Query 006819
Match_columns 630
No_of_seqs 97 out of 116
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 14:57:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4762 DNA replication factor 100.0 5.3E-54 1.2E-58 459.6 19.4 334 104-630 140-490 (498)
2 cd08674 Cdt1_m The middle wing 100.0 5.7E-38 1.2E-42 302.7 13.6 136 97-232 12-151 (185)
3 PF08839 CDT1: DNA replication 100.0 2.5E-36 5.5E-41 285.0 10.4 149 104-262 1-162 (163)
4 cd08767 Cdt1_c The C-terminal 100.0 2.4E-34 5.2E-39 262.9 13.4 125 502-627 2-126 (126)
5 KOG4762 DNA replication factor 99.5 2.5E-14 5.5E-19 155.3 9.7 141 101-243 42-182 (498)
6 TIGR00988 hip integration host 27.0 91 0.002 27.2 3.9 39 562-601 1-39 (94)
7 PF00216 Bac_DNA_binding: Bact 26.6 90 0.002 26.4 3.8 38 562-601 1-38 (90)
8 PF15379 DUF4606: Domain of un 25.8 1.1E+02 0.0023 28.8 4.3 102 505-628 1-102 (104)
9 smart00411 BHL bacterial (prok 25.5 98 0.0021 26.4 3.8 38 562-601 1-38 (90)
10 PRK08402 replication factor A; 23.4 90 0.0019 34.4 3.9 38 560-601 2-39 (355)
11 COG3172 NadR Predicted ATPase/ 22.7 1.1E+02 0.0024 31.2 4.0 50 181-231 114-163 (187)
12 KOG3326 Uncharacterized conser 20.9 1E+02 0.0022 30.5 3.4 48 551-598 62-109 (154)
No 1
>KOG4762 consensus DNA replication factor [Replication, recombination and repair]
Probab=100.00 E-value=5.3e-54 Score=459.61 Aligned_cols=334 Identities=28% Similarity=0.380 Sum_probs=270.3
Q ss_pred CchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccchhhhhhhhccccEEEEEEEeccC-CCCCCCC
Q 006819 104 LPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLGHLAQLKFILPEVIQIKKVLTFDE-KTSCMKP 182 (630)
Q Consensus 104 LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~HLAQIK~IyPeAy~~~qek~~d~-~S~~~k~ 182 (630)
|||||+.|+++|++||++++|+|+|+++|||.+|..+|+.|+|++|+..||||||||||++|.|++.+.+.. +++.+..
T Consensus 140 lp~ky~~L~kvF~~~d~~~~~~h~~~~~~t~~~L~~~v~~~~r~~fsn~hl~qIksv~p~s~~i~~~~t~~~f~~~~~~~ 219 (498)
T KOG4762|consen 140 LPEKYRALRKVFRSMDGIVAKAHPQNRKPTFELLPEPVNRMFRKSFSNTHLAQIKSLYPESYIIRQLETIQRFKAGAKLD 219 (498)
T ss_pred chHHHHHHHHHHHHhhhhhhhcccccCCCchhhccchhhhhhhcccccchhhhhhcccccceeechhhhhhccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999998854 9999999
Q ss_pred CeeEEEeecccccC--CCCCccchhhHHHHHHHHHHHHH--HHhCCCC--------CCCCCCCCCC---CCCCCchhhhh
Q 006819 183 DLHVTVNADAIECD--GKSKCNSKNLNLRTVFRARLMDF--LKDHPEG--------DEIPEETLPE---PFNRSRSDLQL 247 (630)
Q Consensus 183 d~qLtL~p~~~E~~--~~~~s~S~lLeRRrvF~~~Lld~--vK~HHe~--------~dIPEa~LPe---pFN~~~~~~~~ 247 (630)
+|+|++.|++.+.. .....++..++|+++|-..++.+ ++.||.+ +.++|.+|.+ +|+..+..
