GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_068168721.1 HTA01S_RS07505 ABC transporter permease subunit

Query= uniprot:B2TBJ7
         (240 letters)



>NCBI__GCF_001592305.1:WP_068168721.1
          Length = 226

 Score =  158 bits (399), Expect = 1e-43
 Identities = 85/225 (37%), Positives = 128/225 (56%), Gaps = 5/225 (2%)

Query: 14  WGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLV 73
           + G LL  A +TV L L++L VG   G ++AA  LS    LR    + T + RG+PE L+
Sbjct: 7   YAGQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRGIPEFLI 66

Query: 74  IYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGE 133
           + + YFG S L+ +       +G V + PF  G  A+ ++  AY +EV+R +  A+ RG+
Sbjct: 67  VLVCYFGLSNLINN-----HLDGAVEISPFAAGVFALSIVFAAYASEVFRGSFAAIPRGQ 121

Query: 134 LEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVA 193
           +EAA++ G+        + +PQ  R ALP +GN+WQ  LKD++L+SV GL +LL+ S +A
Sbjct: 122 IEAAQAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKSNMA 181

Query: 194 AGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKRNFA 238
           A +THQ F FF+    +Y +    S  VF   E   GR F+   A
Sbjct: 182 AQATHQPFLFFLAAATVYFVFLHASQPVFAWLERRAGRGFEARAA 226


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: 105
Number of extensions: 5
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: 226
Length adjustment: 23
Effective length of query: 217
Effective length of database: 203
Effective search space:    44051
Effective search space used:    44051
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 Apr 09 2024. 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