RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus
Liberibacter asiaticus str. psy62]
         (723 letters)



>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing,
           hydrolase, endonuclease; 2.85A {Escherichia coli} PDB:
           2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
          Length = 517

 Score =  325 bits (835), Expect = 1e-89
 Identities = 172/411 (41%), Positives = 255/411 (62%), Gaps = 3/411 (0%)

Query: 159 DVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGET 218
                   +  I++V++  Q ++VQI KEERGNKGAA+TT++SLAG Y VLMPN  +   
Sbjct: 86  PANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRA-G 144

Query: 219 ISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL 278
              +     DR  LKE    LE+P GMG+I+RTAG  ++   ++ D  + ++ W+ +++ 
Sbjct: 145 GISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKA 204

Query: 279 ALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVR 337
           A +  AP L+++E N+I RA RD   +DI EI++   K    A+  +  L  P ++  ++
Sbjct: 205 AESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIK 264

Query: 338 QYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIED 397
            Y    P+F    IE Q++S  Q EV LPS G ++I+ TEAL +ID+NS R+TR   IE+
Sbjct: 265 LYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEE 324

Query: 398 TALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457
           TA  TNLEAA+EIARQLRLRDL GLIV+DFIDM   ++ R+VE +L+E++++DRAR+Q+ 
Sbjct: 325 TAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQIS 384

Query: 458 AISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAH 517
            IS FGLLEMSRQR+  S+ ES+  VC  C G G +R   S++LSILR +EE  L+    
Sbjct: 385 HISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQ 444

Query: 518 NIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKLFYIEK 567
            +       +  YLLN+KR+ +   E R  GV   +V   ++    +++ +
Sbjct: 445 EVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLR 495



 Score =  131 bits (330), Expect = 6e-31
 Identities = 48/111 (43%), Positives = 66/111 (59%), Gaps = 7/111 (6%)

Query: 3   NKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYG 62
            +MLI+A+  EE RV ++   R+ +LD ES   +Q K NIY  K+TR+EPSL+AAFVDYG
Sbjct: 9   KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYG 68

Query: 63  GNRHGFLPFLEIHPDYYQIPFSDR-----QALLKESN--IAQTDSEAVADD 106
             RHGFLP  EI  +Y+   +S       + +L+E    I Q D E   + 
Sbjct: 69  AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK 119


>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 = 51.5 bits (123), Expect = 7e-07
 Identities = 78/519 (15%), Positives = 151/519 (29%), Gaps = 175/519 (33%)

Query: 19  VLRD-------NRVEELDFESEHKKQIKGNIYLAK-----VTRVEPSLQAAFVD-----Y 61
            L++          E    + E     +    + K      + VEPS    F        
Sbjct: 32  QLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88

Query: 62  GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSL- 120
               + +L   +IH    ++   +   L+K   + +    A    +        ++ +L 
Sbjct: 89  TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI--MAKRPFDKKSNSALF 146

Query: 121 -----EEVAPIANFS-Q---ET--EE------------ESIISANNDVVSN-VEDVKGGS 156
                     +A F  Q   +   EE              +I  + + +S  +       
Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT----- 201

Query: 157 PEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNK----GAAVT----TYLSLAGRYSV 208
             D  K F +   I E ++N              +K       ++      + LA  Y V
Sbjct: 202 TLDAEKVFTQGLNILEWLENP---------SNTPDKDYLLSIPISCPLIGVIQLA-HYVV 251

Query: 209 LMPNTSK--GETISRKITNPVDRKNLKEIARGLEVPAG--MGVILRTAGASRTKIEIKRD 264
               T+K  G T       P       E+   L+   G   G++   A A     E    
Sbjct: 252 ----TAKLLGFT-------P------GELRSYLKGATGHSQGLVTAVAIAETDSWE---S 291

Query: 265 FEYLMR------LWDNVREL---ALNSVAPHLVYE-----EGN----LIKRAIRDLYCKD 306
           F   +R       +  VR        S+ P ++ +     EG     L   +I +L  + 
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML---SISNLTQEQ 348

