Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 303 bits (776), Expect = 5e-87 Identities = 163/367 (44%), Positives = 236/367 (64%), Gaps = 37/367 (10%) Query: 1 MATLELRNVNKTYGAG--LPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETIT 58 MA+L LRN+ K YG G + + +K+GEF+++VGPSGCGKSTL+ +AGLE I+ Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 GGAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVAR 118 GG + IGD+ V+ + P RDIAMVFQ+YALYP M+ EN+ +GLKI K+P+ +I A V + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 119 VAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 AK+L++ HLL RKP +LSGGQ+QRVAMGRA+ R+P+++LFDEPLSNLDAKLR + R E+ Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGS 238 + +H+ L T+++VTHDQ+EAMTL ++ VM G ++QFGTP+E+Y+ PA FVASFIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 239 PPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298 PPMN + + G ILG+RPE + + + EG Sbjct: 241 PPMNLLKNAPGAQPG----------------------------TILGIRPEHLDVRS-EG 271 Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDV-APQVGETLTLQFDPSKVLLF 357 + + V+ E G + L++ ++N +V R+ +P+ + +Q ++ F Sbjct: 272 WAVT-----VETVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAF 326 Query: 358 DANTGER 364 DA TG+R Sbjct: 327 DAATGKR 333 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: 361 Number of extensions: 14 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 ( 7.3 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