RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781206|ref|YP_003065619.1| hypothetical protein
CLIBASIA_05565 [Candidatus Liberibacter asiaticus str. psy62]
         (1246 letters)



>gnl|CDD|163023 TIGR02794, tolA_full, TolA protein.  TolA couples the inner
           membrane complex of itself with TolQ and TolR to the
           outer membrane complex of TolB and OprL (also called
           Pal). Most of the length of the protein consists of
           low-complexity sequence that may differ in both length
           and composition from one species to another,
           complicating efforts to discriminate TolA (the most
           divergent gene in the tol-pal system) from paralogs such
           as TonB. Selection of members of the seed alignment and
           criteria for setting scoring cutoffs are based largely
           conserved operon struction. //The Tol-Pal complex is
           required for maintaining outer membrane integrity. Also
           involved in transport (uptake) of colicins and
           filamentous DNA, and implicated in pathogenesis.
           Transport is energized by the proton motive force. TolA
           is an inner membrane protein that interacts with
           periplasmic TolB and with outer membrane porins ompC,
           phoE and lamB.
          Length = 346

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 20/84 (23%)

Query: 388 LKQATVLARANAQEEKQRREQEAKEKAD-----------------REKADKEAKEKADRE 430
             +A   A+  A+E K++ E EAK KA+                 + KA  EA  KA+ E
Sbjct: 157 KAKAAAEAKKKAEEAKKKAEAEAKAKAEAEAKAKAEEAKAKAEAAKAKAAAEAAAKAEAE 216

Query: 431 KADK---DLQEKTPIKAEGDDFGL 451
            A     + + K      GD FGL
Sbjct: 217 AAAAAAAEAERKADEAELGDIFGL 240



 Score = 38.7 bits (90), Expect = 0.011
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAE 445
           +Q  +  RA A++  ++ EQ AK+  +++K  +EAK K   E   K   E      E
Sbjct: 90  RQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAERKAKE 146



 Score = 33.3 bits (76), Expect = 0.37
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 389 KQATVLARANAQEEKQRREQ-EAKEKAD--REKADKEAKEKADREKADKDLQEKTPIKAE 445
           ++A   A   A+EE + +   EAK+KA+  ++KA+ EAK KA+ E   K   E+   KAE
Sbjct: 142 RKAKEEAAKQAEEEAKAKAAAEAKKKAEEAKKKAEAEAKAKAEAEA--KAKAEEAKAKAE 199



 Score = 32.1 bits (73), Expect = 0.88
 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 387 ELKQATVLARANAQEEKQRREQEAKEKADREKADK---EAKEKADREKADK 434
           E K     A+A A+  K +   EA  KA+ E A     EA+ KAD  +   
Sbjct: 186 EAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKADEAELGD 236



 Score = 29.8 bits (67), Expect = 4.1
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 387 ELKQATVLARANAQEEKQRREQEA--KEKADREKADKEAKEKADREKADKDLQEKTPIKA 444
           +  +     +  A+E K ++  EA  K +A+ E+  KE   K   E+A      +   KA
Sbjct: 109 QAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAERKAKEEAAKQAEEEAKAKAAAEAKKKA 168

Query: 445 E 445
           E
Sbjct: 169 E 169



 Score = 29.4 bits (66), Expect = 5.6
 Identities = 8/44 (18%), Positives = 26/44 (59%)

Query: 396 RANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEK 439
           +A   E+++  EQ  +++ ++  A ++A ++A++     + ++K
Sbjct: 76  QAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQK 119



 Score = 29.0 bits (65), Expect = 8.5
 Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKA--DKDLQEKTPIKAEG 446
           KQA       A E K + E EA+ KA  E+A K+A+E+A  + A   K   E+   KAE 
Sbjct: 119 KQAEEAKAKQAAEAKAKAEAEAERKAK-EEAAKQAEEEAKAKAAAEAKKKAEEAKKKAEA 177

Query: 447 D 447
           +
Sbjct: 178 E 178


>gnl|CDD|181920 PRK09510, tolA, cell envelope integrity inner membrane protein
           TolA; Provisional.
          Length = 387

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 34/119 (28%), Positives = 47/119 (39%), Gaps = 6/119 (5%)

Query: 341 QIKQLRDLASKVKADYH-WAEIRHGNRFKAETRLAYSTIANVANFTSELKQATVLARANA 399
           + K+    A K  A+    AE     +  AE +      A         K+A   A+  A
Sbjct: 152 EAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKA 211

Query: 400 QEE-KQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEG--DDFGLGLPS 455
             E K++   EAK  A   KA  EAK  A++  A K  ++    KA    DD   GL S
Sbjct: 212 AAEAKKKAAAEAKAAA--AKAAAEAKAAAEKAAAAKAAEKAAAAKAAAEVDDLFGGLDS 268



 Score = 32.5 bits (74), Expect = 0.72
 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKAD-REKADKEAKEKAD-----REKADKDLQEKTPI 442
           KQA   A+  A ++KQ  E  AK  A  + KA+ EAK  A        +A K  + +   
Sbjct: 118 KQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAK 177

Query: 443 KAEGD 447
           KA  +
Sbjct: 178 KAAAE 182



 Score = 29.8 bits (67), Expect = 5.2
 Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 396 RANAQEEKQRREQEAKEKADREKADKEAKEKADRE-KADKDLQEK 439
           R  AQE+K++ E+ AK+ A ++K  +EA  KA    KA  + + K
Sbjct: 110 RLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAK 154



 Score = 29.0 bits (65), Expect = 7.8
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAE 445
           KQA    R    E+++   QE K++A+ E A + A ++   E+A          KAE
Sbjct: 95  KQAAEQERLKQLEKERLAAQEQKKQAE-EAAKQAALKQKQAEEAAAKAAAAAKAKAE 150


>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
          Length = 2084

 Score = 39.0 bits (90), Expect = 0.008
 Identities = 50/230 (21%), Positives = 106/230 (46%), Gaps = 14/230 (6%)

Query: 397  ANAQEEKQRREQEAKEKADREKADKEAKEKAD--REKADKDLQEKTPIKAEGDDFGLGLP 454
            A  + E+ ++  EAK+KA+  K   EAK+KA+  ++KAD + ++    K + D+      
Sbjct: 1462 AKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKAD-EAKKAAEAKKKADEAKKAEE 1520

Query: 455  SVPTHSVKLPPKEEELEEVK--------DEGKKGKEPGTTETDDREETERKNQDILDNSL 506
            +      K   + ++ +E K        DE KK +E    E   + E  +K ++  + +L
Sbjct: 1521 AKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMAL 1580

Query: 507  LAGKTHTKNETPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGI-KLTK 565
               +   K E   I        +  K   ++  + +  K  A ++   E +   + +L K
Sbjct: 1581 RKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKK 1640

Query: 566  KEKELQEQEENLRVAEIIQQSRMQSEDLQEKAWDSYKEWKSLSPDEIKQR 615
            KE E +++ E L+ AE  +++++++ +  +KA +  K+ +     E  ++
Sbjct: 1641 KEAEEKKKAEELKKAE--EENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK 1688



 Score = 35.5 bits (81), Expect = 0.093
 Identities = 46/218 (21%), Positives = 89/218 (40%), Gaps = 26/218 (11%)

Query: 397  ANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPSV 456
            A  + E++++  EAK+KA+  K   EAK+KA+  K  ++ ++K     + D+        
Sbjct: 1423 AKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE- 1481

