Align Branched chain amino acid: Na+ symporter (characterized)
to candidate 6938637 Sama_2740 branched-chain amino acid transport system II carrier protein BrnQ (RefSeq)
Query= TCDB::P19072 (437 letters) >FitnessBrowser__SB2B:6938637 Length = 441 Score = 374 bits (961), Expect = e-108 Identities = 203/442 (45%), Positives = 296/442 (66%), Gaps = 22/442 (4%) Query: 8 DLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVVALARVGG 67 D L+LGFMTFA FLGAGN+IFPP AGM AGE++ A GFL+T VG+PL+ ++A+A+ G Sbjct: 10 DTLSLGFMTFAFFLGAGNLIFPPFAGMLAGENMPLAMMGFLVTAVGMPLVGLIAVAKTQG 69 Query: 68 GIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGD-------GGVP 120 R+ + A A A+A+Y+ IGP FA PRT +V+FE+G PF GD G + Sbjct: 70 ---RVMAYLPAVAATALAVAIYIIIGPAFAAPRTGLVAFEIGAKPFLGDTSAVLALGSIS 126 Query: 121 L----LIYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSS 176 L LI+T+ +F+V + L L PG+L+D VGKV+TPVL+ LL L + I P+G+ + Sbjct: 127 LNVAQLIFTLGFFAVTMLLALFPGKLMDSVGKVLTPVLMVLLLSLAISVIMLPSGDTSAP 186 Query: 177 SGEYQSAPLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAAT 236 G+Y S+PL++G ++GY TMDTL +L+FG++I +R +G+ TR + A IAA+ Sbjct: 187 VGDYASSPLIKGVIEGYNTMDTLASLMFGMLIIDLLRKKGVDAPADQTRALVRAAFIAAS 246 Query: 237 GLSLVYLALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVG 296 GL+ VY++LF+LGAT+ IA A+NG QILT YV + FG G+LLL+ V++LACLTTAVG Sbjct: 247 GLAFVYISLFFLGATAGDIAQGAENGGQILTRYVDREFGTLGALLLSTVVSLACLTTAVG 306 Query: 297 LITACGEFFSDLLP-VSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIA 355 L++AC ++F++L P + Y+ VI+FS+ +VAN GLTQLIS+S+PVLV +YP+ I L+A Sbjct: 307 LVSACSDYFNELFPRIKYRQFVILFSIICAVVANVGLTQLISVSIPVLVSVYPVVIALVA 366 Query: 356 LSLFDRLWVSAPRVFVPVMIVALLFGIVDGLGAAKLNGWVPDVFAKLPLADQSLGWLLPV 415 ++ + + V+ VALLFG +DGL AA +N + + +PL + + WLLP Sbjct: 367 VTFMTQYLPNPKVSHRLVLAVALLFGAIDGLKAAGVN---MESLSFMPLYAEGMAWLLPT 423 Query: 416 SIALVLAVVCDRLLGKPREAVA 437 ++ +V+ + +GK A A Sbjct: 424 AVTMVICL----FIGKRAPAAA 441 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: 23 Number of successful extensions: 6 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: 441 Length adjustment: 32 Effective length of query: 405 Effective length of database: 409 Effective search space: 165645 Effective search space used: 165645 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