RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780234|ref|YP_003064647.1| argininosuccinate synthase
[Candidatus Liberibacter asiaticus str. psy62]
         (404 letters)



>gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional.
          Length = 399

 Score =  723 bits (1868), Expect = 0.0
 Identities = 245/400 (61%), Positives = 301/400 (75%), Gaps = 3/400 (0%)

Query: 4   DVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKEVYV 63
             KKVVLAYSGGLDTS+I+KWL+   G EVI F AD+GQGEEL+   +KA   GA E+YV
Sbjct: 1   MKKKVVLAYSGGLDTSVIIKWLKETYGCEVIAFTADVGQGEELEPIREKALKSGASEIYV 60

Query: 64  KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123
           +DLR EFVRD+VFP  RANALYEG Y LGTA+ARPLIAK LV+IA + GADA+AHG TGK
Sbjct: 61  EDLREEFVRDYVFPAIRANALYEGKYPLGTALARPLIAKKLVEIARKEGADAVAHGCTGK 120

Query: 124 GNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSIDT 183
           GNDQVRFEL   +L  D+++IAPWR W  K R++LI +AE+H IPI   K+   P+SID 
Sbjct: 121 GNDQVRFELGIAALAPDLKVIAPWREWDLKSREELIAYAEEHGIPIPVTKKS--PYSIDA 178

Query: 184 NLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQVMSPE 243
           NL H S EG +LEDP    PE VY+  VSPE+APD P  + I+F++G P+AING+ +SP 
Sbjct: 179 NLWHRSIEGGILEDPWNEPPEDVYEWTVSPEDAPDEPEYVEIEFEKGVPVAINGEALSPA 238

Query: 244 VLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGSAH 303
            L+E+LN+    +GIGRIDIVENR VGIKSRGVYETPGGTIL+ AHRA+ES++LD   AH
Sbjct: 239 ELIEELNELAGKHGIGRIDIVENRLVGIKSRGVYETPGGTILIKAHRALESLTLDREVAH 298

Query: 304 LKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESNKS 363
            KD+L  +YA +VY G WFSP RE LQA ID++QE+V G + LKLYKGN +VVGR+S  S
Sbjct: 299 FKDELEPKYAELVYNGLWFSPLREALQAFIDETQEHVTGEVRLKLYKGNAIVVGRKSPNS 358

Query: 364 LYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403
           LY + L T+E+D D Y+Q D+EGFIKL  L  +  A  NK
Sbjct: 359 LYDEDLATYEED-DVYDQKDAEGFIKLWGLPSKIAALVNK 397


>gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional.
          Length = 404

 Score =  612 bits (1581), Expect = e-176
 Identities = 233/400 (58%), Positives = 301/400 (75%), Gaps = 3/400 (0%)

Query: 1   MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQG-EELKIASDKARLLGAK 59
           +   + KVVLAYSGGLDTS+ILKWL+   G EV+ F AD+GQG EEL+    KA+  GAK
Sbjct: 1   LRGKLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFTADVGQGIEELEGLEAKAKASGAK 60

Query: 60  EVYVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHG 119
           ++ VKDLR EFVRD++FP  RANA+YEG YLLGT++ARPLIAK +VDIA E GADA+AHG
Sbjct: 61  QLVVKDLREEFVRDYIFPCLRANAIYEGKYLLGTSMARPLIAKAMVDIAKEVGADAVAHG 120

Query: 120 STGKGNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPF 179
           +TGKGNDQVRFEL+ ++LN +++++APWR W  KGR+DLI++A+KH IP+   K+  + +
Sbjct: 121 ATGKGNDQVRFELTFFALNPELKVVAPWREWDIKGREDLIEYAKKHNIPVPVTKK--SIY 178

Query: 180 SIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQV 239
           S D NL H S EG +LEDP+    E ++ M VSPE APD P  I I+F++G P+AING+ 
Sbjct: 179 SRDRNLWHISYEGDILEDPANEPKEDMFMMSVSPEAAPDQPEYIEIEFEKGLPVAINGKT 238

Query: 240 MSPEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDS 299
           +SP  LL +LN+ G  +GIGRID+VENRFVG+KSRGVYETPGGTIL  AHR +ES++LD 
Sbjct: 239 LSPATLLTKLNEIGGKHGIGRIDMVENRFVGMKSRGVYETPGGTILFAAHRELESLTLDR 298

