RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor
RpoD [Candidatus Liberibacter asiaticus str. psy62]
         (682 letters)



>gnl|CDD|30914 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Transcription].
          Length = 342

 Score =  324 bits (832), Expect = 4e-89
 Identities = 156/354 (44%), Positives = 223/354 (62%), Gaps = 19/354 (5%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L+   +   ++++  I   +   E EL +  +   +  +         +L        + 
Sbjct: 6   LSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVE---LGEDLTDLKLGREPSERA 62

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
                             ++   I++I     ++  E + +   +++GE     AKK++V
Sbjct: 63  -------------RRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE-RDLDAKKKLV 108

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E+NLRLV+S+AKKYT RGL FLDLIQEGNIGLMKA EKFD   G+KFSTYA WW++QAIT
Sbjct: 109 ESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT 168

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVH  + I+K+ R  R +  ++ REPTPEEIA++L +  + VR++LK 
Sbjct: 169 RAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKR 228

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVL 628
             EPISL+TPIGD++ S LGDF+ED  +VSP D+  + +L+E    VLA  LT RE RV+
Sbjct: 229 ASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVI 288

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           R+RFG+      TLEE+G++F ++RER+RQIEAKA+RKL+ HP RS  LRS+LD
Sbjct: 289 RLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYLD 342


>gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma
           subunit [Transcription].
          Length = 247

 Score =  117 bits (295), Expect = 9e-27
 Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 9/231 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E     + ++E  L LV S+A+K+ NRG     DLIQ G IGL+KA E++D   G KFST
Sbjct: 20  EGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFST 79

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA+  ++  I   +      +++P  +R+   ++      +  ++ REPT EEIA++L +
Sbjct: 80  YAVRRIRGEILDYLRKNDS-VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGI 138

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E   + L         +    DED     D   D    +P D   +  L E     + 
Sbjct: 139 DKEEYIEALLAIN---GSQLLSLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAIE 195

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  RE+ VL +R+   +    T +E+ +   ++  R+ ++  KAI+KL+ 
Sbjct: 196 PLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRVSRLHKKAIKKLRK 242


>gnl|CDD|146934 pfam04539, Sigma70_r3, Sigma-70 region 3.  Region 3 forms a
           discrete compact three helical domain within the
           sigma-factor. Region is not normally involved in the
           recognition of promoter DNA, but as some specific
           bacterial promoters containing an extended -10 promoter
           element, residues within region 3 play an important
           role. Region 3 primarily is involved in binding the core
           RNA polymerase in the holoenzyme.
          Length = 78

 Score = 88.0 bits (219), Expect = 7e-18
 Identities = 34/78 (43%), Positives = 55/78 (70%)

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + ++K+ R  R +  ++ REPTPEEIA++L +  E VR+VL+  +EP+SL+ P+G+E+  
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 587 HLGDFIEDKNAVSPLDSA 604
            LGD +ED +A SP D+ 
Sbjct: 61  ELGDLLEDDDAESPEDAV 78


>gnl|CDD|146937 pfam04542, Sigma70_r2, Sigma-70 region 2.  Region 2 of sigma-70 is
           the most conserved region of the entire protein. All
           members of this class of sigma-factor contain region 2.
           The high conservation is due to region 2 containing both
           the -10 promoter recognition helix and the primary core
           RNA polymerase binding determinant. The core binding
           helix, interacts with the clamp domain of the largest
           polymerase subunit, beta prime. The aromatic residues of
           the recognition helix, found at the C-terminus of this
           domain are though to mediate strand separation, thereby
           allowing transcription initiation.
          Length = 71

 Score = 86.1 bits (214), Expect = 3e-17
 Identities = 27/69 (39%), Positives = 41/69 (59%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE  L LV S+A++Y   G    DL+QEG +GL++A E+FD   G  FST+    ++ A
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 508 ITRSIADQS 516
           I  ++  Q 
Sbjct: 61  IIDALRKQR 69


