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 GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components
Query= TCDB::P21627 (307 letters) >FitnessBrowser__psRCH2:GFF3786 Length = 295 Score = 140 bits (352), Expect = 5e-38 Identities = 92/300 (30%), Positives = 160/300 (53%), Gaps = 17/300 (5%) Query: 4 IYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMM 63 I +L QL+ GL GS YA++++G +++G++ +INFAHG YMIG++ ++ LLA + Sbjct: 9 IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYL---LLATL 65 Query: 64 GLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA--V 121 G+ P ++LA I+ IER+A L + L L+ G+++ L+ A Sbjct: 66 GIGYWPALILAP-----IIVGLCSAVIERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120 Query: 122 MLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGR 181 + A+P L G + ++ + + + + + + ++ L I +++LG Sbjct: 121 FYGSSGQPYAVPKELAGGY-----NLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGA 175 Query: 182 ACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKA 241 RA E+ + GIN ++ T+ +GAALA +A +L Y V +P +G I Sbjct: 176 YLRAATENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQV-SPLMGSNLIIVV 234 Query: 242 FTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 F V+GG+GSI GA++ G +LG+ E VF + ++V F ++ +VLL RP G++GR Sbjct: 235 FAVVVVGGMGSILGAIITGYMLGILEGL-TKVFYPEASNIVIFVIMAIVLLVRPAGLMGR 293 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: 290 Number of extensions: 18 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: 307 Length of database: 295 Length adjustment: 27 Effective length of query: 280 Effective length of database: 268 Effective search space: 75040 Effective search space used: 75040 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