RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8580
(274 letters)
>2eqn_A Hypothetical protein LOC92345; NAF1 domain, hypothetical protein
BC008207 [HOMO sapiens], structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 103
Score = 107 bits (268), Expect = 7e-30
Identities = 39/98 (39%), Positives = 67/98 (68%), Gaps = 2/98 (2%)
Query: 13 GDLPPIEDLQISVPED-QCLPVGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKGQRSLG 71
G+LP +E+L I +PED + P+G + +I++ LV+I+++ N P ++ ++V+F +++ G
Sbjct: 7 GELPSVEELTIILPEDIELKPLGMVSSIIEQLVIIESMTNLPPVNEETVIFKS-DRQAAG 65
Query: 72 KIFDVIGPVSGPVYCVRFNSHQHIVDSNIKIDQDVYCA 109
KIF++ GPV+ P Y +RFNS HI IKI + +Y A
Sbjct: 66 KIFEIFGPVAHPFYVLRFNSSDHIESKGIKIKETMYFA 103
>2v3m_A NAF1; ribosomal protein, GAR1, snoRNP, phosphorylation,
hypothetical protein; 2.74A {Saccharomyces cerevisiae}
Length = 131
Score = 95.4 bits (237), Expect = 8e-25
Identities = 16/127 (12%), Positives = 47/127 (37%), Gaps = 7/127 (5%)
Query: 5 RNKGELDLGDLPPIEDLQISVPEDQCLPVGKILNIVDTLVLIKTLKNT--PTLDLDSVLF 62
+K E+ +P + + + P+G + + + ++I + L S+
Sbjct: 5 LSKNEILEETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFC 64
Query: 63 LDKGQRSLGKIFDVIGPVSGPVYCVRFNSHQ--HIVDSNIKIDQDVYCAPQTEHTSYVPL 120
L+ +G + +V GP+ P Y ++ + + +++ + + ++
Sbjct: 65 LEDR-TLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT--PDAHWIDT 121
Query: 121 PDLIKVK 127
+L
Sbjct: 122 FELKHHH 128
>2ey4_C Small nucleolar RNP similar to GAR1; trimeric complex, structural
genomics, PSI, protein structur initiative; 2.11A
{Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3mqk_C 2rfk_C
Length = 82
Score = 42.6 bits (100), Expect = 5e-06
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 7/79 (8%)
Query: 33 VGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKGQRSLGKIFDVIGPVSGPVYCVRFNSH 92
+GK+L+ LI P L+ + DK + +G + DV GPV P ++
Sbjct: 11 LGKVLHYAKQGFLIVRTNWVP--SLNDRVV-DKRLQFVGIVKDVFGPVKMPYVAIKPKVS 67
Query: 93 QHIVDSNIKIDQDVYCAPQ 111
+ I + + +Y +
Sbjct: 68 ----NPEIYVGEVLYVDER 82
>2hvy_B GAR1, small nucleolar RNP similar to GAR1; H/ACA RNA, RNP,
pseudouridine synthase, guide RNA, isomerase
biosynthetic protein-RNA complex; HET: ATP; 2.30A
{Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3hay_B*
Length = 104
Score = 37.7 bits (87), Expect = 5e-04
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 33 VGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKGQRSLGKIFDVIGPVSGPVYCVRFNSH 92
+GK+L+ LI P L+ + DK + +G + DV GPV P ++
Sbjct: 11 LGKVLHYAKQGFLIVRTNWVP--SLNDRVV-DKRLQFVGIVKDVFGPVKMPYVAIKPKV- 66
Query: 93 QHIVDSNIKIDQDVYCAPQT 112
+ I + + +Y +
Sbjct: 67 ---SNPEIYVGEVLYVDERK 83
>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 = 35.2 bits (80), Expect = 0.020
Identities = 17/153 (11%), Positives = 41/153 (26%), Gaps = 52/153 (33%)
Query: 75 DVIGPVSGPVYCVRFNSHQHIVD------SNIKIDQDVYCAPQTEHTSYVPLPDLIKVKG 128
D++ V + F+ + + D S +ID + + + L + K
Sbjct: 20 DIL-SVFEDAFVDNFDC-KDVQDMPKSILSKEEID-HIIMSKDAVSGTLR-LFWTLLSKQ 75
Query: 129 S-------------DASW------ERDQEPPPEVVEFSDDEEERRVKRNQLRTRNNRNTS 169
+ + ++P + + +R++L
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE-------QRDRLYN------- 121
Query: 170 STDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLM 202
D +R + + LR L+
Sbjct: 122 -----DNQVFAKYNVSRL----QPYLKLRQALL 145
Score = 29.8 bits (66), Expect = 1.2
