RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12977
(226 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 = 130 bits (329), Expect = 7e-38
Identities = 62/178 (34%), Positives = 97/178 (54%), Gaps = 14/178 (7%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
GR + A TGSGKTAAFLIPI+ L PK G +A+I+ PTRELA Q +L +
Sbjct: 36 GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH 95
Query: 108 LGLRAHVI--GK-IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
L+ VI G I + K + +++ TP +L+ LL+ L+L+ V++L++
Sbjct: 96 TNLKVVVIYGGTSIDKQIRKL----KRGPHIVVATPGRLLDLLERG--KLDLSKVKYLVL 149
Query: 165 DESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
DE+D++ + GF DQ+ I + + +FSAT ++V R+ L+ V+I
Sbjct: 150 DEADRMLD---MGFEDQIREILKLLP-KDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>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 = 129 bits (327), Expect = 3e-35
Identities = 61/184 (33%), Positives = 101/184 (54%), Gaps = 17/184 (9%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
GR + A TG+GKTAAFL+P++ + + + A+I+ PTRELA Q E +L +
Sbjct: 66 GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKN 125
Query: 108 L-GLRAHVI---GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
L GLR V+ I++ E + D+++ TP +L+ L++ L+L+ VE L+
Sbjct: 126 LGGLRVAVVYGGVSIRKQIEAL----KRGVDIVVATPGRLLDLIKRG--KLDLSGVETLV 179
Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRVQIN 222
+DE+D++ + GF D + I A P ++ +FSAT +D+ + RR L V+I
Sbjct: 180 LDEADRMLD---MGFIDDIEKILKAL--PPDRQTLLFSATMPDDIRELARRYLNDPVEIE 234
Query: 223 VGLR 226
V +
Sbjct: 235 VSVE 238
>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 (307), Expect = 6e-35
Identities = 57/161 (35%), Positives = 90/161 (55%), Gaps = 6/161 (3%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
G+ + APTGSGKT AFL+PI+ +L PK G +A+++ PTRELA+Q Y E +L + L
Sbjct: 14 GKDVLVQAPTGSGKTLAFLLPILQAL-LPKKGGPQALVLAPTRELAEQIYEELKKLFKIL 72
Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
GLR ++ E+ K D+L+ TP +L+ LL+ L N++ L++DE+
Sbjct: 73 GLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR-GKLKLLKNLKLLVLDEAH 131
Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK 209
+L + GF D L I + P+ + + SAT ++
Sbjct: 132 RLLD---MGFGDDLEEILSRLP-PDRQILLLSATLPRNLED 168
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 107 bits (270), Expect = 3e-29
Identities = 63/184 (34%), Positives = 98/184 (53%), Gaps = 8/184 (4%)
Query: 41 TITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
I L R + APTGSGKT A L+P + +L+ + G R +++ PTRELA+Q E
Sbjct: 16 AIEALLSGLRDVILAAPTGSGKTLAALLPALEALK--RGKGGRVLVLVPTRELAEQWAEE 73
Query: 101 TVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
+L LGL+ + E+ + K D+L+TTP +L+ LL+ D L+L+NV+
Sbjct: 74 LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDK--LSLSNVD 131
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQ 220
+I+DE+ +L + GF DQL + N++ + SAT E++ L V
Sbjct: 132 LVILDEAHRLLD---GGFGDQLEKLLKLL-PKNVQLLLLSATPPEEIENLLELFLNDPVF 187
Query: 221 INVG 224
I+VG
Sbjct: 188 IDVG 191
>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 = 95.1 bits (237), Expect = 7e-25
Identities = 43/151 (28%), Positives = 73/151 (48%), Gaps = 10/151 (6%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
+ APTGSGKT A L+PI+ L K G + +++ PTRELA Q ++ G G++
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLK--GGQVLVLAPTRELANQVAER-LKELFGEGIK 59
Query: 112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF 171
+ ++ S K D+++ TP +L+ L+ L+L ++ LI+DE+ +L
Sbjct: 60 VGYLIGGTSIKQQEKLLS-GKTDIVVGTPGRLLDELERLK--LSLKKLDLLILDEAHRLL 116
Query: 172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSAT 202
G L + + + + SAT
Sbjct: 117 NQG----FGLLGLKILLKLPKDRQVLLLSAT 143
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 91.0 bits (226), Expect = 3e-21
Identities = 65/192 (33%), Positives = 97/192 (50%), Gaps = 34/192 (17%)
Query: 49 GRQIFACAPTGSGKTAAFLIPII------HSLRGPKNLGFRAVIVCPTRELAKQTYNETV 102
GR + A TGSGKTA+FL+PII S + A+++ PTREL Q ++
Sbjct: 158 GRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAK 217
Query: 103 RLSEGLGLR-AHVIG---------KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP 152
L +GL + A V+G +IQQ E +++ TP +L+ LL
Sbjct: 218 VLGKGLPFKTALVVGGDAMPQQLYRIQQGVE-----------LIVGTPGRLIDLLSKH-- 264
Query: 153 ALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR 212
+ L NV L++DE D + E RGFRDQ+ I+ A S P + +FSAT + +V K+
Sbjct: 265 DIELDNVSVLVLDEVDCMLE---RGFRDQVMQIFQALSQPQVL--LFSATVSPEVEKFAS 319
Query: 213 RKLKRRVQINVG 224
K + I++G
Sbjct: 320 SLAKDIILISIG 331
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 80.8 bits (200), Expect = 1e-17
Identities = 59/184 (32%), Positives = 92/184 (50%), Gaps = 21/184 (11%)
Query: 49 GRQIFACAPTGSGKTAAFLIPII-HSLRGP-KNLGF-RAVIVCPTRELAKQTYNETVRLS 105
GR + APTG+GKTAAFL+P + H L P + G R +I+ PTRELA Q ++ L+
Sbjct: 38 GRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELA 97
Query: 106 EGLGLRAHVI-GKI--QQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNLANVEW 161
+ L I G + AE F ++ D+++ TP +L+ Y+ + VE
Sbjct: 98 KHTHLDIATITGGVAYMNHAEVF----SENQDIVVATPGRLLQYI---KEENFDCRAVET 150
