RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7655
(110 letters)
>2z3y_A Lysine-specific histone demethylase 1; chromatin, nucleosome,
transcription, LSD1, alternative splicing, chromatin
regulator, coiled coil; HET: F2N; 2.25A {Homo sapiens}
SCOP: a.4.1.18 c.3.1.2 d.16.1.5 PDB: 2ejr_A* 2z5u_A*
3abt_A* 3abu_A* 2y48_A* 2v1d_A* 2h94_A* 2iw5_A* 2uxn_A*
2uxx_A* 2hko_A* 2dw4_A* 2x0l_A* 2l3d_A
Length = 662
Score = 104 bits (260), Expect = 1e-27
Identities = 30/114 (26%), Positives = 51/114 (44%), Gaps = 6/114 (5%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTT----- 55
ME+++D + + + G+ +P+P + + W ++ RGSYS +
Sbjct: 544 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 602
Query: 56 ERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
+ + + P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 603 DLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIAD 656
>2xag_A Lysine-specific histone demethylase 1; amine oxidase, chromatin
regulator, histone inhibitor binding, methylation,
nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A
{Homo sapiens} PDB: 2xaf_A* 2xah_A* 2xaj_A* 2xaq_A*
2xas_A* 2com_A
Length = 852
Score = 102 bits (254), Expect = 6e-27
Identities = 30/114 (26%), Positives = 51/114 (44%), Gaps = 6/114 (5%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTT----- 55
ME+++D + + + G+ +P+P + + W ++ RGSYS +
Sbjct: 715 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 773
Query: 56 ERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
+ + + P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 774 DLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIAD 827
>1b37_A Protein (polyamine oxidase); flavin-dependent amine oxidase,
oxidoreductase; HET: NAG FCA MAN FAD; 1.90A {Zea mays}
SCOP: c.3.1.2 d.16.1.5 PDB: 1b5q_A* 1h81_A* 1h82_A*
1h83_A* 1h84_A* 1h86_A* 3kpf_A* 3ku9_A* 3l1r_A*
Length = 472
Score = 99 bits (249), Expect = 3e-26
Identities = 28/109 (25%), Positives = 49/109 (44%), Gaps = 9/109 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+E +D+Q + E+M+ R +P+ IL W S++ ++G++S
Sbjct: 357 IEQQSDEQTKAEIMQVLRKMFP-GKDVPDATDILVPRWWSDRFYKGTFS--NWPVGVNRY 413
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
+L APV + F GE TSE V+GA +G A+ ++
Sbjct: 414 EYDQLRAPVGR------VYFTGEHTSEHYNGYVHGAYLSGIDSAEILIN 456
>2yg5_A Putrescine oxidase; oxidoreductase, flavin; HET: FAD; 1.90A
{Rhodococcus erythropolis} PDB: 2yg6_A* 2yg3_A* 2yg4_A*
2yg7_A* 3rha_A*
Length = 453
Score = 93.6 bits (233), Expect = 4e-24
Identities = 26/109 (23%), Positives = 47/109 (43%), Gaps = 9/109 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M L+ ++ + ++ + +LG K EP + WGS + RG Y+ + L+
Sbjct: 350 MFELSAEERKATILASLARYLGPK--AEEPVVYYESDWGSEEWTRGCYAA-SFDLGGLHR 406
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
A+ PV + F+ + + Y V+GA+ G R A I+
Sbjct: 407 YGADSRTPVGP------IHFSCSDIAAEGYQHVDGAVRMGQRTAADIIA 449
>1rsg_A FMS1 protein; FAD binding motif, oxidoreductase; HET: FAD; 1.90A
{Saccharomyces cerevisiae} PDB: 1z6l_A* 3bi2_A* 3bi4_A*
3bi5_A* 3bnm_B* 3bnu_B* 3cn8_B* 3cnd_B* 3cnp_B* 3cns_A*
3cnt_B* 1yy5_A* 1xpq_A*
Length = 516
Score = 92.2 bits (228), Expect = 2e-23
Identities = 29/109 (26%), Positives = 44/109 (40%), Gaps = 9/109 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M+ L + V I+ M+ A P I+ ++W + + RG+YS + ++
Sbjct: 406 MKCLDSEDV-IDGMRPIENIANANK--PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDM 462
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
A + FAGE T D GA E+G REA RI
Sbjct: 463 VVAMSNGQD------SRIRFAGEHTIMDGAGCAYGAWESGRREATRISD 505
>1s3e_A Amine oxidase [flavin-containing] B; human monoamine oxidase,
inhibitor binding, rasagiline, enantioselectivity,
oxidoreductase; HET: FAD RHP; 1.60A {Homo sapiens} SCOP:
c.3.1.2 d.16.1.5 PDB: 1gos_A* 1oj9_A* 1ojb_A* 1ojc_A*
1ojd_A* 1s2q_A* 1s2y_A* 1oja_A* 1s3b_A* 2bk3_A* 2byb_A*
2c64_A* 2c65_A* 2c66_A* 2c67_A* 2c70_A* 2v5z_A* 2v60_A*
2v61_A* 2vrl_A* ...
