Query psy14662
Match_columns 237
No_of_seqs 137 out of 171
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 17:27:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14662hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00870 P53: P53 DNA-binding 100.0 2.2E-64 4.8E-69 437.5 13.1 175 22-237 3-179 (196)
2 cd08367 P53 P53 DNA-binding do 100.0 4.9E-59 1.1E-63 399.7 16.2 161 34-237 2-162 (179)
3 PF00870 P53: P53 DNA-binding 98.9 7.5E-10 1.6E-14 96.8 2.3 67 50-128 39-116 (196)
4 cd08367 P53 P53 DNA-binding do 98.6 2.8E-08 6.1E-13 86.1 3.1 66 51-128 26-99 (179)
5 PF09287 CEP1-DNA_bind: CEP-1, 94.9 0.044 9.5E-07 48.5 4.9 146 45-235 15-172 (196)
6 PF11141 DUF2914: Protein of u 54.6 13 0.00028 27.2 2.7 50 178-237 16-65 (66)
7 cd04483 hOBFC1_like hOBFC1_lik 47.1 18 0.00038 28.0 2.5 23 211-233 9-31 (92)
8 cd04478 RPA2_DBD_D RPA2_DBD_D: 28.5 70 0.0015 23.7 3.1 21 213-233 13-33 (95)
9 cd01177 IPT_NFkappaB IPT domai 21.0 96 0.0021 25.2 2.7 28 203-230 9-45 (102)
10 COG4466 Veg Uncharacterized pr 20.6 71 0.0015 25.0 1.8 29 29-57 44-72 (80)
No 1
>PF00870 P53: P53 DNA-binding domain; InterPro: IPR011615 This domain is found in p53 transcription factors, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis []. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilise the protein-DNA complex []. Protein interactions may also serve to stabilise the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coupled to the DNA-binding domain to increase stability []. The DNA-binding domain consists of a beta-sandwich formed of 9 strands in 2 sheets with a Greek-key topology. This structure is found in many transcription factors, often within the DNA-binding domain.; GO: 0044212 transcription regulatory region DNA binding; PDB: 3US2_A 3QYM_E 3QYN_A 3US0_C 3US1_D 2RMN_A 3Q06_B 2VUK_A 2H1L_M 1KZY_B ....
Probab=100.00 E-value=2.2e-64 Score=437.45 Aligned_cols=175 Identities=39% Similarity=0.795 Sum_probs=146.1
Q ss_pred CCCCcccccce-EEEEEcccCCcccccCCeehhhhceeeeeccccccceeEecccCCCCCCCCccceeeccccccccCCC
Q psy14662 22 QGGDIAQVGTT-LALELKQVCDHVFYSIPQYSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGR 100 (237)
Q Consensus 22 ~~~~~~~~~~~-l~~~~~~~~~~~~~s~wtYS~~LnKLf~~m~k~cPi~~~~~~~~~~~~~p~~~~ram~vyk~~~h~~~ 100 (237)
+|+++.++|.+ |+|+|.+ ++.+++++||||++||||||+|+++|||+|+++. +|
T Consensus 3 vPs~~~ypG~~~F~v~f~~-s~t~Ks~~wtYS~~LnKLf~~~~k~cpv~~~~~~------~P------------------ 57 (196)
T PF00870_consen 3 VPSNTDYPGPYNFQVSFQQ-SGTAKSATWTYSPKLNKLFCKMNKTCPVQFKVSS------PP------------------ 57 (196)
