RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8712
(651 letters)
>3toj_A SET1/ASH2 histone methyltransferase complex subun; transcription,
SPRY domain, prote binding, histone methylation, RBBP5,
DPY-30, nuclear; 2.07A {Homo sapiens}
Length = 213
Score = 177 bits (451), Expect = 4e-52
Identities = 54/207 (26%), Positives = 94/207 (45%), Gaps = 23/207 (11%)
Query: 83 QVISPTWILSVWDRDTAMAITPEGLRCQSREQKEWHGCRANKGVYGRGKYYYEATVTD-- 140
+ +L++ DR + I+ + L +K + RA+ GV +G +Y+E TV +
Sbjct: 7 ACLYERVLLALHDRAPQLKISDDRLTVVG--EKGYSMVRASHGVR-KGAWYFEITVDEMP 63
Query: 141 -EGLCRVGWSTSQAVRD--LGTDRFGFGF-GGTGKKSNNKQFDNYGEAFGMHDVIGCLLD 196
+ R+GWS LG D+F + + G K + +Y +G DV+G ++
Sbjct: 64 PDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYIN 123
Query: 197 LDNMTVA--------FTKNGQHLGLAFNISQQLKNSAFYPAVVL-KNAEMSFNFGATPFK 247
L T++ F KNG + G+A+ + + ++PA+ L K+ +S NFG FK
Sbjct: 124 LPEDTISGRGSSEIIFYKNGVNQGVAY---KDIFEGVYFPAISLYKSCTVSINFGP-CFK 179
Query: 248 HEPP-KDYIAVCNAPKQNVKHSESADV 273
+ P Y + + V ADV
Sbjct: 180 YPPKDLTYRPMSDMGWGAVVEHTLADV 206
>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding,
RNA binding protein; 2.10A {Saccharomyces cerevisiae}
SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A
Length = 400
Score = 175 bits (446), Expect = 4e-49
Identities = 76/292 (26%), Positives = 123/292 (42%), Gaps = 63/292 (21%)
Query: 278 VKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG 337
VK N QA+I+ P+RELA QT + K I ++ GG N++D + L+
Sbjct: 83 VKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC---GISCMVTTGGTNLRDDILRLNET 139
Query: 338 VDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGK 397
V I+VGTPGR+ DL S L+ C F++DEAD +L + + +I+++ +P
Sbjct: 140 VHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLP------P 193
Query: 398 RLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVP---------------ETVHHV 442
Q ++ SAT VK+ + ++ P ++L E + ++ +
Sbjct: 194 THQSLLFSATFPL-TVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTL 252
Query: 443 VVKIDPQQ-----------DETWGRLRSH-IQTDGVHA------RDN------------- 471
K+ Q + ++ HA R+
Sbjct: 253 FSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTL 312
Query: 472 ------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
R GIDI + +IN P Y+HRIGR GR +GLAI+L++
Sbjct: 313 VCSDLLTR-GIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLIN 363
Score = 86.5 bits (215), Expect = 3e-18
Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
FE+ + E+ + E + P+ +Q EAIP+ + G D+L A+ G+GKT AF +P ++
Sbjct: 23 FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 82
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
V L +IQ A ++ PT
Sbjct: 83 VKPKLNKIQ---------ALIMVPT 98
>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation,
rRNA processing, mRNA splicing, mRNA transport; HET:
ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB:
2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B
2zu6_A
Length = 410
Score = 173 bits (440), Expect = 4e-48
Identities = 73/290 (25%), Positives = 124/290 (42%), Gaps = 65/290 (22%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
QA+I+ P+RELA Q ++ ++ ++ IGG NV + + L G +V
Sbjct: 103 VRETQALILAPTRELAVQIQKGLLALGDYM---NVQCHACIGGTNVGEDIRKLDYGQHVV 159
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
GTPGR+ D+I L + VLDEAD +L +G+ I +++ +P Q+
Sbjct: 160 AGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLP------PATQV 213
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETV--HHVVVKIDPQQDETWGRLRS 459
++ SATL ++ +M + M P + +K ++ E + V V+ + + +T L
Sbjct: 214 VLISATLPH-EILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 272
Query: 460 HIQTD---------------------------GVHA------RDN--------------- 471
+ +H R++
Sbjct: 273 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLIS 332
Query: 472 ----ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
AR G+D+ + IIN LP+++ Y+HRIGR GR R G+AI+ V
Sbjct: 333 TDVWAR-GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVK 381
Score = 86.9 bits (216), Expect = 3e-18
Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
F+ MG+ ++ + + + P+ +Q AI I+ G DV+ +++G+GKT F + +
Sbjct: 36 TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISV 95
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+Q + ++E Q A +++PT
Sbjct: 96 LQCLDIQVRETQ---------ALILAPT 114
>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis,
cell cycle, nucleus, phosph RNA-binding, ATP-binding,
helicase, hydrolase; 3.50A {Homo sapiens}
Length = 414
Score = 168 bits (428), Expect = 2e-46
Identities = 75/291 (25%), Positives = 133/291 (45%), Gaps = 66/291 (22%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVL-SSGVDI 340
A QA+++ P+RELA+Q ++ ++ IGG NV+ ++ L I
Sbjct: 106 LKATQALVLAPTRELAQQIQKVVMALGDYM---GASCHACIGGTNVRAEVQKLQMEAPHI 162
Query: 341 VVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
+VGTPGR+ D+++ +LS + + FVLDEAD +L +G+ + I + +++ Q
Sbjct: 163 IVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN------SNTQ 216
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETV--HHVVVKIDPQQDETWGRLR 458
+++ SAT+ DV ++ ++ M P + +K E+ E + ++ V+ + + +T L
Sbjct: 217 VVLLSATMPS-DVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLY 275
Query: 459 SHIQTD---------------------------GVHA------RDN-------------- 471
+ +H RD
Sbjct: 276 ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLI 335
Query: 472 -----ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
AR GID+ + +IN LP ++ NY+HRIGR GR R G+AI++V+
Sbjct: 336 TTDLLAR-GIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVT 385
Score = 86.1 bits (214), Expect = 4e-18
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
+ +F++M + + + + + P+ +Q AI + G DV+ A++G+GKT F + I
Sbjct: 39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+Q + LK Q A V++PT
Sbjct: 99 LQQIELDLKATQ---------ALVLAPT 117
>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein,
translation; 2.50A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 2vso_A* 2vsx_A*
Length = 394
Score = 168 bits (427), Expect = 2e-46
Identities = 75/290 (25%), Positives = 121/290 (41%), Gaps = 66/290 (22%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
APQA+++ P+RELA Q ++ + I+ IGG + + L IV
Sbjct: 87 VKAPQALMLAPTRELALQIQKVVMALAFHM---DIKVHACIGGTSFVEDAEGLR-DAQIV 142
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
VGTPGR+ D I + F+LDEAD +L G+ I ++ +P Q+
Sbjct: 143 VGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLP------PTTQV 196
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQD--ETWGRLRS 459
++ SAT+ + DV ++ + M P + +K ++ E + V ++ ++ E L
Sbjct: 197 VLLSATMPN-DVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYD 255
Query: 460 HIQTD---------------------------GVHA------RDN--------------- 471
I +++ RD
Sbjct: 256 SISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIS 315
Query: 472 ----ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
AR GID+ + +IN LP +K NY+HRIGR GR R G+AI+ V+
Sbjct: 316 TDLLAR-GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT 364
Score = 86.4 bits (215), Expect = 3e-18
Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F++M + + + V + P+ +Q AI I+ G DVL A++G+GKTG F + +Q
Sbjct: 23 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
+ ++K Q A +++PT
Sbjct: 83 IDTSVKAPQ---------ALMLAPT 98
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 170 bits (432), Expect = 4e-46
Identities = 75/297 (25%), Positives = 120/297 (40%), Gaps = 76/297 (25%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
PQAI + PSRELA Q + + + K+ +++ I K IV
Sbjct: 187 VPKPQAICLAPSRELARQIMDVVTEMGKYT---EVKTAFGIKDSVPKG----AKIDAQIV 239
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLL-KQGYGNLIDRMHKQIPKITSDGKRLQ 400
+GTPG + DL+ L + FVLDEAD +L +QG G+ R+ +P + Q
Sbjct: 240 IGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLP------RNTQ 293
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQ---------- 450
+++ SAT + V+K AER + LK E+ E + + + ++
Sbjct: 294 IVLFSATFSE-RVEKYAERFAPNANEIRLKTEELSVEGIKQLYMDCQSEEHKYNVLVELY 352
Query: 451 ------------------DETWGRLRSH-IQTDGVH------ARDN-------------- 471
+E R+ + + RD
Sbjct: 353 GLLTIGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLV 412
Query: 472 -----ARPGIDISGLPFIINMTLPDDKA------NYVHRIGRVGRAERMGLAISLVS 517
AR GID+S + ++N +P D+A Y+HRIGR GR R+G++I+ V
Sbjct: 413 TTNVIAR-GIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFVH 468
Score = 66.0 bits (162), Expect = 2e-11
Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 11/63 (17%)
Query: 28 VQAEAIPLILGGG--DVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVI 85
+Q +A+PL+L +++ +++G+GKT AF L ++ V ++ + Q A +
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQ---------AICL 195
Query: 86 SPT 88
+P+
Sbjct: 196 APS 198
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 162 bits (412), Expect = 3e-44
Identities = 70/304 (23%), Positives = 124/304 (40%), Gaps = 72/304 (23%)
Query: 278 VKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG 337
++ V +++ +RELA Q + +F K++ P ++ + GG+++K VL
Sbjct: 70 LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYM--PNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 338 VD-IVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQ-GYGNLIDRMHKQIPKITSD 395
IVVGTPGR+ L L+L H + F+LDE D +L+Q + + + P
Sbjct: 128 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK-- 185
Query: 396 GKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVH-----HVVVKIDPQQ 450
Q+++ SATL +++ + + M P + + E + T+H +V +K D ++
Sbjct: 186 ----QVMMFSATLSK-EIRPVCRKFMQDPMEIFVDDETKL--TLHGLQQYYVKLK-DNEK 237
Query: 451 DETWGRL-------------RSHIQTD--------------GVHA------RDN------ 471
+ L +S + +H R +
Sbjct: 238 NRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK 297
Query: 472 -------------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVST 518
R G+DI + N +P+D Y+HR+ R GR GLAI+ VS
