RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12243
(278 letters)
>3cu0_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
3; glcat-I, glycosyltransferase, heparan sulfate
biosynthesis, glycoprotein; HET: GAL UDP; 1.90A {Homo
sapiens} SCOP: c.68.1.7 PDB: 1kws_A* 1fgg_A*
Length = 281
Score = 263 bits (673), Expect = 3e-88
Identities = 96/234 (41%), Positives = 128/234 (54%), Gaps = 20/234 (8%)
Query: 31 KDLPIIYFITPTYPRREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIP 90
IY +TPTY R Q AEL RL QTL +P LHW++ +D +P++S LL G+
Sbjct: 18 GSHMTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLL 77
Query: 91 YTHIASPMPPVYRTNNAVP----PRGVANRRAALAWIRS-------------YVKSGVVY 133
+TH+ P R P PRGV R AL W+R GVVY
Sbjct: 78 FTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVY 137
Query: 134 FGDDDNTFDLKLFDEIRDTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSWPAKRKFPV 193
F DDDNT+ +LF+E+R T+ +S++PVGL+G P ++ G V+GF +W R FPV
Sbjct: 138 FADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPV 197
Query: 194 DMAGFAVNVDLILKHPNATMPYKA--GYEEDRFISSLGVKLSDIEPKANNCSEV 245
DMAGFAV + L+L PNA A G+ E +S L V D+EP+A NC+ V
Sbjct: 198 DMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHL-VDPKDLEPRAANCTRV 250
>2d0j_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
2; rossmann-like fold, glucuronyltransferase; 2.00A
{Homo sapiens}
Length = 246
Score = 260 bits (666), Expect = 1e-87
Identities = 92/221 (41%), Positives = 132/221 (59%), Gaps = 11/221 (4%)
Query: 33 LPIIYFITPTYPRREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIPYT 92
LP IY ITPTY R Q AELTRL T + LHWI+ +D S ++S L + G+P T
Sbjct: 2 LPTIYAITPTYSRPVQKAELTRLANTFRQVAQLHWILVEDAAARSELVSRFLARAGLPST 61
Query: 93 HIASPMPPVYRTNNAVPPRGVANRRAALAWIRSYV-----KSGVVYFGDDDNTFDLKLFD 147
H+ P P Y+ PR R A LAW+R + GV++F DDDNT+ L+LF
Sbjct: 62 HLHVPTPRRYKR--PGLPRATEQRNAGLAWLRQRHQHQRAQPGVLFFADDDNTYSLELFQ 119
Query: 148 EIRDTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILK 207
E+R T+K+S++PVGL+G P++ G V+G++ W A R F +DMAGFAV++ +IL
Sbjct: 120 EMRTTRKVSVWPVGLVGGRRYERPLVENGKVVGWYTGWRADRPFAIDMAGFAVSLQVILS 179
Query: 208 HPNATMPY---KAGYEEDRFISSLGVKLSDIEPKANNCSEV 245
+P A + G +E F+ + + ++EPKANNC++V
Sbjct: 180 NPKAVFKRRGSQPGMQESDFLKQI-TTVEELEPKANNCTKV 219
>1v84_A Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase
1; glycoprotein, glycocyltransferase, HNK-1 epitop; HET:
GAL NDG NAG TLA UDP; 1.82A {Homo sapiens} SCOP: c.68.1.7
PDB: 1v83_A* 1v82_A*
Length = 253
Score = 258 bits (660), Expect = 9e-87
Identities = 92/226 (40%), Positives = 133/226 (58%), Gaps = 14/226 (6%)
Query: 33 LPIIYFITPTYPRREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIPYT 92
LP I+ +TPTY R Q AELTR+ TL+H+PNLHW+V +D + +P+ + LL G+ YT
Sbjct: 2 LPTIHVVTPTYSRPVQKAELTRMANTLLHVPNLHWLVVEDAPRRTPLTARLLRDTGLNYT 61
Query: 93 HIASPMPPVYRTNNAVP----PRGVANRRAALAWIRSYV-----KSGVVYFGDDDNTFDL 143
H+ P Y+ PRG R AL W+R + GVVYF DDDNT+ L
