RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8891
(203 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 80.1 bits (198), Expect = 4e-18
Identities = 42/204 (20%), Positives = 67/204 (32%), Gaps = 46/204 (22%)
Query: 1 MCAKFLGDPTKVVSGSCDRTLKIWDLRSTETKFAGSSCNDLVT---YDGAGTTIISGHFD 57
F D + S S D+T+K+WD+ + + D V + GT + S D
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQD 156
Query: 58 KKVRFWDFRAEEKVRDIELH-GKITSLDLSKGTETKFAGSSCNDLVTYDGAGTTIISGHF 116
++ WD R + V + H G++ S V + G ++S
Sbjct: 157 GTIKLWDLRTGKCVATLTGHTGEVNS-------------------VAFSPDGEKLLSSSS 197
Query: 117 DKKVRFWDFRAEEKVRDIELHGKITSLDLSKGKYYFVFAEGFKVQCDFTRAVFVVDDDYV 176
D ++ WD + + + H F D +
Sbjct: 198 DGTIKLWDLSTGKCLGTLRGHENG-----------------------VNSVAFSPDGYLL 234
Query: 177 AVGSIDGNIYVWDCNTEQVEAVLK 200
A GS DG I VWD T + L
Sbjct: 235 ASGSEDGTIRVWDLRTGECVQTLS 258
Score = 78.5 bits (194), Expect = 1e-17
Identities = 49/206 (23%), Positives = 72/206 (34%), Gaps = 48/206 (23%)
Query: 1 MCAKFLGDPTKVVSGSCDRTLKIWDLRSTETKFAG---SSCNDLVTYDGAGTTIISGHFD 57
C F D + +GS D T+K+WDL + E + V GT + SG D
Sbjct: 13 TCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSD 72
Query: 58 KKVRFWDFRAEEKVRDIELH-GKITSLDLSKGTETKFAGSSCNDLVTYDGAGTTIISGHF 116
K +R WD E VR + H ++S+ S G + S
Sbjct: 73 KTIRLWDLETGECVRTLTGHTSYVSSVAFSP-------------------DGRILSSSSR 113
Query: 117 DKKVRFWDFRAEEKVRDIELHGK-ITSLDLSKGKYYFVFAEGFKVQCDFTRAVFVVDDDY 175
DK ++ WD + + + H + S+ S D +
Sbjct: 114 DKTIKVWDVETGKCLTTLRGHTDWVNSVAFSP------------------------DGTF 149
Query: 176 VAVGSIDGNIYVWDCNTEQVEAVLKD 201
VA S DG I +WD T + A L
Sbjct: 150 VASSSQDGTIKLWDLRTGKCVATLTG 175
Score = 67.4 bits (165), Expect = 1e-13
Identities = 47/194 (24%), Positives = 69/194 (35%), Gaps = 48/194 (24%)
Query: 1 MCAKFLGDPTKVVSGSCDRTLKIWDLRSTETK--FAGSSCNDL-VTYDGAGTTIISGHFD 57
F D T V S S D T+K+WDLR+ + G + V + G ++S D
Sbjct: 139 NSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSD 198
Query: 58 KKVRFWDFRAEEKVRDIELHGK-ITSLDLSKGTETKFAGSSCNDLVTYDGAGTTIISGHF 116
++ WD + + + H + S V + G + SG
Sbjct: 199 GTIKLWDLSTGKCLGTLRGHENGVNS-------------------VAFSPDGYLLASGSE 239
Query: 117 DKKVRFWDFRAEEKVRDIELH-GKITSLDLSKGKYYFVFAEGFKVQCDFTRAVFVVDDDY 175
D +R WD R E V+ + H +TSL S D
Sbjct: 240 DGTIRVWDLRTGECVQTLSGHTNSVTSLAWSP------------------------DGKR 275
Query: 176 VAVGSIDGNIYVWD 189
+A GS DG I +WD
Sbjct: 276 LASGSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 62.8 bits (151), Expect = 1e-11
Identities = 47/219 (21%), Positives = 74/219 (33%), Gaps = 37/219 (16%)
Query: 5 FLGDPTKVVSGSCDRTLKIWDLRSTETKFAGSSCNDL----VTYDGAGTTIISGHFDKKV 60
F D + + SGS D T+++WDLRS+ + S + V + G + SG D V
Sbjct: 249 FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTV 308
Query: 61 RFWDFRAEEKVRDIELHGKITSLDLSKGTETKFAGSSCNDLVTYDGAGTTIISGHFDKKV 120
R WD + + +L +G + + S L+ + G D +
Sbjct: 309 RLWDLETGKLL-------SSLTLKGHEGPVSSLSFSPDGSLL--------VSGGSDDGTI 353
Query: 121 RFWDFRAEEKVRDIELHGKITSLDLSKGKYYFVFAEG------------------FKVQC 162
R WD R + ++ +E H + S+ S
Sbjct: 354 RLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTS 413
Query: 163 DFTRAVFVVDDDYVAVGSIDGNIYVWDCNTEQVEAVLKD 201
T F D +A GS D I +WD T
Sbjct: 414 RVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSP 452
Score = 48.9 bits (115), Expect = 4e-07
Identities = 55/218 (25%), Positives = 81/218 (37%), Gaps = 20/218 (9%)
Query: 2 CAKFLGDPTKVVSGSCDRTLKIWDLRSTETKFA--------GSSCNDLVTYDGAGTTIIS 53
F D ++SGS D T+K+WDL + E S L + DG + S
Sbjct: 70 SIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLAS 129
Query: 54 GHFDKKVRFWDFR-AEEKVRDIELHGK-ITSLDLSKGTETKFAGSSCNDLV----TYDGA 107
D V+ WD + +R +E H + +TSL S + +GSS + + G
Sbjct: 130 SSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGK 189
