RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy967
(82 letters)
>gnl|CDD|166027 PLN02386, PLN02386, superoxide dismutase [Cu-Zn].
Length = 152
Score = 43.7 bits (103), Expect = 7e-07
Identities = 24/38 (63%), Positives = 28/38 (73%), Gaps = 2/38 (5%)
Query: 4 IKAVCVLN-NEPVKGTIFFTQEHADSPVKVTGEIQGLE 40
+KAV VLN +E VKGTIFFTQE D P VTG + GL+
Sbjct: 2 VKAVAVLNSSEGVKGTIFFTQE-GDGPTTVTGSLSGLK 38
>gnl|CDD|238186 cd00305, Cu-Zn_Superoxide_Dismutase, Copper/zinc superoxide
dismutase (SOD). superoxide dismutases catalyse the
conversion of superoxide radicals to molecular oxygen.
Three evolutionarily distinct families of SODs are
known, of which the copper/zinc-binding family is one.
Defects in the human SOD1 gene causes familial
amyotrophic lateral sclerosis (Lou Gehrig's disease).
Cytoplasmic and periplasmic SODs exist as dimers,
whereas chloroplastic and extracellular enzymes exist
as tetramers. Structure supports independent functional
evolution in prokaryotes (P-class) and eukaryotes
(E-class) [PMID:.8176730].
Length = 144
Score = 40.3 bits (95), Expect = 9e-06
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 5 KAVCVLNNEP--VKGTIFFTQEHADSPVKVTGEIQGLEE 41
AV VL V GT+ FTQ+ V +TGE+ GL
Sbjct: 2 SAVAVLKGPDGKVVGTVTFTQQ--SGGVTITGELSGLTP 38
>gnl|CDD|215700 pfam00080, Sod_Cu, Copper/zinc superoxide dismutase (SODC).
superoxide dismutases (SODs) catalyze the conversion of
superoxide radicals to hydrogen peroxide and molecular
oxygen. Three evolutionarily distinct families of SODs
are known, of which the copper/zinc-binding family is
one. Defects in the human SOD1 gene cause familial
amyotrophic lateral sclerosis (Lou Gehrig's disease).
Structure is an eight-stranded beta sandwich, similar
to the immunoglobulin fold.
Length = 140
Score = 37.2 bits (87), Expect = 1e-04
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 6 AVCVL--NNEPVKGTIFFTQEHADSPVKVTGEIQGLEE 41
AV VL V GT+ FTQ V VT ++ GL
Sbjct: 1 AVAVLKGAGGKVVGTVTFTQVG-GGGVLVTVDLSGLPP 37
>gnl|CDD|183580 PRK12541, PRK12541, RNA polymerase sigma factor; Provisional.
Length = 161
Score = 26.8 bits (59), Expect = 1.1
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 46 NLMNFTVFRAI--LDYYKGQVIK 66
+LM T +R + +DYYKG+ I+
Sbjct: 34 DLMQETFYRMLVHIDYYKGEEIR 56
>gnl|CDD|184514 PRK14110, PRK14110, F0F1 ATP synthase subunit gamma; Provisional.
Length = 291
Score = 25.9 bits (57), Expect = 2.7
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 15/68 (22%)
Query: 6 AVCVLNNEPVKGTIFFTQEHADSPVKVTGEIQGLEEDGGLNL---------------MNF 50
AV ++NNE + + + P +V + + L+E N+ +N+
Sbjct: 170 AVYLINNEMITRATYKPKVRKFLPFEVEAQEKKLDELSVYNIEVSEEEFLDKLLQLYLNY 229
Query: 51 TVFRAILD 58
++RA+++
Sbjct: 230 QLYRALVE 237
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 25.4 bits (56), Expect = 4.1
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 52 VFRAILDYYKGQVIKCPPSVSERAGAL 78
+FR I Y K PP+ +E+ A+
Sbjct: 231 LFRQIEQYLTTGKYKPPPTFAEKLDAI 257
>gnl|CDD|200570 cd10946, CE4_Mll8295_like, Putative catalytic NodB homology
domain of uncharacterized Mll8295 protein encoded from
Rhizobium loti and its bacterial homologs. This family
is represented by a putative polysaccharide deacetylase
Mll8295 encoded from Rhizobium loti. Although its
biological function still remains unknown, Mll8295
shows high sequence homology to the catalytic domain of
Streptococcus pneumoniae polysaccharide deacetylase
PgdA (SpPgdA), which is an extracellular
metal-dependent polysaccharide deacetylase with
de-N-acetylase activity toward a hexamer of
chitooligosaccharide N-acetylglucosamine, but not
shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. Both Mll8295 and SpPgdA
belong to the carbohydrate esterase 4 (CE4)
superfamily. This family also includes many
uncharacterized bacterial polysaccharide deacetylases.
Length = 217
Score = 25.1 bits (55), Expect = 4.9
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 9 VLNNEPVKGTIFFTQEHADSPVKVTGEIQGLEEDGGLNLMNFT 51
+L E VK T+F HAD K ++ ++ G+ L N +
Sbjct: 21 ILKAENVKATVFLVGFHADGGDKAKEALKLYLDNPGIILANHS 63
>gnl|CDD|216943 pfam02237, BPL_C, Biotin protein ligase C terminal domain. The
function of this structural domain is unknown. It is
found to the C terminus of the biotin protein ligase
catalytic domain pfam01317.
Length = 47
Score = 23.6 bits (52), Expect = 5.4
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 31 KVTGEIQGLEEDGGL 45
KV G G+++DG L
Sbjct: 14 KVEGIAVGIDDDGRL 28
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
0.317 0.137 0.402
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,097,686
Number of extensions: 324224
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 8
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)