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)