GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pontibacillus litoralis JSM 072002

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase

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



>NCBI__GCF_000775615.1:WP_036834050.1
          Length = 400

 Score =  230 bits (587), Expect = 5e-65
 Identities = 129/372 (34%), Positives = 211/372 (56%), Gaps = 5/372 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           +D   +EE++M+R +  +F   ++ P + E       DPAI  ++ ++GL+G  IP +YG
Sbjct: 1   MDFTFSEEQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYG 60

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           GSG++Y    ++  E+ER D+ +R+ +SV + L  + + +FGTE QK+KYL   A GE I
Sbjct: 61  GSGMDYNALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKI 120

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GD 190
           G FGLTEP  GSD  S+ T A +    Y L G K WI+    AD F+V+A  D       
Sbjct: 121 GAFGLTEPGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQG 180

Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLN 249
           I  F++E+  +G S+ A  GK+G+RA  TGE+ +++V VP +N +  +  G K     L+
Sbjct: 181 ISAFIVERTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLD 240

Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309
           + R+ ++ GA G   AC   + +Y  +R+ FG+ +  +QL+Q+ +A+M+  + ++     
Sbjct: 241 NGRFTVAAGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVY 300

Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369
           R G +K+ G      TS+ K  +C  A   A  A  + G  G S+E+ V R+L N +   
Sbjct: 301 RAGELKNSGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPV 360

Query: 370 TYEGTHDVHALI 381
            YEGT ++H ++
Sbjct: 361 IYEGTREIHTIM 372


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: 343
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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