Query 020365
Match_columns 327
No_of_seqs 153 out of 370
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 09:09:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020365.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020365hhsearch_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 1.5E-69 3.2E-74 536.7 13.9 231 1-243 262-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 1.1E-67 2.4E-72 538.6 21.1 234 1-242 300-543 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 6.6E-60 1.4E-64 454.3 10.8 232 1-241 254-529 (552)
4 PF04926 PAP_RNA-bind: Poly(A) 100.0 2E-36 4.4E-41 264.2 7.4 135 105-240 1-156 (157)
5 PF04928 PAP_central: Poly(A) 100.0 8.4E-34 1.8E-38 266.5 4.9 99 1-104 156-254 (254)
6 PF03813 Nrap: Nrap protein; 90.2 4.1 8.9E-05 45.8 13.0 183 2-202 224-425 (972)
7 PF03813 Nrap: Nrap protein; 66.6 15 0.00032 41.4 7.0 94 3-103 734-839 (972)
8 PF07357 DRAT: Dinitrogenase r 45.0 8.9 0.00019 36.8 0.6 32 109-140 84-115 (262)
9 PF03828 PAP_assoc: Cid1 famil 42.6 16 0.00035 26.2 1.6 49 2-55 5-58 (60)
10 PF07789 DUF1627: Protein of u 28.1 19 0.00041 32.0 -0.0 51 47-114 102-152 (155)
11 PHA02696 hypothetical protein; 26.6 53 0.0011 25.6 2.1 22 126-147 9-30 (79)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.5e-69 Score=536.66 Aligned_cols=231 Identities=46% Similarity=0.850 Sum_probs=214.3
Q ss_pred ChhHHHHHhhccCCCCCCeeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020365 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (327)
Q Consensus 1 mLv~rFF~vys~W~Wp~PV~L~~i~~~~l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~eEf~Rg~~ 80 (327)
+||+|||++||+|+||+||+|+++++++|+++|||||.|++||+|+|||||||||+||||||||+||++||++||+||++
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 hhhcccchhhhcCccchhhhhcCCccccccccEEEEEEEeCChhhhhhhhhhhhhHHHHHHHHhhhcCCCceeEcCCCCC
Q 020365 81 ICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNK 160 (327)
Q Consensus 81 i~~~~~~~~i~~~~~~W~~Lfep~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~ 160 (327)
||+ +|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.+||++ .+++.|||+|+.
T Consensus 342 I~~-----~i~~~k~~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~-~~i~~ahp~P~~ 415 (562)
T KOG2245|consen 342 ICD-----DIELNKLDWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERN-QVILIAHPNPKK 415 (562)
T ss_pred HHH-----HHHhccccHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhh-cceEEecCCccc
Confidence 999 99999999999999999999999999999999999999999999999999999999996 577889999999
Q ss_pred CCCCCC----CCCceeEEEeeeecccCCCCcCceechHHHHHHHHHHhc----cccccCCC--eEEEEEEeccCCCCCCc
Q 020365 161 YIDPSK----PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGID----NYRVRREG--RDIYFSYVCRRHLPSFV 230 (327)
Q Consensus 161 f~d~~~----~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~~F~~~v~----~~~~~~~~--m~i~v~~Vkr~~LP~~V 230 (327)
|.++.. ..+.+.|||||.+.++. ++||+..+++|.+.++ +...+.+| |++.+.|+||++|+.++
T Consensus 416 f~~~~~~~~~~~~~~~~~igl~~~e~~------~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~krr~l~~~~ 489 (562)
T KOG2245|consen 416 FKDTYNCPLEEDPESLWFIGLEFDENV------KIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVKRRSLIQTI 489 (562)
T ss_pred ccccccCCcccchhHhhhhcccccccc------cchhhhhHHHhhhhhhhcceeeeeeeccccccccccccccccccccc
Confidence 987653 23568899999987654 4899999999999887 45556788 88888899999999999
Q ss_pred CCCCcccCCCCCC
Q 020365 231 FPDGYKWHRPSRH 243 (327)
Q Consensus 231 ~~~g~k~~~~~~~ 243 (327)
+.+++++.+.-++
T Consensus 490 ~~~~l~~~k~~~~ 502 (562)
