Query psy15891
Match_columns 899
No_of_seqs 293 out of 1286
Neff 4.7
Searched_HMMs 46136
Date Sat Aug 17 00:17:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15891hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3657|consensus 100.0 2E-207 5E-212 1748.2 38.2 753 4-898 314-1071(1075)
2 cd08641 DNA_pol_gammaA Pol gam 100.0 9E-122 2E-126 1005.0 33.1 376 467-866 46-425 (425)
3 COG0749 PolA DNA polymerase I 100.0 2.3E-54 5.1E-59 495.0 15.0 323 438-850 238-591 (593)
4 cd06444 DNA_pol_A Family A pol 100.0 1.4E-51 3.1E-56 453.3 22.1 298 465-852 26-346 (347)
5 PF00476 DNA_pol_A: DNA polyme 100.0 2.9E-51 6.3E-56 455.7 18.9 323 433-845 23-377 (383)
6 cd08638 DNA_pol_A_theta DNA po 100.0 4.9E-50 1.1E-54 445.0 23.9 256 514-848 76-370 (373)
7 TIGR00593 pola DNA polymerase 100.0 1.4E-50 3.1E-55 487.9 20.6 320 439-848 535-883 (887)
8 cd08640 DNA_pol_A_plastid_like 100.0 6.3E-50 1.4E-54 443.2 21.5 257 514-848 71-369 (371)
9 cd08637 DNA_pol_A_pol_I_C Poly 100.0 8E-50 1.7E-54 443.8 21.6 248 515-841 103-369 (377)
10 cd08643 DNA_pol_A_pol_I_B Poly 100.0 9.5E-50 2.1E-54 448.5 22.1 320 429-848 55-425 (429)
11 cd08639 DNA_pol_A_Aquificae_li 100.0 2.9E-48 6.4E-53 423.6 23.9 243 514-842 58-317 (324)
12 PRK14975 bifunctional 3'-5' ex 100.0 1.1E-47 2.5E-52 444.8 21.5 250 515-841 283-542 (553)
13 PRK05755 DNA polymerase I; Pro 100.0 8E-46 1.7E-50 449.0 24.6 253 515-846 603-874 (880)
14 cd08642 DNA_pol_A_pol_I_A Poly 100.0 2.4E-44 5.1E-49 398.2 16.3 290 443-845 28-374 (378)
15 smart00482 POLAc DNA polymeras 100.0 1E-42 2.2E-47 358.2 15.7 193 550-807 1-206 (206)
16 KOG3657|consensus 99.5 4.1E-16 8.9E-21 181.8 -7.6 345 435-892 491-840 (1075)
17 COG0749 PolA DNA polymerase I 98.1 6.5E-08 1.4E-12 113.6 -8.0 319 526-890 3-335 (593)
18 PF01612 DNA_pol_A_exo1: 3'-5' 91.6 0.14 3.1E-06 50.1 3.0 56 13-73 119-175 (176)
19 cd06146 mut-7_like_exo DEDDy 3 84.2 2.1 4.6E-05 44.4 6.1 51 11-70 139-192 (193)
20 PF10108 DNA_pol_B_exo2: Predi 82.6 1.8 3.9E-05 46.2 4.8 53 11-72 115-172 (209)
21 cd06141 WRN_exo DEDDy 3'-5' ex 82.3 2.8 6.1E-05 41.8 5.9 49 13-70 116-169 (170)
22 cd05780 DNA_polB_Kod1_like_exo 80.0 2 4.4E-05 44.5 4.1 51 13-69 142-195 (195)
23 cd06129 RNaseD_like DEDDy 3'-5 78.4 4.6 9.9E-05 40.4 5.9 50 13-69 109-159 (161)
24 cd05783 DNA_polB_B1_exo DEDDy 78.3 2.9 6.2E-05 44.1 4.6 45 14-67 158-202 (204)
25 cd05777 DNA_polB_delta_exo DED 78.1 3.1 6.8E-05 44.2 4.9 56 13-72 169-226 (230)
26 cd05781 DNA_polB_B3_exo DEDDy 77.4 2 4.4E-05 44.5 3.2 23 47-69 166-188 (188)
27 cd05782 DNA_polB_like1_exo Unc 76.9 3 6.4E-05 44.0 4.3 48 11-67 155-207 (208)
28 cd06148 Egl_like_exo DEDDy 3'- 72.4 4.4 9.5E-05 42.1 4.1 57 13-76 115-180 (197)
29 cd05160 DEDDy_DNA_polB_exo DED 68.7 6.3 0.00014 40.4 4.3 50 13-66 149-198 (199)
30 cd05779 DNA_polB_epsilon_exo D 68.0 4.8 0.0001 42.6 3.3 47 14-66 156-203 (204)
31 cd05785 DNA_polB_like2_exo Unc 64.1 12 0.00027 39.5 5.5 20 47-66 187-206 (207)
32 cd05784 DNA_polB_II_exo DEDDy 62.6 12 0.00027 39.1 5.1 50 13-67 140-193 (193)
33 PRK05755 DNA polymerase I; Pro 61.0 26 0.00056 44.7 8.5 107 13-155 412-522 (880)
34 smart00474 35EXOc 3'-5' exonuc 55.9 16 0.00036 35.3 4.5 54 13-72 117-170 (172)
35 cd05776 DNA_polB_alpha_exo ina 54.5 20 0.00043 38.5 5.1 49 12-69 172-226 (234)
36 PF13482 RNase_H_2: RNase_H su 52.3 14 0.00031 36.4 3.4 23 47-69 141-163 (164)
37 PRK10829 ribonuclease D; Provi 51.4 25 0.00054 40.7 5.5 54 13-73 116-170 (373)
38 PHA02528 43 DNA polymerase; Pr 44.1 30 0.00066 44.3 5.2 52 14-73 274-330 (881)
39 KOG0950|consensus 42.4 17 0.00037 46.3 2.6 101 550-676 821-923 (1008)
40 PRK14975 bifunctional 3'-5' ex 39.6 55 0.0012 39.7 6.3 53 13-73 91-144 (553)
41 cd05778 DNA_polB_zeta_exo inac 39.5 38 0.00081 36.4 4.4 49 14-66 179-230 (231)
42 cd06142 RNaseD_exo DEDDy 3'-5' 39.2 69 0.0015 31.7 5.9 52 13-73 106-160 (178)
43 smart00486 POLBc DNA polymeras 38.5 52 0.0011 37.5 5.6 52 13-73 166-226 (471)
44 PF00940 RNA_pol: DNA-dependen 37.7 5.6E+02 0.012 30.0 13.8 130 537-677 54-228 (405)
45 TIGR00593 pola DNA polymerase 37.0 87 0.0019 40.3 7.7 57 13-73 420-477 (887)
46 cd00007 35EXOc 3'-5' exonuclea 36.0 52 0.0011 31.1 4.3 58 13-72 97-154 (155)
47 cd09018 DEDDy_polA_RNaseD_like 33.9 52 0.0011 31.4 4.0 55 13-71 96-150 (150)
48 PRK05761 DNA polymerase I; Rev 31.9 58 0.0013 41.3 5.0 45 13-66 290-334 (787)
49 TIGR01388 rnd ribonuclease D. 31.2 90 0.002 36.0 6.0 54 13-73 112-166 (367)
50 PRK05762 DNA polymerase II; Re 30.0 69 0.0015 40.6 5.2 55 14-73 294-354 (786)
51 PHA02524 43A DNA polymerase su 25.8 1.2E+02 0.0025 36.9 5.7 53 14-73 275-330 (498)
52 PF03175 DNA_pol_B_2: DNA poly 23.6 70 0.0015 37.5 3.4 28 46-73 130-157 (459)
53 PHA00452 T3/T7-like RNA polyme 22.8 3.4E+02 0.0074 34.9 9.2 129 537-674 466-638 (807)
54 KOG3337|consensus 22.0 54 0.0012 34.5 1.8 15 66-80 15-29 (201)
55 COG0349 Rnd Ribonuclease D [Tr 20.4 1.5E+02 0.0032 34.6 5.0 55 12-73 111-166 (361)
56 PF14003 YlbE: YlbE-like prote 20.3 17 0.00037 32.4 -1.8 16 257-272 8-23 (65)
No 1
>KOG3657|consensus
Probab=100.00 E-value=2.3e-207 Score=1748.22 Aligned_cols=753 Identities=48% Similarity=0.830 Sum_probs=675.1
Q ss_pred CCcccccccccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHhhhhCCCcchh
Q psy15891 4 ESWTNVSSLNSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLFLERFPHPVTL 83 (899)
Q Consensus 4 ~~W~~~sS~NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F~~~~~~~~~~ 83 (899)
.+|+++||+|||+|||+|||++.++||+.||+||++++++|++|||+||+|||+||.|||+||+++||+|
T Consensus 314 ~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~F---------- 383 (1075)
T KOG3657|consen 314 NPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLF---------- 383 (1075)
T ss_pred hhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHH----------
Confidence 3599999999999999999955569999999999999999999999999999999999999999999999
Q ss_pred hhhhccccccccCchhhHHHHHhhcchhhhcCCCcchhhhhhccccccccCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15891 84 AGMLELSTAYLPDTLATFEVIQALFPLFLERFPHPVTLAGMLELSTAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDK 163 (899)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PHPvt~agml~mgs~~LPvn~~W~~y~~~ae~~y~~~~~~~~~~L~~~ 163 (899)
+|||||||||||||+|||+|||||+||++||+++|++|++++.+++++|+++
T Consensus 384 ----------------------------lercPHPaTlagMLsmGsvyLPvN~nW~rYin~~e~tYeq~~~~~~~kl~~~ 435 (1075)
T KOG3657|consen 384 ----------------------------LERCPHPATLAGMLSMGSVYLPVNSNWERYINEAEQTYEQLKTEAKRKIIES 435 (1075)
T ss_pred ----------------------------HHhCCChHhHHHHHhcCcEEeeccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCccCCcccccCCCCchhhhhccccccccccCcccCCcchhhhhccCCCCchhHHHHHHHHHHHHhhccc
Q psy15891 164 CDQACSLLHDDKYKDSLWLWDQDWSVKDLKLKKKANKTLSVDQETEEPEEFYEINKNGEDQTEDEFVKRRRELVEKFKPL 243 (899)
Q Consensus 164 a~~a~~~~~~~~~~~DpWl~~ldWs~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l 243 (899)
|++||+++.|+.|++|||||++||+.|++|++|+
T Consensus 436 A~~a~~LL~d~~y~~d~wlW~~dw~~~~lk~~~k---------------------------------------------- 469 (1075)
T KOG3657|consen 436 ARDACKLLDDDPYKNDPWLWDLDWTFQELKLKKK---------------------------------------------- 469 (1075)
T ss_pred HHHHHHHhcCCchhccchhcccchhhHHHHHhhc----------------------------------------------
Confidence 9999999999999999999999999999887652
Q ss_pred cccccCCCCCCCCCCCChhhhHhhhcCCCCCCchhhhhhhhcccCCCCCCCCCCCCCcccccccchhhhhhccccCCcce
Q psy15891 244 MQTKDRLPVNSSYLIGYPEWYRKLCVKPHSADKDAVSKQELIHDGISDTSEAWIPGPSLISTSMQITPKLLSLTWKSMPL 323 (899)
Q Consensus 244 ~~~~~~~p~~~~~~~g~P~Wyr~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~g~~~is~~~ri~P~LlrL~W~g~Pl 323 (899)
++|++.++|||+|.|||+||+. + ++|.| .|+++|||+|+|+.|+|+|+||
T Consensus 470 -----g~p~~~~~Lpg~p~wyrkl~p~-~---------------------~~~sp---~isl~~~i~p~l~~l~we~~pl 519 (1075)
T KOG3657|consen 470 -----GLPARKQFLPGSPEWYRKLCPS-D---------------------EVWSP---HISLKSRIIPKLFGLVWEGFPL 519 (1075)
T ss_pred -----CCchhhhcCCCCchhhhhcCCC-C---------------------CCCCC---CCchhhhhHHHHHhhccCCchh
Confidence 3678899999999999999943 1 56777 8999999999999999999999
Q ss_pred eEEcCcceEEeecCCCCCCCCCccCCchHHhhhhhcccccccccccccchhhhhhhhcccccchhhhchhhhhhHHHHHh
Q psy15891 324 HFIRGHGWGYLVPYSTDIKVPDAENIPLEQLKQLYNNITKQDNCEANVDNAQNSLRDSVETNISFIDCSKSAKRLEVIAN 403 (899)
Q Consensus 324 ~~~~~~GW~f~VP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 403 (899)
||++++||||+||++.+. |+++..- +....+|...+.+...++..+..+++++.+.+...+
T Consensus 520 ~~sr~~gwgflvp~~~~~----------e~~~~A~-------~~~~~sD~~~d~~~~~~e~~~~~~~~~~~~~~~~~~-- 580 (1075)
T KOG3657|consen 520 HYSREKGWGFLVPNRKDV----------EKLLQAD-------PNFHEIDAKIDFLPDEAEKKFPNRSFYETLQNNVGM-- 580 (1075)
T ss_pred hhhhhcCceeecCCcchH----------HHHhhcc-------cchhhcchhhhcccchhhhcccccchhhHHhccCcc--
Confidence 999999999999999874 2333200 011233445667777777777777788776544332
Q ss_pred hhhhhhhcccCCCCCCCCCCCCCCeeEEEeccCCCCCCCCCCCCcchhhhhHhhcCCCCCC--chHHHHHHHHHhhhhhh
Q psy15891 404 VLDKKKLAEASSTDTSTDDADTPREIGFIKLPHKDGEHLNVGNPLSRDFINKFSDNSLAGV--DIGAKRIIEISRMLSYW 481 (899)
Q Consensus 404 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~klPHkdG~~~nvg~plsK~fl~~fe~g~L~s~--~~~a~~~le~~~~~syW 481 (899)
+....+|.|+++|.+ ++|+|||||||+|+..|||+||+|||+++|++|+|+++ .+.|..+|++|.|+|||
T Consensus 581 ---~~~q~~g~g~~~~~~-----~~~~f~Klph~~G~S~nvg~pltk~fl~~~~~~vl~~~~~~~~~~r~ldi~~~~s~w 652 (1075)
T KOG3657|consen 581 ---LGTQPDGKGVELDEA-----GLCRFFKLPHPNGPSFNVGNPLTKDFLKKFEEGVLRSGRYEEYADRVLDINQMTSFW 652 (1075)
T ss_pred ---ccccCCCcceeeccc-----ceeeeeecCCCCCCCCccCCcchHhhhhHHHhcccccccccchHHHHHHHHHHHHHH
Confidence 223347999999865 37999999999999999999999999999999999996 58999999999999999
Q ss_pred hhhhhhhhcceeEecccCCCchhhhhcccccCCCCCeEeeeeeeccccccccccCccceecCCCCCcccccccceEecCC
Q psy15891 482 RNNHERVKKQFVVWLNKKDLPRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPD 561 (899)
Q Consensus 482 ~s~r~Ri~~q~vv~~~~~~l~~~~~~~~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~GselRs~f~App 561 (899)
+|+|+||++|||||++...||+.+....+ ....+|.|.|+++++||+|+||+|+||+|+||..++++|++||+|++|||
T Consensus 653 ~s~~~ri~Sqmvvwlp~~~lP~~~~~~~~-k~~~~gaI~p~vvp~gtitrrave~tw~tasNs~~~Rigselkamvqapp 731 (1075)
T KOG3657|consen 653 RSARDRICSQMVVWLPSATLPNAFNLNNE-KEMIYGAIAPQVVPAGTITRRAVEPTWLTASNARPDRIGSELKAMVQAPP 731 (1075)
T ss_pred HHHhhhhhhheeEecccccCchhhhhccc-chhhhhccCccccccchhhhhhhhhhhhhhcccChhhhhHHHHHhhcCCC
Confidence 99999999999999999999987654211 35778999999999999999999999999999999999999999999999
Q ss_pred CceEEEEeccchhhhhhhhcccccccccccccccccccccCccCCCCchhHHHHHHhccchhhhhHHHHHHhhcccHHHH
Q psy15891 562 GYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVGISREHAKIINYARIYGAGERFA 641 (899)
Q Consensus 562 Gy~~VgAD~SqiELRIlal~gDA~~s~~~g~~Afg~m~LeG~K~~GtDlHs~tAs~lGisR~~AKv~nyG~iYGaG~k~A 641 (899)
||+|||||++++|+||+|++|||++.+.||.+|||||+|+|.|++|+|+|+.||+++||||++||+||||+|||+|++||
T Consensus 732 gy~LVgaDvdsqElwiaa~lgda~~~~~hg~ta~gwM~Lag~ks~gtdlhs~ta~~lgiSr~hakv~Ny~riygag~~fa 811 (1075)
T KOG3657|consen 732 GYRLVGADVDSQELWIAALLGDASAEGVHGKTAFGWMTLAGSKSDGTDLHSKTASQLGISRNHAKVFNYARIYGAGQTFA 811 (1075)
T ss_pred cceEeeccccHHHHHHHHHhhhhhhhcccCcchhhhhhhcCccccCchHhHhhhhhccccHhhhhhccHHHHhcCCcchH
Confidence 99999999999999999999999998899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchh
Q psy15891 642 ERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESA 721 (899)
Q Consensus 642 ~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~ 721 (899)
.+|++++||.++.+||+..+.++|..++|.+.++.+++......+..+..+..-++....+..-...+-||.|.|||||.
