RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780976|ref|YP_003065389.1| Holliday junction resolvase
YqgF [Candidatus Liberibacter asiaticus str. psy62]
         (160 letters)



>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2
           function project, S2F, unknown function; 1.60A
           {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A
          Length = 138

 Score =  130 bits (329), Expect = 1e-31
 Identities = 41/134 (30%), Positives = 63/134 (47%), Gaps = 1/134 (0%)

Query: 18  PIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPL 77
            + + D GTK IG+A+       A P P +  +  T     +   +        I+GLPL
Sbjct: 4   TLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63

Query: 78  NMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVD 137
           NM+G+E P     R F +  I  +  V     DERL+TV A+  L +    R     KVD
Sbjct: 64  NMDGTEQPLTARARKFANR-IHGRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 138 SIAAALILQEVLDR 151
           S +A +IL+  +++
Sbjct: 123 SASAVIILESYMEQ 136


>1vhx_A Putative holliday junction resolvase; structural genomics,
           hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8
          Length = 150

 Score =  115 bits (289), Expect = 4e-27
 Identities = 50/137 (36%), Positives = 77/137 (56%), Gaps = 3/137 (2%)

Query: 19  IASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTAL--ELLSFITTENIAAFIIGLP 76
           I  +DLGTK +G+A+SD     A     +   +         L   I    I   ++G P
Sbjct: 5   ILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFP 64

Query: 77  LNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKV 136
            NMNG+ GPR  +++ F   + +    VP V WDERLTT++A+++LI  +VSR+KR + +
Sbjct: 65  KNMNGTVGPRGEASQTFAKVL-ETTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVI 123

Query: 137 DSIAAALILQEVLDRIS 153
           D +AA +ILQ  LD ++
Sbjct: 124 DKMAAVMILQGYLDSLN 140


>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken
           structural genomics/proteomics initiative, RSGI, unknown
           function; NMR {Thermus thermophilus} SCOP: c.55.3.8
          Length = 98

 Score = 95.6 bits (238), Expect = 4e-21
 Identities = 32/97 (32%), Positives = 48/97 (49%), Gaps = 2/97 (2%)

Query: 19  IASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLN 78
           + ++D+G  RIGLA+ + G   A  R +LVRK + +    LL F+  E +   ++GLPL 
Sbjct: 3   VGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLR 62

Query: 79  MNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTT 115
            +  E  +       V  +  R   V    WDER TT
Sbjct: 63  TDLKESAQAGKVLPLVEALRARG--VEVELWDERFTT 97


>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 = 38.8 bits (90), Expect = 5e-04
 Identities = 33/213 (15%), Positives = 66/213 (30%), Gaps = 97/213 (45%)

Query: 5   LIEDLVKSLKPN-QPIASIDLGTKRI---GLAI----SDPGRRFAHPRP---FLVRKKVT 53
           L+ DL+K        +    L  +++   GL I     +P        P   +L+     
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP-----SNTPDKDYLL----- 232

Query: 54  QTA---------LELLSFITTENIAAFIIGL-PLNMN----GSEGPRVHS----TRAFVH 95
            +          ++L  ++    + A ++G  P  +     G+ G   HS    T   + 
Sbjct: 233 -SIPISCPLIGVIQLAHYV----VTAKLLGFTPGELRSYLKGATG---HSQGLVTAVAI- 283

Query: 96  NMID---------RKVYVPFVFWDERLTTVSAQQ----------ILID-----------M 125
              D         RK  +  +F+      V   +          IL D           M
Sbjct: 284 AETDSWESFFVSVRKA-ITVLFF----IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPM 338

Query: 126 ----NVSRK---KRIQKVDS-------IAAALI 144
               N++++     + K +S       +  +L+
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV 371



 Score = 29.9 bits (67), Expect = 0.25
 Identities = 35/154 (22%), Positives = 57/154 (37%), Gaps = 46/154 (29%)

Query: 3    ILLIEDLV-----KSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTAL 57
            ++ IE LV     + +     +   +LG    G+   +PGR         V    +Q AL
Sbjct: 1776 VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGR---------VAASFSQEAL 1826

Query: 58   ELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDER-LTTV 116
            + +     E +               G R       V+  ++ + YV     D R L TV
Sbjct: 1827 QYV----VERV---------------GKRTGWLVEIVNYNVENQQYV--AAGDLRALDTV 1865

Query: 117  SAQQILIDMNVSRKKRIQKVDSI--AAALILQEV 148
            +        NV    ++QK+D I    +L L+EV
Sbjct: 1866 T--------NVLNFIKLQKIDIIELQKSLSLEEV 1891



 Score = 29.9 bits (67), Expect = 0.27
 Identities = 40/252 (15%), Positives = 74/252 (29%), Gaps = 112/252 (44%)

