RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031394
(160 letters)
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 132 bits (336), Expect = 4e-41
Identities = 52/104 (50%), Positives = 68/104 (65%)
Query: 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKI 93
M +K GDTV VIAG DKGK G++ KV + V+V+ +N+ KH K +E QG II+
Sbjct: 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEK 61
Query: 94 EAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEIID 137
EAPIH SNV L + A+RVG K L+DG +VR K+GE+ID
Sbjct: 62 EAPIHISNVALVDPKTGKATRVGFKFLEDGKKVRVAKKSGEVID 105
>gnl|CDD|233263 TIGR01079, rplX_bact, ribosomal protein L24, bacterial/organelle.
This model recognizes bacterial and organellar forms of
ribosomal protein L24. It excludes eukaryotic and
archaeal forms, designated L26 in eukaryotes [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 104
Score = 119 bits (301), Expect = 8e-36
Identities = 53/104 (50%), Positives = 70/104 (67%), Gaps = 1/104 (0%)
Query: 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE-EEQGQIIK 92
KM +K GDTVKVI+G DKGK G++ KV + V+V+ +N+ KHVK + QG II+
Sbjct: 1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIE 60
Query: 93 IEAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEII 136
EAPIH SNVML+ + A+RVG + +DG +VR KTGEII
Sbjct: 61 KEAPIHISNVMLFDPKTGKATRVGIRFEEDGKKVRVFKKTGEII 104
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 98.2 bits (245), Expect = 1e-27
Identities = 46/75 (61%), Positives = 61/75 (81%)
Query: 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKI 93
KMHVK GDTVK+I+G DKGKIGE+ K+ + ++ V+VK IN+K KH+K +E E G+I +
Sbjct: 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQF 65
Query: 94 EAPIHSSNVMLYSKE 108
EAPIHSSNVMLY++E
Sbjct: 66 EAPIHSSNVMLYNEE 80
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 96.6 bits (241), Expect = 9e-27
Identities = 52/105 (49%), Positives = 68/105 (64%), Gaps = 3/105 (2%)
Query: 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKI 93
KM VK GDTVKVIAG DKGK G++ KV V+V+ +N+ KH+K +E +G II
Sbjct: 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIINK 59
Query: 94 EAPIHSSNVMLYSKEME-VASRVGHKVLDDGTRVRYLIKTGEIID 137
EAPIH SNV + +RVG+KV +DG +VR K+GE+ID
Sbjct: 60 EAPIHISNVAIIDPNKTGKPTRVGYKVEEDGKKVRVAKKSGEVID 104
>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26. RPL26 and
its bacterial paralogs RPL24 have a KOW motif at their N
terminal. KOW domain is known as an RNA-binding motif
that is shared so far among some families of ribosomal
proteins, the essential bacterial transcriptional
elongation factor NusG, the eukaryotic chromatin
elongation factor Spt5, the higher eukaryotic KIN17
proteins and Mtr4. RPL26 makes a very minor
contributions to the biogenesis, structure, and function
of 60s ribosomal subunits. However, RPL24 is essential
to generate the first intermediate during 50s ribosomal
subunits assembly. RPL26 have an extra-ribosomal
function to enhances p53 translation after DNA damage.
Length = 65
Score = 86.0 bits (214), Expect = 3e-23
Identities = 36/65 (55%), Positives = 47/65 (72%)
Query: 40 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHS 99
GD V+VI G DKGK G++ KV R + V+V+ +N+ KHVK +E QG II++EAPIH
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60
Query: 100 SNVML 104
SNVML
Sbjct: 61 SNVML 65
>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed.
Length = 76
Score = 70.1 bits (172), Expect = 9e-17
Identities = 30/69 (43%), Positives = 42/69 (60%)
Query: 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKI 93
K+ VK GD VKVIAG DKGK G++ V + V+V+ + + K +K ++ G I+
Sbjct: 4 KLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEK 63
Query: 94 EAPIHSSNV 102
E PIH SNV
Sbjct: 64 EMPIHISNV 72
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 39.9 bits (94), Expect = 7e-05
Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 21 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVK 80
R++ SLPV + GDTVKV+ G KG+ G++ +V + V+ + VK
Sbjct: 36 REKYGIRSLPV------RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVT-----VK 84
Query: 81 KREEEEQGQIIKIEAPIHSSNVM 103
K + E + PIH SNVM
Sbjct: 85 KADGTEVPR------PIHPSNVM 101
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 37.0 bits (87), Expect = 1e-04
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 40 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70
GD V+VI+G KGK G++ +V + V V+
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames
(Kyrpides, Ouzounis and Woese). KOW domain is known as
an RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 33.3 bits (77), Expect = 0.004
Identities = 12/42 (28%), Positives = 17/42 (40%)
Query: 40 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 81
GD V+V+ G KG+ G + + V VK K
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGAELK 42
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 32.3 bits (75), Expect = 0.007
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 36 HVKAGDTVKVIAGCDKGKIGEITKVFRH 63
+ GDTV+VIAG KGK+G++ +V
Sbjct: 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|150132 pfam09356, Phage_BR0599, Phage conserved hypothetical protein
BR0599. This entry describes a family of proteins
found almost exclusively in phage or in prophage
regions of bacterial genomes, including the phage-like
Rhodobacter capsulatus gene transfer agent, which
packages DNA. An apparent exception is Wolbachia
pipientis wMel, a bacterial endosymbiont of the fruit
fly, which has several candidate phage-related genes
physically separate from obvious prophage regions.
