RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9316
(264 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 = 99.3 bits (248), Expect = 9e-25
Identities = 53/204 (25%), Positives = 94/204 (46%), Gaps = 33/204 (16%)
Query: 44 IKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLC 103
+ + H V VA+S DG+ LA+GS D ++ ++ L+ +GHTG V +
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLE---TGELLRTLKGHTGPVRDVA 58
Query: 104 WHATNPDLLSTASGDKTVRIWDARTQKSQI-------------------MLASGSFDKSV 144
A L S S DKT+R+WD T + +L+S S DK++
Sbjct: 59 ASADGTYLAS-GSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTI 117
Query: 145 AIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQIIA 204
++ ++ RGHT V+ + + + ++++S D T+++WD RT K +A
Sbjct: 118 KVWDVETG---KCLTTLRGHTDWVNSVAFS-PDGTFVASSSQDGTIKLWDLRTGK--CVA 171
Query: 205 T-KG--ENIN-ITWAPNGNTIAVG 224
T G +N + ++P+G +
Sbjct: 172 TLTGHTGEVNSVAFSPDGEKLLSS 195
Score = 81.6 bits (202), Expect = 3e-18
Identities = 47/174 (27%), Positives = 69/174 (39%), Gaps = 33/174 (18%)
Query: 23 SQFHLVCKIDDYVKHFNTHND--IKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAIFAL 80
F D +K ++ + H +V+SVA+S DG +L S S D ++ ++ L
Sbjct: 147 GTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDL 206
Query: 81 DKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQIMLASGSF 140
RGH V+ + + + LL++ S D T+R+WD RT + L
Sbjct: 207 STG---KCLGTLRGHENGVNSVAFS-PDGYLLASGSEDGTIRVWDLRTGECVQTL----- 257
Query: 141 DKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 194
GHT SV L W L S S D T+RIWD
Sbjct: 258 ---------------------SGHTNSVTSLAWSPDGKRLAS-GSADGTIRIWD 289
Score = 62.7 bits (153), Expect = 2e-11
Identities = 36/108 (33%), Positives = 51/108 (47%), Gaps = 7/108 (6%)
Query: 20 PSGSQFHLVCKIDDYVKHFNTHND--IKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAI 77
P G + L D +K ++ + + H + V+SVA+S DG LASGS D ++ +
Sbjct: 187 PDGEKL-LSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRV 245
Query: 78 FALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 125
+ L + GHT SV L W L S S D T+RIWD
Sbjct: 246 WDLRTGECVQ---TLSGHTNSVTSLAWSPDGKRLAS-GSADGTIRIWD 289
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 80.5 bits (197), Expect = 3e-17
Identities = 71/253 (28%), Positives = 110/253 (43%), Gaps = 31/253 (12%)
Query: 13 SPEYKLLPSGSQFHLVCKIDDYVKHFNTHNDIKEYQAHGSKVHSVAWSCDGRR-LASGSF 71
SP+ KLL SGS K+ D T + H V S+A+S DG +ASGS
Sbjct: 164 SPDGKLLASGSSLDGTIKLWD----LRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSS 219
Query: 72 DKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKS 131
D ++ ++ L GH+ SV + LL++ S D T+R+WD R+ S
Sbjct: 220 DGTIRLWDLSTG--KLLRSTLSGHSDSVVSSFSP--DGSLLASGSSDGTIRLWDLRSSSS 275
Query: 132 QIM--------------------LASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQL 171
+ LASGS D +V ++ L+ G L + +GH G V L
Sbjct: 276 LLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLET-GKLLSSLTLKGHEGPVSSL 334
Query: 172 CWHATNPDLLSTASGDKTVRIWDARTQKSQIIATKGENIN-ITWAPNGNTIAVGNKEDLV 230
+ L+S S D T+R+WD RT K N+ ++++P+G ++ G+ + V
Sbjct: 335 SFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTV 394
