RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7787
(463 letters)
>gnl|CDD|146345 pfam03660, PHF5, PHF5-like protein. This family of proteins the
superfamily of PHD-finger proteins. At least one
example, from mouse, may act as a chromatin-associated
protein. The S. pombe ini1 gene is essential, required
for splicing. It is localised in the nucleus, but not
detected in the nucleolus and can be complemented by
human ini1.
Length = 105
Score = 127 bits (320), Expect = 1e-35
Identities = 49/66 (74%), Positives = 53/66 (80%)
Query: 322 GLTIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKEC 381
G IGRLCEKCDGKC ICDSYVRP T VRICDEC++GS +C+ICG PGVSDAYYC EC
Sbjct: 15 GTAIGRLCEKCDGKCPICDSYVRPTTKVRICDECSFGSLGNKCIICGSPGVSDAYYCWEC 74
Query: 382 TIQEKD 387
EKD
Sbjct: 75 VRLEKD 80
Score = 126 bits (318), Expect = 3e-35
Identities = 49/64 (76%), Positives = 53/64 (82%)
Query: 13 AIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTI 72
AIGRLCEKCDGKC ICDSYVRP T VRICDEC++GS +C+ICG PGVSDAYYC EC
Sbjct: 17 AIGRLCEKCDGKCPICDSYVRPTTKVRICDECSFGSLGNKCIICGSPGVSDAYYCWECVR 76
Query: 73 QEKD 76
EKD
Sbjct: 77 LEKD 80
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 37.8 bits (88), Expect = 0.014
Identities = 19/64 (29%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 15 GRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGV-SDAYYCKECTIQ 73
C KC GK + T+ C EC C ICG V + C EC +
Sbjct: 53 EIPCPKCRGKGTV--------TVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRK 104
Query: 74 EKDV 77
K V
Sbjct: 105 PKIV 108
Score = 37.8 bits (88), Expect = 0.014
Identities = 19/64 (29%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 326 GRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGV-SDAYYCKECTIQ 384
C KC GK + T+ C EC C ICG V + C EC +
Sbjct: 53 EIPCPKCRGKGTV--------TVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRK 104
Query: 385 EKDV 388
K V
Sbjct: 105 PKIV 108
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 35.3 bits (82), Expect = 0.078
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 39 RICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDVS 78
R C C ++ RC CG Y C C I+ ++
Sbjct: 627 RKCPSCGKETFYRRCPFCGTHTEPV-YRCPRCGIEVEEDE 665
Score = 35.3 bits (82), Expect = 0.078
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 350 RICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDVS 389
R C C ++ RC CG Y C C I+ ++
Sbjct: 627 RKCPSCGKETFYRRCPFCGTHTEPV-YRCPRCGIEVEEDE 665
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 30.7 bits (70), Expect = 1.8
Identities = 16/67 (23%), Positives = 20/67 (29%), Gaps = 18/67 (26%)
Query: 16 RLCEKCDGKCVICDSYVRPCTLVRICDECN-YGSYQGR-----------CVICGGPGVSD 63
C C G S +P T + C CN G + C C G G
Sbjct: 143 VTCSTCHG------SGAKPGTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKII 196
Query: 64 AYYCKEC 70
C +C
Sbjct: 197 KDPCGKC 203
Score = 30.7 bits (70), Expect = 1.8
Identities = 16/67 (23%), Positives = 20/67 (29%), Gaps = 18/67 (26%)
Query: 327 RLCEKCDGKCVICDSYVRPCTLVRICDECN-YGSYQGR-----------CVICGGPGVSD 374
C C G S +P T + C CN G + C C G G
Sbjct: 143 VTCSTCHG------SGAKPGTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKII 196
Query: 375 AYYCKEC 381
C +C
Sbjct: 197 KDPCGKC 203
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 30.4 bits (69), Expect = 2.1
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 240 HYSVIDSFFKAQQEDEIF-------GSSKTKAIKYSSSITSVHIFRLHPVKNGQTSSGFD 292
Y+ I F+ ++ E+F GS +T+ YSS +F P KN + GF
Sbjct: 546 PYASIHYPFENEKFKEVFPADFILEGSDQTRGWFYSSLAIGTALFGQAPYKN-VITHGFT 604
Query: 293 L 293
L
Sbjct: 605 L 605
>gnl|CDD|181400 PRK08351, PRK08351, DNA-directed RNA polymerase subunit E'';
Validated.
Length = 61
Score = 27.2 bits (60), Expect = 2.9
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 39 RICDECNYGSYQGRCVICGGPGVSDAYY 66
+ C C+Y + + RC +CG +SD ++
Sbjct: 4 KACRHCHYITTEDRCPVCGSRDLSDEWF 31
Score = 27.2 bits (60), Expect = 2.9
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 350 RICDECNYGSYQGRCVICGGPGVSDAYY 377
+ C C+Y + + RC +CG +SD ++
Sbjct: 4 KACRHCHYITTEDRCPVCGSRDLSDEWF 31
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 29.6 bits (67), Expect = 4.3
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 14 IGRLCEKCDGKC------VICDSYVRPCTLVRICDECNYGSYQGRCVI 55
+ RLC C +C + S P C+ CN Y+GR I
Sbjct: 394 VRRLCPHCKEECEPEELARLGLSESLPLYRAVGCEACNGSGYKGRTGI 441
Score = 29.6 bits (67), Expect = 4.3
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 325 IGRLCEKCDGKC------VICDSYVRPCTLVRICDECNYGSYQGRCVI 366
+ RLC C +C + S P C+ CN Y+GR I
Sbjct: 394 VRRLCPHCKEECEPEELARLGLSESLPLYRAVGCEACNGSGYKGRTGI 441
>gnl|CDD|165668 PLN00095, PLN00095, chlorophyllide a oxygenase; Provisional.
