Query psy558
Match_columns 692
No_of_seqs 306 out of 483
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 21:06:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy558.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/558hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3701|consensus 100.0 8E-124 2E-128 999.0 35.8 398 1-523 7-410 (411)
2 cd00050 MH2 MH2 domain; C term 100.0 4.7E-71 1E-75 539.3 19.4 175 293-507 2-176 (176)
3 smart00524 DWB Domain B in dwa 100.0 1.1E-69 2.3E-74 527.6 18.1 171 297-507 1-171 (171)
4 PF03166 MH2: MH2 domain; Int 100.0 6.3E-65 1.4E-69 500.4 16.3 176 294-509 2-181 (181)
5 cd00049 MH1 MH1 is a small DNA 100.0 2E-51 4.3E-56 379.7 10.6 119 4-124 1-121 (121)
6 smart00523 DWA Domain A in dwa 100.0 4.6E-49 1E-53 358.1 10.0 108 17-126 1-109 (109)
7 PF03165 MH1: MH1 domain; Int 100.0 6.4E-47 1.4E-51 341.8 1.5 102 22-123 1-103 (103)
8 smart00523 DWA Domain A in dwa 99.9 6E-25 1.3E-29 200.5 6.2 79 508-586 20-108 (109)
9 cd00049 MH1 MH1 is a small DNA 99.9 4.6E-24 9.9E-29 197.9 5.8 77 509-585 36-121 (121)
10 KOG3701|consensus 99.9 2.2E-23 4.8E-28 225.3 11.1 118 508-643 45-174 (411)
11 PF03165 MH1: MH1 domain; Int 99.9 1.4E-24 3.1E-29 196.6 -1.0 77 508-584 17-103 (103)
12 PF10401 IRF-3: Interferon-reg 97.7 0.0017 3.7E-08 64.5 16.9 166 298-516 3-179 (180)
13 PF07624 PSD2: Protein of unkn 73.6 4 8.6E-05 35.4 3.5 47 4-50 26-72 (76)
14 KOG2884|consensus 72.8 6.6 0.00014 41.1 5.4 58 4-61 92-175 (259)
15 KOG3663|consensus 70.8 6.4 0.00014 44.3 5.1 81 20-120 70-169 (518)
16 cd01452 VWA_26S_proteasome_sub 35.0 42 0.0009 34.2 3.7 38 23-61 122-174 (187)
17 PF00498 FHA: FHA domain; Int 30.6 1.2E+02 0.0027 24.5 5.2 43 361-409 23-67 (68)
18 PF15509 DUF4650: Domain of un 29.1 52 0.0011 38.3 3.5 35 15-49 306-340 (520)
19 PF01503 PRA-PH: Phosphoribosy 25.1 95 0.002 27.1 3.7 42 6-50 4-45 (83)
20 PF06576 DUF1133: Protein of u 24.5 99 0.0022 31.4 4.1 43 6-54 46-91 (176)
21 PF09205 DUF1955: Domain of un 21.0 65 0.0014 31.9 2.0 40 10-51 77-116 (161)
22 PF11142 DUF2917: Protein of u 20.4 1.7E+02 0.0036 24.7 4.2 45 354-408 11-55 (63)
No 1
>KOG3701|consensus
Probab=100.00 E-value=8.5e-124 Score=999.00 Aligned_cols=398 Identities=58% Similarity=0.978 Sum_probs=325.4
Q ss_pred CCchhHHHHhhccc-CChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCCC-CCCCcEEecccCCCccccccccCCCeE
Q psy558 1 FTSPAVKKLLGWKQ-GDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGLPHV 78 (692)
Q Consensus 1 ~~~~iV~~Ll~~rQ-G~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~g-~pSkCVTIpRtLDGRLQVagRKg~PHV 78 (692)
|+.|+|+.||+||| |+++|+|||||+||||||||||+++||+||+||+++| ++++||||||+|||||||+||||||||
T Consensus 7 ~~~p~v~~~~~~r~~~~~~e~~~~ka~~slvkklk~~~~~le~l~~av~s~g~~~~~CvtiprslD~Rlq~~~rkg~Phv 86 (411)
T KOG3701|consen 7 FTGPAVKDLLGPRQLGGEDEKFAEKAVESLVKKLKDKKGELENLIKAVESPGTKPTGCVTIPRSLDGRLQVAHRKGFPHV 86 (411)
T ss_pred CCCcchhhccCccccCchhHHHHHHHHHHHHHHhhcccchHHHHHHHhcCCCCCCCceEECCCCCCccccccCCCCCCce
Confidence 78999999999999 9999999999999999999999999999999999998 779999999999999999999999999
Q ss_pred EEEeeecCCCCCCCCCcccCCCCCCCCCCCCCcEEeCCCccccccCCCC-CCcccCCCCCCCCCCCCCcccc--CCCCCC
Q psy558 79 IYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESPVL-PPIVVPRHSEFAPGHSLLPYQQ--MAEPTM 155 (692)
Q Consensus 79 IYcRLWRWPDLh~~nELK~l~~Cq~afdlK~d~VCiNPYHYeRV~sP~i-pp~lv~~~~e~~~~~s~~~~~~--~~~~~~ 155 (692)
||||||||||||+++|||+|++|++||++|+++||||||||+||++|.+ ++.++++..++...++.+.-.+ .....|
T Consensus 87 iy~rlwRwpdl~~~~elk~l~~C~~a~~~~~~~vC~NPyHy~rv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (411)
T KOG3701|consen 87 IYCRLWRWPDLQKNHELKRLECCEHAFESKSDNVCINPYHYSRVESPPILPPPLSPNSPPNDALKTLLDDGGVDIVNRSM 166 (411)
T ss_pred EEEEeecccccccchhheecccCCccccCCCCCeeeCCcccceeecCCCCCcccCCCCCccccccchhhcccccccccCC
Confidence 9999999999999889999999999999999999999999999999944 5666665545443333211000 001233
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccchhhhccccccccCCCCCC-CCCCCCCCCCCCCCC
Q psy558 156 PHNISYSNNGFNQPHSPLSSVSSPASSNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPP-AYSPPQDEKHGSQSP 234 (692)
Q Consensus 156 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~p~~p~~s~~~~~~~~~~~~~~~~~~~~~~~~~p~~-~~~~~~~~~~~~~~~ 234 (692)
|.|..+++ .+++ .++++| +. .. .+.| +..++ .+... +
T Consensus 167 P~n~~~~~-~~~~--------------~~~~tp-------~~-----------~~-----~~~P~~~~~p---~s~~~-~ 204 (411)
T KOG3701|consen 167 PQNNHSSD-LIGP--------------HAPHTP-------DS-----------SQ-----IPAPLGDGGP---SSDSS-A 204 (411)
T ss_pred Cccccccc-cccc--------------CCCCCC-------Cc-----------cc-----CCCCCCCCCC---CCccc-c
Confidence 33333322 1110 000011 00 00 0000 00000 00000 0
Q ss_pred CCCCCCCCCCCCCCcccccccchhhhhhccCCCCCCCCCCCCccccccccccCCCCCCCCCCccEEEEEEeecceeccee
Q psy558 235 HSENAMDTGISSDVTPVPYQVTYFELLTCLMPKMNPNFEEYPTTHIIKMNLYSSFSPPQEQPFWASIAYYELNSRVGEVF 314 (692)
Q Consensus 235 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~WCsIaYyEl~~rVGe~F 314 (692)
. ...++ .+.+..+ ..+.++++||+|+|||+++||||+|
T Consensus 205 ~--~~~P~-~~P~~~~---------------------------------------~~~~~~~~WcsIaYyEl~~rVGE~f 242 (411)
T KOG3701|consen 205 L--PGLPT-DSPDVGP---------------------------------------VHYEEPKSWCSIAYYELNTRVGETF 242 (411)
T ss_pred c--CCCCC-CCCccCc---------------------------------------ccccCCcceeEEEEeeccccccceE
Confidence 0 00000 0001111 2234889999999999999999999
Q ss_pred eeecCeEEEcCCCCCCCCCCeeeecCCcCCCCChhHHHHHhccCCcEEEEEEcCeEEEEecCCCeeEecCCCCCCCCCCC
Q psy558 315 HCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFH 394 (692)
Q Consensus 315 ~v~~~sV~VDGf~dps~~~~RfcLg~lsNv~R~~~~e~~R~~IGkGV~L~~~~G~Vwl~nlS~~pVFVqS~~ld~~~g~~ 394 (692)
+|..++|+||||+|+ ++++|||||+|+|++|++++|++|+|||+||+|++++|+|||+|+|++||||||++||+.+|++
T Consensus 243 ~v~~~~~~vDG~~dp-s~~~rfcLgqlsn~~Rn~~~e~~R~~IG~GV~L~~~~gdVw~~n~sd~pIFVqS~~ln~~~g~~ 321 (411)
T KOG3701|consen 243 HVPGPSITVDGFTDP-SNGSRFCLGQLSNVNRNEKVEKTRAHIGKGVQLSYENGDVWLYNLSDYPIFVQSPNLNYPNGRT 321 (411)
T ss_pred EecCCceEEeeeecC-CCCCceeeccccCCCccchhHHHHhhccCceeeeEecCcEEEEecCCCceeeeCCCCcCCCCCc
Confidence 999999999999999 4669999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeecCCCCeEEEeeHHHHHHHHHHHhhcCchhhhhhccccccCcccccccCCCCCCcccccccccccchhhhheeee
Q psy558 395 QSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYF 474 (692)
Q Consensus 395 ~~~V~KI~pg~slKVFD~~~fa~~L~~~~~~~~~~v~~l~~~c~i~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 474 (692)
+++||||+||++|||||+ +|+++|++++..|++++|+|++||+|
T Consensus 322 ~~~v~ki~Pg~~iKvFd~-~~~~~l~~s~~~g~~~~~~l~~~ctI----------------------------------- 365 (411)
T KOG3701|consen 322 LDTVHKVPPGYSIKVFDF-EFAQQLPTSADPGFESVDQLRKMCTI----------------------------------- 365 (411)
T ss_pred ccceEeeCCCceeEeech-HHHhhhhhcccCCCccccccccceeE-----------------------------------
Confidence 999999999999999999 89999999999999999999999998
Q ss_pred EEEeeEEEeecCCCcccccccccCceeEEEeccChhHHHHHHHhhcCCC
Q psy558 475 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSP 523 (692)
Q Consensus 475 ~~i~RISFvKGWG~~Y~Rq~ItstPCWIEI~L~~~Le~LD~VLsqmg~p 523 (692)
|||||||||++|+||+||+||||||||||+||+|||+||++||.|
T Consensus 366 ----riSFvKGWG~~Y~Rq~It~~PCWiEvhl~~p~~~lD~vl~~~~~~ 410 (411)
T KOG3701|consen 366 ----RISFVKGWGECYSRQDITSTPCWIEVHLNGPLQWLDTVLTQMGSP 410 (411)
T ss_pred ----EEEEeccccccccccccccCcceEEEecCCcHHHHHHHHhhcCCC
Confidence 999999999999999999999999999999999999999999854
No 2
>cd00050 MH2 MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins
Probab=100.00 E-value=4.7e-71 Score=539.28 Aligned_cols=175 Identities=59% Similarity=1.025 Sum_probs=171.3
Q ss_pred CCCCccEEEEEEeecceecceeeeecCeEEEcCCCCCCCCCCeeeecCCcCCCCChhHHHHHhccCCcEEEEEEcCeEEE
Q psy558 293 QEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYA 372 (692)
Q Consensus 293 ~~~~~WCsIaYyEl~~rVGe~F~v~~~sV~VDGf~dps~~~~RfcLg~lsNv~R~~~~e~~R~~IGkGV~L~~~~G~Vwl 372 (692)
.++++||+|+|||||+||||+|+++.++++||||+|| ++++|||||+|+|++|++++++||+|||+||+|++++|+||+
T Consensus 2 ~~~~~WCsIaY~El~~RVGe~f~~~~~~~~VDGf~d~-~~~~rfcLg~lsn~~R~~~ve~~R~~IG~Gv~L~~~~g~Vw~ 80 (176)
T cd00050 2 SEPEHWCSIAYYELNTRVGETFKVSGPNITVDGFTDP-SNGSRFCLGQLSNVNRNETVEKTRRHIGKGVQLSYENGEVWA 80 (176)