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSAT-HTEDVAKWCRRKLKRRV 219
LI+DE+D++ + GF + I A K+ + FSAT + V + R L V
Sbjct: 151 LILDEADRMLDM---GFAQDIETIAAETRWR--KQTLLFSATLEGDAVQDFAERLLNDPV 205
Query: 220 QINV 223
++
Sbjct: 206 EVEA 209
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 78.7 bits (194), Expect = 5e-17
Identities = 66/188 (35%), Positives = 99/188 (52%), Gaps = 22/188 (11%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSL--RGPKNLG---FRAVIVCPTRELAKQTYNETVR 103
GR + A A TG+GKTA F +P++ L R P G RA+I+ PTRELA Q E VR
Sbjct: 38 GRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQI-GENVR 96
Query: 104 -LSEGLGLRAHVI-GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
S+ L +R+ V+ G + + R DVL+ TP +L+ L + A+ L VE
Sbjct: 97 DYSKYLNIRSLVVFGGVSINPQMMKLRGG--VDVLVATPGRLLDLEHQN--AVKLDQVEI 152
Query: 162 LIVDESDKLFEAG-VRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDVAKWCRRKLKRR 218
L++DE+D++ + G + R LA + A KR +FSAT ++D+ + L
Sbjct: 153 LVLDEADRMLDMGFIHDIRRVLAKLPA-------KRQNLLFSATFSDDIKALAEKLLHNP 205
Query: 219 VQINVGLR 226
++I V R
Sbjct: 206 LEIEVARR 213
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 78.7 bits (195), Expect = 5e-17
Identities = 54/183 (29%), Positives = 91/183 (49%), Gaps = 23/183 (12%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG- 107
G+ + A A TGSGKTAAF + ++ L K +A+++CPTRELA Q E RL+
Sbjct: 41 GKDVIAQAKTGSGKTAAFGLGLLQKLD-VKRFRVQALVLCPTRELADQVAKEIRRLARFI 99
Query: 108 -----LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
L L V Q + + G +++ TP +++ L+ L+L + L
Sbjct: 100 PNIKVLTLCGGVPMGPQIDSLEHGAH------IIVGTPGRILDHLRKG--TLDLDALNTL 151
Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDVAKWCRRKLKRRVQ 220
++DE+D++ + GF+D + I +R +FSAT+ E +A +R + V+
Sbjct: 152 VLDEADRMLDM---GFQDAIDAIIRQAPA---RRQTLLFSATYPEGIAAISQRFQRDPVE 205
Query: 221 INV 223
+ V
Sbjct: 206 VKV 208
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 76.0 bits (187), Expect = 5e-16
Identities = 60/195 (30%), Positives = 91/195 (46%), Gaps = 40/195 (20%)
Query: 49 GRQIFACAPTGSGKTAAFLIP-IIH-----SLR---GPKNLGFRAVIVCPTRELAKQTYN 99
GR + A TGSGKT AFL+P I+H LR GP L ++ PTRELA+Q
Sbjct: 167 GRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVL-----VLAPTRELAEQIRE 221
Query: 100 ETVRLSEGLGLRAHVI-----GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL 154
+ + +R V + Q A + G ++LI P +L+ L+ +
Sbjct: 222 QCNKFGASSKIRNTVAYGGVPKRGQIYALRRG------VEILIACPGRLIDFLESN--VT 273
Query: 155 NLANVEWLIVDESDKL----FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW 210
NL V +L++DE+D++ FE +R Q+ P+ + M+SAT ++V
Sbjct: 274 NLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIR--------PDRQTLMWSATWPKEVQSL 325
Query: 211 CRRKLKRR-VQINVG 224
R K V +NVG
Sbjct: 326 ARDLCKEEPVHVNVG 340
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 72.3 bits (177), Expect = 1e-14
Identities = 55/170 (32%), Positives = 90/170 (52%), Gaps = 20/170 (11%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSL--------RGPKNLGFRAVIVCPTRELAKQTYNE 100
G + A TG+GKT AFL+ +++ L R P++ RA+I+ PTRELA Q + +
Sbjct: 46 GGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDP--RALILAPTRELAIQIHKD 103
Query: 101 TVRLSEGLGLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNLAN 158
V+ LGLR A V G + ++ + Q DV+I TP +L+ Y+ Q ++L
Sbjct: 104 AVKFGADLGLRFALVYGGVDYDKQRELLQ--QGVDVIIATPGRLIDYVKQHK--VVSLHA 159
Query: 159 VEWLIVDESDKLFEAG-VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV 207
E ++DE+D++F+ G ++ R L + + L +FSAT + V
Sbjct: 160 CEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTL---LFSATLSHRV 206
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 67.6 bits (165), Expect = 3e-13
Identities = 53/167 (31%), Positives = 82/167 (49%), Gaps = 14/167 (8%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRG--PKNLGF----RAVIVCPTRELAKQTYNETV 102
G A TG+GKTAAFLI II+ L P + RA+I+ PTREL Q +
Sbjct: 124 GHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAA 183
Query: 103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
L++ GL ++ A+ D+L+ TP +L+ Q L++ VE +
Sbjct: 184 ALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDM--VEVM 241
Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDV 207
++DE+D++ + GF Q+ I + +R +FSAT T+DV
Sbjct: 242 VLDEADRMLDM---GFIPQVRQIIRQ-TPRKEERQTLLFSATFTDDV 284
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 66.4 bits (162), Expect = 9e-13
Identities = 58/192 (30%), Positives = 96/192 (50%), Gaps = 31/192 (16%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
GR + A TGSGKTAAF +P++H L+ P+ L ++ PTRELA Q
Sbjct: 43 GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQIL-----VLAPTRELAVQVAEAMTDF 97
Query: 105 SE---GLGLRAHVIGK---IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN 158
S+ G+ + A G+ +Q A + GP+ +++ TP +L L + L+L+
Sbjct: 98 SKHMRGVNVVALYGGQRYDVQLRALRQGPQ------IVVGTPGRL--LDHLKRGTLDLSK 149
Query: 159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR- 217
+ L++DE+D++ GF + + I A + + +FSAT E + + RR +K
Sbjct: 150 LSGLVLDEADEMLRM---GFIEDVETIMAQIPEGH-QTALFSATMPEAIRRITRRFMKEP 205
Query: 218 ---RVQINVGLR 226
R+Q +V R
Sbjct: 206 QEVRIQSSVTTR 217
