RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15735
(574 letters)
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal
regulatory protein Rpn11 and signalosome complex subunit
CSN5. This family contains proteasomal regulatory
protein Rpn11 (26S proteasome regulatory subunit rpn11;
PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the
19S-proteasome; regulatory particle number 11) and
signalosomal CSN5 (COP9 signalosome complex subunit 5;
COP9 complex homolog subunit 5; c-Jun activation
domain-binding protein-1; CSN5/JAB1; JAB1). COP9
signalosome (CSN) and the proteasome lid are paralogous
complexes and their respective subunits CSN5 and Rpn11
are most closely related between the two complexes, both
containing the conserved JAMM (JAB1/MPN/Mov34
metalloenzyme) motif involved in zinc ion coordination
and providing the active site for isopeptidase activity.
Rpn11 is responsible for substrate deubiquitination
during proteasomal degradation. It is essential for
maintaining a correct cell cycle and normal
mitochondrial morphology and physiology; mutations in
Rpn11 cause cell cycle and mitochondrial defects,
temperature sensitivity and sensitivity to DNA damaging
reagents such as UV. It has been shown that the
C-terminal region of Rpn11 is involved in the regulation
of the mitochondrial fission and tubulation processes.
CSN5, one of the eight subunits of CSN, is critical for
nuclear export and the degradation of several tumor
suppressor proteins, including p53, p27, and Smad4. Its
MPN+ domain is critical for the physical interaction of
RUNX3 and Jab1. It has been suggested that the direct
interaction of CSN5/JAB1 with p27 provides p27 with a
leucine-rich nuclear export signal (NES), which is
required for binding to chromosomal region maintenance 1
(CRM1), and facilitates nuclear export. The
over-expression of CSN5/JAB1 also has been implicated in
cancer initiation and progression, including cancer of
the lung, pancreas, mouth, thyroid, and breast,
suggesting that the oncogenic activity of CSN5 is
associated with the down-regulation of RUNX3.
Length = 268
Score = 267 bits (685), Expect = 6e-86
Identities = 87/133 (65%), Positives = 102/133 (76%), Gaps = 4/133 (3%)
Query: 181 DGPVVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGT 240
P D E+VYISSLALLKMLKH RAG P+EVMGLMLG+ VD+YT+ V+DVFA+P GT
Sbjct: 2 WKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGK-VDDYTIIVVDVFALPVEGT 60
Query: 241 GVSVEAVDPVFQAKMLD--MLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSE 298
V A D FQ M+ MLKQTGRPE VVGWYHSHPG+GCWLSG+D+NTQQ + L +
Sbjct: 61 ETRVNAQD-EFQEYMVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQD 119
Query: 299 RAVAVVVDPIQSV 311
VAVVVDPI+S+
Sbjct: 120 PFVAVVVDPIRSL 132
Score = 164 bits (417), Expect = 1e-46
Identities = 66/139 (47%), Positives = 88/139 (63%), Gaps = 10/139 (7%)
Query: 9 GKVVIDAFRLINPNMMVLGQEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNEL 68
GKVVI AFR I P L EPRQTTSN+GHL K ++ G N+ YYS+ I Y K+ L
Sbjct: 135 GKVVIGAFRTIPPGYKPL--EPRQTTSNIGHLPKPKIE-DFGGHNKQYYSLPIEYFKSSL 191
Query: 69 EQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYNKALEEEEKMSPEQLAI 128
++K+LLNL K W++ LSL E+ NE T+ +L+LA+ KA ++EE+++ E+L I
Sbjct: 192 DRKLLLNLWNKYWVNTLSLSPLLENS--NEYTIKQILDLAEKLEKAEQQEERLTGEELDI 249
Query: 129 KNVGKQD-----PKRHLEE 142
NVGK D K HLEE
Sbjct: 250 ANVGKLDKARDSSKIHLEE 268
Score = 44.2 bits (105), Expect = 9e-05
Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 308 IQSVKELAKHYNKALEEEEKMSPEQLAIKNVGKQD-----PKRHLEE 349
I+ + +LA+ KA ++EE+++ E+L I NVGK D K HLEE
Sbjct: 222 IKQILDLAEKLEKAEQQEERLTGEELDIANVGKLDKARDSSKIHLEE 268
>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
eukaryotic. This family contains eukaryotic MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in
proteins with a variety of functions, including AMSH
(associated molecule with the Src homology 3 domain
(SH3) of STAM), H2A-DUB (histone H2A deubiquitinase),
BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as
well as Rpn11 (regulatory particle number 11) and CSN5
(COP9 signalosome complex subunit 5). These domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity. Rpn11 is responsible for
substrate deubiquitination during proteasomal
degradation. It is essential for maintaining a correct
cell cycle and normal mitochondrial morphology and
physiology. CSN5 is critical for nuclear export and the
degradation of several tumor suppressor proteins,
including p53, p27, and Smad4. Over-expression of CSN5
has been implicated in cancer initiation and
progression. AMSH specifically cleaves Lys 63 and not
Lys48-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. It is involved in the
degradation of EGF receptor (EGFR) and possibly other
ubiquitinated endocytosed proteins. BRCC36 is part of
the BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity; it is targeted
to DNA damage foci after irradiation. 2A-DUB is specific
for monoubiquitinated H2A (uH2A), regulating
transcription by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. It is a positive
regulator of androgen receptor (AR) transactivation
activity on a reporter gene and serves as a marker in
prostate tumors.
Length = 119
Score = 160 bits (406), Expect = 4e-47
Identities = 50/123 (40%), Positives = 64/123 (52%), Gaps = 14/123 (11%)
Query: 196 LALLKMLKHGRAGVPMEVMGLMLGEFVDE----YTVRVIDVFAMPQTGTGVSVEAVDPVF 251
ALLKML+H + +EVMGL+ GE V V A P + TG +
Sbjct: 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGEN-------- 52
Query: 252 QAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311
QTGRP +VVGWYHSHP F WLS VDI+TQ S++ + A+A+VV P
Sbjct: 53 --VEELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRN 110
Query: 312 KEL 314
K+
Sbjct: 111 KDT 113
>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Members
of this family are found in proteasome regulatory
subunits, eukaryotic initiation factor 3 (eIF3) subunits
and regulators of transcription factors. This family is
also known as the MPN domain and PAD-1-like domain,
JABP1 domain or JAMM domain. These are metalloenzymes
that function as the ubiquitin isopeptidase/
deubiquitinase in the ubiquitin-based signaling and
protein turnover pathways in eukaryotes. Versions of the
domain in prokaryotic cognates of the
ubiquitin-modification pathway are predicted to have a
similar role.
