RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4574
(343 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 31.6 bits (72), Expect = 0.032
Identities = 14/26 (53%), Positives = 20/26 (76%)
Query: 269 SLANHMNTHTGLKPHCCEICGRSYST 294
+L HM THTG KP+ C +CG+S+S+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 26.6 bits (59), Expect = 1.9
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 297 YLKVHMSCHTGETSHTCHLCPQKFRQ 322
L+ HM HTGE + C +C + F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 32.6 bits (75), Expect = 0.064
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 16/76 (21%)
Query: 66 ECSLCNESFENKKVLFRHLRGKHGMKIKLSRHKT---------------KCVCHYCNRTF 110
+C CN + + + H+ HG I + C YC + F
Sbjct: 1 DCLFCNHTSDTVEENLEHMFKSHGFFIPEREYLVDLEGLLNYLREKIHEGNECLYCGKQF 60
Query: 111 DSKAKIQEHIIS-SHM 125
S +++H+ H
Sbjct: 61 KSLEALRQHMRDKGHC 76
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR
transcriptional regulator proteins. The ros chromosomal
gene is present in octopine and nopaline strains of
Agrobacterium tumefaciens as well as in Rhizobium
meliloti. This gene encodes a 15.5-kDa protein that
specifically represses the virC and virD operons in the
virulence region of the Ti plasmid and is necessary for
succinoglycan production. Sinorhizobium meliloti can
produce two types of acidic exopolysaccharides,
succinoglycan and galactoglucan, that are
interchangeable for infection of alfalfa nodules. MucR
from Sinorhizobium meliloti acts as a transcriptional
repressor that blocks the expression of the exp genes
responsible for galactoglucan production therefore
allowing the exclusive production of succinoglycan.
Length = 130
Score = 31.7 bits (73), Expect = 0.20
Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 15/45 (33%)
Query: 47 SITQTYIHYLECKNRGKLYECSLCNESFENKKVLFRHLRGKHGMK 91
S+T YI LE GK + K L RHLR HG+
Sbjct: 65 SVTPDYIICLED---GKKF------------KTLKRHLRTHHGLT 94
Score = 31.4 bits (72), Expect = 0.25
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 256 VCTICGKMLIDKRSLANHMNTHTGLKP 282
+C GK ++L H+ TH GL P
Sbjct: 72 ICLEDGKKF---KTLKRHLRTHHGLTP 95
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 33.2 bits (76), Expect = 0.22
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 95 SRHKTKCVCHYCNRTFDSKAKIQEHIISSH 124
+ + VC+ C F S ++ EH ++H
Sbjct: 68 PINPSSYVCNVCMAEFSSMDQLAEHQRTTH 97
>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin),
alpha and beta subunits [Energy production and
conversion].
Length = 317
Score = 29.6 bits (67), Expect = 2.1
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 34 DEERCRSCGLL-----SGSIT----QTYIHYLECKNRGKLYECSLCNES-FENKKVLFRH 83
DEE CR CG +G+IT + I +C GK C ++ F +KV
Sbjct: 170 DEELCRGCGKCVKVCPTGAITWDGKKLKIDGSKCIGCGKCIR--ACPKAAFRGEKVGIAI 227
Query: 84 LRGKHGMKI 92
L G +
Sbjct: 228 LVGGKTGRE 236
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.6 bits (67), Expect = 2.7
Identities = 19/87 (21%), Positives = 26/87 (29%), Gaps = 34/87 (39%)
Query: 52 YIHYLECKNRGKLYECSLCNESFENKKVLFRHLRGKHGMKIKLSRHKTKCVCHYCNRTFD 111
Y L C++ G + EC C+ L + + CHYC
Sbjct: 432 YAPLLLCRDCGYIAECPNCDSPLT------------------LHKATGQLRCHYCGY--- 470
Query: 112 SKAKIQEHIISSHMHEKLYQCDFCGSQ 138
QE I C CGS+
Sbjct: 471 -----QEPIPQ--------SCPECGSE 484
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 242
Score = 29.2 bits (66), Expect = 3.2
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 110 FDSKAKIQEHIISSHMH 126
FDSKA+++E+I +S +
Sbjct: 120 FDSKAEVEEYIRASGLP 136
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 26.3 bits (58), Expect = 3.5
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 103 CHYCNRTFDSKAKIQEHIISSHMHEKL 129
C C F K ++ EH++S H KL
Sbjct: 4 CLRCGGIFRKKKEVIEHLLSVHKQNKL 30
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.9 bits (64), Expect = 3.8
Identities = 21/79 (26%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 225 REFICDV--CGKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHMNTHTGLKP 282
+ + C V C K Y + L H HQ +K L + S KP
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQK---------LHENPSPEKMNIFSAKDKP 398
Query: 283 HCCEICGRSYSTAAYLKVH 301
+ CE+C + Y LK H
Sbjct: 399 YRCEVCDKRYKNLNGLKYH 417
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 26.5 bits (58), Expect = 4.1
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 65 YECSLCNESFENKKVLFRHLRGKHGMKIKLSRHK 98
YEC +C E + +K + HLR KH +KLS K
Sbjct: 6 YECPICGEIYIKRKSMITHLR-KHNTNLKLSNCK 38
>gnl|CDD|235984 PRK07272, PRK07272, amidophosphoribosyltransferase; Provisional.
