RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6706
         (119 letters)



>gnl|CDD|217436 pfam03226, Yippee, Yippee putative zinc-binding protein. 
          Length = 109

 Score =  170 bits (432), Expect = 2e-56
 Identities = 59/109 (54%), Positives = 78/109 (71%)

Query: 1   MGRIFLDHIGGSRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRV 60
           MGR+F+ ++ G R++SC  C T L    ++IS  FTG  GRA+LF+RVVN+   + +DR 
Sbjct: 1   MGRLFVVYLTGGRIYSCKHCKTHLALHSDIISKSFTGRHGRAYLFNRVVNVVEGEPEDRQ 60

Query: 61  MLTGRHMVRDVSCKNCNTKLGWVYEFALEETQRYKEGRVILERALVTES 109
           MLTG H VRD+ C  C T LGW YEFA EE+Q+YKEG+ ILERAL+T+ 
Sbjct: 61  MLTGLHTVRDIFCVGCGTTLGWKYEFAYEESQKYKEGKFILERALITKI 109


>gnl|CDD|183375 PRK11908, PRK11908, NAD-dependent epimerase/dehydratase family
           protein; Provisional.
          Length = 347

 Score = 31.6 bits (72), Expect = 0.059
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 14/58 (24%)

Query: 53  YSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEFALEETQR----YKEGRVILERALV 106
           Y DVQ+RV              N   +LGW  +  +++  R       G V   RALV
Sbjct: 299 YQDVQNRV----------PKIDNTMQELGWAPKTTMDDALRRIFEAYRGHVAEARALV 346


>gnl|CDD|100115 cd05804, StaR_like, StaR_like; a well-conserved protein found in
           bacteria, plants, and animals. A family member from
           Streptomyces toyocaensis, StaR is part of a gene cluster
           involved in the biosynthesis of glycopeptide antibiotics
           (GPAs), specifically A47934. It has been speculated that
           StaR could be a flavoprotein hydroxylating a tyrosine
           sidechain. Some family members have been annotated as
           proteins containing tetratricopeptide (TPR) repeats,
           which may at least indicate mostly alpha-helical
           secondary structure.
          Length = 355

 Score = 27.6 bits (62), Expect = 1.3
 Identities = 8/22 (36%), Positives = 9/22 (40%)

Query: 84  YEFALEETQRYKEGRVILERAL 105
             F LEE  +Y        RAL
Sbjct: 120 LAFGLEEAGQYDRAEEAARRAL 141


>gnl|CDD|215415 PLN02776, PLN02776, prenyltransferase.
          Length = 341

 Score = 27.0 bits (60), Expect = 2.4
 Identities = 10/35 (28%), Positives = 13/35 (37%)

Query: 42  AFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNC 76
             L HRV N N  D++    LT     R    +  
Sbjct: 269 LLLLHRVPNDNQVDLRQESELTESLDGRAKGREET 303


>gnl|CDD|233569 TIGR01776, TonB-tbp-lbp, TonB-dependent lactoferrin and transferrin
           receptors.  This family of TonB-dependent receptors are
           responsible for import of iron from the mammalian iron
           carriers lactoferrin and transferrin across the outer
           membrane. These receptors are found only in bacteria
           which can infect mammals such as Moraxella, Mannheimia,
           Neisseria, Actinobacillus, Pasteurella, Haemophilus and
           Histophilus species [Transport and binding proteins,
           Cations and iron carrying compounds, Transport and
           binding proteins, Porins].
          Length = 932

 Score = 27.1 bits (60), Expect = 2.4
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 25  TNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRH-MVRDVSCKNCNTKLGWV 83
           T RR  +  R+       +L    ++L+   ++ R  L   H        KNC   L   
Sbjct: 418 TKRRYGLEYRYKNEDYDRWLDTAKLSLDKQKIELRSRLQELHCSQYPKVDKNCRPSLDKP 477

Query: 84  YEFALEETQRYKEGRVIL 101
           Y F   +   YKE   ++
Sbjct: 478 YSFYKNDRNHYKEKHNVI 495


>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
           [Inorganic ion transport and metabolism].
          Length = 254

 Score = 26.8 bits (60), Expect = 3.2
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 98  RVILERALVTESDVKILD 115
           RV+L RAL    D+ +LD
Sbjct: 147 RVLLARALAQNPDLLLLD 164


>gnl|CDD|181546 PRK08751, PRK08751, putative long-chain fatty acyl CoA ligase;
           Provisional.
          Length = 560

 Score = 26.4 bits (58), Expect = 4.3
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 16/56 (28%)

