RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12456
(162 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 = 89.3 bits (222), Expect = 4e-22
Identities = 39/152 (25%), Positives = 71/152 (46%), Gaps = 3/152 (1%)
Query: 12 TTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAADE 71
+ PDG + D +++WDL+ K V G + +++FS +G L +++ +
Sbjct: 139 NSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSD 198
Query: 72 NCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTD--VRVFLCKQWQELAMF 129
+KLWDL K TL+ N + + F G +A D +RV+ + + +
Sbjct: 199 GTIKLWDLSTGKCLGTLRGHENG-VNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTL 257
Query: 130 NEHTAMVTGVRFGTHAHYLASSSMDRTLKLYS 161
+ HT VT + + LAS S D T++++
Sbjct: 258 SGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 87.8 bits (218), Expect = 1e-21
Identities = 43/156 (27%), Positives = 75/156 (48%), Gaps = 9/156 (5%)
Query: 12 TTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAADE 71
T PDG + G+ D +++WDL+ + + + GP++ ++ S +G YLA+ + +
Sbjct: 13 TCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSD 72
Query: 72 NCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTDVRVFLCKQW-----QEL 126
++LWDL + +TL +Y + + F G ++ + D K W + L
Sbjct: 73 KTIRLWDLETGECVRTLTGHTSY-VSSVAFSPDGRILSSSSRDKT---IKVWDVETGKCL 128
Query: 127 AMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
HT V V F ++ASSS D T+KL+ L
Sbjct: 129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164
Score = 87.0 bits (216), Expect = 2e-21
Identities = 38/149 (25%), Positives = 73/149 (48%), Gaps = 3/149 (2%)
Query: 16 LHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAADENCVK 75
PDG I + D +++WD++ K +T + + +++FS +G ++A+++ + +K
Sbjct: 101 FSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160
Query: 76 LWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTD--VRVFLCKQWQELAMFNEHT 133
LWDLR K TL E+ + F G + + +D ++++ + L H
Sbjct: 161 LWDLRTGKCVATLT-GHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219
Query: 134 AMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
V V F + LAS S D T++++ L
Sbjct: 220 NGVNSVAFSPDGYLLASGSEDGTIRVWDL 248
Score = 78.5 bits (194), Expect = 4e-18
Identities = 40/156 (25%), Positives = 75/156 (48%), Gaps = 7/156 (4%)
Query: 11 LTTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAAD 70
+ DG G+SD +++WDL+ + V + +++FS +G L++++
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSR 113
Query: 71 ENCVKLWDLRKLKNFKTLQ--LDPNYEIRDLCFDQSGTYMAVAGTD--VRVFLCKQWQEL 126
+ +K+WD+ K TL+ D + + F GT++A + D ++++ + + +
Sbjct: 114 DKTIKVWDVETGKCLTTLRGHTDW---VNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCV 170
Query: 127 AMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
A HT V V F L SSS D T+KL+ L
Sbjct: 171 ATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDL 206
Score = 63.9 bits (156), Expect = 7e-13
Identities = 33/114 (28%), Positives = 62/114 (54%), Gaps = 3/114 (2%)
Query: 51 GPIQALSFSENGYYLATAADENCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAV 110
G + ++FS +G LAT + + +K+WDL + +TL+ +RD+ GTY+A
Sbjct: 10 GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKG-HTGPVRDVAASADGTYLAS 68
Query: 111 AGTD--VRVFLCKQWQELAMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
+D +R++ + + + HT+ V+ V F L+SSS D+T+K++ +
Sbjct: 69 GSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
Score = 33.8 bits (78), Expect = 0.021
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 125 ELAMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
HT VT V F LA+ S D T+K++ L
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDL 38
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 74.4 bits (181), Expect = 4e-16
Identities = 39/151 (25%), Positives = 74/151 (49%), Gaps = 6/151 (3%)
Query: 17 HPDG-LIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENG-YYLATAADENCV 74
PDG L+ + D +++WDL+ K ++ P+ +L+FS +G +A+ + + +