Length = 484
Score = 28.9 bits (65), Expect = 4.5
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 198 CHKPNLTNHIQNVHLKSELEKRTAILK 224
H NLTN V L+ ELEK+ AI
Sbjct: 111 AHNGNLTN---AVSLRKELEKQGAIFH 134
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 25.2 bits (56), Expect = 6.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 65 YECSLCNESFENKKVLFRHLRGK 87
+ C LCN +F ++ L HLRGK
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGK 23
>gnl|CDD|150637 pfam09986, DUF2225, Uncharacterized protein conserved in bacteria
(DUF2225). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 214
Score = 28.0 bits (63), Expect = 6.8
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 63 KLYECSLCNESFENKKVLFRHLR 85
K C +CN F+ KKV LR
Sbjct: 4 KKIVCPVCNNEFKTKKVKSSGLR 26
>gnl|CDD|224178 COG1258, COG1258, Predicted pseudouridylate synthase [Translation,
ribosomal structure and biogenesis].
Length = 398
Score = 28.1 bits (63), Expect = 7.0
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 216 LEKRTAILKREFICDVC-GKSYVRKGALTEHHQREHQGKKPVCTICGKMLIDKRSLANHM 274
+EK IL + +CD C G+ + + G E+ +R G+ + +L
Sbjct: 4 IEKALEILAKYPLCDSCLGRCFAKLGTGLENRER------------GRAIKLSLALELDE 51
Query: 275 NTHTGLKPHCCEICG 289
++P C ICG
Sbjct: 52 EYKNEVEPEPCYICG 66
>gnl|CDD|234322 TIGR03709, PPK2_rel_1, polyphosphate:nucleotide phosphotransferase,
PPK2 family. Members of this protein family belong to
the polyphosphate kinase 2 (PPK2) family, which is not
related in sequence to PPK1. While PPK1 tends to act in
the biosynthesis of polyphosphate, or poly(P), members
of the PPK2 family tend to use the terminal phosphate of
poly(P) to regenerate ATP or GTP from the corresponding
nucleoside diphosphate, or ADP from AMP as is the case
with polyphosphate:AMP phosphotransferase (PAP). Members
of this protein family most likely transfer the terminal
phosphate between poly(P) and some nucleotide, but it is
not clear which [Central intermediary metabolism,
Phosphorus compounds].
Length = 264
Score = 27.9 bits (63), Expect = 7.1
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 82 RHLRGKHGMKIKLSRHKTKCVCHYCNRTFDSKAKIQEHIIS-SHMHEKLY 130
R G K+ L+ T Y ++ +++A + E + S + EKLY
Sbjct: 2 DTFRVTPGKKVNLADIDTDDTPGYDSKE-EAEALLAELVARLSDLQEKLY 50
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.7 bits (54), Expect = 7.1
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 311 HTCHLCPQKFRQRSSYTLHYKTH 333
+ C C + F+ +S+ H +TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.7 bits (54), Expect = 8.2
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 283 HCCEICGRSYSTAAYLKVHMSCH 305
+ C CG+ + + + L+ HM H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|223641 COG0567, SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase
(E1) component, and related enzymes [Energy production
and conversion].
Length = 906
Score = 28.0 bits (63), Expect = 8.1
Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 30/95 (31%)
Query: 146 YYHLRDKHLSKPANLSCEFCSRIFTK-KELLRSHLAVHKIGKNYQCYYCRKTYC------ 198
++ L + L + N+ F + +EL+ L +KTYC
Sbjct: 104 FHGLTEADLDETFNIGDGFLGKETMTLRELI-EIL--------------KKTYCGSIGVE 148
Query: 199 --HKPN------LTNHIQNVHLKSELEKRTAILKR 225
H + L I++ E++ AILKR
Sbjct: 149 YMHISDPEEKRWLQERIESGKPTFTAEEKKAILKR 183
>gnl|CDD|238698 cd01407, SIR2-fam, SIR2 family 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.
Length = 218
Score = 27.5 bits (62), Expect = 9.4
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 100 KCVCHYCNRTFDSKAKIQEHIISSHMHEKLYQCDFCGSQQRT 141
+ C C + + ++Q I E++ +C CG R
Sbjct: 109 RVRCTKCGKEYPR-DELQADI----DREEVPRCPKCGGLLRP 145
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 24.6 bits (54), Expect = 9.6
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 256 VCTICGKMLIDKRSLANHMNTH 277
C CGK K +L H+ TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
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
0.324 0.135 0.439
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,093,742
Number of extensions: 1405092
Number of successful extensions: 1999
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1977
Number of HSP's successfully gapped: 104
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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: 59 (26.4 bits)