Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 308 bits (789), Expect = 1e-88 Identities = 165/344 (47%), Positives = 214/344 (62%), Gaps = 24/344 (6%) Query: 4 IKLESVTKNFGP----VEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGT 59 + + + K FG VEV+ +D+ + GEF + VGPSGCGKSTLL +IAGL++ T G Sbjct: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 Query: 60 IRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAA 119 IRI G++ +PP R +AMVFQSYALYP +SV NI F ++M +P E+++RID AA Sbjct: 65 IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAA 124 Query: 120 ALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISEL 179 L ++ LDRRP QLSGGQRQRVA+GRA+ R+P FLFDEPLSNLDA LRV MR EI L Sbjct: 125 MLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRL 184 Query: 180 HKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKM 239 H+ T +YVTHDQVEAMT+ +I V++ GV++Q+G+P E+Y P N +VA FIGSP M Sbjct: 185 HQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTM 244 Query: 240 NLLTG-----------------PQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLG 282 NLL G P + N +G+RPEHL + ET W G + V E G Sbjct: 245 NLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQET-APWRGRVSVVEPTG 303 Query: 283 SDTFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRF 326 DT+ V D +T+R + + GE V L H H F Sbjct: 304 PDTY--VMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWF 345 Lambda K H 0.320 0.138 0.400 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: 333 Number of extensions: 15 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: 334 Length of database: 355 Length adjustment: 29 Effective length of query: 305 Effective length of database: 326 Effective search space: 99430 Effective search space used: 99430 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