RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3426
(360 letters)
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 125 bits (316), Expect = 2e-34
Identities = 55/162 (33%), Positives = 84/162 (51%), Gaps = 4/162 (2%)
Query: 10 CHQYNELLSSKTGHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEATAYAC 69
++ + G +L+R+LKA+ +P D Y QG++ + AP L DE A+ C
Sbjct: 49 TFPHHFFFKNGEGQQQLRRILKAYSIYNP--DVGYCQGMNFIAAPL-LLVVLDEEEAFWC 105
Query: 70 FSTFIPKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLT 129
F + + L +FFL + + L F L+ HD EL H+ ++ P LFA WFLT
Sbjct: 106 FVSLLEYLLRDFFLPSFPGL-QRDLYVFEELLKKHDPELYKHLQKLGLDPSLFASKWFLT 164
Query: 130 MFSHVLPLHKIFHLWDKLLLGDASFPLFIGVSILKQLRETLL 171
+F+ LPL + LWD L G F + ++ILK+ R+ LL
Sbjct: 165 LFARELPLETVLRLWDLFLEGGKFFLFRVALAILKRFRKELL 206
>gnl|CDD|214540 smart00164, TBC, Domain in Tre-2, BUB2p, and Cdc16p. Probable
Rab-GAPs. Widespread domain present in Gyp6 and Gyp7,
thereby giving rise to the notion that it performs a
GTP-activator activity on Rab-like GTPases.
Length = 216
Score = 121 bits (306), Expect = 8e-33
Identities = 50/150 (33%), Positives = 81/150 (54%), Gaps = 4/150 (2%)
Query: 22 GHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEATAYACFSTFIPKYLHNF 81
G L+RVLKA+ +P+ Y QG++ L AP L DE A+ C + +Y NF
Sbjct: 71 GQESLRRVLKAYALYNPEV--GYCQGMNFLAAPL-LLVMEDEEDAFWCLVKLMERYGPNF 127
Query: 82 FLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPLHKIF 141
+L D S + + L + L+ +D +L H+ ++ P L+A+ WFLT+F+ LPL +
Sbjct: 128 YLPDMSGLQLDLL-QLDRLVKEYDPDLYKHLKDLGITPSLYALRWFLTLFARELPLEIVL 186
Query: 142 HLWDKLLLGDASFPLFIGVSILKQLRETLL 171
+WD L + F + +++LK R+ LL
Sbjct: 187 RIWDVLFAEGSDFLFRVALALLKLHRDVLL 216
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 89.1 bits (221), Expect = 2e-19
Identities = 56/200 (28%), Positives = 88/200 (44%), Gaps = 8/200 (4%)
Query: 13 YNELLSSKTGHT--KLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEATAYACF 70
N L ++ L+RVLKA+ +P+ +V QG++ L AP L E A+ C
Sbjct: 270 DNSLFQTEISIRAENLRRVLKAYSLYNPEVGYV--QGMNFLAAPL-LLVLESEEQAFWCL 326
Query: 71 STFI-PKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLT 129
+ L +FL++ S + R+ L+ D EL H+ + +FA WFLT
Sbjct: 327 VKLLKNYGLPGYFLKNLSGLHRDLKV-LDDLVEELDPELYEHLLREGVVLLMFAFRWFLT 385
Query: 130 MFSHVLPLHKIFHLWDKLLLGDASFPLFIGVSILKQLRETLLSSGF-NECILLFSDLPEV 188
+F PL +WD L L +S + ++ILK LR+ LL LL L
Sbjct: 386 LFVREFPLEYALRIWDCLFLEGSSMLFQLALAILKLLRDKLLKLDSDELLDLLLKQLFLH 445
Query: 189 DIEQSVTDSIDIYCVTPRSI 208
+++ + + T R I
Sbjct: 446 SGKEAWSSILKFRHGTDRDI 465
>gnl|CDD|238783 cd01525, RHOD_Kc, Member of the Rhodanese Homology Domain
superfamily. Included in this CD are the rhodanese-like
domains found C-terminal of the serine/threonine protein
kinases catalytic (S_TKc) domain and the Tre-2, BUB2p,
Cdc16p (TBC) domain. The putative active site Cys
residue is not present in this CD.
