RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17586
(106 letters)
>gnl|CDD|239266 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II.
Length = 142
Score = 38.7 bits (91), Expect = 8e-05
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 39 QVDHTIIMYLIDPEGLFVDYYG 60
VDH+ +YL+DP+G V YYG
Sbjct: 120 LVDHSAAIYLVDPDGKLVRYYG 141
>gnl|CDD|224910 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved
in biogenesis of respiratory and photosynthetic systems
[General function prediction only].
Length = 207
Score = 32.4 bits (74), Expect = 0.023
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 40 VDHTIIMYLIDPEGLFVDYYGQNKKPEEV 68
+DH+ YLID +G F+ Y + PEE+
Sbjct: 168 IDHSAGFYLIDADGRFLGTYDYGEPPEEI 196
>gnl|CDD|202321 pfam02630, SCO1-SenC, SCO1/SenC. This family is involved in
biogenesis of respiratory and photosynthetic systems.
SCO1 is required for a post-translational step in the
accumulation of subunits COXI and COXII of cytochrome c
oxidase. SenC is required for optimal cytochrome c
oxidase activity and maximal induction of genes encoding
the light-harvesting and reaction centre complexes of R.
capsulatus.
Length = 152
Score = 32.0 bits (73), Expect = 0.027
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 38 FQVDHTIIMYLIDPEGLFVDYY 59
+ VDH+ YLIDP+G + +Y
Sbjct: 128 YLVDHSSFFYLIDPDGKILKHY 149
>gnl|CDD|176696 cd08348, BphC2-C3-RGP6_C_like, The single-domain
2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC
1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6
and BphC3-RGP6, and similar proteins. This subfamily
contains Rhodococcus globerulus P6 BphC2-RGP6 and
BphC3-RGP6, and similar proteins. BphC catalyzes the
extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, yielding
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. This is
the third step in the polychlorinated biphenyls (PCBs)
degradation pathway (bph pathway). This subfamily of
BphCs belongs to the type I extradiol dioxygenase
family, which require a metal in the active site in its
catalytic mechanism. Most type I extradiol dioxygenases
are activated by Fe(II). Polychlorinated biphenyl
degrading bacteria demonstrate a multiplicity of BphCs.
For example, three types of BphC enzymes have been found
in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all
three enzymes are type I extradiol dioxygenases.
BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases,
which form hexamers. BphC1-RGP6 has an internal
duplication, it is a two-domain dioxygenase which forms
octamers, its two domains do not belong to this
subfamily.
Length = 134
Score = 26.1 bits (58), Expect = 3.3
Identities = 7/22 (31%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 40 VDH--TIIMYLIDPEGLFVDYY 59
VDH +Y DP+G ++ +
Sbjct: 97 VDHGNAWSIYFRDPDGNRLELF 118
>gnl|CDD|226768 COG4318, COG4318, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 221
Score = 26.3 bits (58), Expect = 3.3
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 36 FWFQVDHTIIMYLIDPEGLFVDY 58
FW +D ++ D G Y
Sbjct: 114 FWEVMDENHWVHPFDARGARRPY 136
>gnl|CDD|153126 cd02435, CCC1, CCC1. CCC1: This domain is present in the CCC1, an
iron and manganese transporter of Saccharomyces
cerevisiae. CCC1 is a transmembrane protein that is
located in the vacuole and transfers the iron and
manganese ions from the cytosol to the vacuole. This
domain may be unique to certain fungi and plants.
Length = 241
Score = 25.7 bits (57), Expect = 4.9
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 9/36 (25%)
Query: 8 HFIGGTLPLC---------RPLMYSIISTIPYLLSF 34
+FIGG +PL L+ S+I T+ L F
Sbjct: 164 YFIGGLIPLLPYFFVSTVGEALLLSVIVTLVALFVF 199
>gnl|CDD|182666 PRK10711, PRK10711, hypothetical protein; Provisional.
Length = 231
Score = 25.0 bits (55), Expect = 7.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 14 LPLCRPLMYSIISTIPYLL 32
PL PL+ +++ IP+LL
Sbjct: 28 FPLLNPLLVAMVVIIPFLL 46
>gnl|CDD|237369 PRK13376, pyrB, bifunctional aspartate carbamoyltransferase
catalytic subunit/aspartate carbamoyltransferase
regulatory subunit; Provisional.
Length = 525
Score = 25.5 bits (56), Expect = 7.6
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 53 GLFVDYYGQNKKPEEVSNSI--IVNMMKYENLKKKSW 87
G +D+ + K PEE+ +I I ++K ++
Sbjct: 380 GTVIDHIAKGKTPEEIYETIVKIRKILKLYDVDSADG 416
>gnl|CDD|176681 cd07258, PpCmtC_C, C-terminal domain of
2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This
subfamily contains the C-terminal, catalytic, domain of
PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of
Pseudomonas putida F1) is a dioxygenase involved in the
eight-step catabolism pathway of p-cymene. CmtC acts
upon the reaction intermediate 2,3-dihydroxy-p-cumate,
yielding
2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The
CmtC belongs to the type I family of extradiol
dioxygenases. Fe2+ was suggested as a cofactor, same as
for other enzymes in the family. The type I family of
extradiol dioxygenases contains two structurally
homologous barrel-shaped domains at the N- and
C-terminal. The active-site metal is located in the
C-terminal barrel and plays an essential role in the
catalytic mechanism.
Length = 141
Score = 24.9 bits (54), Expect = 7.7
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 43 TIIMYLIDPEGLFVDY-YGQNKKPE 66
+I Y +DP+G+ V+Y +G + E
Sbjct: 96 SIFFYFLDPDGITVEYSFGMEEFAE 120
>gnl|CDD|227830 COG5543, COG5543, Uncharacterized conserved protein [Function
unknown].
Length = 1400
Score = 25.3 bits (55), Expect = 7.7
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 5/40 (12%)
Query: 58 YYGQNKKPEEVSNSIIVNMMKYENLKKKSWFEDTIESLTS 97
+ + +K I+NM+K + K +L
Sbjct: 1312 FINELQKAMH-----ILNMIKLTSKCYKDQIHHLKSALLE 1346
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
0.322 0.138 0.428
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,450,934
Number of extensions: 469117
Number of successful extensions: 539
Number of sequences better than 10.0: 1
Number of HSP's gapped: 538
Number of HSP's successfully gapped: 27
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (21.9 bits)
S2: 53 (24.1 bits)