GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Desulfovibrio vulgaris Hildenborough

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= uniprot:B2TBJ7
         (240 letters)



>MicrobesOnline__882:206399
          Length = 337

 Score =  121 bits (304), Expect = 2e-32
 Identities = 64/200 (32%), Positives = 115/200 (57%), Gaps = 3/200 (1%)

Query: 16  GVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIY 75
           G+LL    +T+ +++ A+ +G V G +   A++S    LR +   Y  + RG P L+ ++
Sbjct: 125 GILLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVF 184

Query: 76  LFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELE 135
           L+YF   TL+ +   LF   G   +PP   G +A+ + +GAY AE+ R+ + +V RG++E
Sbjct: 185 LWYFVVGTLLNA---LFEKVGLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQME 241

Query: 136 AARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAG 195
           AARS+GM      R++++PQ  R  +P +   +   +KDS+L+ V  + EL + ++    
Sbjct: 242 AARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVT 301

Query: 196 STHQYFTFFVVGGALYLIMT 215
           ++ Q F  ++V   LYL++T
Sbjct: 302 TSLQPFELWIVCALLYLVLT 321


Lambda     K      H
   0.327    0.141    0.403 

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: 141
Number of extensions: 10
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: 240
Length of database: 337
Length adjustment: 26
Effective length of query: 214
Effective length of database: 311
Effective search space:    66554
Effective search space used:    66554
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: 47 (22.7 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