RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8679
(221 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 = 271 bits (694), Expect = 9e-94
Identities = 110/160 (68%), Positives = 136/160 (85%)
Query: 61 IGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKF 120
IG N++LL+DRPDGTYCFR DRV+YVSEKI+ LA N D L++LGTCFGKFTK+ KF
Sbjct: 20 IGENLQLLVDRPDGTYCFRLHNDRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKF 79
Query: 121 RLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDV 180
RLH+TAL YLAPYA++KVW+KP AEQ FLYG+++LKSGL RITENT +YQGV+V +M D+
Sbjct: 80 RLHVTALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADI 139
Query: 181 PLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIRCEDEL 220
PLGFGVAAKST +C+ DP+AIV F+Q+DIGEY+R E+ L
Sbjct: 140 PLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHEETL 179
>2p38_A Protein involved in ribosomal biogenesis; two alpha/beta domains,
PUA domain, biosynthetic protein; 1.80A {Pyrococcus
abyssi}
Length = 166
Score = 128 bits (322), Expect = 9e-38
Identities = 29/138 (21%), Positives = 50/138 (36%), Gaps = 16/138 (11%)
Query: 82 RDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSG----KFRLHITALSYLAPYAQFK 137
V+ V+E++ + E+ +LGT G KF ++ L +
Sbjct: 40 YRDVYAVNEEVWKIIEDINMR-PYSLGTFVGTIRVDENLVEKFYPNLEFF-SLIKLEKNY 97
Query: 138 VWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLA 197
V + P+A F G + K + I + V+VLN +G G+
Sbjct: 98 VILGPKASFLFTTGKDAPKEAVREIKWQGS--KRVVVLNDLGDIIGIGLINP-------- 147
Query: 198 DPLAIVGFNQSDIGEYIR 215
N D+GE++R
Sbjct: 148 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 = 42.4 bits (100), Expect = 2e-05
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 1/80 (1%)
Query: 114 FTKSGKFRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVI 173
++G + L+Y ++ V V AE L G ++ G+ + ++ K +
Sbjct: 50 VFQAGDLIPSVYLLNYR-NPSRNIVTVDEGAEPHILNGSDLFAPGIVSMDDSIRKGDMIF 108
Query: 174 VLNMNDVPLGFGVAAKSTAE 193
V + + G+A E
Sbjct: 109 VKSSKGYFIAVGMAEMDAGE 128
>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 = 41.2 bits (96), Expect = 2e-04
Identities = 35/190 (18%), Positives = 65/190 (34%), Gaps = 58/190 (30%)
Query: 59 GNIGSNVKLLIDRPDGTYCF-REMRDRVFYVSEKILTLA-ENFGPD-------HLLALGT 109
G++ LL+ P ++ +++++ F KIL E F D L+
Sbjct: 14 GSL--EHVLLV--PTASFFIASQLQEQ-FN---KILPEPTEGFAADDEPTTPAELVG--- 62
Query: 110 CFGKFTKSGKFRLHITALSYLAPYAQFKVWVK---PQAEQQFLYGHNI--LKSGLARITE 164
KF ++++L + QF + + E +L G++I L + L + +
Sbjct: 63 ---------KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND 113
Query: 165 NTPK---------YQGVIVLNMNDVPLG----FGVAAKSTAECKLADPLAIVGFN-QSDI 210
T I+ F + A +L AI F Q +
Sbjct: 114 TTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA--QLV---AI--FGGQGNT 166
Query: 211 GEYIRCEDEL 220
+Y +EL
Sbjct: 167 DDYF---EEL 173
Score = 28.1 bits (62), Expect = 3.2
Identities = 37/224 (16%), Positives = 68/224 (30%), Gaps = 70/224 (31%)
Query: 24 CFREMRDRVFY------VSEKILTLAENFGPDHLLALGTC-------FGNIGSNVKLLID 70
F E+RD Y V + I AE L L F G N+ ++
Sbjct: 169 YFEELRD--LYQTYHVLVGDLIKFSAE-----TLSELIRTTLDAEKVFTQ-GLNILEWLE 220
Query: 71 RPDGTYCFREMRDRVF----YVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITA 126
P T D+ + +S ++ + + H + G G+ R ++
Sbjct: 221 NPSNT------PDKDYLLSIPISCPLIGVIQ-LA--HYVVTAKLLGF--TPGELRSYLKG 269
Query: 127 LSYL-------APYAQFKVWVKPQAEQQFLYGHNILKS-------GLARITENTPKYQGV 172
+ A+ W + F ++ K+ G+ R E P
Sbjct: 270 ATGHSQGLVTAVAIAETDSW------ESFF--VSVRKAITVLFFIGV-RCYEAYPNTSLP 320
Query: 173 IVLNMNDVPLGFGVAAKSTAECKLADP-LAIVGFNQSDIGEYIR 215
+ + + GV + P L+I Q + +Y+
Sbjct: 321 PSILEDSLENNEGVPS----------PMLSISNLTQEQVQDYVN 354
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP
assembly, X-linked dyskeratosis congenita; 2.80A
{Saccharomyces cerevisiae}
Length = 195
Score = 36.5 bits (84), Expect = 0.003
Identities = 14/62 (22%), Positives = 25/62 (40%)
Query: 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKL 196
++ VK A YG ++ GL R E Y ++++ + +A ST +
Sbjct: 77 RIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLAS 136
Query: 197 AD 198
D
Sbjct: 137 CD 138
>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 = 0.004
Identities = 33/177 (18%), Positives = 59/177 (33%), Gaps = 42/177 (23%)
Query: 32 VFYVS-EK---ILTLAENFGPDHLLALGTCFGNIGSNVKLLIDRPDGTYCFREMRDRV-- 85
