RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15597
         (204 letters)



>gnl|CDD|167581 PRK03670, PRK03670, competence damage-inducible protein A;
           Provisional.
          Length = 252

 Score = 30.9 bits (70), Expect = 0.36
 Identities = 12/33 (36%), Positives = 20/33 (60%)

Query: 150 CEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQM 182
           CE   E ++ FY+ L K+  +DD +  +AR +M
Sbjct: 93  CEDCLERIKEFYEELYKKGLIDDPTLNEARKKM 125


>gnl|CDD|204831 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
           This domain is found in bacteria. This domain is about
           360 amino acids in length. This domain is found
           associated with pfam00271, pfam00176. The function of
           this domain is not known, but structurally it forms an
           alpha-beta fold in nature with a central beta-sheet
           flanked by helices and loops, the beta-sheet being
           mainly antiparallel and flanked by four alpha helices,
           among which the two longer helices exhibit a coiled-coil
           arrangement.
          Length = 362

 Score = 29.8 bits (68), Expect = 0.97
 Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 5/41 (12%)

Query: 168 HNLDDRSTAQARVQM-----QVVSQLELQLQKERDRLQALK 203
             L  ++   A  Q+     Q   Q++ QL  E  RL+ALK
Sbjct: 281 EQLLQKAEKLAEEQLEEIIEQAKQQMQQQLSAELARLKALK 321


>gnl|CDD|236745 PRK10722, PRK10722, hypothetical protein; Provisional.
          Length = 247

 Score = 28.4 bits (64), Expect = 2.2
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 21  DKSAEAMHDMAFQQNQLIHQLEMTQRKYVLQHAIGLQSQASTSRPGQPMM 70
           D   +A+     QQ +L +QLE+T RK  L++   ++ Q S+ +      
Sbjct: 175 DSELDALRQ---QQQRLQYQLELTTRK--LENLTDIERQLSSRKQAGNFS 219


>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing archaeal-type
           C2H2 Zn-finger [General function prediction only].
          Length = 65

 Score = 26.5 bits (58), Expect = 2.5
 Identities = 11/36 (30%), Positives = 16/36 (44%)

Query: 133 AEKVHFLFGHGVCKWPGCEAVCEDVQAFYKHLNKEH 168
           A KV    G    + P C  V    + + +H+NK H
Sbjct: 6   AIKVRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41


>gnl|CDD|130524 TIGR01457, HAD-SF-IIA-hyp2, HAD-superfamily subfamily IIA
           hydrolase, TIGR01457.  This hypothetical equivalog is a
           member of the Class IIA subfamily of the haloacid
           dehalogenase superfamily of aspartate-nucleophile
           hydrolases. The sequences modelled by this equivalog are
           all gram positive (low-GC) bacteria. Sequences found in
           This model are annotated variously as related to NagD or
           4-nitrophenyl phosphatase, and this hypothetical
           equivalog, of all of those within the Class IIA
           subfamily, is most closely related to the E. coli NagD
           enzyme and the PGP_euk equivalog (TIGR01452). However,
           there is presently no evidence that this hypothetical
           equivalog has the same function of either those [Unknown
           function, Enzymes of unknown specificity].
          Length = 249

 Score = 27.9 bits (62), Expect = 3.3
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 5/48 (10%)

Query: 90  ENQDVSIPAGDKSMFGINGLLVSMGISRREWMNGDDQK---ANESYAE 134
           +N    I AG  +  GI+ LLV  G+++RE M  D +K   A +S AE
Sbjct: 203 DNYATDIMAGINA--GIDTLLVHTGVTKREHMTDDMEKPTHAIDSLAE 248


>gnl|CDD|205086 pfam12808, Mto2_bdg, Micro-tubular organiser Mto1 C-term
           Mto2-binding region.  The C-terminal region of the
           micro-tubular organiser protein 1 (mto1) is the binding
           domain for attachment to Mto2p.The full-length Mto1
           protein is required for microtubule nucleation from
           non-spindle pole body MTOCs in fission yeast. The
           interaction of Mto2p with this region of Mto1 is
           critical for anchoring the cytokinetic actin ring to the
           medial region of the cell and for proper coordination of
           mitosis with cytokinesis.
          Length = 52

 Score = 25.1 bits (55), Expect = 7.4
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 165 NKEHNLDDRSTAQARVQMQVVSQLELQLQKERDR 198
            +E  L DRS A+ R++        L+ + ER R
Sbjct: 16  EREARLLDRSGARERLEELDAENRLLKAELERLR 49


>gnl|CDD|222465 pfam13942, Lipoprotein_20, YfhG lipoprotein.  This family includes
           the YfhG protein from E. coli. Members of this family
           have an N-terminal lipoprotein attachment site. The
           members of this family are functionally uncharacterized.
          Length = 180

 Score = 26.5 bits (59), Expect = 7.4
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 5/49 (10%)

Query: 19  DGDKSAEAMHDMAFQQNQLIHQLEMTQRKYVLQHAIGLQSQASTSRPGQ 67
             D   + + +   QQ +L ++LE T RK  L++   ++ Q S+ + GQ
Sbjct: 127 SSDSELDRLRE---QQARLQYELETTTRK--LENLTDIERQLSSRKQGQ 170


>gnl|CDD|233810 TIGR02283, MltB_2, lytic murein transglycosylase.  Members of this
           family are closely related to the MltB family lytic
           murein transglycosylases described by TIGR02282 and are
           likewise all proteobacterial, although that family and
           this one form clearly distinct clades. Several species
           have one member of each family. Many members of this
           family (unlike the MltB family) contain an additional
           C-terminal domain, a putative peptidoglycan binding
           domain (pfam01471), not included in region described by
           this model. Many sequences appear to contain N-terminal
           lipoprotein attachment sites, as does E. coli MltB in
           TIGR02282 [Cell envelope, Biosynthesis and degradation
           of murein sacculus and peptidoglycan].
          Length = 300

 Score = 26.6 bits (59), Expect = 8.9
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 5/45 (11%)

Query: 30  MAFQQNQLIHQLEMTQRKYV-LQHAIGLQSQASTSRPGQPMMMPS 73
             + + +LI  L++ QR  +      G  + A     GQ   +PS
Sbjct: 125 KDYFRTELIAALKILQRGDLTRAAMKGSWAGAM----GQTQFLPS 165


>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
          Length = 956

 Score = 27.1 bits (61), Expect = 8.9
 Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 6/28 (21%)

Query: 176 AQARVQMQVVSQLELQLQKERDRLQALK 203
            QA+ +         +L  E  RL+ALK
Sbjct: 894 EQAKQEAD------EKLSAELSRLEALK 915


  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
   0.317    0.129    0.379 

Gapped
Lambda     K      H
   0.267   0.0796    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,685,103
Number of extensions: 839405
Number of successful extensions: 779
Number of sequences better than 10.0: 1
Number of HSP's gapped: 779
Number of HSP's successfully gapped: 19
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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 (21.7 bits)
S2: 57 (25.6 bits)