GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Desulfovibrio vulgaris Hildenborough

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase

Query= SwissProt::P31638
         (660 letters)



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

 Score =  591 bits (1523), Expect = e-173
 Identities = 308/654 (47%), Positives = 420/654 (64%), Gaps = 14/654 (2%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           + ++++++E RVF P     + A +   +  +A  ++A      FW   A EL  W + +
Sbjct: 6   ATLDALLREERVFRPLPRVVADAVVNPQDVARAR-EQAGTAPLAFWEEAAEEL-EWFRRW 63

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
             VLD SNAPF +WF     N  +N LDR+++  N  ++A+++E + G   R TY +L+ 
Sbjct: 64  DGVLDDSNAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIWEGEPGDSRRFTYFDLYR 123

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V R AN +++LG+ KGDRVVIYMP   E V AM ACA++GA HS VFGGFSA+SL +R+
Sbjct: 124 EVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRV 183

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEA---VRNVIVYRRTGGKVAWTEG 238
            D     L+T D   R G+ +PLK +ADDA+     EA   + +V+V  R   +    +G
Sbjct: 184 EDARPTLLLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLHHVVVVHRAHLETPMRDG 243

Query: 239 RDRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWT 298
           RD W  D+  GQ      E +SA  PLFVLYTSG+TGKPKG+ HS GGY++    TM+W 
Sbjct: 244 RDIWYHDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWV 303

Query: 299 FDIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVS 358
           FD++P D+FWCTA+ GW+TGH+Y  YGPL AG T V++EG P YP AGR W M+ R  V+
Sbjct: 304 FDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPLYPEAGRLWSMVERWGVT 363

Query: 359 IFYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCP 418
           I YT PT IR L++       ++P ++D+++LRLL TVGEPI+PE W+W+Y+ IG  RCP
Sbjct: 364 ILYTVPTVIRMLMRFG----PLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCP 419

Query: 419 IVDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKR 478
           ++DT+WQTETG  M++PLP  + L PGS   PLPG+   IVD  G  VP G GG+LVVK 
Sbjct: 420 VLDTWWQTETGMIMVSPLP-VSALKPGSVARPLPGVDVDIVDGEGAPVPPGRGGLLVVKN 478

Query: 479 PWPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGH 538
           PWPAM   ++GD E FR+ Y+    G   Y  GD + RD D GY  I GR DDV+ ++GH
Sbjct: 479 PWPAMACGVFGDDEAFRRLYWERFPG--WYCTGDVARRD-DDGYIWIQGRADDVILIAGH 535

Query: 539 RMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598
           R+GT E+E+AL S+P VAE AV+G PD + GE   AFVVL+ +     E   +AT L   
Sbjct: 536 RIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRDTEEAAAEEQALATSLVGH 595

Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAI 652
           V +E+GP+A  +D+ F + LP+ RSGKIMRR+LRS   G E T D STLE+  I
Sbjct: 596 VRRELGPVAVIRDVVFREGLPRNRSGKIMRRILRSEEMGVE-TGDLSTLEDAYI 648


Lambda     K      H
   0.319    0.136    0.422 

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: 1342
Number of extensions: 67
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: 660
Length of database: 648
Length adjustment: 38
Effective length of query: 622
Effective length of database: 610
Effective search space:   379420
Effective search space used:   379420
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)

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