RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5572
(62 letters)
>gnl|CDD|177688 PLN00057, PLN00057, proliferating cell nuclear antigen;
Provisional.
Length = 263
Score = 103 bits (259), Expect = 2e-29
Identities = 40/62 (64%), Positives = 52/62 (83%)
Query: 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
MQEPVSL FA RYL +F KA PLS+ V LS+S ++P+VVE+KI ++G+IRYYLAPKIE D
Sbjct: 199 MQEPVSLTFALRYLNSFTKATPLSDTVTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEED 258
Query: 61 DN 62
++
Sbjct: 259 ED 260
>gnl|CDD|188067 TIGR00590, pcna, proliferating cell nuclear antigen (pcna). All
proteins in this family for which functions are known
form sliding DNA clamps that are used in DNA replication
processes. 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 = 259
Score = 100 bits (250), Expect = 4e-28
Identities = 37/61 (60%), Positives = 50/61 (81%)
Query: 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
M++PV+L FA +YL F KA PLS++V LSMS DVPLVVE+KI D+G +R++LAPKIE +
Sbjct: 199 MKQPVTLTFAIKYLNLFTKATPLSDRVTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDE 258
Query: 61 D 61
+
Sbjct: 259 E 259
>gnl|CDD|202372 pfam02747, PCNA_C, Proliferating cell nuclear antigen, C-terminal
domain. N-terminal and C-terminal domains of PCNA are
topologically identical. Three PCNA molecules are
tightly associated to form a closed ring encircling
duplex DNA.
Length = 128
Score = 94.1 bits (234), Expect = 5e-27
Identities = 36/56 (64%), Positives = 44/56 (78%)
Query: 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
M EPV+L FA RYL +F KA PLS V +SMS ++PLVVE+KI D+G +RYYLAPK
Sbjct: 73 MNEPVTLTFALRYLNSFTKATPLSPTVTISMSSELPLVVEYKIADMGLLRYYLAPK 128
>gnl|CDD|238322 cd00577, PCNA, Proliferating Cell Nuclear Antigen (PCNA) domain
found in eukaryotes and archaea. These polymerase
processivity factors play a role in DNA replication and
repair. PCNA encircles duplex DNA in its central
cavity, providing a DNA-bound platform for the
attachment of the polymerase. The trimeric PCNA ring is
structurally similar to the dimeric ring formed by the
DNA polymerase processivity factors in bacteria (beta
subunit DNA polymerase III holoenzyme) and in
bacteriophages (catalytic subunits in T4 and RB69). This
structural correspondence further substantiates the
mechanistic connection between eukaryotic and
prokaryotic DNA replication that has been suggested on
biochemical grounds. PCNA is also involved with
proteins involved in cell cycle processes such as DNA
repair and apoptosis. Many of these proteins contain a
highly conserved motif known as the PIP-box (PCNA
interacting protein box) which contains the sequence
Qxx[LIM]xxF[FY]. .
Length = 248
Score = 78.8 bits (195), Expect = 5e-20
Identities = 33/58 (56%), Positives = 42/58 (72%)
Query: 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
EPVS ++ +YL +F KAAPLS++V LS D PL +EFKI D GH+ +YLAPKIE
Sbjct: 191 CSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLEFKIADGGHLTFYLAPKIE 248
>gnl|CDD|185661 PTZ00483, PTZ00483, proliferating cell nuclear antigen;
Provisional.
Length = 264
Score = 54.9 bits (132), Expect = 5e-11
Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 7/63 (11%)
Query: 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFK-------IDDIGHIRYYLAP 55
E +S FA RYL+ F+KA L+++V +++S +PL V+F + D I +YLAP
Sbjct: 201 ESLSQEFATRYLVLFSKATSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAP 260
Query: 56 KIE 58
IE
Sbjct: 261 NIE 263
>gnl|CDD|240275 PTZ00113, PTZ00113, proliferating cell nuclear antigen;
Provisional.
Length = 275
Score = 51.4 bits (123), Expect = 1e-09
Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 10/69 (14%)
Query: 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD----------IGHIRY 51
++P+ ++A +YL FAK+ LS+ V L +S + P+ V+++I D +G +++
Sbjct: 202 RKPIKQSYATKYLNMFAKSGCLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKF 261
Query: 52 YLAPKIESD 60
+LAPK++ D
Sbjct: 262 FLAPKMDDD 270
>gnl|CDD|234903 PRK01115, PRK01115, DNA polymerase sliding clamp; Validated.
Length = 247
Score = 48.3 bits (116), Expect = 1e-08
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 13 YLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
YL + KA S++V + D+PL +EF+I G + Y LAP+IE
Sbjct: 202 YLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE 247
>gnl|CDD|177619 PHA03383, PHA03383, PCNA-like protein; Provisional.
