RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18032
(333 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 = 194 bits (496), Expect = 2e-61
Identities = 73/146 (50%), Positives = 98/146 (67%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F+ GL E+L+G+ G++ PTPIQ + IP +L GRDV+ A+TGSGKTA FLIP+LEK
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 99 LKTHAATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASP 158
L G +ALIL+PTRELALQ + ++LGK T L+ + GG S+D Q +L P
Sbjct: 61 LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120
Query: 159 DIVVATPGRFLHIVVEMELKLSSIQY 184
IVVATPGR L ++ +L LS ++Y
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKY 146
Score = 51.7 bits (125), Expect = 8e-08
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
IP +L GRDV+ A+TGSGKTA FL
Sbjct: 29 AIPPLLSGRDVIGQAQTGSGKTAAFL 54
>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 = 171 bits (435), Expect = 4e-49
Identities = 68/163 (41%), Positives = 97/163 (59%), Gaps = 1/163 (0%)
Query: 23 DDNGNTGDKKKKMGGGFQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMAR 82
N ++K F S GL E+L+ + G++ PTPIQ IPL+L GRDV+ A+
Sbjct: 15 AHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQ 74
Query: 83 TGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKELGKFT-KLQSTCL 141
TG+GKTA FL+P+L+K+ V ALIL+PTRELA+Q + +++LGK L+ +
Sbjct: 75 TGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVV 134
Query: 142 LGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQY 184
GG S+ Q L DIVVATPGR L ++ +L LS ++
Sbjct: 135 YGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVET 177
Score = 56.7 bits (137), Expect = 7e-09
Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 18/99 (18%)
Query: 189 VKELGKFT-KLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQ-- 245
+++LGK L+ + GG S+ Q L DIVVATPGR L ++ +L LS ++
Sbjct: 119 LRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETL 178
Query: 246 -LSLTD------FKQDTSRIALDLVGDSTEMIHKQRQSV 277
L D F D +I + + RQ++
Sbjct: 179 VLDEADRMLDMGFIDDIEKI--------LKALPPDRQTL 209
Score = 49.8 bits (119), Expect = 1e-06
Identities = 17/26 (65%), Positives = 21/26 (80%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
IPL+L GRDV+ A+TG+GKTA FL
Sbjct: 59 AIPLILAGRDVLGQAQTGTGKTAAFL 84
>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 = 136 bits (345), Expect = 2e-39
Identities = 54/122 (44%), Positives = 75/122 (61%), Gaps = 3/122 (2%)
Query: 61 TPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELA 120
TPIQ + IP +L G+DV+ A TGSGKT FL+P+L+ L G +AL+L+PTRELA
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPK--KGGPQALVLAPTRELA 58
Query: 121 LQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARL-HASPDIVVATPGRFLHIVVEMELKL 179
Q ++ +K+L K L+ L GG S+ Q +L DI+V TPGR L ++ +LKL
Sbjct: 59 EQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKL 118
Query: 180 SS 181
Sbjct: 119 LK 120
Score = 48.8 bits (117), Expect = 4e-07
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFLFYFF 323
IP +L G+DV+ A TGSGKT FL
Sbjct: 7 AIPAILSGKDVLVQAPTGSGKTLAFLLPIL 36
Score = 46.1 bits (110), Expect = 4e-06
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 185 TFKFVKELGKFTKLQSTCLLGGDSMDNQFARL-HASPDIVVATPGRFLHIVVEMELKLSS 243
++ +K+L K L+ L GG S+ Q +L DI+V TPGR L ++ +LKL
Sbjct: 61 IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 143 bits (362), Expect = 4e-39
Identities = 65/149 (43%), Positives = 99/149 (66%), Gaps = 4/149 (2%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F S GL ++L+ V ++GY+ PTPIQ++ IP VLEGRD++A A+TG+GKTA F +P+L+
Sbjct: 3 FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQH 62
Query: 99 LKTHAATSG----VRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARL 154
L T + VRALIL+PTRELA Q + V++ K+ ++S + GG S++ Q +L
Sbjct: 63 LITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKL 122
Query: 155 HASPDIVVATPGRFLHIVVEMELKLSSIQ 183
D++VATPGR L + + +KL ++
Sbjct: 123 RGGVDVLVATPGRLLDLEHQNAVKLDQVE 151
Score = 43.6 bits (103), Expect = 1e-04
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 189 VKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQLSL 248
V++ K+ ++S + GG S++ Q +L D++VATPGR L + + +KL +++ +