T Consensus 220 ~y~l~i~p~l~~~~~~~~~~~~~~~~~r~q~~s~~~~~~~~ik~~~~~~~~~lsp~~Vd~e~~ltr~~~~f~~~~~~--- 296 (498)
T KOG4762|consen 220 DYELIIKPNLSQENGAVPQPVKSASTPRKQYLSPELFLFTPIKSHHKQALPSLSPAIVDGEESLTRTHPEFALEPHV--- 296 (498)
T ss_pred cceEeccccccccccccccccccccccchhhhhhhhhccCcCchhhhcccccCCcccccchhhhhhccccccccccc---
Confidence 99999999988743 36777888999999999999998 9999998 5556888877 58877665
Q ss_pred hhhcccCCCCCCCCCCchhhhhcccCCCccccccccccccCCccccccccCCCCcccccchhhccccc-ccccchhhhhh
Q 006819 248 NMVKKSTSLTPADSPTDASVEQQQVSSPTCQNSKLLNIVKAPSISMVTGTSASASDNQQPIVASHFSS-RRHFSQKFVNS 326 (630)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~p~~~~~~~~~~~~~~e~~~~~~shl~~-rr~fSqK~~~t 326 (630)
.+.++.++ . ++..+....++..++. +-.+++.
T Consensus 297 -------~i~~s~~~--------------------------------~----~~~~ek~~~a~e~~s~~~~~~~p~---- 329 (498)
T KOG4762|consen 297 -------KICHSEFL--------------------------------E----PPGTEKDSTANEPLSDFRNDKSPR---- 329 (498)
T ss_pred -------cccccccC--------------------------------C----CCcccccccCcCcccccccccCcc----
Confidence 22222222 1 3445555555444443 3333333
Q ss_pred HHHHhhhhhccCCcccCCCCCCCCchhhhcccchhhhhhhhhhhhhhhccccccccccccccCCCCCCCCCCCCCCCccc
Q 006819 327 LAEKKKAERISSGVSIEPSTTPALEPCLRKISSIEETCSTAAISAVELSSKSTSKENCLTYCASPTRLSQSCPPVTPVKE 406 (630)
Q Consensus 327 ~~Ek~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~e~~~~~l~~~p~~~~~~~~~k~~~~~~~~~~~~~~q~~~~~tp~~~ 406 (630)
+++ +++ .+..+
T Consensus 330 -l~~----------------------~~~-----------------------~~~~~----------------------- 340 (498)
T KOG4762|consen 330 -LPL----------------------SVD-----------------------EYPED----------------------- 340 (498)
T ss_pred -hhh----------------------ccc-----------------------ccccc-----------------------
Confidence 222 111 00000
Q ss_pred cCCCCCCCccCcccccCCCCCCccCCCccccccCCCCCCCCCcccCCCCcccCCCCCCcCCCCCCccccccccCCCcccc
Q 006819 407 IDPMESKVSYPIKVDSEQSTPAKLVSTPARLMIGTPALHQPKRCYMTPENVSASSPNKLTRRPPHSRTLKSLKFDTPVKN 486 (630)
Q Consensus 407 i~~~~s~~~~~~~~~~~~stP~k~~stp~~lma~TPa~~~PkR~l~~~~~~s~~~~~k~arrp~~~r~L~~~~F~sp~k~ 486 (630)
+++..+.+. | ++.|+-
T Consensus 341 -----------~rS~~s~~s-------p----~tvp~s------------------------------------------ 356 (498)
T KOG4762|consen 341 -----------LRSMRSDGS-------P----STVPES------------------------------------------ 356 (498)
T ss_pred -----------cccccccCC-------C----ccCCCC------------------------------------------
Confidence 000000000 1 111100
Q ss_pred hhhhccccccccCCCccccCCchhHHHHHHHHHHHHHHhhCchhHHHHHHHHHhhchhHHHHHHHHHHHhhccccccHHH
Q 006819 487 ATVEHKLNEDISVDGDVLDILPENLIQSIREKERKFMEERDPAISQAKWRRQMIASLPKLFNMIHFLFQSIKRSVITKEE 566 (630)
Q Consensus 487 ~~~~~~~~~~~s~d~~~l~~vpesLl~sIrekE~~~~~~q~t~~~~~~~r~~~ia~LP~L~~iir~IF~S~krs~ITKEE 566 (630)
....+...+++++++|+++||+||+++.+++|+++++|++|.+++++||+||||||+||+|++|++|||||
T Consensus 357 ---------~~~~~~s~ls~~~~sLlErIRaKEa~k~~~~m~~~~~~~~r~~~l~~Lp~l~riIr~vF~Serr~~it~e~ 427 (498)
