Query 046838
Match_columns 349
No_of_seqs 130 out of 669
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 04:58:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046838.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046838hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03140 DUF247: Plant protein 100.0 8.9E-89 1.9E-93 673.5 27.6 307 29-349 1-318 (391)
2 KOG3110 Riboflavin kinase [Coe 51.5 12 0.00025 31.8 2.2 59 44-102 65-138 (153)
3 PF09069 EF-hand_3: EF-hand; 49.9 26 0.00057 27.6 3.9 53 67-119 3-76 (90)
4 PHA02103 hypothetical protein 45.0 49 0.0011 27.0 4.7 79 264-345 6-100 (135)
5 PF14579 HHH_6: Helix-hairpin- 31.4 2.2E+02 0.0047 21.9 6.5 78 263-348 1-81 (90)
6 PF07131 DUF1382: Protein of u 25.4 49 0.0011 24.0 1.6 17 252-268 12-28 (61)
7 KOG4134 DNA-dependent RNA poly 22.3 64 0.0014 29.8 2.2 35 28-73 26-60 (253)
8 PF11662 DUF3263: Protein of u 21.5 1E+02 0.0022 23.6 2.8 33 303-336 8-52 (77)
9 PF05391 Lsm_interact: Lsm int 19.0 80 0.0017 18.1 1.3 13 105-117 8-20 (21)
10 COG1777 Predicted transcriptio 17.2 5.5E+02 0.012 23.6 6.9 113 6-124 42-183 (217)
No 1
>PF03140 DUF247: Plant protein of unknown function; InterPro: IPR004158 The function of the plant proteins constituting this family is unknown.
Probab=100.00 E-value=8.9e-89 Score=673.47 Aligned_cols=307 Identities=42% Similarity=0.742 Sum_probs=267.1
Q ss_pred eeecCchhhhcCcCCccceeeeecccCCCCCccchHHHHHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHhccccCCc
Q 046838 29 IFRVPDVLRKLNEKAYEPELLAIGPYHHGKDNLSAFEEHKISYLQTLIEQTG---IPYPDYVRAMWALEERARNCYGGFI 105 (349)
Q Consensus 29 I~rVP~~lr~~~~~aY~P~~VsIGPyHhg~~~L~~mE~~K~~~~~~~l~r~~---~~~~~~~~~i~~~e~~aR~cY~~~~ 105 (349)
|||||+++|++|++||+|++|||||||||+++|+.||++||+|++.|++|++ .++++++++|+++|++||+||++++
T Consensus 1 I~rVP~~lr~~~~~~Y~P~~VsIGPyH~g~~~L~~mE~~K~~~l~~~l~~~~~~~~~l~~~~~~i~~~e~~~R~~Y~~~~ 80 (391)
T PF03140_consen 1 IYRVPESLRDVNPKAYTPQVVSIGPYHHGKPDLQEMEEHKLRYLHRFLKRSGAPAESLEDYVEAIRSLEEEARACYAEDI 80 (391)
T ss_pred CcCCCHHHccCCchhcCCceEEeCCCCCCchhhhhhHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHhcccc
Confidence 8999999999999999999999999999999999999999999999999998 8999999999999999999999999
Q ss_pred C-CChHHHHHHHHhhHHHHHHHHHHhcCCCCCCCCCc-ccccCCcchhHhhHHHHhhccchHHHHHHHHHhhcCCCCCCC
Q 046838 106 S-LGKNEFVQMMLFDGCFIVEVIRKFGLPHLRGDDDP-IFKQGWMLPHIARDMILLENQLPFFVLWKLFIMSEMPNIPGN 183 (349)
Q Consensus 106 ~-~~~~ef~~MmllDgcFlLe~l~~~~~~~~~~~~d~-~~~~~~~~~~i~~DllLLENQIPffVL~~L~~~~~~~~~~~~ 183 (349)
+ +++++|++||++|||||||+|+.+.. ..+.+|| ++..+|....|.+||+|||||||||||++||++.........
