RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030391
(178 letters)
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 242 bits (621), Expect = 1e-83
Identities = 82/145 (56%), Positives = 103/145 (71%), Gaps = 3/145 (2%)
Query: 27 TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNA 86
T+ K A+ ++ WYV+DA K+LGRLAS +A +RGK+ T+TP VD G +VIV+NA
Sbjct: 3 TFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINA 59
Query: 87 EKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELF 146
EKV ++GKK T KIY RHSG PGG+KE TF +L + PER+IE AV+GMLPK LGR +F
Sbjct: 60 EKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMF 119
Query: 147 THLKVYKGPNHPHEAQQPIELPIRD 171
LKVY G HPH AQQP L I+
Sbjct: 120 KKLKVYAGAEHPHAAQQPEVLEIKQ 144
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 219 bits (560), Expect = 2e-74
Identities = 87/145 (60%), Positives = 110/145 (75%), Gaps = 3/145 (2%)
Query: 25 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 84
N T+ P + WY++DA D+ LGRLA+ IA +RGKN +Y PSVD G YVIV+
Sbjct: 2 NKTFIPSKDYKN---RKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVI 58
Query: 85 NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRE 144
NAEK+ V+G K +QK Y RHSGRPGG+K ETF++LQ+R+P RIIE AV+GMLPKG LGR+
Sbjct: 59 NAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRK 118
Query: 145 LFTHLKVYKGPNHPHEAQQPIELPI 169
LFT LKVYKG +HPH AQ+PI++ I
Sbjct: 119 LFTKLKVYKGESHPHVAQKPIKINI 143
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 208 bits (533), Expect = 1e-70
Identities = 74/128 (57%), Positives = 90/128 (70%)
Query: 42 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 101
W+V+DA +ILGRLAS +A +RGK+ TYTP VD G YV+V+NAEK+ ++GKKR QK Y
Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60
Query: 102 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 161
RH+G PGG+K T R PERI+E AVRGMLPK +LGR LKVY G HPH A
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAA 120
Query: 162 QQPIELPI 169
Q+P L I
Sbjct: 121 QKPEVLEI 128
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 205 bits (523), Expect = 9e-69
Identities = 82/129 (63%), Positives = 99/129 (76%)
Query: 39 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 98
+ WYVVDA K LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK Q
Sbjct: 10 KRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQ 69
Query: 99 KIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHP 158
K+Y RHSG PGG+K TF+++ R PER++EHAV+GMLPK RLGR+LF LKVY G HP
Sbjct: 70 KVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHP 129
Query: 159 HEAQQPIEL 167
HEAQ+PI L
Sbjct: 130 HEAQKPIVL 138
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 199 bits (507), Expect = 3e-66
Identities = 77/133 (57%), Positives = 92/133 (69%), Gaps = 1/133 (0%)
Query: 39 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 98
++ WYV+DA K+LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK T
Sbjct: 12 ERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTD 71
Query: 99 KIYRRHSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNH 157
K Y RHSG PGG+K T R PERI+E AVRGMLPK LGR LKVY G H
Sbjct: 72 KKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPH 131
Query: 158 PHEAQQPIELPIR 170
PHEAQ+P L ++
Sbjct: 132 PHEAQKPEALELK 144
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 182 bits (465), Expect = 3e-60
Identities = 64/114 (56%), Positives = 82/114 (71%)
Query: 42 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 101
W+V+DA ++LGRLAS +A + GK+ TYTP VD G YV+VVNAEK+ ++GKK QK+Y
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 102 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGP 155
RH+G PGG+K T L R PERI++ AVRGMLPK +LGR LKVY+G
Sbjct: 61 YRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 96.5 bits (240), Expect = 2e-25
Identities = 52/142 (36%), Positives = 82/142 (57%), Gaps = 5/142 (3%)
Query: 42 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 101
W V DA ++LGRLAS I+ ++GK+ TY P+ D G IV+NA+ ++V+G+K T K Y
Sbjct: 17 WRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFY 76
Query: 102 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 161
R H+G G +KE + + P +I AV MLP+ RL + L+++ G HP
Sbjct: 77 RWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGD 136
Query: 162 Q--QPIELP---IRDKRIQKQR 178
+ +P +P +R+ R + +R
Sbjct: 137 KPLEPFVMPPRQVREMRPRARR 158
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 68.7 bits (169), Expect = 2e-15
Identities = 41/113 (36%), Positives = 57/113 (50%), Gaps = 14/113 (12%)
Query: 44 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSG-KKRTQKIYR 102
V+DA +ILGRLAS +A K L G V++VNAEK ++G ++R + Y+
Sbjct: 6 VIDAEGQILGRLASYVA-----KRLL-------EGEEVVIVNAEKAVITGNRERVIEKYK 53
Query: 103 RHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR-LGRELFTHLKVYKG 154
+ R R P+RI + +RGMLP + GRE LKVY G
Sbjct: 54 QRRERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVG 106
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 60.9 bits (148), Expect = 2e-12
Identities = 42/127 (33%), Positives = 55/127 (43%), Gaps = 15/127 (11%)
Query: 44 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRR 103
V+D + ILGRLAS +A K L G V+VVNAEK+ +SG K+ +
Sbjct: 2 VIDGSGHILGRLASVVA-----KQLLN-------GEKVVVVNAEKIVISGNFYRNKL-KY 48
Query: 104 HSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHEA 161
R P RI VRGMLP K GR LKVY G +
Sbjct: 49 KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDK 108
Query: 162 QQPIELP 168
++ + +P
Sbjct: 109 KKRVVVP 115
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 45.4 bits (108), Expect = 3e-06
Identities = 36/119 (30%), Positives = 49/119 (41%), Gaps = 13/119 (10%)
Query: 43 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYR 102
V+D +LGRLAS +A K L G ++VV E + +SG K+
Sbjct: 6 IVIDCKGHLLGRLASVVA-----KELLL-------GQKIVVVRCEDLNISGSLFRNKVKY 53
Query: 103 RHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHE 160
R HR P I VRGMLP K + G LKV++G P++
Sbjct: 54 EEFLRKRMNTNPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYD 112
>gnl|CDD|234502 TIGR04212, GlyGly_RbtA, Acinetobacter rhombotarget A. Members of
this protein family are found, so far, exclusively in
the genus Acinetobacter. Members average just over 600
amino acids in length, including a 22-amino acid
C-terminal putative protein sorting recognition
sequence, GlyGly-CTERM (TIGR03501). The GlyGly-CTERM
signal always co-occurs with a subfamily of the rhomboid
family intramembrane serine proteases called
rhombosortase (TIGR03902). Members occur paired with a
second rhombosortase target, with which it also shares
an N-terminal motif CSLREA. This protein is designated
Acinetobacter rhombotarget A (rbtA).
