GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate AO356_05195 AO356_05195 sugar ABC transporter substrate-binding protein

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_05195
          Length = 433

 Score =  806 bits (2083), Expect = 0.0
 Identities = 400/433 (92%), Positives = 413/433 (95%), Gaps = 5/433 (1%)

Query: 1   MNAINRLAVAISIASLFPLSAF-----AADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKD 55
           MNAI+RLA  IS+ASL P++AF     AA+SKG+VEVVHWWTSGGEKAAVDVLKAQVEKD
Sbjct: 1   MNAISRLATVISLASLLPVAAFPVTTLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 60

Query: 56  GFVWKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAK 115
           GF WKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTD+LKDVAK
Sbjct: 61  GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDILKDVAK 120

Query: 116 EEKWDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAA 175
            EKWDSLLDKKVSDTVKY+GDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTL+EFYAA
Sbjct: 121 AEKWDSLLDKKVSDTVKYDGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLEEFYAA 180

Query: 176 GDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALT 235
           GDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDN ALTGPEMVKALT
Sbjct: 181 GDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNKALTGPEMVKALT 240

Query: 236 ELKKVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFP 295
           ELKKVATYMD DGKGQDWNLEA KVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFP
Sbjct: 241 ELKKVATYMDADGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFP 300

Query: 296 GTDKAFTYNIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKM 355
           GTDKAFTYNIDSLAVFKQKD GTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDML  M
Sbjct: 301 GTDKAFTYNIDSLAVFKQKDAGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLGDM 360

Query: 356 DSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPAD 415
             YGFDSCAQTAAKDFL DAK+GGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPAD
Sbjct: 361 AKYGFDSCAQTAAKDFLTDAKSGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPAD 420

Query: 416 TAKKLGAAIKSAK 428
            AKKLGAA++SAK
Sbjct: 421 AAKKLGAAVQSAK 433


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: 821
Number of extensions: 23
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: 428
Length of database: 433
Length adjustment: 32
Effective length of query: 396
Effective length of database: 401
Effective search space:   158796
Effective search space used:   158796
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 (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