RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5195
(334 letters)
>gnl|CDD|221827 pfam12881, NUT_N, NUT protein N terminus. This family includes the
NUT protein. The gene encoding for NUT protein (Nuclear
Testis protein) is found fused to BRD3 or BRD4 genes, in
some aggressive types of carcinoma, due to chromosomal
translocations. Proteins of the BRD family contain two
bromodomains that bind transcriptionally active
chromatin through associations with acetylated histones
H3 and H4. Such proteins are crucial for the regulation
of cell cycle progression. On the other hand, little is
known about NUT protein. NUT is known to have a Nuclear
Export Sequence (NES) as well as a Nuclear Localization
Signal (NLS), both located towards the C-terminal end of
the protein. A fused NUT-GFP protein showed either
cytoplasmic or nuclear localization, suggesting that it
is subject to nuclear/cytoplasmic shuttling. Consistent
with this possibility, treatment with leptomycin B an
inhibitor of CRM1-dependent nuclear export resulted in
re-distribution of NUT-GFP to the nucleus. Inspection of
NUT revealed a C-terminal sequence similar to known
nuclear export sequences (NES) which are often regulated
by phosphorylation.
Length = 328
Score = 40.3 bits (94), Expect = 8e-04
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 254 PALPVLPPAPVP-----YIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPS 303
ALP LPPAP P + PPPP++T P +P++ P++T+ P S
Sbjct: 19 AALPFLPPAPQPPDQPFWEPPPPLVTAGFSPGNPLVLSALPSMPLVTEGGGPGLS 73
Score = 30.7 bits (69), Expect = 0.91
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 253 NPALPVLPPAPVPYIPPP--PVITPPVLPQSPVISGVFSP-NPVI 294
NP + P A +P++PP P P P P+++ FSP NP++
Sbjct: 10 NPGASLSPFAALPFLPPAPQPPDQPFWEPPPPLVTAGFSPGNPLV 54
>gnl|CDD|223002 PHA03150, PHA03150, hypothetical protein; Provisional.
Length = 456
Score = 36.4 bits (84), Expect = 0.020
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 2 FGRPSKVSTSQNKSLHLTGIGLAVQAFYINLTLDTVMGGEYAELQPVGPPLINTPGVWGV 61
FGRP ++ LH I L+ ++ D ++ + PL +TP +W +
Sbjct: 290 FGRPRRIDLCAVPRLHCPQILLSWPPNKDSILGDDLL------CPGIDIPLPSTPPIWPL 343
Query: 62 NG 63
N
Sbjct: 344 NV 345
>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA
carboxylase.
Length = 274
Score = 35.2 bits (81), Expect = 0.031
Identities = 23/76 (30%), Positives = 30/76 (39%), Gaps = 10/76 (13%)
Query: 255 ALPVLPPAPVPYI----PPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYP-----SHP 305
ALP PP P P + PPP + P P + + +P T P SHP
Sbjct: 140 ALP-QPPPPAPVVMMQPPPPHAMPPASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHP 198
Query: 306 VGLVTRSSTKYQIPAP 321
+ T Y+ PAP
Sbjct: 199 PLKSPMAGTFYRSPAP 214
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 35.4 bits (81), Expect = 0.048
Identities = 14/52 (26%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHP 305
P PV PV P + PV G + PVI + YP
Sbjct: 336 PVEPVTQTPPVA--SVDVPPAQPTVAWQPV-PGPQTGEPVIAPAPEGYPQQS 384
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 34.0 bits (78), Expect = 0.10
Identities = 15/51 (29%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 254 PALPVLPPAPVPYIPPPPVITP--PVLPQSPVISGVFSPNPVITKNYQPYP 302
P PV A P +PP PV P +P ++ P K P P
Sbjct: 399 PKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAP 449
Score = 32.9 bits (75), Expect = 0.28
Identities = 19/71 (26%), Positives = 22/71 (30%), Gaps = 13/71 (18%)
Query: 254 PALPVLPPAPVPYIPPPPVITP-PVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVTRS 312
A + P PV PP + P PV P P + PV
Sbjct: 393 AAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRA--------AIPVD----E 440
Query: 313 STKYQIPAPTK 323
KY PAP K
Sbjct: 441 KPKYTPPAPPK 451
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 33.9 bits (77), Expect = 0.12
Identities = 45/182 (24%), Positives = 60/182 (32%), Gaps = 10/182 (5%)
Query: 140 RGRNRGHQVAGFSTSYNKHESGNKATYYDDGLGHGGSIQYGSKDHRSRDGVGNAFGGAYH 199
R +G V G N + GN+ TY G H GS S +G+GN G H
Sbjct: 310 RNAIQGDLVRGAPNDKNSFDRGNEKTYQIYGGFHDGSPNAASAGAPF-NGLGNQADGG-H 367
Query: 200 DAHLKTNAHGNKQNFGGGQGFGT-KTGYVNNVGDTKLYGGGVGQGYTGTFNNGF-NPALP 257
+ +A G GG + +N + G G N G NP
Sbjct: 368 INQVHPDARGAWA--GGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGYSNPGNSNPGYN 425
Query: 258 VLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQ--PYPSHPVGLVTRSSTK 315
P + PY PP TP P P + +S P Y P + P +
Sbjct: 426 NAPNSNTPYNNPPNSNTPYSNP--PNSNPPYSNLPYSNTPYSNAPLSNAPPSSAKDHHSA 483
Query: 316 YQ 317
Y
Sbjct: 484 YH 485
>gnl|CDD|117486 pfam08919, F_actin_bind, F-actin binding. The F-actin binding
domain forms a compact bundle of four antiparallel
alpha-helices, which are arranged in a left-handed
topology. Binding of F-actin to the F-actin binding
domain may result in cytoplasmic retention and
subcellular distribution of the protein, as well as
possible inhibition of protein function.
