Query 020698
Match_columns 322
No_of_seqs 155 out of 374
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 04:26:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020698.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020698hhsearch_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 2.6E-70 5.7E-75 540.8 15.5 231 1-238 262-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 2.5E-68 5.4E-73 542.1 21.7 234 1-237 300-543 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 3.4E-61 7.5E-66 462.2 10.8 232 1-236 254-529 (552)
4 PF04926 PAP_RNA-bind: Poly(A) 100.0 1.1E-36 2.4E-41 265.2 7.4 135 100-235 1-156 (157)
5 PF04928 PAP_central: Poly(A) 100.0 2.3E-34 5E-39 269.6 5.5 99 1-99 156-254 (254)
6 PF03813 Nrap: Nrap protein; 92.7 1.5 3.3E-05 49.0 12.9 183 2-197 224-425 (972)
7 PF03813 Nrap: Nrap protein; 72.7 9.2 0.0002 42.9 7.0 94 3-98 734-839 (972)
8 PF03828 PAP_assoc: Cid1 famil 45.2 14 0.00031 26.4 1.6 49 2-55 5-58 (60)
9 PF07357 DRAT: Dinitrogenase r 43.2 9.8 0.00021 36.5 0.6 32 104-135 84-115 (262)
10 PF07789 DUF1627: Protein of u 30.8 26 0.00055 31.1 1.2 51 47-109 102-152 (155)
11 PHA02696 hypothetical protein; 27.6 51 0.0011 25.6 2.2 22 121-142 9-30 (79)
12 PF12921 ATP13: Mitochondrial 25.9 28 0.00061 29.4 0.6 71 32-105 27-104 (126)
13 KOG2054 Nucleolar RNA-associat 22.3 87 0.0019 35.6 3.6 72 56-129 407-479 (1121)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=2.6e-70 Score=540.85 Aligned_cols=231 Identities=46% Similarity=0.850 Sum_probs=213.7
Q ss_pred ChhHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020698 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (322)
Q Consensus 1 mLV~rFF~vys~W~Wp~PV~L~~i~~~~lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~ 80 (322)
+||+|||++||+|+||+||+|+++++++||++|||||.|++||+|+|||||||||+||||||||+||++||++||+||++
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 HHHHHhcCccchhhhccCCCchhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhcCCCceeEcCCCCCCCCCC
Q 020698 81 ICEEIELGKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDPS 160 (322)
Q Consensus 81 i~~~i~~~~~~W~~Lfe~~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~~ 160 (322)
||++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.+||++ ..++.|||+|+.|.+..
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 ICDDIELNKLDWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERN-QVILIAHPNPKKFKDTY 420 (562)
T ss_pred HHHHHHhccccHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhh-cceEEecCCcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999996 57788999999998764
Q ss_pred C----CCCceeEEEceeecccCCCCcCcccchHHHHHHHHHhhc----cccccCCC--eEEEEEEeccCCCCCCcCCCCc
Q 020698 161 K----PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGID----NYRVRREG--RDIYFSYVCRRHLPSFVFPDGY 230 (322)
Q Consensus 161 ~----~~~~~~ffIGL~~~~~~~~~~~~~~dL~~~v~~F~~~v~----~~~~~~~~--m~i~v~~vkr~~LP~~V~~~g~ 230 (322)
. ..+.+.|||||.+.++. ++||+..+++|...++ ++..+.+| |++.+.|+||++|+.+++..++
T Consensus 421 ~~~~~~~~~~~~~igl~~~e~~------~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~krr~l~~~~~~~~l 494 (562)
T KOG2245|consen 421 NCPLEEDPESLWFIGLEFDENV------KIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVKRRSLIQTITKEFL 494 (562)
T ss_pred cCCcccchhHhhhhcccccccc------cchhhhhHHHhhhhhhhcceeeeeeecccccccccccccccccccccCHHHh
Confidence 2 23467899999987654 4899999999999887 45556788 8888889999999999999998
Q ss_pred ccCCCCCC
Q 020698 231 KWHRPSRH 238 (322)
