Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF3451 PS417_17665 ABC transporter permease
Query= TCDB::P21627 (307 letters) >FitnessBrowser__WCS417:GFF3451 Length = 286 Score = 160 bits (404), Expect = 4e-44 Identities = 98/298 (32%), Positives = 166/298 (55%), Gaps = 20/298 (6%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 YL Q++NGL +G Y LI++G T+++G++ +NFAHG +++G+YI + A++L L Sbjct: 5 YLFQILNGLGLGMIYFLISVGLTIIFGLLNFVNFAHGAFFLLGAYICYTAVSLTGNFWL- 63 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVML--S 124 A + +V +A + IERV + + + ++ +G+++ +Q A ++ Sbjct: 64 --------ALLIAPLVVAALAWVIERVLIQRIYHLPHMFQILVTLGIALIIQEASVMIWG 115 Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 K A+P LL G V G+ V Y ++ + V + LV GL L + R+R G R Sbjct: 116 PVGKSVAVPELLRGVLVVGD-----FVYPYYRLFLIVFSGLVGLGLWLLLERTRFGALVR 170 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIG-FLAGIKAFT 243 A +E + +LLG N + ++TF +G ALA VA VL G P +G + G+ AF Sbjct: 171 AGSESTETVSLLGTNIFRLFSMTFALGVALAGVAGVLFAPLRGA-QPFVGPEILGV-AFV 228 Query: 244 AAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 V+GG+GS GA++GGLL+GV ++ ++ Q ++ +G + +V+L RP G+ GR Sbjct: 229 VVVIGGMGSFSGALVGGLLVGVVQSLMTTLW-PQGASLMIYGAMAVVILVRPYGLFGR 285 Lambda K H 0.328 0.145 0.413 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: 258 Number of extensions: 13 Number of successful extensions: 4 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: 307 Length of database: 286 Length adjustment: 26 Effective length of query: 281 Effective length of database: 260 Effective search space: 73060 Effective search space used: 73060 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: 48 (23.1 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