Query 041085
Match_columns 299
No_of_seqs 134 out of 195
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 05:38:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041085.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/041085hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3m66_A Mterf3, mterf domain-co 59.9 1.3 4.3E-05 39.6 -1.1 92 83-192 85-179 (270)
2 3m66_A Mterf3, mterf domain-co 54.1 1.4 4.7E-05 39.4 -2.0 92 82-192 49-143 (270)
3 4b8x_A SCO5413, possible MARR- 41.9 62 0.0021 25.5 6.5 66 60-132 40-108 (147)
4 3eco_A MEPR; mutlidrug efflux 39.3 46 0.0016 25.3 5.2 72 58-136 34-108 (139)
5 3bro_A Transcriptional regulat 38.2 57 0.002 24.7 5.5 71 58-135 37-110 (141)
6 2kp6_A Uncharacterized protein 37.1 7.3 0.00025 29.7 0.1 28 73-100 7-35 (82)
7 3jw4_A Transcriptional regulat 35.1 47 0.0016 25.7 4.6 72 58-136 44-118 (148)
8 4fp9_B Mterf domain-containing 31.4 5.6 0.00019 37.4 -1.7 87 83-192 55-144 (335)
9 3fm5_A Transcriptional regulat 29.7 98 0.0033 23.8 5.7 69 59-135 43-114 (150)
10 3rco_A Tudor domain-containing 29.4 52 0.0018 25.2 3.7 43 59-105 17-69 (89)
11 3nqo_A MARR-family transcripti 29.2 58 0.002 26.7 4.5 70 59-135 45-117 (189)
12 3mva_O Transcription terminati 29.1 9.1 0.00031 35.4 -0.7 108 64-192 44-154 (343)
13 4fx0_A Probable transcriptiona 27.8 81 0.0028 24.9 4.9 69 59-135 37-111 (148)
14 4fp9_B Mterf domain-containing 27.5 7.5 0.00026 36.5 -1.6 117 59-192 62-180 (335)
15 2frh_A SARA, staphylococcal ac 27.0 1.3E+02 0.0044 22.9 5.9 74 58-138 40-116 (127)
16 3s93_A Tudor domain-containing 26.9 81 0.0028 24.5 4.6 55 47-105 2-67 (102)
17 3u2r_A Regulatory protein MARR 25.0 1.3E+02 0.0044 23.7 5.7 73 58-137 49-124 (168)
18 3nrv_A Putative transcriptiona 20.5 2.2E+02 0.0074 21.6 6.1 67 60-135 45-114 (148)
No 1
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A
Probab=59.91 E-value=1.3 Score=39.64 Aligned_cols=92 Identities=16% Similarity=0.283 Sum_probs=52.5
Q ss_pred cCCCCCcchhhhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHHHhhchHHHHHHHH---HHhhccCCCcc
Q 041085 83 QLGLPQDLKLSTFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNALQQNQKDILDRLC---KLLMLTRDRML 159 (299)
Q Consensus 83 ~LgLp~~~~~~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v~~~~e~~~v~rL~---KLLMMS~~rrL 159 (299)
.+|++ +..+.+.+.++|.++..+ +. ++.+... ...++..+ .+.+++.-+. .+|.+|.++-
T Consensus 85 ~~Gls-~~~i~~~l~~~P~lL~~s---------~~--~l~~~v~-~L~~~lG~---~~~~i~~ll~~~P~il~~s~e~~- 147 (270)
T 3m66_A 85 SKNFS-KADVAQMVRKAPFLLNFS---------VE--RLDNRLG-FFQKELEL---SVKKTRDLVVRLPRLLTGSLEPV- 147 (270)
T ss_dssp HTTCC-HHHHHHHHHHSTTGGGSC---------HH--HHHHHHH-HHHHHHCC---CHHHHHHHHHHSGGGGTSCSHHH-
T ss_pred HcCCC-HHHHHHHHHhCCHHHcCC---------HH--HHHHHHH-HHHHHhCC---CHHHHHHHHHhCCcceeechHHH-
Confidence 46775 356777777777777651 10 1222211 12111111 2233333344 6777776541
Q ss_pred chhhHHhhHHhcCCChhhhcccccCCCCCeEEE
Q 041085 160 PLQTIDQLKWDMGLPYDYCDYLITRHPELFSLV 192 (299)
Q Consensus 160 pL~kl~~lr~dLGLP~DF~~~lv~~yP~~Frvv 192 (299)
..++.-+..++|++++=...++.++|+.+...
