RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025562
(251 letters)
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 206 bits (526), Expect = 3e-67
Identities = 67/120 (55%), Positives = 88/120 (73%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ V N ++ G + L+ VF V + ++H+VV QLA +QGTH+TKT SEVSG GKK
Sbjct: 3 LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62
Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
PWRQKGTGRAR G++R PQ+RGG + GPKPR ++ KLNKKVRRL L+ ALS +A EG++
Sbjct: 63 PWRQKGTGRARQGSIRSPQWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRL 122
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family are
ribosomal protein L4. This model recognizes bacterial
and most organellar forms, but excludes homologs from
the eukaryotic cytoplasm and from archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 190 bits (485), Expect = 4e-61
Identities = 65/113 (57%), Positives = 81/113 (71%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF + + ++H+VV+ QLA R+QGTH TKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LNDAVFGIEPNEHLLHQVVKAQLANRRQGTHKTKTRSEVSGGGKKPWRQKGTGRARQGSI 62
Query: 176 RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSL 228
R P +RGG GPKPR ++ KLNKKVRRL L+ ALS +A EGK+ + L
Sbjct: 63 RSPLWRGGGVAFGPKPRDYSYKLNKKVRRLALRSALSEKAREGKLVVVDDFDL 115
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 187 bits (478), Expect = 5e-60
Identities = 72/126 (57%), Positives = 84/126 (66%), Gaps = 8/126 (6%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF IR D++HR V QLA R+QGT STKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LPPAVFGAEIRPDLLHRAVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAGSI 62
Query: 176 RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFS 235
R P +RGG GPKPR ++ KLNKKVRRL L+ ALSA+A EGK L + F
Sbjct: 63 RSPLWRGGGVAFGPKPRDYSYKLNKKVRRLALRSALSAKAREGK--------LVVVDDFE 114
Query: 236 LSLKNT 241
L + T
Sbjct: 115 LEIPKT 120
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 166 bits (423), Expect = 2e-51
Identities = 69/121 (57%), Positives = 85/121 (70%), Gaps = 1/121 (0%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ V + E+ G + L +VF +D+IHR V QLA R+QGTHSTKT EVSG GKK
Sbjct: 4 LKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKK 63
Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAEGK 219
PW QKGTGRAR G++R PQ+RGG HGPKP R ++ KLNKK RRL L+ ALSA+A GK
Sbjct: 64 PWGQKGTGRARQGSIRSPQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGK 123
Query: 220 V 220
+
Sbjct: 124 L 124
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 137 bits (347), Expect = 3e-39
Identities = 61/128 (47%), Positives = 83/128 (64%)
Query: 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG 158
V ++ + G L VFDV +IH+VV Q+A +QGTH TKT +EV G G
Sbjct: 2 ATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGG 61
Query: 159 KKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEG 218
KKPWRQKGTGRAR G++R PQ+RGG T+HGP+PR + + KK+R+ L+ ALS RA +
Sbjct: 62 KKPWRQKGTGRARQGSIRAPQWRGGGTVHGPRPREYNQRTPKKMRQAALRGALSDRARDN 121
Query: 219 KVSLSVSL 226
++ + SL
Sbjct: 122 RLIVVESL 129
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 115 bits (289), Expect = 2e-31
Identities = 45/86 (52%), Positives = 62/86 (72%)
Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHG 188
++HR + Q ++QGT STKT SEV G G+KPW+QKGTGRAR G+ R P ++GG + G
Sbjct: 37 LLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNRSPLWKGGGVIFG 96
Query: 189 PKPRSHAIKLNKKVRRLGLKIALSAR 214
PKP++++ KLNKK RRL L+ L +
Sbjct: 97 PKPKTYSNKLNKKERRLALRTLLYNK 122
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 101 bits (254), Expect = 1e-25
Identities = 47/83 (56%), Positives = 55/83 (66%), Gaps = 1/83 (1%)
Query: 139 AKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-RSHAIK 197
A R+QGTH KT +EVSGTGKKPWRQKGTGRAR G+ R P F GG GP P R++ +K
Sbjct: 130 ASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSPIFVGGGRAFGPTPERNYKLK 189
Query: 198 LNKKVRRLGLKIALSARAAEGKV 220
+NKKVR AL+ A V
Sbjct: 190 VNKKVRFNAFVSALTLLANSKAV 212
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 61.0 bits (149), Expect = 4e-11
Identities = 36/107 (33%), Positives = 48/107 (44%), Gaps = 15/107 (14%)
Query: 119 DVFDVPIRKDIIHRVVRWQLAKRQQ--GT-------HSTKTISEVSGTGKKPWRQKGTGR 169
VF+ P+R D+I R V R Q G S ++ G + P R KG R
Sbjct: 20 AVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVP-RLKGGSR 78
Query: 170 ARHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARA 215
A PQ GG H PK + K+NKK RRL ++ A++A A
Sbjct: 79 AA----FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATA 121
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P. One of the
primary rRNA binding proteins, this protein initially
binds near the 5'-end of the 23S rRNA. It is important
during the early stages of 50S assembly. It makes
multiple contacts with different domains of the 23S rRNA
in the assembled 50S subunit and ribosome.
