RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16627
(713 letters)
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 399 bits (1027), Expect = e-127
Identities = 222/623 (35%), Positives = 349/623 (56%), Gaps = 17/623 (2%)
Query: 97 GDPYRRPEIQSATVEYLATADYTVRDPPQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQL 156
D Y RPE++S V++LA +Y++R PP P +Y+FL+DVS A ++G + +L L
Sbjct: 248 SDRYSRPELKSGVVDFLAPKEYSLRQPP-PPVYVFLIDVSFEAIKNGLVKAAIRAILENL 306
Query: 157 KSMPG-DRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSPEN-ILVNLSEC 214
+P D RT IAII +DS++HF+ L+ +I++D+D+ FLP P ++ L C
Sbjct: 307 DQIPNFDPRTKIAIICFDSSLHFFKLSPD-LDEQMLIVSDLDEPFLPFPSGLFVLPLKSC 365
Query: 215 YDMIVDLLKQLPGKFKDSLDSGSALGPALQAAFKLLQPTGGRITIFQTCLPNRGPGALQS 274
+I LL ++P F+D+ +ALGPAL+AA L+ TGG+I +F + LPN G G LQ
Sbjct: 366 KQIIETLLDRVPRIFQDNKSPKNALGPALKAAKSLIGGTGGKIIVFLSTLPNMGIGKLQL 425
Query: 275 RENPNQRSNDDPPHMNPATDFYKKIALECTSFYIAVDLFILNSQYVDLATLSGVSKFSSG 334
RE+ ++ FYK+ A+EC+ I+VDLF+ + Y+D+ATLS + +++ G
Sbjct: 426 REDKESS------LLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGG 479
Query: 335 CIHHIPLYSGKNMSHVYQLDRMFSRYLTRKIGFESVMRIRCTKGMSIHTFHGNFFVRSTD 394
+ P +S + +L +L+ +IG+E+VMR+RC+ G+ + +F+GNFF RS+D
Sbjct: 480 QTYFYPNFSATRPNDATKLANDLVSHLSMEIGYEAVMRVRCSTGLRVSSFYGNFFNRSSD 539
Query: 395 LLALPNVNPDAGYGIQISIDENLTHIQYACFQVAVLYTSSKGDRRIRVHTLCLPVVSNIN 454
L A + D ++ SIDE L FQVA+LYT + G+RRIRV L LP S+I
Sbjct: 540 LCAFSTMPRDTSLLVEFSIDEKLMT-SDVYFQVALLYTLNDGERRIRVVNLSLPTSSSIR 598
Query: 455 DVLVGADQACIAGLLAKMAVDRSLQHSLSDAREAFLNVVCDVLSTYKMTQAGHLTGSLLA 514
+V ADQ IA +LAK A ++L SL +AR + D+L YK T + L
Sbjct: 599 EVYASADQLAIACILAKKASTKALNSSLKEARVLINKSMVDILKAYKKELVKSNTSTQLP 658
Query: 515 -PSSLKVLPLYVLALLKHPAFRIGQSTRLDDRLFAMTEMKCLPLNSLMLSIYPELYPIHT 573
P++LK+LPL +LALLK AFR G ST D R+ A+ + LPL LM +IYP LY +H
Sbjct: 659 LPANLKLLPLLMLALLKSSAFRSG-STPSDIRISALNRLTSLPLKQLMRNIYPTLYALHD 717
Query: 574 LDQDPTIEWNELQVPIPRILQLSAERLQATGTYLLNMPDLIIILVRHGTSPAICSGLFGF 633
+ +E + +P + ++ L++ G YL++ I + P++ LFG
Sbjct: 718 M-PIEAGLPDEGLLVLPSPINATSSLLESGGLYLIDTGQKIFLWFGKDAVPSLLQDLFGV 776
Query: 634 QSVAQMPETLFELPQLETQLSLKLNSFIS--YLNDDKAYVSPVKVIKDSSPD-RMEFYDK 690
S++ +P F LP + + ++ + I +D + + V V P R+ F+
Sbjct: 777 DSLSDIPSGKFTLPPTGNEFNERVRNIIGELRSVNDDSTLPLVLVRGGGDPSLRLWFFST 836
Query: 691 LIEDKNAGGMAYYEFLLRIREQV 713
L+EDK +Y ++L + E++
Sbjct: 837 LVEDKTLNIPSYLDYLQILHEKI 859
>gnl|CDD|238756 cd01479, Sec24-like, Sec24-like: Protein and membrane traffic in
eukaryotes is mediated by at least in part by the
budding and fusion of intracellular transport vesicles
that selectively carry cargo proteins and lipids from
