Align neutral amino acid transporter B(0) (characterized)
to candidate 6938665 Sama_2768 proton/glutamate symporter (RefSeq)
Query= CharProtDB::CH_091706 (553 letters) >FitnessBrowser__SB2B:6938665 Length = 430 Score = 227 bits (579), Expect = 6e-64 Identities = 149/428 (34%), Positives = 226/428 (52%), Gaps = 56/428 (13%) Query: 61 VVAGVGLGLGVSAAGGADALGPARLTRFAFPGELLLRLLKMIILPLVVCSLIGGAASL-D 119 ++ G+ LG+GV G DA + G L + +KM+I+PLV CSLI G S+ D Sbjct: 22 ILTGMLLGIGVGLVLGPDASALKPI------GTLFVNTIKMLIVPLVFCSLIVGVTSMQD 75 Query: 120 PSALGRVGAWALLFFLVTTLLASALGVGLALALKPGAAVTAITSINDSVVDPCARSAPTK 179 + +GR+G + F+L TT +A ++G+ + L+PGA + S+ + ++AP Sbjct: 76 TARMGRIGFKSFAFYLATTAIAISVGLMVGWLLEPGAGL----SLEGHDLSAEVKTAP-- 129 Query: 180 EALDSFLDLVRNIFPSNLVSAAFRSFATSYEPKDNSCKIPQSCIQREINSTMVQLLCEVE 239 S +D + NI P+N V+A + Sbjct: 130 ----SVMDTLINIVPTNPVAA-------------------------------------LA 148 Query: 240 GMNILGLVVFAIVFGVALRKLGPEGELLIRFFNSFNDATMVLVSWIMWYAPVGILFLVAS 299 IL ++VFA+ GVAL +G G+ I+ F S +A L +M AP G+ L+A Sbjct: 149 SGQILQVIVFAVALGVALVLIGDHGKPAIKVFESLAEAMYKLTDMVMKLAPYGVFGLMAW 208 Query: 300 KIVEMKDVRQLFISLGKYILCCLLGHAIHGLLVLPLIYFLFTRKNPYRFLWGIMTPLATA 359 E + + L K I+ LG A+H L L+ L +P +F GI +A A Sbjct: 209 VAGEYGI--DMLLPLIKVIIAVYLGCALHILGFYSLVLKLVAGLSPIQFFKGISNAMAVA 266 Query: 360 FGTSSSSATLPLMMKCVEEKNGVAKHISRFILPIGATVNMDGAALFQCVAAVFIAQLNGV 419 F TSSS+ TLP MKC E GV K IS F+LP+G T+NMDG AL+Q V A+F+AQ GV Sbjct: 267 FTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTALYQGVTALFVAQAFGV 326 Query: 420 SLDFVKIITILVTATASSVGAAGIPAGGVLTLAIILEAVSLPVKDISLILAVDWLVDRSC 479 L +V +TI++TAT +S+G AG+P G++ L ++L V LP++ +++I +D ++D + Sbjct: 327 DLTWVDYLTIVLTATLASIGTAGVPGAGLVMLTLVLTTVGLPLEGVAIIAGIDRILDMAR 386 Query: 480 TVLNVEGD 487 TV+NV GD Sbjct: 387 TVVNVSGD 394 Lambda K H 0.323 0.138 0.406 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: 443 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 553 Length of database: 430 Length adjustment: 34 Effective length of query: 519 Effective length of database: 396 Effective search space: 205524 Effective search space used: 205524 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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