RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026067
(244 letters)
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 254 bits (651), Expect = 4e-87
Identities = 82/145 (56%), Positives = 103/145 (71%), Gaps = 3/145 (2%)
Query: 93 TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNA 152
T+ K A+ ++ WYV+DA K+LGRLAS +A +RGK+ T+TP VD G +VIV+NA
Sbjct: 3 TFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINA 59
Query: 153 EKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELF 212
EKV ++GKK T KIY RHSG PGG+KE TF +L + PER+IE AV+GMLPK LGR +F
Sbjct: 60 EKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMF 119
Query: 213 THLKVYKGPNHPHEAQQPIELPIRD 237
LKVY G HPH AQQP L I+
Sbjct: 120 KKLKVYAGAEHPHAAQQPEVLEIKQ 144
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 224 bits (573), Expect = 2e-75
Identities = 74/128 (57%), Positives = 90/128 (70%)
Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 167
W+V+DA +ILGRLAS +A +RGK+ TYTP VD G YV+V+NAEK+ ++GKKR QK Y
Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60
Query: 168 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 227
RH+G PGG+K T R PERI+E AVRGMLPK +LGR LKVY G HPH A
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAA 120
Query: 228 QQPIELPI 235
Q+P L I
Sbjct: 121 QKPEVLEI 128
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 224 bits (572), Expect = 4e-75
Identities = 87/145 (60%), Positives = 110/145 (75%), Gaps = 3/145 (2%)
Query: 91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
N T+ P + WY++DA D+ LGRLA+ IA +RGKN +Y PSVD G YVIV+
Sbjct: 2 NKTFIPSKDYKN---RKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVI 58
Query: 151 NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRE 210
NAEK+ V+G K +QK Y RHSGRPGG+K ETF++LQ+R+P RIIE AV+GMLPKG LGR+
Sbjct: 59 NAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRK 118
Query: 211 LFTHLKVYKGPNHPHEAQQPIELPI 235
LFT LKVYKG +HPH AQ+PI++ I
Sbjct: 119 LFTKLKVYKGESHPHVAQKPIKINI 143
>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 = 215 bits (550), Expect = 7e-72
Identities = 82/129 (63%), Positives = 99/129 (76%)
Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 164
+ WYVVDA K LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK Q
Sbjct: 10 KRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQ 69
Query: 165 KIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHP 224
K+Y RHSG PGG+K TF+++ R PER++EHAV+GMLPK RLGR+LF LKVY G HP
Sbjct: 70 KVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHP 129
Query: 225 HEAQQPIEL 233
HEAQ+PI L
Sbjct: 130 HEAQKPIVL 138
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 211 bits (540), Expect = 4e-70
Identities = 77/133 (57%), Positives = 92/133 (69%), Gaps = 1/133 (0%)
Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 164
++ WYV+DA K+LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK T
Sbjct: 12 ERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTD 71
Query: 165 KIYRRHSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNH 223
K Y RHSG PGG+K T R PERI+E AVRGMLPK LGR LKVY G H
Sbjct: 72 KKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPH 131
Query: 224 PHEAQQPIELPIR 236
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 = 195 bits (498), Expect = 3e-64
Identities = 64/114 (56%), Positives = 82/114 (71%)
Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 167
W+V+DA ++LGRLAS +A + GK+ TYTP VD G YV+VVNAEK+ ++GKK QK+Y
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 168 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGP 221
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 = 102 bits (256), Expect = 5e-27
Identities = 52/142 (36%), Positives = 82/142 (57%), Gaps = 5/142 (3%)
Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 167
W V DA ++LGRLAS I+ ++GK+ TY P+ D G IV+NA+ ++V+G+K T K Y