T Consensus 148 -~~~v~~l~~~~G~s~~ei~~~v~~~P~il~~s 179 (270)
T 3m66_A 148 -KENMKVYRLELGFKHNEIQHMITRIPKMLTAN 179 (270)
T ss_dssp -HHHHHHHHHTSCCCHHHHHHHHHHCGGGGTSC
T ss_pred -HHHHHHHHHHcCCCHHHHHHHHHhCChhheec
Confidence 34566677789999888788888888887654
No 2
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A
Probab=54.05 E-value=1.4 Score=39.42 Aligned_cols=92 Identities=21% Similarity=0.323 Sum_probs=60.0
Q ss_pred CcCCCCCcchhhhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHHHhhchHHHHHHH---HHHhhccCCCc
Q 041085 82 GQLGLPQDLKLSTFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNALQQNQKDILDRL---CKLLMLTRDRM 158 (299)
Q Consensus 82 ~~LgLp~~~~~~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v~~~~e~~~v~rL---~KLLMMS~~rr 158 (299)
..+|++ +..+.+.|.++|.+|... +. .+.|...-|. +. .-.+.+++.-+ -.+|.+|.++
T Consensus 49 ~~lG~~-~~~i~~il~~~P~lL~~~---------~e--~l~p~v~~L~--~~---Gls~~~i~~~l~~~P~lL~~s~~~- 110 (270)
T 3m66_A 49 KDVGIE-DNQLGAFLTKNHAIFSED---------LE--NLKTRVAYLH--SK---NFSKADVAQMVRKAPFLLNFSVER- 110 (270)
T ss_dssp HHHTCC-GGGHHHHHHHCTTGGGSC---------HH--HHHHHHHHHH--HT---TCCHHHHHHHHHHSTTGGGSCHHH-
T ss_pred HHcCCC-HHHHHHHHHhCChhhhCC---------HH--HHHHHHHHHH--Hc---CCCHHHHHHHHHhCCHHHcCCHHH-
Confidence 458997 477899999999999872 10 1222222221 11 11233443333 3577777663
Q ss_pred cchhhHHhhHHhcCCChhhhcccccCCCCCeEEE
Q 041085 159 LPLQTIDQLKWDMGLPYDYCDYLITRHPELFSLV 192 (299)
Q Consensus 159 LpL~kl~~lr~dLGLP~DF~~~lv~~yP~~Frvv 192 (299)
-...++.++.++|+|.+=...++.+||..+...
T Consensus 111 -l~~~v~~L~~~lG~~~~~i~~ll~~~P~il~~s 143 (270)
T 3m66_A 111 -LDNRLGFFQKELELSVKKTRDLVVRLPRLLTGS 143 (270)
T ss_dssp -HHHHHHHHHHHHCCCHHHHHHHHHHSGGGGTSC
T ss_pred -HHHHHHHHHHHhCCCHHHHHHHHHhCCcceeec
Confidence 346778887899999988889999999998764
No 3
>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}
Probab=41.94 E-value=62 Score=25.48 Aligned_cols=66 Identities=9% Similarity=0.069 Sum_probs=41.2
Q ss_pred HHHHHhcCCCCcccccchhhhcCcCCCCCcchh---hhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHH
Q 041085 60 LVSIISSASHCFVPIYHLCRHRGQLGLPQDLKL---STFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEG 132 (299)
Q Consensus 60 Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~---~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE 132 (299)
+-.+|...+++.++.+.|++. +|+.. -.+ ..=|.+-=-|=.. .+|..+..-.+.||++|.+++.+=
T Consensus 40 vL~~L~~~~~~~~t~~eLa~~---l~~~~-~tvs~~v~~Le~~Glv~r~---~~~~DrR~~~l~LT~~G~~~~~~~ 108 (147)
T 4b8x_A 40 ALVLLTFSKSGELPMSKIGER---LMVHP-TSVTNTVDRLVRSGLVAKR---PNPNDGRGTLATITDKGREVVEAA 108 (147)
T ss_dssp HHHHHHTSGGGEEEHHHHHHH---HTCCH-HHHHHHHHHHHHTTSEEEE---ECC----CEEEEECHHHHHHHHHH
T ss_pred HHHHHHHCCCCCcCHHHHHHH---HCCCH-HHHHHHHHHHHhCCCEEEe---ecCCcCceeEEEECHHHHHHHHHH
Confidence 445566677888888888876 88863 333 3334444444443 455555567899999999988753
No 4
>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0
Probab=39.32 E-value=46 Score=25.31 Aligned_cols=72 Identities=13% Similarity=0.140 Sum_probs=43.9
Q ss_pred HHHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhH---hhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHH
Q 041085 58 CFLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTF---IRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLN 134 (299)
Q Consensus 58 ~~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~F---lrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~ 134 (299)
..+...|...|+..+++.+|++. +|++. -.+.+. |.+- ++-+- ..+|..+..-.+.||++|.+++.+-..
