RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9094
(185 letters)
>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1) [Translation,
ribosomal structure and biogenesis].
Length = 411
Score = 147 bits (372), Expect = 8e-43
Identities = 58/215 (26%), Positives = 100/215 (46%), Gaps = 34/215 (15%)
Query: 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDP----------- 50
E H + +KV E A+ F+ K + G+IL G K E + D
Sbjct: 191 EAAHEFYKKVGEAASEAFLPIAKKELKGIILGGPGPTKEEFVEGDYLHHELKKKVLGLVD 250
Query: 51 ------------VRFSP--------LKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELG 90
+ + ++ K M ++F E+++D+G +G E+ ALE+G
Sbjct: 251 VSYTGESGLRELIEKAEDALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVREALEMG 310
Query: 91 SVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLL 150
+V+TL+ E+L+ +R K +L ++E ++ F E G E+E VE L+
Sbjct: 311 AVDTLLVSEDLEKERVTYKC---PTCGYENLKSKREFEQKRFRCPECGSEMEEVEVSDLV 367
Query: 151 EWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
+ LA + GA +EII+D + EG+Q ++ FGG+
Sbjct: 368 DELAELAEESGAKVEIISDDTDEGAQLLKAFGGLA 402
>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 = 101 bits (254), Expect = 2e-28
Identities = 38/127 (29%), Positives = 62/127 (48%), Gaps = 38/127 (29%)
Query: 59 KNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRV 118
K + ++ +E+++DTG +GVE+ L+ALE+G+VETL+ + L R V
Sbjct: 5 KKLLEEFLEELAKDTGLAVYGVEEVLKALEMGAVETLLISDELLRSRDV----------- 53
Query: 119 LHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFV 178
++K +EWL N + G +EI++D+S+EG Q
Sbjct: 54 ------ATRNK--------------------IEWLVENAEESGGKVEIVSDESEEGEQL- 86
Query: 179 RGFGGIG 185
+GFGGI
Sbjct: 87 KGFGGIA 93
>gnl|CDD|234307 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and
eukaryotic forms. Directs the termination of nascent
peptide synthesis (translation) in response to the
termination codons UAA, UAG and UGA. This model
identifies both archaeal (aRF1) and eukaryotic (eRF1) of
the protein. Also known as translation termination
factor 1 [Protein synthesis, Translation factors].
Length = 357
Score = 98.5 bits (246), Expect = 8e-25
Identities = 45/215 (20%), Positives = 79/215 (36%), Gaps = 79/215 (36%)
Query: 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDP----------- 50
H + ++V E A F+ + G+++ G K E ++ D
Sbjct: 184 IAAHEFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAEGDYLHYELKKKIIGLFD 243
Query: 51 ------------VRFSP--------LKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELG 90
V + +K K M ++F E+++DTG +G E+ +ALE+G
Sbjct: 244 VSYTGESGLRELVEKAEDLLKDLEYMKEKKLMERFFKELAKDTGLAAYGEEEVRKALEMG 303
Query: 91 SVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLL 150
+V+TL+ SED ++
Sbjct: 304 AVDTLL----------------ISED--------------------------------II 315
Query: 151 EWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
E L+ + GA +EII+ ++EG Q ++ FGGI
Sbjct: 316 EELSELAEESGAKVEIISTDTEEGEQLLKAFGGIA 350
>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
Length = 411
Score = 83.4 bits (207), Expect = 3e-19
Identities = 52/212 (24%), Positives = 96/212 (45%), Gaps = 33/212 (15%)
Query: 5 HNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFD-----------PVRF 53
H + ++V E A F+ + + G+++ G K E + D V +
Sbjct: 195 HEFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYLHYELKKKILGLFDVSY 254
Query: 54 SP--------------LKN------KNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVE 93
+ LK K M ++F E+++D G +G E+ +ALE+G+V+
Sbjct: 255 TGESGLRELVDKASDLLKEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRKALEMGAVD 314
Query: 94 TLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWL 153
TL+ E+L R K + T ++ ++ T + G ELE+VE + ++E L
Sbjct: 315 TLLISEDLRKDRVTYK--CPNCGYEEEKTVKRREELPEKTCPKCGSELEIVEEEDIIEEL 372
Query: 154 ANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
+ + G +E+I+ ++EG Q ++ FGGI
Sbjct: 373 SELAEQSGTKVEVISTDTEEGEQLLKAFGGIA 404
>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 = 60.0 bits (146), Expect = 4e-12
Identities = 27/62 (43%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFSPLKNKN 60
EKRH + RKVAE A F DK N+ G+ILAG K E SD D L K
Sbjct: 47 EEKRHEFYRKVAEAANQYF---DKDNVKGIILAGPGFTKNEFYDSDYLDY----RLLKKK 99
Query: 61 KM 62
K+
Sbjct: 100 KI 101
>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
prediction only].
