Alignments for a candidate for acs in Desulfallas geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfallas geothermicus DSM 3669

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_092485848.1 BM299_RS14480 acetate--CoA ligase

Query= BRENDA::A0B8F1
         (659 letters)



>NCBI__GCF_900115975.1:WP_092485848.1
          Length = 685

 Score =  526 bits (1355), Expect = e-153
 Identities = 276/624 (44%), Positives = 397/624 (63%), Gaps = 33/624 (5%)

Query: 63  YADWFKPYTQILEWNP-----------PYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYY 111
           + + FK +  +L+W+            P  KWF+GGK N ++N VDRH   ++ NK A +
Sbjct: 58  FPECFKEFADLLDWDQYWHTTLDTSDAPCWKWFVGGKLNASYNCVDRHLDKYK-NKTAIH 116

Query: 112 FVGEPVGDTKT-ITYYQLYQAVNKMANGLKS-LGVKKGDRVSIYLPMIPELPITMLACAK 169
           FV EP  +    +TY +LY+ VN+ A  L+  +G+K GDRV+++LPM PELPITMLACA+
Sbjct: 117 FVPEPEDEPIVHMTYQELYRRVNETAAVLRDFVGLKAGDRVTLHLPMTPELPITMLACAR 176

Query: 170 IGAIHSVVFSGFSAGGLQSRVTDAEAKVVVTSDGFYRRGKPLPLKPNVDEAVQNAPS--- 226
           +G IHS VF+GFS      R+ D+E++V++T DG+YR GK L  K N D+AV+ A     
Sbjct: 177 LGVIHSQVFAGFSGQACGERIWDSESRVLITIDGYYRSGKLLDHKVNGDQAVEVAKKLGQ 236

Query: 227 -VEKVVVVKRV----GLDVPMKEGRDIWYHDLVKDQPAECYTEELDP-EDRLFILYTSGT 280
            V+K++V +R         PM EGRD +  DLVK    +       P E  LF++YTSG+
Sbjct: 237 DVDKILVWRRYPGKYSSAAPMVEGRDYFMDDLVKQYRGKIVQPVSMPAEGILFLMYTSGS 296

Query: 281 TGKPKGIEHAHGGFCVGPAYTTAWALDVHEEDVYWCTADCGWITGHSYVVYGPLCLGATS 340
           TG+PKG++H+ GG+     + +    D+H EDVYWC AD GWITGHS++VYGPL   A++
Sbjct: 297 TGRPKGVQHSIGGYLSYVTWMSKNIQDIHPEDVYWCMADIGWITGHSFIVYGPLSAAAST 356

Query: 341 ILYEGAPDYPDIGRWWSIIEEYGVSVFYTAPTAIRMFMKAGDQWPKKYNLKSIRILASVG 400
           +++EG P YPD GR W I EE  V++F+T+PTAIR   KAG   P KYN    + + +VG
Sbjct: 357 VIFEGVPTYPDAGRVWRIAEELDVNIFHTSPTAIRQLRKAGPDEPAKYNY-DFKHMTTVG 415

Query: 401 EPLNPEAYVWFRNNIGGGQAPIIDTWWQTETGCHVIAPLP-MTPEKPGSVAFPLPGFNTD 459
           EP+ PE + W+ N +G G+A I+DTWWQTETG  + + +P ++P KPGS    +PG +  
Sbjct: 416 EPIEPEVWRWYYNVVGKGRAAIVDTWWQTETGGFLCSTVPGLSPMKPGSAGPGVPGIHPV 475

Query: 460 IYDEDGNSVPLGYG--GNIVQKTPWPSMLRAFFRDPERYMKEYWQMY------WDIKPGT 511
           I+D++GN +  G G  GN+  + PWP  ++  ++D +RY+  Y+  Y       D +   
Sbjct: 476 IFDDEGNEIKPGEGKAGNVCIRNPWPGQMQTIWKDRDRYVSTYYGKYNKDPNSKDWRDWP 535

Query: 512 YLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAEVESAAVSHPAVAEAAVIGKPDEVK 571
           Y+AGD A    DGY  I GR+DDV+ VAGHR+   E+ESAA++   VAEAAVI   DE+K
Sbjct: 536 YMAGDAAVMSSDGYVRILGRVDDVINVAGHRLGTKEIESAALTVEEVAEAAVIAAKDEIK 595

Query: 572 GEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVAYPEIVYFVKDVPKTRSGKIMRRVI 631
           G V   ++ LK G + S++L   I++ V +V+G +A P  V+ V D+PKTRSGKIMRR++
Sbjct: 596 GTVPDLYVSLKPGYEASQELAVKISQAVSTVVGKIARPRSVHIVPDMPKTRSGKIMRRIL 655

