RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7597
(188 letters)
>gnl|CDD|99996 cd04300, GT1_Glycogen_Phosphorylase, This is a family of
oligosaccharide phosphorylases. It includes yeast and
mammalian glycogen phosphorylases, plant starch/glucan
phosphorylase, as well as the maltodextrin
phosphorylases of bacteria. The members of this family
catalyze the breakdown of oligosaccharides into
glucose-1-phosphate units. They are important allosteric
enzymes in carbohydrate metabolism. The allosteric
control mechanisms of yeast and mammalian members of
this family are different from that of bacterial
members. The members of this family belong to the GT-B
structural superfamily of glycoslytransferases, which
have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility.
Length = 797
Score = 104 bits (261), Expect = 3e-26
Identities = 34/45 (75%), Positives = 39/45 (86%)
Query: 15 QKLGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
+LG+D+E+LE E DAGLGNGGLGRLAACFLDS+ATLGL YGY
Sbjct: 86 AELGVDLEDLEEQEPDAGLGNGGLGRLAACFLDSLATLGLPGYGY 130
>gnl|CDD|215868 pfam00343, Phosphorylase, Carbohydrate phosphorylase. The
members of this family catalyze the formation of
glucose 1-phosphate from one of the following
polyglucoses; glycogen, starch, glucan or maltodextrin.
Length = 712
Score = 95.9 bits (239), Expect = 3e-23
Identities = 35/44 (79%), Positives = 39/44 (88%)
Query: 16 KLGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
+LGL++EEL E DAGLGNGGLGRLAACFLDS+ATLGL AYGY
Sbjct: 4 ELGLNLEELLEEENDAGLGNGGLGRLAACFLDSLATLGLPAYGY 47
>gnl|CDD|233722 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.
This family consists of phosphorylases. Members use
phosphate to break alpha 1,4 linkages between pairs of
glucose residues at the end of long glucose polymers,
releasing alpha-D-glucose 1-phosphate. The nomenclature
convention is to preface the name according to the
natural substrate, as in glycogen phosphorylase, starch
phosphorylase, maltodextrin phosphorylase, etc. Name
differences among these substrates reflect differences
in patterns of branching with alpha 1,6 linkages.
Members include allosterically regulated and unregulated
forms. A related family, TIGR02094, contains examples
known to act well on particularly small alpha 1,4
glucans, as may be found after import from exogenous
sources [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 794
Score = 92.7 bits (231), Expect = 3e-22
Identities = 35/44 (79%), Positives = 39/44 (88%)
Query: 16 KLGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
+LGLD+EE+ IE DAGLGNGGLGRLAACFLDS+ATLGL A GY
Sbjct: 84 ELGLDLEEILEIENDAGLGNGGLGRLAACFLDSLATLGLPATGY 127
>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
Length = 815
Score = 75.3 bits (185), Expect = 4e-16
Identities = 32/45 (71%), Positives = 36/45 (80%)
Query: 15 QKLGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
+ +GLD+EEL E D GLGNGGLGRLAACFLDS+ATLGL GY
Sbjct: 103 EAMGLDLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGY 147
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 73.1 bits (180), Expect = 2e-15
Identities = 26/43 (60%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 17 LGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
LG + E E D GLG GGLGRLA CFLDS A LGL GY
Sbjct: 97 LGYFLMEFGEHESDPGLG-GGLGRLAGCFLDSAADLGLPLTGY 138
>gnl|CDD|237881 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional.
Length = 798
Score = 68.9 bits (169), Expect = 5e-14
Identities = 26/42 (61%), Positives = 31/42 (73%)
Query: 18 GLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGY 59
+++ +L E D LGNGGLGRLAACFLDSMAT+G A GY
Sbjct: 95 DINLTDLLEEETDPALGNGGLGRLAACFLDSMATVGQPATGY 136
>gnl|CDD|176028 cd08382, C2_Smurf-like, C2 domain present in Smad
ubiquitination-related factor (Smurf)-like proteins. A
single C2 domain is found in Smurf proteins,
C2-WW-HECT-domain E3s, which play an important role in
the downregulation of the TGF-beta signaling pathway.
Smurf proteins also regulate cell shape, motility, and
polarity by degrading small guanosine triphosphatases
(GTPases). C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. Members here have type-II
topology.
Length = 123
Score = 27.7 bits (62), Expect = 2.2
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 7/68 (10%)
Query: 69 TGRIKETLQPQEATLHQKVTVLFEIAGGRKTETVPALSGQRQKHETLAPFTGLAFYKANN 128
T K+TL P+ H +TV G + + Q++ + F G +AN
Sbjct: 37 TDVAKKTLDPKWNE-HFDLTV------GPSSIITIQVFDQKKFKKKDQGFLGCVRIRANA 89
Query: 129 FVSSKAPG 136
+ K G
Sbjct: 90 VLPLKDTG 97
>gnl|CDD|187816 cd09685, Cas7_I-A, CRISPR/Cas system-associated RAMP superfamily
protein Cas7. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas7 is a RAMP superfamily protein; Subunit of the
Cascade complex; also known as DevR family.