T KOG4762|consen 357 ---------TSKADSSQLSGRASSLLERIRAKEAAKRLAQMTERKEQERREQRLALLPELVRIIRSVFVSERRRVITMEE 427 (498)
T ss_pred ---------CcccChhhhccchHHHHHHHHHHHHHHHHHHhhhCchhHHHHHHHHhhHHHHHHHHHHHHhccccceeHHH
Confidence 01134556789999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccccCChhHHHHHHHHHHHhcccchhhcccCCCCeEEEeccCCChHHHHHHhhhcC
Q 006819 567 LIHKIISSHLQITDRREVEEQMNLMLELVPEWISEKLSSCGDLLVCINKMTCPESIRARLEESK 630 (630)
Q Consensus 567 LvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~k~i~sGD~~~ki~K~~dl~sVraRL~e~~ 630 (630)
+|++|++|+..|++++|||+||.||.+++|||||.+.++. |+|+||+|++|.+.|++||++++
T Consensus 428 iv~ki~~s~~~i~s~~eve~hL~LL~e~lP~WiS~~~~~~-d~~v~i~K~~~~~~i~~rl~~e~ 490 (498)
T KOG4762|consen 428 IVKKIQASDSNITSPREVEKHLSLLSELLPDWISEHKSSN-DQLVKISKIADGEHIRARLEEET 490 (498)
T ss_pred HHHHHHhcccccCCHHHHHHHHHHHHHHhHHHHhHHhhcC-ceEEEeehhccHHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999997 99999999999999999998763
No 2
>cd08674 Cdt1_m The middle winged helix fold of replication licensing factor Cdt1 binds geminin to inhibit binding of the MCM complex to origins of replication and DNA. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the origin recognition complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative
Probab=100.00 E-value=5.7e-38 Score=302.74 Aligned_cols=136 Identities=40% Similarity=0.574 Sum_probs=129.7
Q ss_pred CCCCCCCCchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccchhhhhhhhccccEEEEEEEeccCC
Q 006819 97 AGSGSPKLPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLGHLAQLKFILPEVIQIKKVLTFDEK 176 (630)
Q Consensus 97 ~~~~~L~LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~HLAQIK~IyPeAy~~~qek~~d~~ 176 (630)
...+++.||+||+.|+++|++|||+++||++|++.+||.|||++||.|++|+|++.||||||||||++|.|+|+++++++
T Consensus 12 ~~~~~~~lP~ky~~L~~~F~~ldtv~~~l~~R~~~~tf~~ik~~Ve~~~~r~f~~~~LaQI~~l~P~~y~~~~~~~~~~~ 91 (185)
T cd08674 12 SVRPSLKLPEKYEVLAELFRSLDTIVRLLFNRKETCTFDKLKPAVERMTRRRFSEKHLAQIKHIYPEAYTLRQEKNHDEG 91 (185)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHCCCccHHHhhhhheeccCceeEEEEEeccCc
Confidence 35568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCeeEEEeecccccC----CCCCccchhhHHHHHHHHHHHHHHHhCCCCCCCCCC
Q 006819 177 TSCMKPDLHVTVNADAIECD----GKSKCNSKNLNLRTVFRARLMDFLKDHPEGDEIPEE 232 (630)
Q Consensus 177 S~~~k~d~qLtL~p~~~E~~----~~~~s~S~lLeRRrvF~~~Lld~vK~HHe~~dIPEa 232 (630)
++|++++|||+|+|+++|+. ...++++.+++||++||++|++||++||++++++++
T Consensus 92 ~~~~~~~~~l~i~p~~~e~~~~~~~~~~~~~~~~~R~~~F~~~L~~~vk~hh~~fl~~~~ 151 (185)
T cd08674 92 SLCKKPDYQLTLEPNLVEGLELGGSPKLSESRLLARRQVFRSRLLDFVKAHHEEFLISLD 151 (185)
T ss_pred ccccccceEEEEecCccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 99999999999999999875 257788999999999999999999999999999888
No 3
>PF08839 CDT1: DNA replication factor CDT1 like; InterPro: IPR014939 CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin. Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin. This region of CDT1 binds to Geminin []. ; PDB: 2WVR_C 2ZXX_F.