donor to acceptor organelles. The two main classes of
vesicular carriers within the endocytic and the
biosynthetic pathways are COP- and clathrin-coated
vesicles. Formation of COPII vesicles requires the
ordered assembly of the coat built from several
cytosolic components GTPase Sar1, complexes of
Sec23-Sec24 and Sec13-Sec31. The process is initiated by
the conversion of GDP to GTP by the GTPase Sar1 which
then recruits the heterodimeric complex of Sec23 and
Sec24. This heterodimeric complex generates the
pre-budding complex. The final step leading to membrane
deformation and budding of COPII-coated vesicles is
carried by the heterodimeric complex Sec13-Sec31. The
members of this CD belong to the Sec23-like family. Sec
24 is very similar to Sec23. The Sec23 and Sec24
polypeptides fold into five distinct domains: a
beta-barrel, a zinc finger, a vWA or trunk, an all
helical region and a carboxy Gelsolin domain. The
members of this subgroup carry a partial MIDAS motif and
have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 244
Score = 314 bits (806), Expect = e-103
Identities = 120/244 (49%), Positives = 168/244 (68%), Gaps = 2/244 (0%)
Query: 124 PQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDR-RTSIAIITYDSAVHFYSLA 182
PQPA+Y+FL+DVS A +SG L T CE LL+ L ++PGD RT + IT+DS +HF++L
Sbjct: 1 PQPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLK 60
Query: 183 EGQTQPSQMILTDIDDIFLPSPENILVNLSECYDMIVDLLKQLPGKFKDSLDSGSALGPA 242
QP M+++D+DD FLP P+ +LVNL E +I DLL Q+P F+D+ ++ SALGPA
Sbjct: 61 SSLEQPQMMVVSDLDDPFLPLPDGLLVNLKESRQVIEDLLDQIPEMFQDTKETESALGPA 120
Query: 243 LQAAFKLLQPTGGRITIFQTCLPNRGPGALQSRENPNQRSNDD-PPHMNPATDFYKKIAL 301
LQAAF LL+ TGG+I +FQ+ LP G G L+SRE+P S D + P TDFYKK+AL
Sbjct: 121 LQAAFLLLKETGGKIIVFQSSLPTLGAGKLKSREDPKLLSTDKEKQLLQPQTDFYKKLAL 180
Query: 302 ECTSFYIAVDLFILNSQYVDLATLSGVSKFSSGCIHHIPLYSGKNMSHVYQLDRMFSRYL 361
EC I+VDLF+ ++QYVD+ATL +S+ + G +++ P ++ + V +L +RYL
Sbjct: 181 ECVKSQISVDLFLFSNQYVDVATLGCLSRLTGGQVYYYPSFNFSAPNDVEKLVNELARYL 240
Query: 362 TRKI 365
TRKI
Sbjct: 241 TRKI 244
>gnl|CDD|238745 cd01468, trunk_domain, trunk domain. COPII-coated vesicles carry
proteins from the endoplasmic reticulum to the Golgi
complex. This vesicular transport can be reconstituted
by using three cytosolic components containing five
proteins: the small GTPase Sar1p, the Sec23p/24p
complex, and the Sec13p/Sec31p complex. This domain is
known as the trunk domain and has an alpha/beta vWA fold
and forms the dimer interface. Some members of this
family possess a partial MIDAS motif that is a
characteristic feature of most vWA domain proteins.