Length = 117
Score = 141 bits (356), Expect = 5e-40
Identities = 52/117 (44%), Positives = 73/117 (62%), Gaps = 4/117 (3%)
Query: 187 TAEQVYISSLALLKMLKHGRAGVPM--EVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSV 244
+ V I L LLK++ H R G EVMG++LG + + V + FA+PQ+ T V
Sbjct: 1 SVRTVVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDV 60
Query: 245 EAVDPVFQ--AKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSER 299
EAV+ + KML+MLK+ R E VVGWYHSHPG+GCWLS VD++TQ+ ++ +
Sbjct: 61 EAVELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain. Domain in Jun kinase
activation domain binding protein and proteasomal
subunits. Domain at Mpr1p and Pad1p N-termini. Domain of
unknown function.
Length = 135
Score = 132 bits (335), Expect = 1e-36
Identities = 43/122 (35%), Positives = 67/122 (54%), Gaps = 1/122 (0%)
Query: 190 QVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDP 249
+V + L L +LKH P EV G++LG+ + V +VFA+P SV+ D
Sbjct: 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKD-RPEVKEVFAVPNEPQDDSVQEYDE 59
Query: 250 VFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQ 309
+ M + LK+ + +VGWYHSHP + S VD+ T +S++A +V ++VDPI+
Sbjct: 60 DYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK 119
Query: 310 SV 311
S
Sbjct: 120 SF 121
>gnl|CDD|205193 pfam13012, MitMem_reg, Maintenance of mitochondrial structure and
function. This is C-terminal to the Mov24 region of the
yeast proteasomal subunit Rpn11 and seems likely to
regulate the mitochondrial fission and tubulation
processes, ie the outer mitochondrial membrane proteins.
This function appears to be unrelated to the proteasome
activity of the N-terminal region.
Length = 115
Score = 109 bits (274), Expect = 2e-28
Identities = 47/125 (37%), Positives = 65/125 (52%), Gaps = 19/125 (15%)
Query: 28 QEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSL 87
QE Q V+ L+ GLNRHYYS +++ RK ELEQK L NLHK+ W GL L
Sbjct: 1 QEAEQI----------GVEHLLRGLNRHYYS-TLS-RKLELEQKALKNLHKRLWTIGLYL 48
Query: 88 QDYN----EHCKLNEGTVNDMLELAKHY-NKALEEEEKM-SPEQLAIKNVGKQDPKRH-L 140
+D + +L L +Y NK EEE + + +QL + +GK D K+H L
Sbjct: 49 EDVIDGKLPPNHEILRKLQSLLNLLPNYDNKEFEEEFNVETNDQLLVVYLGKLDRKQHAL 108
Query: 141 EEKVD 145
E ++
Sbjct: 109 HELIN 113
Score = 41.8 bits (99), Expect = 9e-05
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 308 IQSVKELAKHY-NKALEEEEKM-SPEQLAIKNVGKQDPKRH-LEEKVD 352
+QS+ L +Y NK EEE + + +QL + +GK D K+H L E ++
Sbjct: 66 LQSLLNLLPNYDNKEFEEEFNVETNDQLLVVYLGKLDRKQHALHELIN 113
>gnl|CDD|219898 pfam08551, DUF1751, Eukaryotic integral membrane protein (DUF1751).
This domain is found in eukaryotic integral membrane
proteins. YOL107W, a Saccharomyces cerervisiae protein,
has been shown to localise COP II vesicles.
Length = 99
Score = 84.6 bits (210), Expect = 5e-20
Identities = 30/68 (44%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 363 LGGKLIEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYIS 422
LGGK +E LWGS E++ F +VN+ + L+Y LYM T + L V I G G ++
Sbjct: 33 LGGKYLERLWGSKELLKFILVVNVITNLLVFLYYLLLYMITRSERYL-DVPISGGYGILA 91
Query: 423 GVLVAVKQ 430
G LVA KQ
Sbjct: 92 GFLVAFKQ 99
>gnl|CDD|224229 COG1310, COG1310, Predicted metal-dependent protease of the
PAD1/JAB1 superfamily [General function prediction
only].
Length = 134
Score = 83.7 bits (207), Expect = 3e-19
Identities = 32/116 (27%), Positives = 44/116 (37%), Gaps = 13/116 (11%)
Query: 206 RAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTG------TGVSVEAVDPVFQAKMLDML 259
+P EV+G +L E+ V + A + G VSVE V+ +
Sbjct: 1 MLVIPKEVLGAILEHARREHPREVCGLLAGTREGERYFPLKNVSVEPVEYFEIDPEYSLF 60
Query: 260 KQTGRP--EMVVGWYHSHPGFGCWLSGVDINTQQSFEALSE-RAVAVVVDPIQSVK 312
E+VVGWYHSHPG + S D L + V V P + K
Sbjct: 61 YLAAEDAGEVVVGWYHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGRVHK 112
>gnl|CDD|163696 cd08065, MPN_eIF3h, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF2h.
Eukaryotic translation initiation factor 3 (eIF3)
subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma;
eIF3-p40) is an evolutionarily non-conserved subunit of
the functional core that comprises eIF3a, eIF3b, eIF3c,
eIF3e, eIF3f, and eIF3h, and contains the MPN domain.
However, it lacks the canonical JAMM motif, and
therefore does not show catalytic isopeptidase
activity.Together with eIF3e and eIF3f, eIF3h stabilizes
the eIF3 complex. Results suggest that eIF3h regulates
cell growth and viability, and that over-expression of
the gene may provide growth advantage to prostate,
breast, and liver cancer cells. For example, EIF3h gene
amplification is common in late-stage prostate cancer
suggesting that it may be functionally involved in the
progression of the disease. It has been shown that
coamplification of MYC, a well characterized oncogene
involved in cell growth, differentiation, and apoptosis,
and EIF3h in patients with non-small cell lung cancer
(NSCLC) improves survival if treated with the Epidermal
Growth Factor Receptor Tyrosine Kinase Inhibitor
(EGFR-TKI), Gefitinib. Plant eIF3h is implicated in
translation of specific mRNAs.
