Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate WP_086510882.1 BZY95_RS15925 ABC transporter ATP-binding protein
Query= TCDB::Q97Q42 (385 letters) >NCBI__GCF_002151265.1:WP_086510882.1 Length = 354 Score = 266 bits (681), Expect = 5e-76 Identities = 146/334 (43%), Positives = 211/334 (63%), Gaps = 9/334 (2%) Query: 20 TKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIMLDGVRINDIPTNKR 79 T +DI+ E+E+G+F +LLG SG GK+T L +IAG ++ T G I++DG I N+R Sbjct: 16 TTAAEDISLEIEKGEFVSLLGPSGCGKTTTLQMIAGFVEPTRGRILMDGEDITHRKPNER 75 Query: 80 DVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVLKMVQLEGYEKRSIRKLS 139 + VFQSYALFPHM V ENV F L +R++ E QRV EVL++V L+ + R R+LS Sbjct: 76 GIGIVFQSYALFPHMTVVENVRFGLEMRRVPATESRQRVGEVLELVHLDQLKDRYPRELS 135 Query: 140 GGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRELQQRLGITFVFVTHDQE 199 GGQRQRVA+ARA++ QP ++LLDEPLS LD KLR DMQ ELR++QQ++G T + VTHDQ Sbjct: 136 GGQRQRVALARALVIQPPLLLLDEPLSNLDAKLREDMQIELRKIQQQVGTTTLMVTHDQS 195 Query: 200 EALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNILPGTM----IEDYLVE 255 EAL++SD + VMN G +VQ P + Y+ P + FV++F+G++N+L G + + + Sbjct: 196 EALSLSDRVVVMNQGRVVQVDEPFNAYERPSDAFVSSFVGKTNLLTGLIGKKQGDQTSIR 255 Query: 256 FNGKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGKLQVKVDTQLFRGVHYEIIAYDEL 315 E G + + V++ IRPE L +T GKL+ +V T+LF G H+ + D Sbjct: 256 LGDATLELTLNGPRTSNQVQISIRPEKLELTDCASGKLKGRVKTRLFLGNHW-LYQVDSS 314 Query: 316 GNEWMIH----STRKAIVGEEIGLDFEPEDIHIM 345 E I R VG+++G+ + P I ++ Sbjct: 315 AGELFITQPNLGKRGVAVGDDVGVSWSPGAIRLL 348 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: 293 Number of extensions: 14 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: 385 Length of database: 354 Length adjustment: 30 Effective length of query: 355 Effective length of database: 324 Effective search space: 115020 Effective search space used: 115020 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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