GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas fluorescens FW300-N2E3

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate AO353_25680 AO353_25680 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25680
          Length = 375

 Score =  207 bits (527), Expect = 4e-58
 Identities = 124/370 (33%), Positives = 188/370 (50%), Gaps = 5/370 (1%)

Query: 21  TDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMN 80
           TD +  + D+AR ++QERL P   E  R  +  +    EM ELG  G  +PEQ+GG    
Sbjct: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63

Query: 81  YVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGL 140
           Y+ Y +   E+   D    ++MSV +S+  VPI +FG+++ K+++L  LA+G  +G F L
Sbjct: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123

Query: 141 TEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----DIRGFV 196
           TEP  GSD  S+ TRAR     Y L+G K +IT+   A V +V+A  D       I  F+
Sbjct: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183

Query: 197 LEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARYG 255
           +     G     +  K+G  AS T +I+ ++V  P  N       G K     L   R G
Sbjct: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243

Query: 256 IAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRL 315
           IA  ++G A A +E AR Y  +R+ FG+P+  +Q +  +LADM T+I +  Q       L
Sbjct: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303

Query: 316 KDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGT 375
           +D G   +   S+ K  +   +  +   A   LGG G   +F + R   ++ V   YEGT
Sbjct: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363

Query: 376 HDIHALILGR 385
            DI  +++ R
Sbjct: 364 SDIQRMVISR 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: 322
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: 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