RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|255764483|ref|YP_003065151.2| hypothetical protein
CLIBASIA_03125 [Candidatus Liberibacter asiaticus str. psy62]
(135 letters)
>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 = 35.7 bits (82), Expect = 0.003
Identities = 29/145 (20%), Positives = 43/145 (29%), Gaps = 60/145 (41%)
Query: 11 NETVRKKGIPTTASQKTPEDNSNRI----RIAVGQSLILQFDVLPKQVIVG--------- 57
N T+RK P+ Q +RI R +F LP V
Sbjct: 390 NLTLRKAKAPSGLDQ-------SRIPFSERKLK---FSNRF--LP----VASPFHSHLLV 433
Query: 58 --DDKIVDVLALE----KEKTVVI------TGKNL--GSTNIIVLGHNNDILLD--T--- 98
D I L K + I G +L S +I + ++D
Sbjct: 434 PASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS------ERIVDCIIRLP 487
Query: 99 ---EIATFANEQST-VRVYTPGTLS 119
E T ++T + + PG S
Sbjct: 488 VKWETTT--QFKATHILDFGPGGAS 510
Score = 33.4 bits (76), Expect = 0.018
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 36/84 (42%)
Query: 74 VITGKNL------------GSTNIIVLGHNNDILLDTEIAT-------FANEQSTVRVYT 114
V+T K L G+T GH+ ++ IA F + + + V
Sbjct: 250 VVTAKLLGFTPGELRSYLKGAT-----GHSQGLVTAVAIAETDSWESFFVSVRKAITV-- 302
Query: 115 PGTLSFLSCTPRCL---P--SSPP 133
L F+ RC P S PP
Sbjct: 303 ---LFFIGV--RCYEAYPNTSLPP 321
Score = 31.8 bits (72), Expect = 0.054
Identities = 26/123 (21%), Positives = 42/123 (34%), Gaps = 41/123 (33%)
Query: 9 IKNETVRKKGIPTTASQ-KTP----EDNSNRIRIAVGQSLILQFDVLPKQVIVGDDKIVD 63
I + + K + A + P D S+ +R + S+ ++IVD
Sbjct: 439 IN-KDLVKNNVSFNAKDIQIPVYDTFDGSD-LR-VLSGSIS--------------ERIVD 481
Query: 64 VLALEK---EKTVVITGKNLGSTNIIVLGHNND----ILLDTEIATFANEQST-VRVYTP 115
+ E T +T+I+ G +L T N+ T VRV
Sbjct: 482 CIIRLPVKWETTT-----QFKATHILDFGPGGASGLGVL------THRNKDGTGVRVIVA 530
Query: 116 GTL 118
GTL
Sbjct: 531 GTL 533
>2ijd_1 Picornain 3C, RNA-directed RNA polymerase; RNA-dependent RNA
polymerase, picornavirus, protease, hydrolase,
transferase; 3.40A {Human poliovirus 1 mahoney} SCOP:
b.47.1.4 e.8.1.4
Length = 644
Score = 30.3 bits (68), Expect = 0.15
Identities = 25/127 (19%), Positives = 41/127 (32%), Gaps = 21/127 (16%)
Query: 10 KNETVRKKGIPTTASQKTPEDNSNRIRIAVGQSLILQFDVLPKQVIV----GDDKIVDVL 65
KN+T KG + T NS + + L+ + + + GDD I
Sbjct: 459 KNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYP 518
Query: 66 ALEKEKTVVITGKNLGSTNIIVLGHNNDILLDTEIATFANEQSTVRVYTPGTLSFLSCTP 125
+ +GK+ G T T A++ +T T ++FL
Sbjct: 519 HEVDASLLAQSGKDYGLT-----------------MTPADKSATFETVTWENVTFLKRFF 561
Query: 126 RCLPSSP 132
R P
Sbjct: 562 RADEKYP 568
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}
Length = 213
Score = 29.3 bits (66), Expect = 0.29
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 10/80 (12%)
Query: 9 IKNETVRKKGIPTTASQKTPEDNSNRIRIAVGQSLILQFDVLPKQVIVGDDKIVDVLALE 68
++++ + Q D I DVL V V D KI +++ ++
Sbjct: 90 VRSKVIAPGNRI----QLGTHDGRT---FITDDKSIKVGDVL--AVSVPDMKISEIIKMQ 140
Query: 69 KEKTVVIT-GKNLGSTNIIV 87
IT G ++ T I
Sbjct: 141 PGNKAYITAGSHVNQTGTIS 160
>2fv4_B Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region;
alpha-beta, complex, coiled-coil, structural protein,
protein binding; NMR {Saccharomyces cerevisiae} SCOP:
d.300.1.2
Length = 77
Score = 26.7 bits (59), Expect = 1.8
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 23 ASQKTPEDNSNRIRIAVGQSLILQFDVLPKQVIVGDDK--IVDVLALEKE 70
S TPE N N +++ + +SL + D+ QV++ +D+L L+
Sbjct: 12 QSAVTPEANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNN 61
>1xr7_A Genome polyprotein; RNA-dependent RNA polymerase, transferase;
2.30A {Human rhinovirus 16} SCOP: e.8.1.4 PDB: 1tp7_A*
1xr6_A
Length = 460