T Consensus 81 ~~~~~~~f~~MmllDgCFlLe~~~~~~~--~~~~~d~~~~~~~~~~~~i~~Dl~LLENQIPffVL~~L~~l~~~~~~~~~ 158 (391)
T PF03140_consen 81 DDMSSDEFVEMMLLDGCFLLEFFLRYSR--SDGENDPGIFSRPWLLSAIRRDLLLLENQIPFFVLEKLFELLFGSKSDVD 158 (391)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHhhhh--ccccccccccccccccccchhheeeecccchHHHHHHHHHHhcccccCcc
Confidence 8 99999999999999999999999875 2345778 888899999999999999999999999999999984444566
Q ss_pred chHHHHHHHhhcccCCCCCccCCCCcccCCCCCCcccchhHHHHhhcCCCCCccCccCC-CCCC----CCCcccccCHHH
Q 046838 184 ESFLVTILRFIYGILPGKGFRRDGVERVNDYPINEIKHLVNLIHDNWLPSPSRIDAYGN-NGKN----NSDWSIICSATE 258 (349)
Q Consensus 184 ~~l~~l~~~ff~~~~~~~~~~~~~~~~~~~~~~~~~~HLLdL~~~~~~~p~~~~~~~~~-~~~~----~~~~~~~~sAte 258 (349)
.++.+++.+||....+.. ... ......+++|||||+| .+++|+.....+.. .... ...+..||||||
T Consensus 159 ~~l~~l~~~~~~~~~~~~-----~~~--~~~~~~~~~HlL~L~~-~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~sA~e 230 (391)
T PF03140_consen 159 ESLIDLVLKFFYKHWPSW-----PPD--EPISNPEPHHLLDLLR-MSLLPSPPSSSPTPPRPPRSNGEKPPPKRIRSATE 230 (391)
T ss_pred chHHHHHHhHhccccccc-----ccc--ccccCCCCCChHHHHH-HHhccccCCcccCCCCcccccccccccccCCCHHH
Confidence 789999999994322211 011 1244567899999999 99999322111111 0111 123578999999
Q ss_pred HHhcCcEEEeecCCCCC-ceeeeEEcCceeeeceEEecccchhhhhhHHHHhhhcCCCCCcchhhHHHHHHhhcCChHHH
Q 046838 259 IQKAGIKFQKVDNHRDG-SLFDIKFKNGVMKIPTLEIGDATETIFQNLIVYEQCSHGINPKHILDYCKFLHCLINSSKDA 337 (349)
Q Consensus 259 L~~aGVkfk~~~~~~~~-~llDI~F~~G~L~IP~l~id~~T~~llrNLiA~Eq~~~~~~~~~vtsYv~fM~~LI~t~eDV 337 (349)
|++|||+||+ +++. +++||+|++|+|+||+|.||++|+++||||||||||+...+ .+|||||.||++||+|++||
T Consensus 231 L~~aGV~fk~---~~~~~~~lDv~F~~G~L~IP~L~id~~T~~~lrNLiA~Eq~~~~~~-~~vtsY~~fm~~Li~t~~DV 306 (391)
T PF03140_consen 231 LREAGVKFKP---SETDRSLLDVKFKKGVLEIPPLYIDDNTESLLRNLIAFEQCHPPTG-SYVTSYVFFMDSLINTPEDV 306 (391)
T ss_pred HHhCCcEEee---ccCccccccceecCCEEEeCeEEECCcchHHHhHHHHHHHHhccCC-chHhHHHHHHHHHhCcHhhH
Confidence 9999999999 7655 59999999999999999999999999999999999999887 89999999999999999999
Q ss_pred HHHHHCCCccCC
Q 046838 338 ELLRRRGIIDNC 349 (349)
Q Consensus 338 ~lL~~~gIi~n~ 349 (349)
++|+++|||+|+
T Consensus 307 ~lL~~kgIi~~~ 318 (391)
T PF03140_consen 307 ELLRRKGIIVNW 318 (391)
T ss_pred HHHHhCCeEecC
Confidence 999999999986
No 2
>KOG3110 consensus Riboflavin kinase [Coenzyme transport and metabolism]
Probab=51.52 E-value=12 Score=31.82 Aligned_cols=59 Identities=15% Similarity=0.233 Sum_probs=40.3
