RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028585
(207 letters)
>gnl|CDD|185439 PTZ00091, PTZ00091, 40S ribosomal protein S5; Provisional.
Length = 193
Score = 353 bits (907), Expect = e-126
Identities = 150/190 (78%), Positives = 170/190 (89%), Gaps = 1/190 (0%)
Query: 18 DVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTN 77
+ KLF +W+++DVQV+D+SL DYI V K + +VPHTAGRY KRFRKAQCPIVERL N
Sbjct: 5 EPKLFGKWSYDDVQVSDLSLKDYIAVTT-KASVFVPHTAGRYQKKRFRKAQCPIVERLVN 63
Query: 78 SLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVV 137
SLM HGRNNGKKL+AVRIVKHA EIIHLLTD+NP+QV+VDAV N GPRED+TR+GS GVV
Sbjct: 64 SLMFHGRNNGKKLLAVRIVKHAFEIIHLLTDKNPLQVLVDAVQNGGPREDSTRVGSGGVV 123
Query: 138 RRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKD 197
RRQAVD+SPLRRVNQAIYLI GARE+AFRNIKTIAECLADE+INA+K SSNSYAIKKKD
Sbjct: 124 RRQAVDVSPLRRVNQAIYLICKGAREAAFRNIKTIAECLADEIINASKESSNSYAIKKKD 183
Query: 198 EIERVAKANR 207
E+ERVAKANR
Sbjct: 184 EVERVAKANR 193
>gnl|CDD|211618 TIGR01028, S7_S5_E_A, ribosomal protein
S7(archaeal)/S5(eukaryotic). This model describes the
members from the eukaryotic cytosol and the Archaea of
the family that includes ribosomal protein S7 of
bacteria and S5 of eukaryotes. A separate model
describes bacterial and organellar S7 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 186
Score = 297 bits (763), Expect = e-104
Identities = 121/190 (63%), Positives = 149/190 (78%), Gaps = 4/190 (2%)
Query: 18 DVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTN 77
++K+F +W+ +DV+V D SL DYI ++ YVPHTAGR++ K+FRKA+ PIVERL N
Sbjct: 1 EIKVFGKWSTDDVEVKDPSLKDYINLEP----KYVPHTAGRHAKKQFRKAKVPIVERLIN 56
Query: 78 SLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVV 137
+M GRNNGKKL A RIVK A EII T +NPIQV+VDA+ N+GPRED TRIG G+V
Sbjct: 57 KVMRSGRNNGKKLKAYRIVKEAFEIIEKRTGENPIQVLVDAIENAGPREDTTRIGYGGIV 116
Query: 138 RRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKD 197
RQAVDISPLRRV+QA+ I GARE+AFRN K+IAECLA+E+I AA G S SYAIKKK+
Sbjct: 117 YRQAVDISPLRRVDQALRNIALGAREAAFRNKKSIAECLAEEIILAANGDSKSYAIKKKE 176
Query: 198 EIERVAKANR 207
E+ERVAK+ R
Sbjct: 177 ELERVAKSAR 186
>gnl|CDD|235204 PRK04027, PRK04027, 30S ribosomal protein S7P; Reviewed.
