Query 001977
Match_columns 987
No_of_seqs 462 out of 2009
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 13:42:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001977.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001977hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0217 Mismatch repair ATPase 100.0 2E-132 5E-137 1161.8 41.0 818 98-986 8-857 (1125)
2 TIGR01070 mutS1 DNA mismatch r 100.0 1E-94 2.3E-99 890.9 64.0 550 327-987 1-558 (840)
3 PRK05399 DNA mismatch repair p 100.0 4.9E-94 1.1E-98 890.2 62.6 560 324-987 5-572 (854)
4 COG0249 MutS Mismatch repair A 100.0 1.4E-87 3E-92 818.1 51.4 568 324-987 3-573 (843)
5 KOG0218 Mismatch repair MSH3 [ 100.0 1.3E-78 2.8E-83 683.0 46.8 611 325-986 160-793 (1070)
6 KOG0219 Mismatch repair ATPase 100.0 1.3E-41 2.9E-46 392.4 45.1 571 326-986 11-607 (902)
7 smart00533 MUTSd DNA-binding d 100.0 1.1E-36 2.3E-41 340.9 29.2 288 669-987 1-290 (308)
8 KOG0220 Mismatch repair ATPase 100.0 3.5E-31 7.5E-36 301.9 36.3 472 452-987 103-589 (867)
9 KOG0221 Mismatch repair ATPase 100.0 2.7E-31 5.9E-36 297.4 32.9 357 601-986 193-563 (849)
10 PF01624 MutS_I: MutS domain I 100.0 9.5E-32 2.1E-36 256.2 10.7 107 328-444 1-113 (113)
11 PRK00409 recombination and DNA 100.0 1.4E-26 2.9E-31 285.5 30.7 291 650-987 2-296 (782)
12 PF05192 MutS_III: MutS domain 99.9 5.2E-25 1.1E-29 231.3 21.2 199 651-967 1-202 (204)
13 TIGR01069 mutS2 MutS2 family p 99.9 5.7E-24 1.2E-28 261.7 30.3 286 649-987 1-291 (771)
14 PF05190 MutS_IV: MutS family 99.5 1.6E-13 3.5E-18 125.7 13.7 92 837-928 1-92 (92)
15 COG1193 Mismatch repair ATPase 99.5 4.3E-13 9.3E-18 163.1 21.5 283 653-987 3-288 (753)
16 PF05188 MutS_II: MutS domain 99.4 1.9E-12 4.2E-17 127.2 13.5 130 453-621 1-130 (137)
17 PF09465 LBR_tudor: Lamin-B re 99.2 6.3E-11 1.4E-15 94.7 6.3 43 105-147 7-49 (55)
18 smart00333 TUDOR Tudor domain. 97.4 0.00022 4.8E-09 59.1 5.2 44 105-150 4-48 (57)
19 KOG4675 Uncharacterized conser 97.4 8.6E-05 1.9E-09 79.1 2.8 84 61-157 122-207 (273)
20 smart00743 Agenet Tudor-like d 97.3 0.00053 1.2E-08 57.8 5.6 36 105-141 4-39 (61)
21 cd04508 TUDOR Tudor domains ar 97.2 0.00054 1.2E-08 54.7 5.2 43 107-150 1-44 (48)
22 PF09038 53-BP1_Tudor: Tumour 96.4 0.006 1.3E-07 57.7 6.0 45 102-147 1-45 (122)
23 PF06003 SMN: Survival motor n 93.3 0.14 3E-06 56.3 6.1 49 102-150 67-116 (264)
24 KOG3064 RNA-binding nuclear pr 88.3 0.29 6.3E-06 52.0 2.3 7 164-170 167-173 (303)
25 PLN00104 MYST -like histone ac 87.3 2.1 4.4E-05 50.1 8.5 39 105-143 55-99 (450)
26 PF11717 Tudor-knot: RNA bindi 85.7 2.8 6E-05 34.6 6.2 43 106-149 3-50 (55)
27 PF05641 Agenet: Agenet domain 84.9 1.8 3.8E-05 37.4 5.0 35 106-141 3-40 (68)
28 PF15057 DUF4537: Domain of un 81.6 3 6.5E-05 40.6 5.7 41 107-148 1-41 (124)
29 KOG0644 Uncharacterized conser 78.1 2.5 5.5E-05 51.9 4.6 47 103-149 978-1036(1113)
30 KOG0127 Nucleolar protein fibr 73.1 2.7 5.8E-05 49.4 3.0 27 99-125 177-203 (678)
31 PF00567 TUDOR: Tudor domain; 73.0 7.1 0.00015 36.5 5.5 52 103-157 51-103 (121)
32 KOG3026 Splicing factor SPF30 63.4 12 0.00026 39.7 5.1 39 102-140 89-127 (262)
33 PF15449 Retinal: Retinal prot 61.5 32 0.0007 44.0 9.0 24 103-126 1136-1159(1287)
34 PLN02782 Branched-chain amino 56.8 36 0.00078 40.0 8.2 71 100-171 76-152 (403)
35 KOG1924 RhoA GTPase effector D 54.8 38 0.00082 42.0 7.9 19 723-741 903-921 (1102)
36 KOG1525 Sister chromatid cohes 52.8 0.85 1.9E-05 59.7 -6.5 59 99-157 982-1041(1266)
37 PF08605 Rad9_Rad53_bind: Fung 51.9 29 0.00062 34.2 5.3 45 109-158 15-59 (131)
38 KOG0526 Nucleosome-binding fac 50.1 10 0.00022 44.8 2.2 22 101-122 338-363 (615)
39 PF11702 DUF3295: Protein of u 49.6 49 0.0011 39.5 7.7 19 72-90 204-222 (507)
40 KOG1118 Lysophosphatidic acid 48.8 47 0.001 36.9 6.8 31 106-139 327-357 (366)
41 PF10851 DUF2652: Protein of u 44.0 13 0.00029 35.2 1.6 29 341-369 80-108 (116)
42 PF02237 BPL_C: Biotin protein 43.5 63 0.0014 25.8 5.2 39 106-147 2-40 (48)
43 PF09026 CENP-B_dimeris: Centr 42.1 8.4 0.00018 35.2 0.0 9 218-226 34-42 (101)
44 KOG0526 Nucleosome-binding fac 41.1 19 0.00042 42.6 2.7 12 193-204 463-474 (615)
45 KOG1473 Nucleosome remodeling 41.0 37 0.00081 43.7 5.2 39 117-157 54-92 (1414)
46 KOG2652 RNA polymerase II tran 40.9 1.7E+02 0.0037 33.2 9.7 12 82-93 156-167 (348)
47 PF05616 Neisseria_TspB: Neiss 39.8 94 0.002 36.8 7.8 7 20-26 294-300 (502)
48 COG5129 MAK16 Nuclear protein 39.5 17 0.00036 38.2 1.7 24 219-242 257-280 (303)
49 KOG0943 Predicted ubiquitin-pr 34.3 27 0.00058 44.9 2.5 18 907-924 2838-2856(3015)
50 PF10446 DUF2457: Protein of u 33.9 17 0.00037 42.2 0.8 28 311-338 181-214 (458)
51 PF11593 Med3: Mediator comple 33.5 64 0.0014 36.8 5.1 27 56-82 173-199 (379)
52 KOG1832 HIV-1 Vpr-binding prot 33.4 23 0.0005 44.4 1.8 6 307-312 1504-1509(1516)
53 PF03652 UPF0081: Uncharacteri 32.8 1.9E+02 0.0041 28.6 7.8 46 470-515 9-58 (135)
54 PF02724 CDC45: CDC45-like pro 32.7 21 0.00046 44.4 1.4 12 497-508 336-347 (622)
55 KOG1924 RhoA GTPase effector D 32.7 1.1E+02 0.0023 38.3 7.1 11 606-616 839-849 (1102)
56 KOG0307 Vesicle coat complex C 31.8 1.1E+02 0.0023 39.8 7.1 31 59-94 808-839 (1049)
57 PRK04778 septation ring format 31.6 2.9E+02 0.0062 34.2 10.9 55 802-859 162-217 (569)
58 PTZ00415 transmission-blocking 31.3 23 0.00049 47.3 1.3 12 174-185 150-161 (2849)
59 KOG3208 SNARE protein GS28 [In 29.4 6.8E+02 0.015 26.9 11.4 96 837-954 2-115 (231)
60 KOG4327 mRNA splicing protein 28.1 48 0.0011 34.4 2.8 45 105-149 69-114 (218)
61 PF07039 DUF1325: SGF29 tudor- 27.4 1.2E+02 0.0026 29.8 5.3 39 106-144 74-113 (130)
62 KOG4825 Component of synaptic 27.3 1.1E+02 0.0023 35.8 5.6 25 20-44 266-290 (666)
63 KOG2141 Protein involved in hi 27.2 48 0.001 40.9 2.9 87 178-327 217-307 (822)
64 PF04147 Nop14: Nop14-like fam 27.1 49 0.0011 42.7 3.3 14 382-395 506-519 (840)
