RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17828
(1061 letters)
>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 = 286 bits (735), Expect = 5e-89
Identities = 107/137 (78%), Positives = 121/137 (88%), Gaps = 2/137 (1%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNS 696
KVVVHPLVLLSVVDH+NR++K G KRVVGVLLG WK KG+LDV+NSFAVPF+ED+KD S
Sbjct: 2 KVVVHPLVLLSVVDHYNRVAK-GTSKRVVGVLLGSWK-KGVLDVTNSFAVPFEEDEKDPS 59
Query: 697 VWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDA 756
VWFLDH+YLENMYGMFKKVNA+EK+VGWY TGPKL ND+ INEL RRYC N VLVIID
Sbjct: 60 VWFLDHNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDV 119
Query: 757 KPKELGLPTEAYRVVDE 773
+PK+LGLPTEAY V+E
Sbjct: 120 RPKDLGLPTEAYIAVEE 136
Score = 254 bits (651), Expect = 4e-77
Identities = 94/129 (72%), Positives = 108/129 (83%)
Query: 858 AREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHD 917
A+EK+VGWY TGPKL ND+ INEL RRYC N VLVIID +PK+LGLPTEAY V+EVHD
Sbjct: 80 AKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVEEVHD 139
Query: 918 DGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTVGSLSQRVTNQLMGLKGLNQQIK 977
DG+PT+KTF HVPSEIGAEEAEEVGVEHLLRDIKD TV +LS RVTN+L LKGL ++K
Sbjct: 140 DGTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLK 199
Query: 978 EIEKYVGQV 986
EI+ Y+ V
Sbjct: 200 EIKDYLQLV 208
Score = 62.6 bits (153), Expect = 2e-10
Identities = 21/29 (72%), Positives = 28/29 (96%)
Query: 512 VVYLAAMIRSIIALHNLINNKITNRDAEK 540
V+YL+++IRS+IALHNLINNKI N++AEK
Sbjct: 252 VIYLSSLIRSVIALHNLINNKIANKEAEK 280
Score = 60.7 bits (148), Expect = 9e-10
Identities = 20/28 (71%), Positives = 27/28 (96%)
Query: 470 VVYLAAMIRSIIALHNLINNKITNRDAE 497
V+YL+++IRS+IALHNLINNKI N++AE
Sbjct: 252 VIYLSSLIRSVIALHNLINNKIANKEAE 279
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 235 bits (602), Expect = 4e-70
Identities = 93/140 (66%), Positives = 116/140 (82%), Gaps = 2/140 (1%)
Query: 636 SKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDN 695
KVVVHPLVLLS+VDH+NR++K +KRVVGVLLG +G +DV+NSFAVPF+EDDKD
Sbjct: 6 EKVVVHPLVLLSIVDHYNRVAK-DTRKRVVGVLLGSSF-RGRVDVTNSFAVPFEEDDKDP 63
Query: 696 SVWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIID 755
S+WFLDH+YLE+M+GMFK++NA+E VVGWY TGPKL +ND+ I+EL Y N VLVIID
Sbjct: 64 SIWFLDHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIID 123
Query: 756 AKPKELGLPTEAYRVVDEDK 775
+PKELG+PT+AY V+E K
Sbjct: 124 VQPKELGIPTKAYYAVEEVK 143
Score = 193 bits (492), Expect = 5e-55
Identities = 76/131 (58%), Positives = 97/131 (74%), Gaps = 1/131 (0%)
Query: 858 AREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHD 917
A+E VVGWY TGPKL +ND+ I+EL Y N VLVIID +PKELG+PT+AY V+EV +
Sbjct: 85 AKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVEEVKE 144
Query: 918 DG-SPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTVGSLSQRVTNQLMGLKGLNQQI 976
+ + K F HVPSEIGA EAEE+GVEHLLRD+KDTTV +L+ VT +L LKGL+ ++
Sbjct: 145 NATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARL 204
Query: 977 KEIEKYVGQVS 987
+EI Y+ V
Sbjct: 205 REIRSYLDLVV 215
Score = 61.7 bits (150), Expect = 5e-10
Identities = 23/46 (50%), Positives = 32/46 (69%)
Query: 512 VVYLAAMIRSIIALHNLINNKITNRDAEKKEITKSKVEDKPQEDKK 557
V+YL+++IRS+IALHNLINNKI N++ EK E K + + K
Sbjct: 258 VIYLSSLIRSVIALHNLINNKILNKEHEKAEDAKPAAKPAKKGSGK 303
Score = 53.6 bits (129), Expect = 2e-07
Identities = 19/28 (67%), Positives = 26/28 (92%)
Query: 470 VVYLAAMIRSIIALHNLINNKITNRDAE 497
V+YL+++IRS+IALHNLINNKI N++ E