T KOG2245|consen 490 TKEFLRLCKQYKK 502 (562)
T ss_pred CHHHhhHHHhhcc
Confidence 9999887776655
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=1.1e-67 Score=538.56 Aligned_cols=234 Identities=35% Similarity=0.665 Sum_probs=214.7
Q ss_pred ChhHHHHHhhccCCCCCCeecccccc-----CCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHH
Q 020365 1 MLVSRFFRVYTQWRWPNPVMMCPIEM-----GELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQF 75 (327)
Q Consensus 1 mLv~rFF~vys~W~Wp~PV~L~~i~~-----~~l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~eEf 75 (327)
+||++||.+|++|+||+||+|+++++ |.+|++||||+.|++|++|+|||||||||+||||||||.||+++|++||
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 58999999999999999999999976 6789999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcccchhhhc-CccchhhhhcCCccccccccEEEEEEEeCChhhhhhhhhhhhhHHHHHHHHhhhcCCCceeE
Q 020365 76 QCGNRICEVRAYFEIEL-GKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQC 154 (327)
Q Consensus 76 ~Rg~~i~~~~~~~~i~~-~~~~W~~Lfep~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~a 154 (327)
+||++||+ +|.. ++..|++||+|++||.+|++||+|++.|.+++++..|.||||||||.|+.+||+. +.+.|
T Consensus 380 ~Ra~~i~~-----~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~~--~~i~~ 452 (593)
T PTZ00418 380 KRAHEIIK-----YIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLETL--NNLKI 452 (593)
T ss_pred HHHHHHHH-----HHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhcc--CCceE
Confidence 99999999 9988 8999999999999999999999999999999999999999999999999999974 44779
Q ss_pred cCCCCCCCCCCC-CCCceeEEEeeeecccCCCCcCceechHHHHHHHHHHhccccc---cCCCeEEEEEEeccCCCCCCc
Q 020365 155 HPYPNKYIDPSK-PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGIDNYRV---RREGRDIYFSYVCRRHLPSFV 230 (327)
Q Consensus 155 hp~P~~f~d~~~-~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~~F~~~v~~~~~---~~~~m~i~v~~Vkr~~LP~~V 230 (327)
||||+.|.+... ..+.++|||||.++..... ...++||+.++++|.+.|++|.. |.++|+|+|+|||++|||+||
T Consensus 453 ~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk~~~Lp~~v 531 (593)
T PTZ00418 453 RPYPKFFKYQDDGWDYASSFFIGLVFFSKNVY-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLKKSQLPAFV 531 (593)
T ss_pred eecCcccccCCCCceeEEEEEEeEeeccCCCC-CCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEeehHhCCHhh
Confidence 999999987653 3567899999999776432 33589999999999999998753 577899999999999999999
Q ss_pred CCCCcccCCCCC
Q 020365 231 FPDGYKWHRPSR 242 (327)
Q Consensus 231 ~~~g~k~~~~~~ 242 (327)
|++|++|+...+
T Consensus 532 ~~~~~~~~~~~~ 543 (593)
T PTZ00418 532 LSQTPEEPVKTK 543 (593)
T ss_pred ccCCCcCCCccc
Confidence 999988876555
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=6.6e-60 Score=454.31 Aligned_cols=232 Identities=33% Similarity=0.639 Sum_probs=212.7
Q ss_pred ChhHHHHHhhccCCCCCCeeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020365 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (327)
Q Consensus 1 mLv~rFF~vys~W~Wp~PV~L~~i~~~~l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~eEf~Rg~~ 80 (327)
.||+|||.++|+|+||+||+|+||+||+++++||||+.|++|++|.|||||||||+||+|||||.||..||..||-||++
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 hhhcccchhhhcCccchhhhhcCCccccccccEEEEEEEeCChhhhhhhhhhhhhHHHHHHHHhhhcCCCceeEcCCCCC
Q 020365 81 ICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNK 160 (327)
Q Consensus 81 i~~~~~~~~i~~~~~~W~~Lfep~~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~ 160 (327)
|++ +|+.+..+|..||+..+||.+||+||.|++.+.++|++.+|.|+|||++|.|+.+||-. .+++.|||||+.
