RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13123
(129 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 37.0 bits (85), Expect = 0.001
Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 11/114 (9%)
Query: 22 CGKQFTRKFSLNAHLHVHYGSSNYKCPL--CGKFFIQLCHMKDH--IQAHGGL---KPYV 74
CGK F+R +L H+ +H S K L F L + + +Q + L K
Sbjct: 329 CGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSE 388
Query: 75 CTY--CGKAFVRASDLKRHIDAHLGV--KKFACETCGKLFSSKHGLKYHVRTHK 124
C + F R S+L HI HL C K F+ + L H + H
Sbjct: 389 TLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442
Score = 36.6 bits (84), Expect = 0.002
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 44 NYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTY--CGKAFVRASDLKRHIDAH 95
CP C F +L H+ HI++H G KP C+Y C K+F R +L RH+ H
Sbjct: 33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 33.1 bits (75), Expect = 0.024
Identities = 22/55 (40%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 71 KPYVCTYCGKAFVRASDLKRHIDAHLGVKKFAC--ETCGKLFSSKHGLKYHVRTH 123
+P C C +F R L RHI +H G K C C K FS L H+RTH
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 30.4 bits (68), Expect = 0.24
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 70 LKPYVCTYCGKAFVRASDLKRHIDAHL----GVKKFAC--ETCGKLFSSKHGLKYHVRTH 123
P C +F R+S L RH+ + +K F+C CGKLFS LK H+ H
Sbjct: 287 SLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346
Score = 30.0 bits (67), Expect = 0.32
Identities = 25/102 (24%), Positives = 33/102 (32%), Gaps = 30/102 (29%)
Query: 17 YQCGECGKQFTRKFSLNAHL-HVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVC 75
+ +C F+R L HL V++ + LKP+ C
Sbjct: 290 IKSKQCNISFSRSSPLTRHLRSVNHSGES-------------------------LKPFSC 324
Query: 76 TY--CGKAFVRASDLKRHIDAHLGVKKFAC--ETCGKLFSSK 113
Y CGK F R LKRHI H + FS
Sbjct: 325 PYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPL 366
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.8 bits (82), Expect = 0.003
Identities = 24/113 (21%), Positives = 38/113 (33%), Gaps = 20/113 (17%)
Query: 21 ECGKQFTRKFSLNAHLHVHYGSSN--------YKCPL--CGKFFIQLCHMKDHIQAHGGL 70
K + ++ S YKCP+ C K + +K H HG
Sbjct: 318 CTNSSSNGKLAHGGERNIDTPSRMLKVKDGKPYKCPVEGCNKKYKNQNGLKYH-MLHG-- 374
Query: 71 KPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHVRTH 123
+ + ++ K + CE C K + + +GLKYH R H
Sbjct: 375 ------HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH-RKH 420
>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 = 32.2 bits (74), Expect = 0.040
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 64 IQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCG 107
I+ HG L CT CGK + R +L+ ID + C CG
Sbjct: 101 IELHGSLFRVRCTKCGKEYPRD-ELQADIDREEVPR---CPKCG 140
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 29.7 bits (67), Expect = 0.050
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 59 HMKDHIQAHGGLKPYVCTYCGKAFVR 84
+++ H++ H G KPY C CGK+F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.1 bits (63), Expect = 0.15
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 87 DLKRHIDAHLGVKKFACETCGKLFSS 112
+L+RH+ H G K + C CGK FSS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 25.0 bits (55), Expect = 2.7
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 31 SLNAHLHVHYGSSNYKCPLCGKFFIQ 56
+L H+ H G YKCP+CGK F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 31.2 bits (71), Expect = 0.075
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 8/49 (16%)
Query: 9 PLATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQL 57
Y+CG CG+ + RK + H Y+C CG +
Sbjct: 112 VSGRKRYIYRCGSCGQLYPRKRRIRRH--------KYRCGRCGGKLKLI 152
>gnl|CDD|224163 COG1242, COG1242, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 312
Score = 31.5 bits (72), Expect = 0.080
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 31 SLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKA 81
+LN +L +G +K L G F C +D GG CT+C A
Sbjct: 10 TLNDYLREKFGEKVFKVTLDGGF---SCPNRDGTIGRGG-----CTFCSVA 52
>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 = 28.5 bits (64), Expect = 0.14
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 74 VCTYCGKAFVRASDLKRHIDAH 95
C CGK+F R S+LKRH+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 0.70
