RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15838
(399 letters)
>gnl|CDD|216666 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists
of FtsJ from various bacterial and archaeal sources FtsJ
is a methyltransferase, but actually has no effect on
cell division. FtsJ's substrate is the 23S rRNA. The 1.5
A crystal structure of FtsJ in complex with its cofactor
S-adenosylmethionine revealed that FtsJ has a
methyltransferase fold. This family also includes the N
terminus of flaviviral NS5 protein. It has been
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 97.3 bits (243), Expect = 6e-24
Identities = 49/218 (22%), Positives = 77/218 (35%), Gaps = 45/218 (20%)
Query: 145 AWCKFHEIVHSYNIVPQQENSFTSIHLCEAPGAFITSLNHYLKLHHPRMQWDWIANTLNP 204
A K EI + + P T + L APG F L +A L P
Sbjct: 5 AAYKLLEIDERFGLKP--GKGKTVLDLGAAPGGFSQVLLERGGAGK------VVAVDLGP 56
Query: 205 HYEGNSFDEMISDDRLILGTHRKWYFGPDNTGNILVQNFVSHFKQHIGFLLIHDTSLAPH 264
E I + G+I + ++ +
Sbjct: 57 -------MEPIQGVYFL-------------RGDITDPETLEKLRELLPGK---------- 86
Query: 265 CTHASHCFLVTADGSFDCQGNPGEQEILVGKLHYREVQIALSLLHNGGNLVIKIFTIFES 324
LV +DG+ + G + +L + +AL +L GGN V+K+F FE
Sbjct: 87 ------VDLVLSDGAPNVSGIENTDSFISLQLVLAALLLALEVLRPGGNFVVKVFKGFE- 139
Query: 325 DTICLMYLLACLFTSVDLFKPATSKEGNSEIYVICRDF 362
++ L+ L F V +FKP S+ +SE Y++C F
Sbjct: 140 FSVELLEKLKKGFEKVGIFKPPASRPSSSEEYLVCLGF 177
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 42.6 bits (101), Expect = 1e-04
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 297 HYREVQIALSLLH-------NGGNLVIKIFTIFESDTICLMYLLACLFTSVDLFKPATSK 349
H R + + L GG+ V K+F + + L+ L LF V +FKP S+
Sbjct: 131 HARSMYLCELALEFALEVLKPGGSFVAKVFQGEDFED--LLKALRRLFRKVKIFKPKASR 188
Query: 350 EGNSEIYVICRDF 362
+ + EIY++ + F
Sbjct: 189 KRSREIYLVAKGF 201
>gnl|CDD|232976 TIGR00438, rrmJ, cell division protein FtsJ. Methylates the 23S
rRNA. Previously known as cell division protein ftsJ.//
Trusted cutoff too high? [SS 10/1/04] [Protein
synthesis, tRNA and rRNA base modification].
Length = 188
Score = 41.7 bits (98), Expect = 2e-04
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 302 QIALSLLHNGGNLVIKIFTIFESDTICLMYLLACLFTSVDLFKPATSKEGNSEIYVICRD 361
IA +L GN V+K+F E D + L LF V + KP S++ ++E+Y++ +
Sbjct: 130 DIAKEVLKPKGNFVVKVFQGEEIDEY--LNELRKLFEKVKVTKPQASRKRSAEVYIVAKR 187
Query: 362 F 362
F
Sbjct: 188 F 188
>gnl|CDD|162022 TIGR00754, bfr, bacterioferritin. Bacterioferritin, predominantly
an iron-storage protein restricted to Bacteria, has also
been designated cytochrome b1 and cytochrome
b-557.Bacterioferritin is a homomultimer most species.
In Neisseria gonorrhoeae, Synechocystis PCC6803,
Magnetospirillum magnetotacticum, and Pseudomonas
aeruginosa, two types of subunit are found in a
heteromultimeric complex, with each species having one
member of each type. At present, both types of subunit
are including in this single model [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 157
Score = 38.6 bits (90), Expect = 0.002
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 170 HLCEAPGAFITSLNHYLKLHHPRMQWDWIANTLNPHYEGNSFDEMISDDRLI 221
HL + +T++N Y H RMQ +W L H S DEM D +I
Sbjct: 10 HLNKQLTNELTAINQYFL--HARMQKNWGLKELADHEYHESIDEMKHADEII 59
>gnl|CDD|222672 pfam14314, Methyltrans_Mon, Virus-capping methyltransferase. This
is the methyltransferase region of the Mononegavirales
single-stranded RNA viral RNA polymerase enzymes. This
region is involved in the mRNA-capping of the virion
particles.
Length = 674
Score = 35.0 bits (81), Expect = 0.068
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 304 ALSLLHNGGNLVIKIF-TIFESDTICLMYLLACLFTSVDLFKPATSKEGNSEIYVICRD 361
LSLL G+L+ K + T ++ + L LF SV L + S SE+YV+ +
Sbjct: 442 VLSLLEEPGSLIFKTYGTYLINENYNALDHLGRLFPSVQLVQTEYSSSFTSEVYVVFKK 500
>gnl|CDD|225104 COG2193, Bfr, Bacterioferritin (cytochrome b1) [Inorganic ion
transport and metabolism].
