RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7268
(134 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 = 94.5 bits (236), Expect = 3e-25
Identities = 38/94 (40%), Positives = 55/94 (58%), Gaps = 7/94 (7%)
Query: 41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
FE+ GL+PE++ G PT IQ +IP LLSG+ I A+TG GKT +FL P++++
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
+ P+ + P ALI+ P REL QI +
Sbjct: 61 LD-------PSPKKDGPQALILAPTRELALQIAE 87
>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 = 93.3 bits (232), Expect = 3e-23
Identities = 37/93 (39%), Positives = 50/93 (53%), Gaps = 7/93 (7%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
F GL+PE++ G PT IQ +IP +L+G+ + A+TG GKT +FL PL+Q
Sbjct: 30 EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQ 89
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+IL E ALI+ P REL QI
Sbjct: 90 KILK-------SVERKYVSALILAPTRELAVQI 115
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 74.8 bits (184), Expect = 9e-17
Identities = 36/95 (37%), Positives = 50/95 (52%), Gaps = 4/95 (4%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
+FE T I+ G T PT IQ P LSG+ I +AETG GKTL+FL P +
Sbjct: 131 SFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIV 190
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
I ++P + + P+ L++ P REL QI +
Sbjct: 191 HIN---AQPLLRYG-DGPIVLVLAPTRELAEQIRE 221
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 74.8 bits (184), Expect = 9e-17
Identities = 37/93 (39%), Positives = 54/93 (58%), Gaps = 2/93 (2%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
+F GL P+++ G PT IQ +IP LSG+S ++ A+TG GKT SFL P++
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+ T R + E PLA+++TP REL Q+
Sbjct: 182 RCCTI--RSGHPSEQRNPLAMVLTPTRELCVQV 212
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 72.7 bits (179), Expect = 4e-16
Identities = 34/92 (36%), Positives = 52/92 (56%), Gaps = 2/92 (2%)
Query: 41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
F D L P++++ K+G T IQ ++P L+G+ A+TG GKT++FL
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+L+ PE + ++N P ALI+ P REL QI
Sbjct: 70 LLS-HPAPEDR-KVNQPRALIMAPTRELAVQI 99
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 73.0 bits (179), Expect = 5e-16
Identities = 35/95 (36%), Positives = 50/95 (52%), Gaps = 9/95 (9%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
TF D GL I++ G P+ IQ IP LL+G+ + +A+TG GKT +F PL+
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
+ PEL AP L++ P REL Q+ +
Sbjct: 67 NL---------DPELKAPQILVLAPTRELAVQVAE 92
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 71.8 bits (176), Expect = 1e-15
Identities = 36/95 (37%), Positives = 58/95 (61%), Gaps = 3/95 (3%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
+F+ GL+P+I+ ++G PT IQ+ +IP +L G+ + A+TG GKT F PL+Q
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
++T + + + + ALI+TP REL QIG+
Sbjct: 62 HLITRQPHAKGRRPVR---ALILTPTRELAAQIGE 93
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 71.9 bits (177), Expect = 1e-15
Identities = 35/93 (37%), Positives = 49/93 (52%), Gaps = 5/93 (5%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
TF + L +++ +G T PT IQ +IP L G+ + A TG GKT +FL P +Q
Sbjct: 2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+L + P K P LI+TP REL Q+
Sbjct: 62 HLLDF---PRRKS--GPPRILILTPTRELAMQV 89
>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 = 68.1 bits (167), Expect = 3e-15
Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 9/72 (12%)
Query: 63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII 122
T IQ +IP +LSGK ++ A TG GKTL+FL P++Q +L P+ P AL++
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALL---------PKKGGPQALVL 51
Query: 123 TPGRELVFQIGQ 134
P REL QI +
Sbjct: 52 APTRELAEQIYE 63
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 62.9 bits (153), Expect = 4e-13
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 54 FTKRGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP 112
K G QK +I LLSG + IL A TG GKTL+ L P ++ +
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK---------- 50
