Query gi|254780297|ref|YP_003064710.1| peptide deformylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 170
No_of_seqs 111 out of 3172
Neff 6.1
Searched_HMMs 39220
Date Sun May 29 15:22:21 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780297.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12846 peptide deformylase; 100.0 0 0 408.3 11.1 165 1-167 1-166 (168)
2 PRK00150 def peptide deformyla 100.0 0 0 406.6 10.4 163 1-165 1-163 (163)
3 COG0242 Def N-formylmethionyl- 100.0 0 0 398.0 12.0 167 1-167 1-168 (168)
4 TIGR00079 pept_deformyl peptid 100.0 0 0 373.6 8.1 160 4-163 2-187 (188)
5 pfam01327 Pep_deformylase Poly 100.0 0 0 372.5 8.4 153 3-155 1-154 (155)
6 cd00487 Pep_deformylase Polype 100.0 0 0 355.9 8.9 141 6-146 1-141 (141)
7 PRK09218 peptide deformylase; 100.0 0 0 317.8 7.8 134 2-146 1-136 (136)
8 KOG3137 consensus 100.0 1.3E-44 0 289.4 7.7 151 4-154 79-246 (267)
9 COG4740 Predicted metalloprote 96.0 0.0021 5.4E-08 41.4 0.8 73 70-144 73-160 (176)
10 TIGR01388 rnd ribonuclease D; 54.6 3.7 9.5E-05 21.8 0.2 80 43-132 35-139 (374)
11 PRK10947 global DNA-binding tr 51.7 3.8 9.7E-05 21.8 -0.2 30 110-139 95-124 (135)
12 pfam09092 Lyase_N Lyase, N ter 42.3 22 0.00056 17.2 2.5 58 92-151 102-160 (178)
13 PRK10328 DNA binding protein, 39.5 8.7 0.00022 19.6 0.1 36 108-145 93-128 (134)
14 KOG0400 consensus 37.6 21 0.00053 17.3 1.8 44 14-57 11-55 (151)
15 cd06401 PB1_TFG The PB1 domain 31.6 19 0.0005 17.5 0.9 37 100-136 34-70 (81)
16 COG0281 SfcA Malic enzyme [Ene 30.0 13 0.00032 18.7 -0.4 60 45-111 274-354 (432)
17 COG3129 Predicted SAM-dependen 26.6 55 0.0014 14.8 2.8 100 9-112 45-159 (292)
18 TIGR01722 MMSDH methylmalonate 24.7 24 0.0006 17.0 0.3 30 110-139 397-427 (478)
19 TIGR02476 BluB cob(II)yrinic a 23.0 51 0.0013 15.0 1.7 32 28-64 29-60 (206)
20 pfam12388 Peptidase_M57 Dual-a 22.9 17 0.00043 17.9 -0.8 25 128-152 131-155 (211)
21 cd04327 ZnMc_MMP_like_3 Zinc-d 22.7 30 0.00076 16.4 0.5 51 92-146 58-108 (198)
22 cd00203 ZnMc Zinc-dependent me 22.2 28 0.00071 16.6 0.2 43 90-145 65-111 (167)
23 pfam09212 CBM27 Carbohydrate b 21.6 53 0.0014 14.9 1.6 81 67-154 92-172 (173)
24 PRK03979 ADP-specific phosphof 21.6 56 0.0014 14.8 1.7 79 42-120 89-192 (451)
25 cd03765 proteasome_beta_bacter 21.3 67 0.0017 14.3 2.0 12 53-64 121-132 (236)
26 TIGR00368 TIGR00368 Mg chelata 20.5 42 0.0011 15.5 0.9 41 92-159 274-316 (505)
No 1
>PRK12846 peptide deformylase; Reviewed
Probab=100.00 E-value=0 Score=408.32 Aligned_cols=165 Identities=41% Similarity=0.637 Sum_probs=157.6
Q ss_pred CCCCCHHHCCCCCCCCCCCCCCCCC-HHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCC
Q ss_conf 9877364576931052121378788-899999999998650047642130220144000377316432334821001644
Q gi|254780297|r 1 MVKKPLVIFPDPILRRVSRPIEKIN-SDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPK 79 (170)
Q Consensus 1 M~~~~Iv~~~dp~L~~~~~~v~~~~-~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~ 79 (170)
|++++|++||||+||++|.||+.++ +++++|++||++||++++|+||||||||+++|+||++++++. ..+.+||||+
T Consensus 1 Mai~~Iv~~pdp~Lr~~a~~V~~~d~~~l~~li~dM~~tM~~~~GvGLAApQIG~~~ri~vi~~~~~~--~~~~v~INP~ 78 (168)
T PRK12846 1 MAIRPILKMPDPRLLTPAEPVTAFDSPELQALIDDMFETMRAANGVGLAAPQIGVSLRVVVFGLGDDA--VPRTVLINPV 78 (168)
T ss_pred CCCCCCCCCCCHHHHCCCEECCCCCCHHHHHHHHHHHHHHHHCCCEEEEHHHCCCCEEEEEEECCCCC--CCCEEEECCE
T ss_conf 98344002799799380627886893999999999999998789959885566974139999758877--7828999984
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHH
Q ss_conf 20100000111000001223210121100000246323585579997297646432700131976853647889999999
Q gi|254780297|r 80 IITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMIT 159 (170)
Q Consensus 80 I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~ 159 (170)
|+..|+++..++|||||+||+++.|+||.+|+|+|+|++|+.++.+++||+|||||||+|||||+||+||+|++||+++.