Sbjct: 298 DFQRRILVATNLFGR-GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD 356
Query: 519 VPEK 522
+
Sbjct: 357 ENDA 360
Score = 85.3 bits (212), Expect = 6e-18
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F + + PE+ +A+ + + P++VQ E IP + G DVL A++G GKT F L +Q
Sbjct: 10 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
+ ++ V+ T
Sbjct: 70 LEPVTGQVS---------VLVMCHT 85
>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD;
ATP-binding, hydrolase, nucleotide-binding, RNA binding
protein, structural genomics; 1.90A {Sulfolobus
tokodaii}
Length = 337
Score = 160 bits (407), Expect = 3e-44
Identities = 59/285 (20%), Positives = 111/285 (38%), Gaps = 62/285 (21%)
Query: 280 LVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVD 339
++ +++++ P+REL Q + I +++ + + GG+ K Q++ + D
Sbjct: 52 ILELGMKSLVVTPTRELTRQVASHIRDIGRYM---DTKVAEVYGGMPYKAQINRVR-NAD 107
Query: 340 IVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRL 399
IVV TPGR+ DL S G + L+ ++DEAD + + G+ + I + Q ++
Sbjct: 108 IVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSN-----RK- 161
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQD-------- 451
+ SAT+ + +++K+ + + ++ V H V +
Sbjct: 162 ITGLFSATIPE-EIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWRSKVQALRE 217
Query: 452 ETWG-------------RLRSHIQT-DGVH------ARDN-------------------A 472
+L + R+ +
Sbjct: 218 NKDKGVIVFVRTRNRVAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277
Query: 473 RPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
R G+DI + +IN P D Y+HRIGR GR R G AI+ +
Sbjct: 278 R-GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL 321
Score = 74.8 bits (185), Expect = 1e-14
Identities = 26/78 (33%), Positives = 47/78 (60%), Gaps = 15/78 (19%)
Query: 11 PEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKE 70
+I +A+ EM + T+VQ++ IPL+L G +V++ A+TGSGKT A+ +PI++
Sbjct: 3 EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------LG 56
Query: 71 IQAGKGQGKAKAQVISPT 88
++ + V++PT
Sbjct: 57 MK---------SLVVTPT 65
>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein,
ATPase, RNA binding protein; 3.00A {Methanocaldococcus
jannaschii} SCOP: c.37.1.19 c.37.1.19
Length = 367
Score = 151 bits (385), Expect = 7e-41
Identities = 74/293 (25%), Positives = 130/293 (44%), Gaps = 78/293 (26%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
NN +AII+ P+RELA Q ++I K ++ I GG + Q+ L +IV
Sbjct: 72 NNGIEAIILTPTRELAIQVADEIESLKGN---KNLKIAKIYGGKAIYPQIKALK-NANIV 127
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
VGTPGR+ D I+ G L+L + ++F+LDEAD +L G+ ++++ K + ++
Sbjct: 128 VGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNK-----DK-RI 181
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDP------------- 448
++ SAT+ ++ +A++ M +++ K + V+++
Sbjct: 182 LLFSATMPR-EILNLAKKYMGDYSFIKAKIN----ANIEQSYVEVNENERFEALCRLLKN 236
Query: 449 ---------------------------------------QQDETWGRLRSH-----IQTD 464
Q+++ + I TD
Sbjct: 237 KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD 296
Query: 465 GVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
V +R GID++ L +IN LP + +Y+HRIGR GRA + G AIS+++
Sbjct: 297 -VMSR-----GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343
Score = 78.7 bits (195), Expect = 7e-16
Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 11/86 (12%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLIL-GGGDVLMAAETGSGKTGAFCLPIIQ 62
F E+ + I A+ + PTD+Q + IPL L +++ A TGSGKT +F +P+I+
Sbjct: 8 FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 67
Query: 63 IVCETLKEIQAGKGQGKAKAQVISPT 88
+V I+ A +++PT
Sbjct: 68 LV-NENNGIE---------AIILTPT 83
>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase,
mRNA-export, nuclear pore, hydrolase-RNA complex; HET:
ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A*
3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A
3pev_A* 3peu_A*
Length = 395
Score = 150 bits (381), Expect = 4e-40
Identities = 80/297 (26%), Positives = 129/297 (43%), Gaps = 76/297 (25%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ +PQAI + PSRELA QT + + KF KI LI+ K++ ++
Sbjct: 73 DASPQAICLAPSRELARQTLEVVQEMGKFT---KITSQLIVPDSFEKNK----QINAQVI 125
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLL-KQGYGNLIDRMHKQIPKITSDGKRLQ 400
VGTPG + DL+ + L + FVLDEAD +L +QG G+ R+ + +P K Q
Sbjct: 126 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLP------KDTQ 179
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQ---------- 450
+++ SAT D V++ A++++ ++L+ + + + + + +
Sbjct: 180 LVLFSATFAD-AVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELY 238
Query: 451 ------------------DETWGRLRSH-IQTDGVH------ARDN-------------- 471
+ +G+L+S + +H RD
Sbjct: 239 GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI 298
Query: 472 -----ARPGIDISGLPFIINMTLP------DDKANYVHRIGRVGRAERMGLAISLVS 517
AR GIDI + ++N LP D A Y+HRIGR GR R G+AIS V
Sbjct: 299 TTNVLAR-GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVH 354
Score = 79.1 bits (196), Expect = 7e-16
Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGG--DVLMAAETGSGKTGAFCLPII 61
F+E+G+ PE+ K + M + P+ +Q A+PL+L +++ +++G+GKT AF L ++
Sbjct: 7 FDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTML 66
Query: 62 QIVCETLKEIQAGKGQGKAKAQVISPT 88
V Q A ++P+
Sbjct: 67 TRVNPEDASPQ---------AICLAPS 84
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 150 bits (381), Expect = 5e-39
Identities = 58/306 (18%), Positives = 115/306 (37%), Gaps = 72/306 (23%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITD-PKIRELLIIGGVNVKDQMSVLS-SGVD 339
+A+I+ P+R+LA Q ++ K K + ++GG + + M+ ++ +
Sbjct: 144 QYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPN 203
Query: 340 IVVGTPGRMEDLISGGHLSLT-HCRFFVLDEADGLLKQGYGNLIDRMHKQIPKI-TSDGK 397
IV+ TPGR+ D++ + VLDEAD LL+ G+ + ++ + + + +
Sbjct: 204 IVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSAD 263
Query: 398 RLQMIVCSATLHDFDVKKMAERLMYFPTWV----DLKGEDAVPETVHH---VVVKIDPQQ 450
++ ++ SATL D V+K+A +M + K E E + + K
Sbjct: 264 NIKTLLFSATLDD-KVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSI 322
Query: 451 DETWGRLRSH----------------------------------IQTDGVH------ARD 470
++ + H R
Sbjct: 323 FAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 382
Query: 471 N-------------------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGL 511
+ AR G+D + ++ + +P + ANY+HRIGR R+ + G
Sbjct: 383 SLVKRFKKDESGILVCTDVGAR-GMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGS 441
Query: 512 AISLVS 517
++ +
Sbjct: 442 SVLFIC 447
Score = 88.3 bits (219), Expect = 2e-18
Identities = 31/87 (35%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGG--GDVLMAAETGSGKTGAFCLPII 61
EE + EI KA+ M++ T VQ + I IL DV+ A+TG+GKT AF +PI
Sbjct: 74 LEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIF 133
Query: 62 QIVCETLKEIQAGKGQGKAKAQVISPT 88
Q + T + Q A +++PT
Sbjct: 134 QHLINTKFDSQYMVK-----AVIVAPT 155
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 150 bits (381), Expect = 5e-39
Identities = 58/306 (18%), Positives = 115/306 (37%), Gaps = 72/306 (23%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITD-PKIRELLIIGGVNVKDQMSVLS-SGVD 339
+A+I+ P+R+LA Q ++ K K + ++GG + + M+ ++ +
Sbjct: 93 QYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPN 152
Query: 340 IVVGTPGRMEDLISGGHLSLT-HCRFFVLDEADGLLKQGYGNLIDRMHKQIPKI-TSDGK 397
IV+ TPGR+ D++ + VLDEAD LL+ G+ + ++ + + + +
Sbjct: 153 IVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSAD 212
Query: 398 RLQMIVCSATLHDFDVKKMAERLMYFPTWV----DLKGEDAVPETVHH---VVVKIDPQQ 450
++ ++ SATL D V+K+A +M + K E E + + K
Sbjct: 213 NIKTLLFSATLDD-KVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSI 271
Query: 451 DETWGRLRSH----------------------------------IQTDGVH------ARD 470
++ + H R
Sbjct: 272 FAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 331
Query: 471 N-------------------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGL 511
+ AR G+D + ++ + +P + ANY+HRIGR R+ + G
Sbjct: 332 SLVKRFKKDESGILVCTDVGAR-GMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGS 390
Query: 512 AISLVS 517
++ +
Sbjct: 391 SVLFIC 396
Score = 85.3 bits (211), Expect = 2e-17
Identities = 31/87 (35%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGG--GDVLMAAETGSGKTGAFCLPII 61
EE + EI KA+ M++ T VQ + I IL DV+ A+TG+GKT AF +PI
Sbjct: 23 LEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIF 82
Query: 62 QIVCETLKEIQAGKGQGKAKAQVISPT 88
Q + T + Q A +++PT
Sbjct: 83 QHLINTKFDSQYMVK-----AVIVAPT 104
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex,
ATPase, riken structural genomics/proteomics initiative,
RSGI; HET: ANP; 2.20A {Drosophila melanogaster}
Length = 434
Score = 141 bits (359), Expect = 1e-36
Identities = 65/288 (22%), Positives = 115/288 (39%), Gaps = 67/288 (23%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
PQ +I+ P+RELA Q FN+ +KF + ++ ++ GG + + Q ++ G +V+ T
Sbjct: 130 PQVVIVSPTRELAIQIFNE---ARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIAT 186
Query: 345 PGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVC 404
PGR+ D + ++ RF VLDEAD +L G+ + M + + +T + Q ++
Sbjct: 187 PGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFS---EDMRRIMTHVTMRPEH-QTLMF 242
Query: 405 SATLHDF--DVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQDETWGRLRSHIQ 462
SAT F ++++MA + +V + V + +++ + +L +
Sbjct: 243 SAT---FPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVN--KYAKRSKLIEILS 297
Query: 463 T------------------------DGVHA-----------RDNA----RPG-------- 475
R+ A + G
Sbjct: 298 EQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIAT 357
Query: 476 ------IDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
+DI + +IN +P +YVHRIGR GR G A S
Sbjct: 358 SVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFD 405
Score = 71.0 bits (175), Expect = 3e-13
Identities = 26/59 (44%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMA-AETGSGKTGAFCLPII 61