Query: 457  PTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQDILDNSLLAGKTHTKNE 516
               + +   K EE ++  DE KK  E      + ++  E K  D    +  A K     +
Sbjct: 1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Query: 517  TPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIKLTKKEKELQEQEEN 576
                  A     +  K  + KK ++++                  K  + +K  +++   
Sbjct: 1542 AEEKKKAD----ELKKAEELKKAEEKK------------------KAEEAKKAEEDKNMA 1579

Query: 577  LRVAEIIQQSRMQSEDLQEKAWDSYKEWKSLSPDEIKQ 614
            LR AE  +++    E   E+    Y+E K +  +E K+
Sbjct: 1580 LRKAEEAKKAE---EARIEEVMKLYEEEKKMKAEEAKK 1614



 Score = 35.1 bits (80), Expect = 0.12
 Identities = 51/223 (22%), Positives = 92/223 (41%), Gaps = 27/223 (12%)

Query: 385  TSELKQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKA 444
              E K+    A+  A+E+K+  E + K + D++KAD+  K  A ++KAD + ++K   K 
Sbjct: 1373 KEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKAD-EAKKKAEEKK 1431

Query: 445  EGDDFGLGLPSVPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQDILDN 504
            + D+                 K EE ++  +  KK +E    E   ++  E K  D    
Sbjct: 1432 KADE--------------AKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKK 1477

Query: 505  SLLAGKTHTKNETPAIPTAKAPPAQAHKGIQDKKPQDQ----REKPLASDIGVGESDYAG 560
                 K   + +  A   AK    +A K  + KK  D+     E   A +    E     
Sbjct: 1478 KAEEAKKADEAKKKA-EEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEE---- 1532

Query: 561  IKLTKKEKELQEQEENLRVAEIIQQSRMQSEDLQEKAWDSYKE 603
                KK  E ++ EE  +  E+ +   ++  + ++KA ++ K 
Sbjct: 1533 ---AKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKA 1572



 Score = 34.7 bits (79), Expect = 0.16
 Identities = 48/204 (23%), Positives = 87/204 (42%), Gaps = 26/204 (12%)

Query: 401  EEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPSVPTHS 460
            EE +++   AK+KA+  K   EA +     +A  D  E    KAE  +            
Sbjct: 1325 EEAKKKADAAKKKAEEAKKAAEAAKA--EAEAAADEAEAAEEKAEAAEK----------- 1371

Query: 461  VKLPPKEEELEEVKDEGKKGKEP--GTTETDDREETERKNQDILDNSLLAGKTHTKNETP 518
                 K+EE ++  D  KK  E      E   + E ++K  D L  +  A K   + +  
Sbjct: 1372 -----KKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK 1426

Query: 519  AIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIKLTKKEKELQEQEENLR 578
            A    KA   +A K  ++ K  D+ +K  A +    E      +  KK  E +++ E  +
Sbjct: 1427 AEEKKKA--DEAKKKAEEAKKADEAKKK-AEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Query: 579  VAEIIQQSRMQSEDLQEKAWDSYK 602
             A+   +++ ++E+ ++KA ++ K
Sbjct: 1484 KAD---EAKKKAEEAKKKADEAKK 1504



 Score = 34.7 bits (79), Expect = 0.16
 Identities = 59/290 (20%), Positives = 118/290 (40%), Gaps = 33/290 (11%)

Query: 340  DQIKQLRDLASKVKADYHWAEIR--HGNRFKAETRLAYSTIANVANFTSELKQATVLARA 397
            ++ K+  + A K + + +  EIR     R     R   +  A  A    ELK+A    +A
Sbjct: 1233 EEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKA 1292

Query: 398  NA--QEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPS 455
            +   + E++++  EAK+KA+  K   EAK+KA+  K   D  +K   +A+          
Sbjct: 1293 DEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAA------- 1345

Query: 456  VPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQDILDNSLLAGKTHTK- 514
                  +     +E E  +++ +  ++         +  ++K ++         K     
Sbjct: 1346 -EAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDK 1404

Query: 515  ---NETPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIKLTKKEKELQ 571
               +E      AK    +A K  ++KK  D+ +K         E      +  KK +E +
Sbjct: 1405 KKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK-------AEEAKKADEAKKKAEEAK 1457

Query: 572  EQEENLRVAEIIQQSRMQSEDLQEKAWDSYKEWKSLSPDEIKQRFQKYAK 621
            + EE  + AE       ++++ ++KA ++ K       DE K++ ++  K
Sbjct: 1458 KAEEAKKKAE----EAKKADEAKKKAEEAKK------ADEAKKKAEEAKK 1497



 Score = 31.6 bits (71), Expect = 1.3
 Identities = 46/203 (22%), Positives = 84/203 (41%), Gaps = 8/203 (3%)

Query: 387  ELKQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTP--IKA 444
            E K+A     A  +E  +  E+E K KA+  K  +EAK KA+  K  ++ ++K     K 
Sbjct: 1585 EAKKAE---EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKK 1641

Query: 445  EGDDFGLGLPSVPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDR--EETERKNQDIL 502
            E ++                   EE ++ +++ KK +E    E D++   E  +K  +  
Sbjct: 1642 EAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEA 1701

Query: 503  DNSLLAGKTHTKNETPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIK 562
              +    K   + +  A    KA      K  + KK + + +K  A +    E +   I 
Sbjct: 1702 KKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKK-EAEEDKKKAEEAKKDEEEKKKIA 1760

Query: 563  LTKKEKELQEQEENLRVAEIIQQ 585
              KKE+E + +E       +I++
Sbjct: 1761 HLKKEEEKKAEEIRKEKEAVIEE 1783


>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
          Length = 567

 Score = 37.2 bits (86), Expect = 0.025
 Identities = 35/118 (29%), Positives = 49/118 (41%), Gaps = 28/118 (23%)

Query: 387 ELKQATVLARANAQEEKQRREQEAKEKADREKADK-------EAKEKADRE--------- 430
           EL++A    R   + E++ R+Q AK K +RE+  K       EA E A R          
Sbjct: 4   ELRRA----REKLEREQRERKQRAKLKLERERKAKEEAAKQREAIEAAQRSRRLDAIEAQ 59

Query: 431 -KADKDLQEKTPIKAEGDDFGLGLPSV----PTHSVKLPPKEEELEEVKDEGKKGKEP 483
            KAD+ +QE       G  F     +V        +KLPP      E+ D+G   K P
Sbjct: 60  IKADQQMQESL-QAGRGIVFSRIFEAVSFQGNGDKIKLPP--SCFTELSDQGAFDKGP 114


>gnl|CDD|178963 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
          Length = 627

 Score = 36.2 bits (85), Expect = 0.049
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 10/61 (16%)

Query: 395 ARANAQEEKQRREQ-EAKEKADR-----EKADKEAKEK---ADREKADKDLQE-KTPIKA 444
           A ANA+E+K+R+E  EA+ +AD      EK  KE  +K    ++EK +  ++E K  +K 
Sbjct: 512 AEANAEEDKKRKELVEARNQADSLIYQTEKTLKELGDKVPADEKEKIEAAIKELKEALKG 571

Query: 445 E 445
           E
Sbjct: 572 E 572


>gnl|CDD|183863 PRK13107, PRK13107, preprotein translocase subunit SecA; Reviewed.
          Length = 908

