Query 010265
Match_columns 514
No_of_seqs 168 out of 376
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 22:30:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010265.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010265hhsearch_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 2E-104 3E-109 831.5 23.3 308 2-316 183-500 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 3E-102 6E-107 836.2 33.9 311 2-315 221-541 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 1.8E-90 3.9E-95 705.3 18.2 307 2-312 175-525 (552)
4 PF04928 PAP_central: Poly(A) 100.0 1.8E-70 3.8E-75 542.8 13.0 178 2-179 77-254 (254)
5 PF04926 PAP_RNA-bind: Poly(A) 100.0 1.2E-33 2.6E-38 259.5 8.7 135 180-315 1-156 (157)
6 PF03813 Nrap: Nrap protein; 98.9 7.9E-08 1.7E-12 111.6 19.5 242 23-277 155-425 (972)
7 COG5260 TRF4 DNA polymerase si 97.6 0.00037 8.1E-09 75.6 10.7 143 15-164 177-342 (482)
8 KOG2054 Nucleolar RNA-associat 97.2 0.0016 3.4E-08 75.8 10.2 168 29-209 305-479 (1121)
9 KOG2277 S-M checkpoint control 97.1 0.0027 5.8E-08 69.6 10.0 142 17-165 245-431 (596)
10 KOG1906 DNA polymerase sigma [ 96.1 0.03 6.5E-07 62.0 10.1 150 11-164 180-341 (514)
11 PF03813 Nrap: Nrap protein; 95.7 0.1 2.2E-06 61.8 12.5 155 18-178 669-839 (972)
12 PRK13300 tRNA CCA-pyrophosphor 94.6 1.1 2.3E-05 49.3 15.5 215 21-278 140-367 (447)
13 TIGR03671 cca_archaeal CCA-add 94.6 1 2.2E-05 48.9 15.2 214 21-278 138-364 (408)
14 smart00572 DZF domain in DSRM 93.6 0.42 9.1E-06 48.7 9.4 124 9-163 105-230 (246)
15 PF09249 tRNA_NucTransf2: tRNA 90.0 0.94 2E-05 41.3 6.4 93 38-152 3-97 (114)
16 PF03828 PAP_assoc: Cid1 famil 89.8 0.26 5.7E-06 38.3 2.5 54 79-136 2-59 (60)
17 COG1746 CCA1 tRNA nucleotidylt 64.2 78 0.0017 35.2 11.5 200 37-278 156-368 (443)
18 PF15431 TMEM190: Transmembran 47.5 12 0.00026 34.5 1.8 38 33-70 72-111 (134)
19 PF07357 DRAT: Dinitrogenase r 34.8 16 0.00035 37.7 0.7 20 196-215 96-115 (262)
20 KOG2054 Nucleolar RNA-associat 30.4 1.3E+02 0.0028 36.8 7.0 121 18-147 805-936 (1121)
21 KOG2303 Predicted NAD synthase 26.2 77 0.0017 36.1 4.0 17 75-91 625-644 (706)
22 PF07789 DUF1627: Protein of u 23.1 39 0.00085 32.5 1.0 43 140-189 110-152 (155)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.6e-104 Score=831.47 Aligned_cols=308 Identities=52% Similarity=0.942 Sum_probs=289.8
Q ss_pred CCcCCCChhhhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCCCChHH
Q 010265 2 SVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSM 81 (514)
Q Consensus 2 slL~nLDe~svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPnas~s~ 81 (514)
++|+||||+|+||||||||||+||+||||.++||.+|||||+||||||||||++||||||+|||||||||||||||+|++
T Consensus 183 slLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARiCQLYPNA~~s~ 262 (562)
T KOG2245|consen 183 SLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARICQLYPNASPST 262 (562)
T ss_pred HhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHccCCCcchHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCceeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhH
Q 010265 82 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTI 161 (514)
Q Consensus 82 Ll~~FF~vYS~W~Wp~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I 161 (514)
||.+||.+|++|.||+||+|+++++++|+++||||+.|++||.|+|||||||||+||||||||+||+++|.+||+||++|
T Consensus 263 Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I 342 (562)
T KOG2245|consen 263 LVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLEI 342 (562)
T ss_pred HHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCcccccccccccHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhcccchhhhcCCcchhhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCCCCCC
Q 010265 162 CEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDTSK 241 (514)
Q Consensus 162 ~~~i~~~~~~W~~LFep~~FF~~Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~~~ 241 (514)
|++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|.|+.+||+.. .++.|||+|+.|.++..
T Consensus 343 ~~~i~~~k~~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~~-~i~~ahp~P~~f~~~~~ 421 (562)
T KOG2245|consen 343 CDDIELNKLDWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERNQ-VILIAHPNPKKFKDTYN 421 (562)
T ss_pred HHHHHhccccHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhhc-ceEEecCCccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999954 67889999999998753
Q ss_pred ----CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHh----hccccCCc--eEEEEEeeccCCCCCCcCCCCcc
Q 010265 242 ----PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSIN----MYMFWKPG--MEICVSHIRRKQIPPYVFPEGYK 311 (514)
Q Consensus 242 ----~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~----~~~~~~~g--m~i~Vs~Vkr~~LP~~V~~~g~~ 311 (514)
..+...|||||...++. ++||+..+++|...++ +...+.+| |.+.+.|+||++|+.++++++.+
T Consensus 422 ~~~~~~~~~~~~igl~~~e~~------~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~krr~l~~~~~~~~l~ 495 (562)
T KOG2245|consen 422 CPLEEDPESLWFIGLEFDENV------KIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVKRRSLIQTITKEFLR 495 (562)
T ss_pred CCcccchhHhhhhcccccccc------cchhhhhHHHhhhhhhhcceeeeeeecccccccccccccccccccccCHHHhh
Confidence 23566899999876542 4999999999999887 45567888 77777899999999999999887
Q ss_pred ccCCC
Q 010265 312 RTRHP 316 (514)
Q Consensus 312 r~~~~ 316 (514)
+.|.-
T Consensus 496 ~~k~~ 500 (562)
T KOG2245|consen 496 LCKQY 500 (562)
T ss_pred HHHhh
Confidence 75554
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=3e-102 Score=836.18 Aligned_cols=311 Identities=43% Similarity=0.829 Sum_probs=290.7
Q ss_pred CCcCCCChhhhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCCCChHH
Q 010265 2 SVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSM 81 (514)
Q Consensus 2 slL~nLDe~svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPnas~s~ 81 (514)
++|+||||+|+||||||||+|+||++|||+++||.+|||||+||||||||||+||||||||||||||||||||||+++++
T Consensus 221 ~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQLyPna~~s~ 300 (593)
T PTZ00418 221 YILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQLYPNFAPSQ 300 (593)
T ss_pred hhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHHhCCCCCHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCceecccccc-----ccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHH
Q 010265 82 LVSRFFRVYTMWRWPNPVMLCAIDE-----AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQ 156 (514)
Q Consensus 82 Ll~~FF~vYS~W~Wp~PV~L~~i~~-----~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~ 156 (514)
||.+||.+|++|+||+||+|+++++ +.++++||||+.|++|++|+|||||||||+||+|||||.||+++|++||+
T Consensus 301 Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt~sT~~vI~~Ef~ 380 (593)
T PTZ00418 301 LIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEFK 380 (593)
T ss_pred HHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCccccccccHHHHHHHHHHHH
Confidence 9999999999999999999999876 67899999999999999999999999999999999999999999999999
Q ss_pred HHHhHhHHhhh-cccchhhhcCCcchhhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCC
Q 010265 157 YGNTICEEVEL-NKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHE 235 (514)
Q Consensus 157 Rg~~I~~~i~~-~~~~W~~LFep~~FF~~Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~ 235 (514)
||++|+++|.. ++.+|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|+.+||+.. .+.+||||++
T Consensus 381 Ra~~i~~~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~~~--~i~~~p~P~~ 458 (593)
T PTZ00418 381 RAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLETLN--NLKIRPYPKF 458 (593)
T ss_pred HHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhccC--CceEeecCcc
Confidence 99999999988 88999999999999999999999999999999999999999999999999999753 3678999999
Q ss_pred CCCCCC-CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHhhcc---ccCCceEEEEEeeccCCCCCCcCCCCcc
Q 010265 236 YVDTSK-PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYM---FWKPGMEICVSHIRRKQIPPYVFPEGYK 311 (514)
Q Consensus 236 f~d~~~-~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~~~~---~~~~gm~i~Vs~Vkr~~LP~~V~~~g~~ 311 (514)
|.+... ..|+++|||||+++.+.. .+..++||+.++++|.+.|++|. .|.++|+|+|+|||+++||++||++|++
T Consensus 459 f~~~~~~~~~~~~ffIGL~~~~~~~-~~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk~~~Lp~~v~~~~~~ 537 (593)
T PTZ00418 459 FKYQDDGWDYASSFFIGLVFFSKNV-YNNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLKKSQLPAFVLSQTPE 537 (593)
T ss_pred cccCCCCceeEEEEEEeEeeccCCC-CCCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEeehHhCCHhhccCCCc
Confidence 988753 357789999999876543 23358999999999999999886 3678899999999999999999999987
Q ss_pred ccCC
Q 010265 312 RTRH 315 (514)
Q Consensus 312 r~~~ 315 (514)
|+.+
T Consensus 538 ~~~~ 541 (593)
T PTZ00418 538 EPVK 541 (593)
T ss_pred CCCc
Confidence 7444
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=1.8e-90 Score=705.34 Aligned_cols=307 Identities=40% Similarity=0.765 Sum_probs=288.2
Q ss_pred CCcCCCChhhhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCCCChHH
Q 010265 2 SVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSM 81 (514)
Q Consensus 2 slL~nLDe~svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPnas~s~ 81 (514)
+||++|||+|++||||.||||+||+|||+..+|+.||||||+|||||.||+|++||+|||+|||||||||||||||+.+.
T Consensus 175 nLLk~~dEkcilsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiCQLYPNA~S~v 254 (552)
T COG5186 175 NLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQLYPNASSFV 254 (552)
T ss_pred hhhhcchHHHHHhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHHhhccCcchHh
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCceeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhH
Q 010265 82 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTI 161 (514)
Q Consensus 82 Ll~~FF~vYS~W~Wp~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I 161 (514)
||++||.++++|+||+||+|+||++++++..+|||+.||+|+.|.|||||||||+||.|||||.||..+|..||-||++|
T Consensus 255 Iv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~vIl~EfvRa~~I 334 (552)
T COG5186 255 IVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHVILMEFVRAHKI 334 (552)
T ss_pred HHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhhhHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhcccchhhhcCCcchhhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCCCC--
Q 010265 162 CEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDT-- 239 (514)
Q Consensus 162 ~~~i~~~~~~W~~LFep~~FF~~Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~-- 239 (514)
+++|+.+..+|..||+..|||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||-.. +++.|||||+.|...
T Consensus 335 ~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~~AhPF~K~F~~~y~ 413 (552)
T COG5186 335 LSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DILYAHPFPKAFRKVYN 413 (552)
T ss_pred hhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhhhcCcCChhhhhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999754 668899999999511
Q ss_pred ------------------------------C-----------CCCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHH
Q 010265 240 ------------------------------S-----------KPCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLS 278 (514)
Q Consensus 240 ------------------------------~-----------~~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~ 278 (514)
+ ...|-+.|||||+.... ..++++||..++++|.+.