F + I V + + +PT +Q +IP+I G D LMA A+TGSGKT AF LPI+
Sbjct: 58 FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRD-LMACAQTGSGKTAAFLLPIL 115
>2yyo_A SPRY domain-containing protein 3; NPPSFA, national project on
protein structural and functional analyses; 2.00A {Homo
sapiens}
Length = 171
Score = 131 bits (331), Expect = 9e-36
Identities = 31/164 (18%), Positives = 51/164 (31%), Gaps = 19/164 (11%)
Query: 95 DRDTAMAITPEGLRCQSREQKEWHGC-RANKGVYGRGKYYYEATVTD---EGLCRVGWST 150
I +G GC A++ + + Y+E ++ D G VG
Sbjct: 4 GSSGFKHILVDGDTLSYHGNSGEVGCYVASRPLT-KDSNYFEVSIVDSGVRGTIAVGLVP 62
Query: 151 SQA--VRDLGTDRFGFGFGGTGKKSNNKQFD--NYGEAFGMHDVIGC-----LLDLDNMT 201
G + K N + +G D IGC D+
Sbjct: 63 QYYSLDHQPGWLPDSVAYHADDGKLYNGRAKGRQFGSKCNSGDRIGCGIEPVSFDVQTAQ 122
Query: 202 VAFTKNGQHLGLAFNISQQLKNSAFYPAVVLK--NAEMSFNFGA 243
+ FTKNG+ +G + +PAV + E+ + A
Sbjct: 123 IFFTKNGKRVGSTI---MPMSPDGLFPAVGMHSLGEEVRLHLNA 163
>3emw_A SPRY domain-containing SOCS box protein 2; apoptosis nucleus,
apoptosis, UBL conjugation pathwayc, CL transcription
regulation, transcription, phosphoprotein; 1.80A {Homo
sapiens} PDB: 3ek9_A
Length = 217
Score = 127 bits (321), Expect = 8e-34
Identities = 36/175 (20%), Positives = 65/175 (37%), Gaps = 26/175 (14%)
Query: 89 WILSVWDRDTAMAITPEGLRCQSREQ-KEWHGCRANKGVYGRGKYYYEATVTDEGL---C 144
+ D + + GL + R + G R +G RG + +E + E
Sbjct: 44 HGWNPKDCSENIEVKEGGLYFERRPVAQSTDGARGKRGYS-RGLHAWEISWPLEQRGTHA 102
Query: 145 RVGWSTSQA-------VRDLGTDRFGFGF---------GGTGKKSNNKQFDNYGEAFGMH 188
VG +T+ A LG++ +G+ G + GE +
Sbjct: 103 VVGVATALAPLQTDHYAALLGSNSESWGWDIGRGKLYHQSKGPGAPQYPAGTQGEQLEVP 162
Query: 189 DVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV--VLKNAEMSFNF 241
+ + +LD++ T+ + G +LG AF + LK YPAV V ++ +
Sbjct: 163 ERLLVVLDMEEGTLGYAIGGTYLGPAF---RGLKGRTLYPAVSAVWGQCQVRIRY 214
>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding
protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19
Length = 206
Score = 126 bits (319), Expect = 1e-33
Identities = 46/147 (31%), Positives = 75/147 (51%), Gaps = 9/147 (6%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ QA++I P+RELA Q I+ K + + + GG N++D + L V +V
Sbjct: 69 KDNIQAMVIVPTRELALQVSQICIQVSKHM--GGAKVMATTGGTNLRDDIMRLDDTVHVV 126
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
+ TPGR+ DLI G + H + VLDEAD LL Q + +++ + +PK R Q+
Sbjct: 127 IATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPK-----NR-QI 180
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVD 428
++ SAT V+K + P ++
Sbjct: 181 LLYSATFPL-SVQKFMNSHLEKPYEIN 206
Score = 87.2 bits (217), Expect = 9e-20
Identities = 29/85 (34%), Positives = 47/85 (55%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
FE+ + E+ + EM W P+ +Q E+IP+ L G D+L A+ G+GK+GA+ +P+++
Sbjct: 5 FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
+ IQ A VI PT
Sbjct: 65 LDLKKDNIQ---------AMVIVPT 80
>2afj_A Gene rich cluster, C9 gene; beta sandwich, gene regulation; NMR
{Mus musculus} SCOP: b.29.1.22
Length = 226
Score = 124 bits (313), Expect = 1e-32
Identities = 36/189 (19%), Positives = 69/189 (36%), Gaps = 27/189 (14%)
Query: 89 WILSVWDRDTAMAITPEGLRCQSRE-QKEWHGCRANKGVYGRGKYYYEATVTDEGL---C 144
+ D + + GL + R + G R +G RG + +E + E
Sbjct: 41 HGWNPKDCSENIDVKEGGLCFERRPVAQSTDGVRGKRGYS-RGLHAWEISWPLEQRGTHA 99
Query: 145 RVGWSTSQAVRD-------LGTDRFGFGF---------GGTGKKSNNKQFDNYGEAFGMH 188
VG +T+ A LG++ +G+ G ++ GE +
Sbjct: 100 VVGVATALAPLQADHYAALLGSNSESWGWDIGRGKLYHQSKGLEAPQYPAGPQGEQLVVP 159
Query: 189 DVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV--VLKNAEMSFNFGATPF 246
+ + +LD++ T+ ++ G +LG AF + LK YP+V V ++ +
Sbjct: 160 ERLLVVLDMEEGTLGYSIGGTYLGPAF---RGLKGRTLYPSVSAVWGQCQVRIRYMGERR 216
Query: 247 KHEPPKDYI 255
E +
Sbjct: 217 V-EETRRIH 224
>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX,
structural genomics, helic binding, HOST-virus
interaction, hydrolase; 1.85A {Homo sapiens} PDB:
2g9n_A*
Length = 237
Score = 124 bits (314), Expect = 2e-32
Identities = 47/152 (30%), Positives = 84/152 (55%), Gaps = 11/152 (7%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVL-SSGVDI 340
QA+++ P+RELA+Q I+ ++ IGG NV+++M L + I
Sbjct: 96 FKETQALVLAPTRELAQQIQKVILALGDYM---GATCHACIGGTNVRNEMQKLQAEAPHI 152
Query: 341 VVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
VVGTPGR+ D+++ +LS + FVLDEAD +L +G+ + I + +++ +Q
Sbjct: 153 VVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN------TSIQ 206
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
+++ SAT+ DV ++ ++ M P + +K E
Sbjct: 207 VVLLSATMPT-DVLEVTKKFMRDPIRILVKKE 237
Score = 83.0 bits (206), Expect = 4e-18
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
+ F++M + + + + + P+ +Q AI + G DV+ A++G+GKT F + I
Sbjct: 29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISI 88
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+Q + KE Q A V++PT
Sbjct: 89 LQQLEIEFKETQ---------ALVLAPT 107
>2jk9_A SPRY domain-containing SOCS box protein 1; transcription
regulation, transcription; 1.79A {Homo sapiens} PDB:
3f2o_A 2fnj_A 2v24_A 2ihs_A
Length = 212
Score = 123 bits (310), Expect = 2e-32
Identities = 36/181 (19%), Positives = 64/181 (35%), Gaps = 28/181 (15%)
Query: 85 ISPTWILSVWDRDTAMAITPEGLRCQSREQ--KEWHGCRANKGVYGRGKYYYEATVTDEG 142
+ + DR + + + R + R G RG + ++ T
Sbjct: 29 VQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYT-RGLHVWQITWAMRQ 87
Query: 143 L---CRVGWSTSQAVRD-------LGTDRFGFGF----------GGTGKKSNNKQFDNYG 182
VG +T+ A +G + +G+ G F
Sbjct: 88 RGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPD 147
Query: 183 EAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV--VLKNAEMSFN 240
E F + D LD+D+ T++F +GQ++G+AF + LK YP V V + E+
Sbjct: 148 ETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAF---RGLKGKKLYPVVSAVWGHCEIRMR 204
Query: 241 F 241
+
Sbjct: 205 Y 205
>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family,
gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 1qva_A
Length = 224
Score = 122 bits (309), Expect = 6e-32
Identities = 44/151 (29%), Positives = 73/151 (48%), Gaps = 11/151 (7%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
APQA+++ P+RELA Q ++ + I+ IGG + + L IV
Sbjct: 80 VKAPQALMLAPTRELALQIQKVVMALAFHM---DIKVHACIGGTSFVEDAEGLR-DAQIV 135
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
VGTPGR+ D I + F+LDEAD +L G+ I ++ +P Q+
Sbjct: 136 VGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLP------PTTQV 189
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
++ SAT+ + DV ++ + M P + +K +
Sbjct: 190 VLLSATMPN-DVLEVTTKFMRNPVRILVKKD 219
Score = 84.5 bits (210), Expect = 1e-18
Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
+ F++M + + + V + P+ +Q AI I+ G DVL A++G+GKTG F +
Sbjct: 13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+Q + ++K Q A +++PT
Sbjct: 73 LQRIDTSVKAPQ---------ALMLAPT 91
>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 2.51A {Homo
sapiens}
Length = 300
Score = 123 bits (311), Expect = 1e-31
Identities = 46/153 (30%), Positives = 76/153 (49%), Gaps = 14/153 (9%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
N PQ + + P+ ELA QT I + KF P+++ + G ++ + IV
Sbjct: 160 NKYPQCLCLSPTYELALQTGKVIEQMGKFY--PELKLAYAVRGNKLERGQKI---SEQIV 214
Query: 342 VGTPGRMEDLIS-GGHLSLTHCRFFVLDEADGLL-KQGYGNLIDRMHKQIPKITSDGKRL 399
+GTPG + D S + + FVLDEAD ++ QG+ + R+ + +P+
Sbjct: 215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC------ 268
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
QM++ SAT D V K A++++ P + LK E
Sbjct: 269 QMLLFSATFED-SVWKFAQKVVPDPNVIKLKRE 300
Score = 79.4 bits (196), Expect = 2e-16
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 11/90 (12%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGG--DVLMAAETGSGKTGAFCL 58
+ +FEE+ + P++ + V M + P+ +Q A+PL+L +++ +++G+GKT AF L
Sbjct: 91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 59 PIIQIVCETLKEIQAGKGQGKAKAQVISPT 88
++ V K Q +SPT
Sbjct: 151 AMLSQVEPANKYPQ---------CLCLSPT 171
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 121 bits (305), Expect = 2e-31
Identities = 49/154 (31%), Positives = 80/154 (51%), Gaps = 8/154 (5%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPK-IRELLIIGGVNVKDQMSVLSSGVDI 340
QA+I P+RELA Q +++ +K KF + I +IGG + + + L+ I
Sbjct: 70 RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHI 129
Query: 341 VVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
V+GTPGR+ D I L + V+DEAD +L G+ +D++ ++P K LQ
Sbjct: 130 VIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMP------KDLQ 183
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDA 434
M+V SAT+ + +K ++ M PT+V +
Sbjct: 184 MLVFSATIPE-KLKPFLKKYMENPTFVHVLEHHH 216
Score = 85.7 bits (213), Expect = 4e-19
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
F P I +A++ + + PT++Q IP L G ++ ++TG+GKT A+ LPI
Sbjct: 3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPI 62
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
++ + E+Q A + +PT
Sbjct: 63 MEKIKPERAEVQ---------AVITAPT 81
>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural
genomics, structural genomics consortium, SGC,
hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*
Length = 230
Score = 121 bits (306), Expect = 2e-31
Identities = 45/154 (29%), Positives = 75/154 (48%), Gaps = 11/154 (7%)
Query: 278 VKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG 337
+ L N + Q +I+ P+RE+A Q + I + + + IGG + + L
Sbjct: 86 LVLENLSTQILILAPTREIAVQIHSVITAIGIKM--EGLECHVFIGGTPLSQDKTRLK-K 142
Query: 338 VDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQG-YGNLIDRMHKQIPKITSDG 396
I VG+PGR++ LI +L+ R F+LDEAD LL++G + I+ ++ +P
Sbjct: 143 CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLP------ 196
Query: 397 KRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLK 430
QM+ SAT + + + M PT+V L
Sbjct: 197 ASKQMLAVSATYPE-FLANALTKYMRDPTFVRLN 229
Score = 83.4 bits (207), Expect = 3e-18
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
