Alignments for a candidate for gtsA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for gtsA in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate PfGW456L13_1894 Glucose ABC transport system, periplasmic sugar-binding protein

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1894
          Length = 432

 Score =  697 bits (1800), Expect = 0.0
 Identities = 344/432 (79%), Positives = 378/432 (87%), Gaps = 4/432 (0%)

Query: 1   MNAINRLAVAISIASL--FPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFV 58
           MNAI+RLA  IS+ASL   PLS  AA+SKG+VEVVHWWTSGGEKAAVDVLKAQVEKDGF 
Sbjct: 1   MNAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFT 60

Query: 59  WKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEK 118
           WKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEW STGLL TD LKDV+K E 
Sbjct: 61  WKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAEN 120

Query: 119 WDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDK 178
           WD LL KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGI K PTTL+EFYAAGDK
Sbjct: 121 WDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDK 180

Query: 179 LKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELK 238
           LKAAGFI LAHGGQPWQDSTVFE VVLSVMGADGYKKALVDLD   L+GPEM K+  ELK
Sbjct: 181 LKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELK 240

Query: 239 KVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTD 298
           K+  YMD +  G+DWN+ A  VI+GKAGMQ+MGDWAKSEWTAAKK+AGKDY+CVAFPGT+
Sbjct: 241 KITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTE 300

Query: 299 KAFTYNIDSLAVFKQK--DKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMD 356
           KAFTYNIDS+AVFK K   KG  A QQD+AKV LG +FQKVFS+NKGSIPVRNDMLN+MD
Sbjct: 301 KAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMD 360

Query: 357 SYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADT 416
             GFD CAQ +AKDF+AD KTGGLQPSMAHNMAT+LAVQGA FDVVTN++ND  ADPA  
Sbjct: 361 KLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKA 420

Query: 417 AKKLGAAIKSAK 428
           + +L +A+K+A+
Sbjct: 421 SAQLASAVKAAQ 432


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: 722
Number of extensions: 19
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: 432
Length adjustment: 32
Effective length of query: 396
Effective length of database: 400
Effective search space:   158400
Effective search space used:   158400
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources