RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4868
(169 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 91.4 bits (228), Expect = 3e-25
Identities = 32/56 (57%), Positives = 42/56 (75%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
R RT+FT +Q++ LEKEFE+ YP RE LA K+GL E +++VWF NRRAKW+R
Sbjct: 2 RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 82.3 bits (204), Expect = 1e-21
Identities = 31/56 (55%), Positives = 42/56 (75%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R RTSFT +Q++ LEKEF++ YP RE LA K+GL E +++VWF NRRAKW+
Sbjct: 2 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 81.9 bits (203), Expect = 2e-21
Identities = 30/58 (51%), Positives = 41/58 (70%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
R RT FT +Q++ LEKEFE+ YP RE LA ++GL E ++++WF NRRAK +R E
Sbjct: 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 53.6 bits (129), Expect = 1e-09
Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
R T++Q+ LE+EFE YP R +L+ + +P +Q+WF N+RAK +++
Sbjct: 53 SKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112
Query: 120 RNQRQRGS 127
+ +++ G
Sbjct: 113 KVEQRPGE 120
>gnl|CDD|220535 pfam10037, MRP-S27, Mitochondrial 28S ribosomal protein S27.
Members of this family of small ribosomal proteins
possess one of three conserved blocks of sequence found
in proteins that stimulate the dissociation of guanine
nucleotides from G-proteins, leaving open the
possibility that MRP-S27 might be a functional partner
of GTP-binding ribosomal proteins.
Length = 417
Score = 36.7 bits (85), Expect = 0.003
Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 11/100 (11%)
Query: 39 PGSNLEPEDDQARLRLKRKLQRNRTSF--TNDQIDNLEK-EFERTHYPDVFARERLAA-- 93
L E ++++ + + L + SF ++ L K E + ERL
Sbjct: 317 DEDLLLEEVEKSKQKFEPLLAQYGESFQEWRSKLQALAKVESRSL----LSVEERLPTIE 372
Query: 94 --KIGLPEARIQVWFSNRRAKWRREEKLRNQRQRGSADPT 131
+ L E R Q+WF R W+R++KLR Q
Sbjct: 373 KEDLELYEQRQQLWFFENRKLWQRKKKLREQADEEYQQRH 412
>gnl|CDD|191179 pfam05053, Menin, Menin. MEN1, the gene responsible for multiple
endocrine neoplasia type 1, is a tumour suppressor gene
that encodes a protein called Menin which may be an
atypical GTPase stimulated by nm23.
Length = 618
Score = 34.2 bits (78), Expect = 0.027
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 109 RRAKWRREEKLRNQRQRGSADPTQAPNNNNNNIVNNNNNSSDGCTPSPA 157
RR RRE K Q G P NNNN +NNNN++ A
Sbjct: 479 RRRGPRRESKS--QEPSGGESPNPELPANNNNSNSNNNNNNGADRKEAA 525
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 27.5 bits (62), Expect = 0.50
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 82 YPDVFARERLAAKIGLPEARIQVWFSNRR 110
YP + LA + GL +I WF N R
Sbjct: 10 YPSEEEKSELARQTGLSRKQIDNWFINAR 38
>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1). All
proteins in this family for which functions are known
are part of a multiprotein complex made up of homologs
of RPA1, RPA2 and RPA3 that bind ssDNA and function in
the recognition of DNA damage for nucleotide excision
repairThis family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford University)
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 608
Score = 29.7 bits (67), Expect = 0.77
Identities = 20/99 (20%), Positives = 30/99 (30%), Gaps = 5/99 (5%)
Query: 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQRQR 125
N + K V ++ KIG P V + W E+ L ++
Sbjct: 85 VNTIGKDGRKVLIVYELEVVKPELKVRDKIGNP-----VTYEKYLDSWHEEQVLASKPAT 139
Query: 126 GSADPTQAPNNNNNNIVNNNNNSSDGCTPSPAPQVSMDP 164
A+P A N NN + + PAP
Sbjct: 140 NPANPPNAKAPKNEVASYNNAANPERGNAPPAPNSGSTR 178
>gnl|CDD|133398 cd04770, HTH_HMRTR, Helix-Turn-Helix DNA binding domain of Heavy
Metal Resistance transcription regulators.
Helix-turn-helix (HTH) heavy metal resistance
transcription regulators (HMRTR): MerR1 (mercury), CueR
(copper), CadR (cadmium), PbrR (lead), ZntR (zinc),
and other related proteins. These transcription
regulators mediate responses to heavy metal stress in
eubacteria. They belong to the MerR superfamily of
transcription regulators that promote transcription of
various stress regulons by reconfiguring the operator
sequence located between the -35 and -10 promoter
elements. A typical MerR regulator is comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 123
Score = 28.3 bits (64), Expect = 0.99
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 45 PEDDQARLRLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQ 103
E D ARLR R+ Q F+ +I L + P R L K+ EA+I
Sbjct: 40 GEADLARLRFIRRAQA--LGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIA 96
>gnl|CDD|188122 TIGR01264, tyr_amTase_E, tyrosine aminotransferase, eukaryotic.
