RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4409
(305 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 34.7 bits (80), Expect = 0.002
Identities = 14/26 (53%), Positives = 20/26 (76%)
Query: 90 DMRRHIRRHTGEKPFKCNFCFQCFTQ 115
++RRH+R HTGEKP+KC C + F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 33.1 bits (76), Expect = 0.008
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 190 SMKRHLRKHTKDKPYECGFCSLKFSR 215
+++RH+R HT +KPY+C C FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 31.2 bits (71), Expect = 0.040
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 1 MRRHLRKHSGEKPYTCYFCNFKSAH 25
+RRH+R H+GEKPY C C +
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|218294 pfam04856, Securin, Securin sister-chromatid separation inhibitor.
Securin is also known as pituitary tumour-transforming
gene product. Over-expression of securin is associated
with a number of tumours, and it has been proposed that
this may be due to erroneous chromatid separation
leading to chromosome gain or loss.
Length = 214
Score = 31.0 bits (70), Expect = 0.58
Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 7/93 (7%)
Query: 214 SRRDNLRRHL--KDQH---SYDSFRSSTKKPGKYGVLIVKGSNISTMRVTSPSSQELTDD 268
R+ L KD + S F S++ K +YG + N+S S ++
Sbjct: 22 RTDSLKRKPLGSKDNNKTSSILPFGSNSVKLPRYGKVFGASLNLSKPSRKSLVLKDKEVK 81
Query: 269 HSEDIEEYHVKHDDTSIQHEETCVQY--EYDDD 299
++E + D SI ++ E D +
Sbjct: 82 SKTELESESDELSDKSIFPLGKKLKSSLEPDIE 114
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.2 bits (70), Expect = 0.74
Identities = 28/111 (25%), Positives = 42/111 (37%), Gaps = 5/111 (4%)
Query: 176 YVCMVCPYHCRQNESMKRHLRKHTKDKPYECGF--CSLKFSRRDNLRRHLKDQHSYDSFR 233
C C + E + RH+R HT +KP +C + C FSR L RHL+ H+ S
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDL 93
Query: 234 SSTKKPGKYGVLIVKGSNISTMRVTSPSSQELTDDHSEDIEEYHVKHDDTS 284
+S P + S+ + + L HS + D
Sbjct: 94 NSKSLPLSNSKASSSSLSSSSS---NSNDNNLLSSHSLPPSSRDPQLPDLL 141
>gnl|CDD|215958 pfam00507, Oxidored_q4, NADH-ubiquinone/plastoquinone
oxidoreductase, chain 3.
Length = 102
Score = 29.4 bits (67), Expect = 0.82
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 197 KHTKDKPYECGFCSLKFSR 215
K PYECGF L +R
Sbjct: 20 DREKLSPYECGFDPLGKAR 38
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 1.9
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 176 YVCMVCPYHCRQNESMKRHLRKH 198
Y C C + +++ H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.3 bits (53), Expect = 8.4
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 76 FTCLVCDYHSPRSIDMRRHIRRH 98
+ C C +R H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.7 bits (66), Expect = 2.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 200 KDKPYECGFCSLKFSRRDNLRRHLKDQH 227
KDKPY C C ++ + L+ H K H
Sbjct: 395 KDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus. This
family represents the C-terminus (approximately 500
residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have been
proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 29.4 bits (66), Expect = 2.6
Identities = 27/112 (24%), Positives = 44/112 (39%), Gaps = 18/112 (16%)
Query: 17 YF--CNFKSAHM-----SSINNHLKIKHLEKIQ--CRYSILKLQSHEESLVQHAK---RC 64
YF C + HM S++N K+K+ + R +L+L E Q K C
Sbjct: 287 YFTHCKLQPVHMILTLRSALNLFFKLKNFKTAASFAR-RLLELAPKPEVAQQARKVLQAC 345
Query: 65 SYVPRPNIQFNFTCLVCDYHSPRSIDMRRHIRRHTGEKPFKCNFCFQCFTQN 116
P Q N+ D H+P + ++ + G+ KC +C F+
Sbjct: 346 EKNPTDAHQLNY-----DEHNPFVVCGASYVPIYRGKPDVKCPYCGASFSPG 392
>gnl|CDD|226123 COG3595, COG3595, Uncharacterized conserved protein [Function
unknown].