T ss_pred CCCCceEEEEEEEccceecccEeccCCcEEEEecccC-CCCCEEEecccCCCCCcHHHHHHHHhccCCEEEEEeCCeEEE
Confidence 3789999999999999999999999999999999999 688999999999999999999999999999999999999999
Q ss_pred EecCCCeeEecCCCCCCCCCCCCCceeecCCCCeEEEeeHHHHHHHHHHHhhcCchhhhhhccccccCcccccccCCCCC
Q psy558 373 ECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRT 452 (692)
Q Consensus 373 ~nlS~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slKVFD~~~fa~~L~~~~~~~~~~v~~l~~~c~i~p~~~~~~~~~~~ 452 (692)
+|+|++||||||++||+++++++++||||+||++|||||+++|+++|+++...+++++|+|++||+|
T Consensus 81 ~~~S~~~VFVqS~~l~~~~~~~~~~V~Kv~pg~~lKvFd~~~f~~~l~~~~~~~~~~~~~l~~~c~i------------- 147 (176)
T cd00050 81 YNLSDHPIFVQSPTLDYPLGRPLLTVHKVPPGYSLKVFDFEQFEQLLRQAAGSTFDGVYDLRRMCTI------------- 147 (176)
T ss_pred EEcCCCCEEEcCCCCCcccCCCCcceEEeCCCCEEEEeCHHHHHHHHHhhhcccCccHHHHHhhceE-------------
Confidence 9999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CcccccccccccchhhhheeeeEEEeeEEEeecCCCcccccccccCceeEEEecc
Q psy558 453 EIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLH 507 (692)
Q Consensus 453 ~~~~~~~~~~~~~~~~~~~~~~~~i~RISFvKGWG~~Y~Rq~ItstPCWIEI~L~ 507 (692)
|||||||||++|+||+||+|||||||+||
T Consensus 148 --------------------------riSFvKGWG~~Y~Rq~it~tPCWiEi~l~ 176 (176)
T cd00050 148 --------------------------RISFVKGWGEDYPRQDITSTPCWIEVHLN 176 (176)
T ss_pred --------------------------EEEEeccccccccccccCCCceEEEEEcC
Confidence 99999999999999999999999999997
No 3
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=100.00 E-value=1.1e-69 Score=527.61 Aligned_cols=171 Identities=59% Similarity=1.028 Sum_probs=167.8
Q ss_pred ccEEEEEEeecceecceeeeecCeEEEcCCCCCCCCCCeeeecCCcCCCCChhHHHHHhccCCcEEEEEEcCeEEEEecC
Q psy558 297 FWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLS 376 (692)
Q Consensus 297 ~WCsIaYyEl~~rVGe~F~v~~~sV~VDGf~dps~~~~RfcLg~lsNv~R~~~~e~~R~~IGkGV~L~~~~G~Vwl~nlS 376 (692)
+||+|+|||+|+||||+|+++.++|+||||+|| ++++|||||+|+|++|++++++||+|||+||+|++++|+||++|+|
T Consensus 1 ~WcsIaYyEl~~rVGe~f~~~~p~v~Vdgf~d~-~~~~rfcLg~lsn~nR~~~~~~~R~~IG~Gv~L~~~~g~Vw~~~~s 79 (171)
T smart00524 1 SWCSIAYYELNTRVGETFKVSSPSVTVDGFTDP-SDGNRFCLGQLSNVNRNEATELIRKHIGKGVQLSYENGDVWLYNRS 79 (171)
T ss_pred CCcEEEEEEecccccceEEccCCeEEEEecccC-CCCCeeEeccCCCCCccHHHHHHHHhccCceEEEEeCCeEEEEEcC
Confidence 699999999999999999999999999999999 6789999999999999999999999999999999999999999999
Q ss_pred CCeeEecCCCCCCCCCCCCCceeecCCCCeEEEeeHHHHHHHHHHHhhcCchhhhhhccccccCcccccccCCCCCCccc
Q psy558 377 DSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPF 456 (692)
Q Consensus 377 ~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slKVFD~~~fa~~L~~~~~~~~~~v~~l~~~c~i~p~~~~~~~~~~~~~~~ 456 (692)
++||||||++||+.+|+++++||||+||++|||||+++|+++|+++...+++++|+|++||+|
T Consensus 80 ~~~VFVqS~~~~~~~~~~~~~V~Kv~pg~~lKvFd~~~f~~~l~~~~~~~~~~~~~l~~~c~i----------------- 142 (171)
T smart00524 80 DSPIFVQSPYLDEPGGRTLDTVHKLPPGYSIKVFDMEKFAQLLARELAKGFEGVYDLARMCTI----------------- 142 (171)
T ss_pred CCCeEEcCCCcccccCCCCcceEEECCCCeEEEeChHHHHHHHHhhhcccCccccchhhheeE-----------------
Confidence 999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccchhhhheeeeEEEeeEEEeecCCCcccccccccCceeEEEecc
Q psy558 457 AVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLH 507 (692)
Q Consensus 457 ~~~~~~~~~~~~~~~~~~~~i~RISFvKGWG~~Y~Rq~ItstPCWIEI~L~ 507 (692)
|||||||||++|+||+||+|||||||+||
T Consensus 143 ----------------------riSFvKGWG~~Y~Rq~it~tPCWiEi~l~ 171 (171)
T smart00524 143 ----------------------RISFVKGWGPDYSRQTITSTPCWIEVHLN 171 (171)
T ss_pred ----------------------EEEEecccCCcccccccccCceEEEEEcC
Confidence 99999999999999999999999999997
No 4
>PF03166 MH2: MH2 domain; InterPro: IPR001132 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the SMAD (Mothers against decapentaplegic (MAD) homologue) (also called MH2 for MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C terminus of MH2 [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1MK2_A 1U7F_A 1MJS_A 1KHU_A 1DD1_C 1G88_A 1U7V_B 1MR1_B 1YGS_A 3DIT_B ....
