GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02869 in Pseudomonas fluorescens FW300-N1B4

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= reanno::Phaeo:GFF2754
         (331 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691 Putrescine transport
           ATP-binding protein PotA (TC 3.A.1.11.1)
          Length = 351

 Score =  245 bits (625), Expect = 1e-69
 Identities = 141/323 (43%), Positives = 194/323 (60%), Gaps = 28/323 (8%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           MT L L NV K +G    +KD+NL + +G+ V F+GPSGCGK+TLLR+I+GLE  T GEI
Sbjct: 1   MTGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            + G+ +  TP  +R   MVFQS AL+PH++V EN+A  LK     K +  ARV E   +
Sbjct: 61  RLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           + L++ +DR  ++LSGGQRQRVAI RA+   PK+ L DEPLS LDA LR + ++EI +L 
Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           ++L+ + I VTHDQ EAMT+AD +VVL + R++QVG+P+E+Y +PAN FVA+FIG+   N
Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSG--N 238

Query: 241 FVPAQRLGGNPGQFIG---------------------IRPEYARISPVGPLAGEVIHVEK 279
             PA  LG       G                     IRPE  ++S     AG      +
Sbjct: 239 IFPATALGNGKVSLPGGDALQVPICSSIVVGEKVKMLIRPEDLQLSQPQATAG-----NR 293

Query: 280 LGGDTNILVDMGEDLTFTARLFG 302
           L G    + D+G  +  T    G
Sbjct: 294 LLGKVTFVRDIGATIETTVECSG 316


Lambda     K      H
   0.320    0.137    0.391 

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: 330
Number of extensions: 16
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: 331
Length of database: 351
Length adjustment: 28
Effective length of query: 303
Effective length of database: 323
Effective search space:    97869
Effective search space used:    97869
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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