Query 007342
Match_columns 607
No_of_seqs 173 out of 402
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 22:16:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007342hhsearch_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 9E-123 2E-127 985.2 25.8 361 1-370 131-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 4E-116 9E-121 961.2 37.8 393 1-401 168-572 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 8E-105 2E-109 822.7 23.0 363 1-369 123-531 (552)
4 PF04928 PAP_central: Poly(A) 100.0 1.1E-69 2.3E-74 548.1 15.9 192 39-232 63-254 (254)
5 PF04926 PAP_RNA-bind: Poly(A) 100.0 4.9E-33 1.1E-37 261.0 9.2 134 233-367 1-156 (157)
6 COG5260 TRF4 DNA polymerase si 99.1 3.4E-10 7.5E-15 123.3 12.4 175 6-215 143-342 (482)
7 KOG1906 DNA polymerase sigma [ 98.8 4.2E-08 9.2E-13 108.8 13.0 173 9-214 153-340 (514)
8 PF03813 Nrap: Nrap protein; 98.7 2.9E-07 6.4E-12 109.2 18.5 189 73-273 154-363 (972)
9 KOG2277 S-M checkpoint control 98.6 1.5E-07 3.3E-12 104.8 11.8 174 8-216 211-431 (596)
10 cd05402 NT_PAP_TUTase Nucleoti 97.7 5.5E-05 1.2E-09 67.1 4.7 36 2-37 63-100 (114)
11 KOG2054 Nucleolar RNA-associat 97.4 0.00076 1.6E-08 79.7 10.9 155 80-247 305-464 (1121)
12 PRK13300 tRNA CCA-pyrophosphor 97.1 0.028 6.1E-07 62.5 18.7 216 16-285 100-327 (447)
13 TIGR03671 cca_archaeal CCA-add 97.0 0.087 1.9E-06 58.1 20.3 253 15-329 97-363 (408)
14 smart00572 DZF domain in DSRM 95.6 0.16 3.4E-06 52.7 12.3 162 14-213 61-229 (246)
15 PF03813 Nrap: Nrap protein; 94.2 0.4 8.6E-06 58.2 12.3 159 66-231 666-839 (972)
16 COG1746 CCA1 tRNA nucleotidylt 92.7 4.2 9.1E-05 45.5 16.0 214 16-285 102-328 (443)
17 PF03828 PAP_assoc: Cid1 famil 91.6 0.15 3.2E-06 40.7 2.5 55 129-187 1-59 (60)
18 PF09249 tRNA_NucTransf2: tRNA 89.3 1.3 2.8E-05 41.2 6.9 93 89-203 3-97 (114)
19 KOG2054 Nucleolar RNA-associat 53.5 32 0.00069 42.5 6.9 123 69-198 805-936 (1121)
20 PF15431 TMEM190: Transmembran 49.5 9.5 0.00021 35.7 1.5 34 84-117 72-107 (134)
21 PF07357 DRAT: Dinitrogenase r 32.7 17 0.00037 38.4 0.5 32 237-268 84-115 (262)
22 KOG2303 Predicted NAD synthase 30.4 87 0.0019 36.4 5.4 17 126-142 625-644 (706)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=9e-123 Score=985.16 Aligned_cols=361 Identities=58% Similarity=1.024 Sum_probs=344.6
Q ss_pred CCCCCCCccceeecCCCccceEEEEECceEEEEEecccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCC
Q 007342 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVP 80 (607)
Q Consensus 1 mL~~~p~Vtel~~V~dA~VPIIKf~~~GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVP 80 (607)
||+++|+||||++|+||+||||||+|+||+|||+||||++++||++|||+||++|+||||+|+||||||||||+||+|||
T Consensus 131 mL~~~~eVteL~~V~dAfVPiikfKf~GI~IDllfArL~l~~VP~dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVP 210 (562)
T KOG2245|consen 131 MLKERPEVTELHAVEDAFVPIIKFKFDGIEIDLLFARLALPVVPEDLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVP 210 (562)
T ss_pred HHhcCccccccccccccccceEEEEecCeeeeeeehhcccccCCCcccccchHhhhcccHHHHHHhcCcCHHHHHHHhCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCC
Q 007342 81 KIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSL 160 (607)
Q Consensus 81 n~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~l 160 (607)
|.++||.+|||||+||||||||||++||||||+|||||||+|||||||++++||.+||.+|++|.||+||+|+.+++|.+
T Consensus 211 n~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARiCQLYPNA~~s~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L 290 (562)
T KOG2245|consen 211 NQENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARICQLYPNASPSTLVAKFFRVFSQWNWPNPVLLKPIEEGNL 290 (562)
T ss_pred CHHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHccCCCcchHHHHHHHHHHHhhccCCCceEecccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhccc
Q 007342 161 GLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240 (607)
Q Consensus 161 g~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~~FF~~Yk~ 240 (607)
+++|||||.|++||||+|||||||||+||||||||+||+++|++||+||++||++|+.++. +|.+|||+++||.+|||
T Consensus 291 ~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~k~--~W~~LFE~~~FF~rYk~ 368 (562)
T KOG2245|consen 291 NLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLEICDDIELNKL--DWSDLFELYNFFSRYKH 368 (562)
T ss_pred CccccCCCCCCCCcceecccccCCcccccccccccHHHHHHHHHHHHHHHHHHHHHHhccc--cHHHHhhhhHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred EEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccCCCCCCCCCC-----CcEEEEEEeeeeccCCCCCCC
Q 007342 241 YLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFSDKSK-----PLYCSYFMGLQRKQGVPVGEG 315 (607)
Q Consensus 241 yL~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~F~~~~~-----~~~~~ffIGL~~~~~~~~~~~ 315 (607)
||+|+++|.++|++.+|.||||||+|+|+.+||++. .++.|||+|+.|.++.. .|...|||||.+.++
T Consensus 369 yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~~-~i~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------ 441 (562)
T KOG2245|consen 369 YLQITASAATEEDLLKWVGWVESRIRQLVLKLERNQ-VILIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------ 441 (562)
T ss_pred HheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhhc-ceEEecCCcccccccccCCcccchhHhhhhccccccc------
Confidence 999999999999999999999999999999999964 67899999999997642 456789999987653
Q ss_pred ceechHHHHHHHHHHHH----hhccCCCC--cEEEEEEecCCCCCCCcCCCCCCCCCCCCC
Q 007342 316 EQFDIRLTVKEFKQAVS----MYTLRKPG--MQISVAHVTRRNLPNFVFPGGVRPSRPSKG 370 (607)
Q Consensus 316 ~~~DL~~~v~eF~~~V~----~~~~~~~~--m~I~Vs~Vkr~~LP~~Vf~~~~r~~~~~k~ 370 (607)
.++||+..+++|+..|+ ++..++.| |++.+.|+||++|+.++++.+.|..|..|.
