RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8796
(536 letters)
>gnl|CDD|109297 pfam00233, PDEase_I, 3'5'-cyclic nucleotide phosphodiesterase.
Length = 237
Score = 243 bits (622), Expect = 2e-77
Identities = 105/241 (43%), Positives = 150/241 (62%), Gaps = 6/241 (2%)
Query: 143 YHNWRHALNVAQTMFAMLKTGKMERFMSDLEILGLLVACLCHDLDHRGTNNAFQTKTESP 202
YHNWRHA +V QT +L T +ER+++DLEIL LL A HD+DHRGTNN+FQ ++S
Sbjct: 1 YHNWRHAADVTQTTHLLLLTLALERYLTDLEILALLFAAAIHDVDHRGTNNSFQINSKSE 60
Query: 203 LAILYTT-STMEHHHFDQCVMILNSDGNNIFQALSPHDYRIVMKLVENSILSTDLAMYFK 261
LAILY S +E+HH Q +L + NIFQ LS D++ + LV IL+TD++++F+
Sbjct: 61 LAILYNDESVLENHHLAQAFKLLQDEECNIFQNLSKKDFQTLRDLVIEMILATDMSLHFQ 120
Query: 262 KKNRFIQLVENGEFDWQSEEKKQLLCGMMMTACDVGAIAKPWEVQHKMAKLVADEFFDQG 321
K +VE + + K LL ++M A D+ KPW++ + A+L+ +EFFDQG
Sbjct: 121 KLKDLKTMVEQKKRLDL-DHKILLLS-LLMHAADLSNPTKPWKLHRRWAELIMEEFFDQG 178
Query: 322 DLEKLQLNTQPVAMMDRERKDELPQMQVGFIDVICLPLYKVMSDTF-PWIQPLYDGTYEN 380
DLE+ +L P M DR +P+ QVGFID I P++K+++D IQPL D +N
Sbjct: 179 DLER-ELGLPPSPMCDRT-SAYVPKSQVGFIDFIVEPIFKLLADVVEKDIQPLLDTIEDN 236
Query: 381 R 381
R
Sbjct: 237 R 237
>gnl|CDD|214679 smart00471, HDc, Metal dependent phosphohydrolases with conserved
'HD' motif. Includes eukaryotic cyclic nucleotide
phosphodiesterases (PDEc). This profile/HMM does not
detect HD homologues in bacterial glycine aminoacyl-tRNA
synthetases (beta subunit).
Length = 124
Score = 67.3 bits (164), Expect = 1e-13
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 16/100 (16%)
Query: 143 YHNWRHALNVAQTMFAMLKTGKMERFMSDLEILGLLVACLCHDLDHRGTNNAFQTKTESP 202
YH + H+L VAQ A+ + + L+I LL+A L HD+ GT ++F KT
Sbjct: 3 YHVFEHSLRVAQLAAALAEE------LGLLDIELLLLAALLHDIGKPGTPDSFLVKTSV- 55
Query: 203 LAILYTTSTMEHHHFDQCVMILNSDGNNIFQALSPHDYRI 242
+E HHF ++L + I + +
Sbjct: 56 ---------LEDHHFIGAEILLEEEEPRILEEILRTAILS 86
>gnl|CDD|238032 cd00077, HDc, Metal dependent phosphohydrolases with conserved 'HD'
motif.
Length = 145
Score = 58.5 bits (141), Expect = 3e-10
Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 35/178 (19%)
Query: 143 YHNWRHALNVAQTMFAMLKTGKMERFMSDLEILGLLVACLCHDLDHRGTNNAFQTKTESP 202
H + H+L VAQ + + + S+ +I L +A L HD+ GT +A
Sbjct: 1 EHRFEHSLRVAQLARRLAEELGL----SEEDIELLRLAALLHDIGKPGTPDAI------- 49
Query: 203 LAILYTTSTMEHHHFDQCVMILNSDGNNIFQALSPHDYRIVMKLVENSILSTDLAMYFKK 262
S +E H IL V+KL++ IL+ D A + ++
Sbjct: 50 ---TEEESELEKDHAIVGAEILREL-----------LLEEVIKLIDELILAVD-ASHHER 94
Query: 263 KNRFIQLVENGEFDWQSEEKKQLLCGMMMTACDV--GAIAKPWEVQHKMAKLVADEFF 318
+ ++ L ++ D E + ++A+ +E
Sbjct: 95 LDGLGYPDGLK-------GEEITLEARIVKLADRLDALRRDSREKRRRIAEEDLEELL 145
>gnl|CDD|214500 smart00065, GAF, Domain present in phytochromes and cGMP-specific
phosphodiesterases. Mutations within these domains in
PDE6B result in autosomal recessive inheritance of
retinitis pigmentosa.
