RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific
exonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
         (600 letters)



>2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair,
           hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A
           2zxp_A 1ir6_A
          Length = 666

 Score =  423 bits (1088), Expect = e-119
 Identities = 151/578 (26%), Positives = 252/578 (43%), Gaps = 51/578 (8%)

Query: 16  FRWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLIL 75
            RW  +L    + +   +     +    A    +R       K+ L+P + LL      L
Sbjct: 5   VRWR-VLSLPPLAQWREVMAALEVGPEAALAYWHRGFR---RKEDLDPPLALLP-----L 55

Query: 76  TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGY 135
               +AA  + +A+   ++I + GDYD DG    A+++R L+    + + +IP R+ +GY
Sbjct: 56  KGLREAAALLEEALRQGKRIRVHGDYDADGLTGTAILVRGLAALGADVHPFIPHRLEEGY 115

Query: 136 GPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALV 195
           G     + + + E + L +TVDCG T++  L+     G++VIV DHH    +  P   +V
Sbjct: 116 GVLMERVPEHL-EASDLFLTVDCGITNHAELRELLENGVEVIVTDHHTP-GKTPPPGLVV 173

Query: 196 NPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVP 255
           +P    DL  +     AGV F        +L   ++       L   DL A+ T+ DV P
Sbjct: 174 HPALTPDL--KEKPTGAGVAF-------LLLWALHERLGLPPPLEYADLAAVGTIADVAP 224

Query: 256 LIGLNRAYVVKGLMVARRQGNPGLKALIERVNISSPITAENLGYMIGPSINAGGRIGESN 315
           L G NRA V +GL         GL+ L E V       A  + + I P INA  R+GE+ 
Sbjct: 225 LWGWNRALVKEGLARIPASSWVGLRLLAEAVGY--TGKAVEVAFRIAPRINAASRLGEAE 282

Query: 316 LGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEG 375
              RLL++DD+ E + L  +L  LN  R+ +E AML +             +A  IV+  
Sbjct: 283 KALRLLLTDDAAEAQALVGELHRLNARRQTLEEAMLRKL------LPQADPEAKAIVLLD 336

Query: 376 DRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILV 435
              HPG++G++A+R+ E   RP F ++     +G G+ RS+      + +  A +  +L+
Sbjct: 337 PEGHPGVMGIVASRILEATLRPVFLVA-----QGKGTVRSLAPISAVEALRSAED--LLL 389

Query: 436 KGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDM 495
           + GGH  AAG  ++   F       + +A      +       +  +L    +   +   
Sbjct: 390 RYGGHKEAAGFAMDEALFPAFKARVEAYAARFPDPVREV---ALLDLLPEPGLLPQVFRE 446

Query: 496 LESAGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGE 555
           L    PYG GNP P+F       ++ R+    HL    +      ++ +A++     L  
Sbjct: 447 LALLEPYGEGNPEPLFLLFGAPEEARRLGEGRHLAFRLKG-----VRVLAWKQGDLAL-- 499

Query: 556 FLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDASPVE 593
                    + V G L  N W G    +++ +D    E
Sbjct: 500 ------PPEVEVAGLLSENAWNGHLAYEVQAVDLRKPE 531


>3dma_A Exopolyphosphatase-related protein; structural genomics, PSI-2,
           protein structure initiative, northeast structural
           genomics consortium, NESG; 2.25A {Bacteroides fragilis}
          Length = 343

 Score = 90.1 bits (222), Expect = 1e-18
 Identities = 41/383 (10%), Positives = 87/383 (22%), Gaps = 84/383 (21%)

Query: 80  KAARRIVQAIYNSEKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYG- 136
                  +    ++KI+I      D D   S   +  FL       N+ +P+   D    
Sbjct: 9   AHIDHFTKWFERADKIVIVSHVSPDGDAIGSSLGLYHFLDSQDKIVNVIVPNAFPDFLKW 68

Query: 137 ----------PNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS 186
                              +   A +I  +D  +                  I       
Sbjct: 69  MPGSKDILLYDRYQEFADKLIMEADVICCLDFNALKRIDEMSDIVAASPGRKIMIDHHLY 128

Query: 187 EEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVA 246
            E      ++   +   S                L++R++ +           +      
Sbjct: 129 PEDFCRITISHPEISSTS---------------ELVFRLICRMGYFSDISKEGAECIYTG 173

