RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 036979
(212 letters)
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 88.4 bits (220), Expect = 7e-23
Identities = 31/54 (57%), Positives = 42/54 (77%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
+ + T++SSGPGGQ+ NK E+AVRL H+PTG++ + E+RSQHKNR AL RL
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERL 67
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 85.7 bits (213), Expect = 7e-20
Identities = 29/64 (45%), Positives = 44/64 (68%), Gaps = 4/64 (6%)
Query: 48 LELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALA 107
+E+ +L + TY+SSG GGQH NK ++AVR+ H+PTG++ Q +RSQH+N+A A
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASA 285
Query: 108 LSRL 111
+ L
Sbjct: 286 MKML 289
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 83.4 bits (207), Expect = 1e-19
Identities = 32/73 (43%), Positives = 45/73 (61%), Gaps = 4/73 (5%)
Query: 39 CPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDR 98
P +E+ DD+L + TY++SG GGQH NK ++AVRL H+PTG++ +R
Sbjct: 96 FPELDISIEIEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNER 151
Query: 99 SQHKNRALALSRL 111
SQH N+ALA L
Sbjct: 152 SQHLNKALARKML 164
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 84.4 bits (210), Expect = 2e-19
Identities = 25/49 (51%), Positives = 38/49 (77%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
T++SSG GGQH N ++AVR+ H+PTG++ + ++RSQHKN+A A+ L
Sbjct: 227 TFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 275
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 81.9 bits (203), Expect = 2e-18
Identities = 25/49 (51%), Positives = 38/49 (77%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
T++SSG GGQH N ++AVR+ H+PTG++ + ++RSQHKN+A A+ L
Sbjct: 229 TFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 277
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 80.6 bits (199), Expect = 5e-18
Identities = 27/49 (55%), Positives = 37/49 (75%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
TY++SG GGQH NK ++AVR+ H+PTG++ Q DRSQHKN+ A+ L
Sbjct: 241 TYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVL 289
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 77.8 bits (192), Expect = 5e-17
Identities = 24/54 (44%), Positives = 39/54 (72%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
+ + T++SSG GGQH N ++AVR+ H+PTG++ + ++RSQHKN+ A+ L
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVL 275
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 76.8 bits (189), Expect = 1e-16
Identities = 34/78 (43%), Positives = 51/78 (65%), Gaps = 5/78 (6%)
Query: 49 ELTDDELLR----ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNR 104
ELTDD+ + + ++ TY++ G GGQH NK E+AVR+ H+PTG++ Q +RSQH N+
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243
Query: 105 ALALSRLPTFLA-LKVRS 121
A+ L + L LK R+
Sbjct: 244 ETAMKMLKSKLVELKERA 261
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 76.5 bits (188), Expect = 1e-16
Identities = 29/54 (53%), Positives = 40/54 (74%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
+ + TY+SSG GGQH N ++AVR+ H+PTG++ Q ++RSQHKNRA A S L
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSML 253
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 72.1 bits (177), Expect = 8e-16
Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 14/82 (17%)
Query: 40 PASKKKNYL----------ELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTG 89
P ++KN+ E T+DE+ E T +SSGPGGQH NK E+AVR H+ +G
Sbjct: 83 PHHRRKNWFIGVQRFSASEEATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASG 138
Query: 90 VIAQAAEDRSQHKNRALALSRL 111
+ + +RSQH N+ LA L
Sbjct: 139 ISVKVQSERSQHANKRLATLLL 160
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 70.5 bits (173), Expect = 3e-15
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 40 PASKKKNYL----ELTDDE--LLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQ 93
P +KN+ + DE E T +SSGPGGQH NK ++AVR H+ +G+ +
Sbjct: 84 PHHGRKNWFVGIGRFSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVK 143
Query: 94 AAEDRSQHKNRALALSRL 111
+RSQH N+ LA +
Sbjct: 144 VQSERSQHANKRLARLLI 161
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 64.7 bits (157), Expect = 2e-12
Identities = 25/48 (52%), Positives = 32/48 (66%)
Query: 64 YKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
Y+SSG GGQH NK E+AVR+ H+PT + RSQH+NR A+ L
Sbjct: 183 YRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKML 230
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 54.7 bits (131), Expect = 4e-09
Identities = 25/61 (40%), Positives = 36/61 (59%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLAL 117
+ ++ TY++SG GGQH N ++AVR+ H PT + +RSQ KNR A+ L L
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQ 257
Query: 118 K 118
K
Sbjct: 258 K 258
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 48.6 bits (117), Expect = 1e-07
Identities = 31/93 (33%), Positives = 42/93 (45%), Gaps = 28/93 (30%)
Query: 48 LELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLK------HVPT------------- 88
L + ++EL E ++SGPGGQ+ NK TAV L+ +P
Sbjct: 8 LVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHR 63
Query: 89 ----GVIA-QAAEDRSQHKNRALALSRLPTFLA 116
GVI +A E RSQ +NR AL RL +
Sbjct: 64 ITKDGVIVIKAQEFRSQERNREDALERLVALIR 96
>gnl|CDD|217292 pfam02928, zf-C5HC2, C5HC2 zinc finger. Predicted zinc finger
with eight potential zinc ligand binding residues. This
domain is found in Jumonji. This domain may have a DNA
binding function.