T Consensus 414 c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~---~~~kkvdi~~p~~EF~el 490 (552)
T COG5186 414 CVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPV---KPGKKVDIEQPVKEFIEL 490 (552)
T ss_pred CccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeec---CCCceeeeeccHHHHHHH
Confidence 0 01255689999998653 235689999999999999
Q ss_pred Hhhcccc-CCceEEEEEeeccCCCCCCcCCCCccc
Q 010265 279 INMYMFW-KPGMEICVSHIRRKQIPPYVFPEGYKR 312 (514)
Q Consensus 279 I~~~~~~-~~gm~i~Vs~Vkr~~LP~~V~~~g~~r 312 (514)
|+.|.++ ..+|.|.|+.+|+.+||+-||.+|++|
T Consensus 491 cr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geer 525 (552)
T COG5186 491 CREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEER 525 (552)
T ss_pred HHHhhccccceeeeehhhccccCCchhhcCCCccC
Confidence 9999654 478999999999999999999999866
No 4
>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=1.8e-70 Score=542.84 Aligned_cols=178 Identities=61% Similarity=1.112 Sum_probs=147.3
Q ss_pred CCcCCCChhhhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCCCChHH
Q 010265 2 SVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSM 81 (514)
Q Consensus 2 slL~nLDe~svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPnas~s~ 81 (514)
++|+|||++|+|||||+||+|+|+++|||.++||.+|||||+|||+||||||++|||||||||||||||||+|||+++++
T Consensus 77 ~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcql~Pn~~~~~ 156 (254)
T PF04928_consen 77 DPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQLYPNASPST 156 (254)
T ss_dssp GGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHHSTT--HHH
T ss_pred hhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHHHCccccccc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCceeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhH
Q 010265 82 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTI 161 (514)
Q Consensus 82 Ll~~FF~vYS~W~Wp~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I 161 (514)
||.+||.+||+|+||+||+|++++++.+++++|+|+.|++|++|+|||||||||+||||||||+||+++|++||+||++|
T Consensus 157 ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~i~~Ef~ra~~i 236 (254)
T PF04928_consen 157 LLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRIIREEFQRAHEI 236 (254)
T ss_dssp HHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhcccchhhhcCCc
Q 010265 162 CEEVELNKAQWSALFEPY 179 (514)
Q Consensus 162 ~~~i~~~~~~W~~LFep~ 179 (514)
++++..++.+|++||+|+
T Consensus 237 ~~~~~~~~~~W~~L~e~~ 254 (254)
T PF04928_consen 237 LSEILKGGASWSDLFEPH 254 (254)
T ss_dssp HHHHHTTSS-HHHCT---
T ss_pred HHHHHcCCCCHHHHcCCC
Confidence 999998999999999985
No 5
>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=1.2e-33 Score=259.49 Aligned_cols=135 Identities=36% Similarity=0.714 Sum_probs=104.9
Q ss_pred chhhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCC------------------CCCC
Q 010265 180 LFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV------------------DTSK 241 (514)
Q Consensus 180 ~FF~~Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------d~~~ 241 (514)
+||.+|||||+|+++|.+++++.+|.||||||||.||.+||+.. .+..|||||+.|. +...
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 69999999999999999999999999999999999999999865 4677999999998 1223
Q ss_pred CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHhhccc---cCCceEEEEEeeccCCCCCCcCCCCccccCC
Q 010265 242 PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF---WKPGMEICVSHIRRKQIPPYVFPEGYKRTRH 315 (514)
Q Consensus 242 ~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~I~~~~~---~~~gm~i~Vs~Vkr~~LP~~V~~~g~~r~~~ 315 (514)
..+.++|||||++......+.++++||+.++++|++.|++|.. +.++|+|+|+|||+++||++||++|.+|+++
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 4578999999999876543344679999999999999999754 6688999999999999999999999988665
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=98.88 E-value=7.9e-08 Score=111.61 Aligned_cols=242 Identities=14% Similarity=0.225 Sum_probs=157.3
Q ss_pred HHHHhCCChHHHHHHHHHHHHHHHHhcccccc-cccchhHHHHHHHHHHHhh---------CCCCChHHHHHHHHHhhhc
Q 010265 23 QILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQL---------YPNAVPSMLVSRFFRVYTM 92 (514)
Q Consensus 23 ~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv-~GyLGGVsWAILVArVCQL---------yPnas~s~Ll~~FF~vYS~ 92 (514)
+|-+..-+...|+.|+.-+|.||++||+.+.. .|-+||..|+||+|+..+- .+..+.-+|+..+..+.|.
T Consensus 155 ~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fLA~ 234 (972)
T PF03813_consen 155 YLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFLAT 234 (972)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHHhc
Confidence 33444456799999999999999999998775 5888999999999999875 4566788999999999999
Q ss_pred CCC-CCceeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhHhHHhhhcccc
Q 010265 93 WRW-PNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQ 171 (514)
Q Consensus 93 W~W-p~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~ 171 (514)
.+| .+|+.++...+....... ...+--|++--.-=.+|.++++|.++++.|+.|-+++.+++++-. ...
T Consensus 235 ~d~~~~~l~~~~~~~~~~~~~~--------~~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~d~ 304 (972)
T PF03813_consen 235 TDLSKKPLFFKSSSDSTESLEE--------FHSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--DDG 304 (972)
T ss_pred cccccCceEEecCCCccchhhh--------hhccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--ccc
Confidence 999 679999865431111111 122334555445567999999999999999999999999987632 345
Q ss_pred hhhhcC-C-cchhhccccEEEEE---EE----eCChhhhhhhhhhhHHHHHHHHH-HhhhccCCceeeccC---CCCCCC
Q 010265 172 WSALFE-P-YLFFESYRNYLQVD---IV----AANADDLLAWKGWVESRLRQLTL-MIERDTYGKLQCHPY---PHEYVD 238 (514)
Q Consensus 172 W~~LFe-p-~~FF~~Yk~YL~I~---v~----a~s~ed~~~w~GwVESRlR~Lv~-~LE~~~~~~l~ahp~---P~~f~d 238 (514)
.+.+|- + .++..+|.+++.|. .. .....+...|..+++.++-.|+. .|-.... .++++ +.++.-
T Consensus 305 F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~~---~i~v~~~~~~~w~i 381 (972)
T PF03813_consen 305 FDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRAK---LIRVLRPSQPPWSI 381 (972)
T ss_pred hhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHH---eEEEeCCCCCCccc
Confidence 777774 4 56778999999991 11 11223334444466777766653 3543221 12332 122211
Q ss_pred CCC--CCceeEEEEeeeeCCCCc---cCCCceecchHHHHHHHH
Q 010265 239 TSK--PCAHCAFFMGLQRKPGEV---VQEGQQFDIRGSVEEFKL 277 (514)
Q Consensus 239 ~~~--~~~~~~ffIGL~~~~~~~---~~~~~~~DL~~~v~eF~~ 277 (514)
.+. ........|||..+.... ...|-..|-.....+|++
T Consensus 382 ~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~ 425 (972)
T PF03813_consen 382 SSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFRE 425 (972)
T ss_pred CCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHH
Confidence 111 111226899998875211 111222233456677776
No 7
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=97.59 E-value=0.00037 Score=75.61 Aligned_cols=143 Identities=17% Similarity=0.230 Sum_probs=110.0
Q ss_pred cchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCC------------------
Q 010265 15 LNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPN------------------ 76 (514)
Q Consensus 15 LNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPn------------------ 76 (514)
=||++.|..|+..+-....+|-+.-.||+||++|.+-+...|-|++.+...||--..|+.|.
