RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10566
(604 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 = 124 bits (313), Expect = 8e-32
Identities = 83/290 (28%), Positives = 126/290 (43%), Gaps = 53/290 (18%)
Query: 300 HCDEVWFCKFSPDGLKLATGSKDTTVIIWDVDPVTFTCQHRKTLEGHTLGVAYLAWSPDS 359
H V S DG LA+GS D T+ +WD++ T + +TL GHT V+ +A+SPD
Sbjct: 50 HTGPVRDVAASADGTYLASGSSDKTIRLWDLE----TGECVRTLTGHTSYVSSVAFSPDG 105
Query: 360 SHLLVVGPEDCHELWVWNIET-ELLRVKLNHSPEDSLTSCSWNRDGTKFVCGGIRGQFYQ 418
+L D + VW++ET + L H D + S +++ DGT FV
Sbjct: 106 -RILSSSSRDK-TIKVWDVETGKCLTTLRGH--TDWVNSVAFSPDGT-FVASS------- 153
Query: 419 CDIEGQVLDSWEG-VRVNCLWCRSDGKSVLAADTHHRIRTYNFEHLTDSNLLQEDHPVMS 477
S +G +++ W T + T L V S
Sbjct: 154 ---------SQDGTIKL---W---------DLRTGKCVAT----------LTGHTGEVNS 182
Query: 478 FTIDATDRLALLNVSTQGVHLWDLRDRILLRKFQGVTQGQFTIHSCFGGANQDFVASGSE 537
L + S + LWDL L +G G ++S + +ASGSE
Sbjct: 183 VAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENG---VNSVAFSPDGYLLASGSE 239
Query: 538 DGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIW 587
DG + +W ++ + TLSGHT +V+ +AW+P + +AS S D T+RIW
Sbjct: 240 DGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDG-KRLASGSADGTIRIW 288
Score = 90.5 bits (225), Expect = 4e-20
Identities = 70/251 (27%), Positives = 111/251 (44%), Gaps = 49/251 (19%)
Query: 339 HRKTLEGHTLGVAYLAWSPDSSHLLVVGPEDCHELWVWNIET-ELLRVKLNHSPEDSLTS 397
R+TL+GHT GV +A+SPD LL G D + VW++ET ELLR H+ +
Sbjct: 1 LRRTLKGHTGGVTCVAFSPD-GKLLATGSGD-GTIKVWDLETGELLRTLKGHT--GPVRD 56
Query: 398 CSWNRDGTKFVCGGIRGQFYQCDIEGQVLDSWEGVRVNCLWCRSDGKSVLAADTHHRIRT 457
+ + DGT G D +R+ W G+ +RT
Sbjct: 57 VAASADGTYLASGS--------------SDK--TIRL---WDLETGEC---------VRT 88
Query: 458 YNFEHLTDSNLLQEDHPVMSFTIDATDRLALLNVSTQG-VHLWDLRDRILLRKFQGVTQG 516
H V S R+ L + S + +WD+ L +G T
Sbjct: 89 L-TGH---------TSYVSSVAFSPDGRI-LSSSSRDKTIKVWDVETGKCLTTLRGHTD- 136
Query: 517 QFTIHSCFGGANQDFVASGSEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIA 576
++S + FVAS S+DG + +W ++ +ATL+GHT V+ VA++P ++++
Sbjct: 137 --WVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLS 194
Query: 577 SVSDDCTVRIW 587
S S D T+++W
Sbjct: 195 S-SSDGTIKLW 204
Score = 80.1 bits (198), Expect = 1e-16
Identities = 62/253 (24%), Positives = 95/253 (37%), Gaps = 48/253 (18%)
Query: 292 ETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWDVDPVTFTCQHRKTLEGHTLGVA 351
E + L H V FSPDG L++ S+D T+ +WDV+ T C TL GHT V
Sbjct: 84 ECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVE--TGKCL--TTLRGHTDWVN 139
Query: 352 YLAWSPDSSHLLVVGPEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCGG 411
+A+SPD + +D + +W++ T V + S +++ DG K +
Sbjct: 140 SVAFSPD-GTFVASSSQD-GTIKLWDLRTGKC-VATLTGHTGEVNSVAFSPDGEKLLSSS 196
Query: 412 IRGQFYQCDIEGQVLDSWEGVRVNCLWCRSDGKSVLAADTHHRIRTYNFEHLTDSNLLQE 471
G ++ LW S GK + T H
Sbjct: 197 SDGT----------------IK---LWDLSTGKC---------LGTL-RGH--------- 218
Query: 472 DHPVMSFTIDATDRLALLNVSTQGVHLWDLRDRILLRKFQGVTQGQFTIHSCFGGANQDF 531
++ V S L + +WDLR ++ G T + S +
Sbjct: 219 ENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNS---VTSLAWSPDGKR 275
Query: 532 VASGSEDGKVYIW 544
+ASGS DG + IW
Sbjct: 276 LASGSADGTIRIW 288
Score = 77.8 bits (192), Expect = 1e-15
Identities = 44/121 (36%), Positives = 60/121 (49%), Gaps = 7/121 (5%)