T Consensus 442 ~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~krr~l~~~~~~~~l~~~k~~~~ 502 (562)
T KOG2245|consen 442 VKIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVKRRSLIQTITKEFLRLCKQYKK 502 (562)
T ss_pred ccchhhhhHHHhhhhhhhcceeeeeeecccccccccccccccccccccCHHHhhHHHhhcc
Confidence 34999999999999998 56778888 888888999999999999998887765543
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=3.9e-116 Score=961.19 Aligned_cols=393 Identities=43% Similarity=0.821 Sum_probs=354.9
Q ss_pred CCCCCCCccceeecCCCccceEEEEECceEEEEEecccCCCCCCCCCCCCcch-hhhcCChhhhhhhchhhhHHHHHHhC
Q 007342 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDS-ILQNADEQTVRSLNGCRVTDQILRLV 79 (607)
Q Consensus 1 mL~~~p~Vtel~~V~dA~VPIIKf~~~GI~IDLlFArL~~~~vPe~ldl~dd~-lL~nlDe~svrSLNG~RVtd~IL~lV 79 (607)
||+++|+|++|++|++|+||||||+|+||+|||+||+|+..+||+++++.+|+ +|++||++|+|||||+||+|+||++|
T Consensus 168 ~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~l~~~~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lV 247 (593)
T PTZ00418 168 KLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANLPLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASV 247 (593)
T ss_pred HHhcCCCcceeeccCccccCeEEEEECCEEEeeeecccCCCCCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHC
Confidence 58899999999999999999999999999999999999999999999988886 99999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceecccccc--
Q 007342 80 PKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEE-- 157 (607)
Q Consensus 80 Pn~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~-- 157 (607)
||+++||.+|||||+||||||||||++||||||+||||||||||||||+++++||.+||++|++|+||+||+|++|++
T Consensus 248 Pn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~ 327 (593)
T PTZ00418 248 PNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVP 327 (593)
T ss_pred CChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred ---CCCCCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHh-ccCCCCcccccCCcc
Q 007342 158 ---GSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEK-NEADVDWDTLFEPFT 233 (607)
Q Consensus 158 ---g~lg~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~-~~~~~~W~~LFep~~ 233 (607)
|.++++||||+.|++|++|+|||||||||+||+|||||+||+++|++||+||++||++|.. ++. +|++||+|++
T Consensus 328 ~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~--~W~~Lfep~~ 405 (593)
T PTZ00418 328 NIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEFKRAHEIIKYIEKNSEN--TWTNVLEPLD 405 (593)
T ss_pred cCCcccCCcccCCCCCcccccccCCeecCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHhcCCC--CHHHHcCCcc
Confidence 7789999999999999999999999999999999999999999999999999999999987 766 9999999999
Q ss_pred hhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccCCCCCCCCC--CCcEEEEEEeeeeccCCC
Q 007342 234 FFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFSDKS--KPLYCSYFMGLQRKQGVP 311 (607)
Q Consensus 234 FF~~Yk~yL~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~F~~~~--~~~~~~ffIGL~~~~~~~ 311 (607)
||.+|++||+|++.+.+++++..|.||||||||.|+.+||+.. .+.+||||++|.+.. ..|+++|||||+++....
T Consensus 406 Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~~~--~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~ 483 (593)
T PTZ00418 406 FFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLETLN--NLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNV 483 (593)
T ss_pred hhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhccC--CceEeecCcccccCCCCceeEEEEEEeEeeccCCC
Confidence 9999999999999999999999999999999999999999863 368899999998765 468899999999876543
Q ss_pred CCCCceechHHHHHHHHHHHHhhc---cCCCCcEEEEEEecCCCCCCCcCCCCCCCCCCCCCccccchhhcccCCCCCCC
Q 007342 312 VGEGEQFDIRLTVKEFKQAVSMYT---LRKPGMQISVAHVTRRNLPNFVFPGGVRPSRPSKGTWDSRRALERKVSSHTKP 388 (607)
Q Consensus 312 ~~~~~~~DL~~~v~eF~~~V~~~~---~~~~~m~I~Vs~Vkr~~LP~~Vf~~~~r~~~~~k~~~~~~~~~~~~~~~~~~~ 388 (607)
. +.+++||+.++++|++.|++|. .|+++|+|+|+|||+++||+|||+.|.++.+..|...+... .+...++|.
T Consensus 484 ~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk~~~Lp~~v~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ 559 (593)
T PTZ00418 484 Y-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLKKSQLPAFVLSQTPEEPVKTKANTKTNT---SSATTSGQS 559 (593)
T ss_pred C-CCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEeehHhCCHhhccCCCcCCCcccccccccc---ccccccccc
Confidence 2 3458999999999999999886 46889999999999999999999998877666664433332 223334444
Q ss_pred CCCCCcccccccc
Q 007342 389 GADDGRKRKQTDD 401 (607)
Q Consensus 389 ~~~~~~kr~~~~~ 401 (607)
|.....+.++.++
T Consensus 560 ~~~~~~~~~~~~~ 572 (593)
T PTZ00418 560 GSSGSTSNSNSNE 572 (593)
T ss_pred cccCcccCCCCCc
Confidence 4444444444443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=8.4e-105 Score=822.72 Aligned_cols=363 Identities=45% Similarity=0.857 Sum_probs=342.5
Q ss_pred CCCCCCCccceeecCCCccceEEEEECceEEEEEecccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCC
Q 007342 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVP 80 (607)
Q Consensus 1 mL~~~p~Vtel~~V~dA~VPIIKf~~~GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVP 80 (607)
||+++|+|+||.+||||+||||||+|.||+|||+||||..++||+.|+|+|+++|++|||+|++||||.||||+||+|||
T Consensus 123 ~Lrer~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~P~Vp~~l~Lsd~nLLk~~dEkcilsLNGtRVTDeiL~LVP 202 (552)
T COG5186 123 ELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSIPVVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVP 202 (552)
T ss_pred HhccCcchhhhccCCcccceeEEEEecCccceeeeeeccCCcCCCcccccchhhhhcchHHHHHhhcCceehHHHHHhCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCC
Q 007342 81 KIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSL 160 (607)
Q Consensus 81 n~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~l 160 (607)
+..+|+.+|||||+|||||.||.|++||+|||+|||||||||||||||+...||.+||.++++|+||+||+|++|++|.+
T Consensus 203 ~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiCQLYPNA~S~vIv~kFF~ils~WnWPqPviLkPieDgpl 282 (552)
T COG5186 203 SVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPL 282 (552)
T ss_pred chHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHHhhccCcchHhHHHHHHHHHHhcCCCCCeEeeeccCCCe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhccc
Q 007342 161 GLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240 (607)
Q Consensus 161 g~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~~FF~~Yk~ 240 (607)
+.+||||+.+++|++|.|||||||||+||+|||+|.||..+|..||-||++|+++|+.+.. +|..||+..+||.+||+
T Consensus 283 qvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~vIl~EfvRa~~I~~di~~n~~--~w~~lFek~DFF~RYk~ 360 (552)
T COG5186 283 QVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHVILMEFVRAHKILSDIERNAL--DWRRLFEKSDFFSRYKL 360 (552)
T ss_pred eEEeeCCccCcccccccCccccCCchhhhhhccccchhhhhHHHHHHHHHHhhhhHhhccc--cHHHHHHhhhHHHHHhH
Confidence 9999999999999999999999999999999999999999999999999999999998877 99999999999999999
Q ss_pred EEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccCCCCCCC-----------------------------
Q 007342 241 YLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFSD----------------------------- 291 (607)
Q Consensus 241 yL~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~F~~----------------------------- 291 (607)
||.|++.+.++|++.+|.|+||||+|.|+.+||-.. +++.|||||+.|..
