RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780788|ref|YP_003065201.1| transcription elongation
factor NusA [Candidatus Liberibacter asiaticus str. psy62]
(526 letters)
>1hh2_P NUSA, N utilization substance protein A; transcription regulation,
termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5
d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Length = 344
Score = 412 bits (1061), Expect = e-116
Identities = 141/341 (41%), Positives = 225/341 (65%), Gaps = 1/341 (0%)
Query: 7 LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLL 66
+ LL+ D + EK I ++ V+ ++ ++ A R +G ++ V I+ TG+I +++LL
Sbjct: 3 IGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLL 62
Query: 67 EVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAE 126
EVVEEVE+ QISL+ A+ DP ++G +V L +FGR+A Q+AKQV+IQ++RE E
Sbjct: 63 EVVEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELE 122
Query: 127 RDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYI 186
+++Q+ ++ + G + + V RV + +G + + + E I E ++ GD VK YI
Sbjct: 123 KEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYI 182
Query: 187 YDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDS 246
DV + +GP++L+SR P+F++ L +E+PE+ NGIV++KA++R+PG R K+AV S+D
Sbjct: 183 IDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDP 242
Query: 247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDV 305
++DP+GAC+G GSR+ A++ EL+ EK+D++ WS D + NAL PA V +V +LD++
Sbjct: 243 NVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKEN 302
Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346
V+VP QLSLAIG+ GQN RLA++LTGW IDI
Sbjct: 303 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMN 343
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology
domains., structural genomics, PSI, protein structure
initiative; 1.70A {Mycobacterium tuberculosis} SCOP:
b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1
Length = 366
Score = 379 bits (975), Expect = e-106
Identities = 132/373 (35%), Positives = 203/373 (54%), Gaps = 32/373 (8%)
Query: 1 MVSANRLEL-LQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGD 59
+VS + + + A+ ++ I + +L + ++ A R G +D R+EI+ +TG
Sbjct: 14 LVSRRHMNIDMAALHAIEVDRGISVNELLETIKSALLTAYRHTQGHQTDARIEIDRKTGV 73
Query: 60 ISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVII 119
+ + AR+ D + ++ D P FGR+A +A+QV++
Sbjct: 74 VRVI--------------------ARETDEAGNLISEWDDT--PEGFGRIAATTARQVML 111
Query: 120 QKVREAERDRQYLEFKDKVGEIISGTVKRVEYGN----VIVDLGNSD----GVIRRDETI 171
Q+ R+AE +R Y EF + GEI++G ++R N V+V +G GVI E +
Sbjct: 112 QRFRDAENERTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV 171
Query: 172 SRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSR 231
E+ G+R++ Y+ V R R P + LSRTHP + KLF +EVPEI +G V++ AV+R
Sbjct: 172 PGESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAR 231
Query: 232 DPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINAL 291
+ G R+K+AV S+ + ++ GAC+G G RV+ V++EL EKIDI+ + D A FV NAL
Sbjct: 232 EAGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANAL 291
Query: 292 RPAIVTKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
PA V V V+D+ V+VP QLSLAIG+ GQN RLA++LTGW IDI +
Sbjct: 292 SPAKVVSVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAXXXXX 351
Query: 351 RQKDFNERTQFFM 363
Q +
Sbjct: 352 GQPEPGVSRGMAH 364
>2asb_A Transcription elongation protein NUSA; protein-RNA complex,
transcription/RNA complex; 1.50A {Mycobacterium
tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB:
2atw_A
Length = 251
Score = 258 bits (661), Expect = 2e-69
Identities = 99/243 (40%), Positives = 141/243 (58%), Gaps = 9/243 (3%)
Query: 133 EFKDKVGEIISGTVKRVEYGN----VIVDLGNSD----GVIRRDETISRENLRPGDRVKS 184
EF + GEI++G ++R N V+V +G GVI E + E+ G+R++
Sbjct: 2 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGESYEHGNRLRC 61
Query: 185 YIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS 244
Y+ V R R P + LSRTHP + KLF +EVPEI +G V++ AV+R+ G R+K+AV S+
Sbjct: 62 YVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVRSN 121
Query: 245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDED 304
+ ++ GAC+G G RV+ V++EL EKIDI+ + D A FV NAL PA V V + +
Sbjct: 122 VAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANALSPAKVVSVSVIDQ 181
Query: 305 VGR-IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFM 363
R V+VP QLSLAIG+ GQN RLA++LTGW IDI + Q +
Sbjct: 182 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAXXXXXGQPEPGVSRGMAH 241
Query: 364 QAI 366
+
Sbjct: 242 DRL 244
>2kwp_A Transcription elongation protein NUSA; NMR {Escherichia coli}
Length = 129
Score = 138 bits (350), Expect = 2e-33
Identities = 47/124 (37%), Positives = 76/124 (61%)
Query: 8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLE 67
E+L + +AV+ EK++ R+ + + ++ A + Y D+RV+I+ ++GD FR
Sbjct: 4 EILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFRRWL 63
Query: 68 VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAER 127
VV+EV T +I+L+ AR D S+++G V D + + F R+ Q+AKQVI+QKVREAER
Sbjct: 64 VVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVREAER 123
Query: 128 DRQY 131
Sbjct: 124 AMLV 127
>2cxc_A NUSA; transcription termination, RNA binding protein, KH domain,
structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1}
PDB: 2cy1_A
Length = 144
Score = 92.0 bits (228), Expect = 3e-19
