RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17926
(95 letters)
>gnl|CDD|237983 cd00016, alkPPc, Alkaline phosphatase homologues; alkaline
phosphatases are non-specific phosphomonoesterases that
catalyze the hydrolysis reaction via a phosphoseryl
intermediate to produce inorganic phosphate and the
corresponding alcohol, optimally at high pH. Alkaline
phosphatase exists as a dimer, each monomer binding 2
zinc atoms and one magnesium atom, which are essential
for enzymatic activity.
Length = 384
Score = 78.1 bits (193), Expect = 1e-18
Identities = 33/60 (55%), Positives = 39/60 (65%), Gaps = 13/60 (21%)
Query: 20 GKATGIVTNTRVTHATPAAFYGHSPSRYWEDDGKVPVISRKSCKDLARQLVEDYPGKDIN 79
GKATGIVT TRVTHATPAAFY H P R WE+ D+A QL+E+ PG+ I+
Sbjct: 109 GKATGIVTTTRVTHATPAAFYAHVPDRNWEE-------------DIAEQLIEEAPGRGID 155
>gnl|CDD|214515 smart00098, alkPPc, Alkaline phosphatase homologues.
Length = 419
Score = 70.9 bits (174), Expect = 6e-16
Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 3 LDLEKVRRVQTYV--AYGTGKATGIVTNTRVTHATPAAFYGHSPSRYWEDDGKVPVISR- 59
+D + V + + A GK+TG+VT TR+THATPAA Y H SR W +D +P +
Sbjct: 79 VDAATGKEVPSVLEWAKKAGKSTGLVTTTRITHATPAATYAHVASRKWYNDADIPAEALE 138
Query: 60 KSCKDLARQLVE 71
C D+ARQL+
Sbjct: 139 NGCGDIARQLIN 150
>gnl|CDD|201110 pfam00245, Alk_phosphatase, Alkaline phosphatase.
Length = 421
Score = 64.0 bits (156), Expect = 1e-13
Identities = 27/53 (50%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 20 GKATGIVTNTRVTHATPAAFYGHSPSRYWEDDGKVPVISRKS-CKDLARQLVE 71
GK+TG+VT TR+THATPAA Y H +R W D +P + CKD+A QL+
Sbjct: 97 GKSTGLVTTTRITHATPAATYAHVTNRKWYGDIAMPASALDEGCKDIAHQLIS 149
>gnl|CDD|224699 COG1785, PhoA, Alkaline phosphatase [Inorganic ion transport and
metabolism].
Length = 482
Score = 60.5 bits (147), Expect = 3e-12
Identities = 22/32 (68%), Positives = 25/32 (78%)
Query: 20 GKATGIVTNTRVTHATPAAFYGHSPSRYWEDD 51
GKATG+VT TR+THATPAAF H SR ED+
Sbjct: 154 GKATGLVTTTRITHATPAAFAAHVTSRDDEDE 185
>gnl|CDD|236706 PRK10518, PRK10518, alkaline phosphatase; Provisional.
Length = 476
Score = 36.2 bits (84), Expect = 0.001
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 15 VAYGTGKATGIVTNTRVTHATPAAFYGHSPSR 46
+A GKATG V+ + ATPAA H SR
Sbjct: 162 LAKAAGKATGNVSTAELQDATPAALVAHVTSR 193
>gnl|CDD|144565 pfam01024, Colicin, Colicin pore forming domain.
Length = 187
Score = 28.1 bits (63), Expect = 0.51
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 63 KDLARQLVEDYPGKDINSFDE 83
K LAR+L +D GK I S DE
Sbjct: 35 KKLARELADDAKGKKIRSVDE 55
>gnl|CDD|237766 PRK14609, PRK14609, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 269
Score = 28.0 bits (63), Expect = 0.55
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 11/50 (22%)
Query: 34 ATPAAFYGHSPSRYWEDDGKVPVISRKSCKDLARQLVEDYPGKDINSFDE 83
+T A+ G P S K++ RQ VE++ K +N F++
Sbjct: 175 STAEAY-----------AGIKPHKPETSLKEIIRQPVEEWKNKLVNDFED 213
>gnl|CDD|234338 TIGR03742, PRTRC_F, PRTRC system protein F. A novel genetic system
characterized by seven (usually) major proteins,
including a ParB homolog and a ThiF homolog, is commonly
found on plasmids or in bacterial chromosomal regions
near phage, plasmid, or transposon markers. It is most
common among the beta Proteobacteria. We designate the
system PRTRC, or ParB-Related,ThiF-Related Cassette.