Sbjct: 258 VIYLSSLIRSVIALHNLINNKILNKEHE 285
>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 = 142 bits (359), Expect = 1e-39
Identities = 53/116 (45%), Positives = 70/116 (60%), Gaps = 6/116 (5%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNS 696
VV+HPLVLL +VDH R K G + V+GVLLG +G +++V+NSFA+P E + D
Sbjct: 4 TVVIHPLVLLKIVDHARRGGKSG--EEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDVE 61
Query: 697 VWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTN 748
LDH+Y+E M M KKVN E+VVGWYH+ P L D+ EL +R
Sbjct: 62 AVELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117
Score = 43.9 bits (104), Expect = 3e-05
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 857 RAREKVVGWYHTGPK----LHQNDIQINELIRRYCTN 889
E+VVGWYH+ P L D+ EL +R
Sbjct: 81 NRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117
>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 = 122 bits (309), Expect = 3e-32
Identities = 48/149 (32%), Positives = 76/149 (51%), Gaps = 13/149 (8%)
Query: 638 VVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSV 697
V +HPLVLL++ DH+ R KRV+GVLLG ++V+NSF +PFDE+++
Sbjct: 1 VQLHPLVLLNISDHYTRRKY--GIKRVIGVLLGYVD-GDKIEVTNSFELPFDEEEES--- 54
Query: 698 WFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKLHQ----NDIQINELIRRY-CTNSVLV 752
F+D +YLE Y + KKV +EK+VGWY G +D ++ N +++
Sbjct: 55 IFIDTEYLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLIL 114
Query: 753 IIDAKPKEL--GLPTEAYRVVDEDKIRPE 779
I+D + L + ++ E
Sbjct: 115 ILDPSLQSDSEKLEISTFTSAQREENGAE 143
Score = 43.2 bits (102), Expect = 1e-04
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 15/91 (16%)
Query: 859 REKVVGWYHTGPKLHQ----NDIQINELIRRY-CTNSVLVIIDAKPKEL--GLPTEAYRV 911
+EK+VGWY G +D ++ N +++I+D + L +
Sbjct: 75 QEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTS 134
Query: 912 VDEVHDDGSPTTKTFDHVPSEIGAEEAEEVG 942
+ + EIG EE E +
Sbjct: 135 A--------QREENGAEITYEIGTEETERIA 157
>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 = 112 bits (282), Expect = 7e-29
Identities = 49/142 (34%), Positives = 69/142 (48%), Gaps = 12/142 (8%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNS 696
+V VHPLV L+++ H R V GVLLG K +V FAVP + D +S
Sbjct: 1 EVKVHPLVPLNILKHAIRDGPE----EVCGVLLGKS-NKDRPEVKEVFAVPNEPQD--DS 53
Query: 697 VWFLDHDYLENMYGMFKKVNAREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLV 752
V D DY M KKVN ++VGWYH+ P + D+ +E + SV++
Sbjct: 54 VQEYDEDYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVL 113
Query: 753 IIDA-KPKELGLPTEAYRVVDE 773
I+D K + L A+R+ E
Sbjct: 114 IVDPIKSFQGRLSLRAFRLTPE 135
Score = 52.0 bits (125), Expect = 8e-08
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 857 RAREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDA-KPKELGLPTEAYRV 911
++VGWYH+ P + D+ +E + SV++I+D K + L A+R+
Sbjct: 73 NKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRL 132
Query: 912 VDE 914
E
Sbjct: 133 TPE 135
>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 = 107 bits (269), Expect = 1e-25
Identities = 46/133 (34%), Positives = 79/133 (59%), Gaps = 8/133 (6%)
Query: 638 VVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSV 697
V VHP+VL S++D + R ++ Q+RV+G LLG +G ++++N FAVP +E + +V
Sbjct: 1 VRVHPVVLFSILDSYERRNE--GQERVIGTLLGTRS-EGEVEITNCFAVPHNESEDQVAV 57
Query: 698 WFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCT--NSVLVIID 755
D +Y MY + +KVN +E +VGWY TG ++ ++ I++ R CT N + + +D
Sbjct: 58 ---DMEYHRTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVD 114
