RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13224
(160 letters)
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 171 bits (435), Expect = 4e-50
Identities = 66/124 (53%), Positives = 88/124 (70%), Gaps = 1/124 (0%)
Query: 38 GKLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKVDQRQVLM 97
GK+ LD +L KLK RVLIF+QMTR+LD+LE +L + G+ Y R+DG T + R +
Sbjct: 471 GKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASI 530
Query: 98 ERFNMD-ARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDV 156
+ FN + F F+LSTR+GG+GINL AD V+ YDSDWNP +D QAQDR HRIGQ ++V
Sbjct: 531 DAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEV 590
Query: 157 HIYR 160
++R
Sbjct: 591 QVFR 594
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 143 bits (362), Expect = 2e-40
Identities = 70/132 (53%), Positives = 92/132 (69%), Gaps = 3/132 (2%)
Query: 32 LIQYDCGKLQSLDVILR-KLKAGGH--RVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTT 88
LIQ GKLQ+LD +L KL GH +VLIF+Q T +LD+LE +L G Y+RLDG+T
Sbjct: 686 LIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGST 745
Query: 89 KVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCH 148
+RQ L++RFN D F+LS ++GG+G+NLTGADTV+ +D WNP ++ QA DR H
Sbjct: 746 PAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAH 805
Query: 149 RIGQTRDVHIYR 160
RIGQ R V +YR
Sbjct: 806 RIGQKRPVKVYR 817
>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 = 2e-28
Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 2/129 (1%)
Query: 31 RLIQYDCGKLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKV 90
++ + KL++L +L++ G +VLIF +MLD L L G L G
Sbjct: 5 YVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQ 64
Query: 91 DQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRI 150
++R+ +++ F +++T GI+L V+ YD W+P+ Q R R
Sbjct: 65 EEREEVLKDFREGE--IVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRA 122
Query: 151 GQTRDVHIY 159
GQ +
Sbjct: 123 GQKGTAILL 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 = 83.0 bits (206), Expect = 7e-22
Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 73 FLNFHGHIYLRLDGTTKVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYD 132
L G RL G ++R+ ++E F +++T G GI+L + V+ YD
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGK--SKVLVATDVAGRGIDLPDVNLVINYD 59
Query: 133 SDWNPTMDAQAQDRCHRIG 151
WNP Q R R G
Sbjct: 60 LPWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 83.0 bits (206), Expect = 1e-21
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 2/84 (2%)
Query: 68 DVLEAFLNFHGHIYLRLDGTTKVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADT 127
+ L L G RL G ++R+ ++++FN +++T G++L G D
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKI--KVLVATDVAERGLDLPGVDL 58
Query: 128 VVFYDSDWNPTMDAQAQDRCHRIG 151
V+ YD W+P Q R R G
Sbjct: 59 VIIYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 36.3 bits (84), Expect = 0.004
Identities = 32/117 (27%), Positives = 54/117 (46%), Gaps = 13/117 (11%)
Query: 38 GKLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKVDQRQ-VL 96
GKL+ L L+++ G ++LIF + + D L L G L + G K ++R VL
Sbjct: 364 GKLKML---LQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVL 420
Query: 97 MERFNMDARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT 153
E + I +++T G+++ V+ +D Q +D HRIG+T
Sbjct: 421 NEFKTGKSPI---MIATDVASRGLDVKDVKYVINFD------FPNQIEDYVHRIGRT 468
>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 = 35.2 bits (81), Expect = 0.011
Identities = 30/116 (25%), Positives = 56/116 (48%), Gaps = 12/116 (10%)
Query: 39 KLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKVDQRQVLME 98
KL+ L +L+ G RV++F + R+++ L L G L G ++R +E
Sbjct: 260 KLELLLKLLKDEDEG--RVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALE 317
Query: 99 RF-NMDARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT 153
+F + + R+ +++T G+++ V+ YD +P +D HRIG+T
Sbjct: 318 KFKDGELRV---LVATDVAARGLDIPDVSHVINYDLPLDP------EDYVHRIGRT 364
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 34.3 bits (79), Expect = 0.019
Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 4/101 (3%)
Query: 29 DPRLIQYDCGKLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTT 88
R+ K+ ++ L A G + LIF + I + G T
Sbjct: 259 ARRIAIASERKIAAVR-GLLLKHARGDKTLIFASDVEHAYEIAKLFL-APGIVEAITGET 316
Query: 89 KVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVV 129
++R+ ++ERF +++ + G+++ AD ++
Sbjct: 317 PKEEREAILERFRTGGIK--VLVTVKVLDEGVDIPDADVLI 355
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 29.9 bits (67), Expect = 0.63
Identities = 26/98 (26%), Positives = 42/98 (42%), Gaps = 8/98 (8%)
Query: 56 RVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKVDQRQVLMERFNMDARIFCFILSTRS 115
RV++F + +E L G +L G +R +E F + +I + +T
Sbjct: 337 RVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFR-EGKIRVLV-ATDV 394
Query: 116 GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT 153
G GI++ G V+ N T+ D HRIG+T
Sbjct: 395 AGRGIHIDGISHVI------NFTLPEDPDDYVHRIGRT 426
>gnl|CDD|220389 pfam09767, DUF2053, Predicted membrane protein (DUF2053). This
entry is of the conserved N-terminal 150 residues of
proteins conserved from plants to humans. The function
is unknown although some annotation suggests it to be a
transmembrane protein.
