RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14249
(60 letters)
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 53.1 bits (128), Expect = 1e-11
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
I+RPMNAFM+++K R+K+ E P N +SK+L
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGD 38
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 46.8 bits (112), Expect = 3e-09
Identities = 16/38 (42%), Positives = 27/38 (71%)
Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
+RP++AF ++++ +R KL ENP L NA++SK+L
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEK 38
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 43.8 bits (104), Expect = 6e-08
Identities = 18/38 (47%), Positives = 28/38 (73%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+ +RPM+AFM++++ R K+ ENPDL NA++SK L
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGE 38
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 43.4 bits (103), Expect = 7e-08
Identities = 11/37 (29%), Positives = 24/37 (64%)
Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+RP++A+ ++++ R ++ ENP L ++SK+L
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGE 37
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 36.8 bits (86), Expect = 3e-05
Identities = 12/36 (33%), Positives = 25/36 (69%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+RP++A+ ++++ +R KL ENPD +++K+L
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGE 37
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include the fungal mating type gene products
MC, MATA1 and Ste11.
Length = 77
Score = 36.5 bits (85), Expect = 5e-05
Identities = 14/38 (36%), Positives = 26/38 (68%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+I RP NAF+++ + + +L ENP L N ++S+++ R
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGR 38
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 27.9 bits (62), Expect = 0.24
Identities = 10/35 (28%), Positives = 23/35 (65%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
+RP++A+ +++ R ++ ENP L ++ K+L+
Sbjct: 72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLS 106
>gnl|CDD|181353 PRK08286, cbiC, cobalt-precorrin-8X methylmutase; Validated.
Length = 214
Score = 25.0 bits (55), Expect = 2.0
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 10 AKEQRIRRPMNAFMVWAKVERKKL 33
AKEQ I R M A + A E KL
Sbjct: 112 AKEQGITRSMAAVDIAAAEEGPKL 135
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 24.4 bits (53), Expect = 3.2
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDL 40
+R ++A+M +AK +R ++ ENP+L
Sbjct: 24 KRALSAYMFFAKEKRAEIIAENPEL 48
>gnl|CDD|235636 PRK05886, yajC, preprotein translocase subunit YajC; Validated.
Length = 109
Score = 24.4 bits (53), Expect = 3.7
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 19 MNAFMVWAKVERKKLADENPDLHNA 43
M FM +A ++K DLH +
Sbjct: 14 MGGFMYFASRRQRKAMQATIDLHES 38
>gnl|CDD|218079 pfam04420, CHD5, CHD5-like protein. Members of this family are
probably coiled-coil proteins that are similar to the
CHD5 (Congenital heart disease 5) protein. In
Saccharomyces cerevisiae this protein localises to the
ER and is thought to play a homeostatic role.
Length = 161
Score = 24.2 bits (53), Expect = 3.9
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 4 HQQQKTAKEQRIRRPMNAFMVWAKVERK--KLADE 36
+ + +E + F WAK+ RK KL DE
Sbjct: 47 KEILELKRELNSISAQDEFAKWAKLNRKLDKLTDE 81
>gnl|CDD|238346 cd00633, Secretoglobin, Secretoglobins are relatively small,
secreted, disulphide-bridged dimeric proteins with
encoding genes sharing substantial sequence similarity.
Their family subunits may be grouped into five
subfamilies, A-E. Uteroglobin (subfamily A), which is
identical to Clara cell protein (CC10), forms a
globular shaped homodimer with a large hydrophobic
pocket located between the two dimers. The uteroglobin
monomer structure is composed of four alpha helices
that do not form a canonical four helix-bundle motif
but rather a boomerang-shaped structure in which
helices H1, H3, and H4 are able to bind a homodimeric
partner. The hydrophobic pocket binds steroids,
particularly progesterone, with high specificity.
