RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2081
(380 letters)
>2vfk_A AKAP18 delta; APO, hydrolase; HET: AMP; 1.50A {Homo sapiens} PDB:
2vfl_A* 2vfy_A
Length = 205
Score = 128 bits (322), Expect = 2e-35
Identities = 36/218 (16%), Positives = 78/218 (35%), Gaps = 23/218 (10%)
Query: 166 THLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVER 225
+ LSIP+ I + ++L +R G HIT+ ++ L + E
Sbjct: 4 NYFLSIPITNKKITAGIKVLQNSILRQDNRLTK----AMVGDGSFHITLLVMQLLNEDEV 59
Query: 226 DQAVEVLQKCGNNIILPILRSQRIKINLKGLEIMNDDPAEVDILYAKVVDDSGL--VQKL 283
+ + L + + IL + + + G+ + + K+ D + + ++
Sbjct: 60 NIGTDALLEL-KPFVEEILEGKHLTLPFHGIGTFQG-----QVGFVKLADGDHVSALLEI 113
Query: 284 CDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYRMRQNPSSDTNSEKRSTFNAKDILE 343
+ + F + +++ + + K H+T M +K + E
Sbjct: 114 AETAKRTFQEKGILAGESRTF---KPHLTFMKLSKAPMLW-------KKGVRKIEPGLYE 163
Query: 344 SLGDFEFGETFVYCVHL-SQRHTHDMDGYFKPSAVISL 380
D FGE +Y + L S +GY+ + I +
Sbjct: 164 QFIDHRFGEEILYQIDLCSMLKKKQSNGYYHCESSIVI 201
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 65.5 bits (160), Expect = 8e-14
Identities = 22/81 (27%), Positives = 37/81 (45%)
Query: 82 DIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYS 141
DI Q IPK + F+IG G + +E +T T++ IPR + I + +
Sbjct: 8 DIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT 67
Query: 142 ERGIASAKRRLDLLLVFARKK 162
+ GI A+ + L+ K+
Sbjct: 68 KEGIEKARHEVLLISAEQDKR 88
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 58.3 bits (141), Expect = 5e-11
Identities = 15/61 (24%), Positives = 26/61 (42%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDLL 155
+P + ++IG KGS R++ E + +P DII + + AK L
Sbjct: 22 EVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLER 81
Query: 156 L 156
+
Sbjct: 82 V 82
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 53.1 bits (128), Expect = 1e-09
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRL 152
+I F+ +IG G+ RI+ + + IP + ++I +G+ AKR L
Sbjct: 10 NIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKREL 66
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 53.7 bits (129), Expect = 1e-09
Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQG---QTGDIIISSYSER 143
+K + ++P IIG KG+ +I E + + P + Q D I + E+
Sbjct: 13 ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 72
Query: 144 GIASAKRRLDLLL 156
+A+ + ++
Sbjct: 73 NTEAARDAILRIV 85
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 52.9 bits (127), Expect = 3e-09
Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 1/82 (1%)
Query: 76 SEDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTG-D 134
S I + + + IIG +G R+I E + P+ G +
Sbjct: 2 SSGSSGRIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPN 61
Query: 135 IIISSYSERGIASAKRRLDLLL 156
+ + + A + L
Sbjct: 62 CVTVTGLPENVEEAIDHILNLE 83
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 46.3 bits (110), Expect = 5e-07
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESE-TNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDL 154
IP + +IG KG R I E + P +G D ++ + AK++L
Sbjct: 22 SIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLH 81
Query: 155 LL 156
L
Sbjct: 82 LA 83
>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 = 49.1 bits (116), Expect = 2e-06
Identities = 55/320 (17%), Positives = 104/320 (32%), Gaps = 72/320 (22%)
Query: 19 DVVNPK-IEIIDGR-RYRVNPSWPSTYEDKSEADPYQRSEYDAGCPGGNQPYEEDDGGLS 76
+V N K + + + T K D + + + L+
Sbjct: 252 NVQNAKAWNAFNLSCKILL------TTRFKQVTDFLSAATT------THISLDHHSMTLT 299
Query: 77 EDEDLDI---YLGKDGQYKYQCHIP---KSFYPFIIGVKGSTKRRIESETNTQLSIPRQG 130
DE + YL Q +P + P + + + R T
Sbjct: 300 PDEVKSLLLKYLDCRPQ-----DLPREVLTTNPRRLSIIAESI-RDGLATWDNWKHVNCD 353
