RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy1723
         (246 letters)



>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 929

 Score =  131 bits (330), Expect = 1e-34
 Identities = 73/226 (32%), Positives = 109/226 (48%), Gaps = 24/226 (10%)

Query: 36  ARFDNILGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFLFHLVGPKMRNFKTSRRS 95
           AR   +L +       ++  EI   F    +V R+A MLNY L  L GPK  + K   + 
Sbjct: 705 ARNSCLLVDGCFDLFTHILDEIPDAFLVDEIVSRLARMLNYNLKILTGPKCTDLKV--KD 762

Query: 96  PGKQEGVGSIPAERKLK------LNISTSPYY---------YFSLSL---PPSLLYLARI 137
           P +        A+  L+      +N+ +   +          F +        +     +
Sbjct: 763 PEQY----GFNAKNLLRRMVMVYINLRSESKFVEAVASDKRSFDIDFFRRALRICENKYL 818

Query: 138 GGASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLD 197
              S I +LR     +EK+      +E  +   PDE+LDP+M TIM +PV LP+SR T+D
Sbjct: 819 ISESQIEELRSFINRLEKVRVIEAVEEEDMGDVPDEFLDPLMFTIMKDPVKLPTSRITID 878

Query: 198 KSTIARHLLSDQTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQK 243
           +STI  HLLSD TDPFNR PLT++ V PN +L+ +I  + +   QK
Sbjct: 879 RSTIKAHLLSDGTDPFNRMPLTLDDVTPNAELREKINRFYKCKGQK 924


>gnl|CDD|203049 pfam04564, U-box, U-box domain.  This domain is related to the Ring
           finger pfam00097 but lacks the zinc binding residues.
          Length = 73

 Score = 98.9 bits (247), Expect = 5e-27
 Identities = 39/71 (54%), Positives = 50/71 (70%), Gaps = 2/71 (2%)

Query: 170 APDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS-DQTDPFNRSPLTMEQVIPNTQ 228
            PDE+LDPI   +M +PV LPS   T D+STI RHLLS D TDPF R PLT +Q+IPN +
Sbjct: 1   IPDEFLDPITLELMKDPVILPSG-ITYDRSTIERHLLSVDPTDPFTREPLTHDQLIPNLE 59

Query: 229 LQTQIQDWIRQ 239
           L+ +I  W+ +
Sbjct: 60  LKEKIDAWLEE 70


>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core.  This is
           the most conserved part of the core region of Ufd2P
           ubiquitin elongating factor or E4, running from helix
           alpha-11 to alpha-38. It consists of 31 helices of
           variable length connected by loops of variable size
           forming a compact unit; the helical packing pattern of
           the compact unit consists of five structural repeats
           that resemble tandem Armadillo (ARM) repeats. This
           domain is involved in ubiquitination as it binds Cdc48p
           and escorts ubiquitinated proteins from Cdc48p to the
           proteasome for degradation. The core is structurally
           similar to the nuclear transporter protein
           importin-alpha. The core is associated with the U-box at
           the C-terminus, pfam04564, which has ligase activity.
          Length = 625

 Score = 94.6 bits (236), Expect = 3e-22
 Identities = 31/69 (44%), Positives = 39/69 (56%)

Query: 22  RKSDSGFLQHIGMMARFDNILGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFLFHL 81
           R+     L+ +   A+    L NET+  L+ LTSEI   F    +VDR+AAMLNY L  L
Sbjct: 480 REERESELRQLERQAKSYLQLANETVKLLKLLTSEIPKPFLSPEIVDRLAAMLNYNLDQL 539

Query: 82  VGPKMRNFK 90
           VGPK  N K
Sbjct: 540 VGPKCSNLK 548


>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain.  Modified RING
           finger domain, without the full complement of
           Zn2+-binding ligands. Probable involvement in
           E2-dependent ubiquitination.
          Length = 63

 Score = 81.1 bits (201), Expect = 3e-20
 Identities = 31/64 (48%), Positives = 41/64 (64%), Gaps = 1/64 (1%)

Query: 173 EYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVIPNTQLQTQ 232
           E+L PI   +M +PV LPS  QT ++S I + LLS  TDP    PLT E +IPN  L++ 
Sbjct: 1   EFLCPISLEVMKDPVILPSG-QTYERSAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSA 59

Query: 233 IQDW 236
           IQ+W
Sbjct: 60  IQEW 63


>gnl|CDD|237449 PRK13616, PRK13616, lipoprotein LpqB; Provisional.
          Length = 591

 Score = 31.5 bits (72), Expect = 0.39
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 129 PSLLYLARIGGASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVT 188
              LY A   G +L+PD R VAV  ++L  +L S   LL   P   L P +  ++    +
Sbjct: 173 RKTLYFADPTGRTLVPDPRWVAVSQDQLATELVS---LLIAGPRPELAPAVRNLLPPGAS 229

Query: 189 L--PSSRQTLDKSTIAR 203
           L  P +R    KS +  
Sbjct: 230 LRGPVTRADGGKSGVGV 246


>gnl|CDD|237620 PRK14136, recX, recombination regulator RecX; Provisional.
          Length = 309

 Score = 30.7 bits (69), Expect = 0.54
 Identities = 15/33 (45%), Positives = 23/33 (69%), Gaps = 3/33 (9%)