Query: 2   GRIFLDHIGGSRLFSCAACDTILTNRR-------ELISTRFTGATGRAFLFHRVVN 50
           G +F+  IGG        C+ +++N R       EL  TRFT  TG   LF+ ++N
Sbjct: 273 GLVFMK-IGG--------CNHLISNPRDMPGFVKELKKTRFTAFTGVNTLFNGLLN 319


>gnl|CDD|225674 COG3132, COG3132, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 215

 Score = 25.9 bits (57), Expect = 4.6
 Identities = 13/26 (50%), Positives = 20/26 (76%), Gaps = 1/26 (3%)

Query: 48 VVNLNYSDVQDRV-MLTGRHMVRDVS 72
          V+NL+ S+VQ+++  L  RH+VR VS
Sbjct: 47 VMNLSESEVQEQLDNLEKRHLVRTVS 72


>gnl|CDD|218816 pfam05936, DUF876, Bacterial protein of unknown function (DUF876). 
           This family consists of a series of hypothetical
           bacterial sequences of unknown function.
          Length = 427

 Score = 25.6 bits (57), Expect = 7.9
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 18/71 (25%)

Query: 2   GRIFLD--------HIGGS-RLFSCAAC-DTILTNRRELISTRFTGATGRAFLFHRVVNL 51
           G + LD        +IG S  L         +L  R E ++ R  G++ + F        
Sbjct: 160 GSVILDEDFIPPCLNIGASPVLTRLLRELLGLLRARAEALAGRLRGSSQQKF-------- 211

Query: 52  NYSDVQDRVML 62
             +DV D ++L
Sbjct: 212 GVADVSDFLLL 222


>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
          heterogeneous nuclear ribonucleoprotein A subfamily.
          This subfamily corresponds to the RRM2 of hnRNP A0,
          hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
          hnRNP A0 is a low abundance hnRNP protein that has been
          implicated in mRNA stability in mammalian cells. It has
          been identified as the substrate for MAPKAP-K2 and may
          be involved in the lipopolysaccharide (LPS)-induced
          post-transcriptional regulation of tumor necrosis
          factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
          macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
          an abundant eukaryotic nuclear RNA-binding protein that
          may modulate splice site selection in pre-mRNA
          splicing. hnRNP A2/B1 is an RNA trafficking response
          element-binding protein that interacts with the hnRNP
          A2 response element (A2RE). Many mRNAs, such as myelin
          basic protein (MBP), myelin-associated oligodendrocytic
          basic protein (MOBP), carboxyanhydrase II (CAII),
          microtubule-associated protein tau, and amyloid
          precursor protein (APP) are trafficked by hnRNP A2/B1.
          hnRNP A3 is also a RNA trafficking response
          element-binding protein that participates in the
          trafficking of A2RE-containing RNA. The hnRNP A
          subfamily is characterized by two RNA recognition
          motifs (RRMs), also termed RBDs (RNA binding domains)
          or RNPs (ribonucleoprotein domains), followed by a long
          glycine-rich region at the C-terminus. .
          Length = 73

 Score = 24.5 bits (54), Expect = 8.2
 Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 4/45 (8%)

Query: 29 ELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSC 73
          E+++ + TG   R F F   V  +  D  D+++L   H +     
Sbjct: 30 EIVTDKETG-KKRGFAF---VTFDDYDPVDKIVLQKYHTINGHRV 70


>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
           metal-type transporters.  This family includes
           transporters involved in the uptake of various metallic
           cations such as iron, manganese, and zinc. The ATPases
           of this group of transporters are very similar to
           members of iron-siderophore uptake family suggesting
           that they share a common ancestor. The best
           characterized metal-type ABC transporters are the
           YfeABCD system of Y. pestis, the SitABCD system of
           Salmonella enterica serovar Typhimurium, and the SitABCD
           transporter of Shigella flexneri. Moreover other
           uncharacterized homologs of these metal-type
           transporters are mainly found in pathogens like
           Haemophilus or enteroinvasive E. coli isolates.
          Length = 213

 Score = 25.2 bits (56), Expect = 8.4
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 98  RVILERALVTESDVKILD 115
           RV+L RALV + D+ +LD
Sbjct: 140 RVLLARALVQDPDLLLLD 157


>gnl|CDD|222644 pfam14279, HNH_5, HNH endonuclease.  This domain is related to
          other HNH domain families such as pfam01844. Suggesting
          that these proteins have a nucleic acid cleaving
          function.
          Length = 69

 Score = 24.2 bits (53), Expect = 9.4
 Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 1/20 (5%)

Query: 62 LTGRHMVRDVSCKNCNTKLG 81
          + G   + +V CK CN+KLG
Sbjct: 23 IGGHLKINNV-CKTCNSKLG 41


  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
   0.326    0.139    0.417 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,030,300
Number of extensions: 508918
Number of successful extensions: 652
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 17
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.2 bits)