Query: 131 QTGDIIISSYSERGIASAKRRLDLLLVFARK--KIPYTHLLSI---------PMNVPN-- 177
+ II SS + A ++ D L VF IP T LLS+ M V N
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVF-PPSAHIP-TILLSLIWFDVIKSDVMVVVNKL 411
Query: 178 -----IQENFAKFKATVLSDFSRCRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVL 232
+++ + ++ S + + E+ + LH ++ V+ +
Sbjct: 412 HKYSLVEKQPKESTISIPSIYLELKVKLENEYA----LHRSI--------VDHYNIPKTF 459
Query: 233 QKCGNNIILPILRS---QRIKINLKGLEIMNDDPAEVDILYAKVVDDSGLVQKLCDDVVQ 289
+++I P L I +LK +E + +++ +D L QK+ D
Sbjct: 460 --DSDDLIPPYLDQYFYSHIGHHLKNIE-HPERMTLFRMVF---LDFRFLEQKIRHDSTA 513
Query: 290 YFISQHLIS-----KAYQKY 304
+ S +++ K Y+ Y
Sbjct: 514 WNASGSILNTLQQLKFYKPY 533
Score = 44.5 bits (104), Expect = 5e-05
Identities = 41/278 (14%), Positives = 97/278 (34%), Gaps = 39/278 (14%)
Query: 81 LDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSY 140
+D G+ QY+Y+ + F V + ++ + LS + + II+S
Sbjct: 7 MDFETGEH-QYQYKDILSVFEDAF---VDNFDCKDVQDMPKSILS---KEEIDHIIMSKD 59
Query: 141 SERGIASAKRRLDLLLVFARKKIPYTHLLSIPMNVPNIQENFAKFKATVLSDFSRCRGIE 200
+ G RL L+ ++++ + + ++ N+ KF + + R +
Sbjct: 60 AVSGT----LRLFWTLLSKQEEMVQKFVEEV------LRINY-KFLMSPIKTEQRQPSMM 108
Query: 201 ESLFQEP-GRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKGLEIM 259
++ E RL+ + +V R Q L++ L LR + + + G +
Sbjct: 109 TRMYIEQRDRLY-NDNQVFAKYNVSRLQPYLKLRQA-----LLELRPAK-NVLIDG---V 158
Query: 260 NDDPAEVDILYAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQKYDTVKMHVTLMNSKYR 319
+ V + K+ + ++++ + ++M L+ Y+
Sbjct: 159 LGSGKTW--VALDVCLSYKVQCKMDFKI--FWLN---LKNCNSPETVLEMLQKLL---YQ 208
Query: 320 MRQNPSSDTNSEKRSTFNAKDILESLGDFEFGETFVYC 357
+ N +S ++ I L + + C
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 44.2 bits (104), Expect = 3e-06
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGI 145
GQ Q +P ++G KG+T +RI+ T+T + P + + ++ E +
Sbjct: 5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPE-NV 63
Query: 146 ASAKRRLD 153
A+ ++
Sbjct: 64 DRAREEIE 71
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 44.2 bits (103), Expect = 4e-05
Identities = 20/143 (13%), Positives = 45/143 (31%), Gaps = 6/143 (4%)
Query: 74 GLSEDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTK--RRIESETNTQLSIPRQGQ 131
GL ++ + + +Y + G + I +ETNT + +P +
Sbjct: 13 GLPLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSV 72
Query: 132 TGDIIISSYSERGIASAKRRLDLLLVFARKKIPYTHLLSIPMNVPNIQENFAKFKATVLS 191
G + I +D AR + ++ M + ++ + +A V
Sbjct: 73 GGTTPDPFAQQVTITGYFGDVDR----ARMLMRRNCHFTVFMALSKMKMPLHELQAHVRQ 128
Query: 192 DFSRCRGIEESLFQEPGRLHITM 214
+ + + E + T
Sbjct: 129 NPIQNVEMSFVDAPEKNGIVTTY 151
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 102
Score = 39.1 bits (91), Expect = 2e-04
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESE-TNTQLSIPRQGQTGDIIISSYSERGIASAKRRLDL 154
P + FIIG KG +I + + D I ++ A+ +++
Sbjct: 32 AAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG---EDKITLEGPTEDVSVAQEQIEG 88
Query: 155 LL 156
++
Sbjct: 89 MV 90
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 37.5 bits (87), Expect = 0.001
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 4/82 (4%)
Query: 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD---IIISSYSE 142
G +P+ +IG G ++I+++ ++ + TG I +
Sbjct: 6 GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 65
Query: 143 RGIASAKRRLDLLLVFARKKIP 164
A R ++ LL R P
Sbjct: 66 -RCEHAARIINDLLQSLRSGPP 86
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
DNA-binding, nucleus, phosph ribonucleoprotein,
RNA-binding, RNA binding protein; NMR {Homo sapiens}
Length = 160
Score = 36.7 bits (85), Expect = 0.004
Identities = 12/66 (18%), Positives = 25/66 (37%)
Query: 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIA 146
K+ + + IIG KG + +++ E+ +++I II + I
