GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Marinicella litoralis KMM 3900

Align 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized)
to candidate WP_099019682.1 CCS90_RS11440 MFS transporter

Query= SwissProt::P9WIS1
         (348 letters)



>NCBI__GCF_002591915.1:WP_099019682.1
          Length = 747

 Score =  143 bits (360), Expect = 2e-38
 Identities = 103/331 (31%), Positives = 166/331 (50%), Gaps = 24/331 (7%)

Query: 28  MVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAIIG 87
           M   INR L D M      ++FGEDVA +GGV+ +T+ L   FGA R F+T L E  I+G
Sbjct: 410 MAIQINRGLQDLMLKYPETVIFGEDVAQKGGVYTITKQLYKKFGAKRIFNTLLDEQTILG 469

Query: 88  IAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFG---G 144
           +A G A  G +P+PEIQ+  + + A DQ+    A  +  + G+   P+ VRI   G   G
Sbjct: 470 LAQGYATLGLLPIPEIQYLAYFHNACDQIRGEAASLQFFSNGQFSNPMVVRIAGLGYQKG 529

Query: 145 IGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACP----------DPV-MYL 193
            G    H+D++ +      G+ V  PS P DA  ++R  +A            +P+ +Y+
Sbjct: 530 FG-GHFHNDNSIAAIRDIPGVTVACPSRPDDAVNMMRTLVALSKVNKRVSLFIEPIALYM 588

Query: 194 EPKRRYHGRGMVDTSRPEP----PIGHAMV-RRSGTDVTVVTYGNLVSTALSSADTAEQQ 248
           +      G G+ +   P+P    P+G   + +    D+ ++TYGN V  +L +    E+ 
Sbjct: 589 QKDLYDEGDGLWNKPYPKPGMYAPLGTPRIYQGKAEDILIITYGNGVLMSLRAIKAFEKT 648

Query: 249 HDWSLEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLE 308
           H   ++++DLR L PL+   I    ++  R +++ EG RS   G G+ + + E   + + 
Sbjct: 649 HKSRVKLMDLRWLQPLNEKAIQKHAEKFDRIIIVDEGRRSACVGEGVISILAE---HGMN 705

Query: 309 APVLR-ACGFDTPYPPARLEKLWLPGPDRLL 338
           +  L+   G DT  P A   KL LP  + +L
Sbjct: 706 SRYLKLITGADTFTPLADAAKLVLPDEEVIL 736


Lambda     K      H
   0.321    0.137    0.417 

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: 580
Number of extensions: 33
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: 348
Length of database: 747
Length adjustment: 34
Effective length of query: 314
Effective length of database: 713
Effective search space:   223882
Effective search space used:   223882
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 (21.9 bits)
S2: 52 (24.6 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