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 Ac3H11_102 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::P21627 (307 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_102 Length = 293 Score = 137 bits (345), Expect = 3e-37 Identities = 88/296 (29%), Positives = 156/296 (52%), Gaps = 21/296 (7%) Query: 10 QLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY--IAFIAITLLAMMGLDS 67 Q++NGL++G L+A+G T+++G++ +IN AHGE Y IG+Y +A +A + L Sbjct: 11 QMINGLSIGVAVVLMALGLTIIFGLLDVINMAHGEFYAIGAYLAVALLATGMSFWWALVL 70 Query: 68 VPLMMLAAFAASIIVTSAFGYSIER-VAYRPLRGGNR-LIPLISAIGMSIFLQNAVMLSQ 125 PL+M + G+ ER + R +R + L+ G+++ L++A+ ++ Sbjct: 71 TPLLM-----------AVLGFVTERGLIQRVFHSKDRHTLTLLLTFGVAVVLEDALKIAF 119 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 + + + G + M G+ ++ + + ++ + L + R+ LG RA Sbjct: 120 GANPLRLEAPISG-----ATEMLGLFFPNYRLFVMLFGGALIAAVWLLVFRTSLGAIVRA 174 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 A D M+ LG+ + A TF G ALA +A VLL Y V P +G + AF+ Sbjct: 175 AAYDRNMSASLGVPVQLVYAGTFAFGVALAGIAGVLLAPIYSVF-PTMGKDFVLIAFSVV 233 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 ++GG+GSI GA+L GLLL ++ + + D + FG+++LVL++RP G+ G+ Sbjct: 234 IIGGMGSIKGALLAGLLLTQVQSISSLYISPVWSDPLLFGIMVLVLMWRPQGLFGK 289 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: 262 Number of extensions: 18 Number of successful extensions: 3 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: 293 Length adjustment: 27 Effective length of query: 280 Effective length of database: 266 Effective search space: 74480 Effective search space used: 74480 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