Query psy9254
Match_columns 167
No_of_seqs 118 out of 166
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 22:45:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4093|consensus 100.0 5.7E-80 1.2E-84 486.6 11.5 144 17-160 1-144 (144)
2 PF04669 Polysacc_synt_4: Poly 100.0 2.2E-36 4.7E-41 249.6 11.5 124 33-157 1-189 (190)
3 PF06881 Elongin_A: RNA polyme 63.6 7.6 0.00016 29.0 2.8 52 51-109 15-75 (109)
4 KOG2297|consensus 52.1 7.7 0.00017 36.1 1.3 55 34-88 310-375 (412)
5 KOG0568|consensus 39.2 19 0.00041 32.4 1.7 28 89-116 287-321 (342)
6 PF15436 PGBA_N: Plasminogen-b 38.5 29 0.00062 30.0 2.6 46 59-107 95-147 (218)
7 PF02845 CUE: CUE domain; Int 37.6 19 0.00041 22.5 1.1 18 68-85 3-20 (42)
8 smart00546 CUE Domain that may 35.3 24 0.00051 22.0 1.3 19 67-85 3-21 (43)
9 smart00339 FH FORKHEAD. FORKHE 34.2 61 0.0013 23.8 3.5 35 45-83 7-41 (89)
10 PF06854 Phage_Gp15: Bacteriop 33.7 24 0.00052 29.2 1.4 53 61-122 106-158 (183)
11 PF09949 DUF2183: Uncharacteri 31.3 37 0.00081 25.5 2.0 31 49-79 56-90 (100)
12 PRK14083 HSP90 family protein; 30.6 60 0.0013 31.5 3.7 64 51-114 405-475 (601)
13 cd00059 FH Forkhead (FH), also 30.5 86 0.0019 22.6 3.7 29 51-83 13-41 (78)
14 PF05676 NDUF_B7: NADH-ubiquin 29.5 33 0.00072 24.4 1.4 24 83-106 2-25 (66)
15 PF14563 DUF4444: Domain of un 25.8 36 0.00079 22.7 1.0 13 112-124 18-30 (42)
16 KOG2387|consensus 25.7 37 0.0008 33.0 1.4 30 134-163 398-427 (585)
17 PF12872 OST-HTH: OST-HTH/LOTU 25.6 54 0.0012 21.8 1.8 47 50-109 12-60 (74)
18 KOG1534|consensus 24.5 90 0.002 27.9 3.4 67 61-128 170-238 (273)
19 PF11880 DUF3400: Domain of un 24.0 24 0.00051 23.9 -0.2 18 136-153 9-26 (45)
20 COG2254 Predicted HD superfami 23.9 57 0.0012 28.3 2.1 42 37-80 106-148 (230)
21 PF08073 CHDNT: CHDNT (NUC034) 23.8 46 0.001 23.1 1.2 10 96-105 44-53 (55)
22 PF00250 Fork_head: Fork head 23.6 1.1E+02 0.0024 22.6 3.3 26 52-81 14-39 (96)
23 COG0621 MiaB 2-methylthioadeni 22.3 1.1E+02 0.0025 28.7 3.9 63 55-117 224-300 (437)
24 PF07181 VirC2: VirC2 protein; 22.2 41 0.0009 28.9 0.9 57 99-155 116-177 (202)
25 PF11467 LEDGF: Lens epitheliu 20.9 48 0.001 25.4 0.9 30 66-107 68-98 (106)
26 PRK06186 hypothetical protein; 20.6 61 0.0013 27.9 1.6 26 135-160 89-114 (229)
27 PF13174 TPR_6: Tetratricopept 20.2 86 0.0019 16.9 1.7 12 68-79 21-32 (33)
No 1
>KOG4093|consensus
Probab=100.00 E-value=5.7e-80 Score=486.62 Aligned_cols=144 Identities=55% Similarity=0.945 Sum_probs=141.1
Q ss_pred hccCCCCcccCCCcHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccCcchHHHHHHHHhhCCCCCccccChhhhcCcccc
Q psy9254 17 ASVLSRPAEEYVNDPSVEAMWVSKAVDHAEVYFNILCSVDPKILRLTAHDDEILKSFRADFPDLKVDVLNEEEMKSPEGK 96 (167)
Q Consensus 17 ~~~~~~~ae~~~N~~~iE~~wAvkA~ehAe~y~~LL~sv~ps~LrLTk~DDeIy~~Fr~~FPe~~v~~i~E~~lKs~~~K 96 (167)