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 18 QCGECGKQFTRKFSLNAHLHVH 39
+C +CGK F+RK +L HL H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.2 bits (58), Expect = 0.93
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 103 CETCGKLFSSKHGLKYHVRTH 123
C CGK FS K LK H+RTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 23.5 bits (51), Expect = 8.7
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 46 KCPLCGKFFIQLCHMKDHIQAH 67
KCP CGK F + ++K H++ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 29.8 bits (67), Expect = 0.19
Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 43 SNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHI 92
S Y CPLC F +K HI+ K VC CGK F H+
Sbjct: 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHV 119
Score = 29.8 bits (67), Expect = 0.22
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 13 TTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHI 64
S Y C C F+ SL H + Y + CP+CGK F DH+
Sbjct: 70 AVSPYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
Score = 29.5 bits (66), Expect = 0.26
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 72 PYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHV 120
PYVC C F + LK+HI K C CGK F + HV
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHV 119
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.1 bits (62), Expect = 0.29
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 45 YKCPLCGKFFIQLCHMKDHIQAH 67
Y+CP+CG+ +I+ M H++ H
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.7 bits (59), Expect = 0.57
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 73 YVCTYCGKAFVRASDLKRHIDAH 95
Y C CGK F S L+ H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 0.64
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 45 YKCPLCGKFFIQLCHMKDHIQAH 67
Y+CP CGK F +++H++ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 0.86
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 17 YQCGECGKQFTRKFSLNAHLHVH 39
Y+C ECGK F K +L H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 1.2
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 101 FACETCGKLFSSKHGLKYHVRTH 123
+ C CGK+F SK L+ H+RTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|130279 TIGR01212, TIGR01212, radical SAM protein, TIGR01212 family.
This family has a cluster of conserved Cys residues
suggestive of Fe-S cluster binding. Members belong to
the radical-SAM family of putative This uncharacterized
protein family shows significant similarity to
TIGR01211, a longer protein that is a histone
acetyltransferase at its C-terminus and is a subunit of
RNA polymerase II (in yeast). This family lacks the
GNAT acetyltransferase domain [Unknown function,
Enzymes of unknown specificity].
Length = 302
Score = 29.0 bits (65), Expect = 0.70
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 31 SLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKA 81
+L +L YG +K L G F C +D + GG CT+C A
Sbjct: 4 TLGDYLKERYGQKVFKITLHGGF---SCPNRDGTKGRGG-----CTFCNDA 46
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or
more acidic residues. The function of members of this
family is unknown.
Length = 104
Score = 28.0 bits (63), Expect = 0.76
Identities = 15/44 (34%), Positives = 16/44 (36%), Gaps = 11/44 (25%)
Query: 47 CPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASDLKR 90
CP CGK F L KD P VC CG+ R
Sbjct: 12 CPTCGKRFYDL--NKD---------PIVCPKCGEEVPPEVAKSR 44
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 28.6 bits (64), Expect = 0.86
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 61 KDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKL 109
K I+ HG ++ Y C CGK + D+ ++ V + C+ C L
Sbjct: 108 KKVIELHGNVEEYYCVRCGKRYT-VEDVIEKLEKS-DVPR--CDDCSGL 152
>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 = 28.5 bits (64), Expect = 0.93
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 7/47 (14%)
Query: 64 IQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLF 110
I+ HG L CT CGK + R L+R C CG L
Sbjct: 105 IELHGSLDRVRCTSCGKEYPRDEVLEREKPPR-------CPKCGGLL 144
>gnl|CDD|217969 pfam04216, FdhE, Protein involved in formate dehydrogenase
formation. The function of these proteins is unknown.
They may possibly be involved in the formation of
formate dehydrogenase.