Sbjct: 164 SPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTI 223
Query: 75 KLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTD--VRVFLCKQW-QELAMFNE 131
+LWDL K ++ L + + F G+ +A +D +R++ + L +
Sbjct: 224 RLWDLSTGKLLRST-LSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSG 282
Query: 132 HTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
H++ V V F LAS S D T++L+ L
Sbjct: 283 HSSSVLSVAFSPDGKLLASGSSDGTVRLWDL 313
Score = 67.4 bits (163), Expect = 1e-13
Identities = 38/152 (25%), Positives = 62/152 (40%), Gaps = 6/152 (3%)
Query: 17 HPDG-LIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAADENCVK 75
PDG L+ G+SD +++WDL K + SFS +G LA+ + + ++
Sbjct: 207 SPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIR 266
Query: 76 LWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTDVRVFLC----KQWQELAMFNE 131
LWDLR + + + + F G +A +D V L +
Sbjct: 267 LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKG 326
Query: 132 HTAMVTGVRFGTHAHYLASS-SMDRTLKLYSL 162
H V+ + F L S S D T++L+ L
Sbjct: 327 HEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDL 358
Score = 65.1 bits (157), Expect = 6e-13
Identities = 39/152 (25%), Positives = 74/152 (48%), Gaps = 6/152 (3%)
Query: 16 LHPDGLIFGIGTSDSQVQIWDLKKQKN-VTDFQLDAGPIQALSFSENGYYLATAADENCV 74
PDG + G+SD +++WDL+ + + + + +++FS +G LA+ + + V
Sbjct: 249 FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTV 308
Query: 75 KLWDLRKLKNFKTLQLDPNY-EIRDLCFDQSGTYMAVAGTD---VRVFLCKQWQELAMFN 130
+LWDL K +L L + + L F G+ + G+D +R++ + + L
Sbjct: 309 RLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLE 368
Query: 131 EHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
H+ V V F ++S S D T++L+ L
Sbjct: 369 GHSN-VLSVSFSPDGRVVSSGSTDGTVRLWDL 399
Score = 64.3 bits (155), Expect = 1e-12
Identities = 50/157 (31%), Positives = 80/157 (50%), Gaps = 7/157 (4%)
Query: 11 LTTAQLHPDGLIFGIGTSDSQVQIWDLKKQK--NVTDFQLDAGPIQALSFSENGYYLATA 68
+ + PDG + G+SD V++WDL+ K + + GP+ +LSFS +G L +
Sbjct: 287 VLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSG 346
Query: 69 -ADENCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTD--VRVFLCKQWQE 125
+D+ ++LWDLR K KTL+ N + + F G ++ TD VR++
Sbjct: 347 GSDDGTIRLWDLRTGKPLKTLEGHSN--VLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSL 404
Query: 126 LAMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYSL 162
L + HT+ VT + F LAS S D T++L+ L
Sbjct: 405 LRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL 441
Score = 58.6 bits (140), Expect = 1e-10
Identities = 37/162 (22%), Positives = 69/162 (42%), Gaps = 9/162 (5%)
Query: 10 TLTTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDF--QLDAGPIQALSF-SENGYYLA 66
++T+ PDG + G+SD +++WDL + + L + L+ S +G +
Sbjct: 67 SITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSIL 126
Query: 67 TAADE--NCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTD---VRVFLCK 121
A+ VKLWDL + + L F G +A + ++++ +
Sbjct: 127 LASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLR 186
Query: 122 QWQELAMFNEHTAMVTGVRF-GTHAHYLASSSMDRTLKLYSL 162
+ L+ HT V+ + F +AS S D T++L+ L
Sbjct: 187 TGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDL 228
Score = 54.7 bits (130), Expect = 2e-09
Identities = 22/85 (25%), Positives = 41/85 (48%)
Query: 7 GGPTLTTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLA 66
G + + PDG + G++D V++WDL + + + +L FS +G LA
Sbjct: 369 GHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLA 428
Query: 67 TAADENCVKLWDLRKLKNFKTLQLD 91
+ + +N ++LWDL+ + D
Sbjct: 429 SGSSDNTIRLWDLKTSLKSVSFSPD 453
Score = 52.0 bits (123), Expect = 2e-08
Identities = 39/161 (24%), Positives = 72/161 (44%), Gaps = 12/161 (7%)
Query: 10 TLTTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSENGYYLATAA 69
+L + G++ SDS V + DL + + I +++FS +G L + +
Sbjct: 29 SLLSLGSSESGILLLALLSDSLVSLPDL----SSLLLRGHEDSITSIAFSPDGELLLSGS 84
Query: 70 DENCVKLWDLRKLKN-FKTLQLDPNYEIRDLCF-DQSGTYMAVAGTD----VRVF-LCKQ 122
+ +KLWDL + K+L+ + + L G + +A + V+++ L
