GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Caulobacter crescentus NA1000

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate CCNA_02994 CCNA_02994 carbamoyl-phosphate synthase large chain

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Caulo:CCNA_02994
          Length = 1099

 Score = 1269 bits (3283), Expect = 0.0
 Identities = 675/1099 (61%), Positives = 812/1099 (73%), Gaps = 33/1099 (3%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI SILI+GAGPIVIGQACEFDYSG QACKALR EGYR+ILVNSNPATIMTDP++
Sbjct: 1    MPKRTDISSILIIGAGPIVIGQACEFDYSGVQACKALRAEGYRIILVNSNPATIMTDPDV 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  E+V KIIEKERPDA+LPTMGGQTALN AL LE  G L +FGV MIGA A
Sbjct: 61   ADATYIEPITPEMVAKIIEKERPDALLPTMGGQTALNTALALEADGTLAKFGVEMIGAKA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            + IDKAEDR++F  AM K+GLE+ RS   HT++EA+     VG P IIRPSFT+ G+GGG
Sbjct: 121  EVIDKAEDRQKFRDAMDKLGLESPRSRACHTLDEAMEGLEFVGLPAIIRPSFTLAGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN EEF+EI  RGLDLSPT E+L++ES++GWKEYEMEVVRDK DNCIIVCSIEN D M
Sbjct: 181  IAYNVEEFKEIVERGLDLSPTTEVLVEESVLGWKEYEMEVVRDKADNCIIVCSIENIDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPA TLTDKEYQ MR AS+AVLREIGVETGGSNVQFAVNP +GR++VIEM
Sbjct: 241  GVHTGDSITVAPALTLTDKEYQWMRAASIAVLREIGVETGGSNVQFAVNPADGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAA+LAVGYTLDEL NDITGG TPASFEPSIDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAARLAVGYTLDELKNDITGGATPASFEPSIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPK--VSLDDP 418
            RF FEK+ G+   LTT MKSVGEVMAIGRT +ES+QKALRGLE G +GFD       DDP
Sbjct: 361  RFAFEKYPGSEPLLTTAMKSVGEVMAIGRTFKESVQKALRGLETGLSGFDEVEIAGADDP 420

Query: 419  E-ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVA 477
            +     + R L     DR+  IA AFR GL+VD V    + + WFL QI E+VR E  V 
Sbjct: 421  DNGKEAVIRALGVPTPDRLRVIAQAFRHGLTVDEVNAACSYEPWFLRQIAEIVRQEGWVK 480

Query: 478  EVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFA 537
              G+    A   R+LK +GF+DARLAKL    E  +R  R   ++ PV+KR+D+CA EF 
Sbjct: 481  AGGLP-QTAQGFRELKAQGFSDARLAKLTASTEKAVRAARQALNVRPVFKRIDSCAGEFL 539

Query: 538  TDTAYMYSTYE-------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
              T YMYSTYE        +CE++PS   +K ++LGGGPNRIGQGIEFDYCC HA+ AL 
Sbjct: 540  ASTPYMYSTYEFGALGQIPQCESDPSA-AKKAVILGGGPNRIGQGIEFDYCCCHAAFALD 598

Query: 591  EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK----GVIVQYGGQT 646
            + G E+IMVNCNPETVSTDYDTSDRLYFEP+T EDVLE++ +E  K    GVIVQ+GGQT
Sbjct: 599  QIGVESIMVNCNPETVSTDYDTSDRLYFEPLTAEDVLELLHVEMSKGTLAGVIVQFGGQT 658

Query: 647  PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706
            PLKLA ALE AGVP++GTSPDAID AEDRERFQ  +  L + QP NA   + + A  +  
Sbjct: 659  PLKLAHALEEAGVPILGTSPDAIDLAEDRERFQQLLNGLNIAQPENAIARSWDEARAEGD 718

Query: 707  EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766
            +IG+P V+RPSYVLGGR MEI+ D   + RY   A  +S + P+LLDH+L  A EVDVDA
Sbjct: 719  KIGFPFVMRPSYVLGGRGMEIIRDHEAMERYIAGAGEISLEHPILLDHYLSRATEVDVDA 778

Query: 767  ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
            +CDG+ V + G++EHIE+AGVHSGDSACS+P ++L  E  + +++Q  ++A  L VRGLM
Sbjct: 779  LCDGKDVFVAGVLEHIEEAGVHSGDSACSMPPFSLKAETVEELKRQTVQMALALNVRGLM 838

Query: 827  NVQFAVK-----NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTK 881
            NVQFA++     N  +Y++EVNPRA+RTVPFV+K  G P+A +AA++MAG+SLA  G+ K
Sbjct: 839  NVQFAIEEPHSDNPRIYVLEVNPRASRTVPFVAKTIGQPVAAIAAKIMAGESLASFGL-K 897