T Consensus 79 I~~~s~~~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~iQHE~DHL~G~Lf~Drls~~kr~~~~ 158 (168)
T PRK12846 79 IEPESPEMEEGWEGCLSVPGLRGEVERYARVRVRGQDLDGKPIEREAEGFLARCVQHEIDHLDGILYPSRLSRLKRFGFL 158 (168)
T ss_pred EECCCCCEEEEECCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEECCEEEEEEHHHHCCCCEEHHHHCCHHHHHHHH
T ss_conf 76478966973067105799777788754999999868998999999772241306273751989606718999999999
Q ss_pred HHHHHHHH
Q ss_conf 99999985
Q gi|254780297|r 160 KKMSKLVQ 167 (170)
Q Consensus 160 ~k~~k~~k 167 (170)
+|++|..+
T Consensus 159 kk~~K~l~ 166 (168)
T PRK12846 159 EVLEKGLD 166 (168)
T ss_pred HHHHHCCC
T ss_conf 99865128
No 2
>PRK00150 def peptide deformylase; Reviewed
Probab=100.00 E-value=0 Score=406.60 Aligned_cols=163 Identities=47% Similarity=0.841 Sum_probs=157.4
Q ss_pred CCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCCC
Q ss_conf 98773645769310521213787888999999999986500476421302201440003773164323348210016442
Q gi|254780297|r 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKI 80 (170)
Q Consensus 1 M~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~I 80 (170)
|++++|++||||+||++|+||+.+++++++|++||++||++++|+||||||||+++|+||++++++. ..+.+||||+|
T Consensus 1 M~i~~Iv~~~dpvLr~~a~~V~~~~~~~~~li~dM~~tM~~~~GvGLAApQIG~~~ri~vi~~~~~~--~~~~v~INP~I 78 (163)
T PRK00150 1 MAILPILRYGDPRLRKVAKPVEPVDDELRKLIDDMLETMYAAPGIGLAAPQVGVSKRIIVIDVSEEK--DEPLVLINPEI 78 (163)
T ss_pred CCCCCCCCCCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHCCCCEEEHHHCCCCEEEEEEECCCCC--CCCEEEECCEE
T ss_conf 9822011079979947373799799899999999999998689948885665975018999825678--86269999864
Q ss_pred CCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHHH
Q ss_conf 01000001110000012232101211000002463235855799972976464327001319768536478899999999
Q gi|254780297|r 81 ITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITK 160 (170)
Q Consensus 81 ~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~~ 160 (170)
++.|+++..++|||||+||+++.|+||.+|+|+|+|++|+.++.+++||+|||||||+|||||+||+||+|+++|+++.+
T Consensus 79 ~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~Drl~~~~~~~~~k 158 (163)
T PRK00150 79 IEKSGELATLEEGCLSVPGVYGEVPRPERVTVKALDRDGKPFELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRQRIKK 158 (163)
T ss_pred ECCCCCEEECCCCCCCCCCCCEEEECCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHHHHCCEECHHHCCHHHHHHHHH
T ss_conf 14689788721551147999656535898999998689969999976444500132758438890067389999999999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780297|r 161 KMSKL 165 (170)
Q Consensus 161 k~~k~ 165 (170)
|++|+
T Consensus 159 k~~kl 163 (163)
T PRK00150 159 KLKKI 163 (163)
T ss_pred HHHCC
T ss_conf 98619
No 3
>COG0242 Def N-formylmethionyl-tRNA deformylase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=398.05 Aligned_cols=167 Identities=49% Similarity=0.884 Sum_probs=160.4
Q ss_pred CCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCC-CCCCCCEECCCC
Q ss_conf 9877364576931052121378788899999999998650047642130220144000377316432-334821001644
Q gi|254780297|r 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHA-HRKNPMVFINPK 79 (170)
Q Consensus 1 M~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~-~~~~~~~~iNP~ 79 (170)
||+++|+++|||+||++|+||..++++++++++||++||++++||||||||||+++|+||++++++. ....+.+||||+
T Consensus 1 m~i~~Iv~~~~p~Lr~~a~~V~~~d~~l~~li~dM~etm~~~~GVGLAApQIGi~kri~vi~~~~~~~~~~~~~vlINP~ 80 (168)
T COG0242 1 MAIREIVKYPDPRLRQVAKPVEEVDDELRQLIDDMLETMYAAEGVGLAAPQIGISKRIFVIDVEEDGRPKEPPLVLINPE 80 (168)
T ss_pred CCCCCCEECCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEHHCCCEEEEEEEECCCCCCCCCCCEEEECCE
T ss_conf 97432110897788303503301599999999999999986799066001149616699999168667676756999999
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHH
Q ss_conf 20100000111000001223210121100000246323585579997297646432700131976853647889999999
Q gi|254780297|r 80 IITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMIT 159 (170)
Q Consensus 80 I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~ 159 (170)
|++.|++....+|||||+||.++.|.||.+|+|+|+|.+|++++.+++||+|||+|||+|||||+||+||+|++++..++
T Consensus 81 I~~~~~~~~~~~EGCLSvP~~~~~V~R~~~I~V~~~D~~G~~~~~~a~G~lA~~iQHEiDHLnGvlf~D~l~~~k~~~~~ 160 (168)
T COG0242 81 IISKSEETLTGEEGCLSVPGVRGEVERPERITVKYLDRNGKPQELEAEGLLARCIQHEIDHLNGVLFIDRLSPLKRDRLK 160 (168)
T ss_pred EEECCCCCCCCCCCEEEECCCEEEEECCCEEEEEEECCCCCEEEEEECCCEEEEEEEECCCCCCEEEEEECCHHHHHHHH
T ss_conf 86637760226756686169601462563899999969999999997472557767650000758750113835440688
Q ss_pred HHHHHHHH
Q ss_conf 99999985
Q gi|254780297|r 160 KKMSKLVQ 167 (170)
Q Consensus 160 ~k~~k~~k 167 (170)
++++|+.+
T Consensus 161 ~~~~~~~~ 168 (168)
T COG0242 161 KKLKKLKK 168 (168)
T ss_pred HHHHHHCC
T ss_conf 87787429
No 4
>TIGR00079 pept_deformyl peptide deformylase; InterPro: IPR000181 Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N-terminus of nascent polypeptide chains in eubacteria 3.5.1.88 from EC. The enzyme acts as a monomer and binds a single zinc ion, catalysing the reaction:: N-formyl-L-methionine + H_2O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal . The structure of these enzymes is known , . PDF, a member of the zinc metalloproteases family, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel beta- strands that surround two perpendicular alpha-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of other metalloproteases, such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloproteases. .; GO: 0005506 iron ion binding, 0042586 peptide deformylase activity, 0006412 translation.
