RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033131
(126 letters)
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 129 bits (328), Expect = 2e-40
Identities = 52/103 (50%), Positives = 68/103 (66%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
M +K GDTV VIAG DKGK G++ KV + V+V+ +N+ KH K +E QG II+ E
Sbjct: 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKE 62
Query: 61 APIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEIID 103
APIH SNV L + A+RVG K L+DG +VR K+GE+ID
Sbjct: 63 APIHISNVALVDPKTGKATRVGFKFLEDGKKVRVAKKSGEVID 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 = 116 bits (292), Expect = 5e-35
Identities = 52/103 (50%), Positives = 69/103 (66%), Gaps = 1/103 (0%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE-EEQGQIIKI 59
M +K GDTVKVI+G DKGK G++ KV + V+V+ +N+ KHVK + QG II+
Sbjct: 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEK 61
Query: 60 EAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEII 102
EAPIH SNVML+ + A+RVG + +DG +VR KTGEII
Sbjct: 62 EAPIHISNVMLFDPKTGKATRVGIRFEEDGKKVRVFKKTGEII 104
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 93.9 bits (234), Expect = 2e-26
Identities = 45/74 (60%), Positives = 60/74 (81%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
MHVK GDTVK+I+G DKGKIGE+ K+ + ++ V+VK IN+K KH+K +E E G+I + E
Sbjct: 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFE 66
Query: 61 APIHSSNVMLYSKE 74
APIHSSNVMLY++E
Sbjct: 67 APIHSSNVMLYNEE 80
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 94.3 bits (235), Expect = 2e-26
Identities = 51/104 (49%), Positives = 67/104 (64%), Gaps = 3/104 (2%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
M VK GDTVKVIAG DKGK G++ KV V+V+ +N+ KH+K +E +G II E
Sbjct: 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIINKE 60
Query: 61 APIHSSNVMLYSKEME-VASRVGHKVLDDGTRVRYLIKTGEIID 103
APIH SNV + +RVG+KV +DG +VR K+GE+ID
Sbjct: 61 APIHISNVAIIDPNKTGKPTRVGYKVEEDGKKVRVAKKSGEVID 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 = 84.9 bits (211), Expect = 3e-23
Identities = 36/65 (55%), Positives = 47/65 (72%)
Query: 6 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHS 65
GD V+VI G DKGK G++ KV R + V+V+ +N+ KHVK +E QG II++EAPIH
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60
Query: 66 SNVML 70
SNVML
Sbjct: 61 SNVML 65
>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed.
Length = 76
Score = 67.0 bits (164), Expect = 5e-16
Identities = 29/68 (42%), Positives = 41/68 (60%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
+ VK GD VKVIAG DKGK G++ V + V+V+ + + K +K ++ G I+ E
Sbjct: 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKE 64
Query: 61 APIHSSNV 68
PIH SNV
Sbjct: 65 MPIHISNV 72
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 39.5 bits (93), Expect = 6e-05
Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 11/67 (16%)
Query: 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAP 62
V+ GDTVKV+ G KG+ G++ +V + V+ + VKK + E + P
Sbjct: 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVT-----VKKADGTEVPR------P 94
Query: 63 IHSSNVM 69
IH SNVM
Sbjct: 95 IHPSNVM 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 = 35.9 bits (84), Expect = 2e-04
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 6 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36
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 = 33.0 bits (76), Expect = 0.004
Identities = 12/42 (28%), Positives = 17/42 (40%)
Query: 6 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 47
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 = 31.5 bits (73), Expect = 0.009
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29
+ 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 = 0.010
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 3 VKAGDTVKVIAGCDK 17
+ 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 = 30.1 bits (69), Expect = 0.051
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 35
+ 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 = 28.3 bits (64), Expect = 0.26
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 34
H K GD VKVI+G +G+ G + KV TV
Sbjct: 1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVF 33
>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 = 0.75
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
+ V+ GD V+++ G KG G+++KV + V+ + E+ G + +
Sbjct: 40 LPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTK---------EKVNGTEVPV- 89
Query: 61 APIHSSNVML 70
PIH SNVM+
Sbjct: 90 -PIHPSNVMI 98
>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 = 0.85
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 13 AGCDKGKIGEITKVFRHNSTVMVKDINLKTK 43
K+ + + R + V V ++ K
Sbjct: 66 DEASDRKLEGVIEHLRQKAEVTVNILSRDNK 96
>gnl|CDD|227736 COG5449, COG5449, Uncharacterized conserved protein [Function
unknown].
