RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780532|ref|YP_003064945.1| aminodeoxychorismate lyase [Candidatus Liberibacter asiaticus str. psy62] (325 letters) >gnl|CDD|145655 pfam02618, YceG, YceG-like family. This family of proteins is found in bacteria. Proteins in this family are typically between 332 and 389 amino acids in length. This family was previously incorrectly annotated and names as aminodeoxychorismate lyase. The structure of YceG was solved by X-ray crystallography. Length = 287 Score = 314 bits (807), Expect = 2e-86 Identities = 118/292 (40%), Positives = 167/292 (57%), Gaps = 16/292 (5%) Query: 36 TIFLVRNNMSLKEISKNLFNGGVIVNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIA 95 + + SL +I+ L GVI + FR + LK GEYE++ G S ++I Sbjct: 1 VVVTIPPGSSLSQIADILEEAGVIKSALAFRLYARLKGKDGNLKAGEYELKPGMSPAEIL 60 Query: 96 EKIMYGKVLMHSISFPEGFTVKQMARRLKDNPLLVGELPLE-----------LPLEGTLC 144 EK++ GKV+ + ++ PEG T++Q+A RL L E L LPLEG L Sbjct: 61 EKLVSGKVVQYKVTIPEGLTLEQIAERLAKAGGLKKEEFLAFLEELGGELPSLPLEGYLF 120 Query: 145 PSTYNFPLGTHRSEILNQAMLKQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRA 204 P TY F GT EIL + + + ++V+ E W+ R P+K+ + +ILASIVEKET A Sbjct: 121 PDTYEFDKGTSAEEILKRMVKRFEKVLAEAWQARAKGLPLKTPYEALILASIVEKETGVA 180 Query: 205 DERAHVASVFINRFSKSIRLQSDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNG 264 +ER +A VF NR K +RLQSD TVIYG+ EGD +++R D +PYN+Y + G Sbjct: 181 EERPKIAGVFYNRLKKGMRLQSDPTVIYGLGEGD-----GRLTRKDLRTDSPYNTYKIKG 235 Query: 265 LPPTAISNPGRLSLEAVAKPLHTEDLYFVGDGKGGHFFSTNFKDHTINVQKW 316 LPP I+NPG+ ++EA P T+ LYFV DG G H+FS +H V+K+ Sbjct: 236 LPPGPIANPGKAAIEAALNPAKTDYLYFVADGDGTHYFSKTLAEHNRAVRKY 287 >gnl|CDD|31747 COG1559, COG1559, Predicted periplasmic solute-binding protein [General function prediction only]. Length = 342 Score = 296 bits (759), Expect = 5e-81 Identities = 130/334 (38%), Positives = 184/334 (55%), Gaps = 21/334 (6%) Query: 2 LKFLIPLITIFLLAIG--VHIHVIRVYNATGPL-QNDTIFLVRNNMSLKEISKNLFNGGV 58 LK L+ L+ + LL +G +I ++ + + PL +N + S+ EI L V Sbjct: 9 LKTLLVLVLVLLLILGGVGYIGILYFFALSPPLGKNKKTVTIPPGSSVSEIGSELEKQKV 68 Query: 59 IVNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIAEKIMYGKVLMHSISFPEGFTVKQ 118 I N +FR ++ + LK GEY + G S + I + + GK ++ PEG+T+KQ Sbjct: 69 IKNARVFRLYLKYNPAAGSLKAGEYRLRPGMSAADILKLLESGKSAQFKVTIPEGYTLKQ 128 Query: 119 MARRLKDNPLLVG--------ELPLELP------LEGTLCPSTYNFPLGTHRSEILNQAM 164 +A++L + P+L G E+ LP LEG L P TY F GT +I+ + + Sbjct: 129 IAKKLAEAPVLDGVLDGLAIAEIAARLPKLDKERLEGYLFPDTYEFTRGTSAEDIIKRMI 188 Query: 165 LKQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRL 224 + +DE WE R D P K+ +L+ LASIVEKE + +ER +ASVF NR K +RL Sbjct: 189 KAMDKKLDEAWEKRADDLPGKTPYELLTLASIVEKEAAVDEERPKIASVFYNRLKKGMRL 248 Query: 225 QSDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSLEAVAKP 284 QSD TVIYG+ IS+ D I TPYN+Y + GLPPT I+NPG +L A P Sbjct: 249 QSDPTVIYGL----GKSHEGAISKKDLEIDTPYNTYKIKGLPPTPIANPGLAALRAALNP 304 Query: 285 LHTEDLYFVGDGKGGHFFSTNFKDHTINVQKWRK 318 T+ LYFV DG GGH FS ++H NV+K+RK Sbjct: 305 AKTDYLYFVADGDGGHVFSKTLEEHNANVEKYRK 338 >gnl|CDD|153433 cd08010, yceG_like, proteins similar to Escherichia coli yceG. The gene product of Escherichia coli yceG has been erroneously annotated as an aminodeoxychorismate lyase. Its overexpression has been reported to cause abnormal biofilm architecture, and it has been reported to be part of a putative five-gene operon. It might function as a periplasmic solute-binding protein. The family also includes Streptomyces caeruleus NovB, an uncharacterized member of the novobiocin biosynthetic gene cluster. Length = 245 Score = 243 bits (622), Expect = 5e-65 Identities = 98/250 (39%), Positives = 140/250 (56%), Gaps = 19/250 (7%) Query: 78 LKTGEYEIEKGSSMSQIAEKIMYGKVLMHSISFPEGFTVKQMARRLKDNP---------L 