Query 030601
Match_columns 174
No_of_seqs 114 out of 163
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 16:12:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030601.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030601hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04062 P21-Arc: ARP2/3 compl 100.0 1E-100 3E-105 627.1 8.1 172 2-173 3-175 (175)
2 KOG3155 Actin-related protein 100.0 7.6E-94 1.6E-98 582.3 11.9 171 1-173 2-173 (173)
3 cd00126 PAH Pancreatic Hormone 72.0 3.3 7.1E-05 26.7 2.0 22 121-142 8-29 (36)
4 PF00159 Hormone_3: Pancreatic 69.0 4.5 9.8E-05 26.0 2.1 22 121-142 8-29 (36)
5 smart00309 PAH Pancreatic horm 67.5 4.7 0.0001 26.0 2.0 22 121-142 8-29 (36)
6 PF09254 Endonuc-FokI_C: Restr 58.8 13 0.00029 31.7 3.7 32 124-165 89-120 (189)
7 PRK09463 fadE acyl-CoA dehydro 48.7 21 0.00045 35.9 3.8 100 42-153 573-678 (777)
8 PF14802 TMEM192: TMEM192 fami 39.4 48 0.001 28.8 4.2 61 80-147 168-234 (236)
9 PF09317 DUF1974: Domain of un 36.3 36 0.00079 30.4 3.1 94 48-153 108-207 (284)
10 PRK03601 transcriptional regul 35.5 24 0.00053 29.1 1.7 21 77-97 6-26 (275)
11 PRK13026 acyl-CoA dehydrogenas 35.1 28 0.00062 35.0 2.4 92 48-151 579-676 (774)
12 COG3765 WzzB Chain length dete 35.1 1.2E+02 0.0027 28.1 6.3 48 103-150 142-190 (347)
13 PF08990 Docking: Erythronolid 31.7 41 0.00088 20.3 1.8 17 126-142 3-19 (27)
14 PF12531 DUF3731: DNA-K relate 29.8 3.7E+02 0.008 23.9 8.1 107 40-161 26-139 (249)
15 PRK11767 SpoVR family protein; 29.4 43 0.00092 32.4 2.5 32 47-81 120-154 (498)
16 PF08606 Prp19: Prp19/Pso4-lik 29.1 81 0.0018 23.1 3.3 18 128-145 25-42 (70)
17 TIGR03779 Bac_Flav_CT_M Bacter 25.5 87 0.0019 29.6 3.7 36 114-150 133-180 (410)
18 KOG3420 Predicted RNA methylas 25.3 30 0.00065 29.3 0.6 56 3-63 40-98 (185)
19 PRK13291 metal-dependent hydro 23.5 2E+02 0.0044 23.1 5.1 36 109-145 3-40 (173)
20 PF01102 Glycophorin_A: Glycop 23.4 68 0.0015 25.4 2.2 39 70-118 78-116 (122)
21 COG2719 SpoVR Uncharacterized 22.2 79 0.0017 30.6 2.8 42 39-83 100-153 (495)
22 CHL00180 rbcR LysR transcripti 22.0 65 0.0014 26.9 2.0 20 78-97 11-30 (305)
23 PF13709 DUF4159: Domain of un 21.9 76 0.0017 26.5 2.4 22 107-136 60-81 (207)
24 COG5500 Predicted integral mem 21.9 54 0.0012 27.1 1.5 26 112-137 108-135 (159)
25 PF04741 InvH: InvH outer memb 21.9 53 0.0011 26.9 1.4 36 14-49 11-51 (147)
26 PF03221 HTH_Tnp_Tc5: Tc5 tran 21.8 1.9E+02 0.0041 18.6 3.9 14 154-167 47-60 (66)
27 COG4114 FhuF Uncharacterized F 21.8 80 0.0017 28.1 2.6 40 127-166 176-223 (251)
28 PF00631 G-gamma: GGL domain; 21.3 93 0.002 21.4 2.4 19 125-143 2-20 (68)
29 PRK09906 DNA-binding transcrip 21.1 78 0.0017 26.0 2.3 20 78-97 7-26 (296)
30 PF10155 DUF2363: Uncharacteri 20.9 63 0.0014 25.5 1.6 23 70-92 53-75 (126)
No 1
>PF04062 P21-Arc: ARP2/3 complex ARPC3 (21 kDa) subunit; InterPro: IPR007204 The Arp2/3 complex is a seven-protein assembly that is critical for actin nucleation and branching in cells. Arp2/3 nucleates new actin filaments while bound to existing filaments, thus creating a branched network []. The complex consists of Arp2, Arp3, p41, p34, p21, p20 and p16. Subunits p34 and p20 constitute the core of the structure, with the remaining subunits located peripherally []. This entry describes the p21 subunit. Proteins such as WASp and Scar1 may mediate receptor signalling through interactions with p21-Arc, resulting in the activation of Arc2/3 complex activity [].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_J 2P9P_E 2P9N_E 2P9K_E 1TYQ_E 1U2V_E 3RSE_E 2P9U_E 3DXM_E 2P9S_E ....
