RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15243
(150 letters)
>gnl|CDD|215646 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).
This family contains, amongst other G-protein-coupled
receptors (GCPRs), members of the opsin family, which
have been considered to be typical members of the
rhodopsin superfamily. They share several motifs, mainly
the seven transmembrane helices, GCPRs of the rhodopsin
superfamily. All opsins bind a chromophore, such as
11-cis-retinal. The function of most opsins other than
the photoisomerases is split into two steps: light
absorption and G-protein activation. Photoisomerases, on
the other hand, are not coupled to G-proteins - they are
thought to generate and supply the chromophore that is
used by visual opsins.
Length = 251
Score = 81.2 bits (201), Expect = 2e-19
Identities = 32/147 (21%), Positives = 67/147 (45%), Gaps = 12/147 (8%)
Query: 4 RMSYSKALMILILIYCYVIPWAMFPYLEKWSRFVPEGYLTSCTFDYLTPTESIRFYVLFM 63
+ +A +++++++ + ++ P L W R V EG +T+C D+ + R Y L
Sbjct: 89 IRTPRRAKVLILVVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESTK-RSYTLLS 147
Query: 64 FIICYCIPMGMIINFYSQIVGHVFSHEKALREQAKKMNVESLRSGQKEGQSSAEVRIAKT 123
++ + +P+ +I+ Y+ I+ + ++ QA+ SS E + AK
Sbjct: 148 TLLGFVLPLLVILVCYTLILRTLRKRARSGASQARAKR-----------SSSKERKAAKM 196
Query: 124 AITLCALFVASWTPYAVVALTGAFGDQ 150
+ + +FV W PY +V L +
Sbjct: 197 LLVVVVVFVLCWLPYHIVLLLDSLCPL 223
>gnl|CDD|238705 cd01417, Ribosomal_L19e_E, Ribosomal protein L19e, eukaryotic.
L19e is found in the large ribosomal subunit of
eukaryotes and archaea. L19e is distinct from the
ribosomal subunit L19, which is found in prokaryotes. It
consists of two small globular domains connected by an
extended segment. It is located toward the surface of
the large subunit, with one exposed end involved in
forming the intersubunit bridge with the small subunit.
The other exposed end is involved in forming the
translocon binding site, along with L22, L23, L24, L29,
and L31e subunits.
Length = 164
Score = 31.9 bits (73), Expect = 0.070
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 78 FYSQIVGHVFSHEKALREQAKKMNVESLRSGQKEGQSSAEVRIAKT 123
Y + G+VF +++ L E K E R KE AE R AK
Sbjct: 120 LYLKAKGNVFKNKRVLMEHIHKAKAEKARE--KELADQAEARRAKN 163
>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional.
Length = 746
Score = 30.5 bits (69), Expect = 0.32
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 6/32 (18%)
Query: 41 YLTSCTFD---YLTPTESI-RFYVL--FMFII 66
YLTS +D YLTPT + RFYV + F I
Sbjct: 705 YLTSKVWDTNNYLTPTFKVKRFYVFKDYAFFI 736
>gnl|CDD|226000 COG3469, COG3469, Chitinase [Carbohydrate transport and
metabolism].
Length = 332
Score = 30.2 bits (68), Expect = 0.40
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 27 FPYLEKWSRFVPEGYLTSC--TFDYLTP 52
FPYL+ W ++P Y+ +D++ P
Sbjct: 182 FPYLQGWGAYIP--YINELRDYYDFIAP 207
>gnl|CDD|192107 pfam08638, Med14, Mediator complex subunit MED14. Saccharomyces
cerevisiae RGR1 mediator complex subunit affects
chromatin structure, transcriptional regulation of
diverse genes and sporulation, required for glucose
repression, HO repression, RME1 repression and
sporulation. This subunit is also found in higher
eukaryotes and Med14 is the agreed unified nomenclature
for this subunit. Med14 is found in the tail region of
Mediator.
