Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Pf6N2E2_2249 Proton/glutamate symport protein @ Sodium/glutamate symport protein
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2249 Length = 420 Score = 307 bits (787), Expect = 3e-88 Identities = 163/400 (40%), Positives = 261/400 (65%), Gaps = 14/400 (3%) Query: 12 IGLILGIIVGAI---FYGNPK----VAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASV 64 +G+ LG++VG F G+ + +A+Y + DIFLR+IKMI+ P+V ++LV G+AS+ Sbjct: 1 MGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLVFATLVGGIASM 60 Query: 65 GDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNE 124 G+ + +G++G + + +F + +++++G+ N+FQPGAG+NM + V+T + Sbjct: 61 GNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHATAAVPVNTGD- 119 Query: 125 VQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKP-VLQFFQGTA 183 S+ ++ P++I E+++ ++L I+ FS+ FG +A + G + + A Sbjct: 120 ---FSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRITDCIEELA 176 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243 + MF +T+ +M FAP GVFA I ++ G+ L+ KL+ Y +L ++A+L G Sbjct: 177 KVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILI-LWALLFGAG 235 Query: 244 KLF-GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFN 302 LF G ++FH+ K++++ ++LA+STASSE+ P+ ++ +EKFG PK ++SFV+P GYSFN Sbjct: 236 YLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLPLGYSFN 295 Query: 303 LDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV 362 LDGS +YQA A +FIAQ Y ID+S +QQ+ +LL LMVTSKG+AGV S VV+ ATL Sbjct: 296 LDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMVTSKGMAGVARASVVVVAATLPMF 355 Query: 363 GIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWE 402 +P GL I GID+ LDMARTA NV+GNS+A +++K E Sbjct: 356 NLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSE 395 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: 431 Number of extensions: 21 Number of successful extensions: 3 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: 420 Length adjustment: 32 Effective length of query: 389 Effective length of database: 388 Effective search space: 150932 Effective search space used: 150932 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: 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