Length = 105
Score = 69.4 bits (170), Expect = 9e-15
Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 7/108 (6%)
Query: 239 LSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESS 298
+S D++ L++ K+ +DIR + ++ I GSINIP + + G +E
Sbjct: 1 ISVYDVIRLLDNS--PAKLAAVDIRSSPDFRRGHIEGSINIPFSSV----FLKEGELEQL 54
Query: 299 PEMNILFNNKGSIIVIVGGEDSMRQAKFARFIVRLGFPKVTYVHEHVN 346
P + L N KG IIVIV A FA F+V+ G P+V + +N
Sbjct: 55 PTVPRLENYKGKIIVIVSHSHK-HAALFAAFLVKCGVPRVCILDGGIN 101
>gnl|CDD|238089 cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold
domain found duplicated in the rhodanese protein. The
cysteine containing enzymatically active version of the
domain is also found in the Cdc25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and certain stress proteins such as
senesence specific protein 1 in plants, PspE and GlpE in
bacteria and cyanide and arsenate resistance proteins.
Inactive versions (no active site cysteine) are also
seen in dual specificity phosphatases, ubiquitin
hydrolases from yeast and in sulfuryltransferases, where
they are believed to play a regulatory role in
multidomain proteins.
Length = 89
Score = 58.1 bits (141), Expect = 6e-11
Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 18/99 (18%)
Query: 243 DLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMN 302
+L +L++ +++D+R+ EEY A I G+INIPL+ + + +
Sbjct: 1 ELKELLD----DEDAVLLDVREPEEYAAGHIPGAINIPLSELEERAALLE---------- 46
Query: 303 ILFNNKGSIIVIVGGEDSMRQAKFARFIVRLGFPKVTYV 341
+K IV+ R A+ A+ + + G V +
Sbjct: 47 ---LDKDKPIVVY-CRSGNRSARAAKLLRKAGGTNVYNL 81
>gnl|CDD|197731 smart00450, RHOD, Rhodanese Homology Domain. An alpha beta fold
found duplicated in the Rhodanese protein. The the
Cysteine containing enzymatically active version of the
domain is also found in the CDC25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and stress proteins such as Senesence
specific protein 1 in plants, PspE and GlpE in bacteria
and cyanide and arsenate resistance proteins. Inactive
versions with a loss of the cysteine are also seen in
Dual specificity phosphatases, ubiquitin hydrolases from
yeast and in sulfuryltransferases. These are likely to
play a role in protein interactions.
Length = 100
Score = 54.0 bits (130), Expect = 2e-09
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 2/90 (2%)
Query: 253 KKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMNILFNNKGSII 312
KV+++D+R EEY I G++NIPL+ + D +L +E + L +K +
Sbjct: 1 NDEKVVLLDVRSPEEYEGGHIPGAVNIPLSELLD-RRGELDILEFEELLKRLGLDKDKPV 59
Query: 313 VIVGGEDSMRQAKFARFIVRLGFPKVTYVH 342
V+ R AK A + LGF V +
Sbjct: 60 VVYCRS-GNRSAKAAWLLRELGFKNVYLLD 88
>gnl|CDD|216005 pfam00581, Rhodanese, Rhodanese-like domain. Rhodanese has an
internal duplication. This Pfam represents a single copy
of this duplicated domain. The domain is found as a
single copy in other proteins, including phosphatases
and ubiquitin C-terminal hydrolases.
