Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate PP_0496 PP_0496 Sodium/alanine symporter
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Putida:PP_0496 Length = 480 Score = 236 bits (601), Expect = 2e-66 Identities = 156/441 (35%), Positives = 233/441 (52%), Gaps = 22/441 (4%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDES----SGEISP 66 +N + G L++VLI+G G Y + +F V FR S ES +G++S Sbjct: 5 INDFLSGKLLIVLIVGLGSYFTIRSRF-------VQFRHFTHMFSVFKESLRGQAGQLSS 57 Query: 67 FQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKD 126 FQALM LA VG GNIAGV A+ LGGPGA+FWMW TALVGM++ F E LA Y+ D Sbjct: 58 FQALMLSLAGRVGAGNIAGVGIAVTLGGPGAVFWMWVTALVGMSSSFFECTLAQVYKRAD 117 Query: 127 ERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPD 186 + GGP Y I++GL ++ + + L IG +Q ++ +L+ +F Sbjct: 118 GDGLYRGGPAYYIQHGLKRKSMAIVFSILLLVTYGFAFIG--LQSYTVTHSLQNAFAFDP 175 Query: 187 WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIF 246 TG+ ++ + +GGI+RI V++ LVP + YI ++ V+ E +P + IF Sbjct: 176 SHTGIVLAVLLAITFIGGIKRIAAVSDLLVPVKTLAYIGVTLYVIGTQIEHVPAMLETIF 235 Query: 247 THAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTA-GIAQAAGTTHSAVRSGLIG 305 AF A G G+A++ GV RG+F+NEAGLG+A +A A H + G++ Sbjct: 236 KSAFGLDPAFAGLLGSAIV----MGVKRGVFANEAGLGSAPNVAAVAAVKHPGAQ-GVVQ 290 Query: 306 MLGTFIDTLIICSLTGLAIITSGVWTSG--ASGAALSSAAFEAAMPGVGHYILSLALVVF 363 F+DT +IC+ T L I+ SG +T G G L+ + A + G +S+AL +F Sbjct: 291 AFSVFLDTFVICTCTALLILLSGFYTPGFEGDGIVLTQNSLAAVVGDWGRVFVSVALSLF 350 Query: 364 AYTTILGWSYYGERCWEYLAGTRAIL-PFRIVWTLAIPFGAMTQLDFAWLVADTLNALMA 422 +T IL Y GE ++L+ R +L FR + + +G+M L + AD +A Sbjct: 351 VFTCILYNYYLGENSLQFLSRNRVVLMVFRGLVLALVVWGSMQDLSTVFAFADITMTCLA 410 Query: 423 IPNLIALLLLSPVVFRLTREY 443 NL+AL LL V R+ R+Y Sbjct: 411 FVNLVALALLFKVGLRVMRDY 431 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: 470 Number of extensions: 25 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: 480 Length adjustment: 33 Effective length of query: 416 Effective length of database: 447 Effective search space: 185952 Effective search space used: 185952 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