Query: 756 AKPKELGLPTEAY 768
+ + +AY
Sbjct: 115 TSLDDGKMSIKAY 127
Score = 53.7 bits (130), Expect = 1e-07
Identities = 31/133 (23%), Positives = 61/133 (45%), Gaps = 9/133 (6%)
Query: 859 REKVVGWYHTGPKLHQNDIQINELIRRYCT--NSVLVIIDAKPKELGLPTEAYRVVDEVH 916
+E +VGWY TG ++ ++ I++ R CT N + + +D + + +AY V +
Sbjct: 75 KEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAY-VSSPLG 133
Query: 917 DDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTVGSLSQRVTNQLMGLKGLNQQI 976
G F +P E+ EAE V ++ L + + R L+ L +
Sbjct: 134 VPGKTLGSMFVPIPLELLYSEAERVALDLLAKTLAS------PSRSAPLTSDLEQLEASL 187
Query: 977 KEIEKYVGQVSRY 989
+++++ + +V RY
Sbjct: 188 EKLQEMLDRVLRY 200
>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 = 102 bits (255), Expect = 1e-25
Identities = 56/128 (43%), Positives = 74/128 (57%), Gaps = 16/128 (12%)
Query: 645 LLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDY 704
L +D + N K V+G+L G K +LDV AVPFDE DKD++VWFL
Sbjct: 1 LKMFLDAAKSI----NGKEVIGLLYGSKT-KKVLDVDEVIAVPFDEGDKDDNVWFL---- 51
Query: 705 LENMYGMFKKVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKE 760
MY FKK+NA ++VGWYHT PK L ND+ +EL +RY V++I+D KPK+
Sbjct: 52 ---MYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKD 108
Query: 761 LGLPTEAY 768
LG + Y
Sbjct: 109 LGNSWKCY 116
Score = 60.2 bits (146), Expect = 6e-11
Identities = 30/109 (27%), Positives = 45/109 (41%), Gaps = 14/109 (12%)
Query: 805 AFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVG 864
L G ++ KV + W + + A ++VG
Sbjct: 18 GLLYGSKTK--KVLDVDEVIAVPFDEGDK------DDNVWFLMYLDF--KKLNAGLRIVG 67
Query: 865 WYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAY 909
WYHT PK L ND+ +EL +RY V++I+D KPK+LG + Y
Sbjct: 68 WYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116
>gnl|CDD|227069 COG4725, IME4, Transcriptional activator, adenine-specific DNA
methyltransferase [Signal transduction mechanisms /
Transcription].
Length = 198
Score = 98.1 bits (244), Expect = 4e-23
Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEG-LLFL 396
QWI+CD+R D VLGKF+V++AD PY MS +E+ L + QL D G L++L
Sbjct: 2 QWIRCDVRKFDFRVLGKFSVVIADMRALRKASAPYDVMSAEEILALPVGQLADMGCLIYL 61
Query: 397 WVTGRAMELGRECLK 411
W T + ECLK
Sbjct: 62 WATAPHLAFTVECLK 76
>gnl|CDD|218409 pfam05063, MT-A70, MT-A70. MT-A70 is the
S-adenosylmethionine-binding subunit of human mRNA:m6A
methyl-transferase (MTase), an enzyme that
sequence-specifically methylates adenines in pre-mRNAs.
Length = 176
Score = 80.9 bits (200), Expect = 2e-17
Identities = 38/67 (56%), Positives = 44/67 (65%), Gaps = 9/67 (13%)
Query: 355 FAVIMADPPWDIHM-------ELPYGTMSDDEMRQLGIPQLQDEG-LLFLWVTGRAM-EL 405
F VI+ADPPW M ELPYGTM+DDE+ L IP+L D+G L+FLW T R E
Sbjct: 1 FDVIIADPPWRNKMVARLKKPELPYGTMNDDELLALPIPELADKGSLIFLWCTNREGEEG 60
Query: 406 GRECLKL 412
GRECLK
Sbjct: 61 GRECLKK 67
>gnl|CDD|163694 cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in COP9
signalosome complex subunit 6. CSN6 (COP9 signalosome
subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one
of the eight subunits of COP9 signalosome, 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. CSN6 is an MPN-domain protein that directly
interacts with the MPN+-domain subunit CSN5. It is
cleaved during apoptosis by activated caspases. CSN6
processing occurs in CSN/CRL (cullin-RING Ub ligase)
complexes and is followed by the cleavage of Rbx1, the
direct interaction partner of CSN6. CSN6 cleavage
enhances CSN-mediated deneddylating activity (i.e.