Sbjct: 1 KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIF 60
Query: 147 SAKRRL 152
A +
Sbjct: 61 KAFAMI 66
Score = 31.7 bits (72), Expect = 0.20
Identities = 8/53 (15%), Positives = 15/53 (28%)
Query: 77 EDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQ 129
+ + +P S +IG G + I T Q+ +
Sbjct: 75 SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD 127
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 36.7 bits (85), Expect = 0.004
Identities = 20/95 (21%), Positives = 30/95 (31%), Gaps = 6/95 (6%)
Query: 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD----IIISSYSERGI 145
Q Q IP IIG KG +++ + + I +II+ E
Sbjct: 2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE-AQ 60
Query: 146 ASAKRRLDLLLVFARKKIPYT-HLLSIPMNVPNIQ 179
A+ R+ L P L + VP
Sbjct: 61 FKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASA 95
Score = 34.7 bits (80), Expect = 0.021
Identities = 10/57 (17%), Positives = 24/57 (42%)
Query: 78 DEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD 134
E+ ++ + + +P S +IG G T +++ T ++ +PR +
Sbjct: 72 KEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDE 128
>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 = 38.5 bits (89), Expect = 0.004
Identities = 52/336 (15%), Positives = 98/336 (29%), Gaps = 137/336 (40%)
Query: 54 RSEYDAGCPGGNQPYEED-DGGL---SEDEDLDIYL--GKDGQ-------------YK-Y 93
++ A +P+++ + L + + + G GQ Y+ Y
Sbjct: 124 KNYITA-RIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG--GQGNTDDYFEELRDLYQTY 180
Query: 94 QCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153
+ I+ T + R + +G L+
Sbjct: 181 H--------VLV-------GDLIKFSAETLSELIRTTLDAE----KVFTQG-------LN 214
Query: 154 LL--LVFARKKIPYTHLLSIPMNVPNI---QENFAKFKATVLSDFSRCRGIEESLFQEPG 208
+L L +LLSIP++ P I Q A + T + L PG
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQ--LAHYVVT-------AK----LLGFTPG 261
Query: 209 RLH--------ITMGMLM-----LADSVER-----DQAVEVLQKCGNNIILPILRSQRIK 250
L + G++ DS E +A+ VL G +R
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG-------VRCYEA- 313
Query: 251 INLKGLEIMNDDPAEVDILYAKVVDDS-----GL------VQKLCDDVVQYFISQ---HL 296
L +++DS G+ + L + VQ ++++ HL
Sbjct: 314 -------------YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL 360
Query: 297 ISKAYQKYDTVKMHVTLMNSKYRMRQN------PSS 326
+ ++ ++L+N +N P S
Sbjct: 361 PAGK-------QVEISLVNG----AKNLVVSGPPQS 385
Score = 33.9 bits (77), Expect = 0.11
Identities = 33/211 (15%), Positives = 63/211 (29%), Gaps = 87/211 (41%)
Query: 205 QEPGRLHITMGM-LMLADSVER---DQAVEVLQKC-GNNIILPILRSQRIKINLKGLEIM 259
QE G MGM L + ++A + G +I L+I+
Sbjct: 1627 QEQG-----MGMDLYKTSKAAQDVWNRADNHFKDTYGFSI----------------LDIV 1665
Query: 260 NDDPAEVDIL-----------------YAKVVDDSGLVQKLCDDVVQYFISQHLISKAYQ 302
++P + I + +VD +K+ + I++H S ++
Sbjct: 1666 INNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE-----INEHSTSYTFR 1720
Query: 303 KYDTVKMHVTLMNSKYRMRQN--PSSDTNSEKRSTFNAKDILESLG----DFEF-----G 351
+ + T Q P+ ++ F L+S G D F G
Sbjct: 1721 -SEKGLLSAT---------QFTQPALTLME--KAAFED---LKSKGLIPADATFAGHSLG 1765
Query: 352 ETFVYC--VHLSQRHTHDMDGYFKPSAVISL 380
E Y L+ +++ +
Sbjct: 1766 E---YAALASLA--------DVMSIESLVEV 1785
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 36.3 bits (84), Expect = 0.006
Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 4/71 (5%)
Query: 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD---IIISSYSE 142
G +P+ +IG G ++I+++ ++ + TG I +
Sbjct: 86 GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 145
Query: 143 RGIASAKRRLD 153
A R ++
Sbjct: 146 -RCEHAARIIN 155
Score = 35.5 bits (82), Expect = 0.010
Identities = 9/61 (14%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD-----IIISSYSERGIASAKRR 151
IP +IG G T ++++ ++ + + G + I + A