Query: 247 LATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISSPITAENLGYMIGPSIN 306
           + T          NR                                   + ++I   ++
Sbjct: 174 MMTDTGGFTYNSNNRE----------------------------------IYFIISELLS 199

Query: 307 AGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQ 366
            G    +         S+    L    +    + ++      ++ ++ + K      D +
Sbjct: 200 KGIDKDDIYRKVYNTYSESRLRLMGYVLSNMKVYKDYNSALISLTKEEQGKFDYIKGDSE 259

Query: 367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVS 426
                          I  +  +          F     E      S RS+  F   ++ +
Sbjct: 260 GF-------VNIPLSIKNVCFSC---------FLREDTEKKMIKISLRSVGKFPCNRLAA 303

Query: 427 FAVEEGILVKGGGHAMAAGLTVE 449
                     GGGH  A+G    
Sbjct: 304 ------EFFNGGGHLNASGGEFY 320


>3dev_A SH1221; alpha-beta protein., structural genomics, PSI-2, protein
           structure initiative; 3.10A {Staphylococcus haemolyticus
           JCSC1435}
          Length = 320

 Score = 68.6 bits (166), Expect = 4e-12
 Identities = 20/106 (18%), Positives = 35/106 (33%), Gaps = 2/106 (1%)

Query: 80  KAARRIVQAIYNSEKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP 137
           +    I+Q +  +E I+I      D D   S   +  +L       N+Y           
Sbjct: 3   EIFNEIMQRVKEAETIIIHRHVRPDPDAYGSQLGLKLYLERKFPEKNIYATGEAEPSLSF 62

Query: 138 NPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ 183
              L E   +  +  ++ V   + +          G  +I IDHH 
Sbjct: 63  IGDLDEIDDSVYSDALVIVCDTANAPRIDDQRYLNGQSLIKIDHHP 108



 Score = 47.0 bits (110), Expect = 1e-05
 Identities = 18/110 (16%), Positives = 36/110 (32%), Gaps = 8/110 (7%)

Query: 340 NQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGRPSF 399
              + +     + Q      +      + +  V++     P         + +  G   +
Sbjct: 195 KDPKLMPFQGYVLQNFELSDSHEYCQIKITNDVLKQFDIQPNEASQFVNTVADISGLKIW 254

Query: 400 AISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVE 449
               +E  +     RS +G  I      A + G    GGGH  A+G++V 
Sbjct: 255 MFGVDEGDQIRCRIRS-KGITIND---VANQFG----GGGHPNASGVSVY 296


>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 = 55.3 bits (133), Expect = 4e-08
 Identities = 93/534 (17%), Positives = 147/534 (27%), Gaps = 206/534 (38%)

Query: 102 DVDGAASVALMMRFLSHCSVNANMYIPDRIVDG-YGPNPSLMEKFINE-------G---- 149
           D +      L+ +FL + S          +     G    ++   + E       G    
Sbjct: 51  DDEPTTPAELVGKFLGYVS--------SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH 102

Query: 150 ---AQLIITVDCGST-------SYDALQYATNQGIDVIVIDHHQ------VKSEEIPAYA 193
              A+L+   D           +Y   +    +  D              V        A
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD----KKSNSALFRAVGEGNAQLVA 158

Query: 194 LVNPNRLDDLSGQGHLCAAGVVF------------LVLVLI-------YRILRQDNKV-- 232
           +          GQG+       F            LV  LI         ++R       
Sbjct: 159 IFG--------GQGN---TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK 207

Query: 233 --PLNFDLLSLL---------DLVALATVCDVVPLIGLNR-A-YVVKGLMVARRQG-NPG 278
                 ++L  L         D +    +    PLIG+ + A YVV     A+  G  PG
Sbjct: 208 VFTQGLNILEWLENPSNTPDKDYLLSIPIS--CPLIGVIQLAHYVV----TAKLLGFTPG 261

Query: 279 -----LKA-------LIERVNISSPITAEN--------------LGY---------MIGP 303
                LK        L+  V I+   + E+              +G           + P
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321

Query: 304 SI------NAGGRIGESNLGSRLLISDDSQE-LEMLAMKLDVLNQNRRLMESAMLEQAEA 356
           SI      N      E      L IS+ +QE ++     ++  N    L     +E +  
Sbjct: 322 SILEDSLEN-----NEGVPSPMLSISNLTQEQVQDY---VNKTNS--HLPAGKQVEIS-- 369