Length = 352
Score = 36.5 bits (85), Expect = 0.005
Identities = 11/36 (30%), Positives = 24/36 (66%)
Query: 61 KMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 96
+ ++ + +++D K +G+E+ +A E G+VETL+
Sbjct: 258 LVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLL 293
>gnl|CDD|131612 TIGR02561, HrpB1_HrpK, type III secretion protein HrpB1/HrpK.
This gene is found within type III secretion operons in
a limited range of species including Xanthomonas,
Ralstonia and Burkholderia.
Length = 153
Score = 30.6 bits (69), Expect = 0.26
Identities = 12/65 (18%), Positives = 22/65 (33%)
Query: 15 ATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFSPLKNKNKMGKYFDEISQDTG 74
+ + P A +L + L + DMFD N ++ + E+ G
Sbjct: 16 VLMYALRSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAG 75
Query: 75 KYCFG 79
+G
Sbjct: 76 APPYG 80
>gnl|CDD|224823 COG1911, RPL30, Ribosomal protein L30E [Translation, ribosomal
structure and biogenesis].
Length = 100
Score = 28.1 bits (63), Expect = 0.97
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 72 DTGKYCFGVEDTLRALELGSVETLICWENL------DIQRY 106
TGK G + T+++L+LG + +I N DI+ Y
Sbjct: 16 KTGKVILGSKRTIKSLKLGKAKLIIIASNCPKELKEDIEYY 56
>gnl|CDD|214617 smart00323, RasGAP, GTPase-activator protein for Ras-like GTPases.
All alpha-helical domain that accelerates the GTPase
activity of Ras, thereby "switching" it into an "off"
position. Improved domain limits from structure.
Length = 344
Score = 28.4 bits (64), Expect = 2.2
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 36 ADFKTELSQSDMFDPVRFSPLKNKNKMGKYFDEISQDTG----KYCFGVEDTLRALELGS 91
A+ S+ +P+ L +K+++ + DE+S K + R L S
Sbjct: 244 ANLSEFGSKEPWMEPLNDFLLSHKDRVKDFLDELSSVPEILVDKVSDSTTISGREL---S 300
Query: 92 VETLICWENLDIQRYVLKN 110
+ + EN D + L N
Sbjct: 301 LLHSLLLENGDALKRELNN 319
>gnl|CDD|143588 cd07564, nitrilases_CHs, Nitrilases, cyanide hydratase (CH)s, and
similar proteins (class 1 nitrilases). Nitrilases
(nitrile aminohydrolases, EC:3.5.5.1) hydrolyze nitriles
(RCN) to ammonia and the corresponding carboxylic acid.
