RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15222
(444 letters)
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA
polymerase, replication protein, transferase; HET: DNA;
1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A*
1eqn_A* 3b39_A*
Length = 338
Score = 356 bits (915), Expect = e-121
Identities = 117/320 (36%), Positives = 183/320 (57%), Gaps = 16/320 (5%)
Query: 1 MICASDFYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NI 57
M + FY+ L+ + A +L+KRGL+ E+I RF +G+AP W+ + K F N
Sbjct: 25 MDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENR 84
Query: 58 NTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNE 117
+L +G++V ++ + YDRFR R+MFPI++ G++IGFGGR++ +
Sbjct: 85 QSLIDAGMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGND-T 132
Query: 118 AKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGT 177
KY+NSPET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+G VA LGT
Sbjct: 133 PKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGT 192
Query: 178 ACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPD 237
+ T+ HI+ + TN++I +DGD+AGR AA RALE L Y TD + ++F+FLPD DPD
Sbjct: 193 STTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPD 252
Query: 238 SYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSS 297
+ +RK G + F ++ +AM L F ++ +L T + L +P +
Sbjct: 253 TLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP-GET 311
Query: 298 LRFKIISSLSKIIKVSFNEI 317
LR + L + + +
Sbjct: 312 LRIYLRQELGNKLGILDDSQ 331
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication,
transf; HET: DNA; 2.00A {Aquifex aeolicus}
Length = 407
Score = 353 bits (908), Expect = e-119
Identities = 91/319 (28%), Positives = 153/319 (47%), Gaps = 24/319 (7%)
Query: 4 ASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASS 63
DFY+ L ++EA ++K RG++ ++ +F+LGYAP+ + + + L +
Sbjct: 112 VCDFYRESLLKNREASEYVKSRGIDPKVARKFDLGYAPSSEALVKVLKENDLLEAYLETK 171
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
L+ K D F R++ PIK+ G++IGFGGR I + KYINS
Sbjct: 172 NLLSP------------TKGVYRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINS 219
Query: 124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
P++ +F K L+GL+EAK I++ G+ ++ EGY D++ L G VA LGTA T
Sbjct: 220 PDSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQNQ 279
Query: 184 IKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
+ +T + +DGD AGR+A + A+ + L + + ++LP+ YDPD +I++F
Sbjct: 280 ANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLL---SAGVEVYPVYLPEGYDPDEFIKEF 336
Query: 244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKII 303
G + + + + L + ++ N KT + Y I RF +
Sbjct: 337 GKEELRRLINSSGELFETLIKTARENLEEKTRE--------FRYYLGFIS-DGVRRFALA 387
Query: 304 SSLSKIIKVSFNEINNLFK 322
S KV + +
Sbjct: 388 SEFHTKYKVPMEILLMKIE 406
>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside
polyph protein-ligand complex, transferase; HET: DNA
ATP; 2.00A {Staphylococcus aureus} PDB: 4edk_A* 4edr_A*
4edt_A* 4edv_A* 4ee1_A*
Length = 329
Score = 336 bits (864), Expect = e-114
Identities = 100/329 (30%), Positives = 155/329 (47%), Gaps = 23/329 (6%)
Query: 4 ASDFYKIQLKNSKE---AINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINT 59
+FY L + E A+ +L++RG + +I +G+AP+ + + +I
Sbjct: 15 IQEFYYYALTKTVEGEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIEL 74
Query: 60 LASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAK 119
+GL+ E + YDRFR RIMFP+KN G+I+G+ GR E K
Sbjct: 75 AYEAGLLSRNE----------ENFSYYDRFRNRIMFPLKNAQGRIVGYSGRTYTGQ-EPK 123
Query: 120 YINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTAC 179
Y+NSPETP+F K LY L +A+ +I K +++ EG+MDVI G VA +GT