Identities = 25/131 (19%), Positives = 52/131 (39%), Gaps = 8/131 (6%)
Query: 213 HMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDE 272
++ V G+ + + + +R V + G +G G ++ + E +
Sbjct: 14 YISVFHSITGVTAYRCIVDEENNRLIFLVSEGE-----AGRAIGRGGRLIKLL-REALGK 67
Query: 273 KIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEV--IVPKEQLSLAIGRRGQNVRL 330
I++V +S D V N + + + E G +V V ++ AIG+ G+NV+
Sbjct: 68 NIEVVEYSSDLERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKR 127
Query: 331 ASQLTGWTIDI 341
A + +
Sbjct: 128 ARLVLSKLFGV 138
Score = 47.3 bits (112), Expect = 1e-05
Identities = 14/77 (18%), Positives = 32/77 (41%)
Query: 294 AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQK 353
+ ++DE+ R+ +V + + AIGR G+ ++L + G I+++ D K
Sbjct: 24 VTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSDLERIVK 83
Query: 354 DFNERTQFFMQAINVDE 370
+ + +
Sbjct: 84 NLFPGVKIESINVRERN 100
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage
lambda protein N, regulation of RNA binding,
transcription antitermination, X-RAY crystallography;
1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A
Length = 70
Score = 83.9 bits (208), Expect = 8e-17
Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 359 TQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE 418
F + +++DE A +LV EGF+ +EELA V + E+ IEG DE T ++ RA+ L
Sbjct: 5 IDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNALA 64
Query: 419 GIDI 422
I
Sbjct: 65 TIAQ 68
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 2006
Score = 57.6 bits (139), Expect = 6e-09
Identities = 69/324 (21%), Positives = 120/324 (37%), Gaps = 96/324 (29%)
Query: 119 IQKVREAERD---RQYLEFKDKVGE-----IISGTVKRVEYGNVIVDLGNSDGV-IRRD- 168
+ K +A +D R FKD G +I+ V N+ + G G IR +
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPV------NLTIHFGGEKGKRIRENY 1688
Query: 169 -----ETISRENLRP-------GDRVKSYIYDVRREQRGPQVLLSRTHPQF-MVKLFHME 215
ETI L+ + SY + R ++G LLS T QF L ME
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTF---RSEKG---LLSAT--QFTQPALTLME 1740
Query: 216 VPEIYN----GIVQVKAV--SRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTEL 269
+ G++ A G A LA + SI+ + V RG +Q V
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVP-- 1798
Query: 270 RDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329
RDE + + + A+ P GR+ +E L + R G+
Sbjct: 1799 RDEL--------GRSNYGMIAINP------------GRVAASFSQEALQYVVERVGKR-- 1836
Query: 330 LASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQA--INVDEIIAHLLVAEGFADVEEL 387
TGW ++I+ ++N Q ++ A + + + ++L F ++++
Sbjct: 1837 -----TGWLVEIV-----------NYNVENQQYVAAGDLRALDTVTNVL---NFIKLQKI 1877
Query: 388 ACVKISEIASIEGFDEETAVEIQG 411
+++ + S+E E++G
Sbjct: 1878 DIIELQKSLSLE--------EVEG 1893
Score = 48.4 bits (115), Expect = 4e-06
Identities = 46/292 (15%), Positives = 79/292 (27%), Gaps = 117/292 (40%)
Query: 283 SATFVINALRPAIVTKVVLDEDVGRIEV--IVPKEQLSLAIGRRGQNVRLASQLTGWTID 340
A + RP ++ G +E +VP +A SQL
Sbjct: 2 DAY----STRPLTLSH-------GSLEHVLLVPTASFFIA-----------SQL------ 33
Query: 341 IITEEEDSINRQKDFNERTQFFMQAINVDEIIA-HLLVAE--GF-AD-VEELACVKISEI 395
++ K E T+ F DE LV + G+ + VE + ++
Sbjct: 34 -----QEQF--NKILPEPTEGFAAD---DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQV 83
Query: 396 --ASIEGFDEETAVEIQGRAREYLEGIDI-TLQKKIRELGVSEELCSIPGIDSKIK---- 448
+ F+ YLEG DI L +L + ++ IK
Sbjct: 84 LNLCLTEFE-----------NCYLEGNDIHAL---AAKLLQENDT-TLVKTKELIKNYIT 128
Query: 449 --VALGENGIKTMED--LAGCSVDD------LLGWSENKG-GNIEK-FD----------G 486
+ + L + + G G GN + F+
Sbjct: 129 ARIMAKRP-FDKKSNSALFRAVGEGNAQLVAIFG-----GQGNTDDYFEELRDLYQTYHV 182
Query: 487 F-----------LSSLGTPKDQVESMIIHARYK-----MGWIEK-EKVADEE 521
LS L E + + + W+E D++
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKV-----FTQGLNILEWLENPSNTPDKD 229
Score = 46.9 bits (111), Expect = 1e-05
Identities = 62/379 (16%), Positives = 116/379 (30%), Gaps = 139/379 (36%)
Query: 40 RSLYGTMSDIRVEINPETGDI------SLFRLLEVVEEVENYTCQISLKVA-----RDRD 88
R LY T + V D+ +L L+ + E L +
Sbjct: 174 RDLYQTYHVL-VG------DLIKFSAETLSELIRTTLDAEKV-FTQGLNILEWLENPSNT 225
Query: 89 PSID--IGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEI---IS 143
P D + +S PL G +Q A V+ K+ L F GE+ +
Sbjct: 226 PDKDYLLSIPISCPL----IG--VIQLAHYVVTAKL---------LGFT--PGELRSYLK 268
Query: 144 GTVKRVEYGNVIVDLGNSDGVI------------------------------RRDETISR 173
G G+S G++ R E
Sbjct: 269 GAT------------GHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPN 316
Query: 174 ENLRP---------GDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPE---IY- 220
+L P + V S + + L++ Q V + +P +
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSIS----N----LTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 221 ---NG---IVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKI 274
NG +V VS P S L + ++ A G+ SR+ + K+
Sbjct: 369 SLVNGAKNLV----VSGPPQS---LYGL--NLTLRKAKAPSGLDQSRI-----PFSERKL 414
Query: 275 DIVV-WSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAI--GRRGQNVR-- 329
+ P ++ F + L PA + ++ +D+ + V + + + + G ++R
Sbjct: 415 KFSNRFLPVASPFHSHLLVPA--SDLIN-KDLVKNNVSFNAKDIQIPVYDTFDGSDLRVL 471
Query: 330 ---LASQLTGWTIDIITEE 345
++ ++ +D I
Sbjct: 472 SGSISERI----VDCIIRL 486
Score = 29.5 bits (66), Expect = 1.7
Identities = 34/230 (14%), Positives = 71/230 (30%), Gaps = 103/230 (44%)