 Score = 35.3 bits (81), Expect = 0.092
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 386 SELKQATVLARANAQE-EKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKA 444
           S L +  V A+++ +E E +RRE++AK + D + A  EA      E     L   TP+  
Sbjct: 824 SVLSKVQVQAQSDVEEMEARRREEDAKIQRDYQHAAAEAL--VGGEDESAALAAHTPMIR 881

Query: 445 EGDDFGLGLP 454
           +G+  G   P
Sbjct: 882 DGEKVGRNDP 891


>gnl|CDD|162816 TIGR02350, prok_dnaK, chaperone protein DnaK.  Members of this
           family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
           chaperone system. All members of the seed alignment were
           taken from completely sequenced bacterial or archaeal
           genomes and (except for Mycoplasma sequence) found
           clustered with other genes of this systems. This model
           excludes DnaK homologs that are not DnaK itself, such as
           the heat shock cognate protein HscA (TIGR01991).
           However, it is not designed to distinguish among DnaK
           paralogs in eukaryotes. Note that a number of dnaK genes
           have shadow ORFs in the same reverse (relative to dnaK)
           reading frame, a few of which have been assigned
           glutamate dehydrogenase activity. The significance of
           this observation is unclear; lengths of such shadow ORFs
           are highly variable as if the presumptive protein
           product is not conserved.
          Length = 595

 Score = 35.0 bits (81), Expect = 0.12
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 377 TIANVANFT-SELKQATVLARANAQEEKQRREQ-EAKEKADR-----EKADKEAKEKADR 429
           TI   +  +  E+++    A ANA+E+K+R+E+ EA+  AD      EK  KEA +K   
Sbjct: 491 TITASSGLSEEEIERMVKEAEANAEEDKKRKEEIEARNNADSLAYQAEKTLKEAGDKLPA 550

Query: 430 EKADK 434
           E+ +K
Sbjct: 551 EEKEK 555


>gnl|CDD|183545 PRK12472, PRK12472, hypothetical protein; Provisional.
          Length = 508

 Score = 34.8 bits (80), Expect = 0.14
 Identities = 30/95 (31%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 338 TYDQIKQLRDLASKVKADYHWAEIRHGNRFKA--ETRLAYSTIANVANFTSELKQATVLA 395
             D+ K     A++  A    A +R   R KA  +  L  +  A  A  T E       A
Sbjct: 205 AADEAKTAAAAAAREAAPLK-ASLRKLERAKARADAELKRADKALAAAKTDE-------A 256

Query: 396 RANAQEEKQRREQEAKEKADR---EKADKEAKEKA 427
           +A A+E +Q+  Q+A E A +    KAD EAK  A
Sbjct: 257 KARAEERQQKAAQQAAEAATQLDTAKADAEAKRAA 291


>gnl|CDD|149170 pfam07946, DUF1682, Protein of unknown function (DUF1682).  The
           members of this family are all hypothetical eukaryotic
           proteins of unknown function. One member is described as
           being an adipocyte-specific protein, but no evidence of
           this was found.
          Length = 322

 Score = 34.5 bits (80), Expect = 0.15
 Identities = 12/62 (19%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 384 FTSELKQATVLARANA------QEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQ 437
            + E+ +     R           E++R+E+  ++K +++K ++EAK      +  +  +
Sbjct: 253 LSPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKYE 312

Query: 438 EK 439
           EK
Sbjct: 313 EK 314



 Score = 30.3 bits (69), Expect = 3.2
 Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 387 ELKQATVLARANAQEEKQRREQEAKEKADREKADK-EAKEKADREK 431
           E ++         +++K+ RE +   K   E+  K E KE+    +
Sbjct: 277 EEERQEEAQEKKEEKKKEEREAK-LAKLSPEEQRKYEEKERKKEAR 321


>gnl|CDD|179887 PRK04863, mukB, cell division protein MukB; Provisional.
          Length = 1486

 Score = 34.2 bits (79), Expect = 0.21
 Identities = 19/106 (17%), Positives = 39/106 (36%), Gaps = 9/106 (8%)

Query: 863 ERSLKNQAHLNAEVERLSGLAQQPSDSTADLKELQ----TQLSRAKKYKESNDERIVSFI 918
           E+ L+ Q      +        +  D   +L++LQ     +L    +      ER     
Sbjct: 526 EQRLRQQQRAERLLAEFCKRLGKNLDDEDELEQLQEELEARLESLSESVSEARER----- 580

Query: 919 RSEFEREIKELKSVIEADAKENPNPNKNQKKLQKTREKLVAQLSSR 964
           R    +++++L++ I+  A   P     Q  L + RE+   +    
Sbjct: 581 RMALRQQLEQLQARIQRLAARAPAWLAAQDALARLREQSGEEFEDS 626


>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein.  Function of MutS2 is
           unknown. It should not be considered a DNA mismatch
           repair protein. It is likely a DNA mismatch binding
           protein of unknown cellular function.
          Length = 771

 Score = 33.3 bits (76), Expect = 0.36
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 13/93 (13%)

Query: 402 EKQRREQEAKEKADREKADKEAKE-----KADREKADKDLQEKTPIKAEGDDFGLGLPSV 456
           E++  E + +E+  + + +KEA+E     K + E   ++L+EK   KA+       L  +
Sbjct: 549 EQEMEELKERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKL 608

Query: 457 PTHSVKLPPKEE--------ELEEVKDEGKKGK 481
                K+P K          +   ++  G+KGK
Sbjct: 609 KETKQKIPQKPTNFQADKIGDKVRIRYFGQKGK 641


>gnl|CDD|161867 TIGR00414, serS, seryl-tRNA synthetase.  This model represents the
           seryl-tRNA synthetase found in most organisms. This
           protein is a class II tRNA synthetase, and is recognized
           by the pfam model tRNA-synt_2b. The seryl-tRNA
           synthetases of two archaeal species, Methanococcus
           jannaschii and Methanobacterium thermoautotrophicum,
           differ considerably and are included in a different
           model.
          Length = 418

 Score = 33.5 bits (77), Expect = 0.37
 Identities = 28/120 (23%), Positives = 51/120 (42%), Gaps = 7/120 (5%)

Query: 385 TSELKQATVLARANAQEEKQRREQEAKE--KADREKADKEAKEKADREKADKDLQEKTP- 441
              L        +  +E + +R + +K+  KA  +K DK  + K + ++  ++L E +  
Sbjct: 32  LIALDDERKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAA 91

Query: 442 ---IKAEGDDFGLGLPSVPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKN 498
              ++AE  D  L +P++P  SV +   EE+  EVK  G              E  E+  
Sbjct: 92  LKALEAELQDKLLSIPNIPHESVPVGKDEEDNLEVKRWGTP-PVFDFKPKPHWELGEKLG 150


>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
           Provisional.
          Length = 482

 Score = 33.4 bits (77), Expect = 0.38
 Identities = 15/60 (25%), Positives = 35/60 (58%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDD 448
           K+AT   +   ++ +++RE+E KEK  +  A K+ +E+ + EK  K+ +++   +   ++
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465


>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR).  This
           family consists of several bovine specific leukaemia
           virus receptors which are thought to function as
           transmembrane proteins, although their exact function is
           unknown.
          Length = 561

 Score = 33.1 bits (75), Expect = 0.41
 Identities = 31/163 (19%), Positives = 61/163 (37%), Gaps = 16/163 (9%)

