Query 005445
Match_columns 696
No_of_seqs 211 out of 502
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 23:33:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005445hhsearch_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 1E-140 3E-145 1137.5 36.4 444 6-459 12-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 1E-132 3E-137 1109.0 48.1 475 7-490 50-572 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 2E-120 3E-125 950.9 31.3 446 6-458 4-531 (552)
4 PF04928 PAP_central: Poly(A) 100.0 8.7E-77 1.9E-81 610.3 19.9 253 7-321 2-254 (254)
5 PF04926 PAP_RNA-bind: Poly(A) 100.0 6.2E-32 1.3E-36 258.7 9.2 133 322-455 1-155 (157)
6 COG5260 TRF4 DNA polymerase si 99.9 2E-23 4.4E-28 228.1 21.9 242 26-304 56-342 (482)
7 KOG1906 DNA polymerase sigma [ 99.9 1.9E-20 4.2E-25 208.4 21.5 248 21-304 57-341 (514)
8 KOG2277 S-M checkpoint control 99.4 1.2E-12 2.6E-17 148.3 16.3 210 60-305 167-431 (596)
9 cd05402 NT_PAP_TUTase Nucleoti 99.3 7.8E-12 1.7E-16 113.0 10.2 66 60-126 32-100 (114)
10 TIGR03671 cca_archaeal CCA-add 99.0 9.3E-08 2E-12 105.4 26.0 293 60-419 53-364 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.0 1.1E-07 2.3E-12 106.2 26.5 294 60-418 54-366 (447)
12 PF03813 Nrap: Nrap protein; 99.0 1.5E-07 3.2E-12 113.9 26.7 281 63-363 12-364 (972)
13 COG1746 CCA1 tRNA nucleotidylt 98.4 7.2E-05 1.6E-09 82.8 23.2 324 29-419 5-368 (443)
14 KOG2054 Nucleolar RNA-associat 97.9 6.5E-05 1.4E-09 89.5 11.9 256 60-336 162-464 (1121)
15 smart00572 DZF domain in DSRM 97.8 0.0012 2.6E-08 69.0 16.8 199 64-303 20-230 (246)
16 PF03828 PAP_assoc: Cid1 famil 97.0 0.00054 1.2E-08 55.7 2.7 55 218-276 1-59 (60)
17 PF03813 Nrap: Nrap protein; 96.0 0.058 1.3E-06 66.4 13.1 158 156-320 667-839 (972)
18 PF09249 tRNA_NucTransf2: tRNA 95.7 0.034 7.4E-07 52.2 7.2 93 178-292 3-97 (114)
19 PF14091 DUF4269: Domain of un 95.3 0.25 5.3E-06 48.7 11.6 117 49-193 5-144 (152)
20 cd05400 NT_2-5OAS_ClassI-CCAas 93.2 0.51 1.1E-05 44.3 8.8 61 63-126 44-110 (143)
21 PF10421 OAS1_C: 2'-5'-oligoad 83.3 2.9 6.3E-05 42.8 6.4 47 171-217 41-88 (190)
22 cd00141 NT_POLXc Nucleotidyltr 81.3 19 0.00042 39.0 12.2 122 39-199 136-278 (307)
23 PF07528 DZF: DZF domain; Int 78.7 92 0.002 33.2 15.9 197 65-302 15-231 (248)
24 PF03281 Mab-21: Mab-21 protei 72.0 1.3E+02 0.0029 31.7 15.2 103 163-297 184-289 (292)
25 KOG2054 Nucleolar RNA-associat 70.5 17 0.00036 45.4 8.8 122 159-287 806-936 (1121)
26 PF01909 NTP_transf_2: Nucleot 64.7 7.3 0.00016 33.4 3.3 19 60-78 27-45 (93)
27 COG1665 Predicted nucleotidylt 59.3 4.1 8.8E-05 44.0 0.9 67 60-127 134-215 (315)
28 cd05397 NT_Pol-beta-like Nucle 56.8 8.1 0.00018 30.8 2.0 13 60-72 30-42 (49)
29 PF15431 TMEM190: Transmembran 47.4 11 0.00024 35.7 1.6 31 173-203 72-104 (134)
30 COG1669 Predicted nucleotidylt 46.8 18 0.00039 33.5 2.8 32 60-93 37-68 (97)
31 cd05403 NT_KNTase_like Nucleot 37.2 67 0.0014 27.1 4.8 20 60-79 31-50 (93)
32 COG1796 POL4 DNA polymerase IV 35.1 89 0.0019 34.7 6.3 66 53-126 185-250 (326)
33 PRK08609 hypothetical protein; 33.9 2.8E+02 0.0062 32.8 10.7 21 178-198 263-283 (570)
34 PF07357 DRAT: Dinitrogenase r 29.9 20 0.00044 38.4 0.5 21 337-357 95-115 (262)
35 PF10281 Ish1: Putative stress 26.6 40 0.00086 25.5 1.4 30 28-58 6-35 (38)
36 PRK13299 tRNA CCA-pyrophosphor 24.6 1E+03 0.023 26.9 12.7 120 109-237 68-211 (394)
37 PF09970 DUF2204: Nucleotidyl 20.2 1.5E+02 0.0032 29.9 4.5 66 62-133 35-100 (181)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.2e-140 Score=1137.52 Aligned_cols=444 Identities=58% Similarity=1.017 Sum_probs=426.3
Q ss_pred CccccccCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc--------------------------
Q 005445 6 GQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ-------------------------- 59 (696)
Q Consensus 6 ~~~~Gvt~PIS~~~Pt~~d~~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~-------------------------- 59 (696)
+++||||+|||+|+||++|+++|.+|+++|+++|+|||+||..+|++||++|++
T Consensus 12 ~~~~Gvt~PiS~a~p~~~d~~lt~~L~~~L~~~g~fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggk 91 (562)
T KOG2245|consen 12 TKSYGVTQPISTAGPTEADIALTQELIKTLKNEGLFESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGK 91 (562)
T ss_pred cccccccCCcccCCCcHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCce
Confidence 489999999999999999999999999999999999999999999999999998
Q ss_pred ----------ccCCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccC
Q 005445 60 ----------VHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSL 129 (696)
Q Consensus 60 ----------V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~ 129 (696)
||+||||||+|||+|+|++|+ |||..|+++|+++++|++|++|++|+||||||+|+||+|||+||+|++
T Consensus 92 IftfGSYRLGVhg~GADIDtLcV~Prhv~R~-DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf~GI~IDllfArL~l 170 (562)
T KOG2245|consen 92 IFTFGSYRLGVHGPGADIDTLCVGPRHVSRS-DFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKFDGIEIDLLFARLAL 170 (562)
T ss_pred EEeccceeecccCCCCCcceeeeccccccHH-HHHHHHHHHHhcCccccccccccccccceEEEEecCeeeeeeehhccc
Confidence 999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred CCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHH
Q 005445 130 WVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 209 (696)
Q Consensus 130 ~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVAr 209 (696)
++||+++||+||++|+++||+|+||||||||||+||+||||.+.||.+|||||+|||+||||||++||||||+|||||||
T Consensus 171 ~~VP~dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVAR 250 (562)
T KOG2245|consen 171 PVVPEDLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVAR 250 (562)
T ss_pred ccCCCcccccchHhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHH
Q 005445 210 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 289 (696)
Q Consensus 210 vCQlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~ 289 (696)
+|||||||++++||.+||.+|++|+||+||+|+.+++|.++++||||+.|+.||||+|||||||||+||+|||||+||++
T Consensus 251 iCQLYPNA~~s~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~ 330 (562)
T KOG2245|consen 251 ICQLYPNASPSTLVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLK 330 (562)
T ss_pred HHccCCCcchHHHHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCcccccccccccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccccce
Q 005445 290 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNML 369 (696)
Q Consensus 290 vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l 369 (696)
+|++||+||++||++|+.++. +|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.+||++. .++
T Consensus 331 Vi~~Ef~~g~~I~~~i~~~k~--~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~~-~i~ 407 (562)
T KOG2245|consen 331 VITEEFKRGLEICDDIELNKL--DWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERNQ-VIL 407 (562)
T ss_pred HHHHHHHHHHHHHHHHHhccc--cHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhhc-ceE
Confidence 999999999999999999998 99999999999999999999999999999999999999999999999999964 678
Q ss_pred eeccCCCCCCCCCC-----CceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHH----hhccCCCC--cEEEEEEec
Q 005445 370 QCHPHPGDFSDKSK-----PLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVS----MYTLRKPG--MQISVAHVT 438 (696)
Q Consensus 370 ~ahp~P~~f~~~~~-----~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~----~~~~~~~g--m~i~V~~vk 438 (696)
.|||+|+.|.++.. .+...|||||.+... .++||+..+++|+..++ .++.++.| |++.+.|+|
T Consensus 408 ~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~k 481 (562)
T KOG2245|consen 408 IAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHVK 481 (562)
T ss_pred EecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeeccccccccccccc
Confidence 99999999997642 466789999987653 34999999999999988 56778889 788888999
Q ss_pred CCCCCCCcCCCCCCCCCCCCC
Q 005445 439 RRNLPNFVFPGGVRPSRPSKG 459 (696)
Q Consensus 439 r~~LP~~v~~~~~~~~~~~~~ 459 (696)
|++|+.++++.+.+..|..+.
T Consensus 482 rr~l~~~~~~~~l~~~k~~~~ 502 (562)
T KOG2245|consen 482 RRSLIQTITKEFLRLCKQYKK 502 (562)
T ss_pred ccccccccCHHHhhHHHhhcc
Confidence 999999999999887775553
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=1.2e-132 Score=1109.01 Aligned_cols=475 Identities=44% Similarity=0.830 Sum_probs=436.4
Q ss_pred ccccccCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc---------------------------
Q 005445 7 QRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ--------------------------- 59 (696)
Q Consensus 7 ~~~Gvt~PIS~~~Pt~~d~~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~--------------------------- 59 (696)
.+||||+|||+++||++|++.+++|+++|+++|+|||+||..+|++||++|++
T Consensus 50 ~~~Gvt~Pis~~~Pt~~d~~~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~g~I 129 (593)
T PTZ00418 50 LSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQISGKL 129 (593)
T ss_pred cccCCCCCccCCCCChHHHhhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCCeEE
Confidence 57999999999999999999999999999999999999999999999999888
Q ss_pred ---------ccCCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccCC
Q 005445 60 ---------VHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLW 130 (696)
Q Consensus 60 ---------V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~ 130 (696)
||+|+||||||||+|+|++|+ +||..|+++|+++++|++|++|++|+||||||+|+||+|||+||+++..
