GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_01204 H281DRAFT_01204 hypothetical protein

Query= BRENDA::Q3JP94
         (395 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01204 H281DRAFT_01204
           hypothetical protein
          Length = 377

 Score =  225 bits (574), Expect = 1e-63
 Identities = 134/375 (35%), Positives = 202/375 (53%), Gaps = 2/375 (0%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73
           +D    +++RM+RDAA  +A  +LAP   +  R     A + R+MG++G LG  +P Q+G
Sbjct: 1   MDSFYTEEQRMIRDAARDFATERLAPNAAQWDRDAQLPADVVRQMGDLGFLGMIVPSQWG 60

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

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

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

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

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

Query: 372 TYEGTHDIHALILGR 386
            YEGT ++  +++ R
Sbjct: 361 IYEGTSEVQRMVIAR 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: 354
Number of extensions: 13
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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