This model describes tyrosine aminotransferase as found
in animals and Trypanosoma cruzi. It is the first enzyme
of a pathway of tyrosine degradation via homogentisate.
Several plant enzyme designated as probable tyrosine
aminotransferases are very closely related to an
experimentally demonstrated nicotianamine
aminotransferase, an enzyme in a siderophore (iron
uptake chelator) biosynthesis pathway. These plant
sequences are excluded from the model seed and score
between the trusted an noise cutoffs [Energy metabolism,
Amino acids and amines].
Length = 401
Score = 28.2 bits (63), Expect = 2.4
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 134 PNNNNNNIVNNNNNSSDGCTPSPAPQVSM------DPTDF 167
P++++NN VN D P P+ + DPT F
Sbjct: 5 PSDHSNNTVNPIRAIVDNMKVKPNPEKPVIKLSIGDPTVF 44
>gnl|CDD|184395 PRK13919, PRK13919, putative RNA polymerase sigma E protein;
Provisional.
Length = 186
Score = 27.6 bits (61), Expect = 2.6
Identities = 22/82 (26%), Positives = 31/82 (37%), Gaps = 11/82 (13%)
Query: 39 PGSNLEPEDDQARLRLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLP 98
PG L+ E R RL R L+ + E+ Y + A +GLP
Sbjct: 114 PGPGLDEEGHLDRTRLGRALK---------ALSPEERRVIEVLYYQGYTHREAAQLLGLP 164
Query: 99 EARIQVWFSNRRAKWRREEKLR 120
++ RRA R +E LR
Sbjct: 165 LGTLKTR--ARRALSRLKEVLR 184
>gnl|CDD|132676 TIGR03637, cas1_YPEST, CRISPR-associated endonuclease Cas1, subtype
I-F/YPEST. The CRISPR-associated protein Cas1 is
virtually universal to CRISPR systems. CRISPR, an
acronym for Clustered Regularly Interspaced Short
Palindromic Repeats, is prokaryotic immunity system for
foreign DNA, mostly from phage. CRISPR systems belong to
different subtypes, distinguished by both nature of the
repeats, the makeup of the cohort of associated Cas
proteins, and by molecular phylogeny within the more
universal Cas proteins such as this one. This model is
of type EXCEPTION and provides more specific information
than the EQUIVALOG model TIGR00287. It describes the
Cas1 protein particular to the YPEST subtype of
CRISPR/Cas system.
Length = 307
Score = 27.8 bits (62), Expect = 2.7
Identities = 13/46 (28%), Positives = 15/46 (32%)
Query: 47 DDQARLRLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLA 92
DD RL + Q R + E YPD A E L
Sbjct: 114 DDDKRLAAAKAFQLIRIELLSQHWKKSLDLREHGFYPDENALEALL 159
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 27.8 bits (62), Expect = 3.3
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 48 DQARLRLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107
+ A L K + Q+++ + Q+ +LE E + + L + R Q+
Sbjct: 46 EIAALEKKIREQQDQRAKLEKQLKSLETEIASL------EAQLIETADDLKKLRKQIADL 99
Query: 108 NRRAKWRREEKLRNQRQR 125
N R E + R QR+R
Sbjct: 100 NARLN-ALEVQEREQRRR 116
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 27.7 bits (61), Expect = 3.9
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 99 EARIQVWFSNRRAKWRREEKLRNQRQRGSADPTQAPNNNNN 139
E + ++ + K R+E LRN+ R S P +P + +
Sbjct: 131 ERKSPKSYNQQSRKKHRDESLRNKHGRPSGPPAMSPGEHFD 171
>gnl|CDD|233243 TIGR01036, pyrD_sub2, dihydroorotate dehydrogenase, subfamily 2.
This model describes enzyme protein dihydroorotate
dehydrogenase exclusively for subfamily 2. It includes
members from bacteria, yeast, plants etc. The
subfamilies 1 and 2 share extensive homology,
particularly toward the C-terminus. This subfamily has a
longer N-terminal region [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 336
Score = 27.4 bits (61), Expect = 4.0
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 44 EPEDDQARLRLKRKLQR----NRTSFTNDQIDNLEKEFERTHY 82
P+ + RL R ++ NR F N DNL + +R Y
Sbjct: 91 RPQPGNPKPRLFRLIEAEGLINRMGFNNHGADNLVENVKRARY 133
>gnl|CDD|150787 pfam10154, DUF2362, Uncharacterized conserved protein (DUF2362).