Length = 266
Score = 75.0 bits (185), Expect = 5e-15
Identities = 47/159 (29%), Positives = 77/159 (48%), Gaps = 11/159 (6%)
Query: 189 EQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVD 248
V I L +LK++KH + +P V G +LG T+ V + F P++ S A +
Sbjct: 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLG-LDVGGTLEVTNCFPFPKSEEDDSDRADE 59
Query: 249 PV--FQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVD 306
+ +Q +M+ +L++ VGWY S G + + I TQ +++ E +V +V D
Sbjct: 60 DIADYQLEMMRLLREVNVDHNHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYD 118
Query: 307 PIQ-SVKELA-KHY---NKALE--EEEKMSPEQLAIKNV 338
P + S L+ K Y K +E +E K S E L N+
Sbjct: 119 PSKTSQGSLSLKAYRLSEKFMELYKEGKFSTESLREANL 157
>gnl|CDD|163699 cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of
BRCA1-A complex. BRCC36 (BRCA1-A complex subunit
BRCC36; BRCA1/BRCA2-containing complex subunit 36;
BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC
complex subunit BRCC36; BRCC36 isopeptidase complex;
Lys-63-specific deubiquitinase BRCC36) and BRCC36-like
domains are members of JAMM/MPN+ deubiquitinases (DUBs),
possibly with Zn2+-dependent ubiquitin isopeptidase
activity. BRCC36 is part of the
BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity. It is targeted
to DNA damage foci after irradiation; RAP80 recruits the
Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand
breaks (DSBs) for DNA repair through specific
recognition of Lys 63-linked polyubiquitinated proteins
by its tandem ubiquitin-interacting motifs. A new
protein, MERIT40 (mediator of RAP80 interactions and
targeting 40 kDa), also named NBA1 (new component of the
BRCA1 A complex), exists in the same BRCA1-containing
complex and is essential for the integrity of the
complex. There are studies suggesting that MERIT40/NBA1
ties BRCA1 complex integrity, DSB recognition, and
ubiquitin chain activities to the DNA damage response.
It has also been shown that BRCA1-containing complex
resembles the lid complex of the 26S proteasome.
Length = 244
Score = 64.3 bits (157), Expect = 1e-11
Identities = 37/127 (29%), Positives = 58/127 (45%), Gaps = 10/127 (7%)
Query: 189 EQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD---EYTVRVIDVFAMPQTGTGVS-- 243
+V++S+ L L H + EVMGL++GE V ++ + A+
Sbjct: 2 SKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRK 61
Query: 244 --VEAVDPVFQAKMLD---MLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSE 298
VE A + + ++TGRP VVGWYHSHP W S VD+ TQ ++ +
Sbjct: 62 DRVEISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDS 121
Query: 299 RAVAVVV 305
V ++
Sbjct: 122 GFVGLIF 128
>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A
deubiquitinase. This family includes histone H2A
deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM
and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or
KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases
(DUBs), with possible Zn2+-dependent ubiquitin
isopeptidase activity. It contains the SWIRM (Swi3p,
Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR,
TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain
can bind directly to DNA. 2A-DUB is specific for
monoubiquitinated H2A (uH2A), regulating transcription
by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. 2A-DUB interacts
with p/CAF (p300/CBP-associated factor) in a
co-regulatory protein complex, where the status of
acetylation of nucleosomal histones modulates its
deubiquitinase activity. 2A-DUB is a positive regulator
of androgen receptor (AR) transactivation activity on a
reporter gene; it participates in transcriptional
regulation events in androgen receptor-dependent gene
activation. In prostate tumors, the levels of uH2A are
dramatically decreased, thus 2A-DUB serving as a
cancer-related marker.
Length = 187
Score = 57.7 bits (140), Expect = 1e-09
Identities = 36/109 (33%), Positives = 56/109 (51%), Gaps = 7/109 (6%)
Query: 190 QVYISSLALLKMLKHGRAGVPM-EVMGLMLGEF-VDEYTVRVIDVFAMPQTGTGVSVEAV 247
+V +SS ALL M H + EV+G + G + + + ++ F TG+ E
Sbjct: 6 KVTVSSNALLLMDFH--CHLTTSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEM- 62
Query: 248 DPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEAL 296
DPV + ++ + L+ G VVGWYHSHP F S DI+TQ ++ +
Sbjct: 63 DPVSETEIRESLESRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIM 109
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 54.4 bits (131), Expect = 4e-09
Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 6/110 (5%)
Query: 198 LLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLD 257
L L ++ EV+GL+ G + + V +V A+P M
Sbjct: 1 LKMFLDAAKSINGKEVIGLLYGSK-TKKVLDVDEVIAVPFDEGDKDDNVW-----FLMYL 54
Query: 258 MLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDP 307
K+ +VGWYH+HP C+LS D+ T + F+ V ++VD
Sbjct: 55 DFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDV 104
>gnl|CDD|163688 cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (MPN) domains
without catalytic isopeptidase activity (non
metal-binding); eukaryotic. This family contains MPN
(also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains
variants lacking key residues in the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif and are unable to coordinate
a metal ion. Comparisons of key catalytic and metal
binding residues explain why the MPN-containing proteins
Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation
initiation factor 3 subunits f and h do not show
catalytic isopeptidase activity. It has been proposed
that the MPN domain in these proteins has a primarily
structural function. Rpn7 is known to be critical for
the integrity of the 26S proteasome complex by
establishing a correct lid structure. It is necessary
for the incorporation/anchoring of Rpn3 and Rpn12 to the
lid and essential for viability and normal mitosis. CSN6
is a highly conserved protein complex with diverse
functions, including several important intracellular
pathways such as the ubiquitin/proteasome system, DNA
repair, cell cycle, developmental changes, and some
aspects of immune responses. It cleaves ubiquitin-like
protein Nedd8 (neural precursor cell expressed,
developmentally downregulated 8)) in the cullin 1 in
cells. EIF3f s a potent inhibitor of HIV-1 replication
as well as an important negative regulator of cell
growth and proliferation. EIF3h regulates cell growth
and viability, and that over-expression of the gene may
provide growth advantage to prostate, breast, and liver
cancer cells.