Query: 231 TFIDVVKSLPPRE 243
D+ R
Sbjct: 395 RLWDLSTGSLLRN 407
Score = 76.3 bits (186), Expect = 7e-16
Identities = 61/268 (22%), Positives = 102/268 (38%), Gaps = 33/268 (12%)
Query: 9 HTPKSPEYKLLPSGSQFHLVCKIDDYVKHFNTHNDIKEYQA----HGSKVHSVAW-SCDG 63
H P G + L D +K ++ N K ++ H S V +A S DG
Sbjct: 64 HEDSITSIAFSPDG-ELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDG 122
Query: 64 RRLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRI 123
+ S + D GH+ SV L + L S +S D T+++
Sbjct: 123 NSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKL 182
Query: 124 WDARTQK--------------------SQIMLASGSFDKSVAIFALDKKGDLNKEVVYRG 163
WD RT K +++ASGS D ++ ++ L G
Sbjct: 183 WDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTG--KLLRSTLSG 240
Query: 164 HTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQIIATKGEN---INITWAPNGNT 220
H+ SV + LL++ S D T+R+WD R+ S + G + +++ ++P+G
Sbjct: 241 HSDSVVSSFSP--DGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKL 298
Query: 221 IAVGNKEDLVTFIDVVKSLPPRERTLTS 248
+A G+ + V D+ TL
Sbjct: 299 LASGSSDGTVRLWDLETGKLLSSLTLKG 326
Score = 73.6 bits (179), Expect = 6e-15
Identities = 56/238 (23%), Positives = 94/238 (39%), Gaps = 34/238 (14%)
Query: 8 FHTPKSPEYKLLPSGSQFHLVCKIDDYVKHFNTHND---IKEYQAHGSKVHSVAWSCDGR 64
D ++ ++ + ++ H S V SVA+S DG+
Sbjct: 238 LSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGK 297
Query: 65 RLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIW 124
LASGS D +V ++ L+ G L + +GH G V L + L+S S D T+R+W
Sbjct: 298 LLASGSSDGTVRLWDLET-GKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLW 356
Query: 125 DARTQKSQIMLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTA 184
D RT K L S SV+ + ++S+
Sbjct: 357 DLRTGKPLKTLEGHSNVLSVSFSP----------------------------DGRVVSSG 388
Query: 185 SGDKTVRIWDARTQKS--QIIATKGENINITWAPNGNTIAVGNKEDLVTFIDVVKSLP 240
S D TVR+WD T + ++ ++P+G ++A G+ ++ + D+ SL
Sbjct: 389 STDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLK 446
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 47.6 bits (113), Expect = 3e-06
Identities = 39/173 (22%), Positives = 77/173 (44%), Gaps = 31/173 (17%)
Query: 93 RGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQIMLASGSFDKSVAIFALDKK 152
+GHT S+ L ++ ++L++ S D T+R+W+ D+SV K
Sbjct: 71 KGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHN-----------DESV-------K 112
Query: 153 GDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKS--QIIATKGENI 210
+ + + +GH + + W+ N ++ ++ D V IWD +K QI K +
Sbjct: 113 EIKDPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIENEKRAFQINMPKKLS- 171
Query: 211 NITWAPNGNTIAVGNKEDLVTFIDVVKSLPPRERTLTSRGHLME----TRSLW 259
++ W GN ++ + ID PR++ + S H+ + T+++W
Sbjct: 172 SLKWNIKGNLLSGTCVGKHMHIID------PRKQEIASSFHIHDGGKNTKNIW 218
Score = 38.8 bits (90), Expect = 0.002
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 61 CDGRRLASGSFDKSVAIFALDKKGDLNKEV-----VYRGHTGSVDQLCWHATNPDLLSTA 115
C LASGS D ++ ++ + + KE+ + +GH + + W+ N ++ ++
Sbjct: 85 CFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKKKISIIDWNPMNYYIMCSS 144
