RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13032
(190 letters)
>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 = 128 bits (323), Expect = 1e-36
Identities = 62/159 (38%), Positives = 87/159 (54%), Gaps = 20/159 (12%)
Query: 1 MERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKY---FN 57
E++ P +VV Y G +ER LRQ K L T D VVIT+Y+++ D K N
Sbjct: 67 FEKWAPALRVVVYHGDGRERSKLRQS-MAKRLDTYD----VVITTYEVLRKDKKLLSLLN 121
Query: 58 RIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPIQNSMAE 117
+++W ++LDEA + + +S +K L RNRLLL+GTPIQN++ E
Sbjct: 122 KVEWDRVVLDEAHRL------------KNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEE 169
Query: 118 LWALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDE 156
LWALL+F+ P F S F EWF+ I + A+NK E
Sbjct: 170 LWALLNFLRPGPFGSFKVFEEWFNIPIANTADNKNKNLE 208
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 104 bits (260), Expect = 4e-26
Identities = 49/143 (34%), Positives = 78/143 (54%), Gaps = 18/143 (12%)
Query: 3 RFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIKWQ 62
RF P + V + G+P+ER R+ + F V +TS+++ + + R W+
Sbjct: 240 RFCPVLRAVKFHGNPEERAHQREELLVAG------KFDVCVTSFEMAIKEKTALKRFSWR 293
Query: 63 YLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPIQNSMAELWALL 122
Y+I+DEA I + E S+ K + FS RLL++GTP+QN++ ELWALL
Sbjct: 294 YIIIDEAHRI------------KNENSLLSKTMRLFSTNYRLLITGTPLQNNLHELWALL 341
Query: 123 HFIMPSMFDSHDEFNEWFSKDIE 145
+F++P +F S + F+EWF E
Sbjct: 342 NFLLPEIFSSAETFDEWFQISGE 364
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 88.3 bits (218), Expect = 1e-20
Identities = 51/155 (32%), Positives = 75/155 (48%), Gaps = 20/155 (12%)
Query: 2 ERFVPDFK-VVPYWGSPQERKILRQFW-DMKNLHTKDASFHVVITSYQLVVS---DFKYF 56
E+F PD + V+ Y G E R+ D+ LH F VVIT+Y+L+ D
Sbjct: 410 EKFAPDLRLVLVYHGEKSELDKKREALRDLLKLH-LVIIFDVVITTYELLRRFLVDHGGL 468
Query: 57 NRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPIQNSMA 116
+I+W ++LDEA I + +QS K L NRL L+GTP++N +
Sbjct: 469 KKIEWDRVVLDEAHRI------------KNDQSSEGKALQFLKALNRLDLTGTPLENRLG 516
Query: 117 ELWALL-HFIMPSMFD-SHDEFNEWFSKDIESHAE 149
ELW+LL F+ P + S F F K I++ +
Sbjct: 517 ELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEED 551
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 57.1 bits (138), Expect = 2e-10
Identities = 27/135 (20%), Positives = 49/135 (36%), Gaps = 24/135 (17%)
Query: 1 MERFVPDF--KVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFK--YF 56
+++ P KVV +G +R+ LR+ + +++T+ ++ +
Sbjct: 74 LKKLGPSLGLKVVGLYGGDSKREQLRKL--------ESGKTDILVTTPGRLLDLLENDKL 125
Query: 57 NRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTP---IQN 113
+ +ILDEA ++D + L L LLLS TP I+N
Sbjct: 126 SLSNVDLVILDEAHRLLDGG---------FGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176
Query: 114 SMAELWALLHFIMPS 128
+ FI
Sbjct: 177 LLELFLNDPVFIDVG 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 = 47.7 bits (114), Expect = 2e-07
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 11/74 (14%)
Query: 39 FHVVITSYQLVVSDFK--YFNRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLL 96