Query: 113 ELNAPLALIITPGRELVFQIGQ 134
L++ P REL Q +
Sbjct: 51 RGKGGRVLVLVPTRELAEQWAE 72
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 62.3 bits (151), Expect = 2e-12
Identities = 35/93 (37%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
TF L P ++ G T T IQ ++P L G A+TG GKTL+FL ++
Sbjct: 10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
++L+ + + KPE P ALI+ P REL QI
Sbjct: 70 RLLSRPALADRKPE--DPRALILAPTRELAIQI 100
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 61.5 bits (149), Expect = 4e-12
Identities = 37/92 (40%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
Query: 41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
F D LAPE++ G T IQ + L+G AI A+TG GKT +FL ++ Q
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+L ++ P + + P ALII P RELV QI
Sbjct: 149 LL--QTPPPKERYMGEPRALIIAPTRELVVQI 178
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 55.0 bits (133), Expect = 9e-10
Identities = 27/83 (32%), Positives = 49/83 (59%), Gaps = 5/83 (6%)
Query: 46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
L P + + F ++ T+ T Q+Y+IP + SG++ +++A TG GKT + P++ ++L
Sbjct: 8 LDPRVREWFKRKF-TSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELL--- 63
Query: 106 SRPEYKPELNAPLALIITPGREL 128
S + K E + AL I+P + L
Sbjct: 64 SLGKGKLE-DGIYALYISPLKAL 85
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 47.1 bits (113), Expect = 4e-07
Identities = 30/94 (31%), Positives = 46/94 (48%), Gaps = 9/94 (9%)
Query: 41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
F L P ++ + G T T IQ S+P +L+GK I A+TG GKT +F L+Q+
Sbjct: 6 FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65
Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
+ + AL++ P REL Q+ +
Sbjct: 66 L---------DVKRFRVQALVLCPTRELADQVAK 90
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 47.1 bits (112), Expect = 4e-07
Identities = 30/93 (32%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
+F+ L +++ G P+ IQ+ I +L G I A++G GKT +F+ +Q
Sbjct: 29 SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQ 88
Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
I +LNA ALI+ P REL QI
Sbjct: 89 LI---------DYDLNACQALILAPTRELAQQI 112
>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 = 45.0 bits (107), Expect = 8e-07
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 10/56 (17%)
Query: 77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
+ +L A TG GKTL+ L P+++ + + K L++ P REL Q+
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ----------VLVLAPTRELANQV 46
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 30/82 (36%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS-FLAPLVQQILTWKS 106
F RG T P Q L G+S +L+A TG GKTL+ FL L+ L
Sbjct: 1 SPFEAWFAARGWT-PRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLID--LAGPE 57
Query: 107 RPEYKPELNAPLALIITPGREL 128
+P K L+ L ITP R L
Sbjct: 58 KP--KKGLH---TLYITPLRAL 74
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 39.1 bits (92), Expect = 3e-04
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 49 EIIDIFT-------KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS-FLA 95
EI+D+ K T T Q+Y+IP + GK+ ++ + TG GKTL+ FLA
Sbjct: 13 EILDLLRPYVREWFKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA 67
>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 = 38.5 bits (90), Expect = 4e-04
Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)
Query: 42 EDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQI 101
+ K G+ Q ++ + G++ ++ TG GKT SFL P++ +
Sbjct: 51 FPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL 110
Query: 102 LTWKSRPEYKPELNAPLALIITPGRELVF 130
L S AL++ P L
Sbjct: 111 LRDPSAR----------ALLLYPTNALAN 129
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 36.3 bits (84), Expect = 0.002
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 11/63 (17%)
Query: 72 TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ 131
L G+ ++ A TG GKTL++L P L + K +I T + L Q
Sbjct: 30 ALKGGEGLLIEAPTGTGKTLAYLLP----ALAYAREEGKK-------VIISTRTKALQEQ 78
Query: 132 IGQ 134
+ +
