RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4056
(227 letters)
>gnl|CDD|223733 COG0661, AarF, Predicted unusual protein kinase [General function
prediction only].
Length = 517
Score = 143 bits (363), Expect = 4e-40
Identities = 54/196 (27%), Positives = 94/196 (47%), Gaps = 10/196 (5%)
Query: 30 RNNYDVNSLVAVRLVRAASCVFNIAYIYKKALYQKATPDPTSEEYSNLKSKVHKEAAEQL 89
R + + L R +A + + + + +SEE L+ K + L
Sbjct: 9 RLPRIIRVRLRYLLGRLLRLTGRLALLLRLLSWLGKSKLASSEE---LREKRAERLRLAL 65
Query: 90 LELCKMNKGVYIKVGQHIGALEYLLPKEYVETMKVLHSKAPMSPMKDILAVLKEDLGKDP 149
EL +IK+GQ + L+P EY E + L + P P ++ +++E+LG+
Sbjct: 66 EEL----GPTFIKLGQILSTRPDLVPPEYAEELAKLQDRVPPFPFEEAERIIEEELGRPI 121
Query: 150 SEIFASIEPNPMGAASLAQVHKATLHDGSTIALKVQHRNVRDNANIDIKCMEALVHVVAW 209
E+F+ EP P+ +AS+AQVH+A L G +A+KVQ +R+ D+K + L ++
Sbjct: 122 EELFSEFEPEPIASASIAQVHRAVLKSGEEVAVKVQRPGIRERIEADLKLLRRLARLIKR 181
Query: 210 VFPEFKFL---WLVDE 222
+ P + L +VDE
Sbjct: 182 LPPGGRRLDLVEVVDE 197
>gnl|CDD|111949 pfam03109, ABC1, ABC1 family. This family includes ABC1 from yeast
and AarF from E. coli. These proteins have a nuclear or
mitochondrial subcellular location in eukaryotes. The
exact molecular functions of these proteins is not
clear, however yeast ABC1 suppresses a cytochrome b mRNA
translation defect and is essential for the electron
transfer in the bc 1 complex and E. coli AarF is
required for ubiquinone production. It has been
suggested that members of the ABC1 family are novel
chaperonins. These proteins are unrelated to the ABC
transporter proteins.
Length = 117
Score = 104 bits (263), Expect = 5e-29
Identities = 34/85 (40%), Positives = 52/85 (61%)
Query: 143 EDLGKDPSEIFASIEPNPMGAASLAQVHKATLHDGSTIALKVQHRNVRDNANIDIKCMEA 202
E+LG E+FA + P+ AAS+AQVH+A L DG +A+KVQ V+ D+K ++
Sbjct: 1 EELGAPVEEVFAEFDEEPIAAASIAQVHRAVLKDGEEVAVKVQRPGVKKRIRSDLKLLKF 60
Query: 203 LVHVVAWVFPEFKFLWLVDETKRNI 227
L ++ FP F WLVDE ++++
Sbjct: 61 LAKILKKFFPGFDLDWLVDEFRKSL 85
>gnl|CDD|233667 TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase. This model
represents the enzyme (UbiB) which catalyzes the first
hydroxylation step in the ubiquinone biosynthetic
pathway in bacteria. It is believed that the reaction is
2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This
model finds hits primarily in the proteobacteria. The
gene is also known as AarF in certain species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 437
Score = 96.2 bits (240), Expect = 4e-23
Identities = 39/119 (32%), Positives = 59/119 (49%)
Query: 99 VYIKVGQHIGALEYLLPKEYVETMKVLHSKAPMSPMKDILAVLKEDLGKDPSEIFASIEP 158
+IK GQ + LLP + E + +L + P K V++ LG E+FA E
Sbjct: 63 TFIKFGQTLSTRADLLPADIAEELSLLQDRVPPFDFKVARKVIEAALGGPLEELFAEFEE 122
Query: 159 NPMGAASLAQVHKATLHDGSTIALKVQHRNVRDNANIDIKCMEALVHVVAWVFPEFKFL 217
P+ AAS+AQVH+A L DG +A+KV + DI + L +V + P+ + L
Sbjct: 123 KPLAAASIAQVHRARLVDGKEVAVKVLRPGIEKTIAADIALLYRLARIVERLSPDSRRL 181
>gnl|CDD|235310 PRK04750, ubiB, putative ubiquinone biosynthesis protein UbiB;
Reviewed.
