Alignments for a candidate for acs in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfobacter vibrioformis DSM 8776

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_035239235.1 Q366_RS12130 acetate--CoA ligase

Query= BRENDA::Q9NR19
         (701 letters)



>NCBI__GCF_000745975.1:WP_035239235.1
          Length = 654

 Score =  798 bits (2062), Expect = 0.0
 Identities = 379/667 (56%), Positives = 483/667 (72%), Gaps = 27/667 (4%)

Query: 32  PPEVSRSAHVPSLQRYRELHRRSVEEPREFWGDIAKEFYWKTPCPGPFLRYNFDVTKGKI 91
           P +   +A + S+  Y+ ++++SVE+P  FWG+IA+ FYW+         +N+ ++KG I
Sbjct: 9   PDKFRENAWIKSMDEYKAMYQKSVEDPEGFWGEIAETFYWEKKWD-KVREFNYSMSKGPI 67

Query: 92  FIEWMKGATTNICYNVLDRNVHEKKLGDKVAFYWEGNEPGETTQITYHQLLVQVCQFSNV 151
            IEW K A TNI YN LDR++  +  GD+ A  WEGN PGE   ITY  L  +VC+F+N 
Sbjct: 68  SIEWFKNARTNITYNCLDRHLDTR--GDQAALIWEGNSPGEDMVITYRALHEKVCRFANA 125

Query: 152 LRKQGIQKGDRVAIYMPMIPELVVAMLACARIGALHSIVFAGFSSESLCERILDSSCSLL 211
           L++ G+ KGDRVAIY+PM+PEL + M+ACARIGA+HSIVF GFSSE+L  RI+DS C +L
Sbjct: 126 LKESGVGKGDRVAIYLPMVPELAITMMACARIGAIHSIVFGGFSSEALANRIMDSLCKVL 185

Query: 212 ITTDAFYRGEKLVNLKELADEALQKCQEKGFPVRCCIVVKHLGRAELGMGDSTSQSPPIK 271
           +T+D   RG K V LK  AD+AL+ C ++G  V  C VVK  G                 
Sbjct: 186 VTSDGVMRGAKSVPLKGNADQALKMCADQGHVVETCFVVKRTGSG--------------- 230

Query: 272 RSCPDVQISWNQGIDLWWHELMQEAGDECEPEWCDAEDPLFILYTSGSTGKPKGVVHTVG 331
                  I+  +  D+WWHE  Q    EC  EW DAEDPLFILYTSGSTG PKGV H VG
Sbjct: 231 -------INMVENRDVWWHEAAQAQSAECPVEWMDAEDPLFILYTSGSTGTPKGVQHNVG 283

Query: 332 GYMLYVATTFKYVFDFHAEDVFWCTADIGWITGHSYVTYGPLANGATSVLFEGIPTYPDV 391
           GYM+Y  TTFKY+FD+H  DV+WCTADIGW+TGHSY+ YGPL+ GATS++FEGIP+YPD 
Sbjct: 284 GYMVYTGTTFKYIFDYHDGDVYWCTADIGWVTGHSYIVYGPLSQGATSIIFEGIPSYPDP 343

Query: 392 NRLWSIVDKYKVTKFYTAPTAIRLLMKFGDEPVTKHSRASLQVLGTVGEPINPEAWLWYH 451
            R W+ VDK+KV +FYTAPTAIR LM  GDE V ++  +SL++LG+VGEPINPEAW WYH
Sbjct: 344 GRFWATVDKWKVNQFYTAPTAIRSLMAQGDEWVAQYDLSSLRLLGSVGEPINPEAWQWYH 403

Query: 452 RVVGAQRCPIVDTFWQTETGGHMLTPLPGATPMKPGSATFPFFGVAPAILNESGEELEGE 511
           + VG ++CPIVDT+WQTETGG M++ LP A   KPGSAT PFF V P +L E G+ELEG 
Sbjct: 404 KHVGKEQCPIVDTWWQTETGGIMISALPYAIDQKPGSATLPFFSVQPVVLGEDGKELEGA 463

Query: 512 AEGYLVFKQPWPGIMRTVYGNHERFETTYFKKFPGYYVTGDGCQRDQDGYYWITGRIDDM 571
            EG L  K+PWPG MRTVY +H+RFE TYF+ F GYY  GDGC+RD+DGY+WITGR+DD+
Sbjct: 464 CEGILAIKEPWPGQMRTVYNSHDRFEMTYFQMFDGYYFAGDGCRRDEDGYFWITGRVDDV 523

Query: 572 LNVSGHLLSTAEVESALVEHEAVAEAAVVGHPHPVKGECLYCFVTLCDGHTFSPKLTEEL 631
           +NVSGH +ST+EVESAL  H+ VAEAAV+G+PH +KG+ +Y F+TL  G + S +L  +L
Sbjct: 524 INVSGHRMSTSEVESALGSHKDVAEAAVIGYPHDIKGQGIYAFITLNIGVSPSDELMADL 583

Query: 632 KKQIREKIGPIATPDYIQNAPGLPKTRSGKIMRRVLRKIAQNDHD-LGDMSTVADPSVIS 690
           K+ +R +IGPIATPD I  A  LPKTRSGKIMRR+LRKIA ++HD LGD+ST++DP V+ 
Sbjct: 584 KRHVRNEIGPIATPDIINFASDLPKTRSGKIMRRILRKIATDEHDQLGDISTLSDPEVVG 643

