Query 025081
Match_columns 258
No_of_seqs 138 out of 187
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:32:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2538 Origin recognition com 100.0 2.6E-34 5.7E-39 278.6 7.4 158 81-256 414-578 (578)
2 KOG2538 Origin recognition com 79.1 1 2.3E-05 45.5 1.6 122 5-130 439-569 (578)
3 PF09079 Cdc6_C: CDC6, C termi 74.5 9.6 0.00021 28.4 5.4 23 220-242 35-57 (85)
4 cd08768 Cdc6_C Winged-helix do 69.3 9.6 0.00021 28.1 4.4 22 221-242 43-64 (87)
5 PF01475 FUR: Ferric uptake re 41.4 89 0.0019 24.5 5.9 48 164-241 12-59 (120)
6 TIGR02928 orc1/cdc6 family rep 40.4 36 0.00079 31.5 4.0 54 164-242 293-349 (365)
7 KOG0502 Integral membrane anky 32.3 17 0.00037 33.6 0.3 19 164-182 207-225 (296)
8 KOG1151 Tousled-like protein k 29.9 35 0.00075 34.8 2.0 73 159-243 511-590 (775)
9 PRK02363 DNA-directed RNA poly 26.0 2.5E+02 0.0054 23.3 6.2 33 159-191 3-35 (129)
10 PHA03358 Alkaline exonuclease; 22.8 51 0.0011 24.9 1.4 16 172-187 19-34 (75)
11 KOG0664 Nemo-like MAPK-related 21.0 1.2E+02 0.0026 29.2 3.8 26 118-143 321-346 (449)
12 PF10668 Phage_terminase: Phag 20.3 1.1E+02 0.0023 22.3 2.6 24 159-182 6-29 (60)
No 1
>KOG2538 consensus Origin recognition complex, subunit 3 [Replication, recombination and repair]
Probab=100.00 E-value=2.6e-34 Score=278.56 Aligned_cols=158 Identities=33% Similarity=0.496 Sum_probs=136.4
Q ss_pred HHHHHHHHHHHHHHHHHhhCCC---CCCCCcceEEEecCchhhhHhhc-CChhhHHHHHhhchhhhhcCc--ccCCCCCC
Q 025081 81 SRAVNEKAASLIECMVRDYMQP---VECSPLHEIVCFKNVETLQLALI-GDPRRRIQIDLLESYKILRCS--CCSRSGHS 154 (258)
Q Consensus 81 ~~~~~~~~~~~l~~l~~~~l~p---~~~lpfhEif~~d~~~~L~~~l~-P~pR~~ie~aL~~p~~yL~~~--~~~~~~~~ 154 (258)
-.+...+++.+++.+++.++-+ ++.-|+||++.|+...+++++|. +.||.++++++.||+.|++|+ ||...++.
T Consensus 414 f~~~~~k~v~l~e~~v~~~~l~~l~~~~~p~~e~l~f~~~~tl~q~l~s~~~RsalhTa~n~P~yyl~~e~~a~e~~~g~ 493 (578)
T KOG2538|consen 414 FEARLLKYVSLIEILVSQSHLSGLNNDIRPVHEVLRFSSISTLRQMLKSGANRSALHTALNDPVYYLHPEMRAVEAADGR 493 (578)
T ss_pred HHHHHHHHhhHHHHHHHHhhccccccchhhHHHHHhcCchHHHHHHHhcccchhHHHHhhcCceeecccHHhhHhhhcCC
Confidence 4566778999999999888765 78899999999999999999998 999999999999999999999 88755554
Q ss_pred C-CCCcchHHHHHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHH
Q 025081 155 L-LPSLHDTSILYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTE 233 (258)
Q Consensus 155 ~-~~s~Pd~silYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~E 233 (258)
+ .+..||+||+||||+|||++||+||||+||.+++..... + .....+.+..+|+||+|||+|
T Consensus 494 l~~~~aPdl~i~yKL~~E~~~liNl~Dw~~AF~e~l~~~~~--E---------------~~n~~~~dP~~~~rF~raV~e 556 (578)
T KOG2538|consen 494 LLLPNAPDLSILYKLYLECGRLINLYDWYIAFREVLLENDR--E---------------YMNPEESDPQIQIRFFRAVDE 556 (578)
T ss_pred cccCcCchHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhhhh--h---------------hccccccCHHHHHHHHHHHHH
