RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7789
(197 letters)
>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 = 159 bits (405), Expect = 1e-46
Identities = 63/182 (34%), Positives = 96/182 (52%), Gaps = 4/182 (2%)
Query: 6 ISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLD 65
+ LR + GGV + + ++ +K+G ++VATPGRL+D++ + + L L LD
Sbjct: 122 LGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLD 181
Query: 66 EADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG-- 123
EADRM+DMGF +D+ I RQTLLFSATMP I+ AR L P+ I V
Sbjct: 182 EADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLE 241
Query: 124 AASMNVVQEVEYVK-QEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGKPFF 181
+ Q V+ +E K+ LL+ L+ + V++F K+ V+ + E L +G
Sbjct: 242 RTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVA 301
Query: 182 TL 183
L
Sbjct: 302 AL 303
>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 = 146 bits (371), Expect = 2e-44
Identities = 49/106 (46%), Positives = 73/106 (68%)
Query: 13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
L+ + GG +++ + +K+G H++VATPGRL+D+L++ + L +YL LDEADRM+D
Sbjct: 98 LKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLD 157
Query: 73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITIN 118
MGFE+ +R I RQTLLFSATMPK++++ AR L P+ I
Sbjct: 158 MGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 144 bits (364), Expect = 1e-40
Identities = 71/173 (41%), Positives = 101/173 (58%), Gaps = 7/173 (4%)
Query: 13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
+R +A GGVP + +++G +++A PGRL+D L+ + +L YL LDEADRM+D
Sbjct: 232 IRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLD 291
Query: 73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK--PITINVGRAG-AASMNV 129
MGFE +R I S R RQTL++SAT PK++Q+ AR L K P+ +NVG A N+
Sbjct: 292 MGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARD-LCKEEPVHVNVGSLDLTACHNI 350
Query: 130 VQEVEYVKQEAKIVYLLECLQKTEPP---VLIFAEKKQDVDAIHEYLLLKGKP 179
QEV V++ K L LQ+ +LIF E K+ D + + L L G P
Sbjct: 351 KQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWP 403
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 123 bits (312), Expect = 1e-33
Identities = 52/156 (33%), Positives = 83/156 (53%), Gaps = 4/156 (2%)
Query: 20 GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
GGVPM +D ++ G H++V TPGR++D L K + LD L LDEADRM+DMGF++ +
Sbjct: 109 GGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAI 168
Query: 80 RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY-VKQ 138
I +RQTLLFSAT P+ I ++ P+ + V +++ Y V
Sbjct: 169 DAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLP--AIEQRFYEVSP 226
Query: 139 EAKIVYLLECLQKTEP-PVLIFAEKKQDVDAIHEYL 173
+ ++ L L +P ++F K++ + + L
Sbjct: 227 DERLPALQRLLLHHQPESCVVFCNTKKECQEVADAL 262
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 109 bits (273), Expect = 4e-28
Identities = 53/131 (40%), Positives = 76/131 (58%)
Query: 11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
+ +R+ + GGV +N + ++ G ++VATPGRL+D+ + V LD L LDEADRM
Sbjct: 102 LNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM 161
Query: 71 VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
+DMGF D+R + + +RQ LLFSAT I+ A L P+ I V R AS V
Sbjct: 162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVT 221
Query: 131 QEVEYVKQEAK 141
Q V +V ++ K
Sbjct: 222 QHVHFVDKKRK 232
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 106 bits (267), Expect = 3e-27
Identities = 61/164 (37%), Positives = 87/164 (53%), Gaps = 6/164 (3%)
Query: 19 IGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEE 77
+GG+ ++ L ++ + C ++VATPGRL+D + V LD+ + LDEADRM+DMGF
Sbjct: 197 VGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIP 256
Query: 78 DVRTI--FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY 135
VR I + + +RQTLLFSAT + N A+ P + + AS V Q V
Sbjct: 257 QVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYA 316
Query: 136 VKQEAKIVYLLECLQKTEP--PVLIFAEKKQDVDAIHEYLLLKG 177