Identities = 46/324 (14%), Positives = 89/324 (27%), Gaps = 104/324 (32%)
Query: 7 KGELDLGDLPPIEDLQISVPEDQCLPVGKILNIVD----TLVLIKTLKNTPTLDLDSVLF 62
D D ++D+ S+ + + I+ D TL L TL + + F
Sbjct: 30 VDNFDCKD---VQDMPKSILSKE--EIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK--F 82
Query: 63 LDKG-QRSLGKIFDVI-----GPVSGP----VYCVR--FNSHQHIVDSNIKIDQDVY--- 107
+++ + + + I P S + +N +Q N+ Q
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQP-SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
Query: 108 -CAPQTEHTSYVPLPDLIKVKGSDASW---------ERDQEPPPEV--VEFSDDEEERRV 155
+ V + + GS +W + + ++ + + V
Sbjct: 142 QALLELRPAKNVLIDGV---LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 156 --KRNQLRTRNNRN-TSSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTASYER---- 208
+L + + N TS +D + + + LR LL + YE
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIH---------SIQAELRRLLKSKPYENCLLV 249
Query: 209 -RNRINDTAT------------TSRPAN-------------------KSFTPG---SI-- 231
N + + T+R + TP S+
Sbjct: 250 LLN-VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308
Query: 232 ----IRAPTLP----DIPPLPLPM 247
R LP P L +
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSI 332
>3u28_C H/ACA ribonucleoprotein complex subunit 1; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_C
Length = 114
Score = 32.6 bits (74), Expect = 0.043
Identities = 15/86 (17%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 26 PEDQCLPVGKILNIV-DTLVLIKTLKNTPTLDLDSVLFLDKGQRSLGKIFDVIGPVSGPV 84
P D L +G L+ +V P + + ++L+ + +GK+ +++GP++
Sbjct: 23 PPDTVLEMGAFLHPCEGDIVCRSINTKIPYFN--APIYLENKTQ-VGKVDEILGPLNEVF 79
Query: 85 YCVRFNSHQHIVDSNIKIDQDVYCAP 110
+ ++ + ++ K Y A
Sbjct: 80 FTIKCGD--GVQATSFKEGDKFYIAA 103
>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 = 31.2 bits (70), Expect = 0.50
Identities = 35/190 (18%), Positives = 60/190 (31%), Gaps = 69/190 (36%)
Query: 14 DLPPIEDLQISVPEDQCLPVGKILNIVDTLVLIKTLKNTPTLDLDSVL-FLDKGQRSLGK 72
LPP L+ S+ ++ +P +L+I + L + V +++K L
Sbjct: 318 SLPP-SILEDSLENNEGVP-SPMLSISN-------------LTQEQVQDYVNKTNSHL-- 360
Query: 73 IFDVIGPVSGPVYCVRFNSHQHIVDS--------------NIK----IDQDVYCAPQTE- 113
P V N +++V S K +DQ P +E
Sbjct: 361 ------PAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR--IPFSER 412
Query: 114 ---------------HTSY-VPLPDLIK--VKGSDASWERDQ--EPPPEVVEFSDDEEER 153
H+ VP DLI + ++ S+ P V + D +
Sbjct: 413 KLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIP----VYDTFDGSDL 468
Query: 154 RVKRNQLRTR 163
RV + R
Sbjct: 469 RVLSGSISER 478
>3iot_A Maltose-binding protein, huntingtin fusion protein; HTT-EX1, HD,
sugar transport, transport, apoptosis, cytoplasm,
disease mutation; 3.50A {Escherichia coli k-12} PDB:
3io6_A 3io4_A 3ior_A 3iou_A 3iov_A 3iow_A
Length = 449
Score = 29.8 bits (67), Expect = 1.1
Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 6/77 (7%)
Query: 145 EFSDDEEERRVKRNQLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTA 204
+ E + + Q + + + PP PP P + P P Q + LL
Sbjct: 376 KLMKAFESLKSFQQQQQQQQQQQQQQQ-QQPPPPPPPPPPPQLPQPPPQA---QPLLPQQ 431
Query: 205 SYERRNRINDTATTSRP 221
SY+ T R
Sbjct: 432 SYQITAGK--LGTGRRF 446
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 29.3 bits (65), Expect = 1.3
Identities = 19/124 (15%), Positives = 33/124 (26%), Gaps = 14/124 (11%)
Query: 144 VEFSDDEEERRVKRN-QLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLM 202
V + +++ R + +N T E ++R+ T Q
