RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5495
(273 letters)
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 81.7 bits (203), Expect = 7e-20
Identities = 44/102 (43%), Positives = 66/102 (64%), Gaps = 8/102 (7%)
Query: 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKK------MGDSQFIIKQEA 208
I KGD V ++ GKDKGK+G V+++ + N VIVEG+N +KK II++EA
Sbjct: 5 IKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNI-VKKHQKPNQENPQGGIIEKEA 63
Query: 209 PLLVTNEVALVDPSDRMGCQVEWRYTEAGDRVRVSKRSGRII 250
P+ ++N VALVDP +V +++ E G +VRV+K+SG +I
Sbjct: 64 PIHISN-VALVDPKTGKATRVGFKFLEDGKKVRVAKKSGEVI 104
>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 = 80.0 bits (198), Expect = 3e-19
Identities = 44/102 (43%), Positives = 63/102 (61%), Gaps = 7/102 (6%)
Query: 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLK-----KMGDSQF-IIKQEA 208
I KGD V+++ GKDKGK+G V+++ + N VIVEG+N K SQ II++EA
Sbjct: 4 IKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEA 63
Query: 209 PLLVTNEVALVDPSDRMGCQVEWRYTEAGDRVRVSKRSGRII 250
P+ ++N V L DP +V R+ E G +VRV K++G II
Sbjct: 64 PIHISN-VMLFDPKTGKATRVGIRFEEDGKKVRVFKKTGEII 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 = 64.5 bits (158), Expect = 8e-14
Identities = 30/66 (45%), Positives = 44/66 (66%), Gaps = 6/66 (9%)
Query: 158 GDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQF-----IIKQEAPLLV 212
GD V+++ GKDKGKQG V+++ ++ N VIVEG+N K + SQ II+ EAP+ +
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60
Query: 213 TNEVAL 218
+N V L
Sbjct: 61 SN-VML 65
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 61.6 bits (150), Expect = 2e-12
Identities = 43/108 (39%), Positives = 68/108 (62%), Gaps = 17/108 (15%)
Query: 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQ-----FIIKQE 207
+ KGD V+++ GKDKGK+G V+++ + V+VEG+N K + SQ II +E
Sbjct: 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIINKE 60
Query: 208 APLLVTNEVALVDPS-----DRMGCQVEWRYTEAGDRVRVSKRSGRII 250
AP+ ++N VA++DP+ R+G +VE E G +VRV+K+SG +I
Sbjct: 61 APIHISN-VAIIDPNKTGKPTRVGYKVE----EDGKKVRVAKKSGEVI 103
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 53.5 bits (129), Expect = 1e-09
Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 14/89 (15%)
Query: 140 KNKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLK---- 195
K KKK+ + GD V+I+ G DKGK G V++I ++ N VIV+G+N K
Sbjct: 2 KKKKKM--------HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKP 53
Query: 196 -KMGDSQFIIKQEAPLLVTNEVALVDPSD 223
K + I + EAP+ +N V L +
Sbjct: 54 NKENEVGEIKQFEAPIHSSN-VMLYNEES 81
>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed.
Length = 76
Score = 48.9 bits (117), Expect = 5e-08
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQF-----IIKQEAP 209
+ KGD V+++ G DKGK G V+ + + N VIVEG+ K + SQ I++E P
Sbjct: 7 VKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMP 66
Query: 210 LLVTN 214
+ ++N
Sbjct: 67 IHISN 71
>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 = 7e-04
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 157 KGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188
KGD V ++ G KGK+G V+++ V VE
Sbjct: 1 KGDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 34.6 bits (81), Expect = 0.002
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 155 IFKGDRVEILVGKDKGKQGYVIQIFQE 181
GD V ++ G KGK G V+++ E
Sbjct: 2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|237883 PRK14991, PRK14991, tetrathionate reductase subunit A; Provisional.
Length = 1031
Score = 35.4 bits (82), Expect = 0.035
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 211 LVTNEVALVDPSDRMGCQVEWRYTEAGDRVRVSKRSGRIIPI------PMAAYETHDYKT 264
L N V + +GC W T+ G RVRV + +I+ I P++ D T
Sbjct: 66 LQPNPQQRVANTQCLGC---W--TQCGVRVRVDNATNKILRIAGNPYHPLSTDHHIDMST 120
Query: 265 P 265
P
Sbjct: 121 P 121
>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 = 29.5 bits (67), Expect = 0.24
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 158 GDRVEILVGKDKGKQGYVIQIFQEINSVIVEG 189
GD V +L G KG++G V+ I V V+G
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKG 32
>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 = 30.5 bits (69), Expect = 0.29
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 141 NKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLN 191
K+ +P+ KGD+V I+ G KG +G V ++ + + VEG+
Sbjct: 36 GKRALPVR--------KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVT 78
>gnl|CDD|129499 TIGR00405, L26e_arch, ribosomal protein L24p/L26e, archaeal. This
protein contains a KOW domain, shared by bacterial NusG
and the L24p/L26e family of ribosomal proteins. Although
called archaeal NusG in several publications, it is the
only close homolog of eukaryotic L26e in archaeal
genomes, shares an operon with L11 in many genomes, and
has been sequenced from purified ribosomes. It is here
designated as a ribosomal protein for these reasons
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 145
Score = 31.0 bits (70), Expect = 0.35
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLN 191
SI KGD VEI+ G KG++ VI++ + V +E +
Sbjct: 86 SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE 123
>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 = 27.9 bits (63), Expect = 0.65
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 158 GDRVEILVGKDKGKQGYVIQIFQ 180
GD V+++ G KG+QG V+ I++
Sbjct: 1 GDTVKVVDGPYKGRQGTVLHIYR 23
>gnl|CDD|181467 PRK08559, nusG, transcription antitermination protein NusG;
Validated.