Sbjct: 8 IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY-KVQQACEM 66
Query: 152 L 152
+
Sbjct: 67 V 67
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1
Length = 94
Score = 34.7 bits (80), Expect = 0.006
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 88 DGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD-----IIISSYSE 142
G + IP S +IG G T ++++ ++ + + G + I+
Sbjct: 12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DP 70
Query: 143 RGIASAKR 150
+ AK
Sbjct: 71 YKVQQAKE 78
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 34.3 bits (79), Expect = 0.010
Identities = 8/49 (16%), Positives = 18/49 (36%)
Query: 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD 134
G + IP +IG G T ++++ ++ + + G
Sbjct: 9 GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT 57
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 34.8 bits (80), Expect = 0.022
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD---IIISSYSERGI 145
G + IP+ +IG G ++I+++ ++ T I+ +R
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR-A 59
Query: 146 ASAKRRLDLLL 156
A + LL
Sbjct: 60 QHAAEIITDLL 70
Score = 28.3 bits (63), Expect = 2.6
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 56 EYDAGCPGGNQPYEEDDGGLSEDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRR 115
AG PGG P G + ++ G ++ +P IIG G T +
Sbjct: 72 SVQAGNPGGPGPGGRGRGRGQGNWNMG---PPGGLQEFNFIVPTGKTGLIIGKGGETIKS 128
Query: 116 IESETNTQLSIPRQG 130
I ++ ++ + R
Sbjct: 129 ISQQSGARIELQRNP 143
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1 PDB: 2opu_A
Length = 92
Score = 32.8 bits (75), Expect = 0.029
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 94 QCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI-PRQGQTGD--IIISSYSERGIASAKR 150
+ +P FIIG G RI+ E+ ++ I P G + +++ E + SAKR
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE-SVQSAKR 76
Query: 151 RLD 153
LD
Sbjct: 77 LLD 79
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 32.3 bits (74), Expect = 0.039
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSI--PRQGQTGDIIISSYSERGIASAKRRLDL 154
IPK IIG G ++I E+ + I P +G II + ++ I +A+ L
Sbjct: 20 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN 79
Query: 155 LL 156
+
Sbjct: 80 SV 81
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1
PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*
Length = 73
Score = 31.5 bits (72), Expect = 0.053
Identities = 13/70 (18%), Positives = 26/70 (37%)
Query: 87 KDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIA 146
K+ + + IIG KG + +++ E+ +++I II + I
Sbjct: 1 KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIF 60
Query: 147 SAKRRLDLLL 156
A + L
Sbjct: 61 KAFAMIIDKL 70
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I domains, fragIle X mental retardation protein,
RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 32.7 bits (74), Expect = 0.082
Identities = 9/60 (15%), Positives = 19/60 (31%), Gaps = 1/60 (1%)
Query: 94 QCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRRLD 153
Q + + IG G+ ++ +I T I + + A+ L+
Sbjct: 7 QFIVREDLMGLAIGTHGANIQQARKVPGVT-AIDLDEDTCTFHIYGEDQDAVKKARSFLE 65
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 32.2 bits (73), Expect = 0.093
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 13/65 (20%)
Query: 105 IIGVKGSTKRRIESETNTQLSI---------PRQGQTGD----IIISSYSERGIASAKRR 151
+ G S + I+ ET ++ + P G+ I IS G+A+AK+
Sbjct: 33 VEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKL 92
Query: 152 LDLLL 156
+ LL
Sbjct: 93 CENLL 97
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein complex; HET: 5BU;
1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 32.5 bits (74), Expect = 0.14
Identities = 11/44 (25%), Positives = 18/44 (40%)