T Consensus 34 ~~vL~~l~~~~~~~~t~~ela~~---l~~~~-~tvs~~l~~Le~~-Gli~r--~~~~~D~R~~~~~LT~~G~~~~~~~~~ 106 (139)
T 3eco_A 34 GHTLGYLYAHQQDGLTQNDIAKA---LQRTG-PTVSNLLRNLERK-KLIYR--YVDAQDTRRKNIGLTTSGIKLVEAFTS 106 (139)
T ss_dssp HHHHHHHHHSTTTCEEHHHHHHH---HTCCH-HHHHHHHHHHHHT-TSEEE--EECCC--CCEEEEECHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCcCHHHHHHH---hCCCc-ccHHHHHHHHHHC-CCEee--cCCCCCCCeeeeEECHHHHHHHHHHHH
Confidence 45556667777667888888866 88863 333333 3333 23332 245555556689999999999886444
Q ss_pred HH
Q 041085 135 AL 136 (299)
Q Consensus 135 v~ 136 (299)
..
T Consensus 107 ~~ 108 (139)
T 3eco_A 107 IF 108 (139)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 5
>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28
Probab=38.20 E-value=57 Score=24.69 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=43.4
Q ss_pred HHHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhH---hhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHH
Q 041085 58 CFLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTF---IRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLN 134 (299)
Q Consensus 58 ~~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~F---lrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~ 134 (299)
..+...|...+++.+++..|.+. +|++. -.+.+. |.+-=-| +. ..+|..+..-.+.||+++.+++.+-..
T Consensus 37 ~~iL~~l~~~~~~~~~~~ela~~---l~~~~-~tvs~~l~~Le~~Gli-~r--~~~~~d~R~~~i~lT~~G~~~~~~~~~ 109 (141)
T 3bro_A 37 MTIIDYLSRNKNKEVLQRDLESE---FSIKS-STATVLLQRMEIKKLL-YR--KVSGKDSRQKCLKLTKKANKLETIILS 109 (141)
T ss_dssp HHHHHHHHHTTTSCCBHHHHHHH---HTCCH-HHHHHHHHHHHHTTSE-EE--EECSSCTTSEEEEECHHHHTTHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHH---HCCCc-chHHHHHHHHHHCCCE-Ee--eCCCcCCCeeeeEECHHHHHHHHHHHH
Confidence 44556667777667888888876 88863 333332 3333223 22 245544455689999999998875444
Q ss_pred H
Q 041085 135 A 135 (299)
Q Consensus 135 v 135 (299)
.
T Consensus 110 ~ 110 (141)
T 3bro_A 110 Y 110 (141)
T ss_dssp H
T ss_pred H
Confidence 3
No 6
>2kp6_A Uncharacterized protein; unknown function, structural genomics, PSI-2, protein struct initiative; NMR {Chromobacterium violaceum}
Probab=37.05 E-value=7.3 Score=29.66 Aligned_cols=28 Identities=29% Similarity=0.271 Sum_probs=22.8
Q ss_pred cccchhhhcCcCCCC-CcchhhhHhhhCC
Q 041085 73 PIYHLCRHRGQLGLP-QDLKLSTFIRRYP 100 (299)
Q Consensus 73 pl~~L~k~r~~LgLp-~~~~~~~FlrkyP 100 (299)
+...|+.+..+|||| +.-.+..||.+||
T Consensus 7 ~~h~l~~LF~QLGL~s~~~~I~~FI~~H~ 35 (82)
T 2kp6_A 7 SNHLLPGLFRQLGLEDEPAAIRAFIDSHP 35 (82)
T ss_dssp TCTHHHHHHHHHTSCCCHHHHHHHHHHSC
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHhCC
Confidence 456788899999999 4456778999997
No 7
>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0
Probab=35.15 E-value=47 Score=25.72 Aligned_cols=72 Identities=13% Similarity=0.116 Sum_probs=34.6
Q ss_pred HHHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhHh---hhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHH
Q 041085 58 CFLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTFI---RRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLN 134 (299)
Q Consensus 58 ~~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~Fl---rkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~ 134 (299)
..+...|...+++.++..+|++. +|++. -.+.+.| .+-=-|=.. .+|..+..-.+.||++|.++..+-..