+V+ + ++ + + + K LILDEA L + LL
Sbjct: 80 TDIVVGTPGRLLDELERLKLSLKKLDLLILDEAH---------RLLNQGFGLLGLKILLK 130
Query: 97 GFSCRNRLLLSGTP 110
R LLLS TP
Sbjct: 131 LPKDRQVLLLSATP 144
>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 = 29.5 bits (67), Expect = 0.69
Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 16/79 (20%)
Query: 40 HVVITSYQLVVS-----DFKYFNRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKL 94
+++ + ++ K +K L+LDEA L D+ + L
Sbjct: 98 DILVGTPGRLLDLLRRGKLKLLKNLK--LLVLDEAH---------RLLDMGFGDDLEEIL 146
Query: 95 LLGFSCRNRLLLSGTPIQN 113
R LLLS T +N
Sbjct: 147 SRLPPDRQILLLSATLPRN 165
>gnl|CDD|233690 TIGR02025, BchH, magnesium chelatase, H subunit. This model
represents the H subunit of the magnesium chelatase
complex responsible for magnesium insertion into the
protoporphyrin IX ring in the biosynthesis of both
chlorophyll and bacteriochlorophyll. In
chlorophyll-utilizing species, this gene is known as
ChlH, while in bacteriochlorophyll-utilizing spoecies it
is called BchH. Subunit H is the largest (~140kDa) of
the three subunits (the others being BchD/ChlD and
BchI/ChlI), and is known to bind protoporphyrin IX.
Subunit H is homologous to the CobN subunit of
cobaltochelatase and by anology with that enzyme,
subunit H is believed to also bind the magnesium ion
which is inserted into the ring. In conjunction with the
hydrolysis of ATP by subunits I and D, a conformation
change is believed to happen in subunit H causing the
magnesium ion insertion into the distorted
protoporphyrin ring [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 1224
Score = 28.6 bits (64), Expect = 2.4
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 8/59 (13%)
Query: 120 ALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDEREYPIVLMLIYSAHNKAEKSLY 178
L H F++ E+ W+ K A P V +L+ H E +
Sbjct: 208 GLYHPDAKGFFETVKEYLAWYKKREGCRAPKA--------PRVGLLLLRKHLLTENQAH 258
>gnl|CDD|215363 PLN02677, PLN02677, mevalonate kinase.
Length = 387
Score = 28.3 bits (63), Expect = 2.7
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 126 MPSMFDSHDEFNEWFSKDIESHAENKTSIDERE 158
M S+F++ D +E + I+S AE++ SI E+E
Sbjct: 261 MKSVFNAVDSISEELATIIQSPAEDELSITEKE 293
>gnl|CDD|181899 PRK09485, mmuM, homocysteine methyltransferase; Provisional.
Length = 304
Score = 28.3 bits (64), Expect = 2.7
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 36/94 (38%)
Query: 46 YQLVVSDFKYFNRIKWQYLI--------------LDEAQAIVDI------NVYSYLNDIE 85
Y L + + F+R + + L LDEA+A+V++ V ++L+
Sbjct: 131 YGLSEEELQDFHRPRIEALAEAGADLLACETIPNLDEAEALVELLKEEFPGVPAWLS--- 187
Query: 86 REQSMRWKLLLGFSCRNRLLLS-GTPIQNSMAEL 118
F+ R+ +S GTP+ + A L
Sbjct: 188 ------------FTLRDGTHISDGTPLAEAAALL 209
>gnl|CDD|180423 PRK06143, PRK06143, enoyl-CoA hydratase; Provisional.
Length = 256
Score = 27.7 bits (62), Expect = 4.0
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 95 LLGFSCRNRLLLSGTPIQNSMAELWALLHFIMP 127
L+G++ LLL+G I + A W L+ ++P
Sbjct: 154 LIGWARTRWLLLTGETIDAAQALAWGLVDRVVP 186
>gnl|CDD|235663 PRK05989, cobN, cobaltochelatase subunit CobN; Reviewed.
