GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sphingobium czechense LL01

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_001046645.1:WP_066607952.1
          Length = 381

 Score =  203 bits (517), Expect = 6e-57
 Identities = 130/376 (34%), Positives = 196/376 (52%), Gaps = 3/376 (0%)

Query: 16  DQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGG 75
           D  L +   M+RDSA +F+ D++AP   E    +     ++  MGE+GL G T+ E+ GG
Sbjct: 5   DFALGDNADMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGG 64

Query: 76  SGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIG 135
            GL Y+ + +   EV R  +         S+L +  I  +G   QK KYLPKL SG+ +G
Sbjct: 65  LGLGYLEHVVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHVG 124

Query: 136 CFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGD--IRG 193
              ++E   GSD  SM  +A K    Y L G+K WITN+P AD  VV+AK   G   I  
Sbjct: 125 SLAMSEAGAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTGEGSKGITT 184

Query: 194 FVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKG-PFTCLNSAR 252
           F++EK  +G S      K+G+R S T E+V D+  VPEENI   + G  G   + L+  R
Sbjct: 185 FLIEKDMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYER 244

Query: 253 YGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLG 312
             ++   LG  +AC  T   Y  +RQQFGRP+ A QL+Q K+ADM   +  A      + 
Sbjct: 245 TVLAGIQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVA 304

Query: 313 RMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYE 372
           R  D G       +     +   A+ +A  A   LGG G + ++ V R++ + ++++   
Sbjct: 305 RACDSGKTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGA 364

Query: 373 GTHDVHALILGRAQTG 388
           GT+++  +++GR   G
Sbjct: 365 GTNEIRRMLIGRELIG 380


Lambda     K      H
   0.320    0.137    0.413 

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: 321
Number of extensions: 17
Number of successful extensions: 4
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: 393
Length of database: 381
Length adjustment: 30
Effective length of query: 363
Effective length of database: 351
Effective search space:   127413
Effective search space used:   127413
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