RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8340
(173 letters)
>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 = 37.1 bits (85), Expect = 0.002
Identities = 21/118 (17%), Positives = 48/118 (40%), Gaps = 22/118 (18%)
Query: 48 SQNQMQEKLAP-KYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNI----PWP 102
+ E++ + +F + + ++K+ ST+ N +L+Q+ Y+ I P
Sbjct: 482 KNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY 541
Query: 103 E----DTIHYSSIVAPPSFKPSL---KYSDISRFECNYKDPQTKLYYYNIEEYKLIRK 153
E + + P + +L KY+D+ R +D + E +K +++
Sbjct: 542 ERLVNAILDFL-----PKIEENLICSKYTDLLRIALMAEDE----AIFE-EAHKQVQR 589
Score = 31.7 bits (71), Expect = 0.12
Identities = 18/126 (14%), Positives = 39/126 (30%), Gaps = 25/126 (19%)
Query: 62 FKNPEYEQRKLSRRSTSSNLPTKQWKSLKQ---ILSYEKNIP-------WPEDTIHYSSI 111
+K+ ++ S+ + L +++ + + +IP W + +
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV 406
Query: 112 VAPPSFKPSL--KYSDISRFE-----CNYKDPQTKLYYYN---IEEYKLIRKLPSD---- 157
V K SL K S K Y + ++ Y + + SD
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 158 -IVNGY 162
++ Y
Sbjct: 467 PYLDQY 472
Score = 27.9 bits (61), Expect = 2.4
Identities = 10/61 (16%), Positives = 16/61 (26%), Gaps = 7/61 (11%)
Query: 103 EDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGY 162
E Y I+ F+ + + F+C K EE I +
Sbjct: 13 EHQYQYKDIL--SVFEDAF----VDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTL 65
Query: 163 L 163
Sbjct: 66 R 66
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 32.4 bits (73), Expect = 0.052
Identities = 25/133 (18%), Positives = 51/133 (38%), Gaps = 20/133 (15%)
Query: 30 SKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSL 89
S G I++ S ++ + + + K+ P E + K++ L
Sbjct: 115 SVGMAIQVNYSSEVKENSVDSDDKAKVPPLIRIV-SGLELSD-------TKQKGKKF--L 164
Query: 90 KQILSYE--KNIPW--PEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNI 145
+++YE +NI P + I +S + + D +C + D +KLYY
Sbjct: 165 --VIAYEPFENIAIELPPNEILFSENNDMDNNNDGV---DELNKKCTFWDAISKLYYVQF 219
Query: 146 EEYKLIRKLPSDI 158
+K + +D+
Sbjct: 220 -FFKQAEQEQADV 231
>1us2_A Xylanase10C, endo-beta-1,4-xylanase; hydrolase, carbohydrate
binding module, xylan degradation; HET: XYP; 1.85A
{Cellvibrio japonicus} SCOP: b.18.1.11 c.1.8.3 PDB:
1us3_A
Length = 530
Score = 30.8 bits (69), Expect = 0.22
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 10/32 (31%)
Query: 135 DPQTKLYY--YNIEE--------YKLIRKLPS 156
DP LYY YNIE+ +++ +
Sbjct: 340 DPAVILYYNDYNIEQNNAKTTKMVDMVKDFQA 371
>1v0l_A Endo-1,4-beta-xylanase A; glycoside hydrolase family 10, xylan
degradation, isofagomine, hydrolase; 0.98A {Streptomyces
lividans} SCOP: c.1.8.3 PDB: 1e0x_A 1e0w_A* 1od8_A
1v0k_A 1v0m_A 1v0n_A 1e0v_A* 1xas_A 2g3i_A 2g3j_A*
2g4f_A 1v6y_A
Length = 313
Score = 30.3 bits (69), Expect = 0.25
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 11/31 (35%)
Query: 135 DPQTKLYY--YNIEE---------YKLIRKL 154
DP KL Y YN+E Y ++R
Sbjct: 162 DPSAKLCYNDYNVENWTWAKTQAMYNMVRDF 192
