RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8828
(81 letters)
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 54.2 bits (130), Expect = 3e-10
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 13/72 (18%)
Query: 8 VSPTKETLLGVGCICPICHDEF-------------KTPVQLTCCHIFCESCVTKWFDREQ 54
+ T+E L C IC DE TP +L C HI C+ W +R+Q
Sbjct: 276 PTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ 335
Query: 55 TCPLCRATLVDD 66
TCP+CR ++ D
Sbjct: 336 TCPICRRPVIFD 347
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 51.2 bits (122), Expect = 3e-09
Identities = 18/41 (43%), Positives = 22/41 (53%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAT 62
C IC D F PV +C H FC C+ + + CPLCRA
Sbjct: 29 CHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAE 69
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 46.6 bits (111), Expect = 6e-09
Identities = 22/43 (51%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 22 CPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
CPIC DEF + V L C H+F + C+ KW TCPLCRA
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRA 45
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 48.9 bits (116), Expect = 2e-08
Identities = 14/40 (35%), Positives = 19/40 (47%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
C IC P + TC H FC C+ + + CP+CR
Sbjct: 28 CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCRE 67
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 45.1 bits (107), Expect = 2e-08
Identities = 23/44 (52%), Positives = 29/44 (65%), Gaps = 2/44 (4%)
Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ-TCPLCRATL 63
CPIC +EF+ PV L C H+FC SC+ KW + TCPLCR +
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 44.8 bits (106), Expect = 3e-08
Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRA 61
CPIC D + PV LT C H+FC C+ ++ ++ CP+CR
Sbjct: 4 ECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 43.3 bits (102), Expect = 1e-06
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT--CPLCRA 61
C +C +E + P C H+FC SC+ + +++ CPLCRA
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRA 259
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 39.8 bits (93), Expect = 2e-06
Identities = 21/40 (52%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 22 CPICHDEF-KTPVQLTCCHIFCESCVTKWFDRE-QTCPLC 59
CPIC +E+ K PV L C H FC SC+ KW + TCP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 42.4 bits (99), Expect = 4e-06
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
+C IC ++++PV C H FC C + + + C +C
Sbjct: 198 LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGK 238
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 40.5 bits (95), Expect = 1e-05
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 37 CCHIFCESCVTKWFDREQTCPLCRATLV 64
C H+FC C+ W + TCP+CR +
Sbjct: 200 CNHVFCIECIDIWKKEKNTCPVCRTPFI 227
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 38.8 bits (90), Expect = 6e-05
Identities = 17/51 (33%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 17 GVGCICPICHDEF---KTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATL 63
G C IC F L C H F CV KW CP+CR +
Sbjct: 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 38.5 bits (89), Expect = 9e-05
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 9/51 (17%)
Query: 22 CPIC------HD-EFKTPVQLTCCHIFCESCVTKWF--DREQTCPLCRATL 63
C IC D + TC + F C+ KWF CPLCR+ +
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 35.5 bits (82), Expect = 1e-04
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 22 CPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE-QTCPLC 59
CPIC +E K PV + C H+FC C+ W + TCPLC
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 37.8 bits (87), Expect = 2e-04
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 22 CPICHDEFKTPVQLTCC-HIFCESCV-TKWFDREQTCPLC 59
CP+CH + P++ CC H FC+ C+ T D + CP C
Sbjct: 277 CPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNC 316
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 34.2 bits (79), Expect = 5e-04
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 6/43 (13%)
Query: 21 ICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQT--CP 57
+CPI + PV L C H++ + K CP
Sbjct: 12 VCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 35.8 bits (82), Expect = 6e-04
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 16/56 (28%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKW-------------FDREQ---TCPLCRA 61
C IC D+ + PV C H+FC C+ KW +D ++ CP+C++
Sbjct: 21 CNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKS 76
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription
initiation. Also known as MAT1 (menage a trois 1). This
family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 309
Score = 35.6 bits (82), Expect = 0.001
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 15/61 (24%)
Query: 22 CPICH-DEFKTP-VQL---TCCHIFCESCVTKWFDR-EQTCPLC---------RATLVDD 66
CP C +++ P ++L C H CESCV F R +CP C R L +D
Sbjct: 6 CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED 65
Query: 67 P 67
P
Sbjct: 66 P 66
>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain. Modified RING
finger domain, without the full complement of
Zn2+-binding ligands. Probable involvement in
E2-dependent ubiquitination.
Length = 63
Score = 33.0 bits (76), Expect = 0.002
Identities = 13/46 (28%), Positives = 19/46 (41%)
Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
+CPI + K PV L + S + KW T P+ L +
Sbjct: 3 LCPISLEVMKDPVILPSGQTYERSAIEKWLLSHGTDPVTGQPLTHE 48
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 32.7 bits (75), Expect = 0.002
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 21 ICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRA 61
+C IC + + V L C H CE C + ++ CP+CR
Sbjct: 4 LCVICLERPRNVVFLPCGHLCLCEECAKRLR-SKKKCPICRQ 44
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to
chromosome metabolism and cell cycle control.
