GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25895
          Length = 367

 Score =  302 bits (774), Expect = 9e-87
 Identities = 164/361 (45%), Positives = 235/361 (65%), Gaps = 7/361 (1%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA L+++N+ K +       +K I+L + + EF++ VGPSGCGKSTL+  IAGLE +T G
Sbjct: 1   MAHLKIKNLQKGFEGF--SIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I +  +D++ +SP  RD+AMVFQ+YALYP MSVR+N+ F L +  + +A+++ +V   A
Sbjct: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           ++L++  +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+  
Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H+ L+ T +YVTHDQ+EAMTL DKV V+  G I+Q G+P E+Y+ PAN FVA F+G+P 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPK 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           M F+  ++ R + +   +L     R  L L+     +    V LG+RPE + LA   GD 
Sbjct: 239 MGFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGA-VTLGIRPEHLNLAL-PGDC 296

Query: 301 ASSIRAEVQVTEPTGPDTLVFV-QLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359
              + A+  V+E  G DT   V   +   +  R+  D+A + GE L+L  D     LFDA
Sbjct: 297 TLQVTAD--VSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDA 354

Query: 360 N 360
           N
Sbjct: 355 N 355


Lambda     K      H
   0.318    0.135    0.382 

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: 379
Number of extensions: 16
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: 386
Length of database: 367
Length adjustment: 30
Effective length of query: 356
Effective length of database: 337
Effective search space:   119972
Effective search space used:   119972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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