Length = 149
Score = 41.2 bits (97), Expect = 3e-04
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 3 DPRFNNEIDRRTGYTTNSILCVPINSYEGEVIGVAQIINKTDGTSSFTDRDIEVA 57
DP F ++ R S L VP+ +GE++GV + NK FT+ D E+
Sbjct: 77 DPLFAEDLLGRYQGVR-SFLAVPLV-ADGELVGVLALHNKKSP-RPFTEEDEELL 128
>gnl|CDD|216590 pfam01590, GAF, GAF domain. This domain is present in
cGMP-specific phosphodiesterases, adenylyl and guanylyl
cyclases, phytochromes, FhlA and NifA. Adenylyl and
guanylyl cyclases catalyze ATP and GTP to the second
messengers cAMP and cGMP, respectively, these products
up-regulating catalytic activity by binding to the
regulatory GAF domain(s). The opposite hydrolysis
reaction is catalyzed by phosphodiesterase.
cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes
the conversion of guanosine 3',5'-cyclic phosphate to
guanosine 5'-phosphate. Here too, cGMP regulates
catalytic activity by GAF-domain binding. Phytochromes
are regulatory photoreceptors in plants and bacteria
which exist in two thermally-stable states that are
reversibly inter-convertible by light: the Pr state
absorbs maximally in the red region of the spectrum,
while the Pfr state absorbs maximally in the far-red
region. This domain is also found in FhlA (formate
hydrogen lyase transcriptional activator) and NifA, a
transcriptional activator which is required for
activation of most Nif operons which are directly
involved in nitrogen fixation. NifA interacts with
sigma-54.
Length = 143
Score = 40.6 bits (95), Expect = 4e-04
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 3 DPRFNNEIDRRTGYTTN----SILCVPINSYEGEVIGVAQIINKTDGTSSFTDRDIEVAL 58
DPRF++ + + S L VP+ GE+IGV + + + FT+ ++E+ L
Sbjct: 77 DPRFSDLTALASDFLRGLGIRSCLAVPLKG-GGELIGVLVLHSTSPRA--FTEEELEL-L 132
Query: 59 ECLSYHA 65
+ L+
Sbjct: 133 QALADQV 139
>gnl|CDD|179373 PRK02118, PRK02118, V-type ATP synthase subunit B; Provisional.
Length = 436
Score = 39.2 bits (92), Expect = 0.004
Identities = 29/78 (37%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 404 EKPIEEFADAGGTKDIEFTVTTLNCDKIATPDSDTSHSIGGSITPSGSTSLHHNRTTRFA 463
EK ++ F D G I VTT+ D + P D + G IT G L R F
Sbjct: 276 EKAVD-FEDGGSITII--AVTTMPGDDVTHPVPDNT----GYIT-EGQFYLRRGRIDPFG 327
Query: 464 SLRRNKQLGKSVRSKFTR 481
SL R KQL V K TR
Sbjct: 328 SLSRLKQL---VIGKKTR 342
>gnl|CDD|222174 pfam13492, GAF_3, GAF domain.
Length = 129
Score = 30.9 bits (70), Expect = 0.59
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 3 DPRFNNEIDRRTGYTTNSILCVPINSYEGEVIGVAQIINKTDGTSSFTDRDIEVALECLS 62
+P D R + S+L VP+ GEVIGV + ++ +FT D+E+ LE L+
Sbjct: 65 EPVSVPAGDNRDLLPSESLLAVPL-RAGGEVIGVLVL--ESTPEEAFTPEDLEL-LELLA 120
Query: 63 YHA 65
Sbjct: 121 SQI 123
>gnl|CDD|225113 COG2203, FhlA, FOG: GAF domain [Signal transduction mechanisms].
