Alignments for a candidate for acs in Methanoculleus horonobensis T10

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanoculleus horonobensis T10

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_067073759.1 MCUHO_RS04125 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_001602375.1:WP_067073759.1
          Length = 632

 Score =  701 bits (1810), Expect = 0.0
 Identities = 340/636 (53%), Positives = 457/636 (71%), Gaps = 6/636 (0%)

Query: 1   MSKDTSVLLEEKRVFKPHYTVVEEAHIKNW-EAELEKGKDHENYWAEKAERLEWFRKWDR 59
           M+++  V LEE + + P     E++ + ++ +A  E   D + +W   A  LEWF+ WDR
Sbjct: 1   MAENFDVKLEEAKYYTPEAHCREQSWVGDYNQAYREFLSDPDGFWDTVARELEWFQPWDR 60

Query: 60  VLDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKL-TYYELYRE 118
           V  E N P+ RWF+NGK+N+T+N +DR +   +RN+VAI++  E  +E ++ TY +L++ 
Sbjct: 61  V-KEWNYPYARWFLNGKLNITHNCLDRHVHNQRRNKVAIMWRGETEEEERIFTYRQLFQA 119

Query: 119 VSRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLN 178
           V R AN LK LG+ KGD V +Y+P+ PE +V+MLACA+IGA+H+V++ G  V AL +R+ 
Sbjct: 120 VCRFANGLKRLGVGKGDRVCIYMPVVPEQIVAMLACARIGAIHTVVFGGFGVSALNQRIT 179

Query: 179 DARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREML 238
              AK++ITAD TYRRG  I LK IV+EA++  P++E  V+++  D+D  +      E+ 
Sbjct: 180 GTDAKVVITADVTYRRGKAIPLKNIVEEAVVNAPSVERIVILRR-DLDKPVELHPEMEVD 238

Query: 239 FDKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIH 298
           +  L EG    C AE MDAEDPLFILYTSG+TG PKG++HT GGYMVG   T    FD+ 
Sbjct: 239 YYDLTEGVERECPAEPMDAEDPLFILYTSGTTGSPKGIVHTCGGYMVGTYYTTRHVFDVK 298

Query: 299 NGDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYT 358
           + D++WCTAD GWITGHSY VYGPLL G T L+ E  PDYPDPG +W+++E+YGVT FYT
Sbjct: 299 DNDIYWCTADPGWITGHSYGVYGPLLNGATCLIAETTPDYPDPGTYWNLIEEYGVTIFYT 358

Query: 359 APTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQT 418
           APTAIR  MR G++ P RYNL SL++LG+VGEP+NPEA+ W+YR IG+++CPI+DTWWQT
Sbjct: 359 APTAIRMFMRVGEEWPDRYNLSSLRVLGSVGEPLNPEAFEWFYRTIGKDRCPIVDTWWQT 418

Query: 419 ETGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTL 478
           ETGMH++  +   P++PG   KP+PG+ ADVVD  G+P P G GG LV+R+PWP+M RT+
Sbjct: 419 ETGMHMVTTMIGEPMRPGFAGKPIPGVVADVVDMAGNPCPPGTGGLLVVREPWPSMMRTI 478

Query: 479 FNDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVF 538
           +ND+ RY   YW  +P G YTA D+A KD+DGY  + GRSDD++ +AGH IGTAEVES  
Sbjct: 479 WNDDDRY-RKYWNTVP-GCYTAADLAVKDKDGYIMVIGRSDDLIVVAGHNIGTAEVESAL 536

Query: 539 VAHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEM 598
           V+H AVAEAAVIGK D +KG  IKAF+IL+ G +    L  +L  H+R  LGP+A+  E+
Sbjct: 537 VSHEAVAEAAVIGKPDALKGNTIKAFVILRNGREPGEKLRNDLVYHVRMTLGPIAIPSEI 596

Query: 599 VQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
             VDSLPKTRSGKIMRR+L+A+E G D GD STLEE
Sbjct: 597 EFVDSLPKTRSGKIMRRVLKAQELGMDPGDISTLEE 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: 1292
Number of extensions: 80
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: 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_067073759.1 MCUHO_RS04125 (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.3357930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-264  863.1   0.0   6.8e-264  862.8   0.0    1.0  1  NCBI__GCF_001602375.1:WP_067073759.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001602375.1:WP_067073759.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  862.8   0.0  6.8e-264  6.8e-264       6     619 ..      29     632 .]      25     632 .] 0.98

