RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13459
(542 letters)
>gnl|CDD|202161 pfam02214, K_tetra, K+ channel tetramerisation domain. The
N-terminal, cytoplasmic tetramerisation domain (T1) of
voltage-gated K+ channels encodes molecular determinants
for subfamily-specific assembly of alpha-subunits into
functional tetrameric channels. It is distantly related
to the BTB/POZ domain pfam00651.
Length = 92
Score = 137 bits (348), Expect = 3e-39
Identities = 47/92 (51%), Positives = 63/92 (68%), Gaps = 2/92 (2%)
Query: 43 LLINVSGRRFETWRNTLEKYPDSLLGSNERE-FFYDEDSKEYFFDRDPDIFRHILNYYRT 101
+ +NV G+RFET ++TL ++PD+LLG + FYD+D+ EYFFDR P F ILN+YRT
Sbjct: 1 VRLNVGGKRFETSKSTLTRFPDTLLGRLLKRCDFYDDDTNEYFFDRSPKHFETILNFYRT 60
Query: 102 -GKLHYPKHECLTSYDEELAFFGILPDVIGDC 132
GKLH P+ CL S+ EEL F+G+ I C
Sbjct: 61 GGKLHRPEEVCLDSFLEELEFYGLGELAIELC 92
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 133 bits (338), Expect = 2e-36
Identities = 60/194 (30%), Positives = 90/194 (46%), Gaps = 19/194 (9%)
Query: 231 CLDTACVMIFTAEYLLRLFAAPDRCKFVRSVMSIIDVVAILPYYIGLGITDNDDVSGAFV 290
LD +IFT E LL+ A + K+ RS +I+D + +LP + L + + SG
Sbjct: 1 ILDYVFTVIFTLEMLLKFIALGFKRKYFRSPWNILDFLVVLPSLVSLILFLLGEDSGLLR 60
Query: 291 TLRVFRVFRIFKFSRHSQGLRILGYTL-KSCAS--ELGFLVFSLAMAIIIFATVMFYAEK 347
LR+ R+ R+ + R GLR L +L +S S L L+ L I +F E
Sbjct: 61 VLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAIIGVQLFGGEL 120
Query: 348 N----------VDGTNFTSIPAAFWYTIVTMTTLGYGD-----MVPETIAGKIVGGV-CS 391
+ +NF S A + T+TT G+GD +VP T+ GKI +
Sbjct: 121 DKCCDKNENPINGNSNFDSYGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFII 180
Query: 392 LSGVLVIALPVPVI 405
L GVL++ L + VI
Sbjct: 181 LGGVLLLNLLIGVI 194
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 84.7 bits (210), Expect = 6e-20
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 2/96 (2%)
Query: 45 INVSGRRFETWRNTLEKYPDSLLGSNEREFFYDEDSKEYFFDRDPDIFRHILNYYRTGKL 104
+ V G++F + L + +F + S+ Y D P+ FR +LN+ TGKL
Sbjct: 4 LVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYTGKL 63
Query: 105 HYPKHECLTSYDEELAFFGILPDVIGDCCYEDYRDR 140
P+ E + E + I P ++ C +
Sbjct: 64 DLPE-ENVEELLELADYLQI-PGLVELCEEFLLKLL 97
>gnl|CDD|221286 pfam11879, DUF3399, Domain of unknown function (DUF3399). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is about 100
amino acids in length. This domain is found associated
with pfam02214, pfam00520.
Length = 104
Score = 72.3 bits (177), Expect = 1e-15
Identities = 26/48 (54%), Positives = 35/48 (72%), Gaps = 1/48 (2%)
Query: 496 VSKKKAAEARMAAQESGLEIDENY-REEDIFEIQHHHLLRCLEKTTNP 542
+ K+ E R+A +ESG E++E + + E IFE+QHHHLL CLEKTTN
Sbjct: 1 LQSKRNGELRLALEESGSEMEELFTKSESIFEMQHHHLLHCLEKTTNH 48
Score = 36.1 bits (83), Expect = 0.006
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 427 DREFVELEVPYNGQAKRPGSPSPLLSPSHSVISTANIFQSCCGR 470
+ EFV+ ++ Y + S S S+ S + +CC R
Sbjct: 47 NHEFVDEQM-YEQSCNEVSLQNYPSSRSPSLSSQPGLTSTCCSR 89
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 66.5 bits (163), Expect = 6e-14
Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 3/70 (4%)
Query: 331 LAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTLGYGDMVPETIAGKIVGGVC 390
L + ++IF TV + E+ G +F A +++ VT+TT+GYGD+VP T AG++ +
Sbjct: 2 LLLLVLIFGTVYYSLEEEGWGWDFLD---ALYFSFVTLTTIGYGDIVPLTDAGRLFTIIY 58
Query: 391 SLSGVLVIAL 400
L G+ + L
Sbjct: 59 ILIGIPLFLL 68
>gnl|CDD|152037 pfam11601, Shal-type, Shal-type voltage-gated potassium channels.
