GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Pseudomonas fluorescens FW300-N2C3

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate AO356_11095 AO356_11095 sodium:alanine symporter

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_11095
          Length = 483

 Score =  273 bits (697), Expect = 1e-77
 Identities = 166/438 (37%), Positives = 242/438 (55%), Gaps = 15/438 (3%)

Query: 11  LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70
           +N  + G +++VLI+G G Y  +  +F+        F +    R     S+ ++S FQAL
Sbjct: 5   INDFLSGKVLIVLIVGLGGYFTIRSRFVQFRHF---FHMFTVFRDSLKSSTDQLSSFQAL 61

Query: 71  MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130
           M  LA  VG GNIAGV  A+ LGGPGA+FWMW TALVGM++ F E  L   Y+  D   +
Sbjct: 62  MLSLAGRVGAGNIAGVGIAVTLGGPGAVFWMWVTALVGMSSSFFECSLGQLYKRCDSEGQ 121

Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIG-NMVQVNSMADALEVSFGVPDWVT 189
           + GGP Y I++GL KRW  +  AF L   L  FG   N +Q +++  +L  +FG     T
Sbjct: 122 YRGGPSYYIQHGLQKRWLGMIMAFLL---LVTFGFAFNGLQAHAVTHSLNNAFGFDTTYT 178

Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249
           G+   ++ GLV +GGI+RI KVA+ LVP   + YI  ++ V+V+  E +PG    I   A
Sbjct: 179 GLGLAVLLGLVFIGGIKRIAKVADLLVPVKTLAYIAVTLYVIVLQFEHVPGMLVTIVKSA 238

Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGT 309
           F    A GG  G+A++     GV RG+F+NEAGLG+A    A  +    V  G++     
Sbjct: 239 FGLDQAFGGLIGSAIV----MGVKRGVFANEAGLGSAPNVAAVASVEHPVAQGVVQAFSV 294

Query: 310 FIDTLIICSLTGLAIITSGVWTSG--ASGAALSSAAFEAAMPGVGHYILSLALVVFAYTT 367
           F+DT +IC+ T L I+ SG +T G    G AL+  +  A +   G   +S+AL +F +T+
Sbjct: 295 FLDTFVICTCTALLILLSGFYTPGFEGDGIALTQNSLAAVVGDWGRIFISVALSLFVFTS 354

Query: 368 ILGWSYYGERCWEYLAG--TRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPN 425
           IL   Y GE    ++ G   +A++ +R +    I +GA+  L   +  AD    L+A  N
Sbjct: 355 ILYNYYLGENNLRFMIGDNRKALMGYRALVLALIFWGAIENLGTVFAFADITMTLLAFVN 414

Query: 426 LIALLLLSPVVFRLTREY 443
           LIAL LL  V  R+ R+Y
Sbjct: 415 LIALFLLFKVGMRILRDY 432


Lambda     K      H
   0.326    0.140    0.437 

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: 514
Number of extensions: 22
Number of successful extensions: 5
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: 449
Length of database: 483
Length adjustment: 33
Effective length of query: 416
Effective length of database: 450
Effective search space:   187200
Effective search space used:   187200
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: 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