RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 039703
(284 letters)
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 173 bits (441), Expect = 5e-53
Identities = 76/210 (36%), Positives = 111/210 (52%), Gaps = 13/210 (6%)
Query: 72 ALRHLRDKDPLLATLIDAHRPPTFESSR--------SPFLSLAKSILYQQLAYKAAKSIY 123
ALR L D DP LA +IDA P + PF +L ++IL QQ++ AA I+
Sbjct: 68 ALRRLFDLDPDLAPIIDALGPLPLLRAPGLRLPLAPDPFEALVRAILSQQVSVAAAAKIW 127
Query: 124 TRFVALFNGEDNIL-----PDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDES 178
R V+L+ I P+ + A + LR G+S RKA Y+ LA +G L
Sbjct: 128 ARLVSLYGNALEIYHSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSE 187
Query: 179 IVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPG 238
+ + D + LT++KGIG W+ MF++F L +PDV P DLG+R+ ++ LY L P
Sbjct: 188 LKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPT 247
Query: 239 ALKMEEVCEKWKPYRSVGSWYMWRLMEAKG 268
++ E+ E+W PYRS + Y+WR A
Sbjct: 248 EKEVRELAERWGPYRSYAALYLWRYARATT 277
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 118 bits (298), Expect = 3e-33
Identities = 40/148 (27%), Positives = 68/148 (45%), Gaps = 11/148 (7%)
Query: 108 SILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI----GVSYRKASYLR 163
+IL QQ + KAA I R + P+ + ++LRE+ G RKA Y++
Sbjct: 3 AILSQQTSDKAANKITKRLFERYGFPT---PEDLAEADEEELRELIKGLGFYRRKAKYIK 59
Query: 164 DLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGV 223
+LA +G L + + L ++ G+G W+ ++F+L +PDV P D V
Sbjct: 60 ELARILVEGYLGLVPLDLEELE----ALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHV 115
Query: 224 RKGLQVLYGLKELPGALKMEEVCEKWKP 251
R+ + L + P ++E E+ P
Sbjct: 116 RRVAKRLGLIDTKPPKKEVERELEELWP 143
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 108 bits (273), Expect = 2e-29
Identities = 48/167 (28%), Positives = 78/167 (46%), Gaps = 15/167 (8%)
Query: 102 FLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVS---YRK 158
F L IL QQ KA Y R + P+A+ A ++LRE+ S RK
Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG----PTPEALAAADEEELRELIRSLGYRRK 56
Query: 159 ASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPV 218
A YL++LA +G +DD + L ++ G+G + ++ ++F+L PD PV
Sbjct: 57 AKYLKELARAIVEGFGGLV----LDDPDAREELLALPGVGRKTANVVLLFALG-PDAFPV 111
Query: 219 GDLGVRKGLQVLYGLKELPGALKMEEVCEKW--KPYRSVGSWYMWRL 263
D VR+ L+ L + + ++EE+ E+ KPY + + L
Sbjct: 112 -DTHVRRVLKRLGLIPKKKTPEELEELLEELLPKPYWGEANQALMDL 157
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 72.3 bits (178), Expect = 1e-15
Identities = 33/157 (21%), Positives = 61/157 (38%), Gaps = 21/157 (13%)
Query: 112 QQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVSYRKASYLRDLAE 167
QQ + R F P+ + A ++L R +G RKA YL +LA
Sbjct: 3 QQTTDERVNKATERLFEKFPT-----PEDLAAADEEELEELIRGLGFYRRKARYLIELAR 57
Query: 168 KYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGL 227
++ + DD + L + G+G + + + F+L KP D V +
Sbjct: 58 I----LVEEYGGEVPDD---REELLKLPGVGRKTANAVLSFALGKP--FIPVDTHVLRIA 108
Query: 228 QVLYGLKELPGALKMEEVCEKWKP---YRSVGSWYMW 261
+ L + + ++E++ EK P +R + +
Sbjct: 109 KRLGLVDKKSTPEEVEKLLEKLLPEEDWRELNLLLID 145
>gnl|CDD|236671 PRK10308, PRK10308, 3-methyl-adenine DNA glycosylase II;
Provisional.
