Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_086509070.1 BZY95_RS06045 alanine:cation symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_002151265.1:WP_086509070.1 Length = 492 Score = 289 bits (740), Expect = 1e-82 Identities = 177/447 (39%), Positives = 247/447 (55%), Gaps = 14/447 (3%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +N ++WG +++ L++ G+ L +F+ FR+L ++ + G +S FQAL Sbjct: 5 INDLLWGKVLIALLIAVGVGFTLSSRFVQFRYFARMFRILGASQAFKRDKHGHLSSFQAL 64 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 + +A VG GNIAGVA AI LGGPGA+FWMW L+GMAT F E LA Y+ Sbjct: 65 LLSIAGRVGGGNIAGVAVAITLGGPGAIFWMWLVGLMGMATSFLECTLAQAYKTAQPDGT 124 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIG-NMVQVNSMADALEVSFGVPDWVT 189 + GGP Y I GLG RW WL A +++ L FG G +Q ++A + + +FG+P T Sbjct: 125 YRGGPAYYIARGLGSRWKWLAALYSVL-LLVTFGFGFTALQSYAVATSFDDAFGIPVLYT 183 Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249 G+ V GL+I GGI+RI +V E LVP M VGY++ + +VL ++ IP F LI A Sbjct: 184 GIGMAAVVGLIIFGGIKRIARVTEVLVPVMAVGYLLIAFVVLGMNLPRIPEVFLLIVNSA 243 Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTA-GIAQAAGTTHSAVRSGLIGMLG 308 F A GG GAA+M GV RG+FSNEAGLG+A +A A H A G++ Sbjct: 244 FGLEPAVGGGIGAAIM----MGVKRGLFSNEAGLGSAPNVAAVAYVPHPA-NQGVVQAFS 298 Query: 309 TFIDTLIICSLTGLAIITSGVW--TSGA--SGAALSSAAFEAAMPGVGHYILSLALVVFA 364 FIDTLIICS T I+ SG + SGA G AL+ + + G +S+AL++F Sbjct: 299 VFIDTLIICSATAFIILLSGAYDPASGADIGGVALTQVSLADHVGEWGRSFVSVALLLFG 358 Query: 365 YTTILGWSYYGERCWEYLAGTRAIL--PFRIVWTLAIPFGAMTQLDFAWLVADTLNALMA 422 ++TIL Y GE Y + L FRI +GA+T L + AD +A Sbjct: 359 FSTILYNYYLGENSLNYFSDGNVTLFNLFRIAIVALCAWGALTDLGTVFAFADVTMGFLA 418 Query: 423 IPNLIALLLLSPVVFRLTREYFAKARS 449 + NLIALL+L RL R++ + R+ Sbjct: 419 LANLIALLMLFKPGLRLMRDFDEQIRA 445 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: 523 Number of extensions: 28 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: 492 Length adjustment: 33 Effective length of query: 416 Effective length of database: 459 Effective search space: 190944 Effective search space used: 190944 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 24 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