Query: 300 GSAHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRE 359
            +  +KD L  +YA +VY GFWF PERE + A ++K  E   GS+ LKLYKGNV V GR+
Sbjct: 299 ETMQVKDSLALKYAELVYNGFWFDPERESMDAFMEKITETTTGSVRLKLYKGNVSVAGRK 358

Query: 360 SNKSLYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLA 399
           S  SLY   + +FE+    YNQ+D+ GFI+L+ALRLRT A
Sbjct: 359 SPYSLYRQDISSFEEGGGIYNQADAAGFIRLYALRLRTRA 398


>gnl|CDD|129143 TIGR00032, argG, argininosuccinate synthase.  argG in bacteria,
           ARG1 in Saccharomyces cerevisiae. There is a very
           unusual clustering in the alignment, with a deep split
           between one cohort of E. coli, H. influenzae, and
           Streptomyces, and the other cohort of eukaryotes,
           archaea, and the rest of the eubacteria.
          Length = 394

 Score =  452 bits (1165), Expect = e-128
 Identities = 191/399 (47%), Positives = 264/399 (66%), Gaps = 7/399 (1%)

Query: 7   KVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVYVKD 65
           KVVLAYSGGLDTS+ LKWL+ EKG EVI + AD+GQ EE +    +KA   GA+  Y  D
Sbjct: 1   KVVLAYSGGLDTSVCLKWLR-EKGYEVIAYTADVGQPEEDIDAIPEKALEYGAENHYTID 59

Query: 66  LRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGKGN 125
            R EFV+D+ F   +ANA YEG Y L TA+ARPLIAK LV+ A + GA+A+AHG TGKGN
Sbjct: 60  AREEFVKDYGFAAIQANAFYEGTYPLSTALARPLIAKKLVEAAKKEGANAVAHGCTGKGN 119

Query: 126 DQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSIDTNL 185
           DQ RFE S   LN D+++IAPWR  +F  R++ I++A +  IP   +K  E P+SID NL
Sbjct: 120 DQERFERSIRLLNPDLKVIAPWRDLNFT-REEEIEYAIQCGIPYPMSK--EKPYSIDENL 176

Query: 186 LHSSSEGRVLEDPSQPAPEYVYKMIVSPEEA-PDTPTTIRIDFQRGDPIAINGQVMSPEV 244
              S E  +LEDPS   PE +Y     P+EA PD P  + IDF++G P+A+NG  + P  
Sbjct: 177 WGRSIEAGILEDPSTEPPEDIYMWTKFPDEATPDEPEVVTIDFEQGVPVALNGVSLDPVE 236

Query: 245 LLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGSAHL 304
           L+ + N+    +G+GRIDI+ENR +G+KSR +YE PG  +L+ AHR +E+++L       
Sbjct: 237 LILEANEIAGKHGVGRIDIIENRIIGLKSREIYEAPGAALLIIAHRDLETLTLTRDVLEF 296

Query: 305 KDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESNKSL 364
           KD +  +Y+ ++YQG WF P  E L A I K+QE V G++ +KL+KGN +V+GR S  SL
Sbjct: 297 KDIVEEQYSELIYQGLWFDPLAEALDAFIRKTQERVTGTVRVKLFKGNAIVIGRTSPYSL 356

Query: 365 YSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403
           Y ++LV+ E D D ++  D+ GFI +  L+++    + K
Sbjct: 357 YDEELVSMEKD-DVFDPRDAIGFITMRGLQIKDYREKKK 394


>gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional.
          Length = 394

 Score =  412 bits (1062), Expect = e-116
 Identities = 191/403 (47%), Positives = 265/403 (65%), Gaps = 13/403 (3%)

Query: 4   DVKKVVLAYSGGLDTSIILKWLQVEKGL-EVIVFIADLGQG-EELKIASDKARLLGAKEV 61
            +KKVVLAYSGGLDTS+ +  L+ + G  EVI    D+GQ  EE+K A +KA+ LG K  
Sbjct: 1   MMKKVVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDVGQPEEEIKEAEEKAKKLGDKH- 59

Query: 62  YVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGST 121
           Y  D + EF +D++FP  +ANALYEGY  LGTA+ARPLIA+ +V++A + GA AIAHG T
Sbjct: 60  YTIDAKEEFAKDYIFPAIKANALYEGY-PLGTALARPLIAEKIVEVAEKEGASAIAHGCT 118