T Consensus 130 ~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~l~~~ 208 (593)
T PTZ00418 130 FTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANLPLP 208 (593)
T ss_pred EEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeeecccCCC
Confidence 899999999999999999995 9999999999999999999999999999999999999999999999999
Q ss_pred CcCCCCCCCchh-hhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHH
Q 005445 131 VIPEDLDISQDS-ILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 209 (696)
Q Consensus 131 ~vpe~ldl~~d~-lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVAr 209 (696)
.||+++++.+++ +|++||++++|||||+||+|+|+++|||.++||.+|||||+|||+||||||++||||||+|||||||
T Consensus 209 ~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvAR 288 (593)
T PTZ00418 209 TIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTAR 288 (593)
T ss_pred CCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHH
Confidence 999999988776 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHhhccCCCCCceecccccc-----CCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccC
Q 005445 210 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEE-----GSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVS 284 (696)
Q Consensus 210 vCQlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~-----g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs 284 (696)
|||+|||+++++||.+||.+|++|+||+||+|+++++ |.++++||||+.+++|++|+||||||+||+||+|||||
T Consensus 289 VCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt 368 (593)
T PTZ00418 289 ICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVT 368 (593)
T ss_pred HHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCcccccccc
Confidence 9999999999999999999999999999999999875 77899999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHh-ccCCCCcccccCCcchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhh
Q 005445 285 TSTLRIMMDEFQRGHEICEAMEK-NEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIER 363 (696)
Q Consensus 285 ~sTl~vI~~Ef~RA~~Il~~i~~-~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~ 363 (696)
.+|+++|++||+||++|+++|.. ++. +|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|+.+||+
T Consensus 369 ~sT~~vI~~Ef~Ra~~i~~~i~~~~~~--~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~ 446 (593)
T PTZ00418 369 YTTKRVITEEFKRAHEIIKYIEKNSEN--TWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLET 446 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCC--CHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhc
Confidence 99999999999999999999987 776 999999999999999999999999999999999999999999999999998
Q ss_pred ccccceeeccCCCCCCCCC--CCceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHHhhc---cCCCCcEEEEEEec
Q 005445 364 HTYNMLQCHPHPGDFSDKS--KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYT---LRKPGMQISVAHVT 438 (696)
Q Consensus 364 ~~~~~l~ahp~P~~f~~~~--~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~~~~---~~~~gm~i~V~~vk 438 (696)
.. .+.+||||++|.+.. ..|+++|||||+++..... +.+++||+.++++|++.|++|. .|+++|+|+|+|||
T Consensus 447 ~~--~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk 523 (593)
T PTZ00418 447 LN--NLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNVY-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLK 523 (593)
T ss_pred cC--CceEeecCcccccCCCCceeEEEEEEeEeeccCCCC-CCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEee
Confidence 53 367899999998765 4588999999998765432 3458999999999999999886 46889999999999
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccccccccccCCCCCCCCCCCccccccccc
Q 005445 439 RRNLPNFVFPGGVRPSRPSKGTWDSRRALERKVSSHTKPGADDGRKRKQTDD 490 (696)
Q Consensus 439 r~~LP~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 490 (696)
+++||+|||+.|.++.+..|.... .+..+...++|.|.....+.++.++
T Consensus 524 ~~~Lp~~v~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 572 (593)
T PTZ00418 524 KSQLPAFVLSQTPEEPVKTKANTK---TNTSSATTSGQSGSSGSTSNSNSNE 572 (593)
T ss_pred hHhCCHhhccCCCcCCCccccccc---cccccccccccccccCcccCCCCCc
Confidence 999999999988877655553222 2234444555666654455554443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=1.5e-120 Score=950.93 Aligned_cols=446 Identities=44% Similarity=0.825 Sum_probs=424.6
Q ss_pred CccccccCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc--------------------------
Q 005445 6 GQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ-------------------------- 59 (696)
Q Consensus 6 ~~~~Gvt~PIS~~~Pt~~d~~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~-------------------------- 59 (696)
.++||||+|||+++.|+++.+++.+|.++|+..|+||++.|.+.|.+||+.|+.
T Consensus 4 ~k~~GiTgP~ST~~aTe~En~Ln~~li~eLk~~g~FE~~~E~~~Rv~VL~~Lq~~~~eFV~~vs~~K~m~dgmar~aGGK 83 (552)
T COG5186 4 KKKYGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGK 83 (552)
T ss_pred cccccccCCcccccccHHHhhhhHHHHHHHHHcCCcCCchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCce
Confidence 489999999999999999999999999999999999999999999999999987
Q ss_pred ----------ccCCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccC
Q 005445 60 ----------VHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSL 129 (696)
Q Consensus 60 ----------V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~ 129 (696)
||+||||||+|||.|+|++|+ |||+.|+.+|++.++++++.+|+||+||||||+|+||+|||.||+|..
T Consensus 84 IFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~-dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~ 162 (552)
T COG5186 84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRS-DFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSI 162 (552)
T ss_pred eeeecceeeeccCCCCCcceEEEecccccHH-HHHHHHHHHhccCcchhhhccCCcccceeEEEEecCccceeeeeeccC
Confidence 999999999999999999995 999999999999999999999999999999999999999999999999
Q ss_pred CCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHH
Q 005445 130 WVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 209 (696)
Q Consensus 130 ~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVAr 209 (696)
+++|..|+++|+++|++|||+|++||||.||||+||+|||+...|+.+|||||+||+||.||.|.+||.|||+|||||||
T Consensus 163 P~Vp~~l~Lsd~nLLk~~dEkcilsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VAR 242 (552)
T COG5186 163 PVVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVAR 242 (552)
T ss_pred CcCCCcccccchhhhhcchHHHHHhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHH
Q 005445 210 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 289 (696)
Q Consensus 210 vCQlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~ 289 (696)
|||||||++..+||.+||.++++|+||+||+|++|++|.++.++|||+.++.|++|+||||||+||+||.|||+|.||..
T Consensus 243 iCQLYPNA~S~vIv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~ 322 (552)
T COG5186 243 ICQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQH 322 (552)
T ss_pred HHhhccCcchHhHHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccccce
Q 005445 290 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNML 369 (696)
Q Consensus 290 vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l 369 (696)
+|..||-||++|+.+|+.+.. +|..||+..|||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||-.. +++
T Consensus 323 vIl~EfvRa~~I~~di~~n~~--~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~ 399 (552)
T COG5186 323 VILMEFVRAHKILSDIERNAL--DWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DIL 399 (552)
T ss_pred hHHHHHHHHHHhhhhHhhccc--cHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhh
Confidence 999999999999999998877 99999999999999999999999999999999999999999999999999764 578
Q ss_pred eeccCCCCCCCC--------------------------------------------CCCceEEEEEeeEecCCCCCCCCc
Q 005445 370 QCHPHPGDFSDK--------------------------------------------SKPLYCSYFMGLQRKQGVPVGEGE 405 (696)
Q Consensus 370 ~ahp~P~~f~~~--------------------------------------------~~~~~~~ffIGL~~~~~~~~~~~~ 405 (696)
.|||||+.|... ...|++.|||||+.... ..++
T Consensus 400 ~AhPF~K~F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~---~~~k 476 (552)
T COG5186 400 YAHPFPKAFRKVYNCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPV---KPGK 476 (552)
T ss_pred hcCcCChhhhhhcCCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeec---CCCc
Confidence 899999999510 01277889999997543 3367
Q ss_pred ccchHHHHHHHHHHHHhhccCC-CCcEEEEEEecCCCCCCCcCC-CCCCCCCCCC
Q 005445 406 QFDIRLTVKEFKQAVSMYTLRK-PGMQISVAHVTRRNLPNFVFP-GGVRPSRPSK 458 (696)
Q Consensus 406 ~~DL~~~v~eF~~~v~~~~~~~-~gm~i~V~~vkr~~LP~~v~~-~~~~~~~~~~ 458 (696)
++|+..++++|.+.|+.|+.+. .+|.|.|..+|+++||+-||. |..||+..+|
T Consensus 477 kvdi~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~~sK 531 (552)
T COG5186 477 KVDIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSNSSK 531 (552)
T ss_pred eeeeeccHHHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccCcccccc
Confidence 8999999999999999998776 579999999999999999995 7777776554
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=8.7e-77 Score=610.27 Aligned_cols=253 Identities=60% Similarity=1.074 Sum_probs=197.5
Q ss_pred ccccccCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhccccCCCCceeEEEecCCCCCccccHHHH
Q 005445 7 QRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQVHGPGADIDTLCVGPRHATREEDFFGE 86 (696)
Q Consensus 7 ~~~Gvt~PIS~~~Pt~~d~~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~V~~pgSDID~LcV~P~~vtr~edFF~~ 86 (696)
++||||+|||+++||++|++.+++|+++|+++|+|||+||..+|++||+.|+++- .++...
T Consensus 2 ~~~Gvt~PIS~~~Pt~~Dl~~s~~L~~~l~~~~~~es~ee~~~R~~vl~~L~~iv-------------------~~wv~~ 62 (254)
T PF04928_consen 2 KQYGVTKPISLAPPTEKDLKRSASLEEFLKDYGLFESEEEEQKREEVLRKLQQIV-------------------KEWVKQ 62 (254)
T ss_dssp GGGSTT--S------HHHHHHHHHHHHHHHHCT-S--HHHHHHHHHHHHHHHHHH-------------------HHHHHH
T ss_pred CccCCCCCccCCCCChhhHHhHHHHHHHHHHcCCCCChHHHhHHHHHHHHHHHHH-------------------HHHHHh
Confidence 7899999999999999999999999999999999999999999999999998710 012211
Q ss_pred HHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccCCCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHH
Q 005445 87 LHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILR 166 (696)
Q Consensus 87 l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~Ilr 166 (696)
...++|+++++.++++|++||++|+|||||+||+|+|++
T Consensus 63 -----------------------------------------~~~~~p~~l~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~ 101 (254)
T PF04928_consen 63 -----------------------------------------ALPRVPEDLDLLDDDPLRNLDEASVRSLNGVRVTDYILR 101 (254)
T ss_dssp -----------------------------------------SSSSB-TT--TT-GGGGTT--HHHHHHHHHHHHHHHHHC
T ss_pred -----------------------------------------hhcCCCcccccCCchhhhCCCHhhccCcccccHHHHHHH
Confidence 566789999999999999999999999999999999999
Q ss_pred hCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceecccccc
Q 005445 167 LVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEE 246 (696)
Q Consensus 167 lVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~ 246 (696)
+||+.+.||.+|||||+|||+||||||++||||||+|||||||+||+|||+++++||.+||.+|++|+||+||+|+.+.+
T Consensus 102 ~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcql~Pn~~~~~ll~~FF~~ys~W~W~~PV~l~~~~~ 181 (254)
T PF04928_consen 102 LVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQLYPNASPSTLLSRFFQIYSQWDWPNPVVLDPIED 181 (254)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHCS-TTS-EESS----
T ss_pred HCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHHHCccccccchHHHHHHHhcCCCCCCceeeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHHHHHhccCCCCcccccCCc
Q 005445 247 GSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPF 321 (696)
Q Consensus 247 g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep~ 321 (696)
+.+++++|+|+.+.+|+.|+||||||+||+||+|+|||++|+++|++||+||+++++++..++. +|++||+|+
T Consensus 182 ~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~i~~Ef~ra~~i~~~~~~~~~--~W~~L~e~~ 254 (254)
T PF04928_consen 182 GPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRIIREEFQRAHEILSEILKGGA--SWSDLFEPH 254 (254)
T ss_dssp -SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHHHHHHHHHHHHHHHHHHTTSS---HHHCT---
T ss_pred CcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHHHHHHHHHHHHHHHHHHcCCC--CHHHHcCCC
Confidence 9999999999998899999999999999999999999999999999999999999999998777 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=99.97 E-value=6.2e-32 Score=258.72 Aligned_cols=133 Identities=40% Similarity=0.774 Sum_probs=105.3
Q ss_pred chhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccccceeeccCCCCCC-------------------CCC
Q 005445 322 TFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFS-------------------DKS 382 (696)
Q Consensus 322 ~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~-------------------~~~ 382 (696)
+||.+|||||+|+|+|.+++++.+|.||||||||.||.+||+.. .+..|||||+.|. +..
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 69999999999999999999999999999999999999999975 4778999999998 112
Q ss_pred CCceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHHhhcc---CCCCcEEEEEEecCCCCCCCcCCCCCCCCC
Q 005445 383 KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTL---RKPGMQISVAHVTRRNLPNFVFPGGVRPSR 455 (696)
Q Consensus 383 ~~~~~~ffIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~~~~~---~~~gm~i~V~~vkr~~LP~~v~~~~~~~~~ 455 (696)
..++++|||||++........++++||+.++++|++.|++|.. +.++|+|+|+||||++||++||+.+.++.+
T Consensus 80 ~~~~~~~fIGL~~~~~~~~~~~~~~dL~~~i~~F~~~v~~~~~~~~~~~~m~i~i~~vk~~~Lp~~v~~~~~~r~~ 155 (157)
T PF04926_consen 80 NEYTSSFFIGLEFDSKESNEGSKKLDLTYAIQEFKDLVRNWEKYYYDEEGMDISISHVKRSQLPDFVFEEGEKRPK 155 (157)
T ss_dssp EEEEEEEEEEEEE--SSSS---S-EE-HHHHHHHHHHHHCCCCTTC-TTTEEEEEEEEEHHHHGGGGS-TTS----
T ss_pred ceeEEEEEEEEEECCCCccccceEEehHHHHHHHHHHHHhhhccccCCCccEEEEEEechHHCChhhhcccCcCCC
Confidence 4588999999999876543334679999999999999999877 567899999999999999999998886664
No 6
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=99.91 E-value=2e-23 Score=228.14 Aligned_cols=242 Identities=22% Similarity=0.313 Sum_probs=191.4
Q ss_pred HhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc--------------------ccCCCCceeEEEecCCCCCccccHHH
Q 005445 26 MRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ--------------------VHGPGADIDTLCVGPRHATREEDFFG 85 (696)
Q Consensus 26 ~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~--------------------V~~pgSDID~LcV~P~~vtr~edFF~ 85 (696)
..|.+|.++... +-||.+|.+.|.+.|++|++ ++.|+||||++++.+....++..=-.