T Consensus 177 ~~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~~~l~~~~~~ 256 (482)
T COG5260 177 TNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNGLLSPLKYNKNI 256 (482)
T ss_pred hhHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCccccccccccchhhccccc
Confidence 37899999999999888999999999999999999999999999999999999999999871
Q ss_pred CChHHHHHHHHHhhh-cCCCCCceeccccccc-c---CCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHH
Q 010265 77 AVPSMLVSRFFRVYT-MWRWPNPVMLCAIDEA-E---LGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVM 151 (514)
Q Consensus 77 as~s~Ll~~FF~vYS-~W~Wp~PV~L~~i~~~-~---lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI 151 (514)
.....|+..||.+|- .|++..-++... .+ . .--..|-- +.. .....|--|. -..|..-...--|...|
T Consensus 257 ~~lgvLf~dFf~~yG~~f~Y~~~~~si~--~g~~~~~K~e~g~~~---~~~-p~~LsiqdP~-td~n~~~~a~s~~ik~i 329 (482)
T COG5260 257 DNLGVLFDDFFELYGKSFNYSLVVLSIN--SGDFYLPKYEKGWLK---PSK-PNSLSIQDPG-TDRNNDISAVSFNIKDI 329 (482)
T ss_pred cccchHHHHHHHHhccccChhheEEEec--CCceeeehhhccccc---ccC-CCcEeecCCC-CCcccccccccchHHHH
Confidence 124679999999998 788877655422 22 0 00122321 111 2567888888 44455445556688999
Q ss_pred HHHHHHHHhHhHH
Q 010265 152 MDQFQYGNTICEE 164 (514)
Q Consensus 152 ~~Ef~Rg~~I~~~ 164 (514)
..+|.+|.+++..
T Consensus 330 ~~~F~~aF~lls~ 342 (482)
T COG5260 330 KAAFIRAFELLSN 342 (482)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999999876
No 8
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=97.20 E-value=0.0016 Score=75.77 Aligned_cols=168 Identities=15% Similarity=0.214 Sum_probs=118.2
Q ss_pred CChHHHHHHHHHHHHHHHHhccccc--ccccchhHHHHHHHHHHH---hhCCCCChHHHHHHHHHhhhcCCCCC-ceecc
Q 010265 29 PNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVC---QLYPNAVPSMLVSRFFRVYTMWRWPN-PVMLC 102 (514)
Q Consensus 29 Pn~e~FR~aLR~IKlWAKrRGIYSN--v~GyLGGVsWAILVArVC---QLyPnas~s~Ll~~FF~vYS~W~Wp~-PV~L~ 102 (514)
-....|+.++--.|.|+++| |. ..|-+||+-|++|+|+.. .+.-+.+..+++..-|++++.|+|.. -+-+.
T Consensus 305 s~~~~f~da~~Llk~WlrqR---s~~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~ 381 (1121)
T KOG2054|consen 305 SSAKGFKDALALLKVWLRQR---SLDIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLV 381 (1121)
T ss_pred hhhhhHHHHHHHHHHHHHhh---hhhcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEec
Confidence 34589999999999999999 33 678899999999999987 35667778899999999999999986 55554
Q ss_pred ccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhHhHHhhhcccchhhhc-CCcch
Q 010265 103 AIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALF-EPYLF 181 (514)
Q Consensus 103 ~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~W~~LF-ep~~F 181 (514)
+-. ..+ |....-+ .+..|.+-=+.-..|..-|++.|+.+.+++|.+-...++++.. ....+.+| ++.+.
T Consensus 382 ~~~-~s~------~~~~~f~-e~~~~~f~D~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~--~~~F~~IFmtkip~ 451 (1121)
T KOG2054|consen 382 PSS-PSL------PALADFH-EGQLVTFIDSSGHLNLCANMTASTYEQVQEEARLTLMLLDSRA--DDGFSLIFMTKIPV 451 (1121)
T ss_pred cCC-CCc------hhhhhhh-hcceeeEeccCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhh--hcCcceeeeecCCc
Confidence 421 000 0000000 1112222223335788889999999999999999999998754 34577776 78999
Q ss_pred hhccccEEEEEEEeCChhhhhhhhhhhH
Q 010265 182 FESYRNYLQVDIVAANADDLLAWKGWVE 209 (514)
Q Consensus 182 F~~Yk~YL~I~v~a~s~ed~~~w~GwVE 209 (514)
|..|.|-+.+.....-+.....-.||.|
T Consensus 452 ~~~yDh~l~l~~~~~l~~~~~~~~~~~~ 479 (1121)
T KOG2054|consen 452 FRAYDHVLHLSPLSRLQAAEHLLSGFCE 479 (1121)
T ss_pred hhhhheeeeccccchhhhHHhhcccchh
Confidence 9999998887665443444444444443
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=97.06 E-value=0.0027 Score=69.63 Aligned_cols=142 Identities=17% Similarity=0.201 Sum_probs=108.6
Q ss_pred hhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccch-hHHHHHHHHHHHhhCCC-------------------
Q 010265 17 GCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG-GVNWALLVARVCQLYPN------------------- 76 (514)
Q Consensus 17 G~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLG-GVsWAILVArVCQLyPn------------------- 76 (514)
|.+.+..+.....--..|+.+--.||.||+++|+.+..-|.+- -.++.+||...-|.++.
T Consensus 245 ~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~ 324 (596)
T KOG2277|consen 245 AILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKP 324 (596)
T ss_pred hhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhccccccc
Confidence 5667777766665445999999999999999999999999998 59999999999987531
Q ss_pred ------------------------CChHHHHHHHHHhhh-cCCCCCceeccccccccCCCcccCCCCCCCCCCCcceeec
Q 010265 77 ------------------------AVPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIIT 131 (514)
Q Consensus 77 ------------------------as~s~Ll~~FF~vYS-~W~Wp~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIIT 131 (514)
.+...|+..||.+|+ .|++++-++=-......... |. ....-.+.|..
T Consensus 325 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~l~~~--~~-----~~~~~~l~i~d 397 (596)
T KOG2277|consen 325 VVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRALKRA--KK-----IKSKKFLCIED 397 (596)
T ss_pred chhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccccccc--ch-----hhhccceeecc
Confidence 012478889999999 89999864422111100000 11 11234588999
Q ss_pred CCCCCcCcccccCcchHHHHHHHHHHHHhHhHHh
Q 010265 132 PAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEV 165 (514)
Q Consensus 132 PayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i 165 (514)
|.....|....++..+..+|+.+|+....++...