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 66.3 bits (162), Expect = 1e-12
Identities = 37/119 (31%), Positives = 59/119 (49%), Gaps = 12/119 (10%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
+ APTGSGKT L+ I+ +L G + V + P + LA++ Y E RL E L
Sbjct: 47 DENVLISAPTGSGKTLIALLAILSTL---LEGGGKVVYIVPLKALAEEKYEEFSRL-EEL 102
Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
G+R G E+ ++DV++TTP KL L + P + ++ +++DE
Sbjct: 103 GIRVGISTGDYDLDDERLA-----RYDVIVTTPEKLDSLTRKRPSWIEEVDL--VVIDE 154
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 61.9 bits (151), Expect = 3e-11
Identities = 51/167 (30%), Positives = 79/167 (47%), Gaps = 25/167 (14%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSL------RGPKNLGFRAVIVCPTRELAKQTYNETV 102
GR + A TG+GKT AFL H L K RA+I+ PTRELA Q + +
Sbjct: 45 GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAE 104
Query: 103 RLSEGLGLRAHVI--GK---IQQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNL 156
L++ GL+ + G Q + G D+LI T +L+ Y Q +NL
Sbjct: 105 PLAQATGLKLGLAYGGDGYDKQLKVLESGV------DILIGTTGRLIDYAKQ---NHINL 155
Query: 157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSAT 202
++ +++DE+D++F+ GF + ++ N + M FSAT
Sbjct: 156 GAIQVVVLDEADRMFDL---GFIKDIRWLFRRMPPANQRLNMLFSAT 199
>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 = 60.1 bits (146), Expect = 1e-10
Identities = 40/124 (32%), Positives = 57/124 (45%), Gaps = 11/124 (8%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHS-LRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
GR + TGSGKT +FL+PI+ LR P RA+++ PT LA L
Sbjct: 85 GRNVVVTTGTGSGKTESFLLPILDHLLRDPS---ARALLLYPTNALANDQAERLRELISD 141
Query: 108 LGLRAHVI---GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALN--LANVEWL 162
L + G E+ D+L+T P+ L YLL + A L N+++L
Sbjct: 142 LPGKVTFGRYTGDTPP--EERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYL 199
Query: 163 IVDE 166
+VDE
Sbjct: 200 VVDE 203
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 57.9 bits (140), Expect = 7e-10
Identities = 43/162 (26%), Positives = 82/162 (50%), Gaps = 14/162 (8%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
G A +G+GKTA F+I + + +A+I+ PTRELA+Q + L + L
Sbjct: 65 GYDTIGQAQSGTGKTATFVIAALQLI-DYDLNACQALILAPTRELAQQIQKVVLALGDYL 123
Query: 109 GLRAHV-IG--KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVD 165
+R H +G ++ K +++ TP + VY + +D L + +++ I+D
Sbjct: 124 KVRCHACVGGTVVRDDINKL----KAGVHMVVGTPGR-VYDM-IDKRHLRVDDLKLFILD 177
Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV 207
E+D++ RGF+ Q+ ++ P+++ +FSAT ++
Sbjct: 178 EADEMLS---RGFKGQIYDVFKKLP-PDVQVALFSATMPNEI 215
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 55.3 bits (134), Expect = 6e-09
Identities = 66/222 (29%), Positives = 89/222 (40%), Gaps = 60/222 (27%)
Query: 29 SNSIFKHFEPH----FTITYLSPLGRQIFAC------------APTGSGKTAAFLIPIIH 72
IF +P F + S Q +A APTGSGKT A +P+I+
Sbjct: 1 DEEIFNILDPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVIN 60
Query: 73 SL----RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV-IGKIQQAAEKFGP 127
L +G G A+ + P + L LG+ V G Q +EK
Sbjct: 61 ELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQ-SEK--- 116
Query: 128 RSAQKF-----DVLITTPNKLVYLLQMDPPAL--NLANVEWLIVDESDKLFEAGVRGFRD 180
QK +LITTP L LL + P L +V ++IVDE L E+ RG
Sbjct: 117 ---QKMLKNPPHILITTPESLAILL--NSPKFRELLRDVRYVIVDEIHALAESK-RG--V 168
Query: 181 QLAVIYAACSGPNLKR-----GMF-----SAT--HTEDVAKW 210
QLA+ +L+R G F SAT E+VAK+
Sbjct: 169 QLAL--------SLERLRELAGDFQRIGLSATVGPPEEVAKF 202
>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 = 49.5 bits (119), Expect = 5e-07
Identities = 53/169 (31%), Positives = 71/169 (42%), Gaps = 22/169 (13%)
Query: 56 APTGSGKT-AAFLIPIIHSLRGPKNL-GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH 113
APTGSGKT A FL +I K G + + P R LA E LGL
Sbjct: 35 APTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALAVDIARNLQAPIEELGLPIR 94
Query: 114 V---IGKIQQAAEKFGPRSAQKF---DVLITTPNKLVYLL-QMDPPALNLANVEWLIVDE 166
V G + R+ Q+ D+L+TTP L LL D L ++ ++VDE
Sbjct: 95 VETRTGDTSSSE-----RARQRKKPPDILLTTPESLALLLSYPDAARL-FKDLRCVVVDE 148
Query: 167 SDKLFEAGVRGFRDQLAVIYA--ACSGPNLKRGMFSAT--HTEDVAKWC 211
+L RG DQL + A P L+R SAT + E+ +
Sbjct: 149 WHELA-GSKRG--DQLELALARLRRLAPGLRRWGLSATIGNLEEARRVL 194
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 46.4 bits (111), Expect = 5e-06
Identities = 46/148 (31%), Positives = 61/148 (41%), Gaps = 44/148 (29%)
Query: 49 GRQIFACAPTGSGKT-AAFLIPIIHSL--RGPKNL---GFRAVIVCPTRELAKQTY-NET 101
G+ + +PTGSGKT AAFL II L G + + V P R L + N
Sbjct: 47 GKNVLISSPTGSGKTLAAFLA-IIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLE 105
Query: 102 VRLSEGLGLRAHVIGKIQQAAEKFGP-----RSA-----------QKF-----DVLITTP 140
L+E I++ A++ G R A QK +LITTP
Sbjct: 106 EPLTE-----------IREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTP 154
Query: 141 NKLVYLLQMDPPALN--LANVEWLIVDE 166
L LL + P L V+W+IVDE
Sbjct: 155 ESLAILL--NSPKFREKLRTVKWVIVDE 180
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 44.9 bits (106), Expect = 2e-05
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 15/131 (11%)
Query: 49 GRQIFACAPTGSGKTA-AFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
