RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781103|ref|YP_003065516.1| penicillin-binding
transmembrane protein [Candidatus Liberibacter asiaticus str. psy62]
         (598 letters)



>gnl|CDD|31111 COG0768, FtsI, Cell division protein FtsI/penicillin-binding
           protein 2 [Cell envelope biogenesis, outer membrane].
          Length = 599

 Score =  365 bits (937), Expect = e-101
 Identities = 175/600 (29%), Positives = 275/600 (45%), Gaps = 70/600 (11%)

Query: 59  FQKRRRKVIAHSKNRIGMTIVVCLVIYIILAIRIIQYGNIHPEPIAPSMNIDEYGMSRPD 118
            +K R      +   + + ++  L+I  +  ++I+Q  +   E    +         R D
Sbjct: 7   KKKGRLFRRRLNLLFLIIFLLFALLILRLFYLQIVQGDDYAKEAANRNQRTVPIPAPRGD 66

Query: 119 IIDRNGEILATDIPTFSLYVEPHKV------ISPDEIIEKLQIVLPNLDSEMIRRKLSSE 172
           I DRNG++LAT++P +SL  +P K+       + DE+  KL  +L +LD   + ++L S+
Sbjct: 67  IYDRNGKVLATNVPVYSLTADPRKITDEPLEATKDELAAKLLALLEDLDKRALLKELKSK 126

Query: 173 TK-FQWLRRK--LSPQQQKRI--LSFGLPGVGFRLEKSRFYP---AASHASHVVGYVDID 224
           ++ F  L RK  L+P+Q  RI  L   LPGV    +  R+YP    ASH +  VG ++ D
Sbjct: 127 SRLFTPLARKTNLTPEQAARIAELLLKLPGVDVETDSRRYYPYGELASHVAGYVGKINED 186

Query: 225 NR--------GITGIEKFLDMQ-----GLTRVFTTNKGE----------KNLQPIRLALD 261
                     G +G+EK  D       G   V    +G           K+ + ++L +D
Sbjct: 187 ELGRLKNEDIGKSGLEKSYDDVLRGKDGYREVEVDRRGNVIPTLKEVKPKDGKDVQLTID 246

Query: 262 LRIQNIVHQELVENKKKYNAESVGTVILNVSTGEVISMVSIPDYDP-----HEAFKGKKE 316
           LR+Q    + L +      A+    V+L+  TGE+++M S P YDP      + +   ++
Sbjct: 247 LRLQKAAEEAL-DKAVANKAKGGAAVVLDPKTGEILAMASSPSYDPNLFVSSKDYDKPRK 305

Query: 317 GWFNRISYGIFEMGSIFKVFTIAMGIDSG---LFTVKDLFDTRNP-IKVGKHVIHDYHPQ 372
              NR   G +E GS FK  T A  +++G   LF    + D   P I++     HDY   
Sbjct: 306 PLLNRAVTGTYEPGSTFKPITAAAALETGNTGLFDPGSVLDGNGPKIRIWGRTGHDYGG- 364

Query: 373 NRILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQAPSYPS--- 429
            R LT+ E  + SSN+G A++A  +G  G  ++L + G   K   +LP   +   PS   
Sbjct: 365 -RPLTLTEALQKSSNVGFAKLALRLGPDGLYDYLKKFGFGQKTGIDLPGETSGLLPSREP 423

Query: 430 -QWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGRLIPPTFMIRSRE-------ESEKV 481
            +W  I   T+S G GL  TPLQ A A A + N G+L+ P  +    +       E   +
Sbjct: 424 WRWGPIDLATLSIGQGLLVTPLQLAQAYATIANGGKLVKPHLVKGIEDPVGENKKEPPVL 483

Query: 482 SRIVLKKNTVKTMRSLLR---EGVTGGSGRRAFVPGFEVGGKTGTAQKVIKK--RYSDTL 536
            + V+   T + +R  +R       GG+G+ A VPG+ + GKTGTAQK       YS   
Sbjct: 484 KKRVISPETAEKVREGMRAVVNDGGGGTGKAAAVPGYRIAGKTGTAQKAGPGGGGYSKGR 543

Query: 537 NFNSFLAVFPTTDPQYIVLSFMDSPKIKERNQLTAGINVAPMVGNIIRRSASMLGVKPVF 596
               F+   P  +P+Y V   +D+P          G   AP+   I+ R    L VKP  
Sbjct: 544 YHAWFVGFAPADNPKYAVAVLVDNPGGG-----YGGAVAAPVFKKIMERLLDYLNVKPDA 598