T Consensus 398 p~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 398 PFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred ccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 9999999999999999999999999999888765
No 10
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=96.13 E-value=0.03 Score=61.96 Aligned_cols=150 Identities=19% Similarity=0.260 Sum_probs=106.9
Q ss_pred hhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCCCC---------hHH
Q 010265 11 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAV---------PSM 81 (514)
Q Consensus 11 svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPnas---------~s~ 81 (514)
|.-..||||-+..|...+-++..+|.++-.+|.|--.|++-....|-+++++.++||-.+-|++|.-. ...
T Consensus 180 SFn~~~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~v 259 (514)
T KOG1906|consen 180 SFNQTNGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGV 259 (514)
T ss_pred eecccCchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccch
Confidence 34457999999999999999999999999999999999999999999999999999999999998641 357
Q ss_pred HHHHHHHhhh-cCCCCC-ceeccccccc-cCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHH
Q 010265 82 LVSRFFRVYT-MWRWPN-PVMLCAIDEA-ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYG 158 (514)
Q Consensus 82 Ll~~FF~vYS-~W~Wp~-PV~L~~i~~~-~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg 158 (514)
|+.+||.+|. +++.-. -|.+....+. .-....|- .+...+.-...|-.|.-|.-+.. -+...+.-|+.+|..|
T Consensus 260 ll~~f~e~yG~~f~~~k~~i~~~~~g~~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndig--r~s~~~~~v~~~F~~a 335 (514)
T KOG1906|consen 260 LLIKFFELYGRNFGYDKLGISLSLGGEYVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIG--RSSFNFSQVKGAFAYA 335 (514)
T ss_pred HHHHHHHHhccccCchhhceeccCCcccccHHhhhhh--cccccCCCccccCCCCCcccccc--cccccHHHHHHHHHHH
Confidence 9999999999 444433 2332211110 00000111 11223445578888888855544 2234566788899888
Q ss_pred HhHhHH
Q 010265 159 NTICEE 164 (514)
Q Consensus 159 ~~I~~~ 164 (514)
..++..
T Consensus 336 f~~l~~ 341 (514)
T KOG1906|consen 336 FKVLTN 341 (514)
T ss_pred HHHHhh
Confidence 776654
No 11
>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=95.67 E-value=0.1 Score=61.79 Aligned_cols=155 Identities=25% Similarity=0.378 Sum_probs=103.4
Q ss_pred hhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHh-hCC---CCChHHHHHHHHHhhhcC
Q 010265 18 CRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQ-LYP---NAVPSMLVSRFFRVYTMW 93 (514)
Q Consensus 18 ~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQ-LyP---nas~s~Ll~~FF~vYS~W 93 (514)
.+-+..|..+--....|-.+.|-+|.|.-.+-+ .|++.--..=+|||.|-. -+| ..++..=+.||.+..|.|
T Consensus 669 p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~~ 744 (972)
T PF03813_consen 669 PKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLSTW 744 (972)
T ss_pred HHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHhC
Confidence 344455555544567899999999999999866 567788899999999983 344 334555577888889999
Q ss_pred CCCC-ceeccccccc--------cCCCcccCCCCCCCCCCCcceeecCCCCCcCcccc---cCcchHHHHHHHHHHHHhH
Q 010265 94 RWPN-PVMLCAIDEA--------ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYN---VSTSTLRVMMDQFQYGNTI 161 (514)
Q Consensus 94 ~Wp~-PV~L~~i~~~--------~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~N---VS~STl~vI~~Ef~Rg~~I 161 (514)
||.+ |++++.-.+- ...|.-|.. .+|......|-|.||.-|.- +..+ -+..-++.|+.=-+.+.++
T Consensus 745 dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g-~~wT~~~Ps~~v~~Rl~~LAk~sl~~ 822 (972)
T PF03813_consen 745 DWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEG-SLWTRNGPSKVVAKRLTALAKASLKL 822 (972)
T ss_pred CCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCC-CEeECCCCCHHHHHHHHHHHHHHHHH
Confidence 9985 9888653211 012333443 34555667899999999853 3333 3444445555444456666
Q ss_pred hHHhhhcccchhhhcCC
Q 010265 162 CEEVELNKAQWSALFEP 178 (514)
Q Consensus 162 ~~~i~~~~~~W~~LFep 178 (514)
++.-..+..+|..||.|
T Consensus 823 l~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 823 LEEQGLSDLDWKSLFRP 839 (972)
T ss_pred HHhcCCCCCCHHHhcCC
Confidence 66333346789999975
No 12
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=94.59 E-value=1.1 Score=49.26 Aligned_cols=215 Identities=17% Similarity=0.214 Sum_probs=120.0
Q ss_pred HHHHHHhCCChHHHHHHHHHHHHHHHHhccccc--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhhcCCCCCc
Q 010265 21 ADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNP 98 (514)
Q Consensus 21 td~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSN--v~GyLGGVsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~P 98 (514)
+.+|++..- +.|+.-.|-+|.|.|.-|||++ +.+-++|+.+-||+++. -+-..++.. .+.| .-|
T Consensus 140 ~~fv~~rl~--~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y------G~F~~~l~~----a~~w--~~~ 205 (447)
T PRK13300 140 TKYVKERLK--GKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKA----ASKW--KPP 205 (447)
T ss_pred HHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHH----HHhC--CCC
Confidence 445544331 3499999999999999999965 55668999999999993 222333333 2445 334
Q ss_pred eeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhHhHHhhhcccchhhhcCC
Q 010265 99 VMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEP 178 (514)
Q Consensus 99 V~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~W~~LFep 178 (514)
+.++.... + . .....+++-||.|.-|..|.|.++|...+..+...-+ .-+.+ +=.++|.|
T Consensus 206 ~~I~~~~~---~-----~---~~~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~aar---~fL~~------Ps~~fF~~ 265 (447)
T PRK13300 206 VKIDLEKH---G-----K---EYKFDDPLVVIDPVDPNRNVAAALSLENLATFILAAR---EFLKN------PSLEFFFP 265 (447)
T ss_pred ceEecccc---C-----c---cccCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHH---HHHhC------CCHHhcCC
Confidence 55432211 0 0 0123578999999999999999999888776654221 22222 23345544
Q ss_pred cc---------hhhccccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCCCCCCCCceeEEE
Q 010265 179 YL---------FFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDTSKPCAHCAFF 249 (514)
Q Consensus 179 ~~---------FF~~Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~~~~~~~~~ff 249 (514)
.+ +-.+=.+.+.|....++.-+-.-| |-++--.+.|...||+.....+.... +.+ .-.|+.+
T Consensus 266 ~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~Dil~-pQl~r~~~~i~~~L~~~gF~v~~~~~----~~d----~~~~~l~ 336 (447)
T PRK13300 266 SDLSPEEILEELERRGTTVLALEFPRPDIVEDILY-PQLERSLRSIVKLLEREGFEVLRSGA----WAD----EDRAYLL 336 (447)
T ss_pred CCCChHHHHHHHhhcCceEEEEEeCCCCCCccchh-HHHHHHHHHHHHHHHHCCCEEEEeee----ecC----CCeEEEE
Confidence 44 111122455555545443333334 66666667777778875443333322 222 1234444
Q ss_pred EeeeeCCC--CccCCCceecchHHHHHHHHH
Q 010265 250 MGLQRKPG--EVVQEGQQFDIRGSVEEFKLS 278 (514)
Q Consensus 250 IGL~~~~~--~~~~~~~~~DL~~~v~eF~~~ 278 (514)
+=|....- -....+-.+.-..-...|.+.