Q Consensus 231 ~~~~~~~~ 238 (322)
++.+.-++
T Consensus 495 ~~~k~~~~ 502 (562)
T KOG2245|consen 495 RLCKQYKK 502 (562)
T ss_pred hHHHhhcc
Confidence 87776654
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=2.5e-68 Score=542.08 Aligned_cols=234 Identities=35% Similarity=0.665 Sum_probs=214.5
Q ss_pred ChhHHHHHhhccCCCCCceecccccc-----CCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHH
Q 020698 1 MLVSRFFRVYTQWRWPNPVMMCPIEM-----GELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQF 75 (322)
Q Consensus 1 mLV~rFF~vys~W~Wp~PV~L~~i~~-----~~lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~~Ef 75 (322)
+||++||.+|++|+||+||+|+++++ |.+|++||||+.|++||+|+|||||||||+||||||||.||+++|++||
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 6789999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhc-CccchhhhccCCCchhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhcCCCceeEcCCCC
Q 020698 76 QCGNRICEEIEL-GKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPN 154 (322)
Q Consensus 76 ~Rg~~i~~~i~~-~~~~W~~Lfe~~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~ 154 (322)
+||++||++|.. ++.+|++||++++||.+|++||+|++.+.+++++..|.||||||||.|+.+||+. +.+.|||||+
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 KRAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLETL--NNLKIRPYPK 457 (593)
T ss_pred HHHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhcc--CCceEeecCc
Confidence 999999999998 8999999999999999999999999999999999999999999999999999974 3467899999
Q ss_pred CCCCCCC-CCCceeEEEceeecccCCCCcCcccchHHHHHHHHHhhccccc---cCCCeEEEEEEeccCCCCCCcCCCCc
Q 020698 155 KYIDPSK-PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGIDNYRV---RREGRDIYFSYVCRRHLPSFVFPDGY 230 (322)
Q Consensus 155 ~f~d~~~-~~~~~~ffIGL~~~~~~~~~~~~~~dL~~~v~~F~~~v~~~~~---~~~~m~i~v~~vkr~~LP~~V~~~g~ 230 (322)
+|.+... ..|.++|||||+++.... .+..++||+.++++|.+.|++|.. |.++|+|+|+|||++|||++||++|.
T Consensus 458 ~f~~~~~~~~~~~~ffIGL~~~~~~~-~~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk~~~Lp~~v~~~~~ 536 (593)
T PTZ00418 458 FFKYQDDGWDYASSFFIGLVFFSKNV-YNNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLKKSQLPAFVLSQTP 536 (593)
T ss_pred ccccCCCCceeEEEEEEeEeeccCCC-CCCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEeehHhCCHhhccCCC
Confidence 9987653 356789999999976543 233589999999999999998863 56789999999999999999999998
Q ss_pred ccCCCCC
Q 020698 231 KWHRPSR 237 (322)
Q Consensus 231 ~~~~~~~ 237 (322)
+|+.+.+
T Consensus 537 ~~~~~~~ 543 (593)
T PTZ00418 537 EEPVKTK 543 (593)
T ss_pred cCCCccc
Confidence 8876655
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=3.4e-61 Score=462.23 Aligned_cols=232 Identities=33% Similarity=0.642 Sum_probs=212.7
Q ss_pred ChhHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020698 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (322)
Q Consensus 1 mLV~rFF~vys~W~Wp~PV~L~~i~~~~lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~ 80 (322)
.||+|||.++|+|+||+||+|+||+||+++++||||++|++|++|.|||||||||+||+|||+|.||..||..||-||++
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 HHHHHhcCccchhhhccCCCchhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhcCCCceeEcCCCCCCCCC-
Q 020698 81 ICEEIELGKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDP- 159 (322)
Q Consensus 81 i~~~i~~~~~~W~~Lfe~~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~- 159 (322)
|+++|+.+..+|..||+..+||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||.. .+++.|||||+.|...
