GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas fluorescens FW300-N1B4

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component

Query= TCDB::O30494
         (367 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847
          Length = 367

 Score =  644 bits (1661), Expect = 0.0
 Identities = 328/367 (89%), Positives = 343/367 (93%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60
           MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVS GTI
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120
           ELDGRDITEV+PAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGV K  VE KV EAARI
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAARI 120

Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           LELGP+LERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLEL RLH
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240
           KELQATMIYVTHDQVEAMT+ADKVVVLN G+IEQVGSPL+LYHQPANLFVAGFLGTPKMG
Sbjct: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240

Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTV 300
           FLKGKVTRV+GQ CEV LDAGT I+LPLSGA+LSVG AVTLGIRPEHLE+A PG  TL V
Sbjct: 241 FLKGKVTRVNGQSCEVLLDAGTRITLPLSGANLSVGGAVTLGIRPEHLELAQPGDCTLQV 300

Query: 301 TADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAVA 360
           TADV ERLGSDTFCHV+TS+GE LTMR+RGD+AS+YGETL LHLD  HCHLFD DGVA+ 
Sbjct: 301 TADVSERLGSDTFCHVLTSSGEALTMRVRGDLASRYGETLSLHLDAEHCHLFDADGVALT 360

Query: 361 VPLRAAA 367
            PLRAAA
Sbjct: 361 RPLRAAA 367


Lambda     K      H
   0.319    0.137    0.387 

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: 583
Number of extensions: 11
Number of successful extensions: 1
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: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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