RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein
[Candidatus Liberibacter asiaticus str. psy62]
(190 letters)
>2f1l_A 16S rRNA processing protein; 9949912, structural genomics, PSI,
protein structure initiative, joint center for
structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas
aeruginosa} SCOP: b.41.1.4 b.43.3.4
Length = 187
Score = 100 bits (249), Expect = 3e-22
Identities = 36/168 (21%), Positives = 76/168 (45%), Gaps = 10/168 (5%)
Query: 5 DKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRY----VLYSNDNRELRILKMYRKNKRF 60
D LV++ I + +G+ GEV + S+ + +L Y + + R+ +++ K
Sbjct: 18 DDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVL 77
Query: 61 IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
A G+D+ A ++ R + LEE E++ LE ++ D+ + G +
Sbjct: 78 AAKLKGLDDREEARTFTGYEICIPRSEL--PSLEEGEYYWHQLEGLKVIDQGRQLLGVID 135
Query: 121 GVYNFGAGSILEIKNTM----EKTFLIPFTKFAVLEVNLQENKILIDP 164
+ GA ++ +K ++ L+P+T VL ++L ++ +D
Sbjct: 136 HLLETGANDVMVVKPCAGSLDDRERLLPYTGQCVLSIDLAAGEMRVDW 183
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural
genomics, PSI-2, protein structure initiative; 2.40A
{Acinetobacter calcoaceticus}
Length = 182
Score = 97.1 bits (241), Expect = 2e-21
Identities = 27/172 (15%), Positives = 72/172 (41%), Gaps = 14/172 (8%)
Query: 5 DKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRKNKRF 60
+ + + + + +GLNG +++ S ++ Y+ + + + + K
Sbjct: 9 EDRIQIGQLRSAYGLNGWLWVYSNTEPMSNMFDYLPWYIETKAGWQTVDVKRWKPHGKGL 68
Query: 61 IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFD----RQGKYW 116
+ + G+ + A L ++ + + DE++ +DL+ + Q
Sbjct: 69 VVSLKGVSDRTGAESLVASNIWIAKSQLPKA--DVDEYYWSDLKGLTVLGLDDEEQEVNL 126
Query: 117 GQVCGVYNFGAGSILEIKNTME----KTFLIPFTKFAVLEVNLQENKILIDP 164
GQ+ ++ GA ++ ++ T + + +IP+ K V V+L+ +I ++
Sbjct: 127 GQIHELFETGANDVMVVRATPDSIDSEERMIPWHKDVVQRVDLEAGRIYVNW 178
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; 2.70A {Haemophilus
influenzae}
Length = 177
Score = 94.0 bits (233), Expect = 2e-20
Identities = 35/169 (20%), Positives = 69/169 (40%), Gaps = 12/169 (7%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY----VLYSNDNRELRILKMYRKNKRFIA 62
+ ++ +G+T+G+ G + I S + Y + + + + + N I
Sbjct: 2 IEVVGKLGSTYGIRGWLRIYSSTEQAESIFDYQPWFLKIKGEWQSIELENWRYHNHEIIV 61
Query: 63 TFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGV 122
G+D+ +A L ++++ F ELEE +++ DL + +G G V +
Sbjct: 62 KLKGVDDREAAQILANVEIGVDLSVFP--ELEEGDYYWHDLIGCTVVNLEGYTMGTVTEM 119
Query: 123 YNFGAGSILEIKNTME-----KTFLIPFTK-FAVLEVNLQENKILIDPI 165
G+ +L +K + + LIPF V V+L I +D
Sbjct: 120 METGSNDVLVVKANTKDAFGKQERLIPFLYEQVVKRVDLTTKTIEVDWD 168
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19,
PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus
thermophilus HB8} PDB: 2dog_A
Length = 162
Score = 92.8 bits (230), Expect = 4e-20
Identities = 35/165 (21%), Positives = 66/165 (40%), Gaps = 14/165 (8%)
Query: 6 KLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFS 65
+LV + G + L G + P+ L+ +Y + I +YR + + +
Sbjct: 2 RLVEIGRFGAPYALKGGLRFRG---EPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLA 58
Query: 66 GIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNF 125
G+ + A L L++Y + LEE ++ L + + + G+V + +
Sbjct: 59 GVTDRTLAEALVGLRVY--AEVADLPPLEEGRYYYFALIGLPVYVEG-RQVGEVVDILDA 115
Query: 126 GAGSILEIKNTME-----KTFLIPFTKFAVLEVNLQENKILIDPI 165
GA +L I+ E L+P V ++E I +DPI
Sbjct: 116 GAQDVLIIRGVGERLRDRAERLVPLQA---PYVRVEEGSIHVDPI 157
>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 = 34.1 bits (78), Expect = 0.020
Identities = 42/203 (20%), Positives = 79/203 (38%), Gaps = 49/203 (24%)
Query: 16 THGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSG------ID- 68
T+G + +D NNP++L + + + K KR +S +D
Sbjct: 1656 TYGFS---ILDIVINNPVNLT--IHFGGE-----------KGKRIRENYSAMIFETIVDG 1699
Query: 69 NIHSASELRDLKLYAKRQDFKDEE--LEEDEFFNTDLEEME--TF-DRQGK--------Y 115
+ + +++ ++ F+ E+ L +F L ME F D + K +
Sbjct: 1700 KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATF 1759
Query: 116 WGQVCGVYNFGA--GSILEIKNTMEKTFLIPFT-KFAVLEVNLQENK---ILIDP--IAA 167
G G Y A ++ I++ +E F T + AV L + I I+P +AA
Sbjct: 1760 AGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAA 1819
Query: 168 GLNNTTMKNPQYDCPLDSAGKKS 190