Length = 179
Score = 32.4 bits (73), Expect = 0.19
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 257 PVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLV-TRSSTK 315
PV P P P PV TPP P+ S SP+ + QP + + L+ TR S +
Sbjct: 6 PVPPAVPKPQSTAKPVGTPP--SPVPLPSTSPSPSKMANGT-QPSSAAFIPLISTRVSLR 62
Query: 316 YQIPAPTKLFVDK 328
P ++ K
Sbjct: 63 KTRQPPERIASGK 75
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 32.7 bits (74), Expect = 0.37
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 10/64 (15%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVTRSS 313
+ V P APV P V++PPV+ +P S P P+ + + S
Sbjct: 1141 VTISVAPAAPVL----PAVVSPPVVSAAPAQSV------ATAVAMAPVAEVPIAVPVQQS 1190
Query: 314 TKYQ 317
Y
Sbjct: 1191 VDYM 1194
>gnl|CDD|220596 pfam10138, Tellurium_res, Tellurium resistance protein. Members of
this family confer resistance to the metalloid element
tellurium and its salts.
Length = 98
Score = 30.4 bits (69), Expect = 0.37
Identities = 15/24 (62%), Positives = 15/24 (62%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPV 277
PA PV PPAP P P PP PPV
Sbjct: 1 PAAPVPPPAPAPPAPAPPPAAPPV 24
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 32.0 bits (73), Expect = 0.40
Identities = 21/74 (28%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 253 NPALPVLPPAPVPY--IPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPY--PSHPVGL 308
+P+ LPPAP + PPP P P P P PV P+ P
Sbjct: 206 SPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPP--- 262
Query: 309 VTRSSTKYQIPAPT 322
+ S+T I T
Sbjct: 263 -SASATPAPIGGIT 275
Score = 27.7 bits (62), Expect = 8.0
Identities = 20/85 (23%), Positives = 25/85 (29%), Gaps = 8/85 (9%)
Query: 244 YTGTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQS-----PVISGVFSPNPVITKNY 298
+ + +P +P P P P + P P S P S NP
Sbjct: 182 ASPSDPPSSSPGVPSFPSPPEDPSSPSDS-SLPPAPSSFQSDTPPPSPESPTNPSPPPGP 240
Query: 299 QPYPSHPVGLVTRSSTKYQIPAPTK 323
P PV V ST P P
Sbjct: 241 AAPPPPPVQQVPPLST--AKPTPPS 263
>gnl|CDD|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa
MW N terminal. This domain is found in eukaryotes. This
domain is about 90 amino acids in length. This domain is
found associated with pfam00076. This domain is part of
U1 snRNP, which is the pre-mRNA binding protein of the
penta-snRNP spliceosome complex. It extends over a
distance of 180 A from its RNA binding domain, wraps
around the core domain of U1 snRNP consisting of the
seven Sm proteins and finally contacts U1-C, which is
crucial for 5'-splice-site recognition.
Length = 94
Score = 29.9 bits (68), Expect = 0.43
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 260 PPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPV 306
P P+PY+PP P ++ I+GV P P
Sbjct: 15 PRPPLPYLPPLDK--APEKRKTNPITGVAQYLSEFKDYKDEPPPEPT 59
>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP). This family
contains bacterial fibronectin-attachment proteins
(FAP). Family members are rich in alanine and proline,
are approximately 300 long, and seem to be restricted to
mycobacteria. These proteins contain a
fibronectin-binding motif that allows mycobacteria to
bind to fibronectin in the extracellular matrix.
Length = 297
Score = 31.4 bits (71), Expect = 0.52
Identities = 17/57 (29%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVT 310
PA P PP P P P P P P P P + N P P+ G +
Sbjct: 57 PAAPPPPPPPAAP-PAPQPDDPNAAPPPPPADPNAPPPPPVDPNAPPPPAPEPGRID 112
Score = 27.6 bits (61), Expect = 8.8
Identities = 13/41 (31%), Positives = 16/41 (39%)
Query: 253 NPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPV 293
+PA P PP+ P P PP P +P PN
Sbjct: 40 DPAPPPPPPSTAAAAPAPAAPPPPPPPAAPPAPQPDDPNAA 80
>gnl|CDD|113398 pfam04625, DEC-1_N, DEC-1 protein, N-terminal region. The
defective chorion-1 gene (dec-1) in Drosophila encodes
follicle cell proteins necessary for proper eggshell
assembly. Multiple products of the dec-1 gene are formed
by alternative RNA splicing and proteolytic processing.