Q ss_pred ccceeeeec--ccCCCCC---ccchHHHHHHHHHHHHHHh-------cC---CCHHHHHHHHHHHHHHHhcccc
Q 046838 44 YEPELLAIG--PYHHGKD---NLSAFEEHKISYLQTLIEQ-------TG---IPYPDYVRAMWALEERARNCYG 102 (349)
Q Consensus 44 Y~P~~VsIG--PyHhg~~---~L~~mE~~K~~~~~~~l~r-------~~---~~~~~~~~~i~~~e~~aR~cY~ 102 (349)
--|+++||| ||..++. ++..++..|.-+..+.++- .. .+++.++++|..-.+.|++.-+
T Consensus 65 v~kMvmSIGwNP~Y~N~~Kt~E~hlih~f~~DFYge~l~~~IvGyiRpe~nf~slesLi~~I~~Di~vA~~~l~ 138 (153)
T KOG3110|consen 65 VFKMVMSIGWNPYYKNKKKTMELHLIHDFGEDFYGETLKVIIVGYIRPELNFDSLESLIEAIHGDIEVAKKVLD 138 (153)
T ss_pred ceeEEEEcccCcccCCcccceeeeeehhcccchhhheeeEEEEEeeccccCcchHHHHHHHHHhhHHHHHHhhc
Confidence 358999999 8887754 4555566665555555542 22 3689999999888888887543
No 3
>PF09069 EF-hand_3: EF-hand; InterPro: IPR015154 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=49.92 E-value=26 Score=27.62 Aligned_cols=53 Identities=19% Similarity=0.365 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhcCC-----CHHHHHHHHH-------------HHHHHHhccccC---CcCCChHHHHHHHHhh
Q 046838 67 HKISYLQTLIEQTGI-----PYPDYVRAMW-------------ALEERARNCYGG---FISLGKNEFVQMMLFD 119 (349)
Q Consensus 67 ~K~~~~~~~l~r~~~-----~~~~~~~~i~-------------~~e~~aR~cY~~---~~~~~~~ef~~MmllD 119 (349)
-|.||+-+++..++. .+..++..+. ..|.-+|+|+.. .-+++.++|+..|..|
T Consensus 3 dKyRylFslisd~~g~~~~~~l~~lL~d~lqip~~vgE~~aFg~~e~sv~sCF~~~~~~~~I~~~~Fl~wl~~e 76 (90)
T PF09069_consen 3 DKYRYLFSLISDSNGCMDQRKLGLLLHDVLQIPRAVGEGPAFGYIEPSVRSCFQQVQLSPKITENQFLDWLMSE 76 (90)
T ss_dssp HHHHHHHHHHS-TTS-B-HHHHHHHHHHHHHHHHHTT-GGGGT--HHHHHHHHHHTTT-S-B-HHHHHHHHHT-
T ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHhCccccccCcHHHHHHHhcccCCCCccCHHHHHHHHHhC
Confidence 588888888876432 2444433322 367889999976 5568999999888765
No 4
>PHA02103 hypothetical protein
Probab=44.97 E-value=49 Score=26.96 Aligned_cols=79 Identities=20% Similarity=0.498 Sum_probs=50.9
Q ss_pred cEEEeecCCCCCcee--eeEEc----Cce--eeeceEEecccchhhhhhHHHHhhhcCCC-----CC---cchhhHHHHH
Q 046838 264 IKFQKVDNHRDGSLF--DIKFK----NGV--MKIPTLEIGDATETIFQNLIVYEQCSHGI-----NP---KHILDYCKFL 327 (349)
Q Consensus 264 Vkfk~~~~~~~~~ll--DI~F~----~G~--L~IP~l~id~~T~~llrNLiA~Eq~~~~~-----~~---~~vtsYv~fM 327 (349)
.||+++.....++.+ .|.|+ +.+ -+||.+..|++..-+-|=.+-+|.|...- +- .++-+|-..+
T Consensus 6 lkf~~fk~kd~rn~f~v~~~fsdkf~d~t~~~e~pai~~~~~~~ei~rl~~f~~kck~~yp~gkgg~~df~~ipdyyryf 85 (135)
T PHA02103 6 LKFTPFKPKDDRNTFMVKMHFSDKFSDATLEYEIPAIDADRTKAEIVRLITFMDKCKAEYPRGKGGQADFNHIPDYYRYF 85 (135)
T ss_pred eeeeccCCccCcceEEEEEecccccCcceeEEeccccccchhhHHHHHHHHHHHHHHhhCCCCCCCccccccChHHHHHh
