Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate 209486 DVU0547 high-affinity branched chain amino acid ABC transporter, periplasmic branched chain amino acid-binding protein
Query= uniprot:G8ALJ3 (366 letters) >MicrobesOnline__882:209486 Length = 372 Score = 208 bits (529), Expect = 2e-58 Identities = 116/365 (31%), Positives = 182/365 (49%), Gaps = 4/365 (1%) Query: 6 SLLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQ 64 +L+ + M V D I + G +G A++G + N GG+ G+ Sbjct: 8 ALIAGMTVAVMAGPVFAGDTIKLGVPGAHSGDLASYGLPSANAAKIVAKMFNDKGGINGK 67 Query: 65 KLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAST 124 +++ DD C P+ A A +L GV V GH CSG++ A +Y E + +SP++T Sbjct: 68 MVEVIPQDDQCKPEMATNAATKLVSDGVDIVLGHICSGATKAALPIYKEANKVVMSPSAT 127 Query: 125 NPKLTEQ-NLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKA 183 P LT+ + FR DDQQ ++ + ++ K +A+LHDK YGKG A+ ++ Sbjct: 128 TPALTQSGDYPMFFRTISSDDQQAKLGVDFAIDKLGAKKIAVLHDKGDYGKGYAEYAKQF 187 Query: 184 LNAGGQKEKI-YEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242 + G+ + +E T G DYSA+V K++ E D V GGYH EA + QM+ + + Sbjct: 188 IEQSGKATVVLFEGVTPGAVDYSAVVQKVRSEGADAVMFGGYHPEASKIVAQMRKKRMTT 247 Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKA-GYEPEGYTLYT 301 P +S D + + + + G E + D +P KEA+E +K G EP + Sbjct: 248 PFISDDGVKDDTFIKVAGKDAEGVYASSSKDVSMLPMYKEAIELHKKEFGTEPGAFYKEA 307 Query: 302 YAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQ 361 +AA Q A ++A ST++ K+ D LR N T IGKI FD +GD + Y+ NG Sbjct: 308 FAAAQALLTAVQRAGSTETPKVVDALRNNFVETAIGKIKFDKRGDAEGTGFSMYQVKNGV 367 Query: 362 YAQVK 366 Y ++K Sbjct: 368 YVELK 372 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: 340 Number of extensions: 18 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: 372 Length adjustment: 30 Effective length of query: 336 Effective length of database: 342 Effective search space: 114912 Effective search space used: 114912 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: 49 (23.5 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