T Consensus 812 ~~ll~~fnp~l~~~Ea~~~A~~l~~~tkG~~~~rlk~e~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~gg~es~ 891 (1075)
T KOG3657|consen 812 EKLLMRFNPSLTQSEAKSKASQLFKLTKGDRAKRLKVEVRMVENSLVCKILTIDGIYLIYSIYENEVEPRRLWVGGTESS 891 (1075)
T ss_pred HHhHHhhCCCCchHHHHHHHHHHHHhhcCceeeehHhHHHHhhhhhhchhhhhhhhhhhhhhhhcccchhhhccCchHHH
Confidence 99999999999999999999999999999888766644211111111111100011111111112567899999999999
Q ss_pred hhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHHHHhccCCc---eeEEEecc
Q psy15891 722 MFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCMRWLVSRDT---RFVISIHD 798 (899)
Q Consensus 722 ~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m~~L~~~~~---rlvlsVHD 798 (899)
|||+||+||.++.||||+|||+|+++|++.+....+|+++++||+|||||+||||+++|+|+||++.|+ ||||+|||
T Consensus 892 ~fn~lesia~~~~prtpvlgc~is~sl~~~~~~~~~f~~srinwvvqssavd~lhlllvsm~wl~~~y~i~~rfcisihd 971 (1075)
T KOG3657|consen 892 MFNKLESIATAHDPRTPVLGCQISRSLEKLPEGEPKFLPSRINWVVQSSAVDFLHLLLVSMQWLCDTYKIDARFCISIHD 971 (1075)
T ss_pred HHHHHHHHhhccCCCCCeeccchhhhhcccccCCcccccceeeEEeeccchhHHHHHHHHHHHHHhhcccceEEEEEehH
Confidence 999999999999999999999999999999866678999999999999999999999999999999886 99999999
Q ss_pred eeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCcccccccccccccccccccCCCccCCCCccCCCccccCCCC
Q psy15891 799 EIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEIDKVLRKESDNDCKTPSNPYGLCKGYGIPLG 878 (899)
Q Consensus 799 EI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdid~vlRKEv~~dc~TPSnp~~~~~~y~Ip~G 878 (899)
||||+|.|++++|+|+||||+|||||+||++|+||+||||+|||||+||||+||||||+|||+||||||||+.+|||++|
T Consensus 972 evrylv~e~d~~raalalqisnl~tr~~~~~r~gi~~lp~svaffs~vdidtvlrkev~mdc~tpsnp~g~~~~ygi~~g 1051 (1075)
T KOG3657|consen 972 EVRYLVKEEDAPRAALALQISNLLTRAMFSQRVGINDLPQSVAFFSQVDIDTVLRKEVTMDCITPSNPHGLEDDYGITGG 1051 (1075)
T ss_pred hHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhhhcccchhhhhhhhccHHHHHHHhcccccCCCCCCCccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCHHHHHHhcCCCCCCCC
Q psy15891 879 EILDIYQTIDKANGVIGTFK 898 (899)
Q Consensus 879 esldi~~~l~~~~g~l~~~~ 898 (899)
+||||+|+||+++|.++.|+
T Consensus 1052 ~sldi~q~ie~~~~d~~k~~ 1071 (1075)
T KOG3657|consen 1052 KSLDIAQLIENRRGDENKKK 1071 (1075)
T ss_pred ccccHHHHHHHccCchhhhh
Confidence 99999999999999988875
No 2
>cd08641 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-nu
Probab=100.00 E-value=9.2e-122 Score=1005.04 Aligned_cols=376 Identities=58% Similarity=0.966 Sum_probs=357.7
Q ss_pred HHHHHHHHHhhhhhhhhhhhhhhcceeEecccCCCchhhhhcccc-cCCCCCeEeeeeeeccccccccccCccceecCCC
Q psy15891 467 GAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIES-EGRDYGVILPQLIVSGTLTRRAVEATWMTASNAV 545 (899)
Q Consensus 467 ~a~~~le~~~~~syW~s~r~Ri~~q~vv~~~~~~l~~~~~~~~~~-~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~ 545 (899)
.|+++||+|++||||+|+|+||++|||||.++.++|+.+..++++ ++..+|||||+++++||+||||+|+|||||+||+
T Consensus 46 ~a~~~l~~~~~~syw~~~r~ri~~q~vv~~~~~~~~~~~~~~~~~~~~~~~Gri~p~~~~~GtvTgRa~~~tW~tas~~~ 125 (425)
T cd08641 46 QAKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPMGTITRRAVEPTWLTASNAK 125 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcceEEEcCCccccccccccccccccCCCCeEeeeeecCcccccccccccccccCCCC
Confidence 577899999999999999999999999999998999888777666 5678999999999999999999999999999999
Q ss_pred CCcccccccceEecCCCceEEEEeccchhhhhhhhcccccccccccccccccccccCccCCCCchhHHHHHHhccchhhh
Q psy15891 546 GERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVGISREHA 625 (899)
Q Consensus 546 ~~~~GselRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~~~g~~Afg~m~LeG~K~~GtDlHs~tAs~lGisR~~A 625 (899)
++++|++||++|+|||||.|||||||||||||++++||+++...|+++|||||+|+|.|.+|+|||+.||+.+|++|++|
T Consensus 126 ~~~iG~eiR~aF~ap~G~~lVgADySQiELRiA~lsgD~~l~~~~~~~AF~~~~l~g~k~~g~DIH~~TA~i~gisR~~A 205 (425)
T cd08641 126 KNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHFGGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRDHA 205 (425)
T ss_pred cchhhHHHHhheecCCCCEEEEEchhHHHHHHHHHcCCHhhhhccccchhhhhhhcccccCCCCHHHHHHHHhCCCHHHh
Confidence 99999999999999999999999999999999999999999779999999999999999999999999999999999999
Q ss_pred hHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcc
Q psy15891 626 KIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSV 705 (899)
Q Consensus 626 Kv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v 705 (899)
|++|||+|||+|.+||.+|++++|+++|.+||++++++||+.|||++.|++.. +..
T Consensus 206 K~~NfG~IYG~g~~~a~~L~~~l~~~is~~EA~~~i~~yF~~y~gVr~~~~~~------------------------~~~ 261 (425)
T cd08641 206 KVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRIAIQRS------------------------TKG 261 (425)
T ss_pred HHHHHHHHHCCCchhhHHHHHHhcCcCCHHHHHHHHHHHHHhCcChhhhhccc------------------------ccc
Confidence 99999999999999999999999999999999999999999999999976541 112
Q ss_pred cccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHHHHh
Q psy15891 706 DKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCMRWL 785 (899)
Q Consensus 706 ~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m~~L 785 (899)
.++++|++|+|||||+|||.+|++|.+..|++|++|++++.+|..++.....++|+|+||+||||||||+|++|++|+++
T Consensus 262 ~~~~~~~~w~gg~es~m~n~le~~A~~~g~~tTllGrr~~~~l~s~n~~~~~~~rsaIN~pIQGSAADiiKlaMV~m~~~ 341 (425)
T cd08641 262 KRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALLEPNLVKNEFMTSRINWVVQSSAVDYLHLMLVSMRWL 341 (425)
T ss_pred cccccccccccchHHHHHHHHHHHHHhcCCCcCccCCEechhhcccchhHHHHHHHHhcccchhhHHHHHHHHHHHHHHH
Confidence 37889999999999999999999999999999999999988898888777788999999999999999999999999998
Q ss_pred ccCCc---eeEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCcccccccccccccccccccCCCccC
Q psy15891 786 VSRDT---RFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEIDKVLRKESDNDCKT 862 (899)
Q Consensus 786 ~~~~~---rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdid~vlRKEv~~dc~T 862 (899)
++.++ |+||||||||+|+||++++|++|+|+||+|+|||+||++++||+||||||||||+|||||||||||||||+|
T Consensus 342 l~~~~i~aRmlLqVHDEL~feV~eed~yr~alalqi~nlltram~a~~lg~~dlPqs~affs~vdid~vlrkev~~dc~t 421 (425)
T cd08641 342 IEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLTRAMFAQKLGINDLPQSVAFFSAVDIDTVLRKEVDMDCVT 421 (425)
T ss_pred HHhcCCCceEEEEECeEeeeeccHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCcchhhhhhhhhhhHHhhcCCCCCCC
Confidence 88664 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCc
Q psy15891 863 PSNP 866 (899)
Q Consensus 863 PSnp 866 (899)
||||
T Consensus 422 ps~p 425 (425)
T cd08641 422 PSNP 425 (425)
T ss_pred CCCC
Confidence 9998
No 3
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.3e-54 Score=495.03 Aligned_cols=323 Identities=25% Similarity=0.372 Sum_probs=272.3
Q ss_pred CCCCCCCCCCcchhhhhHhhcCCCCC-------C-chHHHHHHHHH----hhhhhhhhhhhhhhcceeEecccCCCchhh
Q psy15891 438 DGEHLNVGNPLSRDFINKFSDNSLAG-------V-DIGAKRIIEIS----RMLSYWRNNHERVKKQFVVWLNKKDLPRRL 505 (899)
Q Consensus 438 dG~~~nvg~plsK~fl~~fe~g~L~s-------~-~~~a~~~le~~----~~~syW~s~r~Ri~~q~vv~~~~~~l~~~~ 505 (899)
.|+.+|.+||..-+++ -||+-.|++ + |+++.++||.- ..+..-+-+|+- .+-.+.|.+ .||..+
T Consensus 238 aG~~FNi~SPKQL~~I-LfeKl~Lp~~~kKtktG~yST~~~vLe~L~~~h~i~~~iL~~Rql-~KLksTY~d--~L~~~i 313 (593)
T COG0749 238 AGEEFNINSPKQLGEI-LFEKLGLPPGLKKTKTGNYSTDAEVLEKLADDHPLPKLILEYRQL-AKLKSTYTD--GLPKLI 313 (593)
T ss_pred hcCcCCCCCHHHHHHH-HHHhcCCCccccccCCCCCccHHHHHHHHhhcCccHHHHHHHHHH-HHHHHHhhh--ccHHhh
Confidence 5778999999999999 789888882 3 88999999833 234444445543 223334444 466553
Q ss_pred hhcccccCCCCCeEeeeeeeccccccccccCccceecCCCCCcc------cccccceEecCCCceEEEEeccchhhhhhh
Q psy15891 506 VENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERV------GSELRAMIQAPDGYSIIGADVDSQELWIAS 579 (899)
Q Consensus 506 ~~~~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~------GselRs~f~AppGy~~VgAD~SqiELRIla 579 (899)
...+||||++|+|.||+||| |||++||.+++ |..+|.+|+|++||.+++||||||||||+
T Consensus 314 -------~~~t~RIHTsf~Q~~t~TGR------LSSsdPNLQNIPiRse~Gr~IR~aFva~~g~~~i~aDYSQIELRil- 379 (593)
T COG0749 314 -------NPDTGRIHTSFNQTGTATGR------LSSSDPNLQNIPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRIL- 379 (593)
T ss_pred -------CCCCCccCcchHHHHHHhhc------ccCCCCCcccCCcCCHhHHhhhhceeCCCCCeEEEechHHHHHHHH-
Confidence 23459999999999999999 99999987654 56899999999999999999999999999
Q ss_pred hcccccccc-cccccccccccccCccCCCCchhHHHHHHh-cc--------chhhhhHHHHHHhhcccHHHHHHHHHHhC
Q psy15891 580 VIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GI--------SREHAKIINYARIYGAGERFAERLLKQFN 649 (899)
Q Consensus 580 l~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gi--------sR~~AKv~nyG~iYGaG~k~A~~La~q~n 649 (899)
||+|+ +.+++|| .+|.|+|+.||+.+ |+ .|..||.+|||+|||++ |.+|++++|
T Consensus 380 ----AHls~D~~Ll~AF---------~~g~DiH~~TA~~vFgv~~~~Vt~e~Rr~AKaINFGiiYG~s---afgLa~~L~ 443 (593)
T COG0749 380 ----AHLSQDEGLLRAF---------TEGEDIHTATAAEVFGVPIEEVTSEQRRKAKAINFGLIYGMS---AFGLAQQLG 443 (593)
T ss_pred ----HHhcCCHHHHHHH---------hcCccHHHHHHHHHhCCChhhCCHHHhhhhhhhccceeeccc---hhhHHHHcC
Confidence 99999 9999999 89999999999998 65 39999999999999999 999999999
Q ss_pred CCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHH
Q psy15891 650 PEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEI 729 (899)
Q Consensus 650 ~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~i 729 (899)
+|..||+.++++||+.|||++.|+++ ++++++++|||+ |++||||+
T Consensus 444 --I~~~eA~~~I~~YF~rypgv~~ym~~--~~~~ar~~GyV~---------------Tl~gRRry--------------- 489 (593)
T COG0749 444 --IPRKEAKEYIDRYFERYPGVKEYMER--TKEEAREDGYVE---------------TLFGRRRY--------------- 489 (593)
T ss_pred --CChHHHHHHHHHHHHhChHHHHHHHH--HHHHHHHcCcee---------------eccccccc---------------
Confidence 99999999999999999999999988 999999999998 99999999
Q ss_pred hhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccC--CceeEEEecceeEEecCc
Q psy15891 730 ATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSR--DTRFVISIHDEIRYLVPD 806 (899)
Q Consensus 730 A~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~--~~rlvlsVHDEI~~eVpe 806 (899)
+|.++++... .++.++|.|+|++|||||||++|++|+.| .+|.+. +.|+++|||||++|+||+
T Consensus 490 -------~p~i~s~n~~-------~R~~aER~AiNaPIQGTAADiiK~AMI~vd~~l~~~~~~~rllLQVHDELvfEv~~ 555 (593)
T COG0749 490 -------LPDINSSNRV-------VRAAAERAAINAPIQGTAADIIKLAMIKVDKALKEEKLKARLLLQVHDELVFEVPK 555 (593)
T ss_pred -------CcccccCCHH-------HHHHHHHHHhcCcCcccHHHHHHHHHHhHHHHHhhcchhhhhHHhhhhhhhhcCcH
Confidence 7777765531 47889999999999999999999999999 666653 459999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHHhhccCCCCCCCccccccccccccc
Q psy15891 807 EEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEIDK 850 (899)
Q Consensus 807 e~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdid~ 850 (899)
+.++++...++ ..|..++ . .+||+.|....+-+|+.
T Consensus 556 ~e~e~~~~~v~--~~Me~a~-----~-L~VPL~vdv~~g~nW~e 591 (593)
T COG0749 556 EELEEVKKLLK--AIMENAV-----N-LSVPLEVDVGIGKNWDE 591 (593)
T ss_pred hHHHHHHHHHH--HHHHHhh-----c-cCCceEEecCCCcChhh
Confidence 99988765544 4444443 2 57999988777777663
No 4
>cd06444 DNA_pol_A Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication. DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-
Probab=100.00 E-value=1.4e-51 Score=453.34 Aligned_cols=298 Identities=21% Similarity=0.232 Sum_probs=244.2
Q ss_pred chHHHHHHHHHhhhhhhhhhhhhhhcceeEecccCCCchhhhhcccccCCCCCeEeeeeeeccccccccccCccceecCC
Q psy15891 465 DIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNA 544 (899)
Q Consensus 465 ~~~a~~~le~~~~~syW~s~r~Ri~~q~vv~~~~~~l~~~~~~~~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP 544 (899)
.+.++.+||+.+...+|.+|.+++..+++ .+|||||+|+++||+||| +|+++|
T Consensus 26 hp~~~~ile~r~~~Kl~st~~~~~~~~~~---------------------~~gRih~~~~~~gT~TGR------lSs~~P 78 (347)
T cd06444 26 HPAVPLLLEYKKLAKLWSANGWPWLDQWV---------------------RDGRFHPEYVPGGTVTGR------WASRGG 78 (347)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhc---------------------ccCccccEEEEcccceee------eccCCC
Confidence 57899999999999999999988765443 269999999999999999 999999
Q ss_pred CCCccc------ccccceEecCCCceEEEEeccchhhhhhhhcccccccc-cccccccccccccCccCCCCchhHHHHHH
Q psy15891 545 VGERVG------SELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKA 617 (899)
Q Consensus 545 ~~~~~G------selRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~ 617 (899)
|.++++ +.+|+||+|++||+||++||||||+||+ ||+++ ..++++| ..|.|+|+.||+.
T Consensus 79 NlQniP~~~~~g~~iR~~f~a~~G~~lv~aDysqiElRil-----A~ls~D~~l~~~f---------~~g~Dih~~~A~~ 144 (347)
T cd06444 79 NAQQIPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVL-----AALSGDEALAEAF---------GRGGDLYTATASA 144 (347)
T ss_pred ccccCCCCCchhhhhhheEecCCCCEEEEechhHHHHHHH-----HHHhCCHHHHHHH---------hcCCCHHHHHHHH
Confidence 877655 7899999999999999999999999999 99998 8889988 7899999999999
Q ss_pred hc------cchhhhhHHHHHHhhc----ccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhc
Q psy15891 618 VG------ISREHAKIINYARIYG----AGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKR 687 (899)
Q Consensus 618 lG------isR~~AKv~nyG~iYG----aG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~ 687 (899)
+. ..|+.||++|||++|| +| +.+|++++| +|.+||++++++||+.||+++.|++. +.+.+++.
