RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15631
(213 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 = 51.1 bits (123), Expect = 3e-09
Identities = 15/26 (57%), Positives = 23/26 (88%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27
EK+P+ +EAK+L+ +HMK +PDYK+R
Sbjct: 47 EKQPYYEEAKKLKELHMKLYPDYKWR 72
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP 32
K + + A+ + H +E+PDYKY PR+
Sbjct: 47 VKAYYKELAEEEKERHAREYPDYKYTPRKSS 77
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 37.6 bits (88), Expect = 3e-04
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EK+P+ ++A++ +A + K +P YK
Sbjct: 46 EKKPYEEKAEKEKARYEKAYPAYK 69
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 33.8 bits (78), Expect = 0.007
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EK P+ ++AK+ + + +E P+YK
Sbjct: 47 EKAPYEEKAKKDKERYEEEMPEYK 70
>gnl|CDD|220633 pfam10214, Rrn6, RNA polymerase I-specific transcription-initiation
factor. RNA polymerase I-specific
transcription-initiation factor Rrn6 and Rrn7 represent
components of a multisubunit transcription factor
essential for the initiation of rDNA transcription by
Pol I. These proteins are found in fungi.
Length = 753
Score = 32.0 bits (73), Expect = 0.23
Identities = 22/92 (23%), Positives = 31/92 (33%), Gaps = 12/92 (13%)
Query: 112 QTSQADTKSSN--AAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHP 169
Q +Q D S+ + + + + SS + S S + P +
Sbjct: 650 QATQPDVTDSSQLESQSQIPTIRSS----------QQVSQTRKGGSSVVPSAPAPRLAQS 699
Query: 170 SQFLYGLKSEQLSPSSSPGESQSQSNNQSALE 201
SQ S L PSSS S S QS E
Sbjct: 700 SQPPTSQSSSDLPPSSSQAFSLSDLPMQSQSE 731
>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 = 29.1 bits (66), Expect = 0.34
Identities = 6/21 (28%), Positives = 14/21 (66%)
Query: 2 EKRPFIDEAKRLRAMHMKEHP 22
EK+ + ++A++ + + KE P
Sbjct: 46 EKKKYEEKAEKDKERYEKEMP 66
>gnl|CDD|226159 COG3633, SstT, Na+/serine symporter [Amino acid transport and
metabolism].
Length = 407
Score = 29.3 bits (66), Expect = 1.5
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 121 SNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQ 160
S A AV++SF +PS + PPS + + +
Sbjct: 92 SAALVAVIASF---AFPSTLVLASSAGDISPPSGIVEVLK 128
>gnl|CDD|131710 TIGR02662, dinitro_DRAG, ADP-ribosyl-[dinitrogen reductase]
hydrolase. Members of this family are the enzyme
ADP-ribosyl-[dinitrogen reductase] hydrolase (EC
3.2.2.24), better known as Dinitrogenase Reductase
Activating Glycohydrolase, DRAG. This enzyme reverses a
regulatory inactivation of dinitrogen reductase caused
by the action of NAD(+)--dinitrogen-reductase
ADP-D-ribosyltransferase (EC 2.4.2.37) (DRAT). This
enzyme is restricted to nitrogen-fixing bacteria and
belongs to the larger family of
ADP-ribosylglycohydrolases described by pfam03747
[Central intermediary metabolism, Nitrogen fixation].
Length = 287
Score = 28.2 bits (63), Expect = 2.7
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 8 DEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
EA RL A +H +K+ P R T
Sbjct: 183 REANRLIA----KHRTFKFEPYRGLSTA 206
>gnl|CDD|214000 cd12801, HopAB_KID, Kinase-interacting domains of the HopAB
family of Type III Effector proteins. HopAB family
members are type III effector proteins that are
secreted by the plant pathogen Pseudomonas syringae
into the host plant to inhibit its immune system and
facilitate the spread of the pathogen. AvrPtoB, also
called HopAB3, is the best studied member of the
family. It suppresses host basal defenses by
interfering with PAMP (pathogen-associated molecular
signature)-triggered immunity (PTI) through binding and
inhibiting BAK1, a kinase which serves to activate
defense signaling. It also recognizes the kinase Pto to
activate effector-triggered immunity (ETI). AvrPtoB
contains an N-terminal region that contains two
kinase-interacting domains (KID) and a C-terminal E3
ligase domain. The first KID recognizes the
PTI-associated kinase Bti9 as well as Pto, and is
referred to as the Pto-binding domain (PID). The second
KID interacts with BAK1 and FLS2, which are
leucine-rich repeat-containing receptor-like kinases,
and is called the BAK1-interacting domain (BID). This
family also contains a unique member, HopPmaL, which is
shorter and lacks the C-terminal E3 ligase domain.
Length = 77
Score = 26.9 bits (60), Expect = 2.7
Identities = 10/41 (24%), Positives = 13/41 (31%)
Query: 46 NQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAA 86
AP P+ A + P G HP +L A
Sbjct: 31 MGDAPIPSDIRRALRQVGIFPNIPMEGISLVSHPALNLREA 71
>gnl|CDD|203686 pfam07571, DUF1546, Protein of unknown function (DUF1546).
Associated with pfam02969 in Transcription initiation
factor TFIID subunit 6 (TAF6).
