RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17260
(679 letters)
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 341 bits (876), Expect = e-107
Identities = 146/334 (43%), Positives = 188/334 (56%), Gaps = 38/334 (11%)
Query: 188 EERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKPDLPPLQYEPLLCMRNQCRAILN 247
E DG+R +WNVWPSSK+EAS+ V+P+ LY PLK P+LP L Y+PL C CRA+LN
Sbjct: 7 EAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPELPVLPYDPLRCRT--CRAVLN 64
Query: 248 PLCQVDYKSKLWVCNFCFQRNAFPPQYAAITEQHQPAELHPQFTTIEYTIPKM---QCAP 304
P C+VD+++K+W+C FCFQRN FPP Y++I+E + PAEL PQ+TT+EYT+P +P
Sbjct: 65 PYCRVDFQAKIWICPFCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPPGSGGAPSP 124
Query: 305 LVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHELGCEGISRSYV 364
VF+FVVDTCM EEELGAL+ +L +++LLP+NALVGLITFG V VHELG S+SYV
Sbjct: 125 PVFVFVVDTCMIEEELGALKSALLQAIALLPENALVGLITFGTHVHVHELGFSECSKSYV 184
Query: 365 FRGTKDVPAQRLQEML--RIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLL 422
FRG K+V ++ E L K + A +FL P CE L
Sbjct: 185 FRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPASECEFTLNSAL 244
Query: 423 AALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL------------------------- 457
LQK P V G TG A +A GLL +
Sbjct: 245 EELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSK 304
Query: 458 -----IRSHNDIHKGNNKLPGRMATKITKGLALR 486
IRSH D+ K + A K +GLA +
Sbjct: 305 DLSEPIRSHKDLDKDAAPY-YKKAVKFYEGLAKQ 337
Score = 189 bits (482), Expect = 4e-51
Identities = 63/137 (45%), Positives = 89/137 (64%), Gaps = 2/137 (1%)
Query: 515 GAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGA-PIPQGGP 573
GAIGPC SL K VSD ++G GGT +WK+C L T+LA+FFE+ N + P P G
Sbjct: 418 GAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQSNPQPPGQQ 477
Query: 574 GCIQFITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQ 633
+QF+T YQ +G+ ++RVTT+ R W + + + + +GFDQEAAAV+M R+ ++ E
Sbjct: 478 FFLQFLTRYQHSNGQTRLRVTTVTRRWVEG-SSSEELVAGFDQEAAAVVMARLASHKMET 536
Query: 634 DDGPDVMRWADRTLIRL 650
++ D RW DR LIRL
Sbjct: 537 EEEFDATRWLDRALIRL 553
Score = 109 bits (274), Expect = 1e-24
Identities = 42/102 (41%), Positives = 52/102 (50%), Gaps = 2/102 (1%)
Query: 73 GCEGISRSYVFRGTKDVPAQRLQEML--RIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVE 130
G S+SYVFRG K+V ++ E L K + A + V++FL P
Sbjct: 175 GFSECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPAS 234
Query: 131 ACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLE 172
CE +L L LQKDPWPV G R R TG ALS+A GLL
Sbjct: 235 ECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLG 276
Score = 50.7 bits (122), Expect = 2e-06
Identities = 17/28 (60%), Positives = 22/28 (78%)
Query: 650 LEGGAPVLTEDVSLQVFMEHLKKLAVSS 677
+ G + T+DVSLQVFMEHL++LAV S
Sbjct: 734 MGGSDIIFTDDVSLQVFMEHLQRLAVQS 761
>gnl|CDD|227380 COG5047, SEC23, Vesicle coat complex COPII, subunit SEC23
[Intracellular trafficking and secretion].