T Consensus 44 ~~vL~~l~~~~~~~~t~~eLa~~---l~~~~-~~vs~~l~~L~~~Glv~r~---~~~~DrR~~~~~LT~~G~~~~~~~~~ 116 (148)
T 3jw4_A 44 GRMIGYIYENQESGIIQKDLAQF---FGRRG-ASITSMLQGLEKKGYIERR---IPENNARQKNIYVLPKGAALVEEFNN 116 (148)
T ss_dssp HHHHHHHHHHTTTCCCHHHHHHC----------CHHHHHHHHHHTTSBCCC-----------CCCCBCHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCHHHHHHH---HCCCh-hHHHHHHHHHHHCCCEEee---CCCCCchhheeeECHHHHHHHHHHHH
Confidence 34555566665566788888765 88863 3333322 222222222 33444445688999999999886544
Q ss_pred HH
Q 041085 135 AL 136 (299)
Q Consensus 135 v~ 136 (299)
..
T Consensus 117 ~~ 118 (148)
T 3jw4_A 117 IF 118 (148)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 8
>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}
Probab=31.43 E-value=5.6 Score=37.36 Aligned_cols=87 Identities=16% Similarity=0.211 Sum_probs=54.4
Q ss_pred cCCCCCcchhhhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHHHhhchHHHHHHHH---HHhhccCCCcc
Q 041085 83 QLGLPQDLKLSTFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNALQQNQKDILDRLC---KLLMLTRDRML 159 (299)
Q Consensus 83 ~LgLp~~~~~~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v~~~~e~~~v~rL~---KLLMMS~~rrL 159 (299)
.+|++ +..+..+|.++|.++... +.+ ++ .+...+.-...+++..|+ .+|++|..+ |
T Consensus 55 d~Gfs-~~~i~~il~~~P~il~~~--------------l~~----~i-~~L~~LGls~e~V~kiL~k~P~lL~~s~e~-L 113 (335)
T 4fp9_B 55 DMGFS-NAHINELLSVRRGASLQQ--------------LLD----II-SEFILLGLNPEPVCVVLKKSPQLLKLPIMQ-M 113 (335)
T ss_dssp HTTCC-HHHHHHHHHHCSSCCHHH--------------HHH----HH-HHHHHTTCCHHHHHHHHHHCGGGGGSCHHH-H
T ss_pred HCCCC-HHHHHHHHHhCcccchhH--------------HHH----HH-HHHHHcCCCHHHHHHHHHhChhhccCCHHH-H
Confidence 58997 578999999999987551 111 11 111111113333333333 477777754 2
Q ss_pred chhhHHhhHHhcCCChhhhcccccCCCCCeEEE
Q 041085 160 PLQTIDQLKWDMGLPYDYCDYLITRHPELFSLV 192 (299)
Q Consensus 160 pL~kl~~lr~dLGLP~DF~~~lv~~yP~~Frvv 192 (299)
-.+|..++. +||+.+-...++.++|+.+...
T Consensus 114 -~~~l~fL~~-lGl~~~~i~~ll~~~P~lL~~s 144 (335)
T 4fp9_B 114 -RKRSSYLQK-LGLGEGKLKRVLYCCPEIFTMR 144 (335)
T ss_dssp -HHHHHHHHH-TTCTTTTHHHHHHHCGGGGTSC
T ss_pred -HHHHHHHHH-cCCCHHHHHHHHHhCchhhccC
Confidence 356777754 9999888888999999998654
No 9
>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}
Probab=29.69 E-value=98 Score=23.83 Aligned_cols=69 Identities=12% Similarity=0.155 Sum_probs=33.9
Q ss_pred HHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhHh---hhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHH
Q 041085 59 FLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTFI---RRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNA 135 (299)
Q Consensus 59 ~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~Fl---rkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v 135 (299)
.+...|...++. ++..+|++. +|++. -.+.+.| .+-=-|=. ..+|..+..-.+.||++|.+++.+-...