Length = 605
Score = 32.0 bits (73), Expect = 0.15
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 55 LASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGK 94
LAS AI RGKN + Y D+GA +VVN +++ G+
Sbjct: 424 LASCEAIDQRGKNRSGYDELCDLGAIELVVNRSTISLVGQ 463
>gnl|CDD|99967 cd03793, GT1_Glycogen_synthase_GSY2_like, Glycogen synthase, which
is most closely related to the GT1 family of
glycosyltransferases, catalyzes the transfer of a
glucose molecule from UDP-glucose to a terminal branch
of a glycogen molecule, a rate-limit step of glycogen
biosynthesis. GSY2, the member of this family in S.
cerevisiae, has been shown to possess glycogen synthase
activity.
Length = 590
Score = 28.5 bits (64), Expect = 2.5
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 113 EETFDQLQHRIPERIIEHAVRGMLPKGR--LGRELFTHLK 150
+T + ++ +I +R+ E A++G LP L +E LK
Sbjct: 365 RDTVNSVKEKIGKRLFEAALKGKLPDLEELLDKEDKVMLK 404
>gnl|CDD|130078 TIGR01005, eps_transp_fam, exopolysaccharide transport protein
family. The model describes the exopolysaccharide
transport protein family in bacteria. The transport
protein is part of a large genetic locus which is
associated with exopolysaccharide (EPS) biosynthesis.
Detailed molecular characterization and gene fusion
analysis revealed atleast seven gene products are
involved in the overall regulation, which among other
things, include exopolysaccharide biosynthesis, property
of conferring virulence and exopolysaccharide export
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 754
Score = 28.0 bits (62), Expect = 2.8
Identities = 30/154 (19%), Positives = 45/154 (29%), Gaps = 22/154 (14%)
Query: 8 LTPRHPPLTCRFLWDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKN 67
L P + F D W + +D+ V + ++ A A +
Sbjct: 490 LARPEPGVASAFADDA-ETQWPEAVLEREVADQPRPVAEEELRVK-EEAVAEAKSVAEPE 547
Query: 68 L-ATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRRHSGRPGGM-----KEETFDQLQH 121
+ T P +G I NA + SG KR + GR + E L
Sbjct: 548 VVETQRPRPVLGKSDIEANAAALIASGGKRA--LLIDADGRKAALSQILVAREVSGLLDL 605
Query: 122 RIPERIIEHAV-------RGMLPKGRLGRELFTH 148
R + + ML G LF H
Sbjct: 606 LAGLRSLLLDLTASGAASLPMLDSG-----LFPH 634
>gnl|CDD|148738 pfam07302, AroM, AroM protein. This family consists of several
bacterial and archaeal AroM proteins. In Escherichia
coli the aroM gene is cotranscribed with aroL. The
function of this family is unknown.
Length = 221
Score = 26.9 bits (60), Expect = 6.2
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 115 TFDQLQHRI----PERIIEHAVRGMLPKGRLG 142
F +L R P+RI+ V ++ +LG
Sbjct: 98 EFPKLSARNLLLEPQRILPPLVASIVDGHQLG 129
>gnl|CDD|235303 PRK04517, PRK04517, hypothetical protein; Provisional.
Length = 216
Score = 26.7 bits (59), Expect = 6.7
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 50 KILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSG 93
K + L +A+ G A T V ++V N K +SG
Sbjct: 2 KPIKPLTCLLALCFSGSASADVTMEVPDDVDLLVANGSKPKLSG 45
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 26.5 bits (59), Expect = 9.0
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 118 QLQHRIPERIIEHAV--RGMLPKGRLG 142
Q+ +I ER++E + R LP R G
Sbjct: 951 QVAEKIVERVVERIIREREKLPDRRKG 977
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 0.138 0.437
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,426,861
Number of extensions: 872768
Number of successful extensions: 756
Number of sequences better than 10.0: 1
Number of HSP's gapped: 748
Number of HSP's successfully gapped: 24
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
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: 56 (25.3 bits)