G+ APTG GK+ I + +L+G K I+ PT L KQT + E
Sbjct: 94 GKSFSIVAPTGMGKSTFGAFIALFLALKGKK-----CYIILPTTLLVKQTVEKIESFCEK 148
Query: 108 LGLRAHVIG-----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
L ++ + ++ E FD+L+TT L + P + +++
Sbjct: 149 ANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ----FLARNFPEMKHLKFDFI 204
Query: 163 IVDESDKLFEA 173
VD+ D +A
Sbjct: 205 FVDDVDAFLKA 215
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 44.5 bits (105), Expect = 2e-05
Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 13/119 (10%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
G + PT +GKT I + G +++ + P R LA + Y E RL L
Sbjct: 37 GENVIVSVPTAAGKTLIAYSAIYETFLA----GLKSIYIVPLRSLAMEKYEELSRLRS-L 91
Query: 109 GLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
G+R + IG P +++DV+I T K L+ DP +N +V ++ DE
Sbjct: 92 GMRVKISIGDYDDP-----PDFIKRYDVVILTSEKADSLIHHDPYIIN--DVGLIVADE 143
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 44.0 bits (104), Expect = 3e-05
Identities = 49/173 (28%), Positives = 78/173 (45%), Gaps = 24/173 (13%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
G+ + PT SGKT I +++ L G +AV + P + LA++ Y E + E L
Sbjct: 39 GKNLVLAIPTASGKTLVAEIVMVNKLL---REGGKAVYLVPLKALAEEKYRE-FKDWEKL 94
Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
GLR A G E G K+D++I T K LL+ + +V+ ++ DE
Sbjct: 95 GLRVAMTTGDYDSTDEWLG-----KYDIIIATAEKFDSLLRHGSSWIK--DVKLVVADEI 147
Query: 168 DKLFEAGVRGFRDQ---LAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKL 215
+ G D+ L +I G G+ SAT + E++A+W +L
Sbjct: 148 HLI------GSYDRGATLEMILTHMLGRAQILGL-SATVGNAEELAEWLNAEL 193
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 42.4 bits (100), Expect = 1e-04
Identities = 43/183 (23%), Positives = 69/183 (37%), Gaps = 35/183 (19%)
Query: 56 APTGSGKT------AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE--- 106
APTG GKT + +L G R I+ PT L +Q Y + +E
Sbjct: 104 APTGVGKTTFGLLMSLYL----------AKKGKRVYIIVPTTTLVRQVYERLKKFAEDAG 153
Query: 107 GLGLRAHVIGKI-QQAAEKFGPRSAQ-KFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
L + + + E+ R FD+LITT L L+ +++ V
Sbjct: 154 SLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRF----EELSKLKFDFIFV 209
Query: 165 DESDKLFEAG--------VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK 216
D+ D + +A + GF + VI +A L+R ++ E V + R +
Sbjct: 210 DDVDAILKASKNVDRLLRLLGFSE--EVIESAYELIKLRRKLYGEKRAERVREELREVER 267
Query: 217 RRV 219
R
Sbjct: 268 ERE 270
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 41.3 bits (97), Expect = 3e-04
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
G + APTG+GKT A+L+P + R G + +I T+ L +Q E
Sbjct: 34 GEGLLIEAPTGTGKTLAYLLPALAYAR---EEGKKVIISTRTKALQEQLLEE 82
>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 = 41.3 bits (97), Expect = 3e-04
Identities = 37/139 (26%), Positives = 49/139 (35%), Gaps = 27/139 (19%)
Query: 48 LGRQIFACAPTGSGKT------AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET 101
G APTG GKT + FL G R I+ PT L Q +
Sbjct: 92 RGDSFAIIAPTGVGKTTFGLAMSLFL----------AKKGKRCYIILPTTLLVIQVAEKI 141
Query: 102 VRLSEGLGLRAHVIGKIQ-----QAAEKFGPRSAQ-KFDVLITTPNKLVYLLQMDPPALN 155
L+E G+ IG + ++F R FD+LITT L P +
Sbjct: 142 SSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFD 201
Query: 156 LANVEWLIVDESDKLFEAG 174
VD+ D L +A
Sbjct: 202 FI-----FVDDVDALLKAS 215
>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 = 39.5 bits (92), Expect = 7e-04
Identities = 29/140 (20%), Positives = 49/140 (35%), Gaps = 32/140 (22%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
IF APTG+GKT A+L P++H +A+ + PT L + + R
Sbjct: 17 IFNTAPTGAGKTLAWLTPLLHG-------ENKAIALYPTNALIEDQTEAIKEFVDDANPR 69
Query: 112 --AHVIG----KIQQAAEKFGPRSAQKF-------------DVLITTPN------KLVYL 146
+ + + G +K +L+T P+ + Y+
Sbjct: 70 HQVKSLSASDITLWPNDKNVGSSKGEKLYNLLRNDIGTSTPIILLTNPDIFVYLTRFAYI 129
Query: 147 LQMDPPALNLANVEWLIVDE 166
+ D A +I DE
Sbjct: 130 DRGDIAAGFYTKFSTVIFDE 149
>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 = 38.7 bits (90), Expect = 0.001
Identities = 32/145 (22%), Positives = 52/145 (35%), Gaps = 38/145 (26%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN------ETVRLS 105
IF APTG+GKT A+L P++H + + PT L + + +
Sbjct: 17 IFNTAPTGAGKTLAWLTPLLHG-------ENDTIALYPTNALIEDQTEAIKEFVDVFKPE 69
Query: 106 EGLGLRAHVIGKIQQ-----AAEKFGPRSAQKF-------------DVLITTPN------ 141
+ L HV + A +K G +K +L+T P+
Sbjct: 70 RDVNLL-HVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLT 128
Query: 142 KLVYLLQMDPPALNLANVEWLIVDE 166
+ Y+ + D A +I DE
Sbjct: 129 RFAYIDRGDIAAGFYTKFSTVIFDE 153
>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 = 38.6 bits (90), Expect = 0.002
Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 21/102 (20%)
Query: 56 APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV-RLSEGLG--LRA 112
APTG+GKT +L+P ++ K + VI T+ L Q + + L+E L + A
Sbjct: 271 APTGTGKTLGYLLPALYYAITEKPV----VISTNTKVLQSQLLEKDIPLLNEILNFKINA 326
Query: 113 HVIGKIQQAAEKFGPR---SAQKFDVLIT--TPNKLVYLLQM 149
+I G S KF ++ T N + +M
Sbjct: 327 ALIK---------GKSNYLSLGKFSQILKDNTDNYEFNIFKM 359
Score = 27.8 bits (62), Expect = 5.0