Length = 80
Score = 32.5 bits (75), Expect = 0.017
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 37 VKAGDTVKVIAGCDK 51
+ GD V++ AGCDK
Sbjct: 41 IAVGDAVRLTAGCDK 55
>gnl|CDD|240515 cd06091, KOW_NusG, NusG contains an NGN domain at its N-terminus
and KOW motif at its C-terminus. KOW_NusG motif is one
of the two domains of N-Utilization Substance G (NusG)
a transcription elongation and Rho-termination factor
in bacteria and archaea. KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The eukaryotic ortholog of
NusG is Spt5 with multiple KOW motifs at its
C-terminus.
Length = 56
Score = 30.9 bits (71), Expect = 0.037
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69
+ GDTV++I+G G G++ ++ V V
Sbjct: 4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKV 36
>gnl|CDD|240507 cd06083, KOW_Spt5_3, KOW domain of Spt5, repeat 3. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the
essential bacterial transcriptional elongation factor
NusG, the eukaryotic chromatin elongation factor Spt5,
the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5
domains play critical roles in recruitment of multiple
other eukaryotic transcription elongation and RNA
biogenesis factors and additionally are involved in the
binding of the eukaryotic Spt5 proteins to RNA
polymerases.
Length = 51
Score = 28.6 bits (65), Expect = 0.21
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 68
H K GD VKVI+G +G+ G + KV TV
Sbjct: 1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVF 33
>gnl|CDD|227736 COG5449, COG5449, Uncharacterized conserved protein [Function
unknown].
Length = 225
Score = 29.9 bits (67), Expect = 0.52
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 28 SLPVLHKMHVKAGDTVKVIAGCDK 51
L + +V GD K+ AGCDK
Sbjct: 160 ILEDIIPDYVAPGDEFKITAGCDK 183
>gnl|CDD|130152 TIGR01080, rplX_A_E, ribosomal protein L24p/L26e,
archaeal/eukaryotic. This model represents the archaeal
and eukaryotic branch of the ribosomal protein L24p/L26e
family. Bacterial and organellar forms are represented
by related model TIGR01079 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 114
Score = 28.2 bits (63), Expect = 0.96
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 17/84 (20%)
Query: 21 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVK 80
R++ +LPV + GD V+++ G KG G+++KV + V+ +
Sbjct: 32 REKYGKRALPV------RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTK------ 79
Query: 81 KREEEEQGQIIKIEAPIHSSNVML 104
E+ G + + PIH SNVM+
Sbjct: 80 ---EKVNGTEVPV--PIHPSNVMI 98
>gnl|CDD|240508 cd06084, KOW_Spt5_4, KOW domain of Spt5, repeat 4. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the
essential bacterial transcriptional elongation factor
NusG, the eukaryotic chromatin elongation factor Spt5,
the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5
domains play critical roles in recruitment of multiple
other eukaryotic transcription elongation and RNA
biogenesis factors and additionally are involved in the
binding of the eukaryotic Spt5 proteins to RNA
polymerases.
Length = 43
Score = 26.7 bits (60), Expect = 1.1
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 40 GDTVKVIAGCDKGKIGEITKVFR 62
GDTVKV+ G KG+ G + ++R
Sbjct: 1 GDTVKVVDGPYKGRQGTVLHIYR 23
>gnl|CDD|130335 TIGR01268, Phe4hydrox_tetr, phenylalanine-4-hydroxylase,
tetrameric form. This model describes the larger,
tetrameric form of phenylalanine-4-hydroxylase, as
found in metazoans. The enzyme irreversibly converts
phenylalanine to tryosine and is known to be the
rate-limiting step in phenylalanine catabolism in some
systems. It is closely related to metazoan tyrosine
3-monooxygenase and tryptophan 5-monoxygenase, and more
distantly to monomeric phenylalanine-4-hydroxylases of
some Gram-negative bacteria. The member of this family
from Drosophila has been described as having both
phenylalanine-4-hydroxylase and tryptophan
5-monoxygenase activity (PMID:1371286). However, a
Drosophila member of the tryptophan 5-monoxygenase
clade has subsequently been discovered.
Length = 436
Score = 28.6 bits (64), Expect = 1.7
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 47 AGCDKGKIGEITKVFRHNSTVMVKDINLKTK 77
K+ + + R + V V ++ K
Sbjct: 66 DEASDRKLEGVIEHLRQKAEVTVNILSRDNK 96
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional.
