GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Pseudomonas fluorescens GW456-L13

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate PfGW456L13_554 Glutaryl-CoA dehydrogenase (EC 1.3.99.7)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_554 Glutaryl-CoA
           dehydrogenase (EC 1.3.99.7)
          Length = 393

 Score =  760 bits (1963), Expect = 0.0
 Identities = 373/393 (94%), Positives = 385/393 (97%)

Query: 1   MVGKASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMG 60
           M GKASFNWIDPLLLDQQLTEEERM+RD+A QFAQ  LAPR+LEAFRHE+TDPAIFREMG
Sbjct: 1   MGGKASFNWIDPLLLDQQLTEEERMIRDTAAQFAQQSLAPRILEAFRHEKTDPAIFREMG 60

Query: 61  EVGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQ 120
           EVGLLGATIPEQYGGSGLNYV YGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQ
Sbjct: 61  EVGLLGATIPEQYGGSGLNYVSYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQ 120

Query: 121 KQKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVF 180
           KQKYLPKLASGEWIGCFGLTEPNHGSDPG+MI+RARKV+GGY LTGSKMWITNSPIADVF
Sbjct: 121 KQKYLPKLASGEWIGCFGLTEPNHGSDPGAMISRARKVEGGYSLTGSKMWITNSPIADVF 180

Query: 181 VVWAKDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRG 240
           VVWAKDDAGDIRGFVLEKGW+GLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRG
Sbjct: 181 VVWAKDDAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRG 240

Query: 241 LKGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTE 300
           LKGPFTCLNSARYGISWGALGAAE CWHTARQYTLDRQQFGRPLAA QLIQKKLADMQTE
Sbjct: 241 LKGPFTCLNSARYGISWGALGAAEFCWHTARQYTLDRQQFGRPLAATQLIQKKLADMQTE 300

Query: 301 ITLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVAR 360
           IT+ALQGCLRLGRMKDEGTAAVEITS+MKRNSCGK+LDIARMARDMLGGNGISDEFGVAR
Sbjct: 301 ITMALQGCLRLGRMKDEGTAAVEITSMMKRNSCGKSLDIARMARDMLGGNGISDEFGVAR 360

Query: 361 HLVNLEVVNTYEGTHDVHALILGRAQTGIQAFY 393
           HLVNLEVVNTYEGTHDVHALILGRAQTG+QAFY
Sbjct: 361 HLVNLEVVNTYEGTHDVHALILGRAQTGLQAFY 393


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: 651
Number of extensions: 10
Number of successful extensions: 1
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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