RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780788|ref|YP_003065201.1| transcription elongation
factor NusA [Candidatus Liberibacter asiaticus str. psy62]
         (526 letters)



>gnl|CDD|30544 COG0195, NusA, Transcription elongation factor [Transcription].
          Length = 190

 Score =  181 bits (462), Expect = 3e-46
 Identities = 98/188 (52%), Positives = 131/188 (69%), Gaps = 7/188 (3%)

Query: 160 NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEI 219
             + ++ + E I  EN + GDR+++ +Y+V++E +G Q+ LSRT P+ + KLF +EVPEI
Sbjct: 1   KVEAILPKREQIPGENFKVGDRIRALLYEVQKEAKG-QIELSRTIPELLEKLFEIEVPEI 59

Query: 220 YNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVW 279
            +G++++K V+RDP +    AV S+   IDPVGAC+G RGSRV+AV  EL  EKID+V W
Sbjct: 60  GDGVIEIKCVARDPRA----AVVSNVVKIDPVGACIGKRGSRVKAVSEEL-GEKIDVVEW 114

Query: 280 SPDSATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWT 338
           S D A F+ NAL PA V  V + E D     V+VP +QLSLAIG+ GQNVRLASQLTGW 
Sbjct: 115 SEDPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWE 174

Query: 339 IDIITEEE 346
           IDI T  E
Sbjct: 175 IDIETISE 182



 Score = 27.5 bits (61), Expect = 9.3
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 294 AIVTKVVLDEDVGRIEVIVPKE-QLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347
            I  K V  +    +   V K   +   IG+RG  V+  S+  G  ID++   ED
Sbjct: 63  VIEIKCVARDPRAAVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED 117


>gnl|CDD|88421 cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA),
           S1-like RNA-binding domain. S1-like RNA-binding domains
           are found in a wide variety of RNA-associated proteins.
           NusA is a transcription elongation factor containing an
           N-terminal catalytic domain and three RNA binding
           domains (RBD's). The RBD's include one S1 domain and two
           KH domains that form an RNA binding surface. DNA
           transcription by RNA polymerase (RNAP) includes three
           phases - initiation, elongation, and termination. During
           initiation, sigma factors bind RNAP and target RNAP to
           specific promoters. During elongation, N-utilization
           substances (NusA, B, E, and G) replace sigma factors and
           regulate pausing, termination, and antitermination. NusA
           is cold-shock-inducible..
          Length = 67

 Score = 91.6 bits (228), Expect = 4e-19
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG 195
           D+ GEI++G VKRV+ GNVIVDLG  + ++ + E I  E+ RPGDR+K+Y+ +VR+  +G
Sbjct: 1   DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKG 60

Query: 196 PQVLLSR 202
           PQ++LSR
Sbjct: 61  PQIILSR 67


>gnl|CDD|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
           an essential multifunctional transcription elongation
           factor that is universally conserved among prokaryotes
           and archaea. NusA anti-termination function plays an
           important role in the expression of ribosomal rrn
           operons. During transcription of many other genes,
           NusA-induced RNAP pausing provides a mechanism for
           synchronizing transcription and translation . The
           N-terminal RNAP-binding domain (NTD) is connected
           through a flexible hinge helix to three globular
           domains, S1, KH1 and KH2.   The KH motif is a
           beta-alpha-alpha-beta-beta unit that folds into an
           alpha-beta structure with a three stranded beta-sheet
           interupted by two contiguous helices..
          Length = 61

 Score = 67.5 bits (165), Expect = 8e-12
 Identities = 34/61 (55%), Positives = 42/61 (68%), Gaps = 1/61 (1%)

Query: 283 SATFVINALRPAIVTKVVLDEDVG-RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341
            A F+ NAL PA VT V + +D   R  V+VP +QL LAIG+ GQNVRLAS+L G  IDI
Sbjct: 1   PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60

Query: 342 I 342
           +
Sbjct: 61  V 61



 Score = 30.2 bits (68), Expect = 1.5
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 8/56 (14%)

Query: 224 VQVKAVSRDPGS--RAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV 277
            +V +V+       RA++ V       D +G  +G  G  V+    +L  EKIDIV
Sbjct: 12  AKVTSVTVLDDEEKRARVVV-----PDDQLGLAIGKGGQNVRLAS-KLLGEKIDIV 61


