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_068169054.1 HTA01S_RS08130 ABC transporter permease subunit

Query= uniprot:A0A1N7UBU2
         (233 letters)



>NCBI__GCF_001592305.1:WP_068169054.1
          Length = 233

 Score =  211 bits (536), Expect = 1e-59
 Identities = 107/222 (48%), Positives = 158/222 (71%), Gaps = 6/222 (2%)

Query: 14  LAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILLI 73
           + QG  +T+ ++  AL ++  LGL  AAAKLS  +WL     +Y+T+IR VPDLV +LL+
Sbjct: 8   ILQGLLVTIGVSLGALIVAALLGLAGAAAKLSHHRWLNWLGDIYSTVIRGVPDLVWMLLL 67

Query: 74  FYSLQLWLNDLSEVFGWDYF-EIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEAA 132
           ++  Q+ +ND++E  G+    +I+PF AGV+T+GF+YGAY TE FRGAI+SVP GQ EA 
Sbjct: 68  YFGGQILVNDIAEALGFRSGPQINPFVAGVLTIGFVYGAYMTETFRGAIMSVPKGQSEAG 127

Query: 133 TAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNA---- 188
            A+G+SR+  F  ++ PQ++RFALP   NNWLVLLK+TALVS+IGL+D+   A+ A    
Sbjct: 128 WAFGMSRFYTFRRMVLPQMVRFALPSFTNNWLVLLKATALVSVIGLADITNLAKQAGAAA 187

Query: 189 -GKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIK 229
            G+     + F+  AGL+YL+IT++S  +L+R E+RY++G+K
Sbjct: 188 RGQIPGAAIIFMAFAGLLYLLITSISLLLLRRAEKRYSVGVK 229


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: 203
Number of extensions: 8
Number of successful extensions: 3
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: 233
Length adjustment: 23
Effective length of query: 210
Effective length of database: 210
Effective search space:    44100
Effective search space used:    44100
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