Length = 283
Score = 28.5 bits (64), Expect = 0.97
Identities = 21/97 (21%), Positives = 28/97 (28%), Gaps = 31/97 (31%)
Query: 31 SLNAHLHVHYGSSNYKCPLCGKF----FIQLCHMKDHIQAHGGLK-----------PYV- 74
L+A G CP+CG I GL+ +V
Sbjct: 153 QLDARALPEAGWQRGLCPVCGSAPVASVI-------RGGGAQGLRYLHCSLCETEWHFVR 205
Query: 75 --CTYCGKAFVRASDLKRH--IDAHLGVKKFACETCG 107
CT CG L + GV+ C+TC
Sbjct: 206 VKCTNCG----STKGLAYWSLEEGEPGVRAETCDTCH 238
>gnl|CDD|235290 PRK04351, PRK04351, hypothetical protein; Provisional.
Length = 149
Score = 27.9 bits (63), Expect = 1.0
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 9/38 (23%)
Query: 73 YVCTYCGKAFVRASDLKRHIDAHLGVKKFACETC-GKL 109
Y C CG+ ++R KR I+ K++ C C GKL
Sbjct: 113 YECQSCGQQYLR----KRRIN----TKRYRCGKCRGKL 142
>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 = 28.6 bits (64), Expect = 1.1
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 98 VKKFACETCGKLFSSKHGLKYHVRT 122
+ C C FSS L H RT
Sbjct: 71 PSSYVCNVCMAEFSSMDQLAEHQRT 95
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 27.7 bits (62), Expect = 1.4
Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 12/59 (20%)
Query: 60 MKDHIQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKY 118
MK HG ++ V C ID L + E G+L++ G KY
Sbjct: 98 MKQEGGPHGNMENIVVVVCAN----------KID--LTKHRAVSEDEGRLWAESKGFKY 144
>gnl|CDD|224565 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
modification, protein turnover, chaperones].
Length = 244
Score = 27.9 bits (62), Expect = 1.4
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 43 SNYKCPLCGKFFIQLCHMKDHIQAHGG---LKPYV-----CTYCGKAF 82
+Y CP C + F +L K +I L+ + C YC +A
Sbjct: 92 FDYTCPYCKEAFPEL--KKKYIDDGKVRLVLREFPFLDPACPYCRRAA 137
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 28.2 bits (62), Expect = 1.5
Identities = 18/85 (21%), Positives = 26/85 (30%), Gaps = 8/85 (9%)
Query: 39 HYGSSNYKCPLCGKFFIQLCHMK--DH------IQAHGGLKPYVCTYCGKAFVRASDLKR 90
+ + KCPLC H I + C C + V L
Sbjct: 269 QPPNISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTP 328
Query: 91 HIDAHLGVKKFACETCGKLFSSKHG 115
ID L V+K + K+ +S
Sbjct: 329 DIDKKLEVEKALKKQRKKVGTSDDN 353
>gnl|CDD|223915 COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family
[Transcription].
Length = 250
Score = 27.6 bits (62), Expect = 1.8
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 64 IQAHGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCGKL 109
I+ HG LK C+ CG + D+ + I+ L + C CG
Sbjct: 114 IELHGSLKRVRCSKCGNQYYD-EDVIKFIEDGLIPR---CPKCGGP 155
>gnl|CDD|221420 pfam12099, DUF3575, Protein of unknown function (DUF3575). This
family of proteins are functionally uncharacterized.
This family is only found in bacteria. Proteins in this
family are typically between 187 to 236 amino acids in
length.
Length = 186
Score = 26.8 bits (60), Expect = 2.6
Identities = 7/37 (18%), Positives = 12/37 (32%), Gaps = 9/37 (24%)
Query: 88 LKRH--IDAHLGV-------KKFACETCGKLFSSKHG 115
L R ++ +G+ K+ C CG
Sbjct: 134 LSRRWNLEFSIGLGYLHLEYDKYTCAECGVKVEKGKK 170
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 27.2 bits (61), Expect = 2.6
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 14/43 (32%)
Query: 14 TSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQ 56
+ +C +CG QFT + KCP CG I+
Sbjct: 676 DTIKRCRDCGYQFT--------------DESDKCPRCGSTNIE 704
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 24.8 bits (55), Expect = 2.9
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 100 KFACETCGKLFSSKHGLKYHVRTHK 124
+F C C K F S++ L+ H+++ K
Sbjct: 1 QFYCVACDKYFKSENALENHLKSKK 25
>gnl|CDD|225442 COG2888, COG2888, Predicted Zn-ribbon RNA-binding protein with a
function in translation [Translation, ribosomal
structure and biogenesis].
