GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Rhodococcus qingshengii djl-6-2

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_050655903.1 C1M55_RS30495 alpha-ketoacid dehydrogenase subunit beta

Query= SwissProt::P9WIS1
         (348 letters)



>NCBI__GCF_002893965.1:WP_050655903.1
          Length = 334

 Score =  357 bits (916), Expect = e-103
 Identities = 178/319 (55%), Positives = 228/319 (71%), Gaps = 2/319 (0%)

Query: 26  LTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAI 85
           LTM QA+N AL D++AAD+ V+VFGEDV   GGVFRVT+GL   FG DRCFDTPLAES I
Sbjct: 4   LTMAQALNTALRDSLAADDNVVVFGEDVGTLGGVFRVTDGLTRDFGDDRCFDTPLAESGI 63

Query: 86  IGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGI 145
           IG A+G+A+ GF PV E+QFD F+YPAF+Q+ SH+AK R RT+G + +P+ +R+P  GGI
Sbjct: 64  IGFAIGMAMAGFRPVVEMQFDAFAYPAFEQIASHVAKIRNRTKGALSIPIVIRVPFAGGI 123

Query: 146 GAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGRGMV 205
           G  EHH DS+E Y+ HT GLKVV PST  DAY LLR AI   DPV++LEPK+ Y  R  V
Sbjct: 124 GGVEHHCDSSEGYYAHTPGLKVVAPSTVEDAYSLLRSAIEDLDPVIFLEPKKLYFARADV 183

Query: 206 DTSRPEPPIGHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRSLAPLD 265
           + +  E PIG A+VRR G D T++ YG  V  AL SA+ A  +    +EVID+RS+ P D
Sbjct: 184 ELTACE-PIGRAVVRRPGRDATLIAYGPSVDVALRSAEAAAAE-GRDIEVIDIRSIVPFD 241

Query: 266 FDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTPYPPAR 325
            +T+ AS+++TGRC+V+ E     G GA +AAR+QE  F+ L APVLR  GFD PYP  +
Sbjct: 242 DETVTASVRKTGRCIVIQEAQGFAGVGAEIAARVQERCFHHLHAPVLRVSGFDIPYPAPK 301

Query: 326 LEKLWLPGPDRLLDCVERV 344
           LE+  LP  DR+LD V+R+
Sbjct: 302 LERHHLPSVDRVLDAVDRL 320


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: 378
Number of extensions: 16
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: 334
Length adjustment: 29
Effective length of query: 319
Effective length of database: 305
Effective search space:    97295
Effective search space used:    97295
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