RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7378
(90 letters)
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 65.9 bits (161), Expect = 3e-14
Identities = 22/42 (52%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 41 GGYLVYSTCSILPEENEAVVNYALRKR-DVKLVPTGLDFGTE 81
GG LVYSTCS+ PEENE VV L + D +L P L +G
Sbjct: 281 GGVLVYSTCSLTPEENEEVVERFLERHPDFELEPVRLPWGPL 322
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 63.6 bits (155), Expect = 1e-13
Identities = 30/45 (66%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 40 TGGYLVYSTCSILPEENEAVVNYALRKR-DVKLVPTGLDFGTEGF 83
GG LVYSTCS+LPEENEAV+ Y L+KR DV+LVPTGL G
Sbjct: 206 PGGVLVYSTCSVLPEENEAVIKYFLQKRPDVELVPTGLSEGKIAL 250
Score = 27.7 bits (62), Expect = 0.70
Identities = 19/70 (27%), Positives = 26/70 (37%), Gaps = 11/70 (15%)
Query: 21 KTSLIVILEAIDCLNA-RSPTGGY--------LVYSTCSILPEENEAVVNYALRKRDVK- 70
KT +L+A++ P G Y L YS S+ P EN AV +
Sbjct: 19 KTKRWSLLQALELAGVQLEPLGRYPHALPVGDLPYSIGSLPPFENGAVTVQDASSQLDAI 78
Query: 71 -LVPTGLDFG 79
L P +F
Sbjct: 79 ALNPQEDEFI 88
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 58.6 bits (142), Expect = 6e-12
Identities = 26/48 (54%), Positives = 29/48 (60%), Gaps = 5/48 (10%)
Query: 27 ILEAIDCLNARSPTGGYLVYSTCSILPEENEAVVNYALRKR-DVKLVP 73
I AID L GG LVYSTCS+ EENE V++Y LRKR DV
Sbjct: 182 IDAAIDALKP----GGVLVYSTCSLEVEENEEVIDYILRKRPDVVEEI 225
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 49.8 bits (120), Expect = 1e-08
Identities = 20/37 (54%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 41 GGYLVYSTCSILPEENEAVVNYAL-RKRDVKLVPTGL 76
GG L+Y+TCSILPEENE + L R D +L+ TG
Sbjct: 365 GGTLLYATCSILPEENEQQIKAFLARHPDAELLDTGT 401
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 49.0 bits (118), Expect = 2e-08
Identities = 28/86 (32%), Positives = 37/86 (43%), Gaps = 26/86 (30%)
Query: 22 TSLIVILEAIDCLNARSPT---GGYLVYSTCSILPEENEAVVNYALRKR-DVKLVPTGL- 76
SL I I L + + GG LVYSTC+I EENE V+ L + + +LVP
Sbjct: 352 ESLQEIQLEI--LESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEEHPEFELVPLQHE 409
Query: 77 -------------------DFGTEGF 83
D+GT+GF
Sbjct: 410 KPDELVYEVKDGYLQILPNDYGTDGF 435
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 43.8 bits (104), Expect = 1e-06
Identities = 18/34 (52%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 41 GGYLVYSTCSILPEENEAVVNYAL-RKRDVKLVP 73
GG LVY+TC++ P ENEA + L R D KL P
Sbjct: 377 GGTLVYATCTLHPAENEAQIEQFLARHPDWKLEP 410
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 41.0 bits (96), Expect = 1e-05
Identities = 14/21 (66%), Positives = 17/21 (80%)
Query: 40 TGGYLVYSTCSILPEENEAVV 60
TGG LVY+TCS+LPEEN +
Sbjct: 360 TGGTLVYATCSVLPEENSEQI 380
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 40.7 bits (96), Expect = 2e-05
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 1 MSNWYPLDSTLALRALSTIGKTSLIVILEAIDCLNARSPTGGYLVYSTCSILPEENEAVV 60
+ NW P +S L I T +I A L GG LVYSTC++ EEN+AV
Sbjct: 206 LKNWSP-ESNLE------IAATQRELIESAFHALK----PGGTLVYSTCTLNREENQAVC 254
Query: 61 NY 62
