Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000018545.1:WP_015887278.1 Length = 360 Score = 355 bits (910), Expect = e-102 Identities = 189/368 (51%), Positives = 252/368 (68%), Gaps = 8/368 (2%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+ LE+RN+ K YG +TLK+I+++++ GEFL+L+G SGCGKSTL+N IAGL +GG Sbjct: 1 MSALEIRNIRKRYGD--VETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I+IG++ + G PKDRDIAMVFQSYALYP MSV NI FGL++RK+P A+ + V A Sbjct: 59 DILIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LLQIE+LL+RKP QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +HQ LKTT VYVTHDQIEAMTL ++AVM+DG I+Q GTP EIY+ PA +VA F+GSPP Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPP 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MN + +G L G G R V +G+RPE + L AG+ + Sbjct: 239 MNILD-----AEGTGSGLRILGSENTLPLGGAFPNGTTGRRVKVGIRPEALRL-AGDDAT 292 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360 + A V+V E TGP+ ++ ++ + ++ L P + + G T FD + + LFD Sbjct: 293 GGRLTAIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDPE 352 Query: 361 TGERLGTA 368 +G L A Sbjct: 353 SGLSLRMA 360 Lambda K H 0.318 0.135 0.382 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: 405 Number of extensions: 11 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: 386 Length of database: 360 Length adjustment: 30 Effective length of query: 356 Effective length of database: 330 Effective search space: 117480 Effective search space used: 117480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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