RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7655
(110 letters)
>gnl|CDD|216593 pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase.
This family consists of various amine oxidases,
including maze polyamine oxidase (PAO) and various
flavin containing monoamine oxidases (MAO). The aligned
region includes the flavin binding site of these
enzymes. The family also contains phytoene
dehydrogenases and related enzymes. In vertebrates MAO
plays an important role regulating the intracellular
levels of amines via there oxidation; these include
various neurotransmitters, neurotoxins and trace amines.
In lower eukaryotes such as aspergillus and in bacteria
the main role of amine oxidases is to provide a source
of ammonium. PAOs in plants, bacteria and protozoa
oxidase spermidine and spermine to an aminobutyral,
diaminopropane and hydrogen peroxide and are involved in
the catabolism of polyamines. Other members of this
family include tryptophan 2-monooxygenase, putrescine
oxidase, corticosteroid binding proteins and
antibacterial glycoproteins.
Length = 444
Score = 73.0 bits (179), Expect = 2e-16
Identities = 38/109 (34%), Positives = 55/109 (50%), Gaps = 10/109 (9%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYS-IRTLTTERLN 59
+E L+D+++ V++ R LG + +P+P L + W ++ + RGSYS R
Sbjct: 345 LEDLSDEELLEAVLRDLRKLLGPED-VPDPVNFLVSDWHTDPYARGSYSYPPVGDDSRY- 402
Query: 60 TSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
L PV G L FAGE TS TV GA+E+G R A R+L
Sbjct: 403 --RPALRTPVGPG-----LFFAGEHTSGGYPGTVEGAVESGLRAARRVL 444
>gnl|CDD|215308 PLN02568, PLN02568, polyamine oxidase.
Length = 539
Score = 59.8 bits (145), Expect = 8e-12
Identities = 34/134 (25%), Positives = 56/134 (41%), Gaps = 25/134 (18%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEP--------------------ARILTTSWGS 40
+E L+D+++ V FL + ++L + WG+
Sbjct: 400 LEKLSDEEIIRGVQTTLSSFLKRRVAGLGSQSHPLCNGGASSNDGSRWKFVKVLKSKWGT 459
Query: 41 NKHFRGSYSIRTLTT-----ERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNG 95
+ F GSYS + + +R+ + G LLFAGEAT Y+T +G
Sbjct: 460 DPLFLGSYSYVAVGSSGDDLDRMAEPLPRISDHDQAGGPPLQLLFAGEATHRTHYSTTHG 519
Query: 96 AIETGWREADRILK 109
A +G REA+R+L+
Sbjct: 520 AYFSGLREANRLLQ 533
>gnl|CDD|215362 PLN02676, PLN02676, polyamine oxidase.
Length = 487
Score = 59.7 bits (145), Expect = 8e-12
Identities = 35/107 (32%), Positives = 47/107 (43%), Gaps = 10/107 (9%)
Query: 2 ESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTS 61
E D + + E+M+ R G IPE IL W SN+ F+GSYS + R
Sbjct: 374 EQQPDSETKAEIMEVLRKMFGP--NIPEATDILVPRWWSNRFFKGSYSNWPIGVSRYEFD 431
Query: 62 AAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
+ APV + F GE TSE V+GA G A+ +L
Sbjct: 432 Q--IRAPVGR------VYFTGEHTSEKYNGYVHGAYLAGIDTANDLL 470
>gnl|CDD|177909 PLN02268, PLN02268, probable polyamine oxidase.
