RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy962
(155 letters)
>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 = 190 bits (485), Expect = 2e-63
Identities = 89/145 (61%), Positives = 101/145 (69%), Gaps = 4/145 (2%)
Query: 5 KAVCVLNNEP--VKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNGCTSAG 62
AV VL V GT+ FTQ+ V +TGE+ GL G HGFHIHEFGD TNGCTSAG
Sbjct: 2 SAVAVLKGPDGKVVGTVTFTQQ--SGGVTITGELSGLTPGLHGFHIHEFGDCTNGCTSAG 59
Query: 63 PHFNPLGKDHGAPSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHA 122
HFNP GK HG P+D RH GDLGNIVA + VA V + D +ISL G N+I+GR+LVVHA
Sbjct: 60 GHFNPFGKKHGGPNDEGRHAGDLGNIVADKDGVATVSVLDPLISLKGGNSIIGRSLVVHA 119
Query: 123 DPDDLGKGGHELSKTTGNAGARIAC 147
DDLGKG ELS TGNAG R+AC
Sbjct: 120 GQDDLGKGPDELSGGTGNAGVRVAC 144
>gnl|CDD|166027 PLN02386, PLN02386, superoxide dismutase [Cu-Zn].
Length = 152
Score = 190 bits (484), Expect = 4e-63
Identities = 98/150 (65%), Positives = 113/150 (75%), Gaps = 2/150 (1%)
Query: 4 IKAVCVLN-NEPVKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNGCTSAG 62
+KAV VLN +E VKGTIFFTQE D P VTG + GL+ G HGFH+H GD TNGC S G
Sbjct: 2 VKAVAVLNSSEGVKGTIFFTQE-GDGPTTVTGSLSGLKPGLHGFHVHALGDTTNGCMSTG 60
Query: 63 PHFNPLGKDHGAPSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHA 122
PHFNP GK+HGAP D +RH GDLGN+ + A I D I LTG N+IVGR +VVHA
Sbjct: 61 PHFNPAGKEHGAPEDENRHAGDLGNVTVGDDGTATFTIVDKQIPLTGPNSIVGRAVVVHA 120
Query: 123 DPDDLGKGGHELSKTTGNAGARIACGVIGI 152
DPDDLGKGGHELSK+TGNAG R+ACG+IG+
Sbjct: 121 DPDDLGKGGHELSKSTGNAGGRVACGIIGL 150
>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 = 180 bits (459), Expect = 2e-59
Identities = 84/147 (57%), Positives = 100/147 (68%), Gaps = 9/147 (6%)
Query: 6 AVCVL--NNEPVKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNGCTSAGP 63
AV VL V GT+ FTQ V VT ++ GL G HGFHIHEFGD + GCTSAG
Sbjct: 1 AVAVLKGAGGKVVGTVTFTQVG-GGGVLVTVDLSGLPPGKHGFHIHEFGDCSPGCTSAGG 59
Query: 64 HFNPLGKDHGAPSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHAD 123
HFNP GK HG P+D RH GDLGNIV A+ VAKVEI D ++L+G ++I+GR+LV+HA
Sbjct: 60 HFNPDGKKHGGPNDEGRHAGDLGNIVVDADGVAKVEIVDDRVTLSGGDSIIGRSLVIHAG 119
Query: 124 PDDLGKGGHELSKTTGNAGARIACGVI 150
DDL S+ TGNAGAR+ACGVI
Sbjct: 120 EDDL------KSQPTGNAGARLACGVI 140
>gnl|CDD|178248 PLN02642, PLN02642, copper, zinc superoxide dismutase.
Length = 164
Score = 158 bits (400), Expect = 3e-50
Identities = 81/141 (57%), Positives = 107/141 (75%), Gaps = 1/141 (0%)
Query: 15 VKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNGCTSAGPHFNPLGKDHGA 74
V+G + F Q+ + VTG+I GL G HGFHIH FGD TNGC S GPHFNPL + HG
Sbjct: 20 VRGCLQFVQDIFGT-THVTGKISGLSPGFHGFHIHSFGDTTNGCISTGPHFNPLNRVHGP 78
Query: 75 PSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHADPDDLGKGGHEL 134
P++ +RH GDLGNI+A ++ VA++ I+D I L+G +I+GR +VVHADPDDLGKGGH+L
Sbjct: 79 PNEEERHAGDLGNILAGSDGVAEILIKDKHIPLSGQYSILGRAVVVHADPDDLGKGGHKL 138
Query: 135 SKTTGNAGARIACGVIGIAKA 155
SK+TGNAG+R+ CG+IG+ +
Sbjct: 139 SKSTGNAGSRVGCGIIGLQSS 159
>gnl|CDD|224943 COG2032, SodC, Cu/Zn superoxide dismutase [Inorganic ion transport
and metabolism].
