RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9550
(271 letters)
>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 = 51.6 bits (123), Expect = 1e-07
Identities = 36/170 (21%), Positives = 58/170 (34%), Gaps = 10/170 (5%)
Query: 10 SSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---YGGTSSGYG 66
+ +P S S G S ++P + + P+Y T Y TS Y
Sbjct: 1512 GGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYS 1571
Query: 67 GLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGG 126
+ S + PS S ++P S S +P+ +P P S S +Y+P
Sbjct: 1572 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP------SYSPTSPSYSP-TSP 1624
Query: 127 RMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSSRKLPN 176
S + + S S S Y + S + + S S P+
Sbjct: 1625 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPS 1674
Score = 50.9 bits (121), Expect = 2e-07
Identities = 42/180 (23%), Positives = 62/180 (34%), Gaps = 7/180 (3%)
Query: 2 SYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGSTYGGT 61
++P TS + S SP S S S S ++P + + PSY T
Sbjct: 1518 EATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSY 1577
Query: 62 SSGYGGLTLPSSYSRPSQS--SPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSAN 119
S + S P+ SP S P+S SY+PT+ P P S +S +
Sbjct: 1578 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSP 1635
Query: 120 YTPEGGG---RMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSSRKLPN 176
+P S + + S S S Y + S + + S S PN
Sbjct: 1636 TSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPN 1695
Score = 48.9 bits (116), Expect = 1e-06
Identities = 44/174 (25%), Positives = 61/174 (35%), Gaps = 26/174 (14%)
Query: 1 MSYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSY---GST 57
+Y P +S S S + SP S S S S ++P + + PSY +
Sbjct: 1524 GAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1583
Query: 58 YGGTSSGYGGLTLPSSYSRPSQS------SPRSYHAPPSSYRSS-----YAPTTTPLPPV 106
Y TS Y + S + PS S SP S P+S S Y+PT+ P
Sbjct: 1584 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1643
Query: 107 RPRRSKSSTR-----------SANYTPEGGGRMSRSGSTTSLNSLRSEAPSEGY 149
P S +S S +Y+P S + S S S Y
Sbjct: 1644 SPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPNY 1696
Score = 47.8 bits (113), Expect = 2e-06
Identities = 42/126 (33%), Positives = 54/126 (42%), Gaps = 11/126 (8%)
Query: 1 MSYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGSTYGG 60
S S P S TS S S S SP S + S S S ++P + + PSY
Sbjct: 1580 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP---- 1635
Query: 61 TSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTR---- 116
TS Y + S + PS SP S P+S SY+PT+ P P S +S
Sbjct: 1636 TSPSYSPTSPSYSPTSPSY-SPTSPAYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPT 1692
Query: 117 SANYTP 122
S NY+P
Sbjct: 1693 SPNYSP 1698
Score = 43.9 bits (103), Expect = 4e-05
Identities = 35/173 (20%), Positives = 58/173 (33%), Gaps = 6/173 (3%)
Query: 4 STPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSS----TPYLNSSYPSYGSTYG 59
TP SG + SP + S+ + + Y ++ P
Sbjct: 1470 VTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEA 1529
Query: 60 GTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPL-PPVRPRRSKSSTRSA 118
TS G+G + S + P+ S ++P S S +P+ +P P P S S
Sbjct: 1530 PTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1589
Query: 119 NYTPEGGGRMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSS 171
+Y+P S + + S S S Y + S + + S S
Sbjct: 1590 SYSPTSPS-YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1641
Score = 43.9 bits (103), Expect = 4e-05
Identities = 35/126 (27%), Positives = 49/126 (38%), Gaps = 5/126 (3%)
Query: 1 MSYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST--- 57
SYS P S TS S S S SP S + S S S ++P + + P+Y T
Sbjct: 1610 PSYS--PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPS 1667
Query: 58 YGGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRS 117
Y TS Y + S + PS S ++P S S +P +P P + +
Sbjct: 1668 YSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHN 1727
Query: 118 ANYTPE 123
N
Sbjct: 1728 ENENSR 1733
Score = 41.2 bits (96), Expect = 3e-04
Identities = 33/197 (16%), Positives = 61/197 (30%), Gaps = 21/197 (10%)
Query: 1 MSYSTPPRRSSGRTTSRPRSLYS-------SSPSPQSRNLSSYSSGLSSSTPYLNSSYPS 53
YS + + ++S + + +++P+
Sbjct: 1471 TPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAP 1530
Query: 54 YGSTYGGTSSGYGGLTLPSSYSRPSQS------SPRSYHAPPSS-----YRSSYAPTTTP 102
+G +S G+ + S + P+ S SP S P+S SY+PT+
Sbjct: 1531 TSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1590
Query: 103 LPPVRPRRSKSSTRSANYTPEGG---GRMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTS 159
P P S +S + +P S + + S S S Y + S +
Sbjct: 1591 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1650
Query: 160 RSRVNSESGGSSRKLPN 176
+ S S P+
Sbjct: 1651 SPSYSPTSPAYSPTSPS 1667
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 50.5 bits (120), Expect = 3e-07
Identities = 39/128 (30%), Positives = 54/128 (42%), Gaps = 6/128 (4%)
Query: 15 TSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---YGGTSSGYGGLTLP 71
TS S S S SP S + S+ S S ++P + + PSY T Y TS Y +
Sbjct: 1588 TSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1647
Query: 72 SSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGGRMSRS 131
S + PS SP S P+S SY+PT+ P P S +S + +P
Sbjct: 1648 YSPTSPS-YSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1704
Query: 132 GSTTSLNS 139
T+ S
Sbjct: 1705 SPTSPSYS 1712
Score = 50.1 bits (119), Expect = 4e-07
Identities = 52/181 (28%), Positives = 70/181 (38%), Gaps = 16/181 (8%)
Query: 9 RSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---YGGTSSGY 65
S G +TS S S SP S + S S S ++P + + PSY +T Y TS Y
Sbjct: 1561 SSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSY 1620
Query: 66 GGLTLPSSYS----RPSQSSPR-SYHAPPSSYRS-SYAPTTTPLPPVRPRRSKSSTRSAN 119
SYS S +SP S +P S S SY+PT+ P P S +S +
Sbjct: 1621 S--PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1678
Query: 120 YTPEGGGRMSRSGSTTS----LNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSSRKLP 175
+P S S S TS S S Y + S + + S S P
Sbjct: 1679 TSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1737
Query: 176 N 176
+
Sbjct: 1738 S 1738
Score = 47.4 bits (112), Expect = 3e-06
Identities = 51/185 (27%), Positives = 68/185 (36%), Gaps = 18/185 (9%)
Query: 2 SYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---Y 58
S S L S S SP S S+ S S+P + + PSY T Y
Sbjct: 1534 VQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYST-SPAYMPSSPSYSPTSPSYSPTSPSY 1592
Query: 59 GGTSSGYGGLTLPSS--YSRPSQS-SPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSST 115
TS Y P+S YS S S SP S P+S SY+PT+ P P S +S
