Query 017877
Match_columns 364
No_of_seqs 148 out of 285
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:12:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14215 bHLH-MYC_N: bHLH-MYC 100.0 7.3E-50 1.6E-54 356.3 11.2 155 14-205 1-163 (163)
2 TIGR01817 nifA Nif-specific re 79.3 2.2 4.7E-05 44.6 4.1 75 116-204 68-151 (534)
3 PRK11061 fused phosphoenolpyru 70.8 6.8 0.00015 43.4 5.3 78 116-207 67-149 (748)
4 PF13185 GAF_2: GAF domain; PD 62.2 6 0.00013 31.9 2.2 67 122-204 68-139 (148)
5 smart00065 GAF Domain present 47.1 1.2E+02 0.0026 22.7 9.0 28 10-39 2-29 (149)
6 PRK15429 formate hydrogenlyase 37.2 44 0.00096 36.3 4.5 72 119-201 254-333 (686)
7 COG3340 PepE Peptidase E [Amin 27.4 74 0.0016 31.0 3.7 44 158-210 19-63 (224)
8 PF01590 GAF: GAF domain; Int 27.0 70 0.0015 25.9 3.1 73 116-190 51-131 (154)
9 PRK05022 anaerobic nitric oxid 21.3 1.1E+02 0.0023 32.3 3.9 77 116-205 65-152 (509)
10 KOG1924 RhoA GTPase effector D 14.3 4.7E+02 0.01 30.5 6.8 14 10-23 304-317 (1102)
No 1
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=100.00 E-value=7.3e-50 Score=356.34 Aligned_cols=155 Identities=39% Similarity=0.632 Sum_probs=129.6
Q ss_pred HHHHHHHhccCCCCCceEEEEeeecCCCCCCCCCCCCCccccCCCCCCceeEEecCccccCCccchhhcC------CCC-
Q 017877 14 LQHTLRSLCIHENSQWVYAVFWRILPRNYPPPKWDGQGAYDRSRGNRRNWILVWEDGFCNFAASTAAEIN------SGD- 86 (364)
Q Consensus 14 LQ~~LrsLc~~~~~~WtYAVFWqisprn~ppP~w~~~g~~D~S~~~sg~~iLvWgDGycng~~~~~~E~~------~~~- 86 (364)
|||+||+||+ +++|+||||||+++++ ++|+||||||++++++++..+ +..
T Consensus 1 Lq~~Lr~lv~--~~~W~YaVFWk~~~~~---------------------~~L~W~DG~~~g~~~~~~~~~~~~~~~~~~l 57 (163)
T PF14215_consen 1 LQQRLRSLVE--NSQWTYAVFWKLSPDN---------------------SVLVWGDGYCNGPKETRKNGEEEQEQRSKVL 57 (163)
T ss_pred ChHHHHHHhC--CCCCcEEEEeEEcCCC---------------------CeeeEcceeecCCcccccchhhccchhhhHH
Confidence 7999999999 8899999999999775 499999999999876543210 000
Q ss_pred CCCCCCCCCccccccCCcchHHHHhhccc-cccCCCCeeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhhhh
Q 017877 87 CPSSSVYGNCEFQHYQGLQPELFFKMSHE-IYNYGEGLIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWEAQ 165 (364)
Q Consensus 87 ~~~ss~~g~~~~~~~~~~d~EwFflMSm~-sF~~GeGLpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~AQ 165 (364)
....+.++++...+.+++++||||++||+ +| |+|+|||||++|+|+||++++.. ..+.|+|+|+||
T Consensus 58 ~~l~~~~~~~~~~~~~v~~~e~f~~~s~~~sf--g~G~~G~a~~sg~~~Wi~~~~~~-----------~~~~~~r~~~aq 124 (163)
T PF14215_consen 58 RELHSSFSSYALSPEEVTDTEWFYLVSMSYSF--GEGIPGRAAASGQHIWISGANEL-----------DSSYCERAWLAQ 124 (163)
T ss_pred HHHhhhccccccccchhHHHHHHhhceeeEEe--cCCccEEEeecCccEEEeCCCcc-----------ccccchhhhhhc
Confidence 01122223445678899999999999994 66 99999999999999999999742 345789999999
Q ss_pred hccCcceEEEeEeCCceEeecccccccCChHHHHHHHHHh
Q 017877 166 FQSGIKTIALIAVREGVVQLGAVNKVVEDLNYVVLLRKKF 205 (364)
Q Consensus 166 FsaGIQTIVcIPV~~GVVELGSte~I~Ed~~lV~~IK~lF 205 (364)
.+||||||||||++||||||||++|+||.+||++||++|
T Consensus 125 -~~~~~Tiv~IPv~~GVvELGSt~~I~Ed~~~v~~vk~~F 163 (163)
T PF14215_consen 125 -FAGIQTIVCIPVPNGVVELGSTEKIPEDSNLVQRVKSLF 163 (163)
T ss_pred -ccccceEEEEEecCCEEEeeeeeeeccCHHHHHHHHhhC
Confidence 688889999999999999999999999999999999998
No 2
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=79.32 E-value=2.2 Score=44.57 Aligned_cols=75 Identities=19% Similarity=0.335 Sum_probs=50.7
Q ss_pred cccCCCCeeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhhhhhccCcceEEEeEeC-----CceEeeccccc
Q 017877 116 IYNYGEGLIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWEAQFQSGIKTIALIAVR-----EGVVQLGAVNK 190 (364)
Q Consensus 116 sF~~GeGLpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~AQFsaGIQTIVcIPV~-----~GVVELGSte~ 190 (364)
.|..|+|+.|+|+.+++++.|.+...+ ..|. .+. .-...|+++++|||+. -|||.+.+...
