Alignments for a candidate for carB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Desulfovibrio vulgaris Hildenborough

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate 209094 DVU0162 carbamoyl-phosphate synthase, large subunit

Query= SwissProt::Q42601
         (1187 letters)



>MicrobesOnline__882:209094
          Length = 1077

 Score = 1250 bits (3235), Expect = 0.0
 Identities = 645/1091 (59%), Positives = 814/1091 (74%), Gaps = 25/1091 (2%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            KRTDLK+IM++G+GPI+IGQACEFDYSGTQA KAL+EEGYEV+L+NSNPATIMTDP  A+
Sbjct: 3    KRTDLKRIMVIGSGPIIIGQACEFDYSGTQAVKALKEEGYEVVLVNSNPATIMTDPGLAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
            RTYI P+ PE V  +I KERPDALLPT+GGQT LN A+ALA SG L++ GVELIGA    
Sbjct: 63   RTYIEPIEPETVAAIIRKERPDALLPTLGGQTGLNTALALAASGVLDECGVELIGANRAV 122

Query: 214  IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
            I+KAE RELF+ AM NIGLK P SGI  ++D+   +  ++  FPLIIRPAFT+GGTGGGI
Sbjct: 123  IEKAESRELFRLAMANIGLKVPASGIARSMDDVRRLGTEM-PFPLIIRPAFTMGGTGGGI 181

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN E+ E I   GL AS TS+V++E+S+LGWKEYE+EVMRD ADN VIICSIEN DPMG
Sbjct: 182  AYNMEDLEEIASRGLTASITSEVMIEQSVLGWKEYEMEVMRDKADNCVIICSIENFDPMG 241

Query: 334  VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
            VHTGDSITVAPAQTLTD EYQ +RD SIAI+REIGVE GGSNVQF +NP +G++++IEMN
Sbjct: 242  VHTGDSITVAPAQTLTDVEYQMMRDASIAIMREIGVETGGSNVQFGINPDNGDMVVIEMN 301

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGYTLD+IPNDITR+T ASFEP+IDYVVTKIPRF
Sbjct: 302  PRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITRETMASFEPTIDYVVTKIPRF 361

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
             FEKFPG++  LTT MKSVGE+M++GRTF+ES QK LRSLE G  G G ++ ++   + +
Sbjct: 362  TFEKFPGARDELTTAMKSVGEAMSIGRTFKESLQKGLRSLEVGAPGLG-SRFRDKLPEHE 420

Query: 514  QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
            ++   LR PN  RI  +  AM  GM ID+I+E++ +D WFL Q++ELVD+E  L    L+
Sbjct: 421  EIVAKLRTPNSRRIFYVRLAMLSGMTIDDIHEITNIDPWFLRQMRELVDMEGDLRDFALA 480

Query: 574  EITKED-------LYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAE 626
                 D       L   K+ GFSD+Q+A   K  E +VR  R + G+ P+Y  VDTCA+E
Sbjct: 481  NSMTPDNGELVTLLRRAKEYGFSDRQLAEMWKRPESDVRALRDATGIRPTYYLVDTCASE 540

Query: 627  FEAHTPYMYSSYDVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYET 686
            FEA+TPY YS+Y+   E    +++KV+ILGGGPNRIGQGIEFDYCCCH SFAL++ G + 
Sbjct: 541  FEAYTPYYYSTYETGHEIEAESRRKVIILGGGPNRIGQGIEFDYCCCHASFALKEMGVQA 600

Query: 687  IMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKH 746
            IM+NSNPETVSTDYDTSDRLYFEPLT EDV+++I+ EKPDG+IVQFGGQTPL LA+P++ 
Sbjct: 601  IMVNSNPETVSTDYDTSDRLYFEPLTFEDVMHIIEAEKPDGVIVQFGGQTPLNLAVPLQR 660

Query: 747  YLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALA 806
                        AG V I GTSPD+ID AEDRERF A++ +L + QP      +   A+A
Sbjct: 661  ------------AG-VPILGTSPDAIDRAEDRERFQALIHKLDLRQPANATVMNLRQAIA 707

Query: 807  IAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEID 866
             A  +GYPVVVRPSYVLGGRAMEIVYD+ +L +Y +N+V   PE P+L+DK+L +A E+D
Sbjct: 708  GANSIGYPVVVRPSYVLGGRAMEIVYDEEQLTSYFQNSVGEAPEHPILLDKFLENATEVD 767

Query: 867  VDTLTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNV 926
            VD L+D   +V + GIMEHIE+AG+HSGDSAC +P  ++P+S    I   T  LAK+L V
Sbjct: 768  VDALSDG-TDVYVAGIMEHIEEAGIHSGDSACSIPPYSLPSSITDEISRQTVALAKELRV 826

