Alignments for a candidate for acs in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Moritella dasanensis ArB 0140

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_017223156.1 A923_RS0118350 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000276805.1:WP_017223156.1
          Length = 648

 Score =  959 bits (2478), Expect = 0.0
 Identities = 449/646 (69%), Positives = 531/646 (82%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS    + +PA  A   L+N   Y+AMY+ SI  P+ FWGEQG I+DWIKPY +VK+TSF
Sbjct: 1   MSDTKLYPVPAEFAQNSLLNDSAYQAMYKHSITDPEAFWGEQGHIVDWIKPYSQVKSTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
            PG+V IKW++DG LN++ANCLDRHL++N ++TAIIWEGD+   S+ ++Y++++  VC+F
Sbjct: 61  QPGSVDIKWFQDGQLNVSANCLDRHLKDNANKTAIIWEGDNPEDSEKLTYQDVYEKVCQF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           +N L   GIKKGDVV +YMPMVPEAA+AMLAC RIGAVH+++F GFS EA+A RI +  +
Sbjct: 121 SNALKAQGIKKGDVVCLYMPMVPEAAIAMLACTRIGAVHTIVFAGFSAEALADRIDNCGA 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           +LVIT+DEGVRAGR   LK  VD AL  P VT+V +V+V  RT   I W EGRDLWWHD+
Sbjct: 181 KLVITADEGVRAGRITRLKDCVDTALAKPQVTTVNNVIVFARTKADIAWHEGRDLWWHDV 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           V+    +   E MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYA +TFKYVFD+   D+
Sbjct: 241 VKDQPTECVPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDHQDTDV 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           +WCTADVGW+TGHSYL+YGPLA  ATT++FEGVPN+P  ARM+QVVDKHQV  LYTAPTA
Sbjct: 301 FWCTADVGWITGHSYLVYGPLANAATTVLFEGVPNYPDTARMSQVVDKHQVTTLYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMA+GD AI+GT R+SLR++GSVGEPINPEAW+WY+  IGN   P+VDTWWQTETGG
Sbjct: 361 IRALMAKGDDAIKGTKRTSLRLMGSVGEPINPEAWQWYYNTIGNASTPIVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +ITPLPGAT LK GSATRPFFG+ PALVDNEGN LEGA EG+LVI DSWPGQ R ++GD
Sbjct: 421 ILITPLPGATMLKPGSATRPFFGISPALVDNEGNILEGANEGNLVILDSWPGQMRGIYGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
            +RFE+ YFSTF NMY +GDGA+RD DGYYWITGRVDDVLNVSGHR+GTAEIESALV+H 
Sbjct: 481 EDRFEEAYFSTFPNMYCTGDGAKRDLDGYYWITGRVDDVLNVSGHRMGTAEIESALVSHS 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVG+PH+IKGQ IYAYVTLN GEEP   L AEV+ WVR EIG +ATPD LHWT 
Sbjct: 541 KIAEAAVVGVPHDIKGQGIYAYVTLNAGEEPDAALLAEVKQWVRSEIGAIATPDTLHWTQ 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           +LPKTRSGKIMRRILRK+A  DT +LGDTSTLADP VV+ L+ EKQ
Sbjct: 601 ALPKTRSGKIMRRILRKVATNDTDSLGDTSTLADPSVVDTLIAEKQ 646


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: 1418
Number of extensions: 42
Number of successful extensions: 1
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: 648
Length adjustment: 38
Effective length of query: 614
Effective length of database: 610
Effective search space:   374540
Effective search space used:   374540
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_017223156.1 A923_RS0118350 (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.114902.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1011.3   0.6          0 1011.1   0.6    1.0  1  NCBI__GCF_000276805.1:WP_017223156.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017223156.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1011.1   0.6         0         0       4     628 ..      21     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1011.1 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            ++y+++y+++i+dpe+fw+++++  ++w+kp+++v+++s++p   ++kWf+dg+lnvs+nc+drh++++++k
  NCBI__GCF_000276805.1:WP_017223156.1  21 DSAYQAMYKHSITDPEAFWGEQGH-IVDWIKPYSQVKSTSFQPgsvDIKWFQDGQLNVSANCLDRHLKDNANK 92 
                                           578*********************.6****************99999************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwegd+++ ds+kltY++++++vc+++n+lk++G+kkgd v++Y+pm+pea+iamlac+RiGavh++vfa
  NCBI__GCF_000276805.1:WP_017223156.1  93 TAIIWEGDNPE-DSEKLTYQDVYEKVCQFSNALKAQGIKKGDVVCLYMPMVPEAAIAMLACTRIGAVHTIVFA 164
                                           ********998.6************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfsaeala+Ri ++ aklvitadeg+R g++++lk+ vd al+k +  +v++v+v+ rt++++a w+egrD+w
  NCBI__GCF_000276805.1:WP_017223156.1 165 GFSAEALADRIDNCGAKLVITADEGVRAGRITRLKDCVDTALAKPQVtTVNNVIVFARTKADIA-WHEGRDLW 236
                                           ********************************************9988**************77.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           w+++v++ +++ec pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t+kyvfd++d+d+fwCtaDvG
  NCBI__GCF_000276805.1:WP_017223156.1 237 WHDVVKD-QPTECVPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDHQDTDVFWCTADVG 308
                                           ******7.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           W+tGhsY+vygPLan att+lfegvp+ypd++r+ +v++k++vt++YtaPtaiRalm++g++++k +++ slr
  NCBI__GCF_000276805.1:WP_017223156.1 309 WITGHSYLVYGPLANAATTVLFEGVPNYPDTARMSQVVDKHQVTTLYTAPTAIRALMAKGDDAIKGTKRTSLR 381
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           ++gsvGepinpeaw+Wyy+++G+ ++pivdtwWqtetGgilitplpg at lkpgsat+P+fGi++++vd+eg
  NCBI__GCF_000276805.1:WP_017223156.1 382 LMGSVGEPINPEAWQWYYNTIGNASTPIVDTWWQTETGGILITPLPG-ATMLKPGSATRPFFGISPALVDNEG 453
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           + +e  +e g Lvi ++wP+++r+iygde+rf e+Yf++++++y tGDga+rd dGy+wi+GRvDdv+nvsGh
  NCBI__GCF_000276805.1:WP_017223156.1 454 NILEGANE-GNLVILDSWPGQMRGIYGDEDRFEEAYFSTFPNMYCTGDGAKRDLDGYYWITGRVDDVLNVSGH 525
                                           ****7777.78************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtaeiesalvsh+++aeaavvgvp++ikg+ i+a+v+l++g+e+d+ +l +e+k++vr+eig+ia+pd+++
  NCBI__GCF_000276805.1:WP_017223156.1 526 RMGTAEIESALVSHSKIAEAAVVGVPHDIKGQGIYAYVTLNAGEEPDA-ALLAEVKQWVRSEIGAIATPDTLH 597
                                           ************************************************.5*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++++lPktRsGkimRR+lrk+a+++ ++lgd+stl+dpsvv++l++
  NCBI__GCF_000276805.1:WP_017223156.1 598 WTQALPKTRSGKIMRRILRKVATNDtDSLGDTSTLADPSVVDTLIA 643
                                           *************************99***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (648 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 26.31
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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