RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037430
(198 letters)
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 340 bits (874), Expect = e-120
Identities = 135/198 (68%), Positives = 158/198 (79%)
Query: 1 MGRVIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLAR 60
MGRVIRAQRKG GSVFK+H H R GPA+ R LD+ ER+GY++GVV +I HDPGRGAPLAR
Sbjct: 1 MGRVIRAQRKGNGSVFKAHGHKRLGPAKLRILDYAERHGYIRGVVKDIEHDPGRGAPLAR 60
Query: 61 VTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHV 120
V FR P++Y + KEL +A EGMYTGQ+VYCG KA L +GNVLP+ IPEG +VCNVE
Sbjct: 61 VEFRDPYKYKRVKELMVAPEGMYTGQYVYCGAKAPLAIGNVLPLGQIPEGTIVCNVEEKP 120
Query: 121 GDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLL 180
GDRG LARASG YA II H+ D TR++LPSG KK + S RAMIG VAGGGR +KP+L
Sbjct: 121 GDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGGGRIDKPVL 180
Query: 181 KAGNAYHKFRVKRNCWPK 198
KAGNA+HK+R KRNCWPK
Sbjct: 181 KAGNAFHKYRGKRNCWPK 198
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 209 bits (534), Expect = 8e-69
Identities = 92/199 (46%), Positives = 124/199 (62%), Gaps = 11/199 (5%)
Query: 1 MGRVIRAQRKGAGS-VFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLA 59
MG+ I +QR+G G+ F+S +H KGP ++ LD +G L+G V +I+HDPGR AP+A
Sbjct: 1 MGKRIISQRRGRGTPTFRSPSHRYKGPVKYPPLDK---DGTLRGKVVDILHDPGRNAPVA 57
Query: 60 RVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHH 119
+V F + ++ L +A EG+Y GQ + G A + GN LP+ IPEG VCN+E
Sbjct: 58 KVKFEN-----GEEFLILAPEGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESR 112
Query: 120 VGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPL 179
GD G AR+SG YA+++ H + D V+LPSG K + CRA IG VAGGGR EKP
Sbjct: 113 PGDGGKFARSSGTYALVVGH--EGDKVIVQLPSGKIKELNPRCRATIGVVAGGGRKEKPF 170
Query: 180 LKAGNAYHKFRVKRNCWPK 198
LKAG YHK + K WP+
Sbjct: 171 LKAGKKYHKMKAKAKKWPR 189
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 188 bits (481), Expect = 3e-60
Identities = 71/192 (36%), Positives = 101/192 (52%), Gaps = 11/192 (5%)
Query: 1 MGRVIRAQRKGA--GSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPL 58
MG++I++Q + + K R +DF + G V +I +DP R AP+
Sbjct: 34 MGKLIKSQGRNNRGRITVRHRGGGHKRRY--RLIDFKRNKDGIPGKVEDIEYDPNRSAPI 91
Query: 59 ARVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEH 118
A V + +K +A EG+ G + GK A + GN LP+ +IPEG +V NVE
Sbjct: 92 ALVVYEDG-----EKRYILAPEGLKVGDVIESGKDADIKPGNALPLGNIPEGTIVHNVEL 146
Query: 119 HVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKP 178
GD G LAR++G YA ++ + + V+LPSG + + S CRA IG VA GG KP
Sbjct: 147 KPGDGGQLARSAGTYAQVVGK--EGNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKP 204
Query: 179 LLKAGNAYHKFR 190
L KAG A HK +
Sbjct: 205 LGKAGRARHKGK 216
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 103 bits (260), Expect = 1e-28
Identities = 38/93 (40%), Positives = 55/93 (59%), Gaps = 2/93 (2%)
Query: 96 LMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAK 155
+ +GN LP+++IP G V+ N+E G G LAR++G YA II+ + +KLPSG
Sbjct: 1 IKIGNALPLKNIPIGTVIHNIELIPGKGGQLARSAGTYAQIIAK--EGKYVTLKLPSGEV 58
Query: 156 KIIPSGCRAMIGQVAGGGRTEKPLLKAGNAYHK 188
+++ S CRA IG V+ KPL KAG +
Sbjct: 59 RLVSSNCRATIGVVSNIDHNNKPLGKAGRSRWL 91
>gnl|CDD|162234 TIGR01171, rplB_bact, ribosomal protein L2, bacterial/organellar.