Sbjct: 79 LLE 81
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 34.5 bits (80), Expect = 0.011
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 49 EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLA 95
E F K+ + P +Q+ LL G+S ++A TG GKT +F
Sbjct: 68 EFEKFFKKKTGSKPWSLQRTWAKRLLLGESFAIIAPTGVGKT-TFGL 113
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 33.3 bits (76), Expect = 0.031
Identities = 26/84 (30%), Positives = 31/84 (36%), Gaps = 12/84 (14%)
Query: 49 EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRP 108
E + F K IQK +L GKS +VA TG GK S + L K +
Sbjct: 67 EFEEFFEKITGFEFWSIQKTWAKRILRGKSFSIVAPTGMGK--STFGAFIALFLALKGKK 124
Query: 109 EYKPELNAPLALIITPGRELVFQI 132
Y II P LV Q
Sbjct: 125 CY----------IILPTTLLVKQT 138
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 32.0 bits (73), Expect = 0.072
Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 15/57 (26%)
Query: 75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ 131
+ + ++V TG GKT+ + ++ L++ P +EL+ Q
Sbjct: 54 TERRGVIVLPTGAGKTVVAAE-AIAELKRS--------------TLVLVPTKELLDQ 95
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 31.3 bits (71), Expect = 0.14
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 46 LAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTL 91
+ + + + G+ +Q ++ LL G++ ++V+ T GKTL
Sbjct: 201 IPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTL 247
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 30.8 bits (70), Expect = 0.17
Identities = 19/42 (45%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 72 TLLSGKSAILVAETGCGKTLSFLAPLVQQILTW-KSRPEYKP 112
L GK IL + TG GKTLS L LTW +S PE
Sbjct: 23 VLDRGKIGILESPTGTGKTLSLLC----LTLTWLRSFPERIQ 60
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.4 bits (69), Expect = 0.28
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 49 EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLA 95
E + F K P Q+ L+ GKS ++A TG GKT +F
Sbjct: 70 EFEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKT-TFGL 115
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.7 bits (65), Expect = 0.34
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 12/66 (18%)
Query: 66 QKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG 125
Q+ +I LL K ++V TG GKTL+ A L+ ++ K + L + P
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLTAAA-LIARLAKGKKK-----------VLFVVPR 55
Query: 126 RELVFQ 131
++L+ Q
Sbjct: 56 KDLLEQ 61
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 29.8 bits (68), Expect = 0.44
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 75 SGKSAILVAE--TGCGKTLSFLAP 96
ILV E TG GKTLS+L
Sbjct: 46 LKDGRILVIEAGTGVGKTLSYLLA 69
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 29.7 bits (67), Expect = 0.49
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 75 SGKSAILVAETGCGKTLSFLAP 96
+L A TG GKT + L
Sbjct: 213 RSLLVVLEAPTGYGKTEASLIL 234
>gnl|CDD|182529 PRK10536, PRK10536, hypothetical protein; Provisional.
Length = 262
Score = 27.8 bits (62), Expect = 1.5
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 18 KVLRNAYPTHRGYE---AVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL 74
+VLR +H+ E S + +G E G+A + D + E Q + + +
Sbjct: 16 RVLRRDSRSHKQREEESVTSLVQMGGVEAIGMARDSRD---TSPILARNEAQAHYLKAIE 72
Query: 75 SGKSAILVAETGCGKT 90
S + E GCGKT
Sbjct: 73 SKQLIFATGEAGCGKT 88
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 27.6 bits (62), Expect = 1.9
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 15/56 (26%)
Query: 70 IPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG 125
I LLSGK ++V TG GK+L + QI P L L L+++P
Sbjct: 26 IDALLSGKDTLVVMPTGGGKSLCY------QI------PAL---LLEGLTLVVSPL 66
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 27.2 bits (61), Expect = 2.1
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 57 RGLTTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILT 103
L P ++ + LL G +L G GK+ + L + T
Sbjct: 13 EDLDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKS-TLALDLAAAVAT 59
>gnl|CDD|237493 PRK13762, PRK13762, tRNA-modifying enzyme; Provisional.
