Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate 7024349 Shewana3_1541 sodium/glutamate symporter (RefSeq)
Query= SwissProt::P0AER8 (401 letters) >FitnessBrowser__ANA3:7024349 Length = 407 Score = 351 bits (901), Expect = e-101 Identities = 192/410 (46%), Positives = 269/410 (65%), Gaps = 28/410 (6%) Query: 2 FHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEVN 61 + + L + + A L +G + V ++Y IPEP+ GGL+VA A++ + Sbjct: 5 YTIGELESFLIAIFVLFIGHSINRHVRVFRQYNIPEPIVGGLVVA-AVVAFLHFQDITLA 63 Query: 62 FDMSLRDPLMLAFFATIGLNANIASLRAGGRVVGIFLIVVVGLLVMQNAIGIGMASLLGL 121 F + +++ LML FF+TIGL+AN L +GG+ V IFL V +V+QNA+G+ +ASLLGL Sbjct: 64 FSLPMQNTLMLMFFSTIGLSANYKLLLSGGKKVFIFLGVASVYIVIQNAVGVSLASLLGL 123 Query: 122 DPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPVAR 181 DP++GL+AGSITLSGGHGTG AWS+ F E YG N E+AMA ATFGLV+GG+IGGPVA+ Sbjct: 124 DPILGLIAGSITLSGGHGTGVAWSQTFAENYGI-NTLELAMAAATFGLVMGGIIGGPVAQ 182 Query: 182 YLV--------------KHSTTPNGIPDDQEVPTAFEKPDVGRMITSLVLIETIALIAIC 227 L+ H+T P + DQ E+ V T+ +IET+ ++ IC Sbjct: 183 RLIGKHNLVSSYGMGRKHHATHPQLVTYDQ-----LEEDQV----TAKTIIETLFVLLIC 233 Query: 228 LTVGKIVAQLLAGTAF---ELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLS 284 + K L++ ++P FV LF+GVI++N + Y+ ++ V+G V+LS Sbjct: 234 VAGAKWFTVLVSEYQLNWLKMPDFVYALFLGVIIANITEVTRGYKPHTESIDVIGTVALS 293 Query: 285 LFLAMALMGLKLWELASLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCG 344 LFL+MALM LKLWE+ LA+P+L IL+VQT +A++A FVT+++MG NYDAAV+ GHCG Sbjct: 294 LFLSMALMNLKLWEILDLAIPLLIILLVQTAVLAVFAYFVTFKIMGSNYDAAVITGGHCG 353 Query: 345 FGLGATPTAIANMQAITERFGPSHMAFLVVPMVGAFFIDIVNALVIKLYL 394 FG+GATPTA+ NM A+ R GPS AF+VVP+VGAFFIDIVN +V++ YL Sbjct: 354 FGMGATPTAVMNMGALVSRTGPSPQAFMVVPIVGAFFIDIVNLIVLQGYL 403 Lambda K H 0.329 0.143 0.421 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: 399 Number of extensions: 14 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: 401 Length of database: 407 Length adjustment: 31 Effective length of query: 370 Effective length of database: 376 Effective search space: 139120 Effective search space used: 139120 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 (21.8 bits) S2: 50 (23.9 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