+
Sbjct: 255 LW 256
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 39.7 bits (93), Expect = 5e-05
Identities = 14/19 (73%), Positives = 15/19 (78%)
Query: 39 PTGGYLVYSTCSILPEENE 57
GG LVY+TCSI PEENE
Sbjct: 368 KPGGVLVYATCSIEPEENE 386
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 34.8 bits (80), Expect = 0.002
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 41 GGYLVYSTCSILPEENEAVVN-YALRKRDVKLVPTG---LDFGTEG 82
GG L+YSTC++ EEN VV + ++D +++ +F EG
Sbjct: 359 GGILLYSTCTVTKEENTEVVKRFVYEQKDAEVIDIRDKLEEFEVEG 404
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 27.4 bits (62), Expect = 0.89
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 28 LEAIDCLNARSPTGGYLVYSTCSILPE----ENEAVVNYALRKRDVKLVPTGLDFGTEGF 83
L I L P G + V+ S L ++ L + V +VP G+ FG G+
Sbjct: 308 LNEIPGLECPKPEGAFYVFPNVSKLLGKSITDSLEFAEALLEEAGVAVVP-GIAFGAPGY 366
Query: 84 V 84
V
Sbjct: 367 V 367
>gnl|CDD|218493 pfam05199, GMC_oxred_C, GMC oxidoreductase. This domain found
associated with pfam00732.
Length = 139
Score = 26.2 bits (58), Expect = 2.0
Identities = 8/42 (19%), Positives = 16/42 (38%)
Query: 29 EAIDCLNARSPTGGYLVYSTCSILPEENEAVVNYALRKRDVK 70
+ I + + TC + + ++ VV+ LR V
Sbjct: 69 DEILEYIRAAAVTSWHPMGTCRMGADPDDGVVDPDLRVHGVD 110
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 26.4 bits (59), Expect = 2.2
Identities = 14/36 (38%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 6 PLDSTLALRALSTIGKTSLIVILEA--IDCLNARSP 39
PL LALR LS I L L L R P
Sbjct: 92 PLIRGLALRTLSCIRVPELARDLAPDIKKLLVDRDP 127
>gnl|CDD|188126 TIGR01283, nifE, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifE. This protein is part of the NifEN complex
involved in biosynthesis of the molybdenum-iron cofactor
used by the homologous NifDK complex of nitrogenase. In
a few species, the protein is found as a NifEN fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 453
Score = 25.8 bits (57), Expect = 3.6
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 27 ILEAIDCLNARSPTGGYLVYSTC--SILPEENEAVVNYALRKRDVKLVP 73
+ AI + R VYSTC +++ ++ EAV A K + ++P
Sbjct: 106 LFHAIREIVERYHPPAVFVYSTCVPALIGDDLEAVCKAAAEKTGIPVIP 154
>gnl|CDD|225102 COG2191, COG2191, Formylmethanofuran dehydrogenase subunit E
[Energy production and conversion].
Length = 206
Score = 25.5 bits (56), Expect = 3.8
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 7/56 (12%)
Query: 17 STIGKTSLIVI----LEAIDCLNARSPTGGYLVYSTCSILPEENEAVVNYA-LRKR 67
TIG +LI++ L L R VY IL E+ E + +R
Sbjct: 72 CTIGNGNLILLDYGKLALT--LVKRGSGKAVRVYVKREILDEDPEKTELFPKVRAG 125
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 25.6 bits (57), Expect = 4.0
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 29 EAIDCLNARSPTGGYLVYSTC--SILPEENEAVVNYALRKRDVKLVPTGLDFGTEGFVNY 86
+AI R P VYSTC ++ ++ EAV A ++ + ++P EGF
Sbjct: 77 KAIKEAYERFPPKAIFVYSTCPTGLIGDDIEAVAKEASKELGIPVIP----VNCEGFRGV 132
Query: 87 RQNK 90
Q+
Sbjct: 133 SQSL 136
>gnl|CDD|178032 PLN02410, PLN02410, UDP-glucoronosyl/UDP-glucosyl transferase
family protein.
