RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 044530
(151 letters)
>gnl|CDD|185439 PTZ00091, PTZ00091, 40S ribosomal protein S5; Provisional.
Length = 193
Score = 292 bits (749), Expect = e-103
Identities = 126/151 (83%), Positives = 139/151 (92%)
Query: 1 GRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIV 60
GRY KRFRKAQCPIVERL NSLM HGRNNGKKL+AV IVKHA EIIHLLTD+NP+QV+V
Sbjct: 43 GRYQKKRFRKAQCPIVERLVNSLMFHGRNNGKKLLAVRIVKHAFEIIHLLTDKNPLQVLV 102
Query: 61 DAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECL 120
DAV N GPRED+TR+GS GVVRRQAVD+SPLRRVNQA+YL+ GARE+AFRNIKTIAECL
Sbjct: 103 DAVQNGGPREDSTRVGSGGVVRRQAVDVSPLRRVNQAIYLICKGAREAAFRNIKTIAECL 162
Query: 121 ADELINAAKGSSNSYAIKKKDEIERVAKANR 151
ADE+INA+K SSNSYAIKKKDE+ERVAKANR
Sbjct: 163 ADEIINASKESSNSYAIKKKDEVERVAKANR 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 = 245 bits (628), Expect = 1e-84
Identities = 102/151 (67%), Positives = 121/151 (80%)
Query: 1 GRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIV 60
GR++ K+FRKA+ PIVERL N +M GRNNGKKL A IVK A EII T +NPIQV+V
Sbjct: 36 GRHAKKQFRKAKVPIVERLINKVMRSGRNNGKKLKAYRIVKEAFEIIEKRTGENPIQVLV 95
Query: 61 DAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECL 120
DA+ N+GPRED TRIG G+V RQAVDISPLRRV+QAL + GARE+AFRN K+IAECL
Sbjct: 96 DAIENAGPREDTTRIGYGGIVYRQAVDISPLRRVDQALRNIALGAREAAFRNKKSIAECL 155
Query: 121 ADELINAAKGSSNSYAIKKKDEIERVAKANR 151
A+E+I AA G S SYAIKKK+E+ERVAK+ R
Sbjct: 156 AEEIILAANGDSKSYAIKKKEELERVAKSAR 186
>gnl|CDD|235204 PRK04027, PRK04027, 30S ribosomal protein S7P; Reviewed.
Length = 195
Score = 211 bits (540), Expect = 5e-71
Identities = 83/151 (54%), Positives = 107/151 (70%)
Query: 1 GRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIV 60
GR++ K+F KA+ PIVERL N LM RN GKK A IVK A EII T QNPIQV+V
Sbjct: 45 GRHAKKQFGKAEVPIVERLINKLMRTERNTGKKQKAYNIVKEAFEIIEKRTKQNPIQVLV 104
Query: 61 DAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECL 120
DA+ N+ PRE+ TRI G+ +AVD+SP RRV+ AL + GAR+++F+N K+I E L
Sbjct: 105 DAIENAAPREETTRIKYGGISYPKAVDVSPQRRVDLALRFIAEGARQASFKNKKSIEEAL 164
Query: 121 ADELINAAKGSSNSYAIKKKDEIERVAKANR 151
A+E+I AA SYA++KK+EIERVAK+ R
Sbjct: 165 AEEIIAAANNDPKSYAVRKKEEIERVAKSAR 195
>gnl|CDD|223127 COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 163 bits (415), Expect = 1e-52
Identities = 64/151 (42%), Positives = 84/151 (55%), Gaps = 9/151 (5%)
Query: 1 GRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIV 60
G+ V K IVERL N +M G KK +A IV A +II T QNP+QV
Sbjct: 7 GKREVLPDPKYNSVIVERLINKIMRDG----KKSLAEKIVYGAFDIIEKKTGQNPLQVFE 62
Query: 61 DAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECL 120
A+ N PRE+ G + V++ P RRV AL + GAR+ RN KT+AE L
Sbjct: 63 KAIENVKPREEVKSRRVGGATYQVPVEVRPRRRVALALRWIVEGARK---RNEKTMAERL 119
Query: 121 ADELINAAKGSSNSYAIKKKDEIERVAKANR 151
A+ELI+AA + AIKKK++ R+A+ANR
Sbjct: 120 ANELIDAANNT--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 = 146 bits (372), Expect = 3e-46
Identities = 56/138 (40%), Positives = 80/138 (57%), Gaps = 9/138 (6%)
Query: 14 PIVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDAT 73
+VE+L N LM G KK +A IV A+EII T +NP++V+V A+ N PR +
Sbjct: 21 ALVEKLINKLMKDG----KKSLAEKIVYDALEIIEEKTGKNPLEVLVQAIENVKPRVEVK 76
Query: 74 RIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECLADELINAAKGSSN 133
G + V++SP RRV A+ + AR R+ K++AE LA+ELI+AA
Sbjct: 77 SRRVGGATYQVPVEVSPERRVALAIRWILEAAR---KRSGKSMAEKLANELIDAANN--K 131
Query: 134 SYAIKKKDEIERVAKANR 151
AIKKK+E ++A+ANR
Sbjct: 132 GSAIKKKEETHKMAEANR 149
>gnl|CDD|176994 CHL00053, rps7, ribosomal protein S7.