Probab=100.00 E-value=0 Score=373.59 Aligned_cols=160 Identities=44% Similarity=0.818 Sum_probs=152.7
Q ss_pred CCHHHC-CCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHH----------CC-----CCCEEEHHHCCCCCEEEEECCCC
Q ss_conf 736457-69310521213787888999-999999986500----------47-----64213022014400037731643
Q gi|254780297|r 4 KPLVIF-PDPILRRVSRPIEKINSDIM-NLIDNMLEVMYS----------TD-----GIGLAAVQIGVLYRLVVIDLQDH 66 (170)
Q Consensus 4 ~~Iv~~-~dp~L~~~~~~v~~~~~~~~-~li~dm~~tm~~----------~~-----GvGLAA~QIG~~~ri~vv~~~~~ 66 (170)
.+||.| |++.||++|+||+.+|..++ ++++||++||++ .+ ||||||||||+.+|+|+|++.+.
T Consensus 2 ~~vv~~Lp~~~Lr~~ak~v~~vd~~i~k~~~~dM~~~M~~~~~a~Y~G~A~~Y~~~PGiGLAApQvgi~kr~~~v~~~~~ 81 (188)
T TIGR00079 2 LEVVHYLPDDVLREIAKPVEKVDDKIRKKQLDDMIETMYAYVDASYDGLAEEYKIIPGIGLAAPQVGILKRLIVVDLEDD 81 (188)
T ss_pred CEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC
T ss_conf 50676557722524555211588368899999999999986198758742365237744101010281101587753588
Q ss_pred CC---CCCCCEECCCCCCCHHHHHHHHH--HHCCCCCCC-CHHHHHCCHHEEEEECCC-CCEEEEEEECCEEEEEEEEHH
Q ss_conf 23---34821001644201000001110--000012232-101211000002463235-855799972976464327001
Q gi|254780297|r 67 AH---RKNPMVFINPKIITFSDDFSVYQ--EGCLSIPDY-RADVKRSAFITVRYMDCN-AQHQIIYADGLLATCLQHELD 139 (170)
Q Consensus 67 ~~---~~~~~~~iNP~I~~~s~e~~~~~--EGCLS~Pg~-~~~V~R~~~I~v~~~d~~-G~~~~~~~~g~~Ar~~QHEiD 139 (170)
.+ ....++||||+|+..|.+.+... |||||+|++ ++.|.|+.+|+|+|+|.+ |++++++++||+|||+|||||
T Consensus 82 ~gvqh~~~~~~lINP~I~~~S~e~~~~~SGEGCLSvP~~~~~~V~R~~~v~i~~~d~~~gk~~~~~a~gllA~~iQHE~D 161 (188)
T TIGR00079 82 KGVQHKEKKLVLINPKIIETSEEKSGLESGEGCLSVPGVHYGDVPRAEKVKIRALDRDEGKEFTLEASGLLAICIQHEMD 161 (188)
T ss_pred CCCCCCCCCEEEECCHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEHHHCCEEEEEECCCEEEEEEEEEE
T ss_conf 88311347457756044201576036765672006577521210433128888741322741588625883588764411
Q ss_pred HHCCEEEEEECC-HHH-HHHHHHHHH
Q ss_conf 319768536478-899-999999999
Q gi|254780297|r 140 HLNGILFIDHLS-RLK-RDMITKKMS 163 (170)
Q Consensus 140 HL~G~lf~drls-~~k-r~~~~~k~~ 163 (170)
||||+||+||+| +++ +....+++.
T Consensus 162 HLnGvlF~d~~~~~l~l~~~~~~~~~ 187 (188)
T TIGR00079 162 HLNGVLFVDRISEPLKLPEKLKKELK 187 (188)
T ss_pred CCCCEEEEEECCCHHHHHHHHCCCCC
T ss_conf 25844676532663320132022124
No 5
>pfam01327 Pep_deformylase Polypeptide deformylase.
Probab=100.00 E-value=0 Score=372.46 Aligned_cols=153 Identities=51% Similarity=0.888 Sum_probs=146.3
Q ss_pred CCCHHHCCCCCCCCCCCCCCCCC-HHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCCCC
Q ss_conf 77364576931052121378788-89999999999865004764213022014400037731643233482100164420
Q gi|254780297|r 3 KKPLVIFPDPILRRVSRPIEKIN-SDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKII 81 (170)
Q Consensus 3 ~~~Iv~~~dp~L~~~~~~v~~~~-~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~I~ 81 (170)
+++|++||||+||++|+||+.++ +++++++++|.+||++++|+||||||||+++|+||++.+++.....+.+||||+|+
T Consensus 1 i~~I~~~~dp~Lr~~~~~V~~~~~~~~~~li~dM~~tm~~~~GiGLAApQIG~~~ri~vi~~~~~~~~~~~~v~iNP~I~ 80 (155)
T pfam01327 1 VLPIVTYPDPVLRQKAKPVEEFDDEELKELIDDMLETMYAANGVGLAAPQIGVSKRIFVIDVGDEDGEPEPLVLINPEII 80 (155)
T ss_pred CCEEEECCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEHHHCCCCEEEEEEECCCCCCCCCCEEEECCEEE
T ss_conf 91067739979967251378589399999999999999878996987456697555999991764577785699988057
Q ss_pred CHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHH
Q ss_conf 10000011100000122321012110000024632358557999729764643270013197685364788999
Q gi|254780297|r 82 TFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKR 155 (170)
Q Consensus 82 ~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr 155 (170)
+.|+++..++|||||+||+++.|+||.+|+|+|+|++|+.++.+++||+|||||||+|||+|+||+||+|+.++
T Consensus 81 ~~s~~~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~Dr~~~~~~ 154 (155)
T pfam01327 81 SASEETVEGEEGCLSVPGLRGEVERPKRITVRYQDLNGNEHELEADGFLARVLQHEIDHLDGILFIDRLSKLKR 154 (155)
T ss_pred ECCCCEEEEECCCCCCCCCCEEECCCCEEEEEEECCCCCEEEEEEECEEEEEEEHHHHCCCCEEEHHHCCHHHC
T ss_conf 33895697053614579996676078889999986999699999976033020517270198971582863236
No 6
>cd00487 Pep_deformylase Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents.
