RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6916
(105 letters)
>2gzq_A Phosphatidylethanolamine-binding protein; structural genomics, PSI,
protein structure initiative; HET: MSE; 1.30A
{Plasmodium vivax} PDB: 2r77_A
Length = 200
Score = 110 bits (275), Expect = 5e-32
Identities = 35/100 (35%), Positives = 49/100 (49%), Gaps = 9/100 (9%)
Query: 9 SMLITYNSGKLKVDQGNTLTPSDLKQAPE---VTWNADSSSYYTLVMTDPDAPSRQNPKA 65
M I++ SGK +V+ GN L + P + Y L M DPD PSR+ P
Sbjct: 38 DMYISFKSGK-EVNHGNILDLAGTGSVPRNIKFSEEPPEDYCYILFMIDPDFPSRRRPDG 96
Query: 66 REWRHWLVVNIPGSQISRGQ-----TITPYAGPTPPKGTG 100
R++ HW V I ++ +G T+ PY GP+ KGTG
Sbjct: 97 RDYVHWAVSGIKSKELVKGTDKNCITLLPYVGPSIKKGTG 136
>2iqy_A Phosphatidylethanolamine-binding protein 1; alpha-beta, hydrolase
inhibitor; 1.40A {Rattus norvegicus} PDB: 2iqx_A 1b7a_A*
1a44_A 1beh_A 1bd9_A 2l7w_A 2qyq_A* 1kn3_A
Length = 190
Score = 94.7 bits (235), Expect = 4e-26
Identities = 41/99 (41%), Positives = 60/99 (60%), Gaps = 3/99 (3%)
Query: 7 NGSMLITYNSGKLKVDQGNTLTPSDLKQAPE-VTWNA-DSSSYYTLVMTDPDAPSRQNPK 64
++ + Y + + G LTP+ + P ++W+ D YTLV+TDPDAPSR++PK
Sbjct: 25 QHALRVDYGGVTV-DELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTDPDAPSRKDPK 83
Query: 65 AREWRHWLVVNIPGSQISRGQTITPYAGPTPPKGTGTYI 103
REW H+LVVN+ G+ IS G ++ Y G PPK TG +
Sbjct: 84 FREWHHFLVVNMKGNDISSGTVLSEYVGSGPPKDTGLHR 122
>2jyz_A CG7054-PA, GH14779P, PEBP; PEBP/RKIP, molecular modeling, chemical
shift variations, titration, unknown function; NMR
{Drosophila melanogaster}
Length = 179
Score = 93.1 bits (231), Expect = 2e-25
Identities = 45/96 (46%), Positives = 59/96 (61%), Gaps = 5/96 (5%)
Query: 9 SMLITYNSGKLKVDQGNTLTPSDLKQAPEVTWNA--DSSSYYTLVMTDPDAPSRQNPKAR 66
++ + Y +V QGN LTP+ +K P V+W+ S+ TL+M DPDAP+RQ+PK R
Sbjct: 16 TIKVIYGDDL-EVKQGNELTPTQVKDQPIVSWSGLEGKSNLLTLLMVDPDAPTRQDPKYR 74
Query: 67 EWRHWLVVNIPGSQ--ISRGQTITPYAGPTPPKGTG 100
E HW VVNIPGS S G ++ Y G PPK TG
Sbjct: 75 EILHWSVVNIPGSNENPSGGHSLADYVGSGPPKDTG 110
>1wpx_B Carboxypeptidase Y inhibitor; carboxypeptidase inhibitor, serine
proteinase inhibitor, Pro inhibitor complex; HET: NAG
NDG; 2.70A {Saccharomyces cerevisiae} SCOP: b.17.1.1
Length = 220
Score = 92.8 bits (230), Expect = 5e-25
Identities = 31/126 (24%), Positives = 46/126 (36%), Gaps = 35/126 (27%)
Query: 9 SMLITYNSGKLKVDQGNTLTPSDLKQAPEVTWN----------------ADSSSYYTLVM 52
