Alignments for a candidate for carB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Synechococcus elongatus PCC 7942

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate Synpcc7942_0711 Synpcc7942_0711 carbamoyl phosphate synthase large subunit

Query= SwissProt::Q42601
         (1187 letters)



>FitnessBrowser__SynE:Synpcc7942_0711
          Length = 1097

 Score = 1418 bits (3671), Expect = 0.0
 Identities = 715/1098 (65%), Positives = 875/1098 (79%), Gaps = 22/1098 (2%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            +R D++KI++LG+GPIVIGQACEFDYSGTQACKALREEGYEV+L+NSNPATIMTDPETA+
Sbjct: 3    RRQDIRKILLLGSGPIVIGQACEFDYSGTQACKALREEGYEVVLVNSNPATIMTDPETAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
            RTYI P+TPELV QVIE+ERPDALLPTMGGQTALNLAVALA++G L+++GVELIGAKL A
Sbjct: 63   RTYIEPLTPELVAQVIERERPDALLPTMGGQTALNLAVALAKNGTLDRFGVELIGAKLEA 122

Query: 214  IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
            I+KAEDR LFK+AM+ IG+K  PSGI   + E   IAE+IG +PLIIRPAFT+GGTGGGI
Sbjct: 123  IEKAEDRLLFKEAMERIGVKVCPSGIANNMAEAQAIAEQIGTYPLIIRPAFTMGGTGGGI 182

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN+EEFE I +SGL AS  SQ+LVE+SL+GWKE+ELEVMRDLADNVVIICSIEN+DPMG
Sbjct: 183  AYNQEEFELIVQSGLDASPVSQILVEQSLIGWKEFELEVMRDLADNVVIICSIENLDPMG 242

Query: 334  VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
            VHTGDSITVAPAQTLTD+EYQRLRD +IAIIREIGVE GGSN+QFA+NP DG+V++IEMN
Sbjct: 243  VHTGDSITVAPAQTLTDKEYQRLRDQAIAIIREIGVETGGSNIQFAINPQDGDVIVIEMN 302

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGY+LD++ NDITR+TPASFEP+IDYVVTKIPRF
Sbjct: 303  PRVSRSSALASKATGFPIAKIAAKLAVGYSLDELKNDITRQTPASFEPTIDYVVTKIPRF 362

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
            AFEKFPG+   LTT MKSVGE+MA+GRTF ESFQKALRSLE G SGWGC + + L    +
Sbjct: 363  AFEKFPGTPAQLTTMMKSVGEAMAIGRTFPESFQKALRSLEIGRSGWGCDRPETLP-TLE 421

Query: 514  QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
            Q+K  LR P+PDRI A+  AM  G+   +IY+L+ +D WFL + +E+++ E +L   ++ 
Sbjct: 422  QIKPQLRTPSPDRIFAVRQAMLLGLSDGDIYQLTGIDPWFLEKFREILEGEDFLKRASIE 481

Query: 574  EITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAEFEAHTPY 633
            +IT     EVK+ GFSD+QIAFA  ++EE VR +R   G+ P YK VDTCAAEFEA+TPY
Sbjct: 482  QITPAQWLEVKQLGFSDRQIAFALGSSEEAVRQRRQQQGIKPVYKLVDTCAAEFEAYTPY 541

Query: 634  MYSSYD---------------VECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFA 678
             YS Y+                E E  P+++ KV+ILGGGPNRIGQGIEFDYCCCH +FA
Sbjct: 542  YYSCYESPRSHLAESGLTTIPAESEVRPSDRPKVMILGGGPNRIGQGIEFDYCCCHAAFA 601

Query: 679  LQDAGYETIMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPL 738
            L   GYETIM+NSNPETVSTDYDTSDRLYFEPLT EDVLN+++ E+P G+I+QFGGQTPL
Sbjct: 602  LAADGYETIMVNSNPETVSTDYDTSDRLYFEPLTREDVLNILEAERPQGVIIQFGGQTPL 661

Query: 739  KLALPIKHYLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIA 798
            KLA+P++ +L      +L      +IWGTSPDSID AEDRERF  IL +L I QP  G+A
Sbjct: 662  KLAVPLQTFLQTPEGQALG----TQIWGTSPDSIDTAEDRERFEQILRQLDIAQPANGLA 717