T Consensus 145 ~~~~~v~~~~R~~AK~~~fg~~YG~~~~~g---~~~L~~~~~--is~~ea~~~~~~f~~~~p~v~~~~~~--~~~~a~~~ 217 (347)
T cd06444 145 MFGVPVGGGERQHAKIANLGAMYGATSGIS---ARLLAQLRR--ISTKEAAALIELFFSRFPAFPKAMEY--VEDAARRG 217 (347)
T ss_pred HhCCCCCHHHHHHHHHHHHHHHhCCchhhh---HHHHHHHhC--CCHHHHHHHHHHHHHHCcCHHHHHHH--HHHHHHhc
Confidence 84 5699999999999999 88 999999998 99999999999999999999999987 77888887
Q ss_pred ---CeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhh
Q psy15891 688 ---VYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRIN 764 (899)
Q Consensus 688 ---GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN 764 (899)
|||. |++||++++....|. .++++ ..+.......+..+.|+++|
T Consensus 218 ~~~g~v~---------------T~~GR~r~~~~~~~~----------------~~~~~--~~~~~~~~~~~~~~~r~a~N 264 (347)
T cd06444 218 ERGGYVR---------------TLLGRRSPPPDIRWT----------------EVVSD--PAAASRARRVRRAAGRFARN 264 (347)
T ss_pred cCCceEE---------------EeCCcEeecCCCccc----------------ccccc--cccccccHHHHHHhHHHHhh
Confidence 9987 999999985322210 01111 00111111145678899999
Q ss_pred hhhchHHHHHHHHHHHHHH-HhccC--CceeEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCcccc
Q psy15891 765 WVVQSGAVDFLHLMLVCMR-WLVSR--DTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSIS 841 (899)
Q Consensus 765 ~vIQGSAADilklamv~m~-~L~~~--~~rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svA 841 (899)
++|||||||++|++|+.+. .+.+. ..+++++|||||+++||++++++++..++.++..+..+ ++++|+
T Consensus 265 ~~IQGsaADi~K~ami~~~~~l~~~~~~~~lvl~VHDElv~evp~~~~~~~~~~l~~~M~~~~~~---------~~~~vP 335 (347)
T cd06444 265 FVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRL---------LFGSVP 335 (347)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEccceEEEeCHHHHHHHHHHHHHHHHHHhhc---------cCCCCC
Confidence 9999999999999999994 44442 34999999999999999999999988776555433332 344566
Q ss_pred ccccccccccc
Q psy15891 842 FFSGVEIDKVL 852 (899)
Q Consensus 842 ffs~vdid~vl 852 (899)
+...++|...+
T Consensus 336 l~v~~~ig~~W 346 (347)
T cd06444 336 VRFPVKIGVVW 346 (347)
T ss_pred EEEEeeecCCC
Confidence 66667666543
No 5
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=100.00 E-value=2.9e-51 Score=455.73 Aligned_cols=323 Identities=24% Similarity=0.384 Sum_probs=248.8
Q ss_pred eccCCCCCCCCCCCCcchhhhhHhhcCCCC--------CCchHHHHHHHHHhh-----hhhhhhhhhhhhcceeEecccC
Q psy15891 433 KLPHKDGEHLNVGNPLSRDFINKFSDNSLA--------GVDIGAKRIIEISRM-----LSYWRNNHERVKKQFVVWLNKK 499 (899)
Q Consensus 433 klPHkdG~~~nvg~plsK~fl~~fe~g~L~--------s~~~~a~~~le~~~~-----~syW~s~r~Ri~~q~vv~~~~~ 499 (899)
++++..|..+|.+||.....+- |+...|. +.+++.+++|+.-.. +...+.+|+.-+ ....|.+
T Consensus 23 ~~~~~~g~~fN~~S~~q~~~~L-~~~lgl~~~~~t~~~g~~st~~~~L~~l~~~~~~~~~~~l~~r~~~k-l~~~~~~-- 98 (383)
T PF00476_consen 23 KAYKLAGEEFNPNSPKQLAEVL-FEELGLPPTKKTKKKGKPSTDKEVLKKLAEDAHPIAKLLLEYRKLSK-LRSTYID-- 98 (383)
T ss_dssp HHHHHHTSCSSTTTHHHHHHHH-HTTSSSTTSSBETTCSEBHCTHHHHHHHCCCCHTHHHHHHHHHHHHH-HHHHTTH--
T ss_pred HhHHhcCCccCCCCHHHHHHHH-HHcCCCCCCCCCcccchhhhHHHHHHHhhhhhhhhHHHHHHHHHHHH-HHhhhhh--
Confidence 4556688889999999988764 4555555 234566777763333 333333343311 1111111
Q ss_pred CCchhhhhcccccCCCCCeEeeeeeeccccccccccCccceecCCCCCcc------cccccceEecCCCceEEEEeccch
Q psy15891 500 DLPRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERV------GSELRAMIQAPDGYSIIGADVDSQ 573 (899)
Q Consensus 500 ~l~~~~~~~~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~------GselRs~f~AppGy~~VgAD~Sqi 573 (899)
.+... ....+|||||+++++||+||| +|+++||.+++ |.++|+||+||+||+||++|||||
T Consensus 99 ----~~~~~---~~~~dgrih~~~~~~gt~TGR------ls~~~PNlQniP~~~~~~~~~R~~f~a~~G~~lv~aD~sqi 165 (383)
T PF00476_consen 99 ----NLLDK---VDPEDGRIHPSFNQTGTATGR------LSSSNPNLQNIPKRDPYGKEIRSAFVAPPGYVLVSADYSQI 165 (383)
T ss_dssp ----HHHHH---SBTTTTEE--EEESSSSSSS--------EEESSCTSSSSSSSHHHHGGGGGEEGSSTEEEEEEEESSH
T ss_pred ----HHHHh---ccccCCeecceeeecccccCC------ceeechhhhccccccccCcccceeEecCccceeeeeehhhh
Confidence 11111 123789999999999999999 99999987654 457899999999999999999999
Q ss_pred hhhhhhhcccccccc-cccccccccccccCccCCCCchhHHHHHHh-c--------cchhhhhHHHHHHhhcccHHHHHH
Q psy15891 574 ELWIASVIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-G--------ISREHAKIINYARIYGAGERFAER 643 (899)
Q Consensus 574 ELRIlal~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-G--------isR~~AKv~nyG~iYGaG~k~A~~ 643 (899)
|+||+ ||+++ ..++++| .+|.|+|+.+|+.+ | ..|+.||++|||++|||| +.+
T Consensus 166 ElRvl-----A~ls~D~~l~~~~---------~~g~D~h~~~a~~~~~~~~~~v~~~~R~~aK~~~~g~~YG~g---~~~ 228 (383)
T PF00476_consen 166 ELRVL-----AHLSGDENLIEAF---------RNGEDIHTETASDIFGKPYEEVTKEERQKAKTVNFGLIYGMG---AKG 228 (383)
T ss_dssp HHHHH-----HHHHTHHHHHHHH---------HTTCCHHHHHHHHHTTCHGGGTTHHHHHHHHHHHHHHHTT-T---HHH
T ss_pred hHHHH-----HHhcccHHHHHhh---------cccccHHHHHHHHhcCCCccccchhhHHHHhHHHHhhhhccC---HHH
Confidence 99999 99998 8889999 78999999999986 4 359999999999999999 999
Q ss_pred HHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhh
Q psy15891 644 LLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMF 723 (899)
Q Consensus 644 La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~F 723 (899)
|++++| +|.+||++++++||+.||+++.|++. +.+.+.+.|||+ |++||+++
T Consensus 229 la~~l~--~s~~eA~~~~~~f~~~~p~v~~~~~~--~~~~a~~~g~v~---------------t~~gr~r~--------- 280 (383)
T PF00476_consen 229 LAEQLG--ISEEEAKELIDAFFEAFPGVKKWMER--VKKRARENGYVE---------------TLFGRRRY--------- 280 (383)
T ss_dssp HHHHHT--SCHHHHHHHHHHHHHHSHHHHHHHHH--HHHHHHHHSEEE---------------CTTSSEEE---------
T ss_pred HHHHcc--CCHHHHHHHHHHHHHhCchHHHHHHH--HHHHHhcCCeEE---------------Eecccccc---------
Confidence 999999 99999999999999999999999987 888999999997 99999998
Q ss_pred hhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHHHHhcc-C--CceeEEEeccee
Q psy15891 724 NRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCMRWLVS-R--DTRFVISIHDEI 800 (899)
Q Consensus 724 n~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m~~L~~-~--~~rlvlsVHDEI 800 (899)
+|.+++... ..++...|+++|++|||||||++|.+|+.+.+.+. . ..+++++|||||
T Consensus 281 -------------~p~~~~~~~-------~~~~~~~r~a~N~~iQgsaAdi~k~am~~i~~~l~~~~~~~~l~l~VHDEl 340 (383)
T PF00476_consen 281 -------------LPNIDSRNK-------SLRASAERQAVNTPIQGSAADIMKLAMIRIHEALREKGLGARLVLQVHDEL 340 (383)
T ss_dssp -------------CGGGGSSSH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEESSEE
T ss_pred -------------CCchhcccc-------hhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCcCceeEEEEcCee
Confidence 555544321 13567788999999999999999999999955433 3 249999999999
Q ss_pred EEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCcccccccc
Q psy15891 801 RYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSG 845 (899)
Q Consensus 801 ~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~ 845 (899)
+++||++.+.+++..+ ..+|++++.. .||..|.+--+
T Consensus 341 i~ev~~~~~~~v~~~l--~~~M~~~~~~------~vPl~~~~~iG 377 (383)
T PF00476_consen 341 IFEVPEDEAEEVAEIL--KEIMENAGEL------RVPLPVEVEIG 377 (383)
T ss_dssp EEEEEGGGHHHHHHHH--HHHHHTSSHH------SSCTCEEEEEE
T ss_pred heeecHhHHHHHHHHH--HHHHHhhccC------CCeEEeecCCC
Confidence 9999999998886654 4666666543 67777754433
No 6
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=100.00 E-value=4.9e-50 Score=444.97 Aligned_cols=256 Identities=23% Similarity=0.338 Sum_probs=219.7
Q ss_pred CCCCeEeeeeeeccccccccccCccceecCCCCCcccc---------------------cccceEecCCCceEEEEeccc
Q psy15891 514 RDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGS---------------------ELRAMIQAPDGYSIIGADVDS 572 (899)
Q Consensus 514 ~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~Gs---------------------elRs~f~AppGy~~VgAD~Sq 572 (899)
+.+|||||+++++||+||| ||+++||.+++++ .+|.||+|++||.||++||||
T Consensus 76 ~~~grih~~~~~~gt~TGR------lSs~~PNlQniP~~~~~~~~~~~~~~~~~~~~~~~iR~~f~a~~G~~lv~~Dysq 149 (373)
T cd08638 76 LQMYRIHPTWNQTGTATGR------LSSSEPNLQNVPKDFEIKDAPSPPAGSEGDIPTISLRHAFIPPPGRVLLSADYSQ 149 (373)
T ss_pred CCCCeEeeEEEEccceeee------eeeccCCcCCCCCCCccccccccccccccchhhhhhhheeeCCCCCEEEEechhh
Confidence 5789999999999999999 9999998876665 599999999999999999999
Q ss_pred hhhhhhhhcccccccc-cccccccccccccCccCCCCchhHHHHHHh-ccc--------hhhhhHHHHHHhhcccHHHHH
Q psy15891 573 QELWIASVIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GIS--------REHAKIINYARIYGAGERFAE 642 (899)
Q Consensus 573 iELRIlal~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis--------R~~AKv~nyG~iYGaG~k~A~ 642 (899)
||+||+ ||+|+ ..++++| .+|.|+|+.+|+.+ |++ |+.||++|||++|||| +.
T Consensus 150 iElRvl-----A~ls~D~~l~~~~---------~~g~Dih~~~A~~~~g~~~~~v~~~~R~~aK~~~fg~~YG~g---~~ 212 (373)
T cd08638 150 LELRIL-----AHLSGDPALIELL---------NSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMG---AK 212 (373)
T ss_pred hHHHHH-----HHHhCCHHHHHHH---------hcCCCHHHHHHHHHhCCChhhCCHHHHHHHhHHHHhhHhCCc---HH
Confidence 999999 99998 8999999 77999999999976 764 9999999999999999 99
Q ss_pred HHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhh
Q psy15891 643 RLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAM 722 (899)
Q Consensus 643 ~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~ 722 (899)
+|++++| +|.+||++++++|++.||+++.|+++ +.+.+.+.|||+ |++||+|++
T Consensus 213 ~La~~l~--~s~~eA~~~i~~f~~~~p~v~~~~~~--~~~~a~~~g~v~---------------T~~GRrr~~------- 266 (373)
T cd08638 213 SLAEQLG--VSEEEAKQFIESFKNAYPGVRRFIRE--TIERARRNGFVE---------------TLTGRRRYL------- 266 (373)
T ss_pred HHHHHhC--CCHHHHHHHHHHHHHHCccHHHHHHH--HHHHHHHcCcEE---------------ccCCCEEeC-------
Confidence 9999998 99999999999999999999999988 889999999997 999999994
Q ss_pred hhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccC-------CceeEE
Q psy15891 723 FNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSR-------DTRFVI 794 (899)
Q Consensus 723 Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~-------~~rlvl 794 (899)
|.+++... ..++...|+++|++|||||||++|++|+.+ ++|... ..++++
T Consensus 267 ---------------p~~~~~~~-------~~~~~~~r~a~N~~iQGsaAdi~K~ami~i~~~l~~~~~~~~~~~~~lvl 324 (373)
T cd08638 267 ---------------PEINSGNS-------SERAQAERQAVNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVL 324 (373)
T ss_pred ---------------CCCCCCCH-------HHHHHHHHHHhchhhhhHHHHHHHHHHHHHHHHHHhhcccccCCCeEEEE
Confidence 43333221 135667899999999999999999999999 555442 239999
Q ss_pred EecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCccccccccccc
Q psy15891 795 SIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEI 848 (899)
Q Consensus 795 sVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdi 848 (899)
+||||++++||++++.+++..++ .+|+.++ . ..||+.|....+.+|
T Consensus 325 ~VHDEl~~ev~~~~~~~~~~~i~--~~Me~~~-----~-l~VPl~v~~~iG~~w 370 (373)
T cd08638 325 QIHDELLFEVPESDVDEVARIIK--RSMENAA-----K-LSVPLPVKVSIGKSW 370 (373)
T ss_pred EEccEEEEEeCHHHHHHHHHHHH--HHHhCcc-----C-CCCceEEeecccCCc
Confidence 99999999999999998876554 5555554 2 257877765554444
No 7
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.4e-50 Score=487.89 Aligned_cols=320 Identities=25% Similarity=0.403 Sum_probs=255.2
Q ss_pred CCCCCCCCCcchhhhhHhhcCCCC------CCchHHHHHHHHHh----hhhhhhhhhhhhhcceeEecccCCCchhhhhc
Q psy15891 439 GEHLNVGNPLSRDFINKFSDNSLA------GVDIGAKRIIEISR----MLSYWRNNHERVKKQFVVWLNKKDLPRRLVEN 508 (899)
Q Consensus 439 G~~~nvg~plsK~fl~~fe~g~L~------s~~~~a~~~le~~~----~~syW~s~r~Ri~~q~vv~~~~~~l~~~~~~~ 508 (899)
|..+|.+||....-+ .|++..|. +++++.+++|+..+ .+...+.||+ +.+....|.+ .|++.+
T Consensus 535 g~~fN~~SpkQl~~~-Lf~~lgl~~~kktktg~ST~~~vL~~L~~~hp~~~~ileyR~-l~Kl~sty~~--~l~~~i--- 607 (887)
T TIGR00593 535 GEEFNINSPKQLGEV-LFEKLGLPVGKKTKTGYSTDADVLEKLREKHPIIALILEYRQ-LTKLKSTYVD--GLPELV--- 607 (887)
T ss_pred CCCCCCCCHHHHHHH-HHHhCCCCCCCCCCCCCCChHHHHHHhhhcCcHHHHHHHHHH-HHHHHHHHHH--HHHHHh---
Confidence 667899999664433 25655554 24678888887432 2344445553 3333334443 233321
Q ss_pred ccccCCCCCeEeeeeeeccccccccccCccceecCCCCCcc------cccccceEecCCCceEEEEeccchhhhhhhhcc
Q psy15891 509 IESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERV------GSELRAMIQAPDGYSIIGADVDSQELWIASVIG 582 (899)
Q Consensus 509 ~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~------GselRs~f~AppGy~~VgAD~SqiELRIlal~g 582 (899)
...+|||||+|+|+||+||| |||++||.+++ |.++|++|+|++||+||+||||||||||+
T Consensus 608 ----~~~tgRIh~~~~q~~t~TGR------lSs~~PNLQNIP~r~~~g~~iR~~Fia~~G~~lv~aDySQIELRil---- 673 (887)
T TIGR00593 608 ----NPDTGRIHTTFNQTGTATGR------LSSSNPNLQNIPIRSEEGRKIRKAFVAEKGWLLISADYSQIELRVL---- 673 (887)
T ss_pred ----cCCCCceeeeeEecccceee------ecccCCCccccCCCCcccchhhheEecCCCCeEEEechhHhHHHHH----
Confidence 23459999999999999999 99999987765 56899999999999999999999999999
Q ss_pred cccccc-cccccccccccccCccCCCCchhHHHHHHh-ccc--------hhhhhHHHHHHhhcccHHHHHHHHHHhCCCC
Q psy15891 583 DSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GIS--------REHAKIINYARIYGAGERFAERLLKQFNPEM 652 (899)
Q Consensus 583 DA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis--------R~~AKv~nyG~iYGaG~k~A~~La~q~n~~l 652 (899)
||+|+ ..++++| .+|.|+|+.||+.+ |++ |+.||++|||++|||| +.+|++++| +
T Consensus 674 -Ahls~D~~Li~af---------~~g~DiH~~tA~~~fg~~~e~vt~~~R~~AK~infGiiYG~g---~~~La~~l~--i 738 (887)
T TIGR00593 674 -AHLSQDENLIEAF---------QNGEDIHTETASRLFGVEIEDVTPNMRRIAKTINFGVVYGMS---AFGLAQELG--I 738 (887)
T ss_pred -HHHcCCHHHHHHH---------hcCCChHHHHHHHHhCCChhhCCHHHHhhhhHhhcCcccccc---hhHHHHHcC--C
Confidence 99999 9999999 78999999999987 863 9999999999999999 999999999 9
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhc
Q psy15891 653 SKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATS 732 (899)
Q Consensus 653 S~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~ 732 (899)
|.+||++++++||+.||+++.|+++ +++++++.|||+ |++||||+
T Consensus 739 s~~eA~~~i~~yf~~yp~v~~~~~~--~~~~a~~~Gyv~---------------Tl~GRrr~------------------ 783 (887)
T TIGR00593 739 SRKEAKEFIERYFARYPGVKDYIEN--TVEEARKKGYVE---------------TLFGRRRY------------------ 783 (887)
T ss_pred CHHHHHHHHHHHHHHCccHHHHHHH--HHHHHHHcCcEE---------------ecCCCEee------------------
Confidence 9999999999999999999999987 899999999998 99999999
Q ss_pred cCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccCC--ceeEEEecceeEEecCcchH
Q psy15891 733 LQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSRD--TRFVISIHDEIRYLVPDEEK 809 (899)
Q Consensus 733 ~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~~--~rlvlsVHDEI~~eVpee~~ 809 (899)
+|.++++... .++...|+++|++|||||||++|+||+.+ +.|.+.. .+++++||||++|+||++++
T Consensus 784 ----lp~i~s~n~~-------~r~~aeR~A~N~~iQGsAADi~K~Ami~v~~~l~~~~~~~~lvlqVHDElv~Evp~~~~ 852 (887)
T TIGR00593 784 ----IPDINSRNRN-------VREAAERMAINAPIQGSAADIMKIAMIKLDKRLKERKLKARLLLQVHDELIFEAPEEEA 852 (887)
T ss_pred ----CCCccccchh-------hHhHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCeEEEeeEceEeeeecCHHHH
Confidence 5555543321 46667899999999999999999999999 4554433 59999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhccCCCCCCCccccccccccc
Q psy15891 810 YETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEI 848 (899)
Q Consensus 810 ~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdi 848 (899)
.+++..++ +.|..++ . -+||+.|..-.+-+|
T Consensus 853 ~~v~~~l~--~~Me~a~-----~-l~VPL~v~~~~G~~W 883 (887)
T TIGR00593 853 EEVAALVK--EVMEHAY-----P-LAVPLEVEVGTGKNW 883 (887)
T ss_pred HHHHHHHH--HHHHhhc-----C-CCCcEEEecCccCCH
Confidence 98876654 4444432 2 257887765555444
No 8
>cd08640 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including
Probab=100.00 E-value=6.3e-50 Score=443.25 Aligned_cols=257 Identities=22% Similarity=0.295 Sum_probs=219.7