FE + + + + + + P+ VQ +AIPL G D+++ A++G+GKT F +
Sbjct: 26 FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
+ Q +++PT
Sbjct: 86 LVLENLSTQ---------ILILAPT 101
>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA
dependent ATPase, mRNA export, nucleocytoplasmic
transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens}
PDB: 3ews_A* 3g0h_A* 3fhc_B
Length = 412
Score = 123 bits (310), Expect = 2e-30
Identities = 46/153 (30%), Positives = 75/153 (49%), Gaps = 14/153 (9%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
N PQ + + P+ ELA QT I + KF P+++ + G ++ IV
Sbjct: 93 NKYPQCLCLSPTYELALQTGKVIEQMGKFY--PELKLAYAVRGNKLERG---QKISEQIV 147
Query: 342 VGTPGRMEDLIS-GGHLSLTHCRFFVLDEADGLL-KQGYGNLIDRMHKQIPKITSDGKRL 399
+GTPG + D S + + FVLDEAD ++ QG+ + R+ + +P+
Sbjct: 148 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC------ 201
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
QM++ SAT D V K A++++ P + LK E
Sbjct: 202 QMLLFSATFED-SVWKFAQKVVPDPNVIKLKRE 233
Score = 79.5 bits (197), Expect = 5e-16
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 11/90 (12%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGG--DVLMAAETGSGKTGAFCL 58
+ +FEE+ + P++ + V M + P+ +Q A+PL+L +++ +++G+GKT AF L
Sbjct: 24 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 59 PIIQIVCETLKEIQAGKGQGKAKAQVISPT 88
++ V K Q +SPT
Sbjct: 84 AMLSQVEPANKYPQ---------CLCLSPT 104
Score = 63.0 bits (154), Expect = 1e-10
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 12/69 (17%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKA------NYVHRIGRVGRAER 508
G+ + + T+ V AR GID+ + +IN LP DK Y+HRIGR GR +
Sbjct: 315 GKEKVLVTTN-VCAR-----GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGK 368
Query: 509 MGLAISLVS 517
GLA+++V
Sbjct: 369 RGLAVNMVD 377
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 123 bits (312), Expect = 3e-30
Identities = 46/153 (30%), Positives = 75/153 (49%), Gaps = 14/153 (9%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
N PQ + + P+ ELA QT I + KF P+++ + G ++ IV
Sbjct: 160 NKYPQCLCLSPTYELALQTGKVIEQMGKFY--PELKLAYAVRGNKLERG---QKISEQIV 214
Query: 342 VGTPGRMEDLIS-GGHLSLTHCRFFVLDEADGLL-KQGYGNLIDRMHKQIPKITSDGKRL 399
+GTPG + D S + + FVLDEAD ++ QG+ + R+ + +P+
Sbjct: 215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC------ 268
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
QM++ SAT D V K A++++ P + LK E
Sbjct: 269 QMLLFSATFED-SVWKFAQKVVPDPNVIKLKRE 300
Score = 78.9 bits (195), Expect = 1e-15
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 11/90 (12%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGG--DVLMAAETGSGKTGAFCL 58
+ +FEE+ + P++ + V M + P+ +Q A+PL+L +++ +++G+GKT AF L
Sbjct: 91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 59 PIIQIVCETLKEIQAGKGQGKAKAQVISPT 88
++ V K Q +SPT
Sbjct: 151 AMLSQVEPANKYPQ---------CLCLSPT 171
Score = 62.3 bits (152), Expect = 2e-10
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 12/69 (17%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKA------NYVHRIGRVGRAER 508
G+ + + T+ V AR GID+ + +IN LP DK Y+HRIGR GR +
Sbjct: 382 GKEKVLVTTN-VCAR-----GIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGK 435
Query: 509 MGLAISLVS 517
GLA+++V
Sbjct: 436 RGLAVNMVD 444
>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural
genomics, structural GEN consortium, SGC, ATP-binding,
hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}
Length = 249
Score = 117 bits (294), Expect = 1e-29
Identities = 38/141 (26%), Positives = 70/141 (49%), Gaps = 11/141 (7%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
A+++ P+RELA Q Q I ++ +I+GG++ Q L+ I++ T
Sbjct: 112 LFALVLTPTRELAFQISEQFEALGSSI---GVQSAVIVGGIDSMSQSLALAKKPHIIIAT 168
Query: 345 PGRMEDLI-SGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIV 403
PGR+ D + + +L ++ V+DEAD +L + +D++ K IP+ R + +
Sbjct: 169 PGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPR-----DR-KTFL 222
Query: 404 CSATLHDFDVKKMAERLMYFP 424
SAT+ V+K+ + P
Sbjct: 223 FSATMTK-KVQKLQRAALKNP 242
Score = 95.1 bits (237), Expect = 4e-22
Identities = 36/88 (40%), Positives = 53/88 (60%), Gaps = 9/88 (10%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
F+++GV + +A +++ W PT +Q EAIPL L G D++ AETGSGKTGAF LPI
Sbjct: 42 TKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPI 101
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+ + ET + + A V++PT
Sbjct: 102 LNALLETPQRLF---------ALVLTPT 120
>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic
resolution, AMP complex, ribosome biogenesis,
thermophilic, hydrolase; HET: AMP; 1.20A {Thermus
thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A*
3mwl_A* 3nbf_A* 3nej_A
Length = 207
Score = 114 bits (289), Expect = 2e-29
Identities = 46/151 (30%), Positives = 71/151 (47%), Gaps = 12/151 (7%)
Query: 277 PVKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSS 336
P + P+A+++ P+RELA Q +++ + + + + GG Q L
Sbjct: 65 PSQERGRKPRALVLTPTRELALQVASELTAVAPHL-----KVVAVYGGTGYGKQKEALLR 119
Query: 337 GVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDG 396
G D VV TPGR D + G L L+ VLDEAD +L G+ ++ + P
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPP----- 174
Query: 397 KRLQMIVCSATLHDFDVKKMAERLMYFPTWV 427
R Q ++ SATL K++AER M P +
Sbjct: 175 SR-QTLLFSATLPS-WAKRLAERYMKNPVLI 203
Score = 82.6 bits (205), Expect = 3e-18
Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 8/86 (9%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F++ + PEI +A+ PT +QA A+PL L G D++ A TG+GKT AF LPI +
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 64 VCETLKEIQAGKGQGKA-KAQVISPT 88
+ + +G+ +A V++PT
Sbjct: 63 -------LAPSQERGRKPRALVLTPT 81
>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA
processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP:
c.37.1.19
Length = 220
Score = 114 bits (288), Expect = 3e-29
Identities = 41/152 (26%), Positives = 75/152 (49%), Gaps = 11/152 (7%)
Query: 278 VKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG 337
++ V +++ +RELA Q + +F K++ P ++ + GG+++K VL
Sbjct: 76 LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYM--PNVKVAVFFGGLSIKKDEEVLKKN 133
Query: 338 V-DIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQ-GYGNLIDRMHKQIPKITSD 395
IVVGTPGR+ L L+L H + F+LDE D +L+Q + + + P
Sbjct: 134 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK-- 191
Query: 396 GKRLQMIVCSATLHDFDVKKMAERLMYFPTWV 427
Q+++ SATL +++ + + M P +
Sbjct: 192 ----QVMMFSATLSK-EIRPVCRKFMQDPMEI 218
Score = 83.8 bits (208), Expect = 2e-18
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F + + PE+ +A+ + + P++VQ E IP + G DVL A++G GKT F L +Q
Sbjct: 16 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 75
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
+ ++ V+ T
Sbjct: 76 LEPVTGQVS---------VLVMCHT 91
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 117 bits (295), Expect = 2e-28
Identities = 49/210 (23%), Positives = 95/210 (45%), Gaps = 12/210 (5%)
Query: 262 KQNVKHSESADVSAGPVKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLI 321
+ A G P ++++ P+RELA Q + + KF ++R ++
Sbjct: 79 SDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSY---RSRVRPCVV 135
Query: 322 IGGVNVKDQMSVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNL 381
GG ++ Q+ L G ++V TPGR+ D++ G + L C++ VLDEAD +L G+
Sbjct: 136 YGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQ 195
Query: 382 IDRMHKQIPKITSDGKRLQMIVCSATLHDF--DVKKMAERLMYFPTWVDLKGEDAVPETV 439
I R+ +Q + G R ++ SAT F +++ +A + ++ + + E +
Sbjct: 196 IRRIVEQ-DTMPPKGVR-HTMMFSAT---FPKEIQMLARDFLDEYIFLAVGRVGSTSENI 250
Query: 440 HHVVVKIDPQQDETWGRLRSHIQTDGVHAR 469
VV ++ + + L + G +
Sbjct: 251 TQKVVWVE--ESDKRSFLLDLLNATGKDSL 278
Score = 73.0 bits (180), Expect = 7e-14
Identities = 34/95 (35%), Positives = 48/95 (50%), Gaps = 11/95 (11%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMA-AETGSGKTGAFCLPII- 61
F ++ + I +E + PT VQ AIP+I D LMA A+TGSGKT AF LPI+
Sbjct: 17 FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRD-LMACAQTGSGKTAAFLLPILS 75
Query: 62 ----QIVCETLKEIQAGKGQGKAKAQ----VISPT 88
E L+ ++ G+ K V++PT
Sbjct: 76 QIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPT 110
Score = 59.5 bits (145), Expect = 1e-09
Identities = 26/55 (47%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 463 TDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
T V AR G+DIS + +IN LP D YVHRIGR GR +GLA S +
Sbjct: 333 TA-VAAR-----GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 381
>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA,
N project on protein structural and functional analyses;
2.40A {Dugesia japonica} SCOP: c.37.1.19
Length = 253
Score = 113 bits (285), Expect = 2e-28
Identities = 43/139 (30%), Positives = 77/139 (55%), Gaps = 10/139 (7%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
P+ +I+ P+RELA Q ++ +KF + +R ++ GG + Q+ + G ++V T
Sbjct: 101 PKCLILAPTRELAIQILSE---SQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVAT 157
Query: 345 PGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVC 404
PGR+ D I +SL C++ VLDEAD +L G+ I ++ ++ + S R Q ++
Sbjct: 158 PGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES-NMPSGINR-QTLMF 215
Query: 405 SATLHDF--DVKKMAERLM 421
SAT F +++K+A +
Sbjct: 216 SAT---FPKEIQKLAADFL 231
Score = 82.2 bits (204), Expect = 1e-17
Identities = 32/86 (37%), Positives = 49/86 (56%), Gaps = 2/86 (2%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII-Q 62
F+E+ + P I + + PT +Q AIP IL D++ A+TGSGKT AF +PII
Sbjct: 25 FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH 84
Query: 63 IVCETLKEIQAGKGQGKAKAQVISPT 88
+VC+ L + + K K +++PT
Sbjct: 85 LVCQDLNQQRYSKTAY-PKCLILAPT 109
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 115 bits (290), Expect = 7e-28
Identities = 44/320 (13%), Positives = 92/320 (28%), Gaps = 88/320 (27%)
Query: 280 LVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSS--- 336
