RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.1074_1 (169 letters) >gnl|CDD|146637 pfam04106, APG5, Autophagy protein Apg5. Apg5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway. Length = 195 Score = 31.9 bits (73), Expect = 0.091 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 6/63 (9%) Query: 2 TIVNNTFITSSSTTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHP------EWVVDDL 55 ++ S ++L D +S + PE P + K H I +W+ ++L Sbjct: 122 PVIQALIPPLSEEGQPQTLGDALSELLPELFPSSEELAKPIIHGIEVPLDAPLQWLYENL 181 Query: 56 ASP 58 + P Sbjct: 182 SYP 184 >gnl|CDD|48517 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.. Length = 142 Score = 28.6 bits (64), Expect = 0.96 Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%) Query: 76 TPERMGNYTQIMRKSWI-LSGTQEAVDDV 103 TPE + Y + WI L+GT E ++ + Sbjct: 73 TPEVLKAYAKAFGPGWIGLTGTPEEIEAL 101 >gnl|CDD|133117 cd06907, M14_AGBL2-3_like, Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-2, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This subgroup includes the human AGBL-2, and -3, and the mouse cytosolic carboxypeptidase (CCPs)-2, and -3. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. Length = 261 Score = 26.2 bits (58), Expect = 4.6 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 14/70 (20%) Query: 9 ITSSSTTNKESLSD---VVS-RITPEDTPIYSMIKKGTTHSIHPEWVVDDLASPGPNAQL 64 ITS S+ + + V++ R+ P +T S + KG +D L S P+AQL Sbjct: 33 ITSPSSNPSLAAAKKAVVLTARVHPGETNA-SWMMKG---------FLDFLTSNSPDAQL 82 Query: 65 EGDEYSFKTI 74 D + FK + Sbjct: 83 LRDTFIFKIV 92 >gnl|CDD|73140 cd04642, CBS_pair_29, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 126 Score = 26.0 bits (57), Expect = 5.4 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 2/57 (3%) Query: 2 TIVNNTFITSSSTTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLASP 58 TI + ++ +++ TP T + +I K + +H WVVD+ P Sbjct: 60 TITFKELSEKFTDSDGVKSRPLIT-CTPSST-LKEVITKLVANKVHRVWVVDEEGKP 114 >gnl|CDD|31089 COG0746, MobA, Molybdopterin-guanine dinucleotide biosynthesis protein A [Coenzyme metabolism]. Length = 192 Score = 25.7 bits (56), Expect = 6.0 Identities = 8/22 (36%), Positives = 12/22 (54%) Query: 65 EGDEYSFKTINTPERMGNYTQI 86 + +E SF INTPE + + Sbjct: 170 DLEEDSFFNINTPEDLARAREK 191 >gnl|CDD|36824 KOG1611, KOG1611, KOG1611, Predicted short chain-type dehydrogenase [General function prediction only]. Length = 249 Score = 25.6 bits (56), Expect = 7.5 Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 2/38 (5%) Query: 45 SIHPEWVVDDLASPGPNAQLEGDEYSFKTINTPERMGN 82 SIHP WV D+ G A L +E + K + + ++ N Sbjct: 198 SIHPGWVQTDMG--GKKAALTVEESTSKLLASINKLKN 233 >gnl|CDD|30123 cd00295, RNA_Cyclase, RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ATP-dependent conversion of 3'-phosphate at the end of RNA into 2', 3'-cyclic phosphodiester bond. The enzymes are conserved in eucaryotes, bacteria and archaea. The exact biological role of this enzyme is unknown, but it has been proposed that it is likely to function in cellular RNA metabolism and processing. RNA phosphate cyclase has been characterized in human (with at least three isozymes), and E. coli, and it seems to be taxonomically widespread. The crystal structure of RNA phospate cyclase shows that it consists of two domains. The larger domain contains three repeats of a fold originally identified in the bacterial translation initiation factor IF3.. Length = 338 Score = 25.4 bits (55), Expect = 7.5 Identities = 12/42 (28%), Positives = 19/42 (45%) Query: 56 ASPGPNAQLEGDEYSFKTINTPERMGNYTQIMRKSWILSGTQ 97 A+ G A+ SFK + ER + + R I +GT+ Sbjct: 156 AAGGGGAEENFLCASFKELLLGERGSEFGRQFRGEGIAAGTR 197 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 0.310 0.126 0.351 Gapped Lambda K H 0.267 0.0752 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,922,624 Number of extensions: 90886 Number of successful extensions: 159 Number of sequences better than 10.0: 1 Number of HSP's gapped: 159 Number of HSP's successfully gapped: 10 Length of query: 169 Length of database: 6,263,737 Length adjustment: 87 Effective length of query: 82 Effective length of database: 4,383,754 Effective search space: 359467828 Effective search space used: 359467828 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: 54 (24.5 bits)