VF+ S E + TL + G + LG G +++ L R R
Sbjct: 185 VFWASCEAGTYMRTLCVHLG----MLLGV-----GGHMQELR------------RVRSGA 223
Query: 86 FYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHI----TALSYLAPYAQFKVWVK 141
++ ++TL + ++ + R I T L ++ VK
Sbjct: 224 LSENDNMVTLHD------VMDAQWVYDNTRDESYLRSIIQPLETLLVGYK-----RIVVK 272
Query: 142 PQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLAD 198
A YG ++ GL R E Y ++++ + +A ST + D
Sbjct: 273 DSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCD 329
>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown
function; 1.73A {Pyrococcus horikoshii}
Length = 179
Score = 35.2 bits (81), Expect = 0.008
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 137 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGV-IVLNMNDVPLGFGVAAKSTAE 193
+V V A L G +++ G+ E + V +V PL G+A S
Sbjct: 96 RVVVDEGAVPHILNGADVMAPGIVDADEGIKEGDFVFVVEEKYGRPLAIGIALMSGKV 153
>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 = 29.8 bits (67), Expect = 0.49
Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 5/75 (6%)
Query: 120 FRLHITALSYLAPYAQFKVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGV-IVLNMN 178
L + +L V V A G +++ G+ + + + V + +
Sbjct: 81 QCLKAFGVDWLKG----VVLVDKGAAIALAKGAHLMIPGVVGVEGSFTRGDVVAALYHET 136
Query: 179 DVPLGFGVAAKSTAE 193
P+ GVA ++
Sbjct: 137 RTPVMVGVAEVDSSA 151
>3c0k_A UPF0064 protein YCCW; PUA domain, adoMet dependent
methyltransferase fold; 2.00A {Escherichia coli K12}
Length = 396
Score = 29.2 bits (66), Expect = 0.94
Identities = 7/50 (14%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 137 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 185
++ + E+ L H + +AR+ + + +++ L G
Sbjct: 4 RLVLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARG 53
>2fr5_A Cytidine deaminase; tetrahydrouridine, protein-inhibitor COM
alternate conformation of Arg68, hydrolase; HET: TYU;
1.48A {Mus musculus} SCOP: c.97.1.1 PDB: 1zab_A* 2fr6_A*
1mq0_A*
Length = 146
Score = 28.7 bits (64), Expect = 1.0
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 10/49 (20%)
Query: 3 QVIHNIGSNVKLLIDRPDGTYCFREMRDRVFYVSEKILTLAENFGPDHL 51
QV+ G++ + + +PDGT+ R +++ +L + FGP+ L
Sbjct: 104 QVMREFGTDWAVYMTKPDGTFVVRTVQE--------LLPAS--FGPEDL 142
>2frx_A Hypothetical protein YEBU; rossmann-type
S-adenosylmethionine-dependent methyltransfera domain;
2.90A {Escherichia coli}
Length = 479
Score = 28.9 bits (65), Expect = 1.3
Identities = 14/114 (12%), Positives = 32/114 (28%), Gaps = 13/114 (11%)
Query: 73 DGTYCFREMRDRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAP 132
D + ++ I L LG + + +R A+ LA
Sbjct: 352 DENLRLWQRDKELWLFPVGIEALIGKV---RFSRLGIKLAET-HNKGYRWQHEAVIALAS 407
Query: 133 YAQFKVW-VKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFG 185
+ + PQ +++ G ++ +++ P+G
Sbjct: 408 PDNMNAFELTPQEAEEWYRGRDV--------YPQAAPVADDVLVTFQHQPIGLA 453
>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 = 1.7
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 137 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 185
+V V QA + G + K G+ R+ + V V LG G
Sbjct: 3 RVVVDAQAARAIGKGAMIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKG 52
>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 = 27.9 bits (63), Expect = 2.9
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 88 VSEKILTLAENFGPDHLLALGTCFGK 113
++ IL + F H+ A + FGK
Sbjct: 74 LTPLILATQKQFNYTHICAGASAFGK 99
>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 = 27.3 bits (61), Expect = 4.1
Identities = 6/50 (12%), Positives = 15/50 (30%), Gaps = 5/50 (10%)
Query: 137 KVWVKPQAEQQFLYGH-NILKSGLARITENTPKYQGVIVLNMNDVPLGFG 185
++ V + + L H + + + E G+ + L
Sbjct: 2 RIQVNAKGAARLLSRHLWVFRRDVVSGPETP----GLYPVYWGRRFLALA 47
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
0.324 0.142 0.435
Gapped
Lambda K H
0.267 0.0556 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,458,379
Number of extensions: 206930
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 520
Number of HSP's successfully gapped: 19
Length of query: 221
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,188,903
Effective search space: 548746293
Effective search space used: 548746293
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.4 bits)