Length = 1244
Score = 27.9 bits (63), Expect = 4.2
Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 10/61 (16%)
Query: 120 ALLHFIMPSMFDSHDEFNE----------WFSKDIESHAENKTSIDEREYPIVLMLIYSA 169
LL ++ + + DE K S + R+ P V +L Y A
Sbjct: 152 NLLRYLADTALGTGDEPEPPVPLPAAGIYHPGKAFASLEDYLAWWAPRKAPTVAILFYRA 211
Query: 170 H 170
H
Sbjct: 212 H 212
>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional.
Length = 183
Score = 27.1 bits (60), Expect = 4.8
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 30 KNLHTKDASFHVVITSYQLVVSDFKYFN 57
KNLH K + FH +I + D N
Sbjct: 62 KNLHYKGSIFHRIIPQFMCQGGDITNHN 89
>gnl|CDD|218008 pfam04289, DUF447, Protein of unknown function (DUF447). Archaeal
protein of unknown function.
Length = 177
Score = 27.2 bits (61), Expect = 4.9
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 3/47 (6%)
Query: 48 LVVSDFKYFNRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKL 94
L SDF + +L A A ++ V D + ++L
Sbjct: 66 LEESDFDWPLPGAEGIPVLKGALAWIEFEVKDVEGD---SERPVFEL 109
>gnl|CDD|233795 TIGR02241, TIGR02241, conserved hypothetical phage tail region
protein. This family consists of uncharacterized
proteins. All members so far represent bacterial genes
found in apparent phage or otherwisely laterally
transferred regions of the chromosome. Tentatively
identified neighboring proteins tend to be phage tail
region proteins. In some species, including Photorhabdus
luminescens TTO1, several members of this family may be
encoded near each other.
Length = 140
Score = 26.6 bits (59), Expect = 5.6
Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 49 VVSDFKYFNRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKL 94
V +D + W + N L + E MRW++
Sbjct: 63 VTNDSDLWQ---WANDSMLNDMGTRRKNASIRLYNEAGEPLMRWEV 105
>gnl|CDD|185278 PRK15380, PRK15380, pathogenicity island 1 protein SopD2;
Provisional.
Length = 319
Score = 27.2 bits (60), Expect = 5.6
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 121 LLHFIMPSMFDSHDE-----FNEWFSKDIESHAENKTSIDEREYPIVLMLIYSAHN 171
LL PS+ E F++ +KD + + NK ID +L IY +HN
Sbjct: 253 LLQAYKPSLSSDLIEANTMLFSDVLNKDYDDYQNNKREID-----AILRRIYRSHN 303
>gnl|CDD|237373 PRK13387, PRK13387, 1,4-dihydroxy-2-naphthoate
octaprenyltransferase; Provisional.
Length = 317
Score = 27.1 bits (60), Expect = 5.7
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 23 LRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFN 57
+ F + +HTK ASF VI + K F+
Sbjct: 3 AKLFLKLVEIHTKIASFFPVILGTLFSLYVAKIFD 37
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 26.8 bits (59), Expect = 9.6
Identities = 33/146 (22%), Positives = 62/146 (42%), Gaps = 23/146 (15%)
Query: 16 SPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIKWQ-----YLILDEAQ 70
+P+ER +LR + K H + S + S + V D K F + ++ +E +
Sbjct: 906 TPEER-LLRAIFGDKAGHVVNKSLYCP-PSLEGTVIDVKVFTKKGYEKDARVLSAYEEEK 963
Query: 71 AIVDINVYSYLNDIEREQSMRWKLLLG-------FSCRNRLLLSGTPIQNSMAELWALLH 123
A +D+ + L + RE+ +R LL FS + G I E+ ++
Sbjct: 964 AKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK--EEIASINR 1021
Query: 124 FIMPSMFDSHDEFNEWFSKDIESHAE 149
F + S+ +SK++++H E
Sbjct: 1022 FTLASLVKK-------YSKEVQNHYE 1040
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 0.415
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: 9,876,329
Number of extensions: 908223
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 33
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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 (25.5 bits)