Sbjct: 124 YLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQL 183
Query: 180 TSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSY 239
+ HI I T++I FDGD AG A + + L + + LP DPD Y
Sbjct: 184 SDEHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLL---QQGLNVFVIQLPSGMDPDEY 240
Query: 240 IRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPL--SSS 297
I K+G F+ V + I+ + D+ +Y ++ L I L SS
Sbjct: 241 IGKYGNDAFTTFVKNDKKSFAHYKVSILKDEIAHN--DLSYERY-LKELSHDISLMKSSI 297
Query: 298 LRFKIISSLSKIIKVSFNEINNLFKINTS 326
L+ K I+ ++ VS ++ N + N +
Sbjct: 298 LQQKAINDVAPFFNVSPEQLANEIQFNQA 326
>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 = 65.5 bits (159), Expect = 2e-11
Identities = 71/383 (18%), Positives = 123/383 (32%), Gaps = 143/383 (37%)
Query: 7 FYKIQLKNSKEAINFLKK-----RGL---NE-----EIILRFNLGY-----APNEWNALN 48
F QL+ F K G +E E++ +F LGY P++ +
Sbjct: 28 FIASQLQEQ-----FNKILPEPTEGFAADDEPTTPAELVGKF-LGYVSSLVEPSKVGQFD 81
Query: 49 KV-----------FLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMF-- 95
+V +L+ N+I+ LA+ L+ + V +I+ Y RIM
Sbjct: 82 QVLNLCLTEFENCYLEGNDIHALAAK-LLQENDTTLVKTKELIKNY-----ITARIMAKR 135
Query: 96 PIKN----------TDGQ--IIG-FGG-----------RLIKDSNEAKYINSPETPLFHK 131
P +G ++ FGG R + + Y + L
Sbjct: 136 PFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT----Y-HVLVGDLIKF 190
Query: 132 SNE-LYGLFEAKNAIEK---SGYVLIT----------EGYMD-------VIGLSQFG-FL 169
S E L L EK G ++ + Y+ +IG+ Q ++
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250
Query: 170 QTVAILG---------TACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYAT 220
T +LG + H + ++ T I D ++ + R+A+ V
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHSQGLV--TAVAIAETDSWESFFVSVRKAITV------ 302
Query: 221 DDKIIKFLFL---------PDKYDPDSYIRKFGYKIFSKKVLEA----M----SLLQFFL 263
LF P+ P S + S + E M +L Q +
Sbjct: 303 -------LFFIGVRCYEAYPNTSLPPSILED------SLENNEGVPSPMLSISNLTQEQV 349
Query: 264 EEII--LNYNLKTIKDIEKSKYN 284
++ + N +L K +E S N
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLVN 372
Score = 44.7 bits (105), Expect = 7e-05
Identities = 48/297 (16%), Positives = 78/297 (26%), Gaps = 116/297 (39%)
Query: 75 NQSPVIEK-YKRYDRFRGRIM-FPI-----KNTDGQIIGFGG------------------ 109
S + + R D F I N I FGG
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETI 1696
Query: 110 --------RLIKDSNEA--KYI-NSPETPLFHKSN--------ELYGLFEAKNAIEKSGY 150
++ K+ NE Y S + L E FE ++ G
Sbjct: 1697 VDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME-KAAFED---LKSKG- 1751
Query: 151 VLITEGYMDVIGLSQFGFLQTVAILG--TA--CTSTHIK-----KILFYTNSIIFSFDGD 201
LI G S LG A + + +++FY
Sbjct: 1752 -LIPADAT-FAGHS----------LGEYAALASLADVMSIESLVEVVFY----------- 1788
Query: 202 QAGR-RAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQ 260
R + A+ L ++ +I +P F + V
Sbjct: 1789 ---RGMTMQVAVPRDELGRSNYGMIAI-------NPGRVAASFSQEALQYVVERVGKRTG 1838
Query: 261 FFLEEIILNYNLK--------TIKDIE---------KSKYNIEYLFKIIPLSSSLRF 300
+ +E I+NYN++ ++ ++ K + I II L SL
Sbjct: 1839 WLVE--IVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQ-KI----DIIELQKSLSL 1888
Score = 30.0 bits (67), Expect = 2.1
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 25/79 (31%)
Query: 374 QNYVKMFFQLIDTIHIFKNDIDHS-KFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKT- 431
+NY M IF+ +D K K K+IN++ S F + T
Sbjct: 1686 ENYSAM---------IFETIVDGKLKTEKIFKEINEHSTSYT------FRSEKGLLSATQ 1730
Query: 432 -----LL---DAIYKDRKS 442
L A ++D KS
Sbjct: 1731 FTQPALTLMEKAAFEDLKS 1749
>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 = 54.1 bits (129), Expect = 7e-08
Identities = 82/522 (15%), Positives = 166/522 (31%), Gaps = 144/522 (27%)
Query: 6 DFYKIQ--LKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD---YNNIN 58
