RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780763|ref|YP_003065176.1| hypothetical protein
CLIBASIA_03260 [Candidatus Liberibacter asiaticus str. psy62]
(107 letters)
>1j8b_A YBAB; hypothetical protein, structural genomics, structure 2
function project, S2F, unknown function; HET: MSE; 1.75A
{Haemophilus influenzae rd KW20} SCOP: d.222.1.1 PDB:
1pug_A
Length = 112
Score = 107 bits (269), Expect = 6e-25
Identities = 45/107 (42%), Positives = 69/107 (64%), Gaps = 1/107 (0%)
Query: 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF 60
+ ++ Q +++Q KM+KM+E I LE G +G G+V + ING + + ID SL+
Sbjct: 7 KGGLGGLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME 66
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLKFPF 107
+D E+LEDLI AA +DA ++ E+L K +T G+P+PPG+KFPF
Sbjct: 67 DD-KEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF 112
>1ybx_A Conserved hypothetical protein; structural genomics, PSI, protein
structure initiative, southeast collaboratory for
structural genomics; HET: MSE; 1.80A {Clostridium
thermocellum}
Length = 143
Score = 103 bits (258), Expect = 1e-23
Identities = 36/101 (35%), Positives = 63/101 (62%)
Query: 3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFED 62
NI +V Q +++Q ME+++E + E +AGGG V+V G+ + + I ++ D
Sbjct: 42 NINNLVKQAQKMQRDMERVQEELKEKTVEASAGGGAVTVVATGRKDIKEITIKPEVVDPD 101
Query: 63 NVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGL 103
+VE+L+DLI+AA ++A +K +++V + +IT GL PGL
Sbjct: 102 DVEMLQDLILAAVNEALRKADEMVTAEISKITGGLGGIPGL 142
>3f42_A Protein HP0035; helicobacter pylori unknown-function, structural
genomics, PSI-2, protein structure initiative; HET:
MSE; 1.78A {Helicobacter pylori}
Length = 99
Score = 83.2 bits (206), Expect = 1e-17
Identities = 22/97 (22%), Positives = 46/97 (47%), Gaps = 2/97 (2%)
Query: 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF 60
+ ++ G ++ + +++E +GGGMVSV NG L ++ID SLL
Sbjct: 2 HMDFSQLGGLLDGMKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLL- 60
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGL 97
++ E ++ +++A +D +K +E+ +
Sbjct: 61 -EDKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF 96
>3lhp_S 4E10_D0_1ISEA_004_N (T93); epitope-scaffold, immune system; 2.70A
{Artificial gene} PDB: 1y69_8
Length = 123
Score = 27.8 bits (62), Expect = 0.64
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEG 96
++ + A KKIE +A +T+G
Sbjct: 88 WFDISQSLWDVQKLTDAAIKKIEAALADMEAWLTQG 123
>3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase;
2.99A {Pseudomonas aeruginosa PAO1}
Length = 437
Score = 27.5 bits (59), Expect = 0.74
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 52 VKIDRSLLFE----DNVEILEDLIIAAHSDAHKKIEDLVATKTQ 91
+KID S + + +N EIL+ LI H I V + +
Sbjct: 361 IKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASV 404
>2prg_C Nuclear receptor coactivator SRC-1, peroxisome proliferator
activated receptor gamma; complex
(thiazolidinedione/receptor), ligand-binding domain;
HET: BRL; 2.30A {Homo sapiens} SCOP: j.112.1.1
Length = 88
Score = 26.8 bits (59), Expect = 1.1
Identities = 6/32 (18%), Positives = 12/32 (37%)
Query: 73 AAHSDAHKKIEDLVATKTQEITEGLPIPPGLK 104
+ +S K+ L+ T ++ I K
Sbjct: 2 SKYSQTSHKLVQLLTTTAEQQLRHADIDTSCK 33
>1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A
{Thermus thermophilus} SCOP: d.67.3.1 PDB: 2qbe_6 2qbg_6
2qbi_6* 2qbk_6* 2v46_Y* 2v48_Y* 2z4l_6* 2z4n_6*
Length = 185
Score = 26.6 bits (59), Expect = 1.6
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 14/82 (17%)
Query: 12 KEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLI 71
+ ++ E+ + +I + +R + L + + L ED + E I
Sbjct: 116 RAVRQYAEEGRVAIRN-------------IRREALDKLKKLAKELHLS-EDETKRAEAEI 161
Query: 72 IAAHSDAHKKIEDLVATKTQEI 93
+ K + L K QEI
Sbjct: 162 QKITDEFIAKADQLAEKKEQEI 183
>1c4z_A E6AP, ubiquitin-protein ligase E3A; bilobal structure, elongated
shape, E3 ubiquitin ligase, E2 ubiquitin conjugating
enzyme; 2.60A {Homo sapiens} SCOP: d.148.1.1 PDB:
1d5f_A
Length = 358
Score = 26.2 bits (57), Expect = 1.8
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 52 VKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE 83
+K+ R + +D + LE + + +D K++