>gnl|CDD|144486 pfam00905, Transpeptidase, Penicillin binding protein
           transpeptidase domain.  The active site serine is
           conserved in all members of this family.
          Length = 296

 Score =  188 bits (480), Expect = 3e-48
 Identities = 93/303 (30%), Positives = 150/303 (49%), Gaps = 13/303 (4%)

Query: 285 GTVILNVSTGEVISMVSIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDS 344
             V+L+  TGEV++M   P YDP       KE   NR    ++E GS FK+FT    +D+
Sbjct: 2   SAVVLDPKTGEVLAMAGKPSYDP----NRDKEPLRNRAVQDVYEPGSTFKIFTALAALDN 57

Query: 345 GLFTVKDLFDTRNPIKVGKHVIHDYH-PQNRILTIPEIFRYSSNIGAAQIADAMGIQGHK 403
           G+   ++ FD    + VG + I D++   +  +T+ E   YSSN    Q+A  +G    +
Sbjct: 58  GILKPEETFDDWPGLPVGGYTIKDWNQDGSGTITLREALEYSSNWYFQQLALKLGKDKLR 117

Query: 404 EFLYRLGLLSKLETELPEIQAPSYPSQWKRIHSLTISFGHG-LSTTPLQTAVAAAALINE 462
           ++L + G  +K    LP  ++        R    T ++G G L+ TPLQ A A A + N 
Sbjct: 118 DYLKKFGYGNKTGIGLPG-ESAGILPPRYRGDGATTAWGQGSLTITPLQQAQAYATIANN 176

Query: 463 GRLIPPTFM--IRSREESEKVSRIVLKKNTVKTMRSLLREGVTGGSGRRAFVPGFEVGGK 520
           G+L+PP  +  I+   + + + ++ + K+T + ++ +L+  V    G  A VPG++V GK
Sbjct: 177 GKLVPPHIVKSIKKLVDPKVLGKLPISKSTAEKVKDMLK-LVVNDGGGAAAVPGYKVAGK 235

Query: 521 TGTAQKVIKKRYSDTLNFNSFLAVFPTTDPQYIVLSFMDSPKIKERNQLTAGINVAPMVG 580
           TGTAQ   K  Y D      F+   P  +P+Y     +D PK         G   AP+  
Sbjct: 236 TGTAQVAGKGGYKDGTYNGWFVGYAPADNPKYAFAVLIDDPKGDGG---AGGKVAAPIFK 292

Query: 581 NII 583
           +I+
Sbjct: 293 DIL 295


>gnl|CDD|146381 pfam03717, PBP_dimer, Penicillin-binding Protein dimerization
           domain.  This domain is found at the N terminus of Class
           B High Molecular Weight Penicillin-Binding Proteins. Its
           function has not been precisely defined, but is strongly
           implicated in PBP polymerisation. The domain forms a
           largely disordered 'sugar tongs' structure.
          Length = 165

 Score =  105 bits (263), Expect = 5e-23
 Identities = 51/137 (37%), Positives = 72/137 (52%), Gaps = 17/137 (12%)

Query: 116 RPDIIDRNGEILATDIPTFSLYVEPHKVISP-DEIIEKLQIVLPNLDSEMIRRKLS---- 170
           R +I+DRNG +LAT++P +S+YV+P +V     E  EKL  +L  LD E I +KL     
Sbjct: 5   RGEILDRNGRVLATNVPVYSVYVDPKEVEDELKETAEKLAKIL-GLDPEEILKKLKEKDA 63

Query: 171 SETKFQWLRRKLSPQQQKRILSFGLPGVGFRLEKSRFYPAASHASHVVGYVDIDNR---- 226
              +   L R LSP++  +I    LPGV    E  R+YP    A+HV+GYV   N     
Sbjct: 64  KSYEPVVLARNLSPEEAAKIKELKLPGVSIEEEPKRYYPYGELAAHVLGYVGEINEEELE 123

Query: 227 -------GITGIEKFLD 236
                  G +G+EK  +
Sbjct: 124 RLPGDRVGKSGLEKQYE 140


>gnl|CDD|31087 COG0744, MrcB, Membrane carboxypeptidase (penicillin-binding
           protein) [Cell envelope biogenesis, outer membrane].
          Length = 661

