RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780885|ref|YP_003065298.1| hypothetical protein
CLIBASIA_03910 [Candidatus Liberibacter asiaticus str. psy62]
(207 letters)
>2rde_A Uncharacterized protein VCA0042; C-DI-GMP, structural genomics,
PSI-2, protein structure initiative; HET: C2E; 1.92A
{Vibrio cholerae O395} SCOP: b.45.2.1 b.45.2.2 PDB:
1yln_A*
Length = 251
Score = 44.9 bits (106), Expect = 1e-05
Identities = 21/113 (18%), Positives = 44/113 (38%), Gaps = 14/113 (12%)
Query: 6 HNLQFIDQRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCD--VPMFLVGERSI 63
+ +Q R R +++L G+ +LFD +C +R++S G + + VG+
Sbjct: 127 NTMQVSQLRKEPRFELNLAGK-VLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVA 185
Query: 64 VFV-------EKVGRIEGKVVN-FDSNRGYAVRI---VTSENERRKLADKLIW 105
+ + + + GK+ N S + N + L +L +
Sbjct: 186 LEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKF 238
Score = 38.4 bits (89), Expect = 0.001
Identities = 29/204 (14%), Positives = 73/204 (35%), Gaps = 44/204 (21%)
Query: 32 GTEYNCIVREI-SPGGLCIVCDVPMFLVGERSIVFVEKV--------GRIEGKVVNFDSN 82
GT++ C I + ++ ++P + F E R EG +++F S
Sbjct: 50 GTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQ 109
Query: 83 RGYAVRIVTSENERRKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVLNDNTKH 142
+ + E + +L+ + + + R R + +++ +++
Sbjct: 110 ----LMHILQEPVP------MAFLSIPNTMQVSQLRKEPRFELN---LAGKVLFDEHR-G 155
Query: 143 SCKVIDISESGVS---------------VSVDLQIEMFSKVLFNDILGRVVRIFPGG--- 184
C++ D+S SG V++++ ++ F + G++ +
Sbjct: 156 DCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHA 215
Query: 185 -IAIEFSSVQESNIAFKSLINHCY 207
+EF+ +N K+L+
Sbjct: 216 RYGLEFNEEGRNNA--KNLLAQLK 237
>1ywu_A Hypothetical protein PA4608; PAT7, beta barrel, PILZ domain,
structural genomics, PSI, protein structure initiative;
NMR {Pseudomonas aeruginosa PAO1} SCOP: b.45.2.1
Length = 149
Score = 36.5 bits (84), Expect = 0.004
Identities = 16/118 (13%), Positives = 40/118 (33%), Gaps = 8/118 (6%)
Query: 2 YRGIHNLQFIDQRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVPMFL-VGE 60
++G + Q ++R F R+ D +L + ++ ++S G+ +
Sbjct: 19 FQGHMSDQHDERRRFHRIAFDADSE-ILQGERRWEVLLHDVSLHGILVGQPQDWNGDPQR 77
Query: 61 RSIVFV----EKVGRIEGKVVNFDSNRGYAVRIVTSENERRKLADKLIWLANKDDLHL 114
+ + + R+E + + + + +L+ L N D L
Sbjct: 78 PFEARLYLGLDVLIRMEISLAWAR-DGLLGFECQHIDLDSISHLRRLVEL-NLGDEEL 133
>2gjg_A Hypothetical protein PP4397; structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PSI; 2.25A {Pseudomonas putida KT2440}
Length = 248
Score = 33.5 bits (76), Expect = 0.040
Identities = 9/97 (9%), Positives = 24/97 (24%), Gaps = 8/97 (8%)
Query: 8 LQFIDQRAFQRVKVDLKGRFLLF-------DGTEYNCIVREISPGGLCIVCDVPMFLVGE 60
+ + +R R + L + + +IS G + + + +
Sbjct: 118 VTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRFEGNVEDRLQ 177
Query: 61 RSIVFVEKVGRIEGKVVNFDSNRGYAVRIVTSENERR 97
V+ +V+ + N
Sbjct: 178 LGQVYERFKAGNPLGLVDTMV-ELRHLHYEERINTTF 213
>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 = 31.8 bits (72), Expect = 0.12
Identities = 23/185 (12%), Positives = 50/185 (27%), Gaps = 80/185 (43%)
