RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8832
(144 letters)
>gnl|CDD|238123 cd00202, ZnF_GATA, Zinc finger DNA binding domain; binds
specifically to DNA consensus sequence [AT]GATA[AG]
promoter elements; a subset of family members may also
bind protein; zinc-finger consensus topology is
C-X(2)-C-X(17)-C-X(2)-C.
Length = 54
Score = 57.0 bits (138), Expect = 4e-12
Identities = 22/39 (56%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 39 ECVNCAANSTPLWRRDG-TGHHLCNACGLYNRINGVNRP 76
C NC +TPLWRR G LCNACGLY + +GV RP
Sbjct: 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRP 39
Score = 53.9 bits (130), Expect = 7e-11
Identities = 21/36 (58%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 97 SCANCSTTCTTLWRRN-NNGEPVCNACGLYFKLHNV 131
+C+NC TT T LWRR + G +CNACGLY+K H V
Sbjct: 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36
>gnl|CDD|214648 smart00401, ZnF_GATA, zinc finger binding to DNA consensus sequence
[AT]GATA[AG].
Length = 52
Score = 56.7 bits (137), Expect = 6e-12
Identities = 23/40 (57%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 93 RSGVSCANCSTTCTTLWRRNNNGE-PVCNACGLYFKLHNV 131
SG SC+NC TT T LWRR +G +CNACGLY+K H
Sbjct: 1 GSGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40
Score = 50.5 bits (121), Expect = 1e-09
Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 37 IKECVNCAANSTPLWRRDGTGHH-LCNACGLYNRINGVNRPPVR 79
+ C NC TPLWRR +G+ LCNACGLY + +G + P+
Sbjct: 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLS 46
>gnl|CDD|109380 pfam00320, GATA, GATA zinc finger. This domain uses four cysteine
residues to coordinate a zinc ion. This domain binds to
DNA. Two GATA zinc fingers are found in the GATA
transcription factors. However there are several
proteins which only contains a single copy of the
domain.
Length = 36
Score = 53.0 bits (128), Expect = 1e-10
Identities = 19/35 (54%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 98 CANCSTTCTTLWRRNNNGEP-VCNACGLYFKLHNV 131
C+NC TT T LWRR +G +CNACGLY++ H +
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGLYYRKHGL 35
Score = 50.7 bits (122), Expect = 8e-10
Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 40 CVNCAANSTPLWRRDGTGH-HLCNACGLYNRINGVN 74
C NC TPLWRR G+ LCNACGLY R +G+
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGLYYRKHGLK 36
>gnl|CDD|227928 COG5641, GAT1, GATA Zn-finger-containing transcription factor
[Transcription].
Length = 498
Score = 56.0 bits (135), Expect = 5e-10
Identities = 32/103 (31%), Positives = 43/103 (41%), Gaps = 18/103 (17%)
Query: 40 CVNCAANSTPLWRRD-----GTGHHLCNACGLYNRINGVNRPP------VRTNQKKALQQ 88
C NC STPLWRR G++LCNACGLY +++G R P ++
Sbjct: 161 CSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRSSRSSH 220
Query: 89 TGNKRSGV-----SCANCSTTCTT-LWRRNNNGEPV-CNACGL 124
N +G S N S + T W G + +A L
Sbjct: 221 NNNDSNGENANTESIGNSSASKLTKSWEERPQGRQLLSDAGSL 263
Score = 49.5 bits (118), Expect = 1e-07
Identities = 21/45 (46%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 97 SCANCSTTCTTLWRR-----NNNGEPVCNACGLYFKLHNVFTILF 136
C+NC TT T LWRR + G +CNACGLY KLH
Sbjct: 160 VCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPI 204
Score = 40.2 bits (94), Expect = 1e-04
Identities = 27/93 (29%), Positives = 35/93 (37%), Gaps = 10/93 (10%)
Query: 42 NCAANSTPLWRR-DGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVSCAN 100
+ +TPLWRR CNA G + G RP + + KRS +C N
Sbjct: 303 LTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNS------KRSNATCMN 356
Query: 101 CSTTCTTLWRRNNNGEPVCNACGLYFKLHNVFT 133
CS+T T N+ G KL N
Sbjct: 357 CSSTPTNKILSPPTT---SNSPGAQVKLPNQTR 386
>gnl|CDD|224657 COG1743, COG1743, Adenine-specific DNA methylase containing a
Zn-ribbon [DNA replication, recombination, and repair].
Length = 875
Score = 30.9 bits (70), Expect = 0.23
Identities = 14/65 (21%), Positives = 18/65 (27%), Gaps = 2/65 (3%)
Query: 13 VTDGPFQAYL-TVIDWPQNMMLNMDIK-ECVNCAANSTPLWRRDGTGHHLCNACGLYNRI 70
V G AY+ + N++ E V A D C CG
Sbjct: 199 VKRGKRVAYMDVEEEGKGNIIFEGVGYVEEVEEAEEEGKGTVGDIERRVTCLRCGRVISY 258
Query: 71 NGVNR 75
V R
Sbjct: 259 ADVKR 263
>gnl|CDD|177576 PHA03286, PHA03286, envelope glycoprotein E; Provisional.
