RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8315
(107 letters)
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 29.4 bits (65), Expect = 0.29
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 8/68 (11%)
Query: 19 TLKTPRETPDKTL--KTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLK 76
T K P + DK KT +TPDK+ + K+ +K+L + PD +
Sbjct: 379 TDKPPEKASDKPSPEKTSEKTPDKSHEKQLD------KSSEPVAEKALDKTADKPDAAAR 432
Query: 77 TPRETPDK 84
P ET D+
Sbjct: 433 LPAETADR 440
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 29.5 bits (66), Expect = 0.33
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 2 IWRILKLRNYLSQIP--KRTLKTPRETPDKTLKTPRETPDKTLNTPRETP---DKTLKTP 56
+WR +N +Q P +R+ +TP +TP + + TP K+ TP +TP + P
Sbjct: 260 VWRQ---KNTPAQTPMPERSWQTPAQTPARRISTPMTEEIKSWQTPLQTPAMYSSDYQAP 316
Query: 57 RETPDKSLKTP-RETPDKTLKTPRETPDKISVKSNS 91
+ P + + RE L PD S S+S
Sbjct: 317 KPEPIYTWEELLRERFPSDLFAISSLPDSDSEASDS 352
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 28.7 bits (64), Expect = 0.58
Identities = 15/89 (16%), Positives = 30/89 (33%)
Query: 17 KRTLKTPRETPDKTLKTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLK 76
K+ KT + K KT ++ K ++ K K + + K + K
Sbjct: 239 KKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKK 298
Query: 77 TPRETPDKISVKSNSEVSNGVKTPKVSKK 105
++ K+ ++ K +KK
Sbjct: 299 AGKKAAAGSKAKATAKAPKRGAKGKKAKK 327
>gnl|CDD|233728 TIGR02102, pullulan_Gpos, pullulanase, extracellular, Gram-positive.
Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. In
contrast, a glycogen debranching enzyme such GlgX,
homologous to this family, can release glucose at
alpha,1-6 linkages from glycogen first subjected to limit
degradation by phosphorylase. Characterized members of
this family include a surface-located pullulanase from
Streptococcus pneumoniae (PMID:11083842) and an
extracellular bifunctional amylase/pullulanase with
C-terminal pullulanase activity (PMID:8798645).
Length = 1111
Score = 27.9 bits (62), Expect = 1.1
Identities = 20/83 (24%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 25 ETPDKTLKTPRETPDKTLNTPRETPD--KTLKTPRETPDKSLKTPRETPDKTLKTPRETP 82
E P+KT P P P + PD K +K TP + D+ +TP+
Sbjct: 1008 EAPEKTPPPPEHEPQAP-KPPTQDPDGSKPKDKVDPKDNKDPLTPPGSDDENGETPKGNE 1066
Query: 83 DKISVKSNSEVSNGVKTPKVSKK 105
+K + G P K
Sbjct: 1067 EKKE----EQPDKGANLPNTGTK 1085
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 27.4 bits (61), Expect = 1.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 8 LRNYLSQIPKRTLKTPRE 25
L++ ++QIP + L TP E
Sbjct: 198 LQSIVNQIPMKRLGTPEE 215
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 27.1 bits (60), Expect = 1.8
Identities = 20/73 (27%), Positives = 26/73 (35%), Gaps = 2/73 (2%)
Query: 30 TLKTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLKTPRETPDKISVKS 89
T KTP E K T K KT ++ K + L TP +P ++
Sbjct: 742 TPKTPYEKKTKAKKKSASTKGKAAKTVKKKSKAKSKKTTKKRAGPLYTP--SPALAAMIG 799
Query: 90 NSEVSNGVKTPKV 102
V G T KV
Sbjct: 800 AEPVGRGEATKKV 812
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 26.6 bits (59), Expect = 2.8
Identities = 18/64 (28%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 43 NTPRETPDKTLKTPRETPDKSLKTPRETPDKTLKTPRETPDKISVKSNSEVSNGVKTPKV 102
+ T K +E + K K K ++ P KS E G KTPK
Sbjct: 45 EENKVATTSTKKDKKEDKNNESKKK-SEKKKKKKKEKKEP-----KSEGETKLGFKTPKK 98
Query: 103 SKKP 106
SKK
Sbjct: 99 SKKT 102
>gnl|CDD|114045 pfam05297, Herpes_LMP1, Herpesvirus latent membrane protein 1
(LMP1). This family consists of several latent membrane
protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1
of EBV is a 62-65 kDa plasma membrane protein possessing
six membrane spanning regions, a short cytoplasmic
N-terminus and a long cytoplasmic carboxy tail of 200
amino acids. EBV latent membrane protein 1 (LMP1) is
essential for EBV-mediated transformation and has been
associated with several cases of malignancies. EBV-like
viruses in Cynomolgus monkeys (Macaca fascicularis) have
been associated with high lymphoma rates in
immunosuppressed monkeys.
