RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3407
(749 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 203 bits (519), Expect = 5e-57
Identities = 105/281 (37%), Positives = 140/281 (49%), Gaps = 40/281 (14%)
Query: 1 MLYQRGNDRDYNDW-ERAGNPGWGFKHILPYFLKSEDFQDISRQDAAFHNTGGYLTVS-- 57
M+Y RGN DY++W E G GW + LPYF K+E + + G L+V+
Sbjct: 97 MVYIRGNAMDYDNWAELPGLEGWSYADCLPYFKKAETRDG---GEDDYRGGDGPLSVTRG 153
Query: 58 -PRLSPDETVKIIEA---AGKELKIGTMYDINRDQYIGFGPFDTTTRYGLRCSTSKAFLE 113
P +P + +A AG + D+N Q GFGP D T G R S ++A+L+
Sbjct: 154 KPGTNP-----LFQAFVEAGVQAGYPRTDDLNGYQQEGFGPMDRTVTNGRRWSAARAYLD 208
Query: 114 PAKFRENLIILKNTEVIKILIDSKLKAYGVEYINSQGKICHVNSTREVILSAGAVGSPQL 173
PA R NL I+ + +IL + K +A GVEY G + REVILSAGA+ SPQL
Sbjct: 209 PALKRPNLTIVTHALTDRILFEGK-RAVGVEYERG-GGRETARARREVILSAGAINSPQL 266
Query: 174 LMLSGIGIQKHLKEKNITVIKDLP-VGENLQDH--VCF------PGVLFSSNK---DPAI 221
L LSGIG +HLKE I V+ DLP VGENLQDH V P L+ + K P I
Sbjct: 267 LQLSGIGPAEHLKELGIPVVHDLPGVGENLQDHLEVYIQYECKQPVSLYPALKWWNKPKI 326
Query: 222 TLHYLRYLKVAALKGIST---VEVAKVVGFINTKRNSLYPN 259
+L + G+ E GFI ++ +PN
Sbjct: 327 GAEWL-FTG----TGLGASNHFEAG---GFIRSRAGVDWPN 359
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 188 bits (479), Expect = 1e-51
Identities = 89/212 (41%), Positives = 124/212 (58%), Gaps = 5/212 (2%)
Query: 1 MLYQRGNDRDYNDW-ERAGNPGWGFKHILPYFLKSEDFQDISRQDA-AFHNTGGYLTVSP 58
M+Y RG+ D++ W + +G PGW + +LPYF ++ED + QD +H GG L VSP
Sbjct: 96 MVYVRGHPEDFDAWAQESGAPGWPYDDVLPYFKRAEDLLGVGGQDLRTWHGGGGPLPVSP 155
Query: 59 RLSPDETVKIIEAAGKELKIGTMYDINRDQYIGFGPFDTTTRYGLRCSTSKAFLEPAKFR 118
SP+ + AG++L T D N GFGP+ T G R S ++A+L+PA R
Sbjct: 156 PRSPNPIARAFIEAGEQLGFPTTPDPNGADQEGFGPYCVTICNGRRWSAARAYLKPALKR 215
Query: 119 ENLIILKNTEVIKILIDSKLKAYGVEY-INSQGKICHVNSTREVILSAGAVGSPQLLMLS 177
NL +L V +IL++ +A GVE I G I + REV+L+AGA+ SP+LL+LS
Sbjct: 216 PNLTLLTGARVRRILLEGD-RAVGVEVEIGDGGTIETAVAAREVVLAAGAINSPKLLLLS 274
Query: 178 GIGIQKHLKEKNITVIKDLP-VGENLQDHVCF 208
GIG HL E I V+ LP VG+NLQDH+
Sbjct: 275 GIGPADHLLEHGIDVVGRLPGVGQNLQDHLEI 306
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 162 bits (411), Expect = 1e-42
Identities = 83/210 (39%), Positives = 109/210 (51%), Gaps = 11/210 (5%)
Query: 1 MLYQRGNDRDYNDWERA-GNPGWGFKHILPYFLKSEDFQDISRQDAAFHNTGGYLTVSPR 59
M+YQRGN DY W + G W + LPY+ + E + + G + V R
Sbjct: 91 MIYQRGNPMDYEKWAKPEGMESWDYADCLPYYKRLET-TFGGEKP--YRGHDGPIKVR-R 146
