Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate PP_0996 PP_0996 glutamate:sodium symporter
Query= SwissProt::P0AER8 (401 letters) >FitnessBrowser__Putida:PP_0996 Length = 401 Score = 538 bits (1386), Expect = e-157 Identities = 276/399 (69%), Positives = 327/399 (81%), Gaps = 1/399 (0%) Query: 1 MFHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEV 60 MF LD TLVAA+L LLLGR LV + FL+ Y IPEPVAGGL+VAL+LL L+ S V Sbjct: 1 MFELDFYGTLVAASLVLLLGRGLVARIGFLRAYNIPEPVAGGLVVALSLLALR-SFDVHV 59 Query: 61 NFDMSLRDPLMLAFFATIGLNANIASLRAGGRVVGIFLIVVVGLLVMQNAIGIGMASLLG 120 FD SL+ PLMLAFFATIGL+A+ ASL+ GGRVV +FL+VV GLL++QNA+GIG+A+ LG Sbjct: 60 QFDTSLQTPLMLAFFATIGLSADFASLKKGGRVVAVFLLVVTGLLMVQNAMGIGLATALG 119 Query: 121 LDPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPVA 180 LDPLMGLLAGSI+LSGGHGTGAAW F ER+G +A+E+AMA ATFGLVLGGLIGGPVA Sbjct: 120 LDPLMGLLAGSISLSGGHGTGAAWGATFTERFGLASASELAMASATFGLVLGGLIGGPVA 179 Query: 181 RYLVKHSTTPNGIPDDQEVPTAFEKPDVGRMITSLVLIETIALIAICLTVGKIVAQLLAG 240 R L+K TP + ++P FE+PD R+ITS IET+ALIA+ L G ++ LL G Sbjct: 180 RLLIKRVETPGVQEEAPQLPKGFEQPDKERLITSFSFIETLALIAVSLLTGTLLNGLLKG 239 Query: 241 TAFELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLSLFLAMALMGLKLWELA 300 TAFELPTFVCVLFVGV+L NGL +G Y+VFER VSVLGNVSLSLFLA+ALM LKLW+LA Sbjct: 240 TAFELPTFVCVLFVGVVLRNGLRALGVYKVFEREVSVLGNVSLSLFLAIALMSLKLWDLA 299 Query: 301 SLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCGFGLGATPTAIANMQAI 360 +LALP +L QT+ MAL+AIFVT+++MG+NYDAAVLAAGHCGFGLGATPTAIANMQA+ Sbjct: 300 ALALPFFTLLAAQTLVMALFAIFVTFKVMGRNYDAAVLAAGHCGFGLGATPTAIANMQAV 359 Query: 361 TERFGPSHMAFLVVPMVGAFFIDIVNALVIKLYLMLPIF 399 T+R+G SH+AFLVVPMVGAFFIDI+N +VIKLYL LP F Sbjct: 360 TQRYGASHLAFLVVPMVGAFFIDIINVIVIKLYLALPWF 398 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: 464 Number of extensions: 19 Number of successful extensions: 2 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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