Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 320 bits (820), Expect = 4e-92 Identities = 183/360 (50%), Positives = 236/360 (65%), Gaps = 18/360 (5%) Query: 3 ALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 ++EIR++ +GE++ L +++ +E GEFLVLLGSSGCGKSTLLN IAGL + S G I I Sbjct: 7 SVEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFI 66 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQ 122 ++V P +R I MVFQSYALYP ++V N+ FGL+ R+P+AE K V A +LQ Sbjct: 67 QGQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQ 126 Query: 123 IENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQM 182 IE LL RKP+ LSGGQRQRVAIGRALVR+ VFLFDEPLSNLDAKLR ++R ELKRLHQ Sbjct: 127 IEPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQ 186 Query: 183 LRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNIL 242 L T++YVTHDQ+EAMTLA RIA+M+ GRI QL++PDE+Y+RP LYVAGF+GSP MN++ Sbjct: 187 LANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLI 246 Query: 243 DAEMTANGLKIEGCEEV--LPLPAA---FNGAAWAGRRVKVGIRPEALRLAAGSEAQRLT 297 + G+ I+G L LP + G V +GIRPE + G + R Sbjct: 247 E------GVLIDGVFHAGSLALPMQRYDYRNGPHHGAAV-IGIRPE--HILTGEQITRAD 297 Query: 298 ASVEV----VELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPES 353 A+ EV VE G + + AT G+Q + + + V G FD LFDP + Sbjct: 298 ATAEVLVDLVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNT 357 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: 391 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: 361 Length adjustment: 29 Effective length of query: 331 Effective length of database: 332 Effective search space: 109892 Effective search space used: 109892 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