Length = 537
Score = 64.9 bits (159), Expect = 3e-12
Identities = 31/120 (25%), Positives = 57/120 (47%), Gaps = 1/120 (0%)
Query: 99 VYIKVGQHIGALEYLLPKEYVETMKVLHSKAPMSPMKDILAVLKEDLGKDPSEIFASIEP 158
+++K GQ + L P + + + +L + P A++++ LG E F +
Sbjct: 65 IFVKFGQMLSTRRDLFPPDIADELALLQDRVPPFDGALARAIIEKALGGPVEEWFDDFDI 124
Query: 159 NPMGAASLAQVHKATLHD-GSTIALKVQHRNVRDNANIDIKCMEALVHVVAWVFPEFKFL 217
P+ +AS+AQVH A L D G + +KV ++ + D+ M L V + P+ + L
Sbjct: 125 KPLASASIAQVHFARLKDNGREVVVKVLRPDILPVIDADLALMYRLARWVERLLPDGRRL 184
>gnl|CDD|226717 COG4267, COG4267, Predicted membrane protein [Function unknown].
Length = 467
Score = 32.0 bits (73), Expect = 0.27
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 33 YDVNSLVAVRLVRAASCVFNIA-----YIYKKALYQKATPDPTSEEYSNLKSKVHKEAAE 87
YDV A + + VF I+ K YQ T E N K+ +
Sbjct: 269 YDVPIFYAYLFIIPSMVVFLISLETDFQENYKEYYQAIRGGGTLREIENNLKKMILTLRQ 328
Query: 88 QLLELCKMN 96
+LE+ ++
Sbjct: 329 GILEIMELQ 337
>gnl|CDD|183235 PRK11618, PRK11618, inner membrane ABC transporter permease protein
YjfF; Provisional.
Length = 317
Score = 30.3 bits (69), Expect = 0.78
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 15 LGVGSVIGGTGILLHR--NNYDVNSLVAVRLVRAASCVF 51
L VGSVI TG+ L + +Y + L+A LV F
Sbjct: 63 LSVGSVIAFTGVFLAKLIGDYGWSPLLAFPLVLVMGAAF 101
>gnl|CDD|221888 pfam13001, Ecm29, Proteasome stabiliser. The proteasome consists
of two subunits, and the capacity of the proteasome to
degrade protein depends crucially on the interaction
between these two subunits. This interaction is affected
by a wide range of factors including metabolites, such
as ATP, and proteasome-associated proteins such as
Ecm29. Ecm29 stabilises the interaction between the two
subunits.
Length = 497
Score = 30.3 bits (69), Expect = 0.92
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 120 ETMKVLHSKAPMSPMKDILAVLK--EDLGKDPSEIFASIE 157
E + +L + P KDI V + L ++ ++ SI+
Sbjct: 393 EALGLLAKRDPSLFNKDIDLVEFLFDSLSEESPDVRVSIQ 432
>gnl|CDD|177446 PHA02663, PHA02663, hypothetical protein; Provisional.
Length = 172
Score = 28.4 bits (63), Expect = 2.0
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 3 KILQTRRHIKYALGVGSVIGGTGILL 28
++ +TRR + ++GVG+V+ G G+L
Sbjct: 139 RVHRTRRRLHRSIGVGTVMAGVGLLF 164
>gnl|CDD|217706 pfam03740, PdxJ, Pyridoxal phosphate biosynthesis protein PdxJ.
Members of this family belong to the PdxJ family that
catalyzes the condensation of
1-deoxy-d-xylulose-5-phosphate (DXP) and
1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form
pyridoxine 5'-phosphate (PNP). This reaction is involved
in de novo synthesis of pyridoxine (vitamin B6) and
pyridoxal phosphate.
Length = 238
Score = 28.5 bits (64), Expect = 2.3
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 157 EPNPMGAASLAQVHKATLHDGSTIALKVQHRNVRD 191
P+P+ AA +A+ A DG T+ L+ R+++D
Sbjct: 20 YPDPVEAALIAERAGA---DGITVHLREDRRHIQD 51
>gnl|CDD|199205 cd00411, L-asparaginase_like, Bacterial L-asparaginases and
related enzymes. Asparaginases (amidohydrolases, E.C.
