Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Korea:Ga0059261_0201 Length = 455 Score = 312 bits (799), Expect = 2e-89 Identities = 170/411 (41%), Positives = 253/411 (61%), Gaps = 23/411 (5%) Query: 10 IFIGLILGIIVG-AIFYGNPK---------------VAAYLQPIGDIFLRLIKMIVIPIV 53 I I L+ G IVG + YG VA Y + IFLRLIKMI+ P+V Sbjct: 9 ILIALVAGAIVGLGLHYGIHNSFGADSAGAEAELKTVAGYFSIVTTIFLRLIKMIIAPLV 68 Query: 54 ISSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKT 113 ++LV G+A +GD LG++GG+ + +F + +++ +GL+ N+FQPG G+N L Sbjct: 69 FATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQPGVGLNFP-LPPV 127 Query: 114 DIQSYVDTTNEVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGK 173 D S V E ++ + F ++ P + E+++ ++L I+ FS+ G+ + A+GEK K Sbjct: 128 DATSGV----EKAAFNLKDFFTHVFPASGIEAMAKNEILQIVIFSLFIGVAITAVGEKAK 183 Query: 174 PVLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLF 233 P++ + M VTN +M+FAP VFA + T+++ G + L+ + Y M F Sbjct: 184 PLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIGNLAYFMGTFYIAM-F 242 Query: 234 FIFAVLGGVAKLF-GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITS 292 ++A+L GV L G +++ ++D L+LA+STASSE PR ++ +++FG P I S Sbjct: 243 TLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTLEALDRFGVPPRIAS 302 Query: 293 FVIPTGYSFNLDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSF 352 FV+P GYSFNLDGS +Y A IFIAQ YGID+++ Q+I++LLVLM+TSKGIAGVP S Sbjct: 303 FVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLMITSKGIAGVPRASL 362 Query: 353 VVLLATLGTVGIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEG 403 VV+ ATLG IP GL I GID LDM R+A NV+GN++A+ +++KWEG Sbjct: 363 VVIAATLGFFDIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAVVAKWEG 413 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: 446 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: 421 Length of database: 455 Length adjustment: 32 Effective length of query: 389 Effective length of database: 423 Effective search space: 164547 Effective search space used: 164547 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