RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10953
(181 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 = 112 bits (283), Expect = 9e-31
Identities = 50/151 (33%), Positives = 73/151 (48%), Gaps = 9/151 (5%)
Query: 15 WNVVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALD 74
+V FSPD +V S SQ G I L+ + TGK S+A+S DG + S + D
Sbjct: 139 NSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSD 198
Query: 75 GIINIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTFK 126
G I ++D +T GH + V S AF+ DG S S D T+RVW+ E + T
Sbjct: 199 GTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLS 258
Query: 127 -HADQVWCVCVAPDGDKFVSVGEDKAVHMYS 156
H + V + +PDG + S D + ++
Sbjct: 259 GHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 107 bits (270), Expect = 6e-29
Identities = 48/164 (29%), Positives = 81/164 (49%), Gaps = 9/164 (5%)
Query: 14 MWNVVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGAL 73
+ +V S D Y+ SGS I L+ +ETG+ + + S+A+S DG ++S +
Sbjct: 54 VRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSR 113
Query: 74 DGIINIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTF 125
D I ++D T GH+ WV S AF+ DG F S+S D T+++W+ + + T
Sbjct: 114 DKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATL 173
Query: 126 K-HADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEVNGG 168
H +V V +PDG+K +S D + ++ + + G
Sbjct: 174 TGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRG 217
Score = 106 bits (266), Expect = 3e-28
Identities = 50/158 (31%), Positives = 84/158 (53%), Gaps = 9/158 (5%)
Query: 17 VVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGI 76
V FSPD + + S S+ I ++ VETGK + S+A+S DG ++AS + DG
Sbjct: 99 VAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGT 158
Query: 77 INIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTFK-H 127
I ++D T GH+ V S AF+ DG+ +S+S+D T+++W+ + + + T + H
Sbjct: 159 IKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGH 218
Query: 128 ADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEV 165
+ V V +PDG S ED + ++ + E V+
Sbjct: 219 ENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQT 256
Score = 101 bits (253), Expect = 2e-26
Identities = 51/158 (32%), Positives = 82/158 (51%), Gaps = 9/158 (5%)
Query: 17 VVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGI 76
V FSPD K + +GS G I ++ +ETG+L + +A S DG ++ASG+ D
Sbjct: 15 VAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKT 74
Query: 77 INIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTFK-H 127
I ++D T GH+S+V S AF+ DG+ S+S D T++VW+ + + T + H
Sbjct: 75 IRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGH 134
Query: 128 ADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEV 165
D V V +PDG S +D + ++ + + V
Sbjct: 135 TDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVAT 172
Score = 85.5 bits (212), Expect = 2e-20
Identities = 42/111 (37%), Positives = 63/111 (56%), Gaps = 8/111 (7%)
Query: 13 DMWNVVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGA 72
++ +V FSPD + +LS S G I L+ + TGK S+A+S DG+ +ASG+
Sbjct: 179 EVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGS 238
Query: 73 LDGIINIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWN 115
DG I ++D T GH++ V S A++ DGK S SAD T+R+W+
Sbjct: 239 EDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 78.5 bits (194), Expect = 7e-18
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 9/109 (8%)
Query: 57 LSIAYSTDGHWIASGALDGIINIFD--------ANTGHSSWVLSTAFTRDGKFFISASAD 108
+A+S DG +A+G+ DG I ++D GH+ V A + DG + S S+D
Sbjct: 13 TCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSD 72
Query: 109 HTVRVWNFARRENMHTFK-HADQVWCVCVAPDGDKFVSVGEDKAVHMYS 156
T+R+W+ E + T H V V +PDG S DK + ++
Sbjct: 73 KTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWD 121
Score = 68.1 bits (167), Expect = 4e-14
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 84 TGHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTFK-HADQVWCVCVAPDGDK 142