This family of proteins represents Shal-type
voltage-gated potassium channels which interact with Kv
channel-interacting proteins to modulate cell surface
expression and function of Kv4 channels. The
interaction of the Shal-type protein Kv4.2 and the Kv
interacting protein KChiP1 forms a structure which is
like the structure between calmodulin and its target
peptides when they interact. Interactions of an N
terminal alpha helix in Kv4.2 and a C terminal alpha
helix in KChIP1 are essential for the modulation of
Kv4.2 by KChIPs.
Length = 26
Score = 60.0 bits (145), Expect = 4e-12
Identities = 21/26 (80%), Positives = 23/26 (88%)
Query: 2 ASVAAWLPFARAAAIGWVPIATHPLP 27
A VAAWLPFARAAAIGW+P+A PLP
Sbjct: 1 AGVAAWLPFARAAAIGWMPVANCPLP 26
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 55.8 bits (135), Expect = 2e-08
Identities = 30/109 (27%), Positives = 51/109 (46%), Gaps = 27/109 (24%)
Query: 334 AIIIFATVMFYAEKNVDGTNF---------TSIPAAFWYTIVTMTTLGYGDMVPETIAGK 384
A+I +++FY+ G + S+ AF+++IVTM+T+GYGD+VP + + +
Sbjct: 140 AVISITSLLFYS---TFGALYLGDGFSPPIESLSTAFYFSIVTMSTVGYGDIVPVSESAR 196
Query: 385 ------IVGGVC----SLSGVLVIALPVPVIVSNFSRIYHQNQRADKRK 423
I+ G+ S+S + PVI N R+ RK
Sbjct: 197 LFTISVIILGITVFATSISAIF-----GPVIRGNLKRLVKGRISHMHRK 240
>gnl|CDD|224147 COG1226, Kch, Kef-type K+ transport systems, predicted NAD-binding
component [Inorganic ion transport and metabolism].
Length = 212
Score = 45.1 bits (106), Expect = 3e-05
Identities = 24/161 (14%), Positives = 47/161 (29%), Gaps = 14/161 (8%)
Query: 238 MIFTAEYLLRLFAAPDRCKFVRSVMSIIDVVAILPYYIGLGITDNDDVSGAFVTLRVFRV 297
+IF L R + + V + I + + D+D LR +
Sbjct: 13 LIFAIVRLKRHVIIVGFGRVGQIVARALLASGIP-----VVVIDSD--EDRVELLRELGL 65
Query: 298 FRIFKFSRHSQGLRILGYTLKSCASELGFLVFSLAMAIIIFATVMFYAEKNVDGTNFTSI 357
+ + + L G E V ++ A +
Sbjct: 66 LVVLGDATREEVLEAAGI-------ERARAVIVTLSDDATNVFIVLLARAINPELEILAR 118
Query: 358 PAAFWYTIVTMTTLGYGDMVPETIAGKIVGGVCSLSGVLVI 398
+ T+TT+G ++VP T ++ +L G+
Sbjct: 119 ARDLDEAVETLTTVGADEVVPPTFESALLLARAALVGLGGD 159
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 38.7 bits (90), Expect = 0.009
Identities = 36/135 (26%), Positives = 59/135 (43%), Gaps = 20/135 (14%)
Query: 260 SVMSIIDVVAILPYY-IGLGITDNDDVSGAFVTLRVFRVFRIFK----FSRHSQGLRILG 314
S ++DV + +P+ + IT ++ ++ L + R +R+ + F+R + +R
Sbjct: 138 STWFLMDVASTIPFQALAYLITGTVKLNLSYSLLGLLRFWRLRRVKQLFTRLEKDIR-FS 196
Query: 315 YTLKSCASELG---FLVFSLAMAIIIFATVMFYAEKNVDGT---NFTS-------IPAAF 361
Y CA L FLV + A + K G NF I A +
Sbjct: 197 YFWIRCARLLSVTLFLVHCAGCLYYLIADRYPHQGKTWIGAVIPNFRETSLWIRYISAIY 256
Query: 362 WYTIVTMTTLGYGDM 376
W +I TMTT+GYGD+
Sbjct: 257 W-SITTMTTVGYGDL 270
>gnl|CDD|219699 pfam08016, PKD_channel, Polycystin cation channel. This family
contains the cation channel region of PKD1 and PKD2
proteins.