L ++ ++ P+ L +QT ++ K K++ + +++ S
Sbjct: 60 LARKGKKSALVFPTVTLVKQTLERLQKLADE----KVKIFGFYSSMKKEEKEKFEKSFEE 115
Query: 337 -GVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDR----------- 384
I+V + + LS F +D+ D +LK ID
Sbjct: 116 DDYHILVFSTQFVSKNR--EKLSQKRFDFVFVDDVDAVLKASR--NIDTLLMMVGIPEEI 171
Query: 385 --------MHKQIPKITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVP 436
+I + + K ++V SAT + + L + +V
Sbjct: 172 IRKAFSTIKQGKIYERPKNLKPGILVVSSATA---KPRGIRPLLFRDLLNFTVGRLVSVA 228
Query: 437 ETVHHVVVKIDPQQ-----------------------DETWGRLRSH-IQTDGVHA-RDN 471
+ HV + ++ E + L+ + +
Sbjct: 229 RNITHVRISSRSKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEK 288
Query: 472 -----------------------ARPGIDI-SGLPFIINMTLP--DDKANYVHRIGRVGR 505
R G+D+ + ++I P D Y+ GR R
Sbjct: 289 NFEDFKVGKINILIGVQAYYGKLTR-GVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSR 347
Query: 506 AERMGL--AISLVSTVPEKV 523
L +S++ E++
Sbjct: 348 ILNGVLVKGVSVIFEEDEEI 367
Score = 70.5 bits (173), Expect = 4e-13
Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 12/84 (14%)
Query: 5 EEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIV 64
E + ++ T Q I+ G M A TG GKT + + +
Sbjct: 2 EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWL- 60
Query: 65 CETLKEIQAGKGQGKAKAQVISPT 88
+ GK K+ ++ PT
Sbjct: 61 ------ARKGK-----KSALVFPT 73
>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding,
hydrolase, nucleotide- RNA-binding, methylation, mRNA
processing, mRNA S nucleus; HET: ADP; 2.60A {Homo
sapiens}
Length = 242
Score = 107 bits (270), Expect = 2e-26
Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 18/144 (12%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
P +++ P+RELA+Q ++ +++ I GG Q+ L GV+I + T
Sbjct: 103 PICLVLAPTRELAQQVQQVA---AEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIAT 159
Query: 345 PGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSD--GKRLQMI 402
PGR+ D + G +L + VLDEAD +L G+ QI KI R Q +
Sbjct: 160 PGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFE-------PQIRKIVDQIRPDR-QTL 211
Query: 403 VCSATLHDF--DVKKMAERLMYFP 424
+ SAT + +V+++AE +
Sbjct: 212 MWSAT---WPKEVRQLAEDFLKDY 232
Score = 69.5 bits (171), Expect = 2e-13
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII 61
F E + + ++ PT +QA+ P+ L G D++ A+TGSGKT ++ LP I
Sbjct: 31 FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAI 88
>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX,
structural genomics, structural genomi consortium, SGC,
ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}
Length = 228
Score = 106 bits (268), Expect = 2e-26
Identities = 40/140 (28%), Positives = 69/140 (49%), Gaps = 11/140 (7%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
P +++ P+RELA + K+ ++ + I GG N Q+ +S GVDI++ T
Sbjct: 95 PGMLVLTPTRELALHVEAECSKYSY----KGLKSICIYGGRNRNGQIEDISKGVDIIIAT 150
Query: 345 PGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVC 404
PGR+ DL ++L + V+DEAD +L + I ++ + R Q ++
Sbjct: 151 PGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRP-----DR-QTVMT 204
Query: 405 SATLHDFDVKKMAERLMYFP 424
SAT D V+++A + P
Sbjct: 205 SATWPD-TVRQLALSYLKDP 223
Score = 74.1 bits (183), Expect = 4e-15
Identities = 24/86 (27%), Positives = 47/86 (54%), Gaps = 4/86 (4%)
Query: 4 FEEMGVL-PEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQ 62
F++ P++ K++ + L PT +Q++A P+IL G D+++ A+TG+GKT ++ +P
Sbjct: 21 FKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFI 80
Query: 63 IVCETLKEIQAGKGQGKAKAQVISPT 88
+ + G V++PT
Sbjct: 81 HLDSQPISREQRNG---PGMLVLTPT 103
>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural
genomics, structural genomic consortium, SGC, hydrolase;
HET: ADP; 2.15A {Homo sapiens}
Length = 236
Score = 103 bits (258), Expect = 5e-25
Identities = 46/151 (30%), Positives = 76/151 (50%), Gaps = 12/151 (7%)
Query: 283 NAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVV 342
+ +II P+RELA QTF + K K LIIGG ++K + + + ++I+V
Sbjct: 96 DGLGVLIISPTRELAYQTFEVLRKVGKNH---DFSAGLIIGGKDLKHEAERI-NNINILV 151
Query: 343 GTPGRMED-LISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
TPGR+ + T + VLDEAD +L G+ + ++ + + +PK KR Q
Sbjct: 152 CTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPK-----KR-QT 205
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
++ SAT VK +A + P +V + +
Sbjct: 206 LLFSATQTK-SVKDLARLSLKNPEYVWVHEK 235
Score = 95.0 bits (237), Expect = 3e-22
Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 5/88 (5%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
+ F + + + K ++E + L T++Q + I L L G DVL AA+TGSGKT AF +P+
Sbjct: 24 ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+ E L +Q G +ISPT
Sbjct: 84 L----EALYRLQWTSTDG-LGVLIISPT 106
>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural
genomics, structural GEN consortium, SGC, rRNA,
ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}
Length = 245
Score = 101 bits (255), Expect = 1e-24
Identities = 37/145 (25%), Positives = 62/145 (42%), Gaps = 13/145 (8%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSV-LSSGVDI 340
N +A+II P+RELA Q ++IK + R +I + S DI
Sbjct: 96 NKGFRALIISPTRELASQIHRELIKISEGT---GFRIHMIHKAAVAAKKFGPKSSKKFDI 152
Query: 341 VVGTPGRMEDLIS--GGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITS--DG 396
+V TP R+ L+ + L + V+DE+D L + G D Q+ I
Sbjct: 153 LVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRD----QLASIFLACTS 208
Query: 397 KRLQMIVCSATLHDFDVKKMAERLM 421
+++ + SAT DV++ + +
Sbjct: 209 HKVRRAMFSATFAY-DVEQWCKLNL 232
Score = 80.7 bits (200), Expect = 3e-17
Identities = 27/89 (30%), Positives = 52/89 (58%), Gaps = 12/89 (13%)
Query: 4 FEEM----GVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLP 59
F+++ + + + + + + +PT +Q +AIP++L G ++L +A TGSGKT AF +P
Sbjct: 27 FQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIP 86
Query: 60 IIQIVCETLKEIQAGKGQGKAKAQVISPT 88
I+ +++ +G +A +ISPT
Sbjct: 87 ILM-------QLKQPANKG-FRALIISPT 107
>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics,
structural genomics consort ATP-binding, hydrolase,
nucleotide-binding, RNA-B; 2.80A {Homo sapiens}
Length = 262
Score = 101 bits (253), Expect = 5e-24
Identities = 40/136 (29%), Positives = 68/136 (50%), Gaps = 11/136 (8%)
Query: 283 NAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVV 342
N +I+ P+RELA QTF + + LI+GG N + L +G++I+V
Sbjct: 125 NGTGVLILSPTRELAMQTFGVLKELMTHHV---HTYGLIMGGSNRSAEAQKLGNGINIIV 181
Query: 343 GTPGRMED-LISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
TPGR+ D + + + + V+DEAD +L G+ + ++ K +P +R Q
Sbjct: 182 ATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPT-----RR-QT 235
Query: 402 IVCSATLHDFDVKKMA 417
++ SAT V+ +A
Sbjct: 236 MLFSATQTR-KVEDLA 250
Score = 87.8 bits (218), Expect = 2e-19
Identities = 28/87 (32%), Positives = 49/87 (56%), Gaps = 7/87 (8%)
Query: 4 FEEMGVL--PEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII 61
F + L KA++EM + T++Q ++I +L G D+L AA+TGSGKT AF +P +
Sbjct: 54 FASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAV 113
Query: 62 QIVCETLKEIQAGKGQGKAKAQVISPT 88
++ + +++ G ++SPT
Sbjct: 114 EL----IVKLRFMPRNG-TGVLILSPT 135
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 74.1 bits (183), Expect = 9e-16
Identities = 30/63 (47%), Positives = 36/63 (57%), Gaps = 6/63 (9%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
G R + TD V AR GIDI + +IN LP +K +YVHR GR GRA G AIS
Sbjct: 84 GEYRYLVATD-VAAR-----GIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAIS 137
Query: 515 LVS 517
V+
Sbjct: 138 FVT 140
>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity
A; hydrolase inhibitor-hydrolase complex, DEAD box RNA
helicase; 2.90A {Escherichia coli}
Length = 170
Score = 72.6 bits (179), Expect = 3e-15
Identities = 28/63 (44%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
GR+ + TD V AR GIDI + + N +P Y+HRIGR RA R G AIS
Sbjct: 79 GRVNVLVATD-VAAR-----GIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAIS 132
Query: 515 LVS 517
LV
Sbjct: 133 LVE 135
>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer,
ATP-binding, helicase, hydrolase, nucleotide-binding;
2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A
Length = 212
Score = 71.2 bits (175), Expect = 3e-14
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 449 QQDETWGRLRSH-----IQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRV 503
+++ G R + TD V AR G+DI + +++ LPD Y HR GR
Sbjct: 69 ERERVLGAFRQGEVRVLVATD-VAAR-----GLDIPQVDLVVHYRLPDRAEAYQHRSGRT 122
Query: 504 GRAERMGLAISLVS 517
GRA R G + L
Sbjct: 123 GRAGRGGRVVLLYG 136
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo
sapiens} SCOP: c.37.1.19
Length = 172
Score = 68.4 bits (168), Expect = 1e-13
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
+ R + T+ + R G+DI + N +P+D Y+HR+ R GR GLAI+
Sbjct: 80 FQRRILVATN-LFGR-----GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAIT 133
Query: 515 LVST 518
VS
Sbjct: 134 FVSD 137
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 68.0 bits (167), Expect = 1e-13
Identities = 35/143 (24%), Positives = 53/143 (37%), Gaps = 62/143 (43%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
G R I TD + AR GID+ + +IN LP +K NY+HRIGR GR R G+AI+
Sbjct: 79 GSSRILISTD-LLAR-----GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAIN 132
Query: 515 LVSTVPEKVWYHGEWCATRGRNCSNTQLTDVKGNSQVPIFLLSGTMVNGCCIWFDEKRML 574
V+ ++ +
Sbjct: 133 FVTN--------------------------------------------------EDVGAM 142
Query: 575 GEIEEHLNVTIQQVDDKLEIPAD 597
E+E+ + I+ E+P+D
Sbjct: 143 RELEKFYSTQIE------ELPSD 159
>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA
recognition motif, ATP-BIND helicase,
nucleotide-binding; 2.80A {Thermus thermophilus}
Length = 300
Score = 70.9 bits (174), Expect = 1e-13
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 449 QQDETWGRLRSH-----IQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRV 503