Length = 157
Score = 53.6 bits (129), Expect = 1e-08
Identities = 31/126 (24%), Positives = 56/126 (44%), Gaps = 5/126 (3%)
Query: 191 VYISSLALLKMLKH-GRAGVPME-VMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVD 248
V + L LL + H R ++ V+G++LG +VD + V + F +P S+ +D
Sbjct: 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLG-YVDGDKIEVTNSFELPFDEEEESI-FID 58
Query: 249 PVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERA-VAVVVDP 307
+ K ++ K+ E +VGWY +S D + F +SE + +++DP
Sbjct: 59 TEYLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDP 118
Query: 308 IQSVKE 313
Sbjct: 119 SLQSDS 124
>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family. AMSH (associated
molecule with the Src homology 3 domain (SH3) of STAM
(signal-transducing adapter molecule, also known as
STAMBP)) and AMSH-like proteins (AMSH-LP) are members of
JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent
ubiquitin isopeptidase activity. AMSH specifically
cleaves Lys 63 and not Lys48-linked polyubiquitin
(poly-Ub) chains, thus facilitating the recycling and
subsequent trafficking of receptors to the cell surface.
AMSH and AMSH-LP are anchored on the early endosomal
membrane via interaction with the clathrin coat. AMSH
shares a common SH3-binding site with another endosomal
DUB, UBPY (ubiquitin-specific protease Y; also known as
USP8), the latter being a cysteine protease that does
not discriminate between Lys48 and Lys63-linked
ubiquitin. AMSH is involved in the degradation of EGF
receptor (EGFR) and possibly other ubiquitinated
endocytosed proteins. AMSH also interacts with CHMP1,
CHMP2, and CHMP3 proteins, all of which are components
of ESCRT-III, suggested to be required for EGFR
down-regulation. The function of AMSH-LP has not been
elucidated; however, it exhibits two fundamentally
distinct features from AMSH: first, there is a
substitution in the critical amino acid residue in the
SH3-binding motif (SBM) in the human AMSH-LP, but not in
its mouse ortholog, and lacks STAM-binding ability;
second, AMSH-LP lacks the ability to interact with CHMP
proteins. It is therefore likely that AMSH and AMSH-LP
play different roles on early endosomes.
Length = 173
Score = 47.6 bits (114), Expect = 2e-06
Identities = 16/41 (39%), Positives = 27/41 (65%)
Query: 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDP 307
+ +GW H+HP C+LS VD++T S++ + A+A+V P
Sbjct: 76 ITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP 116
>gnl|CDD|222766 pfam14464, Prok-JAB, Prokaryotic homologs of the JAB domain. These
are metalloenzymes that function as the ubiquitin
isopeptidase/ deubiquitinase in the ubiquitin-based
signaling and protein turnover pathways in eukaryotes.
Prokaryotic JAB domains are predicted to have a similar
role in their cognates of the ubiquitin modification
pathway. The domain is widely found in bacteria, archaea
and phages where they are present in several gene
contexts in addition to those that correspond to the
prokaryotic cognates of the eukaryotic Ub pathway. Other
contexts in which JAB domains are present include gene
neighbor associations with ubiquitin fold domains in
cysteine and siderophore biosynthesis, and phage tail
morphogenesis, where they are shown or predicted to
process the associated ubiquitin. A distinct family, the
RadC-like JAB domains are widespread in bacteria and are
predicted to function as nucleases. In halophilic
archaea the JAB domain shows strong gene-neighborhood
associations with a nucleotidyltransferase suggesting a
role in nucleotide metabolism.
Length = 98
Score = 45.5 bits (108), Expect = 3e-06
Identities = 25/91 (27%), Positives = 33/91 (36%), Gaps = 13/91 (14%)
Query: 197 ALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKML 256
L +L H R P E GL++G RV+ + A+DP
Sbjct: 4 LLEAILAHARRAYPNEACGLLVGT-ERGERTRVVPL------------LALDPEDSFAAA 50
Query: 257 DMLKQTGRPEMVVGWYHSHPGFGCWLSGVDI 287
R +VG YHSHPG + S D
Sbjct: 51 REDAARERGLELVGIYHSHPGGPAYPSETDR 81
>gnl|CDD|163701 cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding). This
family contains archaeal and bacterial MPN (also known
as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These
domains contain the signature JAB1/MPN/Mov34
metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
involved in zinc ion coordination and provides the
active site for isopeptidase activity for the release of
ubiquitin from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. The JAMM proteins likely hydrolyze
ubiquitin conjugates in a manner similar to thermolysin,
in which the zinc-polarized aqua ligand serves as the
nucleophile, compared with the classical DUBs that do so
with a cysteine residue in the active site.
Length = 128
Score = 46.1 bits (110), Expect = 4e-06
Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 4/92 (4%)
Query: 197 ALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVE-AVDPVFQAKM 255
L +L H A P E GL+LG+ T V +V+ + +DP Q
Sbjct: 3 LLEAILAHAEAEYPEECCGLLLGK-GGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAA 61
Query: 256 LDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDI 287
++ G VVG YHSHP S D+
Sbjct: 62 QREARERGLE--VVGIYHSHPDGPARPSETDL 91
>gnl|CDD|163695 cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF3f.
Eukaryotic translation initiation factor 3 (eIF3)
subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic
translation initiation factor 3, subunit 5 epsilon,
47kDa; Mov34/MPN/PAD-1 family protein) is an
evolutionarily non-conserved subunit of the functional
core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f,
and eIF3h, and contains the MPN domain. However, it
lacks the canonical JAMM motif, and therefore does not
show catalytic isopeptidase activity. It has been shown
that eIF3f mRNA expression is significantly decreased in
many human tumors including pancreatic cancer and
melanoma. EIF3f is a potent inhibitor of HIV-1
replication; it mediates restriction of HIV-1 expression
through several factors including the
serine/arginine-rich (SR) protein 9G8, and
cyclin-dependent kinase 11 (CDK11). EIF3f
phosphorylation by CDK11 is important in regulating its
function in translation and apoptosis. It enhances its
association with the core eIF3 subunits during
apoptosis, suggesting that eIF3f may inhibit translation
by increasing the binding to the eIF3 complex during
apoptosis. Thus, eIF3f may be an important negative
regulator of cell growth and proliferation.
