RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11273
(730 letters)
>2ivx_A Cyclin-T2; transcription regulation, cell division,
phosphorylation, NU protein, cell cycle, transcription;
1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A
3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B*
3lq5_B* 3my1_B* 3tn8_B*
Length = 257
Score = 266 bits (681), Expect = 3e-84
Identities = 168/247 (68%), Positives = 207/247 (83%)
Query: 11 SPDRWYFTKEQLENTPSRKCGYDAEKELSCRQQAANLIQDMGQRLQVTQLCINTAIVYMH 70
+ RW+FT+EQLENTPSR+CG +A+KELSCRQQAANLIQ+MGQRL V+QL INTAIVYMH
Sbjct: 1 ASSRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMH 60
Query: 71 RFYVFHSFTQFHRNSIATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPPLDPRSEAYQ 130
RFY+ HSFT+F++N I++ ALFLAAKVEEQ RKLEHVI+VA CL +P LD + +AY
Sbjct: 61 RFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYL 120
Query: 131 EQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFMASNSLHLTTM 190
+Q +E+V+ E ++LQTLGF++ IEHPHT VVKC LVRASKDLAQTSYFMA+NSLHLTT
Sbjct: 121 QQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTF 180
Query: 191 CLQYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLAIFDK 250
CLQY+ TV+AC CIHLACKW+NWEIP S +G+ W+ Y+D VT E L++LT EFL I +K
Sbjct: 181 CLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEK 240
Query: 251 CPSKLKK 257
P++LKK
Sbjct: 241 TPNRLKK 247
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P-
TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1
a.74.1.1 PDB: 2w2h_C
Length = 358
Score = 261 bits (668), Expect = 4e-81
Identities = 173/311 (55%), Positives = 217/311 (69%), Gaps = 3/311 (0%)
Query: 7 QGSHSPDRWYFTKEQLENTPSRKCGYDAEKELSCRQQAANLIQDMGQRLQVTQLCINTAI 66
+ ++ RWYFT+EQLEN+PSR+ G D +KELS RQQAANL+QDMGQRL V+QL INTAI
Sbjct: 4 ERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAI 63
Query: 67 VYMHRFYVFHSFTQFHRNSIATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPPLDPRS 126
VYMHRFY+ SFT+F NS+A AALFLAAKVEEQP+KLEHVI+VA CL + D RS
Sbjct: 64 VYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRS 123
Query: 127 EAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFMASNSLH 186
EAY +Q Q++V+ E+++LQTLGF++ I+HPHT+VVKC LVRASKDLAQTSYFMA+NSLH
Sbjct: 124 EAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLH 183
Query: 187 LTTMCLQYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLA 246
LTT LQY VVAC CIHLACKW+NWEIP S +G+ W+ Y+D VT E L++LT EFL
Sbjct: 184 LTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQ 243
Query: 247 IFDKCPSKLKKRICSISSNQNSTLMA---AFDGDSKKMSGLGNATFAPPHSTSGRVTDDK 303
I +K P++LK+ + A D + + G G + SG T
Sbjct: 244 ILEKTPNRLKRIWNWRACEAAKKTKADDRGTDEKTSEQGGTGGGSGGGSGGGSGGGTSGG 303
Query: 304 RRSEHNGPPPE 314
++ G
Sbjct: 304 VPGQNTGGQEA 314
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive
transcription elongation factor, P-TEFB; 1.50A {Homo
sapiens} SCOP: a.74.1.1 a.74.1.1
Length = 258
Score = 242 bits (620), Expect = 3e-75
Identities = 80/261 (30%), Positives = 139/261 (53%), Gaps = 13/261 (4%)
Query: 2 STNTTQGSHSPDRWYFTKEQLENTPSRKCGYDAEKELSCRQQAANLIQDMGQRLQVTQLC 61
S + H+ WY+ K+ L +TPS+ G D E R++ A I D+G RL +
Sbjct: 2 SVTSANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDT 61
Query: 62 INTAIVYMHRFYVFHSFTQFHRNSIATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPP 121
+ T I+Y HRFY+FHSF QF R LFLA KVEE P+K + +I+ A+ L Q
Sbjct: 62 LATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFG 121
Query: 122 LDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKD----LAQTS 177
+ + +E++V E +LLQT+ FD+ +EHP+ +++K ++ K+ L Q +
Sbjct: 122 -----QFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMA 176
Query: 178 YFMASNSLHLTTMCLQYRSTVVACFCIHLACKWANWEIPQSNEG---RKWFWYIDKEVTQ 234
+ ++SL TT+ LQ+ ++A ++LA + +EI + R+W+ ++V
Sbjct: 177 WTFVNDSLC-TTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPV 235
Query: 235 EQLEQLTEEFLAIFDKCPSKL 255
+ LE + + L ++ + ++
Sbjct: 236 DVLEDICHQILDLYSQGKQQM 256
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET:
BAX; 2.20A {Homo sapiens}
Length = 285
Score = 197 bits (503), Expect = 3e-58
Identities = 56/267 (20%), Positives = 114/267 (42%), Gaps = 12/267 (4%)
Query: 1 MSTNTTQGSHSPDRWYFTKEQLENTPSRKC-GYDAEKELSCRQQAANLIQDMGQRLQVTQ 59
M+ N Q SH +W K+ L + E+ + N+IQ +G+ L++ Q
Sbjct: 3 MAGNFWQSSHY-LQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQ 61
Query: 60 LCINTAIVYMHRFYVFHSFTQFHRNSIATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQ 119
I TA VY RFY +S +A +FLA+KVEE + A + K +
Sbjct: 62 QVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTR 121
Query: 120 PPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYF 179
+ + + I+ E LL+ + + + HP+ +++ + L ++
Sbjct: 122 FS-YAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWR 180
Query: 180 MASNSLHLTTMCLQYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQLEQ 239
+ N + T +CL Y ++A C+H+AC + Q W+ + V E++ +
Sbjct: 181 IV-NDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQ--------WFAELSVDMEKILE 231
Query: 240 LTEEFLAIFDKCPSKLKKRICSISSNQ 266
+ L ++++ + +++ + ++
Sbjct: 232 IIRVILKLYEQWKNFDERKEMATILSK 258
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat
domains, transcription-cell cycle complex; 3.00A
{Schizosaccharomyces pombe}
Length = 235
Score = 182 bits (464), Expect = 3e-53
Identities = 39/238 (16%), Positives = 88/238 (36%), Gaps = 21/238 (8%)
Query: 16 YFTKEQLEN--TPSRKCGYDAEKELSCRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFY 73
Y+ QL + + ++Q G RL++ Q + TAIV + R+
Sbjct: 1 YWASSQLTQLFLSTDLESLEPTCLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYM 60
Query: 74 VFHSFT-QFHRNSIATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPPLDPRSEAYQEQ 132
+ + F ++ ++L+ KVEE P + + A D S +
Sbjct: 61 LKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEAN----------DLWSLKVKLS 110
Query: 133 AQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFMASNSLHLTTMCL 192
I E ++ L + + HP+T + + H ++ + ++ + ++S +++CL
Sbjct: 111 RSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQKQLEFAWSIVNDSY-ASSLCL 169
Query: 193 QYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLAIFDK 250
+A + ++C IP + K ++ + ++I+
Sbjct: 170 MAHPHQLAYAALLISCCNDENTIP-------KLLDLIKSTDAFKVILCVQRIISIYYF 220
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo
sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A
Length = 323
Score = 177 bits (451), Expect = 2e-50
Identities = 40/275 (14%), Positives = 91/275 (33%), Gaps = 43/275 (15%)
Query: 14 RWYFTKEQL--------------------ENTPSRKCGYDAEKELSCRQQAANLIQDMGQ 53
W F+ E+ + P+ + +E++ + + +
Sbjct: 10 HWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCS 69
Query: 54 --RLQVTQLCINTAIVYMHRFYVFHSFTQFHRNSIATAALFLAAKVEEQPRKLEHVIRVA 111
+ + + + TA +Y RFY+ +S ++H I FLA KV+E +
Sbjct: 70 VFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNL 129
Query: 112 QLCLFKNQPPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVK-------CC 164
+ ++ ++I+ E +L+Q L F + + +P+
Sbjct: 130 RESPLG-----------QEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRY 178
Query: 165 HLVRASKDLAQTSYFMASNSLHLTTMCLQYRSTVVACFCIHLACKWANWEIPQSNEGRKW 224
