Alignments for a candidate for acs in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Sulfurihydrogenibium subterraneum DSM 15120

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_028951249.1 Q385_RS0108465 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000619805.1:WP_028951249.1
          Length = 630

 Score =  707 bits (1824), Expect = 0.0
 Identities = 353/633 (55%), Positives = 461/633 (72%), Gaps = 9/633 (1%)

Query: 5   TSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKG-KDHENYWAEKAERLEWFRKWDRVLDE 63
           + +LL+    + P   +V++A +K++E   ++  +D E ++++ AE LEWF+KWD+VL E
Sbjct: 4   SDLLLKVDEKYYPPEDIVQQAWVKDYEYLYKQSIEDREGFYSKIAEELEWFQKWDKVL-E 62

Query: 64  SNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTA 123
            + P+ +WFVNGK N+TYN +DR +   KRN+VA + V+E G+E+K+TY EL   VSR A
Sbjct: 63  WDYPYAKWFVNGKTNITYNCIDRHVKNGKRNKVAFISVDEEGNEKKVTYGELLYLVSRLA 122

Query: 124 NALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAK 183
           N LKSLGIKKGD V++Y+P   E  ++MLACA+IGA+HSV+++G S GAL  R++DA+AK
Sbjct: 123 NGLKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAIHSVVFAGFSEGALKIRVDDAKAK 182

Query: 184 IIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD--K 241
            +ITA  T RRG  I L P V EAI     +E  ++    D D E+SD      + D  K
Sbjct: 183 AVITATYTKRRGKKIPLFPTVKEAIKDLDFVEKIIL---WDRDNELSDEYEEHNVVDFYK 239

Query: 242 LIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGD 301
           LI+     C  E  DAEDPLFILYTSG+TGKPKGVLHTTGGYMV    T +  FD+   D
Sbjct: 240 LIKNSSKECPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDLKEND 299

Query: 302 LWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPT 361
           ++WCTAD+GWITGHSY+VYGPL  G T+++ EG P YP PG+WW  VEKYGV  FYTAPT
Sbjct: 300 IYWCTADVGWITGHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPT 359

Query: 362 AIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETG 421
           AIR LMRFG++ P +Y++ SLK+LG+VGEPINPEAW+WYY+NIGR K  I+DTWWQTETG
Sbjct: 360 AIRMLMRFGEEIPAKYDISSLKVLGSVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETG 419

Query: 422 MHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFND 481
            H+I  +P  P KPG   KP+ GIE  VVD+ G+P+P  + G LVI+ PWP+M RT + +
Sbjct: 420 AHMITTVPSYPAKPGKAGKPMFGIEVAVVDKQGNPMPPNQVGHLVIKNPWPSMLRTCWGE 479

Query: 482 EQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAH 541
            +RY + YW +IP G Y+AGD+A  DE+GY  + GR+DDVL++AGHRIGTAEVES  V +
Sbjct: 480 PERY-EKYWNEIP-GYYSAGDLAAIDEEGYIMVVGRADDVLSVAGHRIGTAEVESAIVEN 537

Query: 542 PAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQV 601
            AVAEAAVIGK + IKGE IKAF+ILK+G++ +  L E +K  +R  LGP+AV  E+  V
Sbjct: 538 HAVAEAAVIGKPNEIKGESIKAFVILKEGYEPSEELKERIKDTVRDVLGPIAVPDEIEFV 597

Query: 602 DSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           D LPKTRSGKIMRR+L+ARE G ++GDTSTLEE
Sbjct: 598 DKLPKTRSGKIMRRLLKARELGLEIGDTSTLEE 630


Lambda     K      H
   0.319    0.138    0.428 

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: 1239
Number of extensions: 43
Number of successful extensions: 4
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: 634
Length of database: 630
Length adjustment: 38
Effective length of query: 596
Effective length of database: 592
Effective search space:   352832
Effective search space used:   352832
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_028951249.1 Q385_RS0108465 (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.12995.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-267  874.1   1.7   2.9e-267  873.9   1.7    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028951249.1  Q385_RS0108465 acetate--CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028951249.1  Q385_RS0108465 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  873.9   1.7  2.9e-267  2.9e-267       4     619 ..      26     630 .]      23     630 .] 0.97

