Align Branched chain amino acid: Na+ symporter (characterized)
to candidate 200133 SO0949 branched-chain amino acid transport system II carrier protein BrnQ (NCBI ptt file)
Query= TCDB::P19072 (437 letters) >FitnessBrowser__MR1:200133 Length = 462 Score = 366 bits (939), Expect = e-106 Identities = 200/450 (44%), Positives = 288/450 (64%), Gaps = 37/450 (8%) Query: 8 DLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVVALARVGG 67 D L LGFMTFA FLGAGN+IFPP AGM AGE++ A GFL+T VGLPL+ ++A+A+ G Sbjct: 5 DTLGLGFMTFAFFLGAGNLIFPPFAGMLAGENMLLAMLGFLITAVGLPLVGLIAVAKAQG 64 Query: 68 GIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGD-------GGVP 120 + + A A AIA+Y+ IGP FA PRT +V++E+G PF + G + Sbjct: 65 KVMAMLPVF---AATALAIAIYIIIGPAFAAPRTGLVAYEIGAKPFIDNTTATIMLGSLS 121 Query: 121 L----LIYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSS 176 L LIYT+ +F V + L L PG+L+D VGKV+TP+LL L+ L + +F PA E+G + Sbjct: 122 LNLSQLIYTLGFFIVTMLLALFPGKLLDSVGKVLTPILLLLLVGLALSVLFLPASEVGVA 181 Query: 177 SGEYQSAPLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAAT 236 G+Y++ PL +G L+GY TMDTL +L+FG++I +R +GI T+Y + A IAA Sbjct: 182 VGDYKNHPLTKGILEGYNTMDTLASLMFGMLIIDLLRKKGIEQPSAQTKYLIRAAFIAAA 241 Query: 237 GLSLVYLALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVG 296 GL+ VY++LF+LGAT+ IA A+NG +ILT YV + FG G++LL+ V+TLACLTTAVG Sbjct: 242 GLAFVYVSLFFLGATAGDIAAGAKNGGEILTNYVTREFGSLGTVLLSAVVTLACLTTAVG 301 Query: 297 LITACGEFFSDLLP-VSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIA 355 L++AC EFF++L+P +SY+ +V+ S L+AN GL+QLI++S+PVL+ +YP+AI L+A Sbjct: 302 LVSACSEFFNELMPKLSYRFLVVALSAICALIANVGLSQLINISIPVLMAVYPVAIALVA 361 Query: 356 LSLFDRLWVSAPRVFVPVMIVALLFGIVDGLGAAK---------------------LNGW 394 ++ + + VALLFGI DG+ A +NG Sbjct: 362 VTFLTEYFPRPQFAHRAALSVALLFGIFDGMKVAAKSLTGEDGRGITEFAQSFIDFVNGM 421 Query: 395 VPDVFAKLPLADQSLGWLLPVSIALVLAVV 424 P + LPL ++ + WLLP + +VL ++ Sbjct: 422 SP-TLSILPLYEEGMAWLLPTLVVIVLCLI 450 Lambda K H 0.327 0.144 0.422 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: 591 Number of extensions: 32 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: 437 Length of database: 462 Length adjustment: 33 Effective length of query: 404 Effective length of database: 429 Effective search space: 173316 Effective search space used: 173316 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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