cleavage of ubiquitin-like protein Nedd8 (neural
precursor cell expressed, developmentally downregulated
8)) in the cullin 1 in cells. The cleavage of Rbx1 and
increased deneddylation of cullins inactivate CRLs and
presumably stabilize pro-apoptotic factors for final
apoptotic steps. While CSN6 shows a typical MPN
metalloprotease fold, it lacks the canonical JAMM motif,
and therefore does not show catalytic isopeptidase
activity.
Length = 288
Score = 71.5 bits (176), Expect = 2e-13
Identities = 43/122 (35%), Positives = 67/122 (54%), Gaps = 6/122 (4%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQK--RVVGVLLGCWKGKGILDVSNSFAVPFDEDDKD 694
V +HPLV+L++ DH R + RVVG LLG G+ I ++ NSF + +D ++
Sbjct: 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREI-EIENSFELKYDTNEDG 60
Query: 695 NSVWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKL-HQNDIQINELIRRYCTNSVLVI 753
V LD ++LE FK+V VGWY TGP ++D+ I++ I + VL++
Sbjct: 61 EIV--LDKEFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLL 118
Query: 754 ID 755
+D
Sbjct: 119 LD 120
Score = 58.4 bits (142), Expect = 5e-09
Identities = 39/132 (29%), Positives = 66/132 (50%), Gaps = 7/132 (5%)
Query: 862 VVGWYHTGPKL-HQNDIQINELIRRYCTNSVLVIIDAKPKELG--LPTEAYRVVDEVHDD 918
VGWY TGP ++D+ I++ I + VL+++D + G LP Y V E+ D
Sbjct: 85 FVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLEL-VD 143
Query: 919 GSPTTKTFDHVPSEIGAEEAEEVGVEHLLR--DIKDTTVGSLSQRVTNQLMGLKGLNQQI 976
G T + F +P I EAE +GV+H+ R + +++ + Q +K LN ++
Sbjct: 144 GEATLR-FRELPYTIETGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRV 202
Query: 977 KEIEKYVGQVSR 988
+ I +Y+ V
Sbjct: 203 ELILEYLKAVPV 214
>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 = 66.5 bits (163), Expect = 4e-13
Identities = 18/51 (35%), Positives = 32/51 (62%)
Query: 936 EEAEEVGVEHLLRDIKDTTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQV 986
+EAE++GVEHLLR + +LS+++ + LK L++++ I Y+ V
Sbjct: 1 QEAEQIGVEHLLRGLNRHYYSTLSRKLELEQKALKNLHKRLWTIGLYLEDV 51
Score = 36.4 bits (85), Expect = 0.015
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 470 VVYLAAMIRSIIALHNLINNK 490
VVYL + R ALH LINN
Sbjct: 95 VVYLGKLDRKQHALHELINNN 115
Score = 36.4 bits (85), Expect = 0.015
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 512 VVYLAAMIRSIIALHNLINNK 532
VVYL + R ALH LINN
Sbjct: 95 VVYLGKLDRKQHALHELINNN 115
>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 = 50.7 bits (122), Expect = 2e-06
Identities = 39/144 (27%), Positives = 61/144 (42%), Gaps = 15/144 (10%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNS 696
V + LV+L ++ H K + V G LLG G G L+V+N F P E+D +
Sbjct: 2 SVQIDGLVVLKIIKH----CKEELPELVQGQLLGLDVG-GTLEVTNCFPFPKSEEDDSDR 56
Query: 697 VWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIR------RYCTNSV 750
DY M + ++VN VGWY + + +LI SV
Sbjct: 57 ADEDIADYQLEMMRLLREVNVDHNHVGWYQS---TYLGSFFTRDLIETQYNYQEAIEESV 113
Query: 751 LVIIDAKPKELG-LPTEAYRVVDE 773
+++ D G L +AYR+ ++
Sbjct: 114 VLVYDPSKTSQGSLSLKAYRLSEK 137
>gnl|CDD|224229 COG1310, COG1310, Predicted metal-dependent protease of the
PAD1/JAB1 superfamily [General function prediction
only].
