Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 186 bits (472), Expect = 9e-52 Identities = 94/248 (37%), Positives = 152/248 (61%), Gaps = 3/248 (1%) Query: 7 DHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRI 66 DHI G + +L +D +G LLGPSGCGKTT+L ++SG QP+ G + Sbjct: 5 DHIIELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEV 64 Query: 67 LFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEM 126 +G+ V + + R + VFQ ++ MTV DN+AF L+ +GVA + RRV D L M Sbjct: 65 RINGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRM 124 Query: 127 IDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRL 186 + L ++A RK + L+ Q+Q++++ R ++ N + +L DEP + +D ++ ++ ++K L Sbjct: 125 VHLENFADRKPRQLSGGQQQRVAIARAVINNPL-VLLLDEPFSALDFKLRKQMQLEIKHL 183 Query: 187 HKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGM 246 +Q G T V+VTHDQ EA +++VVVM +G+I QIG P E++E P++ +V F+G + Sbjct: 184 QRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGD--I 241 Query: 247 NFMPARIE 254 N +P RI+ Sbjct: 242 NALPGRID 249 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: 341 Number of extensions: 22 Number of successful extensions: 2 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: 399 Length adjustment: 30 Effective length of query: 326 Effective length of database: 369 Effective search space: 120294 Effective search space used: 120294 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: 50 (23.9 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