RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2754
(367 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 = 243 bits (622), Expect = 1e-79
Identities = 76/233 (32%), Positives = 112/233 (48%), Gaps = 35/233 (15%)
Query: 28 YRVYELNKRLQQ-RTEESDNLWWDAFATEFFEDDATLTLTFCLEDGP--KRYTIGRTLIP 84
R+ E N+ L R E+ D +W F EFF DA L + EDGP K++ I +P
Sbjct: 2 LRLLEFNEHLSNFRGEDDDISYWQRFVHEFFSPDAVLRYSLSSEDGPEGKQFEITTPALP 61
Query: 85 RYFRSIFDGGITELYYNLKHPKE-SFHNTSITLDCDQCTMVTHHGKPMLTKVCTEGRLIL 143
RYFR+IF+ G+ EL L +E N SI ++C + + + + +V TEG L
Sbjct: 62 RYFRTIFESGVKELQLVLDGAREQVLPNGSIFVECPKASFIYWYDDGS--QVVTEGTLRA 119
Query: 144 EFTFDDLMRIKSWHFAVRQHRELVPRTIVGM-------------QDPSMLEQL------- 183
FD ++I+ W F R H E +PR+++ + S QL
Sbjct: 120 H--FDPDLKIEWWDFCTRSHEEYIPRSVLEPLASPLHTKSKQQSPELSKNSQLRQQKGPQ 177
Query: 184 ------TKNITRQGITNSTLNYLRLCVILEPMQELMSRHKAY-ALSPRDCLKT 229
+ N+TR G+ + + +L + IL PMQ+LMS KA LSPR+ LK
Sbjct: 178 PITSLPSSNVTRFGLPKAVMRFLEIAEILSPMQDLMSFSKANPILSPREALKQ 230
>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 = 29.7 bits (67), Expect = 0.85
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 224 RDCLKT-TLFQKWQRMVAPPGKRESQRPA----NKRRKRKGSQSGGAANSAPPAPSKKRS 278
++C KT L Q++ P KR+ Q+ + K+RK+ S + SA +KKR
Sbjct: 46 KECQKTSQLIHLSQQLQQPQRKRKEQQKSSQTHKKKRKKSRHVS---SRSAKKISAKKRR 102
>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
Length = 521
Score = 30.1 bits (68), Expect = 2.0
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 21/85 (24%)
Query: 148 DDLMRIKSWHFAVRQHRELVPRTIVGMQDPSMLEQLTKNITRQGITNSTLNYLRLCVILE 207
++L I+ H + + + D LEQL K I
Sbjct: 117 EELSAIRELHLRTADELGVDESVVEKLLDE--LEQLLKGIAM------------------ 156
Query: 208 PMQELMSRHKAYALSPRDCLKTTLF 232
M+EL R + Y +S + + T +F
Sbjct: 157 -MKELTPRTRDYLVSFGERMSTRIF 180
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 30.2 bits (67), Expect = 2.6
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 240 APPGKRESQRPANKRRKRKGSQSGGA----ANSAPPAPSKKRSP 279
APPG + R A++RR KG Q G ++S+ + S RSP
Sbjct: 1537 APPGPELADRHADRRRSTKGPQRPGGKRPRSSSSSSSASHDRSP 1580
>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 = 2.8
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 156 WHFAVRQHRELVPRTIVGMQ-----DPSMLEQLTKN 186
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 = 29.1 bits (65), Expect = 3.3
Identities = 7/42 (16%), Positives = 15/42 (35%), Gaps = 5/42 (11%)
Query: 246 ESQRPANKRRKRKGSQSGGAANSA-----PPAPSKKRSPGPN 282
E++ +R + ++ A +A P+ P P
Sbjct: 105 EAKARVQAQRAEQQAKKREEAPAAGEKPTAERPATAARPKPK 146
>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 = 4.5
Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 1/57 (1%)
Query: 204 VILEPMQELMSRH-KAYALSPRDCLKTTLFQKWQRMVAPPGKRESQRPANKRRKRKG 259
+I + + H K ++ L L R ES R NK R G
Sbjct: 93 LISSQQAQYVRDHFKQEGMTDAQALAKYLRSLAWRPADDYTLYESARLHNKIAIRDG 149
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 28.6 bits (64), Expect = 5.6
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 8/57 (14%)
Query: 260 SQSGGAANSAPPAPSKKRSPGPNFSLASQD-------VMVVGEPSLMGGEF-GDEDE 308
S ++ + S+ RS + + PSLMGG F G EDE
Sbjct: 231 DTSESESDESDSEISESRSVSDSEESSPPSKKPKEKKTSSTFLPSLMGGYFSGSEDE 287
>gnl|CDD|203730 pfam07700, HNOB, Heme NO binding. The HNOB (Heme NO Binding)
domain, is a predominantly alpha-helical domain and
binds heme via a covalent linkage to histidine. The HNOB
domain is predicted to function as a heme-dependent
sensor for gaseous ligands, and transduce diverse
downstream signals, in both bacteria and animals.
