RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18035
(104 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 = 102 bits (256), Expect = 1e-28
Identities = 35/78 (44%), Positives = 50/78 (64%)
Query: 16 QQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLS 75
Q + ++LGK T L+ + GG S+D Q +L P IVVATPGR L ++ +L LS
Sbjct: 83 LQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLS 142
Query: 76 SIQYVVFDEADRLFEMGF 93
++Y+V DEADR+ +MGF
Sbjct: 143 KVKYLVLDEADRMLDMGF 160
>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 = 90.2 bits (224), Expect = 1e-22
Identities = 34/86 (39%), Positives = 51/86 (59%), Gaps = 3/86 (3%)
Query: 15 VQQTFKFVKELGKFT-KLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
Q + +++LGK L+ + GG S+ Q L DIVVATPGR L ++ +L
Sbjct: 112 AVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLD 171
Query: 74 LSSIQYVVFDEADRLFEMGF--DVEQ 97
LS ++ +V DEADR+ +MGF D+E+
Sbjct: 172 LSGVETLVLDEADRMLDMGFIDDIEK 197
>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 = 76.9 bits (190), Expect = 3e-19
Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 15 VQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARL-HASPDIVVATPGRFLHIVVEMELK 73
+Q ++ +K+L K L+ L GG S+ Q +L DI+V TPGR L ++ +LK
Sbjct: 58 AEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLK 117
Query: 74 LSS-IQYVVFDEADRLFEMGF 93
L ++ +V DEA RL +MGF
Sbjct: 118 LLKNLKLLVLDEAHRLLDMGF 138
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 70.2 bits (172), Expect = 2e-16
Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMEL 72
+ +Q + +K+LG L+ L GGDS Q +L + DI+V TPGR L ++ +L
Sbjct: 66 LAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKL 125
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
LS++ V+ DEA RL + GF
Sbjct: 126 SLSNVDLVILDEAHRLLDGGF 146
>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 = 67.0 bits (164), Expect = 1e-15
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 13 PIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMEL 72
+ Q + +KEL ++ L+GG S+ Q L DIVV TPGR L + ++L
Sbjct: 41 ELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKL 99
Query: 73 KLSSIQYVVFDEADRLFEMGFDVEQ 97
L + ++ DEA RL GF +
Sbjct: 100 SLKKLDLLILDEAHRLLNQGFGLLG 124
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 67.9 bits (166), Expect = 9e-15
Identities = 27/72 (37%), Positives = 46/72 (63%)
Query: 22 VKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVV 81
V++ K+ ++S + GG S++ Q +L D++VATPGR L + + +KL ++ +V
Sbjct: 95 VRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILV 154
Query: 82 FDEADRLFEMGF 93
DEADR+ +MGF
Sbjct: 155 LDEADRMLDMGF 166
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 67.2 bits (164), Expect = 2e-14
Identities = 33/81 (40%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMEL 72
+V Q K L K+T L +GG D Q +L A DI+VATPGR L E+
Sbjct: 174 LVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEV 233
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
L ++ +V DEADR+ +MGF
Sbjct: 234 HLDMVEVMVLDEADRMLDMGF 254
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 63.1 bits (154), Expect = 4e-13
Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSS 76
Q + L + T L+ GGD D Q L + DI++ T GR + + + L +
Sbjct: 98 QIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGA 157
Query: 77 IQYVVFDEADRLFEMGF 93
IQ VV DEADR+F++GF
Sbjct: 158 IQVVVLDEADRMFDLGF 174
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 61.5 bits (150), Expect = 1e-12
Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 23 KELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVF 82
+EL K T L + GG + N + DIVVATPGR L + E +++ ++
Sbjct: 94 RELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLIL 153
Query: 83 DEADRLFEMGF--DVEQ 97
DEADR+ +MGF D+E
Sbjct: 154 DEADRMLDMGFAQDIET 170
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 56.3 bits (137), Expect = 8e-11
Identities = 24/58 (41%), Positives = 32/58 (55%)
Query: 36 LLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF 93