Length = 61
Score = 25.5 bits (56), Expect = 3.2
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 31 SLNAHLHVHYGSSNYKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCG 79
S + + + CP CG+ I C + G PY C CG
Sbjct: 14 SCGREIAPGETAVKFPCPNCGEVEIYRCAK---CRKLG--NPYRCPKCG 57
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.5 bits (53), Expect = 3.5
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 101 FACETCGKLFSSKHGLKYHVRTHK 124
F C CGK FSSK LK H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 24.5 bits (53), Expect = 3.8
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 73 YVCTYCGKAFVRASDLKRHIDAH 95
+ C CGK+F LKRH+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 23.4 bits (50), Expect = 9.3
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 45 YKCPLCGKFFIQLCHMKDHIQAH 67
+KCPLCGK F +K H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 26.9 bits (60), Expect = 3.7
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 102 ACETCGKLFSSKHGLKYHVRTHKGECK 128
AC+ LF GL Y R HKG+ +
Sbjct: 113 ACQNYSNLFQRDRGL-YLSRAHKGKIR 138
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 26.6 bits (60), Expect = 3.9
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 14/41 (34%)
Query: 11 ATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG 51
A +AY C ECG + + G +CP CG
Sbjct: 2 AKKKTAYVCQECGAESPKWL----------G----RCPECG 28
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 26.9 bits (59), Expect = 4.0
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 80 KAFVRASDLKRHIDAHLGVKKFACETCGKLFSSKHGLKYHV--RTHKGECKR 129
+A R K ++ K C CG+ FS +YH+ + H E +
Sbjct: 218 RAEARGFGKKNGMEGAEWFPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQG 269
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 26.7 bits (59), Expect = 4.0
Identities = 9/42 (21%), Positives = 12/42 (28%), Gaps = 14/42 (33%)
Query: 10 LATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG 51
+A S + C CG + KCP C
Sbjct: 1 MAKAKSKFVCQHCGADSPKWQG--------------KCPACH 28
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 26.8 bits (60), Expect = 4.2
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 14/42 (33%)
Query: 10 LATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG 51
+A +A+ C ECG + KCP CG
Sbjct: 1 MAKKKTAFVCQECGYVSPKWLG--------------KCPACG 28
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 26.1 bits (58), Expect = 4.3
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 13/36 (36%)
Query: 16 AYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG 51
+ C CG + H G + CP+CG
Sbjct: 134 VWVCPVCG-------------YTHEGEAPEVCPICG 156
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 26.6 bits (58), Expect = 4.6
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 43 SNYKCPLCGKFFIQLCH---MKDHIQAHGGLKPYVCTYC--GKAFVRASDLKRHIDAHLG 97
S+ CP CG+ FI L + H G++ +C +C +A + L + +
Sbjct: 459 SSDSCPSCGRAFISLSRPLGTRAHHCRSCGIR--LCVFCITKRAHYSFAKLAKPGSSDEA 516
Query: 98 VKKFACETCGKLFSSKHGLKY 118
++ C+TC K + + L Y
Sbjct: 517 EERLVCDTCYKEYETVSQLHY 537
>gnl|CDD|234777 PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
Length = 242
Score = 26.3 bits (59), Expect = 4.8
Identities = 12/41 (29%), Positives = 14/41 (34%), Gaps = 8/41 (19%)
Query: 67 HGGLKPYVCTYCGKAFVRASDLKRHIDAHLGVKKFACETCG 107
HG L CT CG+ + LK C CG
Sbjct: 117 HGSLLRARCTKCGQTYDLDEYLKPEP--------PRCPKCG 149
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 26.6 bits (59), Expect = 4.9
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 14/33 (42%)
Query: 19 CGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCG 51
C +CG+QF S KCP CG
Sbjct: 697 CRDCGEQFV--------------DSEDKCPRCG 715
>gnl|CDD|217844 pfam04015, DUF362, Domain of unknown function (DUF362). Domain
that is sometimes present in iron-sulphur proteins.