Sbjct: 1593 SPTSPSY----SPTSPSYSATSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSP 1646
Query: 116 R----SANYTPEGGGRMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSS 171
S +Y+P S + + S S S Y + S + + S S
Sbjct: 1647 SYSPTSPSYSP-TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1705
Query: 172 RKLPN 176
P+
Sbjct: 1706 PTSPS 1710
Score = 47.4 bits (112), Expect = 3e-06
Identities = 42/127 (33%), Positives = 56/127 (44%), Gaps = 8/127 (6%)
Query: 1 MSYS-TPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST-- 57
SYS T P S TS S S S SP S + S S S ++P + + PSY T
Sbjct: 1625 PSYSPTSPSYSP---TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1681
Query: 58 -YGGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKS-ST 115
Y TS Y + S + PS S ++P S S +P+ +P P S S S
Sbjct: 1682 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1741
Query: 116 RSANYTP 122
S +Y+P
Sbjct: 1742 TSPSYSP 1748
Score = 47.0 bits (111), Expect = 4e-06
Identities = 47/190 (24%), Positives = 64/190 (33%), Gaps = 26/190 (13%)
Query: 5 TPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSS------STPYLNSSYPSYGSTY 58
TP RS + S +++ SP + S G ++PY P Y S +
Sbjct: 1484 TPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPF 1543
Query: 59 GGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSS---- 114
S GLT P SYS S S PSS SY+PT+ P P S +S
Sbjct: 1544 SSAMSPGYGLTSP-SYSPSSPGYSTSPAYMPSS--PSYSPTSPSYSPTSPSYSPTSPSYS 1600
Query: 115 -------TRSANYTPEGGGRMSRSGSTT------SLNSLRSEAPSEGYESGGDNLSTSRS 161
S +Y+P S S + S S S Y + S +
Sbjct: 1601 PTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1660
Query: 162 RVNSESGGSS 171
+ S S
Sbjct: 1661 SYSPTSPSYS 1670
Score = 45.1 bits (106), Expect = 2e-05
Identities = 42/128 (32%), Positives = 56/128 (43%), Gaps = 12/128 (9%)
Query: 2 SYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---Y 58
SYS P S TS S S S SP S + S S S ++P + + PSY T Y
Sbjct: 1612 SYS--PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1669
Query: 59 GGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTR-- 116
TS Y + S + PS S ++P S SY+PT+ P P S +S
Sbjct: 1670 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS---PSYSPTSPSYSPTSPSYSPTSPSYS 1726
Query: 117 --SANYTP 122
S +Y+P
Sbjct: 1727 PTSPSYSP 1734
Score = 41.2 bits (96), Expect = 3e-04
Identities = 35/107 (32%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 2 SYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGST---Y 58
SYS S TS S S S SP S + S S S ++P + + PSY T Y
Sbjct: 1654 SYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711
Query: 59 GGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPP 105
TS Y P+S S +SP ++P S S +P+ +P P
Sbjct: 1712 SPTSPSYS----PTS-PSYSPTSPS--YSPTSPSYSPTSPSYSPTSP 1751
Score = 40.4 bits (94), Expect = 6e-04
Identities = 44/190 (23%), Positives = 60/190 (31%), Gaps = 24/190 (12%)
Query: 1 MSYSTPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYG--STY 58
S S Y SP S S+ +P + PSY S
Sbjct: 1510 QGGSEGREGFGDYGLLGAASPYKGVQSPGY-----TSPFSSAMSPGYGLTSPSYSPSSPG 1564
Query: 59 GGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRS----SYAPTTTPLPPVRPRRSKSS 114
TS Y + S + PS S ++P S S SY+ T+ P P S +S
Sbjct: 1565 YSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624
Query: 115 TR----SANYTPEGGGRMSRSGSTTSL----NSLRSEAPSEGYESGGDNLSTSRSRVNSE 166
S +Y+P S S S TS S S Y + S + +
Sbjct: 1625 PSYSPTSPSYSPT-----SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1679
Query: 167 SGGSSRKLPN 176
S S P+
Sbjct: 1680 SPSYSPTSPS 1689
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 44.1 bits (104), Expect = 3e-05
Identities = 28/122 (22%), Positives = 44/122 (36%), Gaps = 27/122 (22%)
Query: 172 RKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLS---------- 221
RKL E+ +L + E QA+++ L+ L+K EEEL A +
Sbjct: 1063 RKLEGESSDLHEQ--IAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRE 1120
Query: 222 ------------EQEKRERRTMERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
E EK R E++ ++ EL+ L K E + D +
Sbjct: 1121 LESHISDLQEDLESEKAARNKAEKQKRDLSEELEAL---KTELEDTLDTTATQQELRGSD 1177
Query: 270 SK 271
K
Sbjct: 1178 YK 1179
Score = 39.0 bits (91), Expect = 0.001
Identities = 18/117 (15%), Positives = 47/117 (40%), Gaps = 17/117 (14%)
Query: 172 RKLPNENGELD--YKKLYEES---QAELSRLRETLSKTEEELNQVKATYSK--------N 218
+K+ ++ ++ KL +E + +S L L++ EE+ + +K
Sbjct: 986 KKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELE 1045
Query: 219 SLSEQEKRERRTMERKLSEMEVELKEL----DQFKKENQRLKDENGALIRVISKLSK 271
++E++ R+ +E+ ++E E +L + + + LK + +
Sbjct: 1046 VRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALA 1102
Score = 32.5 bits (74), Expect = 0.14
Identities = 18/103 (17%), Positives = 41/103 (39%), Gaps = 18/103 (17%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRT------------- 230
K+ ++++AEL L + ++ EE N ++ + E E R
Sbjct: 870 KERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEIL 929
Query: 231 --MERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKLSK 271
ME ++ E E ++L + E ++++ + L + +
Sbjct: 930 HEMEARIEEEEERSQQL---QAEKKKMQQQMLDLEEQLEEEEA 969
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 41.7 bits (97), Expect = 7e-05
Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 11/76 (14%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELK 243
+K EE + L L E+E + KA K L E +R+ +E+ + K
Sbjct: 88 RKWREEQRKRLQELDAASKVMEQEWRE-KA---KKDLEEWNQRQSEQVEKNKINNRIADK 143
Query: 244 ELDQFKKENQRLKDEN 259
F ++ D +
Sbjct: 144 A---FYQQ----PDAD 152
Score = 34.0 bits (77), Expect = 0.027
Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 13/86 (15%)
Query: 161 SRVNSESGGSSRKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSL 220
R+ E S RK E ++L S+ RE K +++L +
Sbjct: 78 DRLTQEPE-SIRKWREEQ-RKRLQELDAASKVMEQEWRE---KAKKDLEEWNQRQ----- 127
Query: 221 SEQEKRERRTMERKLSEMEVELKELD 246
E+ E+ + ++++ + ++ D
Sbjct: 128 --SEQVEKNKINNRIAD-KAFYQQPD 150
Score = 30.1 bits (67), Expect = 0.56
Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 42/89 (47%)
Query: 192 AELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE---------- 241
A+ RL + E E S ++ RE + ++L E++
Sbjct: 75 AQADRLTQ-----EPE-------------SIRKWREEQ--RKRLQELDAASKVMEQEWRE 114
Query: 242 --LKELDQF----------KKENQRLKDE 258
K+L+++ K N R+ D+
Sbjct: 115 KAKKDLEEWNQRQSEQVEKNKINNRIADK 143
>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK
snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A
Length = 104
Score = 39.4 bits (91), Expect = 1e-04
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE 241
D+ + YE E + +SK E ++ S + + ++ R R +R + +
Sbjct: 14 DFSETYERYHTESL---QNMSKQELIKEYLELEKSLSRMEDENNRLRLESKRLDARVREL 70
Query: 242 LKELDQFKKENQRLKDENGALIR 264
