RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16262
(222 letters)
>gnl|CDD|240331 PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional.
Length = 249
Score = 357 bits (918), Expect = e-126
Identities = 129/189 (68%), Positives = 153/189 (80%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLL 60
+S G +L+ KEDD+ KML + HIG++N + M++YVYKR +GVHI+NL +TWEKL L
Sbjct: 1 VSSGPKVLTPKEDDIKKMLACKCHIGTKNLENAMKKYVYKRTKEGVHIINLAKTWEKLKL 60
Query: 61 AARAIVAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPR 120
AAR I AIE+PADV V+SSRP GQRAVLKFA YTGA+ IAGRFTPG FTNQIQ F EPR
Sbjct: 61 AARVIAAIENPADVVVVSSRPYGQRAVLKFAQYTGASAIAGRFTPGTFTNQIQKKFMEPR 120
Query: 121 LLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
LL+VTDP TDHQ I EA+YVNIPVIA C+T+SPL +VDIAIPCNN+ SI LM+WLLAR
Sbjct: 121 LLIVTDPRTDHQAIREASYVNIPVIALCDTDSPLEYVDIAIPCNNRGKESIALMYWLLAR 180
Query: 181 EVLRFRGVI 189
EVLR RG +
Sbjct: 181 EVLRLRGTL 189
>gnl|CDD|188101 TIGR01012, Sa_S2_E_A, ribosomal protein Sa(cytosolic)/S2(archaeal).
This model describes the ribosomal protein of the
cytosol and of Archaea, homologous to S2 of bacteria. It
is designated typically as Sa in eukaryotes and Sa or S2
in the archaea. TIGR01011 describes the related protein
of organelles and bacteria [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 196
Score = 293 bits (753), Expect = e-102
Identities = 98/182 (53%), Positives = 135/182 (74%), Gaps = 1/182 (0%)
Query: 11 KEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVAIEH 70
V L A HIG++N + ME+++YK R+DG+++L+LR+T E+L +AA+ +V IE
Sbjct: 2 YLVPVDMYLAAGVHIGTQNKTFDMEKFIYKVRSDGLYVLDLRKTDERLRVAAKFLVRIE- 60
Query: 71 PADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPRLLVVTDPHTD 130
P D+ V+S+R GQ+ VLKFA YTGA IAGRFTPG FTN +Q +FREP ++VVTDP D
Sbjct: 61 PQDILVVSARIYGQKPVLKFAKYTGARAIAGRFTPGTFTNPMQKSFREPEVVVVTDPRAD 120
Query: 131 HQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRGVIG 190
HQ + EA+ V IP++A C+T++PLR+VD+ IP NNK S+ L++WLLARE+LR RG I
Sbjct: 121 HQAVKEASEVGIPIVALCDTDNPLRYVDLVIPTNNKGRRSLALIYWLLAREILRMRGTIS 180
Query: 191 PD 192
PD
Sbjct: 181 PD 182
>gnl|CDD|100106 cd01425, RPS2, Ribosomal protein S2 (RPS2), involved in formation
of the translation initiation complex, where it might
contact the messenger RNA and several components of the
ribosome. It has been shown that in Escherichia coli
RPS2 is essential for the binding of ribosomal protein
S1 to the 30s ribosomal subunit. In humans, most likely
in all vertebrates, and perhaps in all metazoans, the
protein also functions as the 67 kDa laminin receptor
(LAMR1 or 67LR), which is formed from a 37 kDa
precursor, and is overexpressed in many tumors. 67LR is
a cell surface receptor which interacts with a variety
of ligands, laminin-1 and others. It is assumed that the
ligand interactions are mediated via the conserved
C-terminus, which becomes extracellular as the protein
undergoes conformational changes which are not well
understood. Specifically, a conserved palindromic motif,
LMWWML, may participate in the interactions. 67LR plays
essential roles in the adhesion of cells to the basement
membrane and subsequent signalling events, and has been
linked to several diseases. Some evidence also suggests
that the precursor of 67LR, 37LRP is also present in the
nucleus in animals, where it appears associated with
histones.
