RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5261
(267 letters)
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 74.2 bits (182), Expect = 4e-15
Identities = 46/165 (27%), Positives = 58/165 (35%), Gaps = 30/165 (18%)
Query: 119 EFDFVFNCAGLGAQALCR-----DRKLTPIRGQVIKVWAP--------WLSHFYYLDYDV 165
E D V AG A L L P+RGQ + P D
Sbjct: 200 EADKVVLAAGAWAGELAATLGELPLPLRPVRGQALTTEPPEGLLADGLAPVVLVVDDGGG 259
Query: 166 YVIPHSNGAVTLGGC-RHYDSYSRDISRHDT--ASILERCYSLLPRLEEAPVLYEWCGLR 222
Y+ P +G + +GG D R D A +L +LLP L +A + W GLR
Sbjct: 260 YIRPRGDGRLRVGGTDEEGGDDPSDPEREDLVIAELLRVARALLPGLADAGIEAAWAGLR 319
Query: 223 ----PHRSLVIH----------NYGHGGYGVTTAPGTSRYAVQLV 253
P VI GHGG+G T AP R L+
Sbjct: 320 PPTTPDGLPVIGRAAPLPNLYVATGHGGHGFTLAPALGRLLADLI 364
>gnl|CDD|233831 TIGR02352, thiamin_ThiO, glycine oxidase ThiO. This family
consists of the homotetrameric, FAD-dependent glycine
oxidase ThiO, from species such as Bacillus subtilis
that use glycine in thiamine biosynthesis. In general,
members of this family will not be found in species such
as E. coli that instead use tyrosine and the ThiH
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Thiamine].
Length = 337
Score = 66.2 bits (162), Expect = 2e-12
Identities = 38/154 (24%), Positives = 61/154 (39%), Gaps = 20/154 (12%)
Query: 119 EFDFVFNCAGLGAQALCRDRKLTPIRGQVIKVWAPWLSHFYYL------DYDVYVIPHSN 172
+ D V AG A L L P+RGQ +++ AP + VY++P +
Sbjct: 181 QADQVVLAAGAWAGELLPL-PLRPVRGQPLRLEAPAVPLLNRPLRAVVYGRRVYIVPRRD 239
Query: 173 GAVTLGGCRHYDSYSRDISRHDTASILERCYSLLPRLEEAPVLYEWCGLRP--------- 223
G + +G + + +L Y++LP L+EA +L W GLRP
Sbjct: 240 GRLVVGATMEESGFDTTPTLGGIKELLRDAYTILPALKEARLLETWAGLRPGTPDNLPYI 299
Query: 224 ----HRSLVIHNYGHGGYGVTTAPGTSRYAVQLV 253
++ GH G+ AP T+ L+
Sbjct: 300 GEHPEDRRLLIATGHYRNGILLAPATAEVIADLI 333
>gnl|CDD|237093 PRK12409, PRK12409, D-amino acid dehydrogenase small subunit;
Provisional.