Length = 283
Score = 38.2 bits (89), Expect = 0.003
Identities = 34/127 (26%), Positives = 55/127 (43%), Gaps = 15/127 (11%)
Query: 138 PDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGI 197
P+ + A PQ L+ +G+ ++A L LA +G L + D K L + GI
Sbjct: 158 PERLAAADPQALKALGMPLKRAEALIHLANAALEGTL--PLTIPGDVEQAMKTLQTFPGI 215
Query: 198 GAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE-LPG--ALKMEEVCEKWKPYRS 254
G W+ + F + DV D Y +K+ PG ++ E+WKP+RS
Sbjct: 216 GRWTANYFALRGWQAKDVFLPDD----------YLIKQRFPGMTPAQIRRYAERWKPWRS 265
Query: 255 VGSWYMW 261
++W
Sbjct: 266 YALLHIW 272
>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg). All proteins
in this family for which functions are known are
8-oxo-guanaine DNA glycosylases that function in base
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). This family is distantly realted
to the Nth-MutY superfamily [DNA metabolism, DNA
replication, recombination, and repair].
Length = 310
Score = 37.6 bits (87), Expect = 0.004
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 5/87 (5%)
Query: 149 LREIGVSYRKASYLRDLAEKYT---DGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMF 205
LR++G+ YR A Y+R+ A G + I + L + G+G
Sbjct: 178 LRKLGLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCI 236
Query: 206 MIFSLHKPDVLPVGDLGVRKGLQVLYG 232
+ L KP +PV D+ V + Y
Sbjct: 237 CLMGLDKPQAVPV-DVHVWRIANRDYP 262
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 32.0 bits (74), Expect = 0.36
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 15/49 (30%)
Query: 125 RFVALFNGEDNI---------------LPDAVLAVSPQQLREIGVSYRK 158
R V L G D+I L A V +QLRE+G+ RK
Sbjct: 538 RLVMLLAGADSIRDVIAFPKTQSAQDLLTGAPSPVDEKQLRELGIRLRK 586
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 31.0 bits (71), Expect = 0.77
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 15/49 (30%)
Query: 125 RFVALFNGEDNI---------------LPDAVLAVSPQQLREIGVSYRK 158
R V L G ++I L +A V +QL+E+ + R
Sbjct: 536 RLVMLLTGAESIRDVIAFPKTQQAADLLTNAPSEVDEKQLKELSIKVRP 584
>gnl|CDD|187864 cd09733, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily
protein Cas6. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas6 is an endoribonuclease that generates crRNAs,
predicted subunit of Cascade complex; RAMP superfamily
protein; Possesses double RRM/ferredoxin fold; also
known as AF0072 family.
Length = 193
Score = 28.0 bits (63), Expect = 3.9
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 118 AAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKA 159
A ++ R V + + +A L + +QL +G+ +K
Sbjct: 101 PAPVLFARIVVIKGAME---EEAFLQAAQRQLEALGIQAKKM 139
>gnl|CDD|118095 pfam09559, Cas6, Cas6 Crispr. The Cas6 Crispr family of proteins
averaging 140 residues are characterized by having a
GhGxxxxxGhG motif, where h indicates a hydrophobic
residue, at the C-terminus. The CRISPR-Cas system is
possibly a mechanism of defence against invading
pathogens and plasmids that functions analogously to the
RNA interference (RNAi) systems in eukaryotes.
