RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4698
(258 letters)
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 357 bits (917), Expect = e-123
Identities = 152/232 (65%), Positives = 188/232 (81%)
Query: 27 NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
N +A G IE+N+D + ++FD ++L+E+LLRGIY+YGFEKPSAIQQR I P + G D
Sbjct: 8 NQSEQVASTGTIESNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYD 67
Query: 87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
I QAQSGTGKTATF I+ LQ +D ++ CQALILAPTRELAQQIQKVV+ALGD++ V C
Sbjct: 68 TIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRC 127
Query: 147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF 206
HAC+GGT+VRDDI KL+AG +VVGTPGRV+DMI + L +++F+LDEADEMLSRGF
Sbjct: 128 HACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGF 187
Query: 207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
K QIYDVFK L DVQV L SATMP ++L+++ KFMRDP +ILVKK+ELTLE
Sbjct: 188 KGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLE 239
>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 = 304 bits (782), Expect = e-106
Identities = 105/203 (51%), Positives = 138/203 (67%), Gaps = 2/203 (0%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
F+++ LS ELLRGIYA GFEKP+ IQ RAI P + G DVI QAQ+G+GKTA F I IL++
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 109 VD--QNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
+D QALILAPTRELA QI +V LG ++ GGT + IRKL+ G
Sbjct: 61 LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120
Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
+VV TPGR+ D++ RG L +++ VLDEAD ML GF+DQI ++ K L D Q +L
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLF 180
Query: 227 SATMPADVLDVSMKFMRDPIKIL 249
SATMP +V D++ KF+R+P++IL
Sbjct: 181 SATMPKEVRDLARKFLRNPVRIL 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 = 250 bits (639), Expect = 3e-80
Identities = 91/223 (40%), Positives = 128/223 (57%), Gaps = 3/223 (1%)
Query: 38 IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
+ + F + LS ELL+ + GFE+P+ IQ AI + G DV+ QAQ+GTGK
Sbjct: 20 LSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGK 79
Query: 98 TATFSISILQQVDQ--NIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTI 154
TA F + +LQ++ + K ALILAPTRELA QI + + LG + + GG
Sbjct: 80 TAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139
Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
+R I L+ G +VV TPGR+ D+I RG L + VLDEAD ML GF D I +
Sbjct: 140 IRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKIL 199
Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTL 257
K L D Q +L SATMP D+ +++ +++ DP++I V E+L
Sbjct: 200 KALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLER 242
>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 = 182 bits (465), Expect = 2e-58
Identities = 68/169 (40%), Positives = 105/169 (62%), Gaps = 2/169 (1%)
Query: 71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ 130
+ IQ +AI + G DV+ QA +G+GKT F + ILQ + QAL+LAPTRELA+Q
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60
Query: 131 IQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQ 189
I + + L + + GGT +++ RKL+ G A ++VGTPGR+ D++ RG L +
Sbjct: 61 IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120
Query: 190 -IRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV 237
+++ VLDEA +L GF D + ++ L D Q++LLSAT+P ++ D+
Sbjct: 121 NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 172 bits (437), Expect = 9e-54
Identities = 70/196 (35%), Positives = 109/196 (55%), Gaps = 3/196 (1%)
Query: 62 IYAYGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALI 120
I +GFE Q+ AI + G DVI A +G+GKT + L+ + + K + L+
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLV 59
Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDM 179
L PTRELA+Q + + LG + + GG R+ +RKLE+G ++V TPGR+ D+
Sbjct: 60 LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119
Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
+ LS + + +LDEA +L GF DQ+ + K L +VQ++LLSAT P ++ ++
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179
Query: 240 KFMRDPIKILVKKEEL 255
F+ DP+ I V L
Sbjct: 180 LFLNDPVFIDVGFTPL 195
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 166 bits (424), Expect = 7e-49
Identities = 78/207 (37%), Positives = 115/207 (55%), Gaps = 9/207 (4%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