Length = 451
Score = 25.8 bits (56), Expect = 4.1
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 15/86 (17%)
Query: 1 MSNWYPLDSTLALRALSTIGKTSLIVILEAIDCLNARS-------------PTGG-YLVY 46
+S+W L+S + L + +T+ VI+ CL + S P G +LV
Sbjct: 182 VSHWASLESIMELYRNTVDKRTASSVIINTASCLESSSLSRLQQQLQIPVYPIGPLHLVA 241
Query: 47 STCSILPEENEAVVNYALRKRDVKLV 72
S + L EEN++ + + L K+ V
Sbjct: 242 SAPTSLLEENKSCIEW-LNKQKKNSV 266
>gnl|CDD|219681 pfam07983, X8, X8 domain. The X8 domain domain contains at least
6 conserved cysteine residues that presumably form
three disulphide bridges. The domain is found in an
Olive pollen allergen as well as at the C-terminus of
several families of glycosyl hydrolases. This domain
may be involved in carbohydrate binding. This domain is
characteristic of GPI-anchored domains.
Length = 77
Score = 24.5 bits (54), Expect = 4.6
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 29 EAIDC--LNARSPTGGYLVYSTCS 50
+ DC + A TG Y YS CS
Sbjct: 24 QGADCTGIQANGTTGKYGAYSMCS 47
>gnl|CDD|202492 pfam02977, CarbpepA_inh, Carboxypeptidase A inhibitor.
Length = 46
Score = 23.7 bits (51), Expect = 5.9
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 33 CLNARSPTGGYLVYSTCSILP 53
C + GGY S CSILP
Sbjct: 27 CWKLKKTCGGY-TGSACSILP 46
>gnl|CDD|193549 cd05674, M20_yscS, M20 Peptidase, carboxypeptidase yscS. Peptidase
M20 family, yscS (GlyX-carboxypeptidase, CPS1,
carboxypeptidase S, carboxypeptidase a, carboxypeptidase
yscS, glycine carboxypeptidase)-like subfamily. This
group mostly contains proteins that have been
uncharacterized to date, but also includes vacuolar
proteins involved in nitrogen metabolism which are
essential for use of certain peptides that are sole
nitrogen sources. YscS releases a C-terminal amino acid
from a peptide that has glycine as the penultimate
residue. It is synthesized as one polypeptide chain
precursor which yields two active precursor molecules
after carbohydrate modification in the secretory
pathway. The proteolytically unprocessed forms are
associated with the membrane, whereas the mature forms
of the enzyme are soluble. Enzymes in this subfamily
may also cleave intracellularly generated peptides in
order to recycle amino acids for protein synthesis.
Length = 441
Score = 25.2 bits (56), Expect = 6.1
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 11/38 (28%)
Query: 36 ARSPTGGYLVYSTCSI-----------LPEENEAVVNY 62
+ SP LV +T ++ LPEE A VN+
Sbjct: 279 SGSPATNALVRTTTAVTIINGGVKANVLPEEASATVNF 316
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 24.6 bits (54), Expect = 9.0
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 12 ALRALSTIGKTSLIVIL-------EAIDCLNAR 37
AL S GKTSLI ++ E LN R
Sbjct: 28 ALFGPSGSGKTSLINMIAGLTRPDEGRIELNGR 60
>gnl|CDD|175989 cd04022, C2A_MCTP_PRT_plant, C2 domain first repeat found in
Multiple C2 domain and Transmembrane region Proteins
(MCTP); plant subset. MCTPs are involved in Ca2+
signaling at the membrane. Plant-MCTPs are composed of
a variable N-terminal sequence, four C2 domains, two
transmembrane regions (TMRs), and a short C-terminal
sequence. It is one of four protein classes that are
anchored to membranes via a transmembrane region; the
others being synaptotagmins, extended synaptotagmins,
and ferlins. MCTPs are the only membrane-bound C2 domain
proteins that contain two functional TMRs. MCTPs are
unique in that they bind Ca2+ but not phospholipids. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-II topology.
Length = 127
Score = 24.2 bits (53), Expect = 9.5
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 42 GYLVYSTCSILPEENEAVVNYALRKRDV 69
G + S S +P V Y L KR +
Sbjct: 84 GRVRISGTSFVPPSEAVVQRYPLEKRGL 111
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
0.318 0.135 0.397
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,520,343
Number of extensions: 358778
Number of successful extensions: 302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 301
Number of HSP's successfully gapped: 26
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)