Length = 195
Score = 257 bits (658), Expect = 5e-88
Identities = 99/190 (52%), Positives = 129/190 (67%), Gaps = 4/190 (2%)
Query: 18 DVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTN 77
++KLF +W E+V+V D SL YI + VPHT GR++ K+F KA+ PIVERL N
Sbjct: 10 EIKLFGKWDVEEVEVRDPSLKRYINL----TPVLVPHTGGRHAKKQFGKAEVPIVERLIN 65
Query: 78 SLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVV 137
LM RN GKK A IVK A EII T QNPIQV+VDA+ N+ PRE+ TRI G+
Sbjct: 66 KLMRTERNTGKKQKAYNIVKEAFEIIEKRTKQNPIQVLVDAIENAAPREETTRIKYGGIS 125
Query: 138 RRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKD 197
+AVD+SP RRV+ A+ I GAR+++F+N K+I E LA+E+I AA SYA++KK+
Sbjct: 126 YPKAVDVSPQRRVDLALRFIAEGARQASFKNKKSIEEALAEEIIAAANNDPKSYAVRKKE 185
Query: 198 EIERVAKANR 207
EIERVAK+ R
Sbjct: 186 EIERVAKSAR 195
>gnl|CDD|223127 COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 181 bits (461), Expect = 1e-58
Identities = 67/157 (42%), Positives = 88/157 (56%), Gaps = 9/157 (5%)
Query: 51 YVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQN 110
HTAG+ V K IVERL N +M G KK +A +IV A +II T QN
Sbjct: 1 PRRHTAGKREVLPDPKYNSVIVERLINKIMRDG----KKSLAEKIVYGAFDIIEKKTGQN 56
Query: 111 PIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIK 170
P+QV A+ N PRE+ G + V++ P RRV A+ I GAR+ RN K
Sbjct: 57 PLQVFEKAIENVKPREEVKSRRVGGATYQVPVEVRPRRRVALALRWIVEGARK---RNEK 113
Query: 171 TIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207
T+AE LA+ELI+AA + AIKKK++ R+A+ANR
Sbjct: 114 TMAERLANELIDAANNT--GAAIKKKEDTHRMAEANR 148
>gnl|CDD|215771 pfam00177, Ribosomal_S7, Ribosomal protein S7p/S5e. This family
contains ribosomal protein S7 from prokaryotes and S5
from eukaryotes.
Length = 149
Score = 159 bits (404), Expect = 4e-50
Identities = 58/145 (40%), Positives = 83/145 (57%), Gaps = 12/145 (8%)
Query: 63 RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINS 122
++ +VE+L N LM G KK +A +IV A+EII T +NP++V+V A+ N
Sbjct: 17 KYNS---ALVEKLINKLMKDG----KKSLAEKIVYDALEIIEEKTGKNPLEVLVQAIENV 69
Query: 123 GPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELIN 182
PR + G + V++SP RRV AI I AR R+ K++AE LA+ELI+
Sbjct: 70 KPRVEVKSRRVGGATYQVPVEVSPERRVALAIRWILEAAR---KRSGKSMAEKLANELID 126
Query: 183 AAKGSSNSYAIKKKDEIERVAKANR 207
AA AIKKK+E ++A+ANR
Sbjct: 127 AANN--KGSAIKKKEETHKMAEANR 149
>gnl|CDD|176994 CHL00053, rps7, ribosomal protein S7.
Length = 155
Score = 79.2 bits (196), Expect = 6e-19
Identities = 51/136 (37%), Positives = 78/136 (57%), Gaps = 9/136 (6%)
Query: 74 RLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--ATRI 131
RL N L+ +GKK +A RIV A++ I T++NP+ V+ A+ N P + A R+
Sbjct: 21 RLVNMLVNRILKSGKKSLAYRIVYRALKKIQQKTEKNPLSVLRQAIRNVTPDVEVKARRV 80
Query: 132 GSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSY 191
G G + ++I R AI + +R+ + RN +A L+ EL++AAKGS N
Sbjct: 81 G--GSTYQVPIEIGSTRGKALAIRWLLKASRKRSGRN---MAFKLSSELVDAAKGSGN-- 133
Query: 192 AIKKKDEIERVAKANR 207
AI+KK+E R+A+ANR
Sbjct: 134 AIRKKEETHRMAEANR 149
>gnl|CDD|235398 PRK05302, PRK05302, 30S ribosomal protein S7; Validated.
