RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 048058
(157 letters)
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 327 bits (840), Expect = e-113
Identities = 139/157 (88%), Positives = 149/157 (94%)
Query: 1 MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
AAAARPL++VQSL+GDMATD S+TV LPDVM A IRPDIV FVH+NISKNSRQPYAVS+
Sbjct: 1 AAAAARPLVSVQSLDGDMATDKSATVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSK 60
Query: 61 KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK WRRWHRK+N
Sbjct: 61 KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVN 120
Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
VNQKRYA+VSA+AASAVPSLVMARGHKIE VPE+PLV
Sbjct: 121 VNQKRYAVVSALAASAVPSLVMARGHKIENVPEVPLV 157
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 277 bits (710), Expect = 3e-94
Identities = 106/155 (68%), Positives = 123/155 (79%), Gaps = 3/155 (1%)
Query: 3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
ARP+++V S TVPLP V A IRPD+V FVH+N++KN RQ YAV A
Sbjct: 1 MTARPVVSVYSASDKSVV---GTVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLA 57
Query: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
G Q SAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHRK+N+N
Sbjct: 58 GMQHSAESWGTGRAVARIPRVSGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLN 117
Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
QKR+A+ SA+AAS VP+LVMARGH+I VPE+PLV
Sbjct: 118 QKRHAVASALAASGVPALVMARGHRISNVPEVPLV 152
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 132 bits (334), Expect = 5e-39
Identities = 61/148 (41%), Positives = 82/148 (55%), Gaps = 9/148 (6%)
Query: 10 TVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAE 69
V L+G++ + LP V + +RPD++ QP AG +TSAE
Sbjct: 4 KVYDLDGEVV----GEIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAE 59
Query: 70 SWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIV 129
SWG+GR ++R+PR+ GG + AF GGR P K+ + H KIN ++R AI
Sbjct: 60 SWGSGRGIARVPRLKGGS-----RAAFVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIR 114
Query: 130 SAIAASAVPSLVMARGHKIETVPEMPLV 157
SAIAA+A P LV ARGH E VPE+PLV
Sbjct: 115 SAIAATANPELVKARGHVFEGVPELPLV 142
>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 = 119 bits (301), Expect = 4e-34
Identities = 59/149 (39%), Positives = 81/149 (54%), Gaps = 10/149 (6%)
Query: 9 ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
V L+G++ + LP V + +RPD++ N QPY AG +TSA
Sbjct: 3 AKVYDLDGEVV----GEIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSA 58
Query: 69 ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAI 128
ESWG+GR ++R+PR+ GG + A GGR P K+ + H KIN ++R AI
Sbjct: 59 ESWGSGRGIARVPRIKGGS-----RAARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAI 113
Query: 129 VSAIAASAVPSLVMARGHKIETVPEMPLV 157
SAIAA+A P LV ARGH E E+P+V
Sbjct: 114 RSAIAATADPELVKARGHVFEGD-ELPIV 141
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 98.4 bits (246), Expect = 2e-26
Identities = 33/149 (22%), Positives = 57/149 (38%), Gaps = 13/149 (8%)
Query: 6 RPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQ 65
+ V L+G+ + LP+V D++ N RQ ++ G
Sbjct: 1 MMKLKVYDLDGE---EVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEV 57
Query: 66 TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKR 125
+ G+ + R + RGG + K R + +K+N ++R
Sbjct: 58 SGGGKKPWGQKGTGRARQGSIRS---------PQWRGGGVAHGPKPERDYSQKLNKKERR 108
Query: 126 YAIVSAIAASAVP-SLVMARGHKIETVPE 153
A+ SA++A A LV+ RGH E P+
Sbjct: 109 LALRSALSAKARAGKLVVVRGHVFEDAPK 137
>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 = 79.4 bits (197), Expect = 3e-19
Identities = 33/123 (26%), Positives = 49/123 (39%), Gaps = 22/123 (17%)
Query: 29 PDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAE--SW----GTGRAVSRIPR 82
P V A IRPD++ N RQ A + K + S GTGRA R
Sbjct: 5 PAVFGAEIRPDLLHRAVVAQLANRRQGTAST-KTRSEVSGGGKKPWRQKGTGRA--RAGS 61
Query: 83 VPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVM 142
+ R+ + RGG + K R + K+N +R A+ SA++A A ++
Sbjct: 62 I------RS------PLWRGGGVAFGPKP-RDYSYKLNKKVRRLALRSALSAKAREGKLV 108
Query: 143 ARG 145
Sbjct: 109 VVD 111
>gnl|CDD|99983 cd03812, GT1_CapH_like, This family is most closely related to the
GT1 family of glycosyltransferases. capH in
Staphylococcus aureus has been shown to be required for
the biosynthesis of the type 1 capsular polysaccharide
(CP1).