V K LL L P V++FA +K +V I E L+ G
Sbjct: 317 VAGSDK-YKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDG 359
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 102 bits (255), Expect = 1e-25
Identities = 64/185 (34%), Positives = 96/185 (51%), Gaps = 8/185 (4%)
Query: 11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
+P +T L +GG M Q L I++G ++V TPGRL+D+L K + LD L LDE D M
Sbjct: 223 LPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCM 282
Query: 71 VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
++ GF + V IF Q Q LLFSAT+ +++ FA S I I++G + V
Sbjct: 283 LERGFRDQVMQIFQAL-SQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVK 341
Query: 131 QEVEYV---KQEAKIVYLLECLQKTEPPVLIFAEKKQDVD----AIHEYLLLKGKPFFTL 183
Q +V +++ K+ +L+ Q +PP ++F + D AI LK
Sbjct: 342 QLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGE 401
Query: 184 KSLKE 188
KS+KE
Sbjct: 402 KSMKE 406
>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 = 95.8 bits (239), Expect = 3e-25
Identities = 38/99 (38%), Positives = 58/99 (58%), Gaps = 2/99 (2%)
Query: 10 PIPLRTCLAIGGVPMNQSLDVIKKG-CHMMVATPGRLMDMLDKKMVSL-DVCRYLCLDEA 67
+ LR L GG + + +KKG ++V TPGRL+D+L + + L + L LDEA
Sbjct: 71 ILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEA 130
Query: 68 DRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNF 106
R++DMGF +D+ I S RQ LL SAT+P+ +++
Sbjct: 131 HRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 96.4 bits (240), Expect = 4e-25
Identities = 37/114 (32%), Positives = 59/114 (51%), Gaps = 1/114 (0%)
Query: 10 PIPLRTCLAIGGVPMNQSLDVIKKGC-HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD 68
+ L+ GG + L ++ G ++V TPGRL+D+L+ +SL + LDEA
Sbjct: 80 SLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAH 139
Query: 69 RMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRA 122
R++D GF + + + Q LL SAT P++I+N L P+ I+VG
Sbjct: 140 RLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFT 193
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 98.1 bits (244), Expect = 6e-24
Identities = 53/144 (36%), Positives = 82/144 (56%), Gaps = 3/144 (2%)
Query: 13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMV 71
LR L GGV ++ +++++G +++ATPGRL+D + + K+VSL C LDEADRM
Sbjct: 113 LRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMF 172
Query: 72 DMGFEEDVRTIFSFF--RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNV 129
D+GF +D+R + RG RQTLLFSAT+ ++ A + +P + V + V
Sbjct: 173 DLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARV 232
Query: 130 VQEVEYVKQEAKIVYLLECLQKTE 153
Q + + E K LL L ++E
Sbjct: 233 RQRIYFPADEEKQTLLLGLLSRSE 256
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 93.5 bits (233), Expect = 1e-22
Identities = 42/102 (41%), Positives = 62/102 (60%), Gaps = 3/102 (2%)
Query: 20 GGVP-MNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEED 78
GGV MN + +V + ++VATPGRL+ + ++ L LDEADRM+DMGF +D
Sbjct: 109 GGVAYMNHA-EVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQD 167
Query: 79 VRTIFSFFRGQRQTLLFSATMP-KKIQNFARSALVKPITINV 119
+ TI + R ++QTLLFSAT+ +Q+FA L P+ +
Sbjct: 168 IETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEA 209
>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 = 76.6 bits (189), Expect = 4e-18
Identities = 30/95 (31%), Positives = 44/95 (46%)
Query: 5 FISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCL 64
++ IGG + Q ++ ++V TPGRL+D L++ +SL L L
Sbjct: 50 LKELFGEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLIL 109
Query: 65 DEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM 99
DEA R+++ GF I RQ LL SAT
Sbjct: 110 DEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 80.7 bits (199), Expect = 5e-18
Identities = 40/95 (42%), Positives = 55/95 (57%)
Query: 20 GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
GG + L +++G ++V TPGRL+D L + + L L LDEAD M+ MGF EDV
Sbjct: 111 GGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDV 170
Query: 80 RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKP 114