>gnl|CDD|48407 cd02409, KH-II, KH-II  (K homology RNA-binding domain, type II).
           KH binds single-stranded RNA or DNA. It is found in a
           wide variety of proteins including ribosomal proteins
           (e.g. ribosomal protein S3), transcription factors (e.g.
           NusA_K), and post-transcriptional modifiers of mRNA
           (e.g. hnRNP K). There are two different KH domains that
           belong to different protein folds, but they share a
           single KH motif. The KH motif is a
           beta-alpha-alpha-beta-beta unit that folds into an
           alpha-beta structure with a three stranded beta-sheet
           interupted by two contiguous helices. In addition to
           their KH core domain, KH-II proteins have an N-terminal
           alpha helical extension while KH-I proteins have a
           C-terminal alpha helical extension..
          Length = 68

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 286 FVINALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTID 340
           F+   L PA ++ V ++   D   I ++V + Q  L IG++GQN+R   +L    + 
Sbjct: 3   FLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLR 59


>gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain.  The S1 domain occurs in a
           wide range of RNA associated proteins. It is
           structurally similar to cold shock protein which binds
           nucleic acids. The S1 domain has an OB-fold structure.
          Length = 74

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 135 KDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISR------ENLRPGDRVKSYIY 187
           K + G+++ GTV RV  G   VDLGN  +G I   E          E L+ GD V+  + 
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60

Query: 188 DVRREQRGPQV 198
            V +E+    +
Sbjct: 61  KVDKERGRIIL 71


>gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
           metallo-beta-lactamase domain and an RNA-binding KH
           domain [General function prediction only].
          Length = 637

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 12/92 (13%)

Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337
            P+ A  +I  + P  A +T +  D+D G  EVI+  ++  L IG+ G  +R  +  TGW
Sbjct: 73  PPEEARKIILEIVPEEAGITDIYFDDDTG--EVIIEAKKPGLVIGKGGSTLREITAETGW 130

Query: 338 TIDII------TEEEDSINR--QKDFNERTQF 361
              I+      +    SI    + +  ER + 
Sbjct: 131 APKIVRTPPIQSRTIKSIREILRSERKERREI 162


>gnl|CDD|88442 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal
           protein S1 (RPS1) domain. RPS1 is a component of the
           small ribosomal subunit thought to be involved in the
           recognition and binding of mRNA's during translation
           initiation. The bacterial RPS1 domain architecture
           consists of 4-6 tandem S1 domains. In some bacteria, the
           tandem S1 array is located C-terminal to a
           4-hydroxy-3-methylbut-2-enyl diphosphate reductase
           (HMBPP reductase) domain. While RPS1 is found primarily
           in bacteria, proteins with tandem RPS1-like domains have
           been identified in plants and humans, however these lack
           the N-terminal HMBPP reductase domain. This CD includes
           S1 repeat 1 of the Escherichia coli and Homo sapiens
           RPS1 (ec1 and hs1, respectively). Autoantibodies to
           double-stranded DNA from patients with systemic lupus
           erythematosus cross-react with the human RPS1 homolog..
          Length = 70

 Score = 35.1 bits (81), Expect = 0.053
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 139 GEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISREN------LRPGDRVKSYIYDVRR 191
           G+I+ GTV  V+   V+VD+G  S+G+I   E            ++ GD V+ Y+  +R 
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYV--LRV 58

Query: 192 EQRGPQVLLSR 202
           E     V+LS+
Sbjct: 59  EDEEGNVVLSK 69


>gnl|CDD|48408 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
           specificity factor (CPSF) contains an N-terminal K
           homology RNA-binding domain (KH).  The archeal CPSFs are
           predicted to be metal-dependent RNases belonging to the
           beta-CASP family, a subgroup enzymes within the
           metallo-beta-lactamase fold.  The KH motif is a
           beta-alpha-alpha-beta-beta unit that folds into an
           alpha-beta structure with a three stranded beta-sheet
           interupted by two contiguous helices.  In general, KH
           domains are known to bind single-stranded RNA or DNA and
           are found in a wide variety of proteins including
           ribosomal proteins, transcription factors and
           post-transcriptional modifiers of mRNA..
          Length = 145