Length = 273
Score = 27.7 bits (61), Expect = 2.4
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 31 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 63
V+ + + G V V G ++G+IGEI + RH
Sbjct: 166 VVDLIKNRNGKVVMVTGGANRGRIGEIVSIERH 198
>gnl|CDD|235860 PRK06778, PRK06778, hypothetical protein; Validated.
Length = 289
Score = 27.6 bits (61), Expect = 3.4
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 56 EITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASRV 115
T + +D+N KT +KK+ E G++ I M + EME+ +
Sbjct: 83 PATVAVPEETEKKARDVNEKTALLKKKSATELGELATSINTIARDAHMEANLEMEIVPQ- 141
Query: 116 GHKVL--DDGTR 125
G +VL DD R
Sbjct: 142 GLRVLIKDDQNR 153
>gnl|CDD|233522 TIGR01672, AphA, HAD superfamily (subfamily IIIB) phosphatase,
TIGR01672. This family of proteins is a member of the
IIIB subfamily (pfam02767) of the haloacid dehalogenase
(HAD) superfamily of hydrolases. All characterized
members of subfamily III and most characterized members
of the HAD superfamily are phosphatases. HAD superfamily
phosphatases contain active site residues in several
conserved catalytic motifs, all of which are found
conserved here. The AphA gene from E. coli has been
characterized and shown to be an active phosphatase
enzyme. This family has been previously described as the
"class B non-specific bacterial acid phosphatase"
(B-NSAP) family where it is noted that the enzyme is
secreted and has a broad substrate range. The
possibility exists, however, that the enzyme is specific
for an as yet undefined substrate. Supporting evidence
for the inclusion in the HAD superfamily, whose
phosphatase members are magnesium dependent, is the
inhibition by EDTA and calcium ions, and stimulation by
magnesium ion.
Length = 237
Score = 27.2 bits (60), Expect = 3.8
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 14/67 (20%)
Query: 19 WER--KECKPNSLPV-----LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 71
WE+ S+P L MH + GD + + G GK ++K + K+
Sbjct: 102 WEKVNNGWDEFSIPKEVARQLIDMHQRRGDAIFFVTGRTPGKTDTVSK-------TLAKN 154
Query: 72 INLKTKH 78
++ +
Sbjct: 155 FHIPAMN 161
>gnl|CDD|131310 TIGR02257, cobalto_cobN, cobaltochelatase, CobN subunit.
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 1122
Score = 27.4 bits (61), Expect = 4.2
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 105 YSKEMEVASRVGHKV---LDDGTRVRYLIKTGEIIDSAENWKKLKEANRQEK 153
+ +V + + D R+++ + D A NW KL+ E+
Sbjct: 326 FKGVSDVDPALESAITTYRPDPDRIKW------VADLAANWIKLQRKPNAER 371
>gnl|CDD|226223 COG3700, AphA, Acid phosphatase (class B) [General function
prediction only].
Length = 237
Score = 26.8 bits (59), Expect = 5.0
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 14/67 (20%)
Query: 19 WER--KECKPNSLPV-----LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 71
WE+ S+P L MH + GD + + G GK ++K + K+
Sbjct: 102 WEKVNNGWDEFSIPKEVARQLIDMHQRRGDAIYFVTGRTPGKTDTVSK-------TLAKN 154
Query: 72 INLKTKH 78
++ +
Sbjct: 155 FHITNMN 161
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 26.2 bits (58), Expect = 5.1
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 94
M V+ D V V+ G KG+ G++T V+R + ++ I +++ E QI
Sbjct: 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKIT------REKANGEPVQI---- 94
Query: 95 APIHSSNVML 104
IH SNV++
Sbjct: 95 -GIHPSNVII 103
>gnl|CDD|214670 smart00452, STI, Soybean trypsin inhibitor (Kunitz) family of
protease inhibitors.
Length = 172
Score = 26.1 bits (58), Expect = 6.6
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 79 VKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEV--------ASRVGHKVLDDGTRVRYLI 130
V+ E + G +K P S ++ S ++ + A V +D T +
Sbjct: 43 VQSPNEVDNGLPVKFSPPNPSDFIIRESTDLNIEFDAPPLCAQSTVWTVDEDSTPGGLAV 102
Query: 131 KTGEIIDSAENWKKLKEA 148
KTG ++W K+++
Sbjct: 103 KTGGYPGVNDSWFKIEKY 120
>gnl|CDD|220244 pfam09441, Abp2, ARS binding protein 2. This DNA-binding protein
binds to the autonomously replicating sequence (ARS)
binding element. It may play a role in regulating the
cell cycle response to stress signals.
Length = 176
Score = 25.9 bits (57), Expect = 9.8
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 12/27 (44%)
Query: 13 VVRLKRWERKECKPNSLPVLHKMHVKA 39
VRLKRW +H MHV A
Sbjct: 100 AVRLKRW------------MHSMHVDA 114
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
0.315 0.130 0.371
Gapped
Lambda K H
0.267 0.0941 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,729,898
Number of extensions: 682627
Number of successful extensions: 818
Number of sequences better than 10.0: 1
Number of HSP's gapped: 812
Number of HSP's successfully gapped: 57
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 55 (24.6 bits)