Probab=100.00 E-value=6.3e-65 Score=500.42 Aligned_cols=176 Identities=64% Similarity=1.126 Sum_probs=157.7
Q ss_pred CCCccEEEEEEeecceecceeeeecCeEEEcCCCCCCCCCCeeeecCCcCCCCChhHHHHHhccCCcEEEEEE-cCeEEE
Q psy558 294 EQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYV-GGEVYA 372 (692)
Q Consensus 294 ~~~~WCsIaYyEl~~rVGe~F~v~~~sV~VDGf~dps~~~~RfcLg~lsNv~R~~~~e~~R~~IGkGV~L~~~-~G~Vwl 372 (692)
++++||+|+|||+++||||+|+++.++|+||||+|| ++++|||||+|+|++|+++++++|+|||+||+|+++ +|+||+
T Consensus 2 ~~~~Wc~I~Y~E~~~rVG~~f~~~~~~v~idG~~d~-~~~~r~~Lg~~~n~~R~~~~~~~R~~IG~Gi~l~~~~~G~V~l 80 (181)
T PF03166_consen 2 EPEIWCSIAYYELNTRVGEAFKARSPSVIIDGFTDP-SDGDRFCLGQLSNVNRDSKTEKIRRHIGKGIKLSYEEDGNVWL 80 (181)
T ss_dssp S-SSSEEEEEEETTEEESEEEEEESSEEEEESSSSS-SSSSEEECTT---TT--HHHHHHHTTCTT-EEEEEETTTEEEE
T ss_pred CCCeeEEEEEEecCCeEcceeEccCCeEEEeeccCC-CCCCcEecCccCCCCCChHHhhHHheecCcEEEEEecCCeEEE
Confidence 689999999999999999999999999999999999 599999999999999999999999999999999999 699999
Q ss_pred EecCCCeeEecCCCCCCCCCCCCCceeecCCCCeEEEeeHHHHHHHHHHHhhcCchh---hhhhccccccCcccccccCC
Q psy558 373 ECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEA---VYELTKMCTISPIFCIRNKC 449 (692)
Q Consensus 373 ~nlS~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slKVFD~~~fa~~L~~~~~~~~~~---v~~l~~~c~i~p~~~~~~~~ 449 (692)
+|+|++||||||+++|..++.++++|+||+||+++||||+++|+++|+++.+.++++ +++|.+||+|
T Consensus 81 ~n~s~~pVFVqS~~~n~~~~~~~~~V~Kv~pg~~~kvFd~~~f~~~l~~~~~~~~~~~~~~~~l~~~c~i---------- 150 (181)
T PF03166_consen 81 YNRSDSPVFVQSPTLNYQHGFHPGTVCKVPPGYSLKVFDMEKFAQLLRQAVRRGYEAEEDVDELRKMCTI---------- 150 (181)
T ss_dssp EE-SSS-EEEE-HHHHHHTTSTTTSEEEE-TT-EEEEEEHHHHHHHHHHHHTTHHHHTTTHHGGGGGGEE----------
T ss_pred EECCCCCEEEccCCCCcccCcCCCCcEEeCCCceeeccCHHHHHHHHHhhhccccccccchhhhhhcceE----------
Confidence 999999999999999999999999999999999999999999999999999999876 8999999988
Q ss_pred CCCCcccccccccccchhhhheeeeEEEeeEEEeecCCCcccccccccCceeEEEeccCh
Q psy558 450 NRTEIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGP 509 (692)
Q Consensus 450 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~RISFvKGWG~~Y~Rq~ItstPCWIEI~L~~~ 509 (692)
|||||||||++|+||+||+|||||||+||+|
T Consensus 151 -----------------------------riSFvKGWG~~Y~R~~it~~PCWiEi~l~~p 181 (181)
T PF03166_consen 151 -----------------------------RISFVKGWGPEYRRQDITSCPCWIEIHLNGP 181 (181)
T ss_dssp -----------------------------EEEESSB-STTSSSSSGGGSSSEEEEEEHH-
T ss_pred -----------------------------EEEEEcccCCcccccCcccCCeEEEEEccCC
Confidence 9999999999999999999999999999986
No 5
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=100.00 E-value=2e-51 Score=379.72 Aligned_cols=119 Identities=67% Similarity=1.195 Sum_probs=114.3
Q ss_pred hhHHHHhhccc-CChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCCC-CCCCcEEecccCCCccccccccCCCeEEEE
Q psy558 4 PAVKKLLGWKQ-GDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGLPHVIYC 81 (692)
Q Consensus 4 ~iV~~Ll~~rQ-G~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~g-~pSkCVTIpRtLDGRLQVagRKg~PHVIYc 81 (692)
++|++||+||| |||+|+|++|||+||||||||++ +||+|++||+++| .+|+||||||+ ||||||++||++||||||
T Consensus 1 ~~~~~ll~~~~~~~~~e~~~~k~~~sLlKkLKk~~-~le~L~~AV~s~g~~~t~CV~i~r~-D~rl~~~~r~~~phv~~c 78 (121)
T cd00049 1 ALVKRLLGEKKIGGEEEKWKKKAAESLLKKLKKKI-QLEELEDAVESRGGPPTRCVLIPRS-DGRLQVSHRKGLPHVIYC 78 (121)
T ss_pred ChhHHhhcccccCcchHHHHHHHHHHHHHHHhccc-CHHHHHHHHHcCCCCCCCeEEeccc-cccccccccCCCcceEEE
Confidence 47999999999 89999999999999999999964 9999999999986 77999999998 999999999999999999
Q ss_pred eeecCCCCCCCCCcccCCCCCCCCCCCCCcEEeCCCccccccC
Q psy558 82 RVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 124 (692)
Q Consensus 82 RLWRWPDLh~~nELK~l~~Cq~afdlK~d~VCiNPYHYeRV~s 124 (692)
||||||||++++|||++++|+|+|++|.++||||||||+||+.
T Consensus 79 rlwRWpDL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~ 121 (121)
T cd00049 79 RVWRWPDLRSNHELKRLETCEHAFDSKPDEVCINPYHYSRVVR 121 (121)
T ss_pred eeeeccccCchHhheeCccCCCccccCCCeEEeCCceeeeecC
Confidence 9999999999999999999999999999999999999999974
No 6
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=100.00 E-value=4.6e-49 Score=358.08 Aligned_cols=108 Identities=65% Similarity=1.183 Sum_probs=104.3
Q ss_pred hhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCCC-CCCCcEEecccCCCccccccccCCCeEEEEeeecCCCCCCCCCc
Q psy558 17 EEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHEL 95 (692)
Q Consensus 17 EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~g-~pSkCVTIpRtLDGRLQVagRKg~PHVIYcRLWRWPDLh~~nEL 95 (692)
++|+||+|||+|||||||+| +||+|++||+++| .+|+||||||++|||||||+||++||||||||||||||++++||
T Consensus 1 ~~ek~~~k~~~sL~KklK~k--~le~L~~AV~s~g~~~t~CV~i~~~~dgrl~~~~~~~~phvi~crLfRWpdL~s~~eL 78 (109)
T smart00523 1 VEEKWAKKATESLLKKLKKK--QLEELLQAVESKGGPPTRCVLIPRSLDGRLQVAHRKGLPHVLYCRLFRWPDLQSPHEL 78 (109)
T ss_pred CcHHHHHHHHHHHHHHHHHH--HHHHHHHHHHcCCCCCCCeEEeCcccCcccccccCCCCCcEEEEEEeeCCCCCCHHHc
Confidence 47999999999999999994 9999999999987 78999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCCCCCCcEEeCCCccccccCCC
Q psy558 96 KPLEHCQFPFSAKQKDVCINPYHYKRVESPV 126 (692)
Q Consensus 96 K~l~~Cq~afdlK~d~VCiNPYHYeRV~sP~ 126 (692)
|++++|+|||+++.++||||||||+||+.|+
T Consensus 79 k~l~~C~~~~~~~~~~vC~NPyHy~rv~~p~ 109 (109)
T smart00523 79 KALPTCEHAFESKSDEVCCNPYHYSRVERPE 109 (109)
T ss_pred eecccCCCcccCCCCeEEeCCceEEEeecCC
Confidence 9999999999999999999999999999873
No 7
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=100.00 E-value=6.4e-47 Score=341.76 Aligned_cols=102 Identities=67% Similarity=1.223 Sum_probs=80.5
Q ss_pred HHHHHHHHHHHHhhccCcHHHHHHHhcCCC-CCCCcEEecccCCCccccccccCCCeEEEEeeecCCCCCCCCCcccCCC
Q psy558 22 AEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEH 100 (692)
Q Consensus 22 akkAIeSLVKKLKekk~eLesLi~AItt~g-~pSkCVTIpRtLDGRLQVagRKg~PHVIYcRLWRWPDLh~~nELK~l~~ 100 (692)
.||||+||||||||++++||+|++||+|+| .+|+||||||+|||||||++|||+||||||||||||||++++|||+++.
