RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1521
(175 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 51.0 bits (123), Expect = 3e-09
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 42 KGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
GGI V + P G A + L+ GD+ILE+ G +TH +A+ L+
Sbjct: 25 GGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELLK 71
Score = 45.6 bits (109), Expect = 3e-07
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
PGG A G L GD+I+ V+G V + EE ++K
Sbjct: 34 EPGGPAE-RGGLRVGDRILEVNGVSVEGLTHEEAVELLKN 72
Score = 34.1 bits (79), Expect = 0.005
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 143 DVELTKKAGKGFGLSLVGRK-QGPGVFISDLV 173
V L K G G G SL G K G G+F+S +
Sbjct: 3 TVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVE 34
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 43.4 bits (103), Expect = 2e-06
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 36 EVATIMKGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
+ +GG++V + P A + A L+ GD IL + G D +N+T L+
Sbjct: 6 SIRGGTEGGVVVLSVEPGSPAER-AGLQAGDVILAVNGTDVKNLTLEDVAELLK 58
Score = 38.8 bits (91), Expect = 8e-05
Identities = 17/39 (43%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 5 PGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
PG A G L GD I++V+GTDV++ + E+VA ++K
Sbjct: 22 PGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVAELLKK 59
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 42.8 bits (101), Expect = 4e-06
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKGG 44
VPG AA G L GD I+ V+GT V + E ++K
Sbjct: 34 VPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEAVDLLKKA 73
Score = 42.4 bits (100), Expect = 6e-06
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 42 KGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
GG++V + P AAK A L+ GD ILE+ G +TH +A+ L+
Sbjct: 25 GGGVVVSSVVPGSPAAK-AGLRVGDVILEVNGTSVEGLTHLEAVDLLK 71
Score = 27.0 bits (60), Expect = 1.8
Identities = 18/35 (51%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 140 EFVDVELTKKAGKGFGLSLVGRK-QGPGVFISDLV 173
E VEL K G G G SLVG K +G GV +S +V
Sbjct: 1 EPRLVELEKGGG-GLGFSLVGGKDEGGGVVVSSVV 34
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 41.1 bits (97), Expect = 2e-05
Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
+PGG A G L +GD+I+S++G D+ + S +E +KG
Sbjct: 32 LPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLALKG 70
Score = 39.9 bits (94), Expect = 4e-05
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 42 KGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
GI V ++ P GAA L+ GD+IL + G+D N++H +A+ L+
Sbjct: 23 DPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLALK 69
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 36.7 bits (85), Expect = 0.003
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 12 DGRLLKGDQIMSVDGTDVRDKSQEEVATIMKGGILVHDIYPEGAAAKDARLKFGDQILEL 71
DGR+++G + V G D+ + + GI++ + P G AA+ A + D IL+
Sbjct: 249 DGRVIRG--YIGVSGEDINSVVAQGLGLPDLRGIVITGVDPNGPAAR-AGILVRDVILKY 305
Query: 72 TGED 75
G+D
Sbjct: 306 DGKD 309
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 85
Score = 32.6 bits (75), Expect = 0.021
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 2 RAVPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
+PG AA G + GD I+++DG V S E+V +++G
Sbjct: 19 SVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLLRG 59
Score = 31.0 bits (71), Expect = 0.073
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 42 KGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
GG+++ + P AAK A +K GD I+ + GE ++ + LR
Sbjct: 12 DGGLVITSVLPGSPAAK-AGIKAGDIIVAIDGEPVDGLSLEDVVKLLR 58
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 31.0 bits (71), Expect = 0.068
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQ 34
VPG AA G L GD+I++++G ++
Sbjct: 20 VPGSPAAKAG-LKAGDRILAINGQKIKSWED 49
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 90
Score = 30.7 bits (70), Expect = 0.12
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 24 VDGTDVRDKSQEEVATIMKGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNIT 80
V D+ EE+ G+LV + P AAK A LK GD IL + G+ +++
Sbjct: 5 VTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAK-AGLKPGDVILAVNGKPVKSVA 60
Score = 26.4 bits (59), Expect = 3.8
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQ 34
PG AA G L GD I++V+G V+ +
Sbjct: 32 DPGSPAAKAG-LKPGDVILAVNGKPVKSVAD 61
>gnl|CDD|200578 cd10954, CE4_CtAXE_like, Catalytic NodB homology domain of
Clostridium thermocellum acetylxylan esterase and its
bacterial homologs. This family is represented by
Clostridium thermocellum acetylxylan esterase (CtAXE, EC
3.1.1.72), a member of the carbohydrate esterase 4 (CE4)
superfamily. CtAXE deacetylates O-acetylated xylan, a
key component of plant cell walls. It shows no
detectable activity on generic esterase substrates
including para-nitrophenyl acetate. It is specific for
sugar-based substrates and will precipitate acetylxylan,
as a consequence of deacetylation. CtAXE is a monomeric
protein containing a catalytic NodB homology domain with
the same overall topology and a deformed (beta/alpha)8
barrel fold as other CE4 esterases. However, due to
differences in the topography of the substrate-binding
groove, the chemistry of the active center, and metal
ion coordination, CtAXE has different metal ion
preference and lacks activity on N-acetyl substrates. It
is significantly activated by Co2+. Moreover, CtAXE
displays distinctly different ligand coordination to the
metal ion, utilizing an aspartate, a histidine, and four
water molecules, as opposed to the conserved His-His-Asp
zinc-binding triad of other CE4 esterases.
