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 Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_027721031.1 H589_RS0105060 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000425265.1:WP_027721031.1
          Length = 663

 Score =  748 bits (1932), Expect = 0.0
 Identities = 374/649 (57%), Positives = 474/649 (73%), Gaps = 12/649 (1%)

Query: 10  PANIADRCLINPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIK 68
           P N+   C+ + ++Y+A+Y +SIN  + FW E+ + +L W K + KV +  F      IK
Sbjct: 20  PTNVPTACVKSLEEYQAIYDRSINDMEGFWAERAEELLTWDKKWDKVLDYDF--DKPEIK 77

Query: 69  WYEDGTLNLAANCLDRHLQENGDRT--AIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           W+E G LN +ANCLDRH++ NG R   A+IW+G++  + K  +Y  LHR+VCRFAN L +
Sbjct: 78  WFEGGKLNASANCLDRHIK-NGRRNKAALIWQGEEDHEVKVYTYDMLHREVCRFANVLKK 136

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
           +G++KGD V+IY+PM+PE A+AMLAC RIGA HS+IF GFS  ++  RI D  +++ IT 
Sbjct: 137 MGVQKGDRVSIYLPMIPELAIAMLACTRIGAPHSIIFAGFSSNSLRDRINDCGAKIHITG 196

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVE--QA 244
           D  +R GR+IPLK N D+ALK     ++E  +V+ R    I+  EGRD  W DL+   + 
Sbjct: 197 DGVLRGGRAIPLKPNSDEALKE--CPTIEQCIVVPRANNDIEMVEGRDCLWSDLMSDPEI 254

Query: 245 SDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCT 304
           +D    E M+AEDPLFILYTSGSTGKPKGV HTTGGYL YAA T ++VFD    D++WCT
Sbjct: 255 TDNCPYELMDAEDPLFILYTSGSTGKPKGVFHTTGGYLTYAAHTCQWVFDLKDDDVHWCT 314

Query: 305 ADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRAL 364
           AD+GWVTGHSY++YGPLA G+T++MFE VP +P PAR  QV +K +VNI YTAPTAIRAL
Sbjct: 315 ADIGWVTGHSYIVYGPLALGSTSIMFESVPTYPDPARFWQVCEKFRVNIFYTAPTAIRAL 374

Query: 365 MAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMIT 424
           M EGD+  +  D SSLRILG+VGEPINPEAW WY +KIGNEK P+VDTWWQTETGG +++
Sbjct: 375 MREGDQWTQKYDLSSLRILGTVGEPINPEAWMWYHEKIGNEKLPIVDTWWQTETGGHVLS 434

Query: 425 PLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERF 484
           PLP AT LK GSAT P  G+  A+VD  GN +     G L+I   WPG  R ++G+ ERF
Sbjct: 435 PLPYATPLKPGSATLPLPGIDAAIVDRHGNEVGPNEGGFLIIRKPWPGMLRGVWGNQERF 494

Query: 485 EQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAE 544
           +Q YF  F  +Y SGDGAR+D DGY+WI GRVDDV+NVSGHRLGTAEIESALV+HP ++E
Sbjct: 495 KQQYFEGFPGVYESGDGARKDADGYFWIMGRVDDVINVSGHRLGTAEIESALVSHPAVSE 554

Query: 545 AAVVGIPHNIKGQAIYAYVTL--NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSL 602
           AAVVG+PH +KGQ+IYAYVTL  N   +   +L  E+R  VRKEIGPLA+P+V+ +  SL
Sbjct: 555 AAVVGMPHQVKGQSIYAYVTLKSNSDYDEDDDLIKELRMHVRKEIGPLASPEVIQFAPSL 614

Query: 603 PKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMP 651
           PKTRSGKIMRRILRKI  GD +NLGDTSTLADP VV  L+E  + I  P
Sbjct: 615 PKTRSGKIMRRILRKIVEGDAANLGDTSTLADPSVVTDLIEGYEEIINP 663