Query: 60 LSPDETV--KIIEAAGKELKIGTMYDINRDQYIGFGPFDTTTRYGLRCSTSKAFLEPAKF 117
D + IEA G E D+N + GFGP D+T G R S ++A+L PA
Sbjct: 147 GPADNPLFQAFIEA-GVEAGYNKTPDVNGFRQEGFGPMDSTVHNGRRVSAARAYLHPAMK 205
Query: 118 RENLIILKNTEVIKILIDSKLKAYGVEYINSQGKICHVNSTREVILSAGAVGSPQLLMLS 177
R NL + V KI + +A GVE+ G+ H + +EVILSAGA+ SPQLL LS
Sbjct: 206 RPNLEVQTRAFVTKINFEGN-RATGVEFKKG-GRKEHTEANKEVILSAGAINSPQLLQLS 263
Query: 178 GIGIQKHLKEKNITVIKDLP-VGENLQDHV 206
GIG +HL+E I LP VGENLQDH+
Sbjct: 264 GIGDAEHLRELGIEPRIHLPGVGENLQDHL 293
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 126 bits (319), Expect = 8e-31
Identities = 69/199 (34%), Positives = 91/199 (45%), Gaps = 15/199 (7%)
Query: 13 DWERAGNPGWGFKHILPYFLKSE---DFQDISRQDAAFHNTGGYLTVSPRLSPDETVKII 69
D++ PGW + +LP+F E DF D H T G + V D
Sbjct: 102 DFDAWPIPGWSWDDVLPHFRAIETDLDF------DGPLHGTAGPIPVRRTAELDGISAAF 155
Query: 70 EAAGKELKIGTMYDINR---DQYIGFGPFDTTTRYGLRCSTSKAFLEPAKFRENLIILKN 126
AA G + D+N D G G G R ST+ A+L PA R NL + +
Sbjct: 156 VAAALGAGFGWIADLNGSGPDAPTGVGAVPLNVDGGRRVSTAVAYLLPALKRPNLTVEAD 215
Query: 127 TEVIKILIDSKLKAYGVEYINSQGKICHVNSTREVILSAGAVGSPQLLMLSGIGIQKHLK 186
T V++IL S +A GVE + G V+L AGAV S LL+LSGIG + L+
Sbjct: 216 TRVVRILF-SGTRAVGVEVLGDGGP--RTLRADRVVLCAGAVESAHLLLLSGIGPAEQLR 272
Query: 187 EKNITVIKDLPVGENLQDH 205
I V+ DLPVG + DH
Sbjct: 273 AAGIAVVLDLPVGSDFVDH 291
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 115 bits (291), Expect = 2e-29
Identities = 61/215 (28%), Positives = 90/215 (41%), Gaps = 40/215 (18%)
Query: 1 MLYQRGNDRDYNDWE-RAGNPGWGFKHILPYFLKSEDFQDISRQDAAFHNTGGYLTVSPR 59
R ++W G GWG+ LPY K E G L V+ +
Sbjct: 36 SACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE----------------GPLGVTTK 79
Query: 60 LSPDE--TVKIIEAAGKELKIGTMY---DINRDQYIGFGPFDTTTRYGLRCSTSKAFLEP 114
+E + + A +EL + N Y GF G + ST++ +L P
Sbjct: 80 -GIEESPLNQALLKAAEELGYPVEAVPRNSNGCHYCGFCGLGC--PTGAKQSTARTWLRP 136
Query: 115 AKFRENLIILKNTEVIKILID-SKLKAYGVEYINSQGKICH-VNSTREVILSAGAVGSPQ 172
A R NL IL + KI+I +A GVE + G I + + +EV+++AGA+ +P
Sbjct: 137 ALER-NLRILTGAKAEKIIILGRGGRAVGVEARDGGGGIKRLITAAKEVVVAAGALNTPP 195
Query: 173 LLMLSGIGIQKHLKEKNITVIKDLPVGENLQDHVC 207
LL+ SG+G H PVG+NLQ H
Sbjct: 196 LLLRSGLGKNPH------------PVGKNLQLHPV 218
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 67.9 bits (166), Expect = 9e-12