Length = 239
Score = 256 bits (657), Expect = 9e-81
Identities = 103/230 (44%), Positives = 140/230 (60%), Gaps = 5/230 (2%)
Query: 124 PQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE 183
PQP +++F++DVS A + G L + E LL L +PGD R + +ITYDS VHFY+L+
Sbjct: 1 PQPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSS 60
Query: 184 GQTQPSQMILTDIDDIFLPSPENILVNLSECYDMIVDLLKQLPGKFKD--SLDSGSALGP 241
QP +++D+ D+FLP P+ LV LSEC +I DLL+QLP F + LGP
Sbjct: 61 DLAQPKMYVVSDLKDVFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPVPTHRPERCLGP 120
Query: 242 ALQAAFKLLQPT--GGRITIFQTCLPNRGPGALQSRENPNQ-RSNDDPPHMNPATDFYKK 298
ALQAAF LL+ T GGRI +FQ LP GPG L+SRE+ RS+D+ + PAT FYK
Sbjct: 121 ALQAAFLLLKGTFAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSHDEAQLLKPATKFYKS 180
Query: 299 IALECTSFYIAVDLFILNSQYVDLATLSGVSKFSSGCIHHIPLYSGKNMS 348
+A EC I VDLF + YVD+ATL ++K + G ++ + N
Sbjct: 181 LAKECVKSGICVDLFAFSLDYVDVATLKQLAKSTGGQVYLYDSFQAPNDG 230
>gnl|CDD|147125 pfam04811, Sec23_trunk, Sec23/Sec24 trunk domain. COPII-coated
vesicles carry proteins from the endoplasmic reticulum
to the Golgi complex. This vesicular transport can be
reconstituted by using three cytosolic components
containing five proteins: the small GTPase Sar1p, the
Sec23p/24p complex, and the Sec13p/Sec31p complex. This
domain is known as the trunk domain and has an
alpha/beta vWA fold and forms the dimer interface.
Length = 241
Score = 239 bits (613), Expect = 2e-74
Identities = 94/243 (38%), Positives = 140/243 (57%), Gaps = 7/243 (2%)
Query: 124 PQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE 183
PQP ++LF++DVS A +SG L + E LL L +PGD R + IT+DS VHF++L+
Sbjct: 1 PQPPVFLFVIDVSYNAIKSGLLAALKESLLQSLDLLPGDPRALVGFITFDSTVHFFNLSS 60
Query: 184 GQTQPSQMILTDIDDIFLPSPENILVNLSECYDMIVDLLKQLPGKFKDSLDSGSALGPAL 243
QP ++++D+ D+FLP P+ LV LSEC ++ DLL++LP F + LGPAL
Sbjct: 61 SLRQPKMLVVSDLQDMFLPLPDRFLVPLSECRFVLEDLLEELPRMFPVTKRPERCLGPAL 120
Query: 244 QAAFKLLQ--PTGGRITIFQTCLPNRGP-GALQSRENPNQR--SNDDPPHMNPATDFYKK 298
QAA LL+ TGG+I +FQ LP GP G L+SR + + + + A FYK
Sbjct: 121 QAAVLLLKAAFTGGKIMLFQGGLPTVGPGGKLKSRLDESHHDTDKEKAKLVKKADKFYKS 180
Query: 299 IALECTSFYIAVDLFILNSQYVDLATLSGVSKFSSGCIHHIPLYSGKNMSHVYQLDRMFS 358
+A EC + +VDLF + YVD+A L +S+ + G ++ P + + ++ D
Sbjct: 181 LAKECVAQGHSVDLFAFSLDYVDVAELGCLSRLTGGQVYLYPSFQADVDTSKFKQD--LQ 238
Query: 359 RYL 361
RY
Sbjct: 239 RYF 241
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 137 bits (346), Expect = 3e-33
Identities = 125/512 (24%), Positives = 247/512 (48%), Gaps = 41/512 (8%)
Query: 126 PAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQ 185