Cleavage products include S80 (80 kDa) which is
incorporated into the eggshell, and further proteolysis
of S80 gives S60 (60 kDa).
Length = 407
Score = 31.3 bits (70), Expect = 0.67
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 9/50 (18%)
Query: 254 PALPVLP---------PAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVI 294
PA+P +P PAP P P P +P + P I
Sbjct: 94 PAMPSMPGLLGAAAPVPAPAPAPAAAPPAAPAPAADTPAAPIPDAVQPAI 143
>gnl|CDD|221269 pfam11854, DUF3374, Protein of unknown function (DUF3374). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 665 to 712 amino acids in
length.
Length = 675
Score = 31.1 bits (71), Expect = 1.0
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 14/73 (19%)
Query: 61 VNGAYTGAYNTGVNGLSNNGIQALNTYGDRGYGAGGYTDANGFYHG-----------NLG 109
V +G GV + I++ N +G GA G DA+ Y G NLG
Sbjct: 46 VKTGASGEVGVGVGYNDGDDIRSANAFGTDEDGAVGALDADLKYRGEGGYRASFQADNLG 105
Query: 110 TKNGY---DVGHA 119
NG + G
Sbjct: 106 MDNGSAQLEAGKY 118
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 30.7 bits (69), Expect = 1.3
Identities = 14/29 (48%), Positives = 14/29 (48%)
Query: 259 LPPAPVPYIPPPPVITPPVLPQSPVISGV 287
LPP P PPPP PP P P GV
Sbjct: 4 LPPGNPPPPPPPPGFEPPSQPPPPPPPGV 32
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 30.7 bits (69), Expect = 1.3
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 248 FNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGV 287
F G +PA P PPA +P P PPVI P P +
Sbjct: 224 FLPGPSPAQPSAPPASIPAPPIPPVIQYVAPPPVPPPQPI 263
Score = 29.1 bits (65), Expect = 3.7
Identities = 13/33 (39%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 254 PALPVLPPAPV--PYIPPPPVITPPVLPQSPVI 284
A P PAP P I PPV P P+I
Sbjct: 234 SAPPASIPAPPIPPVIQYVAP--PPVPPPQPII 264
>gnl|CDD|218549 pfam05308, Mito_fiss_reg, Mitochondrial fission regulator. In
eukaryotes, this family of proteins induces
mitochondrial fission.
Length = 248
Score = 30.1 bits (68), Expect = 1.4
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLP 279
P L V PP P P PPPP +
Sbjct: 179 PVLEVPPPPPPPPPPPPPSLQQSTSA 204
Score = 29.3 bits (66), Expect = 2.1
Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 254 PALPVLPPAPVPYI---PPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVT 310
+ P+ PP P + PPPP PP P + + + I + + LV
Sbjct: 168 TSFPISPPTEEPVLEVPPPPPP--PPPPPPPSLQQSTSAIDL-IKERKGQRSAAGKTLVL 224
Query: 311 RSSTKYQIP 319
+ P
Sbjct: 225 SKPKSPEFP 233
>gnl|CDD|152960 pfam12526, DUF3729, Protein of unknown function (DUF3729). This
family of proteins is found in viruses. Proteins in this
family are typically between 145 and 1707 amino acids in
length. The family is found in association with
pfam01443, pfam01661, pfam05417, pfam01660, pfam00978.
There is a single completely conserved residue L that
may be functionally important.
Length = 115
Score = 28.9 bits (65), Expect = 1.5
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSP 282
P PP+P+ PP P PP+ P P
Sbjct: 80 VPGPAGPPSPLA--PPAPARKPPLPPPRP 106
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 30.5 bits (69), Expect = 1.5
Identities = 14/52 (26%), Positives = 16/52 (30%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHP 305
P+ P P PPP PPV P +P P P P
Sbjct: 385 PSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPAR 436
>gnl|CDD|237940 PRK15313, PRK15313, autotransport protein MisL; Provisional.
Length = 955
Score = 30.2 bits (67), Expect = 1.7
Identities = 24/69 (34%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 240 VGQGYTGTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQ--SPVISGVFSPNPVITKN 297
V +G + P P++P PV + P PVI PV P PVI P+PV
Sbjct: 546 VQKGKNWYLTSYIEPDEPIIPD-PVDPVIPDPVIPDPVDPDPVDPVIPDPVIPDPVDPDP 604
Query: 298 YQPYPSHPV 306
P P PV
Sbjct: 605 VDPEPVDPV 613
>gnl|CDD|177464 PHA02682, PHA02682, ORF080 virion core protein; Provisional.