Lambda     K      H
   0.317    0.135    0.421 

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: 1433
Number of extensions: 65
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: 652
Length of database: 663
Length adjustment: 38
Effective length of query: 614
Effective length of database: 625
Effective search space:   383750
Effective search space used:   383750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_027721031.1 H589_RS0105060 (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.3439578.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-308 1009.0   0.0   4.3e-308 1008.8   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027721031.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027721031.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1008.8   0.0  4.3e-308  4.3e-308       2     628 ..      29     655 ..      28     656 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1008.8 bits;  conditional E-value: 4.3e-308
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkd 72 
                                           ++leey+++y+++i+d+e fwa+ a+e l+w+k+++kvld ++++ ++kWfe+g+ln+s+nc+drh+++ r++
  NCBI__GCF_000425265.1:WP_027721031.1  29 KSLEEYQAIYDRSINDMEGFWAERAEELLTWDKKWDKVLDYDFDKpEIKWFEGGKLNASANCLDRHIKNgRRN 101
                                           6899***************************************988*************************** PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           k+a+iw g+e++e ++ +tY  l+revcr+anvlk++Gv+kgdrv+iYlpmipe++iamlac+RiGa hs++f
  NCBI__GCF_000425265.1:WP_027721031.1 102 KAALIWQGEEDHE-VKVYTYDMLHREVCRFANVLKKMGVQKGDRVSIYLPMIPELAIAMLACTRIGAPHSIIF 173
                                           *********9985.*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvw 218
                                           aGfs+++l++Ri+d+ ak+ it d+ lRgg++i+lk + deal++++ ++e+++vv r++++++ ++egrD  
  NCBI__GCF_000425265.1:WP_027721031.1 174 AGFSSNSLRDRINDCGAKIHITGDGVLRGGRAIPLKPNSDEALKECP-TIEQCIVVPRANNDIE-MVEGRDCL 244
                                           **********************************************9.7*************66.******** PP

                             TIGR02188 219 weelvek.easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                           w++l+++ e +++c+ e +d+edplfiLYtsGstGkPkGv httgGyl++aa t+++vfd+kd+d++wCtaD+
  NCBI__GCF_000425265.1:WP_027721031.1 245 WSDLMSDpEITDNCPYELMDAEDPLFILYTSGSTGKPKGVFHTTGGYLTYAAHTCQWVFDLKDDDVHWCTADI 317
                                           ******988899************************************************************* PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GWvtGhsYivygPLa G t+++fe+vptypd++rfw+v+ek++v+ifYtaPtaiRalm++g+++++k+dlssl
  NCBI__GCF_000425265.1:WP_027721031.1 318 GWVTGHSYIVYGPLALGSTSIMFESVPTYPDPARFWQVCEKFRVNIFYTAPTAIRALMREGDQWTQKYDLSSL 390
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           r+lg+vGepinpeaw+Wy+e++G+ek pivdtwWqtetGg++++plp  at+lkpgsatlPl+Gi+a++vd++
  NCBI__GCF_000425265.1:WP_027721031.1 391 RILGTVGEPINPEAWMWYHEKIGNEKLPIVDTWWQTETGGHVLSPLPY-ATPLKPGSATLPLPGIDAAIVDRH 462
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g+ev ++e+ g+L+i+kpwP+mlr+++g++erf ++Yf+ ++g+y +GDgar+d+dGy+wi+GRvDdvinvsG
  NCBI__GCF_000425265.1:WP_027721031.1 463 GNEVGPNEG-GFLIIRKPWPGMLRGVWGNQERFKQQYFEGFPGVYESGDGARKDADGYFWIMGRVDDVINVSG 534
                                           ******999.8************************************************************** PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpdk 581
                                           hrlgtaeiesalvsh+av+eaavvg+p+++kg++i+a+v+lk++++ de+ +l kel+++vrkeigp+a+p+ 
  NCBI__GCF_000425265.1:WP_027721031.1 535 HRLGTAEIESALVSHPAVSEAAVVGMPHQVKGQSIYAYVTLKSNSDYDEDdDLIKELRMHVRKEIGPLASPEV 607
                                           ******************************************9998776559********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i+++++lPktRsGkimRR+lrki+eg+  +lgd+stl+dpsvv +l+e
  NCBI__GCF_000425265.1:WP_027721031.1 608 IQFAPSLPKTRSGKIMRRILRKIVEGDaANLGDTSTLADPSVVTDLIE 655
                                           ***************************99**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (663 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: 23.19
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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