Q ss_pred CCCCeEeeeeeeccccccccccCccceecCCCCCcccc------cccceEecCCCceEEEEeccchhhhhhhhccccccc
Q psy15891 514 RDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGS------ELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCA 587 (899)
Q Consensus 514 ~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~Gs------elRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s 587 (899)
..+|||||+++++ |+||| ||+++||.+++++ .+|++|+|++|+.||++|||||||||+ ||+|
T Consensus 71 ~~dgRih~~~~~~-t~TGR------lSs~~PNLQNiP~~~~~~~~iR~~Fva~~G~~lv~aDySQiElRvl-----A~lS 138 (371)
T cd08640 71 DSTGRIHCSLNIN-TETGR------LSSRNPNLQNQPALEKDRYKIRKAFIASPGNTLIVADYSQLELRLL-----AHMT 138 (371)
T ss_pred CCCCCeeeeEeec-cceee------hhcCCCCCCCCCCCCccccchhheEecCCCCEEEEechhhhhHHHH-----HHHc
Confidence 4679999999999 99999 9999999887775 599999999999999999999999999 9999
Q ss_pred c-cccccccccccccCccCCCCchhHHHHHHh-cc-------------------------------chhhhhHHHHHHhh
Q psy15891 588 K-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GI-------------------------------SREHAKIINYARIY 634 (899)
Q Consensus 588 ~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gi-------------------------------sR~~AKv~nyG~iY 634 (899)
+ ..++++| .+|.|+|+.||+.+ |+ .|+.||++|||++|
T Consensus 139 ~D~~Li~af---------~~g~DiH~~tA~~if~~~~e~v~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~AK~infGi~Y 209 (371)
T cd08640 139 RCKSMIEAF---------NAGGDFHSRTASGMYPHVAEAVANGEVLLEWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAY 209 (371)
T ss_pred CCHHHHHHH---------HcCCCHHHHHHHHHhCCCHHHhccccccccccccccccccccccccHHHHHHHHHHHHHHHh
Confidence 8 8999999 78999999999875 32 39999999999999
Q ss_pred cccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccc
Q psy15891 635 GAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQW 714 (899)
Q Consensus 635 GaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~ 714 (899)
|+| +.+|++++| +|.+||++++++||+.||+++.|++. +.++|.+.|||+ |++||||+
T Consensus 210 G~g---~~~La~~lg--is~~eA~~~i~~f~~~fP~v~~~~~~--~~~~a~~~Gyv~---------------T~~GRrr~ 267 (371)
T cd08640 210 GKT---AHGLAKDWK--VKLKEAERTVDAWYSDRPEVEQWQKK--TKKEARERGYTR---------------TLLGRYRY 267 (371)
T ss_pred ccc---hhHHHHHcC--CCHHHHHHHHHHHHHHCccHHHHHHH--HHHHHHHcCcEE---------------ccCCCEEE
Confidence 999 999999999 99999999999999999999999987 889999999997 99999998
Q ss_pred cCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhcc--CCce
Q psy15891 715 YGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVS--RDTR 791 (899)
Q Consensus 715 ~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~--~~~r 791 (899)
+|.+++... ..++...|+++|++|||||||++|.+|+.+ +.|.. ...+
T Consensus 268 ----------------------lp~i~s~~~-------~~~~~~eR~avN~~IQGsAADI~K~Ami~i~~~l~~~~~~~~ 318 (371)
T cd08640 268 ----------------------LPDIKSRNR-------KKRGHAERAAINTPIQGSAADIAMKAMLRIYRNLRLKRLGWK 318 (371)
T ss_pred ----------------------CCCcccccH-------hhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhccCCce
Confidence 444443321 135667899999999999999999999999 55522 3359
Q ss_pred eEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCccccccccccc
Q psy15891 792 FVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEI 848 (899)
Q Consensus 792 lvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdi 848 (899)
++++|||||+++||++.+.+++..+ ..+|+.++.. . .+||+.|....+.+|
T Consensus 319 lvlqVHDElv~evp~~~~~~~~~~v--~~~Me~~~~~---~-l~VPl~v~~~iG~~W 369 (371)
T cd08640 319 LLLQIHDEVILEGPEEKADEALKIV--KDCMENPFFG---P-LDVPLEVDGSVGYNW 369 (371)
T ss_pred EEEEEcceeEEEcCHHHHHHHHHHH--HHHHHhcCcc---C-CCccEEEeccccCCC
Confidence 9999999999999999998887654 3566665432 2 267888765555443
No 9
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=100.00 E-value=8e-50 Score=443.79 Aligned_cols=248 Identities=26% Similarity=0.405 Sum_probs=214.7
Q ss_pred CCCeEeeeeeeccccccccccCccceecCCCCCccc------ccccceEecCCCceEEEEeccchhhhhhhhcccccccc
Q psy15891 515 DYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVG------SELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK 588 (899)
Q Consensus 515 ~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~G------selRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~ 588 (899)
.+|||||+++++||+||| ||+++||.++++ .++|+||+|++||.||++||||||+||+ ||+++
T Consensus 103 ~dgrih~~~~~~gt~TGR------lS~~~PNlQniP~~~~~~~~~R~~f~~~~G~~lv~aDysqiElRil-----A~ls~ 171 (377)
T cd08637 103 KTGRIHTSFNQTVTATGR------LSSSDPNLQNIPIRTEEGREIRKAFVAEEGWVLLSADYSQIELRIL-----AHLSG 171 (377)
T ss_pred CCCceeeeeeeccccccc------hhcccCccccCCCCccchHhHHHheeCCCCCEEEEechhHhHHHHH-----HHHhC
Confidence 489999999999999999 999999988765 6899999999999999999999999999 99998
Q ss_pred -cccccccccccccCccCCCCchhHHHHHHh-ccc--------hhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHH
Q psy15891 589 -EHGATPLGWMTLSGQKSNATDMHSITAKAV-GIS--------REHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAK 658 (899)
Q Consensus 589 -~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis--------R~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~ 658 (899)
..++++| .+|.|+|+.+|+.+ |++ |+.||+++||++|||| +.+|++++| +|.+||+
T Consensus 172 D~~l~~~~---------~~g~Dih~~~A~~~~g~~~~~v~~~~R~~aK~~~~g~~YG~g---~~~la~~lg--~s~~eA~ 237 (377)
T cd08637 172 DEALIEAF---------KNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGIS---AFGLSQQLG--ISRKEAK 237 (377)
T ss_pred CHHHHHHH---------hcCCCHHHHHHHHHhCCChhhCCHHHHhhhhHhhcchhcCcc---hhHHHHHcC--CCHHHHH
Confidence 8889999 78999999999975 875 9999999999999999 999999998 9999999
Q ss_pred HHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCcc
Q psy15891 659 SKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTP 738 (899)
Q Consensus 659 ~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP 738 (899)
+++++|++.||+++.|+++ +.+++.+.|||+ |++|||+++ |
T Consensus 238 ~~~~~f~~~~p~v~~~~~~--~~~~a~~~g~v~---------------t~~GRrr~~----------------------~ 278 (377)
T cd08637 238 EYIDRYFARYPGVKEYMEE--TVEEAREKGYVE---------------TLFGRRRYI----------------------P 278 (377)
T ss_pred HHHHHHHHHCccHHHHHHH--HHHHHHHcCcEE---------------ccCCCEEeC----------------------C
Confidence 9999999999999999987 889999999997 999999994 4
Q ss_pred ccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccC--CceeEEEecceeEEecCcchHHHHHHH
Q psy15891 739 FLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSR--DTRFVISIHDEIRYLVPDEEKYETALA 815 (899)
Q Consensus 739 ~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~--~~rlvlsVHDEI~~eVpee~~~~aA~a 815 (899)
.+++... ..++...|+++|++|||||||++|++|+.+ ++|... ..+++++|||||+++||++++.+++..
T Consensus 279 ~~~~~~~-------~~r~~~~r~a~N~~iQGsaAdi~k~am~~~~~~l~~~~~~~~lvl~vHDEl~~ev~~~~~~~~~~~ 351 (377)
T cd08637 279 EINSKNR-------NVRAFAERIAINTPIQGTAADIIKLAMIRVHKALKEEGLKARMLLQVHDELVFEVPEEELEEVAAL 351 (377)
T ss_pred cccCCcH-------HHhhHHHHhHhcccchhHHHHHHHHHHHHHHHHHHhcCCCeEEEeeEeeeeeEecCHHHHHHHHHH
Confidence 3333221 135667899999999999999999999999 555543 349999999999999999999988766
Q ss_pred HHHHHHHHHHHhhccCCCCCCCcccc
Q psy15891 816 LHVTNLLTRAFCIKKLDMTDIPLSIS 841 (899)
Q Consensus 816 Lqianl~tramf~~~lg~~dlP~svA 841 (899)
++ ++|+++ .. .+||+.|.
T Consensus 352 l~--~~M~~~-----~~-l~VPl~v~ 369 (377)
T cd08637 352 VK--EEMENA-----VE-LSVPLKVD 369 (377)
T ss_pred HH--HHHhhc-----cc-CCCcEEEe
Confidence 54 445554 22 25676664
No 10
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=100.00 E-value=9.5e-50 Score=448.51 Aligned_cols=320 Identities=20% Similarity=0.180 Sum_probs=240.6
Q ss_pred eEEEeccCCCCCCCCCCCCcchhhhhHhhcCCCC-------CCchHHHHHHH-----HHhhhhhhhhhhhhhhcceeEec
Q psy15891 429 IGFIKLPHKDGEHLNVGNPLSRDFINKFSDNSLA-------GVDIGAKRIIE-----ISRMLSYWRNNHERVKKQFVVWL 496 (899)
Q Consensus 429 ~~f~klPHkdG~~~nvg~plsK~fl~~fe~g~L~-------s~~~~a~~~le-----~~~~~syW~s~r~Ri~~q~vv~~ 496 (899)
.-|-|+ ....+|+|||..-.-+ .|++..|. +.+.+..++|+ ..+.+--|+...+++. |++.
T Consensus 55 ~~~~~~---~~~~fN~~S~~ql~~~-L~~~lg~~~~~~t~~G~~std~~vL~~l~~p~~~~ileyr~l~K~~s-t~~~-- 127 (429)
T cd08643 55 APYTKI---KLVTFNPSSRKHIAKR-LKAKYGWEPQEFTESGEPKVDEDVLSKLDYPEAKLLAEYLLVQKRLG-QLAD-- 127 (429)
T ss_pred CCcccc---CCccCCCCCHHHHHHH-HHHhcCCCCCCcCCCCCCCcCHHHHHhccchHHHHHHHHHHHHHHHH-HHHh--
Confidence 345555 3456999999655333 13333332 12455566665 2333344444445553 5442
Q ss_pred ccCCCchhhhhcccccCCCCCeEeeeeeeccccccccccCccceecCCCCCccc-------ccccceEecCCCceEEEEe
Q psy15891 497 NKKDLPRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVG-------SELRAMIQAPDGYSIIGAD 569 (899)
Q Consensus 497 ~~~~l~~~~~~~~~~~~~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~G-------selRs~f~AppGy~~VgAD 569 (899)
....+++. ...+|||||+++|+||+||| ||+++||.++++ .++|++|+||+|++||++|
T Consensus 128 ~~~~~l~~--------v~~dgRIH~~~nq~gt~TGR------lSss~PNLQnIP~~~~~~G~~iR~~Fva~~G~~lv~aD 193 (429)
T cd08643 128 GNNAWLKL--------VHEDGRIHGAVNTNGAVTGR------ATHFSPNMAQVPAVGSPYGKECRELFGVPPGWSLVGAD 193 (429)
T ss_pred hHHHHHHH--------cCCCCceeeeEEeCCccccc------cccCCCcccCCCCCCcccchhhhheEecCCCCEEEEec
Confidence 00011111 24579999999999999999 999999977655 6899999999999999999
Q ss_pred ccchhhhhhhhcccccccccccccccccccccCccCCCCchhHHHHHHhc-cchhhhhHHHHHHhhcccHHHHHHHHHHh
Q psy15891 570 VDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVG-ISREHAKIINYARIYGAGERFAERLLKQF 648 (899)
Q Consensus 570 ~SqiELRIlal~gDA~~s~~~g~~Afg~m~LeG~K~~GtDlHs~tAs~lG-isR~~AKv~nyG~iYGaG~k~A~~La~q~ 648 (899)
||||||||+ ||+|+.....+|.. ...|.|+|+.||+.+| ..|+.||++|||++|||| +.+|++++
T Consensus 194 ySQiELRiL-----Ahls~d~~~~~l~~------~~~~~DiH~~ta~~~g~~~R~~AK~i~fGiiYG~g---~~~La~~l 259 (429)
T cd08643 194 ASGLELRCL-----AHYLARYDGGAYTR------KVLGGDIHWANAQAMGLLSRDGAKTFIYAFLYGAG---DEKLGQIV 259 (429)
T ss_pred HHHHHHHHH-----HHHhcccchHHHHh------hhcccchhHHHHHHhChHHHhhhHHHHHHHHHCCC---hhHHHHHh
Confidence 999999999 89987322233311 2568899999999999 579999999999999999 99999999
Q ss_pred CCCCCHHHHHH------------------------HHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCc
Q psy15891 649 NPEMSKSDAKS------------------------KARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTS 704 (899)
Q Consensus 649 n~~lS~eEA~~------------------------~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~ 704 (899)
| +|.+||++ ++++||+.||+++.|++. +.+.+.++|||+
T Consensus 260 g--~~~~eA~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~f~~~~P~v~~~~~~--~~~~a~~~Gyv~------------- 322 (429)
T cd08643 260 G--DDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVRANFLKGLPALGKLIKK--VKEAAKKRGHLV------------- 322 (429)
T ss_pred C--CCHHHHHhhhhcccccccchhhhhhhhhhHHHHHHHHHHhCccHHHHHHH--HHHHHHhCCcee-------------
Confidence 9 99888876 899999999999999987 889999999997
Q ss_pred ccccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-H
Q psy15891 705 VDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-R 783 (899)
Q Consensus 705 v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~ 783 (899)
|++|||+++ | + .|+++|++|||||||++|++|+.+ +
T Consensus 323 --tl~GRrr~~----------------------~-----------------~--~r~A~Nt~iQGsAADi~K~Ami~i~~ 359 (429)
T cd08643 323 --GLDGRRIRV----------------------R-----------------S--AHAALNTLLQSAGAILMKKWLVLLDD 359 (429)
T ss_pred --CCCCCcccC----------------------c-----------------h--HHHHhChhhhhHHHHHHHHHHHHHHH
Confidence 999999882 1 0 267999999999999999999999 5
Q ss_pred HhccCC------ceeEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCccccccccccc
Q psy15891 784 WLVSRD------TRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSGVEI 848 (899)
Q Consensus 784 ~L~~~~------~rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~vdi 848 (899)
.|.+.+ .+++++||||++|+||++++++++..++ +.|..+. ..+.+ .||+.|.+-.+-+|
T Consensus 360 ~l~~~g~~~~~~~~lvlqVHDElv~ev~~~~ae~v~~~v~--~~Me~a~--~~~~l-~VPL~v~~~iG~nW 425 (429)
T cd08643 360 ELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAV--EAAEKAG--EHFNF-RCPLAGEFDIGRNW 425 (429)
T ss_pred HHHhcCCCcCCCeEEEEEEccceEEEeCHHHHHHHHHHHH--HHHHHhh--hccCC-CcceEeecCccCCH
Confidence 555432 3899999999999999999999877655 4445553 22333 57887765544444
No 11
>cd08639 DNA_pol_A_Aquificae_like Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nucleas
Probab=100.00 E-value=2.9e-48 Score=423.63 Aligned_cols=243 Identities=25% Similarity=0.371 Sum_probs=209.4
Q ss_pred CCCCeEeeeeeeccccccccccCccceecCCCCCccc--ccccceEecCCCceEEEEeccchhhhhhhhcccccccc-cc
Q psy15891 514 RDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVG--SELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK-EH 590 (899)
Q Consensus 514 ~~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~G--selRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~-~~ 590 (899)
..+|||||+++++||+||| +|+++||.++++ ..+|++|+|||||+||++||||||+||+ ||+|+ ..
T Consensus 58 ~~~grih~~~~~~gt~TGR------lS~~~PnlQniP~~~~iR~~f~a~~G~~lv~aDysqiElRil-----A~ls~D~~ 126 (324)
T cd08639 58 PVTGRIHPSFNQIGAASGR------MSCSNPNLQQIPREREFRRCFVAPEGNKLIIADYSQIELRIA-----AEISGDER 126 (324)
T ss_pred CCCCceeeeEEecccceee------hhhccCccccCCCCcccceeEEcCCCCEEEEechhhhHHHHH-----HHHhCCHH
Confidence 3579999999999999999 999999999888 8999999999999999999999999999 99998 88
Q ss_pred cccccccccccCccCCCCchhHHHHHHh-ccc--------hhhhhHHHHHHhhcccHHHHHHHHHH----hCCCCCHHHH
Q psy15891 591 GATPLGWMTLSGQKSNATDMHSITAKAV-GIS--------REHAKIINYARIYGAGERFAERLLKQ----FNPEMSKSDA 657 (899)
Q Consensus 591 g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis--------R~~AKv~nyG~iYGaG~k~A~~La~q----~n~~lS~eEA 657 (899)
++++| .+|.|+|+.+|+.+ |++ |+.||++|||++|||| +.+|+++ +|..+|.+||
T Consensus 127 l~~~~---------~~g~Dih~~~A~~~~g~~~~~v~~~~R~~aK~~~fg~~YG~g---~~~L~~~l~~~~g~~~s~~eA 194 (324)
T cd08639 127 MISAY---------QKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMS---AKGLREYARTNYGVEMSLEEA 194 (324)
T ss_pred HHHHH---------hcCCCHhHHHHHHHhCCChhhCCHHHHHHhhhHHHHHHhCCc---hHHHHHHHhhhcCcCCCHHHH
Confidence 89999 77999999999988 876 9999999999999999 7788775 4567999999
Q ss_pred HHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCc
Q psy15891 658 KSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVT 737 (899)
Q Consensus 658 ~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~Prt 737 (899)
++++++||..||+++.|++. + .+.+.|||+ |++||||++
T Consensus 195 ~~~~~~f~~~~p~v~~~~~~--~--~a~~~g~v~---------------Tl~GRrr~~---------------------- 233 (324)
T cd08639 195 EKFRESFFFFYKGILRWHHR--L--KAKGPIEVR---------------TLLGRRRVF---------------------- 233 (324)
T ss_pred HHHHHHHHHhChhHHHHHHH--H--HHhhcCeEE---------------CCCCCeecc----------------------
Confidence 99999999999999999865 2 256778887 999999882
Q ss_pred cccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccCCceeEEEecceeEEecCcchHHHHHHHH
Q psy15891 738 PFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSRDTRFVISIHDEIRYLVPDEEKYETALAL 816 (899)
Q Consensus 738 P~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~~~rlvlsVHDEI~~eVpee~~~~aA~aL 816 (899)
+....|+++|++|||||||++|++|+.+ +.|.+...+++++|||||+++||++.+.+++..+
T Consensus 234 -----------------~~~~~r~avN~~IQGsaADi~K~ami~i~~~l~~~~~~lvl~VHDElv~ev~~~~~~~~~~~i 296 (324)
T cd08639 234 -----------------EYFTFTEALNYPIQGTGADILKLALALLVDRLKDLDAKIVLCVHDEIVLEVPEDEAEEAKKIL 296 (324)
T ss_pred -----------------cchhhhhHhhhhhhhHHHHHHHHHHHHHHHHHhcCCCeEEeeeceeeeeecCHHHHHHHHHHH
Confidence 1223578999999999999999999999 4555545699999999999999999999887765
Q ss_pred HHHHHHHHHHhhccCCCCCCCccccc
Q psy15891 817 HVTNLLTRAFCIKKLDMTDIPLSISF 842 (899)
Q Consensus 817 qianl~tramf~~~lg~~dlP~svAf 842 (899)
+ ..|.+++. ..+.+||+.|..