Length = 423
Score = 36.2 bits (84), Expect = 0.040
Identities = 34/195 (17%), Positives = 72/195 (36%), Gaps = 28/195 (14%)
Query: 231 CLDTACVMIFTAEYLLRLFAAPDRCKFVRSVMSII--DVVAILPYYIGLGITDNDDVSGA 288
LD A V + +L ++ R + + V + + + A
Sbjct: 244 LLDLAIVALSVVVIVLHIY----RDFLATQLWKQVEASPVDFTDFDRVARLDQLYRIILA 299
Query: 289 FVTLRVFRV-FRIFKFSRHSQGLRILGYTLKSCASEL---GFLVFSLAMAIIIFATVMFY 344
F+ +F ++FK R ++ + + TL EL + L +A ++F
Sbjct: 300 FL---LFLTWLKLFKVLRFNRTMSLFTKTLSRALKELLGFAVMFVILFLAYAQLGYLLF- 355
Query: 345 AEKNVDGTNFTSIPAAFWYTIVTMTTLGYGDMVPETI--AGKIVGGVCSLSGVLVIA--- 399
VD NF++ +I+T+ GD I +++G + L+ V ++
Sbjct: 356 -GSQVD--NFSNFVK----SILTLFRTLCGDFGYTEIFSGNRVLGPLLFLTFVFLVIFIL 408
Query: 400 --LPVPVIVSNFSRI 412
L + +I ++ +
Sbjct: 409 LNLFLAIINDSYVEV 423
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 33.5 bits (77), Expect = 0.31
Identities = 24/126 (19%), Positives = 40/126 (31%), Gaps = 25/126 (19%)
Query: 326 FLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTLGYGDMVPETIAGKI 385
FL ++ +A I F + +K+V + A T G D
Sbjct: 303 FLFLAVLLAAIGF---LLRRKKSVGTKEGGDLGAI--------TLSGSAD---------- 341
Query: 386 VGGVCSLSGVLVIALPVPVIV---SNFSRIYHQNQRADKRKAQRDREFVELEVPYNGQAK 442
G + V A VP+I+ S+ ++ + R F +L +P G
Sbjct: 342 -GAASLGAEQDVSAGTVPLILRLGSDLAKALESIDLDQEIDRMRWALFEDLGIPLPGIHI 400
Query: 443 RPGSPS 448
R
Sbjct: 401 RVDPEG 406
>gnl|CDD|216239 pfam01007, IRK, Inward rectifier potassium channel.
Length = 336
Score = 32.7 bits (75), Expect = 0.43
Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 23/89 (25%)
Query: 326 FLVFSLAMAI--IIFATVMF---------YAEKNVDGT----NFTSIPAAFWYTIVTMTT 370
L+FSLA + + F T+ + + + T N S +AF ++I T TT
Sbjct: 38 LLIFSLAFLLSWLFFGTIWWLIAFAHGDLEPAPDANHTPCVMNVHSFTSAFLFSIETQTT 97
Query: 371 LGYGDMVPETIAGKIVGGVCSLSGVLVIA 399
+GYG + + C L+ L+I
Sbjct: 98 IGYG--------FRCITEECPLAIFLLIL 118
>gnl|CDD|150497 pfam09834, DUF2061, Predicted membrane protein (DUF2061). This
domain, found in various prokaryotic proteins, has no
known function.