Sbjct: 95 VRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILV 154
Query: 249 TD 250
D
Sbjct: 155 LD 156
Score = 42.5 bits (100), Expect = 2e-04
Identities = 17/24 (70%), Positives = 21/24 (87%)
Query: 295 IPLVLEGRDVVAMARTGSGKTACF 318
IP VLEGRD++A A+TG+GKTA F
Sbjct: 32 IPAVLEGRDLMASAQTGTGKTAGF 55
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 117 bits (295), Expect = 8e-32
Identities = 56/135 (41%), Positives = 77/135 (57%), Gaps = 5/135 (3%)
Query: 52 VLKRGYKIPTPIQRKTIPLVLEG-RDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRA 110
+ K G++ P Q++ I +L G RDV+ A TGSGKT L+P LE LK G R
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG---KGGRV 57
Query: 111 LILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFL 169
L+L PTRELA Q + +K+LG L+ L GGDS Q +L + DI+V TPGR L
Sbjct: 58 LVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLL 117
Query: 170 HIVVEMELKLSSIQY 184
++ +L LS++
Sbjct: 118 DLLENDKLSLSNVDL 132
Score = 43.2 bits (102), Expect = 5e-05
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 185 TFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMELKLSS 243
+ +K+LG L+ L GGDS Q +L + DI+V TPGR L ++ +L LS+
Sbjct: 70 WAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSN 129
Query: 244 IQL 246
+ L
Sbjct: 130 VDL 132
Score = 35.9 bits (83), Expect = 0.014
Identities = 16/38 (42%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 294 TIPLVLEG-RDVVAMARTGSGKTACFLFYFFFRFDRGN 330
I +L G RDV+ A TGSGKT L RG
Sbjct: 16 AIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK 53
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 115 bits (291), Expect = 3e-29
Identities = 58/137 (42%), Positives = 75/137 (54%), Gaps = 10/137 (7%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F L +L+ + +GY PT IQ + IP L+GRDV+ A TG+GKTA FL+P L+
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62
Query: 99 L------KTHAATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFA 152
L K+ R LIL+PTRELA+Q +EL K T L + GG + N
Sbjct: 63 LLDFPRRKSGPP----RILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAE 118
Query: 153 RLHASPDIVVATPGRFL 169
+ DIVVATPGR L
Sbjct: 119 VFSENQDIVVATPGRLL 135
Score = 44.2 bits (105), Expect = 7e-05
Identities = 16/26 (61%), Positives = 19/26 (73%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
IP L+GRDV+ A TG+GKTA FL
Sbjct: 31 AIPPALDGRDVLGSAPTGTGKTAAFL 56
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 114 bits (287), Expect = 1e-28
Identities = 56/150 (37%), Positives = 79/150 (52%), Gaps = 5/150 (3%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F F L +V++ + K+G+ TPIQ +PL L GRDV A+TG+GKT FL
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 99 LKTHAATSGV-----RALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFAR 153
L +H A RALI++PTRELA+Q + L + T L+ GGD D Q
Sbjct: 70 LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129
Query: 154 LHASPDIVVATPGRFLHIVVEMELKLSSIQ 183
L + DI++ T GR + + + L +IQ
Sbjct: 130 LESGVDILIGTTGRLIDYAKQNHINLGAIQ 159
Score = 38.0 bits (89), Expect = 0.005
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
+PL L GRDV A+TG+GKT FL
Sbjct: 38 ALPLTLAGRDVAGQAQTGTGKTMAFL 63
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 106 bits (268), Expect = 7e-26
Identities = 55/134 (41%), Positives = 77/134 (57%), Gaps = 7/134 (5%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F + L +L + + GY TPIQ +++P +L G+DV+A A+TGSGKTA F + +L+K
Sbjct: 6 FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65
Query: 99 LKTHAATSGVRALILSPTRELALQTFKFVKELGKFT---KLQSTCLLGGDSMDNQFARLH 155
L V+AL+L PTRELA Q K ++ L +F K+ + C GG M Q L
Sbjct: 66 LD--VKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLC--GGVPMGPQIDSLE 121
Query: 156 ASPDIVVATPGRFL 169
I+V TPGR L
Sbjct: 122 HGAHIIVGTPGRIL 135
Score = 47.1 bits (113), Expect = 7e-06
Identities = 15/25 (60%), Positives = 21/25 (84%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACF 318
++P +L G+DV+A A+TGSGKTA F
Sbjct: 34 SLPAILAGKDVIAQAKTGSGKTAAF 58
Score = 30.9 bits (71), Expect = 1.1
Identities = 13/29 (44%), Positives = 14/29 (48%)
Query: 203 LLGGDSMDNQFARLHASPDIVVATPGRFL 231
L GG M Q L I+V TPGR L
Sbjct: 107 LCGGVPMGPQIDSLEHGAHIIVGTPGRIL 135
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 107 bits (268), Expect = 1e-25