T Consensus 297 ~--~~Me~a~~---~~~~~VPl~v~~ 317 (324)
T cd08639 297 E--SSMEEAGK---RILKKVPVEVEV 317 (324)
T ss_pred H--HHHHHHHH---hcCCCCCeEEec
Confidence 4 55566642 112368887754
No 12
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=100.00 E-value=1.1e-47 Score=444.77 Aligned_cols=250 Identities=22% Similarity=0.294 Sum_probs=217.4
Q ss_pred CCCeEeeeeeeccccccccccCccceecCCCCCcccccccceEecCCCceEEEEeccchhhhhhhhcccccccc-ccccc
Q psy15891 515 DYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK-EHGAT 593 (899)
Q Consensus 515 ~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~GselRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~-~~g~~ 593 (899)
.+|||||.++++||+||| +|+++||.+++++.+|++|+|+|||+||++||||||+||+ ||+|+ ..+++
T Consensus 283 ~~grih~~~~~~gt~TGR------lss~~pnlQniP~~iR~~f~a~~G~~lv~aDysqiElRvl-----A~ls~D~~l~~ 351 (553)
T PRK14975 283 RDGRFHPEYVPGGVVTGR------WASRGPNAQQIPRDIRSAFVADPGWKLVVADASQIELRVL-----AAYSGDERMIE 351 (553)
T ss_pred cCCcccceeeecceeecc------cccCCCccccCCHHHhceEEcCCCCEEEEechhhhHHHHH-----HHHcCCHHHHH
Confidence 679999999999999999 9999999999999999999999999999999999999999 99998 88999
Q ss_pred ccccccccCccCCCCchhHHHHHHh-cc------chhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Q psy15891 594 PLGWMTLSGQKSNATDMHSITAKAV-GI------SREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYT 666 (899)
Q Consensus 594 Afg~m~LeG~K~~GtDlHs~tAs~l-Gi------sR~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~ 666 (899)
+| .+|.|+|+.||+.+ |+ .|+.||++|||++||+| +.+|++++| +.+||++++++||+
T Consensus 352 ~~---------~~g~Dih~~~A~~~~~~~~~~~~~R~~aK~~~~g~~YG~g---~~~l~~~~~---~~~ea~~~~~~~~~ 416 (553)
T PRK14975 352 AF---------RTGGDLHRLTASVGFGKPEEEKEERALAKAANFGAIYGAT---SKGLQEYAK---NYGEAARLLERLRR 416 (553)
T ss_pred HH---------hcCCCHHHHHHHHHhCCCccchhHHHHHHHHHHHhhhCCc---HHHHHHHcC---CHHHHHHHHHHHHH
Confidence 99 77999999999998 44 59999999999999999 999999997 88999999999999
Q ss_pred hChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCcccccccccc
Q psy15891 667 LTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSR 746 (899)
Q Consensus 667 ~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~ 746 (899)
.||+++.|++. +.+.+.+.|||+ |++||++++ |.+++....
T Consensus 417 ~~p~v~~~~~~--~~~~a~~~g~v~---------------T~~GR~~~~----------------------~~~~~~~~~ 457 (553)
T PRK14975 417 AYPRAVGWVER--AAREGERGGVVR---------------TLLGRTSPP----------------------PGFAWRARR 457 (553)
T ss_pred HCccHHHHHHH--HHHHHHHCCeEE---------------CCCCCeecC----------------------CCccccChh
Confidence 99999999988 889999999997 999999994 433332221
Q ss_pred ccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhc-cCCceeEEEecceeEEecCcchHHHHHHHHHHHHHHHH
Q psy15891 747 ALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLV-SRDTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTR 824 (899)
Q Consensus 747 aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~-~~~~rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tr 824 (899)
.++...|+++|++|||||||++|++|+.+ +.|. ....+++++|||||+++||++++.+++..++ +.|++
T Consensus 458 -------~~~~~~r~a~N~~iQGsaAdi~k~am~~~~~~l~~~~~~~lvl~vHDEl~~e~~~~~~~~~~~~i~--~~M~~ 528 (553)
T PRK14975 458 -------RARSRGRFTRNFPVQGTAADWAKLALALLRRRLAEGLDAELVFFVHDEVVVECPEEEAEEVAAAIE--EAMEE 528 (553)
T ss_pred -------HHhHhhhhhcCccchhHHHHHHHHHHHHHHHHHhhcCCcEEEEEecceeEEEecHHHHHHHHHHHH--HHHHH
Confidence 35677899999999999999999999999 5555 3345999999999999999999998877655 44555
Q ss_pred HHhhccCCCCCCCcccc
Q psy15891 825 AFCIKKLDMTDIPLSIS 841 (899)
Q Consensus 825 amf~~~lg~~dlP~svA 841 (899)
++ .+-+..||+.|.
T Consensus 529 a~---~~~~~~Vpl~v~ 542 (553)
T PRK14975 529 AG---RLLFGPVPFPVE 542 (553)
T ss_pred HH---hccCCCccEEEe
Confidence 53 221225777763
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=8e-46 Score=449.01 Aligned_cols=253 Identities=26% Similarity=0.422 Sum_probs=217.4
Q ss_pred CCCeEeeeeeeccccccccccCccceecCCCCCccc------ccccceEecCCCceEEEEeccchhhhhhhhcccccccc
Q psy15891 515 DYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVG------SELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK 588 (899)
Q Consensus 515 ~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~G------selRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~ 588 (899)
.+|||||+++++||+||| +|+++||.++++ ..+|+||+|++||.||++||||||+||+ ||+|+
T Consensus 603 ~~~rih~~~~~~~t~TGR------lss~~PnlQniP~~~~~~~~iR~~f~~~~G~~lv~~DysqiElRil-----A~ls~ 671 (880)
T PRK05755 603 DTGRIHTSFNQTVTATGR------LSSSDPNLQNIPIRTEEGRRIRKAFVAPEGYKLLSADYSQIELRIL-----AHLSG 671 (880)
T ss_pred CCCeecceEeecccceee------eeccCCCcccCCCCCccchhhhheEecCCCCEEEEechhhhHHHHH-----HHHcC
Confidence 446999999999999999 999999988766 5799999999999999999999999999 99998
Q ss_pred -cccccccccccccCccCCCCchhHHHHHHh-ccc--------hhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHH
Q psy15891 589 -EHGATPLGWMTLSGQKSNATDMHSITAKAV-GIS--------REHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAK 658 (899)
Q Consensus 589 -~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis--------R~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~ 658 (899)
..++++| .+|.|+|+.||+.+ |++ |+.||++|||++|||| +.+|++++| +|.+||+
T Consensus 672 D~~l~~~~---------~~g~Dih~~~A~~~~~~~~~~v~~~~R~~aK~~~fg~~YG~g---~~~la~~l~--is~~eA~ 737 (880)
T PRK05755 672 DEGLIEAF---------AEGEDIHTATASEVFGVPLEEVTSEQRRRAKAINFGIIYGMS---AFGLAQQLG--ISRKEAK 737 (880)
T ss_pred CHHHHHHH---------hcCCCHHHHHHHHHhCCChhhCCHHHHHHHHHHhcchhhCCC---hHHHHHHcC--CCHHHHH
Confidence 8899999 78999999999876 864 9999999999999999 999999999 9999999
Q ss_pred HHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCcc
Q psy15891 659 SKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTP 738 (899)
Q Consensus 659 ~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP 738 (899)
+++++||++||+++.|+++ +.+++++.|||+ |++||||+ +|
T Consensus 738 ~~~~~~~~~~p~v~~~~~~--~~~~a~~~g~v~---------------t~~GR~r~----------------------~p 778 (880)
T PRK05755 738 EYIDRYFERYPGVKEYMER--TVEQAREKGYVE---------------TLFGRRRY----------------------LP 778 (880)
T ss_pred HHHHHHHHHCccHHHHHHH--HHHHHHHcCCEE---------------CCCCCeEe----------------------CC
Confidence 9999999999999999988 889999999997 99999999 44
Q ss_pred ccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHH-HHhccC-C-ceeEEEecceeEEecCcchHHHHHHH
Q psy15891 739 FLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM-RWLVSR-D-TRFVISIHDEIRYLVPDEEKYETALA 815 (899)
Q Consensus 739 ~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m-~~L~~~-~-~rlvlsVHDEI~~eVpee~~~~aA~a 815 (899)
.+++... ..++.+.|+++|++|||||||++|++|+.+ +++.+. + .+++++||||++++||++.+.+++..
T Consensus 779 ~~~~~~~-------~~~~~~~r~a~N~~iQgsaAdi~k~am~~~~~~l~~~~~~~~l~l~vHDel~~ev~~~~~~~~~~~ 851 (880)
T PRK05755 779 DINSRNG-------NRRAFAERAAINAPIQGSAADIIKLAMIRVDKALKEEGLKSRMLLQVHDELVFEVPEDELEEVKKL 851 (880)
T ss_pred cccCCCH-------HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEEEEcceeEEEeCHHHHHHHHHH
Confidence 4433221 146678999999999999999999999999 555432 2 49999999999999999999988765
Q ss_pred HHHHHHHHHHHhhccCCCCCCCccccccccc
Q psy15891 816 LHVTNLLTRAFCIKKLDMTDIPLSISFFSGV 846 (899)
Q Consensus 816 Lqianl~tramf~~~lg~~dlP~svAffs~v 846 (899)
++ ++|..++ .+ +||..|.+--+.
T Consensus 852 ~~--~~me~~~-----~l-~vpl~v~~~~g~ 874 (880)
T PRK05755 852 VK--EVMENAV-----EL-SVPLVVDVGVGD 874 (880)
T ss_pred HH--HHHhCcc-----cC-CceEEEeCCcCC
Confidence 43 4444442 22 578777554333
No 14
>cd08642 DNA_pol_A_pol_I_A Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. P
Probab=100.00 E-value=2.4e-44 Score=398.22 Aligned_cols=290 Identities=14% Similarity=0.165 Sum_probs=215.5
Q ss_pred CCCCCcc-hhhhhHhhcCCCCC--CchH-HHHHHH-HHhhhhhhhhhhhhhhcceeEecccCCCchhhhhcccccCCCCC
Q psy15891 443 NVGNPLS-RDFINKFSDNSLAG--VDIG-AKRIIE-ISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIESEGRDYG 517 (899)
Q Consensus 443 nvg~pls-K~fl~~fe~g~L~s--~~~~-a~~~le-~~~~~syW~s~r~Ri~~q~vv~~~~~~l~~~~~~~~~~~~~~dG 517 (899)
|++||.. +.+| |+++.|.+ ...+ ..+.|. ....+..-+.+|..-...-+.|.+ .|++. ...+|
T Consensus 28 n~~SpkQL~~~L--f~~~~l~~~~~k~ttvl~~l~~~~~~~~~iL~~R~~~k~~s~t~~~--~l~~~--------~~~~g 95 (378)
T cd08642 28 NPNSPAQLKDWL--NEQGGEVDSLLKKDVVALLLKTAPGDVKRVLELRQELSKTSVKKYE--AMERA--------VCSDG 95 (378)
T ss_pred CCCCHHHHHHHH--HHcCCCCCCCchhHHHHHHhcccCcHHHHHHHHHHHHhhccHHHHH--HHHHH--------cCCCC
Confidence 7778754 4455 67777754 2122 112221 222334444555553322223332 12222 34579
Q ss_pred eEeeeeeecc-ccccccccCccceecCCCCCcccc----------------------------------cccceEecCCC
Q psy15891 518 VILPQLIVSG-TLTRRAVEATWMTASNAVGERVGS----------------------------------ELRAMIQAPDG 562 (899)
Q Consensus 518 rIhp~~~~~G-TvTGRa~e~tWLSaSnP~~~~~Gs----------------------------------elRs~f~AppG 562 (899)
|||++++++| |.||| +|+++||.++++. .+|++|+||+|
T Consensus 96 Rih~~~~~~gat~TGR------lss~~pnlQNiP~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~iR~aFva~~G 169 (378)
T cd08642 96 RVRGLLQFYGANRTGR------WAGRLVQVQNLPRNYLKDLDLARELVKSGDFDALELLYGSVPDVLSQLIRTAFIPSEG 169 (378)
T ss_pred ceeeeeeeecchhccc------cccCCCCcccCCCCcccchHHHHHHhhccchhhhhhhccccccHHHHHhHHheecCCC
Confidence 9999999999 99999 9999999887765 59999999999
Q ss_pred ceEEEEeccchhhhhhhhcccccccc-cccccccccccccCccCCCCchhHHHHHHh-ccc----------hhhhhHHHH
Q psy15891 563 YSIIGADVDSQELWIASVIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GIS----------REHAKIINY 630 (899)
Q Consensus 563 y~~VgAD~SqiELRIlal~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gis----------R~~AKv~ny 630 (899)
+.||++||||||+||+ ||+|+ ..++++| .+|.|+|+.||+.+ |++ |+.||++||
T Consensus 170 ~~lvsaDySQIElRVL-----AhlS~D~~li~af---------~~g~Dih~~tAs~if~vp~e~~~v~~~~R~~AK~vnf 235 (378)
T cd08642 170 HRFIVSDFSAIEARVI-----AWLAGEQWRLDVF---------ATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAEL 235 (378)
T ss_pred CEEEEecHHHHHHHHH-----HHHhCCHHHHHHH---------hcCCChHHHHHHHHhCCChhhcccCHHHHHHhhhhhc
Confidence 9999999999999999 99999 9999999 78999999999998 542 999999999
Q ss_pred HHhhcccHHHHHHH----HHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhh-hHHHHHHhcCeeecchhhhhcccCCcc
Q psy15891 631 ARIYGAGERFAERL----LKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKD-GHLEELIKRVYSKYEAREVCSAYNTSV 705 (899)
Q Consensus 631 G~iYGaG~k~A~~L----a~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~-e~~~~a~e~GyV~~~~~~~~~~~~~~v 705 (899)
|++||+| +.+| ++++| +|.+||++++++||+.||+++.|+... +..+++.+.||+.
T Consensus 236 GiiYG~g---~~~L~~~aa~~lg--is~~EA~~~i~~yf~~yP~v~~~~~~~~~~~~~a~~~g~v~-------------- 296 (378)
T cd08642 236 ALGYGGS---VGALKAMGALEMG--LTEDELPGIVDAWRNANPNIVKLWWDVDKAAKKAVKERKTV-------------- 296 (378)
T ss_pred cceeccc---hHHHHHhhhhhcC--CCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHHHHcCceE--------------
Confidence 9999999 8888 77888 999999999999999999999988762 2356666777765
Q ss_pred cccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHHHHHHHh
Q psy15891 706 DKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCMRWL 785 (899)
Q Consensus 706 ~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklamv~m~~L 785 (899)
|+ | +.++|.+|||||||++|.+|+.++.
T Consensus 297 -t~-g-------------------------------------------------~r~~~n~IQGtAADi~k~Ami~l~~- 324 (378)
T cd08642 297 -KL-G-------------------------------------------------GKLVENIVQAIARDCLAEAMLRLEK- 324 (378)
T ss_pred -ee-h-------------------------------------------------HhhhhcccchhHHHHHHHHHHHHHh-
Confidence 22 1 1134559999999999999999864
Q ss_pred ccCCceeEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccCCCCCCCcccccccc
Q psy15891 786 VSRDTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFFSG 845 (899)
Q Consensus 786 ~~~~~rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~lg~~dlP~svAffs~ 845 (899)
...+++++||||++|+||+. .. .+-.+..+|+.... +- ..||+..+=|++
T Consensus 325 --~g~~ivLqVHDElv~Evp~~--~~--~~~~v~~iM~~~p~-wa---~~lPl~a~g~~~ 374 (378)
T cd08642 325 --AGYDIVMHVHDEVVIEVPEG--EG--SLEEVNEIMAQPPP-WA---PGLPLNADGFES 374 (378)
T ss_pred --cCCeEEEEECceeEEeeccc--hh--HHHHHHHHHccCCc-cc---cCCccccccccc
Confidence 23699999999999999982 11 12345666665532 11 357888776553
No 15
>smart00482 POLAc DNA polymerase A domain.