Sbjct: 85 SDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTP 144
Query: 123 WQELAMFNEHTAMVTGVRFGTHAHYLAS-SSMDRTLKLYSL 162
+ + H+ VT + F LAS SS+D T+KL+ L
Sbjct: 145 GKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDL 185
Score = 27.0 bits (58), Expect = 5.7
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 11 LTTAQLHPDGLIFGIGTSDSQVQIWDLKKQKNVTDFQLDAGPIQALSFSEN 61
+T+ PDG G+SD+ +++WDLK F D + + S +
Sbjct: 415 VTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGKVLASKSSDLS 465
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 44.3 bits (104), Expect = 9e-06
Identities = 40/142 (28%), Positives = 68/142 (47%), Gaps = 14/142 (9%)
Query: 29 DSQVQIWDLKKQKNVTDFQLDAGPIQALSFSE-NGYYLATAADENCVKLWDLRKLKNFKT 87
+ VQ+WD+ + + VT+ + + ++ +S + LA+ +D+ VKLW + + + T
Sbjct: 554 EGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGT 613
Query: 88 LQLDPNYEIRDLCFDQ----SGTYMAVAGTDVRVF---LCKQWQELAMFNEHTAMVTGVR 140
++ N +C Q SG +A D +V+ L L H+ V+ VR
Sbjct: 614 IKTKAN-----ICCVQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVR 668
Query: 141 FGTHAHYLASSSMDRTLKLYSL 162
F + L SSS D TLKL+ L
Sbjct: 669 F-VDSSTLVSSSTDNTLKLWDL 689
>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 = 40.0 bits (94), Expect = 1e-05
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 122 QWQELAMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYS 161
+ L HT VT V F YLAS S D T+KL+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 36.5 bits (85), Expect = 3e-04
Identities = 13/40 (32%), Positives = 25/40 (62%)
Query: 39 KQKNVTDFQLDAGPIQALSFSENGYYLATAADENCVKLWD 78
+ + + GP+ +++FS +G YLA+ +D+ +KLWD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 26.9 bits (60), Expect = 0.78
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 12 TTAQLHPDGLIFGIGTSDSQVQIWD 36
T+ PDG G+ D +++WD
Sbjct: 16 TSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 25.0 bits (55), Expect = 4.1
Identities = 5/26 (19%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 95 EIRDLCFDQSGTYMAVAGTD--VRVF 118
+ + F G Y+A D ++++
Sbjct: 14 PVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 38.5 bits (90), Expect = 5e-05
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 123 WQELAMFNEHTAMVTGVRFGTHAHYLASSSMDRTLKLYS 161
+ L HT VT V F + LAS S D T++++
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 37.3 bits (87), Expect = 1e-04
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 41 KNVTDFQLDAGPIQALSFSENGYYLATAADENCVKLWD 78
K + + GP+ +++FS +G LA+ +D+ V++WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 26.9 bits (60), Expect = 0.92
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 12 TTAQLHPDGLIFGIGTSDSQVQIWD 36
T+ PDG + G+ D V++WD
Sbjct: 15 TSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 25.4 bits (56), Expect = 3.1
Identities = 7/26 (26%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 95 EIRDLCFDQSGTYMAVAGTD--VRVF 118
+ + F G +A D VRV+
Sbjct: 13 PVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 35.8 bits (82), Expect = 0.005
Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 19/98 (19%)
Query: 11 LTTAQLHP-DGLIFGIGTSDSQVQIWDLKK----------------QKNVTDFQLDAGPI 53
+T+A+ HP +F +S ++++ DL++ +V F+ I
Sbjct: 224 ITSAEFHPEMCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGVDVDFFEEIVSSI 283
Query: 54 QALSFSENGYYLATAADENCVKLWDLRKLKN-FKTLQL 90
FS+NG Y+ + D VK+WD+ KN KT+ +
Sbjct: 284 SDFKFSDNGRYIL-SRDYLTVKIWDVNMAKNPIKTIPM 320
>gnl|CDD|216475 pfam01394, Clathrin_propel, Clathrin propeller repeat. Clathrin
is the scaffold protein of the basket-like coat that
surrounds coated vesicles. The soluble assembly unit, a
triskelion, contains three heavy chains and three light
chains in an extended three-legged structure. Each leg
contains one heavy and one light chain. The N-terminus
of the heavy chain is known as the globular domain, and
is composed of seven repeats which form a beta
propeller.