T Consensus 334 I~~-----di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~v-d~i~~AhPF~K~ 407 (552)
T COG5186 334 ILS-----DIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAV-DDILYAHPFPKA 407 (552)
T ss_pred hhh-----hHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHh-hhhhhcCcCChh
Confidence 999 99999999999999999999999999999999999999999999999999999999975 577889999999
Q ss_pred CCCC----------------------------------C---------CCCCceeEEEeeeecccCCCCcCceechHHHH
Q 020365 161 YIDP----------------------------------S---------KPCPNSAFFWGLSRKEVGTSKECQQFDFQGTV 197 (327)
Q Consensus 161 f~d~----------------------------------~---------~~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v 197 (327)
|... . -+.|.+.|||||++.... .++++||..++
T Consensus 408 F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~~---~~kkvdi~~p~ 484 (552)
T COG5186 408 FRKVYNCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPVK---PGKKVDIEQPV 484 (552)
T ss_pred hhhhcCCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeecC---CCceeeeeccH
Confidence 8510 0 012457899999986543 36789999999
Q ss_pred HHHHHHhccccccC-CCeEEEEEEeccCCCCCCcCCCCcccCCCC
Q 020365 198 KNFRRGIDNYRVRR-EGRDIYFSYVCRRHLPSFVFPDGYKWHRPS 241 (327)
Q Consensus 198 ~~F~~~v~~~~~~~-~~m~i~v~~Vkr~~LP~~V~~~g~k~~~~~ 241 (327)
++|.+.|+.|++++ .+|.|.|+.+|+++||+-||.+|+++|...
T Consensus 485 ~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~~ 529 (552)
T COG5186 485 KEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSNS 529 (552)
T ss_pred HHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccCcccc
Confidence 99999999998776 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=2e-36 Score=264.16 Aligned_cols=135 Identities=34% Similarity=0.683 Sum_probs=105.6
Q ss_pred ccccccccEEEEEEEeCChhhhhhhhhhhhhHHHHHHHHhhhcCCCceeEcCCCCCCC------------------CCCC
Q 020365 105 PFFEAYENYLQVDIVAADADDLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYI------------------DPSK 166 (327)
Q Consensus 105 ~FF~~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------d~~~ 166 (327)
+||.+|||||+|+|+|.+++++.+|.||||||||.||.+||+.. ++..|||||+.|. +...
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 5677999999998 1223
Q ss_pred CCCceeEEEeeeecccCCCCcCceechHHHHHHHHHHhccccc---cCCCeEEEEEEeccCCCCCCcCCCCcccCCC
Q 020365 167 PCPNSAFFWGLSRKEVGTSKECQQFDFQGTVKNFRRGIDNYRV---RREGRDIYFSYVCRRHLPSFVFPDGYKWHRP 240 (327)
Q Consensus 167 ~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~~F~~~v~~~~~---~~~~m~i~v~~Vkr~~LP~~V~~~g~k~~~~ 240 (327)
..+.++|||||++......+.+.++||+.++++|++.|++|.. +.++|+|+|+|||++|||++||++|.+|+++
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 4567999999999887643334689999999999999999877 3578999999999999999999999998875
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=99.98 E-value=8.4e-34 Score=266.46 Aligned_cols=99 Identities=57% Similarity=1.057 Sum_probs=76.3
Q ss_pred ChhHHHHHhhccCCCCCCeeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020365 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (327)
Q Consensus 1 mLv~rFF~vys~W~Wp~PV~L~~i~~~~l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~eEf~Rg~~ 80 (327)
+||.+||.+||+|+||+||+|++++++.+++++|||+.|++|++|+|||||||||+||||||||+||+++|++||+||++
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 hhhcccchhhhcCccchhhhhcCC