Probab=100.00 E-value=1e-42 Score=358.15 Aligned_cols=193 Identities=32% Similarity=0.502 Sum_probs=170.6
Q ss_pred cccccceEecCCCceEEEEeccchhhhhhhhcccccccc-cccccccccccccCccCCCCchhHHHHHHh-cc-------
Q psy15891 550 GSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK-EHGATPLGWMTLSGQKSNATDMHSITAKAV-GI------- 620 (899)
Q Consensus 550 GselRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~-~~g~~Afg~m~LeG~K~~GtDlHs~tAs~l-Gi------- 620 (899)
|+++|+||+|||||.+|++||||||+||+ ||+++ ..+.++| ..|.|+|+.+|+.+ |+
T Consensus 1 g~~iR~~f~a~~G~~lv~~DysqiElRil-----A~ls~D~~l~~~~---------~~g~D~h~~~A~~~~g~~~~~v~~ 66 (206)
T smart00482 1 GREIRRAFVAPPGYVLVSADYSQIELRIL-----AHLSGDENLLEAF---------NNGGDIHSKTAAQVFGVPEEEVTK 66 (206)
T ss_pred CchhhheeeCCCCCEEEEeeHHHHHHHHH-----HHHcCCHHHHHHH---------hcCCCHHHHHHHHHhCCChhhCCH
Confidence 57899999999999999999999999999 99998 8888998 77899999999976 74
Q ss_pred -chhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhhhHHHHHHhcCeeecchhhhhc
Q psy15891 621 -SREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCS 699 (899)
Q Consensus 621 -sR~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~e~~~~a~e~GyV~~~~~~~~~ 699 (899)
.|+.||++|||++||+| +.+|++++| +|.+||++++++|++.||+++.|+++ +.+.+.+.|||+
T Consensus 67 ~~R~~aK~~~~g~~YG~g---~~~la~~lg--~s~~ea~~~~~~f~~~~p~v~~~~~~--~~~~a~~~g~v~-------- 131 (206)
T smart00482 67 ELRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKELIKAYFARFPGVKRYIKR--TLEEARRKGYVT-------- 131 (206)
T ss_pred HHHHHHhHHHHHhhhccc---hhHHHHHcC--CCHHHHHHHHHHHHHHCccHHHHHHH--HHHHHHhCCEEE--------
Confidence 49999999999999999 999999999 99999999999999999999999987 889999999997
Q ss_pred ccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccccchhhhhhhhhhhchHHHHHHHHHH
Q psy15891 700 AYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLML 779 (899)
Q Consensus 700 ~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~~~~~~rsavN~vIQGSAADilklam 779 (899)
|++||++++ |.+++... ..++...|+++|++|||||||++|++|
T Consensus 132 -------t~~Gr~r~~----------------------~~~~~~~~-------~~~~~~~r~a~N~~iQgsaAdi~k~am 175 (206)
T smart00482 132 -------TLFGRRRYI----------------------PDIDSRNP-------VLRAAAERAAVNAPIQGSAADILKLAM 175 (206)
T ss_pred -------ecCCCeeeC----------------------CCCCCCCH-------HHHhHHHHHHHhHhhhhHHHHHHHHHH
Confidence 999999994 43332211 135567899999999999999999999
Q ss_pred HHHH-HhccC--CceeEEEecceeEEecCcc
Q psy15891 780 VCMR-WLVSR--DTRFVISIHDEIRYLVPDE 807 (899)
Q Consensus 780 v~m~-~L~~~--~~rlvlsVHDEI~~eVpee 807 (899)
+.+. .+.+. ..+++++||||++++||++
T Consensus 176 ~~~~~~~~~~~~~~~~vl~vHDElv~evp~~ 206 (206)
T smart00482 176 IKMDEALKEKGLRARLLLQVHDELVFEVPEE 206 (206)
T ss_pred HHHHHHHHhcCCCceEEEeeceeEEeecCCC
Confidence 9994 44443 3499999999999999975
No 16
>KOG3657|consensus
Probab=99.49 E-value=4.1e-16 Score=181.79 Aligned_cols=345 Identities=8% Similarity=-0.118 Sum_probs=249.2
Q ss_pred cCCCCCCCCCCCCcchhhhhHhhcCCCCCCchHHHHHHHHHhhhhhhhhhhhhhhcceeEecccCCCchhhhhcccccCC
Q psy15891 435 PHKDGEHLNVGNPLSRDFINKFSDNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIESEGR 514 (899)
Q Consensus 435 PHkdG~~~nvg~plsK~fl~~fe~g~L~s~~~~a~~~le~~~~~syW~s~r~Ri~~q~vv~~~~~~l~~~~~~~~~~~~~ 514 (899)
+|++++. +.+|++.++.+|+.+++.+.+..+++...+-..|.||..+ .+ .
T Consensus 491 ~~~~~sp---~isl~~~i~p~l~~l~we~~pl~~sr~~gwgflvp~~~~~-----------e~------~---------- 540 (1075)
T KOG3657|consen 491 SDEVWSP---HISLKSRIIPKLFGLVWEGFPLHYSREKGWGFLVPNRKDV-----------EK------L---------- 540 (1075)
T ss_pred CCCCCCC---CCchhhhhHHHHHhhccCCchhhhhhhcCceeecCCcchH-----------HH------H----------
Confidence 4888886 9999999999999999999888888888888888888876 00 0
Q ss_pred CCCeEeeeeeeccccccccccCccceecCCCCCcccccccceEecCCCceEEEEeccchhhhhhhhcccccccccccccc
Q psy15891 515 DYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATP 594 (899)
Q Consensus 515 ~dGrIhp~~~~~GTvTGRa~e~tWLSaSnP~~~~~GselRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~s~~~g~~A 594 (899)
-+ |+ +|+..++. ...|..++.++.|+++|+..- +..+|..+ +. ..
T Consensus 541 -~~---------------A~--~~~~~sD~--------~~d~~~~~~e~~~~~~~~~~~-----~~~~~~~~-~~---q~ 585 (1075)
T KOG3657|consen 541 -LQ---------------AD--PNFHEIDA--------KIDFLPDEAEKKFPNRSFYET-----LQNNVGML-GT---QP 585 (1075)
T ss_pred -hh---------------cc--cchhhcch--------hhhcccchhhhcccccchhhH-----HhccCccc-cc---cC
Confidence 01 22 56777765 355666777999999999876 23344444 22 22
Q ss_pred cccccccCccCCCCchhHHHHHHhccchhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHH
Q psy15891 595 LGWMTLSGQKSNATDMHSITAKAVGISREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLY 674 (899)
Q Consensus 595 fg~m~LeG~K~~GtDlHs~tAs~lGisR~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~ 674 (899)
.|.|+++|.+ ++|.|.+++...|.+++.+++++++++||++.+.- +...+.++..-.-|+.+++..++...+++..=
T Consensus 586 ~g~g~~~~~~--~~~~f~Klph~~G~S~nvg~pltk~fl~~~~~~vl-~~~~~~~~~~r~ldi~~~~s~w~s~~~ri~Sq 662 (1075)
T KOG3657|consen 586 DGKGVELDEA--GLCRFFKLPHPNGPSFNVGNPLTKDFLKKFEEGVL-RSGRYEEYADRVLDINQMTSFWRSARDRICSQ 662 (1075)
T ss_pred CCcceeeccc--ceeeeeecCCCCCCCCccCCcchHhhhhHHHhccc-ccccccchHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 5778888854 49999999999999999999999999999984422 11222332233446667777777777766541
Q ss_pred HhhhhHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCccc
Q psy15891 675 RLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSED 754 (899)
Q Consensus 675 ~~~~e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~~~ 754 (899)
+.. ++. ...+ ++...+ .|++.+..+.=..+++|+...... +..+.-..
T Consensus 663 mvv-----------wlp--~~~l-------------P~~~~~-----~~~k~~~~gaI~p~vvp~gtitrr-ave~tw~t 710 (1075)
T KOG3657|consen 663 MVV-----------WLP--SATL-------------PNAFNL-----NNEKEMIYGAIAPQVVPAGTITRR-AVEPTWLT 710 (1075)
T ss_pred eeE-----------ecc--cccC-------------chhhhh-----cccchhhhhccCccccccchhhhh-hhhhhhhh
Confidence 100 000 0000 001110 466666666666777887544443 33332212
Q ss_pred cchhhhhhhhhhhchHHHHHHHHHHHHHHHhccCC---ceeEEEecceeEEecCcchHHHHHHHHHHHHHHHHHHhhccC
Q psy15891 755 DSKFIQTRINWVVQSGAVDFLHLMLVCMRWLVSRD---TRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKL 831 (899)
Q Consensus 755 ~~~~~rsavN~vIQGSAADilklamv~m~~L~~~~---~rlvlsVHDEI~~eVpee~~~~aA~aLqianl~tramf~~~l 831 (899)
.....+.++||-||+.+.+..+..+|.++...+.+ +++-..+||+ .+.+.++-.|++++.++|..+++.+
T Consensus 711 asNs~~~Rigselkamvqappgy~LVgaDvdsqElwiaa~lgda~~~~-------~hg~ta~gwM~Lag~ks~gtdlhs~ 783 (1075)
T KOG3657|consen 711 ASNARPDRIGSELKAMVQAPPGYRLVGADVDSQELWIAALLGDASAEG-------VHGKTAFGWMTLAGSKSDGTDLHSK 783 (1075)
T ss_pred hcccChhhhhHHHHHhhcCCCcceEeeccccHHHHHHHHHhhhhhhhc-------ccCcchhhhhhhcCccccCchHhHh
Confidence 22333489999999999999999999985544432 2677788888 6678888999999999999999999
Q ss_pred CCCCCCcccccccccccccccccccCCCccCCCCccCCCccccCCCCcccCHHHHH--HhcCC
Q psy15891 832 DMTDIPLSISFFSGVEIDKVLRKESDNDCKTPSNPYGLCKGYGIPLGEILDIYQTI--DKANG 892 (899)
Q Consensus 832 g~~dlP~svAffs~vdid~vlRKEv~~dc~TPSnp~~~~~~y~Ip~Gesldi~~~l--~~~~g 892 (899)
+...||+|+++|+.+|+++|+|+-+.|+|++|++-.| |++||-+.+...+ +.|.|
T Consensus 784 ta~~lgiSr~hakv~Ny~riygag~~fa~~ll~~fnp------~l~~~Ea~~~A~~l~~~tkG 840 (1075)
T KOG3657|consen 784 TASQLGISRNHAKVFNYARIYGAGQTFAEKLLMRFNP------SLTQSEAKSKASQLFKLTKG 840 (1075)
T ss_pred hhhhccccHhhhhhccHHHHhcCCcchHHHhHHhhCC------CCchHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999988 9999888876544 45556
No 17
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=98.10 E-value=6.5e-08 Score=113.58 Aligned_cols=319 Identities=18% Similarity=0.069 Sum_probs=223.0
Q ss_pred ccccccccccCccceecCCCCCcccccccceEecCCCceEEEEeccchhhhhhhhcccccc-cc-cccccccccccccC-
Q psy15891 526 SGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYC-AK-EHGATPLGWMTLSG- 602 (899)
Q Consensus 526 ~GTvTGRa~e~tWLSaSnP~~~~~GselRs~f~AppGy~~VgAD~SqiELRIlal~gDA~~-s~-~~g~~Afg~m~LeG- 602 (899)
.+++|.++.+..|+...+.... ++..+...-..+.+..+||.+++..| -++.+-++|- +. .++.....|+..++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~-~a~~~et~~l~~~~~~lvg~s~~~~~--~~~yi~~~~~~~~~~~~~~l~~~l~~~~~ 79 (593)
T COG0749 3 YGTITDLAVLNAWLTKLNAAAN-IAFDTETDGLDPHGADLVGLSVASEE--EAAYIPLLHGPEQLNVLAALKPLLEDEGI 79 (593)
T ss_pred chhhhHHHHHHHHHHHHhhccc-ceeeccccccCcccCCeeEEEeeccc--cceeEeeccchhhhhhHHHHHHHhhCccc
Confidence 4677888888889988887666 77777777778899999999999999 2212223330 12 34444557887777
Q ss_pred -ccCCCCchhHHHHHHhcc---chhhhhHHHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHhhh
Q psy15891 603 -QKSNATDMHSITAKAVGI---SREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKD 678 (899)
Q Consensus 603 -~K~~GtDlHs~tAs~lGi---sR~~AKv~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~~~ 678 (899)
....+.+.|..+....|| .+.++..++|.+.||.|..+...|++.+. +.+...-+.+..+-... +.....
T Consensus 80 ~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l-~~~~~~~~~i~~kg~~~-~~~~~~---- 153 (593)
T COG0749 80 KKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYL-GLETITFEDIAGKGKKQ-LTFADV---- 153 (593)
T ss_pred chhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhc-CCccchhHHhhcccccc-Cccccc----
Confidence 334678888888888894 68999999999999999655667777762 34433333332222211 111100
Q ss_pred hHHHHHHhcCeeecchhhhhcccCCcccccCCCccccCCCchhhhhhhHHHhhccCCCccccccccccccCCCc-cccch
Q psy15891 679 GHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVS-EDDSK 757 (899)
Q Consensus 679 e~~~~a~e~GyV~~~~~~~~~~~~~~v~tl~GRrr~~gGteS~~Fn~LE~iA~~~~PrtP~Lg~~i~~aL~~~~-~~~~~ 757 (899)
......++.+.++..+..|+.......+..|.| +.+.+.++.-. .+-+.
T Consensus 154 -----------------------------~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L-~~l~~~iE~Pl~~VLa~ 203 (593)
T COG0749 154 -----------------------------KLEKATEYAAEDADATLRLESILEPELLKTPVL-LELYEEIEMPLVRVLAR 203 (593)
T ss_pred -----------------------------hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH-HHHHHHHhccHHHHHHH
Confidence 011122566777888888888887777777766 44443333221 13455
Q ss_pred hhhhhhhhhhchHHHHHHHHHHHHHHHhccCC---c-eeEEEecceeEEecCcchHHH-HHHHHHHHHHHHHHHhhccCC
Q psy15891 758 FIQTRINWVVQSGAVDFLHLMLVCMRWLVSRD---T-RFVISIHDEIRYLVPDEEKYE-TALALHVTNLLTRAFCIKKLD 832 (899)
Q Consensus 758 ~~rsavN~vIQGSAADilklamv~m~~L~~~~---~-rlvlsVHDEI~~eVpee~~~~-aA~aLqianl~tramf~~~lg 832 (899)
.++..+++=+|.......++....+..-.+.| + +|.|.-|+.+....=+..... .+...+.++.+|++++.++|.
T Consensus 204 ME~~Gi~vD~~~L~~l~~el~~~l~~le~eiy~laG~~FNi~SPKQL~~ILfeKl~Lp~~~kKtktG~yST~~~vLe~L~ 283 (593)
T COG0749 204 MERNGIKVDVQYLKELSKELGCELAELEEEIYELAGEEFNINSPKQLGEILFEKLGLPPGLKKTKTGNYSTDAEVLEKLA 283 (593)
T ss_pred hHhcCceecHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCccccccCCCCCccHHHHHHHHh
Confidence 66667899899888877666655554333333 3 899999999877766665555 455667788999999999998
Q ss_pred -CCCCCcccccccccccccccccccCCCccCCCCccCCCccccCCCCcccCHHHHHHhc
Q psy15891 833 -MTDIPLSISFFSGVEIDKVLRKESDNDCKTPSNPYGLCKGYGIPLGEILDIYQTIDKA 890 (899)
Q Consensus 833 -~~dlP~svAffs~vdid~vlRKEv~~dc~TPSnp~~~~~~y~Ip~Gesldi~~~l~~~ 890 (899)
...+|.-|.+|.+++...+-++|.-++||+|++ .- |+++...++.++....
T Consensus 284 ~~h~i~~~iL~~Rql~KLksTY~d~L~~~i~~~t-~R------IHTsf~Q~~t~TGRLS 335 (593)
T COG0749 284 DDHPLPKLILEYRQLAKLKSTYTDGLPKLINPDT-GR------IHTSFNQTGTATGRLS 335 (593)
T ss_pred hcCccHHHHHHHHHHHHHHHHhhhccHHhhCCCC-Cc------cCcchHHHHHHhhccc
Confidence 589999999999999999999999999999997 22 9999988888776544
No 18
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=91.60 E-value=0.14 Score=50.14 Aligned_cols=56 Identities=25% Similarity=0.352 Sum_probs=39.5
Q ss_pred ccHHHHHHHhcCC-ccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEG-KVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g-~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
.||.++..-|| | ..++| .+.+.+... .+.--.+.+.|||.||.+|++||.+|.|..
T Consensus 119 ~~L~~L~~~~l-~~~~~~~--~~~~~~~~~--~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 119 YSLKDLAEEYL-GNIDLDK--KEQMSDWRK--ARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp SSHHHHHHHHH-SEEE-GH--CCTTSSTTT--SSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred ccHHHHHHHHh-hhccCcH--HHhhccCCc--CCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 79999999999 6 44444 445554441 112234556999999999999999998863
No 19
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=84.15 E-value=2.1 Score=44.40 Aligned_cols=51 Identities=27% Similarity=0.326 Sum_probs=40.1
Q ss_pred ccccHHHHHHHhcCCccCCcccccc--cc-cCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHH
Q psy15891 11 SLNSLSEVYKLYCEGKVLDKTDRNI--FV-EGSLEDIENNWHNLMTYCAKDTLATFEVIQALF 70 (899)
Q Consensus 11 S~NsL~dV~~~~c~g~~~dK~~Rd~--F~-~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~ 70 (899)
..-||+++.+.++ |.+++|..+-- -. ..|.++| .|+|.||.+..+||.+|.
T Consensus 139 ~~~sL~~l~~~~l-g~~l~K~~q~SdW~~rpLs~~Qi--------~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 139 KTKGLADLVQEVL-GKPLDKSEQCSNWERRPLREEQI--------LYAALDAYCLLEVFDKLL 192 (193)
T ss_pred ccCCHHHHHHHHh-CCCcCcccccCCCCCCCCCHHHH--------HHHHHHHHHHHHHHHHHh
Confidence 4459999999999 99999987622 21 2355554 899999999999999874
No 20
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=82.59 E-value=1.8 Score=46.20 Aligned_cols=53 Identities=30% Similarity=0.488 Sum_probs=36.5
Q ss_pred ccccHHHHHHHhcCCccC----C-cccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHH
Q psy15891 11 SLNSLSEVYKLYCEGKVL----D-KTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPL 72 (899)
Q Consensus 11 S~NsL~dV~~~~c~g~~~----d-K~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~ 72 (899)
.--||.+++++- |+|- | -+.-+.|.+|++++|+ +||.+||.+|+.||.+.-.+
T Consensus 115 ~~~sLd~la~~l--giPgK~~idGs~V~~~y~~g~i~~I~-------~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 115 ARTSLDELAALL--GIPGKDDIDGSQVAELYQEGDIDEIR-------EYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred ccCCHHHHHHHc--CCCCCCCCCHHHHHHHHHcCCHHHHH-------HHHHHHHHHHHHHHHHHHHh
Confidence 345677777663 5542 2 2345667777776655 79999999999999886543
No 21
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=82.29 E-value=2.8 Score=41.77 Aligned_cols=49 Identities=29% Similarity=0.323 Sum_probs=38.5
Q ss_pred ccHHHHHHHhcCCccCC--ccc-ccccccC--CHHHHHHHHHHHHHHhHHhHHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLD--KTD-RNIFVEG--SLEDIENNWHNLMTYCAKDTLATFEVIQALF 70 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~d--K~~-Rd~F~~~--~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~ 70 (899)
.||++++..|+ |..++ |.. +..+... |.++| .|||.||..+++||.++.
