RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2753
(247 letters)
>gnl|CDD|216712 pfam01803, LIM_bind, LIM-domain binding protein. The LIM-domain
binding protein, binds to the LIM domain pfam00412 of
LIM homeodomain proteins which are transcriptional
regulators of development. Nuclear LIM interactor (NLI)
/ LIM domain-binding protein 1 (LDB1) is located in the
nuclei of neuronal cells during development, it is
co-expressed with Isl1 in early motor neuron
differentiation and has a suggested role in the Isl1
dependent development of motor neurons. It is suggested
that these proteins act synergistically to enhance
transcriptional efficiency by acting as co-factors for
LIM homeodomain and Otx class transcription factors both
of which have essential roles in development. The
Drosophila protein Chip is required for segmentation and
activity of a remote wing margin enhancer. Chip is a
ubiquitous chromosomal factor required for normal
expression of diverse genes at many stages of
development. It is suggested that Chip cooperates with
different LIM domain proteins and other factors to
structurally support remote enhancer-promoter
interactions.
Length = 230
Score = 222 bits (569), Expect = 2e-73
Identities = 70/217 (32%), Positives = 104/217 (47%), Gaps = 34/217 (15%)
Query: 1 ESDNLWWDAFATEFFEDDATLTLTFCLEDGP--KRYTIGRTLIPRYFRSIFDGGITELYY 58
+ D +W F EFF DA L + EDGP K++ I +PRYFR+IF+ G+ EL
Sbjct: 18 DDDISYWQRFVHEFFSPDAVLRYSLSSEDGPEGKQFEITTPALPRYFRTIFESGVKELQL 77
Query: 59 NLKHPKE-SFHNTSITLDCDQCTMVTHHGKPMLTKVCTEGRLILEFTFDDLMRIKSWHFA 117
L +E N SI ++C + + + + +V TEG L FD ++I+ W F
Sbjct: 78 VLDGAREQVLPNGSIFVECPKASFIYWYDDGS--QVVTEGTLRAH--FDPDLKIEWWDFC 133
Query: 118 VRQHRELVPRTIVGM-------------QDPSMLEQL-------------TKNITRQGIT 151
R H E +PR+++ + S QL + N+TR G+
Sbjct: 134 TRSHEEYIPRSVLEPLASPLHTKSKQQSPELSKNSQLRQQKGPQPITSLPSSNVTRFGLP 193
Query: 152 NSTLNYLRLCVILEPMQELMSRHKAY-ALSPRDCLKT 187
+ + +L + IL PMQ+LMS KA LSPR+ LK
Sbjct: 194 KAVMRFLEIAEILSPMQDLMSFSKANPILSPREALKQ 230
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 31.0 bits (69), Expect = 0.78
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 198 APPGKRESQRPANKRRKRKGSQSGGA----ANSAPPAPSKKRSP 237
APPG + R A++RR KG Q G ++S+ + S RSP
Sbjct: 1537 APPGPELADRHADRRRSTKGPQRPGGKRPRSSSSSSSASHDRSP 1580
>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
Length = 521
Score = 30.1 bits (68), Expect = 1.3
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 21/85 (24%)
Query: 106 DDLMRIKSWHFAVRQHRELVPRTIVGMQDPSMLEQLTKNITRQGITNSTLNYLRLCVILE 165
++L I+ H + + + D LEQL K I
Sbjct: 117 EELSAIRELHLRTADELGVDESVVEKLLDE--LEQLLKGIAM------------------ 156
Query: 166 PMQELMSRHKAYALSPRDCLKTALF 190
M+EL R + Y +S + + T +F
Sbjct: 157 -MKELTPRTRDYLVSFGERMSTRIF 180
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 29.1 bits (65), Expect = 1.5
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 114 WHFAVRQHRELVPRTIVGMQ-----DPSMLEQLTKN 144
W + H P +VG Q DPS +E+L KN
Sbjct: 95 WVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKN 130
>gnl|CDD|225651 COG3109, ProQ, Activator of osmoprotectant transporter ProP [Signal
transduction mechanisms].
Length = 208
Score = 28.7 bits (64), Expect = 2.4
Identities = 7/42 (16%), Positives = 15/42 (35%), Gaps = 5/42 (11%)
Query: 204 ESQRPANKRRKRKGSQSGGAANSA-----PPAPSKKRSPGPN 240
E++ +R + ++ A +A P+ P P
Sbjct: 105 EAKARVQAQRAEQQAKKREEAPAAGEKPTAERPATAARPKPK 146
>gnl|CDD|218612 pfam05501, DUF755, Domain of unknown function (DUF755). This
family is predominated by ORFs from Circoviridae. The
function of this family remains to be determined.
Length = 122
Score = 27.8 bits (62), Expect = 2.9
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 182 RDCLKTA-LFQKWQRMVAPPGKRESQRPA----NKRRKRKGSQSGGAANSAPPAPSKKRS 236
++C KT+ L Q++ P KR+ Q+ + K+RK+ S + SA +KKR
Sbjct: 46 KECQKTSQLIHLSQQLQQPQRKRKEQQKSSQTHKKKRKKSRHVS---SRSAKKISAKKRR 102
>gnl|CDD|221073 pfam11311, DUF3114, Protein of unknown function (DUF3114). Some
members in this family of proteins with unknown function
are annotated as cytosolic proteins. This cannot be
confirmed.
