GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Rhodococcus qingshengii djl-6-2

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_019745160.1 C1M55_RS24910 ABC transporter permease subunit

Query= TCDB::Q9KKE2
         (285 letters)



>NCBI__GCF_002893965.1:WP_019745160.1
          Length = 215

 Score = 97.1 bits (240), Expect = 3e-25
 Identities = 57/188 (30%), Positives = 103/188 (54%), Gaps = 4/188 (2%)

Query: 96  LALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKV 155
           ++ ++ + I++ +  V +GILV +S    +I   +   + T+PSF  L   + + GLG  
Sbjct: 23  VSAVIQSVIIATIAAVIIGILVYRSPAGSSIATALASTILTVPSFALLGLLIPILGLGVA 82

Query: 156 PAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAGL 215
           P I A I+YA+ P+IR T +G+  V+  + +AA   G +   +L  +ELP+A P+I+ G+
Sbjct: 83  PTITALILYALLPIIRNTIIGLDAVNPAITDAARGVGMNRMHVLSRIELPIAWPSILTGM 142

Query: 216 NQTIMMALSMVVVASMIGARGLGEQVLNGIQTLD----VGKGLEAGIGIVILAVVLDRIT 271
             +  M + ++ +A+     GLG  + +G+  +     V + L   + IVILA++LD I 
Sbjct: 143 RVSTQMLMGILAIAAYAKGPGLGNLIFSGLSRVGSPNAVPQALVGTVLIVILALILDGIY 202

Query: 272 QGFGKPRT 279
              G+  T
Sbjct: 203 VVIGRLTT 210


Lambda     K      H
   0.327    0.142    0.422 

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: 197
Number of extensions: 11
Number of successful extensions: 2
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: 285
Length of database: 215
Length adjustment: 24
Effective length of query: 261
Effective length of database: 191
Effective search space:    49851
Effective search space used:    49851
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