T ss_dssp S---S-BETTTTEEEEESS-SSSSTTTSEEEETTTTEEEEETTSEEEEEEEESS-------S------------------
T ss_pred CCCCCCcCCCcccEEEecc-CCCCccccEEeehhcCceEEeccCCceEEEEEec------CC------------------
Confidence 57788888877 9999988 5678899999999999999999999999999988 55
Q ss_pred ceeecCCCCCCCCCCCeeeEEEeeecCCCCCCcccCCCCCccccccccccCCCccccCcEEEeCCC-ceeccCCCCCCce
Q psy14662 101 PVERCPLHVCRDPPPLFLRATPIYSQDDHRGRPVERCPLHVSDALCNEINKGFEAVVKHIVRCTSA-HCQYPMDERSGRH 179 (237)
Q Consensus 101 ~v~rcP~h~~~~p~~~~iR~~~~y~~~eh~~e~V~RCp~H~~~~~~~~~n~g~~a~~~HvIRcen~-~A~Y~~d~~t~R~ 179 (237)
|++..||++++|.++||++++|+|||||+ ..+++|+| .++++|||||+++ .|+|++|+.++|+
T Consensus 58 ------------p~g~~iRam~Vy~~~e~~~e~V~RCp~H~---~~~~~~~~-~~~~~HliR~~~~~~a~Y~~d~~t~R~ 121 (196)
T PF00870_consen 58 ------------PPGTYIRAMPVYKKPEHVQEPVKRCPNHE---SSDDFNNG-SAPPSHLIRCEGNQSAQYVEDPNTGRH 121 (196)
T ss_dssp ------------STTEEEEEEEEESSTTTTTSB-B--HHHH---TSSTTTSS-SS-TTBSEEEES-TT-EEEEETTTTEE
T ss_pred ------------CCCCEEEEEEEEcchHhccCchhhCcccc---ccccccCC-CccccceEEEcCCceeEEecCCCCceE
Confidence 77888899999999999999999999994 45565656 4678999999976 9999999999999
Q ss_pred EEeecCCCCCCCCCceeEEEeeEecCCCCCCCCCceeEEEEEEEcCCceEEeEEEeeC
Q psy14662 180 TCVTPLSPPQPGADTVTLMYSFVCKTSCLGGMDRRPVLLLLTLENQHGQILGRRSLSF 237 (237)
Q Consensus 180 SV~VP~e~Pq~Gse~~Ti~~~FmC~sSC~GGmNRRpi~lIfTLE~~~G~VLGRr~~ev 237 (237)
||+||||.||+|++++|++|+|||+|||+||||||||+|||||||++|+|||||+|+|
T Consensus 122 sV~VP~e~pq~g~~~~t~~~~FmC~sSC~gg~nRRpi~~ifTLE~~~g~vlGR~~~~v 179 (196)
T PF00870_consen 122 SVLVPYEPPQVGSEYTTILYNFMCNSSCMGGMNRRPILLIFTLEDSDGQVLGRRSFEV 179 (196)
T ss_dssp EEEEE---SSTTSSSEEEEEEESS-TTGTTTTTTS-EEEEEEEEETTSCEEEEEEEEE
T ss_pred EEEeeccCCccccceeeeeeeeeEcccccCCCCCceEEEEEEEECCCCCEeeeeccCc
Confidence 9999999999999999999999999999999999999999999999999999999986
No 2
>cd08367 P53 P53 DNA-binding domain. P53 is a tumor suppressor gene product; mutations in p53 or lack of expression are found associated with a large fraction of all human cancers. P53 is activated by DNA damage and acts as a regulator of gene expression that ultimatively blocks progression through the cell cycle. P53 binds to DNA as a tetrameric transcription factor. In its inactive form, p53 is bound to the ring finger protein Mdm2, which promotes its ubiquitinylation and subsequent proteosomal degradation. Phosphorylation of p53 disrupts the Mdm2-p53 complex, while the stable and active p53 binds to regulatory regions of its target genes, such as the cyclin-kinase inhibitor p21, which complexes and inactivates cdk2 and other cyclin complexes.