Identities = 36/94 (38%), Positives = 54/94 (57%), Gaps = 8/94 (8%)
Query: 119 ENLIILKNTEVIKILIDS---KLKAYGVEYINSQGKICHV----NSTREVILSAGAVGSP 171
L +L + V KI+ D+ + +A GV + + G N E+ILSAGA+GSP
Sbjct: 233 NKLRVLLHATVQKIVFDTSGKRPRATGVIFKDENGNQHQAFLSNNKGSEIILSAGAIGSP 292
Query: 172 QLLMLSGIGIQKHLKEKNITVI-KDLPVGENLQD 204
Q+L+LSGIG +K LK+ I V+ + VG+ + D
Sbjct: 293 QMLLLSGIGPKKELKKHKIPVVLHNEHVGKGMAD 326
>gnl|CDD|241463 cd13309, PH_SKIP, SifA and kinesin-interacting protein Pleckstrin
homology (PH) domain. SKIP (also called
PLEKHM2/Pleckstrin homology domain-containing family M
member 2) is a soluble cytosolic protein that contains a
RUN domain and a PH domain separated by a unstructured
linker region. SKIP is a target of the Salmonella
effector protein SifA and the SifA-SKIP complex
regulates kinesin-1 on the bacterial vacuole. The PH
domain of SKIP binds to the N-terminal region of SifA
while the N-terminus of SKIP is proposed to bind the TPR
domain of the kinesin light chain. The opposite side of
the SKIP PH domain is proposed to bind
phosphoinositides. TSifA, SKIP, SseJ, and RhoA family
GTPases are also thought to promote host membrane
tubulation. Recently, it was shown that the lysosomal
GTPase Arl8 binds to the kinesin-1 linker SKIP and that
both are required for the normal intracellular
distribution of lysosomes. Interestingly, two kinesin
light chain binding motifs (WD) in SKIP have now been
identified to match a consensus sequence for a kinesin
light chain binding site found in several proteins
including calsyntenin-1/alcadein, caytaxin, and vaccinia
virus A36. SKIP has also been shown to interact with
Rab1A. PH domains have diverse functions, but in general
are involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 103
Score = 56.2 bits (136), Expect = 8e-10
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 9/95 (9%)
Query: 551 RSGNLMYKIND----KSAWTPGFVNLQNGIL-----TVKEAPNSPKNISVIQCHSFSQVY 601
+ G LMYK W PG+ L+NG+L P ++ QC ++
Sbjct: 2 KEGPLMYKTGTSYLGGETWKPGYFLLKNGVLYQYPDRSDRLPLLSISLGGEQCGGCRRIN 61
Query: 602 DKSRPYTFKVNFNPYSFVLFAAPDESQLFDWLQDI 636
+ RP++F++ + AAPDE + +WLQ +
Sbjct: 62 NTDRPHSFELILTDRPSLELAAPDEYEASEWLQSL 96
>gnl|CDD|241452 cd13298, PH1_PH_fungal, Fungal proteins Pleckstrin homology (PH)
domain, repeat 1. The functions of these fungal
proteins are unknown, but they all contain 2 PH domains.