Length = 280
Score = 29.8 bits (66), Expect = 2.0
Identities = 17/52 (32%), Positives = 19/52 (36%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHP 305
PA V PAP P PP T P P + P T+ P P P
Sbjct: 103 PAPAVTCPAPAPACPPATAPTCPPPAVCPAPARPAPACPPSTRQCPPAPPLP 154
>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional.
Length = 663
Score = 30.0 bits (67), Expect = 2.0
Identities = 14/70 (20%), Positives = 18/70 (25%), Gaps = 1/70 (1%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSP-NPVITKNYQPYPSHPVGLVTRS 312
+P PA P PPV P SP + P P P
Sbjct: 388 DGIPYSVPARSPMTAYPPVPQFCGDPGLVSPYNPQSPGTSYGPEPVGPVPPQPTNPYVMP 447
Query: 313 STKYQIPAPT 322
+ + P
Sbjct: 448 ISMANMVYPG 457
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 30.3 bits (68), Expect = 2.1
Identities = 12/47 (25%), Positives = 17/47 (36%)
Query: 260 PPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPV 306
PP P P P +++ LP P + SP P+ P
Sbjct: 2703 PPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPA 2749
Score = 28.0 bits (62), Expect = 9.6
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 255 ALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHP 305
A P + + + PP P PQ+P P P P P P
Sbjct: 2887 ARPAVSRSTESFALPPDQPERPPQPQAPP-----PPQPQPQPPPPPQPQPP 2932
Score = 28.0 bits (62), Expect = 9.7
Identities = 20/88 (22%), Positives = 31/88 (35%), Gaps = 7/88 (7%)
Query: 243 GYTGTFNNGFNPALPVLPP-APVPYIPPPPVITPPVLPQSPVISGVFSPNPV----ITKN 297
+PA P+ PP + P PPPP P P P+ V V +++
Sbjct: 2813 APAAALPPAASPAGPLPPPTSAQPTAPPPP--PGPPPPSLPLGGSVAPGGDVRRRPPSRS 2870
Query: 298 YQPYPSHPVGLVTRSSTKYQIPAPTKLF 325
P+ P R + + T+ F
Sbjct: 2871 PAAKPAAPARPPVRRLARPAVSRSTESF 2898
>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer
membranes [Cell envelope biogenesis, outer membrane].
Length = 244
Score = 29.4 bits (66), Expect = 2.1
Identities = 13/51 (25%), Positives = 14/51 (27%), Gaps = 5/51 (9%)
Query: 254 PALPVLPPAPVPYIP-PPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPS 303
P P PP P P P P P P P +P P
Sbjct: 70 PTEPETPPEPTPPKPKEKPKPEKKPKKPKPKP----KPKPKPKPKVKPQPK 116
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 30.1 bits (68), Expect = 2.1
Identities = 14/68 (20%), Positives = 19/68 (27%), Gaps = 5/68 (7%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVTRSS 313
A P AP PP PV P + + + + P P T +
Sbjct: 408 AAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVAL-----APAPPAQAAPETVAI 462
Query: 314 TKYQIPAP 321
P P
Sbjct: 463 PVRVAPEP 470
>gnl|CDD|234764 PRK00442, tatA, twin arginine translocase protein A; Provisional.
Length = 92
Score = 27.9 bits (62), Expect = 2.2
Identities = 18/61 (29%), Positives = 21/61 (34%), Gaps = 11/61 (18%)
Query: 220 FGTKTGYVNNVGDTKLYGGGVGQ---GYTGTFNNGFNPALPVLPPAPVPYIPPPPVITPP 276
FGTK K G VG+ G+ N P PAP PP T P
Sbjct: 20 FGTKK--------LKNLGSDVGESIKGFRKAMNEDEKEDKPAEQPAPPAQPVPPVQNTAP 71
Query: 277 V 277
+
Sbjct: 72 L 72
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 29.7 bits (68), Expect = 2.2
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 9/35 (25%)
Query: 134 GSYG-DVRGRNRGHQ---VAGFS-----TSYNKHE 159
GS G D RG R HQ V SY + E
Sbjct: 265 GSAGRDTRGLIRVHQFDKVELVKFTKPEDSYAELE 299
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 29.7 bits (66), Expect = 2.3
Identities = 27/77 (35%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 89 DRGYGAG-------GYTDANGFYHGNLGTKNGYDVGHAYGGGKDIGLTNVQGGSYGDVRG 141
DR +G G GYT+ NG +GN G NG GH G GK G V+
Sbjct: 3 DREFGTGNGYSNGNGYTNGNGHTNGN-GNYNGN--GHVNGNGKANGAKVVKMKPMDSELL 59
Query: 142 RNRGHQVAGFSTSYNKH 158
R +GH + F Y K+
Sbjct: 60 REQGHIMVDFIADYYKN 76
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 29.5 bits (66), Expect = 2.3
Identities = 19/73 (26%), Positives = 20/73 (27%), Gaps = 4/73 (5%)
Query: 240 VGQGYTGTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQ 299
V + TGT A P P P P P P P S V S
Sbjct: 74 VSKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATA---- 129
Query: 300 PYPSHPVGLVTRS 312
P P V S
Sbjct: 130 TAPESPSTSVPSS 142
>gnl|CDD|152747 pfam12312, NeA_P2, Nepovirus subgroup A polyprotein. This family
of proteins is found in viruses. Proteins in this family
are typically between 259 and 1110 amino acids in
length. The family is found in association with
pfam03688, pfam03689, pfam03391. This family is one of
the polyproteins expressed by Nepoviruses in subgroup A.
