RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3013
(151 letters)
>gnl|CDD|240514 cd06090, KOW_RPL27, KOW motif of eukaryotic Ribosomal Protein L27.
RPL27e has a KOW motif at its 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. .
Length = 83
Score = 138 bits (349), Expect = 1e-43
Identities = 59/81 (72%), Positives = 72/81 (88%)
Query: 38 KAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKR 97
K GK+V+VLSGRYAG+KAV++K D+GT D+ YGHALVAGIDRYPRKVTK+M+K KR
Sbjct: 1 KPGKVVIVLSGRYAGKKAVIVKNNDEGTKDRPYGHALVAGIDRYPRKVTKKMSKKKIAKR 60
Query: 98 SKIKPFLKVLNYNHLMPTRYT 118
SK+KPF+KV+NYNHLMPTRY+
Sbjct: 61 SKVKPFVKVVNYNHLMPTRYS 81
>gnl|CDD|240428 PTZ00471, PTZ00471, 60S ribosomal protein L27; Provisional.
Length = 134
Score = 123 bits (309), Expect = 7e-37
Identities = 49/119 (41%), Positives = 78/119 (65%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKT 92
M K +K GK+V+V SGRYAGRKAV+++ +D + ++ YGHALVAGI +YP+KV + M+K
Sbjct: 1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKR 60
Query: 93 LFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKKIRFQIRMKFEEK 151
+RS++ FL+V+N+ H +PTRY +E + D KK + + ++ F+ +
Sbjct: 61 TIARRSQVGVFLRVVNHKHFLPTRYNMDMSKELRGRINVSDASKKARSKQLVKKLFQAR 119
>gnl|CDD|201966 pfam01777, Ribosomal_L27e, Ribosomal L27e protein family. The
N-terminal region of the eukaryotic ribosomal L27 has
the KOW motif. C-terminal region is represented by this
family.
Length = 85
Score = 89.6 bits (223), Expect = 2e-24
Identities = 39/70 (55%), Positives = 53/70 (75%), Gaps = 2/70 (2%)
Query: 84 KVTKRMNKTLFKKRSKIKPFLKVLNYNHLMPTRYTY--PDMQEKLQPKELKDPMKKKKIR 141
KVTKRM+K KRSK+KPF+KV+NYNHLMPTRYT D+++ + LKDP K+K+ R
Sbjct: 1 KVTKRMSKKKIAKRSKVKPFVKVVNYNHLMPTRYTVDVEDLKKVVSKDALKDPSKRKEAR 60
Query: 142 FQIRMKFEEK 151
+++ KFEE+
Sbjct: 61 KEVKKKFEER 70
>gnl|CDD|225074 COG2163, RPL14A, Ribosomal protein L14E/L6E/L27E [Translation,
ribosomal structure and biogenesis].
Length = 125
Score = 65.9 bits (161), Expect = 1e-14
Identities = 25/119 (21%), Positives = 50/119 (42%), Gaps = 1/119 (0%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKT 92
M ++ G++V+V +GR+AG+K V++K DD G V G+ R +
Sbjct: 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFV-LITGPKKVKGVPRRRINIKHLEPTD 59
Query: 93 LFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKKIRFQIRMKFEEK 151
+ KV N + L+ K++++P+ + +++ EE+
Sbjct: 60 KVIDLVRGASDEKVKKANEAAGVLAKLDKSAKNLETKKVREPLTDAERFKVMKLVKEER 118
>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 = 33.7 bits (78), Expect = 0.003
Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 10/57 (17%)
Query: 40 GKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKK 96
G +V VL G Y GR+ VV+ D ++G V G K F
Sbjct: 1 GDVVRVLRGPYKGREGVVVD------IDPRFGIVTVKG----ATGSKGAELKVRFDD 47
>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 = 33.2 bits (77), Expect = 0.003
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 40 GKIVLVLSGRYAGRKAVVLKTYDDG 64
G +V V+SG + G+K V++ D
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSK 26
>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 = 0.011
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 38 KAGKIVLVLSGRYAGRKAVVLKTYDD 63
+ G V V++G + G+ VL+ +
Sbjct: 3 EVGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|240520 cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6. RPL6
contains KOW motif that has an extra ribosomal role as
an oncogenic. 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. .
