RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase
[Candidatus Liberibacter asiaticus str. psy62]
(268 letters)
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 1.90A {Rhodobacter sphaeroides}
Length = 249
Score = 182 bits (463), Expect = 7e-47
Identities = 97/239 (40%), Positives = 142/239 (59%), Gaps = 1/239 (0%)
Query: 15 PVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVF 74
PV ILV PQ+GENIG ARAM NF L +LR+V+PRDGWP+ KA + ++ A ++D +F
Sbjct: 5 PVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLF 64
Query: 75 SNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTN 134
+ EAI D +++ATTAR R K V+ P+ A G+ VGI+FG ER GL N
Sbjct: 65 PTVAEAIRDCDYVFATTARGRELTKPVMTPERAMAHGRALTGEGRRVGILFGPERTGLEN 124
Query: 135 EEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKE-QNTPATKGELL 193
E++AL+NAI++ PVNP F SLN++Q VLL+ +E + + + + A+ E+
Sbjct: 125 EDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQHDETPPEVIDMARVDFASGLEVE 184
Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQ 252
D+ E LE G+F P EK M +L +++ R L R +V L G++ + +Q
Sbjct: 185 KLGDHFEEKLEAAGFFFPPEKAPGMKLNLRNMWARLPLTRADVQTLHGMLRQIAWKLKQ 243
>3ic6_A Putative methylase family protein; structural genomics, PSI-2,
protein structure initiative, midwest center for
structural genomics; 2.59A {Neisseria gonorrhoeae fa
1090}
Length = 223
Score = 126 bits (317), Expect = 5e-30
Identities = 56/219 (25%), Positives = 99/219 (45%), Gaps = 20/219 (9%)
Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPS------ 54
MT P L + IIL NIG ARAM L +L +V P
Sbjct: 4 MTALKPALPDYLGNIRIILTRTSHPANIGSAARAMKTMGLHRLTIVTPNLMATPMTENPP 63
Query: 55 -------------EKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSV 101
E++ ++ A V+ + + + L EA+AD A T+R R +
Sbjct: 64 VFNPDDVQSFALPEESFILASGAADVLHNAEIVATLDEALADTTIACALTSRRREITAPL 123
Query: 102 LAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAV 161
P++ L + G+ V ++FG E +GL+ EE+ N +++ NP + SLN++QAV
Sbjct: 124 QTPRDLVPELLQAANRGEKVALVFGNETFGLSIEEVRACNRLMTINGNPDYFSLNLAQAV 183
Query: 162 LLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLE 200
++ +E + S ++++++ AT ++ L ++E
Sbjct: 184 QVVCYEIF-SQTDSPMTHLQQEDHAATHEQIKGMLAHME 221
>3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004,
methylase family protein, haemophilus influenzae RD
KW20; 2.01A {Haemophilus influenzae}
Length = 244
Score = 117 bits (293), Expect = 3e-27
Identities = 70/244 (28%), Positives = 124/244 (50%), Gaps = 12/244 (4%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76
I+L++ NIG ARAM LTQL LV+P+ E++ + SA A+ ++ + RV +
Sbjct: 10 IVLIETSHSGNIGSAARAMKTMGLTQLCLVSPKS--VDEQSYALSAGAENIVKNARVVDS 67
Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136
EA+ D + T+AR R+ +++ P + + + I+FGRER GLTNEE
Sbjct: 68 FDEAVDDCSLVIGTSARLRHLQNTLIEP---RECAEKVVAYKGKIAIVFGRERIGLTNEE 124
Query: 137 IALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEK---NVKEQNTPATKGELL 193
+ + ++ P NP + SLN++ AV L+ +E +V + K + T +L
Sbjct: 125 LLKCHYHLNIPANPDYSSLNLAMAVQLVSYELRMAFLVQNNKKNSLSLIEKNYPTTDQLA 184
Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQS 253
F DY E + G+ + + ++ L ++ R +L + E+ +L G++S ++K +
Sbjct: 185 YFFDYTERIYQSLGFI----QNQGVMRKLKRLYYRAKLEKNELNILNGMLSAVEKRIDLT 240
Query: 254 SRRN 257
N
Sbjct: 241 KEDN 244
>3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase,
adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga
maritima}
Length = 192
Score = 107 bits (267), Expect = 3e-24
Identities = 21/163 (12%), Positives = 51/163 (31%), Gaps = 12/163 (7%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDG-----------WPSEKARSSSANAD 65
I+ ++ +AR +NL +V W + +
