RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14584
(563 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 64.4 bits (158), Expect = 2e-13
Identities = 19/50 (38%), Positives = 34/50 (68%), Gaps = 2/50 (4%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLK 268
R+ H+E E+RRRD++N EL ++P ++KL K +LR+A++++K
Sbjct: 2 RKAHNERERRRRDRINDAFEELRELLP--TPPNKKLSKAEILRLAIEYIK 49
Score = 41.7 bits (99), Expect = 2e-05
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 305 QNHSEIEKRRRDKMNTYITELSAMVPTL 332
+ H+E E+RRRD++N EL ++PT
Sbjct: 3 KAHNERERRRRDRINDAFEELRELLPTP 30
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 63.4 bits (155), Expect = 6e-13
Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 219 RQNHSEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGAVH 275
R+ H+ E+RRR+++N EL +++P S+KL K +LR AV ++K+++ +
Sbjct: 5 REAHNLRERRRRERINDAFDELRSLLP-TLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
Score = 41.4 bits (98), Expect = 4e-05
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 305 QNHSEIEKRRRDKMNTYITELSAMVPTLLPVK---TADI 340
+ H+ E+RRR+++N EL +++PTL P K A+I
Sbjct: 6 EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEI 44
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 59.9 bits (146), Expect = 7e-12
Identities = 16/54 (29%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 223 SEIEKRRRDKMNTYITELSAMVPMCHAMSRKLDKLTVLRMAVQHLKTIRGAVHS 276
+ E+RRR K+N EL +++P ++KL K +LR+A++++K+++ +
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLP-KNKKLSKAEILRLAIEYIKSLQEELQK 53
Score = 38.7 bits (91), Expect = 2e-04
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 308 SEIEKRRRDKMNTYITELSAMVPTLLPVKTAD 339
+ E+RRR K+N EL +++PTL K
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLS 32
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria
and eukarya. Probably the most surprising identification
of a PAS domain was that in EAG-like K+-channels. PAS
domains have been found to bind ligands, and to act as
sensors for light and oxygen in signal transduction.
Length = 103
Score = 36.8 bits (85), Expect = 0.003
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 168 QGELLGQSWFDILHPKDVAKVKEQLFSSDLSPRERLIDV----KSKQVIVGLPVSRQNHS 223
EL+G+S D++HP+D +++E+L + ++V K VI L
Sbjct: 29 PEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIRD 88
Query: 224 EIEKRRR 230
E +
Sbjct: 89 EGGEVIG 95
>gnl|CDD|214512 smart00091, PAS, PAS domain. PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels.
Length = 67
Score = 33.1 bits (76), Expect = 0.040
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 168 QGELLGQSWFDILHPKDVAKVKEQL 192
EL+G+S +++HP+D +V+E L
Sbjct: 38 PEELIGKSLLELIHPEDRERVQEAL 62
>gnl|CDD|201463 pfam00831, Ribosomal_L29, Ribosomal L29 protein.
Length = 58
Score = 29.8 bits (68), Expect = 0.39
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 290 QELKHLILQAAEGFLQNHSEIEKRRRD--KMNTYITE 324
+EL +L Q A G L+N I++ RRD ++ T + E
Sbjct: 21 KELFNLRFQKATGQLENPHRIKEVRRDIARILTVLRE 57
>gnl|CDD|218825 pfam05956, APC_basic, APC basic domain. This region of the APC
family of proteins is known as the basic domain. It
contains a high proportion of positively charged amino
acids and interacts with microtubules.
Length = 359
Score = 32.4 bits (73), Expect = 0.62
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 364 TPASSSSSSSSNSAPSTQP--------GPNTPSPGTGSCVKEEPDTTTGAAASCHRKKKQ 415
TP+SSSS +S+ S P +P G N+ PG G+ + + P T++ A A Q
Sbjct: 79 TPSSSSSQTSTPSQPLPRPLPRPTQSAGRNSILPGPGNSLSQVPRTSSPARALLASSGSQ 138
Query: 416 QQSDR 420
++ +
Sbjct: 139 HKTQK 143
>gnl|CDD|238243 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP. L29 is a
protein of the large ribosomal Subunit. A homolog,
called heparin/heparan sulfate interacting protein
(HIP), has also been identified in mammals. L29 is
located on the surface of the large ribosomal subunit,
where it participates in forming a protein ring that
surrounds the polypeptide exit channel, providing
structural support for the ribosome. L29 is involved in
forming the translocon binding site, along with L19,
L22, L23, L24, and L31e. In addition, L29 and L23 form
the interaction site for trigger factor (TF) on the
ribosomal surface, adjacent to the exit tunnel. L29
forms numerous interactions with L23 and with the 23S
rRNA. In some eukaryotes, L29 is referred to as L35,
which is distinct from L35 found in bacteria and some
eukaryotes (primarily plastids and mitochondria). The
mammalian homolog, HIP, is found on the surface of many
tissues and cell lines. It is believed to play a role in
cell adhesion and modulation of blood coagulation. It
has also been shown to inhibit apoptosis in cancer
cells.
