Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 348 bits (892), Expect = e-100 Identities = 191/361 (52%), Positives = 241/361 (66%), Gaps = 15/361 (4%) Query: 2 SALEIRNIRKRYGE----VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSG 57 S+L+I I KR+G+ VE L+ +DI + GEFL+L+G SGCGKSTLLNIIAGL EP+ Sbjct: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 Query: 58 GDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDT 117 G+I IG ++V+G+ P+DRDIAMVFQSYALYP LSVA NIGF LEMR++P+ E K + + Sbjct: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 Query: 118 ARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELK 177 A +LQI +LLDR+PSQLSGGQRQRVA+GRAL R PQ+FLFDEPLSNLDAKLR+EMR E+K Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 Query: 178 RLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSP 237 RLHQ T VYVTHDQ+EAMTL +RIAVM+ G ++QL PDE+Y+RPA YVA F+GSP Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 Query: 238 PMNILDAEMTANGLKIEGCE-EVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRL 296 MN+L +T I+G + P P++ N V +G+RPE L + E Sbjct: 243 TMNLLRGAVTGGQFGIQGAALNLAPPPSSAN-------EVLLGVRPEHLVM---QETAPW 292 Query: 297 TASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRS 356 V VVE TGP+ + +T +T V G H FD +S Sbjct: 293 RGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEER 352 Query: 357 L 357 L Sbjct: 353 L 353 Lambda K H 0.320 0.136 0.385 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: 393 Number of extensions: 12 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: 360 Length of database: 355 Length adjustment: 29 Effective length of query: 331 Effective length of database: 326 Effective search space: 107906 Effective search space used: 107906 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