RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1937
(307 letters)
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA in
a non-sequence specific fashion and contain two or more
tandem HMG boxes. Class II members include non-histone
chromosomal proteins, HMG1 and HMG2, which bind to bent
or distorted DNA such as four-way DNA junctions,
synthetic DNA cruciforms, kinked cisplatin-modified DNA,
DNA bulges, cross-overs in supercoiled DNA, and can
cause looping of linear DNA. Class III members include
nucleolar and mitochondrial transcription factors, UBF
and mtTF1, which bind four-way DNA junctions.
Length = 66
Score = 63.0 bits (154), Expect = 4e-13
Identities = 20/58 (34%), Positives = 39/58 (67%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 145
P++PL Y +S++ ++K +N D + E+ KI+G+ W++L E++K +Y E E++K
Sbjct: 1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDK 58
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding preferences.
Two phylogenically distinct groups of Class I proteins
bind DNA in a sequence specific fashion and contain a
single HMG box. One group (SOX-TCF) includes
transcription factors, TCF-1, -3, -4; and also SRY and
LEF-1, which bind four-way DNA junctions and duplex DNA
targets. The second group (MATA) includes fungal mating
type gene products MC, MATA1 and Ste11. Class II and III
proteins (HMGB-UBF) bind DNA in a non-sequence specific
fashion and contain two or more tandem HMG boxes. Class
II members include non-histone chromosomal proteins,
HMG1 and HMG2, which bind to bent or distorted DNA such
as four-way DNA junctions, synthetic DNA cruciforms,
kinked cisplatin-modified DNA, DNA bulges, cross-overs
in supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 61.5 bits (150), Expect = 2e-12
Identities = 24/58 (41%), Positives = 40/58 (68%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 145
P++PL Y +S++ +VKA+N L + EI KI+G+MW+ L E++K +Y E E++K
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDK 58
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 53.8 bits (130), Expect = 9e-10
Identities = 23/58 (39%), Positives = 39/58 (67%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 145
P++PL + +S++ ++KA+N LK EI KI+G+ W++L E++K Y E E+EK
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEK 58
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 47.3 bits (113), Expect = 2e-07
Identities = 20/59 (33%), Positives = 38/59 (64%)
Query: 87 PPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 145
P++P+ +M +S++ ++KA+N DL EI K +G+ W+ L E++K Y E +++K
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 44.9 bits (106), Expect = 1e-05
Identities = 18/63 (28%), Positives = 38/63 (60%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYE 142
K P P++PL Y YS + D+++ +N L E+GK++ + W++L +++K Y ++
Sbjct: 66 KDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEAN 125
Query: 143 QEK 145
++
Sbjct: 126 SDR 128
Score = 34.5 bits (79), Expect = 0.046
Identities = 18/63 (28%), Positives = 34/63 (53%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYE 142
P + P+ P++ K+ +V+ + D L E KII + W +L E +K +Y++ Y+
Sbjct: 139 NKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYK 198
Query: 143 QEK 145
+ K
Sbjct: 199 KLK 201
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box
superfamily of DNA-binding proteins. These proteins
contain a single HMG box, and bind the minor groove of
DNA in a highly sequence-specific manner. Members
include the fungal mating type gene products MC, MATA1
and Ste11.
Length = 77
Score = 37.6 bits (88), Expect = 6e-04
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYE 142
K P+P ++ Y + Q+K +N L EI +IIG+MWR + K Y E E
Sbjct: 1 KIPRPRN----AFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAE 56
Query: 143 QEK 145
+EK
Sbjct: 57 EEK 59
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 33.0 bits (76), Expect = 0.021
Identities = 15/58 (25%), Positives = 31/58 (53%)
Query: 90 KPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNL 147
+P+ +M +S++ +V + + I KI+G W+ L ++K Y E+ ++ K L
Sbjct: 4 RPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKEL 61
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 32.9 bits (75), Expect = 0.039
Identities = 20/79 (25%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 69 SQKMLTAKTDGRGPKAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLK--LWEIGKIIGQMW 126
Q + + + R K P P++ L YM ++++ ++ A+N +L + +GK++G+ W
Sbjct: 4 KQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAW 63
Query: 127 RDLPEDQKTEYVEDYEQEK 145
L E++K Y + +++K
Sbjct: 64 NKLSEEEKAPYEKKAQEDK 82
>gnl|CDD|220098 pfam09057, Smac_DIABLO, Second Mitochondria-derived Activator of
Caspases. Second Mitochondria-derived Activator of
Caspases promotes apoptosis by activating caspases in
the cytochrome c/Apaf-1/caspase-9 pathway, and by
opposing the inhibitory activity of inhibitor of
apoptosis proteins (XIAP-BIR3). The protein assumes an
elongated three-helix bundle structure, and forms a
dimer in solution.