>2d1z_A Endo-1,4-beta-D-xylanase; TIM-barrel, retaining enzyme,
catalytic-site mutant, chemica hydrolase; 1.60A
{Streptomyces olivaceoviridis} PDB: 2d20_A* 2d22_A
2d23_A 2d24_A* 1xyf_A 1isw_A* 1isx_A* 1isy_A* 1isv_A*
1it0_A* 1v6u_A* 1v6v_A* 1v6w_A* 1v6x_A* 1isz_A
Length = 436
Score = 30.4 bits (68), Expect = 0.32
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 11/31 (35%)
Query: 135 DPQTKLYY--YNIEE---------YKLIRKL 154
DP KL Y YNIE Y ++R
Sbjct: 162 DPAAKLCYNDYNIENWTWAKTQGVYNMVRDF 192
>1i1w_A Endo-1,4-beta-xylanase; xylan degradation, hydrolase, glycosidase,
enzyme, ultra HIG resolution, cryo temperature, 1; HET:
PCA; 0.89A {Thermoascus aurantiacus} SCOP: c.1.8.3 PDB:
1i1x_A* 2bnj_A* 1gok_A 1gom_A 1goo_A 1goq_A* 1gor_A*
1k6a_A 3o2l_A 3nyd_A* 1tux_A 1b31_A 1b30_A 1b3v_A*
1b3w_A* 1b3x_A* 1b3y_A* 1b3z_A* 1bg4_A
Length = 303
Score = 30.0 bits (68), Expect = 0.36
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 11/31 (35%)
Query: 135 DPQTKLYY--YNIEE---------YKLIRKL 154
DP KLY YN++ ++K
Sbjct: 164 DPNAKLYINDYNLDSASYPKTQAIVNRVKKW 194
>1ta3_B Endo-1,4-beta-xylanase; beta alpha barrel (XIP-I), beta alpha
barrel (xylanase), HYD inhibitor-hydrolase complex; HET:
NAG; 1.70A {Emericella nidulans} SCOP: c.1.8.3
Length = 303
Score = 30.0 bits (68), Expect = 0.39
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 11/31 (35%)
Query: 135 DPQTKLYY--YNIEE---------YKLIRKL 154
DP KLY YN++ ++K
Sbjct: 163 DPDAKLYINDYNLDSASYAKTQAMASYVKKW 193
>1nq6_A XYS1; glycoside hydrolase family 10, xylanase, xylan degradation,,
hydrolase; 1.78A {Streptomyces halstedii} SCOP: c.1.8.3
Length = 302
Score = 30.0 bits (68), Expect = 0.39
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 10/32 (31%)
Query: 135 DPQTKLYY--YNIEE--------YKLIRKLPS 156
D KL Y YN + Y++++
Sbjct: 162 DADAKLCYNDYNTDGQNAKSNAVYEMVKDFKQ 193
>1xyz_A 1,4-beta-D-xylan-xylanohydrolase; glycosyl hydrolase, xylanase,
family F/10 of glycosyl hydrolases, glycosyltransferase;
1.40A {Clostridium thermocellum} SCOP: c.1.8.3
Length = 347
Score = 29.7 bits (67), Expect = 0.47
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 10/30 (33%)
Query: 135 DPQTKLYY--YNIEE--------YKLIRKL 154
DP L+Y YNIE+ + +I+ +
Sbjct: 189 DPDALLFYNDYNIEDLGPKSNAVFNMIKSM 218
>3niy_A Endo-1,4-beta-xylanase; TIM-barrel, hydrolase; 1.58A {Thermotoga
petrophila rku-1} PDB: 3nj3_A* 1vbr_A* 1vbu_A
Length = 341
Score = 29.7 bits (67), Expect = 0.50
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 10/30 (33%)
Query: 135 DPQTKLYY--YNIEE--------YKLIRKL 154
DP L Y Y+IEE Y +I++L
Sbjct: 183 DPDAILIYNDYSIEEINAKSNFVYNMIKEL 212
>1ur1_A Endoxylanase; hydrolase, family 10, glycoside hydrolase,
hemicellulose, xylan degradation; HET: XYS AHR; 1.43A
{Cellvibrio mixtus} SCOP: c.1.8.3 PDB: 1uqy_A* 1uqz_A*
1ur2_A* 2cnc_A*
Length = 378
Score = 29.5 bits (66), Expect = 0.61
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 9/29 (31%)
