RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780801|ref|YP_003065214.1| hypothetical protein CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62] (222 letters) >gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Length = 222 Score = 241 bits (618), Expect = 1e-64 Identities = 89/215 (41%), Positives = 122/215 (56%), Gaps = 10/215 (4%) Query: 11 KQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70 +++I +A A R D V+LVAVSK V ++ IR A+ GQ F EN++QEA K Sbjct: 9 RERIAAAAERAGRDPDEVTLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKA-EELP 67 Query: 71 EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGY 130 + D++ FIG LQ+NKV V LFD+I +V K A L+ K+ R L V +QVN G Sbjct: 68 DPDIEWHFIGHLQTNKVKYAVRLFDLIHSVDSLKLAEELNKRAEKEGRVLDVLVQVNIGG 127 Query: 131 EIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPK---PHFYLLSEIARECK-- 185 E KSG+ P + ++ + L + GLM I P +P+ P+F L E+ E Sbjct: 128 EESKSGVAPEELEELLEEIAALPNLRIRGLMTIAPLTEDPEEVRPYFRELRELRDELGAK 187 Query: 186 ----LTKLSMGMTRDFELAIASGATSVRIGSGIFG 216 L +LSMGM+ DFE+AI GAT VRIG+ IFG Sbjct: 188 GGVNLKELSMGMSGDFEIAIEEGATLVRIGTAIFG 222 >gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General function prediction only]. Length = 228 Score = 220 bits (562), Expect = 3e-58 Identities = 86/227 (37%), Positives = 124/227 (54%), Gaps = 8/227 (3%) Query: 1 MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60 M + L +++I +A A R SV+LVAVSK V ++ IR A GQ F EN++QE Sbjct: 1 MDIKENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYEAGQRHFGENRVQE 60 Query: 61 AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFL 120 A K L+ D++ FIG LQSNKV + FD I ++ R K A L+ ++ + L Sbjct: 61 ALDKIEALKDLPDIEWHFIGPLQSNKVKLVAENFDWIHSLDRLKLAKELNKRALELPKPL 120 Query: 121 PVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEI 180 V IQVN E KSG+ P + + ++ L + GLM IPP +P+ F + ++ Sbjct: 121 NVLIQVNISGEESKSGVPPEELDELAQEVQELPNLELRGLMTIPPLTDDPEEIFAVFRKL 180 Query: 181 A--------RECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219 + + +LSMGM+ D+E+AIA GAT VRIG+ IFG R Sbjct: 181 RKLFDELKAKYPPIDELSMGMSNDYEIAIAEGATMVRIGTAIFGARD 227 >gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn. Length = 224 Score = 167 bits (426), Expect = 2e-42 Identities = 85/224 (37%), Positives = 112/224 (50%), Gaps = 8/224 (3%) Query: 2 SLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEA 61 ++ L KQ+I +A A R SV L+AVSK + IR A + GQ F EN +QEA Sbjct: 1 NIAENLAQVKQRIAQAAKQAGRDPSSVQLLAVSKTKPADAIREAYAAGQRHFGENYVQEA 60 Query: 62 KKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLP 121 +K LR D++ FIG +QSNK I FD + +V R K A L+ + L Sbjct: 61 LEKIEALRDLQDIEWHFIGPIQSNKTKLIAENFDWVHSVDRLKIAKRLNDQRPAGLPPLN 120 Query: 122 VYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPA---MGNPKPHFYLLS 178 V IQVN E KSG+ P + Q L + GLM IP + F L Sbjct: 121 VCIQVNISGEDSKSGVAPEDAAELAEAISQLPNLRLRGLMAIPAPTDDEAAQRAAFKRLR 180 Query: 179 EIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGE 217 ++ + K L LSMGM+ D E AIA+G+T VRIG+ IFG Sbjct: 181 QLFDQLKKQYPDLDTLSMGMSGDLEAAIAAGSTMVRIGTAIFGA 224 >gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins. This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog). Length = 227 Score = 136 bits (345), Expect = 4e-33 Identities = 81/225 (36%), Positives = 118/225 (52%), Gaps = 25/225 (11%) Query: 11 KQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70 +Q ++ ++ K P LVAVSK ++ I+ A GQ F EN +QE +K L Sbjct: 9 RQAVKRAS--KKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI 66 Query: 71 EWDVQLRFIGSLQSNKVSEIVS---LFDVIETVSREKTASLL--SLEMIKQSRFLPVYIQ 125 D++ FIG LQSNKV +++ L+ ++ETV EK A L + E + + L V +Q Sbjct: 67 --DIKWHFIGHLQSNKVKKLLKVPNLY-MVETVDSEKLADKLNKAWEKLGEREPLKVMVQ 123 Query: 126 VNTGYEIQKSGIMPNQTKDFVILCRQKYQ-LNVEGLMCIPPAMGN-----PKPHFYLLSE 