Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate AO353_09955 AO353_09955 sodium:alanine symporter
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__pseudo3_N2E3:AO353_09955 Length = 483 Score = 270 bits (690), Expect = 7e-77 Identities = 166/444 (37%), Positives = 246/444 (55%), Gaps = 15/444 (3%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +N + G +++VLI+G G Y + +F+ L F + + SS ++S FQAL Sbjct: 5 INDFLSGKVLIVLIVGLGSYFTIRSRFVQLRHFLHMFSVFKESLRS---SSEQLSSFQAL 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---LVTFGFAFNGLQSHAVTHSLNNAFGLNTTYT 178 Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249 G+ ++ GLV +GGI+RI KVA+ LVP + YI ++ V+V+ + +PG I A Sbjct: 179 GLGLAVLLGLVFIGGIKRIAKVADLLVPVKTLVYIGVTIYVIVLQFDHVPGMLMTIVKSA 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 FLDTFVICTCTALLILLSGFYTPGFEGDGIALTQNSLAAVVGDWGRMFISVALALFVFTS 354 Query: 368 ILGWSYYGERCWEYLAG--TRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPN 425 IL Y GE +L G + ++ +R + I +GA+ L + AD ++A N Sbjct: 355 ILYNYYLGESNLRFLVGENRKVLIGYRALVLALIFWGAIENLSTVFAFADITMTMLAFVN 414 Query: 426 LIALLLLSPVVFRLTREYFAKARS 449 LIAL LL V R+ +Y A+ R+ Sbjct: 415 LIALFLLFNVGMRILNDYDAQRRA 438 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: 489 Number of extensions: 24 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.
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:
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