Length = 322
Score = 27.5 bits (62), Expect = 2.2
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 48 PEIIDIFTKRGLTT 61
PE+I+ F KRG TT
Sbjct: 148 PELIEEFHKRGFTT 161
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase,
mycofactocin system. Members of this protein family
possess an N-terminal heme-binding domain and
C-terminal flavodehydrogenase domain, and share
homology to yeast flavocytochrome b2, to E. coli
L-lactate dehydrogenase [cytochrome], to (S)-mandelate
dehydrogenase, etc. This enzyme appears only in the
context of the mycofactocin system. Interestingly, it
is absent from the four species detected so far with
mycofactocin but without an F420 biosynthesis system.
Length = 385
Score = 27.4 bits (61), Expect = 2.3
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS 75
F++ G P + KR L+T Q+ S P L+S
Sbjct: 44 FDELGFRPHVAGAPPKRELSTTVMGQEISFPVLIS 78
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 27.4 bits (61), Expect = 2.4
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 66 QKYSIPTLLSGKSAILVAETGCGKTLSFLAP-LVQQILT 103
Q+ I +LSG+ ++V TG GK+L + P LV LT
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLT 68
>gnl|CDD|188902 cd09503, SAM_tumor-p63,p73, SAM domain of tumor-p63,p73 proteins.
SAM (sterile alpha motif) domain of p63, p73
transcriptional factors is a putative protein-protein
interaction domain and lipid-binding domain. p63 and
p73 are homologs to the tumor suppressor p53. They have
a C-terminal SAM domain in their longest spliced alpha
forms, while p53 doesn't have it. p63 or p73 knockout
mice show significant developmental abnormalities but
no increased cancer susceptibility, suggesting that p63
and p73 play a role in regulation of normal
development. It was shown that SAM domain of p73 is
able to bind some membrane lipids. The structural
rearrangements in SAM are necessary to accomplish the
binding. No evidence for homooligomerization through
SAM domains was found for p63/p73 subfamily. It was
suggested that the partner proteins should be either
more distantly related SAM-containing domain proteins
or proteins without the SAM domain.
Length = 65
Score = 25.7 bits (57), Expect = 2.6
Identities = 6/23 (26%), Positives = 15/23 (65%)
Query: 51 IDIFTKRGLTTPTEIQKYSIPTL 73
ID F ++GL + ++ ++++ L
Sbjct: 20 IDNFHQQGLLSIFQLDEFTLEDL 42
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 27.0 bits (61), Expect = 2.8
Identities = 10/17 (58%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 76 GKSAIL-VAETGCGKTL 91
KS IL + TG GKTL
Sbjct: 107 QKSNILLIGPTGSGKTL 123
>gnl|CDD|188971 cd09572, SAM_tumor-p63, SAM domain of tumor-p63 proteins. SAM
(sterile alpha motif) domain of p63 proteins is a
putative protein-protein interaction domain. p63 is
homolog to the tumor suppressor p53. p63 has a
C-terminal SAM domain in the longest spliced alpha
form, while p53 doesn't have it. p63 knockout mice show
significant developmental abnormalities but no
increased cancer susceptibility, suggesting that p63
plays a role in regulation of normal development. No
evidence for homooligomerization through SAM domains
was found for the p63 subfamily. It was suggested that
the partner proteins should be either more distantly
related SAM-containing domain proteins or proteins
without the SAM domain. Mutations in the SAM domain of
p63 are found in AEC syndrome patients.