Length = 179
Score = 122 bits (308), Expect = 5e-36
Identities = 53/147 (36%), Positives = 68/147 (46%), Gaps = 13/147 (8%)
Query: 12 NEPVKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNG------CTSAGPHF 65
GT+ T+ + T + GL G HGFHIHE G T SAG HF
Sbjct: 39 TGKDVGTVTITE--TGYGLLFTPALGGLPPGEHGFHIHEKGSCTPKDGKPVDFLSAGGHF 96
Query: 66 NP-LGKDHGAPSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHADP 124
+P K HG P+ H GDL N+ A+ A + + + L G + GR LV+HA
Sbjct: 97 DPQNTKKHGGPNADGGHAGDLPNLFVNADGKATLPVLAPRLKLKGLLEVKGRALVIHAGG 156
Query: 125 DDLGKGGHELSKTTGNAGARIACGVIG 151
DD + G AGAR+ACGVI
Sbjct: 157 DDYSTQ----PEPLGGAGARVACGVIK 179
>gnl|CDD|215516 PLN02957, PLN02957, copper, zinc superoxide dismutase.
Length = 238
Score = 52.1 bits (125), Expect = 1e-08
Identities = 34/117 (29%), Positives = 53/117 (45%), Gaps = 9/117 (7%)
Query: 15 VKGTIFFTQEHADSPVKVTGEIQGLEEGNHGFHIHEFGDNTNGCTSAGPHFNPLGKDHGA 74
+ G + F Q + ++ GL G HG+ I+E+GD T G S G +NP D
Sbjct: 92 IFGVVRFAQVSMEL-ARIEAAFSGLSPGTHGWSINEYGDLTRGAASTGKVYNPSDDD--- 147
Query: 75 PSDADRHVGDLGNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHADPDDLGKGG 131
+ +GDLG + A N A + + +++GR+L V+A D G G
Sbjct: 148 --TDEEPLGDLGTLEADENGEATFSGTKEKLKVW---DLIGRSLAVYATADKSGPGI 199
>gnl|CDD|182357 PRK10290, PRK10290, superoxide dismutase; Provisional.
Length = 173
Score = 48.7 bits (116), Expect = 7e-08
Identities = 36/134 (26%), Positives = 58/134 (43%), Gaps = 18/134 (13%)
Query: 27 DSPVKVTGEIQGLEEGNHGFHIHEFGD--------NTNGCTSAGPHFNPLGKDHGAPSDA 78
D ++ + +++ L G HGFHIH G + +AG H +P +
Sbjct: 47 DKGLEFSPDLKALPPGEHGFHIHAKGSCQPATKDGKASAAEAAGGHLDPQNTGKHEGPEG 106
Query: 79 DRHVGDLGNIVATANKVAKVEIEDSIIS--LTGANNIVGRTLVVHADPDDLGKGGHELSK 136
H+GDL +V + A D +I+ L + + + L+VH D++ + K
Sbjct: 107 AGHLGDLPALVVNNDGKA----TDPVIAPRLKSLDEVKDKALMVHVGGDNMS----DQPK 158
Query: 137 TTGNAGARIACGVI 150
G G R ACGVI
Sbjct: 159 PLGGGGERYACGVI 172
>gnl|CDD|185286 PRK15388, PRK15388, Cu/Zn superoxide dismutase; Provisional.
Length = 177
Score = 44.7 bits (105), Expect = 2e-06
Identities = 38/125 (30%), Positives = 53/125 (42%), Gaps = 17/125 (13%)
Query: 36 IQGLEEGNHGFHIHE----FGDNTNG----CTSAGPHFNPLGK--DHGAPSDADRHVGDL 85
+ GL G HGFH+H +G AG H +P K H P + H+GDL
Sbjct: 58 LNGLTPGIHGFHVHTNPSCMPGMKDGKEVPALMAGGHLDP-EKTGKHLGPYNDKGHLGDL 116
Query: 86 GNIVATANKVAKVEIEDSIISLTGANNIVGRTLVVHADPDDLGKGGHELSKTTGNAGARI 145
+V A+ A + L + + G +L++H D+ L G GAR
Sbjct: 117 PGLVVNADGTATYPLLAP--RLKSLSELKGHSLMIHKGGDNYSDKPAPL----GGGGARF 170
Query: 146 ACGVI 150
ACGVI
Sbjct: 171 ACGVI 175
>gnl|CDD|179479 PRK02821, PRK02821, hypothetical protein; Provisional.