Length = 251
Score = 55.3 bits (134), Expect = 3e-09
Identities = 37/106 (34%), Positives = 49/106 (46%), Gaps = 15/106 (14%)
Query: 120 VFDVPIRKDIIHRVVRWQLAKRQQ--GT-------HSTKTISEVSGTGKKPWRQKGTGRA 170
VF+ P+R D+I R V R Q G S ++ G + P R KG RA
Sbjct: 21 VFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVP-RIKGGSRA 79
Query: 171 RHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARA 215
R PQ GG H PK + K+NKK RRL ++ A++A A
Sbjct: 80 A----RVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATA 121
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 33.6 bits (77), Expect = 0.076
Identities = 43/130 (33%), Positives = 53/130 (40%), Gaps = 18/130 (13%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAK--RQQGTHSTK----TISE 153
V + DK V DV PIR DI+ V ++K RQ S K T +E
Sbjct: 11 VQSLDGDMATDKSATVALPDVMTAPIRPDIV-NFVHTNISKNSRQPYAVSKKAGHQTSAE 69
Query: 154 VSGTGKKPWR-----QKGTGRARHGTLRGPQFRGGTTMHGPKP---RSHAIKLNKKVRRL 205
GTG+ R GT RA G G RGG M P R H K+N +R
Sbjct: 70 SWGTGRAVSRIPRVPGGGTHRAGQGAF-GNMCRGG-RMFAPTKTWRRWHR-KVNVNQKRY 126
Query: 206 GLKIALSARA 215
+ AL+A A
Sbjct: 127 AVVSALAASA 136
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 30.0 bits (68), Expect = 1.2
Identities = 36/122 (29%), Positives = 49/122 (40%), Gaps = 31/122 (25%)
Query: 120 VFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTIS------EVSGTGKKPWR-----QKGTG 168
VF PIR D++ V +AK ++ ++ K ++ E GTG+ R GT
Sbjct: 26 VFTAPIRPDLVQFVHT-NMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIPRVSGGGTH 84
Query: 169 RARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIAL--------SARAAEGKV 220
R+ G G RGG M P K RR K+ L SA AA G
Sbjct: 85 RSGQGAF-GNMCRGG-RMFAP---------TKTWRRWHRKVNLNQKRHAVASALAASGVP 133
Query: 221 SL 222
+L
Sbjct: 134 AL 135
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 28.8 bits (65), Expect = 3.1
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 79 DLLLKKTVLT----PDITIGLHQDLVIP-VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRV 133
+ + V+T + I L V P V E +++ DV + ++++II R
Sbjct: 97 GIEIDNYVITIPADGEKVIELEGLKVPPCVVEIEGEKGTIILIFKDVGESELKRNIIDRA 156
Query: 134 VR---WQLAKRQQGT 145
++ +L K + T
Sbjct: 157 IKLVEEKLEKLEDLT 171
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 28.3 bits (63), Expect = 4.2
Identities = 25/88 (28%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 12 RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDS 71
R+ F R E + ++ + SP L V S + L L LA T++ D
Sbjct: 235 RYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKL----GSLVQLA-----TSLYECDY 285
Query: 72 SEGAFPSDLLLKKTVLTPDITIGLHQDL 99
G F + L L L D+ +G H DL
Sbjct: 286 G-GDFMNLLYLFCNSLQDDVFLGRHVDL 312
>gnl|CDD|185270 PRK15372, PRK15372, pathogenicity island 2 effector protein SseI;
Provisional.
Length = 292
Score = 28.2 bits (62), Expect = 4.4
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 67 LTPDSSEGAFPSDL----LLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGF 113
LT D A+ +L ++ ++ P +G + L+ PV+NF NE KGF
Sbjct: 118 LTSDIDAAAYLEELKQNPIINNKIMNP---VGQCESLMTPVSNFMNE-KGF 164
>gnl|CDD|217509 pfam03353, Lin-8, Ras-mediated vulval-induction antagonist. LIN-8
is a nuclear protein, present at the sites of
transcriptional repressor complexes, which interacts
with LIN-35 Rb.Lin35 Rb is a product of the class B
synMuv gene lin-35 which silences genes required for
vulval specification through chromatin modification and
remodelling. The biological role of the interaction has
not yet been determined however predictions have been
made. The interaction shows that class A synMuv genes
control vulval induction through the transcriptional
regulation of gene expression. LIN-8 normally functions
as part of a protein complex however when the complex is
absent, other family members can partially replace LIN-8
activity.
Length = 316
Score = 27.4 bits (61), Expect = 8.5
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 76 FPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVF 121
D+ LKK VL+ + ++ T + + ++ +V+
Sbjct: 18 ATKDVTLKKVVLS---LLEKRPEMWKRNTRGQAKK--WAIVGVEVY 58
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 0.135 0.394
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,756,335
Number of extensions: 1204420
Number of successful extensions: 902
Number of sequences better than 10.0: 1
Number of HSP's gapped: 896
Number of HSP's successfully gapped: 21
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
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: 58 (26.1 bits)