RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11904
(199 letters)
>gnl|CDD|220641 pfam10235, Cript, Microtubule-associated protein CRIPT. The CRIPT
protein is a cytoskeletal protein involved in
microtubule production. The C-terminal domain is
essential for binding to the PDZ3 domain of the SAP90
protein, one of a super-family of PDZ-containing
proteins that play an important role in coupling the
membrane ion channels with their signalling partners.
SAP90 is concentrated in the post synaptic density of
glutamatergic neurons.
Length = 89
Score = 104 bits (260), Expect = 2e-29
Identities = 42/70 (60%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 65 GKVITPDNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSH 124
K+ TPD WK G+RNT GGR+I +NK L+ KA+ NPY Q CKIC+ KVHQ GS
Sbjct: 1 TKLATPDVWKKGARNTATLGGRKINKNKLLS-KKAKRNPYAQYSSKCKICKTKVHQKGSK 59
Query: 125 YCQACAYKKG 134
YCQ CAYKKG
Sbjct: 60 YCQRCAYKKG 69
>gnl|CDD|223344 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 273
Score = 30.3 bits (69), Expect = 0.54
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 100 RFNPYTQKFESCKICRQKVHQV-----GSHYCQAC 129
Y + E C+ C + ++ + YC C
Sbjct: 237 ELKVYGRAGEPCRRCGTPIEKIKLGGRSTFYCPVC 271
>gnl|CDD|220082 pfam08960, DUF1874, Domain of unknown function (DUF1874). This
domain is found in a set of hypothetical viral and
bacterial proteins.
Length = 105
Score = 28.5 bits (64), Expect = 1.1
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 3 HCAETWALNN--GDRITSVRISFRHMVYEDALTILSYASPYEVQIETEKEI 51
H A L+N G I RI + V + AL + E ++ T +EI
Sbjct: 45 HDATAQLLSNLLGVNIPMNRIQVKLQVGDKALAFVLKQRLEEGKVLTVEEI 95
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 272
Score = 29.1 bits (65), Expect = 1.3
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 78 RNTIESGGRRIGENKALTASKARF----NPYTQKFESCKICRQKVHQV-----GSHYCQA 128
R IE GG + + F Y + E C C+ + +V SHYC
Sbjct: 210 REAIELGGSSVSDYVDAEGRSGFFQLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPH 269
Query: 129 C 129
C
Sbjct: 270 C 270
>gnl|CDD|240510 cd06086, KOW_Spt5_6, KOW domain of Spt5, repeat 6. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 58
Score = 26.7 bits (60), Expect = 1.8
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 135 EHLVLVTADPEKGDKFALISGEH 157
EHL V PEKGD+ +I GE
Sbjct: 1 EHLEPV--PPEKGDRVKVIKGED 21
>gnl|CDD|212025 cd11635, HR1_PKN2_3, Third Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Protein Kinase N2.
PKN2, also called PKNgamma or Protein-kinase C-related
kinase 2 (PRK2), is a serine/threonine protein kinase
and an effector of the small GTPase Rho/Rac. It
regulates G2/M cell cycle progression and the exit from
cytokinesis. It also phosphorylates hepatitis C virus
(HCV) RNA polymerase and thus, plays a role in HCV RNA
replication. PKN2 shares a common domain architecture
with other PKNs, containing three HR1 domains, a C2
domain, and a kinase domain. In addition, PKN2 contains
a proline-rich region in between its C2 and kinase
domains and has been shown to associate with SH3 domain
containing proteins like NCK and Grb4. This model
characterizes the third HR1 domain of PKN2. HR1 domains
are anti-parallel coiled-coil (ACC) domains that bind
small GTPases from the Rho family; PKN2 specifically
binds to RhoA GTPase in a GTP-dependent manner. The HR1
domains of PKN2, together with its C2 domain, also
facilitate the recruitment of PKN2 to primordial
junctions at nascent cell-cell contacts, where it
promotes junctional maturation.
Length = 74
Score = 26.9 bits (59), Expect = 2.4
Identities = 13/38 (34%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 76 GSRNTIES-GGRRIGENKALTASKARFNPYTQKFESCK 112
G++N ++ G ++ + KAL+ ++ARFN +QK + K
Sbjct: 27 GAKNVMKLLGSGKVTDRKALSEAQARFNESSQKLDLLK 64
>gnl|CDD|222508 pfam14033, DUF4246, Protein of unknown function (DUF4246). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and fungi.
Proteins in this family are typically between 392 and
644 amino acids in length.
Length = 496
Score = 28.0 bits (63), Expect = 3.5
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 16 ITSVRISFRHMV-YEDALTILSYASPYEVQIETEKEIYFIMVCSKCEKKLGKVITP 70
IT R+SFR D + Y +E E++ + ++LG V T
Sbjct: 382 ITESRLSFRQATDDPDDELEVEYEQGDHEWLE---EVFGLEDGDPAVQELGSVSTR 434
>gnl|CDD|150957 pfam10367, Vps39_2, Vacuolar sorting protein 39 domain 2. This
domain is found on the vacuolar sorting protein Vps39
which is a component of the C-Vps complex. Vps39 is
thought to be required for the fusion of endosomes and
other types of transport intermediates with the
vacuole. In Saccharomyces cerevisiae, Vps39 has been
shown to stimulate nucleotide exchange. This domain is
involved in localisation and in mediating the
interactions of Vps39 with Vps11.
Length = 109
Score = 26.4 bits (59), Expect = 4.8
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 55 MVCSKCEKKLGK---VITPDN 72
VC+ C K+LG V+ P+
Sbjct: 79 SVCAVCHKRLGNSVFVVYPNG 99
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 27.3 bits (61), Expect = 5.4
Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 121 VGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTAD 164
+G + +G +V+ P + AL G + V+ D
Sbjct: 18 IGEAVAERYL-AEGARVVIADIKPARARLAALEIGPAAIAVSLD 60
>gnl|CDD|233031 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 272
Score = 27.3 bits (61), Expect = 5.5
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 104 YTQKFESCKIC-----RQKVHQVGSHYCQAC 129
Y +K E C+ C + KV G+H+C C
Sbjct: 241 YGRKGEPCRRCGTPIEKIKVGGRGTHFCPQC 271
>gnl|CDD|234899 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/
5-hydroxymethyluracil DNA glycosylase; Validated.
Length = 274
Score = 27.0 bits (61), Expect = 5.8
Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 5/34 (14%)
Query: 101 FNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 129
Y ++ E C+ C + K + +C C
Sbjct: 238 LQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRC 271
>gnl|CDD|234515 TIGR04234, seadorna_RNAP, seadornavirus RNA-directed RNA
polymerase. Members of this protein family are the
seadornavirus VP1 protein, the RNA-directed RNA
polymerase.
Length = 1144
Score = 27.5 bits (61), Expect = 6.7
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 14 DRITSVRISFRHMVYEDALTIL 35
D +TS + SFR M Y D L L
Sbjct: 757 DSMTSEKNSFREMGYMDGLNTL 778
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
0.318 0.133 0.402
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,917,629
Number of extensions: 880454
Number of successful extensions: 770
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 17
Length of query: 199
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 107
Effective length of database: 6,857,034
Effective search space: 733702638
Effective search space used: 733702638
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: 41 (21.7 bits)
S2: 56 (25.3 bits)