Length = 195
Score = 28.7 bits (65), Expect = 0.84
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 70 IPMGMIINFYSQIVGHVFSHEKALREQAKKMNVESLRSGQKEGQSSAEVRIAKTAITLCA 129
IP+ +++N +Q S+ L + + + E +VRI A L
Sbjct: 3 IPLSLLLNRLAQ-----QSY-NELTQLIELLA----SGDTSEEDVEKKVRILNFAQRLRQ 52
Query: 130 LFV 132
F+
Sbjct: 53 QFI 55
>gnl|CDD|221747 pfam12740, Chlorophyllase2, Chlorophyllase enzyme. This family
consists of several chlorophyllase and chlorophyllase-2
(EC:3.1.1.14) enzymes. Chlorophyllase (Chlase) is the
first enzyme involved in chlorophyll (Chl) degradation
and catalyzes the hydrolysis of an ester bond to yield
chlorophyllide and phytol. The family includes both
plant and Amphioxus members.
Length = 258
Score = 28.2 bits (63), Expect = 1.5
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 51 TPTESIRFYVLFMFIICYCIPMGMIIN-FYSQIVGHVFSHEKALREQAKKMNVESLRSGQ 109
TP+E + VL +F+ Y ++ N FYSQ++ H+ SH + A ++ +
Sbjct: 10 TPSEKGTYPVL-LFLHGY-----LLSNSFYSQLLEHIASHGYIV--VAPQLYTITGPDTT 61
Query: 110 KEGQSSAEVR 119
E S+AEV
Sbjct: 62 DEINSAAEVA 71
>gnl|CDD|181061 PRK07631, PRK07631, amidophosphoribosyltransferase; Provisional.
Length = 475
Score = 27.9 bits (62), Expect = 2.7
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 70 IP--MGMIINFYSQIVGHVFSH-EKALREQAKKMNVESLRSGQKEGQ 113
IP +G+I N Y VG F +ALREQ KM + +R G EG+
Sbjct: 307 IPYELGLIKNRY---VGRTFIQPSQALREQGVKMKLSPVR-GVVEGK 349
>gnl|CDD|116452 pfam07840, FadR_C, FadR C-terminal domain. This family contains
sequences that are similar to the fatty acid metabolism
regulator protein (FadR). This functions as a dimer,
with each monomer being composed of an N-terminal
DNA-binding domain and a regulatory C-terminal domain. A
linker comprising two short alpha helices joins the two
domains. In the C-terminal domain, an antiparallel array
of six alpha helices forms a barrel-like structure,
while a seventh alpha helix forms a 'lid' at the end
closest to the N-terminal domain. This structure was
found to be similar to that of the C-terminal domain of
the Tet repressor. Long-chain acyl-CoA thioesters
interact directly and reversibly with the C-terminal
domain, and this interaction affects the structure and
therefore the DNA binding properties of the N-terminal
domain.
Length = 164
Score = 27.2 bits (61), Expect = 2.7
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 73 GMIIN----FYSQIVGHVFSHEKALREQAKK 99
+I+N YS++ + FS+ +A RE A K
Sbjct: 91 VLILNGFKGLYSRVGRYYFSNPEA-RELALK 120
>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 = 27.7 bits (62), Expect = 3.1
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 95 EQAKKMNVESLRSGQKEGQSSAEVRIAKTAITLCAL 130
E + V+ R A++ +A+ A L AL
Sbjct: 260 ELCIEFGVDGHR---------ADIVMARAARALAAL 286
>gnl|CDD|226407 COG3890, ERG8, Phosphomevalonate kinase [Lipid metabolism].
Length = 337
Score = 26.8 bits (59), Expect = 4.8
Identities = 13/57 (22%), Positives = 23/57 (40%)
Query: 74 MIINFYSQIVGHVFSHEKALREQAKKMNVESLRSGQKEGQSSAEVRIAKTAITLCAL 130
++N + S KA+R +++ E L + Q++A I LC L
Sbjct: 234 RVLNLIKLSLDESNSKSKAIRRSLRRITEEGLADIEPIKQTAALDSIFDLLGVLCDL 290
>gnl|CDD|220817 pfam10593, Z1, Z1 domain. This uncharacterized domain was
identified by Iyer and colleagues. It is found
associated with a helicase domain of superfamily type
II.
