GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas fluorescens FW300-N2E3

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate AO353_03840 AO353_03840 ABC transporter ATP-binding protein

Query= TCDB::O30494
         (367 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  244 bits (623), Expect = 3e-69
 Identities = 138/325 (42%), Positives = 202/325 (62%), Gaps = 14/325 (4%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60
           M  L ++N++K +     +K ++L + + + V F+GPSGCGK+TLLR+IAGLE +S G I
Sbjct: 1   MTGLILENVEKRYGTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120
            LD  DI       R+  MVFQ+ AL+PHM+V +N+++ L L GV K   +++V E   +
Sbjct: 61  RLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLEL 120

Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           ++L  +++R   +LSGGQRQRVAI RAI  +PKI L DEPLS LDA LR  M++E+ +L 
Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240
           + L  T I VTHDQ EAMT+AD VVVL   R++QVG+P+E+Y  PAN FVA F+G+   G
Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGS---G 237

Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTT--- 297
            +       DG   +V L  G  + +P+  +S+ VG  V + +RPE L+++ P  T    
Sbjct: 238 NIFPATALGDG---KVGLPGGDALQVPIC-SSIVVGEKVKMLVRPEDLQLSHPQATAGNR 293

Query: 298 ----LTVTADVGERLGSDTFCHVIT 318
               +T   D+G  + +   C  +T
Sbjct: 294 LLGRVTFVRDIGATIETTVECSGVT 318


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: 311
Number of extensions: 12
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: 351
Length adjustment: 29
Effective length of query: 338
Effective length of database: 322
Effective search space:   108836
Effective search space used:   108836
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.

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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