 Score = 34.8 bits (80), Expect = 0.056
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337
            P+ A  +I  + P  A +T +  D+D G  EVI+  E+  L IG+ G  +R  ++ TGW
Sbjct: 50  PPEEAIKIILEIVPEEAGITDIYFDDDTG--EVIIEAEKPGLVIGKGGSTLREITRETGW 107

Query: 338 TIDII 342
              ++
Sbjct: 108 APKVV 112


>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
           structure and biogenesis].
          Length = 541

 Score = 34.5 bits (79), Expect = 0.067
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 10/87 (11%)

Query: 117 VIIQKVREAERDRQYLEFKD--KVGEIISGTVKRVEYGNVIVDLGNSDGVI-------RR 167
           +  + V E ER  Q  E  +  +VGE++ G VK +      VD+G  DG++       +R
Sbjct: 169 LSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKR 228

Query: 168 DETISRENLRPGDRVKSYIYDVRREQR 194
            +  S E ++ GD VK  +  +  E+ 
Sbjct: 229 VDHPS-EVVKVGDEVKVKVISLDEERG 254



 Score = 34.5 bits (79), Expect = 0.082
 Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 137 KVGEIISGTVKRVEYGNVIVDLGNS-DGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194
           K G ++ G VK V+     V+LG   +G+IR  E +SR+ L+ GD V++ +  + ++ R
Sbjct: 448 KKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSE-LSRDVLKVGDEVEAVVVSIDKKNR 505



 Score = 31.4 bits (71), Expect = 0.70
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISR---ENLRPGDRVKSYIYDVRRE 192
           + G+++ GTV  +E   V+VD+G  S+GVI   E  +    + ++ GD V+  +  +R E
Sbjct: 20  EPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVEDVVQVGDEVEVLV--LRVE 77

Query: 193 QRGPQVLLSRTHPQFM 208
               +++LSR   +  
Sbjct: 78  DGEGELVLSRRKAERE 93


>gnl|CDD|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein
           S1 (RPS1) domain. RPS1 is a component of the small
           ribosomal subunit thought to be involved in the
           recognition and binding of mRNA's during translation
           initiation. The bacterial RPS1 domain architecture
           consists of 4-6 tandem S1 domains. In some bacteria, the
           tandem S1 array is located C-terminal to a
           4-hydroxy-3-methylbut-2-enyl diphosphate reductase
           (HMBPP reductase) domain. While RPS1 is found primarily
           in bacteria, proteins with tandem RPS1-like domains have
           been identified in plants and humans, however these lack
           the N-terminal HMBPP reductase domain. This CD includes
           S1 repeat 3 (ec3) of the Escherichia coli RPS1.
           Autoantibodies to double-stranded DNA from patients with
           systemic lupus erythematosus cross-react with the human
           RPS1 homolog..
          Length = 68

 Score = 34.4 bits (79), Expect = 0.077
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 8/63 (12%)

Query: 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETIS-------RENLRPGDRVKSYIYDVR 190
            G+++ GTVK +      VDLG  DG++   + +S        E +  GD V+  +  + 
Sbjct: 1   EGDVVEGTVKSITDFGAFVDLGGVDGLLHISD-MSWGRVKHPSEVVNVGDEVEVKVLKID 59

Query: 191 REQ 193
           +E+
Sbjct: 60  KER 62


>gnl|CDD|146090 pfam03283, PAE, Pectinacetylesterase. 
          Length = 366

 Score = 34.2 bits (79), Expect = 0.091
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 19/77 (24%)

Query: 213 HMEVPEIYNGIVQVKAVSRDPGS--------RAKL-----AVFSSDSSIDPVGACVGMRG 259
           +ME    ++GI+     S +P          R K+     A FS DS +   G  +  RG
Sbjct: 82  YMEKTLTFSGIL-----SNNPEENPDFYNWNRVKIRYCDGASFSGDSEVVYKGTTLYFRG 136

Query: 260 SR-VQAVVTELRDEKID 275
            R  +AV+ +L  + + 
Sbjct: 137 QRIWEAVIDDLLSKGMK 153


>gnl|CDD|144530 pfam00965, TIMP, Tissue inhibitor of metalloproteinase.  Members of
           this family are common in extracellular regions of
           vertebrate species.
          Length = 174