Probab=100.00 E-value=0 Score=355.91 Aligned_cols=141 Identities=48% Similarity=0.909 Sum_probs=137.1
Q ss_pred HHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCCCCCHHH
Q ss_conf 64576931052121378788899999999998650047642130220144000377316432334821001644201000
Q gi|254780297|r 6 LVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSD 85 (170)
Q Consensus 6 Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~I~~~s~ 85 (170)
|++||||+||++|.+|+.++++++++++||++||++++|+||||||||+++|+||+++++......+.+||||+|+..|+
T Consensus 1 Iv~~pdp~Lr~~a~~V~~~~~~~~~li~dM~~tm~~~~GiGLAApQVG~~~ri~vv~~~~~~~~~~~~v~INP~I~~~s~ 80 (141)
T cd00487 1 IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPDEENKEPPLVLINPEIIESSG 80 (141)
T ss_pred CEECCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHCCCEEEEHHHCCCCEEEEEEECCCCCCCCCCEEEECCEEEECCC
T ss_conf 97759879968171589789899999999999998689959874566975539999857544777736998561573388
Q ss_pred HHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEE
Q ss_conf 0011100000122321012110000024632358557999729764643270013197685
Q gi|254780297|r 86 DFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILF 146 (170)
Q Consensus 86 e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf 146 (170)
++..++|||||+||+++.|+||.+|+|+|+|++|+.++.+++||.|||+|||+|||||+||
T Consensus 81 ~~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~G~~Ar~~QHE~DHL~Gilf 141 (141)
T cd00487 81 ETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELEAEGFLARCIQHEIDHLNGILF 141 (141)
T ss_pred CEEEEECCCCCCCCCCEEEECCCEEEEEEECCCCCEEEEEEECEEEEEEEEHHHHHCCEEC
T ss_conf 5887104605268986774068889999986899999999976156353707472088939
No 7
>PRK09218 peptide deformylase; Validated
Probab=100.00 E-value=0 Score=317.76 Aligned_cols=134 Identities=34% Similarity=0.578 Sum_probs=121.4
Q ss_pred CCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH--HCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCC
Q ss_conf 877364576931052121378788899999999998650--047642130220144000377316432334821001644
Q gi|254780297|r 2 VKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMY--STDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPK 79 (170)
Q Consensus 2 ~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~--~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~ 79 (170)
|+|+|+ +|+|+||++|+||+.+| .+|++||.+||. ..+||||||||||+++|+||++.++ .+.++|||+
T Consensus 1 Mir~Iv-~~~~iLr~~a~pV~~~d---~~l~~dl~dtm~~~~~~gvGLAApQIGv~~ri~vv~~~~-----~~~v~iNP~ 71 (136)
T PRK09218 1 MIKPIV-KDQLFLQQKSQPATKED---LQLAQDLQDTLLANRDECVGMAANMIGVQKRIIIVSMGF-----VPVVMFNPV 71 (136)
T ss_pred CCCCCC-CCCHHHCCCCCCCCHHH---HHHHHHHHHHHHHHCCCCEEECHHHCCCCEEEEEEECCC-----CCEEEECCE
T ss_conf 964420-79777656764297789---999999999998626798696143469875299999689-----877888855
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEE
Q ss_conf 2010000011100000122321012110000024632358557999729764643270013197685
Q gi|254780297|r 80 IITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILF 146 (170)
Q Consensus 80 I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf 146 (170)
|++.|++.. .+|||||+||. ..|.||.+|+|+|+|++|++++.+++||+|||||||+|||||+|+
T Consensus 72 I~~~s~~~~-~~EGCLS~Pg~-~~v~R~~~I~v~~~d~~g~~~~~~~~g~~Ar~~QHE~DHL~GiLi 136 (136)
T PRK09218 72 IVSKSGPYQ-TEEGCLSLSGE-RPTKRYETITVKYLDRNWKPKTQTFTGFTAQIIQHELDHLEGILI 136 (136)
T ss_pred EEECCCCEE-CCCCCCCCCCC-CCCCCCCEEEEEEECCCCCEEEEEEECCEEEEEEHHHHCCCCEEC
T ss_conf 897589687-44577277894-534152089999997999899999967214142718566187979
No 8
>KOG3137 consensus
Probab=100.00 E-value=1.3e-44 Score=289.43 Aligned_cols=151 Identities=34% Similarity=0.616 Sum_probs=139.5
Q ss_pred CCHHHCCCCCCCCCCCCCC---CCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCC-------CC-----
Q ss_conf 7364576931052121378---78889999999999865004764213022014400037731643-------23-----
Q gi|254780297|r 4 KPLVIFPDPILRRVSRPIE---KINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDH-------AH----- 68 (170)
Q Consensus 4 ~~Iv~~~dp~L~~~~~~v~---~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~-------~~----- 68 (170)
.+|+.||||+||.++++|+ ..+++++.|+++|++.|+..+||||||||||++.|+++.+.... .+
T Consensus 79 ~~iv~~gDPVLr~ka~~Vdraqig~e~lq~lvd~m~~VMr~~~gVGLsAPQvGvp~q~~vle~~~alcrecP~~~ra~rq 158 (267)
T KOG3137 79 LKIVEYGDPVLRAKAKRVDRAQIGDENLQNLVDAMFDVMRKTDGVGLSAPQVGVPVQLMVLEPAGALCRECPEPGRAERQ 158 (267)
T ss_pred HHHHCCCCHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCHHHHHHCCCCHHHHHHH
T ss_conf 78632697766411254785560798899999999999971787654675468854799854707777508973466763
Q ss_pred --CCCCCEECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEE
Q ss_conf --348210016442010000011100000122321012110000024632358557999729764643270013197685
Q gi|254780297|r 69 --RKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILF 146 (170)
Q Consensus 69 --~~~~~~~iNP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf 146 (170)
-.+.++|+||++.++|.....+.|||||+||+++.|+||..|.|.++|.+|+.+++-++||.||+||||+|||+|.||
