RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8680
(180 letters)
>1sqw_A Saccharomyces cerevisiae NIP7P homolog; PUA, unknown function;
1.90A {Homo sapiens} SCOP: b.122.1.1 d.17.6.3 PDB:
1t5y_A
Length = 188
Score = 209 bits (534), Expect = 4e-70
Identities = 93/172 (54%), Positives = 115/172 (66%), Gaps = 38/172 (22%)
Query: 2 RDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVK 61
DRV+YVSEKI+ LA N D L++LGTCFGKFTK+ KFRLH+TAL YLAPYA+
Sbjct: 41 NDRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKFRLHVTALDYLAPYAK------ 94
Query: 62 PQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARIT 121
+KVW+KP AEQ FLYG+++LKSGL RIT
Sbjct: 95 --------------------------------YKVWIKPGAEQSFLYGNHVLKSGLGRIT 122
Query: 122 ENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIR 173
ENT +YQGV+V +M D+PLGFGVAAKST +C+ DP+AIV F+Q+DIGEY+R
Sbjct: 123 ENTSQYQGVVVYSMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVR 174
>2p38_A Protein involved in ribosomal biogenesis; two alpha/beta domains,
PUA domain, biosynthetic protein; 1.80A {Pyrococcus
abyssi}
Length = 166
Score = 110 bits (276), Expect = 2e-31
Identities = 29/176 (16%), Positives = 50/176 (28%), Gaps = 54/176 (30%)
Query: 2 RDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSG----KFRLHITALSYLAPYAQFK 57
V+ V+E++ + E+ +LGT G KF ++ L +
Sbjct: 40 YRDVYAVNEEVWKIIEDINMR-PYSLGTFVGTIRVDENLVEKFYPNLEFF-SLIKLEKNY 97
Query: 58 VWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGL 117
V + P+A F G + K + I
Sbjct: 98 VILGPKASFLFTTGKDAPKEAVREIKWQGS------------------------------ 127
Query: 118 ARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIR 173
+ V+VLN +G G+ N D+GE++R
Sbjct: 128 ----------KRVVVLNDLGDIIGIGLINP--------KSDRRFIKNLKDVGEFLR 165
>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR
structure initiative; 2.10A {Thermoplasma acidophilum
dsm 1728} SCOP: b.122.1.1 d.17.6.2
Length = 153
Score = 39.8 bits (93), Expect = 1e-04
Identities = 12/64 (18%), Positives = 22/64 (34%)
Query: 88 KYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAK 147
V V AE L G ++ G+ + ++ K + V + + G+A
Sbjct: 65 YRNPSRNIVTVDEGAEPHILNGSDLFAPGIVSMDDSIRKGDMIFVKSSKGYFIAVGMAEM 124
Query: 148 STAE 151
E
Sbjct: 125 DAGE 128
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_A
Length = 400
Score = 36.7 bits (85), Expect = 0.003
Identities = 14/62 (22%), Positives = 25/62 (40%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 154
++ VK A YG ++ GL R E Y ++++ + +A ST +
Sbjct: 268 RIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLAS 327
Query: 155 AD 156
D
Sbjct: 328 CD 329
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP
assembly, X-linked dyskeratosis congenita; 2.80A
{Saccharomyces cerevisiae}
Length = 195
Score = 35.8 bits (82), Expect = 0.003
Identities = 14/62 (22%), Positives = 25/62 (40%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 154
++ VK A YG ++ GL R E Y ++++ + +A ST +
Sbjct: 77 RIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLAS 136
Query: 155 AD 156
D
Sbjct: 137 CD 138
>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown
function; 1.73A {Pyrococcus horikoshii}
Length = 179
Score = 34.8 bits (80), Expect = 0.007
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGV-IVLNMNDVPLGFGVAAKSTAE 151
+V V A L G +++ G+ E + V +V PL G+A S
Sbjct: 96 RVVVDEGAVPHILNGADVMAPGIVDADEGIKEGDFVFVVEEKYGRPLAIGIALMSGKV 153
>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 = 0.050
Identities = 29/193 (15%), Positives = 56/193 (29%), Gaps = 41/193 (21%)
Query: 3 DRVFYVSEKILTLAENFG-------------PDHLLALGTCFGKFTKSGKFRLHITALSY 49
D + ++ + P L L K ++ LH + + +
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL-----KVKLENEYALHRSIVDH 452