|+.+++|||+|+||++||+||||||+||||||||||+||+||.|||||+||+||+.||+.||+++|..+++++|||..+|
T Consensus 1 a~~~~~~Ae~~~Nd~~IEm~wAvkA~e~aevy~~Li~sv~~s~LkLtk~dD~Iy~~fr~~Fp~l~v~~~t~~elKs~~aK 80 (144)
T KOG4093|consen 1 AMTLSGDAEKYGNDEDIEMAWAVKAVEQAEVYWNLITSVDGSVLKLTKYDDEIYEAFRSSFPELKVEEVTEDELKSAGAK 80 (144)
T ss_pred CCccccCHhhcCChHHHHHHHHHHHHHHHHHHHHHHHccCcceeecccchHHHHHHHHHhcccccccccCHHHHhccchH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccccCccceeeeccCCCCCCCCCceehhhHHHHHHHHHhccCCCcHHHHhhc
Q psy9254 97 AKWREFCEKFKDMIEDYNFGTLLRLDAKGEYSEANTMLSTRIQFYAIELARNKEGLNDSIRDNF 160 (167)
Q Consensus 97 ekWR~F~~~fe~~VeDyNfGTLLR~d~~~eY~e~NTifv~RiQFyAIEIARNReGlNd~~~~~~ 160 (167)
++||+||++|+++|+|||||||||+||+++|+|+|||||||||||||||||||+|||||+++++
T Consensus 81 e~WR~F~~~f~~kvdDyn~GTLlR~daS~ey~~e~TifvpRiqflAiEiARNreGlNd~~~~~~ 144 (144)
T KOG4093|consen 81 EKWRPFCEKFEKKVDDYNFGTLLRIDASKEYSQETTIFVPRIQFLAIEIARNREGLNDWIKEAY 144 (144)
T ss_pred HHHHHHHHHHHhhhcccccceeeeeccccccCCCceEEEeehhhHHHHHHhhhccchhhhhhcC
Confidence 9999999999999999999999999999999999999999999999999999999999998763
No 2
>PF04669 Polysacc_synt_4: Polysaccharide biosynthesis; InterPro: IPR021148 This is a eukaryotic family of uncharacterised proteins. ; PDB: 2JYN_A.
Probab=100.00 E-value=2.2e-36 Score=249.63 Aligned_cols=124 Identities=35% Similarity=0.608 Sum_probs=108.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc-CCCccccCcchHH-----------HHHHHHhhCCCCC-------ccccChhhhcCc
Q psy9254 33 VEAMWVSKAVDHAEVYFNILCSV-DPKILRLTAHDDE-----------ILKSFRADFPDLK-------VDVLNEEEMKSP 93 (167)
Q Consensus 33 iE~~wAvkA~ehAe~y~~LL~sv-~ps~LrLTk~DDe-----------Iy~~Fr~~FPe~~-------v~~i~E~~lKs~ 93 (167)
||++||++|++|+++|||||..+ +|+.|+||++|+. ||++|++.||+++ +..+++++||+.
T Consensus 1 ~E~~~a~~~l~~~~p~cNlLvfgl~~~sl~wt~ln~~GrTvFlee~~~~~~~~~~~fP~l~~~~v~y~t~~~~a~~Ll~~ 80 (190)
T PF04669_consen 1 IEIAWAAKVLQHREPYCNLLVFGLGPDSLLWTSLNDGGRTVFLEEDPAWYSSFRKRFPDLEAYHVRYRTKVIDADELLSK 80 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHS--TTS--SSTTHHH-----------HHHHHHHH-TTT----SHHHHHB--STTTSSH
T ss_pred CcHHHHHHHHHHhCCCceEEEEeCCCccccchhcCcCcccchhhHHHHHHHHHHHHCcCCcccCcccccccCCHHHHhCc
Confidence 79999999999999999999999 9999999999999 9999999999999 679999999999
Q ss_pred c---------------------------ccHHH-HHHHHHhhccccc--------CccceeeeccCCCCCCCCCceehhh
Q psy9254 94 E---------------------------GKAKW-REFCEKFKDMIED--------YNFGTLLRLDAKGEYSEANTMLSTR 137 (167)
Q Consensus 94 ~---------------------------~KekW-R~F~~~fe~~VeD--------yNfGTLLR~d~~~eY~e~NTifv~R 137 (167)
. .|++| +.||+.|++.++| ||+|||+|.+++++|+ +|+|||+|
T Consensus 81 ~~~~~C~~~~~~~~s~C~lal~~LP~~vy~~~WDvi~vd~p~g~~~daPGRM~aIytag~LaR~~~~~~~t-~t~VfVhd 159 (190)
T PF04669_consen 81 ARSPECRPVQNLRFSECKLALNDLPNEVYKEKWDVIFVDAPRGYVPDAPGRMAAIYTAGVLARARASGGYT-ETDVFVHD 159 (190)
