Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO353_12265 AO353_12265 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12265 Length = 274 Score = 498 bits (1282), Expect = e-146 Identities = 255/276 (92%), Positives = 267/276 (96%), Gaps = 2/276 (0%) Query: 1 MSNAAISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEI 60 MSNAA KIEVKNVFKIFG+RS +AL++IRQNK+KDQVLAETGCV+GVNDLSLSI TGEI Sbjct: 1 MSNAA--KIEVKNVFKIFGDRSADALDMIRQNKSKDQVLAETGCVIGVNDLSLSIATGEI 58 Query: 61 FVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFG 120 FVIMGLSGSGKSTLVRH NRLIDPTSG ILVDG DILQ DM+ALREFRRHKISMVFQSFG Sbjct: 59 FVIMGLSGSGKSTLVRHINRLIDPTSGVILVDGVDILQYDMEALREFRRHKISMVFQSFG 118 Query: 121 LLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLA 180 LLPHK+VLDNVAYGLKVRGESKQVCAERA HWINTVGL+GYENKYPHQLSGGMRQRVGLA Sbjct: 119 LLPHKNVLDNVAYGLKVRGESKQVCAERAQHWINTVGLQGYENKYPHQLSGGMRQRVGLA 178 Query: 181 RALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIA 240 RALAADTDIILMDEAFSALDPLIRAEMQDQLLELQ+TLHKTIVFITHDLDEAVRIGNRIA Sbjct: 179 RALAADTDIILMDEAFSALDPLIRAEMQDQLLELQQTLHKTIVFITHDLDEAVRIGNRIA 238 Query: 241 ILKDGKLIQVGTPREILHSPADEYVDRFVQRRAAVV 276 ILKDG+LIQVGTP+EILHSPADEYVDRFVQRRAAVV Sbjct: 239 ILKDGQLIQVGTPKEILHSPADEYVDRFVQRRAAVV 274 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: 376 Number of extensions: 10 Number of successful extensions: 1 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: 274 Length adjustment: 25 Effective length of query: 251 Effective length of database: 249 Effective search space: 62499 Effective search space used: 62499 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: 47 (22.7 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