RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7992
(131 letters)
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 203 bits (518), Expect = 2e-68
Identities = 96/133 (72%), Positives = 109/133 (81%), Gaps = 5/133 (3%)
Query: 4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLT 63
R HSKTY TPRRP+EK RLD ELK+ GEYGL+NKRE+WRV+Y LAKIRKAARELLT
Sbjct: 2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLT 61
Query: 64 LDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKS 118
LDEK+ + ALLRR+ R+G+LDE + KLDYV GL +E LERRLQT+VFKLGLAKS
Sbjct: 62 LDEKDPKRLFEGEALLRRMHRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKS 121
Query: 119 IHHARVLIRQRHI 131
IHHARVLIRQRHI
Sbjct: 122 IHHARVLIRQRHI 134
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
Length = 194
Score = 188 bits (480), Expect = 2e-62
Identities = 92/136 (67%), Positives = 107/136 (78%), Gaps = 5/136 (3%)
Query: 1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
MV+ + KT+ PRRPYEK RLD ELK++GEYGLRNKRE+WRV+YAL++IR AAR
Sbjct: 1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARM 60
Query: 61 LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
LLTLDEK R ALLRR+ R G+LDES+ KLDYV L +E+FLERRLQT VFK G+
Sbjct: 61 LLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGM 120
Query: 116 AKSIHHARVLIRQRHI 131
AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 162
Score = 164 bits (416), Expect = 5e-53
Identities = 78/129 (60%), Positives = 94/129 (72%), Gaps = 3/129 (2%)
Query: 6 VPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLD 65
P K Y TPR P+ K RLD+ELK++G+YGLRNK+EVW+ + L K R+AARELL LD
Sbjct: 3 DPRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD 62
Query: 66 EK---EHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHA 122
++ N LLRRLVR+G+LDE KLD V GL +EDFLERRLQTQVFK GLA++IH A
Sbjct: 63 DEQRLFEGNQLLRRLVRLGILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQA 122
Query: 123 RVLIRQRHI 131
R LI HI
Sbjct: 123 RQLIVHGHI 131
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
Length = 177
Score = 138 bits (350), Expect = 7e-43
Identities = 57/128 (44%), Positives = 77/128 (60%), Gaps = 4/128 (3%)
Query: 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDE 66
P K Y TP P++K R+ +E +++G+YGLRNKRE+W+ + L K R+ AR LL L
Sbjct: 4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPP 63
Query: 67 KEH---RNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
+E LL +L R G+L E LD V L +ED LERRLQT V++ GLA++ AR
Sbjct: 64 EERAKEEEQLLGKLKRYGILKE-NATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQAR 122
Query: 124 VLIRQRHI 131
I HI
Sbjct: 123 QFIVHGHI 130
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 205
Score = 83.9 bits (208), Expect = 4e-21
Identities = 32/116 (27%), Positives = 48/116 (41%), Gaps = 9/116 (7%)
Query: 16 TPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLR 75
P+ K RL +E K+ + G ++ +E W+ + ++L R
Sbjct: 15 LGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAFYGV-LEKQFRR 72
Query: 76 RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
L G L V GL + LERRL V++LG AK+ AR L+ HI
Sbjct: 73 YLKEAGRLKG-------VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHI 121
>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain.
This family includes small ribosomal subunit S9 from
prokaryotes and S16 from metazoans. This domain is
predicted to bind to ribosomal RNA. This domain is
composed of four helices in the known structure. However
the domain is discontinuous in sequence and the
alignment for this family contains only the first three
helices.
Length = 93
Score = 70.4 bits (173), Expect = 5e-17
Identities = 40/97 (41%), Positives = 48/97 (49%), Gaps = 12/97 (12%)
Query: 11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE-- 68
T PRR E RL + K+ GEYGLR + WRVK + +R LL LDEK+
Sbjct: 5 GPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKG-----RLSRYLLRLDEKQKL 59
Query: 69 --HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLE 103
L R+L R GVL KLD GL + D LE
Sbjct: 60 RFFYGLLERQLRRYGVLA---KKLDGSLGLNLLDLLE 93
>gnl|CDD|201819 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 = 35.5 bits (83), Expect = 4e-04
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131
RL + +LGLA S AR LIR H+
Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHV 28
>gnl|CDD|235411 PRK05327, rpsD, 30S ribosomal protein S4; Validated.
