GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Desulfovibrio vulgaris Hildenborough

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase

Query= BRENDA::Q2XNL6
         (634 letters)



>lcl|MicrobesOnline__882:408300 DVU0748 acetyl-CoA synthetase
          Length = 648

 Score =  700 bits (1806), Expect = 0.0
 Identities = 334/638 (52%), Positives = 454/638 (71%), Gaps = 14/638 (2%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64
           LL E+RVF+P   VV +A +   +   A  + G     +W E AE LEWFR+WD VLD+S
Sbjct: 11  LLREERVFRPLPRVVADAVVNPQDVARAREQAGTAPLAFWEEAAEELEWFRRWDGVLDDS 70

Query: 65  NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124
           N PF RWF     N+ +NA+DR ++T  R+++A+++  E GD R+ TY++LYREV+R AN
Sbjct: 71  NAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIWEGEPGDSRRFTYFDLYREVNRLAN 130

Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184
           A++SLG+ KGD V +Y+P  PE V +MLACAKIGAVHS ++ G S  +L +R+ DAR  +
Sbjct: 131 AMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRVEDARPTL 190

Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCPT-----IETTVVVKHTDIDIEMSDISGREMLF 239
           ++T DG YR G V+ LKP+ D+A+          +   VVV    ++  M D  GR++ +
Sbjct: 191 LLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLHHVVVVHRAHLETPMRD--GRDIWY 248

Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299
             L+ G+      E + A DPLF+LYTSG+TGKPKG++H+ GGYMVGV  T+   FD+  
Sbjct: 249 HDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWVFDVRP 308

Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359
            D++WCTA+ GWITGHSY VYGPL+ GTTT+LYEG P YP+ G  WS+VE++GVT  YT 
Sbjct: 309 TDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPLYPEAGRLWSMVERWGVTILYTV 368

Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419
           PT IR LMRFG  +P R+++ +L++L TVGEPI+PE W+W+YR IGR +CP++DTWWQTE
Sbjct: 369 PTVIRMLMRFGPLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCPVLDTWWQTE 428

Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479
           TGM +++PLPV+ LKPGSV +PLPG++ D+VD  G PVP G+GG LV++ PWPAM   +F
Sbjct: 429 TGMIMVSPLPVSALKPGSVARPLPGVDVDIVDGEGAPVPPGRGGLLVVKNPWPAMACGVF 488

Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539
            D++ +  +YW++ PG  Y  GD+AR+D+DGY WIQGR+DDV+ IAGHRIGTAE+E+   
Sbjct: 489 GDDEAFRRLYWERFPGW-YCTGDVARRDDDGYIWIQGRADDVILIAGHRIGTAEMEAALA 547

Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNA---ALIEELKRHLRHELGPVAVVG 596
           +HPAVAE AVIG  D +KGEV KAF++L+   +  A   AL   L  H+R ELGPVAV+ 
Sbjct: 548 SHPAVAECAVIGVPDRLKGEVGKAFVVLRDTEEAAAEEQALATSLVGHVRRELGPVAVIR 607

Query: 597 EMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           ++V  + LP+ RSGKIMRRILR+ E G + GD STLE+
Sbjct: 608 DVVFREGLPRNRSGKIMRRILRSEEMGVETGDLSTLED 645


Lambda     K      H
   0.319    0.138    0.428 

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: 1335
Number of extensions: 63
Number of successful extensions: 5
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: 634
Length of database: 648
Length adjustment: 38
Effective length of query: 596
Effective length of database: 610
Effective search space:   363560
Effective search space used:   363560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 408300 DVU0748 (acetyl-CoA synthetase)
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.2025.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.2e-248  809.8   0.0   8.1e-248  809.6   0.0    1.0  1  lcl|MicrobesOnline__882:408300  DVU0748 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:408300  DVU0748 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.6   0.0  8.1e-248  8.1e-248       5     620 ..      33     646 ..      29     648 .] 0.96

  Alignments for each domain:
  == domain 1  score: 809.6 bits;  conditional E-value: 8.1e-248
                       TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwegde 82 
                                     ++ ++  e+a + p +fw++ a+ elew++ ++ vld+s++p+++Wf ++  n+  n++drh+e+ +++++a+iweg+ 
  lcl|MicrobesOnline__882:408300  33 QDVARAREQAGTAPLAFWEEAAE-ELEWFRRWDGVLDDSNAPFMRWFPGALCNIVHNALDRHIETsNRHRLALIWEGE- 109
                                     6667788999999******9998.6****************************************999**********. PP

                       TIGR02188  83 egedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdae 161
                                     +g dsr++tY +l+rev+rlan++++lGv kgdrv+iY+p +pe+v+amlaca+iGavhs vf+Gfsa +l +R++da+
  lcl|MicrobesOnline__882:408300 110 PG-DSRRFTYFDLYREVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRVEDAR 187
                                     77.59************************************************************************** PP

                       TIGR02188 162 aklvitadeglRggkvielkkivdealekaee....svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekl 236
                                       l++t d+ +R+g+v++lk ++d+a+++ +      +++v+vv+r+  e +++++grD+w+++lv+ ++s+e  +e l
  lcl|MicrobesOnline__882:408300 188 PTLLLTVDGFYRNGRVVPLKPVADDAVDALSPearaGLHHVVVVHRAHLE-TPMRDGRDIWYHDLVR-GQSTEALTEVL 264
                                     *************************99876543445799***********.66**************.6********** PP

                       TIGR02188 237 dsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfeg 315
                                     +++dplf+LYtsG+tGkPkG++h+ gGy++ ++ t+++vfd++++difwCta+ GW+tGhsY vygPL++G tt+l+eg
  lcl|MicrobesOnline__882:408300 265 SANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWVFDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEG 343
                                     ******************************************************************************* PP

                       TIGR02188 316 vptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivd 394
                                      p yp+a+r+w+++e+++vti+Yt Pt+iR+lm+ g   +++hd+ +lr+l +vGepi pe+w W+y+++G+++cp+ d
  lcl|MicrobesOnline__882:408300 344 HPLYPEAGRLWSMVERWGVTILYTVPTVIRMLMRFGPLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCPVLD 422
                                     ******************************************************************************* PP

                       TIGR02188 395 twWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetY 473
                                     twWqtetG i+++plp    +lkpgs ++Pl+G+++++vd eg +v ++++ g+Lv+k+pwP+m+ +++gd+e f + Y
  lcl|MicrobesOnline__882:408300 423 TWWQTETGMIMVSPLPV--SALKPGSVARPLPGVDVDIVDGEGAPVPPGRG-GLLVVKNPWPAMACGVFGDDEAFRRLY 498
                                     ****************9..69***************************999.8************************** PP

                       TIGR02188 474 fkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552
                                     +++++g y tGD arrd+dGyiwi+GR+Ddvi ++Ghr+gtae+e+al sh+avae+av+gvpd +kge+  afvvl++
  lcl|MicrobesOnline__882:408300 499 WERFPGWYCTGDVARRDDDGYIWIQGRADDVILIAGHRIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRD 577
                                     ******************************************************************************9 PP

                       TIGR02188 553 gveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620
                                     ++e+ +e  +l+++l  +vr+e+gp+a  +++ + e lP+ RsGkimRR+lr+   g e +gd+stled 
  lcl|MicrobesOnline__882:408300 578 TEEAAAEeqALATSLVGHVRRELGPVAVIRDVVFREGLPRNRSGKIMRRILRSEEMGVE-TGDLSTLEDA 646
                                     9886554448******************************************9777655.67******97 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.10
//
[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