Length = 37
Score = 26.4 bits (59), Expect = 1.1
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 12 TTAQLHPDGLIFGI-GTSDSQVQIWDL 37
TA + I I T+ VQI D+
Sbjct: 10 PTATMESWKGIIAINLTTKGSVQIVDV 36
>gnl|CDD|178701 PLN03156, PLN03156, GDSL esterase/lipase; Provisional.
Length = 351
Score = 27.8 bits (62), Expect = 2.7
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 90 LDPNYEIRDL----CFDQSGTYMAVAGTDVRVFLCKQWQELAMFNEH 132
LDP+Y I D CF +GT A +DV + + W+EL + E+
Sbjct: 94 LDPSYNISDFATGVCFASAGTGYDNATSDV-LSVIPLWKELEYYKEY 139
>gnl|CDD|132929 cd07018, S49_SppA_67K_type, Signal peptide peptidase A (SppA) 67K
type, a serine protease, has catalytic Ser-Lys dyad.
Signal peptide peptidase A (SppA; Peptidase S49;
Protease IV) 67K type: SppA is found in all three
domains of life and is involved in the cleavage of
signal peptides after their removal from the precursor
proteins by signal peptidases. Members in this subfamily
contain an amino-terminal domain in addition to the
carboxyl-terminal protease domain that is conserved in
all the S49 family members (sometimes referred to as 67K
type), similar to E. coli and Arabidopsis thaliana SppA
peptidases. Unlike the eukaryotic functional homologs
that are proposed to be aspartic proteases,
site-directed mutagenesis and sequence analysis have
shown that members in this subfamily, mostly bacterial,
are serine proteases. The predicted active site serine
for members in this family occurs in a transmembrane
domain. Mutagenesis studies also suggest that the
catalytic center comprises a Ser-Lys dyad (both residues
absolutely conserved within bacteria, chloroplast and
mitochondrial signal peptidase family members) and not
the usual Ser-His-Asp catalytic triad found in the
majority of serine proteases. Interestingly, the single
membrane spanning E. coli SppA carries out catalysis
using a Ser-Lys dyad with the serine located in the
conserved carboxy-terminal protease domain and the
lysine in the non-conserved amino-terminal domain.
Length = 222
Score = 27.5 bits (62), Expect = 3.0
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 55 ALSFSENGYYLATAADE 71
A +S+ YYLA+AADE
Sbjct: 85 ADGYSQGQYYLASAADE 101
>gnl|CDD|238035 cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins
as well as proteins which contain inteins and undergo
protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In
protein splicing an intervening polypeptide sequence -
the intein - is excised from a protein, and the
flanking polypeptide sequences - the exteins - are
joined by a peptide bond. In addition to the
autocatalytic splicing domain, many inteins contain an
inserted endonuclease domain, which plays a role in
spreading inteins. Hedgehog proteins are a major class
of intercellular signaling molecules, which control
inductive interactions during animal development. The
mature signaling forms of hedgehog proteins are the
N-terminal fragments, which are covalently linked to
cholesterol at their C-termini. This modification is
the result of an autoprocessing step catalyzed by the
C-terminal fragments, which are aligned here.