Length = 318
Score = 29.0 bits (65), Expect = 3.3
Identities = 22/90 (24%), Positives = 31/90 (34%), Gaps = 10/90 (11%)
Query: 210 SLKFSRRDNLRRHLKDQHSYDSFRSSTKKPGKYGVLIVKGSNISTMRVTSPSSQELTDDH 269
SL D L Q F S+T G V+IV S S + + S S +D
Sbjct: 83 SLDGFEGDTLIVREVFQVRNVLFISTTLSKGVGDVIIVPWSL-SDVEIESVSGVIRIED- 140
Query: 270 SEDIEEYHVKH-------DDTSIQHEETCV 292
I + VK ++ I+ T
Sbjct: 141 -TKINDLFVKTTSGDISLNNLEIEKSVTIK 169
>gnl|CDD|218820 pfam05943, DUF877, Protein of unknown function (DUF877). This
family consists of a number of uncharacterized bacterial
proteins. The function of this family is unknown.
Length = 423
Score = 28.3 bits (64), Expect = 4.8
Identities = 5/16 (31%), Positives = 10/16 (62%)
Query: 167 AFRENDSYRYVCMVCP 182
+ RE++ RY+ + P
Sbjct: 162 SLRESEDARYLGLTLP 177
>gnl|CDD|235855 PRK06707, PRK06707, amidase; Provisional.
Length = 536
Score = 28.7 bits (64), Expect = 4.9
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 223 LKDQHSYDSFRSSTKKPGKYGVLIVKGSNISTMRVTSPSS 262
+++ D RS KK YG+ +V N+ T +V P+S
Sbjct: 119 MEEARKLDQERSRNKKSNLYGIPVVVKDNVQTAKVM-PTS 157
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins as
well as other related LSM (Like Sm) proteins. The U1,
U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing contain
seven Sm proteins (B/B', D1, D2, D3, E, F and G) in
common, which assemble around the Sm site present in
four of the major spliceosomal small nuclear RNAs. The
U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are also
RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 26.0 bits (58), Expect = 5.4
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 227 HSYDSF----------RSSTKKPGKYGVLIVKGSNISTMRV 257
+D F K K G+++++G+NI +
Sbjct: 26 KGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNNIVLISP 66
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 24.9 bits (55), Expect = 6.3
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 204 YECGFCSLKFSRRDNLRRHLKDQHS 228
+ CG C FS L H K S
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHCS 26
>gnl|CDD|214874 smart00871, AraC_E_bind, Bacterial transcription activator,
effector binding domain. This domain is found in the
probable effector binding domain of a number of
different bacterial transcription activators.and is also
present in some DNA gyrase inhibitors. The absence of a
HTH motif in the DNA gyrase inhibitors is thought to
indicate the fact that these do not bind DNA.
Length = 158
Score = 27.4 bits (61), Expect = 6.8
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 8/75 (10%)
Query: 224 KDQHSYDSFRSSTKKPGKYGVLIVKGSNISTMRVT--------SPSSQELTDDHSEDIEE 275
+ + + + T GKY V KG + ++ P+S D D E
Sbjct: 77 DEVEAPEGVETKTIPAGKYAVFTHKGGSYDEIQEAWEAIYGEWLPNSGYELRDAGPDFEV 136
Query: 276 YHVKHDDTSIQHEET 290
Y DT + T
Sbjct: 137 YLNDPPDTDPEELVT 151
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.5 bits (53), Expect = 8.3
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 204 YECGFCSLKFSRRDNLRRHLKDQH 227
++C C FS +D L+RHL+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|227822 COG5535, RAD4, DNA repair protein RAD4 [DNA replication,
recombination, and repair].
Length = 650
Score = 27.5 bits (61), Expect = 9.6
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 228 SYDSFRSSTKKPGKYGVLIVKGSNISTMRVTSPSSQEL---TDDHSEDIEEYHVKHDDTS 284
S+DSF +K + + G T+ ++ +DDH+E ++ +
Sbjct: 36 SFDSFYQDEEKDIDEEPVELDGDLTVTVNNIRRDRSKVSKYSDDHNEKLQSSQLHLIM-- 93
Query: 285 IQHEETCVQYEYDDDER 301
I + ++ DDER
Sbjct: 94 IPFMLLKSRNKWIDDER 110
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 0.135 0.429
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,494,566
Number of extensions: 1275694
Number of successful extensions: 1583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1577
Number of HSP's successfully gapped: 57
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
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: 40 (21.5 bits)
S2: 59 (26.7 bits)