GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Shewanella loihica PV-4

Align 2-oxoisovalerate dehydrogenase subunit beta 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component beta chain; BCKDE1B; BCKDH E1-beta; Protein DARK INDUCIBLE 4; EC 1.2.4.4 (characterized)
to candidate 5209455 Shew_1926 transketolase, central region (RefSeq)

Query= SwissProt::Q9LDY2
         (358 letters)



>FitnessBrowser__PV4:5209455
          Length = 325

 Score =  427 bits (1097), Expect = e-124
 Identities = 206/322 (63%), Positives = 257/322 (79%), Gaps = 1/322 (0%)

Query: 38  MNLYSAINQALHIALETDPRSYVFGEDVG-FGGVFRCTTGLAERFGKSRVFNTPLCEQGI 96
           +N+  AIN AL IA+ETD ++ +FGEDVG FGGVFR T+GL ++FG+ R FNTPL EQGI
Sbjct: 4   INMLQAINDALTIAMETDDKAVIFGEDVGHFGGVFRATSGLQDKFGRDRCFNTPLTEQGI 63

Query: 97  VGFGIGLAAMGNRVIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTIRAPYGAV 156
            GF  GLA+ G   IAEIQFADYIFPAFDQIVNE+AKFRYRSGN+FN GG+T R PYG  
Sbjct: 64  AGFANGLASNGMTAIAEIQFADYIFPAFDQIVNESAKFRYRSGNEFNVGGITYRTPYGGG 123

Query: 157 GHGGHYHSQSPEAFFCHVPGIKVVIPRSPREAKGLLLSSIRDPNPVVFFEPKWLYRQAVE 216
             GGHYHSQSPEA+F   PG+KVV+PR+  +AKGLLL+SIRD NPVVFFEPK LYR +V 
Sbjct: 124 IAGGHYHSQSPEAYFTQTPGLKVVVPRNAYQAKGLLLASIRDKNPVVFFEPKRLYRASVG 183

Query: 217 DVPEDDYMIPLSEAEVMREGSDITLVGWGAQLTIMEQACLDAENEGISCELIDLKTLIPW 276
           +VP++ Y I L +AEV++EG+DIT++ WGAQ+ I+E+A   A  +GISCE+IDL+TL PW
Sbjct: 184 EVPDEAYEIELGKAEVVQEGTDITVLAWGAQMEIVEEAAKMAAKKGISCEVIDLRTLAPW 243

Query: 277 DKEIVETSVRKTGRLLISHEAPVTGGFGAEIAATIVERCFLRLEAPVSRVCGLDTPFPLV 336
           D + V  SV+KTGRL+I+HEAP+TGGF  EIAATI + CFL LE+P+SRVCGLDTP+PL+
Sbjct: 244 DVDTVAASVKKTGRLVINHEAPLTGGFAGEIAATIQQECFLYLESPISRVCGLDTPYPLI 303

Query: 337 FEPFYMPTKNKILDAIRSTVNY 358
            E  YMP   K  +AI++++ Y
Sbjct: 304 HEKEYMPDALKTFEAIKASMKY 325


Lambda     K      H
   0.322    0.140    0.426 

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: 363
Number of extensions: 9
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: 358
Length of database: 325
Length adjustment: 29
Effective length of query: 329
Effective length of database: 296
Effective search space:    97384
Effective search space used:    97384
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 17 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