RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5884
(195 letters)
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 69.3 bits (170), Expect = 7e-16
Identities = 33/80 (41%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 70 IVKIEATDNDLGVNAEITYSIYHVSNTGLHKFRIDPRSGVIETTGKLI--AGEQYSITVQ 127
++ + ATD D G N E+TYSI VS F IDP +G I T L Y++TV
Sbjct: 16 VLTVSATDPDSGENGEVTYSI--VSGNEDGLFSIDPSTGEITTAKPLDREEQSSYTLTVT 73
Query: 128 ATDTGG--KSSQTIVEVSVV 145
ATD GG SS V ++V+
Sbjct: 74 ATDGGGPPLSSTATVTITVL 93
Score = 34.2 bits (79), Expect = 0.007
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 3 VVSKENLDRDPPNPGKFRFQVIAREKQGTAASVPVSLTVNLNDINDN 49
+ + + LDR+ + V A + G S ++T+ + D+NDN
Sbjct: 54 ITTAKPLDRE--EQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 61.2 bits (149), Expect = 5e-13
Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 75 ATDNDLGVNAEITYSIYHVSNTGLHKFRIDPRSGVIETTGKL--IAGEQYSITVQATDTG 132
ATD D G N ++TYSI +S F IDP +G I TT L +Y++TV+ATD G
Sbjct: 2 ATDADSGENGKVTYSI--LSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGG 59
Query: 133 GKSSQTIVEVSV 144
G + V++
Sbjct: 60 GPPLSSTATVTI 71
Score = 40.0 bits (94), Expect = 4e-05
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 3 VVSKENLDRDPPNPGKFRFQVIAREKQGTAASVPVSLTVNLNDINDNAP 51
+ + + LDR+ ++ V A + G S ++T+ + D+NDNAP
Sbjct: 35 ITTTKPLDRE--EQPEYTLTVEATDGGGPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 53.1 bits (128), Expect = 8e-10
Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 70 IVKIEATDNDLGVNAEITYSIYHVSNTGLHKFRIDPRSGVIETTGKL--IAGEQYSITVQ 127
++ + ATD DLG N I YSI + FRIDP +G + TT L + +Y +TV
Sbjct: 15 VLTVTATDADLGPNGRIFYSI--LGGGPGGWFRIDPDTGDLSTTKPLDRESIGEYELTVL 72
Query: 128 ATDTGGKSSQTIVEVSV 144
ATD+GG + V++
Sbjct: 73 ATDSGGPPLSSTTTVTI 89
>gnl|CDD|225936 COG3401, COG3401, Fibronectin type 3 domain-containing protein
[General function prediction only].
Length = 343
Score = 29.9 bits (67), Expect = 0.83
Identities = 30/127 (23%), Positives = 43/127 (33%), Gaps = 14/127 (11%)
Query: 18 KFRFQVIAREKQGTAASVPVSLTVNLNDINDNAPRLPMIPPIQIQAGEARRQIVKIEATD 77
++V + G + +P TV +P IP +A V E
Sbjct: 227 VEYYKVTTVDNTGFESDLPNEPTVGETG---GRYEVPTIPGETTEASFI---GVAAEQNQ 280
Query: 78 NDLGVNAEITYSIYHVSN-TGLHKFRIDPRSGVIETTGKLIAGEQYSITVQATDTGGKSS 136
V TY++Y V + T F I G ++ G +Y V A D G SS
Sbjct: 281 LRQAV----TYTVYRVEDGTPTKFFTITETDGQDN---DMLTGVEYRYEVVAVDKAGLSS 333
Query: 137 QTIVEVS 143
EV
Sbjct: 334 HPSKEVR 340
>gnl|CDD|99798 cd06201, SiR_like2, Cytochrome p450- like alpha subunits of E.
coli sulfite reductase (SiR) multimerize with beta
subunits to catalyze the NADPH dependent reduction of
sulfite to sulfide. Beta subunits have an Fe4S4
cluster and a siroheme, while the alpha subunits (cysJ
gene) are of the cytochrome p450 (CyPor) family having
FAD and FMN as prosthetic groups and utilizing NADPH.
