RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2928
(744 letters)
>gnl|CDD|221479 pfam12237, PCIF1_WW, Phosphorylated CTD interacting factor 1 WW
domain. This domain family is found in bacteria and
eukaryotes, and is approximately 180 amino acids in
length. This domain is the WW domain of PCIF1. PCIF1
interacts with phosphorylated RNA polymerase II
carboxy-terminal domain (CTD). The WW domain of PCIF1
can directly and preferentially bind to the
phosphorylated CTD compared to the unphosphorylated CTD.
PCIF1 binds to the hyperphosphorylated RNAP II (RNAP
IIO) in vitro and in vivo. Double immunofluorescence
labeling in HeLa cells demonstrated that PCIF1 and
endogenous RNAP IIO are co-localized in the cell
nucleus. Thus, PCIF1 may play a role in mRNA synthesis
by modulating RNAP IIO activity.
Length = 175
Score = 231 bits (592), Expect = 4e-72
Identities = 87/172 (50%), Positives = 106/172 (61%), Gaps = 5/172 (2%)
Query: 496 RNSCFDDKKFELFLPRVWCLLKRYTTFLGQVTAQSGKTQASLPGPVFECLNKHFGVTFEC 555
R + DD + E FL RV+CLL RY T G G QA+LP VF+ L FGV+ EC
Sbjct: 7 RRTSRDDPEDEDFLFRVFCLLLRYDTIFGGEQEAEG-FQAALPEDVFDVLKDKFGVSCEC 65
Query: 556 FASPLNCYFRQYCSMFPDTDSYFGSRGPILDLKAVSGSFQAHPPYCEELMEATVGHFEHL 615
FASPLN QYCS FPDTD YFGS G D K SGSF+A+PP+ EELM+A H E L
Sbjct: 66 FASPLNARLAQYCSAFPDTDKYFGSLGSFFDFKPSSGSFEANPPFDEELMDAMAEHLERL 125
Query: 616 L--ADSPEPLSFIVFVPDFRDPSPSALVKLEASHFKRKQVVVPAFEHEFRIG 665
L + S PLSF+V VP++++ P A KLE S F R+ V+ A EH + G
Sbjct: 126 LDASKSTTPLSFVVIVPEWKE--PPAWSKLENSAFCRRDTVLLAKEHGYYDG 175
>gnl|CDD|238122 cd00201, WW, Two conserved tryptophans domain; also known as the
WWP or rsp5 domain; around 40 amino acids; functions as
an interaction module in a diverse set of signalling
proteins; binds specific proline-rich sequences but at
low affinities compared to other peptide recognition
proteins such as antibodies and receptors; WW domains
have a single groove formed by a conserved Trp and Tyr
which recognizes a pair of residues of the sequence
X-Pro; variable loops and neighboring domains confer
specificity in this domain; there are five distinct
groups based on binding: 1) PPXY motifs 2) the PPLP
motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR
motifs.
Length = 31
Score = 39.4 bits (93), Expect = 1e-04
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 92 GWRKFWSKRENRPYYWNRASGESLWDMPQG 121
GW + W + R YY+N + E+ W+ P+
Sbjct: 3 GWEERWD-PDGRVYYYNHNTKETQWEDPRE 31
>gnl|CDD|215899 pfam00397, WW, WW domain. The WW domain is a protein module with
two highly conserved tryptophans that binds proline-rich
peptide motifs in vitro.
Length = 30
Score = 36.8 bits (86), Expect = 9e-04
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 92 GWRKFWSKRENRPYYWNRASGESLWDMP 119
GW + + RPYY+N +GE+ W+ P
Sbjct: 4 GWEERTD-TDGRPYYYNHNTGETQWERP 30
>gnl|CDD|197736 smart00456, WW, Domain with 2 conserved Trp (W) residues. Also
known as the WWP or rsp5 domain. Binds proline-rich
polypeptides.
