RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy451
(296 letters)
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 116 bits (292), Expect = 2e-31
Identities = 49/169 (28%), Positives = 75/169 (44%), Gaps = 13/169 (7%)
Query: 119 GLIGKIIGQYPLWMKNGEKCRTTLVQVVDNHIIKYIPPEEFKPNRKPYRGEPKRKLGCLL 178
GL+GK +G ++ ++G+ T+++V N + + E + Y +
Sbjct: 1 GLLGKKVGMTQIFTEDGKAVPVTVIEVGPNVVTQVKTVE-----KDGYSA--------VQ 47
Query: 179 VGAESGDPSLYTKEYCGLFKNSGVPPKKKLCRFIITPDAMLPPGTPLTAAHFRPREFLDV 238
+G K G F +GV PK+ L F + G +T F + +DV
Sbjct: 48 LGFGEKKEKRVNKPEAGHFAKAGVEPKRHLREFRVDDLEGYEVGDEITVDIFEAGQKVDV 107
Query: 239 RGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCIASGAGKARVYPG 287
G + +GF GVMKR F G PA+HG +KSHR G I RV+ G
Sbjct: 108 TGTSKGKGFAGVMKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKG 156
>gnl|CDD|234564 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 107 bits (271), Expect = 2e-28
Identities = 48/173 (27%), Positives = 75/173 (43%), Gaps = 19/173 (10%)
Query: 117 RTGLIGKIIGQYPLWMKNGEKCRTTLVQVVDNHIIKYIPPEEFKPNRKPYRGEPKRKLG- 175
G++GK +G ++ ++GE T+++ N + + E K G
Sbjct: 2 MKGILGKKVGMTQIFTEDGESIPVTVIEAGPNVVTQVKTVE---------------KDGY 46
Query: 176 -CLLVGAESGDPSLYTKEYCGLFKNSGVPPKKKLCRFIITPDAMLPPGTPLTAAHFRPRE 234
+ +G K G F +GV PK+ L F G +T F +
Sbjct: 47 NAVQLGFGDKKEKRVNKPEAGHFAKAGVEPKRHLREF--RVVEEYEVGQEITVDIFEAGQ 104
Query: 235 FLDVRGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCIASGAGKARVYPG 287
+DV G + +GF GV+KR F G PA+HG ++SHRR G I + RV+ G
Sbjct: 105 KVDVTGTSKGKGFAGVIKRHNFSGGPASHGNSRSHRRPGSIGARQTPGRVFKG 157
>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 105 bits (265), Expect = 2e-27
Identities = 53/174 (30%), Positives = 77/174 (44%), Gaps = 16/174 (9%)
Query: 117 RTGLIGKIIGQYPLWMKNGEKCRTTLVQVVDNHIIKYIPPEEFKPNRKPYRGEPKRKLGC 176
G +G +G ++ + G T+++V N +++ +
Sbjct: 1 MLGFLGYKVGMTHVFDERGISVPVTVIEVPPNVVVQV-------------KTYETDGYRA 47
Query: 177 LLVGAESGDPSLYTKEYCGLFKNSGVPPKKKLCRFII---TPDAMLPPGTPLTAAHFRPR 233
+ VGA K G F +GV PK+ L F + G +T F+
Sbjct: 48 VQVGAGDRKAKRVNKPLVGHFAKAGVKPKRHLAEFRVGGGDVAEKFEVGQEITVDVFKEG 107
Query: 234 EFLDVRGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCIASGAGKARVYPG 287
E +DV G+T +GFQGVMKRWGFKG PA+HG + SHRR G I RV+ G
Sbjct: 108 ELVDVTGVTKGKGFQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKG 161
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3.
Length = 199
Score = 91.2 bits (227), Expect = 3e-22
Identities = 47/166 (28%), Positives = 69/166 (41%), Gaps = 17/166 (10%)
Query: 125 IGQYPLWMKNGEKCR-TTLVQVVDNHIIKYIPPEEFKPNRKPY-RGEPKRKLGCLLVGAE 182
G ++ + T+++V +++ EE K G K +
Sbjct: 2 AGMTHIFTEKKGVLEPVTVIEVPPMVVVQVKTYEETNDGYKAIQVGLESIKKYRV----- 56
Query: 183 SGDPSLYTKEYCGLFKNSGVPPKKKLCRFIITPDAMLPPGTPLTA-AHFRPREFLDVRGL 241
K G + G PPK + F + PG + FR E++DV G+
Sbjct: 57 -------VKRVLGHTQKRGTPPKAHVMEFRVNGGEEFEPGQTIAVSDVFREGEYVDVTGV 109
Query: 242 TVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCIASGAGKARVYPG 287
T +GFQGVMKRWGFK +P HG HR+ G I + RV+PG
Sbjct: 110 TKGKGFQGVMKRWGFKRLPRKHG-RGYHRKPGSIGAWH-PGRVFPG 153
>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated.