ELD+ + EN +L EN +
Sbjct: 71 ELELDRLRAENLQLLTENELHRQ 93
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 40.9 bits (95), Expect = 3e-04
Identities = 22/127 (17%), Positives = 37/127 (29%), Gaps = 8/127 (6%)
Query: 20 SLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGSTYGGTSSGYGGLTLPSSYSRPSQ 79
+ ++ SS +S + S +PS G G + +
Sbjct: 8 HVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLH--------SPISTL 59
Query: 80 SSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGGRMSRSGSTTSLNS 139
SSP + PP S SS + P P S+ +P S +
Sbjct: 60 SSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLN 119
Query: 140 LRSEAPS 146
+ P+
Sbjct: 120 GVLKVPA 126
Score = 37.8 bits (87), Expect = 0.003
Identities = 21/141 (14%), Positives = 38/141 (26%), Gaps = 7/141 (4%)
Query: 34 SSYSSGLSSSTPYLNSSYPSYGSTYGGTSSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYR 93
+ + ++ S ++ G S P SP H+P S+
Sbjct: 3 HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAA--PSLHPSLGPGIGSPGQLHSPISTLS 60
Query: 94 SSYAPTTTPLPPVRPRRSKSSTRSAN--YTPEGGGRMSRSGSTTSLNSLRSEAPSEGYES 151
S P PP S S + TP G ++ +N + S +
Sbjct: 61 S---PINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLG 117
Query: 152 GGDNLSTSRSRVNSESGGSSR 172
L + + +
Sbjct: 118 LNGVLKVPAHPSGNMASFTKH 138
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon,
coiled post-transcriptional, gene regulation, chaperone;
HET: EPE; 2.20A {Helicobacter pylori}
Length = 256
Score = 38.9 bits (90), Expect = 8e-04
Identities = 19/98 (19%), Positives = 34/98 (34%), Gaps = 2/98 (2%)
Query: 172 RKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTM 231
L E +K +++ + + + EEE +K SKN + Q+ +
Sbjct: 21 DSLEPLIREK--RKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIAS 78
Query: 232 ERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
+K +EL E K+ + R I L
Sbjct: 79 IQKKMSEIKSERELRSLNIEEDIAKERSNQANREIENL 116
>3jsv_C NF-kappa-B essential modulator; ubiquitin, coiled-coil, cellular
signaling, cytoplasm, isopeptide bond, nucleus,
phosphoprotein, UBL conjugation; 2.70A {Mus musculus}
PDB: 3f89_A 2zvo_B 2zvn_B
Length = 94
Score = 36.7 bits (84), Expect = 0.001
Identities = 13/76 (17%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQE-KRERRTMERKLSEMEVEL 242
++ Q + +L+E + + + V ++ + + + + ER E+ + + E
Sbjct: 15 EEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQ 74
Query: 243 KELDQFKKENQRLKDE 258
++L+Q ++E +LK
Sbjct: 75 EQLEQLQREFNKLKVG 90
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 38.2 bits (89), Expect = 0.003
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE 241
YK E+ +EL L +EELN+ + +Q K TME+KL E E
Sbjct: 1016 KYKHETEQLVSELKEQNTLLKTEKEELNR--------RIHDQAKEITETMEKKLVE---E 1064
Query: 242 LKELDQFKKENQRLKDE 258
K+L + ++RL+ +
Sbjct: 1065 TKQL-ELDLNDERLRYQ 1080
Score = 35.9 bits (83), Expect = 0.015
Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 4/87 (4%)
Query: 186 LYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKEL 245
+Y + + L K + E V+ + E + + ++RK+ E E K L
Sbjct: 891 VYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQ---LQRKIDEQNKEYKSL 947
Query: 246 -DQFKKENQRLKDENGALIRVISKLSK 271
++ E L + +L
Sbjct: 948 LEKMNNLEITYSTETEKLRSDVERLRM 974
Score = 31.2 bits (71), Expect = 0.39
Identities = 18/104 (17%), Positives = 40/104 (38%), Gaps = 9/104 (8%)
Query: 172 RKLPNENGELD-YKKLYEESQAELSRLRETLSKTEEELNQVKATYSK-NSLSEQEKRERR 229
+KL E ++ YKKL+ + ++ +L+ + + +E + + E + R
Sbjct: 907 KKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLR 966
Query: 230 TMERKL--SEMEVELKELDQFKKENQRLKDENGALIRVISKLSK 271
+ +L SE E L++E L + + +
Sbjct: 967 SDVERLRMSEEE-----AKNATNRVLSLQEEIAKLRKELHQTQT 1005
>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 = 37.6 bits (87), Expect = 0.003
Identities = 16/103 (15%), Positives = 23/103 (22%)
Query: 4 STPPRRSSGRTTSRPRSLYSSSPSPQSRNLSSYSSGLSSSTPYLNSSYPSYGSTYGGTSS 63
+ SS + S + + ++ Y
Sbjct: 339 FDDKETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQ 398
Query: 64 GYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPV 106
GY P P P+ Y PP AP P V
Sbjct: 399 GYPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGV 441
Score = 27.6 bits (61), Expect = 4.9
Identities = 10/54 (18%), Positives = 15/54 (27%), Gaps = 1/54 (1%)
Query: 71 PSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEG 124
+ + P+ Y PP Y P P P + P+G
Sbjct: 379 QKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPPPQG-APPQG 431
>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein,
nuclear protein, neurogenesis, cytosk LIS1 binding,
differentiation; 2.24A {Rattus norvegicus}
Length = 189
Score = 36.3 bits (83), Expect = 0.004
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 180 ELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEME 239
E D + + +RE ++ +AT SL + E+R + +ER + +E
Sbjct: 94 EDDLSQTRAIKEQLHKYVRELEQANDDLERAKRAT--IMSLEDFEQRLNQAIERN-AFLE 150
Query: 240 VELKELDQFKKENQRLKDE 258
EL E + QRLKDE
Sbjct: 151 SELDEKESLLVSVQRLKDE 169
Score = 32.0 bits (72), Expect = 0.13
Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 6/93 (6%)
Query: 183 YKKLYEESQAELSRLRETLSKTEEELNQVKATYSKN-----SLSEQEKRERRTMERKLSE 237
YK+ ++E++ EL +E + E EL + + +++ K E ++ KL
Sbjct: 22 YKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEH 81
Query: 238 MEVEL-KELDQFKKENQRLKDENGALIRVISKL 269
+ K++ + + + + L + + +L
Sbjct: 82 QYAQSYKQVSVLEDDLSQTRAIKEQLHKYVREL 114
>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO
- IKK gamma - NFKB pathwa darpin, transcription
regulation; 2.9A {Mus musculus}
Length = 110
Score = 34.8 bits (79), Expect = 0.006
Identities = 15/102 (14%), Positives = 41/102 (40%), Gaps = 6/102 (5%)
Query: 161 SRVNSESGGSSRKLPNENGELDYK-----KLYEESQAELSRLRETLSKTEEELNQVKATY 215
+ S + +L + + Q + +L+E + + + V
Sbjct: 9 HHSSGLVPRGSHMASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLK 68
Query: 216 SKNSLSEQE-KRERRTMERKLSEMEVELKELDQFKKENQRLK 256
++ + + + + ER E+ + + E ++L+Q ++E +LK
Sbjct: 69 AQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK 110
>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 361
Score = 35.6 bits (81), Expect = 0.013
Identities = 10/72 (13%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 181 LDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEV 240
D +++ ++ E R + N+ +K+ + +++ E R M+ ++ M+
Sbjct: 285 QDLQEVTQDLHYENFRSERLKRGGRKVENEDM---NKDQILLEKEAELRRMQEMIARMQA 341
Query: 241 ELKELDQFKKEN 252
+++ Q +
Sbjct: 342 QMQMQMQGGDGD 353
Score = 28.3 bits (62), Expect = 2.8
Identities = 8/42 (19%), Positives = 22/42 (52%)
Query: 170 SSRKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQV 211
EN +++ ++ E +AEL R++E +++ + ++
