GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Phaeobacter inhibens BS107

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein

Query= TCDB::O30494
         (367 letters)



>lcl|FitnessBrowser__Phaeo:GFF1645 PGA1_c16680 sugar ABC
           transporter, ATP-binding protein
          Length = 355

 Score =  360 bits (925), Expect = e-104
 Identities = 187/359 (52%), Positives = 250/359 (69%), Gaps = 8/359 (2%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60
           MA ++++++ K +    +++ I+L++ D EF+V VGPSGCGKSTLLR+IAGLE ++ G  
Sbjct: 1   MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120
           E+DG+ + +V P  RD+AMVFQ+YALYPHM V +NM F++++     +   S+V  AA  
Sbjct: 61  EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120

Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           L L  L++R PK LSGGQRQRVA+GRAI+R+P+ FLFDEPLSNLDAALRV+MRLE+ARLH
Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240
           K+L ATMIYVTHDQVEA+TLAD++VVLN G I+QVGSPLELY +PAN FVA F+G+P M 
Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240

Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTV 300
            L      V G    V    G +++L          +AV LGIRPEHL++  PG+  L  
Sbjct: 241 ILP-----VSGAASGVMATNGMMLTL---DHMHDTAAAVELGIRPEHLDVVEPGEGHLIA 292

Query: 301 TADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359
            ADV ERLGSDT  +       PL +R  G++  + GE L L +   + H+FD  G+A+
Sbjct: 293 VADVVERLGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFDDRGIAL 351


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: 401
Number of extensions: 11
Number of successful extensions: 2
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: 355
Length adjustment: 29
Effective length of query: 338
Effective length of database: 326
Effective search space:   110188
Effective search space used:   110188
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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