RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13118
(286 letters)
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 262 bits (671), Expect = 5e-86
Identities = 106/142 (74%), Positives = 121/142 (85%), Gaps = 3/142 (2%)
Query: 19 ARPLITVYS---EKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGH 75
ARPL++V S + TV LP V APIRPD+VNFVH N+SKN RQPYAVSK AGH
Sbjct: 5 ARPLVSVQSLDGDMATDKSATVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGH 64
Query: 76 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQR 135
QTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCR GRMFAPT+ WRRWHRKVNVNQ+
Sbjct: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVNVNQK 124
Query: 136 RYAMVSAIAASSVPALVMSKGH 157
RYA+VSA+AAS+VP+LVM++GH
Sbjct: 125 RYAVVSALAASAVPSLVMARGH 146
Score = 227 bits (581), Expect = 2e-72
Identities = 102/170 (60%), Positives = 122/170 (71%), Gaps = 13/170 (7%)
Query: 116 MFAPTR--IWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARI 173
M AP R I H ++ N R+ VS A GHQTSAESWGTGRAV+RI
Sbjct: 32 MTAPIRPDIVNFVHTNISKNSRQPYAVSKKA-----------GHQTSAESWGTGRAVSRI 80
Query: 174 PRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPAL 233
PRV GGGTHR+GQGAFGNMCR GRMFAPT+ WRRWHRKVNVNQ+RYA+VSA+AAS+VP+L
Sbjct: 81 PRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAVPSL 140
Query: 234 VMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWNDVLKVQSS 283
VM++GH I++VPE PLVVSD + +KT A L +I A+ DV K + S
Sbjct: 141 VMARGHKIENVPEVPLVVSDSAESIEKTSAAIKILKQIGAYADVEKAKDS 190
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 256 bits (657), Expect = 4e-84
Identities = 101/142 (71%), Positives = 119/142 (83%)
Query: 19 ARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTS 78
ARP+++VYS ++ TV LP+VF APIRPD+V FVH N++KN RQ YAV AG Q S
Sbjct: 3 ARPVVSVYSASDKSVVGTVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGMQHS 62
Query: 79 AESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYA 138
AESWGTGRAVARIPRV GGGTHRSGQGAFGNMCR GRMFAPT+ WRRWHRKVN+NQ+R+A
Sbjct: 63 AESWGTGRAVARIPRVSGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLNQKRHA 122
Query: 139 MVSAIAASSVPALVMSKGHQTS 160
+ SA+AAS VPALVM++GH+ S
Sbjct: 123 VASALAASGVPALVMARGHRIS 144
Score = 228 bits (583), Expect = 6e-73
Identities = 91/128 (71%), Positives = 108/128 (84%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G Q SAESWGTGRAVARIPRV GGGTHRSGQGAFGNMCR GRMFAPT+ WRRWHRKVN+N
Sbjct: 58 GMQHSAESWGTGRAVARIPRVSGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLN 117
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
Q+R+A+ SA+AAS VPALVM++GH I +VPE PLVVSD ++ Y+KTK+A FL + A++
Sbjct: 118 QKRHAVASALAASGVPALVMARGHRISNVPEVPLVVSDSVESYEKTKEAVAFLKALGAFD 177
Query: 276 DVLKVQSS 283
DV +V S
Sbjct: 178 DVNRVNDS 185
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 121 bits (305), Expect = 6e-33
Identities = 52/126 (41%), Positives = 79/126 (62%), Gaps = 5/126 (3%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G +TSAESWG+GR +AR+PR++GG + AF GR P ++ + H K+N
Sbjct: 53 GKRTSAESWGSGRGIARVPRLKGGS-----RAAFVPQAVGGRRAHPPKVEKDLHEKINKK 107
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
+RR A+ SAIAA++ P LV ++GH+ + VPE PLVV D + KKTK+ L ++ ++
Sbjct: 108 ERRLAIRSAIAATANPELVKARGHVFEGVPELPLVVVDDFESLKKTKEVRELLEKLGLYD 167
Query: 276 DVLKVQ 281
DV + +
Sbjct: 168 DVERAK 173
Score = 115 bits (290), Expect = 7e-31
Identities = 52/135 (38%), Positives = 75/135 (55%), Gaps = 6/135 (4%)
Query: 24 TVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWG 83
VY E G + LP+VF+ P+RPD++ QP AG +TSAESWG
Sbjct: 4 KVYDLDGEVVG-EIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWG 62
