RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12984
(178 letters)
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 96.8 bits (242), Expect = 2e-25
Identities = 34/67 (50%), Positives = 43/67 (64%), Gaps = 2/67 (2%)
Query: 68 FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
FE L + L+ I +GF K T IQAR IPPLL GRD++G A+TGSGKT AFL+P +
Sbjct: 1 FEELG--LSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPIL 58
Query: 128 ELIYNLK 134
E +
Sbjct: 59 EKLDPSP 65
>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 = 88.3 bits (219), Expect = 7e-21
Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 2/67 (2%)
Query: 64 SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
+ +F +L L+A+ D+GF + T IQ IP +L GRD++G A+TG+GKT AFL
Sbjct: 27 TPPEFASLGLS--PELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFL 84
Query: 124 VPAVELI 130
+P ++ I
Sbjct: 85 LPLLQKI 91
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 78.1 bits (193), Expect = 3e-17
Identities = 33/61 (54%), Positives = 45/61 (73%), Gaps = 2/61 (3%)
Query: 66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
T F L+ + E+ L+A+ D G+T+ T IQA IPP L+GRD++GSA TG+GKT AFL+P
Sbjct: 1 TTFSELE--LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLP 58
Query: 126 A 126
A
Sbjct: 59 A 59
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 69.4 bits (171), Expect = 2e-14
Identities = 22/43 (51%), Positives = 34/43 (79%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF 122
L + ++G+T+MT IQA+++P +L G+D++ AKTGSGKT AF
Sbjct: 16 LANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAF 58
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 66.5 bits (163), Expect = 3e-14
Identities = 23/47 (48%), Positives = 33/47 (70%)
Query: 92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPR 138
T IQA+ IP +L G+D++ A TGSGKTLAFL+P ++ + K P+
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQ 47
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 65.8 bits (161), Expect = 4e-13
Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 6/64 (9%)
Query: 63 LSSTQFE--ALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL 120
L+ +F AL +V ++A+ GF T IQA +P L GRD+ G A+TG+GKT+
Sbjct: 5 LTEQKFSDFALHPQV----VEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTM 60
Query: 121 AFLV 124
AFL
Sbjct: 61 AFLT 64
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 62.6 bits (152), Expect = 6e-12
Identities = 29/55 (52%), Positives = 40/55 (72%), Gaps = 3/55 (5%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
L+A+ D+G+ K + IQA IP LL GRD++G A+TGSGKT AF +P L++NL
Sbjct: 18 LEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLP---LLHNLD 69
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 62.1 bits (151), Expect = 8e-12
Identities = 27/48 (56%), Positives = 37/48 (77%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
LK++ + GFT+ T IQ + P L GRD++G A+TGSGKTLAFL+PA+
Sbjct: 142 LKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAI 189
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 61.0 bits (148), Expect = 2e-11
Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 8/99 (8%)
Query: 36 DSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQ 95
S+ +Q + D EI+ S F+ALK + E+ L+ I GF K + IQ
Sbjct: 3 TSEQKNQSEQVASTGTIESNYD---EIVDS--FDALK--LNEDLLRGIYSYGFEKPSAIQ 55
Query: 96 ARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI-YNL 133
R I P+L+G D +G A++G+GKT F++ A++LI Y+L
Sbjct: 56 QRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL 94
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 59.4 bits (144), Expect = 6e-11
Identities = 24/51 (47%), Positives = 38/51 (74%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
L+A+A+ G+ + T IQ + IP +LEGRDL+ SA+TG+GKT F +P ++ +
Sbjct: 13 LRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHL 63
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 56.7 bits (137), Expect = 2e-10
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 83 IADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
I GF + Q I LL G RD++ +A TGSGKTLA L+PA+E + K
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGR 56
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 56.9 bits (137), Expect = 6e-10
Identities = 24/41 (58%), Positives = 30/41 (73%)
Query: 87 GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
GFT+ T IQA T+P L G D+ G A+TG+GKTLAFLV +
Sbjct: 28 GFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVM 68
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 53.4 bits (128), Expect = 8e-09
Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 139
+ AI D+GF T IQA+ + L G D +G A+TG+GKT AFL + +I L P
Sbjct: 99 MHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFL---ISIINQLLQTPPP 155
Query: 140 GKSWQGKLRPL 150
+ + G+ R L
Sbjct: 156 KERYMGEPRAL 166
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 52.9 bits (127), Expect = 1e-08
Identities = 32/88 (36%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 44 DQTNA----VEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTI 99
Q +E+ + G V ILS + L K+ N + G+ T IQ + I
Sbjct: 98 SQAELLRRKLEIHVKGEAVPPPILSFSSC-GLPPKLLLN----LETAGYEFPTPIQMQAI 152
Query: 100 PPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
P L GR L+ SA TGSGKT +FLVP +
Sbjct: 153 PAALSGRSLLVSADTGSGKTASFLVPII 180
