RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498
methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(245 letters)
>3kw2_A Probable R-RNA methyltransferase; structural genomics, unknown
function, PSI-2, protein structure initiative; HET: MSE
ADN; 2.00A {Porphyromonas gingivalis atcc 33277}
Length = 257
Score = 173 bits (440), Expect = 3e-44
Identities = 48/235 (20%), Positives = 102/235 (43%), Gaps = 9/235 (3%)
Query: 18 IKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRF--KVEYQSRS 75
I+ + D+ ++ VLRM+ GD + L +G+ + + I + + +S
Sbjct: 13 IEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQ 72
Query: 76 QTKQSDVQYIFSPIKTN-RLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISA 134
+ + + +P K + R+++M++K VE+G+ + + + +++ +R+ ISA
Sbjct: 73 KPWRDRITIAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISA 132
Query: 135 AEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHI-----PN 189
+Q + P I ++ ++ + + A + + +
Sbjct: 133 MKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRAEITQGRGYPSDFYHVGQD 192
Query: 190 VAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICGDW 244
V ILIGPEG + E E+ F P+SLG LR++TA + A + + +
Sbjct: 193 VLILIGPEGDFSPSEVESALLAGF-APVSLGESRLRTETAGLVACQWIHTLQACY 246
>1vhy_A Hypothetical protein HI0303; PSI, protein structure initiative, NEW
YORK SGX research center for structural genomics,
nysgxrc; HET: MSE; 1.90A {Haemophilus influenzae} SCOP:
b.122.1.2 c.116.1.5 PDB: 1nxz_A
Length = 257
Score = 164 bits (415), Expect = 2e-41
Identities = 63/252 (25%), Positives = 111/252 (44%), Gaps = 17/252 (6%)
Query: 1 MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISY 60
++I R++ L +TQ S D +++A VLRM EG+ + LF+G + + +KI
Sbjct: 3 LRIP----RIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIE 58
Query: 61 VG--KSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQ 118
+ + + + + R+++ IQKSVE+G+ I P+ +
Sbjct: 59 SNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCG 118
Query: 119 ------NTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETC 172
+ + + I+A EQC +P I P L+ D ++
Sbjct: 119 VKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAH 178
Query: 173 GSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVA 232
S +L + V +LIG EGG ++E F T + LG R+LR++TA++A
Sbjct: 179 YSIKTLPTI----PAGGVRLLIGSEGGLSAQEIAQTEQQGF-TEILLGKRVLRTETASLA 233
Query: 233 AMALVQAICGDW 244
A++ +Q GD
Sbjct: 234 AISALQICFGDL 245
>1vhk_A Hypothetical protein YQEU; structural genomics, unknown function;
2.60A {Bacillus subtilis} SCOP: b.122.1.2 c.116.1.5
Length = 268
Score = 158 bits (399), Expect = 1e-39
Identities = 61/257 (23%), Positives = 107/257 (41%), Gaps = 20/257 (7%)
Query: 7 LKRLFVDF---PLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYV-- 61
L+R F++ + +G++ H++ +V+RM EGD I+ + E ++ V
Sbjct: 3 LQRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSK 62
Query: 62 GKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTH 121
K +E+ + ++ V K ++L+++IQK E+G A P +
Sbjct: 63 DKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKL 122
Query: 122 YNM------DRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSE 175
+ +R AAEQ +P + + + LL+ + V A E +