Query: 927  CGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFEK 986
             GLMN Q+A+   G +F+LE NPRASRT PFVSKA   PL + A  VM GK+LK+L+   
Sbjct: 827  VGLMNIQFAV-KDGVIFILEVNPRASRTAPFVSKATAVPLPRLATQVMLGKTLKELDPWS 885

Query: 987  EVIPKHVSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPL 1046
                 +VSVKE+VFPF +F G D++LGPEMRSTGEVM I+  F  A+   Q+A GQ+LP 
Sbjct: 886  MRRSGYVSVKESVFPFNRFPGVDILLGPEMRSTGEVMGIAPTFEEAYLKGQLAGGQRLPQ 945

Query: 1047 SGTVFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEGRPHA 1106
             G VF+S+ND  K  +  +A  F +LGF+IVAT+GTA  L+  G+P   V K++EGRP+ 
Sbjct: 946  QGKVFISVNDRDKTLVPDVARIFADLGFEIVATAGTAKLLKEHGVPTTHVNKVYEGRPNI 1005

Query: 1107 ADMVANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKSS 1166
             DM+ NG I L++ T+SG    Q D + +RQ  L Y VP  TTV+GA A A+ I + ++ 
Sbjct: 1006 VDMIKNGDIALVVNTASGKRTVQ-DSKSIRQATLMYGVPYSTTVSGARAIAKSIAASRTC 1064

Query: 1167 AIKMTALQDFF 1177
             + + +LQ+++
Sbjct: 1065 GVNVKSLQEYY 1075


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: 3049
Number of extensions: 124
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: 1187
Length of database: 1077
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1031
Effective search space:  1176371
Effective search space used:  1176371
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 209094 DVU0162 (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.22802.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 1519.9   0.0          0 1519.7   0.0    1.0  1  lcl|MicrobesOnline__882:209094  DVU0162 carbamoyl-phosphate synt


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209094  DVU0162 carbamoyl-phosphate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1519.7   0.0         0         0       1    1051 [.       2    1057 ..       2    1058 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1519.7 bits;  conditional E-value: 0
                       TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavekii 77  
                                      pkr+d+k+++viGsGpi+igqA+EFDYsG+qa+kalkeeg+evvLvnsn+At+mtd+ lad++YieP+++e+v+ ii
  lcl|MicrobesOnline__882:209094    2 PKRTDLKRIMVIGSGPIIIGQACEFDYSGTQAVKALKEEGYEVVLVNSNPATIMTDPGLADRTYIEPIEPETVAAII 78  
                                      689************************************************************************** PP

                       TIGR01369   78 ekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseivesveea 154 
                                      +kErpDa+l+tlGGqt+Ln a+ l  +GvL+++gv+l+G++  +i+kae+Re+F+ a+++i+++v++s i++s+++ 
  lcl|MicrobesOnline__882:209094   79 RKERPDALLPTLGGQTGLNTALALAASGVLDECGVELIGANRAVIEKAESRELFRLAMANIGLKVPASGIARSMDDV 155 
                                      ***************************************************************************** PP

                       TIGR01369  155 leaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivc 231 
                                       +  +e+ +P+i+R+aft+gGtG+gia+n+e+l+e+++++l+as +++v++e+s+ gwkE+E+Ev+RD++dnc+i+c
  lcl|MicrobesOnline__882:209094  156 RRLGTEMPFPLIIRPAFTMGGTGGGIAYNMEDLEEIASRGLTASITSEVMIEQSVLGWKEYEMEVMRDKADNCVIIC 232 
                                      ***************************************************************************** PP

                       TIGR01369  232 niEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssA 307 
                                      +iEn+Dp+GvHtGdsi+vaP+qtLtd eyq++Rdas++i+re+gve++ +nvqf+++P++ ++vviE+npRvsRssA
  lcl|MicrobesOnline__882:209094  233 SIENFDPMGVHTGDSITVAPAQTLTDVEYQMMRDASIAIMREIGVETGgSNVQFGINPDNGDMVVIEMNPRVSRSSA 309 
                                      **********************************************988**************************** PP

                       TIGR01369  308 LAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmai 384 
                                      LAskAtG+PiAk+aaklavGy+Lde++nd+t+et+AsfEP++DYvv+kiPr+ ++kf ++ ++l+t mksvGE m+i
  lcl|MicrobesOnline__882:209094  310 LASKATGFPIAKIAAKLAVGYTLDEIPNDITRETMASFEPTIDYVVTKIPRFTFEKFPGARDELTTAMKSVGEAMSI 386 
                                      ***************************************************************************** PP