T Consensus 43 ~vL~~l~~~~~~-~t~~eLa~~---l~i~~-~tvs~~l~~Le~~Glv~r---~~~~~D~R~~~~~LT~~G~~~~~~~~~~ 114 (150)
T 3fm5_A 43 SVLVLACEQAEG-VNQRGVAAT---MGLDP-SQIVGLVDELEERGLVVR---TLDPSDRRNKLIAATEEGRRLRDDAKAR 114 (150)
T ss_dssp HHHHHHHHSTTC-CCSHHHHHH---HTCCH-HHHHHHHHHHHTTTSEEC--------------CEECHHHHHHHHHHHHH
T ss_pred HHHHHHHhCCCC-cCHHHHHHH---HCCCH-hHHHHHHHHHHHCCCEEe---eCCccccchheeeECHHHHHHHHHHHHH
Confidence 344455555543 788888766 88863 3333332 22222222 2344444456899999999988764433
No 10
>3rco_A Tudor domain-containing protein 7; structural genomics, structural genomics consortium, SGC, HL DNA binding protein; 1.80A {Homo sapiens} PDB: 2lh9_A
Probab=29.45 E-value=52 Score=25.19 Aligned_cols=43 Identities=23% Similarity=0.366 Sum_probs=33.0
Q ss_pred HHHHHHhcCCCCcccccchhhh----------cCcCCCCCcchhhhHhhhCCcceee
Q 041085 59 FLVSIISSASHCFVPIYHLCRH----------RGQLGLPQDLKLSTFIRRYPNIFCE 105 (299)
Q Consensus 59 ~Lk~li~~~p~~~lpl~~L~k~----------r~~LgLp~~~~~~~FlrkyP~iF~~ 105 (299)
-|+.+|.|++++ ++++.|.+- .++||. ..+.+||+--|+++.+
T Consensus 17 ~iRslL~S~k~g-vtl~~L~~DYr~l~G~~iP~r~lGy---~sl~~fL~siPdvv~~ 69 (89)
T 3rco_A 17 MLRAVLQSHKNG-VALPRLQGEYRSLTGDWIPFKQLGF---PTLEAYLRSVPAVVRI 69 (89)
T ss_dssp HHHHHHHTCTTC-EEHHHHHHHHHHHHSSCCCTTTTTC---SSHHHHHHTCTTTEEE
T ss_pred HHHHHhhcCCCC-CCHHHHHHHHHHHhCCcCChhhhCc---ccHHHHHhcccCeEEE
Confidence 466778888765 888888774 245666 3568999999999997
No 11
>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}
Probab=29.23 E-value=58 Score=26.75 Aligned_cols=70 Identities=9% Similarity=0.062 Sum_probs=43.9
Q ss_pred HHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhHh---hhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHH
Q 041085 59 FLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTFI---RRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNA 135 (299)
Q Consensus 59 ~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~Fl---rkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v 135 (299)
.+...|...|++.++++.|++. +|++. -.+.+.| .+-=-|=.. .+|..+..-.+.||++|.+++.+-...
T Consensus 45 ~vL~~L~~~~~~~~t~~eLa~~---l~is~-~tvs~~l~~Le~~GlV~r~---~~~~DrR~~~l~LT~~G~~~~~~~~~~ 117 (189)
T 3nqo_A 45 MTILSILHLPEEETTLNNIARK---MGTSK-QNINRLVANLEKNGYVDVI---PSPHDKRAINVKVTDLGKKVMVTCSRT 117 (189)
T ss_dssp HHHHHHHHSCGGGCCHHHHHHH---HTSCH-HHHHHHHHHHHHTTSEEEE---ECSSCSSCEEEEECHHHHHHHHHHHHH
T ss_pred HHHHHHHhccCCCcCHHHHHHH---HCCCH-HHHHHHHHHHHHCCCEEec---cCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence 3445556667778888888866 88863 3333333 333333333 455555567899999999988764443
No 12
>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*
Probab=29.14 E-value=9.1 Score=35.39 Aligned_cols=108 Identities=16% Similarity=0.150 Sum_probs=62.4
Q ss_pred HhcCCCCcccccchhhhcCcCCCCCcchhhhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHHHhhchHHH
Q 041085 64 ISSASHCFVPIYHLCRHRGQLGLPQDLKLSTFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNALQQNQKDI 143 (299)
Q Consensus 64 i~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v~~~~e~~~ 143 (299)
+..+|+..-++ -..=..+|++ .-.+.+.+.+||.++... +. .+.|.-.-|. . +.-...++
T Consensus 44 ~~~s~~~~~~v---l~fL~~~G~s-~~~i~~iv~~~P~lL~~~----~~-------~l~p~l~fL~--~---lG~s~~~i 103 (343)
T 3mva_O 44 FHRMITNEQDL---KMFLLSKGAS-KEVIASIISRYPRAITRT----PE-------NLSKRWDLWR--K---IVTSDLEI 103 (343)
T ss_dssp GGCSCCCHHHH---HHHHHHTTCC-HHHHHHHHHHCGGGGGCC----HH-------HHHHHHHHHT--T---TSSCHHHH
T ss_pred hccCcccHHHH---HHHHHHcCCC-HHHHHHHHHhCcHHHhCC----HH-------HHHHHHHHHH--H---cCCCHHHH
Confidence 44556543333 2233479997 467899999999998651 11 1222111110 0 11123333
Q ss_pred HHHH---HHHhhccCCCccchhhHHhhHHhcCCChhhhcccccCCCCCeEEE
Q 041085 144 LDRL---CKLLMLTRDRMLPLQTIDQLKWDMGLPYDYCDYLITRHPELFSLV 192 (299)
Q Consensus 144 v~rL---~KLLMMS~~rrLpL~kl~~lr~dLGLP~DF~~~lv~~yP~~Frvv 192 (299)
+.-+ -.+|+-+.+..--..+|+-++ ++|+|++-..+++.++|..|...