Length = 234
Score = 31.4 bits (71), Expect = 0.44
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 236 DVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKE 295
D SV N +QV + QV+ + Q EAE + E K E +R +S EL+
Sbjct: 169 DQASVAARNHLQVAQSQVEEV--RQLSKEAEKKLAESKAEEIQRMAEYASSIDLSELEDI 226
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 32.0 bits (73), Expect = 0.48
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 245 RMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQ 289
R+Q + +QS QK+ E +L Q + E +KR E+ +
Sbjct: 608 RLQQAEEALQSAVAKQKQAEEQLVQANAELEEQKRAEAEARTALK 652
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 31.8 bits (72), Expect = 0.48
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 240 VVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKASC 299
N + ++ + Q+ K LE+EL+++ E+ E +++ E+ ++ Q L E+AS
Sbjct: 167 SRIKNDLSEMQCRAQNADTELKLLESELEELREQLEECQKELAEAEKKLQ-SLTSEQASS 225
Query: 300 SENE 303
++N
Sbjct: 226 ADNS 229
>gnl|CDD|187665 cd09805, type2_17beta_HSD-like_SDR_c, human 17beta-hydroxysteroid
dehydrogenase type 2 (type 2 17beta-HSD)-like, classical
(c) SDRs. 17beta-hydroxysteroid dehydrogenases are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. This
classical-SDR subgroup includes the human proteins: type
2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD,
dehydrogenase/reductase SDR family member 9,
short-chain dehydrogenase/reductase family 9C member 7,
3-hydroxybutyrate dehydrogenase type 1, and retinol
dehydrogenase 5. SDRs are a functionally diverse family
of oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 281
Score = 31.5 bits (72), Expect = 0.51
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 114 KLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNLK 148
+LWE K ++W LP + K +Y EDY E K
Sbjct: 192 ELWE--KQAKKLWERLPPEVKKDYGEDYIDELKNK 224
>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 = 31.6 bits (72), Expect = 0.66
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 243 TNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKASCSE 301
+ Q+L+ ++ +L ++LEA+L+++E K + + E E+ EELK+E S
Sbjct: 301 EQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKL-EELKEELESLEA 358
Score = 28.1 bits (63), Expect = 6.8
Identities = 11/51 (21%), Positives = 25/51 (49%)
Query: 244 NRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKK 294
++ L++++ +L +LE + Q + E+ +R+ E Q +E K
Sbjct: 281 EEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESK 331
>gnl|CDD|184284 PRK13732, PRK13732, single-stranded DNA-binding protein;
Provisional.
Length = 175
Score = 30.5 bits (68), Expect = 0.66
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 37 VVTTNRMQVLKRQVQSLTMHQHCQRVSRRGNVSQ--KMLTAKTDGRGPKAPKPPEKPLMP 94
V TT MQ+L R Q Q + + + + K AKT GRG KA +P +P P
Sbjct: 103 VKTTGTMQMLGRAPQQNAQPQPGPQQNGQPQSADATKKGGAKTKGRGRKAAQPEPQPQPP 162
>gnl|CDD|148650 pfam07163, Pex26, Pex26 protein. This family consists of Pex26 and
related mammalian proteins. Pex26 is a type II
peroxisomal membrane protein which recruits Pex6-Pex1
complexes to peroxisomes. Mutations in Pex26 can lead to
human disorders.