Query: 122 GKGNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSI 181
           GKGNDQ+RFE  A    SD+E+IAP R  +   R+  I++A++  IP+   K  E P+SI
Sbjct: 119 GKGNDQLRFE--AVFRASDLEVIAPIRELNLT-REWEIEYAKEKGIPVPVGK--EKPWSI 173

Query: 182 DTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQVMS 241
           D NL   S EG  LEDP+   PE +Y   VSPE+APD P  + I+F+ G P+AING+ M 
Sbjct: 174 DENLWSRSIEGGKLEDPAFEPPEEIYAWTVSPEDAPDEPEIVEIEFEEGVPVAINGEKMD 233

Query: 242 PEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGS 301
              L+ +LN+    +G+GR D++E+R +G+KSR  YE P  T+LL AH+A+E + L    
Sbjct: 234 GVELIRKLNEIAGKHGVGRTDMMEDRVLGLKSRENYEHPAATVLLTAHKALEQLVLTREE 293

Query: 302 AHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESN 361
              K+ + S++A + Y+G    P RE L A IDK+QE V G++T+KLYKG+  VVGRES 
Sbjct: 294 LKFKEIVDSKWAELAYEGLVDEPLREDLNAFIDKTQERVTGTVTVKLYKGSARVVGRESP 353

Query: 362 KSLYSDKLVTFED-DLDAYNQSDSEGFIKLHALRLRTLARRNK 403
            +LYS++LV+F+   +D   Q D+EG  K H L+ R   +  +
Sbjct: 354 YALYSEELVSFDSKTID---QRDAEGMAKYHGLQARLYNKVKR 393


>gnl|CDD|179859 PRK04527, PRK04527, argininosuccinate synthase; Provisional.
          Length = 400

 Score =  201 bits (514), Expect = 2e-52
 Identities = 127/406 (31%), Positives = 189/406 (46%), Gaps = 20/406 (4%)

Query: 6   KKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLG--QGEELKIASDKARLLGAKEVYV 63
           K +VLA+SGGLDTS  + +LQ E+G  V    AD G    EE      +A  LGA     
Sbjct: 3   KDIVLAFSGGLDTSFCIPYLQ-ERGYAVHTVFADTGGVDAEERDFIEKRAAELGAASHVT 61

Query: 64  KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123
            D        FV P+  A   Y+G Y L  +  R LI    +  A E G   IAHG TG 
Sbjct: 62  VDGGPAIWEGFVKPLVWAGEGYQGQYPLLVS-DRYLIVDAALKRAEELGTRIIAHGCTGM 120

Query: 124 GNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKH------AIPIDKNKRGEA 177
           GNDQVRF+L+  +L  D +I+AP R    K       + +K+       +   +      
Sbjct: 121 GNDQVRFDLAVKAL-GDYQIVAPIREIQ-KEHTQTRAYEQKYLEERGFGVRAKQKA---- 174

Query: 178 PFSIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAING 237
            ++I+ NLL  +  G  ++    P  E            P    T+ I F  G+ +A++G
Sbjct: 175 -YTINENLLGVTMSGGEIDRWEAPG-EGARGWCAPRSAWPTEALTVTIKFVEGEAVALDG 232

Query: 238 QVMSPEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISL 297
           + +    +L +LN+     G+GR     +  +G+K R V+E PG   LL AHRA+E   L
Sbjct: 233 KPLPGAQILAKLNKLFAQYGVGRGVYTGDTVIGLKGRIVFEAPGLVSLLTAHRALEDAVL 292

Query: 298 DSGSAHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVG 357
                  K D+  ++  +VY+GF+  P +  ++A +  SQ  V G +TL+   G V  V 
Sbjct: 293 TKQQNRFKPDVARKWVELVYEGFYHDPLKTDIEAFLKSSQAKVNGEVTLETRGGRVDAVA 352

Query: 358 RESNKSLYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403
             S   L + K  T+    D +   ++EGFIKL  +     A+ N+
Sbjct: 353 VRS-PHLLNSKGATYAQSAD-WGVEEAEGFIKLFGMSSTLYAQVNR 396


>gnl|CDD|180043 PRK05370, PRK05370, argininosuccinate synthase; Validated.
          Length = 447

 Score =  128 bits (324), Expect = 3e-30
 Identities = 113/385 (29%), Positives = 179/385 (46%), Gaps = 66/385 (17%)