Length = 195
Score = 28.0 bits (63), Expect = 3.9
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 118 AAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKA 159
A ++ R V + + +A L + +QL +G+ +K
Sbjct: 101 PAPVLFARIVVIKGAME---EEAFLQAAQRQLEALGIQAKKM 139
>gnl|CDD|193546 cd05670, M20_Acy1_YkuR_like, M20 Peptidase Aminoacyclase-1
YkuR-like proteins, including YkuR and Ama/HipO/HyuC
proteins. Peptidase M20 family, Aminoacyclase-1
YkuR-like subfamily including YkuR and Ama/HipO/HyuC
proteins, most of which have not been well characterized
to date. N-terminal acetylation of proteins is a
widespread and highly conserved process that is involved
in the protection and stability of proteins. Several
types of aminoacylases can be distinguished on the basis
of substrate specificity; substrates include
indoleacetic acid (IAA) N-conjugates of amino acids,
N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1
breaks down cytosolic aliphatic N-acyl-alpha-amino acids
(except L-aspartate), especially N-acetyl-methionine and
acetyl-glutamate into L-amino acids and an acyl group.
However, ACY1 can also catalyze the reverse reaction,
the synthesis of acetylated amino acids. ACY1 may also
play a role in xenobiotic bioactivation as well as in
the inter-organ processing of amino acid-conjugated
xenobiotic derivatives
(S-substituted-N-acetyl-L-cysteine). ACY1 appears to
physically interact with Sphingosine kinase type 1
(SphK1) and may influence its physiological functions;
SphK1 and its product sphingosine-1-phosphate have been
shown to promote cell growth and inhibit apoptosis of
tumor cells. Strong expression of the human gene and its
mouse ortholog Acy1 in brain, liver, and kidney suggest
a role of the enzyme in amino acid metabolism of these
organs.
Length = 367
Score = 28.4 bits (64), Expect = 4.4
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 206 MIFSLH-KPDVLPVGDLGVRKGL 227
++LH PD LPVG + R G
Sbjct: 145 EFYALHVAPD-LPVGTIATRPGT 166
>gnl|CDD|179892 PRK04922, tolB, translocation protein TolB; Provisional.
Length = 433
Score = 28.5 bits (64), Expect = 4.5
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 88 DAHRPPTFESSRSPFLSLAKSILYQQLAY 116
D + P T S P LS A S ++LAY
Sbjct: 192 DGYNPQTILRSAEPILSPAWSPDGKKLAY 220
>gnl|CDD|232824 TIGR00099, Cof-subfamily, Cof subfamily of IIB subfamily of
haloacid dehalogenase superfamily. This subfamily of
sequences falls within the Class-IIB subfamily
(TIGR01484) of the Haloacid Dehalogenase superfamily of
aspartate-nucleophile hydrolases. The use of the name
"Cof" as an identifier here is arbitrary and refers to
the E. coli Cof protein. This subfamily is notable for
the large number of recent paralogs in many species.
Listeria, for instance, has 12, Clostridium, Lactococcus
and Streptococcus pneumoniae have 8 each, Enterococcus
and Salmonella have 7 each, and Bacillus subtilus,
Mycoplasma, Staphylococcus and E. coli have 6 each. This
high degree of gene duplication is limited to the gamma
proteobacteria and low-GC gram positive lineages. The
profusion of genes in this subfamily is not coupled with
a high degree of divergence, so it is impossible to
determine an accurate phylogeny at the equivalog level.
Considering the relationship of this subfamily to the
other known members of the HAD-IIB subfamily
(TIGR01484), sucrose and trehalose phosphatases and
phosphomannomutase, it seems a reasonable hypothesis
that these enzymes act on phosphorylated sugars.
Possibly the diversification of genes in this subfamily
represents the diverse sugars and polysaccharides that
various bacteria find in their biological niches. The
members of this subfamily are restricted almost
exclusively to bacteria (one sequences from S. pombe
scores above trusted, while another is between trusted
and noise). It is notable that no archaea are found in
this group, the closest relations to the archaea found
here being two Deinococcus sequences [Unknown function,
Enzymes of unknown specificity].
