RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7749
(319 letters)
>gnl|CDD|185427 PTZ00072, PTZ00072, 40S ribosomal protein S13; Provisional.
Length = 148
Score = 276 bits (707), Expect = 2e-94
Identities = 113/148 (76%), Positives = 129/148 (87%)
Query: 172 MHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQV 231
M+ GKGIS SALPYRR P+WLKL+S +V+D I KL+KKGLTPSQIGVILRDS G+ QV
Sbjct: 1 MYGKGKGISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQV 60
Query: 232 RFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIH 291
+ V+G+KILRI+K GLAP +PEDLY LIKKAV+IRKHLE++RKDKDSKFRLILVESRIH
Sbjct: 61 KNVTGSKILRILKKNGLAPEIPEDLYFLIKKAVSIRKHLEKNRKDKDSKFRLILVESRIH 120
Query: 292 RLARYYKTKAVLPPNWKYESATASALVA 319
RLARYYK LPPNWKYES+TASALVA
Sbjct: 121 RLARYYKRTKQLPPNWKYESSTASALVA 148
Score = 191 bits (486), Expect = 4e-61
Identities = 76/99 (76%), Positives = 87/99 (87%)
Query: 37 VILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDS 96
VILRDS G+ QV+ V+G+KILRI+K GLAP +PEDLY LIKKAV+IRKHLE++RKDKDS
Sbjct: 49 VILRDSMGIPQVKNVTGSKILRILKKNGLAPEIPEDLYFLIKKAVSIRKHLEKNRKDKDS 108
Query: 97 KFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFI 135
KFRLILVESRIHRLARYYK LPPNWKYES+TASA +
Sbjct: 109 KFRLILVESRIHRLARYYKRTKQLPPNWKYESSTASALV 147
>gnl|CDD|236287 PRK08561, rps15p, 30S ribosomal protein S15P; Reviewed.
Length = 151
Score = 181 bits (463), Expect = 2e-57
Identities = 71/151 (47%), Positives = 101/151 (66%)
Query: 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228
M RMHT +G S S P R P W+ + E++++ + +L+K+G +PS IG+ILRD +G+
Sbjct: 1 MARMHTRRRGKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGI 60
Query: 229 AQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVES 288
V+ ++G KI I++ GLAP +PEDL LIKKAV +RKHLE + KD +K L L+ES
Sbjct: 61 PDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQLIES 120
Query: 289 RIHRLARYYKTKAVLPPNWKYESATASALVA 319
+I RL +YYK VLP +W+Y TA LV+
Sbjct: 121 KIRRLVKYYKRTGVLPADWRYSPETAELLVS 151
Score = 123 bits (312), Expect = 8e-35
Identities = 49/95 (51%), Positives = 66/95 (69%)
Query: 37 VILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDS 96
+ILRD +G+ V+ ++G KI I++ GLAP +PEDL LIKKAV +RKHLE + KD +
Sbjct: 52 IILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLHN 111
Query: 97 KFRLILVESRIHRLARYYKTKAVLPPNWKYESATA 131
K L L+ES+I RL +YYK VLP +W+Y TA
Sbjct: 112 KRGLQLIESKIRRLVKYYKRTGVLPADWRYSPETA 146
>gnl|CDD|191937 pfam08069, Ribosomal_S13_N, Ribosomal S13/S15 N-terminal domain.
This domain is found at the N-terminus of ribosomal S13
and S15 proteins. This domain is also identified as
NUC021.
Length = 60
Score = 113 bits (284), Expect = 7e-32
Identities = 40/60 (66%), Positives = 49/60 (81%)
Query: 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228
M RMH+ GKGIS SA PYRR+ P WLK + E+V++ I KL+KKGLTPSQIGVILRD +G+
Sbjct: 1 MARMHSRGKGISGSARPYRRTPPEWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60
>gnl|CDD|238213 cd00353, Ribosomal_S15p_S13e, Ribosomal protein S15
(prokaryotic)_S13 (eukaryotic) binds the central domain
of 16S rRNA and is required for assembly of the small
ribosomal subunit and for intersubunit association, thus
representing a key element in the assembly of the whole
ribosome. S15 also plays an important autoregulatory
role by binding and preventing its own mRNA from being
translated. S15 has a predominantly alpha-helical fold
that is highly structured except for the N-terminal
alpha helix.