++ + L +T+ N + LT L Y + +A I + A + +
Sbjct: 179 PILENPEILRKTADDFL-NRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLS--ES 235
Query: 225 FWYIDKEVTQEQLEQLTEEFLAIFDKCPSKLKKRI 259
+ QL + + + K + +
Sbjct: 236 LMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEV 270
>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 = 67.8 bits (165), Expect = 1e-11
Identities = 79/529 (14%), Positives = 138/529 (26%), Gaps = 200/529 (37%)
Query: 6 TQGS--HS---PDRWYFTKEQL-------ENTPSRKCGYDAEK----ELSCR--QQAANL 47
+ GS H P +F QL P+ D E EL + ++L
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSL 71
Query: 48 IQD--MGQRLQVTQLCINTAIVYMHRFYVFHSFTQF-HRNSIATAALFLAAKVEEQPRKL 104
++ +GQ QV LC+ F + + N I A L + + K
Sbjct: 72 VEPSKVGQFDQVLNLCLTE----------FEN--CYLEGNDIHALAAKLLQENDTTLVKT 119
Query: 105 EHVIRVA-QLCLFKNQPPLDPRSEA----------------------------------- 128
+ +I+ + +P + A
Sbjct: 120 KELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT 179
Query: 129 YQEQAQEIVVNENVLLQTL-------------GFDVG--IEHPHT-----Y--------- 159
Y +++ L L G ++ +E+P Y
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239
Query: 160 ---VVKCCHLVRASKDLAQTSYFMASNSLHLTTMCLQYRSTVVACFCIHLACKWANWEIP 216
V++ H V +K L T + S L T Q +V I W ++
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELRS-YLKGATGHSQ---GLVTAVAIAETDSWESFF-V 294
Query: 217 QSNEGRKW-FW------------YIDKEVTQEQLEQ-------------LTEEFL-AIFD 249
+ F+ + + ++ LE LT+E + +
Sbjct: 295 SVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVN 354
Query: 250 KCPSKL--KKRICSISSNQNSTLMAAFDGDSKKMSGLGNA---TFAPPHSTSGRVTDDKR 304
K S L K++ I S N G + + GL AP R+ +R
Sbjct: 355 KTNSHLPAGKQV-EI-SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSER 412
Query: 305 RSEHNGPPPEYR----------KLMAG------------------------------GRD 324
+ R L+ G D
Sbjct: 413 K-----LKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD 467
Query: 325 MNSRSSTSS---------TAVPINSMPSANTNKPPAHV--FQTSSSSRV 362
+ R + S +P+ + T H+ F +S +
Sbjct: 468 L--RVLSGSISERIVDCIIRLPVK-WETT-TQFKATHILDFGPGGASGL 512
Score = 36.2 bits (83), Expect = 0.044
Identities = 34/296 (11%), Positives = 73/296 (24%), Gaps = 111/296 (37%)
Query: 213 WEIPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLAIFDKCPSKLKKRICSISSNQNST--- 269
+P ++ +F QL E+F I + + ++ +T
Sbjct: 20 LLVPTAS----FFIA----------SQLQEQFNKILPEPTEGF------AADDEPTTPAE 59
Query: 270 LMAAFDGDSKKMSGLGNATFAPPHSTSGRVTDDKRRSEHNGPPPEYRKLM--------AG 321
L+ F LG + G + L
Sbjct: 60 LVGKF---------LG---Y----------VSSLVEPSKVGQFDQVLNLCLTEFENCYLE 97
Query: 322 GRDMNSRSSTSSTAVPINSMPSANTNKPPA--HVFQTSSSSRVPPPPPPHHHHSSAHVPK 379
G D+++ ++ + N + + ++R+ P +SA
Sbjct: 98 GNDIHALAA---------KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRA 148
Query: 380 IKTEHPPM--------KVEPVMKEALLKQ-----PPLIKQEPNVKQEPYIKSEPHSLLPL 426
+ + + + +E L+ L+ IK +L L
Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFEE--LRDLYQTYHVLV--------GDLIKFSAETLSEL 198
Query: 427 RKHEPINPRMMMNKPQSKPVIPHEVRKNGHD----LPVPKPHPPPPPPPPPYMSAA 478
+ ++ V G + L P P Y+ +
Sbjct: 199 IRTT----------LDAEKVFTQ-----GLNILEWL-----ENPSNTPDKDYLLSI 234
Score = 30.0 bits (67), Expect = 3.7
Identities = 23/126 (18%), Positives = 32/126 (25%), Gaps = 44/126 (34%)
Query: 7 QGSHSP--------------DRW----YFTKEQL---------ENTPSRKCGYDAEKELS 39
QGS D W K+ N + + EK
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR 1683
Query: 40 CRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFYVFHS---------FTQFHRNSIATAA 90
R+ + +I + ++ I I Y F S FTQ A
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ--------PA 1735
Query: 91 LFLAAK 96
L L K
Sbjct: 1736 LTLMEK 1741
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent
kinase. protein/protein complex, transferase; 2.50A
{Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1
Length = 252
Score = 62.1 bits (151), Expect = 8e-11
Identities = 34/246 (13%), Positives = 75/246 (30%), Gaps = 31/246 (12%)
Query: 11 SPDRWYFTKEQLENTPSRKCGYDAEKELSC--RQQAANLIQDMGQRLQVTQLCINTAIVY 68
D +R G + ++ + R+ + + + L+ A+
Sbjct: 17 EEDCRQMIYRSEREHDARMVGVNVDQHFTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVAL 76
Query: 69 MHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPPLDPR 125
+ + T+ R + A AL +A KV I+ QL
Sbjct: 77 LDELF---LSTRIDRENYQSTAAVALHIAGKVRAY-----MPIKATQLAYLCG------- 121
Query: 126 SEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFMASNSL 185
A +++ E L TL + + H++ A ++ Y + +
Sbjct: 122 -GATTAD--KLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPREDYLNIYNLCRPKI 178
Query: 186 HLTTM---CLQYRSTVVACFCIHLA--CKWANWEIPQSNEGRKWFWYIDKEVT--QEQLE 238
R ++ C+HL K+ +E + + K + +E+ + ++
Sbjct: 179 FCALCDGRSAMKRPVLITLACMHLTMNQKYDYYE-NRIDGVCKSLYITKEELHQCCDLVD 237
Query: 239 QLTEEF 244
F
Sbjct: 238 IAIVSF 243
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase,
chromosomal rearrangement, ATP-binding, transferase,
polymorphism, cell division; 2.30A {Homo sapiens} PDB:
2w99_A 2w9f_A 2w9z_A
Length = 271
Score = 55.9 bits (135), Expect = 1e-08
Identities = 28/187 (14%), Positives = 68/187 (36%), Gaps = 28/187 (14%)
Query: 60 LCINTAIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLF 116
L +N Y+ RF S ++ + +F+A+K++E + +LC++
Sbjct: 80 LAMN----YLDRFL---SLEPVKKSRLQLLGATCMFVASKMKET-----IPLTAEKLCIY 127
Query: 117 KNQPPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQT 176
+ + + +E++ E +L+ L +++ PH ++ + +++ Q
Sbjct: 128 TD--------NSIR--PEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQI 177
Query: 177 SYFMASNSLHLTTM---CLQYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVT 233
A + L + ++VA + A + N P + V
Sbjct: 178 IRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVI 237
Query: 234 QEQLEQL 240
+ + L
Sbjct: 238 KCDPDCL 244
>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 = 55.2 bits (132), Expect = 7e-08
Identities = 28/176 (15%), Positives = 62/176 (35%), Gaps = 21/176 (11%)
Query: 103 KLEHVIRVAQLCLFKNQPPLDPRSEAYQEQAQEIVVNENV-----LLQTLGFDVGIEHPH 157
KL +I + L P + R + + + V + LL + FDV
Sbjct: 354 KLTTII---ESSL-NVLEPAEYR-KMFDRLS---VFPPSAHIPTILLSLIWFDVIKSDVM 405
Query: 158 TYVVKCCHLVRASKDLAQTSYFMASNSLHLTTMCLQYRS---TVVACFCIHLACKWANWE 214
V K K +++ + S L L + ++V + I + + +
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP--KTFDSDD 463
Query: 215 IPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLAIF-DKCPSKLKKRICSISSNQNST 269
+ + ++ +I + + + F +F D L+++I S+ N++
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF--RFLEQKIRHDSTAWNAS 517
Score = 37.9 bits (87), Expect = 0.014
Identities = 68/545 (12%), Positives = 151/545 (27%), Gaps = 132/545 (24%)
Query: 33 DAEKELSCRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFYVFHSFTQFHRNSIATAALF 92
D K + +++ ++I + T T + +F + F
Sbjct: 40 DMPKSILSKEEIDHIIM-SKDAVSGTLRLFWTLLSKQEEMV-----QKFVEEVLRINYKF 93
Query: 93 LAAKVEEQPRKLEHVIRVAQLC---LFKNQPPLDP----RSEAY---QEQAQEIVVNENV 142
L + ++ + R+ + R+ L+ + R + Y ++ E+ +NV
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNV 153
Query: 143 LLQ-TLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFMASNSLHLTTM--CLQYRSTV- 198
