GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Nitratifractor salsuginis DSM 16511

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score = 71.2 bits (173), Expect = 3e-17
 Identities = 42/128 (32%), Positives = 73/128 (57%), Gaps = 1/128 (0%)

Query: 97  YMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLP 156
           ++  + +L++ TA + AE IR G+ AVP GQ EA  S+GLS    LR VI P A+R  +P
Sbjct: 252 FLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIP 311

Query: 157 AYSTEAVLLVKSTALASLVTVWE-VTGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRL 215
           +   + + L+K+++LA+ +   E VT  A   + QT +  E+ +   L YL ++ ++  +
Sbjct: 312 SIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIVSLI 371

Query: 216 LGMLETRL 223
           L     ++
Sbjct: 372 LNWFNAKM 379



 Score = 47.8 bits (112), Expect = 3e-10
 Identities = 23/54 (42%), Positives = 33/54 (61%)

Query: 22  TLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLVY 75
           TL + F  ++   L+ L+I   R+SP+WL NR A AYI  FR  P+L+Q+   Y
Sbjct: 82  TLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRNIPVLLQILFWY 135


Lambda     K      H
   0.331    0.143    0.431 

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: 212
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 250
Length of database: 384
Length adjustment: 27
Effective length of query: 223
Effective length of database: 357
Effective search space:    79611
Effective search space used:    79611
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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