Query: 402 EKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPSVPTHSV 461
           EK+ ++ + KEK ++EK +++  +K + E     L       A          +   ++V
Sbjct: 196 EKKSKKPKKKEKKEKEK-ERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTV 254

Query: 462 KLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQDILDNSLLAGKTHTKNETPAIP 521
                + E +E KD           ET    + ++K Q          K H  +      
Sbjct: 255 SGTAPDSEPDEPKD-------AEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSD 307

Query: 522 TAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIKLT 564
                P      +Q+   +++   P++S   + E+ Y  IK+T
Sbjct: 308 GGAEQP------VQNGAVEEEPLPPMSSYKLLAENSY--IKMT 342



 Score = 30.4 bits (68), Expect = 3.3
 Identities = 48/237 (20%), Positives = 83/237 (35%), Gaps = 47/237 (19%)

Query: 402 EKQRREQEAKEKADREKADKEAKEKADREK------ADKDL---------QEKTPIKAEG 446
           E++RR ++  EK  REK  +E +++  R        +D+D+          E+ P  A  
Sbjct: 85  EEERRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENALP 144

Query: 447 DDFGLGLPSVP------------THSVKLP---------PKEEELEEVKDEGKKGKEPGT 485
            D     P+ P              S KLP          K  E  +V    KK K+P  
Sbjct: 145 SDEDDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKK 204

Query: 486 TETD----DREETERKNQDILDNSLLAGKTHTKNETPAIPTAKAPPAQAHKGIQDKKPQD 541
            E      +R++ ++K  +   + LLA      +        +A  A    G       D
Sbjct: 205 KEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSEPD 264

Query: 542 QREKPLASDIGVGESDYAGIKLTKKEKELQEQEENLRVAEIIQQSRMQSEDLQEKAW 598
           + +   A +              KK+K+ +E+EE  +  +        S+   E+  
Sbjct: 265 EPKDAEAEETKKSPK-------HKKKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQPV 314


>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
           This model represents a paralogous family of Plasmodium
           yoelii genes preferentially located in the subtelomeric
           regions of the chromosomes. There are no obvious
           homologs to these genes in any other organism.
          Length = 255

 Score = 33.3 bits (76), Expect = 0.41
 Identities = 32/115 (27%), Positives = 53/115 (46%), Gaps = 7/115 (6%)

Query: 851 IKEERYWTIYAFERSL---KNQAHLNAEVERLSGLAQQPSDSTADLKE---LQTQL-SRA 903
           I  ER   I+   R L    NQ  LN   +    LA Q +D   D KE   L+  + S  
Sbjct: 33  ICFERNIKIFRNNRILADADNQFDLNEFYQSTLSLANQFNDCNDDDKEIAHLRNIIDSHI 92

Query: 904 KKYKESNDERIVSFIRSEFEREIKELKSVIEADAKENPNPNKNQKKLQKTREKLV 958
           KK+KE N    ++ +  + ++ I +L+  +E   KE  N   ++  +Q   +K++
Sbjct: 93  KKHKERNTLPDLNNVDKKTKKLINKLQKELEELKKELDNEMNDELTIQPIHDKII 147


>gnl|CDD|180868 PRK07188, PRK07188, nicotinate phosphoribosyltransferase;
           Provisional.
          Length = 352

 Score = 33.0 bits (76), Expect = 0.48
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 11/69 (15%)

Query: 86  VIEAGLKDLKEVGDTLK--RLAETGEVILSDKSDRLLCRFMDMVETEDEHKINKQ----V 139
           VI   LK  +E GD LK  R+  +  +I     D+   R  +++ T D   +N +    +
Sbjct: 215 VITDSLKVAREFGDKLKGVRVDTSKNMI-----DKYFIRHPEVLGTFDPRGVNPELIKAL 269

Query: 140 RDALESAGF 148
           R AL+  G 
Sbjct: 270 RKALDENGG 278


>gnl|CDD|181442 PRK08476, PRK08476, F0F1 ATP synthase subunit B'; Validated.
          Length = 141

 Score = 32.4 bits (74), Expect = 0.73
 Identities = 15/61 (24%), Positives = 33/61 (54%)

Query: 379 ANVANFTSELKQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQE 438
           ++V+    E++     AR  A + +Q+   +AKE+A+++   K+A+ ++  E   K L  
Sbjct: 55  SDVSEIEHEIETILKNAREEANKIRQKAIAKAKEEAEKKIEAKKAELESKYEAFAKQLAN 114

Query: 439 K 439
           +
Sbjct: 115 Q 115


>gnl|CDD|180941 PRK07352, PRK07352, F0F1 ATP synthase subunit B; Validated.
          Length = 174

 Score = 32.2 bits (74), Expect = 0.90
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 13/72 (18%)

Query: 369 AETRLAYSTIANVANFTSELKQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKAD 428
           AE RL  +  A +A    +L QA        Q+E +R   +AK +A+  +A+ E +   D
Sbjct: 62  AEERLRQAAQA-LAEAQQKLAQA--------QQEAERIRADAKARAEAIRAEIEKQAIED 112

Query: 429 ----REKADKDL 436
               ++ A  DL
Sbjct: 113 MARLKQTAAADL 124


>gnl|CDD|178991 PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed.
          Length = 204

 Score = 31.7 bits (73), Expect = 1.1
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 12/66 (18%)

Query: 101 LKR---LAETGEVILSDKSDRLLCRFMDMVETEDEHKINKQVRDALESAGFDLESTQENI 157
           LKR   LAE G  +L DK D L+  F D+++        K++R+ +E     LE   ++ 
Sbjct: 16  LKRRLKLAERGHKLLKDKRDELIMEFFDILDE------AKKLREEVEEE---LEEAYKDF 66

Query: 158 RKVESA 163
               + 
Sbjct: 67  LMARAV 72


>gnl|CDD|115307 pfam06637, PV-1, PV-1 protein (PLVAP).  This family consists of
           several PV-1 (PLVAP) proteins which seem to be specific
           to mammals. PV-1 is a novel protein component of the
           endothelial fenestral and stomatal diaphragms. The
           function of this family is unknown.
          Length = 442

 Score = 31.9 bits (72), Expect = 1.1
 Identities = 28/92 (30%), Positives = 49/92 (53%), Gaps = 19/92 (20%)

Query: 394 LARANAQEEKQRRE--------QEAKEKADREKADKEAKEKADREKADK-DLQEKTPIKA 444
           +AR NA  ++Q+ E        QEAK KA++E   +EAK +A+  +  +  L+EK  ++A
Sbjct: 297 VARENADLQRQKLEAEQAAQAAQEAKAKAEKEAQAREAKLQAECARQTQLALEEKAALRA 356

Query: 445 EGDDFGLGLPSVPTHSVKLPPKEEELEEVKDE 476
           E D+           + +L  K+ E E+++ E
Sbjct: 357 ERDNL----------AKELEAKKREAEQLRME 378


>gnl|CDD|163388 TIGR03674, fen_arch, flap structure-specific endonuclease.
           Endonuclease that cleaves the 5'-overhanging flap
           structure that is generated by displacement synthesis
           when DNA polymerase encounters the 5'-end of a
           downstream Okazaki fragment. Has 5'-endo-/exonuclease
           and 5'-pseudo-Y-endonuclease activities. Cleaves the
           junction between single and double-stranded regions of
           flap DNA.
          Length = 338

 Score = 31.8 bits (73), Expect = 1.2
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 387 ELKQATVLARANAQEEKQRREQEAKEKADREKADKEAK 424
           ELK  T+  R   +EE + + +EA EK D E+A K A+
Sbjct: 85  ELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQ 122