Length = 262
Score = 41.4 bits (97), Expect = 3e-06
Identities = 14/50 (28%), Positives = 34/50 (68%)
Query: 9 FACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
F+ +YL +F KA+ +S+ V + + PL++++ + +G++++ +APK+
Sbjct: 213 FSLKYLTSFTKASGMSSSVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS 262
>gnl|CDD|223665 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair].
Length = 364
Score = 32.3 bits (74), Expect = 0.006
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 13 YLLNFAKAAPLS-NQVCLSMSLDVPLVVEFKIDDI-----GHIRYYLAPKIESDDN 62
YL + K L+ +V LS+ D P E +ID I + LA ++
Sbjct: 273 YLKDRGKKLSLADGEVKLSLGNDEPGKAEEEIDVGYTGEELKIGFNLAYLLDVLKA 328
>gnl|CDD|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional.
Length = 607
Score = 26.9 bits (60), Expect = 0.54
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD--VPLVV 39
+PVSLN +L + A + +V LD +P +
Sbjct: 457 QPVSLNALVEEVLQLFQTAGVQARVDFETELDNELPPIW 495
>gnl|CDD|129429 TIGR00329, gcp_kae1, metallohydrolase, glycoprotease/Kae1 family.
This subfamily includes the well-studied secreted
O-sialoglycoprotein endopeptidase (glycoprotease, EC
3.4.24.57) of Pasteurella haemolytica, a pathogen. A
member from Riemerella anatipestifer, associated with
cohemolysin activity, likewise is exported without
benefit of a classical signal peptide and shows
glycoprotease activity on the test substrate
glycophorin. However, archaeal members of this subfamily
show unrelated activities as demonstrated in Pyrococcus
abyssi: DNA binding, iron binding, apurinic endonuclease
activity, genomic association with a kinase domain, and
no glycoprotease activity. This family thus pulls
together a set of proteins as a homology group that
appears to be near-universal in life, yet heterogeneous
in assayed function between bacteria and archaea
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 305
Score = 25.8 bits (57), Expect = 1.5
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 13/47 (27%)
Query: 15 LNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61
FA++ L++SLD PL+ + +GHI AP+++++
Sbjct: 89 ATFARS--------LALSLDKPLIGVNHL--LGHI---YAPRLDTNI 122
>gnl|CDD|221093 pfam11359, gpUL132, Glycoprotein UL132. Glycoprotein UL132 is a
low-abundance structural component of Human
cytomegalovirus (HCMV). The function of this protein is
not fully understood.
Length = 235
Score = 25.4 bits (55), Expect = 2.1
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 36 PLVVEFKIDDIGHIRYYLA 54
P+ +E DD +IRYY++
Sbjct: 179 PMTIESHADDDENIRYYMS 197
>gnl|CDD|236585 PRK09604, PRK09604, UGMP family protein; Validated.
Length = 332
Score = 25.0 bits (56), Expect = 2.2
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 21/50 (42%)
Query: 15 LNFAKAAPLSNQVCLSMSLDVPLV----VEFKIDDIGHIRYYLAPKIESD 60
++FAKA L+++L+ PL+ +E GH+ LAP +E +
Sbjct: 92 VSFAKA--------LALALNKPLIGVNHLE------GHL---LAPFLEEE 124
>gnl|CDD|223607 COG0533, QRI7, Metal-dependent proteases with possible chaperone
activity [Posttranslational modification, protein
turnover, chaperones].
Length = 342
Score = 24.5 bits (54), Expect = 4.7
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 13/47 (27%)
Query: 15 LNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61
AKA L+++L+ PL+ + GHI A ++E+
Sbjct: 91 ATAAKA--------LALALNKPLIPVNHL--EGHI---EAARLETGL 124
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 24.3 bits (54), Expect = 5.2
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 31 MSLDVPLVVEFKI 43
+ L VPLVV+ +
Sbjct: 860 VELSVPLVVDVGV 872
>gnl|CDD|176474 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with the
single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an incoming
dNTP) and thumb (which binds double-stranded DNA)
subdomains.
Length = 377
Score = 23.9 bits (53), Expect = 5.8
Identities = 5/13 (38%), Positives = 8/13 (61%)
Query: 31 MSLDVPLVVEFKI 43
+ L VPL V+ +
Sbjct: 360 VELSVPLKVDVGV 372
>gnl|CDD|217256 pfam02865, STAT_int, STAT protein, protein interaction domain.
STAT proteins (Signal Transducers and Activators of
Transcription) are a family of transcription factors
that are specifically activated to regulate gene
transcription when cells encounter cytokines and growth
factors. STAT proteins also include an SH2 domain
pfam00017.
Length = 124
Score = 23.4 bits (51), Expect = 8.2
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 48 HIRYYLAPKIESDD 61
+R+YLA IES D
Sbjct: 28 EVRHYLAQWIESQD 41
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
0.323 0.139 0.411
Gapped
Lambda K H
0.267 0.0540 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,043,479
Number of extensions: 205512
Number of successful extensions: 163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 161
Number of HSP's successfully gapped: 18
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.6 bits)