Query 008335
Match_columns 569
No_of_seqs 164 out of 867
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 22:31:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 3.5E-37 7.5E-42 275.9 7.9 126 396-526 1-129 (129)
2 PLN03144 Carbon catabolite rep 63.9 6.4 0.00014 45.4 3.5 34 234-267 172-205 (606)
3 TIGR00547 lolA periplasmic cha 63.1 11 0.00025 37.3 4.7 107 283-410 89-199 (204)
4 PF13473 Cupredoxin_1: Cupredo 56.3 11 0.00023 32.9 2.9 58 343-406 30-93 (104)
5 PF08567 TFIIH_BTF_p62_N: TFII 39.6 1.1E+02 0.0023 26.4 6.3 61 297-368 2-67 (79)
6 PF06027 DUF914: Eukaryotic pr 33.7 90 0.002 33.6 6.1 107 29-138 171-302 (334)
7 PRK00031 lolA lipoprotein chap 32.7 69 0.0015 30.6 4.6 52 348-411 141-193 (195)
8 PF06942 GlpM: GlpM protein; 24.6 27 0.00058 32.3 0.2 40 103-143 7-48 (107)
9 TIGR03096 nitroso_cyanin nitro 22.4 2.2E+02 0.0048 27.3 5.8 61 344-406 57-119 (135)
10 PF03961 DUF342: Protein of un 22.2 2E+02 0.0044 31.7 6.4 87 185-309 115-201 (451)
11 KOG1563 Mitochondrial protein 21.7 2.4E+02 0.0052 30.2 6.4 134 401-564 78-214 (288)
12 cd05171 PIKKc_ATM Ataxia telan 21.7 64 0.0014 33.5 2.3 46 343-388 2-49 (279)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=3.5e-37 Score=275.88 Aligned_cols=126 Identities=33% Similarity=0.625 Sum_probs=93.9
Q ss_pred CCCcccccCCChHHHHHHHHHHHHcCCCCCccCCcceeccCCCCCCCccchhhcccCCCeEEEEEecCC---CCCccccc
Q 008335 396 LPPTVAAFIPTDTELVTYHLMNKVSARSYEQLDRFIKDIELYDYEPSELSSLAYHSGHDKKYFFTRLSQ---PARTVNRQ 472 (569)
Q Consensus 396 LppgvfRF~PTDEELV~~YLrpKI~G~plP~~~~vI~evDVY~~ePWdLP~~~~~~ge~eWYFFSpR~r---kGrR~nRt 472 (569)
|||| |||+|||+|||.+||++|+.|++++ ..++|+++|||++|||+|+.... .++++||||+++.+ +++|.+|+
T Consensus 1 LP~G-~rF~PtD~ELi~~yL~~k~~g~~~~-~~~~i~~~Diy~~~P~~L~~~~~-~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPG-FRFRPTDEELINHYLRPKILGEPLP-CEDVIHDVDIYSAHPWELPAKFK-GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TT-EEE---HHHHHHCTHHHHHTT-HHC-S-CHSEE--GGGS-GGGCHHHSS-S-SSEEEEEEE----------S-EE
T ss_pred CCCc-eEecCChHHHHHHHHHHHhcCCCCC-cccceeecccCccChHHhhhhcc-CCCceEEEEEecccccCCccccccc
Confidence 7999 9999999999999999999999876 35789999999999999995322 25569999999875 36788999
Q ss_pred cccceEEecCCCeeeeCCCCCEEEEEEEEEEEeccCCCCCCCccCeEEEEEEeC
Q 008335 473 AQGGYWRKTGMPSYVNDKDGDAVATKTSLTYFKKQDPTSKPEKTHWLMKEYMLL 526 (569)
Q Consensus 473 tggGyWKatGk~K~I~d~~G~iVG~KKtLvFyegr~P~gkg~KTgWVMhEYrL~ 526 (569)
+++|+||++|+.+.|.+.+|.++|+|++|+||.++.+ ++.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~--~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSP--NGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTT--S-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCC--CCCcCCeEEEEEEeC
Confidence 9999999999999999878899999999999987655 578999999999984
No 2
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=63.94 E-value=6.4 Score=45.43 Aligned_cols=34 Identities=29% Similarity=0.430 Sum_probs=28.7
Q ss_pred cccccCCCCcceeeecccccceEEEEeEeccCCC
Q 008335 234 RHSIEGATEPEYVVTADDINKLIALEHTTIDDEG 267 (569)
Q Consensus 234 ~~~IegA~~p~Y~vTADDv~~~iaie~~p~dd~~ 267 (569)
..-|+=..+..|+.|+||||-.|-+||+|+|...