Length = 156
Score = 76.7 bits (190), Expect = 6e-18
Identities = 47/139 (33%), Positives = 79/139 (56%), Gaps = 13/139 (9%)
Query: 71 IVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--A 128
+V + N LM+ G KK +A +IV A++II T ++P++V A+ N P + +
Sbjct: 22 LVTKFINKLMLDG----KKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPVVEVKS 77
Query: 129 TRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSS 188
R+G G + V++ P RR A+ + AR+ R KT+AE LA+EL++AA
Sbjct: 78 RRVG--GATYQVPVEVRPERRQALAMRWLVEAARK---RGEKTMAERLANELLDAANNRG 132
Query: 189 NSYAIKKKDEIERVAKANR 207
A+KK+++ R+A+AN+
Sbjct: 133 A--AVKKREDTHRMAEANK 149
>gnl|CDD|233238 TIGR01029, rpsG_bact, ribosomal protein S7, bacterial/organelle.
This model describes the bacterial and organellar branch
of the ribosomal protein S7 family (includes prokaroytic
S7 and eukaryotic S5). The eukaryotic and archaeal
branch is described by model TIGR01028 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 154
Score = 70.4 bits (173), Expect = 1e-15
Identities = 45/139 (32%), Positives = 76/139 (54%), Gaps = 13/139 (9%)
Query: 71 IVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--A 128
++ + N +M G KK +A IV A E I T ++P++V A+ N P + +
Sbjct: 20 LLNKFINRVMKDG----KKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVKPLVEVKS 75
Query: 129 TRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSS 188
R+G G + V++ P RR AI + AR+ R K++AE LA+E+++AA +
Sbjct: 76 RRVG--GATYQVPVEVRPSRRYALAIRWLIEAARK---RGGKSMAERLANEILDAANNTG 130
Query: 189 NSYAIKKKDEIERVAKANR 207
AIKK+++ R+A+AN+
Sbjct: 131 A--AIKKREDTHRMAEANK 147
>gnl|CDD|240520 cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6. RPL6
contains KOW motif that has an extra ribosomal role as
an oncogenic. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. .
Length = 152
Score = 29.1 bits (66), Expect = 1.1
Identities = 10/14 (71%), Positives = 11/14 (78%), Gaps = 1/14 (7%)
Query: 146 PLRRVNQAIYLITT 159
PLRRVNQ Y+I T
Sbjct: 50 PLRRVNQR-YVIAT 62
>gnl|CDD|220145 pfam09223, YodA, YodA lipocalin-like domain. Members of this
family of prokaryotic domains have been identified as
part of the response of bacteria to a challenge with
the toxic heavy metal cadmium. They are able to bind to
cadmium, and ensure its subsequent elimination.
Length = 182
Score = 27.6 bits (62), Expect = 3.4
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 27 FEDVQVNDISLSDYIGV 43
FED QV D +LSD+ G
Sbjct: 11 FEDKQVKDRTLSDWEGD 27
>gnl|CDD|226036 COG3505, VirD4, Type IV secretory pathway, VirD4 components
[Intracellular trafficking and secretion].
Length = 596
Score = 27.4 bits (61), Expect = 6.1
Identities = 20/123 (16%), Positives = 33/123 (26%), Gaps = 8/123 (6%)
Query: 46 AKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSL-MMHGRNNGKKLMAVRIVKHAMEIIH 104
G F + + + +SL M+ G L V+ +
Sbjct: 265 GNGVLLTQAIKGL--EGVFGRLRDILSSTELSSLAMLTRILLGDALPWVKAA--LGQFFS 320
Query: 105 LLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARES 164
TD+ V+ A + A DI LR+ +Y R S
Sbjct: 321 NKTDEETSGVLSTASSALTLLMNPLV---AAATSGSDFDIRDLRKKKTTVYFGLDPDRIS 377
Query: 165 AFR 167
+
Sbjct: 378 RVK 380
>gnl|CDD|215312 PLN02574, PLN02574, 4-coumarate--CoA ligase-like.