Length = 265
Score = 43.0 bits (102), Expect = 2e-04
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 213 VMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWY 272
V+G +LG E V + + FA+P + V AVD + M ++ ++ E++VGWY
Sbjct: 25 VIGTLLG-TRSEGEVEITNCFAVPHNESEDQV-AVDMEYHRTMYELHQKVNPKEVIVGWY 82
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 37.8 bits (88), Expect = 0.010
Identities = 33/126 (26%), Positives = 53/126 (42%), Gaps = 10/126 (7%)
Query: 186 DTAEQVYISSLALLKMLKHGR---AGVPMEVMGLMLGEFVDEYTVRVIDVFAMP--QTGT 240
E+V + L LL ++ H V+G++LG V V + FA+P +
Sbjct: 3 RGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGS-SFRGRVDVTNSFAVPFEEDDK 61
Query: 241 GVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERA 300
S+ +D + M M K+ E VVGWY + P L D++ + F
Sbjct: 62 DPSIWFLDHNYLESMFGMFKRINAKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNP 117
Query: 301 VAVVVD 306
V V++D
Sbjct: 118 VLVIID 123
>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
prokaryotic. This family contains bacterial and
archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB,
MPN+)-like domains. These catalytically active domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity for the release of ubiquitin from
ubiquitinated proteins (thus having deubiquitinating
(DUB) activity) that are tagged for degradation. The
JAMM proteins likely hydrolyze ubiquitin conjugates in a
manner similar to thermolysin, in which the
zinc-polarized aqua ligand serves as the nucleophile,
compared with the classical DUBs that do so with a
cysteine residue in the active site.
Length = 101
Score = 34.5 bits (79), Expect = 0.025
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 15/90 (16%)
Query: 201 MLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLK 260
+L H + P E G + G + + ++ +P VS L L+
Sbjct: 6 ILVHAKDAHPDEFCGFLSGSKDN----VMDELIFLPFVSGSVSAV--------IDLAALE 53
Query: 261 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQ 290
+ VVG HSHP C S D++
Sbjct: 54 IGMK---VVGLVHSHPSGSCRPSEADLSLF 80
>gnl|CDD|238345 cd00632, Prefoldin_beta, Prefoldin beta; Prefoldin is a hexameric
molecular chaperone complex, composed of two
evolutionarily related subunits (alpha and beta), which
are found in both eukaryotes and archaea. Prefoldin
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The hexameric
structure consists of a double beta barrel assembly with
six protruding coiled-coils. The alpha prefoldin
subunits have two beta hairpin structures while the beta
prefoldin subunits (this CD) have only one hairpin that
is most similar to the second hairpin of the alpha
subunit. The prefoldin hexamer consists of two alpha and
four beta subunits and is assembled from the beta
hairpins of all six subunits. The alpha subunits
initially dimerize providing a structural nucleus for
the assembly of the beta subunits. In archaea, there is
usually only one gene for each subunit while in
eukaryotes there two or more paralogous genes encoding
each subunit adding heterogeneity to the structure of
the hexamer.
Length = 105
Score = 31.2 bits (71), Expect = 0.43
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 9/59 (15%)
Query: 112 NKALEEEEKMSPEQLAIKNVG-------KQDPKRHLEEKVDTLMTANIIQCLDRNMERL 163
KALEE EK++ + K VG K++ + L+E+++T+ I+ L+R E L
Sbjct: 33 KKALEELEKLADDAEVYKLVGNVLVKQEKEEARTELKERLETIELR--IKRLERQEEDL 89
Score = 30.0 bits (68), Expect = 0.99
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 309 QSVKELAKHYNKALEEEEKMSPEQLAIKNVG-------KQDPKRHLEEKVDTL 354
Q V+ KALEE EK++ + K VG K++ + L+E+++T+
Sbjct: 23 QKVEAQLNENKKALEELEKLADDAEVYKLVGNVLVKQEKEEARTELKERLETI 75
>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in 19S
proteasomal subunits Rpn7 and Rpn8. This family
includes lid subunits of the 26 S proteasome regulatory
particles, Rpn7 (PSMD7; proteasome 26S non-ATPase
subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S
non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be
critical for the integrity of the 26 S proteasome
complex by establishing a correct lid structure. It is
necessary for the incorporation/anchoring of Rpn3 and
Rpn12 to the lid and essential for viability and normal
mitosis. Rpn7 and Rpn8 are ATP-independent components of
the 19S regulator subunit, and contain the MPN
structural motif on its N-terminal region. However,
while they show a typical MPN metalloprotease fold, they
lack the canonical JAMM motif, and therefore do not show
catalytic isopeptidase activity. It is suggested that
Rpn7 function is primarily structural.
Length = 280
Score = 32.6 bits (75), Expect = 0.48
Identities = 30/117 (25%), Positives = 49/117 (41%), Gaps = 7/117 (5%)
Query: 213 VMGLMLGEFVDEYTVRVIDVFAMP--QTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVG 270
V+G++LG + + V + FA+P + SV +D + M M K+ E +VG
Sbjct: 28 VVGVLLGS-WKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAKEKIVG 86
Query: 271 WYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKELAKHYNKALEEEEK 327
WY + P L D++ + F V V++D L A+EE
Sbjct: 87 WYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVEEVHD 139
>gnl|CDD|219882 pfam08524, rRNA_processing, rRNA processing. This is a family of
proteins that are involved in rRNA processing. In a
localisation study they were found to localise to the
nucleus and nucleolus. The family also includes other
metazoa members from plants to mammals where the protein
has been named BR22 and is associated with TTF-1,
thyroid transcription factor 1. In the lungs, the family
binds TTF-1 to form a complex which influences the
expression of the key lung surfactant protein-B (SP-B)
and -C (SP-C), the small hydrophobic surfactant proteins
that maintain surface tension in alveoli.