This cd represents the first PH repeat. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 106
Score = 36.8 bits (86), Expect = 0.005
Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 8/96 (8%)
Query: 546 HDQVFRSGNLMYKINDKSAWTPGFVNLQNGILTV----KEAPNSPKN-ISVIQCHSFSQV 600
D+V +SG L+ + W + L+ L+ KE + I++ + + + +
Sbjct: 3 FDRVLKSGWLLKRSRKTKTWKKRWFVLRPCQLSYYKDEKEY--KLRRVINLSELTAVAPL 60
Query: 601 YDKSRPYTFKVNFNPYSFVLFAAPDESQLFDWLQDI 636
DK R F + + P F A E +W++ I
Sbjct: 61 KDKKRKNVFAI-YTPSKNYHFQASSEKDANEWVEAI 95
>gnl|CDD|214574 smart00233, PH, Pleckstrin homology domain. Domain commonly found
in eukaryotic signalling proteins. The domain family
possesses multiple functions including the abilities to
bind inositol phosphates, and various proteins. PH
domains have been found to possess inserted domains
(such as in PLC gamma, syntrophins) and to be inserted
within other domains. Mutations in Brutons tyrosine
kinase (Btk) within its PH domain cause X-linked
agammaglobulinaemia (XLA) in patients. Point mutations
cluster into the positively charged end of the molecule
around the predicted binding site for
phosphatidylinositol lipids.
Length = 102
Score = 35.6 bits (82), Expect = 0.015
Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 9/102 (8%)
Query: 549 VFRSGNLMYKINDKSA-WTPGFVNLQNGILTV-----KEAPNSPK---NISVIQCHSFSQ 599
V + G L K W + L N L + PK ++S
Sbjct: 1 VIKEGWLYKKSGGGKKSWKKRYFVLFNSTLLYYKSKKDKKSYKPKGSIDLSGCTVREAPD 60
Query: 600 VYDKSRPYTFKVNFNPYSFVLFAAPDESQLFDWLQDIMISIK 641
+P+ F++ + +L A E + W++ + +I
Sbjct: 61 PDSSKKPHCFEIKTSDRKTLLLQAESEEEREKWVEALRKAIA 102
>gnl|CDD|223108 COG0029, NadB, Aspartate oxidase [Coenzyme metabolism].
Length = 518
Score = 37.2 bits (87), Expect = 0.031
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 109 KAFLEPAKFRENLIILKNTEVIKILIDSKLKAYGVEYINSQGKICHVNSTREVILSAGAV 168
A L+ + R N+ +L+ E + ++I+ + GV +N G++ + V+L+ G +
Sbjct: 137 TALLKKVRNRPNITVLEGAEALDLIIEDGIGVAGVLVLNRNGEL-GTFRAKAVVLATGGL 195
Query: 169 G 169
G
Sbjct: 196 G 196
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 32.4 bits (74), Expect = 0.16
Identities = 23/105 (21%), Positives = 42/105 (40%), Gaps = 16/105 (15%)
Query: 549 VFRSGNLMYK-INDKSAWTPGFVNLQNGILTV----KEAPNSPKN-ISVIQCHSFSQVYD 602
V + G L+ K + +W + L +G+L K++ + PK I + C QV
Sbjct: 1 VIKEGWLLKKGSGGRKSWKKRYFVLFDGVLLYYKDSKKSSSRPKGSIPLSGC----QVTK 56
Query: 603 ------KSRPYTFKVNFNPYSFVLFAAPDESQLFDWLQDIMISIK 641
R F++ L A E + +W++ I +I+
Sbjct: 57 VPDSEDGKRKNCFEIRTGDRETFLLQAESEEERKEWVKAIRSAIR 101
>gnl|CDD|219245 pfam06968, BATS, Biotin and Thiamin Synthesis associated domain.
Biotin synthase (BioB), EC:2.8.1.6, catalyzes the last
step of the biotin biosynthetic pathway. The reaction
consists in the introduction of a sulphur atom into
dethiobiotin. BioB functions as a homodimer. Thiamin
synthesis if a complex process involving at least six
gene products (ThiFSGH, ThiI and ThiJ). Two of the
proteins required for the biosynthesis of the thiazole
moiety of thiamine (vitamin B(1)) are ThiG and ThiH
(this family) and form a heterodimer. Both of these
reactions are thought of involve the binding of
co-factors, and both function as dimers. This domain
therefore may be involved in co-factor binding or
dimerisation (Finn, RD personal observation).