Sbjct: 117 VGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS------G 170
Query: 203 TASYERRNRINDTATTSRPANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQH 262
+ A + PG++ P + P PPP F Q
Sbjct: 171 EGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFP-------GPAGPGGPPPPFPAGQT 223
Query: 263 QHQQ 266
H
Sbjct: 224 HHHH 227
>2rjo_A Twin-arginine translocation pathway signal protei; PSI-2, NYSGXRC,
twin arginine translocation pathway signal P structural
genomics; HET: GAL; 2.05A {Burkholderia phytofirmans}
Length = 332
Score = 28.6 bits (64), Expect = 2.2
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 62 FLDKGQRSLGKIFDVIGPVSGPV-YCVRFNSHQH 94
+ + + ++ V+GPV Y + H H
Sbjct: 299 VIARAASPKAEWNNLYARVAGPVVYREGHHHHHH 332
>1e1o_A Lysyl-tRNA synthetase, heat inducible; ligase, aminoacyl-tRNA
synthetase, protein biosynthesis; HET: LYS; 2.12A
{Escherichia coli} SCOP: b.40.4.1 d.104.1.1 PDB: 1e1t_A*
1e22_A* 1e24_A* 1lyl_A 1bbu_A* 1bbw_A 1krs_A 1krt_A
Length = 504
Score = 28.6 bits (65), Expect = 2.7
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 134 ERDQEPPPEVVEFSDDEEERRVKRNQLRTRNN 165
E++ E ++F+D+ RR K LR +
Sbjct: 2 EQETRGANEAIDFNDELRNRREKLAALRQQGV 33
>3pl8_A Pyranose 2-oxidase; substrate complex, H167A mutant, homotetramer,
GMC oxidoredu PHBH fold, rossmann domain,
oxidoreductase; HET: FAD MES G3F; 1.35A {Trametes
ochracea} PDB: 2igo_A* 3lsm_A* 2ign_A* 3k4c_A* 1tt0_A*
2igk_A* 3k4b_A* 3lsk_A* 3bg6_A* 3lsh_A* 3lsi_A* 2igm_A*
3k4j_A* 3k4m_A* 3bg7_A* 3k4k_A* 3k4l_A* 3bly_A* 1tzl_A*
3fdy_A* ...
Length = 623
Score = 28.3 bits (62), Expect = 3.7
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 221 PANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRF 257
A SF + +A +PPLP P + ++
Sbjct: 12 FAKSSFRSAAAQKASA-SSLPPLPGPDKKVPGMDIKY 47
>2g5d_A GNA33; hydrolase, beta barrel; 1.95A {Neisseria gonorrhoeae fa
1090} SCOP: b.52.1.4 PDB: 2g6g_A
Length = 422
Score = 27.6 bits (60), Expect = 4.9
Identities = 8/46 (17%), Positives = 12/46 (26%)
Query: 227 TPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETPLLF 272
+ I+ PD + P P P T T +
Sbjct: 2 SQSRSIQTFPQPDTSVINGPDRPAGIPDPAGTTVAGGGAVYTVVPH 47
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 27.1 bits (59), Expect = 7.8
Identities = 10/42 (23%), Positives = 12/42 (28%), Gaps = 2/42 (4%)
Query: 228 PGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETP 269
+ P P + Q PP P Q Q TP
Sbjct: 25 QPAQFMPPQDP--AAAGMSYGQMGMPPQGAVPSMGQQQFLTP 64
>3gcf_A Terminal oxygenase component of carbazole 1,9A- dioxygenase; rieske
oxygenase, 2Fe-2S, electron transfer, oxidoreductase;
2.30A {Nocardioides aromaticivorans}
Length = 394
Score = 26.9 bits (59), Expect = 9.0
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 168 TSSTDGTDPPDVPPEPKTRRPTPFEQRMNLRN 199
++S + +DP + + P E + N
Sbjct: 2 STSQEISDPAQATSSAQVKWPRYLEATLGFDN 33
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 0.135 0.406
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,232,436
Number of extensions: 248059
Number of successful extensions: 544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 36
Length of query: 274
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 182
Effective length of database: 4,133,061
Effective search space: 752217102
Effective search space used: 752217102
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: 42 (22.0 bits)
S2: 56 (25.2 bits)