T ss_dssp H---------------------------HHHHH-HHHHHHHTTT-S---------TTS-EEEESBTTS-S--TTEEEE-H
T ss_pred cccccccccccccccccccccccccchhhhhhHHHHHHHcCCCCCCccchhhhhhccHHHHhhccCCCCCC-CCEEEEEc
Confidence 9 99999 9999999999999 9999999999999999 99999999
Q ss_pred H----------HHHHHHHHhccCCCcHHHH
Q psy9254 138 I----------QFYAIELARNKEGLNDSIR 157 (167)
Q Consensus 138 i----------QFyAIEIARNReGlNd~~~ 157 (167)
| ||||+||+||++|+|++.+
T Consensus 160 v~R~vE~~~s~eFLc~e~l~~~~G~~~l~h 189 (190)
T PF04669_consen 160 VDRPVEKWFSEEFLCIEILRNREGRNDLWH 189 (190)
T ss_dssp H----------HHHHHHHHHHHTTTTGGG-
T ss_pred ccccccchhHHHHHHHHHHHhCCCchhhcc
Confidence 9 9999999999999999865
No 3
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=63.64 E-value=7.6 Score=28.96 Aligned_cols=52 Identities=37% Similarity=0.687 Sum_probs=32.4
Q ss_pred HHhhcCCCccc--------cCcchHHHHHHH-HhhCCCCCccccChhhhcCccccHHHHHHHHHhhcc
Q psy9254 51 ILCSVDPKILR--------LTAHDDEILKSF-RADFPDLKVDVLNEEEMKSPEGKAKWREFCEKFKDM 109 (167)
Q Consensus 51 LL~sv~ps~Lr--------LTk~DDeIy~~F-r~~FPe~~v~~i~E~~lKs~~~KekWR~F~~~fe~~ 109 (167)
+|..|+|.+|+ |...+|+|+..| .++||+ .+.. .-+.....||+.-.+|++.
T Consensus 15 iL~~~~~~QL~~iE~~np~l~~~tdeLW~~~i~rdFp~-~~~~------~~~~~~~~Wr~~Y~~~~~e 75 (109)
T PF06881_consen 15 ILEKCSPEQLRRIEDNNPHLIEDTDELWKKLIKRDFPE-ESKR------QKPKEPESWRELYEKLKKE 75 (109)
T ss_pred HHccCCHHHHHHHHHhCCCcchhhHHHHHHHHHhHCcC-hhhc------ccccccchHHHHHHHHHHH
Confidence 45555555443 666789998765 679998 2111 1122234899998888765
No 4
>KOG2297|consensus
Probab=52.08 E-value=7.7 Score=36.07 Aligned_cols=55 Identities=25% Similarity=0.375 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhh---cCCCcccc-CcchHHHHH--HHHhhCCCCC-----ccccChh
Q psy9254 34 EAMWVSKAVDHAEVYFNILCS---VDPKILRL-TAHDDEILK--SFRADFPDLK-----VDVLNEE 88 (167)
Q Consensus 34 E~~wAvkA~ehAe~y~~LL~s---v~ps~LrL-Tk~DDeIy~--~Fr~~FPe~~-----v~~i~E~ 88 (167)
|.+-|..|+.|-.+|--||.. .+-|.|-| -|+|..-|+ +|++.||++= .++++|+
T Consensus 310 eelva~qalrhlK~yaPLL~af~s~g~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe 375 (412)
T KOG2297|consen 310 EELVAEQALRHLKQYAPLLAAFCSQGQSELELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEE 375 (412)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHhcCChHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhH
Confidence 667889999999999888755 56666644 388988887 7999999973 3577777
No 5
>KOG0568|consensus
Probab=39.19 E-value=19 Score=32.44 Aligned_cols=28 Identities=39% Similarity=1.025 Sum_probs=22.6
Q ss_pred hhcCccccHHHHHHHHHhh-------cccccCccc
Q psy9254 89 EMKSPEGKAKWREFCEKFK-------DMIEDYNFG 116 (167)
Q Consensus 89 ~lKs~~~KekWR~F~~~fe-------~~VeDyNfG 116 (167)
-|.-+..|..|.-||+.|. +.|+|||+-