D +Q K+ SKE I+ + + ++ + + F++ N
Sbjct: 34 DCKDVQDMPKSILSKEEIDHIIMSK-DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYK 92
Query: 59 TLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEA 118
L S I + P + + Y R R+ D Q+ A
Sbjct: 93 FLMSP-------IKTEQRQPSMM-TRMYIEQRDRL-----YNDNQVF------------A 127
Query: 119 KYINSPETPLFHK-SNELYGLFEAKN-AIE------KSGYVLITEGYMDVIGLSQFGFLQ 170
KY N + K L L AKN I+ K+ + + + + F
Sbjct: 128 KY-NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT--WVALDVCLSYKVQCKMDF-- 182
Query: 171 TVAI----LGTACTSTHIKKILFYTNSIIFSFDGD--QAGRRAARRALEVCLLYATDDKI 224
I L + + ++L +++ D + ++ L + + A ++
Sbjct: 183 --KIFWLNLKNCNSPETVLEML---QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 225 IK-------FLFLPDKYDPDSYIRKFGY--KIF----SKKVLEAMSLLQFFLEEIILNYN 271
+K L L + + + F KI K+V + +S I L+++
Sbjct: 238 LKSKPYENCLLVLLNVQNAKA-WNAFNLSCKILLTTRFKQVTDFLSAATTT--HISLDHH 294
Query: 272 LKTIKDIEK----SKY-NIEY------LFKIIPLSSSL-------------RFKIISS-- 305
T+ E KY + + P S+ +K ++
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDK 354
Query: 306 LSKIIKVSFN-----EINNLFK---I--NTSSIKHKTIEK--KNIQPICIEYQIMKLLIS 353
L+ II+ S N E +F + ++ I + ++ + ++ L
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM-VVVNKLHK 413
Query: 354 YPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHI---FKNDID---HSKFI-KYLKKI 406
Y SL+ + ++ I I +I++ K + + H + Y
Sbjct: 414 Y-SLVEK-QPKESTIS--------------IPSIYLELKVKLENEYALHRSIVDHYNIPK 457
Query: 407 NKNFESIIVKIQDNFEYS--------IEIAKK-TLLDAIYKD 439
+ + +I D + YS IE ++ TL ++ D
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499
Score = 46.8 bits (110), Expect = 1e-05
Identities = 71/557 (12%), Positives = 158/557 (28%), Gaps = 156/557 (28%)
Query: 10 IQLKNSKEAINFL--KKRGLNEEIILRF-NLGYAPN-EW--NALNKVFLDYNNINTLASS 63
I K++ L EE++ +F N ++ + + + + +
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE 114
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKN-----TDGQII------GFG---- 108
D++ N + + +Y+ R + ++ + + G G
Sbjct: 115 --QRDRLYNDN------QVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
Query: 109 --------GRLIKDSNEAKYIN-----SPETPLFHKSNELYGLFEAKNAIEKSGYVLITE 155
K + ++N SPET + +L + I
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPET-VLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 156 GYMDVIG-----LSQFGFLQTVAILGTACTSTHIK------KILFYTN--SIIFSFDGDQ 202
+ L + + +L + KIL T +
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
Query: 203 AGRRA---------ARRALEVCLLYATDDKIIKFLFLP---DKYDPDSYIRKFGYKIFSK 250
+ + L Y + LP +P I ++
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLD----CRPQDLPREVLTTNP------RRLSIIAE 335
Query: 251 KVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNI----EY--LFK---IIPLSSSLRFK 301
+ + ++ + + N + I +S N+ EY +F + P S+ +
Sbjct: 336 SIRDGLATWDNWK-----HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390
Query: 302 IISSL-SKIIKVSFNEINNLF----------KINTSSI-------KHKTIEKKNIQPICI 343
++S + +IK + N K +T SI K K + + +
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450
Query: 344 E-YQIMKLL-----------------ISYPSLINEINSEDMIIFSKCSQNYVKMFFQ--- 382
+ Y I K I + L N + E M +F ++ F +
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGH-HLKNIEHPERMTLFRMVFLDF--RFLEQKI 507
Query: 383 ------------LIDTI--------HIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFE 422
+++T+ +I ND + + + + E ++ +
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLIC--SKYT 565
Query: 423 YSIEIAKKTLLDAIYKD 439
+ IA +AI+++
Sbjct: 566 DLLRIALMAEDEAIFEE 582
Score = 45.2 bits (106), Expect = 4e-05
Identities = 25/168 (14%), Positives = 53/168 (31%), Gaps = 41/168 (24%)
