RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2416
(405 letters)
>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 = 234 bits (598), Expect = 2e-75
Identities = 76/251 (30%), Positives = 124/251 (49%), Gaps = 19/251 (7%)
Query: 22 SLSNCLLPEEKLNPTPSMLDGLDPEVETDLRIIGCELIQTAGILLKLPQVAMATGQVLFQ 81
+ ++ L TPS L+GLDP E R G I G L L +ATG + F
Sbjct: 11 TKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFH 70
Query: 82 RFYYSKSFVRHPMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTT 141
RFY SF + P T C+ LA K+EE P++ +D+I + +
Sbjct: 71 RFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQF------- 123
Query: 142 QYMTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQ--KLMQLA-NYMND 198
K +V+ ER +L+ + F + V+HP++ ++ Y + L +KN+ KL+Q+A ++ND
Sbjct: 124 -GDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVND 182
Query: 199 SLRTDVFVRYDPETIASACIYLTARKLRIPLPR------NPAWYSLF--HVLESDIQDVC 250
SL T + ++++PE IA A +YL R + + W+ F V ++D+C
Sbjct: 183 SLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDIC 242
Query: 251 KRILRLYTRPK 261
+IL LY++ K
Sbjct: 243 HQILDLYSQGK 253
>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 = 228 bits (582), Expect = 6e-72
Identities = 67/342 (19%), Positives = 121/342 (35%), Gaps = 15/342 (4%)
Query: 27 LLPEEKLNPTPSMLDGLDPEVETDLRIIGCELIQTAGILLKLPQVAMATGQVLFQRFYYS 86
E+L +PS G+DP+ E R L+Q G L + Q+ + T V RFY
Sbjct: 13 YFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMI 72
Query: 87 KSFVRHPMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTL 146
+SF R P + A + LA+K+EE P+++ VI V H + P + Y+
Sbjct: 73 QSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLH---PQESLPDTRSEAYLQQ 129
Query: 147 KTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLANYMNDSLRTDVFV 206
++ E +L+ LGF + + HPH +V Q++ K+ N T +
Sbjct: 130 VQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSL 189
Query: 207 RYDPETIASACIYLTARKLRIPLPR---NPAWYSLF--HVLESDIQDVCKRILRLYTRPK 261
+Y P +A CI+L + +P W+ V + ++ L++ +
Sbjct: 190 QYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTP 249
Query: 262 ANTDELERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRT 321
+ + + DR T + S +
Sbjct: 250 NRLKRIWNWRACEAAKKTKADDRG-------TDEKTSEQGGTGGGSGGGSGGGSGGGTSG 302
Query: 322 RSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRSR 363
P + +R + + S +++ R
Sbjct: 303 GVPGQNTGGQEARPNYHCQLCFLRSLGIDYLDASLRKKNKQR 344
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat
domains, transcription-cell cycle complex; 3.00A
{Schizosaccharomyces pombe}
Length = 235
Score = 215 bits (549), Expect = 2e-68
Identities = 47/237 (19%), Positives = 95/237 (40%), Gaps = 19/237 (8%)
Query: 36 TPSMLDGLDPEVETDLRIIGCELIQTAGILLKLPQVAMATGQVLFQRFYYSKSFVR-HPM 94
+ L+ L+P + I +++QT G L+L Q +AT VL +R+ K+ + +
Sbjct: 12 LSTDLESLEPTCLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSL 71
Query: 95 ETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAE 154
E C+ L+ K+EE P IR + N + + + ++ + + E
Sbjct: 72 EALVATCIYLSCKVEECPVHIRTICNEANDLWS-------------LKVKLSRSNISEIE 118
Query: 155 RRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLA-NYMNDSLRTDVFVRYDPETI 213
++ L + V HP+ + NQK ++ A + +NDS + + + P +
Sbjct: 119 FEIISVLDAFLIVHHPYTSLEQAFH--DGIINQKQLEFAWSIVNDSYASSLCLMAHPHQL 176
Query: 214 ASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTDELERQ 270
A A + ++ +P+ + + +RI+ +Y LE
Sbjct: 177 AYAALLISCCNDENTIPKL--LDLIKSTDAFKVILCVQRIISIYYFEDIEAAALEHH 231
>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 = 212 bits (540), Expect = 8e-67
Identities = 59/255 (23%), Positives = 105/255 (41%), Gaps = 12/255 (4%)
Query: 22 SLSNCLLPEEKLNPTPSMLDGLDPEVETDLRIIGCELIQTAGILLKLPQVAMATGQVLFQ 81
+ S E+L TPS G++ + E R LIQ G L + Q+ + T V
Sbjct: 1 ASSRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMH 60
Query: 82 RFYYSKSFVRHPMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTT 141
RFY SF + + + LA+K+EE R++ VI V H +
Sbjct: 61 RFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACL---HPLEPLLDTKCD 117
Query: 142 QYMTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLANYM--NDS 199
Y+ +++ E +L+ LGF + ++HPH +V Q++ ++ L Q + +M N
Sbjct: 118 AYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRA--SKDLAQTSYFMATNSL 175
Query: 200 LRTDVFVRYDPETIASACIYLTARKLRIPLPR---NPAWYSLF--HVLESDIQDVCKRIL 254
T ++Y P IA CI+L + +P W+ V + ++ L
Sbjct: 176 HLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFL 235
Query: 255 RLYTRPKANTDELER 269