This protein family is designated protein F. It is the
most divergent of the families.
Length = 342
Score = 27.4 bits (61), Expect = 0.94
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 13 TYVAYGTGKATGIVTNTRVTHATPAAFYGHSPSRYWEDD 51
V Y +A+ TP A + H YWE +
Sbjct: 135 LDVIY---RASARGPGLY----TPDALFDHFSYIYWEGE 166
>gnl|CDD|132479 TIGR03438, egtD_ergothio, dimethylhistidine N-methyltransferase.
This model represents a distinct set of uncharacterized
proteins found in the bacteria. Analysis by PSI-BLAST
shows remote sequence homology to methyltransferases
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 301
Score = 26.0 bits (58), Expect = 3.1
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 42 HSPSRYWEDDGKVPV-ISRKSCKDLARQLVEDYPGKDI 78
P+RY VP+ IS + K+ A L DYP ++
Sbjct: 86 RQPARY------VPIDISADALKESAAALAADYPQLEV 117
>gnl|CDD|222492 pfam14009, DUF4228, Domain of unknown function (DUF4228). This
domain is found in plants. The function is not known.
Length = 181
Score = 25.8 bits (57), Expect = 3.5
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 51 DGKVPVISRKSCKDLARQLVEDYPGKDINSFDEFYPGKDINA 92
DGKV SR A +L+ +YPG + D Y G+ I A
Sbjct: 24 DGKVREYSRPVT---AAELMLEYPGHFVCDSDSLYIGRRIPA 62
>gnl|CDD|133137 cd05470, pepsin_retropepsin_like, Cellular and retroviral
pepsin-like aspartate proteases. This family includes
both cellular and retroviral pepsin-like aspartate
proteases. The cellular pepsin and pepsin-like enzymes
are twice as long as their retroviral counterparts. The
cellular pepsin-like aspartic proteases are found in
mammals, plants, fungi and bacteria. These well known
and extensively characterized enzymes include pepsins,
chymosin, rennin, cathepsins, and fungal aspartic
proteases. Several have long been known to be medically
(rennin, cathepsin D and E, pepsin) or commercially
(chymosin) important. The eukaryotic pepsin-like
proteases contain two domains possessing similar
topological features. The N- and C-terminal domains,
although structurally related by a 2-fold axis, have
only limited sequence homology except in the vicinity
of the active site. This suggests that the enzymes
evolved by an ancient duplication event. The eukaryotic
pepsin-like proteases have two active site ASP residues
with each N- and C-terminal lobe contributing one
residue. While the fungal and mammalian pepsins are
bilobal proteins, retropepsins function as dimers and
the monomer resembles structure of the N- or C-terminal
domains of eukaryotic enzyme. The active site motif
(Asp-Thr/Ser-Gly-Ser) is conserved between the
retroviral and eukaryotic proteases and between the
N-and C-terminal of eukaryotic pepsin-like proteases.
The retropepsin-like family includes pepsin-like
aspartate proteases from retroviruses, retrotransposons
and retroelements; as well as eukaryotic
DNA-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. Retropepsin is synthesized as
part of the POL polyprotein that contains an
aspartyl-protease, a reverse transcriptase, RNase H,
and an integrase. The POL polyprotein undergoes
specific enzymatic cleavage to yield the mature
proteins. This family of aspartate proteases is
classified by MEROPS as the peptidase family A1 (pepsin
A) and A2 (retropepsin family).
Length = 109
Score = 25.4 bits (56), Expect = 3.7
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 14 YVAYGTGKATGIVTNTRVT 32
+ YGTG +G ++ V+
Sbjct: 58 SITYGTGSLSGGLSTDTVS 76
>gnl|CDD|200935 pfam00022, Actin, Actin.