Query: 1 MVSANRLELLQIADAVAYEKSID---------RDVVLSVM--ADSIQKA--ARSLYGTMS 47
M+S + L Q+ + ++ + V +S++ A ++ + +SLYG
Sbjct: 338 MLSISNLTQEQV------QDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 48 DIRVEINPETG-D-------------------ISL-FR--LLE-----VVEEVENYTCQI 79
+R + +G D ++ F LL + +++
Sbjct: 392 TLR-KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSF 450
Query: 80 S---LKV-------ARD-RDPSIDIGG-----VVSDP--------LPP---MDFGR---- 108
+ +++ D R S I ++ P +DFG
Sbjct: 451 NAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGAS 510
Query: 109 -VAVQSAKQVIIQKVREAERDRQYLEFKDKVGE--IISGTVKR---VEYG 152
+ V + + KD G I++GT+ +YG
Sbjct: 511 GLGVLTHRN------------------KDGTGVRVIVAGTLDINPDDDYG 542
Score = 28.4 bits (63), Expect = 4.1
Identities = 5/49 (10%), Positives = 13/49 (26%), Gaps = 13/49 (26%)
Query: 485 DGFLSSLGTPKDQVE-----SMIIH--ARYKMGWIEKEKVADEEVQDAS 526
+ F L P + + ++ +G+ V+
Sbjct: 35 EQFNKILPEPTEGFAADDEPTTPAELVGKF-LGY-----VSSLVEPSKV 77
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein,
escherichia coli NUSA, transcription regulation,
regulation of RNA binding; NMR {Escherichia coli} PDB:
2jzb_B
Length = 70
Score = 53.9 bits (130), Expect = 7e-08
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 18/82 (21%)
Query: 434 SEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGT 493
+++L ++ G+D + L G+ T+EDLA +DDL G
Sbjct: 6 ADDLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIE-----------------GL 48
Query: 494 PKDQVESMIIHARYKMGWIEKE 515
++ ++I+ AR + W E
Sbjct: 49 TDEKAGALIMAAR-NICWFGDE 69
Score = 35.4 bits (82), Expect = 0.033
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRARE 415
VD +A L A G +E+LA I ++A IEG +E A + AR
Sbjct: 15 VDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARN 62
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 39.3 bits (91), Expect = 0.002
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337
+P+ + +I + P ++++ D D G EVI+ E+ L IG+ G +R ++ GW
Sbjct: 76 TPEDSISIIEEVVPKESVISSYYFDPDSG--EVIIEAEKPGLVIGKHGATLREITKQIGW 133
Query: 338 TIDII 342
++
Sbjct: 134 IPKVV 138
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 37.8 bits (87), Expect = 0.006
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337
P+ A +I + P A +T + D VG EV++ ++ L IG+ G+ +RL +Q W
Sbjct: 81 PPEEAEKLIFEIVPKEAEITNIAFDPSVG--EVLIEAKKPGLVIGKNGETLRLITQKVKW 138
Query: 338 TIDII 342
++
Sbjct: 139 APKVV 143
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric
ring, heptamer, ring, oligomer, RAD51 polymerization
motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP:
a.60.4.1 c.37.1.11
Length = 349
Score = 37.4 bits (86), Expect = 0.009
Identities = 17/78 (21%), Positives = 24/78 (30%), Gaps = 3/78 (3%)
Query: 403 EETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDL 462
E EI E + + +PG+ L E G T+E +
Sbjct: 3 GEEVKEIDEFEELGFEPATEETPXXXXXEKIIRSIEDLPGVGPATAEKLREAGYDTLEAI 62
Query: 463 AGCSVDDLL---GWSENK 477
A S +L G SE
Sbjct: 63 AVASPIELKEVAGISEGT 80
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex,
RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB:
1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y*
1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y*
1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Length = 241
Score = 36.6 bits (84), Expect = 0.013
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 425 QKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLL---GWSENKGGNI 481
++ + EL I G+ +L E G +++ED+ G L G I
Sbjct: 5 EEDVEAEEEYTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARI 64
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain,
transcription, RNA binding protein; 2.27A {Pseudomonas
aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5
c.55.3.13 PDB: 3bzk_A 2oce_A
Length = 785
Score = 36.0 bits (83), Expect = 0.018
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 128 DRQYLEFKD-KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETIS-------RENLRP 178
KD K G ++ G V V VD+G DG++ +S E ++
Sbjct: 643 QEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISA-LSEKFVKDPYEVVKA 701
Query: 179 GDRVKSYIYDVRREQRGPQVLLS 201
GD VK + +V + +V LS
Sbjct: 702 GDIVKVKVMEVDIPRN--RVGLS 722
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 35.7 bits (82), Expect = 0.025
Identities = 11/47 (23%), Positives = 21/47 (44%)
Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQ 352
G I+V VP+ + + IGR G+ ++ G I ++ +
Sbjct: 11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKI 57
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo
sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1
Length = 308
Score = 34.5 bits (79), Expect = 0.059
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 11/80 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETIS-------RENLRPGDRVKSYI 186
+V +++ V+ ++ V L N +G+I E +S + +R G +
Sbjct: 12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSE-LSRRRIRSINKLIRIGRNECVKV 70
Query: 187 YDVRREQRGPQVLLSRTHPQ 206
V +E+ + R P+
Sbjct: 71 IRVDKEKGYIDLSKRRVSPE 90
>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 = 34.4 bits (78), Expect = 0.065
Identities = 14/57 (24%), Positives = 24/57 (42%)
Query: 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE 418
MQ V A L GF +E+++ + E+ IEG +T I + ++
