RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 013857
(435 letters)
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Length = 316
Score = 193 bits (492), Expect = 2e-58
Identities = 58/130 (44%), Positives = 80/130 (61%), Gaps = 4/130 (3%)
Query: 300 LPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA 359
+ T G +V+++KP G TS V G+ RR+ ++VGHAGTLDPMATG+L++ + +A
Sbjct: 1 MSATGPG----IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERA 56
Query: 360 TKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQ 419
TK++ K Y+ RLG+ TST DA+ V+Q P +H+ E I A RGEI Q
Sbjct: 57 TKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQ 116
Query: 420 VPPMFSAIKV 429
VP SAIKV
Sbjct: 117 VPSSVSAIKV 126
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 182 bits (464), Expect = 2e-54
Identities = 49/118 (41%), Positives = 74/118 (62%), Gaps = 1/118 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
++ KPKG TS V ++R+ +K +KVGH GTLDP A G+LI+ V + T++++ Y+ + K
Sbjct: 6 LVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKK 65
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K
Sbjct: 66 VYWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKY 122
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 177 bits (450), Expect = 4e-52
Identities = 45/118 (38%), Positives = 70/118 (59%), Gaps = 1/118 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP+G +S K++R+ + GH G LDP+ATG+L +C+G+ATK K
Sbjct: 28 LLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDK 87
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y + RLG+ T T DAD +++ P E + A +FRG+I Q+P M+SA+K
Sbjct: 88 RYRVIARLGQRTDTSDADGQIVEERPVT-FSAEQLAAALDTFRGDIEQIPSMYSALKY 144
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 155 bits (393), Expect = 1e-43
Identities = 39/120 (32%), Positives = 60/120 (50%), Gaps = 18/120 (15%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
V+V+KP+G TS V +++++ + K GH GTLDP TG+L V + +ATK + + K
Sbjct: 69 VVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPPK 128
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRV 431
Y + L S EDI + F G I+Q PP+ +A+K R+
Sbjct: 129 EYVCLMHLHRDASE------------------EDILRVFKEFTGRIYQRPPLKAAVKRRL 170
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase-structural protein; 2.10A {Pyrococcus abyssi}
PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A*
2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Length = 334
Score = 151 bits (384), Expect = 2e-42
Identities = 37/120 (30%), Positives = 58/120 (48%), Gaps = 18/120 (15%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+ ++KP G TS V ++R++ ++K GH GTLDP +G+L V + +AT++V K
Sbjct: 49 INLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGK 108
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRV 431
Y + L ++ IR F GEI Q PP+ SA+K R+
Sbjct: 109 EYVALMHLHGDVP------------------EDKIRAVMKEFEGEIIQRPPLRSAVKRRL 150
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_A
Length = 400
Score = 135 bits (342), Expect = 7e-36
Identities = 38/121 (31%), Positives = 67/121 (55%), Gaps = 17/121 (14%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP +S V ++R+++ +K GH+GTLDP TG LIVC+ +AT+LV QG
Sbjct: 61 VINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAG 120
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430
K Y + RL +A ++D+ ++ + G ++Q PP+ SA+K +