P ++F+++ S A + YT+ E + ++++ + T IAIIT++S+++FY G+
Sbjct: 952 PPYFVFVVECSYNAIYNNITYTILEGIRYAVQNVKCPQ-TKIAIITFNSSIYFYHCKGGK 1010
Query: 186 TQPSQ-------------MILTDIDDIFLPSP-ENILVNLSECYDMIVDLLKQLPGKFKD 231
+ ++++D+DD FLP P E++ E D I L+ +
Sbjct: 1011 GVSGEEGDGGGGSGNHQVIVMSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSVSTT 1070
Query: 232 SLDSGSALGPALQAAFKLLQPTGG--RITIFQTCLPNRGPGALQSRENPNQRSNDDPPHM 289
GS AL+ A +L+ G I +F T PN G GA++ + Q + +
Sbjct: 1071 MQSYGSCGNSALKIAMDMLKERNGLGSICMFYTTTPNCGIGAIKELKKDLQENFLEVKQ- 1129
Query: 290 NPATDFYKKIALECTSFYIAVDLFILNSQYVDLA--TLSGVSKFSSGCIHHIPLYS-GKN 346
FY + L+ +F I+VD+FI++S V + +L V++ + G I + + K+
Sbjct: 1130 ---KIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQNTGGKILFVENFLWQKD 1186
Query: 347 MSHVYQLDRMFSRYLTRKIGFESVMRIRCTKGMSIHTF---HGNF-FVRSTDLLALPNVN 402
+Y + + I + +++R + MS+ + NF + S D + +P +
Sbjct: 1187 YKEIYM--NIMDTLTSEDIAYCCELKLRYSHHMSVKKLFCCNNNFNSIISVDTIKIPKIR 1244
Query: 403 PDAGYGIQISIDENLTHIQYACFQVAVLYTSSKGDRRIRVHTLCLPVVSNINDVLVGADQ 462
D + ++ + + FQ A +YT+ GDR +R+HT + + S+++ V D
Sbjct: 1245 HDQTFAFLLNYSDISESKKQIYFQCACIYTNLWGDRFVRLHTTHMNLTSSLSTVFRYTDA 1304
Query: 463 ACIAGLLAKMAVDRSLQHSLSDAREAFLNVVCDVLSTYKMTQAGHL-TGSLLAPSSLKVL 521
+ +L K L + + + ++ + +L +Y++ A +G L+ P +LK+L
Sbjct: 1305 EALMNILIKQLCTNILHN--DNYSKIIIDNLAAILFSYRINCASSAHSGQLILPDTLKLL 1362
Query: 522 PLYVLALLKHPAFRIGQSTRLDDRLFAMTEMKCLPLNSLMLSIYPELYPIHTLDQDPTIE 581
PL+ +LLKH + + D +++++ ++ +P+ S +L +YP +Y IH + T E
Sbjct: 1363 PLFTSSLLKHNVTK--KEILHDLKVYSLIKLLSMPIISSLLYVYPVMYVIHI--KGKTNE 1418
Query: 582 WNELQVP----IPRILQLSAERLQATGTYLLN 609
+ + V IP+ + SAE++ + G YLL+
Sbjct: 1419 IDSMDVDDDLFIPKTIPSSAEKIYSNGIYLLD 1450
>gnl|CDD|219707 pfam08033, Sec23_BS, Sec23/Sec24 beta-sandwich domain.
Length = 86
Score = 117 bits (295), Expect = 2e-31
Identities = 41/86 (47%), Positives = 55/86 (63%), Gaps = 1/86 (1%)
Query: 366 GFESVMRIRCTKGMSIHTFHGNFFVRS-TDLLALPNVNPDAGYGIQISIDENLTHIQYAC 424
GF +V+R+R +KG+ + F GNFF RS D LP+++PD Y + IDE L + A
Sbjct: 1 GFNAVLRVRTSKGLKVSGFIGNFFSRSSGDTWKLPSLDPDTSYAFEFDIDEPLDSGKQAY 60
Query: 425 FQVAVLYTSSKGDRRIRVHTLCLPVV 450
Q A+LYT S G+RRIRV T+ LPV
Sbjct: 61 IQFALLYTHSSGERRIRVTTVALPVT 86
>gnl|CDD|218277 pfam04815, Sec23_helical, Sec23/Sec24 helical domain. COPII-coated
vesicles carry proteins from the endoplasmic reticulum
to the Golgi complex. This vesicular transport can be
reconstituted by using three cytosolic components
containing five proteins: the small GTPase Sar1p, the
Sec23p/24p complex, and the Sec13p/Sec31p complex. This
domain is composed of five alpha helices.
