Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc02519 SMc02519 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Smeli:SMc02519 Length = 356 Score = 523 bits (1348), Expect = e-153 Identities = 258/352 (73%), Positives = 296/352 (84%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 MLE++ +K+VG + HI+PTDLVLERGTLNVLLGPTL+GKTSLMRLMAGLD+P GSI F Sbjct: 1 MLEMKKISKVVGGETHIHPTDLVLERGTLNVLLGPTLSGKTSLMRLMAGLDKPASGSIFF 60 Query: 61 DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLK 120 DG DVTG+PVQKR+VAMVYQQFINYPA+TVY NIASPMRI D AT+DREVRKAAELLK Sbjct: 61 DGADVTGVPVQKRSVAMVYQQFINYPAMTVYENIASPMRIKRADGATVDREVRKAAELLK 120 Query: 121 LTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQ 180 LTPYLDRTPLNLSGGQQQRTALARA+VKNA LVL+DEPLANLDYKLREELREELPKIFA Sbjct: 121 LTPYLDRTPLNLSGGQQQRTALARAIVKNADLVLLDEPLANLDYKLREELREELPKIFAA 180 Query: 181 SGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTL 240 SGAIFVYATTEPSEALLLGGNTATL++GR+TQFG TI+VYRRPV++ TA FADPPLNT+ Sbjct: 181 SGAIFVYATTEPSEALLLGGNTATLSEGRITQFGRTIDVYRRPVDIVTARTFADPPLNTI 240 Query: 241 DVTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSE 300 + K+G+ F + VPSHL + DGP T+AF PHHL G L +T +SE Sbjct: 241 GLLKTGSQFVLEGKPVLAVPSHLRSLADGPCTVAFQPHHLSFGQPDGSDEPLTVKTAISE 300 Query: 301 ITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAI 352 ITGSESF+H+ + G RWVMLA GIH+I+PD ++ F+DTRHLMAFG DGRA+ Sbjct: 301 ITGSESFIHVAFAGARWVMLAPGIHEIEPDAMLKVFVDTRHLMAFGPDGRAV 352 Lambda K H 0.319 0.136 0.392 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: 532 Number of extensions: 14 Number of successful extensions: 1 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: 358 Length of database: 356 Length adjustment: 29 Effective length of query: 329 Effective length of database: 327 Effective search space: 107583 Effective search space used: 107583 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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