Sbjct: 62 HLHVETPRNYKLRGDARDPRIPRGTMQRNLALRWLRETFPRNSSQPGVVYFADDDNTYSL 121
Query: 144 KLFDEIRDTKKISMFPVGLIGSYGISSPVLRK-GNVIGFFDSWPAKRKFPVDMAGFAVNV 202
+LF+E+R T+++S++PV +G +P + G V+ + + R F +DMAGFAVN+
Sbjct: 122 ELFEEMRSTRRVSVWPVAFVGGLRYEAPRVNGAGKVVRWKTVFDPHRPFAIDMAGFAVNL 181
Query: 203 DLILKHPNATMPY---KAGYEEDRFISSLGVKLSDIEPKANNCSEV 245
LIL+ A K GY+E + L V L+D+EPKA NC+++
Sbjct: 182 RLILQRSQAYFKLRGVKGGYQESSLLREL-VTLNDLEPKAANCTKI 226
>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 = 49.5 bits (117), Expect = 6e-07
Identities = 45/326 (13%), Positives = 89/326 (27%), Gaps = 106/326 (32%)
Query: 8 DQTHDPITCTTSFKDLR-LFHNVVKDLPIIYFITPTYPRREQVAELTRLGQTLMHIPN-- 64
+ P T + + R +N + Y + R + +L + L N
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAK-YNV----SRLQPYLKLRQALLELRPAKNVL 154
Query: 65 LH--------WIVA----DDTLQC---------------SP-----MISALLPKFGIPYT 92
+ W+ +QC SP M+ LL + +T
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 93 HIASPMPPVYRTNNAVPPRGVANRRAALAWIRSYVKSGVVYFGDDD-------NTFDLK- 144
+ + +++ R L + Y +V + N F+L
Sbjct: 215 SRSDHSSNIKLRIHSIQAE----LRRLLKS-KPYENCLLVL---LNVQNAKAWNAFNLSC 266
Query: 145 ----------LFDEI--RDTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSW------- 185
+ D + T IS+ S L V +
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHH---------SMTLTPDEVKSLLLKYLDCRPQD 317
Query: 186 -P--AKRKFPVDMAGFAVNVDLILKHPNATMPYKAGYEEDRFISSLGVKLSDIEPKANNC 242
P P ++ A + I +K D+ + + L+ +EP
Sbjct: 318 LPREVLTTNPRRLSIIA---ESIRDGLATWDNWKH-VNCDKLTTIIESSLNVLEP----- 368
Query: 243 SEVSEN-----IF----KVPSSNVMS 259
+E + +F +P+ ++S
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTI-LLS 393
Score = 33.7 bits (76), Expect = 0.065
Identities = 34/265 (12%), Positives = 74/265 (27%), Gaps = 86/265 (32%)
Query: 24 RLFHNVVKDLPIIYFITPTYPRREQVA--ELTRLGQTLMHIPNLHWIVADD--------- 72
+L + + + + R EL RL ++ + L +V +
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL--LVLLNVQNAKAWNA 261
Query: 73 -TLQCSPMISALLPKFGIPYTHIASPMPPVYRTNNAVPPRGVANRRAALAWIRSYVKSGV 131
L C ++ T T + V + +A +
Sbjct: 262 FNLSCKILL-----------T-----------TRF----KQVTDFLSAATTTHISLDHHS 295
Query: 132 VYFGDDD------NTFDLKLFDEIRDTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSW 185
+ D+ D + D R+ + + +I +R G + +D+W
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE------SIRDG--LATWDNW 347
Query: 186 --------------------PA--KRKFPVDMAGFAVNVDLILKHPNATMP---YKAGYE 220
PA ++ F ++ F + + P + +
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMF-DRLSVFPPSAHI----PTILLSLIWFDVIKS 402
Query: 221 EDRFISSLGVKLSDIE--PKANNCS 243
+ + + K S +E PK + S
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTIS 427
>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 = 34.3 bits (78), Expect = 0.052
Identities = 55/258 (21%), Positives = 99/258 (38%), Gaps = 75/258 (29%)
Query: 10 THDPITCT----TS--FKDLRL---FHNVVKDLPIIYFITPT--YPRREQ---VAELTRL 55
+H + T+ F +L F+ K LP PT + ++ AEL +
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFN---KILP-----EPTEGFAADDEPTTPAEL--V 61