 Score = 32.0 bits (73), Expect = 0.46
 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 4/50 (8%)

Query: 160 NSDGVIRRDETISRENLR--PGDRVKSYIYDVRREQRGPQVLLSRTHPQF 207
           N+D VIR    +  + L     D+   Y     +  +G     S    Q+
Sbjct: 14  NADFVIRA--KVVGKKLVEQGNDKRIRYKVKQTKMFKGFSKAGSSLDIQY 61


>gnl|CDD|30738 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
           DNA repair [DNA replication, recombination, and repair].
          Length = 354

 Score = 31.8 bits (72), Expect = 0.46
 Identities = 13/56 (23%), Positives = 22/56 (39%)

Query: 418 EGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473
           +GI +   +++  L     +    G+       L   GI T+ DLA   +D L   
Sbjct: 159 DGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKKR 214


>gnl|CDD|143804 pfam00013, KH_1, KH domain.  KH motifs can bind RNA in vitro.
           Autoantibodies to Nova, a KH domain protein, cause
           paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;.
          Length = 57

 Score = 31.0 bits (71), Expect = 0.87
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341
            E+++P   +   IG+ G N++   + TG  I I
Sbjct: 2   EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRI 35


>gnl|CDD|88463 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
           trans-acting factor important for biogenesis of both the
           40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
           distinct regions, an N-terminal region containing
           tandemly repeated S1 RNA-binding domains (12 S1 repeats
           in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
           Homo sapiens Rrp5) and a C-terminal region containing
           tetratricopeptide repeat (TPR) motifs thought to be
           involved in protein-protein interactions.  Mutational
           studies have shown that each region represents a
           specific functional domain. Deletions within the
           S1-containing region inhibit pre-rRNA processing at
           either site A3 or A2, whereas deletions within the TPR
           region confer an inability to support cleavage of A0-A2.
           This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5
           is found in eukaryotes but not in prokaryotes or
           archaea..
          Length = 77

 Score = 31.0 bits (70), Expect = 0.93
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSD--GVIRRDETI------SRENLRPGDRVKSYIYD 188
           KVG+ I GTV+RVE   V +D+  ++  G+  + E        + +  R GD+V++ +  
Sbjct: 1   KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60

Query: 189 VRREQR 194
           +  E++
Sbjct: 61  IDAEKK 66


>gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
           (polynucleotide phosphorylase) [Translation, ribosomal
           structure and biogenesis].
          Length = 692

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 20/93 (21%)

Query: 110 AVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNVIVDLGNSDGVIR-- 166
           + + AK+ I    RE E           VGE+  GTV R+  +G  +  L   DG++   
Sbjct: 602 SAKKAKERIEAITREVE-----------VGEVYEGTVVRIVDFGAFVELLPGKDGLVHIS 650

Query: 167 -----RDETISRENLRPGDRVKSYIYDVRREQR 194
                R E +  + L+ GD VK  + ++ ++ R
Sbjct: 651 QLAKERVEKVE-DVLKEGDEVKVKVIEIDKQGR 682


>gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I.  KH binds
           single-stranded RNA or DNA. It is found in a wide
           variety of proteins including ribosomal proteins,
           transcription factors and post-transcriptional modifiers
           of mRNA. There are two different KH domains that belong
           to different protein folds, but they share a single KH
           motif. The KH motif is folded into a beta alpha alpha
           beta unit. In addition to the core, type II KH domains
           (e.g. ribosomal protein S3) include N-terminal extension
           and type I KH domains (e.g. hnRNP K) contain C-terminal
           extension..
          Length = 64

 Score = 29.8 bits (67), Expect = 2.1
 Identities = 12/44 (27%), Positives = 18/44 (40%)

Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351
             V+VP   +   IG+ G  ++   + TG  I I      S  R
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEER 45


