Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc01626 SMc01626 ABC transporter permease
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__Smeli:SMc01626 Length = 285 Score = 154 bits (388), Expect = 3e-42 Identities = 82/267 (30%), Positives = 140/267 (52%), Gaps = 10/267 (3%) Query: 17 TIYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFT----------DPSW 66 T+ ++F + PI W+ MSF+ N I PTL NY + T D ++ Sbjct: 17 TLVVVFFMFPIVWIFLMSFQTNETILRIPPSVVFTPTLENYAALITGKLQTASGTLDIAF 76 Query: 67 YNGYINSIIYVVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFF 126 NS++ V + +++ +PAAYAF+R++F G + + F LL+ R APP + LP Sbjct: 77 MRNLGNSVLLSVASVALALVLGVPAAYAFARHKFRGSEDIAFTLLSFRFAPPLLVLLPLT 136 Query: 127 QLYSAFGLIDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKI 186 Q + GL +T+ + + L +PL +WI+ G+ + +++ I G+S+ F KI Sbjct: 137 QYFQWLGLSNTYFGLIWIYQLICLPLILWIVRGYFEDISADVEYAYRIAGHSWFSTFRKI 196 Query: 187 FIPLIASGVGVAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAG 246 +PL G+ AG F+F+W + A L + +P++ V+ASG+ +G +AAA Sbjct: 197 ALPLAGPGIAAAGLLAFIFAWNNFVFALVLASADKQPVTVGALAFVTASGIQYGQIAAAI 256 Query: 247 VLTIIPGALVIYFVRNYIAKGFALGRV 273 VL+I P + + + Y+ +G +LG V Sbjct: 257 VLSITPTLALALYAQRYLVEGLSLGAV 283 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: 285 Number of extensions: 12 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: 273 Length of database: 285 Length adjustment: 26 Effective length of query: 247 Effective length of database: 259 Effective search space: 63973 Effective search space used: 63973 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: 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