Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 5207980 Shew_0496 amino acid carrier protein (RefSeq)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__PV4:5207980 Length = 457 Score = 447 bits (1149), Expect = e-130 Identities = 231/442 (52%), Positives = 302/442 (68%), Gaps = 12/442 (2%) Query: 10 DLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQA 69 ++N +VWGP+ L L++GTGLYL L L+ + + +L + RLL++ S G++S F A Sbjct: 9 EINAIVWGPITLCLLVGTGLYLTLRLRLIQVFKLPLALRLLFKPAS----GQGDLSSFAA 64 Query: 70 LMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERN 129 L T L+AT+GTGNI GVATAI +GGPGALFWMW A GMATK+ E +LA+ YR D R Sbjct: 65 LCTALSATIGTGNIVGVATAIKVGGPGALFWMWLAAFFGMATKYGECMLALKYRTTDARG 124 Query: 130 EHVGGPMYAIKNGLGKRWAWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVSFGVPDWV 188 GGPMY I+ GLG WL FALFG G+A FGIG QVN+++DA+ ++F VP WV Sbjct: 125 NIAGGPMYYIERGLGL--GWLAKLFALFGVGVAFFGIGTFAQVNAISDAMTIAFHVPAWV 182 Query: 189 TGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTH 248 T + L+ V LGG++RI KVA+ LVP M +GY++A + +LV +E I A QL+ Sbjct: 183 TALVLTLLVAAVTLGGVKRIAKVAQKLVPSMALGYVLACLWILVTFSEQIIPALQLVIHS 242 Query: 249 AFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLG 308 AF+PI+A GGF GA V AI+ G+ARG+FSNE+GLG+A IA AA T V GL+ M G Sbjct: 243 AFSPISAAGGFLGATVAQAIQIGIARGVFSNESGLGSAPIAAAAAKTKEPVEQGLVSMTG 302 Query: 309 TFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGV-GHYILSLALVVFAYTT 367 TF DTL+IC++TGL +I +GVW+ A+GAA++SAAF V G Y++++ALV FA+TT Sbjct: 303 TFFDTLLICTITGLVLIITGVWSGDAAGAAMTSAAFATGGSAVIGQYLVTIALVCFAFTT 362 Query: 368 ILGWSYYGERCWEYLA----GTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAI 423 ILGW YYGERCW YL G R I ++ ++ I GA QLD WL+ADT+N LMAI Sbjct: 363 ILGWHYYGERCWYYLTGHKLGERGIKIYQFIFLSLIAVGAFIQLDLIWLLADTVNGLMAI 422 Query: 424 PNLIALLLLSPVVFRLTREYFA 445 PNLIAL+ L V+ T YFA Sbjct: 423 PNLIALIGLRKVIIADTLSYFA 444 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: 617 Number of extensions: 31 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: 457 Length adjustment: 33 Effective length of query: 416 Effective length of database: 424 Effective search space: 176384 Effective search space used: 176384 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