++ + ++
Sbjct: 236 QILEKTPNRLKKIRN 250
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET:
BAX; 2.20A {Homo sapiens}
Length = 285
Score = 199 bits (508), Expect = 1e-61
Identities = 68/279 (24%), Positives = 114/279 (40%), Gaps = 14/279 (5%)
Query: 29 PEEKLNPTPSMLDGLDPEVETDLRIIGCELIQTAGILLKLPQVAMATGQVLFQRFYYSKS 88
++ L L L E L+I +IQ G LKL Q +AT V F+RFY S
Sbjct: 20 KQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYS 79
Query: 89 FVRHPMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKT 148
A CV LASK+EE + ++
Sbjct: 80 LKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRF----SYAFPKEFPYRMN 135
Query: 149 QVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLA-NYMNDSLRTDVFVR 207
+++ E +L+ + C+ V HP++ ++ Y+Q + L+ LA +ND+ RTD+ +
Sbjct: 136 HILECEFYLLELMDCCLIVYHPYRPLLQYVQD--MGQEDMLLPLAWRIVNDTYRTDLCLL 193
Query: 208 YDPETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTDEL 267
Y P IA AC+++ + + W++ V I ++ + IL+LY + K N DE
Sbjct: 194 YPPFMIALACLHVACVVQQKDARQ---WFAELSVDMEKILEIIRVILKLYEQWK-NFDER 249
Query: 268 ERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPS 306
+ ++ K + + N+S S S
Sbjct: 250 KEMATILSKMPKPKPPPNSEGEQGPNGSQNSSY---SQS 285
>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 = 198 bits (505), Expect = 9e-61
Identities = 52/321 (16%), Positives = 103/321 (32%), Gaps = 49/321 (15%)
Query: 30 EEKLNPTPSMLDGLDPEVETDLRIIGCELIQTAGILLK--LPQVAMATGQVLFQRFYYSK 87
P+ L+P E L + + + K +P+ + T + F+RFY +
Sbjct: 35 VANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNN 94
Query: 88 SFVRHPMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLK 147
S + + + C LA K++E + +
Sbjct: 95 SVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEK--------------AL 140
Query: 148 TQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLG-----CEKNQKLMQLA-NYMNDSLR 201
Q+++ E ++++L F + V +P++ +L L E + L + A +++N
Sbjct: 141 EQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIAL 200
Query: 202 TDVFVRYDPETIASACIYLTARKLRIPLPRNPA---WYSLFHVLESDIQDVCKRILRLYT 258
TD ++ Y P IA I +A + I + + S + D+ K + L
Sbjct: 201 TDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVK 260
Query: 259 RPKANTDELERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSR 318
+ + E + +K+ S N K R
Sbjct: 261 KYEPPRSEEVAVL-----------KQKL-------------DRCHSAELALNVITKKRKG 296
Query: 319 SRTRSPVTSKSRSRSRSPQPP 339
V+ KS+
Sbjct: 297 YEDDDYVSKKSKHEEEEWTDD 317
>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 = 59.8 bits (145), Expect = 3e-10
Identities = 44/279 (15%), Positives = 85/279 (30%), Gaps = 41/279 (14%)
Query: 30 EEKLNPTPSMLDGLDPEVETDLRIIGCE-LIQTAGILLKLPQV---AMATGQVLFQRFYY 85
EE+ P S + E++ +R + +++ +V AM R+
Sbjct: 49 EERYVPRASYFQCVQREIKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMN----YLDRYLS 104
Query: 86 SKSFVRHPMETTAMGCVCLASKIEE--APRRIRDVINVFHHIRQVMNQKSITPMLLTTQY 143
+ ++ C+ LASK+ E I T +
Sbjct: 105 CVPTRKAQLQLLGAVCMLLASKLRETTPLT-----IEKLCIY---------------TDH 144
Query: 144 MTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQ--LANYMNDSLR 201
Q+ E VL +L + + H + L L ++++ + A
Sbjct: 145 AVSPRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCA 204
Query: 202 TDV-FVRYDPETIASACIYLTARKLRIPLPRNPAWYS-LFHVL---ESDIQDVCKRILRL 256
TD F Y P IA+ I + L L + ++ ++I
Sbjct: 205 TDYTFAMYPPSMIATGSIGAAVQGLGACSMSGDELTELLAGITGTEVDCLRACQEQIEAA 264
Query: 257 YTRPKANTDELERQIEVIKKEYQLSKDRKVLVSGDNTPT 295
++ + + K + S + S +TPT
Sbjct: 265 LR--ESLREAAQTSSSPAPKAPRGSSSQG--PSQTSTPT 299
>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 = 58.3 bits (141), Expect = 6e-10
Identities = 24/179 (13%), Positives = 51/179 (28%), Gaps = 28/179 (15%)
Query: 82 RFYYSKSFVRHPMETTAMGCVCLASKIEEA-PRRIRDVINVFHHIRQVMNQKSITPMLLT 140
+ S R ++TA + +A K+ P + ++
Sbjct: 79 ELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQ----LAYL--------------- 119
Query: 141 TQYMTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGC--EKNQKLMQLANYMND 198
T +++ E + L L + +I L ++ E + L
Sbjct: 120 CGGATTADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPREDYLNIYNLCRPKIF 179
Query: 199 -SLRTDVFVRYDPETIASACIYLTARKLRIPLPRNPAWYSLFHVL---ESDIQDVCKRI 253
+L P I AC++LT + + L + ++ C +
Sbjct: 180 CALCDGRSAMKRPVLITLACMHLTMNQKYD--YYENRIDGVCKSLYITKEELHQCCDLV 236
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*
Length = 269
Score = 57.7 bits (140), Expect = 1e-09
Identities = 35/191 (18%), Positives = 63/191 (32%), Gaps = 38/191 (19%)