Query: 8 YKIQLKNSK-------EAINFLKKRGLNEEIILR-----FN-LGY------APNEWNALN 48
K++L+N + N K ++ I ++ +G+ P
Sbjct: 435 LKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFR 494
Query: 49 KVFLDYNNI-NTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGF 107
VFLD+ + + + + +N ++ YK Y + +++
Sbjct: 495 MVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY-------ICDNDPKYERLV-- 545
Query: 108 GGRLIKD---SNEAKYINSPET-----PLFHKSNELYGLFEAKNAIEK 147
I D E I S T L + ++ EA +++
Sbjct: 546 --NAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFE--EAHKQVQR 589
Score = 39.8 bits (92), Expect = 0.002
Identities = 36/239 (15%), Positives = 82/239 (34%), Gaps = 55/239 (23%)
Query: 235 DPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEK---SKYNIEYLFKI 291
D ++ ++ YK +L F + + N++ K ++D+ K SK I+++
Sbjct: 8 DFETGEHQYQYK----------DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS 57
Query: 292 IPLSSSLRFKIISSLSK---IIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIM 348
S + LSK +++ E + +IN + I+ + QP +
Sbjct: 58 KDAVSGTLRLFWTLLSKQEEMVQKFVEE---VLRINYKFLMSP-IKTEQRQPSMMT---- 109
Query: 349 KLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLID-----------TIH--------- 388
Y + + + D +F+K + + ++ + +L I
Sbjct: 110 ---RMYIEQRDRLYN-DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW 165
Query: 389 ----IFKNDIDHSKF---IKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDR 440
+ + K I +L N N ++++ Y I+ + D +
Sbjct: 166 VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET:
DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11
e.13.1.2
Length = 503
Score = 38.6 bits (89), Expect = 0.003
Identities = 26/145 (17%), Positives = 53/145 (36%), Gaps = 21/145 (14%)
Query: 79 VIEKYK-RYDRFRGRIM--FPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNEL 135
+K + G + ++ +G I+ K + + S++
Sbjct: 27 TCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQ-----------KVRDKDKNFKTTGSHKS 75
Query: 136 YGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAI---LGTACTSTHIKKILFYTN 192
LF K+ +++TEG +D++ + + + + G + Y +
Sbjct: 76 DALF-GKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFD 134
Query: 193 S---IIFSFDGDQAGRRAARRALEV 214
II FD D+AGR+A A +V
Sbjct: 135 QFEQIILMFDMDEAGRKAVEEAAQV 159
>1lng_A SRP19, signal recognition particle 19 kDa protein; protein-RNA
complex, signaling protein/RNA complex; 2.30A
{Methanocaldococcus jannaschii} SCOP: d.201.1.1 PDB:
2v3c_A 3ndb_A 1l9a_A*
Length = 87
Score = 28.5 bits (64), Expect = 1.2
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 69 KIINKVNQSPVIEKYKRYDR----FRGRIMFPIKNTDGQIIGFGGRLIKDSN 116
K + K+ P I + KRY R G + K Q++ ++IK N
Sbjct: 36 KALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN 87
>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 = 29.5 bits (65), Expect = 1.4
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 10/32 (31%)
Query: 16 KEAINFLKKRGLNEEIILRFNLGYAPNEWNAL 47
K+A+ KK L + L YA + AL
Sbjct: 19 KQAL---KK--LQASLKL-----YADDSAPAL 40
>3m1i_C Exportin-1; heat repeat, GTP-binding, nucleotide-binding, NUCL
protein transport, transport, cytoplasm, GTPase
activation; HET: GTP; 2.00A {Saccharomyces cerevisiae}
PDB: 2l1l_B
Length = 1049
Score = 29.9 bits (66), Expect = 2.0
Identities = 28/209 (13%), Positives = 73/209 (34%), Gaps = 8/209 (3%)
Query: 240 IRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLR 299
K K V++ + F++ II + T + + II
Sbjct: 564 FIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSV 623
Query: 300 FKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYP-SLI 358
+ LS ++++ + + + +T++ + + + I I+K ++ S+
Sbjct: 624 AERNRLLSDLMQLPNMAWDTIVEQSTANPT----LLLDSETVKIIANIIKTNVAVCTSMG 679
Query: 359 NEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQ 418