Cypor (including cyt -450 reductase, nitric oxide
synthase, and methionine synthase reductase) are
ferredoxin reductase (FNR)-like proteins with an
additional N-terminal FMN domain and a connecting
sub-domain inserted within the flavin binding portion
of the FNR-like domain. The connecting domain orients
the N-terminal FMN domain with the C-terminal FNR
domain. NADPH cytochrome p450 reductase (CYPOR) serves
as an electron donor in several oxygenase systems and
is a component of nitric oxide synthases and methionine
synthase reductases. CYPOR transfers two electrons from
NADPH to the heme of cytochrome p450 via FAD and FMN.
Ferredoxin-NADP+ (oxido)reductase is an FAD-containing
enzyme that catalyzes the reversible electron transfer
between NADP(H) and electron carrier proteins such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD
as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 289
Score = 29.2 bits (66), Expect = 1.2
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 9 LDRDPPNPGKFRFQVIAREKQGTAASVPVS-LTVNLNDINDNAPRLP 54
LD P +++ R+ G A P + L + LP
Sbjct: 36 LDHKKRLPRTKALELVERKDYGAAVQAPTAILRFKPAKRKLSGKGLP 82
>gnl|CDD|190587 pfam03273, Baculo_gp64, Baculovirus gp64 envelope glycoprotein
family. This family includes the gp64 glycoprotein from
baculovirus as well as other viruses .
Length = 490
Score = 29.0 bits (65), Expect = 1.8
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 52 RLPMIPPIQIQAGEARRQIVKIEATDNDLGVNAEITYSIYHVS---NTGLHKFRIDPRSG 108
LP+ PP E+ ++ V+I + DL N I Y Y+ + N G +DP +G
Sbjct: 16 NLPIKPP-----KESLKKDVEIRIVETDLDENVIIGYKGYYQAYAYNGGS----LDPNTG 66
Query: 109 VIET 112
ET
Sbjct: 67 CEET 70
>gnl|CDD|214484 smart00043, CY, Cystatin-like domain. Cystatins are a family of
cysteine protease inhibitors that occur mainly as single
domain proteins. However some extracellular proteins
such as kininogen, His-rich glycoprotein and fetuin also
contain these domains.
Length = 107
Score = 27.4 bits (61), Expect = 2.3
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 99 HKFRIDPRSGVIETTGKLIAGEQYSITVQATDTGGKSSQT 138
K+ + V+ +++AG Y + V+ +T K
Sbjct: 33 DKYELRVIK-VVSAKSQVVAGTNYYLKVEVGETNCKKLSV 71
>gnl|CDD|214795 smart00736, CADG, Dystroglycan-type cadherin-like domains.
Cadherin-homologous domains present in metazoan
dystroglycans and alpha/epsilon sarcoglycans, yeast
Axl2p and in a very large protein from magnetotactic
bacteria. Likely to bind calcium ions.
Length = 97
Score = 26.9 bits (60), Expect = 2.6
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 86 ITYSIYHVSNTGLHKF-RIDPRSGVIETTGKLIAGEQYSITVQATDTGGKSSQTIVEVSV 144
+TYS + L + D +G + T S+ V ATD+ G S+ ++V
Sbjct: 32 LTYSATLSDGSALPSWLSFDSDTGTLSGTPTNSDVGSLSLKVTATDSSGASASDTFTITV 91
Query: 145 VPGPNT 150
V +
Sbjct: 92 VNTNDA 97
>gnl|CDD|205924 pfam13750, Big_3_3, Bacterial Ig-like domain (group 3). This
family consists of bacterial domains with an Ig-like
fold. Members of this family are found in a variety of
bacterial surface proteins.
Length = 157
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 116 LIAGEQYSITVQATDTGGKSSQTIVEVSVVP 146
L GE Y++TV A D G + V + +P
Sbjct: 118 LEEGESYTLTVTAEDEQGNAKTKTVGFTYLP 148
>gnl|CDD|216843 pfam02010, REJ, REJ domain. The REJ (Receptor for Egg Jelly)
domain is found in PKD1, and the sperm receptor for egg
jelly. The function of this domain is unknown. The
domain is 600 amino acids long so is probably composed
of multiple structural domains. There are six completely
conserved cysteine residues that may form disulphide
bridges. This region contains tandem PKD-like domains.