Query: 100 GCVCL--ASKIEEA-PRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMT----LKTQVIK 152
G + ASK EE P I D ++T K Q+ +
Sbjct: 84 GVTAMFIASKYEEMYPPEIGDFA-----------------------FVTDNTYTKHQIRQ 120
Query: 153 AERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLANYMND-SLRTDVFVRYDPE 211
E ++L+ L F + P + ++ E + + LA Y+ + ++ V + P
Sbjct: 121 MEMKILRALNFGLGRPLPLHFLRRASKI--GEVDVEQHTLAKYLMELTMLDYDMVHFPPS 178
Query: 212 TIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTDELERQI 271
IA+ L A K+ P E + V + + + +
Sbjct: 179 QIAAGAFSL-ALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKH---- 233
Query: 272 EVIKKEYQLSK 282
+K +Y SK
Sbjct: 234 MTVKNKYATSK 244
>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 = 55.4 bits (134), Expect = 7e-09
Identities = 36/192 (18%), Positives = 68/192 (35%), Gaps = 40/192 (20%)
Query: 100 GCVCL--ASKIEEA-PRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMT----LKTQVIK 152
G + ASK EE P + + + Y+T K QV++
Sbjct: 85 GTAAMLLASKFEEIYPPEVAEFV-----------------------YITDDTYTKKQVLR 121
Query: 153 AERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQLANYMND--SLRTDVFVRYDP 210
E VLK L F + ++ + Y N K+ LA ++ + + D +++Y P
Sbjct: 122 MEHLVLKVLTFDLAAPTVNQFLTQYFLHQQ-PANCKVESLAMFLGELSLIDADPYLKYLP 180
Query: 211 ETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTDELERQ 270
IA A +L A + ++ + + Y + +
Sbjct: 181 SVIAGAAFHL-ALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQH------A 233
Query: 271 IEVIKKEYQLSK 282
+ I+++Y+ SK
Sbjct: 234 QQSIREKYKNSK 245
>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 = 54.0 bits (130), Expect = 2e-08
Identities = 25/177 (14%), Positives = 52/177 (29%), Gaps = 35/177 (19%)
Query: 100 GCVCL--ASKIEE--APRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAER 155
G C+ ASK++E T ++++ E
Sbjct: 103 GATCMFVASKMKETIPLT-----AEKLCIY---------------TDNSIRPEELLQMEL 142
Query: 156 RVLKELGFCVHVKHPHKIIVTYLQVLG--CEKNQKLMQLANYMND-SLRTDVFVRYDPET 212
++ +L + + PH I +L + E Q + + A F+ P
Sbjct: 143 LLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSM 202
Query: 213 IASACIYLTARKL-RIPLPRNPAWYSLFHVL-------ESDIQDVCKRILRLYTRPK 261
+A+ + + L ++Y L L ++ ++I L
Sbjct: 203 VAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESSL 259
>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 = 53.2 bits (128), Expect = 3e-08
Identities = 23/170 (13%), Positives = 47/170 (27%), Gaps = 34/170 (20%)
Query: 100 GCVCL--ASKIEE--APRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAER 155
G CL ASK+ + + + ++I E+
Sbjct: 97 GSACLLVASKLRSLTPIS-----TSSLCYA---------------AADSFSRQELIDQEK 136
Query: 156 RVLKELGFCVHVKHPHKIIVTYLQVL--GCEKNQKLMQLANYMND-SLRTDVFVRYDPET 212
+L++L + + L L G + N + +L +
Sbjct: 137 ELLEKLAWRTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASI 196
Query: 213 IASACIYLTARKLRIPLPRNPAWYS---LFHV---LESDIQDVCKRILRL 256
I++A L + + L + S +Q ++IL
Sbjct: 197 ISAAGCAL-LVPANVIPQDTHSGGVVPQLASILGCDVSVLQAAVEQILTS 245
>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 = 51.6 bits (124), Expect = 1e-07
Identities = 20/176 (11%), Positives = 47/176 (26%), Gaps = 43/176 (24%)
Query: 100 GCVCL--ASKIEEA-PRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMT----LKTQVIK 152
G C+ SKI P + + Y++ ++I
Sbjct: 98 GAACVLIGSKIRTVKPMTVSKLT-----------------------YLSCDCFTNLELIN 134
Query: 153 AERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLM--QLANYMND-SLRTDVFVRYD 209
E+ +L+ L + ++ L ++ + A+ +L
Sbjct: 135 QEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLS 194
Query: 210 PETIASACIYLTARKLRIPLPRNPAWYSLFHVL-------ESDIQDVCKRILRLYT 258
P I + + T W L + ++ V ++ ++
Sbjct: 195 PGLICAGGLLTTIETDN---TNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFS 247
>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 = 51.6 bits (123), Expect = 3e-07
Identities = 68/481 (14%), Positives = 131/481 (27%), Gaps = 216/481 (44%)
Query: 3 SHKPESLKAPPKPYGKIALSLSNCLLP-----------EE--KLNPTPSMLDGL----DP 45
S +P +L +G + L L+P E+ K+ P P+ +G +P
Sbjct: 5 STRPLTLS-----HGSLEHVL---LVPTASFFIASQLQEQFNKILPEPT--EGFAADDEP 54
Query: 46 EVETDL--RIIG--CELIQTAGILLKLPQVAMATGQVL---FQRFYYSKSFVR----HPM 94
+L + +G L++ P QVL F ++ H
Sbjct: 55 TTPAELVGKFLGYVSSLVE--------PSKVGQFDQVLNLCLTEF--ENCYLEGNDIH-- 102
Query: 95 ETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQ---KSITPMLLTT---------- 141
A L + + + +++I + R + + K L
Sbjct: 103 -ALA---AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA 158
