Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 158 bits (400), Expect = 1e-43 Identities = 94/239 (39%), Positives = 134/239 (56%), Gaps = 5/239 (2%) Query: 36 DQVLAETGCVVG----VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILV 91 D LA G G ++ LSL++ GE F ++G SG GK+ L+R P +G I + Sbjct: 3 DITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTISI 62 Query: 92 DGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALH 151 GE + + +VFQ + + PH SV DN+ Y LK+ G + L Sbjct: 63 GGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQVLE 122 Query: 152 WINTVGLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQL 211 + V L G EN+ P QLSGG +QRV LARAL ++L+DE LD +R EM+ ++ Sbjct: 123 TVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRFEI 182 Query: 212 LELQKTLHKTIVFITHDLDEAVRIGNRIAILKD-GKLIQVGTPREILHSPADEYVDRFV 269 ELQ+TL TI+++THD + A+ I +R+AI+ G + QVGTP EI PADE+V RF+ Sbjct: 183 KELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRFM 241 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: 212 Number of extensions: 18 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: 366 Length adjustment: 27 Effective length of query: 249 Effective length of database: 339 Effective search space: 84411 Effective search space used: 84411 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