RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3307
(130 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 = 136 bits (345), Expect = 1e-41
Identities = 47/117 (40%), Positives = 68/117 (58%), Gaps = 14/117 (11%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
F+++ ++ + I ++KPTP+Q AIP ++SGRDV+ AQTGSGKTAAFL+PIL +
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
+ P A L+LAPTRELA QI + A+K + L+ V+
Sbjct: 61 LDPSPKKDGPQA--------------LILAPTRELALQIAEVARKLGKHTNLKVVVI 103
>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 = 122 bits (309), Expect = 5e-34
Identities = 44/122 (36%), Positives = 66/122 (54%), Gaps = 15/122 (12%)
Query: 9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
F + ++ + + +++PTP+Q AIP+I++GRDV+ AQTG+GKTAAFL+P
Sbjct: 27 TPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLP 86
Query: 69 ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA-YRSQLRPC 127
+L ++ + A L+LAPTRELA QI +E +K LR
Sbjct: 87 LLQKILKSVERKYVSA--------------LILAPTRELAVQIAEELRKLGKNLGGLRVA 132
Query: 128 VV 129
VV
Sbjct: 133 VV 134
>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 = 96.2 bits (240), Expect = 3e-26
Identities = 45/95 (47%), Positives = 54/95 (56%), Gaps = 16/95 (16%)
Query: 35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 94
TP+Q AIP I+SG+DV+ A TGSGKT AFL+PIL + KK
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLP----------------KKG 44
Query: 95 FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
P LVLAPTRELA QIY+E KK LR ++
Sbjct: 45 GPQALVLAPTRELAEQIYEELKKLFKILGLRVALL 79
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 92.9 bits (231), Expect = 2e-23
Identities = 47/117 (40%), Positives = 67/117 (57%), Gaps = 10/117 (8%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
FD + ++ I +A Y +PTP+Q+ AIP ++ GRD+MA AQTG+GKTA F +P+L
Sbjct: 3 FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQH 62
Query: 73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
+ R P GR P R L+L PTRELA QI + + ++ +R VV
Sbjct: 63 LITRQP---HAKGR-RPVR------ALILTPTRELAAQIGENVRDYSKYLNIRSLVV 109
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 91.9 bits (229), Expect = 6e-23
Identities = 42/112 (37%), Positives = 63/112 (56%), Gaps = 12/112 (10%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
F ++++ E + + Y +PT +Q AIP + GRDV+ A TG+GKTAAFL+P L
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62
Query: 73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL 124
+ + +P RK P L+L PTRELA Q+ D+A++ A + L
Sbjct: 63 LLD------------FPRRKSGPPRILILTPTRELAMQVADQARELAKHTHL 102
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 88.7 bits (220), Expect = 1e-21
Identities = 41/109 (37%), Positives = 58/109 (53%), Gaps = 13/109 (11%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
F + + N+ A Y+ PTP+Q AIP +SGR ++ A TGSGKTA+FLVPI+++
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182
Query: 73 --MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
G ++ PL +VL PTREL Q+ D+AK
Sbjct: 183 CCTIRSG---------HPSEQRN--PLAMVLTPTRELCVQVEDQAKVLG 220
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 84.5 bits (209), Expect = 2e-21
Identities = 36/106 (33%), Positives = 46/106 (43%), Gaps = 18/106 (16%)
Query: 26 IALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA 84
I ++ P QK AI ++SG RDV+ A TGSGKT A L+P L +
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRV--- 57
Query: 85 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL 130
LVL PTRELA Q +E KK L+ +
Sbjct: 58 --------------LVLVPTRELAEQWAEELKKLGPSLGLKVVGLY 89
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 82.9 bits (205), Expect = 1e-19
Identities = 47/129 (36%), Positives = 64/129 (49%), Gaps = 24/129 (18%)
Query: 5 LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA 64
+VS + F D + + +PTP+Q P+ +SGRD++ A+TGSGKT A
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFT-----EPTPIQVQGWPIALSGRDMIGIAETGSGKTLA 183
Query: 65 FLVP----ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY 120
FL+P I Q PL G P+ LVLAPTRELA QI ++ KF
Sbjct: 184 FLLPAIVHINAQ-----PLLRYGDG----------PIVLVLAPTRELAEQIREQCNKFGA 228
Query: 121 RSQLRPCVV 129
S++R V
Sbjct: 229 SSKIRNTVA 237
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 80.8 bits (200), Expect = 5e-19
Identities = 42/118 (35%), Positives = 62/118 (52%), Gaps = 9/118 (7%)
Query: 8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLV 67
L +Q F D + + + + TP+Q A+P+ ++GRDV AQTG+GKT AFL