Probab=100.00 E-value=4.9e-59 Score=399.73 Aligned_cols=161 Identities=39% Similarity=0.746 Sum_probs=145.7
Q ss_pred EEEEcccCCcccccCCeehhhhceeeeeccccccceeEecccCCCCCCCCccceeeccccccccCCCceeecCCCCCCCC
Q psy14662 34 ALELKQVCDHVFYSIPQYSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHVCRDP 113 (237)
Q Consensus 34 ~~~~~~~~~~~~~s~wtYS~~LnKLf~~m~k~cPi~~~~~~~~~~~~~p~~~~ram~vyk~~~h~~~~v~rcP~h~~~~p 113 (237)
+|.+...+. +++++||||+.|||||++|+++|||+|++.. +| |
T Consensus 2 ~v~~~~~~~-~k~~~wtyS~~LnKLfv~m~~~cp~~~~~~~------~p------------------------------p 44 (179)
T cd08367 2 EVTLDESGV-AKSSTWTYSPKLNKLFVKMAKTCPIQFKVNP------SP------------------------------P 44 (179)
T ss_pred eEecCCCCC-ccccCEEEchhhCEEEEecCCeEEEEEEEee------CC------------------------------C
Confidence 455555543 7899999999999999999999999999998 55 7
Q ss_pred CCCeeeEEEeeecCCCCCCcccCCCCCccccccccccCCCccccCcEEEeCCCceeccCCCCCCceEEeecCCCCCCCCC
Q psy14662 114 PPLFLRATPIYSQDDHRGRPVERCPLHVSDALCNEINKGFEAVVKHIVRCTSAHCQYPMDERSGRHTCVTPLSPPQPGAD 193 (237)
Q Consensus 114 ~~~~iR~~~~y~~~eh~~e~V~RCp~H~~~~~~~~~n~g~~a~~~HvIRcen~~A~Y~~d~~t~R~SV~VP~e~Pq~Gse 193 (237)
++..||++++|.++||+.++|+||+||+.. ++. .+++.+|||||+|+.|+|.+|+.++|+||+|||+.||+|++
T Consensus 45 ~~~~vRa~~Vy~~~e~~~~~V~RC~~H~~~---~~~---~~~~~~HviR~~~~~a~Y~~d~~~~R~sV~vP~~~pq~g~~ 118 (179)
T cd08367 45 PGLYVRAMLVYKDPEHVKEPVERCPNHRQG---DDG---HTAPNSHVIRCENPQAEYVGDAFTGRLSVVVPLEPPQVGSE 118 (179)
T ss_pred CCcEEEEEEEEcChhhcCCCcccccccccc---CCC---CCCCcceEEEECCCCcEEeecCCCCcEEEEEECCCCCCCcE
Confidence 899999999999999999999999999643 221 23445699999999999999999999999999999999999
Q ss_pred ceeEEEeeEecCCCCCCCCCceeEEEEEEEcCCceEEeEEEeeC
Q psy14662 194 TVTLMYSFVCKTSCLGGMDRRPVLLLLTLENQHGQILGRRSLSF 237 (237)
Q Consensus 194 ~~Ti~~~FmC~sSC~GGmNRRpi~lIfTLE~~~G~VLGRr~~ev 237 (237)
++|++|+|||+|||+||||||||+|||||||++|+|||||+|+|
T Consensus 119 ~~t~~~~FmC~nSC~gg~nRR~i~liftLE~~~G~vLGR~~i~V 162 (179)
T cd08367 119 YVTVLLQFMCQNSCPGGINRRPIQLVFTLEDENGNVLGRRVIEV 162 (179)
T ss_pred EEEEEEEEECcCcCCCCCCcceEEEEEEEECCCCCEeeEEEEEE
Confidence 99999999999999999999999999999999999999999986
No 3
>PF00870 P53: P53 DNA-binding domain; InterPro: IPR011615 This domain is found in p53 transcription factors, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis []. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilise the protein-DNA complex []. Protein interactions may also serve to stabilise the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coupled to the DNA-binding domain to increase stability []. The DNA-binding domain consists of a beta-sandwich formed of 9 strands in 2 sheets with a Greek-key topology. This structure is found in many transcription factors, often within the DNA-binding domain.; GO: 0044212 transcription regulatory region DNA binding; PDB: 3US2_A 3QYM_E 3QYN_A 3US0_C 3US1_D 2RMN_A 3Q06_B 2VUK_A 2H1L_M 1KZY_B ....
Probab=98.88 E-value=7.5e-10 Score=96.84 Aligned_cols=67 Identities=27% Similarity=0.564 Sum_probs=48.4
Q ss_pred eehhhhceeeeeccccccceeEecccCCCCCCCCccceeeccccccccCCCceeecCCCC-CC------CCCCCeeeEE-
Q psy14662 50 QYSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHV-CR------DPPPLFLRAT- 121 (237)
Q Consensus 50 tYS~~LnKLf~~m~k~cPi~~~~~~~~~~~~~p~~~~ram~vyk~~~h~~~~v~rcP~h~-~~------~p~~~~iR~~- 121 (237)
.|..+-+.+.+++....+.. +. +.||||||||+.||++|+|+|||+|+ .. +++.|+||++
T Consensus 39 Lf~~~~k~cpv~~~~~~~Pp-----------~g-~~iRam~Vy~~~e~~~e~V~RCp~H~~~~~~~~~~~~~~HliR~~~ 106 (196)
T PF00870_consen 39 LFCKMNKTCPVQFKVSSPPP-----------PG-TYIRAMPVYKKPEHVQEPVKRCPNHESSDDFNNGSAPPSHLIRCEG 106 (196)
T ss_dssp EEEETTSEEEEEEEESS-SS-----------TT-EEEEEEEEESSTTTTTSB-B--HHHHTSSTTTSSSS-TTBSEEEES
T ss_pred eEEeccCCceEEEEEecCCC-----------CC-CEEEEEEEEcchHhccCchhhCccccccccccCCCccccceEEEcC
Confidence 56677777778887765543 22 78999999999999999999999996 32 2789999995
Q ss_pred ---EeeecCC
Q psy14662 122 ---PIYSQDD 128 (237)
Q Consensus 122 ---~~y~~~e 128 (237)
|.|.+|.