Query: 307 ISEIIVSGEKGYREAKDFMKLLMPSYARIV-------RQY--EDPHPIFFRS--GIEVQL 355
           + + +                L P+  ++        +      P P   +S  G+ + L
Sbjct: 349 VQDYV----------NKTNSHL-PAGKQVEISLVNGAKNLVVSGP-P---QSLYGLNLTL 393

Query: 356 ------DSLHQTEVTLPSRGYVIINQTEALVSIDV--NSGRSTREHCIEDTA--LQTNLE 405
                   L Q+ +    R     N+    + +    +S      H +   +  +  +L 
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNR---FLPVASPFHS------HLLVPASDLINKDL- 443

Query: 406 AAEEI---ARQLR-----------LRDLAGLIVVDFIDM 430
               +   A+ ++           LR L+G I    +D 
Sbjct: 444 VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC 482



 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 53/215 (24%), Positives = 82/215 (38%), Gaps = 60/215 (27%)

Query: 10   SHVEET------RVVVLRDNRVE-ELDFESEHKKQIKGNIYLAKV--TRVEPSLQAAFVD 60
            +H ++T       +V+  +N V   + F  E  K+I+ N Y A +  T V+  L+   + 
Sbjct: 1651 NHFKDTYGFSILDIVI--NNPVNLTIHFGGEKGKRIREN-YSAMIFETIVDGKLKTEKI- 1706

Query: 61   YGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQ-----TDSEAVADDVTHGDVTIP 115
                      F EI+       F   + LL  +   Q      +  A  D  + G   IP
Sbjct: 1707 ----------FKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG--LIP 1754

Query: 116  ND-----HSLEEVAPIANFSQETEEESIISANNDV---------VSNVEDVKGGS----- 156
             D     HSL E A +A+ +     ES++    +V         V+   D  G S     
Sbjct: 1755 ADATFAGHSLGEYAALASLADVMSIESLV----EVVFYRGMTMQVAVPRDELGRSNYGMI 1810

Query: 157  ---PEDVPKKFKR---QYCIQEVIKNRQILLVQIV 185
               P  V   F +   QY ++ V K R   LV+IV
Sbjct: 1811 AINPGRVAASFSQEALQYVVERVGK-RTGWLVEIV 1844



 Score = 39.5 bits (92), Expect = 0.002
 Identities = 47/274 (17%), Positives = 89/274 (32%), Gaps = 101/274 (36%)

Query: 21  RDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSL---QAAFVD-------YGGNRHGFLP 70
            +   E++    ++  +   N +L    +VE SL       V        YG N      
Sbjct: 342 SNLTQEQVQ---DYVNKT--NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLT---- 392

Query: 71  FL-EI----HPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHG--DVTIPNDHS--LE 121
            L +       D  +IPFS+R+                    ++    V  P  HS  L 
Sbjct: 393 -LRKAKAPSGLDQSRIPFSERKL-----------------KFSNRFLPVASPF-HSHLLV 433

Query: 122 EVAPIANFSQETEEESI-ISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQIL 180
             + +   +++  + ++  +A  D+   V D   G   D          ++ +  +  I 
Sbjct: 434 PASDLI--NKDLVKNNVSFNA-KDIQIPVYDTFDG--SD----------LRVLSGS--IS 476

Query: 181 --LVQIVKEERGNKGAAVT---TYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEI 235
             +V  +               T++   G      P  + G  +   +T+    +N K+ 
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFG------PGGASG--LGV-LTH----RN-KD- 521

Query: 236 ARGLEVPAGMG--VILRTAGASRTKIEIKRDFEY 267
                   G G  VI+  AG     ++I  D +Y
Sbjct: 522 --------GTGVRVIV--AGT----LDINPDDDY 541



 Score = 38.8 bits (90), Expect = 0.005
 Identities = 65/331 (19%), Positives = 124/331 (37%), Gaps = 108/331 (32%)

Query: 244  GMGVIL-RTAGAS-----RTKIEIKRDFEYLMRLWDNVRELALNS---VAPHLVYEEGNL 294
            GMG+ L +T+ A+     R     K  + +      ++ ++ +N+   +  H   E+G  
Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDTYGF------SILDIVINNPVNLTIHFGGEKG-- 1681