Sbjct: 305 KRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQMQ 346
>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1
PDB: 2tma_A 2w49_A 2w4u_A
Length = 284
Score = 34.6 bits (79), Expect = 0.020
Identities = 16/89 (17%), Positives = 40/89 (44%), Gaps = 1/89 (1%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSK-NSLSEQEKRERRTMERKLSEMEVEL 242
+K +ES+ + + K EE++ + + ++E R+ + RKL +E +L
Sbjct: 117 EKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDL 176
Query: 243 KELDQFKKENQRLKDENGALIRVISKLSK 271
+ ++ + ++ E I+ ++ K
Sbjct: 177 ERAEERAELSEGKCAELEEEIKTVTNNLK 205
Score = 31.9 bits (72), Expect = 0.16
Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 1/83 (1%)
Query: 177 ENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERR-TMERKL 235
E+ ++ E + +L + + + +V + ER E K
Sbjct: 131 ESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKC 190
Query: 236 SEMEVELKELDQFKKENQRLKDE 258
+E+E E+K + K + ++
Sbjct: 191 AELEEEIKTVTNNLKSLEAQAEK 213
>3a5t_A Transcription factor MAFG; protein-DNA complex, BZIP factor,
acetylation, DNA-binding, isopeptide bond, nucleus;
2.80A {Mus musculus}
Length = 107
Score = 31.9 bits (72), Expect = 0.050
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 5/96 (5%)
Query: 176 NENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKL 235
+ L ++L S EL++ LSK E + + KN R +R +
Sbjct: 3 HMGTSLTDEELVTMSVRELNQHLRGLSKEEIIQLKQRRRTLKNRGYAASCRVKR--VTQK 60
Query: 236 SEMEVELKELDQFKKENQRLKDENGALIRVISKLSK 271
E+E + EL ++E ++L EN ++ + L
Sbjct: 61 EELEKQKAEL---QQEVEKLASENASMKLELDALRS 93
>3l4q_C Phosphatidylinositol 3-kinase regulatory subunit beta; PI3K,
phosphoinositide-3-kinase, influenza virus, NS1; 2.30A
{Bos taurus} PDB: 2v1y_B
Length = 170
Score = 32.8 bits (74), Expect = 0.053
Identities = 18/88 (20%), Positives = 40/88 (45%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE 241
Y + Y++ E +L E ++T +EL + + + + E+ + K S+ +E
Sbjct: 21 VYHQQYQDKSREYDQLYEEYTRTSQELQMKRTAIEAFNETIKIFEEQGQTQEKSSKEYLE 80
Query: 242 LKELDQFKKENQRLKDENGALIRVISKL 269
+ +KE QR+ + L I+++
Sbjct: 81 RFRREGNEKEMQRILLNSERLKSRIAEI 108
Score = 26.3 bits (57), Expect = 7.8
Identities = 12/93 (12%), Positives = 41/93 (44%), Gaps = 10/93 (10%)
Query: 177 ENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLS 236
E E + +++ S+ SR+ E + +++ + + R ++++++
Sbjct: 85 EGNEKEMQRILLNSERLKSRIAEIHESRTKLEQELR----------AQASDNREIDKRMN 134
Query: 237 EMEVELKELDQFKKENQRLKDENGALIRVISKL 269
++ +L +L + + + + GA + I++
Sbjct: 135 SLKPDLMQLRKIRDQYLVWLTQKGARQKKINEW 167
>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 427
Score = 33.2 bits (75), Expect = 0.089
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 204 TEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKEL--DQFKKENQRLKDENGA 261
E SL E + +R +L + E E++++ + K++ LK+
Sbjct: 304 EEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKE 363
Query: 262 LIRVISKLSK 271
L +L K
Sbjct: 364 LHEKFDRLKK 373
>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 = 32.9 bits (74), Expect = 0.11
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 180 ELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEME 239
++YK L + E R+ T + Q Y+ N + + R KL +
Sbjct: 88 RINYKFLMSPIKTEQ---RQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA- 143
Query: 240 VELKELD 246
L EL
Sbjct: 144 --LLELR 148
>3tnf_B LIDA, RAS-related protein RAB-8A; protein transport, vesicular
trafficking, GTPase, vesicle recuitment, LCV, DRRA,
SIDM; HET: GNP; 2.50A {Legionella pneumophila subsp}
Length = 384
Score = 32.3 bits (72), Expect = 0.14
Identities = 16/92 (17%), Positives = 40/92 (43%), Gaps = 2/92 (2%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYS--KNSLSEQEKRERRTMERKLSEME 239
K +E+ + L + L K E + ++ Y + +L EK + E LSE+
Sbjct: 8 QAIKRAQENIKKGEELEKKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEELSLSEIN 67
Query: 240 VELKELDQFKKENQRLKDENGALIRVISKLSK 271
+++ + ++ +L +++ + + L +
Sbjct: 68 EKMEAFSKDSEKLTQLMEKHKGDEKTVQSLQR 99
>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol
3-phosphate binding, membrane protein; HET: ITP; 2.20A
{Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A*
1hyj_A
Length = 125
Score = 30.7 bits (69), Expect = 0.19
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 16/74 (21%)
Query: 190 SQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQFK 249
+Q E L E K E E+ +++ + +RKL ++EL
Sbjct: 2 NQDERRALLERCLKGEGEIEKLQTKVLEL-------------QRKLDNTTAAVQEL---G 45
Query: 250 KENQRLKDENGALI 263
+ENQ L+ ++ +
Sbjct: 46 RENQSLQIKHTQAL 59
>4f6o_A Metacaspase-1; rossmann fold, hydrolase; HET: DFH; 1.68A
{Saccharomyces cerevisiae}
Length = 350
Score = 31.9 bits (71), Expect = 0.20
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 76 RPSQSSPRSYHAPPSSYRSSYA-PTTTPLPPVRPRRSKSSTRSANYTPEGGGR 127
+ Y+ P + + Y P LPP + + + + + Y+ G R
Sbjct: 2 QAKAQLSNGYNNPNVNASNMYGPPQNMSLPPPQTQTIQGTDQPYQYSQCTGRR 54
>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus
norvegicus}
Length = 96
Score = 29.9 bits (67), Expect = 0.25
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 188 EESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQ 247
E+ Q EL L + +EL V+ ++ ++E ++ + ER E +E +
Sbjct: 7 EQLQRELKELALEEERLIQELEDVEK--NRKVVAENLEKVQAEAERLDQEEAQYQREYSE 64
Query: 248 FKKENQRLKDENGAL 262
FK++ L DE ++
Sbjct: 65 FKRQQLELDDELKSV 79
>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil
(dimeric, parallel), familial hypertrophic
cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo
sapiens} SCOP: h.1.26.1 PDB: 2fxm_A
Length = 129
Score = 30.2 bits (68), Expect = 0.28
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYS--KNSLSEQEKR------ERRTMERKL 235
K+ E+S+A L E + +E N ++ +++L++ E+R + +E K+
Sbjct: 26 KEALEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKV 85
Query: 236 SEMEVELKELDQFKKENQRLKDE 258
EM L++ ++ E K +
Sbjct: 86 KEMNKRLEDEEEMNAELTAKKRK 108
>3fh3_A Putative ECF-type sigma factor negative effector; putative
anti-sigma W factor, MCSG, PSI, structural genomics;
HET: MSE; 2.10A {Bacillus anthracis str} PDB: 3fgg_A
Length = 158
Score = 30.6 bits (68), Expect = 0.29
Identities = 26/131 (19%), Positives = 47/131 (35%), Gaps = 13/131 (9%)
Query: 132 GSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSES-----------GGSSRKLPNENGE 180
GS +L E Y LS ++ + ++ + + NG
Sbjct: 5 GSFENLKKHAGTMTLEAYMRFSAKLSEAKDEMGTKEYEVFTKELKKLTNAKLAYGDSNGN 64
Query: 181 LDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEV 240
+DY L E + E+ ++ L ++LN K+ SK L+++E + V
Sbjct: 65 IDYDALSSEKREEMKKVSMGLQPYFDKLNGHKS--SKEVLTQEEFDRYMEALMTHEIVRV 122
Query: 241 ELKELDQFKKE 251
+ K K E
Sbjct: 123 KTKSTGAIKVE 133
>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing
cluster, hydrophobic core, contractIle protein; 1.80A
{Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A
Length = 155
Score = 30.3 bits (68), Expect = 0.32
Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE 241
+ + E++RL++ L + EE SE + E +E +L +
Sbjct: 11 ELLSKNYHLENEVARLKKLLERAEERAEL----------SEGKSAE---LEEELKTVTNN 57
Query: 242 LKELDQFKKENQRLKDENGALIRVISK 268
LK L+ ++ + +D+ I+V+S
Sbjct: 58 LKSLEAQAEKYSQKEDKYEEEIKVLSD 84
Score = 27.6 bits (61), Expect = 2.6
Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 2/95 (2%)
Query: 177 ENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLS 236
E Y + ++ + E+ L + L + E A S L + + +
Sbjct: 62 EAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAE--FAERSVTKLEKSIDDLEDELYAQKL 119
Query: 237 EMEVELKELDQFKKENQRLKDENGALIRVISKLSK 271
+ + +E+ Q + + + L +N L +++L K
Sbjct: 120 KYKAISEEMKQLEDKVEELLSKNYHLENEVARLKK 154
>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase,
protein-targeting, transport protein; HET: GDP; 1.97A
{Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*
Length = 328
Score = 31.1 bits (71), Expect = 0.32
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 10/67 (14%)
Query: 183 YKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKR---ERRTMERKLSEME 239
+ KL E+ ++ + R+ E + K EEE+ K L ++ + + +++ L E+E
Sbjct: 8 FGKLREKLKSFVKRVEEEVEKEEEEV-------EKKGLLDRILTVEIKEKDVDKALDELE 60
Query: 240 VELKELD 246
++L E D
Sbjct: 61 IDLLEAD 67
>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine
exchange factor, coiled-coil, endocytosis/exocytosis
complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1
Length = 154
Score = 30.6 bits (68), Expect = 0.33
Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 6/81 (7%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSK--NSLSEQEKRERRTMERKLSEMEVE 241
++ + ++ E K +E+ + A+ N++ ++E+ +E + +
Sbjct: 64 REDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQ 123
Query: 242 LKE----LDQFKKENQRLKDE 258
L+E LD + + LK
Sbjct: 124 LREKDTLLDTLTLQLKNLKKV 144
>2xs1_A Programmed cell death 6-interacting protein; protein
transport-viral protein complex, cell cycle; 2.30A {Homo
sapiens} PDB: 2xs8_A 2oev_A 2r05_A 2r02_A 2r03_A 2oex_A
2ojq_A
Length = 704
Score = 31.5 bits (70), Expect = 0.37
Identities = 11/68 (16%), Positives = 22/68 (32%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELK 243
++Y ++ + + + +SK S E R + + L+
Sbjct: 611 DRVYGGLTTKVQESLKKQEGLLKNIQVSHQEFSKMKQSNNEANLREEVLKNLATAYDNFV 670
Query: 244 ELDQFKKE 251
EL KE
Sbjct: 671 ELVANLKE 678
>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 = 31.2 bits (70), Expect = 0.40
Identities = 25/159 (15%), Positives = 45/159 (28%), Gaps = 13/159 (8%)
Query: 71 PSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGGRMSR 130
+ ++R P +R A P R+ S + G
Sbjct: 35 AARWNRGEPQVP--------DFRHLKAEVDAEKPGATDRKGGVGMPSRD-RNIGAPGQDT 85
Query: 131 SGSTTSLNSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSSRKLPNENGELDYKKLYEES 190
G + SL S G ++ + +S S + + +E E + E
Sbjct: 86 PGVSLHPLSLDSPDREPGADAPLELGDSSPQGPMSLESLAPPESTDEGAETE----SPEP 141
Query: 191 QAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERR 229
E R L EE + ++L K + +
Sbjct: 142 GDEGEPGRSGLELEPEEPPGWRELVPPDTLHSLPKSQVK 180
>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP
hydrolysis, GDP, GMP, dynamin related, large GTPase
family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens}
SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A*
2bc9_A* 2d4h_A*
Length = 592
Score = 31.1 bits (69), Expect = 0.40
Identities = 12/87 (13%), Positives = 35/87 (40%), Gaps = 4/87 (4%)
Query: 177 ENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKN--SLSEQEKRERRTMERK 234
+ L + E + E+ R + + KN + ++E+ + +++
Sbjct: 472 TDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQL 531
Query: 235 LSEMEVELKEL--DQFKKENQRLKDEN 259
+ME + +L +Q + +L+++
Sbjct: 532 TEKMENDRVQLLKEQERTLALKLQEQE 558
>3mov_A Lamin-B1; LMNB1, B-type lamins, intermediate filament (IF),
nucleus, coiled coil, structural genomics consortium,
SGC, structural protein; 2.40A {Homo sapiens} PDB:
3tyy_A
Length = 95
Score = 29.1 bits (66), Expect = 0.40
Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 194 LSRLRETLSKTEEELNQVKATYSK-NSLSEQEKR---ERRTMERKLSEMEVELKELDQ 247
+ S+ K + + + E E E+ R L++ E E+ E+
Sbjct: 1 MHHHHHHSSRENLYFQGQKESRACLERIQELEDLLAKEKDNSRRMLTDKEREMAEIRD 58
>2j5u_A MREC protein; bacterial cell shape determining protein MREC, cell
shape regulation; 2.5A {Listeria monocytogenes}
Length = 255
Score = 30.5 bits (69), Expect = 0.55
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 225 KRERRTMERKLSEMEVELKELDQFKKENQRLKD 257
E + ++ +L E+ E+ KKEN+ LK+
Sbjct: 25 YTENQHLKERLEELAQLESEVADLKKENKDLKE 57
>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 = 30.7 bits (69), Expect = 0.57
Identities = 11/92 (11%), Positives = 29/92 (31%), Gaps = 1/92 (1%)
Query: 80 SSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGGRMSRSGSTTSLNS 139
+SP + ++ ++ P T P + + N P+ +G ++ +
Sbjct: 6 TSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNATVAA 65
Query: 140 LRSEAPSEGYESGGDNLSTSRSRVNSESGGSS 171
+ E + + V G++
Sbjct: 66 GHATLR-EHLRDIKAENTDANFYVCPPPTGAT 96
>2qag_C Septin-7; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 418
Score = 30.6 bits (68), Expect = 0.58
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 3/94 (3%)
Query: 181 LDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEK-RERRTMERKLSEME 239
D K + E R R+ + T ++ K + ERR K+ +ME
Sbjct: 276 QDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAKMKKME 335
Query: 240 VELKEL--DQFKKENQRLKDENGALIRVISKLSK 271
+E++++ + K++ Q+LKD L R ++ K
Sbjct: 336 MEMEQVFEMKVKEKVQKLKDSEAELQRRHEQMKK 369
>2wt7_B Transcription factor MAFB; transcription, transcription regulation,
nucleus, activator, repressor, DNA-binding,
phosphoprotein, differentiation; 2.30A {Mus musculus}
PDB: 2wty_A* 1k1v_A
Length = 90
Score = 28.8 bits (64), Expect = 0.60
Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 5/87 (5%)
Query: 185 KLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKE 244
+L S EL+R +K E + K KN Q R +R ++ E E
Sbjct: 2 QLVSMSVRELNRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLE-----NE 56
Query: 245 LDQFKKENQRLKDENGALIRVISKLSK 271
Q ++ ++LK E L R
Sbjct: 57 KTQLIQQVEQLKQEVSRLARERDAYKV 83
>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support,
cytosolic protein; 3.00A {Homo sapiens}
Length = 131
Score = 29.0 bits (66), Expect = 0.69
Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 22/95 (23%)
Query: 183 YKKLYEE--------------SQAELSRLRETLSKTEEELNQVKATYSK--NSLSEQEKR 226
+ EE ++E+S LR T+ E EL + + NSL E + R
