Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000018545.1:WP_015887278.1 Length = 360 Score = 363 bits (931), Expect = e-105 Identities = 198/369 (53%), Positives = 255/369 (69%), Gaps = 10/369 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+ LE+RN+ K YG +TLK+I++ ++ GEFL+L+G SGCGKSTL+N IAGL SGG Sbjct: 1 MSALEIRNIRKRYGD--VETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 IL+ + I G PKDRDIAMVFQSYALYP MSV NI FGL++RK+P AE ++ V + Sbjct: 59 DILIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LLQIE+LL RKP QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQ LKTT VYVTHDQIEAMTL ++AVM+DG I+Q GTP +IY+ PA L+VA F+GSPP Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPP 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPL-GMQDAGLEDREVILGIRPEQIILANGEAN 299 MN + G L +L S LPL G G R V +GIRPE + LA +A Sbjct: 239 MNILD---AEGTGSGLRILGSENT---LPLGGAFPNGTTGRRVKVGIRPEALRLAGDDAT 292 Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 G + A V+V E TGP+ ++ + + ++ L P + G T FD A + LFD Sbjct: 293 G-GRLTAIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDP 351 Query: 360 KTGERLGVA 368 ++G L +A Sbjct: 352 ESGLSLRMA 360 Lambda K H 0.319 0.138 0.393 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: 406 Number of extensions: 13 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 ( 7.4 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