Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_011842475.1 RSPH17029_RS18135 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >NCBI__GCF_000015985.1:WP_011842475.1 Length = 370 Score = 245 bits (626), Expect = 1e-69 Identities = 145/371 (39%), Positives = 208/371 (56%), Gaps = 21/371 (5%) Query: 11 ASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSG 70 A+ A+ P A +WLR NLF++ + LT++ ++L + W ++A + Sbjct: 10 AAPAAAAYDPDARLSAPAWLRANLFSSVWQSLLTLVVAVVLIRFFWFVLDWGVVNAVFYT 69 Query: 71 GGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVP 130 VC + GACWA + K LFG YP DE WR L+ +++ +V Sbjct: 70 TDPDVCRAAT----------GACWAVIVEKHRPMLFGLYPYDEHWRLVLMMAVYLGTVVL 119 Query: 131 MLIPRIPYKGLNALLLLVALPILSA----ILLPGGWFGLTYVETPLWGGLMVTLVLSFVG 186 L PR L LV L I+S+ IL+ GG GL YV T WGGL +T++L Sbjct: 120 SLWPRCWN-----LRFLVPLWIVSSLSIGILMFGGVLGLRYVPTSEWGGLPLTMLLFTGT 174 Query: 187 IAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFD 246 + + +P+ +LLALGRR+ +PV + + VFIE +RGVPLIT+LF+A + PLFLP GV + Sbjct: 175 VLIGMPVAVLLALGRRAPLPVARGVSVVFIEALRGVPLITILFVAVNVFPLFLPAGVEVN 234 Query: 247 KFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVI 306 K LR +G+++F + Y AEV+RGGLQAIP GQYE A SL LS+WQ I+LPQAL++ + Sbjct: 235 KLLRITVGIAIFFACYQAEVIRGGLQAIPTGQYEAAASLSLSYWQTTRRIILPQALRISL 294 Query: 307 PGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCF 366 P I N I K+TS V IIG+FD+L D W + +F V+ F + Sbjct: 295 PAITNHIIAAMKNTSFVIIIGLFDILTATTAVMQDPLWRKFY--IEAYLFVAAVYLFFGY 352 Query: 367 GMSRYSGFMER 377 +S Y+ +E+ Sbjct: 353 ALSLYARQVEK 363 Lambda K H 0.329 0.144 0.454 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: 440 Number of extensions: 24 Number of successful extensions: 3 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: 384 Length of database: 370 Length adjustment: 30 Effective length of query: 354 Effective length of database: 340 Effective search space: 120360 Effective search space used: 120360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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