Query: 116 SGDKTVRIWDARTQK 130
D V IWD +K
Sbjct: 145 GFDSFVNIWDIENEK 159
>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 = 41.5 bits (98), Expect = 8e-06
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 40 THNDIKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAIF 78
+ +K + H V SVA+S DG+ LASGS D ++ ++
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 39.2 bits (92), Expect = 6e-05
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 91 VYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 125
+GHTG V + + L++ S D T+++WD
Sbjct: 7 TLKGHTGPVTSVAFSPDG-KYLASGSDDGTIKLWD 40
Score = 39.2 bits (92), Expect = 6e-05
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 160 VYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 194
+GHTG V + + L++ S D T+++WD
Sbjct: 7 TLKGHTGPVTSVAFSPDG-KYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 40.0 bits (94), Expect = 3e-05
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 91 VYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 125
+GHTG V + + LL++ S D TVR+WD
Sbjct: 6 TLKGHTGPVTSVAFSPDGN-LLASGSDDGTVRVWD 39
Score = 40.0 bits (94), Expect = 3e-05
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 160 VYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWD 194
+GHTG V + + LL++ S D TVR+WD
Sbjct: 6 TLKGHTGPVTSVAFSPDGN-LLASGSDDGTVRVWD 39
Score = 39.6 bits (93), Expect = 3e-05
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 44 IKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAIF 78
++ + H V SVA+S DG LASGS D +V ++
Sbjct: 4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 37.4 bits (86), Expect = 0.007
Identities = 40/190 (21%), Positives = 79/190 (41%), Gaps = 36/190 (18%)
Query: 54 VHSVAWSCDGRRLASGSFDKSVAIFA----LDKKGDLNKEVVYRGHTGSVDQLCWHATNP 109
V ++ + DG A+ +K + IF + D++ VV + +CW++
Sbjct: 486 VCAIGFDRDGEFFATAGVNKKIKIFECESIIKDGRDIHYPVVELASRSKLSGICWNSYIK 545
Query: 110 DLLSTASGDKTVRIWD-ARTQKSQIMLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSV 168
+++++ + V++WD AR+Q M + H V
Sbjct: 546 SQVASSNFEGVVQVWDVARSQLVTEM---------------------------KEHEKRV 578
Query: 169 DQLCWHATNPDLLSTASGDKTVRIWDARTQKS-QIIATKGENINITWAPN--GNTIAVGN 225
+ + + +P LL++ S D +V++W S I TK NI P+ G ++A G+
Sbjct: 579 WSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKA-NICCVQFPSESGRSLAFGS 637
Query: 226 KEDLVTFIDV 235
+ V + D+
Sbjct: 638 ADHKVYYYDL 647
Score = 30.8 bits (69), Expect = 0.82
Identities = 40/175 (22%), Positives = 76/175 (43%), Gaps = 29/175 (16%)
Query: 49 AHGSKVHSVAW-SCDGRRLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHAT 107
A SK+ + W S ++AS +F+ V ++ + + + + + S+D + +
Sbjct: 530 ASRSKLSGICWNSYIKSQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSID---YSSA 586
Query: 108 NPDLLSTASGDKTVRIWDART--------QKSQIM-----------LASGSFDKSVAIFA 148
+P LL++ S D +V++W K+ I LA GS D V +
Sbjct: 587 DPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYD 646
Query: 149 L-DKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQI 202
L + K L + GH+ +V + + + L ++S D T+++WD S I
Sbjct: 647 LRNPKLPLCTMI---GHSKTVSYVRF--VDSSTLVSSSTDNTLKLWDLSMSISGI 696