Probab=100.00 E-value=2.5e-36 Score=285.00 Aligned_cols=149 Identities=33% Similarity=0.555 Sum_probs=103.2
Q ss_pred CchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccchhhhhhhhccccEEEEEEE-eccCCCCCCCC
Q 006819 104 LPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLGHLAQLKFILPEVIQIKKVL-TFDEKTSCMKP 182 (630)
Q Consensus 104 LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~HLAQIK~IyPeAy~~~qek-~~d~~S~~~k~ 182 (630)
||++|+.|+++|++||||++||++|++++||++||++||+|+||+|++.||||||||||+||.|+|++ ....++.+...
T Consensus 1 LP~~y~~L~~~F~~ldtv~~~l~~R~~~~tf~~i~~~Ve~~~kr~F~~~~LaQI~~i~P~a~~~~~~~~~~~~~~~~~~~ 80 (163)
T PF08839_consen 1 LPEKYEFLAELFRALDTVVSMLRNRKETPTFQKIKPSVENMTKRRFTEEHLAQIKYIYPEAYSLKQEKKVPTFDSGSKCM 80 (163)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHTT---BHHHHHHHHHHHHSS---HHHHHHHHHH-GGGEEEEEEE--SS--S---GG
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCCcCHHHHHHHHHhCcccEEEeeeeccccCCcccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999887 43445555555
Q ss_pred CeeEEEeecccc----cCCCCCccchhhHHHHHHHHHHHHHHHhCCCC-----CCCCCCCCCC---CCCCCchhhhhhhh
Q 006819 183 DLHVTVNADAIE----CDGKSKCNSKNLNLRTVFRARLMDFLKDHPEG-----DEIPEETLPE---PFNRSRSDLQLNMV 250 (630)
Q Consensus 183 d~qLtL~p~~~E----~~~~~~s~S~lLeRRrvF~~~Lld~vK~HHe~-----~dIPEa~LPe---pFN~~~~~~~~~~~ 250 (630)
.|+|+|.+++.+ +.....+++.+++||++||++|++||+.||++ ..-|++.|.+ .||.+.++
T Consensus 81 ~~~l~I~p~~~~~~~~~~~~~~~~~~~~~R~~~F~~~L~~~vk~~h~~fL~~l~~~~~~~l~rwHp~F~~~~~p------ 154 (163)
T PF08839_consen 81 KYQLVIEPNLDDVEASDGRKRLSPSRLLERRQVFRQKLLEFVKEHHKEFLASLNPPPDDKLTRWHPKFNLDSCP------ 154 (163)
T ss_dssp GEEEEEEE-SS---TT--SSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTTS-CCC--S--TTS-CCCS-------
T ss_pred CcceEEEeccccccccccccCCChhhHHHHHHHHHHHHHHHHHHhHHHHHHhcCCCchhhHhhcCCCCCcccCC------
Confidence 667777777653 22246678899999999999999999999998 1228889988 99999998
Q ss_pred cccCCCCCCCCC
Q 006819 251 KKSTSLTPADSP 262 (630)
Q Consensus 251 ~~~~~~~~~~~~ 262 (630)
+|.||++|
T Consensus 155 ----~I~~a~LP 162 (163)
T PF08839_consen 155 ----DIPPAELP 162 (163)
T ss_dssp ------------
T ss_pred ----CCCCCCCC
Confidence 88888887
No 4
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=100.00 E-value=2.4e-34 Score=262.85 Aligned_cols=125 Identities=37% Similarity=0.510 Sum_probs=121.4
Q ss_pred ccccCCchhHHHHHHHHHHHHHHhhCchhHHHHHHHHHhhchhHHHHHHHHHHHhhccccccHHHHHHHHHhhccccCCh