Length = 103
Score = 97.2 bits (243), Expect = 3e-24
Identities = 46/104 (44%), Positives = 64/104 (61%), Gaps = 2/104 (1%)
Query: 462 QACIAGLLAKMAVDRSLQHSLSDAREAFLNVVCDVLSTY-KMTQAGHLTGSLLAPSSLKV 520
Q IA LLAK AV+++L SL DAR + D+L+ Y K + +G L+ P SLK+
Sbjct: 1 QEAIAVLLAKKAVEKALTSSLKDARRWLDKKLVDILAAYRKYCASSSSSGQLILPESLKL 60
Query: 521 LPLYVLALLKHPAFRIGQSTRLDDRLFAMTEMKCLPLNSLMLSI 564
LPLY+LALLK PA R G + D+R +A + LP+ +L+L I
Sbjct: 61 LPLYMLALLKSPALR-GGNVSPDERAYARCLLLSLPVENLLLMI 103
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 55.7 bits (135), Expect = 6e-08
Identities = 54/250 (21%), Positives = 86/250 (34%), Gaps = 49/250 (19%)
Query: 106 QSATVEYLATADYTVRDPPQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDRRT 165
Q TVEY T P P +++F++D I + G L + + L P +
Sbjct: 106 QYTTVEY--TLPPGSGGAPSPPVFVFVVDTCMIEEELGALKSALLQAIALL---PENAL- 159
Query: 166 SIAIITYDSAVHFYSLAEG-----------------------------QTQPSQMILTDI 196
+ +IT+ + VH + L + I
Sbjct: 160 -VGLITFGTHVHVHELGFSECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGAR 218
Query: 197 DDIFLPSPENILVNLSEC---YDMIVDLLKQLPGKFKDSLDSGSALGPALQAAFKLLQP- 252
D + L+ SEC + ++ L++ P G AL A LL
Sbjct: 219 DGLSSSGVNRFLLPASECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGAC 278
Query: 253 ---TGGRITIFQTCLPNRGPGALQSRENPNQ-RS-----NDDPPHMNPATDFYKKIALEC 303
TG RI F GPGA+ S++ RS D P+ A FY+ +A +
Sbjct: 279 VPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHKDLDKDAAPYYKKAVKFYEGLAKQL 338
Query: 304 TSFYIAVDLF 313
+ +D+F
Sbjct: 339 VAQGHVLDVF 348
Score = 33.0 bits (76), Expect = 0.68
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 425 FQVAVLYTSSKGDRRIRVHTLCLPVV--SNINDVLVGADQACIAGLLAKMAVDR 476
Q Y S G R+RV T+ V S+ +++ G DQ A ++A++A +
Sbjct: 480 LQFLTRYQHSNGQTRLRVTTVTRRWVEGSSSEELVAGFDQEAAAVVMARLASHK 533
>gnl|CDD|227380 COG5047, SEC23, Vesicle coat complex COPII, subunit SEC23
[Intracellular trafficking and secretion].
Length = 755
Score = 53.3 bits (128), Expect = 3e-07
Identities = 81/443 (18%), Positives = 158/443 (35%), Gaps = 88/443 (19%)
Query: 103 PEIQSATVEYLATADYTVRDPPQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGD 162
QS+T+EY + P ++ F++D + L + L+ L +P +
Sbjct: 104 LLPQSSTIEYT-----LSKPVILPPVFFFVVDACCDEEELTALK---DSLIVSLSLLPPE 155
Query: 163 RRTSIAIITYDSAVHFYSLA----------EGQTQPSQMILTD----------------I 196
+ +ITY +++ + L G + ++ L + I
Sbjct: 156 --ALVGLITYGTSIQVHELNAENHRRSYVFSGNKEYTKENLQELLALSKPTKSGGFESKI 213
Query: 197 DDIFLPSPENILVNLSECYDMIVDLLKQL-------PGKFKDSLDSGSALGPALQAAFKL 249
I + L+ +C ++++L+QL P + +GSAL A +
Sbjct: 214 SGIGQFASSRFLLPTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQC 273
Query: 250 LQPTGGRITIFQTCLPNRGPGALQSRE------NPNQRSNDDPPHMNPATDFYKKIALEC 303
G I +F GPG + S E + + +D H AT FYK +A
Sbjct: 274 FPNAGCHIVLFAGGPCTVGPGTVVSTELKEPMRSHHDIESDSAQHSKKATKFYKGLAERV 333
Query: 304 TSFYIAVDLFILNSQYVDLATLSGVSKFSSGCIHHIPLYSGKNMSHVYQLDRM---FSRY 360
+ A+D+F + + + ++ + G + +S + F R
Sbjct: 334 ANQGHALDIFAGCLDQIGIMEMEPLTTSTGGAL---------VLSDSFTTSIFKQSFQRI 384
Query: 361 LTR------KIGFESVMRIRCTKGMSIHTFHGN---------------FFVRSTDLLALP 399
R K+GF + M ++ +K + I G+ + +T+ +
Sbjct: 385 FNRDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMA 444
Query: 400 NVNPDAGYGI--QISIDENLTHIQYACF---QVAVLYTSSKGDRRIRVHTLCLPVVSNIN 454
+++P + Y + +I++ Q Q Y S G RIRV T+
Sbjct: 445 SLSPKSNYALYFEIALGAASGSAQRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTDGGL 504
