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_068172309.1 HTA01S_RS13395 amino acid ABC transporter permease

Query= uniprot:A0A1N7UBU2
         (233 letters)



>NCBI__GCF_001592305.1:WP_068172309.1
          Length = 228

 Score =  119 bits (297), Expect = 6e-32
 Identities = 77/221 (34%), Positives = 115/221 (52%), Gaps = 11/221 (4%)

Query: 7   LHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPD 66
           L  +GP L  GA +T +L+ +   L+L LG +  A + S A  L V A  Y   +R+VP 
Sbjct: 12  LPDWGPRLVDGALVTARLSLVGFVLALGLGALLVAMQCSGAALLAVAANAYVQFVRTVPL 71

Query: 67  LVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPV 126
           L L+L ++++L      LS            + AG + LG    AY  E  RG + ++  
Sbjct: 72  LALLLALYFALPPLGLTLSG-----------YWAGALGLGLHGSAYVAEILRGGLTAIHR 120

Query: 127 GQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQ 186
           GQ E+A A GLS  Q F  V+FPQ +R  LP L N ++ LLK ++L ++I   +L+ AA+
Sbjct: 121 GQRESALAVGLSPLQVFVHVVFPQALRIMLPPLLNTYVALLKDSSLCALIATDELMLAAR 180

Query: 187 NAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLG 227
                +  PL+  +L GL Y  I    + + + LERR N G
Sbjct: 181 AISSESFLPLHIFLLVGLFYFGIAFPLSMLSRLLERRLNRG 221


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: 111
Number of extensions: 4
Number of successful extensions: 1
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: 228
Length adjustment: 23
Effective length of query: 210
Effective length of database: 205
Effective search space:    43050
Effective search space used:    43050
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.

Links

Downloads

Related tools

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