Length = 175
Score = 29.2 bits (65), Expect = 2.5
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 251 GFNPALPVLPPAPVPYIPPPPVITPP 276
+P P LPP P PPPP+ PP
Sbjct: 110 EAHPGGPCLPPPP----PPPPIQKPP 131
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.7 bits (67), Expect = 2.5
Identities = 18/106 (16%), Positives = 24/106 (22%), Gaps = 11/106 (10%)
Query: 229 NVGDTKLYGGGVGQGYTGTFNNGFNPALPVLPPAPVP-----YIPPPPVITPPVLPQSPV 283
GD G G Q F P A P P +
Sbjct: 364 QKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAG- 422
Query: 284 ISGVFSPNPVITKNYQPYPSHPVGLVTRSSTKYQIPAPTKLFVDKA 329
+P V P +P ++ Q K+ V K
Sbjct: 423 -----TPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVSKV 463
>gnl|CDD|114709 pfam06003, SMN, Survival motor neuron protein (SMN). This family
consists of several eukaryotic survival motor neuron
(SMN) proteins. The Survival of Motor Neurons (SMN)
protein, the product of the spinal muscular
atrophy-determining gene, is part of a large
macromolecular complex (SMN complex) that functions in
the assembly of spliceosomal small nuclear
ribonucleoproteins (snRNPs). The SMN complex functions
as a specificity factor essential for the efficient
assembly of Sm proteins on U snRNAs and likely protects
cells from illicit, and potentially deleterious,
non-specific binding of Sm proteins to RNAs.
Length = 264
Score = 29.2 bits (65), Expect = 2.5
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 246 GTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSP 282
G + P L P P+ PP+I PP P SP
Sbjct: 184 GRHGEKPSGWPPFLSGWPPPFPLGPPMIPPPP-PMSP 219
>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional.
Length = 141
Score = 28.3 bits (63), Expect = 2.9
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 249 NNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSP 282
+ P +PPAP +P P PP P P
Sbjct: 104 PTPPPTSTPAVPPAPAAAVPAPAAAPPPSDPPQP 137
>gnl|CDD|236768 PRK10819, PRK10819, transport protein TonB; Provisional.
Length = 246
Score = 28.9 bits (65), Expect = 3.0
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 4/49 (8%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYP 302
+ P P P + P P P +P+ P + V P +P P
Sbjct: 59 EPPQAVQPPPEPVVEPEP--EPEPIPEPPKEAPV--VIPKPEPKPKPKP 103
>gnl|CDD|147144 pfam04834, Adeno_E3_14_5, Early E3 14.5 kDa protein. The E3B 14.5
kDa was first identified in Human adenovirus type 5. It
is an integral membrane protein oriented with its C
terminus in the cytoplasm. It functions to down-regulate
the epidermal growth factor receptor and prevent tumour
necrosis factor cytolysis. It achieves this through the
interaction with E3 10.4 kDa protein.
Length = 97
Score = 27.4 bits (61), Expect = 3.4
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 246 GTFNNGFN-PALPVLPPAPVP-YIPPPPVITPPVLPQS--PVIS 285
+ G+N P LP P P +IP PP IS
Sbjct: 45 PCLDFGWNAPNALDLPRYPDPQHIPLQQPPPPPEPQPRAPSAIS 88
>gnl|CDD|220708 pfam10349, WWbp, WW-domain ligand protein. The WWbp domain is
characterized by several short PY and PT-like motifs of
the PPPPY form. These appear to bind directly to the WW
domains of WWP1 and WWP2 and other such diverse proteins
as dystrophin and YAP (Yes-associated protein). This is
the WW-domain binding protein WWbp via PY and PY_like
motifs. The presence of a phosphotyrosine residue in the
pWBP-1 peptide abolishes WW domain binding which
suggests a potential regulatory role for tyrosine
phosphorylation in modulating WW domain-ligand
interactions. Given the likelihood that WWP1 and WWP2
function as E3 ubiquitin-protein ligases, it is possible
that initial substrate-specific recognition occurs via
WW domain-substrate protein interaction followed by
ubiquitin transfer and subsequent proteolysis. This
domain lies just downstream of the GRAM (pfam02893) in
many members.