Query: 357 KVLTQCDDIQQASVIVVEGDRWHP-GIVGLLAARLKEKFGRPSFAISFEEDGKGI-GSGR 414
             L     +  A  +VV G    P  + G L   L+ K   PS       D   I  S R
Sbjct: 370 --L-----VNGAKNLVVSG---PPQSLYG-LNLTLR-KAKAPS-----GLDQSRIPFSER 412

Query: 415 SIEGFD-----IGKMVSF------AVEEGIL-------VKGGGHAMAAGLTVERVNFGRL 456
            ++ F      +     F         + I        V      +   + V     G  
Sbjct: 413 KLK-FSNRFLPVA--SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ--IPVYDTFDGS- 466

Query: 457 CDFFQKFAHNIVPAL---ITT-PVF--KIDGVLNASAVNIALIDMLESAGPYGA 504
            D  +  + +I   +   I   PV            A +I  +D     GP GA
Sbjct: 467 -D-LRVLSGSISERIVDCIIRLPVKWET---TTQFKATHI--LDF----GPGGA 509



 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 58/261 (22%), Positives = 107/261 (40%), Gaps = 59/261 (22%)

Query: 133  DGYGPNPSLMEKFINEGAQLIITVDCGST-------SYDALQYATNQGIDVIVIDHHQVK 185
            D YG   S+++  IN    L  T+  G         +Y A+ + T       ++D  ++K
Sbjct: 1655 DTYGF--SILDIVINNPVNL--TIHFGGEKGKRIRENYSAMIFET-------IVDG-KLK 1702

Query: 186  SEEIPAYALVNPNRLDDL--SGQGHLCAAGVVFLVLVLIYRILRQDNK----VPLN--FD 237
            +E+I  +  +N +       S +G L A       L L+ +   +D K    +P +  F 
Sbjct: 1703 TEKI--FKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFA 1760

Query: 238  LLSLLDLVALATVCDVVPLIGLNRAYVVKGLM----VARRQ---GNPGLKALIERVNISS 290
              SL +  ALA++ DV+ +  L      +G+     V R +    N G+ A I    +++
Sbjct: 1761 GHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIA-INPGRVAA 1819

Query: 291  PITAENLGYMIGPSINAGGRIG------ESNL-GSRLLISDDSQELEMLA--------MK 335
              + E L Y++      G R G        N+   + + + D + L+ +          K
Sbjct: 1820 SFSQEALQYVVE---RVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQK 1876

Query: 336  LDVLNQNRRLMESAMLEQAEA 356
            +D++     L +S  LE+ E 
Sbjct: 1877 IDII----ELQKSLSLEEVEG 1893



 Score = 39.9 bits (93), Expect = 0.002
 Identities = 55/336 (16%), Positives = 94/336 (27%), Gaps = 177/336 (52%)

Query: 386 LAARLKEKFGR--PSFAISFEEDGKGIGSGRSIE------GF--------------DIGK 423
           +A++L+E+F +  P     F  D +   +    E      G+               +  
Sbjct: 29  IASQLQEQFNKILPEPTEGFAADDE-PTT--PAELVGKFLGYVSSLVEPSKVGQFDQVLN 85

Query: 424 MVSFAVEEGILVKGGG---HAMAAGLTVE---------RVNFGRLCDFF-------QKFA 464
           +     E   L    G   HA+AA L  E          +    + ++        + F 
Sbjct: 86  LCLTEFENCYL---EGNDIHALAAKLLQENDTTLVKTKEL----IKNYITARIMAKRPFD 138

Query: 465 HNIVPALITTPVFKI--DGVLNAS--AV-----NI---------------ALI-DMLESA 499
                AL     F+   +G  NA   A+     N                 L+ D+++ +
Sbjct: 139 KKSNSAL-----FRAVGEG--NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFS 191

Query: 500 GP---------------YGAG--------NPN-----------PVFAFPNHKLQSIRVVN 525
                            +  G        NP+           P+ + P   L  I V+ 
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI-SCP---L--IGVIQ 245