Probab=100.00 E-value=1.4e-100 Score=627.12 Aligned_cols=172 Identities=50% Similarity=0.920 Sum_probs=126.4
Q ss_pred cccccCCCCCCcceeeCccccccccCCCCCCCCCCCCCcchHHHHHHhhhhhccccccccCCCCceehHhHHHHHHHHHH
Q 030601 2 VYHSSFVDEEGVTKACGCPLLPLKSHIKGPAPASDQDRTDIVDEAITFFRANVFFRNFDIKSSADKLLIYLTFYINVALK 81 (174)
Q Consensus 2 AYHS~f~~~~~~~~~~g~alLPlrt~~rGPAp~~~~~~~DIIDEal~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CLk 81 (174)
||||+|+++++++.+||||||||||++|||||+++++++|||||||+|||||||||||||||+||||||||||||+||||
T Consensus 3 AYHS~f~~~~~~~~iGn~~lLPlrt~~rGPAp~~~~~~~DIIDEaL~~FraNvfFrnfeIKg~aDR~LIYltLyi~eCLk 82 (175)
T PF04062_consen 3 AYHSSFNDDESVRLIGNMALLPLRTKFRGPAPRPDDSDYDIIDEALYLFRANVFFRNFEIKGPADRLLIYLTLYISECLK 82 (175)
T ss_dssp --------TT--EEETTEEE--B--SS-SS--B--SSS--HHHHHHHHHHHHTT-S-----SHHCHHHHHHHHHHHCHHH
T ss_pred CccccccCCCCceeEcCeeeeecccCCCCCCCCCCCCcccHHHHHHHHHHhhhhhhccccCCCCceEeeeHHHHHHHHHH
Confidence 89999999887778888999999999999999877789999999999999999999999999999999999999999999
Q ss_pred HhhcCCCHHHHHHHHHHhcccCCCCCCCCCCCCCccccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhcCCC-CCCchhh
Q 030601 82 RLEGRRTLAEGTKAIINLGLEKVPVPGEPNFPFPGLFALPQSQKEAELFRNYLKQIREETSGRLLSVAYRPN-GTPNKWW 160 (174)
Q Consensus 82 kl~~~~~~~ea~k~l~~la~~~F~iPGd~gFpLn~~y~~P~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy~~~-~~psKwW 160 (174)
||++|++++||+|+|+++|+++|+||||+|||||++|++|+|++|+|+||+||+|+|||+|.|||||||+++ ++|||||
T Consensus 83 kl~~~~sk~ea~k~l~~lal~~F~iPGd~gFpLn~~y~~P~~~~e~d~lR~Yl~QlRqElg~RL~ervf~~~~~~psKwW 162 (175)
T PF04062_consen 83 KLQKCTSKNEAQKELYNLALDNFPIPGDPGFPLNSLYAKPANRQEADLLRQYLTQLRQELGLRLLERVFDDGDGKPSKWW 162 (175)
T ss_dssp HHTT-SSHHHHHHHHHHHHHS----TTSTT-TTTTTS---SSHHHHHHHHHHHHHHHHHHCCCCCHHHB-SSSS-B-HCC
T ss_pred HhccCCCHHHHHHHHHHHHHhcCCCCCCCCCCccccccCCCChhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCChhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999987 8999999
Q ss_pred hhhcccccccccC
Q 030601 161 LAFAKRKFMNIIV 173 (174)
Q Consensus 161 m~FaKRkFM~ksL 173 (174)
|||+|||||||||
T Consensus 163 ~~FaKRkFM~KsL 175 (175)
T PF04062_consen 163 MCFAKRKFMNKSL 175 (175)
T ss_dssp CCCCC--GGG--T
T ss_pred hhhhhhccccccC
Confidence 9999999999998
No 2
>KOG3155 consensus Actin-related protein Arp2/3 complex, subunit ARPC3 [Cytoskeleton]
Probab=100.00 E-value=7.6e-94 Score=582.27 Aligned_cols=171 Identities=51% Similarity=0.922 Sum_probs=165.2
Q ss_pred CcccccCCCCCCcceeeCccccccccCCCCCCCCCCCCCcchHHHHHHhhhhhccccccccCCCCceehHhHHHHHHHHH
Q 030601 1 MVYHSSFVDEEGVTKACGCPLLPLKSHIKGPAPASDQDRTDIVDEAITFFRANVFFRNFDIKSSADKLLIYLTFYINVAL 80 (174)
Q Consensus 1 mAYHS~f~~~~~~~~~~g~alLPlrt~~rGPAp~~~~~~~DIIDEal~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CL 80 (174)
+||||+|.+++++ ..+|||+|||||++|||||+.+ +++|||||||+|||||||||||||||||||+|||+||||||||
T Consensus 2 pAyhSsf~d~~~~-~~~n~alLpl~s~fkGPAp~~~-~d~DIvDEai~yFkaNvFFknfEIK~~ADRtLIYitlyIseCL 79 (173)
T KOG3155|consen 2 PAYHSSFMDPDNK-LIGNMALLPIRSQFKGPAPRET-KDTDIVDEAIYYFKANVFFKNFEIKNPADRTLIYITLYISECL 79 (173)
T ss_pred CcccccccCcCCC-ccCcceeccchhhccCCCCCcc-CccchHHHHHHHhhcccceecceecCccceeEEEeehHHHHHH
Confidence 6999999988765 4568999999999999999976 6899999999999999999999999999999999999999999
Q ss_pred HHhhcCCCHHHHHHHHHHhcccCCCCCCCCCCCCCccccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhcCCC-CCCchh
Q 030601 81 KRLEGRRTLAEGTKAIINLGLEKVPVPGEPNFPFPGLFALPQSQKEAELFRNYLKQIREETSGRLLSVAYRPN-GTPNKW 159 (174)
Q Consensus 81 kkl~~~~~~~ea~k~l~~la~~~F~iPGd~gFpLn~~y~~P~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy~~~-~~psKw 159 (174)
||||+|+|+.||+|+|++||+++|+||||+|||||+||++|.+++|+|.||+|++|+|||+|.|||++||++. ++||||
T Consensus 80 kkLqkc~sk~qg~k~l~~lal~~~~iPGe~GFPln~ly~~p~s~~~~e~mr~Yl~Q~RqE~~~RL~~~v~~~~~d~PsKw 159 (173)
T KOG3155|consen 80 KKLQKCNSKSQGEKELYNLALENFPIPGEPGFPLNALYTLPASKQDAELMRAYLQQFRQETGLRLLEKVYDTPKDKPSKW 159 (173)
T ss_pred HHHHcccchhHHHHHHHHhhhhcccCCCCCCCCchhhhcCCCCCCchHHHHHHHHHHHHHhhhhHHHHhcCCCCCCcchh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999887 899999
Q ss_pred hhhhcccccccccC
Q 030601 160 WLAFAKRKFMNIIV 173 (174)
Q Consensus 160 Wm~FaKRkFM~ksL 173 (174)
|+||+|||||||||
T Consensus 160 W~cF~kRrFMnksl 173 (173)
T KOG3155|consen 160 WLCFAKRRFMNKSL 173 (173)
T ss_pred HHHHHHHHhhhccC
Confidence 99999999999997
No 3
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=71.96 E-value=3.3 Score=26.66 Aligned_cols=22 Identities=32% Similarity=0.549 Sum_probs=17.1
Q ss_pred CCChhHHHHHHHHHHHHHHHHH
Q 030601 121 PQSQKEAELFRNYLKQIREETS 142 (174)
Q Consensus 121 P~~~~e~d~lR~Yl~Q~RqEl~ 142 (174)
|++-.-.|.|++|+++||+=+.
