Alignments for a candidate for carB in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Desulfovibrio vulgaris Miyazaki F

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate 8501587 DvMF_2306 carbamoyl-phosphate synthase, large subunit (RefSeq)

Query= SwissProt::Q42601
         (1187 letters)



>FitnessBrowser__Miya:8501587
          Length = 1078

 Score = 1246 bits (3225), Expect = 0.0
 Identities = 643/1091 (58%), Positives = 807/1091 (73%), Gaps = 25/1091 (2%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            KRTDLK+IM++G+GPIVIGQACEFDYSGTQA KAL+EEGYEV+L+NSNPATIMTDP  A+
Sbjct: 3    KRTDLKRIMVIGSGPIVIGQACEFDYSGTQAVKALKEEGYEVVLVNSNPATIMTDPGLAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
            RTYI P+ PE V  +I KERPDALLPT+GGQT LN A+ALA  G LE+ GV+LIGA    
Sbjct: 63   RTYIEPIEPETVAAIIRKERPDALLPTLGGQTGLNTALALAAMGVLEECGVDLIGANKQV 122

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

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN E+ E I   GLAAS   +V++E+S+LGWKE+E+EVMRD ADN VIICSIEN DPMG
Sbjct: 182  AYNMEDLEEIAARGLAASIKHEVMIEQSVLGWKEFEMEVMRDKADNCVIICSIENFDPMG 241

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

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGYTLD+IPNDITR+T ASFEPSIDY VTKIPRF
Sbjct: 302  PRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITRETMASFEPSIDYCVTKIPRF 361

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
             FEKFPG++  LTT MKSVGE+M++GRTF+ES QK LRSLE G  G G A  +    + +
Sbjct: 362  TFEKFPGAKDELTTSMKSVGEAMSIGRTFKESLQKGLRSLEVGAPGLGSA-FRCKGPERE 420

Query: 514  QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
             +   LR PN  RI  +  AM  GM ++EI+E + +D WFL Q+K+LVD+E  L    L 
Sbjct: 421  DIMRKLRTPNSRRIFYVRHAMLDGMTVEEIHEATAIDPWFLRQMKDLVDMEAELRDFALG 480

Query: 574  EITKEDLYEV-------KKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAE 626
                 D  E+       K+ GFSD+Q+A   K  E +VRT R  +G+ P+Y  VDTCA+E
Sbjct: 481  NAMTVDNAELVALMRRAKEYGFSDRQLAEMWKRPESDVRTLRKQMGIAPTYYLVDTCASE 540

Query: 627  FEAHTPYMYSSYDVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYET 686
            FEA+TPY YS+Y+   E A  ++KKV+ILGGGPNRIGQGIEFDYCCCH SFAL++ G + 
Sbjct: 541  FEAYTPYYYSTYETGHEVAVEDRKKVIILGGGPNRIGQGIEFDYCCCHASFALKEMGVQA 600

Query: 687  IMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKH 746
            IM+NSNPETVSTDYDTSDRLYFEPLT EDV+N+I+ EKPDG++VQFGGQTPL LA+P   
Sbjct: 601  IMVNSNPETVSTDYDTSDRLYFEPLTFEDVMNIIETEKPDGVVVQFGGQTPLNLAVP--- 657

Query: 747  YLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALA 806
                     L  AG V I GTSPDSID AEDRERF A+L +L + QP      S  +A +
Sbjct: 658  ---------LMRAG-VPILGTSPDSIDRAEDRERFQALLQKLGLRQPANATVMSLPEARS 707

Query: 807  IAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEID 866
             A  +GYP VVRPSYVLGGRAMEIVYD+ +L  Y  N+V   P+ P+L+DK+L  AIE+D
Sbjct: 708  AAARIGYPTVVRPSYVLGGRAMEIVYDEEQLAEYFANSVGEKPKHPILIDKFLESAIEVD 767

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

Query: 927  CGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFEK 986
             GLMN Q+A+   G +++LE NPRASRT PFVSKA   PL + A  +M G +LK+L+   
Sbjct: 827  VGLMNIQFAV-KDGLIYILEVNPRASRTAPFVSKATAVPLPRLATQIMLGATLKELDPWS 885