Query: 799  KSEADALAIAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKY 858
            +S  +ALAIA  +GYP VVRPSYVLGGRAMEIVY D+ L  Y+  AVQV+P+ P+L+DK+
Sbjct: 718  RSPEEALAIAHRIGYPTVVRPSYVLGGRAMEIVYSDAELERYMTEAVQVEPDHPILIDKF 777

Query: 859  LSDAIEIDVDTLTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTWTT 918
            L +AIE+DVD L D  G VVIGGIMEHIEQAG+HSGDSAC LPT ++  + L+TIR WTT
Sbjct: 778  LENAIEVDVDALADRTGQVVIGGIMEHIEQAGIHSGDSACSLPTVSLNETVLETIRAWTT 837

Query: 919  KLAKKLNVCGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKS 978
            +LAK LNV GLMN Q+A+     V++LEANPRASRTVPFVSKAIG PLAK AA +MSG++
Sbjct: 838  QLAKALNVIGLMNIQFAVKDE-QVYILEANPRASRTVPFVSKAIGRPLAKIAARLMSGQT 896

Query: 979  LKDLNFEKEVIPKHVSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQI 1038
            L DL    E++P ++SVKEAV PF++F G D +LGPEMRSTGEVM I  +F  AFA A++
Sbjct: 897  LADLGITSELVPSYLSVKEAVLPFDRFPGTDTLLGPEMRSTGEVMGIDVDFGRAFAKAEL 956

Query: 1039 AAGQKLPLSGTVFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLK 1098
            AA Q+LP  GTVF+S++D  K  +  IA  FL+LGF++VAT GT   L  + + VE +LK
Sbjct: 957  AASQRLPRQGTVFISVSDRDKAAIGPIAREFLQLGFRVVATGGTQKVLAEQRLSVEPILK 1016

Query: 1099 LHEGRPHAADMVANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAE 1158
            +HEGRPH  D + N QI L++ T +G A  + D + +R+ AL YKVP +TT+AGA AT E
Sbjct: 1017 VHEGRPHVLDALKNDQIQLIINTPAG-ARAKVDDQIIRRAALDYKVPTVTTIAGAKATVE 1075

Query: 1159 GIKSLKSSAIKMTALQDF 1176
             I++L    +++ +LQD+
Sbjct: 1076 AIRALLEQPLQVKSLQDY 1093



 Score =  240 bits (612), Expect = 5e-67
 Identities = 150/420 (35%), Positives = 229/420 (54%), Gaps = 19/420 (4%)

Query: 75  PVSELADT--TTKPFSPEIVGKRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEG 132
           P S LA++  TT P   E+  + +D  K+MILG GP  IGQ  EFDY    A  AL  +G
Sbjct: 549 PRSHLAESGLTTIPAESEV--RPSDRPKVMILGGGPNRIGQGIEFDYCCCHAAFALAADG 606

Query: 133 YEVILINSNPATIMTDPETANRTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVA 192
           YE I++NSNP T+ TD +T++R Y  P+T E V  ++E ERP  ++   GGQT L LAV 
Sbjct: 607 YETIMVNSNPETVSTDYDTSDRLYFEPLTREDVLNILEAERPQGVIIQFGGQTPLKLAVP 666

Query: 193 L---AESGALEKYGVELIGAKLGAIKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDI 249
           L    ++   +  G ++ G    +I  AEDRE F+  ++ + +  P +G+  + +E   I
Sbjct: 667 LQTFLQTPEGQALGTQIWGTSPDSIDTAEDRERFEQILRQLDIAQPANGLARSPEEALAI 726

Query: 250 AEKIGEFPLIIRPAFTLGGTGGGIAYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYE 309
           A +IG +P ++RP++ LGG    I Y+  E E      +       +L++K L    E +
Sbjct: 727 AHRIG-YPTVVRPSYVLGGRAMEIVYSDAELERYMTEAVQVEPDHPILIDKFLENAIEVD 785

Query: 310 LEVMRDLADNVVIICSIENIDPMGVHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGV 369
           ++ + D    VVI   +E+I+  G+H+GDS    P  +L +   + +R ++  + + + V
Sbjct: 786 VDALADRTGQVVIGGIMEHIEQAGIHSGDSACSLPTVSLNETVLETIRAWTTQLAKALNV 845