Length = 106
Score = 50.6 bits (121), Expect = 4e-08
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 12/96 (12%)
Query: 251 RFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMNILFNNKGS 310
+ V++ID+R EEY I G++NIP L L +ES E +K
Sbjct: 8 LLEADDVVLIDVRSPEEYAKGHIPGAVNIP------LSLPSLDKLESELEELGKKLDKDK 61
Query: 311 IIVIVGGEDSMRQAKFARFIV-----RLGFPKVTYV 341
IV+ R + A ++ LG+ V +
Sbjct: 62 TIVVY-CASGNRSGQAAALLLALILKALGYKNVYVL 96
>gnl|CDD|223680 COG0607, PspE, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 110
Score = 44.5 bits (105), Expect = 5e-06
Identities = 24/104 (23%), Positives = 36/104 (34%), Gaps = 19/104 (18%)
Query: 242 TDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIG-SINIPLARIPDLESTDLGSMESSPE 300
T D +++D+R+ EEY I G +INIPL+ +
Sbjct: 6 TISEDEAALLLAGEDAVLLDVREPEEYERGHIPGAAINIPLSELKA-------------A 52
Query: 301 MNILFNNKGSIIVIV--GGEDSMRQAKFARFIVRLGFPKVTYVH 342
N+L IV+ G S A + GF V +
Sbjct: 53 ENLLELPDDDPIVVYCASGVRSAAAAAALK---LAGFTNVYNLD 93
>gnl|CDD|238777 cd01519, RHOD_HSP67B2, Member of the Rhodanese Homology Domain
superfamily. This CD includes the heat shock protein
67B2 of Drosophila melanogaster and other similar
proteins, many of which are uncharacterized.
Length = 106
Score = 37.2 bits (87), Expect = 0.002
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 255 PKVLVIDIRDNEEYVAESIIGSINIPLARIPD 286
P ++ID+R+ EE I G+INIPL+ +PD
Sbjct: 14 PNKVLIDVREPEELKTGKIPGAINIPLSSLPD 45
>gnl|CDD|238778 cd01520, RHOD_YbbB, Member of the Rhodanese Homology Domain
superfamily. This CD includes several putative ATP /GTP
binding proteins including E. coli YbbB.
Length = 128
Score = 36.9 bits (86), Expect = 0.003
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 239 LSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPL 281
+++ DLL L +ID+R +E+ + G+IN+PL
Sbjct: 1 ITAEDLLALRKAD-----GPLIDVRSPKEFFEGHLPGAINLPL 38
>gnl|CDD|238782 cd01524, RHOD_Pyr_redox, Member of the Rhodanese Homology Domain
superfamily. Included in this CD are the Lactococcus
lactis NADH oxidase, Bacillus cereus NADH dehydrogenase,
and Bacteroides thetaiotaomicron pyridine
nucleotide-disulphide oxidoreductase, and similar
rhodanese-like domains found C-terminal of the pyridine
nucleotide-disulphide oxidoreductase (Pyr-redox) domain
and the Pyr-redox dimerization domain.
Length = 90
Score = 35.7 bits (83), Expect = 0.004
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 257 VLVIDIRDNEEYVAESIIGSINIPLARIPD 286
V +ID+R +E+ I G+INIPL + D
Sbjct: 14 VTLIDVRTPQEFEKGHIKGAINIPLDELRD 43
>gnl|CDD|235526 PRK05597, PRK05597, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 355
Score = 36.0 bits (83), Expect = 0.027
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 238 SLSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARI 284
S ++LD+ V +ID+R+ E+ A SI G+ N+PL+ I
Sbjct: 256 SGGFGEVLDVPRVSALPDGVTLIDVREPSEFAAYSIPGAHNVPLSAI 302
>gnl|CDD|238786 cd01528, RHOD_2, Member of the Rhodanese Homology Domain
superfamily, subgroup 2. Subgroup 2 includes
uncharacterized putative rhodanese-related domains.
Length = 101
Score = 33.1 bits (76), Expect = 0.038
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 13/84 (15%)
Query: 255 PKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMNILFNNKGSIIVI 314
+ ++ID+R+ EE + G +++P++ IP S +L S +P+ +I+ ++
Sbjct: 16 EEPVLIDVREPEELEIAFLPGFLHLPMSEIP-ERSKELDSD--NPDKDIV------VLCH 66
Query: 315 VGGEDSMRQAKFARFIVRLGFPKV 338
GG R + A++++R GF V
Sbjct: 67 HGG----RSMQVAQWLLRQGFENV 86
>gnl|CDD|238720 cd01443, Cdc25_Acr2p, Cdc25 enzymes are members of the Rhodanese
Homology Domain (RHOD) superfamily. Also included in
this CD are eukaryotic arsenate resistance proteins such
as Saccharomyces cerevisiae Acr2p and similar proteins.