Length = 111
Score = 27.8 bits (62), Expect = 3.5
Identities = 18/66 (27%), Positives = 20/66 (30%), Gaps = 3/66 (4%)
Query: 240 VGQGYTGTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQ 299
V + G L LP PPP PP P P GV+ P Y
Sbjct: 40 VSRESGYYPPPGAYVHLEPLPAYGQYAAPPPYGPPPPYYPAPP---GVYPTPPPPNSGYM 96
Query: 300 PYPSHP 305
P P
Sbjct: 97 ADPQEP 102
>gnl|CDD|240109 cd04792, LanM-like, LanM-like proteins. LanM is a bifunctional
enzyme, involved in the synthesis of class II
lantibiotics. It is responsible for both the dehydration
and the cyclization of the precursor-peptide during
lantibiotic synthesis. The C-terminal domain shows
similarity to LanC, the cyclase component of the lan
operon, but the N terminus seems to be unrelated to the
dehydratase, LanB.
Length = 825
Score = 29.2 bits (66), Expect = 3.8
Identities = 13/60 (21%), Positives = 16/60 (26%), Gaps = 10/60 (16%)
Query: 60 GVNGAYTGAYNTGVNGLSNNGIQALNTYGDR----------GYGAGGYTDANGFYHGNLG 109
G G + LS + GD G G + GF HG G
Sbjct: 588 GAAGLILVLLSLYELFLSERFLDLALKCGDHLLENASNEDGGIGPAEQPNLTGFAHGASG 647
>gnl|CDD|184977 PRK15016, PRK15016, isochorismate synthase EntC; Provisional.
Length = 391
Score = 29.1 bits (65), Expect = 4.1
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 34 LDTVMGGEYAELQ-PVGPPLINTPGVWGVNGAYTGAYNTGVNGLS 77
+ V+ +EL P P LI TP +W + + G N N L+
Sbjct: 249 MKEVLRERSSELHVPSSPQLITTPTLWHLATPFEGKANAQENALT 293
>gnl|CDD|219094 pfam06583, Neogenin_C, Neogenin C-terminus. This family represents
the C-terminus of eukaryotic neogenin precursor
proteins, which contains several potential
phosphorylation sites. Neogenin is a member of the N-CAM
family of cell adhesion molecules (and therefore
contains multiple copies of pfam00047 and pfam00041) and
is closely related to the DCC tumour suppressor gene
product - these proteins may play an integral role in
regulating differentiation programmes and/or cell
migration events within many adult and embryonic
tissues.
Length = 295
Score = 28.4 bits (63), Expect = 5.2
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 264 VPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVGLVTRSSTKY 316
VP +P P LP +P+++ P + K+ S VG + R+ +
Sbjct: 197 VPALPASMSTIEPKLPSTPLLT---QQGPTLPKHSVKTAS--VGTLGRARSPL 244
>gnl|CDD|217310 pfam02993, MCPVI, Minor capsid protein VI. This minor capsid
protein may act as a link between the external capsid
and the internal DNA-protein core. The C-terminal 11
residues may function as a protease cofactor leading to
enzyme activation.
Length = 238
Score = 28.2 bits (63), Expect = 5.3
Identities = 9/37 (24%), Positives = 14/37 (37%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSP 290
PA P P P P + PV + + + +P
Sbjct: 143 PAAPEPPSYEETIKPGPAPVEEPVDSMAIAVPAIDTP 179
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 28.7 bits (64), Expect = 5.3
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 221 GTKTGYVNNVGDT--KLYGGGVGQGYTGTFNNGFNPALP-VLPPAPVPYIPPPPVITPPV 277
G + GY + + +++G G G+ T + + P PPAP +PPP PP
Sbjct: 878 GVRVGYAPTLAEALDQVFGPGTGRVATAPGGDAASAPPPGAGPPAPPQAVPPPRTTQPPA 937
Query: 278 LPQS 281
P
Sbjct: 938 APPR 941
>gnl|CDD|177481 PHA02700, PHA02700, ORF017 DNA-binding phosphoprotein; Provisional.