Query: 370 ECGGSNVQFAVNPVDGEVMIIEMNPRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPN 429
             G  N+QFAV   D +V I+E NPR SR+    SKA G P+AK+AA+L  G TL  +  
Sbjct: 846 -IGLMNIQFAVK--DEQVYILEANPRASRTVPFVSKAIGRPLAKIAARLMSGQTLADL-- 900

Query: 430 DITRKTPASFEPSIDYVVTKIPRFAFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKA 489
            IT +   S      Y+  K     F++FPG+  LL  +M+S GE M +   F  +F KA
Sbjct: 901 GITSELVPS------YLSVKEAVLPFDRFPGTDTLLGPEMRSTGEVMGIDVDFGRAFAKA 954


Lambda     K      H
   0.317    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3232
Number of extensions: 126
Number of successful extensions: 16
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1187
Length of database: 1097
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1051
Effective search space:  1199191
Effective search space used:  1199191
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate Synpcc7942_0711 Synpcc7942_0711 (carbamoyl phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01369.hmm
# target sequence database:        /tmp/gapView.22778.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01369  [M=1052]
Accession:   TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1500.1   0.0          0 1499.9   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0711  Synpcc7942_0711 carbamoyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0711  Synpcc7942_0711 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1499.9   0.0         0         0       1    1052 []       2    1077 ..       2    1077 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1499.9 bits;  conditional E-value: 0
                                 TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67  
                                                p+r+di+k+l++GsGpivigqA+EFDYsG+qa+kal+eeg+evvLvnsn+At+mtd+e ad++YieP
  lcl|FitnessBrowser__SynE:Synpcc7942_0711    2 PRRQDIRKILLLGSGPIVIGQACEFDYSGTQACKALREEGYEVVLVNSNPATIMTDPETADRTYIEP 68  
                                                5799*************************************************************** PP

                                 TIGR01369   68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134 
                                                lt+e v+++ie+ErpDa+l+t+GGqtaLnlav l ++G L+++gv+l+G+k+eai+kaedR +Fkea
  lcl|FitnessBrowser__SynE:Synpcc7942_0711   69 LTPELVAQVIERERPDALLPTMGGQTALNLAVALAKNGTLDRFGVELIGAKLEAIEKAEDRLLFKEA 135 
                                                ******************************************************************* PP

                                 TIGR01369  135 lkeineevakseivesveealeaaeeig.yPvivRaaftlgGtGsgiaeneeelkelvekalkaspi 200 
                                                ++ i+++v  s i+++++ea+++ae+ig yP+i+R+aft+gGtG+gia+n+ee++ +v+++l+asp+
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  136 MERIGVKVCPSGIANNMAEAQAIAEQIGtYPLIIRPAFTMGGTGGGIAYNQEEFELIVQSGLDASPV 202 
                                                ***************************889************************************* PP

                                 TIGR01369  201 kqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdas 267 
                                                +q+lve+sl gwkE+E+Ev+RD +dn++i+c+iEnlDp+GvHtGdsi+vaP+qtLtdkeyq+lRd++
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  203 SQILVEQSLIGWKEFELEVMRDLADNVVIICSIENLDPMGVHTGDSITVAPAQTLTDKEYQRLRDQA 269 
                                                ******************************************************************* PP

                                 TIGR01369  268 lkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdel 333 
                                                ++iire+gve++ +n+qfa++P++ +++viE+npRvsRssALAskAtG+PiAk+aaklavGysLdel
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  270 IAIIREIGVETGgSNIQFAINPQDGDVIVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYSLDEL 336 
                                                **********988****************************************************** PP

                                 TIGR01369  334 kndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsle 400 
                                                knd+t++t+AsfEP++DYvv+kiPr++++kf ++  +l+t+mksvGE maigrtf e++qkalrsle
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  337 KNDITRQTPASFEPTIDYVVTKIPRFAFEKFPGTPAQLTTMMKSVGEAMAIGRTFPESFQKALRSLE 403 
                                                ******************************************************************* PP

                                 TIGR01369  401 ekllg..lklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklv 465 
                                                ++ +g  ++ + ++  + e+++ +l++p+++R+fa+ +a+  g+s  ++y+lt id +flek+++++
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  404 IGRSGwgCDRP-ETLPTLEQIKPQLRTPSPDRIFAVRQAMLLGLSDGDIYQLTGIDPWFLEKFREIL 469 
                                                ***99434444.44556678899******************************************** PP

