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.1777319.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.75
//
[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:

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:

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:

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:

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