T Consensus 334 I~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~v-d~i~~AhPF~K~F~~~y 412 (552)
T COG5186 334 ILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAV-DDILYAHPFPKAFRKVY 412 (552)
T ss_pred hhhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHh-hhhhhcCcCChhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999985 5778899999999510
Q ss_pred -------------------------------C-----------CCCCceeEEEceeecccCCCCcCcccchHHHHHHHHH
Q 020698 160 -------------------------------S-----------KPCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRR 197 (322)
Q Consensus 160 -------------------------------~-----------~~~~~~~ffIGL~~~~~~~~~~~~~~dL~~~v~~F~~ 197 (322)
+ -..|.+.|||||++.... .++++||..++++|.+
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 011446899999986543 3578999999999999
Q ss_pred hhccccccC-CCeEEEEEEeccCCCCCCcCCCCcccCCCC
Q 020698 198 GIDNYRVRR-EGRDIYFSYVCRRHLPSFVFPDGYKWHRPS 236 (322)
Q Consensus 198 ~v~~~~~~~-~~m~i~v~~vkr~~LP~~V~~~g~~~~~~~ 236 (322)
.++.|++++ .+|.|.|+.+|+++||+-||.+|..+|...
T Consensus 490 lcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~~ 529 (552)
T COG5186 490 LCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSNS 529 (552)
T ss_pred HHHHhhccccceeeeehhhccccCCchhhcCCCccCcccc
Confidence 999998886 589999999999999999999998776643
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=1.1e-36 Score=265.17 Aligned_cols=135 Identities=34% Similarity=0.679 Sum_probs=106.0
Q ss_pred CchhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhcCCCceeEcCCCCCCC------------------CCCC
Q 020698 100 PFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYI------------------DPSK 161 (322)
Q Consensus 100 ~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------d~~~ 161 (322)
+||.+|||||+|+|+|.+++++.+|.||||||||.||.+||+.. .+..|||||+.|. +...
T Consensus 1 ~FF~~Yk~yl~I~~~a~~~~~~~~W~G~VESrlR~Lv~~LE~~~-~i~~ahp~pk~f~~~~~~~~~~~~~~~~~~~~~~~ 79 (157)
T PF04926_consen 1 DFFSRYKHYLQIDVSAKNEEDHRKWSGWVESRLRHLVQKLERNP-GIKLAHPFPKRFERVYECSEQADENNDEEEEEDPE 79 (157)
T ss_dssp -HHHH-SEEEEEEEEECSHHHHHHHHHHHHCCHHHHHHHHHTST-TEEEEEE-SS-EEEEEE-EBECTTCTTSHHCHCTS
T ss_pred ChhHhCceeEEEEEEeCCHHHHHHhhhHHHHHHHHHHHHHccCC-CeeEecCCCCccccccccccccccccccccccCCC
Confidence 69999999999999999999999999999999999999999974 5677999999997 1223
Q ss_pred CCCceeEEEceeecccCCCCcCcccchHHHHHHHHHhhccccc--c-CCCeEEEEEEeccCCCCCCcCCCCcccCCC
Q 020698 162 PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGIDNYRV--R-REGRDIYFSYVCRRHLPSFVFPDGYKWHRP 235 (322)
Q Consensus 162 ~~~~~~ffIGL~~~~~~~~~~~~~~dL~~~v~~F~~~v~~~~~--~-~~~m~i~v~~vkr~~LP~~V~~~g~~~~~~ 235 (322)
..+.++|||||++......+.++++||+.++++|++.|++|.. + .++|+|+|+||||+|||++||++|.+|+++
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 4567899999999876643334689999999999999999877 3 568999999999999999999999988875
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=100.00 E-value=2.3e-34 Score=269.64 Aligned_cols=99 Identities=57% Similarity=1.057 Sum_probs=76.5