>gnl|CDD|112778 pfam03979, Sigma70_r1_1, Sigma-70 factor, region 1.1.  Region 1.1
          modulates DNA binding by region 2 and 4 when sigma is
          unbound by the core RNA polymerase. Region 1.1 is also
          involved in promoter binding.
          Length = 79

 Score = 73.5 bits (181), Expect = 2e-13
 Identities = 31/71 (43%), Positives = 50/71 (70%), Gaps = 3/71 (4%)

Query: 25 DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGD 81
          D S    KK+I+  ++RGY+T +E+N  LPPD+V SEQ++D ++ML +MGI VV   D +
Sbjct: 3  DLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVEEADSE 62

Query: 82 DLEDEEGSEDS 92
          +L++E  S++ 
Sbjct: 63 ELDEETSSDED 73


>gnl|CDD|146939 pfam04545, Sigma70_r4, Sigma-70, region 4.  Region 4 of sigma-70
           like sigma-factors are involved in binding to the -35
           promoter element via a helix-turn-helix motif. Due to
           the way Pfam works, the threshold has been set
           artificially high to prevent overlaps with other
           helix-turn-helix families. Therefore there are many
           false negatives.
          Length = 50

 Score = 67.4 bits (166), Expect = 1e-11
 Identities = 28/54 (51%), Positives = 38/54 (70%), Gaps = 4/54 (7%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            LASL PRE  VL +RFG       TLEE+G++  ++RER+RQIE +A+RKL+ 
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50


>gnl|CDD|143911 pfam00140, Sigma70_r1_2, Sigma-70 factor, region 1.2. 
          Length = 37

 Score = 56.6 bits (138), Expect = 2e-08
 Identities = 18/33 (54%), Positives = 25/33 (75%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            D VR+YLRE+G + LL+ E E+ +A+RIEAG 
Sbjct: 1   SDSVRLYLREIGRVPLLTAEEEVELARRIEAGD 33


>gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most
           C-terminal of four conserved domains found in
           Escherichia coli (Ec) sigma70, the main housekeeping
           sigma, and related sigma-factors (SFs). A SF is a
           dissociable subunit of RNA polymerase, it directs
           bacterial or plastid core RNA polymerase to specific
           promoter elements located upstream of transcription
           initiation points. The SR4 of Ec sigma70 and other
           essential primary SFs contact promoter sequences located
           35 base-pairs upstream of the initiation point,
           recognizing a 6-base-pair -35 consensus TTGACA.  Sigma70
           related SFs also include SFs which are dispensable for
           bacterial cell growth for example Ec sigmaS, SFs which
           activate regulons in response to a specific signal for
           example heat-shock Ec sigmaH, and a group of SFs which
           includes the extracytoplasmic function (ECF) SFs and is
           typified by Ec sigmaE which contains SR2 and -4 only.
           ECF SFs direct the transcription of genes that regulate
           various responses including periplasmic stress and
           pathogenesis.   Ec sigmaE SR4 also contacts the -35
           element, but recognizes a different consensus (a
           7-base-pair GGAACTT).  Plant SFs recognize sigma70 type
           promoters and direct transcription of the major plastid
           RNA polymerase, plastid-encoded RNA polymerase (PEP)..
          Length = 55

 Score = 56.3 bits (137), Expect = 3e-08
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE     L  L  RE  V+ +RFG G+    + EE+ +   ++R  +RQ   +A++KL+
Sbjct: 1   RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55


>gnl|CDD|146940 pfam04546, Sigma70_ner, Sigma-70, non-essential region.  The domain
           is found in the primary vegetative sigma factor. The
           function of this domain is unclear and can be removed
           without loss of function.
          Length = 210

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 34/149 (22%), Positives = 60/149 (40%), Gaps = 8/149 (5%)