Query: 6   KKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIAS--DKARLLGAKEVYV 63
           ++V +A+SGGLDTS  L W++ +KG     + A+LGQ +E    +   +A   GA+   +
Sbjct: 12  QRVGIAFSGGLDTSAALLWMR-QKGAVPYAYTANLGQPDEDDYDAIPRRAMEYGAENARL 70

Query: 64  KDLRREFVRDFVFPMFRANALYEGYYLLGTA---------IARPLIAKYLVDIANETGAD 114
            D R + V + +       A+  G + + T          + R +    LV    E G +
Sbjct: 71  IDCRAQLVAEGI------AAIQCGAFHISTGGVTYFNTTPLGRAVTGTMLVAAMKEDGVN 124

Query: 115 AIAHGSTGKGNDQVRFELSAYSL--NSDIEIIAPWRHWSF----KGRQDLIDFAEKHAIP 168
               GST KGND  RF    Y L  N +++I  PW    F     GR ++ +F   H   
Sbjct: 125 IWGDGSTYKGNDIERF--YRYGLLTNPELKIYKPWLDQDFIDELGGRAEMSEFLIAHGFD 182

Query: 169 IDKNKRGEAPFSIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSP--------EEAPDTP 220
              +   E  +S D+N+L ++ E + LE  +          IV+P        E+     
Sbjct: 183 YKMSV--EKAYSTDSNMLGATHEAKDLEHLNSGIK------IVNPIMGVAFWDEDVEIKA 234

Query: 221 TTIRIDFQRGDPIAINGQVMSPEV-LLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYET 279
             + + F++G P+A+NG+  S  V L+ + N+ G  +G+G  D +ENR +  KSRG+YE 
Sbjct: 235 EEVTVRFEQGRPVALNGKTFSDPVELMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEA 294

Query: 280 PGGTILLHA--HRAIESISLDSGSAHLKDDLMS------RYASIVYQGFWFSPEREMLQA 331
           P G  LLH    R +  I       H +D +        R   ++YQG WF P+  ML+ 
Sbjct: 295 P-GMALLHIAYERLVTGI-------HNEDTIEQYRINGRRLGRLLYQGRWFDPQALMLR- 345

Query: 332 LIDKSQEYV----EGSITLKLYKGN 352
             +  Q +V     G +TL+L +GN
Sbjct: 346 --ESLQRWVASAITGEVTLELRRGN 368


>gnl|CDD|178276 PLN02671, PLN02671, pectinesterase.
          Length = 359

 Score = 35.6 bits (82), Expect = 0.025
 Identities = 38/160 (23%), Positives = 61/160 (38%), Gaps = 23/160 (14%)

Query: 42  QGEELKIASDKA-----RLLGAKEVYVKDLRREFVR--------DFVFPMFRANALYEGY 88
           Q   L+I+ DKA     R+LGA++  + +    +          DF+F    A +LY+  
Sbjct: 177 QAVALRISGDKAFFYKVRVLGAQDTLLDETGSHYFYQCYIQGSVDFIFG--NAKSLYQDC 234

Query: 89  YLLGTAIARPLIAKYLVDIANE------TGADAIAHGSTGKGNDQVRFELSAYSLNSDIE 142
            +  TA     IA +  D   E              G    G     +  + YS     +
Sbjct: 235 VIQSTAKRSGAIAAHHRDSPTEDTGFSFVNCVINGTGKIYLGRAWGNYSRTVYSNCFIAD 294

Query: 143 IIAP--WRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFS 180
           II P  W  W++  RQ  + F E +      ++ G  P+S
Sbjct: 295 IITPSGWSDWNYPERQRTVMFGEYNCSGRGADRGGRVPWS 334


>gnl|CDD|129369 TIGR00268, TIGR00268, conserved hypothetical protein TIGR00268.
           The N-terminal region of the model shows similarity to
           Argininosuccinate synthase proteins using PSI-blast and
           using the recognize protein identification server.
          Length = 252

 Score = 34.8 bits (80), Expect = 0.037
 Identities = 38/145 (26%), Positives = 64/145 (44%), Gaps = 21/145 (14%)

