RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780425|ref|YP_003064838.1| apolipoprotein N-acyltransferase [Candidatus Liberibacter asiaticus str. psy62] (518 letters) >gnl|CDD|31157 COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope biogenesis, outer membrane]. Length = 518 Score = 223 bits (570), Expect = 9e-59 Identities = 126/523 (24%), Positives = 241/523 (46%), Gaps = 26/523 (4%) Query: 4 IAGKVMLLSGFRRCFIAILAGVIGSFSMPSSDLFLSSFVSFTLLIWLLDGISSNLGRMSA 63 +A + +L RR +A++ G + + + P D + ++ S L+WL+ G A Sbjct: 5 LARQWVLGRPARRLLLALVFGALFALAFPPPDWWWLAWFSLAPLLWLVRG---------A 55 Query: 64 ISRVGSSFFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVVLFFVMISFLLAIFYGV 123 + G+LFG G+FLAG +W+ + G + L ++++ LA+F + Sbjct: 56 PTSWEGLAKSGFLFGFGFFLAGFYWLGTSLGV--GLGLLAVALPLLVLLLAAWLALFLLL 113 Query: 124 ATSLASLLWSTGMGRICVFACAVGFCEWLRSVLGIG-TWNAIGYAAMPIPVMMQSVHWIG 182 L LW + + A EWLR G W +GY+ ++Q G Sbjct: 114 VAVLTCRLWFALLVVPSAWVAA----EWLRGWSLTGFPWLLLGYSQWSPSPLLQLASLGG 169 Query: 183 LFGMNALSVFCFASPALFGTRRDVNIGIILSSTLLILHIAYGWWILTEDSKSSLKFEKIS 242 ++ ++ L V A A +R ++L LL++ +AYG +L + ++ Sbjct: 170 VWLLSFLVVAVNALLASVLLKRATGGRLLLLGLLLVVLLAYGCALLGLAGSVPVGEPTLT 229 Query: 243 PVIRIVQPGINPAIK---EDREKILERYLSLTALPVSAGELEPVIIVWAYLPFPFSIVDQ 299 + +VQ I +K + +++ YL L + +P ++VW PF + Sbjct: 230 --VALVQGNIPQDLKWDADALARLIAGYLEEEFLAA-VDKQKPDLVVWPETALPFDLTRH 286 Query: 300 PSILKKIAS-VLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFA 358 P L ++A + ++ L++G+ G +Y S+ +++ GE + + HLVPF Sbjct: 287 PDALARLAEALQRVGAPLLIGTDVDGPAPGGGIYYNSVLVLDPGGEGVYRYDKVHLVPFG 346 Query: 359 EYLPYRNILKKLNLDFYMFPLDYSSSDISPLLGLSEKLRLYPLLFSDALFHQDI--NNLE 416 EY+P+ +L+ L + D+S +L L+ ++ PL+ +A+F + + + + Sbjct: 347 EYIPFPELLRPLYFFLNLPMSDFSRGPGPQVLLLAGGPKIAPLICYEAIFPELVRASARQ 406 Query: 417 NVSAILNIIDDSGFMGS-GTDHSFRYAQIQAVEIGLPLIRATNNGVSAFLDERGQIISSV 475 +LN+ +D+ F GS G F+ A+++AVE+G PL+RATN G+SA +D RG+I++ + Sbjct: 407 GAELLLNLSNDAWFGGSWGPYQHFQQARVRAVELGRPLVRATNTGISAVIDPRGRILAQL 466 Query: 476 YADRGASIDMHFQPKVRDSFRSSIQMRVFWIIEFILLILAVIV 518 +D K + + W++ + L A++ Sbjct: 467 PYFTRGVLDATVPLKTGLTPYARWGDWPLWLLVGLALAAALLF 509 >gnl|CDD|143595 cd07571, ALP_N-acyl_transferase, Apolipoprotein N-acyl transferase (class 9 nitrilases). ALP N-acyl transferase (Lnt), is an essential membrane-bound enzyme in gram-negative bacteria, which catalyzes the N-acylation of apolipoproteins, the final step in lipoprotein maturation. This is a reverse amidase (i.e. condensation) reaction. