Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate Pf1N1B4_5844 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= CharProtDB::CH_014295 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5844 Length = 259 Score = 226 bits (576), Expect = 4e-64 Identities = 114/259 (44%), Positives = 163/259 (62%), Gaps = 1/259 (0%) Query: 1 MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELC 60 MKK V+ +L L+ S TA A + IR+G + Y PF KN G+L GFD+D+ LC Sbjct: 1 MKKRVMFGALALSMLSLTA-MADDAKPIRLGIEAGYPPFSMKNPDGKLTGFDVDIGDALC 59 Query: 61 KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120 +++ +CT+VE D LIP+LK KKIDAI+SS++IT+ R++ + FT K Y +R V+ + Sbjct: 60 EQMKVKCTWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARFVMKE 119 Query: 121 NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAA 180 +D++ + LKGK+VGVL+ +T + F E P GI +V Y Q D+ AGR+DA Sbjct: 120 GTDVKDPLTELKGKKVGVLRASTHDRFATEVLVPAGINLVRYGSQQEANLDMVAGRLDAM 179 Query: 181 FQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240 D V +GFLK GK + F GP+ +D K FG G G+ +RK D EL + N A E+R Sbjct: 180 LADSVNLDDGFLKTDAGKGFAFVGPTYEDAKYFGGGAGIAVRKGDKELADKFNTAITEIR 239 Query: 241 ADGTYEKLAKKYFDFDVYG 259 A+G Y+++ KYF+FDVYG Sbjct: 240 ANGKYKQVQDKYFNFDVYG 258 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: 178 Number of extensions: 6 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