Length = 134
Score = 42.9 bits (101), Expect = 1e-04
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 18/95 (18%)
Query: 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNS 696
+V+ VL ++++H R V G+L G +G+ + N S
Sbjct: 1 MLVIPKEVLGAILEHARREHPR----EVCGLLAGTREGERYFPLKNV------------S 44
Query: 697 VWFLDHDYLENMYGMFKKVNAR--EKVVGWYHTGP 729
V +++ ++ Y +F E VVGWYH+ P
Sbjct: 45 VEPVEYFEIDPEYSLFYLAAEDAGEVVVGWYHSHP 79
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 37.6 bits (88), Expect = 0.031
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 10/89 (11%)
Query: 16 NSLREKLQKRKQERKDILERDGSLSPARNEEDSVDTSYQTEEDAIKLNPDLELELLEKLC 75
+ L+EKL K ++ ++ +E + EE+ + + +++ +K
Sbjct: 3 DKLKEKLSKFVEKVEEKIEEEEEEEAPEAEEEEEEEDEEEKKEKPGF--------FDKAK 54
Query: 76 DVSLTEEDAIKLNPDLELELLEKLCDVSL 104
+ E+D L +LELELLE DV+L
Sbjct: 55 ITEIKEKDIEDLLEELELELLES--DVAL 81
>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 = 33.4 bits (77), Expect = 0.50
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 708 MYGMFKKVNAREKVVGWYHTGP 729
Y M K+ E VVGWYH+ P
Sbjct: 76 QYEMLKQTGRPENVVGWYHSHP 97
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 31.9 bits (73), Expect = 1.3
Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 7 EIQAIKSKRNSLREKLQKRKQERKDILERDGSLSPARNE-EDSVDTSYQTEEDAIKLNPD 65
E+ ++ + L+E+L + +QE +++ + +L + + Q +AI+L+ +
Sbjct: 74 ELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEE 133
Query: 66 LELELLEKL 74
EL E+L
Sbjct: 134 NR-ELREEL 141
>gnl|CDD|212037 cd10327, SLC5sbd_PanF, Na(+)/pantothenate cotransporters: PanF of
Escherichia coli and related proteins; solute binding
domain. PanF catalyzes the Na+-coupled uptake of
extracellular pantothenate for coenzyme A biosynthesis in
cells. This subfamily belongs to the solute carrier 5
(SLC5) transporter family.
Length = 472
Score = 32.6 bits (75), Expect = 1.4
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 1009 LSGPGRWLLPWGWSIMMWVLVGWGVLGI 1036
L+ G L + + WVLVG+GV+G+
Sbjct: 223 LTPFGPGFLSPPYILSFWVLVGFGVIGL 250
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 32.3 bits (74), Expect = 1.7
Identities = 28/108 (25%), Positives = 49/108 (45%), Gaps = 16/108 (14%)
Query: 6 EEIQAIKSKRNSLREKLQKRKQERKDIL---------------ERDGSLSPARNEEDSVD 50
E+++ +K K L +KL + ++E ++L ER L P NE +
Sbjct: 549 EKLEELKKKLAELEKKLDELEEELAELLKELEELGFESVEELEERLKELEPFYNEYLELK 608
Query: 51 TSYQTEEDAIKLNPDLELELLEKLCDVSLTEEDAIKLNPDLELELLEK 98
+ + E K LE EL + +++ TE+ +L +LE EL +K
Sbjct: 609 DAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELE-ELEKK 655
Score = 32.0 bits (73), Expect = 2.3
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 13/121 (10%)
Query: 6 EEIQAIKSKRNSLREKLQKRKQERKDILERDGSLSPARNEEDSVDTSYQTEEDAIK---- 61
EI I S+ LRE+L+K ++E K++ E + E +S++ S + E+ I+
Sbjct: 207 REINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEE 266
Query: 62 ----LNPDLELELLEKLCDVSLTEEDA---IKLNPDLELELLEKLCDVSLVLPITSQSLM 114
L ++E EL EK+ ++ +E A IKL+ E E L++L ++ L + +