T Consensus 56 ~lt~el~~~y~~--I~ps~eEl~~R~~~leklr~~lk~~~pda~l~vFGS~~t~L~l~~SDiDl~I~s~~~~~~et~~~~ 133 (482)
T COG5260 56 ELTSELLEFYDY--IAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAG 133 (482)
T ss_pred HHHHHHHHHHHh--hCCCHHHHHHHHHHHHHHHHHHHHhCCccceeEecccccccccCcccccEEEecCCccccccccHH
Confidence 455555555543 88999999999999999998 67899999999999766554311111
Q ss_pred HHHHHHhCCCCceEEeecCCCCcceEEEEE--CCeeeEEEeecccCCCcCCCCCCCchhhhcccchhhHhhhchhhhHHH
Q 005445 86 ELHQMLTEMPEVTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQ 163 (696)
Q Consensus 86 ~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~--~GI~iDL~fa~l~~~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~ 163 (696)
.++..|....+..++.+|..|+||||||.. .|++|||.|++. +|++.|..
T Consensus 134 ~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~----------------------------~~~~~akl 185 (482)
T COG5260 134 SLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNT----------------------------NGIVNAKL 185 (482)
T ss_pred HHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEeecCch----------------------------hHHHHHHH
Confidence 455556656788899999999999999998 699999999873 57888999
Q ss_pred HHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhhCCC------------------CCHHHHHHH
Q 005445 164 ILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPN------------------AVPSMLVSR 225 (696)
Q Consensus 164 IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQlyPn------------------as~~~LL~~ 225 (696)
|+.++-..+++|.++..||+||++|.+++...|+|+|+++.+||..++|++|. ..++.|+..
T Consensus 186 ~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~~~l~~~~~~~~lgvLf~d 265 (482)
T COG5260 186 IRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNGLLSPLKYNKNIDNLGVLFDD 265 (482)
T ss_pred HHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCccccccccccchhhccccccccchHHHH
Confidence 99999999999999999999999999999999999999999999999999981 257899999
Q ss_pred HHHhhcc-CCCCCceeccccccC-CC---CccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHH
Q 005445 226 FFRVYTQ-WRWPNPVLLCAIEEG-SL---GLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHE 300 (696)
Q Consensus 226 FF~~Ys~-WdWp~PV~L~~i~~g-~l---g~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~ 300 (696)
||++|+. |+|..-++. +..| .+ .-+.|--.. +...++|+.|. ...|..-....-+.+.|+.+|.+|.+
T Consensus 266 Ff~~yG~~f~Y~~~~~s--i~~g~~~~~K~e~g~~~~~----~p~~LsiqdP~-td~n~~~~a~s~~ik~i~~~F~~aF~ 338 (482)
T COG5260 266 FFELYGKSFNYSLVVLS--INSGDFYLPKYEKGWLKPS----KPNSLSIQDPG-TDRNNDISAVSFNIKDIKAAFIRAFE 338 (482)
T ss_pred HHHHhccccChhheEEE--ecCCceeeehhhccccccc----CCCcEeecCCC-CCcccccccccchHHHHHHHHHHHHH
Confidence 9999996 999875542 3334 21 012332111 12679999999 44444444445579999999999999
Q ss_pred HHHH
Q 005445 301 ICEA 304 (696)
Q Consensus 301 Il~~ 304 (696)
++.+
T Consensus 339 lls~ 342 (482)
T COG5260 339 LLSN 342 (482)
T ss_pred HHhh
Confidence 8864
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.86 E-value=1.9e-20 Score=208.41 Aligned_cols=248 Identities=19% Similarity=0.261 Sum_probs=194.8
Q ss_pred CHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc--------------------ccCCCCceeEEEecCCCCCcc
Q 005445 21 TDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ--------------------VHGPGADIDTLCVGPRHATRE 80 (696)
Q Consensus 21 t~~d~~~t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~--------------------V~~pgSDID~LcV~P~~vtr~ 80 (696)
.+.=..++.++..+++- +.|+.+|...|.+++++++. +|+|+||||+++..+.+..++
T Consensus 57 ~~~s~~l~~eI~~fv~~--l~pt~~e~~~R~~~~~~i~~~v~~~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~~~~e 134 (514)
T KOG1906|consen 57 NLVSERLRNEILDFVQY--LIPTPEEIEVRSELVEKIRDVVKQKWPDASVYVFGSVPTGLYLPDSDIDLVVLSKFLNDKE 134 (514)
T ss_pred chhHHHHHHHHHHHHHH--hcCCchHHHHHHHHHHHHHHHHHHhcccceeEEeeeeeccccccccceEEEEecccccCch
Confidence 34444556666666664 89999999999999999888 689999999999999777764
Q ss_pred ccHHHHHHHHHhC--CCCceEEeecCCCCcceEEEEE--CCeeeEEEeecccCCCcCCCCCCCchhhhcccchhhHhhhc
Q 005445 81 EDFFGELHQMLTE--MPEVTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLN 156 (696)
Q Consensus 81 edFF~~l~~~L~~--~~~V~~l~~V~~A~VPIIKf~~--~GI~iDL~fa~l~~~~vpe~ldl~~d~lL~~lDe~svrSLN 156 (696)
+.+..+..++.. ...-..+..|..|+||||||+. .+|.|||+|++. |
T Consensus 135 -~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~~----------------------------~ 185 (514)
T KOG1906|consen 135 -DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQT----------------------------N 185 (514)
T ss_pred -hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeeccc----------------------------C
Confidence 666666555554 3445678999999999999997 799999999874 6
Q ss_pred hhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhhCCCC---------CHHHHHHHHH
Q 005445 157 GCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA---------VPSMLVSRFF 227 (696)
Q Consensus 157 G~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQlyPna---------s~~~LL~~FF 227 (696)
|||.++.|...+-+++.+|.++..+|.|.-.|+++....|.+++|++++||..+.|++|.. ..+.|+.+||
T Consensus 186 G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~ 265 (514)
T KOG1906|consen 186 GVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFF 265 (514)
T ss_pred chhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999863 3568999999
Q ss_pred Hhhc-cCCCCC-ceeccccccCCCC--ccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHH
Q 005445 228 RVYT-QWRWPN-PVLLCAIEEGSLG--LQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICE 303 (696)
Q Consensus 228 ~~Ys-~WdWp~-PV~L~~i~~g~lg--~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~ 303 (696)
++|+ +|++.. -|.+....+ ..+ ...|- .+...+...+.|.+|..|..+.++. ...+..|+.+|..|+.++.
T Consensus 266 e~yG~~f~~~k~~i~~~~~g~-~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndigr~--s~~~~~v~~~F~~af~~l~ 340 (514)
T KOG1906|consen 266 ELYGRNFGYDKLGISLSLGGE-YVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIGRS--SFNFSQVKGAFAYAFKVLT 340 (514)
T ss_pred HHhccccCchhhceeccCCcc-cccHHhhhhh--cccccCCCccccCCCCCcccccccc--cccHHHHHHHHHHHHHHHh
Confidence 9999 477765 343322111 010 01111 1122455679999999997776532 2447789999999998875
Q ss_pred H
Q 005445 304 A 304 (696)
Q Consensus 304 ~ 304 (696)
.
T Consensus 341 ~ 341 (514)
T KOG1906|consen 341 N 341 (514)
T ss_pred h
Confidence 3
No 8
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.44 E-value=1.2e-12 Score=148.35 Aligned_cols=210 Identities=21% Similarity=0.313 Sum_probs=157.9
Q ss_pred ccCCCCceeEEEecCCCC--C---c-cccHHHHHHHHHhCCCC--ceEEeecCCCCcceEEEEE--CCeeeEEEeecccC
Q 005445 60 VHGPGADIDTLCVGPRHA--T---R-EEDFFGELHQMLTEMPE--VTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSL 129 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~v--t---r-~edFF~~l~~~L~~~~~--V~~l~~V~~A~VPIIKf~~--~GI~iDL~fa~l~~ 129 (696)
+....+|+| +|+.-..- . . ...++..+.++|....+ +..+..|..|+||||||.+ .|+++|+.+....
T Consensus 167 ~~~~~~d~d-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~- 244 (596)
T KOG2277|consen 167 LGERSSDLD-LCVDFTSSFLSFEKIKGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSD- 244 (596)
T ss_pred ccccccCcc-eeecccccccccchhhhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccch-
Confidence 455779999 66632221 1 1 13567778888888553 8999999999999999965 5899999987532
Q ss_pred CCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcc-hHHHHHHHH
Q 005445 130 WVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG-GINWALLVA 208 (696)
Q Consensus 130 ~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLG-GIswAILVA 208 (696)
|.+.+..+.....-..+||.+...||+||+++++++...|.+. .+++.+||+
T Consensus 245 ---------------------------~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi 297 (596)
T KOG2277|consen 245 ---------------------------AILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVI 297 (596)
T ss_pred ---------------------------hhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHH
Confidence 2334444444445556999999999999999999999999988 699999999
Q ss_pred HHHhhCCC-------------------------------------------CCHHHHHHHHHHhhc-cCCCCCceecccc
Q 005445 209 RICQLYPN-------------------------------------------AVPSMLVSRFFRVYT-QWRWPNPVLLCAI 244 (696)
Q Consensus 209 rvCQlyPn-------------------------------------------as~~~LL~~FF~~Ys-~WdWp~PV~L~~i 244 (696)
+++|.++. .+...|+..||.||+ .|+|++-++ .+
T Consensus 298 ~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I--~~ 375 (596)
T KOG2277|consen 298 HFLQTLSPPILPPLSKLLPESDSNDKPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAI--SI 375 (596)
T ss_pred HHHHhcCCcCCCchhhhchhcccccccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhccccccee--ee
Confidence 99997631 124588899999999 799998553 22
Q ss_pred ccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHHHH
Q 005445 245 EEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAM 305 (696)
Q Consensus 245 ~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~~i 305 (696)
+.|.....-|.. ...-.+.|.+|+....|....++.....+|+.+|+....++...
