GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:408300
          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 Aug 03 2021. The underlying query database was built on Aug 03 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