Length = 309
Score = 30.7 bits (69), Expect = 0.98
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 26 FSDSVVPDVRSVVTTNRMQVLKRQVQSLTMHQHCQRVSRRGNVSQKMLT 74
F++ + R Q Q + Q+VS+ G++S K+L+
Sbjct: 187 FTEEQRQAALQAIHDARQQNASSSSQEHSNSNETQKVSKEGSLSLKLLS 235
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 30.4 bits (69), Expect = 1.1
Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 4/107 (3%)
Query: 189 QIGRIDIQPAEDEDEQEDGYSVKHVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQV 248
Q+ I Q + E E G + A + L +I+E + +V+ +
Sbjct: 145 QLELILAQIKQLEAELA-GLQAQLQALRQQLE---VISEELEARRKLKEKGLVSRLELLE 200
Query: 249 LKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKE 295
L+R+ +LEAEL+ ++ + + + + + + F+EE+ +E
Sbjct: 201 LERERAEAQGELGRLEAELEVLKRQIDELQLERQQIEQTFREEVLEE 247
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 29.9 bits (68), Expect = 2.3
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 249 LKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKASCSENEPYL 306
L++Q LT ++LE +LQ ++E +K+ S + QE +++A+ + P +
Sbjct: 225 LQKQRDYLTARIQRLEHQLQLLQEAINSKRLT--LSEKTVQEAQSQDEAARIQANPLV 280
>gnl|CDD|177875 PLN02230, PLN02230, phosphoinositide phospholipase C 4.
Length = 598
Score = 29.7 bits (66), Expect = 2.6
Identities = 21/87 (24%), Positives = 43/87 (49%), Gaps = 12/87 (13%)
Query: 116 WEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNLKASTKLASISRPTWRAKAKASKPKQLRK 175
+++ K+I Q + D+ +E +++ + LK K+ ++P PK+ +
Sbjct: 218 FKVAKMITQTFGDMLYYHDSEGCQEFPSPEELK--EKILISTKP----------PKEYLE 265
Query: 176 SREARPKDSGEKMQIGRIDIQPAEDED 202
+ +A+ KD+GEK + D+ E ED
Sbjct: 266 ANDAKEKDNGEKGKDSDEDVWGKEPED 292
>gnl|CDD|149160 pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein. The sequences
featured in this family are similar to a region of human
TPR protein and to yeast myosin-like proteins 1 (MLP1)
and 2 (MLP2). These proteins share a number of features;
for example, they all have coiled-coil regions and all
three are associated with nuclear pores. TPR is thought
to be a component of nuclear pore complex- attached
intra-nuclear filaments, and is implicated in nuclear
protein import. Moreover, its N-terminal region is
involved in the activation of oncogenic kinases,
possibly by mediating the dimerisation of kinase domains
or by targeting these kinases to the nuclear pore
complex. MLP1 and MLP2 are involved in the process of
telomere length regulation, where they are thought to
interact with proteins such as Tel1p and modulate their
activity.
Length = 132
Score = 28.4 bits (64), Expect = 2.6
Identities = 11/60 (18%), Positives = 27/60 (45%)
Query: 242 TTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKASCSE 301
+Q L++Q+ L +L+AE + + + + + E + ++EL + + E
Sbjct: 57 DIEELQALRKQLNELKKEIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELEKRIEE 116
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 28.8 bits (65), Expect = 2.6
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 236 DVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKE 295
DV+ V+ + K + L KKL+AELQ+ E++ + +++K + + EE +K
Sbjct: 22 DVQKVL--SESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKA 79
Query: 296 KA 297
K
Sbjct: 80 KQ 81
Score = 27.2 bits (61), Expect = 8.1
Identities = 9/50 (18%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 249 LKRQVQSLTMHQKKL-EAELQQIEEKFEAKKRKFVESSEQFQEELKKEKA 297
L+++ Q L L E + +++ + K+++ + + Q+EL++++
Sbjct: 58 LQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQKQQAAQQELQQKQQ 107
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 29.2 bits (66), Expect = 2.8
Identities = 10/52 (19%), Positives = 29/52 (55%)
Query: 246 MQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKA 297
++ + + ++ Q+ L + ++ E+ EA++R + E +Q E+++ E+
Sbjct: 206 IEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAERE 257
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 29.5 bits (66), Expect = 2.8
Identities = 13/60 (21%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 236 DVRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKE 295
D+ +V M L+ + S ++KLE ++ + + + R F+E+ ++ + + KE
Sbjct: 660 DIEAVCREAAMAALRESIGSPA--KEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKE 717
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 29.3 bits (66), Expect = 3.2
Identities = 10/60 (16%), Positives = 31/60 (51%)
Query: 237 VRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEK 296
V R++ L+ V+ L +L+ EL++++ + E + + + +++++K++
Sbjct: 415 REITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDR 474
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 28.6 bits (64), Expect = 3.7
Identities = 12/48 (25%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 247 QVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKK 294
V+++ + T Q++LE E + E++ E ++R ++ E+ Q+ K+
Sbjct: 131 DVIQKNKEKSTREQEELE-EALEFEKEEEEQRRLLLQKEEEEQQMNKR 177
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 4.5
Identities = 16/57 (28%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 242 TTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQE--ELKKEK 296
++ L+++++SL ++KLE +++++EE+ E K++ E E+ +E ELK++
Sbjct: 236 LKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKA 292
>gnl|CDD|235484 PRK05469, PRK05469, peptidase T; Provisional.
