RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4162
(210 letters)
>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat.
Length = 60
Score = 45.6 bits (109), Expect = 3e-07
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 88 IDLSFNNIKNVDKNMFTNFPNLKILYLHKNQIEEYLSVFVLRRVNSLRTLSLYGNPI 144
+DLS N + + F PNLK+L L N + +S + SLR+L L GN +
Sbjct: 5 LDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTS-ISPEAFSGLPSLRSLDLSGNNL 60
Score = 26.7 bits (60), Expect = 1.9
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 108 NLKILYLHKNQIEEYLSVFVLRRVNSLRTLSLYGNPIEKIRE 149
NLK L L N++ + + + +L+ L L GN + I
Sbjct: 1 NLKSLDLSNNRL-TVIPDGAFKGLPNLKVLDLSGNNLTSISP 41
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number of
proteins with diverse functions and cellular locations.
These repeats are usually involved in protein-protein
interactions. Each Leucine Rich Repeat is composed of a
beta-alpha unit. These units form elongated non-globular
structures. Leucine Rich Repeats are often flanked by
cysteine rich domains.
Length = 43
Score = 34.4 bits (80), Expect = 0.002
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 107 PNLKILYLHKNQIEEYLSVFVLRRVNSLRTLSLYGNPIEKIRE 149
NL+ L L NQI + L + +L TL L GN I +
Sbjct: 1 TNLETLDLSNNQIT---DLPPLSNLPNLETLDLSGNKITDLSP 40
Score = 31.3 bits (72), Expect = 0.028
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 88 IDLSFNNIKNVDKNMFTNFPNLKILYLHKNQIEE 121
+DLS N I ++ +N PNL+ L L N+I +
Sbjct: 6 LDLSNNQITDLPP--LSNLPNLETLDLSGNKITD 37
>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function
unknown].
Length = 394
Score = 32.2 bits (73), Expect = 0.18
Identities = 27/92 (29%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 56 RSLWLSHNKISLVYGLDSLVHRTILDPDLIGWIDLSFNNIKNVDKNMFTNFPNLKILYLH 115
+L LS NKIS + I + +DLS N+I + +N NL L L
Sbjct: 189 NNLDLSGNKISDL-------PPEIELLSALEELDLSNNSIIE-LLSSLSNLKNLSGLELS 240
Query: 116 KNQIEEYLSVFVLRRVNSLRTLSLYGNPIEKI 147
N++E+ +++L TL L N I I
Sbjct: 241 NNKLEDLPESIGN--LSNLETLDLSNNQISSI 270
>gnl|CDD|233558 TIGR01752, flav_long, flavodoxin, long chain. Flavodoxins are
small redox-active proteins with a flavin mononucleotide
(FMN) prosthetic group. They can act in nitrogen
fixation by nitrogenase, in sulfite reduction, and
light-dependent NADP+ reduction in during
photosynthesis, among other roles. This model describes
the long chain type, typical for nitrogen fixation but
associated with pyruvate formate-lyase activation and
cobalamin-dependent methionine synthase activity in E.
coli [Energy metabolism, Electron transport].
Length = 167
Score = 30.4 bits (69), Expect = 0.39
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 64 KISLVYGLDSLVHRTILD--PDLIGWIDLSFNNIKNVDKNMFTNFPNL 109
KI + YG D+ I + +G D+ NI K + L
Sbjct: 1 KIGIFYGTDTGNTEGIAEKIQKELGEDDVDVFNIAKASKEDLNAYDKL 48
>gnl|CDD|219401 pfam07404, TEBP_beta, Telomere-binding protein beta subunit (TEBP
beta). This family consists of several telomere-binding
protein beta subunits which appear to be specific to the
family Oxytrichidae. Telomeres are specialised
protein-DNA complexes that compose the ends of
eukaryotic chromosomes. Telomeres protect chromosome
termini from degradation and recombination and act
together with telomerase to ensure complete genome
replication. TEBP beta forms a complex with TEBP alpha
and this complex is able to recognise and bind ssDNA to
form a sequence-specific, telomeric nucleoprotein
complex that caps the very 3' ends of chromosomes.