Sbjct: 5 LTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLT 64
Query: 68 PILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
+ L + PA RK P L++APTRELA QI+ +A+ A + L+
Sbjct: 65 ATFHY------LLSHPAPED---RKVNQPRALIMAPTRELAVQIHADAEPLAQATGLK 113
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 79.1 bits (195), Expect = 3e-18
Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 16/107 (14%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
F D+ + I + Y+KP+P+Q IP +++GRDV+ AQTGSGKTAAF +P+L+
Sbjct: 8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67
Query: 73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
+ P K P LVLAPTRELA Q+ + F+
Sbjct: 68 L--------------DPELKA--PQILVLAPTRELAVQVAEAMTDFS 98
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 77.3 bits (190), Expect = 1e-17
Identities = 42/97 (43%), Positives = 55/97 (56%), Gaps = 9/97 (9%)
Query: 29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY 88
A + + TP+Q +PV + G DV AQTG+GKT AFLV ++N++ R L
Sbjct: 27 AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL--------- 77
Query: 89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
RK P L+LAPTRELA QI+ +A KF LR
Sbjct: 78 ADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLR 114
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 71.4 bits (176), Expect = 1e-15
Identities = 35/89 (39%), Positives = 52/89 (58%), Gaps = 16/89 (17%)
Query: 31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS 90
Y + TP+Q ++P I++G+DV+A A+TGSGKTAAF + +L ++
Sbjct: 24 YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKL--------------DVK 69
Query: 91 RKKVFPLGLVLAPTRELATQIYDEAKKFA 119
R +V LVL PTRELA Q+ E ++ A
Sbjct: 70 RFRV--QALVLCPTRELADQVAKEIRRLA 96
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 68.4 bits (168), Expect = 1e-14
Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERGPLPTPPA 84
++ TP Q+YAIP I SG +V+ A TGSGKT AAFL P++N++ G
Sbjct: 19 KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFL-PVINELLSLGKGKLEDG 73
>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 = 64.3 bits (157), Expect = 4e-14
Identities = 27/70 (38%), Positives = 33/70 (47%), Gaps = 17/70 (24%)
Query: 49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA 108
RDV+ A TGSGKT A L+PIL + LVLAPTRELA
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQV-----------------LVLAPTRELA 43
Query: 109 TQIYDEAKKF 118
Q+ + K+
Sbjct: 44 NQVAERLKEL 53
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 66.1 bits (161), Expect = 9e-14
Identities = 39/107 (36%), Positives = 55/107 (51%), Gaps = 9/107 (8%)
Query: 10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPI 69
K F D + + + I + TP+Q + ++G D + AQTG+GKTAAFL+ I
Sbjct: 86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISI 145
Query: 70 LNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK 116
+NQ+ L TPP Y P L++APTREL QI +A
Sbjct: 146 INQL-----LQTPPPKERYMGE----PRALIIAPTRELVVQIAKDAA 183
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 59.1 bits (144), Expect = 3e-11
Identities = 22/49 (44%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERG 77
++ TP Q+YAIP+I G++V+ + TGSGKT AAFL I+++++ G
Sbjct: 29 KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA-IIDELFRLG 76
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 56.0 bits (135), Expect = 3e-10
Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 16/99 (16%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
FD +++ E + I ++KP+ +Q+ I I+ G D + AQ+G+GKTA F++ L
Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89
Query: 73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
+ L+LAPTRELA QI
Sbjct: 90 I----------------DYDLNACQALILAPTRELAQQI 112
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 50.8 bits (122), Expect = 2e-08
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 18/84 (21%)
Query: 36 PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF 95
P Q+ ++S +V+ A TGSGKT L+ IL+ + E G K V+
Sbjct: 35 PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGG-------------GKVVY 81
Query: 96 PLGLVLAPTRELATQIYDEAKKFA 119
+ P + LA + Y+E +
Sbjct: 82 -----IVPLKALAEEKYEEFSRLE 100
>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 = 46.2 bits (110), Expect = 9e-07
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 17/84 (20%)
Query: 38 QKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 97
Q A+ +I GR+V+ TGSGKT +FL+PIL+ + PS +