65 PRK14637 hypothetical protein; 27.1 73 0.0016 32.2 3.8 45 88-132 79-123 (151)
66 KOG1189 Global transcriptional 25.5 40 0.00087 41.7 1.9 15 70-84 767-781 (960)
67 PF06160 EzrA: Septation ring 25.4 2.8E+02 0.006 34.2 9.2 60 796-858 152-212 (560)
68 PRK13335 superantigen-like pro 23.9 3.8E+02 0.0083 30.4 8.8 16 118-133 172-187 (356)
69 KOG1999 RNA polymerase II tran 23.6 36 0.00078 43.2 1.1 21 642-662 484-504 (1024)
70 smart00026 EPEND Ependymins. E 23.4 39 0.00085 35.4 1.2 19 338-356 48-66 (191)
71 TIGR00250 RNAse_H_YqgF RNAse H 21.8 3.4E+02 0.0074 26.6 7.3 45 470-515 6-55 (130)
72 KOG0917 Uncharacterized conser 21.5 1.7E+02 0.0038 32.0 5.5 11 46-56 248-258 (338)
73 COG0278 Glutaredoxin-related p 21.2 1.4E+02 0.0031 27.9 4.2 37 371-411 19-58 (105)
74 PF12946 EGF_MSP1_1: MSP1 EGF 20.8 54 0.0012 25.0 1.1 18 134-151 11-28 (37)
75 PF06511 IpaD: Invasion plasmi 20.8 9E+02 0.019 27.8 11.2 93 861-959 231-323 (337)
76 PRK00109 Holliday junction res 20.8 8.2E+02 0.018 24.1 12.5 53 454-515 5-61 (138)
77 PF14359 DUF4406: Domain of un 20.7 88 0.0019 28.8 2.8 25 378-402 6-33 (92)
78 PF08181 DegQ: DegQ (SacQ) fam 20.4 3.5E+02 0.0077 20.9 5.3 35 930-964 6-40 (46)
79 PF02576 DUF150: Uncharacteris 20.0 1.1E+02 0.0024 30.2 3.6 53 89-143 69-124 (141)
No 1
>KOG0217 consensus Mismatch repair ATPase MSH6 (MutS family) [Replication, recombination and repair]
Probab=100.00 E-value=2.1e-132 Score=1161.75 Aligned_cols=818 Identities=39% Similarity=0.619 Sum_probs=660.8
Q ss_pred ccccCCccccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceeeecCcceEEEEec--chhhhhhhcccccccc
Q 001977 98 AKSYGEDVLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELLDLGKEKIEWVQE--SVSLLKRLRRDSFKKV 175 (987)
Q Consensus 98 ~~~~~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l~l~~e~~~~~~~--~~~~~~~~~~~~~~~~ 175 (987)
.-..+++.+| .||.+.|..+.....+ |-+++..-+..-+|+-+|... ......|++. +.+
T Consensus 8 ~~t~~~e~~~-----------~~~~~~v~~~~~~e~k----~l~~~t~k~~~~~e~~~~~~~~~r~~~~~rv~~---~e~ 69 (1125)
T KOG0217|consen 8 HMTFFEETPG-----------KLYRNSVGLKPKEEPK----SLRNGTLKIKNLKEKEEFKSGQPREVVSSRVKE---YEA 69 (1125)
T ss_pred ceeecccCcc-----------hhcccccccCCccchh----hhcCCCcCcCccchhhHhhccCccccccccccc---hhh
Confidence 4455677777 7999999988766665 656666555555566666531 1111222221 222
Q ss_pred ccCChhhhhccc-cccCCCCCCCcchhhh-cccCCC-CCCcc-cc---cc---hhhhhhhc--------ccccCCccCCC
Q 001977 176 VVEDDEEMENVE-DEISDDRSDSSDDDWN-KNVGKE-DVSED-EE---VD---LVDEQENK--------VLRGRKRKSSG 237 (987)
Q Consensus 176 ~~~~~~~~~~~~-~~~~~~~~~~~d~~~~-~~~~~~-~~~~~-~~---~~---~~~~~~~~--------~~~~~~~~~~~ 237 (987)
+..+.+...... ...-...+++||+||+ |.+..- ++|++ +| +| ..+|+..+ .+.++.+++..
T Consensus 70 ~~~d~~~~~~~~~~~~k~~~~sDsd~d~g~k~~~~~~~~d~~~~D~~~~d~~~~~~ee~~~~~~~~~~~~~~~r~~~a~~ 149 (1125)
T KOG0217|consen 70 VGDDADIVVESSSEKPKSGLDSDSDEDFGGKEVEEKEDSDEELDDETASDYEVVISEESEGGEPVCRVSDTDSRSRKAES 149 (1125)
T ss_pred cCCCccceeeecccCCccccCCCcccccCcccccccccccccccccccCCcceeccccccCCCcccccCCCcccchhccc
Confidence 222222222222 2233456788889998 111111 22211 11 11 11222211 34455666644
Q ss_pred -----ccCCCCCCCCCCCCccccccCCccc-cCC-CCCCCCC-CCCCcccchhhhhhhccccccccCC-CCCccCCCCCC
Q 001977 238 -----VKKSKSDGNAVNADFKSPIIKPVKI-FGS-DKLSNGF-DNPVMGDVSERFSAREADKFHFLGP-DRRDAKRRRPG 308 (987)
Q Consensus 238 -----~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~fl~~-~~rD~~~r~p~ 308 (987)
+||+.+..++...+.......|.+- .+. ++.+.+. .....++..+|+.++.++++.||.. ++||+++|||+
T Consensus 150 v~k~~~kk~~~~~~~~~~~~~~~~~~p~~~~~~~a~r~~~~~~~i~~~~~~~~~~~a~~~E~~r~l~~e~~RD~~rrr~~ 229 (1125)
T KOG0217|consen 150 VSKGKSKKSPSDSGAVSMGHDLDFNDPMPLREGQASRSASGYCGISNGETELSRMEAFDHEKERYLKLEDVRDALRRRRG 229 (1125)
T ss_pred ccccccCCCCCCccccccccccccCCCCccccCccccccccccccccccccccchhhhcccchhhccHHHhhhhhcCCCC
Confidence 2222233334444555555666651 122 2223333 2233344478888899999888875 57999999999
Q ss_pred CCCCCCccCCCCcccccCCCHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccceeccCCCCccccCcccHH
Q 001977 309 DVYYDPRTLYLPPDFLRNLSEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGEQPHCGFPERNFS 388 (987)
Q Consensus 309 dp~YDp~TL~iP~~~~~~~TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~~~~~~~~~~GfPe~s~~ 388 (987)
||+|||+||||||++|+++||+++|||+||++|||||||||+|||||||++||.+++++|+|+||++++|||||||++|+
T Consensus 230 dp~yDp~TLyiP~s~~~kftpg~kqwWeiKs~~fD~ivfFk~GKFyELye~DA~vg~~~~dl~f~~vN~~~~GfPE~sf~ 309 (1125)
T KOG0217|consen 230 DPEYDPRTLYIPPSFWKKFTPGEKQWWEIKSDNFDTIVFFKKGKFYELYEMDALVGARLFDLKFMDVNMPHSGFPEGSFD 309 (1125)
T ss_pred CCCCCccceecCHHHHhcCCchhhhhhhhhhhcccEEEEEecchHHHHHhhhhhhhhhhcceeecccccccCCCCccchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCeEEEEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCccccccccCCCCCCcEEEEEEecCCCCCCC
Q 001977 389 MNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELLSANPDASYLMALTESNQSPASQ 468 (987)
Q Consensus 389 ~~~~~Lv~~GykVavveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~~l~~~~~~~yLlaI~e~~~~~~~~ 468 (987)
.|+.+|+++|||||+|||+|||.++++|++..|+|+|||+||||+|+|+||+++..++. ++.+.|||||+|...+. .
T Consensus 310 ~~a~q~iq~GYkvarVEQtEt~l~~e~r~~~~~~kdkvvrRev~~ilt~GT~td~~l~~-~~~akylmai~e~~~~~--~ 386 (1125)
T KOG0217|consen 310 YWADQFIQKGYKVARVEQTETPLGKEIRERKTGKKDKVVRREVCRILTNGTLTDIALLT-SDLAKYLMAIKESEESY--S 386 (1125)
T ss_pred hHHHHHHhccceeeeeccccChHHhhhhhcccccchhhHHHHHHHHhcCCcchhHHHhc-cHHHHHHHHHhhcCCCC--C
Confidence 99999999999999999999999999999999999999999999999999999977665 44678999999987642 2
Q ss_pred CCCCEEEEEEEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcCCCccccccCCccccCh
Q 001977 469 STDRCFGICVVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDA 548 (987)
Q Consensus 469 ~~~~~~Gva~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~~~~~~~l~p~~~f~d~ 548 (987)
.+...||+|++|++||+|+++||+||.+|+.|+|+|+|++|+|+|.+.++++..|..+++....+..+..+.|..+||+.
