Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate AO353_17125 AO353_17125 leucine ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17125 Length = 375 Score = 194 bits (493), Expect = 3e-54 Identities = 126/368 (34%), Positives = 191/368 (51%), Gaps = 9/368 (2%) Query: 6 KLTVVAAIAAAAGVASAQ--EQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVT 63 +++ + A AGVAS +KIG P +G YG GA+MAIE++NA+G Sbjct: 7 QISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVTQYGDMQFIGAKMAIEQINAKG-G 65 Query: 64 IGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPH 123 + GK + E DDA DPKQ A A K+ + V VVGHL S +T PAS +Y D G+ Sbjct: 66 VDGKML--EAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIM 123 Query: 124 VTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVAD 183 +T AAT+P++T GYK FR I D+A G Y D +K K VA++ D+ YG+G+A Sbjct: 124 ITPAATSPDITNRGYKMVFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIAT 183 Query: 184 VFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQL 243 KKT KG+KV + DF +I+ +K N D ++YGG P+ G +LRQ ++ Sbjct: 184 AVKKTLEGKGVKVAVFEGLNAGDKDFSSIIQKLKQANVDFVYYGGYHPELGLILRQAKEK 243 Query: 244 GMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQ 303 G+ N K+ G +G+ I+++A A G ++ S + P A + AK + Sbjct: 244 GL-NAKFMGPEGVGNESISQIAQDASE-GLLVTLP--KSFDQDPANKALVDAFAAKKQDP 299 Query: 304 FQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAIT 363 + Y A +I + +K A S D + +FK T ++++ G++KN Sbjct: 300 TGPFVFPAYSAVEVIAEGIKAAKSEDTAKVAAAIHAGTFKTPTGDLSYDAKGDLKNFKFV 359 Query: 364 LYVYKDGK 371 +Y + GK Sbjct: 360 VYQWHFGK 367 Lambda K H 0.315 0.131 0.375 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: 384 Number of extensions: 19 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: 375 Length of database: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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