Length = 150
Score = 31.4 bits (71), Expect = 0.69
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 107 LAKHYNKALEEEEKMSPEQ-------LAIKNVGKQDPKRHLEEK 143
L K Y K LE+E PE+ + K K + K+ L+EK
Sbjct: 34 LKKEYLKLLEKEGYAVPEKESAEKQVKSSKEDRKFEKKKKLDEK 77
Score = 31.4 bits (71), Expect = 0.69
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 314 LAKHYNKALEEEEKMSPEQ-------LAIKNVGKQDPKRHLEEK 350
L K Y K LE+E PE+ + K K + K+ L+EK
Sbjct: 34 LKKEYLKLLEKEGYAVPEKESAEKQVKSSKEDRKFEKKKKLDEK 77
>gnl|CDD|217006 pfam02382, RTX, RTX N-terminal domain. The RTX family of bacterial
toxins are a group of cytolysins and cytotoxins. This
Pfam family represents the N-terminal domain which is
found in association with a glycine-rich repeat domain
and hemolysinCabind pfam00353.
Length = 653
Score = 32.0 bits (73), Expect = 1.0
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 416 GLTGYISGVLVAVKQIMPDHV 436
+TG ISG+L A KQ M +HV
Sbjct: 398 AITGLISGILEASKQAMFEHV 418
>gnl|CDD|224183 COG1263, PtsG, Phosphotransferase system IIC components,
glucose/maltose/N-acetylglucosamine-specific
[Carbohydrate transport and metabolism].
Length = 393
Score = 31.8 bits (73), Expect = 1.0
Identities = 24/136 (17%), Positives = 45/136 (33%), Gaps = 19/136 (13%)
Query: 354 LMTANIIQCLGGKLIEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVR 413
L A ++ +G L ++ + IG AI LF FF + +
Sbjct: 26 LPAAGLLLGIGNLLQAFGLAIPDLAILSDLAAIGNAIFDNLFLFFPIGVAIS-----AAK 80
Query: 414 IHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPT 473
G T ++ V+ +++N L + L + + +
Sbjct: 81 KFGGTAALAAVIGY--------LLVNPALLNAWGLGAAGIPTLDTGVFGFPVPLGIYQ-- 130
Query: 474 MTLFGTLVSWIYLRFY 489
GT++ +Y RFY
Sbjct: 131 ----GTVIPILYNRFY 142
>gnl|CDD|162981 TIGR02707, butyr_kinase, butyrate kinase. This model represents an
enzyme family in which members are designated either
butryate kinase or branched-chain carboxylic acid
kinase. The EC designation 2.7.2.7 describes an enzyme
with relatively broad specificity; gene products whose
context suggests a role in metabolism of aliphatic amino
acids are likely to act as branched-chain carboxylic
acid kinase. The gene typically found adjacent, ptb
(phosphate butyryltransferase), likewise encodes an
enzyme that may have a broad specificity that includes a
role in aliphatic amino acid cabolism [Energy
metabolism, Fermentation].
Length = 351
Score = 31.6 bits (72), Expect = 1.2
Identities = 32/136 (23%), Positives = 53/136 (38%), Gaps = 47/136 (34%)
Query: 191 VYISSLALLKMLKHGRAGVPMEVMGLMLG-EFVDEYTVRVIDVFAMPQTGTGVSVEAVDP 249
Y+ + A+L+ LK G+ G +G ++ E DE + VDP
Sbjct: 83 TYLVNEAMLEDLKSGKRGEHASNLGAIIANELADEL---------------NIPAYIVDP 127
Query: 250 VFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQS-FEALSERAVAVVVDPI 308
V +M D+ + +G PE+ ++S F AL+++AVA
Sbjct: 128 VVVDEMEDVARISGLPEI---------------------ERKSIFHALNQKAVA------ 160
Query: 309 QSVKELAKHYNKALEE 324
+ +AK K EE
Sbjct: 161 ---RRIAKELGKRYEE 173
>gnl|CDD|223769 COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT)
superfamily [Carbohydrate transport and metabolism /
Amino acid transport and metabolism / General function
prediction only].
Length = 292
Score = 31.4 bits (71), Expect = 1.2
Identities = 21/110 (19%), Positives = 44/110 (40%), Gaps = 5/110 (4%)
Query: 377 MMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMPDHV 436
++ F A+ +++S + LL L I G+L+A+ ++ +
Sbjct: 85 LLLFLALKYTSASVASLIIGLLPLFTALLAVLLLLGERLSLL-QILGILLALAGVL---L 140
Query: 437 ILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYL 486
IL G G + LL+ L A++LW + ++ L ++ +
Sbjct: 141 ILLGGGGGGILSLLGLLLALAAALLWALYTA-LVKRLSRLGPVTLALLLQ 189
>gnl|CDD|181644 PRK09088, PRK09088, acyl-CoA synthetase; Validated.
Length = 488
Score = 31.3 bits (71), Expect = 1.4
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 9/70 (12%)
Query: 416 GLTGYISGVLVAVKQIMPDHVILNTG-LGKMTNRNIPLLVILI-ASILWLIGLVDSIRPT 473
G +G GV+++ + + N G LG++ + L A + +IGL+ S+RP
Sbjct: 145 GTSGQPKGVMLSERNL--QQTAHNFGVLGRVDAHS----SFLCDAPMFHIIGLITSVRPV 198
Query: 474 MTLFGT-LVS 482
+ + G+ LVS
Sbjct: 199 LAVGGSILVS 208
>gnl|CDD|221689 pfam12648, TcpE, TcpE family. This family of proteins includes
TcpE a conjugative transposon membrane protein.This
family of proteins is found in bacteria. Proteins in
this family are typically between 122 and 168 amino
acids in length.