T Consensus 376 r~~~~l~~~~~~-----~~~~~l~i~dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 376 RRGRALKRAKKI-----KSKKFLCIEDPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred eecccccccchh-----hhccceeeccccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 323211100111 12346899999999999999999999999999999999998754
No 9
>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=99.32 E-value=7.8e-12 Score=113.02 Aligned_cols=66 Identities=38% Similarity=0.733 Sum_probs=60.0
Q ss_pred ccCCCCceeEEEecCCC-CCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEEC--CeeeEEEeec
Q 005445 60 VHGPGADIDTLCVGPRH-ATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS--GVSIDLLYAR 126 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~-vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~--GI~iDL~fa~ 126 (696)
++.|+||||+++..|.. ... ..++..+.+.|++...+.++..|..|+||||||.+. ||+|||+|++
T Consensus 32 ~~~~~SDiDl~i~~~~~~~~~-~~~l~~l~~~l~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~Dis~~~ 100 (114)
T cd05402 32 LGLPGSDIDLCLLGPNHRVDR-EDFLRKLAKLLKKSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNN 100 (114)
T ss_pred CCCCCCCeeEEEEeCCCCccH-HHHHHHHHHHHHhCCCceeeEEeccCCCCEEEEEEcCCCeEEEEEccc
Confidence 68899999999999986 333 489999999999988889999999999999999998 9999999986
No 10
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.02 E-value=9.3e-08 Score=105.44 Aligned_cols=293 Identities=20% Similarity=0.243 Sum_probs=170.7
Q ss_pred ccCC-CCceeEEEecCCCCCccccHHH---H-HHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccCCCcCC
Q 005445 60 VHGP-GADIDTLCVGPRHATREEDFFG---E-LHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPE 134 (696)
Q Consensus 60 V~~p-gSDID~LcV~P~~vtr~edFF~---~-l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~~vpe 134 (696)
.|++ +||||++++.|....++ ++=. . ....++..+.. -..-|-=|-++..+.|++||+.=|-
T Consensus 53 T~L~G~sDIDIfi~f~~~~~~e-~l~~~gl~i~~~~~~~~~~~----~~~yaeHpYv~~~~~G~~VDiVPcy-------- 119 (408)
T TIGR03671 53 TWLKGDRDIDIFILFPKDTSRE-ELEEYGLEIGHEVLKRGGNY----EERYAEHPYVSGEIEGFEVDVVPCY-------- 119 (408)
T ss_pred CccCCCCceeEEEEeCCCCCHH-HHHHHHHHHHHHHHhhCCCH----hheeccCceEEEEEccEEEEEEeeE--------
Confidence 5778 89999999999887764 3321 1 22222221111 1556788999999999999998542
Q ss_pred CCCCCchh-hhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCC--CCcchHHHHHHHHHHH
Q 005445 135 DLDISQDS-ILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVA--GFLGGINWALLVARIC 211 (696)
Q Consensus 135 ~ldl~~d~-lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~--GfLGGIswAILVArvC 211 (696)
++.+.+ +...+|-. ..=+++++...- +.|+..+|.+|.|+|.-|+|++-. +.++||.+=|||+++
T Consensus 120 --~v~~g~~~~taVDRt-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~y- 187 (408)
T TIGR03671 120 --KVESGEEIISAVDRT-------PFHTRYVLERLD--GKLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHY- 187 (408)
T ss_pred --EccCcCeeeccccCc-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh-
Confidence 122221 11122211 112445554432 238999999999999999996644 779999999999994
Q ss_pred hhCCCCCHHHHHHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHH
Q 005445 212 QLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIM 291 (696)
Q Consensus 212 QlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI 291 (696)
.+-..++..+ ++| ..++.+ +++. +... .-...+.|++|..|..|+|.++|...+..+
T Consensus 188 -----G~F~~~l~~a----~~w--k~~~~i-d~~~-------~~~~----~f~~PlvViDPvDp~RNVAaalS~~~~~~f 244 (408)
T TIGR03671 188 -----GSFENVLKAA----SKW--KPGVVI-DIEE-------HGTK----KFDDPLVVIDPVDPKRNVAAALSLENLARF 244 (408)
T ss_pred -----CCHHHHHHHH----Hhc--CCCeEE-ecCc-------cccc----cCCCCEEEeCCCCCcchHHHHcCHHHHHHH
Confidence 3444555443 334 445554 3221 1110 012579999999999999999999998888
Q ss_pred HHHHHHHHHHHHHHHhccCCCCcccccCCc-----ch---hhhcc-cEEEEEEEecChhhhcchhhhhHHHHHHHHHHHh
Q 005445 292 MDEFQRGHEICEAMEKNEADVDWDTLFEPF-----TF---FEAYK-NYLRIDISAENADDLRNWKGWVESRLRQLTLKIE 362 (696)
Q Consensus 292 ~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep~-----~F---F~~Yk-~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE 362 (696)
...-+++++ . +=..+|.|. ++ +.+-. +.+.|.....+.-+ ...-|-++--.+.|...||
T Consensus 245 v~aar~fl~-------~----Ps~~fF~p~~~~~~~~~~~l~~r~t~~~~~~f~~p~~v~-Dil~pQl~r~~~~i~~~L~ 312 (408)
T TIGR03671 245 ILAARMFLK-------N----PSLEFFFPPEIEPEEFLERLERRGTTLLAIVFRTPDVVD-DILYPQLERSGRSLVKLLE 312 (408)
T ss_pred HHHHHHHHH-------C----CCHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCCCCCc-cchhHHHHHHHHHHHHHHH
Confidence 765555443 1 223455442 11 12222 33444444433222 2334666666667777788
Q ss_pred hccccceeeccCCCCCCCCCCCceEEEEEeeEecCC--CCCCCCcccchHHHHHHHHHH
Q 005445 363 RHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQG--VPVGEGEQFDIRLTVKEFKQA 419 (696)
Q Consensus 363 ~~~~~~l~ahp~P~~f~~~~~~~~~~ffIGL~~~~~--~~~~~~~~~DL~~~v~eF~~~ 419 (696)
+....++....|- +.. .|+.++=|....- .....|..+.-+.....|.+.
T Consensus 313 ~~gF~v~r~~~~~----~~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 364 (408)
T TIGR03671 313 REGFEVLRYGVWA----DEN---TCYLLLELESAELPRVKLHVGPPVWVRDHAEKFIEK 364 (408)
T ss_pred HCCCEEEEeeeec----CCC---eEEEEEEeeccccCCceeeeCCCccchhHHHHHHHH
Confidence 7766566666552 222 1444555543221 111234455555567778763
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.02 E-value=1.1e-07 Score=106.17 Aligned_cols=294 Identities=18% Similarity=0.235 Sum_probs=167.2
Q ss_pred ccCC-CCceeEEEecCCCCCcc---ccHHHHHHHHHhC-CCCceEEeecCCCCcceEEEEECCeeeEEEeecccCCCcCC
Q 005445 60 VHGP-GADIDTLCVGPRHATRE---EDFFGELHQMLTE-MPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPE 134 (696)
Q Consensus 60 V~~p-gSDID~LcV~P~~vtr~---edFF~~l~~~L~~-~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~~vpe 134 (696)
.|.+ ++|||++++.|....++ +........+++. .+. .+++ -|-=|-++..++|++|||.=|-
T Consensus 54 T~L~GdsDIDIFv~fp~~~~~e~L~~~gl~i~~~~~~~~~~~-~~~~---yaeHpyv~~~~~G~~VDiVPcy-------- 121 (447)
T PRK13300 54 TWLSGDRDIDIFVLFPKDTSREELEEKGLEIGKEVAKELLGD-YEER---YAEHPYVTGEIDGFEVDIVPCY-------- 121 (447)
T ss_pred cccCCCCceeEEEEeCCCCCHHHHHHHHHHHHHHHHHhhCCc-ceee---eccCceEEEEECCEEEEEEeeE--------
Confidence 5677 68999999999887763 1122223333333 222 2333 3888999999999999998552
Q ss_pred CCCCCch-hhhcccchhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCC--CCcchHHHHHHHHHHH
Q 005445 135 DLDISQD-SILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVA--GFLGGINWALLVARIC 211 (696)
Q Consensus 135 ~ldl~~d-~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~--GfLGGIswAILVArvC 211 (696)
++.+. .+...+|-. ..=+++|+...- +.++.-+|.+|.|.|.-|+|++-. +.++||.+=+||+++
T Consensus 122 --~v~~~~~~~saVDRt-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y- 189 (447)
T PRK13300 122 --KVESGEEIISAVDRT-------PFHTKYVKERLK--GKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY- 189 (447)
T ss_pred --EccCcCcccccccCc-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh-
Confidence 11111 112222211 112455554432 248999999999999999996644 789999999999994
Q ss_pred hhCCCCCHHHHHHHHHHhhccCCCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHH
Q 005445 212 QLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIM 291 (696)
Q Consensus 212 QlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI 291 (696)
.+-..++..+ ++|.- ++.|. +++. + ... .-...+.|++|..|..|+|.++|...+..+
T Consensus 190 -----G~F~~~l~~a----~~w~~--~~~I~-~~~~--~-----~~~---~f~~PlvViDPvDp~RNVAaa~S~~~~~~f 247 (447)
T PRK13300 190 -----GSFENVLKAA----SKWKP--PVKID-LEKH--G-----KEY---KFDDPLVVIDPVDPNRNVAAALSLENLATF 247 (447)
T ss_pred -----CCHHHHHHHH----HhCCC--CceEe-cccc--C-----ccc---cCCCCEEEeCCCCCcchHHHHcCHHHHHHH
Confidence 4555555554 44543 33331 2211 0 000 113579999999999999999999888776
Q ss_pred HHHHHHHHHHHHHHHhccCCCCcccccCCcc--------hhhh-cccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHh
Q 005445 292 MDEFQRGHEICEAMEKNEADVDWDTLFEPFT--------FFEA-YKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIE 362 (696)
Q Consensus 292 ~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep~~--------FF~~-Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE 362 (696)
...-+ +.++ .. =..+|.|.+ -+.+ =.+.+.|.....+.-+= ..-|-++--.+.|...||
T Consensus 248 v~aar---~fL~----~P----s~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~D-il~pQl~r~~~~i~~~L~ 315 (447)
T PRK13300 248 ILAAR---EFLK----NP----SLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVED-ILYPQLERSLRSIVKLLE 315 (447)
T ss_pred HHHHH---HHHh----CC----CHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHH
Confidence 64322 2232 22 234444433 1111 12444555544443222 234666666667777788
Q ss_pred hccccceeeccCCCCCCCCCCCceEEEEEeeEecC--CCCCCCCcccchHHHHHHHHH
Q 005445 363 RHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQ--GVPVGEGEQFDIRLTVKEFKQ 418 (696)
Q Consensus 363 ~~~~~~l~ahp~P~~f~~~~~~~~~~ffIGL~~~~--~~~~~~~~~~DL~~~v~eF~~ 418 (696)
+....++....| .+.+ .|+.++=|.... ......|..+.-+.-...|.+
T Consensus 316 ~~gF~v~~~~~~----~d~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~ 366 (447)
T PRK13300 316 REGFEVLRSGAW----ADED---RAYLLLELEVAELPNVKLHIGPPVWVREHAENFIE 366 (447)
T ss_pred HCCCEEEEeeee----cCCC---eEEEEEEeecccCCCeeeeeCCCcCchhhHHHHHH
Confidence 776655555444 2211 244444443221 111122444555554778876
No 12
>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=98.96 E-value=1.5e-07 Score=113.88 Aligned_cols=281 Identities=16% Similarity=0.246 Sum_probs=181.9
Q ss_pred CCCceeEEEecCCCCCccccH------------HHHHHHHH--hCCCCceEE---eecCCCCcceEEEEEC-----C---
Q 005445 63 PGADIDTLCVGPRHATREEDF------------FGELHQML--TEMPEVTEL---HPVPDAHVPVMKFKFS-----G--- 117 (696)
Q Consensus 63 pgSDID~LcV~P~~vtr~edF------------F~~l~~~L--~~~~~V~~l---~~V~~A~VPIIKf~~~-----G--- 117 (696)
++-.||+.+.-|..+-.++|| ...++..| ++...+.++ -.=.+.+-|||.+.-. +
T Consensus 12 ~~~~VDl~v~mP~~~fq~KDyln~RY~~KRA~YLa~iA~~L~~~~~~~~~~v~~~~~~gd~~kPil~l~p~~~~~~~~~~ 91 (972)
T PF03813_consen 12 PNLTVDLAVEMPKSLFQEKDYLNYRYFHKRALYLAYIAAHLQKKKSKLFVDVSFEYLNGDPLKPILVLRPKGKKDSDDFS 91 (972)
T ss_pred CCCeeEEEEeCChhhcCchhhccchHHHHHHHHHHHHHHHHhhhccccceeEEEEeCCCCCCCCeEEEEECCcccccccc
Confidence 677899999999765443443 23577777 223333333 3345788999999852 2
Q ss_pred ---eeeEEEeeccc-CC----CcCCC------------------CCCCchhhhcccchhhHhhhchhhhHHHHHHhCCCh
Q 005445 118 ---VSIDLLYARLS-LW----VIPED------------------LDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKI 171 (696)
Q Consensus 118 ---I~iDL~fa~l~-~~----~vpe~------------------ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~ 171 (696)
+.|-|..+.-. .. -.|.- -...|..+|.++-. ..-.+.+.+..-..