3.5.1.1) are dimeric or tetrameric enzymes that
catalyze the hydrolysis of asparagine to aspartic acid
and ammonia. In bacteria, there are two classes of
amidohydrolases, one highly specific for asparagine and
localized to the periplasm (type II L-asparaginase),
and a second (asparaginase- glutaminase) present in the
cytosol (type I L-asparaginase) that hydrolyzes both
asparagine and glutamine with similar specificities and
has a lower affinity for its substrate. Bacterial
L-asparaginases (type II) are potent antileukemic
agents and have been used in the treatment of acute
lymphoblastic leukemia (ALL). A conserved threonine
residue is thought to supply the nucleophile
hydroxy-group that attacks the amide bond. Many
bacterial L-asparaginases have both L-asparagine and
L-glutamine hydrolysis activities, to a different
degree, and some of them are annotated as
asparaginase/glutaminase. This wider family also
includes a subunit of an archaeal Glu-tRNA
amidotransferase.
Length = 320
Score = 27.9 bits (62), Expect = 4.4
Identities = 17/73 (23%), Positives = 31/73 (42%)
Query: 15 LGVGSVIGGTGILLHRNNYDVNSLVAVRLVRAASCVFNIAYIYKKALYQKATPDPTSEEY 74
L G I G G + Y +L +L++A + +A + + L A+ D T +++
Sbjct: 6 LATGGTIAGVGDSATYSAYVAGALGVEKLIKAVPELKELANVKGEQLMNIASEDITPDDW 65
Query: 75 SNLKSKVHKEAAE 87
L +V K
Sbjct: 66 LKLAKEVAKLLDS 78
>gnl|CDD|223923 COG0854, PdxJ, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 243
Score = 27.6 bits (62), Expect = 5.0
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 157 EPNPMGAASLAQVHKATLHDGSTIALKVQHRNVRD 191
P+P+ AA +A+ A DG T+ L+ R+++D
Sbjct: 21 YPDPVEAAFIAEQAGA---DGITVHLREDRRHIQD 52
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 27.6 bits (61), Expect = 5.9
Identities = 23/123 (18%), Positives = 44/123 (35%), Gaps = 15/123 (12%)
Query: 53 IAYIYKKALYQKATPDPTSEEYSNLKSKVHKEAAEQLLELCKMNKGVYIKVGQHIGALE- 111
+A IY+ +K + ++K H+E + L + AL
Sbjct: 450 LAEIYEAEYQRKENESLDGAAGAEKENKEHEEIKSLMGSLFLK-----------LDALSS 498
Query: 112 -YLLPKEYVETMKVLHSKAPMSPMKDILAVLKEDLGK-DPSEIFASIEPNPMGAASLAQV 169
+ +PK E +K++ S P M+++ D P EI+ ++ L +
Sbjct: 499 FHFVPKPAREEVKIV-SNTPAIAMEEVAPTAVSDAALLAPEEIYKKMKAIEKSKTELDRT 557
Query: 170 HKA 172
K
Sbjct: 558 DKN 560
>gnl|CDD|152551 pfam12116, SpoIIID, Stage III sporulation protein D. This stage
III sporulation protein is a small DNA-binding family
that is essential for gene expression of the mother-cell
compartment during sporulation. The domain is found in
bacteria and viruses, and is about 40 amino acids in
length. It has a conserved RGG sequence motif.
Length = 82
Score = 25.8 bits (57), Expect = 6.3
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 50 VFNIA-YIYKKALYQKATPDPTSEEYSNLKSKVHKEAAEQLLELCKMNKGVYIKV 103
V IA YI + KAT ++ + KS VHK+ E+L ++ N + +V
Sbjct: 8 VLEIANYIIEN----KATVRQAAKVFGVSKSTVHKDVTERLPKI---NPQLAKEV 55
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
0.319 0.134 0.388
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,424,266
Number of extensions: 1050950
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1010
Number of HSP's successfully gapped: 28
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.7 bits)