Length = 93
Score = 30.9 bits (71), Expect = 0.52
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 34 SEDFQDISRQDAAFHN---TGGYLTVSPRLSPDETVKIIEAAG 73
D Q ++ A N GGYLT S SPDE + +++ G
Sbjct: 50 LRDLQGLAFMSGA--NSTFVGGYLTTSGNRSPDEDIAMLKDLG 90
>gnl|CDD|162820 TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase
ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF
family of proteins (pfam00899) include a number of
members encoded in the midst of thiamine biosynthetic
operons. This mix of known and putative ThiF proteins
shows a deep split in phylogenetic trees, with the
Escherichia. coli ThiF and the E. coli MoeB proteins
seemingly more closely related than E. coli ThiF and
Campylobacter (for example) ThiF. This model represents
the more widely distributed clade of ThiF proteins such
found in E. coli [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 202
Score = 32.3 bits (74), Expect = 0.56
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 13/72 (18%)
Query: 138 LKAYGVEYINSQGKICHVNSTREVILSAGAVGSPQLLMLSGIGIQKHLKEKNITVIKDLP 197
L G E Q ++ ++ +I+ AG +GSP L L+G G+ I ++ D
Sbjct: 8 LPDIGEE---GQQRL---LNSHVLIIGAGGLGSPAALYLAGAGVGT------IVIVDDDH 55
Query: 198 VG-ENLQDHVCF 208
V NLQ + F
Sbjct: 56 VDLSNLQRQILF 67
>gnl|CDD|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific domain.
This domain is found between domain 3 (pfam04565) and
domain 5 (pfam04565), but shows no homology to domain 4
of Rpb2. The external domains in multisubunit RNA
polymerase (those most distant from the active site) are
known to demonstrate more sequence variability.
Length = 58
Score = 29.1 bits (66), Expect = 1.0
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 224 HYLRYLKVAALKGI-STVEVAKVVGFINTKRNSLYP 258
LRYLKV + T+E +G++ YP
Sbjct: 14 DTLRYLKVEGEHSVPPTLE----IGYVPPSNGGQYP 45
>gnl|CDD|241266 cd01233, PH_KIFIA_KIFIB, KIFIA and KIFIB protein pleckstrin
homology (PH) domain. The kinesin-3 family motors KIFIA
(Caenorhabditis elegans homolog unc-104) and KIFIB
transport synaptic vesicle precursors that contain
synaptic vesicle proteins, such as synaptophysin,
synaptotagmin and the small GTPase RAB3A, but they do
not transport organelles that contain plasma membrane
proteins. They have a N-terminal motor domain, followed
by a coiled-coil domain, and a C-terminal PH domain.