T Consensus 116 ~~l~~l~~~~l-~~~~~k~k~~~~s~W~~rpLt~~qi--------~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 116 VSLARLVEEVL-GLPLSKPKKVRCSNWEARPLSKEQI--------LYAATDAYASLELYRKLL 169 (170)
T ss_pred ccHHHHHHHHc-CcccCCCCCcccCCCCCCCCCHHHH--------HHHHHHHHHHHHHHHHHh
Confidence 59999999999 88888 443 4455443 44554 899999999999999875
No 22
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=79.98 E-value=2 Score=44.46 Aligned_cols=51 Identities=22% Similarity=0.283 Sum_probs=33.9
Q ss_pred ccHHHHHHHhcCCccCCc---ccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDK---TDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQAL 69 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK---~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l 69 (899)
-+|..|++.++|..+.|- +.-+.|.+++ +++.+..||..||..|.+++.++
T Consensus 142 y~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~------~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 142 YTLERVYEELFGIEKEDVPGEEIAEAWDSGE------NLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CcHHHHHHHHhCCCCCcCCHHHHHHHHhCCC------chHHHHHHhHHHHHHHHHHHhhC
Confidence 379999998883322221 1122222221 48889999999999999998753
No 23
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=78.36 E-value=4.6 Score=40.41 Aligned_cols=50 Identities=26% Similarity=0.295 Sum_probs=37.6
Q ss_pred ccHHHHHHHhcCCccCCccccc-ccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRN-IFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQAL 69 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd-~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l 69 (899)
.||+++.+.|+ |..+||..+- .....++. ++-+.|+|.||.++.+||.+|
T Consensus 109 ~~L~~l~~~~l-g~~l~K~~~~s~W~~rpLt------~~qi~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 109 WSLASLVEHFL-GKTLDKSISCADWSYRPLT------EDQKLYAAADVYALLIIYTKL 159 (161)
T ss_pred chHHHHHHHHh-CCCCCccceeccCCCCCCC------HHHHHHHHHHHHHHHHHHHHH
Confidence 59999999999 8899987653 33222221 233489999999999999987
No 24
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=78.25 E-value=2.9 Score=44.10 Aligned_cols=45 Identities=27% Similarity=0.396 Sum_probs=33.0
Q ss_pred cHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHH
Q psy15891 14 SLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQ 67 (899)
Q Consensus 14 sL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~ 67 (899)
+|..|++... |. .|..+ .+.+.+. +.+.|..||..||..|.++.+
T Consensus 158 ~L~~Va~~~l-g~--~K~~~----~~~i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 158 TLDAVAKALL-GE--GKVEL----EKNISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cHHHHHHHhc-CC--CcccC----Cchhhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 7999999888 43 22222 1233343 789999999999999999875
No 25
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=78.10 E-value=3.1 Score=44.23 Aligned_cols=56 Identities=23% Similarity=0.296 Sum_probs=36.9
Q ss_pred ccHHHHHHHhcCCccCCcccccccc--cCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFV--EGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPL 72 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~--~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~ 72 (899)
-+|..|++...+..+.|=+..+++. .++. +.+..|+.||..|+..|.+++.++.-+
T Consensus 169 y~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~----~~~~~l~~Y~~~Da~l~l~L~~kl~~~ 226 (230)
T cd05777 169 YSLNSVSAHFLGEQKEDVHYSIITDLQNGNP----ETRRRLAVYCLKDAYLPLRLLDKLMCL 226 (230)
T ss_pred CcHHHHHHHHhCCCCCCCCHHHHHHHHccCH----hHhHHHHHhhHHHHHHHHHHHHHHhhH
Confidence 4789999888843333222222211 1222 236789999999999999999998654
No 26
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=77.41 E-value=2 Score=44.51 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=20.8
Q ss_pred HHHHHHHHhHHhHHHHHHHHHHH
Q psy15891 47 NWHNLMTYCAKDTLATFEVIQAL 69 (899)
Q Consensus 47 ~f~~Lm~YCA~DV~aT~~v~~~l 69 (899)
+.+.+..||..|+..|..||.++
T Consensus 166 ~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 166 KRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhC
Confidence 56899999999999999999864
No 27
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=76.85 E-value=3 Score=44.04 Aligned_cols=48 Identities=27% Similarity=0.475 Sum_probs=31.2
Q ss_pred ccccHHHHHHHhcCCcc--CC---cccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHH
Q psy15891 11 SLNSLSEVYKLYCEGKV--LD---KTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQ 67 (899)
Q Consensus 11 S~NsL~dV~~~~c~g~~--~d---K~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~ 67 (899)
.--+|.+|+++ | |++ .| ++.-+.|-+| +.+.+..||..||..|..||-
T Consensus 155 ~~~~L~~va~~-l-G~~~K~d~~G~~v~~~y~~g-------~~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 155 ARASLDLLAKL-L-GIPGKMDVDGSQVWELYAEG-------KLDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred CCCCHHHHHHH-h-CCCCCcCCCHHHHHHHHHcC-------ChHHHHHHHHHHHHHHHHHHh
Confidence 34589999985 6 442 11 1222333332 356688999999999999985
No 28
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=72.36 E-value=4.4 Score=42.12 Aligned_cols=57 Identities=18% Similarity=0.310 Sum_probs=41.9
Q ss_pred ccHHHHHHHhcCCccCCcc---------cccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHhhhh
Q psy15891 13 NSLSEVYKLYCEGKVLDKT---------DRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLFLER 76 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~---------~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F~~~ 76 (899)
.||+++.+-|. |.+++|. .+..|..-++. ++-+.|||.||..+.++|..+...+.++
T Consensus 115 ~~L~~l~~~~l-~~~~~k~~~~~~~~~~~~s~W~~RPLt------~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 115 ISLVQLLDKYL-YISISLKEDVKKLMREDPKFWALRPLT------EDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred ccHHHHHHHhh-CCChHHHHHHHHHHhcCchhhhcCCCC------HHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 48999999998 8888752 22344333321 3456999999999999999999999433
No 29
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=68.75 E-value=6.3 Score=40.40 Aligned_cols=50 Identities=18% Similarity=0.104 Sum_probs=32.9
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVI 66 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~ 66 (899)
-||.+|++.+++..+++=+..+++.-.. .++.+.+..||..||..|.+++
T Consensus 149 y~L~~v~~~~l~~~k~~~~~~~~~~~~~----~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 149 YTLDAVAEELLGEGKEKVDGEIIEDAEW----EEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred CCHHHHHHHHhCCCCCcCCHHHHhhccC----cchHHHHHHHHHHHHHHHHHhh
Confidence 4899999999833233222222211000 2578899999999999999987
No 30
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=68.01 E-value=4.8 Score=42.59 Aligned_cols=47 Identities=17% Similarity=0.256 Sum_probs=30.6
Q ss_pred cHHHHHHHhcCCccCCcccccccccCCHHHH-HHHHHHHHHHhHHhHHHHHHHH
Q psy15891 14 SLSEVYKLYCEGKVLDKTDRNIFVEGSLEDI-ENNWHNLMTYCAKDTLATFEVI 66 (899)
Q Consensus 14 sL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i-~~~f~~Lm~YCA~DV~aT~~v~ 66 (899)
||..|++.+.|-.+++=+..+++ +. .++.+.|..||-+||.+|..+|
T Consensus 156 sLd~Va~~~Lg~~K~~~~~~~I~------~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 156 GLKAVTKAKLGYDPVELDPEDMV------PLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred cHHHHHHHHhCCCcCcCCHHHHH------HHHhCCcHHHHhccHHHHHHHHHHh
Confidence 79999998873223322111111 11 1244689999999999999998
No 31
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=64.11 E-value=12 Score=39.47 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=17.4
Q ss_pred HHHHHHHHhHHhHHHHHHHH
Q psy15891 47 NWHNLMTYCAKDTLATFEVI 66 (899)
Q Consensus 47 ~f~~Lm~YCA~DV~aT~~v~ 66 (899)
+-+.|..||..||..|.++.
T Consensus 187 ~~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 187 DPARLLAYALDDVRETEGLA 206 (207)
T ss_pred CHHHHHHHHHHHHHHHHHhh
Confidence 44789999999999999875
No 32
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=62.63 E-value=12 Score=39.15 Aligned_cols=50 Identities=20% Similarity=0.187 Sum_probs=32.9
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHH----HHHHHHHHHhHHhHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIE----NNWHNLMTYCAKDTLATFEVIQ 67 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~----~~f~~Lm~YCA~DV~aT~~v~~ 67 (899)
-+|.+|++.+.+..+.+.. .+-+..+|- ++.+.|..||..||..|.++|.
T Consensus 140 y~L~~Va~~~Lg~~K~~~~-----~~~~~~eI~~~~~~~~~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 140 FSLENVAQELLGEGKLIHD-----VDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193 (193)
T ss_pred CCHHHHHHHHhCCCccccC-----cccCHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhC
Confidence 3799999998843333211 111233333 3567899999999999999873
No 33
>PRK05755 DNA polymerase I; Provisional
Probab=60.99 E-value=26 Score=44.68 Aligned_cols=107 Identities=20% Similarity=0.245 Sum_probs=63.5
Q ss_pred ccHHHHHHHhcCCccCCcccccccccC-CHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHhhhhCCCcchhhhhhcccc
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEG-SLEDIENNWHNLMTYCAKDTLATFEVIQALFPLFLERFPHPVTLAGMLELST 91 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~-~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F~~~~~~~~~~~~~~~~~~ 91 (899)
.||.++++.|+ |+.+..- -++|.++ +..++ ..+....||+.||.+|.+||.++.+.+-+ -+
T Consensus 412 ~~L~~L~~~yl-g~~~~~~-~~~~gk~~~~~~~--ple~~~~YAa~Dv~~~~~L~~~L~~~L~~-~~------------- 473 (880)
T PRK05755 412 HGLDSLAERYL-GHKTISF-EEVAGKQLTFAQV--DLEEAAEYAAEDADVTLRLHEVLKPKLLE-EP------------- 473 (880)
T ss_pred CCHHHHHHHHh-CCCccch-HHhcCCCCCcccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cc-------------
Confidence 79999999999 6653211 1233221 22332 12356689999999999999999998711 00
Q ss_pred ccccCchhhHHHHHhhcchhhhcCCCcchh--hhhhccccccccCCcc-HHHHHHHHHHHHHHHHHH
Q psy15891 92 AYLPDTLATFEVIQALFPLFLERFPHPVTL--AGMLELSTAYLPVNNN-WVKYFNESCQTFNDLNVE 155 (899)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~PHPvt~--agml~mgs~~LPvn~~-W~~y~~~ae~~y~~~~~~ 155 (899)
+.+. ..+.+-||+.. +.|-.-| ++||.. ++++.+..+..-+++..+
T Consensus 474 ------~l~~---------l~~eiE~p~~~~l~~me~~G---i~vD~~~~~~~~~~~~~~~~~l~~~ 522 (880)
T PRK05755 474 ------GLLE---------LYEEIELPLVPVLARMERNG---IKVDREYLKELSAELAQRLAELEQE 522 (880)
T ss_pred ------cHHH---------HHHHhhchHHHHHHHHHhcC---eEeCHHHHHHHHHHHHHHHHHHHHH
Confidence 1111 14567777764 5554444 677864 566655555444444333
No 34
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=55.94 E-value=16 Score=35.26 Aligned_cols=54 Identities=22% Similarity=0.210 Sum_probs=37.0
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPL 72 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~ 72 (899)
+||.++++-|. |..++| .+..++..+ +....+.+.|++.|+.++++++.++.+.
T Consensus 117 ~~l~~l~~~~l-~~~~~~----~~~~~~~~~-~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 117 HGLATLLKEYL-GVELDK----EEQKSDWGA-RPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCHHHHHHHHh-CCCCCc----ccCcccccc-CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 59999999998 766544 222222111 1224557789999999999999988765
No 35
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=54.52 E-value=20 Score=38.48 Aligned_cols=49 Identities=20% Similarity=0.261 Sum_probs=35.3
Q ss_pred cccHHHHHHHhcCCccCCcccccccccCCHHHH------HHHHHHHHHHhHHhHHHHHHHHHHH
Q psy15891 12 LNSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDI------ENNWHNLMTYCAKDTLATFEVIQAL 69 (899)
Q Consensus 12 ~NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i------~~~f~~Lm~YCA~DV~aT~~v~~~l 69 (899)
--+|.+|+..++ |. .|..+- .++| .+.+..|..||..|+.-|.+++.++
T Consensus 172 sY~L~~va~~~L-g~-----~k~di~---~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 172 SYDLTELSQQVL-GI-----ERQDID---PEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred CCChHHHHHHHh-Cc-----CcccCC---HHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 348999999999 43 122221 1222 3568889999999999999999875
No 36
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=52.30 E-value=14 Score=36.36 Aligned_cols=23 Identities=22% Similarity=0.293 Sum_probs=19.9
Q ss_pred HHHHHHHHhHHhHHHHHHHHHHH
Q psy15891 47 NWHNLMTYCAKDTLATFEVIQAL 69 (899)
Q Consensus 47 ~f~~Lm~YCA~DV~aT~~v~~~l 69 (899)
..+.++.||..||.+|.+||..|
T Consensus 141 ~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 141 ALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 68899999999999999999876
No 37
>PRK10829 ribonuclease D; Provisional
Probab=51.37 E-value=25 Score=40.74 Aligned_cols=54 Identities=19% Similarity=0.312 Sum_probs=41.9
Q ss_pred ccHHHHHHHhcCCccCCcccc-cccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDR-NIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~R-d~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
.||+.+.+-+| |+.+||+.+ .....-.+. ++-+.|+|.||....+||.+|....
T Consensus 116 ~gl~~Lv~~~l-gv~ldK~~~~sDW~~RPLs------~~ql~YAa~Dv~~L~~l~~~L~~~L 170 (373)
T PRK10829 116 CGFASMVEEYT-GVTLDKSESRTDWLARPLS------ERQCEYAAADVFYLLPIAAKLMAET 170 (373)
T ss_pred ccHHHHHHHHh-CCccCcccccCCCCCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999 999998763 333332222 1335999999999999999998887
No 38
>PHA02528 43 DNA polymerase; Provisional
Probab=44.10 E-value=30 Score=44.28 Aligned_cols=52 Identities=15% Similarity=0.109 Sum_probs=36.8
Q ss_pred cHHHHHHHhcCCccCC---cccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHH--HHHHh
Q psy15891 14 SLSEVYKLYCEGKVLD---KTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQA--LFPLF 73 (899)
Q Consensus 14 sL~dV~~~~c~g~~~d---K~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~--l~P~F 73 (899)
||..|+..+.|-.+++ ++.-+.|. ++.+.|..||..||..|.+++.+ ++|..
T Consensus 274 sLe~VA~~~LG~~K~d~~~~eI~~l~~--------~d~~~l~~Ynl~Da~Lv~~L~~kl~ll~~~ 330 (881)
T PHA02528 274 RLDYIAEVELGKKKLDYSDGPFKKFRE--------TDHQKYIEYNIIDVELVDRLDDKRKLIELV 330 (881)
T ss_pred CHHHHHHHHhCCCCccCCHHHHHHHHh--------cCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999888322222 23333332 23478999999999999999999 77766
No 39
>KOG0950|consensus
Probab=42.45 E-value=17 Score=46.33 Aligned_cols=101 Identities=8% Similarity=-0.022 Sum_probs=69.9
Q ss_pred cccccceEecCCCceEEEEeccchhhhhhhhc-ccccccccccccccccccccCccCCCCchhHHHHHHhcc-chhhhhH
Q psy15891 550 GSELRAMIQAPDGYSIIGADVDSQELWIASVI-GDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVGI-SREHAKI 627 (899)
Q Consensus 550 GselRs~f~AppGy~~VgAD~SqiELRIlal~-gDA~~s~~~g~~Afg~m~LeG~K~~GtDlHs~tAs~lGi-sR~~AKv 627 (899)
+.-++.-+...---..|+.+|.+.+.|+.|++ +++.|++ +++.| -..++- ++..-+.
T Consensus 821 ~~l~L~~li~espi~~V~~kYk~~rg~lqall~~a~~~a~--~It~F-------------------ce~l~w~~~~~l~~ 879 (1008)
T KOG0950|consen 821 VALALQKLINESPIRTVAEKYKVERGRLQALLSNASSFAS--LITFF-------------------CESIQWFPLRALLS 879 (1008)
T ss_pred HHHHHHHHHhhCcHHHHHHHhCchHHHHHHHHhcchhHHH--HHHHH-------------------HHHhhhcchHHHHH
Confidence 34444445555555669999999999999555 3444443 11111 122221 5677788
Q ss_pred HHHHHhhcccHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhChhhHHHHh
Q psy15891 628 INYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRL 676 (899)
Q Consensus 628 ~nyG~iYGaG~k~A~~La~q~n~~lS~eEA~~~~~~f~~~~pgv~~~~~ 676 (899)
-.|+++|++| ...|..=.- ++...++....-|++.|+++..+..
T Consensus 880 ~~~~rl~~g~---~~eL~~Lmr--v~~~~~~RAr~lf~Agf~tv~~iA~ 923 (1008)
T KOG0950|consen 880 EFYGRLSFGG---HAELIPLMR--VPDVKAERARQLFKAGFTSVGSIAN 923 (1008)
T ss_pred HHHHHHhccc---hhhhhhhhc--CchhHHHHHHHHHHhhccchHHHhc
Confidence 8899999999 777766544 8888999999999999999998753
No 40
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=39.63 E-value=55 Score=39.66 Aligned_cols=53 Identities=23% Similarity=0.216 Sum_probs=40.2
Q ss_pred ccHHHHHHHhcCCccCCccc-ccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTD-RNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~-Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
.+|+++++.|+ +..++|.. |... . +..-.+-..|||.||..+.++|..+.+..
