GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Rhizorhabdus wittichii RW1

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

Query= reanno::Phaeo:GFF1302
         (334 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  147 bits (372), Expect = 2e-40
 Identities = 94/233 (40%), Positives = 129/233 (55%), Gaps = 18/233 (7%)

Query: 4   IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63
           I +  V K +G    +  + L +  GE  V  GPSG GKSTL+R I GLE    G IRI 
Sbjct: 2   IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI- 60

Query: 64  GEDATNIPPAKRGL-------AMVFQSYALYPHMSVRKNIAF-PMKMAGIPADEQKRRID 115
           GED   + P +R L        MVFQ + L+PH+++ +N A  PMK+ G+  D  +    
Sbjct: 61  GED--EVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALAR 118

Query: 116 NAAAALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLE 175
                + + D  D+ P QLSGGQ+QR AI RA+  +P   LFDEP S LDA     M  E
Sbjct: 119 ELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAE----MVKE 174

Query: 176 ISELHKRLAT---TMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAP 225
           + ++ K LAT   TM+ VTH+   A  +AD+I+ + AG I + GSP + + AP
Sbjct: 175 VLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227


Lambda     K      H
   0.320    0.138    0.400 

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: 202
Number of extensions: 9
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: 334
Length of database: 241
Length adjustment: 26
Effective length of query: 308
Effective length of database: 215
Effective search space:    66220
Effective search space used:    66220
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: 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