Query: 84 TGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAI 143
+GR +AR+PR++GG + AF GR P ++ + H K+N +RR A+ SAI
Sbjct: 63 SGRGIARVPRLKGG-----SRAAFVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAI 117
Query: 144 AASSVPALVMSKGHQ 158
AA++ P LV ++GH
Sbjct: 118 AATANPELVKARGHV 132
>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 = 113 bits (285), Expect = 4e-30
Identities = 53/141 (37%), Positives = 77/141 (54%), Gaps = 6/141 (4%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESW 82
VY E G + LP+VF+ P+RPD++ N QPY AG +TSAESW
Sbjct: 3 AKVYDLDGEVVG-EIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESW 61
Query: 83 GTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 142
G+GR +AR+PR++GG + A GR P ++ + H K+N +RR A+ SA
Sbjct: 62 GSGRGIARVPRIKGG-----SRAARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSA 116
Query: 143 IAASSVPALVMSKGHQTSAES 163
IAA++ P LV ++GH +
Sbjct: 117 IAATADPELVKARGHVFEGDE 137
Score = 108 bits (271), Expect = 4e-28
Identities = 47/128 (36%), Positives = 75/128 (58%), Gaps = 6/128 (4%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G +TSAESWG+GR +AR+PR++GG + A GR P ++ + H K+N
Sbjct: 53 GKRTSAESWGSGRGIARVPRIKGGS-----RAARVPQAVGGRRAHPPKVEKDLHEKINKK 107
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
+RR A+ SAIAA++ P LV ++GH+ + E P+VV D + KKTK+ L + ++
Sbjct: 108 ERRLAIRSAIAATADPELVKARGHVFEGD-ELPIVVVDDFESLKKTKEVRELLEALGVYD 166
Query: 276 DVLKVQSS 283
D+ + +
Sbjct: 167 DIERAKEG 174
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 89.2 bits (222), Expect = 2e-21
Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 9/126 (7%)
Query: 20 RPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSA 79
+ VY E G+ LP VF D+++ N RQ +K G +
Sbjct: 1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGG 60
Query: 80 ESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAM 139
G+ R + R G + + R + +K+N +RR A+
Sbjct: 61 GKKPWGQKGTGRARQGSIRS---------PQWRGGGVAHGPKPERDYSQKLNKKERRLAL 111
Query: 140 VSAIAA 145
SA++A
Sbjct: 112 RSALSA 117
Score = 63.0 bits (154), Expect = 7e-12
Identities = 28/127 (22%), Positives = 49/127 (38%), Gaps = 26/127 (20%)
Query: 155 KGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNV 214
+G + G+ R + R G + + R + +K+N
Sbjct: 54 RGEVSGGGKKPWGQKGTGRARQGSIRS---------PQWRGGGVAHGPKPERDYSQKLNK 104
Query: 215 NQRRYAMVSAIAASSVP-ALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKA 273
+RR A+ SA++A + LV+ +GH+ +D P KTK+ FL K
Sbjct: 105 KERRLALRSALSAKARAGKLVVVRGHVFEDAP--------------KTKELVEFLK--KL 148
Query: 274 WNDVLKV 280
DV ++
Sbjct: 149 GLDVKRL 155
>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 = 81.4 bits (202), Expect = 1e-18
Identities = 29/118 (24%), Positives = 47/118 (39%), Gaps = 18/118 (15%)
Query: 40 PSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAE--SWGT--GRAVARIPRVR 95
P+VF A IRPD+++ N RQ A +K + S G AR +R
Sbjct: 5 PAVFGAEIRPDLLHRAVVAQLANRRQGTASTK-TRSEVSGGGKKPWRQKGTGRARAGSIR 63
Query: 96 GGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVM 153
+ R G + + R + K+N RR A+ SA++A + ++
Sbjct: 64 ------------SPLWRGGGVAFGPKP-RDYSYKLNKKVRRLALRSALSAKAREGKLV 108
Score = 53.6 bits (130), Expect = 9e-09
Identities = 28/112 (25%), Positives = 41/112 (36%), Gaps = 29/112 (25%)
Query: 165 GTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 224
GTGRA R +R + R G + + R + K+N RR A+ SA
Sbjct: 53 GTGRA--RAGSIRS------------PLWRGGGVAFGPKP-RDYSYKLNKKVRRLALRSA 97
Query: 225 IAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWND 276
++A + ++ VV D E KTK A L + N
Sbjct: 98 LSAKAREGKLV--------------VVDDFELEIPKTKDAVKLLKNLGLKNK 135
>gnl|CDD|182422 PRK10381, PRK10381, LPS O-antigen length regulator; Provisional.
