Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate AO353_14015 AO353_14015 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14015 Length = 437 Score = 293 bits (750), Expect = 7e-84 Identities = 150/409 (36%), Positives = 251/409 (61%), Gaps = 6/409 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ +GL+LGII G P+ +A L+P+GD F++LIKM++ IV +V G++ GDLK Sbjct: 12 QVVLGLVLGIICGLTL---PEYSAQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGDLK 68 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQH- 127 K+G++G K++IYFE++TTIA+V+GL+ A G+G N+ L++ D QH Sbjct: 69 KVGRIGLKSVIYFEVLTTIALVIGLVFAFSTGIGSGANIH-LDQLSTADMGDIAQRGQHM 127 Query: 128 HSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMF 187 H+ + ++++P ++ + + ++L ++ FSV+FG + +GE + + + +F Sbjct: 128 HTTTQFLMDLIPTSVIGAFADNNILQVLLFSVLFGSALNLVGEAASGISRLINELSHVIF 187 Query: 188 YVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLFG 247 + I++ AP GVF I T SK+G++SL L L+ + Y T F+ +LG V +L G Sbjct: 188 RIMGMIVRLAPIGVFGAIAFTTSKYGLDSLQHLGSLIGLFYLTCTVFVSLILGLVMRLSG 247 Query: 248 INIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGST 307 + + +K L++EL++ TASS+ VLP+IM K+E G + VIPTGYSFNLDG + Sbjct: 248 LRLLPFLKYLREELLIVLGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGFS 307 Query: 308 LYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIPV 366 +Y LA +FIA G +++S +++LLV ++TSKG G+PG + V+L ATL + IPV Sbjct: 308 IYLTLAIVFIANATGTPLAMSDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIPV 367 Query: 367 EGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415 GL + +D + + R N+IGN +A + +++WE + ++ + L+ Sbjct: 368 VGLVLVLAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDVQRANKVLS 416 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: 407 Number of extensions: 19 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: 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