Length = 53
Score = 29.1 bits (66), Expect = 0.63
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 172 WRAFENPHTSTAALVFYYVTGFFIAVSVMANVVETV 207
WR HT+ A LV Y +TG +A ++E
Sbjct: 7 WRIL---HTTVAFLVAYLLTGSLAIGGAIA-LIEPA 38
>gnl|CDD|215101 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 32.0 bits (73), Expect = 0.77
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 35 RRKADDEKLLINVSGRRFETWRNTLEKYP 63
RKA + + +I + FE WR++LE P
Sbjct: 404 LRKAMEAQTIIREESKNFEAWRDSLETVP 432
>gnl|CDD|223742 COG0670, COG0670, Integral membrane protein, interacts with FtsH
[General function prediction only].
Length = 233
Score = 30.7 bits (70), Expect = 1.4
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 326 FLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVT---MTTLGY 373
F V++ + + + ++ YA + +I AAF T + ++ GY
Sbjct: 90 FFVYTALVGLTLSPILLVYAAIS----GGDAIAAAFGITALVFGALSLYGY 136
>gnl|CDD|233196 TIGR00933, 2a38, potassium uptake protein, TrkH family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 390
Score = 30.3 bits (69), Expect = 2.4
Identities = 23/116 (19%), Positives = 44/116 (37%), Gaps = 22/116 (18%)
Query: 259 RSVMSIIDVVAILPYYIGLGITDNDDVSGAFVTLRVFRVFRIFKFSRHSQGLRILGYTLK 318
S+ V+A L GLG T + + R+FK S ++ +R+ L
Sbjct: 156 FHDPSVNLVIAFLIILGGLGFT-------VHYDVYLLLRKRVFKLSLDTK-VRLFVTFL- 206
Query: 319 SCASELGFLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTLGYG 374
L + F L + + T+ Y+ F ++ + ++ T+ T G+
Sbjct: 207 -----LLAIGFILFLLLERGNTLYSYS--------FGALLLSAFFQSSTLRTAGFS 249
>gnl|CDD|234120 TIGR03144, cytochr_II_ccsB, cytochrome c-type biogenesis protein
CcsB. Members of this protein family represent one of
two essential proteins of system II for c-type
cytochrome biogenesis. Additional proteins tend to be
part of the system but can be replaced by chemical
reductants such as dithiothreitol. This protein is
designated CcsB in Bordetella pertussis and some other
bacteria, resC in Bacillus (where there is additional
N-terminal sequence), and CcsA in chloroplast. We use
the CcsB designation here. Member sequences show regions
of strong sequence conservation and variable-length,
poorly conserved regions in between; sparsely filled
columns were removed from the seed alignment prior to
model construction [Energy metabolism, Electron
transport, Protein fate, Protein modification and
repair].
Length = 243
Score = 29.9 bits (68), Expect = 2.7
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 324 LGFLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAA---FWYTI-VTMTTLGYG 374
LG V LA+ I+ FA+++ E T + A W + V++ L Y
Sbjct: 55 LGAFVAPLALLILGFASLVLPVEMQ----QSTPLVPALQSNWLMMHVSVMILSYA 105
>gnl|CDD|218791 pfam05879, RHD3, Root hair defective 3 GTP-binding protein (RHD3).
This family consists of several eukaryotic root hair
defective 3 like GTP-binding proteins. It has been
speculated that the RHD3 protein is a member of a novel
class of GTP-binding proteins that is widespread in
eukaryotes and required for regulated cell enlargement.
The family also contains the homologous yeast synthetic
enhancement of YOP1 (SEY1) protein which is involved in
membrane trafficking.
Length = 743
Score = 30.5 bits (69), Expect = 2.9
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 14/70 (20%)
Query: 108 KHECLTSYDEELAFFGILPDVIGDCCYEDYRDRKRENAERLMDDKLSENGDQNLPQLTNI 167
+ +CL+ YD E + + + KR+ E +D L QL +
Sbjct: 301 REKCLSEYDTEASRY-----------NKGVYQEKRQELEEKLDSHLKPTFQA---QLGAL 346
Query: 168 RQKMWRAFEN 177
+ + +F+
Sbjct: 347 HKGLLESFKE 356
>gnl|CDD|211392 cd11380, Ribosomal_S8e_like, Eukaryotic/archaeal ribosomal
protein S8e and similar proteins. This family contains
the eukaryotic/archaeal ribosomal protein S8, a
component of the small ribosomal subunits, as well as
the NSA2 gene product.