L GG M Q L I+V TPGR L + + L L ++ +V DEADR+ +MGF
Sbjct: 107 LCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGF 164
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 55.9 bits (135), Expect = 2e-10
Identities = 30/93 (32%), Positives = 45/93 (48%), Gaps = 10/93 (10%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
I +Q KF G +K+++T GG Q L +I++A PGR + +
Sbjct: 219 IREQCNKF----GASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTN 274
Query: 74 LSSIQYVVFDEADRLFEMGFD------VEQQSP 100
L + Y+V DEADR+ +MGF+ V Q P
Sbjct: 275 LRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRP 307
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 55.2 bits (133), Expect = 2e-10
Identities = 29/63 (46%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 36 LLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF-- 93
L GG D Q L P IVV TPGR L + L LS + +V DEAD + MGF
Sbjct: 109 LYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIE 168
Query: 94 DVE 96
DVE
Sbjct: 169 DVE 171
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 50.3 bits (120), Expect = 1e-08
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 5/81 (6%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEME-L 72
I + KF +LG L+ + GG D Q L D+++ATPGR + V + + +
Sbjct: 100 IHKDAVKFGADLG----LRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVV 155
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
L + + V DEADR+F++GF
Sbjct: 156 SLHACEICVLDEADRMFDLGF 176
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 49.8 bits (119), Expect = 2e-08
Identities = 24/83 (28%), Positives = 43/83 (51%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
+ QQ K V LG + K++ +GG + + +L A +VV TPGR ++ + L+
Sbjct: 108 LAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLR 167
Query: 74 LSSIQYVVFDEADRLFEMGFDVE 96
+ ++ + DEAD + GF +
Sbjct: 168 VDDLKLFILDEADEMLSRGFKGQ 190
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 49.4 bits (118), Expect = 3e-08
Identities = 23/71 (32%), Positives = 43/71 (60%)
Query: 23 KELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVF 82
K LGK ++ ++GGD+M Q R+ +++V TPGR + ++ + +++L ++ +V
Sbjct: 217 KVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVL 276
Query: 83 DEADRLFEMGF 93
DE D + E GF
Sbjct: 277 DEVDCMLERGF 287
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 32.7 bits (75), Expect = 0.019
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 13 PIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMEL 72
P+V Q +F +++ + + L G+ + L A + VATP VVE +L
Sbjct: 69 PLVLQHAEFCRKVTGIPEDE-IAALTGEVRPEEREELWAKKKVFVATPQ-----VVENDL 122
Query: 73 K-----LSSIQYVVFDEADR 87
K L + ++FDEA R
Sbjct: 123 KAGRIDLDDVSLLIFDEAHR 142
>gnl|CDD|214959 smart00990, VRR_NUC, This model contains proteins with the VRR-NUC
domain. It is associated with members of the PD-(D/E)XK
nuclease superfamily, which include the type III
restriction modification enzymes, for example StyLTI.
Length = 108
Score = 27.9 bits (62), Expect = 0.52
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 53 PDIVVATPGRFLHIVVEMEL---KLSSIQYVVFDEADRLFEMGFDVE 96
PD+++ P + VE++ +LS +Q DRL +GF VE
Sbjct: 59 PDLILFLPQDGRYRFVEVKGPGDRLSPLQKRWI---DRLAGLGFRVE 102
>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253). This
family represents the C-terminal portion (approximately
500 residues) of several hypothetical eukaryotic
proteins of unknown function.
Length = 436
Score = 28.4 bits (64), Expect = 0.61
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 11/46 (23%)
Query: 54 DIVVATP-GRFLHIVVEMELK-------LSSIQYVVFDEADRLFEM 91
DI++A+P G L +++E E K LSSI+ ++ D+AD + M
Sbjct: 128 DIIIASPLG--LRMIIENEDKKKRDYDFLSSIEVLIVDQAD-VILM 170
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 26.7 bits (59), Expect = 2.4
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 53 PDIVVATPGRFLHIVVEMELKLSSIQY--VVFDEADRLFE 90
D+VV L V E ++ + VVFDEA L +
Sbjct: 195 ADLVVTNHALLLADVALEESRILLPENDVVVFDEAHNLPD 234
>gnl|CDD|183711 PRK12738, kbaY, tagatose-bisphosphate aldolase; Reviewed.