Length = 408
Score = 28.6 bits (65), Expect = 4.7
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 264 EAELQQI-----EEKFEAKKRKFVESSEQFQEELKKEKASCSENEPY 305
EAEL I E FEA+K E +++ + + + + Y
Sbjct: 273 EAELSYIIRDFDREGFEARKALMQEIAKKVNAKYGEGRVELEIKDQY 319
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 28.5 bits (64), Expect = 5.8
Identities = 31/208 (14%), Positives = 67/208 (32%), Gaps = 18/208 (8%)
Query: 100 RKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNLKASTKLASISRP 159
+ +Q + E+ + E + + + LKA L +
Sbjct: 691 NEFKEQSEDIGYLEDAGELLRDFAPELEIKVERGNKILAKLFG--RFLKAFNALKKLY-- 746
Query: 160 TWRAKAKASKPKQLRKSREARPKDSGEKMQIGRIDIQPA-EDEDEQEDGYSVKHVA-YAR 217
+ + ++++ + + Q +D+ D E +D S
Sbjct: 747 ----EFAYTLEEEIQYLEDLLKARLEKDYQSKYLDLIDNLNDAREIKDKESKAIDLDDID 802
Query: 218 YLRNHRLINEIFSDSVVPDVRSVVTTNRM-QVLKRQVQSL-------TMHQKKLEAELQQ 269
+ EI D ++ +++ N + LK ++ + +KKL L +
Sbjct: 803 FELELIGKQEINIDYILELLQTFNDKNGAYESLKELIERIIKEWIEDLRQKKKLIERLIE 862
Query: 270 IEEKFEAKKRKFVESSEQFQEELKKEKA 297
++ AKK E E+ KKE+
Sbjct: 863 AINQYRAKKLDTAEKLEELYILAKKEEE 890
>gnl|CDD|129266 TIGR00162, TIGR00162, TIGR00162 family protein. This model
represents one out of two closely related ortholgous
sets of proteins that, so far, are found only in but are
universal among the Archaea. This ortholog set includes
MJ1210 from Methanococcus jannaschii and AF0525 from
Archaeoglobus fulgidus while excluding MJ0106 and AF1251
[Hypothetical proteins, Conserved].
Length = 188
Score = 27.9 bits (62), Expect = 5.8
Identities = 11/43 (25%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 262 KLEAELQQIEEKFEAKKRKFVESSEQFQEE-LKKEKASCSENE 303
LE ++ +EE+ + + K + ++ +EE +++ KA SE +
Sbjct: 142 SLEVSVEALEERAKEME-KIIAKIKEMEEEMVQQWKAKPSEED 183
>gnl|CDD|218311 pfam04888, SseC, Secretion system effector C (SseC) like family.
SseC is a secreted protein that forms a complex together
with SecB and SecD on the surface of Salmonella. All
these proteins are secreted by the type III secretion
system. Many mucosal pathogens use type III secretion
systems for the injection of effector proteins into
target cells. SecB, SseC and SecD are inserted into the
target cell membrane. where they form a small pore or
translocon. In addition to SseC, this family includes
the bacterial secreted proteins PopB, PepB, YopB and
EspD which are thought to be directly involved in pore
formation, and type III secretion system translocon.