Query: 142 ----Q----------------YMTLKTQVIKAERRVLKEL-------------GFCVH-- 166
Q Y L +IK L EL G +
Sbjct: 159 IFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW 218
Query: 167 VKHPHKI-IVTYLQ-------VLGCEKNQKLMQLANYMNDSLRTDVFVR---YDPET--- 212
+++P YL ++G ++QLA+Y+ V + + P
Sbjct: 219 LENPSNTPDKDYLLSIPISCPLIG------VIQLAHYV-------VTAKLLGFTPGELRS 265
Query: 213 ------------IASACI---------YLTARK-LRIPLPRNPAWYSLFHV--------- 241
+ + I +++ RK + + LF +
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITV----------LFFIGVRCYEAYP 315
Query: 242 ---LESDI-QD-------------VCKRILRLYTRPKANTDELERQIEVIKKEYQLSKDR 284
L I +D + + ++++ + L +
Sbjct: 316 NTSLPPSILEDSLENNEGVPSPMLSISNLTQ---------EQVQDYVNKTNSH--LPAGK 364
Query: 285 KVLVSGDNTPTSN--ASP------------NIKSPSRHNNHKRKSRSRSRTRS----PVT 326
+V +S N + + P K+PS + + R S PV
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA 424
Query: 327 S 327
S
Sbjct: 425 S 425
Score = 28.9 bits (64), Expect = 4.6
Identities = 34/210 (16%), Positives = 67/210 (31%), Gaps = 73/210 (34%)
Query: 14 KPYGKIALSLSNCLL--PEEKLNPT----PSML------------DGLDPEVETD----L 51
K + +I ++ + L+ T P++ GL P T L
Sbjct: 1705 KIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL 1764
Query: 52 RIIGCE---LIQTAGILLKLPQVAMATGQVLFQRFYYSKSFV-RHPMETTAMGCV-CLAS 106
G E L A + + + + +V+F R + V R + + G +
Sbjct: 1765 ---G-EYAALASLADV-MSIESLV----EVVFYRGMTMQVAVPRDELGRSNYGMIAINPG 1815
Query: 107 KI-----EEAPRRIRDVIN------VFHHIRQVMN-----QKSITPMLLTTQYMTLKTQV 150
++ +EA + + + + V +++N Q QY V
Sbjct: 1816 RVAASFSQEALQYVVERVGKRTGWLV-----EIVNYNVENQ----------QY------V 1854
Query: 151 IKAERRVLKELGFCVHVKHPHKIIVTYLQV 180
+ R L + ++ KI + LQ
Sbjct: 1855 AAGDLRALDTVTNVLNFIKLQKIDIIELQK 1884
>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 = 49.4 bits (118), Expect = 8e-07
Identities = 23/192 (11%), Positives = 57/192 (29%), Gaps = 40/192 (20%)
Query: 100 GCVCL--ASKIEEA-PRRIRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAERR 156
G L A+K+EE P ++ F ++ T +++ E
Sbjct: 97 GISSLFIAAKLEEIYPPKLHQ----FAYV---------------TDGACSGDEILTMELM 137
Query: 157 VLKELGFCVHVKHPHKIIVTYLQVLGCEKNQKLMQ---------LANYMND-SLRTDVFV 206
++K L + + + Y+QV +++ + D + +
Sbjct: 138 IMKALKWRLSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCL 197
Query: 207 RYDPETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTDE 266
+ +A++ +Y S + DI++ K ++ +
Sbjct: 198 EFPYGILAASALYHF------SSSELMQKVSGYQ--WCDIENCVKWMVPFAMVIRETGSS 249
Query: 267 LERQIEVIKKEY 278
+ + E
Sbjct: 250 KLKHFRGVADED 261
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
DNA-binding, DNA- directed RNA polymerase, isopeptide
bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Length = 345
Score = 46.5 bits (109), Expect = 9e-06
Identities = 29/176 (16%), Positives = 55/176 (31%), Gaps = 12/176 (6%)
Query: 55 GCELIQTAGILLKLPQVAMATGQVLFQRFYYSKSFVRHPMETTAMGCVCLASKIEEAPRR 114
I +LP++ + ++ + K+ ME+ + + + E R
Sbjct: 129 AFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVART 188
Query: 115 IRDVINVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAERRVLKELGFCVHVKHPHKII 174
+++ ++ H + K T + K+E LK + I
Sbjct: 189 FKEIQSLIH-----VKTKEFG----KTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYI 239
Query: 175 VTYLQVLGCEKNQKLMQLANYM-NDSLRTDVFVRYDPETIASACIYLTARKLRIPL 229
+ LG ++ A Y P TIA IYL +IP+
Sbjct: 240 PRFCSHLGL--PMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPI 293
>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 = 45.6 bits (107), Expect = 3e-05
Identities = 56/315 (17%), Positives = 94/315 (29%), Gaps = 101/315 (32%)
Query: 14 KPYGKIA-LSLSNCLLPEEKLNPTPSMLDGLDP-----------------EVETDLRI-- 53
K KI L+L NC PE L +L +DP ++ +LR
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
Query: 54 -------------------------IGCE-LIQT--AGILLKLPQVAMATGQVLFQRFYY 85
+ C+ L+ T + L A T +
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL--SAATTTHISLDHH-- 294
Query: 86 SKSFVRHPMETTAMGCVCLASKIEEAPR---------------RIRDVINVFHHIRQVMN 130
S + P E ++ L + ++ PR IRD + + + + V
Sbjct: 295 SMTL--TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352
Query: 131 QKSITPMLLTTQYMTLKTQVIKAERRVLKELG-FCVHVKHPHKIIVTYLQVLGCE-KNQK 188
K L T +L R++ L F P + L ++ +
Sbjct: 353 DK-----LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL----LSLIWFDVIKSD 403
Query: 189 LMQLANYM-NDSLRTDVFVRYDPETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQ 247
+M + N + SL V + TI+ I +L++ L A H