Length = 175
Score = 31.1 bits (70), Expect = 0.78
Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 3 DPRFNNEIDRRTGYTTNSILCVPINSYEGEVIGVAQIINKTDGTSSFTDRDIEVALE 59
DPRF + S L VP+ +GE++G+ + + ++ +++ ++E+ E
Sbjct: 99 DPRFRDNPLVLLEPPIRSYLGVPL-IAQGELLGLLCVHD-SEPRRQWSEEELELLEE 153
>gnl|CDD|132407 TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.
This clade of FAD dependent oxidoreductases (members of
the pfam01266 family) is syntenically associated with a
family of proposed phosphonatase-like enzymes
(TIGR03351) and is also found (less frequently) in
association with phosphonate transporter components. A
likely role for this enzyme involves the oxidative
deamination of an aminophosphonate differring slightly
from 2-aminoethylphosphonate, possibly
1-hydroxy-2-aminoethylphosphonate (see the comments for
TIGR03351). Many members of the larger FAD dependent
oxidoreductase family act as amino acid oxidative
deaminases.
Length = 365
Score = 31.5 bits (72), Expect = 1.0
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 372 PLYDGTYENRKHWQDLAEKVEM-----GLTWIDHDKIE-KPIEEFADAGGTKDIEFTVTT 425
P +D +R+ W +LA K + G + + E +EEFA + + T
Sbjct: 55 PAWDRARRSREIWLELAAKAGIWVRENGSLHLARTEEELAVLEEFAATREPAEYRVELLT 114
>gnl|CDD|220232 pfam09421, FRQ, Frequency clock protein. The frequency clock
protein, is the central component of the frq-based
circadian negative feedback loop, regulates various
aspects of the circadian clock in Neurospora crassa.
This protein has been shown to interact with itself via
a coiled-coil.
Length = 989
Score = 31.1 bits (70), Expect = 2.0
Identities = 16/57 (28%), Positives = 24/57 (42%)
Query: 433 TPDSDTSHSIGGSITPSGSTSLHHNRTTRFASLRRNKQLGKSVRSKFTRSFYHSNNS 489
P S H + +P S +L H+R R ASL + +S+ S N+S
Sbjct: 3 PPFSSRGHPLPRRASPEKSVTLRHHRLARDASLSASALGVTPSQSQENSSSPRRNSS 59
>gnl|CDD|182279 PRK10163, PRK10163, DNA-binding transcriptional repressor AllR;
Provisional.
Length = 271
Score = 29.6 bits (66), Expect = 3.6
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 396 TWIDHDKIEKPIEEFADAGGTKDIEFTVTTLNCDKIATPDSDTSHSIGGSITPSGSTS 453
T +D + K +E+ + G T D E V LNC IA+ D S+ +I+ SG +S
Sbjct: 185 TLVDMPTLLKDLEQARELGYTVDKEEHVVGLNC--IASAIYDDVGSVVAAISISGPSS 240
>gnl|CDD|224000 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 29.7 bits (67), Expect = 5.1
Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 299 IAKPWEVQHK---MAKLVADEFFDQGDLEK-LQLNTQPVAMMDRERKDELPQMQVGFIDV 354
++ P E + +++++A FF +LE +N++P +++D + G ID+
Sbjct: 1010 LSTPLEDAERAIILSQILA--FFRDPELEFLFPINSRPFSLLDPLSAGSERGLLQGIIDL 1067
Query: 355 ICL 357
+
Sbjct: 1068 LFR 1070
>gnl|CDD|182810 PRK10885, cca, multifunctional tRNA nucleotidyl
transferase/2'3'-cyclic
phosphodiesterase/2'nucleotidase/phosphatase; Reviewed.
