RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032182
(146 letters)
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 191 bits (487), Expect = 8e-64
Identities = 97/144 (67%), Positives = 115/144 (79%), Gaps = 1/144 (0%)
Query: 3 YNPRVSSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTY 62
+N VSSSRRK RKAHFTAPS +RR LMSAPLS +LR KYNVRSMPVRKDDEV VVRG +
Sbjct: 1 FNSIVSSSRRKARKAHFTAPSHLRRKLMSAPLSKELRAKYNVRSMPVRKDDEVMVVRGHH 60
Query: 63 KGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRLDKDRKSLLDRKA 122
KGREGKV VYR+KWVIHIE+ITREK NG V +GI+PS V+ITKL+L+KDRK++L+RKA
Sbjct: 61 KGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLKLNKDRKAILERKA 120
Query: 123 KGRAAADKEKGTKFTPEDIMQSVD 146
+ +DK KG + MQ +D
Sbjct: 121 R-STKSDKGKGKYTAADKAMQQMD 143
>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 = 150 bits (380), Expect = 5e-48
Identities = 63/114 (55%), Positives = 87/114 (76%), Gaps = 1/114 (0%)
Query: 8 SSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREG 67
S RK RKA FTAP VRR LMSAPLS +LR+KY R++PVRK D+V+++RG +KG EG
Sbjct: 1 SKQPRKQRKALFTAPLHVRRKLMSAPLSKELREKYGKRALPVRKGDKVRIMRGDFKGHEG 60
Query: 68 KVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRLDKD-RKSLLDR 120
KV +V +++ I++E +T+EKVNG+ V V I+PS V+ITKL LD + RK +++R
Sbjct: 61 KVSKVDLKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITKLNLDDEKRKKIIER 114
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 115 bits (291), Expect = 2e-34
Identities = 59/117 (50%), Positives = 86/117 (73%), Gaps = 1/117 (0%)
Query: 7 VSSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGRE 66
+S RK RKA + AP +R+ LMSAPLS +LR+KY +RS+PVRK D V+V+RG +KG E
Sbjct: 4 MSKQPRKQRKALYNAPLHLRQKLMSAPLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEE 63
Query: 67 GKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRL-DKDRKSLLDRKA 122
GKVV+V ++ I++E +T +K +G+ V I+PS V+ITKL L D+ R+ +L+R+A
Sbjct: 64 GKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLDLSDERREKILERRA 120
>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 = 61.4 bits (150), Expect = 9e-14
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 11/65 (16%)
Query: 52 DDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVN-----------GSTVNVGINP 100
DEVQV+RG KG++GKV++V R+K + +E + K + V I+
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60
Query: 101 SKVVI 105
S V++
Sbjct: 61 SNVML 65
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 50.4 bits (121), Expect = 5e-09
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 13/80 (16%)
Query: 45 RSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNG-----------ST 93
M V+K D V+V+ G KG+EGKV++V +K + +E + K +
Sbjct: 1 MKMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIIN 58
Query: 94 VNVGINPSKVVITKLRLDKD 113
I+ S V I
Sbjct: 59 KEAPIHISNVAIIDPNKTGK 78
>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 = 40.5 bits (96), Expect = 5e-06
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 51 KDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82
K D V+V+ G +KG++GKVV+V K +H+E
Sbjct: 1 KGDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 37.0 bits (87), Expect = 5e-04
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVN 90
M ++K D V V+ G KG+ GKV++V +K ++ E VN
Sbjct: 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK-----NKVIVEGVN 41
>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 = 0.001
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 48 PVRKDDEVQVVRGTYKGREGKVVQVYRR 75
D V+V+ G +KG+ GKV++V
Sbjct: 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
>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 = 33.8 bits (78), Expect = 0.007
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76
M ++K D V+V+ G KG+ GKV++V +
Sbjct: 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKT 31
>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 = 32.1 bits (74), Expect = 0.009
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 52 DDEVQVVRGTYKGREGKVVQVYRRKWVIHIERIT 85
D V+VV G YKGR+G V+ +YR +H +T
Sbjct: 1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVT 34
>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed.
