GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1894 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_596 Glucose ABC transport system, periplasmic sugar-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894
         (432 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_596 Glucose ABC transport
           system, periplasmic sugar-binding protein
          Length = 435

 Score =  804 bits (2076), Expect = 0.0
 Identities = 401/435 (92%), Positives = 417/435 (95%), Gaps = 3/435 (0%)

Query: 1   MNAISRLATVISLASL---SALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 57
           MNAISRLATVISLASL   +A P+S LAA++KGSVEVVHWWTSGGEKAAVDVLKAQVEKD
Sbjct: 1   MNAISRLATVISLASLLPVAAFPVSALAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 60

Query: 58  GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSK 117
           GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTD LK+VSK
Sbjct: 61  GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDTLKEVSK 120

Query: 118 AENWDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAA 177
           +E WD LL KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGI+KAPTTLEEFYAA
Sbjct: 121 SEGWDNLLIKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIDKAPTTLEEFYAA 180

Query: 178 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFA 237
           GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEM K+F 
Sbjct: 181 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMAKAFT 240

Query: 238 ELKKITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFP 297
           ELKK+TGYMDPNRAGRDWNIAAADVI+GKAGMQMMGDWAKSEWTAAKK+AGKDYQCV FP
Sbjct: 241 ELKKVTGYMDPNRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAKKVAGKDYQCVPFP 300

Query: 298 GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLN 357
           GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALG DFQKVFS+NKGSIPVR DMLN
Sbjct: 301 GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDMLN 360

Query: 358 EMDKLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADP 417
           +M  LGFD CAQ SAKDF+AD+KTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDK+ADP
Sbjct: 361 DMSGLGFDACAQASAKDFLADEKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKNADP 420

Query: 418 AKASAQLASAVKAAQ 432
           AKASAQLASAVKAAQ
Sbjct: 421 AKASAQLASAVKAAQ 435


Lambda     K      H
   0.314    0.129    0.377 

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: 782
Number of extensions: 18
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: 432
Length of database: 435
Length adjustment: 32
Effective length of query: 400
Effective length of database: 403
Effective search space:   161200
Effective search space used:   161200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 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, 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