Length = 435
Score = 53.9 bits (130), Expect = 1e-09
Identities = 29/82 (35%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
EP + L + WGS+ + G YS + L APV N L FAGEATS
Sbjct: 359 TEPVQYLVSRWGSDPNSLGCYSYDLVGKPH--DLYERLRAPVDN------LFFAGEATSS 410
Query: 88 DQYATVNGAIETGWREADRILK 109
D +V+GA TG A+
Sbjct: 411 DFPGSVHGAYSTGVMAAEECRM 432
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 53.3 bits (128), Expect = 1e-09
Identities = 31/86 (36%), Positives = 44/86 (51%), Gaps = 15/86 (17%)
Query: 27 IPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAE----LGAPVSNGMGKPVLLFAG 82
+P+P + T WG + G+YS + ++ E LG PV N L FAG
Sbjct: 1109 VPDPVASVVTDWGRDPFSYGAYSYVAIG------ASGEDYDILGRPVEN-----CLFFAG 1157
Query: 83 EATSEDQYATVNGAIETGWREADRIL 108
EAT ++ TV GA+ +G REA RI+
Sbjct: 1158 EATCKEHPDTVGGAMMSGLREAVRII 1183
>gnl|CDD|178144 PLN02529, PLN02529, lysine-specific histone demethylase 1.
Length = 738
Score = 52.2 bits (125), Expect = 3e-09
Identities = 34/97 (35%), Positives = 50/97 (51%), Gaps = 8/97 (8%)
Query: 13 VMKAFRFFLGAK-YTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSN 71
V+ R K +P+P + + T WGS+ GSYS R+ +S ++ +
Sbjct: 506 VLSVLRGIYNPKGINVPDPIQTICTRWGSDPLSYGSYS-----HVRVQSSGSDYDILAES 560
Query: 72 GMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
G+ L FAGEAT+ AT++GA +G REA RIL
Sbjct: 561 VSGR--LFFAGEATTRQYPATMHGAFLSGLREASRIL 595
>gnl|CDD|215187 PLN02328, PLN02328, lysine-specific histone demethylase 1 homolog.
Length = 808
Score = 46.9 bits (111), Expect = 3e-07
Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 27 IPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATS 86
+P+P + + T WG + GSYS + S+ + ++ +G + FAGEAT+
Sbjct: 601 VPDPVQAVCTRWGKDCFTYGSYSYVAVG------SSGDDYDILAESVGDGRVFFAGEATN 654
Query: 87 EDQYATVNGAIETGWREADRILK 109
+ AT++GA +G REA IL+
Sbjct: 655 KQYPATMHGAFLSGMREAANILR 677
>gnl|CDD|178578 PLN03000, PLN03000, amine oxidase.
Length = 881
Score = 44.6 bits (105), Expect = 2e-06
Identities = 28/81 (34%), Positives = 40/81 (49%), Gaps = 12/81 (14%)
Query: 27 IPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAP---VSNGMGKPVLLFAGE 83
+P+P + + T WG + GSYS N + G ++ +G L FAGE
Sbjct: 545 VPDPLQTVCTRWGGDPFSLGSYS---------NVAVGASGDDYDILAESVGDGRLFFAGE 595
Query: 84 ATSEDQYATVNGAIETGWREA 104
AT+ AT++GA TG REA
Sbjct: 596 ATTRRYPATMHGAFVTGLREA 616
>gnl|CDD|99888 cd05814, CBM20_Prei4, Prei4, N-terminal CBM20 (carbohydrate-binding
module, family 20) domain. Preimplantation protein 4
(Prei4) is a protein of unknown function that is
expressed during mouse preimplantation embryogenesis. In
addition to the N-terminal CBM20 domain, Prei4 contains
a C-terminal glycerophosphoryl diester phosphodiesterase
(GDPD) domain. The CBM20 domain is found in a large
number of starch degrading enzymes including
alpha-amylase, beta-amylase, glucoamylase, and CGTase
(cyclodextrin glucanotransferase). CBM20 is also present
in proteins that have a regulatory role in starch
metabolism in plants (e.g. alpha-amylase) or glycogen
metabolism in mammals (e.g. laforin). CBM20 folds as an
antiparallel beta-barrel structure with two starch
binding sites. These two sites are thought to differ
functionally with site 1 acting as the initial starch
recognition site and site 2 involved in the specific
recognition of appropriate regions of starch.
