Align Branched chain amino acid: Na+ symporter (characterized)
to candidate 5208257 Shew_0769 branched-chain amino acid transport system II carrier protein (RefSeq)
Query= TCDB::P19072 (437 letters) >FitnessBrowser__PV4:5208257 Length = 443 Score = 372 bits (954), Expect = e-107 Identities = 197/436 (45%), Positives = 283/436 (64%), Gaps = 18/436 (4%) Query: 8 DLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVVALARVGG 67 D L LGFMTFA FLGAGN+IFPP AG AGE++ A GFLLT V LPL+T++A+A+ G Sbjct: 10 DTLGLGFMTFAFFLGAGNLIFPPLAGFLAGENMSWAMIGFLLTAVTLPLVTLIAVAKANG 69 Query: 68 GIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGDGGVPL------ 121 + L P+ A AIA+Y+ IGP FA PR +V++EMG PF D Sbjct: 70 KVMGLLPPL---AATMLAIAIYIIIGPAFAAPRAGLVAYEMGYKPFIQDAQASFEVAGVV 126 Query: 122 -----LIYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSS 176 L+YT +F + + L L PG+L+D VGKV+TP+++ L+ L + + P ++ ++ Sbjct: 127 FTSSQLLYTSIFFGIAMLLSLFPGKLLDSVGKVLTPIMIILLVGLAISVVVLPGSDVAAA 186 Query: 177 SGEYQSAPLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAAT 236 G+YQ+ PL +G ++GY TMDTL +L+FG++I +R +G+ R T+Y + A IAA Sbjct: 187 VGDYQTNPLTKGIIEGYNTMDTLASLIFGMLIIDLLRKKGVDSPREQTKYLVRAAFIAAG 246 Query: 237 GLSLVYLALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVG 296 GL+ VY++LFYLGAT+ +A A NG ILT YV FG SG LLLA V+TLACLTT VG Sbjct: 247 GLAFVYVSLFYLGATAGDLAVGADNGGVILTNYVNYQFGASGQLLLAAVVTLACLTTVVG 306 Query: 297 LITACGEFFSDLLP-VSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIA 355 L++AC E+F++L+P +SYK +V+V S+ +VAN GL QLI++S+PVLV +YP+AI L+A Sbjct: 307 LVSACAEYFNELMPSLSYKLLVVVMSVTCAVVANVGLAQLINISIPVLVTIYPVAIALVA 366 Query: 356 LSLFDRLWVSAPRVFVPVMIVALLFGIVDGLGAAKLNGWVPDVFAKLPLADQSLGWLLPV 415 ++ + V+ VAL+FGI+DGL AA +N +F +PL+ Q + WL+P Sbjct: 367 VTYLTERFAQPAFAHRMVLSVALVFGIIDGLKAAGVN---MSMFDVMPLSAQGMAWLIPT 423 Query: 416 SIALVLAVVCDRLLGK 431 +I + ++ R G+ Sbjct: 424 AITIFACLMVKRPRGE 439 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: 602 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: 443 Length adjustment: 32 Effective length of query: 405 Effective length of database: 411 Effective search space: 166455 Effective search space used: 166455 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