Length = 54
Score = 27.6 bits (62), Expect = 0.92
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 35 HHCSCPASKKKNYLELTDDEL 55
CSCP S + T DEL
Sbjct: 30 DLCSCPCSDRTLRYRYTLDEL 50
>gnl|CDD|183173 PRK11519, PRK11519, tyrosine kinase; Provisional.
Length = 719
Score = 28.6 bits (64), Expect = 3.1
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 152 QIGPNNPKFALVLLYSLLLRLLLST-GALSRLIL 184
Q G PK AL++L +++L L+LS G L R +
Sbjct: 416 QPGVLKPKKALIILGAIILGLMLSIVGVLLRSLF 449
>gnl|CDD|216428 pfam01311, Bac_export_1, Bacterial export proteins, family 1. This
family includes the following members; FliR, MopE, SsaT,
YopT, Hrp, HrcT and SpaR All of these members export
proteins, that do not possess signal peptides, through
the membrane. Although the proteins that these exporters
move may be different, the exporters are thought to
function in similar ways.
Length = 249
Score = 28.0 bits (63), Expect = 3.2
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 146 SSEVGPQIGPNNPKFALVLLYSLLLRLLLSTGALSRLILS-DDSLR 190
+S P G + L +L L L++G L+ + DS +
Sbjct: 106 ASSFDPASGSQSSPVGQFLNQLAIL-LFLASGGHLLLLSALYDSYQ 150
>gnl|CDD|216110 pfam00771, FHIPEP, FHIPEP family.
Length = 658
Score = 28.2 bits (64), Expect = 3.9
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 163 VLLYSLLLRLLLSTGALSRLILSD 186
+LL + L RL L+ A +RLIL +
Sbjct: 48 LLLITTLFRLALNV-ASTRLILLE 70
>gnl|CDD|176552 cd08610, GDPD_GDE6, Glycerophosphodiester phosphodiesterase domain
of mammalian glycerophosphodiester phosphodiesterase
GDE6 and similar proteins. This subfamily corresponds
to the glycerophosphodiester phosphodiesterase domain
(GDPD) present in mammalian GDE6 (also known as
glycerophosphodiester phosphodiesterase
domain-containing protein 4 (GDPD4)) and their metazoan
homologs. Mammalian GDE6 is a transmembrane protein
predominantly expressed in the spermatocytes of testis.
Although the specific physiological function of
mammalian GDE6 has not been elucidated, its different
pattern of tissue distribution suggests it might play a
critical role in the completion of meiosis during male
germ cell differentiation.
Length = 316
Score = 27.9 bits (62), Expect = 4.5
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 125 LGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNN 157
LG YSP ++ + L PK TI P + P N
Sbjct: 6 LGIYSPCIREKETLGPKPTIIGHRGAPMLAPEN 38
>gnl|CDD|235672 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 27.8 bits (63), Expect = 4.9
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 7/30 (23%)
Query: 160 FALVLLYSLLLRLLL---STGALSRLILSD 186
F +LL + LLRL L ST RLIL +
Sbjct: 73 FPTLLLITTLLRLALNVAST----RLILLE 98
>gnl|CDD|219086 pfam06553, BNIP3, BNIP3. This family consists of several mammalian
specific BCL2/adenovirus E1B 19-kDa protein-interacting
protein 3 or BNIP3 sequences. BNIP3 belongs to the Bcl-2
homology 3 (BH3)-only family, a Bcl-2-related family
possessing an atypical Bcl-2 homology 3 (BH3) domain,
which regulates PCD from mitochondrial sites by
selective Bcl-2/Bcl-XL interactions. BNIP3 family
members contain a C-terminal transmembrane domain that
is required for their mitochondrial localisation,
homodimerisation, as well as regulation of their
pro-apoptotic activities. BNIP3-mediated apoptosis has
been reported to be independent of caspase activation
and cytochrome c release and is characterized by early
plasma membrane and mitochondrial damage, prior to the
appearance of chromatin condensation or DNA
fragmentation.
Length = 197
Score = 27.2 bits (60), Expect = 6.4
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 130 PPLQLLQILPPKST---IRSSEVGPQIGPNNPKFALVLLYSLLLRLLLSTG 177
PP + + P +S IR + V + G + +F V L +LLL LL G
Sbjct: 130 PPKEFKFVHPKRSVSLSIRKTRVMKKGGLFSAEFLKVFLPTLLLSHLLGLG 180
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 0.408
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,418,089
Number of extensions: 937397
Number of successful extensions: 685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 685
Number of HSP's successfully gapped: 25
Length of query: 212
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 119
Effective length of database: 6,812,680
Effective search space: 810708920
Effective search space used: 810708920
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: 57 (26.0 bits)