RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027797
(218 letters)
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 250 bits (641), Expect = 6e-86
Identities = 82/145 (56%), Positives = 103/145 (71%), Gaps = 3/145 (2%)
Query: 67 TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNA 126
T+ K A+ ++ WYV+DA K+LGRLAS +A +RGK+ T+TP VD G +VIV+NA
Sbjct: 3 TFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINA 59
Query: 127 EKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELF 186
EKV ++GKK T KIY RHSG PGG+KE TF +L + PER+IE AV+GMLPK LGR +F
Sbjct: 60 EKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMF 119
Query: 187 THLKVYKGPNHPHEAQQPIELPIRD 211
LKVY G HPH AQQP L I+
Sbjct: 120 KKLKVYAGAEHPHAAQQPEVLEIKQ 144
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 220 bits (564), Expect = 1e-74
Identities = 74/128 (57%), Positives = 90/128 (70%)
Query: 82 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 141
W+V+DA +ILGRLAS +A +RGK+ TYTP VD G YV+V+NAEK+ ++GKKR QK Y
Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60
Query: 142 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 201
RH+G PGG+K T R PERI+E AVRGMLPK +LGR LKVY G HPH A
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAA 120
Query: 202 QQPIELPI 209
Q+P L I
Sbjct: 121 QKPEVLEI 128
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 221 bits (564), Expect = 2e-74
Identities = 87/145 (60%), Positives = 110/145 (75%), Gaps = 3/145 (2%)
Query: 65 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 124
N T+ P + WY++DA D+ LGRLA+ IA +RGKN +Y PSVD G YVIV+
Sbjct: 2 NKTFIPSKDYKN---RKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVI 58
Query: 125 NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRE 184
NAEK+ V+G K +QK Y RHSGRPGG+K ETF++LQ+R+P RIIE AV+GMLPKG LGR+
Sbjct: 59 NAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRK 118
Query: 185 LFTHLKVYKGPNHPHEAQQPIELPI 209
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 = 212 bits (542), Expect = 5e-71
Identities = 82/129 (63%), Positives = 99/129 (76%)
Query: 79 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 138
+ WYVVDA K LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK Q
Sbjct: 10 KRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQ 69
Query: 139 KIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHP 198
K+Y RHSG PGG+K TF+++ R PER++EHAV+GMLPK RLGR+LF LKVY G HP
Sbjct: 70 KVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHP 129
Query: 199 HEAQQPIEL 207
HEAQ+PI L
Sbjct: 130 HEAQKPIVL 138
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 207 bits (530), Expect = 4e-69
Identities = 77/133 (57%), Positives = 92/133 (69%), Gaps = 1/133 (0%)
Query: 79 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 138
++ WYV+DA K+LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK T
Sbjct: 12 ERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTD 71
Query: 139 KIYRRHSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNH 197
K Y RHSG PGG+K T R PERI+E AVRGMLPK LGR LKVY G H
Sbjct: 72 KKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPH 131
Query: 198 PHEAQQPIELPIR 210
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 = 192 bits (490), Expect = 1e-63
Identities = 64/114 (56%), Positives = 82/114 (71%)
Query: 82 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 141
W+V+DA ++LGRLAS +A + GK+ TYTP VD G YV+VVNAEK+ ++GKK QK+Y
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 142 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGP 195
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 = 101 bits (254), Expect = 4e-27
Identities = 52/142 (36%), Positives = 82/142 (57%), Gaps = 5/142 (3%)
Query: 82 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 141
W V DA ++LGRLAS I+ ++GK+ TY P+ D G IV+NA+ ++V+G+K T K Y
Sbjct: 17 WRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFY 76
Query: 142 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEA 201
R H+G G +KE + + P +I AV MLP+ RL + L+++ G HP
Sbjct: 77 RWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGD 136
Query: 202 Q--QPIELP---IRDKRIQKQR 218
+ +P +P +R+ R + +R
Sbjct: 137 KPLEPFVMPPRQVREMRPRARR 158
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 72.2 bits (178), Expect = 3e-16
Identities = 41/113 (36%), Positives = 57/113 (50%), Gaps = 14/113 (12%)
Query: 84 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSG-KKRTQKIYR 142
V+DA +ILGRLAS +A K L G V++VNAEK ++G ++R + Y+
Sbjct: 6 VIDAEGQILGRLASYVA-----KRLL-------EGEEVVIVNAEKAVITGNRERVIEKYK 53
Query: 143 RHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR-LGRELFTHLKVYKG 194
+ 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 = 64.8 bits (158), Expect = 2e-13
Identities = 42/127 (33%), Positives = 55/127 (43%), Gaps = 15/127 (11%)
Query: 84 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYRR 143
