Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q88P35 (384 letters) >NCBI__GCF_000018545.1:WP_015887278.1 Length = 360 Score = 366 bits (939), Expect = e-106 Identities = 198/369 (53%), Positives = 256/369 (69%), Gaps = 10/369 (2%) Query: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 M+ LE+RN+ K YG +TLK I ++++ GEFL+L+G SGCGKSTL+N IAGL + +GG Sbjct: 1 MSALEIRNIRKRYGD--VETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 Query: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 ILI E+ + G PKDRDIAMVFQSYALYP MSV NI FGL++RK+P A ++ V A Sbjct: 59 DILIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTA 118 Query: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LLQIE+LL RKP+QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 +HQ LKTT VYVTHDQIEAMTL ++AVM+DG I+Q GTP +IY+ PA +VA F+GSPP Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPP 238 Query: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEA-ADALEGREIILGIRPEQIALGAADGN 299 MN + A G L +L S LPLG A + GR + +GIRPE + L D Sbjct: 239 MNILD---AEGTGSGLRILGSENT---LPLGGAFPNGTTGRRVKVGIRPEALRLAGDDAT 292 Query: 300 GLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDA 359 G + A V+V E TGP+L++ + + ++ L P + G T FD A + LFD Sbjct: 293 G-GRLTAIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDP 351 Query: 360 ANGERLHLA 368 +G L +A Sbjct: 352 ESGLSLRMA 360 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: 413 Number of extensions: 12 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 Apr 09 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