T Consensus 287 pl~rp~d~~~w~~~~~~~qddikklnk~iddfn~~ 321 (342)
T KOG0568|consen 287 PLQRPDDKAAWKHFCENFQDDIKKLNKLIDDFNCI 321 (342)
T ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHHhhhcccc
Confidence 3555778999999999885 568899976
No 6
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=38.47 E-value=29 Score=29.99 Aligned_cols=46 Identities=17% Similarity=0.583 Sum_probs=32.4
Q ss_pred ccccCcchHHHHHHHHhhCCCCCc-------cccChhhhcCccccHHHHHHHHHhh
Q psy9254 59 ILRLTAHDDEILKSFRADFPDLKV-------DVLNEEEMKSPEGKAKWREFCEKFK 107 (167)
Q Consensus 59 ~LrLTk~DDeIy~~Fr~~FPe~~v-------~~i~E~~lKs~~~KekWR~F~~~fe 107 (167)
.|-++| |.+||+..+..||+..- .-|.+. +....++-.|+||.+|-
T Consensus 95 allIAP-n~e~Y~~i~~~~~~i~fihpDl~aa~L~~~--g~~P~~~dfrkfc~~~s 147 (218)
T PF15436_consen 95 ALLIAP-NQETYEKIKSSYPNINFIHPDLFAAFLSEN--GHDPTREDFRKFCNQYS 147 (218)
T ss_pred eEEEcC-CHHHHHHHHHhCCCceEecHHHHHHHHHhc--CCCCCHHHHHHHHHHhC
Confidence 344444 78999999999998642 234333 34566999999998873
No 7
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=37.62 E-value=19 Score=22.47 Aligned_cols=18 Identities=33% Similarity=0.755 Sum_probs=13.4
Q ss_pred HHHHHHHhhCCCCCcccc
Q psy9254 68 EILKSFRADFPDLKVDVL 85 (167)
Q Consensus 68 eIy~~Fr~~FPe~~v~~i 85 (167)
+..+.+++.||+++...|
T Consensus 3 ~~v~~L~~mFP~~~~~~I 20 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVI 20 (42)
T ss_dssp HHHHHHHHHSSSS-HHHH
T ss_pred HHHHHHHHHCCCCCHHHH
Confidence 445889999999987655
No 8
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=35.34 E-value=24 Score=21.98 Aligned_cols=19 Identities=37% Similarity=0.742 Sum_probs=14.9
Q ss_pred HHHHHHHHhhCCCCCcccc
Q psy9254 67 DEILKSFRADFPDLKVDVL 85 (167)
Q Consensus 67 DeIy~~Fr~~FPe~~v~~i 85 (167)
++-.+.+++.||+++...|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I 21 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVI 21 (43)
T ss_pred HHHHHHHHHHCCCCCHHHH
Confidence 4556789999999987655
No 9
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=34.16 E-value=61 Score=23.75 Aligned_cols=35 Identities=26% Similarity=0.295 Sum_probs=25.9
Q ss_pred HHHHHHHHhhcCCCccccCcchHHHHHHHHhhCCCCCcc
Q psy9254 45 AEVYFNILCSVDPKILRLTAHDDEILKSFRADFPDLKVD 83 (167)
Q Consensus 45 Ae~y~~LL~sv~ps~LrLTk~DDeIy~~Fr~~FPe~~v~ 83 (167)
|......|.+.++..|.| .+||+-+.+.||-+...
T Consensus 7 ~~lI~~ai~~sp~~~ltl----~~Iy~~I~~~~pyy~~~ 41 (89)
T smart00339 7 IALIAMAILSSPDKRLTL----SEIYKWIEDNFPYYREN 41 (89)
T ss_pred HHHHHHHHHhCCCCCeeH----HHHHHHHHHhCchhhcC
Confidence 344444555667888888 58999999999998643
No 10
>PF06854 Phage_Gp15: Bacteriophage Gp15 protein; InterPro: IPR009660 This entry describes Gp15 from Bacteriophage A500 (Listeria phage A500), related proteins in other bacteriophage, and prophage regions of bacterial genomes. The function is unknown.