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA 173
++A++ +LIT L+ L +P LI+DE+ L +
Sbjct: 408 NRAQKNAEQAQILITNHAYLITRLVDNPELFPSF--RDLIIDEAHHLPDI 455
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 38.2 bits (89), Expect = 0.002
Identities = 24/107 (22%), Positives = 36/107 (33%), Gaps = 4/107 (3%)
Query: 42 ITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET 101
I L + APTG GKT A LI + L L R + V P R + + Y
Sbjct: 207 ILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRA 266
Query: 102 VRLSEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLL 147
+ + ++ Q + +TT + LL
Sbjct: 267 KEIFGLFSVIGKSLHSSSKEPLLLE---PDQDILLTLTTNDSYKKLL 310
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 37.4 bits (87), Expect = 0.004
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 49 GRQIFACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
R+ PTG+GKT AA I L +++ PT+EL Q
Sbjct: 55 ERRGVIVLPTGAGKTVVAAEAI---------AELKRSTLVLVPTKELLDQWAEA 99
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 34.9 bits (81), Expect = 0.005
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 56 APTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY 98
TGSGKT AA LI + + V P ++L +Q
Sbjct: 25 MATGSGKTLTAAALI------ARLAKGKKKVLFVVPRKDLLEQAL 63
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 36.4 bits (85), Expect = 0.010
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 21/103 (20%)
Query: 48 LGRQIFACAPTGSGKT------AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET 101
LG APTG GKT + +L + +G K+ I+ PTR L +Q +
Sbjct: 94 LGESFAIIAPTGVGKTTFGLVMSLYL-----AKKGKKSY-----IIFPTRLLVEQVVEKL 143
Query: 102 VRLSEGLGLRAHVI----GKIQQAAEKFGPRSAQ-KFDVLITT 139
+ E +G ++ ++ E+F R + FD+L+TT
Sbjct: 144 EKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTT 186
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 34.3 bits (79), Expect = 0.040
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 56 APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL-SEGLGLRAH 113
APTG GKT A L+ +HS++ K R +I PTR Y L LGL
Sbjct: 6 APTGYGKTEAALLWALHSIKSQKAD--RVIIALPTRATINAMYRRAKELFGSNLGLLHS 62
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. 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; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 32.4 bits (74), Expect = 0.15
Identities = 22/54 (40%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 56 APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
APTG GKT A L+ +HSL+ K R +I PTR Y R E G
Sbjct: 6 APTGYGKTEAALLWALHSLKSQKAD--RVIIALPTRATINAMYR---RAKEAFG 54
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 32.6 bits (75), Expect = 0.16
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 59 GSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
GSGKT L+ ++ ++ G++A ++ PT LA+Q Y + E LG+R
Sbjct: 293 GSGKTVVALLAMLAAIEA----GYQAALMAPTEILAEQHYESLRKWLEPLGIR 341
>gnl|CDD|233928 TIGR02562, cas3_yersinia, CRISPR-associated helicase Cas3, subtype
I-F/YPEST. The helicase in many CRISPR-associated (cas)
gene clusters is designated Cas3, and most Cas3 proteins
are described by model TIGR01587. Members of this family
are considerably larger, show a number of motifs in
common with TIGR01587 sequences, and replace Cas3 in
some CRISPR/cas loci in a number of Proteobacteria,
including Yersinia pestis, Chromobacterium violaceum,
Erwinia carotovora subsp. atroseptica SCRI1043,
Photorhabdus luminescens subsp. laumondii TTO1,
Legionella pneumophila, etc [Mobile and extrachromosomal
element functions, Other].
Length = 1110
Score = 32.5 bits (74), Expect = 0.16
Identities = 34/132 (25%), Positives = 45/132 (34%), Gaps = 21/132 (15%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT---YNETVRLSEG- 107
A TG GKT A +++LR K G R I R L QT + LS+
Sbjct: 434 GVNMASTGCGKTLANA-RAMYALRDDKQ-GARFAIALGLRSLTLQTGHALKTRLNLSDDD 491
Query: 108 ----------LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLA 157
L KI+Q E G SA F N + +D L
Sbjct: 492 LAVLIGGTAVQTLFDLSKEKIEQVDED-GSESAPIFLAEGQDCNLPDWDGPLDTIELL-- 548
Query: 158 NVEWLIVDESDK 169
L +D+ +K
Sbjct: 549 --GRLSLDDKEK 558
>gnl|CDD|187804 cd09673, Cas3_Cas2_I-F, CRISPR/Cas system-associated protein
Cas3/Cas2. 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;
Cas3/Cas2 fusion; This protein includes both DEAH and HD
motifs for helicase and N-terminal domain corresponding
to Cas2 RNAse; signature gene for Type I and subtype
I-F.
Length = 1106
Score = 32.5 bits (74), Expect = 0.16
Identities = 34/132 (25%), Positives = 45/132 (34%), Gaps = 21/132 (15%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT---YNETVRLSEG- 107
A TG GKT A +++LR K G R I R L QT + LS+
Sbjct: 430 GVNMASTGCGKTLANA-RAMYALRDDKQ-GARFAIALGLRSLTLQTGHALKTRLNLSDDD 487
Query: 108 ----------LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLA 157
L KI+Q E G SA F N + +D L
Sbjct: 488 LAVLIGGTAVQTLFDLSKEKIEQVDED-GSESAPIFLAEGQDCNLPDWDGPLDTIELL-- 544
Query: 158 NVEWLIVDESDK 169
L +D+ +K
Sbjct: 545 --GRLSLDDKEK 554
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family helicase
Csf4. 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;
DinG family DNA helicase.