Cdc25 phosphatases activate the cell division kinases
throughout the cell cycle progression. Cdc25
phosphatases dephosphorylate phosphotyrosine and
phosphothreonine residues, in order to activate their
Cdk/cyclin substrates. The Cdc25 and Acr2p RHOD domains
have the signature motif (H/YCxxxxxR).
Length = 113
Score = 33.5 bits (77), Expect = 0.038
Identities = 18/97 (18%), Positives = 34/97 (35%), Gaps = 12/97 (12%)
Query: 236 CSSLSSTDLLDLINTRFKKPKV--LVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLG 293
+S +L+ L+ +V+D+R ++Y I GSIN+P T
Sbjct: 1 LKYISPEELVALLENSDSNAGKDFVVVDLRR-DDYEGGHIKGSINLPAQ---SCYQT--- 53
Query: 294 SMESSPEMNILFNNKGSIIVIVGGEDSMRQAKFARFI 330
+ + + + G R + AR+
Sbjct: 54 -LPQVYAL--FSLAGVKLAIFYCGSSQGRGPRAARWF 87
>gnl|CDD|238785 cd01527, RHOD_YgaP, Member of the Rhodanese Homology Domain
superfamily. This CD includes Escherichia coli YgaP, and
similar uncharacterized putative rhodanese-related
sulfurtransferases.
Length = 99
Score = 32.8 bits (75), Expect = 0.058
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 259 VIDIRDNEEYVAESIIGSINIPLARIPDLESTDLG 293
++DIR+ +EY+ E I G+ +PL++ LES L
Sbjct: 19 LVDIREPDEYLRERIPGARLVPLSQ---LESEGLP 50
>gnl|CDD|238784 cd01526, RHOD_ThiF, Member of the Rhodanese Homology Domain
superfamily. This CD includes several putative
molybdopterin synthase sulfurylases including the
molybdenum cofactor biosynthetic protein (CnxF) of
Aspergillus nidulans and the molybdenum cofactor
synthesis protein 3 (MOCS3) of Homo sapiens. These
rhodanese-like domains are found C-terminal of the ThiF
and MoeZ_MoeB domains.
Length = 122
Score = 33.1 bits (76), Expect = 0.063
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 13/94 (13%)
Query: 246 DLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMNILF 305
D N K +++D+R + + +INIPL+ + + E +
Sbjct: 14 DYKNILQAGKKHVLLDVRPKVHFEICRLPEAINIPLSELLSKAAELKSLQELPLD----- 68
Query: 306 NNKGSIIVIV--GGEDSMRQAK------FARFIV 331
N+K S I +V G DS + RF+
Sbjct: 69 NDKDSPIYVVCRRGNDSQTAVRKLKELGLERFVR 102
>gnl|CDD|238779 cd01521, RHOD_PspE2, Member of the Rhodanese Homology Domain
superfamily. This CD includes the putative
rhodanese-like protein, Psp2, of Yersinia pestis biovar
Medievalis and other similar uncharacterized proteins.
Length = 110
Score = 32.7 bits (75), Expect = 0.079
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 242 TDLLDL-INTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIP 285
TD D+ I + KP +++D+R E Y + G+IN+P I
Sbjct: 10 TDCWDVAIALKNGKPDFVLVDVRSAEAYARGHVPGAINLPHREIC 54
>gnl|CDD|236337 PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 376
Score = 34.2 bits (79), Expect = 0.10
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 14/85 (16%)
Query: 257 VLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMNILFNNKGSIIVIVG 316
++ID+R+ E + G++ IP LE L P+ + I++I
Sbjct: 18 AVLIDVREAHERASGQAEGALRIPRG---FLE---LRIETHLPDRD------REIVLICA 65
Query: 317 GEDSMRQAKFARFIVRLGFPKVTYV 341
R A A + LG+ +V V
Sbjct: 66 S--GTRSAHAAATLRELGYTRVASV 88
>gnl|CDD|132026 TIGR02981, phageshock_pspE, phage shock operon rhodanese PspE.