Length = 152
Score = 31.4 bits (72), Expect = 0.11
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 11/46 (23%)
Query: 40 GKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKV 85
G ++++L+GR+ G++ V LK D G LV G P K+
Sbjct: 12 GTVLILLAGRFRGKRVVFLKQLDSGL-------LLVTG----PFKI 46
>gnl|CDD|240512 cd06088, KOW_RPL14, KOW motif of Ribosomal Protein L14. RPL14 is a
component of the large ribosomal subunit in both archaea
and eukaryotes with KOW motif at its 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.
Auto-antibodies to RPL14 in humans have been associated
with systemic lupus erythematosus . Although RPL14 is
well conserved, it is not found in all archaea, and
therefore it is presumably not essential.
Length = 76
Score = 29.8 bits (68), Expect = 0.14
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 26/89 (29%)
Query: 38 KAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKR 97
+ G++VL +GR G+ V++ D+ LV G R
Sbjct: 2 EIGRVVLSKAGRDKGKLYVIVDIIDENV-------VLVDG-----------------PLR 37
Query: 98 SKIKPFLKVLNYNHLMPTRYTYPDMQEKL 126
+ +KP K N HL T + +
Sbjct: 38 TGVKP--KKKNLKHLQLTDFVIDIPRGAR 64
>gnl|CDD|238693 cd01399, GlcN6P_deaminase, GlcN6P_deaminase:
Glucosamine-6-phosphate (GlcN6P) deaminase subfamily;
GlcN6P deaminase catalyzes the reversible conversion of
GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium.
The reaction is an aldo-keto isomerization coupled with
an amination or deamination. It is the last step of the
metabolic pathway of N-acetyl-D-glucosamine-6-phosphate
(GlcNAc6P). GlcN6P deaminase is a hexameric enzyme that
is allosterically activated by GlcNAc6P.
Length = 232
Score = 30.5 bits (70), Expect = 0.24
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 17/52 (32%)
Query: 10 NSEEVPTLAHSIFPFLFCRHISKMG--KIMKAGKIVLVLSGRYAGRKAVVLK 59
E+VPT A I+ MG IMKA +I+L+ +G KA +K
Sbjct: 162 GDEDVPTQA-----------IT-MGIGTIMKAKEILLLATGE---GKAEAVK 198
>gnl|CDD|235283 PRK04333, PRK04333, 50S ribosomal protein L14e; Validated.
Length = 84
Score = 27.3 bits (61), Expect = 1.1
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 37 MKA---GKIVLVLSGRYAGRKAVVLKTYDD 63
M A G++ + +GR AGRK V++ D
Sbjct: 1 MPAIEVGRVCVKTAGREAGRKCVIVDIIDK 30
>gnl|CDD|216948 pfam02253, PLA1, Phospholipase A1. Phospholipase A1 is a bacterial
outer membrane bound acyl hydrolase with a broad
substrate specificity EC:3.1.1.32. It has been proposed
that Ser164 is the active site for Escherichia coli
phospholipase A1.
Length = 259
Score = 28.7 bits (65), Expect = 1.1
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 96 KRSKIKPF-LKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKKIRFQIRMKF 148
K S PF + N+L+P YT + P + +K + +FQ+ K
Sbjct: 12 KASSDNPFVITPHKPNYLLPGTYTSDPNRAPFSPTPGAENLKNTEAKFQLSFKV 65
>gnl|CDD|99980 cd03808, GT1_cap1E_like, This family is most closely related to the
GT1 family of glycosyltransferases. cap1E in
Streptococcus pneumoniae is required for the synthesis
of type 1 capsular polysaccharides.
Length = 359
Score = 28.7 bits (65), Expect = 1.1
Identities = 16/102 (15%), Positives = 35/102 (34%), Gaps = 25/102 (24%)
Query: 13 EVPTLAHSIFPFLFCRHISKMGKIMKAGKIVLVLS--------GRYAGRKAVVLKTYDDG 64
+P I PF + + ++ ++++ + +V + GR A R A V K
Sbjct: 52 PIPLDRRGINPFKDLKALLRLYRLLRKERPDIVHTHTPKPGILGRLAARLAGVPKVI--- 108
Query: 65 TADKQYGHALVAGI------DRYPRKVTKRMNKTLFKKRSKI 100
V G+ R++ + + + K+
Sbjct: 109 --------YTVHGLGFVFTSGGLKRRLYLLLERLALRFTDKV 142
>gnl|CDD|240519 cd13155, KOW_KIN17, KOW_Kin17 is a RNA-binding motif. KOW domain
of the KIN17protein contributes to the RNA-binding
properties of the whole protein. 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. KIN17 is conserved from yeast
to human that ubiquitously expressed at low levels in
mammals tissue and have functions in DNA replication,
DNA repair and cell cycle control.
