Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25875 AZOBR_RS25875 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__azobra:AZOBR_RS25875 Length = 367 Score = 400 bits (1029), Expect = e-116 Identities = 215/358 (60%), Positives = 255/358 (71%), Gaps = 5/358 (1%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 L L ++ VG H+ L LERG+LNVLLGPTL+GKTSLMRLMAGLD P+ G + D Sbjct: 3 LVLDKVSRHVGGHVHLENVSLSLERGSLNVLLGPTLSGKTSLMRLMAGLDVPSAGRVLVD 62 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G DVTG V++R+VAMVYQQFINYP+LTVY NIASP+R++ + IDR+VR+AA LLKL Sbjct: 63 GADVTGRHVRERSVAMVYQQFINYPSLTVYENIASPLRVARRPKDEIDRKVREAARLLKL 122 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 YL RTP LSGGQQQRTA+ARALVK A LVL+DEPLANLDYKLREELREELPKIFA + Sbjct: 123 EAYLQRTPQQLSGGQQQRTAIARALVKEAQLVLLDEPLANLDYKLREELREELPKIFAAT 182 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 GA+FVYATTEP+EALLL GNTATL +GR+ QFG T +VYRRP NL +A +F+DPPLNT+ Sbjct: 183 GAVFVYATTEPAEALLLRGNTATLWEGRLAQFGRTPDVYRRPANLTSARVFSDPPLNTMR 242 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEI 301 V K G +G P LA +PD TI F HL L DA L VSEI Sbjct: 243 VHKRGLQIVLATGEHGPARGVLAELPDDDYTIGFRADHLHLTRPHADAIALSGAVAVSEI 302 Query: 302 TGSESFVHLEY---DG--VRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIAA 354 TGSESFVH++ DG RWV + G+ +++P +E F+D R L FG DGR AA Sbjct: 303 TGSESFVHIDLPRTDGGADRWVAVTRGVLEVEPGERIECFIDPRRLFVFGHDGRLAAA 360 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: 430 Number of extensions: 13 Number of successful extensions: 2 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: 367 Length adjustment: 29 Effective length of query: 329 Effective length of database: 338 Effective search space: 111202 Effective search space used: 111202 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