Alignments for a candidate for acs in Methanospirillum lacunae Ki8-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanospirillum lacunae Ki8-1

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109967121.1 DK846_RS01335 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_003173355.1:WP_109967121.1
          Length = 622

 Score =  673 bits (1737), Expect = 0.0
 Identities = 324/622 (52%), Positives = 439/622 (70%), Gaps = 5/622 (0%)

Query: 14  VFKPHYTVVEEAHIKNWEAELEK-GKDHENYWAEKAERLEWFRKWDRVLDESNRPFYRWF 72
           ++ P  +  E A I N+  + ++  KD + +W   A  L WF  WD+V    + PF RWF
Sbjct: 5   IYYPDSSYKETAKIHNYSDKYQEFTKDPDAFWRRIASDLLWFEPWDQVR-VWDHPFARWF 63

Query: 73  VNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANALKSLGIK 132
            N K+N+TYN ++R L+ D+RN+VAI +V E   ER LTYY+L+++V R AN LKSLG+ 
Sbjct: 64  TNAKLNITYNCLERHLNNDRRNKVAICWVGENNRERILTYYQLHKDVMRFANGLKSLGVT 123

Query: 133 KGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKIIITADGTY 192
           KGD V +Y+P  PE+VV+MLACA+IGAVH+V+++G    AL ER+  +++K++ITAD T 
Sbjct: 124 KGDRVCIYMPAIPEMVVAMLACARIGAVHTVVFAGYGAKALNERITGSQSKVVITADSTV 183

Query: 193 RRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEGEGDRCDA 252
           RRGG I LKPIV+EAI+  P +E  VV++  +  + + D    E+ F+ L+     +C  
Sbjct: 184 RRGGSIPLKPIVEEAIINAPMVEKVVVLRTQEPKVGLLD--DLEIDFEDLMSSVPRQCPP 241

Query: 253 EEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWCTADIGWI 312
           E + +EDPLFILYTSG+TG PKG++H  GGYMVG   T +    +   DL+WCTAD GWI
Sbjct: 242 EPVGSEDPLFILYTSGTTGAPKGIVHAAGGYMVGAYYTTKYVLTLQENDLYWCTADPGWI 301

Query: 313 TGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDK 372
           TGH+Y  YGPLL+G T  + E  PDYPDPGVWW ++E+YGV+ FYTAPTAIR  M+ G +
Sbjct: 302 TGHTYGTYGPLLVGGTIFMTEYTPDYPDPGVWWRLIEEYGVSIFYTAPTAIRMFMKVGSE 361

Query: 373 HPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTP 432
            P + +L SL+ILG+VGEP+NPEA+ W+Y NIG++ CPI+DTWWQTETGMH+I  +   P
Sbjct: 362 IPDKSDLSSLRILGSVGEPLNPEAFEWFYHNIGKDHCPILDTWWQTETGMHMITTMVGEP 421

Query: 433 LKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRYIDVYWKQ 492
           +KPG   KP+PGI ADVV++ GDPVP G  GFL I++PWP+M + +  +E+RY   YW  
Sbjct: 422 MKPGFAGKPIPGIVADVVNDEGDPVPSGTTGFLAIKEPWPSMMQMVHQNEERYRG-YWNF 480

Query: 493 IPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVAEAAVIGK 552
                Y+  D+A KD+DGY  + GRSDD++ +AGH +GTAE+ES  V+H +VAEAA IGK
Sbjct: 481 GKYHYYSTNDLAVKDDDGYIMLLGRSDDIIIVAGHNVGTAEIESALVSHQSVAEAAAIGK 540

Query: 553 ADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLPKTRSGKI 612
            D +KG +IKAF+IL+ G      LI +LK H+R  LGP++V  E+  V++LPKTRSGKI
Sbjct: 541 PDDLKGNLIKAFVILRNGVIPTPKLIHDLKYHVRMMLGPISVPAELEFVETLPKTRSGKI 600

Query: 613 MRRILRAREEGEDLGDTSTLEE 634
           MRR+L+ARE G D GD STLEE
Sbjct: 601 MRRVLKAREMGMDPGDVSTLEE 622


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: 1208
Number of extensions: 55
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: 622
Length adjustment: 38
Effective length of query: 596
Effective length of database: 584
Effective search space:   348064
Effective search space used:   348064
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_109967121.1 DK846_RS01335 (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.1228293.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-249  812.7   0.0   1.1e-248  812.5   0.0    1.0  1  NCBI__GCF_003173355.1:WP_109967121.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173355.1:WP_109967121.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.5   0.0  1.1e-248  1.1e-248       3     619 ..      17     622 .]      15     622 .] 0.97

