RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1653
(96 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 80.6 bits (200), Expect = 5e-22
Identities = 32/57 (56%), Positives = 38/57 (66%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
RR R T+T Q ELEKEF N Y + R E+A L LTERQ+K+WFQNRR K K+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 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 = 71.5 bits (176), Expect = 2e-18
Identities = 34/58 (58%), Positives = 39/58 (67%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
RR R +T Q ELEKEF N Y +R R E+A L LTERQ+KIWFQNRR KLK+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 70.7 bits (174), Expect = 4e-18
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
+RR R ++T Q ELEKEF N Y +R R E+A L L+ERQ+K+WFQNRR K K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 49.7 bits (119), Expect = 6e-09
Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+ R+ T Q + LE+EF N Y + RI+++ L + + ++IWFQN+R K KK+
Sbjct: 52 KSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109
>gnl|CDD|226300 COG3777, COG3777, Uncharacterized conserved protein [Function
unknown].
Length = 273
Score = 29.4 bits (66), Expect = 0.21
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 12 QTYTRYQTLELEKEFH----TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
Q YT ++T++ +E H ++T LCL ER+ I + N
Sbjct: 95 QEYTCHETIQYIEEKHGRSGELTFVTVPHVYSSPGQLCLFERRT-IVYTNAPA 146
>gnl|CDD|151367 pfam10920, DUF2705, Protein of unknown function (DUF2705). This
bacterial family of proteins has no known function.
Length = 247
Score = 28.7 bits (64), Expect = 0.34
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 55
+ Y+ L++ +EF +L ++ I + T QI I+F
Sbjct: 69 KDLLISYEFLKISREFKKEKWLMKQFLIIFIRLIIFTLLQIAIFF 113
>gnl|CDD|199823 cd10498, MH2_SMAD_4, C-terminal Mad Homology 2 (MH2) domain in
SMAD4. The MH2 domain is located at the C-terminus of
the SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. The MH2 domain is responsible for
type I receptor interaction, phosphorylation-triggered
homo- and hetero-oligomerization, and transactivation.
It is negatively regulated by the N-terminal MH1 domain.
SMAD4, which belongs to the Dwarfin family of proteins,
is involved in many cell functions such as
differentiation, apoptosis, gastrulation, embryonic
development and the cell cycle. SMAD4 binds receptor
regulated SMADs (R-SMADs) such as SMAD1 or SMAD2, and
forms an oligomeric complex that binds to DNA and serves
as a transcription factor. SMAD4 is often mutated in
several cancers, such as multiploid colorectal cancer,
cervical cancer and pancreatic carcinoma, as well as in
juvenile polyposis syndrome.
Length = 222
Score = 27.8 bits (62), Expect = 0.67
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 74 EQEKQAQAQKAAAAALAAAAVDH 96
+ ++QA +AAAAA AAA +
Sbjct: 127 QMQQQAATAQAAAAAQAAAVAGN 149
Score = 25.1 bits (55), Expect = 7.1
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 75 QEKQAQAQKAAAAALA-AAAVD 95
++ Q QA A AAA A AAAV
Sbjct: 126 RQMQQQAATAQAAAAAQAAAVA 147
>gnl|CDD|216872 pfam02096, 60KD_IMP, 60Kd inner membrane protein.
Length = 193
Score = 27.1 bits (61), Expect = 1.2
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 46 LTERQIKIWFQNRRMK-LKKEIQAIKE--LNEQEKQAQAQKA 84
LT +Q K +M+ L+ EI+ I+E ++ +K Q
Sbjct: 21 LTLKQYK---SMAKMQELQPEIKEIQEKYKDDPQKLQQEMMK 59
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 26.6 bits (60), Expect = 1.4
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
K+++A + E E +A + A A ALA
Sbjct: 44 LKQLEARRA--ELEAKAAEELAEAEALAEK 71
>gnl|CDD|234272 TIGR03592, yidC_oxa1_cterm, membrane protein insertase, YidC/Oxa1
family, C-terminal domain. This model describes
full-length from some species, and the C-terminal
region only from other species, of the YidC/Oxa1 family
of proteins. This domain appears to be univeral among
bacteria (although absent from Archaea). The
well-characterized YidC protein from Escherichia coli
and its close homologs contain a large N-terminal
periplasmic domain in addition to the region modeled
here [Protein fate, Protein and peptide secretion and
trafficking].
Length = 181
Score = 26.7 bits (60), Expect = 1.7
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 46 LTERQIKIWFQNRRMK-LKKEIQAIKEL--NEQEKQAQAQ 82
LT +Q K R+M+ L+ +++ I+E ++ +K Q
Sbjct: 20 LTLKQYK---SMRKMQELQPKLKEIQEKYKDDPQKLQQEM 56
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The
domain, however, is found in various periplasmic
ligand-binding sensor proteins.