+++ G R + TD V AR G+DI + +++ +PD Y HR GR
Sbjct: 66 ERERVMGAFRQGEVRVLVATD-VAAR-----GLDIPQVDLVVHYRMPDRAEAYQHRSGRT 119
Query: 504 GRAERMGLAISLVS 517
GRA R G + L
Sbjct: 120 GRAGRGGRVVLLYG 133
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 70.8 bits (173), Expect = 9e-13
Identities = 74/486 (15%), Positives = 131/486 (26%), Gaps = 173/486 (35%)
Query: 131 KYYYEA-TVTDEGLCRVGWST-SQAVRDLGTDRFGFG-FGGTGKKSNNKQFD-------N 180
K Y A + + S +AV + G + FGG G + + F+
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGE-GNAQL-VAIFGGQG--NTDDYFEELRDLYQT 179
Query: 181 YG---EAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV-VLKNAE 236
Y + L +L T+ K NI + L+N + P L +
Sbjct: 180 YHVLVGDL-IKFSAETLSELIRTTLDAEK---VFTQGLNILEWLENPSNTPDKDYLLSIP 235
Query: 237 MSFNF-GATPFKHEPPKDYIAVCNAPKQNVKHSESADVSAGPVKLVNNAPQAIIIEPSRE 295
+S G H Y+ E G A+ I +
Sbjct: 236 ISCPLIGVIQLAH-----YVVTAKL--LGFTPGELRSYLKGATGHSQGLVTAVAIAETDS 288
Query: 296 LAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQM---------SVLSSGVDIVVGTPG 346
++F + +K I L IG V+ S+L ++ G P
Sbjct: 289 --WESFFVSV--RKA-----ITVLFFIG---VRCYEAYPNTSLPPSILEDSLENNEGVPS 336
Query: 347 RMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPK-----IT-SDGKRLQ 400
M LS++ L ++ + +++ + +P I+ +G +
Sbjct: 337 PM--------LSIS-----------NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-N 376
Query: 401 MIVCS--ATLHDFDVK---------------KMAERLMYF-----PT------------- 425
++V +L+ ++ +ER + F P
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPAS 436
Query: 426 ----------WVDLKGED-AVPETVHHVVVKIDPQQDETWGRLRSH-----------IQT 463
V +D +P V+ LR I
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIP--VYDT---------FDGSDLRVLSGSISERIVDCIIR 485
Query: 464 DGVH----ARDNAR------PGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAI 513
V + A PG SGL HR + G G+ +
Sbjct: 486 LPVKWETTTQFKATHILDFGPG-GASGL------------GVLTHRN-KDGT----GVRV 527
Query: 514 SLVSTV 519
+ T+
Sbjct: 528 IVAGTL 533
Score = 52.4 bits (125), Expect = 5e-07
Identities = 60/339 (17%), Positives = 99/339 (29%), Gaps = 127/339 (37%)
Query: 203 AFTKNGQH-LGLAFNI---SQQL-KNSAFYPAVV---LKNAE-----M------------ 237
+F + + + + F I + N++ P+++ L+N E M
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 238 ----SFNFGATPFKHEPPKD--YIAVCNAPKQNVKHSESADVSAGPVKLVNNAPQA---I 288
N H P I++ N K V VS GP PQ+ +
Sbjct: 351 DYVNKTN------SHLPAGKQVEISLVNGAKNLV-------VS-GP-------PQSLYGL 389
Query: 289 IIEPSRELAEQTFNQI-IKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPGR 347
+ + A +Q I F + R+L L V +P
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSE-------RKLKF--------SNRFL------PVASP-- 426
Query: 348 MEDLISGGHLSLTHCRFFVLDEADGLLKQ---GYGNLIDRMHKQIP-KITSDGKRLQMIV 403
H L A L+ + + QIP T DG L+
Sbjct: 427 ------------FHSHL--LVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR--- 469
Query: 404 CSATLHDFDVKKMAERLMYFPT-WVDLKGEDAVPETVHHVVVKIDPQQDETWGRLRSHIQ 462
L +++ + ++ P W E H++ P G L +H
Sbjct: 470 ---VLSGSISERIVDCIIRLPVKW-----ETTTQFKATHILD-FGPGGASGLGVL-THRN 519
Query: 463 TDGVHARDNARPGIDISGLPFIINMTL---PDDKANYVH 498
DG +G+ I+ TL PDD +
Sbjct: 520 KDG-------------TGVRVIVAGTLDINPDDDYGFKQ 545
Score = 51.2 bits (122), Expect = 1e-06
Identities = 72/432 (16%), Positives = 120/432 (27%), Gaps = 157/432 (36%)
Query: 20 MDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII---Q-----IVCETL--- 68
++WL P D L++ P+I Q + + L
Sbjct: 216 LEWLE----NPSNTP----DKDYLLSI--------PISCPLIGVIQLAHYVVTAKLLGFT 259
Query: 69 -----KEIQA--GKGQGKAKAQVI--SPTWILSVWDRDTAMAITPE---GLRCQSREQKE 116
++ G QG A I + +W + AIT G+RC
Sbjct: 260 PGELRSYLKGATGHSQGLVTAVAIAETDSW--ESFFVSVRKAITVLFFIGVRCYE----- 312
Query: 117 WHGCRANKGVYGRGKYYYEATVTDEGL-CRVGWSTSQ-AVRDLGTDRFGFGFGGTGKKSN 174
Y ++ ++ L G + ++ +L
Sbjct: 313 ---------AYPN--TSLPPSILEDSLENNEGVPSPMLSISNLT---------------- 345
Query: 175 NKQFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSA--FYPAVVL 232
+ + ++ N HL + L N A VV
Sbjct: 346 -------------QEQVQDYVNKTN---------SHLPAGKQVEISLVNGAKNL---VV- 379
Query: 233 KNAEMSFNFGATPFKHEPPKDYIAVCNAPKQNVKHSESADVSAGP-----VKLVNN-APQ 286
S G PP+ + + K D S P +K N P
Sbjct: 380 -----S---G-------PPQSLYGLNLT-LRKAKAPSGLDQSRIPFSERKLKFSNRFLP- 422
Query: 287 AIIIEP--SREL--AEQTFNQIIKFKKFITDPKIRELLI-----IGGVNVKD-QMSVLSS 336
+ P S L A N+ + + K ++ I G +++ S+
Sbjct: 423 --VASPFHSHLLVPASDLINKDLVKNNVSFNAK--DIQIPVYDTFDGSDLRVLSGSISER 478
Query: 337 GVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDG 396
VD ++ P + E TH +LD G G G L R DG
Sbjct: 479 IVDCIIRLPVKWETTT---QFKATH----ILDFGPGGAS-GLGVLTHRN--------KDG 522
Query: 397 KRLQMIVCSATL 408
+++IV + TL
Sbjct: 523 TGVRVIV-AGTL 533
Score = 48.1 bits (114), Expect = 1e-05
Identities = 46/318 (14%), Positives = 85/318 (26%), Gaps = 120/318 (37%)
Query: 366 VLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVCSATLHDFDV---KKMAERLMY 422
V + AD K YG I + P + T+H F K++ E
Sbjct: 1645 VWNRADNHFKDTYGFSILDIVINNPV-------------NLTIH-FGGEKGKRIRENYSA 1690
Query: 423 FPTWVDLKGEDAVPETVHHVVVKIDPQQDE-----TW----GRLRSHIQTDGVHARDNAR 473
+ + E KI + +E T+ G L T +
Sbjct: 1691 M-IFETIVDGKLKTE-------KIFKEINEHSTSYTFRSEKGLLS---AT------QFTQ 1733
Query: 474 PGIDISGLPFIINMTL----------PDDKANYV--HRIG----RVGRAERMGL--AISL 515
P + ++ P D H +G A+ M + + +
Sbjct: 1734 PAL------TLMEKAAFEDLKSKGLIPADA--TFAGHSLGEYAALASLADVMSIESLVEV 1785
Query: 516 VSTVPEKVWYHGEWCATRGRNCSNTQLTDVKGNSQVPIFLLS-GTMVNGCCIWFDEKRML 574
V RG D G S + ++ G +
Sbjct: 1786 V--------------FYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS--------- 1822
Query: 575 GEIEEHLNVTIQQVDDK----LEIPADEFDGK--VVYGQKRVNMGSSYENHVTQMEPSVN 628
+E L +++V + +EI + + V G R +++
Sbjct: 1823 ---QEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLR----------------ALD 1863
Query: 629 KLSKL--ESKAQLIYLKH 644
++ + K Q I +
Sbjct: 1864 TVTNVLNFIKLQKIDIIE 1881
Score = 41.2 bits (96), Expect = 0.001
Identities = 39/278 (14%), Positives = 81/278 (29%), Gaps = 91/278 (32%)
Query: 128 GRGKYYYEAT-----VTDEG----LCRVGWSTSQAVRDLGTDRFGFGFGG-TGKKSNNK- 176
G G Y+ + V + G+S V + FGG GK+
Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVIN-NPVNLTIHFGGEKGKRIRENY 1688
Query: 177 ---QFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVLK 233
F+ + + I +++ + ++T + L+ Q PA+ L
Sbjct: 1689 SAMIFETIVDGKLKTEKI--FKEINEHSTSYTFRSEKGLLSATQFTQ-------PALTL- 1738
Query: 234 NAEMSF-----NFGATPFK-----H---EPPKDYIA-VCNA------------------- 260
E + + G P H E Y A A
Sbjct: 1739 -MEKAAFEDLKSKGLIPADATFAGHSLGE----YAALASLADVMSIESLVEVVFYRGMTM 1793
Query: 261 ----PKQNVKHSESADVSAGPVKLVNNAPQAIIIEPSRELAEQT--------FN----QI 304
P+ + S ++ P ++ + Q + + ++T +N Q
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQY 1853
Query: 305 I---------KFKKFITDPKIRELLIIGGVNVKDQMSV 333
+ + K++++ II ++ +S+
Sbjct: 1854 VAAGDLRALDTVTNVLNFIKLQKIDII---ELQKSLSL 1888
Score = 33.5 bits (76), Expect = 0.25
Identities = 39/246 (15%), Positives = 71/246 (28%), Gaps = 70/246 (28%)
Query: 390 PKITSDGK-RLQMIVCSATLHDFDVKKMAERL-----MYFPTWVDLKGEDAVPETV---- 439
P S G ++V A +L P + D P T
Sbjct: 8 PLTLSHGSLEHVLLV-PTASFFI-----ASQLQEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 440 ----HHVVVKIDPQQDETWGRL---------RSHIQTDGVHARDNARPGIDISGLPFIIN 486
+V ++P + + ++ +++ + +HA + L +
Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHAL--------AAKLLQEND 113
Query: 487 MTLPDDKA---NYVHRIGRVGRAERMGLAISLVSTVPEKVWYHGEWCATRGRNCSNTQLT 543
TL K NY+ R +L V E + + A G Q
Sbjct: 114 TTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG---NAQLVAIFG-----GQ-- 163
Query: 544 DVKGNSQVPIFLLSGTMVNGCCIWFDEKRMLGEI-EEHLNVTIQQVDDKL-EIPADEFDG 601
GN+ +F+E R L + + I+ + L E+ D
Sbjct: 164 ---GNTDD---------------YFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA 205
Query: 602 KVVYGQ 607
+ V+ Q
Sbjct: 206 EKVFTQ 211
Score = 31.6 bits (71), Expect = 1.1
Identities = 21/133 (15%), Positives = 35/133 (26%), Gaps = 64/133 (48%)
Query: 1 MAAFEEM---------------------------GVLP-----EI----GKAVEEMDWLL 24
AAFE++ V+ E+ G ++ +
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQV---AV 1797
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGK--------- 75
P D LG + M A +F +Q V E + + + G
Sbjct: 1798 PRDE--------LGRSNYGMIAINPGRVAASFSQEALQYVVERVGK-RTGWLVEIVNYNV 1848
Query: 76 -GQGKAKAQ-VIS 86
Q Q V +
Sbjct: 1849 ENQ-----QYVAA 1856
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 62.2 bits (152), Expect = 2e-11
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 12/69 (17%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKA------NYVHRIGRVGRAER 508
G+ + I T+ V AR GID+ + ++N LP + Y+HRIGR GR +
Sbjct: 83 GKEKVLITTN-VCAR-----GIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGK 136
Query: 509 MGLAISLVS 517
GLA +++
Sbjct: 137 KGLAFNMIE 145
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 61.4 bits (150), Expect = 4e-11
Identities = 26/57 (45%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 461 IQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
+ T V AR G+DIS + +IN LP D YVHRIGR GR +GLA S +
Sbjct: 101 VATA-VAAR-----GLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 151
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 61.5 bits (150), Expect = 5e-11
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 6/55 (10%)
Query: 463 TDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
TD V ++ G+D + +IN +P++ NYVHRIGR G + G+A + ++
Sbjct: 111 TD-VASK-----GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFIN 159
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 50.9 bits (121), Expect = 9e-07
Identities = 30/191 (15%), Positives = 67/191 (35%), Gaps = 16/191 (8%)
Query: 280 LVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVD 339
L + +++ P++ L Q F++ P + + + G + +++ +
Sbjct: 48 LTKYGGKVLMLAPTKPLVLQ---HAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR-AK 103
Query: 340 IVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRL 399
