GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Acidovorax sp. GW101-3H11

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate Ac3H11_2720 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2720
          Length = 384

 Score =  141 bits (355), Expect = 4e-38
 Identities = 112/372 (30%), Positives = 180/372 (48%), Gaps = 12/372 (3%)

Query: 21  EEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDP-AIFREMGEVGLLGATIPEQYGGSGLN 79
           E+    R+ A +F + ++ P  L A+  E   P +++ + GE GLL +T+PE YGG+G +
Sbjct: 17  EDHEQFREQARRFIEREIVPH-LHAWEAEGIVPKSVWLKAGEAGLLCSTVPEAYGGAGGD 75

Query: 80  YVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGL 139
           +    ++  E+ R+++      +  S +V   I  +GTE QKQ++LPK+ SGE IG   +
Sbjct: 76  FGHSAVMIEELARVNATAVGF-TTHSEIVAPYIVAYGTEEQKQRWLPKMVSGETIGVIAM 134

Query: 140 TEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AGDIRGFVLE 197
           +EP  GSD  SM T A + +  Y + G K +ITN   AD+ V   K D  A ++    +E
Sbjct: 135 SEPGIGSDLRSMRTTAVRGEDIYTINGQKTFITNGGNADLAVTATKLDPAAKELTLICVE 194

Query: 198 KGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLNSARYGIS 256
               G S      K+GL+   T E+  DNV VP  N +  + +G K     L   R  I 
Sbjct: 195 TDQPGFSKGRRLEKIGLKGQDTSELFFDNVSVPMANRLGEEGQGFKYLTHQLAWERTIIG 254

Query: 257 WGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA---LQGCLRLGR 313
             A  + ++      QYT DR+ FG+ +   Q  + KLA+ + + T+    +  CL    
Sbjct: 255 IRAAASIDSLIEQTIQYTRDRKVFGKTVFDFQNTKFKLAECKAQATMLRVFVDDCLAKAM 314

Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373
             +       +  +M     GK LD       + GG G   E+ ++R  V+  V   Y G
Sbjct: 315 RGELSAEVGAMCKLMGSEMQGKILD---ELLQLHGGYGFMSEYMISRAWVDARVARIYGG 371

Query: 374 THDVHALILGRA 385
           T ++   I+ R+
Sbjct: 372 TSEIMKEIISRS 383


Lambda     K      H
   0.320    0.137    0.413 

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: 322
Number of extensions: 17
Number of successful extensions: 4
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: 393
Length of database: 384
Length adjustment: 30
Effective length of query: 363
Effective length of database: 354
Effective search space:   128502
Effective search space used:   128502
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 (21.8 bits)
S2: 50 (23.9 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:

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