Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS08065 HSERO_RS08065 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS08065 Length = 394 Score = 223 bits (569), Expect = 5e-63 Identities = 126/384 (32%), Positives = 203/384 (52%), Gaps = 14/384 (3%) Query: 2 QLKLKLTVVAAIAAAAGVASAQEQV----------VKIGHVAPVSGAQAHYGKDNENGAR 51 +L L +A + A G A+AQ + + IG P+SG GK +NG + Sbjct: 6 RLLAALLALATLGAPVG-ATAQPRAPLPDRQETATLAIGFAGPLSGPSGGVGKSMQNGVQ 64 Query: 52 MAIEELNAQGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIP 111 +A+ E N +G+ IGGK + L+A+DD ADP A+ L +V VVGH SGT++ Sbjct: 65 LALAEANRRGLRIGGKSWQLRLIAQDDRADPATAEFVARSLVQQQVIAVVGHWTSGTSLA 124 Query: 112 ASKVYNDCGIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAII 171 A+ VY+ G+ VT +A + LT Y FR I N+ +LG A YAVD L+ +T+ I Sbjct: 125 AAPVYHRAGVIQVTPSAMSRRLTAMSYPRIFRTIPNNESLGRLAAGYAVDKLETRTIVTI 184 Query: 172 DDRTAYGQGVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDP 231 DDRT +GQG+A+ F +TA+ +G +VV +DK +DF A L + PD IF+GG+D Sbjct: 185 DDRTPFGQGLAEQFARTASERGAQVVGRYSVSDKTSDFNAALLEARKLQPDLIFFGGLDW 244 Query: 232 QGGPMLRQMEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTA 291 Q G + + + +L + + + G T + L + E G KMPG + Sbjct: 245 QAGVLAKSIRRLKL-HARLMASPG--TLGLPFLMRAGPDANGALVLEPGPPQDKMPGWKS 301 Query: 292 WKAKYDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAF 351 ++ +Y + + +Y+ + Y+A I+ +++A S DP+ + + F+GV+ +AF Sbjct: 302 FRQRYSENFDSDMDLYAVFAYEAAQAIIQGIRQAGSADPERIAEAMHRLRFEGVSGPVAF 361 Query: 352 EPNGEMKNPAITLYVYKDGKKTPL 375 G++ P+ T+Y KD + P+ Sbjct: 362 NEEGDLLQPSFTMYEVKDQRWQPV 385 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: 322 Number of extensions: 15 Number of successful extensions: 2 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: 394 Length adjustment: 30 Effective length of query: 345 Effective length of database: 364 Effective search space: 125580 Effective search space used: 125580 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