RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy45
(69 letters)
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 45.6 bits (109), Expect = 2e-07
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 4 EQLKVDNIRRAAAPNDHPLFIDALVDIVSSHL 35
E+ +N RR ND P FI+AL D+V HL
Sbjct: 280 EEAGGENYRRIPCLNDSPAFIEALADLVREHL 311
Score = 27.1 bits (61), Expect = 0.52
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 19 DHPLFIDALVDIVSSHL 35
DHP +I+AL D + L
Sbjct: 157 DHPGYIEALADSIREAL 173
>gnl|CDD|234585 PRK00035, hemH, ferrochelatase; Reviewed.
Length = 333
Score = 44.0 bits (105), Expect = 5e-07
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 4 EQLKVDNIRRAAAPNDHPLFIDALVDIVSSHLR 36
E+ + RR ND P FI+AL D+V +L+
Sbjct: 292 EEAGGEEFRRIPCLNDSPEFIEALADLVRENLQ 324
Score = 30.5 bits (70), Expect = 0.030
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 19 DHPLFIDALVDIVSSHL 35
DHP +I+AL + + L
Sbjct: 164 DHPGYIEALAESIREAL 180
>gnl|CDD|223353 COG0276, HemH, Protoheme ferro-lyase (ferrochelatase) [Coenzyme
metabolism].
Length = 320
Score = 40.3 bits (95), Expect = 1e-05
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 4 EQLKVDNIRRAAAPNDHPLFIDALVDIVSSHL 35
E+ R ND P FIDAL D+V L
Sbjct: 287 EEAGGKKYVRIPCLNDSPEFIDALADLVRELL 318
Score = 26.4 bits (59), Expect = 0.92
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 19 DHPLFIDALVDIVSSHL 35
D PL+I+AL D + L
Sbjct: 161 DEPLYIEALADSIREKL 177
>gnl|CDD|183526 PRK12435, PRK12435, ferrochelatase; Provisional.
Length = 311
Score = 39.2 bits (92), Expect = 3e-05
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 13 RAAAPNDHPLFIDALVDIVSSHLRSK 38
R PN PLFIDAL D+V L+S
Sbjct: 285 RPEMPNADPLFIDALADVVLKKLKSV 310
>gnl|CDD|232827 TIGR00109, hemH, ferrochelatase. Human ferrochelatase, found at
the mitochondrial inner membrane inner surface, was
shown in an active recombinant form to be a homodimer.
This contrasts to an earlier finding by gel filtration
that overexpressed E. coli ferrochelatase runs as a
monomer [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 322
Score = 33.6 bits (77), Expect = 0.003
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 4 EQLKVDNIRRAAAPNDHPLFIDALVDIVSSHL 35
E D +R A N P FI+A+ +V L
Sbjct: 290 EDAGGDKYQRCPALNAKPEFIEAMATLVKKKL 321
>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of
pre-ribosomes [Translation, ribosomal structure and
biogenesis / Intracellular trafficking and secretion].
Length = 657
Score = 26.9 bits (59), Expect = 0.79
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 5/38 (13%)
Query: 30 IVSSHLRSKTK-----INPKFLNRCPHCVNPKCSQAKQ 62
S + K I+ K R C N KCS+
Sbjct: 571 YCCSRSPEEFKGAILDISAKLDIRYSDCSNLKCSEFDI 608
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis
of L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 304
Score = 26.4 bits (59), Expect = 0.89
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 25 DALVDIVSSH----LRSKTKINPKFLNRCPH 51
D L++ + +RSKT++ + L P
Sbjct: 34 DELIEALKDVHLLGIRSKTQLTEEVLEAAPK 64
>gnl|CDD|178602 PLN03034, PLN03034, phosphoglycerate kinase; Provisional.
Length = 481
Score = 26.1 bits (57), Expect = 1.5
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 3 EEQLKVDNIR-RAAAPNDHPLFIDALVDIVSSHLRSKTKINPKF 45
+ Q D+ R RAA P L + I+SSHL + PKF
Sbjct: 107 DNQNITDDTRIRAAIPTIKYLISNGAKVILSSHLGRPKGVTPKF 150
>gnl|CDD|191593 pfam06721, DUF1204, Protein of unknown function (DUF1204). This
family represents the C-terminus of a number of
Arabidopsis thaliana hypothetical proteins of unknown
function. Family members contain a conserved DFD motif.
