RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780762|ref|YP_003065175.1| recombination protein RecR
[Candidatus Liberibacter asiaticus str. psy62]
         (201 letters)



>gnl|CDD|30702 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
           [DNA replication, recombination, and repair].
          Length = 198

 Score =  243 bits (623), Expect = 2e-65
 Identities = 87/198 (43%), Positives = 129/198 (65%)

Query: 4   KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSIC 63
            +    IE LI  L ++PG GP+SA+R   HL+++  + +  LA+A+      +  CS+C
Sbjct: 1   MMYPPPIEKLIDALKKLPGVGPKSAQRLAFHLLQRDREDVERLAKALLEAKENIKHCSVC 60

Query: 64  GNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPE 123
           GN+  +DPC IC D+ RD S + VVE+  D+ ALE++     LYHVLGG LSPLD IGPE
Sbjct: 61  GNLTESDPCDICSDESRDKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGIGPE 120

Query: 124 DIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSEL 183
           D+ I  L++R+    I+E+I A + T+EG+ TA YI   LK + +K+TRLA G+P+G EL
Sbjct: 121 DLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIARLLKPLGLKVTRLAQGVPVGGEL 180

Query: 184 DYLDDGTIFEAIRSRTVL 201
           +Y+D+GT+  A+  R  +
Sbjct: 181 EYVDEGTLSRALEGRRKI 198


>gnl|CDD|173775 cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primase (TOPRIM)
           nucleotidyl transferase/hydrolase domain of the type
           found in Escherichia coli RecR.  RecR participates in
           the RecFOR pathway of homologous recombinational repair
           in prokaryotes. This pathway provides a single-stranded
           DNA molecule coated with RecA to allow invasion of a
           homologous molecule. The RecFOR system directs the
           loading of RecA onto gapped DNA coated with SSB protein.
           The TOPRIM domain has two conserved motifs, one of which
           centers at a conserved glutamate and the other one at
           two conserved aspartates (DxD).  In RecR sequences this
           glutamate in the first turn of the TOPRIM domain is
           semiconserved, the DXD motif is not conserved.
          Length = 112

 Score =  156 bits (396), Expect = 4e-39
 Identities = 54/109 (49%), Positives = 75/109 (68%)

Query: 83  SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142
           + + VVE+  D+ A+E S     LYHVLGG +SPLD IGP+D+ I  L+ERI   +++E+
Sbjct: 1   NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEV 60

Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTI 191
           I A + T+EG+ TA YI   LK   VK+TRLA GIP+G EL+Y D+ T+
Sbjct: 61  ILATNPTVEGEATALYIAKLLKDFGVKVTRLAQGIPVGGELEYADEITL 109


>gnl|CDD|145340 pfam02132, RecR, RecR protein. 
          Length = 41

 Score = 51.7 bits (125), Expect = 1e-07
 Identities = 20/41 (48%), Positives = 25/41 (60%)

Query: 41 QLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRD 81
          +    LAEA+     KV  CS+CGN+  TDPC IC D +RD
Sbjct: 1  EEAERLAEALLEAKEKVRHCSVCGNLTETDPCEICSDPRRD 41


>gnl|CDD|145089 pfam01751, Toprim, Toprim domain.  This is a conserved region from
           DNA primase. This corresponds to the Toprim domain
           common to DnaG primases, topoisomerases, OLD family
           nucleases and RecR proteins. Both DnaG motifs IV and V
           are present in the alignment, the DxD (V) motif may be
           involved in Mg2+ binding and mutations to the conserved
           glutamate (IV) completely abolish DnaG type primase
           activity. DNA primase EC:2.7.7.6 is a
           nucleotidyltransferase it synthesizes the
           oligoribonucleotide primers required for DNA replication
           on the lagging strand of the replication fork; it can
           also prime the leading stand and has been implicated in
           cell division. This family also includes the atypical
           archaeal A subunit from type II DNA topoisomerases. Type
           II DNA topoisomerases catalyse the relaxation of DNA
           supercoiling by causing transient double strand breaks.
          Length = 89

 Score = 43.1 bits (102), Expect = 5e-05
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 83  SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERI-EVKKIRE 141
            V+I+VE  +D  AL ++         L G LS            +  ++ + ++ K  E
Sbjct: 1   KVLIIVEGPSDAIALAKAGGYKGNVVALLGHLS------DVIPLTKEQLKLLKKLAKKDE 54

Query: 142 LIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYG 176
           +I A     EG+  A  +++ LK +  K+ R+   
Sbjct: 55  VILATDPDREGEAIAWKLLELLKPLGKKVRRIFLP 89