++V TP +E+ + G +SL V DEA + I R +K+ K
Sbjct: 104 VIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKR------QAKNP 157
Query: 400 QMIVCSATLHD--FDVKKMAERLM----YFPTWVDLKGEDAVPETVHHVVVKIDPQQDET 453
+I +A+ + ++ L + + V V P+ +
Sbjct: 158 LVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKE 217
Query: 454 WGRLRSHIQTD 464
+L + D
Sbjct: 218 VRKLLREMLRD 228
Score = 38.2 bits (88), Expect = 0.009
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 472 ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
G+D+ + ++ + R GR GR G I L++
Sbjct: 429 GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMA 473
Score = 33.2 bits (75), Expect = 0.31
Identities = 9/33 (27%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 21 DWLLPTDVQAEAIPLILGGGDVLMAAETGSGKT 53
D + P Q + L+ TG GKT
Sbjct: 6 DLIQPRIYQEVIYAKCKET-NCLIVLPTGLGKT 37
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 45.0 bits (105), Expect = 7e-05
Identities = 25/162 (15%), Positives = 53/162 (32%), Gaps = 5/162 (3%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ + + + EQ Q FK I G + + DI+
Sbjct: 294 GRKAKVVFLATKVPVYEQ---QKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDII 350
Query: 342 VGTPGRME-DLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
V TP + G SL+ + DE N++ + + K S + Q
Sbjct: 351 VVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE-QKFNSASQLPQ 409
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHV 442
++ +A++ + K + E + + + A+ ++
Sbjct: 410 ILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENI 451
Score = 29.9 bits (66), Expect = 3.3
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 449 QQDETWGRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAE 507
Q ++ + A A GIDI ++ + + GR GRA
Sbjct: 681 SQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAA 738
>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA
compl protease/ntpase/helicase, hydrolase; 1.95A
{Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A*
1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A*
3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A
Length = 666
Score = 43.1 bits (101), Expect = 3e-04
Identities = 36/279 (12%), Positives = 70/279 (25%), Gaps = 72/279 (25%)
Query: 277 PVKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSS 336
P + +++ PS + + I N++ + +++
Sbjct: 250 PAAYAAQGYKVLVLNPSVAATLGFGAY------------MSKAHGI-DPNIRTGVRTITT 296
Query: 337 GVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEA---DGLLKQGYGNLIDRMHKQIPKIT 393
G + T G+ ++ G S + DE D G G ++D+
Sbjct: 297 GAPVTYSTYGK---FLADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETA----- 348
Query: 394 SDGKRLQMIVCSATLHD---FDVKKMAERLMYFPTWVDLKGEDAVPETVHH--------V 442
+++ +AT + E + + G+ E +
Sbjct: 349 ---GARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHS 405
Query: 443 VVKIDPQQDETWGR----LRSHIQTDGVHARDNAR--------------PGIDI------ 478
K D + G + + D D
Sbjct: 406 KKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTGDFDSVIDCNT 465
Query: 479 ---------SGLPFIINM-TLPDDKANYVHRIGRVGRAE 507
F I T+P D + R GR GR
Sbjct: 466 CVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGR 504
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 43.0 bits (100), Expect = 3e-04
Identities = 31/142 (21%), Positives = 49/142 (34%), Gaps = 4/142 (2%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ + + EQ F K+ R I G + + DI+
Sbjct: 59 GQKGKVVFFANQIPVYEQ---NKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDII 115
Query: 342 VGTPGRME-DLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
+ TP + +L G SL+ + DE KQ N+I + S G Q
Sbjct: 116 ILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQ 175
Query: 401 MIVCSATLHDFDVKKMAERLMY 422
+I +A++ D K E L Y
Sbjct: 176 VIGLTASVGVGDAKTTDEALDY 197
Score = 30.7 bits (68), Expect = 1.9
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGK 75
P + Q E + G + ++ A TG GKT L I + + + Q GK
Sbjct: 14 PRNYQLELALPAMKGKNTIICAPTGCGKTFVSLL-ICEHHLKKFPQGQKGK 63
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 43.0 bits (100), Expect = 3e-04
Identities = 25/137 (18%), Positives = 47/137 (34%), Gaps = 4/137 (2%)
Query: 287 AIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPG 346
+ + EQ Q F ++ I G + + + DI++ TP
Sbjct: 55 VVFFANQIPVYEQ---QATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQ 111
Query: 347 RME-DLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVCS 405
+ +L +G SL+ + DE K N I + S Q++ +
Sbjct: 112 ILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLT 171
Query: 406 ATLHDFDVKKMAERLMY 422
A++ D K E + +
Sbjct: 172 ASVGVGDAKTAEEAMQH 188
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 42.5 bits (99), Expect = 5e-04
Identities = 50/323 (15%), Positives = 96/323 (29%), Gaps = 103/323 (31%)
Query: 193 CLLDLDNMTVAFTKNGQHLGLAFNIS-QQLKNSAFYPAVVLKNAEMSFNFGATPFKHEPP 251
CLL L N V +N + AFN+S + L + + +++ A H
Sbjct: 246 CLLVLLN--V---QNAKAWN-AFNLSCKIL--------LTTRFKQVTDFLSAATTTHISL 291
Query: 252 KDYIAVCNAPKQNVKHSESADVSAG---------PVKLVNNAPQAI-II----------- 290
+ E + P +++ P+ + II
Sbjct: 292 DH-------HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
Query: 291 EPSRELAEQTFNQIIK-FKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPGRME 349
+ + + II+ + + R++ D++SV I +
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMF--------DRLSVFPPSAHI---PTILLS 393
Query: 350 ----DLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQ----IPKITSDGKRLQM 401
D+I V+ + L K L+++ K+ IP I + K
Sbjct: 394 LIWFDVIK----------SDVMVVVNKLHKYS---LVEKQPKESTISIPSIYLELKVKLE 440
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQDETWGRLRSHI 461
LH + + + Y +D +P P D+ + SHI
Sbjct: 441 N--EYALH----RSIVDH--YNIP-KTFDSDDLIP-----------PYLDQYF---YSHI 477
Query: 462 QTDGVHARDNARPGIDISGLPFI 484
G H + N ++ +
Sbjct: 478 ---GHHLK-NIEHPERMTLFRMV 496
Score = 41.4 bits (96), Expect = 0.001
Identities = 44/300 (14%), Positives = 84/300 (28%), Gaps = 122/300 (40%)
Query: 131 KYYYEATVTDEG-------LCRVGW--STSQAVRDLGTDRFGFGFGGTGKKS-NNKQFDN 180
K + +V L + W V + ++ K S KQ
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLI-WFDVIKSDVMVV-VNKLH-------KYSLVEKQPKE 423
Query: 181 YGEAFGMHDVIGCLLDL----DNMTVAFTKNGQHLGL--AFNISQQLKNSAFYPAVV--- 231
+ + L+L +N H + +NI + + P +
Sbjct: 424 S--TISIPSI---YLELKVKLENEYAL------HRSIVDHYNIPKTFDSDDLIPPYLDQY 472
Query: 232 --------LKNAEMS----------FNFGATPFKHEPPKDYIAVCNAPKQNVKHSESADV 273
LKN E +F ++ +Q ++H +A
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDF-----------RFL------EQKIRHDSTAWN 515
Query: 274 SAGPVKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITD--PKIRELLIIGGVNVKDQM 331
++G + T Q+ +K +I D PK L V +
Sbjct: 516 ASGSIL-------------------NTLQQLKFYKPYICDNDPKYERL-------VNAIL 549
Query: 332 SVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPK 391
L P E+LI + L R ++ E + + ++ + KQ+ +
Sbjct: 550 DFL----------PKIEENLICSKYTDLL--RIALMAEDEAIFEEAH--------KQVQR 589
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 37.2 bits (85), Expect = 0.005
Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 9/36 (25%)
Query: 262 KQNVKHSESADVSAGPVKLV--NNAPQAIIIEPSRE 295
KQ +K +++ +KL ++AP A+ I+ + E
Sbjct: 19 KQALKKLQAS------LKLYADDSAP-ALAIKATME 47
Score = 32.2 bits (72), Expect = 0.21
Identities = 6/25 (24%), Positives = 10/25 (40%), Gaps = 9/25 (36%)
Query: 413 VKKMAERL-MYFPTWVDLKGEDAVP 436
+KK+ L +Y D+ P
Sbjct: 22 LKKLQASLKLYAD--------DSAP 38
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 36.7 bits (85), Expect = 0.011
Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 9/90 (10%)
Query: 287 AIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPG 346
I++ L EQ K + R + + G +K + DI++ T
Sbjct: 85 VIVLVNKVLLVEQ---LFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQ 141
Query: 347 RMEDLISG------GHLSLTHCRFFVLDEA 370
+E+ + + L+ ++DE
Sbjct: 142 ILENSLLNLENGEDAGVQLSDFSLIIIDEC 171
Score = 30.2 bits (68), Expect = 1.6
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 29 QAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVISPT 88
Q E L G ++++ TGSGKT + I + L + + GK V+
Sbjct: 38 QMEVAQPALEGKNIIICLPTGSGKT----RVAVYIAKDHLDKKKKASEPGKVI--VLVNK 91
Query: 89 WIL 91
+L
Sbjct: 92 VLL 94
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 37.5 bits (86), Expect = 0.015
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 27 DVQAEAIPLILGGGDVLMAAETGSGKT 53
Q AI I G VL++A T +GKT
Sbjct: 187 PFQDTAISCIDRGESVLVSAHTSAGKT 213
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 37.6 bits (86), Expect = 0.016
Identities = 27/152 (17%), Positives = 51/152 (33%), Gaps = 7/152 (4%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ + + + EQ Q FK I G + + DI+
Sbjct: 294 GRKAKVVFLATKVPVYEQ---QKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDII 350
Query: 342 VGTPGRME-DLISGGHLSLTHCRFFVLDEA-DGLLKQGYGNLIDRMHKQIPKITSDGKRL 399
V TP + G SL+ + DE + Y L+ R +Q K S +
Sbjct: 351 VVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ--KFNSASQLP 408
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKG 431
Q++ +A++ + K + E + + +
Sbjct: 409 QILGLTASVGVGNAKNIEETIEHICSLCSYLD 440
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 37.4 bits (87), Expect = 0.016
Identities = 25/132 (18%), Positives = 49/132 (37%), Gaps = 16/132 (12%)
Query: 287 AIIIEPSRELAEQTFNQIIKF-KKFITDPKIRELLIIGGVNVKDQMSVLSS--GVDIVVG 343
+I P+ L Q I K+ +K + G + +++ + + + IV+
Sbjct: 102 CYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVIT 161
Query: 344 TPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHK-------QIPKITSDG 396
T + S + L H F +D+ D +LK +D++ K
Sbjct: 162 TTQFL----SKHYRELGHFDFIFVDDVDAILKASKN--VDKLLHLLGFHYDLKTKSWVGE 215
Query: 397 KRLQMIVCSATL 408
R ++V +AT
Sbjct: 216 ARGCLMVSTATA 227
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 37.5 bits (86), Expect = 0.017
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 27 DVQAEAIPLILGGGDVLMAAETGSGKT 53