Length = 193
Score = 204 bits (522), Expect = 3e-67
Identities = 69/194 (35%), Positives = 98/194 (50%), Gaps = 28/194 (14%)
Query: 18 MLGAQTHIGSENS--DYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVAIEH-PADV 74
+L A H+G + + +M+ Y+Y RN G+HI++L +T EKL LA I I +
Sbjct: 1 LLEAGVHLGHKTRRWNPKMKPYIYGERN-GIHIIDLEKTLEKLRLALNFIANIAAKGGKI 59
Query: 75 FVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQ----------------------- 111
+ ++P QRAV KFA TG+ + GR+ G TN
Sbjct: 60 LFVGTKPQAQRAVKKFAERTGSFYVNGRWLGGTLTNWKTIRKSIKRLKKLEKEKLEKNLG 119
Query: 112 -IQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHS 170
I+ FR P L++V DP +HQ I EA+ + IPVIA +T +D IP N+ S S
Sbjct: 120 GIKDMFRLPDLVIVLDPRKEHQAIREASKLGIPVIAIVDTNCDPDLIDYPIPANDDSIRS 179
Query: 171 IGLMWWLLAREVLR 184
I L+ WLLAR +L
Sbjct: 180 IALILWLLARAILE 193
>gnl|CDD|235201 PRK04020, rps2P, 30S ribosomal protein S2; Provisional.
Length = 204
Score = 203 bits (519), Expect = 1e-66
Identities = 78/178 (43%), Positives = 114/178 (64%), Gaps = 1/178 (0%)
Query: 15 VTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVAIEHPADV 74
+ + L A HIG++ ME+++Y+ R DG+++L++R+T E++ +AA+ + E P +
Sbjct: 12 LEEYLAAGVHIGTQQKTKDMERFIYRVRPDGLYVLDVRKTDERIRIAAKFLSRYE-PEKI 70
Query: 75 FVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPRLLVVTDPHTDHQPI 134
V+SSR GQ+ V KFA GA I GRF PG TN + EP ++VVTDP D Q +
Sbjct: 71 LVVSSRQYGQKPVQKFAEVVGAKAITGRFIPGTLTNPSLKGYIEPDVVVVTDPRGDAQAV 130
Query: 135 TEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRGVIGPD 192
EA V IPV+A C+T++ VD+ IP NNK ++ L++WLLARE+LR RG I PD
Sbjct: 131 KEAIEVGIPVVALCDTDNLTSNVDLVIPTNNKGRKALALVYWLLAREILRERGEIKPD 188
>gnl|CDD|215856 pfam00318, Ribosomal_S2, Ribosomal protein S2.
Length = 205
Score = 185 bits (473), Expect = 1e-59
Identities = 65/206 (31%), Positives = 94/206 (45%), Gaps = 38/206 (18%)
Query: 18 MLGAQTHIGSENS--DYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVAI-EHPADV 74
+L A H G + + +M+ Y+Y RN G+HI++L +T EKL AA I I +
Sbjct: 1 LLEAGVHFGHQTRRWNPKMKPYIYGERN-GIHIIDLEKTLEKLRKAANFIKEIAAKGGKI 59
Query: 75 FVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQ----------------------- 111
+ ++ Q AV KFA TG + GR+ G TN
Sbjct: 60 LFVGTKKQAQEAVKKFAKRTGQFYVNGRWLGGTLTNWKTIKKSIKRLEELSKKEALKLKR 119
Query: 112 -----------IQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIA 160
I+ + P L++V DP+ +H I EA+ + IPVIA +T +D
Sbjct: 120 ELEKLEKYLGGIKNMKKLPDLVIVVDPNKEHIAIKEASKLGIPVIAIVDTNCDPDLIDYP 179
Query: 161 IPCNNKSPHSIGLMWWLLAREVLRFR 186
IP N+ S SI L+ WLLAR +L R
Sbjct: 180 IPGNDDSIRSIALILWLLARAILEGR 205
>gnl|CDD|223130 COG0052, RpsB, Ribosomal protein S2 [Translation, ribosomal
structure and biogenesis].