F + L LL + G+ + + IQ +++ + G DVIAQA++G+GKTA F + +LQ+
Sbjct: 6 FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-----VSCHACIGGTIVRDDIRKLE 163
+D QAL+L PTRELA Q+ K + L F+ C GG + I LE
Sbjct: 66 LDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLC----GGVPMGPQIDSLE 121
Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
GA ++VGTPGR+ D + +G L + VLDEAD ML GF+D I + + Q
Sbjct: 122 HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQT 181
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV 250
+L SAT P + +S +F RDP+++ V
Sbjct: 182 LLFSATYPEGIAAISQRFQRDPVEVKV 208
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 160 bits (406), Expect = 3e-45
Identities = 81/201 (40%), Positives = 114/201 (56%), Gaps = 7/201 (3%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
F D+ L +L + G+EKPS IQ I + G DV+ AQ+G+GKTA FS+ +L
Sbjct: 8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFM----SVSCHACIGGTIVRDDIRKLEA 164
+D +K Q L+LAPTRELA Q+ + A+ DF V+ A GG +R L
Sbjct: 68 LDPELKAPQILVLAPTRELAVQVAE---AMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ 124
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
G Q+VVGTPGR+ D + RG L ++ VLDEADEML GF + + + + Q
Sbjct: 125 GPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTA 184
Query: 225 LLSATMPADVLDVSMKFMRDP 245
L SATMP + ++ +FM++P
Sbjct: 185 LFSATMPEAIRRITRRFMKEP 205
>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 = 144 bits (364), Expect = 1e-43
Identities = 56/146 (38%), Positives = 82/146 (56%), Gaps = 2/146 (1%)
Query: 85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV 144
DV+ A +G+GKT + IL+ +D K Q L+LAPTRELA Q+ + + L +
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GI 58
Query: 145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
IGGT ++ + L +VVGTPGR+ D + R LS K++ + +LDEA +L++
Sbjct: 59 KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQ 118
Query: 205 GFKDQIYDVFKHLNNDVQVILLSATM 230
GF + L D QV+LLSAT
Sbjct: 119 GFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 142 bits (360), Expect = 1e-39
Identities = 77/209 (36%), Positives = 118/209 (56%), Gaps = 6/209 (2%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
+FD + LS ++LR + G+ +P+ IQQ+AI + G D++A AQ+GTGKTA F++ +LQ
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 108 QVDQNI------KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
+ + +ALIL PTRELA QI + V ++++ GG + + K
Sbjct: 62 HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121
Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV 221
L G V+V TPGR+ D+ + A+ Q+ + VLDEAD ML GF I V L
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR 181
Query: 222 QVILLSATMPADVLDVSMKFMRDPIKILV 250
Q +L SAT D+ ++ K + +P++I V
Sbjct: 182 QNLLFSATFSDDIKALAEKLLHNPLEIEV 210
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 135 bits (342), Expect = 4e-37
Identities = 76/218 (34%), Positives = 119/218 (54%), Gaps = 10/218 (4%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
F D L+ EL+ I+ GF + IQ + + + G+D I +AQ+GTGKTA F ISI+ Q
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 109 VDQN-------IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
+ Q + E +ALI+APTREL QI K AL + ++ +GG +++
Sbjct: 149 LLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQ 208
Query: 162 LEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL--N 218
LEA ++V TPGR+ D RG + + + VLDEAD ML GF Q+ + +
Sbjct: 209 LEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRK 268
Query: 219 NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
+ Q +L SAT DV++++ ++ DP + ++ E +
Sbjct: 269 EERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVA 306
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 127 bits (321), Expect = 8e-34
Identities = 66/207 (31%), Positives = 113/207 (54%), Gaps = 8/207 (3%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
F L +LL + G+E P+ IQ +AI + G ++ A +G+GKTA+F + I+ +
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182
Query: 109 V----DQNIKECQ---ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
+ E + A++L PTREL Q++ LG + +GG + + +
Sbjct: 183 CCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYR 242
Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV 221
++ G +++VGTPGR+ D++S+ + + + VLDE D ML RGF+DQ+ +F+ L+