T Consensus 8 Pg~~a~~eel~~Y~~~L~~Yin 29 (36)
T cd00126 8 PGDDASPEELRQYLAALREYIN 29 (36)
T ss_pred CCCCCCHHHHHHHHHHHHHHHH
Confidence 4555557999999999998654
No 4
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=68.99 E-value=4.5 Score=25.98 Aligned_cols=22 Identities=18% Similarity=0.308 Sum_probs=16.3
Q ss_pred CCChhHHHHHHHHHHHHHHHHH
Q 030601 121 PQSQKEAELFRNYLKQIREETS 142 (174)
Q Consensus 121 P~~~~e~d~lR~Yl~Q~RqEl~ 142 (174)
|++-.-.|.|++|+.+||+=+.
T Consensus 8 P~~~aspeel~~Y~~~L~~Y~~ 29 (36)
T PF00159_consen 8 PGDFASPEELAQYYAALRHYIN 29 (36)
T ss_dssp SSTTSSHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHH
Confidence 4444455779999999998654
No 5
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=67.46 E-value=4.7 Score=25.97 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=16.1
Q ss_pred CCChhHHHHHHHHHHHHHHHHH
Q 030601 121 PQSQKEAELFRNYLKQIREETS 142 (174)
Q Consensus 121 P~~~~e~d~lR~Yl~Q~RqEl~ 142 (174)
|++..-.|.|++|+.+||+=+.
T Consensus 8 Pg~~a~~e~l~~Y~~~L~~Yin 29 (36)
T smart00309 8 PGDDASPEDLRQYLAALREYIN 29 (36)
T ss_pred CCCCCCHHHHHHHHHHHHHHHH
Confidence 4444445679999999998654
No 6
>PF09254 Endonuc-FokI_C: Restriction endonuclease FokI, C terminal; InterPro: IPR015334 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the C-terminal domain of FokI restriction endonucleases, which adopts a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. FokI recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand [, ].; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=58.84 E-value=13 Score=31.71 Aligned_cols=32 Identities=28% Similarity=0.686 Sum_probs=21.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhhcc
Q 030601 124 QKEAELFRNYLKQIREETSGRLLSVAYRPNGTPNKWWLAFAK 165 (174)
Q Consensus 124 ~~e~d~lR~Yl~Q~RqEl~~RL~ervy~~~~~psKwWm~FaK 165 (174)
-..+|.|-.|+.+-|.- ++.-.|+|||-+|-+
T Consensus 89 i~q~DeM~RYI~~n~~R----------d~~~npnkWWe~f~~ 120 (189)
T PF09254_consen 89 ISQADEMIRYIEENQER----------DEKRNPNKWWENFPE 120 (189)
T ss_dssp HHHHHHHHHHHHHHHH------------TTTSTT-GGGGS-T
T ss_pred cccHHHHHHHHHHHhcc----------cccCCCchhHHhccc
Confidence 46778898898877642 222579999999976
No 7
>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed
Probab=48.65 E-value=21 Score=35.90 Aligned_cols=100 Identities=16% Similarity=0.218 Sum_probs=65.2
Q ss_pred hHHHHHHhhhhhccccccccCCCCceehHhHHHHHHHHHHHhhcCCCHHHHHHHHHHhcccCCCCCCCC------CCCCC
Q 030601 42 IVDEAITFFRANVFFRNFDIKSSADKLLIYLTFYINVALKRLEGRRTLAEGTKAIINLGLEKVPVPGEP------NFPFP 115 (174)
Q Consensus 42 IIDEal~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CLkkl~~~~~~~ea~k~l~~la~~~F~iPGd~------gFpLn 115 (174)
+.|=+.++|=+-.--+.||=+|..+--+-+..+++.+|+.+++.. - .-..+|||.++-. =||++
T Consensus 573 l~d~~~~ly~~~a~l~r~~~~~~~~~~~~l~~~~~~~~~~~~~~~------~----~~~~~n~p~~~~~~~~~~~~~p~g 642 (777)
T PRK09463 573 LGDILSQLYLASAVLKRYEDEGRPEADLPLVHWAVQDALYQAEQA------L----DGLLRNFPNRVVAGLLRVLVFPLG 642 (777)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHH------H----HHHHHcCCchHHHHHHHHeeeCCC