Sbjct: 8 LKVRRDHIIDDALVRLEMIAMENPADLKKQLY 39
>2jae_A L-amino acid oxidase; oxidoreductase, dimerisation mode, hydride
transfer mechanism, GR2-family, flavoenzyme, FAD
containing; HET: FAD; 1.25A {Rhodococcus opacus} PDB:
2jb1_A* 2jb2_A* 2jb3_A*
Length = 489
Score = 26.0 bits (55), Expect = 1.8
Identities = 10/62 (16%), Positives = 19/62 (30%)
Query: 24 SITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE 83
+T LEA GG + + R + + + E + + I
Sbjct: 36 KVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCR 95
Query: 84 DL 85
+L
Sbjct: 96 EL 97
>1q1l_A Chorismate synthase; beta alpha beta sandwich, structural genomics,
PSI, protein structure initiative, midwest center for
structural genomics; 2.05A {Aquifex aeolicus} SCOP:
d.258.1.1
Length = 401
Score = 25.6 bits (56), Expect = 2.5
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 17 KMEKMKESITSLEAEGNAGGGMVSVRING 45
K E+ K I ++ +G + GG+ V
Sbjct: 209 KDEEFKTYIDEVKEKGESLGGVFEVFALN 237
>1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta
sandwich; 2.55A {Thermotoga maritima} SCOP: d.67.3.1
PDB: 1t1m_C
Length = 185
Score = 25.7 bits (56), Expect = 2.5
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95
ED+ + LE+ I + +K++++ K +EI E
Sbjct: 150 EDDAKRLENEIQKLTDEFIEKLDEVFEIKKEEIME 184
>3er0_A Eukaryotic translation initiation factor 5A-2; yeast, low
resolution, acetylation, hypusine, phosphoprotein,
protein biosynthesis; 3.35A {Saccharomyces cerevisiae}
Length = 167
Score = 25.6 bits (56), Expect = 2.9
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 8 VGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEI 66
F I+ + K+ + TS G G V + ++ TG K++ N+E+
Sbjct: 38 KNGFVVIKSRPCKIVDMSTS--KTGKHGHAKV--HLVAIDIFTGKKLEDLSPSTHNMEV 92
>1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio
parahaemolyticus} SCOP: d.67.3.1
Length = 185
Score = 25.6 bits (56), Expect = 3.0
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95
ED ++ I A KKI++++A K +E+ E
Sbjct: 150 EDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELME 184
>1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli}
SCOP: d.67.3.1 PDB: 1ek8_A* 1zn0_A 1zn1_A 2rdo_8
Length = 185
Score = 25.6 bits (56), Expect = 3.3
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 19 EKMKESITSLEAEGN-AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSD 77
E+ K+ + E A + +V + + + + D+ + ED+ +D +
Sbjct: 108 ERRKDLTKIVRGEAEQARVAVRNVGRDANDKVKALLKDKEI-SEDDDRRSQDDVQKLTDA 166
Query: 78 AHKKIEDLVATKTQEITE 95
A KKIE +A K E+ +
Sbjct: 167 AIKKIEAALADKEAELMQ 184
>1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle,
protein synthesis; 2.15A {Mycobacterium tuberculosis}
SCOP: d.67.3.1 PDB: 1wqf_A 1wqh_A
Length = 185
Score = 24.9 bits (54), Expect = 4.2
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95
ED V E + +I++LV K E+ E
Sbjct: 150 EDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 25.0 bits (54), Expect = 4.4
Identities = 6/44 (13%), Positives = 15/44 (34%)
Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLK 104
+ + D+I A + + + + P+ GL+
Sbjct: 397 DTEFTEVADIIATALATGSSVDVSALKDRATRLARAFPLYDGLE 440
>2kyy_A Possible ATP-dependent DNA helicase RECG-related; structural
genomics, northeast structural genomics consortiu AAA_4
domain, PSI-2; NMR {Nitrosomonas europaea}
Length = 153
Score = 24.3 bits (52), Expect = 6.6
Identities = 10/61 (16%), Positives = 23/61 (37%)
Query: 11 FKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDL 70
K + + E++ + E GG + + ++ G + R + D ++ DL
Sbjct: 22 AKRASDMGKSVMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDL 81
Query: 71 I 71
Sbjct: 82 A 82
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
0.314 0.134 0.363
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 888,361
Number of extensions: 38288
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 149
Number of HSP's successfully gapped: 35
Length of query: 107
Length of database: 5,693,230
Length adjustment: 71
Effective length of query: 36
Effective length of database: 3,971,906
Effective search space: 142988616
Effective search space used: 142988616
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: 42 (22.0 bits)
S2: 50 (23.2 bits)