RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10096
(125 letters)
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 94.3 bits (234), Expect = 5e-25
Identities = 46/74 (62%), Positives = 59/74 (79%)
Query: 1 MIDTYKKMWRYMENKKPSVFVSTYKEGIDRVLEGNYAFLMESTMLDYIVQRNCNLTQIGG 60
I TY KMW +M +++ SV V + +EGI RVL +YAFLMEST ++++ QRNCNLTQIGG
Sbjct: 151 KISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGG 210
Query: 61 LLDSKGYGIATPMG 74
L+DSKGYG+ TPMG
Sbjct: 211 LIDSKGYGVGTPMG 224
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 90.6 bits (224), Expect = 1e-22
Identities = 43/78 (55%), Positives = 54/78 (69%), Gaps = 3/78 (3%)
Query: 1 MIDTYKKMWRYMENKKPSVFVSTYKEGIDRVL--EGNYAFLMESTMLDYIVQR-NCNLTQ 57
I + KMW YM + +PSVFV T EG+ RV +G YA+L+ESTM +YI QR C+ +
Sbjct: 654 KIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMK 713
Query: 58 IGGLLDSKGYGIATPMGH 75
+GG LDSKGYGIATP G
Sbjct: 714 VGGNLDSKGYGIATPKGS 731
>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor,
membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus
norvegicus} SCOP: c.94.1.1
Length = 312
Score = 87.2 bits (215), Expect = 6e-22
Identities = 46/76 (60%), Positives = 59/76 (77%)
Query: 1 MIDTYKKMWRYMENKKPSVFVSTYKEGIDRVLEGNYAFLMESTMLDYIVQRNCNLTQIGG 60
I TY KMW +M +++ SV V + +EGI RVL +YAFLMEST ++++ QRNCNLTQIGG
Sbjct: 185 KISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGG 244
Query: 61 LLDSKGYGIATPMGHS 76
L+DSKGYG+ TPMG
Sbjct: 245 LIDSKGYGVGTPMGSP 260
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 80.8 bits (199), Expect = 7e-20
Identities = 42/76 (55%), Positives = 53/76 (69%), Gaps = 3/76 (3%)
Query: 2 IDTYKKMWRYMENKKPSVFVSTYKEGIDRVLEGN--YAFLMESTMLDYIVQRN-CNLTQI 58
I + KMW YM + +PSVFV T EG+ RV + YA+L+ESTM +YI QR C+ ++
Sbjct: 152 IAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKV 211
Query: 59 GGLLDSKGYGIATPMG 74
GG LDSKGYGIATP G
Sbjct: 212 GGNLDSKGYGIATPKG 227
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 80.5 bits (198), Expect = 1e-19
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 1 MIDTYKKMWRYMENKKPSVF-VSTYKEGIDRVLEGNYAFLMESTMLDYIVQRN--CNLTQ 57
Y +MWR + S V + GI +V GNYAF+ ++ +L+Y+ + C+
Sbjct: 153 RDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYT 212
Query: 58 IGGLLDSKGYGIATPMG 74
+G + +GYGIA G
Sbjct: 213 VGNTVADRGYGIALQHG 229
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A*
1pb8_A 1pb9_A
Length = 292
Score = 54.3 bits (130), Expect = 5e-10
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 3 DTYKKMWRYMENKKPSVFVSTYKEGIDRVLEGN-YAFLMESTMLDYIVQRNCNLTQIGGL 61
M+R+ME + E I V + +AF+ +S +L++ + C+L G L
Sbjct: 189 VELSTMYRHMEKHN----YESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGEL 244
Query: 62 LDSKGYGIATPMG 74
G+GI
Sbjct: 245 FFRSGFGIGMRKD 257
>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 = 34.4 bits (78), Expect = 0.006
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 17/67 (25%)
Query: 4 TYKKMWRYMENKKPSVFVSTYKEGIDRVLEGNYAFLMES----------TMLDYIVQRN- 52
T + W + ++ ++ ++ VL NY FLM YI QR+
Sbjct: 64 TLRLFWTLLSKQE-----EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR 118
Query: 53 -CNLTQI 58
N Q+
Sbjct: 119 LYNDNQV 125
Score = 25.2 bits (54), Expect = 7.4
Identities = 16/123 (13%), Positives = 41/123 (33%), Gaps = 25/123 (20%)
Query: 5 YKKMWRYMENKK--PSVFVSTYKEGIDRVLEGNYAFLMESTMLDYIVQRNCNLT-QIGGL 61
