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 WP_084935582.1 HA51_RS15840 branched-chain amino acid ABC transporter permease LivH
Query= TCDB::P21627 (307 letters) >NCBI__GCF_002095475.1:WP_084935582.1 Length = 304 Score = 327 bits (837), Expect = 3e-94 Identities = 168/302 (55%), Positives = 221/302 (73%), Gaps = 3/302 (0%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 ++QQ++NGLT+G+ Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y+ I + LL+ G+ Sbjct: 5 FIQQMINGLTLGAVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLCAIGLALLSYFGIH 64 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126 S PL++ +IIVT+A+G++IER+AYRPLR RL PLISAIGMS+ LQN V LSQ Sbjct: 65 SFPLLIFGTLLFTIIVTAAYGWAIERIAYRPLRNSTRLAPLISAIGMSLILQNYVQLSQG 124 Query: 127 SKEKAIPTLLPGNFVFGESSMNGVV-ISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 ++ IPTL+ G V G+V I++ ++ I + F M LT I ++LGR CRA Sbjct: 125 PNQQGIPTLMTG--VLRMEIDGGIVQITWTKVFILIAAFCGMAFLTWIIQYTKLGRICRA 182 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 +D +M ++LGIN++ +I+L FV+GAA+A +A VL+ M YG + GF+ GIKAFTAA Sbjct: 183 VQQDRRMASILGINTDRVISLVFVMGAAMAGLAGVLVTMNYGTFDFYAGFIIGIKAFTAA 242 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305 VLGGIGS+PGAMLGGLLLGVAEA A + YKDV +F LL+++L+FRP G+LGRP V Sbjct: 243 VLGGIGSLPGAMLGGLLLGVAEAQFAGLVNSDYKDVFSFALLVVILIFRPQGLLGRPLVA 302 Query: 306 KV 307 KV Sbjct: 303 KV 304 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: 350 Number of extensions: 16 Number of successful extensions: 2 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: 304 Length adjustment: 27 Effective length of query: 280 Effective length of database: 277 Effective search space: 77560 Effective search space used: 77560 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 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