                       TIGR01369  385 grtfeealqkalrsleekllglklkek.eaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrfflek 460 
                                      grtf+e+lqk+lrsle ++ gl ++ + +  ++ee+  +l++pn rR+f++  a+ +g+++++++e+t+id +fl++
  lcl|MicrobesOnline__882:209094  387 GRTFKESLQKGLRSLEVGAPGLGSRFRdKLPEHEEIVAKLRTPNSRRIFYVRLAMLSGMTIDDIHEITNIDPWFLRQ 463 
                                      *******************99665544044456778999************************************** PP

                       TIGR01369  461 lkklvelekeleeeklk.elkke......llkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaE 530 
                                      +++lv++e +l++ +l   ++ +      ll++ak++Gfsd+q+a+++k  e++vr+lr+++gi p++  vDt+a+E
  lcl|MicrobesOnline__882:209094  464 MRELVDMEGDLRDFALAnSMTPDngelvtLLRRAKEYGFSDRQLAEMWKRPESDVRALRDATGIRPTYYLVDTCASE 540 
                                      ***********99855423333312222279********************************************** PP

                       TIGR01369  531 feaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydi 607 
                                      fea tpY+Ystye+  +++e ++++kv++lG+Gp+Rigqg+EFDyc+ ha+ al+e+g ++i++n+nPEtvstDyd+
  lcl|MicrobesOnline__882:209094  541 FEAYTPYYYSTYETG-HEIEAESRRKVIILGGGPNRIGQGIEFDYCCCHASFALKEMGVQAIMVNSNPETVSTDYDT 616 
                                      **************9.************************************************************* PP

                       TIGR01369  608 adrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikq 684 
                                      +drLyFe+lt+edv++iie ek++gvivq+gGqt+lnla  l++agv+ilGts+++idraEdRe+F++l+++l++ q
  lcl|MicrobesOnline__882:209094  617 SDRLYFEPLTFEDVMHIIEAEKPDGVIVQFGGQTPLNLAVPLQRAGVPILGTSPDAIDRAEDRERFQALIHKLDLRQ 693 
                                      ***************************************************************************** PP

                       TIGR01369  685 pkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDa 761 
                                      p+++++ ++ +a   a++igyPv+vRpsyvlgGrameiv++ee+l++y+++ v  ++e+P+l+dk+le+a+EvdvDa
  lcl|MicrobesOnline__882:209094  694 PANATVMNLRQAIAGANSIGYPVVVRPSYVLGGRAMEIVYDEEQLTSYFQNSVGEAPEHPILLDKFLENATEVDVDA 770 
                                      ***************************************************************************** PP

                       TIGR01369  762 vadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvn 838 
                                      ++dg++v++agi+eHiEeaG+HsGDs++++pp +l ++++++i++++ ++akel+v+Gl+niqf+vkd+ + ++Evn
  lcl|MicrobesOnline__882:209094  771 LSDGTDVYVAGIMEHIEEAGIHSGDSACSIPPYSLPSSITDEISRQTVALAKELRVVGLMNIQFAVKDGVIFILEVN 847 
                                      ***************************************************************************** PP

                       TIGR01369  839 vRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvm 915 
                                      +RasRt Pfvska+ vpl +la++v+lgk+l+el+    ++ +s +v+vk++vf+f+++ gvd++lgpem+stGEvm
  lcl|MicrobesOnline__882:209094  848 PRASRTAPFVSKATAVPLPRLATQVMLGKTLKELDP--WSMRRSGYVSVKESVFPFNRFPGVDILLGPEMRSTGEVM 922 
                                      *********************************998..7778889******************************** PP

                       TIGR01369  916 gigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvs 992 
                                      gi+ ++eea+lk +la +++++++g+v++sv+d+dk+ + ++a+ +a++g++++at+gtak l+e+g+ +++v+kv 
  lcl|MicrobesOnline__882:209094  923 GIAPTFEEAYLKGQLAGGQRLPQQGKVFISVNDRDKTLVPDVARIFADLGFEIVATAGTAKLLKEHGVPTTHVNKVY 999 
                                      ***************************************************************************** PP

                       TIGR01369  993 eeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                      e +++i++++k+++i lv+n++s +k++++++++ir+++++y+vp+ t++++a+a++++
  lcl|MicrobesOnline__882:209094 1000 EGRPNIVDMIKNGDIALVVNTAS-GKRTVQDSKSIRQATLMYGVPYSTTVSGARAIAKS 1057
                                      ********************998.88899999*********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1077 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 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 13.01
//
[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