179 VNT E KSG+ P++ + V ++ L GLM I + G P P F L + Sbjct: 124 VNTSGEESKSGLEPSEAVELVKHIIEECPNLKFSGLMTIG-SFGYSLSSGPNPDFLCLVD 182 Query: 180 IARE-CKLTK-------LSMGMTRDFELAIASGATSVRIGSGIFG 216 ++ C+ LSMGM+ DFE AI G+T+VR+GS IFG Sbjct: 183 CRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227 >gnl|CDD|38367 KOG3157, KOG3157, KOG3157, Proline synthetase co-transcribed protein [General function prediction only]. Length = 244 Score = 129 bits (325), Expect = 7e-31 Identities = 81/233 (34%), Positives = 115/233 (49%), Gaps = 19/233 (8%) Query: 4 GNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKK 63 + L+ ++++ + R +++V LVAVSK + I A GQ F EN +QE + Sbjct: 8 ASALRAVIERVQQAVNQRPRDENAVRLVAVSKTKPASLIIEAYDAGQRHFGENYVQELIE 67 Query: 64 KWIPLRKEWDVQLRFIGSLQSNKVSEI--VSLFDVIETVSREKTASLLSLEMIKQSRFLP 121 K PL + D++ FIG LQSNK ++ V +ETV EK A L K P Sbjct: 68 K-APLLPD-DIKWHFIGHLQSNKCKKLLSVPNLYSVETVDSEKKARKLDSAWSKLGPDNP 125 Query: 122 --VYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQ-LNVEGLMCIPPA----MGNPKPHF 174 V +QVNT E KSGI P++ + + + + L GLM I P F Sbjct: 126 LKVLVQVNTSGEDSKSGIEPSEAPELAEHIKSECKNLKFSGLMTIGSFDNSHSSGENPDF 185 Query: 175 YLLSEIARE-CKLT-------KLSMGMTRDFELAIASGATSVRIGSGIFGERP 219 +L ++ CK +LSMGM+ DF LAI G+T+VR+GS IFG R Sbjct: 186 QVLVKLRESICKKLGIPADQVELSMGMSADFLLAIEQGSTNVRVGSTIFGARE 238 >gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain. Length = 216 Score = 116 bits (294), Expect = 3e-27 Identities = 56/217 (25%), Positives = 85/217 (39%), Gaps = 20/217 (9%) Query: 15 ENSAILAKRPKDSVSLVAVSKM----VDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70 N L +R V L+AV K + ++ AL+ G F LQEA + LR+ Sbjct: 8 HNIRALRERAGRPVKLMAVVKANAYGHGAVRVARALAAGADGFGVATLQEA----LELRE 63 Query: 71 E-WDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTG 129 + +G +++ +D+I TV + A LS K R L V+++V+TG Sbjct: 64 AGITAPILVLGFFPPEELALAAE-YDLIPTVDSLEQAEALSAAAAKLGRPLRVHLKVDTG 122 Query: 130 YEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNP----KPHFYLLSEIAR--E 183 + G P + L +EGLM P + E+A E Sbjct: 123 MG--RLGFTPEELPALAEALALP-GLRLEGLMTHFACADEPDATNRAQLARFRELADALE 179 Query: 184 CKLTKLSMGMTRDFELAI-ASGATSVRIGSGIFGERP 219 LS+G + LA G VR G ++G RP Sbjct: 180 AAGPVLSLGNSAALLLAPLHEGFDMVRPGIALYGARP 216 >gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain 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. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity. Length = 211 Score = 33.4 bits (77), Expect = 0.047 Identities = 16/82 (19%), Positives = 34/82 (41%) Query: 83 QSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQT 142 Q +++ + ++ TV + L +K V ++++TG E K G+ P + Sbjct: 70 QVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGDENGKFGVRPEEL 129 Query: 143 KDFVILCRQKYQLNVEGLMCIP 164 K + ++ L + GL Sbjct: 130 KALLERAKELPHLRLVGLHTHF 151 >gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain 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. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family. Length = 367 Score = 33.2 bits (77), Expect = 0.050 Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%) Query: 94 FDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKY 153 +D+ TVS + A LS + + L V+++++TG + + G P + ++ + + Sbjct: 93 YDLTPTVSSLEQAEALSAAAARLGKTLKVHLKIDTG--MGRLGFRPEEAEELLEALKALP 150 Query: 154 QLNVEGLM 161 L +EG+ Sbjct: 151 GLELEGVF 158 >gnl|CDD|31130 COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer membrane]. Length = 360 Score = 32.9 bits (75), Expect = 0.080 Identities = 13/73 (17%), Positives = 35/73 (47%), Gaps = 3/73 (4%) Query: 89 EIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVIL 148 E+ + +++ V+ + L +++ L V+++++TG + + G+ P + I Sbjct: 92 ELAAAYNLTPVVNSLEQLEALK-NAALKNKPLKVHLKIDTG--MNRLGLRPEEAVALAID 148 Query: 149 CRQKYQLNVEGLM 161 L++EG+ Sbjct: 149 LIALKNLDLEGIF 161 >gnl|CDD|143495 cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase. D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Its activity is present in several genera of bacteria but not in fungi. It requires PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ as cofactors for catalytic activity and thermal stability. Members of this subfamily show similarity to bacterial alanine racemase (AR), a fold type III PLP-dependent enzyme which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists 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. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity. Length = 361 Score = 30.3 bits (69), Expect = 0.39 Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 3/59 (5%) Query: 105 TASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTK-DFVILCRQKYQLNVEGLMC 162 A LS L V + VNTG + ++GI P + + L + GL Sbjct: 114 AAEALSAAAGSAGLTLSVLLDVNTG--MNRTGIAPGEDAEELYRAIATLPGLVLAGLHA 170 >gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 265 Score = 29.0 bits (66), Expect = 1.0 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 3/37 (8%) Query: 177 LSEIARECKLTKLSM---GMTRDFELAIASGATSVRI 210 L I + KL + E A+ +G VRI Sbjct: 57 LRAIRKLVPNVKLQALVRNREKGIERALEAGVDEVRI 93 >gnl|CDD|143490 cd06815, PLPDE_III_AR_like_1, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists 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. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes. Length = 353 Score = 28.7 bits (65), Expect = 1.4 Identities = 54/243 (22%), Positives = 91/243 (37%), Gaps = 55/243 (22%) Query: 6 KLQVFKQKIENSA-ILAKRPKDS-VSLVAVSKMV--DSKKIRVALSCGQVIFAENKLQEA 61 +L++ KI ++A +L + K + + V+K+V D + L G A+++++ Sbjct: 3 RLEINLSKIRHNAKVLVELCKSRGIEVTGVTKVVCGDPEIAEALLEGGITHLADSRIENL 62 Query: 62 KK---------KW---IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLL 109 KK K IP+ E V ++V D+ S +T L Sbjct: 63 KKLKDLGISGPKMLLRIPMLSE---------------VEDVVKYADIS-LNSELETIKAL 106 Query: 110 SLEMIKQSRFLPVYIQVNTG--YEIQKSGIMPNQTKDFVILCRQKYQLNVEG----LMCI 163 S E KQ + + + V+ G E G++P DFV + + + G L C Sbjct: 107 SEEAKKQGKIHKIILMVDLGDLRE----GVLPEDLLDFVEEILKLPGIELVGIGTNLGCY 162 Query: 164 PPAMGNPKPH-FYLLSEIARE------CKLTKLSMGMTRDFELA----IASGATSVRIGS 212 + P L E+ E KL +S G + L + G +RIG Sbjct: 163 GGVL--PTEENMGKLVELKEEIEKEFGIKLPIISGGNSASLPLLLKGELPGGINQLRIGE 220 Query: 213 GIF 215 I Sbjct: 221 AIL 223 >gnl|CDD|36634 KOG1420, KOG1420, KOG1420, Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms]. Length = 1103 Score = 28.1 bits (62), Expect = 1.9 Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 1/46 (2%) Query: 66 IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSL 111 I L + W + LRF+ +L+ V +I+ ++++T S + L+S+ Sbjct: 212 IYLNRSW-LGLRFLRALRLMTVPDILQYLNILKTSSSIRLVQLVSI 256 >gnl|CDD|30933 COG0588, GpmA, Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism]. Length = 230 Score = 28.3 bits (63), Expect = 2.0 Identities = 11/26 (42%), Positives = 17/26 (65%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83 L+E+ + WIP+ K W + R G+LQ Sbjct: 69 LEESDQLWIPVIKSWRLNERHYGALQ 94 >gnl|CDD|133084 cd06226, M14_CPT_like, Peptidase M14-like domain of an uncharacterized group of Peptidase M14 Carboxypeptidase (CP) T (CPT)-like proteins. This group belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding 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. CPT exhibits dual-substrate specificity by cleaving C-terminal hydrophobic amino acid residues and C-terminal positively charged residues. However, CPT does not belong to this CPT-like group. Length = 293 Score = 28.1 bits (63), Expect = 2.1 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%) Query: 168 GNPKPHFYLLSEI-ARECKLTKLSMGMTRD 196 PKP F+++ I ARE +L + D Sbjct: 