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA-EVYRELRSL 297
           D  +      E+  ++E   D+D+DD        E  L P       E A E + ELR  
Sbjct: 35  DAAAATAPAIESELDEEDLEDDDDDDDEDDDEEEEADLGP-----DPEEARERFAELREQ 89

Query: 298 QDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
            +      +K  + S K +  +E L +      L   + D LV+ L  +  R+   E ++
Sbjct: 90  YEKTRKAIEKHGRGSKKAQKAREALAEEFKQFRLVPKQFDRLVDNLRGMVDRVRAQERQI 149

Query: 357 LRLAQSY-GIKRDVFLERHQGRELDPHWV 384
           ++L      + R  F++   G E +  W+
Sbjct: 150 MKLCVERAKMPRKDFIKSFPGNETNLDWL 178


>gnl|CDD|37202 KOG1991, KOG1991, KOG1991, Nuclear transport receptor RANBP7/RANBP8
           (importin beta superfamily) [Nuclear structure,
           Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 1010

 Score = 35.3 bits (81), Expect = 0.052
 Identities = 26/92 (28%), Positives = 43/92 (46%)

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           Q  E+ S+E E +D  E E  I+    + +DD+  +D   E A   E +LD+D+D     
Sbjct: 883 QVEEEDSEEGEEEDDDEEEDFIDDEDDIDEDDQDYLDEYGELALEKEDSLDDDDDFDEDE 942

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           L   ED+L    +  +D        + +LQ +
Sbjct: 943 LDLEEDELFETPLDQVDPFQLFKEAITNLQSS 974


>gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit
            [Transcription].
          Length = 1640

 Score = 34.2 bits (78), Expect = 0.12
 Identities = 18/105 (17%), Positives = 36/105 (34%), Gaps = 13/105 (12%)

Query: 210  KREDSSQEKERDDVQETEGDIESAAKVSKDDRSK----VDSPPENAENDERNLDEDEDDS 265
                    ++ DD  E + D + A+      +++     +S  E+   +ER  + DED+ 
Sbjct: 1327 DEVGGEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEE 1386

Query: 266  AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            +                  D   E   E +  Q      ++ E+S
Sbjct: 1387 SDEDDEEVGL---------DGTPEPEEEDQEGQPEVNAVERREQS 1422


>gnl|CDD|113695 pfam04931, DNA_pol_phi, DNA polymerase phi.  This family includes
           the fifth essential DNA polymerase in yeast EC:2.7.7.7.
           Pol5p is localized exclusively to the nucleolus and
           binds near or at the enhancer region of rRNA-encoding
           DNA repeating units.
          Length = 784

 Score = 33.7 bits (77), Expect = 0.19
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 8/94 (8%)

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
           +E++ DD++ET+ D E   +  +D  S+ +S  E+ E DE    +++D  A+        
Sbjct: 648 EEEDEDDLEETDDD-EDECEAIEDSESESESDGEDGEEDE----QEDDAEANEGVV---P 699

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           +   V  AL ++  +   L         G  DE+
Sbjct: 700 IDKAVRRALPKVLNLPDALDGGDSEDEEGMDDEQ 733


>gnl|CDD|37327 KOG2116, KOG2116, KOG2116, Protein involved in plasmid
           maintenance/nuclear protein involved in lipid metabolism
           [Cell motility, Lipid transport and metabolism].
          Length = 738

 Score = 33.1 bits (75), Expect = 0.26
 Identities = 38/236 (16%), Positives = 71/236 (30%), Gaps = 14/236 (5%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D     +E   EDSLD+   +           D  +  T++ V  ++      EL     
Sbjct: 150 DKRGDANESEQEDSLDIGQRSDTLPGSSFPESDRDNSPTENTVLAFVTPRSDSELEKSGS 209

Query: 139 EIAIAKRIEAGRAMMMASLCE-SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           +  +   +    ++    L E S              N    L RE  D+   I   SK 
Sbjct: 210 KRTLKSELSFSHSLSQRKLSEGSHFQKS---------NKEDALRRETHDMTRRIFLSSKS 260