Length = 492
Score = 29.1 bits (65), Expect = 0.74
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 3 LIVCVLIRH--HVTDGPFQAYLTVIDWPQNMMLNMDIKECVNCAANSTPLW-------RR 53
I + R H T+G FQAY + P N + + C S L ++
Sbjct: 410 CIAGLYRRRRRHRTNGYFQAYPKYMSLPSNDEGDFNSPLSNTCEGLSRGLANEKSRTPKQ 469
Query: 54 DGTGHH 59
G+ +H
Sbjct: 470 KGSRYH 475
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 28.4 bits (64), Expect = 1.1
Identities = 11/28 (39%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 97 SCANCSTTCTTLWRRNNNGEPVCNACGL 124
SC C T + GE VC CGL
Sbjct: 3 SCPECG--STNIITDYERGEIVCADCGL 28
>gnl|CDD|233353 TIGR01311, glycerol_kin, glycerol kinase. This model describes
glycerol kinase, a member of the FGGY family of
carbohydrate kinases [Energy metabolism, Other].
Length = 493
Score = 27.6 bits (62), Expect = 2.6
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 83 KKALQQTGNKRSGVSC---ANCSTTCTTLWRRNNNGEPVCNA 121
+AL + G K ++ N T T +W + G+P+ NA
Sbjct: 58 AEALAKAGIKPDDIAAIGITNQRET-TVVWDKAT-GKPLYNA 97
>gnl|CDD|235832 PRK06567, PRK06567, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase; Validated.
Length = 1028
Score = 27.6 bits (61), Expect = 2.9
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 56 TGHHLCNACG---LYNRINGVNRPPVRTN 81
TGH +CN C +Y + + VN P + +N
Sbjct: 319 TGHRICNDCSKACIYQKQDPVNIPLIESN 347
>gnl|CDD|240158 cd05119, RIO, RIO kinase family, catalytic domain. The RIO kinase
catalytic domain family is part of a larger superfamily,
that includes the catalytic domains of other kinases
such as the typical serine/threonine/tyrosine protein
kinases (PKs), aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase (PI3K).
RIO kinases are atypical protein serine kinases present
in archaea, bacteria and eukaryotes. Serine kinases
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine residues in protein substrates. RIO
kinases contain a kinase catalytic signature, but
otherwise show very little sequence similarity to
typical PKs. The RIO catalytic domain is truncated
compared to the catalytic domains of typical PKs, with
deletions of the loops responsible for substrate
binding. Most organisms contain at least two RIO
kinases, RIO1 and RIO2. A third protein, RIO3, is
present in multicellular eukaryotes. In yeast, RIO1 and
RIO2 are essential for survival. They function as
non-ribosomal factors necessary for late 18S rRNA
processing. RIO1 is also required for proper cell cycle
progression and chromosome maintenance. The biological
substrates for RIO kinases are still unknown.
Length = 187
Score = 27.1 bits (61), Expect = 3.1
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 10/30 (33%)
Query: 22 LTVIDWPQ---------NMMLNMDIKECVN 42
+ +ID PQ L D+ E +N
Sbjct: 153 VYIIDVPQAVEIDHPNAEEFLRRDV-ENIN 181
>gnl|CDD|226711 COG4260, COG4260, Membrane protease subunit, stomatin/prohibitin
family [Amino acid transport and metabolism].
Length = 345
Score = 26.8 bits (59), Expect = 4.3
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 7/63 (11%)
Query: 68 NRINGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTT-------CTTLWRRNNNGEPVCN 120
+ R ++ NQ +A Q + CA C+ C T +N C
Sbjct: 279 QGMMESLRTSLQGNQGQAQAQAAAPAATWPCARCAKLNFCLNCGCGTTADFDNGKAKFCP 338
Query: 121 ACG 123
CG
Sbjct: 339 ECG 341
>gnl|CDD|236637 PRK09970, PRK09970, xanthine dehydrogenase subunit XdhA;
Provisional.
Length = 759
Score = 27.0 bits (60), Expect = 4.5
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 82 QKKALQQTGNKRSGVSCA 99
+ + Q GN R GV A
Sbjct: 428 RAECKNQQGNLRRGVGVA 445
>gnl|CDD|198346 cd07768, FGGY_RBK_like, Ribulokinase-like carbohydrate kinases; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is composed of ribulokinases (RBKs) and
similar proteins from bacteria and eukaryota. RBKs
catalyze the MgATP-dependent phosphorylation of a
variety of sugar substrates including L- and/or
D-ribulose. Members of this subfamily contain two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. Members of this
subfamily belong to the FGGY family of carbohydrate
kinases.