V+D + ILGRLAS +A K L G V+VVNAEK+ +SG K+ +
Sbjct: 2 VIDGSGHILGRLASVVA-----KQLLN-------GEKVVVVNAEKIVISGNFYRNKL-KY 48
Query: 144 HSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLP-KGRLGRELFTHLKVYKGPNHPHEA 201
R P RI VRGMLP K GR LKVY G +
Sbjct: 49 KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDK 108
Query: 202 QQPIELP 208
++ + +P
Sbjct: 109 KKRVVVP 115
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 47.7 bits (114), Expect = 6e-07
Identities = 38/127 (29%), Positives = 52/127 (40%), Gaps = 29/127 (22%)
Query: 83 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGK-KRTQKIY 141
V+D +LGRLAS +A K L G ++VV E + +SG R + Y
Sbjct: 6 IVIDCKGHLLGRLASVVA-----KELLL-------GQKIVVVRCEDLNISGSLFRNKVKY 53
Query: 142 RR-------HSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLP-KGRLGRELFTHLKVYK 193
+ R G HR P I VRGMLP K + G LKV++
Sbjct: 54 EEFLRKRMNTNPRRG--------PFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFE 105
Query: 194 GPNHPHE 200
G P++
Sbjct: 106 GVPAPYD 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 = 30.9 bits (70), Expect = 0.58
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 95 LASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGK 134
LAS AI RGKN + Y D+GA +VVN +++ G+
Sbjct: 424 LASCEAIDQRGKNRSGYDELCDLGAIELVVNRSTISLVGQ 463
>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 = 29.7 bits (66), Expect = 1.2
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 14 SLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRS 59
S +SSSS+ T N+ +T S+++T + ++ STS N+ S
Sbjct: 104 SASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSS 149
Score = 29.4 bits (65), Expect = 2.0
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 13 SSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRS 59
SS +S+S+S+ T N TT S+STT + +S ++S L + S
Sbjct: 110 SSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSSGLTSGAS 156
Score = 28.2 bits (62), Expect = 4.1
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 13 SSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTS 52
SS ++S+S+S T + +T SS++T S +S+ STS
Sbjct: 109 SSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTS 148
>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 = 2.4
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 153 EETFDQLQHRIPERIIEHAVRGMLPKGR--LGRELFTHLK 190
+T + ++ +I +R+ E A++G LP L +E LK
Sbjct: 365 RDTVNSVKEKIGKRLFEAALKGKLPDLEELLDKEDKVMLK 404
>gnl|CDD|178587 PLN03013, PLN03013, cysteine synthase.
Length = 429
Score = 28.2 bits (62), Expect = 3.5
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 6 TPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSFKD 62
+ + ++ + L SSSSSS+ + ISS L FS AS S + RSF D
Sbjct: 38 SSSALLLNPLTSSSSSSTLRRFRCSPEISS-----LSFSSASDFSLAMKRQSRSFAD 89
>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 = 4.4
Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 24/92 (26%)
Query: 109 ATYTPSVDMGAYVIVV---NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFD-------- 157
A P G V+V + ++V VS QKI RR + +E D
Sbjct: 44 AALAPG--PGEDVLVTRLRDGQQVTVS----KQKIERRLQQVIEKLDKEGVDVILLLCTG 97
Query: 158 ---QLQHRI----PERIIEHAVRGMLPKGRLG 182
+L R P+RI+ V ++ +LG
Sbjct: 98 EFPKLSARNLLLEPQRILPPLVASIVDGHQLG 129
>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 = 5.1
Identities = 17/70 (24%), Positives = 22/70 (31%), Gaps = 19/70 (27%)
Query: 153 EETFDQLQHRIPERIIEHAVRGMLPKGRLGR----ELFTHLKVY--------KGPNHPHE 200
E QL R+ RG+LP G GR E + K P E
Sbjct: 873 ERDPAQLAARL-------RARGLLPSGAFGRIFAKEQQQRARQLATAVLAHRKQPPQSVE 925
Query: 201 AQQPIELPIR 210
++ IR
Sbjct: 926 IDLDLQSGIR 935
>gnl|CDD|216208 pfam00941, FAD_binding_5, FAD binding domain in molybdopterin
dehydrogenase.
Length = 171
Score = 26.7 bits (60), Expect = 8.3
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 92 LGRLASTIA-IHIR-----GKNLATYTPSVDMGAYVIVVNAE-KVAVSGKKRTQKI---- 140
L IA IR G N+A +P D+ ++ ++A ++ +RT +
Sbjct: 90 LAEALRKIASPQIRNVATIGGNIANASPISDLPPALLALDATVELRSPEGRRTVPLEDFF 149
Query: 141 --YRRHSGRPG 149
YR+ PG
Sbjct: 150 LGYRKTDLEPG 160
>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 = 8.8
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 15/66 (22%)
Query: 152 KEETFDQLQHRIPERIIEHAVRGMLPKGRLGRELFTHLKVYKGPNHPHEAQQPIELPIRD 211
+ ETF+++ I E ++E A +G + VY P HP A++ ++L + +
Sbjct: 58 EHETFEEVYREIAEELLEEAKKGDV--------------VYAVPGHPLVAEKTVQL-LLE 102
Query: 212 KRIQKQ 217
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 0.130 0.385
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: 10,726,014
Number of extensions: 983432
Number of successful extensions: 985
Number of sequences better than 10.0: 1
Number of HSP's gapped: 974
Number of HSP's successfully gapped: 29
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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: 57 (25.7 bits)