Query: 295  IKRAIRDLYCKDISEIIVSG----EKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRS- 349
             KR IR+ Y   I E IV G    EK ++E  +       SY              FRS 
Sbjct: 1682 -KR-IRENYSAMIFETIVDGKLKTEKIFKEINEHST----SYT-------------FRSE 1722

Query: 350  -GIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVN-SGRSTREHCIEDTALQTNLEAA 407
             G+ +      Q  +TL  +      +++ L+  D   +G S  E+            A 
Sbjct: 1723 KGL-LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYA-----------AL 1770

Query: 408  EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEM 467
              +A  + +  L  ++    + M+              ++ +D    ++G  SN+G++ +
Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQ-------------VAVPRD----ELGR-SNYGMIAI 1812

Query: 468  SRQRIRSS--------VLESTTK-------VCTYCKGAGYIRSQSSVALSILRSVEEYLL 512
            +  R+ +S        V+E   K       +  Y      + +Q  VA   LR+++    
Sbjct: 1813 NPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY-----NVENQQYVAAGDLRALD---- 1863

Query: 513  QYTAHNIIVHTHSDVVLYLLNQKRATIVEYE 543
              T  N         VL  +  ++  I+E +
Sbjct: 1864 --TVTN---------VLNFIKLQKIDIIELQ 1883



 Score = 38.0 bits (88), Expect = 0.007
 Identities = 32/234 (13%), Positives = 70/234 (29%), Gaps = 89/234 (38%)

Query: 506 SVEEYLLQYTAHNIIVH--------THSDVVLYLLNQKRATIVEYEARF--GVSINVVI- 554
           +  E + ++  +  +              V+   L        E+E  +  G  I+ +  
Sbjct: 56  TPAELVGKFLGY--VSSLVEPSKVGQFDQVLNLCLT-------EFENCYLEGNDIHALAA 106

Query: 555 ------GIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPK 608
                    L      I+  + + A +        D ++ S            AL     
Sbjct: 107 KLLQENDTTLVKTKELIK--NYITARIMAKRP--FDKKSNS------------ALF---- 146

Query: 609 SESLEDIQDNIVS------------EESTGVIRKRRRRRRRRRPATDHHD--AGVVSD-V 653
             ++ +    +V+            EE    +R             D +     +V D +
Sbjct: 147 -RAVGEGNAQLVAIFGGQGNTDDYFEE----LR-------------DLYQTYHVLVGDLI 188

Query: 654 SSIQNVI-------DDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTP 700
                 +        D+  ++ +  +I     LEN ++   ++Y +SI P+S P
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLNI--LEWLENPSNTPDKDYLLSI-PISCP 239


>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 = 31.5 bits (70), Expect = 0.63
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 22/50 (44%)

Query: 566 EKGSPVQAL--VNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLE 613
           EK    QAL  +    K+ +D  AP+              L I K+ ++E
Sbjct: 18  EK----QALKKLQASLKLYADDSAPA--------------LAI-KA-TME 47



 Score = 31.5 bits (70), Expect = 0.75
 Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 7/24 (29%)

Query: 432 EKKNNRSVEKKLKESLK---KDRA 452
           EK+   ++ KKL+ SLK    D A
Sbjct: 18  EKQ---AL-KKLQASLKLYADDSA 37



 Score = 30.0 bits (66), Expect = 2.2
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 36/65 (55%)

Query: 444 KESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSI 503
           K++LKK                           L+++ K+  Y          S+ AL+I
Sbjct: 19  KQALKK---------------------------LQASLKL--YA-------DDSAPALAI 42

Query: 504 LRSVE 508
             ++E
Sbjct: 43  KATME 47



 Score = 29.6 bits (65), Expect = 2.9
 Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 10/31 (32%)

Query: 85  DRQALLKESNIAQTDSEAVADDVTHGDVTIP 115
           ++QAL K     Q   +  ADD      + P
Sbjct: 18  EKQALKK----LQASLKLYADD------SAP 38


>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
           degradation, kinase, transferase; 2.60A {Escherichia
           coli} PDB: 1sro_A
          Length = 723

 Score = 30.6 bits (69), Expect = 1.3
 Identities = 24/90 (26%), Positives = 34/90 (37%), Gaps = 28/90 (31%)