Sbjct: 75 QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD------------PSAR----- 117
Query: 98 GLVLAPTRELATQIYDEAKKFAYR 121
L+L PT LA + ++
Sbjct: 118 ALLLYPTNALANDQAERLRELISD 141
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 35.3 bits (82), Expect = 0.002
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 27/94 (28%)
Query: 33 KPTPVQKYAIPVIISGRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPS 90
+ P Q+ AI ++ + + TGSGKT AA L+ L +
Sbjct: 3 ELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAK-----------------G 45
Query: 91 RKKVFPLGLVLAPTRELATQ----IYDEAKKFAY 120
+KKV L + P ++L Q I DEA +
Sbjct: 46 KKKV----LFVVPRKDLLEQALVIIIDEAHHSSA 75
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 36.3 bits (84), Expect = 0.002
Identities = 26/112 (23%), Positives = 42/112 (37%), Gaps = 30/112 (26%)
Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIIS----GRDVMACAQTGSGKT--AAFL 66
D + E + + +A + P Q+ A+ ++ R + TG+GKT AA
Sbjct: 16 LADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA 75
Query: 67 VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF 118
+ E ++ LVL PT+EL Q + KKF
Sbjct: 76 ------IAEL--------------KRST----LVLVPTKELLDQWAEALKKF 103
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 34.0 bits (78), Expect = 0.016
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 19/94 (20%)
Query: 32 DKPTPVQKYAIPVIISGR----DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG 87
+ +Q+ A+ +I+ V+ A TG GKT A L+ L + E+ L
Sbjct: 194 HEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKL-------- 245
Query: 88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR 121
+ + P R + +Y AK+
Sbjct: 246 -------KSRVIYVLPFRTIIEDMYRRAKEIFGL 272
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 32.7 bits (75), Expect = 0.039
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 22/73 (30%)
Query: 48 GRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR 105
GR ++ A TG+GKT A L + + G L LV+ P +
Sbjct: 25 GRGILKMA-TGTGKTLTALAAASKLYE--KIGLLVL-----------------LVVCPYQ 64
Query: 106 ELATQIYDEAKKF 118
L Q EA+KF
Sbjct: 65 HLVDQWAREAEKF 77
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 32.4 bits (74), Expect = 0.061
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 25 NIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT 62
A + P Q+ AI ++ G V+ CA T SGKT
Sbjct: 111 PPAREYPFELDPFQQEAIAILERGESVLVCAPTSSGKT 148
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 30.9 bits (70), Expect = 0.14
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 33 KPTPVQKYAI----PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG 77
+P P Q+ + G ++ A TG+GKT A+L+P L E G
Sbjct: 15 EPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG 63
>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 = 30.9 bits (70), Expect = 0.19
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 17/61 (27%)
Query: 48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL 107
GR V+ T SGK+ A+ +P+L+ + P T L LAPT+ L
Sbjct: 51 GRHVVVATGTASGKSLAYQLPVLSAL-ADDPRAT----------------ALYLAPTKAL 93
Query: 108 A 108
A
Sbjct: 94 A 94
>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 = 30.0 bits (68), Expect = 0.35
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
YD P Q+ I ++ GRDV+ TG GK+ + VP L
Sbjct: 11 YDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL 50
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.5 bits (67), Expect = 0.42
Identities = 25/91 (27%), Positives = 34/91 (37%), Gaps = 27/91 (29%)
Query: 33 KPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG 87
KP Q AI ++ G + TGSGKT + + + PT
Sbjct: 12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFT-----MANVIAKVQRPT------ 60
Query: 88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKF 118
LVLA + LA Q+Y E K+F
Sbjct: 61 -----------LVLAHNKTLAAQLYSEFKEF 80
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 29.7 bits (67), Expect = 0.46
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 55 AQTGSGKTAAFLVPILNQMYER 76
AQTG GKT +L+P+L Q +R
Sbjct: 271 AQTGIGKTYGYLLPLLAQSDQR 292
>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 = 29.4 bits (66), Expect = 0.47
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 36 PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
PVQ I ++ GRD TG GK+ + +P L
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>gnl|CDD|104071 PRK09629, PRK09629, bifunctional thiosulfate
sulfurtransferase/phosphatidylserine decarboxylase;
Provisional.
