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_028950423.1 Q385_RS0103975 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000619805.1:WP_028950423.1
          Length = 632

 Score =  727 bits (1876), Expect = 0.0
 Identities = 354/629 (56%), Positives = 467/629 (74%), Gaps = 4/629 (0%)

Query: 7   VLLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDH-ENYWAEKAERLEWFRKWDRVLDESN 65
           V L+ K +F P   + +E  ++++E+  +K  ++ E +W+E A +L WF+KWD+VL E N
Sbjct: 7   VHLQVKEIFYPPEEIKKECIVQDYESMYKKSIENPEEFWSEIASQLHWFQKWDKVL-EWN 65

Query: 66  RPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANA 125
            P+ +WFVNGK N+TYN +D  ++  +RN+VA + V+E G+E+K+TY EL  +V+R AN 
Sbjct: 66  FPYAKWFVNGKTNITYNCLDANIEKGRRNKVAYISVDEEGNEKKITYGELLEQVNRFANG 125

Query: 126 LKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKII 185
           LKSLG+ KGD V++Y+P   E V++MLACA+IGA+HSV+++G S GAL  R+NDA+AK++
Sbjct: 126 LKSLGVSKGDRVSIYMPNTVEAVIAMLACARIGAIHSVVFAGFSEGALKLRINDAKAKVV 185

Query: 186 ITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEG 245
           ITA  T RRG  I L PIV EAI     ++  V+V   D ++E S+ S + +  ++LI+ 
Sbjct: 186 ITATYTKRRGKKIPLLPIVKEAIKDLDFVKH-VIVWDRDKELEESEFSKKFVSLEELIKS 244

Query: 246 EGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWC 305
               C+ E MDAEDPLFILYTSG+TGKPKGVLHT GGYMV    T ++ F+I    ++WC
Sbjct: 245 SSPNCNPEVMDAEDPLFILYTSGTTGKPKGVLHTVGGYMVNTYLTTKVVFNIKEDTVYWC 304

Query: 306 TADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRH 365
           TADIGWITGHSY+VYGPLL GTT ++ EG P YP PG+WW  V+KY V  FYTAPTAIR 
Sbjct: 305 TADIGWITGHSYIVYGPLLNGTTIVMMEGVPVYPHPGIWWEYVDKYRVNVFYTAPTAIRM 364

Query: 366 LMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLI 425
           LMRFGD+ P +Y+L SLK+LG+VGEPINPEAW+WYY+NIGR +  ++DTWWQTETG H+I
Sbjct: 365 LMRFGDEIPAKYDLSSLKVLGSVGEPINPEAWLWYYKNIGRGRAVVVDTWWQTETGAHMI 424

Query: 426 APLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRY 485
             LP  P KPG   KPL G+  DVVD+ G+ +P    G LVI++PWP+M RT + + +RY
Sbjct: 425 TTLPCYPAKPGKAGKPLFGVIPDVVDKEGNSLPPNTIGHLVIKQPWPSMLRTCWGEPERY 484

Query: 486 IDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVA 545
            + YWK+IPG VY+AGD+A  DEDGY  I GR+DDVL++AGHRIG AEVES  + HPAVA
Sbjct: 485 -EKYWKEIPGNVYSAGDLATIDEDGYIMILGRADDVLSVAGHRIGNAEVESAIIEHPAVA 543

Query: 546 EAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLP 605
           EAAVIGK + IKGE IKAF++LK+G+  +  LIEE+K  ++  LG +AV  E+  VD LP
Sbjct: 544 EAAVIGKPNEIKGESIKAFVVLKEGYSPSIELIEEIKETVKEILGAIAVPDEVEFVDKLP 603

Query: 606 KTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           KTRSGKIMRR+LRARE G+DLGD STLE+
Sbjct: 604 KTRSGKIMRRVLRARELGQDLGDISTLED 632


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: 1209
Number of extensions: 50
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: 632
Length adjustment: 38
Effective length of query: 596
Effective length of database: 594
Effective search space:   354024
Effective search space used:   354024
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_028950423.1 Q385_RS0103975 (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.14065.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   0.4   3.1e-267  873.8   0.4    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028950423.1  Q385_RS0103975 acetate--CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028950423.1  Q385_RS0103975 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  873.8   0.4  3.1e-267  3.1e-267       5     619 ..      28     632 .]      25     632 .] 0.97