T Consensus 107 ~~~a~Y~~d~ 116 (196)
T PF00870_consen 107 NQSAQYVEDP 116 (196)
T ss_dssp -TT-EEEEET
T ss_pred CceeEEecCC
Confidence 8898763
No 4
>cd08367 P53 P53 DNA-binding domain. P53 is a tumor suppressor gene product; mutations in p53 or lack of expression are found associated with a large fraction of all human cancers. P53 is activated by DNA damage and acts as a regulator of gene expression that ultimatively blocks progression through the cell cycle. P53 binds to DNA as a tetrameric transcription factor. In its inactive form, p53 is bound to the ring finger protein Mdm2, which promotes its ubiquitinylation and subsequent proteosomal degradation. Phosphorylation of p53 disrupts the Mdm2-p53 complex, while the stable and active p53 binds to regulatory regions of its target genes, such as the cyclin-kinase inhibitor p21, which complexes and inactivates cdk2 and other cyclin complexes.
Probab=98.59 E-value=2.8e-08 Score=86.12 Aligned_cols=66 Identities=29% Similarity=0.455 Sum_probs=48.6
Q ss_pred ehhhhceeeeeccccccceeEecccCCCCCCCCccceeeccccccccCCCceeecCCCCC-CC----CCCCeeeEE---E
Q psy14662 51 YSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHVC-RD----PPPLFLRAT---P 122 (237)
Q Consensus 51 YS~~LnKLf~~m~k~cPi~~~~~~~~~~~~~p~~~~ram~vyk~~~h~~~~v~rcP~h~~-~~----p~~~~iR~~---~ 122 (237)
|-.+-+.+-+++...-+. . +. +.+|||+||++.||+.++|+|||+|.. .+ |..|+||++ |
T Consensus 26 fv~m~~~cp~~~~~~~~p-----p------~~-~~vRa~~Vy~~~e~~~~~V~RC~~H~~~~~~~~~~~~HviR~~~~~a 93 (179)
T cd08367 26 FVKMAKTCPIQFKVNPSP-----P------PG-LYVRAMLVYKDPEHVKEPVERCPNHRQGDDGHTAPNSHVIRCENPQA 93 (179)
T ss_pred EEecCCeEEEEEEEeeCC-----C------CC-cEEEEEEEEcChhhcCCCccccccccccCCCCCCCcceEEEECCCCc
Confidence 334444445555555554 2 23 789999999999999999999999962 22 556999995 9
Q ss_pred eeecCC
Q psy14662 123 IYSQDD 128 (237)
Q Consensus 123 ~y~~~e 128 (237)
.|..|.
T Consensus 94 ~Y~~d~ 99 (179)
T cd08367 94 EYVGDA 99 (179)
T ss_pred EEeecC
Confidence 999984
No 5
>PF09287 CEP1-DNA_bind: CEP-1, DNA binding; InterPro: IPR015367 This DNA-binding domain is found in the Caenorhabditis transcription factor CEP-1, which is related to human p53. It adopts a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology []. ; PDB: 1T4W_A.