Length = 632
Score = 32.6 bits (74), Expect = 0.17
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL-SE 106
R A TG GKT A ++ + L+ + I PT L Q ++E RL +E
Sbjct: 15 QKRIGMLEASTGVGKTLAMIMAALTMLKERP--DQKIAIAVPTLALMGQLWSELERLTAE 72
Query: 107 GLG 109
GL
Sbjct: 73 GLA 75
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 32.6 bits (74), Expect = 0.17
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL-SE 106
R A TG GKT A ++ + L+ + I PT L Q ++E RL +E
Sbjct: 15 QKRIGMLEASTGVGKTLAMIMAALTMLKERP--DQKIAIAVPTLALMGQLWSELERLTAE 72
Query: 107 GLG 109
GL
Sbjct: 73 GLA 75
>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 = 31.9 bits (73), Expect = 0.22
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 49 GRQIFACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
GR I A TG+GKT A ++ K ++VCP + L Q E
Sbjct: 25 GRGILKMA-TGTGKTLTALAAASKLYE----KIGLLVLLVVCPYQHLVDQWARE 73
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 31.9 bits (73), Expect = 0.23
Identities = 28/117 (23%), Positives = 50/117 (42%), Gaps = 9/117 (7%)
Query: 58 TGSGKTAAFLIPIIHS-LRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA-HVI 115
G GKT I ++ + L+ K+ ++VCP NE + + L + H
Sbjct: 25 MGLGKTLQ-TIALLATYLKEGKDRRGPTLVVCPL-STLHNWLNEFEKWAPALRVVVYHGD 82
Query: 116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW--LIVDESDKL 170
G+ + + + +DV+ITT L + L VEW +++DE+ +L
Sbjct: 83 GRERSKLRQSMAKRLDTYDVVITT---YEVLRKDKKLLSLLNKVEWDRVVLDEAHRL 136
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood
widely spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 32.0 bits (73), Expect = 0.29
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA 94
GR + T SGK+ A+ +P++ +L A+ + PT+ LA
Sbjct: 51 GRHVVVATGTASGKSLAYQLPVLSALADDP--RATALYLAPTKALA 94
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 30.8 bits (70), Expect = 0.58
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 59 GSGKTA-AFL--IPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
GSGKT A L + I + G++ ++ PT LA+Q YN L LG+
Sbjct: 266 GSGKTLVAALAMLAAIEA-------GYQVALMAPTEILAEQHYNSLRNLLAPLGIE 314
>gnl|CDD|238546 cd01126, TraG_VirD4, The TraG/TraD/VirD4 family are bacterial
conjugation proteins involved in type IV secretion.
These proteins aid the transfer of DNA from the plasmid
into the host bacterial chromosome. They contain an ATP
binding domain. VirD4 is involved in DNA transfer to
plant cells and is required for virulence.
Length = 384
Score = 30.4 bits (69), Expect = 0.79
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 10/59 (16%)
Query: 56 APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV 114
APT SGK F+IP + + G V++ P E T LG + V
Sbjct: 6 APTRSGKGVGFVIPNLLTWPGS------VVVLDPKGENF----ELTSEHRRALGRKVFV 54
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 30.6 bits (70), Expect = 0.80
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 55 CAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ 96
PTG GKTA L+ I L G + +I+ PT+ L +Q
Sbjct: 35 VLPTGLGKTAIALLVIAERL---HKKGGKVLILAPTKPLVEQ 73
>gnl|CDD|217088 pfam02534, T4SS-DNA_transf, Type IV secretory system Conjugative
DNA transfer. These proteins contain a P-loop and
walker-B site for nucleotide binding. TraG is essential
for DNA transfer in bacterial conjugation. These
proteins are thought to mediate interactions between the
DNA-processing (Dtr) and the mating pair formation (Mpf)
systems. The C-terminus of this domain interacts with
the relaxosome component TraM via the latter's
tetramerisation domain. TraD is a hexameric ring ATPase
that forms the cytoplasmic face of the conjugative pore.
The family contains a number of different DNA transfer
proteins.
Length = 468
Score = 30.1 bits (68), Expect = 1.0
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
+ A TGSGK +IP + L ++ V++ P EL + T +R +G
Sbjct: 47 VLVFAGTGSGKGVGVVIPNL--LVWKGSI----VVLDPKGELWELTSG--IREKQG 94
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 30.1 bits (69), Expect = 1.1
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 59 GSGKT----AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
GSGKT A L I G++A ++ PT LA+Q Y +L E LG+R
Sbjct: 292 GSGKTVVAALAALAAIEA--------GYQAALMAPTEILAEQHYENLKKLLEPLGIR 340
>gnl|CDD|238662 cd01366, KISc_C_terminal, Kinesin motor domain,
KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a
spindle motor protein necessary for chromosome
segregation in meiosis. KIFC2/KIFC3-like kinesins have
been implicated in motility of the Golgi apparatus as
well as dentritic and axonal transport in neurons. 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 this subgroup the motor domain is found at
the C-terminus (C-type). 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 = 329
Score = 29.8 bits (68), Expect = 1.2
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 25/69 (36%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRG-PKNLGF--RAV--IVCPTRELAKQT--------- 97
IFA TGSGKT +++ G P+N G RA+ + EL ++
Sbjct: 81 IFAYGQTGSGKT--------YTMEGPPENPGIIPRALEQLFNTAEELKEKGWSYTITASM 132
Query: 98 ---YNETVR 103
YNET+R
Sbjct: 133 LEIYNETIR 141
>gnl|CDD|225667 COG3125, CyoD, Heme/copper-type cytochrome/quinol oxidase,
subunit 4 [Energy production and conversion].
