Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 7026278 Shewana3_3420 amino acid carrier protein (RefSeq)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__ANA3:7026278 Length = 452 Score = 455 bits (1170), Expect = e-132 Identities = 230/449 (51%), Positives = 308/449 (68%), Gaps = 8/449 (1%) Query: 3 SLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSG 62 S Q + LNG+VWGP+ L L++GTG+YL L L+ + + RL + LL+ K + G Sbjct: 2 SFQALLSSLNGIVWGPVTLCLLVGTGIYLTLRLRLIQVFRLPMALGLLF----KPAKGHG 57 Query: 63 EISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHY 122 ++S F AL T L+AT+GTGNI GVATAI +GGPGALFWMW A GMATK++E +LAV Y Sbjct: 58 DLSSFAALCTALSATIGTGNIVGVATAIKMGGPGALFWMWLAAFFGMATKYAECMLAVKY 117 Query: 123 REKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVS 181 R D R + GGPMY I+ GLG W + FALFG G+A FGIG QVN+++DAL ++ Sbjct: 118 RTTDARGQIAGGPMYYIERGLGLHW--MAKLFALFGVGVAFFGIGTFAQVNAISDALTIA 175 Query: 182 FGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGA 241 F VP W T + L+ V LGG++RI VA+ LVP M +GY++A V +LV AE+I A Sbjct: 176 FEVPTWATALVLTLLVAAVTLGGVKRISNVAQKLVPAMSIGYVLACVWILVSFAESILPA 235 Query: 242 FQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRS 301 QL+ AFTP++A GGF GA V AI+ G+ARG+FSNE+GLG+A IA AA T+ V Sbjct: 236 LQLVVESAFTPVSAAGGFLGATVAQAIQMGIARGVFSNESGLGSAPIAAAAAKTNEPVEQ 295 Query: 302 GLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFE-AAMPGVGHYILSLAL 360 GL+ M GTF DT+IIC++TGL +I +GVW+ +GAA++SAAF +G Y++++AL Sbjct: 296 GLVSMTGTFFDTIIICTITGLVLIITGVWSGDTAGAAMTSAAFSLGGSAAIGQYLVTIAL 355 Query: 361 VVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNAL 420 V FA+TTILGW YYGERCW YL G R + +++++ I GA +LD WL+ADT+N L Sbjct: 356 VCFAFTTILGWHYYGERCWYYLVGERGLRAYQMLFLGLIAVGAFIKLDVIWLLADTVNGL 415 Query: 421 MAIPNLIALLLLSPVVFRLTREYFAKARS 449 MAIPNLIA++ L V+ T+ YF + S Sbjct: 416 MAIPNLIAIIGLRHVIIAETQSYFVRTLS 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: 602 Number of extensions: 28 Number of successful extensions: 4 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: 452 Length adjustment: 33 Effective length of query: 416 Effective length of database: 419 Effective search space: 174304 Effective search space used: 174304 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