Length = 108
Score = 28.8 bits (65), Expect = 2.4
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 3/70 (4%)
Query: 360 IQCLGGKLIEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTG 419
I +G + P ++E + F I I +A+ L F D + + + G
Sbjct: 12 IYEIGDFSL-PFPVTLEQLGIFVISLIVLALILGLLPGVFS--IFGFDNGWLLLYIVIPG 68
Query: 420 YISGVLVAVK 429
++ K
Sbjct: 69 GLTWFASKKK 78
>gnl|CDD|218603 pfam05482, Serendipity_A, Serendipity locus alpha protein (SRY-A).
The Drosophila serendipity alpha (sry alpha) gene is
specifically transcribed at the blastoderm stage, from
nuclear cycle 11 to the onset of gastrulation, in all
somatic nuclei. SRY-A is required for the
cellularisation of the embryo and is involved in the
localisation of the actin filaments just prior to and
during plasma membrane invagination.
Length = 549
Score = 30.7 bits (69), Expect = 2.5
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 77 HKKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYNKALEEEEKMSPEQLAIKNVGKQDP 136
H + +M+ L+ Q N L E +D+ +L N + LA NV +
Sbjct: 148 HLEAYMEILANQTQNSLHILEENDTDDIDQLGSIVNHIVR-------HALAFANVALESD 200
Query: 137 KRHLEEKVDTLMT 149
K+ L +TL++
Sbjct: 201 KKALSALCETLLS 213
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 30.5 bits (68), Expect = 2.8
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 45 VQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDM 104
+Q + +Y + K ELE++ L N+ D L L E+ +L + +
Sbjct: 457 IQLTAIKTSEEHYLKEVEDLKTELEKEKLKNIELTAHCDKLLL----ENKELTQEASDMT 512
Query: 105 LELAKH---YNKALEEEEKM 121
LEL KH ++EE+M
Sbjct: 513 LELKKHQEDIINCKKQEERM 532
>gnl|CDD|219516 pfam07690, MFS_1, Major Facilitator Superfamily.
Length = 346
Score = 29.7 bits (67), Expect = 3.8
Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 12/98 (12%)
Query: 371 LWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQ 430
L + A++ G A + L Y LY + GL+ ++G+L+ +
Sbjct: 199 LLRDPVLWLLLALLLFGFAFFALLTYLPLYQ-----------EVLGLSALLAGLLLGLAG 247
Query: 431 IMPDHVILNTG-LGKMTNRNIPLLVILIASILWLIGLV 467
++ L G L R LL+ L+ IL +GL
Sbjct: 248 LLGAIGRLLLGRLSDRLGRRRRLLLALLLLILAALGLA 285
>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical
extension region, in the p54nrb/PSF/PSP1 family. All
members in this family contain a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRM1 and RRM2),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1) domain
with a long helical C-terminal extension. The NOPS
domain specifically binds to RRM2 domain of the partner
DBHS protein via a substantial interaction surface. Its
highly conserved C-terminal residues are critical for
functional DBHS dimerization while the highly conserved
C-terminal helical extension, forming a right-handed
antiparallel heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies. PSF
has an additional large N-terminal domain that
differentiates it from other family members. The
p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein 1 (PSP1), which are
ubiquitously expressed and are well conserved in
vertebrates. p54nrb, also termed NONO or NMT55, is a
multi-functional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. PSF, also termed POMp100, is also a
multi-functional protein that binds RNA, single-stranded
DNA (ssDNA), double-stranded DNA (dsDNA) and many
factors, and mediates diverse activities in the cell.
PSP1, also termed PSPC1, is a novel nucleolar factor
that accumulates within a new nucleoplasmic compartment,
termed paraspeckles, and diffusely distributes in the
nucleoplasm. The cellular function of PSP1 remains
unknown currently. The family also includes some
p54nrb/PSF/PSP1 homologs from invertebrate species. For
instance, the Drosophila melanogaster gene
no-ontransient A (nonA) encoding puff-specific protein
Bj6 (also termed NONA) and Chironomus tentans hrp65 gene
encoding protein Hrp65. D. melanogaster NONA is involved
in eye development and behavior and may play a role in
circadian rhythm maintenance, similar to vertebrate
p54nrb. C. tentans Hrp65 is a component of nuclear
fibers associated with ribonucleoprotein particles in
transit from the gene to the nuclear pore.
Length = 90
Score = 28.0 bits (63), Expect = 4.1
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 113 KALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLM 148
KAL E EK EQL + ++ + LE +++
Sbjct: 54 KALYELEKQQREQLEKEL---KEAREKLEAEMEAAR 86
Score = 28.0 bits (63), Expect = 4.1
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 320 KALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLM 355
KAL E EK EQL + ++ + LE +++
Sbjct: 54 KALYELEKQQREQLEKEL---KEAREKLEAEMEAAR 86
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 30.1 bits (68), Expect = 4.2
Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 12/89 (13%)
Query: 58 SISINYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDMLE--LAKHYNKAL 115
S RK+ E+ L K + D+ E D L+ LAK A
Sbjct: 306 SSDSGSRKDVEEENARLEDSPKKRKEEQEDDDFVEDD--------DDLQASLAKQRRLAQ 357
Query: 116 EEEEKMSPEQLA--IKNVGKQDPKRHLEE 142
++ +K+ PE +A I +D + E
Sbjct: 358 KKRKKLRPEDIARQIAEERSEDEEEAAEN 386
>gnl|CDD|223884 COG0814, SdaC, Amino acid permeases [Amino acid transport and
metabolism].