Query: 135 ARIGGASLIPDLRRVAV---LVEKLGAQLQSDE 164
           +R+G A ++ +L+R AV   LVE +GAQL+  E
Sbjct: 224 SRVGSARIVSELKRHAVGDALVESVGAQLRETE 256


>gnl|CDD|220833 pfam10646, Germane, Sporulation and spore germination.  The GerMN
           domain is a region of approximately 100 residues that is
           found, duplicated, in the Bacillus GerM protein and is
           implicated in both sporulation and spore germination.
           The domain is found in a number of different bacterial
           species both alone and in association with other domains
           such as Amidase_3 pfam01520, Gmad1 and Gmad2. It is
           predicted to have a novel alpha-beta fold.
          Length = 116

 Score = 28.1 bits (63), Expect = 2.3
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 132 LYLARIGGASLIPDLRRVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTL 189
           LY     G  L+P  R V        A L   E LL G P + L P + +++     L
Sbjct: 3   LYFVDPDGTKLVPVTRWVPKTDSLATAAL---EELLKG-PSDELAPGLVSVLPPGTKL 56


>gnl|CDD|131824 TIGR02777, LigD_PE_dom, DNA ligase D, 3'-phosphoesterase domain.
           Most sequences in this family are the 3'-phosphoesterase
           domain of a multidomain, multifunctional DNA ligase,
           LigD, involved, along with bacterial Ku protein, in
           non-homologous end joining, the less common of two
           general mechanisms of repairing double-stranded breaks
           in DNA sequences. LigD is variable in architecture, as
           it lacks this domain in Bacillus subtilis, is permuted
           in Mycobacterium tuberculosis, and occasionally is
           encoded by tandem ORFs rather than as a multifuntional
           protein. In a few species (Dehalococcoides ethenogenes
           and the archaeal genus Methanosarcina), sequences
           corresponding to the ligase and polymerase domains of
           LigD are not found, and the role of this protein is
           unclear [DNA metabolism, DNA replication, recombination,
           and repair].
          Length = 156

 Score = 27.7 bits (62), Expect = 3.8
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 85  KMRNF-KTSRRSPGKQEGVGSIPAERKLKLNISTSPYYYFSLSLPPSLLYLARIGGASLI 143
           + R+F KT   S       G+  A   ++ + ++  +Y F L L   L   A   G SL 
Sbjct: 6   RKRDFNKTPEPSGTAARPSGN-QAIFVVQKHHASRLHYDFRLELDGVLKSWAVPKGPSLD 64

Query: 144 PDLRRVAVLVE 154
           P  +R+AV VE
Sbjct: 65  PADKRLAVHVE 75


>gnl|CDD|239442 cd03326, MR_like_1, Mandelate racemase (MR)-like subfamily of the
           enolase superfamily, subgroup 1. Enzymes of this
           subgroup share three conserved carboxylate ligands for
           the essential divalent metal ion (usually Mg2+), two
           aspartates and a glutamate, and conserved catalytic
           residues,  a Lys-X-Lys motif and a conserved
           histidine-aspartate dyad. This subgroup's function is
           unknown.
          Length = 385

 Score = 28.1 bits (63), Expect = 5.2
 Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)

Query: 136 RIGGASLIPDLRRVAVLVEKLG--AQLQSD 163
           +IGGA L  DLRR+   ++ LG  A+L  D
Sbjct: 182 KIGGAPLDEDLRRIEAALDVLGDGARLAVD 211


>gnl|CDD|182464 PRK10441, PRK10441, iron-enterobactin transporter membrane protein;
           Provisional.
          Length = 335

 Score = 27.4 bits (61), Expect = 7.1
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 123 FSLSLPPSLLYLARIGGASLIPDLRRVAVLVEKLGA 158
            +L   P+LL  A I G  L+P   RV+V+   +GA
Sbjct: 284 VTLLATPALLLFADIIGRLLVPGELRVSVVSAFIGA 319


>gnl|CDD|146285 pfam03566, Peptidase_A21, Peptidase family A21. 
          Length = 628

 Score = 27.2 bits (60), Expect = 9.5
 Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 14/74 (18%)

Query: 176 DPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSD-------QTDPFNRS-----PLTMEQV 223
           D +  TI    VT+         + + R + +D        T   NR      PLT  Q 
Sbjct: 378 DNVTITITAPTVTVTVLASLTSSNGVFRGVTADSGARLNLDTAALNRLSIPLPPLTFGQT 437

Query: 224 IPNTQ--LQTQIQD 235
           + NT    Q  +++
Sbjct: 438 MQNTPKTEQFLLKE 451


>gnl|CDD|237360 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
          Length = 410

 Score = 27.2 bits (61), Expect = 9.6
 Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 1/21 (4%)

Query: 215 RSPLTMEQVIPNTQ-LQTQIQ 234
           R  LT EQV  N +    QI 
Sbjct: 89  RKLLTDEQVQHNAKTYTEQIF 109


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.322    0.136    0.393 

Gapped
Lambda     K      H
   0.267   0.0768    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,478,018
Number of extensions: 1187620
Number of successful extensions: 992
Number of sequences better than 10.0: 1
Number of HSP's gapped: 988
Number of HSP's successfully gapped: 17
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
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: 58 (26.0 bits)