Members of this very narrowly defined protein family are
proteins active as rhodanese (EC 2.8.1.1) and found in
the extended variants of the phage shock protein (psp
operon) in Escherichia coli and a few closely related
species. Note that the designation phage shock protein
PspE has been applied, incorrectly, in many instances
where the genome lacks the phage shock regulon entirely.
Length = 101
Score = 31.9 bits (72), Expect = 0.11
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 260 IDIRDNEEYVAESIIGSINIPLARI 284
ID+R E+Y E I G+INIPL I
Sbjct: 22 IDVRIPEQYQQEHIQGAINIPLKEI 46
>gnl|CDD|182356 PRK10287, PRK10287, thiosulfate:cyanide sulfurtransferase;
Provisional.
Length = 104
Score = 32.1 bits (73), Expect = 0.12
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 260 IDIRDNEEYVAESIIGSINIPLARI 284
ID+R E+Y E + G+INIPL +
Sbjct: 24 IDVRVPEQYQQEHVQGAINIPLKEV 48
>gnl|CDD|224697 COG1783, XtmB, Phage terminase large subunit [General function
prediction only].
Length = 414
Score = 33.2 bits (76), Expect = 0.18
Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 4/98 (4%)
Query: 225 LQRHNQALSEFCSSLSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARI 284
Q++ A SS S L I +P + V+ IR+ E +S +
Sbjct: 23 NQKYFIAKGGRGSSKSYATALKNIEKLLSEPGIDVLVIREVENTHKQSTYALF-KEA--L 79
Query: 285 PDLESTDLGSMESSPEMNILFNNKGSIIVIVGGEDSMR 322
+L T + S IL + G I+ G +D +
Sbjct: 80 SELGVTKFFKISKSSPEIILKDT-GQRIIFKGLDDPAK 116
>gnl|CDD|238787 cd01529, 4RHOD_Repeats, Member of the Rhodanese Homology Domain
superfamily. This CD includes putative rhodanese-related
sulfurtransferases which contain 4 copies of the
Rhodanese Homology Domain. Only the second and most of
the fourth repeats contain the putative catalytic Cys
residue. This CD aligns the 1st , 2nd, 3rd, and 4th
repeats.
Length = 96
Score = 30.7 bits (69), Expect = 0.33
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 259 VIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESS-PEMNILFNNKGSIIVIVG 316
++D+R +EY A + G +IP A + L S +L ++E+ + GS++
Sbjct: 15 LLDVRAEDEYAAGHLPGKRSIPGAALV-LRSQELQALEAPGRATRYVLTCDGSLLARFA 72
>gnl|CDD|153325 cd07641, BAR_ASAP1, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with SH3 domain, ANK repeat and PH domain containing
protein 1. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. ASAP1 (ArfGAP with SH3
domain, ANK repeat and PH domain containing protein 1)
is also known as DDEF1 (Development and Differentiation
Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2.
ASAP1 is an Arf GTPase activating protein (GAP) with
activity towards Arf1 and Arf5 but not Arf6 However, it
has been shown to bind GTP-Arf6 stably without GAP
activity. It has been implicated in cell growth,
migration, and survival, as well as in tumor invasion
and malignancy. It binds paxillin and cortactin, two
components of invadopodia which are essential for tumor
invasiveness. It also binds focal adhesion kinase (FAK)
and the SH2/SH3 adaptor CrkL. ASAP1 contains an
N-terminal BAR domain, followed by a Pleckstrin homology
(PH) domain, an Arf GAP domain, ankyrin (ANK) repeats,
and a C-terminal SH3 domain. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions. The BAR domain of ASAP1 mediates membrane
bending, is essential for function, and autoinhibits GAP
activity by interacting with the PH and/or Arf GAP
domains.
