RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1140
(142 letters)
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 91
Score = 93.4 bits (233), Expect = 5e-26
Identities = 29/46 (63%), Positives = 36/46 (78%)
Query: 11 FFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
GTLKGFDQT N+IL + HERVYS GVE+V LGL+++RGDN+
Sbjct: 21 VIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNV 66
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins
as well as other related LSM (Like Sm) proteins. The
U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing
contain seven Sm proteins (B/B', D1, D2, D3, E, F and
G) in common, which assemble around the Sm site present
in four of the major spliceosomal small nuclear RNAs.
The U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are
also RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 51.4 bits (124), Expect = 6e-10
Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
+GTLKGFDQ +N++LDD E + + LGL +IRG+NI
Sbjct: 21 LRGTLKGFDQFMNLVLDDVEETIKDG----KVNKLGLVLIRGNNIV 62
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 51.0 bits (123), Expect = 1e-09
Identities = 22/46 (47%), Positives = 31/46 (67%), Gaps = 3/46 (6%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++GTLKGFDQ +N++L+D E V G ++ LGL IRG+NI
Sbjct: 21 YRGTLKGFDQFMNLVLEDVEETVKD---GEKKRKLGLVFIRGNNIV 63
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. Sm-like proteins exist in archaea as well
as prokaryotes that form heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 63
Score = 48.4 bits (116), Expect = 8e-09
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
GTL FD+ +N++LDD E + VLGL +IRG NI
Sbjct: 19 LTGTLVAFDKYMNLVLDDVVETGRDG----KVRVLGLVLIRGSNIV 60
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 46.5 bits (111), Expect = 7e-08
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++GTL GFDQ +N++LDD E + + + G +IRGDNI
Sbjct: 30 YRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIV 75
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1. The archaeal Sm1
proteins: The Sm proteins are conserved in all three
domains of life and are always associated with U-rich
RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain.
Length = 69
Score = 44.1 bits (105), Expect = 4e-07
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G LKGFDQ +N++L+++ E + G LG ++RGDN+
Sbjct: 24 VRGVLKGFDQHLNLVLENAEEII----EGESVRKLGTVLVRGDNV 64
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1. The eukaryotic LSm proteins
(LSm1-7) assemble into a hetero-heptameric ring around
the 3'-terminus of the gamma-methyl triphosphate
(gamma-m-P3) capped U6 snRNA. Accumulation of
uridylated RNAs in an lsm1 mutant suggests an
involvement of the LSm1-7 complex in recognition of the
3' uridylation tag and recruitment of the decapping
machinery. LSm1-7, together with Pat1, are also called
the decapping activator. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 74
Score = 42.1 bits (100), Expect = 3e-06
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 14 GTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
G L+ FDQ N++L+D+ ER+ + GL IIRG+N+
Sbjct: 27 GILRSFDQFANLVLEDTVERIIVGNQ-YGDIPRGLFIIRGENV 68
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold, containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 80
Score = 40.2 bits (95), Expect = 2e-05
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 12 FQGTLKGFDQTINIILDDSHE-RVYSPTAGV------EQVVLGLHIIRGDNI 56
F GT FD+ +N++L D E R P E+ VLGL ++RG+N+
Sbjct: 23 FVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVLLRGENV 74
>gnl|CDD|212466 cd01719, Sm_G, Sm protein G. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit G
binds subunits E and F to form a trimer which then
assembles onto snRNA along with the D1/D2 and D3/B
heterodimers forming a seven-membered ring structure.
Length = 70
Score = 38.7 bits (91), Expect = 6e-05
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 4/44 (9%)
Query: 13 QGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
G L+GFD +N++LDD+ E E+ +G+ +IRG++I
Sbjct: 24 SGVLRGFDPFMNLVLDDAVE----EVGDGEKTPIGMVVIRGNSI 63
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit E
binds subunits F and G to form a trimer which then
assembles onto snRNA along with the D1/D2 and D3/B
heterodimers forming a seven-membered ring structure.