Sbjct: 20 SIISTAVTNLDVHDIARTARTYNLKGYYIVTNLRAQQDMVSKMLKFWREGFGSRYNPSRA 79
Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125
+ V++ S L++ + D+ + + I + +I
Sbjct: 80 ESLKLVKLKSYLEDVLEDIESVEGERPLIFFTSAKKRENDISFEEGRRIIIETEKPVLIL 139
Query: 126 GRERWGLTNEEIALSNAIISF-PVNPLFPSLNISQAVLLMVWE 167
WGL +E + +S+ ++ F L++ A +++
Sbjct: 140 LGTGWGLPDEILEISDYVLEPIRAQSDFNHLSVRAAAAIIIDR 182
>3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural
genomics, PSI-2, protein structure initiative; 2.30A
{Bordetella pertussis}
Length = 173
Score = 98.8 bits (245), Expect = 1e-21
Identities = 51/164 (31%), Positives = 78/164 (47%), Gaps = 4/164 (2%)
Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPR--DGWPSEKARSSSANAD 65
+ + I+ P N+G ARA+ +L LV PR D +A + ++ A
Sbjct: 4 MTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGAL 63
Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSG--QNVGI 123
V++ V L+EA+A + +A T R R+ +EAA + + V I
Sbjct: 64 DVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAI 123
Query: 124 IFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167
+ G ER GLTN +I L + I P NP + SLN++QA+ L WE
Sbjct: 124 VLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWE 167
>1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH;
2'O-methyltransferase, knot, montreal- kingston
bacterial structural genomics initiative, BSGI; 2.5A
{Escherichia coli} SCOP: c.116.1.1 d.79.3.3
Length = 253
Score = 73.7 bits (180), Expect = 4e-14
Identities = 26/161 (16%), Positives = 55/161 (34%), Gaps = 11/161 (6%)
Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66
+ + + ++IL N+G R+ + + + R + A+ + A
Sbjct: 98 LIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAE 157
Query: 67 VIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFG 126
+ +RV +NL + L L + + ++ G
Sbjct: 158 SVPLIRV-TNLARTMRMLQEENIWIVGTAGEADHTL----------YQSKMTGRLALVMG 206
Query: 127 RERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167
E G+ + +IS P+ SLN+S A + ++E
Sbjct: 207 AEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFE 247
>3n4j_A RNA methyltransferase; center for structural genomics of INF
diseases, csgid; 1.47A {Yersinia pestis} PDB: 3n4k_A*
1mxi_A* 1j85_A*
Length = 165
Score = 73.6 bits (180), Expect = 4e-14
Identities = 30/155 (19%), Positives = 55/155 (35%), Gaps = 10/155 (6%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76
I+L +P++ N G + R N QL L+ P +K + ++ +
Sbjct: 7 IVLFEPEIPPNTGNIIRLCANTGC-QLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHD 65
Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136
+ + AR + A + + N ++FG E GL
Sbjct: 66 YQAFLDSEKLDSTQPAR-------LFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYI 118
Query: 137 IALSN--AIISFPVNPLFPSLNISQAVLLMVWECM 169
+ I P+ S+N+S AV ++V+E
Sbjct: 119 LDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAW 153
>1mxi_A YIBK, hypothetical tRNA/RRNA methyltransferase HI0766;
S-adenosylhomocysteine, SPOU family, structure 2
function project; HET: SAH; 1.70A {Haemophilus
influenzae} SCOP: c.116.1.1 PDB: 1j85_A*
Length = 160
Score = 70.2 bits (171), Expect = 5e-13
Identities = 24/155 (15%), Positives = 50/155 (32%), Gaps = 15/155 (9%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76
I+L +P++ +N G + R N +L L+ P +K S ++
Sbjct: 4 IVLYEPEIPQNTGNIIRLCANTGF-RLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKT 62
Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE- 135
+ + + + ++ ++FG E G+
Sbjct: 63 FEAFLESEKPKRLFALTTKGCPA------------HSQVKFKLGDYLMFGPETRGIPMSI 110
Query: 136 -EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
I P+ S+N+S +V + V+E