 Score = 29.1 bits (66), Expect = 8.2
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 3/35 (8%)

Query: 400 QEEKQRREQEAKEKADREKADKEAKEKADREKADK 434
            E  + R +E +E+A  E+  +EA EK D E+A K
Sbjct: 88  AETLEER-REIREEA--EEKWEEALEKGDLEEARK 119


>gnl|CDD|185669 PTZ00491, PTZ00491, major vault protein; Provisional.
          Length = 850

 Score = 31.5 bits (72), Expect = 1.3
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 397 ANAQEEKQRREQEAKEKADREKADKEAKEKADREK 431
           A A+ + +  EQEA+ + +R+K   +AK +  R K
Sbjct: 666 AAARHQAELLEQEARGRLERQKMHDKAKAEEQRTK 700



 Score = 31.1 bits (71), Expect = 1.8
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 8/53 (15%)

Query: 386 SELKQATVLARA-----NAQEEKQRREQEAKEKADREKADKE---AKEKADRE 430
           +E++QA + A+A      A+ EK R+ QE + + ++ + + E   AKE AD E
Sbjct: 734 AEVEQAELRAKALRIEAEAELEKLRKRQELELEYEQAQNELEIAKAKELADIE 786


>gnl|CDD|180665 PRK06707, PRK06707, amidase; Provisional.
          Length = 536

 Score = 31.4 bits (71), Expect = 1.3
 Identities = 19/76 (25%), Positives = 38/76 (50%)

Query: 896 LQTQLSRAKKYKESNDERIVSFIRSEFEREIKELKSVIEADAKENPNPNKNQKKLQKTRE 955
           +    S+ K     + E I++F + + +R IK  +++IEA  K     ++ +K +Q ++E
Sbjct: 394 VNDYFSQQKNVPVKSLEEIIAFNKKDSKRRIKYGQTLIEASEKSAITKDEFEKVVQTSQE 453

Query: 956 KLVAQLSSRLKELNID 971
               +L   L E  +D
Sbjct: 454 NAKKELDRYLVEKGLD 469


>gnl|CDD|179693 PRK03980, PRK03980, flap endonuclease-1; Provisional.
          Length = 292

 Score = 31.7 bits (73), Expect = 1.4
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 386 SELKQATVLARANAQEEKQRREQEAKEKADREKADKEAK 424
            ELK   +  R   +EE + + +EAKE+ D E+A K A+
Sbjct: 37  PELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQ 75


>gnl|CDD|177950 PLN02316, PLN02316, synthase/transferase.
          Length = 1036

 Score = 31.4 bits (71), Expect = 1.4
 Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 9/48 (18%)

Query: 401 EEKQRR-EQEAKEKADREKADKE--------AKEKADREKADKDLQEK 439
           EEK+R  E+ AKE+A+RE+  +E        A  +ADR +A  +++++
Sbjct: 252 EEKRRELEKLAKEEAERERQAEEQRRREEEKAAMEADRAQAKAEVEKR 299


>gnl|CDD|183692 PRK12704, PRK12704, phosphodiesterase; Provisional.
          Length = 520

 Score = 31.3 bits (72), Expect = 1.5
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 395 ARANAQEEKQRREQEAKEKAD--REKADKEAKEK-ADREKADKDLQEK 439
           A+  A+  K+    EAKE+    R + +KE +E+  + +K +K L +K
Sbjct: 47  AKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQK 94



 Score = 29.4 bits (67), Expect = 6.1
 Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 4/47 (8%)

Query: 397 ANAQEEKQRREQEAKEKADREKADK--EAKEKAD--REKADKDLQEK 439
             A+EE +R  +EAK++A+  K +   EAKE+    R + +K+L+E+
Sbjct: 34  KEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRER 80



 Score = 29.0 bits (66), Expect = 7.6
 Identities = 13/55 (23%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 562 KLTKKEKELQEQEENL-RVAEIIQQSRMQSEDLQEKAWDSYKEWKSLSPDEIKQR 615
            L K+E+EL+++E+ L +  + +++   + E+L E+     +    L+ +E K+ 
Sbjct: 104 LLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEI 158


>gnl|CDD|148216 pfam06476, DUF1090, Protein of unknown function (DUF1090).  This
           family consists of several bacterial proteins of unknown
           function and is known as YqjC in E. coli.
          Length = 115

 Score = 31.1 bits (71), Expect = 1.7
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 370 ETRLAYSTIANVANFTSELKQATVLARANAQEEKQRREQEAK------EKADREKADKEA 423
           ET++ Y+      +  + L++A    +A+  +   R E++AK      E A+RE+  KEA
Sbjct: 30  ETQIEYAKAHGNQHRIAGLEKALKEVQAHCTDAGLRAERQAKVEEKEQEVAEREQELKEA 89

Query: 424 KEKADREKADK 434
           + K D +K +K
Sbjct: 90  QAKGDADKIEK 100


>gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 559

 Score = 31.0 bits (71), Expect = 2.0
 Identities = 27/110 (24%), Positives = 46/110 (41%), Gaps = 20/110 (18%)

Query: 882 LAQQPSDSTADLKELQTQLSRAKKYKESNDERIVSFIRSEFEREIKELKSVIEADAKENP 941
           L +Q + S     EL+  L R ++                 E+E+K+LK+     A E  
Sbjct: 357 LCEQAAASPEYDTELEVLLQRVEQ----------------LEQELKQLKAQPVGVAPEQK 400

Query: 942 NPNKNQKKLQKTREKL-VAQLSSRLKE---LNIDNAYGLWNEYKEDFKAS 987
              K +KK +K + K+   ++   LKE    +++    +W E  E  KA 
Sbjct: 401 EKKKEKKKNKKKKYKVPRGKIYKVLKEATRQDLELLKNVWGEILESLKAQ 450


>gnl|CDD|180874 PRK07194, fliG, flagellar motor switch protein G; Reviewed.
          Length = 334

 Score = 30.7 bits (70), Expect = 2.2
 Identities = 28/127 (22%), Positives = 61/127 (48%), Gaps = 9/127 (7%)

Query: 99  DTLKRLAETGEV--ILSDKSDRLLCRFMDMVETEDEHKIN--KQVRDALESAGFDLESTQ 154
           D L R+A+  +V   + D+ D L+ R + ++  +   K+   KQ  D +     D +   
Sbjct: 158 DILYRIAQLDDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADIINRFPGDRQQLM 217

Query: 155 ENIRKVESALINNNMKDAFRFLELAQKSKETADSHIIEAIDV---GTKLKENTPPTTFTS 211
           E +++ +  ++N    + + F  L+++S+ET    +++ + +      LK  T P    +
Sbjct: 218 EMLKEHDEEVVNEIEDNMYDFFILSRQSEETLQR-LMDEVPMELWAVALK-GTEPALRQA 275

Query: 212 ISKVLLK 218
           I +V+ K
Sbjct: 276 ILRVMPK 282


>gnl|CDD|150853 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3.  This
           protein, which interacts with both microtubules and
           TRAF3 (tumour necrosis factor receptor-associated factor
           3), is conserved from worms to humans. The N-terminal
           region is the microtubule binding domain and is
           well-conserved; the C-terminal 100 residues, also
           well-conserved, constitute the coiled-coil region which
           binds to TRAF3. The central region of the protein is
           rich in lysine and glutamic acid and carries KKE motifs
           which may also be necessary for tubulin-binding, but
           this region is the least well-conserved.
          Length = 506