T Consensus 92 ~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~~--------~~~l~~l~~~~~~~ 163 (972)
T PF03813_consen 92 KTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDMLM--------EEHLKYLHEASKSS 163 (972)
T ss_pred CCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHhH--------HHHHHHHHHHHhcC
Confidence 55555554311 00 00111 11234455544321 11233455555567
Q ss_pred hhHHHHHHHHHHHHHHhcCCcCC-CCCcchHHHHHHHHHHHhh---------CCCCCHHHHHHHHHHhhccCCC-CCcee
Q 005445 172 QNFRTTLRCMRFWAKRRGVYSNV-AGFLGGINWALLVARICQL---------YPNAVPSMLVSRFFRVYTQWRW-PNPVL 240 (696)
Q Consensus 172 ~~FR~~LR~IK~WAKrRGIYsn~-~GfLGGIswAILVArvCQl---------yPnas~~~LL~~FF~~Ys~WdW-p~PV~ 240 (696)
+.|+.++..+|.||++||+.+.. .|.+||+-|+||+|+.+|- .+..+.-+|+..+..+.|..|| .+|+.
T Consensus 164 p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fLA~~d~~~~~l~ 243 (972)
T PF03813_consen 164 PAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFLATTDLSKKPLF 243 (972)
T ss_pred HHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHHhccccccCceE
Confidence 99999999999999999998876 4889999999999999976 3456788999999999999999 56998
Q ss_pred ccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHHHHHhccCCCCcccccCC
Q 005445 241 LCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEP 320 (696)
Q Consensus 241 L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lfep 320 (696)
++.-.+.......| .+.+.+..++| .-.+|.++++|.++++.|+.|-+++.+++++-. .. ..+.+|-.
T Consensus 244 ~~~~~~~~~~~~~~-------~~~~~~vf~D~-sg~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~d--~F~~lFl~ 311 (972)
T PF03813_consen 244 FKSSSDSTESLEEF-------HSAFDPVFVDP-SGGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--DD--GFDSLFLT 311 (972)
T ss_pred EecCCCccchhhhh-------hccCCeEEEeC-CCCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--cc--chhhhhcc
Confidence 86644211111111 12344555555 467999999999999999999999999987421 12 57777743
Q ss_pred --cchhhhcccEEEEE---EE----ecChhhhcchhhhhHHHHHHHH-HHHhh
Q 005445 321 --FTFFEAYKNYLRID---IS----AENADDLRNWKGWVESRLRQLT-LKIER 363 (696)
Q Consensus 321 --~~FF~~Yk~yl~I~---v~----a~~~e~~~~w~GwVESRlR~Lv-~~LE~ 363 (696)
..+..+|.+++.|. .. .....+...|...+..++-.|+ ..|-.
T Consensus 312 ~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgd 364 (972)
T PF03813_consen 312 KVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGD 364 (972)
T ss_pred cCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHH
Confidence 45678999999991 11 1122333444445666776665 34543
No 13
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=98.37 E-value=7.2e-05 Score=82.82 Aligned_cols=324 Identities=19% Similarity=0.198 Sum_probs=178.4
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhhcc------------------------ccCC-CCceeEEEecCCCCCccc--
Q 005445 29 RKLEKYLRDVNLYESQEEAVSREEVLGRLDQ------------------------VHGP-GADIDTLCVGPRHATREE-- 81 (696)
Q Consensus 29 ~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~~------------------------V~~p-gSDID~LcV~P~~vtr~e-- 81 (696)
+.|.+.|+. +-||+||.++=+++.+.|.. .|.+ +.|||+.|+.|....+++
T Consensus 5 ~~l~evl~~--i~P~~eE~~~~~~~~e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~eel~ 82 (443)
T COG1746 5 EVLEEVLKR--IKPTEEERKKLKEVAEELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSEEELE 82 (443)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCCHHHHH
Confidence 345556654 66777776665555554433 6888 679999999999877641
Q ss_pred -cHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccCCCcCCCCCCCchhhhcccchhhHhhhchhhh
Q 005445 82 -DFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRV 160 (696)
Q Consensus 82 -dFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rv 160 (696)
.=.......|.. .. -.+.-|-=|-+.-.++|++||+.=|--... ++ .+...+|-.-. =
T Consensus 83 ~~GL~ig~~~l~~-~~----~~~~YAeHPYV~g~v~G~eVDvVPCy~v~~--~~-------~~~sAVDRTpl-------H 141 (443)
T COG1746 83 EKGLEIGREVLKR-GN----YEERYAEHPYVTGEVDGYEVDVVPCYKVED--GE-------KIISAVDRTPL-------H 141 (443)
T ss_pred HHHHHHHHHHhcC-Cc----hhhhhccCCeeEEEEccEEEEEEecccccC--cc-------cccccccCcch-------h
Confidence 122234444443 11 125568889999999999999996632110 11 01112221000 1
Q ss_pred HHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCC--CCcchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCc
Q 005445 161 TDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVA--GFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNP 238 (696)
Q Consensus 161 td~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~--GfLGGIswAILVArvCQlyPnas~~~LL~~FF~~Ys~WdWp~P 238 (696)
|.++..-+-.. -+.=+|.+|.+.|.=|+|++-+ +.++||-.=+|++++= +-...|..+ + .|.-+
T Consensus 142 t~yv~e~L~~~--~~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~yG------sFe~vl~~a----~--~wrp~ 207 (443)
T COG1746 142 TRYVEEHLKGR--QKDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHYG------SFENVLKAA----S--RWRPG 207 (443)
T ss_pred HHHHHHHhccc--chhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhhc------cHHHHHHHH----h--ccCCC
Confidence 22333222221 1234688999999999999865 8899999999999872 222222222 2 27777
Q ss_pred eeccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHHHHHhccCCCCccccc
Q 005445 239 VLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLF 318 (696)
Q Consensus 239 V~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lf 318 (696)
++| +++ .|.-.. -.| ..|.|++|..|..|+|.+||...+..+. -|.+ ..+++. =..+|
T Consensus 208 ~~I-D~~-------~~~~e~-f~d--~PliVvDPVDP~RNVAAalSl~~la~f~----~aar---~FL~~P----S~efF 265 (443)
T COG1746 208 KII-DLE-------GHKRER-FED--EPLIVVDPVDPKRNVAAALSLENLARFV----HAAR---EFLKNP----SPEFF 265 (443)
T ss_pred eEE-ecc-------chhhhc-cCC--CCeEecCCCCCccchhhhcCHHHHHHHH----HHHH---HHhcCC----Chhhc
Confidence 655 222 121110 011 2799999999999999999987776554 2322 222222 22333
Q ss_pred CCcc--------hhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccccceeeccCCCCCCCCCCCceEEEE
Q 005445 319 EPFT--------FFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFSDKSKPLYCSYF 390 (696)
Q Consensus 319 ep~~--------FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~~~~~~~~~ff 390 (696)
.|.. ...+=.+-+.|.+-..+.-+ ...-|-++---+.|...||.....++..+.| .|... +++-|
T Consensus 266 ~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~~~----~D~~~--~~~v~ 338 (443)
T COG1746 266 FPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSGVW----SDESE--RIYVL 338 (443)
T ss_pred CCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeeeee----ecCCc--ceEEE
Confidence 3211 11111122333333334222 2345777777788888899876666666555 22221 35555
Q ss_pred EeeEecCC--CCCCCCcccchHHHHHHHHHH
Q 005445 391 MGLQRKQG--VPVGEGEQFDIRLTVKEFKQA 419 (696)
Q Consensus 391 IGL~~~~~--~~~~~~~~~DL~~~v~eF~~~ 419 (696)
+=++...- ....-|.++.-..+++ |.+.
T Consensus 339 ~E~~~~~l~~i~~r~GPp~~~e~a~r-F~~k 368 (443)
T COG1746 339 LELESKELPRIELRVGPPVWTEHAVR-FIEK 368 (443)
T ss_pred EEEecccccceeeecCCCccchhHHH-HHHh
Confidence 55543211 0111133344467777 8663
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=97.91 E-value=6.5e-05 Score=89.54 Aligned_cols=256 Identities=18% Similarity=0.238 Sum_probs=158.4
Q ss_pred ccCCCCceeEEEecCCCCCccccHH------------HHHHHHHhCCCCceEEeec---CCCCcceEEEEECCeeeEEEe
Q 005445 60 VHGPGADIDTLCVGPRHATREEDFF------------GELHQMLTEMPEVTELHPV---PDAHVPVMKFKFSGVSIDLLY 124 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~vtr~edFF------------~~l~~~L~~~~~V~~l~~V---~~A~VPIIKf~~~GI~iDL~f 124 (696)
...|+.-+|+++..|+..-..+|++ .-+...|.+.+..-.+... -+-.-||+.+.-.|-..|++-
T Consensus 162 ~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~~pil~i~~~~~~~~~~~ 241 (1121)
T KOG2054|consen 162 CLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHLKPILLIRPRGKDERLVT 241 (1121)
T ss_pred ccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccccchhhccccCCcccccc
Confidence 3568888899888886543223443 2344444444422222211 245568888877776666665
Q ss_pred ecccCCCcCCCCCC-CchhhhcccchhhHhhhchhhh--------------------------HHHHHHhCCChhhHHHH
Q 005445 125 ARLSLWVIPEDLDI-SQDSILQNADEQTVRSLNGCRV--------------------------TDQILRLVPKIQNFRTT 177 (696)
Q Consensus 125 a~l~~~~vpe~ldl-~~d~lL~~lDe~svrSLNG~Rv--------------------------td~IlrlVPn~~~FR~~ 177 (696)
.+-+..-+|..+-+ .++.+|-+. ||.|. .+++.+.....+.|+.+
T Consensus 242 ~~~~~~li~~~~~~f~~~kllp~~--------~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q~L~K~~s~~~~f~da 313 (1121)
T KOG2054|consen 242 VRPPDFLIPCRLLPFKNNKLLPWY--------NGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQLLSKTLSSAKGFKDA 313 (1121)
T ss_pred ccCccccccccccccccccccchh--------cccCccccCCCCCCCCccchhHHHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence 54332223332211 122222110 11111 12333344456899999
Q ss_pred HHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhhccCCCCC-ceeccccccCCCCccc
Q 005445 178 LRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ---LYPNAVPSMLVSRFFRVYTQWRWPN-PVLLCAIEEGSLGLQV 253 (696)
Q Consensus 178 LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQ---lyPnas~~~LL~~FF~~Ys~WdWp~-PV~L~~i~~g~lg~~v 253 (696)
+-..|.|+++|- -+-..|.+||+-|++||++... ++-+.+..+++..-+++++.|||.. -|-++.-. -+
T Consensus 314 ~~Llk~WlrqRs-~~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~~~~-~s----- 386 (1121)
T KOG2054|consen 314 LALLKVWLRQRS-LDIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLVPSS-PS----- 386 (1121)
T ss_pred HHHHHHHHHhhh-hhcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEeccCC-CC-----
Confidence 999999999991 1225688999999999999874 4566788899999999999999986 45443210 00
Q ss_pred cCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHHHHHHHHHHHhccCCCCccccc-CCcchhhhcccEEE
Q 005445 254 WDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLF-EPFTFFEAYKNYLR 332 (696)
Q Consensus 254 WdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~RA~~Il~~i~~~~~~~~W~~Lf-ep~~FF~~Yk~yl~ 332 (696)
.|....-+..+....++ +....|.+.|++.++.+.+++|.+-+..++.+.... .++.+| ++.+.|..|.|-+.