T Consensus 1 ~~k~~~sLlkkLK~~~~~le~L~~Av~s~g~~~t~CV~i~r~~dgrl~v~~~k~~phvl~crlwRwpdL~~~~eLk~l~~ 80 (103)
T PF03165_consen 1 CEKAIKSLLKKLKKKIGQLEELLKAVESRGDPPTKCVTIPRSLDGRLQVSGRKGLPHVLYCRLWRWPDLRHSHELKRLPH 80 (103)
T ss_dssp HHHHHHHHHHHHTTTCTHHHHHHHHHHCTTTSTS---EEE--TTS-EEETTEEE-HHHHHHHHHT-TT--SCCCEEE-TT
T ss_pred ChHHHHHHHHHHccccchHHHHHHHHhcCCCCCCCcEEecCccCccccccccccCceEEEEEEechhhcCCHHhcccCCC
Confidence 489999999999998889999999999875 8999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCcEEeCCCcccccc
Q psy558 101 CQFPFSAKQKDVCINPYHYKRVE 123 (692)
Q Consensus 101 Cq~afdlK~d~VCiNPYHYeRV~ 123 (692)
|+|+|+++.++||||||||+||+
T Consensus 81 C~~~~~~~~~~vC~NPyHy~rv~ 103 (103)
T PF03165_consen 81 CRFAFDSKNDEVCCNPYHYSRVC 103 (103)
T ss_dssp -TT-GGG--SEEE--GGGEEE--
T ss_pred CCChhhcCCCCEEeCCcEeeecC
Confidence 99999999999999999999986
No 8
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=99.91 E-value=6e-25 Score=200.49 Aligned_cols=79 Identities=53% Similarity=1.034 Sum_probs=72.7
Q ss_pred ChhHHHHHHHhhcC-CCCCCCc---------ccccCCCCceEEEeeeecCCCCCCCCCcccCCcccCCCCCCCCcEEeCC
Q psy558 508 GPLQWLDKVLIQMG-SPHQPIS---------SVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINP 577 (692)
Q Consensus 508 ~~Le~LD~VLsqmg-~p~k~is---------sVs~rkg~phvi~crl~RWpdL~~~~ELk~l~~C~~~~~~~~~~vC~NP 577 (692)
..||.|.++++.-| .|++||. +|++++++||||||||||||||++++|||++++|+++|++++++|||||
T Consensus 20 k~le~L~~AV~s~g~~~t~CV~i~~~~dgrl~~~~~~~~phvi~crLfRWpdL~s~~eLk~l~~C~~~~~~~~~~vC~NP 99 (109)
T smart00523 20 KQLEELLQAVESKGGPPTRCVLIPRSLDGRLQVAHRKGLPHVLYCRLFRWPDLQSPHELKALPTCEHAFESKSDEVCCNP 99 (109)
T ss_pred HHHHHHHHHHHcCCCCCCCeEEeCcccCcccccccCCCCCcEEEEEEeeCCCCCCHHHceecccCCCcccCCCCeEEeCC
Confidence 47888999998877 4588883 6889999999999999999999999999999999999999999999999
Q ss_pred ccccccccC
Q psy558 578 YHYKRVESP 586 (692)
Q Consensus 578 yHy~rv~~p 586 (692)
|||+||+.|
T Consensus 100 yHy~rv~~p 108 (109)
T smart00523 100 YHYSRVERP 108 (109)
T ss_pred ceEEEeecC
Confidence 999999987
No 9
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=99.89 E-value=4.6e-24 Score=197.94 Aligned_cols=77 Identities=58% Similarity=1.134 Sum_probs=70.9
Q ss_pred hhHHHHHHHhhcCCC-CCCCc--------ccccCCCCceEEEeeeecCCCCCCCCCcccCCcccCCCCCCCCcEEeCCcc
Q psy558 509 PLQWLDKVLIQMGSP-HQPIS--------SVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYH 579 (692)
Q Consensus 509 ~Le~LD~VLsqmg~p-~k~is--------sVs~rkg~phvi~crl~RWpdL~~~~ELk~l~~C~~~~~~~~~~vC~NPyH 579 (692)
.||.|+++++..|.+ ++||. +|++|+++|||+||||||||||++++|||+|++|+++|+.+.+.|||||||
T Consensus 36 ~le~L~~AV~s~g~~~t~CV~i~r~D~rl~~~~r~~~phv~~crlwRWpDL~~~~eLk~l~~C~~~~~~~~~~vC~NPyH 115 (121)
T cd00049 36 QLEELEDAVESRGGPPTRCVLIPRSDGRLQVSHRKGLPHVIYCRVWRWPDLRSNHELKRLETCEHAFDSKPDEVCINPYH 115 (121)
T ss_pred CHHHHHHHHHcCCCCCCCeEEeccccccccccccCCCcceEEEeeeeccccCchHhheeCccCCCccccCCCeEEeCCce
Confidence 889998888877776 77773 678899999999999999999999999999999999999999999999999
Q ss_pred cccccc
Q psy558 580 YKRVES 585 (692)
Q Consensus 580 y~rv~~ 585 (692)
|+||+.