Sbjct: 243 IQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQP- 301
Query: 222 QVILLSATMPADVLDVSMKFMRDPIKI 248
QV+L SAT+ +V + +D I I
Sbjct: 302 QVLLFSATVSPEVEKFASSLAKDIILI 328
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 120 bits (304), Expect = 8e-32
Identities = 68/206 (33%), Positives = 96/206 (46%), Gaps = 5/206 (2%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
F ++EL E LL + G+ +P+AIQ AI P + G DV+ A +GTGKTA F + LQ
Sbjct: 2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61
Query: 108 QVDQ--NIKECQA--LILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE 163
+ K LIL PTRELA Q+ L + GG +
Sbjct: 62 HLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS 121
Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
+VV TPGR+ I + + +LDEAD ML GF I + Q
Sbjct: 122 ENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQT 181
Query: 224 ILLSATMPAD-VLDVSMKFMRDPIKI 248
+L SAT+ D V D + + + DP+++
Sbjct: 182 LLFSATLEGDAVQDFAERLLNDPVEV 207
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 113 bits (286), Expect = 3e-29
Identities = 73/229 (31%), Positives = 111/229 (48%), Gaps = 20/229 (8%)
Query: 43 DHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--- 98
H+ E F D L +++ + GF + IQ A+ + G DV QAQ+GTGKT
Sbjct: 3 THLTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAF 62
Query: 99 --ATFSISILQQVDQNIKECQ--ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
ATF + ++ K Q ALI+APTRELA QI L + GG
Sbjct: 63 LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDG 122
Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
++ LE+G +++GT GR+ D + ++ I++ VLDEAD M GF I +F
Sbjct: 123 YDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLF 182
Query: 215 -------KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
+ LN +L SAT+ V +++ + M +P + V+ E+ T
Sbjct: 183 RRMPPANQRLN-----MLFSATLSYRVRELAFEHMNNPEYVEVEPEQKT 226
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 115 bits (288), Expect = 3e-29
Identities = 73/220 (33%), Positives = 118/220 (53%), Gaps = 12/220 (5%)
Query: 48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
F +L LL G+ + GF + + IQ + + G DV QAQ+GTGKT F ++++
Sbjct: 10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69
Query: 108 Q-------VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
+ D+ ++ +ALILAPTRELA QI K + G + + A + G + D R
Sbjct: 70 RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLR-FALVYGGVDYDKQR 128
Query: 161 K-LEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL- 217
+ L+ G V++ TPGR+ D + + +S + VLDEAD M GF I + + +
Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188
Query: 218 -NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
Q +L SAT+ VL+++ + M +P K++V+ E +T
Sbjct: 189 ERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETIT 228
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 111 bits (279), Expect = 6e-28
Identities = 65/220 (29%), Positives = 108/220 (49%), Gaps = 14/220 (6%)
Query: 47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF----S 102
+F+ + +L+ + GF +P+ IQ + + G D+I A++G+GKT F
Sbjct: 130 VSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAI 189
Query: 103 ISILQQV-----DQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
+ I Q D I L+LAPTRELA+QI++ G + GG R
Sbjct: 190 VHINAQPLLRYGDGPI----VLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRG 245
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
I L G ++++ PGR+ D + + +++ VLDEAD ML GF+ QI + +
Sbjct: 246 QIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQI 305
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRD-PIKILVKKEELT 256
D Q ++ SAT P +V ++ ++ P+ + V +LT
Sbjct: 306 RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLT 345
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 51.6 bits (124), Expect = 2e-07
Identities = 41/185 (22%), Positives = 80/185 (43%), Gaps = 39/185 (21%)
Query: 74 QQRAIIPCV-RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ 132
QQ A+ + +V+ A +G+GKT ++IL + + + + + P + LA++
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV--VYIVPLKALAEEKY 93
Query: 133 -----------KVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS 181
+V I+ GD+ D + A V+V TP ++ +
Sbjct: 94 EEFSRLEELGIRVGISTGDY---------------DLDDERLARYDVIVTTPEKLDSLTR 138
Query: 182 RGALSTKQIRMFVLDEADEMLS---RG-FKDQIYDVFKHLNNDVQVILLSATMP-----A 232