Identities = 58/145 (40%), Positives = 80/145 (55%), Gaps = 3/145 (2%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F GL +L+ + GY+ P+PIQ + IP +L GRDV+ MA+TGSGKTA F +P+L
Sbjct: 8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67
Query: 99 LKTHAATSGVRALILSPTRELALQTFKFVKELGKFTK-LQSTCLLGGDSMDNQFARLHAS 157
L + L+L+PTRELA+Q + + + K + + L GG D Q L
Sbjct: 68 LD--PELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQG 125
Query: 158 PDIVVATPGRFLHIVVEMELKLSSI 182
P IVV TPGR L + L LS +
Sbjct: 126 PQIVVGTPGRLLDHLKRGTLDLSKL 150
Score = 42.9 bits (101), Expect = 1e-04
Identities = 17/24 (70%), Positives = 20/24 (83%)
Query: 295 IPLVLEGRDVVAMARTGSGKTACF 318
IP +L GRDV+ MA+TGSGKTA F
Sbjct: 37 IPHLLNGRDVLGMAQTGSGKTAAF 60
Score = 34.1 bits (78), Expect = 0.11
Identities = 27/88 (30%), Positives = 35/88 (39%), Gaps = 11/88 (12%)
Query: 157 SPDIVVATPGRFLHIVVEMELKLSSIQYTFKFVKELGKFTKLQSTCLLGGDSMDNQFARL 216
+P I+V P R EL + + F K + + L GG D Q L
Sbjct: 74 APQILVLAPTR--------ELAVQVAEAMTDFSKHM---RGVNVVALYGGQRYDVQLRAL 122
Query: 217 HASPDIVVATPGRFLHIVVEMELKLSSI 244
P IVV TPGR L + L LS +
Sbjct: 123 RQGPQIVVGTPGRLLDHLKRGTLDLSKL 150
>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 = 97.4 bits (243), Expect = 9e-25
Identities = 45/110 (40%), Positives = 62/110 (56%), Gaps = 4/110 (3%)
Query: 75 RDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKELGKFT 134
RDV+ A TGSGKT L+P+LE L + G + L+L+PTRELA Q + +KEL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLK---GGQVLVLAPTRELANQVAERLKELFGE- 56
Query: 135 KLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQY 184
++ L+GG S+ Q L DIVV TPGR L + ++L L +
Sbjct: 57 GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDL 106
Score = 38.1 bits (89), Expect = 0.001
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 185 TFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSI 244
+ +KEL ++ L+GG S+ Q L DIVV TPGR L + ++L L +
Sbjct: 46 VAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKL 104
Query: 245 QL 246
L
Sbjct: 105 DL 106
Score = 33.1 bits (76), Expect = 0.069
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 302 RDVVAMARTGSGKTACFLFY 321
RDV+ A TGSGKT L
Sbjct: 1 RDVLLAAPTGSGKTLAALLP 20
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 103 bits (258), Expect = 1e-24
Identities = 55/158 (34%), Positives = 79/158 (50%), Gaps = 6/158 (3%)
Query: 33 KKMGGGFQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFL 92
++ F F L E++ + G+ TPIQ + + L G D + A+TG+GKTA FL
Sbjct: 83 QEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFL 142
Query: 93 IPMLEKL-----KTHAATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSM 147
I ++ +L RALI++PTREL +Q K L K+T L +GG
Sbjct: 143 ISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDF 202
Query: 148 DNQFARLHAS-PDIVVATPGRFLHIVVEMELKLSSIQY 184
D Q +L A DI+VATPGR L E+ L ++
Sbjct: 203 DKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEV 240
Score = 31.4 bits (71), Expect = 0.64
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 299 LEGRDVVAMARTGSGKTACFL 319
L G D + A+TG+GKTA FL
Sbjct: 122 LAGHDAIGRAQTGTGKTAAFL 142
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 102 bits (255), Expect = 5e-24
Identities = 55/149 (36%), Positives = 88/149 (59%), Gaps = 5/149 (3%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F S GL ++L + GY+ PTPIQ + IP L GR ++ A TGSGKTA FL+P++ +
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182
Query: 99 LKT--HAATSGVR---ALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFAR 153
T S R A++L+PTREL +Q K LGK ++ ++GGD+M Q R
Sbjct: 183 CCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYR 242
Query: 154 LHASPDIVVATPGRFLHIVVEMELKLSSI 182
+ +++V TPGR + ++ + +++L ++
Sbjct: 243 IQQGVELIVGTPGRLIDLLSKHDIELDNV 271
Score = 38.6 bits (90), Expect = 0.004
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
IP L GR ++ A TGSGKTA FL
Sbjct: 151 AIPAALSGRSLLVSADTGSGKTASFL 176
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 95.4 bits (237), Expect = 1e-21
Identities = 54/144 (37%), Positives = 79/144 (54%), Gaps = 5/144 (3%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F SF L +L G+ G+ TPIQ T+P+ L G DV A+TG+GKT FL+ ++ +
