RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17128
(124 letters)
>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 = 76.4 bits (187), Expect = 1e-17
Identities = 22/102 (21%), Positives = 32/102 (31%), Gaps = 22/102 (21%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLL 82
C Q GV A+FG D + S C L V + + F + + P
Sbjct: 53 FCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFP-TDGTHPFVIQMRPD---- 107
Query: 83 NAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
L A +I + W K A +Y+ D
Sbjct: 108 -----------------LKGALLSLIEYYQWDKFAYLYDSDR 132
>3hsy_A Glutamate receptor 2; ligand-gated ION channel, synapse, cell CELL
membrane, endoplasmic reticulum, glycoprotein, ION TRA
ionic channel; HET: NAG BMA; 1.75A {Rattus norvegicus}
PDB: 3h5v_A* 3h5w_A 3o2j_A* 2wjw_A* 2wjx_A 3n6v_A
Length = 376
Score = 68.7 bits (167), Expect = 6e-15
Identities = 21/102 (20%), Positives = 31/102 (30%), Gaps = 22/102 (21%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLL 82
C Q GV A+FG D + S C L V + + F + + P
Sbjct: 53 FCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFP-TDGTHPFVIQMRPDL--- 108
Query: 83 NAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
A +I + W K A +Y+ D
Sbjct: 109 ------------------KGALLSLIEYYQWDKFAYLYDSDR 132
>3h6g_A Glutamate receptor, ionotropic kainate 2; membrane protein
glycoprotein, cell junction, cell membrane,
glycoprotein, ION transport; HET: NAG TLA; 2.70A {Rattus
norvegicus} PDB: 3h6h_A* 3qlv_C 3qlu_C* 3qlt_A* 3olz_A*
Length = 395
Score = 68.2 bits (166), Expect = 8e-15
Identities = 34/104 (32%), Positives = 51/104 (49%), Gaps = 20/104 (19%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKE--FSVNLYPSQK 80
C QL GV A+FGPS + VQSIC AL VPH+++R +++ + F V+LYP
Sbjct: 64 ACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDF- 122
Query: 81 LLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
L+ A D+++F W V +VY++
Sbjct: 123 -----------------SSLSRAILDLVQFFKWKTVTVVYDDST 149
>3o21_A Glutamate receptor 3; periplasmatic binding protein,
oligomerization, membrane, TR protein; HET: NAG; 2.20A
{Rattus norvegicus} PDB: 3p3w_A
Length = 389
Score = 65.6 bits (159), Expect = 8e-14
Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 22/102 (21%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLL 82
C Q GV A+FG D + + S C AL + +F + + P+
Sbjct: 62 FCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFVTPSFP-TDADVQFVIQMRPAL--- 117
Query: 83 NAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
A ++ + W K +Y+ +
Sbjct: 118 ------------------KGAILSLLSYYKWEKFVYLYDTER 141
>3saj_A Glutamate receptor 1; rossman fold, ION channel, membrane,
transport protein; HET: NAG BMA MAN; 2.50A {Rattus
norvegicus}
Length = 384
Score = 63.2 bits (153), Expect = 4e-13
Identities = 22/102 (21%), Positives = 33/102 (32%), Gaps = 22/102 (21%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLL 82
C Q GV A+FG + + S C AL V + ++ S +F + L P
Sbjct: 60 FCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVD-TSNQFVLQLRPE---- 114
Query: 83 NAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
L A +I W +Y+ D
Sbjct: 115 -----------------LQEALISIIDHYKWQTFVYIYDADR 139
>3om0_A Glutamate receptor, ionotropic kainate 5; membrane protein, ION
channel; HET: NAG BMA GOL; 1.40A {Rattus norvegicus}
PDB: 3om1_A* 3qlu_A* 3qlv_A
Length = 393
Score = 58.6 bits (141), Expect = 2e-11
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 20 ESVMCRQLQNGVQALFGPSD-ALLGPHVQSICEALDVPHMESRLDLELNSKE---FSVNL 75
MC+ L GV ++ GPS V IC ++PH++ + + SV+L
Sbjct: 60 TDTMCQILPKGVVSVLGPSSSPASASTVSHICGEKEIPHIKVGPEETPRLQYLRFASVSL 119
Query: 76 YPSQKLLNAAFKDVIRFLNWTK 97
YPS + ++ A +++ N+