Length = 79
Score = 37.9 bits (89), Expect = 1e-04
Identities = 17/44 (38%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13 QGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G + GFD+ +N++LDD+ E V+ T + LG +++GDNI
Sbjct: 34 EGKIIGFDEYMNLVLDDAEE-VHLKTNTRKP--LGRILLKGDNI 74
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 36.9 bits (86), Expect = 3e-04
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F+G L+G+D +N++LD++ E LG +IRGDN+
Sbjct: 27 FRGELQGYDIHMNLVLDNAEEIQDGEVVR----KLGKVVIRGDNV 67
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 89
Score = 36.8 bits (86), Expect = 4e-04
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 13 QGTLKGFDQTINIILDDSHERVYSP----TAGVEQVVLGLHIIRGDNI 56
G LKG+DQ +N++LDD+ E + P E LGL + RG ++
Sbjct: 26 TGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSV 73
>gnl|CDD|212469 cd01722, Sm_F, Sm protein F. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit F is
capable of forming both homo- and hetero-heptamer ring
structures. To form the hetero-heptamer, Sm subunit F
initially binds subunits E and G to form a trimer which
then assembles onto snRNA along with the D3/B and D1/D2
heterodimers.
Length = 69
Score = 34.5 bits (80), Expect = 0.002
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIK 57
++GTL D +N+ L ++ E + G LG +IR +N+
Sbjct: 24 YKGTLVSVDSYMNLQLANTEEYI----DGKFTGNLGEVLIRCNNVL 65
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 76
Score = 34.5 bits (80), Expect = 0.002
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
F GTL GFD +N++L+D E +P G + L ++ G+NI
Sbjct: 26 FVGTLLGFDDYVNMVLEDVTEYEITP-EGRKITKLDQILLNGNNI 69
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein. The archaeal
Sm-like (LSm): The Sm proteins are conserved in all
three domains of life and are always associated with
U-rich RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm-like proteins
exist in archaea as well as prokaryotes that form
heptameric and hexameric ring structures similar to
those found in eukaryotes.
Length = 69
Score = 34.0 bits (78), Expect = 0.003
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQV-VLGLHIIRGDNI 56
QG L D +N+ L D+ E G E+V LG ++RG+NI
Sbjct: 24 LQGRLVAVDDYMNLHLTDTME-----CVGEEKVRSLGTVVLRGNNI 64
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 34.3 bits (79), Expect = 0.004
Identities = 17/44 (38%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13 QGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
+G + GFD+ +N++LDD+ E VY+ + LG +++GDNI
Sbjct: 42 EGKILGFDEYMNMVLDDAEE-VYTKKN--TRKDLGRILLKGDNI 82
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. LSMD1 proteins have a single Sm-like domain
structure. Sm-like proteins exist in archaea as well as
prokaryotes, forming heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 73
Score = 32.1 bits (74), Expect = 0.015
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQV-VLGLHIIRGDNIK 57
GT D+ NIIL ++ E G E+ LGL ++ G +I
Sbjct: 22 LVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLVMVPGKHIV 68
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 68
Score = 28.6 bits (65), Expect = 0.24
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
++G L D +N++L+D+ E Y G G IRG+N+
Sbjct: 24 YRGVLACLDGYMNLVLEDTEE--YVD--GQLVAKYGDAFIRGNNV 64
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 82
Score = 26.4 bits (59), Expect = 2.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 14 GTLKGFDQTINIILDDSHERVYSPT 38
G L +DQ +N+IL D E + +
Sbjct: 26 GRLHAYDQHLNMILGDVEETITTVE 50
>gnl|CDD|237663 PRK14293, PRK14293, chaperone protein DnaJ; Provisional.
Length = 374
Score = 27.3 bits (61), Expect = 2.7
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 46 LGLHIIRGD-----NIKIPTKISSSTR 67
LG + RGD +KIPT+IS R
Sbjct: 319 LGNPVARGDHLITVKVKIPTRISDEER 345
>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase;
Provisional.
