RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1089
(404 letters)
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 171 bits (436), Expect = 7e-47
Identities = 77/178 (43%), Positives = 112/178 (62%), Gaps = 17/178 (9%)
Query: 183 KMTNVTMVLRNIISHPYLIN-----KPYRIVDGKKEMVCDENIVSSSGKMIVLNQLLHKL 237
++ N+ M LR +HPYL PY E++V +SGKM++L++LL KL
Sbjct: 433 RLLNIAMQLRKCCNHPYLFQGAEPGPPY---------TTGEHLVENSGKMVLLDKLLPKL 483
Query: 238 KQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN--GSTEWGV 295
K+ + + L+FS M ++L+ +E+ + Y Y R+ G+ E+R+ ++ FN GS ++ V
Sbjct: 484 KERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKF-V 542
Query: 296 FLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCIYRLVSHST 353
FLLSTRAGG G+NL AD ILYDSDWNPQVD+QA+ R HRIGQ K V ++R + T
Sbjct: 543 FLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYT 600
Score = 55.2 bits (133), Expect = 4e-08
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 1 MHNILKPFFLRRLKCDVNLNLPPKKTTVIDCPMVPAQELMYTKVLTKTI 49
+H +L+PF LRRLK DV LPPKK T++ M Q+ Y +L K +
Sbjct: 374 LHKVLRPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDL 422
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 135 bits (340), Expect = 2e-34
Identities = 74/210 (35%), Positives = 105/210 (50%), Gaps = 15/210 (7%)
Query: 156 CENSSNAQDVPSAEEKNVDEILHHVNVKMT--NVTMVLRNIISHPYLI-----NKPYRIV 208
E + Q + EK + + ++ + LR I +HP L+ RIV
Sbjct: 611 LEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRLRQICNHPALVDEGLEATFDRIV 670
Query: 209 DGKKE-----MVCDENIVSSSGKMIVLNQLL---HKLKQTNHKTLVFSTMVKVLNFIEEL 260
+E + I S GK+ L++LL + HK L+FS VL+ +E+
Sbjct: 671 LLLREDKDFDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDY 730
Query: 261 CVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDS 320
Y RL GS + R + + +FN E VFLLS +AGG GLNLT ADT IL+D
Sbjct: 731 LKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDP 790
Query: 321 DWNPQVDIQAEARCHRIGQTKPVCIYRLVS 350
WNP V++QA R HRIGQ +PV +YRL++
Sbjct: 791 WWNPAVELQAIDRAHRIGQKRPVKVYRLIT 820
Score = 36.6 bits (84), Expect = 0.025
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 2 HNILKPFFLRRLKCDVNL--NLPPKKTTVIDCPMVPAQELMYTKVLTKTIGENREQVAEY 59
+L PF LRR K DV + LPPK V++C + Q +Y +L E +Q+ E
Sbjct: 566 RKLLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALL--EGAEKNQQLLED 623
Query: 60 FNTT 63
Sbjct: 624 LEKA 627
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 101 bits (254), Expect = 4e-26
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 4/128 (3%)
Query: 220 IVSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEE 279
+ K+ L +LL + + K L+F K+L+ + EL LHG EE
Sbjct: 7 LPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEE 66
Query: 280 RNDAVQQFN-GSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIG 338
R + ++ F G L++T +G++L I YD W+P +Q R R G
Sbjct: 67 REEVLKDFREGEIV---VLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAG 123
Query: 339 QTKPVCIY 346
Q +
Sbjct: 124 QKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 85.3 bits (212), Expect = 8e-21
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 2/80 (2%)
Query: 259 ELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTCILY 318
+L RLHG + EER + ++ F L++T G+G++L + I Y
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGK--SKVLVATDVAGRGIDLPDVNLVINY 58
Query: 319 DSDWNPQVDIQAEARCHRIG 338
D WNP IQ R R G
Sbjct: 59 DLPWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 82.6 bits (205), Expect = 8e-20
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 256 FIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTC 315
+ EL RLHG + EER + + +FN L++T +GL+L D
Sbjct: 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGK--IKVLVATDVAERGLDLPGVDLV 59
Query: 316 ILYDSDWNPQVDIQAEARCHRIG 338
I+YD W+P IQ R R G