Length = 136
Score = 26.8 bits (60), Expect = 3.2
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 65 LATAADENCVKLWDLRKLKNFKTLQLDPNYEIR 97
L D K+ +L + K K L LD ++
Sbjct: 7 LVLLEDGGRKKIEELVEKKGDKVLALDETGKLV 39
>gnl|CDD|233097 TIGR00705, SppA_67K, signal peptide peptidase SppA, 67K type. This
model represents the signal peptide peptidase A (SppA,
protease IV) as found in E. coli, Treponema pallidum,
Mycobacterium leprae, and several other species, in
which it has a molecular mass around 67 kDa and a
duplication such that the N-terminal half shares
extensive homology with the C-terminal half. This enzyme
was shown in E. coli to form homotetramers. E. coli
SohB, which is most closely homologous to the C-terminal
duplication of SppA, is predicted to perform a similar
function of small peptide degradation, but in the
periplasm. Many prokaryotes have a single SppA/SohB
homolog that may perform the function of either or both
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 584
Score = 27.1 bits (60), Expect = 5.5
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 40 QKNVTDFQLDAGPIQA--LSFSENGYYLATAADE 71
+++F+ P+ A ++S+ YYLA+ ADE
Sbjct: 116 GSALSEFKDSGKPVYAYGTNYSQGQYYLASFADE 149
>gnl|CDD|203589 pfam07152, YaeQ, YaeQ protein. This family consists of several
hypothetical bacterial proteins of around 180 residues
in length which are often known as YaeQ. YaeQ is
homologous to RfaH, a specialised transcription
elongation protein. YaeQ is known to compensate for loss
of RfaH function.
Length = 174
Score = 26.3 bits (59), Expect = 6.0
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 27 TSDSQVQIW------DLKKQKNVTDFQLDAGPIQALS 57
T +W L + KN++ QLD I AL+
Sbjct: 105 TYGRAADVWWQQNQGKLARLKNLSVVQLDDEFIAALA 141
>gnl|CDD|235426 PRK05352, PRK05352, Na(+)-translocating NADH-quinone reductase
subunit A; Provisional.
Length = 448
Score = 26.7 bits (60), Expect = 6.3
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 113 TDVRVFLCKQWQELAMFNEHTAMVTGVRF---------GTHAHYLASSSMDRT 156
TD +V +CK ++ E+ V F GTH H+L S +T
Sbjct: 186 TDGKVHVCKA-PGASLPGENLKNVEVHTFSGPHPAGLVGTHIHFLDPVSAGKT 237
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit E
binds subunits F and G to form a trimer which then
assembles onto snRNA along with the D1/D2 and D3/B
heterodimers forming a seven-membered ring structure.
Length = 79
Score = 25.2 bits (56), Expect = 6.7
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 16 LHPDGLIFGIGTSDSQVQIWDLKKQKNVT 44
+ P LIF + S+VQIW L +Q ++
Sbjct: 5 VQPINLIFRYLQNKSRVQIW-LYEQTDMR 32
>gnl|CDD|215577 PLN03103, PLN03103, GDP-L-galactose-hexose-1-phosphate
guanyltransferase; Provisional.
Length = 403
Score = 26.6 bits (59), Expect = 8.2
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 63 YYLATA---ADENCVKLWDLRKLKNFKTLQLDPNYEIRDLCFDQSGTYMAVAGTDVRVFL 119
YYLA V++ K +L +Y +R L F+ +A + +
Sbjct: 240 YYLANPFPVEKAPTVRIPHGTAKSGVKVSELV-DYPVRGLVFEGGSDLEDLANSVADACI 298
Query: 120 CKQ 122
C Q
Sbjct: 299 CLQ 301
>gnl|CDD|218801 pfam05896, NQRA, Na(+)-translocating NADH-quinone reductase subunit
A (NQRA). This family consists of several bacterial
Na(+)-translocating NADH-quinone reductase subunit A
(NQRA) proteins. The Na(+)-translocating NADH:
ubiquinone oxidoreductase (Na(+)-NQR) generates an
electrochemical Na(+) potential driven by aerobic
respiration.
Length = 257
Score = 25.9 bits (58), Expect = 9.0
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 10/53 (18%)
Query: 113 TDVRVFLCKQWQELAMFNEHTAMVTGVRF---------GTHAHYLASSSMDRT 156
TD +V +CK + V F GTH H++ + +T
Sbjct: 185 TDGKVHVCKAPGAALPLADLKG-VELHEFSGPHPAGLVGTHIHFIDPVNAGKT 236
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
0.320 0.134 0.406
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,063,857
Number of extensions: 698587
Number of successful extensions: 551
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 50
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (24.8 bits)