Query: 6   KKVVLAYSGGLDTSIILKWLQVEKGLEV--IVFIADLGQGEELKIASDKARLLGAKEVYV 63
           KKV++AYSGG+D+S++      + G EV  I  ++      EL+ A   A+ +G      
Sbjct: 13  KKVLIAYSGGVDSSLLAAVCS-DAGTEVLAITVVSPSISPRELEDAIIIAKEIG------ 65

Query: 64  KDLRREFVR-DFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTG 122
             +  EFV+ D +   FRAN     Y+       + ++   LV  A + G D +  G+  
Sbjct: 66  --VNHEFVKIDKMINPFRANVEERCYF------CKKMVLSILVKEAEKRGYDVVVDGTNA 117

Query: 123 KGNDQVRFELSAYSLNSDIEIIAPW 147
              D +      Y    +   ++PW
Sbjct: 118 ---DDLFDHRPGYRAVKEFNGVSPW 139


>gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA;
           Provisional.
          Length = 362

 Score = 33.0 bits (75), Expect = 0.14
 Identities = 35/130 (26%), Positives = 60/130 (46%), Gaps = 26/130 (20%)

Query: 1   MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDK---ARLLG 57
           M    K+V++  SGG+D++     LQ E+G E++        G  +++  D+   AR L 
Sbjct: 1   MKESKKRVLVGMSGGIDSTATCLMLQ-EQGYEIV--------GVTMRVWGDEPQDARELA 51

Query: 58  AK---EVYVKDLRREF----VRDFVFPMFRANALYEGYYLLGTAIARPLIA-KYLVDIAN 109
           A+   E YV D R  F    V++F+      +   +G       +  PL   + L++ A+
Sbjct: 52  ARMGIEHYVADERVPFKDTIVKNFI------DEYRQGRTPNPCVMCNPLFKFRMLIEWAD 105

Query: 110 ETGADAIAHG 119
           + G   IA G
Sbjct: 106 KLGCAWIATG 115


>gnl|CDD|162854 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
           N-terminal domain.  The only examples in which the
           wobble position of a tRNA must discriminate between G
           and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
           vs. UGG (Trp). In all bacteria, the wobble position of
           the tRNA(Ile) recognizing AUA is lysidine, a lysine
           derivative of cytidine. This family describes a protein
           domain found, apparently, in all bacteria in a single
           copy. Eukaryotic sequences appear to be organellar. The
           domain archictecture of this protein family is variable;
           some, including characterized proteins of E. coli and B.
           subtilis known to be tRNA(Ile)-lysidine synthetase,
           include a conserved 50-residue domain that many other
           members lack. This protein belongs to the ATP-binding
           PP-loop family ( pfam01171). It appears in the
           literature and protein databases as TilS, YacA, and
           putative cell cycle protein MesJ (a misnomer).
          Length = 189

 Score = 32.6 bits (75), Expect = 0.19
 Identities = 36/182 (19%), Positives = 67/182 (36%), Gaps = 34/182 (18%)

Query: 7   KVVLAYSGGLDTSI---ILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKEVYV 63
           ++++A SGG+D+     +L  LQ +  + +I    D G   E    SD+         +V
Sbjct: 1   RILVAVSGGVDSMALLHLLLKLQPKLKIRLIAAHVDHGLRPE----SDEE------AEFV 50

Query: 64  KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123
           +   ++             AL +G        AR     +  +IA + GAD I       
Sbjct: 51  QQFCKKLNIPLEIKKVDVKALAKGKKKNLEEAAREARYDFFEEIAKKHGADYILTAHH-- 108

Query: 124 GNDQV------------RFELSAY----SLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAI 167
            +DQ                LS       L +  +II P    S   + ++ ++ +++ +
Sbjct: 109 ADDQAETILLRLLRGSGLRGLSGMKPIRILGNGGQIIRPLLGIS---KSEIEEYLKENGL 165

Query: 168 PI 169
           P 
Sbjct: 166 PW 167


>gnl|CDD|165411 PHA03139, PHA03139, helicase-primase primase subunit; Provisional.
          Length = 860

 Score = 32.3 bits (73), Expect = 0.24
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 46  LKI-ASDKARLLGAKEVYVKDLRREFVRDFV---FPMFRANALYEGYYLLGTA 94
           L+I ASDK   +  K +Y    RR+ +       FP+FR   L++  +  G +
Sbjct: 378 LEISASDKYVQIQDKRIY----RRQHLHKDYHRPFPVFRVQLLHKNIFCFGNS 426


>gnl|CDD|178898 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
          Length = 346