Length = 157
Score = 32.7 bits (75), Expect = 0.16
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 170 HLCEAPGAFITSLNHYLKLHHPRMQWDWIANTLNPHYEGNSFDEMISDDRLI 221
L EA G + ++N Y H RM +W L H S +EM D+LI
Sbjct: 10 LLNEALGLELAAINQYF--LHSRMYKNWGLTKLAAHEYHESIEEMKHADQLI 59
>gnl|CDD|153099 cd00907, Bacterioferritin, Bacterioferritin, ferritin-like
diiron-binding domain. Bacterioferritins, also known as
cytochrome b1, are members of a broad superfamily of
ferritin-like diiron-carboxylate proteins. Similar to
ferritin in architecture, Bfr forms an oligomer of 24
subunits that assembles to form a hollow sphere with 432
symmetry. Up to 12 heme cofactor groups (iron
protoporphyrin IX or coproporphyrin III) are bound
between dimer pairs. The role of the heme is unknown,
although it may be involved in mediating iron-core
reduction and iron release. Each subunit is composed of
a four-helix bundle which carries a diiron ferroxidase
center; it is here that initial oxidation of ferrous
iron by molecular oxygen occurs, facilitating the
detoxification of iron, protection against dioxygen and
radical products, and storage of ferric-hydroxyphosphate
at the core. Some bacterioferritins are composed of two
subunit types, one conferring heme-binding ability
(alpha) and the other (beta) bestowing ferroxidase
activity.
Length = 153
Score = 31.4 bits (72), Expect = 0.43
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 170 HLCEAPGAFITSLNHYLKLHHPRMQWDWIANTLNPHYEGNSFDEMISDDRLI 221
L +A +T++N Y LH RM DW L + S +EM D+LI
Sbjct: 9 ALNKALTGELTAINQYF-LHA-RMLEDWGLEKLAERFRKESIEEMKHADKLI 58
>gnl|CDD|215523 PLN02969, PLN02969, 9-cis-epoxycarotenoid dioxygenase.
Length = 610
Score = 30.9 bits (70), Expect = 1.4
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 11/51 (21%)
Query: 32 NFSEEALNHFNKKYQLYNASSSYKLSDGETWFSQTK-----WQNTQLAPTL 77
N EE + N + QL+ ++ SY+ WFS + WQN +L P++
Sbjct: 393 NAYEERDDRGNLRIQLHASACSYQ------WFSFHRMFGYDWQNKKLDPSV 437
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 75 PTLFSHFNIKTIPSIKLEN-----FQALKEKLNDVKSNLNH 110
P F +FN+++ ++ E + LK+KL D++ L+
Sbjct: 225 PDKF-YFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264
>gnl|CDD|182604 PRK10635, PRK10635, bacterioferritin; Provisional.
Length = 158
Score = 27.9 bits (62), Expect = 6.2
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 170 HLCEAPGAFITSLNHYLKLHHPRMQWDWIANTLNPHYEGNSFDEMISDDRLI 221
+L + G + ++N Y H RM +W LN S DEM D+ I
Sbjct: 10 YLNKLLGNELVAINQYFL--HARMFKNWGLMRLNDVEYHESIDEMKHADKYI 59
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 28.5 bits (64), Expect = 6.5
Identities = 17/39 (43%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 139 PQLATQ-AWCKFHEIVHSYNIVPQQENSFTSIHLCEAPG 176
PQL Q A C V V + E+SFT HLCE G
Sbjct: 279 PQLHKQMAICGDFRRVFEIGPVFRAEDSFTHRHLCEFTG 317
>gnl|CDD|238840 cd01683, EF2_IV_snRNP, EF-2_domain IV_snRNP domain is a part of
116kD U5-specific protein of the U5 small nucleoprotein
(snRNP) particle, essential component of the
spliceosome. The protein is structurally closely related
to the eukaryotic translational elongation factor EF2.
This domain has been also identified in 114kD
U5-specific protein of Saccharomyces cerevisiae and may
play an important role either in splicing process itself
or the recycling of spliceosomal snRNP.
Length = 178
Score = 27.6 bits (62), Expect = 9.1
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 12/38 (31%)
Query: 228 WYFGPDNTG-NILV---------QNFVSHFKQHI--GF 253
W FGPD G N+L+ +N ++ K+ I GF
Sbjct: 77 WAFGPDTKGPNVLIDDTLPEEVDKNLLNSVKESIVQGF 114
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
0.321 0.134 0.423
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,512,566
Number of extensions: 1799633
Number of successful extensions: 1438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1435
Number of HSP's successfully gapped: 19
Length of query: 399
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 300
Effective length of database: 6,546,556
Effective search space: 1963966800
Effective search space used: 1963966800
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 (21.9 bits)
S2: 60 (26.9 bits)