RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026665
(235 letters)
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 204 bits (522), Expect = 1e-67
Identities = 64/114 (56%), Positives = 83/114 (72%), Gaps = 3/114 (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 EKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR 206
EKV ++GKK T KIY RHSG PGG+KE TF +L + PER+IE AV+GMLPK
Sbjct: 60 EKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNP 113
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 181 bits (462), Expect = 8e-59
Identities = 58/99 (58%), Positives = 73/99 (73%)
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 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR 206
RH+G PGG+K T R PERI+E AVRGMLPK +
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNK 99
>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 = 175 bits (446), Expect = 1e-56
Identities = 56/99 (56%), Positives = 73/99 (73%)
Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIY 167
W+V+DA ++LGRLAS +A + GK+ TYTP VD G YV+VVNAEK+ ++GKK QK+Y
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 168 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGR 206
RH+G PGG+K T L R PERI++ AVRGMLPK +
Sbjct: 61 YRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNK 99
>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 = 176 bits (448), Expect = 1e-56
Identities = 63/104 (60%), Positives = 79/104 (75%)
Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQ 164
+ WYVVDA K LGRLAS +A +RGK+ TYTP VD G YVIV+NAEKV ++GKK Q
Sbjct: 10 KRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQ 69
Query: 165 KIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRVS 208
K+Y RHSG PGG+K TF+++ R PER++EHAV+GMLPK R+
Sbjct: 70 KVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLG 113
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 175 bits (445), Expect = 5e-56
Identities = 67/115 (58%), Positives = 85/115 (73%), Gaps = 3/115 (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 NAEKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKG 205
NAEK+ V+G K +QK Y RHSGRPGG+K ETF++LQ+R+P RIIE AV+GMLPKG
Sbjct: 59 NAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKG 113
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 173 bits (440), Expect = 3e-55
Identities = 63/115 (54%), Positives = 78/115 (67%), Gaps = 4/115 (3%)
Query: 93 TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNA 152
T+ K ++ ++ WYV+DA K+LGRLAS +A +RGK+ TYTP VD G YVIV+NA
Sbjct: 3 TFTAKPSE---VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINA 59
Query: 153 EKVAVSGKKRTQKIYRRHSGRPGGMKEETFDQLQH-RIPERIIEHAVRGMLPKGR 206
EKV ++GKK T K Y RHSG PGG+K T R PERI+E AVRGMLPK
Sbjct: 60 EKVVITGKKLTDKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNP 114
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 94.9 bits (236), Expect = 3e-24
Identities = 42/100 (42%), Positives = 62/100 (62%)
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 RRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRV 207
R H+G G +KE + + P +I AV MLP+ R+
Sbjct: 77 RWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRL 116
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 63.7 bits (156), Expect = 6e-13
Identities = 33/96 (34%), Positives = 48/96 (50%), Gaps = 13/96 (13%)
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 RHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPK 204
+ R R P+RI + +RGMLP
Sbjct: 54 QRRERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPY 89
>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 = 59.0 bits (143), Expect = 3e-11
Identities = 33/96 (34%), Positives = 41/96 (42%), Gaps = 14/96 (14%)
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-RIPERIIEHAVRGMLPK 204
R P RI VRGMLP
Sbjct: 49 KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPH 84
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 46.2 bits (110), Expect = 2e-06
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 34/107 (31%)
Query: 109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVNAEKVAVSGKKRTQKIYR 168
V+D +LGRLAS +A K L G ++VV E + +SG ++R
Sbjct: 6 IVIDCKGHLLGRLASVVA-----KELLL-------GQKIVVVRCEDLNISGS-----LFR 48
Query: 169 RHSGRPGGMKEETFDQLQ-----------HRIPERIIEHAVRGMLPK 204
+K E F + + HR P I VRGMLP
Sbjct: 49 NK------VKYEEFLRKRMNTNPRRGPFHHRAPSDIFWRTVRGMLPH 89
>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 = 32.8 bits (74), Expect = 0.18
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 = 30.1 bits (68), Expect = 1.00
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|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 29.2 bits (65), Expect = 2.3
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|226502 COG4015, COG4015, Predicted dinucleotide-utilizing enzyme of the
ThiF/HesA family [General function prediction only].
