RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027581
(221 letters)
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 139 bits (352), Expect = 3e-41
Identities = 43/79 (54%), Positives = 56/79 (70%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ V N ++ G + L+ VF V + ++H+VV QLA +QGTH+TKT SEVSG GKK
Sbjct: 3 LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62
Query: 161 PWRQKGTGRARHGTLRGPQ 179
PWRQKGTGRAR G++R PQ
Sbjct: 63 PWRQKGTGRARQGSIRSPQ 81
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family are
ribosomal protein L4. This model recognizes bacterial
and most organellar forms, but excludes homologs from
the eukaryotic cytoplasm and from archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 126 bits (320), Expect = 9e-37
Identities = 39/64 (60%), Positives = 48/64 (75%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF + + ++H+VV+ QLA R+QGTH TKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LNDAVFGIEPNEHLLHQVVKAQLANRRQGTHKTKTRSEVSGGGKKPWRQKGTGRARQGSI 62
Query: 176 RGPQ 179
R P
Sbjct: 63 RSPL 66
>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 = 124 bits (315), Expect = 6e-36
Identities = 42/64 (65%), Positives = 47/64 (73%)
Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
L VF IR D++HR V QLA R+QGT STKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3 LPPAVFGAEIRPDLLHRAVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAGSI 62
Query: 176 RGPQ 179
R P
Sbjct: 63 RSPL 66
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 110 bits (278), Expect = 3e-30
Identities = 44/79 (55%), Positives = 54/79 (68%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ V + E+ G + L +VF +D+IHR V QLA R+QGTHSTKT EVSG GKK
Sbjct: 4 LKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKK 63
Query: 161 PWRQKGTGRARHGTLRGPQ 179
PW QKGTGRAR G++R PQ
Sbjct: 64 PWGQKGTGRARQGSIRSPQ 82
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 92.0 bits (228), Expect = 2e-22
Identities = 41/81 (50%), Positives = 51/81 (62%)
Query: 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG 158
V ++ + G L VFDV +IH+VV Q+A +QGTH TKT +EV G G
Sbjct: 2 ATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGG 61
Query: 159 KKPWRQKGTGRARHGTLRGPQ 179
KKPWRQKGTGRAR G++R PQ
Sbjct: 62 KKPWRQKGTGRARQGSIRAPQ 82
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 77.7 bits (192), Expect = 1e-17
Identities = 29/50 (58%), Positives = 37/50 (74%)
Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
++HR + Q ++QGT STKT SEV G G+KPW+QKGTGRAR G+ R P
Sbjct: 37 LLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNRSP 86
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 76.5 bits (188), Expect = 1e-16
Identities = 30/40 (75%), Positives = 33/40 (82%)
Query: 139 AKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
A R+QGTH KT +EVSGTGKKPWRQKGTGRAR G+ R P
Sbjct: 130 ASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSP 169
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 38.3 bits (90), Expect = 0.002
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 119 DVFDVPIRKDIIHRVVRWQLAKRQQ--GT-------HSTKTISEVSGTGKKPWRQKGTGR 169
VF+ P+R D+I R V R Q G S ++ G + P R KG R
Sbjct: 20 AVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVP-RLKGGSR 78
Query: 170 AR 171
A
Sbjct: 79 AA 80
>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 = 32.6 bits (75), Expect = 0.12
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 120 VFDVPIRKDIIHRVVRWQLAKRQQ--GT-------HSTKTISEVSGTGKKPWRQKGTGRA 170
VF+ P+R D+I R V R Q G S ++ G + P R KG RA
Sbjct: 21 VFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVP-RIKGGSRA 79
Query: 171 R 171
Sbjct: 80 A 80
>gnl|CDD|234195 TIGR03396, PC_PLC, phospholipase C, phosphocholine-specific,
Pseudomonas-type. Members of this protein family are
bacterial, phosphatidylcholine-hydrolyzing phospholipase
C enzymes, with a characteristic domain architecture as
found in hemolytyic (PlcH) and nonhemolytic (PlcN)
secreted enzymes of Pseudomonas aeruginosa. PlcH
hydrolyzes phosphatidylcholine to diacylglycerol and
phosphocholine, but unlike PlcN can also hydrolyze
sphingomyelin to ceramide ((N-acylsphingosine)) and
phosphocholine. Members of this family share the
twin-arginine signal sequence for Sec-independent
transport across the plasma membrane. PlcH is secreted
as a heterodimer with a small chaperone, PlcR, encoded
immediately downstream [Cellular processes,
Pathogenesis].
