RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9277
(178 letters)
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 223 bits (571), Expect = 9e-73
Identities = 95/152 (62%), Positives = 115/152 (75%), Gaps = 1/152 (0%)
Query: 14 PEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVI 73
+ S E++ D E+V +FD + L EDLLRGIY+YGFEKPSAIQQR IKPI+ G D I
Sbjct: 11 EQVASTGTIESNYD-EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTI 69
Query: 74 AQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA 133
QAQSGTGKTATF I+ LQ +D L Q L L+PTRELA QIQKVVLALGD++ V+CHA
Sbjct: 70 GQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHA 129
Query: 134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
C+GGT + +D+ KL G H+V GTPGRV+DMI
Sbjct: 130 CVGGTVVRDDINKLKAGVHMVVGTPGRVYDMI 161
>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 = 205 bits (525), Expect = 4e-68
Identities = 68/135 (50%), Positives = 92/135 (68%), Gaps = 2/135 (1%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F+ +GL +LLRGIYA GFEKP+ IQ R+I P++ GRDVI QAQ+G+GKTA F I IL+
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 94 LDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
LD + Q L L+PTRELA+QI +V LG N++ GGT++ + +RKL G
Sbjct: 61 LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120
Query: 152 HVVSGTPGRVFDMIR 166
H+V TPGR+ D++
Sbjct: 121 HIVVATPGRLLDLLE 135
>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 = 154 bits (392), Expect = 3e-45
Identities = 53/162 (32%), Positives = 90/162 (55%), Gaps = 3/162 (1%)
Query: 8 ITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV 67
+ + ++ + + + F ++GL +LL+ + GFE+P+ IQ +I I+
Sbjct: 5 DYDRFVKLKSAHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLIL 64
Query: 68 KGRDVIAQAQSGTGKTATFSISILQSLD--TQLRETQVLCLSPTRELAVQIQKVVLALGD 125
GRDV+ QAQ+GTGKTA F + +LQ + + + L L+PTRELAVQI + + LG
Sbjct: 65 AGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGK 124
Query: 126 FM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
+ ++ GG ++ + + L G +V TPGR+ D+I+
Sbjct: 125 NLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIK 166
>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 = 121 bits (305), Expect = 2e-35
Identities = 46/113 (40%), Positives = 70/113 (61%), Gaps = 1/113 (0%)
Query: 56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ 115
+ IQ ++I I+ G+DV+ QA +G+GKT F + ILQ+L + Q L L+PTRELA Q
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60
Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRS 167
I + + L + ++ GGT+L E RKL G+ ++ GTPGR+ D++R
Sbjct: 61 IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 115 bits (289), Expect = 3e-30
Identities = 60/142 (42%), Positives = 86/142 (60%), Gaps = 7/142 (4%)
Query: 29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
E +TF ++GL+ +L + G+EKPS IQ I ++ GRDV+ AQ+G+GKTA FS+
Sbjct: 3 EFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSL 62
Query: 89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDL 144
+L +LD +L+ Q+L L+PTRELAVQ+ + A+ DF V A GG L
Sbjct: 63 PLLHNLDPELKAPQILVLAPTRELAVQVAE---AMTDFSKHMRGVNVVALYGGQRYDVQL 119
Query: 145 RKLDYGQHVVSGTPGRVFDMIR 166
R L G +V GTPGR+ D ++
Sbjct: 120 RALRQGPQIVVGTPGRLLDHLK 141
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 107 bits (270), Expect = 8e-30
Identities = 43/122 (35%), Positives = 69/122 (56%), Gaps = 3/122 (2%)
Query: 47 IYAYGFEKPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLC 105
I +GFE Q+ +I+ ++ G RDVI A +G+GKT + L++L + +VL
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLV 59
Query: 106 LSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDM 164
L PTRELA Q + + LG + ++ GG + E LRKL+ G+ ++ TPGR+ D+
Sbjct: 60 LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119
Query: 165 IR 166
+
Sbjct: 120 LE 121
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 109 bits (276), Expect = 1e-28