KIF1A adopts a monomeric form in vitro, but acts as a
processive dimer in vivo. KIF1B has alternatively
spliced isoforms distinguished by the presence or
absence of insertion sequences in the conserved
amino-terminal region of the protein; this results in
their different motor activities. KIF1A and KIF1B bind
to RAB3 proteins through the adaptor protein
mitogen-activated protein kinase (MAPK) -activating
death domain (MADD; also calledDENN), which was first
identified as a RAB3 guanine nucleotide exchange factor
(GEF). PH domains have diverse functions, but in general
are involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 111
Score = 29.9 bits (68), Expect = 1.6
Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 9/98 (9%)
Query: 546 HDQVFRSGNLMYKINDKSAWTPGFVNLQNGILTVKEAPNSPKNISVIQCHSFSQV-YDK- 603
V + G L++ + W +V L+ L + + VI + ++V Y
Sbjct: 11 SPVVSKKGYLLFLEDATDGWVRRWVVLRRPYLHIYSSEKDGDERGVINLST-ARVEYSPD 69
Query: 604 -----SRPYTFKVNFNPYSFVLFAAPDESQLFDWLQDI 636
RP F V + P + L A E ++ DWL I
Sbjct: 70 QEALLGRPNVFAV-YTPTNSYLLQARSEKEMHDWLYAI 106
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 31.2 bits (72), Expect = 2.1
Identities = 29/133 (21%), Positives = 48/133 (36%), Gaps = 42/133 (31%)
Query: 224 HYLRYLKVAALKGISTVEVAKVVGFIN----------------TKRNSLYPNVELLSIRI 267
L AALKG+ + + + V ++N ++ + Y N L+++ +
Sbjct: 360 EDTEPLTAAALKGLLSPVLGERVNYVNAPLLAKERGIEVEESKSEESPDYSN--LITVTV 417
Query: 268 PMNSKERNNGKSVMGSLFGQE----VLVDDNDKDVIASPTNL----------TAKVQTIF 313
+ ER SV G++FG V +D D L KV T+
Sbjct: 418 TTDDGER----SVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVIGKVGTL- 472
Query: 314 ESFTKMSETNINI 326
+ E INI
Sbjct: 473 -----LGEAGINI 480
>gnl|CDD|241307 cd10571, PH_beta_spectrin, Beta-spectrin pleckstrin homology (PH)
domain. Beta spectrin binds actin and functions as a
major component of the cytoskeleton underlying cellular
membranes. Beta spectrin consists of multiple spectrin
repeats followed by a PH domain, which binds to
inositol-1,4,5-trisphosphate. The PH domain of
beta-spectrin is thought to play a role in the
association of spectrin with the plasma membrane of
cells. PH domains have diverse functions, but in general
are involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 105
Score = 29.1 bits (66), Expect = 2.3
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 572 LQNGILTV----KEAPNSPKN----ISVIQCHSFSQVYD-KSRPYTFKVNFNPYSFVLFA 622
L+ L+ K A + +++ D K + + F++ + S LF
Sbjct: 30 LKGQELSFYKDQKAAASESYAGEPPLNLSGA-VCEVASDYKKKKHVFRLRLSDGSEYLFQ 88
Query: 623 APDESQLFDWLQDI 636
A DE ++ DW+Q +
Sbjct: 89 AKDEEEMNDWVQKL 102
>gnl|CDD|180442 PRK06175, PRK06175, L-aspartate oxidase; Provisional.
Length = 433
Score = 31.2 bits (71), Expect = 2.4
Identities = 28/114 (24%), Positives = 50/114 (43%), Gaps = 16/114 (14%)
Query: 109 KAFLEPAKFRENLIILKNTEVIKILIDSKLKAYGVEYINSQGKICHVNSTREVILSAGAV 168
K L+ K R+N+ I++N ++ I+ + G K ++ S + IL+ G +
Sbjct: 132 KILLKKVKKRKNITIIENCYLVDIIENDN-TCIGA-ICLKDNKQINIYS-KVTILATGGI 188
Query: 169 G-----SPQLLMLSGIGIQKHLKEKNITVIKDLPVGENLQDHVCFPGVLFSSNK 217
G S +++G GI ++ NI IKDL + +Q H P +
Sbjct: 189 GGLFKNSTNQRIITGDGIAIAIRN-NIK-IKDL---DYIQIH---PTAFYEETI 234
>gnl|CDD|201723 pfam01313, Bac_export_3, Bacterial export proteins, family 3. This
family includes the following members; FliQ, MopD, HrcS,
Hrp, YopS and SpaQ All of these members export proteins,
that do not possess signal peptides, through the
membrane. Although the proteins that these exporters
move may be different, the exporters are thought to
function in similar ways.