Query: 291 CETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWDVDPVTFTCQHRKTLEGHTLGV 350
+ L H EV FSPDG KL + S D T+ +WD+ T C TL GH GV
Sbjct: 167 GKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLS--TGKCLG--TLRGHENGV 222
Query: 351 AYLAWSPDSSHLLVVGPEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCG 410
+A+SPD +LL G ED + VW++ T L +S+TS +W+ DG + G
Sbjct: 223 NSVAFSPD-GYLLASGSEDGT-IRVWDLRTGECVQTL-SGHTNSVTSLAWSPDGKRLASG 279
Query: 411 G 411
Sbjct: 280 S 280
Score = 37.3 bits (87), Expect = 0.018
Identities = 18/39 (46%), Positives = 24/39 (61%)
Query: 291 CETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWD 329
E Q L+ H + V +SPDG +LA+GS D T+ IWD
Sbjct: 251 GECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 100 bits (249), Expect = 2e-22
Identities = 85/311 (27%), Positives = 132/311 (42%), Gaps = 20/311 (6%)
Query: 286 KEEFPCETTQVLNDHCDEVWFCKFSPDGLKLATGS-KDTTVIIWDVDPVTFTCQHRKTLE 344
P + + L H + V FSPDG LA+GS D T+ +WD+ TL
Sbjct: 140 DLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPL----STLA 195
Query: 345 GHTLGVAYLAWSPDSSHLLVVGPEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDG 404
GHT V+ LA+SPD L+ G D + +W++ T L DS+ S ++ DG
Sbjct: 196 GHTDPVSSLAFSPDGGLLIASGSSD-GTIRLWDLSTGKLLRSTLSGHSDSVVSS-FSPDG 253
Query: 405 TKFVCGGIRGQFYQCDIEGQ----VLDSWEGVRVNCLWCRSDGKSVLAADTHHRIRTYNF 460
+ G G D+ S V + DGK + + + +R ++
Sbjct: 254 SLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDL 313
Query: 461 EHLTDS---NLLQEDHPVMSFTIDATDRLALLNVSTQG-VHLWDLRDRILLRKFQGVTQG 516
E L + PV S + L + S G + LWDLR L+ +G +
Sbjct: 314 ETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSN- 372
Query: 517 QFTIHSCFGGANQDFVASGSEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIA 576
+ S + V+SGS DG V +W + + L GHT V+ + ++P + +A
Sbjct: 373 ---VLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSP-DGKSLA 428
Query: 577 SVSDDCTVRIW 587
S S D T+R+W
Sbjct: 429 SGSSDNTIRLW 439
Score = 94.4 bits (233), Expect = 2e-20
Identities = 76/298 (25%), Positives = 121/298 (40%), Gaps = 48/298 (16%)
Query: 294 TQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWDVDPVTFTCQHRKTLEGHTLGVAYL 353
+ +L H D + FSPDG L +GS D T+ +WD+D + H V+ L
Sbjct: 58 SLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLD--NGEKLIKSLEGLHDSSVSKL 115
Query: 354 AW-SPDSSHLLVVGPEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCGGI 412
A SPD + +L+ + +W++ T ++ +S+TS +++ DG G
Sbjct: 116 ALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGS- 174
Query: 413 RGQFYQCDIEGQVLDSWEGVRVNCLWCRSDGKSVLAADTHHRIRTYNFEHLTDSNLLQED 472
LW GK + H
Sbjct: 175 -----------------SLDGTIKLWDLRTGKPLSTLAGHTD------------------ 199
Query: 473 HPVMSFTIDATDRLALLNVSTQG-VHLWDLRDRILLR-KFQGVTQGQFTIHSCFGGANQD 530
PV S L + + S+ G + LWDL LLR G + + S +
Sbjct: 200 -PVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFS----PDGS 254
Query: 531 FVASGSEDGKVYIWHVKREL-PIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIW 587
+ASGS DG + +W ++ + TLSGH+ +V VA++P +++AS S D TVR+W
Sbjct: 255 LLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDG-KLLASGSSDGTVRLW 311
Score = 88.2 bits (217), Expect = 2e-18
Identities = 68/272 (25%), Positives = 107/272 (39%), Gaps = 16/272 (5%)
Query: 292 ETTQVLNDHCDEVWFCKFSPDG-LKLATGSKDTTVIIWDVDPVTFTCQHRKTLEGHTLGV 350
+ L H D V FSPDG L +A+GS D T+ +WD+ T R TL GH+