Length = 274
Score = 28.2 bits (63), Expect = 2.6
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 69 TGRIK---ETLQPQEA----TLHQKVTVLFEIAGGRKTETVPALSGQRQKH 112
+GR++ E L E+ H++ V+ + G VPA+SG+ H
Sbjct: 1 SGRVRVNVEALNGVESAGNYVKHRRAPVVVKTDNGYTVYEVPAISGESLAH 51
>gnl|CDD|226145 COG3618, COG3618, Predicted metal-dependent hydrolase of the
TIM-barrel fold [General function prediction only].
Length = 279
Score = 28.1 bits (63), Expect = 2.8
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 2/53 (3%)
Query: 17 LGLDIE-ELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSAYGYEC-FMMVLI 67
D E EL + E A G +G + C + A L + Y + L
Sbjct: 62 DPRDNEKELAFVAELAERHGGIVGVIDECRPEFAAKLERARYPFFRGVRRNLH 114
>gnl|CDD|216777 pfam01905, DevR, CRISPR-associated negative auto-regulator
DevR/Csa2. This group of families is one of several
protein families that are always found associated with
prokaryotic CRISPRs, themselves a family of clustered
regularly interspaced short palindromic repeats, DNA
repeats found in nearly half of all bacterial and
archaeal genomes. These DNA repeat regions have a
remarkably regular structure: unique sequences of
constant size, called spacers, sit between each pair of
repeats. It has been shown that the CRISPRs are
virus-derived sequences acquired by the host to enable
them to resist viral infection. The Cas proteins from
the host use the CRISPRs to mediate an antiviral
response. After transcription of the CRISPR, a complex
of Cas proteins termed Cascade cleaves a CRISPR RNA
precursor in each repeat and retains the cleavage
products containing the virus-derived sequence. Assisted
by the helicase Cas3, these mature CRISPR RNAs then
serve as small guide RNAs that enable Cascade to
interfere with virus proliferation. Cas5 contains an
endonuclease motif, whose inactivation leads to loss of
resistance, even in the presence of phage-derived
spacers. This family used to be known as DUF73. DevR
appears to be negative auto-regulator within the system.
Length = 258
Score = 27.7 bits (62), Expect = 3.8
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 82 TLHQKVTVLFEIAGGRKTETVPALSGQRQKH 112
T H+K V+ + G K VPA+SG+ KH
Sbjct: 21 TRHRKAPVV--LKTGYKVRYVPAISGESLKH 49
>gnl|CDD|225524 COG2977, EntD, Phosphopantetheinyl transferase component of
siderophore synthetase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 228
Score = 27.3 bits (61), Expect = 4.0
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 9 SRSASHQKLGLDIEELEAIEEDAGL-----GNGGLGRLAACFLDSMATLGL 54
+R + +G+DIE E++ + RLA L + L L
Sbjct: 106 ARRGRVRSIGIDIEPHESLPTAREIADIIITPAERARLARAGLAFLLALTL 156
>gnl|CDD|217083 pfam02521, HP_OMP_2, Putative outer membrane protein. This family
consists of putative outer membrane proteins from
Helicobacter pylori (campylobacter pylori).
Length = 454
Score = 27.4 bits (61), Expect = 5.1
Identities = 29/116 (25%), Positives = 39/116 (33%), Gaps = 23/116 (19%)
Query: 16 KLGLDIEELEAIEEDAGLGNGGLGRLAACFLDSMATLGLSA----YGYECFMMVLIYTG- 70
KL +D+ L ED GL G G L A DS L A +G + + + G
Sbjct: 60 KLQVDVSLLPKGIEDHGLKGGVGGMLGALAYDSTKYLINQATDPIFGSIGWNYIGYWDGY 119
Query: 71 ----RIKETLQPQEATLHQKVTVL------------FEIAGGRKTETVPALSGQRQ 110
T A H + V+ F I GR + +SG Q
Sbjct: 120 LGNKSQATTNAYANA--HVRNYVVYNAFLEYDYKDIFGIKAGRYQSNMDWMSGYNQ 173
>gnl|CDD|233940 TIGR02583, DevR_archaea, CRISPR-associated protein Cas7/Csa2,
subtype I-A/APERN. CRISPR is a term for Clustered
Regularly Interspaced Short Palidromic Repeats. A number
of protein families appear only in association with
these repeats and are designated Cas (CRISPR associated)
proteins. This model represents one such family,
typified by MJ0381 of Methanococcus jannaschii. This
archaeal clade is a member of the DevR family
(TIGR01875) which includes the DevR protein of
Myxococcus xanthus, a protein whose expression appears
to regulated through a number of means, including both
location and autorepression; DevR mutants are incapable
of fruiting body development. This subfamily is found in
a CRISPR/Cas locus we designate APERN, so the family is
designated Csa2, for CRISPR/Cas Subtype Protein 2
[Mobile and extrachromosomal element functions, Other].
Length = 285
Score = 27.0 bits (60), Expect = 5.7
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 69 TGRIK---ETLQPQEA----TLHQKVTVLFEIAGGRKTETVPALSGQRQKH 112
+GR+ E L E+ T H++ V+ + G VPA+SG+ H
Sbjct: 5 SGRVLVNVEALNGVESAGNYTKHRRAPVVVKTDNGYTVYYVPAISGESLAH 55
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
0.318 0.132 0.380
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,219,805
Number of extensions: 823474
Number of successful extensions: 616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 614
Number of HSP's successfully gapped: 15
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
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 (21.7 bits)
S2: 56 (25.4 bits)