GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Nitratifractor salsuginis DSM 16511

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score = 76.3 bits (186), Expect = 8e-19
 Identities = 40/131 (30%), Positives = 78/131 (59%), Gaps = 1/131 (0%)

Query: 87  PAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRM 146
           P F+  +  L IY+  +++E +R  I+++ KGQ EAA S+G+S    +R V+LPQAV   
Sbjct: 250 PEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIA 309

Query: 147 IPPLGNEFIALIKNSALVSLLTIHDLMH-EGQKIISVSYRSLEVYLAIAVVYFILTGATT 205
           IP + N+++ LIKNS+L + +   +L+       ++ + ++LE+ L   + Y +++   +
Sbjct: 310 IPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIVS 369

Query: 206 LVLRRIELRLR 216
           L+L     +++
Sbjct: 370 LILNWFNAKMK 380



 Score = 37.4 bits (85), Expect = 4e-07
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 3   LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62
           + F+P    +     G L T+ ++   ++   ++GLL+GI RL+P   ++  +  AY+  
Sbjct: 63  IPFTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNW-LINRIAAAYIET 121

Query: 63  IRGTPLLVQLFILF 76
            R  P+L+Q+   +
Sbjct: 122 FRNIPVLLQILFWY 135


Lambda     K      H
   0.328    0.143    0.412 

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: 201
Number of extensions: 11
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: 222
Length of database: 384
Length adjustment: 26
Effective length of query: 196
Effective length of database: 358
Effective search space:    70168
Effective search space used:    70168
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 (21.8 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