RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780815|ref|YP_003065228.1| hypothetical protein CLIBASIA_03530 [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >gnl|CDD|34102 COG4395, COG4395, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 281 Score = 122 bits (306), Expect = 1e-28 Identities = 56/239 (23%), Positives = 94/239 (39%), Gaps = 21/239 (8%) Query: 6 MDSGDFLILLFAFITFFVFLQLRGVLGKKTGNEKPF---------------SGFFSGKYV 50 + F L F F +FL L ++G E F + YV Sbjct: 44 LSGMFFGGLFFGIAAFLIFLLLITLIGFVIMLEMRFFDPYRPQRPAYDAAQASVAPDNYV 103 Query: 51 FS-KRDERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARN 109 + E + D + + + G L R + + FDP FLN AR Sbjct: 104 TLPRAPEAQPAS-----AADIPAAGDAIGGAGGPLAAGARAVHNADPSFDPARFLNGARA 158 Query: 110 SYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLVGIDDMKIINASI 169 +YE I ++ G + +L+ V + ++ R+S + +SS V I I A + Sbjct: 159 AYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQSSFVTILQADIARADV 218 Query: 170 EENTVYITIRIVGQFISASYDKDNLLISSDPEIFGKVIDIWTFVRNIPPSNPNWVLIST 228 E + Y T+ I Q I + D+ ++ DP+ + ++WTF R+ +PNW L + Sbjct: 219 EGDEDYATVAIRYQGIDVTRDRSGKVVDGDPDKPEEFAELWTFTRDTGSRDPNWKLAAI 277 >gnl|CDD|146752 pfam04280, Tim44, Tim44-like domain. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane. Length = 146 Score = 111 bits (280), Expect = 1e-25 Identities = 42/144 (29%), Positives = 80/144 (55%) Query: 85 NKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSLST 144 + I + FD ++FL AR +YE I +++ G + + +L+ VY++F ++ Sbjct: 1 ASALAAIKAADPSFDVEEFLEGAREAYEMIQEAWANGDLETLRELLTPEVYEEFAAEIAE 60 Query: 145 RKSNEKNVKSSLVGIDDMKIINASIEENTVYITIRIVGQFISASYDKDNLLISSDPEIFG 204 R++ +++VGI D +++ A +E NT +T+R V Q IS + D ++ DP+ Sbjct: 61 REAQGLTNDATIVGIRDAELLEAKMEGNTAVVTVRFVTQQISVTDDASGEVVEGDPDEPV 120 Query: 205 KVIDIWTFVRNIPPSNPNWVLIST 228 +V ++WTF R++ +PNW L+ Sbjct: 121 EVTEVWTFERDLGSPDPNWRLVGI 144 >gnl|CDD|37791 KOG2580, KOG2580, KOG2580, Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]. Length = 459 Score = 37.6 bits (87), Expect = 0.002 Identities = 28/150 (18%), Positives = 60/150 (40%), Gaps = 5/150 (3%) Query: 82 TRLNKVMRDIVSVYTDFDPKDFLNEARNSY-EAIVDSFFEGKVHAIEKLVDSRVYQDFND 140 T +++V+ +I + FD +DFL E +++++ +G + ++K + Sbjct: 299 TEMSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAA 358 Query: 141 SLSTRKSNEKNVKSSLVGIDDMKIINASIEENTVYITIRIVGQFISASYDKDNLLISSDP 200 + K + S ++ I + I + + E+ + I Q I D ++ DP Sbjct: 359 PIKEYKKHGVYFDSKILDIRGVDIASGKMMEDGPVLIITFQAQEIMCVRDAKGEVVEGDP 418 Query: 201 EIFGKVIDIWTFVRNI----PPSNPNWVLI 226 + +V W R+ P W L+ Sbjct: 419 DKILRVYYAWVLCRDQDELNPDEYAAWRLL 448 >gnl|CDD|145924 pfam03034, PSS, Phosphatidyl serine synthase. Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyses the replacement of the head group of a phospholipid (phosphotidylcholine or phosphotidylethanolamine) by L-serine. Length = 278 Score = 32.3 bits (74), Expect = 0.12 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 13/56 (23%) Query: 179 RIVGQFISASYDKDNLLISSDPEIFGKVIDIWT-------------FVRNIPPSNP 221 R++ QF AS+DK + P+ F +V+ + + IPPS+P Sbjct: 167 RVLLQFTPASWDKYEWKVFKSPKRFLQVLFLVFLILLAELNTFFLKHILWIPPSHP 222 >gnl|CDD|73314 cd02568, PseudoU_synth_PUS1_PUS2, PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).. Length = 245 Score = 30.2 bits (68), Expect = 0.53 Identities = 23/129 (17%), Positives = 50/129 (38%), Gaps = 17/129 (13%) Query: 60 ITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSF- 118 G G +D ++ +N P R+ + R V F+ + + +YE ++ +F Sbjct: 75 DPEGLGIGEDLVEKLNSHLPEDIRVFGITR----VTKSFNARKACD--SRTYEYLLPTFA 128 Query: 119 FEGKVH---AIEKLVDSRVYQDF-NDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENTV 174 E ++ V + + +F S + + S + + +I +E Sbjct: 129 LETLDRFNEILKLYVGTHNFHNFTVRKKFEDPSANRFIIS--FYVSEPFVIEEGLE---- 182 Query: 175 YITIRIVGQ 183 +++I I GQ Sbjct: 183 WVSIEIHGQ 191 >gnl|CDD|39459 KOG4258, KOG4258, KOG4258, Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms]. Length = 1025 Score = 29.6 bits (66), Expect = 0.70 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 9/92 (9%) Query: 117 SFFEGKVHAIEKLVDSRVYQD---FNDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENT 173 E I+ + D++ + N SL+ N N+ S L + IEE T Sbjct: 332 KVCEPGTKTIDSVADAQNLRGCTIINGSLTINIRNGNNIASEL------ENALGLIEEIT 385 Query: 174 VYITIRIVGQFISASYDKDNLLISSDPEIFGK 205 Y+ +R +S S+ ++ LI DP G Sbjct: 386 GYLKVRHSSALVSLSFLRNLRLIRGDPLEEGN 417 >gnl|CDD|36513 KOG1299, KOG1299, KOG1299, Vacuolar sorting protein VPS45/Stt10 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport]. Length = 549 Score = 28.3 bits (63), Expect = 2.0 Identities = 12/38 (31%), Positives = 20/38 (52%) Query: 63 GKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDP 100 G ++ +L N+L PI R K ++ + +VYT P Sbjct: 429 GLHVRQGDLFGPNDLVPIARRFIKGLKGVENVYTQHQP 466 >gnl|CDD|146065 pfam03246, Pneumo_ncap, Pneumovirus nucleocapsid protein. Length = 391 Score = 27.9 bits (62), Expect = 2.3 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 15/77 (19%) Query: 83 RLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSL 142 R N V++D + Y D KD A + YE FE K + I+ V+ +F + Sbjct: 185 RANNVLKDEMKRYPRMDIKDI---ANSFYE-----LFEKKPYYID------VFIEFGKAQ 230 Query: 143 STRKSNEKNVKSSLVGI 159 S+ + V+ VG+ Sbjct: 231 SSTSGGSR-VEGLFVGL 246 >gnl|CDD|112214 pfam03389, MobA_MobL, MobA/MobL family. This family includes of the MobA protein from the E. coli plasmid RSF1010, and the MobL protein from the Thiobacillus ferrooxidans plasmid PTF1. These sequences are mobilisation proteins, which are essential for specific plasmid transfer. Length = 219 Score = 27.9 bits (62), Expect = 2.5 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 6/81 (7%) Query: 56 ERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIV 115 R + G G KK + I L G ++ I D+ K+ + E R ++ Sbjct: 123 LRPLDPDGFGGKKKKSEYI--LDENGNKIRTKRGKIK--TEDWGSKELVEEWRKAWADHA 178 Query: 116 DSFFEGKVHAIEKLVDSRVYQ 136 ++ E I+ +D R Y+ Sbjct: 179 NAHLEL--AGIDARIDHRSYE 197 >gnl|CDD|143487 cd06812, PLPDE_III_DSD_D-TA_like_1, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible members of this family also form dimers in solution. Length = 374 Score = 27.7 bits (62), Expect = 2.5 Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 5/29 (17%) Query: 56 ERGIITLGKGKKKDNLDSINELFPIGTRL 84 E GII L + D PIGTRL Sbjct: 315 EHGIIAL-----RGGSDLSLPDLPIGTRL 338 >gnl|CDD|39890 KOG4692, KOG4692, KOG4692, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. Length = 489 Score = 27.7 bits (61), Expect = 3.0 Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%) Query: 98 FDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVD 131 F P+ ++N +A++D F + A + D Sbjct: 24 FVPEVYVNTLPILLDAVMD--FSHDLKAQFEASD 55 >gnl|CDD|31697 COG1508, RpoN, DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]. Length = 444 Score = 26.8 bits (59), Expect = 4.8 Identities = 29/132 (21%), Positives = 50/132 (37%), Gaps = 26/132 (19%) Query: 34 KTGNEKPFSGFFSGKYVFSKRDERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVS 93 ++ + +P F SG+ + D G+ + N DS+ + RLN+ +VS Sbjct: 220 RSLDPRPGLEFSSGEAEYVVPDVLVRKHNGEWTVELNDDSLPRI-----RLNQEYAALVS 274 Query: 94 VYTDFDPKDFLNEARNSYEAIVDS---------------------FFEGKVHAIEKLVDS 132 + + +DFL E + ++ S FFEG A++ LV Sbjct: 275 RAENDEDQDFLKEKLQEAKWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLR 334 Query: 133 RVYQDFNDSLST 144 V + ST Sbjct: 335 DVADEIGMHEST 346 >gnl|CDD|39760 KOG4560, KOG4560, KOG4560, Transcription factor IIIC box B binding (alpha) subunit [Transcription]. Length = 1897 Score = 26.6 bits (58), Expect = 5.5 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 1/71 (1%) Query: 99 DPKDFLNEARNSYEAIV-DSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLV 157 DP + ++ + K + L +Y+ F++ + N+ S LV Sbjct: 1166 DPASETDLQVAVAHGVLHSNICCAKDKTLLNLQTFEIYKHFSEEVLNSAFNKARADSLLV 1225 Query: 158 GIDDMKIINAS 168 + I +A+ Sbjct: 1226 AVKRRNIQSAA 1236 >gnl|CDD|109933 pfam00895, ATP-synt_8, ATP synthase protein 8. Length = 55 Score = 26.1 bits (58), Expect = 7.6 Identities = 7/17 (41%), Positives = 12/17 (70%) Query: 11 FLILLFAFITFFVFLQL 27 FLI L +++T + +QL Sbjct: 10 FLIFLSSWLTLLIIIQL 26 >gnl|CDD|153131 cd01581, AcnB, Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase B catalytic domain. Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase has an active (4FE-4S) and an inactive (3FE-4S) form. The active cluster is part of the catalytic site that interconverts citrate, cis-aconitase and isocitrate. The domain architecture of aconitase B is different from other aconitases in that the catalytic domain is normally found at C-terminus for other aconitases, but it is at N-terminus for B family. It also has a HEAT domain before domain 4 which plays a role in protein-protein interaction. This alignment is the core domain including domains 1,2 and 3. Length = 436 Score = 25.9 bits (57), Expect = 8.6 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 4/65 (6%) Query: 116 DSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENTVY 175 + F G++ IE L D +V Q F T S E++ + V +D +I +E N V Sbjct: 188 KNVFNGRILEIEGLPDLKVEQAFE---LTDASAERSAAACTVRLDKEPVIE-YLESNVVL 243 Query: 176 ITIRI 180 + I I Sbjct: 244 MKIMI 248 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 0.321 0.140 0.401 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: 2,864,349 Number of extensions: 152240 Number of successful extensions: 468 Number of sequences better than 10.0: 1 Number of HSP's gapped: 467 Number of HSP's successfully gapped: 22 Length of query: 232 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 141 Effective length of database: 4,297,318 Effective search space: 605921838 Effective search space used: 605921838 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: 56 (25.2 bits)