Length = 120
Score = 33.5 bits (77), Expect = 0.006
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 17 FRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTS 61
+R+F+ P +++ W ++ R SI+ L ERLN
Sbjct: 62 YRYFVAVVLNDSGPCQVIVRKWETHLQPR---SIKPLEEERLNDD 103
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 30.3 bits (68), Expect = 0.16
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+++LT +++Q+ + + +G IPEP + L + N +F +Y+ ER+N
Sbjct: 575 VQTLTTEKLQLTSVTSLCMLIGNATVIPEP-QTLFHYYNVNVNFHSNYN------ERIND 627
Query: 61 SAAELGA 67
+ A + A
Sbjct: 628 AVAIITA 634
>gnl|CDD|143428 cd07110, ALDH_F10_BADH, Arabidopsis betaine aldehyde dehydrogenase
1 and 2, ALDH family 10A8 and 10A9-like. Present in
this CD are the Arabidopsis betaine aldehyde
dehydrogenase (BADH) 1 (chloroplast) and 2
(mitochondria), also known as, aldehyde dehydrogenase
family 10 member A8 and aldehyde dehydrogenase family 10
member A9, respectively, and are putative dehydration-
and salt-inducible BADHs (EC 1.2.1.8) that catalyze the
oxidation of betaine aldehyde to the compatible solute
glycine betaine.
Length = 456
Score = 29.6 bits (67), Expect = 0.29
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 56 ERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRILKG 110
ERL T+A + V + + + V L G S+ QY V I G E R+L G
Sbjct: 281 ERLATAAEAI--RVGDPLEEGVRL--GPLVSQAQYEKVLSFIARGKEEGARLLCG 331
>gnl|CDD|129824 TIGR00741, yfiA, ribosomal subunit interface protein. This model
includes a small protein encoded by one of two genes,
both downstream of the gene rpoN for sigma 54, whose
deletion leads to increased expression from sigma
54-dependent promoters. It also includes the N-terminal
half of a light-repressed protein LtrA of Synechococcus
PCC 7002 and the N-terminal region (after removal of
the transit peptide) of a larger plastid-specific
ribosomal protein of spinach. The member of this family
from E. coli is now recognized as a protein at the
interace between ribosomal large and small subunits,
with about 1/3 as many copies per cell as the number of
ribosomes [Protein synthesis, Translation factors].
Length = 95
Score = 28.1 bits (63), Expect = 0.45
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 18/90 (20%)
Query: 9 VQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAP 68
+E+ +A R ++ K AR+ ++F ++ + + N E
Sbjct: 8 NNVEITEALREYVEEKL-----ARL-------ERYFTRIINVDVVLSVERNRFKVEATLY 55
Query: 69 VSNGMGKPVLLFAGEATSEDQYATVNGAIE 98
V+ G V+ A SED YA ++ AI+
Sbjct: 56 VNGG----VIR--ASAESEDMYAAIDLAID 79
>gnl|CDD|226169 COG3643, COG3643, Glutamate formiminotransferase [Amino acid
transport and metabolism].
Length = 302
Score = 27.4 bits (61), Expect = 1.3
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 50 IRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQ 89
++ TTE + ELG V +G PV L+ AT ++
Sbjct: 96 LKDTTTEECVEISKELGKRVGEELGIPVYLYEDAATRPER 135
>gnl|CDD|234221 TIGR03467, HpnE, squalene-associated FAD-dependent desaturase. The
sequences in this family are members of the pfam01593
superfamily of flavin-containing amine oxidases which
include the phytoene desaturases. These sequences also
include a FAD-dependent oxidoreductase domain,
pfam01266. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of squalene, the
condensation product of the polyisoprenoid farnesyl
pyrophosphate. This gene and its association with hopene
biosynthesis in Zymomonas mobilis has been noted in the
literature where the gene symbol hpnE was assigned. This
gene is also found in contexts where the downstream
conversion of squalene to hopenes is not evidence. The
precise nature of the reaction catalyzed by this enzyme
is unknown at this time.
Length = 411
Score = 27.3 bits (61), Expect = 1.6
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 76 PVLLFAGEATSEDQYATVNGAIETGWREADRILK 109
P L AG+ T+ AT+ GA+ +G + A+ +LK
Sbjct: 378 PNLFLAGDWTATGWPATMEGAVRSGVQAAEAVLK 411
>gnl|CDD|130586 TIGR01523, ATPase-IID_K-Na, potassium and/or sodium efflux P-type
ATPase, fungal-type. Initially described as a calcium
efflux ATPase , more recent work has shown that the S.
pombe CTA3 gene is in fact a potassium ion efflux pump.