Query: 882  EVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVM----------GVGRTFAEAFAKA 931
            +V   + +VKE V PF +F GVD +LGPEMRSTGEVM          G+G  FA AFAK+
Sbjct: 898  DVPYDHIAVKEAVFPFARFAGVDTVLGPEMRSTGEVMGLDWKRDGETGMGPAFARAFAKS 957

Query: 932  QLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLV 991
            QLG    +   G A +SV+E DK  +V+    L   GF++ +T GT   L   G+    V
Sbjct: 958  QLGGGVKLPTKGTAFVSVKESDKPWIVEPVKLLQAAGFKVLSTEGTQAYLAAQGVQVEHV 1017

Query: 992  NKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATA 1051
             KV EGRPHI D +KNG    + NTT G++A+EDS  IRR+AL  KV Y TT  G  A A
Sbjct: 1018 KKVLEGRPHIVDVMKNGGVQLVFNTTEGKQALEDSFEIRRTALMMKVPYYTTSAGALAAA 1077

Query: 1052 MALNADATEKVISVQEMHA 1070
             A+ A A  + + V+ + +
Sbjct: 1078 QAI-AGAPAEALDVRPLQS 1095


Lambda     K      H
   0.318    0.135    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: 3085
Number of extensions: 143
Number of successful extensions: 19
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1073
Length of database: 1099
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1053
Effective search space:  1081431
Effective search space used:  1081431
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 CCNA_02994 CCNA_02994 (carbamoyl-phosphate synthase large chain)
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.31727.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 1439.4   0.0          0 1439.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02994  CCNA_02994 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02994  CCNA_02994 carbamoyl-phosphate synthase large chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1439.2   0.0         0         0       1    1051 [.       2    1079 ..       2    1080 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1439.2 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkr+di+++l+iG+GpivigqA+EFDYsG qa+kal+ eg++++Lvnsn+At+mtd+++ad++YieP+t+e
  lcl|FitnessBrowser__Caulo:CCNA_02994    2 PKRTDISSILIIGAGPIVIGQACEFDYSGVQACKALRAEGYRIILVNSNPATIMTDPDVADATYIEPITPE 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 
                                            +v+kiiekErpDa+l+t+GGqtaLn a+ le  G L+k+gv+++G+k e+i+kaedR+kF++a++++++e 
  lcl|FitnessBrowser__Caulo:CCNA_02994   73 MVAKIIEKERPDALLPTMGGQTALNTALALEADGTLAKFGVEMIGAKAEVIDKAEDRQKFRDAMDKLGLES 143 
                                            *********************************************************************** PP

                             TIGR01369  143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 
                                            ++s+++++ +ea+e  e +g+P i+R++ftl+GtG+gia+n ee+ke+ve++l++sp+++vlve+s+ gwk
  lcl|FitnessBrowser__Caulo:CCNA_02994  144 PRSRACHTLDEAMEGLEFVGLPAIIRPSFTLAGTGGGIAYNVEEFKEIVERGLDLSPTTEVLVEESVLGWK 214 
                                            *********************************************************************** PP

                             TIGR01369  214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283 
                                            E+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +R as++++re+gve++ +nvq
  lcl|FitnessBrowser__Caulo:CCNA_02994  215 EYEMEVVRDKADNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQWMRAASIAVLREIGVETGgSNVQ 285 
                                            ****************************************************************988**** PP

                             TIGR01369  284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvv 353 
                                            fa++P + r+vviE+npRvsRssALAskAtG+PiAkvaa+lavGy+Ldelknd+t+  t+AsfEPs+DYvv
  lcl|FitnessBrowser__Caulo:CCNA_02994  286 FAVNPADGRMVVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYTLDELKNDITGgATPASFEPSIDYVV 356 
                                            *******************************************************878************* PP

                             TIGR01369  354 vkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkeke.....aesdeel 419 
                                            +kiPr++++k+ + +  l+t mksvGEvmaigrtf+e++qkalr le++l+g+++ e +      + +e++
  lcl|FitnessBrowser__Caulo:CCNA_02994  357 TKIPRFAFEKYPGSEPLLTTAMKSVGEVMAIGRTFKESVQKALRGLETGLSGFDEVEIAgaddpDNGKEAV 427 
                                            ****************************************************7665443100114556778 PP

