Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 211 bits (536), Expect = 3e-59 Identities = 126/320 (39%), Positives = 193/320 (60%), Gaps = 15/320 (4%) Query: 27 LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVF 86 L ++ E G LLG SGCGK+T+LN ++GLL S G++ G++VT A P ER I VF Sbjct: 26 LNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFIQGQNVTWAEPSERGIGMVF 85 Query: 87 QFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQK 146 Q +Y MTV NL+F L+N ++P+ +I +RV AE+L++ L ++ A L+ +Q+ Sbjct: 86 QSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQIEPLLKRKPAALSGGQRQR 145 Query: 147 ISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTF 206 +++GR LVR DV LFDEPL+ +D L+ LR +LK++H +L T+IYVTHDQVEA+T Sbjct: 146 VAIGRALVR-DVDVFLFDEPLSNLDAKLRADLRVELKRLHQQLANTMIYVTHDQVEAMTL 204 Query: 207 ADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGH--RL 264 AD++ +M G+ +Q+ S D ++ RP + +V FIGSP MN + +G + H L Sbjct: 205 ADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLI----EGVLIDGVFHAGSL 260 Query: 265 ASPVGR-----ALPAGALQVGIRPEYLALA-QPQQAGALPGTVVQ-VQDIGTYQMLTAKV 317 A P+ R GA +GIRPE++ Q +A A +V V+ +G+ ++ A Sbjct: 261 ALPMQRYDYRNGPHHGAAVIGIRPEHILTGEQITRADATAEVLVDLVEGLGSDTLVYATH 320 Query: 318 GEHTVKARFTPETRLPSSGD 337 G ++ R +R+ S+GD Sbjct: 321 GAQNLRLRMDGASRV-SAGD 339 Lambda K H 0.320 0.136 0.395 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: 310 Number of extensions: 17 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: 358 Length of database: 361 Length adjustment: 29 Effective length of query: 329 Effective length of database: 332 Effective search space: 109228 Effective search space used: 109228 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