GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Cupriavidus basilensis 4G11

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate RR42_RS21785 RR42_RS21785 MFS transporter

Query= BRENDA::Q9HIA4
         (319 letters)



>FitnessBrowser__Cup4G11:RR42_RS21785
          Length = 729

 Score =  195 bits (496), Expect = 2e-54
 Identities = 116/292 (39%), Positives = 167/292 (57%), Gaps = 6/292 (2%)

Query: 4   VQALNSAMDLKMSEDDSVIILGEDVGR-DGGVFRVTDGLQAKYGPQRVIDTPLSELGIVG 62
           +  +   M  +M  D SV+++GEDV R  GG    T GL+  + P RV+ TP+SE   VG
Sbjct: 405 IDVVADVMQRRMETDPSVVVMGEDVHRLKGGTNGATRGLRDNF-PDRVLGTPISENAFVG 463

Query: 63  MAIGMAVNG-LKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGIK 121
           +  G+A++G  KP+ E  + DF++ + DQ+ NQ+ K R+  GG+  VPLVLRT V  G  
Sbjct: 464 LGGGLALDGRYKPVVEFMYPDFMWVAADQVFNQIGKARHMFGGESDVPLVLRTKVAMGTG 523

Query: 122 GGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKV-E 180
            G  HS      FA   G  +V+PS P+D  GL+ +A+   DPV+ +E   LY A  V  
Sbjct: 524 YGSQHSMDPAGIFATNPGWRIVAPSTPFDYVGLMNTALACKDPVLVIEHVDLYNASGVGP 583

Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASKSKYDVEVIDLRTI--APMDR 238
           V D  Y +P+ KA V + G+DVT++TY SMV   +    ++  D EVIDLR +  A +D 
Sbjct: 584 VDDFDYHLPVGKAAVRRGGSDVTVITYLSMVGHSLEAVEQTGIDAEVIDLRWLDRASIDW 643

Query: 239 DTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPD 290
           DTI  SV+KT  V+IV +  R    G  ++  I  R  ++L  P+ RVTG +
Sbjct: 644 DTIAQSVRKTNNVLIVEQGARGTSYGGWLADEIQRRYFDWLDQPVQRVTGAE 695


Lambda     K      H
   0.318    0.137    0.388 

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: 544
Number of extensions: 34
Number of successful extensions: 5
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: 319
Length of database: 729
Length adjustment: 34
Effective length of query: 285
Effective length of database: 695
Effective search space:   198075
Effective search space used:   198075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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