Query: 135 DPQTKLYY--YNIEE-------YKLIRKL 154
DP+ L Y YNIE ++I +L
Sbjct: 190 DPKAHLMYNDYNIERTGKREATVEMIERL 218
>3cui_A EXO-beta-1,4-glucanase; CEX, xylanase, isofagomine inhibitor, TIM
barrel, cellulose degradation, glycosidase, hydrolase;
HET: X4S; 1.50A {Cellulomonas fimi} PDB: 3cug_A* 3cuh_A*
3cuf_A* 3cuj_A* 1fh9_A* 1fh7_A 1fh8_A 1exp_A* 1fhd_A*
1j01_A* 2exo_A 2xyl_A 2his_A*
Length = 315
Score = 29.2 bits (66), Expect = 0.64
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 10/30 (33%)
Query: 135 DPQTKLYY--YNIEE--------YKLIRKL 154
DP KL YN+E Y L++
Sbjct: 161 DPTAKLCINDYNVEGINAKSNSLYDLVKDF 190
>2fvy_A D-galactose-binding periplasmic protein; periplasmic binding
protien, hinge, chemotaxis, transport,; HET: BGC; 0.92A
{Escherichia coli} SCOP: c.93.1.1 PDB: 1glg_A* 2fw0_A*
2gbp_A* 2qw1_A* 2hph_A* 2ipn_A* 2ipm_A* 2ipl_A* 1gca_A*
1gcg_A 3ga5_A* 3gbp_A*
Length = 309
Score = 28.9 bits (65), Expect = 0.92
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 12 ALYTLKDP--TNLL-AIQKFFSKGEGIEITMSQSQEDINSQNQMQEKL 56
+Y D + + AI++ +++ M+ SQ D + QN + L
Sbjct: 8 TIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVL 55
>4f8x_A Endo-1,4-beta-xylanase; TIM barrel, hydrolase; HET: NAG BMA; 1.47A
{Penicillium canescens}
Length = 335
Score = 28.6 bits (64), Expect = 0.98
Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 10/32 (31%)
Query: 133 YKDPQTKLYY--YNIEE--------YKLIRKL 154
KLYY Y IE +L+ L
Sbjct: 169 IGANDVKLYYNDYGIENPGTKSTAVLQLVSNL 200
>3emz_A Xylanase, endo-1,4-beta-xylanase; (alpha/beta)8 barrel, GH10 enzyme
complex, hydrolase; HET: HXH; 2.08A {Bacillus SP} PDB:
3emq_A* 3emc_A*
Length = 331
Score = 27.8 bits (62), Expect = 1.8
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 9/29 (31%)
Query: 135 DPQTKLYY--YNIEE-------YKLIRKL 154
DP L+Y YN + Y L+R L
Sbjct: 168 DPNALLFYNDYNETDPVKREKIYNLVRSL 196
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 27.7 bits (61), Expect = 2.5
Identities = 23/108 (21%), Positives = 35/108 (32%), Gaps = 14/108 (12%)
Query: 54 EKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQI-------LSYEKNIPWPEDTI 106
+ L +K + E +R S P + I L + P+ I
Sbjct: 185 DGLRLWGSWKRGKDESDLPEKRLLS---PLEVHTIFTHISSEDLAHLGLNEQYARPDWMI 241
Query: 107 HYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKL 154
V PPS +PS+ SR E D T I+ +R+
Sbjct: 242 ITVLPVPPPSVRPSISVDGTSRGE----DDLTHKLSDIIKANANVRRC 285
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 27.5 bits (61), Expect = 2.5
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 91 QILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLY 141
+IL Y+ PE I V P + +PS+ R E D T
Sbjct: 193 EILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAE----DDLTHKL 239
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 27.8 bits (61), Expect = 2.6
Identities = 20/97 (20%), Positives = 30/97 (30%), Gaps = 19/97 (19%)
Query: 52 MQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQI-------LSYEKNIPWPED 104