Length = 106
Score = 27.2 bits (60), Expect = 5.6
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFS 289
P LP PP PV P P+ P L + ++ G+F+
Sbjct: 60 PQLPPSPPCPVRTPPGSPLAAP--LMPTQMLQGLFT 93
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 28.6 bits (64), Expect = 5.7
Identities = 22/127 (17%), Positives = 30/127 (23%), Gaps = 21/127 (16%)
Query: 191 GNAFGGA-----YHDAHLKTNAHGNKQNFGGGQGFGTKTGYVNNVGDTKLYGGGVGQGYT 245
G+ GGA Y+ + +G + T G G
Sbjct: 388 GSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPT-PMGPG--------GPLRPNGLA 438
Query: 246 -----GTFNNGFNPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQP 300
+ A P PV Y PP + P+ P S K Q
Sbjct: 439 PMNAVRAPSRNAQNAAQKPPMQPVMY--PPNYQSLPLSQDLPQPQSTASQGGQNKKLAQV 496
Query: 301 YPSHPVG 307
S
Sbjct: 497 LASATPQ 503
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 28.6 bits (64), Expect = 6.0
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 255 ALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSP 290
A PPAP P +P V P + V +P
Sbjct: 55 AQAYAPPAPAP-LPAALVAPAPAAASIAAPAAVPAP 89
>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a
role in the biomineralisation of teeth. They seem to
regulate formation of crystallites during the secretory
stage of tooth enamel development and are thought to
play a major role in the structural organisation and
mineralisation of developing enamel. The extracellular
matrix of the developing enamel comprises two major
classes of protein: the hydrophobic amelogenins and the
acidic enamelins. Circular dichroism studies of porcine
amelogenin have shown that the protein consists of 3
discrete folding units: the N-terminal region appears to
contain beta-strand structures, while the C-terminal
region displays characteristics of a random coil
conformation. Subsequent studies on the bovine protein
have indicated the amelogenin structure to contain a
repetitive beta-turn segment and a "beta-spiral" between
Gln112 and Leu138, which sequester a (Pro, Leu, Gln)
rich region. The beta-spiral offers a probable site for
interactions with Ca2+ ions. Muatations in the human
amelogenin gene (AMGX) cause X-linked hypoplastic
amelogenesis imperfecta, a disease characterised by
defective enamel. A 9bp deletion in exon 2 of AMGX
results in the loss of codons for Ile5, Leu6, Phe7 and
Ala8, and replacement by a new threonine codon,
disrupting the 16-residue (Met1-Ala16) amelogenin signal
peptide.
Length = 165
Score = 27.8 bits (62), Expect = 6.1
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 253 NPALPVLPPAPVPYIPPPPVITPPVLPQSPVI 284
P PV P P+P PP P + P+ P P++
Sbjct: 115 QPQPPVHPIPPLPPQPPLPPM-FPMQPLPPLL 145
>gnl|CDD|102370 PRK06425, PRK06425, histidinol-phosphate aminotransferase;
Validated.
Length = 332
Score = 28.3 bits (63), Expect = 6.6
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 7/40 (17%)
Query: 281 SPVISGVFSPNPVITKNYQP------YPSHPVG-LVTRSS 313
S + + + NP I NY P +P+G L++R S
Sbjct: 104 SALPFNLINNNPEILNNYNFDLIFIVSPDNPLGNLISRDS 143
>gnl|CDD|212945 cd12012, SH3_RIM-BP_2, Second Src homology 3 domain of
Rab3-interacting molecules (RIMs) binding proteins.
RIMs binding proteins (RBPs, RIM-BPs) associate with
calcium channels present in photoreceptors, neurons, and
hair cells; they interact simultaneously with specific
calcium channel subunits, and active zone proteins, RIM1
and RIM2. RIMs are part of the matrix at the presynaptic
active zone and are associated with synaptic vesicles
through their interaction with the small GTPase Rab3.
RIM-BPs play a role in regulating synaptic transmission
by serving as adaptors and linking calcium channels with
the synaptic vesicle release machinery. RIM-BPs contain
three SH3 domains and two to three fibronectin III
repeats. Invertebrates contain one, while vertebrates
contain at least two RIM-BPs, RIM-BP1 and RIM-BP2.
RIM-BP1 is also called peripheral-type benzodiazapine
receptor associated protein 1 (PRAX-1). Mammals contain
a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are
predominantly expressed in the brain where they display
overlapping but distinct expression patterns, while
RIM-BP3 is almost exclusively expressed in the testis
and is essential in spermiogenesis. The SH3 domains of
RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and
L-type (alpha1D) and N-type (alpha1B) calcium channel
subunits. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate affinity
and selectivity. They play versatile and diverse roles
in the cell including the regulation of enzymes,
changing the subcellular localization of signaling
pathway components, and mediating the formation of
multiprotein complex assemblies.
Length = 62
Score = 25.7 bits (57), Expect = 6.8
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 8/33 (24%)
Query: 82 QALNTYGDRGYGAGGYTDANGFYHGNLGTKNGY 114
Q + YGD+ DA+GFY G + + G
Sbjct: 30 QLIKVYGDK--------DADGFYLGEINGRRGL 54
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.4 bits (63), Expect = 6.9
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 258 VLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQP 300
V+ PAP P P +T + P++P SP+P QP
Sbjct: 398 VVKPAPAVPTTPSPSLTTALFPEAP------SPSPSALPPGQP 434
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 28.1 bits (62), Expect = 7.4
Identities = 21/51 (41%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 259 LPPAPV-PYIPPPPVITPPVLP-----QSPVISGVFSPNPVITKNYQPYPS 303
LPPAP P+I PPP P LP P + G SP P + N P P+
Sbjct: 337 LPPAPSMPHIKPPPTTPIPQLPNQSHKHPPHLQGP-SPFPQMPSNLPPPPA 386
>gnl|CDD|198185 cd09931, SH2_C-SH2_SHP_like, C-terminal Src homology 2 (C-SH2)
domain found in SH2 domain Phosphatases (SHP) proteins.
