RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62] (354 letters) >gnl|CDD|31380 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]. Length = 248 Score = 220 bits (563), Expect = 3e-58 Identities = 91/236 (38%), Positives = 129/236 (54%), Gaps = 8/236 (3%) Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70 R++K +A AG+ SRRE E++I + RV VNG + V V D +EVDG + Sbjct: 1 DSMRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELK 60 Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTND 127 E L +KP G V++ D +GR TVFD LP R+ VGRLD +TEGLLLLTND Sbjct: 61 EERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLLTND 120 Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGS 185 G LA L PS++ + Y VR G V ++ L L+KG+ + + Sbjct: 121 GELAHRLMHPSSEVEKEYLVRVEGPVTEEDLEKLRKGVTLDDGETKPAKPASLEKEPGKN 180 Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239 N+W+ + L EG+NR+++++FE +V RL RI GP LG L G RE++ + Sbjct: 181 NSWLRITLTEGRNRQVRRMFEAVGLEVLRLKRIRIGPLSLGDLPLPPGEWRELTLE 236 >gnl|CDD|30013 cd02556, PseudoU_synth_RluB, PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.. Length = 167 Score = 200 bits (509), Expect = 6e-52 Identities = 83/167 (49%), Positives = 107/167 (64%), Gaps = 2/167 (1%) Query: 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132 R+ +YHKP GL+ T DP GR TVFD LP + R ISVGRLD+NTEGLLL TNDG LA Sbjct: 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELAN 60 Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192 L PS + R Y VR GQV ++L LKKG+ ++ G + L+ +G N+W V Sbjct: 61 RLMHPSNEIEREYAVRVFGQVTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVT 120 Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSK 238 LREG+NRE+++++E F +V+RLIRI YGP F G L G E+ Sbjct: 121 LREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRGQWEELPP 167 >gnl|CDD|30030 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.. Length = 146 Score = 126 bits (317), Expect = 1e-29 Identities = 55/144 (38%), Positives = 82/144 (56%) Query: 77 LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136 L +KP G+V+T DP+GR TV D L + R+ VGRLD +TEGLLLLTNDG LA L Sbjct: 3 LLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTH 62 Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196 P + Y V+ G +++L L+ G+ + +V + ++ N + V L EG Sbjct: 63 PRYGVEKTYLVKVRGVPSEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEG 122 Query: 197 KNREIKKVFEFFNWKVNRLIRISY 220 +NR+++++FE V RL R+ Sbjct: 123 RNRQVRRMFEAVGHPVLRLKRVRI 146 >gnl|CDD|30010 cd02553, PseudoU_synth_RsuA, PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.. Length = 167 Score = 107 bits (269), Expect = 4e-24 Identities = 54/165 (32%), Positives = 78/165 (47%), Gaps = 7/165 (4%) Query: 77 LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134 + +KP G+V DP TV D LP R + VGRLD +T GLLLLTNDG LA L Sbjct: 4 MLNKPAGVVCATKDPHHP-TVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRL 62 Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194 P + Y V G + +D + +G+++ G + S V + + Sbjct: 63 TSPKKHVPKTYEVTLAGPLTEDDIEAFAEGVLLHD---GYPTKPAKLEILSPTTVRLTIT 119 Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238 EGK ++K++F KV L RI G +L L G R +++ Sbjct: 120 EGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLAPGEWRPLTE 164 >gnl|CDD|30008 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.. Length = 154 Score = 79.6 bits (196), Expect = 1e-15 Identities = 47/152 (30%), Positives = 74/152 (48%), Gaps = 8/152 (5%) Query: 77 LYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135 + +KP GLV +D D TV L RV + GRLD +T GLLLLTNDG L R L Sbjct: 3 VLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLT 62 Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKK-------GIVIQGICYGDMQVTLDTQKGSNAW 188 P + + Y V G++D++ + L G+V +G+ +V + + G Sbjct: 63 EPRREIEKEYLVTVRGELDEEGIEDLATVRRGRLSGLVDEGVPLAVTKVRVIGEHGGTGR 122 Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220 + + L+ G+ +I++ + V RL R+ Sbjct: 123 LRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154 >gnl|CDD|30017 cd02566, PseudoU_synth_RluE, PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.. Length = 168 Score = 79.2 bits (195), Expect = 2e-15 Identities = 47/170 (27%), Positives = 81/170 (47%), Gaps = 18/170 (10%) Query: 75 LWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133 L L++KP G+++ +D + T+ D + V + GRLD ++EGLLLLT+DG L Sbjct: 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD--PGVYAAGRLDRDSEGLLLLTDDGRLQHR 58 Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179 + PS + + Y V+ G +D L L+ G+ + +V Sbjct: 59 ITDPSFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKVDEPPWLWEREPPI 118 Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228 + +W+ + + EGKNR+++++ + RLIR+S G L L Sbjct: 119 RFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSIGDIGLDNL 168 >gnl|CDD|30011 cd02554, PseudoU_synth_RluF, PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.. Length = 164 Score = 76.4 bits (188), Expect = 1e-14 Identities = 46/169 (27%), Positives = 77/169 (45%), Gaps = 8/169 (4%) Query: 76 WLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134 Y+KP+G+ T + F N P R+ +GRLD ++EGL+LLTNDG L + Sbjct: 