Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 202663 SO3562 proton/glutamate symporter, putative (NCBI ptt file)
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__MR1:202663 Length = 413 Score = 371 bits (953), Expect = e-107 Identities = 190/400 (47%), Positives = 268/400 (67%), Gaps = 4/400 (1%) Query: 11 LRLLVRLPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAG 70 L+ + R+P WQ++L G LG G+ G A +L P+G LF++AIKML+ PLVF S+V Sbjct: 3 LQTISRIPFWQKVLTGFILGALVGVLLGESATVLKPLGDLFISAIKMLVAPLVFCSIVVS 62 Query: 71 ITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAPS 130 ITS+ L R+S+KT+ ++++T A IGL G+L G G +A+ + + P Sbjct: 63 ITSLGSQTNLKRLSIKTLGMFMLTGTIASLIGLAVGSLIDMG-GTMQLATTEVRERNIPG 121 Query: 131 LVSILVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKL 190 +L+ ++P NP + AEG +LQIIVFA +G++IN +GE+ P R +A AE ++L Sbjct: 122 FAQVLLDMIPINPFASLAEGKVLQIIVFAALVGIAINKVGEKAEPLKRTIEAGAEVMFQL 181 Query: 191 TDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARL 250 T +V+++ PIGVF L A VVG +G LLPL I IY+A++ H++ VYGG + L A L Sbjct: 182 TRMVLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIAAIYIAALVHMIFVYGGFVKL-AGL 240 Query: 251 NPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTA 310 +P++FF+ PA VAFSTSSS GTLP S A + +GVS+ + FV+P+GAT+NMDG Sbjct: 241 SPIQFFRKALPAQLVAFSTSSSFGTLPASTR-AVETMGVSKRYSAFVMPLGATMNMDGCG 299 Query: 311 -IYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPL 369 IY + A+FIAQ +GI L Y MI +TAT+AS+GTAG+PG+ ++ML + L GLPL Sbjct: 300 GIYPAIAAIFIAQIYGIPLDTLDYVMIAVTATIASVGTAGVPGSAMVMLTVTLGVIGLPL 359 Query: 370 EGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELD 409 EG+A IA IDRI+DM RTT NV GD+MT ++G+SE ELD Sbjct: 360 EGIAFIASIDRIIDMIRTTTNVTGDMMTAVVIGKSENELD 399 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: 525 Number of extensions: 18 Number of successful extensions: 5 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: 413 Length adjustment: 31 Effective length of query: 388 Effective length of database: 382 Effective search space: 148216 Effective search space used: 148216 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