GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:408300
          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.11671.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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.33
//
[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:

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