Length = 358
Score = 28.0 bits (63), Expect = 2.6
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 30 DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAG 63
++K + + DIV H + S S ++KAG
Sbjct: 74 KLIKKN-KYDIV---HVHGSSASGFILLAAKKAG 103
>gnl|CDD|224610 COG1696, DltB, Predicted membrane protein involved in D-alanine
export [Cell envelope biogenesis, outer membrane].
Length = 425
Score = 27.3 bits (61), Expect = 3.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 112 WRRWHRKINVNQKRY 126
WRRWH ++ + Y
Sbjct: 277 WRRWHMSLSTWFRDY 291
>gnl|CDD|215324 PLN02604, PLN02604, oxidoreductase.
Length = 566
Score = 27.5 bits (61), Expect = 3.8
Identities = 16/44 (36%), Positives = 19/44 (43%)
Query: 43 FVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG 86
FV N+ S + Y+V KA S W T VSR P G
Sbjct: 269 FVVKNLFIYSGETYSVLVKADQDPSRNYWVTTSVVSRNNTTPPG 312
>gnl|CDD|184996 PRK15036, PRK15036, hydroxyisourate hydrolase; Provisional.
Length = 137
Score = 26.9 bits (59), Expect = 3.8
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 124 KRYAIVSAIAAS-AVPSLVMARGHKIETV 151
KRY ++S I A+ ++PSLV A I +V
Sbjct: 3 KRYLVLSVITAAFSLPSLVYAAQQNILSV 31
>gnl|CDD|225110 COG2200, Rtn, c-di-GMP phosphodiesterase class I (EAL domain)
[Signal transduction mechanisms].
Length = 256
Score = 26.9 bits (60), Expect = 4.3
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 110 KIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPE 153
KI R + R + + + AIV AI A +A + V E
Sbjct: 176 KIDRSFVRDLETDARDQAIVRAIVA-------LAHKLGLTVVAE 212
>gnl|CDD|115784 pfam07153, Marek_SORF3, Marek's disease-like virus SORF3 protein.
This family consists of several SORF3 proteins from the
Marek's disease-like viruses. Members of this family are
around 350 residues in length. The function of this
family is unknown.
Length = 348
Score = 26.8 bits (59), Expect = 5.4
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 78 SRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKI 119
R RAG G G G ++ ++WR + +++
Sbjct: 282 YESIRARYPSGTRAGYGTTGRPNNGRFKYSRFQVWRNYPQRV 323
>gnl|CDD|215622 PLN03189, PLN03189, Protease specific for SMALL UBIQUITIN-RELATED
MODIFIER (SUMO); Provisional.
Length = 490
Score = 26.4 bits (58), Expect = 7.7
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 46 SNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVP 84
+ISK R A + +G+Q S+ S SRI R P
Sbjct: 25 FHISKKPRFSMAQTPDSGNQHSSNS-----TASRISRYP 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
0.319 0.130 0.393
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,823,214
Number of extensions: 670430
Number of successful extensions: 531
Number of sequences better than 10.0: 1
Number of HSP's gapped: 522
Number of HSP's successfully gapped: 21
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
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: 55 (25.0 bits)