GH+ V AF+ DGK + S D T++VW+ E + T K H V V + DG
Sbjct: 6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTY 65
Query: 143 FVSVGEDKAVHMYSYKPEEEV 163
S DK + ++ + E V
Sbjct: 66 LASGSSDKTIRLWDLETGECV 86
Score = 36.9 bits (86), Expect = 0.003
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 121 NMHTFK-HADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEVNGG 168
T K H V CV +PDG + D + ++ + E + G
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKG 49
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 90.1 bits (222), Expect = 2e-21
Identities = 55/186 (29%), Positives = 82/186 (44%), Gaps = 14/186 (7%)
Query: 2 KQISKINVGPVDMWNVVFSPDDKYVLSGSQS-GKINLYGVETGKLEQIFDTRGKFTLSIA 60
K I + + ++ FSPD K + SGS G I L+ + TGK S+A
Sbjct: 146 KLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLA 205
Query: 61 YSTDGHW-IASGALDGIINIFDANTG---------HSSWVLSTAFTRDGKFFISASADHT 110
+S DG IASG+ DG I ++D +TG HS V+S +F+ DG S S+D T
Sbjct: 206 FSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVS-SFSPDGSLLASGSSDGT 264
Query: 111 VRVWNFA--RRENMHTFKHADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEVNGG 168
+R+W+ H+ V V +PDG S D V ++ + + +
Sbjct: 265 IRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTL 324
Query: 169 GGEEEE 174
G E
Sbjct: 325 KGHEGP 330
Score = 83.6 bits (205), Expect = 3e-19
Identities = 49/183 (26%), Positives = 74/183 (40%), Gaps = 12/183 (6%)
Query: 2 KQISKINVGPVDMWNVVFSPDDKYVLSGSQSGKINLYGVETG-KLEQIFDTRGKFTLSIA 60
K + G D FSPD + SGS G I L+ + + L + LS+A
Sbjct: 232 KLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVA 291
Query: 61 YSTDGHWIASGALDGIINIFDANT----------GHSSWVLSTAFTRDG-KFFISASADH 109
+S DG +ASG+ DG + ++D T GH V S +F+ DG S D
Sbjct: 292 FSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDG 351
Query: 110 TVRVWNFARRENMHTFKHADQVWCVCVAPDGDKFVSVGEDKAVHMYSYKPEEEVEVNGGG 169
T+R+W+ + + T + V V +PDG S D V ++ + G
Sbjct: 352 TIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGH 411
Query: 170 GEE 172
Sbjct: 412 TSR 414
Score = 58.6 bits (140), Expect = 2e-10
Identities = 39/110 (35%), Positives = 62/110 (56%), Gaps = 10/110 (9%)
Query: 15 WNVVFSPD-DKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGAL 73
++ FSPD V GS G I L+ + TGK + + LS+++S DG ++SG+
Sbjct: 332 SSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEG-HSNVLSVSFSPDGRVVSSGST 390
Query: 74 DGIINIFDANT--------GHSSWVLSTAFTRDGKFFISASADHTVRVWN 115
DG + ++D +T GH+S V S F+ DGK S S+D+T+R+W+
Sbjct: 391 DGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWD 440
Score = 44.3 bits (103), Expect = 1e-05
Identities = 24/119 (20%), Positives = 49/119 (41%), Gaps = 8/119 (6%)
Query: 54 KFTLSIAYSTDGHWIASGALDGIINIFDAN----TGHSSWVLSTAFTRDGKFFISASADH 109
LS+ S G + + D ++++ D + GH + S AF+ DG+ +S S+D
Sbjct: 28 LSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDG 87
Query: 110 TVRVWNFARRE---NMHTFKHADQVWCVCVA-PDGDKFVSVGEDKAVHMYSYKPEEEVE 164
T+++W+ E H V + ++ PDG+ + + + +
Sbjct: 88 TIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGK 146
Score = 30.4 bits (67), Expect = 0.45
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 15 WNVVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLS 58
++ FSPD K + SGS I L+ ++T F GK S
Sbjct: 416 TSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPDGKVLAS 459
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 45.4 bits (108), Expect = 1e-07
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 84 TGHSSWVLSTAFTRDGKFFISASADHTVRVWN 115
GH+ V S AF+ DG S S D TVRVW+
Sbjct: 8 KGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 34.6 bits (80), Expect = 0.001
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 119 RENMHTFK-HADQVWCVCVAPDGDKFVSVGEDKAVHMYS 156
+ + T K H V V +PDG+ S +D V ++
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 32.7 bits (75), Expect = 0.009
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 43 GKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGIINIFD 81