  Alignments for each domain:
  == domain 1  score: 873.9 bits;  conditional E-value: 2.9e-267
                                 TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rk 71 
                                               +++y+ ly+++ied+e f++k a+ elew+++++kvl+++  p +kWf++g++n++ync+drhv++ ++
  lcl|NCBI__GCF_000619805.1:WP_028951249.1  26 VKDYEYLYKQSIEDREGFYSKIAE-ELEWFQKWDKVLEWD-YPYAKWFVNGKTNITYNCIDRHVKNgKR 92 
                                               579********************9.5**************.679**********************9** PP

                                 TIGR02188  72 dkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140
                                               +kva i   +e +  ++k+tY ell  v+rlan lk+lG+kkgdrv+iY+p ++ea+iamlacaRiGa+
  lcl|NCBI__GCF_000619805.1:WP_028951249.1  93 NKVAFISVDEEGN--EKKVTYGELLYLVSRLANGLKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAI 159
                                               *****98766554..7***************************************************** PP

                                 TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeeva 209
                                               hsvvfaGfs  al+ R+ da+ak vita  + R+gk+i+l  +v ea+++ +  vek+++  r +e   
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 160 HSVVFAGFSEGALKIRVDDAKAKAVITATYTKRRGKKIPLFPTVKEAIKDLD-FVEKIILWDRDNELSD 227
                                               ***************************************************8.7***********9999 PP

                                 TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdi 278
                                               e++e   v + +l++ ++s+ec+pe  d+edplfiLYtsG+tGkPkGvlhttgGy++ +++t kyvfd+
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 228 EYEEHNVVDFYKLIK-NSSKECPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDL 295
                                               9**************.5**************************************************** PP

                                 TIGR02188 279 kdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRal 347
                                               k++di+wCtaDvGW+tGhsYivygPLanG+t+++ egvp yp+++ +we +eky+v++fYtaPtaiR+l
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 296 KENDIYWCTADVGWITGHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPTAIRML 364
                                               ********************************************************************* PP

                                 TIGR02188 348 mklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatel 416
                                               m+ gee+++k+d+ssl+vlgsvGepinpeaw Wyy+++G++k+ ivdtwWqtetG+++it++p+   ++
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 365 MRFGEEIPAKYDISSLKVLGSVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETGAHMITTVPS--YPA 431
                                               ****************************************************************..6** PP

                                 TIGR02188 417 kpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGD 485
                                               kpg a +P+fGie++vvd++g+++ +++  g Lvik+pwPsmlrt +g++er+  +Y+++++g+y +GD
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 432 KPGKAGKPMFGIEVAVVDKQGNPMPPNQV-GHLVIKNPWPSMLRTCWGEPERYE-KYWNEIPGYYSAGD 498
                                               *************************9999.8*********************95.6************* PP

                                 TIGR02188 486 garrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegv 554
                                                a+ d++Gyi+++GR+Ddv+ v+Ghr+gtae+esa+v+++avaeaav+g+p+eikge+i afv+lkeg+
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 499 LAAIDEEGYIMVVGRADDVLSVAGHRIGTAEVESAIVENHAVAEAAVIGKPNEIKGESIKAFVILKEGY 567
                                               ********************************************************************* PP

                                 TIGR02188 555 eedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619
                                               e++ee l++ +k++vr+ +gpia pd+i++v++lPktRsGkimRRll++   g  ++gd+stle+
  lcl|NCBI__GCF_000619805.1:WP_028951249.1 568 EPSEE-LKERIKDTVRDVLGPIAVPDEIEFVDKLPKTRSGKIMRRLLKARELGL-EIGDTSTLEE 630
                                               ****5.*****************************************9876665.566*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (630 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.05
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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

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