Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate GFF4004 Psest_4077 amino acid carrier protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__psRCH2:GFF4004 Length = 473 Score = 286 bits (732), Expect = 1e-81 Identities = 173/443 (39%), Positives = 249/443 (56%), Gaps = 14/443 (3%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 LN ++W L++V+++G GL + F+ G F + + G++S FQAL Sbjct: 5 LNDLIWSKLLIVMLIGLGLLFTIRSGFVQFRYFGNMFTIFGHAFERQP---GQLSSFQAL 61 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 M +A VG GNIAGV+ AI LGGPGA+FWMW ALVGMAT + E LA Y+ ++ Sbjct: 62 MLSVAGRVGAGNIAGVSVAIMLGGPGAIFWMWVVALVGMATSYFECSLAQLYKRREPDGT 121 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIG-NMVQVNSMADALEVSFGVPDWVT 189 + GGP + I++GLG+RW + + L L FG G N VQ ++A +L +FGVP + Sbjct: 122 YRGGPAFYIQHGLGQRWLGIVVSILL---LMTFGFGFNAVQSFTVASSLHDTFGVPTVAS 178 Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249 G+A LV +I GGIRRI K A+ LVP M Y+ ++ V+ + AIP F LIF A Sbjct: 179 GIALTLVIAGIIFGGIRRIAKWADVLVPVMAFSYLAMALFVIGSNFSAIPETFGLIFRSA 238 Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGT 309 F A G GAA++ GV RG+FSNEAGLG+A A V G++ L Sbjct: 239 FGLEQAFAGGIGAAIL----MGVKRGLFSNEAGLGSAPNVAAVAEVKHPVAQGIVQSLSV 294 Query: 310 FIDTLIICSLTGLAIITSGVWTSG--ASGAALSSAAFEAAMPGVGHYILSLALVVFAYTT 367 FIDT+I+CS T L I+ SGV+ G +G L+ A A + G +S+AL++F +TT Sbjct: 295 FIDTIILCSCTALIILLSGVYEPGMDQAGVVLTQTAVAAVVGEWGRVFVSVALLLFVFTT 354 Query: 368 ILGWSYYGERCWEYLAGTR-AILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNL 426 ++ Y GE + R ++ +RI+ + + +G++ L + AD L+AI NL Sbjct: 355 LIYNYYLGENALGFFTEKRMPVVIYRILVVILVLWGSVQDLGTVFAFADVTMGLLAIANL 414 Query: 427 IALLLLSPVVFRLTREYFAKARS 449 IA+ LL V RL R+Y + R+ Sbjct: 415 IAVALLFKVGLRLMRDYDRQIRA 437 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: 506 Number of extensions: 26 Number of successful extensions: 6 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: 473 Length adjustment: 33 Effective length of query: 416 Effective length of database: 440 Effective search space: 183040 Effective search space used: 183040 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