39 TGPKPVFFIMGAIHAREYTTAELVLRFAED 68 >gnl|CDD|29936 cd00408, DHDPS-like, Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.. Length = 281 Score = 26.7 bits (59), Expect = 5.1 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 5/49 (10%) Query: 136 GIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKP-----HFYLLSE 179 G+ N T++ + L R + +G++ +PP P HF +++ Sbjct: 72 GVGANSTREAIELARHAEEAGADGVLVVPPYYNKPSQEGIVAHFKAVAD 120 >gnl|CDD|32721 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]. Length = 322 Score = 26.7 bits (59), Expect = 5.5 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 12/85 (14%) Query: 70 KEWDVQLRFI-----GSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYI 124 KE QLRFI G S ++ + +SL +++ + A+LL + R Y Sbjct: 177 KERGAQLRFIELMPLGEGNSWRLDKYLSLDEILRKLEER--ATLLPVRKRLHGR--AKYF 232 Query: 125 QVNTGYEIQKSGIMPNQTKDFVILC 149 G EI G + + F C Sbjct: 233 IHPDGGEI---GFIAPVSNPFCATC 254 >gnl|CDD|153344 cd07660, BAR_Arfaptin, The Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin. The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Arfaptins are ubiquitously expressed proteins implicated in mediating cross-talk between Rac, a member of the Rho family GTPases, and Arf (ADP-ribosylation factor) small GTPases. Arfaptins bind to GTP-bound Arf1, Arf5, and Arf6, with strongest binding to GTP-Arf1. Arfaptins also bind to Rac-GTP and Rac-GDP with similar affinities. The Arfs are thought to bind to the same surface as Rac, and their binding is mutually exclusive. Mammals contain at least two isoforms of Arfaptin. Arfaptin 1 has been shown to inhibit the activation of Arf-dependent phospholipase D (PLD) and the secretion of matrix metalloproteinase-9 (MMP-9), an enzyme implicated in cancer invasiveness and metastasis. Arfaptin 2 regulates the aggregation of the protein huntingtin, which is implicated in Huntington disease. Arfaptins are single-domain proteins with a BAR-like structure. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Length = 201 Score = 26.5 bits (59), Expect = 6.1 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%) Query: 54 AENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVS 88 A+ + Q K K+ LR + V+L+F L+ NKV Sbjct: 139 AQRRFQAHKDKYEKLRNDVSVKLKF---LEENKVK 170 >gnl|CDD|145200 pfam01905, DevR, CRISPR-associated negative autoregulator DevR/Csa2. This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers. This family used to be known as DUF73. DevR appears to be negative autoregulator within the system. Length = 293 Score = 26.1 bits (58), Expect = 7.3 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 9/57 (15%) Query: 73 DVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSL-----EMI--KQSRFLPV 122 ++ L IG + +++ + DV E R K A+L +L K++RFLPV Sbjct: 185 NLDLDRIGRPSAEQING-NYVLDVDERKRRIK-AALKALLLLLSGPFGAKRARFLPV 239 >gnl|CDD|35456 KOG0235, KOG0235, KOG0235, Phosphoglycerate mutase [Carbohydrate transport and metabolism]. Length = 214 Score = 26.1 bits (57), Expect = 8.0 Identities = 11/37 (29%), Positives = 17/37 (45%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLF 94 L+E K+K +P+ W + R G LQ E + Sbjct: 73 LEELKQKKVPVLYTWRLNERHYGDLQGLNKRETAKRY 109 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 0.134 0.378 Gapped Lambda K H 0.267 0.0695 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,461,449 Number of extensions: 118539 Number of successful extensions: 284 Number of sequences better than 10.0: 1 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 25 Length of query: 222 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 132 Effective length of database: 4,318,927 Effective search space: 570098364 Effective search space used: 570098364 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: 55 (25.0 bits)