RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781163|ref|YP_003065576.1| hypothetical protein CLIBASIA_05350 [Candidatus Liberibacter asiaticus str. psy62] (214 letters) >gnl|CDD|176858 cd07816, Bet_v1-like, Ligand-binding bet_v_1 domain of major pollen allergen of white birch (Betula verrucosa), Bet v 1, and related proteins. This family includes the ligand binding domain of Bet v 1 (the major pollen allergen of white birch, Betula verrucosa) and related proteins. In addition to birch Bet v 1, this family includes other plant intracellular pathogenesis-related class 10 (PR-10) proteins, norcoclaurine synthases (NCSs), cytokinin binding proteins (CSBPs), major latex proteins (MLPs), and ripening-related proteins. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Members of this family binds a diverse range of ligands. Bet v 1 can bind brassinosteroids, cytokinins, flavonoids and fatty acids. Hyp-1, a PR-10 from Hypericum perforatum/St. John's wort, catalyzes the condensation of two molecules of emodin to the bioactive naphthodianthrone hypericin. NCSs catalyze the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. The role of MLPs is unclear; however, they are associated with fruit and flower development and in pathogen defense responses. A number of PR-10 proteins in this subgroup, including Bet v 1, have in vitro RNase activity, the biological significance of which is unclear. Bet v 1 family proteins have a conserved glycine-rich P (phosphate-binding)-loop proximal to the entrance of the ligand-binding pocket. However, its conformation differs from that of the canonical P-loop structure found in nucleotide-binding proteins. Several PR-10 members including Bet v1 are allergenic. Cross-reactivity of Bet v 1 with homologs from plant foods results in birch-fruit syndrome. Length = 148 Score = 32.9 bits (76), Expect = 0.058 Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 7/46 (15%) Query: 148 FTHFKEYIDEVDKILMRYG---IEGIPLTDFDHEKIKSYLTHIKIV 190 + KE ID VD+ Y IEG L D KSY IK V Sbjct: 61 VKYVKERIDAVDEENKTYKYTVIEGDVLKD----GYKSYKVEIKFV 102 >gnl|CDD|73095 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 110 Score = 30.5 bits (69), Expect = 0.31 Identities = 7/31 (22%), Positives = 18/31 (58%), Gaps = 2/31 (6%) Query: 155 IDEVDKILMRYGIEGIPLTDFDHEKIKSYLT 185 I+E ++L+RYG +P+ + ++ ++ Sbjct: 13 IEEARELLLRYGHTALPV--VEGGRVVGIIS 41 >gnl|CDD|32643 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]. Length = 394 Score = 30.2 bits (68), Expect = 0.44 Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 12/76 (15%) Query: 31 SAEQRKLWSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAY--WFFGEKFSYDVSIKIVLA 88 R L LLR V L TFL+ G F L+ Y F + VS A Sbjct: 198 PGPLRTLLRLLRRPGV--LLGLLATFLF--MTGHFALYTYIRPFLESVAGFSVS-----A 248 Query: 89 INVLLFSFVIA-LLGN 103 ++++L +F IA +GN Sbjct: 249 VSLVLLAFGIAGFIGN 264 >gnl|CDD|112133 pfam03304, Mlp, Mlp lipoprotein family. The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species. This family were previously known as 2.9 lipoprotein genes. These surface expressed genes may represent new candidate vaccinogens for Lyme disease. Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity. Length = 150 Score = 30.2 bits (68), Expect = 0.49 Identities = 22/77 (28%), Positives = 28/77 (36%), Gaps = 20/77 (25%) Query: 131 EKISQKNVEKDFFNS------KFFTHFKEYID---EVDKILMRYGIEGIPLTDFDHEKIK 181 EK K+ E+ F F KE + + K L + D KIK Sbjct: 50 EKPKSKSDEELLFEKLSDDQKTFLDWLKEALGAFGKFYKFL-----------ESDKSKIK 98 Query: 182 SYLTHIKIVRDCLKKDN 198 S LTHIK DC + Sbjct: 99 SALTHIKGELDCCNGNP 115 >gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]. Length = 503 Score = 29.2 bits (65), Expect = 0.92 Identities = 25/88 (28%), Positives = 34/88 (38%), Gaps = 4/88 (4%) Query: 107 EMAKDIAQL--FTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164 EMA +A L I + Q KN E F N+ + EV + + Sbjct: 77 EMAIAMALLGGIGFIHHNCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEVKEAKEK 136 Query: 165 YGIEGIPLTDFDHEKIKSYLTHIKIVRD 192 +G GIP+T+ K S L I RD Sbjct: 137 HGFSGIPVTEDG--KRGSKLVGIITSRD 162 >gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma subunit [Energy production and conversion]. Length = 381 Score = 28.8 bits (64), Expect = 1.2 Identities = 21/130 (16%), Positives = 45/130 (34%), Gaps = 20/130 (15%) Query: 80 DVSIKIVLAINVLLFSFVIALLGNPNIEMAKDIAQLFTLID--NIENGYGQYLEKISQKN 137 D + + A N L+ + V A + + + T+ D + Y + + Sbjct: 82 DTKLSVKKAFNALVQNGVRAAPLWDS--KKQQFVGMLTITDFITVLLRYYKSKSSLDNIE 139 Query: 138 VEKDFFNSK----------FFTHFKEYID------EVDKILMRYGIEGIPLTDFDHEKIK 181 V +D SK I + +L++ I +P+ D + ++ Sbjct: 140 VLEDSQLSKRREVECLLKETLKPPFVSISPESSLLDAVLLLIKSRIHRVPVIDPETGEVL 199 Query: 182 SYLTHIKIVR 191 LT +I++ Sbjct: 200 YILTQRRILK 209 >gnl|CDD|37313 KOG2102, KOG2102, KOG2102, Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]. Length = 941 Score = 28.1 bits (62), Expect = 2.0 Identities = 11/59 (18%), Positives = 18/59 (30%), Gaps = 4/59 (6%) Query: 143 FNSKFFTHF----KEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRDCLKKD 197 S +THF + Y D + + T D + S + + KK Sbjct: 775 LASPLYTHFTSPIRRYADIIVHRQLAAAFLERSPTAPDRPNLSSLAANCNERKKAAKKA 833 >gnl|CDD|39018 KOG3814, KOG3814, KOG3814, Signaling protein van gogh/strabismus [Signal transduction mechanisms]. Length = 531 Score = 27.7 bits (61), Expect = 2.7 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 14/85 (16%) Query: 27 GLFDSAEQRKLWSLLRYWSVEFWEL----LCRTFLW---LLCLGFFTLFAYW-FFGEK-- 76 GL S + L L+ W++ F+ + R F+ LL L F +FAYW F+ + Sbjct: 156 GLLISMAFKLLILLIGIWAL-FFRKAMADMPRVFVVRALLLVLVFLIVFAYWLFYIVRIL 214 Query: 77 FSYDVSIKIVLAINVLLFSFVIALL 101 + K ++ S V ALL Sbjct: 215 DERYRNYKGIVQYAT---SLVDALL 236 >gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. Length = 467 Score = 27.6 bits (62), Expect = 3.0 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%) Query: 136 KNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRD 192 K E F + E ++ RYGI G+P+T + K+ L I+ RD Sbjct: 82 KRFESGFITDPVTVSPDTTVAEALELKERYGISGVPVT--EDGKLLGGLVGIRTSRD 136 >gnl|CDD|36273 KOG1055, KOG1055, KOG1055, GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms]. Length = 865 Score = 26.9 bits (59), Expect = 4.0 Identities = 11/28 (39%), Positives = 13/28 (46%) Query: 45 SVEFWELLCRTFLWLLCLGFFTLFAYWF 72 SV + LC W+L LGF F F Sbjct: 529 SVNAFPFLCTARTWILGLGFTLAFGAMF 556 >gnl|CDD|144229 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). Length = 373 Score = 27.1 bits (61), Expect = 4.0 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 3/52 (5%) Query: 133 ISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYL 184 I++ +V++ F S H KEY E K + E E+ L Sbjct: 92 INKSSVDRGLFTS---IHIKEYEIEARKTKLGPIEEITRDPPNVSEEAYRKL 140 >gnl|CDD|36500 KOG1286, KOG1286, KOG1286, Amino acid transporters [Amino acid transport and metabolism]. Length = 554 Score = 26.8 bits (59), Expect = 4.8 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 3/47 (6%) Query: 59 LLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPN 105 +L + F + AY +FS KI+ A+ ++ + VI G P Sbjct: 166 ILIINLFGVLAY--GEVEFSL-AFNKILTAVGFIILAIVIIAGGGPA 209 >gnl|CDD|38951 KOG3747, KOG3747, KOG3747, Concentrative Na+-nucleoside cotransporter CNT1/CNT2 [Nucleotide transport and metabolism, Inorganic ion transport and metabolism]. Length = 602 Score = 26.8 bits (59), Expect = 5.0 Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 24/81 (29%) Query: 43 YWSVEFWELLCRTFLWLLCLGFFTLFAYWFF----------------GEKFSYDVSIK-- 84 W + L + L LL L W F G F + +I Sbjct: 203 NWRIVTSGLGLQFLLGLLVLR--WPTGRWIFQWLGEQVQIFLEYAQAGASFVFGDNICDL 260 Query: 85 IVLAINVL----LFSFVIALL 101 V A +L FS V+++L Sbjct: 261 AVFAFAILPIIIFFSAVVSIL 281 >gnl|CDD|153334 cd07650, F-BAR_Syp1p_like, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Syp1p is associated with septins, a family of GTP-binding proteins that serve as elements of septin filaments, which are required for cell morphogenesis and division. Syp1p regulates cell-cycle dependent septin cytoskeletal dynamics in yeast. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCH domain Only (FCHO) proteins and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Length = 228 Score = 26.5 bits (59), Expect = 5.2 Identities = 7/32 (21%), Positives = 15/32 (46%) Query: 110 KDIAQLFTLIDNIENGYGQYLEKISQKNVEKD 141 ++A +E Y Q L K++++N + Sbjct: 22 TELADWLQERRRLERQYVQGLRKLARRNEPLN 53 >gnl|CDD|33694 COG3907, COG3907, PAP2 (acid phosphatase) superfamily protein [General function prediction only]. Length = 249 Score = 26.1 bits (57), Expect = 6.6 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 55 TFLWLLCLGFFTLFAY 70 T WL+ LGFF LF Sbjct: 224 TICWLVALGFFYLFFV 239 >gnl|CDD|73050 cd03291, ABCC_CFTR1, The CFTR subfamily domain 1. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.. Length = 282 Score = 26.1 bits (57), Expect = 6.9 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 3/41 (7%) Query: 123 ENGYGQYLEKISQKNVEKDFFN---SKFFTHFKEYIDEVDK 160 + G+G+ LEK Q+N ++ + + FF++ V K Sbjct: 14 DEGFGELLEKAKQENNDRKHSSDDNNLFFSNLCLVGAPVLK 54 >gnl|CDD|110588 pfam01594, UPF0118, Domain of unknown function DUF20. This transmembrane region is found in putative permeases and predicted transmembrane proteins it has no known function. It is not clear what source suggested that these proteins may be permeases and this information should be treated with caution. Length = 327 Score = 26.0 bits (58), Expect = 7.5 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 8/83 (9%) Query: 56 FLWLLCLGFFTLFAY-----WFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPNIEMAK 110 L L + + + ++I +VL + ++ + LL I Sbjct: 21 LLVPLLIALVLAYLLNPVVRFLKRRGIPRSLAILLVLLLFLVALVLLGLLLIPLLIIQ-- 78 Query: 111 DIAQLFTLIDNIENGYGQYLEKI 133 + QL + + +L ++ Sbjct: 79 -LTQLIKSLPQYIDSLLNWLNEL 100 >gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit. Length = 327 Score = 26.1 bits (58), Expect = 7.8 Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 13/71 (18%) Query: 141 DFFNSKFFTHFKE---YIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKI------VR 191 D F F H +E ++ + + LTD K + L I I VR Sbjct: 216 DLFIP--FLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIALKQIFIEQLELSVR 273 Query: 192 --DCLKKDNIH 200 +CLK+ NIH Sbjct: 274 AYNCLKRANIH 284 >gnl|CDD|146277 pfam03552, Cellulose_synt, Cellulose synthase. Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterized genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity. Length = 716 Score = 25.9 bits (57), Expect = 8.1 Identities = 27/101 (26%), Positives = 40/101 (39%), Gaps = 18/101 (17%) Query: 113 AQLFTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPL 172 A +F L D E + +SQ ++EK F S F + LM G G+P Sbjct: 334 APIFNLEDIDEGDEDEKSSLMSQLSLEKRFGQSPVF---------IASTLMEEG--GVPR 382 Query: 173 TDFDHEKIKSYLTHIKIVRDCLKKDNIHYAKELRNDWI-GS 212 + +K + I C +D + KE+ WI GS Sbjct: 383 SPLPATLVKEAIHVIS----CGYEDKTEWGKEI--GWIYGS 417 >gnl|CDD|31481 COG1290, QcrB, Cytochrome b subunit of the bc complex [Energy production and conversion]. Length = 381 Score = 26.0 bits (57), Expect = 8.6 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%) Query: 38 WSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFV 97 W + YW L ++ T W FG D ++ A++VLL + Sbjct: 145 WDQMSYWGATVITNLFSAIPFI-----GTWLVQWLFGGFSVSDPTLNRFFALHVLLLPAI 199 Query: 98 IALLGNPNI 106 I L ++ Sbjct: 200 ILALVGLHL 208 >gnl|CDD|48065 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.. Length = 215 Score = 25.6 bits (56), Expect = 9.2 Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 3/39 (7%) Query: 126 YGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164 Y + LE K+ F FF FK+ + + +K++++ Sbjct: 45 YAKMLE---HDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80 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 0.327 0.143 0.450 Gapped Lambda K H 0.267 0.0711 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,847,001 Number of extensions: 159493 Number of successful extensions: 850 Number of sequences better than 10.0: 1 Number of HSP's gapped: 847 Number of HSP's successfully gapped: 93 Length of query: 214 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 124 Effective length of database: 4,318,927 Effective search space: 535546948 Effective search space used: 535546948 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: 55 (25.0 bits)