RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16978
(154 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 84.8 bits (211), Expect = 7e-23
Identities = 32/57 (56%), Positives = 38/57 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
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 = 75.0 bits (185), Expect = 6e-19
Identities = 34/58 (58%), Positives = 39/58 (67%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
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 = 74.2 bits (183), Expect = 1e-18
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
+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 = 52.4 bits (126), Expect = 3e-09
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
P + R+ T Q + LE+EF N Y + RI+++ L + + ++IWFQN+R K KK+
Sbjct: 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109
Query: 97 LRAVKE--INEQARRERE 112
E E+ +
Sbjct: 110 RSGKVEQRPGEEEADLAK 127
>gnl|CDD|221563 pfam12407, Abdominal-A, Homeobox protein. This domain family is
found in eukaryotes, and is approximately 30 amino acids
in length. The family is found in association with
pfam00046. This family is a homeobox protein involved in
differentiation of embryonic cells to form the abdominal
region.
Length = 24
Score = 34.1 bits (78), Expect = 0.001
Identities = 20/24 (83%), Positives = 23/24 (95%)
Query: 96 ELRAVKEINEQARREREEQDRLKQ 119
ELRAVKEINEQARREREEQ++ K+
Sbjct: 1 ELRAVKEINEQARREREEQEKDKR 24
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 32.3 bits (74), Expect = 0.037
Identities = 13/44 (29%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 86 FQNRRMKLKKELRAVKEINEQARRER-EEQDRLKQEKHAKMDHH 128
F R+ + +K+ A +E E+ R ER EE+ R+++E+ +++
Sbjct: 27 FHKRKQQRRKK--AQEEAKEKEREERIEERKRIREERKQELEKQ 68
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 32.5 bits (74), Expect = 0.064
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 93 LKKELRAVKEINEQARREREEQDRLKQEKHAKMDHHSHHQSM 134
+++E + +++ E+ RR REE R K EK A+M +++
Sbjct: 429 VEEEHQIYRKLQEE-RRLREEAIRAKAEKTARMKAEMKEKTL 469
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 30.9 bits (71), Expect = 0.16
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 87 QNRRMKLKKELRAVKEINEQARREREEQD 115
+ R KL+KEL VK+ E R R+
Sbjct: 12 RERIAKLRKELEKVKKQRELQRARRKRSG 40
>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 = 28.6 bits (65), Expect = 0.20
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 58 HFNH-YLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
H ++ Y + + E+A L+ +QI WF N R
Sbjct: 5 HLHNPYPSEEEKSELARQTGLSRKQIDNWFINARR 39
>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex. Med21 has been
known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in
Drosophila. The heterodimer of the two subunits Med7 and
Med21 appears to act as a hinge between the middle and
the tail regions of Mediator.
Length = 132
Score = 28.4 bits (64), Expect = 1.0
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 13/57 (22%)
Query: 70 EIAHALCLTERQIKIWF------------QNRRM-KLKKELRAVKEINEQARREREE 113
E+A + L +QI+ Q RR+ +L++ELR V+ E+A +E+E+
Sbjct: 61 ELARDIILKAQQIEYLIDSLPGIESSEEEQLRRIKELEEELREVEAEREEAVKEKEK 117
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 29.0 bits (66), Expect = 1.1
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 87 QNRRMKLKKELRAVKEINEQARREREEQD 115
+ R +LKKEL V++ E+ RR R+ D
Sbjct: 160 RERIAQLKKELEKVEKQRERQRRRRKRAD 188
>gnl|CDD|224060 COG1137, YhbG, ABC-type (unclassified) transport system, ATPase
component [General function prediction only].
Length = 243
Score = 27.6 bits (62), Expect = 2.8
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 52 ELEKEFHFNHYLTR---------RRRIEIAHALCLT 78
L +EFH H RRR+EIA AL
Sbjct: 122 ALLEEFHITHLRDSKAYSLSGGERRRVEIARALAAN 157
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 27.7 bits (62), Expect = 3.0
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 79 ERQIKIWFQNRRMK-LKKELRAVKEINEQARREREEQDRLKQEKHAKMD 126
R++++ R++ L++EL ++E ++A E EE QE K++
Sbjct: 222 LRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLE 270
>gnl|CDD|238006 cd00047, PTPc, Protein tyrosine phosphatases (PTP) catalyze the
dephosphorylation of phosphotyrosine peptides; they
regulate phosphotyrosine levels in signal transduction
pathways. The depth of the active site cleft renders the
enzyme specific for phosphorylated Tyr (pTyr) residues,
instead of pSer or pThr. This family has a distinctive
active site signature motif, HCSAGxGRxG. Characterized
as either transmembrane, receptor-like or
non-transmembrane (soluble) PTPs. Receptor-like PTP
domains tend to occur in two copies in the cytoplasmic
region of the transmembrane proteins, only one copy may
be active.