Sbjct: 123 DDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQ 182
Query: 176 NSLEKLHAIAHIP----NVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAV 231
+ AI ++ I+ GPEGG E E L V LGPRILR++TA +
Sbjct: 183 GEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGV-TCGLGPRILRTETAPL 241
Query: 232 AAMALVQAI----CGDW 244
A++ + GD
Sbjct: 242 YALSAISYQTELLRGDQ 258
>1v6z_A Hypothetical protein TTHA0657; structural genomics, riken
structural genomics/proteomics initiative, RSGI,
transferase; 2.00A {Thermus thermophilus HB8} SCOP:
b.122.1.2 c.116.1.5 PDB: 2cx8_A* 2z0y_A*
Length = 228
Score = 134 bits (338), Expect = 2e-32
Identities = 68/246 (27%), Positives = 118/246 (47%), Gaps = 23/246 (9%)
Query: 1 MKIHSHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISY 60
M+ H R F G + +L VLR + GD +F+G+ E L+++
Sbjct: 1 MRPH----RAF-----SPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGE-REALAEVVD 50
Query: 61 VGKSIRFKV-EYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQN 119
+G +R++V E + + +V + +K ++L +++ + E+G I+P++TR++
Sbjct: 51 LGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVP 110
Query: 120 THYNMD---RVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSEN 176
R+R + AA+Q + +P + PP L+ + + V A
Sbjct: 111 KEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVL 170
Query: 177 SLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMAL 236
EK +A+ +GPEGG+ EE L + F TP+SLG RILR++TAA+A +AL
Sbjct: 171 DPEK--------PLALAVGPEGGFAEEEVALLEARGF-TPVSLGRRILRAETAALALLAL 221
Query: 237 VQAICG 242
A G
Sbjct: 222 CTAGEG 227
>1z85_A Hypothetical protein TM1380; structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PSI; 2.12A {Thermotoga maritima MSB8}
Length = 234
Score = 118 bits (297), Expect = 9e-28
Identities = 47/232 (20%), Positives = 92/232 (39%), Gaps = 20/232 (8%)
Query: 9 RLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFK 68
LF + + H++ V+R+KEGD I +G + + + K
Sbjct: 15 HLFYGTA--QNGEVIFDEREAHHM-RVVRLKEGDVIEATDGNGFSYTCILKSLKKKTAAA 71
Query: 69 VEY-QSRSQTKQSDVQYIFSPIKTNRL-DYMIQKSVEMGMGAIRPVITRYTQNTHYNMDR 126
+ + ++ + PI ++I+K VE+G+ I ++D+
Sbjct: 72 KIVKVEEKEKEPTEKLSVVVPIGRWERTRFLIEKCVELGVDEIFFHK-FERSQHEISLDK 130
Query: 127 VRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAH 186
+ AA+QC P + + + + ++ D L
Sbjct: 131 AKIVVREAAKQCKRYLFPKVSFL-------EKLEFSGNVITLDLDASQNLLDANLEG--- 180
Query: 187 IPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238
++ +++GPEGG+ +E+E L S T +SLG +ILR +TAA+ + +
Sbjct: 181 --SITVVVGPEGGFSEKERELLRS--STTIVSLGKKILRFETAAILTVGYIA 228
>2egv_A UPF0088 protein AQ_165; RSME, methyltransferase, rRNA modification,
PUA domain, M3U, SAM, structural genomics, NPPSFA; HET:
SAM; 1.45A {Aquifex aeolicus} PDB: 2egw_A*
Length = 229
Score = 117 bits (294), Expect = 2e-27
Identities = 35/220 (15%), Positives = 87/220 (39%), Gaps = 15/220 (6%)
Query: 25 SGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK-SIRFKVEYQSRSQTKQSDVQ 83
+ + V R+++ + + + ++ K+ K I ++ + ++ D+
Sbjct: 17 REGEVKHF-RVRRIEKDEEFGVIHE-GKIYVCKVRREDKREISCEIVEELETKLPPKDIT 74
Query: 84 YIFSPIK-TNRLDYMIQKSVEMGMGAIRPVITRYT----QNTHYNMDRVRTYTISAAEQC 138
