RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5322
(476 letters)
>gnl|CDD|217340 pfam03055, RPE65, Retinal pigment epithelial membrane protein.
This family represents a retinal pigment epithelial
membrane receptor which is abundantly expressed in
retinal pigment epithelium, and binds plasma retinal
binding protein. The family also includes the sequence
related neoxanthin cleavage enzyme in plants and
lignostilbene-alpha,beta-dioxygenase in bacteria.
Length = 469
Score = 300 bits (771), Expect = 3e-97
Identities = 139/490 (28%), Positives = 201/490 (41%), Gaps = 87/490 (17%)
Query: 46 WFRDCHTEVDQPVQGTVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKIS 105
F E+ VEG IP+ ++G L RNGPG G + H FD G+LH F+
Sbjct: 1 NFAPVREELPDAEDLEVEGEIPADLNGTLYRNGPGPLERGGFRYHHWFDGDGMLHAFRFE 60
Query: 106 SGLVTYQCKFIKSESYIKNHAARRIVVTGFGTRFVPDPCASIFQRIATLFKPGSDNTLVS 165
G VTY+ +F+++E Y AA R + G PDPC +IF R + + +
Sbjct: 61 DGRVTYRNRFVRTEGYKAERAAGRRLYPGEFGTLKPDPCKNIFPR---VPGKLKNVANTN 117
Query: 166 VYPIQDQVYALGDSNYMHRIDPATLDTLEKMDLARDVTILHQ-TSHPLT-TSDGETFNLG 223
V ++ AL ++ +R+DP TL+TL + D + T+HP GE N G
Sbjct: 118 VVYHGGRLLALWEAGLPYRLDPETLETLGRYDFGGKLKPGPPFTAHPKVDPVTGELVNFG 177
Query: 224 VTLRPTGPRYCILQLNDVADHRVKLVTSVPVRWKFHPGYMHTFAMTPHYFIIVEQPLSIS 283
++L P P D KLV VP+ P +H FA+T +Y I + PL
Sbjct: 178 LSLGPKPPYLTYY----EVDADGKLVREVPIFSLPGPSMIHDFAITENYVIFPDLPLVFD 233
Query: 284 VPRLIKNSVTNRPLATCLKF------------------------------------FEKQ 307
RL+ A L++ +E+
Sbjct: 234 PLRLLLGG-----RADPLRWDPEKPTRFGVIPRRGGKSDVRWFEAPPCFVFHTANAWEEG 288
Query: 308 SNIH---------------------STPRYAQMFRARPLRFRLDLASPRTAPTGKVRPSV 346
I + R+R R+RLDL + V V
Sbjct: 289 GEIVLDACRYDDPDFLDPFYLDNLRPDAFADKKPRSRLTRWRLDLKTGG-----DVTEEV 343
Query: 347 ICDVGCETPRMNGQHQGRPYTYFYAISADIDRDNPG---TLIKVNVQNNTCKSWSQKD-V 402
+ D CE PR+N ++ GR Y Y Y +AD G L+KV+++ + WS
Sbjct: 344 LLDRPCEFPRINPRYVGRKYRYVYMAAADPRPPGSGPFDGLVKVDLETGEVQVWSFGPGC 403
Query: 403 YPSEPVFVATPNAVKEDEGVLLSVLLWSHHPTRVS-LLVLNARTMQE--LGRVNFTTPTP 459
YP EP+FV P A ED+G LLSV+ T S LL+L+A+ + E + RV P
Sbjct: 404 YPGEPIFVPRPGAADEDDGWLLSVVYDED--TGRSELLILDAKDLTEGPVARVEL--PHR 459
Query: 460 VPKCLHGWYF 469
VP HG +
Sbjct: 460 VPYGFHGTWV 469
>gnl|CDD|226196 COG3670, COG3670, Lignostilbene-alpha,beta-dioxygenase and related
enzymes [Secondary metabolites biosynthesis, transport,
and catabolism].