Length = 231
Score = 26.4 bits (59), Expect = 5.1
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 4/32 (12%)
Query: 75 IINFYSQIVGHVFSHEKALREQAKKMNVESLR 106
+ ++ I E+ LREQ K+M L
Sbjct: 186 LYEWFRHIA----EAEEELREQLKRMAEAGLT 213
>gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase;
Reviewed.
Length = 212
Score = 26.3 bits (59), Expect = 6.9
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 80 SQIVGHVFSHE--KALREQAKK 99
+ +V VFS E K L+ +AK+
Sbjct: 97 AHLVRRVFSVERIKTLQWEAKR 118
>gnl|CDD|226192 COG3666, COG3666, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 161
Score = 25.9 bits (57), Expect = 7.6
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 2 DGRMSYSKALMILILIYCYVIPW 24
GR +Y M+ I++Y Y+
Sbjct: 49 TGRPAYHPKRMLKIILYGYLQGI 71
>gnl|CDD|191120 pfam04884, DUF647, Protein of unknown function (DUF647). In
plants, this domain plays a role in auxin-transport,
plant growth and development.
Length = 251
Score = 26.1 bits (58), Expect = 7.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 7/32 (21%)
Query: 34 SRFVPEGYLTSCTFDYLTPTESIRFYVLFMFI 65
+ F+PEGY S T DYL Y L+ +
Sbjct: 20 NVFLPEGYPDSVTEDYLP-------YQLWDSL 44
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 26.1 bits (58), Expect = 8.2
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 80 SQIVGHVFS--HEKALREQAKKMNVESLR 106
+++VG V S + L EQA++ N+E+L
Sbjct: 91 ARLVGRVVSIERIEELAEQARR-NLETLG 118
>gnl|CDD|111661 pfam02788, RuBisCO_large_N, Ribulose bisphosphate carboxylase large
chain, N-terminal domain. The N-terminal domain of
RuBisCO large chain adopts a ferredoxin-like fold.
Length = 126
Score = 25.5 bits (56), Expect = 8.7
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 21/95 (22%)
Query: 19 CYVI-PWAMFPYLEKWSRFVPE---GYLTSCTFDYLTPTESIRFYV------------LF 62
+ + P E + E G T D LT + + F
Sbjct: 19 AFRMTPQPGVDPEEAAAAVAAESSTGTWTVVWTDLLTALDRYKARAYEVDPVPGEDEQYF 78
Query: 63 MFIICYCIPM---GMIINFYSQIVGHVFSHEKALR 94
+I Y + + G I N + I+G+VF KA+R
Sbjct: 79 AYI-AYPLDLFEEGSIANLLTSIIGNVFGF-KAVR 111
>gnl|CDD|223143 COG0065, LeuC, 3-isopropylmalate dehydratase large subunit [Amino
acid transport and metabolism].
Length = 423
Score = 26.0 bits (58), Expect = 9.5
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 36 FVPEGYLTSCTFDYLTPTESIRFYVLFMFIICYCIPMGMIINFY---SQIVGHVFSHEKA 92
PE T TFD+ PT I+ + G I+NFY Q + H E+
Sbjct: 54 RDPE--KTVATFDHNVPTPDIKAAEQQKELRENAKEFG-IVNFYDVGDQGIVHQVGPEQG 110
Query: 93 L 93
L
Sbjct: 111 L 111
>gnl|CDD|233273 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane [Transport and
binding proteins, Cations and iron carrying compounds,
Energy metabolism, Other].
Length = 582
Score = 25.9 bits (57), Expect = 9.8
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 11/32 (34%)
Query: 65 IICYCIPMGMIINFYSQIVGHVFSHEKALREQ 96
I+ +P GM+ N SQ L+EQ
Sbjct: 286 ILVAQVPGGMLSNLESQ-----------LKEQ 306
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
0.329 0.139 0.439
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,662,860
Number of extensions: 669999
Number of successful extensions: 1013
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1008
Number of HSP's successfully gapped: 58
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.5 bits)