GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Desulfovibrio vulgaris Hildenborough

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 209323 DVU0387 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q9HU30
         (231 letters)



>MicrobesOnline__882:209323
          Length = 225

 Score =  133 bits (334), Expect = 3e-36
 Identities = 75/210 (35%), Positives = 118/210 (56%), Gaps = 10/210 (4%)

Query: 12  LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71
           +L G+ +T+   L ++ +G  +G+  A+A+      +R+L G Y    RG+P  + + + 
Sbjct: 15  ILEGSAVTIATVLGSLALGFCMGVPMAVAQVYGGRPVRYLVGLYVWFFRGMPILVLLFLF 74

Query: 72  YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131
           YFG          LF   DL LS F A  L LG+   AY +++FRG++L++P+G  +A +
Sbjct: 75  YFG----------LFQALDLNLSAFTASCLVLGMASAAYQSQIFRGSILALPQGQLKAAR 124

Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191
           ALG+S G     IVLPQ  R+++P   N Y ILLKD+AL  ++   EIM +    ++ T 
Sbjct: 125 ALGMSDGAAIRSIVLPQALRLSIPAWSNEYSILLKDSALAFVLGTPEIMARTHFVASRTY 184

Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERR 221
           E    YMTA A+Y  +T+  +  L  LER+
Sbjct: 185 EHLPLYMTAGALYFIITLAGLKVLRHLERK 214


Lambda     K      H
   0.327    0.143    0.431 

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: 123
Number of extensions: 7
Number of successful extensions: 4
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: 231
Length of database: 225
Length adjustment: 23
Effective length of query: 208
Effective length of database: 202
Effective search space:    42016
Effective search space used:    42016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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