Alignments for a candidate for acs in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfovibrio oxyclinae DSM 11498

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_018124331.1 B149_RS0106290 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000375485.1:WP_018124331.1
          Length = 658

 Score =  749 bits (1933), Expect = 0.0
 Identities = 365/617 (59%), Positives = 463/617 (75%), Gaps = 11/617 (1%)

Query: 35  PDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRT 93
           P+ FW E+ + ++ W KP+ KV +  F      I W++ G LN++ NCLD+H+ ENG R 
Sbjct: 44  PEGFWAERAEELVSWFKPWDKVLDYDFH--KPEINWFKGGKLNVSYNCLDKHI-ENGRRN 100

Query: 94  --AIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAAVAMLA 151
             A+IW+G+     K  +Y+ L+ +VC+FAN L ++G++KGD VA+Y+PMVPE ++AMLA
Sbjct: 101 KAALIWQGEPDEDVKVFTYQMLYTEVCKFANALKKMGVRKGDRVALYLPMVPELSIAMLA 160

Query: 152 CARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDALKNPNV 211
           CARIGA+HSV+F GFS  ++  RI D  +++++T+D  +RAG++IPLK N D+A KN   
Sbjct: 161 CARIGAMHSVVFAGFSAISLQSRIQDCEAKVLVTADAVIRAGKTIPLKPNADEACKN--C 218

Query: 212 TSVEHVVVLKRTGGKIDWQEGRDLWWHDLV--EQASDQHQAEEMNAEDPLFILYTSGSTG 269
            SVE VVV++R G  ++  EGRD WWH++V  +        EEM+AED LFILYTSGSTG
Sbjct: 219 PSVEQVVVVQRGGNDVEMVEGRDRWWHEVVGEDDVRGDCPPEEMDAEDILFILYTSGSTG 278

Query: 270 KPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGATTLM 329
           KPKGV+HTTGGYL YAA T ++VFD    D+YWCTAD+GW+TGHSY+LYGPL  GAT+LM
Sbjct: 279 KPKGVVHTTGGYLTYAAHTLQWVFDLQEDDVYWCTADIGWITGHSYILYGPLCLGATSLM 338

Query: 330 FEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSVGEP 389
           FEGVP++P P R  Q+V+K +VN+ YTAPT IRALM EG+   +  D S+LRILGSVGEP
Sbjct: 339 FEGVPSYPKPDRFWQIVEKFKVNLFYTAPTVIRALMREGEAWTQNYDLSTLRILGSVGEP 398

Query: 390 INPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQPALV 449
           INPEAW WY + IGN K P+VDTWWQTETGGFMI+PLP AT LK GSATRP  GV   +V
Sbjct: 399 INPEAWRWYHQNIGNGKLPIVDTWWQTETGGFMISPLPYATPLKPGSATRPMPGVSAKVV 458

Query: 450 DNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGY 509
             +G+P +    G LV+   WPG  R +FGD ERF+ TYF  F  MY SGDGAR D+DGY
Sbjct: 459 RADGSPADPDEGGHLVVDKPWPGMLRGVFGDPERFKSTYFQRFPGMYESGDGARCDKDGY 518

Query: 510 YWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGE 569
            WI GR+DDV+NVSGHRLGTAEIESALVAH  ++EAAVVG+PH +KGQ+IYAYVTL   E
Sbjct: 519 MWIMGRLDDVINVSGHRLGTAEIESALVAHSAVSEAAVVGMPHQVKGQSIYAYVTLKSDE 578

Query: 570 EPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDT 629
           E S E+ AE++ WVR EIGP+ATP+V+ + D LPKTRSGKIMRR+LRKIAA D  + GDT
Sbjct: 579 EESDEIRAELKKWVRSEIGPIATPEVIQFADGLPKTRSGKIMRRVLRKIAA-DQDDFGDT 637

