Query 013882
Match_columns 434
No_of_seqs 160 out of 368
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:20:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013882hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2245 Poly(A) polymerase and 100.0 1.6E-67 3.5E-72 543.1 16.3 229 1-236 262-500 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 7E-66 1.5E-70 545.5 26.4 232 1-235 300-541 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 2.3E-59 5E-64 469.0 11.9 231 1-235 254-528 (552)
4 PF04926 PAP_RNA-bind: Poly(A) 100.0 1.3E-35 2.7E-40 268.3 8.8 135 100-235 1-156 (157)
5 PF04928 PAP_central: Poly(A) 100.0 1.1E-32 2.5E-37 268.8 5.6 99 1-99 156-254 (254)
6 PF03813 Nrap: Nrap protein; 90.9 2.6 5.7E-05 49.3 12.8 183 2-197 224-425 (972)
7 PF03813 Nrap: Nrap protein; 63.2 18 0.00038 42.6 7.0 94 3-98 734-839 (972)
8 PF03828 PAP_assoc: Cid1 famil 44.6 14 0.00031 27.8 1.6 52 2-55 5-58 (60)
9 PF07357 DRAT: Dinitrogenase r 37.2 14 0.00031 37.2 0.8 33 103-135 83-115 (262)
10 PF07789 DUF1627: Protein of u 30.6 25 0.00054 32.9 1.2 43 60-109 110-152 (155)
11 PF12921 ATP13: Mitochondrial 21.7 54 0.0012 29.2 1.6 73 32-106 27-105 (126)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.6e-67 Score=543.14 Aligned_cols=229 Identities=44% Similarity=0.825 Sum_probs=211.8
Q ss_pred ChHHHHHHhhccCCCCCceeccccccccCCccccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHHHHHHH
Q 013882 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNT 80 (434)
Q Consensus 1 mLV~kFF~vyS~W~WP~PV~L~~i~~~~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf~RG~~ 80 (434)
+||+|||.+|++|+||+||+|+++++++|+++|||||.|++||+|+|||||||||+||||||||+||++||++||+||++
T Consensus 262 ~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~ 341 (562)
T KOG2245|consen 262 TLVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLE 341 (562)
T ss_pred HHHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCcccccccccccHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccchhhhcCCcchhhccccEEEEEEEeCCHhHhHhHHHHHHHHHHHHHHHhhhccCCceeeccCCCCCCCCC
Q 013882 81 ICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDTS 160 (434)
Q Consensus 81 I~~~I~~g~~~W~~LFep~~FF~~Yk~YL~I~vsA~see~~~~W~GwVESRLR~Lv~~LE~~~~~~l~ahP~P~~F~d~~ 160 (434)
||++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||||.|+.+||++. .++.|||+|+.|.++.
T Consensus 342 I~~~i~~~k~~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~~-~i~~ahp~P~~f~~~~ 420 (562)
T KOG2245|consen 342 ICDDIELNKLDWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERNQ-VILIAHPNPKKFKDTY 420 (562)
T ss_pred HHHHHHhccccHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhhc-ceEEecCCcccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999965 5677999999999875
Q ss_pred C----CCceeeEEEeeeeCCCCccCCCceeehhhHHHHHHHHHh----hhcccCCc--cEEEEEeeccCCCCCCCCCCCc
Q 013882 161 K----PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSIN----MYMFWKPG--MEICVSHIRRKQIPPYVFPEGY 230 (434)
Q Consensus 161 ~----~~~~~~fFIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~----~~~~~~~g--M~I~VshVkrsqLP~~Vf~~g~ 230 (434)
. ..+...|||||.+..+ .++||+..+++|...++ +...+.+| |++.+.|+||++|+.+++.+++
T Consensus 421 ~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~krr~l~~~~~~~~l 494 (562)
T KOG2245|consen 421 NCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVKRRSLIQTITKEFL 494 (562)
T ss_pred cCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeecccccccccccccccccccccCHHHh
Confidence 3 2456789999998754 34999999999999887 44456788 8888889999999999999998
Q ss_pred cccCCC
Q 013882 231 KRTRHP 236 (434)
Q Consensus 231 kr~r~~ 236 (434)
++.|.-
T Consensus 495 ~~~k~~ 500 (562)
T KOG2245|consen 495 RLCKQY 500 (562)
T ss_pred hHHHhh
Confidence 776554