Query: 526 LAHLQMTFESQDSETLQAIAFRVYG-TPLGEFLMQSR--GKRMHVTGH------------ 570
           LAH    +          +  ++ G TP GE   +S   G     TGH            
Sbjct: 246 LAH----Y---------VVTAKLLGFTP-GEL--RSYLKG----ATGHSQGLVTAVAIAE 285

Query: 571 ------------LCVN--YWRGSKRCQLRVLDASPV 592
                         +   ++ G  RC     +A P 
Sbjct: 286 TDSWESFFVSVRKAITVLFFIGV-RCY----EAYPN 316



 Score = 32.6 bits (74), Expect = 0.24
 Identities = 47/195 (24%), Positives = 77/195 (39%), Gaps = 47/195 (24%)

Query: 266  KGLMVARRQGNPGLKALIERVNISSPITAENL---GYMIGPSINAGGRIGESNLGSRLLI 322
            KGL+ A +   P L  L+E+         E+L   G +   +  AG  +GE         
Sbjct: 1723 KGLLSATQFTQPAL-TLMEKAAF------EDLKSKGLIPADATFAGHSLGE--------- 1766

Query: 323  SDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGI 382
                     LA   DV++     +ES ++E    + +T      Q +V   E  R + G+
Sbjct: 1767 ------YAALASLADVMS-----IES-LVEVVFYRGMTM-----QVAVPRDELGRSNYGM 1809

Query: 383  VGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAM 442
            + +   R+   F + +     E  GK   +G  +E      +V++ VE    V  G   +
Sbjct: 1810 IAINPGRVAASFSQEALQYVVERVGK--RTGWLVE------IVNYNVENQQYVAAGD--L 1859

Query: 443  AAGLTVERV-NFGRL 456
             A  TV  V NF +L
Sbjct: 1860 RALDTVTNVLNFIKL 1874


>3cvj_A Putative phosphoheptose isomerase; NP_244191.1, structural
           genomics, joint center for structural genomics, JCSG;
           HET: MSE; 2.00A {Bacillus halodurans c-125}
          Length = 243

 Score = 37.5 bits (86), Expect = 0.008
 Identities = 18/116 (15%), Positives = 38/116 (32%), Gaps = 18/116 (15%)

Query: 79  DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN 138
            K A  + +A+ N  +  +FG      +  +A  +   +         +P  ++    PN
Sbjct: 29  IKGAHLVSEAVMNGGRFYVFG---SGHSHMIAEEIYNRAGGLALVTAILPPELMLHERPN 85

Query: 139 PS-------------LMEKFINEGAQLIITVDCGSTSY--DALQYATNQGIDVIVI 179
            S             L    +     ++I  + G  +   +    + N G  VI +
Sbjct: 86  KSTYLERIEGLSKSYLKLHQVTNKDVIMIISNSGRNTVPVEMAIESRNIGAKVIAM 141


>2gx8_A NIF3-related protein; structural genomics, unknown function, PSI,
           protein structure initiative; HET: EPE; 2.20A {Bacillus
           cereus atcc 14579} SCOP: c.135.1.1
          Length = 397

 Score = 35.0 bits (80), Expect = 0.052
 Identities = 9/57 (15%), Positives = 22/57 (38%), Gaps = 6/57 (10%)

Query: 140 SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVN 196
             + +   +GA + +T   G   Y     A   G++++   H+    E++    +  
Sbjct: 319 KYINQAKFKGADVYVT---GDMYYHVAHDAMMLGLNIVDPGHN---VEKVMKQGVQK 369


>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 = 34.6 bits (78), Expect = 0.065
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 18/47 (38%)

Query: 79  DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANM 125
           +K A + +QA   S K+  + D   D A ++A          + A M
Sbjct: 18  EKQALKKLQA---SLKL--YAD---DSAPALA----------IKATM 46



 Score = 29.2 bits (64), Expect = 2.9
 Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 4/22 (18%)

Query: 534 ESQDSETLQAIAFRVYG---TP 552
           E Q  + LQA + ++Y     P
Sbjct: 18  EKQALKKLQA-SLKLYADDSAP 38


>2haw_A Manganese-dependent inorganic pyrophosphatase; substrate complex,
           hydrolase; HET: 1PE PG4; 1.75A {Bacillus subtilis} SCOP:
           c.107.1.1 PDB: 1k23_A* 1wpm_A* 2iw4_A*
          Length = 309