Sbjct: 648 LMQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLGKNVK 704
Score = 33.3 bits (75), Expect = 0.16
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 422 ITLQKKIRELGVSEELC---SIPGIDSKIKVALGENGIKTMEDLAGCSVDDL---LGWSE 475
TL+ ++ + G+ EEL +P + + AL +G +++ED++ ++L G
Sbjct: 631 ETLRVRV-KYGIREELIPLMQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGV 689
Query: 476 NKGGNIEKF 484
I KF
Sbjct: 690 KTVEAIFKF 698
>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 = 34.2 bits (77), Expect = 0.078
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 18/42 (42%)
Query: 261 RVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLD 302
++QA L+ +++ DSA PA+ K ++
Sbjct: 24 KLQA---SLK-------LYADDSA--------PALAIKATME 47
Score = 31.9 bits (71), Expect = 0.39
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 78 QISLKV-ARDRDPSIDI 93
Q SLK+ A D P++ I
Sbjct: 26 QASLKLYADDSAPALAI 42
Score = 28.0 bits (61), Expect = 5.6
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 10/31 (32%)
Query: 236 RAKLAVFSSDSSIDPVGACVGMRGSRVQAVV 266
+A L +++ DS+ P A ++A +
Sbjct: 26 QASLKLYADDSA--PALA--------IKATM 46
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP
complex, calcium stimulation, RECA, DMC1; HET: DNA ANP;
1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11
PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A*
3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ewa_A* 3ew9_A* 3etl_A*
2gdj_A*
Length = 322
Score = 33.8 bits (76), Expect = 0.095
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 434 SEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDL---LGWSENK 477
+ L +PG+ L E G +A +V +L G SE
Sbjct: 2 GDNLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKA 48
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus
musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB:
1kdh_A* 1kej_A*
Length = 381
Score = 33.9 bits (77), Expect = 0.100
Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 7/74 (9%)
Query: 392 ISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRE---LGVSEELCSIPGIDSKIK 448
+ + I ++ I+ +E + + K + + S+ G+ K
Sbjct: 79 MKDTEGIPCLGDKVKSIIE----GIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTA 134
Query: 449 VALGENGIKTMEDL 462
G +T+ +
Sbjct: 135 EKWFRMGFRTLSKI 148
>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA
binding, molecular switch, RECA, DMC1; HET: DNA; 1.93A
{Sulfolobus solfataricus P2} PDB: 2bke_A* 2dfl_A*
2zub_A* 2zuc_A* 2zud_A*
Length = 324
Score = 33.7 bits (76), Expect = 0.10
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 435 EELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLL 471
+ + +PGI + L E G ++E LA S DL
Sbjct: 12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLS 48
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 33.7 bits (77), Expect = 0.10
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
E+ +P + IGR+G N+ Q++G I I E S R
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGR 51
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA
complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus
horikoshii} PDB: 1yz6_A
Length = 275
Score = 33.5 bits (76), Expect = 0.12
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 11/80 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSDGV----------IRRDETISRENLRPGDRVKSYI 186
+ GE + TVKR+ ++L G I + L+ G +V + +
Sbjct: 10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIR-DYLKEGQKVVAKV 68
Query: 187 YDVRREQRGPQVLLSRTHPQ 206
V + + L R Q
Sbjct: 69 IRVDPRKGHIDLSLRRVTQQ 88
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2,
initiation factor 2 alpha subunit, initiation factor 2
beta subunit; 2.80A {Sulfolobus solfataricus} PDB:
2aho_B
Length = 266
Score = 33.3 bits (76), Expect = 0.13
Identities = 18/84 (21%), Positives = 29/84 (34%), Gaps = 11/84 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSDGV----------IRRDETISRENLRPGDRVKSYI 186
GEI+ TVK+V V L G+ + + I + L+ +V +
Sbjct: 10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIR-DVLKENRKVIVKV 68
Query: 187 YDVRREQRGPQVLLSRTHPQFMVK 210
V R + V L + K
Sbjct: 69 IRVDRRKGTVDVSLKKVTDDERRK 92
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 33.1 bits (74), Expect = 0.14
Identities = 11/60 (18%), Positives = 22/60 (36%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAIN 367
I+V +P+ + + IGR G+ ++ G I ++ + R A
Sbjct: 5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAE 64
Score = 30.4 bits (67), Expect = 1.2
Identities = 22/143 (15%), Positives = 41/143 (28%), Gaps = 7/143 (4%)
Query: 214 MEVPEIYNGIV------QVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVT 267
+ +P GIV +K + D G R + + G A
Sbjct: 7 VPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIA-QITGPPDRAQHAAEI 65
Query: 268 ELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQN 327
+ R + + IVP + L IG+ G+
Sbjct: 66 ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGET 125
Query: 328 VRLASQLTGWTIDIITEEEDSIN 350
++ SQ +G I++ + +
Sbjct: 126 IKSISQQSGARIELQRNPPPNAD 148
>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 = 33.3 bits (75), Expect = 0.14
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 4/61 (6%)
Query: 424 LQKKIRELGVSEELC---SIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGN 480
L ++I+ GV EEL I I L GI+ ED+