Length = 65
Score = 25.7 bits (56), Expect = 2.8
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 51 IDIFTKRGLTTPTEIQKYSIPTLLSGK 77
+D FT +GLTT +I+ YS+ L S K
Sbjct: 20 LDYFTTQGLTTIYQIEHYSMDDLSSLK 46
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 27.5 bits (61), Expect = 2.9
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 49 EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKT 90
E + F K + P IQK +L G S ++A TG GKT
Sbjct: 66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKT 107
>gnl|CDD|236898 PRK11308, dppF, dipeptide transporter ATP-binding subunit;
Provisional.
Length = 327
Score = 27.2 bits (61), Expect = 2.9
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 72 TLLSGKSAILVAETGCGKTLSFLAPLVQQI 101
TL GK+ +V E+GCGK S LA L+ I
Sbjct: 37 TLERGKTLAVVGESGCGK--STLARLLTMI 64
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 26.9 bits (60), Expect = 3.3
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 22/82 (26%)
Query: 33 VSRIDLGTFE------------DTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAI 80
+++IDL E D G + GL + LL+GK +
Sbjct: 117 LNKIDLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEE--------LAELLAGKITV 168
Query: 81 LVAETGCGKT--LSFLAPLVQQ 100
L+ ++G GK+ ++ L P + Q
Sbjct: 169 LLGQSGVGKSTLINALLPELNQ 190
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 26.8 bits (59), Expect = 3.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 83 AETGCGKTLSFLAPLVQQILT 103
A TG GKTL++L PL+
Sbjct: 21 APTGAGKTLAWLTPLLHGENK 41
>gnl|CDD|234202 TIGR03417, chol_sulfatase, choline-sulfatase.
Length = 500
Score = 27.0 bits (60), Expect = 3.6
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 19/53 (35%)
Query: 21 RNAYPTHRGYEAVSRID------LGTFEDTGLAPEIIDIFT--------KRGL 59
R AY + A+S ID L T E+T A + I +FT +RGL
Sbjct: 252 RRAY-----FGAISYIDDKIGELLDTLEETRQADDTIIVFTSDHGDMLGERGL 299
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1);
Provisional.
Length = 1466
Score = 26.9 bits (59), Expect = 3.7
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 64 EIQKYSIPTLLSGKSAILVAETGCGKT 90
EI K TL GK+ V E+GCGK+
Sbjct: 399 EIYKDLNFTLTEGKTYAFVGESGCGKS 425
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 26.8 bits (59), Expect = 3.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 83 AETGCGKTLSFLAPLVQQ 100
A TG GKTL++L PL+
Sbjct: 21 APTGAGKTLAWLTPLLHG 38
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 26.6 bits (59), Expect = 4.2
Identities = 29/103 (28%), Positives = 43/103 (41%), Gaps = 14/103 (13%)
Query: 33 VSRIDLGTFEDTGLAPEIIDIFTK----RGLTTPTEIQKYS----IP-----TLLSGKSA 79
VSR G FE+ P I D K RG +I S P ++L+G
Sbjct: 17 VSRFLGGRFEE-QYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPFPAMRRLSILTGDVF 75
Query: 80 ILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII 122
ILV ++ + L +QIL KS + K + N + ++I
Sbjct: 76 ILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVI 118
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1
and is thought to have a role in resistance to
oxidative stress. Interestingly, subfamily B is more
closely related to the carboxyl-terminal component of
subfamily C than the two halves of ABCC molecules are
with one another.
Length = 238
Score = 26.3 bits (59), Expect = 5.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 72 TLLSGKSAILVAETGCGKT 90
T+ GK+ LV +GCGK+
Sbjct: 25 TIPPGKTVALVGSSGCGKS 43
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 26.4 bits (59), Expect = 5.3
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 76 GKSAIL-VAETGCGKTLSFLAPLVQQIL 102
KS IL + TG GKTL LA + +IL
Sbjct: 96 SKSNILLIGPTGSGKTL--LAQTLAKIL 121
>gnl|CDD|233331 TIGR01255, pyr_form_ly_1, formate acetyltransferase 1. Alternate
names: pyruvate formate-lyase; formate
C-acetyltransferase This enzyme converts formate +
acetyl-CoA into pyruvate + CoA. This model describes
formate acetyltransferase 1. More distantly related
putative formate acetyltransferases have also been
identified, including formate acetyltransferase 2 from
E. coli, which is excluded from this model [Energy
metabolism, Fermentation].
