Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3083 HP15_3026 TRAP dicarboxylate transporter, DctM subunit
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Marino:GFF3083 Length = 499 Score = 323 bits (828), Expect = 8e-93 Identities = 172/452 (38%), Positives = 273/452 (60%), Gaps = 23/452 (5%) Query: 7 LGPM---MFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMA 63 +GP+ MF V L G P+AF GG+ ++F + D + L+ +P RIF +MA Sbjct: 52 IGPLTYLMFGSLAVALMMGLPLAFVTGGLGVMFIYLVG-----DAMMLNIVPGRIFPLMA 106 Query: 64 NGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVA 123 N + AIP FIF+ SMLER+G+ E++ + +G + GGLA A I+ T+LAA GV+ Sbjct: 107 NPDIAAIPLFIFMASMLERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIG 166 Query: 124 ATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFI 183 A VV MG+I+LP ML+ Y ++A G I+A GTLG +IPPS++ I+ A SVG+L++ Sbjct: 167 AAVVTMGIIALPAMLKRHYDHKIAIGSIMAGGTLGILIPPSILAILYAVVAQQSVGELYL 226 Query: 184 GSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILL 243 GSLLPGLM++G + YVL+ +WL P L P +P E R ++L +++ ++ PL L+ L Sbjct: 227 GSLLPGLMLSGLYLTYVLVRSWLNPKLGPPIPVEDRISLKEKL--KLLGNLIAPLALVGL 284 Query: 244 VLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGST 303 VLG +F GIA+P EA +GS GAI +A +++ + L E T + ++MV+ I+ G++ Sbjct: 285 VLGLLFGGIATPVEAAGIGSFGAIIVAMMHKKFSIAGLREASVTTAKASAMVLWIMFGAS 344 Query: 304 AFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPV 363 F + G +F+ D + G L + M+ + +LG F+D+ I + +P+F P+ Sbjct: 345 VFVGFYILQGGQQFVTDAILGTGMSAYGILFLLMVLLVVLGMFLDWVGILLLAVPIFIPI 404 Query: 364 AEALNLD-------------LIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQ 410 +AL ++W+GV+ N+Q SFL+PPFG+ALFY+RGV P ++ G Sbjct: 405 VKALEFPGLFGFPPVAGDDVVLWFGVLYLVNMQMSFLSPPFGYALFYIRGVCPPEISMGT 464 Query: 411 IYRGAVPFIGLQVLVLLLIIIFPALINWLPSL 442 I++ ++ F+ +Q L + ++ P ++ WLP L Sbjct: 465 IFKSSLVFLAIQAFGLFMCVLIPGIVTWLPGL 496 Score = 24.6 bits (52), Expect = 0.007 Identities = 38/179 (21%), Positives = 70/179 (39%), Gaps = 29/179 (16%) Query: 282 WEVCDATLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQI--------GFL 333 W + AT+ + ++ + L+ L + ++F+F L +L G +I G L Sbjct: 8 WLMIIATVGLAFVICVELINI----LFYDPWSDEKFLFKLSGSLSGVEIGPLTYLMFGSL 63 Query: 334 AISMITIFILGFFIDFFEIAFI---------------VLPLF-KPVAEALNLDLIWYGVI 377 A++++ L F + FI + PL P A+ L + ++ Sbjct: 64 AVALMMGLPLAFVTGGLGVMFIYLVGDAMMLNIVPGRIFPLMANPDIAAIPLFIFMASML 123 Query: 378 VGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436 A L + + + G+A A++ I V IG V V + II PA++ Sbjct: 124 ERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIGAAV-VTMGIIALPAML 181 Lambda K H 0.331 0.148 0.443 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: 717 Number of extensions: 49 Number of successful extensions: 7 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: 445 Length of database: 499 Length adjustment: 33 Effective length of query: 412 Effective length of database: 466 Effective search space: 191992 Effective search space used: 191992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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