Sbjct: 121 KEYVCIVRLHDALKD-----------------EKDLGRSLENLTGALFQRPPLISAVKRQ 163
Query: 431 V 431
+
Sbjct: 164 L 164
>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 = 55.1 bits (132), Expect = 4e-08
Identities = 89/571 (15%), Positives = 158/571 (27%), Gaps = 206/571 (36%)
Query: 1 MSLLLLRPKLITS-SRTLSLLLPPP-------LKDNFIKKNVYLLSTKAFSSSI-TSTPY 51
M RP ++ S LL+P L++ F K T+ F++ +TP
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKI--LPEPTEGFAADDEPTTPA 58
Query: 52 PL--QYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGELGFD--SWVDKKLEKEAK 107
L ++ +++ +P + + + EN +G D + KL +E
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNL-CLTEFENCYLEGN---DIHALA-AKLLQEND 113
Query: 108 TRQPGSDNAEMTKSMRKYYNKR----RQRMYGTDS------EDE----Y------GKNDD 147
T + ++ Y R R ++S + G DD
Sbjct: 114 TTLVKTKEL-----IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDD 168
Query: 148 GFVEL-------KPEVVEF-NRLHKREEELYFYDTFAYPWEKDKHYKMVYQ----LEKKY 195
F EL V + + EL + +K + LE
Sbjct: 169 YFEELRDLYQTYHVLVGDLIKFSAETLSELI-----RTTLDAEKVFTQGLNILEWLEN-- 221
Query: 196 FPDQCLDKAFLD------P---------------SADQNVKKMRKK-------------- 220
P DK +L P ++R
Sbjct: 222 -PSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA 280
Query: 221 ---AGGKSEEKKYNKEDDK--RLVFF-----------DDQEKKSEKDSI-LGEDV----- 258
A S E + K ++FF +DS+ E V
Sbjct: 281 VAIAETDSWE-SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 259 NVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYI-VSRSTELPPTWDGPFGTMVLVNKP 317
++ +++++V+++ + K N + +S LVN
Sbjct: 340 SISN-LTQEQVQDY---VNKT----NSHLPAGKQVEIS-----------------LVNGA 374
Query: 318 KGWTSFTVCG---KLRRLV-KVKKVGHAGTLD----PMA-------TGLLIVCV------ 356
K + V G L L ++K LD P + L V
Sbjct: 375 K---NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHL 431
Query: 357 -GKATKLVDRYQGMIKGYSGVFRLGEATSTWDADS---PVIQREPWEHIKD-EDIRKAAA 411
A+ L+++ L + +++A PV D D+R +
Sbjct: 432 LVPASDLINK------------DLVKNNVSFNAKDIQIPV------YDTFDGSDLRVLSG 473
Query: 412 SFRGEI----------WQVPPMFSAIKVRVF 432
S I W+ F A + F
Sbjct: 474 SISERIVDCIIRLPVKWETTTQFKATHILDF 504
Score = 29.6 bits (66), Expect = 2.6
Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 39/99 (39%)
Query: 358 KATKLVDRYQGMI--KGYSG------VFR-LGEATS--TWDADSPVI------QREP--- 397
K ++ + Y MI G +F+ + E ++ T+ ++ ++ Q P
Sbjct: 1680 KGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ--PALT 1737
Query: 398 ------WEHIKDEDIRKAAASFR----GEIWQVPPMFSA 426
+E +K + + A A+F GE ++A
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGE-------YAA 1769
Score = 28.9 bits (64), Expect = 5.0
Identities = 21/109 (19%), Positives = 33/109 (30%), Gaps = 40/109 (36%)
Query: 35 YLLSTKAFSSSITSTPYPLQYDMIINNPTQ------PQQSQTRRRPARVNSTNSDENQNP 88
+ T FS I D++INNP ++ + R N +
Sbjct: 1652 HFKDTYGFS--IL--------DIVINNPVNLTIHFGGEKGKR----IRENYSAMIFETIV 1697
Query: 89 DGELG----FDSWVDKKL-------EKEA--KTR--QPGSDNAEMTKSM 122
DG+L F +++ EK T+ QP A
Sbjct: 1698 DGKLKTEKIFKE-INEHSTSYTFRSEKGLLSATQFTQP----ALTLMEK 1741
>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 = 51.4 bits (122), Expect = 5e-07
Identities = 48/327 (14%), Positives = 87/327 (26%), Gaps = 97/327 (29%)
Query: 3 LLLLRPKLITSSRTLSLLLPPPLKDN---FIKKNVYLLSTKAFSSSITSTP------YPL 53
LL R K +T + + L + V L K P P
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 54 QYDMI----INNPTQPQQSQTRRRPARVNST--NSDENQNPDG------ELG-F--DSWV 98