L+ LG G K + + + C + +
Sbjct: 154 LIDGVLGS--G---------KTWVALDVCLSYKVQCKM--DFKIFWLNLKNCNSPETVLE 200
Query: 199 -VACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQLEQLTEEFLAIFDKCPSKLKK 257
+ + W + SN + ++ + E + SK +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSN-------------IKLRIHSIQAELRRLLK---SKPYE 244
Query: 258 RICSISSN-QNSTLMAAFDGDSKKM---SGLGNATFAPPHSTSGRVTDDKRRSEHNGPPP 313
+ N QN+ AF+ K + F +T+ D + P
Sbjct: 245 NCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT---PD 301
Query: 314 EYRKLMAGGRDMNSRSSTSSTAVPINSMPSANTNKPPAHVFQTSSSSRVPPPPPPHHHHS 373
E + L+ +P P + + S R +
Sbjct: 302 EVKSLLL-----------KYLDCRPQDLPREVLTTNPRRLSIIAESIR-------DGLAT 343
Query: 374 SAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQE---------PNVKQEPYIKSEPHSLL 424
+ + + K+ +++ +L P ++ P+ I P LL
Sbjct: 344 WDNWKHVNCD----KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH----I---PTILL 392
Query: 425 PL--RKHEPINPRMMMNKPQSKPVI---PHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAK 479
L + +++NK ++ P E + + Y+ K
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI---------------YLE-LK 436
Query: 480 LPPPS----HSDVITNVIKEVTY-----SKQMEKSSILNHKESSISHPPHLSMSIPQTKA 530
+ + H ++ + T+ +H I H HL +I +
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH----IGH--HLK-NIEHPER 489
Query: 531 PSIFS 535
++F
Sbjct: 490 MTLFR 494
Score = 35.2 bits (80), Expect = 0.097
Identities = 72/609 (11%), Positives = 164/609 (26%), Gaps = 183/609 (30%)
Query: 227 YIDKEVTQEQ------LEQLTEEFLAIFDKCPSKLKKRICSISSNQNSTLMAAFDGDSKK 280
++D E + Q L + F+ FD C K + Q+ +
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFD-C-----KDV------QDMPKSILSKEEIDH 53
Query: 281 MSGLGNATFAPPHSTSGRVTDDKRRSEHNGPPPEYRKLMAGGRDMNSRSSTSSTAVPINS 340
+ + S + R+ + +K + +N + S
Sbjct: 54 IIMSKD-----AVSGTLRLFWTLLSKQEEM----VQKFVEEVLRINYKFLMSPIKTEQRQ 104
Query: 341 MPSANTNKPPAHVFQTSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQ 400
PS T ++ Q ++ V +++ +++ALL+
Sbjct: 105 -PSMMTRM---YIEQRDRLYNDNQVFAKYN------VSRLQPYL-------KLRQALLE- 146
Query: 401 PPLIKQEPNV---------KQ----EPYIKSEPHSLLPLRKH-----EPINPRMMMNKPQ 442
++ NV K + + + + + +P ++ Q
Sbjct: 147 ---LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203
Query: 443 SKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAA-----KLPPPSHS-----DV-ITN 491
+ +++ N H + A K P + +V
Sbjct: 204 K---LLYQIDPNWTSRS---DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 492 VIKE--------VT--YSKQMEKSSILNHKESSISHPPHLSMSIPQTKAPSIFSPEKNTS 541
+T + + + S S+ H ++++ + K S+ K
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHS-MTLTPDEVK--SLLL--KYLD 312
Query: 542 PVINKTPFKMKTPTPPSFSPI---------------KISPSKSSEGLKAKLEPELVPVIT 586
P ++ T P S I ++ K + +++ L L P
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN-VLEPAEY 371
Query: 587 K-----LG---DDILTKPKILA---SEIISETKQE-PHESHS-----QHPKKKKKH---- 625
+ L +L+ ++I ++ H + PK+
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 626 ----KEKDKDRDKKHKE--------KKKHKDDKHKDKRKDK-------HRESSHVDPAPI 666
K K ++ H+ K DD D+ H H+
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP-YLDQYFYSHIGH----HLKNIE- 485
Query: 667 KITIPKDKIIEMPCSSNL--------KKIKMKDSFENP--------LKIRISKDFLSKDS 710
+++ + +KI+ + N +++ K ++ +
Sbjct: 486 ----HPERMTLFR---MVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDND 538
Query: 711 KKRERDTDD 719
K ER +
Sbjct: 539 PKYERLVNA 547
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between
N-terminal and C-TERM domain of kinase, cell
cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus
saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A*
1xo2_A* 1bu2_A
Length = 254
Score = 52.4 bits (126), Expect = 1e-07
Identities = 19/154 (12%), Positives = 52/154 (33%), Gaps = 28/154 (18%)
Query: 60 LCINTAIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLF 116
L ++ + R+ Q + + I A + + +K+ + V++L
Sbjct: 75 LSVS----ILDRYL---CKKQGTKKTLQKIGAACVLIGSKIRTV-----KPMTVSKLTYL 122
Query: 117 KNQPPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQT 176
+ + E++ E +L+ L +D +++ C+ ++ +DL
Sbjct: 123 SC--------DCFTNL--ELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQ 172
Query: 177 SYFMASNSLHLTTM---CLQYRSTVVACFCIHLA 207
Y AS ++ + ++ +
Sbjct: 173 LYEAASTTICKALIQPNIALLSPGLICAGGLLTT 206
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation,
ATP-BIN cell division, disease mutation, kinase; 3.00A
{Homo sapiens}
Length = 306
Score = 52.5 bits (126), Expect = 2e-07
Identities = 25/150 (16%), Positives = 49/150 (32%), Gaps = 26/150 (17%)
Query: 65 AIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEE-QPRKLEHVIRVAQLCLFKNQP 120
A+ Y+ R+ S + + + LA+K+ E P +E +
Sbjct: 95 AMNYLDRYL---SCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTD-------- 143
Query: 121 PLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTSYFM 180
A + ++ E ++L L +D+ H ++ H + +D
Sbjct: 144 ------HAVSPR--QLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKH 195
Query: 181 ASNSLHLTTM---CLQYRSTVVACFCIHLA 207
A L L Y +++A I A
Sbjct: 196 AQTFLALCATDYTFAMYPPSMIATGSIGAA 225
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin,
cell cycle, signaling protein; 2.90A {Human herpesvirus
8} SCOP: a.74.1.1 a.74.1.1
Length = 257
Score = 48.6 bits (116), Expect = 2e-06
Identities = 23/199 (11%), Positives = 55/199 (27%), Gaps = 39/199 (19%)
Query: 65 AIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPP 121
A+ + R Q + +A L +A+K+ I + LC
Sbjct: 75 ALNLLDRLL---LIKQVSKEHFQKTGSACLLVASKLRSL-----TPISTSSLCYAAA--- 123
Query: 122 LDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASK--DLAQTSYF 179
+++ Q E++ E LL+ L + L++ +
Sbjct: 124 -----DSFSRQ--ELIDQEKELLEKLAWRTEAVLATDVT--SFLLLKLVGGSQHLDFWHH 174
Query: 180 MASNSLHLTTM---CLQYRSTVVACFCIHLACKWANWEIPQSNEGRKWFWYIDKEVTQEQ 236
+ + + +++++ L IPQ Q
Sbjct: 175 EVNTLITKALVDPLTGSLPASIISAAGCALLVP--ANVIPQDTHSGGV---------VPQ 223
Query: 237 LEQLTEEFLAIFDKCPSKL 255
L + +++ ++
Sbjct: 224 LASILGCDVSVLQAAVEQI 242
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*
Length = 269
Score = 44.6 bits (106), Expect = 4e-05
Identities = 21/153 (13%), Positives = 52/153 (33%), Gaps = 26/153 (16%)
Query: 60 LCINTAIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLF 116
+ ++ + RF + + A+F+A+K EE + +
Sbjct: 61 MTVS----IIDRFM---QNNSVPKKMLQLVGVTAMFIASKYEEM-----YPPEIGDFAFV 108
Query: 117 KNQPPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVKCCHLVRASKDLAQT 176
+ Y + +I E +L+ L F +G P ++ + + +
Sbjct: 109 TD--------NTYTKH--QIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTL 158
Query: 177 SYFMASNSLHLTTMCLQYRSTVVACFCIHLACK 209
+ ++ ++ L + + + +A LA K
Sbjct: 159 AKYLMELTM-LDYDMVHFPPSQIAAGAFSLALK 190
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division),
ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear
protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP:
a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B*
1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B*
2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B*
2x1n_B* 1vyw_B* ...
