GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas stutzeri RCH2

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate GFF2397 Psest_2445 Acyl-CoA dehydrogenases

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__psRCH2:GFF2397
          Length = 379

 Score =  204 bits (519), Expect = 3e-57
 Identities = 124/373 (33%), Positives = 186/373 (49%), Gaps = 5/373 (1%)

Query: 22  DTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNY 81
           + +  + + AR ++QERL P  ++  R  +       EM  LG  G  +PEQ+GGS   Y
Sbjct: 5   EDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGY 64

Query: 82  VCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGLT 141
           + Y +   E+   D    ++MSV +S+  VPI  FG+E+ K  +L  LA GE +G F LT
Sbjct: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFALT 124

Query: 142 EPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDD----AGDIRGFVL 197
           EP  GSD  S+ TRAR+    Y L+GAK +IT+   A   +V+A  D     G I  F++
Sbjct: 125 EPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGISAFIV 184

Query: 198 EKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARYGI 256
                G     +  K+G  AS T +I  +++  P  N       G +     L   R GI
Sbjct: 185 PTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGI 244

Query: 257 AWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLK 316
           A  A+G A A +E AR Y  DR+ FG+P+  +Q +  +LADM T+I +  Q       L+
Sbjct: 245 AAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAALR 304

Query: 317 DEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTH 376
           + G   +   S+ K  +   +  +   A   LGG G   +F + R   ++ V   YEGT 
Sbjct: 305 EVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYEGTS 364

Query: 377 DIHALILGRAITG 389
           DI  L++ R + G
Sbjct: 365 DIQRLVISRNLGG 377


Lambda     K      H
   0.319    0.136    0.409 

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: 319
Number of extensions: 10
Number of successful extensions: 2
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