>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa.  Pol IV, also
           known as Pol kappa, DinB, and Dpo4, is a translesion
           synthesis (TLS) polymerase.  Translesion synthesis is a
           process that allows the bypass of a variety of DNA
           lesions.  TLS polymerases lack proofreading activity and
           have low fidelity and low processivity.  They use
           damaged DNA as templates and insert nucleotides opposite
           the lesions.  Known primarily as Pol IV in prokaryotes
           and Pol kappa in eukaryotes, this polymerase has a
           propensity for generating frameshift mutations.  The
           eukaryotic Pol kappa differs from Pol IV and Dpo4 by an
           N-terminal extension of ~75 residues known as the
           "N-clasp" region.  The structure of Pol kappa shows DNA
           that is almost totally encircled by Pol kappa, with the
           N-clasp region augmenting the interactions between DNA
           and the polymerase. Pol kappa is more resistant than Pol
           eta and Pol iota to bulky guanine adducts and is
           efficient at catalyzing the incorporation of dCTP.
           Bacterial pol IV has a higher error rate than other
           Y-family polymerases.
          Length = 334

 Score = 29.0 bits (66), Expect = 3.0
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 425 QKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKG 478
           ++ +  L V +    IPG+       L E GIKT+ DLA   V+ L       G
Sbjct: 165 EEFLAPLPVRK----IPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKLFGKSG 214


>gnl|CDD|38787 KOG3580, KOG3580, KOG3580, Tight junction proteins [Signal
           transduction mechanisms].
          Length = 1027

 Score = 28.9 bits (64), Expect = 3.1
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG 195
            +  +   G   R  Y        NS G   R    S E  RP +R +S   D+ R++RG
Sbjct: 118 FEDEDEFDGRSFRSGYSER--SRLNSHGGRSRSWEDSPERGRPHERARSRERDLSRDRRG 175

Query: 196 PQ 197
           P+
Sbjct: 176 PR 177


>gnl|CDD|30441 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
           structure and biogenesis].
          Length = 233

 Score = 29.1 bits (65), Expect = 3.4
 Identities = 10/44 (22%), Positives = 20/44 (45%)

Query: 286 FVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329
           F+   L  A ++ V ++       V +   +  L IG++G N+ 
Sbjct: 31  FLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIE 74


>gnl|CDD|37490 KOG2279, KOG2279, KOG2279, Kinase anchor protein AKAP149, contains
           KH and Tudor RNA-binding domains [Signal transduction
           mechanisms].
          Length = 608

 Score = 28.9 bits (64), Expect = 3.5
 Identities = 17/38 (44%), Positives = 27/38 (71%)

Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE 345
           IE++VP+E + L IGR+G N++   + TG  ID+ TE+
Sbjct: 70  IEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED 107


>gnl|CDD|34769 COG5169, HSF1, Heat shock transcription factor [Transcription].
          Length = 282

 Score = 28.5 bits (63), Expect = 4.8
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 7/52 (13%)

Query: 255 VGMRGSRVQAVVTEL-----RDEKIDIVVWSPDSATFVINALRPAIVTKVVL 301
           +  R S+ +  V +L       E   ++ WSPD  +FVI  L P   TKV+L
Sbjct: 3   MSSRWSQPKEFVHKLYQILEEPEYYKLIQWSPDGRSFVI--LDPEEFTKVIL 52


>gnl|CDD|28890 cd00006, PTS_IIA_man, PTS_IIA, PTS system, mannose/sorbose specific
           IIA subunit. The bacterial phosphoenolpyruvate: sugar
           phosphotransferase system (PTS) is a multi-protein
           system involved in the regulation of a variety of
           metabolic and transcriptional processes. This family is
           one of four structurally and functionally distinct group
           IIA PTS system cytoplasmic enzymes, necessary for the
           uptake of carbohydrates across the cytoplasmic membrane
           and their phosphorylation. IIA subunits receive
           phosphoryl groups from HPr and transfer them to IIB
           subunits, which in turn phosphorylate the substrate..
          Length = 122

 Score = 28.3 bits (63), Expect = 5.8
 Identities = 9/51 (17%), Positives = 21/51 (41%)

Query: 371 IIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGID 421
           I  H   A G  +  E+   +   + +I+    E+  ++  + +  L  +D
Sbjct: 5   IATHGGFASGLLNSAEMILGEQENVEAIDFPPGESPDDLLEKIKAALAELD 55


>gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein).
           HypE is involved in Ni-Fe hydrogenase biosynthesis.
           HypE dehydrates its own carbamoyl moiety in an
           ATP-dependent process to yield the enzyme thiocyanate.
           The N-terminal domain of HypE is related to the
           ATP-binding domains of the AIR synthases,
           selenophosphate synthetase (SelD), and FGAM synthase and
           is thought to bind ATP..
          Length = 293

 Score = 28.2 bits (64), Expect = 6.6
 Identities = 11/20 (55%), Positives = 14/20 (70%)

Query: 163 GVIRRDETISRENLRPGDRV 182
           GVI R   IS  N+RPGD++
Sbjct: 137 GVIPRGVIISPSNIRPGDKI 156


>gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
           [Transcription].
          Length = 183

 Score = 27.9 bits (62), Expect = 6.6
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYD 188
           L FK   GE++ G V  V      V +G  DG++   + I  + +   ++ K  I +
Sbjct: 75  LVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQ-IMDDYIDYDEKNKVLIGE 130


>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
           only].
          Length = 604

 Score = 27.9 bits (62), Expect = 6.7
 Identities = 13/43 (30%), Positives = 23/43 (53%)

Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
           GR  V VP++ +   IG+ G+ ++   +  G  ID+   EE+ 
Sbjct: 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEE 528


>gnl|CDD|35793 KOG0573, KOG0573, KOG0573, Asparagine synthase [Amino acid
           transport and metabolism].
          Length = 520

 Score = 28.0 bits (62), Expect = 6.8
 Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 1/85 (1%)

Query: 219 IYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV 278
            Y+         RD   R  L       +   V + VG  G  +  V    R++  D V 
Sbjct: 122 YYDVRSDKLYFGRDDIGRRSLLYSLDPFNFSLVLSTVGTSGKLIYEVPPVFRNKLTDRVP 181

Query: 279 WSPDSATFVINALRPAIVTKVVLDE 303
           W   S T + N+L P++     + E
Sbjct: 182 WPYLS-TKLENSLGPSLPPLCDISE 205


>gnl|CDD|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein
           S1 (RPS1) domain. RPS1 is a component of the small
           ribosomal subunit thought to be involved in the
           recognition and binding of mRNA's during translation
           initiation. The bacterial RPS1 domain architecture
           consists of 4-6 tandem S1 domains. In some bacteria, the
           tandem S1 array is located C-terminal to a
           4-hydroxy-3-methylbut-2-enyl diphosphate reductase
           (HMBPP reductase) domain. While RPS1 is found primarily
           in bacteria, proteins with tandem RPS1-like domains have
           been identified in plants and humans, however these lack
           the N-terminal HMBPP reductase domain. This CD includes
           S1 repeat 6 (ec6) of the Escherichia coli RPS1.
           Autoantibodies to double-stranded DNA from patients with
           systemic lupus erythematosus cross-react with the human
           RPS1 homolog..
          Length = 73

 Score = 27.8 bits (62), Expect = 7.1
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 9/64 (14%)

Query: 139 GEIISGTVKRVEYGNVIVDLGNS-DGVIRRDETISRE-------NLRPGDRVKSYIYDVR 190
           G I++G V  V+     V LG+  +G +R  E +SR+         + GD V++ I +V 
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAE-LSRDRVEDATERFKVGDEVEAKITNVD 59

Query: 191 REQR 194
           R+ R
Sbjct: 60  RKNR 63


>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
           DnaJ-type Zn finger domain [DNA replication,
           recombination, and repair].
          Length = 715

 Score = 28.0 bits (62), Expect = 7.3
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSD--GVIRRDETISRENLRPGDRVKSYIYDVRREQR 194
           + G+   G V RVE   V V+L NS   G+I R +     +   GD +   + DVR E+ 
Sbjct: 121 EAGKYYKGIVSRVEKYGVFVEL-NSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKG 179


  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
   0.317    0.136    0.375 

Gapped
Lambda     K      H
   0.267   0.0643    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,170,171
Number of extensions: 337363
Number of successful extensions: 973
Number of sequences better than 10.0: 1
Number of HSP's gapped: 966
Number of HSP's successfully gapped: 55
Length of query: 526
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 428
Effective length of database: 4,146,055
Effective search space: 1774511540
Effective search space used: 1774511540
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: 41 (21.6 bits)
S2: 60 (27.1 bits)