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_037574209.1 BS73_RS19260 alpha-ketoacid dehydrogenase subunit beta

Query= SwissProt::P9WIS1
         (348 letters)



>NCBI__GCF_000744815.1:WP_037574209.1
          Length = 326

 Score =  363 bits (933), Expect = e-105
 Identities = 187/325 (57%), Positives = 235/325 (72%), Gaps = 2/325 (0%)

Query: 22  ITQSLTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLA 81
           + +  TMV+A+N AL  ++ AD + LV GEDV   GGVFRVT+GL   FG DR  DTPLA
Sbjct: 1   MAEKYTMVKALNEALRRSLDADPKTLVMGEDVGRLGGVFRVTDGLYKDFGEDRVIDTPLA 60

Query: 82  ESAIIGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPS 141
           ES I+G A+GL LRG+ PV EIQFDGF YPAFDQ+VS LAK   R+ G+V +PVT+RIP 
Sbjct: 61  ESGIVGTAIGLCLRGYRPVLEIQFDGFVYPAFDQIVSQLAKMHARSLGKVRLPVTIRIPW 120

Query: 142 FGGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHG 201
            GGIGA EHHS+S E+Y+ HTAGLKVV P++P DA+W+LR AIA  DPV++LEPKRRY  
Sbjct: 121 AGGIGAVEHHSESHEAYFAHTAGLKVVAPASPADAHWMLRQAIASDDPVIFLEPKRRYWD 180

Query: 202 RGMVDTSRPEPPIGH-AMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRS 260
           +  VD     P   H A V RSGTD+T++ YG +V   L +A  A  +   S+EV+DLRS
Sbjct: 181 KAEVDPDGEAPAGLHDARVVRSGTDLTLLAYGPMVKVCLEAA-AAAAEDGRSIEVVDLRS 239

Query: 261 LAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTP 320
           L+P+DFDT+ AS++RTGR VV+HE P  LG G+ LAAR+ E  FY LEAPVLR  GF  P
Sbjct: 240 LSPVDFDTLEASVRRTGRAVVVHEAPVFLGMGSELAARLTERCFYALEAPVLRVGGFFAP 299

Query: 321 YPPARLEKLWLPGPDRLLDCVERVL 345
           YPP+R+E  +LP  DR+LD V+R +
Sbjct: 300 YPPSRVEDTFLPDLDRVLDAVDRAM 324


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: 391
Number of extensions: 15
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: 326
Length adjustment: 28
Effective length of query: 320
Effective length of database: 298
Effective search space:    95360
Effective search space used:    95360
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