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K+    Q K   ++           K  ++     D    + E D +N
Sbjct: 261 LETFNAATLPIDKK---LQGKSDSELASKVDSPSR-KKDKREANDGADDLRLDDEGDYKN 316

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
            D +   ++     + +  +      +D   E    L S+  +      D + ++K
Sbjct: 317 ADPENSVTSSKWGELSESRQSVKSKGVDSGVEKTMRLASILCSLCLSLGDGREALK 372


>gnl|CDD|31168 COG0826, COG0826, Collagenase and related proteases
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 347

 Score = 32.6 bits (74), Expect = 0.37
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 24 FDFSDDSWKKMIKLARQRG---YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           +FS +   + ++LA   G   YV +   N  L  DE+  E +E  +  L  +G++ V
Sbjct: 44 LNFSVEDLAEAVELAHSAGKKVYVAV---NTLLHNDEL--ETLERYLDRLVELGVDAV 96


>gnl|CDD|36189 KOG0971, KOG0971, KOG0971, Microtubule-associated protein dynactin
           DCTN1/Glued [Cell cycle control, cell division,
           chromosome partitioning, Cytoskeleton].
          Length = 1243

 Score = 31.9 bits (72), Expect = 0.66
 Identities = 43/196 (21%), Positives = 72/196 (36%), Gaps = 24/196 (12%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE--------KERDDVQ 224
           E  D      EI+  E     E KG    G    SYQ ++   Q         + RD   
Sbjct: 339 ERVDELETDLEILKAEM----EEKGS--DGQAASSYQFKQLEQQNARLKDALVRLRDLSA 392

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQ 275
             + D +   K  +   S+++      E   R LD+ E          D+A     M +Q
Sbjct: 393 SEKQDHQKLQKELEKKNSELEELRRQKERLSRELDQAESTIADLKEQVDAALGAEEMVEQ 452

Query: 276 LRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           L  K +   +++  +   +  L+    +N Q  E +      L+E+L    G+    Q R
Sbjct: 453 LTDKNLNLEEKVKLLEETVGDLEALEEMNEQLQESNRELELDLREELDMAKGARKELQKR 512

Query: 335 IDLLVEQLYDISKRIM 350
           ++   E +YD  + I 
Sbjct: 513 VEAAQETVYDRDQTIK 528


>gnl|CDD|37532 KOG2321, KOG2321, KOG2321, WD40 repeat protein [General function
           prediction only].
          Length = 703

 Score = 31.5 bits (71), Expect = 0.82
 Identities = 26/173 (15%), Positives = 56/173 (32%), Gaps = 4/173 (2%)

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S + R  +    +    Q  E      A    D+  + ++   +A   E + +E  DD A
Sbjct: 500 SEEYRLLAPVASKMSKKQPKELRELLEA-EESDEEEESENGESDAG-KEESDEEASDDDA 557

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              S+ E+  +          A V R  +  +++    +K +    K    + +   + G
Sbjct: 558 DEASSDEETRKLYERKMEKHAAAVKRRRKEQKEDERTIRKPQTERSKQI--ENRAGNIFG 615

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
               +        + L    +     +GE+       G ++  F  R +    
Sbjct: 616 ETKDSLLGQGGSKKSLQARLRSTARGDGEVTFEDGQRGKRQMTFTLRLKKSND 668


>gnl|CDD|40022 KOG4825, KOG4825, KOG4825, Component of synaptic membrane glycine-,
           glutamate- and thienylcyclohexylpiperidine-binding
           glycoprotein (43kDa) [Signal transduction mechanisms].
          Length = 666

 Score = 30.5 bits (68), Expect = 1.7
 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 9/88 (10%)

