Alignments for a candidate for acs in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Maridesulfovibrio zosterae DSM 11974

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_027720495.1 H589_RS0102105 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000425265.1:WP_027720495.1
          Length = 626

 Score =  703 bits (1815), Expect = 0.0
 Identities = 340/616 (55%), Positives = 442/616 (71%), Gaps = 8/616 (1%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWEAELEK---GKDHENYWAEKAERLEWFRKWDRVLDES 64
           LL E+RVF+P   ++ EA +   +    +     D   YW E AE+L+WF KW++VLD+S
Sbjct: 14  LLHEERVFRPLPQMIIEAGVNPQDLRAARELADNDLCAYWEEAAEKLDWFTKWEKVLDDS 73

Query: 65  NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124
           N P YRWF   + N+ YNA+DR ++T  +N++A+++  E GD R+ TYYELYR V+R AN
Sbjct: 74  NAPDYRWFAGARCNIVYNALDRHIETVNKNRLALIWEGEPGDSRQYTYYELYRAVNRFAN 133

Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184
            LK LG+ KGD V LY+P  PE V+SMLACA+IGAVH +++SG S   L ER+ +   K+
Sbjct: 134 GLKRLGVGKGDHVVLYMPQLPETVISMLACARIGAVHCLVFSGFSARLLRERVRELNPKV 193

Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCP--TIETTVVVKHTDIDIEMSDISGREMLFDKL 242
           ++T DG YR G VI+LK  VD A+L  P    E+ VVV   +++++M   S R+  ++ L
Sbjct: 194 VVTVDGFYRNGQVIRLKEEVDRALLDTPQDVPESVVVVHRANVEVDMD--SARDCWYEDL 251

Query: 243 IEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDL 302
           +  E     AE M A+DPLFIL+TSG+TG PKG++H+ GGYMVGV  T +  FD+   D+
Sbjct: 252 VRHERSHAPAEIMAADDPLFILHTSGTTGSPKGMIHSHGGYMVGVHRTFKWVFDLRPTDI 311

Query: 303 WWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTA 362
           +WC+AD GWITGHSY+VYGPLL GTTT++YEG   YP     W+I+ KYGV+ FYT+PT 
Sbjct: 312 FWCSADPGWITGHSYLVYGPLLAGTTTVMYEGHSLYPQADRMWNIISKYGVSIFYTSPTQ 371

Query: 363 IRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGM 422
           IR LMRFG K+P++++L +L+ILG VGEP NPEAW+W Y NIG+ +CP++DTWWQTETGM
Sbjct: 372 IRTLMRFGHKYPEQHDLSTLRILGAVGEPFNPEAWIWLYENIGKGQCPVLDTWWQTETGM 431

Query: 423 HLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDE 482
            +I+P+PV+ LKPGSVT+PLPGI ADVVD  G+PVP GKGGFLVI+KPWP+MF  +  D 
Sbjct: 432 IMISPMPVSVLKPGSVTRPLPGIYADVVDREGNPVPAGKGGFLVIKKPWPSMFSGVLGDN 491

Query: 483 QRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHP 542
           +   + YW  IPG  Y AGD+ARKDEDGYFWIQGR+DDVLNI+GHRIGTAEVES   +HP
Sbjct: 492 EAVRNHYWGHIPGMFY-AGDVARKDEDGYFWIQGRADDVLNISGHRIGTAEVESALTSHP 550

Query: 543 AVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVD 602
            VAEAAVIG AD IKG+V KA + L  G   +  L  ELK H+R ELGP+ +V  +   D
Sbjct: 551 HVAEAAVIGVADKIKGQVAKAHVTLNHGITESDDLHRELKEHIRRELGPIVIVRSIEFCD 610

Query: 603 SLPKTRSGKIMRRILR 618
            LPKT SGKI R  L+
Sbjct: 611 ELPKTSSGKIKRSALK 626


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: 1238
Number of extensions: 54
Number of successful extensions: 3
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: 626
Length adjustment: 38
Effective length of query: 596
Effective length of database: 588
Effective search space:   350448
Effective search space used:   350448
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_027720495.1 H589_RS0102105 (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.1944816.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-252  825.2   0.0   1.8e-252  825.0   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027720495.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027720495.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  825.0   0.0  1.8e-252  1.8e-252       8     601 ..      39     625 ..      33     626 .] 0.97