Length = 415
Score = 29.5 bits (67), Expect = 4.5
Identities = 23/133 (17%), Positives = 40/133 (30%), Gaps = 14/133 (10%)
Query: 396 YFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNI-PLLV 454
Y FF L YI G + ++ + N R + L+
Sbjct: 81 YLGKKGGILIGLSYFFALYGLLVAYIVG----IGNLLA-SFLGNQFGLNPLPRKLGSLIF 135
Query: 455 ILIASILWLIGLVDSIRPTMTLFGTLVSWI-----YLRFYQYHTNGTRGDMADNFNFANF 509
L+ + L +G + ++ T L V ++ YL + N A +
Sbjct: 136 ALVLAFLSWLGTLAVLKITSLLVFGKVIYLVLLVVYLIPHWNPANLFALPSASQSFWKYL 195
Query: 510 FPTIIQPPIAVVC 522
I P+ V
Sbjct: 196 LLAI---PVFVFS 205
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 28.4 bits (64), Expect = 4.7
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 112 NKALEEEEKMSPEQLAIKNVG-------KQDPKRHLEEKVDTLMTANIIQCLDRNMERL 163
KALEE EK+ + K VG K++ LEE+ +TL I+ L++ E+L
Sbjct: 40 EKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERKETL--ELRIKTLEKQEEKL 96
Score = 27.7 bits (62), Expect = 7.4
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 293 FEALSERAVAVVVDPIQSVKELAKHYNKALEEEEKMSPEQLAIKNVG-------KQDPKR 345
+ L ++ V++ Q ++ K KALEE EK+ + K VG K++
Sbjct: 15 LQQLQQQLQKVILQ-KQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVD 73
Query: 346 HLEEKVDTL 354
LEE+ +TL
Sbjct: 74 ELEERKETL 82
>gnl|CDD|214022 cd12959, MMACHC-like, Methylmalonic aciduria and homocystinuria
type C protein and similar proteins. MMACHC, also
called CblC, is involved in the intracellular processing
of vitamin B12 by catalyzing two reactions: the
reductive decyanation of cyanocobalamin in the presence
of a flavoprotein oxidoreductase and the dealkylation of
alkylcobalamins through the nucleophilic displacement of
the alkyl group by glutathione. Mutations in MMACHC
cause combined methylmalonic acidemia/aciduria and
homocystinuria (CblC type), the most common inherited
disorder of cobalamin metabolism. The structure of
MMACHC reveals it to be the most divergent member of the
NADPH-dependent flavin reductase family that can use FMN
or FAD to catalyze reductive decyanation; it is also the
first enzyme with glutathione transferase (GST) activity
that is unrelated to the GST superfamily in structure
and sequence.
Length = 226
Score = 29.2 bits (66), Expect = 5.0
Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 15/73 (20%)
Query: 275 HPGFGCWLS--GVDI--NTQQSFEALSERAVAVVVDPIQSVKELAKHYNK---------A 321
HP +G W + GV I + L E + + L + +N
Sbjct: 147 HPKYGGWFAFRGVIIFPDVLPPD--LPEPEPVDCLTTEEDRIALLELFNYHWRDWRYRDV 204
Query: 322 LEEEEKMSPEQLA 334
E+ S EQ
Sbjct: 205 GPPVERYSEEQKE 217
>gnl|CDD|66449 pfam02764, Diphtheria_T, Diphtheria toxin, T domain. Central
domain of diphtheria toxin is the translocation (T)
domain. pH induced conformational change in this domain
triggers insertion into the endosomal membrane and
facilitates the transfer of the catalytic domain into
the cytoplasm.
Length = 180
Score = 28.6 bits (63), Expect = 7.0
Identities = 28/122 (22%), Positives = 48/122 (39%), Gaps = 14/122 (11%)
Query: 106 ELAKHYNKALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMTANIIQCLDR----NME 161
E AK Y + + PE +K V + N+ Q +D N+E
Sbjct: 42 EKAKQYLEEFHQTALEHPELSELKTVTGTN--PVFAGANYAAWAVNVAQVIDSETADNLE 99
Query: 162 RLLRLGSGMPGLSQAPPVSDGPVVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEF 221
+ S +PG+ ++DG V E++ S+AL ++ +P ++GE
Sbjct: 100 KTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMV--AQAIP------LVGEL 151
Query: 222 VD 223
VD
Sbjct: 152 VD 153
>gnl|CDD|191973 pfam08232, Striatin, Striatin family. Striatin is an intracellular
protein which has a caveolin-binding motif, a
coiled-coil structure, a calmodulin-binding site, and a
WD (pfam00400) repeat domain. It acts as a scaffold
protein and is involved in signalling pathways.
Length = 133
Score = 27.7 bits (62), Expect = 8.8
Identities = 7/47 (14%), Positives = 17/47 (36%)
Query: 310 SVKELAKHYNKALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMT 356
S +E + + +EE + + ++ L+E L +
Sbjct: 83 SKEEEEEELEEDDDEESNSEKVDESELKKSRLYLRKSLQEIGYLLKS 129
>gnl|CDD|237708 PRK14418, PRK14418, membrane protein; Provisional.
Length = 236
Score = 28.2 bits (63), Expect = 9.4
Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 5/87 (5%)
Query: 381 FAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMPDHVILNT 440
A+V + + T + + + + + V + G+ V + I P +
Sbjct: 59 IALVVFALDVLKT--LLAILIVSIVVNFVPAVNAFYVIPQAVGLGVVIGHIFPIYFKFKG 116
Query: 441 GLGKMTNRNIPLLVILIASILWLIGLV 467
G G L+I I IL LI +
Sbjct: 117 GKGAACTVG---LIISINIILALIAGI 140
>gnl|CDD|215858 pfam00324, AA_permease, Amino acid permease.
Length = 473
Score = 28.8 bits (65), Expect = 9.7
Identities = 23/145 (15%), Positives = 44/145 (30%), Gaps = 20/145 (13%)
Query: 390 ISSTLFYFFLYMCT-FNTD--LLFFVRIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMT 446
+ ST + N F + I GL G I L+++ + K
Sbjct: 338 LLSTAISLLAVLLASLNPAIVFNFLLAISGLIGLIVWGLISLSHL-----RFRKAF-KYQ 391
Query: 447 NRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRFYQYHTNGTRGDMADNFNF 506
R+I L + + L + T+ L L + L N+
Sbjct: 392 GRSIDELPFKACLGPFGVILGLAALITILLIQAL--YASLPV---------PKPPKNWGA 440
Query: 507 ANFFPTIIQPPIAVVCNTIHEFLVR 531
A+F + + ++ + V+
Sbjct: 441 ASFAALYLIALLFLILLIGVKLHVK 465
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 0.137 0.407
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,946,047
Number of extensions: 3029361
Number of successful extensions: 3509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3483
Number of HSP's successfully gapped: 76
Length of query: 574
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 472
Effective length of database: 6,413,494
Effective search space: 3027169168
Effective search space used: 3027169168
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: 62 (27.7 bits)