RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13
[Candidatus Liberibacter asiaticus str. psy62]
(122 letters)
>gnl|CDD|30448 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 151 bits (384), Expect = 4e-38
Identities = 76/121 (62%), Positives = 93/121 (76%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV+IP KRVV AL YI+GIG + +++IC K I P++RV +L E E+ ++R AI
Sbjct: 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
+ Y VEGDLRR V M+IKRLM +GCYRG+RHRRGLPVRGQRT TNARTRK KG +
Sbjct: 61 QNKYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKK 120
Query: 121 K 121
K
Sbjct: 121 K 121
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 144 bits (364), Expect = 7e-36
Identities = 66/122 (54%), Positives = 88/122 (72%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
M RIAGV++PR KR+ AL YI+GIG S+++I K I P+ R L + ++ +R+ I
Sbjct: 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
E++YQVEGDLRR ++NIKRLM++ CYRG RHR GLPVRGQRT TNARTR+ K +
Sbjct: 61 EENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGK 120
Query: 121 KR 122
K+
Sbjct: 121 KK 122
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 120 bits (304), Expect = 8e-29
Identities = 53/107 (49%), Positives = 68/107 (63%), Gaps = 1/107 (0%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RI N+ K++ AL YI GIG + + I K + ++RV +L E E+ +IR I
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 63 DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNART 109
Y VE DLRR + +I+RL + CYRGLRH RGLPVRGQRT TNART
Sbjct: 61 -YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRGQRTKTNART 106
>gnl|CDD|38521 KOG3311, KOG3311, KOG3311, Ribosomal protein S18 [Translation,
ribosomal structure and biogenesis].
Length = 152
Score = 63.7 bits (155), Expect = 1e-11
Identities = 44/144 (30%), Positives = 69/144 (47%), Gaps = 25/144 (17%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RI N+ ++V AL I GIG + ++ +C K + +R +L E ++++I Q +
Sbjct: 12 ILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQIL 71
Query: 61 E--------------QDYQVEGD--------LRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
Q ++G L + +I+RL + C+RGLRH GL V
Sbjct: 72 NDPRQYKIPDWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRV 131
Query: 99 RGQRTHTNARTRKKFGKGGVARKR 122
RGQRT TN R K GV+ K+
Sbjct: 132 RGQRTKTNGRRGKTV---GVSGKK 152
>gnl|CDD|33585 COG3790, COG3790, Predicted membrane protein [Function unknown].
Length = 97
Score = 28.7 bits (64), Expect = 0.39
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 2 ARIAGVNIPRAKRVVRALC--YIHGIGFKSSQ 31
AR + + ++ A+C IHG+GF+
Sbjct: 41 ARTSSLEAWHGLLMIWAVCAGVIHGVGFRPRS 72
>gnl|CDD|113842 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 28.0 bits (62), Expect = 0.69
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 40 PPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVA 75
R ++V+SE +I I QD + EG +RR +A
Sbjct: 198 KNSRDAGKVVDSETAEICDEIFQDEETEGYVRRFIA 233
>gnl|CDD|147324 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyse the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 27.1 bits (61), Expect = 1.3
Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 55 QIRQAIEQ-DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRG 95
+ IE D +V ++ + + ++RL+ LR+RR
Sbjct: 1299 ALWDEIEALDNKVPAAVQLRLLLELRRLLRRATRWLLRNRRQ 1340
>gnl|CDD|37512 KOG2301, KOG2301, KOG2301, Voltage-gated Ca2+ channels, alpha1
subunits [Inorganic ion transport and metabolism, Signal
transduction mechanisms].
Length = 1592
Score = 25.6 bits (56), Expect = 3.4
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 6/43 (13%)
Query: 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLV 49
+ R RV+RAL + G + L + QLV
Sbjct: 160 IRALRTFRVLRALKLV--SGIPGLKTRVGAL----IKASKQLV 196
>gnl|CDD|38025 KOG2814, KOG2814, KOG2814, Transcription coactivator complex, P50
component (LigT RNA ligase/phosphodiesterase family)
[Transcription].
