RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14375
(206 letters)
>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide;
transcription, nucleotidyltransferase; 2.70A {Homo
sapiens} SCOP: a.60.8.2
Length = 152
Score = 155 bits (392), Expect = 9e-49
Identities = 104/130 (80%), Positives = 113/130 (86%)
Query: 77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFR 136
VEEDA L FPKEFE AETLL SEVHMLL+HRK QNE+AE+EQE SEVF KTL YT RF
Sbjct: 23 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 82
Query: 137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
+FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct: 83 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 142
Query: 197 DIQTKRSLQY 206
DIQTKRS QY
Sbjct: 143 DIQTKRSFQY 152
>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 135
Score = 140 bits (354), Expect = 4e-43
Identities = 47/132 (35%), Positives = 71/132 (53%), Gaps = 2/132 (1%)
Query: 75 QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNEN-AEEEQEFSEVFQKTLTYTE 133
+ EEDA L+ EFEN + L +SE +L++ Q E ++V +KT+ Y
Sbjct: 4 AIFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFN 63
Query: 134 RFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQ 193
F +FK E + +L + HKFE A + LC E EEA+ LIPSL + +++ L+
Sbjct: 64 VFARFKTAEATYACERIL-GNRFHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQG 122
Query: 194 ILDDIQTKRSLQ 205
ILD++ T R Q
Sbjct: 123 ILDELSTLRKFQ 134
>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide;
transferase; 2.30A {Saccharomyces cerevisiae} SCOP:
a.60.8.2
Length = 187
Score = 105 bits (262), Expect = 1e-28
Identities = 35/129 (27%), Positives = 62/129 (48%), Gaps = 12/129 (9%)
Query: 88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEF------------SEVFQKTLTYTERF 135
E+ + L + +E E+E E ++ + T+ Y F
Sbjct: 58 TAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNF 117
Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
+F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL + ++EL +IL
Sbjct: 118 SRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERIL 177
Query: 196 DDIQTKRSL 204
++ +L
Sbjct: 178 KELSNLETL 186
>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II,
metal-binding, transcription bubble; HET: BRU; 3.20A
{Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D
1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D*
2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D*
3hov_D* 3how_D* 3hox_D* ...
Length = 221
Score = 105 bits (262), Expect = 2e-28
Identities = 35/127 (27%), Positives = 62/127 (48%), Gaps = 12/127 (9%)
Query: 90 FENAETLLISEVHMLLQHRKTQNENAEEEQEF------------SEVFQKTLTYTERFRK 137
E+ + L + +E E+E E ++ + T+ Y F +
Sbjct: 94 VEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSR 153
Query: 138 FKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL + ++EL +IL +
Sbjct: 154 FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKE 213
Query: 198 IQTKRSL 204
+ +L
Sbjct: 214 LSNLETL 220
>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A
{Schizosaccharomyces pombe}
Length = 136
Score = 62.8 bits (152), Expect = 5e-13
Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 2/113 (1%)
Query: 90 FENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTY--TERFRKFKNRETITSV 147
E L E + ++ A + + + L Y ++ + +E
Sbjct: 21 AEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDC 80
Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQT 200
+ + +L K E+ I N P + E A I +E RF+EE++ ++++ I T
Sbjct: 81 IAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKLVEKINT 133
>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase,
transcription; 1.75A {Methanococcus jannaschii} SCOP:
a.60.8.2
Length = 107
Score = 49.4 bits (118), Expect = 2e-08
Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 8/110 (7%)
Query: 88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
K+ + +SE ++ N + E S L Y ++F K ++E +
Sbjct: 4 KKILGERYVTVSEAAEIM-------YNRAQIGELSYEQGCALDYLQKFAKL-DKEEAKKL 55
Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
L + + IA++ PE ++ +A+ E EE+ +I+
Sbjct: 56 VEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRK 105
>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 = 47.5 bits (112), Expect = 1e-06
Identities = 49/299 (16%), Positives = 85/299 (28%), Gaps = 108/299 (36%)
Query: 1 MVCLGLGQNKEKTVSFLLSTSRISPGD-----C-----VVSLFPRKI-----------QP 39
+ + ++ S LL P D +S+ I
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350
Query: 40 KSNQIKSALSKSVPPRTPYSDR-----VSI---GYIIMTHVL--------DQVVEEDAGD 83
+++ + + S+ P R +S+ I T +L V