Sbjct: 404 VMVVVNKLHKYSL---VEKQPKESTIS---IPSIYLELKVKLENEYA----LH------- 446
Query: 248 DVCKRILRLYTRPKA 262
+ I+ Y PK
Sbjct: 447 ---RSIVDHYNIPKT 458
Score = 43.3 bits (101), Expect = 1e-04
Identities = 32/272 (11%), Positives = 74/272 (27%), Gaps = 52/272 (19%)
Query: 123 HHIRQVMNQ-----KSITPMLLTTQYMTLKTQ-VIKAERRVLKELGFCVHVKHPHKIIVT 176
HH+ + K I + + V + +L + + + T
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 177 YLQVLGCEKNQKLMQLANYMNDSLRTDVFVRYD--PETIASACIYLTARKLRIPLPRNPA 234
+ +++ + ++ + LR + Y I + R P
Sbjct: 65 LR-LFWTLLSKQEEMVQKFVEEVLRIN----YKFLMSPIKTEQ--------RQPSMMTRM 111
Query: 235 WYSLFHVLESDIQDVCKRILRLYTRPKANTDELERQIEVIKKE-YQLSKDRKVLV----- 288
+ L +D Q K + +R + +++ +L + VL+
Sbjct: 112 YIEQRDRLYNDNQVFAKYNV---SRLQ--------PYLKLRQALLELRPAKNVLIDGVLG 160
Query: 289 SGDNTPTSNASPNIKSPSRHNNH------KRKSRSRSRTRSPVTSKSRSRSRSPQPPKHK 342
SG + + K + + K + + + H
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH- 219
Query: 343 KSKKYSSRARSRSKSPRSRSRT--PDRKYKKS 372
SS + R S ++ R + Y+
Sbjct: 220 -----SSNIKLRIHSIQAELRRLLKSKPYENC 246
>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 = 43.5 bits (102), Expect = 3e-05
Identities = 31/170 (18%), Positives = 63/170 (37%), Gaps = 22/170 (12%)
Query: 59 IQTAGILLKLPQVAMATGQVLFQRFYYSKSFVRHPMETTAMGCVCLASKIEEAPRRIRDV 118
I T + LP+ + LF++ Y KS + A C+ +A + E PR +++
Sbjct: 12 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEI 71
Query: 119 INVFHHIRQVMNQKSITPMLLTTQYMTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYL 178
V +++K I + + +LK L V + + +
Sbjct: 72 CAVSR-----ISKKEIG----------------RCFKLILKALETSVDLITTGDFMSRFC 110
Query: 179 QVLGCEKNQKLMQLANYMNDSLRTDVFVRYDPETIASACIYLTARKLRIP 228
L K + M + ++ D+ P ++A+A IY+ ++
Sbjct: 111 SNLCLPKQVQ-MAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEK 159
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 44.5 bits (104), Expect = 4e-05
Identities = 16/138 (11%), Positives = 42/138 (30%)
Query: 268 ERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTS 327
+R + ++ + S++R + + + +S + + + RS+ + R
Sbjct: 232 DRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRR 291
Query: 328 KSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRSRTPDRKYKKSHKSHKDSKDYYTPPS 387
SRSR R+ + + K+ + + + ++
Sbjct: 292 SSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRD 351
Query: 388 PDRSPYSSHSRSHSRKSS 405
+R R R
Sbjct: 352 RERRRSHRSERERRRDRD 369
Score = 41.8 bits (97), Expect = 3e-04
Identities = 13/103 (12%), Positives = 26/103 (25%)
Query: 303 KSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRS 362
K R + + K + R R R S+ R+R + + + + +P
Sbjct: 271 KEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDG 330
Query: 363 RTPDRKYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSHSRKSS 405
+ + +D R R
Sbjct: 331 PPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRD 373
Score = 41.0 bits (95), Expect = 6e-04
Identities = 17/103 (16%), Positives = 29/103 (28%)
Query: 303 KSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRS 362
+ + +S+ + R R +S+SR R+R + K + A
Sbjct: 269 RDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPD 328
Query: 363 RTPDRKYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSHSRKSS 405
P + + K RS S R R
Sbjct: 329 DGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRD 371
Score = 40.2 bits (93), Expect = 9e-04
Identities = 13/104 (12%), Positives = 26/104 (25%), Gaps = 1/104 (0%)
Query: 303 KSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRS 362
P + + R R RS + + ++ + R R R R
Sbjct: 325 APPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERG 384
Query: 363 RTPDR-KYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSHSRKSS 405
R + + + + S D S + +
Sbjct: 385 SERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPEN 428
Score = 40.2 bits (93), Expect = 0.001
Identities = 10/102 (9%), Positives = 24/102 (23%), Gaps = 1/102 (0%)
Query: 304 SPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRSR 363
R K + R + + + P + + R + R R R
Sbjct: 298 RARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRD-RERRR 356
Query: 364 TPDRKYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSHSRKSS 405
+ + ++ +D +R +
Sbjct: 357 SHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGG 398
Score = 31.0 bits (69), Expect = 0.67
Identities = 10/88 (11%), Positives = 22/88 (25%)
Query: 304 SPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRSR 363
P + + R RS + R R R + + +