Query: 108 GTTIISGHFDKKVRFWDFRAEEKVR--DIELHGKITSLDLSKGKYYFVFAEGFKVQCDFT 165
+ ++GH V F + + G I DLS GK G
Sbjct: 190 PLSTLAGH-TDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVV-- 246
Query: 166 RAVFVVDDDYVAVGSIDGNIYVWDCNTEQVEAVLKDMH 203
+ F D +A GS DG I +WD + H
Sbjct: 247 -SSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGH 283
Score = 44.3 bits (103), Expect = 2e-05
Identities = 43/205 (20%), Positives = 68/205 (33%), Gaps = 14/205 (6%)
Query: 7 GDPTKVVSGSCDRTLKIWDLRSTETKFA-----GSSCNDLVTYDGAGTTIISGHFDKKVR 61
G+ + S S D T+K+WDL + S L D ++
Sbjct: 122 GNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIK 181
Query: 62 FWDFRAEEKVRDIELH-GKITSLDLSKGTETKFAGSSC-NDLVTYDGAG----TTIISGH 115
WD R + + + H ++SL S A S + +D + + +SGH
Sbjct: 182 LWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGH 241
Query: 116 FDKKVRFWDFRAEEKVRDIELHGKITSLDLSKGKYYFVFAEGFKVQCDFTRAVFVVDDDY 175
D V + + G I DL G F D
Sbjct: 242 SDSVVSSFSPD-GSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSS--VLSVAFSPDGKL 298
Query: 176 VAVGSIDGNIYVWDCNTEQVEAVLK 200
+A GS DG + +WD T ++ + L
Sbjct: 299 LASGSSDGTVRLWDLETGKLLSSLT 323
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 31.2 bits (71), Expect = 0.030
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 1 MCAKFLGDPTKVVSGSCDRTLKIWD 25
F D + SGS D T+++WD
Sbjct: 15 TSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 27.3 bits (61), Expect = 0.84
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 172 DDDYVAVGSIDGNIYVWD 189
D + +A GS DG + VWD
Sbjct: 22 DGNLLASGSDDGTVRVWD 39
Score = 25.8 bits (57), Expect = 2.5
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 42 VTYDGAGTTIISGHFDKKVRFWD 64
V + G + SG D VR WD
Sbjct: 17 VAFSPDGNLLASGSDDGTVRVWD 39
Score = 25.8 bits (57), Expect = 2.5
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 102 VTYDGAGTTIISGHFDKKVRFWD 124
V + G + SG D VR WD
Sbjct: 17 VAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 30.7 bits (70), Expect = 0.047
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 2 CAKFLGDPTKVVSGSCDRTLKIWD 25
F D + SGS D T+K+WD
Sbjct: 17 SVAFSPDGKYLASGSDDGTIKLWD 40
Score = 27.3 bits (61), Expect = 0.72
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 172 DDDYVAVGSIDGNIYVWD 189
D Y+A GS DG I +WD
Sbjct: 23 DGKYLASGSDDGTIKLWD 40
Score = 26.5 bits (59), Expect = 1.6
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 42 VTYDGAGTTIISGHFDKKVRFWD 64
V + G + SG D ++ WD
Sbjct: 18 VAFSPDGKYLASGSDDGTIKLWD 40
Score = 26.5 bits (59), Expect = 1.6
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 102 VTYDGAGTTIISGHFDKKVRFWD 124
V + G + SG D ++ WD
Sbjct: 18 VAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 30.7 bits (69), Expect = 0.52
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 53 SGHFDKKVRFWDFRAE-EKVRDIELHGKITSLDLSKGTETKFAGSSCNDLVTYDGAGTTI 111
SG D +R W+ E V++I+ + KG + K + N + Y +
Sbjct: 92 SGSEDLTIRVWEIPHNDESVKEIK-----DPQCILKGHKKKISIIDWNPMNYY-----IM 141
Query: 112 ISGHFDKKVRFWDFRAEEKVRDIELHGKITSL 143
S FD V WD E++ I + K++SL
Sbjct: 142 CSSGFDSFVNIWDIENEKRAFQINMPKKLSSL 173
>gnl|CDD|173920 cd02169, Citrate_lyase_ligase, Citrate lyase ligase. Citrate lyase
ligase, also known as [Citrate (pro-3S)-lyase] ligase,
is responsible for acetylation of the
(2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A)
prosthetic group of the gamma subunit of citrate lyase,
converting the inactive thiol form of this enzyme to the
active form. The acetylation of 1 molecule of
deacetyl-citrate lyase to enzymatically active citrate
lyase requires 6 molecules of ATP. The
Adenylylyltranferase activity of the enzyme involves the
formation of AMP and and pyrophosphate in the
acetylation reaction.
