GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Shewanella halifaxensis HAW-EB4

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 WP_012277322.1 SHAL_RS11655 2-oxoisovalerate dehydrogenase subunit beta

Query= SwissProt::Q9LDY2
         (358 letters)



>NCBI__GCF_000019185.1:WP_012277322.1
          Length = 325

 Score =  431 bits (1107), Expect = e-125
 Identities = 207/322 (64%), Positives = 256/322 (79%), Gaps = 1/322 (0%)

Query: 38  MNLYSAINQALHIALETDPRSYVFGEDVG-FGGVFRCTTGLAERFGKSRVFNTPLCEQGI 96
           MN+  AINQAL   +E+D    VFGEDVG FGGVFR T+GL E+FG+ R FNTPL EQGI
Sbjct: 4   MNMLQAINQALSSEMESDETMTVFGEDVGHFGGVFRATSGLQEKFGRDRCFNTPLTEQGI 63

Query: 97  VGFGIGLAAMGNRVIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTIRAPYGAV 156
            GF  GLA+ G   +AEIQFADYIFPA DQIVNE+AKFRYRSGN+F+ GGLT R PYG  
Sbjct: 64  AGFANGLASNGMTAVAEIQFADYIFPAIDQIVNESAKFRYRSGNEFDVGGLTFRTPYGGG 123

Query: 157 GHGGHYHSQSPEAFFCHVPGIKVVIPRSPREAKGLLLSSIRDPNPVVFFEPKWLYRQAVE 216
             GGHYHSQSPEA+F   PG+KVV+PR+P +AKGLL++SIRD NPV+FFEPK LYR +V 
Sbjct: 124 IAGGHYHSQSPEAYFTQTPGLKVVVPRNPEQAKGLLIASIRDKNPVIFFEPKRLYRASVG 183

Query: 217 DVPEDDYMIPLSEAEVMREGSDITLVGWGAQLTIMEQACLDAENEGISCELIDLKTLIPW 276
           +VPE DY+I L +AEV+++GSDITL+GWGAQ+ ++E+A   A  +GISCE++DL+TL PW
Sbjct: 184 EVPEGDYVIELGKAEVVKQGSDITLLGWGAQMEVLEKAAEMAAKKGISCEIVDLRTLSPW 243

Query: 277 DKEIVETSVRKTGRLLISHEAPVTGGFGAEIAATIVERCFLRLEAPVSRVCGLDTPFPLV 336
           D + V  SV+KTGRLLI+HEAP+TGGF  EIAATI E CFL LE+P++RVCGLDTP+PL+
Sbjct: 244 DIDTVAASVKKTGRLLINHEAPLTGGFAGEIAATIQEECFLYLESPIARVCGLDTPYPLI 303

Query: 337 FEPFYMPTKNKILDAIRSTVNY 358
            E  YMP   K  +AI+++V +
Sbjct: 304 HEKEYMPDALKTFEAIKASVKF 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: 8
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 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