T Consensus 387 ~~~~s~gvc~iDtstge~~~~eF~DDr~~s~L~tlLs~~rp~E~I~e~~~ls~~t~~~ik~~~~~~~~~n~~~~~eFwds 466 (1125)
T KOG0217|consen 387 TGEVSFGVCFIDTSTGEINIGEFCDDRHCSKLDTLLSQVRPVELIEERKNLSDPTKVIIKLKLSSNLVENLVPKSEFWDS 466 (1125)
T ss_pred cCceeeeEEEEEcccceEEEEEeecchhhhHHHHHHHcccHHHHHHHhhccCCceeeeeeeeecchhhhcccChhhhcch
Confidence 46788999999999999999999999999999999999999999999999999888777766666667777888899999
Q ss_pred hhhHHHH--HHHHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHHHHHHHhcchhhhhc
Q 001977 549 ETTVLEI--KNIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLR 626 (987)
Q Consensus 549 ~~~~~~l--~~~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL~YL~~~~ld~~ll~ 626 (987)
+++..++ ..||... |...+|.++..- ..+++++++|||++++||+++++|+.|++
T Consensus 467 ek~~~eii~~dy~~~~--------------------g~e~~~sil~~p---~~~~~la~safg~~~~Ylk~~~id~~lls 523 (1125)
T KOG0217|consen 467 EKTGREIISEDYFESL--------------------GLEDSPSILKSP---NTDKELALSAFGGLFYYLKKLLIDEELLS 523 (1125)
T ss_pred hhHHHHHhhhhhhhcc--------------------cccCchhhccCC---CccchhhHHHHHHHHHHHHHHhhHHHHhh
Confidence 9998765 2444310 123455554332 24568999999999999999999999999
Q ss_pred ccccccccCCCccccCCCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHH
Q 001977 627 FAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706 (987)
Q Consensus 627 ~~~f~~~~~~~~~~~~~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~Rl 706 (987)
+++|..|+... ...|+||++||+|||||.|.++|+.+||||.++|+|.||||||||++||++||+|.+.|++||
T Consensus 524 m~n~~ey~~~~------~s~mvlD~~tL~NleIf~Ns~~G~~~gtL~~~~~~csTpfGKRllk~Wl~~Pl~~~~~I~~R~ 597 (1125)
T KOG0217|consen 524 MKNFEEYDSLD------QSEMVLDGATLENLEIFSNSRNGGDEGTLFYAVNRCSTPFGKRLLKTWLMAPLCDKEDIKQRQ 597 (1125)
T ss_pred hhhhhhcchhc------ccceeecchhhhhhhhhccCCCCCCchhHHHHHhhccChHHHHHHHHHhhCcCCCHHHHHHHH
Confidence 99999886322 234999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCChHHHHHHHHhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 001977 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLG 786 (987)
Q Consensus 707 daVe~L~~~n~~l~~~lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~ 786 (987)
|+|+.|.. ++..+..+...|+++||+||+|.|||.++.. +++++.+|+++|.+|+.+...+..+.
T Consensus 598 dav~~l~~-~~~~~~~~~e~l~klPDlERlL~Rih~~~~~--------------~~k~i~~f~rvLegfk~~~~~~~~~~ 662 (1125)
T KOG0217|consen 598 DAVDSLGK-APMDRTKVGETLKKLPDLERLLVRIHNGGEK--------------NKKKIADFIRVLEGFKEINKLLGSLI 662 (1125)
T ss_pred HHHHHHhc-CchhHHHHHHHHhhCCcHHHHHHHHHhcCcc--------------chhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999997 6678889999999999999999999976532 25789999999999999998887766
Q ss_pred HHhhhc-ChHHHHHhhcCCCCchhHHHHHHHHHhhcchhhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 787 AILENT-ESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRK 865 (987)
Q Consensus 787 ~~l~~~-~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k 865 (987)
+.+... ...+|..++ .++|++..-++.+..+||+..|.++|.|+|..|++.|||++.+.+++++++|..+|+++++
T Consensus 663 ~v~~~~~~~~~is~~~---~~~p~~~~~i~~~~~af~r~~a~~eg~i~P~~Gfd~eyD~a~k~~~e~e~~L~~~L~~~rk 739 (1125)
T KOG0217|consen 663 NVLKEGEGLRLISELL---ESMPNLSEEIENWTEAFDRVKAVKEGVIVPLEGFDEEYDEAMKRVDEAENELLAYLEEYRK 739 (1125)
T ss_pred HHHHhhHHHHHHHHHh---cCcchhhHHHHHHHHHHHHHHHhhcCccCCCccccHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 554322 223333333 3589999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 866 LLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFC 945 (987)
Q Consensus 866 ~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~ 945 (987)
.++|++|.|+++++..|++|||.+...++|.+|+..+++||..||+||++.+|..++.++++++.....++.++++.+|.
T Consensus 740 ~l~c~si~~~~vGk~~y~lEvP~n~~~~s~~~~~~~S~~Kg~~RY~tp~~~kli~~l~~aee~~~~~~~d~~~r~~~~f~ 819 (1125)
T KOG0217|consen 740 RLGCSSIVFVDVGKDVYQLEVPENGGVPSSLRYELMSAKKGVSRYYTPDLRKLIAHLDEAEERKKSSLSDLKRRLIVRFD 819 (1125)
T ss_pred hcCCCceeEeecCceEEEEecCcccCCCCchHHHHHHhhcCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999987777777999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceeccc
Q 001977 946 EHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEM 986 (987)
Q Consensus 946 ~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~i 986 (987)
+|+..|++++.++|.||||+|+|.. .-+...++|||+|
T Consensus 820 ~~~~~w~~tv~~~a~iD~l~sla~~---s~~~~~~~Crp~i 857 (1125)
T KOG0217|consen 820 EHYIIWQATVKALASIDCLLSLAET---SKGLGGPMCRPEI 857 (1125)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHh---hccCCCCccccee
Confidence 9999999999999999999998443 3356788999987
No 2
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=100.00 E-value=1e-94 Score=890.89 Aligned_cols=550 Identities=25% Similarity=0.362 Sum_probs=461.8
Q ss_pred CCHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccceeccC------CCCccccCcccHHHHHHHHHHcCCe
Q 001977 327 LSEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKG------EQPHCGFPERNFSMNVEKLARKGYR 400 (987)
Q Consensus 327 ~TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~~~~~------~~~~~GfPe~s~~~~~~~Lv~~Gyk 400 (987)
+||||+|||+||++|||+|||||||+|||||++||+++|++|||++|.+ .+||||||+|+++.|+++||++|||
T Consensus 1 ~TPm~~Qy~~iK~~~~D~iLffr~GdFYElf~eDA~~~a~~L~i~lt~r~~~~~~~~pm~GvP~ha~~~yl~kLv~~G~k 80 (840)
T TIGR01070 1 LTPMMQQYLKLKAEHPDALLFFRMGDFYELFYEDAKKAAQLLDISLTSRGQSADEPIPMAGIPYHAVEAYLEKLVKQGES 80 (840)
T ss_pred CCHHHHHHHHHHHhCCCEEEEEEcCCEEEEehhhHHHHHHHhCeEEeecCCCCCCCCCcccCCHHHHHHHHHHHHHCCCE
Confidence 6999999999999999999999999999999999999999999999975 2799999999999999999999999
Q ss_pred EEEEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCccccccccCCCCCCcEEEEEEecCCCCCCCCCCCEEEEEEEe
Q 001977 401 VLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELLSANPDASYLMALTESNQSPASQSTDRCFGICVVD 480 (987)
Q Consensus 401 VavveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~~l~~~~~~~yLlaI~e~~~~~~~~~~~~~~Gva~vD 480 (987)
||||||+|+|... .++|+||||+||||||+++++++.. .+++||+||.+.. ..||+||+|
T Consensus 81 Vai~eQ~e~~~~~----------kg~v~Rev~ri~TpGT~~~~~~l~~-~~~nyl~ai~~~~---------~~~gla~~D 140 (840)
T TIGR01070 81 VAICEQIEDPKTA----------KGPVEREVVQLITPGTVSDEALLPE-RQDNLLAAIAQES---------NGFGLATLD 140 (840)
T ss_pred EEEEEecCCchhc----------CCceeeEEEEEECCCcccccccccC-CCCceEEEEEeCC---------CeEEEEEEE
Confidence 9999999998642 2599999999999999999998864 3789999997421 249999999
Q ss_pred CCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcCCCccccccCCccccChhhhHHHHHHHHh
Q 001977 481 VATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAETTVLEIKNIYN 560 (987)
Q Consensus 481 ~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~~~~~~~l~p~~~f~d~~~~~~~l~~~~~ 560 (987)
+|||+|++++|.|+ ..|.+.|.+++|+|||++.+. +......+ . .|+...+...+...|+
T Consensus 141 ~sTG~~~~~~~~d~---~~l~~~l~~~~P~Eil~~~~~-~~~~~~~~---------~-------~f~~~~~~~~l~~~f~ 200 (840)
T TIGR01070 141 LTTGEFKVTELADK---ETLYAELQRLNPAEVLLAEDL-SEMEAIEL---------R-------EFRKDTAVMSLEAQFG 200 (840)
T ss_pred ccccEEEEEEecCH---HHHHHHHhccCCeEEEEcCCC-ChHHHHHh---------H-------hcchhHHHHHHHHhcC
Confidence 99999999999874 369999999999999998764 22221110 0 2333344444555543
Q ss_pred hhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHHHHHHHhcchhhhhcccccccccCCCccc
Q 001977 561 RITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLRFAKFELLPCSGFGD 640 (987)
Q Consensus 561 ~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL~YL~~~~ld~~ll~~~~f~~~~~~~~~~ 640 (987)
... + ..++ + ....++++|+|+++.||+.+... .+.... .+..