+ +++ + V+DE +L RG + I + LN ++++ LSAT+P A
Sbjct: 139 KRPSWIEEVDLVVIDEI-HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEEVA 197
Query: 233 DVLDV 237
D L+
Sbjct: 198 DWLNA 202
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 38.2 bits (89), Expect = 0.003
Identities = 35/166 (21%), Positives = 66/166 (39%), Gaps = 29/166 (17%)
Query: 84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ-QIQKVVIALGDF- 141
G +V+ +G+GKT +F + IL + ++ +AL+L PT LA Q +++ + D
Sbjct: 85 GRNVVVTTGTGSGKTESFLLPILDHLLRD-PSARALLLYPTNALANDQAERLRELISDLP 143
Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALS--------TKQIRMF 193
V+ G T + + +++ P DM+ L + ++
Sbjct: 144 GKVTFGRYTGDTPPEERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKYL 199
Query: 194 VLDEAD----------EMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
V+DE +L R + + +Q+I SAT
Sbjct: 200 VVDELHTYRGVQGSEVALLLRRLL----RRLRRYGSPLQIICTSAT 241
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 36.9 bits (86), Expect = 0.007
Identities = 27/120 (22%), Positives = 48/120 (40%), Gaps = 8/120 (6%)
Query: 81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD 140
+ N ++ +G GKT ++ I ++ + L LAPT+ L Q +
Sbjct: 27 ALFKNTLVV-LPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAE---FCRK 80
Query: 141 FMSVSCHACIGGT-IVRDDIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEA 198
+ T VR + R+ A +V V TP V + + G + + + + DEA
Sbjct: 81 VTGIPEDEIAALTGEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEA 140
>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 = 36.6 bits (85), Expect = 0.011
Identities = 36/152 (23%), Positives = 62/152 (40%), Gaps = 17/152 (11%)
Query: 56 EELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKE 115
+++ + A G +P Q RA G V+ + +GK+ + + +L + + +
Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRA 82
Query: 116 CQALILAPTRELAQQIQKVVIALG-DFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPG 174
AL LAPT+ LA + V L + + + T R R A+ V+ P
Sbjct: 83 T-ALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWAR---EHARYVLTNP- 137
Query: 175 RVFDMISRGALSTKQ--------IRMFVLDEA 198
DM+ RG L + +R V+DE
Sbjct: 138 ---DMLHRGILPSHARWARFLRRLRYVVIDEC 166
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 35.9 bits (83), Expect = 0.018
Identities = 31/155 (20%), Positives = 55/155 (35%), Gaps = 30/155 (19%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ---KVVIALG 139
+ +G GKT + ++ ++ L+L PT+EL Q K + L
Sbjct: 54 TERRGVIVLPTGAGKTVVA-AEAIAELKRST-----LVLVPTKELLDQWAEALKKFLLLN 107
Query: 140 DFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF---VLD 196
D + + GG K A+V V T V + R L F + D
Sbjct: 108 DEIGI-----YGGG------EKELEPAKVTVAT---VQTLARRQLLDEFLGNEFGLIIFD 153
Query: 197 EADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
E + + ++ + + L+ + L+AT
Sbjct: 154 EVHHLPAPSYR----RILELLSAAYPRLGLTATPE 184
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 35.4 bits (82), Expect = 0.028
Identities = 53/198 (26%), Positives = 87/198 (43%), Gaps = 27/198 (13%)
Query: 41 NWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT-- 98
++D V D E +L Y FE QQ AI RG V+ A + +GKT
Sbjct: 96 DYDMV----PDAESPFDLAPPAREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVV 150
Query: 99 ATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL-GDFMSVSCHACIGGTIVRD 157
A ++I++ + Q + + +P + L+ Q + ++A GD A + G + D
Sbjct: 151 AEYAIALALRDGQ-----RVIYTSPIKALSNQKYRDLLAKFGD------VADMVGLMTGD 199
Query: 158 -DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM--LSRGFKDQIYDVF 214
I A +V T + +M+ RG+ S + I V DE + RG + +V
Sbjct: 200 VSI---NPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWE--EVI 254
Query: 215 KHLNNDVQVILLSATMPA 232
L + V+ + LSAT+P
Sbjct: 255 ILLPDHVRFVFLSATVPN 272
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 35.4 bits (82), Expect = 0.028
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 90 QAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI-QKVVIALGDFMSVSCHA 148
+AQ+G GKT + + +L Q DQ Q ++ PT+ L QI + V A+ + + CH+
Sbjct: 270 EAQTGIGKTYGYLLPLLAQSDQ----RQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCHS 325
Query: 149 CIG 151
G
Sbjct: 326 LKG 328
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 32.6 bits (75), Expect = 0.050
Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK 133
