RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9578
(122 letters)
>gnl|CDD|179959 PRK05185, rplT, 50S ribosomal protein L20; Provisional.
Length = 114
Score = 186 bits (475), Expect = 9e-63
Identities = 70/114 (61%), Positives = 91/114 (79%)
Query: 2 PRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLW 61
RVKRGV ARAR KK+LK AKGY G R+ +YRVAKQAVM A+QYAYRDRR KKR FR LW
Sbjct: 1 ARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQKKRDFRKLW 60
Query: 62 ISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKE 115
I+RINAA R++ ++Y+ F+NGLKK+ I++DRK+LA +A+ D F+++V + K
Sbjct: 61 IARINAAARQNGLSYSRFINGLKKAGIEIDRKVLADLAVNDPAAFAALVEKAKA 114
>gnl|CDD|223369 COG0292, RplT, Ribosomal protein L20 [Translation, ribosomal
structure and biogenesis].
Length = 118
Score = 173 bits (441), Expect = 2e-57
Identities = 73/117 (62%), Positives = 93/117 (79%)
Query: 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSL 60
M RVKRGV ARAR KK+LK AKGY G R+ +YRVAKQAVM A+QYAYRDRR +KR FR L
Sbjct: 1 MARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQRKRDFRKL 60
Query: 61 WISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117
WI+RINAA RE+ ++Y+ F+NGLKK+ I++DRK+LA +AI D F+++V + K L
Sbjct: 61 WIARINAAARENGLSYSRFINGLKKAGIEIDRKVLADLAINDPAAFAALVEKAKAAL 117
>gnl|CDD|201238 pfam00453, Ribosomal_L20, Ribosomal protein L20.
Length = 108
Score = 161 bits (410), Expect = 5e-53
Identities = 65/108 (60%), Positives = 85/108 (78%)
Query: 2 PRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLW 61
RVKRGV AR R KK+LK AKG+ G R+ ++R AKQ VM A+QYAYRDR+ KKR FR LW
Sbjct: 1 TRVKRGVVARKRRKKILKLAKGFRGARSKLFRTAKQQVMKALQYAYRDRKKKKRDFRRLW 60
Query: 62 ISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSI 109
I+RINAA REH ++Y+ F+NGLKK++I+L+RK+LA +AI D F ++
Sbjct: 61 ITRINAAAREHGLSYSRFINGLKKANIELNRKVLAQLAINDPEAFKAL 108
>gnl|CDD|197305 cd07026, Ribosomal_L20, Ribosomal protein L20. The ribosomal
protein family L20 contains members from eubacteria, as
well as their mitochondrial and plastid homologs. L20 is
an assembly protein, required for the first in-vitro
reconstitution step of the 50S ribosomal subunit, but
does not seem to be essential for ribosome activity. L20
has been shown to partially unfold in the absence of
RNA, in regions corresponding to the RNA-binding sites.
L20 represses the translation of its own mRNA via
specific binding to two distinct mRNA sites, in a manner
similar to the L20 interaction with 23S ribosomal RNA. .
Length = 106
Score = 153 bits (389), Expect = 8e-50
Identities = 63/106 (59%), Positives = 83/106 (78%)
Query: 6 RGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRI 65
RGV AR R KK+LK AKG+ GRR+ ++R AKQAVM A+ YAYRDR+ KKR FR LWI+RI
Sbjct: 1 RGVVARKRRKKILKLAKGFRGRRSRLFRTAKQAVMKALAYAYRDRKQKKRDFRRLWITRI 60
Query: 66 NAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVN 111
NAA REH ++Y+ F++GLKK++I L+RK+LA +AI D F ++V
Sbjct: 61 NAAAREHGLSYSRFIHGLKKANILLNRKVLAQLAILDPKAFKALVE 106
>gnl|CDD|130104 TIGR01032, rplT_bact, ribosomal protein L20. This model describes
bacterial ribosomal protein L20 and its chloroplast
equvalent. This protein binds directly to 23s ribosomal
RNA and is necessary for the in vitro assembly process
of the 50s ribosomal subunit. It is not involved in the
protein synthesizing functions of that subunit. GO
process changed accordingly (SS 5/09/03) [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 144 bits (365), Expect = 4e-46
Identities = 68/112 (60%), Positives = 87/112 (77%)
Query: 3 RVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWI 62
RVKRGV AR R KK+LKQAKG+ G R YRVAKQ V+ AM YAYRDRR +KR FRSLWI
Sbjct: 2 RVKRGVVARRRRKKILKQAKGFRGTRKRHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLWI 61
Query: 63 SRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114
+RINAA R+H ++Y+ F+NGLKK++I+++RK+L+ +AI D F IV + K
Sbjct: 62 TRINAAARQHGLSYSRFINGLKKANIEINRKVLSELAINDPEAFKEIVEKAK 113
>gnl|CDD|214352 CHL00068, rpl20, ribosomal protein L20.