                                 TIGR01369  466 elekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfe 532 
                                                e e  l++ ++++++  ++ ++k+lGfsd+qia ++++se++vr+ r+++gi pv+k vDt+aaEfe
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  470 EGEDFLKRASIEQITPAQWLEVKQLGFSDRQIAFALGSSEEAVRQRRQQQGIKPVYKLVDTCAAEFE 536 
                                                ******************************************************************* PP

                                 TIGR01369  533 aktpYlYstyeee..............kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalr 585 
                                                a tpY+Ys ye+               + +v+ +++ kv++lG+Gp+Rigqg+EFDyc+ ha+ al 
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  537 AYTPYYYSCYESPrshlaesglttipaESEVRPSDRPKVMILGGGPNRIGQGIEFDYCCCHAAFALA 603 
                                                ***********9878888899999988889999999******************************* PP

                                 TIGR01369  586 eagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakelee. 651 
                                                  gy+ti++n+nPEtvstDyd++drLyFe+lt edvl+i+e e+++gvi+q+gGqt+l+la  l+  
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  604 ADGYETIMVNSNPETVSTDYDTSDRLYFEPLTREDVLNILEAERPQGVIIQFGGQTPLKLAVPLQTf 670 
                                                *************************************************************999752 PP

                                 TIGR01369  652 ........agvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvR 710 
                                                         g++i Gts++sid+aEdRe+F+++l++l+i qp++  a+s eea  ia++igyP +vR
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  671 lqtpegqaLGTQIWGTSPDSIDTAEDRERFEQILRQLDIAQPANGLARSPEEALAIAHRIGYPTVVR 737 
                                                222221114699******************************************************* PP

                                 TIGR01369  711 psyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadg.eevliagileH 776 
                                                psyvlgGrameiv++++elery++eav+v +++P+lidk+le+a+EvdvDa+ad  ++v+i gi+eH
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  738 PSYVLGGRAMEIVYSDAELERYMTEAVQVEPDHPILIDKFLENAIEVDVDALADRtGQVVIGGIMEH 804 
                                                *****************************************************96369********* PP

                                 TIGR01369  777 iEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasR 843 
                                                iE+aG+HsGDs+++lp+ +l+e v+++i++ ++++ak+l+v Gl+niqf+vkde+vy++E+n+RasR
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  805 IEQAGIHSGDSACSLPTVSLNETVLETIRAWTTQLAKALNVIGLMNIQFAVKDEQVYILEANPRASR 871 
                                                ******************************************************************* PP

                                 TIGR01369  844 tvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemks 910 
                                                tvPfvska+g pl+k+a++++ g++l++   g+++e  +++++vk+av++f ++ g+d +lgpem+s
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  872 TVPFVSKAIGRPLAKIAARLMSGQTLAD--LGITSELVPSYLSVKEAVLPFDRFPGTDTLLGPEMRS 936 
                                                ****************************..668999******************************* PP

                                 TIGR01369  911 tGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakv 977 
                                                tGEvmgi+ d+ +a++ka la++++++++g+v++sv+d+dk ++ ++a+++ ++g++v+at gt+kv
  lcl|FitnessBrowser__SynE:Synpcc7942_0711  937 TGEVMGIDVDFGRAFAKAELAASQRLPRQGTVFISVSDRDKAAIGPIAREFLQLGFRVVATGGTQKV 1003
                                                ******************************************************************* PP

                                 TIGR01369  978 leeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvtelet 1044
                                                l+e+  ++e +lkv+e ++++l++lk+++i+l+in+++ +++a+ ++ +irr+a++ykvp+vt++++
  lcl|FitnessBrowser__SynE:Synpcc7942_0711 1004 LAEQRLSVEPILKVHEGRPHVLDALKNDQIQLIINTPA-GARAKVDDQIIRRAALDYKVPTVTTIAG 1069
                                                ***********************************998.77788899******************** PP

                                 TIGR01369 1045 aealleal 1052
                                                a+a++ea+
  lcl|FitnessBrowser__SynE:Synpcc7942_0711 1070 AKATVEAI 1077
                                                ****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1097 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 13.13
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis