RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780980|ref|YP_003065393.1| hypothetical protein CLIBASIA_04405 [Candidatus Liberibacter asiaticus str. psy62] (121 letters) >gnl|CDD|35385 KOG0163, KOG0163, KOG0163, Myosin class VI heavy chain [Cytoskeleton]. Length = 1259 Score = 31.9 bits (72), Expect = 0.042 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%) Query: 22 DIVIGRTEDLLNKLQKNSTQMIKEANF--KISETHRLAQERVEAAEKRVKEVEERATASR 79 D+ + E L+ +L Q I+E KI E ++R EA EKR +E EE+ A Sbjct: 899 DVAVKNYEKLVKRLDSKEQQQIEELERLRKIQELAEAERKRREAEEKRRREEEEKKRAKA 958 Query: 80 KL 81 ++ Sbjct: 959 EM 960 >gnl|CDD|146000 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979 Score = 28.1 bits (62), Expect = 0.55 Identities = 11/26 (42%), Positives = 18/26 (69%) Query: 55 RLAQERVEAAEKRVKEVEERATASRK 80 +LA++R EA EK +E E++A R+ Sbjct: 576 KLAKKREEAVEKAKREAEQKAREERE 601 >gnl|CDD|34624 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]. Length = 373 Score = 27.9 bits (62), Expect = 0.61 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 4/77 (5%) Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQ----ERVEAAEKRVKEVEERATASRKLS 82 RTE L + + +++E R + E++ EKR++E+E+ RK Sbjct: 288 RTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKEL 347 Query: 83 VDELANAFWDLSDEDKN 99 +L L D +K Sbjct: 348 NSKLEEIQKKLEDLEKR 364 >gnl|CDD|147016 pfam04654, DUF599, Protein of unknown function, DUF599. This family includes several uncharacterized proteins. Length = 216 Score = 27.5 bits (62), Expect = 0.91 Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 2/27 (7%) Query: 7 MTSAF--STTLLTIGGCDIVIGRTEDL 31 M + F ST +L I G ++G T+ L Sbjct: 61 MGTTFFASTAILLIAGIAALLGSTDRL 87 >gnl|CDD|38820 KOG3614, KOG3614, KOG3614, Ca2+/Mg2+-permeable cation channels (LTRPC family) [Inorganic ion transport and metabolism, Signal transduction mechanisms]. Length = 1381 Score = 27.6 bits (61), Expect = 0.94 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 16/80 (20%) Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER---------ATASR 79 E+ L K + E N E R RV+ R+ E+E+R + +R Sbjct: 1125 ENFLRKREM-------EQNSSTEERIRRTANRVDLILNRLIELEQREKTLKDSVQNSETR 1177 Query: 80 KLSVDELANAFWDLSDEDKN 99 SV + + + ++ N Sbjct: 1178 LASVLQFSEEYVNILKILVN 1197 >gnl|CDD|38830 KOG3624, KOG3624, KOG3624, M13 family peptidase [Amino acid transport and metabolism]. Length = 687 Score = 26.7 bits (58), Expect = 1.5 Identities = 9/40 (22%), Positives = 24/40 (60%) Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRV 68 +++ L+K +M++E ++ ET + A +++ A +K + Sbjct: 381 SEMIEDLKKAFEEMLQELDWLDEETRKSAIKKLNAMKKNI 420 >gnl|CDD|33777 COG4018, COG4018, Uncharacterized protein conserved in archaea [Function unknown]. Length = 505 Score = 26.5 bits (58), Expect = 1.6 Identities = 12/33 (36%), Positives = 18/33 (54%) Query: 74 RATASRKLSVDELANAFWDLSDEDKNAFTGNVK 106 + KL VDE+ +A DLSDE+ N++ Sbjct: 20 KLAYEGKLDVDEVVDAVGDLSDEELEKLGDNLR 52 >gnl|CDD|36445 KOG1231, KOG1231, KOG1231, Proteins containing the FAD binding domain [Energy production and conversion]. Length = 505 Score = 26.5 bits (58), Expect = 1.8 Identities = 13/57 (22%), Positives = 24/57 (42%) Query: 42 MIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELANAFWDLSDEDK 98 +I A K+ + QER+ + VE A +R + + ++L DE + Sbjct: 227 IITRARIKLEPAPKRDQERLISVCGSFDTVEGAAIVARNGLQSNIRVSRFELLDEVQ 283 >gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1174 Score = 26.1 bits (57), Expect = 2.7 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 9/102 (8%) Query: 23 IVIGRTEDLLNKLQKNSTQMIKEANFKIS---ETHRLAQERVEAAEKRVKEVEERATASR 79 I I + +KNS I+E KI+ E+ + +E+ EK +KE+E++ A Sbjct: 233 ICIAYEYLQAEEKRKNSAHEIEEMKDKIAKLDESLGKTDKEIESLEKEIKEIEQQRDAEM 292 Query: 80 KLSVDELANAFWDLSDE------DKNAFTGNVKQEVCKVKKI 115 V L + L +E N + E K+++I Sbjct: 293 GGEVKALEDKLDSLQNEITREETSLNLKKETLNGEEEKLEEI 334 >gnl|CDD|31753 COG1565, COG1565, Uncharacterized conserved protein [Function unknown]. Length = 370 Score = 26.0 bits (57), Expect = 2.7 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 