Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 168 bits (426), Expect = 1e-46 Identities = 88/226 (38%), Positives = 140/226 (61%), Gaps = 10/226 (4%) Query: 48 VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107 +N ++L I +GE+ ++G SG GK++L+R L P SG+I+ GED+ + R+ Sbjct: 18 LNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVFHGEDV------SSRDV 71 Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGE----SKQVCAERALHWINTVGLKGYEN 163 R + VFQ + L H +V +NVA+GL+++ + S+ V AE+ + V L + Sbjct: 72 RDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELLGLVQLDWLAD 131 Query: 164 KYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIV 223 +YP QLSGG RQR+ LARALA + ++L+DE F ALD +R E++ L L + +H T V Sbjct: 132 RYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLARLHEDVHLTSV 191 Query: 224 FITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 F+THD +EA+ + +RI ++ G + Q+GTP E+ +PA E+V F+ Sbjct: 192 FVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFL 237 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: 213 Number of extensions: 17 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: 334 Length adjustment: 27 Effective length of query: 249 Effective length of database: 307 Effective search space: 76443 Effective search space used: 76443 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