GapMind for catabolism of small carbon sources

 

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

Align Histidine transport system permease protein HisM (characterized)
to candidate WP_068168721.1 HTA01S_RS07505 ABC transporter permease subunit

Query= SwissProt::P0A2I7
         (235 letters)



>NCBI__GCF_001592305.1:WP_068168721.1
          Length = 226

 Score =  112 bits (280), Expect = 6e-30
 Identities = 72/211 (34%), Positives = 112/211 (53%), Gaps = 3/211 (1%)

Query: 17  GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLL 76
           G    G  +T+ L +SS+V+G  L ++LA G +S    +R  + L T + RG P ++ +L
Sbjct: 9   GQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRGIPEFLIVL 68

Query: 77  VFYSGMYTLEIVKGTDLLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAA 136
           V Y G+  L       L  A   S     V AL++   AY +E+F G+  ++P G+IEAA
Sbjct: 69  VCYFGLSNLI---NNHLDGAVEISPFAAGVFALSIVFAAYASEVFRGSFAAIPRGQIEAA 125

Query: 137 RAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINSAT 196
           +A+G ++ + +  + LP A RIALP+  N    +L  T+L     + DLLK +     AT
Sbjct: 126 QAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKSNMAAQAT 185

Query: 197 YQPFTAFGIAAVLYLLISYVLISLFRRAERR 227
           +QPF  F  AA +Y +  +    +F   ERR
Sbjct: 186 HQPFLFFLAAATVYFVFLHASQPVFAWLERR 216


Lambda     K      H
   0.330    0.141    0.429 

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: 142
Number of extensions: 4
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: 235
Length of database: 226
Length adjustment: 23
Effective length of query: 212
Effective length of database: 203
Effective search space:    43036
Effective search space used:    43036
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 (21.9 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