T Consensus 172 ~~w~~vg~~~~y~p~~~d~g~~lk~~~~~~~~~~ 205 (606)
T PLN03144 172 ETWIEVGRSKTYTPTADDVGHVLKFECVVVDAET 205 (606)
T ss_pred CceEEeCCCccccCChhhCCceEEEEEEEccccc
Confidence 3345655788999999999999999999998864
No 3
>TIGR00547 lolA periplasmic chaperone LolA. This protein, LolA, is known so far only in the gamma and beta subdivisions of the Proteobacteria. The E. coli major outer lipoprotein (Lpp) of E. coli is released from the inner membrane as a complex with this chaperone in an energy-requiring process, and is then delivered to LolB for insertion into the outer membrane. LolA is involved in the delivery of lipoproteins generally, rather than just Lpp, and is an essential protein in E. coli, unlike Lpp itself.
Probab=63.13 E-value=11 Score=37.33 Aligned_cols=107 Identities=14% Similarity=0.284 Sum_probs=58.1
Q ss_pred cccChhhHHHHHHhhhc--eeeEEEEEEeeCCCCCcccceeEEEEecceEEEEcCccceeeecccCcceEEEe-ccCCcc
Q 008335 283 IKCDPDMQSKVDMHISR--GQAAFRVLLLINSSENTWEPATLSFTQSRFHVKINSTDVVISEGDLFNIIEIEI-PIGLSR 359 (569)
Q Consensus 283 I~cdp~mq~~I~~~~~~--g~a~f~V~l~~~~~~~~wE~atL~i~r~~y~ik~~~~~~~~i~ekfs~~~~iki-p~g~~~ 359 (569)
..+||+....+.+.+.. |..- ..++.+..++.|+...+.-.-..|.|+..... . .| ..+.|.+ +.|...
T Consensus 89 w~Ydp~leQvt~~~~~~~~~~TP--~~lL~~~~~~~~~~f~v~~~~~~~~L~Pk~~~-~----~f-~~~~l~fd~~~~l~ 160 (204)
T TIGR00547 89 WFYDPFVEQATAQWLKDATGNTP--FMLIARNDKSDWHQYNIKQNGDDFVLKPKASN-G----NI-KQFDINVDADGIIH 160 (204)
T ss_pred EEECCCCceeeeeeccccccCCc--HHhhcCCchhhhhceEEEecCCEEEEEECCCC-C----Ce-EEEEEEECCCCCEE
Confidence 34566655544333332 2222 22344444444776654432234666543211 0 11 1234555 577899
Q ss_pred eEEEEccCCCeeeeecCCccccceeeeeehhhcccCCCCcccccC-CChHHH
Q 008335 360 QFILRRLDGESHYFITNNDRMRDTLVLTMRTFRRMVLPPTVAAFI-PTDTEL 410 (569)
Q Consensus 360 qfvIi~SDG~Eh~Lr~~d~r~RD~~VltlR~F~rmaLppgvfRF~-PTDEEL 410 (569)
++.+..+.|....+++.+. + +..++++.|.|. |.+.|+
T Consensus 161 ~~~v~D~~Gq~t~i~f~~~--~-----------n~~l~~~~F~F~pP~GvdV 199 (204)
T TIGR00547 161 NFSATEKDDQRNLYQLKNI--Q-----------NGALDAAKFQFKPEKGVEV 199 (204)
T ss_pred EEEEEecCCCEEEEEEcCC--c-----------CCCCChhhEEEcCCCCCee
Confidence 9999999998777776542 2 345778889997 455554
No 4
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=56.26 E-value=11 Score=32.87 Aligned_cols=58 Identities=19% Similarity=0.182 Sum_probs=36.8
Q ss_pred cccCcceEEEeccCCcceEEEEccCCCeeeeecCCcc------ccceeeeeehhhcccCCCCcccccCCC
Q 008335 343 GDLFNIIEIEIPIGLSRQFILRRLDGESHYFITNNDR------MRDTLVLTMRTFRRMVLPPTVAAFIPT 406 (569)
Q Consensus 343 ekfs~~~~ikip~g~~~qfvIi~SDG~Eh~Lr~~d~r------~RD~~VltlR~F~rmaLppgvfRF~PT 406 (569)
-.|+|+ .|+++-|++..+.+...|...|.|..++.. --++..+++ .++.||.|.|.-+
T Consensus 30 ~~f~P~-~i~v~~G~~v~l~~~N~~~~~h~~~i~~~~~~~~l~~g~~~~~~f-----~~~~~G~y~~~C~ 93 (104)
T PF13473_consen 30 FGFSPS-TITVKAGQPVTLTFTNNDSRPHEFVIPDLGISKVLPPGETATVTF-----TPLKPGEYEFYCT 93 (104)