Length = 689
Score = 31.1 bits (71), Expect = 0.40
Identities = 18/82 (21%), Positives = 28/82 (34%), Gaps = 7/82 (8%)
Query: 106 FFNEDKGFMVLAGD-VFDVPIRKDIIHRVVRWQLAKRQQGTHSTK-TISEVSGTGKKPWR 163
F E +G A V +V + D+ + + L G T+++ + G P
Sbjct: 577 FLREFRGNAAAAAGAVPEVRVCYDVANGNLYLTL--SNAGRSPVTVTVTDNAYGGAGPRT 634
Query: 164 QKGTGRAR---HGTLRGPQGWY 182
R H L GWY
Sbjct: 635 VTVAPGQRVELHWDLSASGGWY 656
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 29.4 bits (66), Expect = 1.6
Identities = 30/95 (31%), Positives = 37/95 (38%), Gaps = 17/95 (17%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAK--RQQGTHSTKTISEVSGT 157
V + DK V DV PIR DI+ V ++K RQ S K + S
Sbjct: 11 VQSLDGDMATDKSATVALPDVMTAPIRPDIV-NFVHTNISKNSRQPYAVSKKAGHQTSA- 68
Query: 158 GKKPWRQKGTGRARH--------GTLRGPQGWYYN 184
+ W GTGRA GT R QG + N
Sbjct: 69 --ESW---GTGRAVSRIPRVPGGGTHRAGQGAFGN 98
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 28.1 bits (63), Expect = 3.7
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 79 DLLLKKTVLT----PDITIGLHQDLVIP-VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRV 133
+ + V+T + I L V P V E +++ DV + ++++II R
Sbjct: 97 GIEIDNYVITIPADGEKVIELEGLKVPPCVVEIEGEKGTIILIFKDVGESELKRNIIDRA 156
Query: 134 VR---WQLAKRQQGT 145
++ +L K + T
Sbjct: 157 IKLVEEKLEKLEDLT 171
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 28.0 bits (62), Expect = 4.3
Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 10/88 (11%)
Query: 12 RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDS 71
R+ F R E + ++ + SP L V S + L L + L +
Sbjct: 235 RYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYG-------- 286
Query: 72 SEGAFPSDLLLKKTVLTPDITIGLHQDL 99
G F + L L L D+ +G H DL
Sbjct: 287 --GDFMNLLYLFCNSLQDDVFLGRHVDL 312
>gnl|CDD|185270 PRK15372, PRK15372, pathogenicity island 2 effector protein SseI;
Provisional.
Length = 292
Score = 27.4 bits (60), Expect = 5.7
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 67 LTPDSSEGAFPSDL----LLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGF 113
LT D A+ +L ++ ++ P +G + L+ PV+NF NE KGF
Sbjct: 118 LTSDIDAAAYLEELKQNPIINNKIMNP---VGQCESLMTPVSNFMNE-KGF 164
>gnl|CDD|236238 PRK08320, PRK08320, branched-chain amino acid aminotransferase;
Reviewed.
Length = 288
Score = 27.1 bits (61), Expect = 7.8
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 12/38 (31%)
Query: 39 YVA-CSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGA 75
YVA +GDN+F +K+G ++TP + GA
Sbjct: 181 YVAEGTGDNIFIVKNG-----------KLITPPTYAGA 207
>gnl|CDD|214534 smart00138, MeTrc, Methyltransferase, chemotaxis proteins.
Methylates methyl-accepting chemotaxis proteins to form
gamma-glutamyl methyl ester residues.
Length = 264
Score = 26.9 bits (60), Expect = 7.9
Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVR-W 136
+ T FF E K F L V + I R VR W
Sbjct: 65 LMTTNETRFFRESKHFEALEEKVLPLLIASRRHGRRVRIW 104
>gnl|CDD|234238 TIGR03508, decahem_SO, decaheme c-type cytochrome, DmsE family.
