Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 203 bits (516), Expect = 7e-57 Identities = 126/366 (34%), Positives = 196/366 (53%), Gaps = 10/366 (2%) Query: 6 SLLVAVAATAMTASVA-KADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQ 64 +L +A+AA+ + A+ A A + + P+TG++A+ G+ M+ + ++N AGG+ G Sbjct: 7 ALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKAGGINGN 66 Query: 65 KLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAST 124 K++L V DD DP+ A A +L +GV G + S + + +Y E GV+QI+ ST Sbjct: 67 KVELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGVVQIATGST 126 Query: 125 NPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184 +LTE+ LK R RDD+QG +A K L++ K VA+LHD S+Y KGLADET+ L Sbjct: 127 AVRLTEKGLKRFLRTAPRDDEQGMVAAK-LIKAKGYKAVALLHDNSSYAKGLADETKALL 185 Query: 185 NAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPI 244 + G K Y+A T GE+DY+A+++KLK D+++ GY+ E G+L RQ + N P+ Sbjct: 186 DKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQKMEMKWNVPM 245 Query: 245 VSGDALVTNEYWAITG---PAGENTMMTFGPDPREMPEAKEAVEKFRKA--GYEPEGYTL 299 + GDA + I+G G + GP + P AK + ++ G +++ Sbjct: 246 MGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAKYNGVPGSVWSV 305 Query: 300 YTYAALQIWAEAAKQANSTDSAKIADVLRK--NSYNTVIGKIGFDAKGDVTSPAYVWYRW 357 A + EA K DS IA+ L+ +Y G+I F+ KGD Y Y Sbjct: 306 LAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDRVGDLYRVYEV 365 Query: 358 N-NGQY 362 N NG + Sbjct: 366 NANGDF 371 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: 369 Number of extensions: 24 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: 375 Length adjustment: 30 Effective length of query: 336 Effective length of database: 345 Effective search space: 115920 Effective search space used: 115920 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