Score = 26.1 bits (57), Expect = 3.0
Identities = 21/127 (16%), Positives = 38/127 (29%), Gaps = 21/127 (16%)
Query: 10 KNETVRKKGIPTTASQKTPEDNSNRIRIAVGQSLILQFDVLP----KQVIVGDDKIVDVL 65
K+ +G + T NS I + ++ + + K + GDD I
Sbjct: 275 KSTYYEVEGGVPSGCSGTSIFNSMINNIIIRTLVLDAYKHIDLDKLKIIAYGDDVIFSYK 334
Query: 66 ALEKEKTVVITGKNLGSTNIIVLGHNNDILLDTEIATFANEQSTVRVYTPGTLSFLSCTP 125
+ + G+ G T T A++ S + G ++FL
Sbjct: 335 YKLDMEAIAKEGQKYGLT-----------------ITPADKSSEFKELDYGNVTFLKRGF 377
Query: 126 RCLPSSP 132
R
Sbjct: 378 RQDDKYK 384
>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding,
complete proteome, DNA binding, DNA repair; HET: DNA
ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12
c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A*
1oh7_A* 1oh8_A* 1w7a_A* 1wbd_A* 1ng9_A*
Length = 800
Score = 25.3 bits (54), Expect = 4.6
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 110 VRVYTPGTL 118
VR+ TPGT+
Sbjct: 111 VRIVTPGTI 119
>2o8b_A DNA mismatch repair protein MSH2; DNA damage response, somatic
hypermutation, protein-DNA complex, DNA mispair, cancer,
ABC transporter ATPase; HET: DNA ADP; 2.75A {Homo
sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 2o8e_A*
Length = 934
Score = 25.0 bits (53), Expect = 5.2
Identities = 4/10 (40%), Positives = 5/10 (50%)
Query: 110 VRVYTPGTLS 119
+PG LS
Sbjct: 120 AYKASPGNLS 129
>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic
hypermutation, protein-DNA complex, DNA mispair, cancer,
ABC transporter ATPase; HET: DNA ADP; 2.75A {Homo
sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*
Length = 1022
Score = 25.0 bits (53), Expect = 6.0
Identities = 4/10 (40%), Positives = 6/10 (60%)
Query: 110 VRVYTPGTLS 119
R+ T GT +
Sbjct: 176 CRIITKGTQT 185
>2l04_A Major tail protein V; bacteriophage lambda, phage tail, GPV,
IG-like domain, viral; NMR {Enterobacteria phage
lambda}
Length = 91
Score = 24.7 bits (54), Expect = 7.2
Identities = 14/64 (21%), Positives = 17/64 (26%), Gaps = 9/64 (14%)
Query: 31 NSNRIRIAVGQSLILQFDVLP-----KQVI--VGDDKIVDVLALEKEKTVVITGKNLGST 83
+ GQS L P K D V T+ + G G
Sbjct: 12 TPASTSVVKGQSTTLTVAFQPEGVTDKSFRAVSADKTKATVS--VSGMTITVNGVAAGKV 69
Query: 84 NIIV 87
NI V
Sbjct: 70 NIPV 73
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli K12}
Length = 671
Score = 24.8 bits (53), Expect = 7.3
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 32 SNRIRIAVGQSLILQFDVLPKQVIVGDDKIVDVLALEKEKTVVITGK 78
+ V L+ + P +++ ++I A KTVV+TG
Sbjct: 565 AEESNRNVISELLAEGVHWPAPIVINAEEIDSPFA---GKTVVLTGS 608
>1gml_A CCT-gamma; chaperone, chaperonin, actin, tubulin; 2.2A {Mus
musculus} SCOP: c.8.5.2 PDB: 1gn1_A
Length = 178
Score = 24.5 bits (53), Expect = 8.1
Identities = 12/74 (16%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 15 RKKGIPTTASQKTPEDNSNRIRIAVGQSLILQFDVLPKQVIVGDDKIVDVLALEKEKTVV 74
+ + A ++ + ++NRI A G ++ + + L + + ++++ + E
Sbjct: 97 MRANVT--AIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTF 154
Query: 75 ITGKNLGSTNIIVL 88
IT I+L
Sbjct: 155 ITDCKDPKACTILL 168
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
0.316 0.133 0.372
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,112,942
Number of extensions: 47887
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 16
Length of query: 135
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 53
Effective length of database: 3,705,222
Effective search space: 196376766
Effective search space used: 196376766
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 (21.6 bits)
S2: 51 (23.5 bits)