T Consensus 159 mepf~l~V~VNP~lk~~s~klv~F~EGClSv~Gf~A~V~R~q~V~i~g~D~~Ger~~~~aSgw~ARI~QHE~DHL~G~Lf 238 (267)
T KOG3137 159 MEPFKLIVLVNPKLKKYSDKLVPFDEGCLSVPGFYAEVVRPQSVKIDGRDITGERFSISASGWPARIFQHEYDHLEGVLF 238 (267)
T ss_pred CCCCCEEEEECCHHHHHCCCCCCCCCCCCCCCCHHHCCCCCCEEEEEEECCCCCEEEEECCCCHHHHHHHHHHHHCCEEE
T ss_conf 36787699956067542365233655322454366400333067874005888789996264358898867642025055
Q ss_pred EEECCHHH
Q ss_conf 36478899
Q gi|254780297|r 147 IDHLSRLK 154 (170)
Q Consensus 147 ~drls~~k 154 (170)
+|+|.+.-
T Consensus 239 ~DkM~~rt 246 (267)
T KOG3137 239 FDKMTDRT 246 (267)
T ss_pred EEECCCHH
T ss_conf 54135176
No 9
>COG4740 Predicted metalloprotease [General function prediction only]
Probab=96.01 E-value=0.0021 Score=41.38 Aligned_cols=73 Identities=32% Similarity=0.381 Sum_probs=54.0
Q ss_pred CCCCEECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEE-------CC--------CCCEEEEEEECCEEEEE
Q ss_conf 4821001644201000001110000012232101211000002463-------23--------58557999729764643
Q gi|254780297|r 70 KNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYM-------DC--------NAQHQIIYADGLLATCL 134 (170)
Q Consensus 70 ~~~~~~iNP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~-------d~--------~G~~~~~~~~g~~Ar~~ 134 (170)
...+.++||+|++..+ +..--|-|-|= ..+..|+||.+++|..- |. .-++-+..++|-.|--+
T Consensus 73 E~~YLflNPeIi~~EG-t~~RlEKCG~r-~eRelv~RPyR~~vr~d~~l~a~vdPg~~~IRvreL~k~~lrl~G~pAy~~ 150 (176)
T COG4740 73 EDLYLFLNPEIIRAEG-TLTRLEKCGRR-RERELVKRPYRLEVRHDGGLIARVDPGRRRIRVRELDKGTLRLEGIPAYNL 150 (176)
T ss_pred HHEEEEECHHHEECCC-EEEEHHHHCCH-HHHHHHCCCEEEEEECCCEEEEEECCCCCEEEEEECCCCEEEEECCCCCHH
T ss_conf 1444650731240554-48725542336-778875487389991584589997776315787752787178844732015
Q ss_pred EEEHHHHCCE
Q ss_conf 2700131976
Q gi|254780297|r 135 QHELDHLNGI 144 (170)
Q Consensus 135 QHEiDHL~G~ 144 (170)
.||+.||.|-
T Consensus 151 aHEleHLeg~ 160 (176)
T COG4740 151 AHELEHLEGD 160 (176)
T ss_pred HHHHHHHHCC
T ss_conf 7778775067
No 10
>TIGR01388 rnd ribonuclease D; InterPro: IPR006292 These proteins represent ribonuclease D, a 3-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Members of this family are restricted to the Proteobacteria; Aquifex, Mycobacteria and eukaryotes. Ribonuclease D is not essential in Escherichia coli but is deleterious when overexpressed. The precise biological role of ribonuclease D is still unknown. ; GO: 0004540 ribonuclease activity, 0008033 tRNA processing, 0005737 cytoplasm.
Probab=54.57 E-value=3.7 Score=21.85 Aligned_cols=80 Identities=19% Similarity=0.248 Sum_probs=52.7
Q ss_pred CCCCEEEHHHCCCCCEEEEECCCCCCCCCCC--EECCCCCCC----HHHHHHHHHHHCCCCC------------------
Q ss_conf 7642130220144000377316432334821--001644201----0000011100000122------------------
Q gi|254780297|r 43 DGIGLAAVQIGVLYRLVVIDLQDHAHRKNPM--VFINPKIIT----FSDDFSVYQEGCLSIP------------------ 98 (170)
Q Consensus 43 ~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~--~~iNP~I~~----~s~e~~~~~EGCLS~P------------------ 98 (170)
|-.|| .||+.+.++.+||.---+..-.|+ +|-||+|+| .|+..++|.--|=++|
T Consensus 35 P~LgL--iQ~a~g~~~~LIDPL~~~~~~~Pl~~lL~d~~v~KvlHAaseDlEvF~~l~g~lP~PLfDTQi~Aa~~G~g~s 112 (374)
T TIGR01388 35 PQLGL--IQVADGEQLALIDPLVIDIDLSPLLELLADESVVKVLHAASEDLEVFLNLFGVLPKPLFDTQIAAAFLGFGES 112 (374)
T ss_pred HHHCC--EECCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCC
T ss_conf 20400--3113787568765888752347999997389815853045047999998705798883058899998367852
Q ss_pred -CCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEE
Q ss_conf -3210121100000246323585579997297646
Q gi|254780297|r 99 -DYRADVKRSAFITVRYMDCNAQHQIIYADGLLAT 132 (170)
Q Consensus 99 -g~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar 132 (170)
|+..-|.+...|.+ ++.-.+++|.+|
T Consensus 113 ~gY~~LV~~~~~v~L--------dKse~rtDW~~R 139 (374)
T TIGR01388 113 MGYDKLVQEVLGVEL--------DKSETRTDWLAR 139 (374)
T ss_pred HHHHHHHHHHHCEEC--------CCCCCCCHHHCC
T ss_conf 108999999737031--------788872221047
No 11
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=51.66 E-value=3.8 Score=21.81 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=27.9
Q ss_pred HEEEEECCCCCEEEEEEECCEEEEEEEEHH
Q ss_conf 002463235855799972976464327001
Q gi|254780297|r 110 ITVRYMDCNAQHQIIYADGLLATCLQHELD 139 (170)
Q Consensus 110 I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiD 139 (170)
.+++|.|.+|+.++++..|=.-..||..+|
T Consensus 95 aKY~y~denGe~ktWTGqGR~P~~iq~ald 124 (135)
T PRK10947 95 AKYSYVDENGETKTWTGQGRTPAVIKKAMD 124 (135)
T ss_pred CCCEEECCCCCEEEEECCCCCCHHHHHHHH
T ss_conf 995035589986223278988599999999
No 12
>pfam09092 Lyase_N Lyase, N terminal. Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a jelly-roll fold topology consisting of a two-layered bent beta-sheet sandwich with one short alpha-helix. The convex beta sheet is composed of five antiparallel strands, whilst the concave beta-sheet contains five antiparallel beta-strands with a loop between two consecutive strands folding back onto the concave surface. This domain is required for binding of the protein to long glycosaminoglycan chains.