Sbjct: 111 LNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAW 145
>3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode,
structural genomics; 2.40A {Burkholderia pseudomallei
305}
Length = 160
Score = 66.9 bits (162), Expect = 5e-12
Identities = 27/155 (17%), Positives = 45/155 (29%), Gaps = 13/155 (8%)
Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76
++LV+P++ N G V R N + K R + +
Sbjct: 8 VVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDW 67
Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136
A A + + A +FG E GL
Sbjct: 68 -----------DAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPAL 116
Query: 137 IALSNA--IISFPVNPLFPSLNISQAVLLMVWECM 169
+ + P+ P SLN+S V ++V+E
Sbjct: 117 VDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAW 151
>3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance
methyltransferase, 23S R methyltransferase; 2.00A
{Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A*
Length = 277
Score = 65.8 bits (160), Expect = 1e-11
Identities = 24/155 (15%), Positives = 56/155 (36%), Gaps = 10/155 (6%)
Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72
G V++L ++ NIG + R + LV+ +++ ++
Sbjct: 118 GGDVVVLDGVKIVGNIGAIVRTSLALGAAGIVLVDSDLATIADRRLLRASRGYVFSL--- 174
Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132
+ A + N+ ++ + + + + + ++FG E+ G
Sbjct: 175 -------PVVLADREEAVSFLRDNDIALMVLDTDGDLGVKDLGDRADRMALVFGSEKGGP 227
Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167
+ S +S P+ SLN+S +V + + E
Sbjct: 228 SGLFQEASAGTVSIPMLSSTESLNVSVSVGIALHE 262
>1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot,
rossmann fold, EL30-like fold, riken structural
genomics/proteomics initiative; 2.40A {Thermus
thermophilus} SCOP: c.116.1.1 d.79.3.3
Length = 274
Score = 64.5 bits (156), Expect = 2e-11
Identities = 27/164 (16%), Positives = 56/164 (34%), Gaps = 13/164 (7%)
Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANAD 65
+ + S +++ V + N+G V R+ + + D + + R+S+
Sbjct: 108 EEYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVF 167
Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125
+ S + + I + T + A L V I
Sbjct: 168 SLRTLAASESEVLDWIKQHNLPLVATTPH-------------AEALYWEANLRPPVAIAV 214
Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
G E GL + + + P+ SLN+S + L+++E +
Sbjct: 215 GPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEAL 258
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying
enzyme, topological knot; 1.85A {Aquifex aeolicus}
Length = 211
Score = 61.7 bits (149), Expect = 1e-10
Identities = 20/162 (12%), Positives = 60/162 (37%), Gaps = 11/162 (6%)
Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67
L+ K ++ + + N + R + L + +G ++ + +
Sbjct: 19 LEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHA-EGKKAKINEGITQGSHKW 77
Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127
+ +V + +++ + + + A + + + ++ G
Sbjct: 78 VFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVN----------FREVDYTKPTVLVVGN 127
Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
E G++ E + +++ I P+ + SLN+S A ++++E
Sbjct: 128 ELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQ 169
>1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A
{Streptomyces viridochromogenes} PDB: 1x7p_A*
Length = 287
Score = 57.7 bits (138), Expect = 2e-09
Identities = 24/154 (15%), Positives = 47/154 (30%), Gaps = 6/154 (3%)
Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75
++ P NIG + R+ L + K + S+
Sbjct: 128 GVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPK------SVRSSTGSLFSLP 181
Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135
