RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9740
(189 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 = 97.9 bits (245), Expect = 8e-26
Identities = 37/76 (48%), Positives = 54/76 (71%), Gaps = 4/76 (5%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ATPGRL D L+ L+++K+LVLDEADR+L F++Q+R I +PK +QTLLFS
Sbjct: 123 VVATPGRLLDLLER-GKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLFS 181
Query: 61 ATMTDTLEQVKSITKK 76
ATM ++V+ + +K
Sbjct: 182 ATMP---KEVRDLARK 194
>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 = 93.3 bits (232), Expect = 2e-22
Identities = 47/154 (30%), Positives = 77/154 (50%), Gaps = 12/154 (7%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ATPGRL D + L+ ++ LVLDEADR+L F + + I A+P +QTLLFS
Sbjct: 154 VVATPGRLLDLIKR-GKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFS 212
Query: 61 ATMTDTLEQV-KSITKKQVGTLLFSATMTDTLEQVKSITKKQVGTMKKKSSYQAFLLCQQ 119
ATM D + ++ + V + + TL+++K + V + ++K LL +
Sbjct: 213 ATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLE-VESEEEKLELLLKLL-KD 270
Query: 120 HIVAQIITQLDPVHVFVWESKQDVATVEELDQYY 153
++I VFV +K+ V + E +
Sbjct: 271 EDEGRVI-------VFV-RTKRLVEELAESLRKR 296
>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 = 80.8 bits (200), Expect = 1e-19
Identities = 29/70 (41%), Positives = 38/70 (54%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
++ TPGRL D L L +K LVLDEA RLL F + + I +P +Q LL S
Sbjct: 100 LVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLS 159
Query: 61 ATMTDTLEQV 70
AT+ LE +
Sbjct: 160 ATLPRNLEDL 169
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 81.4 bits (202), Expect = 2e-18
Identities = 29/70 (41%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
++ TPGR+ DHL T L+ + LVLDEADR+L F + + I P ++QTLLFS
Sbjct: 127 IVGTPGRILDHLRK-GTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFS 185
Query: 61 ATMTDTLEQV 70
AT + + +
Sbjct: 186 ATYPEGIAAI 195
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 71.4 bits (175), Expect = 8e-15
Identities = 35/76 (46%), Positives = 47/76 (61%), Gaps = 4/76 (5%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ TPGRL DHL T L+++ LVLDEAD +L F E + TI +P+ QT LFS
Sbjct: 129 VVGTPGRLLDHLKR-GTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFS 187
Query: 61 ATMTDTLEQVKSITKK 76
ATM E ++ IT++
Sbjct: 188 ATMP---EAIRRITRR 200
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 69.1 bits (169), Expect = 9e-15
Identities = 31/94 (32%), Positives = 50/94 (53%), Gaps = 1/94 (1%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
++ TPGRL D L+ + SL+ + ++LDEA RLL G F +Q+ + +PK Q LL S
Sbjct: 109 LVTTPGRLLDLLEN-DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLS 167
Query: 61 ATMTDTLEQVKSITKKQVGTLLFSATMTDTLEQV 94
AT + +E + + + T + +EQ
Sbjct: 168 ATPPEEIENLLELFLNDPVFIDVGFTPLEPIEQF 201
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 67.5 bits (165), Expect = 2e-13
Identities = 32/76 (42%), Positives = 50/76 (65%), Gaps = 4/76 (5%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
++ATPGRL D L+ N L++++ LVLDEADR+L F +R + +P ++Q LLFS
Sbjct: 129 LVATPGRLLD-LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFS 187
Query: 61 ATMTDTLEQVKSITKK 76
AT +D +K++ +K
Sbjct: 188 ATFSD---DIKALAEK 200
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 66.3 bits (162), Expect = 5e-13
Identities = 30/61 (49%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 2 IATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFSA 61
IA PGRL D L++ N +L R+ +LVLDEADR+L F+ Q+R I + +QTL++SA
Sbjct: 258 IACPGRLIDFLES-NVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSA 316
Query: 62 T 62
T
Sbjct: 317 T 317
