GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Paraburkholderia bryophila 376MFSha3.1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein

Query= BRENDA::Q92947
         (438 letters)



>FitnessBrowser__Burk376:H281DRAFT_02091
          Length = 378

 Score =  177 bits (449), Expect = 5e-49
 Identities = 113/376 (30%), Positives = 183/376 (48%), Gaps = 8/376 (2%)

Query: 60  LTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGV 118
           L  D +++RD  RT+ +E + P     +R   F +++  ++ ELG  G  + + YG AG+
Sbjct: 3   LDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGAGM 62

Query: 119 SSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGELLGCFG 178
            ++A  L+  E+   D G  +A+SV +  V   +  YG++ Q++++L  LA+GE+LG F 
Sbjct: 63  DALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGAFC 122

Query: 179 LTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCEDGC----IR 234
           LTEP +GSD S++ T A  +    +Y LNG K +IT+    D+ +V A  +       I 
Sbjct: 123 LTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRGIS 182

Query: 235 GFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGC--LNN 292
            F++    +G    R++ K    +S T  II +   VP  N++ GA   G       L  
Sbjct: 183 AFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLI-GAEGEGYRIALSGLEG 241

Query: 293 ARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLGLHACLQ 352
            R GIA   +G +      A  YA +R  FG PL  +Q +Q +LADM T++         
Sbjct: 242 GRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIWH 301

Query: 353 LGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNT 412
              LKD  +      ++ K      A  I   A  + GG G   ++ V R   ++     
Sbjct: 302 AASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQI 361

Query: 413 YEGTHDIHALILGRAI 428
           YEGT DI  +++ R +
Sbjct: 362 YEGTSDIQKILIARGL 377


Lambda     K      H
   0.319    0.135    0.400 

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: 349
Number of extensions: 15
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: 438
Length of database: 378
Length adjustment: 31
Effective length of query: 407
Effective length of database: 347
Effective search space:   141229
Effective search space used:   141229
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