Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 169 bits (429), Expect = 9e-47 Identities = 119/358 (33%), Positives = 184/358 (51%), Gaps = 23/358 (6%) Query: 4 ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63 +++ + YGA D D+SL + E+ ALLGPSG GK++LL I++GL P Sbjct: 3 LSIRQLTRRYGAFAALD-DFSLDIAEGEF-----VALLGPSGSGKSSLLRILAGLDDPDR 56 Query: 64 GRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEA----DVDRR 119 G +L DG D+ L Q R+I VFQ ++ MTV DN+AF LR R A D+ R Sbjct: 57 GDVLRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAAR 116 Query: 120 VRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVL 179 V D+L + L RR L+ Q+Q+++L R L + + +L DEP +D ++ L Sbjct: 117 VEDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAV-EPSLLLLDEPFGALDAQVRGTL 175 Query: 180 RSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGY 239 R L+ L + G T V VTHDQ EAL A++VVVM G+I Q+G P+E++ P+ FV Sbjct: 176 RVWLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHG 235 Query: 240 FIGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREGMPITI 299 F+G N + +E + +G + E +G + E +RPE + L G+ Sbjct: 236 FVGR--ANRIRGHVERDRLHLGGHSFQGELPGDLAG-REIEAWLRPEHLALASRGLGGWT 292 Query: 300 SKVEDIG-RQKIVRARFADQPIAIVVPED---ADIPADAR-----VTFDPSAISIYAD 348 +++ + + RAR A +V+ + A++ A VT P +++AD Sbjct: 293 GRLQHLDLAGPVARARLAMHGDGLVLDAEWNAAEVAAHGLAIGEVVTLQPREFTLFAD 350 Lambda K H 0.321 0.137 0.405 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: 326 Number of extensions: 15 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: 356 Length of database: 384 Length adjustment: 30 Effective length of query: 326 Effective length of database: 354 Effective search space: 115404 Effective search space used: 115404 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