 Score = 93.6 bits (232), Expect = 1e-19
 Identities = 67/287 (23%), Positives = 108/287 (37%), Gaps = 51/287 (17%)

Query: 256 IRLALDLRIQNIVHQELVEN-KKKYNAESVGTVILNVSTGEVISMVSIPDYDPHEAFKGK 314
           +   LD  +Q    + +  +   K        V+++  TG V ++V   DY P       
Sbjct: 299 VYTTLDPELQEAAEKAVQADPLYKLRDVQAALVLIDPKTGAVRALVGGRDYQPSG----- 353

Query: 315 KEGWFNRISYGIFEMGSIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYHPQN- 373
               FNR +    + GS FK F     ++ G  T   +     P+  G     ++ P+N 
Sbjct: 354 ----FNRATQAKRQPGSTFKPFLYYAALEEGKATPSTIVVDA-PVTYG-----NWSPKNY 403

Query: 374 ------RILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQAPSY 427
                   +T+ E    S NI A ++   +G+    +   +LG+ S L            
Sbjct: 404 DGRYEGGSVTLREALATSLNIPAVRLLQKVGLDKVVDTAKKLGINSPLVP---------- 453

Query: 428 PSQWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGRLIPPTFMIRSREESEKV------ 481
                     +++ G     +PL+ A A A   N G   PP F IR   +++ V      
Sbjct: 454 --------GPSLALG-ASEVSPLEMASAYATFANGGTYYPPHF-IRKVTDADGVLYDNPP 503

Query: 482 -SRIVLKKNTVKTMRSLLREGVT-GGSGRRAFVPGFEVGGKTGTAQK 526
             + VL       M  +L+  VT  G+G  A +PG    GKTGT   
Sbjct: 504 KVKRVLSPQAAYLMTDMLQGVVTPTGTGAAAKLPGPYAAGKTGTTND 550


>gnl|CDD|34614 COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding protein
           [Cell envelope biogenesis, outer membrane].
          Length = 797

 Score = 67.6 bits (165), Expect = 1e-11
 Identities = 64/274 (23%), Positives = 105/274 (38%), Gaps = 63/274 (22%)

Query: 287 VILNVSTGEVISMVSIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGL 346
           V L+  TG ++++V    +   +         FNR +  + + GS FK F  +  +D G 
Sbjct: 424 VSLDPKTGAILALVGGFSFAQSK---------FNRATQALRQPGSSFKPFVYSAALDKG- 473

Query: 347 FTVKDLFDTRNPIKVGKHVIHDYHPQNR------ILTIPEIFRYSSNIGAAQIADAMGIQ 400
            T   + +              + P+N        +T+ +    S N+ A ++ DA+G+ 
Sbjct: 474 LTPASVINDAPISFWDGGGGGVWRPKNYGGKFAGPITLRQGLEQSRNLVAVRLLDAVGVD 533

Query: 401 GHKEFLYRLGLLSKLETELPEIQAPSYPSQWKRIHSLTISFGHGLSTTPLQTAVAAAALI 460
              E++ R G  +    ELP                L+++ G G  TTPLQ A A A   
Sbjct: 534 YAAEYIKRFGFYTD---ELP--------------PVLSMALGSG-ETTPLQMARAYAVFA 575

Query: 461 NEGRLIPPTFMIR--------------------------SREESEKVSRI--VLKKNTVK 492
           N G+ + P F+ R                          ++EE         V+   T  
Sbjct: 576 NGGKRVEPYFIDRIEDRNGKVIFRAEPRVCCRCNADEANNQEEQTLADYAPQVIDPMTAY 635

Query: 493 TMRSLLREGVTGGSGRRAFVPG-FEVGGKTGTAQ 525
            + S+LR  V  G+  RA   G  ++ GKTGT  
Sbjct: 636 QITSMLRGVVQRGTAARAGRLGRPDIAGKTGTTN 669


>gnl|CDD|34561 COG4953, PbpC, Membrane carboxypeptidase/penicillin-binding protein
           PbpC [Cell envelope biogenesis, outer membrane].
          Length = 733

 Score = 51.1 bits (122), Expect = 9e-07
 Identities = 71/343 (20%), Positives = 121/343 (35%), Gaps = 55/343 (16%)

Query: 256 IRLALDLRIQNIVHQELVENKKKYNAESVGTVILNVSTGEVISMVSIPDYDPHEAFKGKK 315
           +   L  R++            +    S   ++++  T EV++ V   D+     F   +
Sbjct: 271 LDANLQRRLEEQARDYASRLGPR---NSAAVLVVDNRTMEVLAYVGSADF-----FDASR 322