Length = 755
Score = 283 bits (725), Expect = 4e-85
Identities = 143/335 (42%), Positives = 185/335 (55%), Gaps = 33/335 (9%)
Query: 184 FYQNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKPDLPPLQYEPLLCMRNQCR 243
F EE DGIR TWNV+P+++ +A+R V+P+ CLY PL E L YEP+ C C+
Sbjct: 3 FEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDALTVNYYEPVKCTA-PCK 61
Query: 244 AILNPLCQVDYKSKLWVCNFCFQRNAFPPQYAAITEQHQPAELHPQFTTIEYTIPKMQCA 303
A+LNP C +D +++ W+C FC QRN PPQY I+ + P EL PQ +TIEYT+ K
Sbjct: 62 AVLNPYCHIDERNQSWICPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKPVIL 121
Query: 304 PLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHELGCEGISRSY 363
P VF FVVD C DEEEL AL+DSL +SLSLLP ALVGLIT+G +QVHEL E RSY
Sbjct: 122 PPVFFFVVDACCDEEELTALKDSLIVSLSLLPPEALVGLITYGTSIQVHELNAENHRRSY 181
Query: 364 VFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLA 423
VF G K+ + LQE+L + K + S + G + A ++FL P + CE ++L
Sbjct: 182 VFSGNKEYTKENLQELLALSKPTKSGGFESKISGI-GQFASSRFLLPTQQCEFKLLNILE 240
Query: 424 ALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL-------------------------- 457
LQ P V G+ TG A IA LLE
Sbjct: 241 QLQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPNAGCHIVLFAGGPCTVGPGTVVSTE 300
Query: 458 ----IRSHNDIHKGNNKLPGRMATKITKGLALRAA 488
+RSH+DI + + + ATK KGLA R A
Sbjct: 301 LKEPMRSHHDIESDSAQHSKK-ATKFYKGLAERVA 334
Score = 144 bits (365), Expect = 5e-36
Identities = 66/142 (46%), Positives = 84/142 (59%), Gaps = 3/142 (2%)
Query: 510 ELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIP 569
L + G IG VS+ K +SD ++G+G T SWKM +LSP + AL+FEI +
Sbjct: 408 NLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASGSA 467
Query: 570 QGGP-GCIQFITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVV 628
Q IQFIT YQ SG ++RVTT+AR + D L I+ FDQEAAAV M R+
Sbjct: 468 QRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTDG--GLPKINRSFDQEAAAVFMARIAA 525
Query: 629 NRAEQDDGPDVMRWADRTLIRL 650
+AE +D DV RW DR LIRL
Sbjct: 526 FKAETEDIIDVFRWIDRNLIRL 547
Score = 82.2 bits (203), Expect = 4e-16
Identities = 43/100 (43%), Positives = 54/100 (54%), Gaps = 1/100 (1%)
Query: 73 GCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVEAC 132
E RSYVF G K+ + LQE+L + K + S + G +FL P + C
Sbjct: 173 NAENHRRSYVFSGNKEYTKENLQELLALSKPTKSGGFESKISGIGQFAS-SRFLLPTQQC 231
Query: 133 EMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLE 172
E L ++L LQ DPWPV GKR LR TG AL+IA LLE
Sbjct: 232 EFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLE 271
Score = 39.1 bits (91), Expect = 0.008
Identities = 16/27 (59%), Positives = 21/27 (77%)
Query: 652 GGAPVLTEDVSLQVFMEHLKKLAVSST 678
G +LT+DV+LQ FM HL+KLAVS +
Sbjct: 729 GSETILTDDVNLQKFMNHLRKLAVSKS 755
>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 = 210 bits (536), Expect = 4e-63
Identities = 106/218 (48%), Positives = 120/218 (55%), Gaps = 33/218 (15%)
Query: 303 APLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHELGCEGISRS 362
+P VFLFVVDTCMDEEEL AL++SL MSLSLLP NALVGLITFG MVQVHELG E S+S
Sbjct: 2 SPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELGFEECSKS 61
Query: 363 YVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRP--ARTQFLQPVEACEMYATD 420
YVFRG KD A+++Q+ML +G +M A P P A ++FL PV CE TD
Sbjct: 62 YVFRGNKDYTAKQIQDMLGLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTD 121
Query: 421 LLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL----------------------- 457
LL LQ P V G TGVA IAVGLLE
Sbjct: 122 LLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACFPNTGARIMLFAGGPCTVGPGAVV 181
Query: 458 -------IRSHNDIHKGNNKLPGRMATKITKGLALRAA 488
IRSH+DI K N K + A K LA R A
