Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 3608576 Dshi_1970 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Dino:3608576 Length = 688 Score = 363 bits (931), Expect = e-104 Identities = 192/458 (41%), Positives = 289/458 (63%), Gaps = 27/458 (5%) Query: 11 MFVGALVFLGCGYPVAFSLGGVAI--------------LFAIIGAALGSFDPIFLSAMPQ 56 MF+ + L GYPVA+ L GV + L+ + L D + L A Sbjct: 232 MFITFIALLFTGYPVAWVLSGVGVAYCGLAFLFDNDLMLWTGLEGTLTGLDYLTLGATVN 291 Query: 57 RIFGIMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLA 116 R++ M+N L+A+P FIF+G ML+ SG+AE+L+ +M + G RGGLA+ V ++G +LA Sbjct: 292 RVYATMSNAVLVALPMFIFMGLMLDESGVAERLMTSMQRLFGKTRGGLAITVTMIGIILA 351 Query: 117 ATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGV 176 A+TG++ A+VV +G++SLP M++ YS LA+GV+ ASGTLG +IPPS++L+++ADQ+ + Sbjct: 352 ASTGIIGASVVLLGVLSLPAMMQQKYSPRLAAGVVSASGTLGILIPPSIMLVIMADQMAL 411 Query: 177 SVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLP 236 SVGDLF+ ++ PG+++ G + +Y+ +I++LKPD+AP +P ++ Q ++ +V V LP Sbjct: 412 SVGDLFMAAVFPGVIIGGLYLVYIFVISYLKPDVAP-VPEGAQSPDWQAVKDVMVAV-LP 469 Query: 237 PLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVM 296 L LIL VLGSIF GI +PTEA +G++GA LA ++L L V +T T+ + Sbjct: 470 TLGLILAVLGSIFAGICTPTEASGIGALGATLLALGYRKLTLHKLVNVLVSTFNTTAYIF 529 Query: 297 LILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIV 356 I LG+T FS V R L GD + ++A G G + + +F+LGF +D+ EI IV Sbjct: 530 AIFLGATVFSYVLRELGGDALIEHMIAATGLGPNGTILFILFIVFLLGFVLDWIEITLIV 589 Query: 357 LPLFKPVAEALNLD-----------LIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPAS 405 LPL +P+ AL +D L+W+ ++V LQTSFLTPP GFALFYL+GV P Sbjct: 590 LPLMRPIVNALGMDIPGFGVLDEPTLVWFVILVAVTLQTSFLTPPVGFALFYLKGVCPPE 649 Query: 406 LTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSLS 443 + IY+G +PF+ LQ+ L L+ + PAL WLPS++ Sbjct: 650 IKLLDIYKGIIPFVLLQLTGLALVFLLPALATWLPSVA 687 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: 838 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 688 Length adjustment: 36 Effective length of query: 409 Effective length of database: 652 Effective search space: 266668 Effective search space used: 266668 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: 53 (25.0 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