Confidence 345566677666667777766543333677888888888876542 1 1234578877544 49999
Q ss_pred ccccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 030601 116 GLFALPQSQKEAELFRNYLKQIREETSGRLLSVAYRPN 153 (174)
Q Consensus 116 ~~y~~P~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy~~~ 153 (174)
..|.+|+|+-..+.-+.-++. -++-.||..-+|-.+
T Consensus 643 ~~~~~p~d~~~~~~~~~~~~~--~~~r~~l~~~~~~~~ 678 (777)
T PRK09463 643 RRYRAPSDKLDHQVAKLLQTP--SATRDRLTRGQYLPP 678 (777)
T ss_pred CCCCCCCHHHHHHHHHHHhCC--cHHHHHHhCCCCCCC
Confidence 999999987665554443322 355678888888643
No 8
>PF14802 TMEM192: TMEM192 family
Probab=39.44 E-value=48 Score=28.79 Aligned_cols=61 Identities=21% Similarity=0.280 Sum_probs=42.7
Q ss_pred HHHhhcCCCHHHHHHHHHHh-cccCCCCCCCCCCCCCccccCCCChh-----HHHHHHHHHHHHHHHHHHHHHh
Q 030601 80 LKRLEGRRTLAEGTKAIINL-GLEKVPVPGEPNFPFPGLFALPQSQK-----EAELFRNYLKQIREETSGRLLS 147 (174)
Q Consensus 80 Lkkl~~~~~~~ea~k~l~~l-a~~~F~iPGd~gFpLn~~y~~P~~~~-----e~d~lR~Yl~Q~RqEl~~RL~e 147 (174)
..|.++.+...|+.++.... ...+-+++|+-|| -.+ .+.+ .+| |=.||+|=-..|+.||++
T Consensus 168 V~kFN~~~~~PDv~~~~~~~~~~~~~~~~~e~g~-r~~-----~~~eellEkQad-lI~yLk~hn~~L~~ril~ 234 (236)
T PF14802_consen 168 VRKFNKARPPPDVLREEYSRSYLYPSSSSSELGF-RDG-----SSLEELLEKQAD-LIRYLKEHNARLSRRILA 234 (236)
T ss_pred HHHHhccCCCCCCchhhhccccCCCCCCccccCC-cCC-----CCHHHHHHHHHH-HHHHHHHHHHHHHHHHHh
Confidence 45567776777888877665 5678899999999 222 2222 234 446999999999999875
No 9
>PF09317 DUF1974: Domain of unknown function (DUF1974); InterPro: IPR015396 This C-terminal domain is functionally uncharacterised and is predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases. ; GO: 0003995 acyl-CoA dehydrogenase activity, 0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase, 0055114 oxidation-reduction process
Probab=36.30 E-value=36 Score=30.39 Aligned_cols=94 Identities=18% Similarity=0.295 Sum_probs=66.3
Q ss_pred HhhhhhccccccccCCCCceehHhHHHHHHHHHHHhhcCCCHHHHHHHHHHhcccCCCCCCCC------CCCCCccccCC
Q 030601 48 TFFRANVFFRNFDIKSSADKLLIYLTFYINVALKRLEGRRTLAEGTKAIINLGLEKVPVPGEP------NFPFPGLFALP 121 (174)
Q Consensus 48 ~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CLkkl~~~~~~~ea~k~l~~la~~~F~iPGd~------gFpLn~~y~~P 121 (174)
++|-+-..-|.||=.|.-+--+-++-+-+++||-++|.. +.. .+.|||.|+-. -||++--|.+|
T Consensus 108 ~LYl~sAvLKr~ed~Gr~~~Dlplv~wa~~~~l~~~q~A---------l~~-~~~NfP~r~~~~llR~l~fP~G~~~~~P 177 (284)
T PF09317_consen 108 QLYLASAVLKRFEDEGRPEEDLPLVHWAMQDALYRIQEA---------LDG-ILRNFPNRALAWLLRALVFPLGRRYRKP 177 (284)
T ss_pred HHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHH---------HHH-HHHhCCChHHHHHHHHhhcCCCCCCCCC
Confidence 466677777889988877777888888999999876542 222 35688887654 49999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 030601 122 QSQKEAELFRNYLKQIREETSGRLLSVAYRPN 153 (174)
Q Consensus 122 ~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy~~~ 153 (174)
+|+-..+.-+.-++ =-+.-.||..-+|-+.