Confidence 456553223333333 44454 455 58999999999999999999999998431 10 3455665443
Q ss_pred HhhcCChHHHHHHHHCCC
Q 046838 328 HCLINSSKDAELLRRRGI 345 (349)
Q Consensus 328 ~~LI~t~eDV~lL~~~gI 345 (349)
-..+|-|++-.+-||
T Consensus 86 ---~ee~e~ie~we~ygv 100 (135)
T PHA02103 86 ---GEEAEGVELWEEYGV 100 (135)
T ss_pred ---cccchhhhHHHHhCc
Confidence 346677777777776
No 5
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=31.37 E-value=2.2e+02 Score=21.90 Aligned_cols=78 Identities=18% Similarity=0.249 Sum_probs=51.9
Q ss_pred CcEEEeecCCCCCceeeeEEcC--ceeeeceEEecccchhhhhhHHHHhhhcCCCCCcchhhHHHHHHhh-cCChHHHHH
Q 046838 263 GIKFQKVDNHRDGSLFDIKFKN--GVMKIPTLEIGDATETIFQNLIVYEQCSHGINPKHILDYCKFLHCL-INSSKDAEL 339 (349)
Q Consensus 263 GVkfk~~~~~~~~~llDI~F~~--G~L~IP~l~id~~T~~llrNLiA~Eq~~~~~~~~~vtsYv~fM~~L-I~t~eDV~l 339 (349)
||++.+.+- ..|-.+-+..+ |.+.+|--.|..-.+.....+++-=+ . ..++|+..|...+ --+..+++.
T Consensus 1 Gi~v~ppdI--n~S~~~~~~~~~~~~Ir~gl~~Ikglg~~~a~~I~~~R~-~-----g~f~s~~df~~R~~~i~~~~le~ 72 (90)
T PF14579_consen 1 GIKVLPPDI--NKSDADFTVEDKNNAIRLGLSAIKGLGEEVAEKIVEERE-N-----GPFKSLEDFIQRLPKINKRQLEA 72 (90)
T ss_dssp T-EEE---T--TT-BSS-EEETT-TEEE-BGGGSTTS-HHHHHHHHHHHH-C-----SS-SSHHHHHHHS-TS-HHHHHH
T ss_pred CCEEeCCee--cccCCCeEEECCCCEEeehHhhcCCCCHHHHHHHHHhHh-c-----CCCCCHHHHHHHHhcCCHHHHHH
Confidence 788877321 22333555555 79999999999998888887776544 2 2378888999888 778999999
Q ss_pred HHHCCCccC
Q 046838 340 LRRRGIIDN 348 (349)
Q Consensus 340 L~~~gIi~n 348 (349)
|.+.|.+..
T Consensus 73 Li~aGafd~ 81 (90)
T PF14579_consen 73 LIKAGAFDS 81 (90)
T ss_dssp HHHTTTTTT
T ss_pred HHHCCCccc
Confidence 999998764
No 6
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=25.38 E-value=49 Score=23.99 Aligned_cols=17 Identities=24% Similarity=0.403 Sum_probs=14.2
Q ss_pred cccCHHHHHhcCcEEEe
Q 046838 252 IICSATEIQKAGIKFQK 268 (349)
Q Consensus 252 ~~~sAteL~~aGVkfk~ 268 (349)
.+--|-.|..+||+|.+
T Consensus 12 ~lE~A~~La~~GIRFVp 28 (61)
T PF07131_consen 12 ALEMAHSLAHIGIRFVP 28 (61)
T ss_pred HHHHHHHHHHcCceeec
Confidence 35567889999999998
No 7
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=22.31 E-value=64 Score=29.84 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=26.2
Q ss_pred eeeecCchhhhcCcCCccceeeeecccCCCCCccchHHHHHHHHHH
Q 046838 28 SIFRVPDVLRKLNEKAYEPELLAIGPYHHGKDNLSAFEEHKISYLQ 73 (349)
Q Consensus 28 ~I~rVP~~lr~~~~~aY~P~~VsIGPyHhg~~~L~~mE~~K~~~~~ 73 (349)
|++++|..+ .+|+||||-.++.-..||+|=-..+.
