Query psy12411
Match_columns 161
No_of_seqs 182 out of 416
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 18:34:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0334|consensus 99.7 2.2E-17 4.7E-22 158.7 6.9 146 1-159 186-349 (997)
2 KOG0339|consensus 99.7 2E-17 4.4E-22 151.1 1.8 133 20-161 68-210 (731)
3 PTZ00110 helicase; Provisional 97.8 1.4E-05 3.1E-10 73.5 3.6 43 119-161 74-116 (545)
4 KOG0336|consensus 97.1 0.00029 6.4E-09 64.5 2.3 36 124-161 164-199 (629)
5 PLN00206 DEAD-box ATP-dependen 94.9 0.024 5.2E-07 51.9 3.3 40 122-161 67-108 (518)
6 PF10453 NUFIP1: Nuclear fragi 29.1 45 0.00097 22.2 1.9 25 136-160 6-30 (56)
7 PF08621 RPAP1_N: RPAP1-like, 26.3 55 0.0012 21.2 1.9 15 144-158 11-25 (49)
8 PF00140 Sigma70_r1_2: Sigma-7 25.4 37 0.00079 20.4 0.9 12 30-41 2-13 (37)
9 PF08164 TRAUB: Apoptosis-anta 21.4 1E+02 0.0022 21.9 2.7 30 128-158 49-80 (83)
10 PF13865 FoP_duplication: C-te 19.7 74 0.0016 22.0 1.6 11 31-41 48-58 (74)
No 1
>KOG0334|consensus
Probab=99.69 E-value=2.2e-17 Score=158.68 Aligned_cols=146 Identities=37% Similarity=0.548 Sum_probs=101.5
Q ss_pred CcccccCCCCcccc-c--c-----------ccccCCCCCcccCChHHHHHhhhHHHhhhhCCCCCCCCCCCCCCCCCCCC
Q psy12411 1 MKKWNLEDDSDEDE-N--D-----------NKDENGKTAEEDIDPLDAFMQGVHEEMRKVNKPAVPTTADVKPADSGSKP 66 (161)
Q Consensus 1 ~k~w~Ledd~dde~-~--~-----------~~~~~~~~eeeEiDPLDAFM~~v~~ev~k~~~~~~~~~~~~~~~~~g~~~ 66 (161)
+|+|+|++++++++ + + ...+..-..++++|||||||..+..++..-+....... .
T Consensus 186 ~k~~~l~~~~d~~~~~~~~~~~s~q~~~~~~~~p~~~~~dd~~d~ld~~m~~~~~~~~~~~~~~~~~~----~------- 254 (997)
T KOG0334|consen 186 KKLWELEDEDDDDSANPAELGWSEQDVPELMKAPNLMLVDDEEDPLDAFMEQMVGKVLAKFSNSSHSK----A------- 254 (997)
T ss_pred ccceEecCCCCccccCccccchhhccchhhccCccccccccccchHHHHHHHHHHHHHHHhcCCCccc----c-------
Confidence 58999999988665 1 0 11112224578899999999998755433222111100 0
Q ss_pred CcceEEeccchhhhh-hhhcccccc---ccCCCCCCchhhhhhHHHHHHhHHHhhcccCCCCCCCCCCcCcccccCCCCC
Q psy12411 67 AGVVIVTGVVKKSVE-KAKGELMEE---NQDGLEYSSEEEQEDLTSTAANLASKQKKELSKVDHSTIEYLPFRKDFYVEV 142 (161)
Q Consensus 67 ~~~~~~~~~~~~~~~-~~~ge~~e~---d~d~~e~~~eeed~d~~~~~~~~~~k~kk~L~~vdhs~i~y~pF~KnFY~E~ 142 (161)
.++..+....+... +..|.++++ +.|.+++.++.+ ++...++++++.++++.|..++||++.|.|||||||+++
T Consensus 255 -~~~~~s~~~~~~~~~~~~g~v~e~~~~~~D~~e~~~~~~-~d~~~~~~~~~~~~~~~~~~~~~S~~~~epFRknfy~e~ 332 (997)
T KOG0334|consen 255 -QVVEVSKDARKGLNPKLSGFVIEPGLVNGDNEEVELNGS-FDNRNAAKNMNLKAKKNLIQVDHSKISYEPFRKNFYIEV 332 (997)
T ss_pred -cccccchhhhccCCccccceeccCCcCCcchhhhhhccc-cchHHHHHHhccccccceeecccccccchhhhhcccccc
Confidence 01111122222222 367899987 566677765544 778888888888888889999999999999999999999
Q ss_pred hhhhcCCHHHHHHHHhh
Q psy12411 143 PEIARMTPEEVEKYKEV 159 (161)
Q Consensus 143 ~ei~~ms~eEV~~~R~~ 159 (161)
++|+.||.+||..||..