Query: 8   DLVKSLK-----PNQ------PIASIDLGTKRIGL------AIS------DPG---RRFA 41
           ++++ L+     P++      PI S  L    IG+       ++       PG       
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPI-SCPL----IGVIQLAHYVVTAKLLGFTPGELRSYLK 268

Query: 42  ----H---------------PRPFLVRKKVTQTALELLSFITTENIAAF-IIGLPLNM-- 79
               H                  F       + A+ +L FI      A+    LP ++  
Sbjct: 269 GATGHSQGLVTAVAIAETDSWESFF---VSVRKAITVLFFIGVRCYEAYPNTSLPPSILE 325

Query: 80  ----NGSEG-P----RVHS-TRAFVHNMID---------RKVYV-----P--FV------ 107
               N  EG P     + + T+  V + ++         ++V +         V      
Sbjct: 326 DSLENN-EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ 384

Query: 108 ----FWDERLTTVSAQQILIDMN----VSRKKRIQK----VDS--------IAAALILQE 147
                 +  L    A   L D +      RK +       V S         A+ LI ++
Sbjct: 385 SLYGL-NLTLRKAKAPSGL-DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442

Query: 148 VLDR-ISFLESS 158
           ++   +SF    
Sbjct: 443 LVKNNVSFNAKD 454


>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 = 29.6 bits (65), Expect = 0.34
 Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 15/38 (39%)

Query: 119 QQILIDMNVSRKKRIQ---KV---DSIAAALILQEVLD 150
           +Q L        K++Q   K+   DS A AL ++  ++
Sbjct: 19  KQAL--------KKLQASLKLYADDS-APALAIKATME 47


>3ces_A MNMG, tRNA uridine 5-carboxymethylaminomethyl modification enzyme
           GIDA, GIDA; tRNA modification, FAD binding domain,
           structural genomics; 2.41A {Escherichia coli} PDB:
           3cp2_A
          Length = 651

 Score = 26.9 bits (59), Expect = 2.2
 Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 4/25 (16%)

Query: 79  MNGSEGPRVHSTRAFVHNMIDRKVY 103
           +N S+GP V +TRA      DR +Y
Sbjct: 106 LNASKGPAVRATRA----QADRVLY 126


>2zxi_A TRNA uridine 5-carboxymethylaminomethyl modification enzyme MNMG;
           5-carboxymethylaminomethyl uridine, wobble uridine, FAD,
           FAD-binding protein; HET: FAD; 2.30A {Aquifex aeolicus}
           PDB: 2zxh_A* 2e57_A*
          Length = 637

 Score = 26.6 bits (58), Expect = 2.6
 Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 4/25 (16%)

Query: 79  MNGSEGPRVHSTRAFVHNMIDRKVY 103
           +N  +G  V S RA      D+K Y
Sbjct: 105 LNTRKGKAVQSPRA----QADKKRY 125


>3cer_A Possible exopolyphosphatase-like protein; NESG, BLR13, Q8G5J2,
          X-RAY, structure, structural genomics, PSI-2; 2.40A
          {Bifidobacterium longum NCC2705}
          Length = 343

 Score = 26.8 bits (58), Expect = 2.6
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 14 KPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKV 52
          K +  +A ID GT  I L I+       H     + + +
Sbjct: 13 KESVTVAGIDCGTNSIRLKIARVDADGMHEVVPRILRVI 51


>3hi0_A Putative exopolyphosphatase; 17739545, structural genomics, joint
          center for structural genomics, JCSG; HET: MSE; 2.30A
          {Agrobacterium tumefaciens str}
          Length = 508

 Score = 26.6 bits (58), Expect = 2.8
 Identities = 7/27 (25%), Positives = 14/27 (51%)

Query: 13 LKPNQPIASIDLGTKRIGLAISDPGRR 39
          L    P++ ID+G+  + L + +   R
Sbjct: 11 LTGLAPVSVIDIGSNSVRLVVYEGLSR 37


>1kcf_A Hypothetical 30.2 KD protein C25G10.02 in chromosome I;
          beta-alpha-beta motif, RUVC resolvase family,
          hydrolase; 2.30A {Schizosaccharomyces pombe} SCOP:
          a.140.2.1 c.55.3.7
          Length = 258

 Score = 26.5 bits (58), Expect = 3.2
 Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 1/32 (3%)

Query: 5  LIEDLVKSL-KPNQPIASIDLGTKRIGLAISD 35
          L+  +V S   P   +  IDLG K      + 
Sbjct: 27 LLRRIVDSPIYPTSRVLGIDLGIKNFSYCFAS 58


>2v4j_B Sulfite reductase, dissimilatory-type subunit beta; dissimilatory
           sulfite reductase, complex, siroheme, oxidoreductase;
           HET: SRM; 2.10A {Desulfovibrio vulgaris} SCOP: d.58.1.5
           d.58.36.2 d.134.1.1
          Length = 381

 Score = 26.2 bits (57), Expect = 3.3
 Identities = 5/19 (26%), Positives = 9/19 (47%)