Sbjct: 189 KPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLS--TGKL-LRSTLSGHS-DS 244
Query: 351 AYLAWSPDSSHLLVVGPEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCG 410
++SPD S L + + +W++ + ++ S+ S +++ DG G
Sbjct: 245 VVSSFSPDGSLLASGSSD--GTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
Query: 411 GIRGQFYQCDIEGQVLDSWEGV-----RVNCL-WCRSDGKSVLAADTHHRIRTYNFEHLT 464
G D+E L S + V+ L + V IR ++
Sbjct: 303 SSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGK 362
Query: 465 DSNLLQEDHPVMSFTIDATDRLALLNVSTQGVHLWDLRDRILLRKFQGVTQGQFTIHSCF 524
L+ V+S + R+ + V LWDL LLR G T + S
Sbjct: 363 PLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHT---SRVTSLD 419
Query: 525 GGANQDFVASGSEDGKVYIWHVKRELPIATLS 556
+ +ASGS D + +W +K L + S
Sbjct: 420 FSPDGKSLASGSSDNTIRLWDLKTSLKSVSFS 451
Score = 70.5 bits (171), Expect = 8e-13
Identities = 46/183 (25%), Positives = 78/183 (42%), Gaps = 23/183 (12%)
Query: 433 RVNCLWCRSDGKSVLAADTHHRIRTYNF---EHLTDSNLLQEDHPVMSFTIDATDRLALL 489
+ + DG+ +L+ + I+ ++ E L S D V + + D ++L
Sbjct: 67 SITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSIL 126
Query: 490 NVSTQG---VHLWDLRDRILLRKFQGVTQGQFTIHS------CFGGANQDFVASGSEDGK 540
S+ V LWDL G HS F + + S DG
Sbjct: 127 LASSSLDGTVKLWDLST-------PGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGT 179
Query: 541 VYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIWGPHLNTNKSPHLA 600
+ +W ++ P++TL+GHT VS +A++P +IAS S D T+R+W + + L
Sbjct: 180 IKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLW----DLSTGKLLR 235
Query: 601 SSL 603
S+L
Sbjct: 236 STL 238
Score = 46.6 bits (109), Expect = 3e-05
Identities = 31/121 (25%), Positives = 49/121 (40%), Gaps = 6/121 (4%)
Query: 270 DESLENVSLLVDHLCTKEEFPCETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWD 329
D SL D + + V FSPDG +++GS D TV +WD
Sbjct: 339 DGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWD 398
Query: 330 VDPVTFTCQHRKTLEGHTLGVAYLAWSPDSSHLLVVGPEDCHELWVWNIETELLRVKLNH 389
+ + + L+GHT V L +SPD L + + +W+++T L V +
Sbjct: 399 LSTGSL----LRNLDGHTSRVTSLDFSPDGKSLASGS--SDNTIRLWDLKTSLKSVSFSP 452
Query: 390 S 390
Sbjct: 453 D 453
Score = 35.4 bits (80), Expect = 0.095
Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 11/96 (11%)
Query: 496 VHLWDLRDRILLRKFQGVTQGQFTIHSCFGGANQDFVASGSEDGKVYIWHV-KRELPIAT 554
V L DL +L +T F+ + + SGS DG + +W + E I +
Sbjct: 51 VSLPDLSSLLLRGHEDSITSIAFSPDG-------ELLLSGSSDGTIKLWDLDNGEKLIKS 103
Query: 555 LSG-HTRTVSCVAW-NPVYHQMIASVSD-DCTVRIW 587
L G H +VS +A +P + ++ + S D TV++W
Sbjct: 104 LEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLW 139
Score = 30.4 bits (67), Expect = 3.0
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 536 SEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIWGPHLNTNK 595
+L L GH +++ +A++P +++ S S D T+++W
Sbjct: 42 LLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSP-DGELLLSGSSDGTIKLWDLDNGEKL 100
Query: 596 SPHL 599
L
Sbjct: 101 IKSL 104
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 48.1 bits (115), Expect = 9e-08
Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 551 PIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIW 587
+ TL GHT V+ VA++P ++AS SDD TVR+W
Sbjct: 3 LLRTLKGHTGPVTSVAFSP-DGNLLASGSDDGTVRVW 38
Score = 47.3 bits (113), Expect = 2e-07
Identities = 17/39 (43%), Positives = 21/39 (53%)