                             TIGR01369  420 eealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakkl 490 
                                             +al  p+++Rl +ia+a+r+g++v+ev+ ++ ++ +fl++++++v+ e  ++   l   +++ ++++k++
  lcl|FitnessBrowser__Caulo:CCNA_02994  428 IRALGVPTPDRLRVIAQAFRHGLTVDEVNAACSYEPWFLRQIAEIVRQEGWVKAGGLP-QTAQGFRELKAQ 497 
                                            899999**********************************************977776.77899******* PP

                             TIGR01369  491 GfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee......kddvevtekk 555 
                                            Gfsd+++akl+ ++e++vr++r++l++ pv+kr+D +a+Ef a+tpY+Ystye        + +++ +  k
  lcl|FitnessBrowser__Caulo:CCNA_02994  498 GFSDARLAKLTASTEKAVRAARQALNVRPVFKRIDSCAGEFLASTPYMYSTYEFGalgqipQCESDPSAAK 568 
                                            ****************************************************9765555555566667779 PP

                             TIGR01369  556 kvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiie 626 
                                            k ++lG+Gp+Rigqg+EFDyc+ ha+ al + g ++i++n+nPEtvstDyd++drLyFe+lt edvl++++
  lcl|FitnessBrowser__Caulo:CCNA_02994  569 KAVILGGGPNRIGQGIEFDYCCCHAAFALDQIGVESIMVNCNPETVSTDYDTSDRLYFEPLTAEDVLELLH 639 
                                            *********************************************************************99 PP

                             TIGR01369  627 kekve....gvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsv 693 
                                             e  +    gvivq+gGqt+l+la++leeagv+ilGts+++id aEdRe+F++ll+ l+i qp++++a+s 
  lcl|FitnessBrowser__Caulo:CCNA_02994  640 VEMSKgtlaGVIVQFGGQTPLKLAHALEEAGVPILGTSPDAIDLAEDRERFQQLLNGLNIAQPENAIARSW 710 
                                            8865422228************************************************************* PP

                             TIGR01369  694 eeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavad 764 
                                            +ea+   ++ig+P ++RpsyvlgGr+mei++++e +ery+  a e+s e+P+l+d+yl+ a+EvdvDa++d
  lcl|FitnessBrowser__Caulo:CCNA_02994  711 DEARAEGDKIGFPFVMRPSYVLGGRGMEIIRDHEAMERYIAGAGEISLEHPILLDHYLSRATEVDVDALCD 781 
                                            *********************************************************************** PP

                             TIGR01369  765 geevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkd.....e 830 
                                            g++v++ag+leHiEeaGvHsGDs++++pp +l++e+++++k+++ ++a +l+v+Gl+n+qf++++      
  lcl|FitnessBrowser__Caulo:CCNA_02994  782 GKDVFVAGVLEHIEEAGVHSGDSACSMPPFSLKAETVEELKRQTVQMALALNVRGLMNVQFAIEEphsdnP 852 
                                            **************************************************************986432224 PP

                             TIGR01369  831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvd 901 
                                            ++yv+Evn+RasRtvPfv+k++g p++++a+k+++g++l++ +    k+  ++++avk+avf+f+++agvd
  lcl|FitnessBrowser__Caulo:CCNA_02994  853 RIYVLEVNPRASRTVPFVAKTIGQPVAAIAAKIMAGESLASFGL---KDVPYDHIAVKEAVFPFARFAGVD 920 
                                            69***************************************886...99999******************* PP

                             TIGR01369  902 vvlgpemkstGEvmgigrd..........leeallkallaskakikkkgsvllsvkdkdkeellelakkla 962 
                                             vlgpem+stGEvmg++ +          +++a++k++l  + k+++kg++++svk++dk  ++e +k l+
  lcl|FitnessBrowser__Caulo:CCNA_02994  921 TVLGPEMRSTGEVMGLDWKrdgetgmgpaFARAFAKSQLGGGVKLPTKGTAFVSVKESDKPWIVEPVKLLQ 991 
                                            **************9763211222222226788889999999***************************** PP

                             TIGR01369  963 ekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreave 1033
                                            ++g+kv++tegt+++l+ +g+++e+v+kv e +++i++++k++ ++lv+n+t+ +k+a e+++ irr+a++
  lcl|FitnessBrowser__Caulo:CCNA_02994  992 AAGFKVLSTEGTQAYLAAQGVQVEHVKKVLEGRPHIVDVMKNGGVQLVFNTTE-GKQALEDSFEIRRTALM 1061
                                            **************************************************997.888999*********** PP

                             TIGR01369 1034 ykvplvteletaeallea 1051
                                            +kvp+ t+ ++a a+++a
  lcl|FitnessBrowser__Caulo:CCNA_02994 1062 MKVPYYTTSAGALAAAQA 1079
                                            *********999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1099 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.11
# Mc/sec: 10.39
//
[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:

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:

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:

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:

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