Alignments for a candidate for acs in Methanospirillum stamsii Pt1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanospirillum stamsii Pt1

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109939574.1 DLD82_RS02360 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_003173335.1:WP_109939574.1
          Length = 629

 Score =  680 bits (1754), Expect = 0.0
 Identities = 322/596 (54%), Positives = 433/596 (72%), Gaps = 5/596 (0%)

Query: 39  DHENYWAEKAERLEWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAI 98
           D + +WA+KA  L+W + WD++ D    P  RWF  GK+N++ N +DR +   +RN++A+
Sbjct: 39  DPDGFWAKKARELDWIKPWDKIRDWE-WPQARWFCGGKLNVSANCLDRHVKNGRRNKLAL 97

Query: 99  LYVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIG 158
           ++  ERG E   TY +LYR V R ANALK+LG+KKGD V LY+P+ PE V++MLAC +IG
Sbjct: 98  IWKGERGKEEIYTYRQLYRAVMRFANALKNLGVKKGDCVCLYMPLVPEHVIAMLACTRIG 157

Query: 159 AVHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTV 218
           AVHS++++G    AL  R+ DA AK++ITAD   RRG  I L+ IVDEA+   P++E  V
Sbjct: 158 AVHSIVFAGFGAEALHTRIRDADAKVVITADVGIRRGKFIPLRSIVDEAVKNAPSVEKIV 217

Query: 219 VVKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLH 278
           V+      +E+   S  E+ F  + EG  + C  EEMD+EDPLFILYTSG+TG+PKG++H
Sbjct: 218 VLSRERCPVEL--YSEMEVDFYAIQEGVSEECPPEEMDSEDPLFILYTSGTTGQPKGIVH 275

Query: 279 TTGGYMVGVASTLEMTFDIHNGDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDY 338
           TTGGY+VG   T +  FD+   D+ WCTAD GWITGHSY+VYGPL +G T ++ E   DY
Sbjct: 276 TTGGYLVGTHYTSKYIFDLKENDVHWCTADTGWITGHSYIVYGPLSVGATVVITETTLDY 335

Query: 339 PDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWM 398
           PDPGVWW I+E++GVT FYTAPTAIR  MR G++ P +YNL SL+I+G+VGEP+NPEA+ 
Sbjct: 336 PDPGVWWKIIEEFGVTIFYTAPTAIRMFMRVGEEWPNKYNLSSLRIIGSVGEPLNPEAFE 395

Query: 399 WYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVP 458
           WYYR IG+ +CPI+DTWWQTETG+H+I      P+KPG    P+PG+ ADVVD+ G PVP
Sbjct: 396 WYYRVIGKNQCPILDTWWQTETGIHMITTPLGQPMKPGFAGVPIPGVVADVVDKEGKPVP 455

Query: 459 LGKGGFLVIRKPWPAMFRTLFNDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRS 518
            G+GG LVI++PWP+M RT+  +++RY+  YW QI    YT GD+A +DEDGY  + GRS
Sbjct: 456 AGQGGLLVIKEPWPSMMRTVHKNKERYLQ-YWNQI-NHWYTVGDLAVRDEDGYIMVLGRS 513

Query: 519 DDVLNIAGHRIGTAEVESVFVAHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALI 578
           DD++ +AGH +GTAEVES  VAH A+AEAAVIG  D +KG+ +KAF++L +G++ +  LI
Sbjct: 514 DDIIIVAGHNLGTAEVESALVAHEAIAEAAVIGVPDDMKGQAVKAFVVLCQGYEPSQKLI 573

Query: 579 EELKRHLRHELGPVAVVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
            EL  H+R  +GP+A+   +  +D LPKTRSGKIMRR+L+A+E G D GD STLEE
Sbjct: 574 SELIYHVRMTIGPIAMPSGIEFMDKLPKTRSGKIMRRVLKAKEMGVDPGDISTLEE 629


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: 1240
Number of extensions: 60
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: 629
Length adjustment: 38
Effective length of query: 596
Effective length of database: 591
Effective search space:   352236
Effective search space used:   352236
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_109939574.1 DLD82_RS02360 (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.76372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.2e-269  878.9   0.1   1.1e-268  878.6   0.1    1.0  1  NCBI__GCF_003173335.1:WP_109939574.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173335.1:WP_109939574.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  878.6   0.1  1.1e-268  1.1e-268       4     619 ..      26     629 .]      23     629 .] 0.97