Length = 520
Score = 90.7 bits (225), Expect = 7e-23
Identities = 25/109 (22%), Positives = 41/109 (37%), Gaps = 8/109 (7%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+ LT ++ ++ + + LG+ EP +W ++ G Y+ L
Sbjct: 352 LARLTKEERLKKLCELYAKVLGSL-EALEPVHYEEKNWCEEQYSGGCYTTY-FPPGILTQ 409
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
L PV + FAG T+ + GA+E G R A IL
Sbjct: 410 YGRVLRQPVDR------IYFAGTETATHWSGYMEGAVEAGERAAREILH 452
>2vvm_A Monoamine oxidase N; FAD, peroxisome, flavoprotein, oxidoreductase,
enantioselectivity, directed evolution variant; HET:
FAD; 1.85A {Aspergillus niger} PDB: 2vvl_A* 2vvl_G*
Length = 495
Score = 81.1 bits (200), Expect = 2e-19
Identities = 17/109 (15%), Positives = 38/109 (34%), Gaps = 11/109 (10%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+ + E +KA R++ +W ++ +G++ ++
Sbjct: 386 ANHIQPDEDVRETLKAVGQLAPG---TFGVKRLVFHNWVKDEFAKGAWF--FSRPGMVSE 440
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
L ++FA + + ++GAIE G R A +L+
Sbjct: 441 CLQGLREKHGG------VVFANSDWALGWRSFIDGAIEEGTRAARVVLE 483
>3k7m_X 6-hydroxy-L-nicotine oxidase; enantiomeric substrates,
flavoenzymes, nicotine degradation, oxidoreductase; HET:
FAD GP7; 1.95A {Arthrobacter nicotinovorans} PDB:
3k7q_X* 3ng7_X* 3ngc_X* 3nh3_X* 3nho_X* 3nk0_X* 3nk1_X*
3nk2_X* 3nn0_X* 3nn6_X* 3k7t_A*
Length = 431
Score = 72.9 bits (179), Expect = 1e-16
Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 12/97 (12%)
Query: 12 EVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSN 71
V A ++L E I W ++ F G + + + ELG P
Sbjct: 339 AVKDAVLYYLPEV----EVLGIDYHDWIADPLFEGPWV--APRVGQFSRVHKELGEPAGR 392
Query: 72 GMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
+ F G S + + GA+ET + IL
Sbjct: 393 ------IHFVGSDVSLEFPGYIEGALETAECAVNAIL 423
>2jae_A L-amino acid oxidase; oxidoreductase, dimerisation mode, hydride
transfer mechanism, GR2-family, flavoenzyme, FAD
containing; HET: FAD; 1.25A {Rhodococcus opacus} PDB:
2jb1_A* 2jb2_A* 2jb3_A*
Length = 489
Score = 71.5 bits (175), Expect = 4e-16
Identities = 22/111 (19%), Positives = 42/111 (37%), Gaps = 8/111 (7%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
ESLT +Q + + G KY + + + SW K+ +++ +
Sbjct: 379 FESLTHRQRLAKAIAEGSEIHGEKY-TRDISSSFSGSWRRTKYSESAWANWAGSGGSHGG 437
Query: 61 SAAELGAPVSNGMGKPV--LLFAGEATSEDQYATVNGAIETGWREADRILK 109
+A + +PV + FAG+ S A +GA+ + I +
Sbjct: 438 AATPEY----EKLLEPVDKIYFAGDHLSNA-IAWQHGALTSARDVVTHIHE 483
>2iid_A L-amino-acid oxidase; flavoenzyme, FAD binding domain, reaction
mechanism, sustrat binding, oxidoreductase; HET: NAG FUC
PHE FAD; 1.80A {Calloselasma rhodostoma} SCOP: c.3.1.2
d.16.1.5 PDB: 1f8s_A* 1f8r_A* 1reo_A* 1tdk_A* 1tdn_A*
1tdo_A* 3kve_A* 4e0v_A*
Length = 498
Score = 64.5 bits (157), Expect = 1e-13
Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 11/111 (9%)
Query: 1 MESLTDKQVQIEVMKAFR--FFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERL 58
++L K V L K + W +K+ G + T T +
Sbjct: 381 FQALDFKDCADIVFNDLSLIHQLPKKDIQSFCYPSVIQKWSLDKYAMGGIT--TFTPYQF 438
Query: 59 NTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