Query: 455 DVLVGA-DQACIAGLLAKMAVDR 476
+ + DQ A +A++A +
Sbjct: 505 PKINRSFDQEAAAVFMARIAAFK 527
>gnl|CDD|238755 cd01478, Sec23-like, Sec23-like: Protein and membrane traffic in
eukaryotes is mediated by at least in part by the
budding and fusion of intracellular transport vesicles
that selectively carry cargo proteins and lipids from
donor to acceptor organelles. The two main classes of
vesicular carriers within the endocytic and the
biosynthetic pathways are COP- and clathrin-coated
vesicles. Formation of COPII vesicles requires the
ordered assembly of the coat built from several
cytosolic components GTPase Sar1, complexes of
Sec23-Sec24 and Sec13-Sec31. The process is initiated by
the conversion of GDP to GTP by the GTPase Sar1 which
then recruits the heterodimeric complex of Sec23 and
Sec24. This heterodimeric complex generates the
pre-budding complex. The final step leading to membrane
deformation and budding of COPII-coated vesicles is
carried by the heterodimeric complex Sec13-Sec31. The
members of this CD belong to the Sec23-like family. Sec
23 is very similar to Sec24. The Sec23 and Sec24
polypeptides fold into five distinct domains: a
beta-barrel, a zinc finger, a vWA or trunk, an all
helical region and a carboxy Gelsolin domain. The
members of this subgroup lack the consensus MIDAS motif
but have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 267
Score = 46.2 bits (110), Expect = 2e-05
Identities = 55/236 (23%), Positives = 89/236 (37%), Gaps = 55/236 (23%)
Query: 124 PQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLA- 182
P ++LF++D + L E L+ L +P + + +IT+ + V + L
Sbjct: 1 TSPPVFLFVVDTCMDEEELDALK---ESLIMSLSLLPPN--ALVGLITFGTMVQVHELGF 55
Query: 183 ---------EGQTQPSQMILTDIDDIFLPS-------------------PENILVNLSEC 214
G + + D+ + P+ L+ +S+C
Sbjct: 56 EECSKSYVFRGNKDYTAKQIQDMLGLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQC 115
Query: 215 YDMIVDLLKQL-------PGKFKDSLDSGSALGPA---LQAAFKLLQPTGGRITIFQTCL 264
+ DLL+QL P + +G AL A L+A F TG RI +F
Sbjct: 116 EFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACFP---NTGARIMLFAGGP 172
Query: 265 PNRGPGALQSRE--NPNQRS-----NDDPPHMNPATDFYKKIALECTSFYIAVDLF 313
GPGA+ S E +P RS D+ + A FY +A + AVD+F
Sbjct: 173 CTVGPGAVVSTELKDP-IRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIF 227
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 35.5 bits (82), Expect = 0.12
Identities = 22/98 (22%), Positives = 30/98 (30%), Gaps = 16/98 (16%)
Query: 1 AQPGNYPSVPVGY------------PSLNQAGYQQQQQQQQQQTLNSQFSNLSVNQGMNK 48
QP YP P G+ PS A Q QQ Q ++Q M
Sbjct: 198 EQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPP 257
Query: 49 MWGYEPHDLLNTRDILPATKVEPPPIRLPQNLPEIHEQ 86
P + P + +PPP P P + +
Sbjct: 258 PPPQPPQQ----QQQPPQPQAQPPPQNQPTPHPGLPQG 291
Score = 30.1 bits (68), Expect = 5.6
Identities = 15/86 (17%), Positives = 21/86 (24%), Gaps = 15/86 (17%)
Query: 2 QPGNYPSVPVGYPSLNQAGYQQQQQQQQQQTLNSQFSNLSVNQGMNKMWGYEPHDLLNTR 61
+P G P A QQ +Q + + +
Sbjct: 173 PQPPQQVLPQGMPPRQAAFPQQGPPEQPPG---------------YPQPPQGHPEQVQPQ 217
Query: 62 DILPATKVEPPPIRLPQNLPEIHEQF 87
LPA P LP LP+
Sbjct: 218 QFLPAPSQAPAQPPLPPQLPQQPPPL 243
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins
is found in bacteria. Proteins in this family are
typically between 115 and 181 amino acids in length.
There are two completely conserved residues (F and G)
that may be functionally important.