Probab=33.72 E-value=24 Score=29.16 Aligned_cols=53 Identities=21% Similarity=0.441 Sum_probs=36.3
Q ss_pred ccCcchHHHHHHHHhhCCCCCccccChhhhcCccccHHHHHHHHHhhcccccCccceeeecc
Q psy9254 61 RLTAHDDEILKSFRADFPDLKVDVLNEEEMKSPEGKAKWREFCEKFKDMIEDYNFGTLLRLD 122 (167)
Q Consensus 61 rLTk~DDeIy~~Fr~~FPe~~v~~i~E~~lKs~~~KekWR~F~~~fe~~VeDyNfGTLLR~d 122 (167)
-++.=.+-||.+|++..- +|+ -...++--|.+||.-|.+.-+|--||+.+..+
T Consensus 106 d~~~Da~~IyasF~~~Yg-IdL--------~~~~~~lhW~~F~aL~~~L~~~t~~~~ii~~R 158 (183)
T PF06854_consen 106 DFEQDADYIYASFLQQYG-IDL--------IEEQGYLHWWKFKALFNGLSEDTPFKQIIGIR 158 (183)
T ss_pred cHHHhHHHHHHHHHHHhC-ccH--------HHhcccCcHHHHHHHHhcCCCCCHHHHHHHHh
Confidence 344455779999999873 232 11335788999999999986666666555443
No 11
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=31.32 E-value=37 Score=25.49 Aligned_cols=31 Identities=29% Similarity=0.389 Sum_probs=25.3
Q ss_pred HHHHhhcCCCcccc----CcchHHHHHHHHhhCCC
Q psy9254 49 FNILCSVDPKILRL----TAHDDEILKSFRADFPD 79 (167)
Q Consensus 49 ~~LL~sv~ps~LrL----Tk~DDeIy~~Fr~~FPe 79 (167)
-+|+...|..+.-| +..|-+||.++.++||+
T Consensus 56 ~~i~~~fP~~kfiLIGDsgq~DpeiY~~ia~~~P~ 90 (100)
T PF09949_consen 56 ERILRDFPERKFILIGDSGQHDPEIYAEIARRFPG 90 (100)
T ss_pred HHHHHHCCCCcEEEEeeCCCcCHHHHHHHHHHCCC
Confidence 34677777777666 56899999999999998
No 12
>PRK14083 HSP90 family protein; Provisional
Probab=30.63 E-value=60 Score=31.53 Aligned_cols=64 Identities=20% Similarity=0.355 Sum_probs=48.5
Q ss_pred HHhhcCCCccccC-cchHHHHHHHHhhCCCCCccccChhhhc------CccccHHHHHHHHHhhcccccCc
Q psy9254 51 ILCSVDPKILRLT-AHDDEILKSFRADFPDLKVDVLNEEEMK------SPEGKAKWREFCEKFKDMIEDYN 114 (167)
Q Consensus 51 LL~sv~ps~LrLT-k~DDeIy~~Fr~~FPe~~v~~i~E~~lK------s~~~KekWR~F~~~fe~~VeDyN 114 (167)
+..+-+=.-|-+| ++|..+..++++.||+..+..|+.+++. +....+.+..+++.+++.+.|.-
T Consensus 405 ~~~~kg~eVl~~~~~iDe~~l~~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~ 475 (601)
T PRK14083 405 IARAQGMGVINGGYTYDSELLERLPRLRPGLTVERLDPAELTDRLEPLTPEEELALRPFLAEAREVLAPFG 475 (601)
T ss_pred HHHHCCCeEEEeCCccHHHHHHHHHhhCCCCcEEEechhhhhhhccccchhhHHHHHHHHHHHHHHhCccc
Confidence 3444444456677 8999999999999999998777765442 23457789999999999998864
No 13
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=30.53 E-value=86 Score=22.56 Aligned_cols=29 Identities=31% Similarity=0.371 Sum_probs=23.1
Q ss_pred HHhhcCCCccccCcchHHHHHHHHhhCCCCCcc
Q psy9254 51 ILCSVDPKILRLTAHDDEILKSFRADFPDLKVD 83 (167)
Q Consensus 51 LL~sv~ps~LrLTk~DDeIy~~Fr~~FPe~~v~ 83 (167)
.|.+.++..|.| .|||+-+++.||-+...