Query: 93  FVHNMIDRKVYVPFVFWDE 111
           F H++ID      +  W +
Sbjct: 357 FSHHLIDDFRDPAYYTWRQ 375


>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 = 26.3 bits (57), Expect = 3.3
 Identities = 25/106 (23%), Positives = 42/106 (39%), Gaps = 35/106 (33%)

Query: 1    MSILLIEDLVKSLKPNQPIASI----DLGTKRIGLAISDPGR-------------RFAHP 43
            + I++  DL  +LK   PI  I       T +IG ++  PG+             ++A P
Sbjct: 1185 IQIIMQADL--ALKMGVPIYGIVAMAATATDKIGRSVPAPGKGILTTAREHHSSVKYASP 1242

Query: 44   R---PFLVRKKVTQTA---------LELLSF----ITTENIAAFII 73
                 +  R+ VT+ A         LE L      I +E+   F++
Sbjct: 1243 NLNMKYRKRQLVTREAQIKDWVENELEALKLEAEEIPSEDQNEFLL 1288


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 26.0 bits (56), Expect = 3.5
 Identities = 7/19 (36%), Positives = 16/19 (84%), Gaps = 1/19 (5%)

Query: 129 RKKRIQKVDSIAAALILQE 147
           ++KR+Q++D+ A+ ++ QE
Sbjct: 94  QRKRLQELDA-ASKVMEQE 111


>2nac_A NAD-dependent formate dehydrogenase;
           oxidoreductase(aldehyde(D),NAD+(A)); 1.80A {Pseudomonas
           SP} SCOP: c.2.1.4 c.23.12.1 PDB: 2nad_A* 2go1_A 2gug_A*
           2gsd_A*
          Length = 393

 Score = 25.6 bits (55), Expect = 4.8
 Identities = 8/26 (30%), Positives = 11/26 (42%)

Query: 53  TQTALELLSFITTENIAAFIIGLPLN 78
           T TA    +  T E +  F  G P+ 
Sbjct: 337 TLTAQARYAAGTREILECFFEGRPIR 362


>1eex_A Propanediol dehydratase; coenzyme B12, potassium ION, TIM barrel,
           lyase; HET: COY; 1.70A {Klebsiella oxytoca} SCOP:
           c.1.19.3 PDB: 1dio_A* 1egm_A* 1egv_A* 1iwb_A* 1uc4_A*
           1uc5_A* 1iwp_A* 1mmf_A*
          Length = 554

 Score = 25.9 bits (57), Expect = 4.8
 Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 122 LIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLE 156
           L D NV R + +    ++  A I+ EV+  ++ +E
Sbjct: 91  LCDPNVKRSEIVPLTTAMTPAKIV-EVVSHMNVVE 124


>3c7b_B Sulfite reductase, dissimilatory-type subunit beta; alpha/beta
           fold, 4Fe-4S, heme, iron, iron-sulfur, membrane,
           metal-binding; HET: SRM; 2.00A {Archaeoglobus fulgidus}
           SCOP: d.58.1.5 d.58.36.2 d.134.1.1
          Length = 366

 Score = 25.4 bits (55), Expect = 6.2
 Identities = 6/23 (26%), Positives = 12/23 (52%)

Query: 93  FVHNMIDRKVYVPFVFWDERLTT 115
           F  ++ID     P+ + + R +T
Sbjct: 340 FTQHLIDDYRITPYFYSEFRAST 362


>2vx2_A Enoyl-COA hydratase domain-containing protein 3; isomerase,
          alternative splicing, fatty acid metabolism, enoyl
          coenzyme A hydratase; 2.3A {Homo sapiens}
          Length = 287

 Score = 25.3 bits (54), Expect = 6.9
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 22 IDLGTKRIGLAISDPGRRFAHPRPFLVRK 50
          +DLGT+ +       GRR + PRP   R+
Sbjct: 11 VDLGTENLYFQSMGAGRRESEPRPTSARQ 39


>3kgl_A Cruciferin; 11S SEED globulin, rapeseed, SEED storage protein,
           storage protein, plant protein; 2.98A {Brassica napus}
          Length = 466

 Score = 25.1 bits (54), Expect = 8.3
 Identities = 9/32 (28%), Positives = 14/32 (43%)

Query: 36  PGRRFAHPRPFLVRKKVTQTALELLSFITTEN 67
            G+  + P+ F V K+ T      + F T  N
Sbjct: 374 QGQLLSIPQGFSVVKRATSEQFRWIEFKTNAN 405


  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
   0.323    0.138    0.385 

Gapped
Lambda     K      H
   0.267   0.0524    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,294,408
Number of extensions: 56050
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 28
Length of query: 160
Length of database: 5,693,230
Length adjustment: 85
Effective length of query: 75
Effective length of database: 3,632,490
Effective search space: 272436750
Effective search space used: 272436750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.7 bits)