The SH2 domain phosphatases (SHP-1, SHP-2/Syp,
Drosophila corkscrew (csw), and Caenorhabditis elegans
Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic
signaling enzymes. They are both targeted and regulated
by interactions of their SH2 domains with
phosphotyrosine docking sites. These proteins contain
two SH2 domains (N-SH2, C-SH2) followed by a tyrosine
phosphatase (PTP) domain, and a C-terminal extension.
Shp1 and Shp2 have two tyrosyl phosphorylation sites in
their C-tails, which are phosphorylated differentially
by receptor and nonreceptor PTKs. Csw retains the
proximal tyrosine and Ptp-2 lacks both sites.
Shp-binding proteins include receptors, scaffolding
adapters, and inhibitory receptors. Some of these bind
both Shp1 and Shp2 while others bind only one. Most
proteins that bind a Shp SH2 domain contain one or more
immuno-receptor tyrosine-based inhibitory motifs
(ITIMs): [SIVL]xpYxx[IVL]. Shp1 N-SH2 domain blocks the
catalytic domain and keeps the enzyme in the inactive
conformation, and is thus believed to regulate the
phosphatase activity of SHP-1. Its C-SH2 domain is
thought to be involved in searching for phosphotyrosine
activators. The SHP2 N-SH2 domain is a conformational
switch; it either binds and inhibits the phosphatase, or
it binds phosphoproteins and activates the enzyme. The
C-SH2 domain contributes binding energy and specificity,
but it does not have a direct role in activation. Csw
SH2 domain function is essential, but either SH2 domain
can fulfill this requirement. The role of the csw SH2
domains during Sevenless receptor tyrosine kinase (SEV)
signaling is to bind Daughter of Sevenless rather than
activated SEV. Ptp-2 acts in oocytes downstream of
sheath/oocyte gap junctions to promote major sperm
protein (MSP)-induced MAP Kinase (MPK-1)
phosphorylation. Ptp-2 functions in the oocyte
cytoplasm, not at the cell surface to inhibit multiple
RasGAPs, resulting in sustained Ras activation. It is
thought that MSP triggers PTP-2/Ras activation and ROS
production to stimulate MPK-1 activity essential for
oocyte maturation and that secreted MSP domains and
Cu/Zn superoxide dismutases function antagonistically to
control ROS and MAPK signaling. In general SH2 domains
are involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 99
Score = 26.5 bits (59), Expect = 8.2
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 201 AHLKTNAHGNKQNFGGGQGFGTKTGYVNN 229
H+ G K + GGG+ F + T V +
Sbjct: 49 THIMIRCQGGKYDVGGGEEFDSLTDLVEH 77
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 28.1 bits (63), Expect = 8.3
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 144 RGHQVAGFSTSYNKHESGNKATYYDDGLGHG 174
G V+G S S+ K +G A DG+G G
Sbjct: 562 DGELVSGDSYSFGKLSAGKYAVAISDGMGSG 592
>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional.
Length = 226
Score = 27.7 bits (62), Expect = 8.4
Identities = 12/55 (21%), Positives = 14/55 (25%)
Query: 253 NPALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITKNYQPYPSHPVG 307
PAPV P PV P P+ K + P G
Sbjct: 93 PNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPKPEPKPVVEEKAAPTG 147
>gnl|CDD|222828 PHA01732, PHA01732, proline-rich protein.
Length = 94
Score = 26.2 bits (57), Expect = 8.8
Identities = 13/43 (30%), Positives = 16/43 (37%)
Query: 254 PALPVLPPAPVPYIPPPPVITPPVLPQSPVISGVFSPNPVITK 296
P P P P PPP PP P + V + P I +
Sbjct: 7 PKPPEPPAPLPPAPVPPPPPAPPAPVPEPTVKPVNAEAPKIRE 49
>gnl|CDD|234165 TIGR03303, OM_YaeT, outer membrane protein assembly complex, YaeT
protein. Members of this protein family are the YaeT
protein of the YaeT/YfiO complex for assembling proteins
into the outer membrane of Gram-negative bacteria. This
protein is similar in sequence and function to a
non-essential paralog, YtfM, that is also in the Omp85
family. Members of this family typically have five
tandem copies of the surface antigen variable number
repeat (pfam07244), followed by an outer membrane
beta-barrel domain (pfam01103), while the YtfM family
typically has a single pfam07244 repeat [Protein fate,
Protein and peptide secretion and trafficking].
Length = 741
Score = 27.9 bits (63), Expect = 9.6
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 80 GIQALNTYGDRG------YGAGGYTDANGFYHGNLGTKNGYDVGHAYGG 122
+ N YG + + AGG GF +G ++ D G + GG
Sbjct: 598 RLGYGNGYGGKDLPFYERFYAGGIGSVRGFESNGIGPRDINDSGDSIGG 646
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
0.313 0.138 0.426
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,487,658
Number of extensions: 1721380
Number of successful extensions: 1935
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1699
Number of HSP's successfully gapped: 142
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.8 bits)