RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18092
(183 letters)
>2yyb_A Hypothetical protein TTHA1606; structural genomics, unknown
function; 2.60A {Thermus thermophilus}
Length = 242
Score = 83.1 bits (206), Expect = 4e-20
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 122 MINSIAVCAGSGGELLRGKKADLYITGEMSHHDVLDATHRGTTVLLLEHSDSERPFLQFF 181
+ ++ + +GSG LL ADL++TGE H + RG V+ H D+E ++
Sbjct: 162 HVETVILVSGSGTGLLPKVDADLFVTGEPKHSVFHETFERGLNVIYAGHYDTETFGVKAL 221
>2fyw_A Conserved hypothetical protein; structural genomics, PSI, midwest
CENT structural genomics, MCSG, protein structure
initiative; 2.40A {Streptococcus pneumoniae} SCOP:
c.135.1.1
Length = 267
Score = 80.8 bits (200), Expect = 4e-19
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 107 TSTHVLIKDSDLDEIMINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVLDATHRGT 163
S ++ D + I+ +A+C GSG K AD+YITG++ +H D G
Sbjct: 161 DSLRMVHYQEDDLQKPISRVAICGGSGQSFYKDALAKGADVYITGDIYYHTAQDMLSDGL 220
Query: 164 TVLLLEHSDSERPFLQFF 181
L H E F++
Sbjct: 221 LALDPGHY-IEVIFVEKI 237
>2nyd_A UPF0135 protein SA1388; hypothetical protein SA1388,
selenomethionine SAD, unknown F; 2.00A {Staphylococcus
aureus subsp} PDB: 3lnl_A*
Length = 370
Score = 82.0 bits (202), Expect = 5e-19
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 122 MINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVLDATHRGTTVLLLEHSDSERPFL 178
I IA+ GSG + AD+++TG++ HHD LDA G ++ + H SE
Sbjct: 279 KIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHY-SEYVMK 337
Query: 179 QFF 181
+
Sbjct: 338 EGL 340
>1nmo_A Hypothetical protein YBGI; toroidal structure, structure 2 project,
S2F, structural genomics, unknown function; 2.20A
{Escherichia coli} SCOP: c.135.1.1 PDB: 1nmp_A
Length = 247
Score = 77.7 bits (192), Expect = 5e-18
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 122 MINSIAVCAGSGGELL---RGKKADLYITGEMSHHDVLDATHRGTTVLLLEHSDSERPFL 178
++ +A C G G + D +ITGE+S + A +G H +ER +
Sbjct: 164 VVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGI 223
Query: 179 QFF 181
+
Sbjct: 224 RAL 226
>2gx8_A NIF3-related protein; structural genomics, unknown function,
protein structure initiative, midwest center for
structural genomics, MCSG; HET: EPE; 2.20A {Bacillus
cereus} SCOP: c.135.1.1
Length = 397
Score = 69.7 bits (170), Expect = 1e-14
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 122 MINSIAVCAGSGGELLRG---KKADLYITGEMSHHDVLDATHRGTTVLLLEHSDSERPFL 178
+ +AV G G + + K AD+Y+TG+M +H DA G ++ H+ E+
Sbjct: 306 KVRKVAVLGGDGNKYINQAKFKGADVYVTGDMYYHVAHDAMMLGLNIVDPGHN-VEKVMK 364
Query: 179 QFF 181
Q
Sbjct: 365 QGV 367
>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 = 43.5 bits (102), Expect = 2e-05
Identities = 38/218 (17%), Positives = 66/218 (30%), Gaps = 60/218 (27%)
Query: 10 GSPAFIRVCLL--------STRPRVCF----PPGTDNVRSRNGWLSPI--LSSFSLRF-- 53
GS + LL +++ + F P T+ + + +P + F L +
Sbjct: 14 GS---LEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF-LGYVS 69