Members of this family are small, decaheme c-type
cytochromes, related DmsE of Shewanella oneidensis MR-1,
which has been shown to be part of an anaerobic dimethyl
sulfoxide reductase.
Length = 258
Score = 27.0 bits (60), Expect = 8.2
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 7/36 (19%)
Query: 186 RSKAQKPCYK--VEQEGAAAW-----VEDCSICSSS 214
++ + CYK E+ G W EDCS C S
Sbjct: 163 KTTLNETCYKCHAEKRGPFLWEHAPVTEDCSTCHSP 198
>gnl|CDD|133159 cd06095, RP_RTVL_H_like, Retropepsin of the RTVL_H family of human
endogenous retrovirus-like elements. This family
includes aspartate proteases from retroelements with LTR
(long terminal repeats) including the RTVL_H family of
human endogenous retrovirus-like elements. While fungal
and mammalian pepsins are bilobal proteins with
structurally related N- and C-termini, retropepsins are
half as long as their fungal and mammalian counterparts.
The monomers are structurally related to one lobe of the
pepsin molecule and retropepsins function as homodimers.
The active site aspartate occurs within a motif
(Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral
aspartyl protease is synthesized as part of the POL
polyprotein that contains an aspartyl protease, a
reverse transcriptase, RNase H, and an integrase. The
POL polyprotein undergoes specific enzymatic cleavage to
yield the mature proteins. In aspartate peptidases, Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 86
Score = 25.8 bits (57), Expect = 8.6
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQK------GTGRARHGTLRGP 178
H V++ L +Q+ + ++ I VSG ++P G H L P
Sbjct: 20 HSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVP 73
>gnl|CDD|217509 pfam03353, Lin-8, Ras-mediated vulval-induction antagonist. LIN-8
is a nuclear protein, present at the sites of
transcriptional repressor complexes, which interacts
with LIN-35 Rb.Lin35 Rb is a product of the class B
synMuv gene lin-35 which silences genes required for
vulval specification through chromatin modification and
remodelling. The biological role of the interaction has
not yet been determined however predictions have been
made. The interaction shows that class A synMuv genes
control vulval induction through the transcriptional
regulation of gene expression. LIN-8 normally functions
as part of a protein complex however when the complex is
absent, other family members can partially replace LIN-8
activity.
Length = 316
Score = 27.0 bits (60), Expect = 9.3
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 76 FPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVF 121
D+ LKK VL+ + ++ T + + ++ +V+
Sbjct: 18 ATKDVTLKKVVLS---LLEKRPEMWKRNTRGQAKK--WAIVGVEVY 58
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal metallophosphatase
domain. Mre11 (also known as SbcD in Escherichia coli)
is a subunit of the MRX protein complex. This complex
includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital
role in several nuclear processes including DNA
double-strand break repair, telomere length maintenance,
cell cycle checkpoint control, and meiotic
recombination, in eukaryotes. During double-strand
break repair, the MRX complex is required to hold the
two ends of a broken chromosome together. In vitro
studies show that Mre11 has 3'-5' exonuclease activity
on dsDNA templates and endonuclease activity on dsDNA
and ssDNA templates. In addition to the N-terminal
phosphatase domain, the eukaryotic MRE11 members of this
family have a C-terminal DNA binding domain (not
included in this alignment model). MRE11-like proteins
are found in prokaryotes and archaea was well as in
eukaryotes. Mre11 belongs to the metallophosphatase
(MPP) superfamily. MPPs are functionally diverse, but
all share a conserved domain with an active site
consisting of two metal ions (usually manganese, iron,
or zinc) coordinated with octahedral geometry by a cage
of histidine, aspartate, and asparagine residues. The
MPP superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 26.6 bits (59), Expect = 9.9
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 113 FMVLAGDVFDVP-IRKDIIHRVVRWQLAK 140
F+++AGD+FD + + ++ L +
Sbjct: 44 FVLIAGDLFDSNNPSPEALELLIE-ALRR 71
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
0.320 0.135 0.411
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,326,725
Number of extensions: 1043360
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 749
Number of HSP's successfully gapped: 23
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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: 57 (25.7 bits)