++ + R ++ E Q ++ G E GL+N
Sbjct: 182 AVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNA 241
Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
L + +S P+ SLN + A +++E +
Sbjct: 242 WRTLCDYTVSIPMAGSASSLNAANAATAILYEAV 275
>2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural
genomics, structural genomics consortium, SGC, RNA
binding protein; HET: SAH; 1.60A {Homo sapiens}
Length = 184
Score = 56.5 bits (135), Expect = 7e-09
Identities = 24/165 (14%), Positives = 52/165 (31%), Gaps = 9/165 (5%)
Query: 5 APQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANA 64
A +L S +++ N+G + R F + L + + + + S +
Sbjct: 17 AARLGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVSAE 76
Query: 65 DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGII 124
+ L + + T K + + + ++
Sbjct: 77 QWLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQTAK---------SLDLTQYCFPEKSLLL 127
Query: 125 FGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
G ER G+ I + + P + SLN+ + L++WE
Sbjct: 128 LGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYT 172
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP:
c.116.1.1
Length = 194
Score = 53.4 bits (127), Expect = 6e-08
Identities = 27/162 (16%), Positives = 54/162 (33%), Gaps = 12/162 (7%)
Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67
L+ ++L + N+ + R + + VNP G P
Sbjct: 16 LRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVP------------TF 63
Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127
++ A F + + ++FG
Sbjct: 64 NETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGA 123
Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
E+WG++ E +AL++ I P+ + SLN+S A ++++E
Sbjct: 124 EKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQ 165
>3gyq_A RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase,
spout mtases, SAM, trefoil knot, antibiotic resistance;
HET: SAM; 2.45A {Streptomyces cyaneus}
Length = 272
Score = 50.7 bits (120), Expect = 3e-07
Identities = 28/169 (16%), Positives = 61/169 (36%), Gaps = 10/169 (5%)
Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSS 60
P S +G V++L ++ NIG + R + + LV+ +
Sbjct: 106 PRPARFGDIASRRGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIA------ 159
Query: 61 SANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQN 120
D + + A + + + + I + E +
Sbjct: 160 ----DRRLQRASRGYVFSLPVVLSGREEAIAFIRDSGMQLMTLKADGDISVKELGDNPDR 215
Query: 121 VGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169
+ ++FG E+ G ++ S+A +S P+ SLN+S ++ + + E +
Sbjct: 216 LALLFGSEKGGPSDLFEEASSASVSIPMMSQTESLNVSVSLGIALHERI 264
>2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, knot,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.85A {Porphyromonas gingivalis
W83}
Length = 257
Score = 43.9 bits (102), Expect = 4e-05
Identities = 25/172 (14%), Positives = 54/172 (31%), Gaps = 14/172 (8%)
Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSS 60
+ + + +G ++L Q N+G + R F + + L S K +
Sbjct: 90 VFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQA 149
Query: 61 SANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQN 120
S A + + + R + ++ +
Sbjct: 150 SMGALARVQPTPLKN---------TVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEP 200
Query: 121 VGIIFGRERWGLTNEEIALSNAIISFPVNPL-----FPSLNISQAVLLMVWE 167
++ G E G++ E A ++ P + L SLN++ A ++ E
Sbjct: 201 AILVLGSEGRGISPEVAAEITDRLTIPASGLSVKGHTESLNVAIATAILCSE 252
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 41.9 bits (98), Expect = 2e-04
Identities = 24/133 (18%), Positives = 45/133 (33%), Gaps = 31/133 (23%)
Query: 139 LSNAII--SFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELL-SF 195