Query: 291 CETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWD 329
+ + L H V FSPDG LA+GS D TV +WD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 31.2 bits (71), Expect = 0.091
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 337 CQHRKTLEGHTLGVAYLAWSPDSSHLLVVGPEDCHELWVWN 377
+ +TL+GHT V +A+SPD + L +D + VW+
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGS-DDGT-VRVWD 39
Score = 27.7 bits (62), Expect = 1.8
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 528 NQDFVASGSEDGKVYIWH 545
+ + +ASGS+DG V +W
Sbjct: 22 DGNLLASGSDDGTVRVWD 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 = 48.1 bits (115), Expect = 1e-07
Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 551 PIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIW 587
+ TL GHT V+ VA++P + +AS SDD T+++W
Sbjct: 4 LLKTLKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLW 39
Score = 45.0 bits (107), Expect = 1e-06
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 295 QVLNDHCDEVWFCKFSPDGLKLATGSKDTTVIIWD 329
+ L H V FSPDG LA+GS D T+ +WD
Sbjct: 6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 31.9 bits (73), Expect = 0.046
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 336 TCQHRKTLEGHTLGVAYLAWSPDSSHLLVVGPEDCHELWVWN 377
+ + KTL+GHT V +A+SPD +L +D + +W+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGS-DDGT-IKLWD 40
Score = 27.3 bits (61), Expect = 2.0
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 528 NQDFVASGSEDGKVYIWH 545
+ ++ASGS+DG + +W
Sbjct: 23 DGKYLASGSDDGTIKLWD 40
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 47.6 bits (113), Expect = 1e-05
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 523 CFGGANQDFVASGSEDGKVYIWHVKREL--------PIATLSGHTRTVSCVAWNPVYHQM 574
CF + +ASGSED + +W + P L GH + +S + WNP+ + +
Sbjct: 85 CF----SEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKKKISIIDWNPMNYYI 140
Query: 575 IASVSDDCTVRIW 587
+ S D V IW
Sbjct: 141 MCSSGFDSFVNIW 153
Score = 43.0 bits (101), Expect = 3e-04
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 520 IHSCFGGANQDFVA------SGSEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQ 573
I SC + FVA G G + + + R+ P+ L GHT ++ + +NP + +
Sbjct: 29 IDSCGIACSSGFVAVPWEVEGGGLIGAIRLENQMRKPPVIKLKGHTSSILDLQFNPCFSE 88
Query: 574 MIASVSDDCTVRIWG-PHLNTN 594
++AS S+D T+R+W PH + +
Sbjct: 89 ILASGSEDLTIRVWEIPHNDES 110
Score = 33.8 bits (77), Expect = 0.27
Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 7/94 (7%)
Query: 316 LATGSKDTTVIIWDVDPVTFTCQHRK----TLEGHTLGVAYLAWSPDSSHLLVVGPEDCH 371
LA+GS+D T+ +W++ + + K L+GH ++ + W+P + +++ D
Sbjct: 90 LASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSF 149
Query: 372 ELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGT 405
+ +W+IE E ++N + L+S WN G
Sbjct: 150 -VNIWDIENEKRAFQINMPKK--LSSLKWNIKGN 180
>gnl|CDD|128914 smart00668, CTLH, C-terminal to LisH motif. Alpha-helical motif of
unknown function.
Length = 58
Score = 42.2 bits (100), Expect = 2e-05
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 121 SAAKFRQHIMDGDWSKADHDLNDLEYLLDSRGDLVEMKFLILEQKYLEYLEDGRVLD 177
+ R+ I+ GDW +A L+ L+ L R +++F + +QK+LE + G++ +
Sbjct: 4 ERKRIRELILKGDWDEALEWLSSLKPPLLERNS--KLEFELRKQKFLELVRQGKLEE 58
>gnl|CDD|223893 COG0823, TolB, Periplasmic component of the Tol biopolymer
transport system [Intracellular trafficking and
secretion].