T Consensus 201 ~~~---l------------~~~~----------~----~~~~~~~~a~g~ll~Yl~~~~~~-~~~~~~--------~~~~ 242 (840)
T TIGR01070 201 TED---L------------GGLG----------L----RNAPLGLTAAGCLLQYAKRTQRT-ALPHLQ--------PVRL 242 (840)
T ss_pred ccc---h------------hhcC----------C----CCCHHHHHHHHHHHHHHHHhChh-hhhhCC--------CcEE
Confidence 110 0 0000 0 12467899999999999998654 222222 2334
Q ss_pred cCCCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHH
Q 001977 641 MAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFA 720 (987)
Q Consensus 641 ~~~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~ 720 (987)
+..+++|+||++|++||||+.|.. |+.+||||++||+|+|+||+|+||+||++||+|+++|++|||+|++|++ +..++
T Consensus 243 ~~~~~~m~lD~~t~~~LEl~~~~~-~~~~gSL~~~ld~t~T~~G~RlLr~wl~~Pl~d~~~I~~Rld~Ve~l~~-~~~l~ 320 (840)
T TIGR01070 243 YELQDFMQLDAATRRNLELTENLR-GGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDTVEVLLR-HFFLR 320 (840)
T ss_pred ECCCCEEEeCHHHHHhccCCccCC-CCCCCcHHHHHhhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHh-CHHHH
Confidence 566889999999999999999986 5578999999999999999999999999999999999999999999997 56788
Q ss_pred HHHHHhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHh
Q 001977 721 LEFRKALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHI 800 (987)
Q Consensus 721 ~~lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l 800 (987)
..++..|++++||||+++|+..+. + ++++|..+..+|..+..+.+.+.. ..++.|..+
T Consensus 321 ~~l~~~L~~i~Dlerll~ri~~~~-~--------------~~~dl~~l~~~l~~~~~l~~~l~~-------~~~~~l~~l 378 (840)
T TIGR01070 321 EGLRPLLKEVGDLERLAARVALGN-A--------------RPRDLARLRTSLEQLPELRALLEE-------LEGPTLQAL 378 (840)
T ss_pred HHHHHHhccCcCHHHHHHHHHcCC-C--------------CHHHHHHHHHHHHHHHHHHHHHHh-------cCcHHHHHH
Confidence 899999999999999999998642 2 257888999998888877665432 345667776
Q ss_pred hcCCCCchhHHHHHHHHHhhcchhh--hcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEc
Q 001977 801 LTPGKGLPAIVSILKHFKDAFDWVE--ANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIG 878 (987)
Q Consensus 801 ~~~~~~lp~l~~ll~~i~~~iD~~~--a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~ 878 (987)
.. .++++.++.+.|+++|+... ...+|++| ++|+|++||++|+.++++++.+.++.+++++.++++++++....
T Consensus 379 ~~---~l~~~~~l~~~i~~~i~~~~~~~~~~~~~I-~~g~~~~Ld~lr~~~~~~~~~l~~l~~~~~~~~~i~~lk~~~~~ 454 (840)
T TIGR01070 379 AA---QIDDFSELLELLEAALIENPPLVVRDGGLI-REGYDEELDELRAASREGTDYLARLEARERERTGIPTLKVGYNA 454 (840)
T ss_pred HH---hcccHHHHHHHHHHHHhcCCccccccCCee-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEEec
Confidence 64 35677778888888887422 22356666 99999999999999999999999999999999999888876666
Q ss_pred CeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 879 KDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAAT 958 (987)
Q Consensus 879 k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~i 958 (987)
..||+|+|+++...++|++|++.++++|.+||+||+++++++++.++++++..++.+|+.+|+..+.+|.+.|..++++|
T Consensus 455 ~~gy~iev~~~~~~~vp~~~i~~~s~~~~~rf~tpel~~l~~~l~~~~~~~~~~e~~i~~~L~~~i~~~~~~l~~~~~~l 534 (840)
T TIGR01070 455 VFGYYIEVTRGQLHLVPAHYRRRQTLKNAERYITPELKEKEDKVLEAEGKILALEKELFEELRELLKKYLEALQEAARAL 534 (840)
T ss_pred CceEEEEEehhhhhcCCcceEEEEeccCceEEcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcccchhhhhhcccCCceecccC
Q 001977 959 AGLTLILLDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 959 AeLD~L~Sla~l~kA~~A~~~~yvRP~in 987 (987)
|+||||+|| |.+|.+++||||+|+
T Consensus 535 a~lD~l~s~-----A~~a~~~~~~~P~~~ 558 (840)
T TIGR01070 535 AELDVLANL-----AEVAETLHYTRPRFG 558 (840)
T ss_pred HHHHHHHHH-----HHHHHHCCCcCceec
Confidence 999999998 888999999999984
No 3
>PRK05399 DNA mismatch repair protein MutS; Provisional
Probab=100.00 E-value=4.9e-94 Score=890.22 Aligned_cols=560 Identities=27% Similarity=0.384 Sum_probs=472.4
Q ss_pred ccCCCHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccceeccCC------CCccccCcccHHHHHHHHHHc
Q 001977 324 LRNLSEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGE------QPHCGFPERNFSMNVEKLARK 397 (987)
Q Consensus 324 ~~~~TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~~~~~~------~~~~GfPe~s~~~~~~~Lv~~ 397 (987)
.+++||||+|||+||++|||+|||||||+|||||++||+++|++|||++|.++ .||||||+|+++.|+++||++
T Consensus 5 ~~~~TP~~~Qy~~iK~~~~D~ilffr~GdFYElf~eDA~~~s~~L~i~lt~r~~~~~~~~pm~GvP~h~~~~yl~kLv~~ 84 (854)
T PRK05399 5 MSKLTPMMQQYLEIKAQYPDALLFFRMGDFYELFFEDAKKASRLLDITLTKRGKSAGEPIPMAGVPYHAAEGYLAKLVKK 84 (854)
T ss_pred cCCCCHHHHHHHHHHhhCCCEEEEEEcCCEEEEeHhhHHHHHHHhCeEEeeccCCCCCCCCEecCcHHHHHHHHHHHHHC
Confidence 35799999999999999999999999999999999999999999999999753 499999999999999999999
Q ss_pred CCeEEEEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCccccccccCCCCCCcEEEEEEecCCCCCCCCCCCEEEEE
Q 001977 398 GYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELLSANPDASYLMALTESNQSPASQSTDRCFGIC 477 (987)
Q Consensus 398 GykVavveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~~l~~~~~~~yLlaI~e~~~~~~~~~~~~~~Gva 477 (987)
|||||||||+|||..+ .++|+|+||+||||||+++++++.. .+++||+||.+. ...||+|
T Consensus 85 GyKVaI~EQ~e~~~~~----------k~~v~R~v~~i~TpGT~~~~~~l~~-~~~~yl~ai~~~---------~~~~Gia 144 (854)
T PRK05399 85 GYKVAICEQVEDPATA----------KGPVKREVVRIVTPGTVTDEALLDE-KQNNYLAAIAQD---------GGGYGLA 144 (854)
T ss_pred CCEEEEEEecCChhhc----------CCccceEEEEEECCCeeecccccCC-CCCcEEEEEEEC---------CCeEEEE
Confidence 9999999999999642 2599999999999999999998864 478999999864 2369999
Q ss_pred EEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcCCCccccccCCccccChhhhHHHHHH
Q 001977 478 VVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAETTVLEIKN 557 (987)
Q Consensus 478 ~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~~~~~~~l~p~~~f~d~~~~~~~l~~ 557 (987)
|+|++||+|++++| .+++|+++|.+++|+|||++.+..+.. +... . ..... .+.. .|+...+.+.|..
T Consensus 145 ~~D~stg~~~~~~~----~~~~L~~~l~~~~P~Eil~~~~~~~~~----~~~~-~-~~~~~-~~~~-~f~~~~~~~~l~~ 212 (854)
T PRK05399 145 YLDLSTGEFRVTEL----DEEELLAELARLNPAEILVPEDFSEDE----LLLL-R-RGLRR-RPPW-EFDLDTAEKRLLE 212 (854)
T ss_pred EEECCCCeEEEEEE----cHHHHHHHHHhcCCcEEEEcCCcchhh----Hhhc-c-cccee-cccc-ccChHHHHHHHHH
Confidence 99999999999999 357899999999999999998754432 1111 1 11111 1212 3477777777887
Q ss_pred HHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHHHHHHHhcchhhhhcccccccccCCC
Q 001977 558 IYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLRFAKFELLPCSG 637 (987)
Q Consensus 558 ~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL~YL~~~~ld~~ll~~~~f~~~~~~~ 637 (987)
+|...+. . .+ . ....++++|+|+++.||+.+... .+.....
T Consensus 213 ~f~~~~~---------------~-----~~--------~--~~~~~~~~a~~all~Yl~~~~~~-~~~~~~~-------- 253 (854)
T PRK05399 213 QFGVASL---------------D-----GF--------G--VDLPLAIRAAGALLQYLKETQKR-SLPHLRS-------- 253 (854)
T ss_pred HhCcCCc---------------c-----cc--------C--CCCHHHHHHHHHHHHHHHHhchh-hhhccCC--------
Confidence 7752110 0 01 0 02367899999999999998763 2322222
Q ss_pred ccccCCCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCCh
Q 001977 638 FGDMAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQ 717 (987)
Q Consensus 638 ~~~~~~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~ 717 (987)
+..+...++|+||++|++||||+.|.. |+.+||||++||||+|+||+|+||+||++||+|+++|++|||+|++|++ +.