Length = 234
Score = 26.9 bits (60), Expect = 1.7
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 67 QAIKELNEQEKQAQAQKAAAAA 88
A+K+ N + ++ +AQ +
Sbjct: 55 AALKQANARIEELEAQAQHPQS 76
>gnl|CDD|233430 TIGR01477, RIFIN, variant surface antigen, rifin family. This
model represents the rifin branch of the rifin/stevor
family (pfam02009) of predicted variant surface antigens
as found in Plasmodium falciparum. This model is based
on a set of rifin sequences kindly provided by Matt
Berriman from the Sanger Center. This is a global model
and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 20 bits.
Length = 353
Score = 27.0 bits (60), Expect = 1.7
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 58 RRMKLKKEIQAIKELNE 74
R+ K+KK++Q IK LNE
Sbjct: 337 RKKKMKKKLQYIKLLNE 353
>gnl|CDD|215395 PLN02742, PLN02742, Probable galacturonosyltransferase.
Length = 534
Score = 26.7 bits (59), Expect = 1.8
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 60 MKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAV 94
M LK IQA L E+ A Q LAA A+
Sbjct: 157 MTLKAHIQA---LEERANAATVQSTKFGQLAAEAL 188
>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 = 25.1 bits (56), Expect = 1.8
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 29 NHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
N Y + + E+A L+ +QI WF N R
Sbjct: 8 NPYPSEEEKSELARQTGLSRKQIDNWFINARR 39
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 26.5 bits (58), Expect = 2.1
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 1 MGANGLRRRGRQTYTRYQ 18
MG N + RGRQ R+Q
Sbjct: 317 MGMNNMVHRGRQKKQRFQ 334
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 26.5 bits (58), Expect = 2.4
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAAA 93
K+++ A + E+ + A A AAAAA AA A
Sbjct: 297 KQDVLAAAKAAEEARAAAAAPAAAAAPAAPA 327
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 26.4 bits (59), Expect = 2.5
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 15/49 (30%)
Query: 31 YLTRR----------RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 69
YLTRR R + C T R I + +N M + IQ +
Sbjct: 201 YLTRRLVEVVQHIVVRETD-----CGTTRGISVSPRNGMMIERILIQTL 244
>gnl|CDD|217451 pfam03249, TSA, Type specific antigen. There are several antigenic
variants in Rickettsia tsutsugamushi, and a
type-specific antigen (TSA) of 56-kilodaltons located on
the rickettsial surface is responsible for the
variation. TSA proteins are probably integral membrane
proteins.
Length = 502
Score = 26.4 bits (58), Expect = 2.7
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 75 QEKQAQAQKAAAAALAAAAV 94
Q +Q QAQ A A AAAAV
Sbjct: 315 QGQQQQAQATAQEAAAAAAV 334
>gnl|CDD|200473 cd11334, AmyAc_TreS, Alpha amylase catalytic domain found in
Trehalose synthetase. Trehalose synthetase (TreS)
catalyzes the reversible interconversion of trehalose
and maltose. The enzyme catalyzes the reaction in both
directions, but the preferred substrate is maltose.
Glucose is formed as a by-product of this reaction. It
is believed that the catalytic mechanism may involve the
cutting of the incoming disaccharide and transfer of a
glucose to an enzyme-bound glucose. This enzyme also
catalyzes production of a glucosamine disaccharide from
maltose and glucosamine. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 447
Score = 26.4 bits (59), Expect = 2.7
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 35 RRRIEMAHALCLT 47
RRRIE+A++L +
Sbjct: 348 RRRIELAYSLLFS 360
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 26.0 bits (58), Expect = 3.1
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 56 QNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAAL 89
+ + K +++ +ELN Q + QKA A +
Sbjct: 48 EAKAEKAERD----RELNRQRQAEAEQKAIVAQI 77
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 25.9 bits (57), Expect = 3.4
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAAA 93
K ++A K++NE +A A+K AA A A AA
Sbjct: 130 KAALEAEKKVNEARAEAVAEKKAAEAAAVAA 160
>gnl|CDD|106978 PHA00670, PHA00670, hypothetical protein.
Length = 540
Score = 26.0 bits (57), Expect = 4.1
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 60 MKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAAVD 95
+ K+++Q+I++ Q++QA Q A A A A AA
Sbjct: 493 IVPKEQVQSIRKQRAQQQQAAQQAAIAEAAANAAKA 528
>gnl|CDD|224060 COG1137, YhbG, ABC-type (unclassified) transport system, ATPase
component [General function prediction only].
Length = 243
Score = 25.6 bits (57), Expect = 4.2
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 6 LRRRGRQTYTRYQTLELE---KEFHTNHYLTR---------RRRIEMAHALCLT 47
L R + + EL+ +EFH H RRR+E+A AL
Sbjct: 104 LEIREKDLKKAERKEELDALLEEFHITHLRDSKAYSLSGGERRRVEIARALAAN 157
>gnl|CDD|218003 pfam04281, Tom22, Mitochondrial import receptor subunit Tom22. The
mitochondrial protein translocase family, which is
responsible for movement of nuclear encoded pre-proteins
into mitochondria, is very complex with at least 19
components. These proteins include several chaperone
proteins, four proteins of the outer membrane
translocase (Tom) import receptor, five proteins of the
Tom channel complex, five proteins of the inner membrane
translocase (Tim) and three "motor" proteins. This
family represents the Tom22 proteins. The N terminal
region of Tom22 has been shown to have chaperone-like
activity, and the C terminal region faces the
intermembrane face.
