Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate PfGW456L13_1449 probable dicarboxylate transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1449 Length = 420 Score = 286 bits (733), Expect = 6e-82 Identities = 147/403 (36%), Positives = 249/403 (61%), Gaps = 6/403 (1%) Query: 15 ILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLKKLGKLG 74 +LGI+ G P+ +A L+P+GD F++LIKM++ IV +V G++ GDLKK+G++G Sbjct: 1 VLGIVCGLTL---PEYSAQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGDLKKVGRIG 57 Query: 75 GKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQH-HSMVET 133 K++IYFE++TTIA+V+GL+ A G+G N+ LE+ D QH H+ + Sbjct: 58 LKSVIYFEVLTTIALVIGLVFAFSTGIGSGANIH-LEQLSAADMGDIAQRGQHMHTTTQF 116 Query: 134 FVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFYVTNQI 193 ++++P ++ + + ++L ++ FSV+FG + +GE + + + +F + I Sbjct: 117 LMDLIPTSVIGAFADNNILQVLLFSVLFGSALNLVGEAASGISRLINELSHVIFRIMGMI 176 Query: 194 MKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLFGINIFHI 253 ++ AP GVF I T SK+G++SL L LV + Y T + F+ +LG V +L G+ ++ + Sbjct: 177 VRLAPIGVFGAIAFTTSKYGLDSLQHLGSLVGLFYLTCVAFVALILGLVMRLSGLKMWPL 236 Query: 254 IKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTLYQALA 313 +K L++EL++ TASS+ VLP+IM K+E G + VIPTGYSFNLDG ++Y LA Sbjct: 237 LKYLREELLIVMGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGFSIYLTLA 296 Query: 314 AIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIPVEGLAFI 372 +FIA G ++++ +++LLV ++TSKG G+PG + V+L ATL + IPV GL + Sbjct: 297 IVFIANATGTPLAMTDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIPVVGLVLV 356 Query: 373 AGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415 +D + + R N+IGN +A + +++WE + ++ + L+ Sbjct: 357 LAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDIQRANKVLS 399 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: 386 Number of extensions: 16 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