Alignments for a candidate for carB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Dinoroseobacter shibae DFL-12

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate 3609253 Dshi_2639 carbamoyl-phosphate synthase, large subunit (RefSeq)

Query= SwissProt::Q42601
         (1187 letters)



>FitnessBrowser__Dino:3609253
          Length = 1105

 Score = 1178 bits (3047), Expect = 0.0
 Identities = 627/1120 (55%), Positives = 795/1120 (70%), Gaps = 57/1120 (5%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            KRTD+K IMI+GAGPI+IGQACEFDYSG QACKALREEGY VIL+NSNPATIMTDP  A+
Sbjct: 3    KRTDIKSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGLAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
             TYI P+TPE+V ++IEKERPDALLPTMGGQT LN ++AL E G L KYGVE+IGAK  A
Sbjct: 63   ATYIEPITPEIVAKIIEKERPDALLPTMGGQTGLNTSLALEEMGVLAKYGVEMIGAKREA 122

Query: 214  IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
            I+ AEDR+LF++AM  +G++ P + I TT+DEC    + IG  P IIRPAFTLGGTGGG+
Sbjct: 123  IEMAEDRKLFREAMDRLGIENPRATIATTMDECMAALDDIG-LPAIIRPAFTLGGTGGGV 181

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN++++E  CKSGL AS  +Q+L+++SLLGWKE+E+EV+RD ADN +I+C+IEN+DPMG
Sbjct: 182  AYNRDDYEHFCKSGLDASPVNQILIDESLLGWKEFEMEVVRDKADNAIIVCAIENVDPMG 241

Query: 334  VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
            VHTGDSITVAPA TLTD+EYQ +R+ SIA++REIGVE GGSNVQ+AVNP DG +++IEMN
Sbjct: 242  VHTGDSITVAPALTLTDKEYQIMRNGSIAVLREIGVETGGSNVQWAVNPADGRMVVIEMN 301

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGYTLD++ NDIT+ TPASFEP+IDYVVTKIPRF
Sbjct: 302  PRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITKVTPASFEPTIDYVVTKIPRF 361

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
            AFEKFPG++P LTT MKSVGE+M++GRTF ES QKAL S+E G +G+    I  +  D  
Sbjct: 362  AFEKFPGAEPNLTTAMKSVGEAMSIGRTFHESVQKALASMETGLTGFDEIAIPGISADHR 421

Query: 514  Q-------LKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQY 566
                    +  +L    PDR+  I  AM+ G+  DEI   +  D WFL +++E+V+ E  
Sbjct: 422  SDAPDTAAVVKALARQTPDRLRVIAQAMRHGLSDDEIQAATSYDPWFLARIREIVETEAQ 481

Query: 567  LMSGTLSEITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAE 626
            +    L  +  E L ++K  GF+D ++A  T   E +VR  R  LGV   +KR+DTCAAE
Sbjct: 482  VRRDGL-PLEAEGLRKLKMMGFTDARLAKLTGRDEGQVRRARTRLGVTAQFKRIDTCAAE 540

Query: 627  FEAHTPYMYSSY------DVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQ 680
            FEA TPYMYS+Y      + ECES P +  KV+ILGGGPNRIGQGIEFDYCCCH  FAL 
Sbjct: 541  FEAQTPYMYSTYETPVMGEAECESRPTDATKVVILGGGPNRIGQGIEFDYCCCHACFALT 600

Query: 681  DAGYETIMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPD----GIIVQFGGQT 736
            +AGYETIM+N NPETVSTDYDTSDRLYFEPLT E V+ ++  E+ +    G+IVQFGGQT
Sbjct: 601  EAGYETIMVNCNPETVSTDYDTSDRLYFEPLTFEHVMEILRAEQENGTLHGVIVQFGGQT 660

Query: 737  PLKLALPIKHYLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGG 796
            PLKLA  ++             A  + I GT+PD+ID AEDRERF A++++L ++QP   
Sbjct: 661  PLKLANALE-------------AEGIPILGTTPDAIDLAEDRERFQALVNDLGLKQPHNA 707

Query: 797  IAKSEADALAIAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVD 856
            IA ++A+A A A ++G+P+V+RPSYVLGGRAMEIV D  +L  Y+  AV V  + PVL+D
Sbjct: 708  IASTDAEAFAAAGDIGFPLVIRPSYVLGGRAMEIVRDMGQLERYIAEAVVVSGDSPVLLD 767

Query: 857  KYLSDAIEIDVDTLTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTW 916
             YL+ A+E+DVD L D   NV + GIM+HIE+AGVHSGDSAC LP  ++    L  IR  
Sbjct: 768  SYLAGAVELDVDALCDG-ENVHVAGIMQHIEEAGVHSGDSACSLPPYSLSDDVLARIRVQ 826

Query: 917  TTKLAKKLNVCGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSG 976
            T  LA+ L V GLMN Q+AI    +++L+E NPRASRTVPFV+KA    +A  AA +M+G
Sbjct: 827  TEALARALRVKGLMNVQFAI-KDDEIYLIEVNPRASRTVPFVAKATDSAIASIAARLMAG 885

Query: 977  KSLKDLNF---------EKEVIP------------KHVSVKEAVFPFEKFQGCDVILGPE 1015
            + L +            E + +P               SVKEAV PF +F G D ILGPE
Sbjct: 886  EPLSNFPLRDPLPHDAPEDQHLPIGDPMTLAHPDTPWFSVKEAVLPFARFPGVDTILGPE 945

Query: 1016 MRSTGEVMSISSEFSSAFAMAQIAAGQKLPLSGTVFLSLNDMTKPH-LEKIAVSFLELGF 1074
            MRSTGEVM     F  AF  AQ+ AG  LP  GTVFLS+ +  K   L + A    ELG 
Sbjct: 946  MRSTGEVMGWDRSFPRAFLKAQMGAGTVLPTEGTVFLSIKEADKTEMLVETAAMLTELGL 1005

Query: 1075 KIVATSGTAHFLELKGIPVERVLKLHEGRPHAADMVANGQIHLMLITSSGDALDQKDGRQ 1134
             IVAT GTA FL+  GI  + V K++EGRP   DM+ +G+I L++ T+ G A    D R+
Sbjct: 1006 DIVATRGTAAFLKDHGIASKVVNKVYEGRPDVVDMLKDGRIALVMNTTEG-AQAVNDSRE 1064

Query: 1135 LRQMALAYKVPVITTVAGALATAEGIKSLKSSAIKMTALQ 1174
            +R +AL  ++P  TT+A + A A+ + + +   I + ALQ
Sbjct: 1065 IRSVALYDRIPYFTTLAASHAAAQAMIARREGEIGVRALQ 1104



 Score =  230 bits (587), Expect = 4e-64
 Identities = 151/417 (36%), Positives = 220/417 (52%), Gaps = 28/417 (6%)

Query: 90  EIVGKRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDP 149
           E   + TD  K++ILG GP  IGQ  EFDY    AC AL E GYE I++N NP T+ TD 
Sbjct: 561 ECESRPTDATKVVILGGGPNRIGQGIEFDYCCCHACFALTEAGYETIMVNCNPETVSTDY 620

Query: 150 ETANRTYIAPMTPELVEQVIEKERPD----ALLPTMGGQTALNLAVALAESGALEKYGVE 205
           +T++R Y  P+T E V +++  E+ +     ++   GGQT L LA       ALE  G+ 
Sbjct: 621 DTSDRLYFEPLTFEHVMEILRAEQENGTLHGVIVQFGGQTPLKLA------NALEAEGIP 674

Query: 206 LIGAKLGAIKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFT 265
           ++G    AI  AEDRE F+  + ++GLK P + I +T  E F  A  IG FPL+IRP++ 
Sbjct: 675 ILGTTPDAIDLAEDRERFQALVNDLGLKQPHNAIASTDAEAFAAAGDIG-FPLVIRPSYV 733

Query: 266 LGGTGGGIAYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICS 325
           LGG    I  +  + E      +  S  S VL++  L G  E +++ + D  +NV +   
Sbjct: 734 LGGRAMEIVRDMGQLERYIAEAVVVSGDSPVLLDSYLAGAVELDVDALCD-GENVHVAGI 792

Query: 326 IENIDPMGVHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDG 385
           +++I+  GVH+GDS    P  +L+D    R+R  + A+ R + V+ G  NVQFA+   D 
Sbjct: 793 MQHIEEAGVHSGDSACSLPPYSLSDDVLARIRVQTEALARALRVK-GLMNVQFAIK--DD 849