T Consensus 337 ~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 367 (447)
T PRK13300 337 LELEVAELPNVKLHIGPPVWVREHAENFIEK 367 (447)
T ss_pred EEeecccCCCeeeeeCCCcCchhhHHHHHHH
Confidence 44442221 111123345555557788763
No 13
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=94.57 E-value=1 Score=48.87 Aligned_cols=214 Identities=19% Similarity=0.235 Sum_probs=121.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHHHHHHHhccccc--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhhcCCCCCc
Q 010265 21 ADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNP 98 (514)
Q Consensus 21 td~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSN--v~GyLGGVsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~P 98 (514)
+++|+...- +.|+.-.|-+|.|.|.-|+|+. +.+-+.|+.+-||+++. -+-..++.. .+.| ..+
T Consensus 138 ~~fv~~rl~--~~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~y------G~F~~~l~~----a~~w--k~~ 203 (408)
T TIGR03671 138 TRYVLERLD--GKLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHY------GSFENVLKA----ASKW--KPG 203 (408)
T ss_pred HHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHH----HHhc--CCC
Confidence 344444332 2489999999999999999965 45567999999999992 222333332 2444 446
Q ss_pred eeccccccccCCCcccCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhHhHHhhhcccchhhhcCC
Q 010265 99 VMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEP 178 (514)
Q Consensus 99 V~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~W~~LFep 178 (514)
+.++....+. ....+++-||.|.-|..|.|.++|...+..+...-++.. . .+=..+|.|
T Consensus 204 ~~id~~~~~~------------~~f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl---~------~Ps~~fF~p 262 (408)
T TIGR03671 204 VVIDIEEHGT------------KKFDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFL---K------NPSLEFFFP 262 (408)
T ss_pred eEEecCcccc------------ccCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHH---H------CCCHHHcCC
Confidence 7763221101 123578999999999999999999988877765433222 1 122345544
Q ss_pred c-----ch---hhc-cccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCCCCCCCCceeEEE
Q 010265 179 Y-----LF---FES-YRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDTSKPCAHCAFF 249 (514)
Q Consensus 179 ~-----~F---F~~-Yk~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~~~~~~~~~ff 249 (514)
. ++ +.+ -.+.+.|....++.-+-.-| |-++--.+.|...||+.....+....| .+. -.|+.+
T Consensus 263 ~~~~~~~~~~~l~~r~t~~~~~~f~~p~~v~Dil~-pQl~r~~~~i~~~L~~~gF~v~r~~~~----~~~----~~~~l~ 333 (408)
T TIGR03671 263 PEIEPEEFLERLERRGTTLLAIVFRTPDVVDDILY-PQLERSGRSLVKLLEREGFEVLRYGVW----ADE----NTCYLL 333 (408)
T ss_pred CCCChHHHHHHHhhcCcEEEEEEeCCCCCCccchh-HHHHHHHHHHHHHHHHCCCEEEEeeee----cCC----CeEEEE
Confidence 3 11 122 22344444444443232333 666666677777788654444444433 121 125555
Q ss_pred EeeeeCCCC--ccCCCceecchHHHHHHHHH
Q 010265 250 MGLQRKPGE--VVQEGQQFDIRGSVEEFKLS 278 (514)
Q Consensus 250 IGL~~~~~~--~~~~~~~~DL~~~v~eF~~~ 278 (514)
+=|....-. ....+-.+.-+.-...|.+.
T Consensus 334 ~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 364 (408)
T TIGR03671 334 LELESAELPRVKLHVGPPVWVRDHAEKFIEK 364 (408)
T ss_pred EEeeccccCCceeeeCCCccchhHHHHHHHH
Confidence 555433211 11123345555667778763
No 14
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=93.63 E-value=0.42 Score=48.66 Aligned_cols=124 Identities=13% Similarity=0.084 Sum_probs=95.4
Q ss_pred hhhhhccchhhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCC-CChHHHHHHHH
Q 010265 9 EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPN-AVPSMLVSRFF 87 (514)
Q Consensus 9 e~svRSLNG~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQLyPn-as~s~Ll~~FF 87 (514)
++|+.+|-..|-+.......-....|+.+.|.+|-|.+|--.++. |.+..+-+|+++++--... ..+..-+.+||
T Consensus 105 ~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~p----L~~w~iELl~~~~i~~~~~~l~~~~a~RR~f 180 (246)
T smart00572 105 KKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQP----LSGWPLELLVEKAIGSARQPLGLGDAFRRVF 180 (246)
T ss_pred HHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhcccccc----cccccHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 457788888999999999888899999999999999999766544 8888999999999863222 23678899999
Q ss_pred HhhhcCCCCCceeccccccccCCCcccCCCCCCCCCCCcceeecCCCC-CcCcccccCcchHHHHHHHHHHHHhHhH
Q 010265 88 RVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYP-CMNSSYNVSTSTLRVMMDQFQYGNTICE 163 (514)
Q Consensus 88 ~vYS~W~Wp~PV~L~~i~~~~lg~~vW~P~~~~rdr~hlMPIITPayP-~mNSt~NVS~STl~vI~~Ef~Rg~~I~~ 163 (514)
.+.|+=- +|. + + --|+.|+.+ ..|.+...|.-...-|...-+.+.+++.