T Consensus 116 y~rv~~ 121 (121)
T cd00049 116 YSRVVR 121 (121)
T ss_pred eeeecC
Confidence 999974
No 10
>KOG3701|consensus
Probab=99.89 E-value=2.2e-23 Score=225.27 Aligned_cols=118 Identities=48% Similarity=0.902 Sum_probs=98.7
Q ss_pred ChhHHHHHHHhhcCCC-CCCCc---------ccccCCCCceEEEeeeecCCCCCCCCCcccCCcccCCCCCCCCcEEeCC
Q psy558 508 GPLQWLDKVLIQMGSP-HQPIS---------SVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINP 577 (692)
Q Consensus 508 ~~Le~LD~VLsqmg~p-~k~is---------sVs~rkg~phvi~crl~RWpdL~~~~ELk~l~~C~~~~~~~~~~vC~NP 577 (692)
+.||.|.+||...|.. ++|+. +|+||||+||||||||||||||++.+|||++++|+++|+++.+.|||||
T Consensus 45 ~~le~l~~av~s~g~~~~~CvtiprslD~Rlq~~~rkg~Phviy~rlwRwpdl~~~~elk~l~~C~~a~~~~~~~vC~NP 124 (411)
T KOG3701|consen 45 GELENLIKAVESPGTKPTGCVTIPRSLDGRLQVAHRKGFPHVIYCRLWRWPDLQKNHELKRLECCEHAFESKSDNVCINP 124 (411)
T ss_pred chHHHHHHHhcCCCCCCCceEECCCCCCccccccCCCCCCceEEEEeecccccccchhheecccCCccccCCCCCeeeCC
Confidence 6799999999999887 88883 9999999999999999999999999999999999999999999999999
Q ss_pred ccccccccCCcccccccccccccccccCCCCceeccCCCCCCCCCCCCcccCC--CCCCCCCCCCCCC
Q psy558 578 YHYKRVESPVTLFDILTHLKIYSFYFLPVLPPIVVPRHSEFAPGHSLLPYQQM--AEPTMPHNISYSN 643 (692)
Q Consensus 578 yHy~rv~~p~~~~~~~~~~~~~~~~~~p~~~p~lvp~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 643 (692)
|||+||+.| ++++|.+++++.++....+.+..... .++.||.|..+++
T Consensus 125 yHy~rv~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~n~~~~~ 174 (411)
T KOG3701|consen 125 YHYSRVESP------------------PILPPPLSPNSPPNDALKTLLDDGGVDIVNRSMPQNNHSSD 174 (411)
T ss_pred cccceeecC------------------CCCCcccCCCCCccccccchhhcccccccccCCCccccccc
Confidence 999999998 45777777777665444443322211 2578899988875
No 11
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=99.88 E-value=1.4e-24 Score=196.58 Aligned_cols=77 Identities=55% Similarity=1.087 Sum_probs=56.1
Q ss_pred ChhHHHHHHHh-hcCCCCCCCc---------ccccCCCCceEEEeeeecCCCCCCCCCcccCCcccCCCCCCCCcEEeCC
Q psy558 508 GPLQWLDKVLI-QMGSPHQPIS---------SVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINP 577 (692)
Q Consensus 508 ~~Le~LD~VLs-qmg~p~k~is---------sVs~rkg~phvi~crl~RWpdL~~~~ELk~l~~C~~~~~~~~~~vC~NP 577 (692)
+.||.|.++++ +-+.+++||. +|++++|.||||+|||||||||++++|||+|+.|+++|+.++++|||||
T Consensus 17 ~~le~L~~Av~s~g~~~t~CV~i~r~~dgrl~v~~~k~~phvl~crlwRwpdL~~~~eLk~l~~C~~~~~~~~~~vC~NP 96 (103)
T PF03165_consen 17 GQLEELLKAVESRGDPPTKCVTIPRSLDGRLQVSGRKGLPHVLYCRLWRWPDLRHSHELKRLPHCRFAFDSKNDEVCCNP 96 (103)
T ss_dssp THHHHHHHHHHCTTTSTS---EEE--TTS-EEETTEEE-HHHHHHHHHT-TT--SCCCEEE-TT-TT-GGG--SEEE--G
T ss_pred chHHHHHHHHhcCCCCCCCcEEecCccCccccccccccCceEEEEEEechhhcCCHHhcccCCCCCChhhcCCCCEEeCC
Confidence 58999999998 5567788883 5899999999999999999999999999999999999999999999999
Q ss_pred ccccccc
Q psy558 578 YHYKRVE 584 (692)
Q Consensus 578 yHy~rv~ 584 (692)
|||+|||
T Consensus 97 yHy~rv~ 103 (103)
T PF03165_consen 97 YHYSRVC 103 (103)
T ss_dssp GGEEE--
T ss_pred cEeeecC
Confidence 9999986
No 12
>PF10401 IRF-3: Interferon-regulatory factor 3; InterPro: IPR019471 This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha, beta-stimulated gene). IRF-3 pre-exists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1J2F_A 1QWT_A 3A77_B 1ZOQ_A 3DSH_A.
Probab=97.72 E-value=0.0017 Score=64.46 Aligned_cols=166 Identities=15% Similarity=0.152 Sum_probs=102.4
Q ss_pred cEEEEEEeecceecceeeeecCe-EEEcC-CCCCC------CCCCeeeecCCcCCC-C--ChhHHHHHhccCCcEEEEEE
Q psy558 298 WASIAYYELNSRVGEVFHCQSHS-VIVDG-FTNPS------NNLNRFCLGQLSNVN-R--NSTIENTRRHIGKGVHLYYV 366 (692)
Q Consensus 298 WCsIaYyEl~~rVGe~F~v~~~s-V~VDG-f~dps------~~~~RfcLg~lsNv~-R--~~~~e~~R~~IGkGV~L~~~ 366 (692)
+-.|..|=.+..|+++- ++++. +-|=. -.+.. .+..+..|=.-.... . .+.++++-.+.++||.|...
T Consensus 3 ~l~V~v~Y~G~~V~~~~-v~~~~GcRl~~~~~~~~~~~~~~~~~~~v~lP~p~~~~~~~q~~~~~~lL~~l~rGl~L~~~ 81 (180)
T PF10401_consen 3 SLEVTVYYRGRLVLETT-VSNPEGCRLSYGPPPSQGHLCGPSSPEQVWLPSPPPIPDQKQREYTERLLNHLERGLLLWSN 81 (180)
T ss_dssp EEEEEEEETTCEEEEEE-EEETT-EEEESSSTCCCCCHH--TTSEEEE---GCC---HHHHHHHHHHHCCTTT-EEEEEE
T ss_pred EEEEEEEECCEEEEEEE-EeCCCcEEEEecCCCccccccCCCCCCeeECCCCCccCChhHHHHHHHHHHhhcCcEEEEEe
Confidence 45677777888888763 55443 33321 11110 022333332222211 1 35789999999999999999
Q ss_pred cCeEEEEecCCCeeEecCCCCCCCCCCCCCceeecCCCCeEEEeeHHHHHHHHHHHhhcCchhhhhhccccccCcccccc
Q psy558 367 GGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIR 446 (692)
Q Consensus 367 ~G~Vwl~nlS~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slKVFD~~~fa~~L~~~~~~~~~~v~~l~~~c~i~p~~~~~ 446 (692)
+++||++++....||...+.-.... .-.|+..+...||||+++|-+.|++..+.+-. .|
T Consensus 82 ~~gI~akRlc~~~Vfw~g~~~~~~~-----~P~kL~r~~~~~lFd~~~F~~~L~~~~~~~~~-----------~P----- 140 (180)
T PF10401_consen 82 PQGIYAKRLCQCRVFWSGPEAPPSD-----EPNKLEREEPVKLFDTQQFLRELQRFPQGGGP-----------SP----- 140 (180)
T ss_dssp TTEEEEEE-SSS-EEEECCTSS-S------S-SE--CTS-EEEEEHHHHHHHHHHHHTTSSS------------------
T ss_pred CCEEEEEecCCceEEEEcCCccCCC-----CCcccCcCCceeeccHHHHHHHHHHHhcCCCC-----------CC-----
Confidence 9999999999999999998875432 33499999999999999999988776543210 00
Q ss_pred cCCCCCCcccccccccccchhhhheeeeEEEeeEEEeecCCCcccccccccCceeEEEeccChhHHHHHH
Q psy558 447 NKCNRTEIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKV 516 (692)
Q Consensus 447 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~RISFvKGWG~~Y~Rq~ItstPCWIEI~L~~~Le~LD~V 516 (692)
. +-|.++|..=|-. .+.....+-+++|...-+=++++.+
T Consensus 141 ---------~-------------------~~i~LcfGe~~~~---~~~~~~klI~v~v~p~~a~~l~~~~ 179 (180)
T PF10401_consen 141 ---------D-------------------YQIYLCFGEEWPD---GRPWEKKLITVQVEPVFARQLLEMA 179 (180)
T ss_dssp ------------------------------EEEEEESSSSTT---SSCCCCSSEEEEEEEHHHHHHHHHH
T ss_pred ---------C-------------------cEEEEEEcccCCC---CCCccCceEEEEEEeHHHHHHHHHh
Confidence 0 1126777655532 1678888999999887777777654
No 13
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=73.58 E-value=4 Score=35.40 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=42.0
Q ss_pred hhHHHHhhcccCChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCC
Q psy558 4 PAVKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCP 50 (692)
Q Consensus 4 ~iV~~Ll~~rQG~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~ 50 (692)
-.+.+||.|--|.+-+.--+.+|+.++.++|+...-+.+||.||.+.