Query: 56 GQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIPY-----TH-IASPMPPVYRTN---- 105
G+ L ++ +L + Q +++ L +F Y H +A+ + T
Sbjct: 62 GKFLGYVSSL--VEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT 119
Query: 106 -----NAVPPRGVANR----RAALAWIRSYVKSGV--VY--FGDDDNTFDLKLFDEIRDT 152
N + R +A R ++ A R+ V G + FG NT D F+E+RD
Sbjct: 120 KELIKNYITARIMAKRPFDKKSNSALFRA-VGEGNAQLVAIFGGQGNTDDY--FEELRDL 176
Query: 153 KKISMFPVG-LIGSYGISSPVLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLI--LKHP 209
+ VG LI S+ L + + A++ F G +++ L++P
Sbjct: 177 YQTYHVLVGDLIKF---SAETLSELI----RTTLDAEKVFT---QGL----NILEWLENP 222
Query: 210 NATMPYKAGYEEDRFISS 227
+ T P ++D +S
Sbjct: 223 SNT-P-----DKDYLLSI 234
Score = 30.8 bits (69), Expect = 0.54
Identities = 29/164 (17%), Positives = 48/164 (29%), Gaps = 70/164 (42%)
Query: 102 YRTNNAVPPRGVANR-----RAALAW-----IRSYVKSGVVYFG---------------- 135
Y+T+ A + V NR + + + + + ++FG
Sbjct: 1636 YKTSKAA--QDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIF 1693
Query: 136 ---DDDNTFDLKLFDEIRDTKKISMF--PVGLIGSYGISSPVLRKGNVIGFFDSWPAKRK 190
D K+F EI + F GL+ + + P L
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL----------------- 1736
Query: 191 FPVDMAGFAVNVDLILKH-----PNATMPYKAGYEEDRFISSLG 229
++ A F LK +AT AG+ SLG
Sbjct: 1737 TLMEKAAFED-----LKSKGLIPADATF---AGH-------SLG 1765
>2qee_A BH0493 protein; amidohydrolase, structural genomics, PSI-2, protein
structure initiative; 1.65A {Bacillus halodurans c-125}
PDB: 3hka_A* 2q6e_A 3hk5_A* 3hk7_A* 3hk8_A* 3hk9_A*
2q08_A* 2pnk_A*
Length = 437
Score = 30.8 bits (69), Expect = 0.49
Identities = 18/145 (12%), Positives = 40/145 (27%), Gaps = 18/145 (12%)
Query: 24 RLFHNVVKDLPIIYFITPTYPRREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISAL 83
N V + P+ T + E+ + H++VA+ +
Sbjct: 13 EKVKNAVNNQPVTDMHTHLFS--PNFGEILLWDID--ELLTYHYLVAE-----------V 57
Query: 84 LPKFGIPYTHIASPMPPVYRTNNAVPPRGVANRRAALAWIRSYVKSGVVYFGDDDNTFDL 143
+ + + + + R R V + + G D T DL
Sbjct: 58 MRWTDVSIEAFWAMSKR--EQADLIWEELFIKRSPVSEACR-GVLTCLQGLGLDPATRDL 114
Query: 144 KLFDEIRDTKKISMFPVGLIGSYGI 168
+++ E K ++ +
Sbjct: 115 QVYREYFAKKTSEEQVDTVLQLANV 139
>1ear_A Urease accessory protein UREE; chaperone, putative NI-chaperone,
urease operon; 1.7A {Bacillus pasteurii} SCOP: b.107.1.1
d.58.38.1 PDB: 1eb0_A
Length = 147
Score = 29.1 bits (65), Expect = 0.89
Identities = 10/60 (16%), Positives = 22/60 (36%), Gaps = 7/60 (11%)
Query: 45 RREQVAELTRLGQTLMHIPNLHW--IVADDTLQCSP--MISALLPKFGIPYTHIASPMPP 100
+ + + E+ ++ I N H I+ DD + + L+ + G+ Y
Sbjct: 82 KPQTMQEMGKMA---FEIGNRHTMCIIEDDEILVRYDKTLEKLIDEVGVSYEQSERRFKE 138
>1qqp_1 FMDV, protein (genome polyprotein); heparan sulphate,
virus-receptor interactions/protein carbohydrate
interactions; HET: IDX SGN IDS; 1.90A {Foot-and-mouth
disease virus} SCOP: b.121.4.1 PDB: 1bbt_1 1fod_1
Length = 213
Score = 27.4 bits (60), Expect = 4.1
Identities = 10/38 (26%), Positives = 13/38 (34%)