Query: 316 EGWFNRISYGIFEMGSIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYHPQNR- 374
            G  + +   +   GS  K F   +  D GL   + L     P + G     DY P+N  
Sbjct: 323 SGHID-MVRALRSPGSTLKPFVYGLAFDQGLIHPETLLKDV-PTRFG-----DYRPENFD 375

Query: 375 -----ILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQAPSYPS 429
                 +++ E    S NI A ++ +A+G       L + G+       LPE  AP    
Sbjct: 376 SNFHGPVSVREALIKSLNIPAVRLLEAVGPPRFAARLRQAGVHLY----LPEGAAP---- 427

Query: 430 QWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGRLIPPTFMIRSREESEKVSRIVLKKN 489
                  L++  G G   T    A   AAL N+G+  P    +     +E+    +L   
Sbjct: 428 ------GLSLILG-GAGITLEDLAQLYAALANQGKAGPLRDTLDDDPLTERT---LLSPG 477

Query: 490 TVKTMRSLLREGVTGGSGRRAFVPGFEVGGKTGTAQKVIKKRYSDTLNFNSFLAVFPTTD 549
               +  +L +    G    A      +  KTGT+       Y D  +   F        
Sbjct: 478 AAWQILDILSDVARPGLPNGALPSVRPIAWKTGTSYG-----YRDAWSVGVF-------- 524

Query: 550 PQYIVLSFMDSPKIKERNQLTAGINVAPM---VGNIIRRSASM 589
            +Y++  ++          L+     AP+   V NII RS  +
Sbjct: 525 GRYVLGVWVGRFDGTPVPGLSGVATAAPLLFQVNNIIARSGRL 567


>gnl|CDD|35676 KOG0455, KOG0455, KOG0455, Homoserine dehydrogenase [Amino acid
           transport and metabolism].
          Length = 364

 Score = 31.5 bits (71), Expect = 0.73
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 126 ILATDIPTFSLYVEPHK-VISPDEIIEKLQIVLPNLDSEMIRRKLSSETKFQWLR 179
                 P  SL  EP   ++S DE +  L      LD  +  R   + ++ + LR
Sbjct: 239 ESMDSFPVESLIPEPLPSLMSADEFLHGL----VKLDQNIEERVKEASSEGKVLR 289


>gnl|CDD|73263 cd01379, MYSc_type_III, Myosin motor domain, type III myosins.
           Myosin III has been shown to play a role in  the vision
           process in insects and in hearing in mammals. Myosin
           III, an unconventional myosin, does not form dimers.
           This catalytic (head) domain has ATPase activity and
           belongs to the larger group of P-loop NTPases. Myosins
           are actin-dependent molecular motors that play important
           roles in muscle contraction, cell motility, and
           organelle transport. The head domain is a molecular
           motor, which utilizes ATP hydrolysis to generate
           directed movement toward the plus end along actin
           filaments. A cyclical interaction between myosin and
           actin provides the driving force. Rates of ATP
           hydrolysis and consequently the speed of movement along
           actin filaments vary widely, from about 0.04 micrometer
           per second for myosin I to 4.5 micrometer per second for
           myosin II in skeletal muscle. Myosin II moves in
           discrete steps about 5-10 nm long and generates 1-5
           piconewtons of force. Upon ATP binding, the myosin head
           dissociates from an actin filament. ATP hydrolysis
           causes the head to pivot and associate with a new actin
           subunit. The release of Pi causes the head to pivot and
           move the filament (power stroke). Release of ADP
           completes the cycle..
          Length = 653

 Score = 31.1 bits (70), Expect = 0.83
 Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 59  FQKRRRKVIAHSKNRIGMTIVVCLVIYIILAIRIIQYGNIHPEPIAPSMNIDEYGMSRPD 118
           F K + + I      IG T      +Y ILA  I+  G+I    +A     D+  +S   
Sbjct: 234 FYKDQFEQIEQCFRVIGFTDEEVGSVYRILA-AILNLGDIEFGSVASEHQTDKSRVSNVA 292

Query: 119 IIDRNGEILATDIPTFSLYVEPHKVISPDEII 150
            ++    +L          +  H V++  E I
Sbjct: 293 ALENAASLLCIRSDELQEALTSHCVVTRGETI 324