T ss_dssp EEEES--EEEEETTCEEEEEEEE-SSS-EEEEEGGGTEEEEE-TT-EEEEEE-----EE-S-EEEEEB-S
T ss_pred CeEecC-EEEEcCCCeEEEEEEECCCCcEEEEECCCceEEEECCCCEEEEEE-----cCCCCEEEEEEcC
Confidence 367887 789999999999999888888998875422 234444433 2567998888744
No 5
>PF08567 TFIIH_BTF_p62_N: TFIIH p62 subunit, N-terminal domain; InterPro: IPR013876 The N-terminal region of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal region reveals that it adopts a pleckstrin homology (PH) fold [, ]. ; PDB: 1Y5O_A 2LOX_A 2GS0_A 2L2I_A 2K2U_A 1PFJ_A 2RNR_B.
Probab=39.63 E-value=1.1e+02 Score=26.43 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=42.0
Q ss_pred hhceeeEEEEEEeeCCCCCcccceeEEEEecc--eEEEEcCcccee-eecccCcceEEEe-ccCCc-ceEEEEccCC
Q 008335 297 ISRGQAAFRVLLLINSSENTWEPATLSFTQSR--FHVKINSTDVVI-SEGDLFNIIEIEI-PIGLS-RQFILRRLDG 368 (569)
Q Consensus 297 ~~~g~a~f~V~l~~~~~~~~wE~atL~i~r~~--y~ik~~~~~~~~-i~ekfs~~~~iki-p~g~~-~qfvIi~SDG 368 (569)
+..|+|+|+ ..+.||.|+..+ ....-++.+... +.-.|..-++.++ |.|.+ -|.-|+..++
T Consensus 2 ~~~~~~~yK-----------K~~G~L~l~~d~~~~~W~~~~~~~~~~v~i~~~~I~~lq~Sp~~s~Kv~Lki~~~~~ 67 (79)
T PF08567_consen 2 LPSGAASYK-----------KKDGTLTLTEDRKPLEWTPKASDGPSTVSIPLNDIKNLQQSPEGSPKVMLKIVLKDD 67 (79)
T ss_dssp CCECEEEET-----------TEEEEEEEETTCSSEEEEECCSSSSSEEEEETTTEEEEEE--TTSSTEEEEEEETTS
T ss_pred CccceEEEE-----------cCCcEEEEecCCceEEEeecCCCCCceEEEEHHHhhhhccCCCCCcceEEEEEEecC
Confidence 356888885 356889998888 888887766654 8888888888888 55554 3444444444
No 6
>PF06027 DUF914: Eukaryotic protein of unknown function (DUF914); InterPro: IPR009262 This family consists of several hypothetical proteins of unknown function. Some of the sequences in this family are annotated as putative membrane proteins.
Probab=33.71 E-value=90 Score=33.64 Aligned_cols=107 Identities=36% Similarity=0.469 Sum_probs=57.8
Q ss_pred chhhhHHHHHhhhhhhhhhhccCcchhHHH--HHhhhhccee-eeeeeeeec-cccccccccccccchhhHHHHHH-HHH
Q 008335 29 GLAILFFILEAVSVVLDIFEKSKGASLAAF--LFSAFGFAMT-IYVCFLERT-FTAIKPQADRQLGILDIAFSVLQ-LIA 103 (569)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~ 103 (569)
-++++--++-|++.|+.=+- -|.++...+ ..+.||+... |....+||+ +..++ -+.+.+.+-++|++.. +.-
T Consensus 171 ll~l~~a~lya~~nV~~E~~-v~~~~~~~~lg~~Glfg~ii~~iq~~ile~~~i~~~~--w~~~~~~~~v~~~~~lf~~y 247 (334)
T PF06027_consen 171 LLALLGAILYAVSNVLEEKL-VKKAPRVEFLGMLGLFGFIISGIQLAILERSGIESIH--WTSQVIGLLVGYALCLFLFY 247 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHh-cccCCHHHHHHHHHHHHHHHHHHHHHheehhhhhccC--CChhhHHHHHHHHHHHHHHH
Confidence 36677778888887764221 122333333 2344454333 233347765 22222 3455566667676532 333
Q ss_pred HHHHHhhhhcccc--------------------ccccceehhhhHHHHhheeeee
Q 008335 104 TLIHLILLVSDAK--------------------YNYNASVLFPLAFAIIAVLFVF 138 (569)
Q Consensus 104 ~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~~ 138 (569)
++.-+++..|+|- +.|..+.+++++|++|.+-++.