Length = 180
Score = 31.4 bits (72), Expect = 0.14
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 6/41 (14%)
Query: 23 SVDGTDVRDKS-QEEVATIMKGG-----ILVHDIYPEGAAA 57
SVD D + K+ ++ V+T++K IL+HDIYP A
Sbjct: 119 SVDTEDWKSKNAEKIVSTVLKQAKDGDIILMHDIYPSTVEA 159
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 31.9 bits (73), Expect = 0.15
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 36 EVATIMKGGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLRLTP 92
E+ GG+ V AAK A +K GD I+++ G+ ++ +A+ +R P
Sbjct: 105 ELQMEDIGGVKVVSPIDGSPAAK-AGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKP 160
Score = 31.5 bits (72), Expect = 0.18
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
+ G AA G + GD I+ +DG V S +E +++G
Sbjct: 120 IDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIRG 158
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 31.4 bits (72), Expect = 0.21
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 34 QEEVATIMK----GGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNITHAKAMAHLR 89
++A + G LV + P A K A LK GD I + G+ + A LR
Sbjct: 244 TSDLAKSLGLEKQRGALVAQVLPGSPAEK-AGLKAGDVITSVNGKPISS------FADLR 296
Query: 90 LTPAKAKPCPTVP 102
KP V
Sbjct: 297 RAIGTLKPGKKVT 309
Score = 27.6 bits (62), Expect = 4.2
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQ--EEVATIMKG 43
+PG A G L GD I SV+G + + + T+ G
Sbjct: 265 LPGSPAEKAG-LKAGDVITSVNGKPISSFADLRRAIGTLKPG 305
Score = 27.6 bits (62), Expect = 4.3
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 43 GGILVHDIYPEGAAAKDARLKFGDQILELTGEDFRNI 79
G++V + G+ A A L+ GD IL + + ++
Sbjct: 362 KGVVVTKVVS-GSPAARAGLQPGDVILSVNQQPVSSV 397
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 30.8 bits (70), Expect = 0.27
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 4 VPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKG 43
G A G + GD+I+ ++G V S ++ +++G
Sbjct: 70 FEGSPAEKAG-IKPGDKIIKINGKSVAGMSLDDAVALIRG 108
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 30.1 bits (68), Expect = 0.65
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 3 AVPGGIAATDGRLLKGDQIMSVDGTDVRDKSQEEVATIMKGG 44
PGG AA G + GD I+++DGT S E A ++G
Sbjct: 109 PAPGGPAARAG-IRPGDVILAIDGTSTEGLSLYEAADRLQGP 149
>gnl|CDD|200571 cd10947, CE4_SpPgdA_BsYjeA_like, Catalytic NodB homology domain of
Streptococcus pneumoniae peptidoglycan deacetylase PgdA,
Bacillus subtilis BsYjeA protein, and their bacterial
homologs. This family is represented by Streptococcus
pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA), a
member of the carbohydrate esterase 4 (CE4) superfamily.
SpPgdA protects gram-positive bacterial cell wall from
host lysozymes by deacetylating peptidoglycan
N-acetylglucosamine (GlcNAc) residues. It consists of
three separate domains: N-terminal, middle and
C-terminal (catalytic) domains. The catalytic NodB
homology domain is similar to the deformed (beta/alpha)8
barrel fold adopted by other CE4 esterases, which
harbors a mononuclear metalloenzyme employing a
conserved His-His-Asp zinc-binding triad closely
associated with conserved catalytic base (aspartic acid)
and acid (histidine) to carry out acid/base catalysis.
The enzyme is able to accept GlcNAc3 as a substrate,
with the N-acetyl of the middle sugar being removed by
the enzyme. This family also includes Bacillus subtilis
BsYjeA protein encoded by the yjeA gene, which is one of
the six polysaccharide deacetylase gene homologs (pdaA,
pdaB/ybaN, yheN, yjeA, yxkH and ylxY) in the Bacillus
subtilis genome. Although homology comparison shows that
the BsYjeA protein contains a polysaccharide deacetylase
domain, and was predicted to be a membrane-bound
xylanase or a membrane-bound chitooligosaccharide
deacetylase, more recent research indicates BsYjeA might
be a novel non-specific secretory endonuclease which
creates random nicks progressively on the two strands of
dsDNA, resulting in highly distinguishable
intermediates/products very different in chemical and
physical compositions over time. In addition, BsYjeA
shares several enzymatic properties with the
well-understood DNase I endonuclease. Both enzymes are
active on ssDNA and dsDNA, both generate random nicks,
and both require Mg2+ or Mn2+ for hydrolytic activity.