Sbjct: 342 GPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDN 401
Query: 364 TPDRKYKKSHKSHKDSKDYYTPPSPDRS 391
+ S + +S+ +P+
Sbjct: 402 GLEGLGNDSRDMYMESEGGDGYLAPENG 429
Score = 30.6 bits (68), Expect = 0.95
Identities = 8/65 (12%), Positives = 13/65 (20%)
Query: 303 KSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRS 362
+ R HKR R R R + + + Y
Sbjct: 370 RDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENG 429
Query: 363 RTPDR 367
+
Sbjct: 430 YLMEA 434
>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 = 39.6 bits (92), Expect = 7e-04
Identities = 22/174 (12%), Positives = 51/174 (29%), Gaps = 24/174 (13%)
Query: 57 ELIQTAGILLKLPQVAMATGQVLFQRFYYSKSFVRHPMETTAMGCVCLASKIEEAPRRIR 116
+ LKLP+ L++ +E+ CV A ++ + PR +
Sbjct: 14 SELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLD 73
Query: 117 DVINVFHHIRQVMNQ--KSITPMLLTTQYMTLKTQVIKAERRVLKELGFCVHVKHPHKII 174
++ ++ ++ + + + I L T + ELG V+ I
Sbjct: 74 EIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFA-DELGLSEKVRRRAIEI 132
Query: 175 VTYLQVLGCEKNQKLMQLANYMNDSLRTDVFVRYDPETIASACIYLTARKLRIP 228
+ + + P + +A +Y+ +
Sbjct: 133 LDEAY---------------------KRGLTSGKSPAGLVAAALYIASLLEGEK 165
>3uwp_A Histone-lysine N-methyltransferase, H3 lysine-79; epigenetics,
tubercidin, structu genomics, structural genomics
consortium, SGC; HET: 5ID; 2.05A {Homo sapiens} PDB:
4eqz_A* 3sx0_A* 4er0_A* 4er7_A* 1nw3_A* 4er6_A* 4er5_A*
3qow_A* 3qox_A* 4er3_A* 3sr4_A*
Length = 438
Score = 33.3 bits (75), Expect = 0.12
Identities = 18/105 (17%), Positives = 28/105 (26%), Gaps = 5/105 (4%)
Query: 263 NTDELERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRTR 322
+ LE +K + SNA+ K P + S
Sbjct: 336 DRTILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGPEGKVAGPADAPMDSGAE 395
Query: 323 SPVTSKSRSRSRSPQPPKHKKSKKYSSRARSRSKSPRSRSRTPDR 367
+ + SP + KK K + R + R R R
Sbjct: 396 EEKAGAATVKKPSPSKARKKKLNK-----KGRKMAGRKRGRPKKM 435
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial;
mitochondrion, DNA binding protein, transcription
factor, transcription termination; 1.60A {Homo sapiens}
PDB: 3opg_A 3my3_A
Length = 270
Score = 32.1 bits (73), Expect = 0.23
Identities = 23/129 (17%), Positives = 40/129 (31%), Gaps = 13/129 (10%)
Query: 136 PMLLTTQYMTLKTQVIKAERRVLKELGFCVHVKHPHKIIVTYLQVLGCEKN---QKLMQL 192
P LLT +K + ELGF +I ++L K + +
Sbjct: 137 PRLLTGSLEPVKENMKV----YRLELGF--KHNEIQHMITRIPKMLTANKMKLTETFDFV 190
Query: 193 ANYMNDSLRTDV----FVRYDPETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQD 248
N M+ V + ++LT P P + SL ++ +
Sbjct: 191 HNVMSIPHHIIVKFPQVFNTRLFKVKERHLFLTYLGRAQYDPAKPNYISLDKLVSIPDEI 250
Query: 249 VCKRILRLY 257
C+ I +
Sbjct: 251 FCEEIAKAS 259
>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 = 31.2 bits (70), Expect = 0.83
Identities = 33/122 (27%), Positives = 46/122 (37%), Gaps = 6/122 (4%)
Query: 289 SGDNTPTSNA-SPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKY 347
S +PTS + SP S S + + SP S + P S Y
Sbjct: 1574 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1633
Query: 348 SSRARSRSKSPRSRSRTPDRKYKKSHKSHKDSKDYYTPPSPDRSP----YSSHSRSHSRK 403
S + S S + S S T Y + ++ + Y+P SP SP YS S S+S
Sbjct: 1634 SPTSPSYSPTSPSYSPTSPS-YSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1692
Query: 404 SS 405
S
Sbjct: 1693 SP 1694
Score = 27.8 bits (61), Expect = 9.2
Identities = 34/125 (27%), Positives = 47/125 (37%), Gaps = 9/125 (7%)
Query: 289 SGDNTPTS-NASPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHK-KSKK 346
S +PTS + SP S S + + SP S + S S SP P + S
Sbjct: 1609 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPAYSPTSPS 1667
Query: 347 YSSRARSRSKSPRSRSRTPDRKYKKSHKSHKDSKDY------YTPPSPDRSPYSSHSRSH 400
YS + S S + S S T S S Y Y+P SP SP + +
Sbjct: 1668 YSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHN 1727
Query: 401 SRKSS 405
++S
Sbjct: 1728 ENENS 1732
>3rrx_A EXO-1,3/1,4-beta-glucanase; (alpha/beta)8 barrel,(alpha/beta)6
sheet, hydrolase; 1.90A {Pseudoalteromonas SP} PDB:
3usz_A 3f93_A 3f94_A 3ut0_A
Length = 822
Score = 30.0 bits (68), Expect = 1.6
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 29/81 (35%)
Query: 241 VLESDIQDVCKRILR------LYTRPKANTDELERQIEVI-KKEYQ-------------- 279
+ ES I D +R LR ++T+ K + + + + E++
Sbjct: 342 IAESRINDAVRRFLRAKIRWGVFTKSKPSARPESQHPQWLGAAEHRTLAREAVRKSLVLL 401
Query: 280 --------LSKDRKVLVSGDN 292
+ ++LV+G
Sbjct: 402 KNNESILPIKASSRILVAGKG 422
>2y94_A 5'-AMP-activated protein kinase catalytic subunit; transferase,
