Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 5208721 Shew_1224 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:L0GT47 (419 letters) >FitnessBrowser__PV4:5208721 Length = 416 Score = 365 bits (936), Expect = e-105 Identities = 184/396 (46%), Positives = 265/396 (66%), Gaps = 3/396 (0%) Query: 16 RLPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQ 75 ++P WQ++L G LGV G+ G A L P+G LF+ AIKML+ PL+F ++V ITS+ Sbjct: 7 QIPFWQKVLAGFILGVGLGVVLGEQATQLKPLGDLFIAAIKMLVAPLIFCAIVVSITSLG 66 Query: 76 DSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAPSLVSIL 135 + L R+S+KT+A++++T A IGL G+L G + + A+ + + P +L Sbjct: 67 NDVSLKRLSIKTLAMFMLTGTIASLIGLAIGSLIDMGGSLEL-ATTEVRERNVPGFAQVL 125 Query: 136 VGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVM 195 + ++P NP + AEG +LQIIVFA +G++IN IGE+ P R +A AE ++LT +V+ Sbjct: 126 LDMIPVNPFASLAEGKVLQIIVFAALVGIAINKIGEKAEPLKRTIEAGAEVMFQLTRMVL 185 Query: 196 RVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRF 255 ++ PIGVF L A VVG +G LLPL IG IY+A++ H++ VYGGL+ A L+ ++F Sbjct: 186 QLTPIGVFGLMAWVVGEYGLSTLLPLGKFIGAIYIAALIHMVFVYGGLVRFGAGLSAVQF 245 Query: 256 FQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGT-AIYQG 314 F+ PA VAF+T+SS GTLP S A + +GVS+ FVLP+GAT+NMDG IY Sbjct: 246 FRKAMPAQLVAFTTASSFGTLPASTR-ATETMGVSKKYGAFVLPLGATMNMDGCGGIYPA 304 Query: 315 VLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVAL 374 + A+FIAQ +GI L Y +I +TAT+AS+GTAG+PG+ ++ML + L GLPLEG+A Sbjct: 305 IAAIFIAQIYGIPLEMTDYMLIAVTATVASVGTAGVPGSAMVMLSVTLGVVGLPLEGIAF 364 Query: 375 IAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDR 410 IA IDR++DM RT NV GD+MT +VG+SE +LD+ Sbjct: 365 IASIDRVIDMIRTATNVTGDMMTAVVVGKSEGQLDQ 400 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: 545 Number of extensions: 25 Number of successful extensions: 4 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: 416 Length adjustment: 32 Effective length of query: 387 Effective length of database: 384 Effective search space: 148608 Effective search space used: 148608 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