Length = 138
Score = 29.0 bits (66), Expect = 3.0
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 30 PIPKDRRKADDEKLLINVSGRRFE 53
P K +RKA K + R++E
Sbjct: 1 PQGKHKRKATGGKFKVVRKKRKYE 24
>gnl|CDD|235672 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 30.1 bits (69), Expect = 3.2
Identities = 11/46 (23%), Positives = 27/46 (58%), Gaps = 9/46 (19%)
Query: 326 FLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTL 371
L F++A++++I + + ++ +D F++ P T++ +TTL
Sbjct: 46 LLTFNIALSVLILLVAL-FIQRPLD---FSAFP-----TLLLITTL 82
>gnl|CDD|219062 pfam06496, DUF1097, Protein of unknown function (DUF1097). This
family consists of several bacterial putative membrane
proteins.
Length = 140
Score = 28.7 bits (65), Expect = 3.6
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 329 FSLAMAII--IFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTLG--YGDMVPETIAGK 384
LA I+ I A VM K V +F IP F T +G + ++P G
Sbjct: 69 NPLAGYILTGIVAFVMCLQAK-VPLLSF--IPGTFLGCASTFAAIGGDWLVVLPSLAVGA 125
Query: 385 IVGGVCSLSGVLVIA 399
++G G + A
Sbjct: 126 LLGYASEWLGSWLAA 140
>gnl|CDD|222413 pfam13843, DDE_Tnp_1_7, Transposase IS4.
Length = 352
Score = 29.5 bits (67), Expect = 4.4
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 13/61 (21%)
Query: 70 NEREFFYDEDSKEYFFDRDPDIFRHILNY---YRTGKL--HYPKHECLTSYDEELAFFGI 124
E F FFD +I + I+ Y K T+ +E AF G+
Sbjct: 1 TPVELF------NLFFD--DEILQLIVRETNLYARQKRAKQKDSVWRPTTAEEIKAFLGL 52
Query: 125 L 125
L
Sbjct: 53 L 53
>gnl|CDD|177625 PHA03389, polh, polyhedrin; Provisional.
Length = 246
Score = 29.4 bits (66), Expect = 4.6
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 37 KADDEKLLINVSGRRF--ETWRNTLEKYPDSLLGSNEREF 74
K D KL++N SG+ F ETW +E DS N++E
Sbjct: 80 KPDTMKLVVNWSGKEFLRETWTRFME---DSFPIVNDQEV 116
>gnl|CDD|200482 cd11344, AmyAc_GlgE_like, Alpha amylase catalytic domain found in
GlgE-like proteins. GlgE is a
(1,4)-a-D-glucan:phosphate a-D-maltosyltransferase,
involved in a-glucan biosynthesis in bacteria. It is
also an anti-tuberculosis drug target. GlgE isoform I
from Streptomyces coelicolor has the same catalytic and
very similar kinetic properties to GlgE from
Mycobacterium tuberculosis. GlgE from Streptomyces
coelicolor forms a homodimer with each subunit
comprising five domains (A, B, C, N, and S) and 2
inserts. Domain A is a catalytic alpha-amylase-type
domain that along with domain N, which has a
beta-sandwich fold and forms the core of the dimer
interface, binds cyclodextrins. Domain A, B, and the 2
inserts define a well conserved donor pocket that binds
maltose. Cyclodextrins competitively inhibit the binding
of maltooligosaccharides to the S. coelicolor enzyme,
indicating that the hydrophobic patch overlaps with the
acceptor binding site. This is not the case in M.
tuberculosis GlgE because cyclodextrins do not inhibit
this enzyme, despite acceptor length specificity being
conserved. Domain C is hypothesized to help stabilize
domain A and could be involved in substrate binding.
Domain S is a helix bundle that is inserted within the N
domain and it plays a role in the dimer interface and
interacts directly with domain B. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 355
Score = 29.5 bits (67), Expect = 4.6
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 54 TWRNT---LEKYPDSLLGSNEREFFYDEDSKEYFFDRDPDIFRHILNY 98
TWRNT L +Y L + RE+F + F+ PDI L +
Sbjct: 238 TWRNTKQELTEYLTELTQTEVREYF-----RPNFWPNTPDILPEYLQF 280
>gnl|CDD|237906 PRK15086, PRK15086, ethanolamine utilization protein EutH;
Provisional.