T Consensus 178 sD~l~~~vA~~l~~--p~~~RdRLt~~~y~~~ 207 (284)
T PF09317_consen 178 SDKLGHEVARLLMT--PGAARDRLTAGIYLPR 207 (284)
T ss_pred ChHHHHHHHHHHcC--ChHHHHHHhCCCCCCC
Confidence 98765555443321 2345578888888644
No 10
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=35.51 E-value=24 Score=29.12 Aligned_cols=21 Identities=5% Similarity=0.158 Sum_probs=16.3
Q ss_pred HHHHHHhhcCCCHHHHHHHHH
Q 030601 77 NVALKRLEGRRTLAEGTKAII 97 (174)
Q Consensus 77 ~~CLkkl~~~~~~~ea~k~l~ 97 (174)
-+++..+.++.|-..|.+.|+
T Consensus 6 l~~f~~v~~~gs~s~AA~~L~ 26 (275)
T PRK03601 6 LKTFLEVSRTRHFGRAAESLY 26 (275)
T ss_pred HHHHHHHHHcCCHHHHHHHhC
Confidence 367778888888888888774
No 11
>PRK13026 acyl-CoA dehydrogenase; Reviewed
Probab=35.14 E-value=28 Score=35.03 Aligned_cols=92 Identities=15% Similarity=0.227 Sum_probs=65.5
Q ss_pred HhhhhhccccccccCCCCceehHhHHHHHHHHHHHhhcCCCHHHHHHHHHHhcccCCCCCCCC------CCCCCccccCC
Q 030601 48 TFFRANVFFRNFDIKSSADKLLIYLTFYINVALKRLEGRRTLAEGTKAIINLGLEKVPVPGEP------NFPFPGLFALP 121 (174)
Q Consensus 48 ~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CLkkl~~~~~~~ea~k~l~~la~~~F~iPGd~------gFpLn~~y~~P 121 (174)
+++-+-...|.||=.|.-.-=|.++-+-+++||-++++. +.. .++|||.++-. =||+|..|.+|
T Consensus 579 ~ly~~~a~lk~~~~~~~~~~~~~~~~~~~~~~~~~~~~a---------~~~-~~~n~p~~~~~~~~~~~~~p~g~~~~~p 648 (774)
T PRK13026 579 QLYLASATLKRFEDNGRQQDDLPAVHYAMQDCLHLAAKA---------LDE-FLRNFPNRPVAWLLRALIFPLGNHFRAP 648 (774)
T ss_pred HHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHHHHHHH---------HHH-HHHhCCchHHHHHHhheeeCCCCCCCCC
Confidence 466677778899998866666688888899999876542 222 35788887543 49999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 030601 122 QSQKEAELFRNYLKQIREETSGRLLSVAYR 151 (174)
Q Consensus 122 ~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy~ 151 (174)
+|+-..+.-+.-++. -+.-.||..-+|-
T Consensus 649 ~d~~~~~~a~~~~~~--~~~r~~l~~~~~~ 676 (774)
T PRK13026 649 SDKLARQLAELMMTP--GPARDRLTALCYI 676 (774)
T ss_pred CHHHHHHHHHHHhCC--hHHHHHHhCcCCC
Confidence 987665554443332 2555788888885
No 12
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=35.13 E-value=1.2e+02 Score=28.12 Aligned_cols=48 Identities=15% Similarity=0.206 Sum_probs=37.3
Q ss_pred CCCCCCCCCCC-CCccccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhc
Q 030601 103 KVPVPGEPNFP-FPGLFALPQSQKEAELFRNYLKQIREETSGRLLSVAY 150 (174)
Q Consensus 103 ~F~iPGd~gFp-Ln~~y~~P~~~~e~d~lR~Yl~Q~RqEl~~RL~ervy 150 (174)
.|..+|+.+++ ++..|..+....-++.+++|++++=|.....+++++=
T Consensus 142 ~~~~~~~~~~~~~~vs~~a~t~edAq~~L~gyI~~~s~~v~~el~~~l~ 190 (347)
T COG3765 142 SFKPGGFDLATNLTVSFTAETAEDAQDLLRGYIAFVSQKVAQELLDNLK 190 (347)
T ss_pred hccCCccccchhheeeeecCCcHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 34556666665 7777888876666799999999999999988887764
No 13
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=31.72 E-value=41 Score=20.27 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 030601 126 EAELFRNYLKQIREETS 142 (174)
Q Consensus 126 e~d~lR~Yl~Q~RqEl~ 142 (174)
+.|.||.||+++=-||-
T Consensus 3 ~e~kLr~YLkr~t~eL~ 19 (27)
T PF08990_consen 3 NEDKLRDYLKRVTAELR 19 (27)
T ss_dssp -HCHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 56889999998766653
No 14
>PF12531 DUF3731: DNA-K related protein ; InterPro: IPR021030 Proteins in this family are bacterial proteins of approximately 250 amino acids in length. There are two conserved sequence motifs: RPG and WRR. The proteins in this family are frequently annotated as DNA-K related proteins however there is little accompanying literature to confirm this.
Probab=29.78 E-value=3.7e+02 Score=23.86 Aligned_cols=107 Identities=18% Similarity=0.306 Sum_probs=66.4
Q ss_pred cchHHHHHHhhhhhccccccccCCCCceehHhHHHHHHHHHHHhhcCCCHHHHHHHHHHhcccCCCCCCCCCC-CCCccc
Q 030601 40 TDIVDEAITFFRANVFFRNFDIKSSADKLLIYLTFYINVALKRLEGRRTLAEGTKAIINLGLEKVPVPGEPNF-PFPGLF 118 (174)
Q Consensus 40 ~DIIDEal~~FrAN~fFrnfEIKg~aDR~LIYltLyi~~CLkkl~~~~~~~ea~k~l~~la~~~F~iPGd~gF-pLn~~y 118 (174)
.-=|++.-.+|...+-|. ..+.--.=|-||+ .+++..-+ .+.|.+++. .+..+--|+...= +++
T Consensus 26 ~wRv~qlW~l~~~g~q~~-----~~~q~w~ewW~lW-----RRiAGGL~-~~qQ~~l~~-~ia~~l~p~~~~~~~~~--- 90 (249)
T PF12531_consen 26 DWRVEQLWKLYQQGIQFP-----KDAQVWSEWWTLW-----RRIAGGLN-EGQQEQLFD-DIAPYLQPAAQRNRKKP--- 90 (249)
T ss_pred HHHHHHHHHHhhcccCCC-----CcchHHHHHHHHH-----HHHHcCCC-HHHHHHHHH-HHHHHhCcccccccccc---
Confidence 344666666666655553 1222233355555 88998888 444555554 3344445555442 333
Q ss_pred cCCCChhHHHHHHHHH------HHHHHHHHHHHHhhhcCCCCCCchhhh
Q 030601 119 ALPQSQKEAELFRNYL------KQIREETSGRLLSVAYRPNGTPNKWWL 161 (174)
Q Consensus 119 ~~P~~~~e~d~lR~Yl------~Q~RqEl~~RL~ervy~~~~~psKwWm 161 (174)
..+...+..|++|-.- -+.+.|+|..|++|+=.++..+.-||.