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 35.3 bits (81), Expect = 0.027
Identities = 27/110 (24%), Positives = 44/110 (40%), Gaps = 27/110 (24%)
Query: 90 VVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKSQIMLASGSFDKSVAIFAL 149
V +GHT V + +H + ++L++A D V +WD K+
Sbjct: 119 VHLQGHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERGKA------------------ 160
Query: 150 DKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQK 199
EV+ + H+ + L W+ + LL T S DK + I D R
Sbjct: 161 -------VEVI-KCHSDQITSLEWN-LDGSLLCTTSKDKKLNIIDPRDGT 201
Score = 35.3 bits (81), Expect = 0.029
Identities = 44/194 (22%), Positives = 79/194 (40%), Gaps = 34/194 (17%)
Query: 74 SVAIFALDKKGDL--NKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVRIWDARTQKS 131
S A+ G L N ++ G G + + ++ +P L TAS D T+ W +
Sbjct: 52 STAVLKHTDYGKLASNPPILL-GQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEG- 109
Query: 132 QIMLASGSFDKSVAIFALDKKGDLNKEVVYRGHTGSVDQLCWHATNPDLLSTASGDKTVR 191
L D V + +GHT V + +H + ++L++A D V
Sbjct: 110 ---LTQNISDPIVHL---------------QGHTKKVGIVSFHPSAMNVLASAGADMVVN 151
Query: 192 IWDARTQKS-QIIATKGENI-NITWAPNGNTIAVGNKEDLVTFIDVVKSLPPRERTLTSR 249
+WD K+ ++I + I ++ W +G+ + +K+ + ID PR+ T+ S
Sbjct: 152 VWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIID------PRDGTIVSS 205
Query: 250 GHLMET----RSLW 259
+ R LW
Sbjct: 206 VEAHASAKSQRCLW 219
Score = 30.6 bits (69), Expect = 0.95
Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 24/124 (19%)
Query: 50 HGSKVHSVAWSCDGRRLASGSFDKSVAIFALDKKGDLNKEVVYRG--HTGSVDQLCWHAT 107
H ++ S+ W+ DG L + S DK + I +D + + +V H + Q C A
Sbjct: 167 HSDQITSLEWNLDGSLLCTTSKDKKLNI--IDPR---DGTIVSSVEAHASAKSQRCLWAK 221
Query: 108 NPDLLSTASGDKT----VRIWDART-----------QKSQIMLASGSFDKSVAIFALDKK 152
DL+ T K+ + +WD R Q S + + FD+ + + K
Sbjct: 222 RKDLIITLGCSKSQQRQIMLWDTRKMASPYSTVDLDQSSALFIP--FFDEDTNLLYIGSK 279
Query: 153 GDLN 156
G+ N
Sbjct: 280 GEGN 283
>gnl|CDD|203719 pfam07676, PD40, WD40-like Beta Propeller Repeat. This family
appears to be related to the pfam00400 repeat This This
repeat corresponds to the RIVW repeat identified in cell
surface proteins [Adindla et al. Comparative and
Functional Genomics 2004; 5:2-16].
Length = 37
Score = 28.7 bits (65), Expect = 0.31
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 201 QIIATKGENINITWAPNGNTIA 222
++ T G +W+P+G +A
Sbjct: 3 RLTNTPGNEGEPSWSPDGKRLA 24
>gnl|CDD|235312 PRK04792, tolB, translocation protein TolB; Provisional.
Length = 448
Score = 31.1 bits (71), Expect = 0.50
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 56 SVAWSCDGRRLASGSFDKSVA-IFALD-KKGDLNKEVVYRGHTGS 98
S AWS DGR+LA SF+ A IF D K + G G+
Sbjct: 222 SPAWSPDGRKLAYVSFENRKAEIFVQDIYTQVREKVTSFPGINGA 266
>gnl|CDD|234377 TIGR03866, PQQ_ABC_repeats, PQQ-dependent catabolism-associated
beta-propeller protein. Members of this protein family
consist of seven repeats each of the YVTN family
beta-propeller repeat (see TIGR02276). Members occur
invariably as part of a transport operon that is
associated with PQQ-dependent catabolism of alcohols
such as phenylethanol.
