Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate BWI76_RS04265 BWI76_RS04265 sodium:alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Koxy:BWI76_RS04265 Length = 476 Score = 263 bits (671), Expect = 1e-74 Identities = 167/451 (37%), Positives = 253/451 (56%), Gaps = 25/451 (5%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDES----SGEISP 66 +N ++WG +M+ L+LG G++ KF + FR + Q S G ++ Sbjct: 8 INEILWGSVMIYLLLGAGVWFTWRTKF-------IQFRYIRQFSKSLKRSLQPQPGGLTS 60 Query: 67 FQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKD 126 FQAL LAA VG+GN+AGVA AI GGPGA+FWMW +AL+GMA+ F+E LA Y+E+D Sbjct: 61 FQALCMSLAARVGSGNMAGVALAIAAGGPGAVFWMWLSALLGMASSFAECSLAQLYKERD 120 Query: 127 ERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPD 186 R + GGP + + GLG R W+G F++F LA I N VQ NS+A A+ +F +P+ Sbjct: 121 SRGQFRGGPAWYMARGLGMR--WMGVLFSIFLLLAYGIIFNTVQANSVAHAMAYAFHLPE 178 Query: 187 WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIF 246 +TG ++T LVI+ GIR + ++ + LVP M + ++ S+++ + H A+P F+ IF Sbjct: 179 AITGGVLAVLTLLVIVRGIRGVARMMQWLVPVMALLWVATSLVIGLWHITALPTIFETIF 238 Query: 247 THAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGT---AGIAQAAGTTHSAVRSGL 303 AF A G G + A+ G RG+FSNEAG+G+ + A A+ H A + G+ Sbjct: 239 RCAFGWQEAAAGAVGYTISQALTSGFQRGMFSNEAGMGSTPNSAAAAASWPPHPAAQ-GI 297 Query: 304 IGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGV----GHYILSLA 359 + M+G FIDT++IC T A+I G A A + +M + G +++ Sbjct: 298 VQMIGVFIDTIVIC--TASAVIIMLAPRDGNGEAVNGIQAIQHSMNNLIGDWGSSFVAIV 355 Query: 360 LVVFAYTTILGWSYYGERCWEYLA--GTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTL 417 +++FA+++I+ Y E +L R I R++ + GAM L W +ADT+ Sbjct: 356 VLLFAFSSIVANYIYAENNLIFLRMDSDRNIWLLRLLTLCMVATGAMIGLPVVWQMADTI 415 Query: 418 NALMAIPNLIALLLLSPVVFRLTREYFAKAR 448 ALMAI NL A+LLLSP V + +Y + R Sbjct: 416 MALMAITNLTAILLLSPTVRIIASDYLRQRR 446 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: 558 Number of extensions: 30 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: 476 Length adjustment: 33 Effective length of query: 416 Effective length of database: 443 Effective search space: 184288 Effective search space used: 184288 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