nucleotide-binding, staurosporine-binding,
serine/threonine-protein kinase; HET: TPO STU AMP; 3.24A
{Rattus norvegicus}
Length = 476
Score = 29.8 bits (67), Expect = 1.7
Identities = 8/85 (9%), Positives = 17/85 (20%), Gaps = 2/85 (2%)
Query: 278 YQLSKDRKVLVSGDNTPTSNASP--NIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRS 335
Y L D + +++ SP + + +P +
Sbjct: 326 YHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNP 385
Query: 336 PQPPKHKKSKKYSSRARSRSKSPRS 360
+ K P
Sbjct: 386 QKSKHQGVRKAKWHLGIRSQSRPND 410
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 29.5 bits (66), Expect = 2.4
Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 7/95 (7%)
Query: 294 PTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKKSKKYSSRARS 353
PTS +P + + ++ N + + + T P+P K+KK K + +
Sbjct: 5 PTSPGTPGVAAATQAANGGPATPAPPALGAAPTG-------DPKPKKNKKPKNPTPPRPA 57
Query: 354 RSKSPRSRSRTPDRKYKKSHKSHKDSKDYYTPPSP 388
+ + R++ + K+ ++Y P P
Sbjct: 58 GDNATVAAGHATLREHLRDIKAENTDANFYVCPPP 92
>3pe5_A Uncharacterized protein; structural genomics, PSI-biology, protein
structure initiati northeast structural genomics
consortium, NESG; 2.38A {Clostridium leptum}
Length = 403
Score = 29.2 bits (65), Expect = 2.8
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 317 SRSRTRSPVTSKSRSRSRSPQPPKHKKSKK 346
S R + P SRS P K +K
Sbjct: 3 SNRRYQEPQNRDISSRSNGKNPFKRSTGRK 32
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 29.3 bits (65), Expect = 3.0
Identities = 43/138 (31%), Positives = 55/138 (39%), Gaps = 26/138 (18%)
Query: 289 SGDNTPTSNA----SPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQPPKHKK- 343
S +PTS + SP+ SP+ ++ S S S T SP S + S S SP P +
Sbjct: 1596 SPSYSPTSPSYSATSPSY-SPTS-PSYSPTSPSYSPT-SPSYSPT-SPSYSPTSPSYSPT 1651
Query: 344 SKKYSSRARSRSKSPRSRSRTPDRKYKKSHKSHKDSKDY-------------YTPPSPDR 390
S YS + S S + S S T S S Y Y+P SP
Sbjct: 1652 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711
Query: 391 SP----YSSHSRSHSRKS 404
SP YS S S+S S
Sbjct: 1712 SPTSPSYSPTSPSYSPTS 1729
>1esw_A Amylomaltase; (beta,alpha)8-barrel, glucanotransferase,
alpha-amylase FAMI acarbose, transferase; HET: ACR;
1.90A {Thermus aquaticus} SCOP: c.1.8.1 PDB: 1cwy_A*
1fp8_A 1fp9_A 2owc_A* 2oww_A* 2owx_A* 2x1i_A*
Length = 500
Score = 29.2 bits (66), Expect = 3.1
Identities = 6/15 (40%), Positives = 6/15 (40%)
Query: 384 TPPSPDRSPYSSHSR 398
P SPY S S
Sbjct: 50 GPTGYGDSPYQSFSA 64
>3odw_A RHO guanine nucleotide exchange factor 1; regulation of RHOA
GTPase, rhogef, DH, PH, signaling PR; 3.20A {Homo
sapiens} PDB: 3odx_A
Length = 536
Score = 28.9 bits (64), Expect = 3.2
Identities = 15/124 (12%), Positives = 27/124 (21%), Gaps = 12/124 (9%)
Query: 293 TPTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTS------------KSRSRSRSPQPPK 340
T +I +R N + + ++ V + SR R+ P
Sbjct: 23 AKTKKGLSSILDAARWNRGEPQVPDFRHLKAEVDAEKPGATDRKGGVGMPSRDRNIGAPG 82
Query: 341 HKKSKKYSSRARSRSKSPRSRSRTPDRKYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSH 400
S + P S + + P S D +
Sbjct: 83 QDTPGVSLHPLSLDSPDREPGADAPLELGDSSPQGPMSLESLAPPESTDEGAETESPEPG 142
Query: 401 SRKS 404
Sbjct: 143 DEGE 146
>3h2b_A SAM-dependent methyltransferase; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; HET: SAH;
2.00A {Corynebacterium glutamicum atcc 13032}
Length = 203
Score = 27.8 bits (62), Expect = 4.4
Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 234 AWYSLFHVLESDIQDVCKRILRLYTRP 260
AWYSL H+ ++ D +
Sbjct: 108 AWYSLIHMGPGELPDALVALRMA-VED 133
>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 = 27.2 bits (59), Expect = 5.8
Identities = 6/23 (26%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 370 KKSHKSHKDSKDYYTPPSPDRSP 392
K++ K + S Y + D +P
Sbjct: 19 KQALKKLQASLKLY---ADDSAP 38
>3dxq_A Choline/ethanolamine kinase family protein; NP_106042.1, STR
genomics, joint center for structural genomics, JCSG,
prote structure initiative; HET: MSE; 2.55A
{Mesorhizobium loti}
Length = 301
Score = 27.8 bits (61), Expect = 6.8
Identities = 13/89 (14%), Positives = 29/89 (32%), Gaps = 6/89 (6%)
Query: 206 VRYDPETIASACIYLTARKLRIPLPRNPAWYSLFHVLESDIQDVCKRILRLYTRPKANTD 265
+ P + A A RKL P + LF +++ ++ + + + L A
Sbjct: 100 FKTRPGSPARAGEAF--RKLHGSGAVFPFRFELFAMIDDYLKVLSTKNVTLP----AGYH 153
Query: 266 ELERQIEVIKKEYQLSKDRKVLVSGDNTP 294
++ R+ ++ D
Sbjct: 154 DVVREAGGVRSALAAHPLPLAACHCDPLC 182
>2oga_A Transaminase; PLP-dependent enzyme, desosamine, deoxysugars,