+ + QY ++ GK++
Sbjct: 1820 SFSQEAL---QY--VVERVGKRT 1837
Score = 28.8 bits (64), Expect = 0.73
Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 14/69 (20%)
Query: 52 KMYRKNKRFIATFSGIDNIHSA-SELRDLKLYAKRQDFKDEELEE-DEFFNTDLEEMETF 109
++ A F G N ELRD LY + ++ E + +
Sbjct: 155 QLV-------AIFGGQGNTDDYFEELRD--LYQTYHVLVGDLIKFSAETLSELIRTTLDA 205
Query: 110 DRQGKYWGQ 118
+ K + Q
Sbjct: 206 E---KVFTQ 211
>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 = 30.4 bits (67), Expect = 0.30
Identities = 14/66 (21%), Positives = 16/66 (24%), Gaps = 45/66 (68%)
Query: 73 ASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILE 132
AS LKLYA D+ + L
Sbjct: 27 AS----LKLYA------------DD-----------------------------SAPALA 41
Query: 133 IKNTME 138
IK TME
Sbjct: 42 IKATME 47
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.5 bits (60), Expect = 2.0
Identities = 23/103 (22%), Positives = 38/103 (36%), Gaps = 31/103 (30%)
Query: 3 KLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIA 62
++D + L + E +I S +P ++ +YV S +
Sbjct: 1008 QVDPITLFVLVSVV-----EAFIASGITDPYEMYKYVHVSE-----------------VG 1045
Query: 63 TFSGIDNIHSASELRDLKLYAKRQDFKDEELEED----EFFNT 101
SG + S LR ++ R FKDE ++ D F NT
Sbjct: 1046 NCSG-SGMGGVSALRG--MFKDR--FKDEPVQNDILQESFINT 1083
>2gjj_A A21 single-chain antibody fragment against ERBB2; IG family, SCFV,
immune system; 2.10A {Mus musculus}
Length = 264
Score = 27.2 bits (60), Expect = 2.6
Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 115 YWGQVCG-VYNFGAGSILEIKNTMEKTFLIPFTKFAVL----EVNLQE 157
Y Q + FG G+ LEIK + EV LQ+
Sbjct: 97 YCQQYSNYPWTFGGGTRLEIKRGGGGSGGGGSGGGGSGGGGSEVQLQQ 144
>2gki_A Nuclease; anti-DNA antibody, catalytic antibody, immune system;
2.88A {Mus musculus}
Length = 291
Score = 26.4 bits (58), Expect = 4.1
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 123 YNFGAGSILEIKNTMEKTFLIP 144
Y FG+G+ LEIK +
Sbjct: 260 YTFGSGTKLEIKXXXXXGLVPR 281
>1zb9_A OHR, organic hydroperoxide resistance protein; oxidoreductase;
HET: PE4; 1.80A {Xylella fastidiosa 9A5C} PDB: 1zb8_A*
Length = 143
Score = 25.8 bits (56), Expect = 5.6
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDS 27
M L+K++ A + T G +G V
Sbjct: 1 MNSLEKVLYTAIVTATGGRDGSVVSSD 27
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 25.6 bits (55), Expect = 6.9
Identities = 11/77 (14%), Positives = 23/77 (29%)
Query: 38 YVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDE 97
+V Y + +++ Y + S DL Y D + + +
Sbjct: 609 HVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEGFDDLIK 668
Query: 98 FFNTDLEEMETFDRQGK 114
E ++ QG+
Sbjct: 669 NCREQHEALKAQLEQGR 685
>1jqo_A Phosphoenolpyruvate carboxylase; beta barrel, carbon dioxide
fixation, lyase; 3.00A {Zea mays} SCOP: c.1.12.3
Length = 970
Score = 25.8 bits (56), Expect = 7.1
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 40 LYSNDNRELRILK-MYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEF 98
D R ++LK MY + F T ++ + + + LY + EEL+ F
Sbjct: 801 AIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLV--AEELK--PF 856
Query: 99 FNTDLEEME 107
++
Sbjct: 857 GKQLRDKYV 865
>2gjx_A Beta-hexosaminidase alpha chain; beta-hexosaminidase A,
glycosidase, TAY-sachs disease, GM2 ganglisode, TIM
barrel, hydrolase; HET: NAG BMA NDG; 2.80A {Homo
sapiens} SCOP: c.1.8.6 d.92.2.1 PDB: 2gk1_A*
Length = 507
Score = 25.6 bits (55), Expect = 7.9
Identities = 10/66 (15%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 24 YIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYA 83
+D A N LN + + D+ +++ + +I++A +++++ YA
Sbjct: 167 TLDVMAYN--KLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYA 224
Query: 84 KRQDFK 89
+ + +
Sbjct: 225 RLRGIR 230
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 0.137 0.392
Gapped
Lambda K H
0.267 0.0587 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,659,578
Number of extensions: 77322
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 27
Length of query: 190
Length of database: 5,693,230
Length adjustment: 87
Effective length of query: 103
Effective length of database: 3,584,002
Effective search space: 369152206
Effective search space used: 369152206
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: 54 (24.9 bits)