Length = 436
Score = 27.8 bits (62), Expect = 4.2
Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 106 RSGVIETTGK-LIAGEQYSITVQATDTGGKSSQTIVEVSVVPGP 148
S + L AG Y+ + + +S+ T + +V G
Sbjct: 148 SSSSLTIPASTLKAGTTYTFKLTVSKDSRRSASTEQTILIVEGN 191
>gnl|CDD|219430 pfam07495, Y_Y_Y, Y_Y_Y domain. This domain is mostly found at the
end of the beta propellers (pfam07494) in a family of
two component regulators. However they are also found
tandemly repeated in Clostridium tetani CTC_02402
without other signal conduction domains being present.
It's named after the conserved tyrosines found in the
alignment. The exact function is not known.
Length = 64
Score = 25.4 bits (56), Expect = 5.4
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 9/54 (16%)
Query: 100 KFRIDPRSGVIETTGK--------LIAGEQYSITVQATDTGGKSSQTIVEVSVV 145
++R++ G G L G+ Y++ V+A D G S ++
Sbjct: 10 RYRLEGFDGEWVELGDYSEASYTNLPPGK-YTLKVKAKDNDGNWSYDDASLNFT 62
>gnl|CDD|192725 pfam11228, DUF3027, Protein of unknown function (DUF3027). This
family of proteins with unknown function appears to be
restricted to Actinobacteria.
Length = 194
Score = 26.5 bits (59), Expect = 7.4
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 119 GEQYSITVQATDTGGKSSQTIVEVSVVPGP 148
G ++++TV A + T+ EV +VPGP
Sbjct: 27 GWRWAVTV-ARAPRARHV-TVNEVVLVPGP 54
>gnl|CDD|176241 cd08281, liver_ADH_like1, Zinc-dependent alcohol dehydrogenases
(ADH) and class III ADG (AKA formaldehyde
dehydrogenase). NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of
alcohols and aldehydes or ketones. This group contains
members identified as zinc dependent alcohol
dehydrogenases (ADH), and class III ADG (aka
formaldehyde dehydrogenase, FDH). Alcohol dehydrogenase
in the liver converts ethanol and NAD+ to acetaldehyde
and NADH, while in yeast and some other microorganisms
ADH catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
Class III ADH are also know as glutathione-dependent
formaldehyde dehydrogenase (FDH), which convert
aldehydes to the corresponding carboxylic acid and
alcohol. ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which
contacts a mononucleotide. A GxGxxG motif after the
first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H) binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose
of NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 371
Score = 26.6 bits (59), Expect = 9.0
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 11/50 (22%)
Query: 7 ENLDRDPPNPGKFRFQVIAREKQGTAASVPVSLTVNLNDINDNAPR-LPM 55
E ++ DPP PG+ ++ AA + S +L+ IN + PR LPM
Sbjct: 24 EEVELDPPGPGEVLVKI-------AAAGLCHS---DLSVINGDRPRPLPM 63
>gnl|CDD|215667 pfam00031, Cystatin, Cystatin domain. Very diverse family.
Attempts to define separate sub-families failed.
Typically, either the N-terminal or C-terminal end is
very divergent. But splitting into two domains would
make very short families. pfam00666 are related to this
family but have not been included.
Length = 92
Score = 25.3 bits (56), Expect = 9.8
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 109 VIETTGKLIAGEQYSITVQATDTGGKSSQTIVE 141
V+ +++AG Y I V+ +T S+ +E
Sbjct: 38 VLRAKSQVVAGMNYYIKVEVGETNCSKSKKDLE 70
>gnl|CDD|177816 PLN02156, PLN02156, gibberellin 2-beta-dioxygenase.
Length = 335
Score = 26.5 bits (58), Expect = 9.8
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 36 PVSLTVNLNDINDNAPRLPMIPPIQIQAGEARRQIVK 72
P + NL P +IP I + +A+ QIVK
Sbjct: 7 PATFDSNLYVNPKCKPVPVLIPVIDLTDSDAKTQIVK 43
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
0.312 0.129 0.355
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,415,157
Number of extensions: 837002
Number of successful extensions: 470
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 33
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
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 (21.8 bits)
S2: 56 (25.4 bits)