Query: 89 GQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQT 132
QY + IP IIG G T +++ ET + + +
Sbjct: 4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF 47
Score = 31.4 bits (71), Expect = 0.26
Identities = 9/49 (18%), Positives = 21/49 (42%)
Query: 86 GKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD 134
D + + +P S IIG G+T + I ++ + + ++ +
Sbjct: 99 NPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN 147
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA
recognition, complex E, KH domain, QUA2 homology; NMR
{Homo sapiens} SCOP: d.51.1.1
Length = 131
Score = 31.8 bits (72), Expect = 0.16
Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 25/96 (26%)
Query: 86 GKDGQYKYQCHIPKSFYP------FIIGVKGSTKRRIESETNTQLSIPRQGQTGD----- 134
+ + IP+ YP +IG +G+T + IE E N ++ I +G +
Sbjct: 2 AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR 61
Query: 135 --------------IIISSYSERGIASAKRRLDLLL 156
++++ + + A ++ +L
Sbjct: 62 KDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNIL 97
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 30.3 bits (69), Expect = 0.18
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI--PRQGQTGDIIISSYSERGIASAKR 150
Q IPK IIG G ++I E+ + I P +G II + ++ I +A+
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQY 68
Query: 151 RL 152
L
Sbjct: 69 LL 70
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 31.9 bits (72), Expect = 0.19
Identities = 7/39 (17%), Positives = 15/39 (38%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDI 135
+ +IG +G K I T T +++ + +
Sbjct: 10 VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIV 48
Score = 30.4 bits (68), Expect = 0.69
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 6/97 (6%)
Query: 75 LSEDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD 134
L ED+ L + K Q H K IIG G +R IE T+T +++
Sbjct: 83 LEEDQILVVVDLKQVVGDSQNH-LKRIKGRIIGEGGRARRTIEEMTDTYINV--GEYE-- 137
Query: 135 IIISSYSERGIASAKRRLDLLLVFARKKIPYTHLLSI 171
+ I E +AK+ +++L Y HL I
Sbjct: 138 VAIIGDYE-RAMAAKQAIEMLAEGRMHSTVYRHLERI 173
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 32.5 bits (75), Expect = 0.23
Identities = 8/59 (13%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRR 151
+P S +G G +++++ET +S + + + + A+
Sbjct: 569 ETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQ---VDEETFSVFAPTPSAMHEARDF 624
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 32.6 bits (75), Expect = 0.23
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 105 IIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRR 151
+IG K +I+ +T +++I G I I + +A+
Sbjct: 612 VIGPKRQMINQIQEDTGAEITI---EDDGTIYIGAADGPAAEAARAT 655
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 30.6 bits (69), Expect = 0.25
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 96 HIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD------IIISSYSERGIASAK 149
IP +IG G + I +T + I RQ II S + I AK
Sbjct: 12 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAK 70
Query: 150 R 150
+
Sbjct: 71 Q 71
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 32.5 bits (75), Expect = 0.27
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRR 151
+IP +IG G R I + T ++ I G + +S+ I +A
Sbjct: 572 ETINIPTDKIREVIGSGGKVIREIVATTGAKVDI---NDDGVVKVSASDGAKIKAAIDW 627
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 32.1 bits (74), Expect = 0.33
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 93 YQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAKRR 151
+ I +IG GS R + ET T + I G + I++ A RR
Sbjct: 562 HTIKINPDKIKDVIGKGGSVIRALTEETGTTIEI---EDDGTVKIAATDGEKAKHAIRR 617
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif, immune system; 2.00A
{Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 29.2 bits (66), Expect = 0.44
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQG 130
+ + +P++ I+G G T + T ++ I ++G
Sbjct: 2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing
factor, RNA binding protein; 2.30A {Pyrococcus
horikoshii} PDB: 3aev_B
Length = 219
Score = 31.2 bits (70), Expect = 0.45
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGDIIISSYSERGIASAK 149
IPK +IG KG TK+ IE T T+++I + I + +E +A K
Sbjct: 40 IPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWK 92
Score = 30.1 bits (67), Expect = 0.86
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 5/90 (5%)
Query: 67 PYEEDDGGLSEDEDLDIYLGKDGQYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI 126
E L+E E L+I D + + IIG KG T++ IE + +S+
Sbjct: 105 SPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV 164
Query: 127 PRQGQTGDIIISSYSERGIASAKRRLDLLL 156
G+T + I + I AK ++ L
Sbjct: 165 --YGKT--VAIIG-NPIQIEIAKTAIEKLA 189
>1we8_A Tudor and KH domain containing protein; structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 29.8 bits (67), Expect = 0.46
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQGQTGD-----IIISSYSERGIASAKRR 151
+P+ IIG G T R I + +++ ++ + I IS + +A+AK
Sbjct: 21 VPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-EVAAAKHL 79
Query: 152 LD 153
+
Sbjct: 80 IL 81
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 28.8 bits (65), Expect = 0.57
Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 3/52 (5%)
Query: 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSI-PRQGQTGD--IIIS 138
++ IP IIG +G+ I + Q+ I + D + I+
Sbjct: 4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA
binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 29.9 bits (67), Expect = 0.67
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 97 IPKSFYP------FIIGVKGSTKRRIESETNTQLSIPRQG 130
+P YP I+G +G T +++E+ET ++ + +G
Sbjct: 8 VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKG 47
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding
motif, protein/RNA structure, RNA binding protein/RNA
complex; 2.40A {Homo sapiens} SCOP: d.51.1.1
Length = 87
Score = 28.8 bits (65), Expect = 0.72
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 90 QYKYQCHIPKSFYPFIIGVKGSTKRRIESETNTQLSIPRQG 130
+ + +P++ I+G G T + T ++ I ++G
Sbjct: 2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42
>2h2b_A Tight junction protein ZO-1; PDZ domain, phage derived high
affinity ligand, cell adhesio; 1.60A {Homo sapiens} PDB:
2h2c_A 2h3m_A 2rrm_A
Length = 107
Score = 28.5 bits (64), Expect = 1.2
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 221 DSVERDQAVEVLQKCGNNIILPILR 245
D+VE AV+ L+K G N + I R
Sbjct: 71 DNVEHAFAVQQLRKSGKNAKITIRR 95
>1n7t_A 99-MER peptide of densin-180-like protein; PDZ domain, C-terminal
peptide complex, high affnity ligand, signaling protein;
NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2h3l_A
Length = 103
Score = 28.2 bits (63), Expect = 1.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 221 DSVERDQAVEVLQKCGNNIILPILR 245
++E QAV +L+ N + L I+R
Sbjct: 75 INIEHGQAVSLLKTFQNTVELIIVR 99
>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone,
H2A/H2B, tata-DNA, transcription initiation, NC2,
negative cofactor, structural genomics, PSI; 2.62A {Homo
sapiens} SCOP: a.22.1.3
Length = 179
Score = 29.0 bits (64), Expect = 1.7
Identities = 5/25 (20%), Positives = 13/25 (52%)
Query: 328 TNSEKRSTFNAKDILESLGDFEFGE 352
N ++ T + + ++++L FG
Sbjct: 61 CNKSEKKTISPEHVIQALESLGFGS 85
>1rgw_A ZAsp protein; PDZ, cypher, oracle, muscle, Z-DISK, sarcomere,
structural protein; NMR {Homo sapiens} SCOP: b.36.1.1
PDB: 1wjl_A
Length = 85
Score = 27.6 bits (62), Expect = 2.1