Sbjct: 15 FFTKTEELNREVATNSELVQSGKSEISELRRTMQNLEIELQSQLSMKASLENSLEETKGR 74
Query: 227 ERRTMER---KLSEMEVELKELDQFKKENQRLKDE 258
+ + + +E +L +L + E ++ E
Sbjct: 75 YCMQLAQIQEMIGSVEEQLAQL---RCEMEQQNQE 106
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure,
structural genomics, protein structure initiative; NMR
{Corynebacterium glutamicum} SCOP: a.4.1.19
Length = 97
Score = 28.5 bits (64), Expect = 0.81
Identities = 7/37 (18%), Positives = 12/37 (32%)
Query: 223 QEKRERRTMERKLSEMEVELKELDQFKKENQRLKDEN 259
+ S E +++ Q KKEN +
Sbjct: 46 KYGSNHNVQGTTPSAAVSEAEQIRQLKKENALQRART 82
>1t3w_A DNA primase; DNAG, DNA-directed RNA polymerase, E. coli, DNA
replication, replication; HET: DNA MSE; 2.80A
{Escherichia coli} SCOP: a.236.1.1 PDB: 2haj_A*
Length = 148
Score = 29.1 bits (65), Expect = 0.82
Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 164 NSESGGSSRKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQ 223
+ + + KL + D + L+ + ++L E ++ A + LS +
Sbjct: 76 GTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLL--ELRQEELIARERTHGLSNE 133
Query: 224 EKRERRTMERKLS 236
E+ E T+ ++L+
Sbjct: 134 ERLELWTLNQELA 146
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural
genomics, PSI-2, protein structure initiative; NMR
{Shigella flexneri}
Length = 108
Score = 28.1 bits (62), Expect = 1.1
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 185 KLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKE 244
++ ESQ E T+ ++ T + +E + LKE
Sbjct: 17 RMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQHERDTGGDDGGLTTAERQ-RLKE 75
Query: 245 LDQFKKENQRLKDEN 259
++EN+ L+ N
Sbjct: 76 P---ERENRELRRSN 87
>3ahc_A Phosphoketolase, xylulose 5-phosphate/fructose 6-phosphate phospho;
thiamine diphosphate-dependent enzyme, alpha-beta fold;
HET: TPP 2PE; 1.70A {Bifidobacterium breve} PDB: 3ahd_A*
3ahe_A* 3ahf_A* 3ahj_A* 3ahi_A* 3ahh_A* 3ahg_A* 3ai7_A*
Length = 845
Score = 29.7 bits (66), Expect = 1.1
Identities = 9/49 (18%), Positives = 12/49 (24%)
Query: 76 RPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEG 124
S PR H + + P+ R NY G
Sbjct: 10 HSSGLVPRGSHMTNPVIGTPWQKLDRPVSEEAIEGMDKYWRVTNYMSIG 58
>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil,
endocytosis/exocytosis complex; 3.00A {Saccharomyces
cerevisiae} SCOP: h.1.33.1
Length = 135
Score = 28.7 bits (63), Expect = 1.1
Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATY--SKNSLSEQEKRERRTMERKLSEME 239
++ + ++ E K +E+ + A+ N+L + E+ +E +
Sbjct: 50 RLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNLVADARMEKYAIEILNKRLT 109
Query: 240 VELKELDQ 247
+L+E D
Sbjct: 110 EQLREKDM 117
>2pms_C Pneumococcal surface protein A (PSPA); lactoferrin, protein-protein
metal transport, hydrolase; HET: NAG; 2.91A
{Streptococcus pneumoniae} SCOP: h.4.19.1
Length = 125
Score = 28.3 bits (62), Expect = 1.2
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 189 ESQAELSRLRETLSKTEEELNQ----VKATYSKNSLSEQEKRERRTMERKLSEMEVELKE 244
QA+++ L + + E+EL + Y+K + + + KLS++E +
Sbjct: 10 APQAKIAELENQVHRLEQELKEIDESESEDYAKEGFRAPLQSKLDAKKAKLSKLEELSDK 69
Query: 245 LDQFKKENQRLKDE 258
+D+ E +L+D+
Sbjct: 70 IDELDAEIAKLEDQ 83
>3ami_A Zinc peptidase; alpha/beta, zinc binding, hydrolase; 2.40A
{Sphingomonas} PDB: 3amj_C
Length = 445
Score = 29.2 bits (66), Expect = 1.4
Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 174 LPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMER 233
+P++ + +L + +A++ + TE EL++VK+ + EQ+ + +
Sbjct: 317 VPSKGVTIA--QLETDLRAQVRDIAAKGV-TEAELSRVKSQMVAGKVYEQDSLMGQATQ- 372
Query: 234 KLSEMEVELKELDQFKKENQRLK 256
+ +EV + Q+L+
Sbjct: 373 -IGGLEVLGLSWRDDDRFYQQLR 394
>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support,
cytosolic protein; 3.00A {Homo sapiens}
Length = 129
Score = 28.3 bits (64), Expect = 1.4
Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 19/82 (23%)
Query: 183 YKKLYEE--------------SQAELSRLRETLSKTEEELNQVKATYSK--NSLSEQEKR 226
Y+ YEE ++ E+S + + + E++ VK + N++++ E+R
Sbjct: 13 YQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQR 72
Query: 227 ERRTMER---KLSEMEVELKEL 245
++ KL+E+E L++
Sbjct: 73 GELALKDARNKLAELEEALQKA 94
>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP:
h.1.3.1
Length = 63
Score = 26.9 bits (60), Expect = 1.5
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 220 LSEQEKRER------RTMERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
+ + +K E+ R ++K +E E E + +K+N+ LK+ +L + I L
Sbjct: 1 MKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYL 56
>2wqd_A Phosphoenolpyruvate-protein phosphotransferase; kinase, cytoplasm,
transport, magnesium, PEP- utilising enzyme,
phosphotransferase system; 2.40A {Staphylococcus aureus}
PDB: 2hro_A
Length = 572
Score = 29.0 bits (66), Expect = 1.6
Identities = 6/56 (10%), Positives = 21/56 (37%), Gaps = 1/56 (1%)
Query: 169 GSSRKLPNENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQE 224
+ L + D + + + E+++ + ++ EL +++ L +
Sbjct: 17 AKAYLLVEPDLTFDKNEKVTDVEGEVAKFNSAIEASKVELTKIRNNAEVQ-LGADK 71
>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET:
MSE; 2.33A {Homo sapiens}
Length = 168
Score = 28.5 bits (63), Expect = 1.6
Identities = 14/94 (14%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSK-NSLSEQEKRERRTMERKLSEMEV 240
+ L E Q L + S+T+++ Q++A + ++ +++ ++
Sbjct: 45 QLESLNRELQERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQE 104
Query: 241 ELK----ELDQFKKENQRLKDENGALIRVISKLS 270
E+K L++ + E + +D + + L
Sbjct: 105 EVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLE 138
>1zym_A Enzyme I; phosphotransferase; 2.50A {Escherichia coli} SCOP:
a.60.10.1 c.8.1.2 PDB: 1eza_A 1ezb_A 1ezc_A 1ezd_A
2eza_A 2ezb_A 2ezc_A 3ezb_A 3eze_A 3eza_A
Length = 258
Score = 28.8 bits (65), Expect = 1.7
Identities = 7/43 (16%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQE 224
K ++ E+ R +K +L +K + E++
Sbjct: 28 RKKISADQVDQEVERFLSGRAKASAQLETIKTKAGET-FGEEK 69
>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil,
endocytosis/exocytosis complex; 2.70A {Saccharomyces
cerevisiae} SCOP: h.1.33.1
Length = 97
Score = 27.5 bits (60), Expect = 1.8
Identities = 10/65 (15%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 184 KKLYEESQAELSRLRETLSKTEEELNQVKATY--SKNSLSEQEKRERRTMERKLSEMEVE 241
++ + ++ E K +E+ + A+ N++ ++E+ +E + +
Sbjct: 32 REDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQ 91
Query: 242 LKELD 246
L+E D
Sbjct: 92 LREKD 96
>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold,
coiled coil, riken structural genomics/proteomics
initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus}
SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A*
1iyw_A
Length = 862
Score = 29.1 bits (66), Expect = 1.8
