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_028311034.1 H566_RS0108010 urea ABC transporter permease subunit UrtB
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000482785.1:WP_028311034.1 Length = 539 Score = 142 bits (358), Expect = 2e-38 Identities = 92/296 (31%), Positives = 153/296 (51%), Gaps = 8/296 (2%) Query: 5 YHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMG 64 Y L L +G+++GS L A+G + YG++G+IN AHGE+ MIG+Y ++ L Sbjct: 240 YEMLANLFSGISLGSILLLAALGLAITYGLMGIINMAHGELLMIGAYSTYVVQGLFRKYA 299 Query: 65 LDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA--VM 122 + ++AA + +VT+A G +ER R L G L L++ G+S+ L A + Sbjct: 300 PGAFDWYVVAALPVAFLVTAAVGMVLERTIIRWLY-GRPLETLLTTWGISLLLIQACRTI 358 Query: 123 LSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRA 182 + E P+ + G G + G+VI + +I+I + +F V+F + L I+R+RLG Sbjct: 359 FGAQNVEVENPSWMSG----GIALAGGIVIPFNRIIIVLFSFAVLFAVYLLIARTRLGLF 414 Query: 183 CRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAF 242 RA ++ KM + G+ ++ I LTF +GA +A + V L Q G + P +G + +F Sbjct: 415 VRAVTQNRKMASCCGVPTHRIDMLTFGLGAGVAGLGGVALS-QIGNVGPDLGRSYIVDSF 473 Query: 243 TAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGI 298 V GG+G + G ++ L LG F G ++ +IL + RP G+ Sbjct: 474 MVVVFGGVGQLAGTVIAALGLGSLSKFLEPWSGAVLAKIMVLVFIILFIQKRPQGL 529 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: 336 Number of extensions: 18 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: 539 Length adjustment: 31 Effective length of query: 276 Effective length of database: 508 Effective search space: 140208 Effective search space used: 140208 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: 50 (23.9 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