T Consensus 91 ~~~~~~~~~emvRl~asLErL~~~~K~elg~wll~rL~~~~~~~~~wWA 139 (249)
T PF12531_consen 91 KGPQPQSYDEMVRLAASLERLPVEDKIELGEWLLKRLQKPSESAQHWWA 139 (249)
T ss_pred cccCccCHHHHHHHHHhhccCCHHHHHHHHHHHHHHhcCCCCCcchHHH
Confidence 4556666677777553 367999999999997776677888985
No 15
>PRK11767 SpoVR family protein; Provisional
Probab=29.41 E-value=43 Score=32.44 Aligned_cols=32 Identities=34% Similarity=0.710 Sum_probs=21.8
Q ss_pred HHhhhhhccccccccCCCCceehHhHHH---HHHHHHH
Q 030601 47 ITFFRANVFFRNFDIKSSADKLLIYLTF---YINVALK 81 (174)
Q Consensus 47 l~~FrAN~fFrnfEIKg~aDR~LIYltL---yi~~CLk 81 (174)
.+|||.|.+||... .|+.+|=|+.. ||.+|-.
T Consensus 120 ndFFKNN~~F~~~t---~a~~ild~~~~~~~~I~~~e~ 154 (498)
T PRK11767 120 NSFFKNNYLFRTWT---DASSIIDYLVFAKNYIAECEE 154 (498)
T ss_pred hhhhhccHHhhCCc---chHHHHHHHHHHHHHHHHHHH
Confidence 47999999999763 36666666543 5666643
No 16
>PF08606 Prp19: Prp19/Pso4-like; InterPro: IPR013915 This region is found specifically in PRP19-like protein. The region represented by this protein covers the sequence implicated in self-interaction and a coiled-coiled motif []. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly [].
Probab=29.06 E-value=81 Score=23.06 Aligned_cols=18 Identities=39% Similarity=0.373 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 030601 128 ELFRNYLKQIREETSGRL 145 (174)
Q Consensus 128 d~lR~Yl~Q~RqEl~~RL 145 (174)
=.+|+=|.|+||||+..|
T Consensus 25 f~LRk~l~~~rqELs~aL 42 (70)
T PF08606_consen 25 FTLRKQLDQTRQELSHAL 42 (70)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 358999999999998654
No 17
>TIGR03779 Bac_Flav_CT_M Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=25.46 E-value=87 Score=29.56 Aligned_cols=36 Identities=14% Similarity=0.393 Sum_probs=27.5
Q ss_pred CCccccCCCChhHHHHHHHHHHHHHHHHH------------HHHHhhhc
Q 030601 114 FPGLFALPQSQKEAELFRNYLKQIREETS------------GRLLSVAY 150 (174)
Q Consensus 114 Ln~~y~~P~~~~e~d~lR~Yl~Q~RqEl~------------~RL~ervy 150 (174)
|+++|..|.+..|.+ ++.=+.|++.++. ..|+||-|
T Consensus 133 LgsFYe~~~~~~e~e-l~~~veel~~~l~~~~~~~~~~~eq~almEKsy 180 (410)
T TIGR03779 133 LGSFYEYPKTDEEKE-LLREVEELESRLATEPSPAPELEEQLALMEKSY 180 (410)
T ss_pred hhhhccCCCCchhHH-HHHHHHHHHHHHhhhcccccchhHHHHHHHHhH
Confidence 778899999888888 7777888877664 45677665
No 18
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=25.31 E-value=30 Score=29.34 Aligned_cols=56 Identities=27% Similarity=0.492 Sum_probs=38.6
Q ss_pred ccccCCCCCCc---ceeeCccccccccCCCCCCCCCCCCCcchHHHHHHhhhhhccccccccCC
Q 030601 3 YHSSFVDEEGV---TKACGCPLLPLKSHIKGPAPASDQDRTDIVDEAITFFRANVFFRNFDIKS 63 (174)
Q Consensus 3 YHS~f~~~~~~---~~~~g~alLPlrt~~rGPAp~~~~~~~DIIDEal~~FrAN~fFrnfEIKg 63 (174)
.|+++-|-++- ..-|||+.|-+-+..-||..-- ..||=+|||..|+-|.- .|||.-
T Consensus 40 Ih~TygdiEgkkl~DLgcgcGmLs~a~sm~~~e~vl---GfDIdpeALEIf~rNae--EfEvqi 98 (185)
T KOG3420|consen 40 IHNTYGDIEGKKLKDLGCGCGMLSIAFSMPKNESVL---GFDIDPEALEIFTRNAE--EFEVQI 98 (185)
T ss_pred HHhhhccccCcchhhhcCchhhhHHHhhcCCCceEE---eeecCHHHHHHHhhchH--Hhhhhh
Confidence 47888643332 2235699998777666665432 48999999999999974 566654
No 19
>PRK13291 metal-dependent hydrolase; Provisional
Probab=23.51 E-value=2e+02 Score=23.07 Aligned_cols=36 Identities=11% Similarity=0.378 Sum_probs=24.7
Q ss_pred CCCCCCCccccCCC--ChhHHHHHHHHHHHHHHHHHHHH
Q 030601 109 EPNFPFPGLFALPQ--SQKEAELFRNYLKQIREETSGRL 145 (174)
Q Consensus 109 d~gFpLn~~y~~P~--~~~e~d~lR~Yl~Q~RqEl~~RL 145 (174)
+.-||++. |.+|. +..+-+.+-+-|.+.+++|...|
T Consensus 3 ~~~~~~~~-~~~~~~~~~~~~~~~i~~l~~~~~~l~~~l 40 (173)
T PRK13291 3 DLRYPIGQ-FQYPEEITEEQIQEWIAEIEALPNELRAAV 40 (173)
T ss_pred CCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35699999 88885 45555666666777777775444
No 20