T Consensus 248 ~l~p~~l~~ssAt~~nLsLLTsd~~ali~~i~~f~~~~~~ly~~af~lIiiG~vv 302 (334)
T PF06027_consen 248 SLVPIVLRMSSATFFNLSLLTSDFYALIIDIFFFGYKFSWLYILAFALIIIGFVV 302 (334)
T ss_pred HHHHHHHHhCccceeehHHHHhhHHHHHHHHHhcCccccHHHHHHHHHHHHHhhe
Confidence 4444444444442 5677788899999977654443
No 7
>PRK00031 lolA lipoprotein chaperone; Reviewed
Probab=32.67 E-value=69 Score=30.56 Aligned_cols=52 Identities=19% Similarity=0.215 Sum_probs=33.6
Q ss_pred ceEEEeccCCcceEEEEccCCCeeeeecCCccccceeeeeehhhcccCCCCcccccC-CChHHHH
Q 008335 348 IIEIEIPIGLSRQFILRRLDGESHYFITNNDRMRDTLVLTMRTFRRMVLPPTVAAFI-PTDTELV 411 (569)
Q Consensus 348 ~~~ikip~g~~~qfvIi~SDG~Eh~Lr~~d~r~RD~~VltlR~F~rmaLppgvfRF~-PTDEELV 411 (569)
.+.|.+..+.+.+..+..++|....+++.+.+. +..+|+..|.|+ |.+.|+|
T Consensus 141 ~i~l~~~~~~i~~i~i~d~~g~~t~i~f~~~~~------------n~~l~~~~F~f~~P~g~~Vv 193 (195)
T PRK00031 141 QFTIGFRNGTLASFSLVDQDGQRTLITFSNIQK------------NPALDADKFTFTPPKGVDVD 193 (195)
T ss_pred EEEEEECCCeEEEEEEEcCCCCEEEEEeccccc------------CCCCChhhEEEcCCCCcccC
Confidence 455555456778888888888666555444321 356788888988 5666655
No 8
>PF06942 GlpM: GlpM protein; InterPro: IPR009707 This family consists of several bacterial GlpM membrane proteins. GlpM is a hydrophobic protein containing 109 amino acids. It is thought that GlpM may play a role in alginate biosynthesis in Pseudomonas aeruginosa [].
Probab=24.56 E-value=27 Score=32.30 Aligned_cols=40 Identities=45% Similarity=0.573 Sum_probs=30.0
Q ss_pred HHHHHHhhhhccccccccceehhhh--HHHHhheeeeeeccCC
Q 008335 103 ATLIHLILLVSDAKYNYNASVLFPL--AFAIIAVLFVFKERDT 143 (569)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 143 (569)
|+..-+|-+.|-.|+.|-|. |.|| .||+||-.+|-+||+.