Length = 252
Score = 171 bits (435), Expect = 3e-53
Identities = 57/219 (26%), Positives = 94/219 (42%), Gaps = 49/219 (22%)
Query: 17 KMLGAQTHIGSENS--DYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVAI-EHPAD 73
++L A H G + + +M+ +++ RN G+HI++L++T E+L A + + I +
Sbjct: 8 QLLEAGVHFGHQTRRWNPKMKPFIFGERN-GIHIIDLQKTLERLREAYKFLRRIAANGGK 66
Query: 74 VFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTN----------------------- 110
+ + ++ Q V +FA TGA + GR+ G TN
Sbjct: 67 ILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTNFKTIRKSIKRLKELEKMEEDGFD 126
Query: 111 ----------------------QIQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFC 148
I+ P +L V DP + + EA + IPV+A
Sbjct: 127 GLTKKEALMLTRELEKLEKSLGGIKDMKGLPDVLFVIDPRKEKIAVKEANKLGIPVVALV 186
Query: 149 NTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 187
+T VD IP N+ + SI L++WLLAR +L RG
Sbjct: 187 DTNCDPDGVDYVIPGNDDAIRSIALIYWLLARAILEGRG 225
>gnl|CDD|130084 TIGR01011, rpsB_bact, ribosomal protein S2, bacterial type. This
model describes the bacterial, ribosomal, and
chloroplast forms of ribosomal protein S2. TIGR01012
describes the archaeal and cytosolic forms [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 225
Score = 67.0 bits (164), Expect = 1e-13
Identities = 54/231 (23%), Positives = 92/231 (39%), Gaps = 57/231 (24%)
Query: 7 ILSLKEDDVTKMLGAQTHIGSENS--DYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARA 64
++S+K+ +L A H G + + +M+ +++ RN G+HI++L++T + L A
Sbjct: 1 VVSMKD-----LLEAGVHFGHQTRRWNPKMKPFIFGERN-GIHIIDLQKTLQLLKEAYNF 54
Query: 65 I--VAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTN------------ 110
+ VA +FV ++ + + + A G + R+ G TN
Sbjct: 55 VKDVAANGGKILFV-GTKKQAKEIIKEEAERCGMFYVNQRWLGGMLTNFKTIRKSIKKLK 113
Query: 111 -----QIQAAF------------RE-----------------PRLLVVTDPHTDHQPITE 136
+ F RE P LL V DP + + E
Sbjct: 114 KLEKMEEDGTFDDLTKKEALMLSREKEKLEKSLGGIKDMKKLPDLLFVIDPVKEKIAVAE 173
Query: 137 AAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 187
A + IPV+A +T VD IP N+ + SI L+ L+A VL +
Sbjct: 174 ARKLGIPVVAIVDTNCDPDLVDYPIPGNDDAIRSIRLLTNLIADAVLEGKQ 224
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
Length = 258
Score = 50.5 bits (122), Expect = 1e-07
Identities = 23/65 (35%), Positives = 33/65 (50%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLL 178
P L V DP+ +H + EA + IPV+A +T VD IP N+ + SI L +
Sbjct: 158 PDALFVVDPNKEHIAVKEARKLGIPVVAIVDTNCDPDGVDYPIPGNDDAIRSIKLYTSKI 217
Query: 179 AREVL 183
A +L
Sbjct: 218 ADAIL 222
Score = 30.5 bits (70), Expect = 0.47
Identities = 13/40 (32%), Positives = 26/40 (65%), Gaps = 3/40 (7%)
Query: 17 KMLGAQTHIGSENS--DYQMEQYVYKRRNDGVHILNLRRT 54
++L A H G + + +M+ Y++ RN G+HI++L++T
Sbjct: 8 QLLEAGVHFGHQTRRWNPKMKPYIFGERN-GIHIIDLQKT 46
>gnl|CDD|177007 CHL00067, rps2, ribosomal protein S2.
Length = 230
Score = 37.1 bits (87), Expect = 0.003
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 17 KMLGAQTHIGSENSDY--QMEQYVYKRRNDGVHILNLRRT 54
+ML A H G + + +M Y+Y RN G+HI+NL +T
Sbjct: 12 EMLEAGVHFGHQTRKWNPKMAPYIYAERN-GIHIINLVQT 50
Score = 32.1 bits (74), Expect = 0.14
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGL 173
P ++++ D ++ + E + IP I+ +T DI IP N+ + SI L
Sbjct: 162 PDIVIIIDQQEEYTALRECRKLGIPTISILDTNCDPDLADIPIPANDDAIASIKL 216
>gnl|CDD|183428 PRK12311, rpsB, 30S ribosomal protein S2/unknown domain fusion
protein; Provisional.
Length = 326
Score = 36.7 bits (85), Expect = 0.005
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLL 178
P LL V D + + I EA + IPV A +T + +P N+ + +I L L+
Sbjct: 153 PDLLFVIDTNKEDIAIQEAQRLGIPVAAIVDTNCDPDGITYPVPGNDDAGRAIALYCDLI 212
Query: 179 AREVL----RFRGVIGPD 192
AR + R +G +G D
Sbjct: 213 ARAAIDGISRAQGDLGID 230
>gnl|CDD|220226 pfam09412, XendoU, Endoribonuclease XendoU. This is a family of
endoribonucleases involved in RNA biosynthesis which has
been named XendoU in Xenopus laevis. XendoU is a
U-specific metal dependent enzyme that produces products
with a 2'-3' cyclic phosphate termini.
