Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Dsui_3482 Dsui_3482 Na+/H+ dicarboxylate symporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__PS:Dsui_3482 Length = 437 Score = 286 bits (731), Expect = 1e-81 Identities = 150/394 (38%), Positives = 244/394 (61%), Gaps = 10/394 (2%) Query: 29 KVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIA 88 ++A Y + DIFLRLIKMI+ P++ ++LV G+A++GD K +G++GG+ + +F + + Sbjct: 36 EIAGYFSILTDIFLRLIKMIIAPLIFATLVAGLANMGDAKAVGRVGGRALGWFICASFCS 95 Query: 89 IVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHHSMVETFVNIVPKNIFESLST 148 + +GLL AN+ QPG +++ E S + ++ + ++ PK+I E+++ Sbjct: 96 LFIGLLFANVLQPGHALSVPLPE-----SAAGLNLKTSALNLKDFITHVFPKSIMEAMAG 150 Query: 149 GDMLPIIFFSVMFGLGVAAI-GEKGKPVLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGV 207 ++L I+ F+V FGL + + + + ++ M VT+ +M+FAPFGVF + Sbjct: 151 NEVLQILVFAVFFGLALGHLHNQAARSLVNTMDEVVHVMLKVTDYVMRFAPFGVFGAVAG 210 Query: 208 TVSKFGVESLIPLSKLVIVVYATML-FFIFAVLGGVAKLFGINIFHIIKILKDELILAYS 266 ++ G+ L+ K ++ Y + + +L G L G ++F +IK+++ L++ +S Sbjct: 211 AITTNGLGMLLVFGKFMLSFYVALAALWALLILAGFIVL-GKDVFRLIKLVRGPLLVGFS 269 Query: 267 TASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTLYQALAAIFIAQLYGIDMS 326 TASSE+V P++M+++EKFG +T FV+P GYSFNLDGS +Y A+FIAQ Y I MS Sbjct: 270 TASSESVYPKLMEQLEKFGIKTRVTGFVLPLGYSFNLDGSMMYTTFLALFIAQAYDIPMS 329 Query: 327 VSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVGIPVEGLAFIAGIDRILDMARTAV 386 ++ QI++LLVLMV+SKGIAGVP S VV+ A L +P GL + GID LDM RT Sbjct: 330 LTAQITMLLVLMVSSKGIAGVPRASLVVVAAVLPMFNLPEAGLLLVLGIDHFLDMGRTVT 389 Query: 387 NVIGNSLAAIIMSKWEGQYNEEKGKQYLAELQQS 420 NV+GNS+A +++KWEG + + LAE ++S Sbjct: 390 NVLGNSIATAVVAKWEGAI--DPVSEELAEAEES 421 Lambda K H 0.326 0.143 0.402 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: 406 Number of extensions: 18 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: 421 Length of database: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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 (21.6 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