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_012758690.1 RLEG_RS16360 urea ABC transporter permease subunit UrtB
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000023185.1:WP_012758690.1 Length = 545 Score = 140 bits (354), Expect = 5e-38 Identities = 92/297 (30%), Positives = 152/297 (51%), Gaps = 9/297 (3%) Query: 4 IYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMM 63 ++ +Q + GL++GS L AIG + +G++G+IN AHGE+ MIG+Y ++ + Sbjct: 246 LWDIVQNIWYGLSLGSVLLLAAIGLAITFGVMGVINMAHGEMVMIGAYTTYVVQEYITSA 305 Query: 64 GLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVML 123 + + A A+ + T G IER R L G L L++ G+S+ LQ AV Sbjct: 306 FPELADYSLAFAVPAAFVFTGFVGLVIERAVIRYLY-GRPLETLLATWGVSLILQQAVRS 364 Query: 124 S--QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGR 181 S ++E PT + G F G G+ I++ ++ I V + +V L L + RS G Sbjct: 365 SFGPTNREVRNPTWMSGVFDLG-----GLSITWNRLWIIVFSMVVFVALLLLLKRSAFGL 419 Query: 182 ACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKA 241 RA ++ +M + +GI + + A TF +G+ +A +A V L Q ++P +G I + Sbjct: 420 QMRAVTQNRRMASSMGIRTGWVDAFTFALGSGIAGIAGVALS-QIDNVSPNLGQSYIIDS 478 Query: 242 FTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGI 298 F V GG+G++ G ++G L LGV F G ++ L+IL + RP G+ Sbjct: 479 FMVVVFGGVGNLWGTLVGALSLGVVNKFLEPFAGAVLGKILVLVLIILFIQKRPRGL 535 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: 380 Number of extensions: 23 Number of successful extensions: 4 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: 545 Length adjustment: 31 Effective length of query: 276 Effective length of database: 514 Effective search space: 141864 Effective search space used: 141864 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