Length = 303
Score = 27.8 bits (62), Expect = 7.0
Identities = 10/37 (27%), Positives = 25/37 (67%)
Query: 260 QKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEK 296
+K+ +++LQQ+E + +++K E EQ ++ ++K +
Sbjct: 14 EKQAKSKLQQLERARDKQEKKAEEYQEQIKKAIEKAE 50
>gnl|CDD|148511 pfam06936, Selenoprotein_S, Selenoprotein S (SelS). This family
consists of several mammalian selenoprotein S (SelS)
sequences. SelS is a plasma membrane protein and is
present in a variety of tissues and cell types. The
function of this family is unknown.
Length = 190
Score = 27.5 bits (61), Expect = 7.4
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 260 QKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEK 296
Q+ LEA +++E +AK KF E +Q +EE +++K
Sbjct: 82 QEALEAARLRMQEDLDAKAAKFKEKQKQLEEEKRRQK 118
>gnl|CDD|185748 cd09235, V_Alix, Middle V-domain of mammalian Alix and related
domains are dimerization and protein interaction
modules. This family contains the middle V-shaped (V)
domain of mammalian Alix (apoptosis-linked gene-2
interacting protein X) and related domains. It belongs
to the V_Alix_like superfamily which includes the
V-domains of Bro1 and Rim20 (also known as PalA) from
Saccharomyces cerevisiae, mammalian His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), and related domains. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1), is
part of the ESCRT (Endosomal Sorting Complexes Required
for Transport) system, and participates in membrane
remodeling processes, including the budding of enveloped
viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), the abscission reactions
of mammalian cell division, and in apoptosis. The Alix
V-domain is a dimerization domain, and contains a
binding site, partially conserved in the V_Alix_like
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. In addition to the V-domain, Alix also has
an N-terminal Bro1-like domain, which binds components
of the ESCRT-III complex, in particular CHMP4. The
Bro1-like domain of Alix can also bind to human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1), and
the apoptotic protein ALG-2.
Length = 339
Score = 27.6 bits (62), Expect = 7.8
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 247 QVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKKEKASCSEN 302
L++QVQ Q+ L A +Q ++F +K+ S +EE+ K+ A+ +
Sbjct: 250 GPLQKQVQESLSRQESLLANIQVAHQEFSKEKQS--NSGANEREEVLKDLAAAYDA 303
>gnl|CDD|218953 pfam06245, DUF1015, Protein of unknown function (DUF1015). Family
of proteins with unknown function found in archaea and
bacteria.
Length = 415
Score = 27.9 bits (63), Expect = 7.9
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 264 EAELQQIEEKFEAKKRKFV-------ESSEQFQEELKKEKASCSENEPYLF 307
+ +I+E FEA ++ S+ +++E ++E + NEPY +
Sbjct: 186 PELIAKIQEAFEAIPALYIADGHHRYASALNYRDERREENPEHTGNEPYNY 236
>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869). This
bacterial family of proteins has no known function.
Length = 131
Score = 26.8 bits (60), Expect = 8.1
Identities = 11/53 (20%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 249 LKRQVQSLTMHQKKLEAE--------LQQIEEKFEAKKRKFVESSEQFQEELK 293
L++++Q L +K E ++QI+++ E ++ K +E Q +++
Sbjct: 32 LEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQQVEQERAKRLEQKNQLLFQIE 84
>gnl|CDD|223081 COG0002, ArgC, Acetylglutamate semialdehyde dehydrogenase [Amino
acid transport and metabolism].