Query: 632 KAKALGKPVGDISALANPESVENI 655
            + +    VGD+++LANP+ VE I
Sbjct: 656 ASISNRGDVGDVTSLANPDVVEQI 679


Lambda     K      H
   0.318    0.137    0.438 

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: 1391
Number of extensions: 82
Number of successful extensions: 9
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: 659
Length of database: 685
Length adjustment: 39
Effective length of query: 620
Effective length of database: 646
Effective search space:   400520
Effective search space used:   400520
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_092485848.1 BM299_RS14480 (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.7994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-231  754.8   0.0     4e-231  754.5   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092485848.1  BM299_RS14480 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092485848.1  BM299_RS14480 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  754.5   0.0    4e-231    4e-231      16     628 ..      56     681 ..      43     682 .. 0.96

  Alignments for each domain:
  == domain 1  score: 754.5 bits;  conditional E-value: 4e-231
                                 TIGR02188  16 edpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrkdkvaiiwegdeeg 84 
                                               ++  + +++ a   l+w++ ++++ld+s +p  kWf++g+ln+syncvdrh+ k k+k+ai++  + e+
  lcl|NCBI__GCF_900115975.1:WP_092485848.1  56 DNFPECFKEFAD-LLDWDQYWHTTLDTSDAPCWKWFVGGKLNASYNCVDRHLDKYKNKTAIHFVPEPED 123
                                               556667788887.7***************************************************9888 PP

                                 TIGR02188  85 edsrkltYaellrevcrlanvlke.lGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                               e   ++tY+el+r+v+++a+vl++ +G+k gdrv+++lpm+pe+ i+mlacaR+G++hs vfaGfs +a
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 124 EPIVHMTYQELYRRVNETAAVLRDfVGLKAGDRVTLHLPMTPELPITMLACARLGVIHSQVFAGFSGQA 192
                                               89**********************88******************************************* PP

                                 TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtg...eevaewkegr 215
                                                 eRi d+e++++it d+ +R gk ++ k + d+a+e a++   +v+k+lv +r     ++ a+++egr
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 193 CGERIWDSESRVLITIDGYYRSGKLLDHKVNGDQAVEVAKKlgqDVDKILVWRRYPgkySSAAPMVEGR 261
                                               ************************************988777779*********8622234578***** PP

                                 TIGR02188 216 DvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedif 284
                                               D+ +++lv++   + ++p ++ +e +lf++YtsGstG+PkGv+h+ gGyl +++   k + di++ed++
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 262 DYFMDDLVKQYRGKIVQPVSMPAEGILFLMYTSGSTGRPKGVQHSIGGYLSYVTWMSKNIQDIHPEDVY 330
                                               **********9999******************************************************* PP

                                 TIGR02188 285 wCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee 353
                                               wC+aD+GW+tGhs+ivygPL++ a+t++fegvptypda+r+w++ e+ +v+if+t+PtaiR l k+g +
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 331 WCMADIGWITGHSFIVYGPLSAAASTVIFEGVPTYPDAGRVWRIAEELDVNIFHTSPTAIRQLRKAGPD 399
                                               ********************************************************************* PP

                                 TIGR02188 354 lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsat 422
                                                ++k++ + ++ + +vGepi+pe w+Wyy+vvGk++++ivdtwWqtetGg+l +++pg + ++kpgsa 
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 400 EPAKYNYD-FKHMTTVGEPIEPEVWRWYYNVVGKGRAAIVDTWWQTETGGFLCSTVPG-LSPMKPGSAG 466
                                               ****9986.7999*********************************************.5********* PP

                                 TIGR02188 423 lPlfGieaevvdeegkeve.eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..........l 480
                                                 ++Gi++++ d+eg+e++  e ++g ++i++pwP++++ti++d +r+v+tY+ k+++           
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 467 PGVPGIHPVIFDDEGNEIKpGEGKAGNVCIRNPWPGQMQTIWKDRDRYVSTYYGKYNKdpnskdwrdwP 535
                                               *******************5444569******************************999999***9999 PP

                                 TIGR02188 481 yftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvv 549
                                               y++GD a++ +dGy+ ilGRvDdvinv+Ghrlgt+eiesa ++ e+vaeaav++++deikg +   +v 
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 536 YMAGDAAVMSSDGYVRILGRVDDVINVAGHRLGTKEIESAALTVEEVAEAAVIAAKDEIKGTVPDLYVS 604
                                               ********************************************************************* PP

                                 TIGR02188 550 lkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstle 618
                                               lk g+e+++e l+ ++ ++v++ +g+ia+p+++++v+++PktRsGkimRR+l +i + +  +gdv+ l+
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 605 LKPGYEASQE-LAVKISQAVSTVVGKIARPRSVHIVPDMPKTRSGKIMRRILASISN-RGDVGDVTSLA 671
                                               ********95.*******************************************987.55677****** PP

                                 TIGR02188 619 dpsvveelke 628
                                               +p vve++++
  lcl|NCBI__GCF_900115975.1:WP_092485848.1 672 NPDVVEQIRR 681
                                               *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (685 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 13.59
//
[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