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=23.35 E-value=68 Score=25.42 Aligned_cols=39 Identities=15% Similarity=0.370 Sum_probs=12.7
Q ss_pred HhHHHHHHHHHHHhhcCCCHHHHHHHHHHhcccCCCCCCCCCCCCCccc
Q 030601 70 IYLTFYINVALKRLEGRRTLAEGTKAIINLGLEKVPVPGEPNFPFPGLF 118 (174)
Q Consensus 70 IYltLyi~~CLkkl~~~~~~~ea~k~l~~la~~~F~iPGd~gFpLn~~y 118 (174)
|=+||+|.=|++|+.|..+- +.+- -|-|+|..=||+++=
T Consensus 78 Ig~Illi~y~irR~~Kk~~~-~~~p---------~P~~~d~~~p~~~~~ 116 (122)
T PF01102_consen 78 IGIILLISYCIRRLRKKSSS-DVQP---------LPEEDDTDVPLSSVE 116 (122)
T ss_dssp HHHHHHHHHHHHHHS----------------------------------
T ss_pred HHHHHHHHHHHHHHhccCCC-CCCC---------CCCCCCCCCCcceee
Confidence 44678999999999987552 2111 344456888888853
No 21
>COG2719 SpoVR Uncharacterized conserved protein [Function unknown]
Probab=22.17 E-value=79 Score=30.62 Aligned_cols=42 Identities=29% Similarity=0.523 Sum_probs=32.2
Q ss_pred CcchHHHHH---------HhhhhhccccccccCCCCceehHhHH---HHHHHHHHHh
Q 030601 39 RTDIVDEAI---------TFFRANVFFRNFDIKSSADKLLIYLT---FYINVALKRL 83 (174)
Q Consensus 39 ~~DIIDEal---------~~FrAN~fFrnfEIKg~aDR~LIYlt---Lyi~~CLkkl 83 (174)
+.++++.|| +|||.|.+||.+ +.|--.+=|+. =||.+|..++
T Consensus 100 eNtl~~Q~LV~AHv~GHndFFKNN~lFr~w---tdas~iv~~l~~aa~~I~~~e~~~ 153 (495)
T COG2719 100 ENTLAMQALVMAHVYGHNDFFKNNYLFRLW---TDASDIVDYLEFAADYIAECEERH 153 (495)
T ss_pred hhHHHHHHHHHHHHHhhhhhhcCCeeeecc---CchHHHHHHHHHHHHHHHHHHHHh
Confidence 567888877 799999999999 55555555554 4899999874
No 22
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=22.00 E-value=65 Score=26.89 Aligned_cols=20 Identities=10% Similarity=0.247 Sum_probs=14.9
Q ss_pred HHHHHhhcCCCHHHHHHHHH
Q 030601 78 VALKRLEGRRTLAEGTKAII 97 (174)
Q Consensus 78 ~CLkkl~~~~~~~ea~k~l~ 97 (174)
+++..+.++.|...|.++|+
T Consensus 11 ~~f~~v~e~gs~s~AA~~L~ 30 (305)
T CHL00180 11 RILKAIATEGSFKKAAESLY 30 (305)
T ss_pred HHHHHHHHcCCHHHHHHHhc
Confidence 56667777888888888774
No 23
>PF13709 DUF4159: Domain of unknown function (DUF4159)
Probab=21.86 E-value=76 Score=26.52 Aligned_cols=22 Identities=41% Similarity=0.857 Sum_probs=16.9
Q ss_pred CCCCCCCCCccccCCCChhHHHHHHHHHHH
Q 030601 107 PGEPNFPFPGLFALPQSQKEAELFRNYLKQ 136 (174)
Q Consensus 107 PGd~gFpLn~~y~~P~~~~e~d~lR~Yl~Q 136 (174)
||...++| +.+|.+.||+||++
T Consensus 60 ~g~~~~~~--------s~~e~~~Lr~Yl~~ 81 (207)
T PF13709_consen 60 PGHGDFPL--------SDEEIANLRRYLEN 81 (207)
T ss_pred eCCCCCCC--------CHHHHHHHHHHHHc
Confidence 66666644 67899999999865
No 24
>COG5500 Predicted integral membrane protein [Function unknown]
Probab=21.85 E-value=54 Score=27.07 Aligned_cols=26 Identities=31% Similarity=0.528 Sum_probs=20.7
Q ss_pred CCCCcccc--CCCChhHHHHHHHHHHHH
Q 030601 112 FPFPGLFA--LPQSQKEAELFRNYLKQI 137 (174)
Q Consensus 112 FpLn~~y~--~P~~~~e~d~lR~Yl~Q~ 137 (174)
-|||.-.+ .|++.+-++.|.+||+|-
T Consensus 108 VPLNdALAaa~Pas~~ga~lW~~yLt~W 135 (159)
T COG5500 108 VPLNDALAAANPASTDGAKLWTSYLTNW 135 (159)
T ss_pred ccchHHHhhcCCCcccHHHHHHHHHHhH
Confidence 57886543 388999999999999983
No 25
>PF04741 InvH: InvH outer membrane lipoprotein; InterPro: IPR006830 This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion [, ].; GO: 0009405 pathogenesis
Probab=21.85 E-value=53 Score=26.88 Aligned_cols=36 Identities=28% Similarity=0.466 Sum_probs=27.2
Q ss_pred ceeeCccccccccCCCCCCCCCC-----CCCcchHHHHHHh
Q 030601 14 TKACGCPLLPLKSHIKGPAPASD-----QDRTDIVDEAITF 49 (174)
Q Consensus 14 ~~~~g~alLPlrt~~rGPAp~~~-----~~~~DIIDEal~~ 49 (174)
..++|||-+|.-+...-|+..++ .-..|-|||+..+
T Consensus 11 f~ligcaqv~~~ss~s~p~qq~~~qkeq~a~a~sid~c~sl 51 (147)
T PF04741_consen 11 FLLIGCAQVPSPSSGSKPAQQPEAQKEQQANADSIDECMSL 51 (147)
T ss_pred HHHhhhccCCCCcccCCcccCcchhHHHHhccccHHHHHcC
Confidence 35789999999999888887543 1236889998754
No 26
