GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pontibacillus litoralis JSM 072002

Align Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial; SBCAD; 2-methyl branched chain acyl-CoA dehydrogenase; 2-MEBCAD; 2-methylbutyryl-coenzyme A dehydrogenase; 2-methylbutyryl-CoA dehydrogenase; EC 1.3.8.5 (characterized)
to candidate WP_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase

Query= SwissProt::P45954
         (432 letters)



>NCBI__GCF_000775615.1:WP_036834050.1
          Length = 400

 Score =  260 bits (664), Expect = 6e-74
 Identities = 137/374 (36%), Positives = 215/374 (57%), Gaps = 1/374 (0%)

Query: 56  TFTDEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGTG 115
           TF++E+ M++ +V++F  ++I P +   DE    + +++  L   GLMG+ +  +YGG+G
Sbjct: 4   TFSEEQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYGGSG 63

Query: 116 ASFLSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYL-PQLTTEKVGSF 174
             + +  +V EEL + D +      +   L +  + + GTEEQK  YL PQ   EK+G+F
Sbjct: 64  MDYNALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKIGAF 123

Query: 175 CLSEAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITS 234
            L+E GAGSD  +++T A ++GDYY LNG K WIS  + A  FLV A  D    ++GI++
Sbjct: 124 GLTEPGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQGISA 183

Query: 235 FLVDRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGR 294
           F+V+R   G      + KLG+RA +T  L  E+V VP  N LG+ G G+K A+ SL+ GR
Sbjct: 184 FIVERTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLDNGR 243

Query: 295 IGIAAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAA 354
             +AA   GL   C + ++ Y  ER  FGK +   Q +Q  +A++   L+ +RLL Y A 
Sbjct: 244 FTVAAGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVYRAG 303

Query: 355 RLLEAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYE 414
            L  +GK   +E S+AK+ A + A +     ++  G  GY+ +Y VE+Y R++K   IYE
Sbjct: 304 ELKNSGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPVIYE 363

Query: 415 GASNIQLNTIAKHI 428
           G   I     A+++
Sbjct: 364 GTREIHTIMQAEYV 377


Lambda     K      H
   0.318    0.134    0.385 

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: 400
Number of extensions: 19
Number of successful extensions: 2
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: 432
Length of database: 400
Length adjustment: 31
Effective length of query: 401
Effective length of database: 369
Effective search space:   147969
Effective search space used:   147969
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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