GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas putida KT2440

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Putida:PP_1018
          Length = 384

 Score =  327 bits (839), Expect = 2e-94
 Identities = 175/366 (47%), Positives = 244/366 (66%), Gaps = 6/366 (1%)

Query: 1   MTSVSVRDLSLNFGA--VTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58
           M ++ +R+++  +G+     L  + L I  GEFL+L+G SGCGKSTL+NCIAGL  ++ G
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60

Query: 59  QIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRAS 118
            I I +++V+   PKDR I MVFQSYALYP M+V +N+ FGLK+ K+P A I++ V R +
Sbjct: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120

Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178
           ++LQI+ LL RKP++LSGGQ+QRVA+GRAL R   ++LFDEPLSNLDAKLR E+R E+K 
Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238
           +HQ LK T +YVTHDQIEA+TL D++AVMK G+IQQ   P  IYN P N FVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240

Query: 239 MNFFRGEVEPKDGR--SFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEA-RD 295
           MNF    +  +DGR  + + +G    ++    A   L+ G++++LG+RPE + +  A  +
Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALE-GREIILGIRPEQIALGAADGN 299

Query: 296 GEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDA 355
           G P  +A V + EP G D L+++T     +  R+A       G T+ L FD     +FDA
Sbjct: 300 GLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDA 359

Query: 356 ESENRL 361
            +  RL
Sbjct: 360 ANGERL 365


Lambda     K      H
   0.320    0.137    0.392 

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: 395
Number of extensions: 12
Number of successful extensions: 3
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: 361
Length of database: 384
Length adjustment: 30
Effective length of query: 331
Effective length of database: 354
Effective search space:   117174
Effective search space used:   117174
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