Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate PP_3593 PP_3593 Amino acid ABC transporter, periplasmic binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Putida:PP_3593 Length = 250 Score = 178 bits (451), Expect = 1e-49 Identities = 103/255 (40%), Positives = 146/255 (57%), Gaps = 9/255 (3%) Query: 2 KKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEM 61 K + LLGA AL + A + L+ E AYPPF D + GFD DI +ALCE+M Sbjct: 3 KSMALLGACALLLAGA---ASAETLRFATEGAYPPFNYVDADNKLHGFDVDITHALCEQM 59 Query: 62 KVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTA 121 KV+C V Q+++G+IPAL RK DAI++SM TE+R+K + FT+ YY TP + + + Sbjct: 60 KVECTLVAQDWEGIIPALMARKYDAIVASMIDTEERRKKIAFTDHYYRTPLTVAVAKDSK 119 Query: 122 VSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVAD 181 + + G +G Q S +A +V GA++K Y + +E D+AAGRLDG +AD Sbjct: 120 IDSAQTDFVGYTVGAQSSSTQAIYAEDVYGKAGADVKLYPTMDEANADLAAGRLDGVIAD 179 Query: 182 ATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGD-ALKDKINTAIAAIRENG 240 L + ++ + G +G DV IAVRK D AL+ ++NTA+ I NG Sbjct: 180 KFPLHE-WMNKNGGDCCKILG----DVADTKADAAIAVRKDDEALRQRLNTALQQIVANG 234 Query: 241 KYKQIQDKYFAFDIY 255 Y++I KYFAFDIY Sbjct: 235 TYQKIASKYFAFDIY 249 Lambda K H 0.318 0.138 0.394 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: 161 Number of extensions: 8 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: 257 Length of database: 250 Length adjustment: 24 Effective length of query: 233 Effective length of database: 226 Effective search space: 52658 Effective search space used: 52658 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