+ + Y+S V GNTL + P+ + +TLVM
Sbjct: 36 ILAVEYSSSA-PVAMGNTLPTEKARSKPQFQFTFNKQMQKSVPQANAYVPQDDDLFTLVM 94
Query: 53 TDPDAPSRQNPKAREWRHWLVVNIPGS------------------QISRGQTITPYAGPT 94
TDPDAPS+ + K E+ H + ++ T+ Y GP
Sbjct: 95 TDPDAPSKTDHKWSEFCHLVECDLKLLNEATHETSGATEFFASEFNTKGSNTLIEYMGPA 154
Query: 95 PPKGTG 100
PPKG+G
Sbjct: 155 PPKGSG 160
>3axy_A Protein heading DATE 3A; phosphatidylethanolamine-binding protein,
14-3-3 protein, BZ protein, floral induction; HET: SEP;
2.40A {Oryza sativa japonica group} PDB: 1wkp_A
Length = 170
Score = 90.8 bits (225), Expect = 8e-25
Identities = 38/93 (40%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 9 SMLITYNSGKLKVDQGNTLTPSDLKQAPEVTWNA-DSSSYYTLVMTDPDAPSRQNPKARE 67
++ +TY S V G L PS + P V D ++YTLVM DPDAPS +P RE
Sbjct: 29 NLKVTYGSKT--VSNGLELKPSMVTHQPRVEVGGNDMRTFYTLVMVDPDAPSPSDPNLRE 86
Query: 68 WRHWLVVNIP-GSQISRGQTITPYAGPTPPKGT 99
+ HWLV +IP + S GQ + Y P P G
Sbjct: 87 YLHWLVTDIPGTTAASFGQEVMSYESPRPTMGI 119
>1wko_A Terminal flower 1 protein; CIS-peptide, PEBP, signaling protein;
1.80A {Arabidopsis thaliana} PDB: 1qou_A
Length = 180
Score = 89.2 bits (221), Expect = 4e-24
Identities = 34/97 (35%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 9 SMLITYNSGKLKVDQGNTLTPSDLKQAPEVTW-NADSSSYYTLVMTDPDAPSRQNPKARE 67
M ++YN + V G+ L PS + P V D S++TLVM DPD P +P +E
Sbjct: 33 KMNVSYNKKQ--VSNGHELFPSSVSSKPRVEIHGGDLRSFFTLVMIDPDVPGPSDPFLKE 90
Query: 68 WRHWLVVNIPG-SQISRGQTITPYAGPTPPKGTGTYI 103
HW+V NIPG + + G+ + Y P P G ++
Sbjct: 91 HLHWIVTNIPGTTDATFGKEVVSYELPRPSIGIHRFV 127
>3n08_A Putative phosphatidylethanolamine-binding protein; eukarytic
homolog RAF kinase inhibitor protein (RKIP). csgid
structural genomics; 1.25A {Chlamydia trachomatis}
Length = 153
Score = 49.6 bits (119), Expect = 5e-09
Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 16/83 (19%)
Query: 36 PEVTWNA--DSSSYYTLVMTDPDAPSRQNPKAREWRHWLVVNIPGSQISRGQTITP---- 89
P ++++ + L++ DPD P W HW+V N+ + +
Sbjct: 30 PPLSFSDVPREAKSLVLIVEDPDVPPSVRED-GLWIHWIVYNLSPVVSNLAEGAQIFAVQ 88
Query: 90 ---------YAGPTPPKGTGTYI 103
Y P PP Y
Sbjct: 89 GLNTAGEIGYCPPCPPDAKHRYY 111
>2evv_A Hypothetical protein HP0218; alpha-beta structure, dimer,
structural genomics, PSI, prote structure initiative;
HET: MSE; 2.59A {Helicobacter pylori}
Length = 207
Score = 43.4 bits (102), Expect = 2e-06
Identities = 19/102 (18%), Positives = 32/102 (31%), Gaps = 37/102 (36%)