Length = 136
Score = 25.3 bits (56), Expect = 4.7
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 72 LNEQEKQAQAQKAAAAALAA 91
L E EK+ QK A LA
Sbjct: 117 LVEMEKEMDLQKGANEVLAP 136
>gnl|CDD|133191 cd05060, PTKc_Syk_like, Catalytic domain of Spleen Tyrosine
Kinase-like Protein Tyrosine Kinases. Protein Tyrosine
Kinase (PTK) family; Spleen Tyrosine Kinase (Syk)
subfamily; catalytic (c) domain. The Syk subfamily is
composed of Syk, ZAP-70, Shark, and similar proteins.
The PTKc family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
protein serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Syk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing two Src homology 2 (SH2) domains
N-terminal to the catalytic tyr kinase domain. They are
involved in the signaling downstream of activated
receptors (including B-cell, T-cell, and Fc receptors)
that contain ITAMs (immunoreceptor tyr activation
motifs), leading to processes such as cell
proliferation, differentiation, survival, adhesion,
migration, and phagocytosis. Syk is important in B-cell
receptor (BCR) signaling, while Zap-70 is primarily
expressed in T-cells and NK cells, and is a crucial
component in T-cell receptor (TCR) signaling. Syk also
plays a central role in Fc receptor-mediated
phagocytosis in the adaptive immune system. Shark is
exclusively expressed in ectodermally derived
epithelia, and is localized preferentially to the
apical surface of the epithelial cells, it may play a
role in a signaling pathway for epithelial cell
polarity.
Length = 257
Score = 25.4 bits (56), Expect = 5.1
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 59 RMKLKKEIQ-AIKELNEQEKQAQAQKAAAAALAAAAVDH 96
MK KE++ A+K L ++ A ++ A A +DH
Sbjct: 17 LMKSGKEVEVAVKTLKQEHIAAGKKEFLREASVMAQLDH 55
>gnl|CDD|215264 PLN02475, PLN02475,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase.
Length = 766
Score = 25.5 bits (56), Expect = 6.0
Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 8/47 (17%)
Query: 58 RRMKLKKEI--------QAIKELNEQEKQAQAQKAAAAALAAAAVDH 96
KL KE+ Q + E+ K QK A A AA
Sbjct: 340 NETKLDKELKSWLAFAAQKVVEVVALAKALAGQKDEAFFSANAAAQA 386
>gnl|CDD|215222 PLN02397, PLN02397, aspartate transaminase.
Length = 423
Score = 25.3 bits (56), Expect = 6.1
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 18 QTLELEKEFHTNHYLTRRRRIEMA 41
Q + KE+H Y+TR RI MA
Sbjct: 380 QVDRMTKEYHI--YMTRDGRISMA 401
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 25.4 bits (56), Expect = 6.8
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 48 ERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQ 80
E + + Q R KLKK+ + K+ E+ ++A+
Sbjct: 558 EEKEALKEQKRLRKLKKQEEKKKKELEKLEKAK 590
>gnl|CDD|178439 PLN02847, PLN02847, triacylglycerol lipase.
Length = 633
Score = 24.8 bits (54), Expect = 9.1
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 7/36 (19%)
Query: 52 KIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAA 87
++W++ L+KE+Q ++ E + QAQ ++AAAA
Sbjct: 498 ELWYE-----LEKELQ--RQETEVDAQAQEEEAAAA 526
>gnl|CDD|233905 TIGR02515, IV_pilus_PilQ, type IV pilus secretin (or competence
protein) PilQ. A number of proteins homologous to PilQ
are involved in type IV pilus formation, competence for
transformation, type III secretion, and type II
secretion (also called the main terminal branch of the
general secretion pathway). Members of this family
include PilQ itself, which is a component of the type
IV pilus structure, from a number of species. In
Haemophilus influenzae, the member of this family is
associated with competence for transformation with
exogenous DNA rather than with formation of a type IV
pilus; the surface structure required for competence
may be considered an unusual, incomplete type IV pilus
structure [Cell envelope, Surface structures].
Length = 418
Score = 24.6 bits (54), Expect = 9.8
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 66 IQAIKELNEQEKQAQAQKAAAAALA 90
I + EL QEK K L
Sbjct: 71 IAPLDELAAQEKDELEAKKQIENLE 95
>gnl|CDD|235948 PRK07157, PRK07157, acetate kinase; Provisional.
Length = 400
Score = 24.7 bits (54), Expect = 9.9
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 48 ERQIKIWFQNRRMKLKKEIQAI 69
I+IW +N+ ++ +EI+ I
Sbjct: 66 AVLIEIWEENKLIEDLEEIELI 87
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 0.128 0.359
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: 5,039,627
Number of extensions: 428886
Number of successful extensions: 1671
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1587
Number of HSP's successfully gapped: 203
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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 (22.0 bits)
S2: 53 (24.1 bits)