However, the true biological function of uteroglobin is
poorly understood. In mammals, uteroglobin has
immunosuppressive and anti-inflammatory properties
through the inhibition of phospholipase A2. The other
four main subfamilies of secretoglobins are found in
heterodimeric combinations, with B and C subfamilies
disulphide-bridged to the E and D subfamilies,
respectively. [See review by Laukaitis C.M. & Karn R.C.
(2005). Biological Journal of the Linnean Society 84,
493]. These include rat prostatic steroid-binding
protein (PBP or prostatein), human mammaglobin (or
heteroglobin), lipophilins, major cat allergen Fel dI,
the hamster Harderian gland proteins and mouse salivary
androgen-binding protein (ABP). Example of such a
heterodimer: ABPalpha-like sequences are closely
related to cat Fel dI chain 1, whereas
ABPbeta-gamma-like sequences are closely related to Fel
dI chain 2. Thus, the heterodimeric structure of
ABPalpha-beta and ABPalpha-gamma is recapitulated by
the sequence-similar Fel dI chains 1 and 2. This
conservation of primary and quaternary structure
indicates that the genome of the eutherian common
ancestor of cats, rodents, and primates contained a
similar gene pair.
Length = 67
Score = 23.4 bits (51), Expect = 4.7
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 20 NAFMVWAKVERKKLADENPDLHNADLSKMLARILL 54
V AK + K+ DE +++K+L +IL
Sbjct: 29 TPEAVEAKEKLKQCVDEQSLETKENIAKLLEKILA 63
>gnl|CDD|236573 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 24.2 bits (53), Expect = 5.0
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 8 KTAKEQRIRRPMNAFMVWAKVERKKLADENPD 39
K +++ +R N F W +++ + A P
Sbjct: 64 KLCDQEKWKREENPFDAWDRLKAQAAAGAFPK 95
>gnl|CDD|163713 cd08157, catalase_fungal, Fungal catalases similar to yeast
catalases A and T. Catalase is a ubiquitous enzyme
found in both prokaryotes and eukaryotes, which is
involved in the protection of cells from the toxic
effects of peroxides. It catalyzes the conversion of
hydrogen peroxide to water and molecular oxygen.
Catalases also utilize hydrogen peroxide to oxidize
various substrates such as alcohol or phenols. This
family of fungal catalases has a relatively small
subunit size, and binds a protoheme IX (heme b) group
buried deep inside the structure. Fungal catalases also
bind NADPH as a second redox-active cofactor. They form
tetramers; in eukaryotic cells, catalases are typically
located in peroxisomes. Saccharomyces cerevisiae
catalase T is found in the cytoplasm, though.
Length = 451
Score = 24.2 bits (53), Expect = 5.1
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 29 ERKKLADENPDLHNADLSKMLAR 51
E +LA NPD DL + + R
Sbjct: 198 EAARLAGSNPDYATKDLFEAIER 220
>gnl|CDD|215003 smart01060, Catalase, Catalases are antioxidant enzymes that
catalyse the conversion of hydrogen peroxide to water
and molecular oxygen, serving to protect cells from its
toxic effects. Hydrogen peroxide is produced as a
consequence of oxidative cellular metabolism and can be
converted to the highly reactive hydroxyl radical via
transition metals, this radical being able to damage a
wide variety of molecules within a cell, leading to
oxidative stress and cell death. Catalases act to
neutralise hydrogen peroxide toxicity, and are produced
by all aerobic organisms ranging from bacteria to man.
Most catalases are mono-functional, haem-containing
enzymes, although there are also bifunctional
haem-containing peroxidase/catalases that are closely
related to plant peroxidases, and non-haem,
manganese-containing catalases that are found in
bacteria.
Length = 373
Score = 24.0 bits (53), Expect = 5.1
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 22 FMVWAKVERKKLADENPDLHNADL 45
+ W E KLA ++PD H DL
Sbjct: 214 NLTWE--EAAKLAGKDPDYHRRDL 235
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
0.320 0.127 0.373
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,943,559
Number of extensions: 195855
Number of successful extensions: 195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 195
Number of HSP's successfully gapped: 16
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
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: 53 (24.0 bits)