>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
           nucleotidyl transferase/hydrolase domain found in type
           IA, type IIA and type IIB topoisomerases, bacterial
           DnaG-type primases, small primase-like proteins from
           bacteria and archaea, OLD family nucleases from
           bacterial and archaea, and bacterial DNA repair proteins
           of the RecR/M family. This domain has two conserved
           motifs, one of which centers at a conserved glutamate
           and the other one at two conserved aspartates (DxD).
           This glutamate and two aspartates, cluster together to
           form a highly acid surface patch. The conserved
           glutamate may act as a general base in nucleotide
           polymerization by primases and in strand joining in
           topoisomerases and, as a general acid in strand cleavage
           by topisomerases and nucleases. The DXD motif may
           co-ordinate Mg2+, a cofactor required for full catalytic
           function.
          Length = 83

 Score = 40.1 bits (94), Expect = 5e-04
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 10/92 (10%)

Query: 83  SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142
             +I+VE  +D  AL ++         LGG               + L++R+   + +E+
Sbjct: 1   KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNK---------TRELLKRLL-GEAKEV 50

Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLA 174
           I A  A  EG+  A  +++ LK +  K+ RL 
Sbjct: 51  IIATDADREGEAIALRLLELLKSLGKKVRRLL 82


>gnl|CDD|145942 pfam03059, NAS, Nicotianamine synthase protein.  Nicotianamine
           synthase EC:2.5.1.43 catalyses the trimerisation of
           S-adenosylmethionine to yield one molecule of
           nicotianamine. Nicotianamine has an important role in
           plant iron uptake mechanisms. Plants adopt two
           strategies (termed I and II) of iron acquisition.
           Strategy I is adopted by all higher plants except
           graminaceous plants, which adopt strategy II. In
           strategy I plants, the role of nicotianamine is not
           fully determined: possible roles include the formation
           of more stable complexes with ferrous than with ferric
           ion, which might serve as a sensor of the physiological
           status of iron within a plant, or which might be
           involved in the transport of iron. In strategy II
           (graminaceous) plants, nicotianamine is the key
           intermediate (and nicotianamine synthase the key enzyme)
           in the synthesis of the mugineic family (the only known
           family in plants) of phytosiderophores.
           Phytosiderophores are iron chelators whose secretion by
           the roots is greatly increased in instances of iron
           deficiency.
          Length = 277

 Score = 30.4 bits (69), Expect = 0.35
 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 14/80 (17%)

Query: 87  VVEDVADLWA-------LERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKI 139
           +VE + DL+A       L  S  VNAL+  L  +  P     P  I +  L   I+  +I
Sbjct: 9   LVEKILDLYAAISKLESLSPSPDVNALFTQLVTTCIP-----PSPIDVTKLGPEIQ--EI 61

Query: 140 RELIFAISATIEGQTTAHYI 159
           R L+  + +  EG   +HY 
Sbjct: 62  RSLLIRLCSEAEGLLESHYS 81


>gnl|CDD|33999 COG4277, COG4277, Predicted DNA-binding protein with the
           Helix-hairpin-helix motif [General function prediction
           only].
          Length = 404

 Score = 28.0 bits (62), Expect = 1.8
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 15  KILARIPGFGPRSARR 30
           K L R+PG G +SARR
Sbjct: 330 KELLRVPGIGVKSARR 345


>gnl|CDD|146710 pfam04216, FdhE, Protein involved in formate dehydrogenase
           formation.  The function of these proteins is unknown.
           They may possibly be involved in the formation of
           formate dehydrogenase.
          Length = 287

 Score = 27.7 bits (62), Expect = 2.0
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 24/64 (37%)

Query: 60  CSICGN--------VDTTDP------CAIC------IDQQRDASVIIVVEDVA----DLW 95
           C+ CG+        ++  +P      C  C      +DQ++D  +  V +D+A    DL 
Sbjct: 212 CTNCGSTKGLAYWSLEEGEPGVRAETCDTCHSYLKILDQEKDPDLEPVADDLASLALDLL 271

Query: 96  ALER 99
           A E+
Sbjct: 272 AREK 275


>gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit
           [DNA replication, recombination, and repair].
          Length = 201

 Score = 27.5 bits (61), Expect = 2.4
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 14  IKILARIPGFGPRSARRATLHLVKKKEQLLG 44
           +K L++IPG G ++A R  L L  K    L 
Sbjct: 107 VKALSKIPGIGKKTAERIVLELKGKLAAFLK 137


>gnl|CDD|36325 KOG1109, KOG1109, KOG1109, Vacuole membrane protein VMP1 [General
           function prediction only].
          Length = 440

 Score = 27.7 bits (61), Expect = 2.4
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 10  IENLIKILARIPGFGPRSARRATLHLVKKKEQLL 43
            E  + IL  +PG G R  R     L++K++QLL
Sbjct: 339 FEERVSILDTVPGLGHR-LREPFRWLLEKQKQLL 371


>gnl|CDD|31216 COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy
           production and conversion].
          Length = 472

 Score = 27.6 bits (61), Expect = 2.6
 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 9/62 (14%)

Query: 82  ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141
           AS +IV E V D +         +L   +G  L P   +GP       LI   ++ ++  
Sbjct: 279 ASRLIVHESVYDEFVERLVARAASL--KVGDPLDPSTDLGP-------LISEEQLDRVEG 329