+ + I+ Q Y + + + + ++ L+ I K ++
Sbjct: 680 ADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYI 739
Query: 419 DNFEYSIEIAK---KTLLDAIYKDRKSVV 444
++ K + LL+A+ +D + V
Sbjct: 740 SKARNLDDVVKVLVEPLLNAVLEDYMNNV 768
>3bpo_A Interleukin 13; IL4, IL13, IL4R, IL13R, cytokine, glycoprotein, IM
response, membrane, phosphoprotein, secreted; HET: NAG;
3.00A {Homo sapiens} PDB: 1ijz_A 1ik0_A 3g6d_A 3l5w_I
3l5x_A* 3l5y_A 1ga3_A
Length = 127
Score = 28.2 bits (62), Expect = 2.6
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 384 IDTIHIFKNDIDHSKFIKYLKKINKNFESIIV 415
I+ K+ + H K + + N+NFESII+
Sbjct: 91 IEVAQFVKDLLLHLKKLFREGQFNRNFESIII 122
>1t6t_1 Putative protein; structural genomics, PSI, protein structur
initiative, midwest center for structural genomics,
MCSG, U function; 1.80A {Aquifex aeolicus} SCOP:
c.136.1.1
Length = 118
Score = 28.0 bits (62), Expect = 2.7
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 1/68 (1%)
Query: 146 EKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGR 205
V++ EG D LS+F + + G + + +I FD D G
Sbjct: 18 ASREAVILVEGKNDKKALSKFSIKNVIDLSGKRYADV-VDMLEGKWEKVILLFDLDTHGE 76
Query: 206 RAARRALE 213
R ++ E
Sbjct: 77 RINQKMKE 84
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD,
FCPH, BRCT, hydrolase, ALF4, transition state analog,
cobalt, magnesium; 2.10A {Schizosaccharomyces pombe}
Length = 372
Score = 28.6 bits (63), Expect = 4.7
Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 365 DMIIFSKCSQNYVKMFFQLIDTI------HIFKNDIDHSKFIKYLKKINKNFESIIVKIQ 418
++ I++ ++ Y K ++ID + D S K L+++ S++V +
Sbjct: 92 ELHIYTMGTKAYAKEVAKIIDPTGKLFQDRVLSRDDSGSLAQKSLRRLFPCDTSMVV-VI 150
Query: 419 DNFEYS 424
D+
Sbjct: 151 DDRGDV 156
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD,
FCPH, BRCT, hydrolase, BEF3, acylphosphate analog,
cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces
pombe}
Length = 442
Score = 28.0 bits (61), Expect = 7.1
Identities = 13/66 (19%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 365 DMIIFSKCSQNYVKMFFQLIDTIH-IFKNDI---DHS--KFIKYLKKINKNFESIIVKIQ 418
++ I++ ++ Y K ++ID +F++ + D S K L+++ S++V +
Sbjct: 100 ELHIYTMGTKAYAKEVAKIIDPTGKLFQDRVLSRDDSGSLAQKSLRRLFPCDTSMVV-VI 158
Query: 419 DNFEYS 424
D+
Sbjct: 159 DDRGDV 164
>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix
motif, structural genom transcription; 2.05A {Pyrococcus
horikoshii} SCOP: a.4.5.28
Length = 100
Score = 26.2 bits (58), Expect = 8.2
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 294 LSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSI-KH 330
L + +R I+ L K F++I + + ++ H
Sbjct: 13 LGNPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSH 50
>3fz4_A Putative arsenate reductase; APC61768, structural genomics, PSI-2,
protein structure initiative; HET: MSE; 1.38A
{Streptococcus mutans UA159}
Length = 120
Score = 26.4 bits (59), Expect = 9.4
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 306 LSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLI 358
+ ++ S E+ F NTS ++ + K+ + LL S LI
Sbjct: 45 IRNWLENSGLELKKFF--NTSGQSYRALGLKDKLHQLSLDEAANLLASDGMLI 95
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
0.323 0.140 0.394
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,782,513
Number of extensions: 424356
Number of successful extensions: 1383
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1367
Number of HSP's successfully gapped: 42
Length of query: 444
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 347
Effective length of database: 3,993,456
Effective search space: 1385729232
Effective search space used: 1385729232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.6 bits)