Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 304 bits (779), Expect = 2e-87 Identities = 170/366 (46%), Positives = 229/366 (62%), Gaps = 14/366 (3%) Query: 3 TLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAI 62 ++E+R+++ +G L + L I++GEFL+L+G SGCGKSTL+NCIAGL I+ G I Sbjct: 7 SVEIRDLDLHFGE--LQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQI 64 Query: 63 MIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKL 122 I Q+V+ P +R I MVFQSYALYP M+V N+ FGLK ++P+A+I VAR A++ Sbjct: 65 FIQGQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEV 124 Query: 123 LQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMH 182 LQIE LL RKP LSGGQ+QRVA+GRAL R ++LFDEPLSNLDAKLR ++R E+K +H Sbjct: 125 LQIEPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLH 184 Query: 183 QRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMN 242 Q+L T +YVTHDQ+EAMTL D++A+MK G I Q +P EIYN P N +VA FIGSP MN Sbjct: 185 QQLANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMN 244 Query: 243 FVPLRLQRKDGRLV-ALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSA 301 + +G L+ + +G + G ++G+RPE I+ GE + Sbjct: 245 LI-------EGVLIDGVFHAGSLALPMQRYDYRNGPHHGAAVIGIRPEHIL--TGEQITR 295 Query: 302 SSIRAEVQV--TEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 + AEV V E G DTLV+ + R+ G+ L + FD + LFD Sbjct: 296 ADATAEVLVDLVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDP 355 Query: 360 NTGERL 365 NT RL Sbjct: 356 NTEARL 361 Lambda K H 0.318 0.135 0.382 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: 378 Number of extensions: 14 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: 386 Length of database: 361 Length adjustment: 30 Effective length of query: 356 Effective length of database: 331 Effective search space: 117836 Effective search space used: 117836 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: 50 (23.9 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