S +D +++++ E+G+ P+I+ + + ++ + I A +Q
Sbjct: 75 LYQSVTVDLKTMDTIVRQATELGVLTFVPIISERSFQKEEAILKKTEKWKRIVIEAMKQS 134
Query: 139 DILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG 198
I P L L+ + N + ++ ++++GPEG
Sbjct: 135 RRPIPMEIKKPVRLSDLIPESEENIILDN------FYEGVKPKDVNLEAKTYSVVVGPEG 188
Query: 199 GYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238
G+ E + L F + L P LR++TA V+ ++++
Sbjct: 189 GFSKRESQILREKGF-KSVLLEPYTLRTETAVVSIVSILM 227
>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 = 38.0 bits (88), Expect = 0.002
Identities = 51/314 (16%), Positives = 82/314 (26%), Gaps = 140/314 (44%)
Query: 12 VDFPL-CIKTQGKASGDQYHYL--AHVLRMKEGDNILLFNGKDGE--------------- 53
+ PL + Q A HY+ A +L G+ G G
Sbjct: 236 ISCPLIGV-IQ-LA-----HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS 288
Query: 54 WLSKISYVGKSIR--FKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMG------ 105
W S V K+I F + R ++ P +++ S+E
Sbjct: 289 WESFFVSVRKAITVLFFIGV--RCY--EAYPNTSLPPS-------ILEDSLENNEGVPSP 337
Query: 106 MGAIR----PVITRYTQ--NTHYNMDRVRTYTIS---AAEQCDILTLPFIY--PPTTLEF 154
M +I + Y N+H + + IS A+ + PP +L
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGK-QVE-ISLVNGAKN-------LVVSGPPQSL-- 386
Query: 155 LLKNWDHNCQIVFADETCGSENSLEKLHA-----IAHIPNVAILIGPEGGYHSEEKETLH 209
G +L K A + IP SE K
Sbjct: 387 -----------------YGLNLTLRKAKAPSGLDQSRIP------------FSERKLKFS 417
Query: 210 ------SLPFVTPL-----------------SLGP---RI----------LRSDTAAVAA 233
+ PF + L S +I LR + +++
Sbjct: 418 NRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISE 477
Query: 234 MALVQAICG---DW 244
+V I W
Sbjct: 478 -RIVDCIIRLPVKW 490
Score = 29.1 bits (65), Expect = 0.99
Identities = 40/267 (14%), Positives = 67/267 (25%), Gaps = 101/267 (37%)
Query: 51 DGEWLSKISYVGKSIRF---KVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSV----- 102
D E + VGK + + VE Q Q + + + Y+ +
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQV-LNLCLTEFEN---CYLEGNDIHALAA 106
Query: 103 ------EMGMGAIRPVITRYTQNTHY-----------------NMDRVRTYTI----SAA 135
+ + + +I Y + I
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNT 166
Query: 136 EQC--DILTLPFIYPPTTLEFLLKNWDHNCQIVFADET----CGSENSLEKLHA------ 183
+ ++ L Y L+ + I F+ ET + EK+
Sbjct: 167 DDYFEELRDLYQTYHV-----LVGDL-----IKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 184 --IAH---IPNVAILIG-PEGGYHSEEKETLHSLPF----------VTPLSLG--PRILR 225
+ + P+ L+ P S P VT LG P LR
Sbjct: 217 EWLENPSNTPDKDYLLSIPI------------SCPLIGVIQLAHYVVTAKLLGFTPGELR 264
Query: 226 SDTAA--------VAAMALVQAICGDW 244
S V A+A+ A W
Sbjct: 265 SYLKGATGHSQGLVTAVAI--AETDSW 289
Score = 28.8 bits (64), Expect = 1.2
Identities = 21/147 (14%), Positives = 45/147 (30%), Gaps = 26/147 (17%)
Query: 107 GAIRPVITRYTQNTHYNMDRVR-TYTISAAEQCDILTLPFIYPPTT-LEFLLKNWDHNCQ 164
G++ V+ T + + +++ + E + PTT E + K +
Sbjct: 14 GSLEHVLLVPT-ASFFIASQLQEQFNKILPEPTEGFAAD--DEPTTPAELVGKFLGYVSS 70
Query: 165 IVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPR-- 222
+V G + + L + L G + H+ L +L
Sbjct: 71 LV-EPSKVGQFDQVLNL-CLTEF-ENCYLEGND--IHA----LAAKLLQENDTTLVKTKE 121
Query: 223 ILRSDTAAVAAM----------ALVQA 239
++++ A AL +A