Length = 203
Score = 35.5 bits (83), Expect = 0.003
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 102 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
LE RL V++LG A + AR L+ HI
Sbjct: 91 LESRLDNVVYRLGFAPTRRQARQLVSHGHI 120
>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed.
Length = 201
Score = 34.4 bits (80), Expect = 0.006
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 101 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
LE RL +F+LG+A +I AR L+ HI
Sbjct: 86 LLEMRLDNILFRLGMAPTIPAARQLVNHGHI 116
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 200
Score = 32.7 bits (75), Expect = 0.028
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 102 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
LE RL V++LG A + AR L+ HI
Sbjct: 88 LESRLDNVVYRLGFAPTRFAARQLVSHGHI 117
>gnl|CDD|238095 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 = 29.1 bits (66), Expect = 0.16
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131
RL + +LGLA S AR LI+ H+
Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHV 28
>gnl|CDD|217010 pfam02387, IncFII_repA, IncFII RepA protein family. This protein
is plasmid encoded and found to be essential for plasmid
replication.
Length = 279
Score = 29.2 bits (66), Expect = 0.45
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 21 YEKARLDQELKIIG--EYGLRNKREVWRV-------KYALAKIRKAARELLTLDEKEHRN 71
K + L + E R K + A K R+ AR+L LDEK+ R
Sbjct: 179 ENKKLKKKGLIPLTLDEARRRAKEFHIERAFSYRTERKAFGKKRRRARKLAKLDEKDIRK 238
Query: 72 ALLRRLVR 79
+L LV+
Sbjct: 239 KILNALVK 246
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 27.6 bits (62), Expect = 0.50
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131
RRL + +LGLA S AR LI Q +
Sbjct: 1 RRLDKFLARLGLAPSRSQARRLIEQGRV 28
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is
a monomer which aminoacylates the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in
ATP binding. IleRS has an insertion in the core
domain, which is subject to both deletions and
rearrangements. This editing region hydrolyzes
mischarged cognate tRNAs and thus prevents the
incorporation of chemically similar amino acids.
Length = 338
Score = 28.0 bits (63), Expect = 1.5
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 29 ELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
ELK+ E G+ K+++ K +A+ RE
Sbjct: 55 ELKVEKELGISGKKDI--EKMGIAEFNAKCRE 84
>gnl|CDD|204930 pfam12464, Mac, Maltose acetyltransferase. This domain family is
found in bacteria, archaea and eukaryotes, and is
approximately 50 amino acids in length. The family is
found in association with pfam00132. Mac uses
acetyl-CoA as acetyl donor to acetylated cytoplasmic
maltose.
Length = 55
Score = 25.9 bits (58), Expect = 1.9
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRL 77
L R AR LL D+ E R LL+ L
Sbjct: 17 LVAERLRARRLLREYNATPPDDPEKRRELLKEL 49
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 27.5 bits (62), Expect = 2.5
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 38 LRNKR-------EVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGV 82
LRN+R E+ R + +A +R ELL +E+E + LV GV
Sbjct: 1335 LRNRRQPLDIAAEIERFRPGVAALRPQLPELLPGEEREALEERAQALVEAGV 1386
>gnl|CDD|236109 PRK07827, PRK07827, enoyl-CoA hydratase; Provisional.