+ +I + + ++ + +S P L F + +
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCD-KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 99 -DKKLE---KEAKTRQPGSDNAEM-TKSM-RKYYNKRRQRMYGTDSEDEYGKNDDGFVEL 152
L + ++ S+ K + + ++EL
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP------------SIYLEL 435
Query: 153 KPEVVEFNRLHKR-------------------EEELYFYDTFAYPWEKDKHYKMVYQLEK 193
K ++ LH+ + YFY + H K + E+
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH------HLKNIEHPER 489
Query: 194 -KYFPDQCLDKAFLDPSADQNVKKMRK-----KAGGKSEE-----KKY------NKEDDK 236
F LD FL+ +K+R A G K Y N +
Sbjct: 490 MTLFRMVFLDFRFLE-------QKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYE 542
Query: 237 RLVFFDDQEK---KSEKDSILGEDVNV 260
RLV + K E++ I + ++
Sbjct: 543 RLV--NAILDFLPKIEENLICSKYTDL 567
Score = 41.4 bits (96), Expect = 6e-04
Identities = 57/449 (12%), Positives = 119/449 (26%), Gaps = 120/449 (26%)
Query: 8 PKLITSSRTLSLLLPPPLKDNFIKKNVYLLSTK------AFSSSITSTPYPLQYDMIINN 61
PK I S + ++ + + + L +K F + Y I
Sbjct: 42 PKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE 101
Query: 62 PTQPQQSQTRRRPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKS 121
QP TR + + +D NQ K +R +
Sbjct: 102 QRQPSM-MTRMYIEQRDRLYND-NQ--------------VFAKYNVSRL------QPYLK 139
Query: 122 MRKY-YNKRRQR------MYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYFYDT 174
+R+ R + + G+ GK + +V ++ + + F+
Sbjct: 140 LRQALLELRPAKNVLIDGVLGS------GKT----W-VALDVCLSYKVQCKMDFKIFWLN 188
Query: 175 FAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKE- 233
+ +M+ +L + P+ ++ + + ++ + + K Y
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWT-SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
Query: 234 ---DD---KRLV-FFDDQEK-------KSEKDSILGED------VNVKGEVSEKKVEEFF 273
+ + F+ K K D + + ++ +V+
Sbjct: 248 LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 274 -KCLKKVPNKE-NEVGSGEPYIVS----RSTELPPTWDGPFGTMVLVNKPKGWTSFTVCG 327
K L P EV + P +S + TWD W C
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD-------------NWKHVN-CD 353
Query: 328 KLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387
KL +++ L+P + + + VF
Sbjct: 354 KLTTIIESS----LNVLEP-------------AEYRKMFDRL-----SVFPP-------S 384
Query: 388 ADSP--VIQREPWEHIKDEDIRKAAASFR 414
A P ++ W + D+
Sbjct: 385 AHIPTILLSLI-WFDVIKSDVMVVVNKLH 412
Score = 32.9 bits (74), Expect = 0.23
Identities = 46/330 (13%), Positives = 89/330 (26%), Gaps = 98/330 (29%)
Query: 2 SLLLLRP-KLIT---------SSRTLSLLLPPPLKDNFIKKNVYLLSTKAFSSSITSTPY 51
+LL LRP K + + L + L ++ ++ L+ K +S +
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM-DFKIFWLNLKN-CNSPETVLE 200
Query: 52 PLQ--YDMIINNPTQPQQSQTRRRPARVNSTNSD------ENQNPDGELGFD----SWVD 99
LQ I N T + + R++S ++ + L +
Sbjct: 201 MLQKLLYQIDPNWTS-RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259
Query: 100 KKLEKEAK----TRQPG-SDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKN-DDGFVELK 153
K TR +D + + + + + K D +L
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 154 PEVVEFNRLH-------KREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFL 206
EV+ N R+ T+ W+ K+ +E L+ L
Sbjct: 320 REVLTTNPRRLSIIAESIRD----GLATWDN-WKHVNCDKLTTIIES------SLNV--L 366
Query: 207 DPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNV------ 260
+P+ E +K FD S+ ++
Sbjct: 367 EPA----------------EYRKM----------FDRL-------SVFPPSAHIPTILLS 393
