GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas fluorescens FW300-N1B4

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Pf1N1B4_4787 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4787
          Length = 375

 Score =  200 bits (508), Expect = 6e-56
 Identities = 121/369 (32%), Positives = 186/369 (50%), Gaps = 5/369 (1%)

Query: 22  DTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNY 81
           D +  + D+AR ++QERL P   E  R  +  +    EM  LG  G  +PEQ+GG    Y
Sbjct: 5   DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64

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

Query: 142 EPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----DIRGFVL 197
           EP  GSD  S+ TRAR     Y L+G K +IT+   A V +V+A  D       I   ++
Sbjct: 125 EPQAGSDASSLKTRARLDGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGITALIV 184

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

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

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

Query: 377 DIHALILGR 385
           DI  +++ R
Sbjct: 365 DIQRMVISR 373


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: 318
Number of extensions: 9
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: 375
Length adjustment: 30
Effective length of query: 365
Effective length of database: 345
Effective search space:   125925
Effective search space used:   125925
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