Most nitrilases prefer aromatic nitriles, some prefer
arylacetonitriles and others aliphatic nitriles. This
group includes the nitrilase cyanide dihydratase (CDH),
which hydrolyzes inorganic cyanide (HCN) to produce
formate. It also includes cyanide hydratase (CH), which
hydrolyzes HCN to formamide. This group includes four
Arabidopsis thaliana nitrilases (Ath)NIT1-4. AthNIT1-3
have a strong substrate preference for
phenylpropionitrile (PPN) and other nitriles which may
originate from the breakdown of glucosinolates. The
product of PPN hydrolysis, phenylacetic acid has auxin
activity. AthNIT1-3 can also convert indoacetonitrile to
indole-3-acetic acid (IAA, auxin), but with a lower
affinity and velocity. From their expression patterns,
it has been speculated that NIT3 may produce IAA during
the early stages of germination, and that NIT3 may
produce IAA during embryo development and maturation.
AthNIT4 has a strong substrate specificity for the
nitrile, beta-cyano-L-alanine (Ala(CN)), an intermediate
of cyanide detoxification. AthNIT4 has both a nitrilase
activity and a nitrile hydratase (NHase) activity, which
generate aspartic acid and asparagine respectively from
Ala(CN). NHase catalyzes the hydration of nitriles to
their corresponding amides. This subgroup belongs to a
larger nitrilase superfamily comprised of belong to a
larger nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13),
this subgroup corresponds to class 1.
Length = 297
Score = 27.5 bits (62), Expect = 4.1
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 82 DTLRA--LELGSVETLICWENL 101
LR +G + LICWEN
Sbjct: 140 SGLRVVDTPIGRLGALICWENY 161
>gnl|CDD|184174 PRK13602, PRK13602, putative ribosomal protein L7Ae-like;
Provisional.
Length = 82
Score = 25.9 bits (57), Expect = 5.1
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 66 FDEISQDTGKYCFGVEDTLRALELGSVETLICWENLD 102
++++SQ G + T++AL+ GSV+ ++ E+ D
Sbjct: 3 YEKVSQ-AKSIVIGTKQTVKALKRGSVKEVVVAEDAD 38
>gnl|CDD|179205 PRK01018, PRK01018, 50S ribosomal protein L30e; Reviewed.
Length = 99
Score = 26.1 bits (58), Expect = 5.8
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 72 DTGKYCFGVEDTLRALELGSVETLICWENL------DIQRY 106
DTGK G + T++A++LG + +I N DI+ Y
Sbjct: 13 DTGKVILGSKRTIKAIKLGKAKLVIVASNCPKDIKEDIEYY 53
>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 = 26.7 bits (59), Expect = 7.0
Identities = 10/44 (22%), Positives = 28/44 (63%)
Query: 62 MGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQR 105
+ ++ + +++D K +G ++ ++A E G++E L+ + + +QR
Sbjct: 264 IDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVLVQR 307
>gnl|CDD|184103 PRK13512, PRK13512, coenzyme A disulfide reductase; Provisional.
Length = 438
Score = 26.7 bits (59), Expect = 8.9
Identities = 8/30 (26%), Positives = 11/30 (36%)
Query: 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDK 135
Y + L TPE+ D+ T K
Sbjct: 47 YYIGEVVEDRKYALAYTPEKFYDRKQITVK 76
>gnl|CDD|215357 PLN02665, PLN02665, pectinesterase family protein.
Length = 366
Score = 26.5 bits (59), Expect = 9.4
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 12/59 (20%)
Query: 23 DKPNIAGLILAGSADFKTELSQSDMFDPVRFSPLKNKNKM------GKYFDEISQDTGK 75
P I + GS DFKT + D ++ P N ++ G+Y ++I+ D K
Sbjct: 65 AAPRIIKVRKDGSGDFKT------ITDAIKSIPAGNTQRVIIDIGPGEYNEKITIDRSK 117
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
0.316 0.134 0.389
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,201,759
Number of extensions: 823145
Number of successful extensions: 654
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 24
Length of query: 185
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 94
Effective length of database: 6,901,388
Effective search space: 648730472
Effective search space used: 648730472
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 (21.6 bits)
S2: 56 (25.3 bits)