Length = 297
Score = 29.5 bits (67), Expect = 0.97
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 163 DFTRAVFVVDDDYVAVGSIDGNI 185
D+T +F + +A GSI GN+
Sbjct: 5 DYTVGIFDDAGELIATGSIAGNV 27
>gnl|CDD|222231 pfam13570, YWTD, YWTD domain. The YWTD repeat appears on the
low-density lipoprotein receptor (LDLR) up to six times,
being preceded and followed by an EGF domain. The region
of the LDLR carrying these two types of repeat appears
to control the related processes of lipoprotein release
at low pH and the recycling of the receptor to the cell
surface. The YWTD repeats form a six-bladed
beta-propeller that packs tightly against the C-terminal
EGF module.
Length = 39
Score = 26.8 bits (60), Expect = 1.2
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 170 VVDDDYVAVGSIDGNIYVWD 189
V V VG+ DG +Y D
Sbjct: 18 AVAGGLVYVGTGDGTLYALD 37
>gnl|CDD|114767 pfam06064, Gam, Host-nuclease inhibitor protein Gam. The Gam
protein inhibits RecBCD nuclease and is found in both
bacteria and bacteriophage.
Length = 98
Score = 27.7 bits (61), Expect = 1.9
Identities = 19/49 (38%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 84 DLSKGTETKFAGSSCNDLVTYDGAGTTIISGHFDKKVRFWDFRAEEKVR 132
DL KG S C D + GA IS FD V F + RA E +R
Sbjct: 34 DLEKGIPLHLFESLCIDELPRHGANKKAISRAFDDDVEFQE-RAAEFIR 81
>gnl|CDD|225595 COG3053, CitC, Citrate lyase synthetase [Energy production and
conversion].
Length = 352
Score = 28.1 bits (63), Expect = 3.1
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 161 QCDFTRAVFVVDDDYVAVGSIDGNI--YVWDCNTEQVEAVL 199
++ A++ +++ +A GSI GN+ V + Q E +
Sbjct: 34 TVEYFVAIYRDNEEIIACGSIAGNVIKCVAVSESLQGEGLA 74
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 28.5 bits (63), Expect = 3.2
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 8 DPTKVVSGSCDRTLKIWDL 26
D + +VS S D TLK+WDL
Sbjct: 671 DSSTLVSSSTDNTLKLWDL 689
Score = 28.1 bits (62), Expect = 4.1
Identities = 31/126 (24%), Positives = 52/126 (41%), Gaps = 29/126 (23%)
Query: 7 GDPTKVVSGSCDRTLKIWDLR------STETKFAGSSCNDLVTYDGAGTTIISGHFDKKV 60
DPT + SGS D ++K+W + + +TK A C + +G ++ G D KV
Sbjct: 586 ADPTLLASGSDDGSVKLWSINQGVSIGTIKTK-ANICCVQFPS--ESGRSLAFGSADHKV 642
Query: 61 RFWDFRAEE-KVRDIELHGKITSLDLSKGTETKFAGSSCNDLVTYDGAGTTIISGHFDKK 119
++D R + + + H K S +F SS T++S D
Sbjct: 643 YYYDLRNPKLPLCTMIGHSKTVSY-------VRFVDSS------------TLVSSSTDNT 683
Query: 120 VRFWDF 125
++ WD
Sbjct: 684 LKLWDL 689
Score = 27.7 bits (61), Expect = 4.9
Identities = 31/152 (20%), Positives = 61/152 (40%), Gaps = 36/152 (23%)
Query: 42 VTYDGAGTTIISGHFDKKVRFWDFRAEEKVRD-IELHGKITSLDLSKGTETKFAGSSCND 100
+ +D G + +KK++ F E ++D ++H + L + +K +G N
Sbjct: 489 IGFDRDGEFFATAGVNKKIKI--FECESIIKDGRDIHYPVVEL----ASRSKLSGICWNS 542
Query: 101 LVTYDGAGTTIISGHFDKKVRFWDFRAEEKVRDIELHGK-ITSLDLSKGKYYFVFAEGFK 159
+ + + S +F+ V+ WD + V +++ H K + S+D S
Sbjct: 543 YIK-----SQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSA----------- 586
Query: 160 VQCDFTRAVFVVDDDYVAVGSIDGNIYVWDCN 191
D +A GS DG++ +W N
Sbjct: 587 ------------DPTLLASGSDDGSVKLWSIN 606
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 28.3 bits (63), Expect = 3.6
Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 12/99 (12%)
Query: 107 AGTTIISGHFDKKVRFWDFRAEEKVRDIELHGKITSLDLS-KGKYYFVFAEGFKVQCDF- 164