Probab=42.33 E-value=22 Score=17.21 Aligned_cols=58 Identities=16% Similarity=0.083 Sum_probs=28.7
Q ss_pred HHCCCCCCCCHHHHHCCHHEEEEE-CCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECC
Q ss_conf 000012232101211000002463-235855799972976464327001319768536478
Q gi|254780297|r 92 EGCLSIPDYRADVKRSAFITVRYM-DCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLS 151 (170)
Q Consensus 92 EGCLS~Pg~~~~V~R~~~I~v~~~-d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls 151 (170)
|-|.+||-. .+-.=.+.+.|.|. |.+|.+.+. ...+.+-.+.------.|.+|+||+-
T Consensus 102 ~~~~~F~~~-LnFtGWRa~wV~y~~Dm~G~~~~g-~~~m~~lrivAP~~~~~G~lfiD~l~ 160 (178)
T pfam09092 102 EPDAGFKVG-INFTGWRAVWVSFQNDLEGRKIEG-KADMDSIRIVAPLKAPKGRLFIDRVM 160 (178)
T ss_pred CCCEEEEEE-EECCCCCEEEEECHHHCCCCCCCC-CCCCEEEEEECCCCCCCCEEEEEEEE
T ss_conf 720788877-606511014553002237984567-67510799986688888229999998
No 13
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=39.55 E-value=8.7 Score=19.65 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=30.5
Q ss_pred CHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEE
Q ss_conf 00002463235855799972976464327001319768
Q gi|254780297|r 108 AFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGIL 145 (170)
Q Consensus 108 ~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~l 145 (170)
.-.+++|.|.+|+.++++..|=.-..||..+| .|..
T Consensus 93 RPaKY~y~D~nGe~ktWtG~GR~P~~~~~~l~--~Gk~ 128 (134)
T PRK10328 93 RPAKYRFTDVNGETKTWTGQGRTPKPIAQALA--EGKS 128 (134)
T ss_pred CCCCEEEECCCCCEEEEECCCCCCHHHHHHHH--CCCC
T ss_conf 99872235699977453389989679999998--6997
No 14
>KOG0400 consensus
Probab=37.63 E-value=21 Score=17.35 Aligned_cols=44 Identities=25% Similarity=0.384 Sum_probs=32.4
Q ss_pred CCCCCCCCC-CCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCC
Q ss_conf 052121378-78889999999999865004764213022014400
Q gi|254780297|r 14 LRRVSRPIE-KINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYR 57 (170)
Q Consensus 14 L~~~~~~v~-~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~r 57 (170)
+..-+.|.. .+-.-++..++|+.+-.+...--||.++|||+-.|
T Consensus 11 is~SAlPY~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400 11 ISGSALPYRRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred CCCCCCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCCHHHCEEEEE
T ss_conf 356766553578378763889999999999866998658126653
No 15
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=31.65 E-value=19 Score=17.54 Aligned_cols=37 Identities=19% Similarity=0.334 Sum_probs=27.5
Q ss_pred CCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEE
Q ss_conf 2101211000002463235855799972976464327
Q gi|254780297|r 100 YRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQH 136 (170)
Q Consensus 100 ~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QH 136 (170)
+.++..-...+.++|.|++|..++..-+--++-.+|+
T Consensus 34 f~~~l~~~d~~~iKYkDedgDlITi~d~sDlsfAiq~ 70 (81)
T cd06401 34 FRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQC 70 (81)
T ss_pred HHCCCCCCCCEEEEEECCCCCEEEEECCCCHHHHHHH
T ss_conf 7264898745489975378998998456404778752
No 16
>COG0281 SfcA Malic enzyme [Energy production and conversion]
Probab=29.95 E-value=13 Score=18.68 Aligned_cols=60 Identities=27% Similarity=0.402 Sum_probs=28.4
Q ss_pred CCEEEHHHCCCCCEEEEECCCCCCCCCC--CEECCCCCCCHHHHHHHHHHH-----------------CCCCCCCC--HH
Q ss_conf 4213022014400037731643233482--100164420100000111000-----------------00122321--01
Q gi|254780297|r 45 IGLAAVQIGVLYRLVVIDLQDHAHRKNP--MVFINPKIITFSDDFSVYQEG-----------------CLSIPDYR--AD 103 (170)
Q Consensus 45 vGLAA~QIG~~~ri~vv~~~~~~~~~~~--~~~iNP~I~~~s~e~~~~~EG-----------------CLS~Pg~~--~~ 103 (170)
+|+|++ |.-..=.|=.+.. +| +.|-||.-...-++...+..| +|.|||++ +-
T Consensus 274 iG~S~~--G~~t~e~V~~Ma~-----~PiIfalaNP~pEi~Pe~a~~~~~~aaivaTGrsd~PnQvNNvL~FPgIfrGaL 346 (432)
T COG0281 274 IGVSGV--GAFTEEMVKEMAK-----HPIIFALANPTPEITPEDAKEWGDGAAIVATGRSDYPNQVNNVLIFPGIFRGAL 346 (432)
T ss_pred EECCCC--CCCCHHHHHHHCC-----CCEEEECCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCCCCEEECCCCCHHHH
T ss_conf 976778--8769999997564-----987875489973269999964588978998289898643442557550013456
Q ss_pred HHHCCHHE
Q ss_conf 21100000
Q gi|254780297|r 104 VKRSAFIT 111 (170)
Q Consensus 104 V~R~~~I~ 111 (170)
..|.+.|+
T Consensus 347 d~rA~~It 354 (432)
T COG0281 347 DVRAKTIT 354 (432)
T ss_pred HHCCCCCC
T ss_conf 50654488
No 17
>COG3129 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=26.61 E-value=55 Score=14.85 Aligned_cols=100 Identities=13% Similarity=0.117 Sum_probs=53.8
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEE--ECC-------CCCCC------CCCC
Q ss_conf 76931052121378788899999999998650047642130220144000377--316-------43233------4821
Q gi|254780297|r 9 FPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVI--DLQ-------DHAHR------KNPM 73 (170)
Q Consensus 9 ~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv--~~~-------~~~~~------~~~~ 73 (170)
+|+-.| |.||..-.+-++.|++-|.+|--.-+|-++++--||...+-++= .+. ..+-. -...