Sbjct: 182 STELKDPIRSHHDIDKDNAKYY-KKAVKFYDSLAKRLA 218
Score = 138 bits (350), Expect = 8e-37
Identities = 55/102 (53%), Positives = 64/102 (62%), Gaps = 2/102 (1%)
Query: 73 GCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPP--VHKFLQPVE 130
G E S+SYVFRG KD A+++Q+ML +G +M A P P +FL PV
Sbjct: 54 GFEECSKSYVFRGNKDYTAKQIQDMLGLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVS 113
Query: 131 ACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLE 172
CE +LTDLL LQ DPWPV G R LR TGVALSIAVGLLE
Sbjct: 114 QCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLE 155
>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 = 111 bits (281), Expect = 8e-28
Identities = 62/215 (28%), Positives = 74/215 (34%), Gaps = 61/215 (28%)
Query: 304 PLVFLFVVDTCMD---EEELGALRDSLQMSLSLLPK--NALVGLITFGQMVQVHELGCEG 358
P VFLFV+D + L AL++SL SL LLP ALVG ITF V L
Sbjct: 3 PPVFLFVIDVSYNAIKSGLLAALKESLLQSLDLLPGDPRALVGFITFDSTVHFFNLSSSL 62
Query: 359 ISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYA 418
R K + LQ+M P P R FL P+ C
Sbjct: 63 -------RQPKMLVVSDLQDMF------------------LPLPDR--FLVPLSECRFVL 95
Query: 419 TDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTLI-------------------- 458
DLL L + V + E C G A AV LL+
Sbjct: 96 EDLLEELPR-MFPVTKRPERC--LGPALQAAVLLLKAAFTGGKIMLFQGGLPTVGPGGKL 152
Query: 459 -----RSHNDIHKGNNKLPGRMATKITKGLALRAA 488
SH+D K KL + A K K LA
Sbjct: 153 KSRLDESHHDTDKEKAKL-VKKADKFYKSLAKECV 186
Score = 56.1 bits (136), Expect = 1e-08
Identities = 27/89 (30%), Positives = 34/89 (38%), Gaps = 23/89 (25%)
Query: 84 RGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVEACEMSLTDLLGGL 143
R K + LQ+M P +FL P+ C L DLL L
Sbjct: 63 RQPKMLVVSDLQDMF--------------------LPLPDRFLVPLSECRFVLEDLLEEL 102
Query: 144 QKDPWPVHQGKRALRSTGVALSIAVGLLE 172
+ +PV KR R G AL AV LL+
Sbjct: 103 PR-MFPV--TKRPERCLGPALQAAVLLLK 128
>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 = 106 bits (266), Expect = 9e-26
Identities = 53/162 (32%), Positives = 65/162 (40%), Gaps = 39/162 (24%)
Query: 303 APLVFLFVVDTCM---DEEELGALRDSLQMSLSLLPK--NALVGLITFGQMVQVHELGCE 357
P VF+FV+D E L AL++SL SL LLP A VGLIT+ V + L +
Sbjct: 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSD 61
Query: 358 GI-SRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEM 416
+ YV KDV P P R FL P+ C+
Sbjct: 62 LAQPKMYVVSDLKDV--------------------------FLPLPDR--FLVPLSECKK 93
Query: 417 YATDLLAALQK--GPVAVHQGREHCGPTGVAHVIAVGLLEGT 456
DLL L PV H+ E C G A A LL+GT
Sbjct: 94 VIHDLLEQLPPMFWPVPTHR-PERC--LGPALQAAFLLLKGT 132
Score = 60.0 bits (146), Expect = 5e-10
Identities = 24/95 (25%), Positives = 30/95 (31%), Gaps = 29/95 (30%)
Query: 78 SRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVEACEMSLT 137
+ YV KD P +FL P+ C+ +
Sbjct: 65 PKMYVVSDLKD----------------------------VFLPLPDRFLVPLSECKKVIH 96
Query: 138 DLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLE 172
DLL L WPV R R G AL A LL+
Sbjct: 97 DLLEQLPPMFWPV-PTHRPERCLGPALQAAFLLLK 130
>gnl|CDD|219707 pfam08033, Sec23_BS, Sec23/Sec24 beta-sandwich domain.
Length = 86
Score = 85.6 bits (213), Expect = 2e-20
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 18/87 (20%)
Query: 515 GAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGGPG 574
G IG S + G T WK+ +L P+T+ A F+I P+ G
Sbjct: 18 GFIGNFFSRS------------SGDT--WKLPSLDPDTSYAFEFDIDE----PLDSGKQA 59
Query: 575 CIQFITHYQAPSGEKKVRVTTIARNWA 601
IQF Y SGE+++RVTT+A
Sbjct: 60 YIQFALLYTHSSGERRIRVTTVALPVT 86
>gnl|CDD|203092 pfam04810, zf-Sec23_Sec24, Sec23/Sec24 zinc finger. 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 found to be zinc binding domain.