T Consensus 333 ~di~~ms~~eV~~yr~~ 349 (997)
T KOG0334|consen 333 RDIKRMSAAEVDEYRCE 349 (997)
T ss_pred hhHHHHHHHHHHHhhcC
Confidence 99999999999999963
No 2
>KOG0339|consensus
Probab=99.66 E-value=2e-17 Score=151.15 Aligned_cols=133 Identities=30% Similarity=0.472 Sum_probs=91.1
Q ss_pred cCCCCCcccCChHHHHHhhhHHHhhhhCCCCCCCCCCCCCCCCCCCCCcceEEeccchhhhhhhhccccccccCC-----
Q psy12411 20 ENGKTAEEDIDPLDAFMQGVHEEMRKVNKPAVPTTADVKPADSGSKPAGVVIVTGVVKKSVEKAKGELMEENQDG----- 94 (161)
Q Consensus 20 ~~~~~eeeEiDPLDAFM~~v~~ev~k~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ge~~e~d~d~----- 94 (161)
.....+.+|+|||||||+.+.+++..............+...+. ..+ ..++.+++....++++.++|.++.-.
T Consensus 68 ~~a~~~~de~d~ldafMA~~~d~~~sd~~~~e~kk~eRkn~dd~-~p~-~~vr~dI~~e~aae~~~kym~e~k~~~~~~e 145 (731)
T KOG0339|consen 68 AAAGGEVDEIDPLDAFMAKIEDQAQSDKKPLEQKKKERKNDDDD-DPT-ATVRADIDEEDAAEALFKYMSENKRAGAAKE 145 (731)
T ss_pred hhccCCCCCCCCcchhhhhhhhhhhccCCccchHHHhhhccCCC-ccc-hhhhcchhhHHhHHHHHHHhhhcccchhhhh
Confidence 33456779999999999999999876443332111101000000 011 23456777777788888888765533
Q ss_pred -----CCCCchhhhhhHHHHHHhHHHhhcccCCCCCCCCCCcCcccccCCCCChhhhcCCHHHHHHHHhhcC
Q psy12411 95 -----LEYSSEEEQEDLTSTAANLASKQKKELSKVDHSTIEYLPFRKDFYVEVPEIARMTPEEVEKYKEVDN 161 (161)
Q Consensus 95 -----~e~~~eeed~d~~~~~~~~~~k~kk~L~~vdhs~i~y~pF~KnFY~E~~ei~~ms~eEV~~~R~~~~ 161 (161)
++|+++ .+.++. .||..++|++|+|++|+|+||+||||.+|.+|..|+..+|-.||+.-|
T Consensus 146 ~~~~~leydsd------~nPi~~-~kr~idpl~~idhs~i~y~p~~kdfy~e~esI~gl~~~d~~~~r~~Ln 210 (731)
T KOG0339|consen 146 CDDMCLEYDSD------GNPIAP-DKRQIDPLPPIDHSEIDYEPFNKDFYEEHESIEGLTKMDVIDLRLTLN 210 (731)
T ss_pred cccceeecCCC------CCccCc-ccccCCCCCCcchhhccccccccccccChhhhhccccccchhhHhhhc
Confidence 233322 123333 467889999999999999999999999999999999999999998644
No 3
>PTZ00110 helicase; Provisional
Probab=97.82 E-value=1.4e-05 Score=73.52 Aligned_cols=43 Identities=33% Similarity=0.712 Sum_probs=40.0
Q ss_pred ccCCCCCCCCCCcCcccccCCCCChhhhcCCHHHHHHHHhhcC
Q psy12411 119 KELSKVDHSTIEYLPFRKDFYVEVPEIARMTPEEVEKYKEVDN 161 (161)
Q Consensus 119 k~L~~vdhs~i~y~pF~KnFY~E~~ei~~ms~eEV~~~R~~~~ 161 (161)
..|+.++|+.++|+||+||||.+++.++.|+.++|..+|..++
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (545)
T PTZ00110 74 KRLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKE 116 (545)
T ss_pred cccCCCCCccccccchhhhcccCChhhhcCCHHHHHHHHHhcC
Confidence 4689999999999999999999999999999999999998763
No 4
>KOG0336|consensus
Probab=97.08 E-value=0.00029 Score=64.53 Aligned_cols=36 Identities=19% Similarity=0.506 Sum_probs=32.6
Q ss_pred CCCCCCCcCcccccCCCCChhhhcCCHHHHHHHHhhcC
Q psy12411 124 VDHSTIEYLPFRKDFYVEVPEIARMTPEEVEKYKEVDN 161 (161)
Q Consensus 124 vdhs~i~y~pF~KnFY~E~~ei~~ms~eEV~~~R~~~~ 161 (161)
..|. +++|+.||||+|+++.++||+.++..||.+|+
T Consensus 164 ~kW~--~lpPi~knfYke~~e~s~ls~~q~~~~r~en~ 199 (629)
T KOG0336|consen 164 FKWA--KLPPIKKNFYKESNETSNLSKEQLQEWRKENF 199 (629)
T ss_pred cccc--cCCchhhhhhhcCchhccCCHHHHHHHHHcCC
Confidence 3454 79999999999999999999999999999875
No 5