Sbjct: 17 WRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFY 76
Query: 168 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 227
R H+G G +KE + + P +I AV MLP+ RL + L+++ G HP
Sbjct: 77 RWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGD 136
Query: 228 Q--QPIELP---IRDKRIQKQR 244
+ +P +P +R+ R + +R
Sbjct: 137 KPLEPFVMPPRQVREMRPRARR 158
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 73.4 bits (181), Expect = 2e-16
Identities = 41/113 (36%), Positives = 57/113 (50%), Gaps = 14/113 (12%)
Query: 110 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSG-KKRTQKIYR 168
V+DA +ILGRLAS +A K L G V++VNAEK ++G ++R + Y+
Sbjct: 6 VIDAEGQILGRLASYVA-----KRLL-------EGEEVVIVNAEKAVITGNRERVIEKYK 53
Query: 169 RHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR-LGRELFTHLKVYKG 220
+ 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 = 65.9 bits (161), Expect = 9e-14
Identities = 42/127 (33%), Positives = 55/127 (43%), Gaps = 15/127 (11%)
Query: 110 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRR 169
V+D + ILGRLAS +A K L G V+VVNAEK+ +SG K+ +
Sbjct: 2 VIDGSGHILGRLASVVA-----KQLLN-------GEKVVVVNAEKIVISGNFYRNKL-KY 48
Query: 170 HSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHEA 227
R P RI VRGMLP K GR LKVY G +
Sbjct: 49 KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDK 108
Query: 228 QQPIELP 234
++ + +P
Sbjct: 109 KKRVVVP 115
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 48.5 bits (116), Expect = 5e-07
Identities = 38/127 (29%), Positives = 52/127 (40%), Gaps = 29/127 (22%)
Query: 109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGK-KRTQKIY 167
V+D +LGRLAS +A K L G ++VV E + +SG R + Y
Sbjct: 6 IVIDCKGHLLGRLASVVA-----KELLL-------GQKIVVVRCEDLNISGSLFRNKVKY 53
Query: 168 RR-------HSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLP-KGRLGRELFTHLKVYK 219
+ R G HR P I VRGMLP K + G LKV++
Sbjct: 54 EEFLRKRMNTNPRRG--------PFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFE 105
Query: 220 GPNHPHE 226
G P++
Sbjct: 106 GVPAPYD 112
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 34.7 bits (79), Expect = 0.041
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 14 SLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPD 73
S +SSSS+ T N+ +T S+++T + ++ STS N+ S +SL+ D
Sbjct: 104 SASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSSGLTSGASVVSLI-D 162
Query: 74 NQRWMFEQSEV 84
W+++ S V
Sbjct: 163 TCAWVYQDSSV 173
>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 = 30.9 bits (70), Expect = 0.70
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 121 LASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGK 160
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 = 28.8 bits (65), Expect = 2.8
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 179 EETFDQLQHRIPERIIEHAVRGMLPKGR--LGRELFTHLK 216
+T + ++ +I +R+ E A++G LP L +E LK
Sbjct: 365 RDTVNSVKEKIGKRLFEAALKGKLPDLEELLDKEDKVMLK 404
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 28.8 bits (64), Expect = 3.1
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 5 CTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTK--RSFKV 62
+ + ++ S SSS SSS + + + S T F + +T+ + + RSF V
Sbjct: 9 SSSSSLLLPSSSSSSPSSSTFSFKSTSGKLKSLTLSSSFLSPFSTTTTSTSQRRRRSFTV 68
Query: 63 R 63
R
Sbjct: 69 R 69
>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 = 27.6 bits (62), Expect = 4.6
Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 24/92 (26%)
Query: 135 ATYTPSVDMGAYVIVV---NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD-------- 183
A P G V+V + ++V VS QKI RR + +E D
Sbjct: 44 AALAPG--PGEDVLVTRLRDGQQVTVS----KQKIERRLQQVIEKLDKEGVDVILLLCTG 97
Query: 184 ---QLQHRI----PERIIEHAVRGMLPKGRLG 208
+L R P+RI+ V ++ +LG
Sbjct: 98 EFPKLSARNLLLEPQRILPPLVASIVDGHQLG 129
>gnl|CDD|216208 pfam00941, FAD_binding_5, FAD binding domain in molybdopterin
dehydrogenase.