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED-DSAHTLSAMED 274
            E +++ V + + D+   AK++  D  K     E  END+     DED D A       +
Sbjct: 177 DENKQEAVAKEDFDLAKKAKLAIADLKKSGEELEELENDKGCAVADEDFDLAKDKKDEIE 236

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAV 302
            LR +++  LD        L  L+D  +
Sbjct: 237 ALRAEILAQLD--------LHLLEDAEL 256


>gnl|CDD|34730 COG5129, MAK16, Nuclear protein with HMG-like acidic region
           [General function prediction only].
          Length = 303

 Score = 30.1 bits (67), Expect = 2.0
 Identities = 16/56 (28%), Positives = 26/56 (46%)

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           ++  D+  E   DD ++ +   +   K    D+S   S  E  E+ E   DEDED+
Sbjct: 207 EEESDTELEAVTDDSEKEKTKKKDLEKWLGSDQSMETSESEEEESSESESDEDEDE 262


>gnl|CDD|36161 KOG0943, KOG0943, KOG0943, Predicted ubiquitin-protein
            ligase/hyperplastic discs protein, HECT superfamily
            [Posttranslational modification, protein turnover,
            chaperones].
          Length = 3015

 Score = 30.2 bits (67), Expect = 2.1
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 207  SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            S     D++ + E  + QE E   E        D    D   ++AE ++ + D+D+DD  
Sbjct: 1709 SGNTTNDTNADNEEREGQEGEFAGEE----DHHDDDNDDDDDDDAEAEDDDDDDDDDDED 1764

Query: 267  HTLSAMEDQ 275
              L A    
Sbjct: 1765 MDLDAEAAA 1773


>gnl|CDD|37249 KOG2038, KOG2038, KOG2038, CAATT-binding transcription factor/60S
           ribosomal subunit biogenesis protein [Translation,
           ribosomal structure and biogenesis, Transcription].
          Length = 988

 Score = 30.0 bits (67), Expect = 2.5
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 10/63 (15%)

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           ED S  +E DD  E E   E      KDD++K D       +D+ + DED+D+  ++L +
Sbjct: 844 EDGSLPEEEDDDYEFEFGAE------KDDKNKKD----MTSDDDVDADEDDDEDENSLGS 893

Query: 272 MED 274
            ED
Sbjct: 894 EED 896


>gnl|CDD|39545 KOG4344, KOG4344, KOG4344, Uncharacterized conserved protein
           [Function unknown].
          Length = 1121

 Score = 29.8 bits (66), Expect = 2.7
 Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 15/103 (14%)

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVD--------SPPENAENDERN--LDEDE 262
           +S +E ER+   E + D ++A  + +D+   +            E+ END+ +  L+E++
Sbjct: 142 NSMEEAERNAEIEEKADFDAAKNLMEDEEMDIAALLDEDFLDEEEDDENDQLSDPLEEED 201

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRE--LRSLQDNAVN 303
            D    L   E+  + +    LDE A V  E    S+ +  VN
Sbjct: 202 CDIQTDLKPDEEIDQNR---KLDECARVKDEADDASVLEGHVN 241


>gnl|CDD|143182 cd04981, IgV_H, Immunoglobulin (Ig) heavy chain (H), variable (V)
           domain.  IgV_H: Immunoglobulin (Ig) heavy chain (H),
           variable (V) domain. The basic structure of Ig molecules
           is a tetramer of two light chains and two heavy chains
           linked by disulfide bonds. In Ig, each chain is composed
           of one variable domain (IgV) and one or more constant
           domains (IgC); these names reflect the fact that the
           variability in sequences is higher in the variable
           domain than in the constant domain. There are five types
           of heavy chains (alpha, gamma, delta, epsilon, and mu),
           which determine the type of immunoglobulin: IgA, IgG,
           IgD, IgE, and IgM, respectively. In higher vertebrates,
           there are two types of light chain, designated kappa and
           lambda, which can associate with any of the heavy
           chains. This family includes alpha, gamma, delta,
           epsilon, and mu heavy chains.
          Length = 117

