GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Shewanella amazonensis SB2B

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate 6937192 Sama_1362 isovaleryl-CoA dehydrogenase (RefSeq)

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__SB2B:6937192
          Length = 389

 Score =  224 bits (570), Expect = 4e-63
 Identities = 136/378 (35%), Positives = 206/378 (54%), Gaps = 16/378 (4%)

Query: 18  LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77
           L +D  M+RDA + +A+G++AP   +  R       ++ + G++GLLG T+ E+YGG  +
Sbjct: 12  LGEDVDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEEYGGVNM 71

Query: 78  DYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFG 137
            Y+++ +   E+ R  +         S+L +  I+  G++AQ+ KYLPKL +GE IG   
Sbjct: 72  GYLAHVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGEHIGALA 131

Query: 138 LTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDEIRGF 196
           ++EPN GSD  SM   ARK    Y L+G+KMWITN P A  +V++AK D D G   I  F
Sbjct: 132 MSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTDLDKGPHGITAF 191

Query: 197 ILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLNSARY 255
           I+E+G KG S      K+G+R S T E+V ++  VPEENIL  +  G++   + L+  R 
Sbjct: 192 IVERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVKVLMSGLDYERV 251

Query: 256 GIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGR 315
            ++ G LG   +C  I   YV +R QFG+ +   QL+Q KLADM T +      V  + R
Sbjct: 252 VLSGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSYVYNVAR 311

Query: 316 MKDEGTAAVEITSIMKRNSCGKALDIARLARDM-------LGGNGISDEFGVARHLVNLE 368
             D G          ++++ G  L  A LA  M       LGGNG  +E+   R L + +
Sbjct: 312 ACDRGETT-------RKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAK 364

Query: 369 VVNTYEGTHDIHALILGR 386
           +     GT +I  +++GR
Sbjct: 365 LYEIGAGTSEIRRMLIGR 382


Lambda     K      H
   0.320    0.138    0.414 

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: 387
Number of extensions: 19
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: 395
Length of database: 389
Length adjustment: 31
Effective length of query: 364
Effective length of database: 358
Effective search space:   130312
Effective search space used:   130312
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