Length = 92
Score = 26.4 bits (59), Expect = 4.3
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 129 SSFYSSLYPSVTSAQTKTF---STPPPSHLSALF 159
S Y+SL P +T K P +H A+
Sbjct: 38 SDSYNSLRPRLTRTLLKALLDPKKPLGTHYGAIR 71
>gnl|CDD|152771 pfam12336, SOXp, SOX transcription factor. This domain family is
found in eukaryotes, and is approximately 80 amino
acids in length. The family is found in association
with pfam00505. There are two conserved sequence
motifs: KKDK and LPG. This family is made up of SOX
transcription factors. These are involved in
upregulation of nestin, a neural promoter.
Length = 84
Score = 26.0 bits (57), Expect = 5.2
Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 5/72 (6%)
Query: 26 YRPRRKPKT----PGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLD 81
YRPRRK KT S+P P GAP + + + N G S
Sbjct: 1 YRPRRKTKTLLKKDKYSLPGGLLPANGAPVQRAVGVGMDGYAHMNGYMN-GAYSMMQDDQ 59
Query: 82 SLSAAYPPMNMP 93
+P MN
Sbjct: 60 LHYPQHPGMNSA 71
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 27.8 bits (62), Expect = 5.4
Identities = 22/77 (28%), Positives = 26/77 (33%), Gaps = 1/77 (1%)
Query: 13 LRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHG 72
L A+ KE K RKPKTP P + S ++A A H
Sbjct: 626 LDALSPKEGDGKKSSADRKPKTPPSRAPPASLSKPASSPDASQTSASFDLDPDFELATH- 684
Query: 73 GGSHPHPLDSLSAAYPP 89
L S SA PP
Sbjct: 685 QSVPEAALASGSAPAPP 701
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 27.4 bits (61), Expect = 7.7
Identities = 27/166 (16%), Positives = 35/166 (21%), Gaps = 15/166 (9%)
Query: 32 PKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMN 91
P+ P Q +P P Q A P +P PP G P
Sbjct: 173 PQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPP------QGHPEQVQPQQFLPAPSQA 226
Query: 92 MPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPP 151
P + Q Q S P AQ PP
Sbjct: 227 PAQP---PLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQ------PP 277
Query: 152 PSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQ 197
P + + P + L + Q Q
Sbjct: 278 PQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQ 323
>gnl|CDD|132012 TIGR02967, guan_deamin, guanine deaminase. This model describes
guanine deaminase, which hydrolyzes guanine to xanthine
and ammonia. Xanthine can then be converted to urate by
xanthine dehydrogenase, and urate subsequently degraded.
In some bacteria, the guanine deaminase gene is found
near the xdhABC genes for xanthine dehydrogenase.
Non-homologous forms of guanine deaminase also exist, as
well as distantly related forms outside the scope of
this model [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 401
Score = 26.8 bits (60), Expect = 8.6
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 72 GGGSHPHPLDSLSAAYPPMNMPHYFGSPFDA 102
GGG+ L +L AY + SPF+A
Sbjct: 298 GGGTSFSMLQTLREAYKVSQLQGARLSPFEA 328
>gnl|CDD|215570 PLN03091, PLN03091, hypothetical protein; Provisional.
Length = 459
Score = 26.9 bits (59), Expect = 9.6
Identities = 35/175 (20%), Positives = 66/175 (37%), Gaps = 32/175 (18%)
Query: 34 TPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMP 93
+ I N+ + N S SN P +F + SH +S + + P ++
Sbjct: 191 SSSSKINNSNNNN------HSNSNLMTPTPNKDFFLDRFTTSH----ESSTTSCRPSDLV 240
Query: 94 HYFGSPFDAMNFSKLVQGQTSQADT---KSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTP 150
+F PF +N++ + T+ T ++ + + S F SS+ P S
Sbjct: 241 GHF--PFQQLNYASNARLSTNPNPTLWFSQNSKSFEMNSEFSSSMTP----------SIL 288
Query: 151 PPSHLSALFQHP-------TAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQS 198
PPS S+ P + S +PS + + + + + + + SN S
Sbjct: 289 PPSVTSSFLPTPMSYKPSISLPSDNPSIPSFTVNGVRNWEAGAFSNNSNSSNGSS 343
>gnl|CDD|212087 cd11518, SLC6sbd_SIT1, Na(+)- and Cl(-)-dependent imino acid
transporter SIT1; solute-binding domain. SIT1 (also
called XTRP3, XT3, IMINO) transports imino acids, such
as proline, pipecolate, MeAIB, and sarcosine. It has
weak affinity for neutral amino acids such as
phenylalanine. Human SIT1 is encoded by the SLC6A20
gene. SIT1 is expressed in brain, kidney, small
intestine, thymus, spleen, ovary, and lung. SLC6A20 is a
candidate gene for the rare disorder iminoglycinuria.
This subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 576
Score = 26.7 bits (59), Expect = 9.6
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 14/72 (19%)
Query: 125 AAVVSSFYSSLYPSVTSAQT-----KTFSTPPP-------SHLSALFQHPTAASSHPSQF 172
A+VV SF+ S+Y +V +A +F P P S+ + + AS P+Q+
Sbjct: 89 ASVVVSFFLSMYYNVINAWAFWYLFHSFQDPLPWSVCPLNSNRTGYTEECEKAS--PTQY 146
Query: 173 LYGLKSEQLSPS 184
+ ++ +SPS
Sbjct: 147 FWYRETLNISPS 158
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
0.311 0.125 0.369
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,541,133
Number of extensions: 901440
Number of successful extensions: 871
Number of sequences better than 10.0: 1
Number of HSP's gapped: 847
Number of HSP's successfully gapped: 74
Length of query: 213
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 120
Effective length of database: 6,812,680
Effective search space: 817521600
Effective search space used: 817521600
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 (21.8 bits)
S2: 57 (26.0 bits)