128 LK GEYE+ G S+++I E++ GK ++ PEG+T+KQ+A+ L Sbjct: 1 LKAGEYELSPGMSLAEILERLTSGKSAQVKVTIPEGYTLKQIAKALSKAGGLSDAEFLAA 60 Query: 129 LVGELPLEL-----PLEGTLCPSTYNFPLGTHRSEILNQAMLKQKQVVDEVWEIRDVDHP 183 L + L PLEG L P TY FP G ++L + + + +V++E W R P Sbjct: 61 LKDPAFILLGDPKYPLEGYLFPDTYEFPKGATPEDLLKRMVKRFDKVLEEAWAAR-AGLP 119 Query: 184 IKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRLQSDSTVIYGILEGDYDLTN 243 + +++ LASIVEKE +ER +A VF NR K +RLQSD TVIYG+ + Sbjct: 120 GLTPYEVLTLASIVEKEAGLPEERPLIAGVFYNRLKKGMRLQSDPTVIYGL----GEHKK 175 Query: 244 RKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSLEAVAKPLHTEDLYFVGDGKGGHFFS 303 I++ D I +PYN+Y + GLPP I+NPG +LEA P T+ LYFV DG G H+FS Sbjct: 176 GTITKKDLEIDSPYNTYKIKGLPPGPIANPGLAALEAALNPAKTDYLYFVADGTGTHYFS 235 Query: 304 TNFKDHTINV 313 +++H NV Sbjct: 236 KTYEEHNKNV 245 >gnl|CDD|146135 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognized by T cells. Length = 577 Score = 29.7 bits (67), Expect = 1.2 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%) Query: 163 AMLKQKQVVDEVWEIRDVDHPIKSKEDLVILASI---VEKETSRADERA 208 A+LK + ++ + R+ +K KE L +LA I +E+E R D + Sbjct: 454 ALLKSRGLLKKNQLERERREFLKEKERLKLLAEIRERIERERDRNDGKY 502 >gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction only]. Length = 849 Score = 28.0 bits (62), Expect = 3.5 Identities = 9/50 (18%), Positives = 16/50 (32%) Query: 173 EVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSI 222 I + + + LA+ ++K E A+ NRF Sbjct: 279 WQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLKAAACIGNRFDLDT 328 >gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit [Posttranslational modification, protein turnover, chaperones]. Length = 786 Score = 28.0 bits (62), Expect = 3.9 Identities = 10/18 (55%), Positives = 16/18 (88%) Query: 115 TVKQMARRLKDNPLLVGE 132 T++ ++RR K+NP+LVGE Sbjct: 182 TIQILSRRTKNNPVLVGE 199 >gnl|CDD|163680 cd07942, DRE_TIM_LeuA, Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Alpha-isopropylmalate synthase (LeuA), a key enzyme in leucine biosynthesis, catalyzes the first committed step in the pathway, converting acetyl-CoA and alpha-ketoisovalerate to alpha-isopropyl malate and CoA. Although the reaction catalyzed by LeuA is similar to that of the Arabidopsis thaliana IPMS1 protein, the two fall into phylogenetically distinct families within the same superfamily. LeuA has and N-terminal TIM barrel catalytic domain, a helical linker domain, and a C-terminal regulatory domain. LeuA forms a homodimer in which the linker domain of one monomer sits over the catalytic domain of the other, inserting residues into the active site that may be important for catalysis. Homologs of LeuA are found in bacteria as well as fungi. This family includes alpha-isopropylmalate synthases I (LEU4) and II (LEU9) from Saccharomyces cerevisiae. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 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 = 284 Score = 27.5 bits (62), Expect = 4.6 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%) Query: 17 GVHIHVIRVYNATGPLQNDTIFLVRNNMSLKEI 49 G ++ +YNAT PLQ +F S +EI Sbjct: 90 GAKKAIVHLYNATSPLQRRVVF----GKSKEEI 118 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 0.138 0.398 Gapped Lambda K H 0.267 0.0785 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,912,449 Number of extensions: 204601 Number of successful extensions: 453 Number of sequences better than 10.0: 1 Number of HSP's gapped: 443 Number of HSP's successfully gapped: 16 Length of query: 325 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 231 Effective length of database: 4,232,491 Effective search space: 977705421 Effective search space used: 977705421 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: 57 (25.6 bits)