Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate 5210738 Shew_3166 extracellular solute-binding protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__PV4:5210738 Length = 242 Score = 90.5 bits (223), Expect = 3e-23 Identities = 71/251 (28%), Positives = 113/251 (45%), Gaps = 15/251 (5%) Query: 2 KKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPF--ASKAPDGSIVGFDYDIGNALCE 59 K ++L G AL +LS ++ L +G AA+PPF ++GFD D+ + E Sbjct: 3 KSILLAGFTALLLLS-GCGKEQDYLVVGTNAAFPPFEYVGGVSGDQVMGFDIDLARKVAE 61 Query: 60 EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAG 119 + +FD LI AL KID I S M+IT +R+ SVDF+ YY +++ Sbjct: 62 DAGKTLKVENMKFDSLIVALNAGKIDMIASGMTITPERQASVDFSEPYYEATQVVLVNKQ 121 Query: 120 TQVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179 +LA+L GK VQ GS A+ + K + + + E +++ G++D + Sbjct: 122 DDSIHSLADLTGKHFAVQLGST----ADMMAKKYTQSVTAFNTGFEAIMELKNGKVDLVL 177 Query: 180 ADATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRA 239 D+ + K K + F E Y G AV K L IN + ++ Sbjct: 178 FDSEPAANYLAKNPELK---LISLDFPPEFY-----GFAVAKSQPELLASINKTLATMKQ 229 Query: 240 NGKYKQIQDKY 250 NG+Y + K+ Sbjct: 230 NGEYDALLAKH 240 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: 141 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 258 Length of database: 242 Length adjustment: 24 Effective length of query: 234 Effective length of database: 218 Effective search space: 51012 Effective search space used: 51012 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: 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