LS+ + V P+ + A L E + + + P T EL+ F
Sbjct: 11 LSHGSLEHVLLV----PTASFFIASQL--QEQFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 196 LDYLEISLEE--RGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRG-----IVSTLDK 248
L Y+ +E G F V L+ + F E + L G + + L +
Sbjct: 65 LGYVSSLVEPSKVGQFDQV------LNLCLTEF-------ENCY-LEGNDIHALAAKLLQ 110
Query: 249 FSRQS-SRRNNVL 260
+ + + ++
Sbjct: 111 ENDTTLVKTKELI 123
Score = 41.1 bits (96), Expect = 3e-04
Identities = 34/204 (16%), Positives = 64/204 (31%), Gaps = 66/204 (32%)
Query: 25 GENIGMVARAMWNFNLTQLRLVNP----------RDGWPSEKARSS----SANADCVIDS 70
G +I +A + N T L P +K +S + +
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG----N 153
Query: 71 VRVFS------NLKEAIADLHFIYATTARNRNNFKSVLAP--KEAAIVLNERIFSGQNVG 122
++ + N + +L +Y T + ++ K +A L+E I + +
Sbjct: 154 AQLVAIFGGQGNTDDYFEELRDLYQT-------YHVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 123 IIFGR----ERWGLTNEEIA-----LSNAIISFPVNPLFPSLNISQ-AVLLMVWECMENS 172
+F + W L N L + IS P+ + + ++ V +
Sbjct: 207 KVFTQGLNILEW-LENPSNTPDKDYLLSIPISCPLIGV---IQLAHYVVTAKLLGF---- 258
Query: 173 IVSSEKNVKEQNTPATKGELLSFL 196
TP GEL S+L
Sbjct: 259 ------------TP---GELRSYL 267
Score = 38.4 bits (89), Expect = 0.002
Identities = 39/268 (14%), Positives = 79/268 (29%), Gaps = 97/268 (36%)
Query: 31 VARAMWNFNLTQLR------LVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADL 84
V A + F +QL+ L P +G+ ++ ++ A E +
Sbjct: 22 VPTASF-FIASQLQEQFNKILPEPTEGFAADDEPTTPA----------------ELVG-- 62
Query: 85 HFIYATTAR----NRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALS 140
F+ ++ F VL + L E F E L +I
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVL-----NLCLTE--F-----------ENCYLEGNDI--- 101
Query: 141 NAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLE 200
+A+ + L + + + + + + +++ +++ A L +
Sbjct: 102 HALAA----KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSA----LFRAVGEGN 153
Query: 201 ISL----------EERGYFRPVEKKKKMLDDLYSI---FIRPELMREEVFLLRGIVSTLD 247
L ++ YF E L DLY + L++ TL
Sbjct: 154 AQLVAIFGGQGNTDD--YFE--E-----LRDLYQTYHVLVGD--------LIKFSAETLS 196
Query: 248 KFSRQSSRRN-------NVL--LQKTEK 266
+ R + N+L L+
Sbjct: 197 ELIRTTLDAEKVFTQGLNILEWLENPSN 224
Score = 36.1 bits (83), Expect = 0.008
Identities = 47/206 (22%), Positives = 75/206 (36%), Gaps = 73/206 (35%)
Query: 87 IYATTAR-----NR--NNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIAL 139
+Y T+ NR N+FK IV+N + N+ I FG E+ E
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPV----NLTIHFGGEKGKRIRE---- 1686
Query: 140 SNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPAT-------KGEL 192
N S M++E + + + +EK KE N +T KG L
Sbjct: 1687 ----------------NYSA----MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG-L 1725
Query: 193 LSFLDYLE--ISLEERGYFRPVEKKKKM-------------------LDDLYSIFIRPEL 231
LS + + ++L E+ F ++ K + L D+ SI E
Sbjct: 1726 LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI----ES 1781
Query: 232 MREEVFLLRGIVSTL----DKFSRQS 253
+ E VF RG+ + D+ R +
Sbjct: 1782 LVEVVF-YRGMTMQVAVPRDELGRSN 1806
Score = 31.1 bits (70), Expect = 0.26
Identities = 23/137 (16%), Positives = 43/137 (31%), Gaps = 47/137 (34%)
Query: 2 TPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNP----RDGWPSEKA 57
+ L ++ +I D + + +FN +++ P DG
Sbjct: 429 SHL---LVPASD---LINKD---------LVKNNVSFNAKDIQI--PVYDTFDG---SDL 468
Query: 58 RSSSANADCVIDSVRVFSNLKEAIADL--HFIYATTARNRNNFKS----VLAPKEAA-I- 109
R S + + + + + I L + T FK+ P A+ +
Sbjct: 469 RVLSGS---ISER------IVDCIIRLPVKWETTT------QFKATHILDFGPGGASGLG 513
Query: 110 VLNERIFSGQNVGIIFG 126
VL R G V +I
Sbjct: 514 VLTHRNKDGTGVRVIVA 530