Query: 386 EVMIIEMNPRVSRSSALASKATGFPIAKMAAKLSVGYTL------DQIPNDITRKTPASF 439
           E+ +IE+NPR SR+    +KAT   IA +AA+L  G  L      D +P+D         
Sbjct: 850 EIYLIEVNPRASRTVPFVAKATDSAIASIAARLMAGEPLSNFPLRDPLPHDAPEDQHLPI 909

Query: 440 -------EPSIDYVVTKIPRFAFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKA 489
                   P   +   K     F +FPG   +L  +M+S GE M   R+F  +F KA
Sbjct: 910 GDPMTLAHPDTPWFSVKEAVLPFARFPGVDTILGPEMRSTGEVMGWDRSFPRAFLKA 966


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: 3005
Number of extensions: 135
Number of successful extensions: 22
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: 1105
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1059
Effective search space:  1208319
Effective search space used:  1208319
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 3609253 Dshi_2639 (carbamoyl-phosphate synthase, large subunit (RefSeq))
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.27196.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 1459.4   0.0          0 1459.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609253  Dshi_2639 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609253  Dshi_2639 carbamoyl-phosphate synthase, large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1459.2   0.0         0         0       1    1052 []       2    1090 ..       2    1090 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1459.2 bits;  conditional E-value: 0
                         TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavek 75  
                                        pkr+dik++++iG+Gpi+igqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+ lad++YieP+t+e+v+k
  lcl|FitnessBrowser__Dino:3609253    2 PKRTDIKSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGLADATYIEPITPEIVAK 76  
                                        689************************************************************************ PP

                         TIGR01369   76 iiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                        iiekErpDa+l+t+GGqt+Ln ++ lee+GvL+kygv+++G+k eai+ aedR++F+ea++ +++e ++++i+++
  lcl|FitnessBrowser__Dino:3609253   77 IIEKERPDALLPTMGGQTGLNTSLALEEMGVLAKYGVEMIGAKREAIEMAEDRKLFREAMDRLGIENPRATIATT 151 
                                        *************************************************************************** PP

                         TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskd 225 
                                        ++e+++a ++ig+P i+R+aftlgGtG+g+a+n+++ ++ ++++l+asp++q+l+++sl gwkE+E+EvvRD++d
  lcl|FitnessBrowser__Dino:3609253  152 MDECMAALDDIGLPAIIRPAFTLGGTGGGVAYNRDDYEHFCKSGLDASPVNQILIDESLLGWKEFEMEVVRDKAD 226 
                                        *************************************************************************** PP

                         TIGR01369  226 nciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvn 299 
                                        n+iivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+ s++++re+gve++ +nvq+a++P + r+vviE+n
  lcl|FitnessBrowser__Dino:3609253  227 NAIIVCAIENVDPMGVHTGDSITVAPALTLTDKEYQIMRNGSIAVLREIGVETGgSNVQWAVNPADGRMVVIEMN 301 
                                        ****************************************************988******************** PP

                         TIGR01369  300 pRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtq 374 
                                        pRvsRssALAskAtG+PiAk+aaklavGy+Ldel nd+tk t+AsfEP++DYvv+kiPr++++kf +++ +l+t 
  lcl|FitnessBrowser__Dino:3609253  302 PRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITKVTPASFEPTIDYVVTKIPRFAFEKFPGAEPNLTTA 376 
                                        *************************************************************************** PP

                         TIGR01369  375 mksvGEvmaigrtfeealqkalrsleekllg........lklkek.eaesdeeleealkkpndrRlfaiaealrr 440 
                                        mksvGE m+igrtf+e++qkal+s+e++l+g        ++ +++  a ++ ++ +al +++++Rl +ia+a+r+
  lcl|FitnessBrowser__Dino:3609253  377 MKSVGEAMSIGRTFHESVQKALASMETGLTGfdeiaipgISADHRsDAPDTAAVVKALARQTPDRLRVIAQAMRH 451 
                                        *****************************9944433333222333033445667899****************** PP

