RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13598
(163 letters)
>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic
domain.
Length = 184
Score = 84.6 bits (210), Expect = 3e-21
Identities = 35/98 (35%), Positives = 61/98 (62%), Gaps = 3/98 (3%)
Query: 2 CRYVQQTTNSPVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMEQSGLPGRVHIS 61
+ V + + +RVGIHTG V+AGV+G R+ ++DV+ V LA++ME +G+PG++H+S
Sbjct: 89 IKSVNIHSFEGLRVRVGIHTGPVVAGVIGARRPRYDVWGDTVNLASRMESTGVPGKIHVS 148
Query: 62 EKTLCYIDGNFEVEPAFGENREEALRQAG-LKTFFIVN 98
E+T + + E F E E ++ G ++T+F+
Sbjct: 149 EETYRLLKTREQFE--FTERGEVEVKGKGKMETYFLNG 184
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 77.3 bits (191), Expect = 3e-18
Identities = 23/53 (43%), Positives = 39/53 (73%)
Query: 12 PVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMEQSGLPGRVHISEKT 64
+ +R+GIHTG V+AGV+G R ++ ++ V LA++ME +G PG++ +SE+T
Sbjct: 129 GLRVRIGIHTGPVVAGVVGIRMPRYCLFGDTVNLASRMESAGDPGQIQVSEET 181
>gnl|CDD|143636 cd07302, CHD, cyclase homology domain. Catalytic domains of the
mononucleotidyl cyclases (MNC's), also called cyclase
homology domains (CHDs), are part of the class III
nucleotidyl cyclases. This class includes eukaryotic and
prokaryotic adenylate cyclases (AC's) and guanylate
cyclases (GC's). They seem to share a common catalytic
mechanism in their requirement for two magnesium ions to
bind the polyphosphate moiety of the nucleotide.
Length = 177
Score = 68.8 bits (169), Expect = 4e-15
Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 12 PVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMEQSGLPGRVHISEKTLCYI-DG 70
P+ +R+GIHTG V+AGV+G + ++ V V LA ++E PG++ +SE T + D
Sbjct: 94 PLRLRIGIHTGPVVAGVVGSERPEYTVIGDTVNLAARLESLAKPGQILVSEATYELLGDA 153
Query: 71 NFEVEP 76
FE E
Sbjct: 154 GFEFEE 159
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.
Class III nucleotidyl cyclases are the largest, most
diverse group of nucleotidyl cyclases (NC's) containing
prokaryotic and eukaryotic proteins. They can be divided
into two major groups; the mononucleotidyl cyclases
(MNC's) and the diguanylate cyclases (DGC's). The
MNC's, which include the adenylate cyclases (AC's) and
the guanylate cyclases (GC's), have a conserved cyclase
homology domain (CHD), while the DGC's have a conserved
GGDEF domain, named after a conserved motif within this
subgroup. Their products, cyclic guanylyl and adenylyl
nucleotides, are second messengers that play important
roles in eukaryotic signal transduction and prokaryotic
sensory pathways.
Length = 133
Score = 58.1 bits (141), Expect = 1e-11
Identities = 24/55 (43%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 5 VQQTTNSPVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMEQSGLPGRVH 59
+ Q+ +PV +R+GIHTG V+ GV+G R Q+DV+ V LA++ME G+V
Sbjct: 80 LNQSEGNPVRVRIGIHTGPVVVGVIGSR-PQYDVWGALVNLASRMESQAKAGQVL 133
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 40.6 bits (95), Expect = 1e-04
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 12 PVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMEQSGLPGRVHISEKTL 65
+ +R+GIHTG V+ G G + V V A ++E PG+V +SE T
Sbjct: 134 SLRVRIGIHTGEVVVGNTG----GYTVVGSAVNQAARLESLAKPGQVLLSEATY 183
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 423
Score = 35.2 bits (82), Expect = 0.010
Identities = 20/75 (26%), Positives = 27/75 (36%), Gaps = 23/75 (30%)
Query: 44 ELANKM-EQSGLPGRVHISEKTLCYIDGNFEVEPAFGENREEALRQAGLKTFFIVNTIVP 102
LA K+ E+ G P ++ E T +R EAL A F++NTI
Sbjct: 47 ILAKKIVEELGAPLKI---EAT---------------TDRREALDGAD----FVINTIQV 84
Query: 103 DNKNSFVIRVHISEK 117
I EK
Sbjct: 85 GGHEYTETDFEIPEK 99
>gnl|CDD|236318 PRK08639, PRK08639, threonine dehydratase; Validated.
