Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_018124026.1 B149_RS0104760 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_000375485.1:WP_018124026.1 Length = 380 Score = 191 bits (486), Expect = 2e-53 Identities = 111/345 (32%), Positives = 169/345 (48%), Gaps = 6/345 (1%) Query: 25 IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKLEVGDDACDPKQAVAVA 84 + + AG +G A++G + INA GGVLG ++++ DD C P+ A A Sbjct: 36 LVLGVAGAHSGDLASYGLPTVNAAKLVAKKINAEGGVLGMQVEVMAQDDQCKPEMATNAA 95 Query: 85 NQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKLTEQ-NLKNVFRVCGRD 143 +L VK V GH CSG++ A ++Y + ++ +SP++TNP LT+ N N FR D Sbjct: 96 TKLLSEDVKIVLGHICSGATKAALEIYKDGNIVCMSPSATNPPLTQSGNYPNFFRTIASD 155 Query: 144 DQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL-NAGGQKEKIYEAYTAGEK 202 D Q + + + KN+A++HDK YGKG A Q+ + G ++E T G Sbjct: 156 DAQASLEVDF-AKKLGLKNIAVIHDKGDYGKGFASFCQQFIEEEDGMSVALFEGVTPGAV 214 Query: 203 DYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGDALVTNEYWAITGPA 262 DYSA+V K+K D V GGYH EA + M+ + + P +S D + + + G Sbjct: 215 DYSAVVQKIKNSGADGVIFGGYHPEASKIVTSMRKKNIEVPFLSDDGVKDETFIKVAGEY 274 Query: 263 GENTMMTFGPDPREMP--EAKEAVEKFRKAGYEPEGYTLYTYAALQIWAEAAKQANSTDS 320 E T D P E+ K + G +P + YAA Q A ++A + D Sbjct: 275 AEGVYATGPRDISGNPLYSVAESAHK-EEFGSDPGAFYYQAYAAAQALLNAVEKAGAVDY 333 Query: 321 AKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQYAQV 365 KI + LR T +GKI FD +GD + Y+ +GQY ++ Sbjct: 334 DKIVEALRTEYVETPLGKIKFDDRGDAEGVGFSMYQVKDGQYVEI 378 Lambda K H 0.312 0.129 0.366 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: 359 Number of extensions: 25 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: 366 Length of database: 380 Length adjustment: 30 Effective length of query: 336 Effective length of database: 350 Effective search space: 117600 Effective search space used: 117600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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