Q+ AI + + +G+GKT T + +++ ++ + K+ L + P ++L +Q
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLT-AAALIARLAKGKKK--VLFVVPRKDLLEQ-AL 63
Query: 134 VVI 136
V+I
Sbjct: 64 VII 66
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 31.6 bits (72), Expect = 0.063
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 76 RAIIPCVRGNDV-IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV 134
A+ G + + GTGKTAT + +I+ ++ + L++APT A+++++
Sbjct: 1 EAVEAAASGRSLFVVDGGPGTGKTAT-AAAIIARLLAAGRSV--LVVAPTGRAARRLRER 57
Query: 135 VIALGDFMSVSCHA 148
+ AL + + HA
Sbjct: 58 LAALDLADASTLHA 71
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 31.9 bits (73), Expect = 0.13
Identities = 27/134 (20%), Positives = 48/134 (35%), Gaps = 31/134 (23%)
Query: 92 QSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIG 151
+SG+GKT R LA+Q+ + V +
Sbjct: 12 ESGSGKTTL-----------------------LRRLARQLPNRRVVY-----VEAPSLGT 43
Query: 152 GTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY 211
+ I + G + GT + + I AL + + ++DEA LS +++
Sbjct: 44 PKDLLRKILR-ALGLPLSGGTTAELLEAILD-ALKRRGRPLLIIDEAQ-HLSLEALEELR 100
Query: 212 DVFKHLNNDVQVIL 225
D++ +QVIL
Sbjct: 101 DLYDLSEKGIQVIL 114
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 32.7 bits (75), Expect = 0.18
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 17/72 (23%)
Query: 69 KPSAIQQRAI----------IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA 118
K + Q+R + +P R + Q G+GKT ++++L ++ Q
Sbjct: 235 KLTRAQKRVVKEILQDLKSDVPMNR----LLQGDVGSGKTLVAALAMLAAIEAGY---QV 287
Query: 119 LILAPTRELAQQ 130
++APT LA+Q
Sbjct: 288 ALMAPTEILAEQ 299
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 30.8 bits (70), Expect = 0.32
Identities = 35/162 (21%), Positives = 55/162 (33%), Gaps = 62/162 (38%)
Query: 94 GTGKTATFSISILQQVDQNIKE-CQALILAPTR----ELAQQIQKVVI------------ 136
G GKT + + V + I + L+LAPTR E+ + ++ + I
Sbjct: 12 GAGKTRKV---LPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHT 68
Query: 137 --ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV 194
+ D M CHA T + R L P RV + +
Sbjct: 69 GREIVDVM---CHA----TFTQ---RLLS---------PVRV-----------PNYEVII 98
Query: 195 LDEA---DEM--LSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
+DEA D +RG+ + I ++AT P
Sbjct: 99 MDEAHFTDPASIAARGYIST-----LVELGEAAAIFMTATPP 135
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 30.8 bits (70), Expect = 0.49
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 74 QQRAIIPCVRGNDV-IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT 124
Q+ AI + +D+ + Q GTGKT T + I++Q+ N + L+ AP+
Sbjct: 6 QREAIKKALSSSDITLIQGPPGTGKTTT-IVEIIKQLLSNAPGKKVLVCAPS 56
>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 = 31.4 bits (72), Expect = 0.59
Identities = 39/159 (24%), Positives = 68/159 (42%), Gaps = 14/159 (8%)
Query: 83 RGNDVIAQAQSGTGKT-ATF--SISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG 139
G + A +G+GKT A F S+ L ++ K L + P R LA I + + A
Sbjct: 27 EGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALAVDIARNLQAPI 86
Query: 140 DFMSVSCHACI--GGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALST--KQIRMFVL 195
+ + + G T + R+ + +++ TP + ++S + K +R V+
Sbjct: 87 EELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLSYPDAARLFKDLRCVVV 146
Query: 196 DEADEMLS--RGFKDQI---YDVFKHLNNDVQVILLSAT 229
DE E+ RG DQ+ + L ++ LSAT
Sbjct: 147 DEWHELAGSKRG--DQLELALARLRRLAPGLRRWGLSAT 183
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 30.5 bits (69), Expect = 0.67
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 163 EAGAQVVVG--TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
EAGA V++ T ++ ++ + + ++ + D A + G Q + F L D
Sbjct: 32 EAGADVLIAARTESQLDEVAEQIRAAGRRAHVVAADLAHPEATAGLAGQAVEAFGRL--D 89
Query: 221 VQVILLSATMPADVLDVSMKFMRD 244
+ V + TMP +L S K + D
Sbjct: 90 IVVNNVGGTMPNPLLSTSTKDLAD 113
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 30.7 bits (70), Expect = 0.70
Identities = 40/204 (19%), Positives = 84/204 (41%), Gaps = 38/204 (18%)
Query: 51 DMELSEELLRGIYAY-GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQV 109
E ++++L+ ++ Y F QQ I + G D + +G GK+ + I L
Sbjct: 1 MREEAQQVLKQVFGYASFRPG---QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL--- 54
Query: 110 DQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA--- 166
+ E L+++P L + + A G + A + T+ R++ +++