T Consensus 181 e~lAsG~-----l~p---~------------~-------~gI~DPce~~~~nv~~~lT~qqrd~It~sAQ~alRl~A 230 (246)
T smart00572 181 ECLASGI-----LLP---G------------S-------PGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLA 230 (246)
T ss_pred HHHHhcc-----CcC---C------------C-------CCCcCCCCCCcccHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 9988421 110 0 0 136778886 7888888888888888888887777764
No 15
>PF09249 tRNA_NucTransf2: tRNA nucleotidyltransferase, second domain; InterPro: IPR015329 This domain adopts a structure consisting of a five helical bundle core. It is predominantly found in Archaeal tRNA nucleotidyltransferases, following the catalytic nucleotidyltransferase domain []. ; GO: 0004810 tRNA adenylyltransferase activity, 0016437 tRNA cytidylyltransferase activity; PDB: 3OUY_B 2ZHB_A 2ZH1_A 2ZH2_A 1UET_A 2ZH7_A 1R8B_A 2DR5_A 1TFW_C 3OVA_A ....
Probab=90.00 E-value=0.94 Score=41.34 Aligned_cols=93 Identities=24% Similarity=0.343 Sum_probs=57.1
Q ss_pred HHHHHHHHHHhccccc--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhhcCCCCCceeccccccccCCCcccC
Q 010265 38 LRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWD 115 (514)
Q Consensus 38 LR~IKlWAKrRGIYSN--v~GyLGGVsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~~~lg~~vW~ 115 (514)
.|-.|...|.-|||+. +.+-++|+..-+|+.+.=- ....-+.-+ .|..|+.++....+..
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yGs----------F~~~l~~a~--~W~~~~~Id~~~~~~~------ 64 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYGS----------FENVLEAAA--KWKPPVVIDLEDHGEP------ 64 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHSS----------HHHHHHHHT--T--TTEEEETT-TTE-------
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHCC----------HHHHHHHHH--hcCCCeEEccCccchh------
Confidence 5788999999999997 4577788888888877522 122222223 6777888865321110
Q ss_pred CCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHH
Q 010265 116 PRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMM 152 (514)
Q Consensus 116 P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~ 152 (514)
.....+++.||.|.-|..|.|.+||...+..+.
T Consensus 65 ----~~~f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 65 ----SKKFDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp -----EEE-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred ----hhhcCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 112357899999999999999999988766544
No 16
>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=89.81 E-value=0.26 Score=38.31 Aligned_cols=54 Identities=20% Similarity=0.381 Sum_probs=33.9
Q ss_pred hHHHHHHHHHhhh-cCCCCCceecccccccc-C--CCcccCCCCCCCCCCCcceeecCCCCC
Q 010265 79 PSMLVSRFFRVYT-MWRWPNPVMLCAIDEAE-L--GFSVWDPRKNRRDKTHHMPIITPAYPC 136 (514)
Q Consensus 79 ~s~Ll~~FF~vYS-~W~Wp~PV~L~~i~~~~-l--g~~vW~P~~~~rdr~hlMPIITPayP~ 136 (514)
.+.|+..||.+|+ .|+|.+-|+-- ..+. + ....|.. ....+...|.|..|.-|.
T Consensus 2 lg~Ll~~Ff~~Y~~~Fd~~~~~Isi--~~g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~~ 59 (60)
T PF03828_consen 2 LGELLLGFFEYYGRKFDYENNVISI--RNGGYFPKEEKNWSK--SRNQRKKRLCIEDPFDPS 59 (60)
T ss_dssp HHHHHHHHHHHHHHTS-TTTEEEES--SSSSEEEHHHHTGCH--CCCCECSSSEBBESSSTT
T ss_pred HHHHHHHHHHHhCCcCCCCceEEEe--cCCceEEhhhccccc--cccCCCCeEEEECCCCCC
Confidence 4689999999999 99999865532 1221 1 1123431 112345789999998774
No 17
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=64.24 E-value=78 Score=35.17 Aligned_cols=200 Identities=19% Similarity=0.175 Sum_probs=107.1
Q ss_pred HHHHHHHHHHHhccccc--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhhcC-CCCCceeccccccccCCCcc
Q 010265 37 TLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMW-RWPNPVMLCAIDEAELGFSV 113 (514)
Q Consensus 37 aLR~IKlWAKrRGIYSN--v~GyLGGVsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W-~Wp~PV~L~~i~~~~lg~~v 113 (514)
=.|-.|.+-|.=|+|++ +.+-++|+-.-||+.+.= .|=.+...- .|..|++++.- .
T Consensus 156 eVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~yG-------------sFe~vl~~a~~wrp~~~ID~~--------~ 214 (443)
T COG1746 156 EVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHYG-------------SFENVLKAASRWRPGKIIDLE--------G 214 (443)
T ss_pred HHHHHHHHHhccCccceeeeeccchHHHHHHHHhhhc-------------cHHHHHHHHhccCCCeEEecc--------c
Confidence 46788999999999997 456677887777776642 122222222 27777887542 1
Q ss_pred cCCCCCCCCCCCcceeecCCCCCcCcccccCcchHHHHHHHHHHHHhHhHHhhhcccchhhhcCCc---c-----hhhcc
Q 010265 114 WDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPY---L-----FFESY 185 (514)
Q Consensus 114 W~P~~~~rdr~hlMPIITPayP~mNSt~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~W~~LFep~---~-----FF~~Y 185 (514)
|... +-...+|-|+.|.-|..|+|.+||.-.+..+. -|.+.. + +.+=.++|.|. . ...+=
T Consensus 215 ~~~e---~f~d~PliVvDPVDP~RNVAAalSl~~la~f~----~aar~F---L--~~PS~efF~p~~~~~~~~~~~~~rg 282 (443)
T COG1746 215 HKRE---RFEDEPLIVVDPVDPKRNVAAALSLENLARFV----HAAREF---L--KNPSPEFFFPRKPKPLLLSKLRRRG 282 (443)
T ss_pred hhhh---ccCCCCeEecCCCCCccchhhhcCHHHHHHHH----HHHHHH---h--cCCChhhcCCCCcCcccccchhhcC
Confidence 2111 11123899999999999999999987766544 222221 1 12223444331 1 22222
Q ss_pred ccEEEEEEEeCChhhhhhhhhhhHHHHHHHHHHhhhccCCceeeccCCCCCCCCCCCCceeEEEEeeeeCCCCc--cCCC
Q 010265 186 RNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVDTSKPCAHCAFFMGLQRKPGEV--VQEG 263 (514)
Q Consensus 186 k~YL~I~v~a~s~ed~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~d~~~~~~~~~ffIGL~~~~~~~--~~~~ 263 (514)
.+-+.|.+-.++.-+-. .-+-++---+.|...||......+..+.| .|... +|+-|+=+....-.. ...+
T Consensus 283 t~v~~l~~~~pd~vdDi-lypQl~r~~~~l~r~Le~~gF~vl~~~~~----~D~~~---~~~v~~E~~~~~l~~i~~r~G 354 (443)
T COG1746 283 THVLALVFPKPDLVDDI-LYPQLERTARSLFRALEEEGFRVLRSGVW----SDESE---RIYVLLELESKELPRIELRVG 354 (443)
T ss_pred ceEEEEEeCCCCCCcch-hhHHHHHHHHHHHHHHHHcCCEEeeeeee----ecCCc---ceEEEEEEecccccceeeecC
Confidence 23333433344433333 34777777788888888765444433333 23221 344555554222110 1112
Q ss_pred ceecchHHHHHHHHH
Q 010265 264 QQFDIRGSVEEFKLS 278 (514)
Q Consensus 264 ~~~DL~~~v~eF~~~ 278 (514)
-+++-+.+++ |.+.