T Consensus 361 yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~~AhPF~K~F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~ 439 (552)
T COG5186 361 YLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DILYAHPFPKAFRKVYNCVAEESIEKIGSGVTLEVAYESTDHE 439 (552)
T ss_pred hhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhhhcCcCChhhhhhcCCccHHHHHHHhcccceeehhhccchh
Confidence 999999999999999999999999999999999764 67899999999961
Q ss_pred -----C----------CCCcEEEEEEeeeeccCCCCCCCceechHHHHHHHHHHHHhhccCCC-CcEEEEEEecCCCCCC
Q 007342 292 -----K----------SKPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLRKP-GMQISVAHVTRRNLPN 355 (607)
Q Consensus 292 -----~----------~~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~V~~~~~~~~-~m~I~Vs~Vkr~~LP~ 355 (607)
+ ...|++.|||||+.... ..++++||..++++|.+.|+.|++++. +|.|.|+.+|+.+||+
T Consensus 440 kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~---~~~kkvdi~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpd 516 (552)
T COG5186 440 KLANDTVPEEESMEDGMKVYCTTFYIGLDVIPV---KPGKKVDIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPD 516 (552)
T ss_pred hhccccCchhhhhccccceeeeEEEEEEEeeec---CCCceeeeeccHHHHHHHHHHhhccccceeeeehhhccccCCch
Confidence 0 01277889999997643 336789999999999999999987764 7999999999999999
Q ss_pred CcCC-CCCCCCCCCC
Q 007342 356 FVFP-GGVRPSRPSK 369 (607)
Q Consensus 356 ~Vf~-~~~r~~~~~k 369 (607)
-||. ++.||+..+|
T Consensus 517 eVF~~geerPs~~sK 531 (552)
T COG5186 517 EVFYPGEERPSNSSK 531 (552)
T ss_pred hhcCCCccCcccccc
Confidence 9996 6667765333
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=1.1e-69 Score=548.12 Aligned_cols=192 Identities=64% Similarity=1.162 Sum_probs=155.4
Q ss_pred CCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHH
Q 007342 39 SLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLV 118 (607)
Q Consensus 39 ~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILV 118 (607)
+..++|+++++.++++|++||++|+|||||+||+|+|+++|||.++||.+|||||+|||+||||||++||||||||||||
T Consensus 63 ~~~~~p~~l~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILv 142 (254)
T PF04928_consen 63 ALPRVPEDLDLLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILV 142 (254)
T ss_dssp SSSSB-TT--TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHH
T ss_pred hhcCCCcccccCCchhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCCCCcccCCCCCCCCCcccceeecCCCCCCCcccccChhh
Q 007342 119 ARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTST 198 (607)
Q Consensus 119 ArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~ST 198 (607)
|||||+|||+++++||.+||.+||+|+||+||+|+++.++.+++++|||+.+.+|++|+||||||+||+||||||||+||
T Consensus 143 Arvcql~Pn~~~~~ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st 222 (254)
T PF04928_consen 143 ARVCQLYPNASPSTLLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRST 222 (254)
T ss_dssp HHHHHHSTT--HHHHHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHH
T ss_pred HHHHHHCccccccchHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCcccccCCc
Q 007342 199 LRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPF 232 (607)
Q Consensus 199 l~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~ 232 (607)
+++|++||+||++|++++..++. +|++||+|+
T Consensus 223 ~~~i~~Ef~ra~~i~~~~~~~~~--~W~~L~e~~ 254 (254)
T PF04928_consen 223 LRIIREEFQRAHEILSEILKGGA--SWSDLFEPH 254 (254)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSS---HHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC--CHHHHcCCC
Confidence 99999999999999999998777 999999985
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=99.98 E-value=4.9e-33 Score=261.00 Aligned_cols=134 Identities=40% Similarity=0.767 Sum_probs=105.5
Q ss_pred chhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccCCCCCC-------------------CCC
Q 007342 233 TFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFS-------------------DKS 293 (607)
Q Consensus 233 ~FF~~Yk~yL~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~F~-------------------~~~ 293 (607)
+||.+|||||+|+++|.+++++.+|.||||||||.|+.+||+.. .+..|||||+.|. +..
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 69999999999999999999999999999999999999999875 4778999999998 122
Q ss_pred CCcEEEEEEeeeeccCCCCCCCceechHHHHHHHHHHHHhhcc---CCCCcEEEEEEecCCCCCCCcCCCCCCCCCC
Q 007342 294 KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTL---RKPGMQISVAHVTRRNLPNFVFPGGVRPSRP 367 (607)
Q Consensus 294 ~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~V~~~~~---~~~~m~I~Vs~Vkr~~LP~~Vf~~~~r~~~~ 367 (607)
..++++|||||++........++++||+.++++|++.|++|++ +.++|+|+|+|||+++||++||+.|.++.++
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 4588999999999876544334689999999999999999877 5678999999999999999999988877553
No 6
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=99.13 E-value=3.4e-10 Score=123.33 Aligned_cols=175 Identities=21% Similarity=0.322 Sum_probs=137.7
Q ss_pred CCccceeecCCCccceEEEEE--CceEEEEEecccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChh
Q 007342 6 PEVTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQ 83 (607)
Q Consensus 6 p~Vtel~~V~dA~VPIIKf~~--~GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~ 83 (607)
-...++..|..|+||||||.. .|++||+.|.+- +|++.|..|+..+-...
T Consensus 143 ~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~----------------------------~~~~~akl~~~~~~~~P 194 (482)
T COG5260 143 NLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNT----------------------------NGIVNAKLIRSYLKEDP 194 (482)
T ss_pred ccCeeeEEEEecccceEEEecCccceEEEeecCch----------------------------hHHHHHHHHHHHHhcCc
Confidence 455678999999999999999 689999999883 58889999999999999
Q ss_pred hHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCC------------------CChHHHHHHHHHhhc-cC
Q 007342 84 NFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPN------------------AVPSMLVSRFFRVYT-QW 144 (607)
Q Consensus 84 ~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPn------------------as~s~Ll~~FF~vYS-~W 144 (607)
.+|.+.-.||+||++|.+.+...|.|++.+...||....|+.|- .....|+..||++|. .|
T Consensus 195 ~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~~~l~~~~~~~~lgvLf~dFf~~yG~~f 274 (482)
T COG5260 195 RLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSF 274 (482)
T ss_pred ccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCccccccccccchhhccccccccchHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999971 245689999999998 78
Q ss_pred CCCCceeccccccC-CC---CCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHH
Q 007342 145 RWPNPVLLCAIEEG-SL---GLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEA 215 (607)
Q Consensus 145 ~Wp~PV~L~~i~~g-~l---g~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~ 215 (607)
++..-++. +..| .+ --.-|--.. . .....|..|. -..|..-....-|...|+.+|.+|.+++.+
T Consensus 275 ~Y~~~~~s--i~~g~~~~~K~e~g~~~~~---~-p~~LsiqdP~-td~n~~~~a~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 275 NYSLVVLS--INSGDFYLPKYEKGWLKPS---K-PNSLSIQDPG-TDRNNDISAVSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred ChhheEEE--ecCCceeeehhhccccccc---C-CCcEeecCCC-CCcccccccccchHHHHHHHHHHHHHHHhh
Confidence 88775543 3333 10 001222111 1 1456788888 444444445566788999999999998864
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=98.79 E-value=4.2e-08 Score=108.80 Aligned_cols=173 Identities=20% Similarity=0.306 Sum_probs=130.1
Q ss_pred cceeecCCCccceEEEEE--CceEEEEEecccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChhhHH
Q 007342 9 TELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFR 86 (607)
Q Consensus 9 tel~~V~dA~VPIIKf~~--~GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~FR 86 (607)
..+..|..|+||||||+. .+|.||+.|.+. ||||.++.|...+-++..+|
T Consensus 153 ~~v~~v~karvpiik~~d~~s~i~vDISFn~~----------------------------~G~~aa~~i~~~~~~~p~~~ 204 (514)
T KOG1906|consen 153 FHVKVVQKARVPIIKFKDPVSNIHVDISFNQT----------------------------NGVKAAKFIKDFLRDHPFLR 204 (514)
T ss_pred ceEEEeeeeeeeeEEeecCccceEEEeeeccc----------------------------CchhHHHHHHHHHhcCccch
Confidence 457889999999999998 799999999984 57999999999999999999
Q ss_pred HHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCCC---------ChHHHHHHHHHhhc-cCCCCC-ceecccc
Q 007342 87 TTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA---------VPSMLVSRFFRVYT-QWRWPN-PVLLCAI 155 (607)
Q Consensus 87 ~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPna---------s~s~Ll~~FF~vYS-~W~Wp~-PV~L~~i 155 (607)
.++-.+|.|--.|++.....|.+++++.++||..+.|++|.- ....|+.+||++|+ +++... -|.+...