Length = 215
Score = 31.2 bits (70), Expect = 0.56
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 20 KTGHTKLKRVLKAWVTS---HPQFDFVYWQGLDSLCAPFVFLNFNDEATAYACFSTFIPK 76
+T K+K+ +KA S H Q + Y Q LD + F+ + D TA+ FST
Sbjct: 15 RTALQKVKKSVKAIYNSGQDHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKFSTLT-- 72
Query: 77 YLHNFFLRDNSAVVREYLSKFSHLIAF 103
++ S +++ L SH + F
Sbjct: 73 -------KELSTLLKNLLQGLSHNVIF 92
>gnl|CDD|184680 PRK14434, PRK14434, acylphosphatase; Provisional.
Length = 92
Score = 29.3 bits (66), Expect = 0.73
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 8/51 (15%)
Query: 306 NNKGSIIVIVGGEDSMRQAKFARFI--VRLG---FPKVTYVHEHVNSFECY 351
N+ G++ ++ +DS AK A+FI +R G + KVTYV + +FE +
Sbjct: 38 NDDGTVEILAQSDDS---AKLAKFIQEIRKGPSKWAKVTYVDVTMANFEDF 85
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 30.2 bits (69), Expect = 0.84
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 18/69 (26%)
Query: 254 KPKVLVIDIRDNEEYVAE------SIIGSINIPLARIPDLESTD-LGSMESSPEMNILFN 306
+ + DI N EY+AE +IG++ IP AR P L + + + +M
Sbjct: 63 FAEFVETDIFSNCEYLAEAIAEADLVIGTVLIPGARAPKLVTREMVKTM----------- 111
Query: 307 NKGSIIVIV 315
GS+IV V
Sbjct: 112 KPGSVIVDV 120
>gnl|CDD|180967 PRK07411, PRK07411, hypothetical protein; Validated.
Length = 390
Score = 31.2 bits (71), Expect = 0.91
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 239 LSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLES 289
++ T+L L+++ ++ID+R+ EY I GS+ +PL PD+E+
Sbjct: 284 MTVTELKALLDS--GADDFVLIDVRNPNEYEIARIPGSVLVPL---PDIEN 329
>gnl|CDD|238723 cd01446, DSP_MapKP, N-terminal regulatory rhodanese domain of dual
specificity phosphatases (DSP), such as Mapk
Phosphatase. This domain is believed to determine
substrate specificity by binding the substrate, such as
ERK2, and activating the C-terminal catalytic domain by
inducing a conformational change. This domain has
homology to the Rhodanese Homology Domain.
Length = 132
Score = 29.6 bits (67), Expect = 1.0
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 238 SLSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARI 284
++ L L+ ++L++D R EY + I G++N+ I
Sbjct: 1 TIDCAWLAALLREG--GERLLLLDCRPFLEYSSSHIRGAVNVCCPTI 45
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 29.9 bits (68), Expect = 1.8
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 258 LVIDIRDNEEYVAESIIGSINIPL 281
+ID+R E+ + G+IN+PL
Sbjct: 4 PLIDVRSPAEFAEGHLPGAINLPL 27
>gnl|CDD|119001 pfam10481, Cenp-F_N, Cenp-F N-terminal domain. Mitosin or
centromere-associated protein-F (Cenp-F) is found bound
across the centromere as one of the proteins of the
outer layer of the kinetochore. Most of the
kinetochore/centromere functions appear to depend upon
binding of the C-terminal par to f the molecule, whereas
the N-terminal part, here, may be a cytoplasmic player
in controlling the function of microtubules and dynein.
Length = 288
Score = 30.2 bits (67), Expect = 1.8
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 214 ESESTLLEGALLQRHNQALSEFCSSLSST 242
E+E T EGA L+R NQ L E C L T
Sbjct: 56 ENEKT--EGANLKRENQRLMEICEHLEKT 82
>gnl|CDD|143475 cd06567, Peptidase_S41, C-terminal processing peptidase family S41.
Peptidase family S41 (C-terminal processing peptidase
or CTPase family) contains very different subfamilies;
it includes photosystem II D1 C-terminal processing
protease (CTPase), interphotoreceptor retinoid-binding
protein IRBP and tricorn protease (TRI). CTPase and TRI
both contain the PDZ domain while IRBP, although being
very similar to the tail-specific protease domain, lacks
the PDZ insertion domain and hydrolytic activity. These
serine proteases have distinctly different active sites:
in CTPase, the active site consists of a serine/lysine
catalytic dyad while in tricorn core protease, it is a
tetrad (serine, histidine, serine, glutamate). CPases
with different substrate specificities in different
species include processing of D1 protein of the
photosystem II reaction center in higher plants and
cleavage of a peptide of 11 residues from the precursor
form of penicillin-binding protein; and others such as
tricorn protease (TRI) act as a carboxypeptidase,
involved in the degradation of proteasomal products.