  Alignments for each domain:
  == domain 1  score: 812.5 bits;  conditional E-value: 1.1e-248
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                           ++++y++ y+e ++dp++fw++ a++ l w++p+++v+ ++ +p+++Wf++++ln++ync++rh+++ r++kv
  NCBI__GCF_003173355.1:WP_109967121.1  17 KIHNYSDKYQEFTKDPDAFWRRIASD-LLWFEPWDQVRVWD-HPFARWFTNAKLNITYNCLERHLNNdRRNKV 87 
                                           7899*********************6.*************9.78**********************99***** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           ai w g+++   +r ltY++l+++v r+an lk+lGv kgdrv+iY+p ipe+v+amlacaRiGavh+vvfaG
  NCBI__GCF_003173355.1:WP_109967121.1  88 AICWVGENNR--ERILTYYQLHKDVMRFANGLKSLGVTKGDRVCIYMPAIPEMVVAMLACARIGAVHTVVFAG 158
                                           *******776..5************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           + a+al+eRi+ +++k+vitad ++R+g +i+lk iv+ea+ +a+ +vekv+v++ ++ +v  + ++ ++ +e
  NCBI__GCF_003173355.1:WP_109967121.1 159 YGAKALNERITGSQSKVVITADSTVRRGGSIPLKPIVEEAIINAP-MVEKVVVLRTQEPKVG-LLDDLEIDFE 229
                                           ********************************************9.7******999888866.99******** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           +l+++ ++++c+pe+++sedplfiLYtsG+tG PkG++h++gGy++ a++t+kyv  ++++d +wCtaD GW+
  NCBI__GCF_003173355.1:WP_109967121.1 230 DLMSS-VPRQCPPEPVGSEDPLFILYTSGTTGAPKGIVHAAGGYMVGAYYTTKYVLTLQENDLYWCTADPGWI 301
                                           ****6.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+Y  ygPL++G t ++ e +p+ypd++ +w++ie+y+v+ifYtaPtaiR++mk+g+e+++k dlsslr+l
  NCBI__GCF_003173355.1:WP_109967121.1 302 TGHTYGTYGPLLVGGTIFMTEYTPDYPDPGVWWRLIEEYGVSIFYTAPTAIRMFMKVGSEIPDKSDLSSLRIL 374
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGep+npea+eW+y+++Gk++cpi dtwWqtetG ++it++ g   ++kpg a +P++Gi a+vv++eg++
  NCBI__GCF_003173355.1:WP_109967121.1 375 GSVGEPLNPEAFEWFYHNIGKDHCPILDTWWQTETGMHMITTMVGE--PMKPGFAGKPIPGIVADVVNDEGDP 445
                                           *********************************************5..************************* PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                           v ++++ g+L+ik+pwPsm++ ++++eer+   Y++  k  +y t D a++d+dGyi++lGR Dd+i v+Gh+
  NCBI__GCF_003173355.1:WP_109967121.1 446 VPSGTT-GFLAIKEPWPSMMQMVHQNEERYRG-YWNFGKYhYYSTNDLAVKDDDGYIMLLGRSDDIIIVAGHN 516
                                           ***999.8**********************75.7775554488899*************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584
                                           +gtaeiesalvsh++vaeaa++g+pd++kg+ i afv+l++gv ++  +l ++lk +vr ++gpi+ p+++++
  NCBI__GCF_003173355.1:WP_109967121.1 517 VGTAEIESALVSHQSVAEAAAIGKPDDLKGNLIKAFVILRNGVIPTP-KLIHDLKYHVRMMLGPISVPAELEF 588
                                           **********************************************9.5************************ PP

                             TIGR02188 585 veelPktRsGkimRRllrkiaegeellgdvstled 619
                                           ve+lPktRsGkimRR+l++   g    gdvstle+
  NCBI__GCF_003173355.1:WP_109967121.1 589 VETLPKTRSGKIMRRVLKAREMGM-DPGDVSTLEE 622
                                           *****************9876655.567*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (622 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: 21.35
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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