Query: 261 ------KGEVSEKKVEEFFK--CLKKVPNK 282
V + K ++K P +
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Score = 31.4 bits (70), Expect = 0.69
Identities = 27/203 (13%), Positives = 61/203 (30%), Gaps = 49/203 (24%)
Query: 166 EEELYFYD---TFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNV-------- 214
E + + D F + + K V + K + +D + A
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72
Query: 215 ---KKMRKKAGGKSEEKKYN----------KEDDKRLVFFDDQEKKSEKDSILGEDVNVK 261
++M +K + Y ++ + +Q + D+ V K
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN----QVFAK 128
Query: 262 GEVS-EKKVEEFFKCLKKVPNKENEV-----GSGEPYIVS---RSTELPPTWDGP-FGTM 311
VS + + + L ++ +N + GSG+ ++ S ++ D F
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--- 185
Query: 312 VLVNKPKGWTSFTVCGKLRRLVK 334
W + C +++
Sbjct: 186 --------WLNLKNCNSPETVLE 200
Score = 30.6 bits (68), Expect = 1.4
Identities = 67/481 (13%), Positives = 119/481 (24%), Gaps = 174/481 (36%)
Query: 23 PPLKDNFIK----KNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRR------ 72
+D F+ K+V + S + D II + S T R
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSKE--------EIDHIIMSKDA--VSGTLRLFWTLL 72
Query: 73 -RPARVNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPG--------------SDNAE 117
+ + +E + + ++ ++ E RQP +DN
Sbjct: 73 SKQEEMVQKFVEEVLRINYK-----FLMSPIKTE--QRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 118 MTK---SMRKYYNKRRQRMYGTDSEDE--------YGK--------NDDGFVELKP-EV- 156
K S + Y K RQ + GK ++
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF 185
Query: 157 -VEFNRLHKREEELYFYDTFAYPWEKD------------------KHYKMVYQLEKKYFP 197
+ + E L Y + + + K Y
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY-- 243
Query: 198 DQCL---D--------KAF------LDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVF 240
+ CL AF L + + V + + D +
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVT-----DFLSAATTTHISLDHHSMTL 298
Query: 241 FDDQEKK--------SEKD-------------SILGEDV--------NVKGEVSEKKVEE 271
D+ K +D SI+ E + N K V+ K+
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-HVNCDKLTT 357
Query: 272 FFK-CLKKVPNKENEVGSGEPY----IVSRSTELPPT-----WDG--PFGTMVLVNKPKG 319
+ L + E + + + S +P W MV+VNK
Sbjct: 358 IIESSLNVLEPAEYR----KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK--- 410
Query: 320 WTSFTVCGKLRRLVKVKKVG----HAGTLDPMATGLLIVCVGKAT---KLVDRYQGMIKG 372
K + K K + L+ L + + +VD Y + K
Sbjct: 411 ------LHKYSLVEKQPKESTISIPSIYLE-----LKVKLENEYALHRSIVDHYN-IPKT 458
Query: 373 Y 373
+
Sbjct: 459 F 459
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.1 bits (72), Expect = 0.25
Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 23/87 (26%)
Query: 224 KSEE----KKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLK-- 277
++E +K+ +E KRL D K E++ E ++K +EE+ +
Sbjct: 80 LTQEPESIRKWREEQRKRLQELDAASKVMEQEWR---------EKAKKDLEEWNQRQSEQ 130
Query: 278 ----KVPNKENEVGSGEPYIVSRSTEL 300
K+ N+ + + + ++
Sbjct: 131 VEKNKINNRIAD----KAFYQQPDADI 153
Score = 28.2 bits (62), Expect = 4.0
Identities = 12/92 (13%), Positives = 30/92 (32%), Gaps = 27/92 (29%)
Query: 154 PEVV-----EFN-RLHKREEELYFYDTFAYPWEKDKHYKMVYQLEKKYFPDQCLDKAFLD 207
PE + E RL + + K + + +K L++
Sbjct: 84 PESIRKWREEQRKRLQELDAA-----------SKVMEQEWREKAKKD------LEEWN-- 124
Query: 208 PSADQNVKKMRKKAGGKSEEKKYNKEDDKRLV 239
Q+ + + K + +K + ++ D ++