Length = 155
Score = 71.8 bits (177), Expect = 1e-16
Identities = 50/136 (36%), Positives = 77/136 (56%), Gaps = 9/136 (6%)
Query: 18 RLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--ATRI 75
RL N L+ +GKK +A IV A++ I T++NP+ V+ A+ N P + A R+
Sbjct: 21 RLVNMLVNRILKSGKKSLAYRIVYRALKKIQQKTEKNPLSVLRQAIRNVTPDVEVKARRV 80
Query: 76 GSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECLADELINAAKGSSNSY 135
G G + ++I R A+ L +R+ + RN +A L+ EL++AAKGS N
Sbjct: 81 G--GSTYQVPIEIGSTRGKALAIRWLLKASRKRSGRN---MAFKLSSELVDAAKGSGN-- 133
Query: 136 AIKKKDEIERVAKANR 151
AI+KK+E R+A+ANR
Sbjct: 134 AIRKKEETHRMAEANR 149
>gnl|CDD|235398 PRK05302, PRK05302, 30S ribosomal protein S7; Validated.
Length = 156
Score = 70.5 bits (174), Expect = 3e-16
Identities = 48/139 (34%), Positives = 78/139 (56%), Gaps = 13/139 (9%)
Query: 15 IVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--A 72
+V + N LM+ G KK +A IV A++II T ++P++V A+ N P + +
Sbjct: 22 LVTKFINKLMLDG----KKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPVVEVKS 77
Query: 73 TRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECLADELINAAKGSS 132
R+G G + V++ P RR A+ L AR+ R KT+AE LA+EL++AA
Sbjct: 78 RRVG--GATYQVPVEVRPERRQALAMRWLVEAARK---RGEKTMAERLANELLDAANNRG 132
Query: 133 NSYAIKKKDEIERVAKANR 151
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 = 63.5 bits (155), Expect = 1e-13
Identities = 45/139 (32%), Positives = 76/139 (54%), Gaps = 13/139 (9%)
Query: 15 IVERLTNSLMMHGRNNGKKLMAVLIVKHAMEIIHLLTDQNPIQVIVDAVINSGPRED--A 72
++ + N +M G KK +A IV A E I T ++P++V A+ N P + +
Sbjct: 20 LLNKFINRVMKDG----KKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVKPLVEVKS 75
Query: 73 TRIGSAGVVRRQAVDISPLRRVNQALYLLTTGARESAFRNIKTIAECLADELINAAKGSS 132
R+G G + V++ P RR A+ L AR+ R K++AE LA+E+++AA +
Sbjct: 76 RRVG--GATYQVPVEVRPSRRYALAIRWLIEAARK---RGGKSMAERLANEILDAANNTG 130
Query: 133 NSYAIKKKDEIERVAKANR 151
AIKK+++ R+A+AN+
Sbjct: 131 A--AIKKREDTHRMAEANK 147
>gnl|CDD|212578 cd11705, DHR2_DOCK4, Dock Homology Region 2, a GEF domain, of Class
B Dedicator of Cytokinesis 4. Dock4 is an atypical
guanine nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for free
GTP. It plays a role in regulating dendritic growth and
branching in hippocampal neurons, where it is highly
expressed. It may also regulate spine morphology and
synapse formation. Dock4 activates the Ras family GTPase
Rap1, probably indirectly through interaction with Rap
regulatory proteins. DOCK proteins are divided into four
classes (A-D) based on sequence similarity and domain
architecture; class B includes Dock3 and 4. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock4, which
contains the catalytic GEF activity for Rac and/or
Cdc42. Class B DOCKs also contain an SH3 domain at the
N-terminal region and a PxxP motif at the C-terminus.