Length = 560
Score = 27.5 bits (61), Expect = 6.1
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 13/54 (24%)
Query: 115 IVDAVINSGPREDATRIGSAGVVRRQ-------------AVDISPLRRVNQAIY 155
I+DA + + P ++ I A VVRRQ A ++P ++V + ++
Sbjct: 478 IIDAAVTAVPDKECGEIPVAFVVRRQGSTLSQEAVINYVAKQVAPYKKVRKVVF 531
>gnl|CDD|238370 cd00728, malate_synt_G, Malate synthase G (MSG), monomeric enzyme
present in some bacteria. In general, malate synthase
catalyzes the Claisen condensation of glyoxylate and
acetyl-CoA to malyl-CoA , which hydrolyzes to malate and
CoA. This reaction is part of the glyoxylate cycle,
which allows certain organisms to derive their carbon
requirements from two-carbon compounds, by bypassing the
two carboxylation steps of the citric acid cycle.
Length = 712
Score = 27.4 bits (61), Expect = 7.5
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 86 NGKKLMAVRIVKHAMEIIHLLT-DQNPI-QVIVDAVINS 122
G+ LM VR V H M +L D N + + I+DAVI S
Sbjct: 324 PGRSLMFVRNVGHLMTNDAILDSDGNEVPEGIMDAVITS 362
>gnl|CDD|233547 TIGR01730, RND_mfp, RND family efflux transporter, MFP subunit.
This model represents the MFP (membrane fusion protein)
component of the RND family of transporters. RND refers
to Resistance, Nodulation, and cell Division. It is, in
part, a subfamily of pfam00529 (Pfam release 7.5) but
hits substantial numbers of proteins missed by that
model. The related HlyD secretion protein, for which
pfam00529 is named, is outside the scope of this model.
Attributed functions imply outward transport. These
functions include nodulation, acriflavin resistance,
heavy metal efflux, and multidrug resistance proteins.
Most members of this family are found in Gram-negative
bacteria. The proposed function of MFP proteins is to
bring the inner and outer membranes together and enable
transport to the outside of the outer membrane. Note,
however, that a few members of this family are found in
Gram-positive bacteria, where there is no outer membrane
[Transport and binding proteins, Unknown substrate].
Length = 322
Score = 26.9 bits (60), Expect = 8.6
Identities = 10/47 (21%), Positives = 18/47 (38%)
Query: 102 IIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLR 148
I L + I V AVI + + + G V ++ V++
Sbjct: 243 TISLKVRSSAIVVPTQAVIEDLNGKYVYVVKNDGKVSKRPVEVGLRN 289
>gnl|CDD|153380 cd07368, PhnC_Bs_like, PhnC is a Class III Extradiol ring-cleavage
dioxygenase involved in the polycyclic aromatic
hydrocarbon (PAH) catabolic pathway. This subfamily is
composed of Burkholderia sp. PhnC and similar poteins.
PhnC is one of nine protein products encoded by the phn
locus. These proteins are involved in the polycyclic
aromatic hydrocarbon (PAH) catabolic pathway. PhnC is a
member of the class III extradiol dioxygenase family, a
group os enzymes which use a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. LigAB-like enzymes are
usually composed of two subunits, designated A and B,
which form a tetramer composed of two copies of each
subunit. This model represents the catalytic subunit, B.
Length = 277
Score = 26.7 bits (59), Expect = 9.7
Identities = 17/62 (27%), Positives = 21/62 (33%), Gaps = 10/62 (16%)
Query: 66 KAQCPIVERLTNSLMMHGRNNGKKLMAVR--IVKHAMEIIHLLTDQNPIQVIVDAVINSG 123
+A E L + +M HG G R V HA I PI + V V G
Sbjct: 88 RAVIENNEPLAHHIMQHGLEYGIDWAVARSFTVDHAATI--------PIHLAVRPVRAKG 139
Query: 124 PR 125
Sbjct: 140 KG 141
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
0.319 0.131 0.368
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,445,529
Number of extensions: 978698
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 766
Number of HSP's successfully gapped: 27
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
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 (25.6 bits)