Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate 5207569 Shew_0103 sodium/glutamate symporter (RefSeq)
Query= SwissProt::P0AER8 (401 letters) >FitnessBrowser__PV4:5207569 Length = 407 Score = 353 bits (905), Expect = e-102 Identities = 188/405 (46%), Positives = 276/405 (68%), Gaps = 16/405 (3%) Query: 1 MFHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEV 60 ++ + L + + A L L +G + V+ +KY IPEP+ GGLLVA + +L S + Sbjct: 4 VYTVGELESFLVAILVLFIGHSVNRHVASFRKYNIPEPIVGGLLVAAVITILH-SYNISL 62 Query: 61 NFDMSLRDPLMLAFFATIGLNANIASLRAGGRVVGIFLIVVVGLLVMQNAIGIGMASLLG 120 F +S+++ LML FF+++GL A+ L GG V +FL + +++QNA+G+ MA+ LG Sbjct: 63 EFSLSMQNTLMLMFFSSVGLAASYKLLMKGGSKVFLFLAIASLYIIIQNAVGVSMATALG 122 Query: 121 LDPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPVA 180 L+PLMGL+AGSITLSGGHGTGAAW++ F ++YG N E+AMA ATFGLV+GG+IGGPVA Sbjct: 123 LEPLMGLIAGSITLSGGHGTGAAWAQTFSDQYGI-NTLELAMAAATFGLVMGGIIGGPVA 181 Query: 181 RYLVK-------HSTTPNGIPDDQEVPTAFEKPDVGRMITSLVLIETIALIAICLT---- 229 + L+ + N D ++ T +++ + R +T+ ++E + ++ +C+ Sbjct: 182 QRLINKNGLLSSYGVGGNHHKDHPDLVT-YDQLEEDR-VTAKSILEVLFILLLCVAGAKW 239 Query: 230 VGKIVAQLLAGTAFELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLSLFLAM 289 G ++A L G ++P FV LF GV+++N + +++ V VLG VSL+LFLAM Sbjct: 240 FGSLIAYLDIGW-LKMPDFVYALFFGVVITNITEVSRGFKINRECVDVLGTVSLALFLAM 298 Query: 290 ALMGLKLWELASLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCGFGLGA 349 ALM LKLWE+ LA+P+L IL+VQT +A++A +VT+++MG NYDAAV+A GHCGFGLGA Sbjct: 299 ALMNLKLWEIFDLAVPLLIILLVQTAVLAVFAYWVTFKLMGANYDAAVMAGGHCGFGLGA 358 Query: 350 TPTAIANMQAITERFGPSHMAFLVVPMVGAFFIDIVNALVIKLYL 394 TPTA+ NM A+ R GPS AF+VVP+VGAFFIDIVNA++++ YL Sbjct: 359 TPTAVMNMGALVSRTGPSPQAFMVVPIVGAFFIDIVNAIILQGYL 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: 379 Number of extensions: 19 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: 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