AG +IS + + DF +E+ R I ++ S+ +G Y + DF
Sbjct: 41 AGAGMISEELAGQQLYLDFDEQEQERGITINAANVSMVHEYEGNEYLINLIDTPGHVDFG 100
Query: 165 ---TRAVFVVDDDYVAVGSIDGNIYVWDCNTEQVEAVLK 200
TRA+ VD V V +++G + Q E VL+
Sbjct: 101 GDVTRAMRAVDGAIVVVCAVEGVM-------PQTETVLR 132
>gnl|CDD|184619 PRK14322, glmM, phosphoglucosamine mutase; Provisional.
Length = 429
Score = 27.6 bits (61), Expect = 5.5
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 69 EKVRDIELHGKITSLDLSKGTETKFA 94
E RD++L G++ SLDL+ G T A
Sbjct: 156 EMFRDLDLTGEMVSLDLANGATTTTA 181
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 318
Score = 27.2 bits (61), Expect = 5.8
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 165 TRAVFVVDDDYVAVGSIDGNIYV 187
T A F+VD D + GN++V
Sbjct: 174 TAAEFLVDYDTILGADKFGNLHV 196
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 27.0 bits (60), Expect = 6.2
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 169 FVVDDDYVAVGSIDGNIYVWDCNT 192
VD + V + G + D T
Sbjct: 30 VAVDGGRLYVATGKGELVALDAAT 53
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 27.2 bits (61), Expect = 6.3
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 113 SGHFDKK--VRFWDFRAEEKVRDIELHGKITSLDLSKGKYYFVFAEG 157
+GHFD + V + A EK E+ ++ +L GK + AEG
Sbjct: 295 AGHFDVEIDVAGLEELAVEK---REVRPQVDEYELPDGKRIILLAEG 338
>gnl|CDD|188873 cd09213, Luminal_IRE1_like, The Luminal domain, a dimerization
domain, of Inositol-requiring protein 1-like proteins.
The Luminal domain is a dimerization domain present in
Inositol-requiring protein 1 (IRE1), eukaryotic
translation Initiation Factor 2-Alpha Kinase 3
(EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are
serine/threonine protein kinases (STKs) and are type I
transmembrane proteins that are localized in the
endoplasmic reticulum (ER). They are kinase receptors
that are activated through the release of BiP, a
chaperone bound to their luminal domains under
unstressed conditions. This results in dimerization
through their luminal domains, allowing
trans-autophosphorylation of their kinase domains and
activation. They play roles in the signaling of the
unfolded protein response (UPR), which is activated when
protein misfolding is detected in the ER in order to
decrease the synthesis of new proteins and increase the
capacity of the ER to cope with the stress. IRE1, also
called Endoplasmic reticulum (ER)-to-nucleus signaling
protein (or ERN), contains an endoribonuclease domain in
its cytoplasmic side and acts as an ER stress sensor. It
is the oldest and most conserved component of the UPR in
eukaryotes. Its activation results in the cleavage of
its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans,
promoting a splicing event that enables translation into
a transcription factor which activates the UPR. EIF2AK3,
also called PKR-like Endoplasmic Reticulum Kinase
(PERK), phosphorylates the alpha subunit of eIF-2,
resulting in the downregulation of protein synthesis. It
functions as the central regulator of translational
control during the UPR pathway. In addition to the eIF-2
alpha subunit, EIF2AK3 also phosphorylates Nrf2, a
leucine zipper transcription factor which regulates
cellular redox status and promotes cell survival during
the UPR.
