GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  140 bits (353), Expect = 4e-38
 Identities = 85/232 (36%), Positives = 131/232 (56%), Gaps = 12/232 (5%)

Query: 11  KGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEV 70
           K + G+  ++ + L+V   E +V  GPSG GKSTL+R I GLE    G I + G D  EV
Sbjct: 9   KWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI-GED--EV 65

Query: 71  SPAKRDL-------AMVFQTYALYPHMSVRKNMSFA-LDLAGVAKAEVEKKVSEAARILE 122
            P +R L        MVFQ + L+PH+++ +N + A + + G+A+   E    E    + 
Sbjct: 66  RPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVR 125

Query: 123 LGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKE 182
           +    ++ P QLSGGQ+QR AI RA+   P+I LFDEP S LDA + V+  L++++    
Sbjct: 126 IADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEM-VKEVLDIMKALAT 184

Query: 183 LQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFL 234
              TM+ VTH+   A  +AD+++ ++ G+I + GSP D +  P +     FL
Sbjct: 185 EGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236


Lambda     K      H
   0.320    0.137    0.389 

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: 223
Number of extensions: 12
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: 367
Length of database: 241
Length adjustment: 26
Effective length of query: 341
Effective length of database: 215
Effective search space:    73315
Effective search space used:    73315
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 (21.8 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