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 9. Length = 270 Score = 137 bits (347), Expect = 9e-33 Identities = 73/258 (28%), Positives = 120/258 (46%), Gaps = 24/258 (9%) Query: 245 IRIVQPGINPAIK---EDREKILERYLSLTALPVSAGELEPVIIVWAYLP---FPFSIVD 298 + +VQ I K E R+ L+RYL LT P ++VW P PF + Sbjct: 3 VALVQGNIPQDEKWDPEQRQATLDRYLDLTRELADEK---PDLVVW---PETALPFDLQR 56 Query: 299 QPSILKKIASVLK-INQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPF 357 P L ++A + + L+ G+ R+E G +Y S +++ G IL + HLVPF Sbjct: 57 DPDALARLARAARAVGAPLLTGAPRRE--PGGGRYYNSALLLDPGGGILGRYDKHHLVPF 114 Query: 358 AEYLPYRNILKKLNLDFYMFPLDYSSSDISPLLGLSEKLRLYPL-----LFSDALFHQDI 412 EY+P R++L+ L L F + D+S L L +R+ PL +F + + Sbjct: 115 GEYVPLRDLLRFLGLLFDLPMGDFSPGTGPQPLLLGGGVRVGPLICYESIFPELVRDAV- 173 Query: 413 NNLENVSAILNIIDDSGFMGS-GTDHSFRYAQIQAVEIGLPLIRATNNGVSAFLDERGQI 471 + ++NI +D+ F S G A+++A+E G PL+RA N G+SA +D G+I Sbjct: 174 --RQGADLLVNITNDAWFGDSAGPYQHLAMARLRAIETGRPLVRAANTGISAVIDPDGRI 231 Query: 472 ISSVYADRGASIDMHFQP 489 ++ + + Sbjct: 232 VARLPLFEAGVLVAEVPL 249 >gnl|CDD|144405 pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase. This family contains hydrolases that break carbon-nitrogen bonds. The family includes: Nitrilase EC:3.5.5.1, Aliphatic amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12, Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins. Length = 172 Score = 35.4 bits (82), Expect = 0.040 Identities = 29/145 (20%), Positives = 55/145 (37%), Gaps = 15/145 (10%) Query: 245 IRIVQPGINPAIKEDREKILERYLSLTALPVSAG-------ELEPVIIVWAYLPFPFSIV 297 + +VQ + P+ D E L++ L L G EL + Sbjct: 2 VALVQ--LPPS-AFDLEANLQKLLELIEEAARQGADLIVFPELFIPGYAHGAAEYLELAE 58 Query: 298 DQPSI-LKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVP 356 P L+ ++++ + N + +V + Y ++ +I+ GE+L +HLVP Sbjct: 59 AIPGEVLQALSALARKNGITVVAGI---PERDGGGLYNTLVLIDPDGELLGKYRKRHLVP 115 Query: 357 FAEYLPYRNILKKLNLDFYMFPLDY 381 F E++ R + F +F Sbjct: 116 FGEWVE-RPLFGPGGATFPVFDTPV 139 >gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes. This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy. Length = 253 Score = 33.5 bits (77), Expect = 0.15 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 6/57 (10%) Query: 303 LKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFAE 359 L ++A L I ++ G K Y + +I+ GEI+ HL F E Sbjct: 68 LAELAKELGIY--IVAGIAEK----DGDKLYNTAVVIDPDGEIIGKYRKIHLFDFGE 118 >gnl|CDD|144721 pfam01231, IDO, Indoleamine 2,3-dioxygenase. Length = 407 Score = 32.6 bits (75), Expect = 0.29 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 11/54 (20%) Query: 388 PLLGLSEKLRLYPLLFSDAL--------FHQDINNLENVSAILNI---IDDSGF 430 PLL +SE L L P+L L D +L+N+S I D+S F Sbjct: 104 PLLEVSEHLGLPPILTYADLVLWNWKPIDPDDPLDLDNLSTINTFTGTKDESWF 157 >gnl|CDD|143898 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Length = 257 Score = 31.0 bits (71), Expect = 0.74 Identities = 33/109 (30%), Positives = 45/109 (41%), Gaps = 18/109 (16%) Query: 71 FFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVVLFFVMISFLLAIF-----YGVAT 125 F+VGW FGV + G I+ + W +LF F LA+ YG+ Sbjct: 1 FYVGW-FGVLSIIFGALGAF--IIGFNAAASVTWNPLLFGRNF-FWLAVEPPSAEYGL-- 54 Query: 126 SLASLLWSTGMGRICVFACAVGFCEW-LRSV-----LGIGTWNAIGYAA 168 S A LW G+ +I F F W LR LG+G A ++A Sbjct: 55 SFA-PLWEGGLWQIITFFATGAFLSWWLREYEIARKLGMGPHVAWAFSA 102 >gnl|CDD|143607 cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Length = 253 Score = 30.2 bits (69), Expect = 1.6 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%) Query: 301 SILKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFA 358 S L ++A +N ++ GS+ E G Y + Y+I+ GE++A+ HL Sbjct: 64 SFLSELAKKHGVN--IVAGSV-AEKEGG--KLYNTAYVIDPDGELIATYRKIHLFGLM 116 >gnl|CDD|38864 KOG3660, KOG3660, KOG3660, Sodium-neurotransmitter symporter [Signal transduction mechanisms]. Length = 629 Score = 29.9 bits (67), Expect = 1.6 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 8/67 (11%) Query: 63 AISRVGSSFFVGWLFGVGYFLAGL---WWVREGIVDQIGSRFP-----FWGVVLFFVMIS 114 A++++ S LF L GL + + E IV I FP W VVLF ++ Sbjct: 374 ALAQMPLSPLWSGLFFFMLLLLGLDSQFAIVETIVTAIVDEFPRLRNRRWIVVLFVCVVG 433 Query: 115 FLLAIFY 121 FLL + Sbjct: 434 FLLGLPL 440 >gnl|CDD|143643 cd07883, RHD-n_NFkB, N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-kappa B). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 and B2 families of transcription factors, also referred to as class I members of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. Family members include NF-kappa B1 and NF-kappa B2. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form), while NF-kappa B2 is called p100 or p52 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and REL). p105 and p100 may also act as I-kappa Bs due to their C-terminal ankyrin repeats. Length = 197 Score = 29.8 bits (67), Expect = 2.2 Identities = 13/26 (50%), Positives = 14/26 (53%) Query: 7 KVMLLSGFRRCFIAILAGVIGSFSMP 32 K M LS R CF A L GSF+ P Sbjct: 159 KSMDLSVVRLCFQAFLPDSNGSFTRP 184 >gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This family contains uncharacterized integral membrane proteins. Length = 771 Score = 27.5 bits (62), Expect = 9.5 Identities = 19/83 (22%), Positives = 28/83 (33%), Gaps = 15/83 (18%) Query: 64 ISRVGSSFFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVV------------LFFV 111 ++R+G V +F + FL L R S F + L + Sbjct: 46 LTRIGLFLLVFLIFFLFLFLNLLLAYRARPPFVPLSPEQFGDPLARYRSVILPRRRLLLL 105 Query: 112 MISFLLAIFYGVATSLASLLWST 134 IS +L + G AS W T Sbjct: 106 GISLVLGLLAG---LSASSRWET 125 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 0.328 0.143 0.438 Gapped Lambda K H 0.267 0.0746 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 6,568,865 Number of extensions: 379065 Number of successful extensions: 1609 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1563 Number of HSP's successfully gapped: 164 Length of query: 518 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 420 Effective length of database: 4,146,055 Effective search space: 1741343100 Effective search space used: 1741343100 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 (21.7 bits) S2: 60 (26.9 bits)