RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780848|ref|YP_003065261.1| co-chaperonin GroES
[Candidatus Liberibacter asiaticus str. psy62]
         (111 letters)



>gnl|CDD|30583 COG0234, GroS, Co-chaperonin GroES (HSP10) [Posttranslational
           modification, protein turnover, chaperones].
          Length = 96

 Score = 91.0 bits (226), Expect = 6e-20
 Identities = 47/98 (47%), Positives = 72/98 (73%), Gaps = 4/98 (4%)

Query: 9   LRPTRGRVVVRRLQSEIKTATGNILIPDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEV 68
           ++P   RV+V+R++ E KTA G I++PD+  EKP    GE++ VG G  D++G+++  +V
Sbjct: 3   IKPLGDRVLVKRVEEEEKTAGG-IVLPDSAKEKPQ--EGEVVAVGPGRRDENGELVPLDV 59

Query: 69  SKGDIVLFGKWSGTEIKLNDGEEYLVMQESDIMGIVVE 106
             GD VLFGK++GTE+K+ DGEEYL++ ESDI+ IV +
Sbjct: 60  KVGDRVLFGKYAGTEVKI-DGEEYLILSESDILAIVEK 96


>gnl|CDD|73192 cd00320, cpn10, Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10
           cooperates with chaperonin 60 (cpn60 or GroEL), an
           ATPase, to assist the folding and assembly of proteins
           and is found in eubacterial cytosol, as well as in the
           matrix of mitochondria and chloroplasts. It forms
           heptameric rings with a dome-like structure, forming a
           lid to the large cavity of the tetradecameric cpn60
           cylinder and thereby tightly regulating release and
           binding of proteins to the cpn60 surface..
          Length = 93

 Score = 88.3 bits (219), Expect = 4e-19
 Identities = 42/96 (43%), Positives = 69/96 (71%), Gaps = 4/96 (4%)

Query: 9   LRPTRGRVVVRRLQSEIKTATGNILIPDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEV 68
           ++P   RV+V+R+++E KT  G I++PD+  EKP    G+++ VG G  +++G+ +   V
Sbjct: 2   IKPLGDRVLVKRIEAEEKTKGG-IILPDSAKEKPQ--EGKVVAVGPGRRNENGERVPLSV 58

Query: 69  SKGDIVLFGKWSGTEIKLNDGEEYLVMQESDIMGIV 104
             GD VLF K++GTE+KL DGEEYL+++ESDI+ ++
Sbjct: 59  KVGDKVLFPKYAGTEVKL-DGEEYLILRESDILAVI 93


>gnl|CDD|109232 pfam00166, Cpn10, Chaperonin 10 Kd subunit.  This family contains
           GroES and Gp31-like chaperonins. Gp31 is a functional
           co-chaperonin that is required for the folding and
           assembly of Gp23, a major capsid protein, during phage
           morphogenesis.
          Length = 92

 Score = 83.4 bits (207), Expect = 1e-17
 Identities = 42/96 (43%), Positives = 68/96 (70%), Gaps = 5/96 (5%)

Query: 9   LRPTRGRVVVRRLQSEIKTATGNILIPDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEV 68
           ++P   RV+V+R++ E KT  G I++PD+  EKP+   GE++ VG G  + +G+ +  EV
Sbjct: 2   IKPLGDRVLVKRVEEEEKTKGG-IILPDSAKEKPN--QGEVVAVGPGARN-NGERVPLEV 57

Query: 69  SKGDIVLFGKWSGTEIKLNDGEEYLVMQESDIMGIV 104
             GD VLF K++GTE+K+ DGEEYL+++E DI+ ++
Sbjct: 58  KVGDKVLFPKYAGTEVKI-DGEEYLILKEKDILAVI 92


>gnl|CDD|36854 KOG1641, KOG1641, KOG1641, Mitochondrial chaperonin
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 104

 Score = 66.5 bits (162), Expect = 1e-12
 Identities = 33/97 (34%), Positives = 57/97 (58%), Gaps = 3/97 (3%)

Query: 9   LRPTRGRVVVRRLQSEIKTATGNILIPDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEV 68
           + P   RV+V+R+++  KTA G IL+P+    K     G ++ VG G  D+ G+++   V
Sbjct: 11  VVPLLDRVLVQRIEAPTKTAGG-ILLPEKSVGKLL--QGTVVAVGPGSRDKGGEIVPVSV 67

Query: 69  SKGDIVLFGKWSGTEIKLNDGEEYLVMQESDIMGIVV 105
             GD VL  ++ GT++KL D +EY + ++ D +  +V
Sbjct: 68  KVGDRVLLPEYGGTKVKLGDEDEYHLFRDEDDLLAIV 104


>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
           Sorting Nexin Vps5p.  BAR domains are dimerization,
           lipid binding and curvature sensing modules found in
           many different proteins with diverse functions. Sorting
           nexins (SNXs) are Phox homology (PX) domain containing
           proteins that are involved in regulating membrane
           traffic and protein sorting in the endosomal system.
           SNXs differ from each other in their lipid-binding
           specificity, subcellular localization and specific
           function in the endocytic pathway. A subset of SNXs also
           contain BAR domains. The PX-BAR structural unit
           determines the specific membrane targeting of SNXs.
           Vsp5p is the yeast counterpart of human SNX1 and is part
           of the retromer complex, which functions in the
           endosome-to-Golgi retrieval of vacuolar protein sorting
           receptor Vps10p, the Golgi-resident membrane protein
           A-ALP, and endopeptidase Kex2. BAR domains form dimers
           that bind to membranes, induce membrane bending and
           curvature, and may also be involved in protein-protein
           interactions.
          Length = 216