Length = 286
Score = 26.2 bits (57), Expect = 3.2
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 52 SPDIVVATPGRFLHIVVEMELKLSSIQYVVFD 83
SP I+ TPG F HI +E L S ++
Sbjct: 43 SPVILAGTPGTFKHIALEEIYALCSAYSTTYN 74
>gnl|CDD|219965 pfam08676, MutL_C, MutL C terminal dimerisation domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognises mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerisation.
Length = 144
Score = 26.1 bits (58), Expect = 3.4
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 72 LKLSSIQYVVFDE-ADRLFEMGFDVEQQSP 100
L+LS + + +E + L +GF++E+ P
Sbjct: 58 LELSPEEAALLEEHKELLARLGFELEEFGP 87
>gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
Length = 374
Score = 26.1 bits (58), Expect = 3.7
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 1 MGFANINYLISFPIVQQTFKFVKE-LGKFTKLQST 34
+GF NIN + F + QT + KE L K +L
Sbjct: 147 LGFNNINVDLMFGLPNQTLEDWKETLEKVVELNPE 181
>gnl|CDD|238807 cd01573, modD_like, ModD; Quinolinate phosphoribosyl transferase
(QAPRTase or QPRTase) present in some modABC operons in
bacteria, which are involved in molybdate transport. In
general, QPRTases are part of the de novo synthesis
pathway of NAD in both prokaryotes and eukaryotes. They
catalyse the reaction of quinolinic acid (QA) with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to produce nicotinic acid mononucleotide (NAMN),
pyrophosphate and carbon dioxide.
Length = 272
Score = 25.7 bits (57), Expect = 5.0
Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 17/62 (27%)
Query: 36 LLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGFDV 95
LGG ARL A P + IVVE++ +EA E G D+
Sbjct: 164 FLGGPEPLKALARLRA------TAPEK--KIVVEVD---------SLEEALAAAEAGADI 206
Query: 96 EQ 97
Q
Sbjct: 207 LQ 208
>gnl|CDD|237172 PRK12683, PRK12683, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 25.8 bits (57), Expect = 5.0
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 43 DNQFARLHASPDIVV-ATPGRFLHIVVEMELKLSSIQYVVFD----------EADRLFEM 91
D FA PDIV+ A + VE+ + + + + +D + D LFE
Sbjct: 208 DQAFAEAGLVPDIVLTALDADVIKTYVELGMGVGIVAAMAYDPQRDTGLVALDTDHLFEA 267
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 25.7 bits (57), Expect = 5.8
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 53 PDIVVATPGRFLHIVV--EMELKLSSIQYVVFDE 84
P I++ TP ++ + L ++YV+ DE
Sbjct: 124 PHILITTPESLAILLNSPKFRELLRDVRYVIVDE 157
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 24.9 bits (55), Expect = 9.0
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 31 LQSTCLLGGDSMDNQFARLHASP----DIVVATPGRFLHIVVEMELKLSSIQYVVFDEAD 86
+++ L S + + L+ ++ +P R + LK I V DEA
Sbjct: 82 IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAH 141
Query: 87 RLFEMGFD 94
+ + G D
Sbjct: 142 CISQWGHD 149
>gnl|CDD|131210 TIGR02155, PA_CoA_ligase, phenylacetate-CoA ligase.
Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the
first step in aromatic catabolism of phenylacetic acid
(PA) into phenylacetyl-CoA (PA-CoA). Often located in a
conserved gene cluster with enzymes involved in
phenylacetic acid activation (paaG/H/I/J),
phenylacetate-CoA ligase has been found among the
proteobacteria as well as in gram positive prokaryotes.
In the B-subclass proteobacterium Azoarcus evansii,
phenylacetate-CoA ligase has been shown to be induced
under aerobic and anaerobic growth conditions. It
remains unclear however, whether this induction is due
to the same enzyme or to another isoenzyme restricted to
specific anaerobic growth conditions [Energy metabolism,
Other].
Length = 422
Score = 25.2 bits (55), Expect = 9.4
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 53 PDIVVATPGRFLHIVVEMELKL-----SSIQYVVF 82
PDI++ TP L+++ E++ +S+Q +F
Sbjct: 168 PDIIMVTPSYMLNLLEELKRMGIDPAQTSLQVGIF 202
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 0.139 0.405
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,195,420
Number of extensions: 428636
Number of successful extensions: 524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 29
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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: 53 (24.4 bits)