Length = 33
Score = 36.0 bits (84), Expect = 0.002
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 92 GWRKFWSKRENRPYYWNRASGESLWDMPQG 121
GW + + RPYY+N + E+ W+ P+
Sbjct: 5 GWEERKDP-DGRPYYYNHETKETQWEKPRE 33
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 34.0 bits (78), Expect = 0.37
Identities = 15/101 (14%), Positives = 24/101 (23%), Gaps = 8/101 (7%)
Query: 11 PAPTTSWDSMSVPQGPPIPITHENIQQVMVPVPIKMQPPPNLNPMME-------HGNPMQ 63
PAP+ + +P P Q PPP + P
Sbjct: 221 PAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQN 280
Query: 64 QGPMTPHQGVQMGGSYIDHELPPELIQQGWRKFWSKRENRP 104
Q P P+L+ + +R +
Sbjct: 281 QPTPHPGLPQGQNAPLPPP-QQPQLLPLVQQPQGQQRGPQF 320
Score = 33.6 bits (77), Expect = 0.47
Identities = 26/197 (13%), Positives = 38/197 (19%), Gaps = 48/197 (24%)
Query: 17 WDSMSVPQGPPIPITH---------------ENIQQVMVPVPIKMQPPPNLNPMMEHGNP 61
W + P+ P E ++ + Q P ++ G P
Sbjct: 126 WGTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMP 185
Query: 62 MQQGPMTPHQGVQMGGSYIDHELPPELIQQGWRKFWSKRENRPYYWNRASGESLWDMPQG 121
+Q + Y P
Sbjct: 186 PRQAAFPQQGPPEQPPGYPQPPQGH-----------------PEQVQPQQ------FLPA 222
Query: 122 SGFDPIGDPLGICAGPPPPHTPNMNMPPQPMKRRASEGMAMGAPLPKKFILSGPWDLEIP 181
P PL P P + P P + M P P + P P
Sbjct: 223 PSQAPAQPPL---PPQLPQQPPPLQQPQFPGLSQ---QMPPPPPQPPQQQQQPPQPQAQP 276
Query: 182 TNVIILERAPTSMPQPH 198
PT P
Sbjct: 277 PPQ----NQPTPHPGLP 289
Score = 29.4 bits (66), Expect = 9.4
Identities = 16/81 (19%), Positives = 20/81 (24%), Gaps = 7/81 (8%)
Query: 19 SMSVPQGPPIPITHENIQQVMVPVPIKMQPPPNLNPMMEH----GNPMQQ---GPMTPHQ 71
+ Q P P QQ P P PP N N P
Sbjct: 248 FPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPL 307
Query: 72 GVQMGGSYIDHELPPELIQQG 92
Q G + +L+Q
Sbjct: 308 VQQPQGQQRGPQFREQLVQLS 328
>gnl|CDD|181561 PRK08818, PRK08818, prephenate dehydrogenase; Provisional.
Length = 370
Score = 33.3 bits (76), Expect = 0.47
Identities = 24/63 (38%), Positives = 31/63 (49%), Gaps = 12/63 (19%)
Query: 614 HLLADSPEPLSFIVFVPDFRDPSPSAL--------VKLEASHFKRKQVVVPAFEHEFRIG 665
+LLAD EPL+ V++P+ R S L V L + H R PA E FRIG
Sbjct: 287 YLLADLTEPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHSSR----TPAGELHFRIG 342
Query: 666 VQP 668
+P
Sbjct: 343 FEP 345
>gnl|CDD|177328 PHA01929, PHA01929, putative scaffolding protein.
Length = 306
Score = 30.8 bits (69), Expect = 2.2
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 11 PAPTTSWDSMSVPQGPPIPITHENIQQVMVPVPIKMQPPPNLNPMMEHGNPMQQGPMTP 69
APT + + PQ P P QQ+ +P + QP P + M H +QQ P P
Sbjct: 23 AAPTPQPNPVIQPQAPVQPGQPGAPQQLAIPTQ-QPQPVP-TSAMTPH--VVQQAPAQP 77
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 30.1 bits (68), Expect = 5.7
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 283 DARKQLSKYAEAAKKLIESRNAN---SESRKVVKWNAEDTFL-WLRKTVGATYDDFQERL 338
+A+ L Y + K ++ S+S K A D L WL K A ++F+ +
Sbjct: 539 EAKNGLENYCYSMKNTLQDEKVKGKLSDSDKATIEKAIDEALEWLEKNQLAEKEEFEHKQ 598
Query: 339 NHLKTQCQPHLTE 351
+++ C P +T+
Sbjct: 599 KEVESVCNPIMTK 611
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form a
pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 29.1 bits (66), Expect = 6.1
Identities = 22/108 (20%), Positives = 44/108 (40%), Gaps = 29/108 (26%)
Query: 279 KYTGDARKQLSKYA-EAAKKLIESRNANSESRKVVKWNAEDTFLWLRKTVGATYDDFQER 337
Y + ++QL YA E +L +++T LR+ + +D + R
Sbjct: 12 SYAEELQEQLGPYAQEFWARL-----------------SKET-EALREELQKDLEDVRAR 53
Query: 338 LNHLKTQCQPHLTE---TVKDSVEKICLKIQHLSTEHAKKIRDKNSDL 382
L QP+L E V ++E++ ++ + E K++ +L
Sbjct: 54 L-------QPYLDELKAKVGQNLEELRQRLAPYAEELRKRLNRDAEEL 94
>gnl|CDD|172967 PRK14495, PRK14495, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/unknown domain fusion protein;
Provisional.