 Score = 34.6 bits (79), Expect = 0.068
 Identities = 21/112 (18%), Positives = 34/112 (30%), Gaps = 11/112 (9%)

Query: 93  EKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYIPD-------RIVDGYGPNPSLME 143
           EKI+IFG  + D D   S        +    NA               +D +      + 
Sbjct: 2   EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLV 61

Query: 144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALV 195
           +        +I VD              +   + VIDHH++ + E       
Sbjct: 62  ETAANEVNGVILVDHNERQQ--SIKDIEEVQVLEVIDHHRIANFETAEPLYY 111


>2fyw_A Conserved hypothetical protein; structural genomics, PSI, midwest
           center for structural genomics, MCSG; 2.40A
           {Streptococcus pneumoniae TIGR4} SCOP: c.135.1.1
          Length = 267

 Score = 34.3 bits (78), Expect = 0.069
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQ 172
           +R + +   +    I    + G G   S  +  + +GA + IT   G   Y   Q   + 
Sbjct: 163 LRMVHYQEDDLQKPISRVAICG-GSGQSFYKDALAKGADVYIT---GDIYYHTAQDMLSD 218

Query: 173 GIDVIVIDHH 182
           G+  +   H+
Sbjct: 219 GLLALDPGHY 228


>2xbl_A Phosphoheptose isomerase; capsule; HET: M7P PGE PG4; 1.62A
           {Burkholderia pseudomallei} PDB: 2x3y_A
          Length = 198

 Score = 33.5 bits (76), Expect = 0.13
 Identities = 23/149 (15%), Positives = 49/149 (32%), Gaps = 23/149 (15%)

Query: 51  NVSIDYAKDFLNPSIRLL---MPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAA 107
           N  + Y  + +  + R++   + D  +L    K A   + +I    K+++ G     G+A
Sbjct: 4   NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAG---NGGSA 60

Query: 108 SVALMMRF-LSHCSVNANMYIPDRIVDGYGPNPS--------------LMEKFINEGAQL 152
           + A  +              +P   +       +               ++   NEG  L
Sbjct: 61  ADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVL 120

Query: 153 IITVDCGSTSY--DALQYATNQGIDVIVI 179
           I     G +     A + A  +G+  +  
Sbjct: 121 IGYSTSGKSPNILAAFREAKAKGMTCVGF 149


>2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase
           maturation, [4Fe-4S] cluster, thiol redox; HET: CSW;
           2.07A {Thermococcus kodakarensis KOD1}
          Length = 372

 Score = 33.1 bits (76), Expect = 0.19
 Identities = 19/127 (14%), Positives = 42/127 (33%), Gaps = 16/127 (12%)

Query: 165 ALQYATNQGID--VIVIDHHQVKSEEIPAYA--LVNPNRLDDLSGQGHLCAAGVVFLVLV 220
            L  A  + ++   I   H        PA    L        L   GH+       ++ V
Sbjct: 159 MLNVAAQEELENFKIYSVHRLT----PPAVEVLLKQGTVFQGLIAPGHVST-----IIGV 209

Query: 221 LIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVV-KGLMVARRQGNPGL 279
             +  L +   +P         D+  L  +  ++ +     A ++ +     + +GN   
Sbjct: 210 KGWEYLTEKYGIPQVVAGFEPNDV--LMAILMLIRMYKEGEARIINEYERAVKYEGNVVA 267

Query: 280 KALIERV 286
           + +I++ 
Sbjct: 268 QKMIDKF 274


>2nyd_A UPF0135 protein SA1388; hypothetical protein SA1388,
           selenomethionine SAD, unknown function; 2.00A
           {Staphylococcus aureus subsp}
          Length = 370

 Score = 33.2 bits (75), Expect = 0.20
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 136 GPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYAL 194
           G       + + +GA + +T   G   +     A   G+++I I+H+   SE +    L
Sbjct: 288 GSGIGYEYQAVQQGADVFVT---GDIKHHDALDAKIHGVNLIDINHY---SEYVMKEGL 340


>1zcl_A Protein tyrosine phosphatase 4A1; PRL-1 PTP4A dual specific
           phosphatase, hydrolase; 2.90A {Rattus norvegicus} PDB:
           1x24_A
          Length = 180

 Score = 32.2 bits (73), Expect = 0.30
 Identities = 24/110 (21%), Positives = 36/110 (32%), Gaps = 12/110 (10%)

