Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate Pf6N2E2_1743 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1743 Length = 368 Score = 271 bits (693), Expect = 2e-77 Identities = 150/360 (41%), Positives = 225/360 (62%), Gaps = 19/360 (5%) Query: 4 PIIEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGD 63 P+IEF V K + D T V+KD+N + G+F TLLGASGSGK+T L ++AG T G+ Sbjct: 13 PLIEFNGVQKSY-DGKTLVIKDLNLAISRGEFLTLLGASGSGKTTTLMMLAGFETPTRGE 71 Query: 64 IMLDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVLK 123 I++ G I P ++R + VFQ+YALFPHM+V EN+A+PL++R +++ +++ +V + Sbjct: 72 ILMGGTPIQKKPAHQRGMGMVFQNYALFPHMSVEENLAYPLKMRGLNRSDLQAKVKRAID 131 Query: 124 MVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELREL 183 MVQL G ++R I +LSGGQ+QRVA+ARA++ +P V+L+DEPL ALD LR MQYE+++L Sbjct: 132 MVQLHGMQQRRITELSGGQQQRVALARAMVFEPEVILMDEPLGALDKNLREHMQYEIKQL 191 Query: 184 QQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNI 243 + LG+T V+VTHDQ EAL MSD I V ++G+I Q G+P +Y+ P N +VA FIGE+N+ Sbjct: 192 HKSLGVTVVYVTHDQSEALTMSDRIAVFHEGDIAQIGSPTALYEHPENAYVANFIGENNV 251 Query: 244 LPGTMIE------DYLVEFNGKRFEAVDGGMKPNEP--VEVVIRPEDLRITLPEEGKLQV 295 L GT+ D +E NG +K P VE+VIRPE++R+ Q Sbjct: 252 LVGTVQHRDGQTCDVTLE-NGLHVTGSAKALKGLRPERVELVIRPENIRLGPVASMPWQA 310 Query: 296 KVDTQLFRGVHYEIIAYDELGNEWMI-------HSTRKAIVGEEIGLDFEPEDIHIMRLN 348 V ++ G H + + LG++ + ++ G+ G D+ +D H+ L+ Sbjct: 311 TVIDSIYLGDHLRV--HLRLGHQQALIVKVANNGFFKQLRTGQVTGFDWSTDDAHLFELS 368 Lambda K H 0.318 0.138 0.386 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: 325 Number of extensions: 11 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: 385 Length of database: 368 Length adjustment: 30 Effective length of query: 355 Effective length of database: 338 Effective search space: 119990 Effective search space used: 119990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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