Query: 23  NRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIP 82
            R+EE+  E E      G +Y  KVTR+        VD+G        F+ I        
Sbjct: 616 RRIEEITAEIE-----VGRVYTGKVTRI--------VDFGA-------FVAIGG------ 649

Query: 83  FSDRQALLKESNIAQTDSEAVADDVTHGDV 112
              ++ L+  S IA    E V D +  G  
Sbjct: 650 --GKEGLVHISQIADKRVEKVTDYLQMGQE 677


>1iru_N 20S proteasome; cell cycle, immune response, proteolysis,
           ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
          Length = 219

 Score = 28.9 bits (64), Expect = 4.4
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 285 PHLVYEEG-NLIKRAIRDLYCKDIS-----EIIVSGEKGYREAKDFMKLLMPSYARIVRQ 338
           P L   E  +L++R +R LY +D       +     EKG               A ++  
Sbjct: 158 PVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKGVEIEGPLSTETNWDIAHMISG 217

Query: 339 YE 340
           +E
Sbjct: 218 FE 219


>2epj_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA,
           structural genomics, NPPSFA; HET: PMP; 1.70A {Aeropyrum
           pernix K1} PDB: 2zsl_A* 2zsm_A*
          Length = 434

 Score = 28.8 bits (63), Expect = 5.0
 Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 6/45 (13%)

Query: 309 EIIVSGEKG---YREAKDFMKLLMPSYARIVRQYEDPHPIFFRSG 350
           +++ SGEK    +   K+     + S    VR    P+P + + G
Sbjct: 4   DVLASGEKSRMLFERTKELFPGGVNSP---VRAAVKPYPFYVKRG 45


>2pe4_A Hyaluronidase-1; hyaluronan, EGF-like domain, alternative splicing,
           hydrolase; HET: NAG BMA MAN; 2.00A {Homo sapiens}
          Length = 424

 Score = 28.2 bits (63), Expect = 6.9
 Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 1/29 (3%)

Query: 400 LQTNLE-AAEEIARQLRLRDLAGLIVVDF 427
           L  +L    ++I   +   D +GL V+D+
Sbjct: 83  LIAHLARTFQDILAAIPAPDFSGLAVIDW 111


>1knv_A BSE634I restriction endonuclease; APO-enzyme, hydrolase; 2.17A
           {Geobacillus stearothermophilus} SCOP: c.52.1.7
          Length = 293

 Score = 28.0 bits (62), Expect = 7.2
 Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 3/45 (6%)

Query: 262 KRDFEYLMRLWDNV---RELALNSVAPHLVYEEGNLIKRAIRDLY 303
           K +F+Y     + V    + AL + A H +    +  +RA+ D++
Sbjct: 231 KAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIF 275


>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
           transferase, ATP-GTP diphosphotransferase RNA
           processing, RNA degradation; 2.5A {Streptomyces
           antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
           d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
          Length = 757

 Score = 27.8 bits (62), Expect = 7.6
 Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 2/35 (5%)

Query: 40  GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74
           G   L  V +       AFV     + G L   +I
Sbjct: 668 GERILGSVVKTTTF--GAFVSLLPGKDGLLHISQI 700


>1d6t_A Ribonuclease P, RNAse P protein; endonuclease, subunit; NMR
           {Staphylococcus aureus} SCOP: d.14.1.2
          Length = 117

 Score = 27.8 bits (62), Expect = 9.3
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 7/63 (11%)

Query: 216 GETISRKITNPVDRKNLKEIARGLEVPAGMG-------VILRTAGASRTKIEIKRDFEYL 268
           G ++S+K+ N V R  +K   R                VI R      T ++I+   E++
Sbjct: 46  GISVSKKLGNAVLRNKIKRAIRENFKVHKSHILAKDIIVIARQPAKDMTTLQIQNSLEHV 105

Query: 269 MRL 271
           +++
Sbjct: 106 LKI 108


  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    0.132    0.369 

Gapped
Lambda     K      H
   0.267   0.0664    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 6,130,040
Number of extensions: 295659
Number of successful extensions: 1256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1235
Number of HSP's successfully gapped: 32
Length of query: 723
Length of database: 5,693,230
Length adjustment: 99
Effective length of query: 624
Effective length of database: 3,293,074
Effective search space: 2054878176
Effective search space used: 2054878176
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: 60 (27.0 bits)