GapMind for catabolism of small carbon sources

 

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

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate Pf6N2E2_1098 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

Query= CharProtDB::CH_003045
         (260 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1098
          Length = 260

 Score =  222 bits (565), Expect = 7e-63
 Identities = 106/256 (41%), Positives = 161/256 (62%), Gaps = 2/256 (0%)

Query: 6   LALSL-LIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQ 64
           +AL L L+ L A   S  A   ++RIG +  Y PF+SK      +GFD D+G  +C  M+
Sbjct: 6   IALKLGLVSLLAFGTSLQAAESSLRIGIEAAYPPFASKTPDNAIVGFDYDIGQALCAEMK 65

Query: 65  VKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI 124
           V+C W   +FD LIP+LK KK+DA+ISS+SIT +R + + F+D+ Y   +RL+  KGS I
Sbjct: 66  VRCVWQEQEFDGLIPALKVKKVDAVISSMSITPERLKSVDFTDRYYRIPARLVFRKGSGI 125

Query: 125 QPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDE 184
                 L GK +GV + +  + Y  D++   G +VV Y +Q+ I+ DL  GRLDA +   
Sbjct: 126 NDIPAQLNGKRIGVQRATNFDRYVTDHFAPAGAEVVRYGSQNEIFLDLLGGRLDATMASS 185

Query: 185 VAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGT 244
           V   E  LK+P G ++ F GP+  +++YFG G G+ +RK+DT L   F++AL  +R +GT
Sbjct: 186 VVIDESLLKRPEGNDFEFVGPNFTEEQYFGTGIGIAVRKNDT-LAGRFNQALATIRANGT 244

Query: 245 YDKMAKKYFDFNVYGD 260
           Y+++ +KYFDF++YG+
Sbjct: 245 YERIRQKYFDFDIYGE 260


Lambda     K      H
   0.315    0.132    0.374 

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: 190
Number of extensions: 8
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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: 47 (22.7 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