GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas litoralis 2SM5

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_090271903.1 BLU11_RS02525 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_900105005.1:WP_090271903.1
          Length = 378

 Score =  208 bits (530), Expect = 2e-58
 Identities = 133/371 (35%), Positives = 187/371 (50%), Gaps = 5/371 (1%)

Query: 20  LTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGM 79
           + D +R + + AR ++QERLLP   E  R  +       EMG+LG LG  +PEQ+GG   
Sbjct: 3   INDEQREITNVARQFAQERLLPFAAEWDREHRFPTEALAEMGQLGFLGMLVPEQWGGCDT 62

Query: 80  NYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFG 139
            Y+ Y L   E+   D    ++MSV +S+   PI  FGSEE K ++LP LA GE +G F 
Sbjct: 63  GYLTYALALEEIAAGDGACSTIMSVHNSVGCAPILRFGSEEQKDRFLPPLARGEQIGGFA 122

Query: 140 LTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWA--KDDAG--DIRGF 195
           LTEP+ GSD GS+ TRAR+    Y L GAK +IT+   A   +V+A    DAG   I  F
Sbjct: 123 LTEPHAGSDAGSLRTRARRDGDSYVLDGAKQFITSGREAGTVIVFAVTDPDAGKRGITAF 182

Query: 196 VLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARY 254
           ++     G     +  K+G  AS T +I  D +     N       G +     L   R 
Sbjct: 183 IVPTDSPGYEVVRVEEKLGQHASDTCQIAFDGLRLSAANRLGGEGEGYRIALANLEGGRI 242

Query: 255 GIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGR 314
           GIA  A+G A A +E AR Y  +R+ FG+ L  +Q +  +LADM T+I +  Q       
Sbjct: 243 GIAAQAVGMARAAFEVARDYARERQAFGKALTEHQAVAFRLADMATQIAVARQMVHHAAA 302

Query: 315 LKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEG 374
           L+D G   +   S+ K  +   +      A   LGG G   +F + R   ++ V   YEG
Sbjct: 303 LRDAGQPALVEASMAKLFASEMAEKACSAAIQTLGGYGYLKDFPLERIYRDVRVCQIYEG 362

Query: 375 THDIHALILGR 385
           T DI  L++ R
Sbjct: 363 TSDIQRLVIAR 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: 343
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: 378
Length adjustment: 30
Effective length of query: 365
Effective length of database: 348
Effective search space:   127020
Effective search space used:   127020
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 24 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