Length = 420
Score = 32.5 bits (75), Expect = 0.086
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 59 HISEKT-LCYIDG-NFEVEPAFGENREEALRQAGLKTFFIVN 98
I KT +C I G N ++E E +E +L GLK +FIVN
Sbjct: 302 EIKGKTVVCVISGGNNDIE-RMPEIKERSLIYEGLKHYFIVN 342
Score = 32.5 bits (75), Expect = 0.086
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 113 HISEKT-LCYIDG-NFEVEPAFGENREEALRQAGLKTFFIVN 152
I KT +C I G N ++E E +E +L GLK +FIVN
Sbjct: 302 EIKGKTVVCVISGGNNDIE-RMPEIKERSLIYEGLKHYFIVN 342
>gnl|CDD|233712 TIGR02079, THD1, threonine dehydratase. This model represents
threonine dehydratase, the first step in the pathway
converting threonine into isoleucine. At least two other
clades of biosynthetic threonine dehydratases have been
charcterized (TIGR01124 and TIGR01127). Those sequences
described by this model are exclusively found in species
containg the rest of the isoleucine pathway and which
are generally lacking in members of the those other two
clades of threonine dehydratases. Members of this clade
are also often gene clustered with other elements of the
isoleucine pathway [Amino acid biosynthesis, Pyruvate
family].
Length = 409
Score = 30.5 bits (69), Expect = 0.34
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 19 IHTGAVLAGVLGQRQWQFDVYSKD---VELANKMEQSGLP-GRVHISEKT-LCYIDG-NF 72
+ GAV +L D+Y+ + E A + + L I KT +C + G N
Sbjct: 254 VPEGAVCTTIL-------DLYNLEGIVAEPAGALSIAALERLGEEIKGKTVVCVVSGGNN 306
Query: 73 EVEPAFGENREEALRQAGLKTFFIVN 98
++E E RE +L GLK +FIV
Sbjct: 307 DIE-RTEEIRERSLLYEGLKHYFIVR 331
Score = 29.3 bits (66), Expect = 0.95
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 111 RVHISEKT-LCYIDG-NFEVEPAFGENREEALRQAGLKTFFIVN 152
I KT +C + G N ++E E RE +L GLK +FIV
Sbjct: 289 GEEIKGKTVVCVVSGGNNDIE-RTEEIRERSLLYEGLKHYFIVR 331
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 30.2 bits (68), Expect = 0.59
Identities = 33/135 (24%), Positives = 51/135 (37%), Gaps = 29/135 (21%)
Query: 13 VDMRVGIHTGAVLA---GVLGQRQWQFDVYSKDVELANKMEQSGLPGRVHISEKTLCYID 69
V++ GIHTG VLA G A +M+ PG++ +SE +
Sbjct: 386 VEIAAGIHTGLVLAQAPHASGGTT---------PNAAVRMQAQAEPGQILVSEAARKLLR 436
Query: 70 GNFEVEPAFGENREEALRQAGLKTFFIVNTIVPDNKNSFVIRVHISEKTLCYIDGNFEVE 129
+ + +P EEA AG V ++ + + +DG
Sbjct: 437 RHADFDPT---ALEEAA--AGA-ESQPVFELLGE---------RAARTPFTSLDGG-TTT 480
Query: 130 PAFGENRE-EALRQA 143
P G +RE EALR+
Sbjct: 481 PLVGRSRELEALRRR 495
>gnl|CDD|219209 pfam06870, RNA_pol_I_A49, A49-like RNA polymerase I associated
factor. Saccharomyces cerevisiae A49 is a specific
subunit associated with RNA polymerase I (Pol I) in
eukaryotes. Pol I maintains transcription activities in
A49 deletion mutants. However, such mutants are
deficient in transcription activity at low temperatures.