Query: 126 YIPDRIVDGYGPNPSLMEKFINEGAQLIIT--VDCGSTSYDALQYATNQGIDV--IVIDH 181
           Y   R +  + P  + + KFI E  +  +T  V     +YD       +GI V     D 
Sbjct: 34  YKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDT-TLVEKEGIHVLDWPFDD 92

Query: 182 HQVKSEEIPAYALVNPNRLDDLSGQGHL---CAAGV----VFLVLVLIYR 224
               S +I    L              +     AG+    V + L LI  
Sbjct: 93  GAPPSNQIVDDWLSLVKIKFREEPGCCIAVHSVAGLGRAPVLVALALIEG 142


>1wpn_A Manganese-dependent inorganic pyrophosphatase; metal binding,
           hydrolase; 1.30A {Bacillus subtilis} SCOP: c.107.1.1
          Length = 188

 Score = 32.1 bits (72), Expect = 0.33
 Identities = 19/107 (17%), Positives = 32/107 (29%), Gaps = 7/107 (6%)

Query: 93  EKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGA 150
           EKI+IFG  + D D   S        +    NA      ++           ++      
Sbjct: 2   EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLV 61

Query: 151 QLIITVDCGSTSYDA-----LQYATNQGIDVIVIDHHQVKSEEIPAY 192
           +       G    D            +   + VIDHH++ + E    
Sbjct: 62  ETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEP 108


>1nmo_A Hypothetical protein YBGI; toroidal structure, structure 2 function
           project, S2F, structural genomics, unknown functio;
           2.20A {Escherichia coli} SCOP: c.135.1.1 PDB: 1nmp_A
          Length = 247

 Score = 31.9 bits (72), Expect = 0.40
 Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 4/65 (6%)

Query: 118 HCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI 177
            C       +  R+    G   S ++     G    IT   G  S   +  A  QG+   
Sbjct: 156 WCGDTGPEVV-QRVAWCTGGGQSFIDSAARFGVDAFIT---GEVSEQTIHSAREQGLHFY 211

Query: 178 VIDHH 182
              HH
Sbjct: 212 AAGHH 216


>1k20_A Manganese-dependent inorganic pyrophosphatase; family II ppase,
           binuclear metal centre, hydrolase; 1.50A {Streptococcus
           gordonii} SCOP: c.107.1.1 PDB: 1wpp_A 2enx_A* 1i74_A
          Length = 310

 Score = 30.3 bits (68), Expect = 1.2
 Identities = 19/113 (16%), Positives = 34/113 (30%), Gaps = 13/113 (11%)

Query: 94  KIMIFG--DYDVDGAASVALMMRFLSHC-SVNANMYIPDRIVDGYG--------PNPSLM 142
           KI++FG  + D D   S             ++          +             P ++
Sbjct: 2   KILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVI 61

Query: 143 EKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALV 195
                EGA+ +I  D              +     V+DHH+V + E      +
Sbjct: 62  TSAKAEGAEQVILTDHNEFQQSVADI--AEVEVYGVVDHHRVANFETANPLYM 112


>2vh3_A Ranasmurfin, RSF-1; LTQ, bisltq, unknown function; HET: TY3 TY2;
           1.16A {Polypedates leucomystax} PDB: 2vh3_B*
          Length = 113

 Score = 30.5 bits (68), Expect = 1.2
 Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 18/99 (18%)

Query: 380 PGIVGLLAARLK--EKFGRPSFAI-----SFEEDGKGIGSGRSIEGFDIGKMVSFAVEEG 432
           PG    LA  L+  + F + S+A+     +++ED +     R+ E FD     +   +EG
Sbjct: 12  PGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYE--RAAEDFDSAVKCT-GCKEG 68

Query: 433 I--------LVKGGGHAMAAGLTVERVNFGRLCDFFQKF 463
           +        L++ G     A L ++R   G LC  FQK 
Sbjct: 69  VDLHEGNPELIEEGFEKFLASLKIDRKALGSLCTLFQKL 107


>2eih_A Alcohol dehydrogenase; zinc ION binding protein, structural
           genomics, NPPSFA; 2.30A {Thermus thermophilus HB8}
          Length = 343

 Score = 30.1 bits (67), Expect = 1.6
 Identities = 19/153 (12%), Positives = 39/153 (25%), Gaps = 3/153 (1%)