T Consensus 205 ~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~ 284 (514)
T KOG1906|consen 205 SLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLG 284 (514)
T ss_pred hHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhccccCchhhceeccCC
Confidence 999999999999999999999999999999999999999864 23579999999999 444432 2222111
Q ss_pred ccCCCC--CcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHH
Q 007342 156 EEGSLG--LQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICE 214 (607)
Q Consensus 156 ~~g~lg--~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~ 214 (607)
.+ ..+ ..-|- .+...+.....|-.|.-|.-+.. -+...+.-|+.+|..|+.++.
T Consensus 285 g~-~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndig--r~s~~~~~v~~~F~~af~~l~ 340 (514)
T KOG1906|consen 285 GE-YVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIG--RSSFNFSQVKGAFAYAFKVLT 340 (514)
T ss_pred cc-cccHHhhhhh--cccccCCCccccCCCCCcccccc--cccccHHHHHHHHHHHHHHHh
Confidence 10 000 00111 11223344678888888844443 222446688999999998764
No 8
>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=98.74 E-value=2.9e-07 Score=109.25 Aligned_cols=189 Identities=16% Similarity=0.282 Sum_probs=133.6
Q ss_pred HHHHHhCCChhhHHHHHHHHHHHHHhhcCccCc-cccchhHHHHHHHHHHHhh---------CCCCChHHHHHHHHHhhc
Q 007342 73 DQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV-AGFLGGINWALLVARICQL---------YPNAVPSMLVSRFFRVYT 142 (607)
Q Consensus 73 d~IL~lVPn~~~FR~aLR~IKlWAKrRGIYSNv-~GfLGGIsWAILVArVCQL---------yPnas~s~Ll~~FF~vYS 142 (607)
+.|-+..-+...|+.|+.-+|.||++||+.+.. .|.+||+-|++|+|...|- .+..+..+|+..+.++.|
T Consensus 154 ~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fLA 233 (972)
T PF03813_consen 154 KYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFLA 233 (972)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHHh
Confidence 445555556789999999999999999998765 5889999999999999865 455688899999999999
Q ss_pred cCCC-CCceeccccccCCCCCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccC
Q 007342 143 QWRW-PNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEA 221 (607)
Q Consensus 143 ~W~W-p~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~ 221 (607)
..+| .+|+.++.-++.......| ..+--|++--.-=.+|.++++|.++++.|+.|-+++.+++++-. ..
T Consensus 234 ~~d~~~~~l~~~~~~~~~~~~~~~--------~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~d 303 (972)
T PF03813_consen 234 TTDLSKKPLFFKSSSDSTESLEEF--------HSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--DD 303 (972)
T ss_pred ccccccCceEEecCCCccchhhhh--------hccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--cc
Confidence 9999 6799887654311100011 11223343333467999999999999999999999999886421 12
Q ss_pred CCCcccccC-C-cchhhhcccEEEEE---EE----ecChhhhcchhhhhHHHHHHHHH-HHh
Q 007342 222 DVDWDTLFE-P-FTFFEAYKNYLRID---IS----AENADDLRNWKGWVESRLRQLTL-KIE 273 (607)
Q Consensus 222 ~~~W~~LFe-p-~~FF~~Yk~yL~I~---vs----a~~~e~~~~W~GwVESRlR~Lv~-~LE 273 (607)
..+.+|- + .++..+|.+++.|. .. .....+...|..+++.++-.|+. .|-
T Consensus 304 --~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLg 363 (972)
T PF03813_consen 304 --GFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALG 363 (972)
T ss_pred --chhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHH
Confidence 5676664 4 46778999999991 11 12223334444456667766653 354
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=98.64 E-value=1.5e-07 Score=104.77 Aligned_cols=174 Identities=22% Similarity=0.338 Sum_probs=131.1
Q ss_pred ccceeecCCCccceEEEEE--CceEEEEEecccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChhhH
Q 007342 8 VTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNF 85 (607)
Q Consensus 8 Vtel~~V~dA~VPIIKf~~--~GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~F 85 (607)
+..+..|..|+|||||+.. .|+++|+.+-... .+.+..+|+... .--.+|
T Consensus 211 ~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~--------~~~nS~ll~~~~--------------------~~d~r~ 262 (596)
T KOG2277|consen 211 VREVQQILSARVPIIKFNDSGSGLECDLSVNNSD--------AILNSQLLRNYS--------------------EIDPRV 262 (596)
T ss_pred cceeeeeeecCCCEEEecCCCCCCceeeeeccch--------hhhhhHHHHHhH--------------------hcCCCc
Confidence 8889999999999999955 5899999987532 223444444332 223389
Q ss_pred HHHHHHHHHHHHhhcCccCccccch-hHHHHHHHHHHHhhCCC-------------------------------------
Q 007342 86 RTTLRCMRFWAKRRGVYSNVAGFLG-GINWALLVARICQLYPN------------------------------------- 127 (607)
Q Consensus 86 R~aLR~IKlWAKrRGIYSNv~GfLG-GIsWAILVArVCQLyPn------------------------------------- 127 (607)
+.+--.||.||+++|+++..-|.+. -+++.+||....|.++-
T Consensus 263 ~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 342 (596)
T KOG2277|consen 263 RPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKPVVKKKVLCSFLRVFQRNP 342 (596)
T ss_pred chHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhcccccccchhhhhhhcccccccccc
Confidence 9999999999999999999999988 69999999999887531
Q ss_pred ------CChHHHHHHHHHhhc-cCCCCCceeccccccCCCCCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHH
Q 007342 128 ------AVPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 200 (607)
Q Consensus 128 ------as~s~Ll~~FF~vYS-~W~Wp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~ 200 (607)
.+...|+..||.+|+ .|++++-++ .+..|.....-|.. ...-.+-|..|.....|....++..+..