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 220 ADSVERDQAVEVLQKCGNNIILPILRSQR 248
D++ +A ++ N+ L + +S+R
Sbjct: 57 TDTMTHLEAQNKIKSASYNLSLTLQKSKR 85
>1mfg_A ERB-B2 interacting protein; PDZ domain, protein-peptide complex,
erbin., signaling protein; 1.25A {Homo sapiens} SCOP:
b.36.1.1 PDB: 1mfl_A
Length = 95
Score = 27.8 bits (62), Expect = 2.2
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 221 DSVERDQAVEVLQKCGNNIILPILR 245
++E QAV +L+ N + L I+R
Sbjct: 67 INIEHGQAVSLLKTFQNTVELIIVR 91
>2pa1_A PDZ and LIM domain protein 2; PDZ domain, structural genomics,
structural genomics consort metal binding protein; 1.70A
{Homo sapiens} PDB: 3pdv_A
Length = 87
Score = 27.2 bits (61), Expect = 2.7
Identities = 4/30 (13%), Positives = 14/30 (46%)
Query: 220 ADSVERDQAVEVLQKCGNNIILPILRSQRI 249
A+ + +A +++ + + L + R +
Sbjct: 58 AEGMLHAEAQSKIRQSPSPLRLQLDRITSL 87
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 26.9 bits (60), Expect = 2.8
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 97 IPKSFYPFIIGVKGSTKRRIESETNTQLSI--PRQGQTGDIIISSYSERGIASAKRRLD 153
IP + IIG +G+ I + Q+ I P +G +G + + S I+ A+ ++
Sbjct: 12 IPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLIN 70
>2csj_A TJP2 protein; PDZ domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: b.36.1.1
Length = 117
Score = 27.4 bits (61), Expect = 3.1
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 221 DSVERDQAVEVLQKCGNNIILPILRSQRIKIN 252
+ V AV+ L+K G + + R +++++
Sbjct: 78 EDVLHSFAVQQLRKSGKIAAIVVKRPRKVQVA 109
>2djt_A Unnamed protein product; PDZ domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 104
Score = 27.3 bits (61), Expect = 3.1
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 208 GRLHITMGMLMLA------DSVERDQAVEVLQKCGNNIILPILRSQR 248
GRL + G L+L + QAVE ++ G + L I R
Sbjct: 55 GRLEV--GDLVLHINGESTQGLTHAQAVERIRAGGPQLHLVIRRPLS 99
>2w4f_A Protein LAP4; structural protein, phosphoprotein, UBL conjugation,
leucine-rich repeat, alternative splicing, cytoplasm,
circletail, coiled coil; 1.30A {Homo sapiens}
Length = 97
Score = 26.9 bits (60), Expect = 3.7
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 226 DQAVEVLQKCGNNIILPILRSQRIKI 251
+AVE L+ G + + + R + +
Sbjct: 72 HEAVEALRGAGTAVQMRVWRERETSV 97
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 26.9 bits (60), Expect = 3.9
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 28 IDGRRYRVNPSWPSTYEDKSEADPYQRSEYD 58
I G R RV S + + P +R +
Sbjct: 62 ICGSRVRVELSTGMPRRSRFDRPPARRKLLE 92
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 93
Score = 26.7 bits (59), Expect = 3.9
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 328 TNSEKRSTFNAKDILESLGDFEFGE 352
+ EKR T N +DIL ++ F
Sbjct: 55 CHQEKRKTINGEDILFAMSTLGFDS 79
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_B
Length = 128
Score = 27.3 bits (60), Expect = 4.2
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 328 TNSEKRSTFNAKDILESLGDFEFGE 352
+ + T AKDIL++L + +F
Sbjct: 56 AHKQNHKTITAKDILQTLTELDFES 80
>1x5q_A LAP4 protein; PDZ domain, scribble homolog protein, hscrib,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.36.1.1
Length = 110
Score = 26.9 bits (60), Expect = 5.1
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 226 DQAVEVLQKCGNNIILPILR 245
+AVE L+ G + + + R
Sbjct: 84 HEAVEALRGAGTAVQMRVWR 103
>1cpy_A Serine carboxypeptidase; hydrolase (carboxypeptidase); HET: NAG;
2.60A {Saccharomyces cerevisiae} SCOP: c.69.1.5 PDB:
1wpx_A* 1ysc_A*
Length = 421
Score = 28.0 bits (63), Expect = 5.3
Identities = 12/72 (16%), Positives = 19/72 (26%), Gaps = 8/72 (11%)
Query: 243 ILRSQRIKINLKGLEIMN-------DDPAEVDILYAKVVDDSGLVQKLCDDVVQYFIS-Q 294
IL + NL + I N + + + S L + C +
Sbjct: 159 ILSHKDRNFNLTSVLIGNGLTDPLTQYNYYEPMACGEGGEPSVLPSEECSAMEDSLERCL 218