T Consensus 91 ~~l~~la~~~l-~~~l~k~~~~sdw-----~--rpls~~q~~YAa~Dv~~l~~L~~~L~~qL 144 (553)
T PRK14975 91 SSLSAAAARAL-GEGLDKPPQTSAL-----S--DPPDEEQLLYAAADADVLLELYAVLADQL 144 (553)
T ss_pred CCHHHHHHHHh-CCCCCChhhhccc-----c--ccchHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 49999999999 99998844 3222 1 11233456699999999999999999987
No 41
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=39.52 E-value=38 Score=36.39 Aligned_cols=49 Identities=18% Similarity=0.304 Sum_probs=33.9
Q ss_pred cHHHHHHHhcCCcc--C-CcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHH
Q psy15891 14 SLSEVYKLYCEGKV--L-DKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVI 66 (899)
Q Consensus 14 sL~dV~~~~c~g~~--~-dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~ 66 (899)
||..|+....+..+ + -++.-+.|-+++.++ ...+..||.+|+..|.+++
T Consensus 179 sL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~----r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 179 TLENVVYHVLHQRIPLYSNKTLTEWYKSGSASE----RWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred CHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhH----hHHHHHHHHHHHHHHHHhh
Confidence 68999988883222 2 144445554555544 5679999999999999876
No 42
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=39.17 E-value=69 Score=31.68 Aligned_cols=52 Identities=19% Similarity=0.207 Sum_probs=38.0
Q ss_pred ccHHHHHHHhcCCccCCccccccccc-C--CHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVE-G--SLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~-~--~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
+||.++++-|+ |..+.|+. .+.+ + .++ .....|+|.|+.++.+++.++.+..
T Consensus 106 ~~l~~l~~~~l-~~~~~~~~--~~~~w~~~~l~------~~~~~yaa~~a~~l~~L~~~l~~~L 160 (178)
T cd06142 106 VGLAALVEELL-GVELDKGE--QRSDWSKRPLT------DEQLEYAALDVRYLLPLYEKLKEEL 160 (178)
T ss_pred ccHHHHHHHHh-CCCCCccc--ccccCCCCCCC------HHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 58999999898 76655532 3332 1 111 4457899999999999999999887
No 43
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=38.54 E-value=52 Score=37.52 Aligned_cols=52 Identities=27% Similarity=0.551 Sum_probs=35.6
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHH-------HHHHHHHHHhHHhHHHHHHHHHHH--HHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIE-------NNWHNLMTYCAKDTLATFEVIQAL--FPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~-------~~f~~Lm~YCA~DV~aT~~v~~~l--~P~F 73 (899)
-+|.+|+.... |. .++.+ +..+|. +..+.+..||..|+..|.+++.++ +|..
T Consensus 166 ~~L~~va~~~l-~~-----~k~d~---~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l~~~~~~ 226 (471)
T smart00486 166 YKLDTVAEYLL-GK-----EKDDL---PYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKLNVIPLI 226 (471)
T ss_pred CCHHHHHHHHh-CC-----CCCCC---CHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 46888888877 41 11222 222333 356779999999999999999995 5555
No 44
>PF00940 RNA_pol: DNA-dependent RNA polymerase; InterPro: IPR002092 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The phage-type enzymes are family of single chain polymerases found in bacteriophages and mitochondria [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=37.70 E-value=5.6e+02 Score=30.05 Aligned_cols=130 Identities=18% Similarity=0.126 Sum_probs=69.4
Q ss_pred ccceecCCCCCc--ccccccceEecC--CC---ceEEEEeccchhhhhhh-hcccccccc-cccccccccccccCccCCC
Q psy15891 537 TWMTASNAVGER--VGSELRAMIQAP--DG---YSIIGADVDSQELWIAS-VIGDSYCAK-EHGATPLGWMTLSGQKSNA 607 (899)
Q Consensus 537 tWLSaSnP~~~~--~GselRs~f~Ap--pG---y~~VgAD~SqiELRIla-l~gDA~~s~-~~g~~Afg~m~LeG~K~~G 607 (899)
-|..|.+|= +- .--|++.....+ ++ +.-|..|.|-==+-++| +++|...+. .+++. + ..-
T Consensus 54 ~w~~Ad~P~-qfLA~c~e~~~~~~~~~~~~~~s~lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip--------~--~~p 122 (405)
T PF00940_consen 54 WWLKADKPW-QFLAACFELAKALRSGNPEEFVSHLPVHQDGSCSGLQHYSALLRDEVGAKAVNLIP--------S--DKP 122 (405)
T ss_dssp GGGGSSSHH-HHHHHHHHHHHHHCCCSGCCSEE-SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSS--------S--SS-
T ss_pred HHhcCCcHH-HHHHHHHHHHHHHhcCCchheeecceeeecCcccHHHHHHHHccCHhhChhcCCCC--------C--CCC
Confidence 677777771 11 112344443322 33 35588999877777773 335665433 22221 1 234
Q ss_pred CchhHHHHHHh-----------------------ccchhhhhHHHHHHhhcccHHH-HHHHHHHhCCCC--------CHH
Q psy15891 608 TDMHSITAKAV-----------------------GISREHAKIINYARIYGAGERF-AERLLKQFNPEM--------SKS 655 (899)
Q Consensus 608 tDlHs~tAs~l-----------------------GisR~~AKv~nyG~iYGaG~k~-A~~La~q~n~~l--------S~e 655 (899)
-|+|+.+|..+ +++|+..|...--.+||++... +..+..++.... ..+
T Consensus 123 ~DiY~~V~~~v~~~l~~~~~~~~~~~~~~~~l~~~i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~ 202 (405)
T PF00940_consen 123 QDIYSEVAEEVKKRLEEDADDAEEDNSLAKWLKGGITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYK 202 (405)
T ss_dssp --HHHHHHHHHHHHHHHHHHEHHCCHHHHHHCCCT--HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHH
T ss_pred CchHHHHHHHHHHHHHHhhcccccchHHHHHhcCCCChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHH
Confidence 69999887653 4689999999999999998332 334444332111 122
Q ss_pred HHH----HHHHHHHHhChhhHHHHhh
Q psy15891 656 DAK----SKARKMYTLTKGKKLYRLK 677 (899)
Q Consensus 656 EA~----~~~~~f~~~~pgv~~~~~~ 677 (899)
.|. .+.+.+.+.||+.+..++.
T Consensus 203 ~~~~la~~i~~~i~~~~~~a~~~m~w 228 (405)
T PF00940_consen 203 AAMYLAKIIFEAIKEVFPGARNIMDW 228 (405)
T ss_dssp HHHHHHHHHHHHHHCCSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 344 3445566668887775443
No 45
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.05 E-value=87 Score=40.34 Aligned_cols=57 Identities=16% Similarity=0.094 Sum_probs=38.9
Q ss_pred ccHHHHHHHhcCCccCCcccccccccC-CHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEG-SLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~-~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
+||.++++-|+ +..+.+.. +++.++ +..++ ....+..||+.|+.+|.++|.++.|..
T Consensus 420 ~~l~~la~~yl-~~~~~~~~-~~~~~~~~~~~~--~~~~~~~ya~~d~~~~~~L~~~l~~~l 477 (887)
T TIGR00593 420 STLDTLARRYL-VEELILDE-KIGGKLAKFAFP--PLEEATEYLARRAAATKRLAEELLKEL 477 (887)
T ss_pred CCHHHHHHHHc-CcccccHH-HhccCCCCcccc--cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999 54433211 233332 11222 134567899999999999999999998
No 46
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=35.95 E-value=52 Score=31.13 Aligned_cols=58 Identities=28% Similarity=0.375 Sum_probs=37.5
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPL 72 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~ 72 (899)
.||.++++.|. +..+.+.. +.+..+.....+....+...|++.|+.++++++.++.+.
T Consensus 97 ~~l~~l~~~~l-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 97 HSLDDLAKEYL-GIELDKDE-QIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred CCHHHHHHHHc-CCCCccHH-HHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 48999999998 66543311 122222100012236668889999999999999998764
No 47
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=33.93 E-value=52 Score=31.42 Aligned_cols=55 Identities=18% Similarity=0.189 Sum_probs=37.1
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFP 71 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P 71 (899)
.+|.++++-|+ +..+.|.. +.+.++..++ ....+...|.+.|+.+.++++.++.|
T Consensus 96 ~~l~~l~~~~l-~~~~~~~~-~~~~~~~~~~--~~~~~~~~ya~~~a~~l~~L~~~l~~ 150 (150)
T cd09018 96 WDMDSLVERWL-GHKLIKFE-SIAGKLWFNQ--PLTEEQGRYAAEDADVTLQIHLKLWP 150 (150)
T ss_pred CCHHHHHHHHh-CCCcccHH-HhcCCCCccc--CCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 48999999998 76654411 1443332111 11555667999999999999998865
No 48
>PRK05761 DNA polymerase I; Reviewed
Probab=31.85 E-value=58 Score=41.29 Aligned_cols=45 Identities=16% Similarity=0.195 Sum_probs=32.6
Q ss_pred ccHHHHHHHhcCCccCCcccccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHH
Q psy15891 13 NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVI 66 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~ 66 (899)
=||..|++-+.|..++|-. .+ +.+ .+.+.|..||..|+..|.+++
T Consensus 290 ysL~~Va~~~Lg~~K~~~~-~~------i~~--~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 290 ARLDAVGRALLGISKVELE-TN------ISE--LDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred CChHHHHHHHhCCCccccc-cc------ccc--cCHHHHHHHHHHHHHHHHHHH
Confidence 3799999988844444332 12 222 378999999999999999985
No 49
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=31.21 E-value=90 Score=35.96 Aligned_cols=54 Identities=17% Similarity=0.215 Sum_probs=40.5
Q ss_pred ccHHHHHHHhcCCccCCccc-ccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 13 NSLSEVYKLYCEGKVLDKTD-RNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 13 NsL~dV~~~~c~g~~~dK~~-Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
.||+++.+-|| |+.++|.. |..... +.-.++...|+|.||.+.+++|.++....
T Consensus 112 ~~l~~Lv~~~L-g~~l~K~~~~sdW~~------rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L 166 (367)
T TIGR01388 112 MGYAKLVQEVL-GVELDKSESRTDWLA------RPLTDAQLEYAAADVTYLLPLYAKLMERL 166 (367)
T ss_pred ccHHHHHHHHc-CCCCCcccccccCCC------CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999 88899863 222111 11144567999999999999999998877
No 50
>PRK05762 DNA polymerase II; Reviewed
Probab=30.02 E-value=69 Score=40.56 Aligned_cols=55 Identities=22% Similarity=0.349 Sum_probs=36.6
Q ss_pred cHHHHHHHhcCCccCCcccccccccCCHHHHH----HHHHHHHHHhHHhHHHHHHHHH--HHHHHh
Q psy15891 14 SLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIE----NNWHNLMTYCAKDTLATFEVIQ--ALFPLF 73 (899)
Q Consensus 14 sL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i~----~~f~~Lm~YCA~DV~aT~~v~~--~l~P~F 73 (899)
+|..|++... |.. |...|.. ...++|- ++.+.|..||..|+..|.++|. .++|..
T Consensus 294 sL~~Va~~~L-g~~--K~~~d~~--~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl~ll~~~ 354 (786)
T PRK05762 294 SLEYVSQRLL-GEG--KAIDDPY--DRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKTKLLPFL 354 (786)
T ss_pred CHHHHHHHHh-CCC--eeccCcc--ccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 6888888666 321 1111111 1234443 4567899999999999999999 568877
No 51
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=25.82 E-value=1.2e+02 Score=36.85 Aligned_cols=53 Identities=21% Similarity=0.365 Sum_probs=32.3
Q ss_pred cHHHHHHHhcCCccCCcccccccccCCHHHH-HHHHHHHHHHhHHhHHHHHHHH--HHHHHHh
Q psy15891 14 SLSEVYKLYCEGKVLDKTDRNIFVEGSLEDI-ENNWHNLMTYCAKDTLATFEVI--QALFPLF 73 (899)
Q Consensus 14 sL~dV~~~~c~g~~~dK~~Rd~F~~~~~~~i-~~~f~~Lm~YCA~DV~aT~~v~--~~l~P~F 73 (899)
||..|+.+..+-.++|- .+++.+. .++.+.|..||..|+..|..++ ..+++..
T Consensus 275 sL~~Vs~~~Lg~~K~d~-------~~~I~~l~~~d~~rla~YclkDa~L~~~L~~~~~ll~~~ 330 (498)
T PHA02524 275 KLGNVGYREVKADKLDY-------EGPINKFRKADHQRYVDYCVRDTDIILLIDGRRCFIDLI 330 (498)
T ss_pred CHHHHHHHhcCCccccc-------hhhHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67788775543233331 1122222 1245899999999999999887 4455543
No 52
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=23.58 E-value=70 Score=37.51 Aligned_cols=28 Identities=18% Similarity=0.539 Sum_probs=21.1
Q ss_pred HHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 46 NNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 46 ~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
+-.+++..||..||.++++|+.+.--.|
T Consensus 130 d~~~e~l~Yc~~DV~iL~~~~~~f~~~~ 157 (459)
T PF03175_consen 130 DFKKEILEYCKQDVRILYKVLEKFRKIF 157 (459)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4457899999999999998888865555
No 53
>PHA00452 T3/T7-like RNA polymerase
Probab=22.76 E-value=3.4e+02 Score=34.92 Aligned_cols=129 Identities=17% Similarity=0.144 Sum_probs=66.6
Q ss_pred ccceecCCCC-CcccccccceEecCCC---ceEEEEeccchhhhhhh-hcccccccccccccccccccccCccCCCCchh
Q psy15891 537 TWMTASNAVG-ERVGSELRAMIQAPDG---YSIIGADVDSQELWIAS-VIGDSYCAKEHGATPLGWMTLSGQKSNATDMH 611 (899)
Q Consensus 537 tWLSaSnP~~-~~~GselRs~f~AppG---y~~VgAD~SqiELRIla-l~gDA~~s~~~g~~Afg~m~LeG~K~~GtDlH 611 (899)
-|+.+.+|=. -..--|++.++..+.. +.-|.-|.|-==+-..| +.+|...+. +- +.+ -+++ --|+|
T Consensus 466 ww~~Ad~P~qfLA~c~El~~a~~~~~~~~s~lPI~qDgSCnGlQHyAAL~rD~~ga~-----~V-NL~-p~d~--p~DvY 536 (807)
T PHA00452 466 WWAEADSPLCFLAACFEYAAAVHSGTSYVSGLPVAMDGTCSGLQHFSAMLRDEVGGR-----AV-NLL-PSDK--PQDIY 536 (807)
T ss_pred hhhcCCCHHHHHHHHHHHHHHHhCCCccccccccccCCcccHHHHHHHHhCCHHhHH-----Hh-CCC-CCCC--CccHH
Confidence 4777777710 0011234444433332 23366666655555553 334544322 11 111 1222 45888
Q ss_pred HHHHHHh-------------------------ccchhhhhHHHHHHhhcccHHH-HHHHHHHh---CCCCC------HHH
Q psy15891 612 SITAKAV-------------------------GISREHAKIINYARIYGAGERF-AERLLKQF---NPEMS------KSD 656 (899)
Q Consensus 612 s~tAs~l-------------------------GisR~~AKv~nyG~iYGaG~k~-A~~La~q~---n~~lS------~eE 656 (899)
+.+|..+ +|+|+..|...--.+||.+... ..++.+++ +.... -+.
T Consensus 537 ~~Va~~v~~~i~~d~~~~~~~~~~~~~~~l~~~i~RkvvKqtVMT~vYGvT~~g~~~qI~~~l~~~~~~~~~~~~~~~~~ 616 (807)
T PHA00452 537 GIVAEVVNEKLERDAINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQPGIDEGDGAMFTNQA 616 (807)
T ss_pred HHHHHHHHHHHHHHHhCCCcchHHHHHHHHhCCCChhhcccccccceeCCchhhhHHHHHHHHHhcCCCcccchhhhHHH
Confidence 8877542 4789999999999999998333 33344333 21111 111
Q ss_pred ----HHHHHHHHHHhChhhHHH
Q psy15891 657 ----AKSKARKMYTLTKGKKLY 674 (899)
Q Consensus 657 ----A~~~~~~f~~~~pgv~~~ 674 (899)
|+.+.+.+.+.||+...-
T Consensus 617 ~~yla~~i~~ai~~~f~~a~~i 638 (807)
T PHA00452 617 ASYMAKLIWDAISETVPAAVEA 638 (807)
T ss_pred HHHHHHHHHHHHHHHHHhHHHH
Confidence 455556677777776663
No 54
>KOG3337|consensus
Probab=21.97 E-value=54 Score=34.50 Aligned_cols=15 Identities=27% Similarity=0.696 Sum_probs=8.8
Q ss_pred HHHHHHHhhhhCCCc
Q psy15891 66 IQALFPLFLERFPHP 80 (899)
Q Consensus 66 ~~~l~P~F~~~~~~~ 80 (899)
|..+.-.||+|||||
T Consensus 15 ~d~VssAfw~RYPNp 29 (201)
T KOG3337|consen 15 WDQVSSAFWQRYPNP 29 (201)
T ss_pred HHHHHHHHHHhCCCc
Confidence 344555666666664
No 55
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=20.42 E-value=1.5e+02 Score=34.59 Aligned_cols=55 Identities=20% Similarity=0.308 Sum_probs=45.1
Q ss_pred cccHHHHHHHhcCCccCCccc-ccccccCCHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHh
Q psy15891 12 LNSLSEVYKLYCEGKVLDKTD-RNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLF 73 (899)
Q Consensus 12 ~NsL~dV~~~~c~g~~~dK~~-Rd~F~~~~~~~i~~~f~~Lm~YCA~DV~aT~~v~~~l~P~F 73 (899)
-.||++..+-+| |+.+||.. |.....-++.+ +=++|-|.||.--+++|.+|--..
T Consensus 111 ~~gl~~Lv~~ll-~v~ldK~~q~SDW~~RPLs~------~Ql~YAa~DV~yL~~l~~~L~~~L 166 (361)
T COG0349 111 SHGLADLVEELL-GVELDKSEQRSDWLARPLSE------AQLEYAAADVEYLLPLYDKLTEEL 166 (361)
T ss_pred cccHHHHHHHHh-CCcccccccccccccCCCCH------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999999 99999875 55666555544 458999999999999999998877
No 56
>PF14003 YlbE: YlbE-like protein
Probab=20.31 E-value=17 Score=32.36 Aligned_cols=16 Identities=38% Similarity=0.798 Sum_probs=12.8
Q ss_pred CCCChhhhHhhhcCCC
Q psy15891 257 LIGYPEWYRKLCVKPH 272 (899)
Q Consensus 257 ~~g~P~Wyr~l~~~~~ 272 (899)
+.-.|.|||.|.+.+.
T Consensus 8 iR~~P~WYR~LsR~P~ 23 (65)
T PF14003_consen 8 IREQPIWYRILSRNPE 23 (65)
T ss_pred HHHCcHHHHHHccCHH
Confidence 3447999999998775
Done!