This model distinguishes bacterial and organellar
ribosomal protein L2 from its counterparts in the
archaea nad in the eukaryotic cytosol. Plant
mitochondrial examples tend to have long, variable
inserts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 273
Score = 86.2 bits (214), Expect = 1e-20
Identities = 54/171 (31%), Positives = 83/171 (48%), Gaps = 9/171 (5%)
Query: 20 THHRKGPA--QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFI 77
+ HR G +R +DF + VA I +DP R A +A + + +K +
Sbjct: 49 SRHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYAD-----GEKRYIL 103
Query: 78 AAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVII 137
A +G+ G V G +A + GN LP+R+IP G V N+E G G LAR++G A I+
Sbjct: 104 APKGLKVGDTVISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQIL 163
Query: 138 SHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAGNAYHK 188
+ + ++LPSG +++ CRA IG+V L KAG +
Sbjct: 164 AK--EGGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRSRWL 212
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 82.6 bits (205), Expect = 2e-19
Identities = 54/178 (30%), Positives = 80/178 (44%), Gaps = 20/178 (11%)
Query: 22 HRKG--PAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMK-QKELFIA 78
HR G +R +DF + G + I +DP R A + + Y +K +
Sbjct: 51 HRGGGHKRLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLI------HYGDGEKRYILH 104
Query: 79 AEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIIS 138
G+ G + G +A + +GN LP+ +IP G + N+E G G LARA+G A +I+
Sbjct: 105 PRGLKIGDTIVSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIA 164
Query: 139 HNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCW 196
+ + +KLPSG ++I C A IGQV K L KAG W
Sbjct: 165 K--EGKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAG---------SKRW 211
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 77.8 bits (193), Expect = 2e-17
Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 15/131 (11%)
Query: 43 GVVAEIIHDPGRGAPLARVTF----RHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMV 98
V I +DP R A +A + + + RY+ +A +G+ G V G A +
Sbjct: 76 AKVERIEYDPNRSARIALLHYADGEK---RYI------LAPKGLKVGDTVVSGPDADIKP 126
Query: 99 GNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKII 158
GN LP+R+IP G V N+E G G LAR++G A +++ + ++LPSG + +
Sbjct: 127 GNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAK--EGKYATLRLPSGEVRKV 184
Query: 159 PSGCRAMIGQV 169
+ CRA IG+V
Sbjct: 185 LAECRATIGEV 195
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 75.3 bits (185), Expect = 2e-16
Identities = 60/194 (30%), Positives = 87/194 (44%), Gaps = 17/194 (8%)
Query: 2 GRVI------RAQRKGAGSVFKSHTHHRKGP--AQFRSLDFGERNGYLKGVVAEIIHDPG 53
GRV+ R + G +V + T HR G + R +DF + V I +DP
Sbjct: 58 GRVVKQLSCRRVKNSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPS 117
Query: 54 RGAPLARVTFRHP-FRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAV 112
R A +A + + Y+ +A + G + K A + GN LP+R+IP G++
Sbjct: 118 RSAHIALLQYEDGVLSYI------LAPLLLRPGDKIIASKYANINPGNSLPLRNIPVGSI 171
Query: 113 VCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGG 172
V NVE G G + RA G YA ++S D +KL S + P C A IGQV+
Sbjct: 172 VHNVEMRPGAGGQIIRAGGTYATVVSK--DEQFATLKLKSTEIRKFPLDCWATIGQVSNL 229
Query: 173 GRTEKPLLKAGNAY 186
+ L KAG
Sbjct: 230 EHHMRILGKAGVNR 243
>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding
domain.
Length = 77
Score = 67.2 bits (165), Expect = 3e-15
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 11 GAGSVFKSHTHHRKG--PAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFR 68
G + + HR G +R +DF G +KG V +I +DP R AP+A V +
Sbjct: 1 GRNNPGRITVRHRGGGHKRLYRLIDFKRNKGNIKGKVIDIEYDPNRSAPIALVKYEDG-- 58
Query: 69 YMKQKELFIAAEGMYTGQFVYC 90
+K +A EG+ G +
Sbjct: 59 ---EKRYILAPEGLKVGDTIES 77
>gnl|CDD|225882 COG3345, GalA, Alpha-galactosidase [Carbohydrate transport and
metabolism].
Length = 687
Score = 29.4 bits (66), Expect = 1.3
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 66 PFRYMKQKELFIAAEGMYTG-QFVYCGKKATLMVGNVLPVRSIPEGAVVCNVE 117
P R + Q + F G G Y G A + + P + +G + + E
Sbjct: 193 PERNL-QSDGFTEEAGEVYGFGLTYSGNFAAFVEVHQHPFFRVQDGILPFDGE 244
>gnl|CDD|214625 smart00332, PP2Cc, Serine/threonine phosphatases, family 2C,
catalytic domain. The protein architecture and deduced
catalytic mechanism of PP2C phosphatases are similar to
the PP1, PP2A, PP2B family of protein Ser/Thr
phosphatases, with which PP2C shares no sequence
similarity.
Length = 252
Score = 28.1 bits (63), Expect = 2.5
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 119 HVGD-RGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGG 172
+VGD R VL R + H P N+ R +I +G + G+V G
Sbjct: 118 NVGDSRAVLCRNGKAVQLTEDHKPSNEDER-------ARIEAAGGFVINGRVNGV 165
>gnl|CDD|183829 PRK12921, PRK12921, 2-dehydropantoate 2-reductase; Provisional.
