Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 295 bits (756), Expect = 1e-84 Identities = 160/368 (43%), Positives = 230/368 (62%), Gaps = 39/368 (10%) Query: 1 MATLELRNVNKTYG--PGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETIS 58 MA+L LRN+ K YG P + + ++ DGEF+++VGPSGCGKSTL+ +AGLE IS Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 GGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVAR 118 GG + + D ++ + P RDIAMVFQ+YALYP M+ +N+A+GLKI K+P EI V + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 +K+L++ HLL RKP +LSGGQ+QRVAMGRA+ R+P+++LFDEPLSNLDAKLR + R E+ Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238 + +H+ L T+++VTHDQ+EAMTL ++ VM G ++QFGTP+++Y+ PA FVASFIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 239 PPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI-ILANGE 297 PPMN +++A ILGIRPE + + + G Sbjct: 241 PPMNL----------------------------LKNAPGAQPGTILGIRPEHLDVRSEGW 272 Query: 298 ANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDV-APAVGETLTLQFDPAKVLL 356 A V+ E G + L++ +N +V R+ +P + +Q ++ Sbjct: 273 A-------VTVETVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHA 325 Query: 357 FDAKTGER 364 FDA TG+R Sbjct: 326 FDAATGKR 333 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: 378 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: 386 Length of database: 334 Length adjustment: 29 Effective length of query: 357 Effective length of database: 305 Effective search space: 108885 Effective search space used: 108885 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: 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