Deletion analysis of the fusion yeast homolog indicate
that only the C-terminal two thirds are required for
function. Transcript analysis has demonstrated that A49
is maximising transcription of ribosomal DNA.
Length = 385
Score = 27.3 bits (61), Expect = 4.5
Identities = 15/53 (28%), Positives = 19/53 (35%), Gaps = 8/53 (15%)
Query: 84 EALRQAGLKTFFIVNTIVPDNKNSFVIRVHISEKTLCYI------DGNFEVEP 130
E L LK F + + S I +K LCYI NF V+
Sbjct: 269 EILIDKILKRFTDPTSN--NGGRSNRISPTHEDKLLCYILALALHLDNFSVDL 319
>gnl|CDD|202395 pfam02785, Biotin_carb_C, Biotin carboxylase C-terminal domain.
Biotin carboxylase is a component of the acetyl-CoA
carboxylase multi-component enzyme which catalyzes the
first committed step in fatty acid synthesis in animals,
plants and bacteria. Most of the active site residues
reported in reference are in this C-terminal domain.
Length = 107
Score = 25.9 bits (58), Expect = 5.3
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 131 AFGENREEALR--QAGLKTFFI--VNTIVPYSFAIL 162
G +REEA+ + L I V T +P+ AIL
Sbjct: 56 VHGPDREEAIARLRRALAETRIEGVKTNIPFLRAIL 91
>gnl|CDD|214878 smart00878, Biotin_carb_C, Biotin carboxylase C-terminal domain.
Biotin carboxylase is a component of the acetyl-CoA
carboxylase multi-component enzyme which catalyses the
first committed step in fatty acid synthesis in animals,
plants and bacteria. Most of the active site residues
reported in reference are in this C-terminal domain.
Length = 107
Score = 25.5 bits (57), Expect = 9.1
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 131 AFGENREEALR--QAGLKTFFI--VNTIVPYSFAIL 162
+GE+REEA+ + L F I V T +P+ A+L
Sbjct: 56 VWGEDREEAIARLRRALDEFRIRGVKTNIPFLRALL 91
>gnl|CDD|220584 pfam10120, Aldolase_2, Putative aldolase. Members of this family
of archaeal and bacterial proteins are likely to be
aldolases.
Length = 169
Score = 25.7 bits (57), Expect = 9.3
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 11/78 (14%)
Query: 77 AFGENREEALRQAGLKTFFIVNTIVPDNKNSFVIRVHISEK--------TLCYIDGNFEV 128
+ E EAL++ GLK P+ ++ I E + Y G
Sbjct: 89 RYDEEIVEALKKLGLKVSEFDREEEPEEVKGKTMQWGIEEAIESLGGVPDVIYDLGGVGK 148
Query: 129 EPA---FGENREEALRQA 143
EP G + E + +
Sbjct: 149 EPMIRVLGRDPVEVVEKL 166
>gnl|CDD|163513 TIGR03801, asp_4_decarbox, aspartate 4-decarboxylase. This enzyme,
aspartate 4-decarboxylase (EC 4.1.1.12), removes the
side-chain carboxylate from L-aspartate, converting it
to L-alanine plus carbon dioxide. It is a PLP-dependent
enzyme, homologous to aspartate aminotransferase (EC
2.6.1.1) [Energy metabolism, Amino acids and amines].
Length = 521
Score = 26.1 bits (58), Expect = 9.7
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 84 EALRQAGLKTFFIVNTIVPDNKNSFVIRVHISEKTLCYI 122
E LR +K F+VN P N S V +S++++ I
Sbjct: 234 EKLRDPSIKALFVVN---PSNPPS----VAMSDESIEKI 265
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
0.322 0.138 0.414
Gapped
Lambda K H
0.267 0.0887 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,387,048
Number of extensions: 766695
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 738
Number of HSP's successfully gapped: 21
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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 (21.9 bits)
S2: 55 (24.7 bits)