Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_924 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_924 Length = 258 Score = 307 bits (787), Expect = 1e-88 Identities = 161/258 (62%), Positives = 189/258 (73%), Gaps = 2/258 (0%) Query: 1 MKKLVLLGALALSVLSLPT-FADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCE 59 MKK L+ LALS+L+ + FA EK L+IGIEAAYPPFASK G IVGFDYDIGNALC Sbjct: 1 MKKFPLITGLALSLLACSSLFAAEKDLRIGIEAAYPPFASKTDKGEIVGFDYDIGNALCA 60 Query: 60 EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAG 119 +MKVKCVWVE EFDGLIP+LKV+KID LSSM+I +DRKKSVDFT+KYY T +RLVMK G Sbjct: 61 QMKVKCVWVEGEFDGLIPSLKVKKIDMALSSMTINEDRKKSVDFTHKYYFTSSRLVMKDG 120 Query: 120 TQVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179 V D A LKGK IGVQR + +R+A EV +P G +K YG+ EIY+D+AAGRLD Sbjct: 121 AVVDDQYASLKGKNIGVQRATTTDRYATEVFEPKGINVKRYGNNEEIYMDLAAGRLDAIF 180 Query: 180 ADATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRA 239 AD L D FL GKG+AFVGP D KY G+G GIAVRKG+ + +N AI IRA Sbjct: 181 ADTIPLSD-FLAMPRGKGYAFVGPELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDEIRA 239 Query: 240 NGKYKQIQDKYFNFDIYG 257 NG+Y++I KYF DIYG Sbjct: 240 NGEYQKISQKYFKSDIYG 257 Lambda K H 0.318 0.138 0.395 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: 241 Number of extensions: 10 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 (21.7 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