Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate Pf6N2E2_5395 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= CharProtDB::CH_014295 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5395 Length = 244 Score = 209 bits (533), Expect = 3e-59 Identities = 103/243 (42%), Positives = 150/243 (61%), Gaps = 1/243 (0%) Query: 17 ATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDA 76 A+++ A + +RIG + Y PF SK S+G++VGFD D+ LC ++ +C ++E D Sbjct: 2 ASSSLFAAEKTLRIGIEAAYPPFASKTSEGKIVGFDYDIGNALCAQMQVKCEWIEGEFDG 61 Query: 77 LIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRV 136 LIP+LK KKID +SS++ITE+R++ + FT K Y SRLV+ + + + +LKGK V Sbjct: 62 LIPALKVKKIDLALSSMTITEERKKSVDFTHKYYFTSSRLVMKEGAVVDDQYVNLKGKTV 121 Query: 137 GVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPV 196 GV + TT + + E PKG+ + Y + IY DL +GR+DA F D + E FL P Sbjct: 122 GVQRATTTDRYATEVLEPKGVSVKRYSNNEEIYMDLASGRLDAIFADTIPL-EDFLSMPR 180 Query: 197 GKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFD 256 GK Y F GP +KD K G G G+ +RK + +L LNKA +RA+G Y+K+ KYF D Sbjct: 181 GKGYAFVGPELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDGIRANGEYQKIQGKYFKSD 240 Query: 257 VYG 259 +YG Sbjct: 241 IYG 243 Lambda K H 0.315 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: 166 Number of extensions: 5 Number of successful extensions: 2 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: 244 Length adjustment: 24 Effective length of query: 236 Effective length of database: 220 Effective search space: 51920 Effective search space used: 51920 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: 46 (22.3 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