Sbjct: 55 ---LLEGLTLVVSPLISLMKDQVDQLEAAG--IRA---AYLNSTLSREERQQVLNQLKSG 106
Query: 167 --QVVVGTP-----GRVFDMISRGALSTKQIRMFVLDEADEMLSR---GFK---DQIYDV 213
+++ +P R +++ R +S + +DEA +S+ F+ ++ +
Sbjct: 107 QLKLLYISPERLMSPRFLELLKRLPIS-----LVAIDEA-HCISQWGHDFRPDYRRLGRL 160
Query: 214 FKHLNNDVQVILLSATMPADVLDV 237
L N V+ L+AT V D
Sbjct: 161 RAGLPN-PPVLALTATATPRVRDD 183
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 30.6 bits (70), Expect = 0.79
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 27/91 (29%)
Query: 53 ELSEELLRGIYAYGFEKPSAIQQRAI----------IPCVR---GNDVIAQAQSGTGKTA 99
EL + L A F K + Q+R I +P R G DV G+GKT
Sbjct: 250 ELLAKFLA---ALPF-KLTNAQKRVIKEILADLASPVPMNRLLQG-DV------GSGKTV 298
Query: 100 TFSISILQQVDQNIKECQALILAPTRELAQQ 130
+++L ++ QA ++APT LA+Q
Sbjct: 299 VALLAMLAAIEAGY---QAALMAPTEILAEQ 326
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 30.6 bits (70), Expect = 0.83
Identities = 30/112 (26%), Positives = 51/112 (45%), Gaps = 17/112 (15%)
Query: 94 GTGKT--ATFSI-SILQQVDQNIKECQALILAPTRELAQQIQ---KVVIALGDFMSVSCH 147
G GKT A I L + + LILAPT+ L +Q + + + + V
Sbjct: 39 GLGKTAIALLVIAERLHKKGG-----KVLILAPTKPLVEQHAEFFRKFLNIPEEKIVV-- 91
Query: 148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGALSTKQIRMFVLDEA 198
G + + +L A+V+V TP + D+I+ G +S + + + + DEA
Sbjct: 92 --FTGEVSPEKRAELWEKAKVIVATPQVIENDLIA-GRISLEDVSLLIFDEA 140
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 30.1 bits (68), Expect = 1.2
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 6/64 (9%)
Query: 74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL----APTRELAQ 129
Q +AI RG D++ A +G+GKTA I++++ + + + L++ A RE+ +
Sbjct: 6 QWQAIY--TRGQDILVSASAGSGKTAVLVERIIRKITRGVDVDRLLVVTFTNAAAREMKE 63
Query: 130 QIQK 133
+I +
Sbjct: 64 RIAE 67
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.9 bits (68), Expect = 1.7
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 15/70 (21%)
Query: 69 KPSAIQQRAIIPCVRGNDVIAQAQ-----SGTGKTATFSISILQQVDQNIKECQ--ALIL 121
KP+ Q AI V G + + Q +G+GKT T + V I + Q L+L
Sbjct: 12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA-----NV---IAKVQRPTLVL 63
Query: 122 APTRELAQQI 131
A + LA Q+
Sbjct: 64 AHNKTLAAQL 73
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 29.4 bits (66), Expect = 1.9
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 49 FDDMELSEELLRGIYAYGFEKPSAIQQ---RAIIPCV-RGNDVIAQAQSGTGKTATFSIS 104
DD L+ GFE P Q+ A+ + G ++ +A +GTGKT + +
Sbjct: 2 SDDGYLAVAFP------GFE-PRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLP 54
Query: 105 ILQQVDQNIKECQALILAPTRELAQQI 131
L + K+ +I T+ L +Q+
Sbjct: 55 ALAYAREEGKK--VIISTRTKALQEQL 79
>gnl|CDD|222737 pfam14400, Transglut_i_TM, Inactive transglutaminase fused to 7
transmembrane helices. A family of inactive
transglutaminases fused to seven transmembrane helices.
The transglutaminase domain is predicted to be
extracellularly located. Members of this family are
associated in gene neighborhoods with a pepsin-like
peptidase and an ATP-grasp of the RimK-family. The
ATP-grasp is predicted to modify the 7TM protein or a
cofactor that interacts with it.
Length = 164
Score = 28.7 bits (65), Expect = 2.1
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 10 EDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLR 60
+P P E + P ++ P A + L+E A+N + EL++
Sbjct: 97 AEPPAVPPPPEPKAPQWDEPEKTAAEALLEEARSRSADNL---TFARELIK 144
>gnl|CDD|224370 COG1453, COG1453, Predicted oxidoreductases of the aldo/keto
reductase family [General function prediction only].
Length = 391
Score = 29.2 bits (66), Expect = 2.4
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 104 SILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHAC 149
+ +Q+++N+K L + T E Q ++KV + + V C C
Sbjct: 253 NTPEQLEENLKIASELEPSLTEEELQILEKVEEIYRESLKVPCTGC 298
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 29.3 bits (67), Expect = 2.4
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 13/86 (15%)
Query: 94 GTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI-QKVVIALGDF-MSVSCHACIG 151
G+GKT +++ L ++ QA ++APT LA+Q + + L + V A +
Sbjct: 292 GSGKTVVAALAALAAIEAG---YQAALMAPTEILAEQHYENLKKLLEPLGIRV---ALLT 345
Query: 152 GTI---VRDDI-RKLEAG-AQVVVGT 172
G++ R +I + +G A +V+GT
Sbjct: 346 GSLKGKERREILEAIASGEADIVIGT 371
>gnl|CDD|216146 pfam00843, Arena_nucleocap, Arenavirus nucleocapsid protein.