Identities = 7/68 (10%), Positives = 19/68 (27%), Gaps = 18/68 (26%)
Query: 191 QAELSRLRETLSKTEEELNQVKATYSKNSLS-------------EQEKRERRTMERKLSE 237
+ R + L + + + K L+ E E+ + +
Sbjct: 799 EEWRRRQEKRLKELLALAERSQR---K--LASPGFREKAPKEVVEAEEARLKENLEQAER 853
Query: 238 MEVELKEL 245
+ L ++
Sbjct: 854 IREALSQI 861
>3sfv_B LIDA protein, substrate of the DOT/ICM system; LIDA-RAB complex,
coiled-coil domain, type IV effector prote legionella,
GDP binding; HET: GDP; 1.73A {Legionella pneumophila}
Length = 344
Score = 28.8 bits (63), Expect = 1.8
Identities = 14/85 (16%), Positives = 30/85 (35%)
Query: 176 NENGELDYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKL 235
EN E K L + + LS + E + ++ ++ K+ E+ + + +
Sbjct: 21 EENLEGFEKLLTDSEELSLSEINEKMKAFSKDSEKLTQLMEKHKGDEKTVQSLQREHHDI 80
Query: 236 SEMEVELKELDQFKKENQRLKDENG 260
L+ L + +E G
Sbjct: 81 KAKLANLQVLHDAHTGKKSYVNEKG 105
>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic
vesicle, protein transport, transport, vacuole; 2.80A
{Saccharomyces cerevisiae}
Length = 152
Score = 27.9 bits (61), Expect = 2.2
Identities = 22/129 (17%), Positives = 44/129 (34%), Gaps = 12/129 (9%)
Query: 138 NSLRSEAPSEGYESGGDNLSTSRSRVNSESGGSSRKLPNENGELDYKKLYEESQA---EL 194
E S D+L R ++ +L +N + A L
Sbjct: 11 RKKAKEERSNPQTDSMDDLLIRRLTDRNDKEAHLNELFQDNSGAIGGNIVSHDDALLNTL 70
Query: 195 SRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQFKKENQR 254
+ L++ L E+E+ + L E + + ER + + E + +++
Sbjct: 71 AILQKELKSKEQEIRR---------LKEVIALKNKNTERLNAALISGTIENNVLQQKLSD 121
Query: 255 LKDENGALI 263
LK E+ L+
Sbjct: 122 LKKEHSQLV 130
>4ew8_A Sensor protein DIVL; signal transduction, two-component regulatory
system, hiska GHKL domain, structural genomics; 2.50A
{Caulobacter crescentus}
Length = 268
Score = 28.3 bits (64), Expect = 2.5
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 220 LSEQEKRERRTMERKLSEMEVELKELDQFKKE 251
S R ++ L++ L E ++ K++
Sbjct: 11 SSGLVPRGSHMLQSALADRSAALAEAERLKRD 42
>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A
{Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A
Length = 86
Score = 26.8 bits (60), Expect = 2.6
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 207 ELNQVKATYSK--NSLSEQEKR---ERRTMERKLSEMEVELKELDQFKKENQRLKDE 258
+L+Q++ + L + E ER T R L+E E E+ E+ + Q+ DE
Sbjct: 4 QLSQLQCQLAAKEAKLRDLEDSLARERDTSRRLLAEKEREMAEM---RARMQQQLDE 57
>3kin_B Kinesin heavy chain; motor protein, cytoskeleton; HET: ADP; 3.10A
{Rattus norvegicus} SCOP: c.37.1.9
Length = 117
Score = 27.3 bits (61), Expect = 2.8
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 183 YKKLYEESQAELSRLRETLSKTEEELNQVK 212
+KK YE+ + + L+ + E ELN+ +
Sbjct: 87 WKKKYEKEKEKNKALKSVIQHLEVELNRWR 116
>2wg5_A General control protein GCN4, proteasome-activating nucleotidase;
transcription hydrolase complex, nucleotide-binding;
2.10A {Saccharomyces cerevisiae} PDB: 2wg6_A
Length = 109
Score = 27.1 bits (60), Expect = 2.8
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 229 RTMERKLSEMEVELKELDQFKKENQRLKDENGAL 262
++ ++E +++EL +N L++E L
Sbjct: 3 HHHHHRMKQLEDKVEEL---LSKNYHLENEVARL 33
>3ajw_A Flagellar FLIJ protein; flagellum, type III secretion, coiled-coil,
protein transpor; 2.10A {Salmonella typhimurium}
Length = 150
Score = 27.6 bits (61), Expect = 2.9
Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 191 QAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQFKK 250
Q + L + + + +L Q S +EK++R + L + + L + +
Sbjct: 73 QQFIQTLEKAIEQHRLQLTQWTQKVDLALKSWREKKQRLQAWQTLQDRQTAAALLAENRM 132
Query: 251 ENQRLKDE 258
+ Q+ DE
Sbjct: 133 D-QKKMDE 139
>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase,
hypertherm protein, replication; HET: DNA BOG; 1.50A
{Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1d2m_A*
Length = 664
Score = 28.3 bits (64), Expect = 3.1
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 229 RTMERKLSEMEVELKE-LDQFKKEN-----QRLK 256
+E L E+E EL E + F++ QRLK
Sbjct: 248 EGLEEILKEIEKELWERVRYFEERGEVLYAQRLK 281
>2hwg_A Phosphoenolpyruvate-protein phosphotransferase; enzyme I,
phosphoenolpyruvate:sugar phosphotransferase system,
PTS; HET: NEP; 2.70A {Escherichia coli} PDB: 2kx9_A
2xdf_A 2l5h_A
Length = 575
Score = 28.3 bits (64), Expect = 3.5
Identities = 7/42 (16%), Positives = 15/42 (35%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQ 223
K ++ E+ R +K +L +K + E+
Sbjct: 28 RKKISADQVDQEVERFLSGRAKASAQLETIKTKAGETFGEEK 69
>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA
complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1
Length = 55
Score = 25.5 bits (56), Expect = 3.9
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 217 KNSLSEQEKRERRTMERKLSEMEVELKELDQFKKENQRLKDENGAL 262
KN + +E R ++ + + +E + L + +N+ L +E AL
Sbjct: 8 KNREAARESRRKK--KEYVKSLENRVAVL---ENQNKTLIEELKAL 48
>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex,
hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus
subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A*
1d9x_A 2d7d_B* 2nmv_B*
Length = 661
Score = 27.9 bits (63), Expect = 4.1
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 228 RRTMERKLSEMEVELKE-LDQFKKEN-----QRLK 256
ME+ + +E EL+E L + QRL+
Sbjct: 253 AEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLE 287
>3lay_A Zinc resistance-associated protein; salmonella typhimurium L
structural genomics, center for structural genomics of
INFE diseases; 2.70A {Salmonella enterica subsp}
Length = 175
Score = 27.1 bits (59), Expect = 4.5
Identities = 10/68 (14%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 183 YKKLYEESQAELSRLRETLSKTEEELNQVKATYSKN-----SLSEQEKRERRTMERKLSE 237
+K+Y++ + S LR+ L E N + S + +++++ + + ++ + +
Sbjct: 76 AQKIYDDYYTQTSALRQQLISKRYEYNALLTASSPDTAKINAVAKEMESLGQKLDEQRVK 135
Query: 238 MEVELKEL 245
+V + +
Sbjct: 136 RDVAMAQA 143
>1t9b_A Acetolactate synthase, mitochondrial; acetohydroxyacid synthase,
herbicide, sulfonylurea, thiamin diphosphate, FAD,
inhibitor; HET: 1CS P25 FAD NSP P22 YF3; 2.20A
{Saccharomyces cerevisiae} SCOP: c.31.1.3 c.36.1.5
c.36.1.9 PDB: 1n0h_A* 1t9a_A* 1t9c_A* 1t9d_A* 1jsc_A*
Length = 677
Score = 27.6 bits (62), Expect = 4.8
Identities = 10/76 (13%), Positives = 19/76 (25%), Gaps = 2/76 (2%)
Query: 69 TLPSSYSRPSQSSPRSYHAPPSSYRSSYAPTTTPLPPVRPRRSKSSTRSANYTPEGGGRM 128
T + + R SP AP+ P +P + P+
Sbjct: 21 TAAAKFERQHMDSPDLGTDDDDK-AMGSAPSFNVDPLEQPAEPSKLAKKLRAEPDMDTSF 79
Query: 129 SR-SGSTTSLNSLRSE 143
+G + +
Sbjct: 80 VGLTGGQIFNEMMSRQ 95
>1pp9_A Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_A* 1be3_A* 1l0n_A* 1ntk_A* 1ntm_A*
1ntz_A* 1nu1_A* 1l0l_A* 1ppj_A* 1sqq_A* 1sqv_A* 1sqx_A*
2a06_A* 2fyu_A* 2ybb_A* 1sqb_A* 1sqp_A* 1qcr_A* 1bcc_A*
2bcc_A* ...