Length = 490
Score = 148 bits (375), Expect = 2e-39
Identities = 129/486 (26%), Positives = 196/486 (40%), Gaps = 80/486 (16%)
Query: 47 FRDCHTEVDQPVQGTVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKISS 106
F TE D VEG IP+ +DG L RNGP + G + H FD G++H
Sbjct: 26 FAPVRTEFDATDLTDVEGRIPADLDGTLYRNGPNPLHRGGIATYHWFDGDGMIHAVAFRD 85
Query: 107 GL-VTYQCKFIKSESYIKNHAARRIVVTGFGTRFVPDPCASIFQRIATLFKPGSDNTLVS 165
G TY+ +F++++ Y+ + A + + G G P K + NT V
Sbjct: 86 GGRATYRNRFVRTQGYLAENEAGKPLWGGLGE---TQPPGVRPHSRTGDLKNAA-NTSVI 141
Query: 166 VYPIQDQVYALGDSNYMHRIDPATLDTLEKMDLARDVTILHQTSHPLTTSD-GETFNLGV 224
++ D++ AL + +R+DP TL+TL K D D ++HP D GE FN G
Sbjct: 142 MHG--DELLALWEGGSPYRLDPDTLETLGKEDFGGDPLGGPFSAHPKVDPDTGELFNFGY 199
Query: 225 TLRPTGPRYCILQLNDVADHRVKLVT-SVPVRWKFHPGYMHTFAMTPHYFIIVEQPLSIS 283
+ Y ++ D + V +P P MH FA+T +Y I + P++
Sbjct: 200 SFALPYLTYYVV---DADGELRRTVDIPLP-----GPPMMHDFAITENYLIFFDLPVTFD 251
Query: 284 -VPRLIKNS-----------------VTNRPLATCLKFFEKQS-------NIHSTPR--- 315
VPRL+ V R + +++FE + N +
Sbjct: 252 PVPRLLGRPADGHAMRWRPELPTRILVLPREGDSEIRWFEAEPGFVFHFLNAYEEGDEVV 311
Query: 316 ---------YAQMF---------------RARPLRFRLDLASPRTAPTGKVRPSVICDVG 351
++Q R R+ L+L TGKV + D
Sbjct: 312 LVDFLRYDDFSQTLDTLGEGPGGDFRTLAPPRLHRWTLNLK------TGKVAEEQLDDRA 365
Query: 352 CETPRMNGQHQGRPYTYFYAISADIDRDNP---GTLIKVNVQNNTCKSWS-QKDVYPSEP 407
CE PR+N ++ G+PY Y Y A TL K +++ T + +S Y SEP
Sbjct: 366 CEFPRINPRYVGQPYRYTYMSGARPGTFLFQGLQTLAKHDLETGTSQVYSFGPRGYGSEP 425
Query: 408 VFVATPNAVKEDEGVLLSVLLWSHHPTRVSLLVLNARTMQELGRVNFTTPTPVPKCLHGW 467
VFV P + ED+G LL+ L++ LLV +A+ + P VP HG
Sbjct: 426 VFVPRPGSSAEDDGWLLT-LVYDGDRHASELLVFDAQRVTAEPIARLALPQRVPYGFHGN 484
Query: 468 YFPHER 473
+ P E
Sbjct: 485 WVPTEE 490
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 55.5 bits (134), Expect = 3e-08
Identities = 35/104 (33%), Positives = 49/104 (47%), Gaps = 8/104 (7%)
Query: 21 DATIAALERRVENGDSIFDNVDAGVWFRDCHTEVD-QPVQG--TVEGVIPSWIDGVLIRN 77
DA +AL +E + D V V QPV+ V G IP IDGV +RN
Sbjct: 89 DAVESALVSHLERQHPLPKTADPAVQIAGNFAPVPEQPVRHNLPVTGRIPDCIDGVYVRN 148
Query: 78 GPGSWNVGEE--SFDHLFDCSGLLHRFKISSGLVTYQCKFIKSE 119
G N E + HLFD G++H +I +G +Y C+F ++
Sbjct: 149 GA---NPLFEPVAGHHLFDGDGMVHAVRIGNGSASYACRFTETN 189
>gnl|CDD|215271 PLN02491, PLN02491, carotenoid 9,10(9',10')-cleavage dioxygenase.
Length = 545
Score = 43.7 bits (103), Expect = 1e-04
Identities = 56/256 (21%), Positives = 93/256 (36%), Gaps = 51/256 (19%)
Query: 61 TVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKISSGLVTYQCKFIKS-- 118
V G +P ++G +R GP + H FD G++H +I G TY +++K+
Sbjct: 70 PVRGHLPECLNGEFVRVGPNPKFSPVAGY-HWFDGDGMIHGMRIKDGKATYVSRYVKTSR 128
Query: 119 ---ESYIKNHAARRI-VVTGFGTRFVPDPCASIFQRIATLFKPGSDNTLVSVYPIQDQVY 174
E + +I + G + + Q++ K + D Y
Sbjct: 129 LKQEEFFGGAKFMKIGDLKGLFGLLMVN-----MQQLRAKLK------------VLDFSY 171
Query: 175 ALGDSNY-----------MHRID-PATLDTLEKMDLAR------DVTILHQ-TSHP-LTT 214
G N + D P + LE DL D + H T+HP +
Sbjct: 172 GNGTGNTALIYHHGKLLALSEADKPYVVKVLEDGDLQTLGLLDYDKRLKHSFTAHPKVDP 231
Query: 215 SDGETFNLGVTLRPTGPRYCILQLNDVADHRVKLVTSVPVRWKFHPGYMHTFAMTPHYFI 274
GE F G + P Y ++ + V + S P+ MH FA+T +Y I
Sbjct: 232 FTGEMFTFGYSHEPPYITYRVISKDGAMHDPVPITISEPI-------MMHDFAITENYAI 284
Query: 275 IVEQPLSISVPRLIKN 290
++ PL ++K
Sbjct: 285 FMDLPLYFRPKEMVKE 300
>gnl|CDD|215523 PLN02969, PLN02969, 9-cis-epoxycarotenoid dioxygenase.