Sbjct: 267 RIEELKKEIE-ELEEKVKELKELKEKAEEYIKLSEFYE-EYLDELREIEKRLSRLEEEIN 324
Query: 115 G 115
G
Sbjct: 325 G 325
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 31.3 bits (71), Expect = 3.8
Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 8/98 (8%)
Query: 2 SDAWEEIQAIKSKRNSLREKLQKRKQERKDILERDGSLSPARNEEDSVDTSYQTEEDAIK 61
S+A E++ + + S EKL Q + L + +L + + ++ + E I+
Sbjct: 622 SEAENELEEAEEELESELEKLN--LQAELEELLQA-ALEELEEKVEELEAEIRRELQRIE 678
Query: 62 LNPDLELELLEKLCDVSLTEEDAIKLNPDLELELLEKL 99
E +L EKL ++ EE+ +L +LE ELL+KL
Sbjct: 679 ----NEEQLEEKLEELEQLEEELEQLREELE-ELLKKL 711
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 31.2 bits (71), Expect = 4.2
Identities = 39/228 (17%), Positives = 98/228 (42%), Gaps = 24/228 (10%)
Query: 6 EEIQAIKSKRNSLREKLQKRKQE----RKDILERDGSLSPARNEEDSVDTSYQTEEDAIK 61
+EI+ +KS+ LRE+L++ ++E +++I E +G +S R + ++ + E+ ++
Sbjct: 267 KEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLE 326
Query: 62 LNPDLELELLEKLCDVSLTEEDAIKLNPDLELELLEKLCDVSLVLPITSQSLMGTLNQEY 121
EL EK+ +E+ + LE EL + L ++ + L L +
Sbjct: 327 -------ELKEKI---EALKEELEERETLLE-ELEQLLAELEEAKEELEEKLSALLEELE 375
Query: 122 THLCLINLLHKFATQKLITIN-ESKDDDNQVEIVSVEHVKLLGMVNEVSKGIKRKADTDT 180
+ ++L + E + N++E + E L + +S+ ++ +
Sbjct: 376 ELFEALR-------EELAELEAELAEIRNELEELKREIESLEERLERLSERLE-DLKEEL 427
Query: 181 SDYEDDEDLKKFKDNGDETDVMSLLSKPSIREKQVKQIGEEILDLLTK 228
+ E + + + + ++ L + ++K++ E+ +L +
Sbjct: 428 KELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEE 475
Score = 30.8 bits (70), Expect = 5.0
Identities = 23/101 (22%), Positives = 47/101 (46%), Gaps = 8/101 (7%)
Query: 1 MSDAWEEIQAIKSKRNSLREKLQKRKQERKDILERDGSLSPARNEEDSVDTSYQTEEDAI 60
+ + EEI+ ++ K + L E+L++ ++E +++ E L E++ ++ + E+
Sbjct: 830 IEELEEEIEELEEKLDELEEELEELEKELEELKEE---LEELEAEKEELEDELKELEEEK 886
Query: 61 KLNPDLELELLEKLCDVSLTEEDAIKLNPDLELELLEKLCD 101
+ +LE E L +L L E LE LE +
Sbjct: 887 E---ELEEE-LRELES-ELAELKEEIEKLRERLEELEAKLE 922
>gnl|CDD|234486 TIGR04156, cyanoexo_CrtB, cyanoexosortase B. This model describes
a cyanobacterial-restricted form of exosortase,
associated with a PEP-CTERM domain subclass described in
model TIGR04155. This is one of two such
cyanoexosortases, either of which is sufficient to
accompany TIGR04155 family members. The cyanoexosortase
is TIGR03763 [Protein fate, Protein and peptide
secretion and trafficking].
Length = 280
Score = 30.4 bits (69), Expect = 4.7
Identities = 32/129 (24%), Positives = 49/129 (37%), Gaps = 32/129 (24%)
Query: 382 QLGIPQLQDEGLLFLWVTGRAMELGRECLKLFMLQDE---GLLFLWVTGRAMELGRECLK 438
Q G+ D ++L+V GR +E+ C L ML L+ L+ TG +
Sbjct: 152 QFGMDVTVDG--IYLYVNGRIVEVAPYCAGLKMLFTSLYVSLMLLYWTGALSSRRKTIFF 209
Query: 439 LSL------------NCQLS------QDVEFTWPYLGWMSKFSLHHFFQVVYLAAMIRSI 480
LS N L+ QD F W + GW +Y A M+ +
Sbjct: 210 LSSAVLISVIANIIRNTLLTLFHGTGQDAAFKWLHEGWGGD---------LYSAGMLGLL 260
Query: 481 IALHNLINN 489
+ L N ++N
Sbjct: 261 VPLLNWMDN 269
>gnl|CDD|130749 TIGR01688, dltC, D-alanine--poly(phosphoribitol) ligase, subunit 2.