Query: 295 HLISKAYQKYDT 306
LI Y
Sbjct: 219 GLIESCYDSQSV 230
>1vb7_A PDZ and LIM domain 2; PDZ domain PDZ-LIM protein, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, unknown function; NMR {Mus musculus}
SCOP: b.36.1.1
Length = 94
Score = 26.5 bits (59), Expect = 5.5
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 220 ADSVERDQAVEVLQKCGNNIILPILRSQR 248
A+++ +A +++ + + L + RS
Sbjct: 62 AENMLHAEAQSKIRQSASPLRLQLDRSSG 90
>1vbg_A Pyruvate,orthophosphate dikinase; transferase, maize, riken
structural genomics/proteomics INI RSGI, structural
genomics; 2.30A {Zea mays} SCOP: c.1.12.2 c.8.1.1
d.142.1.5 PDB: 1vbh_A*
Length = 876
Score = 28.2 bits (63), Expect = 5.7
Identities = 18/68 (26%), Positives = 23/68 (33%), Gaps = 13/68 (19%)
Query: 196 CRGIEESLFQEPGRLHITMGMLMLADSVERDQAVEVLQKCGNNIILPILRSQRIKINLKG 255
CR E F R+ M+M R QA++ L LP RS I
Sbjct: 563 CR-TEHMFFASDERIKAVRQMIMAPTLELRQQALDRL--------LPYQRSDFEGI---- 609
Query: 256 LEIMNDDP 263
M+ P
Sbjct: 610 FRAMDGLP 617
>2fcf_A Multiple PDZ domain protein; adaptor molecule, protein linker,
structural genomics, struc genomics consortium, SGC,
structural protein; 1.76A {Homo sapiens} SCOP: b.36.1.1
Length = 103
Score = 26.6 bits (59), Expect = 6.6
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 208 GRLHITMGMLMLA------DSVERDQAVEVLQKCGNNIILPILRSQRIKI 251
G L G ++ +QAVE ++K GN ++ + ++
Sbjct: 56 GTLKP--GDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL 103
>3cyy_A Tight junction protein ZO-1; protein-ligand complex, cell junction,
membrane, phosphoprot domain, tight junction,
transmembrane; 2.40A {Homo sapiens}
Length = 92
Score = 26.2 bits (58), Expect = 7.5
Identities = 6/47 (12%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 208 GRLHITMGMLMLA------DSVERDQAVEVLQKCGNNIILPILRSQR 248
G + G ++L +++ A ++++ + + + R +R
Sbjct: 40 GNIQE--GDVVLKINGTVTENMSLTDAKTLIERSKGKLKMVVQRDER 84
>2o2t_A Multiple PDZ domain protein; structural protein, structural
genomics, structural genomics consortium, SGC; 2.70A
{Homo sapiens}
Length = 117
Score = 26.2 bits (58), Expect = 8.3
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 219 LADSVERDQAVEVLQKCGNNIILPILR 245
L ++ QA+ +LQK + + L I R
Sbjct: 82 LDQTITHQQAISILQKAKDTVQLVIAR 108
>1d5g_A Human phosphatase HPTP1E; protein-peptide complex, hydrolase; NMR
{Homo sapiens} SCOP: b.36.1.1 PDB: 3lnx_A 3lny_A 3pdz_A
1vj6_A 1gm1_A 1ozi_A
Length = 96
Score = 26.0 bits (58), Expect = 8.5
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 208 GRLHITMGMLMLA------DSVERDQAVEVLQKCGNNIILPILRSQ 247
GR+H G +LA + QAVE L+ G + L + + Q
Sbjct: 50 GRIHK--GDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQ 93
>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase,
protein translocation, protein transport; 2.00A
{Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A
3bxz_A*
Length = 853
Score = 27.5 bits (62), Expect = 8.7
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 12/37 (32%)
Query: 9 AQRTKHLF----DYDVVNPKIEIID--------GRRY 33
A R LF DY V + ++ I+D GRR+
Sbjct: 305 ALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRW 341
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
0.319 0.137 0.399
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,846,917
Number of extensions: 349434
Number of successful extensions: 766
Number of sequences better than 10.0: 1
Number of HSP's gapped: 760
Number of HSP's successfully gapped: 76
Length of query: 380
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 285
Effective length of database: 4,049,298
Effective search space: 1154049930
Effective search space used: 1154049930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (25.9 bits)