Length = 232
Score = 25.9 bits (56), Expect = 1.8
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 9 DNIRRAAAPNDHPLFIDALVDIVSSHLRSKTKINPKFLNRCPHCVNPK 56
+ RR A + LF A ++ V +HL K PKF + C N
Sbjct: 79 EFQRRKALDHMADLF-QARMNRVKAHLDDKIAAEPKFFDFNQVCGNIA 125
>gnl|CDD|130861 TIGR01802, CM_pl-yst, monofunctional chorismate mutase,
eukaryotic type. This model represents the plant and
yeast (plastidic) chorismate mutase. These CM's are
distinct from other forms by the presence of an
extended regulatory domain [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 246
Score = 25.5 bits (56), Expect = 2.4
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 11 IRRAAAPNDHPLFIDAL 27
+RR +P++HP F D L
Sbjct: 64 VRRFESPDEHPFFPDKL 80
>gnl|CDD|200455 cd11316, AmyAc_bac2_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Chloroflexi, Dictyoglomi, and Fusobacteria. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 403
Score = 25.2 bits (56), Expect = 2.5
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 18 NDHPLFIDALVDIVSSH 34
++HP F +A S +
Sbjct: 97 SEHPWFQEAASSPDSPY 113
>gnl|CDD|147459 pfam05271, Tobravirus_2B, Tobravirus 2B protein. This family
consists of several tobravirus 2B proteins. It is known
that the 2B protein is required for transmission by
both Paratrichodorus pachydermus and P. anemones
nematodes.
Length = 117
Score = 24.8 bits (54), Expect = 2.8
Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 20/59 (33%)
Query: 17 PNDHPLFI---------DALVDIVS-SHLRSK-----TKINPKFL----NRCPHCVNPK 56
PND LF+ D L D V H S+ + I F+ NR P C+N K
Sbjct: 9 PNDQ-LFLSDTYQLVWFDILRDKVEHKHFVSQVSTDLSSIPKSFISFVDNRLPMCINHK 66
>gnl|CDD|224080 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 25.3 bits (56), Expect = 3.0
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 3 EEQL-KVDNIRRAAAPNDHPLFIDALVDIVSSHLRSKTKINPKFLN 47
++L K+ +RR +P D I+ L+D + KTK N +FL
Sbjct: 376 PDELQKMWVLRRILSPMDEIDAIEFLIDKL-----KKTKTNDEFLE 416
>gnl|CDD|199216 cd10321, RNase_Ire1_like, RNase domain (also known as the kinase
extension nuclease domain) of Ire1 and RNase L. This
RNase domain is found in the multi-functional protein
Ire1; Ire1 also contains a type I transmembrane
serine/threonine protein kinase (STK) domain, and a
Luminal dimerization domain. Ire1 is essential for the
endoplasmic reticulum (ER) unfolded protein response
(UPR). The UPR is activated when protein misfolding is
detected in the ER in order to reduce the synthesis of
new proteins and increase the capacity of the ER to
cope with the stress. IRE1 acts as an ER stress sensor;
IRE1 dimerizes through its N-terminal luminal domain
and forms oligomers, promoting
trans-autophosphorylation by its cytosolic kinase
domain which stimulates its endoribonuclease (RNase)
activity and results in the cleavage of its mRNA
substrate, Hac1 in yeast and Xbp1 in metazoans, thus
promoting a splicing event that enables translation
into a transcription factor which activates the UPR.
