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)