GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pedobacter sp. GW460-11-11-14-LB5

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__Pedo557:CA265_RS22715
          Length = 379

 Score =  232 bits (591), Expect = 2e-65
 Identities = 136/372 (36%), Positives = 209/372 (56%), Gaps = 2/372 (0%)

Query: 17  QLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPG 76
           +L++++ M+R AA  +AQ +L P V E   H+   A   +++GE+G LG  + E+Y G G
Sbjct: 4   ELSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYNGSG 63

Query: 77  LDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCF 136
           LD +SY L+  E+ ++D+    ++SV +SLV   +  +GS+AQKEKYL  LA GE IG F
Sbjct: 64  LDAISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEKIGAF 123

Query: 137 GLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDE-IRG 195
            L+EP  GSD  S  T A      Y L+G+K WITN   A  ++V A+   + R + I  
Sbjct: 124 CLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHKGINA 183

Query: 196 FILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEEN-ILPHVKGLRGPFTCLNSAR 254
           FI+EKG +G +      K+G+R S T  ++ ++  VP+EN I     G +     L   R
Sbjct: 184 FIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTLEGGR 243

Query: 255 YGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLG 314
            GIA  ALG A+  + +A QY  +RK FG+P++ +Q I  KLADM T+I      V +  
Sbjct: 244 IGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLVYKAA 303

Query: 315 RMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYE 374
            +KD+G    +  S+ K  +   A+D+   A  + GG G   E+ V R + + ++   YE
Sbjct: 304 WLKDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKITQIYE 363

Query: 375 GTHDIHALILGR 386
           GT +I  +++ R
Sbjct: 364 GTSEIQKMVISR 375


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: 341
Number of extensions: 18
Number of successful extensions: 3
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: 379
Length adjustment: 30
Effective length of query: 365
Effective length of database: 349
Effective search space:   127385
Effective search space used:   127385
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