Length = 207
Score = 73.9 bits (182), Expect = 1e-15
Identities = 39/111 (35%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 177 LLVGAESGDPSLYTKEYCGLFKNSGVPPKKKLCRFIITPDAMLPPGTPLTAAHFRPREFL 236
+ +G + TK G + S VPP K L F + G PLT F + +
Sbjct: 49 IQIGYKQVSTKKLTKPQLGHLQKSNVPPLKYLKEFRVKSSEEFEVGQPLTVDAFSVGQLV 108
Query: 237 DVRGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCIASGAGKARVYPG 287
+V G ++ +GF G+ KR F P THG +K+HR G I +G RVYPG
Sbjct: 109 NVSGKSIGKGFAGLQKRHNFSRGPMTHG-SKNHRAPGSIGAGTTPGRVYPG 158
>gnl|CDD|235260 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
Length = 337
Score = 49.5 bits (119), Expect = 8e-07
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 230 FRPREFLDVRGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCI 275
F+ + +DV +T +GFQGV+KRWG K +P H R G +
Sbjct: 193 FKEGQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKRRGGSRHIGTL 238
>gnl|CDD|234286 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam family
pfam00297. Eukaryotic proteins are excluded from this
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 330
Score = 48.9 bits (117), Expect = 1e-06
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 230 FRPREFLDVRGLTVDRGFQGVMKRWGFKGMPATHGVTKSHRRGGCI 275
F+ + +DV +T +GFQGV+KRWG K +P H K R G +
Sbjct: 188 FKEGQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKRRKGGRHIGTL 233
>gnl|CDD|240267 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
Length = 390
Score = 40.5 bits (95), Expect = 7e-04
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 230 FRPREFLDVRGLTVDRGFQGVMKRWGFKGMP-ATHGVTKSHRRGGCIAS 277
F+ E +DV G+T GF+GV+KRWG +P TH + R+ CI +
Sbjct: 208 FQQNEMIDVIGVTKGHGFEGVVKRWGVTRLPRKTH---RGLRKVACIGA 253
>gnl|CDD|234429 TIGR03984, TIGR03984, CRISPR-associated protein, TIGR03984 family.
Members of this protein family are found exclusively in
CRISPR-containing organisms, in operon contexts with
RAMP (repeat-associated mystery protein) proteins also
linked to CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats).
Length = 147
Score = 29.6 bits (67), Expect = 1.0
Identities = 9/48 (18%), Positives = 14/48 (29%)
Query: 123 KIIGQYPLWMKNGEKCRTTLVQVVDNHIIKYIPPEEFKPNRKPYRGEP 170
I + LW + E + ++ K I P E K
Sbjct: 72 AIDARQLLWGEPVEAPTGGWTLLAESRGGKLIVPLELLLKNKLKSAAR 119
>gnl|CDD|202716 pfam03646, FlaG, FlaG protein. Although important for flagella the
exact function of this protein is unknown.
Length = 107
Score = 28.3 bits (64), Expect = 1.6
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 3/20 (15%)
Query: 143 VQVVDNH---IIKYIPPEEF 159
V+VVD +I+ IP EE
Sbjct: 70 VKVVDKETGEVIRQIPSEEA 89
>gnl|CDD|226763 COG4313, COG4313, Protein involved in meta-pathway of phenol
degradation [Energy production and conversion].
Length = 304
Score = 28.1 bits (63), Expect = 4.9
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 215 PDAMLPPGTPLTAA-----HFRPREFLDVRGLTVDRGFQG 249
PD PP TP A H+ +D G +V G
Sbjct: 42 PDGAAPPPTPGVAFAVYLNHYSASRLMDNSGNSVPVDVTG 81
>gnl|CDD|232924 TIGR00334, 5S_RNA_mat_M5, ribonuclease M5. This family of
orthologous proteins shows a weak but significant
similarity to the central region of the DnaG-type DNA
primase. The region of similarity is termed the Toprim
(topoisomerase-primase) domain and is also shared by
RecR, OLD family nucleases, and type IA and II
topoisomerases [Transcription, RNA processing].
Length = 174
Score = 27.9 bits (62), Expect = 5.4
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 94 IETYNTPLKIEPLQPLEITTSSKRTGLIGKIIGQYPLWMKNGEKCRTTLVQVVDNHIIKY 153
IET + LK E + I + K+ G+I +P GEK R + Q + + +
Sbjct: 26 IETNGSALKDETIN--LIKKAQKKQGVIILTDPDFP-----GEKIRKKIEQHLPGYENCF 78
Query: 154 IPPEEFKPNRK 164
IP KPN+K
Sbjct: 79 IPKHLAKPNKK 89
>gnl|CDD|181059 PRK07627, PRK07627, dihydroorotase; Provisional.
Length = 425
Score = 27.7 bits (62), Expect = 9.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 276 ASGAGKARVYPGGVLQRGLK 295
A +A VYP G L GLK
Sbjct: 113 ARNLNQAHVYPLGALTVGLK 132
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 27.7 bits (62), Expect = 9.8
Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 21/57 (36%)
Query: 214 TPDAMLPPGTPLTAAHFRPREFLD---------------------VRGLTVDRGFQG 249
+L P PL + RPR+ D +RGLTV+R F
Sbjct: 4 DDKTVLLPVGPLGYVYARPRDDEDLEELSLLSARSRDSDVAVAPLIRGLTVERDFVV 60
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
0.321 0.140 0.442
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,514,353
Number of extensions: 1497023
Number of successful extensions: 1081
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1074
Number of HSP's successfully gapped: 18
Length of query: 296
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 200
Effective length of database: 6,679,618
Effective search space: 1335923600
Effective search space used: 1335923600
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: 59 (26.4 bits)