Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 119 bits (298), Expect = 9e-32 Identities = 72/234 (30%), Positives = 126/234 (53%), Gaps = 7/234 (2%) Query: 31 QNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAIL 90 +N TK + G G+ ++S I G++ I+G SGSGKSTL++ L+ G I Sbjct: 9 KNLTKQYQAEQAG---GIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIF 65 Query: 91 VDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERAL 150 + + + D + ++ K MV Q F L + V DN+A L + AE+ L Sbjct: 66 FEDKRVKGPDEQLIPGHKQMK--MVTQDFSLNIYAKVYDNIASQLS--NTDLKTKAEKTL 121 Query: 151 HWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQ 210 + + + +NK +LSGG +QRV +A+A+ ADT ++L+DE FS +D L++ +++ Sbjct: 122 QIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRAD 181 Query: 211 LLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEY 264 + + T++ ++HD + + + +++ ILK+G+L+Q G P EI P Y Sbjct: 182 IKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIY 235 Lambda K H 0.321 0.138 0.387 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: 218 Number of extensions: 12 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: 276 Length of database: 330 Length adjustment: 27 Effective length of query: 249 Effective length of database: 303 Effective search space: 75447 Effective search space used: 75447 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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