GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Rhizorhabdus wittichii RW1

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  135 bits (340), Expect = 8e-37
 Identities = 83/228 (36%), Positives = 126/228 (55%), Gaps = 10/228 (4%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L +VSL +  G+  VI G SGSGKSTL+R IN L     G +    D +     + L+  
Sbjct: 17  LRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRP-DRRVLQRI 75

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYG-QRVRGVSKDDAREIGMKWIDTVGLSGYDAKFP 161
           R R V MVFQ F L PH T+L+N      +VRG+++D A  +  + ++ V ++    K+P
Sbjct: 76  RAR-VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYP 134

Query: 162 HQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAK---TIV 218
            QLSGG +QR  +ARALA   ++IL DE  SALD     +M  ++L + + LA    T++
Sbjct: 135 AQLSGGQQQRTAIARALAMQPEIILFDEPTSALD----AEMVKEVLDIMKALATEGITML 190

Query: 219 FITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQR 266
            +TH++  A  +   I  +  GQ+V+ G+P D    P ++    F+ R
Sbjct: 191 CVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSR 238


Lambda     K      H
   0.323    0.139    0.397 

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: 194
Number of extensions: 13
Number of successful extensions: 4
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: 275
Length of database: 241
Length adjustment: 24
Effective length of query: 251
Effective length of database: 217
Effective search space:    54467
Effective search space used:    54467
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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