TI + QT LFSATMP+ I+ R + +P
Sbjct: 171 ETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEP 205
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 79.6 bits (197), Expect = 9e-18
Identities = 50/166 (30%), Positives = 85/166 (51%), Gaps = 7/166 (4%)
Query: 13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
L+ LA GG ++ L V++ G +++ T GRL+D + ++L + + LDEADRM D
Sbjct: 112 LKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFD 171
Query: 73 MGFEEDVRTIFSFFR----GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMN 128
+GF +D+R + F R QR +LFSAT+ +++ A + P + V
Sbjct: 172 LGFIKDIR--WLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHR 229
Query: 129 VVQEVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYL 173
+ +E+ Y E K+ L +++ P +IFA K + I +L
Sbjct: 230 IKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHL 275
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 79.5 bits (196), Expect = 1e-17
Identities = 37/101 (36%), Positives = 55/101 (54%)
Query: 19 IGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEED 78
+GG + ++ +K G HM+V TPGR+ DM+DK+ + +D + LDEAD M+ GF+
Sbjct: 131 VGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQ 190
Query: 79 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
+ +F Q LFSATMP +I + P I V
Sbjct: 191 IYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILV 231
>gnl|CDD|179606 PRK03606, PRK03606, ureidoglycolate hydrolase; Provisional.
Length = 162
Score = 32.9 bits (76), Expect = 0.048
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 76 EEDVRTIFSFFRGQRQTLLFSATM 99
E R + S FR Q + L M
Sbjct: 49 GEGGRALISIFRAQPRALPLEIRM 72
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 28.7 bits (65), Expect = 1.2
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 128 NVVQEVEYVK--QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKS 185
+ Q V V+ + ++ LL+ K VLIF K+ +D + E L G L
Sbjct: 1 PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 186 -LKEDQNNQTLEN 197
+++ + L++
Sbjct: 61 DGSQEEREEVLKD 73
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C;
Provisional.
Length = 317
Score = 28.2 bits (63), Expect = 3.3
Identities = 19/67 (28%), Positives = 34/67 (50%)
Query: 111 LVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIH 170
L KP V S V++ + ++ EA+ + L+ L + VL+ A+K+ + ++H
Sbjct: 105 LNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLH 164
Query: 171 EYLLLKG 177
E L KG
Sbjct: 165 EQLREKG 171
>gnl|CDD|225482 COG2930, COG2930, Uncharacterized conserved protein [Function
unknown].
Length = 227
Score = 26.8 bits (59), Expect = 6.4
Identities = 8/48 (16%), Positives = 14/48 (29%)
Query: 73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVG 120
S F Q L +P + A+ ++ P + G
Sbjct: 19 ASETNKAAKTNSSFVLTEQRLGPDQVIPPSLLERAKGIVIIPSVLKAG 66
>gnl|CDD|182234 PRK10091, PRK10091, MFS transport protein AraJ; Provisional.
Length = 382
Score = 27.0 bits (60), Expect = 6.9
Identities = 14/48 (29%), Positives = 21/48 (43%)
Query: 83 FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
F F R L+F+ATM FA + +KP + + SM +
Sbjct: 193 FHFLRSPAPWLIFAATMFGNAGVFAWFSYIKPYMMFISGFSETSMTFI 240
>gnl|CDD|225735 COG3194, DAL3, Ureidoglycolate hydrolase [Nucleotide transport
and metabolism].
Length = 168
Score = 26.2 bits (58), Expect = 9.1
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 43 GRLMDMLDKKMVSLD---VCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM 99
G +++ KM ++ RY L + ED RT+ + FR Q + +M
Sbjct: 18 GDVIETDQAKMFHINGGTAERYHDLARVE-----AAGEDARTLINIFRAQPAVHPLTISM 72
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
0.324 0.138 0.399
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,898,792
Number of extensions: 911455
Number of successful extensions: 728
Number of sequences better than 10.0: 1
Number of HSP's gapped: 716
Number of HSP's successfully gapped: 32
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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: 41 (22.0 bits)
S2: 56 (25.3 bits)