Length = 354
Score = 27.4 bits (62), Expect = 2.9
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 99 GYRPSVDVLHLSASAL 114
+RPSVDVL SA+
Sbjct: 264 RHRPSVDVLFRSAAKA 279
>gnl|CDD|149796 pfam08850, DUF1820, Domain of unknown function (DUF1820). This
family includes small functionally uncharacterized
proteins around 100 amino acids in length.
Length = 99
Score = 26.1 bits (58), Expect = 3.4
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 19 FDQTINIILDDSHERVYSPTAGVEQVVLGLH-IIRGDNI------KIPTKISSSTRSPVP 71
F + +++D S E++ + AGV++ + +H IIR D + KI +P P
Sbjct: 38 FGERSQVVVDPSEEKLKNEFAGVKRSYIPMHSIIRIDEVEKEGTAKITEAKPKGNVTPFP 97
Query: 72 DP 73
P
Sbjct: 98 SP 99
>gnl|CDD|173361 PTZ00066, PTZ00066, pyruvate kinase; Provisional.
Length = 513
Score = 26.3 bits (58), Expect = 6.6
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 100 YRPSVDVLHLSASALKVESMAFIMGLTLPCVLS 132
YRPS +L LSAS V+S++ G+T V S
Sbjct: 431 YRPSCTILALSASPSVVKSLSVARGVTTYVVNS 463
>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
receiver domain and a methylesterase domain [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 350
Score = 26.1 bits (58), Expect = 6.9
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 97 RFGYRPSVDVLHLSASAL 114
G+RPSVDVL S + L
Sbjct: 255 VNGHRPSVDVLFRSVAEL 272
>gnl|CDD|99791 cd06194, FNR_N-term_Iron_sulfur_binding, Iron-sulfur binding
ferredoxin reductase (FNR) proteins combine the FAD and
NAD(P) binding regions of FNR with an N-terminal
Iron-Sulfur binding cluster domain. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD
as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 222
Score = 26.1 bits (58), Expect = 7.2
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 21 QTINIILDDSHERVYSPTAGV-EQVVLGLHIIRGDN 55
Q +N+ R YSPT+ L HI R N
Sbjct: 28 QYVNLRRAGGLARSYSPTSLPDGDNELEFHIRRKPN 63
>gnl|CDD|213029 cd11375, Peptidase_M54, Peptidase family M54, also called
archaemetzincins or archaelysins. Peptidase M54
(archaemetzincin or archaelysin) is a zinc-dependent
aminopeptidase that contains the consensus zinc-binding
sequence HEXXHXXGXXH/D and a conserved Met residue at
the active site, and is thus classified as a metzincin.
Archaemetzincins, first identified in archaea, are also
found in bacteria and eukaryotes, including two human
members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1
is mainly found in the liver and heart while AMZ2 is
primarily expressed in testis and heart; both have been
reported to degrade synthetic substrates and peptides.
The Peptidase M54 family contains an extended metzincin
concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that
a second zinc ion is bound to four cysteines, thus
resembling a zinc finger. Phylogenetic analysis of this
family reveals a complex evolutionary process involving
a series of lateral gene transfer, gene loss and genetic
duplication events.
Length = 173
Score = 25.7 bits (57), Expect = 7.8
Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 11/66 (16%)
Query: 78 NFILLPQIWGIERRTLSFMRFGYRPS--VDVLHLSASALKVESMAFIMGLTLPCVLSHDL 135
+LP I + R Y +D L LK ++G+T DL
Sbjct: 29 PVEVLPSIPVPPLEAYNPSRGQYLADDILDALL----KLKPPDADCVLGVT-----DVDL 79
Query: 136 FLPPWN 141
+ P N
Sbjct: 80 YEPGLN 85
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.325 0.140 0.424
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,323,399
Number of extensions: 657221
Number of successful extensions: 612
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 36
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.4 bits)