Length = 367
Score = 25.6 bits (57), Expect = 4.1
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 15 VAYGTGKATGIVTNT--RVTHATP 36
AY +G+ TG+V ++ VT P
Sbjct: 134 SAYASGRTTGLVVDSGAGVTSVVP 157
>gnl|CDD|185727 cd08986, GH43_7, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
(EC 3.2.1.99), xylanase (EC 3.2.1.8),
endo-alpha-L-arabinanase and galactan
1,3-beta-galactosidase (EC 3.2.1.145) activities. These
are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 269
Score = 25.4 bits (56), Expect = 4.6
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 30 RVTHATPAAFYGHSPSRYWEDDGKV 54
+ F G PS + +DDGKV
Sbjct: 120 KHITGNKPLFPGIDPSLFEDDDGKV 144
>gnl|CDD|100097 cd05805, MPG1_transferase, GTP-mannose-1-phosphate
guanyltransferase (MPG1 transferase), also known as
GDP-mannose pyrophosphorylase, is a bifunctional enzyme
with both phosphomannose isomerase (PMI) activity and
GDP-mannose phosphorylase (GMP) activity. The protein
contains an N-terminal NTP transferase domain, an
L-beta-H domain, and a C-terminal PGM-like domain that
belongs to the alpha-D-phosphohexomutase superfamily.
This subfamily is limited to bacteria and archaea. The
alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Members
of this group appear to lack conserved residues
necessary for metal binding and catalytic activity.
Other members of this superfamily include the
phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 441
Score = 25.7 bits (57), Expect = 4.8
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 11/35 (31%)
Query: 48 WEDDGKVPVISRKSCKDLARQLVEDYPGKDINSFD 82
WE G+V R+L+E+ P K I D
Sbjct: 373 WEAKGRV-----------MRRLIEEAPDKSIELID 396
>gnl|CDD|130208 TIGR01138, cysM, cysteine synthase B. CysM differs from CysK in
that it can also use thiosulfate instead of sulfide, to
produce cysteine thiosulfonate instead of cysteine.
Alternate name: O-acetylserine (thiol)-lyase [Amino acid
biosynthesis, Serine family].
Length = 290
Score = 25.3 bits (55), Expect = 5.5
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 63 KDLARQLVEDYPGKDINSFDEFYPGKDINAHQH 95
+DLA +L GK D+F + AH
Sbjct: 121 RDLALELANRGEGK---LLDQFNNPDNPYAHYT 150
>gnl|CDD|225152 COG2243, CobF, Precorrin-2 methylase [Coenzyme metabolism].
Length = 234
Score = 24.9 bits (55), Expect = 6.3
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 52 GKVPVI---SRKSCKDLARQLVEDY 73
K V+ S+K LAR++VEDY
Sbjct: 26 KKADVVYVPSKKGKGSLAREIVEDY 50
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and
other members of the AlkA family.
Length = 144
Score = 24.6 bits (54), Expect = 7.0
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 63 KDLARQLVEDYPGKDINSFDE 83
K+LAR LVE Y G +E
Sbjct: 59 KELARILVEGYLGLVPLDLEE 79
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I
amino acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in
ATP binding.
Length = 143
Score = 24.7 bits (54), Expect = 7.6
Identities = 11/63 (17%), Positives = 19/63 (30%)
Query: 20 GKATGIVTNTRVTHATPAAFYGHSPSRYWEDDGKVPVISRKSCKDLARQLVEDYPGKDIN 79
G IVT + A Y +D G + + A+ VE + +
Sbjct: 15 GHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANKKGENAKAFVERWIERIKE 74
Query: 80 SFD 82
+
Sbjct: 75 DVE 77
>gnl|CDD|197612 smart00263, LYZ1, Alpha-lactalbumin / lysozyme C.
Length = 127
Score = 24.6 bits (54), Expect = 8.3
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 45 SRYWEDDGKVPVISRKSCKDLARQLVEDYPGKDIN 79
S+YW +DGK P S +C +L++D D+
Sbjct: 60 SKYWCNDGKTPG-SVNACGISCSKLLDDDITDDVK 93
>gnl|CDD|223707 COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase
[Nucleotide transport and metabolism].
Length = 178
Score = 24.8 bits (55), Expect = 8.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 59 RKSCKDLARQLVEDYPGKDI 78
+ K+LA Q+ EDY GKD
Sbjct: 18 KARIKELAAQITEDYGGKDP 37
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 0.134 0.410
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,015,410
Number of extensions: 405385
Number of successful extensions: 407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 28
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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: 53 (24.2 bits)