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRA 148
>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 = 31.1 bits (69), Expect = 0.26
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 7/36 (19%)
Query: 204 EKETLHSLPFVTPLSLGPRILRSDTA-AVAAMALVQ 238
EK+ L L SL ++ D+A A+A A ++
Sbjct: 18 EKQALKKL----QASL--KLYADDSAPALAIKATME 47
Score = 26.1 bits (56), Expect = 7.0
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 18/40 (45%)
Query: 175 ENSLEKLHAIAHI------PNVAILIGPEGGYHSEEKETL 208
+ +L+KL A + P +AI K T+
Sbjct: 19 KQALKKLQASLKLYADDSAPALAI------------KATM 46
>2p3w_A Probable serine protease HTRA3; PDZ domain, phage derived high
affinity ligand, protein binding; 1.70A {Homo sapiens}
Length = 112
Score = 26.8 bits (59), Expect = 4.0
Identities = 8/48 (16%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 33 AHVLRMKEGDNILLFNGK---DGEWLSKISYVGKSIRFKVEYQSRSQT 77
+ +++GD I+ NG+ D L + + +V +
Sbjct: 48 SQRGGIQDGDIIVKVNGRPLVDSSELQEAVLTESPLLLEVRRGNDDLL 95
>2j42_A C2-II, C2 toxin component-II; 3.13A {Clostridium botulinum}
Length = 721
Score = 26.8 bits (59), Expect = 4.4
Identities = 4/43 (9%), Positives = 13/43 (30%), Gaps = 5/43 (11%)
Query: 44 ILLFNGK----DGEWLSKISYV-GKSIRFKVEYQSRSQTKQSD 81
+ NG+ + ++ + G ++E +
Sbjct: 89 RVELNGEIFNLSLNTSNTVNLIQGNVYDIRIEQLMSENQLLKN 131
>2joa_A Serine protease HTRA1; PDZ, beta-sandwich, cyclically-permuted,
protein binding; NMR {Homo sapiens}
Length = 105
Score = 26.8 bits (59), Expect = 4.8
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 3/48 (6%)
Query: 33 AHVLRMKEGDNILLFNGK---DGEWLSKISYVGKSIRFKVEYQSRSQT 77
A +KE D I+ NG+ +S + ++ V +
Sbjct: 48 AEAGGLKENDVIISINGQSVVSANDVSDVIKRESTLNMVVRRGNEDIM 95
>3khf_A Microtubule-associated serine/threonine-protein kinase 3; MAST3,
microtubule associated serine/threonine kinase 3, PDZ
domain, structural genomics; 1.20A {Homo sapiens} PDB:
2w7r_A
Length = 99
Score = 26.0 bits (57), Expect = 7.9
Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 6/52 (11%)
Query: 33 AHVLRMKEGDNILLFNGKDGEWLS------KISYVGKSIRFKVEYQSRSQTK 78
A ++ GD I NG+ L + G I + ++T
Sbjct: 47 AQEAGLRAGDLITHINGESVLGLVHMDVVELLLKSGNKISLRTTALENTETS 98
>2fcf_A Multiple PDZ domain protein; adaptor molecule, protein linker,
structural genomics, structural genomics consortium,
SGC, structural protein; 1.76A {Homo sapiens} SCOP:
b.36.1.1
Length = 103
Score = 25.7 bits (56), Expect = 9.2
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 37 RMKEGDNILLFNGKDGEWLS------KISYVGKSIRFKVEYQSRSQ 76
+K GD I+ +G D S I G + F V+ ++
Sbjct: 57 TLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR 102
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
0.321 0.136 0.414
Gapped
Lambda K H
0.267 0.0482 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,111,005
Number of extensions: 92849
Number of successful extensions: 398
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 20
Length of query: 245
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 155
Effective length of database: 3,511,270
Effective search space: 544246850
Effective search space used: 544246850
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: 55 (25.6 bits)