>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 = 61.6 bits (150), Expect = 1e-12
Identities = 28/63 (44%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ TPGRL D L+ SL ++ L+LDEA RLL+ F I +PK +Q LL S
Sbjct: 83 VVGTPGRLLDELER-LKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLS 141
Query: 61 ATM 63
AT
Sbjct: 142 ATP 144
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 60.7 bits (148), Expect = 3e-11
Identities = 29/63 (46%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ATPGRL ++ N F ++ L+LDEADR+L F + + TI +KQTLLFS
Sbjct: 127 VVATPGRLLQYIKEEN-FDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLFS 185
Query: 61 ATM 63
AT+
Sbjct: 186 ATL 188
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 59.2 bits (143), Expect = 1e-10
Identities = 31/67 (46%), Positives = 43/67 (64%), Gaps = 3/67 (4%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPK--QKQTLL 58
++ATPGRL D + L+ ++ +VLDEADR+L F Q+R I P+ ++QTLL
Sbjct: 217 LVATPGRLLD-FNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLL 275
Query: 59 FSATMTD 65
FSAT TD
Sbjct: 276 FSATFTD 282
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 56.9 bits (137), Expect = 8e-10
Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQ--KQTLL 58
+IATPGRL D++ SL+ + VLDEADR+ F + +R + +P++ +QTLL
Sbjct: 138 IIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLL 197
Query: 59 FSATMT 64
FSAT++
Sbjct: 198 FSATLS 203
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 55.6 bits (134), Expect = 2e-09
Identities = 31/78 (39%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
++ TPGRL D L + + L+ + LVLDE D +L F +Q+ IF A+ Q Q LLFS
Sbjct: 250 IVGTPGRLIDLL-SKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFS 307
Query: 61 ATMTDTLEQVKSITKKQV 78
AT++ +E+ S K +
Sbjct: 308 ATVSPEVEKFASSLAKDI 325
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 55.2 bits (133), Expect = 2e-09
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFS 60
V+ TPGR+ D +D ++ +K +LDEAD +LS F Q+ +F +P Q LFS
Sbjct: 150 VVGTPGRVYDMIDK-RHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFS 208
Query: 61 ATMTD 65
ATM +
Sbjct: 209 ATMPN 213
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 48.0 bits (115), Expect = 6e-07
Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 1 VIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLLSGIFDEQMRTIFGAVP--KQKQTLL 58
+I T GRL D+ N +L I+ +VLDEADR+ F + +R +F +P Q+ +L
Sbjct: 137 LIGTTGRLIDYAKQ-NHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQRLNML 195
Query: 59 FSATMT 64
FSAT++
Sbjct: 196 FSATLS 201
>gnl|CDD|235883 PRK06901, PRK06901, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 322
Score = 30.5 bits (69), Expect = 0.45
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 33 RLLSGI-FDE-QMRTIFGAVPKQKQTLLFSATMTDTLEQVKSITKKQVGTLLF 83
RLL+GI DE + R F P Q + Q++++T + +F
Sbjct: 176 RLLNGIPLDEEEQRLAFDVFPANAQN--LELQLQKIFPQLENVTFHSIQVPVF 226
>gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional.
Length = 216
Score = 29.6 bits (67), Expect = 0.72
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 122 VAQIITQLDPVHVFVWES---KQDVATVEELDQYYVLCPYDVKDGYLVETVRLYREKSPR 178
V Q+I + P V E+ +Q + E LD +L ++ +ET+ REKS
Sbjct: 22 VKQLI-SMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLS 80
Query: 179 GAIVIFT 185
G IV+F+
Sbjct: 81 GRIVVFS 87
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.6 bits (67), Expect = 0.90
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 5 PGRLADHLDTCNTFSLNRIKFLVLDEADRLL 35
PG A +DT + R K L +D D LL
Sbjct: 87 PGGKAAFIDTEHALDPERAKQLGVDLLDNLL 117
>gnl|CDD|218749 pfam05788, Orbi_VP1, Orbivirus RNA-dependent RNA polymerase (VP1).
