Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF1015 HP15_994 glycine betaine/carnitine/choline ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Marino:GFF1015 Length = 315 Score = 177 bits (449), Expect = 3e-49 Identities = 97/232 (41%), Positives = 144/232 (62%), Gaps = 6/232 (2%) Query: 43 GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102 G V V+ ++L++ TGE+ V++G SG GKST +R N+L+ + G ILVDG D+ ++ + Sbjct: 12 GDAVAVDRINLTVETGEVCVLVGSSGCGKSTTLRMINQLLPHSEGQILVDGNDVTAMNPE 71 Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKG-- 160 LR + V Q GL PH +V N+A ++ ++ ER + + L Sbjct: 72 QLRL----NMGYVIQGTGLFPHWTVARNIAMVPQLLKWPRERVDERVHELLTLLDLDPAT 127 Query: 161 YENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHK 220 + NKYP QLSGG QRVG+ARALAA+ +I+LMDE F ALD + R +Q ++L +Q L K Sbjct: 128 HANKYPQQLSGGQAQRVGVARALAANPNILLMDEPFGALDAITRENLQLEMLRIQSQLRK 187 Query: 221 TIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFVQRR 272 T VF+THD+DEA+R+ RIA++ G++IQ TP IL PA +V+ V ++ Sbjct: 188 TTVFVTHDIDEALRLATRIAVMDQGRIIQHDTPENILRRPASVFVENLVGKQ 239 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: 226 Number of extensions: 10 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: 315 Length adjustment: 26 Effective length of query: 250 Effective length of database: 289 Effective search space: 72250 Effective search space used: 72250 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