T Consensus 26 clv~~t~dl-----------hlalaP~yl~npl~~~i~ehld~~vl 60 (253)
T KOG4134|consen 26 CLVCITTDL-----------HLALAPYYLANPLHALIEEHLDTKVL 60 (253)
T ss_pred eEEEeeehe-----------eeeecchhhcchhHHHHHHHhhHHHh
Confidence 699999764 79999999988765567776544443
No 8
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.54 E-value=1e+02 Score=23.61 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=25.2
Q ss_pred hhHHHHhhhcCCC------------CCcchhhHHHHHHhhcCChHH
Q 046838 303 QNLIVYEQCSHGI------------NPKHILDYCKFLHCLINSSKD 336 (349)
Q Consensus 303 rNLiA~Eq~~~~~------------~~~~vtsYv~fM~~LI~t~eD 336 (349)
+-++|||...+.. + .--|.|-..++.||++++=
T Consensus 8 ~~iL~fE~~ww~~~GaKe~aIre~fG-ls~~rYyq~Ln~LiD~p~A 52 (77)
T PF11662_consen 8 RAILDFERRWWRHGGAKEEAIREEFG-LSPTRYYQRLNALIDDPAA 52 (77)
T ss_pred HHHHHHHHHhCcCCCCcHHHHHHHHC-CCHHHHHHHHHHHhCChHH
Confidence 3478999876542 2 3578999999999999863
No 9
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=19.01 E-value=80 Score=18.07 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=10.7
Q ss_pred cCCChHHHHHHHH
Q 046838 105 ISLGKNEFVQMML 117 (349)
Q Consensus 105 ~~~~~~ef~~Mml 117 (349)
..+|.++|.+|+|
T Consensus 8 ~p~SNddFrkmfl 20 (21)
T PF05391_consen 8 KPKSNDDFRKMFL 20 (21)
T ss_pred CccchHHHHHHHc
Confidence 3489999999976
No 10
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=17.15 E-value=5.5e+02 Score=23.62 Aligned_cols=113 Identities=14% Similarity=0.159 Sum_probs=59.0
Q ss_pred cchHHHHHHHHhhccCCCCCCCeeeecCchhhhcCcCCccce-----eeeecccCCCCCc----cchHHHHHHHH-----
Q 046838 6 PNKVLDLVGEKLHRLTPTCSQFSIFRVPDVLRKLNEKAYEPE-----LLAIGPYHHGKDN----LSAFEEHKISY----- 71 (349)
Q Consensus 6 ~~~~~~~i~~~l~~~~~~~~~~~I~rVP~~lr~~~~~aY~P~-----~VsIGPyHhg~~~----L~~mE~~K~~~----- 71 (349)
+..++++++-.=.-.--+| .|-++|. +..+++|.|. .|.+||+-.|-.. .-..|..|..+
T Consensus 42 qkAVl~HL~~LE~AGlveS---~ie~~~R---g~~rKYY~Is~~~rleV~lsp~~f~~~~~~~~~~~l~~~r~~~~~~~~ 115 (217)
T COG1777 42 QKAVLKHLRILERAGLVES---RIEKIPR---GRPRKYYMISRNLRLEVTLSPNFFGAERFDLEEDDLESERSEVSKLFK 115 (217)
T ss_pred HHHHHHHHHHHHHcCCchh---hcccccc---CCCcceeeccCCeEEEEEecCcccceeccCccccchhhhhcchhhhcc
Confidence 3455565543222244455 6777776 6677888774 6899999998431 11122333333
Q ss_pred ----HHHHHHhc----------CCCHHHHHHHHHHHHHHHhccccCCcC-CChHHHHHHHHhhHHHHH
Q 046838 72 ----LQTLIEQT----------GIPYPDYVRAMWALEERARNCYGGFIS-LGKNEFVQMMLFDGCFIV 124 (349)
Q Consensus 72 ----~~~~l~r~----------~~~~~~~~~~i~~~e~~aR~cY~~~~~-~~~~ef~~MmllDgcFlL 124 (349)
+..++++. .....++.....++-+++..-|.+..+ +.....+.-++.+|.+-+
T Consensus 116 s~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~rik~~ied~~~~~~~~~vl~~l~~n~~~~v 183 (217)
T COG1777 116 SPEGISELISRLLEINREIEELSRAQTELQKQLNELMDRIKEEIEDKDGDMTERIVLEYLLKNGAADV 183 (217)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHhhhhhHH
Confidence 12222221 112334444455556666666665544 445555555555554433
Done!