Length = 111
Score = 28.1 bits (63), Expect = 1.8
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 8/45 (17%)
Query: 12 FTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACA 56
+ IGFV+SII+T + + T+ I A
Sbjct: 20 YLIGFVLSIILTLIPFWV-VMTGALSSTVTLII-------ILGLA 56
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 29.3 bits (65), Expect = 1.8
Identities = 27/117 (23%), Positives = 44/117 (37%), Gaps = 13/117 (11%)
Query: 59 GSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT-------RELAKQTYNETVRLSEGLGLR 111
G GKT + ++ L K A+IV P RE K + + G +
Sbjct: 368 GLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNWKREFEKFA-PDLRLVLVYHGEK 426
Query: 112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW--LIVDE 166
+ + K + + FDV+ITT L + L +EW +++DE
Sbjct: 427 SELDKKREALRDLLKLHLVIIFDVVITT---YELLRRFLVDHGGLKKIEWDRVVLDE 480
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 29.5 bits (66), Expect = 1.9
Identities = 35/139 (25%), Positives = 51/139 (36%), Gaps = 37/139 (26%)
Query: 56 APTGSGKT-AAFLIPI--IHSLRGP--KNLGFRA----VIVCPTRELAKQTYNETVRLSE 106
APTGSGKT AAFL + + G + R + + P + L +
Sbjct: 3 APTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTD-------VQR 55
Query: 107 GLGLRAHVIGKIQQ-------------------AAEKFGPRSAQKFDVLITTPNKLVYLL 147
L + I ++ A E+ + D+LITTP L YL+
Sbjct: 56 NLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSK-LTRNPPDILITTPESL-YLM 113
Query: 148 QMDPPALNLANVEWLIVDE 166
L VE +I+DE
Sbjct: 114 LTSRARETLRGVETVIIDE 132
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 29.0 bits (66), Expect = 2.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 56 APTGSGKTAAFLIPII 71
A TG GKT ++L+ I
Sbjct: 56 AGTGVGKTLSYLLAGI 71
>gnl|CDD|215197 PLN02347, PLN02347, GMP synthetase.
Length = 536
Score = 28.5 bits (64), Expect = 3.3
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRG-PKNLGFRAVIVCPTRELAK 95
I +C P GSG+T + I H++ G PK++ + ++ P + L K
Sbjct: 349 IESCPPPGSGRTHSHTIKSHHNVGGLPKDMKLK--LIEPLKLLFK 391
>gnl|CDD|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 372
Score = 28.5 bits (64), Expect = 3.3
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 15/72 (20%)
Query: 88 CPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLL 147
C T A+Q +N +R+SE +IG++ +AA+ G V P V ++
Sbjct: 120 CST---AQQGFNRNLRVSE-------IIGQVWRAAKIIG-----AAKVTGQRPITNVVMM 164
Query: 148 QMDPPALNLANV 159
M P LNL NV
Sbjct: 165 GMGEPLLNLNNV 176
>gnl|CDD|187827 cd09696, Cas3_I, CRISPR/Cas system-associated protein Cas3;
Distinct Cas3 family with HD domain fused to C-termus of
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; DNA helicase Cas3; This protein includes
both DEAH and HD motifs; signature gene for Type I.
Length = 843
Score = 28.4 bits (63), Expect = 3.5
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 57 PTGSGKT---AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH 113
PTG GKT AA+L+ + + P+ R V V R + Q E ++ E L
Sbjct: 38 PTGLGKTSIIAAWLLAVEIGAKVPR----RLVYVVNRRTVVDQVTEEAEKIGERLPDVPE 93
Query: 114 VIGKIQQAAEKFGPRSA 130
V + EK P+
Sbjct: 94 VEAALWTRPEKPDPKKD 110
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 28.4 bits (64), Expect = 3.7
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 56 APTGSGKTAAFLIPIIH 72
A TG+GK+ A+L+P +
Sbjct: 283 AGTGTGKSLAYLLPAAY 299
>gnl|CDD|237549 PRK13897, PRK13897, type IV secretion system component VirD4;
Provisional.
Length = 606
Score = 28.2 bits (63), Expect = 3.8
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 56 APTGSGKTAAFLIP 69
APTGSGK F+IP
Sbjct: 165 APTGSGKGVGFVIP 178
>gnl|CDD|223506 COG0429, COG0429, Predicted hydrolase of the alpha/beta-hydrolase
fold [General function prediction only].
Length = 345
Score = 28.1 bits (63), Expect = 4.0
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 188 ACSG-PNLKRGMFSATHTEDVAKWCRRKLKRR 218
CSG N ++ + TED+ + LK R
Sbjct: 114 GCSGEANTSPRLYHSGETEDIR-FFLDWLKAR 144
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 28.0 bits (63), Expect = 4.2
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
G+ + A PT SGKT LI + L+ G +A+ + P R LA + + E R E L
Sbjct: 39 GKNLLAAIPTASGKT---LIAELAMLKAIAR-GGKALYIVPLRALASEKFEEFERFEE-L 93
Query: 109 GLR 111
G+R
Sbjct: 94 GVR 96
>gnl|CDD|225806 COG3267, ExeA, Type II secretory pathway, component ExeA (predicted
ATPase) [Intracellular trafficking and secretion].
Length = 269
Score = 27.8 bits (62), Expect = 4.4
Identities = 23/134 (17%), Positives = 44/134 (32%), Gaps = 19/134 (14%)
Query: 55 CAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV 114
GSGKT ++ SL + AV+V L+ T E + + +V
Sbjct: 57 TGEVGSGKTVL-RRALLASLNEDQV----AVVVIDKPTLSDATLLEAIVADLESQPKVNV 111
Query: 115 IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG 174
++Q + L+ + V L+ + LN + E+ +L
Sbjct: 112 NAVLEQIDREL--------AALVKKGKRPVVLMVDEAHDLNDS------ALEALRLLTNL 157
Query: 175 VRGFRDQLAVIYAA 188
L+++
Sbjct: 158 EEDSSKLLSIVLIG 171
>gnl|CDD|233953 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, subtype
Dpsyc. This model describes a CRISPR-associated
putative DEAH-box helicase, or Cas3, of a subtype found
in Actinomyces naeslundii MG1, Geobacter sulfurreducens
PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea
psychrophila. This protein includes both DEAH and HD
motifs [Mobile and extrachromosomal element functions,
Other].