Sbjct: 619 LTERIKH-GVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVASLIGRGIAER 677
Query: 481 I 481
+
Sbjct: 678 V 678
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix,
fidelity, processivity, transferase; 2.30A {Sulfolobus
solfataricus} SCOP: e.8.1.7
Length = 221
Score = 33.2 bits (75), Expect = 0.15
Identities = 12/52 (23%), Positives = 27/52 (51%)
Query: 419 GIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDL 470
G+ + ++++ ++ IPGI S + L E GI+ + D+ + ++L
Sbjct: 168 GLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNEL 219
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 109
Score = 33.0 bits (75), Expect = 0.16
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 9/73 (12%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR-------ENLRPGDRVKSYIYDV 189
K G I++G V V+ V+L + R SR L GD V++ V
Sbjct: 30 KKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGV 89
Query: 190 RREQRGPQVLLSR 202
R+ R + LS
Sbjct: 90 DRKNR--AISLSV 100
>1yz6_A Probable translation initiation factor 2 alpha subunit; beta
barrel, helical domain and alpha beta domain; 3.37A
{Pyrococcus abyssi}
Length = 274
Score = 33.0 bits (75), Expect = 0.16
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 11/80 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSDGVI----------RRDETISRENLRPGDRVKSYI 186
+ GE + TVKR+ ++L G I + L+ G +V + +
Sbjct: 9 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIR-DYLKEGQKVVAKV 67
Query: 187 YDVRREQRGPQVLLSRTHPQ 206
V + + L R Q
Sbjct: 68 IRVDPRKGHIDLSLRRVTQQ 87
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I KH domains, fragIle X mental retardation protein,
RNA binding protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 32.9 bits (74), Expect = 0.16
Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 7/118 (5%)
Query: 309 EVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSI-------NRQKDFNERTQF 361
+ IV ++ + LAIG G N++ A ++ G T + E+ + + K +F
Sbjct: 7 QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEF 66
Query: 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEG 419
I V + ++ + ++E+ IE +E+ + +G G
Sbjct: 67 AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVG 124
>3go5_A Multidomain protein with S1 RNA-binding domains; structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4}
Length = 285
Score = 32.7 bits (74), Expect = 0.20
Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 4/59 (6%)
Query: 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194
+ I G + V + ++E GD VK + Y +++
Sbjct: 4 TNLASFIVGLIIDENDRFYFVQKDGQTYALAKEE----GQHTVGDTVKGFAYTDMKQKL 58
Score = 27.3 bits (60), Expect = 9.6
Identities = 8/62 (12%), Positives = 20/62 (32%)
Query: 133 EFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRRE 192
+ + + V R++ V L ++ + + R G + + + R
Sbjct: 147 AYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAEPRLGQVLDARVIGFREV 206
Query: 193 QR 194
R
Sbjct: 207 DR 208
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 32.7 bits (74), Expect = 0.20
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 309 EVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQK 353
E+++P + L IG+ G+ ++ + G + +I + + N K
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDK 61
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA
binding protein; NMR {Bacillus subtilis}
Length = 130
Score = 32.7 bits (74), Expect = 0.21
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 9/78 (11%)
Query: 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGNS-------DGVIRRDETISRENLRPGDRVKS 184
+ K +VG + +G V ++ V L V E+L GD V+
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 185 YIYDVRREQRGPQVLLSR 202
+ V E+ ++ LS
Sbjct: 61 KVLAVDEEKG--KISLSI 76
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 32.5 bits (74), Expect = 0.22
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
E+ +P + + IGR+G + Q++G I I E S +R
Sbjct: 7 HELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDR 50
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 32.5 bits (74), Expect = 0.23
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 18/85 (21%)
Query: 395 IASIEGFDEETAVEIQGRAREYLEGIDITLQKKIREL---GVSE--------------EL 437
S+E +EET + + + + ++ + G +L
Sbjct: 41 ARSLEELNEETPELLAREFTG-IPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDL 99
Query: 438 CSIPGIDSKIKVALGENGIKTMEDL 462
+ G+ K +L GI ++E L
Sbjct: 100 LGVRGLGPKKIRSLWLAGIDSLERL 124
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 32.6 bits (74), Expect = 0.25
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAIN 367
I+V VP + L +G +G ++ Q T I +++ + E + I
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI- 70
Query: 368 VDEIIA 373
+ I
Sbjct: 71 -EAHIT 75
>1we8_A Tudor and KH domain containing protein; structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 32.3 bits (73), Expect = 0.29
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
++ VP+ + IGR G+ +R + +G I E E +
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT 57
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transferase; 2.30A {Saccharomyces cerevisiae} SCOP:
b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G
1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G*
2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H
3hou_G* 3hov_G* ...
