Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 202182 SO3063 sodium:alanine symporter family protein (NCBI ptt file)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__MR1:202182 Length = 495 Score = 275 bits (702), Expect = 3e-78 Identities = 165/455 (36%), Positives = 246/455 (54%), Gaps = 37/455 (8%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +N +VW P ++ L LG GL+ L +F+ L L RL++ G+S D +S FQAL Sbjct: 8 VNNIVWSPALVYLCLGVGLFFSLRSRFLQLRHLPEMIRLMFDGKSTD----AGVSSFQAL 63 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 LA VGTGNIAGVATAI GGPGALFWMW A +G ++ F E L Y+EK E Sbjct: 64 AMTLAGRVGTGNIAGVATAITFGGPGALFWMWMVAFLGASSAFVESTLGQVYKEK-INGE 122 Query: 131 HVGGPMYAIKNGLGKRW-AWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVSFGVPDWV 188 + GGP + I+ GLG +W AW A +F G+ G VQ NS+ +L+ +F + V Sbjct: 123 YRGGPAFYIEKGLGMKWYAWTFAIATIFACGVLLPG----VQANSIGASLKTAFDIDPNV 178 Query: 189 TGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTH 248 T ++ G +I GG++RI A +VPFM +GYI+ + +++ ++ + +PG LI Sbjct: 179 TAAVLAMLLGFIIFGGVKRIANFATLVVPFMALGYIIVACVIIALNIDQLPGILWLIIKS 238 Query: 249 AFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLG 308 AF A G G A+M +GV RG++SNEAG GT A +A + GL+ Sbjct: 239 AFGFDAGFGAILGLAIM----WGVKRGVYSNEAGQGTGPHASSAAAVTHPAKQGLVQAFS 294 Query: 309 TFIDTLIICSLTGLAIITSGVW-TSGASGAALSS-------------AAFEAAMPGVGHY 354 +IDTL +CS TG ++ +G++ G GAAL + A E+ MPG G+ Sbjct: 295 VYIDTLFVCSATGFMLLITGLYNVQGPDGAALYTGIAGVAAGSGYVQTAMESMMPGFGNM 354 Query: 355 ILSLALVVFAYTTILGWSYYGERCWEYLAGTRAI------LPFRIVWTLAIPFGAMTQLD 408 +++AL FA+TTI+ + Y E Y+ R + + +++ + +G + D Sbjct: 355 FVAIALFFFAFTTIVAYYYIAETNIAYI--NRKVNRPWLTVMLKVIIMASTVYGTVKTAD 412 Query: 409 FAWLVADTLNALMAIPNLIALLLLSPVVFRLTREY 443 AW + D +MA N+IA++LL V F ++Y Sbjct: 413 LAWGMGDIGVGIMAWLNIIAIILLQKVAFTCLKDY 447 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: 574 Number of extensions: 37 Number of successful extensions: 8 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: 495 Length adjustment: 33 Effective length of query: 416 Effective length of database: 462 Effective search space: 192192 Effective search space used: 192192 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