Length = 349
Score = 27.6 bits (62), Expect = 8.4
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 9 HVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQV 45
H AY + + + + PD ++V +N +
Sbjct: 263 HAAYEEFYAGEPFV-RVVPEGGYPDTKAVAGSNFCDI 298
Score = 27.6 bits (62), Expect = 8.4
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 212 HVAYARYLRNHRLINEIFSDSVVPDVRSVVTTNRMQV 248
H AY + + + + PD ++V +N +
Sbjct: 263 HAAYEEFYAGEPFV-RVVPEGGYPDTKAVAGSNFCDI 298
>gnl|CDD|153271 cd07307, BAR, The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization
module that binds membranes and detects membrane
curvature. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions including organelle
biogenesis, membrane trafficking or remodeling, and cell
division and migration. Mutations in BAR containing
proteins have been linked to diseases and their
inactivation in cells leads to altered membrane
dynamics. A BAR domain with an additional N-terminal
amphipathic helix (an N-BAR) can drive membrane
curvature. These N-BAR domains are found in amphiphysins
and endophilins, among others. BAR domains are also
frequently found alongside domains that determine lipid
specificity, such as the Pleckstrin Homology (PH) and
Phox Homology (PX) domains which are present in beta
centaurins (ACAPs and ASAPs) and sorting nexins,
respectively. A FES-CIP4 Homology (FCH) domain together
with a coiled coil region is called the F-BAR domain and
is present in Pombe/Cdc15 homology (PCH) family
proteins, which include Fes/Fes tyrosine kinases, PACSIN
or syndapin, CIP4-like proteins, and srGAPs, among
others. The Inverse (I)-BAR or IRSp53/MIM homology
Domain (IMD) is found in multi-domain proteins, such as
IRSp53 and MIM, that act as scaffolding proteins and
transducers of a variety of signaling pathways that link
membrane dynamics and the underlying actin cytoskeleton.
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions. The I-BAR domain
induces membrane protrusions in the opposite direction
compared to classical BAR and F-BAR domains, which
produce membrane invaginations. BAR domains that also
serve as protein interaction domains include those of
arfaptin and OPHN1-like proteins, among others, which
bind to Rac and Rho GAP domains, respectively.
Length = 194
Score = 27.4 bits (61), Expect = 8.6
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 258 MHQKKLEAELQQIEEKFEAKKRKFVESSEQFQEELKK 294
+KK ++L + EE+ + K K+ E E+ E+L K
Sbjct: 121 RKKKKDSSKLAEAEEELQEAKEKYEELREELIEDLNK 157
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.9 bits (63), Expect = 8.8
Identities = 13/48 (27%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 251 RQVQSLTMHQKKLEAELQQIEEKFEAKKRKFVESSEQ-FQEELKKEKA 297
+ ++L +KL+ EL++ +EK + ++ K +E +E+ Q+ +K+ K
Sbjct: 537 EEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKK 584
>gnl|CDD|218369 pfam04994, TfoX_C, TfoX C-terminal domain. TfoX may play a key
role in the development of genetic competence by
regulating the expression of late competence-specific
genes. This family corresponds to the C-terminal
presumed domain of TfoX. The domain is found associated
with pfam00383 in a member from Neisseria meningitidis
serogroup B. It is also found as an isolated domain in
some proteins suggesting this is an autonomous domain.
Length = 77
Score = 25.6 bits (57), Expect = 9.4
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 100 RKVWDQVKAQNLDLKLWEI-GKIIGQMWRDLPEDQKTE 136
K+ + +L+L L+ + G + G+ W LPE++K E
Sbjct: 36 LKLKRSGSSVSLNL-LYALEGALEGKHWNVLPEERKEE 72
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 27.7 bits (62), Expect = 9.7
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 237 VRSVVTTNRMQVLKRQVQSLTMHQKKLEAELQQIEEKFEAKKRKFV-ESSEQFQEELKKE 295
RS+ R +LK++ L Q+ AE Q E K + K + + + + E+ +
Sbjct: 852 GRSLKAKKRFSLLKKETIYLQSAQRVELAERQLQELKIDVKSISSLKLVNLELESEIIEL 911
Query: 296 KASCSENE 303
K S S +
Sbjct: 912 KKSLSSDL 919
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
0.314 0.128 0.361
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: 15,087,023
Number of extensions: 1390766
Number of successful extensions: 2291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2211
Number of HSP's successfully gapped: 237
Length of query: 307
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 210
Effective length of database: 6,635,264
Effective search space: 1393405440
Effective search space used: 1393405440
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 (22.0 bits)
S2: 59 (26.4 bits)