Sbjct: 125 --QRQSEQVEKNKINNRIADKAFYQQPDADII 154
>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 = 7/24 (29%), Positives = 8/24 (33%), Gaps = 5/24 (20%)
Query: 100 KKLEKEAKTRQPGSD-----NAEM 118
KKL+ K S A M
Sbjct: 23 KKLQASLKLYADDSAPALAIKATM 46
Score = 27.6 bits (60), Expect = 6.0
Identities = 6/22 (27%), Positives = 10/22 (45%), Gaps = 7/22 (31%)
Query: 180 EKDKHYKMVYQLE---KKYFPD 198
EK + + +L+ K Y D
Sbjct: 18 EK----QALKKLQASLKLYADD 35
>2ykt_A Brain-specific angiogenesis inhibitor 1-associate protein 2;
signaling protein, NPY motif, binding pocket; 2.11A
{Homo sapiens} PDB: 1y2o_A 1wdz_A
Length = 253
Score = 29.1 bits (64), Expect = 2.7
Identities = 24/151 (15%), Positives = 54/151 (35%), Gaps = 11/151 (7%)
Query: 141 EYGKNDDGFVELKPEVVEFNRLHKREEELY------FYDTFAYPWEK--DKHYKMVYQLE 192
E G EL + + +H++ + F++ E+ + + +
Sbjct: 64 ELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAAL 123
Query: 193 KKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDS 252
KKY +Q LD +KK+RKK+ G +KY+ ++ + + K+ E ++
Sbjct: 124 KKYQTEQRSKGDALD-KCQAELKKLRKKSQGSKNPQKYSDKELQYID--AISNKQGELEN 180
Query: 253 ILGEDVNVKGEVSEKKVEEFFKCLKKVPNKE 283
+ + ++ + V
Sbjct: 181 YVSDGYKTALTEERRRFCFLVEKQCAVAKNS 211
>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative
initiation, ATP-binding, DNA- binding, hydrolase,
nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB:
3ezk_A*
Length = 592
Score = 28.4 bits (62), Expect = 5.4
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 228 KKYNKEDDKRLVFFDDQEKKSEKDSILGED----VNVKGEVSEKKVEEFFKCLK 277
K DK +F ++K +++ +G N+K + + + VEE+ KC
Sbjct: 87 VKIPNNSDKPELFQTYKDKNNKRSRYMGLPNLKRANIKTQWTREMVEEWKKCRD 140
>2d1l_A Metastasis suppressor protein 1; IRSP53, actin binding, IMD,
protein binding; HET: MSE; 1.85A {Mus musculus}
Length = 253
Score = 27.9 bits (61), Expect = 6.8
Identities = 19/140 (13%), Positives = 40/140 (28%), Gaps = 7/140 (5%)
Query: 151 ELKPEVVEFNRLHKREEELY------FYDTFAYPWEKD-KHYKMVYQLEKKYFPDQCLDK 203
E+ + H+ E D P ++ + +K V K +
Sbjct: 77 EIGSALTRMCMRHRSIEAKLRQFSSALIDCLINPLQEQMEEWKKVANQLDKDHAKEYKKA 136
Query: 204 AFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGE 263
+ K++KKA + + + + D +K + + V
Sbjct: 137 RQEIKKKSSDTLKLQKKAKKVDAQGRGDIQPQLDSALQDVNDKYLLLEETEKQAVRKALI 196
Query: 264 VSEKKVEEFFKCLKKVPNKE 283
+ F L+ V +E
Sbjct: 197 EERGRFCTFISMLRPVIEEE 216
>2v2g_A Peroxiredoxin 6; oxidoreductase, antioxidant enzymes; 1.60A
{Arenicola marina} PDB: 2v32_A 2v41_A
Length = 233
Score = 27.2 bits (61), Expect = 9.3
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 255 GEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGEPYIVSRSTELPPTWDG 306
G+ V VS ++ + F ++ V SG+ Y+ R T P + G
Sbjct: 180 GDRCMVVPGVSAEEAKTLFPNMEVK-----AVPSGKGYL--RYTPQPKSMGG 224
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
0.315 0.133 0.394
Gapped
Lambda K H
0.267 0.0556 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,660,481
Number of extensions: 397882
Number of successful extensions: 645
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 43
Length of query: 435
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 339
Effective length of database: 4,021,377
Effective search space: 1363246803
Effective search space used: 1363246803
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: 42 (22.0 bits)
S2: 59 (26.9 bits)