Query: 691 HLF-SHR 696
            L  SH+
Sbjct: 644 TLINSHK 650


Lambda     K      H
   0.320    0.138    0.440 

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: 1349
Number of extensions: 64
Number of successful extensions: 5
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: 701
Length of database: 654
Length adjustment: 39
Effective length of query: 662
Effective length of database: 615
Effective search space:   407130
Effective search space used:   407130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_035239235.1 Q366_RS12130 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# 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.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.3896604.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-302  990.1   0.2   2.3e-302  989.9   0.2    1.0  1  NCBI__GCF_000745975.1:WP_035239235.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035239235.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  989.9   0.2  2.3e-302  2.3e-302       2     628 ..      19     647 ..      18     648 .. 0.98

  Alignments for each domain:
  == domain 1  score: 989.9 bits;  conditional E-value: 2.3e-302
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.....kvkWfedgelnvsyncvdrhvek 69 
                                           ++++eyk++y++++edpe fw++ a+ ++ w k+++kv++ + +      +++Wf+++++n++ync+drh+ +
  NCBI__GCF_000745975.1:WP_035239235.1  19 KSMDEYKAMYQKSVEDPEGFWGEIAE-TFYWEKKWDKVREFNYSMskgpiSIEWFKNARTNITYNCLDRHLDT 90 
                                           789**********************9.6**********9765543336689********************** PP

                             TIGR02188  70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhs 142
                                           r d++a+iweg+++ge    +tY+ l+++vcr+an+lke Gv kgdrvaiYlpm+pe++i+m+acaRiGa+hs
  NCBI__GCF_000745975.1:WP_035239235.1  91 RGDQAALIWEGNSPGE-DMVITYRALHEKVCRFANALKESGVGKGDRVAIYLPMVPELAITMMACARIGAIHS 162
                                           **************96.99****************************************************** PP

                             TIGR02188 143 vvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewk 212
                                           +vf+Gfs+eala+Ri+d+ +k+++t+d+ +Rg k+++lk ++d+al+++ +    ve++ vvkrtg+ ++ ++
  NCBI__GCF_000745975.1:WP_035239235.1 163 IVFGGFSSEALANRIMDSLCKVLVTSDGVMRGAKSVPLKGNADQALKMCADqghVVETCFVVKRTGSGIN-MV 234
                                           ************************************************98777789************66.** PP

                             TIGR02188 213 egrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifw 285
                                           e+rDvww+e+ +  +saec++e++d+edplfiLYtsGstG+PkGv+h++gGy++++ +t+ky+fd++d+d++w
  NCBI__GCF_000745975.1:WP_035239235.1 235 ENRDVWWHEAAQA-QSAECPVEWMDAEDPLFILYTSGSTGTPKGVQHNVGGYMVYTGTTFKYIFDYHDGDVYW 306
                                           ************5.*********************************************************** PP

                             TIGR02188 286 CtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkh 358
                                           CtaD+GWvtGhsYivygPL++Gat+++feg+p+ypd++rfw++++k+kv++fYtaPtaiR+lm++g+e+v+++
  NCBI__GCF_000745975.1:WP_035239235.1 307 CTADIGWVTGHSYIVYGPLSQGATSIIFEGIPSYPDPGRFWATVDKWKVNQFYTAPTAIRSLMAQGDEWVAQY 379
                                           ************************************************************************* PP

                             TIGR02188 359 dlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieae 431
                                           dlsslr+lgsvGepinpeaw+Wy+++vGke+cpivdtwWqtetGgi+i++lp  a+++kpgsatlP+f ++++
  NCBI__GCF_000745975.1:WP_035239235.1 380 DLSSLRLLGSVGEPINPEAWQWYHKHVGKEQCPIVDTWWQTETGGIMISALPY-AIDQKPGSATLPFFSVQPV 451
                                           *****************************************************.6****************** PP

                             TIGR02188 432 vvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdv 504
                                           v+ e+gke+e   e g+L+ik+pwP+++rt+y+ ++rf  tYf+ ++g+yf+GDg+rrd+dGy+wi+GRvDdv
  NCBI__GCF_000745975.1:WP_035239235.1 452 VLGEDGKELEGACE-GILAIKEPWPGQMRTVYNSHDRFEMTYFQMFDGYYFAGDGCRRDEDGYFWITGRVDDV 523
                                           **********8888.8********************************************************* PP

                             TIGR02188 505 invsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpia 577
                                           invsGhr++t+e+esal sh++vaeaav+g+p++ikg+ i+af++l+ gv++++e l ++lk++vr+eigpia
  NCBI__GCF_000745975.1:WP_035239235.1 524 INVSGHRMSTSEVESALGSHKDVAEAAVIGYPHDIKGQGIYAFITLNIGVSPSDE-LMADLKRHVRNEIGPIA 595
                                           ******************************************************5.***************** PP

                             TIGR02188 578 kpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +pd i+++++lPktRsGkimRR+lrkia++e ++lgd+stl+dp+vv +l++
  NCBI__GCF_000745975.1:WP_035239235.1 596 TPDIINFASDLPKTRSGKIMRRILRKIATDEhDQLGDISTLSDPEVVGTLIN 647
                                           *******************************9***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (654 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 39.76
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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

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 catabolism of small carbon sources