Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 309 bits (791), Expect = 8e-89 Identities = 167/357 (46%), Positives = 223/357 (62%), Gaps = 26/357 (7%) Query: 1 MAGIKIDKINKFYGTTQALFD----INLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVS 56 MA I + ++ K YG D I+ +I DGEF+V VGPSGCGKSTLLR +AGLE +S Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 SGRIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAE 116 SG+I IG R V +EP +RD+AMVFQ+YALYPHMTV +NM +G+K+ G R+ Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 117 AARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVEL 176 AA +L+L L+R P QLSGGQRQRVA+GRAIV+ P+VFLFDEPLSNLDAKLRVQMR+E+ Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 177 EGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGS 236 + LH L T +YVTHDQVEAMT+ +++V+NRG EQ+G+P ++Y +P + FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 237 PAMNVFSSDVGLQDISLDASAA--------------------FVGCRPEHIEIVPDGD-G 275 P MN+ + S + S +G RPEH+ + DG Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDGSAA 300 Query: 276 HIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD 332 ++ V + E LG E L++ GG +V R + + + G + F +H FD Sbjct: 301 QLSLEVELVEALGAELLVHARC-GGQALVLRCPANVQVRTGQRIGASFGAGDVHWFD 356 Lambda K H 0.320 0.139 0.396 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: 368 Number of extensions: 15 Number of successful extensions: 1 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: 338 Length of database: 364 Length adjustment: 29 Effective length of query: 309 Effective length of database: 335 Effective search space: 103515 Effective search space used: 103515 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