Length = 159
Score = 28.5 bits (64), Expect = 1.00
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 30 PRLIQYDCGKLQSLDVILRKLKAGGHRVLIFTQMTRMLDVLEAFL 74
P I Y L + +KA G I TQ+ ++L +L F
Sbjct: 15 PYYIVYKASGLSEYGAFWKCVKAAG--GYILTQLLKLL-LLATFF 56
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 29.1 bits (65), Expect = 1.0
Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 8/103 (7%)
Query: 51 KAGGHRVLIFTQMTRMLDVLEAFLNFHGHIYLRLDGTTKVDQRQVLMERFNMDARIFCFI 110
++ G R ++F ++ + L HG+ L G +R+ L+ RF +
Sbjct: 254 RSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQ--LEIL 311
Query: 111 LSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT 153
++T G+++ G V YD ++ A+D HRIG+T
Sbjct: 312 VATDVAARGLHIDGVKYVYNYDLPFD------AEDYVHRIGRT 348
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 28.1 bits (63), Expect = 2.1
Identities = 24/110 (21%), Positives = 53/110 (48%), Gaps = 15/110 (13%)
Query: 35 YDCGKLQSLDVILRK--LKAGGHRVLIFTQMTRMLDVLEAFLNFHG----HIYL------ 82
+ KL+ L IL++ K G RV++FT+ + + FL G ++
Sbjct: 345 VEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASRE 404
Query: 83 RLDGTTKVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYD 132
G ++ +Q++++ ++F + +++T G G+++ D V+FY+
Sbjct: 405 GDKGMSQKEQKEII-DQFRKG--EYNVLVATSVGEEGLDIPEVDLVIFYE 451
>gnl|CDD|232919 TIGR00322, diphth2_R, diphthamide biosynthesis enzyme Dph1/Dph2
domain. Archaea and Eukaryotes, but not Eubacteria,
share the property of having a covalently modified
residue,
2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine,
as a part of a cytosolic protein. The modified His,
termed diphthamide, is part of translation elongation
factor EF-2 and is the site for ADP-ribosylation by
diphtheria toxin. This model includes both Dph1 and Dph2
from Saccharomyces cerevisiae, although only Dph2 is
found in the Archaea (see TIGR03682). Dph2 has been
shown to act analogously to the radical SAM (rSAM)
family (pfam04055), with 4Fe-4S-assisted cleavage of
S-adenosylmethionine to create a free radical, but a
different organic radical than in rSAM.
Length = 319
Score = 27.9 bits (63), Expect = 2.5
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 90 VDQRQVLMERFN-----MDARIFCFILSTRSG 116
D ++L R+ DA+ I+ T G
Sbjct: 215 YDANKLLRRRYALIEKAKDAKKVGIIVGTLGG 246
>gnl|CDD|216748 pfam01866, Diphthamide_syn, Putative diphthamide synthesis protein.
Human DPH1 is a candidate tumour suppressor gene. DPH2
from yeast, which confers resistance to diphtheria
toxin, has been found to be involved in diphthamide
synthesis. Diphtheria toxin inhibits eukaryotic protein
synthesis by ADP-ribosylating diphthamide, a
posttranslationally modified histidine residue present
in EF2. The exact function of the members of this family
is unknown.
Length = 300
Score = 27.6 bits (62), Expect = 3.3
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 84 LDGTTKVDQRQVLMERFNMDARIFCFILSTRSG 116
D + +R +E+ DA+ F I+ T+ G
Sbjct: 184 YDADKMLRRRYAAIEKA-KDAKSFGIIVGTKGG 215
>gnl|CDD|224663 COG1749, FlgE, Flagellar hook protein FlgE [Cell motility and
secretion].