Sbjct: 11 FSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNR 70
Query: 99 LKTHAATSG-----VRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFAR 153
L + A + RALIL+PTRELA+Q K + G L+ + GG D Q
Sbjct: 71 LLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQREL 130
Query: 154 LHASPDIVVATPGRFLHIVVEMEL 177
L D+++ATPGR + V + ++
Sbjct: 131 LQQGVDVIIATPGRLIDYVKQHKV 154
Score = 36.1 bits (83), Expect = 0.024
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACFL 319
T+P+ L G DV A+TG+GKT FL
Sbjct: 39 TLPVALPGGDVAGQAQTGTGKTLAFL 64
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 92.6 bits (230), Expect = 5e-21
Identities = 47/129 (36%), Positives = 77/129 (59%), Gaps = 2/129 (1%)
Query: 39 FQSFGLGFEVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEK 98
F + L ++L+G+ G++ P+ IQ++ I +L+G D + A++G+GKTA F+I L+
Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89
Query: 99 LKTHAATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASP 158
+ + +ALIL+PTRELA Q K V LG + K++ +GG + + +L A
Sbjct: 90 IDY--DLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGV 147
Query: 159 DIVVATPGR 167
+VV TPGR
Sbjct: 148 HMVVGTPGR 156
Score = 35.6 bits (82), Expect = 0.035
Identities = 18/64 (28%), Positives = 34/64 (53%)
Query: 187 KFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQL 246
K V LG + K++ +GG + + +L A +VV TPGR ++ + L++ ++L
Sbjct: 114 KVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKL 173
Query: 247 SLTD 250
+ D
Sbjct: 174 FILD 177
Score = 29.0 bits (65), Expect = 3.3
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 295 IPLVLEGRDVVAMARTGSGKTACF 318
I +L+G D + A++G+GKTA F
Sbjct: 59 IKPILDGYDTIGQAQSGTGKTATF 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 85.6 bits (212), Expect = 2e-18
Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 3/140 (2%)
Query: 48 VLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAAT-- 105
+LK + G+ PTPIQ + P+ L GRD++ +A TGSGKT FL+P + +
Sbjct: 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRY 200
Query: 106 -SGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVAT 164
G L+L+PTRELA Q + + G +K+++T GG Q L +I++A
Sbjct: 201 GDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIAC 260
Query: 165 PGRFLHIVVEMELKLSSIQY 184
PGR + + L + Y
Sbjct: 261 PGRLIDFLESNVTNLRRVTY 280
Score = 37.1 bits (86), Expect = 0.011
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 296 PLVLEGRDVVAMARTGSGKTACFL 319
P+ L GRD++ +A TGSGKT FL
Sbjct: 162 PIALSGRDMIGIAETGSGKTLAFL 185
>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 = 62.8 bits (153), Expect = 8e-11
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 7/117 (5%)
Query: 52 VLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGV-RA 110
++K G + Q + L+ EGR+VV TGSGKT FL+P+L+ H RA
Sbjct: 63 LVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILD----HLLRDPSARA 118
Query: 111 LILSPTRELAL-QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHAS-PDIVVATP 165
L+L PT LA Q + + + + GD+ + + + PDI++ P
Sbjct: 119 LLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNP 175
Score = 36.2 bits (84), Expect = 0.026
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 293 DTIPLVLEGRDVVAMARTGSGKTACFLF 320
D + L+ EGR+VV TGSGKT FL
Sbjct: 77 DALRLIREGRNVVVTTGTGSGKTESFLL 104
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 61.5 bits (150), Expect = 2e-10
Identities = 38/130 (29%), Positives = 60/130 (46%), Gaps = 19/130 (14%)
Query: 47 EVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKT-ACFL--IPMLEKLKTHA 103
++ KR + TP QR IP + G +V+ +A TGSGKT A FL I L L
Sbjct: 10 PRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGK 69
Query: 104 ATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLG-------GDSMDNQFARLHA 156
G+ AL +SP + L + ++E + LG GD+ ++ ++
Sbjct: 70 LEDGIYALYISPLKALNNDIRRRLEEPLR--------ELGIEVAVRHGDTPQSEKQKMLK 121
Query: 157 SP-DIVVATP 165
+P I++ TP
Sbjct: 122 NPPHILITTP 131
Score = 34.9 bits (81), Expect = 0.062
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 266 STEMIHKQRQSVRKWDPAKKKYVQVTD---DTIPLVLEGRDVVAMARTGSGKT-ACFL 319
E+ + VR+W K+K+ +T IP + G +V+ +A TGSGKT A FL
Sbjct: 1 DEEIFNILDPRVREW--FKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFL 56