 Score = 30.6 bits (69), Expect = 2.4
 Identities = 24/157 (15%), Positives = 58/157 (36%), Gaps = 6/157 (3%)

Query: 398 NAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPS-- 455
           + +EE++ +EQ  +EK  +++  KE  +    ++  K+ +     K +  +  +  P   
Sbjct: 102 SGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKE-KEKEKEKKVEEPRDR 160

Query: 456 -VPTHSVKLPPKE-EELEEVKDEGKKGKEPGTTETDDREETERKNQDILDNSLLAGKTHT 513
                  ++  K   +    K    K K+P   E   +   E       +  +   +   
Sbjct: 161 EEEKKRERVRAKSRPKKPPKKKPENKKKDPPEREKKKQASREAVKGKPEEPDVPEEREKE 220

Query: 514 KNETPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASD 550
           +++ P   T  +PP++  +  Q  +   +    L   
Sbjct: 221 EDDGPDPETNTSPPSE-DESRQSSEISRRSSGSLKKP 256


>gnl|CDD|179919 PRK05035, PRK05035, electron transport complex protein RnfC;
           Provisional.
          Length = 695

 Score = 30.7 bits (70), Expect = 2.7
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 10/47 (21%)

Query: 399 AQEEKQRREQEAKEKAD-------REKADKEAKEK---ADREKADKD 435
           A E+++++ +EAK + +       REKA +EA+ K     R   DKD
Sbjct: 440 AIEQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARAAKDKD 486


>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
           component YidC; Validated.
          Length = 429

 Score = 30.6 bits (69), Expect = 2.7
 Identities = 19/104 (18%), Positives = 34/104 (32%), Gaps = 2/104 (1%)

Query: 396 RANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLPS 455
            A   E K+ R  E  E   R+K   + +  A+RE  +++ +++                
Sbjct: 326 HAENAEIKKTRTAEKNEAKARKKEIAQKRRAAERE-INREARQERAAAMARARARRAAVK 384

Query: 456 VPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQ 499
                +       E    ++E  KG  P    T   E     +Q
Sbjct: 385 AKKKGLI-DASPNEDTPSENEESKGSPPQVEATTTAEPNREPSQ 427


>gnl|CDD|184062 PRK13455, PRK13455, F0F1 ATP synthase subunit B; Provisional.
          Length = 184

 Score = 30.5 bits (69), Expect = 3.0
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 386 SELKQATVLARANAQE---EKQRREQEAKEKADREKADKEAKEKADREKADKDLQE 438
           SEL++A  L R  AQ      +R+++E +E+ADR  A  + + +A  E+A  DL+ 
Sbjct: 65  SELEEARAL-REEAQTLLASYERKQREVQEQADRIVAAAKDEAQAAAEQAKADLEA 119


>gnl|CDD|149595 pfam08597, eIF3_subunit, Translation initiation factor eIF3
           subunit.  This is a family of proteins which are
           subunits of the eukaryotic translation initiation factor
           3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
           cerevisiae protein eIF3j has been shown to be required
           for processing of 20S pre-rRNA and binds to 18S rRNA and
           eIF3 subunits Rpg1p and Prt1p.
          Length = 242

 Score = 30.4 bits (69), Expect = 3.2
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 399 AQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAE 445
            +EEK ++  +AK K   +   +E KEKA REK +K L+E   I  E
Sbjct: 45  KEEEKAKKAAKAKAKKALKAKIEE-KEKAKREKEEKALRELEEITPE 90


>gnl|CDD|178775 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
          Length = 1465

 Score = 30.2 bits (68), Expect = 3.2
 Identities = 35/163 (21%), Positives = 58/163 (35%), Gaps = 21/163 (12%)

Query: 395  ARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGLP 454
            A+A    EK +R     E    +K  ++A +K   +K  K        KA   +      
Sbjct: 1173 AKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTK--------KASESE-----T 1219

Query: 455  SVPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDDREETERKNQDILDNSLLAGKTHTK 514
            +  T+       E   E VK +G+ G +         +E E +  D+ D        +  
Sbjct: 1220 TEETYGSSAMETENVAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKD----RLAAYNL 1275

Query: 515  NETPAIPTAKAPPAQAHKGIQDKKPQDQREKPLASDIGVGESD 557
            +  PA         +A       +    R+KPLAS   + +SD
Sbjct: 1276 DSAPAQSAKMEETVKA----VPARRAAARKKPLASVSVISDSD 1314


>gnl|CDD|185597 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
          Length = 651

 Score = 30.0 bits (68), Expect = 3.5
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 400 QEEKQRREQEAKEKADREKADKEAKEKADREK 431
           Q EK+ +E   ++K  R+   +E K+K + EK
Sbjct: 554 QREKEEKEALKEQKRLRKLKKQEEKKKKELEK 585


>gnl|CDD|150410 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
           Mitofilin controls mitochondrial cristae morphology.
           Mitofilin is enriched in the narrow space between the
           inner boundary and the outer membranes, where it forms a
           homotypic interaction and assembles into a large
           multimeric protein complex. The first 78 amino acids
           contain a typical amino-terminal-cleavable mitochondrial
           presequence rich in positive-charged and hydroxylated
           residues and a membrane anchor domain. In addition, it
           has three centrally located coiled coil domains.
          Length = 561

 Score = 30.1 bits (68), Expect = 3.6
 Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 17/106 (16%)

Query: 867 KNQAHLNAEVER--LSGLAQQPSDSTADLKELQTQLSRAKKYKESNDERIVSFIRSEFER 924
           K  A L AE E      L ++       L +L+ +L    + KE+  E+    +R EFER
Sbjct: 245 KKLAELKAEEEEELERALKEK---REELLSKLEEELLARLEEKEAALEKQ---LRLEFER 298

Query: 925 EIKELKSVIEADAKENPNPNKNQKKLQKTREKLVAQLSSRLKELNI 970
           E +EL+   E          K + +L++  E    +L + L E  I
Sbjct: 299 EKEELRKKYE---------EKLRTELERQAEAHEQKLKNELAEQAI 335


>gnl|CDD|151926 pfam11489, DUF3210, Protein of unknown function (DUF3210).  This is
           a family of proteins conserved in yeasts. The function
           is not known. The Schizosaccharomyces pombe member is
           the uncharacterized serine-rich protein C18E5.07 and the
           Saccharomyces cerevisiae member is the uncharacterized
           protein YIR003W.
          Length = 672

 Score = 29.9 bits (67), Expect = 3.8
 Identities = 28/140 (20%), Positives = 48/140 (34%), Gaps = 31/140 (22%)

Query: 466 KEEELEEVKDEGKKGKEPGTTETDDREETER---KNQDILDNSLLAGKTHTKNETPAIPT 522
           +E E    +DE +   +  T E+  R E E+    ++DI ++S  + +      TP+ P 
Sbjct: 377 EEYEPLFPEDESEIAVKKPTEESSRRPEEEKHRFPSEDIWEDSPSSLQLTATVSTPSNPP 436

Query: 523 AKAP--PAQAHKGIQDKKPQDQREKPLASDIGVGESDYAGIKLTKKEKELQEQEENLRVA 580
            +    P Q          +   E  L                 K E +    E      
Sbjct: 437 PRPSETPEQETS-------RSSSEVSLKPQ-----------SELKSEDKKARPE------ 472