Length = 446
Score = 27.5 bits (62), Expect = 5.3
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 3/52 (5%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMER 233
+ Q + RL + TE E+ + K +S + E
Sbjct: 330 SIDDMMFVLQGQWMRLCTSA--TESEVLRGKNLLRNALVSHLDGTTPV-CED 378
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic
dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP;
2.27A {Mus musculus}
Length = 536
Score = 27.3 bits (61), Expect = 5.3
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 6/87 (6%)
Query: 173 KLPNENGELDYKKLYEE--SQAELSRLRETLSKTEEELNQVKATYSKNS-LSEQEKRERR 229
+ EN E S A ++++ ++ S + + +
Sbjct: 114 IIMRENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNYEIVNRASLAAGPMVKWAIAQL 173
Query: 230 TMERKLSEMEV---ELKELDQFKKENQ 253
L +E EL++L+ K+NQ
Sbjct: 174 NYADMLKRVEPLRNELQKLEDDAKDNQ 200
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 25.5 bits (56), Expect = 5.5
Identities = 8/43 (18%), Positives = 20/43 (46%)
Query: 198 RETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEV 240
KT+E++ +KA++ ++ + + R L+ E+
Sbjct: 6 HHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEI 48
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain,
coiled-coil domain, DNA and cleavage, nucleus; HET: DNA
EVP; 2.16A {Homo sapiens}
Length = 803
Score = 27.4 bits (60), Expect = 5.6
Identities = 14/117 (11%), Positives = 38/117 (32%), Gaps = 24/117 (20%)
Query: 145 PSEGYESGGDNLSTSRSRVNSESGGSSRKLPNENGELDY---KKLYEESQAELSRLRETL 201
P + ++ + + N SS + +Y L+ ++ ++ L +
Sbjct: 684 PVKAWKEAQEKAAEEDETQNQHDDSSSDSGTPSGPDFNYILNMSLWSLTKEKVEELIKQR 743
Query: 202 SKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQFKKENQRLKDE 258
E+N +K S ++ ++L F +E +++ +
Sbjct: 744 DAKGREVNDLKRK---------------------SPSDLWKEDLAAFVEELDKVESQ 779
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 27.3 bits (61), Expect = 6.1
Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 2/75 (2%)
Query: 185 KLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKE 244
K ++ L + L K E N + + L + E +
Sbjct: 871 KRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNET-GDSITAVQAKLKNLEAFDGECQS 929
Query: 245 L-DQFKKENQRLKDE 258
L Q + + +
Sbjct: 930 LEGQSNSDLLSILAQ 944
>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription
regulation, nucleus, activator, repressor, DNA-binding,
phosphoprotein, differentiation; 2.30A {Mus musculus}
PDB: 1fos_E* 1a02_F* 1s9k_D
Length = 63
Score = 25.1 bits (55), Expect = 6.5
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 224 EKRERRTM----------ERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
EKR R R+ + E DQ + E L+ E L++ KL
Sbjct: 1 EKRRIRRERNKMAAAKCRNRRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKL 56
>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA
complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F
2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A
Length = 62
Score = 25.0 bits (55), Expect = 7.0
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 223 QEKRERRTM------ERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
+ KR R + +RKL + +++ K +N L L +++L
Sbjct: 3 ERKRMRNRIAASKSRKRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQL 55
>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 = 27.1 bits (59), Expect = 7.2
Identities = 16/102 (15%), Positives = 28/102 (27%), Gaps = 1/102 (0%)
Query: 62 SSGYGGLTLPSSYSRPSQSSPRSYHAPPSSYRSS-YAPTTTPLPPVRPRRSKSSTRSANY 120
S LP+ Y Q P ++ + +S + +
Sbjct: 10 SDSNFMANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSP 69
Query: 121 TPEGGGRMSRSGSTTSLNSLRSEAPSEGYESGGDNLSTSRSR 162
GGG S S + + A + + GG + R
Sbjct: 70 GSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGG 111
>3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently
linked comple supercoiling; HET: DNA PTR TSP; 2.48A
{Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A
2rgr_A*
Length = 757
Score = 27.3 bits (60), Expect = 7.2
Identities = 20/119 (16%), Positives = 35/119 (29%), Gaps = 12/119 (10%)
Query: 145 PSEGYESGGDNLSTSRSRVNSESGGSSRKLPNENGELDYKKLYEESQAELSRLRETLSK- 203
EG G ++N G +S + E+ D + + + L
Sbjct: 641 NKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMR 700
Query: 204 ----TEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQFKKENQRLKDE 258
T+E ++ QEK KLS ++ +L F+ Q
Sbjct: 701 IWSLTKERYQKLLKQK-------QEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQR 752
>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle
protein; 2.50A {Gallus gallus}
Length = 101
Score = 25.6 bits (56), Expect = 7.2
Identities = 9/60 (15%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMERKLSEMEVE 241
+K + ++ E+ + E++ + +E+L + + E ++ R++ +E E
Sbjct: 48 GLQKKLKGTEDEVEKYSESVKEAQEKLE------QAEKKATDAEAEVASLNRRIQLVEEE 101
>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 = 25.7 bits (56), Expect = 7.3
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 225 KRERRTMERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
++ R + + E + ++ EL EN+RL+ + L R +S L
Sbjct: 28 RKSRDKAKMRNLETQHKVLEL---TAENERLQKKVEQLSRELSTL 69
>2wd5_A Structural maintenance of chromosomes protein 1A; DNA damage, cell
cycle, cell division; 2.70A {Mus musculus}
Length = 233
Score = 26.5 bits (59), Expect = 7.8
Identities = 6/35 (17%), Positives = 13/35 (37%)
Query: 213 ATYSKNSLSEQEKRERRTMERKLSEMEVELKELDQ 247
A+ K +++ ++ K + EL E
Sbjct: 196 ASDLKAKARRWDEKAVDKLKEKKGRLTEELLEHHH 230
>2f1m_A Acriflavine resistance protein A; helical hairpin, lipoyl domain,
beta barrel, transport prote; 2.71A {Escherichia coli}
Length = 277
Score = 26.8 bits (60), Expect = 7.9
Identities = 7/42 (16%), Positives = 22/42 (52%)
Query: 183 YKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQE 224
Y+ Y+ ++ +L++ + + + +N+ + +S+QE
Sbjct: 58 YQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQE 99
>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 = 25.2 bits (55), Expect = 8.7
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 225 KRERRTMERKLSEMEVELKELDQFKKENQRLKDENGALIRVISKL 269
++ R + + E + ++ EL EN+RL+ + L R +S L
Sbjct: 28 RKSRDKAKMRNLETQHKVLEL---TAENERLQKKVEQLSRELSTL 69
>3d3y_A Uncharacterized protein; APC29635, conserved protein, enterococcus
faecalis V583, STR genomics, PSI-2, protein structure
initiative; 1.95A {Enterococcus faecalis}
Length = 425
Score = 26.9 bits (60), Expect = 9.2
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 2/52 (3%)
Query: 182 DYKKLYEESQAELSRLRETLSKTEEELNQVKATYSKNSLSEQEKRERRTMER 233
+ ++ EL +R E E+ Q KA KN +E+
Sbjct: 325 NRNQVLRLISTELENIRLG-KIRELEIEQTKAML-KNQYILALDNAGAWLEK 374
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
0.300 0.118 0.312
Gapped
Lambda K H
0.267 0.0437 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,591,192
Number of extensions: 193927
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 187
Length of query: 271
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 179
Effective length of database: 4,133,061
Effective search space: 739817919
Effective search space used: 739817919
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.7 bits)
S2: 56 (26.1 bits)