Length = 39
Score = 68.7 bits (169), Expect = 6e-15
Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 234 PLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQY 274
P+ C R CRA LNP CQ D+ + W CN C QRN PP+Y
Sbjct: 1 PVRCRR--CRAYLNPYCQFDFGGRRWTCNLCGQRNDLPPEY 39
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 48.2 bits (115), Expect = 1e-05
Identities = 36/146 (24%), Positives = 62/146 (42%), Gaps = 24/146 (16%)
Query: 185 YQNEERDGIRCTWNVWP--SSKLEASRLVMPVGCLYQP---LKEKPDLPPLQYE--PLLC 237
N +R T P + L+ S++ P G + +P L + D PL + + C
Sbjct: 145 QSNCSPKYVRSTMYAIPETNDLLKKSKI--PFGLVIRPFLELYPEEDPVPLVEDGSIVRC 202
Query: 238 MRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQYAAITEQHQP-------AELHPQF 290
R CR+ +NP Q + + W CN C +N P + + + P EL +
Sbjct: 203 RR--CRSYINPFVQFIEQGRKWRCNICRSKNDVPEGFDNPSGPNDPRSDRYSRPEL--KS 258
Query: 291 TTIEYTIPKM----QCAPLVFLFVVD 312
+++ PK Q P V++F++D
Sbjct: 259 GVVDFLAPKEYSLRQPPPPVYVFLID 284
Score = 29.8 bits (67), Expect = 5.6
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 575 CIQFITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRA 631
Q Y GE+++RV ++ ++ + + + DQ A A I+ + +A
Sbjct: 568 YFQVALLYTLNDGERRIRVVNLS---LPTSSSIREVYASADQLAIACILAKKASTKA 621
>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 = 42.5 bits (101), Expect = 4e-05
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 616 QEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRL 650
QEA AV++ + V +A D RW D+ L+ +
Sbjct: 1 QEAIAVLLAKKAVEKALTSSLKDARRWLDKKLVDI 35
>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 = 36.7 bits (85), Expect = 0.043
Identities = 29/153 (18%), Positives = 40/153 (26%), Gaps = 19/153 (12%)
Query: 8 SMSAPAPAPRPGQPPRVHELGCEGISRSYVFRGTKDVPAQRLQEML-------RIGKYSM 60
AP P+P P + L E + R Q Q++L +
Sbjct: 136 PPQAPESQPQPQTPAQ-KMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQ 194
Query: 61 SAPAPAPRPGQPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTP 120
P P G P V Q Q + + P P P QPP
Sbjct: 195 GPPEQPP--GYPQPPQGHPEQV---------QPQQFLPAPSQAPAQPPLPPQLPQQPPPL 243
Query: 121 PVHKFLQPVEACEMSLTDLLGGLQKDPWPVHQG 153
+F + Q+ P P Q
Sbjct: 244 QQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQP 276
>gnl|CDD|131869 TIGR02822, adh_fam_2, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). The gene neighborhood of members
of this family is not conserved and it appears that no
members are characterized. The sequence of the family
includes 6 invariant cysteine residues and one invariant
histidine. It appears that no member is characterized
[Energy metabolism, Fermentation].
Length = 329
Score = 32.2 bits (73), Expect = 0.80
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 400 PRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEG 455
PRP + L V AC + TDL + +G + VH+ R G V V G G
Sbjct: 23 PRPGPGELLVRVRACGVCRTDL--HVSEGDLPVHRPRVTPGHEVVGEVAGRGADAG 76
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 31.6 bits (72), Expect = 1.6
Identities = 24/123 (19%), Positives = 31/123 (25%), Gaps = 9/123 (7%)
Query: 11 APAPAPRPGQPPRVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPG 70
A A P P +++ PA + AP AP
Sbjct: 382 ARPEAAAPAAAPV---------AQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAA 432
Query: 71 QPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVE 130
P + PAQ E + I PA A P P L P E
Sbjct: 433 APAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTE 492
Query: 131 ACE 133
+
Sbjct: 493 EGD 495
>gnl|CDD|226709 COG4258, COG4258, Predicted exporter [General function prediction
only].
