GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hcl in Desulfovibrio vulgaris Miyazaki F

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 8499484 DvMF_0256 AMP-dependent synthetase and ligase (RefSeq)

Query= SwissProt::Q8GQN9
         (527 letters)



>lcl|FitnessBrowser__Miya:8499484 DvMF_0256 AMP-dependent synthetase
           and ligase (RefSeq)
          Length = 583

 Score =  181 bits (459), Expect = 7e-50
 Identities = 135/487 (27%), Positives = 215/487 (44%), Gaps = 35/487 (7%)

Query: 71  GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130
           G++  D+V + + +       F   +K G V +  N L  E +  + + DS AR  +   
Sbjct: 75  GVRRGDKVSIMLPNLPQTVIAFWAVLKAGGVVVMTNPLYMEKELVHQIHDSGARFMIALD 134

Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAG---------------EDSLAAL------------ 163
            + P   P+  K+   ++ +   G G               E +   L            
Sbjct: 135 LVWPKIEPLREKLGIDKYFLTRIGDGLAFPLNFLYAFKAKREGTWRELPFDGRHVLPWKT 194

Query: 164 LATGSEQFEAAPTRP-DDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGD 222
           L  G  +       P +D     Y+ G+TG  KG +  H ++    +     +   R+ D
Sbjct: 195 LLKGKVRHSTTTCNPTEDLAVLQYTGGTTGISKGVMLTHHNMSVNVQQITTILGDARDMD 254

Query: 223 VVFSAAKLFF-AYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLY 281
             F     +F  YGL   L  P A+ AT V    R  P  V   +++H+P IF G P++Y
Sbjct: 255 HCFLGLMPYFHVYGLTTCLTLPTALAATIVPFP-RYVPRDVLVGIQKHKPTIFPGAPSIY 313

Query: 282 ASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHI-FLSN 340
            S++   +        +R C S    +P +  +R++   G  +++G G TE   +  L+ 
Sbjct: 314 ISLMQQKEVGDYDLTSIRYCISGSAPMPVEHIKRFRELTGAQVIEGFGLTEASPVTHLNP 373

Query: 341 RAGDVHYGTSGKPVPGYRLRLIDEDGAEITT-AGVAGELQISGPSSAVMYWNNPEKTAAT 399
             G    G+ G P P    R++D +  ++   AG  GEL I GP     YWN P++TA T
Sbjct: 374 IHGVSKTGSIGIPFPDTEARIVDMEVGQVPLPAGKVGELIIRGPQVMKGYWNRPDETANT 433

Query: 400 FMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGW 459
               W  +GD  +++++GY+    R  DM  V G  V P E++  L  H  + EA  VG 
Sbjct: 434 LRNGWLYTGDIAIMDEDGYFTIVDRKKDMFLVGGYNVYPREIDEVLHEHPKIKEAVTVGV 493

Query: 460 EDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKI 519
                    KAF+V+KPG    +  + ++ AH +  LA YK P+ +EF DDLPKT  GK+
Sbjct: 494 PHPTRGEMIKAFVVVKPG---EKLTKAEVVAHCREKLASYKVPKQVEFRDDLPKTVVGKV 550

Query: 520 QRFKLRS 526
            R  LR+
Sbjct: 551 LRRILRT 557


Lambda     K      H
   0.319    0.138    0.412 

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: 746
Number of extensions: 44
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 527
Length of database: 583
Length adjustment: 36
Effective length of query: 491
Effective length of database: 547
Effective search space:   268577
Effective search space used:   268577
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: 53 (25.0 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