T Consensus 355 Pp~~~e~a~r-F~~k 368 (443)
T COG1746 355 PPVWTEHAVR-FIEK 368 (443)
T ss_pred CCccchhHHH-HHHh
Confidence 2333366776 7663
No 18
>PF15431 TMEM190: Transmembrane protein 190
Probab=47.47 E-value=12 Score=34.45 Aligned_cols=38 Identities=32% Similarity=0.549 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHhcccccc--cccchhHHHHHHHHHH
Q 010265 33 HFCTTLRCLKFWAKRRGVYSNV--TGFLGGVNWALLVARV 70 (514)
Q Consensus 33 ~FR~aLR~IKlWAKrRGIYSNv--~GyLGGVsWAILVArV 70 (514)
.|...+-|+=-|||||++|.|. -|||.||--.=|.-.|
T Consensus 72 l~Li~~iclFWWAkRrd~~k~lh~P~fL~~~~c~kls~~v 111 (134)
T PF15431_consen 72 LLLICSICLFWWAKRRDMCKHLHMPRFLSGFKCDKLSRTV 111 (134)
T ss_pred HHHHHHHHHHHHHHHhchHhhccCchhhccCccchhhchh
Confidence 4666777888999999999874 5899887654443333
No 19
>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=34.79 E-value=16 Score=37.74 Aligned_cols=20 Identities=45% Similarity=0.719 Sum_probs=16.6
Q ss_pred CChhhhhhhhhhhHHHHHHH
Q 010265 196 ANADDLLAWKGWVESRLRQL 215 (514)
Q Consensus 196 ~s~ed~~~w~GwVESRlR~L 215 (514)
+|.-+...++||||||+-.+
T Consensus 96 Sn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 96 SNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCChhhhhhhhhhhhccCcC
Confidence 46778899999999998644
No 20
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=30.43 E-value=1.3e+02 Score=36.80 Aligned_cols=121 Identities=21% Similarity=0.326 Sum_probs=73.4
Q ss_pred hhHHHHHHHhCCChHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhh----CCCCChHHHHHHHHHhhhcC
Q 010265 18 CRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQL----YPNAVPSMLVSRFFRVYTMW 93 (514)
Q Consensus 18 ~RVtd~ILrlVPn~e~FR~aLR~IKlWAKrRGIYSNv~GyLGGVsWAILVArVCQL----yPnas~s~Ll~~FF~vYS~W 93 (514)
.|.|-.|..+--.+..|-.+.|-.|.|-...=+-+ |.+ -=++-+|||..-+- .|..++..=..||-+..|+|
T Consensus 805 p~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~~---h~~-De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~ 880 (1121)
T KOG2054|consen 805 PLHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSG---HHL-DEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTW 880 (1121)
T ss_pred HHHHHHHHHHhhcccchhHHHHHHHHHHHHHhhcc---chH-HHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcC
Confidence 45555555555567889999999999976542111 122 34567888887743 34555666688999999999
Q ss_pred CCCC-ceeccccccccCCCcccC------CCCCCCCCCCcceeecCCCCCcCcccccCcch
Q 010265 94 RWPN-PVMLCAIDEAELGFSVWD------PRKNRRDKTHHMPIITPAYPCMNSSYNVSTST 147 (514)
Q Consensus 94 ~Wp~-PV~L~~i~~~~lg~~vW~------P~~~~rdr~hlMPIITPayP~mNSt~NVS~ST 147 (514)
+|.. |.+++- . .+++.=+ --...|.....|-|||| |=..++.+.=+.++
T Consensus 881 dW~~~PLIvd~-n---n~~~ed~~~e~~e~f~s~R~~lp~m~vit~-yD~~~~~~t~~~P~ 936 (1121)
T KOG2054|consen 881 DWKFDPLIVDF-N---NGFPEDERSELEEKFISARKQLPPMVVITP-YDHLGSKFTRTSPN 936 (1121)
T ss_pred cccCCceEEEc-C---CCCcHHHHHHHHHHHhhhcccCCceEEeec-cccccccccccCch
Confidence 9986 777753 1 1111100 00112334458999997 44455555555555
No 21
>KOG2303 consensus Predicted NAD synthase, contains CN hydrolase domain [Coenzyme transport and metabolism; General function prediction only]
Probab=26.21 E-value=77 Score=36.11 Aligned_cols=17 Identities=35% Similarity=0.641 Sum_probs=11.8
Q ss_pred CCCCh---HHHHHHHHHhhh
Q 010265 75 PNAVP---SMLVSRFFRVYT 91 (514)
Q Consensus 75 Pnas~---s~Ll~~FF~vYS 91 (514)
+..+| +.=|.+||.+|+
T Consensus 625 ~klsp~qvaEKVk~FF~~Y~ 644 (706)
T KOG2303|consen 625 DKLSPRQVAEKVKRFFSYYS 644 (706)
T ss_pred CcCCHHHHHHHHHHHHhhhe
Confidence 44454 455889999986
No 22
>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=23.14 E-value=39 Score=32.52 Aligned_cols=43 Identities=9% Similarity=0.232 Sum_probs=35.5
Q ss_pred ccccCcchHHHHHHHHHHHHhHhHHhhhcccchhhhcCCcchhhccccEE
Q 010265 140 SYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYL 189 (514)
Q Consensus 140 t~NVS~STl~vI~~Ef~Rg~~I~~~i~~~~~~W~~LFep~~FF~~Yk~YL 189 (514)
+.++--++++.+..|++||..=+++ |..++...-=+.+|++-|
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 3788899999999999999877665 999998877777777643
Done!