Length = 423
Score = 27.3 bits (61), Expect = 3.8
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 111 LSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDR 146
+T + NL V + +NPT A +
Sbjct: 157 KATTNVSFSANLNSGAIVPSITAPFNPTDTATYNYK 192
>gnl|CDD|197280 cd09183, PLDc_FAM83C_N, N-terminal phospholipase D-like domain of
the uncharacterized protein, Family with sequence
similarity 83C. N-terminal phospholipase D (PLD)-like
domain of the uncharacterized protein, Family with
sequence similarity 83C (FAM83C). Since the N-terminal
PLD-like domain of FAM83 proteins shows only trace
similarity to the PLD catalytic domain and lacks the
functionally important histidine residue, FAM83 proteins
may share a similar three-dimensional fold with PLD
enzymes, but are most unlikely to carry PLD activity.
The N-terminus of FAM83C shows high homology to other
FAM83 family members, indicating that FAM83C might have
arisen early in vertebrate evolution by duplication of a
gene in the FAM83 family.
Length = 274
Score = 27.1 bits (60), Expect = 3.8
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 5 MTAELRPKLRLLHPVTSAMCTQFPDPRLIQYDCGKLQSLDVILRKLKAGGHRVL-----I 59
M+ P L L P P I + K ++ ++R L + V+ +
Sbjct: 90 MSDFDPPDLELGWPEIPLATKASPTEAQIFFQRDKANNIKDLIRSLISMAKTVIAIVMDL 149
Query: 60 FTQMTRMLDVLEAFLNFHGHIYLRLD 85
FT + + D++EA +YL LD
Sbjct: 150 FTDVDILCDLMEASNKRRVPVYLLLD 175
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 27.1 bits (61), Expect = 4.7
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 146 RCHRIGQTRDVHIY 159
R RIGQ D+ I+
Sbjct: 586 RLDRIGQKHDIQIH 599
>gnl|CDD|130395 TIGR01328, met_gam_lyase, methionine gamma-lyase. This model
describes a methionine gamma-lyase subset of a family of
PLP-dependent trans-sulfuration enzymes. The member from
the parasite Trichomonas vaginalis is described as
catalyzing alpha gamma- and alpha-beta eliminations and
gamma-replacement reactions on methionine, cysteine, and
some derivatives. Likewise, the enzyme from Pseudomonas
degrades cysteine as well as methionine [Energy
metabolism, Amino acids and amines].
Length = 391
Score = 26.8 bits (59), Expect = 5.8
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 96 LMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTM 139
+ +F + FI V ++ +V++++ NPTM
Sbjct: 118 ALTKFGIQVD---FINMAIPEEVKAHIKDNTKIVYFETPANPTM 158
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 26.1 bits (58), Expect = 6.8
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 86 GTTKVDQRQVLMERFNMDARIFCFILSTRSGGVGINLTGADTVVFYD 132
G K +Q V E D I I G + I L ADT++F D
Sbjct: 43 GVPKEEQITVQNELVKEDEWI---IDGNYGGTMDIRLNAADTIIFLD 86
>gnl|CDD|224650 COG1736, DPH2, Diphthamide synthase subunit DPH2 [Translation,
ribosomal structure and biogenesis].
Length = 347
Score = 26.5 bits (59), Expect = 7.1
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 91 DQRQVLMERFN-----MDARIFCFILSTRSG 116
+ + L +R+ +DA+ F I+ST+ G
Sbjct: 219 EADRFLRKRYAAISKALDAKSFGIIVSTKGG 249
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 26.3 bits (59), Expect = 8.8
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 26 QFPDPRLIQYD---CGKLQSLDVILRKLKAGGHRVLIFTQM 63
FP+ R+++ D + +L+ +L + G +LI TQM
Sbjct: 449 LFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQM 489
>gnl|CDD|238902 cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type
peptidylprolyl cis- trans isomerase domain occuring with
a C-terminal RNA recognition motif domain (RRM). This
subfamily of the cyclophilin domain family contains a
number of eukaryotic cyclophilins having the RRM domain
including the nuclear proteins: human hCyP-57,
Arabidopsis thaliana AtCYP59, Caenorhabditis elegans
CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241
protein has been shown to have a role in cell
morphogenesis.
Length = 166
Score = 25.8 bits (57), Expect = 9.6
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 11/80 (13%)
Query: 6 TAELRPKLRLLHPVTSAMCTQFPDPRLIQYDCGKLQSLDVILRKLKAGGHRVLIFTQMTR 65
E+ P L+ T +M + Q+ ++LD + K H +F Q+
Sbjct: 76 EPEILPLLKHSKKGTVSMVNAGDNLNGSQFYITLGENLDYLDGK-----H--TVFGQVVE 128
Query: 66 MLDVL----EAFLNFHGHIY 81
DVL +A ++ G
Sbjct: 129 GFDVLEKINDAIVDDDGRPL 148
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
0.329 0.141 0.432
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: 8,196,896
Number of extensions: 748200
Number of successful extensions: 883
Number of sequences better than 10.0: 1
Number of HSP's gapped: 877
Number of HSP's successfully gapped: 29
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 55 (24.9 bits)