RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy993
(164 letters)
>gnl|CDD|216846 pfam02014, Reeler, Reeler domain.
Length = 127
Score = 129 bits (327), Expect = 2e-39
Identities = 50/131 (38%), Positives = 71/131 (54%), Gaps = 7/131 (5%)
Query: 28 VCADMTPKHPQTVPQDSESPYKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQARVGDK 87
C+DM P H PQ ++SPY I + +S PG + +V IS G +F+GF +QAR GD
Sbjct: 1 ACSDMLPGHGGASPQTTDSPYTITVSPESYVPGQTYTVTISKSSGDTFRGFLLQARNGDP 60
Query: 88 P---VGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNESVNFVAT 144
P VG F + + +++NC NA TH + K+ +++TWVAP V F AT
Sbjct: 61 PGDMVGTFQLADDDETSQLLNC----PNAVTHANTNPKTEISVTWVAPAAGGGCVVFRAT 116
Query: 145 VAKDGGEYWVG 155
V + YWV
Sbjct: 117 VVQSRDVYWVD 127
>gnl|CDD|176096 cd08544, Reeler, Reeler, the N-terminal domain of reelin,
F-spondin, and a variety of other proteins. This domain
is found at the N-terminus of F-spondin, a protein
attached to the extracellular matrix, which plays roles
in neuronal development and vascular remodelling. The
F-spondin reeler domain has been reported to bind
heparin. The reeler domain is also found at the
N-terminus of reelin, an extracellular glycoprotein
involved in the development of the brain cortex, and in
a variety of other eukaryotic proteins with different
domain architectures, including the animal
ferric-chelate reductase 1 or stromal cell-derived
receptor 2, a member of the cytochrome B561 family,
which reduces ferric iron before its transport from the
endosome to the cytoplasm. Also included is the insect
putative defense protein 1, which is expressed upon
bacterial infection and appears to contain a single
reeler domain.
Length = 135
Score = 127 bits (322), Expect = 1e-38
Identities = 47/137 (34%), Positives = 65/137 (47%), Gaps = 4/137 (2%)
Query: 28 VCADMTPKHPQTVPQDSESPYKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQARVGD- 86
C DM P + SPY I + S PG + +V +S F+GF +QAR
Sbjct: 1 ACVDMPPGPGHGGDPQTTSPYSITISGNSYVPGETYTVTLSGSSPSPFRGFLLQARDASS 60
Query: 87 -KPVGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNESVNFVATV 145
+PVG F P K++ C GS NA TH + K+ VT TW AP + + V F ATV
Sbjct: 61 NEPVGTFQ-LPPDSGTKLLTC-CGSDNAVTHSNNSKKTSVTFTWTAPSNGSGCVTFRATV 118
Query: 146 AKDGGEYWVGQQSEPVT 162
+ +WV S+ +
Sbjct: 119 VQSYDVFWVDVLSKTLC 135
>gnl|CDD|220261 pfam09484, Cas_TM1802, CRISPR-associated protein TM1802
(cas_TM1802). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This minor cas protein is
found in at least five prokaryotic genomes:
Methanosarcina mazei, Sulfurihydrogenibium azorense,
Thermotoga maritima, Carboxydothermus hydrogenoformans,
and Dictyoglomus thermophilum, the first of which is
archaeal while the rest are bacterial.
Length = 584
Score = 31.6 bits (72), Expect = 0.16
Identities = 21/145 (14%), Positives = 36/145 (24%), Gaps = 33/145 (22%)
Query: 38 QTVPQDSESPYKIVLKKKSVAPGGSISVVISSPPGLS--FKGFFVQARVGDKPVGQFTKS 95
+ Y+ VLK I +VI K + S
Sbjct: 26 LQENPNKGGNYQHVLKIDFDTEENEIEIVIGEEFDKKTARKYLYKG--QAGNGNSSQWYS 83
Query: 96 PSSKF---------YKVINCLGGSQNAATHIDAKAKSRVTLTWVAPEDL----------- 135
P++K K+ + K R L + + L
Sbjct: 84 PTNKITYDPEETLNKKLKSIFKKFYKD---KGEINKYRYFLKDI-KKVLEKNFEKIIKDL 139
Query: 136 -----NESVNFVATVAKDGGEYWVG 155
NE V + K+ G+ ++
Sbjct: 140 IDLKKNEGVLYTIYFLKNDGKKYLS 164
>gnl|CDD|153217 cd01746, GATase1_CTP_Synthase, Type 1 glutamine amidotransferase
(GATase1) domain found in Cytidine Triphosphate
Synthetase. Type 1 glutamine amidotransferase (GATase1)
domain found in Cytidine Triphosphate Synthetase (CTP).