This is a family of proteins conserved from nematodes to
humans. The function is not known.
Length = 501
Score = 27.1 bits (60), Expect = 5.2
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 117 EKLRNQRQRGSADPTQAPNNNNNNIVNNNNNSS 149
EK ++ ADP + + V + S
Sbjct: 71 EKAYSETLLEHADPEEPNWEEDFAQVYHQLIHS 103
>gnl|CDD|180883 PRK07206, PRK07206, hypothetical protein; Provisional.
Length = 416
Score = 26.9 bits (60), Expect = 5.4
Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 5/50 (10%)
Query: 89 ERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQ-----RQRGSADPTQA 133
+RLA + + S RR K L RQ +AD +A
Sbjct: 86 DRLAEILTPQYSNDPALSSARRNKAEMINALAEAGLPAARQINTADWEEA 135
>gnl|CDD|237974 PRK15489, nfrB, bacteriophage N4 adsorption protein B; Provisional.
Length = 703
Score = 26.6 bits (59), Expect = 7.0
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 76 EFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111
EF H D+ RE L + P A + FS RRA
Sbjct: 216 EFAEWHQKDLVVRESLTGTV--PSAGVGTCFS-RRA 248
>gnl|CDD|183576 PRK12534, PRK12534, RNA polymerase sigma factor; Provisional.
Length = 187
Score = 26.2 bits (57), Expect = 7.5
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 45 PEDDQARL-RLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQ 103
D + L R +R R R +++ E RT + + E LAA+ P ++
Sbjct: 112 RAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVK 171
Query: 104 VWFSNRRAKWR 114
W AK +
Sbjct: 172 SWIRRGLAKLK 182
>gnl|CDD|131098 TIGR02043, ZntR, Zn(II)-responsive transcriptional regulator. This
model represents the zinc and cadmium (II) responsive
transcriptional activator of the gamma proteobacterial
zinc efflux system. This protein is a member of the MerR
family of transcriptional activators (pfam00376) and
contains a distinctive pattern of cysteine residues in
its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a
conserved and critical cysteine at the N-terminal end of
the dimerization helix [Regulatory functions, DNA
interactions].
Length = 131
Score = 26.0 bits (57), Expect = 8.0
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 34 GDNSNPGSNLEPEDDQARLRLKRKLQRNRTSFTNDQI-DNLEKEFERTHYPDVFARERLA 92
++ G L ++DQ RLR K + FT D+I + L + + T + + +
Sbjct: 30 AGRTDSGYRLYTDEDQKRLRFILKAK--ELGFTLDEIKELLSIKLDATEHSCAEVKAIVD 87
Query: 93 AKIGLPEARIQVWFSNRRA 111
AK+ L + +I RR+
Sbjct: 88 AKLELVDEKINELTKIRRS 106
>gnl|CDD|176758 cd08780, Death_TRADD, Death Domain of Tumor Necrosis Factor
Receptor 1-Associated Death Domain protein. Death
domain (DD) of TRADD (TNF Receptor 1-Associated Death
Domain or TNFRSF1A-associated via death domain)
protein. TRADD is a central signaling adaptor for
TNF-receptor 1 (TNFR1), mediating activation of Nuclear
Factor -kappaB (NF-kB) and c-Jun N-terminal kinase
(JNK), as well as caspase-dependent apoptosis. It also
carries important immunological roles including
germinal center formation, DR3-mediated T-cell
stimulation, and TNFalpha-mediated inflammatory
responses. In general, DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 90
Score = 25.2 bits (55), Expect = 8.0
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 53 RLKRKLQRNRTSFTNDQIDNLEKEFER 79
+ R LQ+N + + IDNL E++R
Sbjct: 18 PVGRSLQKNCRALRDPAIDNLAYEYDR 44
>gnl|CDD|216978 pfam02331, P35, Apoptosis preventing protein. This viral protein
functions to block the host apoptotic response caused by
infection by the virus. The apoptosis preventing protein
(or early 35kD protein, P35) acts by blocking caspase
protease activity.
Length = 300
Score = 26.3 bits (58), Expect = 8.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 57 KLQRNRTSFTNDQIDNLEKEFERTHY 82
+L+RN + + Q+D K F+ HY
Sbjct: 77 QLERNYHNKRSTQMDGFHKYFKDEHY 102
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 0.129 0.378
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,711,569
Number of extensions: 791823
Number of successful extensions: 822
Number of sequences better than 10.0: 1
Number of HSP's gapped: 811
Number of HSP's successfully gapped: 51
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 55 (24.9 bits)