Q 020365 81 ICEVRAYFEIELGKAEWSALFEHY 104 (327)
Q Consensus 81 i~~~~~~~~i~~~~~~W~~Lfep~ 104 (327)
||+ ++..++.+|++||+|+
T Consensus 236 i~~-----~~~~~~~~W~~L~e~~ 254 (254)
T PF04928_consen 236 ILS-----EILKGGASWSDLFEPH 254 (254)
T ss_dssp HHH-----HHHTTSS-HHHCT---
T ss_pred HHH-----HHHcCCCCHHHHcCCC
Confidence 999 9999999999999985
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=90.18 E-value=4.1 Score=45.77 Aligned_cols=183 Identities=10% Similarity=0.132 Sum_probs=105.8
Q ss_pred hhHHHHHhhccCCC-CCCeeccccccCCCCccccCCCCCCCCCCCcceeeccCCCCCCcccccchhHHHHHHHHHHHHHH
Q 020365 2 LVSRFFRVYTQWRW-PNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNR 80 (327)
Q Consensus 2 Lv~rFF~vys~W~W-p~PV~L~~i~~~~l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~NVs~STl~vI~eEf~Rg~~ 80 (327)
|+.-+....|..+| -+|+.++.-.+... .. .....+--||+--.-=.+|-.+++|.++++.|+.|-+++.+
T Consensus 224 lFr~~l~fLA~~d~~~~~l~~~~~~~~~~-------~~-~~~~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~ 295 (972)
T PF03813_consen 224 LFRAVLQFLATTDLSKKPLFFKSSSDSTE-------SL-EEFHSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLE 295 (972)
T ss_pred HHHHHHHHHhccccccCceEEecCCCccc-------hh-hhhhccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHH
Confidence 44556667799999 56999987653110 00 11123445555555568999999999999999999999999
Q ss_pred hhhcccchhhhcCccchhhhhc-C-CccccccccEEEEE---EEe----CChhhhhhhhhhhhhHHHHHH-HHhhhcCCC
Q 020365 81 ICEVRAYFEIELGKAEWSALFE-H-YPFFEAYENYLQVD---IVA----ADADDLLTWKGWVESRFRQLT-LKIEQDTNG 150 (327)
Q Consensus 81 i~~~~~~~~i~~~~~~W~~Lfe-p-~~FF~~Yk~yL~I~---v~a----~~~e~~~~W~GwVESRlR~Lv-~~LE~~~~~ 150 (327)
+++ +- ....-+.+|- + .++..+|.+++.|. ... ....+...+...++.++-.|+ ..|-...
T Consensus 296 lL~-----~~--~~d~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~-- 366 (972)
T PF03813_consen 296 LLD-----DS--SDDGFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRA-- 366 (972)
T ss_pred Hhc-----cc--cccchhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHH--
Confidence 988 32 2234666664 4 45678999999991 111 222333444445666775543 3453221
Q ss_pred ceeEcCCC---CCCC--CCCCCCCceeEEEeeeecccCC---CCcCceechHHHHHHHHH
Q 020365 151 LLQCHPYP---NKYI--DPSKPCPNSAFFWGLSRKEVGT---SKECQQFDFQGTVKNFRR 202 (327)
Q Consensus 151 ~l~ahp~P---~~f~--d~~~~~~~~~ffIGL~~~~~~~---~~~~~~~DL~~~v~~F~~ 202 (327)
-.++++. ..+. ............|||.++.... +.-|...|-.....+|++
T Consensus 367 -~~i~v~~~~~~~w~i~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~ 425 (972)
T PF03813_consen 367 -KLIRVLRPSQPPWSISSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFRE 425 (972)
T ss_pred -HeEEEeCCCCCCcccCCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHH
Confidence 1233331 1221 1111111226789999876321 112223345567777876
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=66.60 E-value=15 Score=41.43 Aligned_cols=94 Identities=22% Similarity=0.366 Sum_probs=57.7
Q ss_pred hHHHHHhhccCCCCC-CeeccccccCC--------CCccccCCCCCCCCCCCcceeeccCCCCCCcccc---cchhHHHH
Q 020365 3 VSRFFRVYTQWRWPN-PVMMCPIEMGE--------LGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSYK---VSLGTLQV 70 (327)
Q Consensus 3 v~rFF~vys~W~Wp~-PV~L~~i~~~~--------l~~~vWdPr~n~~Dr~hlMPIITPayP~mNSt~N---Vs~STl~v 70 (327)
+-||.+..|.|+|-+ |++++.-.+-. -.|..|.. .+|......|-|.||.=|.- +... -+..-++.