 Score = 30.8 bits (71), Expect = 0.58
 Identities = 41/138 (29%), Positives = 55/138 (39%), Gaps = 36/138 (26%)

Query: 6   KKVVLAYSGGLDTSIILKWLQVEKGLEVI-VFIADLGQGEELKI--------ASDKARLL 56
           K+VV+  SGG+D+S+    L  E+G EVI VF+  L   ++               AR +
Sbjct: 1   KRVVVGMSGGVDSSVAA-ALLKEQGYEVIGVFMK-LWDDDDETGKGGCCAEEDIADARRV 58

Query: 57  GAK---EVYVKDLRREFVRDFVF-PMFRANALYEGYYLLG-TAIARPLIA-------KYL 104
             K     YV D  +EF  D V              Y  G T    P +        K  
Sbjct: 59  ADKLGIPHYVVDFEKEF-WDRVIDYFLDE-------YKAGRTPN--PCVLCNKEIKFKAF 108

Query: 105 VDIANETGADAIAHGSTG 122
           ++ A E GAD IA   TG
Sbjct: 109 LEYARELGADYIA---TG 123


>gnl|CDD|148238 pfam06508, ExsB, ExsB.  This family includes putative
          transcriptional regulators from Bacteria and Archaea.
          Length = 137

 Score = 29.9 bits (68), Expect = 1.4
 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 7  KVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGE--ELKIASDKARLLGAK 59
          K V+  SGGLD++  L W + ++G EV     D GQ    EL+ A   A+ LG +
Sbjct: 1  KAVVLLSGGLDSTTCLAWAK-KEGYEVYALTFDYGQRHSKELECAKKIAKALGVE 54


>gnl|CDD|129461 TIGR00364, TIGR00364, exsB protein.  This protein family is
          represented by a single member in nearly every
          completed large (> 1000 genes) prokaryotic genome. In
          Rhizobium meliloti, a species in which the exo genes
          make succinoglycan, a symbiotically important
          exopolysaccharide, exsB is located nearby and affects
          succinoglycan levels, probably through polar effects on
          exsA expression or the same polycistronic mRNA. In
          Arthrobacter viscosus, the homologous gene is
          designated ALU1 and is associated with an aluminum
          tolerance phenotype. The function is unknown.
          Length = 201

 Score = 29.7 bits (67), Expect = 1.5
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 9  VLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQ--GEELKIASDKARLLGAKE 60
          V+  SGG D++  L   + E G EV     D GQ    EL+ A   A  LG + 
Sbjct: 2  VVVLSGGQDSTTCLAIAKDE-GYEVHAITFDYGQRHSRELESARKIAEALGIEH 54


>gnl|CDD|131719 TIGR02671, cas_csx9, CRISPR-associated protein (provisional), Csx9
           family.  Members of this family, so far, are archaeal
           proteins found in CRISPR-associated (cas) gene regions.
           So far, this rare cas protein is found in only three
           genomes: Pyrococcus horikoshii shinkaj OT3, Pyrococcus
           abyssi GE5, and Thermococcus kodakarensis KOD1. In each
           case it is found immediately upstream of cas3 in loci
           that resemble the Apern type but lack Csa1 and Csa4
           genes.
          Length = 377

 Score = 29.5 bits (66), Expect = 1.6
 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 10/95 (10%)

Query: 1   MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKE 60
           ++  VKK+     GG+D  + LK          +  + D+ + E  K  S    +L    
Sbjct: 260 LAEYVKKIENYRVGGVDLLVELKEGGATVEKYPLWALVDIAEKELWKGVSGDREMLAY-- 317

Query: 61  VYVKDL-------RREFVRDFVFPMFR-ANALYEG 87
           ++VKDL       R+E + D +F +FR   AL EG
Sbjct: 318 IFVKDLYRAINSGRKELIEDSIFRLFRQGRALLEG 352


>gnl|CDD|118190 pfam09658, Cas_Csx9, CRISPR-associated protein (Cas_Csx9).
           Clusters of short DNA repeats with nonhomologous
           spacers, which are found at regular intervals in the
           genomes of phylogenetically distinct prokaryotic
           species, comprise a family with recognisable features.
           This family is known as CRISPR (short for Clustered,
           Regularly Interspaced Short Palindromic Repeats). A
           number of protein families appear only in association
           with these repeats and are designated Cas
           (CRISPR-Associated) proteins. This entry describes
           archaeal proteins encoded in cas gene regions.
          Length = 377