Query: 13 QRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVPMFLVGERSIVFVEKVGRI 72
A + DL + + + I P+
Sbjct: 433 VPASDLINKDLVKNNV------------SFNAKDIQI----PV----------------- 459
Query: 73 EGKVVNFDSNRGYAVRIVTSENERRKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDA 132
+D+ G +R++ S + ++++++ DC I R V
Sbjct: 460 ------YDTFDGSDLRVL-SGS----ISERIV-----------DC------IIRLP-VKW 490
Query: 133 QLVLNDNTKHSCKVIDI---SESGVSVSVDLQIEMFSKVLFNDILGRVVRIFPGGIAIEF 189
+ H ++D SG+ V + G VR+ G ++
Sbjct: 491 ETTTQFKATH---ILDFGPGGASGLGVLTHRNKD-----------GTGVRVIVAG-TLDI 535
Query: 190 SSVQE 194
+ +
Sbjct: 536 NPDDD 540
Score = 29.1 bits (65), Expect = 0.80
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 17/51 (33%)
Query: 160 LQIEMFSKVLF-----------NDILGR----VVRIFPGGIAIEFSSVQES 195
+ IE +V+F D LGR ++ I PG +A FS QE+
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS--QEA 1825
>3kyf_A PP4397, putative uncharacterized protein; C-DI-GMP, PILZ domain,
VCA0042, unknown function; HET: 5GP; 2.10A {Pseudomonas
putida} PDB: 2gjg_A
Length = 231
Score = 31.3 bits (70), Expect = 0.15
Identities = 8/80 (10%), Positives = 22/80 (27%), Gaps = 7/80 (8%)
Query: 8 LQFIDQRAFQRVKVDLKGRFLLF-------DGTEYNCIVREISPGGLCIVCDVPMFLVGE 60
+ + +R R + L + + +IS G + + + +
Sbjct: 110 VTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRFEGNVEDRLQ 169
Query: 61 RSIVFVEKVGRIEGKVVNFD 80
V+ +V+
Sbjct: 170 LGQVYERFKAGNPLGLVDTM 189
Score = 30.9 bits (69), Expect = 0.24
Identities = 24/140 (17%), Positives = 49/140 (35%), Gaps = 15/140 (10%)
Query: 31 DGTEYNCIVREISPGGLCIVCDVPMFLVGERSIVFVEKV---GRIEGKVVNFDSNRGYAV 87
+ V + + D + GE+ I E G +G + ++ + A+
Sbjct: 34 RSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDGVRIAWECDH--AL 91
Query: 88 RIVTSENERRKLADKLIWLANKDDL-HLQDCRAYGRKITRDREVDAQLV---LNDNTKHS 143
+I + R ++ + Q A+ + + VD L L N
Sbjct: 92 KISEVDGHR------CYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMR 145
Query: 144 CKVIDISESGVSVSVDLQIE 163
K++DIS +G + + +E
Sbjct: 146 GKLLDISATGCKLRFEGNVE 165
>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 = 0.31
Identities = 8/39 (20%), Positives = 18/39 (46%), Gaps = 15/39 (38%)
Query: 12 DQRAFQRVKVDLKGRFLLF-DGTEYNCIVREISPGGLCI 49
+++A ++++ LK L+ D + +P L I
Sbjct: 18 EKQALKKLQASLK----LYADDS---------AP-ALAI 42
>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L*
1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K*
1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O 1voy_O 1vp0_O
Length = 116
Score = 28.3 bits (63), Expect = 1.2
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 88 RIVTSEN---ERRKLADKLIWLANKDDLHLQDCRAYGRKITRDREV 130
RI T+ E R ++LI A DLH R + D++V
Sbjct: 33 RIQTTLTKAKELRPFVEQLITTAKGGDLH---SRRLVAQDIHDKDV 75
>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like
domain, Trp repressor-like domain, helix-turn-helix
motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB:
1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q
2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R
2wdj_R 2wdl_R 2wdn_R 2wh2_R ...