Length = 788
Score = 31.4 bits (71), Expect = 2.1
Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 17/76 (22%)
Query: 392 PAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVG 451
P G P RP +A L + A + + VA +A
Sbjct: 399 PWLCRGAPVRPVPA----------------MARLARWLAAWRRNKWLLAGLLVALALASL 442
Query: 452 LLEGTL-IRSHNDIHK 466
LL G +R +DI +
Sbjct: 443 LLPGMSWLRVDDDISQ 458
>gnl|CDD|152115 pfam11679, DUF3275, Protein of unknown function (DUF3275). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 211
Score = 30.6 bits (69), Expect = 2.1
Identities = 21/75 (28%), Positives = 27/75 (36%), Gaps = 20/75 (26%)
Query: 10 SAPAPAPRPGQPPRVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRP 69
SAPAPAP P P SR +M RI + M+A APA
Sbjct: 113 SAPAPAPSPQSPKP----ASRRASR----------------DMRRIAPFGMNASAPAQEA 152
Query: 70 GQPGCEGISRSYVFR 84
Q + + +F
Sbjct: 153 AQASSDEDEDAELFG 167
>gnl|CDD|200529 cd11268, Sema_6C, The Sema domain, a protein interacting module, of
semaphorin 6C (Sema6C, also called semaphorin Y).
Sema6C is highly expressed in adult brain and skeletal
muscle and it shows growth cone collapsing activity. It
may play a role in the maintenance and remodelling of
neuronal connections. In adult skeletal muscle, this
role includes prevention of motor neuron sprouting and
uncontrolled motor neuron growth. The expression of
Sema6C in adult skeletal muscle is down-regulated
following denervation. Sema6C is a member of the class 6
semaphorin family of proteins, which are membrane
associated semaphorins. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 465
Score = 30.4 bits (68), Expect = 3.2
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 65 PAPRPGQPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQP 117
P+PRPG C G+ + +F ++D+P L I + + PA P QP
Sbjct: 314 PSPRPG--SCAGVGGAALFSSSRDLPDDVLT---FIKAHPLLDPAVPPVTHQP 361
>gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease,
includes microcin C7 self immunity protein.
LD-carboxypeptidase (Muramoyltetrapeptide
carboxypeptidase; EC 3.4.17.13; Merops family S66;
initially described as Carboxypeptidase II) family also
includes the microcin c7 self-immunity protein (MccF) as
well as uncharacterized proteins including hypothetical
proteins. LD-carboxypeptidase hydrolyzes the amide bond
that links the dibasic amino acids to C-terminal
D-amino acids. The physiological substrates of
LD-carboxypeptidase are tetrapeptide fragments (such as
UDP-MurNAc-tetrapeptides) that are produced when
bacterial cell walls are degraded; they contain an
L-configured residue (L-lysine or meso-diaminopimelic
acid residue) as the penultimate residue and D-alanine
as the ultimate residue. A possible role of
LD-carboxypeptidase is in peptidoglycan recycling
whereby the resulting tripeptide (precursor for murein
synthesis) can be reconverted into peptidoglycan by
attachment of preformed D-Ala-D-Ala dipeptides. Some
enzymes possessing LD-carboxypeptidase activity also act
as LD-transpeptidase by replacing the terminal D-Ala
with another D-amino acid. MccF contributes to
self-immunity towards microcin C7 (MccC7), a ribosomally
encoded peptide antibiotic that contains a
phosphoramidate linkage to adenosine monophosphate at
its C-terminus. Its possible biological role is to
defend producer cells against exogenous microcin from
re-entering after having been exported. It is suggested
that MccF is involved in microcin degradation or
sequestration in the periplasm.
Length = 282
Score = 29.8 bits (68), Expect = 4.3
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 605 TQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGAPVLT 658
TQL +G + A +I+GR D G + L L G PVL
Sbjct: 213 TQLKL--AGVLDKVAGIILGRFTDCEDNDDFGYTLEEVLKEVLGDL--GIPVLY 262
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 30.0 bits (67), Expect = 4.8
Identities = 26/113 (23%), Positives = 33/113 (29%), Gaps = 19/113 (16%)
Query: 8 SMSAPAPAPRPGQPPRVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAP 67
+M P AP P +PP AQR + +AP A
Sbjct: 693 TMQPPPRAPTPMRPPAA-----------------PPGRAQRPAAATGRARPPAAAPGRAR 735
Query: 68 RPGQPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTP 120
P G +R + P R + AP P P P PP P
Sbjct: 736 PPA--AAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAP 786
>gnl|CDD|223041 PHA03321, PHA03321, tegument protein VP11/12; Provisional.
