RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780482|ref|YP_003064895.1| ribonuclease P [Candidatus Liberibacter asiaticus str. psy62] (123 letters) >gnl|CDD|144425 pfam00825, Ribonuclease_P, Ribonuclease P. Length = 107 Score = 74.1 bits (183), Expect = 1e-14 Identities = 40/104 (38%), Positives = 59/104 (56%), Gaps = 5/104 (4%) Query: 7 LKKRRQF-ALVKKGELRKGPFFSLEVLNNNNSNLLPRVGFTVTKKQGC-AVERNRMRRRL 64 LKKR++F A+ +KG F L N+ PR+G +V+KK G AV RNR++R L Sbjct: 5 LKKRKEFQAVFRKGRRVASRHFVLYYRPNSLGY--PRLGISVSKKVGKRAVVRNRIKRLL 62 Query: 65 KEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRR 108 +EA RL + L G D V+IA++ AL F EL + +++ Sbjct: 63 REAFRLNKD-RLPPGLDIVVIARKGALEADFAELLKELEKLLKK 105 >gnl|CDD|30939 COG0594, RnpA, RNase P protein component [Translation, ribosomal structure and biogenesis]. Length = 117 Score = 60.3 bits (146), Expect = 1e-10 Identities = 45/107 (42%), Positives = 65/107 (60%), Gaps = 5/107 (4%) Query: 7 LKKRRQFALV-KKGELRKGPFFSLEVLNNNNSNLLPRVGFTVTKKQ-GCAVERNRMRRRL 64 LKKR++F V KKG+ R+ F + + NN PR+G TV+KK+ G AVERNR++R + Sbjct: 7 LKKRKEFQAVFKKGKRRRNSLFFV-LYGRNNGLDHPRIGLTVSKKKVGNAVERNRIKRLI 65 Query: 65 KEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRRNKR 111 +EA RL L G D V+IA++ L + F EL + ++R KR Sbjct: 66 REAFRL--LQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRAKR 110 >gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain. Length = 216 Score = 28.7 bits (65), Expect = 0.39 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 13/56 (23%) Query: 54 AVERN--RMRRRLKEAVRLCAEGVLK---HGHDYVLIAKRDALFIPFKELCNHFVE 104 A+ N +R R V+L A V+K +GH V +A+ A + F Sbjct: 5 ALRHNIRALRERAGRPVKLMA--VVKANAYGHGAVRVARALA------AGADGFGV 52 >gnl|CDD|30783 COG0434, SgcQ, Predicted TIM-barrel enzyme [General function prediction only]. Length = 263 Score = 27.5 bits (61), Expect = 0.92 Identities = 11/29 (37%), Positives = 16/29 (55%) Query: 51 QGCAVERNRMRRRLKEAVRLCAEGVLKHG 79 +G A E R R RL V++ A+ +KH Sbjct: 129 EGNAAELARYRARLGSRVKVLADVHVKHA 157 >gnl|CDD|176451 cd08769, DAP_dppA_2, Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized putative peptidases. Length = 270 Score = 24.9 bits (55), Expect = 5.2 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 3/59 (5%) Query: 58 NRMRRRLKEAVRLCAEGVLKHGHDYVLIAKRDALF--IPFKELCNHFVERVRRNKRSYY 114 RR + E + E + + G + +++A I ++EL V V R Sbjct: 29 KEARRLMTEELNAVLEELFESGFEEIVVADSHGRMDNIDYEELD-PRVSLVSGYPRPLS 86 >gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, and other MDR family members. This group contains enzymes of the zinc-dependent alcohol dehydrogenase family, including members (aka MDR) identified as 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and N-benzyl-3-pyrrolidinol dehydrogenase. 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase catalyzes the conversion of 6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to 6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This group displays the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 338 Score = 24.9 bits (55), Expect = 6.3 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 11/50 (22%) Query: 61 RRRLKEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRRNK 110 L E + L A+G L + P E+ +ER+ + K Sbjct: 291 PEDLPEVLDLIAKGKLD------PQVET----RPLDEI-PEVLERLHKGK 329 >gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. Length = 312 Score = 24.6 bits (54), Expect = 6.7 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%) Query: 54 AVERNR--MRRRLKEAVRLCAEGVLK----HGHDYVLIAKRDAL 91 AVER+ ++EAV+L A+G L H++ L DA Sbjct: 253 AVERDPRIGLEGMREAVKLIADGRLDLGSLLTHEFPLEELGDAF 296 >gnl|CDD|38059 KOG2848, KOG2848, KOG2848, 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid transport and metabolism]. Length = 276 Score = 24.4 bits (53), Expect = 7.6 Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 5/37 (13%) Query: 79 GHDYVLIAKRDALFIPFKELCNH-----FVERVRRNK 110 + V+IAKR ++P L + F++R RR K Sbjct: 111 PKNCVVIAKRSLFYVPIFGLAMYLSGVVFIDRSRREK 147 >gnl|CDD|145134 pfam01813, ATP-synt_D, ATP synthase subunit D. This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase. Length = 194 Score = 24.1 bits (53), Expect = 9.9 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 10/40 (25%) Query: 59 RMRRRLKEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKEL 98 R++RRLK A R GH +L KRDAL + F+ L Sbjct: 5 RLKRRLKLAQR---------GHK-LLKKKRDALILEFRAL 34 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 0.326 0.139 0.412 Gapped Lambda K H 0.267 0.0797 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,510,466 Number of extensions: 72212 Number of successful extensions: 216 Number of sequences better than 10.0: 1 Number of HSP's gapped: 212 Number of HSP's successfully gapped: 14 Length of query: 123 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 41 Effective length of database: 4,491,799 Effective search space: 184163759 Effective search space used: 184163759 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 (21.6 bits) S2: 51 (23.3 bits)