>gnl|CDD|119431 cd05171, PIKKc_ATM, Ataxia telangiectasia mutated (ATM), catalytic
           domain; The ATM catalytic domain subfamily is part of a
           larger superfamily that includes the catalytic domains
           of other kinases such as the typical
           serine/threonine/tyrosine protein kinases (PKs),
           aminoglycoside phosphotransferase, choline kinase, and
           RIO kinases. ATM is a member of the phosphoinositide
           3-kinase-related protein kinase (PIKK) subfamily. PIKKs
           have intrinsic serine/threonine kinase activity and are
           distinguished from other PKs by their unique catalytic
           domain, similar to that of lipid PI3K, and their large
           molecular weight (240-470 kDa). ATM contains a FAT
           (FRAP, ATM and TRRAP) domain, a catalytic domain, and a
           FATC domain at the C-terminus. ATM is critical in the
           response to DNA double strand breaks (DSBs) caused by
           radiation. It is activated at the site of a DSB and
           phosphorylates key substrates that trigger pathways that
           regulate DNA repair and cell cycle checkpoints at the
           G1/S, S phase, and G2/M transition. Patients with the
           human genetic disorder Ataxia telangiectasia (A-T),
           caused by truncating mutations in ATM, show genome
           instability, increased cancer risk, immunodeficiency,
           compromised mobility, and neurodegeneration. A-T
           displays clinical heterogeneity, which is correlated to
           the degree of retained ATM activity..
          Length = 279

 Score = 29.9 bits (68), Expect = 2.0
 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 7/32 (21%)

Query: 372 QNRILTIPEI--FRYSSNIGAAQIADAMGIQG 401
           Q +IL +PE   FR + +     I D MGI G
Sbjct: 213 QGKILPVPETVPFRLTRD-----IVDGMGITG 239


>gnl|CDD|144524 pfam00957, Synaptobrevin, Synaptobrevin. 
          Length = 89

 Score = 29.8 bits (68), Expect = 2.2
 Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 44 NLCQKGCHMEDGQDLFQKRRRKV-----IAHSKNRIGMTIVVCLVIYIILAI 90
           L  K  +++     F+K+ RK+       + K +I + ++V ++I II+ +
Sbjct: 35 ELVDKTENLQSQAQQFRKQARKLKRKMWWKNMKLKIILGLIVLILILIIIIV 86


>gnl|CDD|143914 pfam00144, Beta-lactamase, Beta-lactamase.  This family appears to
           be distantly related to pfam00905 and PF00768
           D-alanyl-D-alanine carboxypeptidase.
          Length = 327

 Score = 29.0 bits (65), Expect = 3.9
 Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 11/64 (17%)

Query: 326 IFEMGSIFKVFT---IAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYHPQNRILTIPEIF 382
           +F + S+ K FT   +   ++ G   + D         V K++          +T+ ++ 
Sbjct: 49  LFRIASVTKTFTAAAVLALVERGKLDLDD--------PVSKYLPEFAGSGKGGVTLRDLL 100

Query: 383 RYSS 386
            ++S
Sbjct: 101 THTS 104


>gnl|CDD|48199 cd03324, rTSbeta_L-fuconate_dehydratase, Human rTS beta is encoded
           by the rTS gene which, through alternative RNA splicing,
           also encodes rTS alpha whose mRNA is complementary to
           thymidylate synthase mRNA. rTS beta expression is
           associated with the production of small molecules that
           appear to mediate the down-regulation of thymidylate
           synthase protein by a novel intercellular signaling
           mechanism. A member of this family, from Xanthomonas,
           has been characterized to be a L-fuconate dehydratase.
           rTS beta belongs to the enolase superfamily of enzymes,
           characterized by the presence of an enolate anion
           intermediate which is generated by abstraction of the
           alpha-proton of the carboxylate substrate by an active
           site residue and is stabilized by coordination to the
           essential Mg2+ ion..
          Length = 415

 Score = 29.1 bits (65), Expect = 4.0
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 160 LDSEMIRRKLSSETKFQWLRRKLSPQQQKRILSFGLPGVGFRLE--KSRFYPAASHASHV 217
           L  +M   +L S   F+++   L+P++   IL  G PG   R     +  YPA + ++  
Sbjct: 133 LLVDMTPEELVSCIDFRYITDALTPEEALEILRRGQPGKAAREADLLAEGYPAYTTSAGW 192