GKL + S+A+S DG+ +ASG+ DG + ++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 28.5 bits (64), Expect = 0.28
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 15 WNVVFSPDDKYVLSGSQSGKINLY 38
+V FSPD + SGS G + ++
Sbjct: 15 TSVAFSPDGNLLASGSDDGTVRVW 38
>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 = 44.6 bits (106), Expect = 3e-07
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 84 TGHSSWVLSTAFTRDGKFFISASADHTVRVWN 115
GH+ V S AF+ DGK+ S S D T+++W+
Sbjct: 9 KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 35.0 bits (81), Expect = 0.001
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 119 RENMHTFK-HADQVWCVCVAPDGDKFVSVGEDKAVHMYS 156
E + T K H V V +PDG S +D + ++
Sbjct: 2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 33.8 bits (78), Expect = 0.003
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 42 TGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGIINIFD 81
+G+L + S+A+S DG ++ASG+ DG I ++D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 28.4 bits (64), Expect = 0.26
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 15 WNVVFSPDDKYVLSGSQSGKINLY 38
+V FSPD KY+ SGS G I L+
Sbjct: 16 TSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 43.3 bits (102), Expect = 3e-05
Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 11/101 (10%)
Query: 20 SPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGI--- 76
SPD K V+ + ++ + ++ G + I + + + WIA +G
Sbjct: 410 SPDGKKVVVANDRFELWVIDIDNGNVRLIDKSEYGLITDFDWHPNSRWIAYAFPEGYYTQ 469
Query: 77 -INIFDANTGH-------SSWVLSTAFTRDGKFFISASADH 109
I ++D + G +++ S AF DG++ SA
Sbjct: 470 SIKLYDMDGGKIYDVTTPTAYDFSPAFDPDGRYLYFLSARS 510
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 33.5 bits (76), Expect = 0.052
Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 11/114 (9%)
Query: 14 MWNVVFSPDDKYVL-SGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGA 72
+W++ +S D +L SGS G + L+ + G T+ S G +A G+
Sbjct: 578 VWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGS 637
Query: 73 LDGIINIFDANT---------GHSSWVLSTAFTRDGKFFISASADHTVRVWNFA 117
D + +D GHS V F D +S+S D+T+++W+ +
Sbjct: 638 ADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDLS 690
Score = 29.3 bits (65), Expect = 1.3
Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 10/101 (9%)
Query: 68 IASGALDGIINIFDANTG--------HSSWVLSTAFTR-DGKFFISASADHTVRVWNFAR 118
+AS +G++ ++D H V S ++ D S S D +V++W+ +
Sbjct: 548 VASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQ 607
Query: 119 RENMHTFKHADQVWCVCVAPDGDKFVSVGE-DKAVHMYSYK 158
++ T K + CV + + ++ G D V+ Y +
Sbjct: 608 GVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYDLR 648
>gnl|CDD|202169 pfam02239, Cytochrom_D1, Cytochrome D1 heme domain. Cytochrome cd1
(nitrite reductase) catalyzes the conversion of nitrite
to nitric oxide in the nitrogen cycle. This family
represents the d1 heme binding domain of cytochrome cd1,
in which His/Tyr side chains ligate the d1 heme iron of
the active site in the oxidized state.
Length = 369
Score = 31.7 bits (72), Expect = 0.19
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 17 VVFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTR-GKFTLSIAYSTDGHWIASGA-LD 74
+FS D +YV + G + + LE + + R G S+A S +G ++ G
Sbjct: 42 RMFSSDGRYVYVIGRDGGLTKI--DLWNLEIVAEVRQGGNARSVAVSYEGRYVIVGNYWP 99
Query: 75 GIINIFDANT 84
G I D T
Sbjct: 100 GQYVIMDGRT 109
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 31.7 bits (72), Expect = 0.22
Identities = 26/114 (22%), Positives = 37/114 (32%), Gaps = 21/114 (18%)
Query: 54 KFTLSIAYSTDGHWIA-----SGALDGIINIFDAN-----TGHSSWVLSTAFT---RDGK 100
K T S + W S L + + SS ST + +G+
Sbjct: 173 KLTRSSGDTDGAVWKETLYGPSSWLRSLRGLLPFQRYGKDRLASSAAASTIVSSSEVNGQ 232
Query: 101 FFI-SASADHTVRVWNF---ARRENMHTFKH-ADQVWCVCVAPDGD---KFVSV 146
F+ + S D T+RVWN + CV +P KF SV
Sbjct: 233 TFLFTLSLDGTLRVWNLDTGQCAFLPSRADSGGSRYLCVTYSPFSSGEFKFFSV 286
>gnl|CDD|183181 PRK11534, PRK11534, DNA-binding transcriptional regulator CsiR;
Provisional.
