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_068172435.1 HTA01S_RS13655 amino acid ABC transporter permease

Query= uniprot:A0A1N7UBU2
         (233 letters)



>NCBI__GCF_001592305.1:WP_068172435.1
          Length = 221

 Score =  114 bits (284), Expect = 2e-30
 Identities = 67/220 (30%), Positives = 114/220 (51%), Gaps = 10/220 (4%)

Query: 4   FLNLHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRS 63
           FL+   +   + +G   + +L  +A+   +ALG + A  +LS  KWL +PA  Y   +RS
Sbjct: 7   FLDWSVFSSFVLKGLIFSAQLTLVAMLGGIALGTVLALMRLSGKKWLVMPAAFYVNTLRS 66

Query: 64  VPDLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILS 123
           +P +++IL  F  + L +             +    + +IT      AY++E  R  I S
Sbjct: 67  IPLVMVILWFFLLIPLLIGQ----------PMGAELSAIITFTVFEAAYYSEIMRAGIQS 116

Query: 124 VPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVK 183
           VP GQ+ A  A G++  Q   L++ PQ  R  LP L    ++L + T+LV  IG  DL+K
Sbjct: 117 VPKGQVNAGYAVGMTYGQTMQLIVLPQAFRNMLPVLMTQTIILFQDTSLVYAIGAYDLLK 176

Query: 184 AAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERR 223
             + AGK  N P+   ++A ++Y VI    + +++RL+++
Sbjct: 177 GFEVAGKNFNRPVETYLVAAVVYFVICFSLSMLVRRLQKK 216


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: 124
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: 221
Length adjustment: 22
Effective length of query: 211
Effective length of database: 199
Effective search space:    41989
Effective search space used:    41989
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