This model describes the clade of fungal P-type ATPases
responsible for potassium and sodium efflux. The degree
to which these pumps show preference for sodium or
potassium varies. This group of ATPases has been
classified by phylogentic analysis as type IID. The
Leishmania sequence (GP|3192903), which falls between
trusted and noise in this model, may very well turn out
to be an active potassium pump.
Length = 1053
Score = 26.9 bits (59), Expect = 2.8
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEAT----SEDQYATVNGAIETGWREADRI 107
+T + +N S + A V MG A +A+ S+D +A++ AIE G R D I
Sbjct: 749 AMTGDGVNDSPSLKMANVGIAMGINGSDVAKDASDIVLSDDNFASILNAIEEGRRMFDNI 808
Query: 108 LK 109
+K
Sbjct: 809 MK 810
>gnl|CDD|224152 COG1231, COG1231, Monoamine oxidase [Amino acid transport and
metabolism].
Length = 450
Score = 26.6 bits (59), Expect = 2.9
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 80 FAGEATSEDQYATVNGAIETGWREADRILK 109
FAG + + + GAI +G R A I
Sbjct: 416 FAGTEHASEFGGWLEGAIRSGQRAAAEIHA 445
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 26.1 bits (58), Expect = 4.6
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 42 KHFRGSYS----IRTLTTERLNTSAAELGAPVS-----NGMGK-PVLLFA--GEATSED 88
+H R ++++T + L A EL AP +G+ PV+ FA G AT D
Sbjct: 164 RHMRKINGEIRRLQSMTEDELYVVAKELQAPYELVKEVAKLGRLPVVNFAAGGVATPAD 222
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
Length = 293
Score = 25.9 bits (58), Expect = 4.7
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 42 KHFRGSYS-IRTLTT---ERLNTSAAELGAPVS-----NGMGK-PVLLFA--GEATSED 88
+H R IR LT+ + L T+A EL AP +G+ PV+ FA G AT D
Sbjct: 161 RHMRQINGEIRRLTSMSEDELYTAAKELQAPYELVKEVAELGRLPVVNFAAGGIATPAD 219
>gnl|CDD|197341 cd08524, Reelin_subrepeat_like, Tandem repeat subunit of reelin
and related proteins. Reelin is an extracellular
glycoprotein involved in neuronal development,
specifically in the brain cortex. It contains 8
tandemly repeated units, each of which is composed of
two highly similar subrepeats and a central EGF domain.
This model characterizes the subrepeats, which directly
contact each other in a compact arrangement.
Consecutive reelin repeat units are packed together to
form an overall rod-like molecular structure. Reelin
repeats 5 and 6 are reported to interact with neuronal
receptors, the apolipoprotein E receptor 2 (ApoER2) and
the very-low-density lipoprotein receptor (VLDLR),
triggering a signaling cascade upon binding and
subsequent tyrosine phosphorylation of the cytoplasmic
disabled-1 (Dab1). Genetic deficiency of reelin, or
ApoER2 and VLDLR, or Dab1, all exhibit the same
phenotypes, including ataxia, cortical layer inversion
and abnormal positioning patterns.
Length = 144
Score = 25.1 bits (55), Expect = 6.6
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 39 GSNKHFRGSYSIRTLTTERLNTSAAEL 65
G+ F Y R L T LNT+ A
Sbjct: 32 GNALVFNEPYGPRELVTTDLNTNEASF 58
>gnl|CDD|172382 PRK13861, PRK13861, type IV secretion system protein VirB9;
Provisional.
Length = 292
Score = 25.2 bits (55), Expect = 7.7
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 19 FFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLT 54
FF +K P+P +LT S + + S S +TL+
Sbjct: 86 FFKASKVLPPQPVIVLTASDAGMRRYVFSISSKTLS 121
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
0.315 0.130 0.375
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,407,013
Number of extensions: 439259
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 30
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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 (21.6 bits)
S2: 53 (24.1 bits)