Length = 57
Score = 29.0 bits (66), Expect = 0.75
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 290 QELKHLILQAAEGFLQNHSEIEKRRRD--KMNTYITE 324
+EL +L Q A G L+N I K R+D ++ T + E
Sbjct: 20 KELFNLRFQKATGQLENPHRIRKVRKDIARIKTVLNE 56
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 32.1 bits (73), Expect = 0.91
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 364 TPASSSSSSSSNSAPSTQPG----PNTPSPGTGSCVKEEPDTTTGAAAS 408
T ++S+ + + P NT +P + E P ++ A S
Sbjct: 33 TTTPATSTEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETS 81
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 31.8 bits (72), Expect = 1.1
Identities = 40/139 (28%), Positives = 56/139 (40%), Gaps = 25/139 (17%)
Query: 36 SHSVYYDLQPVQRSTCSTSTYVED-GQIPSSSV---HPMEYQQADSTRKSKKRKGGSSFH 91
SH V PV + +YVED +P S + + Q+ TRK+KKRK G +
Sbjct: 343 SHPVCNGASPVSITPEENESYVEDAVSLPDSEIKDGKLSKLQRV--TRKAKKRKLGDMAY 400
Query: 92 GSD------------FEEDTGEDSGKSLKLDDSKKSTCSTSTYVEDGQIPSSSVHPMEYQ 139
D E + DS +S K D S+ S S E+G + S ++ +
Sbjct: 401 EGDADWETLINEQGFLENPSACDSDRSFKTRDKSDSS-SVSKEGENGGAAAVSAG-LKAR 458
Query: 140 QADSTRKSK-----KRKGG 153
K K KRKGG
Sbjct: 459 AVGPIEKIKFKEVLKRKGG 477
>gnl|CDD|178971 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed.
Length = 66
Score = 28.7 bits (65), Expect = 1.3
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 13/51 (25%)
Query: 287 LTDQELKHLIL-----------QAAEGFLQNHSEIEKRRRD--KMNTYITE 324
L+ +EL +L Q A G L+N + + RRD ++ T + E
Sbjct: 9 LSVEELNEKLLELKKELFNLRFQKATGQLENTHRLREVRRDIARIKTVLRE 59
>gnl|CDD|234314 TIGR03694, exosort_acyl, N-acyl amino acid synthase,
PEP-CTERM/exosortase system-associated. Members of this
protein family are restricted to bacterial species with
the PEP-CTERM/exosortase system predicted to act in
exopolysaccharide-associated protein targeting.
PSI-BLAST and CDD reveal relationships to the
acyltransferase family that includes N-acyl-L-homoserine
lactone synthetase, and recent work shows long-chain
N-acyl amino acid biosynthesis activity. Several members
of this family may be found in a single genome. These
acyltransferases may produce a quorum signalling
molecule or may contribute to chemical modifications in
exopolysaccharide and biofilm structural material
production.
Length = 241
Score = 30.4 bits (69), Expect = 2.3
Identities = 17/63 (26%), Positives = 20/63 (31%), Gaps = 6/63 (9%)
Query: 330 PTLLPVKTADIPAEVSRLCPGARRSFFCRMKCKHTPASSSSSSSSNSAPSTQPGPNTPSP 389
P LP AEVSRL + F R K P S + + S P
Sbjct: 103 PRRLPRSR---IAEVSRLA--VSKDFRRRKGEKLKP-SGVGVIETEAPFSESERRRFPHI 156
Query: 390 GTG 392
G
Sbjct: 157 PLG 159
>gnl|CDD|222915 PHA02670, PHA02670, ORF112 putative chemokine-binding protein;
Provisional.