Length = 260
Score = 44.2 bits (105), Expect = 6e-05
Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 26/152 (17%)
Query: 60 LCINTAIVYMHRFYVFHSFTQFHRNS---IATAALFLAAKVEEQPRKLEHVIRVAQLCLF 116
L +N Y+ RF S R + TAA+ LA+K EE + VA+
Sbjct: 62 LAVN----YIDRFL---SSMSVLRGKLQLVGTAAMLLASKFEEI-----YPPEVAEFVYI 109
Query: 117 KNQPPLDPRSEAYQEQAQEIVVNENVLLQTLGFDVGIEHPHTYVVK-CCHLVRASKDLAQ 175
+ + Y + ++++ E+++L+ L FD+ + ++ + H A+ +
Sbjct: 110 TD--------DTYTK--KQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVES 159
Query: 176 TSYFMASNSLHLTTMCLQYRSTVVACFCIHLA 207
+ F+ SL L+Y +V+A HLA
Sbjct: 160 LAMFLGELSLIDADPYLKYLPSVIAGAAFHLA 191
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET:
TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1
Length = 283
Score = 40.5 bits (95), Expect = 0.001
Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 27/133 (20%)
Query: 86 IATAALFLAAKVEE-QPRKLEHVIRVAQLCLFKNQPPLDPRSEAYQEQAQEIVVNENVLL 144
I ++LF+AAK+EE P KL V A EI+ E +++
Sbjct: 96 IGISSLFIAAKLEEIYPPKLHQFAYVT--------------DGACSG--DEILTMELMIM 139
Query: 145 QTLGFDVGIEHPHTYVVKCCHLVRASKDLAQTS-------YFMASNSLHLTTM---CLQY 194
+ L + + +++ + + + + L L + CL++
Sbjct: 140 KALKWRLSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEF 199
Query: 195 RSTVVACFCIHLA 207
++A ++
Sbjct: 200 PYGILAASALYHF 212
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 38.6 bits (89), Expect = 0.002
Identities = 12/62 (19%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 605 SETKQEPHESHSQHPKKKKKH-KEKDKDRDKKHKE----KKKHKDD--KHKDKRKDKHRE 657
QEP ES + ++++K +E D +E KK ++ + + ++ +K++
Sbjct: 78 DRLTQEP-ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136
Query: 658 SS 659
++
Sbjct: 137 NN 138
Score = 35.9 bits (82), Expect = 0.022
Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 15/76 (19%)
Query: 578 EPELV--------PVITKLGDDILTKPKILASEIISETKQEPHESHSQHPKKKKKHKEKD 629
EPE + + +L D +K E + K++ E + + ++ +K+K +
Sbjct: 83 EPESIRKWREEQRKRLQEL--DAASKVME--QEWREKAKKDLEEWNQRQSEQVEKNKINN 138
Query: 630 KDRDKKHKEKKKHKDD 645
+ D K + D
Sbjct: 139 RIAD---KAFYQQPDA 151
Score = 32.8 bits (74), Expect = 0.22
Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 601 SEIIS----ETKQEPHESHSQHPKKKKKHKEK-DKDRD---KKHKEK--KKHKDDKHKDK 650
E I E ++ E + +++ +EK KD + ++ E+ K +++ DK
Sbjct: 84 PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK 143
Query: 651 RKDKHRESS 659
+ ++
Sbjct: 144 AFYQQPDAD 152
>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin,
armadillo repeat, nuclear receptor LIGA binding domain,
protein binding; HET: P6L; 2.76A {Homo sapiens}
Length = 352
Score = 36.1 bits (83), Expect = 0.038
Identities = 28/160 (17%), Positives = 45/160 (28%), Gaps = 9/160 (5%)
Query: 354 FQTSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQEPNVKQE 413
+ + S+V P SSA I+ H K P+ AL P + P V
Sbjct: 2 LKLEAMSQVIQAMPSDLTISSA----IQNIHSASKGLPLNHAAL--PPTDYDRSPFVTSP 55
Query: 414 PYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPP 473
+ PH L + P + P G+ P P
Sbjct: 56 ISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHL 115
Query: 474 Y---MSAAKLPPPSHSDVITNVIKEVTYSKQMEKSSILNH 510
+ P + ++ + +E + EK S
Sbjct: 116 ILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGL 155
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex,
inter-protein beta sheet, protein-protein, metal
transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A
{Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Length = 229
Score = 34.3 bits (78), Expect = 0.088
Identities = 32/140 (22%), Positives = 47/140 (33%), Gaps = 10/140 (7%)
Query: 369 HHHHSSAHVPKI------KTEHPPMKVEPVMKE----ALLKQPPLIKQEPNVKQEPYIKS 418
HHHHSS VP+ + P +P+ A L+ P ++ P EP +
Sbjct: 6 HHHHSSGLVPRGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEP 65
Query: 419 EPHSLLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAA 478
EP P I KP+ KPV + + PV P P +
Sbjct: 66 EPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTS 125
Query: 479 KLPPPSHSDVITNVIKEVTY 498
+ S +T+V
Sbjct: 126 STATAATSKPVTSVASGPRA 145
Score = 29.7 bits (66), Expect = 2.5
Identities = 21/152 (13%), Positives = 35/152 (23%), Gaps = 12/152 (7%)
Query: 332 SSTAVPINSMPSANTNKPPAHVFQTSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMKVEP 391
SS VP S S + Q S + V P + P + P
Sbjct: 10 SSGLVPRGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIP 69
Query: 392 VMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIPHEV 451
+ + P +I++ + + P R +P+ R + P
Sbjct: 70 EPPK---EAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARL--- 123
Query: 452 RKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPP 483
P L
Sbjct: 124 ------TSSTATAATSKPVTSVASGPRALSRN 149
Score = 29.3 bits (65), Expect = 4.0
Identities = 22/141 (15%), Positives = 40/141 (28%), Gaps = 6/141 (4%)
Query: 329 SSTSSTAVPINSMPSANTNKPPAHVFQTSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMK 388
S +P + P + T PA + + P P PP +
Sbjct: 21 SVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVE------PEPEPEPIPEPPKE 74
Query: 389 VEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIP 448
V+++ K P K V+++P +P P E P + + +
Sbjct: 75 APVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSK 134
Query: 449 HEVRKNGHDLPVPKPHPPPPP 469
+ + P P
Sbjct: 135 PVTSVASGPRALSRNQPQYPA 155
>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA
complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP:
d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A*
1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A*
1lpq_A* 1rr8_C* 1ej9_A*
Length = 591
Score = 33.6 bits (76), Expect = 0.29
Identities = 12/84 (14%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 602 EIISETKQEPHESHSQHPKKKKKHKEKDKDRDKKHKEK------KKHKDDKHKDKRKDKH 655
E +++ +++ + + K +K + KK ++ K +++ K
Sbjct: 482 EQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIA 541
Query: 656 RESSHVDPAPIKITIPKDKIIEMP 679
+S ++ +IT+ K +P
Sbjct: 542 LGTSKLNYLDPRITVAWCKKWGVP 565
