Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate AO356_12080 AO356_12080 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_12080 Length = 366 Score = 440 bits (1132), Expect = e-128 Identities = 211/367 (57%), Positives = 272/367 (74%), Gaps = 2/367 (0%) Query: 2 MKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETG-IKVVYDVY 60 M R + + A + G QA + + L VYNW DYI P LE F + +K+VYD++ Sbjct: 1 MNRLKRFMAPAVCAALLCGAVQA-EERTLRVYNWFDYITPKALEDFKAQNSQVKLVYDIF 59 Query: 61 DSNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEV 120 D+NE LEAKLL G SGYDVVVPSN FLAKQI+AGV+Q LD+SKLPNW +L+ LM +E Sbjct: 60 DTNEALEAKLLTGNSGYDVVVPSNVFLAKQIEAGVFQPLDRSKLPNWNHLDPKLMKLIEA 119 Query: 121 SDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDS 180 +DPGN+ A+PYM+GTI IG+NPDK+KAA GDNAPVDSWDL+FK ENI KLKQCGV+ LDS Sbjct: 120 NDPGNKFAVPYMYGTILIGFNPDKIKAALGDNAPVDSWDLIFKEENISKLKQCGVALLDS 179 Query: 181 PTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIG 240 P+EILP AL +LG P++ P + AE L +KIRP++TYFHSSKY++D+ANG+ICVA+G Sbjct: 180 PSEILPLALQHLGLDPNSKKPADYAKAEALMMKIRPHITYFHSSKYMADIANGDICVAVG 239 Query: 241 YSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPE 300 YSG QA +RA+EAKN VTV +PKEGA +FDM+AIPK A N A F+N+L++P+ Sbjct: 240 YSGSFSQAANRAKEAKNGVTVDMRLPKEGAPIWFDMLAIPKGAANPGDAYTFINYLLQPQ 299 Query: 301 IMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSW 360 ++A ++D V +PN N AT +V AIRN+P +YP+E M LYT LP +RA TR+W Sbjct: 300 VIAPVSDFVGYPNPNKDATEMVDPAIRNNPNLYPTEAAMTTLYTLQPLPRDAERARTRAW 359 Query: 361 TKIKSGK 367 T+IKSG+ Sbjct: 360 TRIKSGQ 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: 477 Number of extensions: 23 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