Length = 372
Score = 29.5 bits (67), Expect = 4.7
Identities = 37/201 (18%), Positives = 79/201 (39%), Gaps = 44/201 (21%)
Query: 227 IVFFCLDTACVMIFTAEYLLRLFAAPDRCKFVRSVMSIID---VVAILPYYIGLGITDND 283
++ F + A + F E +++ F F + ++++I AI+ G +
Sbjct: 176 VIIFAILLALGLKFIPEKMIKGFL-----IFGKFIVALITIGLAAAIVQSLTGWKLIPGF 230
Query: 284 D----------------VSGAFVTLRVFRVFRIFKFSRHSQGL-RILGYTLKSCASELGF 326
D ++GAF + + F + + ++LG + A
Sbjct: 231 DPIKFEAIEIVGSIAIVLAGAFPMVYLITKV----FKKPLMKVGKLLGMNEVAAAG---- 282
Query: 327 LVFSLAMAIIIFATVMFYAEKN-VDGTNFTSIPAAFWYTIVTMTTLGYG-----DMVPET 380
+V +LA I +F + + V F ++ AAF V LG+ M+
Sbjct: 283 MVATLANNIPMFGMMKDMDPRGKVINVAF-AVSAAF----VLGDHLGFTAGVQPTMIFPM 337
Query: 381 IAGKIVGGVCSLSGVLVIALP 401
I GK++GG+ ++ +++++
Sbjct: 338 IVGKLIGGITAIGVAILLSVK 358
>gnl|CDD|224287 COG1368, MdoB, Phosphoglycerol transferase and related proteins,
alkaline phosphatase superfamily [Cell envelope
biogenesis, outer membrane].
Length = 650
Score = 29.3 bits (66), Expect = 5.7
Identities = 27/162 (16%), Positives = 57/162 (35%), Gaps = 22/162 (13%)
Query: 256 KFVRSVMSIIDVVAILPYYIGLGITDNDDVSGAFVTLRVFRVFRIFKFSRHSQGLRILGY 315
F + ++ L + + L + + L F+ R+ + +L
Sbjct: 13 LFFPIFLGFGILLVFLLWLLTL-LIYFLGFVLPILLL--FQGLRLLFSLPILFIVSLLLL 69
Query: 316 TL--KSC-ASELGFLVFSLAMAIIIFATVMFYAEKNVDGTNFTSIPAAFWYTIVTMTTLG 372
L K A + L+ +L ++I++ ++FY F +IP A + LG
Sbjct: 70 LLLFKGVDALNIFRLILALLISILLILDILFYRFFID----FLTIPNALLIEDFNLGKLG 125
Query: 373 YGDM---VPETIAGKIVGGVCSLSGVLVIALPVPVIVSNFSR 411
+ + PE I +V L++ + + V +
Sbjct: 126 FSALSLLYPEDILF-VVD--------LILLILLLVFYWRLAG 158
>gnl|CDD|216251 pfam01027, Bax1-I, Inhibitor of apoptosis-promoting Bax1.
Programmed cell-death involves a set of Bcl-2 family
proteins, some of which inhibit apoptosis (Bcl-2 and
Bcl-XL) and some of which promote it (Bax and Bak).
Human Bax inhibitor, BI-1, is an evolutionarily
conserved integral membrane protein containing multiple
membrane-spanning segments predominantly localised to
intracellular membranes. It has 6-7 membrane-spanning
domains. The C termini of the mammalian BI-1 proteins
are comprised of basic amino acids resembling some
nuclear targeting sequences, but otherwise the predicted
proteins lack motifs that suggest a function. As plant
BI-1 appears to localise predominantly to the ER, we
hypothesized that plant BI-1 could also regulate cell
death triggered by ER stress. BI-1 appears to exert its
effect through an interaction with calmodulin.
Length = 205
Score = 28.7 bits (65), Expect = 6.3
Identities = 10/83 (12%), Positives = 23/83 (27%), Gaps = 21/83 (25%)
Query: 294 VFRVFRIFKFSRHSQGLRILGYTLKSCASELGFLVFSLAMAIIIFATVMFYAEKNVDGTN 353
+F + + S + +F+L + + ++ Y T
Sbjct: 51 IFVFLLFSRIKKKSSSAALAL-----------LFLFTLLEGLTLGPILLVY-------TA 92
Query: 354 FTSIPAAFWYTIVT---MTTLGY 373
+ I AF T ++
Sbjct: 93 GSIILQAFLGTAAIFGGLSLYAL 115
>gnl|CDD|177516 PHA03070, PHA03070, DNA-binding virion core protein; Provisional.