Q ss_pred ChhHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020698 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (322)
Q Consensus 1 mLV~rFF~vys~W~Wp~PV~L~~i~~~~lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~ 80 (322)
+||.+||.+||+|+||+||+|++++++.+++++|||+.|++|++|+|||||||||+||||||||+||+++|++||+||++
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 HHHHHhcCccchhhhccCC
Q 020698 81 ICEEIELGKAEWSALFEHY 99 (322)
Q Consensus 81 i~~~i~~~~~~W~~Lfe~~ 99 (322)
|++++..++.+|++||+|+
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=92.68 E-value=1.5 Score=48.98 Aligned_cols=183 Identities=10% Similarity=0.126 Sum_probs=107.0
Q ss_pred hhHHHHHhhccCCC-CCceeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020698 2 LVSRFFRVYTQWRW-PNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (322)
Q Consensus 2 LV~rFF~vys~W~W-p~PV~L~~i~~~~lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~ 80 (322)
|+.-+....|..+| -+|+.++.-.+.. +.. .....+--|++--.-=.+|-.+++|.++++.|+.|-+++.+
T Consensus 224 lFr~~l~fLA~~d~~~~~l~~~~~~~~~-------~~~-~~~~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~ 295 (972)
T PF03813_consen 224 LFRAVLQFLATTDLSKKPLFFKSSSDST-------ESL-EEFHSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLE 295 (972)
T ss_pred HHHHHHHHHhccccccCceEEecCCCcc-------chh-hhhhccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHH
Confidence 45566677799999 6699998765311 000 11123445555555557999999999999999999999999
Q ss_pred HHHHHhcCccchhhhccC--CCchhccccEEEEE-------EEeCChhhhhhhhhhhHHHHHHHHH-HhhhcCCCceeEc
Q 020698 81 ICEEIELGKAEWSALFEH--YPFFEAYENYLQVD-------IVAADADDLLTWKGWVESRFRQLTL-KIEQDTNGLLQCH 150 (322)
Q Consensus 81 i~~~i~~~~~~W~~Lfe~--~~FF~~Yk~yL~I~-------v~a~~~e~~~~W~GwVESRlR~Lv~-~LE~~~~~~l~ah 150 (322)
++++- .....+.+|-. ..+..+|.+++.|. .......+...+...++.++-.|+. .|-... -.++
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 98863 23456777744 35678999999991 1112223344454566677755544 353322 1123
Q ss_pred CC---CCCCC--CCCCCCCceeEEEceeecccCC---CCcCcccchHHHHHHHHH
Q 020698 151 PY---PNKYI--DPSKPCPNSAFFWGLSRKEVGT---SKECQQFDFQGTVKNFRR 197 (322)
Q Consensus 151 p~---P~~f~--d~~~~~~~~~ffIGL~~~~~~~---~~~~~~~dL~~~v~~F~~ 197 (322)
++ +..+. ............|||.++.... +..|...|-.....+|++
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 22221 1111111226789999876321 112223344566777876
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=72.73 E-value=9.2 Score=42.93 Aligned_cols=94 Identities=22% Similarity=0.366 Sum_probs=58.6
Q ss_pred hHHHHHhhccCCCCC-ceeccccccCC--------CCccccCCCCCCCCCCCcceeeccCCCCCCcccc---cchhHHHH
Q 020698 3 VSRFFRVYTQWRWPN-PVMMCPIEMGE--------LGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYK---VSLGTLQV 70 (322)
Q Consensus 3 V~rFF~vys~W~Wp~-PV~L~~i~~~~--------lg~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~N---Vs~STl~v 70 (322)
+-||.+..|.|+|-+ |++++.-.+-. -.|..|.. .+|......|-|.||.=|.- +... -+..-++.