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 50.1 bits (120), Expect = 1e-06
Identities = 30/108 (27%), Positives = 48/108 (44%), Gaps = 10/108 (9%)
Query: 62 PIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELAL 121
P Q +L +V+ A TGSGKT L+ +L L G + + + P + LA
Sbjct: 35 PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG----GGKVVYIVPLKALAE 90
Query: 122 QTFKFVKELGKFTKLQ-STCLLGGDSMDNQFARLHASPDIVVATPGRF 168
+ + +E + +L + GD D RL A D++V TP +
Sbjct: 91 EKY---EEFSRLEELGIRVGISTGD-YDLDDERL-ARYDVIVTTPEKL 133
Score = 29.3 bits (66), Expect = 3.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 296 PLVLEGRDVVAMARTGSGKTA 316
+L +V+ A TGSGKT
Sbjct: 42 KGLLSDENVLISAPTGSGKTL 62
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 47.6 bits (114), Expect = 6e-06
Identities = 29/71 (40%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 54 KRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKT-ACFL--IPMLEKL-KTHAATSGVR 109
K + TP QR IPL+ EG++V+ + TGSGKT A FL I L +L + V
Sbjct: 27 KEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVY 86
Query: 110 ALILSPTRELA 120
L +SP R L
Sbjct: 87 CLYVSPLRALN 97
Score = 34.5 bits (80), Expect = 0.082
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 6/50 (12%)
Query: 274 RQSVRKWDPAKKKYVQVTD---DTIPLVLEGRDVVAMARTGSGKT-ACFL 319
R VR+W K+K+ T IPL+ EG++V+ + TGSGKT A FL
Sbjct: 19 RPYVREW--FKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFL 66
>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 = 47.1 bits (112), Expect = 6e-06
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 13/95 (13%)
Query: 62 PIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELAL 121
P+Q + I VL GRD + TG GK+ C+ +P L + G+ L++SP L
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL-------CSDGI-TLVISPLISLME 65
Query: 122 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHA 156
+K G L Q +
Sbjct: 66 DQVLQLKASGI-----PATFLNSSQSKEQQKNVLT 95
Score = 31.3 bits (71), Expect = 0.84
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 294 TIPLVLEGRDVVAMARTGSGKTACF 318
I VL GRD + TG GK+ C+
Sbjct: 19 VINAVLLGRDCFVVMPTGGGKSLCY 43
>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 = 46.8 bits (112), Expect = 1e-05
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 55 RGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKT-ACFLIPMLEKLKTHAATSGVRALIL 113
RG+ P P Q + LEGR + +A TGSGKT A FL +++ G+ L +
Sbjct: 10 RGWT-PRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYI 68
Query: 114 SPTRELA 120
+P R LA
Sbjct: 69 TPLRALA 75
>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 = 46.3 bits (110), Expect = 1e-05
Identities = 34/112 (30%), Positives = 51/112 (45%), Gaps = 7/112 (6%)
Query: 47 EVLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATS 106
+V+ + G P Q + L GR VV T SGK+ + +P+L L A
Sbjct: 24 DVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSAL---ADDP 80
Query: 107 GVRALILSPTRELALQTFKFVKELGKFTKLQSTCLLGGDS--MDNQFARLHA 156
AL L+PT+ LA + V+EL +T GD+ + ++AR HA
Sbjct: 81 RATALYLAPTKALAADQLRAVRELTLRGVRPAT--YDGDTPTEERRWAREHA 130
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 42.7 bits (101), Expect = 2e-04
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 52 VLKR--GYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPML 96
VLK+ GY P Q++ I +L G+D + + TG GK+ C+ IP L
Sbjct: 8 VLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL 54
Score = 35.0 bits (81), Expect = 0.058
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 295 IPLVLEGRDVVAMARTGSGKTACF 318
I +L G+D + + TG GK+ C+
Sbjct: 26 IDALLSGKDTLVVMPTGGGKSLCY 49
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 42.2 bits (100), Expect = 4e-04
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 83 TGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKELGKFTKLQSTCLL 142
TG GKTA L+ + E+L G + LIL+PT+ L Q +F ++ + +
Sbjct: 38 TGLGKTAIALLVIAERLHKK----GGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFT 93
Query: 143 GGDSMDNQFARLHASPDIVVATP 165
G S + + A L ++VATP
Sbjct: 94 GEVSPEKR-AELWEKAKVIVATP 115
>gnl|CDD|203859 pfam08147, DBP10CT, DBP10CT (NUC160) domain. This C terminal
domain is found in the Dbp10p subfamily of hypothetical
RNA helicases.
