RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3939
(123 letters)
>3u5e_g 60S ribosomal protein L34-A, 60S ribosomal protein L33-A;
translation, ribosome, ribosomal R ribosomal protein,
STM1, eukaryotic ribosome; 3.00A {Saccharomyces
cerevisiae} PDB: 3u5i_g 3izc_i 3izs_i
Length = 121
Score = 66.6 bits (162), Expect = 1e-15
Identities = 33/79 (41%), Positives = 42/79 (53%)
Query: 7 SVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLC 66
VKTPGG L ++KK P+CG C L GI R + + +S+ K V R+YGG C
Sbjct: 22 VVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRC 81
Query: 67 HKCVKEKFIYCFFYSHCKI 85
CVKE+ I F KI
Sbjct: 82 ANCVKERIIRAFLIEEQKI 100
Score = 40.0 bits (93), Expect = 2e-05
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 51 SRRRKMVKRSYGGVLCHKCVKE-KFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVK 109
S + K+VK G + K C C L GI R + + +S+ K V
Sbjct: 17 SNKIKVVKTPGGILRAQHVKKLATRPKC---GDCGSALQGISTLRPRQYATVSKTHKTVS 73
Query: 110 RSYGGVLCHKCVKE 123
R+YGG C CVKE
Sbjct: 74 RAYGGSRCANCVKE 87
>3iz5_I 60S ribosomal protein L10 (L10E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_I 1s1i_I 3jyw_I
Length = 224
Score = 66.2 bits (161), Expect = 2e-15
Identities = 4/81 (4%), Positives = 15/81 (18%), Gaps = 2/81 (2%)
Query: 7 SVKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKARSIE--RSRMSRRRKMVKRSYGGV 64
+ + Y K + ++ +R +
Sbjct: 22 YCRGVPDPKIRIYDVGMKKKGVDEFPYCVHLVSWEKENVSSEALEAARIACNKYMTKNAG 81
Query: 65 LCHKCVKEKFIYCFFYSHCKI 85
++ + K+
Sbjct: 82 KDAFHLRVRVHPFHVLRINKM 102
>4a18_L RPL34; ribosome, eukaryotic initiation factor 6, EIF6, transla
large ribosomal subunit, rRNA; 3.52A {Tetrahymena
thermophila} PDB: 4a19_L 4a1b_L 4a1d_L 4adx_4
Length = 123
Score = 63.9 bits (155), Expect = 2e-14
Identities = 35/81 (43%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 7 SVKTPGGRLVYHYLKKAGKVPRCGH--CKIKLPGIEKARSIERSRMSRRRKMVKRSYGGV 64
VKTPGGRLV Y+KK +C C + L GI + R E + ++R K V R YGG
Sbjct: 22 KVKTPGGRLVAQYVKKVVNYTKCSEAGCNVALNGIAQVRPAEYATIARSAKTVSRVYGGE 81
Query: 65 LCHKCVKEKFIYCFFYSHCKI 85
LCH CV+ + I F KI
Sbjct: 82 LCHTCVRSRIIRAFLTEEVKI 102
Score = 44.7 bits (105), Expect = 4e-07
Identities = 23/73 (31%), Positives = 34/73 (46%)
Query: 51 SRRRKMVKRSYGGVLCHKCVKEKFIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVKR 110
S + + VK G ++ K + C + L GI + R E + ++R K V R
Sbjct: 17 SNKVRKVKTPGGRLVAQYVKKVVNYTKCSEAGCNVALNGIAQVRPAEYATIARSAKTVSR 76