Length = 224
Score = 30.6 bits (69), Expect = 0.36
Identities = 25/115 (21%), Positives = 44/115 (38%), Gaps = 7/115 (6%)
Query: 18 VFSPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGII 77
F PD+K +S S Y + G L + L + G+ +AS + ++
Sbjct: 24 NFQPDEKLRMSLLTS----RYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELL 79
Query: 78 NIFDANTGHSSWVLSTAFTRDGKFFISASADHTVRVWNFARRENMHTFKHADQVW 132
+IFDA + ++S A R G + AD + ++ E + W
Sbjct: 80 DIFDARANMEAMLVSLAIARGGDEW---EADVLAKAHLLSKLEACDASEKMLDEW 131
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 28.9 bits (65), Expect = 1.2
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 53 GKFTLSIAYSTDGHWIASGALDGIINIFDANTGHSSWVLSTA 94
G +S+A S DGH+ A+G ++G F +TG +S L+
Sbjct: 92 GYQEVSLAKSRDGHFEANGRVNGKKVDFLVDTGATSVALNEE 133
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to pfam05362, which is
the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 29.4 bits (66), Expect = 1.2
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 10/93 (10%)
Query: 21 PDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGIINIF 80
P Y ++ ++SGK+ LY E Q+ GK ++S G + A + I F
Sbjct: 495 PGVVYAVTQNESGKVGLYRFEV----QVSAGSGKHSVS------GLGSNTTAKESIRVAF 544
Query: 81 DANTGHSSWVLSTAFTRDGKFFISASADHTVRV 113
D G+ + ++A + + + H
Sbjct: 545 DYFKGNLVRISASAKFSEHDYHLHVVDLHNTGP 577
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 28.1 bits (63), Expect = 2.2
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 6/77 (7%)
Query: 19 FSPDDKYVLSGSQSGKINLYGVETGKL--EQIFDTRGKFTLSIAYSTDGHWIASGALDGI 76
+ D + + G++ TGKL + ++A G + DG
Sbjct: 30 VAVDGGRLYVATGKGELVALDAATGKLLWRKDLSGEILGAPTVA----GGVVVVVTADGS 85
Query: 77 INIFDANTGHSSWVLST 93
+ DA TG W
Sbjct: 86 LYALDAETGKLLWSYQR 102
>gnl|CDD|219038 pfam06459, RR_TM4-6, Ryanodine Receptor TM 4-6. This region covers
TM regions 4-6 of the ryanodine receptor 1 family.
Length = 217
Score = 27.7 bits (62), Expect = 3.0
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 156 SYKPEEEVEVN----GGGGEEEEEEQMV 179
S P EE E G GEE+EEE +V
Sbjct: 148 STSPAEEEEEEGSGSGDDGEEDEEEGIV 175
>gnl|CDD|235150 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
Length = 248
Score = 27.6 bits (62), Expect = 3.4
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 123 HTFKHADQVW 132
HT +HAD+VW
Sbjct: 195 HTLRHADRVW 204
>gnl|CDD|199835 cd10277, PQQ_ADH_I, Ethanol dehydrogenase, a bacterial quinoprotein
(PQQ-dependent type I alcohol dehydrogenase). This
bacterial family of homodimeric ethanol dehydrogenases
utilize pyrroloquinoline quinone (PQQ) as a cofactor. It
represents proteins whose expression may be induced by
ethanol, and which are similar to quinoprotein methanol
dehydrogenases, but have higher specificities for
ethanol and other primary and secondary alcohols.
Dehydrogenases with PQQ cofactors, such as ethanol,
methanol, and membrane-bound glucose dehydrogenases,
form an 8-bladed beta-propeller.