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=7e-66 Score=545.54 Aligned_cols=232 Identities=34% Similarity=0.706 Sum_probs=213.2
Q ss_pred ChHHHHHHhhccCCCCCceecccccc-----ccCCccccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHH
Q 013882 1 MLVSRFFRVYTMWRWPNPVMLCAIDE-----AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQF 75 (434)
Q Consensus 1 mLV~kFF~vyS~W~WP~PV~L~~i~~-----~~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf 75 (434)
+||.+||.+|++|+||+||+|+++++ +.+|++||||+.|++||+|+|||||||||+||+|||||.||+++|++||
T Consensus 300 ~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt~sT~~vI~~Ef 379 (593)
T PTZ00418 300 QLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEF 379 (593)
T ss_pred HHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCccccccccHHHHHHHHHHH
Confidence 58999999999999999999999876 5788999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhh-cccchhhhcCCcchhhccccEEEEEEEeCCHhHhHhHHHHHHHHHHHHHHHhhhccCCceeeccCCC
Q 013882 76 QYGNTICEEVEL-NKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPH 154 (434)
Q Consensus 76 ~RG~~I~~~I~~-g~~~W~~LFep~~FF~~Yk~YL~I~vsA~see~~~~W~GwVESRLR~Lv~~LE~~~~~~l~ahP~P~ 154 (434)
+||++|+++|.. ++.+|++||+|++||.+|+|||+|++.|.+++++..|.||||||||.|+.+||+.. .+.+||||+
T Consensus 380 ~Ra~~i~~~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~~~--~i~~~p~P~ 457 (593)
T PTZ00418 380 KRAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLETLN--NLKIRPYPK 457 (593)
T ss_pred HHHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhccC--CceEeecCc
Confidence 999999999998 89999999999999999999999999999999999999999999999999999853 357899999
Q ss_pred CCCCCCC-CCceeeEEEeeeeCCCCccCCCceeehhhHHHHHHHHHhhhcc---cCCccEEEEEeeccCCCCCCCCCCCc
Q 013882 155 EYVDTSK-PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF---WKPGMEICVSHIRRKQIPPYVFPEGY 230 (434)
Q Consensus 155 ~F~d~~~-~~~~~~fFIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~~~~~---~~~gM~I~VshVkrsqLP~~Vf~~g~ 230 (434)
+|.+... ..|.++|||||.++..... ...++||+.++++|.+.|++|.. |.++|+|+|+|||++|||+|||++|+
T Consensus 458 ~f~~~~~~~~~~~~ffIGL~~~~~~~~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk~~~Lp~~v~~~~~ 536 (593)
T PTZ00418 458 FFKYQDDGWDYASSFFIGLVFFSKNVY-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLKKSQLPAFVLSQTP 536 (593)
T ss_pred ccccCCCCceeEEEEEEeEeeccCCCC-CCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEeehHhCCHhhccCCC
Confidence 9988753 4678899999999765432 33589999999999999998863 57889999999999999999999998
Q ss_pred cccCC
Q 013882 231 KRTRH 235 (434)
Q Consensus 231 kr~r~ 235 (434)
+|++.
T Consensus 537 ~~~~~ 541 (593)
T PTZ00418 537 EEPVK 541 (593)
T ss_pred cCCCc
Confidence 88555
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=2.3e-59 Score=469.02 Aligned_cols=231 Identities=34% Similarity=0.673 Sum_probs=212.6
Q ss_pred ChHHHHHHhhccCCCCCceeccccccccCCccccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHHHHHHH
Q 013882 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNT 80 (434)
Q Consensus 1 mLV~kFF~vyS~W~WP~PV~L~~i~~~~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf~RG~~ 80 (434)
.||.|||.++++|+||+||+|+||++++++.+||||+.|++|++|.|||||||||+||+|||+|.||..||..||-||++
T Consensus 254 vIv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~vIl~EfvRa~~ 333 (552)
T COG5186 254 VIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHVILMEFVRAHK 333 (552)
T ss_pred hHHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhhhHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccchhhhcCCcchhhccccEEEEEEEeCCHhHhHhHHHHHHHHHHHHHHHhhhccCCceeeccCCCCCCCC-
Q 013882 81 ICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDT- 159 (434)
Q Consensus 81 I~~~I~~g~~~W~~LFep~~FF~~Yk~YL~I~vsA~see~~~~W~GwVESRLR~Lv~~LE~~~~~~l~ahP~P~~F~d~- 159 (434)
|+++|+.+..+|.+||+..+||.+||+||.|++.+.++|++.+|.|+||||||.|+.+||-.. +++.|||||+.|...