T Consensus 254 ~~~~~~~~~m~lD~~tl~~Lei~~~~~-~~~~gSL~~~ld~t~T~~G~RlLr~wl~~Pl~d~~~I~~R~d~Ve~l~~-~~ 331 (854)
T PRK05399 254 PKRYEESDYLILDAATRRNLELTENLR-GGRKNSLLSVLDRTVTAMGGRLLRRWLHRPLRDREAIEARLDAVEELLE-DP 331 (854)
T ss_pred CEEECCCCEEEcCHHHHHhccCCccCC-CCCCCcHHHHhccCCCcHHHHHHHHHHhCcCCCHHHHHHHHHHHHHHHh-CH
Confidence 344567889999999999999999874 5678999999999999999999999999999999999999999999997 67
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHH
Q 001977 718 PFALEFRKALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQL 797 (987)
Q Consensus 718 ~l~~~lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL 797 (987)
.++..++..|+++|||+|+++|+..+. + .+++|..++.+|..+..+.+.+. ...++.|
T Consensus 332 ~~~~~l~~~L~~i~Dlerll~ri~~~~-~--------------~~~dl~~l~~~l~~~~~l~~~l~-------~~~~~~l 389 (854)
T PRK05399 332 LLREDLRELLKGVYDLERLLSRIALGR-A--------------NPRDLAALRDSLEALPELKELLA-------ELDSPLL 389 (854)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcC-C--------------CHHHHHHHHHHHHHHHHHHHHHH-------hcCcHHH
Confidence 888999999999999999999997642 1 24688888888888777765443 2346677
Q ss_pred HHhhcCCCCchhHHHHHHHHHhhcchhh--hcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEE
Q 001977 798 HHILTPGKGLPAIVSILKHFKDAFDWVE--ANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYV 875 (987)
Q Consensus 798 ~~l~~~~~~lp~l~~ll~~i~~~iD~~~--a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~ 875 (987)
..+... ++++.++++.|+++||... ...++.++ ++|+|++||++|+.++++.+.++++++++++.++++++++.
T Consensus 390 ~~l~~~---l~~~~~l~~~i~~~i~~~~~~~~~~~~~i-~~g~~~~Ld~lr~~~~~~~~~l~~~~~~~~~~~~~~~l~~~ 465 (854)
T PRK05399 390 AELAEQ---LDPLEELADLLERAIVEEPPLLIRDGGVI-ADGYDAELDELRALSDNGKDWLAELEARERERTGISSLKVG 465 (854)
T ss_pred HHHHhh---cccHHHHHHHHHHHHccCCchhcccCCEE-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEE
Confidence 777653 5667788888889998532 22346666 99999999999999999999999999999999999888887
Q ss_pred EEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 876 TIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMV 955 (987)
Q Consensus 876 ~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~ 955 (987)
..+..||+|+|+++...++|++|++.+++++..||+||++++|++++.++++++.+++.+|+++|++.+.+|...|..++
T Consensus 466 ~~~~~gy~iev~~~~~~~vp~~~~~~~s~~~~~rf~t~~l~~l~~~l~~~~~~~~~~e~~i~~~l~~~i~~~~~~l~~~~ 545 (854)
T PRK05399 466 YNKVFGYYIEVTKANLDKVPEDYIRRQTLKNAERYITPELKELEDKILSAEEKALALEYELFEELREEVAEHIERLQKLA 545 (854)
T ss_pred EcCceeEEEEEEcchhhhCChhhhheeeccCeEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77789999999999888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcccchhhhhhcccCCceecccC
Q 001977 956 AATAGLTLILLDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 956 ~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~in 987 (987)
++||+||||+|| |.+|..++||||+|+
T Consensus 546 ~~la~lD~l~s~-----A~~a~~~~~~~P~~~ 572 (854)
T PRK05399 546 KALAELDVLASL-----AEVAEENNYVRPEFT 572 (854)
T ss_pred HHHHHHHHHHHH-----HHHHHHCCccccEEe
Confidence 999999999999 888899999999983
No 4
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-87 Score=818.08 Aligned_cols=568 Identities=29% Similarity=0.402 Sum_probs=470.7
Q ss_pred ccCCCHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccceeccCC-CCccccCcccHHHHHHHHHHcCCeEE
Q 001977 324 LRNLSEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGE-QPHCGFPERNFSMNVEKLARKGYRVL 402 (987)
Q Consensus 324 ~~~~TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~~~~~~-~~~~GfPe~s~~~~~~~Lv~~GykVa 402 (987)
++++||||||||+||++|+|++|||+||+|||+|++||.+++++|+|++|+|+ +||||||+|+++.|+.+||++|||||
T Consensus 3 ~~~~tP~m~qy~~ik~~~~d~llffr~GdfYelf~~DA~~~s~~l~itlT~r~~~pm~gvP~h~~~~yl~~li~~g~kVA 82 (843)
T COG0249 3 KAKLTPMMQQYLEIKAQYPDTLLFFRMGDFYELFFEDAKIAARLLDITLTKRGNIPMAGVPYHALDYYLAKLIELGYKVA 82 (843)
T ss_pred cccCCcHHHHHHHHHHhCCccEEEEecccchhhhHHHHHHHHHhhCceeecCCCCcCCCCccccHHHHHHHHHhCCCeEE
Confidence 56899999999999999999999999999999999999999999999999876 59999999999999999999999999
Q ss_pred EEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCccccccccCCCCCCcEEEEEEecCCCCCCCCCCCEEEEEEEeCC
Q 001977 403 VVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELLSANPDASYLMALTESNQSPASQSTDRCFGICVVDVA 482 (987)
Q Consensus 403 vveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~~l~~~~~~~yLlaI~e~~~~~~~~~~~~~~Gva~vD~s 482 (987)
||||+|+|..+ .++|+|+|++|+||||++|+.++... +++||+||..... . .||+||+|++
T Consensus 83 iceQ~e~~~~~----------k~~v~R~v~rv~TpGt~~d~~~l~~~-~~n~l~a~~~~~~-------~-~~gla~~dls 143 (843)
T COG0249 83 ICEQLEDPAEA----------KGVVERKVVRVVTPGTLTDEALLSDR-ENNYLAALAIDRD-------G-KVGLAFIDLS 143 (843)
T ss_pred EEEcccChhhh----------cCcceeEEEEEECCCeeecccccccc-ccceEEEEEecCC-------C-EEEEEEEEcc
Confidence 99999999753 24999999999999999999988643 7899999986431 2 7999999999
Q ss_pred CCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcCCCccccccCCccccChhhhHHHHHHHHhhh
Q 001977 483 TSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAETTVLEIKNIYNRI 562 (987)
Q Consensus 483 TG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~~~~~~~l~p~~~f~d~~~~~~~l~~~~~~~ 562 (987)
||+|.+.+|. +.+|.+.|.+++|+|||++....+......... +.....+ ..+|+...+...|..+|...
T Consensus 144 tGef~~~~~~----~~~l~~~l~r~~p~Eil~~~~~~~~~~~~~~~~-----~~~~~~~-~~~f~~~~~~~~l~~~~~~~ 213 (843)
T COG0249 144 TGEFFVSEFE----REKLLSELKRLQPKELLLSESLLSSTLAEIQKG-----LFVVRLP-ASFFDEDDAEEILSEYFGVR 213 (843)
T ss_pred cCeEEEEEee----HHHHHHHHHhCCCcEEEeccccCchhhhhhhhc-----eeeeecc-hhhcCccHHHHHHHHHhCcc
Confidence 9999999998 678999999999999999988665432221111 1111112 24566666777777777532
Q ss_pred ccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHHHHHHHhcchhhhhcccccccccCCCccccC
Q 001977 563 TAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLRFAKFELLPCSGFGDMA 642 (987)
Q Consensus 563 ~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL~YL~~~~ld~~ll~~~~f~~~~~~~~~~~~ 642 (987)
+. ..++. ....++++|+|+++.|++.++... + .++ ..+..+.
T Consensus 214 ~l---------------~~~~~--------------~~~~~~~~a~~~ll~Y~~~t~~~~-l---~~~-----~~~~~~~ 255 (843)
T COG0249 214 DL---------------DGFGL--------------ISTPLALSAAGALLSYLKDTQKTF-L---PHI-----QIIQRYD 255 (843)
T ss_pred cc---------------ccccc--------------ccchHHHHHHHHHHHHHHHhhhcc-c---ccc-----ccceeec
Confidence 21 11111 113689999999999998776541 2 222 2334567
Q ss_pred CCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHH
Q 001977 643 KKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALE 722 (987)
Q Consensus 643 ~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~ 722 (987)
..++|.||.+|++||||++|.++++.+||||++||+|+|+||+|||++||++||+|.++|+.|||+|++|.. +..++..
