GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate WP_013403449.1 CALHY_RS07945 ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_09615
         (283 letters)



>NCBI__GCF_000166355.1:WP_013403449.1
          Length = 217

 Score = 87.0 bits (214), Expect = 3e-22
 Identities = 63/198 (31%), Positives = 109/198 (55%), Gaps = 21/198 (10%)

Query: 94  QTLALMLVATLISVLIGIPLGILSARSNR--------LRSVLMPLLDIMQTMPSFVYLIP 145
           QT+ +++++TLI+ ++GIPLG+    +++        L  +L  +++I +++P FV L+ 
Sbjct: 14  QTIYMVVISTLIATVLGIPLGVFLMVTDKGQILQNDILNKILSTIVNIFRSIP-FVILLI 72

Query: 146 VLMLF-------GLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRWQQ 198
           VLM F        +G   AI    I A P + R+T+  +R+VD  V+EA  A GA+ +Q 
Sbjct: 73  VLMPFTRLIVGTSIGTTAAIVPLSIAAIPFMGRITETALREVDHGVIEAAQAMGASPFQI 132

Query: 199 LFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGE-DVLVGIQTLNVGRGLEAG 257
           +  V +P ALPSI++GI  T +  +    +A +IG  GLG+  V  G Q   +    +  
Sbjct: 133 ITKVLIPEALPSIVSGITITAINLVGYSAMAGVIGGGGLGDLAVRYGYQRFMI----DIM 188

Query: 258 LAIVILAVVIDRITQAYG 275
           L  V + + + ++TQ  G
Sbjct: 189 LWTVAILIAMVQLTQLIG 206


Lambda     K      H
   0.328    0.142    0.429 

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: 165
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 283
Length of database: 217
Length adjustment: 24
Effective length of query: 259
Effective length of database: 193
Effective search space:    49987
Effective search space used:    49987
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 Sep 24 2021. 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