T Consensus 334 I~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~~AhPF~K~F~~~y 412 (552)
T COG5186 334 ILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DILYAHPFPKAFRKVY 412 (552)
T ss_pred hhhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhhhcCcCChhhhhhc
Confidence 999999999999999999999999999999999999999999999999999999999999865 567899999999511
Q ss_pred -------------------------------C-----------CCCceeeEEEeeeeCCCCccCCCceeehhhHHHHHHH
Q 013882 160 -------------------------------S-----------KPCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKL 197 (434)
Q Consensus 160 -------------------------------~-----------~~~~~~~fFIGL~~~~~~~~~~~~~~DL~~~v~eF~~ 197 (434)
+ .+.|.+.|||||++.... ..+++||..++++|.+
T Consensus 413 ~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~~---~~kkvdi~~p~~EF~e 489 (552)
T COG5186 413 NCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPVK---PGKKVDIEQPVKEFIE 489 (552)
T ss_pred CCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeecC---CCceeeeeccHHHHHH
Confidence 0 012566899999987543 3578999999999999
Q ss_pred HHhhhcccC-CccEEEEEeeccCCCCCCCCCCCccccCC
Q 013882 198 SINMYMFWK-PGMEICVSHIRRKQIPPYVFPEGYKRTRH 235 (434)
Q Consensus 198 ~I~~~~~~~-~gM~I~VshVkrsqLP~~Vf~~g~kr~r~ 235 (434)
.|+.|++++ .+|.|.|+.+|+++||+-||.+|+.|+..
T Consensus 490 lcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~ 528 (552)
T COG5186 490 LCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSN 528 (552)
T ss_pred HHHHhhccccceeeeehhhccccCCchhhcCCCccCccc
Confidence 999998876 68999999999999999999999877444
No 4
>PF04926 PAP_RNA-bind: Poly(A) polymerase predicted RNA binding domain; InterPro: IPR007010 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase. ; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0043631 RNA polyadenylation, 0005634 nucleus; PDB: 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A 1Q79_A 1Q78_A 1F5A_A.
Probab=100.00 E-value=1.3e-35 Score=268.26 Aligned_cols=135 Identities=36% Similarity=0.711 Sum_probs=106.2
Q ss_pred chhhccccEEEEEEEeCCHhHhHhHHHHHHHHHHHHHHHhhhccCCceeeccCCCCCC------------------CCCC
Q 013882 100 LFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV------------------DTSK 161 (434)
Q Consensus 100 ~FF~~Yk~YL~I~vsA~see~~~~W~GwVESRLR~Lv~~LE~~~~~~l~ahP~P~~F~------------------d~~~ 161 (434)
+||.+|||||+|+++|.+++++.+|.||||||||.||.+||+... +..|||||+.|. +...