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=94.86 E-value=0.024 Score=51.90 Aligned_cols=40 Identities=15% Similarity=0.166 Sum_probs=34.5
Q ss_pred CCCCCCCCCc-CcccccCCCCChhhhc-CCHHHHHHHHhhcC
Q psy12411 122 SKVDHSTIEY-LPFRKDFYVEVPEIAR-MTPEEVEKYKEVDN 161 (161)
Q Consensus 122 ~~vdhs~i~y-~pF~KnFY~E~~ei~~-ms~eEV~~~R~~~~ 161 (161)
..++|+++.| ++|+|+||+.++.+.. |+..++..||..++
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~ 108 (518)
T PLN00206 67 VAVGAPKPKRLPATDECFYVRDPGSTSGLSSSQAELLRRKLE 108 (518)
T ss_pred CCcCCCchhhcCCcCCcCCccCcchhccCCHHHHHHHHHHCC
Confidence 4688888776 8899999999998865 99999999998754
No 6
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=29.13 E-value=45 Score=22.23 Aligned_cols=25 Identities=40% Similarity=0.530 Sum_probs=18.3
Q ss_pred ccCCCCChhhhcCCHHHHHHHHhhc
Q psy12411 136 KDFYVEVPEIARMTPEEVEKYKEVD 160 (161)
Q Consensus 136 KnFY~E~~ei~~ms~eEV~~~R~~~ 160 (161)
++|+++-..|+--|+++|..||.++
T Consensus 6 ~~~~~~g~~~~L~t~eeI~~W~eER 30 (56)
T PF10453_consen 6 KDFHIPGTSIKLQTPEEIAKWIEER 30 (56)
T ss_pred ccccCCCceeecCCHHHHHHHHHHH
Confidence 4555565666667999999999764
No 7
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=26.29 E-value=55 Score=21.19 Aligned_cols=15 Identities=47% Similarity=0.833 Sum_probs=12.6
Q ss_pred hhhcCCHHHHHHHHh
Q psy12411 144 EIARMTPEEVEKYKE 158 (161)
Q Consensus 144 ei~~ms~eEV~~~R~ 158 (161)
-|++||++||.+-|.
T Consensus 11 rL~~MS~eEI~~er~ 25 (49)
T PF08621_consen 11 RLASMSPEEIEEERE 25 (49)
T ss_pred HHHhCCHHHHHHHHH
Confidence 478999999988775
No 8
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=25.35 E-value=37 Score=20.37 Aligned_cols=12 Identities=17% Similarity=0.509 Sum_probs=10.1
Q ss_pred ChHHHHHhhhHH
Q psy12411 30 DPLDAFMQGVHE 41 (161)
Q Consensus 30 DPLDAFM~~v~~ 41 (161)
|||..||..|..
T Consensus 2 D~l~~Yl~ei~~ 13 (37)
T PF00140_consen 2 DSLRLYLKEIGR 13 (37)
T ss_dssp HHHHHHHHHHHH
T ss_pred cHHHHHHHHHcC
Confidence 799999998854
No 9
>PF08164 TRAUB: Apoptosis-antagonizing transcription factor, C-terminal; InterPro: IPR012617 This C-terminal domain is found in traube proteins [].; GO: 0005634 nucleus
Probab=21.36 E-value=1e+02 Score=21.95 Aligned_cols=30 Identities=13% Similarity=0.315 Sum_probs=24.5
Q ss_pred CCCcCcccc--cCCCCChhhhcCCHHHHHHHHh
Q psy12411 128 TIEYLPFRK--DFYVEVPEIARMTPEEVEKYKE 158 (161)
Q Consensus 128 ~i~y~pF~K--nFY~E~~ei~~ms~eEV~~~R~ 158 (161)
+|.|.+.+| ||..+ +.....+++.+++|-.
T Consensus 49 KlRY~VheKL~NFmaP-~~~~~w~~~~~delf~ 80 (83)
T PF08164_consen 49 KLRYHVHEKLVNFMAP-EDRPTWSDEQIDELFA 80 (83)
T ss_pred eeeeeeHHHHhhhcCC-CCCCCCCHHHHHHHHH
Confidence 789999998 89966 6667888888888754
No 10
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=19.71 E-value=74 Score=21.99 Aligned_cols=11 Identities=36% Similarity=0.604 Sum_probs=7.7
Q ss_pred hHHHHHhhhHH
Q psy12411 31 PLDAFMQGVHE 41 (161)
Q Consensus 31 PLDAFM~~v~~ 41 (161)
-|||||+....
T Consensus 48 ELD~Ym~~~~~ 58 (74)
T PF13865_consen 48 ELDAYMSKTKS 58 (74)
T ss_pred HHHHHHHHHHH
Confidence 59999965433
Done!