RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17307
(342 letters)
>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
prediction only].
Length = 352
Score = 184 bits (470), Expect = 1e-55
Identities = 83/306 (27%), Positives = 143/306 (46%), Gaps = 36/306 (11%)
Query: 73 IDFDTQACVLRLK-ES-EDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLT 130
++ D + V++L E+ +D+WH YN+I +GD V A T R+ +S S R+ L
Sbjct: 4 LEEDKKRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGERIPMTLG 63
Query: 131 ISVESIDFDTQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIE 190
I VE I+FD A LR+KG ++ + V G+YHT+++ + + E+ K EW+ LER++
Sbjct: 64 IKVEKIEFDKFANRLRIKGPIVEGPEEVVKGSYHTINVTIGTEIEIEKEEWNKDQLERLK 123
Query: 191 VACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLSPI- 249
A K +VA V++ EG A I ++ ++ KI + IP KR + ++ I
Sbjct: 124 EAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRSGIPGKREGDIRAERKFFDEIA 183
Query: 250 -TTVEAVKMDNKVL-----------------LENKSKFLLVHSSSAFKHSLKEILADPTV 291
E +D ++ + ++ +S+ + + E+L V
Sbjct: 184 KALKEYANLDIIIVAGPGFAKEDFYDFLRERYPELANIVIEDTSTGGRAGINEVLKRGAV 243
Query: 292 TSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSD 336
+ +T+ A D + YG V A E A++TLL+ D L R+ D
Sbjct: 244 DKILSETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRSDD 303
Query: 337 LNERKK 342
+ ER+
Sbjct: 304 VEERED 309
Score = 78.5 bits (194), Expect = 3e-16
Identities = 34/85 (40%), Positives = 49/85 (57%), Gaps = 4/85 (4%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSS 60
M+++ ++ K GV+ LVPE +D+WH YN+I +GD V A T R+ +S S
Sbjct: 1 MRILEEDK----KRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGE 56
Query: 61 RVRTMLTISVESIDFDTQACVLRLK 85
R+ L I VE I+FD A LR+K
Sbjct: 57 RIPMTLGIKVEKIEFDKFANRLRIK 81
>gnl|CDD|217574 pfam03463, eRF1_1, eRF1 domain 1. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 133
Score = 129 bits (326), Expect = 6e-37
Identities = 45/113 (39%), Positives = 63/113 (55%), Gaps = 2/113 (1%)
Query: 85 KESEDMWHAYNLITEGDSVRASTIRKVQSE--SNTGSSTSSRVRTMLTISVESIDFDTQA 142
+ D+WH +LI GD V + T RK+Q E + T RV++ LTI+VE + FD +
Sbjct: 21 ETLGDLWHLISLIIPGDRVISDTTRKLQDEYSNIKSKVTRERVQSALTIAVERLKFDPEN 80
Query: 143 CVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNI 195
+LR G I+EN+ K+G YHTLD+E R +SK WDS L + A
Sbjct: 81 GLLRFCGTIIEENEDGKLGKYHTLDIEPPRPITISKYRWDSKFLTELLEAMLE 133
Score = 87.3 bits (217), Expect = 4e-21
Identities = 36/87 (41%), Positives = 52/87 (59%), Gaps = 3/87 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSE--SNTGSST 58
MKL+ KNI +K G++ L+PE D+WH +LI GD V + T RK+Q E + T
Sbjct: 1 MKLLEKNI-EKYGKGLIKLLPETLGDLWHLISLIIPGDRVISDTTRKLQDEYSNIKSKVT 59
Query: 59 SSRVRTMLTISVESIDFDTQACVLRLK 85
RV++ LTI+VE + FD + +LR
Sbjct: 60 RERVQSALTIAVERLKFDPENGLLRFC 86
>gnl|CDD|129217 TIGR00111, pelota, mRNA surveillance protein pelota. This model
describes the Drosophila protein Pelota, the budding
yeast protein DOM34 which it can replace, and a set of
closely related archaeal proteins. Members contain a
proposed RNA binding motif. The meiotic defect in pelota
mutants may be a complex result of a protein translation
defect, as suggested in yeast by ribosomal protein
RPS30A being a multicopy suppressor and by an altered
polyribosome profile in DOM34 mutants rescued by RPS30A.
This family is homologous to a family of peptide chain
release factors. Pelota is proposed to act in protein
translation [Protein synthesis, Translation factors].