T Consensus 343 ~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I--~~r~~~~l~~~~~~-----~~~~~l~i~dp~~~~~n~~~~~~~~~~~ 415 (596)
T KOG2277|consen 343 SNSQNTGSLGELLLGFFSYYASLFDFRKNAI--SIRRGRALKRAKKI-----KSKKFLCIEDPFEVSHNADAGVTLKVLL 415 (596)
T ss_pred ccccccchHHHHHHHHHHHHhhhccccccee--eeeecccccccchh-----hhccceeeccccccccCccccchHHHHH
Confidence 012477889999999 899998653 22222211100111 1124688999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 007342 201 IMMDEFQRGHEICEAM 216 (607)
Q Consensus 201 vI~~Ef~RA~~Il~~i 216 (607)
+|+.+|+....++...
T Consensus 416 ~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 416 LIQDEFQESRRVFKDV 431 (596)
T ss_pred HHHHHHHHHHHHhhhh
Confidence 9999999999988653
No 10
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=97.66 E-value=5.5e-05 Score=67.10 Aligned_cols=36 Identities=33% Similarity=0.672 Sum_probs=32.9
Q ss_pred CCCCCCccceeecCCCccceEEEEEC--ceEEEEEecc
Q 007342 2 LTEMPEVTELHPVPDAHVPVMKFKFS--GVSIDLLYAR 37 (607)
Q Consensus 2 L~~~p~Vtel~~V~dA~VPIIKf~~~--GI~IDLlFAr 37 (607)
|++.+.+.++..|..|+||||||... |++|||+|+.
T Consensus 63 l~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~Dis~~~ 100 (114)
T cd05402 63 LKKSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNN 100 (114)
T ss_pred HHhCCCceeeEEeccCCCCEEEEEEcCCCeEEEEEccc
Confidence 55667788999999999999999998 9999999997
No 11
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=97.42 E-value=0.00076 Score=79.68 Aligned_cols=155 Identities=15% Similarity=0.228 Sum_probs=111.1
Q ss_pred CChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHH---hhCCCCChHHHHHHHHHhhccCCCCC-ceecccc
Q 007342 80 PKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARIC---QLYPNAVPSMLVSRFFRVYTQWRWPN-PVLLCAI 155 (607)
Q Consensus 80 Pn~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVC---QLyPnas~s~Ll~~FF~vYS~W~Wp~-PV~L~~i 155 (607)
.....|+.++--.|.|+++|-. +-..|.+||+-|++|+++.. .+.-+.+..+++..-+++++.|+|.. -+-+++-
T Consensus 305 s~~~~f~da~~Llk~WlrqRs~-~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~~~ 383 (1121)
T KOG2054|consen 305 SSAKGFKDALALLKVWLRQRSL-DIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLVPS 383 (1121)
T ss_pred hhhhhHHHHHHHHHHHHHhhhh-hcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEeccC
Confidence 3467999999999999999911 12567899999999999986 35666788999999999999999986 4443321
Q ss_pred ccCCCCCcccCCCCCCCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCccccc-CCcch
Q 007342 156 EEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLF-EPFTF 234 (607)
Q Consensus 156 ~~g~lg~~vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LF-ep~~F 234 (607)
. -+ .|....-+.++. |.+-=+.-..|..-|+|.++.+.+++|.+-...++++.... ..+.+| ++.+.
T Consensus 384 ~-~s------~~~~~~f~e~~~-~~f~D~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~----~F~~IFmtkip~ 451 (1121)
T KOG2054|consen 384 S-PS------LPALADFHEGQL-VTFIDSSGHLNLCANMTASTYEQVQEEARLTLMLLDSRADD----GFSLIFMTKIPV 451 (1121)
T ss_pred C-CC------chhhhhhhhcce-eeEeccCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhhhc----CcceeeeecCCc
Confidence 0 00 011111111222 22222334688888999999999999999999999865432 577776 67899
Q ss_pred hhhcccEEEEEEE
Q 007342 235 FEAYKNYLRIDIS 247 (607)
Q Consensus 235 F~~Yk~yL~I~vs 247 (607)
|..|.|=+.+...
T Consensus 452 ~~~yDh~l~l~~~ 464 (1121)
T KOG2054|consen 452 FRAYDHVLHLSPL 464 (1121)
T ss_pred hhhhheeeecccc
Confidence 9999998877654
No 12
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=97.13 E-value=0.028 Score=62.53 Aligned_cols=216 Identities=17% Similarity=0.224 Sum_probs=127.8
Q ss_pred CCccceEEEEECceEEEEEec-ccCCCCCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChhhHHHHHHHHHH
Q 007342 16 DAHVPVMKFKFSGVSIDLLYA-RLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRF 94 (607)
Q Consensus 16 dA~VPIIKf~~~GI~IDLlFA-rL~~~~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~FR~aLR~IKl 94 (607)
-|--|-++..|+|++||++=| .+.-. ..+...+|-+ .-=+++|++..- +.++.-.|.+|.
T Consensus 100 yaeHpyv~~~~~G~~VDiVPcy~v~~~----------~~~~saVDRt-------p~H~~fv~~rl~--~~~~d~VRLlK~ 160 (447)
T PRK13300 100 YAEHPYVTGEIDGFEVDIVPCYKVESG----------EEIISAVDRT-------PFHTKYVKERLK--GKLEDEVRLLKQ 160 (447)
T ss_pred eccCceEEEEECCEEEEEEeeEEccCc----------CcccccccCc-------hHHHHHHHHhhh--hhHHHHHHHHHH
Confidence 467799999999999999877 22210 0111122211 122456665442 238999999999
Q ss_pred HHHhhcCccC--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCCCCcccCCCCCCC
Q 007342 95 WAKRRGVYSN--VAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPK 172 (607)
Q Consensus 95 WAKrRGIYSN--v~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~lg~~vWdP~~~~~ 172 (607)
|.|.-|+|++ ..+.++|+.+=+|+++. -+-..++..+ +.|. -|+.+...+.+.. .
T Consensus 161 f~k~~gvYGsE~k~~GFSGYl~ELLv~~y------G~F~~~l~~a----~~w~--~~~~I~~~~~~~~-----------~ 217 (447)
T PRK13300 161 FLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKAA----SKWK--PPVKIDLEKHGKE-----------Y 217 (447)
T ss_pred HHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH----HhCC--CCceEeccccCcc-----------c
Confidence 9999999965 45668999999999993 3334444443 4454 3343321111110 0
Q ss_pred CCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCcc---------hhhhcccEEE
Q 007342 173 DKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFT---------FFEAYKNYLR 243 (607)
Q Consensus 173 Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~~---------FF~~Yk~yL~ 243 (607)
.-...+.||.|.-|..|.|.++|...+..+...-+ + ..+... ..+|.|.+ +-.+=.+.+.
