Align Branched chain amino acid: Na+ symporter (characterized)
to candidate GFF2441 Psest_2489 branched-chain amino acid uptake carrier
Query= TCDB::P19072 (437 letters) >FitnessBrowser__psRCH2:GFF2441 Length = 438 Score = 675 bits (1742), Expect = 0.0 Identities = 342/431 (79%), Positives = 386/431 (89%) Query: 1 MTHLKGFDLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVV 60 M LKGFDLLALGFMTFALFLGAGNIIFPPSAGMA+GE VW AA GFLLTGVGLPLLTVV Sbjct: 1 MNRLKGFDLLALGFMTFALFLGAGNIIFPPSAGMASGEFVWHAALGFLLTGVGLPLLTVV 60 Query: 61 ALARVGGGIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGDGGVP 120 ALARVGGG+ RLT P+G AG A+AVYLAIGPLFATPRTAVVSFEMG+APF+G+ G+P Sbjct: 61 ALARVGGGMDRLTAPLGNVAGTVLAVAVYLAIGPLFATPRTAVVSFEMGIAPFSGNAGMP 120 Query: 121 LLIYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSSSGEY 180 L +YT+ +F+ +LFLVLNPG+LV+R+GK ITPVLL+ALLVLGGAAIFAPAGE+G+++ Y Sbjct: 121 LFLYTLVFFAAMLFLVLNPGQLVNRIGKFITPVLLAALLVLGGAAIFAPAGEVGAATESY 180 Query: 181 QSAPLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAATGLSL 240 +++PL++GFL+GYLTMDTLGALVFGIVIATAIRDRG+++ LVTRYSMIAGVIAA GLSL Sbjct: 181 RASPLIKGFLEGYLTMDTLGALVFGIVIATAIRDRGVTEPALVTRYSMIAGVIAAIGLSL 240 Query: 241 VYLALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVGLITA 300 VYLALFYLGATSQGIA A+NGVQILT YVQ TFG GSLLLAVVITLACLTTAVGL TA Sbjct: 241 VYLALFYLGATSQGIAAGAENGVQILTTYVQHTFGTPGSLLLAVVITLACLTTAVGLTTA 300 Query: 301 CGEFFSDLLPVSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIALSLFD 360 CGEFFS LLPVSY+TVV+VF+LFSLLVANQGLTQLIS+SVPVLVGLYPLAIVL+ALSL D Sbjct: 301 CGEFFSALLPVSYRTVVVVFALFSLLVANQGLTQLISVSVPVLVGLYPLAIVLVALSLLD 360 Query: 361 RLWVSAPRVFVPVMIVALLFGIVDGLGAAKLNGWVPDVFAKLPLADQSLGWLLPVSIALV 420 R WVS RVFVPVM V L+FG+VDGL AA L WVP +FA+LPLADQS+GWL+PV + LV Sbjct: 361 RFWVSPTRVFVPVMGVTLIFGVVDGLAAAGLGNWVPALFAQLPLADQSMGWLVPVLVMLV 420 Query: 421 LAVVCDRLLGK 431 LAV DRLLG+ Sbjct: 421 LAVATDRLLGR 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: 777 Number of extensions: 29 Number of successful extensions: 1 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: 438 Length adjustment: 32 Effective length of query: 405 Effective length of database: 406 Effective search space: 164430 Effective search space used: 164430 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