This protein is part of the teichoic acid operon in
gram-positive organisms. Gram positive organisms
incorporate teichoic acid in their cell walls, and in
the fatty acid residues of the glycolipid component of
the outer layer of the cytoplasmic membrane. This gene,
dltC, encodes the alanyl carrier protein [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 73
Score = 28.3 bits (63), Expect = 4.8
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 69 ELLEKLCDVSLTEEDAIKLNPDLEL---ELLEKLCDVSLVLPITSQ 111
+L+ L +V T D +K NPDLEL LL+ V L+L I +Q
Sbjct: 3 GVLDILAEV--TGSDDVKENPDLELFEEGLLDSFGTVQLLLEIQNQ 46
>gnl|CDD|119363 cd06546, GH18_CTS3_chitinase, GH18 domain of CTS3 (chitinase 3), an
uncharacterized protein from the human fungal pathogen
Coccidioides posadasii. CTS3 has a chitinase-like
glycosyl hydrolase family 18 (GH18) domain; and has
homologs in bacteria as well as fungi.
Length = 256
Score = 30.0 bits (68), Expect = 5.7
Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 17/113 (15%)
Query: 107 PITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDD-------NQVEIVSVEHV 159
PI+S L+ THL ++ LH I +N+ D ++ I+ V
Sbjct: 16 PISSLLLVTEKGIALTHL-IVAALHINDDG-NIHLNDHPPDHPRFTTLWTELAILQSSGV 73
Query: 160 KLLGMVNEVSKGIKRKADTDTSDYED-----DEDLKKFKDNGDETDV---MSL 204
K++GM+ + G + D D D+E + +++ +G + DV MSL
Sbjct: 74 KVMGMLGGAAPGSFSRLDDDDEDFERYYGQLRDMIRRRGLDGLDLDVEEPMSL 126
>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal
subunit [Translation, ribosomal structure and
biogenesis].
Length = 591
Score = 30.4 bits (68), Expect = 6.4
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 3/68 (4%)
Query: 142 NESKDDDNQVEIVSVEHVKLLGMVNEVSKGIKRKADTDTSDYEDDEDLKKFKDNGDETDV 201
ES D V + + E+S+ I +E L F+DN D+
Sbjct: 280 VESLDSSTLKSAVCNDPGNIDVSKEELSEKIPELMVECR---LVEEKLDTFEDNNKNKDI 336
Query: 202 MSLLSKPS 209
M ++SKP
Sbjct: 337 MEMVSKPC 344
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase 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.
Length = 331
Score = 30.1 bits (68), Expect = 6.5
Identities = 12/61 (19%), Positives = 21/61 (34%)
Query: 712 FKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 771
F E + W H + + DI + + + + V A L P + Y V
Sbjct: 30 FDIAPPGEALSAWQHPNIEFLKGDITDRNDVEQALSGADCVFHTAAIVPLAGPRDLYWEV 89
Query: 772 D 772
+
Sbjct: 90 N 90
>gnl|CDD|221177 pfam11708, Slu7, Pre-mRNA splicing Prp18-interacting factor. The
spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and
U5) and proteins, catalyzes the excision of introns from
pre-mRNAs in two successive trans-esterification
reactions. Step 2 depends upon integral spliceosome
constituents such as U5 snRNA and Prp8 and
non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22.
ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a
conformational change in the spliceosome that leads to
protection of the 3'ss from targeted RNase H cleavage.
This change, which probably reflects binding of the 3'ss
PyAG in the catalytic centre of the spliceosome,
requires the ordered recruitment of Slu7, Prp18, and
Prp22 to the spliceosome. There is a close functional
relationship between Prp8, Prp18, and Slu7, and Prp18
interacts with Slu7, so that together they recruit Prp22
to the spliceosome. Most members of the family carry a
zinc-finger of the CCHC-type upstream of this domain.