Q 006819 502 DVLDILPENLIQSIREKERKFMEERDPAISQAKWRRQMIASLPKLFNMIHFLFQSIKRSVITKEELIHKIISSHLQITDR 581 (630)
Q Consensus 502 ~~l~~vpesLl~sIrekE~~~~~~q~t~~~~~~~r~~~ia~LP~L~~iir~IF~S~krs~ITKEELvhKIias~~~I~d~ 581 (630)
+.|+|+|++||++||+||+++.+++||+.+.+++|++|+++||++||+||+||+|++|++||||+|+|||++||++++++
T Consensus 2 ~~lkg~~~sLLerIr~ke~~~~~~~~t~~~~~~kr~~~~~rLP~la~~v~~if~s~~k~~l~~e~l~~kl~~S~~~~~s~ 81 (126)
T cd08767 2 EALKGVPKSLLERIRAKEAAKALEKMTRRPEQEKRRRMYARLPELARILRNIFVSEKKTVLPLEELVYKLQASYPSILSR 81 (126)
T ss_pred cchhhCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHhHHHHHHHHHHHHHhcccccccHHHHHHHHHHhCCCCCCH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhcccchhhcccCCCCeEEEeccCCChHHHHHHhh
Q 006819 582 REVEEQMNLMLELVPEWISEKLSSCGDLLVCINKMTCPESIRARLE 627 (630)
Q Consensus 582 gEvEEqL~LLeeLvPDWIS~k~i~sGD~~~ki~K~~dl~sVraRL~ 627 (630)
||||+||+||+|++||||+.+.++ |++|++++|..|+++|++||+
T Consensus 82 ~E~E~~l~LL~el~P~Wis~~~~~-~~~~lk~~k~~~~~~V~~rL~ 126 (126)
T cd08767 82 GEVEEHLRLLAELAPDWISEKSLR-KGDYLKIDKKVDLEKVRKRLE 126 (126)
T ss_pred HHHHHHHHHHHHhChHHheeeeeC-CceEEEECccccHHHHHHHhC
Confidence 999999999999999999999997 688999999999999999995
No 5
>KOG4762 consensus DNA replication factor [Replication, recombination and repair]
Probab=99.52 E-value=2.5e-14 Score=155.29 Aligned_cols=141 Identities=35% Similarity=0.470 Sum_probs=133.1
Q ss_pred CCCCchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccchhhhhhhhccccEEEEEEEeccCCCCCC
Q 006819 101 SPKLPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLGHLAQLKFILPEVIQIKKVLTFDEKTSCM 180 (630)
Q Consensus 101 ~L~LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~HLAQIK~IyPeAy~~~qek~~d~~S~~~ 180 (630)
...+|+.|.+|..+|+.+|.+.++...|+ .++|.+.++..+.||-|+|.+.|++|++||+|+++.+..++.+|++.+||
T Consensus 42 ~~k~~~~~~~l~~~~~~ld~~~~~q~~r~-~~l~~~~~~~~~s~ta~~~~~~~~~e~~~iip~~~~lk~~~~~d~~e~~~ 120 (498)
T KOG4762|consen 42 RAKLPHENNILIKFFQVLDMSMGLQKLRG-KCLRSNRKSSIRSLTARILHYMHKPELDHIIPGLKELKRVLKFDEHECCM 120 (498)
T ss_pred hhhcchhhhhHHHHHHHHHHhhhhhcccC-CcccccCCcchhhhhhcccccccccchhhhhhhhhhhhcccccccchhcc
Confidence 45899999999999999999999999999 99999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEeecccccCCCCCccchhhHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCch
Q 006819 181 KPDLHVTVNADAIECDGKSKCNSKNLNLRTVFRARLMDFLKDHPEGDEIPEETLPEPFNRSRS 243 (630)
Q Consensus 181 k~d~qLtL~p~~~E~~~~~~s~S~lLeRRrvF~~~Lld~vK~HHe~~dIPEa~LPepFN~~~~ 243 (630)
+.+++..++.++++....+ ....|+++|++|+..+.++.+.|.+...++.+.|+++||....