Length = 110
Score = 32.4 bits (74), Expect = 0.23
Identities = 17/53 (32%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 2 QPGNYPSVPVGYPSLNQAGYQQQQQQQQQQTLNSQFSN----LSVNQGMNKMW 50
Q P P YP QQQQ Q + SQF N N+ MN +
Sbjct: 41 QGHFMPPQPQPYPK----QSPQQQQPPQFSSFLSQFKNSDGTFDFNKMMNTVG 89
>gnl|CDD|227823 COG5536, BET4, Protein prenyltransferase, alpha subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 328
Score = 31.0 bits (70), Expect = 2.0
Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 9/86 (10%)
Query: 49 MWGYEPHDLLNTRDILPATKVEPPPIRLPQNLPEIHEQFLYDRNTEMFG-DPYRRPEIQS 107
M G + DL I+ ++ + +NLP +H + R Q
Sbjct: 246 MIGEKVEDLGKYIVIINGKEL---DLGPKENLPCLHSLLELEFLCHAEKALLTERDIEQK 302
Query: 108 ATVEYLATADYTVRDPPQPAMYLFLL 133
A VE DP + +Y L
Sbjct: 303 ALVELAIKV-----DPARRNLYSTLH 323
>gnl|CDD|223716 COG0643, CheA, Chemotaxis protein histidine kinase and related
kinases [Cell motility and secretion / Signal
transduction mechanisms].
Length = 716
Score = 31.1 bits (71), Expect = 2.6
Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 17/84 (20%)
Query: 541 RLDDRLFAMTEMKCLPLNSLMLSIYPELYPIHTLDQDPTIEWNELQVPIPR---ILQLSA 597
R+ ++A +PL S+ ++ + I ++ + +P+ R +L +
Sbjct: 584 RVGGEVYA------IPLASVEETLRIDPEDIKPVEGQEVLRLRGEVLPLVRLGELLNVPP 637
Query: 598 ERLQATGTYLLNMPDLIIILVRHG 621
+ +++VR G
Sbjct: 638 ASPEPE--------QGPVVIVRSG 653
>gnl|CDD|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain. VWA
domains in extracellular eukaryotic proteins mediate
adhesion via metal ion-dependent adhesion sites (MIDAS).
Intracellular VWA domains and homologues in prokaryotes
have recently been identified. The proposed VWA domains
in integrin beta subunits have recently been
substantiated using sequence-based methods.
Length = 175
Score = 29.7 bits (67), Expect = 3.7
Identities = 24/123 (19%), Positives = 39/123 (31%), Gaps = 35/123 (28%)
Query: 131 FLLDVSQ-IAAQSGYLYTVCEVLLNQLKSMP-GDRRTSIAIITYDSAVHFYSLAEGQTQP 188
FLLD S + E +L ++ + G + ++T+
Sbjct: 4 FLLDGSGSMGGN--RFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAR----------- 50
Query: 189 SQMILTDIDDIFLPSPENILVNLSECYDMIVDLLKQLPGKFKDSLDSGSALGPALQAAFK 248
+N S D +++ L L K L G+ LG ALQ A +
Sbjct: 51 ----------------VLFPLNDSRSKDALLEALASLSYK----LGGGTNLGAALQYALE 90
Query: 249 LLQ 251
L
Sbjct: 91 NLF 93
>gnl|CDD|221872 pfam12954, DUF3843, Protein of unknown function (DUF3843). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 325
Score = 30.0 bits (68), Expect = 4.0
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 31 QTLNSQFSNLSVNQGMNKMWGYEPHDLLNTRDILPATKVEPPPIRLPQNLPEIHEQFL 88
L F +N G + ++ L RD+L PPI + LPE +E+FL
Sbjct: 140 GLLEEAFETAPINDGPSSLF------LHEGRDLLKMPFTPLPPIEPEEKLPEDYEKFL 191
>gnl|CDD|220172 pfam09309, FCP1_C, FCP1, C-terminal. The C-terminal domain of
FCP-1 is required for interaction with the carboxy
terminal domain of RAP74. Interaction relies extensively
on van der Waals contacts between hydrophobic residues
situated within alpha-helices in both domains.