  Alignments for each domain:
  == domain 1  score: 862.8 bits;  conditional E-value: 6.8e-264
                             TIGR02188   6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaii 77 
                                           +y++ y+e  +dp+ fw++ a+e lew++p+++v++++  p ++Wf +g+ln++ nc+drhv++ r++kvai+
  NCBI__GCF_001602375.1:WP_067073759.1  29 DYNQAYREFLSDPDGFWDTVARE-LEWFQPWDRVKEWN-YPYARWFLNGKLNITHNCLDRHVHNqRRNKVAIM 99 
                                           799*******************5.*************9.679********************9989******* PP

                             TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                           w g+ e+ ++r +tY++l++ vcr+an lk+lGv kgdrv+iY+p++pe ++amlacaRiGa+h+vvf+Gf  
  NCBI__GCF_001602375.1:WP_067073759.1 100 WRGETEE-EERIFTYRQLFQAVCRFANGLKRLGVGKGDRVCIYMPVVPEQIVAMLACARIGAIHTVVFGGFGV 171
                                           ****776.69*************************************************************** PP

                             TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelv 223
                                           +al++Ri+ ++ak+vitad ++R+gk+i+lk+iv+ea+ +a+ sve++++++r  ++ +e++ +++v + +l+
  NCBI__GCF_001602375.1:WP_067073759.1 172 SALNQRITGTDAKVVITADVTYRRGKAIPLKNIVEEAVVNAP-SVERIVILRRDLDKPVELHPEMEVDYYDLT 243
                                           *****************************************9.7********99888788************* PP

                             TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGh 296
                                           e ++++ec++e++d+edplfiLYtsG+tG PkG++ht gGy++ +++t++ vfd+kd+di+wCtaD GW+tGh
  NCBI__GCF_001602375.1:WP_067073759.1 244 E-GVERECPAEPMDAEDPLFILYTSGTTGSPKGIVHTCGGYMVGTYYTTRHVFDVKDNDIYWCTADPGWITGH 315
                                           *.6********************************************************************** PP

                             TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369
                                           sY vygPL+nGat l+ e++p+ypd++ +w++ie+y+vtifYtaPtaiR++m++gee++++++lsslrvlgsv
  NCBI__GCF_001602375.1:WP_067073759.1 316 SYGVYGPLLNGATCLIAETTPDYPDPGTYWNLIEEYGVTIFYTAPTAIRMFMRVGEEWPDRYNLSSLRVLGSV 388
                                           ************************************************************************* PP

                             TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442
                                           Gep+npea+eW+y+++Gk++cpivdtwWqtetG +++t++ g   +++pg a +P++G+ a+vvd  g+++ +
  NCBI__GCF_001602375.1:WP_067073759.1 389 GEPLNPEAFEWFYRTIGKDRCPIVDTWWQTETGMHMVTTMIGE--PMRPGFAGKPIPGVVADVVDMAGNPCPP 459
                                           ******************************************5..**************************** PP

                             TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515
                                           +++ g+Lv+++pwPsm+rti++d++r+  +Y+++++g+y + D a++dkdGyi+++GR Dd+i v+Gh++gta
  NCBI__GCF_001602375.1:WP_067073759.1 460 GTG-GLLVVREPWPSMMRTIWNDDDRYR-KYWNTVPGCYTAADLAVKDKDGYIMVIGRSDDLIVVAGHNIGTA 530
                                           999.8**********************7.5******************************************* PP

                             TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588
                                           e+esalvsheavaeaav+g+pd +kg++i afv+l++g+e+ e +l+++l  +vr ++gpia p++i++v++l
  NCBI__GCF_001602375.1:WP_067073759.1 531 EVESALVSHEAVAEAAVIGKPDALKGNTIKAFVILRNGREPGE-KLRNDLVYHVRMTLGPIAIPSEIEFVDSL 602
                                           ******************************************9.5**************************** PP

                             TIGR02188 589 PktRsGkimRRllrkiaegeellgdvstled 619
                                           PktRsGkimRR+l++   g    gd+stle+
  NCBI__GCF_001602375.1:WP_067073759.1 603 PKTRSGKIMRRVLKAQELG-MDPGDISTLEE 632
                                           *************986665.5567*****85 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 37.75
//
[ok]

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

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Protein sequences (fasta format)
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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