T Consensus 26 ~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~y~~~~Li~~iv~S 72 (76)
T PF07624_consen 26 CFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANGYRLRDLILAIVTS 72 (76)
T ss_pred HHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 46889999999998887888999999999999888999999999764
No 14
>KOG2884|consensus
Probab=72.79 E-value=6.6 Score=41.09 Aligned_cols=58 Identities=29% Similarity=0.339 Sum_probs=42.8
Q ss_pred hhHHHHhhcccCC-----------hhhHHHHHHHHHHHHHHhhcc---------------CcHHHHHHHhcCCCCCCCcE
Q psy558 4 PAVKKLLGWKQGD-----------EEEKWAEKAVDSLVKKLKKSK---------------GDIEELERALSCPGQPSKCV 57 (692)
Q Consensus 4 ~iV~~Ll~~rQG~-----------EeE~fakkAIeSLVKKLKekk---------------~eLesLi~AItt~g~pSkCV 57 (692)
.|.|--|-|||+. ..-+-.||....|.|+|||.+ .-|+++|.|+-..|.-|.||
T Consensus 92 ~iA~lalkhRqnk~~~~riVvFvGSpi~e~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv 171 (259)
T KOG2884|consen 92 QIAQLALKHRQNKNQKQRIVVFVGSPIEESEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLV 171 (259)
T ss_pred HHHHHHHHhhcCCCcceEEEEEecCcchhhHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEE
Confidence 4667778899964 122234568888999999854 23678888887667889999
Q ss_pred Eecc
Q psy558 58 TIPR 61 (692)
Q Consensus 58 TIpR 61 (692)
++|+
T Consensus 172 ~Vpp 175 (259)
T KOG2884|consen 172 SVPP 175 (259)
T ss_pred EeCC
Confidence 9998
No 15
>KOG3663|consensus
Probab=70.80 E-value=6.4 Score=44.25 Aligned_cols=81 Identities=31% Similarity=0.660 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHhh--ccCcHHHHHHHhcCCCCCCCcEEecccCCCccccccccCCCeEEEE-----eeecCC-----
Q psy558 20 KWAEKAVDSLVKKLKK--SKGDIEELERALSCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYC-----RVWRWP----- 87 (692)
Q Consensus 20 ~fakkAIeSLVKKLKe--kk~eLesLi~AItt~g~pSkCVTIpRtLDGRLQVagRKg~PHVIYc-----RLWRWP----- 87 (692)
|||-| |+-|||| +.+.-|+++.+|+- ..+.+||.=--.--|+++ -|=| ++||--
T Consensus 70 KWASR----LLaKlrKDIr~e~rEdFVltItG-kk~p~CVlSnpDQKGKmR---------RIDCLRQADKVWRLDLVmVI 135 (518)
T KOG3663|consen 70 KWASR----LLAKLRKDIRPEYREDFVLTITG-KKPPCCVLSNPDQKGKMR---------RIDCLRQADKVWRLDLVMVI 135 (518)
T ss_pred HHHHH----HHHHHHhhcchHHHHHHHhhhcC-CCCCceeecCccccCcee---------ehhhhhhhchheeeeeeeEE
Confidence 55554 6777776 22456788887763 357889875433334442 2333 577742
Q ss_pred -----CCCC--CCCcccCCCCCCCCCCCCCcEEeCCCccc
Q psy558 88 -----DLQS--HHELKPLEHCQFPFSAKQKDVCINPYHYK 120 (692)
Q Consensus 88 -----DLh~--~nELK~l~~Cq~afdlK~d~VCiNPYHYe 120 (692)
-|.+ ...|..-+.|-.+ -.||||||.-
T Consensus 136 LFKgIPLESTDGERL~ksp~C~hP------~LCVqPhHi~ 169 (518)
T KOG3663|consen 136 LFKGIPLESTDGERLEKSPQCSHP------GLCVQPHHIG 169 (518)
T ss_pred eecccccccCchhhhhcCcccCCC------ccccccceee
Confidence 1222 2345555666543 5899999974
No 16
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=34.99 E-value=42 Score=34.18 Aligned_cols=38 Identities=29% Similarity=0.412 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhhcc---------------CcHHHHHHHhcCCCCCCCcEEecc
Q psy558 23 EKAVDSLVKKLKKSK---------------GDIEELERALSCPGQPSKCVTIPR 61 (692)
Q Consensus 23 kkAIeSLVKKLKekk---------------~eLesLi~AItt~g~pSkCVTIpR 61 (692)
++.+..+.|||||+. +-|+.|++||.++ ..|.+|+||-
T Consensus 122 ~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~~~~~-~~s~~~~~~~ 174 (187)
T cd01452 122 EKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNGK-DGSHLVSVPP 174 (187)
T ss_pred HHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHHhcCC-CCceEEEeCC
Confidence 345667778887732 4588899999644 3499999985
No 17
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=30.56 E-value=1.2e+02 Score=24.51 Aligned_cols=43 Identities=16% Similarity=0.312 Sum_probs=28.8
Q ss_pred EEEEEEcC-eEEEEec-CCCeeEecCCCCCCCCCCCCCceeecCCCCeEEE
Q psy558 361 VHLYYVGG-EVYAECL-SDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKI 409 (692)
Q Consensus 361 V~L~~~~G-~Vwl~nl-S~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slKV 409 (692)
..|.++++ .+|++.+ |.+.+||+...+. +..-++|..|..|++
T Consensus 23 a~i~~~~~~~~~i~d~~s~ngt~vng~~l~------~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 23 ARISFDDDGQFYIEDLGSTNGTFVNGQRLG------PGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEEEEETTEEEEEEESSSSS-EEETTEEES------STSEEEE-TTEEEEE
T ss_pred eEEEEeceeeEEEEeCCCCCcEEECCEEcC------CCCEEECCCCCEEEc
Confidence 56788887 9999997 7999999653332 234567777766653
No 18
>PF15509 DUF4650: Domain of unknown function (DUF4650)
Probab=29.13 E-value=52 Score=38.30 Aligned_cols=35 Identities=31% Similarity=0.304 Sum_probs=27.3
Q ss_pred CChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcC
Q psy558 15 GDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSC 49 (692)
Q Consensus 15 G~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt 49 (692)
|+-.|.-..|--=-|+||||-||+-|.+|..--..