  Alignments for each domain:
  == domain 1  score: 873.8 bits;  conditional E-value: 3.1e-267
                                 TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkd 72 
                                               ++y+++y+++ie+pe+fw++ a+ +l+w+++++kvl+++++  +kWf++g++n++ync+d ++ek r++
  lcl|NCBI__GCF_000619805.1:WP_028950423.1  28 QDYESMYKKSIENPEEFWSEIAS-QLHWFQKWDKVLEWNFP-YAKWFVNGKTNITYNCLDANIEKgRRN 94 
                                               79*********************.5*************975.89************************* PP

                                 TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavh 141
                                               kva i   +e +  ++k+tY ell++v+r+an lk+lGv kgdrv+iY+p ++eaviamlacaRiGa+h
  lcl|NCBI__GCF_000619805.1:WP_028950423.1  95 KVAYISVDEEGN--EKKITYGELLEQVNRFANGLKSLGVSKGDRVSIYMPNTVEAVIAMLACARIGAIH 161
                                               ***997766444..7****************************************************** PP

                                 TIGR02188 142 svvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevae 210
                                               svvfaGfs  al+ Ri+da+ak+vita  + R+gk+i+l  iv ea+++ +  v++v+v  r +e  ++
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 162 SVVFAGFSEGALKLRINDAKAKVVITATYTKRRGKKIPLLPIVKEAIKDLD-FVKHVIVWDRDKELEES 229
                                               **************************************************8.7********99887666 PP

                                 TIGR02188 211 wkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279
                                                 +++ v +eel+++ +s +c+pe +d+edplfiLYtsG+tGkPkGvlht+gGy++ ++lt+k+vf+ik
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 230 EFSKKFVSLEELIKS-SSPNCNPEVMDAEDPLFILYTSGTTGKPKGVLHTVGGYMVNTYLTTKVVFNIK 297
                                               677888999999995.***************************************************** PP

                                 TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalm 348
                                               ++ ++wCtaD+GW+tGhsYivygPL+nG t ++ egvp yp+++ +we ++ky+v++fYtaPtaiR+lm
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 298 EDTVYWCTADIGWITGHSYIVYGPLLNGTTIVMMEGVPVYPHPGIWWEYVDKYRVNVFYTAPTAIRMLM 366
                                               ********************************************************************* PP

                                 TIGR02188 349 klgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelk 417
                                               + g+e+++k+dlssl+vlgsvGepinpeaw Wyy+++G++++ +vdtwWqtetG+++it+lp    ++k
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 367 RFGDEIPAKYDLSSLKVLGSVGEPINPEAWLWYYKNIGRGRAVVVDTWWQTETGAHMITTLPC--YPAK 433
                                               **************************************************************9..6*** PP

                                 TIGR02188 418 pgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGD 485
                                               pg a +PlfG+ ++vvd+eg+++ +++  g Lvik+pwPsmlrt +g++er+  +Y+k+++g +y +GD
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 434 PGKAGKPLFGVIPDVVDKEGNSLPPNTI-GHLVIKQPWPSMLRTCWGEPERYE-KYWKEIPGnVYSAGD 500
                                               ************************9999.8*********************95.699*999889***** PP

                                 TIGR02188 486 garrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegv 554
                                                a+ d+dGyi+ilGR+Ddv+ v+Ghr+g ae+esa+++h+avaeaav+g+p+eikge+i afvvlkeg+
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 501 LATIDEDGYIMILGRADDVLSVAGHRIGNAEVESAIIEHPAVAEAAVIGKPNEIKGESIKAFVVLKEGY 569
                                               ********************************************************************* PP

                                 TIGR02188 555 eedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619
                                               +++ e l +e+k++v++ +g+ia pd++++v++lPktRsGkimRR+lr+   g + lgd+stled
  lcl|NCBI__GCF_000619805.1:WP_028950423.1 570 SPSIE-LIEEIKETVKEILGAIAVPDEVEFVDKLPKTRSGKIMRRVLRARELG-QDLGDISTLED 632
                                               ****5.******************************************87665.5677*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (632 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: 11.81
//
[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