 Score = 29.5 bits (66), Expect = 1.6
 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 10/95 (10%)

Query: 1   MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKE 60
           ++  VKK+     GG+D  + LK          +  + D+ + E  K  S    +L    
Sbjct: 260 LAEYVKKIENYRVGGVDLLVELKEGGATVEKYPLWALVDIAEKELWKGVSGDREMLAY-- 317

Query: 61  VYVKDL-------RREFVRDFVFPMFR-ANALYEG 87
           ++VKDL       R+E + D +F +FR   AL EG
Sbjct: 318 IFVKDLYRAINSGRKELIEDSIFRLFRQGRALLEG 352


>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
          Length = 436

 Score = 29.2 bits (66), Expect = 2.1
 Identities = 7/17 (41%), Positives = 17/17 (100%)

Query: 6  KKVVLAYSGGLDTSIIL 22
          +++++A+SGGLD++++L
Sbjct: 16 RQILVAFSGGLDSTVLL 32


>gnl|CDD|161871 TIGR00420, trmU, tRNA
          (5-methylaminomethyl-2-thiouridylate)-
          methyltransferase.  tRNA
          (5-methylaminomethyl-2-thiouridylate)-methyltransferase
          (trmU, asuE, or mnmA) is involved in the biosynthesis
          of the modified nucleoside
          5-methylaminomethyl-2-thiouridine (mnm5s2U34) present
          in the wobble position of some tRNAs. This enzyme
          appears not to occur in the Archaea.
          Length = 352

 Score = 28.9 bits (65), Expect = 2.3
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 14/88 (15%)

Query: 6  KKVVLAYSGGLDTSIILKWLQVEKGLEVI-VFIA-----DLGQG------EELKIASDKA 53
          KKV++  SGG+D+S+   +L  ++G EV+ VF+      D   G      E+L+ A    
Sbjct: 1  KKVIVGLSGGVDSSVSA-YLLKQQGYEVVGVFMKNWEEDDKNDGHGCTSAEDLRDAQAIC 59

Query: 54 RLLGAKEVYVKDLRREFVRDFVFPMFRA 81
            LG   +   + ++E+      P  + 
Sbjct: 60 EKLGIP-LEKVNFQKEYWNKVFEPFIQE 86


>gnl|CDD|118641 pfam10113, Fibrillarin_2, Fibrillarin-like archaeal protein.
           Members of this family of proteins include archaeal
           fibrillarin homologs.
          Length = 505

 Score = 28.2 bits (63), Expect = 3.8
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 42  QGEELKIASDKARLLGAKEVYVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIA 101
           Q EEL+  +   R LG+  VY +D+   ++ D  +    ++  YE          R  + 
Sbjct: 352 QKEELEALARAVRFLGSNLVYPRDIGGTYIGDAHWAALPSSPAYE----------RSDVV 401

Query: 102 KYLVDIANETGADAIA 117
           K + D+ +E  AD +A
Sbjct: 402 KTVDDLESEVIADTVA 417


>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
          Length = 251

 Score = 28.1 bits (63), Expect = 4.1
 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 4/32 (12%)

Query: 91  LGTAIARPLI---AK-YLVDIANETGADAIAH 118
           LG AIAR +    AK +L DI +  G DA A 
Sbjct: 11  LGRAIARRMAEQGAKVFLTDINDAAGLDAFAA 42


>gnl|CDD|163331 TIGR03569, NeuB_NnaB, N-acetylneuraminate synthase.  This family is
           a subset of the Pfam model pfam03102 and is believed to
           include only authentic NeuB N-acetylneuraminate (sialic
           acid) synthase enzymes. The majority of the genes
           identified by this model are observed adjacent to both
           the NeuA and NeuC genes which together effect the
           biosynthesis of CMP-N-acetylneuraminate from
           UDP-N-acetylglucosamine.
          Length = 329

 Score = 27.9 bits (63), Expect = 4.4
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 100 IAKYLVDIANETGADAIAH 118
           +AK LVD A E GADA+  
Sbjct: 17  LAKKLVDAAAEAGADAVKF 35


>gnl|CDD|182880 PRK10982, PRK10982, galactose/methyl galaxtoside transporter
           ATP-binding protein; Provisional.
          Length = 491