+ ++ + + + + + I + L + ++++ ++ T I +
Sbjct: 375 FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE---KQPKESTISIPSI 431
Query: 62 -LDSKGYGIATPMGHSGLVGH---IACW--------RWDDYFWSYNNVHSSGHWRDMEEI 109
L+ K H +V H + D YF+S+ H ++ I
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH-------LKNI 484
Query: 110 QHE 112
+H
Sbjct: 485 EHP 487
>3g3d_A UMP synthase, uridine 5'-monophosphate synthase; C-terminal domain,
orotidine 5'-monophosphate decarboxylase, human,
5-fluoro-6-azido-UMP; HET: 5FU; 1.70A {Homo sapiens}
PDB: 3bvj_A* 3mw7_A* 2p1f_A 2eaw_A 3bgg_A* 3bgj_A*
Length = 312
Score = 27.7 bits (61), Expect = 1.2
Identities = 20/128 (15%), Positives = 38/128 (29%), Gaps = 22/128 (17%)
Query: 6 KKMWRYMENKKPSVFVS----TYKEGID--RVLEGNYAFLMESTMLDY-------IVQRN 52
K+ R M+ K+ ++ +S +E + L + L T +D +++
Sbjct: 73 SKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICML--KTHVDILNDFTLDVMKEL 130
Query: 53 CNLTQIGGL---LDSKGYGIATPMGHSGLVGHIACWRWDDYFWSYNNVHSSGHWRDMEEI 109
L + D K I + G W D N H ++ +
Sbjct: 131 ITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLV----NAHVVPGSGVVKGL 186
Query: 110 QHETQGKK 117
Q
Sbjct: 187 QEVGLPLH 194
>3opt_A DNA damage-responsive transcriptional repressor R; RPH1, histone
demethylase, catalytic core, oxidoreductase; HET: DNA
AKG; 2.20A {Saccharomyces cerevisiae} PDB: 3opw_A*
Length = 373
Score = 26.9 bits (58), Expect = 2.1
Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 3/53 (5%)
Query: 54 NLTQIGGLLDSKGY---GIATPMGHSGLVGHIACWRWDDYFWSYNNVHSSGHW 103
N+ ++ +LD G+ ++GL W +D N G
Sbjct: 200 NVAKLPNILDHMETKVPGVNDSYLYAGLWKASFSWHLEDQDLYSINYIHFGAP 252
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix
two-turns helix; 2.00A {Sulfolobus shibatae} SCOP:
a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A*
1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Length = 471
Score = 26.3 bits (57), Expect = 3.3
Identities = 7/35 (20%), Positives = 17/35 (48%)
Query: 50 QRNCNLTQIGGLLDSKGYGIATPMGHSGLVGHIAC 84
+++ + ++ LD K YGI + ++ H+
Sbjct: 384 EKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCS 418
>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger,
ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding
protein, USP; NMR {Homo sapiens}
Length = 126
Score = 25.8 bits (56), Expect = 3.5
Identities = 7/32 (21%), Positives = 9/32 (28%), Gaps = 6/32 (18%)
Query: 80 GHIACWRWDDYFWSYNNVHSSGHWRDMEEIQH 111
GH C R H+ H+ H
Sbjct: 61 GHQGCGRN------SQEQHALKHYLTPRSEPH 86
>2xhz_A KDSD, YRBH, arabinose 5-phosphate isomerase; lipopolysaccharide
biogenesis; 2.60A {Escherichia coli}
Length = 183
Score = 25.6 bits (57), Expect = 3.7
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 61 LLDSKGYGIATPMGHSGLVGH-IA 83
+ KG + MG SG +G +A
Sbjct: 45 MFWCKGKVVVMGMGASGHIGRKMA 68
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 0.134 0.435
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,977,353
Number of extensions: 102307
Number of successful extensions: 232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 225
Number of HSP's successfully gapped: 24
Length of query: 125
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,412,271
Effective search space: 189727653
Effective search space used: 189727653
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: 51 (24.0 bits)