Length = 231
Score = 27.2 bits (61), Expect = 3.3
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 24 MLCQLKQSGPNGC----PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTE 79
ML +L + G C P G TY T+ L E + Y R +++++
Sbjct: 71 MLTELVEKGREKCAQYWPEEEGSLTYGDI-TVTLVSEEKLDDYT--VRTLKLSNTGTGET 127
Query: 80 RQIK-IWFQN 88
R + +
Sbjct: 128 RTVTHFQYTG 137
>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC;
Provisional.
Length = 276
Score = 27.3 bits (61), Expect = 3.5
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 87 QNRRMKLKKELRAVKEINEQARREREEQDRLKQ 119
+N LKKEL ++ ++ + E RL++
Sbjct: 77 ENEE--LKKELLELESRLQELEQLEAENARLRE 107
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 26.9 bits (60), Expect = 4.1
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 80 RQIKIWFQNRRMKLKKELRAVKEINEQARREREEQDRLKQEKHAKMD 126
RQ + F+ RR EL + + E RR REE++R K++ +
Sbjct: 158 RQQQRQFEQRR---NAELAETQRLEEAERRRREEKERRKKQDKERKQ 201
>gnl|CDD|223994 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational
modification, protein turnover, chaperones].
Length = 647
Score = 27.3 bits (61), Expect = 4.2
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 99 AVKEINEQARREREEQDRL 117
AV+E+ +A R +Q++L
Sbjct: 343 AVEELIREAARRAGDQNKL 361
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 26.7 bits (60), Expect = 4.9
Identities = 9/34 (26%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 87 QNRRMKLKKELRAVKEINEQARREREEQDRLKQE 120
Q R+++LK +++ + + E +RLK E
Sbjct: 16 QIRQLELKL-----RDLEAENEKLERELERLKSE 44
>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 435 to 791 amino acids in
length. This family is related to pfam00589 suggesting
it may be an integrase enzyme.
Length = 418
Score = 26.9 bits (60), Expect = 5.0
Identities = 14/81 (17%), Positives = 32/81 (39%)
Query: 60 NHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELRAVKEINEQARREREEQDRLKQ 119
HYL RR ++ + Q + RM ++ R +++ ++ + EE L++
Sbjct: 233 RHYLPRRVDRDVQAVVLGLPPQEALIRAATRMSRTRDPRRPRDLTDEQKASVEEDPELQE 292
Query: 120 EKHAKMDHHSHHQSMMGGLDK 140
+ ++ G + K
Sbjct: 293 LIRKRDHLKKEIIALYGQVAK 313
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 26.8 bits (60), Expect = 5.0
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 80 RQIK--IWFQNRRMKLKKELRAVKEINE--QARREREEQDRLKQEKHAK 124
RQ K I + KK A K E QAR ERE+ R + +H K
Sbjct: 432 RQAKAEIR--AIEQEKKKAEEA-KARFEARQARLEREKAAR--EARHKK 475
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 27.1 bits (60), Expect = 5.1
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 96 ELRAVKEINEQARREREEQDRLKQEKHAK 124
ELR +E E+ +RER+++ +LK E+ K
Sbjct: 4 ELRRAREKLEREQRERKQRAKLKLERERK 32
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 26.6 bits (59), Expect = 5.2
Identities = 9/44 (20%), Positives = 25/44 (56%)
Query: 85 WFQNRRMKLKKELRAVKEINEQARREREEQDRLKQEKHAKMDHH 128
W ++ + +K+L+ + E ++ RE+E ++ +++ AK +
Sbjct: 92 WLSAKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYE 135
>gnl|CDD|216534 pfam01499, Herpes_UL25, Herpesvirus UL25 family. The herpesvirus
UL25 gene product is a virion component involved in
virus penetration and capsid assembly. The product of
the UL25 gene is required for packaging but not cleavage
of replicated viral DNA. This family includes a number
of herpesvirus proteins: EHV-1 36, EBV BVRF1, HCMV UL77,
ILTV ORF2, and VZV gene 34.
