Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate Pf6N2E2_1770 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1770 Length = 357 Score = 406 bits (1044), Expect = e-118 Identities = 193/350 (55%), Positives = 254/350 (72%), Gaps = 3/350 (0%) Query: 18 VAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSGY 77 + AQAAD + +YNWS YIAPDTL+ FT +TG + YD+YDSNEVL+AKL+AG SGY Sbjct: 11 IVSTAQAADT--VRIYNWSSYIAPDTLQNFTTQTGHQTQYDLYDSNEVLDAKLMAGHSGY 68 Query: 78 DVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTIG 137 DVV PSN F+A+QI AG + LD+SKLPNW NLN LM LE +DPGN + PY+WG+ G Sbjct: 69 DVVFPSNHFMARQITAGALKPLDRSKLPNWHNLNPTLMKVLEANDPGNRYGFPYLWGSTG 128 Query: 138 IGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPD 197 IGYN KVKA GD P+DSWD+VFKPEN++KL +CGV+ LD+ EILP AL+YLG Sbjct: 129 IGYNVAKVKAVLGD-VPIDSWDIVFKPENMKKLARCGVAMLDNGPEILPIALNYLGLPHH 187 Query: 198 TDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKN 257 + + + + A+ L LK+RPYV+YFH+SKY SDLA G++C+ +G+SGD+ QA +RA EA N Sbjct: 188 SKDKADYEKAQALLLKVRPYVSYFHNSKYTSDLATGDVCLVVGFSGDVMQAAARANEAGN 247 Query: 258 KVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAA 317 + Y IPKEG+ +FDMVA+P DA N F+N+L+ P++MA I++ V + NGN A Sbjct: 248 GQQIAYAIPKEGSPMWFDMVAMPADAPNEGAGYEFLNYLLDPKVMAGISNHVHYANGNTA 307 Query: 318 ATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 A LV +AIRNDP +YP + VMKKL+ +P + R TR W++IKSG+ Sbjct: 308 AEGLVDKAIRNDPMVYPPDSVMKKLFVLEAMPLENDRLRTRVWSRIKSGQ 357 Lambda K H 0.315 0.133 0.390 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: 480 Number of extensions: 18 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: 367 Length of database: 357 Length adjustment: 29 Effective length of query: 338 Effective length of database: 328 Effective search space: 110864 Effective search space used: 110864 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: 42 (22.0 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