Align Branched chain amino acid: Na+ symporter (characterized)
to candidate WP_104485719.1 UN63_RS05165 branched-chain amino acid transport system II carrier protein
Query= TCDB::P19072 (437 letters) >NCBI__GCF_002936955.1:WP_104485719.1 Length = 434 Score = 371 bits (952), Expect = e-107 Identities = 198/434 (45%), Positives = 278/434 (64%), Gaps = 9/434 (2%) Query: 4 LKGFDLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVVALA 63 L FD++ LGFMTFA FLGAGNIIFPP AG AGE++ SA FGFL+T VGLPL+T++A A Sbjct: 5 LSTFDVMGLGFMTFAFFLGAGNIIFPPLAGFLAGENLNSAMFGFLITAVGLPLVTLIAAA 64 Query: 64 RVGGGIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGDGG-VPLL 122 GGG+ + + + A A+++ IGP FA PRT +V++EMG+ PF D G L Sbjct: 65 LAGGGLPTMGRYLPAAVVTVMATAIFIIIGPAFAAPRTGLVAYEMGLKPFLNDPGQTTLT 124 Query: 123 IYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSSSGEYQS 182 +YT+ +F +VL L LN GRL+D VGKV+TP+LL L+ L A P G + Y + Sbjct: 125 LYTIGFFGLVLLLSLNQGRLLDAVGKVLTPILLLLLVALAVAVFVNPQGTQPQVAEAYLT 184 Query: 183 APLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAATGLSLVY 242 P V+GF++GY TMDT AL+FG++I +R +G++D+R +RY MIA +IAA GL VY Sbjct: 185 QPFVKGFIEGYNTMDTFAALMFGMLILDVLRQKGVTDTRAQSRYLMIAALIAAAGLGFVY 244 Query: 243 LALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVGLITACG 302 ++LF LG TS G+ A NG +I++AYV FG G +LA +++LAC+TTAVGL+++C Sbjct: 245 VSLFILGGTSFGVVESASNGGEIISAYVLSLFGAPGLWILAAIVSLACITTAVGLVSSCA 304 Query: 303 EFFSDLL-PVSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIALSLFDR 361 ++F L SY+ V + ++ +LVAN GL LIS+S+PVLV YP+A+ L+ + Sbjct: 305 DYFHRLTGKGSYRRWVAINAVACMLVANVGLNTLISVSIPVLVACYPVAVALVMATYLTP 364 Query: 362 LWVSAPRVFVPVMIVALLFGIVDGLGAAKLNGWVPDVFAKLPLADQSLGWLLPVSIALVL 421 L S F +M VA FG++DG+ AA LN F LP+ D + W+LP A V+ Sbjct: 365 LMRSPVFAFRLIMTVAFAFGLIDGMQAAGLN---MSAFTFLPMFDIGMAWVLPTIAAAVI 421 Query: 422 AVVCDRLLGKPREA 435 + GK ++A Sbjct: 422 GLAA----GKAKQA 431 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: 595 Number of extensions: 33 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: 434 Length adjustment: 32 Effective length of query: 405 Effective length of database: 402 Effective search space: 162810 Effective search space used: 162810 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 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