Length = 80
Score = 90.6 bits (226), Expect = 3e-23
Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 55 KILRIMKAMGLAPN----LPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 110
K I+K GLA L L ++ V + +HLE+++KDK SK L+L+ S+ RL
Sbjct: 1 KKQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRL 60
Query: 111 ARYYKTKAVLPPNWKYESAT 130
+Y K K L W E
Sbjct: 61 LKYLKRKDRLRYEWLIEKLG 80
Score = 90.6 bits (226), Expect = 3e-23
Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 238 KILRIMKAMGLAPN----LPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 293
K I+K GLA L L ++ V + +HLE+++KDK SK L+L+ S+ RL
Sbjct: 1 KKQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRL 60
Query: 294 ARYYKTKAVLPPNWKYESAT 313
+Y K K L W E
Sbjct: 61 LKYLKRKDRLRYEWLIEKLG 80
>gnl|CDD|223262 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 89.2 bits (222), Expect = 2e-22
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 16/104 (15%)
Query: 212 GLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLE 271
S+I LRD +G+ +V SG L L ++ + +HL+
Sbjct: 1 MSLTSEIKQELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLK 44
Query: 272 RSRKDKDSKFRLILVESRIHRLARYYKTKAVLPPNWKYESATAS 315
+KD S+ L+L+ S+ RL +Y K K VL W +
Sbjct: 45 EHKKDHHSRRGLLLLVSKRRRLLKYLKRKDVLRYRWLIKKLGLR 88
Score = 81.1 bits (201), Expect = 2e-19
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 16/95 (16%)
Query: 38 ILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSK 97
LRD +G+ +V SG L L ++ + +HL+ +KD S+
Sbjct: 10 ELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLKEHKKDHHSR 53
Query: 98 FRLILVESRIHRLARYYKTKAVLPPNWKYESATAS 132
L+L+ S+ RL +Y K K VL W +
Sbjct: 54 RGLLLLVSKRRRLLKYLKRKDVLRYRWLIKKLGLR 88
>gnl|CDD|109373 pfam00312, Ribosomal_S15, Ribosomal protein S15.
Length = 83
Score = 80.8 bits (200), Expect = 2e-19
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 234 VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 293
+G I +KA ++ + L ++ V +RKHLE +KD SK LI + S+ RL
Sbjct: 2 ATGLIISEFLKAEKDTGSVEVQIALLTERIVRLRKHLEEHKKDYHSKRGLIKMVSKRRRL 61
Query: 294 ARYYKTKAVLPPNWKYESATASALV 318
Y K K +YE+ +
Sbjct: 62 LAYLKKKDT----ARYENLIEQLGL 82
Score = 80.1 bits (198), Expect = 4e-19
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 51 VSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 110
+G I +KA ++ + L ++ V +RKHLE +KD SK LI + S+ RL
Sbjct: 2 ATGLIISEFLKAEKDTGSVEVQIALLTERIVRLRKHLEEHKKDYHSKRGLIKMVSKRRRL 61
Query: 111 ARYYKTKAVLPPNWKYESATASAFI 135
Y K K +YE+ +
Sbjct: 62 LAYLKKKDT----ARYENLIEQLGL 82
>gnl|CDD|238361 cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain.
This short domain consists of a helix-turn-helix
structure, which can bind to several types of RNA. It is
found in the ribosomal protein S15, the influenza A
viral nonstructural protein (NSA) and in several
eukaryotic aminoacyl tRNA synthetases (aaRSs), where it
occurs as a single or a repeated unit. It is involved in
both protein-RNA interactions by binding tRNA and
protein-protein interactions in the formation of
tRNA-synthetases into multienzyme complexes. While this
domain lacks significant sequence similarity between the
subgroups in which it is found, they share similar
electrostatic surface potentials and thus are likely to
bind to RNA via the same mechanism.
Length = 46
Score = 56.4 bits (137), Expect = 6e-11
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 70 PEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYK 115
+ L ++ +++HL +++KDK SK L L+ S+ RL +Y K
Sbjct: 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46
Score = 56.4 bits (137), Expect = 6e-11
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 253 PEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRLARYYK 298
+ L ++ +++HL +++KDK SK L L+ S+ RL +Y K
Sbjct: 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46
>gnl|CDD|240278 PTZ00119, PTZ00119, 40S ribosomal protein S15; Provisional.