T Consensus 45 iPeg~L---CPpvPgRAdYih~laDLL~s~~g~~~~~~i~~LDIGvGAnCIYPliG~~eYgwrfvGseid~~sl~sAk~i 121 (292)
T COG3129 45 IPEGFL---CPPVPGRADYIHHLADLLASTSGQIPGKNIRILDIGVGANCIYPLIGVHEYGWRFVGSEIDSQSLSSAKAI 121 (292)
T ss_pred CCCCCC---CCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCEEECCEEECCCCCHHHHHHHHHH
T ss_conf 788773---89999736799999999874389877676478850457642002133212122001574687788888999
Q ss_pred EECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEE
Q ss_conf 001644201000001110000012232101211000002
Q gi|254780297|r 74 VFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITV 112 (170)
Q Consensus 74 ~~iNP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v 112 (170)
+.-||.....=.-..--.-+|+ |||+.+.-+||+-..+
T Consensus 122 i~~N~~l~~~I~lr~qk~~~~i-f~giig~nE~yd~tlC 159 (292)
T COG3129 122 ISANPGLERAIRLRRQKDSDAI-FNGIIGKNERYDATLC 159 (292)
T ss_pred HHCCCCHHHHEEEEECCCCCCC-CCCCCCCCCEEEEEEC
T ss_conf 8709041533367752685434-1651034433305751
No 18
>TIGR01722 MMSDH methylmalonate-semialdehyde dehydrogenase; InterPro: IPR010061 These proteins are involved in valine catabolism, methylmalonate-semialdehyde dehydrogenase catalyzes the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA. Methylmalonate-semialdehyde dehydrogenase has been characterised in both prokaryotes , and eukaryotes , functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in Pseudomonas aeruginosa does not correspond with the N-terminal sequence predicted for rat liver. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase . In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2 . The preceding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus.; GO: 0004491 methylmalonate-semialdehyde dehydrogenase (acylating) activity, 0006573 valine metabolic process.
Probab=24.66 E-value=24 Score=17.04 Aligned_cols=30 Identities=27% Similarity=0.325 Sum_probs=19.9
Q ss_pred HEEEEECCCCC-EEEEEEECCEEEEEEEEHH
Q ss_conf 00246323585-5799972976464327001
Q gi|254780297|r 110 ITVRYMDCNAQ-HQIIYADGLLATCLQHELD 139 (170)
Q Consensus 110 I~v~~~d~~G~-~~~~~~~g~~Ar~~QHEiD 139 (170)
|++--.+.-|| +=..+-+|-.||-|||+||
T Consensus 397 i~liN~sPyGNGTaIFT~~GaaAR~fqh~ie 427 (478)
T TIGR01722 397 IKLINESPYGNGTAIFTSDGAAARKFQHEIE 427 (478)
T ss_pred HHHHCCCCCCCCCEEECCCCHHHHHEEEEEE
T ss_conf 8864176588864113177521201102563
No 19
>TIGR02476 BluB cob(II)yrinic acid a,c-diamide reductase; InterPro: IPR012825 The BluB protein is related to nitroreductase, and is found to substitute for the FldA cobalt reductase in aerobic species (by phylogenetic profiling). The bluB gene is also found to be preceded by B12 promoter elements . The gene in R. capsulatus has been shown to be essential for cobalamin biosynthesis ..
Probab=22.97 E-value=51 Score=15.03 Aligned_cols=32 Identities=13% Similarity=0.364 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECC
Q ss_conf 9999999998650047642130220144000377316
Q gi|254780297|r 28 IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQ 64 (170)
Q Consensus 28 ~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~ 64 (170)
-.+++..+++++..+|-||++= |-+++.|.-+
T Consensus 29 pe~vL~rll~Aa~~APSVG~~q-----PW~f~~V~~~ 60 (206)
T TIGR02476 29 PEEVLERLLDAAHLAPSVGFSQ-----PWRFVRVESP 60 (206)
T ss_pred CHHHHHHHHHHHHHCCCCCCCC-----CCCEEEECCH
T ss_conf 6889999999985078878778-----8325886678
No 20
>pfam12388 Peptidase_M57 Dual-action HEIGH metallo-peptidase. The catalytic triad for this family of proteases is HE-H-H, which in many members is in the sequence motif HEIGH.
Probab=22.90 E-value=17 Score=17.93 Aligned_cols=25 Identities=24% Similarity=0.397 Sum_probs=19.6
Q ss_pred CCEEEEEEEEHHHHCCEEEEEECCH
Q ss_conf 9764643270013197685364788
Q gi|254780297|r 128 GLLATCLQHELDHLNGILFIDHLSR 152 (170)
Q Consensus 128 g~~Ar~~QHEiDHL~G~lf~drls~ 152 (170)
...++++.|||-|+-|.=-+|..++
T Consensus 131 ~~~~~vi~HEiGHciGfRHTDyfnR 155 (211)
T pfam12388 131 NVNEHVITHEIGHSIGFRHTDYFDR 155 (211)
T ss_pred CHHHHHHHHHHHCEECCCCCCCCCC
T ss_conf 0334545232022222211355574
No 21
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=22.72 E-value=30 Score=16.42 Aligned_cols=51 Identities=18% Similarity=0.145 Sum_probs=28.2
Q ss_pred HHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEE
Q ss_conf 0000122321012110000024632358557999729764643270013197685
Q gi|254780297|r 92 EGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILF 146 (170)
Q Consensus 92 EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf 146 (170)
-||-|+-|-.+.-.+...-+...-...... ...-..+.+.||+-|.-|..-
T Consensus 58 ~G~wS~VGtd~~~~~~~~~Tmnlg~~~~~~----~~~~~~~~~~he~~h~~g~~h 108 (198)
T cd04327 58 DGYWSYVGTDALLIGADAPTMNLGWFTDDT----PDPEFSRVVLHEFGHALGFIH 108 (198)
T ss_pred CCCCCCCCCCCCCCCCCCCCEECCCCCCCC----CCCCCCEEHHHHHHHHHCCCC
T ss_conf 975376686523578888714546567877----553300100577676642600
No 22
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=22.17 E-value=28 Score=16.61 Aligned_cols=43 Identities=19% Similarity=0.129 Sum_probs=24.6
Q ss_pred HHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEEC----CEEEEEEEEHHHHCCEE
Q ss_conf 100000122321012110000024632358557999729----76464327001319768
Q gi|254780297|r 90 YQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADG----LLATCLQHELDHLNGIL 145 (170)
Q Consensus 90 ~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g----~~Ar~~QHEiDHL~G~l 145 (170)
...||.|+-|-.. +..+........+ ..+..++||+-|.-|..