T Consensus 7 a~~VllIalLsKsk~~yiaG-LvPLFPTFALIahyiVg~er~~ 48 (107)
T PF06942_consen 7 ALVVLLIALLSKSKNYYIAG-LVPLFPTFALIAHYIVGSERGM 48 (107)
T ss_pred HHHHHHHHHHHhchhhHHhh-HHHHhHHHHHHHHHHHHhcCCH
Confidence 44455677788888888765 4444 5999999999999964
No 9
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=22.39 E-value=2.2e+02 Score=27.26 Aligned_cols=61 Identities=7% Similarity=-0.079 Sum_probs=39.0
Q ss_pred ccCcceEEEeccCCcceEEEEccCCCeeeeecCCccccceeee--eehhhcccCCCCcccccCCC
Q 008335 344 DLFNIIEIEIPIGLSRQFILRRLDGESHYFITNNDRMRDTLVL--TMRTFRRMVLPPTVAAFIPT 406 (569)
Q Consensus 344 kfs~~~~ikip~g~~~qfvIi~SDG~Eh~Lr~~d~r~RD~~Vl--tlR~F~rmaLppgvfRF~PT 406 (569)
-|+|+ .|+++.|.+-++.+...|+..|.+...+-.. +..+- .-.+++-.+..||.|.|+-+
T Consensus 57 ~~~P~-~I~VkaGD~Vtl~vtN~d~~~H~f~i~~~gi-s~~I~pGet~TitF~adKpG~Y~y~C~ 119 (135)
T TIGR03096 57 LNEPE-ALVVKKGTPVKVTVENKSPISEGFSIDAYGI-SEVIKAGETKTISFKADKAGAFTIWCQ 119 (135)
T ss_pred EEcCC-EEEECCCCEEEEEEEeCCCCccceEECCCCc-ceEECCCCeEEEEEECCCCEEEEEeCC
Confidence 44665 5779999999999998888888877654222 11111 01223445778888877643
No 10
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=22.23 E-value=2e+02 Score=31.66 Aligned_cols=87 Identities=26% Similarity=0.376 Sum_probs=52.0
Q ss_pred cccCCCCCCcccceeEeccccCCCceeeeecCCeeeeeEEEEEEecccccccccCCCCcceeeecccccceEEEEeEecc
Q 008335 185 LSGQVQEGPGIEKFRIIGEAKPGGKLLGYPVNGTTLSTFQWIRFLEDDTRHSIEGATEPEYVVTADDINKLIALEHTTID 264 (569)
Q Consensus 185 ~~~~~d~lp~i~gl~I~Gda~pG~~L~g~~vngtt~c~FqWvRhledgt~~~IegA~~p~Y~vTADDv~~~iaie~~p~d 264 (569)
.+.-..|-||..|..+.|+.+|...-.-.++. ..++-.+..+|=.+++|-
T Consensus 115 la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~------------------------~g~~~~~~~~d~~~~~A~------ 164 (451)
T PF03961_consen 115 LAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLK------------------------AGKNTEVSEEDGNKLYAA------ 164 (451)
T ss_pred EEEEccCCCCCCCcccCCCCcCCCCCCcccee------------------------CCCCEEEEcCCCCEEEEe------
Confidence 55557789999999999999987665511111 112333343443344331
Q ss_pred CCCCcceEEEEeecCCCccccChhhHHHHHHhhhceeeEEEEEEe
Q 008335 265 DEGHEGKLVTVFANEHSKIKCDPDMQSKVDMHISRGQAAFRVLLL 309 (569)
Q Consensus 265 d~~rkGelv~~~an~~~kI~cdp~mq~~I~~~~~~g~a~f~V~l~ 309 (569)
..|-++.. ++.|.-+|.+.=. +--+++|+..|.=.+.
T Consensus 165 ---~~G~~~~~----~~~i~V~~~l~i~-dVd~~TGnI~f~G~V~ 201 (451)
T PF03961_consen 165 ---IDGRPVFE----NGKISVDPVLEIN-DVDYSTGNIDFDGDVI 201 (451)
T ss_pred ---cCCEEEEE----CCEEEEEEeeEeC-CCCCCCCCEeeeEEEE
Confidence 13444322 3447777777767 7778889888855544
No 11
>KOG1563 consensus Mitochondrial protein Surfeit 1/SURF1/SHY1, required for expression of cytochrome oxidase [Energy production and conversion]
Probab=21.74 E-value=2.4e+02 Score=30.19 Aligned_cols=134 Identities=16% Similarity=0.263 Sum_probs=71.5
Q ss_pred cccCCChHHHHHHHHHHHHcCCCCCccCCcceeccCCCCCCCccchhh--cccCCCeEEEEEecCCCCCccccccccceE
Q 008335 401 AAFIPTDTELVTYHLMNKVSARSYEQLDRFIKDIELYDYEPSELSSLA--YHSGHDKKYFFTRLSQPARTVNRQAQGGYW 478 (569)
Q Consensus 401 fRF~PTDEELV~~YLrpKI~G~plP~~~~vI~evDVY~~ePWdLP~~~--~~~ge~eWYFFSpR~rkGrR~nRttggGyW 478 (569)
+++.=.-.|||.+ |..++.-.+.+++.++ -.+++|+--..- ++..+++-.|..||.+.+. .+.+ .||.