Length = 529
Score = 27.3 bits (61), Expect = 5.1
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 62 STDGHWIASGALDGIINIFDANTGHSSW-------VLS--TAFTRDGKFFIS 104
+T G + +G DG FDA TG W ++ + DGK +++
Sbjct: 444 TTAGGLVFTGTPDGYFRAFDAKTGKELWEFQTGSGIIGPPVTWEVDGKQYVA 495
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 27.0 bits (60), Expect = 6.0
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 20 SPDDKYVLSGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDGIINI 79
PDD YVL GS + L E G + + + GK +S W + G+ +
Sbjct: 106 YPDDPYVLRGSCGLEYRLELTEEG--RRKYGSSGKDHGRGGFSGYSGWSSGDGGSGLFTV 163
Query: 80 F 80
F
Sbjct: 164 F 164
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 26.8 bits (59), Expect = 7.4
Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 21/111 (18%)
Query: 17 VVFSPDDKYVL-SGSQSGKINLYGVETGKLEQIFDTRGKFTLSIAYSTDGHWIASGALDG 75
V F P VL S +N++ VE GK ++ S+ ++ DG + + + D
Sbjct: 131 VSFHPSAMNVLASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDK 190
Query: 76 IINIFDANTGHSSWVLSTAFTRDGKFFISASADHTVR----VWNFARRENM 122
+NI D RDG S A + + +W A+R+++
Sbjct: 191 KLNIIDP--------------RDGTIVSSVEAHASAKSQRCLW--AKRKDL 225
>gnl|CDD|233950 TIGR02608, delta_60_rpt, delta-60 repeat domain. This domain
occurs in tandem repeats, as many as 13, in proteins
from Bdellovibrio bacteriovorus, Azotobacter
vinelandii, Geobacter sulfurreducens, Pirellula sp. 1,
Myxococcus xanthus, and others, many of which are
Deltaproteobacteria. The periodicity of the repeat
ranges from about 57 to 61 amino acids, and a core
region of about 54 is represented by this model and
seed alignment.
Length = 54
Score = 24.5 bits (54), Expect = 8.5
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 13 DMWNVVFSPDDKYVLSGS--QSGKINLYGVE---TGKLEQIFDTRGKFTLSIA 60
+ V D K +++G SG + G L+ F T GK T +
Sbjct: 2 RAYAVAVQSDGKILVAGYVDNSGNNDFVLARLNADGSLDTTFGTGGKVTFDLG 54
>gnl|CDD|212052 cd11483, SLC-NCS1sbd_Mhp1-like, nucleobase-cation-symport-1 (NCS1)
transporter Mhp1-like; solute-binding domain. This NCS1
subfamily includes Microbacterium liquefaciens Mhp1, and
various uncharacterized NCS1s. Mhp1 mediates the uptake
of indolyl methyl- and benzyl-hydantoins as part of a
metabolic salvage pathway for their conversion to amino
acids. Mhp1 has 12 transmembrane (TM) helices (an
inverted topology repeat: TMs1-5 and TMs6-10, and
TMs11-12; TMs numbered to conform to the Solute carrier
6 (SLC6) family Aquifex aeolicus LeuT). NCS1s are
essential components of salvage pathways for nucleobases
and related metabolites; their other known substrates
include allantoin, uracil, thiamine, and nicotinamide
riboside. NCS1s belong to a superfamily which also
contains the solute carrier 5 family sodium/glucose
transporters (SLC5s), and SLC6 neurotransmitter
transporters.
Length = 434
Score = 26.5 bits (59), Expect = 9.7
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 67 WIASGALDGIINIFDANTGHSSWVL 91
W+ + AL+ I I G + VL
Sbjct: 112 WLGALALNEISKIL---FGFDNLVL 133
>gnl|CDD|214340 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
Length = 200
Score = 26.0 bits (58), Expect = 9.7
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 76 IINIFDANTGHSSWVLSTAFTRDGKFFISA 105
I ++ TG WV+S RD F+SA
Sbjct: 154 ITRVYAQRTGKPLWVISEDMERD--VFMSA 181
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
0.316 0.133 0.410
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: 9,323,842
Number of extensions: 840772
Number of successful extensions: 833
Number of sequences better than 10.0: 1
Number of HSP's gapped: 789
Number of HSP's successfully gapped: 56
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.4 bits)