T Consensus 13 Ai~~sp~~~lTL----~eIy~~I~~~~pyyr~~ 41 (78)
T cd00059 13 AIQSSPEKRLTL----SEIYKWISDNFPYFRDA 41 (78)
T ss_pred HHHhCCCCCeeH----HHHHHHHHHhCCccccC
Confidence 355567788888 59999999999998643
No 14
>PF05676 NDUF_B7: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7); InterPro: IPR008698 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of Homo sapiens mitochondrial encephalomyopathies [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=29.53 E-value=33 Score=24.42 Aligned_cols=24 Identities=21% Similarity=0.581 Sum_probs=21.2
Q ss_pred cccChhhhcCccccHHHHHHHHHh
Q psy9254 83 DVLNEEEMKSPEGKAKWREFCEKF 106 (167)
Q Consensus 83 ~~i~E~~lKs~~~KekWR~F~~~f 106 (167)
.++|++||.+..-...||++|..+
T Consensus 2 m~aTqeEM~~a~lPl~~RDyCAh~ 25 (66)
T PF05676_consen 2 MIATQEEMEDAKLPLQYRDYCAHL 25 (66)
T ss_pred CCcCHHHHHHcCCChhhhhhHHHH
Confidence 367999999999999999999765
No 15
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=25.83 E-value=36 Score=22.67 Aligned_cols=13 Identities=54% Similarity=0.779 Sum_probs=7.0
Q ss_pred cCccceeeeccCC
Q psy9254 112 DYNFGTLLRLDAK 124 (167)
Q Consensus 112 DyNfGTLLR~d~~ 124 (167)
|=|||-|||.+.+
T Consensus 18 DE~FGmLLr~~~~ 30 (42)
T PF14563_consen 18 DEDFGMLLRDDDT 30 (42)
T ss_dssp -TT--EEEE-SS-
T ss_pred ccccceEEEeCCc
Confidence 6689999998864
No 16
>KOG2387|consensus
Probab=25.71 E-value=37 Score=33.02 Aligned_cols=30 Identities=37% Similarity=0.579 Sum_probs=25.2
Q ss_pred ehhhHHHHHHHHHhccCCCcHHHHhhcCCc
Q psy9254 134 LSTRIQFYAIELARNKEGLNDSIRDNFKPS 163 (167)
Q Consensus 134 fv~RiQFyAIEIARNReGlNd~~~~~~~~~ 163 (167)
+|-=||--+||.|||..|+-|+.-..+.++
T Consensus 398 iCLGmQ~AvIEfaRnvLg~~dAnStEF~p~ 427 (585)
T KOG2387|consen 398 ICLGMQLAVIEFARNVLGLKDANSTEFDPE 427 (585)
T ss_pred eehhhhHHHHHHHHHhhCCCCCCccccCCC
Confidence 467799999999999999999877666554
No 17
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=25.62 E-value=54 Score=21.80 Aligned_cols=47 Identities=19% Similarity=0.322 Sum_probs=27.8
Q ss_pred HHHhhcCCC--ccccCcchHHHHHHHHhhCCCCCccccChhhhcCccccHHHHHHHHHhhcc
Q psy9254 50 NILCSVDPK--ILRLTAHDDEILKSFRADFPDLKVDVLNEEEMKSPEGKAKWREFCEKFKDM 109 (167)
Q Consensus 50 ~LL~sv~ps--~LrLTk~DDeIy~~Fr~~FPe~~v~~i~E~~lKs~~~KekWR~F~~~fe~~ 109 (167)
.+|.+..+. .+.|+.+ -..+++.||+|++.. =|-.+|++|++.+.+.
T Consensus 12 ~ll~~~~~~~g~v~ls~l----~~~~~~~~~~f~~~~---------yG~~~l~~ll~~~~~~ 60 (74)
T PF12872_consen 12 ELLESQKGEDGWVSLSQL----GQEYKKKYPDFDPRD---------YGFSSLSELLESLPDV 60 (74)
T ss_dssp HHHHHTCTTTSSEEHHHH----HHHHHHHHTT--TCC---------TTSSSHHHHHHT-TTT
T ss_pred HHHHhCcCCCceEEHHHH----HHHHHHHCCCCCccc---------cCCCcHHHHHHhCCCe
Confidence 355455443 6888654 455556667788773 3677888888776654
No 18
>KOG1534|consensus
Probab=24.53 E-value=90 Score=27.91 Aligned_cols=67 Identities=21% Similarity=0.271 Sum_probs=44.9
Q ss_pred ccCcch--HHHHHHHHhhCCCCCccccChhhhcCccccHHHHHHHHHhhcccccCccceeeeccCCCCCC
Q psy9254 61 RLTAHD--DEILKSFRADFPDLKVDVLNEEEMKSPEGKAKWREFCEKFKDMIEDYNFGTLLRLDAKGEYS 128 (167)
Q Consensus 61 rLTk~D--DeIy~~Fr~~FPe~~v~~i~E~~lKs~~~KekWR~F~~~fe~~VeDyNfGTLLR~d~~~eY~ 128 (167)
-|||+| ..+-+.-.+.|=+-+...+.+++= +..+.+|.++.+..--..|+|||.-.++-+|++.+=|
T Consensus 170 vlsKMDLlk~~~k~~l~~Fl~~d~~~l~~~~~-~~~~s~Kf~~L~~~i~~~v~d~~Mv~FlPl~~~~eeS 238 (273)
T KOG1534|consen 170 VLSKMDLLKDKNKKELERFLNPDEYLLLEDSE-INLRSPKFKKLTKCIAQLVDDYSMVNFLPLDSSDEES 238 (273)
T ss_pred hhhHHHHhhhhhHHHHHHhcCCchhhhhcccc-cccccHHHHHHHHHHHHHhccccceeeeecCCCCHHH