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK 410
Query: 84 L-------QFPKEFENAETLLISEVHMLLQ---------HRK------------------ 109
L + PKE T+ I +++ L+ HR
Sbjct: 411 LHKYSLVEKQPKES----TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 110 ---------------TQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETIT------SVR 148
E+ E F VF L + RF + K R T S+
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDF--RFLEQKIRHDSTAWNASGSIL 521
Query: 149 NLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELR-QILDDIQTKRSLQY 206
N L Q K +K I + P+ A++ L + EE + + D ++ +L
Sbjct: 522 NTLQQLKFYK---PYICDNDPKYERLVNAILDFLP-KIEENLICSKYTDLLR--IALMA 574
Score = 39.1 bits (90), Expect = 7e-04
Identities = 45/228 (19%), Positives = 69/228 (30%), Gaps = 55/228 (24%)
Query: 1 MVCLGLGQNKEKTVSFL-LSTSRISPGDCVVSLFPRKI---------QPKS--NQIKSAL 48
+ LG G KT + L V KI P++ ++ L
Sbjct: 158 V--LGSG----KTW--VALDVCLSYK---VQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206
Query: 49 SKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLI-SEVHMLLQH 107
+ P T SD S + H + + L K +EN LL+ V
Sbjct: 207 YQIDPNWTSRSDH-SSNIKLRIHSIQAELR----RLLKSKPYENC--LLVLLNV------ 253
Query: 108 RKTQNENAEEEQEFSEVFQ-KTLTYTERFRK---FKNRETITSVRNLLTQKKLHKFE--- 160
+NA+ F+ K L T RF++ F + T T + L E
Sbjct: 254 -----QNAKAWNAFN--LSCKILL-TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 161 -LAAIANLCPET-PEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY 206
L + P+ P E P E +R L + +
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNP-RRLSIIAESIRDGLATWDNWKHVNC 352
Score = 37.5 bits (86), Expect = 0.002
Identities = 26/222 (11%), Positives = 58/222 (26%), Gaps = 43/222 (19%)
Query: 9 NKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSDRVSIGYII 68
+ L T + V ++ + S + R P YI
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE--QRQPSMMTRM--YIE 114
Query: 69 MTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHR--------------KT---- 110
L + F K + + LL+ R KT
Sbjct: 115 QRDRLYNDNQV------FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168
Query: 111 ---QNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANL 167
+ + + +F ++F L + ++ LL Q + + ++
Sbjct: 169 DVCLSYKVQCKMDF-KIFWLNLK-----NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 168 CPETPEEAKALIPSLECRFEEEELRQ---ILDDIQTKRSLQY 206
+A + L + + +L ++Q ++
Sbjct: 223 IKLRIHSIQAELRRL---LKSKPYENCLLVLLNVQNAKAWNA 261
Score = 34.1 bits (77), Expect = 0.026
Identities = 10/72 (13%), Positives = 23/72 (31%), Gaps = 7/72 (9%)
Query: 142 ETITSVRNLLTQKKLHKFELAAIANL-CPETPEEAKALIPSLECRF------EEEELRQI 194
+ T + L FE A + N C + + K+++ E ++
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 195 LDDIQTKRSLQY 206
+ +K+
Sbjct: 68 FWTLLSKQEEMV 79
>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F
2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F
Length = 113
Score = 44.5 bits (105), Expect = 1e-06
Identities = 22/110 (20%), Positives = 45/110 (40%), Gaps = 9/110 (8%)
Query: 88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
+ S LL + + S + Q+T Y K + E+ V
Sbjct: 4 VYIVEEHYIPYSVAKKLL-------SDVIKSGSSSNLLQRTYDYLNSVEKC-DAESAQKV 55
Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECR-FEEEELRQILD 196
L+ + A +A++CP TP+E ++++ R + E++++I+D
Sbjct: 56 VEELSSIISREDVRAVLASICPITPDEVRSILIMDSNRTYTSEDIQKIID 105
>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein
complex, nucleotidyltransferase, nuclear protein,
hypothetical protein; 3.2A {Saccharomyces cerevisiae}
Length = 161
Score = 41.8 bits (97), Expect = 3e-05
Identities = 16/93 (17%), Positives = 34/93 (36%)
Query: 108 RKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANL 167
+N +E++ + + E+ + L KL K E I N
Sbjct: 67 SINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQ 126
Query: 168 CPETPEEAKALIPSLECRFEEEELRQILDDIQT 200
P +++ + RF+E+ + ++L+ I
Sbjct: 127 LPANMVHLYSIVEECDARFDEKTIEEMLEIISA 159
>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 = 39.3 bits (91), Expect = 6e-04
Identities = 33/206 (16%), Positives = 58/206 (28%), Gaps = 70/206 (33%)
Query: 13 TVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRT--------PYSDRVSI 64
L+ T+ F ++Q++ +K +P T P +
Sbjct: 17 EHVLLVPTA----------SFFI-----ASQLQEQFNKILPEPTEGFAADDEPTT---PA 58
Query: 65 GYI--IMTHVLDQVVEEDAGD----LQFP-KEFENAETLLISEVHMLLQHRKTQNENAEE 117
+ + +V V G L EFEN L +++H L +N+
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC-YLEGNDIHALAAKLLQENDTTLV 117
Query: 118 EQEFSEVFQKTLTYTERFRKFKNRETITSVRN-LLTQKKLHKFELAAIANLCPETPEEAK 176
+ E+ + Y R R + L +L AI
Sbjct: 118 KT--KELIK---NYITA-RIMAKRPFDKKSNSALFRAVGEGNAQLVAI------------ 159