Length = 300
Score = 30.4 bits (69), Expect = 0.90
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 184 ASGDKTVRIWDARTQKSQIIATKGENIN-ITWAPNGNTIAVGNKED-LVTFIDV 235
AS TV++ D T + G + PNG + + N++D LVT ID+
Sbjct: 49 ASDSDTVQVIDPATGEVLHTLPSGPDPELFALHPNGKILYIANEDDALVTVIDI 102
>gnl|CDD|179329 PRK01742, tolB, translocation protein TolB; Provisional.
Length = 429
Score = 30.6 bits (69), Expect = 0.96
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 56 SVAWSCDGRRLASGSFDKSVAIFALDKKGDLNKEVV--YRGHTGS 98
S AWS DG +LA SF+ + + ++VV +RGH G+
Sbjct: 208 SPAWSPDGSKLAYVSFENKKSQLVVHDLRSGARKVVASFRGHNGA 252
>gnl|CDD|217299 pfam02949, 7tm_6, 7tm Odorant receptor. This family is composed of
7 transmembrane receptors, that are probably drosophila
odorant receptors.
Length = 313
Score = 29.6 bits (67), Expect = 1.5
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 21/64 (32%)
Query: 102 LCWHATNPDLLSTASGD------------------KTVRIWDARTQKSQIMLASGSFDKS 143
C++ L+ AS + +T+ I+ R Q+ + A G F S
Sbjct: 245 YCYYGN---ELTEASEELANAIYSSNWYDASRRYRRTLLIFIMRAQRPITIKAGGFFPIS 301
Query: 144 VAIF 147
+ F
Sbjct: 302 LPTF 305
>gnl|CDD|184683 PRK14450, PRK14450, acylphosphatase; Provisional.
Length = 91
Score = 27.9 bits (62), Expect = 1.8
Identities = 13/29 (44%), Positives = 21/29 (72%), Gaps = 3/29 (10%)
Query: 217 NGN---TIAVGNKEDLVTFIDVVKSLPPR 242
NGN +A G+K+ L+ F+D+++S PPR
Sbjct: 39 NGNEVEVVAEGDKDSLLEFLDLLRSGPPR 67
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 29.2 bits (66), Expect = 2.7
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 23/92 (25%)
Query: 25 FHLVCKIDDYVKHF----------NTHNDIKEYQAHGSKVHSVAW--SCDGRRLASGSFD 72
F + Y ++F DI+ A G V A+ D
Sbjct: 209 FQ----TESYARNFLDLCSRLLGVTGDADIRFNGADGRIVKVGAFPIGIDPEEFERALKS 264
Query: 73 KSVAIFALDKKGDL--NKEVVYRGHTGSVDQL 102
SV L+ K +L NK+++ VD+L
Sbjct: 265 PSVQEKVLELKAELGRNKKLIV-----GVDRL 291
>gnl|CDD|165346 PHA03054, PHA03054, IMV membrane protein; Provisional.
Length = 72
Score = 26.9 bits (59), Expect = 2.9
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 226 KEDLVTFIDVVKSLPPRERTLTS 248
++DL FI++VKS+ E+T+TS
Sbjct: 17 EDDLTDFIEIVKSVLSDEKTVTS 39
>gnl|CDD|236491 PRK09377, tsf, elongation factor Ts; Provisional.
Length = 290
Score = 28.5 bits (65), Expect = 2.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 179 DLLSTASGDKTVRIWDARTQKSQIIATKGENINI 212
LL+ TV +ART+ I GENI++
Sbjct: 110 ALLALKLDGGTVE--EARTELIAKI---GENISL 138
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 29.1 bits (65), Expect = 3.0
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 40 THNDIKEYQAHGSKVHSVAWSCDGRRLA--SGSFDKSVAIFALDKK 83
T I + VH W R A SG SV++F L
Sbjct: 263 TERSIPVEKDLKDPVHDFTWEPLSSRFAVISGYMPASVSVFDLRGN 308
>gnl|CDD|211904 TIGR04108, HutX, putative heme utilization carrier protein HutX.
