Alignments for a candidate for acs in Archaeoglobus veneficus SNP6

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Archaeoglobus veneficus SNP6

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_013683570.1 ARCVE_RS04375 acetate--CoA ligase

Query= BRENDA::A0B8F1
         (659 letters)



>NCBI__GCF_000194625.1:WP_013683570.1
          Length = 647

 Score =  709 bits (1831), Expect = 0.0
 Identities = 341/642 (53%), Positives = 461/642 (71%), Gaps = 20/642 (3%)

Query: 27  SNSYQWMKKKGFKTEKEMREWC----------AQNYLDFWDEMAQTYADWFKPYTQILE- 75
           SNS ++   + ++  +E R++           AQ+YL FWDE+A+   +WF+PY  +L+ 
Sbjct: 2   SNSKEFSPGEIYEPSEETRKYAWVNNERIYEMAQDYLTFWDEVAKNDVEWFEPYEDVLDD 61

Query: 76  WNPPYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYYFVGEPVGDTKTITYYQLYQAVNKM 135
            N P+ +WF+GGK N+ HN +DRH K  + +K A  + GEP  + + ITY++LYQ V + 
Sbjct: 62  SNAPFYRWFVGGKINITHNCLDRHIKL-KGDKTAIIWQGEPENEKEKITYHELYQRVCRF 120

Query: 136 ANGLKSLGVKKG-DRVSIYLPMIPELPITMLACAKIGAIHSVVFSGFSAGGLQSRVTDAE 194
           AN L++LGV++  D V+IY+ M+PELPI MLACA+IGAIHSVVF GFS+  L+ R+ DAE
Sbjct: 121 ANALRTLGVEEEEDVVTIYMGMVPELPIAMLACARIGAIHSVVFGGFSSKALRDRINDAE 180

Query: 195 AKVVVTSDGFYRRGKPLPLKPNVDEAVQNAPSVEKVVVVKRVGLDVPMKEGRDIWYHDLV 254
           +KVVVT DG+YRRGK +  K  VDEA++NAPSVE VVV++R G DV M EGRD+W+H+L 
Sbjct: 181 SKVVVTMDGYYRRGKVVETKRIVDEALENAPSVESVVVLERTGNDVNMVEGRDVWWHELE 240

Query: 255 KDQPAECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYTTAWALDVHEEDVY 314
           +  P +C    LD E  LFILYTSGTTGKPKG+ H HGG+ VG   TT W  D+ + D++
Sbjct: 241 EGLPDKCECRPLDSEHTLFILYTSGTTGKPKGVLHVHGGYNVGTHITTKWVFDLKDRDIF 300

Query: 315 WCTADCGWITGHSYVVYGPLCLGATSILYEGAPDYPDIGRWWSIIEEYGVSVFYTAPTAI 374
           WCTAD GWITGHSYVVYGPL +GAT ++YEGAPD+P   RWWSIIE+YGV++ YTAPTAI
Sbjct: 301 WCTADIGWITGHSYVVYGPLSVGATVLMYEGAPDHPQPDRWWSIIEQYGVTILYTAPTAI 360

Query: 375 RMFMKAGDQWPKKYNLKSIRILASVGEPLNPEAYVWFRNNIGGGQAPIIDTWWQTETGCH 434
           R FMK G++WPKK++L S+R+L +VGE ++P+A+ W+  +IG  + PI+DTWWQTETG  
Sbjct: 361 RYFMKLGEEWPKKHDLSSLRLLGTVGETIDPKAWKWYYKHIGNERCPIVDTWWQTETGMI 420

Query: 435 VIAPLP-MTPEKPGSVAFPLPGFNTDIYDEDGNSVPLGYGGNIVQKTPWPSMLRAFFRDP 493
           +I PLP +T  KPGS   P PG   DI DE G S      G +V   PWP+M R  + +P
Sbjct: 421 MITPLPGITKLKPGSATLPFPGIEVDIRDEKGYSAD---SGELVITNPWPAMFRTLWGEP 477

Query: 494 ERYMKEYWQMYWDIKPGTYLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAEVESAAV 553
           ER+ K+YW+    +    Y  GD A +D++GY+WI GRID+VLKV+GHR+ +AE+E A +
Sbjct: 478 ERFAKQYWRSNGGL---IYYTGDGARKDENGYYWIIGRIDEVLKVSGHRLGSAEIEGALI 534

Query: 554 SHPAVAEAAVIGKPDEVKGEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVAYPEIVY 613
           SH AV+EAAV+GKP E+KGE  VAF++LK G + S +L++D+ KHVR+ +G +A PE +Y
Sbjct: 535 SHEAVSEAAVVGKPHEIKGETPVAFVVLKTGYEPSVELEEDLKKHVRNEIGAIAVPEGIY 594

Query: 614 FVKDVPKTRSGKIMRRVIKAKALGKPVGDISALANPESVENI 655
           FV+ +PKTRSGKIMRR++ A   G+ VGDI+ L +   VE I
Sbjct: 595 FVEQLPKTRSGKIMRRILLAIEKGEEVGDITTLEDVTVVEKI 636


