GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araUsh in Pseudomonas fluorescens FW300-N2E2

Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate Pf6N2E2_522 Inositol transport system sugar-binding protein

Query= uniprot:A0KWY4
         (313 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_522
          Length = 308

 Score =  144 bits (363), Expect = 3e-39
 Identities = 104/283 (36%), Positives = 145/283 (51%), Gaps = 11/283 (3%)

Query: 9   ALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQR--GIDLKFADAQQKQEN 66
           AL L   S        +G S    +  W T   E++  +AK    G+ L+F DA+     
Sbjct: 11  ALSLMLTSGAALADLKIGVSMSQFDDTWLTYLRESMDKKAKSLPDGVTLQFEDARSDVVK 70

Query: 67  QIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL--FLTR 124
           Q+  V SFI+Q VDAII+ PV     + + K A  A IP+V V+R  + DD  L   +  
Sbjct: 71  QLSQVESFISQKVDAIIVNPVDTAATQRITKAAVAAGIPLVYVNR--RPDDLKLPAGVVT 128

Query: 125 IASDFSEEGRKIGQWLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRS 184
           +ASD  E GR   Q+L +K  G  DI  L G +   +  +R  G   V+A YPN KI + 
Sbjct: 129 VASDDLEAGRMQMQYLAEKMGGKGDIVILLGDLANNSTTNRTKGVKDVLAKYPNIKIEQE 188

Query: 185 QTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSV 244
           QTG + R KG  ++  +L    G+   AV ++NDEMA+GA  A+K+AG K G  +LI  V
Sbjct: 189 QTGTWLRDKGMTLVNDWL--TQGREFQAVVANNDEMAIGAAMALKQAGTKKG-SVLIAGV 245

Query: 245 DGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQ 287
           DG PD   A+  GD+   V +     G A  +ID  +K  K Q
Sbjct: 246 DGTPDGLNAIKKGDM--AVSVFQDAKGQADGSIDTAVKMVKKQ 286


Lambda     K      H
   0.316    0.131    0.376 

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: 225
Number of extensions: 14
Number of successful extensions: 4
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: 313
Length of database: 308
Length adjustment: 27
Effective length of query: 286
Effective length of database: 281
Effective search space:    80366
Effective search space used:    80366
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: 41 (21.6 bits)
S2: 48 (23.1 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