T Consensus 218 ~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~aar---~----fL~~Ps----~~fF~~~~~~~~~~~~~l~~R~t~~~~ 286 (447)
T PRK13300 218 KFDDPLVVIDPVDPNRNVAAALSLENLATFILAAR---E----FLKNPS----LEFFFPSDLSPEEILEELERRGTTVLA 286 (447)
T ss_pred cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHH---H----HHhCCC----HHhcCCCCCChHHHHHHHhhcCceEEE
Confidence 11368999999999999999999998877664322 2 222222 23444433 1111224555
Q ss_pred EEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccC
Q 007342 244 IDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPH 285 (607)
Q Consensus 244 I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~ 285 (607)
|....++.-+-. .-|-++-=.+.|...||+....++....|
T Consensus 287 v~f~~p~~v~Di-l~pQl~r~~~~i~~~L~~~gF~v~~~~~~ 327 (447)
T PRK13300 287 LEFPRPDIVEDI-LYPQLERSLRSIVKLLEREGFEVLRSGAW 327 (447)
T ss_pred EEeCCCCCCccc-hhHHHHHHHHHHHHHHHHCCCEEEEeeee
Confidence 555544433323 33666666666777788776555555444
No 13
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=96.96 E-value=0.087 Score=58.11 Aligned_cols=253 Identities=19% Similarity=0.227 Sum_probs=145.5
Q ss_pred CCCccceEEEEECceEEEEEecccCCCCCCCCCCCCcc-hhhhcCChhhhhhhchhhhHHHHHHhCCChhhHHHHHHHHH
Q 007342 15 PDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQD-SILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMR 93 (607)
Q Consensus 15 ~dA~VPIIKf~~~GI~IDLlFArL~~~~vPe~ldl~dd-~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~FR~aLR~IK 93 (607)
.-|--|-++..|+|++||++=|-- +.+- .+...+|-. ..=+++++...- +.|+.-.|.+|
T Consensus 97 ~yaeHpYv~~~~~G~~VDiVPcy~----------v~~g~~~~taVDRt-------p~H~~fv~~rl~--~~~~d~VRLlK 157 (408)
T TIGR03671 97 RYAEHPYVSGEIEGFEVDVVPCYK----------VESGEEIISAVDRT-------PFHTRYVLERLD--GKLRDDVRLLK 157 (408)
T ss_pred eeccCceEEEEEccEEEEEEeeEE----------ccCcCeeeccccCc-------hHHHHHHHHhhh--hhHHHHHHHHH
Confidence 456669999999999999986631 1111 111111211 112455554432 23889999999
Q ss_pred HHHHhhcCccC--ccccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCCCCcccCCCCCC
Q 007342 94 FWAKRRGVYSN--VAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNP 171 (607)
Q Consensus 94 lWAKrRGIYSN--v~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~lg~~vWdP~~~~ 171 (607)
.|.|.-|+|++ ..+.++|+.+=+|+++. -+-..++..+ +.| ..++.+ +++.. ...
T Consensus 158 ~f~k~igvYGsE~~~~GFSGYl~ELLv~~y------G~F~~~l~~a----~~w--k~~~~i-d~~~~-------~~~--- 214 (408)
T TIGR03671 158 QFLKGIGVYGSELKTRGFSGYLCELLVIHY------GSFENVLKAA----SKW--KPGVVI-DIEEH-------GTK--- 214 (408)
T ss_pred HHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH----Hhc--CCCeEE-ecCcc-------ccc---
Confidence 99999999965 45568999999999993 2333444433 444 445654 32211 110
Q ss_pred CCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCc-----ch---hhh-cccEE
Q 007342 172 KDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPF-----TF---FEA-YKNYL 242 (607)
Q Consensus 172 ~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~-----~F---F~~-Yk~yL 242 (607)
.-.+.+.||.|.-|..|.|.++|...+..+...-+++++ .. =..+|.|. ++ +.+ -.+.+
T Consensus 215 -~f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl~-------~P----s~~fF~p~~~~~~~~~~~l~~r~t~~~ 282 (408)
T TIGR03671 215 -KFDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFLK-------NP----SLEFFFPPEIEPEEFLERLERRGTTLL 282 (408)
T ss_pred -cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHHH-------CC----CHHHcCCCCCChHHHHHHHhhcCcEEE
Confidence 113589999999999999999999999888766555443 22 12455442 11 122 22444
Q ss_pred EEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccCCCCCCCCCCCcEEEEEEeeeeccCC--CCCCCceech
Q 007342 243 RIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQGV--PVGEGEQFDI 320 (607)
Q Consensus 243 ~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~F~~~~~~~~~~ffIGL~~~~~~--~~~~~~~~DL 320 (607)
.|....++.-+- ..-|-++-=.+.|...||+....++....|- +.. .|+.++=|...+-. ....|-.+.-
T Consensus 283 ~~~f~~p~~v~D-il~pQl~r~~~~i~~~L~~~gF~v~r~~~~~----~~~---~~~l~~el~~~~lp~~~~h~GPpv~~ 354 (408)
T TIGR03671 283 AIVFRTPDVVDD-ILYPQLERSGRSLVKLLEREGFEVLRYGVWA----DEN---TCYLLLELESAELPRVKLHVGPPVWV 354 (408)
T ss_pred EEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEEeeeec----CCC---eEEEEEEeeccccCCceeeeCCCccc
Confidence 444444443222 3346666666667777887766556666552 222 25555555432211 1112333455
Q ss_pred HHHHHHHHH
Q 007342 321 RLTVKEFKQ 329 (607)
Q Consensus 321 ~~~v~eF~~ 329 (607)
+.....|.+
T Consensus 355 ~~~a~~F~~ 363 (408)
T TIGR03671 355 RDHAEKFIE 363 (408)
T ss_pred hhHHHHHHH
Confidence 455677876
No 14
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=95.62 E-value=0.16 Score=52.71 Aligned_cols=162 Identities=17% Similarity=0.163 Sum_probs=114.0
Q ss_pred cCCCccceEEEEEC----ceEEEEEecccCCCCCCCCCCCCcchhhhcCC-hhhhhhhchhhhHHHHHHhCCChhhHHHH
Q 007342 14 VPDAHVPVMKFKFS----GVSIDLLYARLSLWVIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTT 88 (607)
Q Consensus 14 V~dA~VPIIKf~~~----GI~IDLlFArL~~~~vPe~ldl~dd~lL~nlD-e~svrSLNG~RVtd~IL~lVPn~~~FR~a 88 (607)
|....+|.++..|. -...+..- ..+|+++...+. -..+| +.|+.+|-..|-+...-...-....|+.+
T Consensus 61 ~~~~~~~~~~~~i~ltSp~~r~~~~~-----~~~~~~~~~~~p--~~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iv 133 (246)
T smart00572 61 VTSTKEPTMEVGILITSPLARVELLI-----TTVPENLRKLDP--EDHLDRKKCLSALASLRHAKWFQARASGLQSCVIV 133 (246)
T ss_pred eeccCCCceeEEEEEecccccccccc-----cccCcccccCCc--cccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhH
Confidence 44555576666552 11122222 334555443222 12334 67899999999999999999999999999
Q ss_pred HHHHHHHHHhhcCccCccccchhHHHHHHHHHHHhhCCC-CChHHHHHHHHHhhccCCCCCceeccccccCCCCCcccCC
Q 007342 89 LRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPN-AVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDP 167 (607)
Q Consensus 89 LR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQLyPn-as~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~lg~~vWdP 167 (607)
.|.+|-|.+|--.++. |.+...=+|+++++--... .+++.-+.|||++.|+=-. +. |+
T Consensus 134 iRilKd~~~R~~~~~p----L~~w~iELl~~~~i~~~~~~l~~~~a~RR~fe~lAsG~l-----~p----~~-------- 192 (246)
T smart00572 134 IRVLRDLCNRVPTWQP----LSGWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGIL-----LP----GS-------- 192 (246)
T ss_pred HHHHHHHHHhcccccc----cccccHHHHHHHHhccCCCCCCHHHHHHHHHHHHHhccC-----cC----CC--------
Confidence 9999999999766544 8888899999999863322 3578889999999874222 10 00
Q ss_pred CCCCCCCcccceeecCCCC-CCCcccccChhhHHHHHHHHHHHHHHH
Q 007342 168 RRNPKDKYHLMPIITPAYP-CMNSSYNVSTSTLRIMMDEFQRGHEIC 213 (607)
Q Consensus 168 ~~~~~Dr~hlMPIITPayP-~~NST~NVT~STl~vI~~Ef~RA~~Il 213 (607)
--|+.|+.+ ..|.+...|.-..+.|+..-+.+.+++
T Consensus 193 ----------~gI~DPce~~~~nv~~~lT~qqrd~It~sAQ~alRl~ 229 (246)
T smart00572 193 ----------PGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLL 229 (246)
T ss_pred ----------CCCcCCCCCCcccHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 125677776 788888889999999999888888876
No 15
>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=94.20 E-value=0.4 Score=58.17 Aligned_cols=159 Identities=22% Similarity=0.375 Sum_probs=104.4
Q ss_pred hchhhhHHHHHHhCCChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHH-hhCCCC---ChHHHHHHHHHhh
Q 007342 66 LNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARIC-QLYPNA---VPSMLVSRFFRVY 141 (607)
Q Consensus 66 LNG~RVtd~IL~lVPn~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVC-QLyPna---s~s~Ll~~FF~vY 141 (607)
+-..+-+..|..+--....|-.+.|.+|.|.-.+-+ .|++.--..=+|||.|- +-+|-. ++.+=+.||.+..