Length = 452
Score = 29.6 bits (66), Expect = 6.8
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 167 PKKFILSGPWDLEIPTNVIILER-APTSM-------PQPHPEIELFR 205
P++ IL+ E P ILER AP + +PHP+IE+FR
Sbjct: 67 PRRLILTREHRGEPPRLAAILERMAPVDLVLVEGYKTEPHPKIEVFR 113
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 29.5 bits (67), Expect = 7.0
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 13/62 (20%)
Query: 335 QERLNHLKTQCQPHLT-ETVKDSVEKICLKIQHLSTEHAK----------KIRDKNSDLL 383
Q+ + +L+ + + +T E ++D VEK+ ++ H T AK +IR+ SDL+
Sbjct: 45 QKVIKYLEEKYKEEVTVEDIQDLVEKVLIENGHAET--AKAYILYRAERTRIREIKSDLM 102
Query: 384 TA 385
A
Sbjct: 103 KA 104
>gnl|CDD|224079 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 29.5 bits (67), Expect = 7.5
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 121 GSGFDPIGDPLGICAGPPPPHT---PNMNMPPQPMKRR 155
G D +G PL G P T P PP P+KRR
Sbjct: 106 GRVLDGLGRPLD--GGGLPDGTERRPLDAPPPNPLKRR 141
>gnl|CDD|165425 PHA03154, PHA03154, hypothetical protein; Provisional.
Length = 304
Score = 29.3 bits (65), Expect = 8.3
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 421 EYHPDKEQIMLRFQNDTVTVNSLH--FQKL-EHLYRY-SCFDDKKFE 463
+Y D+ ++F D +T+ S H Q L E++Y Y CF +++F+
Sbjct: 258 DYEADRMAKFIKFSADQITILSTHTDLQGLAEYIYSYKKCFINRRFD 304
>gnl|CDD|217931 pfam04153, NOT2_3_5, NOT2 / NOT3 / NOT5 family. NOT1, NOT2, NOT3,
NOT4 and NOT5 form a nuclear complex that negatively
regulates the basal and activated transcription of many
genes. This family includes NOT2, NOT3 and NOT5.
Length = 131
Score = 28.1 bits (63), Expect = 9.0
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 394 PPSTLNSRKVWCYPIQFSTPSCRMPSIEYH-----PDKEQIMLRFQNDT 437
PPS ++R+ P Q+ P C + + + P +F ++T
Sbjct: 8 PPSPSDARER---PPQYDIPECYLNTPSSYPQNPPPLSPSKFQKFDDET 53
>gnl|CDD|233401 TIGR01413, Dyp_perox_fam, Dyp-type peroxidase family. A defined
member of this superfamily is Dyp, a dye-decolorizing
peroxidase that lacks a typical heme-binding region. A
distinct, uncharacterized branch (TIGR01412) of this
superfamily has a typical twin-arginine dependent signal
sequence characteristic of exported proteins with bound
redox cofactors.
Length = 308
Score = 28.9 bits (65), Expect = 9.8
Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 536 SLP-GPVFECLNKHFGVTFECFASPLNCYFRQYCSMFPDTDSYFGSRGPILD-LKAVSGS 593
SLP G + + G+ F + L Q MF D D G+ +L+ + V G
Sbjct: 242 SLPYGDGSDDTGQDAGLLFIAYQRSLENGEIQLQRMFGDND---GATDRLLEFTRPVGGG 298
Query: 594 FQAHPPYCE 602
+ P
Sbjct: 299 YFFAPSGVA 307
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
0.319 0.136 0.433
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,516,832
Number of extensions: 3766495
Number of successful extensions: 3404
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3340
Number of HSP's successfully gapped: 33
Length of query: 744
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 640
Effective length of database: 6,324,786
Effective search space: 4047863040
Effective search space used: 4047863040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.2 bits)