 Score = 29.3 bits (66), Expect = 3.5
 Identities = 7/15 (46%), Positives = 12/15 (80%)

Query: 493 GYKFSTYAMWWVKQA 507
           G+ F++Y + WV+QA
Sbjct: 23  GFTFTSYGVNWVRQA 37


>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
            (vWA) domain [General function prediction only].
          Length = 4600

 Score = 29.3 bits (65), Expect = 3.7
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 16/87 (18%)

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN------------ 250
            T+     + E+S  E+E  D+ E   DI      S +++   +   E+            
Sbjct: 3868 TKDSVVSENENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQS 3927

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLR 277
            A N+E +L   EDD+     A+ED+ R
Sbjct: 3928 AANNESDLVSKEDDN----KALEDKDR 3950



 Score = 28.9 bits (64), Expect = 4.4
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 11/74 (14%)

Query: 211  REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD-------SPPENAEND---ERNLDE 260
            +ED ++  E  D QE E + E +  V  DD  + D        PPEN + D   +  LDE
Sbjct: 3938 KEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDE 3997

Query: 261  DEDDSAHTLSAMED 274
             E D +   S +ED
Sbjct: 3998 KEGDVSKD-SDLED 4010


>gnl|CDD|31783 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma
           subunit, sigma24 homolog [Transcription].
          Length = 182

 Score = 28.9 bits (64), Expect = 4.7
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E   A    +  +     E   R LA L PR+     +R+  G+    + EE+ +   ++
Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGL----SYEEIAEILGIS 156

Query: 653 RERIRQIEAKAIRKLK 668
              ++    +A +KL+
Sbjct: 157 VGTVKSRLHRARKKLR 172


>gnl|CDD|39027 KOG3823, KOG3823, KOG3823, Uncharacterized conserved protein
           [Function unknown].
          Length = 630

 Score = 28.9 bits (64), Expect = 5.1
 Identities = 10/62 (16%), Positives = 21/62 (33%)

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + Q+    S E +     + +G +E   +    D++     P+ A   +        D
Sbjct: 555 HLAGQEEAHESHESQSVSCDKPQGIVEIGREAELLDKTAQSEEPKIAAASQAGRPGCGGD 614

Query: 265 SA 266
            A
Sbjct: 615 VA 616


>gnl|CDD|37043 KOG1832, KOG1832, KOG1832, HIV-1 Vpr-binding protein [Cell cycle
            control, cell division, chromosome partitioning].
          Length = 1516

 Score = 28.9 bits (64), Expect = 5.3
 Identities = 11/53 (20%), Positives = 26/53 (49%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
            E+  + ++ D+  + E D++    +  D+    D    + +N++   DED D+
Sbjct: 1410 EEDDETEDEDEDDDEEDDLDRDDGLEGDNSDSGDDDLSSEDNEDEVSDEDGDE 1462



 Score = 28.1 bits (62), Expect = 8.8
 Identities = 11/56 (19%), Positives = 22/56 (39%)

Query: 210  KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +R  +  + + ++  ETE + E   +    DR        +   D+    ED +D 
Sbjct: 1399 RRRPTDDDSDEEEDDETEDEDEDDDEEDDLDRDDGLEGDNSDSGDDDLSSEDNEDE 1454


>gnl|CDD|32632 COG2771, CsgD, DNA-binding HTH domain-containing proteins
           [Transcription].
          Length = 65

 Score = 28.4 bits (63), Expect = 6.2
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             A LTPRE  +LR+     +    + +E+ +   ++ E ++       RKL   +R 
Sbjct: 1   RTADLTPREREILRL-----VAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRV 53


>gnl|CDD|37045 KOG1834, KOG1834, KOG1834, Calsyntenin [Extracellular structures].
          Length = 952