Length = 73
Score = 33.2 bits (76), Expect = 0.002
Identities = 13/41 (31%), Positives = 17/41 (41%)
Query: 20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
C + V C H F C+++W TCPLCR
Sbjct: 33 CPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73
>gnl|CDD|227545 COG5220, TFB3, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH, subunit TFB3 [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 314
Score = 33.4 bits (76), Expect = 0.004
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 22 CPICH-DEFKTP-----VQLTCCHIFCESCVTKWFDREQT-CP 57
CP+C D + P + C H CESCV + F R CP
Sbjct: 13 CPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCP 55
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 30.6 bits (69), Expect = 0.022
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 36 TCCHIFCESCVTKWFDREQTCPLCRATLV 64
C H F + C+ +W D + CPL R T V
Sbjct: 53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 31.6 bits (71), Expect = 0.023
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 6/31 (19%)
Query: 36 TCCHIFCESCVTKWF-DREQT-----CPLCR 60
+C HIFC +C+ W R +T CP+CR
Sbjct: 196 SCNHIFCITCINIWHRTRRETGASDNCPICR 226
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 29.5 bits (67), Expect = 0.12
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 42 CESCVTKWFDREQTCPLCRATLVDD 66
C C ++ D CP C +T ++D
Sbjct: 681 CRDCGYQFTDESDKCPRCGSTNIED 705
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of
Di19 is unknown.
Length = 209
Score = 28.9 bits (65), Expect = 0.21
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLC 59
CP C+++F V L CCHI E + CP+C
Sbjct: 36 CPFCYEDFDI-VSL-CCHIDEEHPFEA---KNGVCPVC 68
>gnl|CDD|220669 pfam10272, Tmpp129, Putative transmembrane protein precursor. This
is a family of proteins conserved from worms to humans.
The proteins are purported to be transmembrane
protein-precursors but the function is unknown.
Length = 356
Score = 28.5 bits (64), Expect = 0.30
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 13/43 (30%)
Query: 33 VQLTCCHIFCESCVTKWFDREQ-------------TCPLCRAT 62
C ++C +C+ KWF Q CP CRA
Sbjct: 305 QNCYCRPMWCLTCMAKWFASRQDQQERETWLSSKCPCPTCRAK 347
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 27.1 bits (60), Expect = 0.50
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 37 CCHIFCESCVTKWFDREQT---CPLCRATLV 64
C H F C+ KW E + CP+CR T V
Sbjct: 52 CKHNFHMHCILKWLATETSKGLCPMCRQTFV 82
>gnl|CDD|188428 TIGR03913, rad_SAM_trio, Y_X(10)_GDL-associated radical SAM
protein. This narrowly distributed protein family
contains an N-terminal radical SAM domain. It occurs in
Pseudomonas fluorescens Pf0-1, Ralstonia solanacearum,
and numerous species and strains of Burkholderia.
Members always occur next to a trio of three mutually
homologous genes, all of which contain the domain
pfam08898 as the whole of the protein (about 60 amino
acids) or as the C-terminal domain. The function is
unknown, but the fact that all phylogenetically
correlated proteins are mutually homologous with
prominent invariant motifs (an invariant tyrosine and a
GDL motif) and as small as 60 amino acids suggests that
post-translational modification of pfam08898
domain-containing proteins may be its function. This
view is supported by closer homology to the PqqE radical
SAM protein involved in PQQ biosynthesis from the PqqA
precursor peptide than to other characterized radical
SAM proteins [Unknown function, Enzymes of unknown
specificity].
Length = 477
Score = 27.2 bits (60), Expect = 0.74
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 27 DEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
+ + P QL C SC++ EQTCP C A
Sbjct: 420 EVGRVPPQLA----LCRSCLSYIHAHEQTCPHCGA 450
>gnl|CDD|118392 pfam09862, DUF2089, Protein of unknown function (DUF2089). This
domain, found in various hypothetical prokaryotic
proteins, has no known function. This domain is a
zinc-ribbon.
Length = 113
Score = 26.4 bits (59), Expect = 1.1
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 6/41 (14%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAT 62
CP+C +E +L C C + + F C CR T
Sbjct: 1 CPVCGEELTV-TRLECSK--CGTTIEGRFT---LCKFCRLT 35
>gnl|CDD|192832 pfam11789, zf-Nse, Zinc-finger of the MIZ type in Nse subunit.
Nse1 and Nse2 are novel non-SMC subunits of the fission
yeast Smc5-6 DNA repair complex. This family is the
zinc-finger domain similar to the MIZ type of
zinc-finger.