Length = 171
Score = 32.3 bits (73), Expect = 0.29
Identities = 14/95 (14%), Positives = 27/95 (28%), Gaps = 16/95 (16%)
Query: 123 REAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI----------- 171
E + + FK GE++ GTV V +G + +
Sbjct: 68 AEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNP 127
Query: 172 -----SRENLRPGDRVKSYIYDVRREQRGPQVLLS 201
S + + R++ I + + S
Sbjct: 128 PSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGS 162
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein/RNA complex; HET:
5BU; 1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 31.5 bits (70), Expect = 0.43
Identities = 19/159 (11%), Positives = 48/159 (30%), Gaps = 15/159 (9%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAIN 367
++V++P IG+ GQ + + TG TI + ++ +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETA------------VEIQGRARE 415
V IA + + + ++ + G +
Sbjct: 68 VHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 416 YLE---GIDITLQKKIRELGVSEELCSIPGIDSKIKVAL 451
+ G + L +K + + + ++ G + + A+
Sbjct: 128 AIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV 166
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-binding,
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 31.8 bits (71), Expect = 0.45
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 423 TLQKKIRELGVSEELC---SIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGG 479
L ++R+ G+ EEL I G+ K L NGIK + D+ + G
Sbjct: 643 ILNLRVRD-GIKEELLELVQISGVGRKRARLLYNNGIKELGDVVMNPDKVKNLLGQKLGE 701
Query: 480 NI 481
+
Sbjct: 702 KV 703
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1 PDB: 2opu_A
Length = 92
Score = 31.4 bits (71), Expect = 0.46
Identities = 12/44 (27%), Positives = 17/44 (38%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
E VP + IGR G+ + Q +G I I + R
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPER 60
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif; 2.00A {Homo sapiens}
SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 31.4 bits (71), Expect = 0.47
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
+E+ VP+ + +G+ G+ + +LTG I I + E
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG 47
>1kl9_A Eukaryotic translation initiation factor 2 subunit 1; OB fold,
helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1
b.40.4.5
Length = 182
Score = 31.4 bits (71), Expect = 0.50
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 9/67 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDE------TISRENLRPGDRVKSYIY 187
+V +++ V+ + V L N +G+I E + +R G +
Sbjct: 14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73
Query: 188 DVRREQR 194
V +E+
Sbjct: 74 RVDKEKG 80
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 172
Score = 31.2 bits (70), Expect = 0.51
Identities = 9/84 (10%), Positives = 23/84 (27%), Gaps = 16/84 (19%)
Query: 134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI----------------SRENLR 177
++ GE++ V V ++G + + + +
Sbjct: 80 WRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIE 139
Query: 178 PGDRVKSYIYDVRREQRGPQVLLS 201
G V+ I R + + +
Sbjct: 140 KGSNVRLKIVGTRTDATEIFAIAT 163
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase,
transcription; 1.75A {Methanococcus jannaschii} SCOP:
b.40.4.5 d.230.1.1
Length = 187
Score = 31.2 bits (70), Expect = 0.68
Identities = 21/110 (19%), Positives = 35/110 (31%), Gaps = 22/110 (20%)
Query: 105 DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGV 164
D G V V + L + ++ E+I G V V V LG DG+
Sbjct: 53 DIGEGKVVHGDGSAYHPVV-----FETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGL 107
Query: 165 IRRDE-----------------TISRENLRPGDRVKSYIYDVRREQRGPQ 197
I + + + L GD V++ I + + +
Sbjct: 108 IHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR 157
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium; 1.80A {Deinococcus radiodurans R1} SCOP:
b.40.4.5 b.40.4.16 PDB: 2r7f_A
Length = 469
Score = 30.7 bits (68), Expect = 0.75
Identities = 8/74 (10%), Positives = 18/74 (24%), Gaps = 9/74 (12%)
Query: 123 REAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNS--DGVIRRDETISRENLRPGD 180
R + R + + V + + + D + PG
Sbjct: 388 RLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTP-------AAPGT 440
Query: 181 RVKSYIYDVRREQR 194
++ D+ Q
Sbjct: 441 ALQVQFADIDLPQM 454
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 30.6 bits (69), Expect = 0.82
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
+V +PK+ IG+ GQ ++ +G +I I E S +R
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDR 59
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha
subunit; transferase, protein biosynthesis, protein
synthesis/transferase complex; HET: TPO ANP; 2.50A
{Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A
Length = 175
Score = 30.8 bits (69), Expect = 0.84
Identities = 5/28 (17%), Positives = 13/28 (46%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSDGV 164
++ +I+ V+++ V L D +
Sbjct: 14 EIDDIVMVNVQQIAEMGAYVKLLEYDNI 41
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 30.5 bits (68), Expect = 1.0
Identities = 30/149 (20%), Positives = 47/149 (31%), Gaps = 8/149 (5%)
Query: 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAI 366
RI V V E+L IG RG+ + TG I + TE I + M+A
Sbjct: 5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAA 64
Query: 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQK 426
V + I+ L + + R + + G ++
Sbjct: 65 EVVKAISL---GFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARR 121
Query: 427 KIREL-----GVSEELCSIPGIDSKIKVA 450
I E+ V E +I G + A
Sbjct: 122 TIEEMTDTYINVGEYEVAIIGDYERAMAA 150
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1
Length = 94
Score = 30.3 bits (68), Expect = 1.1
Identities = 9/46 (19%), Positives = 22/46 (47%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQK 353
E+++P + L IG+ G+ ++ + G + +I + + K
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADK 62
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 29.9 bits (67), Expect = 1.3
Identities = 13/79 (16%), Positives = 22/79 (27%), Gaps = 8/79 (10%)
Query: 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETIS--------RENLRPGDRVK 183
+E + I G V V + + T E + GD+V
Sbjct: 16 MENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVW 75
Query: 184 SYIYDVRREQRGPQVLLSR 202
+ + +V LS
Sbjct: 76 VKLIGREMKNDRIKVSLSM 94
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 29.8 bits (67), Expect = 1.6