CTPase homolog IRBP, secreted by photoreceptors into the
interphotoreceptor matrix, having arisen in the early
evolution of the vertebrate eye, promotes the release of
all-trans retinol from photoreceptors and facilitates
its delivery to the retinal pigment epithelium.
Length = 224
Score = 29.2 bits (66), Expect = 2.5
Identities = 18/97 (18%), Positives = 34/97 (35%), Gaps = 25/97 (25%)
Query: 232 LSEFCSSLSSTDLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTD 291
+ F + ++ +L + + K K L++D+R+N G
Sbjct: 66 IPSFSAESTAEELREALAELKKGVKGLILDLRNN--------PG---------------- 101
Query: 292 LGSMESSPEMNILFNNKGSIIVIVGGEDSMRQAKFAR 328
G + ++ E+ LF KG I+V A
Sbjct: 102 -GLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAP 137
>gnl|CDD|225450 COG2897, SseA, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 285
Score = 28.8 bits (65), Expect = 4.2
Identities = 17/100 (17%), Positives = 31/100 (31%), Gaps = 4/100 (4%)
Query: 243 DLLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSMESSPEMN 302
+ LD ++++ D D EEY+ I G++ + S +
Sbjct: 20 ENLDDPAVVIVDARIILPDPDDAEEYLEGHIPGAVFFDWEADLSDPVPLPHMLPSPEQFA 79
Query: 303 ILFNNKG----SIIVIVGGEDSMRQAKFARFIVRLGFPKV 338
L G +V+ A+ + LG V
Sbjct: 80 KLLGELGIRNDDTVVVYDDGGGFFAARAWWLLRYLGHENV 119
>gnl|CDD|188475 TIGR03960, rSAM_fuse_unch, radical SAM family uncharacterized
protein. This model describes a radical SAM protein, or
protein region, regularly found paired with or fused to
a region described by TIGR03936. PSI-BLAST analysis of
TIGR03936 suggests a relationship to the tRNA
pseudouridine synthase TruA, suggesting that this system
may act in RNA modification [Unknown function, Enzymes
of unknown specificity].
Length = 605
Score = 28.8 bits (65), Expect = 5.5
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 202 CVTPRSITFRMHESESTLLEGAL 224
+ RSI + H+S++++LEG L
Sbjct: 478 KIKSRSIKYNWHDSDTSVLEGVL 500
>gnl|CDD|176744 cd08332, CARD_CASP2, Caspase activation and recruitment domain of
Caspase-2. Caspase activation and recruitment domain
(CARD) similar to that found in caspase-2. Caspases are
aspartate-specific cysteine proteases with functions in
apoptosis and immune signaling. Caspase-2 (also known as
ICH1, NEDD2, or CASP2) is one of the most evolutionarily
conserved caspases, and plays a role in apoptosis, DNA
damage response, cell cycle regulation, and tumor
suppression. It is localized in the nucleus and exhibits
properties of both an initiator and an effector caspase.