Length = 409
Score = 29.1 bits (66), Expect = 5.9
Identities = 16/51 (31%), Positives = 17/51 (33%), Gaps = 16/51 (31%)
Query: 140 PVKYH----NWRHALNVAQTMFAMLKTGKMERFMSDLEILGLLVACLCHDL 186
P K+H H L V A L RF A LCHDL
Sbjct: 219 PAKWHPEIDTGIHTLMVLD-QAAKLSPSLDVRF-----------AALCHDL 257
>gnl|CDD|223667 COG0594, RnpA, RNase P protein component [Translation, ribosomal
structure and biogenesis].
Length = 117
Score = 27.6 bits (62), Expect = 7.7
Identities = 8/37 (21%), Positives = 13/37 (35%), Gaps = 6/37 (16%)
Query: 461 RFASLRRNKQ------LGKSVRSKFTRSFYHSNNSHP 491
+ L++ K+ GK R+ Y NN
Sbjct: 3 KELRLKKRKEFQAVFKKGKRRRNSLFFVLYGRNNGLD 39
>gnl|CDD|225116 COG2206, COG2206, c-di-GMP phosphodiesterase class II (HD-GYP
domain) [Signal transduction mechanisms].
Length = 344
Score = 28.6 bits (64), Expect = 8.9
Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 86 YNLYSFTFIDFDLSDMDTCRATIRMFLECDLVKQFHIPYDV--LCRWVLSVKKNYRPVKY 143
L + + AT+ + +E V + + + L R + K +Y
Sbjct: 94 AALVLNFEEIGEDILIAKLDATLAVRIELSKVAREIVKKALVALARGDIKAKDDYT---- 149
Query: 144 HNWRHALNVAQTMFAMLKTGKMERFMSDLEILGLLVACLCHDLD 187
+ H++ VA+ A+ K + +S+ +I L +A L HD+
Sbjct: 150 --YGHSVRVAELAEAIAK----KLGLSEEKIEELALAGLLHDIG 187
>gnl|CDD|198455 cd10487, EphR_LBD_A10, Ligand Binding Domain of Ephrin type-A
Receptor 10. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA10, which contains an inactive tyr kinase
domain, may function to attenuate signals of
co-clustered active receptors. EphA10 is mainly
expressed in the testis. EphRs contain a ligand binding
domain and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyrosine kinase
domain. Binding of the ephrin ligand to EphR requires
cell-cell contact since both are anchored to the plasma
membrane. The resulting downstream signals occur
bidirectionally in both EphR-expressing cells (forward
signaling) and ephrin-expressing cells (reverse
signaling). Ephrin/EphR interaction results in cell-cell
repulsion or adhesion.
Length = 173
Score = 28.1 bits (62), Expect = 9.6
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 308 KMAKLVADEFFDQGDL--EKLQLNTQPVAMMDRERKDELPQMQVGFIDV-ICLPLYKV 362
K+ + ADE F QGDL K++LNT+ + R+ + F DV C+ L V
Sbjct: 114 KIDTIAADESFTQGDLGERKMKLNTEVREIGHLSRRG----FHLAFQDVGACVALVSV 167
>gnl|CDD|164934 PHA02538, N, capsid protein; Provisional.
Length = 348
Score = 28.5 bits (64), Expect = 9.9
Identities = 22/113 (19%), Positives = 32/113 (28%), Gaps = 48/113 (42%)
Query: 20 SILCVPINSYEGEVI--GVAQIINKTDGTSSFTDRDIEVALECLSYHATASGEDTRKLIK 77
I VP++ +GE + GV+ +I T+ FT R +
Sbjct: 54 RINVVPVDEIKGEKLGLGVSGLIASRTDTTGFTKR------------------------Q 89
Query: 78 DTIPSAQVYNLYSFTFIDFDLSDMDTCRATIRMFLECDLVKQFHIPYDVLCRW 130
P+A N Y D D I Y L +W
Sbjct: 90 GVDPTALDGNKYECEETDSD----------------------TAITYAKLDQW 120
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.409
Gapped
Lambda K H
0.267 0.0564 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,946,105
Number of extensions: 2567341
Number of successful extensions: 2086
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2080
Number of HSP's successfully gapped: 23
Length of query: 536
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 434
Effective length of database: 6,413,494
Effective search space: 2783456396
Effective search space used: 2783456396
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 (21.9 bits)
S2: 61 (27.6 bits)