Length = 260
Score = 26.6 bits (59), Expect = 4.4
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 47 VKYALAKIRKAARELLTLDEKEHRNALLRRLV 78
V+YA+ A LTLD +RNAL RLV
Sbjct: 8 VRYAVD--GGVAT--LTLDSPHNRNALSARLV 35
>gnl|CDD|217357 pfam03079, ARD, ARD/ARD' family. The two acireductone dioxygenase
enzymes (ARD and ARD', previously known as E-2 and E-2')
from Klebsiella pneumoniae share the same amino acid
sequence, but bind different metal ions: ARD binds Ni2+,
ARD' binds Fe2+. ARD and ARD' can be experimentally
interconverted by removal of the bound metal ion and
reconstitution with the appropriate metal ion. The two
enzymes share the same substrate,
1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield
different products. ARD' yields the alpha-keto precursor
of methionine (and formate), thus forming part of the
ubiquitous methionine salvage pathway that converts
5'-methylthioadenosine (MTA) to methionine. This pathway
is responsible for the tight control of the
concentration of MTA, which is a powerful inhibitor of
polyamine biosynthesis and transmethylation reactions.
ARD yields methylthiopropanoate, carbon monoxide and
formate, and thus prevents the conversion of MTA to
methionine. The role of the ARD catalyzed reaction is
unclear: methylthiopropanoate is cytotoxic, and carbon
monoxide can activate guanylyl cyclase, leading to
increased intracellular cGMP levels. This family also
contains other members, whose functions are not well
characterized.
Length = 157
Score = 26.2 bits (58), Expect = 4.5
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 18/89 (20%)
Query: 20 PYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVR 79
P EKA D+ K+ Y W++ A + A ELL + + +H + +
Sbjct: 21 PKEKAETDELAKLGVLY--------WKLD---ADDEETAEELLRIRKYKHYD---DVDID 66
Query: 80 IGVLDESKMKLDYVWGLKIEDFLERRLQT 108
+ V E+ D K++ F E L T
Sbjct: 67 VTVCPETTPNFDE----KLKKFFEEHLHT 91
>gnl|CDD|235458 PRK05427, PRK05427, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 308
Score = 26.3 bits (59), Expect = 5.2
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 33 IGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVL 83
I YGL E+ + K ++ K+A EL+ +D KE + + V IG +
Sbjct: 176 IEAYGL----EMLKAKSDVSG--KSAEELIDMDAKEF--EMNGKKVGIGQV 218
>gnl|CDD|213072 cd11756, GH94N_ChvB_NdvB_1_like, First GH94N domain of cyclic beta
1-2 glucan synthetase and similar domains. The
glycoside hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cyclic beta 1-2
glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the
chromosomal chvB virulence gene). This first of two
tandemly repeated GH94-N-terminal-like domains has not
been characterized functionally. Some beta 1-2 glucan
synthetases are annotated as NdvB (nodule development B)
gene products, glycosyltransferases required for the
synthesis of cyclic beta-(1,2)-glucans, which play a
role in interactions between bacteria and plants.
Length = 284
Score = 26.3 bits (59), Expect = 5.7
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 110 VFKLGLAKSIHHARVLIRQ 128
VF LG A AR LIR+
Sbjct: 264 VFLLGEADDAEEARALIRR 282
>gnl|CDD|234302 TIGR03664, fut_nucase, futalosine nucleosidase. This enzyme
catalyzes the conversion of futalosine to
de-hypoxanthine futalosine in a pathway for the
biosynthesis of menaquinone distinct from the pathway
observed in E. coli.
Length = 222
Score = 26.1 bits (58), Expect = 6.2
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 29 ELKIIGEY-GLRNKREVWRVKYALAKIRKAARELL 62
EL+ I G R+ R WR+K ALA + +AA +LL
Sbjct: 189 ELRGISNLVGPRD-RSAWRIKEALAALTRAAAKLL 222
>gnl|CDD|235231 PRK04160, PRK04160, diphthine synthase; Provisional.
Length = 258
Score = 26.0 bits (58), Expect = 6.8
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 54 IRKAARELLTLDEKEHRNALLRR-----LVRIGVLDESKMKLDYVWGLKIEDF 101
+A LL L+EK + + R G D ++ + L DF
Sbjct: 177 ANEALELLLELEEKRGEGVISEDTLAVVVARAGSPDP-VVRAGRLEELADYDF 228
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
0.324 0.139 0.399
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,996,202
Number of extensions: 654048
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 968
Number of HSP's successfully gapped: 77
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)