Query: 84 LPKFGIPYTHIASPMPPVYRTNNAVPPRGVANRRAALA 121
L + +PYT + VY V N R L
Sbjct: 112 LTRLALPYTAPHRVLATVYNGECRYSRNAVPNLRGDLQ 149
>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 = 26.5 bits (57), Expect = 7.0
Identities = 12/66 (18%), Positives = 17/66 (25%), Gaps = 37/66 (56%)
Query: 148 EIRDTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILK 207
E + KK+ S + + DS PA A+
Sbjct: 18 EKQALKKLQ-------ASLKLYAD-----------DSAPA----------LAI------- 42
Query: 208 HPNATM 213
ATM
Sbjct: 43 --KATM 46
>3iac_A Glucuronate isomerase; IDP02065, structural genom center for
structural genomics of infectious diseases, CSGI; 2.22A
{Salmonella typhimurium}
Length = 473
Score = 27.3 bits (60), Expect = 7.1
Identities = 4/13 (30%), Positives = 6/13 (46%)
Query: 24 RLFHNVVKDLPII 36
L+H +PI
Sbjct: 21 TLYHKYAAPMPIY 33
>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase,
nuclease, double strand DNA repair, protein-DNA CO
hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus
subtilis} PDB: 3u44_B*
Length = 1166
Score = 27.4 bits (60), Expect = 7.3
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 45 RREQVAELTRLGQTLMHIPNLHW----IVADDTLQCSPMISALLPKFGIPYT 92
RR ++ + R L+ + I+A M+ + + IPY
Sbjct: 320 RRAELEGIAREIHALVREKGYRYKDVAILARQPEDYKDMVKEVFADYEIPYF 371
>3gwq_A D-serine deaminase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, lyase; HET: MSE; 2.00A {Burkholderia xenovorans
LB400}
Length = 426
Score = 27.0 bits (59), Expect = 7.7
Identities = 17/130 (13%), Positives = 37/130 (28%), Gaps = 8/130 (6%)
Query: 5 MQLDQTHDPITCTTSFKDLRLFHNVVKDLPIIYFITPTYPRREQVAELTRLGQTLMHIPN 64
QL+ IT T+ + +H V + + + + L+ P
Sbjct: 89 RQLETGAWGITLATAHQVRAAYHGGVSRVLMANQLVGRRN--------MMMVAELLSDPE 140
Query: 65 LHWIVADDTLQCSPMISALLPKFGIPYTHIASPMPPVYRTNNAVPPRGVANRRAALAWIR 124
+ D+++ + + P RT + A A +
Sbjct: 141 FEFFCLVDSVEGVEQLGEFFKSVNKQLQVLLELGVPGGRTGVRDAAQRNAVLEAITRYPD 200
Query: 125 SYVKSGVVYF 134
+ +GV +
Sbjct: 201 TLKLAGVELY 210
>3hxj_A Pyrrolo-quinoline quinone; all beta protein. incomplete 8-blade
beta-propeller., struct genomics, PSI-2, protein
structure initiative; 2.00A {Methanococcus maripaludis}
Length = 330
Score = 26.6 bits (59), Expect = 8.8
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 127 VKSGVVYFGDDDNTFDLKLFDEIRDTKKISMFPVGLIGSYGISSPVLRKGNVI 179
+ +YFG D L + D + F GS+ I++PV+ + I
Sbjct: 263 GNTDTIYFGSYDGH--LYAIN--PDGTEKWNFET---GSWIIATPVIDENGTI 308
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
0.322 0.138 0.423
Gapped
Lambda K H
0.267 0.0519 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,358,440
Number of extensions: 262831
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 18
Length of query: 278
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 186
Effective length of database: 4,133,061
Effective search space: 768749346
Effective search space used: 768749346
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 (21.9 bits)
S2: 57 (26.2 bits)