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
V +PKE IG+ G+ ++ T I I ++ S
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS 59
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 29.5 bits (66), Expect = 1.8
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
IEV VP + IG++G +R I + E S
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQS 59
>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding
protein; structural genomics, NPPSFA; 1.94A {Pyrococcus
horikoshii}
Length = 362
Score = 29.5 bits (66), Expect = 1.8
Identities = 25/104 (24%), Positives = 35/104 (33%), Gaps = 13/104 (12%)
Query: 84 ARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIIS 143
A+ D + I P+P V +VII R E GE I
Sbjct: 244 AKVEDGKLVITEKSKLPIPKQYVEIVKETGITEVII-GFRP-----HDAEIVKGEGEGIV 297
Query: 144 GTVKRVEY-GN---VIVDLGNSDGVIRRDETISRENLRPGDRVK 183
G V E G V V + +S + E E+ G++V
Sbjct: 298 GEVYSFEPLGREQIVTVSVNDSIVKVFAPE---GEHFSFGEKVT 338
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
mutation, deletion, streisinger, slippage, transferase,
lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A*
2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A*
1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A*
1rzt_A* 3hx0_A* 1nzp_A*
Length = 335
Score = 29.4 bits (65), Expect = 1.9
Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 5/73 (6%)
Query: 391 KISEIASIEGFDEETAVEIQGRAREYLE-GIDITLQKKIRELGVSEELCSIPGIDSKIKV 449
E SI G + A +I E LE G L + V E +I G +K
Sbjct: 55 SYQEACSIPGIGKRMAEKII----EILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQ 110
Query: 450 ALGENGIKTMEDL 462
+ G +++ED+
Sbjct: 111 MWYQQGFRSLEDI 123
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding
motif, protein/RNA structure, RNA binding protein/RNA
complex; 2.40A {Homo sapiens} SCOP: d.51.1.1
Length = 87
Score = 29.5 bits (66), Expect = 1.9
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
+E+ VP+ + +G+ G+ + +LTG I I + E
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG 47
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 29.4 bits (66), Expect = 1.9
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
+V +PK+ IG+ GQ ++ +G +I I E S +R
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDR 52
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform
B'; KH domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.51.1.1
Length = 91
Score = 29.1 bits (65), Expect = 2.2
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 309 EVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
E +V ++ + LAIG G N++ A ++ G T + E+ +
Sbjct: 18 EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRI 60
>2knj_A Microplusin preprotein; antimicrobial peptide, rhipicephalus
(boophilus) microplus, antimicrobial protein; NMR
{Rhipicephalus microplus}
Length = 90
Score = 29.1 bits (65), Expect = 2.4
Identities = 8/54 (14%), Positives = 17/54 (31%), Gaps = 7/54 (12%)
Query: 423 TLQKKIRELGVSEELCSI------PGIDSKIKVALGENGIKTMEDLAG-CSVDD 469
+++L C+ ++ + V IK + D A C +
Sbjct: 31 AFDNAVQQLNCLNRACAYRKMCATNNLEQAMSVYFTNEQIKEIHDAATACDPEA 84
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.0 bits (64), Expect = 2.6
Identities = 60/267 (22%), Positives = 109/267 (40%), Gaps = 67/267 (25%)
Query: 314 KEQLSL-AIGRRGQNVRLASQLT------GWTI--------DIITEEEDSINRQKDFNER 358
+ +LSL + R + A+QLT GWT +II E + + + F+++
Sbjct: 642 ESKLSLETLFNRWHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGIEKMG-VRTFSQK 700
Query: 359 TQFF-MQAINVDEIIAHLLVAEGFAD-------VEELA---------CVKISEI---ASI 398
F + + E++ + AD V EL V+ SE+ SI
Sbjct: 701 EMAFNLLGLLTPEVVELCQKSPVMADLNGGLQFVPELKEFTAKLRKELVETSEVRKAVSI 760
Query: 399 E---------GFDEETA---VEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSK 446
E G + A VEIQ RA L+ ++ K+++++ + EL + ++
Sbjct: 761 ETALEHKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQVKQIAPA-ELEGLLDLERV 819
Query: 447 IKV-ALGENG----IKT---ME-----DLAGC-SVDDLLGWSENKGGNIE--KFDGFLSS 490
I V E G +T ME L GC + ++G+ GN++ + G++ S
Sbjct: 820 IVVTGFAEVGPWGSARTRWEMEAFGEFSLEGCVEMAWIMGFISYHNGNLKGRPYTGWVDS 879
Query: 491 LGTPKDQVESMIIHARYKMGWIEKEKV 517
K+ V+ + A+Y+ +E +
Sbjct: 880 --KTKEPVDDKDVKAKYETSILEHSGI 904
Score = 28.6 bits (63), Expect = 3.2
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 43 YGTMSDIRVEINPETGDISLFRLLEVVE 70
YG DI +++P I+LF L+ VVE
Sbjct: 999 YGISDDIISQVDP----ITLFVLVSVVE 1022
>2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair,
hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A
2zxp_A 1ir6_A
Length = 666
Score = 28.9 bits (64), Expect = 3.0
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 357 ERTQFFMQAINVDEIIAHLLVAEGFADVEEL 387
+ + M A+ V A GF E+L
Sbjct: 16 AQWREVMAALEVGPEAALAYWHRGFRRKEDL 46
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 28.8 bits (63), Expect = 3.1
Identities = 10/47 (21%), Positives = 23/47 (48%)
Query: 309 EVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF 355
E+++P + L IG+ G+ ++ + G + +I + + N K
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPL 51
Score = 28.4 bits (62), Expect = 4.4
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
I+V VP+ + + IGR G+ ++ G I ++ +
Sbjct: 93 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEK 136
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide;
DNA-dependent RNA polymerase, cellular RNA polymerase;
4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5
d.230.1.1 PDB: 2bbm_B 2bbn_B
Length = 215
Score = 28.5 bits (63), Expect = 3.4
Identities = 15/107 (14%), Positives = 31/107 (28%), Gaps = 16/107 (14%)
Query: 111 VQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDET 170
+Q + + E + + FK GE++ GTV V +G + +
Sbjct: 56 IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLM 115
Query: 171 I----------------SRENLRPGDRVKSYIYDVRREQRGPQVLLS 201
S + + R++ I + + S
Sbjct: 116 PQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGS 162
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 28.6 bits (64), Expect = 3.5
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
+E+ + + IG+ G N+ ++ I + E S
Sbjct: 7 VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS 47
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein/DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1
PDB: 2pqu_A 2py9_A 1ztg_A
Length = 73
Score = 28.2 bits (63), Expect = 5.0
Identities = 8/41 (19%), Positives = 22/41 (53%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
