RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10002
(145 letters)
>gnl|CDD|232799 TIGR00049, TIGR00049, Iron-sulfur cluster assembly accessory
protein. Proteins in this subfamily appear to be
associated with the process of FeS-cluster assembly. The
HesB proteins are associated with the nif gene cluster
and the Rhizobium gene IscN has been shown to be
required for nitrogen fixation. Nitrogenase includes
multiple FeS clusters and many genes for their assembly.
The E. coli SufA protein is associated with SufS, a NifS
homolog and SufD which are involved in the FeS cluster
assembly of the FhnF protein. The Azotobacter protein
IscA (homologs of which are also found in E.coli) is
associated which IscS, another NifS homolog and IscU, a
nifU homolog as well as other factors consistent with a
role in FeS cluster chemistry. A homolog from Geobacter
contains a selenocysteine in place of an otherwise
invariant cysteine, further suggesting a role in redox
chemistry [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 105
Score = 118 bits (298), Expect = 1e-35
Identities = 44/99 (44%), Positives = 57/99 (57%), Gaps = 15/99 (15%)
Query: 47 AGLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKA 106
GL+VGV+ GC+GL Y L + + + DE QD GV++ +D K+
Sbjct: 22 LGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQD---------------GVKVVVDPKS 66
Query: 107 QLTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
L G+E+DYVE L S F F NPN KGTCGCG+SFSV
Sbjct: 67 LPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKSFSV 105
>gnl|CDD|223393 COG0316, sufA, Fe-S cluster assembly scaffold protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 110
Score = 106 bits (268), Expect = 6e-31
Identities = 42/98 (42%), Positives = 55/98 (56%), Gaps = 15/98 (15%)
Query: 48 GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQ 107
GL+VGV+ GC+G Y L + + + D QD GV++ +D K+
Sbjct: 28 GLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQD---------------GVKVVVDPKSL 72
Query: 108 LTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
L GTE+DYVE+ L S F F NPN K +CGCGESFSV
Sbjct: 73 PYLEGTEIDYVEDLLGSGFTFKNPNAKSSCGCGESFSV 110
>gnl|CDD|213674 TIGR02011, IscA, iron-sulfur cluster assembly protein IscA. This
model represents the IscA component of the ISC system
for iron-sulfur cluster assembly. The ISC system
consists of IscRASU, HscAB and an Isc-specific
ferredoxin. IscA previously was believed to act as a
scaffold and now is seen as an iron donor protein. This
clade is limited to the proteobacteria [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 105
Score = 83.3 bits (206), Expect = 8e-22
Identities = 39/98 (39%), Positives = 56/98 (57%), Gaps = 15/98 (15%)
Query: 48 GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQ 107
GL++GV+ GC+G++Y L + D+ D+ V F GV+I ID K+
Sbjct: 23 GLRLGVKTSGCSGMAYVLEFV-DEPTPDDIV--------------FEDKGVKIVIDGKSL 67
Query: 108 LTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
L GT++D+V+ L+ F F NPN+K CGCGESF V
Sbjct: 68 QYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 105
>gnl|CDD|131052 TIGR01997, sufA_proteo, FeS assembly scaffold SufA. This model
represents the SufA protein of the SUF system of
iron-sulfur cluster biosynthesis. This system performs
FeS biosynthesis even during oxidative stress and tends
to be absent in obligate anaerobic and microaerophilic
bacteria [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 107
Score = 80.6 bits (199), Expect = 1e-20
Identities = 36/112 (32%), Positives = 59/112 (52%), Gaps = 16/112 (14%)
Query: 35 NKIHCIIFISSQA-GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFF 93
I ++ +A G+++GV++ GC G+ Y L+ + +K D+ + D
Sbjct: 11 IHIRELVAKRPEAVGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHD------------ 58
Query: 94 HVSGVRIFIDRKAQLTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
G ++F+ +A L +LGT++D+V L F FNNPN CGCGESF +
Sbjct: 59 ---GAKVFVAPEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGESFEL 107
>gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional.
Length = 107
Score = 80.7 bits (199), Expect = 1e-20
Identities = 36/98 (36%), Positives = 57/98 (58%), Gaps = 15/98 (15%)
Query: 48 GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQ 107
GL++GV+ GC+G++Y L + D+ ++ V +D GV++ +D K+
Sbjct: 25 GLRLGVRTSGCSGMAYVLEFV-DEPTPEDIVFED--------------KGVKVVVDGKSL 69
Query: 108 LTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
L GT++D+V+ L+ F F NPN+K CGCGESF V
Sbjct: 70 QFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 107
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 72.8 bits (179), Expect = 2e-17
Identities = 34/98 (34%), Positives = 50/98 (51%), Gaps = 15/98 (15%)
Query: 48 GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQ 107
G+++GV+Q GC G Y L+ + +K D F G ++F+ +A
Sbjct: 40 GVRLGVKQTGCAGFGYVLDSVSEPDKDD---------------LVFEHDGAKLFVPLQAM 84
Query: 108 LTLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
+ GTE+DYV L+ F F+NP + CGCGESF V
Sbjct: 85 PFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGESFGV 122
>gnl|CDD|110518 pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis. This
family is involved in iron-sulphur cluster biosynthesis.