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 32.8 bits (74), Expect = 0.33
Identities = 19/93 (20%), Positives = 28/93 (30%), Gaps = 12/93 (12%)
Query: 286 NATFAPPHSTSGRVTDDKRRSEHNGPPPEYRKLMAGGRDMNSRSSTSSTAVPINSMPSAN 345
T S ++ ++ E + AG +SR++ P A
Sbjct: 143 VVTPVNKQFLSQFEMQSRKTTQSGQMSGEGK---AGPPGGSSRAAFPQGGRGRGRFPGAV 199
Query: 346 TNKPPAHVFQTSSSSRVPPPP------PPHHHH 372
P F + PPPP HHHH
Sbjct: 200 ---PGGDRFPGPAGPGGPPPPFPAGQTHHHHHH 229
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 32.2 bits (72), Expect = 0.67
Identities = 20/230 (8%), Positives = 48/230 (20%), Gaps = 27/230 (11%)
Query: 369 HHHHSSAHV-------------------------PKIKTEHPPMKVEPVMKEALLKQPPL 403
HHHH H ++EH + + + ++ L
Sbjct: 3 HHHHHHGHHHQLENLYFQGEETAVPENSGANTELVSGESEHSTNEADKQNEGEHARENKL 62
Query: 404 IKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIP--HEVRKNGHDLPVP 461
K E + E + K E +
Sbjct: 63 EKAEGVATASETASPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEA 122
Query: 462 KPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKEVTYSKQMEKSSILNHKESSISHPPHL 521
KP + A + ++ K+++ +S +
Sbjct: 123 KPEATNQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGAREDD 182
Query: 522 SMSIPQTKAPSIFSPEKNTSPVINKTPFKMKTPTPPSFSPIKISPSKSSE 571
+++ S + + + + T + +
Sbjct: 183 AINRGSVVLASRRTGHLVNEKASKEAKVQALSNTNSKAKDHASVGGEEFK 232
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 31.2 bits (70), Expect = 0.86
Identities = 10/73 (13%), Positives = 19/73 (26%), Gaps = 20/73 (27%)
Query: 1 MSTNTTQGSHSPDRWYFTKEQLENTPSRKCGYDAEKELSCRQQAANLIQD--MGQRLQVT 58
M T + + R L C E C+ +++ G
Sbjct: 1 MMTRESIDKRAGRR----GPNLNIV--LTC-----PE--CKVYPPKIVERFSEGDV---- 43
Query: 59 QLCINTAIVYMHR 71
+C +V +
Sbjct: 44 -VCALCGLVLSDK 55
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB);
hyperthermophIle, ribosome binding, complex (ribosome
binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei}
SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*
Length = 200
Score = 31.1 bits (70), Expect = 0.92
Identities = 13/75 (17%), Positives = 29/75 (38%)
Query: 40 CRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFYVFHSFTQFHRNSIATAALFLAAKVEE 99
+ + + L +++ AI + Y + + AAL++A+ +E
Sbjct: 104 LFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEG 163
Query: 100 QPRKLEHVIRVAQLC 114
+ R V VA++
Sbjct: 164 EKRTQREVAEVARVT 178
>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay,
ribosomal protein,hydrolase; 9.50A {Saccharomyces
cerevisiae}
Length = 611
Score = 31.6 bits (72), Expect = 1.1
Identities = 17/111 (15%), Positives = 32/111 (28%), Gaps = 2/111 (1%)
Query: 504 KSSILNHKESSISHPPHLSMSIPQTKAPSIFSPEKNTSPVINKTPFKMKT--PTPPSFSP 561
K ++ ++ S L ++ + K P N S + + + P P
Sbjct: 57 KLALFDNNFDLESTLAELKKTLKKKKTPKKPIAAANGSANVTQKLANISISQQRPNDRLP 116
Query: 562 IKISPSKSSEGLKAKLEPELVPVITKLGDDILTKPKILASEIISETKQEPH 612
+ +S + + V + TKPK PH
Sbjct: 117 DWLDEEESEGERNGEEANDEKTVQRYYKTTVPTKPKKPHDISAFVKSALPH 167
>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp,
transferase; HET: DNA; 2.89A {Mycobacterium
tuberculosis} PDB: 3rb9_A*
Length = 408
Score = 31.5 bits (72), Expect = 1.1
Identities = 5/32 (15%), Positives = 11/32 (34%), Gaps = 1/32 (3%)
Query: 369 HHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQ 400
HHHH + + +++E+
Sbjct: 1 HHHHHHMDAATTRVGLTDLTFR-LLRESFADA 31
>1up8_A Vanadium-dependent bromoperoxidase 1; haloperoxidase, vanadate;
2.20A {Corallina pilulifera} SCOP: a.111.1.2 PDB: 1qhb_A
Length = 598
Score = 31.4 bits (70), Expect = 1.1
Identities = 23/116 (19%), Positives = 36/116 (31%), Gaps = 12/116 (10%)
Query: 264 SNQNSTLMAAFDGDSKKMSGLGNATFAPPHSTSGRVTDDK-----RRSEHNGPPPEYRKL 318
+N L D D+ S + + T PH +G + D R+ ++G E L
Sbjct: 36 ANGEELLYRNPDPDNTDPSFIASFTKGLPHDDNGAIIDPDDFLAFVRAINSGDEKEIADL 95
Query: 319 MAGGRDMNSRSSTSSTAVPINSMPSAN---TNKPPAHVFQT----SSSSRVPPPPP 367
G + NS+ N F + S +PP P
Sbjct: 96 TLGPARDPETGLPIWRSDLANSLELEVRGWENSSAGLTFDLEGPDAQSIAMPPAPV 151
>1xma_A Predicted transcriptional regulator; southea collaboratory for
structural genomics, secsg, protein struc initiative,
PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61
Length = 145
Score = 30.1 bits (68), Expect = 1.2
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 368 PHHHHSSAHVPKIKTEHPPMKVEPVMK 394
HHHHSS VP+ K +M
Sbjct: 6 HHHHHSSGLVPRGSQSTSLYKKAGLMV 32
>2obd_A Cholesteryl ester transfer protein; lipid transfer protein, lipid
transport; HET: NDG FU4 2OB PCW EPE 1PE PG4; 2.10A {Homo
sapiens}
Length = 476
Score = 31.4 bits (70), Expect = 1.3
Identities = 19/194 (9%), Positives = 45/194 (23%), Gaps = 21/194 (10%)
Query: 389 VEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIP 448
+ +K L Q + ++++ + + ++ + + + +
Sbjct: 171 ISFTLKLVLKGQICKEINVISNIMADFVQTRA-ASILSDGDIGVDISLTGDPVITASYL- 228
Query: 449 HEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKEV---TYSKQMEKS 505
E GH + P P P S ++ E + +K +
Sbjct: 229 -ESHHKGHFIYKDVSEDLPLPTFSP-------TLLGDSRMLYFWFSERVFHSLAKVAFQD 280
Query: 506 SILNHKESSISHPPHLSMSIPQTKAPSIFSPE-KNTSPVINKTPFKMKTPTPPSFSPIKI 564
L L T E P ++ + P S
Sbjct: 281 GRLMLSLMGDEFKAVLETWGFNTNQEIF--QEVVGGFP--SQAQVTVHCLKMPKIS---C 333
Query: 565 SPSKSSEGLKAKLE 578
++
Sbjct: 334 QNKGVVVDSSVMVK 347
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like
fold, helix-turn-helix, transcription/DNA complex; 2.65A
{Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A
2phg_A 1vol_A*
Length = 207
Score = 30.4 bits (68), Expect = 1.6
Identities = 10/83 (12%), Positives = 27/83 (32%)
Query: 32 YDAEKELSCRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFYVFHSFTQFHRNSIATAAL 91
A + + + L + + A + S+A AA+
Sbjct: 90 LKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAI 149
Query: 92 FLAAKVEEQPRKLEHVIRVAQLC 114
++A++ + R + + +A +
Sbjct: 150 YMASQASAEKRTQKEIGDIAGVA 172
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A
Length = 419
Score = 30.7 bits (69), Expect = 1.6
Identities = 17/81 (20%), Positives = 36/81 (44%)