antibiotics, hydrolase; HET: PGU; 2.05A {Streptomyces
venezuelae} PDB: 2oge_A*
Length = 399
Score = 27.5 bits (62), Expect = 7.5
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 123 HHIRQVMNQKSITPML----LTTQYMTLKTQVIKAERRVLK 159
+ + M+ ++ TP + L Y L+ + A RVL
Sbjct: 15 LYFQGHMSSRAETPRVPFLDLKAAYEELRAETDAAIARVLD 55
>3bbn_T Ribosomal protein S20; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 202
Score = 27.4 bits (60), Expect = 7.9
Identities = 17/106 (16%), Positives = 41/106 (38%), Gaps = 14/106 (13%)
Query: 281 SKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQP-- 338
S+ + + + G + + ++S + + + S S+S ++ S + P
Sbjct: 16 SQFKVLSLKGISCSSPSSSFSNRRGASATLSSSLSFSQSVSQCVAFSTGNLWVQKPMRQL 75
Query: 339 ---------PKHKKSKK---YSSRARSRSKSPRSRSRTPDRKYKKS 372
K + K + + R +KS +S +RT +K ++
Sbjct: 76 IVCEAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVLEA 121
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 27.9 bits (61), Expect = 8.2
Identities = 21/111 (18%), Positives = 41/111 (36%), Gaps = 4/111 (3%)
Query: 34 NPTPSMLDGLDPEVE-TDLRIIGCELIQTAGILLKLPQVAMATGQVLFQRFYYSKSFVRH 92
S +D LDP + + +I + IL++ + QV +
Sbjct: 643 KGLQSAIDVLDPLTKDPVDFVRQAAMIALSMILIQQTEKLNP--QVADINKNFLSVITNK 700
Query: 93 PMETTAMGCVCLASKIEEAPRRIRDVINVFHHIRQVMNQKSITPMLLTTQY 143
E A C+A I A R I + + ++ KS+ +++ +Q+
Sbjct: 701 HQEGLAKFGACVAQGIMNAGGR-NVTIQLENADTGTLDTKSVVGLVMFSQF 750
>3a98_B Engulfment and cell motility protein 1; protein-protein complex,
DOCK2, ELMO1, SH3 domain, PH domain bundle, proline-rich
sequence, cytoskeleton; 2.10A {Homo sapiens} PDB: 2vsz_A
Length = 203
Score = 26.9 bits (59), Expect = 8.9
Identities = 12/72 (16%), Positives = 22/72 (30%)
Query: 278 YQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTSKSRSRSRSPQ 337
+LS + KVL GD + S + P + + ++ +
Sbjct: 53 CRLSPNHKVLHYGDLEESPQGEVPHDSLQDKLPVADIKAVVTGKDCPHMKEKGALKQNKE 112
Query: 338 PPKHKKSKKYSS 349
+ S Y S
Sbjct: 113 VLELAFSILYDS 124
>2cp6_A Restin; microtubule binding, cytoskeleton associated protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.34.10.1
Length = 172
Score = 27.0 bits (59), Expect = 9.7
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 1/67 (1%)
Query: 270 QIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNNHKRKSRSRSRTRSPVTSKS 329
++ I K T++AS +SPS + S + S + P +
Sbjct: 104 KVTKIGFPSTTPAKAKANAVRRVMATTSASLK-RSPSASSLSSMSSVASSVSSRPSRTGL 162
Query: 330 RSRSRSP 336
+ + P
Sbjct: 163 LTETSGP 169
>3hkw_A NS5B RNA-dependent RNA polymerase; HCV polymerase,
1,5-benzodiazepine, transferase; HET: IX6; 1.55A
{Hepatitis c virus subtype 1A} PDB: 3qgi_A* 3qgh_A*
2xi3_A* 2xi2_A* 3e51_A* 3bsa_A* 3bsc_A* 3br9_A* 3co9_A*
3cvk_A* 3cwj_A* 3d28_A* 3d5m_A* 3cde_A* 3gyn_A* 3h2l_A*
3igv_A* 2ax0_A* 2awz_A* 2ax1_A* ...
Length = 581
Score = 27.4 bits (60), Expect = 9.8
Identities = 21/99 (21%), Positives = 32/99 (32%), Gaps = 9/99 (9%)
Query: 315 SRSRSRTRSPVTSKSRSRSRSPQPP-----KHKKSKKYSSRARSRS----KSPRSRSRTP 365
S S S T + VT + + P + YS+ +RS K R +
Sbjct: 4 SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNMVYSTTSRSACQRQKKVTFDRLQVL 63
Query: 366 DRKYKKSHKSHKDSKDYYTPPSPDRSPYSSHSRSHSRKS 404
D Y+ K K + S + HS +S
Sbjct: 64 DSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSARS 102
>3u0r_A Apoptosis inhibitor 5; heat repeat, armadillo repeat, lysine
acetylation; 2.50A {Homo sapiens} PDB: 3v6a_A
Length = 507
Score = 27.6 bits (60), Expect = 9.9
Identities = 19/113 (16%), Positives = 41/113 (36%), Gaps = 4/113 (3%)
Query: 251 KRILRLYTRPKANTDELERQIEVIKKEYQLSKDRKVLVSGDNTPTSNASPNIKSPSRHNN 310
+ L+ T T+E + ++ +K ++ K L + S + + K +
Sbjct: 395 RLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEI 454
Query: 311 HKRKSRSRSRTRSPVTSKSRSRSRSPQ----PPKHKKSKKYSSRARSRSKSPR 359
++++ + + SP S R + PP K S + RS +
Sbjct: 455 GQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKYSSNLGNFNYERSLQGK 507
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
0.316 0.130 0.377
Gapped
Lambda K H
0.267 0.0487 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,846,151
Number of extensions: 337067
Number of successful extensions: 937
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 72
Length of query: 405
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 309
Effective length of database: 4,021,377
Effective search space: 1242605493
Effective search space used: 1242605493
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 (21.7 bits)
S2: 58 (26.7 bits)