+ L A + FAGE T++ + ++ I++G R A +
Sbjct: 439 QHFSDPLTASQGR------IYFAGEYTAQA-HGWIDSTIKSGLRAARDVNL 482
>2e1m_C L-glutamate oxidase; L-amino acid oxidase, FAD, L-GOX, flavo
oxidoreductase; HET: FAD; 2.80A {Streptomyces SP}
Length = 181
Score = 59.9 bits (145), Expect = 1e-12
Identities = 21/109 (19%), Positives = 41/109 (37%), Gaps = 9/109 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+S D + ++ + G + + T SW + + G + T ++
Sbjct: 51 WDSFDDAERYGYALENLQSVHGRRIEVFYTGAGQTQSWLRDPYACGEAA--VYTPHQMTA 108
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
++ P + FAGE S +A + GA+ET R A + +
Sbjct: 109 FHLDVVRPEGP------VYFAGEHVSLK-HAWIEGAVETAVRAAIAVNE 150
>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 = 32.9 bits (74), Expect = 0.015
Identities = 24/139 (17%), Positives = 48/139 (34%), Gaps = 36/139 (25%)
Query: 1 MESLTDKQVQI------EVMKA-FRFFLGA---KYTIPEPARILTTS-----WGSNKHFR 45
+L KQ ++ EV++ ++F + + P + + N+ F
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127
Query: 46 GSYSI-RTLTTERLNTSAAELGAPVSN----GM---GKPVLLFAGEA-TSEDQYATVNGA 96
Y++ R +L + EL P N G+ GK + A + S ++
Sbjct: 128 -KYNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWV--ALDVCLSYKVQCKMDFK 183
Query: 97 IETGW------READRILK 109
I W + +L+
Sbjct: 184 IF--WLNLKNCNSPETVLE 200
>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 = 30.4 bits (68), Expect = 0.089
Identities = 11/38 (28%), Positives = 12/38 (31%), Gaps = 13/38 (34%)
Query: 72 GMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
GMG D Y T A + W AD K
Sbjct: 1630 GMGM------------DLYKTSKAAQDV-WNRADNHFK 1654
Score = 28.9 bits (64), Expect = 0.30
Identities = 17/116 (14%), Positives = 38/116 (32%), Gaps = 25/116 (21%)
Query: 13 VMKAF-RFFLG--------AKYTIPEPARILTTSWGSNKHFRGSYSIRTLT---TERLNT 60
+ F +L AK ++ + + + + R + ++ +
Sbjct: 87 CLTEFENCYLEGNDIHALAAKLLQENDTTLVK----TKELIKNYITARIMAKRPFDKKSN 142
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSED-------QYATVNGAIETGWREADRILK 109
SA L V G + V +F G+ ++D Y T + + + + L
Sbjct: 143 SA--LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
>3ayj_A Pro-enzyme of L-phenylalanine oxidase; amino acid oxidase,
flavoenzyme, L- binding, oxidoreductase; HET: FAD PHE;
1.10A {Pseudomonas} PDB: 2yr4_A* 2yr6_A* 3ayi_A* 2yr5_A*
3ayl_A*
Length = 721
Score = 29.8 bits (65), Expect = 0.17
Identities = 11/104 (10%), Positives = 24/104 (23%), Gaps = 8/104 (7%)
Query: 9 VQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKH---FRGSYSIRTLTTERLNTSAAEL 65
A ++ A W +NK F+ + +
Sbjct: 579 KYAGASNAQPWWFYQLLAEARTADRFVFDWTTNKTAGGFKLDMTGDHHQSNLCFRYHTHA 638
Query: 66 GAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
A + A ++ S + GA + ++
Sbjct: 639 LAASLDNR----FFIASDSYSHLG-GWLEGAFMSALNAVAGLIV 677
>3v26_X ORF3, ORF95, probable sigma(54) modulation protein; ribosome
hibernation factor, YHBH, protein E, stress respons
stationary phase; 3.10A {Escherichia coli} PDB: 3v28_X
2rql_A
Length = 101
Score = 26.8 bits (60), Expect = 0.95
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 41 NKHFRGSYSIR-TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
