GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17595 in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate WP_068168721.1 HTA01S_RS07505 ABC transporter permease subunit

Query= uniprot:A0A1N7UBU2
         (233 letters)



>NCBI__GCF_001592305.1:WP_068168721.1
          Length = 226

 Score =  171 bits (432), Expect = 1e-47
 Identities = 92/223 (41%), Positives = 130/223 (58%), Gaps = 4/223 (1%)

Query: 10  YGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVL 69
           Y   L QGAW+T++LA  +L + LALGL+ AA  LS    LR    L T L+R +P+ ++
Sbjct: 7   YAGQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRGIPEFLI 66

Query: 70  ILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQL 129
           +L+ ++ L   +N+  +       EI PF AGV  L  ++ AY +E FRG+  ++P GQ+
Sbjct: 67  VLVCYFGLSNLINNHLD----GAVEISPFAAGVFALSIVFAAYASEVFRGSFAAIPRGQI 122

Query: 130 EAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAG 189
           EAA A+GL+  Q F  V  PQ  R ALP LGN W  LLK T+LVS++GL DL+K +  A 
Sbjct: 123 EAAQAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKSNMAA 182

Query: 190 KTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIKGMA 232
           + T++P  F + A  +Y V    S  V   LERR   G +  A
Sbjct: 183 QATHQPFLFFLAAATVYFVFLHASQPVFAWLERRAGRGFEARA 225


Lambda     K      H
   0.327    0.141    0.428 

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: 159
Number of extensions: 6
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: 233
Length of database: 226
Length adjustment: 23
Effective length of query: 210
Effective length of database: 203
Effective search space:    42630
Effective search space used:    42630
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