Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate SM_b21216 SM_b21216 sugar ABC transporter ATP-binding protein
Query= TCDB::Q88P35 (384 letters) >FitnessBrowser__Smeli:SM_b21216 Length = 360 Score = 357 bits (915), Expect = e-103 Identities = 187/367 (50%), Positives = 250/367 (68%), Gaps = 8/367 (2%) Query: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 M+ LE+RN+ K YG +TLK I ++++ GEFL+L+G SGCGKSTL+N IAGL + +GG Sbjct: 1 MSALEIRNIRKRYGE--VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 Query: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 ILI E+ V G+ PKDRDIAMVFQSYALYP +SV NI FGL++R++PQA D+ V A Sbjct: 59 DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118 Query: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LLQIE+LL RKP+QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 +HQ L+TT VYVTHDQIEAMTL ++AVM+DG I+Q P ++Y+ PA +VA F+GSPP Sbjct: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 Query: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGNG 300 MN + + + ++ + LP A GR + +GIRPE + L A G+ Sbjct: 239 MNILDAEMTANGLK----IEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAA--GSE 292 Query: 301 LPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDAA 360 + A V+V E TGP+L+ T+ ++ L P A +G FD + LFD Sbjct: 293 AQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPE 352 Query: 361 NGERLHL 367 +G L + Sbjct: 353 SGRSLRM 359 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: 387 Number of extensions: 10 Number of successful extensions: 4 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: 360 Length adjustment: 30 Effective length of query: 354 Effective length of database: 330 Effective search space: 116820 Effective search space used: 116820 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 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