RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17172
(80 letters)
>gnl|CDD|109297 pfam00233, PDEase_I, 3'5'-cyclic nucleotide phosphodiesterase.
Length = 237
Score = 56.7 bits (137), Expect = 2e-11
Identities = 28/65 (43%), Positives = 35/65 (53%), Gaps = 13/65 (20%)
Query: 28 YHNSIHATD-------------IKRHLTHLEIMASLLAAVAHDLDHPGVNQPFLIATSNH 74
YHN HA D ++R+LT LEI+A L AA HD+DH G N F I + +
Sbjct: 1 YHNWRHAADVTQTTHLLLLTLALERYLTDLEILALLFAAAIHDVDHRGTNNSFQINSKSE 60
Query: 75 LAALY 79
LA LY
Sbjct: 61 LAILY 65
>gnl|CDD|220395 pfam09778, Guanylate_cyc_2, Guanylylate cyclase. Members of this
family of proteins catalyze the conversion of guanosine
triphosphate (GTP) to 3',5'-cyclic guanosine
monophosphate (cGMP) and pyrophosphate.
Length = 212
Score = 28.5 bits (64), Expect = 0.26
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 2 EHFNLDVVRVWKLFSLIEEGYHGTNPYHNSIHATDIKRHL 41
+HF+ D VRV +LF E G + S+ +I+ HL
Sbjct: 83 KHFDADEVRVNELFQKAES--AGIDVECRSVSIQEIQEHL 120
>gnl|CDD|183950 PRK13287, amiF, formamidase; Provisional.
Length = 333
Score = 27.0 bits (60), Expect = 0.93
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 10 RVWKLFSLIEEGYHGTNPYHNSI 32
+VW +FS++E G PY+ +I
Sbjct: 96 KVWGVFSIMERNPDGNEPYNTAI 118
>gnl|CDD|214679 smart00471, HDc, Metal dependent phosphohydrolases with conserved
'HD' motif. Includes eukaryotic cyclic nucleotide
phosphodiesterases (PDEc). This profile/HMM does not
detect HD homologues in bacterial glycine
aminoacyl-tRNA synthetases (beta subunit).
Length = 124
Score = 26.1 bits (57), Expect = 1.5
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 26 NPYHNSIH-------ATDIKRHLTHLEIMASLLAAVAHDLDHPGVNQPFLIATSNHL 75
+ YH H A + L L+I LLAA+ HD+ PG FL+ TS
Sbjct: 1 SDYHVFEHSLRVAQLAAALAEELGLLDIELLLLAALLHDIGKPGTPDSFLVKTSVLE 57
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other enzymes)
catalyzes NADP-dependent sterol C-4 demethylation, as
part of steroid biosynthesis. 3-keto reductase is a
classical SDR, with a well conserved canonical active
site tetrad and fairly well conserved characteristic
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 290
Score = 26.2 bits (58), Expect = 1.6
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 13 KLFSLIE-EGYHGTNPYHNSIHATDIKRHLTHLEIMASLLAAVAHDLDHPGVNQPFLIAT 71
K FSL + + G PY +S + D+ L L V + HPG+ L
Sbjct: 186 KYFSLEDIQHLKGPAPYSSSKYLVDL-LSLALNRKFNKL--GVYSYVVHPGICTTNLTYG 242
Query: 72 S 72
Sbjct: 243 I 243
>gnl|CDD|219473 pfam07580, Peptidase_M26_C, M26 IgA1-specific Metallo-endopeptidase
C-terminal region. These peptidases, which cleave
mammalian IgA, are found in Gram-positive bacteria.
Often found associated with pfam00746, they may be
attached to the cell wall.
Length = 731
Score = 26.5 bits (59), Expect = 1.7
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 13 KLFSLIEEGYHGTNPYHNSIHATDIKRHLTHLEIMASL 50
K F IE Y + N H D+ R LT E L
Sbjct: 497 KWFKKIENKYV-KDRDGNDTHQWDVVRDLTAEEKAKKL 533
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 25.7 bits (57), Expect = 2.6
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 39 RHLT-HLEIMA----SLLAAVAHDLDHPGVNQPFLIATSNHLAALY 79
RH T H+E+ LLA D PG NQP L + LA +
Sbjct: 211 RHTTRHVELFELPNGGLLA------DTPGFNQPDLDCSPRELAHYF 250
>gnl|CDD|143589 cd07565, aliphatic_amidase, aliphatic amidases (class 2
nitrilases). Aliphatic amidases catalyze the hydrolysis
of short-chain aliphatic amides to form ammonia and the
corresponding organic acid. This group includes
Pseudomonas aeruginosa (Pa) AmiE, the amidase from
Geobacillus pallidus RAPc8 (RAPc8 amidase), and
Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and
HpAmiE hydrolyze various very short aliphatic amides,
including propionamide, acetamide and acrylamide. HpAmiF
is a formamidase which specifically hydrolyzes
formamide. These proteins belong to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to class 2. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer. HpAmiE ,
HpAmiF, and RAPc8 amidase, and PaAimE appear to be
homohexameric enzymes, trimer of dimers.