Length = 610
Score = 40.9 bits (96), Expect = 0.001
Identities = 32/132 (24%), Positives = 62/132 (46%), Gaps = 14/132 (10%)
Query: 352 CETPRMNGQHQGRPYTYFYAISADIDRDN----P-GTLIKVNVQNNTCKSWSQ-KDVYPS 405
+ P +N G+ Y YA +A R P +++K++V + + +SWS +
Sbjct: 479 ADFPVINPSFSGQKNEYTYAAAASGSRKTLPHFPFDSVVKLDVPDGSARSWSTGARRFVG 538
Query: 406 EPVFVATPNAV---KEDEGVLLSVLLWSHHPTRVSLLVLNARTMQELG----RVNFTTPT 458
EPVFV ++ +ED+G +L V+ ++ R L++L+A+ + E ++
Sbjct: 539 EPVFVPRKSSQGGGEEDDGYVL-VVEYAVSDERCYLVILDAKRIGERDAVVAKLEVPKHL 597
Query: 459 PVPKCLHGWYFP 470
P HG++
Sbjct: 598 TFPMGFHGFWAD 609
Score = 34.8 bits (80), Expect = 0.096
Identities = 30/99 (30%), Positives = 42/99 (42%), Gaps = 9/99 (9%)
Query: 36 SIFDNVDAGVW-----FRDCHTEVDQPVQGT-VEGVIPS-WIDGVLIRNGPGSWNVGEES 88
+ D+ A W F +E PV+ VEG IPS + G GPG + S
Sbjct: 48 TEDDSTSAAFWDYQFLFVSQRSETKDPVRLRVVEGAIPSDFPSGTYYLAGPGLFTDDHGS 107
Query: 89 FDHLFDCSGLLHRFKISSG--LVTYQCKFIKSESYIKNH 125
H D G L F I G V Y +++K+E+ + H
Sbjct: 108 TVHPLDGHGYLRAFHIDGGDRPVQYSARYVKTEAKKEEH 146
>gnl|CDD|132648 TIGR03609, S_layer_CsaB, polysaccharide pyruvyl transferase CsaB.
The CsaB protein (cell surface anchoring B) of Bacillus
anthracis adds a pyruvoyl group to
peptidoglycan-associated polysaccharide. This addition
is required for proteins with an S-layer homology domain
(pfam00395) to bind. Within the larger group of proteins
described by pfam04230, this model represents a distinct
clade that nearly exactly follows the phylogenetic
distribution of the S-layer homology domain (pfam00395)
[Cell envelope, Surface structures, Protein fate,
Protein and peptide secretion and trafficking].
Length = 298
Score = 36.1 bits (84), Expect = 0.034
Identities = 17/84 (20%), Positives = 26/84 (30%), Gaps = 8/84 (9%)
Query: 186 DPATLDTLE----KMDLARDVTILHQTSHPLTTSDGETFNLGVTLRPTGP--RYCILQLN 239
D A+ L+ +LA D L + V+LRP +L+L
Sbjct: 135 DAASYRLLKRLGIPAELAADPVWLLPPEPWPGGEPLPEPVIVVSLRPWPLLDVSRLLRLL 194
Query: 240 DVADHRVKLVTSVPVRW-KFHPGY 262
D + T V + F
Sbjct: 195 RALDRLQR-DTGAFVLFLPFQQPQ 217
>gnl|CDD|237591 PRK14036, PRK14036, citrate synthase; Provisional.
Length = 377
Score = 30.7 bits (70), Expect = 1.5
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 119 ESYIKNHAARRIVVTGFGTRF--VPDPCASIFQRIA-TLFK 156
Y+ A + + GFG R V DP A+I Q++A LF
Sbjct: 241 RPYLDERLANKQKIMGFGHREYKVKDPRATILQKLAEELFA 281
>gnl|CDD|153272 cd07588, BAR_Amphiphysin, The Bin/Amphiphysin/Rvs (BAR) domain of
Amphiphysins. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Amphiphysins
function primarily in endocytosis and other membrane
remodeling events. They contain an N-terminal BAR domain
with an additional N-terminal amphipathic helix (an
N-BAR), a variable central domain, and a C-terminal SH3
domain. This subfamily is composed of different isoforms
of amphiphysin and Bridging integrator 2 (Bin2).