T Consensus 1 ~FF~~Yk~yl~I~~~a~~~~~~~~W~G~VESrlR~Lv~~LE~~~~-i~~ahp~pk~f~~~~~~~~~~~~~~~~~~~~~~~ 79 (157)
T PF04926_consen 1 DFFSRYKHYLQIDVSAKNEEDHRKWSGWVESRLRHLVQKLERNPG-IKLAHPFPKRFERVYECSEQADENNDEEEEEDPE 79 (157)
T ss_dssp -HHHH-SEEEEEEEEECSHHHHHHHHHHHHCCHHHHHHHHHTSTT-EEEEEE-SS-EEEEEE-EBECTTCTTSHHCHCTS
T ss_pred ChhHhCceeEEEEEEeCCHHHHHHhhhHHHHHHHHHHHHHccCCC-eeEecCCCCccccccccccccccccccccccCCC
Confidence 699999999999999999999999999999999999999999764 567999999998 1223
Q ss_pred CCceeeEEEeeeeCCCCccCCCceeehhhHHHHHHHHHhhhcc--c-CCccEEEEEeeccCCCCCCCCCCCccccCC
Q 013882 162 PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF--W-KPGMEICVSHIRRKQIPPYVFPEGYKRTRH 235 (434)
Q Consensus 162 ~~~~~~fFIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~~~~~--~-~~gM~I~VshVkrsqLP~~Vf~~g~kr~r~ 235 (434)
..+.++|||||.+......+..+++||+.++++|+..|++|.. | .++|+|+|+||||+|||++||++|.+|+++
T Consensus 80 ~~~~~~~fIGL~~~~~~~~~~~~~~dL~~~i~~F~~~v~~~~~~~~~~~~m~i~i~~vk~~~Lp~~v~~~~~~r~~k 156 (157)
T PF04926_consen 80 NEYTSSFFIGLEFDSKESNEGSKKLDLTYAIQEFKDLVRNWEKYYYDEEGMDISISHVKRSQLPDFVFEEGEKRPKK 156 (157)
T ss_dssp EEEEEEEEEEEEE--SSSS---S-EE-HHHHHHHHHHHHCCCCTTC-TTTEEEEEEEEEHHHHGGGGS-TTS-----
T ss_pred ceeEEEEEEEEEECCCCccccceEEehHHHHHHHHHHHHhhhccccCCCccEEEEEEechHHCChhhhcccCcCCCC
Confidence 5678899999999876543344689999999999999999876 3 578999999999999999999999988765
No 5
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=99.97 E-value=1.1e-32 Score=268.79 Aligned_cols=99 Identities=55% Similarity=1.052 Sum_probs=76.5
Q ss_pred ChHHHHHHhhccCCCCCceeccccccccCCccccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHHHHHHH
Q 013882 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNT 80 (434)
Q Consensus 1 mLV~kFF~vyS~W~WP~PV~L~~i~~~~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf~RG~~ 80 (434)
+||.+||.+|++|+||+||+|++++++.+++++|||+.|++|++|+|||||||||+||||||||+||+++|++||+||++
T Consensus 156 ~ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~i~~Ef~ra~~ 235 (254)
T PF04928_consen 156 TLLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRIIREEFQRAHE 235 (254)
T ss_dssp HHHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccchhhhcCCc
Q 013882 81 ICEEVELNKAQWSALFEPY 99 (434)
Q Consensus 81 I~~~I~~g~~~W~~LFep~ 99 (434)
|++++..++.+|++||+|+
T Consensus 236 i~~~~~~~~~~W~~L~e~~ 254 (254)
T PF04928_consen 236 ILSEILKGGASWSDLFEPH 254 (254)
T ss_dssp HHHHHHTTSS-HHHCT---
T ss_pred HHHHHHcCCCCHHHHcCCC
Confidence 9999999999999999985
No 6
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=90.94 E-value=2.6 Score=49.25 Aligned_cols=183 Identities=10% Similarity=0.162 Sum_probs=104.9
Q ss_pred hHHHHHHhhccCCC-CCceeccccccccCCccccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHHHHHHH
Q 013882 2 LVSRFFRVYTMWRW-PNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNT 80 (434)
Q Consensus 2 LV~kFF~vyS~W~W-P~PV~L~~i~~~~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf~RG~~ 80 (434)
|+..+....|..+| -+|+.++.-.+..-. ......+--||+--.-=.+|-.+++|.++++.|+.|-+++.+
T Consensus 224 lFr~~l~fLA~~d~~~~~l~~~~~~~~~~~--------~~~~~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~ 295 (972)
T PF03813_consen 224 LFRAVLQFLATTDLSKKPLFFKSSSDSTES--------LEEFHSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLE 295 (972)
T ss_pred HHHHHHHHHhccccccCceEEecCCCccch--------hhhhhccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHH
Confidence 45566677799999 679999876531100 001112334444444457999999999999999999999998
Q ss_pred HHHHHhhcccchhhhcC-C-cchhhccccEEEEE---EE----eCCHhHhHhHHHHHHHHHHHHHHH-hhhccCCceeec
Q 013882 81 ICEEVELNKAQWSALFE-P-YLFFESYRNYLQVD---IV----AANADDLLAWKGWVESRLRQLTLM-IERDTYGKLQCH 150 (434)
Q Consensus 81 I~~~I~~g~~~W~~LFe-p-~~FF~~Yk~YL~I~---vs----A~see~~~~W~GwVESRLR~Lv~~-LE~~~~~~l~ah 150 (434)
++++- .......+|- + ..+..+|.+++.|. .. .....+...|..++..+|-.|+.+ |-... -.++
T Consensus 296 lL~~~--~~d~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~---~~i~ 370 (972)
T PF03813_consen 296 LLDDS--SDDGFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRA---KLIR 370 (972)
T ss_pred Hhccc--cccchhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHH---HeEE
Confidence 88763 2345677774 4 45678999999991 11 122233445555666676666543 53321 1133
Q ss_pred cC---CCCCCCCCC--CCceeeEEEeeeeCCCCcc---CCCceeehhhHHHHHHH
Q 013882 151 PY---PHEYVDTSK--PCAHCAFFMGLQRKPGEVV---QEGQQFDIRGSVEEFKL 197 (434)
Q Consensus 151 P~---P~~F~d~~~--~~~~~~fFIGL~~~~~~~~---~~~~~~DL~~~v~eF~~ 197 (434)
++ +..+.-.+. ........|||.++..... ..|-..|-.....+|++
T Consensus 371 v~~~~~~~w~i~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~ 425 (972)
T PF03813_consen 371 VLRPSQPPWSISSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFRE 425 (972)
T ss_pred EeCCCCCCcccCCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHH
Confidence 33 222211111 1112267899998763211 11122234556677876
No 7
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=63.23 E-value=18 Score=42.60 Aligned_cols=94 Identities=24% Similarity=0.441 Sum_probs=56.4
Q ss_pred HHHHHHhhccCCCCC-ceeccccccc--------cCCccccCCCCCCCCCCCcceEecCCCCCCcchhh---cChhhHHH
Q 013882 3 VSRFFRVYTMWRWPN-PVMLCAIDEA--------ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYN---VSTSTLRV 70 (434)
Q Consensus 3 V~kFF~vyS~W~WP~-PV~L~~i~~~--------~lg~~vWdPr~n~rDr~hlMPIITPayP~mNST~N---VT~STl~v 70 (434)
..||.+..+.|+|-+ |++++.-.+- .-.|..|.. ..|......|-|.||.=|.- +..+ -+..-++.
T Consensus 734 FlRfL~lLs~~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g-~~wT~~~Ps~~v~~R 811 (972)
T PF03813_consen 734 FLRFLHLLSTWDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEG-SLWTRNGPSKVVAKR 811 (972)
T ss_pred HHHHHHHHHhCCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCC-CEeECCCCCHHHHHH
Confidence 358889999999985 9888653211 012444544 23444567899999988753 3343 33444444
Q ss_pred HHHHHHHHHHHHHHHhhcccchhhhcCC
Q 013882 71 MMDQFQYGNTICEEVELNKAQWSALFEP 98 (434)
Q Consensus 71 I~eEf~RG~~I~~~I~~g~~~W~~LFep 98 (434)
|+.==+.++++++.-..+..+|..||.+
T Consensus 812 l~~LAk~sl~~l~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 812 LTALAKASLKLLEEQGLSDLDWKSLFRP 839 (972)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHhcCC
Confidence 4443344555555222236799999975
No 8
>PF03828 PAP_assoc: Cid1 family poly A polymerase; InterPro: IPR002058 These PAP/25A associated domains are found in uncharacterised eukaryotic proteins, a number of which are described as 'topoisomerase 1-related' though they appear to have little or no homology to topoisomerase 1. The signatures that define this group of sequences often occur towards the C terminus after the PAP/25A core domain IPR001201 from INTERPRO.; PDB: 2B4V_A 2B56_A 2B51_A 4EP7_B 2NOM_B 2Q0G_B 2Q0D_B 2Q0C_A 2Q0F_A 2Q0E_A ....