Length = 533
Score = 28.9 bits (65), Expect = 2.9
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 20/61 (32%)
Query: 157 DDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
DDIRKL DM R + +++ +++ +R F+D+++D F H
Sbjct: 454 DDIRKL--------------LDMHGRRDIKLIDVKL----TSEQ--ARKFEDKVWDKFGH 493
Query: 217 L 217
L
Sbjct: 494 L 494
>gnl|CDD|184200 PRK13640, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 282
Score = 28.2 bits (63), Expect = 3.8
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 191 RMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
++ +LDE+ ML K+QI + + L + ++S T
Sbjct: 163 KIIILDESTSMLDPAGKEQILKLIRKLKKKNNLTVISIT 201
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 28.2 bits (64), Expect = 4.0
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 75 QRAI---IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ 129
RAI +P +G + SGTGKT I + ++ E LI RE+A+
Sbjct: 3 IRAIDLLLPIGKGQRIGIFGGSGTGKT-VLLGMIARNAKADVVEVYVLIGERGREVAE 59
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 27.5 bits (61), Expect = 4.8
Identities = 25/150 (16%), Positives = 48/150 (32%), Gaps = 47/150 (31%)
Query: 93 SGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGG 152
GTGKT R +A ++ + F+ ++ + G
Sbjct: 28 PGTGKTTL-----------------------ARAIANELFR---PGAPFLYLNASDLLEG 61
Query: 153 TIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD 212
+V + V + + + +DE D + SRG ++ +
Sbjct: 62 LVVAELFG------------HFLVRLLFELAEKAKPGV--LFIDEIDSL-SRGAQNALLR 106
Query: 213 VFKHLNN------DVQVILLSATMPADVLD 236
V + LN+ +V+VI + LD
Sbjct: 107 VLETLNDLRIDRENVRVIGATNRPLLGDLD 136
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 27.8 bits (62), Expect = 6.3
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 184 ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
AL+ I +LDEA ML + + D+ + + ++ + ++S T
Sbjct: 158 ALNPSVI---ILDEATSMLDPDARQNLLDLVRKVKSEHNITIISIT 200
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 27.0 bits (59), Expect = 6.4
Identities = 25/161 (15%), Positives = 52/161 (32%), Gaps = 23/161 (14%)
Query: 93 SGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGG 152
G+GKT T + ++ +++ + E ++I G S S G
Sbjct: 11 PGSGKT-TLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS-----GE 64
Query: 153 TIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD 212
+R + V+ + D I+ +LD E L ++
Sbjct: 65 LRLRLALALARKLKPDVL-----ILDEITS-----------LLDAEQEALLLLLEELRLL 108
Query: 213 VFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
+ ++ VI L+ D+ ++ D +L+
Sbjct: 109 LLLKSEKNLTVI-LTTNDEKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative,
glycosyltransferase domain. This family consists of the
N-terminal regions, or in some cases the entirety, of
bacterial proteins closely related to plant
sucrose-phosphate synthases (SPS). The C-terminal domain
(TIGR02471), found with most members of this family,
resembles both bona fide plant sucrose-phosphate
phosphatases (SPP) and the SPP-like domain of plant SPS.
At least two members of this family lack the SPP-like
domain, which may have binding or regulatory rather than
enzymatic activity by analogy to plant SPS. This enzyme
produces sucrose 6-phosphate and UDP from UDP-glucose
and D-fructose 6-phosphate, and may be encoded near the
gene for fructokinase.
Length = 439
Score = 27.8 bits (62), Expect = 6.5
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 156 RDDIRKLEAGAQVVVGTPGRVFDMISR 182
RDDIRK+E+ + V+ +V +I R
Sbjct: 289 RDDIRKMESQQREVL---QKVLLLIDR 312
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 27.8 bits (62), Expect = 6.7
Identities = 38/189 (20%), Positives = 67/189 (35%), Gaps = 26/189 (13%)
Query: 83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA-PTRELAQQIQKVVIALGDF 141
R V+ +A +G GKT I L +D+ IK +I P R + + + + +
Sbjct: 213 RSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGL 272
Query: 142 MSVSCHACIGG---------------TIVRDDIRKLEAGAQVVVGT------PGRVFDMI 180
SV + T+ +D K A +VV + F
Sbjct: 273 FSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFE 332
Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATMPADVLDVSM 239
L T + +LDE + + + L V V+L+SAT+P + +
Sbjct: 333 FLALLLTSLV---ILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLK 389
Query: 240 KFMRDPIKI 248
K + ++
Sbjct: 390 KALGKGREV 398
>gnl|CDD|119350 cd02871, GH18_chitinase_D-like, GH18 domain of Chitinase D (ChiD).