Length = 382
Score = 26.5 bits (58), Expect = 2.8
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 18 RTLKTPRETPDKTLKTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLKT 77
+ L P PD + P T D N P++ PD T + PD + + PD T
Sbjct: 240 QNLGAPGGGPDNGPQDPDNTDD---NGPQD-PDNTDDNGPQDPDNTDDNGPQDPDNTADN 295
Query: 78 PRETPD 83
+ PD
Sbjct: 296 GPQDPD 301
Score = 26.1 bits (57), Expect = 3.7
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 25 ETPDKTLKTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKT 74
+ PD T + PD T + + PD T + PD + + PD T
Sbjct: 254 QDPDNTDDNGPQDPDNTDDNGPQDPDNTDDNGPQDPDNTADNGPQDPDNT 303
>gnl|CDD|227114 COG4773, FhuE, Outer membrane receptor for ferric coprogen and
ferric-rhodotorulic acid [Inorganic ion transport and
metabolism].
Length = 719
Score = 26.6 bits (59), Expect = 3.1
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 39 DKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLKTPRETPDKISVKSNSEV 93
D +L+T T +T +T ++ T K T RETP +SV + +
Sbjct: 41 DASLDTVTVTGSRTASITEKTGSYTVSGMS-TATKLPMTLRETPQSVSVITRQRM 94
>gnl|CDD|234504 TIGR04216, halo_surf_glyco, major cell surface glycoprotein.
Members of this family are the S-layer-forming
halobacterial major cell surface glycoprotein. The
highest scores below model cutoffs are fragmentary
paralogs to actual members of the family. Modifications
include at N-linked and O-linked glycosylation, a
C-terminal diphytanylglyceryl modification, and probable
cleavage of the PGF-CTERM tail.
Length = 782
Score = 26.4 bits (58), Expect = 3.9
Identities = 13/55 (23%), Positives = 17/55 (30%), Gaps = 7/55 (12%)
Query: 25 ETPDKTLKTPRETPDKTLNTPRETPDKTLK-TPRETPDKSLKTPRETPDKTLKTP 78
E PD T T + T T + T P + + P E TP
Sbjct: 712 ERPDTT------TSEDPTTTTTPTTTGPEETTETAEPTTTTEEPTEETTTGSSTP 760
>gnl|CDD|215130 PLN02217, PLN02217, probable pectinesterase/pectinesterase
inhibitor.
Length = 670
Score = 26.2 bits (57), Expect = 4.7
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 16 PKRTLKTPRETPDKTLKTPRETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTL 75
P L +P TP K + P L +P TP + E+ K T +P+ ++
Sbjct: 600 PAGHLGSPPATPSKIVSPSTSPPASHLGSPSTTP-----SSPESSIKVASTETASPESSI 654
Query: 76 K 76
K
Sbjct: 655 K 655
>gnl|CDD|233819 TIGR02307, RNA_lig_RNL2, RNA ligase, Rnl2 family. Members of this
family ligate (seal breaks in) RNA. Members so far
include phage proteins that can counteract a host
defense of cleavage of specific tRNA molecules,
trypanosome ligases involved in RNA editing, but no
prokaryotic host proteins [Mobile and extrachromosomal
element functions, Prophage functions, Transcription,
RNA processing].
Length = 325
Score = 25.6 bits (56), Expect = 5.6
Identities = 13/49 (26%), Positives = 17/49 (34%), Gaps = 6/49 (12%)
Query: 7 KLRNYLSQIPKRTLKTPRETPDKTLK-----TPRETPDKTLNTPRETPD 50
+L N LS+I K + RETP T NT +
Sbjct: 255 RLNNVLSKIGTEPPKDFGMVMGLLAQDALKEFLRETPGIT-NTQADNRK 302
>gnl|CDD|218941 pfam06217, GAGA_bind, GAGA binding protein-like family. This
family includes gbp a protein from Soybean that binds to
GAGA element dinucleotide repeat DNA. It seems likely
that the this domain mediates DNA binding. This putative
domain contains several conserved cysteines and a
histidine suggesting this may be a zinc-binding DNA
interaction domain.
Length = 301
Score = 25.2 bits (55), Expect = 7.2
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 35 RETPDKTLNTPRETPDKTLKTPRETPDKSLKTPRETPDKTLKTPRETPDKISVKSNSE-V 93
P + + ++ K P+ K K ++++K P P + + V
Sbjct: 138 STAPPEAKEVKKPKKGQSPKVPKAPKPKKPKKKGSVSNRSVKMPGIDPRSKPDWKSQDLV 197
Query: 94 SNGV 97
NGV
Sbjct: 198 INGV 201
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.305 0.126 0.355
Gapped
Lambda K H
0.267 0.0666 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,055,102
Number of extensions: 389171
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 67
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 53 (24.3 bits)