GapMind for catabolism of small carbon sources

 

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

Align putrescine transport system permease protein PotH (characterized)
to candidate Pf6N2E2_4817 Spermidine Putrescine ABC transporter permease component PotB (TC 3.A.1.11.1)

Query= CharProtDB::CH_088338
         (317 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4817
          Length = 415

 Score =  162 bits (411), Expect = 1e-44
 Identities = 83/222 (37%), Positives = 138/222 (62%), Gaps = 5/222 (2%)

Query: 82  NLGNFLQLT-DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVI 140
           +LG     T D  +Y D + ++  +  + T  CL++ YPLA+ +A+      N+L++LV+
Sbjct: 179 DLGELAPATPDQAIYLDIFTRTFWMGLVITAICLVLAYPLAYLLANLPSRQSNLLMILVL 238

Query: 141 LPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMV 200
           LP WTS L+RV AW+ +L++ G++N+ L+ +GVID+PL ++     VYI +V+  +PFM+
Sbjct: 239 LPFWTSILVRVAAWIVLLQSGGLINSALMAMGVIDKPLELVFNRTGVYISMVHILLPFMI 298

Query: 201 LPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPE 260
           LPIY+ +  I  + + AA+ LG  P  +F+ V  P T  G+ AG +LVFI A+G ++ P 
Sbjct: 299 LPIYSVMKGISPTYMRAAISLGCHPFASFWRVYFPQTYAGVGAGCLLVFILAIGYYITPA 358

Query: 261 LLGGPDSIMIGRVLWQEFFNNR--DWPVASAVAIIMLLLLIV 300
           LLG P+  M+    +  F+ N   +W +A+A+  ++LL  IV
Sbjct: 359 LLGSPNDQMVS--YFVAFYTNTSINWGMATALGGLLLLATIV 398


Lambda     K      H
   0.328    0.144    0.457 

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: 347
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: 317
Length of database: 415
Length adjustment: 29
Effective length of query: 288
Effective length of database: 386
Effective search space:   111168
Effective search space used:   111168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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