This family consists of the RNA-dependent RNA polymerase
protein VP1 from the Orbiviruses. VP1 may have both
enzymatic and structural roles in the virus life cycle.
Length = 1301
Score = 29.4 bits (66), Expect = 1.5
Identities = 32/112 (28%), Positives = 48/112 (42%), Gaps = 14/112 (12%)
Query: 38 IFDEQMRTIFGAVPK-------QKQTLL-FSATMTDTLEQVKSITKKQVGTLLFSATMTD 89
FD+ + TIF + K K T+L FS T T + + + Q + S+
Sbjct: 777 KFDKIITTIFDTIAKCGHEASPSKTTILPFSVEKTQTHAK-QGVYIPQDRMMFISSERRK 835
Query: 90 TLEQVKSITKKQVGTMKKKSSYQAFLLCQQHIVAQIITQLDPVHVFVWESKQ 141
+E VK + QV T K S + F H +AQII L + V + K+
Sbjct: 836 DIEDVKGYMRSQVQTFVTKCS-RGF----SHELAQIILMLKTIFVGYRKLKR 882
>gnl|CDD|223391 COG0314, MoaE, Molybdopterin converting factor, large subunit
[Coenzyme metabolism].
Length = 149
Score = 27.6 bits (62), Expect = 2.9
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 165 LVETVRLYREKSPRGAIVIFTDTCR 189
+ E + E S GAIV F R
Sbjct: 15 VEELIEALSEPSEAGAIVTFVGIVR 39
>gnl|CDD|113196 pfam04415, DUF515, Protein of unknown function (DUF515). Family of
hypothetical Archaeal proteins.
Length = 416
Score = 28.0 bits (62), Expect = 3.0
Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 8/111 (7%)
Query: 53 QKQTLLFSATMTDTLEQVKSITKKQVGTLLFSATMTDTLEQVKSITKKQVGTMKKKSSYQ 112
QKQ + + +E++ SI + L A L+Q K+ Q K ++
Sbjct: 86 QKQAYINKIQAANNIEEINSIDVVGICEQLEEAKKYKELKQYKNQAINQ-----IKDAFG 140
Query: 113 AFLLCQ--QHIVAQIITQLDPVHVFVWESKQDVATVEELDQYYVLCPYDVK 161
L + +I L+ + V +S + + V E+ L
Sbjct: 141 PLLSLSLPDELKRKITATLNSLLKQV-DSAKTIDEVLEISPDKYLLSLWKY 190
>gnl|CDD|163452 TIGR03740, galliderm_ABC, gallidermin-class lantibiotic protection
ABC transporter, ATP-binding subunit. Model TIGR03731
represents the family of all lantibiotics related to
gallidermin, including epidermin, mutatin, and nisin.
This protein family describes the ATP-binding subunit of
a gallidermin/epidermin class lantibiotic protection
transporter. It is largely restricted to
gallidermin-family lantibiotic biosynthesis and export
cassettes, but also occurs in orphan transporter
cassettes in species that lack candidate lantibiotic
precursor and synthetase genes.
Length = 223
Score = 27.0 bits (60), Expect = 5.0
Identities = 15/51 (29%), Positives = 29/51 (56%)
Query: 20 LNRIKFLVLDEADRLLSGIFDEQMRTIFGAVPKQKQTLLFSATMTDTLEQV 70
LN K L+LDE L I +++R + + P+Q T++ S+ + ++Q+
Sbjct: 140 LNHPKLLILDEPTNGLDPIGIQELRELIRSFPEQGITVILSSHILSEVQQL 190
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
0.322 0.135 0.383
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,341,024
Number of extensions: 836222
Number of successful extensions: 745
Number of sequences better than 10.0: 1
Number of HSP's gapped: 726
Number of HSP's successfully gapped: 34
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.3 bits)