T Consensus 666 ~~~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lL 741 (972)
T PF03813_consen 666 IHLPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLL 741 (972)
T ss_pred HhhHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHH
Confidence 345556666666666678999999999999999977 46778899999999997 344533 4444456777778
Q ss_pred ccCCCCC-ceeccccccCC--------CCCcccCCCCCCCCCcccceeecCCCCCCCc--ccccChhhHHHHHHHHHHHH
Q 007342 142 TQWRWPN-PVLLCAIEEGS--------LGLQVWDPRRNPKDKYHLMPIITPAYPCMNS--SYNVSTSTLRIMMDEFQRGH 210 (607)
Q Consensus 142 S~W~Wp~-PV~L~~i~~g~--------lg~~vWdP~~~~~Dr~hlMPIITPayP~~NS--T~NVT~STl~vI~~Ef~RA~ 210 (607)
+.|||.+ |+++..-.+-. ..+..|.. ..+......|-|-||.-|.-.. ...-+..-++.|+.=-+.+.
T Consensus 742 s~~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl 820 (972)
T PF03813_consen 742 STWDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASL 820 (972)
T ss_pred HhCCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHH
Confidence 9999985 88775322100 01222322 1233345689999999985432 12355556666766666677
Q ss_pred HHHHHHHhccCCCCcccccCC
Q 007342 211 EICEAMEKNEADVDWDTLFEP 231 (607)
Q Consensus 211 ~Il~~i~~~~~~~~W~~LFep 231 (607)
++++. .+-...+|..||.+
T Consensus 821 ~~l~~--~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 821 KLLEE--QGLSDLDWKSLFRP 839 (972)
T ss_pred HHHHh--cCCCCCCHHHhcCC
Confidence 76662 22224489999976
No 16
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=92.70 E-value=4.2 Score=45.49 Aligned_cols=214 Identities=18% Similarity=0.183 Sum_probs=118.7
Q ss_pred CCccceEEEEECceEEEEEecccC-CC-CCCCCCCCCcchhhhcCChhhhhhhchhhhHHHHHHhCCChhhHHHHHHHHH
Q 007342 16 DAHVPVMKFKFSGVSIDLLYARLS-LW-VIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMR 93 (607)
Q Consensus 16 dA~VPIIKf~~~GI~IDLlFArL~-~~-~vPe~ldl~dd~lL~nlDe~svrSLNG~RVtd~IL~lVPn~~~FR~aLR~IK 93 (607)
-|-=|-+.-+++|+++|++=|--. -+ .+-... |..+|- |.++..-+-.... .=.|-.|
T Consensus 102 YAeHPYV~g~v~G~eVDvVPCy~v~~~~~~~sAV---DRTplH---------------t~yv~e~L~~~~~--deVrLLK 161 (443)
T COG1746 102 YAEHPYVTGEVDGYEVDVVPCYKVEDGEKIISAV---DRTPLH---------------TRYVEEHLKGRQK--DEVRLLK 161 (443)
T ss_pred hccCCeeEEEEccEEEEEEecccccCcccccccc---cCcchh---------------HHHHHHHhcccch--hHHHHHH
Confidence 455699999999999999988432 11 011111 111111 2233322222111 2346779
Q ss_pred HHHHhhcCccCc--cccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCC-CCCceeccccccCCCCCcccCCCCC
Q 007342 94 FWAKRRGVYSNV--AGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWR-WPNPVLLCAIEEGSLGLQVWDPRRN 170 (607)
Q Consensus 94 lWAKrRGIYSNv--~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~-Wp~PV~L~~i~~g~lg~~vWdP~~~ 170 (607)
.+-|.=|+|++- .+.++|+-.-+|+.+. -.|=.+...-. |.-|++|.. + .|.-..
T Consensus 162 ~FlK~iGvYGaE~rt~GFSGYL~ELLII~y-------------GsFe~vl~~a~~wrp~~~ID~-~-------~~~~e~- 219 (443)
T COG1746 162 QFLKGIGVYGAELRTQGFSGYLCELLIIHY-------------GSFENVLKAASRWRPGKIIDL-E-------GHKRER- 219 (443)
T ss_pred HHHhccCccceeeeeccchHHHHHHHHhhh-------------ccHHHHHHHHhccCCCeEEec-c-------chhhhc-
Confidence 999999999974 5667888888887765 12222222222 777766532 2 121000
Q ss_pred CCCCcccceeecCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCcc--------hhhhcccEE
Q 007342 171 PKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFT--------FFEAYKNYL 242 (607)
Q Consensus 171 ~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~LFep~~--------FF~~Yk~yL 242 (607)
-.| ..|-|+.|.-|..|.|.+||.-.+..+.- |.+ ..+++.+ ..+|.|.. ...+=.+-+
T Consensus 220 f~d--~PliVvDPVDP~RNVAAalSl~~la~f~~----aar---~FL~~PS----~efF~p~~~~~~~~~~~~~rgt~v~ 286 (443)
T COG1746 220 FED--EPLIVVDPVDPKRNVAAALSLENLARFVH----AAR---EFLKNPS----PEFFFPRKPKPLLLSKLRRRGTHVL 286 (443)
T ss_pred cCC--CCeEecCCCCCccchhhhcCHHHHHHHHH----HHH---HHhcCCC----hhhcCCCCcCcccccchhhcCceEE
Confidence 011 28999999999999999999888766542 222 2222222 23333211 122222333
Q ss_pred EEEEEecChhhhcchhhhhHHHHHHHHHHHhhccCcceeeccC
Q 007342 243 RIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPH 285 (607)
Q Consensus 243 ~I~vsa~~~e~~~~W~GwVESRlR~Lv~~LE~~~~~~l~ahp~ 285 (607)
.|.+-.++.-+ ...-|-++---+.|...||...+.++..+.|
T Consensus 287 ~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~~~ 328 (443)
T COG1746 287 ALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSGVW 328 (443)
T ss_pred EEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeeeee
Confidence 33333444322 3345777777778888899876666665555
No 17
>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=91.58 E-value=0.15 Score=40.67 Aligned_cols=55 Identities=22% Similarity=0.428 Sum_probs=34.7
Q ss_pred ChHHHHHHHHHhhc-cCCCCCceeccccccCCC---CCcccCCCCCCCCCcccceeecCCCCC
Q 007342 129 VPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSL---GLQVWDPRRNPKDKYHLMPIITPAYPC 187 (607)
Q Consensus 129 s~s~Ll~~FF~vYS-~W~Wp~PV~L~~i~~g~l---g~~vWdP~~~~~Dr~hlMPIITPayP~ 187 (607)
+.+.|+..||++|+ .|+|.+-|+ .+..|.. ....|.. ....+...|.|..|.-|.