Length = 256
Score = 27.6 bits (62), Expect = 7.3
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 124 TRFVALFNGEDNILPDAVLAVSPQQLREI---GVSYRKASYLRDLAEKYTDGILSDESIV 180
+ N + +V++ P + EI GVS K S L+ LAE GI ++ I
Sbjct: 155 DLLIEALNKLELEENVSVVSSGPYSI-EITAKGVS--KGSALQSLAEAL--GISLEDVIA 209
Query: 181 ---EMDDVTMFKM 190
M+D+ M +
Sbjct: 210 FGDGMNDIEMLEA 222
>gnl|CDD|99794 cd06197, FNR_like_2, FAD/NAD(P) binding domain of ferredoxin
reductase-like proteins. Ferredoxin reductase (FNR) was
intially identified as a chloroplast reductase activity,
catalyzing the electron transfer from reduced
iron-sulfur protein ferredoxin to NADP+ as the final
step in the electron transport mechanism of photosystem
I. FNR transfers electrons from reduced ferredoxin to
FAD (forming FADH2 via a semiquinone intermediate) and
then transfers a hydride ion to convert NADP+ to NADPH.
FNR has since been shown to utilize a variety of
electron acceptors and donors and have a variety of
physiological functions in a variety of organisms
including nitrogen assimilation, dinitrogen fixation,
steroid hydroxylation, fatty acid metabolism, oxygenase
activity, and methane assimilation. FNR has an
NAD(P)-binding sub-domain of the alpha/beta class and a
discrete (usually N-terminal) flavin sub-domain which
varies in orientation with respect to the NAD(P)
binding domain. The N-terminal moeity may contain a
flavin prosthetic group (as in flavoenzymes) or use
flavin as a substrate. Because flavins such as FAD can
exist in oxidized, semiquinone (one-electron reduced),
or fully reduced hydroquinone forms, FNR can interact
with one and two electron carriers. FNR has a strong
preference for NADP(H) vs NAD(H).
Length = 220
Score = 27.4 bits (61), Expect = 8.7
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 63 LTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSP 101
L F E+D H+ D DP ++ TF S +P
Sbjct: 34 LDFSSELDSGYSHMADDDP---QSLNDDFVRTFTVSSAP 69
>gnl|CDD|233292 TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit. This
model describes the ATP synthase gamma subunit in
bacteria and its equivalents in organelles, namely,
mitochondria and chloroplast. F1/F0-ATP synthase is a
multisubunit, membrane associated enzyme found in
bacteria and organelles of higher eukaryotes, namely,
mitochondria and chloroplast. This enzyme is principally
involed in the synthesis of ATP from ADP and inorganic
phosphate by coupling the energy derived from the proton
electrochemical gradient across the biological membrane.
A brief description of this multisubunit enzyme complex:
F1 and F0 represent two major clusters of subunits. The
gamma subunit is the part of F1 cluster. Surrounding the
gamma subunit in a cylinder-like structure are three
alpha and three subunits in an alternating fashion. This
is the central catalytic unit whose different
conformations permit the binding of ADP and inorganic
phosphate and release of ATP [Energy metabolism,
ATP-proton motive force interconversion].
Length = 286
Score = 27.3 bits (61), Expect = 9.4
Identities = 21/103 (20%), Positives = 40/103 (38%), Gaps = 15/103 (14%)
Query: 76 LRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSIL--YQQLAYKAAKSIYTRFVALFNGE 133
R D ++A++ PTFE + A +L + + +Y +FV++ + E
Sbjct: 126 KRRGDNIVASVTGLSDQPTFEEASGI----ADKLLDAFDSGEFDEVYIVYNKFVSVISQE 181
Query: 134 DNILPDAVLAVSPQQLREIGVSYRKASY-------LRDLAEKY 169
+ +L +S Q E + + L DL +Y
Sbjct: 182 PTVKQ--LLPLSEQGPDEGFKFSQDYIFEPDEEEILDDLLPRY 222
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
0.318 0.133 0.386
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,514,692
Number of extensions: 1392364
Number of successful extensions: 1170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1156
Number of HSP's successfully gapped: 27
Length of query: 284
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 188
Effective length of database: 6,679,618
Effective search space: 1255768184
Effective search space used: 1255768184
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 (21.7 bits)
S2: 58 (25.9 bits)