Length = 425
Score = 42.8 bits (101), Expect = 4e-04
Identities = 36/142 (25%), Positives = 60/142 (42%), Gaps = 17/142 (11%)
Query: 292 ETTQVLNDHCDEVWFCKFSPDGLKLATGSKDTT----VIIWDVDPVTFTCQHRK-TLEGH 346
Q L D + +SPDG KLA S + + D++ + G+
Sbjct: 183 YNQQKLTDSGSLILTPAWSPDGKKLAYVSFELGGCPRIYYLDLN---TGKRPVILNFNGN 239
Query: 347 TLGVAYLAWSPDSSHLLVVG-PEDCHELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGT 405
A+SPD S L + ++++ +++ + L +L + + TS SW+ DG+
Sbjct: 240 NG---APAFSPDGSKLAFSSSRDGSPDIYLMDLDGKNLP-RLTNGFGIN-TSPSWSPDGS 294
Query: 406 KFVCGGIRG---QFYQCDIEGQ 424
K V RG Q Y D+EG
Sbjct: 295 KIVFTSDRGGRPQIYLYDLEGS 316
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 40.6 bits (95), Expect = 0.002
Identities = 38/144 (26%), Positives = 61/144 (42%), Gaps = 15/144 (10%)
Query: 308 KFSP-DGLKLATGSKDTTVIIWDV--DPVTFTC-QHRKTLEGHTLGVAYLAWSPDSSHLL 363
F+P D KL T S+D T++ W + + +T L+GHT V +++ P + ++L
Sbjct: 82 AFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVSFHPSAMNVL 141
Query: 364 VVGPEDCHELWVWNIETEL-LRVKLNHSPEDSLTSCSWNRDGTKFVCGGIRGQFYQ---- 418
D + VW++E + V HS D +TS WN DG+ C + +
Sbjct: 142 ASAGAD-MVVNVWDVERGKAVEVIKCHS--DQITSLEWNLDGSLL-CTTSKDKKLNIIDP 197
Query: 419 --CDIEGQVLDSWEGVRVNCLWCR 440
I V CLW +
Sbjct: 198 RDGTIVSSVEAHASAKSQRCLWAK 221
Score = 34.9 bits (80), Expect = 0.14
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 534 SGSEDGKVYIWHVKRE-------LPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRI 586
+ SEDG + W + E PI L GHT+ V V+++P ++AS D V +
Sbjct: 93 TASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVSFHPSAMNVLASAGADMVVNV 152
Query: 587 W 587
W
Sbjct: 153 W 153
Score = 30.2 bits (68), Expect = 3.6
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 532 VASGSEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIWGP 589
+AS D V +W V+R + + H+ ++ + WN + ++ + S D + I P
Sbjct: 141 LASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWN-LDGSLLCTTSKDKKLNIIDP 197
>gnl|CDD|128913 smart00667, LisH, Lissencephaly type-1-like homology motif.
Alpha-helical motif present in Lis1, treacle, Nopp140,
some katanin p60 subunits, muskelin, tonneau, LEUNIG and
numerous WD40 repeat-containing proteins. It is
suggested that LisH motifs contribute to the regulation
of microtubule dynamics, either by mediating
dimerisation, or else by binding cytoplasmic dynein
heavy chain or microtubules directly.
Length = 34
Score = 35.5 bits (83), Expect = 0.002
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 87 EDIVRLIGQYLRTIGLDRTADLLMQESGCKL 117
++ RLI +YL G + TA+ L +ESG L
Sbjct: 4 SELNRLILEYLLRNGYEETAETLQKESGLSL 34
>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
Length = 430
Score = 39.7 bits (93), Expect = 0.003
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 14/122 (11%)
Query: 309 FSPDGLKLATGSKDT---TVIIWDVDPVTFTCQHRKTLEGHTLGVAYLAWSPDSSHLLVV 365
+SPDG ++A S + + + ++D T + EG L A AWSPD S L V
Sbjct: 206 WSPDGKRIAYVSFEQKRPRIFVQNLD--TGRREQITNFEG--LNGA-PAWSPDGSKLAFV 260
Query: 366 GPEDCH-ELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCGGIRG---QFYQCDI 421
+D + E++V ++ + L NH D T W +DG RG Q Y+ ++
Sbjct: 261 LSKDGNPEIYVMDLASRQLSRVTNHPAID--TEPFWGKDGRTLYFTSDRGGKPQIYKVNV 318
Query: 422 EG 423
G
Sbjct: 319 NG 320
>gnl|CDD|234019 TIGR02800, propeller_TolB, tol-pal system beta propeller repeat
protein TolB. Members of this protein family are the