T Consensus 78 vkRlkWK~~lI~~-l~~rL~~~pi~LP~~~------~~l~~lEyrrV~~rG~F~H~kEm~vgPR~r~~~--~g~~-~Gy~ 147 (288)
T KOG1563|consen 78 VKRLKWKLELIAS-LKQRLEQEPIPLPKDL------DDLEGLEYRRVKLRGIFLHDKEMYVGPRTRSGP--KGSE-IGYY 147 (288)
T ss_pred ehhHHHHHHHHHH-HHhhhcCCCccCCCCh------hHhcccceEEEEEEEEEcccceEEeccccccCC--CCcc-cceE
Confidence 4667788899996 8999988887754443 234555432211 1112334466777755331 2222 3443
Q ss_pred EecCCCeeeeCCCCCEEEEEEEEEEEeccCCCCCCCccCeEEEEEEeCCCCCCCCCCCCCe-EEEEEEEeccccCCCCCc
Q 008335 479 RKTGMPSYVNDKDGDAVATKTSLTYFKKQDPTSKPEKTHWLMKEYMLLKSQQPNQNDETPW-TLCVLYDFQRKRREGPFK 557 (569)
Q Consensus 479 KatGk~K~I~d~~G~iVG~KKtLvFyegr~P~gkg~KTgWVMhEYrL~~~~~~n~~~~~d~-VLCKIYkKkrKrr~gp~k 557 (569)
-.|- -+.+.+|.+| -+.-||+=.+|-..+...+....++.. ++|-|.+...+-+=.+.+
T Consensus 148 vvTP---F~~~d~g~~I-----------------LVNRGWvp~~~v~petR~~~~~~~~~v~l~gvVRk~e~r~~f~~~n 207 (288)
T KOG1563|consen 148 VVTP---FILDDNGSII-----------------LVNRGWVPRKKVEPETRYPSGQPEGHVELVGVVRKTETRPQFTPVN 207 (288)
T ss_pred Eeee---eEECCCCCEE-----------------EEecCccchhhcCcccccccCCccceEEEEEEEecCCCCCCccccc
Confidence 2221 0111222211 123567777776666553332333444 677776555555567778
Q ss_pred ccccccc
Q 008335 558 RTEKNLW 564 (569)
Q Consensus 558 s~~~~~w 564 (569)
..++++|
T Consensus 208 ~pe~~~w 214 (288)
T KOG1563|consen 208 KPESNVW 214 (288)
T ss_pred CCcccce
Confidence 8888888
No 12
>cd05171 PIKKc_ATM Ataxia telangiectasia mutated (ATM), catalytic domain; The ATM catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. ATM is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). ATM contains a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. ATM is critical in the response to DNA double strand breaks (DSBs) caused by radiation. It is activated at the site of a DSB and phosphorylates key substrates that trigger pathways that regulate DNA repair and cell cycle checkpoints at the G1/S, S phase, and G2/M transi
Probab=21.68 E-value=64 Score=33.46 Aligned_cols=46 Identities=11% Similarity=0.141 Sum_probs=36.2
Q ss_pred cccCcceEEEeccCCcceEEEEccCCCeeeeecC--Cccccceeeeee
Q 008335 343 GDLFNIIEIEIPIGLSRQFILRRLDGESHYFITN--NDRMRDTLVLTM 388 (569)
Q Consensus 343 ekfs~~~~ikip~g~~~qfvIi~SDG~Eh~Lr~~--d~r~RD~~Vltl 388 (569)
+.|.|.+.|--....|.+..+.++||..|.+-+. +...+|+.+++|
T Consensus 2 ~~f~~~v~v~~s~~~Pkri~~~gsdG~~y~fl~K~~dDlR~D~rimQl 49 (279)
T cd05171 2 SKFKDVFTTAGGINAPKIITCVGSDGKKYKQLLKGGDDDRQDAVMEQV 49 (279)
T ss_pred CCccCeEEEecCCCCCEEEEEECCCCCEEEEEecCCCcccHHHHHHHH
Confidence 4788999998888899999999999999988873 233357666644
Done!