T Consensus 121 k~~~~~~lna~~ve~s~~~-lp~ky~~L~kvF~~~d~~~~~~h~~~~~~t~~~L~~~v~~~~r 182 (498)
T KOG4762|consen 121 KPGLHESLNADLVEPSIRG-LPEKYRALRKVFRSMDGIVAKAHPQNRKPTFELLPEPVNRMFR 182 (498)
T ss_pred cccccchhhhhhhccccCC-chHHHHHHHHHHHHhhhhhhhcccccCCCchhhccchhhhhhh
Confidence 9999999999999876544 6688999999999999999999999999999999999995543
No 6
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=27.00 E-value=91 Score=27.16 Aligned_cols=39 Identities=28% Similarity=0.478 Sum_probs=32.8
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|...+.. .+.+++++-|.-+.+.+=+||..
T Consensus 1 m~k~eli~~i~~~~~~-~s~~~v~~vv~~~~~~i~~~L~~ 39 (94)
T TIGR00988 1 MTKSELIERIATQQSH-LPAKDVEDAVKTMLEHMASALAQ 39 (94)
T ss_pred CCHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHHHHHHHc
Confidence 7999999999765543 47899999999999999998866
No 7
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=26.58 E-value=90 Score=26.43 Aligned_cols=38 Identities=26% Similarity=0.510 Sum_probs=30.9
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+.+|-..+. .+.+++++-|.-|.+.+-+=|..
T Consensus 1 Mtk~eli~~ia~~~~--~s~~~v~~vl~~~~~~i~~~L~~ 38 (90)
T PF00216_consen 1 MTKKELIKRIAEKTG--LSKKDVEAVLDALFDVIKEALKE 38 (90)
T ss_dssp EBHHHHHHHHHHHHT--SSHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHHHHhc
Confidence 799999999966555 59999999999998887665543
No 8
>PF15379 DUF4606: Domain of unknown function (DUF4606)
Probab=25.82 E-value=1.1e+02 Score=28.78 Aligned_cols=102 Identities=22% Similarity=0.179 Sum_probs=56.8
Q ss_pred cCCchhHHHHHHHHHHHHHHhhCchhHHHHHHHHHhhchhHHHHHHHHHHHhhccccccHHHHHHHHHhhccccCChhHH
Q 006819 505 DILPENLIQSIREKERKFMEERDPAISQAKWRRQMIASLPKLFNMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREV 584 (630)
Q Consensus 505 ~~vpesLl~sIrekE~~~~~~q~t~~~~~~~r~~~ia~LP~L~~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEv 584 (630)
+.||+.|+++|+=|-......|.....++. .-+--++-..=..+-..-|.-.||..+...-|..||
T Consensus 1 c~VP~~l~nRi~~kn~~~~~kq~~~~k~H~-~s~Cp~C~kkraeLa~~~Flr~KktlLE~~ll~EKi------------- 66 (104)
T PF15379_consen 1 CTVPDELVNRIYLKNMRATLKQVATAKQHN-SSQCPSCNKKRAELAQSAFLRRKKTLLESLLLQEKI------------- 66 (104)
T ss_pred CcCcHHHHHHHHHHHHHHHHHHHhcccccC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------
Confidence 369999999998766655554433222222 111122223334556677888889888888887776
Q ss_pred HHHHHHHHHhcccchhhcccCCCCeEEEeccCCChHHHHHHhhh
Q 006819 585 EEQMNLMLELVPEWISEKLSSCGDLLVCINKMTCPESIRARLEE 628 (630)
Q Consensus 585 EEqL~LLeeLvPDWIS~k~i~sGD~~~ki~K~~dl~sVraRL~e 628 (630)
||||+-=.-| --|-+ ..+++ = .-.-|+..|++||.+
T Consensus 67 eehl~tkD~L--tlIgE-i~~~l---P--rlSddP~~IW~rL~~ 102 (104)
T PF15379_consen 67 EEHLYTKDFL--TLIGE-IHRSL---P--RLSDDPRIIWKRLNE 102 (104)
T ss_pred HHHHhcccHH--HHHHH-HHHcC---C--CCCCCHHHHHHHHhh
Confidence 7777631110 00111 11110 0 112389999999976
No 9
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.49 E-value=98 Score=26.36 Aligned_cols=38 Identities=24% Similarity=0.494 Sum_probs=31.4
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|.. +..+ +.+++++-|..|.+.+-++|..
