Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate WP_040660796.1 ON16_RS07490 sodium:glutamate symporter
Query= SwissProt::P0AER8 (401 letters) >NCBI__GCF_000307265.1:WP_040660796.1 Length = 416 Score = 208 bits (530), Expect = 2e-58 Identities = 127/396 (32%), Positives = 214/396 (54%), Gaps = 11/396 (2%) Query: 2 FHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEVN 61 F + L+ L A + LGR +V L+KY IP PV GL+ +L + +K S + Sbjct: 22 FKFEYLSALGFAAFVIFLGRAIVRHSKLLQKYAIPAPVVSGLIFSLVVSFIKMSGAMAFS 81 Query: 62 FDMS-LRDPLMLAFFATIGLNANIASLR-AGGRVVGIFLIVVVGLLVMQNAIGIGMASLL 119 FD++ ++D FF +G + ++ AGG++ + + L+ +Q+ +G+ + +L+ Sbjct: 82 FDVTVMKDLCQNLFFLCVGFGFSWKMIKHAGGKLCVLIAVGACLLITLQDLLGVAIGNLV 141 Query: 120 GLDPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPV 179 GL PL+ L S +SGG GT +A+ +F E G AT + +A T G ++G LIGGPV Sbjct: 142 GLHPLLALQCSSSAMSGGVGTASAFGPIF-ENMGAPEATTIGVAAGTLGNIMGSLIGGPV 200 Query: 180 ARYLVKHSTTPNGIPDDQEVPTAFE--KPDVGRMITSLVLIETIALIAICLTVGKIVAQL 237 A +L+ D E + E + D GRMI+ + +A + + I L Sbjct: 201 AAFLISRHGLKADPNDKPEAVMSGEATRLDNGRMISMFAMCLLLAALGM-----PIYMLL 255 Query: 238 LAGTAFELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLSLFLAMALMGLKLW 297 + E+P F+ LF G I N + + + V + ++ L L+LA+ LM + + Sbjct: 256 DSIPMIEMPKFIGCLFAGAIARNVMEAFHI-KFYTPEVDAIEHMFLELYLALVLMTIDIT 314 Query: 298 ELASLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCGFGLGATPTAIANM 357 +LA +A M IL+ Q I MAL+ IFV++ M G++Y AAV+AAG+CG+G G+ P A+AN Sbjct: 315 KLAPVAGQMGVILIGQAILMALFGIFVSYNMFGRDYGAAVMAAGNCGWGCGSGPNAVANE 374 Query: 358 QAITERFGPSHMAFLVVPMVGAFFIDIVNALVIKLY 393 +A+ +++G ++A+++ P DI N + + L+ Sbjct: 375 KAVMDQYGWHNIAWVLYPSFAVIIDDIYNPIFLSLF 410 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: 381 Number of extensions: 12 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: 416 Length adjustment: 31 Effective length of query: 370 Effective length of database: 385 Effective search space: 142450 Effective search space used: 142450 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 24 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