Probab=94.93 E-value=0.044 Score=48.49 Aligned_cols=146 Identities=19% Similarity=0.328 Sum_probs=70.8
Q ss_pred cccCCee---hhhhceeeeeccccccceeEecccCCCCCCCCccceeeccccccccCCCceeecCCCCCCCCCCCeeeEE
Q psy14662 45 FYSIPQY---SYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHVCRDPPPLFLRAT 121 (237)
Q Consensus 45 ~~s~wtY---S~~LnKLf~~m~k~cPi~~~~~~~~~~~~~p~~~~ram~vyk~~~h~~~~v~rcP~h~~~~p~~~~iR~~ 121 (237)
+.|...| ++-=+-||.+|.+..|+.|+|.-.+ .+| ..+..||+.
T Consensus 15 k~sd~~~~~~~~~~~~lwtkm~cnVpiev~wni~~-------------~~~--------------------nknl~LriR 61 (196)
T PF09287_consen 15 KVSDFAYKQMPNGEKYLWTKMKCNVPIEVRWNIDS-------------CHY--------------------NKNLSLRIR 61 (196)
T ss_dssp T-SSEEEEE-TT--EEEEE-TT--EEEEEEEE--T-------------TTT--------------------T---EEEEE
T ss_pred hcccchheecCCCCeEEeccccccceEEEEeccCc-------------eee--------------------cccceEEEe
Confidence 4444444 3335579999999999999998721 122 456777774
Q ss_pred -EeeecCCCC-------CCcccCCCCCccccccccccCCCccccCcEEEeCCCceeccCCCCCCceEEeecCCCCCCCCC
Q psy14662 122 -PIYSQDDHR-------GRPVERCPLHVSDALCNEINKGFEAVVKHIVRCTSAHCQYPMDERSGRHTCVTPLSPPQPGAD 193 (237)
Q Consensus 122 -~~y~~~eh~-------~e~V~RCp~H~~~~~~~~~n~g~~a~~~HvIRcen~~A~Y~~d~~t~R~SV~VP~e~Pq~Gse 193 (237)
.-|...+.+ ..-|.-|.+|...+ ..+ |.+.++++-|....|... ..+-+++.+-+. +|..
T Consensus 62 lV~y~~~~nie~airnp~~~V~KCr~H~~~e------~~f--P~esFFyIvnS~~hwtin-s~kg~~fst~I~---pg~~ 129 (196)
T PF09287_consen 62 LVNYDKSENIENAIRNPNSDVKKCRNHIMRE------QKF--PRESFFYIVNSGHHWTIN-SKKGNTFSTIIN---PGTN 129 (196)
T ss_dssp EEEE-SSS-HHHHTT-TT-B----HHHHHT--------SS--STT-SEEEES-SSEEEEE--TTSSEEEEE-----TT--
T ss_pred eecccccccHHHHHhCchhhHHHHHHHHHHH------hhC--CcccEEEEEccCcceEEe-cCCCcEEEEEEC---CCcc
Confidence 445444332 23468899995321 123 346666666555554432 111222332221 2555
Q ss_pred ceeEEEeeEecCCCCCCCC-CceeEEEEEEEcCCceEEeEEEe
Q psy14662 194 TVTLMYSFVCKTSCLGGMD-RRPVLLLLTLENQHGQILGRRSL 235 (237)
Q Consensus 194 ~~Ti~~~FmC~sSC~GGmN-RRpi~lIfTLE~~~G~VLGRr~~ 235 (237)
-...-+-|||+-+|++--. |+...|..-|||.+|+-+-..++
T Consensus 130 ~v~FDIIf~cqe~cm~l~dkrktmcla~fledengnei~h~vi 172 (196)
T PF09287_consen 130 QVNFDIIFMCQENCMDLDDKRKTMCLAVFLEDENGNEILHAVI 172 (196)
T ss_dssp EEEEEEEESS-GGGS-HHHHTSEEEEEEEEE-TTS-EEEEEEE
T ss_pred eeeeeehhhhHHHhcchhhhhhhheeeeeeeccCCCchhHHHh
Confidence 5667777999999996333 56678999999999987766554
No 6
>PF11141 DUF2914: Protein of unknown function (DUF2914); InterPro: IPR022606 This bacterial family of proteins has no known function.
