Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMa1341 SMa1341 ABC transporter permease
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__Smeli:SMa1341 Length = 319 Score = 159 bits (402), Expect = 7e-44 Identities = 85/296 (28%), Positives = 144/296 (48%), Gaps = 40/296 (13%) Query: 18 IYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPS------------ 65 + + + PIYW+ + +FK + T P + + +FT S Sbjct: 22 VITLLFLAPIYWITSTAFKPRNLATTIPPTVIFEPEISPFVKLFTKRSQLRSAPEPEDYA 81 Query: 66 ---WY-------------------------NGYINSIIYVVMNTVISVAAALPAAYAFSR 97 W+ N ++NS+I + +TV++VA AY FSR Sbjct: 82 AAPWWERLVFDGGEKVVRSGRGQVQLSGYPNRFMNSLIVAITSTVLAVAMGTFTAYGFSR 141 Query: 98 YRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFGLIDTHIAVALAHCLFNVPLAVWIL 157 ++ G+ L F++L+ RM PP V A+P F +Y A GL DTH + + + FN+ +VW++ Sbjct: 142 FKVKGEADLLFFILSTRMLPPVVVAIPMFLMYRAVGLNDTHWGLIILYTAFNLSFSVWLM 201 Query: 158 EGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIASGVGVAGFFCFMFSWVELLLARTLT 217 +GF+ +PKE +E A +DGY+ F KI +P A+G+ FCF+ +W E A +T Sbjct: 202 KGFIDEIPKEYEEAALVDGYTRLEAFFKIVLPEAATGIAATAVFCFITAWNEYAFALIMT 261 Query: 218 TTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPGALVIYFVRNYIAKGFALGRV 273 A+ + V + DW V+AA L ++P A+ + +RN++ +G + G + Sbjct: 262 NRRAQTAPPFIPSQVGSGLPDWTVIAAGTFLFLLPVAIFTFLLRNHLLRGMSFGAI 317 Lambda K H 0.330 0.142 0.456 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: 286 Number of extensions: 16 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: 2 Length of query: 273 Length of database: 319 Length adjustment: 26 Effective length of query: 247 Effective length of database: 293 Effective search space: 72371 Effective search space used: 72371 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: 48 (23.1 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