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: 1375
Number of extensions: 73
Number of successful extensions: 7
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: 647
Length adjustment: 38
Effective length of query: 621
Effective length of database: 609
Effective search space:   378189
Effective search space used:   378189
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_013683570.1 ARCVE_RS04375 (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.2308577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-292  957.5   1.4   1.8e-292  957.2   1.4    1.0  1  NCBI__GCF_000194625.1:WP_013683570.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000194625.1:WP_013683570.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  957.2   1.4  1.8e-292  1.8e-292      12     628 ..      31     638 ..      21     639 .. 0.97

  Alignments for each domain:
  == domain 1  score: 957.2 bits;  conditional E-value: 1.8e-292
                             TIGR02188  12 eeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrkdkvaiiwegdeeg 84 
                                            e ++d+ +fw++ ak+ +ew++p+e vld+s++p+++Wf++g++n++ nc+drh++ + dk+aiiw g+ e+
  NCBI__GCF_000194625.1:WP_013683570.1  31 YEMAQDYLTFWDEVAKNDVEWFEPYEDVLDDSNAPFYRWFVGGKINITHNCLDRHIKLKGDKTAIIWQGEPEN 103
                                           456789****************************************************************555 PP

                             TIGR02188  85 edsrkltYaellrevcrlanvlkelGvkk.gdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeR 156
                                            +++k+tY+el+++vcr+an+l++lGv++  d v+iY+ m+pe+ iamlacaRiGa+hsvvf+Gfs++al++R
  NCBI__GCF_000194625.1:WP_013683570.1 104 -EKEKITYHELYQRVCRFANALRTLGVEEeEDVVTIYMGMVPELPIAMLACARIGAIHSVVFGGFSSKALRDR 175
                                           .69************************86268899************************************** PP

                             TIGR02188 157 ivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeasa 229
                                           i+dae+k+v+t d+ +R+gkv+e+k+ivdeale+a+ sve+v+v++rtg++v+ ++egrDvww+el e + ++
  NCBI__GCF_000194625.1:WP_013683570.1 176 INDAESKVVVTMDGYYRRGKVVETKRIVDEALENAP-SVESVVVLERTGNDVN-MVEGRDVWWHELEE-GLPD 245
                                           ***********************************9.7*************66.************99.6*** PP

                             TIGR02188 230 ecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                           +ce+++ldse+ lfiLYtsG+tGkPkGvlh  gGy + +++t+k+vfd+kd difwCtaD+GW+tGhsY+vyg
  NCBI__GCF_000194625.1:WP_013683570.1 246 KCECRPLDSEHTLFILYTSGTTGKPKGVLHVHGGYNVGTHITTKWVFDLKDRDIFWCTADIGWITGHSYVVYG 318
                                           ************************************************************************* PP

                             TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinp 375
                                           PL++Gat l++eg+p++p+++r+w++ie+y+vti+YtaPtaiR +mklgee++kkhdlsslr+lg+vGe i+p
  NCBI__GCF_000194625.1:WP_013683570.1 319 PLSVGATVLMYEGAPDHPQPDRWWSIIEQYGVTILYTAPTAIRYFMKLGEEWPKKHDLSSLRLLGTVGETIDP 391
                                           ************************************************************************* PP

                             TIGR02188 376 eaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                           +aw+Wyy+++G+e+cpivdtwWqtetG i+itplpg +t+lkpgsatlP++Gie+++ de+g ++++    g 
  NCBI__GCF_000194625.1:WP_013683570.1 392 KAWKWYYKHIGNERCPIVDTWWQTETGMIMITPLPG-ITKLKPGSATLPFPGIEVDIRDEKGYSADS----GE 459
                                           ************************************.5************************98765....67 PP

                             TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesa 520
                                           Lvi++pwP+m+rt++g++erf ++Y+++  g +y+tGDgar+d++Gy+wi+GR+D+v++vsGhrlg+aeie a
  NCBI__GCF_000194625.1:WP_013683570.1 460 LVITNPWPAMFRTLWGEPERFAKQYWRSNGGlIYYTGDGARKDENGYYWIIGRIDEVLKVSGHRLGSAEIEGA 532
                                           9*************************9888789**************************************** PP

                             TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRs 593
                                           l+sheav+eaavvg+p+eikge+ vafvvlk+g+e++ e le++lkk+vr+eig+ia p+ i++ve+lPktRs
  NCBI__GCF_000194625.1:WP_013683570.1 533 LISHEAVSEAAVVGKPHEIKGETPVAFVVLKTGYEPSVE-LEEDLKKHVRNEIGAIAVPEGIYFVEQLPKTRS 604
                                           **************************************5.********************************* PP

                             TIGR02188 594 GkimRRllrkiaegeellgdvstledpsvveelke 628
                                           GkimRR+l +i +gee+ gd++tled +vve++ke
  NCBI__GCF_000194625.1:WP_013683570.1 605 GKIMRRILLAIEKGEEV-GDITTLEDVTVVEKIKE 638
                                           ***********998776.5*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (647 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: 00:00:00.02
# Mc/sec: 16.72
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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