Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate BPHYT_RS08805 BPHYT_RS08805 sulfate ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__BFirm:BPHYT_RS08805 Length = 352 Score = 212 bits (539), Expect = 1e-59 Identities = 121/310 (39%), Positives = 184/310 (59%), Gaps = 16/310 (5%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I V+N+ K F G VALDNV+++ GE +LGPSG GKTT +R+IAGL+ G++ Sbjct: 3 ITVRNLQKRF--GDFVALDNVSLDFPPGELVALLGPSGCGKTTLLRVIAGLEYADGGQVV 60 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEE-----IR 118 + VA+ G +R++G VFQ +AL+ ++T FEN+AF L +K KE IR Sbjct: 61 LQGQDVATVGA-----REREVGFVFQHYALFRHMTVFENVAFGL-RVKPRKERPSEAVIR 114 Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178 ++V E+ K++ + + +P ELSGGQ+QR+ALARAL +P +LLLDEPF LDA++R Sbjct: 115 EKVHELLKLVQLDWLAQRYPSELSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKE 174 Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238 R+ ++ + L ++ + V+HD + +ADR+ VL +G + QVG P+D+YD+P + V Sbjct: 175 LRSWLRRLHDDLHISTIFVTHDQEEALEVADRIVVLNRGHVEQVGSPQDVYDHPQTSFVY 234 Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSD---RAIIGIRPEDVKLSKDVIKDDSWIL 295 +G N L G V G V+ PVS+ +D A +RP D++L I+ Sbjct: 235 EFLGAANRLHGNVDASGFVVDGAALPVSIKADFSGPAFAYVRPHDLQLYPQASGHREGIV 294 Query: 296 VGKGKVKVIG 305 V +V +G Sbjct: 295 VDVRRVVTLG 304 Lambda K H 0.319 0.139 0.390 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: 308 Number of extensions: 11 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: 353 Length of database: 352 Length adjustment: 29 Effective length of query: 324 Effective length of database: 323 Effective search space: 104652 Effective search space used: 104652 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 (21.7 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