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 45.7 bits (109), Expect = 4e-06
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 88 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
FT +T Q IP + G +++ A TGSGKT A +P + +
Sbjct: 20 FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINEL 62
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 43.5 bits (103), Expect = 2e-05
Identities = 27/132 (20%), Positives = 50/132 (37%), Gaps = 28/132 (21%)
Query: 21 LKILQSKEKSKPAEKDS--DANEDEDQTNAVEVQLPGSDVALEILSSTQF-----EALKG 73
L ++ S + + D +D + ++ P EI + E
Sbjct: 4 LSVVASLRSAFKFITEYLEDEFKDAEGQEGSILRDP------EIEARPGKTSEFPELRDE 57
Query: 74 KVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE----- 128
+ +KA G ++ Q + + EGR++V + TGSGKT +FL+P ++
Sbjct: 58 SLKSALVKA----GIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD 113
Query: 129 ------LIYNLK 134
L+Y
Sbjct: 114 PSARALLLYPTN 125
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 38.9 bits (91), Expect = 3e-04
Identities = 17/32 (53%), Positives = 24/32 (75%)
Query: 106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
RD++ +A TGSGKTLA L+P +EL+ +LK
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ 32
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 37.2 bits (87), Expect = 0.003
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 13/71 (18%)
Query: 88 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL-AFLVPAVELIYNLKFMPRNGKSWQGK 146
F T Q IP + EG++++ S+ TGSGKTL AFL +I L + R G+
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA----IIDELFRLGREGE----- 80
Query: 147 LRPLTNGVYLV 157
L + VY +
Sbjct: 81 ---LEDKVYCL 88
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 33.8 bits (78), Expect = 0.038
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 77 ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
+ LK + G+ Q I LL G+D + TG GK+L + +PA+
Sbjct: 6 QQVLKQV--FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL 54
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 33.6 bits (77), Expect = 0.040
Identities = 24/80 (30%), Positives = 32/80 (40%), Gaps = 22/80 (27%)
Query: 83 IADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLA-----------------FLV 124
+ G ++ +Q + LLEG +L+ + T SGKTL FLV
Sbjct: 209 LKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLV 268
Query: 125 PAVELIYNLK---FMPRNGK 141
P V L N K F R K
Sbjct: 269 PLVALA-NQKYEDFKERYSK 287
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 32.9 bits (76), Expect = 0.086
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 95 QARTIPPLLEGRDLVGSAKTGSGKTLA-FLVPAVELIYNLKFMPRNG 140
Q LEGR + A TGSGKTLA FL ++L K P+ G
Sbjct: 18 QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK--PKKG 62
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 32.0 bits (73), Expect = 0.17
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA 126
+ A+ G + + QAR GR +V + T SGK+LA+ +P
Sbjct: 26 VAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPV 72
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 31.3 bits (71), Expect = 0.22
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 87 GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
G + +Q I +L GRD TG GK+L + +PA+
Sbjct: 8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 31.6 bits (72), Expect = 0.23
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 100 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM 136
LL +++ SA TGSGKTL L+ + +
Sbjct: 42 KGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGK 78
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 31.5 bits (72), Expect = 0.26
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 112 AKTGSGKTLAFLVPAV 127
A TG+GK+LA+L+PA
Sbjct: 283 AGTGTGKSLAYLLPAA 298
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 31.0 bits (71), Expect = 0.31
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 104 EGRDLVGSAKTGSGKTLAFLVPAV 127
+GR LV A TG GKTL++L+ +
Sbjct: 48 DGRILVIEAGTGVGKTLSYLLAGI 71
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 30.0 bits (68), Expect = 0.39
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 3 KDTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNA 48
KD EK + KR+KKK K + K+ K +K+ + ++
Sbjct: 78 KDEEKTAKKRA-KRQKKKQKKKKKKKAKKGNKKEEKEGSKSSEESS 122
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 30.4 bits (69), Expect = 0.45
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 95 QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA 126
Q I +L+GRD++ TG GK+L + VPA
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVPA 49
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 30.4 bits (69), Expect = 0.54
Identities = 24/127 (18%), Positives = 37/127 (29%), Gaps = 15/127 (11%)
Query: 3 KDTEKHLMNKITK----REKKKLKI-----LQSKEKSKPAEKDSDANEDEDQTNAVEVQL 53
E+ L N R K Q K K +E +S +L
Sbjct: 29 TAEEESLKNIDISDLFERSVDMNKDPKEATDQVKAVDKHSEIESLNVGMRLDVRLSSKEL 88
Query: 54 PGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAK 113
V + E+ + + F ++ Q I L G ++ A
Sbjct: 89 SDVAVPDDYDMVPDAESPF-----DLAPPAREYPF-ELDPFQQEAIAILERGESVLVCAP 142
Query: 114 TGSGKTL 120
T SGKT+
Sbjct: 143 TSSGKTV 149
>gnl|CDD|206005 pfam13834, DUF4193, Domain of unknown function (DUF4193). This
domain of unknown function contains four conserved
cysteines and a conserved histidine, including a CXXXXH
motif.