T Consensus 65 ~~~gc~S~vG~~~-------------~~~~q~~~l~~~~~~~~~~~gti~HElgHaLGf~ 111 (167)
T cd00203 65 GGTGGWAYLGRVC-------------DSLRGVGVLQDNQSGTKEGAQTIAHELGHALGFY 111 (167)
T ss_pred CCCEEEECCCCCC-------------CCCCCEEEECCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 9984485189886-------------7998538965897433255424899999984887
No 23
>pfam09212 CBM27 Carbohydrate binding module 27. Members of this family are carbohydrate binding modules that bind to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. They adopt a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom.
Probab=21.60 E-value=53 Score=14.91 Aligned_cols=81 Identities=16% Similarity=0.268 Sum_probs=44.2
Q ss_pred CCCCCCCEECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEE
Q ss_conf 23348210016442010000011100000122321012110000024632358557999729764643270013197685
Q gi|254780297|r 67 AHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILF 146 (170)
Q Consensus 67 ~~~~~~~~~iNP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf 146 (170)
.+.-.|+++.||-++++...+..-.=--|+.-.+-+.--+.-.|++.+ | ....+.|+.--++--.+| ++|..|
T Consensus 92 ~g~lRpya~L~~gW~K~g~d~~~~nv~Dle~v~idg~~Y~~~~V~Ie~-d-----~~~~~~~l~l~IVGd~l~-~~G~IY 164 (173)
T pfam09212 92 NGALRPYAALNPGWIKIGLDMNHTNIDDGELVSFDGKKYKKFHVNIEF-D-----AMPGVNELFIGIVGDHLA-YDGPIF 164 (173)
T ss_pred CCCEEEEEEECCCCEEECCCCCCCCCCCCEEEEECCEEEEEEEEEEEE-E-----CCCCCCCCEEEEECCCCC-CCCCEE
T ss_conf 765656787289857866754422345430899889999999999985-1-----377987408998635325-679789
Q ss_pred EEECCHHH
Q ss_conf 36478899
Q gi|254780297|r 147 IDHLSRLK 154 (170)
Q Consensus 147 ~drls~~k 154 (170)
+|-+.=+|
T Consensus 165 IDNI~l~k 172 (173)
T pfam09212 165 IDNVRLFK 172 (173)
T ss_pred EEEEEEEC
T ss_conf 76454314
No 24
>PRK03979 ADP-specific phosphofructokinase; Provisional
Probab=21.57 E-value=56 Score=14.77 Aligned_cols=79 Identities=19% Similarity=0.202 Sum_probs=42.4
Q ss_pred CCC-CCEEEHHHCCCCCEEEE-ECCCCCCC------CCC----------CEECCCCCCCHHH-HH-----HHHHHH-CCC
Q ss_conf 476-42130220144000377-31643233------482----------1001644201000-00-----111000-001
Q gi|254780297|r 42 TDG-IGLAAVQIGVLYRLVVI-DLQDHAHR------KNP----------MVFINPKIITFSD-DF-----SVYQEG-CLS 96 (170)
Q Consensus 42 ~~G-vGLAA~QIG~~~ri~vv-~~~~~~~~------~~~----------~~~iNP~I~~~s~-e~-----~~~~EG-CLS 96 (170)
.+| +|+.||..+.....-|| ..+.-... +.+ +++..|+=-..++ +. ..+.+| +.+
T Consensus 89 mGGqaGI~ANll~~l~~~~vi~~~p~ls~~qa~lf~~~~i~~P~~e~g~l~l~~p~ea~~~~~~~~Ih~IfEf~~G~~~~ 168 (451)
T PRK03979 89 MGGQAGIIANLLSGLGAKKVIAYVPVLSKKQAELFVDGPLYFPKVENGKLVLKKPREAFKGGDELKINRIFEFSEGEKFS 168 (451)
T ss_pred ECCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHCCCCEEEEEEECCEEEECCCHHHCCCCCCCEEEEEEEECCCCEEE
T ss_conf 17499999999976398027982687888999870578843116678976404816640789875169999937998885
Q ss_pred CCCCCHHHHHCCHHEEEEECCCCC
Q ss_conf 223210121100000246323585
Q gi|254780297|r 97 IPDYRADVKRSAFITVRYMDCNAQ 120 (170)
Q Consensus 97 ~Pg~~~~V~R~~~I~v~~~d~~G~ 120 (170)
++|-...++|..+.-+.+.+.+..
T Consensus 169 ~~~~~i~aPrsNRFI~s~d~~n~~ 192 (451)
T PRK03979 169 LGGEEITVPRENRFIASSRPENLR 192 (451)
T ss_pred CCCCEEEECCCCEEEEECCCCCCC
T ss_conf 378428824786689866887765
No 25
>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=21.32 E-value=67 Score=14.31 Aligned_cols=12 Identities=42% Similarity=0.307 Sum_probs=6.7
Q ss_pred CCCCCEEEEECC
Q ss_conf 144000377316
Q gi|254780297|r 53 GVLYRLVVIDLQ 64 (170)
Q Consensus 53 G~~~ri~vv~~~ 64 (170)
|-+-++|-|...
T Consensus 121 g~~p~LflIYpe 132 (236)
T cd03765 121 GEEPRLFLIYPQ 132 (236)
T ss_pred CCCCEEEEEECC
T ss_conf 998438999369
No 26
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482 This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=20.52 E-value=42 Score=15.51 Aligned_cols=41 Identities=27% Similarity=0.515 Sum_probs=28.5
Q ss_pred HHCCCCCCCC--HHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHH
Q ss_conf 0000122321--0121100000246323585579997297646432700131976853647889999999
Q gi|254780297|r 92 EGCLSIPDYR--ADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMIT 159 (170)
Q Consensus 92 EGCLS~Pg~~--~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~ 159 (170)
.-.-|.|++- |..+||-+|.+- -||+||.|=+.-+||+.++
T Consensus 274 HHsAS~~~lvGGG~~P~PGEiSLA---------------------------hnGvLFLDEl~EF~r~vL~ 316 (505)
T TIGR00368 274 HHSASKPALVGGGSIPKPGEISLA---------------------------HNGVLFLDELPEFKRKVLD 316 (505)
T ss_pred CCCCCCCCCCCCCCCCCCCCEEHH---------------------------CCCCHHHHCCHHHHHHHHH
T ss_conf 500256664058752228512020---------------------------0541043222044678998
Done!