Members of this protein family are HutX, found paired
with HutW in some heme utilization loci although not
shown directly to be necessary for heme utilization.
This protein is homologous to the heme carrier protein
HemS, while its partner HutW is homologous to (but does
not complement) HemN, the radical SAM enzyme
oxygen-independent coproporphyrinogen III oxidase
involved in heme biosynthesis.
Length = 153
Score = 28.0 bits (63), Expect = 3.6
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 230 VTFIDVVKSLPPRERTLTSRGH---LMETRSLWG 260
V+ ++VV++LP TL +++ S WG
Sbjct: 22 VSELEVVRALPEEMVTLVPGDRFDEILQDLSGWG 55
>gnl|CDD|148467 pfam06868, DUF1257, Protein of unknown function (DUF1257). This
family contains hypothetical proteins of unknown
function that are approximately 120 residues long.
Family members include eukaryotic and bacterial
proteins.
Length = 104
Score = 26.8 bits (60), Expect = 5.5
Identities = 8/35 (22%), Positives = 19/35 (54%)
Query: 185 SGDKTVRIWDARTQKSQIIATKGENINITWAPNGN 219
G++ VR + +T ++ I+ + +I + NG+
Sbjct: 12 EGEQPVRGYRGQTTRADIVIPQNNGYDIGFRWNGD 46
>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 = 28.0 bits (63), Expect = 5.6
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 182 STASGDKTVRIWDARTQKSQIIAT-KGENINITWAPNGNTIAV 223
S SG + + D T + + +A+ G N ++P+G+ +AV
Sbjct: 208 SFESGKPEIYVQDLATGQREKVASFPGMNGAPAFSPDGSKLAV 250
>gnl|CDD|227471 COG5142, OXR1, Oxidation resistance protein [DNA replication,
recombination, and repair].
Length = 212
Score = 27.5 bits (61), Expect = 5.8
Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 4/84 (4%)
Query: 4 PVIQFHTPKSPEYKLLPSGSQFHLVCKIDDYVKHFNTHNDIKEYQAHGSKVHSVAWSCDG 63
H KS + LL + + D K+ + + +G + + S
Sbjct: 22 QFDLMHDGKSYKASLLTEEIVTRIRESLPDRYKYSTSWRLLYSLFENGFSLRTFYESFGE 81
Query: 64 RRLASGSFDKSVAIFAL-DKKGDL 86
F + + A DK GDL
Sbjct: 82 N---EWPFRRVGFVLACRDKDGDL 102
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 27.8 bits (63), Expect = 6.0
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 204 ATKGENINITWAPNGNTIAV 223
A K I +T P N+ +V
Sbjct: 86 AAKKRGIVVTNTPGANSNSV 105
>gnl|CDD|215555 PLN03063, PLN03063, alpha,alpha-trehalose-phosphate synthase
(UDP-forming); Provisional.
Length = 797
Score = 27.5 bits (61), Expect = 9.1
Identities = 20/48 (41%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 40 THNDIKEYQAHGSKVHSVAWSCDGRRLASGSFDKSVAIFALDKKGDLN 87
T ND+ EYQ S+VH + +GR GS SV I LD D N
Sbjct: 324 TRNDVPEYQKLKSQVHELVGRINGR---FGSV-SSVPIHHLDCSVDFN 367
>gnl|CDD|235083 PRK02889, tolB, translocation protein TolB; Provisional.
Length = 427
Score = 27.3 bits (61), Expect = 9.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 56 SVAWSCDGRRLASGSFDK 73
S AWS DG +LA SF+
Sbjct: 200 SPAWSPDGTKLAYVSFES 217
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
0.317 0.132 0.406
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: 12,946,704
Number of extensions: 1165575
Number of successful extensions: 1088
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1016
Number of HSP's successfully gapped: 48
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
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 (21.7 bits)
S2: 58 (26.1 bits)