GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pseudomonas simiae WCS417

Align Amino acid:proton symporter (characterized, see rationale)
to candidate GFF3721 PS417_19045 amino acid:proton symporter

Query= uniprot:A0A0N9WTL5
         (431 letters)



>FitnessBrowser__WCS417:GFF3721
          Length = 420

 Score =  731 bits (1887), Expect = 0.0
 Identities = 379/413 (91%), Positives = 393/413 (95%)

Query: 1   MKKNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLV 60
           M KNKLPRRIA+GIALGVLVGWACHH+AGSEQ+AK +A YFSMVTDIFLRMIKMIIAPLV
Sbjct: 1   MNKNKLPRRIAVGIALGVLVGWACHHYAGSEQAAKALAGYFSMVTDIFLRMIKMIIAPLV 60

Query: 61  FATLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHA 120
           FATLVGGIASMGNSRSVGRIG RAM WFVTAS+VSL++GM LVNLFQPGAGLNM V QHA
Sbjct: 61  FATLVGGIASMGNSRSVGRIGMRAMLWFVTASLVSLMLGMALVNLFQPGAGLNMQVVQHA 120

Query: 121 TAAVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT 180
           TAAVPVNTGDFSLK FI HVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT
Sbjct: 121 TAAVPVNTGDFSLKTFISHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT 180

Query: 181 DSIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWA 240
           D+++ELAKVMFKITDYVMAFAPIGVFAAIASAITT GLGLL DY KLIAEFYLGI +LW 
Sbjct: 181 DTVDELAKVMFKITDYVMAFAPIGVFAAIASAITTNGLGLLADYAKLIAEFYLGIALLWV 240

Query: 241 LLFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLP 300
           LLF AGYLFLGRSVF LGKLIREPILLAFSTASSESAYPKT+EALEKFGAPKRVSSFVLP
Sbjct: 241 LLFAAGYLFLGRSVFTLGKLIREPILLAFSTASSESAYPKTMEALEKFGAPKRVSSFVLP 300

Query: 301 LGYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA 360
           LGYSFNLDGSMMYQAFAI+FIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA
Sbjct: 301 LGYSFNLDGSMMYQAFAIMFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA 360

Query: 361 ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADE 413
           ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSE+ EE  E
Sbjct: 361 ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSEAEEEPAE 413


Lambda     K      H
   0.325    0.138    0.392 

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: 647
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: 431
Length of database: 420
Length adjustment: 32
Effective length of query: 399
Effective length of database: 388
Effective search space:   154812
Effective search space used:   154812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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