GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Burkholderia phytofirmans PsJN

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__BFirm:BPHYT_RS28040
          Length = 377

 Score =  222 bits (565), Expect = 2e-62
 Identities = 135/375 (36%), Positives = 202/375 (53%), Gaps = 2/375 (0%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73
           +D    D++RM+RDAA  +A  +LAP   +  R     A + R+MGE+G LG  +P ++G
Sbjct: 1   MDSFYTDEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWG 60

Query: 74  GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133
           G   DYV+Y L   E+    +   ++MSV +S+   PI  FG++AQK++YL  LATG  I
Sbjct: 61  GSYTDYVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLATGRRI 120

Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDE 192
           G F LTEP  GS+  ++ TRA    G + L+GSK ++TN   AD+ +V+A  D D G+  
Sbjct: 121 GAFCLTEPQAGSEANNLRTRAVLRDGKWILNGSKQFVTNGSRADLAIVFAVTDPDRGKRG 180

Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLN 251
           +  FI+     G +      K+G+RAS T  I LD+  VPE N+L    +GLR   + L 
Sbjct: 181 LTAFIVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPGEGLRIALSNLE 240

Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311
             R GIA  A+G A + +  AR Y  +R QFG+ L  +Q I   LADM T +      V 
Sbjct: 241 GGRIGIAAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNAARLLVH 300

Query: 312 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVN 371
              R++  G   +   S  K  +   A +I   A  + GG G  +++ V RH  +  +  
Sbjct: 301 HAARLRTAGKPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYRDARITQ 360

Query: 372 TYEGTHDIHALILGR 386
            YEGT ++  +++ R
Sbjct: 361 IYEGTSEVQRMLIAR 375


Lambda     K      H
   0.320    0.138    0.414 

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: 360
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: 395
Length of database: 377
Length adjustment: 30
Effective length of query: 365
Effective length of database: 347
Effective search space:   126655
Effective search space used:   126655
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