  Alignments for each domain:
  == domain 1  score: 825.0 bits;  conditional E-value: 1.8e-252
                             TIGR02188   8 kelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwe 79 
                                           ++  e a +d  ++w++ a+ +l+w++++ekvld+s++p+++Wf++++ n+ yn++drh+e+ +k+++a+iwe
  NCBI__GCF_000425265.1:WP_027720495.1  39 RAARELADNDLCAYWEEAAE-KLDWFTKWEKVLDDSNAPDYRWFAGARCNIVYNALDRHIETvNKNRLALIWE 110
                                           56677789999*****9888.6*************************************************** PP

                             TIGR02188  80 gdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                           g+ +g dsr++tY+el+r v+r+an lk+lGv kgd+v++Y+p +pe+vi mlacaRiGavh +vf+Gfsa  
  NCBI__GCF_000425265.1:WP_027720495.1 111 GE-PG-DSRQYTYYELYRAVNRFANGLKRLGVGKGDHVVLYMPQLPETVISMLACARIGAVHCLVFSGFSARL 181
                                           **.77.59***************************************************************** PP

                             TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesv.ekvlvvkrtgeevaewkegrDvwweelve 224
                                           l+eR+ + + k+v+t d+ +R+g+vi+lk+ vd+al +++++v e+v+vv+r++ ev  +++ rD w+e+lv+
  NCBI__GCF_000425265.1:WP_027720495.1 182 LRERVRELNPKVVVTVDGFYRNGQVIRLKEEVDRALLDTPQDVpESVVVVHRANVEVD-MDSARDCWYEDLVR 253
                                           *****************************************77478999*******66.************** PP

                             TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhs 297
                                           + ++++ ++e + ++dplfiL+tsG+tG PkG++h+ gGy++ ++ t+k+vfd++++difwC+aD GW+tGhs
  NCBI__GCF_000425265.1:WP_027720495.1 254 H-ERSHAPAEIMAADDPLFILHTSGTTGSPKGMIHSHGGYMVGVHRTFKWVFDLRPTDIFWCSADPGWITGHS 325
                                           6.99999****************************************************************** PP

                             TIGR02188 298 YivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvG 370
                                           Y+vygPL++G tt+++eg   yp+a+r+w++i ky+v+ifYt+Pt iR+lm+ g++ +++hdls+lr+lg+vG
  NCBI__GCF_000425265.1:WP_027720495.1 326 YLVYGPLLAGTTTVMYEGHSLYPQADRMWNIISKYGVSIFYTSPTQIRTLMRFGHKYPEQHDLSTLRILGAVG 398
                                           ************************************************************************* PP

                             TIGR02188 371 epinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveee 443
                                           ep npeaw W+ye++Gk++cp+ dtwWqtetG i+i+p+p     lkpgs t+Pl+Gi a+vvd+eg++v ++
  NCBI__GCF_000425265.1:WP_027720495.1 399 EPFNPEAWIWLYENIGKGQCPVLDTWWQTETGMIMISPMPV--SVLKPGSVTRPLPGIYADVVDREGNPVPAG 469
                                           ****************************************9..589**************************9 PP

                             TIGR02188 444 eeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtae 516
                                           ++ g+LvikkpwPsm+ ++ gd+e   + Y+ +++g++++GD ar+d+dGy+wi+GR+Ddv+n+sGhr+gtae
  NCBI__GCF_000425265.1:WP_027720495.1 470 KG-GFLVIKKPWPSMFSGVLGDNEAVRNHYWGHIPGMFYAGDVARKDEDGYFWIQGRADDVLNISGHRIGTAE 541
                                           99.8********************************************************************* PP

                             TIGR02188 517 iesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelP 589
                                           +esal sh++vaeaav+gv+d+ikg++  a+v+l++g++e+++ l++elk+++r+e+gpi   ++i++ +elP
  NCBI__GCF_000425265.1:WP_027720495.1 542 VESALTSHPHVAEAAVIGVADKIKGQVAKAHVTLNHGITESDD-LHRELKEHIRRELGPIVIVRSIEFCDELP 613
                                           ****************************************995.***************************** PP

                             TIGR02188 590 ktRsGkimRRll 601
                                           kt sGki R  l
  NCBI__GCF_000425265.1:WP_027720495.1 614 KTSSGKIKRSAL 625
                                           *******99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (626 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: 28.17
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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