 Score = 27.3 bits (61), Expect = 0.89
 Identities = 8/41 (19%), Positives = 20/41 (48%)

Query: 67  EVSKGDIVLFGKWSGTEIKLNDGEEYLVMQESDIMGIVVEE 107
           E+SK    L    +  + ++ +  E   +Q+   +G+ ++E
Sbjct: 55  ELSKSLSDLLAALAEVQKRIKESLERQALQDVLTLGVTLDE 95


>gnl|CDD|36390 KOG1175, KOG1175, KOG1175, Acyl-CoA synthetase [Lipid transport and
           metabolism].
          Length = 626

 Score = 27.2 bits (60), Expect = 1.00
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 27  TATGNILI---PDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEVSKGDIVLFGKW 79
           T TG I I   P  +  KP ++          ++D++G  + P    G++ L   W
Sbjct: 395 TETGGICITPKPGKLPIKPGSAGKPFPGYDVQILDENGNELPPSTGNGELRLKPPW 450


>gnl|CDD|143499 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzyme, Alanine Racemase 2.  This
           subfamily is composed of bacterial alanine racemases (EC
           5.1.1.1) with similarity to Yersinia pestis and Vibrio
           cholerae alanine racemase (AR) 2. ARs catalyze the
           interconversion between L- and D-alanine, an essential
           component of the peptidoglycan layer of bacterial cell
           walls. These proteins are similar to other bacterial ARs
           and are fold type III PLP-dependent enzymes containing
           contains an N-terminal PLP-binding TIM-barrel domain and
           a C-terminal beta-sandwich domain. They exist as
           homodimers with active sites that lie at the interface
           between the TIM barrel domain of one subunit and the
           beta-sandwich domain of the other subunit. Homodimer
           formation and the presence of the PLP cofactor are
           required for catalytic activity.
          Length = 365

 Score = 26.9 bits (60), Expect = 1.2
 Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 1/28 (3%)

Query: 66  PEVSKGD-IVLFGKWSGTEIKLNDGEEY 92
           P V  GD +VLFGK  G EI   + EE 
Sbjct: 317 PGVKAGDEVVLFGKQGGAEITAAEIEEG 344


>gnl|CDD|110955 pfam02007, MtrH, Tetrahydromethanopterin S-methyltransferase MtrH
           subunit.  The enzyme tetrahydromethanopterin
           S-methyltransferase EC:2.1.1.86 is composed of eight
           subunits. The enzyme is a membrane- associated enzyme
           complex which catalyses an energy-conserving,
           sodium-ion-translocating step in methanogenesis from
           hydrogen and carbon dioxide.
          Length = 296

 Score = 25.5 bits (56), Expect = 3.7
 Identities = 25/98 (25%), Positives = 35/98 (35%), Gaps = 16/98 (16%)

Query: 20  RLQSEIKTATGNILIPDTVSEKPSASSGEIMWVGAGVMDQSGKVIEPEVSKGDIVLFGKW 79
             Q E+   TGN  +     E P A    I +V A V D    +   E   G++ L    
Sbjct: 54  NTQEELSDETGNPYLVQIFGETPEAIIRYIDFV-ADVTDAPFLIDSTE---GEVRLAAAK 109

Query: 80  SGTEIKLND------------GEEYLVMQESDIMGIVV 105
             TE+ L D              E   + ESD+   +V
Sbjct: 110 YATEVGLADRAIYNSINASIEDSEIEALAESDVEAAIV 147


>gnl|CDD|146502 pfam03903, Phage_T4_gp36, Phage T4 tail fibre. 
          Length = 219

 Score = 25.2 bits (55), Expect = 4.2
 Identities = 7/23 (30%), Positives = 13/23 (56%)

Query: 27  TATGNILIPDTVSEKPSASSGEI 49
           T TGN+  P+  S+ P++    +
Sbjct: 179 TMTGNLTAPNFFSQNPASQPSHV 201


>gnl|CDD|58640 cd03584, NTR_complement_C4, NTR/C345C domain, complement C4
          subfamily; The NTR domain found in complement C4 is
          also known as the C345C domain because it occurs at the
          C-terminus of complement C3, C4 and C5. Complement C4
          is a key player in the activation of the component
          classical pathway. C4 is cleaved by activated C1 to
          yield C4a anaphylatoxin, and the larger fragment C4b,
          an essential component of the C3- and C5-convertase
          enzymes. C4b binds covalently to the surface of
          pathogens through a reactive thioester. The role of the
          NTR/C345C domain in C4 (C4b) is unclear..
          Length = 153

 Score = 24.5 bits (53), Expect = 6.8
 Identities = 9/28 (32%), Positives = 16/28 (57%)

Query: 68 VSKGDIVLFGKWSGTEIKLNDGEEYLVM 95
          V   +  +F K    +++L  G+EYL+M
Sbjct: 70 VKPEETRVFLKRLSCKLELKKGKEYLIM 97


  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
   0.311    0.132    0.371 

Gapped
Lambda     K      H
   0.267   0.0603    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,296,561
Number of extensions: 58412
Number of successful extensions: 89
Number of sequences better than 10.0: 1
Number of HSP's gapped: 79
Number of HSP's successfully gapped: 13
Length of query: 111
Length of database: 6,263,737
Length adjustment: 77
Effective length of query: 34
Effective length of database: 4,599,844
Effective search space: 156394696
Effective search space used: 156394696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.7 bits)