GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_0481 N515DRAFT_0481 2-oxoisovalerate dehydrogenase E1 component

Query= SwissProt::P9WIS1
         (348 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0481
          Length = 755

 Score =  156 bits (394), Expect = 2e-42
 Identities = 114/333 (34%), Positives = 166/333 (49%), Gaps = 22/333 (6%)

Query: 32  INRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAIIGIAVG 91
           I +AL++ MA     L+FGEDVA++GGV+ VT+GL  TF  +R F+T L E+ I+G+A G
Sbjct: 426 IGQALHEVMAKYPESLLFGEDVALKGGVYTVTKGLFKTFKGNRVFNTLLDETVILGLAQG 485

Query: 92  LALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFG---GIGAA 148
            A  G +P+PEIQ+  + + A DQ+       +  +  +   P+ +R+ + G   G G  
Sbjct: 486 YANMGMLPMPEIQYLAYFHNACDQIRGEACSLQFFSNDQYRNPLVMRVAALGYQKGFG-G 544

Query: 149 EHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACP----------DPVMYLEPKRR 198
             H+D++ +      GL V  PS   DA  +LR  +A            +P+     K  
Sbjct: 545 HFHNDNSIAALRDIPGLVVGCPSRGDDAAAMLRTLMALAKVDGRVCAFLEPIALYMTKDL 604

Query: 199 YH-GRGMVDTSRPEP----PIGHAMV-RRSGTDVTVVTYGNLVSTALSSADTAEQQHDWS 252
           Y  G G    + P P    P+G   V  +   D+ V T+GN V  AL +A   E++H W 
Sbjct: 605 YEAGDGQWQFAYPAPGEALPLGEGRVYEQDADDLVVFTFGNGVPMALRAAREIEKKHGWR 664

Query: 253 LEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVL 312
             V+DLR LAPL+   IA   +   R +V+ EG RS G G G+   I E        P+ 
Sbjct: 665 TRVVDLRWLAPLNDKFIAGQARNARRILVLDEGRRSAGVGEGIITAIVEGGCG--ATPLQ 722

Query: 313 RACGFDTPYPPARLEKLWLPGPDRLLDCVERVL 345
           R  G DT  P A    L LPG   ++   ER+L
Sbjct: 723 RVVGADTYTPLAGAALLVLPGEAEIVAAAERML 755


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: 630
Number of extensions: 26
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: 755
Length adjustment: 34
Effective length of query: 314
Effective length of database: 721
Effective search space:   226394
Effective search space used:   226394
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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