ChiD, a chitinase found in Bacillus circulans,
hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine
in chitin and chitodextrins. The domain architecture of
ChiD includes a catalytic glycosyl hydrolase family 18
(GH18) domain, a chitin-binding domain, and a
fibronectin type III domain. The chitin-binding and
fibronectin type III domains are located either
N-terminal or C-terminal to the catalytic domain. This
family includes exochitinase Chi36 from Bacillus cereus.
Length = 312
Score = 27.7 bits (62), Expect = 7.1
Identities = 13/33 (39%), Positives = 15/33 (45%)
Query: 200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA 232
+ML GF D F L D VI L A+ A
Sbjct: 219 DMLLTGFPIAGNDRFPPLPADKVVIGLPASPSA 251
>gnl|CDD|153286 cd07602, BAR_RhoGAP_OPHN1-like, The Bin/Amphiphysin/Rvs (BAR)
domain of Oligophrenin1-like Rho GTPase Activating
Proteins. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. This subfamily is
composed of Rho and Rac GTPase activating proteins
(GAPs) with similarity to oligophrenin1 (OPHN1). Members
contain an N-terminal BAR domain, followed by a
Pleckstrin homology (PH) domain, and a Rho GAP domain.
Some members contain a C-terminal SH3 domain.
Vertebrates harbor at least three Rho GAPs in this
subfamily including OPHN1, GTPase Regulator Associated
with Focal adhesion kinase (GRAF), GRAF2, and an
uncharacterized protein called GAP10-like. OPHN1, GRAF
and GRAF2 show GAP activity towards RhoA and Cdc42. In
addition, OPHN1 is active towards Rac. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions. The BAR domains of OPHN1
and GRAF directly interact with their Rho GAP domains
and inhibit their activity. The autoinhibited proteins
are able to bind membranes and tubulate liposomes,
showing that the membrane-tubulation and GAP-inhibitory
functions of the BAR domains can occur simultaneously.
Length = 207
Score = 27.3 bits (61), Expect = 7.2
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI 159
+ + + IKEC+ LI A T+ L++ + L +F CIG T D+I
Sbjct: 16 KAIKELIKECKNLISA-TKNLSKAQRSFAQTLQNFKFE----CIGETQTDDEI 63
>gnl|CDD|227198 COG4861, COG4861, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 345
Score = 27.6 bits (61), Expect = 7.3
Identities = 13/49 (26%), Positives = 19/49 (38%)
Query: 154 IVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML 202
+V +R++ A A V VGT D + L DE+L
Sbjct: 161 LVDAPLREIAASAGVSVGTAKETMDTLRETGFLEHLGSRRRLVRTDELL 209
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 27.4 bits (61), Expect = 7.6
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 77 AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
A+IP RG + TGKTA +IL Q +N+
Sbjct: 155 ALIPIGRGQRELILGDRQTGKTAIAIDTILNQKGRNV 191
>gnl|CDD|220999 pfam11144, DUF2920, Protein of unknown function (DUF2920). This
bacterial family of proteins has no known function.
Length = 403
Score = 27.6 bits (62), Expect = 8.0
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 12/62 (19%)
Query: 199 DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF-------MRDPIKILVK 251
DE+ K+++YD+ K L D + L+ D + KF M +K L K
Sbjct: 304 DELAPAKDKEELYDILKELGFDATLHLIK-----DESQIDGKFIKNLEHGMGISMKALFK 358
Query: 252 KE 253
KE
Sbjct: 359 KE 360
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the form
of molybdenum cofactor (Moco) which is associated with
the metabolism of nitrogen, carbon and sulfur by redox
active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe and
mog. The mob locus contains mobA and mobB genes. MobB
catalyzes the attachment of the guanine dinucleotide to
molybdopterin.
Length = 159
Score = 26.8 bits (60), Expect = 8.1
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 131 IQKVVIAL-GDFMSVSC--HACIGGTIVR---DDIRKLEAGAQVVVGTPGRVFDMIS--R 182
++K++ AL + V+ H I D R EAGA+ V+ + R + +I R
Sbjct: 18 LEKLIPALSARGLRVAVIKHDHHDFDIDTPGKDSYRHREAGAEEVLVSSPRRWALIRELR 77
Query: 183 GALSTKQIRMFVLDEADEMLSRGFKD 208
+ + L + D +L GFK+
Sbjct: 78 DEPEPDLLLLLRLLDVDLVLVEGFKE 103
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 27.2 bits (61), Expect = 9.8
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 67 FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT 98
F + Q+ AI G +V+ A +G+GKT
Sbjct: 20 FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKT 51
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
0.319 0.135 0.388
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: 13,391,336
Number of extensions: 1307283
Number of successful extensions: 1389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1349
Number of HSP's successfully gapped: 61
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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 (21.7 bits)
S2: 58 (26.3 bits)