Length = 610
Score = 29.3 bits (65), Expect = 0.52
Identities = 17/43 (39%), Positives = 21/43 (48%)
Query: 75 ERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
ERGP+ G + + GLV P REL T YDEA +
Sbjct: 515 ERGPMAVVLVGAMIVASVETVWAGLVTPPKRELKTFSYDEAAR 557
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.5 bits (67), Expect = 0.57
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 20/68 (29%)
Query: 52 MACAQTGSGKTA-AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
+ TG GKTA A LV I +++++G KV L+LAPT+ L Q
Sbjct: 33 LVVLPTGLGKTAIALLV-IAERLHKKG--------------GKV----LILAPTKPLVEQ 73
Query: 111 IYDEAKKF 118
+ +KF
Sbjct: 74 HAEFFRKF 81
>gnl|CDD|213255 cd03288, ABCC_SUR2, ATP-binding cassette domain 2 of the
sulfonylurea receptor SUR. The SUR domain 2. The
sulfonylurea receptor SUR is an ATP binding cassette
(ABC) protein of the ABCC/MRP family. Unlike other ABC
proteins, it has no intrinsic transport function,
neither active nor passive, but associates with the
potassium channel proteins Kir6.1 or Kir6.2 to form the
ATP-sensitive potassium (K(ATP)) channel. Within the
channel complex, SUR serves as a regulatory subunit
that fine-tunes the gating of Kir6.x in response to
alterations in cellular metabolism. It constitutes a
major pharmaceutical target as it binds numerous drugs,
K(ATP) channel openers and blockers, capable of up- or
down-regulating channel activity.
Length = 257
Score = 28.7 bits (64), Expect = 0.78
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 20 EIITNNIALARYDKP-TPVQKYAIPVIISGRDVMACAQTGSGKTA 63
EI +++ + RY+ PV K+ I G+ V C +TGSGK++
Sbjct: 19 EIKIHDLCV-RYENNLKPVLKHVKAYIKPGQKVGICGRTGSGKSS 62
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 28.8 bits (65), Expect = 0.82
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
Y P Q+ I ++SG+D + TG GK+ + +P L
Sbjct: 15 YASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL 54
>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 = 28.7 bits (65), Expect = 0.97
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 33 KPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERGP 78
P P Q + GR + A TGSGKT A FL +++ P
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKP 59
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 27.7 bits (62), Expect = 1.3
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 18/66 (27%)
Query: 58 GSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
G+GKT L ++ + +R L T LVLAPTR + ++ + +
Sbjct: 12 GAGKTRKVLPELVRECIDRR-LRT-----------------LVLAPTRVVLAEMEEALRG 53
Query: 118 FAYRSQ 123
R
Sbjct: 54 LPIRYH 59
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of
double-stranded breaks by homologous recombination. The
term AddAB is used broadly, with AddA homologous
between the Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of
species [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1230
Score = 28.1 bits (63), Expect = 1.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
T Q AI G+D++ A GSGKTA + I+ +
Sbjct: 3 TDEQWQAI--YTRGQDILVSASAGSGKTAVLVERIIRK 38
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 27.7 bits (62), Expect = 1.9
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQ-KYAIPVIISGRDVMACAQTGSGKT 62
VS F + ++ L Y +P Q Y I + + ++ C T SGKT
Sbjct: 100 VSPNGSSFTIRKFSDEPITPEDLIEYGTISPEQAAYLWLAIEARKSIIICGGTASGKT 157
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.0 bits (63), Expect = 1.9
Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 31/93 (33%)
Query: 33 KPTPVQKYAIPVIISGRDVMACAQTGSGKT------AAFLVPILNQMYERGPLPTPPAGR 86
KP +Q+ ++ G A TG GKT + +L A +