Length = 203
Score = 26.3 bits (59), Expect = 4.9
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 2/21 (9%)
Query: 53 FFIQLCHMKDHIQAH--GGLK 71
I L +K H Q G +K
Sbjct: 105 VIINLPKLKTHGQTGVTGAVK 125
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. 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. 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. 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 = 300
Score = 26.1 bits (58), Expect = 5.2
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 97 GVKKFACETCGKLFSSKHGLKYHV 120
G+ K A E +L+ +GL Y V
Sbjct: 139 GISKLAIEKYLRLYQYLYGLDYTV 162
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 26.0 bits (57), Expect = 6.2
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 45 YKCPLCGKFFIQLCHMKDHI--QAHGGLKPYVC 75
+ CP C + F LC D I + GG Y+
Sbjct: 90 FTCPECLRGFYSLCAKYDFIGSRRDGGNAEYIV 122
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 26.1 bits (58), Expect = 7.5
Identities = 10/52 (19%), Positives = 16/52 (30%), Gaps = 11/52 (21%)
Query: 6 PRDPLATTTSAYQCGECGKQFTRKFSLNAHLHVHYGSSNYKCPLCGKFFIQL 57
PRD + +C CG++ CP C + +L
Sbjct: 382 PRDSKEGSKGTRECKVCGREEPIA----------EDEDEGLCPTC-ERLYEL 422
>gnl|CDD|223100 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 26.0 bits (58), Expect = 7.5
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 64 IQAHGGLKPYVCTY 77
I HGG PY T+
Sbjct: 421 IALHGGFIPYGGTF 434
>gnl|CDD|213729 TIGR02605, CxxC_CxxC_SSSS, putative regulatory protein, FmdB
family. This model represents a region of about 50
amino acids found in a number of small proteins in a
wide range of bacteria. The region begins usually with
the initiator Met and contains two CxxC motifs
separated by 17 amino acids. One member of this family
is has been noted as a putative regulatory protein,
designated FmdB (SP:Q50229, PMID:8841393 ). Most
members of this family have a C-terminal region
containing highly degenerate sequence, such as
SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in
Mycobacterium tuberculosis and
VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces
avermitilis. These low complexity regions, which are
not included in the model, resemble low-complexity
C-terminal regions of some heterocycle-containing
bacteriocin precursors [Regulatory functions, DNA
interactions].
Length = 52
Score = 24.2 bits (53), Expect = 7.6
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 11/38 (28%)
Query: 17 YQCGECGKQFT--RKFSLNAHLHVHYGSSNYKCPLCGK 52
Y+C CG +F +K S + CP CG
Sbjct: 6 YRCTACGHRFEVLQKMSDDPLA---------TCPECGS 34
>gnl|CDD|132916 cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of
1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and related proteins. Thiamine
pyrophosphate (TPP) family, pyrimidine (PYR) binding
domain of 1-deoxy-D-xylulose-5-phosphate synthase
(DXS), transketolase (TK), and the beta subunits of the
E1 component of the human pyruvate dehydrogenase
complex (E1- PDHc), subfamily. The PYR domain is found
in many key metabolic enzymes which use TPP (also known
as thiamine diphosphate) as a cofactor. TPP binds in
the cleft formed by a PYR domain and a PP domain. The
PYR domain, binds the aminopyrimidine ring of TPP, the
PP domain binds the diphosphate residue. A polar
interaction between the conserved glutamate of the PYR
domain and the N1' of the TPP aminopyrimidine ring is
shared by most TPP-dependent enzymes, and participates
in the activation of TPP. The PYR and PP domains have a
common fold, but do not share strong sequence
conservation. The PP domain is not included in this
sub-family. Like many TPP-dependent enzymes DXS and TK
are homodimers having a PYR and a PP domain on the same
subunit. TK has two active sites per dimer which lie
between PYR and PP domains of different subunits. For
DXS each active site is located at the interface of a
PYR and a PP domain from the same subunit. E1-PDHc is
an alpha2beta2 dimer-of-heterodimers having two active
sites but having the PYR and PP domains arranged on
separate subunits, the PYR domains on the beta