Confidence 345544 124445556665555444444332 2334589999999999999999999999999987644
No 19
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=24.01 E-value=24 Score=23.86 Aligned_cols=18 Identities=28% Similarity=0.449 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHhccCCCc
Q psy9254 136 TRIQFYAIELARNKEGLN 153 (167)
Q Consensus 136 ~RiQFyAIEIARNReGlN 153 (167)
+-.-|..+|+||...|=|
T Consensus 9 ~~aDYIVVEmA~~lLGe~ 26 (45)
T PF11880_consen 9 LEADYIVVEMARHLLGEN 26 (45)
T ss_pred CccceehHHHHHHHhhhh
Confidence 445577899999999975
No 20
>COG2254 Predicted HD superfamily hydrolase, possibly a nuclease [DNA replication, recombination, and repair]
Probab=23.91 E-value=57 Score=28.34 Aligned_cols=42 Identities=17% Similarity=0.048 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCccccCc-chHHHHHHHHhhCCCC
Q psy9254 37 WVSKAVDHAEVYFNILCSVDPKILRLTA-HDDEILKSFRADFPDL 80 (167)
Q Consensus 37 wAvkA~ehAe~y~~LL~sv~ps~LrLTk-~DDeIy~~Fr~~FPe~ 80 (167)
.|...+.|++++++-..+ |+.++|+. +.+.+|+.+.+.||+.
T Consensus 106 Val~~~~H~~i~~~~~~~--~~~~~l~~~~~~~~~~~~~e~~~~~ 148 (230)
T COG2254 106 VALALMLHHEIRMGAPRS--ISNLKLNLEVVEVKYDEIDEDKEKL 148 (230)
T ss_pred HHHHHHHHHHHHhhcccc--chhhccchhhhhhHHHHhhhhhhhh
Confidence 456667888877776655 55888884 7788888888888884
No 21
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.82 E-value=46 Score=23.14 Aligned_cols=10 Identities=70% Similarity=1.278 Sum_probs=7.8
Q ss_pred cHHHHHHHHH
Q psy9254 96 KAKWREFCEK 105 (167)
Q Consensus 96 KekWR~F~~~ 105 (167)
-.|||+|++.
T Consensus 44 ~AKwrEF~~~ 53 (55)
T PF08073_consen 44 QAKWREFQEH 53 (55)
T ss_pred HHHHHHHHhc
Confidence 5789999863
No 22
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=23.59 E-value=1.1e+02 Score=22.63 Aligned_cols=26 Identities=31% Similarity=0.434 Sum_probs=20.9
Q ss_pred HhhcCCCccccCcchHHHHHHHHhhCCCCC
Q psy9254 52 LCSVDPKILRLTAHDDEILKSFRADFPDLK 81 (167)
Q Consensus 52 L~sv~ps~LrLTk~DDeIy~~Fr~~FPe~~ 81 (167)
|.+.+...|.| .|||+-+.+.||-+.
T Consensus 14 i~~sp~~~Ltl----~eIy~~i~~~~pyyr 39 (96)
T PF00250_consen 14 ILSSPDKRLTL----SEIYEWIEENFPYYR 39 (96)
T ss_dssp HHTSTTSEBEH----HHHHHHHHHHCGHHH
T ss_pred HHhCCCCCccH----HHHHHHHHHhhcccc
Confidence 44466778888 699999999999874
No 23
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.34 E-value=1.1e+02 Score=28.69 Aligned_cols=63 Identities=19% Similarity=0.323 Sum_probs=48.6
Q ss_pred cCC-CccccC-----cchHHHHHHHHhh---CCCCC--ccccChh---hhcCccccHHHHHHHHHhhcccccCccce
Q psy9254 55 VDP-KILRLT-----AHDDEILKSFRAD---FPDLK--VDVLNEE---EMKSPEGKAKWREFCEKFKDMIEDYNFGT 117 (167)
Q Consensus 55 v~p-s~LrLT-----k~DDeIy~~Fr~~---FPe~~--v~~i~E~---~lKs~~~KekWR~F~~~fe~~VeDyNfGT 117 (167)
+++ ..+|+| +++|++-+.+++. .|-|+ |+.-+.. .|+-+-..+..+.++++++..++|..++|
T Consensus 224 I~G~~riR~~~~~P~~~~d~lI~~~~~~~kv~~~lHlPvQsGsd~ILk~M~R~yt~e~~~~~i~k~R~~~Pd~~i~t 300 (437)
T COG0621 224 IPGIERIRFGSSHPLEFTDDLIEAIAETPKVCPHLHLPVQSGSDRILKRMKRGYTVEEYLEIIEKLRAARPDIAIST 300 (437)
T ss_pred CCCceEEEEecCCchhcCHHHHHHHhcCCcccccccCccccCCHHHHHHhCCCcCHHHHHHHHHHHHHhCCCceEec
Confidence 553 566665 4788888888875 66665 5666665 56677778999999999999999999886
No 24
>PF07181 VirC2: VirC2 protein; InterPro: IPR009841 This family consists of several VirC2 proteins which seem to be found exclusively in Agrobacterium species and Rhizobium etli. VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear [, ].; PDB: 2RH3_A.
