Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate AO356_29815 AO356_29815 spermidine/putrescine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29815 Length = 361 Score = 409 bits (1051), Expect = e-119 Identities = 198/367 (53%), Positives = 263/367 (71%), Gaps = 6/367 (1%) Query: 1 MMKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVY 60 + R K+++ L L +A AQAAD + +YNWS YIAPDTL+ FT +TG + YD+Y Sbjct: 1 LRSRMLKSIVPLLL---IASTAQAADT--VRIYNWSSYIAPDTLQNFTTQTGHQTQYDLY 55 Query: 61 DSNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEV 120 DSNEVL+AKL+AG SGYDVV PSN F+A+QI AG + LD+SKLPNW NLN LM LE Sbjct: 56 DSNEVLDAKLMAGHSGYDVVFPSNHFMARQITAGALKPLDRSKLPNWHNLNPTLMKVLEA 115 Query: 121 SDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDS 180 +DPGN + PY+WG+ GIGYN KVKA GD P+DSWD+VFKPEN++KL +CGV+ LD+ Sbjct: 116 NDPGNRYGFPYLWGSTGIGYNVAKVKAVLGD-VPIDSWDIVFKPENMKKLARCGVAMLDN 174 Query: 181 PTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIG 240 EILP AL+YLG + + + + A+ L LK+RPYV+YFH+SKY SDLA G++C+ +G Sbjct: 175 GPEILPIALNYLGLPHHSKDKADYEKAQALLLKVRPYVSYFHNSKYTSDLATGDVCLVVG 234 Query: 241 YSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPE 300 +SGD+ QA +RA EA N + Y IPKEG+ +FDMVA+P DA N F+N+L+ P+ Sbjct: 235 FSGDVMQAAARANEAGNGQQIAYAIPKEGSPMWFDMVAMPADAPNEGAGYEFLNYLLDPK 294 Query: 301 IMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSW 360 +MA I++ V + NGN AA LV +AIRNDP +YP + VMKKL+ +P + R TR W Sbjct: 295 VMAGISNHVHYANGNTAAEGLVDKAIRNDPMVYPPDSVMKKLFVLEAMPLENDRLRTRVW 354 Query: 361 TKIKSGK 367 ++IKSG+ Sbjct: 355 SRIKSGQ 361 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: 482 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: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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