T Consensus 256 ~~~~m~lD~~t~~nLEl~~~~~~~~~~gSL~~~ld~t~T~mG~RlL~~wl~~PL~~~~~I~~Rld~Ve~l~~-~~~l~~~ 334 (843)
T COG0249 256 LEDYMVLDAATRRNLELFSNLRGNGKKGSLFWLLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKD-NPELREK 334 (843)
T ss_pred cCcEEEEcHHHHhcccccccCCCCCCCCcHHHHhccCCCchhHHHHHHHhhCcccCHHHHHHHHHHHHHHHh-hhHHHHH
Confidence 788999999999999999999888999999999999999999999999999999999999999999999997 5578999
Q ss_pred HHHhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhc
Q 001977 723 FRKALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHILT 802 (987)
Q Consensus 723 lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~ 802 (987)
++..|+++||+||+++|+..+. + ++++|..+..+|..+..+.+.+.... ....+..+..
T Consensus 335 L~~~L~~v~DleRl~~Rl~~~~-~--------------~~rDl~~l~~~l~~~~~i~~~l~~~~------~~~~l~~~~~ 393 (843)
T COG0249 335 LREMLKKVPDLERLLSRLSLGR-A--------------SPRDLLRLRDSLEKIPEIFKLLSSLK------SESDLLLLLE 393 (843)
T ss_pred HHHHHhcCcCHHHHHHHHHcCC-C--------------ChhhHHHHHHHHHHHHHHHHHHhccc------cchhhhHHhh
Confidence 9999999999999999998653 2 25688889999888888776554321 1112222222
Q ss_pred CCCCchhHHHHHHHHHhhcchhhh--cCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCe
Q 001977 803 PGKGLPAIVSILKHFKDAFDWVEA--NNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKD 880 (987)
Q Consensus 803 ~~~~lp~l~~ll~~i~~~iD~~~a--~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~ 880 (987)
....++.+.++...++.+|..... ..+ .+ ++.|++++||++|..++..++.+.++..+.+...|+.+++....+..
T Consensus 394 ~i~~~~~~~e~~~ll~~~i~~~~~~~~~~-~i-i~~g~~~eLd~lr~~~~~~~~~i~~le~~~r~~~gi~slki~~n~v~ 471 (843)
T COG0249 394 DIESLDYLAELLELLETAINEDPPLAVRD-GI-IKEGYNIELDELRDLLNNAKEWIAKLELEERERTGIKSLKIKYNKVY 471 (843)
T ss_pred hhhccccHHHHHHHHHHHhhhcchhhcch-hH-HhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhhhccc
Confidence 112345456777777778875332 223 34 49999999999999999999999999988999999887654444458
Q ss_pred eEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 881 LYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAG 960 (987)
Q Consensus 881 gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAe 960 (987)
||+|+|++.....+|.+|++.++.|+..||+|+++++++.++.++++++..++.+++.++++.+..|.+.|++++.+||+
T Consensus 472 Gy~ievt~~~~~~~p~~~ir~qt~kn~~rf~t~el~~~e~~i~~a~~~i~~lE~~l~~~~~~~i~~~~~~l~~~a~aLa~ 551 (843)
T COG0249 472 GYYIEVTKSNAKLVPDDYIRRQTLKNAERFTTPELKELEEKLLDAEEKILALEYELFDELREKILAHINELQALAKALAE 551 (843)
T ss_pred eeEEEechhccccCchHHHHHHHHhcceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcccchhhhhhcccCCceecccC
Q 001977 961 LTLILLDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 961 LD~L~Sla~l~kA~~A~~~~yvRP~in 987 (987)
||||+|| |..|...+||||+|+
T Consensus 552 lD~l~sl-----A~~a~~~~y~rP~~~ 573 (843)
T COG0249 552 LDVLSSL-----AEIAAEQNYVRPEFV 573 (843)
T ss_pred HHHHHHH-----HHHHhhCCCCCceec
Confidence 9999999 888999999999974
No 5
>KOG0218 consensus Mismatch repair MSH3 [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-78 Score=682.97 Aligned_cols=611 Identities=25% Similarity=0.360 Sum_probs=463.3
Q ss_pred cCCCHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccce-eccCCCCccccCcccHHHHHHHHHHcCCeEEE
Q 001977 325 RNLSEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQ-YMKGEQPHCGFPERNFSMNVEKLARKGYRVLV 403 (987)
Q Consensus 325 ~~~TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~-~~~~~~~~~GfPe~s~~~~~~~Lv~~GykVav 403 (987)
.++||+++||.|+|++|.|+||+.+||+.|.+|++||+|++++|||. ++.+++..|.||.++++.|+++||++||||||
T Consensus 160 s~yTPLeqQ~~elK~~h~d~VL~ievGYkyRfFgeDAeiasrvLgIych~dhnFmtaS~P~~Rl~vHleRLv~~g~KVaV 239 (1070)
T KOG0218|consen 160 SKYTPLEQQVKELKMHHRDKVLVIEVGYKYRFFGEDAEIASRVLGIYCHNDHNFMTASFPDVRLNVHLERLVHHGLKVAV 239 (1070)
T ss_pred cccCcHHHHHHHHHhhCCceEEEEEecceEEeecccHHHHHHhhceEEEeccceeeccCCcchhhHHHHHHHhcCceEEE
Confidence 36899999999999999999999999999999999999999999996 57788999999999999999999999999999
Q ss_pred EeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCcccccc--ccCC----CCCCcEEEEEEecCCCCCCCCCCCEEEEE
Q 001977 404 VEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGE--LLSA----NPDASYLMALTESNQSPASQSTDRCFGIC 477 (987)
Q Consensus 404 veQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~--~l~~----~~~~~yLlaI~e~~~~~~~~~~~~~~Gva 477 (987)
|+|+||++.+. .+.+++.++.|.|++|||+||+.++. .+.. +..++|++|+.++....-...+...+|+.
T Consensus 240 VkQtETAAiKs----~gasRsslF~RklsavyTKaTl~eds~~~~r~e~~~~~~ssfllcv~dn~~ksk~ksg~v~vgli 315 (1070)
T KOG0218|consen 240 VKQTETAAIKS----HGASRSSLFERKLSAVYTKATLGEDSTFVLRGERILGDTSSFLLCVRDNVHKSKEKSGVVKVGLI 315 (1070)
T ss_pred EeehhhHHHHh----cCCcccchHHHHHHHHhhhhhhccccccccchhhhcCCcceEEEEEehhhhhhhhhcCceEEEEE
Confidence 99999998642 23467889999999999999998653 1111 12578999999855432223457889999
Q ss_pred EEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhh-cCCCccccccCCccccChhhh-HHHH
Q 001977 478 VVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRH-TRNPLVNDLVPLSEFWDAETT-VLEI 555 (987)
Q Consensus 478 ~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~-~~~~~~~~l~p~~~f~d~~~~-~~~l 555 (987)
-|.++||++.+.+|.|+..++.|+|.|..++|.|+|++.. +++.+...+.+. .+.. ...... ++-+.+ .+.+
T Consensus 316 gVqlstGevVydeFqdnf~rseLqtrisslqP~ElLl~~~-ls~qt~all~~~~Vsve----~~~~rv-~r~~naV~q~i 389 (1070)
T KOG0218|consen 316 GVQLSTGEVVYDEFQDNFARSELQTRISSLQPIELLLNTD-LSPQTVALLFKDNVSVE----LIHKRV-YRLENAVVQAI 389 (1070)
T ss_pred EEecCCCcEehHhhhhhHHHHHHHHHHhccCcceeecCCC-CcHHHHHHHHhcccchh----hhhhhh-hhchhHHHHHH
Confidence 9999999999999999999999999999999999999865 677777665532 2211 111111 222221 2222
Q ss_pred HHHHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchH-HHHHHHHHHHHHHHhcchhhhhccccccccc
Q 001977 556 KNIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQ-VLSALGGTLFYLKKSFLDETLLRFAKFELLP 634 (987)
Q Consensus 556 ~~~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~l-al~AlgalL~YL~~~~ld~~ll~~~~f~~~~ 634 (987)
+-.+....+..-+|+ -..+. +++.-+++. ..+ .++.++.++.||.+..+++ ++..++|.
T Consensus 390 kla~e~~q~f~~~k~-------~l~gs------~ii~li~nl---~~psvic~la~~is~lkefnlE~-~l~~psf~--- 449 (1070)
T KOG0218|consen 390 KLANEKIQNFEDDKE-------MLEGS------EIICLIMNL---SHPSVICLLAKLISHLKEFNLEQ-VLLIPSFY--- 449 (1070)
T ss_pred HHHHHHHhhhhhhhh-------hhhhh------hhhhhhhcC---CCchHHHHHHHHHHHHHHhchHH-heeccccc---
Confidence 211111110000000 00000 111122222 134 4455999999999998875 44445663
Q ss_pred CCCccccCCCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHH-
Q 001977 635 CSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLR- 713 (987)
Q Consensus 635 ~~~~~~~~~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~- 713 (987)
+++....+|.|+++||++||||.|.+||+.+|||||+||||.|.||.||||.|+.+||+|...|++|+|||+++.