4/68 (5%) Query: 29 EDLLNKLQKNSTQMIKEANFKISETH----RLAQERVEAAEKRVKEVEERATASRKLSVD 84 D+L L++ ++ + ++ I E +E ++A E ++ VE +K Sbjct: 93 SDILRTLRRLYPELYEALSYYIIEPSPELRARQKETLKATEDLIRWVEWVEDLPKKFPGI 152 Query: 85 ELANAFWD 92 ++N +D Sbjct: 153 VVSNELFD 160 >gnl|CDD|30092 cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.. Length = 338 Score = 26.0 bits (57), Expect = 2.8 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 2/58 (3%) Query: 30 DLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELA 87 +LL K +N TQ EAN S +H + Q V ++ ++ KLS+ +LA Sbjct: 188 ELLMKGNRNRTQEPTEANATSSRSHAVLQITVRQKDRTASINQQVRIG--KLSLIDLA 243 >gnl|CDD|37332 KOG2121, KOG2121, KOG2121, Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]. Length = 746 Score = 25.7 bits (56), Expect = 3.3 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 13/63 (20%) Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDEL 86 R + L K K++T +I EA + EA EK +T S +SV + Sbjct: 629 RPCEDLVKAGKDATLLIHEATLEDDLEE-------EAVEK------GHSTTSEAISVAKK 675 Query: 87 ANA 89 NA Sbjct: 676 MNA 678 >gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]. Length = 3738 Score = 25.5 bits (55), Expect = 3.9 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%) Query: 57 AQERVEAAEKRVKEVEERATASRKLSV----DELANAFWDLSDEDKN 99 ++E K + + + T+SR + D FW+ DEDKN Sbjct: 2874 SEESFVMCLKDLTSIVDIKTSSRPAMIGSLTDGSTETFWESGDEDKN 2920 >gnl|CDD|33327 COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]. Length = 372 Score = 25.3 bits (55), Expect = 3.9 Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%) Query: 35 LQKNSTQMIKEANFKI-SETHRLAQERVEAAEKRVKEVEERATASR 79 + K S ++I + + + +T R A+E V+ AE+RVK+ T R Sbjct: 161 ILKQSEKLINQLSERARRDTVRFAEEEVQKAEERVKKASNDLTDYR 206 >gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]. Length = 1758 Score = 25.5 bits (55), Expect = 4.2 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 7/71 (9%) Query: 41 QMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELANAFWD-LSDEDKN 99 M++EA SE AQ+ + A ++ + S + + L D L+ D + Sbjct: 1436 SMVREAKLSASE----AQQSAQRALEQANASRSQMEESNRE-LRNLIQQVRDFLTQPDAD 1490 Query: 100 AFT-GNVKQEV 109 + V +EV Sbjct: 1491 PDSIEEVAEEV 1501 >gnl|CDD|35462 KOG0241, KOG0241, KOG0241, Kinesin-like protein [Cytoskeleton]. Length = 1714 Score = 25.4 bits (55), Expect = 4.4 Identities = 11/52 (21%), Positives = 25/52 (48%) Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRK 80 E L +L++ + E K+ E+ +L +E E+++++ EE + Sbjct: 374 EKLREQLEQAEAMKLPELKEKLEESEKLIKEITVTWEEKLRKTEEINQERQA 425 >gnl|CDD|111928 pfam03087, DUF241, Arabidopsis protein of unknown function. This family represents a number of Arabidopsis proteins. Their functions are unknown. Length = 230 Score = 25.1 bits (55), Expect = 4.4 Identities = 7/38 (18%), Positives = 19/38 (50%) Query: 36 QKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73 ++ + E + +E + +R+E E ++E+E+ Sbjct: 174 IRSELSRLDEEKRRDNEEVKDILKRLEELENSIEELED 211 >gnl|CDD|36302 KOG1086, KOG1086, KOG1086, Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]. Length = 594 Score = 25.4 bits (55), Expect = 4.5 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%) Query: 31 LLNKLQK-NSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73 LL +L K N + ++ AN I + + ++E KRVK +EE Sbjct: 177 LLARLLKSNHPEDLQAANKLIKTLVKEEEHKLEKISKRVKALEE 220 >gnl|CDD|38926 KOG3722, KOG3722, KOG3722, Lipocalin-interacting membrane receptor (LIMR) [Defense mechanisms]. Length = 538 Score = 24.9 bits (54), Expect = 4.9 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 5/52 (9%) Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATAS 78 RT ++ K K+ + K NF E E V+ + +E+R TAS Sbjct: 289 RTTPIVRKWDKDVPKK-KNPNFDYRELK----EYVKELRTQRSSLEKRRTAS 335 >gnl|CDD|73362 cd00311, TIM, Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually homodimeric, but in some organisms tetrameric, is ubiqitous and conserved in function across eukaryotes, bacteria and archaea.. Length = 242 Score = 25.2 bits (55), Expect = 5.2 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 