Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PP_5341 PP_5341 putrescine-binding periplasmic protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__Putida:PP_5341 Length = 367 Score = 452 bits (1164), Expect = e-132 Identities = 220/362 (60%), Positives = 277/362 (76%), Gaps = 2/362 (0%) Query: 7 KTLLALTLAGSV-AGMAQA-ADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNE 64 K LLA +A ++ AG A A+ + L VYNW DYI P TL F K++G+K+VYD++D+NE Sbjct: 5 KRLLAPFIAATLFAGALHAQAEQRTLRVYNWFDYITPQTLTAFQKDSGVKLVYDIFDTNE 64 Query: 65 VLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPG 124 LEAKLL G SGYDVVVPSN FLAKQI+AGV+Q LD+SKLPNW++L+ LM +E +DPG Sbjct: 65 ALEAKLLTGNSGYDVVVPSNVFLAKQIEAGVFQPLDRSKLPNWQHLDPALMKLIEANDPG 124 Query: 125 NEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEI 184 N+ A+PYM+GT+ IG+NP KVKAA GDNAPVDSWDL+FK ENI KLKQCGV+ LDSP+EI Sbjct: 125 NKFAVPYMYGTVLIGFNPAKVKAALGDNAPVDSWDLIFKEENIAKLKQCGVALLDSPSEI 184 Query: 185 LPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGD 244 LP AL YLG P++D P + K AEEL LKIRP++TYFHSSKY++D+ANG+ICVA+GYSG Sbjct: 185 LPLALQYLGLPPNSDKPADYKKAEELMLKIRPHITYFHSSKYMADIANGDICVAVGYSGS 244 Query: 245 IYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAE 304 QA +RA EA N V V +PKEGA +FDM+AIPK A N E A F+N+L++PE++A Sbjct: 245 FSQAANRAREANNGVVVDMRLPKEGAPIWFDMLAIPKGAANPEDAHTFINYLLRPEVIAP 304 Query: 305 ITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIK 364 I+D V +PN N AT V+ IRN+P +YP+ E M KLYT L +RA TR+WT+IK Sbjct: 305 ISDFVGYPNPNKDATDKVNPTIRNNPNLYPTAEAMAKLYTLKPLTRNAERARTRAWTRIK 364 Query: 365 SG 366 SG Sbjct: 365 SG 366 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: 469 Number of extensions: 21 Number of successful extensions: 1 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: 367 Length adjustment: 30 Effective length of query: 337 Effective length of database: 337 Effective search space: 113569 Effective search space used: 113569 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