Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 268 bits (686), Expect = 1e-76 Identities = 155/358 (43%), Positives = 206/358 (57%), Gaps = 24/358 (6%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 VQ + + F + + ++ + I +GEF ++LGPSG GKTT LRLIAG E +G I + Sbjct: 5 VQFTHVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIH 64 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 E+ +P R VNTVFQ YALFPHM V +NVA+GL+++ E R EAL MV L Sbjct: 65 GEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVAL 124 Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 + RKP QLSGGQ+QRVA+ARA+VN+PR+LLLDE L ALD KLR+QMQ+ELK LQR+L Sbjct: 125 GGYGDRKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQL 184 Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257 GITF+FVTHDQ EAL+MSDR+ V GRIEQ TPR +Y +P FVA F+G N+ Sbjct: 185 GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGTSNVIRGE 244 Query: 258 VIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIGYV 317 + +RL G +RPE +R E + G + Sbjct: 245 LAQRLG-----------------------GTAQPFSIRPEHVRFAEGPLGTGEVEISGLL 281 Query: 318 RERNYKGMTLESVVELENGKMVMVSEFFNE-DDPDFDHSLDQKMAINWVESWEVVLAD 374 + Y+G ++LENG+ + +S N+ D H + Q + W V L D Sbjct: 282 HDIQYQGSATRYELKLENGQALNISRANNQWLDTTAGHQVGQTLTARWAREAMVPLTD 339 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: 315 Number of extensions: 14 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: 378 Length of database: 344 Length adjustment: 29 Effective length of query: 349 Effective length of database: 315 Effective search space: 109935 Effective search space used: 109935 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: 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