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 Pf1N1B4_3217 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::P21627 (307 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3217 Length = 307 Score = 511 bits (1317), Expect = e-150 Identities = 255/307 (83%), Positives = 283/307 (92%) Query: 1 MPEIYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLL 60 MP+IYH+ QQLVNGLT+GSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY+AFIAI L Sbjct: 1 MPDIYHFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60 Query: 61 AMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA 120 AM+GLDSVPL+M AAF A+I+VTSA+GYSIER+AYRPLRG NRLIPLISAIGMSIFLQN Sbjct: 61 AMLGLDSVPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120 Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180 V+L+QDSK+K+I L+PGNF G + V+ISYMQI++FVVT + M GLTLFISRSRLG Sbjct: 121 VLLAQDSKDKSISNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180 Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240 RACRACAED+KM NLLGIN+NNIIALTFVIGAALAA+AAVLL MQYGVINP GFL G+K Sbjct: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 240 Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300 AFTAAVLGGIGSIPGAMLGGL+LGVAEAFGAD+FGDQYKDVVAFGLL+LVLLFRPTG+LG Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGLLG 300 Query: 301 RPEVEKV 307 RPEVEKV Sbjct: 301 RPEVEKV 307 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: 468 Number of extensions: 10 Number of successful extensions: 1 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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