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=21.78 E-value=1.9e+02 Score=18.60 Aligned_cols=14 Identities=29% Similarity=0.563 Sum_probs=9.1
Q ss_pred CCCchhhhhhcccc
Q 030601 154 GTPNKWWLAFAKRK 167 (174)
Q Consensus 154 ~~psKwWm~FaKRk 167 (174)
.-.+.|+-.|-||-
T Consensus 47 ~~s~~W~~~F~~Rh 60 (66)
T PF03221_consen 47 KASKGWLDRFKKRH 60 (66)
T ss_dssp S--CHHHHHHHHHT
T ss_pred CcccHHHHHHHHHc
Confidence 34457888898874
No 27
>COG4114 FhuF Uncharacterized Fe-S protein [General function prediction only]
Probab=21.77 E-value=80 Score=28.11 Aligned_cols=40 Identities=25% Similarity=0.489 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh-----hcC---CCCCCchhhhhhccc
Q 030601 127 AELFRNYLKQIREETSGRLLSV-----AYR---PNGTPNKWWLAFAKR 166 (174)
Q Consensus 127 ~d~lR~Yl~Q~RqEl~~RL~er-----vy~---~~~~psKwWm~FaKR 166 (174)
.-.|-=||+.+||++|.++++- +|. ++|.+|-+|.|...|
T Consensus 176 gyli~wyl~e~k~~lg~~~~~s~r~~lf~e~ll~nG~dnPl~rtv~~r 223 (251)
T COG4114 176 GYLINWYLTEMKQLLGEDLVESLRHALFFEKLLPNGQDNPLWRTVVLR 223 (251)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhccCCCCCcHHHHHHHh
Confidence 4567789999999999999873 221 348999999988766
No 28
>PF00631 G-gamma: GGL domain; InterPro: IPR015898 This entry represents the G protein gamma subunit and the GGL (G protein gamma-like) domain, which are related in sequence and are comprised of an extended alpha-helical polypeptide. The G protein gamma subunit forms a stable dimer with the beta subunit, but it does not make any contact with the alpha subunit, which contacts the opposite face of the beta subunit. The GGL domain is found in several RGS (regulators of G protein signaling) proteins. GGL domains can interact with beta subunits to form novel dimers that prevent gamma subunit binding, and may prevent heterotrimer formation by inhibiting alpha subunit binding. The interaction between G protein beta-5 neuro-specific isoforms and RGS GGL domains may represent a general mode of binding between beta-propeller proteins and their partners [].; GO: 0004871 signal transducer activity, 0007186 G-protein coupled receptor protein signaling pathway, 0005834 heterotrimeric G-protein complex; PDB: 3PSC_G 3SN6_G 1OMW_G 2BCJ_G 1GG2_G 3PVW_G 3PVU_G 3AH8_G 3CIK_G 1GP2_G ....
Probab=21.28 E-value=93 Score=21.44 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 030601 125 KEAELFRNYLKQIREETSG 143 (174)
Q Consensus 125 ~e~d~lR~Yl~Q~RqEl~~ 143 (174)
++.+.++.-+.|||+|+..
T Consensus 2 ~~~~~l~~ei~~L~~el~~ 20 (68)
T PF00631_consen 2 QEKDQLKREIEQLRQELER 20 (68)
T ss_dssp THHHHHHHHHHHHHHHHTS
T ss_pred hHHHHHHHHHHHHHHHHcc
Confidence 4677888888999999863
No 29
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=21.13 E-value=78 Score=25.98 Aligned_cols=20 Identities=0% Similarity=0.027 Sum_probs=13.8
Q ss_pred HHHHHhhcCCCHHHHHHHHH
Q 030601 78 VALKRLEGRRTLAEGTKAII 97 (174)
Q Consensus 78 ~CLkkl~~~~~~~ea~k~l~ 97 (174)
+++..+.++.|-..|.+.|+
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~ 26 (296)
T PRK09906 7 RYFVAVAEELNFTKAAEKLH 26 (296)
T ss_pred HHHHHHHhhCCHHHHHHHhC
Confidence 34556667778788887775
No 30
>PF10155 DUF2363: Uncharacterized conserved protein (DUF2363); InterPro: IPR019312 This entry represents a region of 120 amino acids in proteins conserved from plants to humans. Their function is not known.
Probab=20.87 E-value=63 Score=25.45 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=17.7
Q ss_pred HhHHHHHHHHHHHhhcCCCHHHH
Q 030601 70 IYLTFYINVALKRLEGRRTLAEG 92 (174)
Q Consensus 70 IYltLyi~~CLkkl~~~~~~~ea 92 (174)
=|+..||+.|++.++.-+.+...
T Consensus 53 efl~~yI~~cI~~ce~~kd~~~q 75 (126)
T PF10155_consen 53 EFLHMYISNCIKSCESIKDKYMQ 75 (126)
T ss_pred HHHHHHHHHHHHHHHhhcccccc
Confidence 48899999999999876554333
Done!