RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3437
(132 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 = 69.6 bits (171), Expect = 6e-17
Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 20/86 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFM++++ RR + +YP N +SK LG WK LS+
Sbjct: 6 MNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWK--------------------ALSN 45
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKY 86
+K+P+ EEA++L+++H +P+YK+
Sbjct: 46 EEKQPYYEEAKKLKELHMKLYPDYKW 71
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 66.9 bits (164), Expect = 6e-16
Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++AF +++Q R L + P L NAE+SK LG WK LS+
Sbjct: 5 LSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWK--------------------NLSE 44
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
+KKP+ E+AE+ + ++ +P YK
Sbjct: 45 EEKKPYEEKAEKEKARYEKAYPAYK 69
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 55.4 bits (134), Expect = 2e-11
Identities = 27/85 (31%), Positives = 44/85 (51%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
M+AFM+++Q R + + P L NAE+SK LG WK LS+
Sbjct: 6 MSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWK--------------------LLSE 45
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
+K P+ E+A++ ++ ++ E P YK
Sbjct: 46 EEKAPYEEKAKKDKERYEEEMPEYK 70
>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 = 52.6 bits (127), Expect = 2e-10
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 20/82 (24%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+ +++Q R + + P L E+SK LG +WK LS+
Sbjct: 5 LSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWK--------------------SLSE 44
Query: 61 SDKKPFIEEAERLRQIHKSEHP 82
+KK + E+AE+ ++ ++ E P
Sbjct: 45 EEKKKYEEKAEKDKERYEKEMP 66
>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 = 52.3 bits (126), Expect = 3e-10
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
NAF+++ Q L + P L N E+S+ +G +W++ S
Sbjct: 6 RNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSE--------------------SP 45
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
K + E AE ++ H E+P+YKY PR+
Sbjct: 46 EVKAYYKELAEEEKERHAREYPDYKYTPRKSS 77
>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 = 43.8 bits (104), Expect = 4e-07
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 20/80 (25%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+ +++Q R L + P E++K LG WK +LS+
Sbjct: 5 LSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWK--------------------ELSE 44
Query: 61 SDKKPFIEEAERLRQIHKSE 80
+KK + E+AE+ ++ ++ E
Sbjct: 45 EEKKKYEEKAEKDKERYEKE 64
>gnl|CDD|233148 TIGR00844, c_cpa1, na(+)/h(+) antiporter. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals. Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in (1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles. This model is specific for the
fungal members of this family [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 810
Score = 30.3 bits (68), Expect = 0.29
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 17 NQYPSLHNAELSKTLGVLWKTLKVETH-YHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQ 75
N L + V T Y + S +D YT +DS+ E R+++
Sbjct: 583 NTIYGLDKLARDTENRDVTY---VPTSRYDGIESEIDDVYTYENDSESIASSER-RRIKK 638
Query: 76 IHKSEHPNY 84
+ + E Y
Sbjct: 639 LREEEQQAY 647
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 28.7 bits (64), Expect = 0.68
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+ +++ R + + P L E+ K L WK +L+D
Sbjct: 75 LSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWK--------------------ELTD 114
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
+K+P+ +EA R+ ++ E Y
Sbjct: 115 EEKEPYYKEANSDRERYQREKEEYN 139
>gnl|CDD|182803 PRK10878, PRK10878, hypothetical protein; Provisional.
Length = 72
Score = 26.2 bits (58), Expect = 2.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 47 VMSPFEDTYTKLSDSDKKPFI 67
+M FE Y LSD +K+ FI
Sbjct: 8 IMPFFEHEYDSLSDDEKRIFI 28
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 25.1 bits (55), Expect = 5.6
Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 21/81 (25%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHN-AELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLS 59
NA+ + Q R L + P + AE SK WK + S
Sbjct: 8 RNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAM--------------------S 47
Query: 60 DSDKKPFIEEAERLRQIHKSE 80
+ +K+ + E+A ++ + E
Sbjct: 48 EEEKEKYEEKAREDKKRYDRE 68
>gnl|CDD|199877 cd06910, M14_ASTE_ASPA_like_7, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like;
uncharacterized subgroup. A functionally
uncharacterized subgroup of the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily
which is part of the M14 family of
metallocarboxypeptidases. ASTE catalyzes the fifth and
last step in arginine catabolism by the arginine
succinyltransferase pathway, and aspartoacylase (ASPA,
also known as aminoacylase 2, and ACY-2; EC:3.5.1.15)
cleaves N-acetyl L-aspartic acid (NAA) into aspartate
and acetate. NAA is abundant in the brain, and
hydrolysis of NAA by ASPA may help maintain white
matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 272
Score = 26.1 bits (58), Expect = 5.6
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 64 KPFIEEAERLRQIHKSEHPN-----YKYQPRRRKCSKNLGTSA 101
+P I+ A+ L +H + P+ + R ++ +G A
Sbjct: 88 RPVIDTADYLLDLHSMQWPSPPLILAGDLQKGRALARAVGDPA 130
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 26.4 bits (58), Expect = 5.9
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 78 KSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKK 116
K EHP+ K R+ S + G + + +KS+S +S K
Sbjct: 817 KPEHPSRKRPRRQEDTSSSSGPFSASSTKSSSKSSSTSK 855
>gnl|CDD|236529 PRK09465, tolC, outer membrane channel protein; Reviewed.
Length = 446
Score = 26.1 bits (58), Expect = 6.4
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 66 FIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKKGQLNEQS 123
F+ +E+L H R + + +S NN++ S SSIN+ ++ ++ QS
Sbjct: 326 FVGASEQLESAH-------------RSVVQTVRSSFNNINASISSINAYEQAVVSAQS 370
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 26.1 bits (58), Expect = 7.7
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 111 INSLKKGQLNEQSLQIRRGIRE 132
+N K +LNE+ Q+ + I E
Sbjct: 968 LNDEKIDELNEEIKQLEQAIEE 989
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 25.9 bits (57), Expect = 8.8
Identities = 12/71 (16%), Positives = 25/71 (35%)
Query: 53 DTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSIN 112
D DS + + + + N + + +L T NL S I+
Sbjct: 75 DKKFSTIDSSTSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDIS 134
Query: 113 SLKKGQLNEQS 123
++ + +E+S
Sbjct: 135 DYEQPRNSEKS 145
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
0.313 0.126 0.361
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,330,623
Number of extensions: 512459
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 412
Number of HSP's successfully gapped: 25
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.2 bits)