Length = 76
Score = 27.8 bits (63), Expect = 3.9
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 677 DKVISFMRSAPFSAIIMVGALVCPDTIVG----IIEASMTLN-PEIPFTLKVGSTTLVGS 731
+ VI R A + +++ L+ +VG + +A+ + + F K+ + L
Sbjct: 1 EDVIDLGRQALWLVLLLSAPLLLVALVVGLVVSLFQAATQIQEQTLSFVPKLLAVLLTLL 60
Query: 732 SLGP 735
GP
Sbjct: 61 LAGP 64
>gnl|CDD|204173 pfam09231, RDV-p3, Rice dwarf virus p3. Members of this family are
core structural proteins found in the double-stranded
RNA virus Phytoreovirus. They are large proteins without
apparent domain division, with a number of all-alpha
regions and one all beta domain near the C-terminal end.
Length = 967
Score = 30.3 bits (68), Expect = 4.2
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 469 VISSIDIDAVSTLISNVEIMCLKQHYTPSSVSAKQRHTLMR-----LLEHISSQTQYFNK 523
+I +D+DA + I ++ + PS+++A QR + L++ + Q
Sbjct: 324 IIGGLDLDAFNDFIYGACLLLFQAIIPPSAIAAMQRLDINNAFAYFLIKCHAPQATTARL 383
Query: 524 CDEIILYSWSWIEQFSDISR 543
I+ I+++ R
Sbjct: 384 LPNEIIPPLDAIDEWQSNDR 403
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 30.0 bits (68), Expect = 6.3
Identities = 26/170 (15%), Positives = 50/170 (29%), Gaps = 13/170 (7%)
Query: 296 KDVIASPTNLTAKVQTIFESFTKMSETNININKKQFMSNMDKVFETI-KTKFEPFAEGEI 354
D + + + E K+SE K + S ++ +K E
Sbjct: 344 NDFMNDEGGFAELFRKLSE---KLSE-----KKLKRYSYLELAALNPRDSKEGSKGTREC 395
Query: 355 PIESRSSYWNNNSDGTSKEACE-MGKLGSSTPIKKHSVITSNNNSLNLENILDNIVFKVL 413
+ R + D CE + +LG ++T + +
Sbjct: 396 KVCGREEPIAEDEDEGLCPTCERLYELGKELLKDDSFLVTEKEDGGKKLPKFNGYYLLFA 455
Query: 414 NKYGEPVMLFLTRRLLIMYNVNTENYKSLVLKDMDNIVVGEHTVSFDCKG 463
+ E L L L+ +Y+ N + L+ I VG++
Sbjct: 456 YEADEYEELALEDELVRIYSKNKPDTGDLI---ATKIWVGDYVPRNGDGK 502
>gnl|CDD|227273 COG4937, COG4937, Predicted regulatory domain of prephenate
dehydrogenase [Translation, ribosomal structure and
biogenesis].
Length = 171
Score = 28.3 bits (63), Expect = 9.1
Identities = 31/108 (28%), Positives = 47/108 (43%), Gaps = 13/108 (12%)
Query: 135 DSKLKAYGVEYI---NSQGKIC---HVNSTREVILSAGAVGSPQLLMLSGIGIQKHLKEK 188
D + A E NS GK H+ S R + V P L+L+ G K K K
Sbjct: 2 DKAIFALTSEIEKLNNSVGKDVGVKHIYSGRVHVGVLKDVE-PDYLILNKSGKGKEQKFK 60
Query: 189 --NITVIKDLPVG----ENLQDHVCFPGVLFSSNKDPAITLHYLRYLK 230
N+ V+ + + E+L+ V VLF + DP + L+ ++ LK
Sbjct: 61 ILNVRVLSEDELRKWKKEHLEKKVIDVSVLFKKDVDPEVILNAVKLLK 108
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
0.318 0.135 0.391
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,588,689
Number of extensions: 3702065
Number of successful extensions: 3245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3224
Number of HSP's successfully gapped: 27
Length of query: 749
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 645
Effective length of database: 6,324,786
Effective search space: 4079486970
Effective search space used: 4079486970
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 (21.7 bits)
S2: 63 (27.9 bits)