T Consensus 104 ~~il~~~P~iLl~s~~~~~l~p~v~fL~-~lGl~~~~i~~ll~~~P~il~~~ 154 (343)
T 3mva_O 104 VNILERSPESFFRSNNNLNLENNIKFLY-SVGLTRKCLCRLLTNAPRTFSNS 154 (343)
T ss_dssp HHHHHHCSHHHHSCCCHHHHHHHHHHHH-HTTCCHHHHHHHHHHCGGGGTSC
T ss_pred HHHHHHCCHHHhCCChHhhHHHHHHHHH-HhCCCHHHHHHHHHhCChhheeC
Confidence 3333 233455554323344677777 89999999999999999998653
No 13
>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*
Probab=27.78 E-value=81 Score=24.90 Aligned_cols=69 Identities=14% Similarity=0.206 Sum_probs=32.4
Q ss_pred HHHHHHhcCCC---CcccccchhhhcCcCCCCCcchhhh---HhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHH
Q 041085 59 FLVSIISSASH---CFVPIYHLCRHRGQLGLPQDLKLST---FIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEG 132 (299)
Q Consensus 59 ~Lk~li~~~p~---~~lpl~~L~k~r~~LgLp~~~~~~~---FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE 132 (299)
.+-..|...|+ ..++..+|++. +|+.. -.+.+ =|.+-=-| .. .+|..+..-.+.||++|.+++.+=
T Consensus 37 ~vL~~l~~~~~~~~~~~t~~eLa~~---l~~~~-~tvsr~v~~Le~~glV-r~---~~~~DrR~~~v~LT~~G~~~~~~~ 108 (148)
T 4fx0_A 37 STLAVISLSEGSAGIDLTMSELAAR---IGVER-TTLTRNLEVMRRDGLV-RV---MAGADARCKRIELTAKGRAALQKA 108 (148)
T ss_dssp HHHHHHHC---------CHHHHHHH---HTCCH-HHHHHHHHHHHHTTSB-C--------------CCBCHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCCcCHHHHHHH---HCCCh-hhHHHHHHHHHHCCCE-Ee---eCCCCCCeeEEEECHHHHHHHHHH
Confidence 34455555554 46788888866 88853 22332 23344334 43 344444556899999999998764
Q ss_pred HHH
Q 041085 133 LNA 135 (299)
Q Consensus 133 ~~v 135 (299)
..+
T Consensus 109 ~~~ 111 (148)
T 4fx0_A 109 VPL 111 (148)
T ss_dssp HHH
T ss_pred HHH
Confidence 433
No 14
>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}
Probab=27.50 E-value=7.5 Score=36.51 Aligned_cols=117 Identities=10% Similarity=0.121 Sum_probs=70.2
Q ss_pred HHHHHHhcCCCCccc--ccchhhhcCcCCCCCcchhhhHhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHHH
Q 041085 59 FLVSIISSASHCFVP--IYHLCRHRGQLGLPQDLKLSTFIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNAL 136 (299)
Q Consensus 59 ~Lk~li~~~p~~~lp--l~~L~k~r~~LgLp~~~~~~~FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v~ 136 (299)
.+..+|...|.- ++ +..+-..-..||++ .-.+.+.|.++|.++..+ +- +|.+...-| ++..+-
T Consensus 62 ~i~~il~~~P~i-l~~~l~~~i~~L~~LGls-~e~V~kiL~k~P~lL~~s---------~e--~L~~~l~fL--~~lGl~ 126 (335)
T 4fp9_B 62 HINELLSVRRGA-SLQQLLDIISEFILLGLN-PEPVCVVLKKSPQLLKLP---------IM--QMRKRSSYL--QKLGLG 126 (335)
T ss_dssp HHHHHHHHCSSC-CHHHHHHHHHHHHHTTCC-HHHHHHHHHHCGGGGGSC---------HH--HHHHHHHHH--HHTTCT
T ss_pred HHHHHHHhCccc-chhHHHHHHHHHHHcCCC-HHHHHHHHHhChhhccCC---------HH--HHHHHHHHH--HHcCCC
Confidence 577888888862 21 11111122458997 577899999999998762 10 244443333 112222
Q ss_pred hhchHHHHHHHHHHhhccCCCccchhhHHhhHHhcCCChhhhcccccCCCCCeEEE
Q 041085 137 QQNQKDILDRLCKLLMLTRDRMLPLQTIDQLKWDMGLPYDYCDYLITRHPELFSLV 192 (299)
Q Consensus 137 ~~~e~~~v~rL~KLLMMS~~rrLpL~kl~~lr~dLGLP~DF~~~lv~~yP~~Frvv 192 (299)
...-..++.+.-.+|.+|..+ -..++..++..+|+..+=...++.++|..+...
