GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas fluorescens GW456-L13

Align MalF, component of Maltose/trehalose porter (characterized)
to candidate PfGW456L13_2614 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)

Query= TCDB::O51924
         (300 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2614
          Length = 288

 Score =  127 bits (319), Expect = 3e-34
 Identities = 81/265 (30%), Positives = 143/265 (53%), Gaps = 9/265 (3%)

Query: 25  MILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFWYSTFVTV 84
           ++LP+  +V    ++P+M     S+ +D+     + FVG   Y +VL       S     
Sbjct: 12  LVLPVFLLVAFSAVIPMMTVVNYSV-QDIFDQSSRYFVGADWYKQVLLDPRLHDSLLRQF 70

Query: 85  SFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSYGL 144
            +S   + +E  LG++ AL +  + +   V+  I+ IP  +P  +    W++      GL
Sbjct: 71  IYSACVLLIEIPLGIAIALTMPTKGRWSSVVLIILAIPLLIPWNVVGTIWQIFGRADIGL 130

Query: 145 FNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLYEAALID 204
               L  +G+S  N+    + A+  +++ DVW  T L+ LL  +GL+AIP   Y+AA ID
Sbjct: 131 LGASLKAMGIS-YNYAANTMDAWVTVLVMDVWHWTSLVALLCFSGLRAIPDVYYQAARID 189

Query: 205 GASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATT----SISLL 260
            AS +  F+ I LP LK VL++A++LR +D+  ++   +VLTGGGPG +TT    +++ +
Sbjct: 190 RASAWAVFRHIQLPKLKSVLLIAVMLRFMDSFMIYTEPFVLTGGGPGNSTTFLSQTLTQM 249

Query: 261 AFNYYNLGDYGIGSAISILTFVLVL 285
           A   ++LG     +A S++ F+++L
Sbjct: 250 AIGQFDLGP---AAAFSLVYFLIIL 271


Lambda     K      H
   0.329    0.145    0.436 

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: 247
Number of extensions: 22
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: 300
Length of database: 288
Length adjustment: 26
Effective length of query: 274
Effective length of database: 262
Effective search space:    71788
Effective search space used:    71788
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 (21.8 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