Confidence 4 468999999999999999999999999999999982210 0 001234567899999999999
Q ss_pred HHHcCcccCCCCCCcceeeeecc
Q 025081 234 LQITGLIRMPTKRRPDFVQRVAF 256 (258)
Q Consensus 234 L~~lGfIK~~skrK~DhV~K~~W 256 (258)
||+||+|| ||+||+|||+|++|
T Consensus 557 Lq~lG~IK-pss~KtDhv~k~~w 578 (578)
T KOG2538|consen 557 LQFLGLIK-PSSRKTDHVLKLTW 578 (578)
T ss_pred HHhccccC-ccccchHHHHHhcC
Confidence 99999999 69999999999999
No 2
>KOG2538 consensus Origin recognition complex, subunit 3 [Replication, recombination and repair]
Probab=79.14 E-value=1 Score=45.52 Aligned_cols=122 Identities=18% Similarity=0.153 Sum_probs=83.3
Q ss_pred hhHHHHHHHhccCChhHHHHHHHHHHHhhhChHHHHH----HHHHHHHHHhhcCCCcccccccccCccccCcccccCcHH
Q 025081 5 RLICQAVQKVRDLPIAQLYKLLKRWEELTVDINEIHA----KLKELLSVIKLENGRSSRQDMADSSKRPVSRSQLNIEKE 80 (258)
Q Consensus 5 ~~i~~~~~~~r~l~~~~l~~~l~~w~~~~~~~~e~~~----~~~~~~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~~~~~ 80 (258)
+++.-+-+.+++.+..+|.+.|.+|+...+-.++++. .+.+|+++...++--..-.-|..++-.+|.+- ...
T Consensus 439 ~~~~p~~e~l~f~~~~tl~q~l~s~~~RsalhTa~n~P~yyl~~e~~a~e~~~g~l~~~~aPdl~i~yKL~~E----~~~ 514 (578)
T KOG2538|consen 439 NDIRPVHEVLRFSSISTLRQMLKSGANRSALHTALNDPVYYLHPEMRAVEAADGRLLLPNAPDLSILYKLYLE----CGR 514 (578)
T ss_pred cchhhHHHHHhcCchHHHHHHHhcccchhHHHHhhcCceeecccHHhhHhhhcCCcccCcCchHHHHHHHHHH----HhH
Confidence 6677889999999999999999999999999999995 77778888433332222234433333333322 112
Q ss_pred HHHHHHHHHHHHHHHH---HhhCCCCCCCCcceEEEecCchhhhHh--hcCChhh
Q 025081 81 SRAVNEKAASLIECMV---RDYMQPVECSPLHEIVCFKNVETLQLA--LIGDPRR 130 (258)
Q Consensus 81 ~~~~~~~~~~~l~~l~---~~~l~p~~~lpfhEif~~d~~~~L~~~--l~P~pR~ 130 (258)
...+.+....|.+-+. ++++.|++.-|.++|-++-++.-|+-. +-|.-|.
T Consensus 515 liNl~Dw~~AF~e~l~~~~~E~~n~~~~dP~~~~rF~raV~eLq~lG~IKpss~K 569 (578)
T KOG2538|consen 515 LINLYDWYIAFREVLLENDREYMNPEESDPQIQIRFFRAVDELQFLGLIKPSSRK 569 (578)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhccccccCHHHHHHHHHHHHHHHhccccCccccc
Confidence 4555555555555555 888899999999999878777666543 4555554
No 3
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=74.48 E-value=9.6 Score=28.44 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHcCcccC
Q 025081 220 EASIQARFCKAVTELQITGLIRM 242 (258)
Q Consensus 220 e~~~qArF~rAv~EL~~lGfIK~ 242 (258)
+...+-||..-+.||+++|+|..
T Consensus 35 ~pls~~r~~~~l~eL~~~gli~~ 57 (85)
T PF09079_consen 35 DPLSYRRFSDYLSELEMLGLIES 57 (85)
T ss_dssp ----HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCHHHHHHHHHHHHhCCCeEE
Confidence 45678999999999999999984
No 4
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=69.33 E-value=9.6 Score=28.14 Aligned_cols=22 Identities=27% Similarity=0.483 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHcCcccC
Q 025081 221 ASIQARFCKAVTELQITGLIRM 242 (258)
Q Consensus 221 ~~~qArF~rAv~EL~~lGfIK~ 242 (258)
...+-+|..-+.||+++|+|..
