Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 6938850 Sama_2953 sodium:alanine symporter family protein (RefSeq)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__SB2B:6938850 Length = 464 Score = 447 bits (1151), Expect = e-130 Identities = 231/439 (52%), Positives = 302/439 (68%), Gaps = 8/439 (1%) Query: 8 VVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPF 67 + LN +VWGP+ L L++GTG+Y + LK + LV+L + LL++ S GE+S F Sbjct: 7 LTQLNAIVWGPVTLCLLVGTGVYFTVRLKLLQLVKLPLALSLLFKPAS----GKGELSSF 62 Query: 68 QALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDE 127 AL T L+AT+GTGNI GVATAI LGGPGALFWMW A GMATK++E +LA+ YR D Sbjct: 63 GALCTALSATIGTGNIVGVATAIKLGGPGALFWMWVAAFFGMATKYAECLLALKYRTTDA 122 Query: 128 RNEHVGGPMYAIKNGLGKRWAWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVSFGVPD 186 R GGPMY I+ GLG WL FA+FG G+A FGIG QVN+++DA+ V+F VP Sbjct: 123 RGNIAGGPMYYIERGLGL--GWLARLFAIFGVGVAFFGIGTFAQVNAISDAMTVAFAVPT 180 Query: 187 WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIF 246 WVT L+ V LGG++RI VA+ LVP M +GY++A + VL+ +AI A L+ Sbjct: 181 WVTASVLTLLVAAVTLGGVKRIASVAQTLVPAMAIGYVLACLWVLLSLHDAIVPALSLVV 240 Query: 247 THAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGM 306 AFTP+AA GGF GA V AI+ G+ARG+FSNE+GLG+A IA A T V GL+ M Sbjct: 241 NGAFTPVAAGGGFLGATVALAIQTGIARGVFSNESGLGSAPIAAATARTKEPVEQGLVSM 300 Query: 307 LGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAM-PGVGHYILSLALVVFAY 365 GTF DTLIIC++TGL +I +GVW+ ++GAA++SAAF AA P +G Y++++ALV FA+ Sbjct: 301 TGTFFDTLIICTMTGLVLIITGVWSGDSAGAAMTSAAFSAATNPLLGQYLVTVALVCFAF 360 Query: 366 TTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPN 425 TTILGW+YYGERCW YL G R +R+V+ L I GA +LD WL+AD +N LMAIPN Sbjct: 361 TTILGWNYYGERCWSYLTGGRYAGLYRLVFLLLIAGGAFIKLDLIWLLADIVNGLMAIPN 420 Query: 426 LIALLLLSPVVFRLTREYF 444 LIAL+ L V+ ++ YF Sbjct: 421 LIALIGLRSVILAESQRYF 439 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: 660 Number of extensions: 29 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 416 Effective length of database: 431 Effective search space: 179296 Effective search space used: 179296 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