T Consensus 1 mtk~eli~~ia~-~~~~-~~~~v~~vl~~l~~~i~~~L~~ 38 (90)
T smart00411 1 MTKSELIDAIAE-KAGL-SKKDAKAAVDAFLEIITEALKK 38 (90)
T ss_pred CCHHHHHHHHHH-HhCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 689999998844 5544 7999999999999988888765
No 10
>PRK08402 replication factor A; Reviewed
Probab=23.41 E-value=90 Score=34.38 Aligned_cols=38 Identities=37% Similarity=0.555 Sum_probs=32.3
Q ss_pred ccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 560 SVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 560 s~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
.+||||+++..| ++.++ +++.|+|+.|+.|-+-+| +.+
T Consensus 2 ~~~~~~~i~e~~-~~~~~-vs~eei~~~l~~lv~~~~--~~e 39 (355)
T PRK08402 2 TVLTKEEIIERI-ERKTG-MSREEIEEKIREIMKEEG--ISE 39 (355)
T ss_pred ccccHHHHHHHH-HHhhC-CCHHHHHHHHHHHHHHcC--CCH
Confidence 479999999998 55576 899999999999988888 665
No 11
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=22.75 E-value=1.1e+02 Score=31.22 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=32.8
Q ss_pred CCCeeEEEeecccccCCCCCccchhhHHHHHHHHHHHHHHHhCCCCCCCCC
Q 006819 181 KPDLHVTVNADAIECDGKSKCNSKNLNLRTVFRARLMDFLKDHPEGDEIPE 231 (630)
Q Consensus 181 k~d~qLtL~p~~~E~~~~~~s~S~lLeRRrvF~~~Lld~vK~HHe~~dIPE 231 (630)
..|+.|.|.|+ ++..+++.-.-.-.+-|+.||+.|...+..|-....+-+
T Consensus 114 r~DL~lLl~p~-t~wvaDG~R~~~~~~~R~~F~~~l~~~L~~~~~~~v~i~ 163 (187)
T COG3172 114 RFDLTLLLEPN-TPWVADGLRSLGSSVQRQEFQNLLEQMLEENNIPFVVIE 163 (187)
T ss_pred ccceEEEcCCC-CceeCCCccccccHhHHHHHHHHHHHHHHHhCCcEEEEc
Confidence 45777777787 455443333333456679999999999999865533333
No 12
>KOG3326 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.86 E-value=1e+02 Score=30.54 Aligned_cols=48 Identities=23% Similarity=0.464 Sum_probs=44.6
Q ss_pred HHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccc
Q 006819 551 HFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEW 598 (630)
Q Consensus 551 r~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDW 598 (630)
|.++||.||-.+--.-|+..-.+-|++-++-.++++-.+||-+..=||
T Consensus 62 RLlYqSrKRGiLEnDLLLs~Fa~~~l~~m~e~~l~~YD~LiN~~~~dW 109 (154)
T KOG3326|consen 62 RLLYQSRKRGILENDLLLSNFAAKNLKKMSEEQLKEYDQLINEESNDW 109 (154)
T ss_pred HHHHHHhhcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcCCc
Confidence 568999999999999999999999999999999999999999987777
Done!