RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.1080_1 (110 letters) >gnl|CDD|146059 pfam03237, Terminase_6, Terminase-like family. This family represents a group of terminase proteins. Length = 380 Score = 32.0 bits (73), Expect = 0.033 Identities = 11/25 (44%), Positives = 12/25 (48%) Query: 1 MAGNQLGKTLAGAAEAAMHLSGCYP 25 + Q GKT A A EA H G P Sbjct: 3 LGSRQSGKTFAFAREALRHALGNGP 27 >gnl|CDD|173801 cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases. Streptococcal C5a peptidase (SCP), is a highly specific protease and adhesin/invasin. The subtilisin-like protease domain is located at the N-terminus and contains a protease-associated domain inserted into a loop. There are three fibronectin type III (Fn) domains at the C-terminus. SCP binds to integrins with the help of Arg-Gly-Asp motifs which are thought to stabilize conformational changes required for substrate binding. Peptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Length = 346 Score = 27.2 bits (61), Expect = 1.1 Identities = 7/21 (33%), Positives = 11/21 (52%) Query: 59 GEPMSPDQQGSGMIPANKVLN 79 SP +QG+G+I K + Sbjct: 326 KTYYSPRRQGAGLIDVAKAIA 346 >gnl|CDD|31988 COG1803, MgsA, Methylglyoxal synthase [Carbohydrate transport and metabolism]. Length = 142 Score = 26.4 bits (58), Expect = 1.6 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 6/57 (10%) Query: 26 SWWRGYR-FLQPIVMVAGSVTYELTRDG----IQRLLLGEPMSPDQQGSGMIPANKV 77 ++ + ++ L + A T L ++ + RL G PM DQQ +I K+ Sbjct: 21 NFVQAHKELLSRHDLYATGTTGGLIQEATGLNVHRLKSG-PMGGDQQIGALIAEGKI 76 >gnl|CDD|31521 COG1330, RecC, Exonuclease V gamma subunit [DNA replication, recombination, and repair]. Length = 1078 Score = 26.1 bits (57), Expect = 2.1 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%) Query: 50 RDGIQRLLLGEPMSPDQQ-GSGMIPANKV 77 R G++R+LLG M D G++P ++V Sbjct: 492 RFGLERMLLGYAMDEDAGEWQGVLPYDEV 520 >gnl|CDD|39179 KOG3976, KOG3976, KOG3976, Mitochondrial F1F0-ATP synthase, subunit b/ATP4 [Energy production and conversion]. Length = 247 Score = 26.1 bits (57), Expect = 2.1 Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 2/50 (4%) Query: 61 PMSPDQQGSGMIPANKVLNMTRRSNIAGAYSTVT--VRHLSGRDIGFIIE 108 P P + G+IP + ++ + G Y + + +++ I + Sbjct: 47 PEYPGKVRLGIIPDEWFTFLYTKTGVTGPYLFGAGLIAYAISKELYVIED 96 >gnl|CDD|146611 pfam04072, LCM, Leucine carboxyl methyltransferase. Family of leucine carboxyl methyltransferases EC:2.1.1.-. This family may need divides a the full alignment contains a significantly shorter mouse sequence. Length = 175 Score = 25.2 bits (56), Expect = 4.1 Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 5/38 (13%) Query: 25 PSWWR-----GYRFLQPIVMVAGSVTYELTRDGIQRLL 57 W G+ +P + VA + LT + + LL Sbjct: 134 DDWLDALRAAGFDPSRPTLFVAEGLLMYLTEEAVDALL 171 >gnl|CDD|173814 cd07489, Peptidases_S8_5, Peptidase S8 family domain, uncharacterized subfamily 5. gap in seq This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Length = 312 Score = 24.9 bits (55), Expect = 5.4 Identities = 9/25 (36%), Positives = 13/25 (52%) Query: 57 LLGEPMSPDQQGSGMIPANKVLNMT 81 L + QQG+G++ A K L T Sbjct: 276 ALPDLAPVAQQGAGLVNAYKALYAT 300 >gnl|CDD|153115 cd01057, AAMH_A, Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphthol. Both enzyme systems consist of three components: the hydroxylase, a coupling protein and a reductase. In the MMO hydroxylase, dioxygen and substrate interact with the diiron center in a hydrophobic cavity at the active site. The reductase component and protein coupling factor provide electrons from NADH for reducing the oxidized binuclear iron-oxo cluster to its reduced form. Reaction with dioxygen produces a peroxy-bridged complex and dehydration leads to the formation of complex Q, which is thought to be the oxygenating species that carries out the insertion of an oxygen atom into a C-H bond of the substrate. The toluene monooxygenase systems, toluene 2-, 3-, and 4-monooxygenase, are similar to MMO but with an additional component, a Rieske-type ferredoxin. The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Alkane omega-hydroxylase (AlkB) and xylene monooxygenase are members of a distinct class of integral membrane diiron proteins and are not included in this CD. Length = 465 Score = 24.6 bits (54), Expect = 6.1 Identities = 4/12 (33%), Positives = 7/12 (58%) Query: 27 WWRGYRFLQPIV 38 +WR +R +V Sbjct: 248 FWRQHRLFDALV 259 >gnl|CDD|133035 cd04192, GT_2_like_e, Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. Length = 229 Score = 24.2 bits (53), Expect = 7.6 Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 3/26 (11%) Query: 25 PSWW-RGYRFLQ--PIVMVAGSVTYE 47 +W F+Q I +VAG V Y Sbjct: 97 SNWLLTFVAFIQKEQIGLVAGPVIYF 122 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 0.320 0.135 0.407 Gapped Lambda K H 0.267 0.0783 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,296,256 Number of extensions: 58960 Number of successful extensions: 107 Number of sequences better than 10.0: 1 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 10 Length of query: 110 Length of database: 6,263,737 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,621,453 Effective search space: 157129402 Effective search space used: 157129402 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (23.3 bits)