Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= uniprot:G8ALJ3 (366 letters) >MicrobesOnline__882:206137 Length = 376 Score = 204 bits (518), Expect = 4e-57 Identities = 124/355 (34%), Positives = 191/355 (53%), Gaps = 12/355 (3%) Query: 11 VAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKLEV 70 +AATA A + V P+TG++A+ G+ M+ +E ++N AGG+ G K++L V Sbjct: 18 MAATAFAAG----PVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAGGINGNKVELIV 73 Query: 71 GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKLTE 130 DD DP+ A A +L+ +GV V G + S + + +Y E G+ QI+ STN +LTE Sbjct: 74 EDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGSTNVRLTE 133 Query: 131 QNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGGQK 190 + LK R C RDD+QG++A K +++N K VA+LHD S+Y KGLADET+ L+ G K Sbjct: 134 KGLKLFLRTCPRDDEQGRVAAK-VIKNKGYKAVALLHDNSSYAKGLADETKALLDKDGTK 192 Query: 191 EKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGDAL 250 Y+A T GE+DY+A+++KLK D+++ GY+ E G+L RQ + N P++ GDA Sbjct: 193 IVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEMKWNVPMMGGDAA 252 Query: 251 VTNEYWAITGPAGENTMMTFGPD-PREMPEAKE----AVEKFRKAGYEPEGYTLYTYAAL 305 + I G A P P++ A+ A K + +++ A Sbjct: 253 NNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNALPNSVWSVLAGDAF 312 Query: 306 QIWAEAAKQANSTDSAKIADVLRK--NSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358 ++ EA ++ D A IA L+ +Y + G+I F+ KGD Y Y N Sbjct: 313 KVIVEAVQKGGKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLYRVYDVN 367 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: 376 Number of extensions: 24 Number of successful extensions: 3 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: 376 Length adjustment: 30 Effective length of query: 336 Effective length of database: 346 Effective search space: 116256 Effective search space used: 116256 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