GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8501039 DvMF_1775 acetate/CoA ligase (RefSeq)

Query= SwissProt::Q8ZKF6
         (652 letters)



>lcl|FitnessBrowser__Miya:8501039 DvMF_1775 acetate/CoA ligase
           (RefSeq)
          Length = 667

 Score =  748 bits (1932), Expect = 0.0
 Identities = 370/627 (59%), Positives = 468/627 (74%), Gaps = 10/627 (1%)

Query: 22  EQYETKYKQSINDPDTFWGEQGK-ILDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80
           ++Y    +++  DP+ FWG++ + +LDW TP+ KV +         I+W++  TLN+A N
Sbjct: 38  DEYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADM--NEPRIEWFKGATLNVAYN 95

Query: 81  CLDRHLQENGDRT--AIIWEGDDTSQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138
           CLDRHL  NG R   AIIW+G+     + ++Y+ L+ +VCRFA+ L  LG++KGD VA+Y
Sbjct: 96  CLDRHLV-NGRRNKAAIIWQGEPEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALY 154

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198
           MPM+PE AVAMLACARIGAVHS++F GFS  ++  RI D  +++V+TAD  +RAGRSIPL
Sbjct: 155 MPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQNRIQDCEAKVVVTADAVLRAGRSIPL 214

Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRD-LIEKASPEHQPEA-MNAE 256
           K NVD+ALK+    SVE V+V+ R  S+   +EGRD+WW + + ++      P A M++E
Sbjct: 215 KVNVDEALKD--CPSVERVVVVDRAHSNCAMREGRDMWWHEAMADRTLDTSCPCAKMDSE 272

Query: 257 DPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYL 316
           D LFILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD H  D+YWCTAD+GW+TGHSY+
Sbjct: 273 DMLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYI 332

Query: 317 LYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTD 376
           +YGPLA G TTLMFEGVP+WP P R   +V+K +VNI YTAPT IRALM EG    +  D
Sbjct: 333 VYGPLALGGTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHD 392

Query: 377 RSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGS 436
            SSLR+LGSVGEPINPEAW WY + IG  + P+VDTWWQTETGG MI+ LP A  LK GS
Sbjct: 393 LSSLRVLGSVGEPINPEAWMWYHEHIGHSRLPIVDTWWQTETGGIMISALPYATTLKPGS 452

Query: 437 ATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496
           AT P  G+  A+V  +G P      G+LV+   WPG  R +FG  ER++ TYF  F  MY
Sbjct: 453 ATMPLPGIDAAVVKADGTPCGPNEGGHLVVRKPWPGMLRGVFGSPERYKSTYFERFPGMY 512

Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKG 556
            SGDGAR DEDGY W+ GR+DDV+NVSGHR+GTAE+ESALV+HP +AEAAVVG+PHAIKG
Sbjct: 513 ESGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHAIKG 572

Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           +AIYAYVTL+ G E + EL A +R WVRKEIGP+ATP+V+ + + LPKTRSGKIMRRILR
Sbjct: 573 EAIYAYVTLSAGTEETEELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILR 632

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLE 643
           KIA+G  S+ GDTSTLADPGVV+ L+E
Sbjct: 633 KIASGAGSDFGDTSTLADPGVVQDLIE 659


Lambda     K      H
   0.317    0.135    0.423 

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: 1442
Number of extensions: 62
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: 667
Length adjustment: 38
Effective length of query: 614
Effective length of database: 629
Effective search space:   386206
Effective search space used:   386206
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 8501039 DvMF_1775 (acetate/CoA ligase (RefSeq))
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.3962.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-304  996.4   0.0   2.7e-304  996.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501039  DvMF_1775 acetate/CoA ligase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501039  DvMF_1775 acetate/CoA ligase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  996.2   0.0  2.7e-304  2.7e-304       3     628 ..      36     659 ..      34     660 .. 0.98

  Alignments for each domain:
  == domain 1  score: 996.2 bits;  conditional E-value: 2.7e-304
                         TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkdkvaii 77 
                                        ++ey +  e+a +dpe fw++ a++ l+w++p++kv+d+++++ +++Wf++++lnv+ync+drh+ + r++k+aii
  lcl|FitnessBrowser__Miya:8501039  36 GMDEYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADMNEpRIEWFKGATLNVAYNCLDRHLVNgRRNKAAII 112
                                       6899***********************************998877*********************999******** PP

                         TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeala 154
                                       w g+ +++d+r ltY+ l++evcr+a vl+ lGv+kgdrva+Y+pmipe+++amlacaRiGavhs+vfaGfsa +l+
  lcl|FitnessBrowser__Miya:8501039 113 WQGE-PEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALYMPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQ 188
                                       ****.5568******************************************************************** PP

                         TIGR02188 155 eRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek.easae 230
                                       +Ri+d+eak+v+tad  lR g++i+lk +vdeal++++ sve+v+vv r+ ++ a ++egrD+ww+e++++ + +++
  lcl|FitnessBrowser__Miya:8501039 189 NRIQDCEAKVVVTADAVLRAGRSIPLKVNVDEALKDCP-SVERVVVVDRAHSNCA-MREGRDMWWHEAMADrTLDTS 263
                                       *************************************9.7*************55.**************977899* PP

                         TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanG 307
                                       c+++k+dsed+lfiLYtsGstGkPkGv+httgGyl +aa t+++vfd++d+d++wCtaD+GW+tGhsYivygPLa G
  lcl|FitnessBrowser__Miya:8501039 264 CPCAKMDSEDMLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYIVYGPLALG 340
                                       ***************************************************************************** PP

                         TIGR02188 308 attllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyev 384
                                        ttl+fegvp++p ++rfw+++ek++v+ifYtaPt+iRalm++g ++++khdlsslrvlgsvGepinpeaw+Wy+e+
  lcl|FitnessBrowser__Miya:8501039 341 GTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHDLSSLRVLGSVGEPINPEAWMWYHEH 417
                                       ***************************************************************************** PP

                         TIGR02188 385 vGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrt 461
                                       +G+++ pivdtwWqtetGgi+i++lp  at lkpgsat+Pl+Gi+a+vv+ +g+++ ++e+ g Lv++kpwP+mlr+
  lcl|FitnessBrowser__Miya:8501039 418 IGHSRLPIVDTWWQTETGGIMISALPY-ATTLKPGSATMPLPGIDAAVVKADGTPCGPNEG-GHLVVRKPWPGMLRG 492
                                       ***************************.6*****************************999.8************** PP

                         TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538
                                       ++g +er+ +tYf++++g+y +GDgar+d+dGy w++GR+DdvinvsGhr+gtae+esalvsh+avaeaavvg+p+ 
  lcl|FitnessBrowser__Miya:8501039 493 VFGSPERYKSTYFERFPGMYESGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHA 569
                                       ***************************************************************************** PP

                         TIGR02188 539 ikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdv 614
                                       ikgeai+a+v+l++g+ee+e el++ l+++vrkeigpia+p+ i+++e lPktRsGkimRR+lrkia+g+ +  gd+
  lcl|FitnessBrowser__Miya:8501039 570 IKGEAIYAYVTLSAGTEETE-ELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILRKIASGAgSDFGDT 645
                                       *****************999.5************************************************99***** PP

                         TIGR02188 615 stledpsvveelke 628
                                       stl+dp vv++l+e
  lcl|FitnessBrowser__Miya:8501039 646 STLADPGVVQDLIE 659
                                       **********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (667 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 13.12
//
[ok]

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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