Length = 287
Score = 30.3 bits (68), Expect = 2.7
Identities = 17/59 (28%), Positives = 21/59 (35%), Gaps = 2/59 (3%)
Query: 361 CKHTPASSSSSSSSNSAPSTQPGPNTPSPGTGSCVKEEPDTTTGAAASCHRKKKQQQSD 419
C H + PST PGP T + +EP TT S RK+ D
Sbjct: 165 CDHQKFPEEPTPKPEPTPSTTPGPTLLE--TTLDLTDEPTTTPPVDTSVDRKRNPDPVD 221
>gnl|CDD|145047 pfam01692, Paramyxo_C, Paramyxovirus non-structural protein c.
This family consist of the C proteins (C', C, Y1, Y2)
found in Paramyxovirinae; human parainfluenza, and
sendai virus. The C proteins effect viral RNA synthesis
having both a positive and negative effect during the
course of infection. Paramyxovirus have a negative
strand ssRNA genome of 15.3kb form which six mRNAs are
transcribed, five of these are monocistronic. The P/C
mRNA is polycistronic and has two overlapping open
reading frames P and C, C encodes the nested C proteins
C', C, Y1 and Y2.
Length = 204
Score = 29.2 bits (65), Expect = 4.4
Identities = 18/55 (32%), Positives = 24/55 (43%)
Query: 367 SSSSSSSSNSAPSTQPGPNTPSPGTGSCVKEEPDTTTGAAASCHRKKKQQQSDRK 421
S S SS NS P++ P P G+ D+ A S + K KQQ+ K
Sbjct: 23 SMRSDSSLNSYPTSAPTPEKTEAGSMVSSTTPKDSAHHAKPSVNTKTKQQKRRPK 77
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 29.7 bits (66), Expect = 5.1
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 362 KHTPASSSSSSSSNSAPSTQPGPNTPSPGTGSCVKEEPDT 401
K S++SS +A + P P++ S + + P
Sbjct: 1222 KAAQLQLSAASSPPAATTPTPPPSSSSSSSAQSISTSPGQ 1261
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed.
Length = 592
Score = 29.3 bits (65), Expect = 6.9
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 366 ASSSSSSSSNSAPSTQPGPNTPSPGTGSCVK 396
A S++S ++ S PST + PS GT + K
Sbjct: 376 AGSTTSDTNTSKPSTGTSTSKPSTGTSTNAK 406
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 29.1 bits (64), Expect = 8.8
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 362 KHTPASSSSSSSSNSAPSTQPGPN-TPSPGTGSCVKEEPDTTTGAAASCHRKKKQQQSDR 420
+ + +SSSSSSSS+S+PS++P + TPS + P A R ++++ DR
Sbjct: 1815 RSSSSSSSSSSSSSSSPSSRPSRSATPS------LSPSPSPPRRAPVDRSRSGRRRERDR 1868
>gnl|CDD|220204 pfam09362, DUF1996, Domain of unknown function (DUF1996). This
family of proteins are functionally uncharacterized.
Length = 228
Score = 28.4 bits (64), Expect = 8.8
Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 29/70 (41%)
Query: 57 VEDGQIPSSSVHPMEYQQADSTRKSKKRKGGSSFHGSD-FEEDTGEDSGKSLKLDDSKKS 115
V GQIPS+ VH G + F ++ D S
Sbjct: 4 VNPGQIPSAHVH--------------------QIVGGNAF--------DATMTYDLLLAS 35
Query: 116 TCSTSTYVED 125
TC++ T ED
Sbjct: 36 TCTSCTNAED 45
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 28.9 bits (64), Expect = 9.0
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 366 ASSSSSSSSNSAPSTQPGPNTPSPGTGSCVKEEPDTTTGAAAS 408
ASSS S SA S G + S S +E T +G A++
Sbjct: 144 ASSSDGKSKASAKS---GSKSASKHGESNSSDESATDSGKASA 183
>gnl|CDD|221287 pfam11881, DUF3401, Domain of unknown function (DUF3401). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 231 to 250 amino acids in length. This domain is
found associated with pfam02145, pfam00595.
Length = 240
Score = 28.2 bits (63), Expect = 9.0
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 352 RRSFFCRMKCKHTPASSSSSSSSNSAPSTQPGPNTPSPGTGSCVKEEPDTTTG 404
R + F + P S + + S + Q TP G +E P T TG
Sbjct: 183 RAASFFSLTESQRPESLAPARSLVLQVAPQTPRTTPLSG-----EESPSTLTG 230
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 0.128 0.372
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,269,270
Number of extensions: 2530193
Number of successful extensions: 1917
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1892
Number of HSP's successfully gapped: 30
Length of query: 563
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 461
Effective length of database: 6,413,494
Effective search space: 2956620734
Effective search space used: 2956620734
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 (21.9 bits)
S2: 62 (27.6 bits)