T Consensus 450 ----s~~ss~e~Mtls~ntLq~Leif~nqtd~~~kGSLfwvldhT~TsfG~RmLr~WvtkPLvd~~~I~eRLDAVeeits 525 (1070)
T KOG0218|consen 450 ----SPFSSKEHMTLSPNTLQSLEIFTNQTDGSEKGSLFWVLDHTRTSFGLRMLREWVTKPLVDVHQIEERLDAVEEITS 525 (1070)
T ss_pred ----CcccccceeeechhhhhceeeeeecCCCCcccceEEEeccchhHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHh
Confidence 234566799999999999999999999999999999999999999999999999999999999999999999993
Q ss_pred cC-ChHHHHHHHHhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHH--HHhh
Q 001977 714 GV-NQPFALEFRKALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLG--AILE 790 (987)
Q Consensus 714 ~~-n~~l~~~lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~--~~l~ 790 (987)
.. |...+..++..|.++|||+|-|.||+.+.+ ++|. .+++ -+..|+.+...|+.+...+.... .--.
T Consensus 526 hssnS~vf~si~~~l~rlpDl~rgL~rIy~~tC-tp~~--eff~-------vlk~iy~a~s~fq~~~~~~~~~~~s~~~s 595 (1070)
T KOG0218|consen 526 HSSNSIVFESINQMLNRLPDLLRGLNRIYYGTC-TPRK--EFFF-------VLKQIYSAVSHFQMHQSYLEHFKSSDGRS 595 (1070)
T ss_pred cccchHHHHHHHHHHHhCcHhHhhHHHHhcccC-CcHH--HHHH-------HHHHHHHHHHHHHHHhhhhhhhccccccc
Confidence 32 444788899999999999999999987653 3321 1111 12333333333333221111110 0012
Q ss_pred hcChHHHHHhhcCCCCchhHHHHHHHHHhhcchhhhcCCCC--eeeCCC-CCHhHHHHHHH---HHHHH---HHHHHHHH
Q 001977 791 NTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGR--IIPHGG-VDMDYDSACKK---VKEIE---ASLTKHLK 861 (987)
Q Consensus 791 ~~~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~~a~~~g~--iipk~G-~d~eLD~lr~~---i~~ie---~~L~~~l~ 861 (987)
.++|++|+.++..+. -|.+...+.+|..+++..++.+... ++ ++- --|.+++.+.. +++++ .+|.++|+
T Consensus 596 ~~qS~LLrrlisel~-~p~~~s~~~hfL~mln~~aa~~gnk~d~f-kd~snfpl~~e~~di~~virE~~ms~~~~~~hLa 673 (1070)
T KOG0218|consen 596 GKQSPLLRRLISELN-EPLSTSQLPHFLTMLNVSAAMEGNKDDQF-KDFSNFPLYDESEDIIKVIRESEMSRSQLKEHLA 673 (1070)
T ss_pred hhccHHHHHHHHHhc-CccccccHHHHHHHhhHHHHhhCChHHhh-hhhccCcchhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 357899999885421 2666677778888888655542211 11 111 13555554443 23332 35677999
Q ss_pred HHHHHhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 862 EQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLI 941 (987)
Q Consensus 862 ~~~k~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~ 941 (987)
++|+.+..|++.|..+++..|+|||+.+..+++|.+|+.+++||...||+||+++++..+|..+++.+.......+..+.
T Consensus 674 eiRk~Lk~pnlef~~vsgv~flIEvkns~~kkiP~dWiKvnsTk~vsRfhtP~iq~~l~eL~~~~e~L~i~sea~~~sFL 753 (1070)
T KOG0218|consen 674 EIRKYLKRPNLEFRQVSGVDFLIEVKNSQIKKIPDDWIKVNSTKMVSRFHTPRIQKLLQELEYYKELLIIESEAQYKSFL 753 (1070)
T ss_pred HHHHHhcCCCceeEEecCeeEEEEecccccccCCccceeeccceeeeecCCHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceeccc
Q 001977 942 GQFCEHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEM 986 (987)
Q Consensus 942 ~~~~~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~i 986 (987)
++|.+||..|+++...+|.||||+|| |..+...|||||+|
T Consensus 754 ~kiSehYtelrkat~~LatlDCi~Sl-----A~~s~n~nYvRPtf 793 (1070)
T KOG0218|consen 754 NKISEHYTELRKATLNLATLDCILSL-----AATSCNVNYVRPTF 793 (1070)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHhccCCccCccc
Confidence 99999999999999999999999999 88999999999997
No 6
>KOG0219 consensus Mismatch repair ATPase MSH2 (MutS family) [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-41 Score=392.41 Aligned_cols=571 Identities=22% Similarity=0.280 Sum_probs=408.6
Q ss_pred CCCHHHHHHHHHHhhCC---CeEEEEeeCCeEEEechhHHHHHHhcc-----ceeccC----CCCccccCcccHHHHHHH
Q 001977 326 NLSEGQKQWWEFKSKHM---DKVIFFKMGKFYELFEMDAHVGAKELD-----LQYMKG----EQPHCGFPERNFSMNVEK 393 (987)
Q Consensus 326 ~~TP~~~Qyw~iK~~~~---D~Vlffk~GkFYEly~~DA~i~~~~L~-----l~~~~~----~~~~~GfPe~s~~~~~~~ 393 (987)
+-+.+.+-|..+=+.-+ +||.||..|+||-.|++||..+|+..- ++++.. +.-.|.+.-..|...++.
T Consensus 11 ~d~~~~~~f~~f~~~l~~p~~tvr~fdrge~ytv~geDa~~va~~v~kt~~~~k~l~~~~~~~~~~v~ls~~~~e~~vr~ 90 (902)
T KOG0219|consen 11 KDEAADRNFLKFYEGLPKPTTTVRFFDRGEYYTVHGEDAEFVARNVYKTQAVIKTLSPDNAKNTKEVSLSKGNFEKVVRE 90 (902)
T ss_pred ccchhHHHHHHHHhcCCCCCceEEEecCcceEEEeccchhhhhhhhhhhhhhheecCCcccccceEEEecHHHHHHHHHH
Confidence 44556666666655443 799999999999999999999998653 343322 233456667788889976
Q ss_pred H-HHcCCeEEEEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCcccccc-ccCCCCC-Cc---EEEEEEecCCCCCC
Q 001977 394 L-ARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGE-LLSANPD-AS---YLMALTESNQSPAS 467 (987)
Q Consensus 394 L-v~~GykVavveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~-~l~~~~~-~~---yLlaI~e~~~~~~~ 467 (987)
| +..+|+|.+++--|+ .+++..=-+||.+.+.+ ++..+.+ +. |+...+-.
T Consensus 91 ~l~~~~~~Ve~y~~~~~------------------~w~l~~~~sPGN~~~fedll~~~~~v~is~~~~~v~~~~------ 146 (902)
T KOG0219|consen 91 LLLVLRYRVEVYSSNQG------------------DWKLTKRGSPGNLVQFEDLLFSNNDVPISIISLIVKHPG------ 146 (902)
T ss_pred HHHHhccceEEeecCcc------------------ceeEEecCCCCcHHHHHHHHcccccchhhhhheeEEeec------
Confidence 5 589999999974321 23444445899987754 3322111 11 22222221
Q ss_pred CCCCCEEEEEEEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcCCCccccccCCccccC
Q 001977 468 QSTDRCFGICVVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWD 547 (987)
Q Consensus 468 ~~~~~~~Gva~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~~~~~~~l~p~~~f~d 547 (987)
..+.+.+|+|++|++.-.+++.+|.||..+++|+.+|.+++|+|+|++.+....+..++..-..++.++...+..++|-+
T Consensus 147 ~~~~~~vgv~~~d~~~~k~~~~ef~Dn~~~snle~~l~~lg~kEcll~~~~~~~~~~kl~~~~~r~g~~~t~~~~~e~~~ 226 (902)
T KOG0219|consen 147 VDGQRRVGVAFVDTINVKIGLSEFVDDDSFSNLEALLIQLGPKECVLPEGSVAGEMKKLRNIIDRCGVLITLRKKSESSW 226 (902)
T ss_pred cCCCceeEEEEechhheeeehhhhcCcHHHHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhccCeEEEEecccchhH
Confidence 13467899999999999999999999999999999999999999999954333333333222234555544443333311
Q ss_pred hhhhHHHHHHHHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHHHHHHHhcchhhhhcc
Q 001977 548 AETTVLEIKNIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLRF 627 (987)
Q Consensus 548 ~~~~~~~l~~~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL~YL~~~~ld~~ll~~ 627 (987)
...++.+...+.... ....+|+ + ...++++++.+++.||.-. -+... .