Length = 391
Score = 27.3 bits (60), Expect = 3.8
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 80 VVRRQAVDISPLRRV-------NQALYLLTTGARESAFRNIKTIAECLADELINAAKGSS 132
V +R+ V++SPL NQ L L + + +NI + CL + A G
Sbjct: 262 VEKREVVEMSPLENAIEVLENKNQQLRTLISQCQTRQMQNINPLTMCLNGVIDAAVNGGV 321
Query: 133 NSY 135
+ Y
Sbjct: 322 SRY 324
>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 = 26.4 bits (59), Expect = 4.9
Identities = 9/14 (64%), Positives = 11/14 (78%), Gaps = 1/14 (7%)
Query: 90 PLRRVNQALYLLTT 103
PLRRVNQ Y++ T
Sbjct: 50 PLRRVNQR-YVIAT 62
>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 = 5.1
Identities = 10/47 (21%), Positives = 18/47 (38%)
Query: 46 IIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLR 92
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 = 26.4 bits (58), Expect = 7.0
Identities = 16/62 (25%), Positives = 21/62 (33%), Gaps = 10/62 (16%)
Query: 10 KAQCPIVERLTNSLMMHGRNNGK--KLMAVLIVKHAMEIIHLLTDQNPIQVIVDAVINSG 67
+A E L + +M HG G + V HA I PI + V V G
Sbjct: 88 RAVIENNEPLAHHIMQHGLEYGIDWAVARSFTVDHAATI--------PIHLAVRPVRAKG 139
Query: 68 PR 69
Sbjct: 140 KG 141
>gnl|CDD|213272 cd05904, 4CL, 4-Coumarate-CoA Ligase (4CL). 4-Coumarate:coenzyme A
ligase is a key enzyme in the phenylpropanoid metabolic
pathway for monolignol and flavonoid biosynthesis. It
catalyzes the synthesis of hydroxycinnamate-CoA
thioesters in a two-step reaction, involving the
formation of hydroxycinnamate-AMP anhydride and the
nucleophilic substitution of AMP by CoA. The
phenylpropanoid pathway is one of the most important
secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 504
Score = 26.4 bits (59), Expect = 8.1
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 59 IVDAVINSGPREDATRIGSAGVVRRQAVDISP 90
I DA + P E+A I A VVR+ ++S
Sbjct: 434 IADAAVIPYPDEEAGEIPMAFVVRQPGSELSE 465
>gnl|CDD|215312 PLN02574, PLN02574, 4-coumarate--CoA ligase-like.
Length = 560
Score = 26.3 bits (58), Expect = 8.1
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 13/54 (24%)
Query: 59 IVDAVINSGPREDATRIGSAGVVRRQ-------------AVDISPLRRVNQALY 99
I+DA + + P ++ I A VVRRQ A ++P ++V + ++
Sbjct: 478 IIDAAVTAVPDKECGEIPVAFVVRRQGSTLSQEAVINYVAKQVAPYKKVRKVVF 531
>gnl|CDD|224208 COG1289, COG1289, Predicted membrane protein [Function unknown].
Length = 674
Score = 26.2 bits (58), Expect = 9.0
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 56 IQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQALYLLTT 103
+++ A N+ + + + ++R + S RR N LY L
Sbjct: 189 GELLDTARQNAALVDALAQTLTLRLLRSAGFEGSRGRRRNLRLYFLAQ 236
>gnl|CDD|143468 cd07150, ALDH_VaniDH_like, Pseudomonas putida vanillin
dehydrogenase-like. Vanillin dehydrogenase (Vdh,
VaniDH) involved in the metabolism of ferulic acid and
other related sequences are included in this CD. The
E. coli vanillin dehydrogenase (LigV) preferred NAD+ to
NADP+ and exhibited a broad substrate preference,
including vanillin, benzaldehyde, protocatechualdehyde,
m-anisaldehyde, and p-hydroxybenzaldehyde.
Length = 451
Score = 26.1 bits (58), Expect = 9.7
Identities = 22/75 (29%), Positives = 28/75 (37%), Gaps = 6/75 (8%)
Query: 50 LTDQNPIQVIVDAVINSGPREDATR-IGSAGVVRRQAVDISPLRRVNQALYLLTTGARES 108
D NP V A + G R+DA R I +A +P R LL A E
Sbjct: 1 FDDLNPADGSVYARVAVGSRQDAERAIAAAYDAFPAWAATTPSER---ERILLK--AAEI 55
Query: 109 AFRNIKTIAECLADE 123
R + + L DE
Sbjct: 56 MERRADDLIDLLIDE 70
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 0.133 0.362
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: 7,637,470
Number of extensions: 700131
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 583
Number of HSP's successfully gapped: 26
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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: 54 (24.4 bits)