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 358888999999995 99886432211 12333433 23444567899999999843 3333 44444555
Q ss_pred HHHHHHHHHHHHHHHhcCccchhhhccC
Q 020698 71 MTEQFQCGNRICEEIELGKAEWSALFEH 98 (322)
Q Consensus 71 I~~Ef~Rg~~i~~~i~~~~~~W~~Lfe~ 98 (322)
|+.==+.++++++.-..+..+|..||.+
T Consensus 812 l~~LAk~sl~~l~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 812 LTALAKASLKLLEEQGLSDLDWKSLFRP 839 (972)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHhcCC
Confidence 5554455566666322246799999986
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=45.20 E-value=14 Score=26.43 Aligned_cols=49 Identities=24% Similarity=0.449 Sum_probs=28.9
Q ss_pred hhHHHHHhhc-cCCCCCcee-ccccccCCC-C--ccccCCCCCCCCCCCcceeeccCCC
Q 020698 2 LVSRFFRVYT-QWRWPNPVM-MCPIEMGEL-G--FSVWDPRKNPKDRSHRMPIITPAYH 55 (322)
Q Consensus 2 LV~rFF~vys-~W~Wp~PV~-L~~i~~~~l-g--~~vWdPr~n~~Dr~hlMPIITPayP 55 (322)
|+..||..|+ .|+|.+=|+ +.. |.. . ...|.. ....+...|.|.=|.-|
T Consensus 5 Ll~~Ff~~Y~~~Fd~~~~~Isi~~---g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~ 58 (60)
T PF03828_consen 5 LLLGFFEYYGRKFDYENNVISIRN---GGYFPKEEKNWSK--SRNQRKKRLCIEDPFDP 58 (60)
T ss_dssp HHHHHHHHHHHTS-TTTEEEESSS---SSEEEHHHHTGCH--CCCCECSSSEBBESSST
T ss_pred HHHHHHHHhCCcCCCCceEEEecC---CceEEhhhccccc--cccCCCCeEEEECCCCC
Confidence 6889999999 999998544 322 211 0 123431 11234577888888655
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=43.24 E-value=9.8 Score=36.47 Aligned_cols=32 Identities=34% Similarity=0.471 Sum_probs=21.5
Q ss_pred ccccEEEEEEEeCChhhhhhhhhhhHHHHHHH
Q 020698 104 AYENYLQVDIVAADADDLLTWKGWVESRFRQL 135 (322)
Q Consensus 104 ~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~L 135 (322)
.|-.+|+==..-.|.-+...++||||||+-.+
T Consensus 84 sYLRlLrGW~fDSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 84 SYLRLLRGWGFDSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred hHHHHHhccCcCCCChhhhhhhhhhhhccCcC
Confidence 34444433333467788899999999998544
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=30.76 E-value=26 Score=31.11 Aligned_cols=51 Identities=10% Similarity=0.211 Sum_probs=39.4
Q ss_pred ceeeccCCCCCCcccccchhHHHHHHHHHHHHHHHHHHHhcCccchhhhccCCCchhccccEE
Q 020698 47 MPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNRICEEIELGKAEWSALFEHYPFFEAYENYL 109 (322)
Q Consensus 47 MPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~i~~~i~~~~~~W~~Lfe~~~FF~~Yk~yL 109 (322)
.|-.|..+| .|+--.+++.+..|+.||-.-++. |..++...-=+++|++-|
T Consensus 102 ~Psfte~~~-----d~li~pslr~a~rElRRak~kvqk-------wErvcaAlRELnKhRdiv 152 (155)
T PF07789_consen 102 IPSFTEKRA-----DDLILPSLRKANRELRRAKSKVQK-------WERVCAALRELNKHRDIV 152 (155)
T ss_pred CCCcccccC-----cceechhHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Confidence 444444444 789999999999999999887776 999998777677777643
No 11
>PHA02696 hypothetical protein; Provisional
Probab=27.59 E-value=51 Score=25.58 Aligned_cols=22 Identities=32% Similarity=0.915 Sum_probs=19.2
Q ss_pred hhhhhhhhHHHHHHHHHHhhhc
Q 020698 121 LLTWKGWVESRFRQLTLKIEQD 142 (322)
Q Consensus 121 ~~~W~GwVESRlR~Lv~~LE~~ 142 (322)
+-.|.||+.-|+|.|+..|-+.
