Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_011840946.1 RSPH17029_RS06720 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000015985.1:WP_011840946.1 Length = 362 Score = 405 bits (1041), Expect = e-118 Identities = 211/354 (59%), Positives = 253/354 (71%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 LEL+ ++MVG HI+PTDL L+ GT+NVLLGPTLAGKTSLMRLMAGLD P+ G + ++ Sbjct: 3 LELQGVSRMVGGRVHIHPTDLALQGGTMNVLLGPTLAGKTSLMRLMAGLDAPSSGRLLWN 62 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G DVTG VQ R VAMVYQQFINYP+++VY NIASP+R+ G+ I+R V + AE+LKL Sbjct: 63 GQDVTGQRVQDRRVAMVYQQFINYPSMSVYENIASPLRLQGRSRTEIERAVGEVAEMLKL 122 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 TP L R PL LSGGQQQR ALARALVK A LVL+DEPLANLDYKLREELR E+PKIF S Sbjct: 123 TPMLRRKPLELSGGQQQRCALARALVKGAGLVLLDEPLANLDYKLREELRLEIPKIFEAS 182 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 GAIFVYATTEP EALLLGG+TATL +GRVTQFGPT +VYR+PV+ TA +F+DPP+N L Sbjct: 183 GAIFVYATTEPEEALLLGGHTATLWEGRVTQFGPTPQVYRQPVDATTARVFSDPPMNFLP 242 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEI 301 VTK+G T P LA + DG F +HL L +G A R +EI Sbjct: 243 VTKTGARLTFGHLANAPAEGALAGLADGRYLAGFRANHLALNRHSGRAVEFSCRLTATEI 302 Query: 302 TGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIAAA 355 TGSE+F+HL + WV L GIHD+ P EV +LD H+ F ++G A A Sbjct: 303 TGSETFLHLAHGSDLWVGLVPGIHDLPPGSEVSVWLDPAHVYLFDAEGALAAPA 356 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: 442 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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 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