CTP is involved in pyrimidine
ribonucleotide/ribonucleoside metabolism. CTPs produce
CTP from UTP and glutamine and regulate intracellular
CTP levels through interactions with four ribonucleotide
triphosphates. The enzyme exists as a dimer of identical
chains that aggregates as a tetramer. CTP is derived
form UTP in three separate steps involving two active
sites. In one active site, the UTP O4 oxygen is
activated by Mg-ATP-dependent phosphorylation, followed
by displacement of the resulting 4-phosphate moiety by
ammonia. At a separate site, ammonia is generated via
rate limiting glutamine hydrolysis (glutaminase)
activity. A gated channel that spans between the
glutamine hydrolysis and amidoligase active sites
provides a path for ammonia diffusion. CTPs belong to
the triad family of amidotransferases having a conserved
Cys-His-Glu catalytic triad in the glutaminase active
site.
Length = 235
Score = 30.2 bits (69), Expect = 0.34
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 89 VGQFTKSPSSKFYK-VINCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNES 138
VG++ + P + Y V+ L ++A + K + + W+ EDL E
Sbjct: 6 VGKYVELPDA--YLSVLEAL---KHAGIALGVK----LEIKWIDSEDLEEE 47
>gnl|CDD|165153 PHA02790, PHA02790, Kelch-like protein; Provisional.
Length = 480
Score = 28.1 bits (62), Expect = 2.3
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 1/94 (1%)
Query: 71 PGLSFKGFFVQARVG-DKPVGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLTW 129
P S+K F++ + D+ + F S+ +V+ +GG N H +A A + ++ W
Sbjct: 240 PRKSYKYPFIEYPMNMDQIIDIFHMCTSTHVGEVVYLIGGWMNNEIHNNAIAVNYISNNW 299
Query: 130 VAPEDLNESVNFVATVAKDGGEYWVGQQSEPVTV 163
+ +N + + V + Y VG P +V
Sbjct: 300 IPIPPMNSPRLYASGVPANNKLYVVGGLPNPTSV 333
>gnl|CDD|239932 cd04486, YhcR_OBF_like, YhcR_OBF_like: A subfamily of OB-fold
domains similar to the OB folds of Bacillus subtilis
YhcR. YhcR is a sugar-nonspecific nuclease, which is
active in the presence of Ca2+ and Mn2+. It cleaves RNA
endonucleolytically, producing 3'-monophosphate
nucleosides. YhcR appears to be the major Ca2+
activated nuclease of B. subtilis. YhcR may be
localized in the cell wall.
Length = 78
Score = 26.5 bits (59), Expect = 3.0
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 65 VVISSPPGLSFKGFFVQARVGD 86
VV + G GF++Q GD
Sbjct: 5 VVTAVFSGGGLGGFYIQDEDGD 26
>gnl|CDD|216192 pfam00920, ILVD_EDD, Dehydratase family.
Length = 521
Score = 27.8 bits (63), Expect = 3.1
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 103 VINCLGGSQNAATHIDAKAKS-RVTLTWVAPEDLNESVNFVATVAKDGGEYWV 154
V+ GGS NA H+ A A+ V LT + ++ V +A + K G+Y +
Sbjct: 230 VLMATGGSTNAVLHLLAIAREAGVDLTLDDFDRISRKVPLLADL-KPSGKYLM 281
>gnl|CDD|177855 PLN02205, PLN02205, alpha,alpha-trehalose-phosphate synthase
[UDP-forming].
Length = 854
Score = 27.7 bits (61), Expect = 3.3
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 88 PVGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLT-WVAP 132
P KSPSSK ++N L +N I A+SR TL W +P
Sbjct: 609 PQASIDKSPSSKSIDILNTLCRDKNNMVFI-VSARSRKTLADWFSP 653
>gnl|CDD|233332 TIGR01256, modA, molybdenum ABC transporter, periplasmic
molybdate-binding protein. The model describes the
molybdate ABC transporter periplasmic binding protein in
bacteria and archae. Several of the periplasmic
receptors constitute a diverse class of binding proteins
that differ widely in size, sequence and ligand
specificity. It has been shown experimentally by
radioactive labeling that ModA represent hydrophylioc
periplasmic-binding protein in gram-negative organisms
and its counterpart in gram-positive organisms is a
lipoprotein. The other components of the system include
the ModB, an integral membrane protein and ModC the
ATP-binding subunit. Invariably almost all of them
display a common beta/alpha folding motif and have
similar tertiary structures consisting of two globular
domains [Transport and binding proteins, Anions].