Sbjct: 60 IIYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 55.8 bits (135), Expect = 9e-09
Identities = 23/47 (48%), Positives = 30/47 (63%)
Query: 1 MHNILKPFFLRRLKCDVNLNLPPKKTTVIDCPMVPAQELMYTKVLTK 47
+H +LKPF LRR K DV +LPPK V+ C + Q +Y K+LTK
Sbjct: 217 LHKLLKPFLLRRTKDDVEKSLPPKTEHVLYCNLSDEQRKLYKKLLTK 263
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 44.0 bits (104), Expect = 9e-05
Identities = 52/240 (21%), Positives = 88/240 (36%), Gaps = 52/240 (21%)
Query: 112 KRRKCSLN--KTYDLTEIDRMFDSMIERDDTSDTEVQVEDKIKVEPCENSSNAQDV---- 165
KR K L+ +T L E DRM D D +E +K P + Q +
Sbjct: 166 KRGKLDLSGVETLVLDEADRMLDMGFIDD--------IEKILKALP----PDRQTLLFSA 213
Query: 166 --PSAEEKNVDEILH---HVNVKMTNVTMVLRNIISHPYLINKPYRIVDGKKEMVCDENI 220
P + L+ + V + + L+ I YL +
Sbjct: 214 TMPDDIRELARRYLNDPVEIEVSVEKLERTLKKI-KQFYLEVESEE-------------- 258
Query: 221 VSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEER 280
K+ +L +LL + + +VF +++ + E + LHG + EER
Sbjct: 259 ----EKLELLLKLLKDEDEG--RVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEER 312
Query: 281 NDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQT 340
+ A+++F L++T +GL++ I YD +P E HRIG+T
Sbjct: 313 DRALEKFKDGELR--VLVATDVAARGLDIPDVSHVINYDLPLDP------EDYVHRIGRT 364
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 39.3 bits (92), Expect = 0.002
Identities = 41/151 (27%), Positives = 70/151 (46%), Gaps = 18/151 (11%)
Query: 156 CENSSNAQDVPSAEEKNVDEILHHVNVKMTNVTMVLRNIISHPYLINKPY--RIVDGKKE 213
CE SS+ +D+ E + + + L + +HPYL+ Y + + K+
Sbjct: 35 CETSSSKEDIIKLLEDLTE--------SIKLLFENLSLVATHPYLLIDHYMPKSLLLKEP 86
Query: 214 MVCDENIVSSSGKMIVLNQLLHKLKQTNHKT--LVFSTMVKVLNFIEELCVLENYNYYRL 271
E++ +SGK +VLN L++ L ++ L+ S VK L+ +E L + + NY RL
Sbjct: 87 P---EHLAETSGKFLVLNDLINLLIRSERDLHVLIISRSVKTLDLVEALLLGKGLNYKRL 143
Query: 272 HG-SIRNEERNDAVQQFNGSTEWGVFLLSTR 301
G S+ E N V GS + L ++
Sbjct: 144 SGESLYEE--NHKVSDKKGSLSLWIHLTTSD 172
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 36.7 bits (85), Expect = 0.019
Identities = 31/123 (25%), Positives = 54/123 (43%), Gaps = 10/123 (8%)
Query: 219 NIVSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNE 278
+V K L LL ++ + K L+F K +F+ + L+ + +HG + E
Sbjct: 355 FVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQE 414
Query: 279 ERNDAVQQF-NGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRI 337
ER + +F G + +++T +GL++ I +D P Q E HRI
Sbjct: 415 ERTWVLNEFKTGKSP---IMIATDVASRGLDVKDVKYVINFDF---PN---QIEDYVHRI 465
Query: 338 GQT 340
G+T
Sbjct: 466 GRT 468
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 30.7 bits (70), Expect = 1.2
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 230 LNQLLHKLKQTNHKTLVFST--MVKVLNFIEELCVLEN 265
L +LL KLK+ KT++ T + VL + + + VL++
Sbjct: 177 LLELLKKLKEEGGKTIIIVTHDLELVLEYADRVVVLDD 214
>gnl|CDD|222918 PHA02687, PHA02687, ORF061 late transcription factor VLTF-4;
Provisional.
Length = 231
Score = 30.4 bits (68), Expect = 1.6
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 14/92 (15%)
Query: 99 EQTIDSNQL----------VQQPKRRKCSLNKTYDLTEIDRMFDSMIERDDTSDTEVQVE 148
EQ QL V+ PKRR K + + + + DD D + E
Sbjct: 64 EQECQQEQLPVPESVPPAPVKTPKRRTKKKAKADKPEKSPKAVEKLCPPDDRDDKNEEKE 123
Query: 149 DKIKVEPCENSSNAQDVPS----AEEKNVDEI 176
+ + E S +A+ S +++ N+DE+
Sbjct: 124 PTEEAQRNEESGDAEGGASGRSPSDDDNLDEM 155
>gnl|CDD|114933 pfam06241, DUF1012, Protein of unknown function (DUF1012). Family
of uncharacterized proteins found in both eukaryotes and
bacteria.
Length = 208
Score = 29.6 bits (66), Expect = 2.4
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 151 IKVEPCENSSNAQDVPSAEEKNVDEILHHVNVKMTNVTMVLRNIISHPYLINKPYR 206
+KVEP ENS++ V + +K++ +I H + N + + N+ S P L YR
Sbjct: 57 LKVEPVENSTSKLFVQCSRQKDLIKIYRH----LLNYSKNVFNLCSFPNLTGMKYR 108
>gnl|CDD|224279 COG1360, MotB, Flagellar motor protein [Cell motility and
secretion].
