Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 6936087 Sama_0284 sodium/alanine symporter (RefSeq)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__SB2B:6936087 Length = 477 Score = 296 bits (758), Expect = 1e-84 Identities = 181/448 (40%), Positives = 250/448 (55%), Gaps = 20/448 (4%) Query: 16 WGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQALMTCLA 75 WGP MLVL++G GL+ ++ P L ++ +G+ + +++G IS AL + +A Sbjct: 21 WGPHMLVLLVGGGLFFLIYSGLAPFRYLKHAIDIV-RGKYPEADAAGNISHAGALSSAMA 79 Query: 76 ATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNEHVGGP 135 TVG GNI GVA AI GGPGA+FWMW +ALVGMATKF LA+ YR DE GGP Sbjct: 80 GTVGMGNIGGVALAIVAGGPGAIFWMWVSALVGMATKFFTCSLAIMYRGTDETGRVRGGP 139 Query: 136 MYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQ-VNSMADALEVSFG----------- 183 MY I +GLG++W L F L G + F + N Q V + + L +S G Sbjct: 140 MYIITHGLGQKWKPLAVFFCLVGLVGNFPLFNTNQLVQILKEYLFLSPGDTGVAVGSGEH 199 Query: 184 -VPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAF 242 + G+A M + LVILGGI+RI VA +VP M + Y+ ++ V++ H +P Sbjct: 200 FALELGLGLAIMSLVALVILGGIKRIAAVAIRVVPTMILLYVGCALYVILSHLGDVPMHL 259 Query: 243 QLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSG 302 I AF+ + GG G + GV R FSNEAG+GT + T V+ G Sbjct: 260 WRIVEDAFSVQSVAGGILGTMLT-----GVKRAAFSNEAGIGTEVMVHGNAKTSEPVKEG 314 Query: 303 LIGMLGTFIDTLIICSLTGLAIITSGVW-TSGASGAALSSAAFEAAMPGVGHYILSLALV 361 L+ MLG IDTL++C+ T L I+ SGVW GA+G +LSSAAF A MPG+G Y+L + + Sbjct: 315 LVAMLGPAIDTLLVCTATALIILISGVWEQGGANGISLSSAAFAATMPGIGPYLLLVCVS 374 Query: 362 VFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALM 421 FA TTI ++YG +C+ +L G R + ++ LAI F A L + D LM Sbjct: 375 FFAITTIFTQAFYGSQCFAFLFGARRERWYLYLYLLAILFAATNSLTDIVNIIDGAYGLM 434 Query: 422 AIPNLIALLLLSPVVFRLTREYFAKARS 449 AIP + A LLL+P V ++YF + RS Sbjct: 435 AIPTMTAALLLAPRVRAAAKDYFRRLRS 462 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: 556 Number of extensions: 33 Number of successful extensions: 6 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: 477 Length adjustment: 33 Effective length of query: 416 Effective length of database: 444 Effective search space: 184704 Effective search space used: 184704 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