Length = 115
Score = 130 bits (330), Expect = 1e-40
Identities = 58/114 (50%), Positives = 79/114 (69%)
Query: 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSL 60
M RVKRG AR R KK+LK A G+ G + ++R A Q M A+ +YRDR+ KKR FR L
Sbjct: 1 MTRVKRGYIARKRRKKILKFASGFRGAHSRLFRTANQQKMKALVSSYRDRKKKKRDFRRL 60
Query: 61 WISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114
WI+RINAA+RE+ ++Y+ F++ L K+ I L+RK+LA IAI D F +I N+I
Sbjct: 61 WITRINAAIRENGVSYSKFIHNLYKNQILLNRKILAQIAILDPNCFYTISNKII 114
>gnl|CDD|185406 PTZ00030, PTZ00030, 60S ribosomal protein L20; Provisional.
Length = 121
Score = 105 bits (265), Expect = 8e-31
Identities = 49/105 (46%), Positives = 72/105 (68%)
Query: 10 ARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAV 69
+ KV K AKG+ GR + +++A+ VM A+ Y+Y RR +KR+ R WI INAA
Sbjct: 1 MKIPRDKVFKLAKGFRGRSKNCFKLARNRVMKALLYSYISRRKRKRILRVHWIQTINAAT 60
Query: 70 REHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114
REH MTY+ F+NGL S+IQL+RK+LA++AIT+ F ++V++ K
Sbjct: 61 REHNMTYSRFINGLNNSNIQLNRKILANLAITEPFSFKALVDESK 105
>gnl|CDD|237748 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
protein; Provisional.
Length = 230
Score = 100 bits (251), Expect = 2e-27
Identities = 48/108 (44%), Positives = 70/108 (64%)
Query: 13 RHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREH 72
R KKVLK AKGYFG ++++Y+ A + VM ++QYAYRDR+ +KR FR LWISRINA
Sbjct: 13 RRKKVLKMAKGYFGSKSTLYKTAHEQVMRSLQYAYRDRKQRKRDFRKLWISRINAGAMLC 72
Query: 73 KMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLTNK 120
+ Y+ M+GL + + ++RK+L+ +A VF V K+ L+
Sbjct: 73 GIKYSRLMHGLALAKVDINRKVLSDLAHLQPEVFVQYVELAKKFLSQF 120
>gnl|CDD|219601 pfam07835, COX4_pro_2, Bacterial aa3 type cytochrome c oxidase
subunit IV. Bacterial cytochrome c oxidase is found
bound to the to the cell membrane, where it is involved
in the generation of the transmembrane proton
electrochemical gradient. It is composed of four
subunits. Subunit IV consists of one transmembrane helix
that does not interact directly with the other subunits,
but maintains its position by indirect contacts via
phospholipid molecules found in the structure. The
function of subunit IV is as yet unknown.
Length = 43
Score = 24.6 bits (54), Expect = 4.5
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 69 VREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVN 111
EH+ TY+ F+ K +I A I + L+ +I
Sbjct: 10 YPEHEKTYDGFIKLTKWGTI-------AIIVL---LILMAIFL 42
>gnl|CDD|236839 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional.
Length = 542
Score = 26.0 bits (58), Expect = 6.2
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 94 LLASIAITDKLVFSSIVNQIKENLTNKAF 122
+ + + + L FS I ++ L KA
Sbjct: 28 VFSVLLVVHLLYFSQISRMTRDGLAEKAL 56
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 26.0 bits (58), Expect = 6.3
Identities = 9/43 (20%), Positives = 22/43 (51%), Gaps = 10/43 (23%)
Query: 34 VAKQAVMHAMQYAYR--DRRNKKRVFRSLWISRINAAVREHKM 74
+ Q + HA++Y++ D++ K+R + + R+ +M
Sbjct: 341 INPQGINHALKYSWDLLDKKVKRR--------HLKPSERDKQM 375
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 26.1 bits (58), Expect = 6.3
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 10/45 (22%)
Query: 4 VKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYR 48
+K + RAR+KK+LK+A ++A+ +MQY Y+
Sbjct: 629 LKTFLEERARYKKLLKEAT----------SSVEKAIYDSMQYTYK 663
>gnl|CDD|239541 cd03458, Catechol_intradiol_dioxygenases, Catechol intradiol
dioxygenases can be divided into several subgroups
according to their substrate specificity for catechol,
chlorocatechols and hydroxyquinols. Almost all members
of this family are homodimers containing one ferric ion
(Fe3+) per monomer. They belong to the intradiol
dioxygenase family, a family of mononuclear non-heme
iron intradiol-cleaving enzymes that catalyze the
oxygenation of catecholates to aliphatic acids via the
cleavage of aromatic rings.
Length = 256
Score = 25.6 bits (57), Expect = 8.1
Identities = 7/31 (22%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 54 KRVFRSLWISRINAAVREHKMTYNTFMNGLK 84
K++ L + ++ +RE ++T + +M G+
Sbjct: 3 KQIMARL-VRHLHDFIREVELTEDEWMAGVD 32
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
0.324 0.132 0.367
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,969,135
Number of extensions: 504249
Number of successful extensions: 600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 600
Number of HSP's successfully gapped: 27
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)