Length = 244
Score = 28.9 bits (65), Expect = 4.1
Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 45 LTKTIGENREQVAEYFNTTVNTSSSSDSSGNESYIWFSEESTLSNASSVKAGKREQTIDS 104
++ E +Q+A YF + + S S G +S + +E L+ +V ++ +
Sbjct: 37 MSSISPEKFQQIAAYFRIAFSGAPGSASEGGKS-MQQVKEKELAEELNVGEAIEKK--EL 93
Query: 105 NQLVQQPKRR 114
++ + +
Sbjct: 94 SEKLGDLAKE 103
>gnl|CDD|237960 PRK15407, PRK15407, lipopolysaccharide biosynthesis protein RfbH;
Provisional.
Length = 438
Score = 29.1 bits (66), Expect = 4.6
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 193 NIISHPYLINKPYRIV 208
N+ PY YR+V
Sbjct: 381 NLTRQPYFKGVKYRVV 396
>gnl|CDD|165303 PHA03002, PHA03002, Hypothetical protein; Provisional.
Length = 679
Score = 28.9 bits (65), Expect = 6.1
Identities = 11/65 (16%), Positives = 28/65 (43%)
Query: 130 MFDSMIERDDTSDTEVQVEDKIKVEPCENSSNAQDVPSAEEKNVDEILHHVNVKMTNVTM 189
F I + + D I+ +P + + + + EE ++++IL H++ +
Sbjct: 310 EFRDKIMIKENRVITMNKGDSIRKKPMKLKCSMKKIIKDEENSIEDILIHIDNARKKRKL 369
Query: 190 VLRNI 194
+ +I
Sbjct: 370 SIEDI 374
>gnl|CDD|240399 PTZ00393, PTZ00393, protein tyrosine phosphatase; Provisional.
Length = 241
Score = 28.4 bits (63), Expect = 6.3
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 156 CENSSNAQDVPSAEEKNVDEILHHVNVKMTNVTMVLRNIISH----PYLINKPYRIVDGK 211
C SS + +N D+++H V VK + L NI + ++N P +I GK
Sbjct: 33 CSRSSASI-PNIGRRRNCDQVIHTVYVKYFAMDSYLGNINYNMDYLNPVLNHPTKIEHGK 91
Query: 212 KEMV 215
+++
Sbjct: 92 IKIL 95
>gnl|CDD|222487 pfam13981, SopA, SopA-like central domain. This domain is found in
the E. coli Type III secretion effector proteins SopA
and NleL. These proteins have been shown to act as E3
ubiquitin ligase enzymes.
Length = 135
Score = 27.7 bits (62), Expect = 6.5
Identities = 12/23 (52%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 182 VKMTNVTMVLRNIISH-PYLINK 203
V +TNVT+ L +I+S PY+I+K
Sbjct: 20 VNLTNVTLSLLDILSKPPYIIDK 42
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 28.4 bits (64), Expect = 7.3
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 51 ENREQVAEYFNTTVNTS-SSSDSSGNESYI 79
E +AEYF T + + + D S + +
Sbjct: 53 EQLIGIAEYFRTPLKVALTGGDRSSDSTSP 82
>gnl|CDD|215095 PLN00191, PLN00191, enolase.
Length = 457
Score = 28.5 bits (64), Expect = 7.8
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 321 DWNPQVDIQAEARCHRIGQ----TKPVCIYRLVSHSTYQVHLFTIDSSGSVSWSSQSVK 375
DW + + +G T P + + + L ++ G+V+ S ++VK
Sbjct: 324 DWEHWAKLTSLEDVQIVGDDLLVTNPKRVAKAIQEKACNALLLKVNQIGTVTESIEAVK 382
>gnl|CDD|161862 TIGR00407, proA, gamma-glutamyl phosphate reductase. The related
model TIGR01092 describes a full-length fusion protein
delta l-pyrroline-5-carboxylate synthetase that includes
a gamma-glutamyl phosphate reductase region as described
by this model. Alternate name: glutamate-5-semialdehyde
dehydrogenase. The prosite motif begins at residue 332
of the seed alignment although not all of the members of
the family exactly obey the motif [Amino acid
biosynthesis, Glutamate family].
Length = 398
Score = 28.2 bits (63), Expect = 9.3
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 61 NTTVNTSSSSDSSGNESYIWFSEESTLSNASSVKAGKR--EQT---IDSNQLVQQPKRRK 115
N TV+ +S +GN + +E+ SN + V+ + QT + + QL++ P R
Sbjct: 116 NVTVDIASLCLKTGNAVILRGGKEAVRSNKALVEVIQDALAQTGLPVGAVQLIETPSREL 175
Query: 116 CSLNKTYDLTEIDRMFDSMIER 137
S +L ++D D +I R
Sbjct: 176 VS-----ELLDLDEYIDLLIPR 192
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
0.316 0.130 0.379
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,314,916
Number of extensions: 1762392
Number of successful extensions: 1449
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1439
Number of HSP's successfully gapped: 25
Length of query: 404
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 305
Effective length of database: 6,546,556
Effective search space: 1996699580
Effective search space used: 1996699580
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 (21.6 bits)
S2: 60 (26.8 bits)