Sbjct: 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYL-----------------AKK 122
Query: 87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
G KK ++ PTR L Q+ ++ +KF
Sbjct: 123 G----KKS----YIIFPTRLLVEQVVEKLEKFG 147
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 27.8 bits (62), Expect = 2.0
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 21/62 (33%)
Query: 35 TPVQKYAIPV-IISGRDVMACAQTGSGKTAA-----------------FLVPIL---NQM 73
PVQ A+ ++ G +++ + T SGKT FLVP++ NQ
Sbjct: 218 LPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQK 277
Query: 74 YE 75
YE
Sbjct: 278 YE 279
>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 = 27.5 bits (61), Expect = 2.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 50 DVMACAQTGSGKTAAFLVPILNQ 72
+ A TG+GKT +L+P L
Sbjct: 266 KSLIEAPTGTGKTLGYLLPALYY 288
>gnl|CDD|233090 TIGR00682, lpxK, tetraacyldisaccharide 4'-kinase. Also called
lipid-A 4'-kinase. This essential gene encodes an
enzyme in the pathway of lipid A biosynthesis in
Gram-negative organisms. A single copy of this protein
is found in Gram-negative bacteria. PSI-BLAST converges
on this set of apparent orthologs without identifying
any other homologs [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 311
Score = 27.4 bits (61), Expect = 2.3
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 39 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 97
+ +PV+I G + G+GKT +V + + +RG L RGY S+ K + L
Sbjct: 25 RAPVPVVIVGN----LSVGGTGKTP-VVVWLAELLKDRG-LRVGVLSRGYGSKTKKYTL 77
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 27.3 bits (61), Expect = 2.6
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 26/64 (40%)
Query: 57 TGSGKTA--AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE 114
TGSGKT A ++ +N PT LV+A + LA Q+Y+E
Sbjct: 38 TGSGKTFTMANVIAQVN-------RPT-----------------LVIAHNKTLAAQLYNE 73
Query: 115 AKKF 118
K+F
Sbjct: 74 FKEF 77
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 27.4 bits (61), Expect = 2.7
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
Y + P Q+ I ++SGRD + TG GK+ + +P L
Sbjct: 23 YQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPAL 62
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 27.2 bits (60), Expect = 3.2
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 36 PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
P Q+ I +SG DV TG GK+ + +P L
Sbjct: 463 PNQREIINATMSGYDVFVLMPTGGGKSLTYQLPAL 497
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 26.8 bits (60), Expect = 3.5
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 19/61 (31%)
Query: 58 GSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
GSGKT L+ +L E G + ++APT LA Q Y+ +K
Sbjct: 293 GSGKTVVALLAML-AAIEAG--------------YQA----ALMAPTEILAEQHYESLRK 333
Query: 118 F 118
+
Sbjct: 334 W 334
>gnl|CDD|132949 cd06618, PKc_MKK7, Catalytic domain of the dual-specificity Protein
Kinase, MAP kinase kinase 7. Protein kinases (PKs), MAP
kinase kinase 7 (MKK7) subfamily, catalytic (c) domain.
PKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine or tyrosine residues on
protein substrates. The MKK7 subfamily is part of a
larger superfamily that includes the catalytic domains
of other protein serine/threonine kinases, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. The mitogen-activated protein (MAP) kinase
signaling pathways are important mediators of cellular
responses to extracellular signals. The pathways involve
a triple kinase core cascade comprising the MAP kinase
(MAPK), which is phosphorylated and activated by a MAPK
kinase (MAPKK or MKK), which itself is phosphorylated
and activated by a MAPK kinase kinase (MAPKKK or MKKK).