TolB periplasmic protein of Gram-negative bacteria. TolB
is part of the Tol-Pal (peptidoglycan-associated
lipoprotein) multiprotein complex, comprising five
envelope proteins, TolQ, TolR, TolA, TolB and Pal, which
form two complexes. The TolQ, TolR and TolA
inner-membrane proteins interact via their transmembrane
domains. The {beta}-propeller domain of the periplasmic
protein TolB is responsible for its interaction with
Pal. TolB also interacts with the outer-membrane
peptidoglycan-associated proteins Lpp and OmpA. TolA
undergoes a conformational change in response to changes
in the proton-motive force, and interacts with Pal in an
energy-dependent manner. The C-terminal periplasmic
domain of TolA also interacts with the N-terminal domain
of TolB. The Tol-PAL system is required for bacterial
outer membrane integrity. E. coli TolB is involved in
the tonB-independent uptake of group A colicins
(colicins A, E1, E2, E3 and K), and is necessary for the
colicins to reach their respective targets after initial
binding to the bacteria. It is also involved in uptake
of filamentous DNA. Study of its structure suggest that
the TolB protein might be involved in the recycling of
peptidoglycan or in its covalent linking with
lipoproteins. The Tol-Pal system is also implicated in
pathogenesis of E. coli, Haemophilus ducreyi ,
Salmonella enterica and Vibrio cholerae, but the
mechanism(s) is unclear [Transport and binding proteins,
Other, Cellular processes, Pathogenesis].
Length = 417
Score = 39.6 bits (93), Expect = 0.004
Identities = 37/136 (27%), Positives = 56/136 (41%), Gaps = 22/136 (16%)
Query: 308 KFSPDGLKLA---TGSKDTTVIIWDVDPVTFTCQHRKTL--EGHTLGVAYLAWSPDSSHL 362
+SPDG KLA S + + D+ T Q K G A +SPD S L
Sbjct: 196 AWSPDGQKLAYVSFESGKPEIYVQDL----ATGQREKVASFPGMNGAPA---FSPDGSKL 248
Query: 363 LVV-GPEDCHELWVWNIETELLRVKLNHSPE-DSLTSCSWNRDGTKFVCGGIRG---QFY 417
V + +++V +++ + L +L + P D T SW+ DG RG Q Y
Sbjct: 249 AVSLSKDGNPDIYVMDLDGKQLT-RLTNGPGID--TEPSWSPDGKSIAFTSDRGGSPQIY 305
Query: 418 QCDIEG--QVLDSWEG 431
D +G ++ G
Sbjct: 306 MMDADGGEARRLTFRG 321
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 38.5 bits (89), Expect = 0.011
Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 532 VASGSEDGKVYIWHVKR-ELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIWGPH 590
+A GS D KVY + ++ +LP+ T+ GH++TVS V + V + S S D T+++W
Sbjct: 633 LAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRF--VDSSTLVSSSTDNTLKLWDLS 690
Query: 591 LNT---NKSP 597
++ N++P
Sbjct: 691 MSISGINETP 700
Score = 35.8 bits (82), Expect = 0.065
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 523 CFGGANQDFVASGSEDGKVYIWHVKRELPIATLSGHTRTVSCVAWNPVYHQMIASVSDDC 582
C+ + VAS + +G V +W V R + + H + V + ++ ++AS SDD
Sbjct: 539 CWNSYIKSQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDG 598
Query: 583 TVRIW 587
+V++W
Sbjct: 599 SVKLW 603
>gnl|CDD|179892 PRK04922, tolB, translocation protein TolB; Provisional.
Length = 433
Score = 34.3 bits (79), Expect = 0.19
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 354 AWSPDSSHLLVVGPEDCH-ELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCGGI 412
++SPD L + D + E++V ++ + L NH D T +W DG
Sbjct: 254 SFSPDGRRLALTLSRDGNPEIYVMDLGSRQLTRLTNHFGID--TEPTWAPDGKSIYFTSD 311
Query: 413 RG---QFYQCDIEG 423
RG Q Y+ G
Sbjct: 312 RGGRPQIYRVAASG 325
>gnl|CDD|235312 PRK04792, tolB, translocation protein TolB; Provisional.