Length = 694
Score = 29.9 bits (67), Expect = 5.8
Identities = 24/123 (19%), Positives = 31/123 (25%), Gaps = 32/123 (26%)
Query: 11 APAPAPRPGQPPRVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPG 70
P P RPG P C +R+ R L + R+ PA A P
Sbjct: 443 PPPPRARPGSTP-----ACARRARAQRARDAGPEYVDPLGALRRL-------PAGAAPPP 490
Query: 71 QPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVE 130
+P +Y R M P P T + P
Sbjct: 491 EPAAAPSPATYYTR--------------------MGGGPPRLPPRNRATETLRPDWGPPA 530
Query: 131 ACE 133
A
Sbjct: 531 AAP 533
>gnl|CDD|235086 PRK02919, PRK02919, oxaloacetate decarboxylase subunit gamma;
Provisional.
Length = 82
Score = 27.3 bits (61), Expect = 6.3
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 100 IGKYSMSAPAPAPRPGQPPTPPVHKF--LQPV 129
I ++ P AP P P PV F L+PV
Sbjct: 39 INRFF-PEPVAAPAPRPVPVAPVDDFTRLKPV 69
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 29.4 bits (66), Expect = 7.3
Identities = 24/110 (21%), Positives = 37/110 (33%), Gaps = 15/110 (13%)
Query: 313 TCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVP 372
T +DE+ R S +SL L +AL+ L R
Sbjct: 313 TALDEQMERFARRSDALSLELALLHALLALGGAPSEGVAAVAPPAPAPADLTQR------ 366
Query: 373 AQRLQEMLRIGKYSMSAPAPA---------PRPGQPPRPARTQFLQPVEA 413
RL++ +R + + +A A A PRP PP P + +
Sbjct: 367 LNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRPRGPPAPEPARSAEAPPL 416
>gnl|CDD|238742 cd01465, vWA_subgroup, VWA subgroup: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Not much is known about the function of the VWA
domain in these proteins. The members do have a
conserved MIDAS motif. The biochemical function however
is not known.
Length = 170
Score = 28.4 bits (64), Expect = 7.4
Identities = 9/47 (19%), Positives = 23/47 (48%)
Query: 305 LVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQV 351
LVF+ MD +L ++ +L++ + L + + ++T+ +
Sbjct: 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAET 49
>gnl|CDD|226696 COG4245, TerY, Uncharacterized protein encoded in toxicity
protection region of plasmid R478, contains von
Willebrand factor (vWF) domain [General function
prediction only].
Length = 207
Score = 28.6 bits (64), Expect = 7.8
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 300 MQCAPLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNAL------VGLITFGQMVQVH 352
M+ P L M E + AL LQM + L ++ + ++TFG +V
Sbjct: 1 MRRLPCYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVI 59
>gnl|CDD|223067 PHA03380, PHA03380, transactivating tegument protein VP16;
Provisional.
Length = 432
Score = 28.9 bits (65), Expect = 9.1
Identities = 9/38 (23%), Positives = 11/38 (28%), Gaps = 1/38 (2%)
Query: 387 MSAPAP-APRPGQPPRPARTQFLQPVEACEMYATDLLA 423
+ P+P A PG P P M L
Sbjct: 372 LDPPSPSAVLPGDPVPPLTVSVASTAADAAMPPALALD 409
>gnl|CDD|236754 PRK10760, PRK10760, murein hydrolase B; Provisional.
Length = 359
Score = 28.9 bits (65), Expect = 9.9
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 373 AQRLQEMLRIGKYSMSAPAPAPRPGQPPRPA----RTQFLQP 410
A+RL +LR+ M AP RP P A R +F+ P
Sbjct: 85 AKRLDWVLRL----MDRQAPTTRPPSGPNGAWLRYRKKFITP 122
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 0.425
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,779,504
Number of extensions: 3411573
Number of successful extensions: 3808
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3729
Number of HSP's successfully gapped: 66
Length of query: 679
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 576
Effective length of database: 6,369,140
Effective search space: 3668624640
Effective search space used: 3668624640
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: 62 (27.9 bits)