Query: 50 LAPYAQFKVW--VKPQADQ---QFLYGHNILKSGLARITENTPK-YQGVIF---KV---- 96
F + P DQ + GH++ + F K+
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHI-GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDS 511
Query: 97 --WVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 154
W + L LK I +N PKY+ ++ ++ +P ++ K
Sbjct: 512 TAWNASGSILNTL---QQLKFYKPYICDNDPKYERLVNAILDFLP----KIEENLICSKY 564
Query: 155 ADPLAIVGFNQSD 167
D L I + +
Sbjct: 565 TDLLRIALMAEDE 577
>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 = 31.6 bits (71), Expect = 0.13
Identities = 35/195 (17%), Positives = 55/195 (28%), Gaps = 82/195 (42%)
Query: 1 MRDRVFYVSEKILTLA-ENFGPD-------HLLALGTCFGKFTKSGKFRLHITALSYLAP 52
++++ F KIL E F D L+ KF L Y++
Sbjct: 33 LQEQ-FN---KILPEPTEGFAADDEPTTPAELVG------------KF------LGYVSS 70
Query: 53 YAQFKVWVKPQADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNI 112
V+P QF +L L F E +L G++I
Sbjct: 71 L------VEPSKVGQF---DQVLNLCLTE------------F--------ENCYLEGNDI 101
Query: 113 --LKSGLARITENTPK---------YQGVIVLNMNDVPLG----FGVAAKSTAECKLADP 157
L + L + + T I+ F + A +L
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA--QLV-- 157
Query: 158 LAIVGFN-QSDIGEY 171
AI F Q + +Y
Sbjct: 158 -AI--FGGQGNTDDY 169
>3c0k_A UPF0064 protein YCCW; PUA domain, adoMet dependent
methyltransferase fold; 2.00A {Escherichia coli K12}
Length = 396
Score = 29.6 bits (67), Expect = 0.56
Identities = 7/50 (14%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 95 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 143
++ + E+ L H + +AR+ + + +++ L G
Sbjct: 4 RLVLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARG 53
>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics,
NPPSFA, national project on structural and functional
analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1
d.17.6.4 PDB: 2cx1_A* 1zs7_A
Length = 187
Score = 28.3 bits (63), Expect = 1.00
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGV-IVLNMNDVPLGFGVAAKSTAE 151
V V A G +++ G+ + + + V + + P+ GVA ++
Sbjct: 94 VVLVDKGAAIALAKGAHLMIPGVVGVEGSFTRGDVVAALYHETRTPVMVGVAEVDSSA 151
>2as0_A Hypothetical protein PH1915; RNA methyltransferase, structural
genomics, PSI, protein structure initiative; 1.80A
{Pyrococcus horikoshii} SCOP: b.122.1.9 c.66.1.51
Length = 396
Score = 28.6 bits (64), Expect = 1.1
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 95 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 143
+V V QA + G + K G+ R+ + V V LG G
Sbjct: 3 RVVVDAQAARAIGKGAMIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKG 52
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A
Length = 419
Score = 28.8 bits (64), Expect = 1.1
Identities = 6/23 (26%), Positives = 15/23 (65%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P+A++G N + +Y+ ++ + L
Sbjct: 336 PVALLGMNADLMNQYVEFVADRL 358
>1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase,
ribonucleotide reductase, dinuclear metal-cluster; 2.2A
{Mus musculus} SCOP: a.25.1.2 PDB: 1h0n_A 1w68_A 1w69_A
1xsm_A 2uw2_A 3hf1_A 2vux_A
Length = 390
Score = 28.3 bits (63), Expect = 1.5
Identities = 6/23 (26%), Positives = 15/23 (65%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P+ ++G N + + +YI ++ + L
Sbjct: 310 PVKLIGMNCTLMKQYIEFVADRL 332
>1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1sms_A
Length = 345
Score = 28.3 bits (63), Expect = 1.6
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P+ G + I YI ++ + L
Sbjct: 263 PVEKFGMDLKSIHTYIEFVADGL 285
>2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb
PY03671, S genomics consortium, SGC, oxidoreductase;
2.70A {Plasmodium yoelii yoelii}
Length = 349
Score = 27.9 bits (62), Expect = 1.7
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P ++G N + +YI ++ + L