Length = 375
Score = 29.7 bits (66), Expect = 1.1
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 106 FPNLKILYLHKNQIEEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQL 161
FPN+ I+ LH I LRRVNS + Y N E R +V + P L
Sbjct: 74 FPNVNIVDLHDKVIVINNWSLELRRVNSAEVFTSYAN-----LEARLIVHSFKPNL 124
>gnl|CDD|226016 COG3485, PcaH, Protocatechuate 3,4-dioxygenase beta subunit
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 226
Score = 28.5 bits (64), Expect = 1.9
Identities = 12/51 (23%), Positives = 17/51 (33%)
Query: 33 QKLKPNVHRLGESPPMLVGRYDTRSLWLSHNKISLVYGLDSLVHRTILDPD 83
Q L P VH E+ + G Y G L+ +LD +
Sbjct: 33 QTLGPYVHIGLETEGTVFGPYYLNDAPNDLLTNDKARGERILLEGRVLDGN 83
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 28.4 bits (64), Expect = 2.5
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 13/52 (25%)
Query: 103 FTNFPNLKILYLHKNQIEEYLSVFVLRRVNSLRTLSLYGNPIEKIRE-YRAV 153
NFPNL+++YL EE+L+ F V++LR N IE ++ YR V
Sbjct: 59 LRNFPNLRVVYLTS---EEFLNDF----VDALRD-----NKIEAFKKSYRNV 98
>gnl|CDD|235362 PRK05192, PRK05192, tRNA uridine 5-carboxymethylaminomethyl
modification enzyme GidA; Validated.
Length = 618
Score = 28.5 bits (65), Expect = 3.3
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 14 KIPLDLSFQQIQSLDKVAVQKLK 36
KIP D+ + I L A +KL
Sbjct: 559 KIPEDIDYDAISGLSNEAREKLN 581
>gnl|CDD|204266 pfam09537, DUF2383, Domain of unknown function (DUF2383).
Members of this protein family are found mostly in the
Proteobacteria, although one member is found in the the
marine planctomycete Pirellula sp. strain 1. The
function is unknown.
Length = 87
Score = 26.4 bits (59), Expect = 4.3
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 5 YKTSI----DPEFKIPLDLSFQQIQSLDKVAVQKLKPNVHRLGESPP 47
Y+ + DPE K FQ+ + + A +L+ + LG P
Sbjct: 20 YEKAAEKVKDPELKA----LFQRRAAERRQAAAELQAEIRALGGEPE 62
>gnl|CDD|223522 COG0445, GidA, Flavin-dependent tRNA uridine
5-carboxymethylaminomethyl modification enzyme GidA
[Cell cycle control, cell division, chromosome
partitioning].
Length = 621
Score = 27.9 bits (63), Expect = 4.9
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 14 KIPLDLSFQQIQSLDKVAVQKLK 36
KIP D+ + +I L A +KL
Sbjct: 564 KIPEDIDYDKIPGLSNEAREKLN 586
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 27.5 bits (61), Expect = 5.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 17 LDLSFQQIQSLDKVAVQKLKPNVHR 41
D ++ ++ LD VA ++ PN HR
Sbjct: 166 EDHGYELLKELDPVAANRIHPNNHR 190
>gnl|CDD|206103 pfam13932, GIDA_assoc_3, GidA associated domain 3. The GidA
associated domain 3 is a motif that has been identified
at the C-terminus of protein GidA. It consists of 4
helices, the last three being rather short and forming
small bundle at the top end of the first longer one. It
is here named helical domain 3 because in GidA it is
preceded by two other C-terminal helical domain (based
on crystal structures). GidA is an tRNA modification
enzyme found in bacteria and mitochondrial. Based on
mutational analysis this domain has been suggested to
be implicated in binding of the D-stem of tRNA and to
be responsible for the interaction with protein MnmE.
Structures of GidA in complex with either tRNA or MnmE
are missing. Reported to bind to Pfam family MnmE,
pfam12631.
Length = 72
Score = 25.2 bits (56), Expect = 8.1
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 14 KIPLDLSFQQIQSLDKVAVQKLK 36
+IP D+ + +I L A +KL
Sbjct: 24 RIPEDIDYARISGLSNEAREKLA 46
>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein
kinase; Provisional.
Length = 968
Score = 26.7 bits (59), Expect = 9.9
Identities = 37/146 (25%), Positives = 66/146 (45%), Gaps = 36/146 (24%)
Query: 14 KIPLDL-SFQQIQSLD---KVAVQKLKPNVHRL--------------GESPPMLVGRYDT 55
+IP D+ SF ++ LD V V K+ ++ L G+ P L
Sbjct: 155 EIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSL 214
Query: 56 RSLWLSHNKIS-----LVYGLDSLVHRTILDPDLIGWIDLSFNNIKNVDKNMFTNFPNLK 110
+ ++L +N +S + GL SL H +DL +NN+ + N NL+
Sbjct: 215 KWIYLGYNNLSGEIPYEIGGLTSLNH-----------LDLVYNNLTGPIPSSLGNLKNLQ 263
Query: 111 ILYLHKNQIEEYL--SVFVLRRVNSL 134
L+L++N++ + S+F L+++ SL
Sbjct: 264 YLFLYQNKLSGPIPPSIFSLQKLISL 289
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 0.136 0.383
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,739,235
Number of extensions: 1006631
Number of successful extensions: 798
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 40
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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 (21.7 bits)
S2: 57 (25.7 bits)