Query: 581 EIIQQSRMQSEDLQEKAWDS 600
             + + R  S D+ E A +S
Sbjct: 473 --VSKQRFPSRDVWEDAPES 490


>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
            archaeal type.  SMC (structural maintenance of
            chromosomes) proteins bind DNA and act in organizing and
            segregating chromosomes for partition. SMC proteins are
            found in bacteria, archaea, and eukaryotes. It is found
            in a single copy and is homodimeric in prokaryotes, but
            six paralogs (excluded from this family) are found in
            eukarotes, where SMC proteins are heterodimeric. This
            family represents the SMC protein of archaea and a few
            bacteria (Aquifex, Synechocystis, etc); the SMC of other
            bacteria is described by TIGR02168. The N- and C-terminal
            domains of this protein are well conserved, but the
            central hinge region is skewed in composition and highly
            divergent.
          Length = 1164

 Score = 30.0 bits (68), Expect = 3.8
 Identities = 45/220 (20%), Positives = 87/220 (39%), Gaps = 18/220 (8%)

Query: 7    SIDYQTNNLDQDKIPSEDVAKTLTSIQDNIKHLREFIIAWSSDLNPHKDRYDYIVGPIEQ 66
             I+ + N L  +K   E   + L   + ++K   + I     +LN  K+  +  +  +E 
Sbjct: 816  EIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEA 875

Query: 67   RLKKVSERYERVVSRDLTLVIEAGLKDLKEVGDTLKRLAETGEVILSDKSDRLLCRFMDM 126
             L+ +  R   +      L  EA L++L+   + L+   E     LS+   +L     ++
Sbjct: 876  ALRDLESRLGDLKKERDEL--EAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEEL 933

Query: 127  VETEDEHKINKQVRDALESAGFDLESTQENIRKVESAL-----INNNMKDAF-----RFL 176
             E ED    ++++ +        LE  Q  +++VE  +     +N      +     R  
Sbjct: 934  SEIEDPKGEDEEIPEEE----LSLEDVQAELQRVEEEIRALEPVNMLAIQEYEEVLKRLD 989

Query: 177  ELAQKSK--ETADSHIIEAIDVGTKLKENTPPTTFTSISK 214
            EL +K    E     I+E I+   K K       F +I++
Sbjct: 990  ELKEKRAKLEEERKAILERIEEYEKKKREVFMEAFEAINE 1029


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 30.0 bits (68), Expect = 4.2
 Identities = 24/117 (20%), Positives = 54/117 (46%), Gaps = 10/117 (8%)

Query: 861 AFERSLKNQAHLNAEVERLSGLAQQPSDSTADLKELQTQLSRA-KKYKESNDERI----- 914
           A++   +    +   +ERL    ++  +    +KE + +L    ++  E + E       
Sbjct: 163 AYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREE 222

Query: 915 VSFIRSEFEREIKELKSVIEADAKENPNPNKNQKKLQ---KTREKLVAQLSSRLKEL 968
           +  +  E + E++ELK  IE   KE  +   +++KL+   +  E+ + +L   ++EL
Sbjct: 223 LEKLEKEVK-ELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEEL 278


>gnl|CDD|179218 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase; Validated.
          Length = 451

 Score = 29.7 bits (68), Expect = 4.4
 Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 246 KLRGLAFDHTYFNDKLNQFLKEIKNHQKEYDESEKGSSKARYHAAYAHIYW----DLAND 301
           +LRG  F ++         L  +++        E+G  +    A+Y H+++    D A  
Sbjct: 385 RLRGHEFHYSTLETPEEAPLYRVRDADGR-PLGEEGYRRGNVLASYLHLHFASNPDAAAR 443

Query: 302 WVN 304
           ++ 
Sbjct: 444 FLA 446


>gnl|CDD|161824 TIGR00335, primase_sml, DNA primase, eukaryotic-type, small subunit,
            putative.  This model is named putative because the
            assignment is putative for archaeal proteins. Eukaryotic
            proteins scoring above the trusted cutoff can be
            considered authentic.
          Length = 297

 Score = 29.9 bits (67), Expect = 4.4
 Identities = 20/110 (18%), Positives = 36/110 (32%), Gaps = 4/110 (3%)

Query: 918  IRSEFEREIKELKSVIEADAKENPNPNKNQKKLQKTREKLVAQLSSRLKELNIDNAYGLW 977
            +R     E      ++  + K   N N  ++ L +   K + +     K   + N    W
Sbjct: 162  LREIVRYERLRYPKIVRVE-KRFLNSNAVKRVLNRLLLKALEEEILTSKLKILPNDLRKW 220

Query: 978  NEYKEDFKAS--FEYP-LGTYEPAILGAMKDMDRLHPIYSVSKTIQKAGG 1024
               KE    S   +Y  L  Y   I+   K       +    K++ +  G
Sbjct: 221  KLIKEVIFKSEKKDYSALEIYIDKIVLDDKVTLDRIRLLRHPKSLHRVTG 270


>gnl|CDD|150933 pfam10337, DUF2422, Protein of unknown function (DUF2422).  This is
           a family of proteins conserved in fungi. The function is
           not known. This family is the C-terminal half of some
           member proteins which contain the DUF2421 pfam10334
           domain at their N-terminus.
          Length = 448

 Score = 29.6 bits (67), Expect = 4.6
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 10/68 (14%)

Query: 921 EFEREIKELKSVIEADAK-------ENPNPNKNQKKLQKTREKL---VAQLSSRLKELNI 970
                +  L+S ++   K        NP    N KKL+K   K+    A+L + L  L +
Sbjct: 221 GMAGILGLLRSALKLHTKFLATLEPSNPFFALNFKKLKKDITKIRSLYAKLEADLGFLKL 280

Query: 971 DNAYGLWN 978
           + +YG  +
Sbjct: 281 EFSYGRLS 288


>gnl|CDD|178414 PLN02819, PLN02819, lysine-ketoglutarate reductase/saccharopine
            dehydrogenase.
          Length = 1042

 Score = 29.8 bits (67), Expect = 4.7
 Identities = 8/40 (20%), Positives = 18/40 (45%)

Query: 1047 DLAKRFKALLSWKGWHQLTPAPKISTPSFEVSSYVNPKRM 1086
            + A +    + + G  + T  PK     F+V+ Y   +++
Sbjct: 902  ETAAKAAKTIVFLGLDEETEVPKSCKSIFDVTCYRMEEKL 941


>gnl|CDD|163506 TIGR03794, NHPM_micro_HlyD, NHPM bacteriocin system secretion
           protein.  Members of this protein family are homologs of
           the HlyD membrane fusion protein of type I secretion
           systems. Their occurrence in prokaryotic genomes is
           associated with the occurrence of a novel class of
           microcin (small bacteriocins) with a propeptide region
           related to nitrile hydratase. We designate the class of
           bacteriocin as Nitrile Hydratase Propeptide Microcin, or
           NHPM. This family, therefore, is designated as NHPM
           bacteriocin system secretion protein. Some but not all
           NHPM-class putative microcins belong to the TOMM
           (thiazole/oxazole modified microcin) class as assessed
           by the presence of the scaffolding protein and/or
           cyclodehydratase in the same gene clusters.
          Length = 421

 Score = 29.4 bits (66), Expect = 5.7
 Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 5/97 (5%)