Length = 302
Score = 29.5 bits (66), Expect = 2.1
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 55 KILRIMKAMGLAP----NLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 110
K L I + + P + P + CL +K + +R HL KD K + ++ +R +L
Sbjct: 109 KKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKL 168
Query: 111 ARY-YKT 116
+Y YKT
Sbjct: 169 MKYLYKT 175
Score = 29.5 bits (66), Expect = 2.1
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 238 KILRIMKAMGLAP----NLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRIHRL 293
K L I + + P + P + CL +K + +R HL KD K + ++ +R +L
Sbjct: 109 KKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKL 168
Query: 294 ARY-YKT 299
+Y YKT
Sbjct: 169 MKYLYKT 175
>gnl|CDD|185416 PTZ00052, PTZ00052, thioredoxin reductase; Provisional.
Length = 499
Score = 28.6 bits (64), Expect = 4.6
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 17/78 (21%)
Query: 192 NWLKLTSEDVKDHIFKLS---KKGLTPSQIGVI-----LRDSHGVA-----QVRFVSGNK 238
NW KL V++HI L+ + GL S++ I L+D H V+ Q ++
Sbjct: 89 NWGKLV-TTVQNHIRSLNFSYRTGLRSSKVEYINGLAKLKDEHTVSYGDNSQEETITAKY 147
Query: 239 ILRIMKAMGLAPNLPEDL 256
IL A G P++PED+
Sbjct: 148 IL---IATGGRPSIPEDV 162
>gnl|CDD|176889 cd08880, RHO_alpha_C_ahdA1c-like, C-terminal catalytic domain of
the large/alpha subunit (ahdA1c) of a ring-hydroxylating
dioxygenase from Sphingomonas sp. strain P2 and related
proteins. C-terminal catalytic domain of the large
subunit (ahdA1c) of the AhdA3A4A2cA1c salicylate
1-hydroxylase complex from Sphingomonas sp. strain P2,
and related Rieske-type non-heme iron aromatic
ring-hydroxylating oxygenases (RHOs, also known as
aromatic ring hydroxylating dioxygenases). AhdA3A4A2cA1c
is one of three known isofunctional salicylate
1-hydroxylase complexes in strain P2, involved in
phenanthrene degradation, which catalyze the
monooxygenation of salicylate, the metabolite of
phenanthene degradation, to produce catechol. This
complex prefers salicylate over other substituted
salicylates; the other two salicylate 1-hydroxylases
have different substrate preferences. RHOs utilize
non-heme Fe(II) to catalyze the addition of hydroxyl
groups to the aromatic ring, an initial step in the
oxidative degradation of aromatic compounds. RHOs are
composed of either two or three protein components, and
are comprised of an electron transport chain (ETC) and
an oxygenase. The ETC transfers reducing equivalents
from the electron donor to the oxygenase component,
which in turn transfers electrons to the oxygen
molecules. The oxygenase components are oligomers,
either (alpha)n or (alpha)n(beta)n. The alpha subunits
are the catalytic components and have an N-terminal
domain, which binds a Rieske-like 2Fe-2S cluster, and a
C-terminal domain which binds the non-heme Fe(II). The
Fe(II) is co-ordinated by conserved His and Asp
residues. Other oxygenases belonging to this subgroup
include the alpha subunits of anthranilate
1,2-dioxygenase from Burkholderia cepacia DBO1, a
polycyclic aromatic hydrocarbon dioxygenase from
Cycloclasticus sp. strain A5 (PhnA dioxygenase),
salicylate-5-hydroxylase from Ralstonia sp. U2,
ortho-halobenzoate 1,2-dioxygenase from Pseudomonas
aeruginosa strain JB2, and the terephthalate
1,2-dioxygenase system from Delftia tsuruhatensis strain
T7. This subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 222
Score = 27.6 bits (62), Expect = 7.1
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 11/51 (21%)
Query: 186 YRRSVP-NWLKLTSEDVKD-------HIFKLSKKGL-TPSQIGVILRDSHG 227
YR+ +P NW KL +E+VKD H+F GL Q I+ D HG
Sbjct: 4 YRQRIPGNW-KLYAENVKDPYHASLLHLF-FVTFGLWRADQKSSIIDDEHG 52
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
0.324 0.138 0.413
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,424,467
Number of extensions: 1603654
Number of successful extensions: 1799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1795
Number of HSP's successfully gapped: 30
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (26.3 bits)