Length = 64
Score = 36.5 bits (85), Expect = 0.001
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 261 DLVGDSTEMIHKQRQSVRKWDPAKKKYVQVTDDTIPLVLEGRDVVAMARTGSGK 314
DLV D +Q+Q +R WD KKKYV + + R SG+
Sbjct: 1 DLVNDDGAGEPQQKQLMR-WDKKKKKYVNRRNG-------SKGDKKKIRGESGQ 46
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 39.6 bits (93), Expect = 0.002
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)
Query: 71 VLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKEL 130
L +V + TG GKT + + +L+ L L+PT+ L LQ +F +++
Sbjct: 27 ALFKNTLVVLP-TGLGKTFIAAMVIANRLRWFGGK----VLFLAPTKPLVLQHAEFCRKV 81
Query: 131 GKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 178
+ + L G+ + L A + VATP VVE +LK
Sbjct: 82 TGIPEDE-IAALTGEVRPEEREELWAKKKVFVATPQ-----VVENDLK 123
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 39.0 bits (91), Expect = 0.003
Identities = 43/128 (33%), Positives = 62/128 (48%), Gaps = 18/128 (14%)
Query: 47 EVLKGVLK-RGYKIPTPIQRKTIPL-VLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAA 104
E +K VLK RG + P Q + + VLEG+++V T SGKT I M+ KL
Sbjct: 10 ERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKL----L 65
Query: 105 TSGVRALILSPTRELA---LQTFKFVKELGKFTKLQSTCLLGG-DSMDNQFARLHASPDI 160
G +A+ L P + LA + FK ++LG L+ G DS D + DI
Sbjct: 66 REGGKAVYLVPLKALAEEKYREFKDWEKLG----LRVAMTTGDYDSTDEWLGKY----DI 117
Query: 161 VVATPGRF 168
++AT +F
Sbjct: 118 IIATAEKF 125
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 39.1 bits (92), Expect = 0.003
Identities = 37/136 (27%), Positives = 57/136 (41%), Gaps = 15/136 (11%)
Query: 60 PTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTREL 119
P +QR +L G +A TG GKT F + M L A G ++ I+ PTR L
Sbjct: 81 PWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYL----AKKGKKSYIIFPTRLL 135
Query: 120 ALQTFKFVKELGKFTKLQSTCLLGGDSM-----DNQFARLHASP-DIVVATPGRFLHIVV 173
Q + +++ G+ L S+ + RL DI+V T +FL
Sbjct: 136 VEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTS-QFLSKNF 194
Query: 174 EMELKLSSIQYTFKFV 189
+ +L ++ F FV
Sbjct: 195 D---ELPKKKFDFVFV 207
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 38.2 bits (89), Expect = 0.005
Identities = 18/41 (43%), Positives = 25/41 (60%)
Query: 56 GYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPML 96
GY+ P Q++ I VL GRD + + TG GK+ C+ IP L
Sbjct: 22 GYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPAL 62
>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 = 37.7 bits (88), Expect = 0.007
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 49 LKGVLKR--GYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPML 96
+ VLKR GY P Q + I VL+GRDV+ + TG GK+ C+ +P L
Sbjct: 1 AQQVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL 50
>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 = 0.017
Identities = 24/94 (25%), Positives = 35/94 (37%), Gaps = 21/94 (22%)
Query: 73 EGRDVVAMARTGSGKT--ACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKEL 130
E R V+ + TG+GKT A I A L+L PT+EL Q + +K+
Sbjct: 55 ERRGVIVLP-TGAGKTVVAAEAI----------AELKRSTLVLVPTKELLDQWAEALKK- 102
Query: 131 GKFTKLQSTCLLGGDSMDNQFARLHASPDIVVAT 164
+ GG + + VAT
Sbjct: 103 -FLLLNDEIGIYGGGE------KELEPAKVTVAT 129
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 35.5 bits (82), Expect = 0.038
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 47 EVLKGVLK-RGYKIPTPIQRKTIPL-VLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAA 104
E K +LK G + P+Q + +LEG +++ ++ T SGKT LI L +
Sbjct: 203 EKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKT---LIGELAGIP-RLL 258
Query: 105 TSGVRALILSPTRELALQTFKFVKELGKFTKL 136
+ G + L L P LA Q ++ KE +++KL
Sbjct: 259 SGGKKMLFLVPLVALANQKYEDFKE--RYSKL 288
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 35.3 bits (82), Expect = 0.040
Identities = 36/99 (36%), Positives = 51/99 (51%), Gaps = 19/99 (19%)
Query: 71 VLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKEL 130
+L+G++++A T SGKT LI L LK A G +AL + P R LA + F +E
Sbjct: 36 LLDGKNLLAAIPTASGKT---LIAELAMLK--AIARGGKALYIVPLRALASEKF---EEF 87
Query: 131 GKFTKLQ-----STCLLGGDSMDNQFARLHASPDIVVAT 164
+F +L ST GD D++ L DI+VAT
Sbjct: 88 ERFEELGVRVGIST----GD-YDSRDEWL-GDNDIIVAT 120
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 34.8 bits (80), Expect = 0.056
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 11/90 (12%)
Query: 57 YKIPTPIQRKTIPLV---LEGRDVVAM-ARTGSGKTACFLIPMLEKLKTHAATSGVRALI 112
P P QR+ V L+G + + + A TG+GKT +L+P L +A G + +I
Sbjct: 13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALA----YAREEGKKVII 68
Query: 113 LSPTRELALQTFKFVKELGKFTKLQSTCLL 142
+ T+ ALQ + ++E KL
Sbjct: 69 STRTK--ALQ-EQLLEEDLPIHKLLKKLGG 95
>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 = 34.0 bits (78), Expect = 0.11