                         TIGR01369  441 gvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkel 515 
                                        g+s +e+  +t +d +fl +++++ve+e ++++  l  l++e l+k+k +Gf+d+++akl++ +e +vr++r++l
  lcl|FitnessBrowser__Dino:3609253  452 GLSDDEIQAATSYDPWFLARIREIVETEAQVRRDGLP-LEAEGLRKLKMMGFTDARLAKLTGRDEGQVRRARTRL 525 
                                        *******************************977776.************************************* PP

                         TIGR01369  516 givpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalr 585 
                                        g++  +kr+Dt+aaEfea+tpY+Ystye+      + +++ t+  kv++lG+Gp+Rigqg+EFDyc+ ha+ al 
  lcl|FitnessBrowser__Dino:3609253  526 GVTAQFKRIDTCAAEFEAQTPYMYSTYETPvmgeaECESRPTDATKVVILGGGPNRIGQGIEFDYCCCHACFALT 600 
                                        ***************************986544334455666779****************************** PP

                         TIGR01369  586 eagyktilinynPEtvstDydiadrLyFeeltvedvldiiekek....vegvivqlgGqtalnlakeleeagvki 656 
                                        eagy+ti++n+nPEtvstDyd++drLyFe+lt+e+v++i++ e+     +gvivq+gGqt+l+la++le++g++i
  lcl|FitnessBrowser__Dino:3609253  601 EAGYETIMVNCNPETVSTDYDTSDRLYFEPLTFEHVMEILRAEQengtLHGVIVQFGGQTPLKLANALEAEGIPI 675 
                                        ****************************************99873333578************************ PP

                         TIGR01369  657 lGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeler 731 
                                        lGt++++id aEdRe+F++l+++lg+kqp++++a++  ea  +a +ig+P+++RpsyvlgGrameiv+++ +ler
  lcl|FitnessBrowser__Dino:3609253  676 LGTTPDAIDLAEDRERFQALVNDLGLKQPHNAIASTDAEAFAAAGDIGFPLVIRPSYVLGGRAMEIVRDMGQLER 750 
                                        *************************************************************************** PP

                         TIGR01369  732 yleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkike 806 
                                        y+ eav vs ++Pvl+d yl  avE+dvDa++dge+v +agi++HiEeaGvHsGDs+++lpp +ls++v+ +i+ 
  lcl|FitnessBrowser__Dino:3609253  751 YIAEAVVVSGDSPVLLDSYLAGAVELDVDALCDGENVHVAGIMQHIEEAGVHSGDSACSLPPYSLSDDVLARIRV 825 
                                        *************************************************************************** PP

                         TIGR01369  807 ivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleele........ 873 
                                        +++++a++l+vkGl+n+qf++kd+e+y+iEvn+RasRtvPfv+ka++  ++++a+++++g+ l++          
  lcl|FitnessBrowser__Dino:3609253  826 QTEALARALRVKGLMNVQFAIKDDEIYLIEVNPRASRTVPFVAKATDSAIASIAARLMAGEPLSNFPlrdplphd 900 
                                        *****************************************************************9999****** PP

                         TIGR01369  874 ...........kgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakik 937 
                                                        ++++  ++vk+av++f+++ gvd +lgpem+stGEvmg +r++ +a+lka++ ++++++
  lcl|FitnessBrowser__Dino:3609253  901 apedqhlpigdPMTLAHPDTPWFSVKEAVLPFARFPGVDTILGPEMRSTGEVMGWDRSFPRAFLKAQMGAGTVLP 975 
                                        ********9985577889999****************************************************** PP

                         TIGR01369  938 kkgsvllsvkdkdkee.llelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvi 1011
                                        ++g+v+ls+k++dk+e l+e+a++l+e+gl ++at+gta++l+++gi ++vv+kv e +++++++lk++ i lv+
  lcl|FitnessBrowser__Dino:3609253  976 TEGTVFLSIKEADKTEmLVETAAMLTELGLDIVATRGTAAFLKDHGIASKVVNKVYEGRPDVVDMLKDGRIALVM 1050
                                        ***********9996516899****************************************************** PP

                         TIGR01369 1012 nltskkkkaaekgykirreaveykvplvteletaealleal 1052
                                        n+t+ +++a++++  ir  a+  ++p++t+l++ +a+++a+
  lcl|FitnessBrowser__Dino:3609253 1051 NTTE-GAQAVNDSREIRSVALYDRIPYFTTLAASHAAAQAM 1090
                                        *987.8889999*******************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1105 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 0.03s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 12.89
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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