Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate YP_004139565.1 Mesci_0342 TRAP dicarboxylate transporter subunit DctM
Query= TCDB::P74224 (445 letters) >NCBI__GCF_000185905.1:YP_004139565.1 Length = 593 Score = 335 bits (860), Expect = 2e-96 Identities = 213/522 (40%), Positives = 295/522 (56%), Gaps = 104/522 (19%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFD--------PIFLSAMPQRI 58 + P+MF ++FL GYPVAFSL ++F IG L + P+ L A+P Sbjct: 8 MAPIMFASLIIFLLIGYPVAFSLAANGLMFFFIGVLLSPYSGGSINLAWPL-LHALPDNF 66 Query: 59 FG--IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLA 116 +G +M+N TLLAIPFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LA Sbjct: 67 YGSRVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIFVGALLA 126 Query: 117 ATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGV 176 ATTGVVAA+V+AMGLISLPIMLRYGY + LASGVI ASGTL QIIPPS+VLIVLADQLG Sbjct: 127 ATTGVVAASVIAMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVLADQLGR 186 Query: 177 SVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLP 236 SVGD++ G+L+PGL++ G + Y+LI++ ++P+ PALP E R +G + Sbjct: 187 SVGDMYAGALIPGLVLTGLYMSYILIMSIIRPNSMPALPLEARTLGHGVM---------- 236 Query: 237 PLVLILLVLGSIFFG---IASPTEAGAVGSIGAIA-------LAHFNQRLNWKALWEVCD 286 L++ LLV ++ + +P +GA A +A ++RLN+ + + Sbjct: 237 SLLVALLVTSAVSYAAYRYLAPAHGDNADILGATAGVLFIYIVAIADKRLNFNMMSRLAQ 296 Query: 287 ATL--RITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMI------ 338 + I + ++ L+ T F + EG M + A G L++ ++ Sbjct: 297 QVIIVLIPPLALIFLVLGTIFLGIATPTEGGA-MGSVGALFMAAAKGRLSLDVVKQALAS 355 Query: 339 -------TIFIL-------------------------------GFFI------------- 347 +FIL GF I Sbjct: 356 TTRLSSFVLFILIGARVFSLTFYGVNGHIWVEHLLTSLPGGEVGFLIGVNMLVFFLAFFL 415 Query: 348 DFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAP---- 403 DFFE+AFI++PL P A+ L +DLIW+GV++G N+QTSF+ PPFGFALFYLR VA Sbjct: 416 DFFELAFIIVPLLAPAADKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAARVPY 475 Query: 404 ---------ASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436 A +TTGQIY GAVPF+ +QV+++ L I FP ++ Sbjct: 476 LDRLTGKQIAPVTTGQIYWGAVPFVCIQVIMIGLTIAFPQMV 517 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: 861 Number of extensions: 53 Number of successful extensions: 4 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: 593 Length adjustment: 35 Effective length of query: 410 Effective length of database: 558 Effective search space: 228780 Effective search space used: 228780 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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