Identities = 52/136 (38%), Positives = 81/136 (59%), Gaps = 1/136 (0%)
Query: 32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
+ F + L LL + G+ + + IQ +S+ I+ G+DVIAQA++G+GKTA F + +L
Sbjct: 4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63
Query: 92 QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
Q LD + Q L L PTRELA Q+ K + L F+ N++ GG + + L++G
Sbjct: 64 QKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG 123
Query: 151 QHVVSGTPGRVFDMIR 166
H++ GTPGR+ D +R
Sbjct: 124 AHIIVGTPGRILDHLR 139
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 103 bits (259), Expect = 2e-26
Identities = 54/138 (39%), Positives = 88/138 (63%), Gaps = 6/138 (4%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
+FD++GL D+LR + G+ +P+ IQQ++I +++GRD++A AQ+GTGKTA F++ +LQ
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 93 SLDTQ------LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK 146
L T+ R + L L+PTRELA QI + V ++N++ GG +++ + K
Sbjct: 62 HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121
Query: 147 LDYGQHVVSGTPGRVFDM 164
L G V+ TPGR+ D+
Sbjct: 122 LRGGVDVLVATPGRLLDL 139
>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 = 89.3 bits (222), Expect = 3e-23
Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 2/100 (2%)
Query: 70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV 129
RDV+ A +G+GKT + IL+ LD L+ QVL L+PTRELA Q+ + + L +
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLD-SLKGGQVLVLAPTRELANQVAERLKELFGE-GI 58
Query: 130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ 169
+ IGGT++ + + L +V GTPGR+ D + +
Sbjct: 59 KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLK 98
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 91.9 bits (229), Expect = 3e-22
Identities = 48/137 (35%), Positives = 67/137 (48%), Gaps = 4/137 (2%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
TF + L E LL + G+ +P+AIQ +I P + GRDV+ A +GTGKTA F + LQ
Sbjct: 2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61
Query: 93 SLDTQLRE----TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
L R ++L L+PTRELA+Q+ L ++ GG
Sbjct: 62 HLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS 121
Query: 149 YGQHVVSGTPGRVFDMI 165
Q +V TPGR+ I
Sbjct: 122 ENQDIVVATPGRLLQYI 138
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 92.3 bits (229), Expect = 3e-22
Identities = 53/171 (30%), Positives = 84/171 (49%), Gaps = 10/171 (5%)
Query: 2 AAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQR 61
R +K P L +E E E + F + L +L+ I+ GF + IQ +
Sbjct: 57 KKDKPRRERKPKPASLWKLEDFVVEPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQ 116
Query: 62 SIKPIVKGRDVIAQAQSGTGKTATFSISILQSL-------DTQLRETQVLCLSPTRELAV 114
+ + G D I +AQ+GTGKTA F ISI+ L + + E + L ++PTREL V
Sbjct: 117 VLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVV 176
Query: 115 QIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH--VVSGTPGRVFD 163
QI K AL + + +GG + + L++L+ + ++ TPGR+ D
Sbjct: 177 QIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLE-ARFCDILVATPGRLLD 226
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 77.7 bits (192), Expect = 3e-17
Identities = 43/144 (29%), Positives = 68/144 (47%), Gaps = 9/144 (6%)
Query: 34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
F + L ++ + GF + IQ ++ + GRDV QAQ+GTGKT F +
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 94 L-------DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK 146
L D ++ + + L ++PTRELAVQI L ++ GG + L+
Sbjct: 70 LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129
Query: 147 LDYGQHVVSGTPGRVFDMIRSSQG 170
L+ G ++ GT GR+ D + Q
Sbjct: 130 LESGVDILIGTTGRLIDYAK--QN 151
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 77.3 bits (190), Expect = 5e-17
Identities = 46/141 (32%), Positives = 74/141 (52%), Gaps = 7/141 (4%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
TF + L LL G+ + GF + + IQ ++ + G DV QAQ+GTGKT F ++++