Length = 118
Score = 28.2 bits (63), Expect = 1.5
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 88 RIVTSEN---ERRKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLV 135
RI T+ E R D LI LA + DLH R + +D ++ +L
Sbjct: 33 RITTTVPKAKELRGFVDHLIHLAKRGDLH---ARRLVLRDLQDVKLVRKLF 80
>3i1n_N 50S ribosomal protein L17; ribosome structure, protein-RNA complex,
acetylation, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1p85_L 1p86_L 1vs8_N 2aw4_N
2awb_N 1vs6_N 2i2v_N 2j28_N 2i2t_N* 2qao_N* 2qba_N*
2qbc_N* 2qbe_N 2qbg_N 2qbi_N* 2qbk_N* 2qov_N 2qox_N
2qoz_N* 2qp1_N* ...
Length = 127
Score = 27.9 bits (62), Expect = 1.9
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 88 RIVTSEN---ERRKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLV 135
I T+ E R++ + LI LA D + R TRD E+ A+L
Sbjct: 33 IIKTTLPKAKELRRVVEPLITLAKTDSVA---NRRLAFARTRDNEIVAKLF 80
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 26.4 bits (58), Expect = 4.8
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 21/69 (30%)
Query: 92 SENER--RKLADKLIWLANKDDLHLQDCRAYGRKITRDRE------VDAQLVLNDNTKHS 143
S ++R R+ + L L +C+ Y KI LVL+D
Sbjct: 6 SIDKRAGRRGPN----LNIV--LTCPECKVYPPKIVERFSEGDVVCALCGLVLSDK---- 55
Query: 144 CKVIDI-SE 151
++D SE
Sbjct: 56 --LVDTRSE 62
>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.188.1.1 PDB: 2ftc_J 3iy9_S
Length = 122
Score = 26.4 bits (58), Expect = 5.2
Identities = 11/43 (25%), Positives = 15/43 (34%), Gaps = 3/43 (6%)
Query: 88 RIVTSEN---ERRKLADKLIWLANKDDLHLQDCRAYGRKITRD 127
RI E R A+KLI D + + R +T
Sbjct: 21 RIEAPWARVDEMRGYAEKLIDYGKLGDTNERAMRMADFWLTEK 63
>1x6o_A Eukaryotic initiation factor 5A; SGPP, structural genomics, PSI,
protein structure initiative; 1.60A {Leishmania
braziliensis} SCOP: b.34.5.2 b.40.4.5 PDB: 1xtd_A
Length = 174
Score = 26.1 bits (57), Expect = 5.5
Identities = 20/138 (14%), Positives = 42/138 (30%), Gaps = 11/138 (7%)
Query: 24 KGRFLLFDGTEYNCIVREISPGGLCIVCDVPMFLVGERSIVFVEKVGRIEGKVVNFDSNR 83
KG ++ +G I +S G V + + +E V
Sbjct: 38 KGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKT 97
Query: 84 GYAVRIVTSENERRKLADKLIWLAN----KDDLHLQDCRAYGRKI----TRDREVDAQLV 135
+ NE L L + + ++DL + A +I ++V +V
Sbjct: 98 YTYSVLDIQANEDPSLPAHLSLMDDEGESREDLDMPPDPALATQIKEQFDSGKDVLV-VV 156
Query: 136 LNDNTKHSCKVIDISESG 153
++ +V+ +
Sbjct: 157 VSAMGTE--QVLQTKNAA 172
>3hly_A Flavodoxin-like domain; Q5MZP6_SYNP6, flavoprotein, DFA1, SNR135D,
NESG, structural genomics, PSI-2; 2.40A {Synechococcus
elongatus pcc 6301}
Length = 161
Score = 25.7 bits (56), Expect = 7.6
Identities = 5/39 (12%), Positives = 12/39 (30%), Gaps = 7/39 (17%)
Query: 110 DDLHLQDCRAYGRKITRDREVDAQLVLNDNTKHSCKVID 148
+ Q C G + Q + + + K ++
Sbjct: 124 TEAIYQQCEESGTDL-------GQWLTRADAIQTMKSLE 155
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
0.326 0.142 0.418
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,768,367
Number of extensions: 80182
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 21
Length of query: 207
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 119
Effective length of database: 3,559,758
Effective search space: 423611202
Effective search space used: 423611202
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: 40 (21.6 bits)
S2: 54 (24.7 bits)