Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate WP_008812970.1 M988_RS12725 arginine ABC transporter substrate-binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >NCBI__GCF_001655005.1:WP_008812970.1 Length = 243 Score = 171 bits (434), Expect = 1e-47 Identities = 98/251 (39%), Positives = 150/251 (59%), Gaps = 10/251 (3%) Query: 1 MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 MKK+++ A L+ +S+ A E ++ EA+YPPF + + GFD D+ NA+C++ Sbjct: 1 MKKIII--ATVLAGISVSASAAET-IRFAAEASYPPFEFMDANNQMQGFDIDLANAICKQ 57 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGT 120 MK C + Q FD LIP+LK ++IDA++S M IT +R+K V FT YY+ A + + G Sbjct: 58 MKATCTFTNQSFDSLIPSLKFKRIDAVISGMDITPERQKQVAFTAPYYDNSALFIAEKG- 116 Query: 121 QVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180 +V+D +A LKGK++G+Q GS H ++ +E K PY S LD+ GRLD Sbjct: 117 KVAD-IAALKGKRVGMQNGSTHQKYLQE--KHPEITPVPYDSYQNAILDLKNGRLDAVFG 173 Query: 181 DATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRAN 240 D ++++ +LK +S VG TD YFG G+GIAVR+ + L++ NAA+ ++ + Sbjct: 174 DTAVVNE-WLKQNS--ALTAVGDKVTDPNYFGTGLGIAVRQNNAELLNQFNAALNQLKQD 230 Query: 241 GKYKQIQDKYF 251 G YK I K+F Sbjct: 231 GTYKTIYSKWF 241 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: 181 Number of extensions: 6 Number of successful extensions: 4 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: 243 Length adjustment: 24 Effective length of query: 234 Effective length of database: 219 Effective search space: 51246 Effective search space used: 51246 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 24 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