Its members include proteins that are involved in
nitrogen fixation such as the HesB and HesB-like
proteins.
Length = 91
Score = 69.9 bits (172), Expect = 9e-17
Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 15/84 (17%)
Query: 48 GLKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQ 107
GL++GV+ GC+G SY L + + ++ DE QD GV + +D K+
Sbjct: 23 GLRIGVRYGGCSGFSYGLTFEDEPDEGDEVFEQD---------------GVTVVVDEKSL 67
Query: 108 LTLLGTEMDYVENKLSSEFVFNNP 131
L GTE+D+VE L S F F+NP
Sbjct: 68 PYLEGTEIDFVEELLGSGFTFSNP 91
>gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA;
Provisional.
Length = 115
Score = 64.6 bits (158), Expect = 2e-14
Identities = 34/97 (35%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 49 LKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQL 108
L+V + GC+G Y + DE+V +D GV + +D +
Sbjct: 34 LRVYITGGGCSGFQYGFTF-------DEQVNED--------DTTIEKQGVTLVVDPMSLQ 78
Query: 109 TLLGTEMDYVENKLSSEFVFNNPNIKGTCGCGESFSV 145
L+G E+DY E S FV NPN K TCGCG SFS+
Sbjct: 79 YLVGAEVDYTEGLEGSRFVIKNPNAKTTCGCGSSFSI 115
>gnl|CDD|215564 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional.
Length = 163
Score = 46.8 bits (111), Expect = 3e-07
Identities = 30/98 (30%), Positives = 44/98 (44%), Gaps = 16/98 (16%)
Query: 49 LKVGVQQRGCNGLSYTLNYAKDKEKMDEEVIQDVKYWALILTCFFHVSGVRIFIDRKAQL 108
L++ V+ GC+G Y DK D+ V F GV++ +D +
Sbjct: 80 LRLSVETGGCSGFQYVFEL-DDKTNSDDRV--------------FEKDGVKLVVDNISYD 124
Query: 109 TLLGTEMDYVENKLSSEFVFN-NPNIKGTCGCGESFSV 145
+ G +DYVE + S FV + NP+ G C C SF V
Sbjct: 125 FVKGATVDYVEELIRSAFVVSTNPSAVGGCSCKSSFMV 162
>gnl|CDD|200593 cd10971, CE4_DAC_u2_5s, Putative catalytic NodB homology domain
of uncharacterized prokaryotic polysaccharide
deacetylases which consist of a 5-stranded beta/alpha
barrel. This family contains many uncharacterized
prokaryotic polysaccharide deacetylases. Although their
biological functions remain unknown, all members of
this family are predicted to contain a conserved domain
with a 5-stranded beta/alpha barrel, which is similar
to the catalytic NodB homology domain of rhizobial
NodB-like proteins, belonging to the larger
carbohydrate esterase 4 (CE4) superfamily.
Length = 198
Score = 26.1 bits (58), Expect = 6.4
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 29 HGLLKINKIHCIIFI 43
H +L +NKIH I+FI
Sbjct: 40 HKVLDVNKIHFILFI 54
>gnl|CDD|214855 smart00851, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS)
where it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also
includes inosicase. The known structures in this family
show a common phosphate binding site.
Length = 91
Score = 25.1 bits (56), Expect = 6.5
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 21 LSDDRTQIHGLLKINKIHCIIFISS 45
+ QI L+K +I +I
Sbjct: 41 VHGGIPQILDLIKNGEIDLVINTLY 65
>gnl|CDD|165199 PHA02865, PHA02865, MHC-like TNF binding protein; Provisional.
Length = 338
Score = 26.0 bits (57), Expect = 8.2
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 35 NKIHCIIFISSQAGLKVGVQQRGCNGLSYTLNYAKDKEK--MDEE 77
N+I C++F S+ ++ GCNG Y D+E DEE
Sbjct: 294 NQIVCVVFHSTLEP-QIYRCSEGCNGPLPDHQYRGDEEGDEEDEE 337
>gnl|CDD|239306 cd03008, TryX_like_RdCVF, Tryparedoxin (TryX)-like family,
Rod-derived cone viability factor (RdCVF) subfamily;
RdCVF is a thioredoxin (TRX)-like protein specifically
expressed in photoreceptors. RdCVF was isolated and
identified as a factor that supports cone survival in
retinal cultures. Cone photoreceptor loss is responsible
for the visual handicap resulting from the inherited
disease, retinitis pigmentosa. RdCVF shows 33%
similarity to TRX but does not exhibit any detectable
thiol oxidoreductase activity.
Length = 146
Score = 25.5 bits (56), Expect = 9.7
Identities = 14/40 (35%), Positives = 19/40 (47%)
Query: 85 WALILTCFFHVSGVRIFIDRKAQLTLLGTEMDYVENKLSS 124
+A L FF ++DR AQL L+ MD E + S
Sbjct: 43 FAPKLKDFFVRLTDEFYVDRSAQLALVYVSMDQSEQQQES 82
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
0.324 0.139 0.422
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,177,274
Number of extensions: 623190
Number of successful extensions: 443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 19
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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: 41 (22.0 bits)
S2: 54 (24.4 bits)