RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021591
(310 letters)
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 280 bits (719), Expect = 1e-95
Identities = 99/203 (48%), Positives = 139/203 (68%), Gaps = 2/203 (0%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ V N ++ G + L+ VF V + ++H+VV QLA +QGTH+TKT SEVSG GKK
Sbjct: 3 LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62
Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKL 220
PWRQKGTGRAR G++R PQ+RGG + GPKPR ++ KLNKKVRRL L+ ALS +A EG+L
Sbjct: 63 PWRQKGTGRARQGSIRSPQWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRL 122
Query: 221 LVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLN 280
+V +DL + + KTK + + KKVL+ + E L L+ +NL V+VLP+ GLN
Sbjct: 123 VVVDDLSLEAPKTKELAAKLKNL-GLKKVLIVTDE-VDENLYLSARNLPNVDVLPAQGLN 180
Query: 281 VYSILQHDTLVMSRDAVNKIVDR 303
VY +L+ D +V+++ AV K+ +R
Sbjct: 181 VYDLLRADKVVLTKAAVKKLEER 203
>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 = 266 bits (682), Expect = 3e-90
Identities = 94/187 (50%), Positives = 126/187 (67%), Gaps = 1/187 (0%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF + + ++H+VV+ QLA R+QGTH TKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LNDAVFGIEPNEHLLHQVVKAQLANRRQGTHKTKTRSEVSGGGKKPWRQKGTGRARQGSI 62
Query: 176 RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKF 235
R P +RGG GPKPR ++ KLNKKVRRL L+ ALS +A EGKL+V +D ++ KTK
Sbjct: 63 RSPLWRGGGVAFGPKPRDYSYKLNKKVRRLALRSALSEKAREGKLVVVDDFDLEEPKTKD 122
Query: 236 IVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSRD 295
+ + KKVL+ + E L L+ +NL V VLP+ GLNVY +L+ D +V++
Sbjct: 123 LAKILKNLGLDKKVLIVTDE-VDENLYLSARNLPNVKVLPANGLNVYDLLRADKVVLTEA 181
Query: 296 AVNKIVD 302
AV K+ +
Sbjct: 182 AVEKLEE 188
>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 = 255 bits (655), Expect = 5e-86
Identities = 98/189 (51%), Positives = 125/189 (66%), Gaps = 2/189 (1%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF IR D++HR V QLA R+QGT STKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LPPAVFGAEIRPDLLHRAVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAGSI 62
Query: 176 RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKF 235
R P +RGG GPKPR ++ KLNKKVRRL L+ ALSA+A EGKL+V +D E+ KTK
Sbjct: 63 RSPLWRGGGVAFGPKPRDYSYKLNKKVRRLALRSALSAKAREGKLVVVDDFELEIPKTKD 122
Query: 236 IVNYYNQME-NTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSR 294
V + KKVL+ E L L+ +NL V+V+ GLNVY +L D +V+++
Sbjct: 123 AVKLLKNLGLKNKKVLIVVDE-KDENLYLSARNLPGVDVVTVDGLNVYDLLPADKVVITK 181
Query: 295 DAVNKIVDR 303
A+ K+ +R
Sbjct: 182 SALEKLEER 190
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 219 bits (559), Expect = 4e-71
Identities = 97/206 (47%), Positives = 127/206 (61%), Gaps = 3/206 (1%)
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 LLVFEDLEV-PSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVG 278
L+V + KTK +V + ++ K LL G KL+ +NL V V+ VG
Sbjct: 124 LVVVRGHVFEDAPKTKELVEFLKKLGLDVKRLLIVKGERDGNGKLSARNLKNVKVVLVVG 183
Query: 279 -LNVYSILQHDTLVMSRDAVNKIVDR 303
L V +L+ D LV+++ A KI +R
Sbjct: 184 GLPVVDVLRADKLVITKLAPGKIEER 209
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 161 bits (409), Expect = 9e-48
Identities = 83/208 (39%), Positives = 123/208 (59%), Gaps = 10/208 (4%)
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 KLLVFEDL-EVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKL----KLATQNLHYVNV 273
+L+V E L + TK + + ME+ + +L+ + E+ +L+ +NL V+V
Sbjct: 122 RLIVVESLQDGDPPSTKAVAQALSVMEDQRALLV-----VAERSDAVERLSVRNLARVHV 176
Query: 274 LPSVGLNVYSILQHDTLVMSRDAVNKIV 301
L + LN Y +L D +V ++ A+ V
Sbjct: 177 LGADQLNTYDVLNVDWVVFTQSALEAFV 204
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 145 bits (368), Expect = 2e-42
Identities = 68/179 (37%), Positives = 109/179 (60%), Gaps = 13/179 (7%)
Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHG 188
++HR + Q ++QGT STKT SEV G G+KPW+QKGTGRAR G+ R P ++GG + G
Sbjct: 37 LLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNRSPLWKGGGVIFG 96
Query: 189 PKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSH--KTKFIVNYYNQME-- 244
PKP++++ KLNKK RRL L+ L + + V E+ E KTK +N ++
