RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022312
(299 letters)
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 245 bits (628), Expect = 7e-82
Identities = 87/175 (49%), Positives = 118/175 (67%), Gaps = 2/175 (1%)
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 LVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
+V +DL + + KTK + + KKVL+ + E L L+ +NL V+VLP
Sbjct: 123 VVVDDLSLEAPKTKELAAKLKNL-GLKKVLIVTDE-VDENLYLSARNLPNVDVLP 175
>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 = 232 bits (595), Expect = 3e-77
Identities = 83/160 (51%), Positives = 107/160 (66%), Gaps = 1/160 (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 IVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
+ + KKVL+ + E L L+ +NL V VLP
Sbjct: 123 LAKILKNLGLDKKVLIVTDE-VDENLYLSARNLPNVKVLP 161
>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 = 224 bits (573), Expect = 1e-73
Identities = 87/161 (54%), Positives = 106/161 (65%), Gaps = 2/161 (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-NTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
V + KKVL+ E L L+ +NL V+V+
Sbjct: 123 AVKLLKNLGLKNKKVLIVVDE-KDENLYLSARNLPGVDVVT 162
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 197 bits (504), Expect = 5e-63
Identities = 86/180 (47%), Positives = 110/180 (61%), Gaps = 2/180 (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-PSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVV 278
L+V + KTK +V + ++ K LL G KL+ +NL V V+ V
Sbjct: 124 LVVVRGHVFEDAPKTKELVEFLKKLGLDVKRLLIVKGERDGNGKLSARNLKNVKVVLVVG 183
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 151 bits (382), Expect = 8e-44
Identities = 69/156 (44%), Positives = 97/156 (62%), Gaps = 5/156 (3%)
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---EVPSHKTKFIVNYYNQMENTKKVLL 251
+L+V E L + P TK + + ME+ + +L+
Sbjct: 122 RLIVVESLQDGDPP--STKAVAQALSVMEDQRALLV 155
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 128 bits (324), Expect = 4e-36
Identities = 62/153 (40%), Positives = 92/153 (60%), Gaps = 13/153 (8%)
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---LKLATQNLHYVNVL 274
+K+L+ + EK L L+T+NL V ++
Sbjct: 155 LDQKILI----IVPEKTENLYLSTRNLKNVELI 183
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 109 bits (274), Expect = 4e-28
Identities = 59/138 (42%), Positives = 81/138 (58%), Gaps = 7/138 (5%)
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 CIHEKLKLATQNLHYVNV 273
E + + +NL V V
Sbjct: 248 --DENIFKSARNLQNVIV 263
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 62.9 bits (154), Expect = 2e-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 = 59.5 bits (145), Expect = 2e-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 = 35.2 bits (81), Expect = 0.035
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 = 29.6 bits (67), Expect = 1.7
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|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 28.9 bits (65), Expect = 3.3
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|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 28.1 bits (63), Expect = 5.9
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|198445 cd10477, EphR_LBD_B2, Ligand Binding Domain of Ephrin type-B
Receptor 2. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphB receptors bind to transmembrane ephrin-B
ligands. There are six vertebrate EhpB receptors
(EphB1-6), which display promiscuous interactions with
three ephrin-B ligands. EphB2 plays a role in cell
positioning in the gastrointestinal tract by being
expressed in proliferating progenitor cells. It also has
been implicated in colorectal cancer. A loss of EphB2,
as well as EphA4, also precedes memory decline in a
murine model of Alzheimers disease. EphRs contain a
ligand binding domain and two fibronectin repeats
extracellularly, a transmembrane segment, and a
cytoplasmic tyrosine kinase domain. Binding of the
ephrin ligand to EphR requires cell-cell contact since
both are anchored to the plasma membrane. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling).
Length = 178
Score = 27.3 bits (60), Expect = 7.6
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 3/39 (7%)
Query: 257 IHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFD 295
IH ++K + ++ + +PSV S ++F +YYY DFD
Sbjct: 68 IHVEMKFSVRD---CSSIPSVPGSCKETFNLYYYESDFD 103
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 27.6 bits (61), Expect = 8.6
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
0.322 0.138 0.407
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: 15,357,306
Number of extensions: 1458210
Number of successful extensions: 1067
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1057
Number of HSP's successfully gapped: 16
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
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)