Identities = 24/72 (33%), Positives = 31/72 (43%), Gaps = 5/72 (6%)
Query: 60 PTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTREL 119
P IQ+ VL G +A TG GKT F + M L A G R I+ PT L
Sbjct: 79 PWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFL----AKKGKRCYIILPTTLL 133
Query: 120 ALQTFKFVKELG 131
+Q + + L
Sbjct: 134 VIQVAEKISSLA 145
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 33.9 bits (78), Expect = 0.13
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 56 GYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSP 115
G++ P QR ++ G+ +A TG GKT F + M L A G R I+ P
Sbjct: 80 GFR-PWSAQRVWAKRLVRGKSFAIIAPTGVGKTT-FGLLMSLYL----AKKGKRVYIIVP 133
Query: 116 TRELALQTFKFVKELG 131
T L Q ++ +K+
Sbjct: 134 TTTLVRQVYERLKKFA 149
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 31.0 bits (71), Expect = 0.21
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 10/56 (17%)
Query: 70 LVLEGRDVVAMARTGSGKT--ACFLIPMLEKLKTHAATSGVRALILSPTRELALQT 123
L+ + R ++ MA TGSGKT A LI L K K + L + P ++L Q
Sbjct: 15 LLEKKRGLIVMA-TGSGKTLTAAALIARLAKGKK-------KVLFVVPRKDLLEQA 62
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 33.1 bits (76), Expect = 0.25
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 12/89 (13%)
Query: 60 PTPIQRKTIPLVLEGRDVVAMARTGSGKT--ACFLIPMLEKLKTHAATSGVRALILSPTR 117
P Q++ I ++ G V+ A T SGKT A + I + A G R + SP +
Sbjct: 120 LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIAL-------ALRDGQRVIYTSPIK 172
Query: 118 ELALQTFK-FVKELGKFTKLQSTCLLGGD 145
L+ Q ++ + + G + L+ GD
Sbjct: 173 ALSNQKYRDLLAKFGDVADMVG--LMTGD 199
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 32.4 bits (74), Expect = 0.37
Identities = 21/90 (23%), Positives = 31/90 (34%), Gaps = 6/90 (6%)
Query: 73 EGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKELGK 132
VV A TG GKT LI L L R + + P R + ++ KE+
Sbjct: 213 RSLLVVLEAPTGYGKTEASLILALALLDEKIKLKS-RVIYVLPFRTIIEDMYRRAKEIFG 271
Query: 133 FTKLQSTCLLGGDSMDNQFARLHASPDIVV 162
++G + L PD +
Sbjct: 272 LFS-----VIGKSLHSSSKEPLLLEPDQDI 296
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 31.8 bits (73), Expect = 0.55
Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 11/62 (17%)
Query: 78 VAMAR-----TGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTF-KFVKELG 131
V M R GSGKT L+ ML A +G +A +++PT LA Q + K L
Sbjct: 282 VPMNRLLQGDVGSGKTVVALLAML-----AAIEAGYQAALMAPTEILAEQHYESLRKWLE 336
Query: 132 KF 133
Sbjct: 337 PL 338
>gnl|CDD|218447 pfam05123, S_layer_N, S-layer like family, N-terminal region.
Length = 279
Score = 30.4 bits (69), Expect = 1.3
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 5 DPEDIEGFEDPTVTISSNDDNGNTGD---KKKKMGGG---FQSFGLGFEVLKGVLKRGYK 58
D D + FED V I+S+ N T K +M F+ GF K VLK G +
Sbjct: 174 DNSDDDAFEDLFVRITSDALNNTTDKLKVNKDEMVYASLAFKEDKSGFAGTK-VLKEGMR 232
Query: 59 IP 60
IP
Sbjct: 233 IP 234
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.9 bits (67), Expect = 2.3
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 60 PTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTREL 119
IQ+ +L G+ +A TG GK+ F + A G + I+ PT L
Sbjct: 80 FWSIQKTWAKRILRGKSFSIVAPTGMGKST-FGAFI----ALFLALKGKKCYIILPTTLL 134
Query: 120 ALQTFKFVKELGKFTK 135
QT V+++ F +
Sbjct: 135 VKQT---VEKIESFCE 147
>gnl|CDD|184507 PRK14101, PRK14101, bifunctional glucokinase/RpiR family
transcriptional regulator; Provisional.
Length = 638
Score = 29.5 bits (66), Expect = 2.8
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 248 LTDFKQDTSRIALDLVGDSTEMIHKQRQSVRKWDPAKKKYVQVTDDTIPLVLEGRD 303
L+DFK ++A L G + M H Q V D A +V D+T+ +L+ R+
Sbjct: 403 LSDFKL---KLATGLTG-TIPMSHSQ---VHLGDTATDFGAKVLDNTVSAILQLRE 451
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 29.6 bits (67), Expect = 3.0
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 11/62 (17%)
Query: 78 VAMAR-----TGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTF-KFVKELG 131
V M R GSGKT + ML A +G + +++PT LA Q + L
Sbjct: 255 VPMNRLLQGDVGSGKTLVAALAMLA-----AIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
Query: 132 KF 133
Sbjct: 310 PL 311
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 29.4 bits (66), Expect = 3.1
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 8 DIEGFEDPTVTISSNDDNGNT 28
D++G ED ++SS DD N
Sbjct: 324 DVDGLEDAPGSVSSKDDRRNL 344
>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 = 29.1 bits (65), Expect = 3.3
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 77 VVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKEL 130
+ A TG+GKT +L P+L +A+ L PT L + +KE
Sbjct: 17 IFNTAPTGAGKTLAWLTPLL--------HGENKAIALYPTNALIEDQTEAIKEF 62
>gnl|CDD|237549 PRK13897, PRK13897, type IV secretion system component VirD4;
Provisional.