Sbjct: 10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69
Query: 93 SL-------DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
L D + + + L L+PTRELA+QI K + G + ++ GG + +
Sbjct: 70 RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRE 129
Query: 146 KLDYGQHVVSGTPGRVFDMIR 166
L G V+ TPGR+ D ++
Sbjct: 130 LLQQGVDVIIATPGRLIDYVK 150
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 75.2 bits (185), Expect = 3e-16
Identities = 43/141 (30%), Positives = 74/141 (52%), Gaps = 9/141 (6%)
Query: 33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL- 91
+F + GL LL + G+E P+ IQ ++I + GR ++ A +G+GKTA+F + I+
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181
Query: 92 -------QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL 144
Q R + L+PTREL VQ++ LG + + +GG + + L
Sbjct: 182 RCCTIRSGHPSEQ-RNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL 240
Query: 145 RKLDYGQHVVSGTPGRVFDMI 165
++ G ++ GTPGR+ D++
Sbjct: 241 YRIQQGVELIVGTPGRLIDLL 261
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 71.3 bits (175), Expect = 5e-15
Identities = 42/143 (29%), Positives = 71/143 (49%), Gaps = 5/143 (3%)
Query: 31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
V +F+ + +L+ + GF +P+ IQ + + GRD+I A++G+GKT F +
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPA 188
Query: 91 LQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
+ ++ Q LR VL L+PTRELA QI++ G ++ GG +
Sbjct: 189 IVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIY 248
Query: 146 KLDYGQHVVSGTPGRVFDMIRSS 168
L G ++ PGR+ D + S+
Sbjct: 249 ALRRGVEILIACPGRLIDFLESN 271
>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 = 41.6 bits (98), Expect = 8e-05
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
E L + G E+ + Q +++ I +GR+V+ +G+GKT +F + IL L +
Sbjct: 55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL-LRD 113
Query: 99 RETQVLCLSPTRELA 113
+ L L PT LA
Sbjct: 114 PSARALLLYPTNALA 128
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 39.6 bits (93), Expect = 5e-04
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKT-ATF--SISILQSLDTQLRETQVLCL-- 106
F + Q+ +I I G +V+ A +G+GKT A F I+ L SL E + L
Sbjct: 20 FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYI 79
Query: 107 SPTRELAVQIQKVVLALGDFMN 128
SP + L I++ + +
Sbjct: 80 SPLKALNNDIRRRLEEPLRELG 101
>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 = 38.6 bits (90), Expect = 0.001
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 40 REDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR 99
D++ + A G +P Q R+ + GR V+ + +GK+ + + +L +L R
Sbjct: 22 HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPR 81
Query: 100 ETQVLCLSPTRELAVQIQKVVLALG 124
T L L+PT+ LA + V L
Sbjct: 82 AT-ALYLAPTKALAADQLRAVRELT 105
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 37.9 bits (89), Expect = 0.001
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL----DTQLRETQVLCL- 106
F + Q+ +I I +G++V+ + +G+GKT ++I+ L E +V CL
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLY 89
Query: 107 -SPTRELAVQIQK 118
SP R L I +
Sbjct: 90 VSPLRALNNDIHR 102
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 33.1 bits (76), Expect = 0.062
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI-QKVVLALGDFMNVQCHA 133
+AQ+G GKT + + +L Q + Q++ PT+ L QI + V A+ + ++ CH+
Sbjct: 270 EAQTGIGKTYGYLLPLLA----QSDQRQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCHS 325
Query: 134 CIGGTN 139
G N
Sbjct: 326 LKGPQN 331
>gnl|CDD|221912 pfam13086, AAA_11, AAA 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 = 220
Score = 31.2 bits (71), Expect = 0.18
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 59 QQRSIKPIVKGRDV-IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT 109
Q+ +IK + D+ + Q GTGKT T + I++ L + +VL +P+
Sbjct: 6 QREAIKKALSSSDITLIQGPPGTGKTTT-IVEIIKQLLSNAPGKKVLVCAPS 56
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 31.6 bits (72), Expect = 0.19