Length = 99
Score = 28.7 bits (65), Expect = 0.56
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 25 QSKEKSKPAEKD-SDANEDEDQTNAVEV-QLPGSDVALEILS 64
S E+ K D D D+ A E +LPG+D++ E LS
Sbjct: 19 DSLEELKARRADAQSGVVDVDEGEAAESFELPGADLSGEELS 60
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 29.2 bits (66), Expect = 1.3
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 102 LLEGRDLVGSAKTGSGKTL 120
LL+G++L+ + T SGKTL
Sbjct: 36 LLDGKNLLAAIPTASGKTL 54
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 29.0 bits (65), Expect = 1.5
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
L G L+ A TG+GKTLA+L+PA+
Sbjct: 31 LKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG 63
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 27.6 bits (62), Expect = 1.5
Identities = 13/43 (30%), Positives = 19/43 (44%)
Query: 12 KITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLP 54
K RE K + Q K K + A D + + E T + +LP
Sbjct: 44 KAKAREADKARKQQLKAKQRQAANDDEEDTIESVTQSQSNKLP 86
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 28.5 bits (64), Expect = 2.0
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 95 QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA 126
Q I +L GRD + TG GK+L + +PA
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPA 61
>gnl|CDD|219285 pfam07065, D123, D123. This family contains a number of
eukaryotic D123 proteins approximately 330 residues
long. It has been shown that mutated variants of D123
exhibit temperature-dependent differences in their
degradation rate. D123 proteins are regulators of eIF2,
the central regulator of translational initiation.
Length = 295
Score = 28.1 bits (63), Expect = 2.6
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 14/73 (19%)
Query: 23 ILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKA 82
+L S+E S P ++S NE D D ++ +F L K+ E A
Sbjct: 31 LLPSEESSLPIYQESSDNEYSDWFE-------DDDDEDTDVTRPEFPELHQKIRE----A 79
Query: 83 IADMG---FTKMT 92
I ++G F K+
Sbjct: 80 IEELGGAVFPKLN 92
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 27.8 bits (62), Expect = 3.2
Identities = 12/57 (21%), Positives = 24/57 (42%)
Query: 2 SKDTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDV 58
D ++ + K E+K+ + KE AEK+ + +E+E++ E
Sbjct: 53 KSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKE 109
>gnl|CDD|214787 smart00721, BAR, BAR domain.
Length = 239
Score = 27.3 bits (61), Expect = 3.9
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 7 KHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVE 50
K + K E+K L ++ K K A+K + +DE A E
Sbjct: 134 KEIKKARKKLERKLLDYDSARHKLKKAKKSKEKKKDEKLAKAEE 177
>gnl|CDD|151502 pfam11056, UvsY, Recombination, repair and ssDNA binding protein
UvsY. UvsY protein enhances the rate of
single-stranded-DNA-dependant ATP hydrolysis by UvsX
protein. The enhancement of ATP hydrolysis by UvsY
protein is shown to result from the ability of UvsY
protein to increase the affinity of UvsX protein for
single-stranded DNA.