Length = 410
Score = 41.2 bits (97), Expect = 4e-04
Identities = 53/173 (30%), Positives = 72/173 (41%), Gaps = 39/173 (22%)
Query: 116 LESEFDFVFNCAGLGAQALCR---DR-KLTPIRGQVIKVW---------APWLSHFYYLD 162
EFD V CAG+G++AL DR + P++G I V APW+S LD
Sbjct: 243 RTLEFDGVVVCAGVGSRALAAMLGDRVNVYPVKGYSITVNLDDEASRAAAPWVS---LLD 299
Query: 163 YDVYVIPHSNGAVTL--GGCRHYDSYSRDISRHDTASIL----ERCYSLLPRLEEAPVLY 216
++ GA G ++ Y+RDI R D L R + P + V+
Sbjct: 300 DSAKIVTSRLGADRFRVAGTAEFNGYNRDI-RADRIRPLVDWVRRNF---PDVSTRRVV- 354
Query: 217 EWCGLRP------------HRSLVIHNYGHGGYGVTTAPGTSRYAVQLVKQAL 257
W GLRP R V +N GHG G T + T+ Q+V Q L
Sbjct: 355 PWAGLRPMMPNMMPRVGRGRRPGVFYNTGHGHLGWTLSAATADLVAQVVAQKL 407
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 36.5 bits (85), Expect = 0.012
Identities = 34/141 (24%), Positives = 48/141 (34%), Gaps = 16/141 (11%)
Query: 94 AMKRVSKQGGKFRRGTVSSFSGLESEFDFVFNCAGLGAQAL--CRDRKLTPIRGQVIKVW 151
+ + + G + + +G V G A L L P+RGQV +
Sbjct: 156 EITSLERDGEGW---QLLDANGEVIAASVVVLANGAQAGQLAQTAHLPLRPVRGQVSHLP 212
Query: 152 A----PWLSHFYYLDYDVYVIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLLP 207
A L L YD Y+ P +NG +G + + D A LER LP
Sbjct: 213 ATEALSALKTV--LCYDGYLTPANNGEHCIGASYDRNDDDLALREADHAENLERLAECLP 270
Query: 208 RLEEA-----PVLYEWCGLRP 223
L A L G+R
Sbjct: 271 ALAWASEVDISALQGRVGVRC 291
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 36.5 bits (85), Expect = 0.012
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 26/72 (36%)
Query: 121 DFVFNCAGLGAQALCR------DRKLTPIRGQVIKVWAPWLSHFYYLDYD--------VY 166
FV N AGL A L + D K+ P+RG+ + LD + +Y
Sbjct: 201 KFVINAAGLYADPLAQMAGIPEDFKIFPVRGE-----------YLVLDNEVKALLRHKIY 249
Query: 167 VIPHSNGAVTLG 178
+P+ G LG
Sbjct: 250 PVPNP-GLPGLG 260
>gnl|CDD|227908 COG5621, COG5621, Predicted secreted hydrolase [General function
prediction only].
Length = 354
Score = 31.0 bits (70), Expect = 0.57
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 221 LRPHRSLVIHNYGHGGYGVTTAPGTSRYAVQLVKQALDPTSSLKSKL 267
L+ V+ G GY V +A G + Y L + + T S+ +
Sbjct: 171 LQATGPPVLQ--GDRGYSVKSALGQASYYYSLPRYEVSGTVSVDGET 215
>gnl|CDD|114274 pfam05543, Peptidase_C47, Staphopain peptidase C47. Staphopains
are one of four major families of proteinases secreted
by the Gram-positive Staphylococcus aureus. These
staphylococcal cysteine proteases are secreted as
preproenzymes that are proteolytically cleaved to
generate the mature enzyme.
Length = 174
Score = 29.5 bits (66), Expect = 1.1
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 146 QVIKVWAPWLSHFYYLDYDVYVIPHSNGAVTLGGCRHYDSYS 187
+VI +W PW + F D +IP SNG HY YS
Sbjct: 135 EVIIIWNPWDNGFMTQDAKSNIIPVSNG-------DHYQWYS 169
>gnl|CDD|146870 pfam04441, Pox_VERT_large, Poxvirus early transcription factor
(VETF), large subunit. The poxvirus early transcription
factor (VETF), in addition to the viral RNA polymerase,
is required for efficient transcription of early genes
in vitro. VETF is a heterodimeric protein that binds
specifically to early gene promoters. The heterodimer is
comprised of an 82 kDa (this family) subunit and a 70
kDa subunit.
Length = 700
Score = 30.1 bits (68), Expect = 1.4
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 3 FPVISVDASVQNEDGSRTLTLSQTKFSADGSTGKAMISTYQTSLLKNASIEN 54
FP I+ ++ +E+G LTL+ F DG +ST T+ KN +
Sbjct: 599 FPYITNIRTIISENG---LTLTTDGFYIDGELFTEKLSTKFTTFTKNITTSP 647
>gnl|CDD|173672 cd05581, STKc_PDK1, Catalytic domain of the Protein
Serine/Threonine Kinase, Phosphoinositide-dependent
kinase 1. Serine/Threonine Kinases (STKs),
Phosphoinositide-dependent kinase 1 (PDK1) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PDK1 subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase (PI3K). PDK1
carries an N-terminal catalytic domain and a C-terminal
pleckstrin homology (PH) domain that binds
phosphoinositides. It phosphorylates the activation loop
of AGC kinases that are regulated by PI3K such as PKB,
SGK, and PKC, among others, and is crucial for their
activation. Thus, it contributes in regulating many
processes including metabolism, growth, proliferation,
and survival. PDK1 also has the ability to
autophosphorylate and is constitutively active in
mammalian cells. PDK1 is essential for normal embryo
development and is important in regulating cell volume.
