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 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 210 bits (535), Expect = 3e-59 Identities = 115/308 (37%), Positives = 189/308 (61%), Gaps = 12/308 (3%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLA--MMG 64 ++Q L N L GS YALIA+GYT+VYG++ +INFAHG+++M+G+YIAF +LL ++G Sbjct: 4 FIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGDLLG 63 Query: 65 LDSVPLMMLAAFAA--SIIVTSAFGYSIERVAYRPLR--GGNRLIPLISAIGMSIFLQNA 120 + ++P A ++++T+ G ++ER+AYRPLR G +RL +I+A+ + L+N Sbjct: 64 VFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLILENG 123 Query: 121 VMLSQDSKEKAIPTLLPGN-FVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRL 179 + + + +P ++ + FG S ++ +++ + + FLV F L ++R+R+ Sbjct: 124 NLALLGASRRKLPDMVDKVVYTFGSVS-----VTNLKVWVIITAFLVFFLLQFIVTRTRI 178 Query: 180 GRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGI 239 G A RA A D L+GI ++II TFV+G+ A +A +L M Y +++P +G + G Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238 Query: 240 KAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGIL 299 KAF AAV+GGIG I GA +GG LL E A ++D+ AF +L+++L RPTG+ Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLF 298 Query: 300 GRPEVEKV 307 G + K+ Sbjct: 299 GVAKTTKI 306 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: 280 Number of extensions: 14 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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