Length = 252
Score = 28.5 bits (64), Expect = 3.0
Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 1/57 (1%)
Query: 162 VILEPMQELMSRH-KAYALSPRDCLKTALFQKWQRMVAPPGKRESQRPANKRRKRKG 217
+I + + H K ++ L L R ES R NK R G
Sbjct: 93 LISSQQAQYVRDHFKQEGMTDAQALAKYLRSLAWRPADDYTLYESARLHNKIAIRDG 149
>gnl|CDD|184155 PRK13574, PRK13574, anthranilate synthase component I; Provisional.
Length = 420
Score = 28.2 bits (63), Expect = 4.3
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 40 LIPRYFRSIFDGGITELYYNLK 61
++ R++R +F G +YYNL+
Sbjct: 180 VLSRFYRYLFSGDPLRIYYNLR 201
>gnl|CDD|182501 PRK10503, PRK10503, multidrug efflux system subunit MdtB;
Provisional.
Length = 1040
Score = 28.2 bits (63), Expect = 5.2
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 132 MQDPSMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSR 173
+QDP+ ++ LT + G TN +LN RL + L+P+ E R
Sbjct: 597 LQDPA-VQSLTSFVGVDG-TNPSLNSARLQINLKPLDERDDR 636
>gnl|CDD|217495 pfam03326, Herpes_TAF50, Herpesvirus transcription activation
factor (transactivator). This family includes EBV BRLF1
and similar ORF 50 proteins from other herpesviruses.
Length = 500
Score = 27.8 bits (62), Expect = 5.8
Identities = 8/63 (12%), Positives = 20/63 (31%), Gaps = 1/63 (1%)
Query: 176 AYALSPRDCLKTALFQKWQRMVAPPGK-RESQRPANKRRKRKGSQSGGAANSAPPAPSKK 234
+ LS + + ++ P ++ + ++K+ GS + PS
Sbjct: 375 SPLLSSLADTPSGAAHQPASLLPPAVVQQQLEDASDKQPPTPGSSLVPQPDEQELGPSVM 434
Query: 235 RSP 237
Sbjct: 435 ALL 437
>gnl|CDD|218970 pfam06278, DUF1032, Protein of unknown function (DUF1032). This
family consists of several conserved eukaryotic proteins
of unknown function.
Length = 565
Score = 27.2 bits (60), Expect = 8.6
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 10/71 (14%)
Query: 179 LSPRDCLKTALFQKWQRMVAPPGKRESQRPANKRRKRKGS---QSGG----AANSAPPAP 231
L P D ++ F+K + PPG E+ P+ K RKRKG Q A +
Sbjct: 268 LDPFDSFESKPFKKGKPYSVPPGVEEA--PSQK-RKRKGPSKLQDFHKWFLKAYADHEDA 324
Query: 232 SKKRSPGPNFS 242
+ R GP F+
Sbjct: 325 RRSRRKGPTFA 335
>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed.
Length = 327
Score = 27.0 bits (60), Expect = 9.0
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 8/61 (13%)
Query: 194 QRMVAPPGKRESQRPANKRRK----RKGSQSGGAANSAPPAPSKKRSPGPNFSL----AS 245
P + N + + SG + A A + +P +++L AS
Sbjct: 195 THPTPPQKPATKKPAVNHHKTATVAVPPATSGKPKSGAASARALSSAPASHYTLQLSSAS 254
Query: 246 Q 246
+
Sbjct: 255 R 255
>gnl|CDD|222158 pfam13474, SnoaL_3, SnoaL-like domain. This family contains a
large number of proteins that share the SnoaL fold.
Length = 121
Score = 26.2 bits (58), Expect = 9.1
Identities = 22/122 (18%), Positives = 37/122 (30%), Gaps = 20/122 (16%)
Query: 8 DAFATEFFEDDATLTLTFCLED------GPKRYTIGRTLIPRYFRSIFDGGITELYYNLK 61
DA+ E D +D G GR + Y R FD G +
Sbjct: 6 DAWHEAAAEGDLDAYFALFADDVSFIGTGADELWRGREAVRAYLRPDFDKGEPWSF---- 61
Query: 62 HPKESFHNTSITLDCDQ---CTMVTHHGKPMLTKVCTEGR--LILEFTFDDLMRIKSWHF 116
+ +T+ D ++ T++ R +L T D +I +H
Sbjct: 62 ----ELLDRRVTVSGDVAWVDELLDIQMPADGTELSGPCRGTGVLRKT-DGGWKIAHYHL 116
Query: 117 AV 118
+
Sbjct: 117 SF 118
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
0.321 0.134 0.417
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,428,050
Number of extensions: 1140843
Number of successful extensions: 1062
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 20
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.2 bits)