Length = 261
Score = 30.3 bits (69), Expect = 0.73
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 27 SENSDYQMEQYVYKRRNDGVHILNLRRTWEKLL 59
N DY+ Y+ R N +L ++ TW LL
Sbjct: 175 KGNVDYK--GYIKDRENGTDDVLTVQFTWNGLL 205
>gnl|CDD|184410 PRK13945, PRK13945, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 282
Score = 28.4 bits (64), Expect = 2.9
Identities = 12/30 (40%), Positives = 12/30 (40%), Gaps = 9/30 (30%)
Query: 147 FCNTESPLRFVDIAIPCNNKSPHSIGLMWW 176
F LRFVDI S G MWW
Sbjct: 105 FFEKNQELRFVDI---------RSFGQMWW 125
>gnl|CDD|99959 cd01635, Glycosyltransferase_GTB_type, Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. The structures of the formed
glycoconjugates are extremely diverse, reflecting a wide
range of biological functions. The members of this
family share a common GTB topology, one of the two
protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility.
Length = 229
Score = 28.0 bits (62), Expect = 3.7
Identities = 18/104 (17%), Positives = 30/104 (28%), Gaps = 8/104 (7%)
Query: 52 RRTWEK---LLLAARAIVAIEHPADVFVI-SSRPIGQRAVLKFASYTGATPIAGRFTPGA 107
R EK L+ A A++ P VI P + A+ +
Sbjct: 112 RLAPEKGLDDLIEAFALLKERGPDLKLVIAGDGPEREYLEELLAALLLLDRVI-FLGGLD 170
Query: 108 FTNQIQAAFREPRLLVVTDPHTDHQPIT--EAAYVNIPVIAFCN 149
+ + V+ + + EA +PVIA
Sbjct: 171 PEELLALLLAAADVFVLP-SLREGFGLVVLEAMACGLPVIATDV 213
>gnl|CDD|220931 pfam10995, DUF2819, Protein of unknown function (DUF2819). This
bacterial family of proteins has no known function.
Length = 316
Score = 27.6 bits (62), Expect = 4.8
Identities = 20/77 (25%), Positives = 29/77 (37%), Gaps = 16/77 (20%)
Query: 51 LRRTWEKLLLAARA--IVAIEHPADVFV---------ISSRPIGQ--RAVLKFASYTGAT 97
LR E+LLLA A +V P F+ I +RP+ A+L
Sbjct: 148 LRYQDERLLLALGANLVVPRNTPLSRFLTQIESIQGQIFTRPVPSDIEALLS---ADLPL 204
Query: 98 PIAGRFTPGAFTNQIQA 114
+ G P F ++A
Sbjct: 205 GLKGYLPPDEFCEYVRA 221
>gnl|CDD|178104 PLN02486, PLN02486, aminoacyl-tRNA ligase.
Length = 383
Score = 27.8 bits (62), Expect = 5.1
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 89 KFASYTGATPIA-----GRFTPGAFTNQIQAAFREPRLLVVTD 126
KF YTG P + G P FT +Q AF+ P ++ +TD
Sbjct: 73 KFYLYTGRGPSSEALHLGHLIPFMFTKYLQDAFKVPLVIQLTD 115
>gnl|CDD|222939 PHA02878, PHA02878, ankyrin repeat protein; Provisional.
Length = 477
Score = 27.5 bits (61), Expect = 5.9
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 11 KEDDVTKML---GAQTHIGSENSDYQMEQYVYKRRNDGVHIL 49
K+ +T++L GA +I + ++ + V VHIL
Sbjct: 179 KDQRLTELLLSYGANVNIPDKTNNSPLHHAVKHYNKPIVHIL 220
>gnl|CDD|233460 TIGR01543, proheadase_HK97, phage prohead protease, HK97 family.
This model describes the prohead protease of HK97 and
related phage. It is generally encoded next to the gene
for the capsid protein that it processes, and in some
cases may be fused to it. This family does not show
similarity to the prohead protease of phage T4 (see
pfam03420) [Mobile and extrachromosomal element
functions, Prophage functions, Protein fate, Other].
Length = 145
Score = 26.7 bits (59), Expect = 7.2
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 103 FTPGAFTNQIQAAFREPRLLV 123
F PGAFTN + + RLL
Sbjct: 23 FLPGAFTNTLAEWNDKVRLLY 43
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
0.323 0.139 0.427
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,743,817
Number of extensions: 1130152
Number of successful extensions: 975
Number of sequences better than 10.0: 1
Number of HSP's gapped: 964
Number of HSP's successfully gapped: 31
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.9 bits)