Query: 36 PEVTW-NADSSSYYTLVMTDPDAPSRQNPKAREWRHWLVVNIPGSQISRGQTITP----- 89
P+++W + + Y L + D DA + HW+V NI + + ++
Sbjct: 61 PKISWQKVEGAQSYALELIDHDAQK---VCGMPFVHWVVGNIAHNVLEENASMMDKRIVQ 117
Query: 90 ----------------------------YAGPTPPKGTGTYI 103
Y GP PP G Y+
Sbjct: 118 GVNSLTQGFIRSPLNESEKQRSNLNNSVYIGPMPPNGDHHYL 159
>1fux_A Hypothetical 19.5 kDa protein in EMRE-RUS intergenic region; beta
protein, unknown function; 1.81A {Escherichia coli}
SCOP: b.17.1.2
Length = 166
Score = 40.9 bits (96), Expect = 9e-06
Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 28/89 (31%)
Query: 36 PEVTWNA--DSSSYYTLVMTDPDAPSRQNPKAREWRHWLVVNIPGSQIS-------RGQT 86
P +TW+ + + + + + DPDAP+ W HW VVNIP + R T
Sbjct: 34 PSLTWSGVPEGTKSFAVTVYDPDAPTGSG-----WWHWTVVNIPATVTYLPVDAGRRDGT 88
Query: 87 ITP--------------YAGPTPPKGTGT 101
P + G PPKG
Sbjct: 89 KLPTGAVQGRNDFGYAGFGGACPPKGDKP 117
>1fjj_A Hypothetical 17.1 kDa protein in MODC-BIOA intergenic region; PEPB
family, lipid binding protein; HET: MSE EPE; 1.66A
{Escherichia coli} SCOP: b.17.1.2 PDB: 1vi3_A*
Length = 159
Score = 33.7 bits (77), Expect = 0.004
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 27/85 (31%)
Query: 36 PEVTWNA--DSSSYYTLVMTDPDAPSRQNPKAREWRHWLVVNIPGSQ------ISRGQTI 87
P + W+ + + + DPDAP+ W HW+VVN+P G
Sbjct: 33 PHLAWDDVPAGTKSFVVTCYDPDAPTGSG-----WWHWVVVNLPADTRVLPQGFGSGLVA 87
Query: 88 TP--------------YAGPTPPKG 98
P Y G PPKG
Sbjct: 88 MPDGVLQTRTDFGKTGYDGAAPPKG 112
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology,
possible helix-turn-helix motif, ribosome; NMR
{Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB:
1c06_A 1eg0_A 1qd7_C
Length = 159
Score = 25.9 bits (58), Expect = 1.9
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 9/39 (23%)
Query: 57 APSRQNPKAREW---RHWLV----VNIPGSQISRGQTIT 88
A +R +AR+ H LV VNIP ++ GQTI
Sbjct: 63 ARTR--RQARQLVTHGHILVDGSRVNIPSYRVKPGQTIA 99
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 201
Score = 26.0 bits (58), Expect = 2.1
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 57 APSRQNPKAREW---RHWLV----VNIPGSQISRGQTIT 88
AP+ P AR+ RH LV V+IP + TI
Sbjct: 101 APTI--PGARQLVNHRHILVNGRIVDIPSYRCKPQDTIM 137
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D*
2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D*
2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D*
...