Query: 111 SYGGVLCHKCVKE 123
YGG LCH CV+
Sbjct: 77 VYGGELCHTCVRS 89
>2b3y_A Iron-responsive element binding protein 1; IRP1 IRE-IRP1 aconitase
activity, lyase; 1.85A {Homo sapiens} SCOP: c.8.2.1
c.83.1.1 PDB: 2b3x_A 3snp_A 3sn2_A 2ipy_A
Length = 888
Score = 29.8 bits (68), Expect = 0.22
Identities = 9/22 (40%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 6 PSVKT---PGGRLVYHYLKKAG 24
P +KT PG +V +YL+++G
Sbjct: 464 PYIKTSLSPGSGVVTYYLQESG 485
>1f0l_A Diphtheria toxin; bacterial toxin, ADP-ribosylation, transmembrane;
HET: APU; 1.55A {Corynebacterium diphtheriae} SCOP:
b.2.1.1 d.166.1.1 f.1.2.1 PDB: 1ddt_A* 1mdt_A* 1sgk_A
1tox_A* 1xdt_T 4ae0_A 4ae1_A 1dtp_A*
Length = 535
Score = 28.0 bits (61), Expect = 0.82
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 22 KAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSYGGVLCHKCVKEKFIYCF--F 79
KAG G K+ PG+ K +++ +K + S L + E+FI F
Sbjct: 76 KAG-----GVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDG 130
Query: 80 YSHCKIKLPGIEKARSIE 97
S + LP E + S+E
Sbjct: 131 ASRVVLSLPFAEGSSSVE 148
>3idv_A Protein disulfide-isomerase A4; thioredoxin-like fold, disulfide
bond, endoplasmic reticulum isomerase, redox-active
center; 1.95A {Homo sapiens} PDB: 2dj2_A
Length = 241
Score = 27.1 bits (60), Expect = 1.3
Identities = 11/28 (39%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 15 LVYHYLKKAGKVPRCGHCKIKLPGIEKA 42
L+ Y P CGHCK P EK
Sbjct: 36 LLEFY------APWCGHCKQFAPEYEKI 57
>3ed3_A Protein disulfide-isomerase MPD1; thioredoxin-like domain, CXXC,
endoplasmic reticulum, glycoprotein, redox-active
center; 2.00A {Saccharomyces cerevisiae}
Length = 298
Score = 26.6 bits (58), Expect = 2.2
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK KA
Sbjct: 45 PWCGHCKKLSSTFRKA 60
>3aps_A DNAJ homolog subfamily C member 10; thioredoxin fold, CXXC motif,
endoplasmic reticulum, oxidore; 1.90A {Mus musculus}
Length = 122
Score = 25.8 bits (57), Expect = 2.5
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CG C+ P E
Sbjct: 31 PWCGPCQNFAPEFELL 46
>1u19_A Rhodopsin; G protein-coupled receptor, membrane protein, retinal
protei photoreceptor, signaling protein; HET: MAN NAG
BMA RET PLM HTO HTG; 2.20A {Bos taurus} SCOP: f.13.1.2
PDB: 1hzx_A* 1gzm_A* 1l9h_A* 2g87_A* 2hpy_A* 2i35_A*
2i36_A* 2i37_A* 2ped_A* 3oax_A* 3c9l_A* 1jfp_A* 1ln6_A*
1f88_A* 3cap_A* 3dqb_A* 3pqr_A* 3pxo_A* 3c9m_A* 2x72_A*
...