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~~~~~I--si~~g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~~ 59 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDYENNVI--SIRNGGYFPKEEKNWSK--SRNQRKKRLCIEDPFDPS 59 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-TTTEEE--ESSSSSEEEHHHHTGCH--CCCCECSSSEBBESSSTT
T ss_pred CHHHHHHHHHHHhCCcCCCCceEE--EecCCceEEhhhccccc--cccCCCCeEEEECCCCCC
Confidence 35789999999999 999999665 2333431 1123431 112345789999998764
No 18
>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=89.28 E-value=1.3 Score=41.25 Aligned_cols=93 Identities=20% Similarity=0.297 Sum_probs=56.1
Q ss_pred HHHHHHHHHhhcCccCc--cccchhHHHHHHHHHHHhhCCCCChHHHHHHHHHhhccCCCCCceeccccccCCCCCcccC
Q 007342 89 LRCMRFWAKRRGVYSNV--AGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWD 166 (607)
Q Consensus 89 LR~IKlWAKrRGIYSNv--~GfLGGIsWAILVArVCQLyPnas~s~Ll~~FF~vYS~W~Wp~PV~L~~i~~g~lg~~vWd 166 (607)
.|..|.+.|.-|||+.- .+.++|+-.-+||.+.= +-..+|.. -+ .|..|+.|..-..+...
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yG------sF~~~l~~----a~--~W~~~~~Id~~~~~~~~----- 65 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYG------SFENVLEA----AA--KWKPPVVIDLEDHGEPS----- 65 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHS------SHHHHHHH----HT--T--TTEEEETT-TTE-------
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHC------CHHHHHHH----HH--hcCCCeEEccCccchhh-----
Confidence 47889999999999974 56788998888888762 21222222 23 67667766432111100
Q ss_pred CCCCCCCCcccceeecCCCCCCCcccccChhhHHHHH
Q 007342 167 PRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMM 203 (607)
Q Consensus 167 P~~~~~Dr~hlMPIITPayP~~NST~NVT~STl~vI~ 203 (607)
..-...+.||.|.-|..|.|.+||..++..+.
T Consensus 66 -----~~f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 66 -----KKFDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp -----EEE-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred -----hhcCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 00125799999999999999999998877655
No 19
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=53.50 E-value=32 Score=42.46 Aligned_cols=123 Identities=18% Similarity=0.274 Sum_probs=71.2
Q ss_pred hhhHHHHHHhCCChhhHHHHHHHHHHHHHhhcCccCccccchhHHHHHHHHHHHh-hC---CCCChHHHHHHHHHhhccC
Q 007342 69 CRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ-LY---PNAVPSMLVSRFFRVYTQW 144 (607)
Q Consensus 69 ~RVtd~IL~lVPn~~~FR~aLR~IKlWAKrRGIYSNv~GfLGGIsWAILVArVCQ-Ly---Pnas~s~Ll~~FF~vYS~W 144 (607)
.|.+-.|-.+--.+..|-.+.|--|.|-...=+-+ |.+ -=+.-+|||..-+ -+ |-.++..=..||-+..|+|
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 34445555554557789999999999977653221 122 3456788888764 23 3455555578999999999
Q ss_pred CCCC-ceeccccccCCCCCc----ccCCCCCCCCCcccceeecCCCCCCCcccccChhh
Q 007342 145 RWPN-PVLLCAIEEGSLGLQ----VWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTST 198 (607)
Q Consensus 145 ~Wp~-PV~L~~i~~g~lg~~----vWdP~~~~~Dr~hlMPIITPayP~~NST~NVT~ST 198 (607)
+|.. |.++.- ..+ ++.. .-.--...+..+..|-||||- =..++.+.=+.++
T Consensus 881 dW~~~PLIvd~-nn~-~~ed~~~e~~e~f~s~R~~lp~m~vit~y-D~~~~~~t~~~P~ 936 (1121)
T KOG2054|consen 881 DWKFDPLIVDF-NNG-FPEDERSELEEKFISARKQLPPMVVITPY-DHLGSKFTRTSPN 936 (1121)
T ss_pred cccCCceEEEc-CCC-CcHHHHHHHHHHHhhhcccCCceEEeecc-ccccccccccCch
Confidence 9986 876643 111 1000 000001112234589999984 4445544444455
No 20
>PF15431 TMEM190: Transmembrane protein 190
Probab=49.48 E-value=9.5 Score=35.71 Aligned_cols=34 Identities=29% Similarity=0.580 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHhhcCccCc--cccchhHHHHHH
Q 007342 84 NFRTTLRCMRFWAKRRGVYSNV--AGFLGGINWALL 117 (607)
Q Consensus 84 ~FR~aLR~IKlWAKrRGIYSNv--~GfLGGIsWAIL 117 (607)
.|...+-|+=-|||||++|.|. -|||.||-..=|
T Consensus 72 l~Li~~iclFWWAkRrd~~k~lh~P~fL~~~~c~kl 107 (134)
T PF15431_consen 72 LLLICSICLFWWAKRRDMCKHLHMPRFLSGFKCDKL 107 (134)
T ss_pred HHHHHHHHHHHHHHHhchHhhccCchhhccCccchh
Confidence 4667788899999999999875 588888654433
No 21
>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=32.75 E-value=17 Score=38.35 Aligned_cols=32 Identities=38% Similarity=0.408 Sum_probs=21.4
Q ss_pred hcccEEEEEEEecChhhhcchhhhhHHHHHHH
Q 007342 237 AYKNYLRIDISAENADDLRNWKGWVESRLRQL 268 (607)
Q Consensus 237 ~Yk~yL~I~vsa~~~e~~~~W~GwVESRlR~L 268 (607)
.|-.+|+==..-+|.-+...++||||||+-.+
T Consensus 84 sYLRlLrGW~fDSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 84 SYLRLLRGWGFDSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred hHHHHHhccCcCCCChhhhhhhhhhhhccCcC
Confidence 34444333233467778899999999998654
No 22
>KOG2303 consensus Predicted NAD synthase, contains CN hydrolase domain [Coenzyme transport and metabolism; General function prediction only]
Probab=30.35 E-value=87 Score=36.37 Aligned_cols=17 Identities=35% Similarity=0.616 Sum_probs=12.1
Q ss_pred CCCChH---HHHHHHHHhhc
Q 007342 126 PNAVPS---MLVSRFFRVYT 142 (607)
Q Consensus 126 Pnas~s---~Ll~~FF~vYS 142 (607)
+..+|. .=|.+||.+|+
T Consensus 625 ~klsp~qvaEKVk~FF~~Y~ 644 (706)
T KOG2303|consen 625 DKLSPRQVAEKVKRFFSYYS 644 (706)
T ss_pred CcCCHHHHHHHHHHHHhhhe
Confidence 445554 44899999997
Done!