MKK7 is a dual-specificity PK that phosphorylates and
activates its downstream target, c-Jun N-terminal kinase
(JNK), on specific threonine and tyrosine residues.
Although MKK7 is capable of dual phosphorylation, it
prefers to phosphorylate the threonine residue of JNK.
Thus, optimal activation of JNK requires both MKK4 (not
included in this subfamily) and MKK7. MKK7 is primarily
activated by cytokines. MKK7 is essential for liver
formation during embryogenesis. It plays roles in G2/M
cell cycle arrest and cell growth. In addition, it is
involved in the control of programmed cell death, which
is crucial in oncogenesis, cancer chemoresistance, and
antagonism to TNFalpha-induced killing, through its
inhibition by Gadd45beta and the subsequent suppression
of the JNK cascade.
Length = 296
Score = 27.0 bits (60), Expect = 3.5
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 11/67 (16%)
Query: 46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR 105
ISGR V + A+T S AA++ P ER + P Y R V+ LG+ L
Sbjct: 161 ISGRLVDSKAKTRSAGCAAYMAP------ER--IDPPDPNPKYDIRADVWSLGISLV--- 209
Query: 106 ELATQIY 112
ELAT +
Sbjct: 210 ELATGQF 216
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 26.9 bits (61), Expect = 3.9
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 26/64 (40%)
Query: 57 TGSGKTA--AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE 114
TGSGKT A ++ L + PT LVLA + LA Q+Y E
Sbjct: 41 TGSGKTFTMANVIARLQR-------PT-----------------LVLAHNKTLAAQLYSE 76
Query: 115 AKKF 118
K+F
Sbjct: 77 FKEF 80
>gnl|CDD|219697 pfam08014, DUF1704, Domain of unknown function (DUF1704). This
family contains many hypothetical proteins.
Length = 348
Score = 26.8 bits (60), Expect = 4.1
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 60 GKTAAFLVPILNQMYERGPLPTPP 83
GKTA +P++ ++ ERG L P
Sbjct: 299 GKTALEDLPLIRELVERGLLTPPK 322
>gnl|CDD|238668 cd01372, KISc_KIF4, Kinesin motor domain, KIF4-like subfamily.
Members of this group seem to perform a variety of
functions, and have been implicated in neuronal
organelle transport and chromosome segregation during
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type).
N-type kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a
speed of about 6400 Angstroms per second. To achieve
that, kinesin head groups work in pairs. Upon replacing
ADP with ATP, a kinesin motor domain increases its
affinity for microtubule binding and locks in place.
Also, the neck linker binds to the motor domain, which
repositions the other head domain through the
coiled-coil domain close to a second tubulin dimer,
about 80 Angstroms along the microtubule. Meanwhile,
ATP hydrolysis takes place, and when the second head
domain binds to the microtubule, the first domain again
replaces ADP with ATP, triggering a conformational
change that pulls the first domain forward.
Length = 341
Score = 26.5 bits (59), Expect = 4.2
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 51 VMACAQTGSGKT 62
V+A QTGSGKT
Sbjct: 77 VLAYGQTGSGKT 88
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 26.6 bits (59), Expect = 4.3
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 35 TPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLV-PILNQMYERGPL 79
T Q+ AI + R+++ TGSGKT LV I+N+M + P
Sbjct: 134 TAAQREAIIAAVRAHRNILVIGGTGSGKTT--LVNAIINEMVIQDPT 178
>gnl|CDD|234555 TIGR04344, ovoA_Nterm, 5-histidylcysteine sulfoxide synthase.