Sbjct: 269 PCDLIGMNSRLMSQYIEFVADRL 291
>1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen
activation, iron coupled radical, immune EVAS
replication, oxidoreductase; 1.70A {Chlamydia
trachomatis} SCOP: a.25.1.2 PDB: 4d8g_A 4d8f_A 2ani_A
Length = 346
Score = 27.7 bits (62), Expect = 1.9
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P I+G S +Y++++ +
Sbjct: 277 PRGILGLRASMFIDYVQHIADRR 299
>1wxx_A TT1595, hypothetical protein TTHA1280; thermus thermophillus,
methyltransferase, adoMet, structural genomics; 1.80A
{Thermus thermophilus} SCOP: b.122.1.9 c.66.1.51 PDB:
1wxw_A 2cww_A*
Length = 382
Score = 27.7 bits (62), Expect = 2.3
Identities = 6/50 (12%), Positives = 15/50 (30%), Gaps = 5/50 (10%)
Query: 95 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 143
++ V + + L H + + + E G+ + L
Sbjct: 2 RIQVNAKGAARLLSRHLWVFRRDVVSGPETP----GLYPVYWGRRFLALA 47
>3olj_A Ribonucleoside-diphosphate reductase subunit M2; metal-binding,
HRRM2, oxidoreductase; 2.10A {Homo sapiens}
Length = 286
Score = 27.5 bits (61), Expect = 2.5
Identities = 6/23 (26%), Positives = 15/23 (65%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P+ ++G N + + +YI ++ + L
Sbjct: 245 PVKLIGMNCTLMKQYIEFVADRL 267
>2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide
reductase, oxidoreductase, DNA replication, iron,
DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax}
Length = 311
Score = 27.5 bits (61), Expect = 2.5
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 157 PLAIVGFNQSDIGEYIRYMTNML 179
P ++G N + +YI ++ + L
Sbjct: 268 PCDLIGMNSRLMSQYIEFVADRL 290
>1efv_A Electron transfer flavoprotein; electron transport, glutaric
acidemia type II; HET: FAD AMP; 2.10A {Homo sapiens}
SCOP: c.26.2.3 c.31.1.2 PDB: 2a1u_A* 1t9g_R* 2a1t_R*
Length = 315
Score = 27.5 bits (62), Expect = 2.7
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 8 VSEKILTLAENFGPDHLLALGTCFGK 33
++ IL + F H+ A + FGK
Sbjct: 74 LTPLILATQKQFNYTHICAGASAFGK 99
>4a58_A Ribonucleoside-diphosphate reductase small chain; oxidoreductase,
epstein-BARR virus, R2 subunit; 1.68A {Human herpesvirus
4} PDB: 4a5c_A 4a5d_A 4a5e_A 4a5f_A 4a5h_A 4a5i_A 4a5j_A
Length = 324
Score = 27.2 bits (61), Expect = 3.3
Identities = 2/31 (6%), Positives = 10/31 (32%), Gaps = 2/31 (6%)
Query: 151 ECKLAD--PLAIVGFNQSDIGEYIRYMTNML 179
E + + + I +++ + +
Sbjct: 247 ETAFIEARGEGVTLVDVRAIKQFLEATADRI 277
>2rcc_A Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1,
putative class I ribonucleotide reductase,
ribonucleotide reductase; HET: MSE PGE PG4; 1.90A
{Bacillus halodurans c-125}
Length = 346
Score = 26.9 bits (60), Expect = 3.6
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 160 IVGFNQSDIGEYIRYMTN 177
I G N D+ YI ++ N
Sbjct: 273 IPGINPEDMETYISFIAN 290
>1mxr_A Ribonucleotide reductase R2; radical protein, DI iron,
oxidoreductase; 1.42A {Escherichia coli} SCOP: a.25.1.2
PDB: 1jpr_A 1jqc_A 1xik_A 3uus_E* 1yfd_A 1piy_A 1r65_A
2xof_A* 1biq_B* 1rsv_A 1piz_A 1piu_A 1pim_A 1rsr_A
1biq_A* 1rib_A 1mrr_A 1rnr_A* 1pj0_A 1pj1_A ...
Length = 375
Score = 26.2 bits (58), Expect = 6.7
Identities = 6/19 (31%), Positives = 14/19 (73%)
Query: 159 AIVGFNQSDIGEYIRYMTN 177
+++G N+ + +Y+ Y+TN
Sbjct: 295 SMIGLNKDILCQYVEYITN 313
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
0.323 0.139 0.419
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,714,420
Number of extensions: 152666
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 27
Length of query: 180
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 92
Effective length of database: 4,244,745
Effective search space: 390516540
Effective search space used: 390516540
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 (24.6 bits)