Sbjct: 120 YPSNEDVSLAVSRILKSFNYPS 141
>3qek_A NMDA glutamate receptor subunit; amino terminal domain, ION
channel, NMDA receptor, allosteri modulation,
phenylethanolamine, polyamine; HET: NAG BMA; 2.00A
{Xenopus laevis} PDB: 3qel_A* 3qem_A* 3q41_A*
Length = 384
Score = 51.7 bits (123), Expect = 6e-09
Identities = 15/112 (13%), Positives = 35/112 (31%), Gaps = 28/112 (25%)
Query: 23 MCRQLQN-GVQALF-----GPSDALLGPHVQSICEALDVPHME--SRLDLELNSKEFS-- 72
+C L + V A+ P+D L + +P + +R+ + +
Sbjct: 57 VCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSF 116
Query: 73 VNLYPSQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
+ P + +++R NW V ++ +D+
Sbjct: 117 LRTVPPYSHQALVWFEMMRLFNWNH------------------VILIVSDDH 150
>3qel_B Glutamate [NMDA] receptor subunit epsilon-2; ION channel,
allosteric modulation, phenylethanolamine,
N-glycosylation, extracellular; HET: NAG BMA MAN FUC
QEL; 2.60A {Rattus norvegicus} PDB: 3qem_B* 3jpw_A*
3jpy_A*
Length = 364
Score = 49.8 bits (118), Expect = 2e-08
Identities = 8/105 (7%), Positives = 29/105 (27%), Gaps = 17/105 (16%)
Query: 23 MCRQLQN-GVQALFGP---SDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPS 78
+C + + +Q + + + I P + ++ S
Sbjct: 55 ICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPIL-------------GIHGGSS 101
Query: 79 QKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEED 123
+ + + + + + +++ +W +IV
Sbjct: 102 MIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYF 146
>1jdp_A NPR-C, atrial natriuretic peptide clearance receptor;
hormone-receptor complex, natriuretic peptide receptor,
ALLO activation, signaling protein; HET: NDG NAG; 2.00A
{Homo sapiens} SCOP: c.93.1.1 PDB: 1jdn_A* 1yk0_A*
1yk1_A*
Length = 441
Score = 34.7 bits (79), Expect = 0.004
Identities = 16/103 (15%), Positives = 30/103 (29%), Gaps = 15/103 (14%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKEFSVNLYPSQKL 81
+ + GP V + D+P + L K+ + Y L
Sbjct: 77 VAAARGAKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQHKD---SEYSH--L 131
Query: 82 LNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
A + + R +W++ A+VY +D
Sbjct: 132 TRVAPAY---------AKMGEMMLALFRHHHWSRAALVYSDDK 165
>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 = 33.7 bits (76), Expect = 0.012
Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 29/128 (22%)
Query: 7 LVEVNVNTGLEEEES--VMCRQLQNGVQALFGPSDALLG-PHVQSICEALDVPHMESRLD 63
+ + + L +E ++ + L Q L P + L P SI + + D
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLKYLDCRPQDL--PREVLTTNPRRLSIIAES-IRDGLATWD 345
Query: 64 --LELNSKEF------SVN-LYPS--QKLLN--AAF-KDVIRFLNWTKKLL-----NAAF 104
+N + S+N L P+ +K+ + + F + LL +
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA----HIPTILLSLIWFDVIK 401
Query: 105 KDVIRFLN 112
DV+ +N
Sbjct: 402 SDVMVVVN 409
Score = 32.1 bits (72), Expect = 0.037
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 62 LDLELNSKEFSVNLYPSQKLLNAAFKDVIRFL-NWTKKLLNAAFKDVIRFLNWTKVAIVY 120
L+ N ++L+N ++ FL + L+ + + D++R + ++
Sbjct: 525 QQLKFYKPYICDNDPKYERLVN----AILDFLPKIEENLICSKYTDLLRIALMAEDEAIF 580
Query: 121 EE 122
EE
Sbjct: 581 EE 582
Score = 26.4 bits (57), Expect = 3.0
Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 16/84 (19%)
Query: 46 VQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLLNAAFKDVIRFLNWTKKLLNAAFK 105
+ + D ++ L+ +E ++ S+ ++ L WT LL+ +
Sbjct: 26 EDAFVDNFDCKDVQDMPKSILSKEEID-HIIMSKDAVSG-----TLRLFWT--LLSKQEE 77
Query: 106 DVIRFL--------NWTKVAIVYE 121
V +F+ + I E
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTE 101
>1dp4_A Atrial natriuretic peptide receptor A; periplasmic binding protein
fold, dimer, hormone/growth FACT receptor, lyase
complex; HET: NAG; 2.00A {Rattus norvegicus} SCOP:
c.93.1.1 PDB: 1t34_A* 3a3k_A*
Length = 435
Score = 31.7 bits (71), Expect = 0.045
Identities = 16/98 (16%), Positives = 24/98 (24%), Gaps = 16/98 (16%)
Query: 28 QNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKEFSVNLYPSQKLLNAAF 86
++ GP V VP + L + K+ Y
Sbjct: 75 EHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIGVKD----EYAL-------- 122
Query: 87 KDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
R + L + R L W A+V D
Sbjct: 123 --TTRTG-PSHVKLGDFVTALHRRLGWEHQALVLYADR 157
>4f11_A Gamma-aminobutyric acid type B receptor subunit 2; venus flytrap
module, G-protein coupled receptor, signaling; 2.38A
{Homo sapiens} PDB: 4f12_A*
Length = 433
Score = 30.6 bits (69), Expect = 0.11
Identities = 4/25 (16%), Positives = 12/25 (48%)
Query: 100 LNAAFKDVIRFLNWTKVAIVYEEDN 124
+N A +++ W +V + ++
Sbjct: 141 VNPAILKLLKHYQWKRVGTLTQDVQ 165
>2yim_A Probable alpha-methylacyl-COA racemase MCR (2-methylacyl-COA
racemase) (2-arylpropionyl-COA...; isomerase, methyl-COA
racemase; HET: MC4; 1.41A {Mycobacterium tuberculosis}
PDB: 2gce_A* 1x74_A* 2gd0_A* 2gd2_A* 2gd6_A* 2gci_A*
Length = 360
Score = 27.9 bits (63), Expect = 0.82
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 33 ALFGPSDALLGPHVQSICEALDVPHMESR 61
A+F SDA + P V + E + PH+ R
Sbjct: 289 AVFANSDACVTP-VLAFGEVHNEPHIIER 316
>2g04_A Probable fatty-acid-COA racemase FAR; isomerase; 2.70A
{Mycobacterium tuberculosis}
Length = 359
Score = 27.9 bits (63), Expect = 0.88
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 33 ALFGPSDALLGPHVQSICEALDVPHMESR 61
+F +DA + P V + EA + H+++R
Sbjct: 291 RVFAGTDACVTP-VLAWSEAANNDHLKAR 318
>3zy2_A Putative GDP-fucose protein O-fucosyltransferase;
glycosyltransferase, GT-B, catalytic mechanism,; HET:
GDP; 1.54A {Caenorhabditis elegans} PDB: 3zy3_A* 3zy4_A*
3zy5_A* 3zy6_A*
Length = 362
Score = 26.2 bits (57), Expect = 3.3
Identities = 8/42 (19%), Positives = 17/42 (40%)
Query: 77 PSQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAI 118
P+ + ++L W+ ++ A K + L VA+
Sbjct: 175 PAPFPSKGKVWSIQKYLRWSSRITEQAKKFISANLAKPFVAV 216
>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 = 25.4 bits (55), Expect = 7.0
Identities = 16/94 (17%), Positives = 28/94 (29%), Gaps = 32/94 (34%)
Query: 34 LFGPSDALLGPHVQSICE---------ALDVPHMESRLDLELNSKEFSVNLYPSQKLLN- 83
FG G + I E +D ++ E+N S + LL+
Sbjct: 1675 HFG------GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSA 1728
Query: 84 -------------AAFKDVIRFLNWTKKLLNAAF 104
AAF+ ++ + +A F
Sbjct: 1729 TQFTQPALTLMEKAAFE-DLK--SKGLIPADATF 1759
>1ni5_A Putative cell cycle protein MESJ; structural genomics, ATPase,
PP-type, putative cell cycle PR PSI, protein structure
initiative; 2.65A {Escherichia coli} SCOP: b.153.1.2
c.26.2.5 d.229.1.1
Length = 433
Score = 25.1 bits (55), Expect = 8.8
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 45 HVQSICEALDVPHMESRLDLE 65
H +++C+ VP + R+ L
Sbjct: 64 HCENVCQQWQVPLVVERVQLA 84
>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA
complex; 3.65A {Geobacillus kaustophilus}
Length = 464
Score = 25.0 bits (55), Expect = 9.7
Identities = 3/31 (9%), Positives = 11/31 (35%)
Query: 45 HVQSICEALDVPHMESRLDLELNSKEFSVNL 75
V+ C + +++D+ + +
Sbjct: 69 FVKRFCVERRILCETAQIDVPAFQRSAGLGA 99
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 0.396
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,853,290
Number of extensions: 95794
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 30
Length of query: 124
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,412,271
Effective search space: 185315382
Effective search space used: 185315382
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 (23.3 bits)