Probab=22.15 E-value=41 Score=28.87 Aligned_cols=57 Identities=25% Similarity=0.333 Sum_probs=32.6
Q ss_pred HHHHHHHhhcccccCccceeeeccCCCCCCCCCceehhhHHH--HHHHHHhc---cCCCcHH
Q psy9254 99 WREFCEKFKDMIEDYNFGTLLRLDAKGEYSEANTMLSTRIQF--YAIELARN---KEGLNDS 155 (167)
Q Consensus 99 WR~F~~~fe~~VeDyNfGTLLR~d~~~eY~e~NTifv~RiQF--yAIEIARN---ReGlNd~ 155 (167)
-|.=+..||.++.|-+|-++...=+-..-.+.-+|+-|+=-| -++||||| +.|||..
T Consensus 116 LrrAL~dfE~mL~dGsF~~~pksYpi~~~~~k~~IV~TsRmfpv~lle~Ar~hFDplgleta 177 (202)
T PF07181_consen 116 LRRALDDFEAMLADGSFSKAPKSYPIPQTVEKSIIVQTSRMFPVSLLEVARNHFDPLGLETA 177 (202)
T ss_dssp HHHHHHHHHHHHHTSGGGGS--------ST-----EEEEEE--HHHHHHHHHHHSTTS-S-H
T ss_pred HHHHHHHHHHHHcCCccccccccCCCccccCCceEEEecccCcHHHHHHHHHhcCchhhHHH
Confidence 466678899999999999887665555555555887776433 68999998 6788764
No 25
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=20.90 E-value=48 Score=25.44 Aligned_cols=30 Identities=33% Similarity=0.826 Sum_probs=11.7
Q ss_pred hHHHHHHHHhhC-CCCCccccChhhhcCccccHHHHHHHHHhh
Q psy9254 66 DDEILKSFRADF-PDLKVDVLNEEEMKSPEGKAKWREFCEKFK 107 (167)
Q Consensus 66 DDeIy~~Fr~~F-Pe~~v~~i~E~~lKs~~~KekWR~F~~~fe 107 (167)
=.+||..|+..| |+-+.. ..-|..||++-+
T Consensus 68 A~~lYnkfK~~f~~~~e~~------------~~~~~~~~~~~~ 98 (106)
T PF11467_consen 68 ATELYNKFKSLFLPEPESE------------QNFWEEFCEEVK 98 (106)
T ss_dssp HHHHHHHHHHHHH--S-SH------------------------
T ss_pred HHHHHHHHHHHhCCCchHH------------HHHHHHHHHHHH
Confidence 468999999999 774432 344777776543
No 26
>PRK06186 hypothetical protein; Validated
Probab=20.59 E-value=61 Score=27.88 Aligned_cols=26 Identities=27% Similarity=0.266 Sum_probs=21.0
Q ss_pred hhhHHHHHHHHHhccCCCcHHHHhhc
Q psy9254 135 STRIQFYAIELARNKEGLNDSIRDNF 160 (167)
Q Consensus 135 v~RiQFyAIEIARNReGlNd~~~~~~ 160 (167)
|-=||-..||.|||..|+-|......
T Consensus 89 ClGmQ~avIe~arnv~g~~dA~s~E~ 114 (229)
T PRK06186 89 CGGFQHALLEYARNVLGWADAAHAET 114 (229)
T ss_pred chhhHHHHHHHHhhhcCCcCCCcCCC
Confidence 66799999999999999988654433
No 27
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=20.24 E-value=86 Score=16.92 Aligned_cols=12 Identities=25% Similarity=0.625 Sum_probs=9.4
Q ss_pred HHHHHHHhhCCC
Q psy9254 68 EILKSFRADFPD 79 (167)
Q Consensus 68 eIy~~Fr~~FPe 79 (167)
++|+.|.+.||+
T Consensus 21 ~~~~~~~~~~P~ 32 (33)
T PF13174_consen 21 EYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHSTT
T ss_pred HHHHHHHHHCcC
Confidence 578888888886
Done!