Ovothiol A is N1-methyl-4-mercaptohistidine. In the
absence of S-adenosylmethione, a methyl donor, the
intermediate produced is 4-mercaptohistidine. In both
Erwinia tasmaniensis and Trypanosoma cruzi, a protein
occurs with 5-histidylcysteine sulfoxide synthase
activity, but these two enzymes and most homologs share
an additional C-terminal methyltransferase domain. Thus
OvoA may be a bifunctional enzyme with
5-histidylcysteine sulfoxide synthase and
4-mercaptohistidine N1-methyltranferase activity. This
model describes the 5-histidylcysteine sulfoxide
synthase domain, a homolog of the ergothioneine
biosynthesis protein EgtB [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 442
Score = 26.5 bits (59), Expect = 4.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 14 DDIQMTEIITNNIALARYDKPTPVQKYA 41
DD T+ N+ LA PV ++A
Sbjct: 336 DDPVWTDEAPANLNLAYGASSCPVDRFA 363
>gnl|CDD|214371 CHL00122, secA, preprotein translocase subunit SecA; Validated.
Length = 870
Score = 26.5 bits (59), Expect = 5.9
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 18/82 (21%)
Query: 8 LKKQGFDDIQMTEIITNNIALAR-----------YDKPTPVQKYAIPVIISGRDVMACAQ 56
LKK+ + + +II + AL R +D VQ V+ G+ +A +
Sbjct: 44 LKKRLSNGQNLNKIIPESFALTREASFRTLGLRHFD----VQLIGGLVLNDGK--IAEMK 97
Query: 57 TGSGKT-AAFLVPILNQMYERG 77
TG GKT A L LN + +G
Sbjct: 98 TGEGKTLVATLPAYLNALTGKG 119
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 26.1 bits (58), Expect = 6.1
Identities = 23/93 (24%), Positives = 33/93 (35%), Gaps = 27/93 (29%)
Query: 33 KPTPVQKYAIPVIIS--GRDVMACAQ-----TGSGKTAAFLVPILNQMYERGPLPTPPAG 85
K T QK + I+ DV + GSGKT LV L +
Sbjct: 235 KLTRAQKRVVKEILQDLKSDV-PMNRLLQGDVGSGKT---LVAALAML------------ 278
Query: 86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF 118
+ +V ++APT LA Q Y+ +
Sbjct: 279 AAIEAGYQV----ALMAPTEILAEQHYNSLRNL 307
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 26.2 bits (58), Expect = 6.5
Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 31/93 (33%)
Query: 33 KPTPVQKYAIPVIISGRDVMACAQTGSGKT------AAFLVPILNQMYERGPLPTPPAGR 86
+P Q+ ++ G+ A TG GKT + +L A +
Sbjct: 82 RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYL-----------------AKK 124
Query: 87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
G K+V ++ PT L Q+Y+ KKFA
Sbjct: 125 G----KRV----YIIVPTTTLVRQVYERLKKFA 149
>gnl|CDD|191851 pfam07798, DUF1640, Protein of unknown function (DUF1640). This
family consists of sequences derived from hypothetical
eukaryotic proteins. A region approximately 100
residues in length is featured.
Length = 177
Score = 25.7 bits (57), Expect = 7.1
Identities = 8/27 (29%), Positives = 16/27 (59%), Gaps = 7/27 (25%)
Query: 7 SLKKQGFDDIQ-------MTEIITNNI 26
SL++ GF + Q +T++I ++I
Sbjct: 10 SLEENGFTEEQAEAIVSALTDVINDSI 36
>gnl|CDD|226636 COG4166, OppA, ABC-type oligopeptide transport system, periplasmic
component [Amino acid transport and metabolism].
Length = 562
Score = 26.2 bits (58), Expect = 7.1
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 81 TPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
TPPA G P ++ L E A ++ EA
Sbjct: 351 TPPAASGLPGKELALLAPLPQKDPPEKAKELLKEAGY 387
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and
move along the microtubule at a speed of about 6400
Angstroms per second. To achieve that, kinesin head
groups work in pairs. Upon replacing ADP with ATP, a
kinesin motor domain increases its affinity for
microtubule binding and locks in place. Also, the neck
linker binds to the motor domain, which repositions the
other head domain through the coiled-coil domain close
to a second tubulin dimer, about 80 Angstroms along the
microtubule. Meanwhile, ATP hydrolysis takes place, and
when the second head domain binds to the microtubule,
the first domain again replaces ADP with ATP,
triggering a conformational change that pulls the first
domain forward.