Length = 291
Score = 25.7 bits (57), Expect = 2.9
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 10 RVWKLFSLIE--EGYHGTNPYHNSI 32
+VW +FS++E HG NPY+ +I
Sbjct: 83 KVWGVFSIMERNPD-HGKNPYNTAI 106
>gnl|CDD|188641 cd00954, NAL, N-Acetylneuraminic acid aldolase, also called
N-acetylneuraminate lyase (NAL). N-Acetylneuraminic
acid aldolase, also called N-acetylneuraminate lyase
(NAL), which catalyses the reversible aldol reaction of
N-acetyl-D-mannosamine and pyruvate to give
N-acetyl-D-neuraminic acid (D-sialic acid). It has a
widespread application as biocatalyst for the synthesis
of sialic acid and its derivatives. This enzyme has been
shown to be quite specific for pyruvate as the donor,
but flexible to a variety of D- and, to some extent,
L-hexoses and pentoses as acceptor substrates. NAL is
member of dihydrodipicolinate synthase family that
comprises several pyruvate-dependent class I aldolases.
Length = 288
Score = 25.0 bits (55), Expect = 4.3
Identities = 16/85 (18%), Positives = 24/85 (28%), Gaps = 16/85 (18%)
Query: 4 FNLDVVRVWKLFSLIEEG--------YHGTNPYHNSIHATDIKRHLTHLEIMASLLAAVA 55
+N++ R K+F G H N + + + T I+
Sbjct: 208 YNVNGKRYRKIFEAFNAGDIDTARELQHVINDVITVLIKNGL--YPTLKAILR------L 259
Query: 56 HDLDHPGVNQPFLIATSNHLAALYE 80
LD P T LA E
Sbjct: 260 MGLDAGPCRLPLRKVTEKALAKAKE 284
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 25.0 bits (55), Expect = 4.7
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 9/51 (17%)
Query: 15 FSLIEEGYHGTNPYHNSIHATDIKRHL---------THLEIMASLLAAVAH 56
+++E G +P A I HL THL +A L + H
Sbjct: 102 LYILDEIDRGLDPRDGQALAEAILEHLVKGAQVIVITHLPELAELADKLIH 152
>gnl|CDD|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G
(eIF4G). Also occurs in NMD2p and CBP80. The domain is
rich in alpha-helices and may contain multiple
alpha-helical repeats. In eIF4G, this domain binds
eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G
domain homologues (in press).
Length = 200
Score = 24.6 bits (54), Expect = 5.3
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 7/60 (11%)
Query: 2 EHFNLDVVRVWKLFSLIEEGYHGTNPYHNSIHATDIKRHLTHLEIMASLLAAVAHDLDHP 61
E +N V+ + L++E N + D R +E + SLL DL+
Sbjct: 105 ELYNFQVLTSKIILELLKELL-------NDLTKLDPPRSDFSVECLLSLLPTCGKDLERE 157
>gnl|CDD|226848 COG4424, COG4424, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 250
Score = 24.5 bits (53), Expect = 6.9
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 45 EIMASLLAAVAHDLDHPGVNQPFLIATS 72
+ A AAVA L+ GV+ P A
Sbjct: 196 VLSADPTAAVASVLEALGVDPPLAPAPM 223
>gnl|CDD|220877 pfam10797, YhfT, Protein of unknown function. This family is
conserved in Firmicutes and Proteobacteria. The function
is not known but several members are annotated as being
homologues of E coli YhfT, a protein thought to be
involved in fatty acid oxidation.
Length = 421
Score = 24.6 bits (54), Expect = 7.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 37 IKRHLTHLEIMASLLAAVAH 56
IK++L L IM +L+AA A
Sbjct: 227 IKKNLPLLAIMGALIAAAAS 246
>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 24.3 bits (53), Expect = 8.7
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 54 VAHDLDHPGVNQPFLIATSNHLAALY 79
++H L+ V +PF+IAT+ L+ L+
Sbjct: 520 ISHWLNTHAVIEPFVIATNRQLSVLH 545
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 0.136 0.419
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,187,257
Number of extensions: 324845
Number of successful extensions: 290
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 22
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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 (22.0 bits)
S2: 53 (24.2 bits)