RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17899
(145 letters)
>gnl|CDD|197673 smart00352, POU, Found in Pit-Oct-Unc transcription factors.
Length = 75
Score = 97.9 bits (244), Expect = 6e-28
Identities = 36/55 (65%), Positives = 39/55 (70%), Gaps = 3/55 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 71
G TQADVG AL L P A SQ+TICRFE+L LS NM LKP+LQ WLEEAE
Sbjct: 24 GFTQADVGLALGALYGP---AFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEAE 75
>gnl|CDD|189427 pfam00157, Pou, Pou domain - N-terminal to homeobox domain.
Length = 75
Score = 83.9 bits (208), Expect = 2e-22
Identities = 34/55 (61%), Positives = 38/55 (69%), Gaps = 3/55 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 71
G TQADVG AL L P SQ+TICRFE+L LS NM LKP+L+ WLEEAE
Sbjct: 24 GYTQADVGLALGALYGP---VFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 47.5 bits (114), Expect = 2e-08
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
+RKRT+ + LE F PS E+ +A+KL L + V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 43.8 bits (104), Expect = 5e-07
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
K+RKRTS + LE F P PS E+ +A+KL L + V+
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
>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 = 40.7 bits (96), Expect = 9e-06
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
+RKRT + LE F P PS E+ +A++L L + V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 27.6 bits (62), Expect = 2.0
Identities = 13/71 (18%), Positives = 31/71 (43%)
Query: 64 QAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIA 123
+ LEEA+A+ + +R + A AGEK++ P+ ++ + + +
Sbjct: 100 RKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHT 159
Query: 124 AIAEKLDLKKN 134
+++ +L
Sbjct: 160 PVSDISELTVG 170
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 26.8 bits (59), Expect = 2.2
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 13/62 (20%)
Query: 11 SRVLFTG-----VTQADVGKAL--------ANLKLPGVGALSQSTICRFESLTLSHNNMI 57
+R LF G VT+ D+ +A ++K PG G S +FE+L ++H +
Sbjct: 7 NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66
Query: 58 AL 59
A+
Sbjct: 67 AM 68
>gnl|CDD|233993 TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein
FixG. Member of this ferredoxin-like protein family are
found exclusively in species with an operon encoding the
cbb3 type of cytochrome c oxidase (cco-cbb3), and near
the cco-cbb3 operon in about half the cases. The
cco-cbb3 is found in a variety of proteobacteria and
almost nowhere else, and is associated with oxygen use
under microaerobic conditions. Some (but not all) of
these proteobacteria are also nitrogen-fixing, hence the
gene symbol fixG. FixG was shown essential for
functional cco-cbb3 expression in Bradyrhizobium
japonicum.
Length = 434
Score = 26.9 bits (60), Expect = 4.3
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 81 PDAPSVLPAGEKKRKRTSIAAPEKR 105
P AP + AGEK + + P
Sbjct: 379 PGAPIHVKAGEKVKLPVFLRTPPDA 403
>gnl|CDD|237110 PRK12472, PRK12472, hypothetical protein; Provisional.
Length = 508
Score = 26.8 bits (59), Expect = 4.9
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 88 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAI 125
AG+ KR AAP + A PR +GE I AI
Sbjct: 27 LAGDAAAKRARPAAPTE-------ATAPREAGEPIMAI 57
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 26.4 bits (58), Expect = 7.6
Identities = 26/87 (29%), Positives = 33/87 (37%), Gaps = 2/87 (2%)
Query: 58 ALKPILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRP 117
ALK I EAE A AP+ P + T AAP + A + +P
Sbjct: 4 ALKKIFGK--GEAEQPAPAPPSPAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKPKKDKP 61
Query: 118 SGEKIAAIAEKLDLKKNVVRPINGHTR 144
E+ A L+ VV P G TR
Sbjct: 62 RRERKPKPASLWKLEDFVVEPQEGKTR 88
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 25.9 bits (57), Expect = 7.7
Identities = 10/42 (23%), Positives = 15/42 (35%)
Query: 88 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKL 129
+ K KR + LE F + P PS ++ L
Sbjct: 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLL 88
>gnl|CDD|220905 pfam10923, DUF2791, P-loop Domain of unknown function (DUF2791).
This is a family of proteins found in archaea and
bacteria. This domain contains a P-loop motif suggesting
it binds to a nucleotide such as ATP.
Length = 417
Score = 26.0 bits (58), Expect = 8.3
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 58 ALKPILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKK 93
AL+ I+ W+ E + ++L A E
Sbjct: 119 ALRSIVDRWIYAIEEDVLAEGGLDPDEALLDAVEAL 154
>gnl|CDD|115120 pfam06443, SEF14_adhesin, SEF14-like adhesin. Family of
enterotoxigenic bacterial adhesins.
Length = 165
Score = 25.8 bits (56), Expect = 8.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 5 PMPDVYSRVLFTGVTQADVGKALANLKLPGVGALS 39
P D + LF G A +G A+AN PG+ L+
Sbjct: 93 PFKDGAGQPLFRGRINAAIGNAMAN---PGIDGLA 124
>gnl|CDD|187879 cd09748, Cmr3_III-B, CRISPR/Cas system-associated RAMP superfamily
protein Cmr3. 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;
RAMP superfamily protein; This protein is a subunit of
Cmr complex.
Length = 356
Score = 25.8 bits (57), Expect = 9.4
Identities = 24/109 (22%), Positives = 33/109 (30%), Gaps = 10/109 (9%)
Query: 3 LFPMPDVYSRVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPI 62
LFP P + L L+ S T L ++ K
Sbjct: 82 LFPAPLDLLVKRKKEDG----LRFLLRLEP---RPFSTGTDPEDALEGLLEPDIGDKKKP 134
Query: 63 LQAWLEEAEAQAKNKRRDPDAPSVLPAGE--KKRKRTSIA-APEKRSLE 108
+L Q PDA V+ E + R IA PE R++E
Sbjct: 135 APGYLSWEGLQKYLLGEAPDAREVVEGSELWEPETRIGIALDPETRTVE 183
>gnl|CDD|217859 pfam04045, P34-Arc, Arp2/3 complex, 34 kD subunit p34-Arc. Arp2/3
protein complex has been implicated in the control of
actin polymerisation in cells. The human complex
consists of seven subunits which include the actin
related Arp2 and Arp3, and five others referred to as
p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This
family represents the p34-Arc subunit.
Length = 240
Score = 25.7 bits (57), Expect = 9.4
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 85 SVLPAGEKKR--------KRTSIAAPEKRSLEAYFAVQPRPSGEKIAAI 125
LPA E++ KR +AAP +++ E + GE++A I
Sbjct: 46 EELPADEREELIEKIALLKRNCMAAPFEKAFEKQAELAEEAEGEEVAVI 94
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
0.315 0.130 0.367
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,381,467
Number of extensions: 654803
Number of successful extensions: 751
Number of sequences better than 10.0: 1
Number of HSP's gapped: 747
Number of HSP's successfully gapped: 45
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.5 bits)