Query: 555 TPPSFSPIKISPSKSSEGLKAKLEPELVPVITKLGDDILTKPKILASEIISETKQEPHES 614
P K +PSK++ + LE + + L + + S+++ E + E+
Sbjct: 15 VPRGSHMPKETPSKAAADALSDLEIKDSKSNLNKELETLREENRVKSDMLKEKLSKDAEN 74
Query: 615 HSQHPKKKKKHKEKDKDRDKK 635
H + K + H+ K K+ +K+
Sbjct: 75 HKAYLKSHQVHRHKLKEMEKE 95
>1y8q_B Anthracycline-, ubiquitin-like 2 activating enzyme E1B; SUMO,
heterodimer, UBL, ligase; HET: ATP; 2.25A {Homo sapiens}
PDB: 1y8r_B* 3kyc_B* 3kyd_B* 2px9_A
Length = 640
Score = 30.9 bits (69), Expect = 1.9
Identities = 15/108 (13%), Positives = 37/108 (34%), Gaps = 6/108 (5%)
Query: 538 KNTSPVINKTPFKMKTPTPPSFSPIKISPSKSSEGLKAKLEPELVPVITKLGDDILTKPK 597
++ + F++ P P + + S + + + DD+L
Sbjct: 533 LHSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLI--- 589
Query: 598 ILASEIISETKQEPHESHSQHPKKKKKHKEKDKDRDKKHKEKKKHKDD 645
+ E + + +K+K EK+ K+ + ++K + D
Sbjct: 590 ---VDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELD 634
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 30.0 bits (67), Expect = 2.1
Identities = 19/122 (15%), Positives = 23/122 (18%), Gaps = 2/122 (1%)
Query: 362 VPPPPPPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPH 421
+ PP A VP P + P Q P P
Sbjct: 80 MTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM--PQAPAGLAGPVRGVGGP 137
Query: 422 SLLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLP 481
S + + G P P PPP P
Sbjct: 138 SQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRP 197
Query: 482 PP 483
P
Sbjct: 198 PM 199
>3c8w_A Acetoacetate decarboxylase ADC; YP_094708.1, structural GE joint
center for structural genomics, JCSG, protein structu
initiative; HET: LCK CIT; 1.60A {Legionella pneumophila
subsp} SCOP: d.347.1.1
Length = 255
Score = 30.0 bits (67), Expect = 2.5
Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 438 MNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSA 477
M+K S + V N +P P+ P P +++
Sbjct: 2 MDKYLSANSL-EGVIDNEFSMPAPRWLNTYPAGPYRFINR 40
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 30.1 bits (67), Expect = 2.9
Identities = 15/73 (20%), Positives = 20/73 (27%)
Query: 418 SEPHSLLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSA 477
S H P M++ + + VP P PPPPP P
Sbjct: 3 SSHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPP 62
Query: 478 AKLPPPSHSDVIT 490
+ S I
Sbjct: 63 DTVTGDSVLQRIL 75
Score = 29.7 bits (66), Expect = 3.8
Identities = 22/132 (16%), Positives = 28/132 (21%), Gaps = 2/132 (1%)
Query: 367 PPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPL 426
HHHHSS VP+ P L P+ P P
Sbjct: 5 HHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAA-GNPPD 63
Query: 427 RKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVP-KPHPPPPPPPPPYMSAAKLPPPSH 485
+ ++ P P P P PP P P
Sbjct: 64 TVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGLYHHPVPEP 123
Query: 486 SDVITNVIKEVT 497
V +
Sbjct: 124 DPVRVEEVSRRI 135
Score = 29.0 bits (64), Expect = 6.1
Identities = 26/167 (15%), Positives = 39/167 (23%), Gaps = 32/167 (19%)
Query: 329 SSTSSTAVPINSMPSANTNKPPAHVFQTSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMK 388
SS +P + P+ +++S + PP P
Sbjct: 3 SSHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPP--------------VTVPDP 48
Query: 389 VEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIP 448
P PP S +L P P S
Sbjct: 49 APPPPPAPAAGNPPDTVTGD---------SVLQRILR----GPTGP-----GTTSLAPAV 90
Query: 449 HEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKE 495
R+ G + P P P Y P P + ++ IK
Sbjct: 91 RYGRQPGPEAPASAPPAAGRAVPGLYHHPVPEPDPVRVEEVSRRIKR 137
>3gyk_A 27KDA outer membrane protein; APC61738.2, silicibacter pomeroyi
DSS-3, thioredoxin-like, oxidoreductase, structural
genomics, PSI-2; HET: MSE; 1.76A {Silicibacter pomeroyi}
Length = 175
Score = 29.2 bits (66), Expect = 3.3
Identities = 19/118 (16%), Positives = 32/118 (27%), Gaps = 30/118 (25%)
Query: 30 CGYDAEKELSCRQQAANLIQDMGQRLQVTQLCINTAIVYMHRFYVFHSFTQFHRNSIATA 89
C Y CR+ A + + V V+ + S A
Sbjct: 34 CPY-------CRRAMAEVQGLVDADPNVR--------------LVYREWPILGEGSDFAA 72
Query: 90 ALFLAAKVEEQPRKLEHVIRVAQLCLFKNQPPLDPRSEAYQEQAQEIVVNENVLLQTL 147
LAA+ Q K E L + A+E+ ++ L + +
Sbjct: 73 RAALAAR---QQGKYEAFHWA----LMGMSGKANE--TGVLRIAREVGLDTEQLQRDM 121
>3bn9_D E2 FAB heavy chain; antibody-protease complex, protein-protein
complex, enzyme- inhibitor complex, disease mutation,
glycoprotein, hydrolase; 2.17A {Homo sapiens} SCOP:
b.1.1.1 b.1.1.2 PDB: 3kr3_H 2xtj_E
Length = 257
Score = 29.4 bits (67), Expect = 3.3
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 329 SSTSSTAVPINSMPSA----NTNKPPAHVFQTSSSSRVPPPPPPHHHHSSAHVPKIKTE 383
S +S VP +S+ + N N P++ HHHH A K+ +E
Sbjct: 192 SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHHGAAEQKLISE 250
>3d2f_A Heat shock protein homolog SSE1; nucleotide exchange factor,
protein folding, ATP-binding, Ca binding, chaperone,
nucleotide-binding, phosphoprotein; HET: ATP; 2.30A
{Saccharomyces cerevisiae} PDB: 3d2e_A* 3c7n_A* 2qxl_A*
Length = 675
Score = 30.0 bits (68), Expect = 3.4
Identities = 22/103 (21%), Positives = 31/103 (30%), Gaps = 16/103 (15%)
Query: 567 SKSSEGLKAKLEPELVPVITKLGDDILTKPK-----------ILASEIISETKQEPHE-- 613
+S+ K KL+ L L D+ K L + I + E
Sbjct: 573 PFASDAEKTKLQGMLNKAEEWLYDEGFDSIKAKYIAKYEELASLGNIIRGRYLAKEEEKK 632
Query: 614 ---SHSQHPKKKKKHKEKDKDRDKKHKEKKKHKDDKHKDKRKD 653
Q + EK + K EKK+ K D D D
Sbjct: 633 QAIRSKQEASQMAAMAEKLAAQRKAEAEKKEEKKDTEGDVDMD 675
>1jer_A Cucumber stellacyanin; electron transport, copper, glycoprotein,
hydroxylation; 1.60A {Cucumis sativus} SCOP: b.6.1.1
Length = 138
Score = 28.5 bits (63), Expect = 3.7
Identities = 10/28 (35%), Positives = 11/28 (39%)
Query: 459 PVPKPHPPPPPPPPPYMSAAKLPPPSHS 486
PP PP M +PPPS S
Sbjct: 111 ATVSMPPPSSSPPSSVMPPPVMPPPSPS 138
>2wvr_C DNA replication factor CDT1; DNA replication license, DNA
replication inhibitor, phosphoprotein, UBL conjugation,
DNA-binding, polymorphism; HET: DNA; 3.30A {Homo
sapiens} PDB: 2klo_A*
Length = 546