Query: 987  EVIPKHVSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPL 1046
                 + SVKE+VFPF +F G D++LGPEMRSTGEVM I+S F  A+   Q+A GQ+LP 
Sbjct: 886  MRRTGYFSVKESVFPFNRFPGVDILLGPEMRSTGEVMGIASSFEEAYLKGQLAGGQRLPQ 945

Query: 1047 SGTVFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEGRPHA 1106
            SG +F+S+ND  K  + ++A  F +LGF+++ATSGTA  L   G+P   V K++EGRP+ 
Sbjct: 946  SGKIFISVNDRDKLLITEVASMFADLGFEVLATSGTAKLLREGGVPATSVHKVYEGRPNI 1005

Query: 1107 ADMVANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKSS 1166
             D + NG I L+L T+SG    Q D + +RQ  L Y VP  TTV+GA A A+ I++ +  
Sbjct: 1006 VDFIKNGDIALVLNTASGKRTVQ-DSKSIRQATLMYGVPYSTTVSGAKAIAQAIRASRCC 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: 3006
Number of extensions: 119
Number of successful extensions: 20
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: 1078
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1032
Effective search space:  1177512
Effective search space used:  1177512
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 8501587 DvMF_2306 (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.21523.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 1530.0   0.0          0 1529.8   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501587  DvMF_2306 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501587  DvMF_2306 carbamoyl-phosphate synthase, large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1529.8   0.0         0         0       1    1052 []       2    1058 ..       2    1058 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1529.8 bits;  conditional E-value: 0
                         TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavek 75  
                                        pkr+d+k+++viGsGpivigqA+EFDYsG+qa+kalkeeg+evvLvnsn+At+mtd+ lad++YieP+++e+v+ 
  lcl|FitnessBrowser__Miya:8501587    2 PKRTDLKRIMVIGSGPIVIGQACEFDYSGTQAVKALKEEGYEVVLVNSNPATIMTDPGLADRTYIEPIEPETVAA 76  
                                        689************************************************************************ PP

                         TIGR01369   76 iiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                        ii+kErpDa+l+tlGGqt+Ln a+ l  +GvLe++gv l+G++ ++i+kae+Re+F+ea+++i+++v++s i+++
  lcl|FitnessBrowser__Miya:8501587   77 IIRKERPDALLPTLGGQTGLNTALALAAMGVLEECGVDLIGANKQVIEKAESRELFREAMANIGLKVPASGIART 151 
                                        *************************************************************************** PP

                         TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskd 225 
                                        +e+  +  +e+ +P+i+R+aft+gGtG+gia+n+e+l+e+++++l+as  ++v++e+s+ gwkE+E+Ev+RD++d
  lcl|FitnessBrowser__Miya:8501587  152 MEDVRRLGTEMPFPLIIRPAFTMGGTGGGIAYNMEDLEEIAARGLAASIKHEVMIEQSVLGWKEFEMEVMRDKAD 226 
                                        ************************************************99************************* PP

                         TIGR01369  226 nciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvn 299 
                                        nc+i+c+iEn+Dp+GvHtGdsi+vaP+qtLtd eyq++Rdas++i+re+gve++ +nvqf+++P++ ++vviE+n
  lcl|FitnessBrowser__Miya:8501587  227 NCVIICSIENFDPMGVHTGDSITVAPAQTLTDVEYQMMRDASIAIMREIGVETGgSNVQFGINPQNGDMVVIEMN 301 
                                        ****************************************************988******************** PP

                         TIGR01369  300 pRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtq 374 
                                        pRvsRssALAskAtG+PiAk+aaklavGy+Lde++nd+t+et+AsfEPs+DY+v+kiPr+ ++kf +++++l+t+
  lcl|FitnessBrowser__Miya:8501587  302 PRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITRETMASFEPSIDYCVTKIPRFTFEKFPGAKDELTTS 376 
                                        *************************************************************************** PP

                         TIGR01369  375 mksvGEvmaigrtfeealqkalrsleekllglklkek.eaesdeeleealkkpndrRlfaiaealrrgvsveevy 448 
                                        mksvGE m+igrtf+e+lqk+lrsle ++ gl +  + +  ++e+++++l++pn rR+f++ +a+ +g++vee++
  lcl|FitnessBrowser__Miya:8501587  377 MKSVGEAMSIGRTFKESLQKGLRSLEVGAPGLGSAFRcKGPEREDIMRKLRTPNSRRIFYVRHAMLDGMTVEEIH 451 
                                        *******************************766544055677899***************************** PP