Length = 744
Score = 26.4 bits (58), Expect = 5.4
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 26 THRGYEAVSRIDLGTFEDTGLAPEIIDIFT----KRGLTTPTEIQKY 68
+ GY AV ++ G G +DI+ RG T E Q++
Sbjct: 243 VYFGYLAVVKVINGAAMSLGRTSTFLDIYIERDLARGTITEQEAQEF 289
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 26.1 bits (58), Expect = 6.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYS 69
L E TGL EI+ K L +PTE Q++
Sbjct: 113 LVKAESTGL--EIVLCLNKADLVSPTEQQQWQ 142
>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 = 26.3 bits (58), Expect = 6.2
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 66 QKYSIPTLLSGKSAILVAETGCGKTLSF-LAPLV 98
Q I +L G+ +V TG GK+L + L L
Sbjct: 16 QLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC 49
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 26.2 bits (58), Expect = 6.7
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 83 AETGCGKTLSFLAPLVQQ 100
A+TG GKT +L PL+ Q
Sbjct: 271 AQTGIGKTYGYLLPLLAQ 288
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 25.7 bits (57), Expect = 7.2
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 88 GKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII 122
+TL LA + +L K++P Y P ++ +I+
Sbjct: 23 DQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIV 57
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication,
recombination, and repair].
Length = 845
Score = 26.1 bits (58), Expect = 7.8
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 80 ILVAETGCGKT 90
I+V ETG GKT
Sbjct: 69 IIVGETGSGKT 79
>gnl|CDD|234423 TIGR03972, rSAM_TYW1, wyosine biosynthesis protein TYW1. Members
of this protein family are the archaeal protein TWY1, a
radical SAM protein that catalyzes the second step in
creating the wye-bases, wyosine and derivatives such as
wybutosine, for tRNA base modification [Protein
synthesis, tRNA and rRNA base modification].
Length = 297
Score = 25.7 bits (57), Expect = 7.9
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 48 PEIIDIFTKRGLTT 61
PE+I+ F KRG TT
Sbjct: 137 PELIEEFHKRGFTT 150
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 25.8 bits (57), Expect = 8.3
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTL 91
Q+ +I L G+S ++ A T GKT+
Sbjct: 119 ELDPFQQEAIAILERGESVLVCAPTSSGKTV 149
>gnl|CDD|132210 TIGR03166, alt_F1F0_F1_eps, alternate F1F0 ATPase, F1 subunit
epsilon. A small number of taxonomically diverse
prokaryotic species have what appears to be a second ATP
synthase, in addition to the normal F1F0 ATPase in
bacteria and A1A0 ATPase in archaea. These enzymes use
ion gradients to synthesize ATP, and in principle may
run in either direction. This model represents the F1
epsilon subunit of this apparent second ATP synthase.
Length = 122
Score = 25.4 bits (56), Expect = 8.6
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 81 LVAETGCG------KTLSFLAPLVQQILTWKSRPE 109
+VAET G + +A LV IL +++
Sbjct: 20 IVAETESGSFGLLPGHVDCVAALVPGILIYETADG 54
>gnl|CDD|169553 PRK08690, PRK08690, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 261
Score = 25.7 bits (56), Expect = 9.9
Identities = 12/49 (24%), Positives = 21/49 (42%)
Query: 46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFL 94
L+ + +D ++ T EI YS+P L ++ LS+L
Sbjct: 100 LSGDFLDSISREAFNTAHEISAYSLPALAKAARPMMRGRNSAIVALSYL 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
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,849,131
Number of extensions: 597971
Number of successful extensions: 681
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 77
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.6 bits)