Length = 177
Score = 28.9 bits (65), Expect = 1.1
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 1 MRAVPGGIAATDGRLLKGDQIM-SVDGTDVRDKS-QEEVATIMK----GGI-LVHDIYPE 53
+R G + ++ + VD D ++ + V +M G I L+HDI+
Sbjct: 96 LRPPYGATNRSIRQIAGLTIALWDVDTRDWSKRNKDKIVTIVMNQVQPGSIVLMHDIHRT 155
Query: 54 GAAAKDARLKF 64
A A L +
Sbjct: 156 TADALPRILDY 166
>gnl|CDD|203730 pfam07700, HNOB, Heme NO binding. The HNOB (Heme NO Binding)
domain, is a predominantly alpha-helical domain and
binds heme via a covalent linkage to histidine. The
HNOB domain is predicted to function as a
heme-dependent sensor for gaseous ligands, and
transduce diverse downstream signals, in both bacteria
and animals.
Length = 171
Score = 28.4 bits (64), Expect = 1.3
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 21 IMSVDGTDVRDKSQEEVATIMKGGILVHDIYPE-------GAAAKDARLKFGDQILELTG 73
+ G DV ++ E+ +G VH+ Y + AA+K + ++I E G
Sbjct: 13 VQRKYGEDVWEQILEKAGFEPEGVFTVHESYDDSELYDLVAAASKVLGIPA-EEIWEAFG 71
Query: 74 EDF 76
F
Sbjct: 72 RFF 74
>gnl|CDD|184614 PRK14314, glmM, phosphoglucosamine mutase; Provisional.
Length = 450
Score = 28.0 bits (63), Expect = 2.7
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 13 GRLLKGDQIMSVDGTDVRDKSQEE----VATIMKGGILVHDIYPEGAAAKDARLKFGD 66
G ++ GDQIM++ TD++ + VAT+M L ++ + + R GD
Sbjct: 257 GHIVDGDQIMAICATDLKKRGALPKNTLVATVMSNMGL--EVAMKELGGQVLRTPVGD 312
>gnl|CDD|220016 pfam08786, DUF1795, Domain of unknown function (DUF1795). This is
a bacterial domain of unknown function. It forms an
antiparallel beta sheet structure and contains some
alpha helical regions.
Length = 130
Score = 26.4 bits (59), Expect = 5.7
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 121 FQVKLVVLRDTVTKEDDLLEFVDVELTKKAGKGFGLSLVGRKQG-----PGVFI 169
+ LV+ RD + + L +++ +L + G +L+ R+ PGV +
Sbjct: 26 AGLSLVISRDPLEPGETLETYLERQLALLKKQLPGFTLLERQPATLGGHPGVEL 79
>gnl|CDD|220197 pfam09351, DUF1993, Domain of unknown function (DUF1993). This
family of proteins are functionally uncharacterized.
Length = 162
Score = 26.4 bits (59), Expect = 6.4
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 53 EGAAAKDARLKFGDQILELTGEDF 76
+GA +D L G + + TGE +
Sbjct: 105 DGAEDRDITLPLGGKEFDFTGEAY 128
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 25.3 bits (56), Expect = 8.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 15 LLKGDQIMSVDGTDVRDKSQ 34
L GD I+S+DG V ++
Sbjct: 31 LKPGDIILSIDGKKVNSLTE 50
>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional.
Length = 667
Score = 26.8 bits (60), Expect = 8.3
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 4 VPGGIAATDGRLLKGDQIMSV--DGTDVRD----KSQEEVATIM--KGGILVHDIYPEGA 55
V GG AA +L GD+I+ V DG + D + + VA I KG + +I P G
Sbjct: 263 VAGGPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWRLDDVVALIKGPKGSKVRLEILPAGK 322
Query: 56 AAK 58
K
Sbjct: 323 GTK 325
>gnl|CDD|191653 pfam06962, rRNA_methylase, Putative rRNA methylase. This family
contains a number of putative rRNA methylases. Note that
many family members are hypothetical proteins.
Length = 138
Score = 26.0 bits (58), Expect = 8.6
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 40 IMKGGILVHDIY---PEGAAAKDARLKFGDQI 68
+ GG+++ IY EG KDA L F +
Sbjct: 80 LKPGGLIILVIYHGHEEGKKEKDAVLDFVSNL 111
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
0.317 0.136 0.385
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,886,941
Number of extensions: 813753
Number of successful extensions: 692
Number of sequences better than 10.0: 1
Number of HSP's gapped: 686
Number of HSP's successfully gapped: 53
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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 (21.6 bits)
S2: 56 (25.4 bits)