Length = 128
Score = 26.9 bits (60), Expect = 4.0
Identities = 15/86 (17%), Positives = 34/86 (39%)
Query: 12 KITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEAL 71
+ + E +K K+L+ + D + + + + ++ + + ++I + Q+
Sbjct: 37 EKIRLEAQKKKLLKERLLYYTGRADDEVCMEIYEKSEIKTVIAADEEVIKIDAKIQYIDQ 96
Query: 72 KGKVCENTLKAIADMGFTKMTEIQAR 97
E L AI GF I+ R
Sbjct: 97 VLDFLEEALDAIKQRGFQIKNAIEWR 122
>gnl|CDD|217553 pfam03430, TATR, Trans-activating transcriptional regulator. This
family of trans-activating transcriptional regulator
(TATR), also known as intermediate early protein 1, are
common to the Nucleopolyhedroviruses.
Length = 571
Score = 27.2 bits (60), Expect = 5.4
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 4 DTEKHLMNKITKREKKKLKILQSKEKSKPAEKDS 37
K L+NK KR+K K +QS E +
Sbjct: 142 SKGKKLVNKPKKRQKYKKATIQSPTSLTEEENYN 175
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 27.1 bits (60), Expect = 5.6
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 112 AKTGSGKTLAFLVPA 126
A TG+GKTL +L+PA
Sbjct: 271 APTGTGKTLGYLLPA 285
>gnl|CDD|117527 pfam08961, DUF1875, Domain of unknown function (DUF1875). The MIT
domain, found in Nuclear receptor-binding factor 2, has
no known function.
Length = 243
Score = 27.1 bits (59), Expect = 6.0
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 11 NKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEA 70
N+ ++E K+LK +++ P EK+ D + D +T+ + V ++ A + +F A
Sbjct: 145 NERLRKENKQLKAEKARLLKGPIEKELDVDADFVETSELWVLPQHNEEATASSTWQKFAA 204
Query: 71 LKGK 74
GK
Sbjct: 205 NTGK 208
>gnl|CDD|205225 pfam13044, DUF3904, Protein of unknown function (DUF3904). This
family of proteins is functionally uncharacterized. This
family of proteins is found in viruses. Proteins in this
family are typically between 437 and 448 amino acids in
length.
Length = 436
Score = 26.9 bits (59), Expect = 6.3
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 55 GSDVALEILSSTQFEALKGKVCEN-TLKAIADMGFTKMTE 93
D +S T FEA++G EN +KA+ D F +T+
Sbjct: 68 DGDTKNGKVSQTLFEAIQGTQMENCAVKAVFDTSFVNLTK 107
>gnl|CDD|184638 PRK14345, PRK14345, lipoate-protein ligase B; Provisional.
Length = 234
Score = 26.5 bits (59), Expect = 7.7
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 76 CENTLKA--------IADMGFTKMTEIQARTIPP 101
C+N L A I+D G T ++ RT+
Sbjct: 167 CDNDLAAFDAIVPCGISDAGVTTLSAELGRTVTV 200
>gnl|CDD|239319 cd03021, DsbA_GSTK, DsbA family, Glutathione (GSH) S-transferase
Kappa (GSTK) subfamily; GSTK is a member of the GST
family of enzymes which catalyzes the transfer of the
thiol of GSH to electrophilic substrates. It is
specifically located in the mitochondria and
peroxisomes, unlike other members of the canonical GST
family, which are mainly cytosolic. The biological
substrates of GSTK are not yet known. It is presumed to
have a protective role during respiration when large
amounts of reactive oxygen species are generated. GSTK
has the same general fold as DsbA, consisting of a
thioredoxin domain interrupted by an alpha-helical
domain and its biological unit is a homodimer. GSTK is
closely related to the bacterial enzyme,
2-hydroxychromene-2-carboxylate (HCCA) isomerase. It
shows little sequence similarity to the other members of
the GST family.
Length = 209
Score = 26.2 bits (58), Expect = 8.5
Identities = 10/53 (18%), Positives = 23/53 (43%)
Query: 36 DSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGF 88
E + + A + ++ A ++L + +K ++ ENT +A+ F
Sbjct: 126 TEPITESQSISVAADKLGGSAEQAEKLLKAASTPEVKNRLKENTDEALKYGAF 178
>gnl|CDD|235163 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 26.5 bits (59), Expect = 8.7
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 63 LSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR 106
L+S+++ + + CE LK + ++TE +PPLL R
Sbjct: 192 LASSEY-NERRQECEEALKILGKKSSKEVTEEDLSKLPPLLRKR 234
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
0.313 0.130 0.357
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,521,342
Number of extensions: 763683
Number of successful extensions: 804
Number of sequences better than 10.0: 1
Number of HSP's gapped: 797
Number of HSP's successfully gapped: 74
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.4 bits)