Length = 76
Score = 30.8 bits (70), Expect = 0.061
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76
+ V+K D V+V+ G KG+ GKV+ V +K
Sbjct: 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK 34
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 28.5 bits (64), Expect = 0.40
Identities = 10/38 (26%), Positives = 25/38 (65%)
Query: 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERI 84
M V+ D V+++ G+ KG+ G+V+++ ++ + ++ I
Sbjct: 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44
>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 = 27.4 bits (62), Expect = 0.72
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 53 DEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82
D V+++ G + G EGKV ++ K + +
Sbjct: 8 DTVRIISGPFAGFEGKVEEIDEEKGKVKVL 37
>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 = 26.4 bits (59), Expect = 1.3
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 53 DEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVN 90
D V+V+RG YKGREG VV + R ++ ++ T K
Sbjct: 2 DVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGA 39
>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
Length = 561
Score = 27.4 bits (61), Expect = 3.3
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 78 VIHIERITREKVNGSTVNVGINPSKVVI 105
V IER T + G+ VNVG PSK++I
Sbjct: 124 VTLIERGT---IGGTCVNVGCVPSKIMI 148
>gnl|CDD|202989 pfam04379, DUF525, Protein of unknown function (DUF525). Members
of this family include the bacterial protein ApaG and
the C termini of some F-box proteins (pfam00646). F-box
proteins contain a carboxyl-terminal domain that
interacts with protein substrates, so this family may
be involved in protein-protein interaction. The
function of ApaG proteins is unknown, but mutations in
the Salmonella typhimurium ApaG homologue corD gives a
phenotype of low-level cobalt resistance and decreased
magnesium efflux by effects on the CorA magnesium
transport system.
Length = 90
Score = 26.3 bits (59), Expect = 3.4
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 70 VQVYRRKWVIHIERITREKVNGSTVNVG 97
VQ+ R W+I E+V G V VG
Sbjct: 28 VQLLSRHWIITDANGKVEEVRGEGV-VG 54
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 26.7 bits (59), Expect = 6.8
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 6/67 (8%)
Query: 28 ILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIH----IER 83
+LMSA L L++K R+ V+ + K E + + R +
Sbjct: 374 LLMSATLPPFLKEKLKKALGKGRE--VVENAKFCPKEDEPGLKRKERVDVEDGPQEELIE 431
Query: 84 ITREKVN 90
+ E+V
Sbjct: 432 LISEEVK 438
>gnl|CDD|235479 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase;
Provisional.
Length = 326
Score = 26.1 bits (58), Expect = 7.6
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 96 VGINPSKVVITKLR 109
VGI P KV ITK++
Sbjct: 167 VGIGPGKVCITKIK 180
>gnl|CDD|237790 PRK14694, PRK14694, putative mercuric reductase; Provisional.
Length = 468
Score = 26.1 bits (57), Expect = 8.8
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 84 ITREKVNGSTVNVGINPSKVVITKLRLDKDRK 115
I R + G+ VN+G PSK++I + R+
Sbjct: 35 IERGTIGGTCVNIGCVPSKIMIRAAHIAHLRR 66
>gnl|CDD|240241 PTZ00045, PTZ00045, apical membrane antigen 1; Provisional.
Length = 595
Score = 26.1 bits (57), Expect = 9.6
Identities = 19/93 (20%), Positives = 30/93 (32%), Gaps = 2/93 (2%)
Query: 20 TAPSSVRRILMSAPLSTDLRQKYNVRS-MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWV 78
+ R P S L Q + S + K + KG G + W
Sbjct: 38 LNQNQTRLTSSRTPASLSLIQSNSSLSPIHNPKRAGLSERNPFGKGEIGGRSNRKQNPWK 97
Query: 79 IHIERITREKVNGSTVNVGINPSKVV-ITKLRL 110
+E+ +V+GS + V + V K R
Sbjct: 98 KFMEKFDIPRVHGSGIYVDLGEDAEVGGKKYRE 130
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 0.131 0.361
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: 7,309,702
Number of extensions: 648743
Number of successful extensions: 631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 629
Number of HSP's successfully gapped: 45
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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: 54 (24.2 bits)