Query: 146 INEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE---EIPAYALVNPNRLDD 202
           +  G  +++       S  A+Q A   G  VI     + K      + A   VN    D 
Sbjct: 164 VRPGDDVLVMAAGSGVSVAAIQIAKLFGARVIATAGSEDKLRRAKALGADETVNYTHPDW 223

Query: 203 LSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRA 262
                 L        V+     +  +             +   +      +       R 
Sbjct: 224 PKEVRRLTGGKGADKVVDHTGALYFEGVIKATANGGRIAIAGASSGYEGTLPFAHVFYRQ 283

Query: 263 YVVKGLMVARRQGNPGLKALIERVNISSPITAE 295
             + G  +A +     +   +E   +   +   
Sbjct: 284 LSILGSTMASKSRLFPILRFVEEGKLKPVVGQV 316


>2i2w_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 1.95A
           {Escherichia coli} PDB: 2i22_A 1x94_A
          Length = 212

 Score = 29.4 bits (65), Expect = 2.1
 Identities = 18/156 (11%), Positives = 44/156 (28%), Gaps = 9/156 (5%)

Query: 55  DYAKDFLNPSIRLL---MPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVAL 111
           D  ++ LN +   L   + D   +    +AA  +  +     K++  G+    G+   A+
Sbjct: 24  DLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGN---GGSHCDAM 80

Query: 112 MMRFLSHCSVNANMYIPDRI-VDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT 170
                       N      I +        +   F             G      L  +T
Sbjct: 81  HFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGIST 140

Query: 171 NQGIDVIVIDHHQVKSEEIPAYALV--NPNRLDDLS 204
           +     ++      + + +    L   +  ++   +
Sbjct: 141 SGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTA 176


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

 Score = 29.1 bits (64), Expect = 2.6
 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 4/32 (12%)

Query: 573 VNYWRGSKRCQLRVLD-ASPV---EGHHFAKK 600
           +  WR  +R +L+ LD AS V   E    AKK
Sbjct: 87  IRKWREEQRKRLQELDAASKVMEQEWREKAKK 118


>2yva_A DNAA initiator-associating protein DIAA; intermolecular disulfide
           bonding, putative phosphosugar binding protein, DNAA
           binding protein; 1.85A {Escherichia coli}
          Length = 196

 Score = 29.0 bits (64), Expect = 3.0
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 4/77 (5%)

Query: 55  DYAKDFLNPSIRLLMP-DPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMM 113
           +  K     SI+  +     +     +AA  +VQ++ N  KI+  G+     +A+ A   
Sbjct: 3   ERIKACFTESIQTQIAAAEALPDAISRAAMTLVQSLLNGNKILCCGN---GTSAANAQHF 59

Query: 114 RFLSHCSVNANMYIPDR 130
                            
Sbjct: 60  AASMINRFETERPSLPA 76


>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 = 28.6 bits (63), Expect = 4.4
 Identities = 22/104 (21%), Positives = 46/104 (44%), Gaps = 28/104 (26%)

Query: 47  LVNRNVSID--YAKDFLNP--SIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMI----- 97
           +VN N S D  YA+  + P  +I+L  P+        + A   ++ + + E++++     
Sbjct: 768 VVNGN-SADAAYAQVEIQPRANIQLDFPELKPYKQVKQIAPAELEGLLDLERVIVVTGFA 826

Query: 98  ----------------FGDYDVDGAASVALMMRFLSHCSVNANM 125
                           FG++ ++G   +A +M F+S+   N N+
Sbjct: 827 EVGPWGSARTRWEMEAFGEFSLEGCVEMAWIMGFISYH--NGNL 868


>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
           baumannii} PDB: 2xkk_A*
          Length = 767

 Score = 28.5 bits (63), Expect = 4.8
 Identities = 8/25 (32%), Positives = 9/25 (36%)

Query: 94  KIMIFGDYDVDGAASVALMMRFLSH 118
           KI I  D D DG     L+      
Sbjct: 116 KICILADADSDGLHIATLLCALFVK 140


>1wou_A Thioredoxin -related protein, 14 kDa; electron transport; 1.80A
           {Homo sapiens} SCOP: c.47.1.16 PDB: 1v9w_A
          Length = 123