Length = 538
Score = 26.6 bits (59), Expect = 6.0
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 10/45 (22%)
Query: 56 EFHFNHY----LTRRRRIEI------AHALCLTERQIKIWFQNRR 90
EF +Y +E+ AL L E W +RR
Sbjct: 427 EFLMENYVVPTYRANPNVELSQLFPGLAALALDESVRLGWGHSRR 471
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 26.2 bits (58), Expect = 6.4
Identities = 8/51 (15%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 87 QNRRMKLKKELRAVKEINEQARREREEQD--RLKQEKHAKMDHHSHHQSMM 135
Q + +L+K ++ ++ +A+ + + +L++++ MD +M
Sbjct: 71 QEKMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQMEMMDDQR---ELM 118
>gnl|CDD|226300 COG3777, COG3777, Uncharacterized conserved protein [Function
unknown].
Length = 273
Score = 26.3 bits (58), Expect = 6.6
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 43 QTYTRFQTLELEKEFHF----NHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98
Q YT +T++ +E H ++T LCL ER+ I + N
Sbjct: 95 QEYTCHETIQYIEEKHGRSGELTFVTVPHVYSSPGQLCLFERRT-IVYTNAPASKPAVKM 153
Query: 99 AVKE 102
+V E
Sbjct: 154 SVAE 157
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 26.5 bits (59), Expect = 6.7
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 19 VHFAKMLCQLKQSGPNG 35
V A++L QL P+G
Sbjct: 144 VQLARVLAQLWPPVPSG 160
>gnl|CDD|234279 TIGR03607, TIGR03607, patatin-related protein. This bacterial
protein family contains an N-terminal patatin domain,
where patatins are plant storage proteins capable of
phospholipase activity (see pfam01734). Regions of
strong sequence conservation are separated by regions of
significant sequence and length variability. Members of
the family are distributed sporadically among bacteria.
The function is unknown [Unknown function, General].
Length = 739
Score = 26.6 bits (59), Expect = 6.9
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 96 ELRAVKEINEQARREREEQDRLKQEK 121
+L A++ N + RR R D + E
Sbjct: 350 DLEAIRRHNRRVRRLRAIVDARRPEV 375
>gnl|CDD|227111 COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit
[Lipid metabolism].
Length = 645
Score = 26.5 bits (59), Expect = 7.4
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 20/64 (31%)
Query: 62 YLTRRRRIEI-------AHALCLTERQIKIWFQNRRMK---------LKKELRAVKEINE 105
YL + R IEI + + L ER + Q R K L +E R + + E
Sbjct: 202 YLDKPRHIEIQVFADQHGNVVHLGERDCSL--QRRHQKVIEEAPAPFLTEETR--EAMGE 257
Query: 106 QARR 109
A
Sbjct: 258 AAVA 261
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 26.5 bits (59), Expect = 7.7
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 89 RRM-KLKKELRAVKEINEQARREREEQD 115
RR+ KLK+EL V++ E R++R
Sbjct: 164 RRIAKLKRELENVEKAREPRRKKRSRSG 191
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 26.2 bits (58), Expect = 8.0
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 97 LRAVKEINEQARREREEQDRLKQEKHAKM-DHHSHHQSMMGGLDKNSD 143
L+ E +A ++R+E +R++++K KM S M GL + SD
Sbjct: 199 LQEEYEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESD 246
>gnl|CDD|219308 pfam07146, DUF1389, Protein of unknown function (DUF1389). This
family consists of several hypothetical bacterial
proteins which seem to be specific to Chlamydia
pneumoniae. Members of this family are typically around
400 residues in length. The function of this family is
unknown.
Length = 311
Score = 26.1 bits (58), Expect = 8.7
Identities = 11/37 (29%), Positives = 14/37 (37%)
Query: 12 QLVIVLNVHFAKMLCQLKQSGPNGCPRRRGRQTYTRF 48
QL+ L+ LC L QS G R Y +
Sbjct: 254 QLIKSLDSDSWDFLCALDQSRGGGGLARLAGALYPDY 290
>gnl|CDD|171849 PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory
protein; Reviewed.
Length = 133
Score = 25.8 bits (56), Expect = 9.0
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 95 KELRAVKEINEQARREREEQDRLKQEKHAKMDHH 128
K L K + +QA+++ E D+L +E + +
Sbjct: 35 KGLEIAKNLADQAKKDDERIDKLMKESDKNLTPY 68
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
0.325 0.135 0.403
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,813,757
Number of extensions: 712385
Number of successful extensions: 1846
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1773
Number of HSP's successfully gapped: 179
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.1 bits)