Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 200106 SO0922 proton/glutamate symporter (NCBI ptt file)
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__MR1:200106 Length = 424 Score = 469 bits (1208), Expect = e-137 Identities = 235/400 (58%), Positives = 307/400 (76%), Gaps = 1/400 (0%) Query: 17 LPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQD 76 +PLW QI +G+ LG+ G+ G A L PIGTLF+N IKMLIVPLVF SL+ G+TSM+D Sbjct: 3 VPLWLQIFVGMVLGILVGVTLGEQASYLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMED 62 Query: 77 SAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVA-SGNEQAKQAPSLVSIL 135 +AK+GRI K+ + YL TTA A+S+GL+ G + PG G+ ++ AK+ PS++ L Sbjct: 63 TAKMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPLLQHEAVNTAKEVPSVMQTL 122 Query: 136 VGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVM 195 + +VP NPV A A G ILQ+IVFA+ALG+++ LIG+ G PA+++F++LAE YKLTD+VM Sbjct: 123 IDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLTDMVM 182 Query: 196 RVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRF 255 ++AP GVF L A V G +G ++L PL VI +Y+ I HVL Y +L L A+LNPL F Sbjct: 183 KLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFAKLNPLHF 242 Query: 256 FQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGV 315 F+GI+ A+AVAF+TSSS+GTLP S++CA + LGV++ ++ FVLP+G TINMDGTA+YQGV Sbjct: 243 FKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTALYQGV 302 Query: 316 LALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALI 375 ALF+AQAFGIDL+ Y IILTATLASIGTAG+PGAGL+ML LVL+ GLPLEGVALI Sbjct: 303 TALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVGLPLEGVALI 362 Query: 376 AGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYDS 415 AGIDRILDMART VNV+GDL+ TT++ +SE ELD Y++ Sbjct: 363 AGIDRILDMARTVVNVSGDLVATTVIAKSENELDVEHYNA 402 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: 608 Number of extensions: 24 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: 424 Length adjustment: 32 Effective length of query: 387 Effective length of database: 392 Effective search space: 151704 Effective search space used: 151704 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: 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