Length = 862
Score = 28.0 bits (62), Expect = 4.5
Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 57 PTGSGKTA---AFLIPIIHSLRGPKNLGF--RAVIVCPTRELAKQTYNETVRLSEGLGLR 111
PTG GKTA +L + + R V V R + Q+ E ++ E LG
Sbjct: 38 PTGLGKTAVIAGWLYALTQDAEQVRRRKVPRRLVYVVDRRTVVDQSTREAEKIQEALGEA 97
Query: 112 AHV 114
Sbjct: 98 PER 100
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 27.9 bits (62), Expect = 5.0
Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 30/113 (26%)
Query: 49 GRQIFACAPTGSGKT--------------AAFLIPII----HSLRG---PKNLGFRAVIV 87
G+ I AC G+GKT FL+P I +LR K L FRA V
Sbjct: 183 GKLIMAC---GTGKTFTSLKISEALAAARILFLVPSISLLSQTLREWTAQKELDFRASAV 239
Query: 88 CPTRELAKQTYNETVRLSEGLGLRAHVIGK-IQQAAEKFGPRSAQKFDVLITT 139
C ++++ E ++ S+ L + + I E + A V+ +T
Sbjct: 240 CSDDKVSRS--AEDIKASD-LPIPVSTDLEDILSEMEHR--QKANGLTVVFST 287
>gnl|CDD|238670 cd01374, KISc_CENP_E, Kinesin motor domain, CENP-E/KIP2-like
subgroup, involved in chromosome movement and/or spindle
elongation 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 = 321
Score = 27.7 bits (62), Expect = 5.1
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 23/67 (34%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRG-PKNLG---------FRAVIVCPTREL-----AKQ 96
IFA T SGKT ++ G + G F+ + P RE +
Sbjct: 77 IFAYGQTSSGKT--------FTMSGDEQEPGIIPLAVRDIFQRIQDTPDREFLLRVSYLE 128
Query: 97 TYNETVR 103
YNE ++
Sbjct: 129 IYNEKIK 135
>gnl|CDD|177609 PHA03372, PHA03372, DNA packaging terminase subunit 1; Provisional.
Length = 668
Score = 27.8 bits (62), Expect = 5.3
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 2 KNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFA------C 55
KN+L I I F I VT L V++N + ++ F I +LS IF
Sbjct: 157 KNLL-----IHVIFF---IAVTKLPVLANRVLEYLLHVFDIEFLSESSLNIFKQKATVFL 208
Query: 56 APTGSGKTAAFLIPII 71
P GKT F+IPII
Sbjct: 209 VPRRHGKT-WFIIPII 223
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 27.7 bits (62), Expect = 6.3
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 49 GRQIFACAPTGSGKT 63
G + CAPT SGKT
Sbjct: 134 GESVLVCAPTSSGKT 148
>gnl|CDD|224361 COG1444, COG1444, Predicted P-loop ATPase fused to an
acetyltransferase [General function prediction only].
Length = 758
Score = 27.7 bits (62), Expect = 6.6
Identities = 26/119 (21%), Positives = 37/119 (31%), Gaps = 19/119 (15%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE-TVRLSEG 107
R + A G GK+AA I + R ++ PT QT E + E
Sbjct: 231 KRALVLTADRGRGKSAALGIALA--AAARLAGSVRIIVTAPTPA-NVQTLFEFAGKGLEF 287
Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
LG + V S F + + PP + L+VDE
Sbjct: 288 LGYKRKVAPDALGE---IREVSGDGFRI------------EYVPPDDAQEEADLLVVDE 331
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 27.4 bits (61), Expect = 6.7
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 9/65 (13%)
Query: 49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNL---GFRAVIVCPTRELAKQTYNETVRLS 105
G + + T SGKT +I L G L G + + + P LA Q Y +
Sbjct: 232 GENLLVVSATASGKT------LIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERY 285
Query: 106 EGLGL 110
LGL
Sbjct: 286 SKLGL 290
>gnl|CDD|219016 pfam06417, DUF1077, Protein of unknown function (DUF1077). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 124
Score = 26.5 bits (59), Expect = 7.9
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 8 ALGIFTIGFVISIIVTTL-AVVS-NSIFKHFE 37
+L IF I V ++ + A++S NS FK E
Sbjct: 41 SLQIFPIMMVGMLLWNPIKAILSTNSAFKPLE 72
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 27.5 bits (61), Expect = 8.0
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 136 LITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG 177
+I N+L LL + P + + N + ++ + D LF+ G RG
Sbjct: 350 VINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRG 391
>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 = 27.0 bits (60), Expect = 8.4
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 7/63 (11%)
Query: 52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY---NETVRLSEGL 108
+ P+GSGK+ + + L G R +++ P E + E + L G
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLA----RGGRVIVIDPKGEYSGLARALGGEVIDLGPGS 59
Query: 109 GLR 111
G+
Sbjct: 60 GIS 62
>gnl|CDD|203575 pfam07081, DUF1349, Protein of unknown function (DUF1349). This
family consists of several hypothetical bacterial
proteins but contains one sequence from Saccharomyces
cerevisiae. Members of this family are typically around
200 residues in length. The function of this family is
unknown.
Length = 182
Score = 26.8 bits (60), Expect = 8.6
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 52 IFACAPTGSGKTAAF 66
AC+P GSG T F
Sbjct: 155 FMACSPEGSGFTVRF 169
>gnl|CDD|206379 pfam14211, DUF4323, Domain of unknown function (DUF4323). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
eukaryotes. Proteins in this family are typically
between 85 and 171 amino acids in length.
Length = 126
Score = 26.3 bits (58), Expect = 9.1
Identities = 8/31 (25%), Positives = 11/31 (35%)
Query: 46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRG 76
L R F CA + + HS +G
Sbjct: 46 LALFRLAFRCASMHRLTSPRASNSLAHSTKG 76
>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 = 9.2
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 11/45 (24%)
Query: 58 TGSGKTA--AFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
TGSGKT A +I + +++ + LA Q YNE
Sbjct: 38 TGSGKTFTMANVI---------AQVNRPTLVIAHNKTLAAQLYNE 73
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 27.0 bits (60), Expect = 9.8
Identities = 9/33 (27%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 32 IFKHFEPHFTITYLSPLGRQIFA-CAPTGSGKT 63
K+F I IF P G+GK+
Sbjct: 7 RLKNFRSFKDIDIEKLFDSGIFLIVGPNGAGKS 39
>gnl|CDD|226775 COG4325, COG4325, Predicted membrane protein [Function unknown].
Length = 464
Score = 27.1 bits (60), Expect = 9.9
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 15/70 (21%)
Query: 11 IFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQ----IFACAPTGSGKTAAF 66
I G V SI V L + S+ F P T+L + Q IF C T +
Sbjct: 91 ISVTGIVFSITVVALQLASSQ----FSPRLLRTFLRDVPNQVVLAIFLC-------TFVY 139
Query: 67 LIPIIHSLRG 76
+ ++ ++
Sbjct: 140 SLGVLRTVGE 149
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
0.325 0.140 0.415
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: 11,633,826
Number of extensions: 1112928
Number of successful extensions: 2144
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2080
Number of HSP's successfully gapped: 114
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.9 bits)