In general, CARDs are death domains (DDs) found
associated with caspases. They are known to be important
in the signaling pathways for apoptosis, inflammation,
and host-defense mechanisms. DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including PYRIN and DED (Death Effector Domain). They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 90
Score = 27.0 bits (60), Expect = 5.6
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 12/69 (17%)
Query: 192 QSVTDSIDIYCVTPRSITFRMHE---------SESTLLEGALLQRHNQALSEFCSSLSST 242
+ V D + I+ + +T M E S++ L L +R +A S FC +L T
Sbjct: 19 ELVLDELLIHLLQKDILTDSMAESIMAKPTSFSQNVALLNLLPKRGPRAFSAFCEALRET 78
Query: 243 D---LLDLI 248
L DL+
Sbjct: 79 SQEHLCDLL 87
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 28.7 bits (65), Expect = 6.0
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 21/77 (27%)
Query: 251 RFKKPKVLVIDIRDNEEYVAESII---GS-------INIPLARIPDLESTDLGSMESSPE 300
RF P + + D E A++II GS I ARI L+S+D + P+
Sbjct: 117 RFVDPHTVEVTGEDKETITADNIIIATGSRPRIPPGPGIDGARI--LDSSDALFLLELPK 174
Query: 301 MNILFNNKGSIIVIVGG 317
S++++ GG
Sbjct: 175 ---------SLVIVGGG 182
>gnl|CDD|109986 pfam00951, Arteri_Gl, Arterivirus GL envelope glycoprotein.
Arteriviruses encode 4 envelope proteins, Gl, Gs, M and
N. Gl envelope protein, is encoded in ORF5, and is 30-
45 kDa in size. Gl is heterogenously glycosylated with
N-acetyllactosamine in a cell-type-specific manner. The
Gl glycoprotein expresses the neutralisation
determinants.
Length = 179
Score = 27.8 bits (62), Expect = 6.7
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 5/69 (7%)
Query: 95 SKFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPLHKIFHLWDKLLLGDASF 154
+ S + ++ ++ F W + F L +F L LL A F
Sbjct: 8 NGNSSTYQYIYNLTICELNGTGWLGTHFD--WAVETFPLFPYLTHLFSLG---LLTTAHF 62
Query: 155 PLFIGVSIL 163
F+ +S L
Sbjct: 63 LDFLNLSAL 71
>gnl|CDD|184994 PRK15034, PRK15034, nitrate/nitrite transport protein NarU;
Provisional.
Length = 462
Score = 28.3 bits (63), Expect = 7.0
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 135 LPLHKIFHLWDKLLLGDASFPLFIGVSILKQLRETLLSSGFNECILLFSDLPEVDIEQ 192
LP+ + HLW LL A+F FIG S+GF +L + P+V+I +
Sbjct: 246 LPVLQRLHLWLLSLLYLATFGSFIG-----------FSAGF--AMLAKTQFPDVNILR 290
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 28.3 bits (64), Expect = 7.0
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 256 KVLVIDIRDNEEYVAESIIGSINIPL 281
+ID+R E+ I G+IN+PL
Sbjct: 15 DTPLIDVRSPIEFAEGHIPGAINLPL 40
>gnl|CDD|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 28.3 bits (64), Expect = 7.6
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 24/76 (31%)
Query: 223 ALLQRHNQALSE------FCSSLSSTDLLDLINTRFKKPKV------------------L 258
A + L E F S ++D++D + K+ V
Sbjct: 83 AFFEELGVPLKEEDHGRLFPVSDKASDIVDALLNELKELGVKIRTRTRVLSVEKDDDGRF 142
Query: 259 VIDIRDNEEYVAESII 274
+D EE A+S++
Sbjct: 143 RVDTDGGEELEADSLV 158
>gnl|CDD|176020 cd08374, C2F_Ferlin, C2 domain sixth repeat in Ferlin. Ferlins are
involved in vesicle fusion events. Ferlins and other
proteins, such as Synaptotagmins, are implicated in
facilitating the fusion process when cell membranes fuse
together. There are six known human Ferlins: Dysferlin
(Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3),
Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can
lead to a wide range of diseases including muscular
dystrophy (dysferlin), deafness (otoferlin), and
infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the sixth C2
repeat, C2E, and has a type-II topology.
Length = 133
Score = 27.2 bits (61), Expect = 8.1
Identities = 11/42 (26%), Positives = 23/42 (54%)
Query: 244 LLDLINTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIP 285
L T +K P L + + DN+++ + +GS+ + L+ +P
Sbjct: 81 FWSLDETEYKIPPKLTLQVWDNDKFSPDDFLGSLELDLSILP 122
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
0.325 0.140 0.428
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,577,684
Number of extensions: 1826243
Number of successful extensions: 2212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2197
Number of HSP's successfully gapped: 52
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
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: 60 (27.0 bits)