                         TIGR01369  449 eltkidrffleklkklvelekeleeeklk...elkk....ellkkakklGfsdeqiaklvkvseaevrklrkelg 516 
                                        e+t id +fl+++k+lv++e el++ +l     +++     l+++ak++Gfsd+q+a+++k  e++vr+lrk++g
  lcl|FitnessBrowser__Miya:8501587  452 EATAIDPWFLRQMKDLVDMEAELRDFALGnamTVDNaelvALMRRAKEYGFSDRQLAEMWKRPESDVRTLRKQMG 526 
                                        ************************985432222332111146799****************************** PP

                         TIGR01369  517 ivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagykt 591 
                                        i+p++  vDt+a+Efea tpY+Ystye+  ++v+v+++kkv++lG+Gp+Rigqg+EFDyc+ ha+ al+e+g ++
  lcl|FitnessBrowser__Miya:8501587  527 IAPTYYLVDTCASEFEAYTPYYYSTYETG-HEVAVEDRKKVIILGGGPNRIGQGIEFDYCCCHASFALKEMGVQA 600 
                                        ****************************9.********************************************* PP

                         TIGR01369  592 ilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidr 666 
                                        i++n+nPEtvstDyd++drLyFe+lt+edv++iie+ek++gv+vq+gGqt+lnla  l +agv+ilGts++sidr
  lcl|FitnessBrowser__Miya:8501587  601 IMVNSNPETVSTDYDTSDRLYFEPLTFEDVMNIIETEKPDGVVVQFGGQTPLNLAVPLMRAGVPILGTSPDSIDR 675 
                                        *************************************************************************** PP

                         TIGR01369  667 aEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevsk 741 
                                        aEdRe+F++ll++lg+ qp+++++ s+ ea+++a++igyP +vRpsyvlgGrameiv++ee+l++y+ + v   +
  lcl|FitnessBrowser__Miya:8501587  676 AEDRERFQALLQKLGLRQPANATVMSLPEARSAAARIGYPTVVRPSYVLGGRAMEIVYDEEQLAEYFANSVGEKP 750 
                                        *************************************************************************** PP

                         TIGR01369  742 ekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelk 816 
                                        ++P+lidk+le+a+EvdvDa++dg++v++agi+eHiEeaG+HsGDs++v+pp++l e ++++i +++ ++a+el+
  lcl|FitnessBrowser__Miya:8501587  751 KHPILIDKFLESAIEVDVDALSDGTDVYVAGIMEHIEEAGIHSGDSACVIPPHTLPEAIVNEIARQTVELARELR 825 
                                        *************************************************************************** PP

                         TIGR01369  817 vkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaav 891 
                                        v+Gl+niqf+vkd+ +y++Evn+RasRt Pfvska+ vpl +la++++lg++l+el+    ++ ++ +++vk++v
  lcl|FitnessBrowser__Miya:8501587  826 VVGLMNIQFAVKDGLIYILEVNPRASRTAPFVSKATAVPLPRLATQIMLGATLKELDP--WSMRRTGYFSVKESV 898 
                                        *******************************************************998..6677778******** PP

                         TIGR01369  892 fsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekgl 966 
                                        f+f+++ gvd++lgpem+stGEvmgi++++eea+lk +la ++++++ g++++sv+d+dk  ++e+a+++a++g+
  lcl|FitnessBrowser__Miya:8501587  899 FPFNRFPGVDILLGPEMRSTGEVMGIASSFEEAYLKGQLAGGQRLPQSGKIFISVNDRDKLLITEVASMFADLGF 973 
                                        *************************************************************************** PP

                         TIGR01369  967 kvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvte 1041
                                        +v+at+gtak l+e g+ a+ v+kv e +++i++ +k+++i lv+n++s +k++++++++ir+++++y+vp+ t+
  lcl|FitnessBrowser__Miya:8501587  974 EVLATSGTAKLLREGGVPATSVHKVYEGRPNIVDFIKNGDIALVLNTAS-GKRTVQDSKSIRQATLMYGVPYSTT 1047
                                        **********************************************998.88899999***************** PP

                         TIGR01369 1042 letaealleal 1052
                                        +++a+a+++a+
  lcl|FitnessBrowser__Miya:8501587 1048 VSGAKAIAQAI 1058
                                        ******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1078 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: 00:00:00.09
# Mc/sec: 12.03
//
[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