Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 305 bits (780), Expect = 1e-87 Identities = 178/359 (49%), Positives = 228/359 (63%), Gaps = 37/359 (10%) Query: 1 MTGLLLKDIRKSYG----AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEIT 56 M L L++I K YG A VIHG++ ++K+GEFVV VGPSGCGKSTLLRM+AGLEEI+ Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 GGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRG 116 GG++ I VND+ P++R IAMVFQ+YALYPHMT ++NMA+G++IA+ K+EI RV Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 117 AADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEI 176 AA +L+L L+R P+ LSGGQRQRVA+GRAI R P+VFLFDEPLSNLDA LR TR+EI Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 177 AKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIG 236 KL + T ++VTHDQVEAMTLA R++V++AG++EQ G P E+Y PA FVA FIG Sbjct: 181 QKLHRELG-ITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIG 239 Query: 237 SPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDF 296 SP MN++ A G Q L G+RPE L V Sbjct: 240 SPPMNLLK---NAPGAQPGTIL-----------------------GIRPEHLDVRSEG-- 271 Query: 297 LFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKA-KLHLFD 354 + TV VE LG L+Y G + E +I ++ D V +A +LH FD Sbjct: 272 -WAVTVETVELLGAERLIY--GRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFD 327 Lambda K H 0.320 0.137 0.387 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: 346 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: 362 Length of database: 334 Length adjustment: 29 Effective length of query: 333 Effective length of database: 305 Effective search space: 101565 Effective search space used: 101565 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 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