Amphiphysin I proteins, enriched in the brain and
nervous system, contain domains that bind clathrin,
Adaptor Protein complex 2 (AP2), dynamin and
synaptojanin. They function in synaptic vesicle
endocytosis. Some amphiphysin II isoforms, also called
Bridging integrator 1 (Bin1), are localized in many
different tissues and may function in intracellular
vesicle trafficking. In skeletal muscle, Bin1 plays a
role in the organization and maintenance of the T-tubule
network. Bin2 is mainly expressed in hematopoietic cells
and is upregulated during granulocyte differentiation.
The N-BAR domains of amphiphysins form a curved dimer
with a positively-charged concave face that can drive
membrane bending and curvature.
Length = 211
Score = 30.0 bits (68), Expect = 1.8
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 1 MNKRGRQVVDIARYFHHL--------DNDATIAALERRVENGDSIFD 39
+ KRGR++VD H+L +D + E ++ +++
Sbjct: 110 IAKRGRKLVDYDSARHNLEALKAKKKVDDQKLTKAEEELQQAKKVYE 156
>gnl|CDD|218575 pfam05390, KRE9, Yeast cell wall synthesis protein KRE9/KNH1. This
family contains several KRE9 and KNH1 proteins which are
involved in encoding cell surface O glycoproteins, which
are required for beta -1,6-glucan synthesis in yeast.
Length = 107
Score = 28.5 bits (63), Expect = 3.0
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 452 VNFTTPTPVPKCLHGWYFPHER 473
VN+ TP P+P GWY P +R
Sbjct: 72 VNYATPAPMPSDNGGWYNPSKR 93
>gnl|CDD|239185 cd02784, MopB_CT_PHLH, The MopB_CT_PHLH CD includes a group of
related uncharacterized putative hydrogenase-like
homologs (PHLH) of molybdopterin binding proteins. This
CD is of the PHLH region homologous to the conserved
molybdopterin-binding C-terminal (MopB_CT) region
present in many, but not all, MopB homologs.
Length = 137
Score = 28.6 bits (64), Expect = 3.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 210 HPLTTSDGETFNLGVTLRPTGPRYCILQ 237
+P TSD F GV + TG +Y ++
Sbjct: 105 YPFRTSDVPDFVAGVEVTKTGRKYPLVT 132
>gnl|CDD|215729 pfam00117, GATase, Glutamine amidotransferase class-I.
Length = 186
Score = 28.8 bits (65), Expect = 4.8
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 31 VENGDSIFDNVDAGVWFRDCHTEVDQPVQGTVEGVIPSWIDGVLIRNGPGS 81
++NGDS N+ + EV P E ++ DG++I GPGS
Sbjct: 3 IDNGDSFTYNLARALRELGVEVEVV-PNDTPAEEILELNPDGIIISPGPGS 52
>gnl|CDD|183784 PRK12838, PRK12838, carbamoyl phosphate synthase small subunit;
Reviewed.
Length = 354
Score = 29.1 bits (66), Expect = 5.3
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 48 RDCHTEVDQPVQGTVEGVIPSWIDGVLIRNGPG 80
R C V P ++E + DG+++ NGPG
Sbjct: 188 RGCKVTV-LPYDTSLEEIKNLNPDGIVLSNGPG 219
>gnl|CDD|240366 PTZ00334, PTZ00334, trans-sialidase; Provisional.
Length = 780
Score = 29.1 bits (65), Expect = 6.9
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 40 NVDAGVWFRDCHTEVDQPVQGTVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLF 93
N W RD + VD V+ GV + DGV + W VG++ + L+
Sbjct: 521 NFSGNTW-RDEYLGVDATVKKGTNGVATGYADGVTFQGAWAEWPVGKQGENQLY 573
>gnl|CDD|99865 cd06112, citrate_synt_like_1_1, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism.
Length = 373
Score = 28.5 bits (64), Expect = 7.7
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 121 YIKNHAARRIVVTGFGTRF--VPDPCASIFQRIA 152
Y+ A + + GFG R DP A+I Q++A
Sbjct: 242 YLDKKLANKQKIWGFGHRVYKTKDPRATILQKLA 275
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 0.137 0.433
Gapped
Lambda K H
0.267 0.0550 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,493,436
Number of extensions: 2339467
Number of successful extensions: 1756
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1742
Number of HSP's successfully gapped: 24
Length of query: 476
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 375
Effective length of database: 6,457,848
Effective search space: 2421693000
Effective search space used: 2421693000
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: 61 (27.7 bits)