3 IAYNKPVGIDCTLERADEDNIIDFVNPPP---RIFPIGRLDKDSEGLILLTNDGDLVNKI 59 Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194 + Y V + + + + + G+VI G +V + + L Sbjct: 60 LHADNNHEKEYLVTVNKPITDEFIEGMSNGVVILGTVTKPCKVERLAKDK----FRIVLT 115 Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243 +G NR+I+++ E ++V L R+ +LG L G R ++ L E Sbjct: 116 QGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDAELFE 164 >gnl|CDD|30012 cd02555, PSSA_1, PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA. . Length = 177 Score = 65.3 bits (159), Expect = 3e-11 Identities = 41/166 (24%), Positives = 70/166 (42%), Gaps = 12/166 (7%) Query: 77 LYHKPIGLVTTHSDP--------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128 L HKP G+V+ + + L F+R+ +G LD + GLL+ + DG Sbjct: 8 LLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDG 67 Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188 + R L +++ + Y V G++ L L G+ G +V+ + Sbjct: 68 RVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQ----NEQR 123 Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234 + L+E + +I+++ E +V L RI G LG L G R Sbjct: 124 LRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLPLGQWR 169 >gnl|CDD|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA. Length = 151 Score = 50.1 bits (120), Expect = 9e-07 Identities = 29/150 (19%), Positives = 54/150 (36%), Gaps = 18/150 (12%) Query: 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLA 131 + +KP G+ +D ++ + L R+ V RLD +T GLLLL DG A Sbjct: 1 YIVVNKPAGVPVHPTDLSDLLSLTELLLVAELGKFRLYPVHRLDRDTSGLLLLAKDGEAA 60 Query: 132 RVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLLKKGIVIQGICYGDMQVTL----- 179 L P + + Y G + + + K + + D + + Sbjct: 61 NKLNKLFPERKVEKEYLALVDGPEEEEGTIKAPIKKDKNKVPRRKKEELDGKKAVTHLRV 120 Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFE 206 ++ + V + L G+ +I+ Sbjct: 121 LRSGSKIEDVSLVELELVTGRKHQIRAHLA 150 >gnl|CDD|30910 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]. Length = 289 Score = 46.9 bits (111), Expect = 8e-06 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 21/172 (12%) Query: 6 IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65 V E QR+ K +A+ SR ++++I + RV+VNG + + + D + + Sbjct: 5 EVPEEEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNG-KKVKPSYKLKPGDVVRIPLP 63 Query: 66 PLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSR 107 + E+ L + +KP GLV T+ + L R Sbjct: 64 EEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVER 123 Query: 108 VISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157 V RLD +T GLLL+ + + + + Y G + +D+ Sbjct: 124 PGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDE 175 >gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.. Length = 70 Score = 45.3 bits (107), Expect = 2e-05 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 1/59 (1%) Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71 R+ K++AR G+A SR E ++I V VNG ++ + + V D IEVDG + + Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDI 59 >gnl|CDD|144902 pfam01479, S4, S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Length = 48 Score = 39.0 bits (92), Expect = 0.002 Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%) Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60 R+ KV+AR G+A SR E ++I V+VNG +++ + V D I Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48 >gnl|CDD|73332 cd02868, PseudoU_synth_hTruB2_like, PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).. Length = 226 Score = 34.9 bits (80), Expect = 0.036 Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 9/97 (9%) Query: 79 HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE 135 +KP G+ H R T+ NL F V RLD + G+L+L + G + Sbjct: 6 YKPPGVHWKHV----RDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGNKLLSH 61 Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172 L S RVY +R G + + N G VI+ Y Sbjct: 62 LYSNHPTRVYTIR--GLLGKATENFFHTGRVIEKTTY 96 >gnl|CDD|32457 COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown]. Length = 257 Score = 32.1 bits (73), Expect = 0.21 Identities = 15/50 (30%), Positives = 29/50 (58%) Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 R+ VI+ SR + +++I + +VKVN ++++A+ V D I + G Sbjct: 182 RLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG 231 >gnl|CDD|30511 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 401 Score = 29.0 bits (65), Expect = 2.0 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 3/66 (4%) Query: 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 + + ++ AG+A SR E R+I Q VK+NG +E N + +D ++ + L Sbjct: 331 KQKLEDGLVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVED--ENYVLSDLLDNGLLVL 388 Query: 68 RKAERT 73 R+ ++ Sbjct: 389 RRGKKK 394 >gnl|CDD|30868 COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]. Length = 205 Score = 28.8 bits (64), Expect = 2.1 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 1/62 (1%) Query: 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 +R+ V+ R G A +RR+ ++++ + VNG + + V D I V Sbjct: 89 LALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSK 148 Query: 68 RK 69 Sbjct: 149 SP 150 >gnl|CDD|33817 COG4059, MtrE, Tetrahydromethanopterin