Sbjct: 97 PKPKTYSNKLNKKERRLALRTLLYNK--SNNITVVENFESSITNPKTKAFINLLKKLNIN 154
Query: 245 NTKKVLLCDGGCIHEK---LKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSRDAVNKI 300
+K+L+ + EK L L+T+NL V ++ + LN+ S+L+ ++++++A+ I
Sbjct: 155 LDQKILI----IVPEKTENLYLSTRNLKNVELISADTLNIKSLLKAKQIIITKEALKII 209
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 117 bits (294), Expect = 6e-31
Identities = 65/162 (40%), Positives = 96/162 (59%), Gaps = 7/162 (4%)
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 LNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQME--NTKKVLLCDGG 255
+NKKVR AL+ A +LV +D ++ TK ++ +++ N K +L+
Sbjct: 190 VNKKVRFNAFVSALTLLANSKAVLV-DDFKLEKISTKDLIKKLTKLKINNLKHILIVSN- 247
Query: 256 CIHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSRDAV 297
E + + +NL V V+ L+V ++ D LV+S++++
Sbjct: 248 --DENIFKSARNLQNVIVVKPTSLSVELLIAADVLVLSKESI 287
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 62.2 bits (152), Expect = 3e-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 = 58.8 bits (143), Expect = 4e-10
Identities = 44/126 (34%), Positives = 57/126 (45%), Gaps = 23/126 (18%)
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------AEGKLLVF 223
R PQ GG H PK + K+NKK RRL ++ A++A A A G VF
Sbjct: 80 A----RVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGH--VF 133
Query: 224 EDLEVP 229
E E+P
Sbjct: 134 EGDELP 139
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 34.8 bits (80), Expect = 0.057
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|239004 cd02049, bacterial_SERPIN, SERine Proteinase INhibitors (serpins),
prokaryotic subgroup. Little information about specific
functions is available for this subgroup, most likely
they are inhibitory members of the serpin superfamily.
In general, serpins exhibit conformational polymorphism
shifting from native to cleaved, latent, delta, or
polymorphic forms. Many serpins, such as antitrypsin and
antichymotrypsin, function as serine protease
inhibitors.
Length = 364
Score = 30.0 bits (68), Expect = 1.4
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 14/85 (16%)
Query: 157 TGKKPWRQ-KGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARA 215
T +K WR+ R R G+L P+F+ I+L ++ LG++ A + A
Sbjct: 240 TAEK-WRKWIEQFRMREGSLSLPRFQLEYE----------IELRDALKALGMEEAFTPDA 288
Query: 216 AEGKLLVFEDLEVPS--HKTKFIVN 238
A+ L +L + HKT VN
Sbjct: 289 ADFSKLGEGNLYISKVIHKTFIEVN 313
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 28.4 bits (64), Expect = 4.9
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|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 28.5 bits (64), Expect = 5.5
Identities = 35/118 (29%), Positives = 47/118 (39%), Gaps = 31/118 (26%)
Query: 120 VFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTIS------EVSGTGKKPWR-----QKGTG 168
VF PIR D++ V +AK ++ ++ K ++ E GTG+ R GT
Sbjct: 26 VFTAPIRPDLVQFVHT-NMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIPRVSGGGTH 84
Query: 169 RARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIAL--------SARAAEG 218
R+ G G RGG M P K RR K+ L SA AA G
Sbjct: 85 RSGQGAF-GNMCRGG-RMFAP---------TKTWRRWHRKVNLNQKRHAVASALAASG 131
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 28.0 bits (62), Expect = 7.4
Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 10/88 (11%)
Query: 12 RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDS 71
R+ F R E + ++ + SP L V S + L L + L +
Sbjct: 235 RYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYG-------- 286
Query: 72 SEGAFPSDLLLKKTVLTPDITIGLHQDL 99
G F + L L L D+ +G H DL
Sbjct: 287 --GDFMNLLYLFCNSLQDDVFLGRHVDL 312
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 0.137 0.402
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: 15,808,118
Number of extensions: 1507003
Number of successful extensions: 1068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1054
Number of HSP's successfully gapped: 15
Length of query: 310
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 213
Effective length of database: 6,635,264
Effective search space: 1413311232
Effective search space used: 1413311232
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 (21.9 bits)
S2: 59 (26.5 bits)