Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 6938665 Sama_2768 proton/glutamate symporter (RefSeq)
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__SB2B:6938665 Length = 430 Score = 476 bits (1225), Expect = e-139 Identities = 237/400 (59%), Positives = 311/400 (77%), Gaps = 1/400 (0%) Query: 17 LPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQD 76 +PLW QIL G+ LG+ G+ G DA L PIGTLF+N IKMLIVPLVF SL+ G+TSMQD Sbjct: 16 VPLWLQILTGMLLGIGVGLVLGPDASALKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMQD 75 Query: 77 SAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASG-NEQAKQAPSLVSIL 135 +A++GRI K+ A YL TTA A+S+GL+ G L PG G+++ + + K APS++ L Sbjct: 76 TARMGRIGFKSFAFYLATTAIAISVGLMVGWLLEPGAGLSLEGHDLSAEVKTAPSVMDTL 135 Query: 136 VGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVM 195 + +VP NPV A A G ILQ+IVFA+ALGV++ LIG+ G PA+++F++LAE YKLTD+VM Sbjct: 136 INIVPTNPVAALASGQILQVIVFAVALGVALVLIGDHGKPAIKVFESLAEAMYKLTDMVM 195 Query: 196 RVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRF 255 ++AP GVF L A V G +G ++LLPL VI +YL H+L Y +L L+A L+P++F Sbjct: 196 KLAPYGVFGLMAWVAGEYGIDMLLPLIKVIIAVYLGCALHILGFYSLVLKLVAGLSPIQF 255 Query: 256 FQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGV 315 F+GI+ A+AVAF+TSSS+GTLP S++CA + LGV++ ++ FVLP+G TINMDGTA+YQGV Sbjct: 256 FKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTALYQGV 315 Query: 316 LALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALI 375 ALF+AQAFG+DL+ Y I+LTATLASIGTAG+PGAGL+ML LVLT GLPLEGVA+I Sbjct: 316 TALFVAQAFGVDLTWVDYLTIVLTATLASIGTAGVPGAGLVMLTLVLTTVGLPLEGVAII 375 Query: 376 AGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYDS 415 AGIDRILDMART VNV+GDL+ TT++ RSE E+D A Y++ Sbjct: 376 AGIDRILDMARTVVNVSGDLVATTVIARSEGEIDIAHYNA 415 Lambda K H 0.324 0.140 0.386 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: 652 Number of extensions: 27 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: 419 Length of database: 430 Length adjustment: 32 Effective length of query: 387 Effective length of database: 398 Effective search space: 154026 Effective search space used: 154026 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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