This RNase domain is also found in Ribonuclease L
(RNase L), sometimes referred to as the 2-5A-dependent
RNase. RNase L is a highly regulated, latent
endoribonuclease widely expressed in most mammalian
tissues. It is involved in the mediation of the
antiviral and pro-apoptotic activities of the
interferon-inducible 2-5A system; the interferon
(IFN)-inducible 2'-5'-oligoadenylate synthetase
(OAS)/RNase L pathway blocks infections by certain
types of viruses through cleavage of viral and cellular
single-stranded RNA. RNase L has been shown to have an
impact on the pathogenesis of prostate cancer; the
RNase L gene, RNASEL, has been identified as a strong
candidate for the hereditary prostate cancer 1 (HPC1)
allele.
Length = 127
Score = 24.7 bits (54), Expect = 3.6
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 23 FIDALVDIVSSHLRSKTKINPKFLNRCPHCVNPKCS 58
FIDA+++++ + +N K LN V+
Sbjct: 6 FIDAVLNLLKDSNLPPSTLN-KLLNPGSDTVSSSFL 40
>gnl|CDD|180334 PRK05978, PRK05978, hypothetical protein; Provisional.
Length = 148
Score = 24.6 bits (54), Expect = 4.1
Identities = 5/8 (62%), Positives = 5/8 (62%)
Query: 45 FLNRCPHC 52
F RCP C
Sbjct: 32 FRGRCPAC 39
>gnl|CDD|212688 cd11738, HSPA4L_NBD, Nucleotide-binding domain of HSPA4L. Human
HSPA4L (also known as 70-kDa heat shock protein 4-like,
APG-1, HSPH3, and OSP94; the human HSPA4L gene maps to
4q28) is expressed ubiquitously and predominantly in the
testis. It is required for normal spermatogenesis and
plays a role in osmotolerance. HSPA4L belongs to the
105/110 kDa heat shock protein (HSP105/110) subfamily of
the HSP70-like family. HSP105/110s are believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 383
Score = 24.6 bits (53), Expect = 5.3
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 23 FIDALVDIVSSHLRSKTKINPKFLNRCPHCVNPKCSQAKQWFS 65
F +ALVD ++K KIN K +R + +C + K+ S
Sbjct: 235 FDEALVDYFCDEFKTKYKINVKENSRALLRLYQECEKLKKLMS 277
>gnl|CDD|188518 TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-activating
enzyme. Members of this radical SAM protein family are
[benzylsuccinate synthase]-activating enzyme, a glycyl
radical active site-creating enzyme related to
[pyruvate formate-lyase]-activating enzyme and
additional uncharacterized homologs activating
additional glycyl radical-containing enzymes [Protein
fate, Protein modification and repair].
Length = 314
Score = 24.5 bits (53), Expect = 6.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 48 RCPHCVNPKCSQAKQWF 64
RCP C NP+ +Q F
Sbjct: 29 RCPWCHNPETQDTRQEF 45
>gnl|CDD|224063 COG1140, NarY, Nitrate reductase beta subunit [Energy production
and conversion].
Length = 513
Score = 24.3 bits (53), Expect = 6.8
Identities = 6/9 (66%), Positives = 7/9 (77%)
Query: 49 CPHCVNPKC 57
C HC+NP C
Sbjct: 183 CEHCLNPSC 191
>gnl|CDD|218910 pfam06144, DNA_pol3_delta, DNA polymerase III, delta subunit. DNA
polymerase III, delta subunit (EC 2.7.7.7) is required
for, along with delta' subunit, the assembly of the
processivity factor beta(2) onto primed DNA in the DNA
polymerase III holoenzyme-catalyzed reaction. The delta
subunit is also known as HolA.
Length = 172
Score = 23.8 bits (52), Expect = 8.4
Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 2/45 (4%)
Query: 27 LVDIVSSHLRSKTKINPKFLNRCP--HCVNPKCSQAKQWFSQLCA 69
L+ L + K+ + C K + QW +
Sbjct: 94 LIIEAPGKLDERKKLTKLLKKKATVVECFTLKEEELIQWIQKRAK 138
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
0.323 0.133 0.425
Gapped
Lambda K H
0.267 0.0511 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,407,694
Number of extensions: 238293
Number of successful extensions: 412
Number of sequences better than 10.0: 1
Number of HSP's gapped: 412
Number of HSP's successfully gapped: 22
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.7 bits)