Length = 345
Score = 25.3 bits (55), Expect = 4.0
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 66 VEGDL--RRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122
VE D + +R+++ GL + ++ T N+R RK G+ G+ ++
Sbjct: 240 VEPDDYEKFLQHRCGERILERFVASGLIKKESSSLKLHCTVMNSRYRKNGGEPGLVKES 298
>gnl|CDD|146739 pfam04257, Exonuc_V_gamma, Exodeoxyribonuclease V, gamma subunit.
The Exodeoxyribonuclease V enzyme is a multi-subunit
enzyme comprised of the proteins RecB, RecC (this
family) and RecD. This enzyme plays an important role in
homologous genetic recombination, repair of double
strand DNA breaks resistance to UV irradiation and
chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyses
ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of
ssDNA or dsDNA and unwinding of dsDNA. This family
consists of two AAA domains.
Length = 1008
Score = 25.3 bits (56), Expect = 4.2
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 23/76 (30%)
Query: 32 DICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGL- 90
++ + L +P RR L E ++ ++RQ +E+ G GL
Sbjct: 431 ELLDLLEVPAVRRRFGLDEDDLERLRQWLEE---------------------AGIRWGLD 469
Query: 91 -RHRRGLPVRGQRTHT 105
HR+ L + G ++
Sbjct: 470 AEHRQALGLPGDEQNS 485
>gnl|CDD|36584 KOG1370, KOG1370, KOG1370, S-adenosylhomocysteine hydrolase
[Coenzyme transport and metabolism].
Length = 434
Score = 25.3 bits (55), Expect = 4.8
Identities = 14/67 (20%), Positives = 25/67 (37%)
Query: 23 HGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLM 82
H K+ +CN E V L + + D + + + + + RL+
Sbjct: 287 HFDQMKNDAIVCNIGHFDTEIDVKWLNTPALTWENVKPQVDRYILPNGKHIILLAEGRLV 346
Query: 83 DLGCYRG 89
+LGC G
Sbjct: 347 NLGCATG 353
>gnl|CDD|145898 pfam02990, EMP70, Endomembrane protein 70.
Length = 518
Score = 24.6 bits (54), Expect = 6.7
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 47 QLVESEVIQIRQAIEQDYQVE 67
+L +V R+AIE+ Y V+
Sbjct: 54 KLTSEDVKFFRKAIEEGYYVQ 74
>gnl|CDD|34920 COG5343, COG5343, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 240
Score = 24.2 bits (52), Expect = 8.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 57 RQAIEQDYQVEGDLRRTVAMNIKRLMDLG 85
R+A E+ + +GD VA +RL L
Sbjct: 31 RRAAERRIETDGDFAALVARWQERLAPLD 59
>gnl|CDD|173756 cd08216, PK_STRAD, Pseudokinase domain of STE20-related kinase
adapter protein. Protein Kinase family, STE20-related
kinase adapter protein (STRAD) subfamily, pseudokinase
domain. The STRAD subfamily is part of a larger
superfamily that includes the catalytic domains of
serine/threonine kinases (STKs), protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
pseudokinase domain shows similarity to protein kinases
but lacks crucial residues for catalytic activity. STRAD
forms a complex with the scaffolding protein MO25, and
the STK, LKB1, resulting in the activation of the
kinase. In the complex, LKB1 phosphorylates and
activates adenosine monophosphate-activated protein
kinases (AMPKs), which regulate cell energy metabolism
and cell polarity. LKB1 is a tumor suppressor linked to
the rare inherited disease, Peutz-Jeghers syndrome,
which is characterized by a predisposition to benign
polyps and hyperpigmentation of the buccal mucosa. There
are two forms of STRAD, alpha and beta, that complex
with LKB1 and MO25. The structure of STRAD-alpha is
available and shows that this protein binds ATP, has an
ordered activation loop, and adopts a closed
conformation typical of fully active protein kinases. It
does not possess activity due to nonconservative
substitutions of essential catalytic residues. ATP
binding enhances the affinity of STRAD for MO25. The
conformation of STRAD-alpha stabilized through ATP and
MO25 may be needed to activate LKB1.
Length = 314
Score = 24.2 bits (53), Expect = 9.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 13 KRVVRALCYIHGIGF 27
K V+ AL YIH GF
Sbjct: 108 KDVLNALDYIHSKGF 122
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.326 0.141 0.416
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,462,241
Number of extensions: 68564
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 20
Length of query: 122
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,491,799
Effective search space: 179671960
Effective search space used: 179671960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.2 bits)