T Consensus 127 ~~~i~~ll~~~P~lL~~s~e~--i~~~v~~L~~~lGfS~~ev~~mv~r~P~lL~~S 180 (335)
T 4fp9_B 127 EGKLKRVLYCCPEIFTMRQQD--INDTVRLLKEKCLFTVQQVTKILHSCPSVLRED 180 (335)
T ss_dssp TTTHHHHHHHCGGGGTSCHHH--HHHHHHHHHHTSCCCHHHHHHHHHHCGGGGTSC
T ss_pred HHHHHHHHHhCchhhccChHH--HHHHHHHHHHHcCCCHHHHHHHHHhCChhhhCC
Confidence 222233444444566666553 234556677889998888888999999888664
No 15
>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D
Probab=27.02 E-value=1.3e+02 Score=22.89 Aligned_cols=74 Identities=9% Similarity=0.031 Sum_probs=44.3
Q ss_pred HHHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhHh---hhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHH
Q 041085 58 CFLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTFI---RRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLN 134 (299)
Q Consensus 58 ~~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~Fl---rkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~ 134 (299)
..+...|...+++.++..+|++. +|++. -.+.+.| .+-=-|=.. .+|..+..-.+.||++|.+++.+-..
T Consensus 40 ~~vL~~l~~~~~~~~t~~eLa~~---l~~~~-~tvs~~l~~Le~~Glv~r~---~~~~D~R~~~i~LT~~G~~~~~~~~~ 112 (127)
T 2frh_A 40 FAVLTYISENKEKEYYLKDIINH---LNYKQ-PQVVKAVKILSQEDYFDKK---RNEHDERTVLILVNAQQRKKIESLLS 112 (127)
T ss_dssp HHHHHHHHHTCCSEEEHHHHHHH---SSSHH-HHHHHHHHHHHHTTSSCCB---CCSSSSCCCEEECCSHHHHHHHHHHH
T ss_pred HHHHHHHHhccCCCcCHHHHHHH---HCCCH-HHHHHHHHHHHHCCCEEec---CCCCCCCeeEEEECHHHHHHHHHHHH
Confidence 34445555665567888888866 88852 3333333 222222222 34444455789999999999987655
Q ss_pred HHhh
Q 041085 135 ALQQ 138 (299)
Q Consensus 135 v~~~ 138 (299)
...+
T Consensus 113 ~~~~ 116 (127)
T 2frh_A 113 RVNK 116 (127)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 5443
No 16
>3s93_A Tudor domain-containing protein 5; structural genomics consortium, SGC, transcription; 2.28A {Homo sapiens}
Probab=26.93 E-value=81 Score=24.48 Aligned_cols=55 Identities=13% Similarity=0.094 Sum_probs=38.6
Q ss_pred HHHhhhchHHHHH-HHHHHhcCCCCcccccchhhhc----------CcCCCCCcchhhhHhhhCCcceee
Q 041085 47 VVAAEKDLRAACF-LVSIISSASHCFVPIYHLCRHR----------GQLGLPQDLKLSTFIRRYPNIFCE 105 (299)
Q Consensus 47 ~v~r~k~l~~v~~-Lk~li~~~p~~~lpl~~L~k~r----------~~LgLp~~~~~~~FlrkyP~iF~~ 105 (299)
.+++++-+..+-+ |+.+|.++++ .++++.|.+-. +.||. ..+.+||+--|+++++
T Consensus 2 ~~~~~~~l~~vkk~irslLiS~K~-gvtl~~L~~dYr~~~G~~iP~r~lGy---~sl~~fL~sipdvv~~ 67 (102)
T 3s93_A 2 MSEQERIQECLRKEIRSLLISTKD-GLSPQELEKEYLLMVGNHLPLRILGY---RSTMELVLDMPDVVRV 67 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSSSS-CBCHHHHHHHHHHHHSSCCCTGGGTC---SSHHHHHHTCTTTEEE
