GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_596 Glucose ABC transport system, periplasmic sugar-binding protein

Query= reanno::WCS417:GFF4324
         (428 letters)



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

 Score =  699 bits (1805), Expect = 0.0
 Identities = 348/435 (80%), Positives = 380/435 (87%), Gaps = 7/435 (1%)

Query: 1   MNAINRLAVAISIASL-----FPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKD 55
           MNAI+RLA  IS+ASL     FP+SA AAD+KG+VEVVHWWTSGGEKAAVDVLKAQVEKD
Sbjct: 1   MNAISRLATVISLASLLPVAAFPVSALAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 60

Query: 56  GFVWKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAK 115
           GF WKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEW STGLL TD LK+V+K
Sbjct: 61  GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDTLKEVSK 120

Query: 116 EEKWDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAA 175
            E WD+LL KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGI K PTTL+EFYAA
Sbjct: 121 SEGWDNLLIKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIDKAPTTLEEFYAA 180

Query: 176 GDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALT 235
           GDKLKAAGFI LAHGGQPWQDSTVFE VVLSVMGADGYKKALVDLD   L+GPEM KA T
Sbjct: 181 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMAKAFT 240

Query: 236 ELKKVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFP 295
           ELKKV  YMD +  G+DWN+ A  VINGKAGMQ+MGDWAKSEWTAAKKVAGKDY+CV FP
Sbjct: 241 ELKKVTGYMDPNRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAKKVAGKDYQCVPFP 300

Query: 296 GTDKAFTYNIDSLAVFKQK--DKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLN 353
           GT+KAFTYNIDS+AVFK K   KG  A QQD+AKV LG++FQKVFSINKGSIPVR DMLN
Sbjct: 301 GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDMLN 360

Query: 354 KMDSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADP 413
            M   GFD+CAQ +AKDFLAD KTGGLQPSMAHNMAT+LAVQGA FDVVTN++ND  ADP
Sbjct: 361 DMSGLGFDACAQASAKDFLADEKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKNADP 420

Query: 414 ADTAKKLGAAIKSAK 428
           A  + +L +A+K+A+
Sbjct: 421 AKASAQLASAVKAAQ 435


Lambda     K      H
   0.314    0.131    0.388 

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: 723
Number of extensions: 24
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: 428
Length of database: 435
Length adjustment: 32
Effective length of query: 396
Effective length of database: 403
Effective search space:   159588
Effective search space used:   159588
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: 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