T Consensus 9 lFvwAgW~aRRVr~Lc~~lRrr 30 (79)
T PHA02696 9 LFVWAGWLARRVRRLCIWLRRR 30 (79)
T ss_pred hhhhHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999764
No 12
>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=25.86 E-value=28 Score=29.43 Aligned_cols=71 Identities=17% Similarity=0.219 Sum_probs=46.8
Q ss_pred cccCCCCCCCCCCCc-ceeeccCCCCCCcccccchhHHHHHHHHHHHHHHHHHHHhc------CccchhhhccCCCchhc
Q 020698 32 SVWDPRKNPKDRSHR-MPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNRICEEIEL------GKAEWSALFEHYPFFEA 104 (322)
Q Consensus 32 ~vWdPr~n~~Dr~hl-MPIITPayP~mNSt~NVs~STl~vI~~Ef~Rg~~i~~~i~~------~~~~W~~Lfe~~~FF~~ 104 (322)
.+|+...+... .+. .+.-.|.||..+.-.+|-.| + --..+|..|.++++.+.. .+.-|..||+-.....+
T Consensus 27 ~~WgI~~~~~~-~~~~~~~~spl~Pt~~lL~AIv~s-f-~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~ 103 (126)
T PF12921_consen 27 SVWGIDVNGKK-KEGDYPPSSPLYPTSRLLIAIVHS-F-GYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSS 103 (126)
T ss_pred HhcCCCCCCcc-ccCccCCCCCCCCCHHHHHHHHHH-H-HhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcC
Confidence 47876655322 222 88889999988876666544 3 334678889999888653 35568888876544443
Q ss_pred c
Q 020698 105 Y 105 (322)
Q Consensus 105 Y 105 (322)
+
T Consensus 104 ~ 104 (126)
T PF12921_consen 104 K 104 (126)
T ss_pred C
Confidence 3
No 13
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=22.26 E-value=87 Score=35.61 Aligned_cols=72 Identities=17% Similarity=0.255 Sum_probs=53.0
Q ss_pred CCCcccccchhHHHHHHHHHHHHHHHHHHHhcCccchhhhc-cCCCchhccccEEEEEEEeCChhhhhhhhhhhH
Q 020698 56 CMNSSYKVSLGTLQVMTEQFQCGNRICEEIELGKAEWSALF-EHYPFFEAYENYLQVDIVAADADDLLTWKGWVE 129 (322)
Q Consensus 56 ~mNSt~NVs~STl~vI~~Ef~Rg~~i~~~i~~~~~~W~~Lf-e~~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVE 129 (322)
..|-.-|++.|+...+++|..-.+.++++...+ ..+.+| ++.+.|..|.|=+.+.....-+.....-.||.|
T Consensus 407 ~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~--~F~~IFmtkip~~~~yDh~l~l~~~~~l~~~~~~~~~~~~ 479 (1121)
T KOG2054|consen 407 HLNLCANMTASTYEQVQEEARLTLMLLDSRADD--GFSLIFMTKIPVFRAYDHVLHLSPLSRLQAAEHLLSGFCE 479 (1121)
T ss_pred cchhhhhccHHHHHHHHHHHHHHHHHHhhhhhc--CcceeeeecCCchhhhheeeeccccchhhhHHhhcccchh
Confidence 567777999999999999999999999986543 355555 678999999998887766544444444444443
Done!