RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780279|ref|YP_003064692.1| dihydrodipicolinate reductase [Candidatus Liberibacter asiaticus str. psy62] (280 letters) >gnl|CDD|30637 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]. Length = 266 Score = 290 bits (743), Expect = 3e-79 Identities = 119/269 (44%), Positives = 161/269 (59%), Gaps = 4/269 (1%) Query: 4 SPMRISVLG-GGRMGQALIKEIHNNPSITLHSIIVRSGSPLIGQDVGNFVGISPMGIKFS 62 S ++++V G GRMG+ LI+ + P + L + R GS +G D G G+ +G+ + Sbjct: 1 SMIKVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGSLSLGSDAGELAGLGLLGVPVT 60 Query: 63 DNLAMAIQSVDGIIDFSSPALTLQSLNISAQHNIVHIIGTTGFSVKENEVISSFARNAPI 122 D+L + D +IDF++P TL++L + +H +IGTTGF+ ++ E + A P+ Sbjct: 61 DDLLLVKADADVLIDFTTPEATLENLEFALEHGKPLVIGTTGFTEEQLEKLREAAEKVPV 120 Query: 123 VKSSNMSLGINFLGFLVETAAEYLLPAKDWDFEILEMHHRRKLDSPSGTALLLGEAIANG 182 V + N SLG+N L L E AA+ L D+D EI+E HHR K D+PSGTAL L EAIA Sbjct: 121 VIAPNFSLGVNLLFKLAEQAAKVL---DDYDIEIIEAHHRHKKDAPSGTALKLAEAIAEA 177 Query: 183 RKVNLTDHMVLNRHIQQCARTEGSIGIASLRAGSIVGEHSVVIAGEGESITLSHSAYDRR 242 R +L D V R AR EG IGI S+R G IVGEH V+ AGEGE I + H A R Sbjct: 178 RGQDLKDEAVYGREGATGARKEGEIGIHSVRGGDIVGEHEVIFAGEGERIEIRHRATSRD 237 Query: 243 IFARGSLTAALWAKSQIPGLYSMRDVLGI 271 FARG+L AA W + PGLY M DVLG+ Sbjct: 238 SFARGALLAARWLVGKPPGLYDMEDVLGL 266 >gnl|CDD|147385 pfam05173, DapB_C, Dihydrodipicolinate reductase, C-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain. Length = 137 Score = 170 bits (434), Expect = 4e-43 Identities = 69/140 (49%), Positives = 87/140 (62%), Gaps = 4/140 (2%) Query: 131 GINFLGFLVETAAEYLLPAKDWDFEILEMHHRRKLDSPSGTALLLGEAIANGRKVNLTDH 190 G+N L L E AA+YL D+D EI+E+HHR+K D+PSGTAL L EAIA R L Sbjct: 1 GVNLLMKLAEEAAKYL--GDDYDIEIIEIHHRQKKDAPSGTALKLAEAIAEARGEALEVV 58 Query: 191 MVLNRHIQQCARTEGSIGIASLRAGSIVGEHSVVIAGEGESITLSHSAYDRRIFARGSLT 250 R R+ IGI S+R G +VGEH V+ G+GE I ++H A+ R IFA G+L Sbjct: 59 ADE-REGGTRGRSVNEIGIHSVRGGGVVGEHEVIFGGDGERIEITHDAHSREIFAPGALL 117 Query: 251 AALW-AKSQIPGLYSMRDVL 269 AA W A ++PGLY M DVL Sbjct: 118 AAEWLAGKKLPGLYGMEDVL 137 >gnl|CDD|144632 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH. Length = 122 Score = 122 bits (308), Expect = 1e-28 Identities = 44/124 (35%), Positives = 73/124 (58%), Gaps = 3/124 (2%) Query: 6 MRISVLG-GGRMGQALIKEIHNNPSITLHSIIVRSGSPLIGQDVGNFVGISPMGIKFSDN 64 ++++V+G GRMG+ LIK I P L + + R GS L+G D G G P+G+ +D+ Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVAAVDRPGSSLLGSDAGELAG--PLGVPVTDD 58 Query: 65 LAMAIQSVDGIIDFSSPALTLQSLNISAQHNIVHIIGTTGFSVKENEVISSFARNAPIVK 124 L + D +IDF++P TL++L ++ +H +IGTTGF+ ++ + A+ PIV Sbjct: 59 LEEVLADADVLIDFTTPEATLENLELALKHGKPLVIGTTGFTEEQLAELKEAAKKIPIVI 118 Query: 125 SSNM 128 + N Sbjct: 119 APNF 122 >gnl|CDD|30693 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]. Length = 266 Score = 35.6 bits (82), Expect = 0.014 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 5/72 (6%) Query: 5 PMRISVLGGGRMGQALIKEIHNNPSITLHSIIVRSGSPLIGQDVGNFVGISPMGIKFSDN 64 M+I +G G MG+A++ + + ++ IIV + S + + G+ + + Sbjct: 1 MMKIGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRSEEKRAAL-----AAEYGVVTTTD 55 Query: 65 LAMAIQSVDGII 76 A++ D + Sbjct: 56 NQEAVEEADVVF 67 >gnl|CDD|30589 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion]. Length = 329 Score = 32.1 bits (73), Expect = 0.16 Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 17/126 (13%) Query: 5 PMRISVLGGGRMGQALIKEIHNNPSITLHSIIVRSGSPLIGQDVGN-------FVGIS-P 56 M+I+V+G G G AL K + N H + + I ++ GI P Sbjct: 1 MMKIAVIGAGSWGTALAKVLARNG----HEVRLWGRDEEIVAEINETRENPKYLPGILLP 56 Query: 57 MGIKFSDNLAMAIQSVDGIIDFSSPA----LTLQSLNISAQHNIVHIIGTTGFSVKENEV 112 +K + +LA A+ D I+ + P+ L+ L + + + T G + + Sbjct: 57 PNLKATTDLAEALDGADIIV-IAVPSQALREVLRQLKPLLLKDAIIVSATKGLEPETGRL 115 Query: 113 ISSFAR 118 +S Sbjct: 116 LSEIIE 121 >gnl|CDD|30808 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and metabolism]. Length = 333 Score = 29.8 bits (67), Expect = 0.75 Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 9/82 (10%) Query: 5 PMRISVLGGGRMGQALIKEIHNNPS---------ITLHSIIVRSGSPLIGQDVGNFVGIS 55 +++ +LG G +G +++ + I + ++ R GS + D+ N + Sbjct: 3 TVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVADRDGSLVRDLDLLNAEVWT 62 Query: 56 PMGIKFSDNLAMAIQSVDGIID 77 G + + + +D +++ Sbjct: 63 TDGALSLGDEVLLDEDIDVVVE 84 >gnl|CDD|133148 cd05481, retropepsin_like_LTR_1, Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Length = 93 Score = 29.5 bits (67), Expect = 0.98 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%) Query: 2 HQSPMRISVLGGGR---MGQALIKEIHNNPSITLHSIIVRS-GSPLIG 45 SP+R++ GG G +K + NP L +V+ G PL+G Sbjct: 41 RPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVKEEGPPLLG 88 >gnl|CDD|37827 KOG2616, KOG2616, KOG2616, Pyridoxalphosphate-dependent enzyme/predicted threonine synthase [Amino acid transport and metabolism]. Length = 266 Score = 27.6 bits (61), Expect = 3.7 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%) Query: 62 SDNLAMAIQSVDGIIDFSSPALTLQSLNISAQHN-IVHIIGTTGFSVKENEVISSFARNA 120 D ++++ G ++F+ L ++ L I+ N I+H TG +V ++ + Sbjct: 37 FDECQDPVKTIFGDVEFAKMGLPIRKLVIATNENDILHRFVKTGDYELSEKVAATLSPAM 96 Query: 121 PIVKSSNM 128 I+ SSN Sbjct: 97 DILVSSNF 104 >gnl|CDD|37509 KOG2298, KOG2298, KOG2298, Glycyl-tRNA synthetase and related class II tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 599 Score = 26.9 bits (59), Expect = 6.2 Identities = 10/36 (27%), Positives = 16/36 (44%) Query: 153 DFEILEMHHRRKLDSPSGTALLLGEAIANGRKVNLT 188 ++ ++L S + LGEA+A G N T Sbjct: 259 AEKLRLFPRDKQLSGQSAQKVALGEAVAKGTVNNET 294 >gnl|CDD|147655 pfam05602, CLPTM1, Cleft lip and palate transmembrane protein 1 (CLPTM1). This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis. Length = 437 Score = 26.5 bits (59), Expect = 8.2 Identities = 8/24 (33%), Positives = 13/24 (54%) Query: 20 LIKEIHNNPSITLHSIIVRSGSPL 43 + KE+ NN ++ H + SG L Sbjct: 102 IPKEVQNNGTLYAHVYLGLSGYSL 125 >gnl|CDD|147078 pfam04735, Baculo_helicase, Baculovirus DNA helicase. Length = 1173 Score = 26.4 bits (59), Expect = 9.0 Identities = 9/29 (31%), Positives = 18/29 (62%) Query: 137 FLVETAAEYLLPAKDWDFEILEMHHRRKL 165 +L E+ +Y+L A + +IL+++H K Sbjct: 549 YLPESVFDYMLNAIKNELDILKIYHAAKF 577 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 0.319 0.135 0.382 Gapped Lambda K H 0.267 0.0737 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,230,360 Number of extensions: 168216 Number of successful extensions: 443 Number of sequences better than 10.0: 1 Number of HSP's gapped: 439 Number of HSP's successfully gapped: 22 Length of query: 280 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 187 Effective length of database: 4,254,100 Effective search space: 795516700 Effective search space used: 795516700 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 (21.7 bits) S2: 57 (25.7 bits)