Length = 236
Score = 29.7 bits (67), Expect = 6.8
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 15/75 (20%)
Query: 4 AWEE--------IQAIKSK-----RNSLREKLQKRKQERKDILER--DGSLSPARNEEDS 48
AWE +QA +K + +K Q + Q+++ +LE+ +E
Sbjct: 139 AWEAAEKGGDVHLQANPTKLELLRKKEKEKKEQLKIQKKQSLLEKYGGEEHLDKPPKELL 198
Query: 49 VDTSYQTEEDAIKLN 63
+ S E
Sbjct: 199 LGQSEDYVEYDRAGK 213
>gnl|CDD|233604 TIGR01863, cas_Csd1, CRISPR-associated protein Cas8c/Csd1, subtype
I-C/DVULG. CRISPR loci appear to be mobile elements
with a wide host range. This model represents a protein
that tends to be found near CRISPR repeats of the DVULG
subtype of CRISPR/Cas locus. We designate this family
Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species
range for this subtype, so far, is exclusively bacterial
and mesophilic, although CRISPR loci in general are
particularly common among archaea and thermophilic
bacteria. In a few species (Xanthomonas axonopodis pv.
citri str. 306 and Streptococcus mutans UA159), homology
to this protein family is split across two tandem genes;
the trusted cutoff to this family is set low enough to
capture at least the longer of the two [Mobile and
extrachromosomal element functions, Other].
Length = 584
Score = 30.0 bits (68), Expect = 6.9
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 748 NSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPSANKAAI 793
+++D + L L E R D K+ P P+ +
Sbjct: 27 IPFFIVLDEDGQFLRL--EDLRKTDGKKLIPRTLLVPQRVGRTVGL 70
>gnl|CDD|178102 PLN02484, PLN02484, probable pectinesterase/pectinesterase
inhibitor.
Length = 587
Score = 30.3 bits (68), Expect = 7.0
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 498 VNIEFNFSLQHFSQVVYLAAMI 519
++I FN +LQHFS+ +YL++ I
Sbjct: 108 IHISFNMTLQHFSKALYLSSTI 129
>gnl|CDD|221775 pfam12794, MscS_TM, Mechanosensitive ion channel inner membrane
domain 1. The small mechanosensitive channel, MscS, is a
part of the turgor-driven solute efflux system that
protects bacteria from lysis in the event of osmotic
shock. The MscS protein alone is sufficient to form a
functional mechanosensitive channel gated directly by
tension in the lipid bilayer. The MscS proteins are
heptamers of three transmembrane subunits with seven
converging M3 domains, and this domain is one of the
inner membrane domains.
Length = 339
Score = 29.9 bits (68), Expect = 7.1
Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 18/71 (25%)
Query: 972 LNQQIKEIEKYVGQVS--RYWPPFYVVVINLIDKRSVTHLSGPGRWLLPWGWSIMMWVLV 1029
+ +++ I K VG+V+ + +++ L+ L+ LP + + +
Sbjct: 24 IKARLERIAKRVGKVTQDSFLHTPRALLLTLL-------LA------LPLPL---LLLAI 67
Query: 1030 GWGVLGIGWNS 1040
G+ + G W S
Sbjct: 68 GYALQGAAWQS 78
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
archaeal 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. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and C-terminal
domains of this protein are well conserved, but the
central hinge region is skewed in composition and highly
divergent [Cellular processes, Cell division, DNA
metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.4 bits (69), Expect = 7.1
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 4 AWEEIQAIKSKRNSLREKLQKRKQERKDILER 35
A +E + + + + L+EK K ++ERK ILER
Sbjct: 977 AIQEYEEVLKRLDELKEKRAKLEEERKAILER 1008
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.7 bits (68), Expect = 9.3
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 14/95 (14%)
Query: 11 IKSKRNSLREKLQKRKQERKDILERDGSLSPARNEE-DSVDTSYQTEEDAIKLN----PD 65
++ +RN L +KL+KR ++++ L+R L R EE + + + ++ ++ +
Sbjct: 77 LRERRNEL-QKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEE 135
Query: 66 LELELLEKLCDVS-LTEEDAIKLNPDLELELLEKL 99
L E L++L +S LT E+A + LLEK+
Sbjct: 136 LIEEQLQELERISGLTAEEAKE-------ILLEKV 163
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.405
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 53,984,495
Number of extensions: 5413948
Number of successful extensions: 5625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5570
Number of HSP's successfully gapped: 77
Length of query: 1061
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 954
Effective length of database: 6,191,724
Effective search space: 5906904696
Effective search space used: 5906904696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.5 bits)