Length = 312
Score = 27.1 bits (60), Expect = 7.0
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 16/77 (20%)
Query: 136 LHGKITSLDLSKGKYYFVFAEG----------FKVQCDFTRAVFVVDDDYVAVGSIDGNI 185
L G I ++D S G+ + F G + + + + D DGN+
Sbjct: 7 LDGTIYAVDASSGEIQWSFDGGGPLYSSYQSSRDGNAESSSTMLIPSLDG------DGNL 60
Query: 186 YVWDCNTEQVEAVLKDM 202
Y D ++ + +
Sbjct: 61 YQHDKGHGSLQRLPLTI 77
>gnl|CDD|233470 TIGR01567, S_layer_rel_Mac, S-layer family duplication domain.
This model represents a sequence region found tandemly
duplicated in two proven archaeal S-layer glycoproteins,
MA0829 from Methanosarcina acetivorans C2A and MM1976
from Methanosarcina mazei Go1, as well as in several
paralogs of those L-layer proteins from both species.
Members of the family show regions of local similarity
to another known family of archaeal S-layer proteins
described by model TIGR01564. Some members of this
family, including the proven S-layer proteins, have the
archaeosortase A target motif, PGF-CTERM (TIGR04126), at
the protein C-terminus [Cell envelope, Surface
structures].
Length = 256
Score = 26.7 bits (59), Expect = 7.9
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 142 SLDLSKG---KYYFVFAEGFKVQCDFTRAVFVVDDDYVAVGSIDGNIYVWD 189
SLDL +G V +G KV ++ VD + ++V ++D + + +
Sbjct: 104 SLDLGEGYSLNVNQVDVDGEKVWLSLSKDGEEVDSEIISVSTVDDDDFTYT 154
>gnl|CDD|197200 cd00138, PLDc_SF, Catalytic domain of phospholipase D superfamily
proteins. Catalytic domain of phospholipase D (PLD)
superfamily proteins. The PLD superfamily is composed of
a large and diverse group of proteins including plant,
mammalian and bacterial PLDs, bacterial cardiolipin (CL)
synthases, bacterial phosphatidylserine synthases (PSS),
eukaryotic phosphatidylglycerophosphate (PGP) synthase,
eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and
some bacterial endonucleases (Nuc and BfiI), among
others. PLD enzymes hydrolyze phospholipid
phosphodiester bonds to yield phosphatidic acid and a
free polar head group. They can also catalyze the
transphosphatidylation of phospholipids to acceptor
alcohols. The majority of members in this superfamily
contain a short conserved sequence motif (H-x-K-x(4)-D,
where x represents any amino acid residue), called the
HKD signature motif. There are varying expanded forms of
this motif in different family members. Some members
contain variant HKD motifs. Most PLD enzymes are
monomeric proteins with two HKD motif-containing
domains. Two HKD motifs from two domains form a single
active site. Some PLD enzymes have only one copy of the
HKD motif per subunit but form a functionally active
dimer, which has a single active site at the dimer
interface containing the two HKD motifs from both
subunits. Different PLD enzymes may have evolved through
domain fusion of a common catalytic core with separate
substrate recognition domains. Despite their various
catalytic functions and a very broad range of substrate
specificities, the diverse group of PLD enzymes can bind
to a phosphodiester moiety. Most of them are active as
bi-lobed monomers or dimers, and may possess similar
core structures for catalytic activity. They are
generally thought to utilize a common two-step ping-pong
catalytic mechanism, involving an enzyme-substrate
intermediate, to cleave phosphodiester bonds. The two
histidine residues from the two HKD motifs play key
roles in the catalysis. Upon substrate binding, a
histidine from one HKD motif could function as the
nucleophile, attacking the phosphodiester bond to create
a covalent phosphohistidine intermediate, while the
other histidine residue from the second HKD motif could
serve as a general acid, stabilizing the leaving group.
Length = 119
Score = 25.9 bits (57), Expect = 9.4
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 168 VFVVDDDYVAVGSIDGNIYVWDCNTE 193
V V+D + VGS + + N E
Sbjct: 89 VVVIDGEVAYVGSANLSTASAAQNRE 114
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
0.321 0.138 0.425
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,235,689
Number of extensions: 944849
Number of successful extensions: 798
Number of sequences better than 10.0: 1
Number of HSP's gapped: 756
Number of HSP's successfully gapped: 43
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
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 (21.8 bits)
S2: 57 (25.7 bits)