T Consensus 68 ~~~~~~gi~g~v~~~~~pvii~Dv~~d--~~~~----------~~~--~~~~~~~~S~l~VPL~~~g~viGvL~v~s~~~ 133 (534)
T TIGR01817 68 RYRVGEGAIGQIVATGNSLVVPDVAAE--PLFL----------DRL--SLYDPGPVPFIGVPIKADSETIGVLAADRDFR 133 (534)
T ss_pred cccCCccHHHHHHhcCCeEEecccccC--chhh----------hcc--ccccCCcceEEEEEEcCCCEEEEEEEEEeccc
Confidence 567789999999999999999876432 1111 000 0114678999999984 48999998854
Q ss_pred ----ccCChHHHHHHHHH
Q 017877 191 ----VVEDLNYVVLLRKK 204 (364)
Q Consensus 191 ----I~Ed~~lV~~IK~l 204 (364)
-.+|.+++..|-..
T Consensus 134 ~~~ft~~d~~lL~~lA~~ 151 (534)
T TIGR01817 134 SRERLEEEVRFLEMVANL 151 (534)
T ss_pred cccccHHHHHHHHHHHHH
Confidence 34565666554433
No 3
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=70.83 E-value=6.8 Score=43.40 Aligned_cols=78 Identities=13% Similarity=0.112 Sum_probs=51.9
Q ss_pred cccCCCCeeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhhhhhccCcceEEEeEeC-----CceEeeccccc
Q 017877 116 IYNYGEGLIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWEAQFQSGIKTIALIAVR-----EGVVQLGAVNK 190 (364)
Q Consensus 116 sF~~GeGLpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~AQFsaGIQTIVcIPV~-----~GVVELGSte~ 190 (364)
.|..|+|+.|+|+.+++++.|.+...+ ..|. ..++. . ..+++..+|||+. =|||.+.+.+.
T Consensus 67 ~l~~geGi~G~Va~tg~pV~V~Dv~~d--prf~--------~~~~~---~-~~~~~S~L~VPL~~~geVIGVL~v~~~~~ 132 (748)
T PRK11061 67 TLAFDEGIVGLVGRLAEPINLADAQKH--PSFK--------YIPSV---K-EERFRAFLGVPIIYRRQLLGVLVVQQREL 132 (748)
T ss_pred eccCCcchHHHHhccCceEEECCcccC--cccc--------cCccc---c-CccceEEEEEEEeeCCEEEEEEEEeeCCC
Confidence 578899999999999999999766432 2221 11111 1 3679999999985 37888877765
Q ss_pred ccCChHHHHHHHHHhhc
Q 017877 191 VVEDLNYVVLLRKKFSY 207 (364)
Q Consensus 191 I~Ed~~lV~~IK~lF~~ 207 (364)
-.-+.+-+..+..+...
T Consensus 133 ~~Fs~~d~~lL~~LA~~ 149 (748)
T PRK11061 133 RQFDESEESFLVTLATQ 149 (748)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 55555445555555443
No 4
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=62.22 E-value=6 Score=31.95 Aligned_cols=67 Identities=22% Similarity=0.208 Sum_probs=38.9
Q ss_pred CeeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhhhhhccCcceEEEeEeC--C---ceEeecccccccCChH
Q 017877 122 GLIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWEAQFQSGIKTIALIAVR--E---GVVQLGAVNKVVEDLN 196 (364)
Q Consensus 122 GLpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~AQFsaGIQTIVcIPV~--~---GVVELGSte~I~Ed~~ 196 (364)
|+.+.++.+++++++. ... .. ..+..... ..||+.++|||+. + |||.|.+.+.-.=+..