Length = 171
Score = 28.0 bits (63), Expect = 6.2
Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 13/85 (15%)
Query: 26 PDYRVYELNKRLQQRTEESDNLWWDAFATEFFEDDATLTLTFCLEDGPKR--YTIGRTLI 83
D +Y+L + W+AF FF TF E G +GR L
Sbjct: 44 DDSELYDLVAAASKVLGIPAEEIWEAFGRFFF--------TFFSESGYDELLRVLGRNL- 94
Query: 84 PRYFRSIFDGG--ITELYYNLKHPK 106
+ +S+ + +T+LY + P
Sbjct: 95 RDFLQSLDNIHVEVTKLYPGARPPS 119
>gnl|CDD|226450 COG3941, COG3941, Mu-like prophage protein [General function
prediction only].
Length = 633
Score = 28.3 bits (63), Expect = 6.8
Identities = 17/83 (20%), Positives = 23/83 (27%), Gaps = 14/83 (16%)
Query: 233 QKWQRMVAPPGKRESQRPANKRRKRKG-----------SQSGGAANSAPPAPSKKRSPGP 281
+ P ++ P K K G S SGG A A P R G
Sbjct: 440 STRESPRRPAQRKRGVPPRRKAGKAGGLAARSLPALGFSASGGLAAMAGKVPRLSRLAGR 499
Query: 282 NFSLASQDVMVVGE---PSLMGG 301
N L ++ L+
Sbjct: 500 NAPLLGASSLIAVAEVYSVLLDE 522
>gnl|CDD|181231 PRK08114, PRK08114, cystathionine beta-lyase; Provisional.
Length = 395
Score = 28.1 bits (63), Expect = 7.8
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 313 RLENTQYDAGANCLDHDPHFSDSPSWGG 340
+L + Q AN LD+ FS + SWGG
Sbjct: 318 KLTDEQL---ANYLDNFSLFSMAYSWGG 342
>gnl|CDD|182501 PRK10503, PRK10503, multidrug efflux system subunit MdtB;
Provisional.
Length = 1040
Score = 28.5 bits (64), Expect = 7.9
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 174 MQDPSMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSR 215
+QDP+ ++ LT + G TN +LN RL + L+P+ E R
Sbjct: 597 LQDPA-VQSLTSFVGVDG-TNPSLNSARLQINLKPLDERDDR 636
>gnl|CDD|184155 PRK13574, PRK13574, anthranilate synthase component I; Provisional.
Length = 420
Score = 28.2 bits (63), Expect = 8.1
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 82 LIPRYFRSIFDGGITELYYNLK 103
++ R++R +F G +YYNL+
Sbjct: 180 VLSRFYRYLFSGDPLRIYYNLR 201
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
0.319 0.135 0.423
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: 18,748,887
Number of extensions: 1778975
Number of successful extensions: 1561
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1547
Number of HSP's successfully gapped: 30
Length of query: 367
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 269
Effective length of database: 6,590,910
Effective search space: 1772954790
Effective search space used: 1772954790
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 (21.7 bits)
S2: 60 (27.0 bits)