Length = 153
Score = 29.1 bits (66), Expect = 1.7
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 142 KKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188
K K +E IK +GD VE++ G KG++ V+++ + V VE
Sbjct: 87 KPKPIVEGIK-----EGDIVELIAGPFKGEKARVVRVDESKEEVTVE 128
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 28.3 bits (64), Expect = 1.7
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 157 KGDRVEILVGKDKGKQGYVIQIFQEINSVIVEG 189
KGD V+++ G KG++G V+++ + + VEG
Sbjct: 48 KGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG 80
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 28.6 bits (64), Expect = 1.8
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFI 203
+ K D V ++ G KG++G V ++++ + +E + K G+ I
Sbjct: 47 VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITRE-KANGEPVQI 94
>gnl|CDD|169065 PRK07696, PRK07696, sulfur carrier protein ThiS; Provisional.
Length = 67
Score = 27.0 bits (60), Expect = 2.7
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 139 EKNKKKIPIEPIKDWSIFKGDRVEIL 164
E+NK + + D S+F GD++EI+
Sbjct: 36 ERNKDILQKDDHTDTSVFDGDQIEIV 61
>gnl|CDD|240510 cd06086, KOW_Spt5_6, KOW domain of Spt5, repeat 6. 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 = 58
Score = 26.3 bits (59), Expect = 3.1
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 157 KGDRVEILVGKDKGKQGYVIQI 178
KGDRV+++ G+D+G G +I I
Sbjct: 10 KGDRVKVIKGEDRGSTGELISI 31
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 28.7 bits (65), Expect = 3.3
Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 18/72 (25%)
Query: 140 KNKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSV-------------- 185
KNK+ + EP RVE+ GY I +N++
Sbjct: 198 KNKELLSPEPTYIEGEKDNIRVEVAFQYT---DGYSENIVSFVNNIATTEGGTHENGFKD 254
Query: 186 -IVEGLNTYLKK 196
+ +N Y KK
Sbjct: 255 ALTRVINEYAKK 266
>gnl|CDD|214510 smart00089, PKD, Repeats in polycystic kidney disease 1 (PKD1) and
other proteins. Polycystic kidney disease 1 protein
contains 14 repeats, present elsewhere such as in
microbial collagenases.
Length = 79
Score = 26.3 bits (58), Expect = 6.3
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 259 THDYKTPGTYKVT 271
TH Y PGTY VT
Sbjct: 48 THTYTKPGTYTVT 60
>gnl|CDD|185673 cd00560, PanC, Pantoate-beta-alanine ligase. PanC
Pantoate-beta-alanine ligase, also known as pantothenate
synthase, catalyzes the formation of pantothenate from
pantoate and alanine. PanC belongs to a large
superfamily of nucleotidyltransferases that includes ,
ATP sulfurylase (ATPS), phosphopantetheine
adenylyltransferase (PPAT), and the amino-acyl tRNA
synthetases. The enzymes of this family are structurally
similar and share a dinucleotide-binding domain.
Length = 277
Score = 27.5 bits (62), Expect = 8.5
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 79 TFEMD--IMEEHKIEVLFLGQVYHVYPKGPQYTVVDQGKDSD 118
T E D ++EE +++LF V +YP+G T VD G S+
Sbjct: 74 TLEADLALLEEAGVDLLFAPSVEEMYPEGLFSTFVDVGPLSE 115
>gnl|CDD|185466 PTZ00130, PTZ00130, heat shock protein 90; Provisional.
Length = 814
Score = 27.7 bits (61), Expect = 9.4
Identities = 45/181 (24%), Positives = 78/181 (43%), Gaps = 17/181 (9%)
Query: 37 YPKIVNEYERKYATGCFSDIENEDKDTKEQDVLAVTYQPK---LSTFEMDIMEEHKIEVL 93
Y I EY + TGC+ D N +K K + + PK L T+ ++ + K
Sbjct: 496 YKLIYKEYRKYLKTGCYEDDINRNKIVKLLLFKTMLH-PKSISLDTYIENMKPDQKFIYY 554
Query: 94 FLGQVYHVYPKGPQYTVVDQGKDSDFDFSTDRPWEVPFLARNRPWEKNKKKIPIEPIKDW 153
G Y K PQ + + K+ D F T+ E + R + ++ K K
Sbjct: 555 ASGDSYEYLSKIPQLQIFKK-KNIDVVFLTESVDE-SCVQRVQEYDGKKFK--------- 603
Query: 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFIIKQEAPLLVT 213
SI KG+ L +K K+ V ++++ + VI + L + K+ S+ ++ +AP V
Sbjct: 604 SIQKGEITFELTEDEKKKEEKVKKMYKALIDVISDTLRNQIFKVEISRRLV--DAPCAVV 661
Query: 214 N 214
+
Sbjct: 662 S 662
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
0.318 0.139 0.422
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: 14,190,326
Number of extensions: 1364727
Number of successful extensions: 1206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1200
Number of HSP's successfully gapped: 35
Length of query: 273
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 178
Effective length of database: 6,723,972
Effective search space: 1196867016
Effective search space used: 1196867016
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 (21.7 bits)
S2: 58 (25.8 bits)