Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 200 bits (508), Expect = 6e-56 Identities = 124/330 (37%), Positives = 181/330 (54%), Gaps = 8/330 (2%) Query: 18 LYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMPVRDRNVA 77 L + + + G +L+G + GK++L+ I+AGLD PT G + + GK+V GMP RDR++A Sbjct: 24 LRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDIA 83 Query: 78 MVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHIDMFLDRYPAELSGGQ 135 MV+Q + YP++ VA NI L++R + R+ E+A+ L I LDR P++LSGGQ Sbjct: 84 MVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGGQ 143 Query: 136 QQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGEAL 195 +QRVA+ RALA+ L L DEPL NLD KLR E+R E+ +L A T VY T + EA+ Sbjct: 144 RQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEAM 203 Query: 196 LLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATAQGVRLQGGAE 255 LG AV+ G + Q G E+++ P + VA P MNL+ + T +QG A Sbjct: 204 TLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVTGGQFGIQGAAL 263 Query: 256 LTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEISGSDTFVHASTPWGDL 315 P P ++A + +GVR L + G V + E +G DT+V T G + Sbjct: 264 NLAPPP---SSANEVLLGVRPEHLVMQE---TAPWRGRVSVVEPTGPDTYVMVDTAAGSV 317 Query: 316 VAQLTGVHYFELGTAITLHLDPAQAYVFGA 345 + + G + L L PA A+ F A Sbjct: 318 TLRTDAQTRVQPGEHVGLALAPAHAHWFDA 347 Lambda K H 0.318 0.133 0.375 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: 295 Number of extensions: 13 Number of successful extensions: 3 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: 363 Length of database: 355 Length adjustment: 29 Effective length of query: 334 Effective length of database: 326 Effective search space: 108884 Effective search space used: 108884 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