T Consensus 387 -~~~~~~f~e~~~~~f~D-~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~----~F~~IFmtkip~~~~yDh~l~ 460 (1121)
T KOG2054|consen 387 -LPALADFHEGQLVTFID-SSGHLNLCANMTASTYEQVQEEARLTLMLLDSRADD----GFSLIFMTKIPVFRAYDHVLH 460 (1121)
T ss_pred -chhhhhhhhcceeeEec-cCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhhhc----CcceeeeecCCchhhhheeee
Confidence 01111111122222222 355789999999999999999999999999865422 577766 77899999998887
Q ss_pred EEEE
Q 005445 333 IDIS 336 (696)
Q Consensus 333 I~v~ 336 (696)
+...
T Consensus 461 l~~~ 464 (1121)
T KOG2054|consen 461 LSPL 464 (1121)
T ss_pred cccc
Confidence 7554
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=97.75 E-value=0.0012 Score=69.04 Aligned_cols=199 Identities=15% Similarity=0.157 Sum_probs=137.5
Q ss_pred CCceeEEEecCCCCCccccHHHHHHHHH----hCCCCceEEeecCCCCcceEEEEEC----CeeeEEEeecccCCCcCCC
Q 005445 64 GADIDTLCVGPRHATREEDFFGELHQML----TEMPEVTELHPVPDAHVPVMKFKFS----GVSIDLLYARLSLWVIPED 135 (696)
Q Consensus 64 gSDID~LcV~P~~vtr~edFF~~l~~~L----~~~~~V~~l~~V~~A~VPIIKf~~~----GI~iDL~fa~l~~~~vpe~ 135 (696)
+-+.|+|+++....|. .-.+.+.+.| +...+=.....|..+.+|.++..+. -...+... ..+|++
T Consensus 20 d~~~~lVv~c~~~PT~--~ll~~v~~~l~e~l~~~~~~e~~~~~~~~~~~~~~~~i~ltSp~~r~~~~~-----~~~~~~ 92 (246)
T smart00572 20 DNVAELVLLCKEKPTS--ELVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGILITSPLARVELLI-----TTVPEN 92 (246)
T ss_pred CCceeEEEEecCCCcH--HHHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEEEecccccccccc-----cccCcc
Confidence 4578889998888885 3444444333 3322112223456667788877762 12222222 233555
Q ss_pred CCCCchhhhcccc-hhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhhC
Q 005445 136 LDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLY 214 (696)
Q Consensus 136 ldl~~d~lL~~lD-e~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQly 214 (696)
+...+.. .-+| +.|+.+|-..|-+.......-....|+.++|++|-|.+|--..+ -|.++.+=+|+++++-..
T Consensus 93 ~~~~~p~--~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~----pL~~w~iELl~~~~i~~~ 166 (246)
T smart00572 93 LRKLDPE--DHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQ----PLSGWPLELLVEKAIGSA 166 (246)
T ss_pred cccCCcc--ccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhccccc----ccccccHHHHHHHHhccC
Confidence 4332222 2233 57888899999999999998889999999999999999876544 388999999999998633
Q ss_pred CC-CCHHHHHHHHHHhhccC-CCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCCC-CCCcccccChhHHHHH
Q 005445 215 PN-AVPSMLVSRFFRVYTQW-RWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP-CMNSSYNVSTSTLRIM 291 (696)
Q Consensus 215 Pn-as~~~LL~~FF~~Ys~W-dWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P-~~Nst~NVs~sTl~vI 291 (696)
.. .+++.-+.+||++.|+= =+|.- --|++|+.+ ..|++...|....+.|
T Consensus 167 ~~~l~~~~a~RR~fe~lAsG~l~p~~----------------------------~gI~DPce~~~~nv~~~lT~qqrd~I 218 (246)
T smart00572 167 RQPLGLGDAFRRVFECLASGILLPGS----------------------------PGLTDPCEKDNTDALTALTLQQREDV 218 (246)
T ss_pred CCCCCHHHHHHHHHHHHHhccCcCCC----------------------------CCCcCCCCCCcccHHHhcCHHHHHHH
Confidence 22 36789999999998851 12210 146788886 8999999999999999
Q ss_pred HHHHHHHHHHHH
Q 005445 292 MDEFQRGHEICE 303 (696)
Q Consensus 292 ~~Ef~RA~~Il~ 303 (696)
...-+.|.+++.
T Consensus 219 t~sAQ~alRl~A 230 (246)
T smart00572 219 TASAQTALRLLA 230 (246)
T ss_pred HHHHHHHHHHHH
Confidence 999999888773
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=96.97 E-value=0.00054 Score=55.71 Aligned_cols=55 Identities=22% Similarity=0.428 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHhhc-cCCCCCceeccccccCCC---CccccCCCCCCCCCcccceeeCCCCCC
Q 005445 218 VPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSL---GLQVWDPRRNPKDKYHLMPIITPAYPC 276 (696)
Q Consensus 218 s~~~LL~~FF~~Ys-~WdWp~PV~L~~i~~g~l---g~~vWdP~~~~~Dr~hlMpIiTPa~P~ 276 (696)
+++.||..||+||+ .|||.+-|+ .+..|.. ....|.. ....+...|+|++|+.|.
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 47899999999999 899999665 3444542 1223431 111345789999999875
No 17
>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=96.04 E-value=0.058 Score=66.39 Aligned_cols=158 Identities=22% Similarity=0.378 Sum_probs=105.8
Q ss_pred chhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHH-hhCC---CCCHHHHHHHHHHhhc
Q 005445 156 NGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARIC-QLYP---NAVPSMLVSRFFRVYT 231 (696)
Q Consensus 156 NG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvC-QlyP---nas~~~LL~~FF~~Ys 231 (696)
-..+-+..|..+--..+.|..++|.+|.|.-.+-+ .|++.--.+=+|||++. +-+| ..++.+=+.+|.++.+
T Consensus 667 ~~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs 742 (972)
T PF03813_consen 667 HLPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLS 742 (972)
T ss_pred hhHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHH
Confidence 34555666666666778999999999999888866 46788899999999997 3344 3455555677888889
Q ss_pred cCCCCC-ceeccccccCC--------CCccccCCCCCCCCCcccceeeCCCCCCCCc--ccccChhHHHHHHHHHHHHHH
Q 005445 232 QWRWPN-PVLLCAIEEGS--------LGLQVWDPRRNPKDKYHLMPIITPAYPCMNS--SYNVSTSTLRIMMDEFQRGHE 300 (696)
Q Consensus 232 ~WdWp~-PV~L~~i~~g~--------lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Ns--t~NVs~sTl~vI~~Ef~RA~~ 300 (696)
+|||.+ |+++.--.+-. -.+..|-. ..+......|.|.||..|.-.. ...-+..-+++|+.--+.+.+
T Consensus 743 ~~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~ 821 (972)
T PF03813_consen 743 TWDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLK 821 (972)
T ss_pred hCCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHH
Confidence 999995 88764321100 01222322 1122344689999999985432 123555567788887778888
Q ss_pred HHHHHHhccCCCCcccccCC
Q 005445 301 ICEAMEKNEADVDWDTLFEP 320 (696)
Q Consensus 301 Il~~i~~~~~~~~W~~Lfep 320 (696)
+++. .+-...+|..||.+
T Consensus 822 ~l~~--~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 822 LLEE--QGLSDLDWKSLFRP 839 (972)
T ss_pred HHHh--cCCCCCCHHHhcCC
Confidence 8772 22224599999976
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=95.72 E-value=0.034 Score=52.21 Aligned_cols=93 Identities=19% Similarity=0.279 Sum_probs=57.6
Q ss_pred HHHHHHHHHHhcCCcCCC--CCcchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeccccccCCCCccccC
Q 005445 178 LRCMRFWAKRRGVYSNVA--GFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWD 255 (696)
Q Consensus 178 LR~IK~WAKrRGIYsn~~--GfLGGIswAILVArvCQlyPnas~~~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWd 255 (696)
+|.+|.+.|.-|+|++-. +.++||-.=+||+++= +-..+|. .-+ +|..|+.|..-..+... +.
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yG------sF~~~l~----~a~--~W~~~~~Id~~~~~~~~-~~-- 67 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYG------SFENVLE----AAA--KWKPPVVIDLEDHGEPS-KK-- 67 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHS------SHHHHHH----HHT--T--TTEEEETT-TTE---EE--
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHC------CHHHHHH----HHH--hcCCCeEEccCccchhh-hh--
Confidence 588999999999999865 8899999999999872 2223333 234 66667765321111100 00
Q ss_pred CCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHH
Q 005445 256 PRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMM 292 (696)
Q Consensus 256 P~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~ 292 (696)
-...+.|++|..|..|+|.+||..++..+.
T Consensus 68 -------f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 68 -------FDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp -------E-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred -------cCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 025799999999999999999988776554
No 19
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=95.26 E-value=0.25 Score=48.75 Aligned_cols=117 Identities=21% Similarity=0.380 Sum_probs=72.7
Q ss_pred HHHHHHHhhcc------------ccCCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEE-eecCCCCcceEEEEE
Q 005445 49 SREEVLGRLDQ------------VHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTEL-HPVPDAHVPVMKFKF 115 (696)
Q Consensus 49 ~Re~VL~~L~~------------V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l-~~V~~A~VPIIKf~~ 115 (696)
.+-.|++.|.. ...++||||.+|-.+.. +.|=..+...-.+.++.+-- ..|..-..=+..|.+
T Consensus 5 ~~~~i~~~L~~~~PiL~GTiPi~Idi~~SDLDIic~~~d~----~~F~~~l~~~f~~~~~f~~~~~~i~~~~~~~~~F~~ 80 (152)
T PF14091_consen 5 NELGILEKLAAYDPILVGTIPIGIDIPGSDLDIICEVPDP----EAFEQLLQSLFGQFEGFTIKEKTIRGEPSIVANFRY 80 (152)
T ss_pred HHhhHHHHhhcCCCEEecccccccCCCCCCccEEEEeCCH----HHHHHHHHHHhccCCCceeeeceeCCceeEEEEEEE
Confidence 45567777777 68899999999988842 23334444444445553321 234444555677888
Q ss_pred CCeeeEEEeec-ccCCCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHHhCCCh-hhHHHHHHHHH--------HHH
Q 005445 116 SGVSIDLLYAR-LSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKI-QNFRTTLRCMR--------FWA 185 (696)
Q Consensus 116 ~GI~iDL~fa~-l~~~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~-~~FR~~LR~IK--------~WA 185 (696)
.|.+|.| |++ .+ ++.-||+|=-.-=.+++-.. +.||.-+|-+| +||
T Consensus 81 ~~~~~Ei-F~Q~~P-----------------------v~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa 136 (152)
T PF14091_consen 81 EGFPFEI-FGQPIP-----------------------VEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFA 136 (152)
T ss_pred CCceEEE-eecCCC-----------------------hhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHH
Confidence 9999987 443 22 23467887544333333334 78999999888 466
Q ss_pred HHhcCCcC
Q 005445 186 KRRGVYSN 193 (696)
Q Consensus 186 KrRGIYsn 193 (696)
+-=||-++
T Consensus 137 ~lLgL~GD 144 (152)
T PF14091_consen 137 KLLGLEGD 144 (152)
T ss_pred HHhCCCCC
Confidence 66665544
No 20
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It 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 dis
Probab=93.21 E-value=0.51 Score=44.34 Aligned_cols=61 Identities=25% Similarity=0.339 Sum_probs=42.1
Q ss_pred CCCceeEEEecCCCCC----ccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEEC--CeeeEEEeec
Q 005445 63 PGADIDTLCVGPRHAT----REEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS--GVSIDLLYAR 126 (696)
Q Consensus 63 pgSDID~LcV~P~~vt----r~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~--GI~iDL~fa~ 126 (696)
+.||||++++.+.... ...++...+.+.|.+...- .......-|.|.++|. |++|||+=|.