T ss_pred CccHHHHHHHHHHHHHHhheeCCC-CcCHHHHHHHHHHHcCCcCCchhcCc---CCHHHHHHcCCCeEEE
Confidence 3566777766655 4556666654 78888888742 34555 3468999999999987
No 17
>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}
Probab=25.01 E-value=1.3e+02 Score=23.73 Aligned_cols=73 Identities=8% Similarity=0.040 Sum_probs=40.7
Q ss_pred HHHHHHHhcCCCCcccccchhhhcCcCCCCCcchhhhH---hhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHH
Q 041085 58 CFLVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLSTF---IRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLN 134 (299)
Q Consensus 58 ~~Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~F---lrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~ 134 (299)
..+...|....+..+++..|++. +|+.. -.+.+. |.+-=-|=.. .+|..+..-.+.||++|.+++.+=..
T Consensus 49 ~~vL~~l~~~~~~~~t~~eLa~~---l~~~~-~tvs~~l~~Le~~Glv~r~---~~~~DrR~~~l~LT~~G~~~~~~~~~ 121 (168)
T 3u2r_A 49 YNTLRLLRSVHPEGMATLQIADR---LISRA-PDITRLIDRLDDRGLVLRT---RKPENRRVVEVALTDAGLKLLKDLEE 121 (168)
T ss_dssp HHHHHHHHHHTTSCEEHHHHHHH---C---C-THHHHHHHHHHHTTSEEEE---EETTEEEEEEEEECHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCcCHHHHHHH---HCCCh-hhHHHHHHHHHHCCCEeec---CCCCCCCeeEeEECHHHHHHHHHHHH
Confidence 34445555554456788888866 88863 333333 3333333333 34544445689999999998886544
Q ss_pred HHh
Q 041085 135 ALQ 137 (299)
Q Consensus 135 v~~ 137 (299)
...
T Consensus 122 ~~~ 124 (168)
T 3u2r_A 122 PVR 124 (168)
T ss_dssp HHH
T ss_pred HHH
Confidence 433
No 18
>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}
Probab=20.46 E-value=2.2e+02 Score=21.56 Aligned_cols=67 Identities=19% Similarity=0.179 Sum_probs=34.1
Q ss_pred HHHHHhcCCCCcccccchhhhcCcCCCCCcchhhh---HhhhCCcceeeecccCCCCCCcCceecCHHHHHHHHHHHHH
Q 041085 60 LVSIISSASHCFVPIYHLCRHRGQLGLPQDLKLST---FIRRYPNIFCESHVLDSGGTRVPCFGLTPEAADVHHEGLNA 135 (299)
Q Consensus 60 Lk~li~~~p~~~lpl~~L~k~r~~LgLp~~~~~~~---FlrkyP~iF~~~~~~~p~~~~~p~~rLT~~a~~L~~eE~~v 135 (299)
+-..|...+ .++..+|++. +|++. -.+.+ -|.+- ++.+- ..+|..+..-.+.||++|.+++.+-...
T Consensus 45 iL~~l~~~~--~~t~~ela~~---l~~~~-~tvs~~l~~Le~~-Glv~r--~~~~~D~R~~~~~lT~~G~~~~~~~~~~ 114 (148)
T 3nrv_A 45 IISVLSSAS--DCSVQKISDI---LGLDK-AAVSRTVKKLEEK-KYIEV--NGHSEDKRTYAINLTEMGQELYEVASDF 114 (148)
T ss_dssp HHHHHHHSS--SBCHHHHHHH---HTCCH-HHHHHHHHHHHHT-TSEEC-----------CCBEECHHHHHHHHHHHHH
T ss_pred HHHHHHcCC--CCCHHHHHHH---HCCCH-HHHHHHHHHHHHC-CCEEe--ecCCCCcceeEeEECHhHHHHHHHHHHH
Confidence 334444444 5677777755 78752 22322 23333 44443 3445444456899999999988764433
Done!