 Score = 28.5 bits (63), Expect = 7.0
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 207 SYQKREDSSQEKERDDVQETEGD-----IESAAKVSKDDRSKVDSPPENAENDERNLDED 261
            Y+K     +E E ++ +ETE +      +SA   S+D+    +  P + +N++R +  +
Sbjct: 886 DYEKGGSIEEESEEEEEEETEDEEESSDSDSADSESEDEEEGTEVGP-HLQNNQRQVQLE 944

Query: 262 EDDS 265
            DDS
Sbjct: 945 WDDS 948


>gnl|CDD|146113 pfam03313, SDH_alpha, Serine dehydratase alpha chain.  L-serine
           dehydratase (EC:4.2.1.13) is a found as a heterodimer of
           alpha and beta chain or as a fusion of the two chains in
           a single protein. This enzyme catalyses the deamination
           of serine to form pyruvate. This enzyme is part of the
           gluconeogenesis pathway.
          Length = 269

 Score = 28.2 bits (64), Expect = 7.7
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 6/67 (8%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E G+SISE       + K E    +     V   +   +        +GL+ L+ I  G+
Sbjct: 2   EKGLSISE------NILKNEMSVGVPGTGEVGLKMAAALGAMGGDVEKGLEVLEGITPGD 55

Query: 479 IGLMKAA 485
           +   + A
Sbjct: 56  LKKARRA 62


>gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated
           protein/mitoxantrone resistance protein, ABC superfamily
           [Secondary metabolites biosynthesis, transport and
           catabolism].
          Length = 1381

 Score = 28.3 bits (63), Expect = 7.8
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           K F    E +RQ E K +RK  + S
Sbjct: 400 KPFLKKIEDLRQKELKLLRKSAYLS 424


>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of  class I
           lysyl tRNA synthetase.  Class I lysyl tRNA synthetase
           (LysRS) catalytic core domain. This class I enzyme is a
           monomer which aminoacylates the 2'-OH of the nucleotide
           at the 3' of the appropriate tRNA. The core domain is
           based on the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding. The class I LysRS is found only in archaea and
           some bacteria and has evolved separately from class II
           LysRS, as the two do not share structural or sequence
           similarity.
          Length = 353

 Score = 28.1 bits (63), Expect = 8.1
 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 11/51 (21%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHI--------VSMVRKG 437
           W + +A   + I++ R   +   V +GIS S   HI          +V + 
Sbjct: 3   WADVIA---EKIIEERKGKEKYVVASGISPSGHIHIGNFREVITADLVARA 50


>gnl|CDD|30988 COG0643, CheA, Chemotaxis protein histidine kinase and related
           kinases [Cell motility and secretion / Signal
           transduction mechanisms].
          Length = 716

 Score = 28.0 bits (62), Expect = 9.2
 Identities = 32/152 (21%), Positives = 59/152 (38%), Gaps = 2/152 (1%)

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           E  +  +E + V  TE D E    V  +   + +     A   +  L E  +        
Sbjct: 229 EAEAAFEESEVVLATEQDEELIRDVL-ELVVEAEELEIAAVELDAELLELAESEQAADDV 287

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-EKLVKLVGSLSL 330
           +  Q  P    +  E A++     +    A        SS++  V K ++L+ LVG L +
Sbjct: 288 LAAQAEPLAEKSAAEAAKLSALEAAPAAKAAAAAAGASSSIRVDVEKLDRLMNLVGELVI 347

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            +SR+  L  +L ++ + +     +L RL   
Sbjct: 348 TRSRLSQLASELDEVREELDEALRQLSRLTTD 379


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.315    0.131    0.366 

Gapped
Lambda     K      H
   0.267   0.0574    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,835,413
Number of extensions: 413758
Number of successful extensions: 1259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1225
Number of HSP's successfully gapped: 98
Length of query: 682
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 582
Effective length of database: 4,102,837
Effective search space: 2387851134
Effective search space used: 2387851134
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: 42 (22.0 bits)
S2: 61 (27.6 bits)