+ + E E R LS + K I L + + PE
Sbjct: 182 VGSWKKDRATGDADEPELRVLS--------TEEILNIFKHISVKDFTSLGFNEVFSRPEW 233
Query: 105 TIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLY 141
I V PP +PS+ +++ R E D T
Sbjct: 234 MILTCLPVPPPPVRPSISFNESQRGE----DDLTFKL 266
>1n82_A Xylanase, intra-cellular xylanase; hydrolase; 1.45A {Geobacillus
stearothermophilus} SCOP: c.1.8.3 PDB: 3mua_A* 2q8x_A*
3msd_A* 3msg_A* 3mui_A* 3ms8_A
Length = 331
Score = 27.4 bits (61), Expect = 2.7
Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 9/29 (31%)
Query: 135 DPQTKLYY--YNIEE-------YKLIRKL 154
DP L+Y YN + L++ L
Sbjct: 169 DPDALLFYNDYNECFPEKREKIFALVKSL 197
>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 = 26.9 bits (59), Expect = 4.0
Identities = 9/46 (19%), Positives = 22/46 (47%), Gaps = 10/46 (21%)
Query: 11 EALYTLKDPTNLLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKL 56
AL T+ + N + +QK I + + Q+ ++ + +++ L
Sbjct: 1860 RALDTVTNVLNFIKLQK---------IDIIELQKSLSLE-EVEGHL 1895
>2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target
base partner, 5-methylpyr 2(1H)-ONE, base flipping; HET:
5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27
d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A*
2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A*
Length = 421
Score = 26.5 bits (58), Expect = 5.5
Identities = 15/112 (13%), Positives = 32/112 (28%), Gaps = 1/112 (0%)
Query: 40 SQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNI 99
S + + + P + P +E + + + L +
Sbjct: 211 SGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAA 270
Query: 100 PWPEDTIHYSSIVAP-PSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKL 150
PE H + P P P L ++ +Y+ + L+ +L
Sbjct: 271 RSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKEL 322
>4dkl_A MU-type opioid receptor, lysozyme chimera; G-protein coupled
receptor, 7 transmembrane receptor, signal
protein-antagonist complex; HET: BF0 CLR MPG 1PE; 2.80A
{Mus musculus} PDB: 4ej4_A* 4djh_A*
Length = 464
Score = 26.1 bits (57), Expect = 7.7
Identities = 12/117 (10%), Positives = 36/117 (30%), Gaps = 3/117 (2%)
Query: 37 ITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQ-ILSY 95
IT ++++ N + + P Y+ RR+ N+ + ++ +
Sbjct: 269 ITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNS 328
Query: 96 EKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIR 152
+ + ++ S + + R ++ Y + ++ R
Sbjct: 329 LRMLQQKRWDEAAVNL--AKSRWYNQTPNRAKRVITTFRTGTWDAYEKDRNLRRITR 383
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
0.313 0.131 0.379
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,611,434
Number of extensions: 137293
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 30
Length of query: 173
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 86
Effective length of database: 4,272,666
Effective search space: 367449276
Effective search space used: 367449276
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 (21.9 bits)
S2: 54 (24.7 bits)