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 54 KPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT 109
+ Q+ ++ +VK R + +G GKT ++ + + L L PT
Sbjct: 36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKT------VVAAEAIAELKRSTLVLVPT 89
Query: 110 RELAVQIQK 118
+EL Q +
Sbjct: 90 KELLDQWAE 98
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 30.8 bits (70), Expect = 0.42
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 64 KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI 116
K ++ +V+ A +G+GKT ++IL +L +V+ + P + LA +
Sbjct: 42 KGLLSDENVLISAPTGSGKTLIALLAILSTL--LEGGGKVVYIVPLKALAEEK 92
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 30.4 bits (69), Expect = 0.46
Identities = 27/123 (21%), Positives = 52/123 (42%), Gaps = 14/123 (11%)
Query: 10 KKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG 69
++ ++LS+V D+ + Y FE QQ +I + +G
Sbjct: 81 VRLSSKELSDVAVPDDYDMVPDAESPFDLAPPAR-----EYPFE-LDPFQQEAIAILERG 134
Query: 70 RDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL-GDF 126
V+ A + +GKT A ++I++ +V+ SP + L+ Q + +LA GD
Sbjct: 135 ESVLVCAPTSSGKTVVAEYAIAL-----ALRDGQRVIYTSPIKALSNQKYRDLLAKFGDV 189
Query: 127 MNV 129
++
Sbjct: 190 ADM 192
>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 = 30.6 bits (70), Expect = 0.47
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKT-ATF--SISILQSLDTQLRETQVLCLSPTR 110
P Q ++GR + A +G+GKT A F S+ L + + L ++P R
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLR 72
Query: 111 ELAVQIQK 118
LAV I +
Sbjct: 73 ALAVDIAR 80
>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 = 30.6 bits (69), Expect = 0.53
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA 113
+P +IQ+ K +++G A +G GKT TF +++ SL + + + PT L
Sbjct: 78 EPWSIQKMWAKRVLRGDSFAIIAPTGVGKT-TFGLAM--SLFLAKKGKRCYIILPTTLLV 134
Query: 114 VQI 116
+Q+
Sbjct: 135 IQV 137
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.9 bits (67), Expect = 0.84
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 4/96 (4%)
Query: 51 GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR 110
GFE +IQ+ K I++G+ A +G GK+ TF I L + ++ ++ PT
Sbjct: 77 GFE-FWSIQKTWAKRILRGKSFSIVAPTGMGKS-TFGAFIALFLALKGKKCYIIL--PTT 132
Query: 111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK 146
L Q + + + + N+ +NL + ++
Sbjct: 133 LLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKE 168
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 29.4 bits (66), Expect = 1.2
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 51 GFEKPSAIQQRSIKPIV----KGRDVIAQAQSGTGKT-ATFSISILQSLDTQLRETQVLC 105
GFE P Q+ + + G ++ +A +GTGKT A ++ + + + V+
Sbjct: 13 GFE-PRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKK---VII 68
Query: 106 LSPTRELAVQI 116
+ T+ L Q+
Sbjct: 69 STRTKALQEQL 79
>gnl|CDD|227392 COG5059, KIP1, Kinesin-like protein [Cytoskeleton].
Length = 568
Score = 28.9 bits (65), Expect = 1.4
Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 27/94 (28%)
Query: 7 RITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEK---PSAIQQ--- 60
RI + E L N ++ +E Y F+K PSA Q+
Sbjct: 29 RIIPGELGERLINTSKKSHVSLEKS--------------KEGTYAFDKVFGPSATQEDVY 74
Query: 61 -RSIKPIV----KGRD--VIAQAQSGTGKTATFS 87
+IKP++ G + V A Q+G+GKT T S
Sbjct: 75 EETIKPLIDSLLLGYNCTVFAYGQTGSGKTYTMS 108
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 28.9 bits (65), Expect = 1.5
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP 108
A GF P + Q+ K +V+G+ A +G GKT TF + + SL + +V + P
Sbjct: 78 ATGFR-PWSAQRVWAKRLVRGKSFAIIAPTGVGKT-TFGLLM--SLYLAKKGKRVYIIVP 133
Query: 109 TRELAVQIQKVVLALGD 125
T L Q+ + + +
Sbjct: 134 TTTLVRQVYERLKKFAE 150
>gnl|CDD|204301 pfam09735, Nckap1, Membrane-associated apoptosis protein.
Expression of this protein was found to be markedly
reduced in patients with Alzheimer's disease. It is
involved in the regulation of actin polymerisation in
the brain as part of a WAVE2 signalling complex.