Length = 465
Score = 26.7 bits (59), Expect = 5.5
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 76 PPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNA 121
P VRT + A+ G V+ T T+ + G+P+ A
Sbjct: 52 PAVRTAVRAAVAAAGVDPDQVAALGVDATSCTVVPLDAEGQPLTPA 97
>gnl|CDD|234345 TIGR03755, conj_TIGR03755, integrating conjugative element protein,
PFL_4711 family. Members of this protein family are
found in genomic regions associated with conjugative
transfer and integrated TOL-like plasmids. The specific
function is unknown [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 418
Score = 26.5 bits (59), Expect = 5.7
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 66 LYNRING---VNRPPVRTNQKKALQQTGNKRSGVSCAN 100
+Y I G V+ PP R Q KA+ R+ + C N
Sbjct: 4 VYYSIGGGSAVSAPPGRAGQMKAIGVGAGWRANLMCGN 41
>gnl|CDD|129374 TIGR00273, TIGR00273, iron-sulfur cluster-binding protein. Members
of this family have a perfect 4Fe-4S binding motif
C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or
imperfect (the first Cys replaced by Ser) second copy.
Members probably bind two 4fe-4S iron-sulfur clusters
[Energy metabolism, Electron transport].
Length = 432
Score = 26.4 bits (58), Expect = 7.2
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 15 DGPFQAYLTVIDWPQNMMLNMDIKE---CVNCAA--NSTPLWRRDGTGH 58
DGP + +L ++D ++ +L + +E C+ C A N P++R G GH
Sbjct: 267 DGPEEFHLILLDNGRSNILATEFREVLACIRCGACQNECPVYRHIG-GH 314
>gnl|CDD|238184 cd00296, SIR2, SIR2 superfamily of proteins includes silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation, where the
acetyl group from the lysine epsilon-amino group is
transferred to the ADP-ribose moiety of NAD+, producing
nicotinamide and the novel metabolite
O-acetyl-ADP-ribose. Sir2 proteins, also known as
sirtuins, are found in all eukaryotes and many archaea
and prokaryotes and have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
The most-studied function, gene silencing, involves the
inactivation of chromosome domains containing key
regulatory genes by packaging them into a specialized
chromatin structure that is inaccessible to DNA-binding
proteins. The oligomerization state of Sir2 appears to
be organism-dependent, sometimes occurring as a monomer
and sometimes as a multimer. Also included in this
superfamily is a group of uncharacterized Sir2-like
proteins which lack certain key catalytic residues and
conserved zinc binding cysteines.
Length = 222
Score = 26.2 bits (58), Expect = 7.2
Identities = 8/37 (21%), Positives = 10/37 (27%)
Query: 96 VSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNVF 132
V C +C P C CG + V
Sbjct: 114 VRCTSCGKEYPRDEVLEREKPPRCPKCGGLLRPDVVD 150
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription
factor TFIIB contains a zinc-binding motif near the
N-terminus. This domain is involved in the interaction
with RNA pol II and TFIIF and plays a crucial role in
selecting the transcription initiation site. The domain
adopts a zinc ribbon like structure.
Length = 40
Score = 23.8 bits (52), Expect = 8.5
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 98 CANCSTTCTTLWRRNNNGEPVCNACGL 124
C NC +T GE VC CGL
Sbjct: 3 CPNCGSTEIV--FDYERGEYVCTECGL 27
>gnl|CDD|227611 COG5291, COG5291, Predicted membrane protein [Function unknown].
Length = 313
Score = 26.1 bits (57), Expect = 8.7
Identities = 17/89 (19%), Positives = 24/89 (26%), Gaps = 14/89 (15%)
Query: 45 ANSTPLWRRDGTGHHLCNACGLYNRINGVNR---------PPVRTNQKKALQQTGN-KRS 94
STP W + H + C I + +Q A G+
Sbjct: 204 ILSTPCWVKKLFNEHPSSFCSARKGITIRHERNMGYSNASTTTEESQCCAETFKGSGVVL 263
Query: 95 GVSCANCSTTCTTLWRRNNN----GEPVC 119
G ST + NN E +C
Sbjct: 264 GTKSMAVSTVVGSSTEAKNNYLDFTEALC 292
>gnl|CDD|233239 TIGR01031, rpmF_bact, ribosomal protein L32. This protein
describes bacterial ribosomal protein L32. The noise
cutoff is set low enough to include the equivalent
protein from mitochondria and chloroplasts. No related
proteins from the Archaea nor from the eukaryotic
cytosol are detected by this model. This model is a
fragment model; the putative L32 of some species shows
similarity only toward the N-terminus [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 55
Score = 24.2 bits (53), Expect = 9.6
Identities = 9/31 (29%), Positives = 11/31 (35%), Gaps = 8/31 (25%)
Query: 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYNR 69
C NC P H +C +CG Y
Sbjct: 28 VCPNCGEFKLP--------HRVCPSCGYYKG 50
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
0.325 0.137 0.466
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,864,560
Number of extensions: 539670
Number of successful extensions: 529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 519
Number of HSP's successfully gapped: 40
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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 (21.6 bits)
S2: 54 (24.6 bits)