Query: 177 ALIPSLECRF------EE--EELRQI 194
F ++ EELR +
Sbjct: 160 ---------FGGQGNTDDYFEELRDL 176
Score = 38.9 bits (90), Expect = 7e-04
Identities = 30/155 (19%), Positives = 54/155 (34%), Gaps = 52/155 (33%)
Query: 1 M-VCLGLGQNK-----EKTVSFLLSTSRISPGDCVVSLF--PRKI----QPKS-NQIKSA 47
M L Q + KT S L + ++ +SL + + P+S +
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVE-----ISLVNGAKNLVVSGPPQSLYGLNLT 392
Query: 48 LSK-SVPP-----RTPYSDR---VSIGYIIMT---H------VLDQVVEE--------DA 81
L K P R P+S+R S ++ + H D + ++ +A
Sbjct: 393 LRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA 452
Query: 82 GDLQFP-KEFENAETL-----LISE--VHMLLQHR 108
D+Q P + + L ISE V +++
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLP 487
Score = 36.6 bits (84), Expect = 0.004
Identities = 24/111 (21%), Positives = 44/111 (39%), Gaps = 27/111 (24%)
Query: 87 PKE----FENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKN-R 141
P F + I E + + + + E+ F E+ + + +YT F++ +
Sbjct: 1669 PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT-----FRSEK 1723
Query: 142 ETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIP--------SL-E 183
+++ + TQ L E AA +L ++K LIP SL E
Sbjct: 1724 GLLSATQF--TQPALTLMEKAAFEDL------KSKGLIPADATFAGHSLGE 1766
>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 = 30.3 bits (67), Expect = 0.27
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 7/36 (19%)
Query: 153 QKK-LHKFELAAIANLCPETPEEAKALIPSLECRFE 187
+K+ L K + A+L + A AL +++ E
Sbjct: 18 EKQALKKLQ----ASLKLYADDSAPAL--AIKATME 47
>2qgu_A Probable signal peptide protein; NESG, RSR89, Q8XV73, structural
genomics, PSI-2, protein STR initiative; HET: MSE PEF;
1.50A {Ralstonia solanacearum}
Length = 211
Score = 28.7 bits (64), Expect = 1.2
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 106 QHRKTQNENAEEEQEFSEVFQKTL--TYTERFRKFKNRE 142
+ E++Q+ + F+ L TY +N+
Sbjct: 84 RFWSQATP--EQQQQIQDGFKSLLIRTYAGALANVRNQT 120
>3fb2_A Spectrin alpha chain, brain spectrin; non-erythroid alpha chain
alpha-II spectrin, fordrin alpha chain, sptan1,
SPTA2_human, NESG, HR5563A; 2.30A {Homo sapiens}
Length = 218
Score = 27.6 bits (61), Expect = 2.5
Identities = 18/103 (17%), Positives = 42/103 (40%), Gaps = 6/103 (5%)
Query: 104 LLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRE----TITSVRNLLTQKKLHKF 159
+ H + ++ + Q F F+ +++ R + + +T LL + + H+
Sbjct: 1 MGHHHHHHSHDSHDLQRFLSDFRDLMSWINGIRGLVSSDELAKDVTGAEALLERHQEHRT 60
Query: 160 ELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR 202
E+ A A + + L+ + E++Q LD + +R
Sbjct: 61 EIDARAGTFQAFEQFGQQLL--AHGHYASPEIKQKLDILDQER 101
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 3.4
Identities = 4/18 (22%), Positives = 8/18 (44%)
Query: 106 QHRKTQNENAEEEQEFSE 123
Q K + N ++ F +
Sbjct: 130 QVEKNKINNRIADKAFYQ 147
>2shp_A SHP-2, SYP, SHPTP-2; tyrosine phosphatase, insulin signaling, SH2
protein; HET: CAT; 2.00A {Homo sapiens} SCOP: c.45.1.2
d.93.1.1 d.93.1.1
Length = 525
Score = 27.1 bits (60), Expect = 5.4
Identities = 31/158 (19%), Positives = 58/158 (36%), Gaps = 26/158 (16%)
Query: 6 LGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSD-RVSI 64
L K K SFL+ S+ PGD V+S+ + +SN SK + + +
Sbjct: 125 LLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESN---DGKSKVTHVMIRCQELKYDV 181
Query: 65 G----YIIMTHVLDQ-----VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENA 115
G + +T +++ +VE LQ + + +E+ ++ E
Sbjct: 182 GGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR-INAAEIESRVRELSKLAETT 240
Query: 116 EE-----EQEFSEVFQKTLTYTERFR-------KFKNR 141
++ +EF + Q+ + K KNR
Sbjct: 241 DKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNR 278
>1yo7_A Regulatory protein ROP; protein design, RE-engineering of topology,
four-helix bundle, replication regulator; 2.80A
{Escherichia coli}
Length = 120
Score = 25.9 bits (56), Expect = 5.7
Identities = 10/51 (19%), Positives = 20/51 (39%)
Query: 140 NRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEE 190
N + L +KL++ + A++C + A L S F++
Sbjct: 10 NMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLASFKKNG 60
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 0.131 0.362
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,877,996
Number of extensions: 156596
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 452
Number of HSP's successfully gapped: 29
Length of query: 206
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,216,824
Effective search space: 493368408
Effective search space used: 493368408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.3 bits)