Score = 29.7 bits (65), Expect = 4.2
Identities = 19/178 (10%), Positives = 33/178 (18%), Gaps = 2/178 (1%)
Query: 298 RVTD--DKRRSEHNGPPPEYRKLMAGGRDMNSRSSTSSTAVPINSMPSANTNKPPAHVFQ 355
RVTD +RR P + + +S
Sbjct: 5 RVTDFFARRRPGPPRIAPPKLACRTPSPARPALRAPASATSGSRKRARPPAAPGRDQARP 64
Query: 356 TSSSSRVPPPPPPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQEPNVKQEPY 415
+ + P K++ A Q+ + E
Sbjct: 65 PARRRLRLSVDEVSSPSTPEAPDIPACPSPGQKIKKSTPAAGQPPHLTSAQDQDTISELA 124
Query: 416 IKSEPHSLLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPP 473
+ L R + + G P + P P
Sbjct: 125 SCLQRARELGARVRALKASAQDAGESCTPEAEGRPEEPCGEKAPAYQRFHALAQPGLP 182
>2dm9_A V-type ATP synthase subunit E; A-ATPase, structural genomics,
NPPSFA, national project on P structural and functional
analyses; 1.85A {Pyrococcus horikoshii} SCOP: d.81.4.1
PDB: 2dma_A 4dt0_A
Length = 198
Score = 28.8 bits (64), Expect = 4.2
Identities = 9/57 (15%), Positives = 22/57 (38%)
Query: 585 ITKLGDDILTKPKILASEIISETKQEPHESHSQHPKKKKKHKEKDKDRDKKHKEKKK 641
+ +I + + I++E +Q+ + + + + E R K E +K
Sbjct: 4 AELIIQEINKEAERKIEYILNEARQQAEKIKEEARRNAEAKAEWIIRRAKTQAELEK 60
>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 9.00A {Bos
taurus}
Length = 205
Score = 29.1 bits (64), Expect = 4.5
Identities = 10/58 (17%), Positives = 27/58 (46%)
Query: 601 SEIISETKQEPHESHSQHPKKKKKHKEKDKDRDKKHKEKKKHKDDKHKDKRKDKHRES 658
E I + ++E + + K +++ +++ KK E+ + + +K K +R +
Sbjct: 99 PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIA 156
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 29.7 bits (66), Expect = 4.9
Identities = 27/148 (18%), Positives = 46/148 (31%), Gaps = 5/148 (3%)
Query: 428 KHEPINPRMMMNKPQSKPVIPH---EVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPS 484
+ P +P P P P P P P P P S
Sbjct: 1583 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1642
Query: 485 HSDVITNVIKEVTYSKQMEKSSILNHKESSISHPPHLSMSIPQTKAPSIFSPEKN-TSPV 543
S + + + + ++ +S S+ P P + + S SP + TSP
Sbjct: 1643 TSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPS 1702
Query: 544 INKTPFKMKTPTPPSFSPIKISPSKSSE 571
+ T +P P++SP + +
Sbjct: 1703 YSPTSPGY-SPGSPAYSPKQDEQKHNEN 1729
>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA
complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1
Length = 87
Score = 27.3 bits (60), Expect = 5.3
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 620 KKKKKHKEKDKDRDKKHKEKKKHKDDKHKDKRKDKHRE 657
K KK +K D K +E+ K +DK K ++ E
Sbjct: 3 SKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLE 40
>3v26_X ORF3, ORF95, probable sigma(54) modulation protein; ribosome
hibernation factor, YHBH, protein E, stress respons
stationary phase; 3.10A {Escherichia coli} PDB: 3v28_X
2rql_A
Length = 101
Score = 27.5 bits (62), Expect = 5.3
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 646 KHKDKRKDKHRESSH 660
KHKDK K H H
Sbjct: 87 KHKDKLKQHHHHHHH 101
>3tj1_A RNA polymerase I-specific transcription initiatio RRN3; heat
repeat, transcription factor, nucleus; 2.85A
{Saccharomyces cerevisiae}
Length = 649
Score = 29.5 bits (65), Expect = 5.4
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 369 HHHHSSAHVPKIKTEHPPMKVEPVMK 394
HHHHSS VP+ M E K
Sbjct: 7 HHHHSSGLVPRGSH-MAMMAFENTSK 31
>2efk_A CDC42-interacting protein 4; EFC domain, structural genomics,
NPPSFA, national project on structural and functional
analyses; 2.30A {Homo sapiens} SCOP: a.238.1.4
Length = 301
Score = 28.9 bits (64), Expect = 5.5
Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 2/95 (2%)
Query: 567 SKSSEGLKAKLEPELVPVITKLGDDILTKPKILASEIISETKQEPHESHSQHPKKKKKHK 626
+ E + L + +TK ++ + K+ + +Q+ Q K+K +
Sbjct: 82 AGQRELVAENLSVRVCLELTKYSQEMKQERKMH-FQEGRRAQQQLENGFKQLENSKRKFE 140
Query: 627 EKDKDRDKKHKEKKKHKDDKHKDKRK-DKHRESSH 660
++ +K + ++ D + K +K ++ +H
Sbjct: 141 RDCREAEKAAQTAERLDQDINATKADVEKAKQQAH 175
>3vr8_D Succinate dehydrogenase [ubiquinone] cytochrome B subunit,
mitochondrial; membrane protein, reductase, mitochondria
MEMB oxidoreductase; HET: FAD HEM RQX EPH; 2.81A
{Ascaris suum} PDB: 3vrb_D*
Length = 156
Score = 28.2 bits (62), Expect = 5.5
Identities = 6/45 (13%), Positives = 12/45 (26%)
Query: 442 QSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPSHS 486
++ + +++ PP P P SH
Sbjct: 12 SARILRTSLIQRCAGATSAAVTGAAPPQFDPIAAEKGFKPLHSHG 56
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 29.2 bits (66), Expect = 5.9
Identities = 9/31 (29%), Positives = 11/31 (35%), Gaps = 10/31 (32%)
Query: 198 VVACFCI--HLACKWANWEIPQSNEGRKWFW 226
VA F L W +WE G + F
Sbjct: 382 TVATFLTRGGL---WQSWE-----HGLQHFL 404
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 29.4 bits (65), Expect = 6.0
Identities = 25/206 (12%), Positives = 52/206 (25%), Gaps = 9/206 (4%)
Query: 303 KRRSEHNGPPPEYRKLMAGGRDMNSRSSTSSTAVPINSMPSANTNKPPAHVFQTSSSSRV 362
K+R + + A M PP + +
Sbjct: 5 KKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAG---MSYGQMGMPPQGAVPSMGQQQF 61
Query: 363 PPPPPPHHHHSSAHVPKIKTEHPPMKVEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHS 422
P H M + L+ ++ + V+ ++ +
Sbjct: 62 LTPAQEQLHQQIDQAT------TSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQP 115
Query: 423 LLPLRKHEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPP 482
+ +P +P ++ + + + PPP PP M
Sbjct: 116 MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELS 175
Query: 483 PSHSDVITNVIKEVTYSKQMEKSSIL 508
+ D I + + V + + K S L
Sbjct: 176 NASPDYIRSTLNAVPKNSSLLKKSKL 201
>3n2s_A NADPH-dependent nitro/flavin reductase; alpga-beta-alpha sandwich,
oxidoreductase; HET: FMN; 1.95A {Bacillus subtilis}
Length = 249
Score = 28.5 bits (64), Expect = 6.3
Identities = 9/59 (15%), Positives = 23/59 (38%), Gaps = 20/59 (33%)
Query: 222 RKWFWYIDKEVTQEQLEQLTE--------------EFLAIFDKCPSKLKKRICSISSNQ 266
R + D+ +T E+++ L + + + D + K+ + ++ NQ
Sbjct: 15 RS---FTDQLLTAEEIDTLVKSAQAASTSSYVQAYSIIGVSDP---EKKRELSVLAGNQ 67
>1bkj_A NADPH-flavin oxidoreductase; luminescence, flavoprotein; HET: FMN;
