GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Streptacidiphilus oryzae TH49

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_037568597.1 BS73_RS01200 alpha-ketoacid dehydrogenase subunit beta

Query= SwissProt::P9WIS1
         (348 letters)



>NCBI__GCF_000744815.1:WP_037568597.1
          Length = 347

 Score =  318 bits (814), Expect = 2e-91
 Identities = 167/328 (50%), Positives = 219/328 (66%), Gaps = 6/328 (1%)

Query: 23  TQSLTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAE 82
           T  LTM QAINRAL + +  D R LV GEDV   GGVFRVT+GL   FG  R  DTPLAE
Sbjct: 19  TTGLTMQQAINRALAELLEEDPRTLVLGEDVGRLGGVFRVTDGLQQRFGRRRVMDTPLAE 78

Query: 83  SAIIGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSF 142
           SAI+G++VGLA+ G+ P+PE+QFDGF+YPA DQ+V+ LA+ R R+RG + MPVT+R+PS+
Sbjct: 79  SAIVGMSVGLAMAGWKPIPELQFDGFAYPAIDQIVNQLARMRYRSRGALPMPVTLRVPSY 138

Query: 143 GGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGR 202
           GGI A EHH +S E+ + H  GLKVV PSTPG+AY LL+ A+  PDPV+++EPK RY  R
Sbjct: 139 GGIQAPEHHGESLEAVFAHVPGLKVVSPSTPGEAYRLLKTAVRDPDPVVFMEPKSRYWDR 198

Query: 203 GMVDTSRPEPPIG-----HAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVID 257
           G VD++      G        + R G   T+VT+G +V   L  A+ A       LEV+D
Sbjct: 199 GPVDSAAGAAEDGPEDEPRLRIARPGRHATLVTWGAMVRRCLQVAELAAAD-GVDLEVVD 257

Query: 258 LRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGF 317
           LR L P+D D +AA+++RT R VV+HE PR+ G GA ++A + E  F  L +PV R  G+
Sbjct: 258 LRWLKPVDADGLAAAVRRTRRAVVVHEAPRTAGLGAEISALLMERCFADLRSPVRRVTGY 317

Query: 318 DTPYPPARLEKLWLPGPDRLLDCVERVL 345
           D P P   LE+ +LP  DR+L  V+ VL
Sbjct: 318 DVPTPAGPLEEHYLPDADRILLAVQNVL 345


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: 396
Number of extensions: 12
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: 348
Length of database: 347
Length adjustment: 29
Effective length of query: 319
Effective length of database: 318
Effective search space:   101442
Effective search space used:   101442
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: 49 (23.5 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