Length = 394
Score = 28.9 bits (64), Expect = 5.6
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 300 RSCPLSLGKILKLRLEPHSHSLGLTIGRLCEK 331
R+CPLSLGK++ + + H G C K
Sbjct: 118 RACPLSLGKLVDGKAQCPYHGWEYETGGECAK 149
>gnl|CDD|153108 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit,
ferritin-like diiron-binding domain. Ribonucleotide
Reductase, R2/beta subunit (RNRR2) is a member of a
broad superfamily of ferritin-like diiron-carboxylate
proteins. The RNR protein catalyzes the conversion of
ribonucleotides to deoxyribonucleotides and is found in
all eukaryotes, many prokaryotes, several viruses, and
few archaea. The catalytically active form of RNR is a
proposed alpha2-beta2 tetramer. The homodimeric alpha
subunit (R1) contains the active site and redox active
cysteines as well as the allosteric binding sites. The
beta subunit (R2) contains a diiron cluster that, in its
reduced state, reacts with dioxygen to form a stable
tyrosyl radical and a diiron(III) cluster. This
essential tyrosyl radical is proposed to generate a
thiyl radical, located on a cysteine residue in the R1
active site that initiates ribonucleotide reduction. The
beta subunit is composed of 10-13 helices, the 8 longest
helices form an alpha-helical bundle; some have 2
addition beta strands. Yeast is unique in that it
assembles both homodimers and heterodimers of RNRR2. The
yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2
homolog (Y4) that lacks the diiron center and is
proposed to only assist in cofactor assembly, and
perhaps stabilize R1 (Y1) in its active conformation.
Length = 288
Score = 28.7 bits (65), Expect = 6.0
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 236 IHTRHYS-VIDSFFKAQQEDEIFGSSKT-KAIKY 267
IH+ YS ++D+ K ++ DE+F + +T A+K
Sbjct: 92 IHSESYSYILDTLGKDEERDELFEAIETDPALKK 125
>gnl|CDD|227495 COG5166, COG5166, Uncharacterized conserved protein [Function
unknown].
Length = 657
Score = 28.8 bits (64), Expect = 7.1
Identities = 21/114 (18%), Positives = 37/114 (32%), Gaps = 4/114 (3%)
Query: 206 ALKKRFSLLQALQQVDNLSLLLHVFHFLNHIHTRHYSVIDSFFKAQQEDEIFGSSKTKAI 265
+ Q+ Q S H F + + VI F + + + I
Sbjct: 161 GFSNGLNEQQSFYQRHLESTR-HEFSCQKNAEMSFFIVIYGAFCSVEHARSRVLALMDEI 219
Query: 266 KYSSSI---TSVHIFRLHPVKNGQTSSGFDLLSKTSRRSCPLSLGKILKLRLEP 316
+ S I TSV + K +++G + + P KI +L+ P
Sbjct: 220 RGLSVIFIATSVSSQPILVGKAFSSTAGMKATESINIYTLPFCSDKIPRLQTYP 273
>gnl|CDD|132961 cd06630, STKc_MEKK1, Catalytic domain of the Protein
Serine/Threonine Kinase, MAP/ERK kinase kinase 1.
Serine/threonine kinases (STKs), MAP/ERK kinase kinase 1
(MEKK1) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
MEKK1 subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. MEKK1 is a mitogen-activated protein kinase
(MAPK) kinase kinase (MAPKKK or MKKK or MAP3K), that
phosphorylates and activates MAPK kinases (MAPKKs or
MKKs or MAP2Ks), which in turn phosphorylate and
activate MAPKs during signaling cascades that are
important in mediating cellular responses to
extracellular signals. MEKK1 activates the extracellular
signal-regulated kinase 1/2 (ERK1/2) and c-Jun
N-terminal kinase (JNK) pathways by activating their
respective MAPKKs, MEK1/2 and MKK4/MKK7, respectively.
MEKK1 is important in regulating cell survival and
apoptosis. MEKK1 also plays a role in cell migration,
tissue maintenance and homeostasis, and wound healing.
Length = 268
Score = 28.3 bits (63), Expect = 8.7
Identities = 8/39 (20%), Positives = 23/39 (58%)
Query: 409 QKNTYWDIFVNTLSTLSIATCLNGFGTCAEFMSVEYCYQ 447
+++++++FV ++ S++ L+ +G E + + Y Q
Sbjct: 73 CEDSHFNLFVEWMAGGSVSHLLSKYGAFKEAVIINYTEQ 111
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
0.324 0.139 0.445
Gapped
Lambda K H
0.267 0.0641 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,488,621
Number of extensions: 2084721
Number of successful extensions: 1480
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1476
Number of HSP's successfully gapped: 31
Length of query: 463
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 363
Effective length of database: 6,502,202
Effective search space: 2360299326
Effective search space used: 2360299326
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.5 bits)