Probab=54.57 E-value=13 Score=27.23 Aligned_cols=50 Identities=20% Similarity=0.211 Sum_probs=31.7
Q ss_pred ceEEeecCCCCCCCCCceeEEEeeEecCCCCCCCCCceeEEEEEEEcCCceEEeEEEeeC
Q psy14662 178 RHTCVTPLSPPQPGADTVTLMYSFVCKTSCLGGMDRRPVLLLLTLENQHGQILGRRSLSF 237 (237)
Q Consensus 178 R~SV~VP~e~Pq~Gse~~Ti~~~FmC~sSC~GGmNRRpi~lIfTLE~~~G~VLGRr~~ev 237 (237)
+.--.|||+- .|..+-+...+..=. ..+=.=-+.++|.+|++||+..|+|
T Consensus 16 ~~~~~i~l~i--~g~r~Rt~S~k~~~~--------~~~G~WrV~V~~~~G~~l~~~~F~V 65 (66)
T PF11141_consen 16 KLVARIPLPI--SGGRWRTWSSKQNFP--------DQPGDWRVEVVDEDGQVLGSLRFSV 65 (66)
T ss_pred EEEEEEEEec--cCCCEEEEEEeecCC--------CCCcCEEEEEEcCCCCEEEEEEEEE
Confidence 3444455533 355577777774432 1222334788899999999999975
No 7
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=47.15 E-value=18 Score=27.95 Aligned_cols=23 Identities=9% Similarity=0.115 Sum_probs=19.3
Q ss_pred CCCceeEEEEEEEcCCceEEeEE
Q psy14662 211 MDRRPVLLLLTLENQHGQILGRR 233 (237)
Q Consensus 211 mNRRpi~lIfTLE~~~G~VLGRr 233 (237)
.+.++..+.|||+|+.|.|-++.
T Consensus 9 v~~~~~~~~~tLdDgTG~Ie~~~ 31 (92)
T cd04483 9 RRERETFYSFGVDDGTGVVNCVC 31 (92)
T ss_pred EEecCCeEEEEEecCCceEEEEE
Confidence 45788999999999999986654
No 8
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=28.52 E-value=70 Score=23.67 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=17.3
Q ss_pred CceeEEEEEEEcCCceEEeEE
Q psy14662 213 RRPVLLLLTLENQHGQILGRR 233 (237)
Q Consensus 213 RRpi~lIfTLE~~~G~VLGRr 233 (237)
.++..+.|||+|+.|.|-++.
T Consensus 13 ~~~~~~~~tL~D~TG~I~~~~ 33 (95)
T cd04478 13 EQSTNITYTIDDGTGTIEVRQ 33 (95)
T ss_pred EcccEEEEEEECCCCcEEEEE
Confidence 346789999999999987765
No 9
>cd01177 IPT_NFkappaB IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to certain chemicals. NFkappaB blocking cell apoptosis in several cell types, gives it an important role in cell proliferation and differentiation.
Probab=21.00 E-value=96 Score=25.19 Aligned_cols=28 Identities=14% Similarity=0.291 Sum_probs=19.7
Q ss_pred ecCCCCCC---------CCCceeEEEEEEEcCCceEE
Q psy14662 203 CKTSCLGG---------MDRRPVLLLLTLENQHGQIL 230 (237)
Q Consensus 203 C~sSC~GG---------mNRRpi~lIfTLE~~~G~VL 230 (237)
|..||.|| .++--|++.|.-|+.++.+|
T Consensus 9 ~sgsv~GG~Ev~LLcdKV~K~dI~VrF~e~~~~~~~W 45 (102)
T cd01177 9 TSGSVKGGDEVYLLCDKVQKEDIQVRFFEEDEEETVW 45 (102)
T ss_pred cccccCCCcEEEEEecccCCCCCEEEEEEcCCCCCce
Confidence 44566666 46778999999887765554
No 10
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.61 E-value=71 Score=24.99 Aligned_cols=29 Identities=21% Similarity=0.093 Sum_probs=23.7
Q ss_pred ccceEEEEEcccCCcccccCCeehhhhce
Q psy14662 29 VGTTLALELKQVCDHVFYSIPQYSYELNK 57 (237)
Q Consensus 29 ~~~~l~~~~~~~~~~~~~s~wtYS~~LnK 57 (237)
+-+.|.|++.+..+..---+|+||+.|-+
T Consensus 44 YpSvFIiel~~d~~~~~~vSYsYsDILTe 72 (80)
T COG4466 44 YPSVFIIELDQDEGNFERVSYSYSDILTE 72 (80)
T ss_pred cCcEEEEEecccCCCceEEEEEehhheee
Confidence 45678999999888777788999999854
Done!