RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17809
(294 letters)
>gnl|CDD|219844 pfam08447, PAS_3, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 90
Score = 45.1 bits (107), Expect = 2e-06
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 145 INKGQVLTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVN 189
+ KG+ + YR+ K+G Y WV++ + +N +I V
Sbjct: 47 LKKGEPYSGEYRIRRKDGEYRWVEARGRPIR-DENGKPVRVIGVA 90
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria
and eukarya. Probably the most surprising identification
of a PAS domain was that in EAG-like K+-channels. PAS
domains have been found to bind ligands, and to act as
sensors for light and oxygen in signal transduction.
Length = 103
Score = 42.2 bits (99), Expect = 3e-05
Identities = 23/104 (22%), Positives = 33/104 (31%), Gaps = 25/104 (24%)
Query: 113 LDGFAFALGSDGRFLYISETVSIYLGLSQWQVINK------------------------G 148
L L DGR LY + LG S ++I K G
Sbjct: 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGG 60
Query: 149 QVLTHYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVI 192
+ +T RL K+G WV T + + ++ V I
Sbjct: 61 EPVTLEVRLRRKDGSVIWVLVSLTPIRDEGG-EVIGLLGVVRDI 103
Score = 28.8 bits (64), Expect = 1.3
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 4 FEQHQGTHILQVEMTGSSVFDYIHQADHTELAEQL 38
EQ G E+ G S+ D IH D EL E+L
Sbjct: 21 AEQLLG--YSPEELIGKSLLDLIHPEDREELRERL 53
>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to
contribute to PAS structural domain). PAC motif occurs
C-terminal to a subset of all known PAS motifs. It is
proposed to contribute to the PAS domain fold.
Length = 43
Score = 39.1 bits (92), Expect = 9e-05
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 152 THYYRLMNKNGGYTWVQSCATVVCSSKNADEQNIICVNYVISGR 195
T YRL K+G Y WV A+ + + + I+ V I+ R
Sbjct: 1 TVEYRLRRKDGSYIWVLVSASPIRDEDG-EVEGILGVVRDITER 43
>gnl|CDD|214512 smart00091, PAS, PAS domain. PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels.
Length = 67
Score = 34.3 bits (79), Expect = 0.006
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 112 SLDGFAFALGSDGRFLYISETVSIYLGLSQWQVINK 147
SL F L DGR LY + LG S ++I K
Sbjct: 9 SLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGK 44
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 32.7 bits (75), Expect = 0.22
Identities = 13/60 (21%), Positives = 21/60 (35%)
Query: 212 QQRGVKREEPSNNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTSEGDNSGDQRGR 271
+Q K E+ PE PD ++ D ++ P D E D + G+
Sbjct: 315 EQPQGKDEKDLEEKPEEPGPDPEKPDEGEDDAEQSGPRGHPTPGNDDEKEPDPQEEADGQ 374
>gnl|CDD|216228 pfam00989, PAS, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 113
Score = 29.7 bits (67), Expect = 0.74
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 112 SLDGFAFALGSDGRFLYISETVSIYLGLSQWQVINK 147
SL F + DGR LY++ LGLS+ +VI K
Sbjct: 9 SLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGK 44
>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional.
Length = 413
Score = 30.7 bits (69), Expect = 0.80
Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 1/70 (1%)
Query: 220 EPSNNDPENDSPDA-DREDGRNSGDSRNHDHLSPPDIEDGTSEGDNSGDQRGRNHLDHVT 278
EP ++PE DSP E +S ++ + + Q+ H D T
Sbjct: 179 EPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPT 238
Query: 279 QLHNISTPPE 288
+ P
Sbjct: 239 EPEREGPPFP 248
>gnl|CDD|238737 cd01460, vWA_midasin, VWA_Midasin: Midasin is a member of the AAA
ATPase family. The proteins of this family are unified
by their common archetectural organization that is based
upon a conserved ATPase domain. The AAA domain of
midasin contains six tandem AAA protomers. The AAA
domains in midasin is followed by a D/E rich domain that
is following by a VWA domain. The members of this
subgroup have a conserved MIDAS motif. The function of
this domain is not exactly known although it has been
speculated to play a crucial role in midasin function.