Length = 57
Score = 25.3 bits (56), Expect = 1.3
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 22 CPICHDEFKTPV-QLTCCHIFCESCVTKWFDREQT--CP 57
CP+ F+ PV C H+F + + R +T CP
Sbjct: 14 CPLTLQPFEEPVTSKKCNHVFEKDAILSMLRRNKTVKCP 52
>gnl|CDD|182763 PRK10832, PRK10832, phosphatidylglycerophosphate synthetase;
Provisional.
Length = 182
Score = 26.0 bits (57), Expect = 1.8
Identities = 18/45 (40%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 10 PTKETLLGVGCICPICHDEFKTPVQ---LTCCHIFCESCVTKWFD 51
PT TL V I P F P C IFC + VT WFD
Sbjct: 6 PTLLTLFRVILI-PFFVLVFYLPFTWAPFVCALIFCVAAVTDWFD 49
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 25.8 bits (56), Expect = 2.8
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTK--WFDREQTCPLCRAT 62
C IC + C H C +C + ++ CPLCR
Sbjct: 63 NCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106
>gnl|CDD|176887 cd08878, RHO_alpha_C_DMO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of dicamba O-demethylase and
related aromatic ring hydroxylating dioxygenases.
C-terminal catalytic domain of the oxygenase alpha
subunit of Stenotrophomonas maltophilia dicamba
O-demethylase (DMO) and related Rieske-type non-heme
iron aromatic ring-hydroxylating oxygenases (RHOs, also
known as aromatic ring hydroxylating dioxygenases). RHOs
utilize non-heme Fe(II) to catalyze the addition of
hydroxyl groups to the aromatic ring, an initial step in
the oxidative degradation of aromatic compounds. RHOs
are composed of either two or three protein components,
and are comprised of an electron transport chain (ETC)
and an oxygenase. The ETC transfers reducing equivalents
from the electron donor to the oxygenase component,
which in turn transfers electrons to the oxygen
molecules. The oxygenase components are oligomers,
either (alpha)n or (alpha)n(beta)n. The alpha subunits
are the catalytic components and have an N-terminal
domain, which binds a Rieske-like 2Fe-2S cluster, and
the C-terminal catalytic domain which binds the non-heme
Fe(II). The Fe(II) is co-ordinated by conserved His and
Asp residues. Oxygenases belonging to this subgroup
include the alpha subunits of carbazole
1,9a-dioxygenase, phthalate dioxygenase, vanillate
O-demethylase, Pseudomonas putida 2-oxoquinoline
8-monooxygenase, and Comamonas testosteroni T-2
p-toluenesulfonate dioxygenase. It also includes the
C-terminal domain of the lignin biphenyl-specific
O-demethylase (LigX) of the 5,5'-dehydrodivanillic acid
O- demethylation system of Sphingomonas paucimobilis
SYK-6. This subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 196
Score = 25.5 bits (56), Expect = 3.4
Identities = 12/59 (20%), Positives = 16/59 (27%), Gaps = 11/59 (18%)
Query: 24 ICHDEFKTPVQLTCCHIFCESCVTKW-FDREQTCPLCRATLVDDPAWRDGATSYFVQIF 81
+ + TP+ T H F W F R DD + S F
Sbjct: 107 MRVTHWITPIDETTTHYF-------WFFVRNFAPD---EEKKDDEELTETLRSGLSGAF 155
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine
sulfoxide reductase A/B protein; Provisional.
Length = 521
Score = 25.6 bits (56), Expect = 3.7
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 56 CPLCRATLVDDPAWRD 71
CPLC + L + W
Sbjct: 68 CPLCLSELGETEKWAQ 83
>gnl|CDD|236572 PRK09566, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 513
Score = 25.4 bits (56), Expect = 3.9
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 49 WFDREQTCPLCRATLVDDPAWRD 71
W ++ LCRA L +RD
Sbjct: 239 WVKPDEVVRLCRAIL---EVYRD 258
>gnl|CDD|150637 pfam09986, DUF2225, Uncharacterized protein conserved in bacteria
(DUF2225). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 214
Score = 24.9 bits (55), Expect = 4.7
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 20 CICPICHDEFKTP 32
+CP+C++EFKT
Sbjct: 6 IVCPVCNNEFKTK 18
>gnl|CDD|218794 pfam05883, Baculo_RING, Baculovirus U-box/Ring-like domain. This
family consists of several Baculovirus proteins of
around 130 residues in length. The function of this
family is unknown, but it appears to be related to the
U-box and ring finger domain by profile-profile
comparison.
Length = 135
Score = 24.1 bits (53), Expect = 8.2
Identities = 9/37 (24%), Positives = 13/37 (35%), Gaps = 9/37 (24%)
Query: 22 CPICHD---EFKTPVQLTCC------HIFCESCVTKW 49
C IC D + V +T +F C +W
Sbjct: 29 CAICLDRINDNDGVVAVTDGGTLNLEKMFHAECDKRW 65
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
0.329 0.143 0.517
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,843,430
Number of extensions: 258159
Number of successful extensions: 445
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 59
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)