GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Magnetospirillum magneticum AMB-1

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate WP_083763391.1 AMB_RS00370 hypothetical protein

Query= BRENDA::Q9HIA4
         (319 letters)



>NCBI__GCF_000009985.1:WP_083763391.1
          Length = 654

 Score =  137 bits (346), Expect = 6e-37
 Identities = 95/287 (33%), Positives = 145/287 (50%), Gaps = 21/287 (7%)

Query: 3   MVQALNSAMDLKMSEDDSVIILGEDVGRD-GGVFRVTDGLQAKYGPQRVIDTPLSELGIV 61
           +V+ + + +D  M+ DD +++LGED+    GG F+VT GL   Y P RV +TP+SE G+V
Sbjct: 329 LVEHIRAGLDAAMAADDRLLLLGEDICSPYGGAFKVTSGLSDSY-PGRVFNTPISEAGLV 387

Query: 62  GMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGIK 121
           G+  G+A+ G + + EI F DF+    DQ+IN  AK     G D  VPL++RTP+GG   
Sbjct: 388 GVGAGLALAGRRVVAEIMFGDFLTLVADQLINHAAKFTQMYGEDVEVPLLVRTPMGGRRG 447

Query: 122 GGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAI-ESPDPVIFLEPK--------- 171
            G  HSQS E +F    GLTV++  +  DA       I  +  P + +E K         
Sbjct: 448 YGPTHSQSLETHFFGVPGLTVLAIHHRMDAAAFYARLIATAKTPHLIIENKVAYGVDCAR 507

Query: 172 -RLYRAQKVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASKSKYDVEVIDL 230
            RL     VE  D+  T+ +R     +    VTI+ YG M+  +     +   D +++  
Sbjct: 508 DRLQGFSYVETDDDLPTLVVRPCVQAQ----VTILGYGGMLLEMEKAMDRLFEDADIVTE 563

Query: 231 R----TIAPMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISE 273
                 + P +   ++ SV  T R+V+V E     G GAE  A + +
Sbjct: 564 AICPVALYPSNMQALLDSVSLTRRLVVVEEGQGYAGYGAEAVAFLHQ 610


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: 468
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 319
Length of database: 654
Length adjustment: 33
Effective length of query: 286
Effective length of database: 621
Effective search space:   177606
Effective search space used:   177606
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