Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 214 bits (544), Expect = 4e-60 Identities = 124/322 (38%), Positives = 191/322 (59%), Gaps = 7/322 (2%) Query: 26 PLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQV 85 PL ++ DG ++GPSGCGK+T+L +++GL + G + + + VT P++R IA V Sbjct: 22 PLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGDIWINDQRVTEMEPKDRGIAMV 81 Query: 86 FQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQ 145 FQ +Y M+V EN+A+ L+ R + + QI +RV A +LE+ G L +R L+ +Q Sbjct: 82 FQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAARILELDGLLKRRPRELSGGQRQ 141 Query: 146 KISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALT 205 ++++GR +VR D A LFDEPL+ +D L+ Q+R +L+Q+H LK T +YVTHDQVEA+T Sbjct: 142 RVAMGRAIVR-DPAVFLFDEPLSNLDAKLRVQMRLELQQLHRRLKTTSLYVTHDQVEAMT 200 Query: 206 FADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSV---AGH 262 A +V+VM G A Q+G+ ++E+PA FV FIGSP MN L + E G Sbjct: 201 LAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAMNLLTGRVNNEGTHFELDGGI 260 Query: 263 RLASPVGRALPAG-ALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVGEHT 321 L G AG + +GIRPE++AL+ Q G +P + ++ +G + + GE Sbjct: 261 ELPLNGGYRQYAGRKMTLGIRPEHIALSS-QAEGGVPMVMDTLEILGADNLAHGRWGEQK 319 Query: 322 VKARFTPETRLPSSGDTAWLQV 343 + R + R P++G T WL + Sbjct: 320 LVVRLAHQER-PTAGSTLWLHL 340 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: 302 Number of extensions: 12 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: 356 Length adjustment: 29 Effective length of query: 329 Effective length of database: 327 Effective search space: 107583 Effective search space used: 107583 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