 Score = 27.8 bits (62), Expect = 5.0
 Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 11/45 (24%)

Query: 257 GIGRIDIVENRFVGIKSRGVYETPGGTILLHA-----HRAIESIS 296
           G  R DIVE  F      G+ E   GTI LH      H A E+I+
Sbjct: 284 GAKRTDIVETLF------GIREKSAGTITLHGKKINNHNANEAIN 322


>gnl|CDD|148126 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA).
           This family consists of several Ribosomal protein L11
           methyltransferase (EC:2.1.1.-) sequences.
          Length = 294

 Score = 28.0 bits (63), Expect = 5.1
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%)

Query: 18  TSIILKWL--QVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVYVKDL 66
           T++ L+ L   V+ G  V+    D+G G   L IA   A  LGAK+V   D+
Sbjct: 147 TALCLEALESLVKPGETVL----DVGCGSGILAIA---ALKLGAKKVVGVDI 191


>gnl|CDD|173128 PRK14665, mnmA, tRNA-specific 2-thiouridylase MnmA; Provisional.
          Length = 360

 Score = 28.0 bits (62), Expect = 5.1
 Identities = 35/125 (28%), Positives = 52/125 (41%), Gaps = 11/125 (8%)

Query: 1   MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEV----IVFIADLGQGEELKIASDKARLL 56
           M    K+V+L  SGG D+S+    L  E G EV      F    G  E L+ A   A  L
Sbjct: 1   MMEKNKRVLLGMSGGTDSSVAAMLLL-EAGYEVTGVTFRFYEFNGSTEYLEDARALAERL 59

Query: 57  GAKEVY--VKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGAD 114
           G   +    + + R+ + D+    + +        L    +  PL+AK    IA+E G  
Sbjct: 60  GIGHITYDARKVFRKQIIDYFIDEYMSGHTPVPCTLCNNYLKWPLLAK----IADEMGIF 115

Query: 115 AIAHG 119
            +A G
Sbjct: 116 YLATG 120


>gnl|CDD|150740 pfam10100, DUF2338, Uncharacterized protein conserved in bacteria
           (DUF2338).  Members of this family of hypothetical
           bacterial proteins have no known function.
          Length = 429

 Score = 27.4 bits (61), Expect = 6.4
 Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 3/26 (11%)

Query: 199 SQPAPEYVYKMIVSPEEAPDTPTTIR 224
               P+YVYK+     E P TPT IR
Sbjct: 231 ETKVPKYVYKLY---PEGPITPTLIR 253


>gnl|CDD|179053 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
          Length = 250

 Score = 27.4 bits (62), Expect = 7.4
 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 10/48 (20%)

Query: 18  TSIILKWL--QVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVY 62
           T + L+ L   V  G  V+    D+G G   L IA   A  LGAK+V 
Sbjct: 106 TRLCLEALEKLVLPGKTVL----DVGCGSGILAIA---AAKLGAKKVL 146


>gnl|CDD|181524 PRK08654, PRK08654, pyruvate carboxylase subunit A; Validated.
          Length = 499

 Score = 27.3 bits (61), Expect = 8.4
 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 12/44 (27%)

Query: 82  NALYEGY----YLLGTAIARPLIAKYL-----VDIANETGADAI 116
           NAL+  Y    Y +G A   P    YL     +D+A + GADAI
Sbjct: 38  NALFVKYADEAYPIGPA---PPSKSYLNIERIIDVAKKAGADAI 78


>gnl|CDD|182110 PRK09849, PRK09849, putative oxidoreductase; Provisional.
          Length = 702

 Score = 26.9 bits (60), Expect = 9.0
 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 154 GRQDLIDFAEKHAIPIDKNKRGEAPFSIDTNLLHSS 189
           G +D  D   K+  PI+  K   A +S+  N LH S
Sbjct: 522 GSEDAYD-ETKNYTPINDAKAKFAKWSLLRNCLHDS 556


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.318    0.137    0.393 

Gapped
Lambda     K      H
   0.267   0.0790    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,795,843
Number of extensions: 456501
Number of successful extensions: 918
Number of sequences better than 10.0: 1
Number of HSP's gapped: 890
Number of HSP's successfully gapped: 40
Length of query: 404
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 308
Effective length of database: 3,920,105
Effective search space: 1207392340
Effective search space used: 1207392340
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 (21.7 bits)
S2: 58 (26.0 bits)