T Consensus 306 ~ds~e~q~hKLRLKLLKKLKAKKkKLAsL~s~~~~ 340 (520)
T PF15509_consen 306 GDSVEDQTHKLRLKLLKKLKAKKKKLASLMSSPQN 340 (520)
T ss_pred CCcchhhHHHHHHHHHHHHHHhHHHHHHHHhhhhc
Confidence 45556777788888999999999999998764433
No 19
>PF01503 PRA-PH: Phosphoribosyl-ATP pyrophosphohydrolase; InterPro: IPR021130 Phosphoribosyl-ATP pyrophosphatase, 3.6.1.31 from EC catalyses the second step in the histidine biosynthetic pathway: 5-phosphoribosyl-ATP + H2O = 5-phosphoribosyl-AMP + PPi The Neurospora crassa enzyme also catalyzes the reactions of histidinol dehydrogenase (1.1.1.23 from EC) and phosphoribosyl-AMP cyclohydrolase (3.5.4.19 from EC). This entry also includes the Bacillus subtilis Cof proteins, which catalyze the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate []. ; PDB: 2A7W_K 3NL9_A 1YXB_D 1YVW_A 2YFD_C 2YFC_B 2YF3_C 2YF4_A 2YEU_E 2YF9_A ....
Probab=25.11 E-value=95 Score=27.07 Aligned_cols=42 Identities=19% Similarity=0.219 Sum_probs=29.9
Q ss_pred HHHHhhcccCChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCC
Q psy558 6 VKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCP 50 (692)
Q Consensus 6 V~~Ll~~rQG~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~ 50 (692)
.++.++.|+....+..-++-.+...|||.| |+.+++.|+..+
T Consensus 4 f~~~~~~~~~~~p~~~~~~l~~~~~~kl~E---E~~E~~~A~~~~ 45 (83)
T PF01503_consen 4 FHRTIDQRKKEAPEGSTKELLDLRLKKLGE---EAGELIEAAKNG 45 (83)
T ss_dssp HHHHHHHCCHSSTTTHHHHHHHHHHHHHHH---HHHHHHHHHHCS
T ss_pred HHHHHHhHhhCCCCCCcHHHHHHHHHHHHH---HHHHHHHHHHcC
Confidence 356777787664444455555568889988 899999998754
No 20
>PF06576 DUF1133: Protein of unknown function (DUF1133); InterPro: IPR010557 This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
Probab=24.51 E-value=99 Score=31.41 Aligned_cols=43 Identities=28% Similarity=0.410 Sum_probs=32.8
Q ss_pred HHHHhhcccCChhhHHHHHHHHHHHHHHhh---ccCcHHHHHHHhcCCCCCC
Q psy558 6 VKKLLGWKQGDEEEKWAEKAVDSLVKKLKK---SKGDIEELERALSCPGQPS 54 (692)
Q Consensus 6 V~~Ll~~rQG~EeE~fakkAIeSLVKKLKe---kk~eLesLi~AItt~g~pS 54 (692)
-.+||+.++ +.|.||.-.++.||| +++||+...+-+..+.+.|
T Consensus 46 fnqLl~s~k------itKtaI~~aLr~mkKsGi~k~EL~~~~~eil~gK~kS 91 (176)
T PF06576_consen 46 FNQLLASKK------ITKTAINEALRRMKKSGISKPELEAFLREILNGKQKS 91 (176)
T ss_pred HHHHHhccc------ccHHHHHHHHHHHHHhcCCcHHHHHHHHHHhCccccc
Confidence 445666554 788999999999999 6689999988887665333
No 21
>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.
Probab=20.95 E-value=65 Score=31.93 Aligned_cols=40 Identities=20% Similarity=0.294 Sum_probs=27.1
Q ss_pred hhcccCChhhHHHHHHHHHHHHHHhhccCcHHHHHHHhcCCC
Q psy558 10 LGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG 51 (692)
Q Consensus 10 l~~rQG~EeE~fakkAIeSLVKKLKekk~eLesLi~AItt~g 51 (692)
-|+-.-+-..+|.-.|+.+||++=|+ |+||.+..-+-.++
T Consensus 77 ~C~~~~n~~se~vD~ALd~lv~~~kk--DqLdki~~~l~kn~ 116 (161)
T PF09205_consen 77 ECYAKRNKLSEYVDLALDILVKQGKK--DQLDKIYNELKKNE 116 (161)
T ss_dssp HHHHHTT---HHHHHHHHHHHHTT-H--HHHHHHHHHH----
T ss_pred HHHHHhcchHHHHHHHHHHHHHhccH--HHHHHHHHHHhhcc
Confidence 35555566667999999999999887 89999999886443
No 22
>PF11142 DUF2917: Protein of unknown function (DUF2917); InterPro: IPR021317 This bacterial family of proteins appears to be restricted to Proteobacteria.
Probab=20.40 E-value=1.7e+02 Score=24.71 Aligned_cols=45 Identities=13% Similarity=0.162 Sum_probs=30.2
Q ss_pred HhccCCcEEEEEEcCeEEEEecCCCeeEecCCCCCCCCCCCCCceeecCCCCeEE
Q psy558 354 RRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLK 408 (692)
Q Consensus 354 R~~IGkGV~L~~~~G~Vwl~nlS~~pVFVqS~~ld~~~g~~~~~V~KI~pg~slK 408 (692)
+.++++|.+|.+.+|.|||+.-.+.- |+ =..++..+.|.+|..+-
T Consensus 11 ~lr~~~~~~l~v~~G~vWlT~~g~~~--------D~--~L~~G~~l~l~~g~~vv 55 (63)
T PF11142_consen 11 SLRAAAGQRLRVESGRVWLTREGDPD--------DY--WLQAGDSLRLRRGGRVV 55 (63)
T ss_pred EeEcCCCcEEEEccccEEEECCCCCC--------CE--EECCCCEEEeCCCCEEE
Confidence 45678899999999999999865311 11 12355667777776553
Done!