Query: 54 ----RDDKTARDTVSRVVTRLF------------AMEKIPGSNPTINKKKLD---SYFDG 94
D V + F K+ N T K + +Y
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Query: 95 KHFGVSIHTVANTSTHVLIKDSDLDEIMINSIAVCAGSG------GELLRGKKADLYITG 148
+ ++ S L + + +A+ G G EL DLY
Sbjct: 130 RI--MAKRPFDKKSNSALFRAVGEGNAQL--VAIFGGQGNTDDYFEEL-----RDLY--- 177
Query: 149 EMSHHDVLDATHRGTTVL--LLEHS-DSERPFLQFFSI 183
+ H V D L L+ + D+E+ F Q +I
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
Score = 33.5 bits (76), Expect = 0.038
Identities = 37/191 (19%), Positives = 63/191 (32%), Gaps = 55/191 (28%)
Query: 22 TRPRVCFPPGT--DNVRSRNGWLSPILSSFSLRFRDDKTARDTVSRVVTRLFAMEKI--- 76
P PP D++ + G SP+L S+ + +D V++ + L A +++
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPML---SISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
Query: 77 -------------PGS----NPTINKKKLDSYFD-------------GKHFG-VSI--HT 103
P S N T+ K K S D F V+ H+
Sbjct: 370 LVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHS 429
Query: 104 -VANTSTHVLIKDSDLDEIMINS----IAVCAGSGGELLRGKKADLY--ITGEMSHHDV- 155
+ ++ ++ KD + + N+ I V G LR + I + V
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489
Query: 156 ------LDATH 160
ATH
Sbjct: 490 WETTTQFKATH 500
Score = 30.8 bits (69), Expect = 0.25
Identities = 42/211 (19%), Positives = 64/211 (30%), Gaps = 81/211 (38%)
Query: 6 VSTIGSPAFIRVCLLSTRPRVCFPPGTDNVRSRNGWLSPILSS-----FSLRFRDDKTA- 59
VS G P + L+ R + P G D +SR I S FS RF +
Sbjct: 379 VS--GPPQSLYGLNLTLR-KAKAPSGLD--QSR------IPFSERKLKFSNRF-LPVASP 426
Query: 60 ------RDTVSRVVTRLFAME--------KIP------GSNPTINKKKLDSYFDGKH--- 96
+ L +IP GS+ + L +
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL----RVLSGSISERIVDC 482
Query: 97 -FGVSIH---TVANTSTHVLIKDSDLDEIMINSIAVCAGSGGELLRGKKADLYITGEMSH 152
+ + T +TH+L D G GG + L G ++H
Sbjct: 483 IIRLPVKWETTTQFKATHIL----DF------------GPGGA------SGL---GVLTH 517
Query: 153 HDVLDATHRGTTVLL---LEHS-DSERPFLQ 179
D T G V++ L+ + D + F Q
Sbjct: 518 R-NKDGT--GVRVIVAGTLDINPDDDYGFKQ 545
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 0.76
Identities = 5/29 (17%), Positives = 10/29 (34%), Gaps = 8/29 (27%)
Query: 60 RDTVSRVVTRL--FAMEKIPGSNP--TIN 84
+ + ++ L +A S P I
Sbjct: 19 KQALKKLQASLKLYA----DDSAPALAIK 43
>3r8n_I 30S ribosomal protein S9; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_I 3fih_I* 3iy8_I 2wwl_I
3oar_I 3oaq_I 3ofb_I 3ofa_I 3ofp_I 3ofx_I 3ofy_I 3ofo_I
3r8o_I 4a2i_I 2qal_I* 1p6g_I 1p87_I 2aw7_I 2avy_I
2i2u_I ...
Length = 127
Score = 25.9 bits (58), Expect = 4.6
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 11/37 (29%)
Query: 57 KTARDTVSRVVTRLFAMEKIPGS-NPTINKKKLDSYF 92
K++ +RV + PG+ IN++ L+ YF
Sbjct: 10 KSS---AARV--FI-----KPGNGKIVINQRSLEQYF 36
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
d.14.1.1 PDB: 1gix_L* 1hnw_I* 1hnx_I* 1hnz_I* 1hr0_I
1i94_I* 1i95_I* 1i96_I* 1i97_I* 1ibk_I* 1ibl_I* 1ibm_I
1j5e_I 1jgo_L* 1jgp_L* 1jgq_L* 1ml5_L* 1n32_I* 1n33_I*
1n34_I ...