Length = 54
Score = 26.0 bits (58), Expect = 2.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 40 GKIVLVLSGRYAGRKAVVLK 59
G VLV++G Y G +A +
Sbjct: 2 GGRVLVVNGAYRGCEATLES 21
>gnl|CDD|179028 PRK00443, nagB, glucosamine-6-phosphate deaminase; Provisional.
Length = 261
Score = 27.9 bits (63), Expect = 2.3
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 12 EEVPTLAHSIFPFLFCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLK 59
E+VP A ++ +G I+ A +I+L+ G KA +K
Sbjct: 179 EQVPKYALTV----------GVGTILDAKEIMLLAPGH---NKAEAVK 213
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 26.2 bits (59), Expect = 4.2
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 32 KMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGI 78
M KI K G V+V++G+ G++ VLK +V G+
Sbjct: 1 MMMKI-KKGDTVIVIAGKDKGKRGKVLKVLPKK------NKVIVEGV 40
>gnl|CDD|238343 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
the methyltransferase Sun. The rRNA-specific
5-methylcytidine transferase Sun, also known as RrmB or
Fmu shares the RNA-binding non-catalytic domain with the
transcription termination factor NusB. The precise
biological role of this domain in Sun is unknown,
although it is likely to be involved in
sequence-specific RNA binding. The C-terminal
methyltransferase domain of Sun has been shown to
catalyze formation of m5C at position 967 of 16S rRNA in
Escherichia coli.
Length = 126
Score = 25.8 bits (57), Expect = 6.5
Identities = 12/51 (23%), Positives = 19/51 (37%)
Query: 57 VLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVL 107
L+ D D+ LV G R+ + +N L K P ++ L
Sbjct: 27 ALQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNL 77
>gnl|CDD|179794 PRK04223, rpl22p, 50S ribosomal protein L22P; Reviewed.
Length = 153
Score = 25.6 bits (57), Expect = 8.1
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 27 CRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVT 86
R I + MK + L A ++AV K ++ ++ AG RYP K
Sbjct: 34 AREI----RGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAG--RYPVKAA 87
Query: 87 KRMNKTL 93
K K L
Sbjct: 88 KAFLKLL 94
>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 = 24.4 bits (54), Expect = 9.3
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 40 GKIVLVLSGRYAGRKAVVLKTYDD 63
G V V+ G+ G++ VLK
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRK 24
>gnl|CDD|198414 cd10432, BI-1-like_bacterial, Bacterial BAX inhibitor
(BI)-1/YccA-like proteins. This family is comprised of
bacterial relatives of the mammalian members of the BAX
inhibitor (BI)-1 like family of small transmembrane
proteins, which have been shown to have an antiapoptotic
effect either by stimulating the antiapoptotic function
of Bcl-2, a well-characterized oncogene, or by
inhibiting the proapoptotic effect of Bax, another
member of the Bcl-2 family. In plants, BI-1 like
proteins play a role in pathogen resistance. A
characterized prokaryotic member, Escherichia coli YccA,
has been shown to interact with ATP-dependent protease
FtsH, which degrades abnormal membrane proteins as part
of a quality control mechanism to keep the integrity of
biological membranes.
Length = 211
Score = 25.6 bits (57), Expect = 9.8
Identities = 6/28 (21%), Positives = 16/28 (57%)
Query: 20 SIFPFLFCRHISKMGKIMKAGKIVLVLS 47
S++ + + +S +G + G I L+++
Sbjct: 110 SLYGYTTKKDLSFLGSFLFMGLIGLIIA 137
>gnl|CDD|182489 PRK10477, PRK10477, outer membrane lipoprotein Blc; Provisional.
Length = 177
Score = 25.8 bits (57), Expect = 9.8
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 67 DKQYGHALVAGIDR 80
D++Y HALV G DR
Sbjct: 122 DREYRHALVCGPDR 135
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
0.322 0.137 0.396
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: 7,758,577
Number of extensions: 704249
Number of successful extensions: 680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 678
Number of HSP's successfully gapped: 38
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.2 bits)