>1pvv_A Otcase, ornithine carbamoyltransferase; dodecamer; 1.87A
{Pyrococcus furiosus} SCOP: c.78.1.1 c.78.1.1 PDB:
1a1s_A
Length = 315
Score = 32.0 bits (72), Expect = 0.15
Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 4/85 (4%)
Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARS-SSANADCVIDSVRVF 74
V+ + D + M+A ++ + P P EK + NA S +
Sbjct: 158 VVYVGDGNNVAHSLMIAGTKLGADV---VVATPEGYEPDEKVIKWAEQNAAESGGSFELL 214
Query: 75 SNLKEAIADLHFIYATTARNRNNFK 99
+ +A+ D IY +
Sbjct: 215 HDPVKAVKDADVIYTDVWASMGQEA 239
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3dxj_D* 3eql_D*
1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 30.1 bits (67), Expect = 0.48
Identities = 15/73 (20%), Positives = 26/73 (35%)
Query: 170 ENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRP 229
IV K P K +LL+ +Y E+ ++ + ++ D +
Sbjct: 130 SKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQ 189
Query: 230 ELMREEVFLLRGI 242
EL V L G+
Sbjct: 190 ELAPGVVSRLDGV 202
>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2
function project, S2F, structural genomics, transferase;
HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1
Length = 206
Score = 28.9 bits (64), Expect = 1.2
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 18/102 (17%)
Query: 13 KGPVIILVDPQLGEN----IGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSAN----- 63
P + V P L EN + + TQL RD E+ + +
Sbjct: 104 TAPYTLFVVPLLIENKLTALCDRILVVDVSPQTQLARSAQRDNNNFEQIQRIMNSQVSQQ 163
Query: 64 -----ADCVIDS----VRVFSNLKEAIADLHFIYATTARNRN 96
AD VI++ + +L++ + +LH Y A N+N
Sbjct: 164 ERLKWADDVINNDAELAQNLPHLQQKVLELHQFYLQQAENKN 205
>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand
binding domain, AF-2, androgen, testosterone, DHT,
alpha-helical sandwich; HET: DHT; 1.40A {Pan
troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A*
1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A*
2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A*
2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...
Length = 269
Score = 27.7 bits (61), Expect = 3.0
Identities = 17/118 (14%), Positives = 36/118 (30%), Gaps = 28/118 (23%)
Query: 129 RWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLM---VWECMENSIVSSEKNVKEQNT 185
+T +E A++ F L + + + ++ I KN
Sbjct: 146 WLQITPQEFLCMKALLLFS-IIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSC-- 202
Query: 186 PATKGELLSFLDYL-EISLEERGYFRPVEKKKKMLDDLYSIFIR--------PELMRE 234
+L LD + I+ +++ + + I+ PE+M E
Sbjct: 203 SRRFYQLTKLLDSVQPIA-------------RELHQFTFDLLIKSHMVSVDFPEMMAE 247
>2k3i_A Uncharacterized protein YIIS; GFT protein structure, PSI, NESG,
structural genomics, protein structure initiative; NMR
{Shigella flexneri 2A}
Length = 109
Score = 27.1 bits (60), Expect = 4.8
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 8/70 (11%)
Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNRN------NFKSVLAPKEAAIVLNERI- 115
N +C R F+ +EA + + A + + + E + L+
Sbjct: 25 NDNCTSKFSRFFATREEAESFMTK-LKELAAAASSADEGASVAYKIKDLEGQVELDAAFT 83
Query: 116 FSGQNVGIIF 125
FS Q IIF
Sbjct: 84 FSCQAEMIIF 93
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.318 0.133 0.380
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,178,967
Number of extensions: 98632
Number of successful extensions: 270
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 31
Length of query: 268
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 177
Effective length of database: 3,487,026
Effective search space: 617203602
Effective search space used: 617203602
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: 41 (21.7 bits)
S2: 56 (25.8 bits)