Length = 266
Score = 30.4 bits (69), Expect = 1.0
Identities = 12/50 (24%), Positives = 19/50 (38%)
Query: 6 QHQGTHILQVEMTGSSVFDYIHQADHTELAEQLGLGLSQGHGLASPGSAN 55
Q T I + + +F+ + QL L +S G G S G+
Sbjct: 135 QQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFSEGAQK 184
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 29.9 bits (68), Expect = 1.8
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 213 QRGVKREEPSNNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTSEGDNSGDQRGR 271
R + + + R R+ D+R D+ + G +GD+ + GR
Sbjct: 207 DRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDN----REDRGDRDGDDGEGRGGR 261
Score = 28.3 bits (64), Expect = 5.4
Identities = 13/69 (18%), Positives = 20/69 (28%), Gaps = 6/69 (8%)
Query: 212 QQRGVKREEPSNNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTSEGDNSGDQ--- 268
+RG + E + D + ++ D R R+ D GD
Sbjct: 188 GERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRR--GRRRRRDRRDARGDDNRE 245
Query: 269 -RGRNHLDH 276
RG D
Sbjct: 246 DRGDRDGDD 254
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 30.1 bits (68), Expect = 1.8
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 16/96 (16%)
Query: 207 LEDYIQQRGVKREEPSNNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTS------ 260
+ED +R + EE + E D + ++ + + D S + DG S
Sbjct: 381 IEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSLAVGY 440
Query: 261 EGDNS----GDQRG------RNHLDHVTQLHNISTP 286
+ D S GD+ G + L+ VT ++N+S P
Sbjct: 441 KNDRSYVVRGDKIGVFKHTDDDSLEFVTAINNVSDP 476
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 29.6 bits (67), Expect = 2.4
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 239 RNSGDSRNH-----DHLSPPDIEDGTSEGD 263
RN+ +R + PP+IED GD
Sbjct: 363 RNTDYARRNADALGSFPVPPEIEDDGPAGD 392
>gnl|CDD|216073 pfam00709, Adenylsucc_synt, Adenylosuccinate synthetase.
Length = 420
Score = 28.3 bits (64), Expect = 6.0
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 186 ICVNYVISGREYENFIMDCCQLEDY 210
+CV Y G+E + F LE
Sbjct: 341 VCVAYRYDGKEIDYFPASLEDLEKV 365
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 28.0 bits (62), Expect = 6.2
Identities = 17/75 (22%), Positives = 32/75 (42%)
Query: 201 IMDCCQLEDYIQQRGVKREEPSNNDPENDSPDADREDGRNSGDSRNHDHLSPPDIEDGTS 260
+ D + E+ I++ G + EE + + ++D D D +D + D + D D +D S
Sbjct: 28 LNDTMKKENAIRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDS 87
Query: 261 EGDNSGDQRGRNHLD 275
+ N D
Sbjct: 88 TLHDDSSADDGNETD 102
>gnl|CDD|222046 pfam13324, GCIP, Grap2 and cyclin-D-interacting. GCIP, or Grap2
and cyclin-D-interacting protein, is found in
eukaryotes, and in the human protein CCNDBP1, residues
149-190 constitute a helix-loop-helix domain, residues
190-240 an acidic region, and 240-261 a leucine zipper
domain. GCIP interacts with full-length Grap2 protein
and with the COOH-terminal unique and SH3 domains
(designated QC domain) of Grap2. It is potentially
involved in the regulation of cell differentiation and
proliferation through Grap2 and cyclin D-mediated
signalling pathways. In mice, it is involved in
G1/S-phase progression of hepatocytes, which in older
animals is associated with the development of liver
tumours. In vitro it acts as an inhibitory HLH protein,
for example, blocking transcription of the HNF-4
promoter. In its function as a cyclin D1-binding protein
it is able to reduce CDK4-mediated phosphorylation of
the retinoblastoma protein and to inhibit E2F-mediated
transcriptional activity. GCIP has also been shown to
have interact physically with Rad (Ras associated with
diabetes), Rad being important in regulating cellular
senescence.
Length = 271
Score = 27.4 bits (61), Expect = 7.9
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 207 LEDYIQQRGVKREEPSNNDPE-NDSPDADREDGRNSGDSRNHDHLSPPDIE 256
++D +++ +E SN+D E S +D D + + S ++E
Sbjct: 135 VKDVLREMKEAKEGCSNDDSEDPFSDGHHDDDDVEGDDLNDDRYWSEEEME 185
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
0.313 0.130 0.387
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,437,996
Number of extensions: 1318214
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 20
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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 (21.9 bits)
S2: 59 (26.6 bits)