Length = 225
Score = 28.4 bits (63), Expect = 0.96
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 2 HVKAGDTVKVIAGCDK 17
+V GD K+ AGCDK
Sbjct: 168 YVAPGDEFKITAGCDK 183
>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 = 25.9 bits (58), Expect = 1.3
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 6 GDTVKVIAGCDKGKIGEITKVFR 28
GDTVKV+ G KG+ G + ++R
Sbjct: 1 GDTVKVVDGPYKGRQGTVLHIYR 23
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional.
Length = 273
Score = 27.7 bits (61), Expect = 1.8
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 6 GDTVKVIAGCDKGKIGEITKVFRH 29
G V V G ++G+IGEI + RH
Sbjct: 175 GKVVMVTGGANRGRIGEIVSIERH 198
>gnl|CDD|131310 TIGR02257, cobalto_cobN, cobaltochelatase, CobN subunit.
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 1122
Score = 27.8 bits (62), Expect = 2.0
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 71 YSKEMEVASRVGHKV---LDDGTRVRYLIKTGEIIDSAENWKKLKEANRQEK 119
+ +V + + D R+++ + D A NW KL+ E+
Sbjct: 326 FKGVSDVDPALESAITTYRPDPDRIKW------VADLAANWIKLQRKPNAER 371
>gnl|CDD|214670 smart00452, STI, Soybean trypsin inhibitor (Kunitz) family of
protease inhibitors.
Length = 172
Score = 26.5 bits (59), Expect = 3.3
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 45 VKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEV--------ASRVGHKVLDDGTRVRYLI 96
V+ E + G +K P S ++ S ++ + A V +D T +
Sbjct: 43 VQSPNEVDNGLPVKFSPPNPSDFIIRESTDLNIEFDAPPLCAQSTVWTVDEDSTPGGLAV 102
Query: 97 KTGEIIDSAENWKKLKEA 114
KTG ++W K+++
Sbjct: 103 KTGGYPGVNDSWFKIEKY 120
>gnl|CDD|235860 PRK06778, PRK06778, hypothetical protein; Validated.
Length = 289
Score = 26.8 bits (59), Expect = 3.3
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 22 EITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASRV 81
T + +D+N KT +KK+ E G++ I M + EME+ +
Sbjct: 83 PATVAVPEETEKKARDVNEKTALLKKKSATELGELATSINTIARDAHMEANLEMEIVPQ- 141
Query: 82 GHKVL--DDGTR 91
G +VL DD R
Sbjct: 142 GLRVLIKDDQNR 153
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 26.2 bits (58), Expect = 3.6
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIE 60
M V+ D V V+ G KG+ G++T V+R + ++ I +++ E QI
Sbjct: 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKIT------REKANGEPVQI---- 94
Query: 61 APIHSSNVML 70
IH SNV++
Sbjct: 95 -GIHPSNVII 103
>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 = 26.4 bits (58), Expect = 4.1
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKH 44
MH + GD + + G GK ++K + K+ ++ +
Sbjct: 125 MHQRRGDAIFFVTGRTPGKTDTVSK-------TLAKNFHIPAMN 161
>gnl|CDD|226223 COG3700, AphA, Acid phosphatase (class B) [General function
prediction only].
Length = 237
Score = 26.4 bits (58), Expect = 4.9
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKH 44
MH + GD + + G GK ++K + K+ ++ +
Sbjct: 125 MHQRRGDAIYFVTGRTPGKTDTVSK-------TLAKNFHITNMN 161
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
0.312 0.128 0.349
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: 6,042,995
Number of extensions: 523488
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 60
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (21.9 bits)
S2: 53 (23.8 bits)