T Consensus 44 ~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~---~~~~~~~~~~v~v~~~~~~~~vDvvP~~ 110 (143)
T cd05400 44 GDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA---NEEVKAQHRSVTVKFKGQGFHVDVVPAF 110 (143)
T ss_pred CCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc---ccccccCceEEEEEEcCCCeEEEEEEEe
Confidence 5899999999886643 1136677777778774321 1122355588999987 8999997664
No 21
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=83.35 E-value=2.9 Score=42.78 Aligned_cols=47 Identities=11% Similarity=0.089 Sum_probs=32.6
Q ss_pred hhhHHHHHHHHHHHHHHhcCCcCCC-CCcchHHHHHHHHHHHhhCCCC
Q 005445 171 IQNFRTTLRCMRFWAKRRGVYSNVA-GFLGGINWALLVARICQLYPNA 217 (696)
Q Consensus 171 ~~~FR~~LR~IK~WAKrRGIYsn~~-GfLGGIswAILVArvCQlyPna 217 (696)
....+.++|.||+|-+.----.... +-+..|++-+|+++....-.+.
T Consensus 41 P~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~~ 88 (190)
T PF10421_consen 41 PTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCGA 88 (190)
T ss_dssp -HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT-S
T ss_pred CHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCCC
Confidence 4788999999999998754443333 4577899999999999776544
No 22
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup 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. These three carboxylate residues are fairly well conserved in this
Probab=81.29 E-value=19 Score=38.98 Aligned_cols=122 Identities=20% Similarity=0.207 Sum_probs=72.3
Q ss_pred CCCCCHHHHHHHHHHHHhhcc--------cc-------CCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeec
Q 005445 39 NLYESQEEAVSREEVLGRLDQ--------VH-------GPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPV 103 (696)
Q Consensus 39 ~l~eS~EE~~~Re~VL~~L~~--------V~-------~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V 103 (696)
+-++=.|-....+.|+..|+. +. .-.+|||+|+..|.... ..++..+.+.|.+.+.++.+
T Consensus 136 ~ri~r~ea~~~a~~i~~~l~~~~~~~~v~i~GS~RRg~et~gDiDilv~~~~~~~--~~~~~~v~~~l~~~~~~~~~--- 210 (307)
T cd00141 136 QRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS--RGLLEKVVDALVELGFVTEV--- 210 (307)
T ss_pred CCeEHHHHHHHHHHHHHHHHhCCCceEEEEcccccCCCCccCCEEEEEecCCccc--cccHHHHHHHHHhCCCeehh---
Confidence 345555555556666666665 11 24479999988776544 26788888999988876542
Q ss_pred CCCCcceEEEEEC------CeeeEEEeecccCCCcCCCCCCCchhhhcccchhhHhhhchhhhHHHHHHhCCChhhHHHH
Q 005445 104 PDAHVPVMKFKFS------GVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTT 177 (696)
Q Consensus 104 ~~A~VPIIKf~~~------GI~iDL~fa~l~~~~vpe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~~ 177 (696)
...-..-....+. |+.|||.++.-..+ .-.++..-.+. . -
T Consensus 211 ~~~g~~k~~~~~~~~~~~~~~rVDl~~~p~~~~------------------------------~~all~fTGs~-~---~ 256 (307)
T cd00141 211 LSKGDTKASGILKLPGGWKGRRVDLRVVPPEEF------------------------------GAALLYFTGSK-Q---F 256 (307)
T ss_pred hhCCCceEEEEEecCCCCCceEEEEEEeCHHHH------------------------------HHHHHHhhCCH-H---H
Confidence 1112222222222 89999998753211 00122222222 2 2
Q ss_pred HHHHHHHHHHhcCCcCCCCCcc
Q 005445 178 LRCMRFWAKRRGVYSNVAGFLG 199 (696)
Q Consensus 178 LR~IK~WAKrRGIYsn~~GfLG 199 (696)
.|.++.||++||..=|..|..-
T Consensus 257 nr~lR~~A~~~G~~L~~~GL~~ 278 (307)
T cd00141 257 NRALRRLAKEKGLKLNEYGLFD 278 (307)
T ss_pred HHHHHHHHHHcCCeeecccccc
Confidence 5667999999999888877653
No 23
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=78.68 E-value=92 Score=33.20 Aligned_cols=197 Identities=15% Similarity=0.199 Sum_probs=125.1
Q ss_pred CceeEEEecCCCCCccccHHHHHHHHHhC----CCCceEEeecCCC------CcceEEEEE--C--CeeeEEEeecccCC
Q 005445 65 ADIDTLCVGPRHATREEDFFGELHQMLTE----MPEVTELHPVPDA------HVPVMKFKF--S--GVSIDLLYARLSLW 130 (696)
Q Consensus 65 SDID~LcV~P~~vtr~edFF~~l~~~L~~----~~~V~~l~~V~~A------~VPIIKf~~--~--GI~iDL~fa~l~~~ 130 (696)
-+.|+|+++..-.|. ++.+.+.+.|.+ ...-+-...++.+ ..|.+...+ . .+.+.+..+.
T Consensus 15 ~~~eLVVlck~kPT~--~lL~~v~~~L~~~L~~~~~~ev~~~~e~~~~~~~~~~~~~~~~~~lts~~~r~~~~~~~---- 88 (248)
T PF07528_consen 15 NDVELVVLCKEKPTK--ELLNRVAEKLPEQLKKVTPEEVTNSVEAAIIIDSCKEPKLEVGIDLTSPVMRVRVLITT---- 88 (248)
T ss_pred ceEeEEEEcCCCCcH--HHHHHHHHHHHHHHhhhCccccccchhhhhhhcccccccceeeEEecCCceEEEEeccc----
Confidence 478999999888885 577665555554 2111112222222 235555443 2 2333433322
Q ss_pred CcCCCCCCCchhhhcccc-hhhHhhhchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHH
Q 005445 131 VIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 209 (696)
Q Consensus 131 ~vpe~ldl~~d~lL~~lD-e~svrSLNG~Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVAr 209 (696)
.+++..-.+.. ..|| ..|..+|-..|=+..+..........+.++|.+|--.+|-- .++.|.+..+=+|+-+
T Consensus 89 -~~~~~~~~dp~--~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p----~w~~L~~W~leLL~~~ 161 (248)
T PF07528_consen 89 -IPENLSKLDPE--DHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVP----TWQPLSSWALELLVEK 161 (248)
T ss_pred -cCccccccChh--hcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCC----CCCCCChhHHHHHHHH
Confidence 23433222211 2344 37788888899999999888888889999999999988753 3556888888888877
Q ss_pred HHhhCCC---CCHHHHHHHHHHhhcc-CCCCCceeccccccCCCCccccCCCCCCCCCcccceeeCCCC-CCCCcccccC
Q 005445 210 ICQLYPN---AVPSMLVSRFFRVYTQ-WRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAY-PCMNSSYNVS 284 (696)
Q Consensus 210 vCQlyPn---as~~~LL~~FF~~Ys~-WdWp~PV~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~-P~~Nst~NVs 284 (696)
..---|+ .+++.-+.+||+..|. +=-|. . | =|.+|+. ...++..+.|
T Consensus 162 ~i~~~~~~~~l~~g~a~RRvle~lasGillp~----------~-------~-----------gl~DPcE~~~~~~~~~lt 213 (248)
T PF07528_consen 162 AISNNSSRQPLSPGDAFRRVLECLASGILLPG----------S-------P-----------GLRDPCEKDPVDVLDTLT 213 (248)
T ss_pred HeeeCCCCCCCChHHHHHHHHHHHhCceecCC----------C-------C-----------CCcCCCCCCCceeeccCC
Confidence 7653333 4678899999999874 22221 1 1 1235555 5577788888
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 005445 285 TSTLRIMMDEFQRGHEIC 302 (696)
Q Consensus 285 ~sTl~vI~~Ef~RA~~Il 302 (696)
...+..|..--+.+.+++
T Consensus 214 ~qq~e~it~sAQ~~LRll 231 (248)
T PF07528_consen 214 LQQREDITSSAQTALRLL 231 (248)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 888888988777777766
No 24
>PF03281 Mab-21: Mab-21 protein
Probab=72.03 E-value=1.3e+02 Score=31.66 Aligned_cols=103 Identities=19% Similarity=0.275 Sum_probs=70.0
Q ss_pred HHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhhCCCC---CHHHHHHHHHHhhccCCCCCce
Q 005445 163 QILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA---VPSMLVSRFFRVYTQWRWPNPV 239 (696)
Q Consensus 163 ~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQlyPna---s~~~LL~~FF~~Ys~WdWp~PV 239 (696)
++++.+ ....+.+||++|.-.++.. ...+-|+++++-.++.+.|..+|.. ....|-.+|.++...
T Consensus 184 ~ll~~~--~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~------- 251 (292)
T PF03281_consen 184 QLLKNL--NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDF------- 251 (292)
T ss_pred HHHHhc--cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHH-------
Confidence 444443 4567889999999877766 5667899999999999999999876 245565666655431
Q ss_pred eccccccCCCCccccCCCCCCCCCcccceeeCCCCCCCCcccccChhHHHHHHHHHHH
Q 005445 240 LLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQR 297 (696)
Q Consensus 240 ~L~~i~~g~lg~~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sTl~vI~~Ef~R 297 (696)
+++-.++|.+ | --+.|.+|.=.+.+..++..+..++.+
T Consensus 252 L~~~L~~~~L------p--------------hff~~~~NLf~~~~~~~~~~~~~~~~~ 289 (292)
T PF03281_consen 252 LIKCLQEGRL------P--------------HFFIPNLNLFQHLSPEELDELARKLER 289 (292)
T ss_pred HHHHHhcCCC------C--------------ccCCCCcccCCCCCHHHHHHHHHHHHH
Confidence 1222333332 1 114577888888888888877776654
No 25
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=70.54 E-value=17 Score=45.38 Aligned_cols=122 Identities=18% Similarity=0.287 Sum_probs=70.8
Q ss_pred hhHHHHHHhCCChhhHHHHHHHHHHHHHHhcCCcCCCCCcchHHHHHHHHHHHhh-C---CCCCHHHHHHHHHHhhccCC
Q 005445 159 RVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQL-Y---PNAVPSMLVSRFFRVYTQWR 234 (696)
Q Consensus 159 Rvtd~IlrlVPn~~~FR~~LR~IK~WAKrRGIYsn~~GfLGGIswAILVArvCQl-y---Pnas~~~LL~~FF~~Ys~Wd 234 (696)
|.+-.|..+--.+..|-.++|.-|.|...+=+-+ |.+ -=++-+|||...+. + |..++..=..+|-.+.|+||
T Consensus 806 ~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~~---h~~-De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~d 881 (1121)
T KOG2054|consen 806 LHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSG---HHL-DEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWD 881 (1121)
T ss_pred HHHHHHHHHhhcccchhHHHHHHHHHHHHHhhcc---chH-HHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCc
Confidence 4444444444457899999999999966552211 122 44567888887643 3 45666666789999999999
Q ss_pred CCC-ceeccccccCCCCc----cccCCCCCCCCCcccceeeCCCCCCCCcccccChhH
Q 005445 235 WPN-PVLLCAIEEGSLGL----QVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTST 287 (696)
Q Consensus 235 Wp~-PV~L~~i~~g~lg~----~vWdP~~~~~Dr~hlMpIiTPa~P~~Nst~NVs~sT 287 (696)
|.. |.++.- ..+ +.. +..+-....+..+..|.|+||- -..++...-+..+
T Consensus 882 W~~~PLIvd~-nn~-~~ed~~~e~~e~f~s~R~~lp~m~vit~y-D~~~~~~t~~~P~ 936 (1121)
T KOG2054|consen 882 WKFDPLIVDF-NNG-FPEDERSELEEKFISARKQLPPMVVITPY-DHLGSKFTRTSPN 936 (1121)
T ss_pred ccCCceEEEc-CCC-CcHHHHHHHHHHHhhhcccCCceEEeecc-ccccccccccCch
Confidence 985 776643 211 100 0000011112234579999995 3344444444444
No 26
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=64.72 E-value=7.3 Score=33.43 Aligned_cols=19 Identities=26% Similarity=0.288 Sum_probs=16.6
Q ss_pred ccCCCCceeEEEecCCCCC
Q 005445 60 VHGPGADIDTLCVGPRHAT 78 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~vt 78 (696)
.+.|+||||++++.+....