S-methyltransferase, subunit E [Coenzyme metabolism]. Length = 304 Score = 28.8 bits (64), Expect = 2.2 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 6/68 (8%) Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV-----FEFFNWKVNRLI 216 K G + G+ +G + V L + + V ++ G + + +N KV Sbjct: 229 KFGGPLTGLAFG-LIVFLSSWVTTVFDPAVSIQGGWISIVAGLIIVLILIIWNRKVEVKA 287 Query: 217 RISYGPFQ 224 R +YGP++ Sbjct: 288 RNAYGPYK 295 >gnl|CDD|143359 cd07854, STKc_MAPK4_6, Catalytic domain of the Serine/Threonine Kinases, Mitogen-Activated Protein Kinases 4 and 6. Serine/Threonine Kinases (STKs), Mitogen-Activated Protein Kinase 4 (MAPK4) and MAPK6 subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAPK4/6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MAPKs are important mediators of cellular responses to extracellular signals. MAPK4 is also called ERK4 or p63MAPK, while MAPK6 is also called ERK3 or p97MAPK. MAPK4 and MAPK6 are atypical MAPKs that are not regulated by MAP2Ks. MAPK6 is expressed ubiquitously with highest amounts in brain and skeletal muscle. It may be involved in the control of cell differentiation by negatively regulating cell cycle progression in certain conditions. It may also play a role in glucose-induced insulin secretion. MAPK6 and MAPK4 cooperate to regulate the activity of MAPK-activated protein kinase 5 (MK5), leading to its relocation to the cytoplasm and exclusion from the nucleus. The MAPK6/MK5 and MAPK4/MK5 pathways may play critical roles in embryonic and post-natal development. Length = 342 Score = 27.8 bits (62), Expect = 4.1 Identities = 25/92 (27%), Positives = 36/92 (39%), Gaps = 23/92 (25%) Query: 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129 E RL++Y GL HS ++ R + + INTE L+L D G Sbjct: 113 EEHARLFMYQLLRGLKYIHS------------ANVLHRDLKPANVFINTEDLVLKIGDFG 160 Query: 130 LARVL-----------ELPSTQWLRVYRVRFH 150 LAR++ E T+W R R+ Sbjct: 161 LARIVDPHYSHKGYLSEGLVTKWYRSPRLLLS 192 >gnl|CDD|31382 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]. Length = 245 Score = 27.5 bits (61), Expect = 5.5 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%) Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72 R+ ++ G+ SR + + +I V VNG + + + V D IEV G R Sbjct: 3 MRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSR 62 >gnl|CDD|147651 pfam05597, Phasin, Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon. Length = 132 Score = 27.6 bits (62), Expect = 5.7 Identities = 11/24 (45%), Positives = 18/24 (75%) Query: 14 QRVSKVIARAGIASRREVERMIAQ 37 +RV+K + R G+ SR+EVE + A+ Sbjct: 94 ERVAKALNRLGVPSRKEVEALSAR 117 >gnl|CDD|30057 cd01314, D-HYD, D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine or hydantoin. The hydrolysis of dihydropyrimidines is the second step of reductive catabolism of pyrimidines in human. The hydrolysis of 5-substituted hydantoins in microorganisms leads to enantiomerically pure N-carbamyl amino acids, which are used for the production of antibiotics, peptide hormones, pyrethroids, and pesticides. HYDs are classified depending on their stereoselectivity. This family also includes collapsin response regulators (CRMPs), cytosolic proteins involved in neuronal differentiation and axonal guidance which have strong homology to DHPases, but lack most of the active site residues.. Length = 447 Score = 27.5 bits (61), Expect = 5.9 Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 13/71 (18%) Query: 47 LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106 L + + +DH P A K G P+G V +P ++S Sbjct: 302 LSSGTLQTVGSDH-----CPFNFA--------QKARGKDDFTKIPNGVPGVETRMPLLWS 348 Query: 107 RVISVGRLDIN 117 ++ GR+ + Sbjct: 349 EGVAKGRITLE 359 >gnl|CDD|30029 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. . Length = 185 Score = 27.3 bits (60), Expect = 6.1 Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 8/87 (9%) Query: 79 HKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLAR 132 +KP GL T+ + L + R V RLD +T GLLL+ + A Sbjct: 5 NKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAA 64 Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDK 157 L + + + Y G+ +D+ Sbjct: 65 KLSKQFKERKVKKTYLALVDGKPPEDE 91 >gnl|CDD|39858 KOG4659, KOG4659, KOG4659, Uncharacterized conserved protein (Rhs family) [Function unknown]. Length = 1899 Score = 26.9 bits (59), Expect = 8.2 Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 2/40 (5%) Query: 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113 R Y GL+ T D G + V++ + R+ R Sbjct: 799 RDATYLGYTGLLLTKRDDTGTAVVYEYDE--YGRLTGAKR 836 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 0.318 0.134 0.385 Gapped Lambda K H 0.267 0.0747 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,158,068 Number of extensions: 216207 Number of successful extensions: 470 Number of sequences better than 10.0: 1 Number of HSP's gapped: 456 Number of HSP's successfully gapped: 30 Length of query: 354 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 259 Effective length of database: 4,210,882 Effective search space: 1090618438 Effective search space used: 1090618438 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.1 bits)