T Consensus 68 ~~~~~~~~~~~~~~~~-~~~--~~------------~~~~~~~~-~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~~~ 131 (148)
T PF13185_consen 68 GLWEGVLRTGEPIIIN-DDD--SS------------FPPWELAR-HPGIRSILCVPLRSGGEVIGVLSLYSKEPNAFSEE 131 (148)
T ss_dssp ETTSHHHHHTS-EEES-CCC--GG------------GSTTHHHC-CTT-SEEEEEEEEETTEEEEEEEEEESSTT---HH
T ss_pred hHHHHHHhcCceEEEe-Ccc--cc------------ccchhhhc-cccCCEEEEEEEeECCEEEEEEEEeeCCCCCcCHH
Confidence 3444448899999998 110 00 11112223 6899999999984 3 9999999877555555
Q ss_pred HHHHHHHH
Q 017877 197 YVVLLRKK 204 (364)
Q Consensus 197 lV~~IK~l 204 (364)
-+..++.+
T Consensus 132 ~~~~l~~l 139 (148)
T PF13185_consen 132 DLELLEAL 139 (148)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 55555444
No 5
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=47.07 E-value=1.2e+02 Score=22.72 Aligned_cols=28 Identities=18% Similarity=0.078 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhccCCCCCceEEEEeeecC
Q 017877 10 MTHLLQHTLRSLCIHENSQWVYAVFWRILP 39 (364)
Q Consensus 10 l~~~LQ~~LrsLc~~~~~~WtYAVFWqisp 39 (364)
++..++..++.++. ..++..+.++.+..
T Consensus 2 ~~~~~~~~~~~l~~--~~~~~~~~i~~~~~ 29 (149)
T smart00065 2 LEELLQTILEELRQ--LLGADRVLIYLVDE 29 (149)
T ss_pred HHHHHHHHHHHHHH--HhCCceEEEEEEec
Confidence 45667777777776 56888898988874
No 6
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=37.21 E-value=44 Score=36.27 Aligned_cols=72 Identities=17% Similarity=0.218 Sum_probs=44.2
Q ss_pred CCCCeeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhhhhhccCcceEEEeEeC-----CceEeecccccc--
Q 017877 119 YGEGLIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWEAQFQSGIKTIALIAVR-----EGVVQLGAVNKV-- 191 (364)
Q Consensus 119 ~GeGLpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~AQFsaGIQTIVcIPV~-----~GVVELGSte~I-- 191 (364)
.+.|+.|+|+.+++++=+...... . ...+++.....+..+|+++++||+. -|||.+++...-
T Consensus 254 ~~~~l~g~V~~~~~p~lv~~~~~d-~----------~~~~~~~~~~~~~~~~~s~l~vPL~~~~~v~GvL~l~~~~~~~F 322 (686)
T PRK15429 254 EAGTLTERVFKSKEMLLINLHERD-D----------LAPYERMLFDTWGNQIQTLCLLPLMSGDTMLGVLKLAQCEEKVF 322 (686)
T ss_pred cccchHHHHHhcCceEEEECccCc-c----------cchhhhhhhhcccccceEEEEEeEEECCEEEEEEEEeeCCCCcC
Confidence 345899999999999977544211 0 1112333323334679999999973 499999865432
Q ss_pred -cCChHHHHHH
Q 017877 192 -VEDLNYVVLL 201 (364)
Q Consensus 192 -~Ed~~lV~~I 201 (364)
.+|.+++..|
T Consensus 323 ~~~dl~lL~~i 333 (686)
T PRK15429 323 TTTNLKLLRQI 333 (686)
T ss_pred CHHHHHHHHHH
Confidence 2455555444
No 7
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=27.37 E-value=74 Score=31.03 Aligned_cols=44 Identities=32% Similarity=0.311 Sum_probs=35.7
Q ss_pred CCchhhhhhccC-cceEEEeEeCCceEeecccccccCChHHHHHHHHHhhcccC
Q 017877 158 HPRTWEAQFQSG-IKTIALIAVREGVVQLGAVNKVVEDLNYVVLLRKKFSYIES 210 (364)
Q Consensus 158 ~~Ra~~AQFsaG-IQTIVcIPV~~GVVELGSte~I~Ed~~lV~~IK~lF~~l~~ 210 (364)
+-..|.+.|..| -+||++||...++ .|+..+|+.+|..|..++.