T Consensus 27 ~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 27 DATPDSDIDLLIILDEPED 45 (93)
T ss_dssp SSCTTSCEEEEEEESSTSC
T ss_pred cCCCCCCEEEEEEeCCccc
Confidence 5789999999999998765
No 27
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=59.31 E-value=4.1 Score=43.97 Aligned_cols=67 Identities=22% Similarity=0.383 Sum_probs=35.0
Q ss_pred ccCCCCceeEEEecCCCCCccccHHHHHHHH-HhCCCCceEEeecCCCCcceEEEE--------------ECCeeeEEEe
Q 005445 60 VHGPGADIDTLCVGPRHATREEDFFGELHQM-LTEMPEVTELHPVPDAHVPVMKFK--------------FSGVSIDLLY 124 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~vtr~edFF~~l~~~-L~~~~~V~~l~~V~~A~VPIIKf~--------------~~GI~iDL~f 124 (696)
.|..+||||.++-|+.+..-.+.+-..+.+- |.. ..-...+.|-.-+.|=|.|. +.|+-|||+|
T Consensus 134 l~~~nSDIDfVVYG~~~~~aRea~~~~~e~~~l~~-ldd~~W~~iyrkr~~~l~f~ef~~~E~RK~nRgiv~gt~fdlLf 212 (315)
T COG1665 134 LYDENSDIDFVVYGQMWFRAREAILDAIEDFPLGE-LDDAEWERIYRKRIPELSFDEFLYHERRKGNRGIVGGTYFDLLF 212 (315)
T ss_pred ccCCCCCceEEEEcHHHHHHHHHHHhhhhccCccC-cCHHHHHHHHHcccCCCCHHHHHHHhhhccCceeecCEEEEEEE
Confidence 6789999999999954422111111111111 111 01112234444555555542 4689999999
Q ss_pred ecc
Q 005445 125 ARL 127 (696)
Q Consensus 125 a~l 127 (696)
++=
T Consensus 213 vrd 215 (315)
T COG1665 213 VRD 215 (315)
T ss_pred ecc
Confidence 873
No 28
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=56.83 E-value=8.1 Score=30.77 Aligned_cols=13 Identities=38% Similarity=0.654 Sum_probs=11.2
Q ss_pred ccCCCCceeEEEe
Q 005445 60 VHGPGADIDTLCV 72 (696)
Q Consensus 60 V~~pgSDID~LcV 72 (696)
.+.+.||||++|+
T Consensus 30 ~~~~~SDIDi~v~ 42 (49)
T cd05397 30 LLKKSSDIDLACV 42 (49)
T ss_pred CCCCCCCEEEEEE
Confidence 5679999999887
No 29
>PF15431 TMEM190: Transmembrane protein 190
Probab=47.36 E-value=11 Score=35.71 Aligned_cols=31 Identities=29% Similarity=0.607 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHHHhcCCcCCC--CCcchHHH
Q 005445 173 NFRTTLRCMRFWAKRRGVYSNVA--GFLGGINW 203 (696)
Q Consensus 173 ~FR~~LR~IK~WAKrRGIYsn~~--GfLGGIsw 203 (696)
.|-....|+=-|||||++|.|.. |||.||--
T Consensus 72 l~Li~~iclFWWAkRrd~~k~lh~P~fL~~~~c 104 (134)
T PF15431_consen 72 LLLICSICLFWWAKRRDMCKHLHMPRFLSGFKC 104 (134)
T ss_pred HHHHHHHHHHHHHHHhchHhhccCchhhccCcc
Confidence 45567788899999999998764 88888643
No 30
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=46.84 E-value=18 Score=33.52 Aligned_cols=32 Identities=28% Similarity=0.311 Sum_probs=18.7
Q ss_pred ccCCCCceeEEEecCCCCCccccHHHHHHHHHhC
Q 005445 60 VHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 93 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~ 93 (696)
-..|+||||+++-.-...+- -+|| .+...|.+
T Consensus 37 E~~~~SDIDILVef~~~~~l-l~~~-~l~~~L~~ 68 (97)
T COG1669 37 EQKPDSDIDILVEFEPGKTL-LDLV-RLEDELSD 68 (97)
T ss_pred CCCCCCCceeEEeecCCccH-HHHH-HHHHHHHH
Confidence 35699999998865444332 1333 24555554
No 31
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=37.22 E-value=67 Score=27.06 Aligned_cols=20 Identities=25% Similarity=0.233 Sum_probs=15.9
Q ss_pred ccCCCCceeEEEecCCCCCc
Q 005445 60 VHGPGADIDTLCVGPRHATR 79 (696)
Q Consensus 60 V~~pgSDID~LcV~P~~vtr 79 (696)
-+.++||||++++.+.....
T Consensus 31 ~~~~~SDiDl~vi~~~~~~~ 50 (93)
T cd05403 31 DARPDSDIDLLVIFDDPLDP 50 (93)
T ss_pred CCCCCCCeeEEEEeCCCCCH
Confidence 35589999999999877653
No 32
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=35.08 E-value=89 Score=34.73 Aligned_cols=66 Identities=26% Similarity=0.350 Sum_probs=49.5
Q ss_pred HHHhhccccCCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeec
Q 005445 53 VLGRLDQVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYAR 126 (696)
Q Consensus 53 VL~~L~~V~~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~ 126 (696)
+.+.+++.---.+|||.+|... +.. .+.+.|.++|+|.++.+-.+..|-++.--..|++|||-.+.
T Consensus 185 ~aGs~RR~retv~DiD~~~s~~-~~~-------~v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~ 250 (326)
T COG1796 185 IAGSLRRGRETVGDIDILISTS-HPE-------SVLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVP 250 (326)
T ss_pred eccchhhccccccceeeEeccC-CcH-------HHHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcC
Confidence 3444555445668999887543 322 25566677899999999999999999988999999998764
No 33
>PRK08609 hypothetical protein; Provisional
Probab=33.86 E-value=2.8e+02 Score=32.84 Aligned_cols=21 Identities=33% Similarity=0.172 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhcCCcCCCCCc
Q 005445 178 LRCMRFWAKRRGVYSNVAGFL 198 (696)
Q Consensus 178 LR~IK~WAKrRGIYsn~~GfL 198 (696)
.|.++.||++||..-|-.|..
T Consensus 263 n~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 263 NVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred HHHHHHHHHHcCCcccccccc
Confidence 466699999999999998885
No 34
>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=29.91 E-value=20 Score=38.39 Aligned_cols=21 Identities=43% Similarity=0.639 Sum_probs=17.1
Q ss_pred ecChhhhcchhhhhHHHHHHH
Q 005445 337 AENADDLRNWKGWVESRLRQL 357 (696)
Q Consensus 337 a~~~e~~~~w~GwVESRlR~L 357 (696)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 346678889999999998755
No 35
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=26.59 E-value=40 Score=25.55 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=24.0
Q ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHhhc
Q 005445 28 TRKLEKYLRDVNLYESQEEAVSREEVLGRLD 58 (696)
Q Consensus 28 t~~L~~~L~~~~l~eS~EE~~~Re~VL~~L~ 58 (696)
+.+|.+.|+..|+..++.. ..|++.|..++
T Consensus 6 ~~~L~~wL~~~gi~~~~~~-~~rd~Ll~~~k 35 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPKSA-KTRDELLKLAK 35 (38)
T ss_pred HHHHHHHHHHcCCCCCCCC-CCHHHHHHHHH
Confidence 5789999999998766555 78888887764
No 36
>PRK13299 tRNA CCA-pyrophosphorylase; Provisional
Probab=24.56 E-value=1e+03 Score=26.89 Aligned_cols=120 Identities=14% Similarity=0.260 Sum_probs=68.0
Q ss_pred ceEEEEECCeeeEEEeecccC----CCcCCCC----CCCchhhhcccch---------hhHhhhchhhhHH-HHHHhCCC
Q 005445 109 PVMKFKFSGVSIDLLYARLSL----WVIPEDL----DISQDSILQNADE---------QTVRSLNGCRVTD-QILRLVPK 170 (696)
Q Consensus 109 PIIKf~~~GI~iDL~fa~l~~----~~vpe~l----dl~~d~lL~~lDe---------~svrSLNG~Rvtd-~IlrlVPn 170 (696)
..+.+..+|..+|+...+... ..-|..+ ++..|-.-++..- .-+-=.+|.++.+ .++|.|.+
T Consensus 68 gt~~v~~~~~~~ei~t~R~e~~~~d~~~p~~~~~~~~i~eDl~RRDFTINAma~~~~g~liDpf~G~~DL~~~~iR~v~~ 147 (394)
T PRK13299 68 GTVLVLENGEEYEVTTFRTESEYVDYRRPSEVTFVRSLEEDLKRRDFTINAIAMDENGEIIDLFDGLEDLKNRLIRAVGN 147 (394)
T ss_pred CEEEEEECCEEEEEEeeccccCccCCCCCccccCCCCHHHHHHhccccHHHhhcCCCCCEeeCCCCHHHHhCCceeecCC
Confidence 445556789999999887631 1112111 2222222222221 1111246766654 66777754
Q ss_pred h-hhHH----HHHHHHHHHHHHhcCCcCCCCC-cchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCC
Q 005445 171 I-QNFR----TTLRCMRFWAKRRGVYSNVAGF-LGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPN 237 (696)
Q Consensus 171 ~-~~FR----~~LR~IK~WAKrRGIYsn~~Gf-LGGIswAILVArvCQlyPnas~~~LL~~FF~~Ys~WdWp~ 237 (696)
. ++|+ .+||++++-|+ +|| +.--.+..+... ..+....+..-|...|..++..-+|..
T Consensus 148 ~~~~f~eDplRiLRa~Rfaa~--------l~f~i~~~t~~~i~~~-~~~l~~vs~eRI~~El~kll~~~~~~~ 211 (394)
T PRK13299 148 AEERFQEDALRMMRAVRFASQ--------LGFDLETETFEAMKTQ-APLLEKISVERIFVEFEKLLLGPFWRK 211 (394)
T ss_pred HHHhhccCHHHHHHHHHHHHH--------HCCCCCHHHHHHHHHH-HHHHhcCCHHHHHHHHHHHHcCCCHHH
Confidence 3 3454 57899998874 456 555555555433 455677778888888888877555443
No 37
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=20.18 E-value=1.5e+02 Score=29.93 Aligned_cols=66 Identities=23% Similarity=0.207 Sum_probs=35.0
Q ss_pred CCCCceeEEEecCCCCCccccHHHHHHHHHhCCCCceEEeecCCCCcceEEEEECCeeeEEEeecccCCCcC
Q 005445 62 GPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIP 133 (696)
Q Consensus 62 ~pgSDID~LcV~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~A~VPIIKf~~~GI~iDL~fa~l~~~~vp 133 (696)
....|||+++..+.... +.++|..+.....-.-+-+++ .....++++...++.||| +.++....+|
T Consensus 35 r~T~DIDlfi~~~~~~~-~~~~~~~~a~~~g~~~~~~~~----~~~~~~~~~~~~~v~IDl-~~ni~~~~v~ 100 (181)
T PF09970_consen 35 RTTKDIDLFIENPSPNL-EADALREVAEENGWDLGWTDF----GTPRYVVKVGGEDVRIDL-LENIGDFYVP 100 (181)
T ss_pred CCCCCeEEEeCCCchHH-HHHHHHHHHHHcCCCcCcccc----CCCceEEEeCCCCeEEEc-hhccCCcccC
Confidence 35789998876664433 235555554322211122221 123445666668899999 5555433333
Done!