Length = 205
Score = 26.1 bits (58), Expect = 2.3
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 57 APSRQNPKAREW---RHWLV----VNIPGSQISRGQTIT 88
+R +AR+ + +V VNI Q+S ++
Sbjct: 107 GATR--AEARQLVSHKAIMVNGRVVNIASYQVSPNDVVS 143
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D*
1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D*
1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G
2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Length = 209
Score = 25.7 bits (57), Expect = 2.7
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 57 APSRQNPKAREW---RHWLV----VNIPGSQISRGQTIT 88
A SR +AR+ H V V++P ++ G I
Sbjct: 111 AVSR--RQARQLVRHGHITVNGRRVDLPSYRVRPGDEIA 147
>3iko_C Nucleoporin NUP84; NPC, transport, WD repeat, autocatalytic
cleavage, mRNA transport, nuclear pore complex, nucleus,
phosphoprotein; 3.20A {Saccharomyces cerevisiae} PDB:
3jro_C
Length = 460
Score = 25.9 bits (56), Expect = 3.2
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 23 QGNTLTPSDLKQAPEVTWNADSSSYYTLVMT-DPDAPSRQNPK 64
+ NT K P W +S + + D D P R+N
Sbjct: 127 KENTYVMERPKNVPTSKWLNSITS--GGLKSCDLDFPLRENTN 167
>3g68_A Putative phosphosugar isomerase; SIS domain, double-SIS DOMA
protein, structural genomics, joint center for
structural G JCSG; HET: MSE CIT; 1.80A {Clostridium
difficile}
Length = 352
Score = 25.2 bits (56), Expect = 4.3
Identities = 3/23 (13%), Positives = 6/23 (26%), Gaps = 2/23 (8%)
Query: 73 VVNIPGSQISR--GQTITPYAGP 93
+ + I +T G
Sbjct: 115 MAGCKNALIDEISDYILTVNCGE 137
>2g8s_A Glucose/sorbosone dehydrogenases; bladed beta-propellor,
pyrolloquinoline quinone (PQQ), quinoprotein, sugar
binding protein; HET: MSE; 1.50A {Escherichia coli K12}
Length = 353
Score = 25.4 bits (56), Expect = 4.6
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 7 NGSMLITYNSGKLKVDQGNTLTPSDLKQAPEV 38
N MLIT G+L+ Q + L P+V
Sbjct: 29 NHGMLITLRGGELRHWQAGKGLSAPLSGVPDV 60
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT,
cytoplasmic vesicle, membrane, Ca structural protein;
7.94A {Bos taurus}
Length = 190
Score = 25.1 bits (54), Expect = 5.4
Identities = 6/16 (37%), Positives = 7/16 (43%), Gaps = 2/16 (12%)
Query: 55 PDAPSRQNP-KAREWR 69
D Q P R+WR
Sbjct: 77 ADR-LTQEPESIRKWR 91
>3ol2_B Plexin-B1; beta-propeller, signalling, extacellular, signaling
protein; HET: NAG BMA; 2.99A {Homo sapiens}
Length = 528
Score = 24.7 bits (52), Expect = 7.8
Identities = 4/27 (14%), Positives = 7/27 (25%)
Query: 63 PKAREWRHWLVVNIPGSQISRGQTITP 89
+ + WL P +G
Sbjct: 499 SRGQGPEQWLWSFQPELGCLQGTKHHH 525
>3knz_A Putative sugar binding protein; structural genomics, joint C
structural genomics, JCSG, protein structure initiative;
2.50A {Salmonella enterica subsp}
Length = 366
Score = 24.4 bits (54), Expect = 8.5
Identities = 4/23 (17%), Positives = 8/23 (34%), Gaps = 2/23 (8%)
Query: 73 VVNIPGSQISR--GQTITPYAGP 93
+ + + I R +T G
Sbjct: 130 MAGVAPATIDRAADYILTVPCGE 152
>3das_A Putative oxidoreductase; aldose sugar dehydrogenase, beta
propellor, PQQ, SGDH; HET: MSE ARA PQQ; 1.60A
{Streptomyces coelicolor}
Length = 347
Score = 24.2 bits (53), Expect = 9.2
Identities = 6/33 (18%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 7 NGSMLIT-YNSGKLKVDQGNTLTPSDLKQAPEV 38
G +L++ + + T ++L + P V
Sbjct: 42 GGDLLVSSRDEATITRVDAKTGRKTELGEVPGV 74
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
0.311 0.129 0.394
Gapped
Lambda K H
0.267 0.0644 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,627,936
Number of extensions: 82473
Number of successful extensions: 177
Number of sequences better than 10.0: 1
Number of HSP's gapped: 160
Number of HSP's successfully gapped: 30
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.6 bits)