I +++ +++ IG++G++V+ + +G I+I
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE 47
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 27.9 bits (62), Expect = 5.5
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 20/82 (24%)
Query: 110 AVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRV-EYGNVIVDLGNSDGVI--- 165
+ A + I + E E VG + +G V R+ ++G + G +G++
Sbjct: 610 KAKHAIRRIEEITAEIE-----------VGRVYTGKVTRIVDFGAFVAIGGGKEGLVHIS 658
Query: 166 ----RRDETISRENLRPGDRVK 183
+R E ++ + L+ G V
Sbjct: 659 QIADKRVEKVT-DYLQMGQEVP 679
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 103
Score = 27.9 bits (62), Expect = 6.0
Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 11/67 (16%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNS----DGVIRRDETIS-------RENLRPGDRVKSY 185
+G+I +G V + V L +G++ E + + G RVK
Sbjct: 11 TIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVK 70
Query: 186 IYDVRRE 192
+
Sbjct: 71 VLSFTGT 77
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 115
Score = 27.7 bits (61), Expect = 6.6
Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 10/79 (12%)
Query: 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI--------RRDETISRENLRPGDRVK 183
+ + G ++G V + V++ + + + GD V+
Sbjct: 24 IAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVE 83
Query: 184 SYIYDVRREQRGPQVLLSR 202
+ D+ E+R ++ L
Sbjct: 84 VMVLDIDEERR--RISLGL 100
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 27.7 bits (61), Expect = 6.8
Identities = 7/44 (15%), Positives = 16/44 (36%)
Query: 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
++ V V + IGR+G + I +++ +
Sbjct: 18 KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQP 61
>3f2v_A General stress protein 14; alpha-beta protein., structural
genomics, PSI-2, protein structure initiative; HET: FMN;
2.00A {Treponema denticola}
Length = 192
Score = 27.7 bits (61), Expect = 6.9
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKK 427
V E++ + + + + I S G+ E E++ AR+YL +D LQ+
Sbjct: 126 VAEVLRPFELTAKYCNADYRPPFTFHTIDSNAGYSEAARQEVERSARDYLAWLD-ALQQT 184
Query: 428 I 428
+
Sbjct: 185 L 185
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 27.7 bits (61), Expect = 7.0
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
G + +P + L IGR G+NV+ +Q TG ++I + + +
Sbjct: 7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGD 51
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription
regulation, DNA-directed RNA polymer
nucleotidyltransferase; HET: MLY; 2.05A {Escherichia
coli k-12} PDB: 1lb2_B* 1xs9_D
Length = 86
Score = 27.3 bits (61), Expect = 7.7
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 10/52 (19%)
Query: 420 IDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLL 471
D L + + +L ++ + L I + DL + +LL
Sbjct: 6 FDPILLRPVDDLELT----------VRSANCLXAEAIHYIGDLVQRTEVELL 47
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 27.4 bits (60), Expect = 7.7
Identities = 10/43 (23%), Positives = 22/43 (51%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSIN 350
++V +P + + IG++GQ+++ S+ +I I E
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSK 47
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 27.6 bits (61), Expect = 8.0
Identities = 11/78 (14%), Positives = 20/78 (25%)
Query: 303 EDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFF 362
E + +V + + IG RG+ +R I N
Sbjct: 14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 73
Query: 363 MQAINVDEIIAHLLVAEG 380
++ + L G
Sbjct: 74 EAIDHILNLEEEYLADSG 91
>1d5g_A Human phosphatase HPTP1E; protein-peptide complex, hydrolase; NMR
{Homo sapiens} SCOP: b.36.1.1 PDB: 3pdz_A 1vj6_A 1gm1_A
1ozi_A
Length = 96
Score = 27.5 bits (61), Expect = 8.5
Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 4/65 (6%)
Query: 26 VVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVAR 85
V +V+ A D + +N + + VE + N + L + +
Sbjct: 36 YVKAVIPQGA--AESDGRIHKGDRVLAVNGV--SLEGATHKQAVETLRNTGQVVHLLLEK 91
Query: 86 DRDPS 90
+ P+
Sbjct: 92 GQSPT 96
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 27.2 bits (60), Expect = 8.7
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 303 EDVGRIEVIVPKEQLSLAIGRRGQNVR-LASQLTGWTIDIITEEEDS 348
++ +EV +P + + IG +G+ +R + + G I E S
Sbjct: 14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS 60
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
cytoplasm, DNA-binding, nucleus, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Homo sapiens}
Length = 160
Score = 27.5 bits (60), Expect = 8.7
Identities = 22/150 (14%), Positives = 52/150 (34%), Gaps = 12/150 (8%)
Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAIN 367
I +++ +++ IG++G++V+ + +G I+I F A+
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMI 66
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEI------ASIEGFDEETAVEIQGRAREYLEGID 421
+D++ + + + V + + S+ G EI+ G
Sbjct: 67 IDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST-----GAQ 121
Query: 422 ITLQKKIRELGVSEELCSIPGIDSKIKVAL 451
+ + +E +I GI I +
Sbjct: 122 VQVAGD-MLPNSTERAITIAGIPQSIIECV 150
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanocaldococcus jannaschii}
Length = 80
Score = 27.3 bits (60), Expect = 8.8
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 137 KVGEIISGTVKRV-EYGNVIVDLGNSDGVIRRDE--TISRENLRPGDRVKSYIYDVRREQ 193
+ G+ G V R+ +YG I G++R + ++ ENL GD + DVR E+
Sbjct: 4 EPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAIDVRPEK 63
Query: 194 R 194
R
Sbjct: 64 R 64
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 27.4 bits (61), Expect = 9.0
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 282 DSATFVINALRPAIVTKVVLDEDVGRIEVI-VPKEQLSLAIGRRGQNVRLASQLTGWTID 340
D+ +++ + AI T + + RI + +P +++ IG + Q + + TG I
Sbjct: 573 DARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEIT 632
Query: 341 I 341
I
Sbjct: 633 I 633
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.317 0.136 0.375
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 4,557,345
Number of extensions: 226569
Number of successful extensions: 928
Number of sequences better than 10.0: 1
Number of HSP's gapped: 898
Number of HSP's successfully gapped: 130
Length of query: 526
Length of database: 5,693,230
Length adjustment: 97
Effective length of query: 429
Effective length of database: 3,341,562
Effective search space: 1433530098
Effective search space used: 1433530098
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.7 bits)