Length = 349
Score = 26.2 bits (58), Expect = 3.3
Identities = 2/36 (5%), Positives = 10/36 (27%)
Query: 74 FIYCFFYSHCKIKLPGIEKARSIERSRMSRRRKMVK 109
+ F Y + + + +++ +
Sbjct: 218 IVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTR 253
>2c0n_A A197; thermophil protein, thermophilic virus, STIV, sulfolobus
turreted ICOS virus; 1.86A {Sulfolobus turreted
icosahedral virus}
Length = 203
Score = 25.8 bits (56), Expect = 4.4
Identities = 6/42 (14%), Positives = 12/42 (28%), Gaps = 3/42 (7%)
Query: 44 SIERSRMSRRRKMVKRSYGG---VLCHKCVKEKFIYCFFYSH 82
S+ R + + + G + EK F +
Sbjct: 98 SVYRKDWEKEIFDGEVNGCGLGFTFIKREFLEKIKRPAFLAF 139
>2b5e_A Protein disulfide-isomerase; 2.40A {Saccharomyces cerevisiae} SCOP:
c.47.1.2 c.47.1.2 c.47.1.2 c.47.1.2 PDB: 3boa_A
Length = 504
Score = 25.6 bits (55), Expect = 5.4
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P ++
Sbjct: 386 PWCGHCKRLAPTYQEL 401
Score = 25.2 bits (54), Expect = 7.6
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P KA
Sbjct: 41 PWCGHCKNMAPEYVKA 56
>3qll_A Citrate lyase; beta barrel; 2.45A {Yersinia pestis}
Length = 316
Score = 25.7 bits (57), Expect = 5.5
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 17 YHYLKKAGKVPRCGHCKIKLPGIEKARSIERSRMSRRRKMVKRSY 61
+H+ +G VPR H G + R MS RS+
Sbjct: 6 HHHHHSSGLVPRGSHMASMTGGQQMGRG--SEFMSNLDTYQTRSW 48
>2dml_A Protein disulfide-isomerase A6; thioredoxin domain-containing
protein 7, endoplasmic reticulum, redox-active center,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 130
Score = 24.7 bits (54), Expect = 6.5
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHC+ P +KA
Sbjct: 45 PWCGHCQRLTPEWKKA 60
>2r2j_A Thioredoxin domain-containing protein 4; CRFS motif, chaperone,
endoplasmic reticulum, S response; 2.60A {Homo sapiens}
Length = 382
Score = 25.3 bits (55), Expect = 6.8
Identities = 4/16 (25%), Positives = 7/16 (43%)
Query: 27 PRCGHCKIKLPGIEKA 42
C ++ P E+A
Sbjct: 32 DWCRFSQMLHPIFEEA 47
>3uvt_A Thioredoxin domain-containing protein 5; thioredoxin-like fold,
isomerase; 2.00A {Homo sapiens} PDB: 2diz_A
Length = 111
Score = 24.6 bits (54), Expect = 8.2
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P E+
Sbjct: 31 PWCGHCKTLAPTWEEL 46
>1x5d_A Protein disulfide-isomerase A6; PDIA6, ERP5, TXNDC7, thioredoxin
like domain, redox, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 133
Score = 24.7 bits (54), Expect = 8.4
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P A
Sbjct: 35 PWCGHCKNLEPEWAAA 50
>3mae_A 2-oxoisovalerate dehydrogenase E2 component, dihydrolipamide
acetyltransferase; 2-oxoacid dehydrogenases
acyltransferase; 2.50A {Listeria monocytogenes}
Length = 256
Score = 24.9 bits (55), Expect = 8.7
Identities = 4/21 (19%), Positives = 9/21 (42%)
Query: 37 PGIEKARSIERSRMSRRRKMV 57
P + A + ++ RK +
Sbjct: 10 PPVRSAAGDKEIPINGVRKAI 30
Score = 24.9 bits (55), Expect = 8.7
Identities = 4/21 (19%), Positives = 9/21 (42%)
Query: 88 PGIEKARSIERSRMSRRRKMV 108
P + A + ++ RK +
Sbjct: 10 PPVRSAAGDKEIPINGVRKAI 30
>2djj_A PDI, protein disulfide-isomerase; thioredoxin fold; NMR {Humicola
insolens} SCOP: c.47.1.2 PDB: 2kp1_A
Length = 121
Score = 24.3 bits (53), Expect = 9.4
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGHCK P E+
Sbjct: 35 PWCGHCKALAPKYEEL 50
>3f8u_A Protein disulfide-isomerase A3ERP57; endoplasmic reticulum,
glycoprotein, immunoglobulin domain, microsome, protein
disulfide isomerase, thioredoxin-like FO like domain;
HET: NAG; 2.60A {Homo sapiens} PDB: 2dmm_A 2alb_A
Length = 481
Score = 24.8 bits (53), Expect = 9.5
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 27 PRCGHCKIKLPGIEKA 42
P CGH K P E A
Sbjct: 31 PWCGHAKRLAPEYEAA 46
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
0.328 0.140 0.444
Gapped
Lambda K H
0.267 0.0542 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,918,510
Number of extensions: 103323
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 42
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.9 bits)