11/71 (15%) Query: 46 ANFKISETHRLAQERVEAAEKRVKEVEER-----------ATASRKLSVDELANAFWDLS 94 N+K++ T A E +A +K+ A + L ++ ++S Sbjct: 5 GNWKMNGTLAEALELAKALNAVLKDESGVEVVVAPPFTYLAAVAEALEGSKIKVGAQNVS 64 Query: 95 DEDKNAFTGNV 105 ED AFTG + Sbjct: 65 PEDSGAFTGEI 75 >gnl|CDD|32264 COG2081, COG2081, Predicted flavoproteins [General function prediction only]. Length = 408 Score = 24.8 bits (54), Expect = 5.8 Identities = 10/53 (18%), Positives = 18/53 (33%) Query: 30 DLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLS 82 L K +K + T + V A KE++ + S+K+ Sbjct: 317 QLSPKELAQLAAALKAWPITPNGTEPYREAEVTAGGVDTKEIDSKTMESKKVP 369 >gnl|CDD|40045 KOG4848, KOG4848, KOG4848, Extracellular matrix-associated peroxidase [Extracellular structures, Defense mechanisms]. Length = 225 Score = 24.7 bits (53), Expect = 6.1 Identities = 7/47 (14%), Positives = 22/47 (46%), Gaps = 1/47 (2%) Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73 R ++ ++K Q + + + + + A + E+ ++E++E Sbjct: 133 REAEIAKNMKK-YPQTLAKYEASLVKQEQEADAKEVRLERLIREIQE 178 >gnl|CDD|145274 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria. Length = 375 Score = 24.6 bits (54), Expect = 6.2 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 15/68 (22%) Query: 56 LAQERVEAAEKRVKEVEERATASRKLSVDELANA--FWDLSDEDKNAFTGNVKQEVCKVK 113 +E +E AE +E +R KL +EL + ++DL ++ V Sbjct: 284 FVEEMLEIAESPPEEFSKRILGLLKLIKEELLDVPLYYDLH-------------QLASVL 330 Query: 114 KITVPPSN 121 K++VPP Sbjct: 331 KLSVPPLQ 338 >gnl|CDD|38122 KOG2911, KOG2911, KOG2911, Uncharacterized conserved protein [Function unknown]. Length = 439 Score = 24.5 bits (53), Expect = 6.7 Identities = 12/58 (20%), Positives = 23/58 (39%) Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDEL 86 EDL +KN ++ + RL+ + E +++ E K V++L Sbjct: 380 EDLEADEKKNEDLVLPLNSVSRDFLKRLSDLELLTNEDSLEKTEGPLNQISKSLVEQL 437 >gnl|CDD|112811 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator. Length = 220 Score = 24.3 bits (53), Expect = 8.2 Identities = 8/38 (21%), Positives = 20/38 (52%) Query: 53 THRLAQERVEAAEKRVKEVEERATASRKLSVDELANAF 90 + + ++E +++ K++E +A A+ +ELA Sbjct: 52 RQKQLERKLEEQKEQAKKLENKARAALTKGNEELAREA 89 >gnl|CDD|145010 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA. Length = 517 Score = 24.3 bits (53), Expect = 9.0 Identities = 20/117 (17%), Positives = 36/117 (30%), Gaps = 36/117 (30%) Query: 17 TIGGCDIV--------IGRTEDLLNKLQKNSTQMIKEANFKISETH-------------- 54 +GG + +G D ++ +N+ +++E E+ Sbjct: 319 VLGGTQSLHTNPFDEALGLPTDFSARIARNTQLILQE------ESGVARVIDPWGGSYYV 372 Query: 55 -RLAQERVEAAEKRVKEVEER-------ATASRKLSVDELANAFWDLSDEDKNAFTG 103 L E A K +E+EE KL ++E A D + G Sbjct: 373 EELTDRIAEEAWKLFQEIEEAGGMAKAIEDGLPKLRIEESAARRQARIDSGREVIVG 429 >gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.. Length = 307 Score = 24.4 bits (53), Expect = 9.0 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%) Query: 25 IGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER 74 +G E L K Q + +KE F +S RL + +E E+E + Sbjct: 218 LGEAEGLGPKTQSEALAFLKEWGFPVSPETRLC-KNIEEVLAFYDEIEAK 266 >gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]. Length = 1592 Score = 24.1 bits (52), Expect = 9.2 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 1/59 (1%) Query: 30 DLLNKLQKNSTQMIKE-ANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELA 87 + ++ L++ + +I E + F + + +R E+ ER A R L+ ELA Sbjct: 1203 EAISLLERLNLSLITELSRFISTLEAKGLLDREVEFLPSDAELAERNAAGRGLTRPELA 1261 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 0.312 0.126 0.337 Gapped Lambda K H 0.267 0.0790 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,255,070 Number of extensions: 53647 Number of successful extensions: 245 Number of sequences better than 10.0: 1 Number of HSP's gapped: 243 Number of HSP's successfully gapped: 80 Length of query: 121 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 39 Effective length of database: 4,491,799 Effective search space: 175180161 Effective search space used: 175180161 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (23.3 bits)