Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 382 bits (980), Expect = e-110 Identities = 202/391 (51%), Positives = 261/391 (66%), Gaps = 32/391 (8%) Query: 17 LVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIML 76 +++L G+ K F+ + +DLTI NGEFLTLLGPSGCGKTT+LRL++G E SG + + Sbjct: 7 IIELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRI 66 Query: 77 DNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQ 136 + + + VP E R VNTVFQ+YALFPHMTV +NVAFGL+MQ A E RV++ALRMV Sbjct: 67 NGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVH 126 Query: 137 LETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRK 196 LE FA RKP QLSGGQQQRVAIARAV+N P +LLLDE SALD+KLRKQMQ E+K LQR+ Sbjct: 127 LENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQ 186 Query: 197 LGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNA 256 LGITFVFVTHDQEEA MSDR+VVM +GRIEQ G P+EIYEEP N++VA F+G+IN Sbjct: 187 LGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGDINALPG 246 Query: 257 TV-IERLD-----------------------------EQRVRANVEGRECNIYVNFAVEP 286 + RLD E A V G + + P Sbjct: 247 RIDAVRLDWSAAPGTPLAPPAPGTPEHAALPPDLKPGEHLYDATVGGTVFPVRSRRRLAP 306 Query: 287 GQKLHVLLRPEDLRVEEI--NDDNHAEGLIGYVRERNYKGMTLESVVELENGKMVMVSEF 344 G + VLLRPEDLR++ I + L G + E YKG T++ V+ L++G+ +M +EF Sbjct: 307 GDGVQVLLRPEDLRIDRIAVAETPDWPHLWGRIEESVYKGATVDLVITLDDGQRLMAAEF 366 Query: 345 FNEDDPDFDHSLDQKMAINWVESWEVVLADE 375 FNEDD D +++ +++A++WV+ WEV+L D+ Sbjct: 367 FNEDDEDINYNPGERVAVSWVDGWEVLLPDD 397 Lambda K H 0.319 0.136 0.385 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: 464 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 378 Length of database: 399 Length adjustment: 30 Effective length of query: 348 Effective length of database: 369 Effective search space: 128412 Effective search space used: 128412 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: 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