Length = 377
Score = 31.2 bits (71), Expect = 0.54
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 210 RKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVV-SDKIQ 256
N+ + Y++ A AA + V S G ++D P+F + + +D ++
Sbjct: 233 LDANIQRLNYSLSIANAAG-IKKPVYSNGQAVKDDPDFSIALGADGLE 279
>gnl|CDD|114908 pfam06216, RTBV_P46, Rice tungro bacilliform virus P46 protein.
This family consists of several Rice tungro bacilliform
virus P46 proteins. The function of this family is
unknown.
Length = 392
Score = 30.0 bits (67), Expect = 1.5
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 244 VPE-FPLVVSDKIQEYKKTKQATIFLHR-IKAWN 275
+PE PL++++KI +YK TI + + I W+
Sbjct: 256 LPEGIPLIIAEKIMDYKFPGANTILIEKEIPKWD 289
>gnl|CDD|183726 PRK12756, PRK12756, phospho-2-dehydro-3-deoxyheptonate aldolase;
Provisional.
Length = 348
Score = 29.5 bits (67), Expect = 2.0
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 51 VVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWGTGRAVARI 91
VV+F H N K HR+ V++D Q S A+A I
Sbjct: 262 VVDFSHGNCQKQHRRQLDVAEDICQQIRNGS----TAIAGI 298
>gnl|CDD|181107 PRK07765, PRK07765, para-aminobenzoate synthase component II;
Provisional.
Length = 214
Score = 28.1 bits (63), Expect = 5.2
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 138 AMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGT---HRSGQGAF 189
MV A AA+ P L + GHQ ++G V R P + G T H +G G
Sbjct: 67 DMVRACAAAGTPLLGVCLGHQAIGVAFGA--TVDRAPELLHGKTSSVHHTGVGVL 119
>gnl|CDD|236236 PRK08315, PRK08315, AMP-binding domain protein; Validated.
Length = 559
Score = 27.9 bits (63), Expect = 6.5
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 244 VPEFPLVVSDKIQEYK 259
V EFP+ V+ KIQ++K
Sbjct: 529 VDEFPMTVTGKIQKFK 544
>gnl|CDD|224610 COG1696, DltB, Predicted membrane protein involved in D-alanine
export [Cell envelope biogenesis, outer membrane].
Length = 425
Score = 27.7 bits (62), Expect = 7.3
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 123 WRRWHRKVNVNQRRY 137
WRRWH ++ R Y
Sbjct: 277 WRRWHMSLSTWFRDY 291
Score = 27.7 bits (62), Expect = 7.3
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 205 WRRWHRKVNVNQRRY 219
WRRWH ++ R Y
Sbjct: 277 WRRWHMSLSTWFRDY 291
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 27.6 bits (61), Expect = 8.0
Identities = 26/71 (36%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 76 QTSAESWGTGRAVARIP-RVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQ 134
+T AE GTG+ P R +G G R+G GR F PT R + KVN
Sbjct: 140 KTRAEVSGTGKK----PWRQKGTGRARAGSTRSPIFVGGGRAFGPTPE-RNYKLKVNKKV 194
Query: 135 RRYAMVSAIAA 145
R A VSA+
Sbjct: 195 RFNAFVSALTL 205
Score = 27.6 bits (61), Expect = 8.0
Identities = 26/71 (36%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 158 QTSAESWGTGRAVARIP-RVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQ 216
+T AE GTG+ P R +G G R+G GR F PT R + KVN
Sbjct: 140 KTRAEVSGTGKK----PWRQKGTGRARAGSTRSPIFVGGGRAFGPTPE-RNYKLKVNKKV 194
Query: 217 RRYAMVSAIAA 227
R A VSA+
Sbjct: 195 RFNAFVSALTL 205
>gnl|CDD|144353 pfam00720, SSI, Subtilisin inhibitor-like.
Length = 95
Score = 26.1 bits (58), Expect = 9.8
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 150 ALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGA 188
ALV++ G SA + RAV GTH + A
Sbjct: 5 ALVLTVGQGESAATATVQRAVTLTCAPTASGTHPAPAAA 43
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 0.132 0.413
Gapped
Lambda K H
0.267 0.0550 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,302,198
Number of extensions: 1309346
Number of successful extensions: 1067
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 27
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
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 (22.0 bits)
S2: 58 (26.5 bits)