Length = 1118
Score = 28.5 bits (64), Expect = 1.9
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 15/88 (17%)
Query: 17 LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQA 76
LS++ + E+ E FD GLR D R + AY S++ R +
Sbjct: 463 LSSLSVKQVENGEA---FDFRGLRLDWFR-LQAYTSVAKSSLNLRDNPKLAS-------- 510
Query: 77 QSGTGKTATFSISILQSLDTQLRETQVL 104
T F ++ SL+ L ET L
Sbjct: 511 ---EMNTIVFHSKMVDSLEEMLVETSDL 535
>gnl|CDD|236420 PRK09229, PRK09229, N-formimino-L-glutamate deiminase; Validated.
Length = 456
Score = 28.3 bits (64), Expect = 2.4
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQA 177
H I +L E+LR L+YGQ + + + S GRR + A
Sbjct: 324 HVSI---DLVEELRLLEYGQRLRDRRRNVLAAAAQPSVGRRLFDAA 366
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.8 bits (60), Expect = 3.1
Identities = 13/57 (22%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ 115
Q+ +I+ +++ + + +G+GKT T + I + + +VL + P ++L Q
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAK---GKKKVLFVVPRKDLLEQ 61
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 27.7 bits (61), Expect = 4.4
Identities = 27/104 (25%), Positives = 44/104 (42%), Gaps = 11/104 (10%)
Query: 13 IPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGI-----YAYGFEKPSAIQQRSIKPIV 67
I + + NV+ T E+ FD + +D GI Y+Y E +I +
Sbjct: 1851 ISKSIENVKNSTDEN----LLFDILNKTKDAYAGIIGKKYYSYKDEAEKIF--INISKLA 1904
Query: 68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE 111
++ Q SG +I+IL SLD++ +T SP +E
Sbjct: 1905 NSINIQIQNNSGIDLFDNINIAILSSLDSEKEDTLKFIPSPEKE 1948
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 25.4 bits (56), Expect = 5.7
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC 131
+ GTGKTAT + +I+ L R VL ++PT A ++++ + AL
Sbjct: 13 FVVDGGPGTGKTAT-AAAIIARLLAAGRS--VLVVAPTGRAARRLRERLAALDLADASTL 69
Query: 132 HA 133
HA
Sbjct: 70 HA 71
>gnl|CDD|239510 cd03418, GRX_GRXb_1_3_like, Glutaredoxin (GRX) family, GRX
bacterial class 1 and 3 (b_1_3)-like subfamily; composed
of bacterial GRXs, approximately 10 kDa in size, and
proteins containing a GRX or GRX-like domain. GRX is a
glutathione (GSH) dependent reductase, catalyzing the
disulfide reduction of target proteins such as
ribonucleotide reductase. It contains a redox active
CXXC motif in a TRX fold and uses a similar dithiol
mechanism employed by TRXs for intramolecular disulfide
bond reduction of protein substrates. Unlike TRX, GRX
has preference for mixed GSH disulfide substrates, in
which it uses a monothiol mechanism where only the
N-terminal cysteine is required. The flow of reducing
equivalents in the GRX system goes from NADPH -> GSH
reductase -> GSH -> GRX -> protein substrates. By
altering the redox state of target proteins, GRX is
involved in many cellular functions including DNA
synthesis, signal transduction and the defense against
oxidative stress. Different classes are known including
E. coli GRX1 and GRX3, which are members of this
subfamily.
Length = 75
Score = 25.2 bits (56), Expect = 6.7
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQ 176
C C+ L + + +DY + V G P +MI S GRRT Q
Sbjct: 10 CPYCVRAKALLDK-KGVDYEEIDVDGDPALREEMINRSGGRRTVPQ 54
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. 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 = 352
Score = 26.5 bits (59), Expect = 9.2
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 17/53 (32%)
Query: 50 YGFEK---PSAIQ----QRSIKPIVKGRDVI--------AQAQSGTGKTATFS 87
Y F+K P A Q + + PI+ +V+ A Q+GTGKT T
Sbjct: 50 YTFDKVFGPEADQIEVYSQVVSPILD--EVLMGYNCTIFAYGQTGTGKTYTME 100
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
0.317 0.133 0.368
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: 8,846,207
Number of extensions: 799588
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 691
Number of HSP's successfully gapped: 44
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.5 bits)