1.80A {Vibrio harveyi} SCOP: d.90.1.1 PDB: 2bkj_A*
Length = 240
Score = 28.5 bits (64), Expect = 6.4
Identities = 8/59 (13%), Positives = 19/59 (32%), Gaps = 20/59 (33%)
Query: 222 RKWFWYIDKEVTQEQLEQLTE--------------EFLAIFDKCPSKLKKRICSISSNQ 266
RK + +T EQ + + + + + D + + + + NQ
Sbjct: 15 RK---FTAVPITDEQRQTIIQAGLAASSSSMLQVVSIVRVTDS---EKRNELAQFAGNQ 67
>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA
complex, transcription factor, BZIP, C/EBP; 1.80A {Homo
sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A
1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A
Length = 78
Score = 26.8 bits (59), Expect = 6.7
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 620 KKKKKHKEKDKDRDKKHKEKKKHKDDKHKDKRKDKHRE 657
K KK +K D K +E+ K +DK K ++ E
Sbjct: 3 SKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLE 40
>1mv3_A MYC box dependent interacting protein 1; tumor suppressor,
endocytosis/exocytosis complex; NMR {Homo sapiens} SCOP:
b.34.2.1
Length = 213
Score = 28.5 bits (62), Expect = 7.0
Identities = 23/147 (15%), Positives = 38/147 (25%), Gaps = 12/147 (8%)
Query: 329 SSTSSTAVPINSMPSANTNKPPAHVFQTSSS--SRVPPPPPPHHHHSSAHVPKIKTEHPP 386
S ++ + +N P P S S + PP PPP H S V + +
Sbjct: 3 SPAATPEIRVNHEPEPAGGATPGATLPKSPSQLRKGPPVPPPPKHTPSKEVKQEQILSLF 62
Query: 387 MKVEPVMKEALLKQPPLIKQEPNVKQEPYIKSEPHSLLPLRKHEPINPRMMMNKPQSKPV 446
+ +P E ++P + + S P
Sbjct: 63 EDTFVP------EISVTTPSQPAEASEVAGGTQPAAGAQEPGETAASE----AASSSLPA 112
Query: 447 IPHEVRKNGHDLPVPKPHPPPPPPPPP 473
+ E + V PP
Sbjct: 113 VVVETFPATVNGTVEGGSGAGRLDLPP 139
>3u28_C H/ACA ribonucleoprotein complex subunit 1; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_C
Length = 114
Score = 27.6 bits (61), Expect = 7.2
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 369 HHHHSSAHVPKIKTEHPPMKVEPV 392
HHHHSS VP+ PP V +
Sbjct: 7 HHHHSSGLVPRGSHMGPPDTVLEM 30
>3vf0_A Vinculin, metavinculin; cytoskeletal F-actin binding protein, CEL
adhesion-protein binding complex; HET: EPE; 2.54A {Homo
sapiens}
Length = 283
Score = 28.5 bits (62), Expect = 7.2
Identities = 19/106 (17%), Positives = 34/106 (32%), Gaps = 3/106 (2%)
Query: 459 PVPKPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKEVTYSKQMEKSSILNHKESSISHP 518
P+P+ PPP PPPP + P +VI + + ++Q+ + + I
Sbjct: 13 PLPEGEVPPPRPPPPEEKDEEFPEQKAGEVINQPM--MMAARQLHDEARKWSSKPGIPAA 70
Query: 519 PHLSMSIPQTKAPSIFSPEKNTSPVINKTP-FKMKTPTPPSFSPIK 563
+ + A + P + P PI
Sbjct: 71 EVGIGVVAEADAADAAGFPVPPDMEDDYEPELLLMPSNQPVNQPIL 116
>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis
lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A*
1u0y_A* 1yt2_A*
Length = 269
Score = 28.3 bits (64), Expect = 7.3
Identities = 6/42 (14%), Positives = 19/42 (45%)
Query: 604 ISETKQEPHESHSQHPKKKKKHKEKDKDRDKKHKEKKKHKDD 645
++E + + + +E+++++ K K+ +K D
Sbjct: 223 EPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWD 264
>2vbi_A Pyruvate decarboxylase; thiamine pyrophosphate, lyase, pyruv
flavoprotein, THDP-dependent enzyme; HET: TPP; 2.75A
{Acetobacter pasteurianus}
Length = 566
Score = 28.7 bits (65), Expect = 7.4
Identities = 10/63 (15%), Positives = 17/63 (26%), Gaps = 12/63 (19%)
Query: 442 QSKPV---IPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKEVTY 498
+ KP I N P +P P P ++ S + + +
Sbjct: 158 ERKPAYLDIA----CNIASEPCVRPGPVSSLLSEP-----EIDHTSLKAAVDATVALLEK 208
Query: 499 SKQ 501
S
Sbjct: 209 SAS 211
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 28.7 bits (63), Expect = 8.3
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 457 DLPVPKPHPPPPPPPPPYMSAAKLPPPS 484
DL P+P PPPP P + +
Sbjct: 25 DLQRPQPPPPPPSAASPGATPGSAAASA 52
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 28.9 bits (65), Expect = 8.3
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 570 SEGLKAKLEPELVP-VITKLGDDILTKPKILASEIISETKQEPHESHSQHPKKKKKHKEK 628
GL +++ LV + D L + + L + E KQ E +++ E
Sbjct: 968 EAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQL------AEQYDEL 1021
Query: 629 DKDRDKKHKEKKK 641
+ +KK + K++
Sbjct: 1022 KHEFEKKLEAKRR 1034
>2wvg_A PDC, pyruvate decarboxylase; thiamine diphosphate, lyase,
flavoprotein, metal-binding, alcohol fermentation; HET:
TPU; 1.75A {Zymomonas mobilis} PDB: 2wva_A* 2wvh_A
3oe1_A* 1zpd_A*
Length = 568
Score = 28.7 bits (65), Expect = 9.1
Identities = 10/63 (15%), Positives = 17/63 (26%), Gaps = 12/63 (19%)
Query: 442 QSKPV---IPHEVRKNGHDLPVPKPHPPPPPPPPPYMSAAKLPPPSHSDVITNVIKEVTY 498
+ KPV I N +P P P S + + +K +
Sbjct: 158 EKKPVYLEIA----CNIASMPCAAPGPASALFNDE-----ASDEASLNAAVEETLKFIAN 208
Query: 499 SKQ 501
+
Sbjct: 209 RDK 211
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 28.4 bits (63), Expect = 9.8
Identities = 13/60 (21%), Positives = 16/60 (26%), Gaps = 4/60 (6%)
Query: 429 HEPINPRMMMNKPQSKPVIPHEVRKNGHDLPVPKPHP----PPPPPPPPYMSAAKLPPPS 484
+ + MM Q G+ P P P PP Y PPP
Sbjct: 366 ADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPPPQ 425
>1f5v_A Oxygen-insensitive NADPH nitroreductase; flavoprotein,
oxidoreduction, nitrocompound, oxidoreductase; HET: FMN;
1.70A {Escherichia coli} SCOP: d.90.1.1
Length = 240
Score = 28.0 bits (63), Expect = 10.0
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 20/59 (33%)
Query: 222 RKWFWYIDKEVTQEQLEQLTE--------------EFLAIFDKCPSKLKKRICSISSNQ 266
R + D+ +++ Q E + + I DK L++ + +++ Q
Sbjct: 15 RH---FTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDK---ALREELVTLTGGQ 67
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
0.313 0.128 0.382
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,812,732
Number of extensions: 640234
Number of successful extensions: 3672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3240
Number of HSP's successfully gapped: 167
Length of query: 730
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 629
Effective length of database: 3,881,772
Effective search space: 2441634588
Effective search space used: 2441634588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (28.0 bits)