Query: 385 TSELKQATVLARANAQEEKQR--REQEAKEKADREKADKEAKEKADREKADKDLQEKTPI 442
               KQ  +L+R  A  ++ R  ++Q  +E+   + ADK     A + KAD+   E    
Sbjct: 153 REVGKQRGLLSRGLATFKRDRILQQQWREEQEKYDAADKARAIYALQTKADERNLETVLQ 212

Query: 443 KAEGDDFGLGLPS---VPTHSVKLPPKEEELEEVKDE 476
                DF L   +   + T   ++     E+EE++++
Sbjct: 213 SLSQADFQLAGVAEKELETVEARIKEARYEIEELENK 249


>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
           subunit G; Reviewed.
          Length = 197

 Score = 29.6 bits (66), Expect = 5.8
 Identities = 14/60 (23%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDD 448
           K+ +++ R    E+ ++  +E +E+ + E+ +++  E+ D+E+ +++ +E+T I+ + DD
Sbjct: 117 KKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQT-IEEQSDD 175


>gnl|CDD|130078 TIGR01005, eps_transp_fam, exopolysaccharide transport protein
           family.  The model describes the exopolysaccharide
           transport protein family in bacteria. The transport
           protein is part of a large genetic locus which is
           associated with exopolysaccharide (EPS) biosynthesis.
           Detailed molecular characterization and gene fusion
           analysis revealed atleast seven gene products are
           involved in the overall regulation, which among other
           things, include exopolysaccharide biosynthesis, property
           of conferring virulence and exopolysaccharide export.
          Length = 754

 Score = 29.2 bits (65), Expect = 6.1
 Identities = 39/215 (18%), Positives = 59/215 (27%), Gaps = 24/215 (11%)

Query: 374 AYSTIANVANFTSELKQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKADREKAD 433
           AY      A   S    A  LA   A   KQ R+ EA+  A R ++D      A      
Sbjct: 179 AYIAGQGAAKSESNTAAADFLAPEIADLSKQSRDAEAEVAAYRAQSDLLMGNNATLATQQ 238

Query: 434 KDLQEKTPIKAEGDDFGLGLPSVPTHSVKLPPKEEELEEVKDEGKKGKEPGTTETDD--- 490
                    +A  +            SVK   +     +V  E    +            
Sbjct: 239 LAELNTELSRARANRAA---AEGTADSVKKALQNGGSLDVLPEVLSSQLKLEDLIQRLRE 295

Query: 491 REETERKNQDILDNSLLAGKTHTKNETPAIPTAKAPPAQ-------AHKGIQDKKPQDQR 543
           R+   R     L  ++LA          ++    A           +     D      R
Sbjct: 296 RQAELRATIADLSTTMLANHPRVVAAKSSLADLDAQIRSELQKITKSLLMQADA--AQAR 353

Query: 544 EKPLASDIGVGESDYAGIKLTKKEKELQEQEENLR 578
           E  L SD+          +L     +  EQ+ +L 
Sbjct: 354 ESQLVSDVN---------QLKAASAQAGEQQVDLD 379


>gnl|CDD|183249 PRK11637, PRK11637, AmiB activator; Provisional.
          Length = 428

 Score = 28.9 bits (65), Expect = 7.9
 Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 6/62 (9%)

Query: 394 LARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADKDLQEKTPIKAEGDDFGLGL 453
           +ARA   E K R E+EA+E A      K+AK K    K  +   E++ +   G   GLG 
Sbjct: 249 IARAER-EAKARAEREAREAARVRDKQKQAKRKGSTYKPTES--ERSLMSRTG---GLGR 302

Query: 454 PS 455
           P 
Sbjct: 303 PR 304


>gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional.
          Length = 562

 Score = 28.8 bits (65), Expect = 7.9
 Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 8/120 (6%)

Query: 887  SDSTADLKELQTQLSRAKKYKESNDERIVSFIRSEFEREIKELKSVIEADAKENPNPNKN 946
            +     LKELQ  L +     +  +E +  F  +E  +++ ELK+ I  + +        
Sbjct: 302  TKIKDKLKELQHSLEKLDTAIDELEEIMDEF--NEQSKKLLELKNKISTNKQSLITLVDK 359

Query: 947  QKKLQKTREKLVAQLSSRLKELNIDNAYGLWNEYKEDFKASFEYPLGTYEPAILGAM-KD 1005
             KK++   E+L A+     +EL       L +E  +  K   E     Y   I+  + KD
Sbjct: 360  AKKVKAAIEELQAEFVDNAEELA-----KLQDELDKIVKTKSELVKEKYHRGIVTDLLKD 414


>gnl|CDD|185517 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
          Length = 393

 Score = 28.8 bits (65), Expect = 8.1
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 387 ELKQATVLARANAQEEKQRREQEAKEKADREKADKEAK 424
           ELK   +  R   +EE +   ++A E+ D E+  K++K
Sbjct: 93  ELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSK 130


>gnl|CDD|180236 PRK05753, PRK05753, nucleoside diphosphate kinase regulator;
           Provisional.
          Length = 137

 Score = 28.8 bits (65), Expect = 8.2
 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)

Query: 876 VERLSGLAQQPSDSTADLKE-LQTQLSRAK 904
            ERL  L +QP+ +   + E L  +L RA+
Sbjct: 14  AERLDRLLEQPAFAGPPIAEALNAELDRAQ 43


>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
          Length = 1021

 Score = 28.9 bits (64), Expect = 8.6
 Identities = 10/41 (24%), Positives = 25/41 (60%)

Query: 394 LARANAQEEKQRREQEAKEKADREKADKEAKEKADREKADK 434
           + R   + E+  RE+  +++ +R++ D+  +E+ DR + D+
Sbjct: 479 IERERLERERLERERLERDRLERDRLDRLERERVDRLERDR 519


>gnl|CDD|178093 PLN02475, PLN02475,
           5-methyltetrahydropteroyltriglutamate--homocysteine
           methyltransferase.
          Length = 766

 Score = 28.6 bits (64), Expect = 9.3
 Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 421 KEAKEKADREKADKDLQEKTPIKAEGD--DFGLGLPSVPTHSVKLPPKEEELEEVKDEGK 478
            EA +KA       D +  TP+ A  D     L LP +PT ++   P+  EL  V+ E K
Sbjct: 396 NEAVQKAAAALKGSDHRRATPVSARLDAQQKKLNLPILPTTTIGSFPQTVELRRVRREYK 455

Query: 479 KGK 481
             K
Sbjct: 456 AKK 458


>gnl|CDD|184614 PRK14314, glmM, phosphoglucosamine mutase; Provisional.
          Length = 450

 Score = 28.8 bits (65), Expect = 9.7
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 5/53 (9%)

Query: 97  VGDTLKRLAETGEVILSDKSDRLLCRFMDMVETEDEHKIN---KQVRDALESA 146
           + D  + L ++G V+L       LCR M  VE ED+H+++   K++ D +E  
Sbjct: 398 IKDVEEALGDSGRVLLRYSGTENLCRVM--VEGEDKHQVDSLAKEIADVVEKE 448


  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
   0.312    0.130    0.366 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 20,191,530
Number of extensions: 1349660
Number of successful extensions: 3783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3454
Number of HSP's successfully gapped: 230
Length of query: 1246
Length of database: 5,994,473
Length adjustment: 105
Effective length of query: 1141
Effective length of database: 3,725,633
Effective search space: 4250947253
Effective search space used: 4250947253
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 63 (28.3 bits)