Length = 448
Score = 32.7 bits (75), Expect = 0.65
Identities = 43/165 (26%), Positives = 68/165 (41%), Gaps = 39/165 (23%)
Query: 310 SPDGLKLATGS---KDTTVIIWDVDPVTFTCQHRK--TLEGHTLGVAYLAWSPDSSHLLV 364
SPDG KLA S + + + D+ +T K + G G +SPD L +
Sbjct: 226 SPDGRKLAYVSFENRKAEIFVQDI----YTQVREKVTSFPGIN-GAP--RFSPDGKKLAL 278
Query: 365 VGPEDCH-ELWVWNIETELLRVKLNHSPEDSLTSCSWNRDGTKFVCGGIRG---QFYQCD 420
V +D E++V +I T+ L H D T SW+ DG + RG Q Y+ +
Sbjct: 279 VLSKDGQPEIYVVDIATKALTRITRHRAID--TEPSWHPDGKSLIFTSERGGKPQIYRVN 336
Query: 421 IEGQVLD--SWEG---------------VRVNCLWCRSDGKSVLA 448
+ + ++EG + VN R++GK +A
Sbjct: 337 LASGKVSRLTFEGEQNLGGSITPDGRSMIMVN----RTNGKFNIA 377
>gnl|CDD|227663 COG5369, COG5369, Uncharacterized conserved protein [Function
unknown].
Length = 743
Score = 32.6 bits (74), Expect = 0.78
Identities = 29/136 (21%), Positives = 52/136 (38%), Gaps = 8/136 (5%)
Query: 98 RTIGLDRTADLLMQESGCKLDHPSAAKFRQHIMDGDWSKADHDLNDLEYLLDSRGDLVEM 157
R D D+ + L+ +H+ G K D N ++ LD V++
Sbjct: 213 RVFKNDCNPDIQIINL---LNELLDEYLGKHVKIGRIRKRRDDSNGVKNKLDVLSCCVKL 269
Query: 158 KFLILEQ---KYLEYLEDGRVLDALHVLRNELTPLNHNTAKVHELSSFMMCSGVEQLLER 214
F+ + + E +LD L R E TP+N+ + L F + V+ L
Sbjct: 270 YFMSHSEDKVRIFERWIFYPLLDELIQYRKESTPMNNPVLVL--LGIFCVQDDVQACLSL 327
Query: 215 AKWDGKGSQSRTKLMD 230
+ K + +K++D
Sbjct: 328 PQLFEKDIELTSKIID 343
>gnl|CDD|204739 pfam11768, DUF3312, Protein of unknown function (DUF3312). This is
a eukaryotic family of uncharacterized proteins. This
family shows similarity to WD40 repeat proteins.
Length = 544
Score = 32.4 bits (74), Expect = 0.87
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 10/62 (16%)
Query: 307 CKFSPDGLKLATGSKDTTVIIWDVDPVTFTCQHRKT--LEGHTLGVAYLAWSPDSSHLLV 364
C SPD KL G D++++++D +HR L + +AW PDS+ +LV
Sbjct: 264 CARSPDEEKLLLGCIDSSLVLYD--------EHRGVTLLAQAAVIPHLIAWHPDSAIVLV 315
Query: 365 VG 366
Sbjct: 316 AN 317
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
RecG helicase involved in DNA repair. Replication factor
A is a heterotrimeric complex, that contains a subunit
in this family. This domain is also found at the
C-terminus of bacterial DNA polymerase III alpha chain.
Length = 75
Score = 29.5 bits (67), Expect = 0.91
Identities = 6/37 (16%), Positives = 14/37 (37%)
Query: 552 IATLSGHTRTVSCVAWNPVYHQMIASVSDDCTVRIWG 588
TL T ++ V + ++ + + V + G
Sbjct: 19 FLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVLVTG 55
>gnl|CDD|220824 pfam10607, CLTH, CTLH/CRA C-terminal to LisH motif domain. RanBPM
is a scaffolding protein and is important in regulating
cellular function in both the immune system and the
nervous system. This domain is at the C-terminus of the
proteins and is the binding domain for the CRA motif
(for CT11-RanBPM), which is comprised of approximately
100 amino acids at the C terminal of RanBPM. It was
found to be important for the interaction of RanBPM with
fragile X mental retardation protein (FMRP), but its
functional significance has yet to be determined. This
region contains CTLH and CRA domains annotated by SMART;
however, these may be a single domain, and it is
refereed to as a C-terminal to LisH motif.