Length = 171
Score = 27.1 bits (61), Expect = 6.4
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 118 LGRLASTIA-IHIR-----GKNLATYTPSVDMGAYVIVVNAE-KVAVSGKKRTQKI---- 166
L IA IR G N+A +P D+ ++ ++A ++ +RT +
Sbjct: 90 LAEALRKIASPQIRNVATIGGNIANASPISDLPPALLALDATVELRSPEGRRTVPLEDFF 149
Query: 167 --YRRHSGRPG 175
YR+ PG
Sbjct: 150 LGYRKTDLEPG 160
>gnl|CDD|215191 PLN02333, PLN02333, glucose-6-phosphate 1-dehydrogenase.
Length = 604
Score = 27.6 bits (61), Expect = 7.2
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 3/73 (4%)
Query: 1 MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSF 60
MATL + S S S + ++ + L F A + +P
Sbjct: 1 MATLSSSHS---CPYARSYSYSLSPSSSSSHSSVVDPHRSLSFLSAIPQGLNPAKLCVRS 57
Query: 61 KVRCCQNLSLVPD 73
+ QN+ L+ D
Sbjct: 58 QRNSYQNVVLMQD 70
>gnl|CDD|233419 TIGR01450, recC, exodeoxyribonuclease V, gamma subunit. This model
describes the gamma subunit of exodeoxyribonuclease V.
Species containing this protein should also have the
alpha (TIGR01447) and beta (TIGR00609) subunits.
Candidates from Borrelia and from the Chlamydias differ
dramatically and score between trusted and noise cutoffs
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1067
Score = 27.8 bits (62), Expect = 7.3
Identities = 17/70 (24%), Positives = 22/70 (31%), Gaps = 19/70 (27%)
Query: 179 EETFDQLQHRIPERIIEHAVRGMLPKGRLGR----ELFTHLKVY--------KGPNHPHE 226
E QL R+ RG+LP G GR E + K P E
Sbjct: 873 ERDPAQLAARL-------RARGLLPSGAFGRIFAKEQQQRARQLATAVLAHRKQPPQSVE 925
Query: 227 AQQPIELPIR 236
++ IR
Sbjct: 926 IDLDLQSGIR 935
>gnl|CDD|221217 pfam11777, DUF3316, Protein of unknown function (DUF3316). This
family of bacterial proteins has no known function.
Several members are, however, annotated as being
putative acyl-CoA synthetase, but this could not be
confirmed.
Length = 114
Score = 26.5 bits (59), Expect = 7.9
Identities = 8/64 (12%), Positives = 21/64 (32%), Gaps = 4/64 (6%)
Query: 3 TLCTPTCVIFSSL---QSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLN-TKR 58
+ ++ S+ + S++ +L T + GF+ + S N +
Sbjct: 4 LILLALLLLLSATAFAGNYVSTTQTDSLQTDVYATKQAAYGAGFTNLNDLYLSSSNELGK 63
Query: 59 SFKV 62
+
Sbjct: 64 ELNI 67
>gnl|CDD|212509 cd11723, YabN_N, N-terminal S-AdoMet dependent methylase domain of
Bacillus subtilis YabN and related proteins. This
family contains proteins similar to Bacillus subtilis
YabN, which is a fusion of an N-terminal TP-methylase
and a C-terminal MazG-type nucleotide
pyrophosphohydrolase domain. MazG-like NTP-PPases have
been implicated in house-cleaning functions such as
degrading abnormal (d)NTPs. TP-methylases use S-AdoMet
(S-adenosyl-L-methionine or SAM) in the methylation of
diverse substrates. Most members catalyze various
methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The specific function of YabN's
TP-methylase domain is not known.
Length = 220
Score = 26.8 bits (60), Expect = 8.6
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 15/66 (22%)
Query: 178 KEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPIRD 237
+ ETF+++ I E ++E A +G + VY P HP A++ ++L + +
Sbjct: 58 EHETFEEVYREIAEELLEEAKKGDV--------------VYAVPGHPLVAEKTVQL-LLE 102
Query: 238 KRIQKQ 243
K +
Sbjct: 103 KAEKAG 108
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
0.317 0.131 0.393
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,918,520
Number of extensions: 1091133
Number of successful extensions: 1041
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1031
Number of HSP's successfully gapped: 27
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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 (26.1 bits)