GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Algoriphagus aquaeductus T4

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_003253485.1:WP_111393797.1
          Length = 379

 Score =  223 bits (567), Expect = 9e-63
 Identities = 134/377 (35%), Positives = 201/377 (53%), Gaps = 5/377 (1%)

Query: 16  LDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYG 75
           ++ QLT+    V+++AR ++Q  LLP V +     K       +MG+LG LG  +  +Y 
Sbjct: 1   MNFQLTEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYN 60

Query: 76  GSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWV 135
           G GM+ + Y +   E+ ++D+     MSV +SLV   + ++GSEE KQKYL +LATGE +
Sbjct: 61  GGGMDTISYVIAMEELSKIDASASVSMSVNNSLVCWGLEKYGSEEQKQKYLTRLATGEIL 120

Query: 136 GCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----D 191
           G F L+EP  GSD  S  T A      Y L+G K WITN   A V++V A+ DA      
Sbjct: 121 GAFCLSEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKG 180

Query: 192 IRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVR-GLKGPFTCLN 250
           I  F++EKGW+G        K+G+R S T  ++  +V  P EN       G       LN
Sbjct: 181 ISVFLVEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLN 240

Query: 251 SARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCL 310
             R GIA  ALG A   YE A  Y+ +RK FG+P++ +Q IQ KLADM T+I        
Sbjct: 241 GGRIGIAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVY 300

Query: 311 RLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVN 370
           +   LKD+G      +++ K  +   ++++   A  + GG G   E+ + R + + ++  
Sbjct: 301 KAAWLKDQGEDYAHASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQ 360

Query: 371 TYEGTHDIHALILGRAI 387
            YEGT +I  +++ R I
Sbjct: 361 IYEGTSEIQRIVISRGI 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: 336
Number of extensions: 20
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 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