Length = 249
Score = 28.9 bits (65), Expect = 6.4
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 233 DTACVMIFTAEYLLRLFAAPDRCKFVRSVMSIIDVV 268
D T L L A + KF RS +SI ++V
Sbjct: 12 DALFAAGITRYDDLELVIAGAKVKFPRSFLSIFNIV 47
>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Yggs-like proteins. This subfamily contains mainly
uncharacterized proteobacterial proteins with similarity
to the hypothetical Escherichia coli protein YggS, a
homolog of yeast YBL036c, which is homologous to a
Pseudomonas aeruginosa gene that is co-transcribed with
a known proline biosynthetic gene. Like yeast YBL036c,
Yggs is a single domain monomeric protein with a typical
TIM-barrel fold. Its structure, which shows a
covalently-bound PLP cofactor, is similar to the
N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. YggS has not been characterized extensively
and its biological function is still unkonwn.
Length = 224
Score = 28.7 bits (65), Expect = 6.6
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 12/72 (16%)
Query: 478 KARLARI--RIAKASSGAAF---------VSKKKAAEARMAAQESGL-EIDENYREEDIF 525
LA++ RIA+A+ A VSK K A+A A +G ENY +E +
Sbjct: 3 AENLAQVKQRIAQAAKQAGRDPSSVQLLAVSKTKPADAIREAYAAGQRHFGENYVQEALE 62
Query: 526 EIQHHHLLRCLE 537
+I+ L+ +E
Sbjct: 63 KIEALRDLQDIE 74
>gnl|CDD|191366 pfam05757, PsbQ, Oxygen evolving enhancer protein 3 (PsbQ). This
family consists of the plant specific oxygen evolving
enhancer protein 3 (PsbQ). Photosystem II (PSII)1 is a
pigment-protein complex, which consists of at least 25
different protein subunits, at present denoted PsbA-Z
according to the genes that encode them. PsbQ plays an
important role in the lumenal oxygen-evolving activity
of PSII from higher plants and green algae.
Length = 203
Score = 28.6 bits (64), Expect = 7.1
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 1 MASVAAWLPFARAAAIGWVPIATHPLPPPPIPK 33
+A+ A FA+AAA PI LPPPP
Sbjct: 40 VATGLAGGAFAQAAAAAAKPIKV-GLPPPPSGG 71
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 29.1 bits (65), Expect = 8.3
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 457 VISTANIFQSCCGRCCGQRYQ 477
VI A+IF S CGR C Q Q
Sbjct: 369 VIYEASIFPSICGRVCPQETQ 389
>gnl|CDD|218929 pfam06182, ABC2_membrane_6, ABC-2 family transporter protein. This
family acts as the transmembrane domain (TMD) of ABC
transporters. The family includes proteins responsible
for the transport of herbicides.
Length = 229
Score = 28.4 bits (64), Expect = 8.5
Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 23/104 (22%)
Query: 294 VFRVFRIFKFSRHSQGLRILGYTLKSC------ASELGFLVFSLAMAIIIFATVMFYAEK 347
FR F I++ R G+ +L Y +K A L +++ ++ +I ++ +F+
Sbjct: 78 SFRRFNIWRVGRLLVGIILLIYAVKKLGINWTPAKILLYIISLISGTLIYYS--LFFI-- 133
Query: 348 NVDGTNFTSIPAAFW-YTIVTMTTLGYG----DMVPETIAGKIV 386
S+ +FW +T + YG P TI I+
Sbjct: 134 ------LGSL--SFWFVRSYNITYITYGLLTFAKYPMTIYPLII 169
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 27.3 bits (61), Expect = 8.9
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 212 RPGRAGSLPCGERYKIVFFCLDTACV 237
R GR LP G RYK+V LD A V
Sbjct: 82 RGGRVKDLP-GVRYKVVRGALDVAGV 106
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
0.324 0.139 0.428
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,934,574
Number of extensions: 2935104
Number of successful extensions: 4257
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4240
Number of HSP's successfully gapped: 58
Length of query: 542
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 440
Effective length of database: 6,413,494
Effective search space: 2821937360
Effective search space used: 2821937360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.3 bits)