Q AI I G VL++A T +GKT
Sbjct: 89 PFQDTAISCIDRGESVLVSAHTSAGKT 115
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 36.8 bits (84), Expect = 0.020
Identities = 28/162 (17%), Positives = 53/162 (32%), Gaps = 7/162 (4%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
+ + + + EQ Q FK I G + + DI+
Sbjct: 53 GRKAKVVFLATKVPVYEQ---QKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDII 109
Query: 342 VGTPGRME-DLISGGHLSLTHCRFFVLDEADGLLK-QGYGNLIDRMHKQIPKITSDGKRL 399
V TP + G SL+ + DE Y L+ R +Q K S +
Sbjct: 110 VVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ--KFNSASQLP 167
Query: 400 QMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHH 441
Q++ +A++ + K + E + + + A+ +
Sbjct: 168 QILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVREN 209
Score = 28.4 bits (62), Expect = 8.4
Identities = 17/72 (23%), Positives = 24/72 (33%), Gaps = 7/72 (9%)
Query: 20 MDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGK 79
M+ Q E + G + L+ A TGSGKT L Q K
Sbjct: 3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILIC-------EHHFQNMPAGRK 55
Query: 80 AKAQVISPTWIL 91
AK ++ +
Sbjct: 56 AKVVFLATKVPV 67
>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome
segregation, cell adhesion, kleisin, MIT cell cycle;
HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP:
c.37.1.12
Length = 430
Score = 35.8 bits (83), Expect = 0.036
Identities = 24/101 (23%), Positives = 42/101 (41%), Gaps = 24/101 (23%)
Query: 294 RELAEQTFNQI-IKFK---KFITDPKIRELLIIGG---VNVKDQMSVLSSGVDIVVGTPG 346
+EL E+TF+ + + +T + + GG + ++D+ ++G+ P
Sbjct: 266 KELFEKTFDYVSDHLDAIYRELTKNPNSNVELAGGNASLTIEDEDEPFNAGIKYHATPPL 325
Query: 347 ----RMEDLISGGHLSLT---------HCR---FFVLDEAD 371
ME L SGG ++ + FFVLDE D
Sbjct: 326 KRFKDMEYL-SGGEKTVAALALLFAINSYQPSPFFVLDEVD 365
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 33.6 bits (77), Expect = 0.21
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 27 DVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLK 69
QAEA+ + G ++L+A T +GKT + +++ + K
Sbjct: 28 PPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGK 70
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 33.6 bits (77), Expect = 0.26
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 27 DVQAEAIPLILGGGD-VLMAAETGSGKTGAFCLPIIQIVCET 67
Q EA+ L G+ +L+ + TGSGKT + II + +
Sbjct: 33 PPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN 74
>3kta_B Chromosome segregation protein SMC; structural maintenance of
chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A,
transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB:
1xew_Y 1xex_B*
Length = 173
Score = 29.6 bits (67), Expect = 2.2
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 21/76 (27%)
Query: 333 VLSSGVDIVVGTPG----RMEDLISGGHLSLT---------HCR---FFVLDEADGLLKQ 376
S G++I G R+E +SGG +LT + F++ DE D L
Sbjct: 43 PFSGGLEIEAKPAGKDVKRIE-AMSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDD 101
Query: 377 G----YGNLIDRMHKQ 388
+LI K+
Sbjct: 102 ANVKRVADLIKESSKE 117
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold,
ATP-binding, hydrolase, nucleotide- binding; 2.00A
{Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 30.2 bits (68), Expect = 2.3
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 27 DVQAEAIPLILGGGD-VLMAAETGSGKTGAFCLPIIQIVCET 67
QAEA+ + G L++ T SGKT + ++ +
Sbjct: 26 PPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ 67
Score = 28.7 bits (64), Expect = 7.3
Identities = 25/122 (20%), Positives = 51/122 (41%), Gaps = 13/122 (10%)
Query: 287 AIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPG 346
A+ I P + LAE+ F + ++K ++ G + KD+ DI++ T
Sbjct: 71 AVYIVPLKALAEEKFQEFQDWEKI--GLRVAMA--TGDYDSKDE---WLGKYDIIIATAE 123
Query: 347 RMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIVCSA 406
+ + L+ G + + V DE + + G ++ + + + Q+I SA
Sbjct: 124 KFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVI------LAHMLGKAQIIGLSA 177
Query: 407 TL 408
T+
Sbjct: 178 TI 179
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease,
double strand DNA repair, protein-DNA CO hydrolase-DNA
complex; HET: DNA; 2.80A {Bacillus subtilis} PDB:
3u44_A*
Length = 1232
Score = 29.6 bits (66), Expect = 4.1
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 26 TDVQAEAIPLILGGGDVLMAAETGSGKT 53
TD Q AI G D+L+AA GSGKT
Sbjct: 12 TDDQWNAIVST--GQDILVAAAAGSGKT 37
>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
repair, nucleotide-binding, DNA-binding, polymorphism,
nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
PDB: 2wwy_A*
Length = 591
Score = 29.6 bits (67), Expect = 4.2
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 29 QAEAIPLILGGGD--VLMAAETGSGK 52
Q E I + + G + ++M TG GK
Sbjct: 49 QLETINVTMAGKEVFLVMP--TGGGK 72
>1bc4_A Ribonuclease, RC RNAse; hydrolase, phosphoric diester, cytotoxic
protein, sialic acid binding lectin; HET: PCA; NMR {Rana
catesbeiana} SCOP: d.5.1.1 PDB: 1km8_A 1km9_A 1m07_A
Length = 111
Score = 27.9 bits (62), Expect = 4.3
Identities = 4/26 (15%), Positives = 6/26 (23%)
Query: 246 FKHEPPKDYIAVCNAPKQNVKHSESA 271
F A+C S +
Sbjct: 40 FIISSATTVKAICTGVINMNVLSTTR 65
>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A
{Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3
Length = 229
Score = 29.0 bits (64), Expect = 4.4
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 35 LILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVISPTWIL 91
L L G V+ + TGA + ++Q T GQ K +++ W+L
Sbjct: 141 LQLCGASVVKELPLLTRDTGAHPIVLVQPSAWTEDNDCPDIGQ-LCKGRLVMWDWVL 196
>2p7s_A Amphinase-2; cytotoxic RNAse, enzyme efficiency, substrate SPE
hydrolase; HET: NAG; 1.80A {Rana pipiens} PDB: 2p6z_A*
Length = 114
Score = 27.5 bits (61), Expect = 5.4
Identities = 7/35 (20%), Positives = 8/35 (22%), Gaps = 5/35 (14%)
Query: 246 FKHEPPKDYIAVCNAPKQNVKHSESADVSAGPVKL 280
F H +C V S S L
Sbjct: 47 FIHSTTGPVKEICRRATGRVNKS-----STQQFTL 76
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae}
PDB: 4a4k_A
Length = 997
Score = 29.0 bits (64), Expect = 5.9
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 27 DVQAEAIPLILGGGDVLMAAETGSGKT 53
Q EA+ + G V +AA T +GKT
Sbjct: 42 TFQKEAVYHLEQGDSVFVAAHTSAGKT 68
>2jgp_A Tyrocidine synthetase 3; multifunctional enzyme, antibiotic
biosynthesis, condensatio domain, peptide bond
formation, ligase; 1.85A {Brevibacillus brevis}
Length = 520
Score = 28.7 bits (65), Expect = 7.4
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 16/39 (41%)
Query: 334 LSSGVDIVVGTP--GR----MEDLISGGHLSLTHCRFFV 366
+ DI+VGTP GR +E ++ G FV
Sbjct: 344 YAGQEDIIVGTPITGRSHADLEPIV-G---------MFV 372
>2fyt_A Protein arginine N-methyltransferase 3; structural genomics,
structural genomics consortium, SGC; HET: SAH; 2.00A
{Homo sapiens} SCOP: c.66.1.6 PDB: 3smq_A* 1f3l_A*
Length = 340
Score = 28.5 bits (63), Expect = 7.6
Identities = 17/150 (11%), Positives = 43/150 (28%), Gaps = 7/150 (4%)
Query: 326 NVKDQMSVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFF---VLDEADGLLKQGYGNLI 382
++D ++++ ++ V +++ +IS VL + L +G
Sbjct: 110 KLEDTITLIKGKIEEVHLPVEKVDVIISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYP 169
Query: 383 DRMHKQIPKITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHV 442
D + ++ K I ++ F + M + ++ L + + E
Sbjct: 170 DICTISLVAVSDVNKHADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIK 229
Query: 443 VVKIDPQQDETWGR---LRSHIQTDG-VHA 468
+ I A
Sbjct: 230 HIDCHTTSISDLEFSSDFTLKITRTSMCTA 259
>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic
subunit]; helicase, flavivirus, DEAD-BOX, ATPase,
rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP:
c.37.1.14 c.37.1.14 PDB: 1ymf_A*
Length = 440
Score = 28.3 bits (63), Expect = 8.7
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 473 RPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAE 507
+P + G I L ++ R GR+GR
Sbjct: 252 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNP 286
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 28.4 bits (64), Expect = 8.8
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 296 LAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKD---QMSVLSSG-VDIVVGT 344
LA Q + + + + I L+IG + S L +G +D+V+GT
Sbjct: 429 LAIQHYR---RTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGT 478
>1h4g_A Xylanase; glycoside hydrolase, oligosaccharide, transition-state,
intermediate, mutant, BOAT conformation; HET: FXP; 1.1A
{Bacillus agaradhaerens} SCOP: b.29.1.11 PDB: 1qh6_A*
1qh7_A* 1h4h_A* 2f6b_A 2nqy_A* 1igo_A
Length = 207
Score = 27.9 bits (62), Expect = 9.4
Identities = 9/64 (14%), Positives = 18/64 (28%)
Query: 119 GCRANKGVYGRGKYYYEATVTDEGLCRVGWSTSQAVRDLGTDRFGFGFGGTGKKSNNKQF 178
G + G + + + L R G ++ +G + + N
Sbjct: 23 GGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYL 82
Query: 179 DNYG 182
YG
Sbjct: 83 CVYG 86
>1e69_A Chromosome segregation SMC protein; structural maintenance of
chromosomes, coiled coil; 3.1A {Thermotoga maritima}
SCOP: c.37.1.12
Length = 322
Score = 28.0 bits (63), Expect = 9.8
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 19/81 (23%)
Query: 327 VKDQMSVLSSGVDIVVGTPG---RMEDLISGGHLSLT---------HCR---FFVLDEAD 371
V + S+L +G +I + PG + L+SGG +L + F+VLDE D
Sbjct: 192 VSEAKSILDAGFEISIRKPGRRDQKLSLLSGGEKALVGLALLFALMEIKPSPFYVLDEVD 251
Query: 372 GLLKQG----YGNLIDRMHKQ 388
L + L+ K
Sbjct: 252 SPLDDYNAERFKRLLKENSKH 272
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.136 0.412
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,330,930
Number of extensions: 653389
Number of successful extensions: 1684
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1588
Number of HSP's successfully gapped: 149
Length of query: 651
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 551
Effective length of database: 3,909,693
Effective search space: 2154240843
Effective search space used: 2154240843
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: 60 (27.5 bits)