Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate AO353_28165 AO353_28165 ABC transporter substrate-binding protein
Query= CharProtDB::CH_018185 (260 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28165 Length = 259 Score = 249 bits (635), Expect = 5e-71 Identities = 116/249 (46%), Positives = 165/249 (66%) Query: 11 VLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELCKRINTQCTFV 70 V+ F + Q I+ G DP+Y PFE K G L GFDIDL LC ++ +C +V Sbjct: 10 VMLFGLIITPLSQAQQVIKFGVDPSYPPFEQKQPDGSLSGFDIDLGNALCAELSVKCIWV 69 Query: 71 ENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVAS 130 E D ++P+LKAKK DAI+S+ S TE R+Q++ F+ K+Y A S LV KN+ + PT AS Sbjct: 70 EQNFDGMVPALKAKKFDAILSAFSATEARRQQVDFSHKIYTAPSSLVARKNAGLLPTAAS 129 Query: 131 LKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEG 190 LKGK VGV+QG+ QE+F W +G+EI+SYQ QD ++SDL GR++AAFQ V A G Sbjct: 130 LKGKSVGVVQGSLQESFAKSEWGSQGVEILSYQTQDQVFSDLINGRLEAAFQASVQADIG 189 Query: 191 FLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAK 250 L++P G+ + F G + D+++ G G +G+RK + +LRE LN A A +R G Y+++AK Sbjct: 190 LLQKPQGQGFAFAGDPITDKRIIGDGVAIGVRKNEPDLREQLNTAIAGIRQSGQYDRIAK 249 Query: 251 KYFDFDVYG 259 +YF+FD+YG Sbjct: 250 QYFNFDIYG 258 Lambda K H 0.316 0.133 0.372 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: 187 Number of extensions: 3 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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