Length = 305
Score = 28.3 bits (64), Expect = 2.6
Identities = 25/114 (21%), Positives = 33/114 (28%), Gaps = 26/114 (22%)
Query: 4 VIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKG---VVAEIIHDPGRGAPLAR 60
I AQ G G V R L FGE G V + + L+
Sbjct: 126 FISAQLNGDGVV-----VQRADHR----LTFGEIPGQRSERTRAVRDALAGARLEVVLSE 176
Query: 61 VTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVC 114
R + + +K LF A T L V + S P G +
Sbjct: 177 -NIR---QDIWRKLLFNAVMNGMT----------ALGRATVGGILSRPGGRDLA 216
>gnl|CDD|153101 cd01042, DMQH, Demethoxyubiquinone hydroxylase, ferritin-like
diiron-binding domain. Demethoxyubiquinone hydroxylases
(DMQH) are members of the ferritin-like,
diiron-carboxylate family which are present in
eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the
Coq7 family). DMQH participates in one of the last steps
of ubiquinone biosysnthesis and is responsible for DMQ
hydroxylation, resulting in the formation of
hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a
mitochondrial inner membrane protein and Coq7 is a
proposed interfacial integral membrane protein.
Mutations in the Caenorhabditis elegans gene clk-1
affect biological timing and extend longevity. The
conserved residues of a diiron center are present in
this domain.
Length = 165
Score = 27.1 bits (61), Expect = 4.5
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 142 DNDTTRVKLPSGAKKIIPSGCRAMI 166
+ + L + K +I +GC+ I
Sbjct: 136 ELGAEKAPLYALLKALIKAGCKVAI 160
>gnl|CDD|238457 cd00915, MD-1_MD-2, MD-1 and MD-2 are cofactors required for LPS
signaling through cell surface receptors. MD-2 and its
binding partner, Toll-like receptor 4 (TLR4), are
essential for the innate immune responses of mammalian
cells to bacterial lipopolysaccharide (LPS); MD-2
directly binds the lipid A moiety of LPS. The TLR4-like
receptor, RP105, which mediates LPS-induced lymphocyte
proliferation, interacts with MD-1; MD-1 enhances
RP105-mediated LPS-induced growth of B cells. These
proteins belong to the ML domain family.
Length = 130
Score = 26.8 bits (59), Expect = 4.6
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 81 GMYTGQFVYCGKKATLMVGNVLPV----RSIPEGAVVCNVEHHVGDRGVLA 127
Y ++ +CG V V P IP+G C E V +R +A
Sbjct: 74 HGYLDKYSFCGALKGETVYYVGPFSFKGILIPQGQYRCVAELIVENRETVA 124
>gnl|CDD|220428 pfam09826, Beta_propel, Beta propeller domain. Members of this
family comprise secreted bacterial proteins containing
C-terminal beta-propeller domain distantly related to
WD-40 repeats.
Length = 521
Score = 26.9 bits (60), Expect = 9.3
Identities = 9/36 (25%), Positives = 13/36 (36%)
Query: 130 SGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAM 165
GD V+I + D K S A + P +
Sbjct: 63 DGDRLVVIGDRYEEDNIPPKGVSEAATMPPPAYSST 98
>gnl|CDD|132732 cd06934, NR_LBD_PXR_like, The ligand binding domain of xenobiotic
receptors:pregnane X receptor and constitutive
androstane receptor. The ligand binding domain of
xenobiotic receptors: This xenobiotic receptor family
includes pregnane X receptor (PXR), constitutive
androstane receptor (CAR) and other related nuclear
receptors. They function as sensors of toxic
byproducts of cell metabolism and of exogenous
chemicals, to facilitate their elimination. The nuclear
receptor pregnane X receptor (PXR) is a
ligand-regulated transcription factor that responds to
a diverse array of chemically distinct ligands,
including many endogenous compounds and clinical drugs.
The ligand binding domain of PXR shows remarkable
flexibility to accommodate both large and small
molecules. PXR functions as a heterodimer with retinoic
X receptor-alpha (RXRa) and binds to a variety of
response elements in the promoter regions of a diverse
set of target genes involved in the metabolism,
transport, and elimination of these molecules from the
cell. Constitutive androstane receptor (CAR) is a
closest mammalian relative of PXR, which has also been
proposed to function as a xenosensor. CAR is activated
by some of the same ligands as PXR and regulates a
subset of common genes. The sequence homology and
functional similarity suggests that the CAR gene arose
from a duplication of an ancestral PXR gene. Like other
nuclear receptors, xenobiotic receptors have a central
well conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 226
Score = 26.6 bits (59), Expect = 9.4
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 24 KGPAQFRSLDFGERNGYLKGVVAEIIH 50
K FRSL ++ LKG EI
Sbjct: 56 KDLPYFRSLPIEDQISLLKGATFEICQ 82
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 0.139 0.430
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,329,907
Number of extensions: 976925
Number of successful extensions: 681
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 18
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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 (21.9 bits)
S2: 56 (25.4 bits)