Length = 216
Score = 27.0 bits (60), Expect = 3.8
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 118 DAKAKSRVTLTWVAPEDLNESVNFVATVAKDG 149
D +V PEDL + + + A + K G
Sbjct: 159 DVIPSKKVGSVATFPEDLYKPIRYPAVIVKGG 190
>gnl|CDD|223207 COG0129, IlvD, Dihydroxyacid dehydratase/phosphogluconate
dehydratase [Amino acid transport and metabolism /
Carbohydrate transport and metabolism].
Length = 575
Score = 27.5 bits (62), Expect = 3.9
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 107 LGGSQNAATHIDAKAKS-RVTLTWVAPEDLNESVNFVATVAKDGGEY 152
GGS NA H+ A A+ V LT + ++ V +A V +GG+Y
Sbjct: 275 TGGSTNAVLHLLAIAREAGVDLTLDDFDRISRKVPLLAKVYPNGGKY 321
>gnl|CDD|215504 PLN02934, PLN02934, triacylglycerol lipase.
Length = 515
Score = 27.4 bits (61), Expect = 4.1
Identities = 9/32 (28%), Positives = 21/32 (65%), Gaps = 4/32 (12%)
Query: 79 FVQARVGDKPVGQFTKS----PSSKFYKVINC 106
F Q R+G++ +G+F ++ P ++++V+ C
Sbjct: 360 FGQPRIGNRQLGKFMEAQLNYPVPRYFRVVYC 391
>gnl|CDD|182164 PRK09953, wcaD, putative colanic acid biosynthesis protein;
Provisional.
Length = 404
Score = 27.2 bits (60), Expect = 4.2
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 49 KIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQARVGDKPVGQFTKSPSSKFYKVINCLG 108
K +KKK ++ + G+ ++ R+GD SS +Y+++ L
Sbjct: 236 KEAIKKK---LPLALVSLAVFLVGVVIAFPYISTRLGD-----LGTEGSSSYYRIVGPLV 287
Query: 109 GSQNAATHID 118
+ THID
Sbjct: 288 MVGYSLTHID 297
>gnl|CDD|232926 TIGR00337, PyrG, CTP synthase. CTP synthase is involved in
pyrimidine ribonucleotide/ribonucleoside metabolism. The
enzyme catalyzes the reaction L-glutamine + H2O + UTP +
ATP = CTP + phosphate + ADP + L-glutamate. The enzyme
exists as a dimer of identical chains that aggregates as
a tetramer. This gene has been found circa 500 bp 5'
upstream of enolase in both beta (Nitrosomonas europaea)
and gamma (E.coli) subdivisions of proteobacterium (FEMS
Microbiol Lett 1998 Aug 1;165(1):153-7) [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 525
Score = 26.5 bits (59), Expect = 8.1
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 89 VGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNES 138
VG++ + S Y + A H AK ++V + W+ EDL E
Sbjct: 295 VGKYVELKDS--YLSVI------EALKHAGAKLDTKVNIKWIDSEDLEEE 336
>gnl|CDD|131058 TIGR02003, PTS-II-BC-unk1, PTS system, IIBC component. This model
represents a family of fused B and C components of PTS
enzyme II. This clade is a member of a larger family
which contains enzyme II's specific for a variety of
sugars including glucose (TIGR02002) and
N-acetylglucosamine (TIGR01998). None of the members of
this clade have been experimentally characterized. This
clade includes sequences from Streptococcus and
Enterococcus which also include a C-terminal A domain as
well as Bacillus and Clostridium which do not. In nearly
all cases, these species also contain an authentic
glucose-specific PTS transporter [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 548
Score = 26.5 bits (58), Expect = 9.1
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 98 SKFYKVINCLGGSQNAATHIDAKAKSRVT---LTWVAPEDLNESVNFVATVAKDGG 150
S K+I+ LGG++N A + RVT L VA E + + + + KD G
Sbjct: 471 SLATKIIDLLGGAENIADVDACMTRLRVTVKDLAKVAAEADWKKADALGLIQKDKG 526
>gnl|CDD|223378 COG0301, ThiI, Thiamine biosynthesis ATP pyrophosphatase [Coenzyme
metabolism].
Length = 383
Score = 26.1 bits (58), Expect = 9.6
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 25 PEGVCADMTPKHPQTVPQDSE 45
PE C P P+T P+ E
Sbjct: 340 PEDCCVIFAPPTPKTKPKLIE 360
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
0.314 0.129 0.380
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,834,885
Number of extensions: 664024
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 22
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.0 bits)