Length = 263
Score = 30.0 bits (67), Expect = 4.5
Identities = 28/121 (23%), Positives = 41/121 (33%), Gaps = 31/121 (25%)
Query: 63 ILPATKVEPPPIRL-PQNLPEIHEQFLYDRNTEMF---------GDPYRRPEIQSATVEY 112
+L P PI Q PE+ +YD T P+ P S+ ++
Sbjct: 35 VLQTALFHPAPIHPKAQPGPEVR---IYDPVTGKLIRRGPQASAPAPFHAPG-PSSLPDH 90
Query: 113 LATADYTVRDPPQPAMYLFLLDVSQIAAQSG--------------YLYTVCEVLLNQLKS 158
+ + P QP M+ SQ Q G LYT+C+ L+S
Sbjct: 91 GEPSSFRAVQPHQPQMFGEEAPSSQDGEQPGPSRRKRQPSMSETMPLYTLCK---EDLES 147
Query: 159 M 159
M
Sbjct: 148 M 148
>gnl|CDD|184029 PRK13399, PRK13399, fructose-1,6-bisphosphate aldolase;
Provisional.
Length = 347
Score = 29.4 bits (66), Expect = 6.6
Identities = 23/59 (38%), Positives = 25/59 (42%), Gaps = 12/59 (20%)
Query: 590 PRILQLSA-ERLQATGTYLLNM--------PDLIIIL-VRHGTSPAICSGLF--GFQSV 636
P ILQ S R A L +M PD+ I L HG SPA C GF SV
Sbjct: 44 PVILQASRGARKYAGDAMLRHMVLAAAEMYPDIPICLHQDHGNSPATCQSAIRSGFTSV 102
>gnl|CDD|226036 COG3505, VirD4, Type IV secretory pathway, VirD4 components
[Intracellular trafficking and secretion].
Length = 596
Score = 29.7 bits (67), Expect = 7.2
Identities = 20/113 (17%), Positives = 33/113 (29%), Gaps = 15/113 (13%)
Query: 107 SATVEYLATADYTVRDP---PQPAMYLFLLDVSQIAAQSGYLYTVCEVLLNQLKSMPGDR 163
+ ++ L +RD + + L + A + L Q S D
Sbjct: 271 TQAIKGLEGVFGRLRDILSSTELSSLAMLTRILLGDALPW-----VKAALGQFFSNKTDE 325
Query: 164 RTSIAIITYDSAVHFYSLAE--GQTQPSQMILTDI-----DDIFLPSPENILV 209
TS + T SA+ T S + D+ F P+ I
Sbjct: 326 ETSGVLSTASSALTLLMNPLVAAATSGSDFDIRDLRKKKTTVYFGLDPDRISR 378
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. Mediator is a
large complex of up to 33 proteins that is conserved
from plants to fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 29.2 bits (65), Expect = 8.8
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 22 QQQQQQQQQQTLNSQFSNLSVNQGMNKMWGYEPHDLLN 59
Q Q QQ Q N Q ++N GMN + ++ DL N
Sbjct: 337 NQNQTPQQLQPQNQQ----NMNMGMNDVNNFDLLDLNN 370
>gnl|CDD|233760 TIGR02171, Fb_sc_TIGR02171, Fibrobacter succinogenes paralogous
family TIGR02171. This model describes a paralogous
family of the rumen bacterium Fibrobacter succinogenes.
Eleven members are found in Fibrobacter succinogenes
S85, averaging over 900 amino acids in length. More than
half are predicted lipoproteins. The function is
unknown.
Length = 912
Score = 29.4 bits (66), Expect = 9.1
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 436 GDRRIRVHTLCLPVVSNINDVLVGADQACIAGLLAKMAVDRSL 478
G R +R H V + +DV +QAC A LAK R+L
Sbjct: 469 GARLLRAHVANEDVDNGKDDVWYNGEQACNAS-LAKDGSKRTL 510
>gnl|CDD|223555 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
protein subunit [Energy production and conversion].
Length = 234
Score = 28.8 bits (65), Expect = 9.3
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 660 FISYLNDDKAYVSP---VKVIKDSSPDRMEFYDKL 691
+ L + + P VI+D D EFY+KL
Sbjct: 76 LMKDLEEGVITIEPLPNFPVIRDLVVDMEEFYEKL 110
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
0.321 0.137 0.402
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,534,780
Number of extensions: 3594451
Number of successful extensions: 3726
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3653
Number of HSP's successfully gapped: 38
Length of query: 713
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 609
Effective length of database: 6,324,786
Effective search space: 3851794674
Effective search space used: 3851794674
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: 63 (28.2 bits)