Query: 630 STLADPGVVEKLLEEKQ 646
           STLADPGV+  L+E K+
Sbjct: 638 STLADPGVITDLVEGKK 654


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: 1459
Number of extensions: 65
Number of successful extensions: 6
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: 658
Length adjustment: 38
Effective length of query: 614
Effective length of database: 620
Effective search space:   380680
Effective search space used:   380680
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_018124331.1 B149_RS0106290 (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.3798888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-306 1003.8   0.0   1.7e-306 1003.5   0.0    1.0  1  NCBI__GCF_000375485.1:WP_018124331.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_018124331.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1003.5   0.0  1.7e-306  1.7e-306       5     627 ..      31     650 ..      27     652 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1003.5 bits;  conditional E-value: 1.7e-306
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           ++  el ++a+edpe fwa+ a+e ++w+kp++kvld ++++ +++Wf++g+lnvsync+d+h+e+ r++k+a
  NCBI__GCF_000375485.1:WP_018124331.1  31 DKLVELEKRAEEDPEGFWAERAEELVSWFKPWDKVLDYDFHKpEINWFKGGKLNVSYNCLDKHIENgRRNKAA 103
                                           66778999*******************************9988****************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           +iw g+ ++ed++ +tY+ l++evc++an+lk++Gv+kgdrva+Ylpm+pe+ iamlacaRiGa+hsvvfaGf
  NCBI__GCF_000375485.1:WP_018124331.1 104 LIWQGE-PDEDVKVFTYQMLYTEVCKFANALKKMGVRKGDRVALYLPMVPELSIAMLACARIGAMHSVVFAGF 175
                                           ******.6678************************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           sa +l++Ri+d+eak+++tad  +R gk+i+lk ++dea ++++ sve+v+vv+r g++v+ ++egrD ww+e
  NCBI__GCF_000375485.1:WP_018124331.1 176 SAISLQSRIQDCEAKVLVTADAVIRAGKTIPLKPNADEACKNCP-SVEQVVVVQRGGNDVE-MVEGRDRWWHE 246
                                           *******************************************9.7*************66.*********** PP

                             TIGR02188 222 lvek.easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           +v + +++ +c+pe++d+ed+lfiLYtsGstGkPkGv+httgGyl++aa t ++vfd++++d++wCtaD+GW+
  NCBI__GCF_000375485.1:WP_018124331.1 247 VVGEdDVRGDCPPEEMDAEDILFILYTSGSTGKPKGVVHTTGGYLTYAAHTLQWVFDLQEDDVYWCTADIGWI 319
                                           **8768999**************************************************************** PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYi+ygPL+ Gat+l+fegvp+yp+++rfw+++ek+kv+ fYtaPt+iRalm++ge++++++dls+lr+l
  NCBI__GCF_000375485.1:WP_018124331.1 320 TGHSYILYGPLCLGATSLMFEGVPSYPKPDRFWQIVEKFKVNLFYTAPTVIRALMREGEAWTQNYDLSTLRIL 392
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw+Wy++++G++k pivdtwWqtetGg++i+plp  at+lkpgsat+P++G++a+vv  +g++
  NCBI__GCF_000375485.1:WP_018124331.1 393 GSVGEPINPEAWRWYHQNIGNGKLPIVDTWWQTETGGFMISPLPY-ATPLKPGSATRPMPGVSAKVVRADGSP 464
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++++e+ g Lv++kpwP+mlr+++gd+erf +tYf++++g+y +GDgar dkdGy+wi+GR+DdvinvsGhrl
  NCBI__GCF_000375485.1:WP_018124331.1 465 ADPDEG-GHLVVDKPWPGMLRGVFGDPERFKSTYFQRFPGMYESGDGARCDKDGYMWIMGRLDDVINVSGHRL 536
                                           ***999.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtaeiesalv+h+av+eaavvg+p+++kg++i+a+v+lk+ +ee++ e+++elkk+vr+eigpia+p+ i+++
  NCBI__GCF_000375485.1:WP_018124331.1 537 GTAEIESALVAHSAVSEAAVVGMPHQVKGQSIYAYVTLKSDEEESD-EIRAELKKWVRSEIGPIATPEVIQFA 608
                                           *******************************************999.5************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           + lPktRsGkimRR+lrkia++++  gd+stl+dp v+ +l 
  NCBI__GCF_000375485.1:WP_018124331.1 609 DGLPKTRSGKIMRRVLRKIAADQDDFGDTSTLADPGVITDLV 650
                                           **************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (658 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: 38.03
//
[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