Length = 77
Score = 27.3 bits (61), Expect = 1.2
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 115 GRTLVVHADPDDLGK 129
GRTL V PDDLGK
Sbjct: 30 GRTLEVRVHPDDLGK 44
>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 = 28.1 bits (63), Expect = 1.7
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 11/69 (15%)
Query: 9 VLNNEPVKGTIFFTQEHADSPVKVTGEIQ------GLEEGNHGF-HIH----EFGDNTNG 57
+L E VK T+F HAD K ++ G+ NH + H + F NT+
Sbjct: 21 ILKAENVKATVFLVGFHADGGDKAKEALKLYLDNPGIILANHSYTHANNNYTLFYSNTDK 80
Query: 58 CTSAGPHFN 66
Sbjct: 81 VVEDILKAQ 89
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 28.2 bits (63), Expect = 1.8
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 9/48 (18%)
Query: 107 LTGANNIVGRTLV---------VHADPDDLGKGGHELSKTTGNAGARI 145
+TGA +G LV VHA D K H LSK R+
Sbjct: 15 VTGATGYIGSWLVKLLLQRGYTVHATLRDPAKSLHLLSKWKEGDRLRL 62
>gnl|CDD|240542 cd13137, MATE_NorM_like, Subfamily of the multidrug and toxic
compound extrusion (MATE)-like proteins similar to
Thermotoga marina NorM. The integral membrane proteins
from the MATE family are involved in exporting
metabolites across the cell membrane and are responsible
for multidrug resistance (MDR) in many bacteria and
animals. A number of family members are involved in the
synthesis of peptidoglycan components in bacteria.
Length = 432
Score = 27.9 bits (63), Expect = 2.1
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 82 VGDLGNIVATANKVAKVEIEDSIISLTG-ANNIVGRTLVVHADPDDLGKGGHELSKTTGN 140
V G A ++ + IE S+ + G ++ TLV LG G + ++ G
Sbjct: 253 VASYGTAALAAYQIG-LRIE-SLAFMPGFGFSMAASTLVGQN----LGAGDPDEARRYGK 306
Query: 141 AGARIACGVIGI 152
R+ +G+
Sbjct: 307 RALRLGVLFMGL 318
>gnl|CDD|236342 PRK08862, PRK08862, short chain dehydrogenase; Provisional.
Length = 227
Score = 27.4 bits (61), Expect = 3.2
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 99 EIEDSIISLTGANNIVGRTLVVH 121
+I+ SII +T A +++GRT+ H
Sbjct: 2 DIKSSIILITSAGSVLGRTISCH 24
>gnl|CDD|182393 PRK10343, PRK10343, RNA-binding protein YhbY; Provisional.
Length = 97
Score = 25.8 bits (56), Expect = 5.4
Identities = 13/35 (37%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 89 VATANKVAKVEIEDSIISLTGANN--IVGRTLVVH 121
+AT ++ K I ++I+ TGA N ++G+TLV++
Sbjct: 51 IATEDRETKTLIVEAIVRETGACNVQVIGKTLVLY 85
>gnl|CDD|215481 PLN02889, PLN02889, oxo-acid-lyase/anthranilate synthase.
Length = 918
Score = 27.1 bits (60), Expect = 5.4
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 112 NIVGRTLVVHADPDDLGKGG 131
NIV RT+V+H +G GG
Sbjct: 863 NIVIRTVVIHEGEASIGAGG 882
>gnl|CDD|232908 TIGR00292, TIGR00292, thiazole biosynthesis enzyme. This enzyme is
involved in the biosynthesis of the thiamine precursor
thiazole, and is repressed by thiamine. This family
includes c-thi1, a Citrus gene induced during natural
and ethylene induced fruit maturation and is highly
homologous to plant and yeast thi genes involved in
thiamine biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Thiamine].
Length = 254
Score = 26.0 bits (57), Expect = 8.8
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 61 AGPHFNPLGKDHGAPSDADRHVGDLGNIVATANKVAKVEIEDSIISLTG 109
AG H +PL + DA H ++ + A K+ +ED + L G
Sbjct: 148 AGLHVDPLTQRSRVVVDATGHDAEIVAVCAK-----KIVLEDQVPKLGG 191
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
0.314 0.135 0.403
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,782,730
Number of extensions: 695283
Number of successful extensions: 402
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 20
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
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: 42 (21.9 bits)
S2: 55 (24.9 bits)