Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PfGW456L13_736 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_736 Length = 366 Score = 442 bits (1137), Expect = e-129 Identities = 213/361 (59%), Positives = 271/361 (75%), Gaps = 1/361 (0%) Query: 7 KTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKF-TKETGIKVVYDVYDSNEV 65 K +A L ++ G A A+ + L VYNW DYI P LE F + T K+VYD++D+NE Sbjct: 5 KRFIAPALCATLLGGAVHAEERTLRVYNWFDYITPKALEDFKAQNTQTKLVYDIFDTNEA 64 Query: 66 LEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGN 125 LEAKLL G SGYDVVVPSN FLAKQI+AGV+Q LD+SKLPNW +L+ LM +E +DPGN Sbjct: 65 LEAKLLTGNSGYDVVVPSNVFLAKQIEAGVFQPLDRSKLPNWNHLDPKLMKLIEANDPGN 124 Query: 126 EHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEIL 185 + A+PYM+GTI IG+NPDKVKAA G +APVDSWDL+FK ENI KLKQCGV+ LDSP+EIL Sbjct: 125 KFAVPYMYGTILIGFNPDKVKAALGADAPVDSWDLIFKEENISKLKQCGVALLDSPSEIL 184 Query: 186 PAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDI 245 P AL +LG P++ P + AE L +KIRPY+TYFHSSKY++D+ANG+ICVA+GYSG Sbjct: 185 PLALQHLGLDPNSKKPADYDKAEALLMKIRPYITYFHSSKYMADIANGDICVAVGYSGSF 244 Query: 246 YQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEI 305 QA +RA+EAKN V V +PKEGA +FDM+AIPK A+N E A F+N+L++P+++A + Sbjct: 245 SQAANRAKEAKNGVVVDMRLPKEGAPIWFDMLAIPKGAKNPEDAYTFINYLLQPQVIAPV 304 Query: 306 TDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKS 365 +D V +PN N AT LV AIRN+P +YP++ M LYT LP +RA TR+WTKIKS Sbjct: 305 SDFVGYPNPNKDATELVDPAIRNNPNLYPTDAAMGTLYTLQPLPRDAERARTRAWTKIKS 364 Query: 366 G 366 G Sbjct: 365 G 365 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: 481 Number of extensions: 22 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: 366 Length adjustment: 30 Effective length of query: 337 Effective length of database: 336 Effective search space: 113232 Effective search space used: 113232 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