Length = 280
Score = 28.3 bits (64), Expect = 4.6
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 77 GSYSET-LVIENSDFLPWAMKRVSKQ 101
GS+S L E +A+K + K+
Sbjct: 12 GSFSTVVLAKEKETNKEYAIKILDKR 37
>gnl|CDD|182654 PRK10695, PRK10695, hypothetical protein; Provisional.
Length = 859
Score = 28.3 bits (64), Expect = 5.4
Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 12/85 (14%)
Query: 151 WAPWLSHFYYLDYDVYVIPHSNGAVTLGGCRHYDSYSRDISRHDTASILERCYSLLPRLE 210
L YL D + SN ++ H + + DT ++ C S LP E
Sbjct: 52 GGLRLPDLRYLVGDCPLATVSNLSL-----SHPSRWRLNA---DTVTLDSACLSKLPASE 103
Query: 211 EAPV----LYEWCGLRPHRSLVIHN 231
E+P L +W + P L I +
Sbjct: 104 ESPAAPLTLAQWQSMLPETWLNIDH 128
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 27.9 bits (63), Expect = 5.5
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 14 NEDGSRTLT----LSQTKFSADGSTGKAMISTYQTSLLKNASIE 53
ED R + SQ F + T +AM + Q LL+ S+E
Sbjct: 153 QEDALRMMRAVRFASQLGFDLETETFEAMKT--QAPLLEKISVE 194
>gnl|CDD|185280 PRK15382, PRK15382, non-LEE encoded effector protein NleB;
Provisional.
Length = 326
Score = 27.9 bits (62), Expect = 6.4
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 195 TASILERCYSLLPRLEEAPVLYEWCGLRPHR 225
T S + Y L P E+ P+L++W RP R
Sbjct: 23 TVSFAGKEYELEPIDEKTPILFQWFEARPER 53
>gnl|CDD|218411 pfam05067, Mn_catalase, Manganese containing catalase. Catalases
are important antioxidant metalloenzymes that catalyze
disproportionation of hydrogen peroxide, forming
dioxygen and water. Two families of catalases are known,
one having a heme cofactor, and this family that is a
structurally distinct family containing non-heme
manganese.
Length = 283
Score = 27.6 bits (61), Expect = 7.5
Identities = 12/65 (18%), Positives = 22/65 (33%)
Query: 38 MISTYQTSLLKNASIENLVPVYRDAQPDELVVGNKTYKYGSYSETLVIENSDFLPWAMKR 97
MI+T LLK A+ + + ++ G + +S +PW
Sbjct: 72 MIATMIARLLKGATFDQQEDAAEEPVIGSVLGGMNPQHAIVSGLGAMPMDSMGVPWTADY 131
Query: 98 VSKQG 102
+ G
Sbjct: 132 IVASG 136
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 27.2 bits (61), Expect = 8.9
Identities = 7/45 (15%), Positives = 16/45 (35%)
Query: 106 RRGTVSSFSGLESEFDFVFNCAGLGAQALCRDRKLTPIRGQVIKV 150
+ + ++D +F+ G +L R G+ + V
Sbjct: 195 TTEDFVALTAGGEKYDVIFDAVGNSPFSLYRASLALKPGGRYVSV 239
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 0.134 0.408
Gapped
Lambda K H
0.267 0.0584 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,357,605
Number of extensions: 1246000
Number of successful extensions: 975
Number of sequences better than 10.0: 1
Number of HSP's gapped: 967
Number of HSP's successfully gapped: 20
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
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 (26.4 bits)