Query: 218 VGYVD 222
           +GY D
Sbjct: 193 LGYSD 197


>gnl|CDD|176331 cd01255, PH_TIAM, TIAM Pleckstrin homology (PH) domain.  TIAM
           Pleckstrin homology (PH) domain. TIAM (T-cell invasion
           and metastasis) is a guanine nucleotide exchange factor
           specific for RAC1. It consists of an N-terminal PH
           domain followed by  Raf-like ras binding domain(RDB), a
           PDZ domain, a RhoGEF (DH) domain and a PH domain. PH
           domains share little sequence conservation, but all have
           a common fold, which is electrostatically polarized. PH
           domains also have diverse functions. They are often
           involved in targeting proteins to the plasma membrane,
           but few display strong specificity in lipid binding.
           Any specificity is usually determined by loop regions or
           insertions in the N-terminus of the domain, which are
           not conserved across all PH domains. This subfamily
           contains the alignment of the PH domain that follows the
           DH domain.
          Length = 160

 Score = 28.7 bits (64), Expect = 4.2
 Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 19/107 (17%)

Query: 405 FLYRLGLLSKLETELPEIQAPSYPSQWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGR 464
            +Y+  L  K + +L  +   +  ++          F   +  T LQ   ++AA +    
Sbjct: 62  LVYKERL--KQKKKLMGVSRKNATNEVD-----PFRFRVLIPVTALQVRASSAADMESNF 114

Query: 465 LIPPTFMIRSREESEKVSRIVL---------KKNTVKTMRSLLREGV 502
           L     +I  + E E     V          +   +KT+RS+LRE V
Sbjct: 115 LWE---LIHLKSELEGRPEKVFVLCCSTAESRNAFLKTIRSILRESV 158


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

 Score = 28.8 bits (64), Expect = 4.8
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 21/104 (20%)

Query: 100 PEPIAPSMN-----IDEYGMSRPDIIDRNGEILATDIPTFSLYVEPHKVISPDEIIEKLQ 154
           PE IA  +      + E      + I  +  I   +      ++E  K +SP++ +E   
Sbjct: 208 PEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVE--- 264

Query: 155 IVLPNLDSEMIRRKLSSETKFQWLRRKLSPQQQKRI-LSFGLPG 197
                       R+   E   + L   L+ ++++ I L FGL  
Sbjct: 265 ------------RESLKEDLNEVLAEALTERERRVIRLRFGLDD 296


>gnl|CDD|38006 KOG2795, KOG2795, KOG2795, Catalytic subunit of the meiotic double
           strand break transesterase [Replication, recombination
           and repair].
          Length = 372

 Score = 28.7 bits (64), Expect = 5.0
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 3/101 (2%)

Query: 179 RRKLSPQQQKRILSFGLPGVGF-RLEKSRFYPAASHASHVVGYVDIDNRGITGIEKFLDM 237
            + L  +Q   + S  L  V   R+E          A      + + NR  +      D+
Sbjct: 4   AQGLGGRQSLTLNSNDLSAVVLARIEDFVLSVLVQLARPEGFSLSVINRKRSNSLSSPDL 63

Query: 238 QGLTRV--FTTNKGEKNLQPIRLALDLRIQNIVHQELVENK 276
             L      T      + +  + A+ LR+  IVH+ L   K
Sbjct: 64  DTLVSKSHNTLRFTFSSKKAKKFAILLRVLEIVHELLELGK 104


>gnl|CDD|30609 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
           metabolism].
          Length = 485

 Score = 27.9 bits (62), Expect = 7.9
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 18/78 (23%)

Query: 526 KVIKKRYSDTLNFNSFLAVF--PTTDPQYIVLSFMDSPKIKERNQL--------TAGINV 575
           +V+ ++  + L   + LAV       P+ IVL +    K K+   L        + GI++
Sbjct: 205 EVLDEKDLEKLGMGALLAVGKGSARPPRLIVLEYNGKGKAKKPIALVGKGITFDSGGISI 264

Query: 576 APMVGNIIRRSASMLGVK 593
            P        +A M  +K
Sbjct: 265 KP--------AAGMDTMK 274


  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
   0.322    0.138    0.401 

Gapped
Lambda     K      H
   0.267   0.0813    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,391,283
Number of extensions: 409013
Number of successful extensions: 1004
Number of sequences better than 10.0: 1
Number of HSP's gapped: 982
Number of HSP's successfully gapped: 26
Length of query: 598
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 499
Effective length of database: 4,124,446
Effective search space: 2058098554
Effective search space used: 2058098554
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: 60 (26.7 bits)