Length = 606
Score = 29.4 bits (66), Expect = 3.4
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 22/74 (29%)
Query: 48 VLKGVLKRGYKIPTPIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPMLE---------- 97
+L G K GY + Q + A TGSGK F+IP L
Sbjct: 143 MLLGKDKGGYFVADGFQHALL-----------FAPTGSGKGVGFVIPNLLFWEDSVVVHD 191
Query: 98 -KLKTHAATSGVRA 110
KL+ + TSG R
Sbjct: 192 IKLENYELTSGWRE 205
>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 = 29.1 bits (65), Expect = 3.7
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 77 VVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSPTRELALQTFKFVKEL 130
+ A TG+GKT +L P+L + L PT L + +KE
Sbjct: 17 IFNTAPTGAGKTLAWLTPLL--------HGENDTIALYPTNALIEDQTEAIKEF 62
>gnl|CDD|234344 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
family. Members of this protein are assigned by
homology to the TraD family of conjugative coupling
factor. This particular clade serves as a marker for an
extended gene region that occurs occasionally on
plasmids, including the toluene catabolism TOL plasmid.
More commonly, the gene region is chromosomal, flanked
by various markers of conjugative transfer and
insertion.
Length = 643
Score = 28.5 bits (64), Expect = 5.5
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 71 VLEG-RDVVAMARTGSGKTACFLIPMLEKLKTHAATSGVRALILSP 115
VL+G R V +T K L P+LEKL T+G A +LSP
Sbjct: 378 VLDGLRSAVRYDKTYFDKIVASLGPLLEKL-----TTGKTAKLLSP 418
>gnl|CDD|236499 PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component;
Reviewed.
Length = 924
Score = 28.5 bits (65), Expect = 6.0
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 92 LIPMLEKLKTHAATSGVRALIL 113
LIPML+++ A GV+ +++
Sbjct: 226 LIPMLDEIIRRAGKLGVKEIVI 247
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 27.7 bits (62), Expect = 6.1
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 84 GSGKTACFLIPMLEKLKTHAATSGVRALILSPTR 117
G+GKT L ++ + +R L+L+PTR
Sbjct: 12 GAGKTRKVLPELVRE----CIDRRLRTLVLAPTR 41
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 28.7 bits (64), Expect = 6.2
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 62 PIQRKTIPLVLEGRDVVAMARTGSGKTACFLIPML 96
P QR+ I + G DV + TG GK+ + +P L
Sbjct: 463 PNQREIINATMSGYDVFVLMPTGGGKSLTYQLPAL 497
>gnl|CDD|238682 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 767
Score = 28.3 bits (63), Expect = 7.4
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 64 QRKTIPLVLEGRD--VVAMARTGSGKTACF 91
Q L+ RD ++ + R+G+GKT
Sbjct: 74 QTAYRALLETRRDQSIIFLGRSGAGKTTSC 103
>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 = 8.2
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 56 GYKIPTPIQRKTIPLVLE-GRDVVAMARTGSGKT-----ACFLIPMLEKL 99
Y +P Q + L +E + ++ T SGKT IP E++
Sbjct: 124 EYGTISPEQAAYLWLAIEARKSIIICGGTASGKTTLLNALLDFIPPEERI 173
>gnl|CDD|223430 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 198
Score = 27.2 bits (61), Expect = 9.1
Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 20/102 (19%)
Query: 64 QRKTIPLVLEGRDVVAMARTGSGKTACF-----LIPM---------LEKLKTHAATSGVR 109
+ + +V E +DV+A+ +TG + L P+ +++L A ++
Sbjct: 78 DKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGIGPEDLNIDELLQRLAEGSIK 137
Query: 110 ALIL--SPTRE---LALQTFKFVKELG-KFTKLQSTCLLGGD 145
+IL +PT E AL + +K LG K T+L +GG+
Sbjct: 138 EVILATNPTVEGEATALYIARLLKPLGLKVTRLAQGVPVGGE 179
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 0.397
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: 17,060,173
Number of extensions: 1634637
Number of successful extensions: 1611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1578
Number of HSP's successfully gapped: 100
Length of query: 333
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 236
Effective length of database: 6,635,264
Effective search space: 1565922304
Effective search space used: 1565922304
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: 59 (26.7 bits)