T Consensus 19 ~~~~~i~n~l~g~~~~i~FIPtAs~~---------~~~~~Yv~k~~~~l~~lg~ 63 (224)
T COG3340 19 HFLPFIANFLQGKRKTIAFIPTASVD---------SEDDFYVEKVRNALAKLGL 63 (224)
T ss_pred hhhHHHHHHhcCCCceEEEEecCccc---------cchHHHHHHHHHHHHHcCC
Confidence 345677777888 7899999998764 4568899999999999864
No 8
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=27.03 E-value=70 Score=25.88 Aligned_cols=73 Identities=18% Similarity=0.194 Sum_probs=41.3
Q ss_pred cccCCCCeeeeEeeCCCeeeeeCCCCchhhh---hhhhcccCCCCCCchhhhhhccCcceEEEeEeC-----CceEeecc
Q 017877 116 IYNYGEGLIGKVAADHSHKWIYKEPNDQEIN---FLSAWHNAADSHPRTWEAQFQSGIKTIALIAVR-----EGVVQLGA 187 (364)
Q Consensus 116 sF~~GeGLpGKaaasg~h~WI~~~~~~~e~~---f~s~w~~s~d~~~Ra~~AQFsaGIQTIVcIPV~-----~GVVELGS 187 (364)
.+..+.++.|+++.+++.+.|.+........ ....-......+.+.... ..|+++++|+|+. -|||.|.+
T Consensus 51 ~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~s~l~vPi~~~g~~~G~l~l~~ 128 (154)
T PF01590_consen 51 RLSMDESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLA--EYGVRSYLCVPIISGGRLIGVLSLYR 128 (154)
T ss_dssp EEETTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHH--TTTESEEEEEEEEETTEEEEEEEEEE
T ss_pred cccccccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccc--cccCceeeEeeeecccCcEEEEEEEE
Confidence 3444467789999999999987653210000 000000000001111121 3699999999984 58999998
Q ss_pred ccc
Q 017877 188 VNK 190 (364)
Q Consensus 188 te~ 190 (364)
++.
T Consensus 129 ~~~ 131 (154)
T PF01590_consen 129 TRP 131 (154)
T ss_dssp ESS
T ss_pred CCC
Confidence 887
No 9
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=21.34 E-value=1.1e+02 Score=32.25 Aligned_cols=77 Identities=8% Similarity=-0.043 Sum_probs=48.6
Q ss_pred cccCCCC-eeeeEeeCCCeeeeeCCCCchhhhhhhhcccCCCCCCchhh--hhhccCcceEEEeEeC-----CceEeecc
Q 017877 116 IYNYGEG-LIGKVAADHSHKWIYKEPNDQEINFLSAWHNAADSHPRTWE--AQFQSGIKTIALIAVR-----EGVVQLGA 187 (364)
Q Consensus 116 sF~~GeG-LpGKaaasg~h~WI~~~~~~~e~~f~s~w~~s~d~~~Ra~~--AQFsaGIQTIVcIPV~-----~GVVELGS 187 (364)
.|..|+| ..|.++.+|..+-|..+... . +.+.|... +. ..||...+|||+. -|||.+-+
T Consensus 65 ~~~~geGP~l~av~~~g~~v~v~~~~~~--p----------~~~~~~~~~~~~-~~gi~S~l~vPL~~~~~~~GvL~l~~ 131 (509)
T PRK05022 65 RFALEEHPRLEAILRAGDPVRFPADSEL--P----------DPYDGLIPGVQE-SLPVHDCMGLPLFVDGRLIGALTLDA 131 (509)
T ss_pred ccCCCcchHHHHHHhcCCeEEEecCCCC--C----------cccccccccccc-cCCcceEEEEEEEECCEEEEEEEEee
Confidence 7889999 78999988999977744311 0 11222211 12 3589999999983 58889877
Q ss_pred ccc---ccCChHHHHHHHHHh
Q 017877 188 VNK---VVEDLNYVVLLRKKF 205 (364)
Q Consensus 188 te~---I~Ed~~lV~~IK~lF 205 (364)
.+. -.+|..++..+-..+
T Consensus 132 ~~~~~f~~~~~~~l~~~a~~~ 152 (509)
T PRK05022 132 LDPGQFDAFSDEELRALAALA 152 (509)
T ss_pred CCCCcCCHHHHHHHHHHHHHH
Confidence 653 334455555544433
No 10
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=14.33 E-value=4.7e+02 Score=30.47 Aligned_cols=14 Identities=7% Similarity=0.090 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHhcc
Q 017877 10 MTHLLQHTLRSLCI 23 (364)
Q Consensus 10 l~~~LQ~~LrsLc~ 23 (364)
++-.+.+....|+.
T Consensus 304 l~vacmq~INal~t 317 (1102)
T KOG1924|consen 304 LQVACMQFINALVT 317 (1102)
T ss_pred HHHHHHHHHHHhcC
Confidence 33344444444443
Done!