Length = 328
Score = 25.7 bits (57), Expect = 7.5
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 45 IISGRDVMACA--QTGSGKT 62
++ G + A QTGSGKT
Sbjct: 74 VLEGYNGTIFAYGQTGSGKT 93
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 26.0 bits (57), Expect = 7.7
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 55 AQTGSGKT-AAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
A TGSGKT AAFL + E G T A + SR L ++P + L T +
Sbjct: 3 APTGSGKTLAAFLYALDRLFREGGE-DTREAHKRKTSRI------LYISPIKALGTDV 53
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 25.6 bits (57), Expect = 7.9
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 51 VMACAQTGSGKT 62
+ A QTGSGKT
Sbjct: 77 IFAYGQTGSGKT 88
>gnl|CDD|233800 TIGR02247, HAD-1A3-hyp, epoxide hydrolase N-terminal domain-like
phosphatase. This model represents a small clade of
sequences including C. elegans and mammalian sequences
as well as a small number of bacteria. In eukaryotes,
this domain exists as an N-terminal fusion to the
soluble epoxide hydrolase enzyme and has recently been
shown to be an active phosphatase, although the nature
of the biological substrate is unclear. These appear to
be members of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases by
general homology and the conservation of all of the
recognized catalytic motifs (although the first motif is
unusual in the replacement of the more common aspartate
with glycine...). The variable domain is found in
between motifs 1 and 2, indicating membership in
subfamily I and phylogeny and prediction of the alpha
helical nature of the variable domain (by PSI-PRED)
indicate membership in subfamily IA.
Length = 211
Score = 25.6 bits (56), Expect = 7.9
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 1 MQECLVSLKKQGFDDIQMTEIITNNIALAR 30
M + +L+ +GF T ITNN
Sbjct: 99 MMAAIKTLRAKGFK----TACITNNFPTDH 124
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 25.6 bits (57), Expect = 7.9
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 52 MACAQTGSGKTAAFLVPILNQMYERG 77
+ TG+GKT A +L+Q+ RG
Sbjct: 19 LIVGTTGTGKTQALR-ELLDQIRARG 43
>gnl|CDD|236730 PRK10641, btuB, vitamin B12/cobalamin outer membrane transporter;
Provisional.
Length = 614
Score = 25.7 bits (57), Expect = 7.9
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 85 GRGYPSRKKV---FPLGLVLAPTRELATQIYDEAKKFA---YRSQL 124
G GY +R + G L TR+L +Q +D ++ Y SQL
Sbjct: 240 GYGYDNRTDYDAYYSPGSPLIDTRQLYSQSWDAGLRYNGGIYSSQL 285
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 25.8 bits (57), Expect = 8.6
Identities = 6/28 (21%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 51 VMACAQTGSGKTAAFLVPILNQMYERGP 78
++ +GSGK+ + + ++ RG
Sbjct: 4 MLIVGPSGSGKSTLLKL-LALRLLARGG 30
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of
organelles and in cell division.
Length = 335
Score = 25.6 bits (57), Expect = 8.9
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 41 AIPVIISGRD-----VMACAQTGSGKT 62
A P++ S + + A QTGSGKT
Sbjct: 68 AAPLVDSVLEGYNATIFAYGQTGSGKT 94
>gnl|CDD|222919 PHA02688, PHA02688, ORF059 IMV protein VP55; Provisional.
Length = 323
Score = 25.4 bits (56), Expect = 9.2
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 2 QECLVSLKKQGFDDIQMTEIITNN 25
+ ++K++ D +Q+ E + NN
Sbjct: 136 HPIIKAMKEKNIDILQLRETLHNN 159
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 25.9 bits (58), Expect = 9.2
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 100 VLAPTRELATQIYDEAKKF 118
++APT LA Q Y+ KK
Sbjct: 315 LMAPTEILAEQHYENLKKL 333
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 0.138 0.407
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,787,764
Number of extensions: 605668
Number of successful extensions: 718
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 83
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
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 (21.9 bits)
S2: 53 (24.4 bits)