Length = 128
Score = 25.9 bits (58), Expect = 4.7
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 11/37 (29%)
Query: 57 KTARDTVSRVVTRLFAMEKIPGS-NPTINKKKLDSYF 92
K A V+RV L PG+ T+N + + YF
Sbjct: 11 KEA---VARV--FL-----RPGNGKVTVNGQDFNEYF 37
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 26.3 bits (59), Expect = 5.7
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 63 VSRVVTRLFAMEKIPGSNPTINK 85
V RV+ R +A+ PG NK
Sbjct: 141 VKRVLARCYAVSGWPGKKEVENK 163
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 197
Score = 26.3 bits (58), Expect = 6.0
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 11/39 (28%)
Query: 57 KTARDTVSRVVTRLFAMEKIPGS-NPTINKKKLDSYFDG 94
K A ++RV L G+ IN + Y G
Sbjct: 79 KCA---IARV--VL-----QEGTGKFIINYRDAKEYLQG 107
>1nmb_N N9 neuraminidase; complex (hydrolase-immunoglobulin), complex
(hydrolase- immunoglobulin) complex; HET: NAG BMA MAN;
2.20A {Influenza a virus} SCOP: b.68.1.1
Length = 470
Score = 26.5 bits (58), Expect = 6.0
Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 11/74 (14%)
Query: 26 VCFPPGTDNVRSR-----------NGWLSPILSSFSLRFRDDKTARDTVSRVVTRLFAME 74
+C P TDN R G + + FS + T+S + M
Sbjct: 319 ICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEML 378
Query: 75 KIPGSNPTINKKKL 88
K+P + K
Sbjct: 379 KVPNALTDDRSKPT 392
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 26.1 bits (58), Expect = 6.5
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 63 VSRVVTRLFAMEKIPGSNPTINK 85
V+RV+ R+ A+ P S +
Sbjct: 161 VARVLCRVRAIGADPSSTLVSQQ 183
>3f2v_A General stress protein 14; alpha-beta protein., structural
genomics, PSI-2, protein structure initiative; HET: FMN;
2.00A {Treponema denticola}
Length = 192
Score = 25.9 bits (57), Expect = 7.7
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 131 GSGGELLRGKKADLYIT 147
GS G+ L+G+K L ++
Sbjct: 92 GSKGKALKGRKIALAVS 108
>2xp1_A SPT6; transcription, IWS1, histone chaperone, mRNA export; 2.20A
{Antonospora locustae}
Length = 178
Score = 25.6 bits (56), Expect = 8.0
Identities = 7/60 (11%), Positives = 20/60 (33%), Gaps = 12/60 (20%)
Query: 94 GKHFGVSIHTVANTSTHVLIKD------------SDLDEIMINSIAVCAGSGGELLRGKK 141
+ + I ++ H+ I++ D+DE++ + + + K
Sbjct: 44 HGYCVLVIKFASDVFVHMKIEEHSEHYTCSNKHFEDIDEVISVYVRPILRNLKSIKAHAK 103
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 25.7 bits (57), Expect = 9.4
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 63 VSRVVTRLFAMEKIPGSNPTINKKKL 88
V RV++RLF + T +K+
Sbjct: 150 VMRVLSRLFLVTDDIAKPST--RKRF 173
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
0.322 0.137 0.404
Gapped
Lambda K H
0.267 0.0852 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,810,346
Number of extensions: 163707
Number of successful extensions: 322
Number of sequences better than 10.0: 1
Number of HSP's gapped: 318
Number of HSP's successfully gapped: 24
Length of query: 183
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 95
Effective length of database: 4,244,745
Effective search space: 403250775
Effective search space used: 403250775
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 (21.9 bits)
S2: 54 (24.4 bits)