subunits, the PP domains on the alpha subunits. DXS is
a regulatory enzyme of the mevalonate-independent
pathway involved in terpenoid biosynthesis, it
catalyzes a transketolase-type condensation of pyruvate
with D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon
dioxide. TK catalyzes the transfer of a two-carbon unit
from ketose phosphates to aldose phosphates. In
heterotrophic organisms, TK provides a link between
glycolysis and the pentose phosphate pathway and
provides precursors for nucleotide, aromatic amino acid
and vitamin biosynthesis. TK also plays a central role
in the Calvin cycle in plants. PDHc catalyzes the
irreversible oxidative decarboxylation of pyruvate to
produce acetyl-CoA in the bridging step between
glycolysis and the citric acid cycle. This subfamily
includes the beta subunits of the E1 component of the
acetoin dehydrogenase complex (ADC) and the branched
chain alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). ADC participates in the
breakdown of acetoin. BCADC catalyzes the oxidative
decarboxylation of 4-methyl-2-oxopentanoate,
3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate
during the breakdown of branched chain amino acids.
Length = 156
Score = 25.5 bits (57), Expect = 8.1
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 66 AHGGLKPYVCTYCGKAFV-RASDLKRHIDA--HLGVK 99
A GLKP+V T+ F+ RA D RH A +L VK
Sbjct: 59 ALHGLKPFVSTFS--FFLQRAYDQIRHDVALQNLPVK 93
>gnl|CDD|233890 TIGR02486, RDH, reductive dehalogenase. This model represents a
family of corrin and 8-iron Fe-S cluster-containing
reductive dehalogenases found primarily in halorespiring
microorganisms such as dehalococcoides ethenogenes which
contains as many as 17 enzymes of this type with varying
substrate ranges. One example of a characterized species
is the tetrachloroethene reductive dehalogenase
(1.97.1.8) which also acts on trichloroethene converting
it to dichloroethene.
Length = 314
Score = 25.9 bits (57), Expect = 8.2
Identities = 12/17 (70%), Positives = 13/17 (76%), Gaps = 3/17 (17%)
Query: 92 IDAHLGVKKFACETCGK 108
IDA G+ KF CETCGK
Sbjct: 199 IDA--GMAKF-CETCGK 212
>gnl|CDD|163663 cd07420, MPP_RdgC, Drosophila melanogaster RdgC and related
proteins, metallophosphatase domain. RdgC (retinal
degeneration C) is a vertebrate serine-threonine protein
phosphatase that is required to prevent light-induced
retinal degeneration. In addition to its catalytic
domain, RdgC has two C-terminal EF hands. Homologs of
RdgC include the human phosphatases protein phosphatase
with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1
transcripts are present at low levels in the retina,
PPEF-2 transcripts and PPEF-2 protein are present at
high levels in photoreceptors. The PPP (phosphoprotein
phosphatase) family, to which RdgC belongs, is one of
two known protein phosphatase families specific for
serine and threonine. The PPP family also includes:
PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1,
PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic
domain is defined by three conserved motifs (-GDXHG-,
-GDXVDRG- and -GNHE-). The PPP enzyme family is ancient
with members found in all eukaryotes, and in most
bacterial and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 321
Score = 25.4 bits (56), Expect = 9.4
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 110 FSSKHGLKYHVRTHKGECK 128
KHGL +R+H ECK
Sbjct: 259 VLQKHGLSLLIRSH--ECK 275
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 25.5 bits (57), Expect = 10.0
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 45 YKCPLCGKFFIQLCHMKDHIQAHGGLKPYVCTYCGKAFVRASD 87
CP CG+ + H++ + C CG+ ++ +D
Sbjct: 128 RICPACGRTY--------HVKFNPPKVEGKCDVCGEELIQRAD 162
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
0.327 0.139 0.466
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: 6,089,873
Number of extensions: 486433
Number of successful extensions: 1023
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1000
Number of HSP's successfully gapped: 136
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)