 Score = 27.8 bits (61), Expect = 6.6
 Identities = 10/80 (12%), Positives = 24/80 (30%), Gaps = 10/80 (12%)

Query: 77  DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIP-------- 128
           DC +A   + + + +  +  +F    V                       +P        
Sbjct: 45  DCVQAEPVVREGLKHISEGCVFIYCQVG--EKPYWKDPNNDFRKNLKVTAVPTLLKYGTP 102

Query: 129 DRIVDGYGPNPSLMEKFINE 148
            ++V+      +L+E   +E
Sbjct: 103 QKLVESECLQANLVEMLFSE 122


>2va1_A Uridylate kinase; UMPK, transferase, pyrimidine biosynthesis, amino
           acid kinase family; 2.50A {Ureaplasma parvum}
          Length = 256

 Score = 27.6 bits (60), Expect = 7.7
 Identities = 12/117 (10%), Positives = 39/117 (33%), Gaps = 4/117 (3%)

Query: 68  LMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI 127
           ++          +++   ++     E++MIF         +        +  + ++ + +
Sbjct: 118 VLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILM 177

Query: 128 PDRIVDGYGPNPSLMEK----FINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID 180
               VDG   +   +      + +    + +T +       AL       I+++V +
Sbjct: 178 GKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFN 234


>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
           isomera; HET: DNA; 3.10A {Escherichia coli}
          Length = 420

 Score = 27.7 bits (61), Expect = 8.6
 Identities = 9/25 (36%), Positives = 13/25 (52%)

Query: 94  KIMIFGDYDVDGAASVALMMRFLSH 118
            I+I  D DVDG+    L++ F   
Sbjct: 108 SIIIMTDADVDGSHIRTLLLTFFYR 132


>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
           helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
           c.37.1.16 e.10.1.1 PDB: 1gl9_B*
          Length = 1054

 Score = 27.3 bits (60), Expect = 9.0
 Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 8/54 (14%)

Query: 363 DDIQ---QASVIVVEGDRW-HPGIVGLLAARLKEKFGRPSFAI----SFEEDGK 408
           DD+Q   Q  V+VVEG RW H  +  L+  R      RP   +    S E DGK
Sbjct: 856 DDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGK 909


>3gos_A 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
           succinyltransferase;
           2,3,4,5-tetrahydropyridine-2-carboxylate N-
           succinyltransferase; 1.80A {Yersinia pestis} PDB:
           1kgq_A* 1kgt_A* 2tdt_A* 3tdt_A* 3bxy_A 1tdt_A
          Length = 276

 Score = 27.5 bits (61), Expect = 9.1
 Identities = 27/145 (18%), Positives = 61/145 (42%), Gaps = 14/145 (9%)

Query: 103 VDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEK--FINEGAQLI--ITVDC 158
           VD  A+V    +   +  ++  + I   +++    NP+++E   F+   ++++  + V+ 
Sbjct: 142 VDTWATVGSCAQIGKNVHLSGGVGI-GGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEE 200

Query: 159 GSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLV 218
           GS     +     Q   +   +  +V    +PA ++V    L    G   L  A      
Sbjct: 201 GSVISMGVFIG--QSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCA------ 252

Query: 219 LVLIYRILRQDNKVPLNFDLLSLLD 243
           +++     +  +KV +N +LL  +D
Sbjct: 253 VIVKKVDAKTRSKVGIN-ELLRTID 276


>1bjt_A Topoisomerase II; quaternary change, DNA-binding, DNA topology;
           2.50A {Saccharomyces cerevisiae} SCOP: e.11.1.1 PDB:
           1bgw_A 2rgr_A*
          Length = 793

 Score = 27.5 bits (60), Expect = 9.7
 Identities = 9/23 (39%), Positives = 13/23 (56%)

Query: 94  KIMIFGDYDVDGAASVALMMRFL 116
            +MI  D D DG+    L++ FL
Sbjct: 112 HLMIMTDQDHDGSHIKGLIINFL 134


  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
   0.322    0.139    0.406 

Gapped
Lambda     K      H
   0.267   0.0575    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 5,211,265
Number of extensions: 250797
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 819
Number of HSP's successfully gapped: 48
Length of query: 600
Length of database: 5,693,230
Length adjustment: 98
Effective length of query: 502
Effective length of database: 3,317,318
Effective search space: 1665293636
Effective search space used: 1665293636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.8 bits)