Length = 144
Score = 30.6 bits (70), Expect = 1.0
Identities = 22/102 (21%), Positives = 46/102 (45%), Gaps = 12/102 (11%)
Query: 126 RQHIMDGDWSKADHDLNDLEYLLDSRGDLVEMKFLILEQKYLEYLEDGRVLDALHVLRNE 185
R+ +++GD +A N+ + L +E + + Q+++E + +G++L+AL R
Sbjct: 9 RESLLNGDLEEALEWCNENKPELLKINSNLEFELRL--QQFIELIREGKILEALEYAREN 66
Query: 186 LTPLNHNTAKVHELSSFM---------MCSGVEQLLERAKWD 218
L P + E+ M S + LL ++W+
Sbjct: 67 LAPFFNEQHL-KEIQKLMGLLAFPDPTDSSPYKSLLSPSRWE 107
>gnl|CDD|224086 COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and
metabolism].
Length = 598
Score = 31.9 bits (73), Expect = 1.1
Identities = 28/126 (22%), Positives = 45/126 (35%), Gaps = 4/126 (3%)
Query: 143 DLEYLLDSRGDLVEMKFLILEQKYLEYLEDGRVLDALHVLRNELTPLNHNTAKVHELSSF 202
DL L +L E +FL ++ L+ LE ++ + L L + L ++
Sbjct: 14 DLSDLY-PGDELWEAEFLEESKELLKALEFYELILSAEDLLEALEEYEKLEELLGRLYAY 72
Query: 203 --MMCSGVEQLLERAKWDGKGSQSRTKLMDKLQSFLPPTVMLPPRRLQTLLSQAVDLQKY 260
M S E K K + L F P + L +Q+LL+ +L Y
Sbjct: 73 ASMKLSTDTTDEEAQKLYQKLEEFYADFSSALSFFEPELLELDEEVIQSLLTSGPELADY 132
Query: 261 HCPYHN 266
Y
Sbjct: 133 R-FYLE 137
>gnl|CDD|237557 PRK13918, PRK13918, CRP/FNR family transcriptional regulator;
Provisional.
Length = 202
Score = 30.6 bits (69), Expect = 1.9
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 68 PEINGEVPAPAVKTMTRTDEDIVRLIGQYLRT------IGLDRTADLLMQESG 114
E N + V+T+ R E I RL+GQ L+ + L T ++SG
Sbjct: 92 AEDNLVLTQHLVRTLARAYESIYRLVGQRLKNRIAAALLELSDTPLATQEDSG 144
>gnl|CDD|220051 pfam08873, DUF1834, Domain of unknown function (DUF1834). This
family of proteins are functionally uncharacterized. One
member is the Gp37 protein from the FluMu prophage.
Length = 193
Score = 29.7 bits (67), Expect = 3.5
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 18/76 (23%)
Query: 207 GVEQLLERAKWDGKGSQSRTKLMDKLQSFLPPTVMLPPRRLQTLLSQAVDLQK------- 259
G+ QL+E R L Q P L P ++ L + + Q
Sbjct: 96 GIYQLVEAL---------RALLN--GQDLGLPIGPLRPGAVRNLFNGKLKGQGVSVYALE 144
Query: 260 YHCPYHNTKVDESLEN 275
+ P+ ++D +
Sbjct: 145 FETPWPLRQLDLDALD 160
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 29.3 bits (66), Expect = 8.1
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 162 LEQKYLEYLEDGRVLDALHVLRNELTPL-NHNTAKVHELSSFMMCSGVEQLLE 213
L Q E+LE+GRV + L R E H A+ HE + +E+ +E
Sbjct: 468 LAQALYEFLEEGRVPEQLQTERQEAELNGRHVEAEEHEQVWNALIELLEEFVE 520
>gnl|CDD|222991 PHA03119, PHA03119, helicase-primase primase subunit; Provisional.
Length = 1085
Score = 29.1 bits (65), Expect = 9.5
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 12/71 (16%)
Query: 247 LQTLLSQAV-DLQKYHCPYHNTK---------VDESLENVSLLVDHLCTKEEFPCETTQV 296
LQ L S+AV D + C ++ T D + ++++ + D + +
Sbjct: 695 LQLLFSEAVVDWNSHPCYFYKTSCPPQPRHTICDINSQDINEIQDFMW--DADILYQDVE 752
Query: 297 LNDHCDEVWFC 307
LN+ DE +
Sbjct: 753 LNELHDEGAYD 763
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
0.319 0.135 0.423
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,372,684
Number of extensions: 2914602
Number of successful extensions: 2271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2205
Number of HSP's successfully gapped: 50
Length of query: 604
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 502
Effective length of database: 6,413,494
Effective search space: 3219573988
Effective search space used: 3219573988
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 (21.7 bits)
S2: 62 (27.5 bits)