++F + L E+ T ++ V+ G + A A +D YA ++G I+
Sbjct: 28 EQYFDRINQVYVVLKVEK-VTHTSDATLHVNGGE-----IHA-SAEGQDMYAAIDGLID 79
>3v2c_Y Ribosome-associated inhibitor A; RAIA, protein Y, stress RES
stationary phase, ribosome hibernation,
ribosome-inhibitor; 2.70A {Escherichia coli k-12} PDB:
3v2e_Y 1n3g_A 1l4s_A 1voq_a 1vos_a 1vov_a 1vox_a 1voz_a
Length = 119
Score = 26.8 bits (60), Expect = 1.0
Identities = 13/59 (22%), Positives = 18/59 (30%), Gaps = 8/59 (13%)
Query: 41 NKHFRGSYSIR-TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
K + L+ E A + NG +L A ED Y +N I
Sbjct: 28 EKWQTHLINPHIILSKEPQGFVA-DATINTPNG-----VLVA-SGKHEDMYTAINELIN 79
>2ywq_A Protein Y, ribosomal subunit interface protein; sigma-54
modulation protein family, structural genomics; 2.64A
{Thermus thermophilus} SCOP: d.204.1.1
Length = 105
Score = 26.0 bits (58), Expect = 1.5
Identities = 10/63 (15%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 41 NKHFRGSYSIR-TLTTERL----NTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNG 95
+++ G + L+ + AE+ + G+ + E D YA ++
Sbjct: 29 DRYQDGELMAKVVLSLAGSPHVEKKARAEIQVDLPGGL-----VRV-EEEDADLYAAIDR 82
Query: 96 AIE 98
A++
Sbjct: 83 AVD 85
>4fyl_A Ribosome hibernation protein YHBH;
beta-alpha-beta-BETA-beta-alpha secondary structure
fold SIM YFIA of E. coli; HET: FME; 1.60A {Vibrio
cholerae}
Length = 95
Score = 26.0 bits (58), Expect = 1.7
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 41 NKHFRGSYSIR-TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
+ F ++ L E+L AE V+ + A A E+ YA ++ ++
Sbjct: 28 ERFFDHINHVQVILRVEKLR-QIAEATLHVNQAE-----IHA-HADDENMYAAIDSLVD 79
>3tqm_A Ribosome-associated factor Y; protein synthesis, protein binding;
2.45A {Coxiella burnetii}
Length = 96
Score = 25.6 bits (57), Expect = 2.2
Identities = 8/59 (13%), Positives = 17/59 (28%), Gaps = 8/59 (13%)
Query: 41 NKHFRGSYSIR-TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
+I + + + + A +A S+D Y TV+ +
Sbjct: 28 QPCRDEISNIHIIFHINK-LKKIVDANVKLPGST-----INA-QAESDDMYKTVDLLMH 79
>1imu_A Hypothetical protein HI0257; dsRNA binding protein, proteome,
solution structure, ribosome, structure 2 function
project, S2F; NMR {Haemophilus influenzae} SCOP:
d.204.1.1
Length = 107
Score = 25.6 bits (57), Expect = 2.3
Identities = 15/59 (25%), Positives = 18/59 (30%), Gaps = 8/59 (13%)
Query: 41 NKHFRGSYSIR-TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
K S L N + E G L A ATS+D Y +N E
Sbjct: 28 GKWQTQLISPHFVLNKVP-NGFSVEASIGTPLGN-----LLA-SATSDDMYKAINEVEE 79
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
0.315 0.130 0.375
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,604,427
Number of extensions: 81094
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 24
Length of query: 110
Length of database: 6,701,793
Length adjustment: 74
Effective length of query: 36
Effective length of database: 4,635,639
Effective search space: 166883004
Effective search space used: 166883004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.3 bits)