Probab=44.56 E-value=14 Score=27.84 Aligned_cols=52 Identities=21% Similarity=0.351 Sum_probs=28.6
Q ss_pred hHHHHHHhhc-cCCCCCcee-ccccccccCCccccCCCCCCCCCCCcceEecCCCC
Q 013882 2 LVSRFFRVYT-MWRWPNPVM-LCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYP 55 (434)
Q Consensus 2 LV~kFF~vyS-~W~WP~PV~-L~~i~~~~lg~~vWdPr~n~rDr~hlMPIITPayP 55 (434)
|+..||.+|+ .|+|.+-|+ +.....-......|.. ....+...|.|.=|.=|
T Consensus 5 Ll~~Ff~~Y~~~Fd~~~~~Isi~~g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~ 58 (60)
T PF03828_consen 5 LLLGFFEYYGRKFDYENNVISIRNGGYFPKEEKNWSK--SRNQRKKRLCIEDPFDP 58 (60)
T ss_dssp HHHHHHHHHHHTS-TTTEEEESSSSSEEEHHHHTGCH--CCCCECSSSEBBESSST
T ss_pred HHHHHHHHhCCcCCCCceEEEecCCceEEhhhccccc--cccCCCCeEEEECCCCC
Confidence 7889999999 999998554 3221100001122431 11223467888887654
No 9
>PF07357 DRAT: Dinitrogenase reductase ADP-ribosyltransferase (DRAT); InterPro: IPR009953 This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions [].
Probab=37.24 E-value=14 Score=37.21 Aligned_cols=33 Identities=36% Similarity=0.441 Sum_probs=22.3
Q ss_pred hccccEEEEEEEeCCHhHhHhHHHHHHHHHHHH
Q 013882 103 ESYRNYLQVDIVAANADDLLAWKGWVESRLRQL 135 (434)
Q Consensus 103 ~~Yk~YL~I~vsA~see~~~~W~GwVESRLR~L 135 (434)
..|-.+|+==..-+|.-+...++||||||+-.+
T Consensus 83 ~sYLRlLrGW~fDSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 83 ASYLRLLRGWGFDSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred hhHHHHHhccCcCCCChhhhhhhhhhhhccCcC
Confidence 334444443333467778899999999998644
No 10
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=30.64 E-value=25 Score=32.92 Aligned_cols=43 Identities=9% Similarity=0.232 Sum_probs=36.6
Q ss_pred hhhcChhhHHHHHHHHHHHHHHHHHHhhcccchhhhcCCcchhhccccEE
Q 013882 60 SYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYL 109 (434)
Q Consensus 60 T~NVT~STl~vI~eEf~RG~~I~~~I~~g~~~W~~LFep~~FF~~Yk~YL 109 (434)
.+++--++++.+..|+.|+-.-.+. |..++...-=+++|++-|
T Consensus 110 ~d~li~pslr~a~rElRRak~kvqk-------wErvcaAlRELnKhRdiv 152 (155)
T PF07789_consen 110 ADDLILPSLRKANRELRRAKSKVQK-------WERVCAALRELNKHRDIV 152 (155)
T ss_pred CcceechhHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Confidence 3789999999999999999887775 999998888888887754
No 11
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=21.74 E-value=54 Score=29.21 Aligned_cols=73 Identities=22% Similarity=0.259 Sum_probs=47.8
Q ss_pred cccCCCCCCCCCCCcceEecCCCCCCcchhhcChhhHHHHHHHHHHHHHHHHHHhh------cccchhhhcCCcchhhcc
Q 013882 32 SVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVEL------NKAQWSALFEPYLFFESY 105 (434)
Q Consensus 32 ~vWdPr~n~rDr~hlMPIITPayP~mNST~NVT~STl~vI~eEf~RG~~I~~~I~~------g~~~W~~LFep~~FF~~Y 105 (434)
.+|+...+......-.+.-.|.||..+.-.+|-.+= --..+|..|.++++.+.. .+.-|..||+-...+.++
T Consensus 27 ~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf--~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~~ 104 (126)
T PF12921_consen 27 SVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSF--GYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSSK 104 (126)
T ss_pred HhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHH--HhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCC
Confidence 467765443221111788899999888877766553 444678889999887743 345699988765555544
Q ss_pred c
Q 013882 106 R 106 (434)
Q Consensus 106 k 106 (434)
+
T Consensus 105 ~ 105 (126)
T PF12921_consen 105 R 105 (126)
T ss_pred c
Confidence 4
Done!