  Alignments for each domain:
  == domain 1  score: 878.6 bits;  conditional E-value: 1.1e-268
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           l +yk+ y+e  +dp+ fwak+a+e l+w+kp++k++d++  p+++Wf +g+lnvs+nc+drhv++ r++k+a
  NCBI__GCF_003173335.1:WP_109939574.1  26 LGDYKKAYAEFLSDPDGFWAKKARE-LDWIKPWDKIRDWE-WPQARWFCGGKLNVSANCLDRHVKNgRRNKLA 96 
                                           568*********************5.*************9.5699**************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           +iw g+  +  ++ +tY++l+r v r+an+lk+lGvkkgd v++Y+p++pe viamlac+RiGavhs+vfaGf
  NCBI__GCF_003173335.1:WP_109939574.1  97 LIWKGERGK--EEIYTYRQLYRAVMRFANALKNLGVKKGDCVCLYMPLVPEHVIAMLACTRIGAVHSIVFAGF 167
                                           ******554..699*********************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                            aeal++Ri da+ak+vitad g+R+gk i+l++ivdea+++a+ svek++v+ r   +v+ + ++++v +  
  NCBI__GCF_003173335.1:WP_109939574.1 168 GAEALHTRIRDADAKVVITADVGIRRGKFIPLRSIVDEAVKNAP-SVEKIVVLSRERCPVE-LYSEMEVDFYA 238
                                           *******************************************9.7*************77.88899999999 PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           + e ++s+ec+pe++dsedplfiLYtsG+tG+PkG++httgGyl+ +++t ky+fd+k++d++wCtaD GW+t
  NCBI__GCF_003173335.1:WP_109939574.1 239 IQE-GVSEECPPEEMDSEDPLFILYTSGTTGQPKGIVHTTGGYLVGTHYTSKYIFDLKENDVHWCTADTGWIT 310
                                           999.6******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsYivygPL++Gat ++ e++ +ypd++ +w++ie+++vtifYtaPtaiR++m++gee+++k++lsslr++g
  NCBI__GCF_003173335.1:WP_109939574.1 311 GHSYIVYGPLSVGATVVITETTLDYPDPGVWWKIIEEFGVTIFYTAPTAIRMFMRVGEEWPNKYNLSSLRIIG 383
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGep+npea+eWyy+v+Gk++cpi dtwWqtetG ++it+  g   ++kpg a +P++G+ a+vvd+egk+v
  NCBI__GCF_003173335.1:WP_109939574.1 384 SVGEPLNPEAFEWYYRVIGKNQCPILDTWWQTETGIHMITTPLG--QPMKPGFAGVPIPGVVADVVDKEGKPV 454
                                           ***************************************99888..6************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                            ++++ g+Lvik+pwPsm+rt+++++er+ + Y++++++ y  GD a+rd+dGyi++lGR Dd+i v+Gh+lg
  NCBI__GCF_003173335.1:WP_109939574.1 455 PAGQG-GLLVIKEPWPSMMRTVHKNKERYLQ-YWNQINHWYTVGDLAVRDEDGYIMVLGRSDDIIIVAGHNLG 525
                                           **999.8**********************85.***************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           tae+esalv+hea+aeaav+gvpd++kg+a+ afvvl +g+e+++ +l +el+ +vr +igpia p+ i++++
  NCBI__GCF_003173335.1:WP_109939574.1 526 TAEVESALVAHEAIAEAAVIGVPDDMKGQAVKAFVVLCQGYEPSQ-KLISELIYHVRMTIGPIAMPSGIEFMD 597
                                           *********************************************.5************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaegeellgdvstled 619
                                           +lPktRsGkimRR+l++   g    gd+stle+
  NCBI__GCF_003173335.1:WP_109939574.1 598 KLPKTRSGKIMRRVLKAKEMGV-DPGDISTLEE 629
                                           ***************9866655.556*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (629 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: 35.47
//
[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