Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_091524012.1 BM253_RS11210 ABC transporter ATP-binding protein
Query= TCDB::Q88P35 (384 letters) >NCBI__GCF_900115115.1:WP_091524012.1 Length = 312 Score = 117 bits (294), Expect = 3e-31 Identities = 89/334 (26%), Positives = 160/334 (47%), Gaps = 49/334 (14%) Query: 4 LELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAIL 63 L++ ++ +Y + L D+ +K G L+G SG GKSTL+ + GL G+I Sbjct: 2 LQVNQLSFSYNNS--QILSDVSFQLKAGNSYALIGASGSGKSTLLKLVYGLLDADSGSIF 59 Query: 64 IDEQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARV 119 +E+ + G + P + + Q + L P +SV EN+ R L + E+ RV Sbjct: 60 WNEKQILGPAYHLVPGMDYMKYLAQDFDLMPFVSVAENVG-----RFLSNFYLKEKKNRV 114 Query: 120 AKLLQIEHLLAR---KPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 +LL++ + K LSGGQ QR A+ R LA P+ L DEP S++D + E+ T Sbjct: 115 DELLELVDMTEFANVKAKFLSGGQMQRTALARVLALEPEFLLLDEPFSHIDPFQKRELAT 174 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFI 236 ++ ++ T ++ +H EA+ D++ V+++GI+ + PQ IY +P N+++A Sbjct: 175 QLFQYCKQKGITILFTSHTPEEALMYADEILVLQNGILIEKDIPQNIYENPKNEYIARLT 234 Query: 237 GSPPMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAA 296 G +N IP +L + E +L +RP ++ + + Sbjct: 235 GD--VNIIPANY-----------------FDLNINE----------VLYVRPHELQI-SN 264 Query: 297 DGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVC 330 DG+ +++ + TG + L++ LN ++C Sbjct: 265 DGS-----EVKIKHSYFTGKNYLIYAVLNDLEIC 293 Lambda K H 0.320 0.137 0.391 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: 233 Number of extensions: 11 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: 384 Length of database: 312 Length adjustment: 29 Effective length of query: 355 Effective length of database: 283 Effective search space: 100465 Effective search space used: 100465 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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