Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate PfGW456L13_1692 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= CharProtDB::CH_018185 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1692 Length = 258 Score = 221 bits (562), Expect = 2e-62 Identities = 114/259 (44%), Positives = 158/259 (61%), Gaps = 2/259 (0%) Query: 1 MKKLALSLSLVLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELC 60 MKK L L L+ + ++ FAA + +RIG + Y PF SK +GE+VGFD D+ LC Sbjct: 1 MKKFPLITGLALSLLACSSVFAA-EKTLRIGIEAAYPPFASKTDKGEIVGFDYDIGNALC 59 Query: 61 KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120 ++ +C +VE D LIPSLK KKID +SS++I E R++ + FT K Y SRLV+ Sbjct: 60 AQMKAKCVWVEGEFDGLIPSLKVKKIDMALSSMTINEDRKKSVDFTHKYYFTSSRLVMKD 119 Query: 121 NSDIQPTVASLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAA 180 + + ASLKGK VGV + TT + + +E + PKGI + Y + IY DL AGR+DA Sbjct: 120 GAVVDDQYASLKGKTVGVQRATTTDRYASEVFEPKGINVKRYSNNEEIYMDLAAGRLDAI 179 Query: 181 FQDEVAASEGFLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240 F D + ++ FL P GK Y F GP +KD K G G G+ +RK + EL LN A +R Sbjct: 180 FADTIPLND-FLSMPRGKGYAFVGPELKDPKYVGEGAGIAVRKGNTELVSELNTAIDGIR 238 Query: 241 ADGTYEKLAKKYFDFDVYG 259 A G Y+K+++KYF D+YG Sbjct: 239 ASGEYQKISEKYFKSDIYG 257 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: 176 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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