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 358888999999996 99887532211 12333443 23444567899999998743 3333 44444555
Q ss_pred HHHHHHHHHHhhhcccchhhhcCccchhhhhcC
Q 020365 71 MTEQFQCGNRICEVRAYFEIELGKAEWSALFEH 103 (327)
Q Consensus 71 I~eEf~Rg~~i~~~~~~~~i~~~~~~W~~Lfep 103 (327)
|+.==+.+.++++ .-..+..+|..||.+
T Consensus 812 l~~LAk~sl~~l~-----~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 812 LTALAKASLKLLE-----EQGLSDLDWKSLFRP 839 (972)
T ss_pred HHHHHHHHHHHHH-----hcCCCCCCHHHhcCC
Confidence 5544445555555 222347799999986
No 8
>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=44.97 E-value=8.9 Score=36.85 Aligned_cols=32 Identities=34% Similarity=0.471 Sum_probs=21.3
Q ss_pred ccccEEEEEEEeCChhhhhhhhhhhhhHHHHH
Q 020365 109 AYENYLQVDIVAADADDLLTWKGWVESRFRQL 140 (327)
Q Consensus 109 ~Yk~yL~I~v~a~~~e~~~~W~GwVESRlR~L 140 (327)
.|-.+|+==..-+|.-+...++||||||+-.+
T Consensus 84 sYLRlLrGW~fDSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 84 SYLRLLRGWGFDSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred hHHHHHhccCcCCCChhhhhhhhhhhhccCcC
Confidence 34444433333357788899999999998544
No 9
>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=42.62 E-value=16 Score=26.20 Aligned_cols=49 Identities=24% Similarity=0.449 Sum_probs=28.7
Q ss_pred hhHHHHHhhc-cCCCCCCee-ccccccCCC-C--ccccCCCCCCCCCCCcceeeccCCC
Q 020365 2 LVSRFFRVYT-QWRWPNPVM-MCPIEMGEL-G--FSVWDPRKNPKDRSHRMPIITPAYH 55 (327)
Q Consensus 2 Lv~rFF~vys-~W~Wp~PV~-L~~i~~~~l-~--~~vWdPr~n~~Dr~hlMPIITPayP 55 (327)
|+..||..|+ .|+|.+=|+ +.. +.. . -..|.. ....+...|.|.=|.=|
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 999998554 322 210 0 123431 11234567888877654
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=28.14 E-value=19 Score=31.96 Aligned_cols=51 Identities=10% Similarity=0.211 Sum_probs=39.3
Q ss_pred ceeeccCCCCCCcccccchhHHHHHHHHHHHHHHhhhcccchhhhcCccchhhhhcCCccccccccEE
Q 020365 47 MPIITPAYHCMNSSYKVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYL 114 (327)
Q Consensus 47 MPIITPayP~mNSt~NVs~STl~vI~eEf~Rg~~i~~~~~~~~i~~~~~~W~~Lfep~~FF~~Yk~yL 114 (327)
.|-+|..+| .++--++|+.+..|+.||-.-++ .|..++....=+.+|++-|
T Consensus 102 ~Psfte~~~-----d~li~pslr~a~rElRRak~kvq------------kwErvcaAlRELnKhRdiv 152 (155)
T PF07789_consen 102 IPSFTEKRA-----DDLILPSLRKANRELRRAKSKVQ------------KWERVCAALRELNKHRDIV 152 (155)
T ss_pred CCCcccccC-----cceechhHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHH
Confidence 444454444 78999999999999999988777 5999988777677776643
No 11
>PHA02696 hypothetical protein; Provisional
Probab=26.59 E-value=53 Score=25.59 Aligned_cols=22 Identities=32% Similarity=0.915 Sum_probs=19.1
Q ss_pred hhhhhhhhhhHHHHHHHHhhhc
Q 020365 126 LLTWKGWVESRFRQLTLKIEQD 147 (327)
Q Consensus 126 ~~~W~GwVESRlR~Lv~~LE~~ 147 (327)
+-.|.||+.-|+|.|...|-+.
T Consensus 9 lFvwAgW~aRRVr~Lc~~lRrr 30 (79)
T PHA02696 9 LFVWAGWLARRVRRLCIWLRRR 30 (79)
T ss_pred hhhhHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999764
Done!