T Consensus 43 ~l~~~~~~~~l~~L~~~gli~~ 64 (87)
T cd08768 43 PLTQRRISDLLSELEMLGLLET 64 (87)
T ss_pred CCcHHHHHHHHHHHHHcCCeEE
Confidence 3568999999999999999984
No 5
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=41.45 E-value=89 Score=24.49 Aligned_cols=48 Identities=23% Similarity=0.385 Sum_probs=38.9
Q ss_pred HHHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHHcCccc
Q 025081 164 ILYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQITGLIR 241 (258)
Q Consensus 164 ilYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~lGfIK 241 (258)
.++.+..+++.-++++++|....+.- ...-.+-.||++..|.=.|+|.
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~~------------------------------~~is~~TVYR~L~~L~e~Gli~ 59 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKKG------------------------------PRISLATVYRTLDLLEEAGLIR 59 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHTT------------------------------TT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhcc------------------------------CCcCHHHHHHHHHHHHHCCeEE
Confidence 56788888888999999999998621 1234899999999999999998
No 6
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=40.39 E-value=36 Score=31.50 Aligned_cols=54 Identities=22% Similarity=0.386 Sum_probs=38.1
Q ss_pred HHHHHHHH---hCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHHcCcc
Q 025081 164 ILYNLAQE---HGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQITGLI 240 (258)
Q Consensus 164 ilYkLY~E---aG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~lGfI 240 (258)
+|+.+... .+..|+..|+|..|+...+.- + .+.....+|...+.+|+.+|+|
T Consensus 293 ~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~---~----------------------~~~~~~~~~~~~l~~l~~~gli 347 (365)
T TIGR02928 293 VLLAIANLAANDEDPFRTGEVYEVYKEVCEDI---G----------------------VDPLTQRRISDLLNELDMLGLV 347 (365)
T ss_pred HHHHHHHHHhcCCCCccHHHHHHHHHHHHHhc---C----------------------CCCCcHHHHHHHHHHHHhcCCe
Confidence 35555432 334689999999998865421 1 1234578999999999999999
Q ss_pred cC
Q 025081 241 RM 242 (258)
Q Consensus 241 K~ 242 (258)
..
T Consensus 348 ~~ 349 (365)
T TIGR02928 348 EA 349 (365)
T ss_pred EE
Confidence 94
No 7
>KOG0502 consensus Integral membrane ankyrin-repeat protein Kidins220 (protein kinase D substrate) [General function prediction only]
Probab=32.25 E-value=17 Score=33.58 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=16.4
Q ss_pred HHHHHHHHhCCcccHHHHH
Q 025081 164 ILYNLAQEHGDHINLHDWY 182 (258)
Q Consensus 164 ilYkLY~EaG~lINlyDw~ 182 (258)
.+-+|.++++.-||+|||=
T Consensus 207 diV~lLL~r~vdVNvyDwN 225 (296)
T KOG0502|consen 207 DIVELLLTREVDVNVYDWN 225 (296)
T ss_pred HHHHHHHhcCCCcceeccC
Confidence 4568999999999999993
No 8
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=29.88 E-value=35 Score=34.81 Aligned_cols=73 Identities=19% Similarity=0.230 Sum_probs=53.0
Q ss_pred cchHHHHHHHHHH--hCCcccHHHHHH----HHHhhhcCccc-ccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHH
Q 025081 159 LHDTSILYNLAQE--HGDHINLHDWYQ----SFKSKVCSSRS-KGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAV 231 (258)
Q Consensus 159 ~Pd~silYkLY~E--aG~lINlyDw~~----AF~~~l~~~~~-~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv 231 (258)
.--.|.=|..++| +.+.|-+||+|. +||++++=.+. ..++-.|+. ---.|+++-+--||-|
T Consensus 511 hKHAcREyrIHKeLDHpRIVKlYDyfslDtdsFCTVLEYceGNDLDFYLKQh------------klmSEKEARSIiMQiV 578 (775)
T KOG1151|consen 511 HKHACREYRIHKELDHPRIVKLYDYFSLDTDSFCTVLEYCEGNDLDFYLKQH------------KLMSEKEARSIIMQIV 578 (775)
T ss_pred HHHHHHHHhhhhccCcceeeeeeeeeeeccccceeeeeecCCCchhHHHHhh------------hhhhHHHHHHHHHHHH
Confidence 4567889999988 799999999995 89999975441 000100100 0135788889999999
Q ss_pred HHHHHcCcccCC
Q 025081 232 TELQITGLIRMP 243 (258)
Q Consensus 232 ~EL~~lGfIK~~ 243 (258)
.-|.||.=||+|
T Consensus 579 nAL~YLNEikpP 590 (775)
T KOG1151|consen 579 NALKYLNEIKPP 590 (775)
T ss_pred HHHHHHhccCCC
Confidence 999999999854
No 9
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=25.95 E-value=2.5e+02 Score=23.29 Aligned_cols=33 Identities=12% Similarity=0.256 Sum_probs=29.1
Q ss_pred cchHHHHHHHHHHhCCcccHHHHHHHHHhhhcC
Q 025081 159 LHDTSILYNLAQEHGDHINLHDWYQSFKSKVCS 191 (258)
Q Consensus 159 ~Pd~silYkLY~EaG~lINlyDw~~AF~~~l~~ 191 (258)
+.-+-++|.+..+.|..++.+|.+....+.++.
T Consensus 3 ~S~idvAy~iL~~~~~~m~f~dL~~ev~~~~~~ 35 (129)
T PRK02363 3 LSLIEVAYEILKEKKEPMSFYDLVNEIQKYLGK 35 (129)
T ss_pred ccHHHHHHHHHHHcCCcccHHHHHHHHHHHhCC
Confidence 456789999999999999999999999887664
No 10
>PHA03358 Alkaline exonuclease; Provisional
Probab=22.84 E-value=51 Score=24.88 Aligned_cols=16 Identities=38% Similarity=0.547 Sum_probs=14.6
Q ss_pred hCCcccHHHHHHHHHh
Q 025081 172 HGDHINLHDWYQSFKS 187 (258)
Q Consensus 172 aG~lINlyDw~~AF~~ 187 (258)
.|..||||+=|.+|..
T Consensus 19 ~G~~INl~eDFE~fS~ 34 (75)
T PHA03358 19 DGGIINLYNDYEEFSL 34 (75)
T ss_pred CCCEechHHHHHHHhh
Confidence 5999999999999976
No 11
>KOG0664 consensus Nemo-like MAPK-related serine/threonine protein kinase [Signal transduction mechanisms]
Probab=21.01 E-value=1.2e+02 Score=29.21 Aligned_cols=26 Identities=31% Similarity=0.360 Sum_probs=22.7
Q ss_pred hhhhHhhcCChhhHHHHHhhchhhhh
Q 025081 118 ETLQLALIGDPRRRIQIDLLESYKIL 143 (258)
Q Consensus 118 ~~L~~~l~P~pR~~ie~aL~~p~~yL 143 (258)
..+.+.|.|.||.+|..++..|+.||
T Consensus 321 ~~~~~~l~~d~dkris~~~A~~~~~~ 346 (449)
T KOG0664|consen 321 DLLQKLLHFDPDKRISVEEALQHRYL 346 (449)
T ss_pred HHHHHHhCCCCcccccHhhhcccccc
Confidence 36778899999999999999999888
No 12
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=20.29 E-value=1.1e+02 Score=22.27 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=20.5
Q ss_pred cchHHHHHHHHHHhCCcccHHHHH
Q 025081 159 LHDTSILYNLAQEHGDHINLHDWY 182 (258)
Q Consensus 159 ~Pd~silYkLY~EaG~lINlyDw~ 182 (258)
-|+=-.+|.+|+|+|.-|.+-|-=
T Consensus 6 sp~rdkA~e~y~~~~g~i~lkdIA 29 (60)
T PF10668_consen 6 SPNRDKAFEIYKESNGKIKLKDIA 29 (60)
T ss_pred CcCHHHHHHHHHHhCCCccHHHHH
Confidence 478889999999999889988753
Done!