Query: 142 LI 143
            I
Sbjct: 330 YI 331


>gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily.  Arl9/Arl10 was
           identified from a human cancer-derived EST dataset.  No
           functional information about the subfamily is available
           at the current time, but crystal structures of human
           Arl10b and Arl10c have been solved.
          Length = 159

 Score = 26.5 bits (59), Expect = 5.1
 Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 13/80 (16%)

Query: 80  RDASVIIVVEDVADLWALERSKAVNALYHVLGG-SLS--PLDRIG-----PEDIGIQSLI 131
           R  + I+ V D AD  ALE +K  N L+ +L   SL   PL  +G     P  + +  LI
Sbjct: 66  RGVNAIVYVVDAADRTALEAAK--NELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELI 123

Query: 132 ERIEVKKI--RE-LIFAISA 148
           E++ +K I  RE   ++IS 
Sbjct: 124 EQMNLKSITDREVSCYSISC 143


>gnl|CDD|112424 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier. 
          Length = 456

 Score = 26.5 bits (59), Expect = 5.8
 Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 109 VLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTA 156
           V+GG    ++R G  D G+++L++ ++  +    I  ++A      T 
Sbjct: 82  VVGGFAGVMNRTGAIDAGVKALVKPLKGIES-PYILLLAAYFSLGGTV 128


>gnl|CDD|133068 cd03856, M14_Nna1_like, Peptidase M14-like domain of Nna-1 (Nervous
           system Nuclear protein induced by Axotomy), also known
           as ATP/GTP binding protein (AGTPBP-1) and cytosolic
           carboxypeptidase (CCP), and related proteins. The
           Peptidase M14 family of metallocarboxypeptidases are
           zinc-binding carboxypeptidases (CPs) which hydrolyze
           single, C-terminal amino acids from polypeptide chains,
           and have a recognition site for the free C-terminal
           carboxyl group, which is a key determinant of
           specificity. This subfamily includes the human AGTPBP-1
           and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1
           and CCP -2 through -6. Nna1-like proteins are active
           metallopeptidases that are thought to act on cytosolic
           proteins such as alpha-tubulin, to remove a C-terminal
           tyrosine. Nna1 is widely expressed in the developing and
           adult nervous systems, including cerebellar Purkinje and
           granule neurons, miral cells of the olfactory bulb and
           retinal photoreceptors. Nna1 is also induced in
           axotomized motor neurons. Mutations in Nna1 cause
           Purkinje cell degeneration (pcd). The Nna1 CP domain is
           required to prevent the retinal photoreceptor loss and
           cerebellar ataxia phenotypes of pcd mice, and a
           functional zinc-binding domain is needed for Nna-1 to
           support neuron survival in these mice. Nna1-like
           proteins from the different phyla are highly diverse,
           but they all contain a characteristic N-terminal
           conserved domain right before the CP domain. It has been
           suggested that this N-terminal domain might act as a
           folding domain.
          Length = 269

 Score = 25.9 bits (57), Expect = 7.4
 Identities = 15/56 (26%), Positives = 23/56 (41%)

Query: 105 ALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIM 160
           AL   L G+   L  I     G     E +     ++ IF I+    G+T A ++M
Sbjct: 18  ALCESLQGNSCDLLTITSPPEGNDIKYEHLCSFANKKYIFLIARVHPGETNASWVM 73


>gnl|CDD|143443 cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate
           dehydrogenase, PutA.  The proline catabolic enzymes of
           the aldehyde dehydrogenase (ALDH) protein superfamily,
           proline dehydrogenase and
           Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH,
           (EC=1.5.1.12 )), catalyze the two-step oxidation of
           proline to glutamate; P5CDH catalyzes the oxidation of
           glutamate semialdehyde, utilizing NAD+ as the electron
           acceptor. In some bacteria, the two enzymes are fused
           into the bifunctional flavoenzyme, proline utilization A
           (PutA) These enzymes play important roles in cellular
           redox control, superoxide generation, and apoptosis. In
           certain prokaryotes such as Escherichia coli, PutA is
           also a transcriptional repressor of the proline
           utilization genes.
          Length = 518

 Score = 25.6 bits (57), Expect = 8.8
 Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)

Query: 126 GIQSLIERIEVKKIRELIFA 145
           GI S  ER E++  RE + A
Sbjct: 440 GIHSRDER-EIEYWRERVEA 458


>gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 221

 Score = 25.6 bits (56), Expect = 8.8
 Identities = 8/22 (36%), Positives = 14/22 (63%)

Query: 80  RDASVIIVVEDVADLWALERSK 101
           RD+SV ++V D+ D  + E + 
Sbjct: 93  RDSSVAVIVYDITDRNSFENTS 114


  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    0.139    0.398 

Gapped
Lambda     K      H
   0.267   0.0702    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,379,398
Number of extensions: 120659
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 26
Length of query: 201
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,340,536
Effective search space: 486140032
Effective search space used: 486140032
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: 55 (25.0 bits)