Length = 217
Score = 27.9 bits (62), Expect = 3.6
Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 153 EKVAVSGKKRTQK---IYRRHSGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRVSS 209
E++ V +R ++ I+RR + G K + +L R + A + K +
Sbjct: 46 ERIYVFDGQRVEEDDIIHRRLGAKVGEYKVDFIKRLGRVHFGRRV-EAFPENITKDNL-H 103
Query: 210 LILNQILCVCM 220
L+ ++ +C+
Sbjct: 104 LLKGDVVVICI 114
>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 = 4.1
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 179 EETFDQLQHRIPERIIEHAVRGMLPKG 205
+T + ++ +I +R+ E A++G LP
Sbjct: 365 RDTVNSVKEKIGKRLFEAALKGKLPDL 391
>gnl|CDD|211992 TIGR04269, SAM_SPASM_FxsB, radical SAM/SPASM domain, FxsB family.
This model describes a radical SAM (pfam04055)/SPASM
domain (TIGR04085) fusion subfamily distinct from PqqE,
MftC, anaerobic sulfatase maturases, and other peptide
maturases. The combined region described in this model
can itself be fused to another domain, such as
TIGR04267, or stand alone. Members occurring in the same
cassette as a member of family TIGR04268 should be
designated FxsB.
Length = 363
Score = 28.2 bits (63), Expect = 4.5
Identities = 12/37 (32%), Positives = 13/37 (35%), Gaps = 4/37 (10%)
Query: 171 SGRPGGMKEETFDQLQHRIPERIIEHAVRGMLPKGRV 207
RP M ET R+ EHA LP V
Sbjct: 30 RARPKVMSAETRR----AFARRLAEHAAAHDLPSVAV 62
>gnl|CDD|215191 PLN02333, PLN02333, glucose-6-phosphate 1-dehydrogenase.
Length = 604
Score = 28.0 bits (62), Expect = 5.1
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 7/75 (9%)
Query: 1 MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPF--LGFSVASAKSTSPLNTKR 58
MATL + ++ S S S S + ++ SS P L F A + +P
Sbjct: 1 MATLSSSHSCPYARSYSYSLSPS-----SSSSHSSVVDPHRSLSFLSAIPQGLNPAKLCV 55
Query: 59 SFKVRCCQNLSLVPD 73
+ QN+ L+ D
Sbjct: 56 RSQRNSYQNVVLMQD 70
>gnl|CDD|216208 pfam00941, FAD_binding_5, FAD binding domain in molybdopterin
dehydrogenase.
Length = 171
Score = 27.1 bits (61), Expect = 5.3
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|234412 TIGR03951, Fe_III_red_FhuF, siderophore-iron reductase FhuF.
Members of this protein family, including FhuF of E.
coli, are siderophore ferric iron reductases that appear
to play a role in iron removal from certain
hydroxamate-type siderophores, including coprogen,
ferrichrome, ferrioxamine B, and aerobactin. Genes occur
in regularly in siderophore transport and/or
biosynthesis clusters. The C-terminus includes four Cys
residues in a C-C-10(X)-C-X-X-C motif that binds a
2Fe-2S cluster. Family TIGR03950 is similar, but
especially in the C-terminal region, but likely acts on
a different panel of siderophores [Energy metabolism,
Electron transport, Transport and binding proteins,
Cations and iron carrying compounds].
Length = 182
Score = 26.5 bits (59), Expect = 9.6
Identities = 5/33 (15%), Positives = 8/33 (24%), Gaps = 5/33 (15%)
Query: 81 QSEVNGPDIWNNT-----WYPKAADHRHSDKTW 108
+N +W+N WY
Sbjct: 90 YGGINPRLLWSNAGYYIDWYLGELAELLGPAPL 122
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
0.320 0.130 0.392
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: 11,243,486
Number of extensions: 1013913
Number of successful extensions: 1042
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1033
Number of HSP's successfully gapped: 29
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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 (21.8 bits)
S2: 57 (25.7 bits)