Length = 351
Score = 127 bits (320), Expect = 8e-34
Identities = 79/280 (28%), Positives = 121/280 (43%), Gaps = 39/280 (13%)
Query: 88 EDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRL 147
+D+WH Y +I +GD A T R+ Q S S L I VES++FD + LR
Sbjct: 23 DDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDKSKDT-VKLGIEVESVEFDMKTERLRY 81
Query: 148 KGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMM 206
KG + V +G+YHTL+++ + K W L+R+ A I K AAV+M
Sbjct: 82 KGVIVTGPEDDVPVGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAVVM 141
Query: 207 QEGLANIMLITASMSLVRTKIETNIPRKRR--DNKDLLKELLSPITTVEAVKMDNKVLL- 263
+EG+A++ L+ KIE ++P K+R +L KE I D K ++
Sbjct: 142 EEGIAHVGLVRQYSVEEIQKIEYHMPGKKRTLKFGELRKEFYKEIAKKLLNFDDLKTIIV 201
Query: 264 -------------------ENKSKFLLVHSSSAFKHSLKEILADPTVTSKMQDTK----- 299
E +K +L + S+ + + E+L V +Q+T+
Sbjct: 202 AGPGFYKNDFYDFIFERYPEEANKAVLENCSTGGRAGINEVLKRGLVARILQETRYAKEI 261
Query: 300 ----------ALDPSRAFYGYRHVSAANESQAIDTLLIAD 329
A D +A YG V A E AI+ LL+ D
Sbjct: 262 MVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTD 301
Score = 57.9 bits (140), Expect = 2e-09
Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSS 60
M +V ++ N V+ L+PE +D+WH Y +I +GD A T R+ Q S S
Sbjct: 1 MSIVEESFNKGG--AVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDKSK 58
Query: 61 RVRTMLTISVESIDFDTQACVLRLK 85
L I VES++FD + LR K
Sbjct: 59 DT-VKLGIEVESVEFDMKTERLRYK 82
>gnl|CDD|217575 pfam03464, eRF1_2, eRF1 domain 2. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 129
Score = 57.7 bits (140), Expect = 2e-10
Identities = 27/129 (20%), Positives = 42/129 (32%), Gaps = 31/129 (24%)
Query: 200 DVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRR-------DNKDLLKELLSPI--- 249
D A++M EG A I L+T + KI +P K ++ E +
Sbjct: 1 DYGAIVMDEGEALIGLLTGYGIEILGKITVGLPGKHGRGGQSARRFEEKRHEFYRKVAEA 60
Query: 250 --TTVEAVKMDNKVL-------------------LENKSKFLLVHSSSAFKHSLKEILAD 288
+ + +L L K K +LV S + L E+L
Sbjct: 61 ANQYFDKDNVKGIILAGPGFTKNEFYDSDYLDYRLLKKKKIVLVDVSYGGEAGLNEVLER 120
Query: 289 PTVTSKMQD 297
P V + D
Sbjct: 121 PAVADVLSD 129
>gnl|CDD|146221 pfam03465, eRF1_3, eRF1 domain 3. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 100
Score = 48.3 bits (116), Expect = 2e-07
Identities = 19/43 (44%), Positives = 24/43 (55%)
Query: 300 ALDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSDLNERKK 342
A D A YG V A E A++TLLI+D L R+ D+ R K
Sbjct: 16 AKDTGLAVYGVEEVLKALEMGAVETLLISDELLRSRDVATRNK 58
>gnl|CDD|173111 PRK14648, PRK14648, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 354
Score = 30.1 bits (67), Expect = 1.6
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 11/55 (20%)
Query: 53 NTGSSTSSRVRTMLTISVESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRAST 107
NTG++T+ +VRT+L + + R+ E+ +W +I G+SVR ++
Sbjct: 306 NTGNATAHQVRTLLRVVRQ-----------RVFETHGVWLEREIIFSGESVRMTS 349
>gnl|CDD|198453 cd10485, EphR_LBD_A7, Ligand Binding Domain of Ephrin type-A
Receptor 7. 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. EphA7 has been implicated in various cancers,
including prostate, gastic and colorectal cancers. 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).
Length = 177
Score = 28.8 bits (64), Expect = 2.7
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 10/84 (11%)
Query: 78 QACVLRLKESEDMWHAYNLITEGDSVRAST-IRKVQSESNTGSSTSSRVRTMLTISVESI 136
Q C + ++ +++ W N I++G++ R ++ + N+ + +
Sbjct: 43 QVCQV-MEPNQNNWLRTNWISKGNAQRIFVELKFTLRDCNSLPGVLGTCKETFNLYYYET 101
Query: 137 DFDTQACVLRLKGRNIQENQYVKM 160
D+DT GRNI+ENQYVK+
Sbjct: 102 DYDT--------GRNIRENQYVKI 117
>gnl|CDD|217606 pfam03543, Peptidase_C58, Yersinia/Haemophilus virulence surface
antigen.
Length = 203
Score = 27.4 bits (61), Expect = 9.0
Identities = 15/69 (21%), Positives = 23/69 (33%), Gaps = 13/69 (18%)
Query: 273 HSSSAFKHSLKEILADPT---------VTSKMQDTK----ALDPSRAFYGYRHVSAANES 319
H+ +A + SL I + DT L+PS G V+ +
Sbjct: 52 HARAAERQSLYSIKKLQLLSRGAGAQFFQFQATDTWLQEAGLEPSGEEKGLGSVAGTVSA 111
Query: 320 QAIDTLLIA 328
+ LL A
Sbjct: 112 SNVSRLLKA 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
0.314 0.126 0.341
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,022,317
Number of extensions: 1459103
Number of successful extensions: 806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 796
Number of HSP's successfully gapped: 18
Length of query: 342
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 244
Effective length of database: 6,590,910
Effective search space: 1608182040
Effective search space used: 1608182040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 59 (26.4 bits)