T Consensus 227 -kdv~~~l~~~l~~~~-------------------~~~~~~e----~-----~~q~a~~~~~~~i~yl~~~-~e~~~--s 274 (902)
T KOG0219|consen 227 -KDVEQDLNRLLKSQE-------------------HAAYLPE----L-----ELQLAMSALSALIKYLDLE-NEYSN--S 274 (902)
T ss_pred -HHHHHHHHhcccchh-------------------hhccchH----H-----HhHHHHHHHHHHHHHHhhc-ccccc--c
Confidence 122222222222100 0012232 2 2468999999999999432 22221 1
Q ss_pred cccccccCCCccccCCCCeeecCHHHHHhccCcccCCC-CCCcchhhh-hhhccCChHHHHHHHHHhhCcCCCHHHHHHH
Q 001977 628 AKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRS-GDSSGTLYA-QLNHCVTAFGKRLLRTWLARPLYNSGLIRER 705 (987)
Q Consensus 628 ~~f~~~~~~~~~~~~~~~~M~LD~~TL~nLEI~~n~~~-g~~~gSL~~-lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~R 705 (987)
+++++ .......+|.||.+|+++|++|+...+ -....+|.. +||||.|++|.|||++|+.+||++++.|++|
T Consensus 275 ~~~ei------~~~~~~~~m~ld~~av~alnlf~~~~~~~~~s~~L~~~~LN~c~t~~G~rll~~w~~qpL~~~~ri~~r 348 (902)
T KOG0219|consen 275 GKYEL------TNHGLHQFMRLDSAAVRALNLFPLPYNNPEKSNNLALSLLNHCKTLQGERLLRQWLKQPLRDIDRINER 348 (902)
T ss_pred ceEEE------eecchHHHhhHHHHHHHHHhhcCCCCCCccccchhhHHHHhhcccccchhhhhhhhhcchHHHHHHHHH
Confidence 23332 234566799999999999999985422 123347777 9999999999999999999999999999999
Q ss_pred HHHHHHHHcCChHHHHHHH-HhcCCCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 001977 706 QDAVAGLRGVNQPFALEFR-KALSRLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSS 784 (987)
Q Consensus 706 ldaVe~L~~~n~~l~~~lr-~~Lk~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~ 784 (987)
+|.|+.|+. +...+..++ ..|..+|||-|++.|+. .+ ...+...+++....+..+.+.+.+
T Consensus 349 ~d~v~~l~~-~~~~rq~L~~~lL~~~pdi~rl~~~l~-~~----------------~L~d~~r~yq~~~~l~~~~~~l~~ 410 (902)
T KOG0219|consen 349 HDLVEALVE-DAEIRQKLRDDLLRRIPDISRLARRLM-KA----------------NLQDVNRIYQAAKLLPTVVQVLIS 410 (902)
T ss_pred hhhHHHHHh-hhHHHHHHHHHHhhcChhHHHhhhhhh-hc----------------chHHHHHHHHHHHHhHHHHHHHHh
Confidence 999999997 455666554 57899999999999986 21 123455555555555555554433
Q ss_pred HHHHhhhcChHHHHHhhcCCCCchhHHHHHHHHHhhcchhhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 785 LGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQR 864 (987)
Q Consensus 785 l~~~l~~~~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~ 864 (987)
+.. . ...+|..-+. ....++..+.+.++.++|.+.+.+ +.++++..+|++|-++|+.+++++..+++...++.
T Consensus 411 ~~~---~-~~~ll~~~l~--~~~~~~~kf~~~ve~t~D~da~ee-~ey~VR~eFdeeL~eLrq~LdeL~~~m~~~hkrv~ 483 (902)
T KOG0219|consen 411 LSE---S-HNRLLKSPLT--EHLKKLEKFQEMVETTVDLDAEEE-NEYRVRVDFDEELQELREKLDELERKMEKLHKKVS 483 (902)
T ss_pred hhh---h-hhhhhhhhhh--hhhhhHHHHHHHHHHHhhHhHHhc-CcEEEecccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 321 1 1122222111 123456677777889999876665 77777999999999999999999999999999998
Q ss_pred HHhCCC---CeeEEEEcCeeEEEEecccccCCC--CCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 865 KLLGDT---SITYVTIGKDLYLLEVPESLRGSV--PRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQR 939 (987)
Q Consensus 865 k~l~~~---~iky~~~~k~gY~IeVp~~~~~kv--P~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~ 939 (987)
..++.. +|+.......||++.++....+.+ .++|+..++.||+++|+|..|..||+++.+.+.++...+..|.++
T Consensus 484 ~dl~~D~~kklkLe~~~~~G~~~RlTr~e~~~LR~~k~y~eLstqK~GV~FTtk~L~slN~e~~~~qk~Y~~~Q~~ivre 563 (902)
T KOG0219|consen 484 ADLGLDPKKQLKLENSAQFGWYFRVTRKEEKVLRKKKNYTELSTQKGGVKFTTKKLSSLNDEFMSLQKEYDEAQNEIVRE 563 (902)
T ss_pred hhcCCCcccceeeeccchhheeeeeeehhhhHhhccCCceEEEEeeCcEEEEhhhHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 888764 477777778999999998765433 368999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceeccc
Q 001977 940 LIGQFCEHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEM 986 (987)
Q Consensus 940 L~~~~~~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~i 986 (987)
++.....|.+.+..+.+.+|.|||+.|||. |....-.+|+||.+
T Consensus 564 vikia~tY~Ppleal~~vlAhLDv~~SFa~---~st~a~~pYvRP~~ 607 (902)
T KOG0219|consen 564 IIKIAATYTPPLEALNQVLAHLDVFVSFAH---AATVAPIPYVRPKL 607 (902)
T ss_pred HHHHHhhcCCcHHHHHHHHHHHHhheeehh---hcccCCCCccCccc
Confidence 999999999999999999999999999933 33344789999976
No 7
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=100.00 E-value=1.1e-36 Score=340.93 Aligned_cols=288 Identities=33% Similarity=0.453 Sum_probs=236.0
Q ss_pred cchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcCCCCCHHHHHHHHhcCccccC
Q 001977 669 SGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRLPDMERLLARLFASSEANG 748 (987)
Q Consensus 669 ~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk~lpDLERll~Ri~~~~~~~~ 748 (987)
+||||++||+|+|++|+|+|++||++|++|.++|++||++|++|+. +..+...++..|++++|++|++.|+..+. .
T Consensus 1 ~~sL~~~l~~~~T~~G~r~L~~wl~~Pl~~~~~I~~R~~~v~~~~~-~~~l~~~l~~~L~~~~Di~~~l~~~~~~~-~-- 76 (308)
T smart00533 1 KGSLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVE-NPELRQKLRQLLKRIPDLERLLSRIERGR-A-- 76 (308)
T ss_pred CCCHHHHHccCCCcHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHh-ChHHHHHHHHHHccCCcHHHHHHHHHcCC-C--
Confidence 4799999999999999999999999999999999999999999997 66778889999999999999999997532 1
Q ss_pred cCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCchhHHHHHHHHHhhcchh-hhc
Q 001977 749 RNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWV-EAN 827 (987)
Q Consensus 749 r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~-~a~ 827 (987)
++.+|..|+.++..+..+.+.+..... ....+++..+.. .+...+..+...++.. ...
T Consensus 77 ------------~~~el~~l~~~l~~~~~l~~~l~~~~~---~~~~~~~~~~~~------~~~~~~~~l~~~~~~~~~~~ 135 (308)
T smart00533 77 ------------SPRDLLRLYDSLEGLKEIRQLLESLDG---PLLGLLLKVILE------PLLELLELLLELLNDDDPLE 135 (308)
T ss_pred ------------CHHHHHHHHHHHHHHHHHHHHHHhcCc---HHHHHHHHhhcc------chHHHHHHHHHHhccCCccc
Confidence 246888888888888877766543210 001122332221 1112222222222211 111
Q ss_pred -CCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecC
Q 001977 828 -NSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKG 906 (987)
Q Consensus 828 -~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg 906 (987)
.++..+ ++|+|++||.+|+.+++++.+++++++++.+.++++.+++..+...||+|+||.+...++|++|+..+++++
T Consensus 136 ~~~~~~i-~~~~s~~Ld~lr~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~g~~i~v~~~~~~~~~~~~~~~s~s~~ 214 (308)
T smart00533 136 VNDGGLI-KDGFDPELDELREKLEELEEELEELLKKEREELGIDSLKLGYNKVHGYYIEVTKSEAKKVPKDFIRRSSLKN 214 (308)
T ss_pred ccCCCee-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCceEEeEeccEEEEEEecchhhccCChHHHHHhhhcc
Confidence 222344 999999999999999999999999999999888877777655556789999999988899999999999999
Q ss_pred eEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceeccc
Q 001977 907 FFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEM 986 (987)
Q Consensus 907 ~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~i 986 (987)
+.+|+++++.+|++++.++++++.+++..++++|++.|.+|.+.|..+++++|+|||++|+ |.+|..++||||+|
T Consensus 215 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~l~~~i~~~~~~l~~~~~~i~~lD~l~s~-----a~~a~~~~~~~P~i 289 (308)
T smart00533 215 TERFTTPELKELENELLEAKEEIERLEKEILRELLEKVLEYLEELRALAEALAELDVLLSL-----ATLAAEGNYVRPEF 289 (308)
T ss_pred cceeeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHCCCcCCee
Confidence 9999999999999999999999999999999999999999999999999999999999998 88899999999998
Q ss_pred C
Q 001977 987 N 987 (987)
Q Consensus 987 n 987 (987)
+
T Consensus 290 ~ 290 (308)
T smart00533 290 V 290 (308)
T ss_pred C
Confidence 4
No 8
>KOG0220 consensus Mismatch repair ATPase MSH4 (MutS family) [Replication, recombination and repair]
Probab=100.00 E-value=3.5e-31 Score=301.90 Aligned_cols=472 Identities=17% Similarity=0.196 Sum_probs=349.4
Q ss_pred CcEEEEEEecCCCCCCCCCCCEEEEEEEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhc
Q 001977 452 ASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHT 531 (987)
Q Consensus 452 ~~yLlaI~e~~~~~~~~~~~~~~Gva~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~ 531 (987)
...++|+.|.... ....+|+|.+|+.++++++++|.|+..|.++.+.|.-+.|-||+++.........+++....
T Consensus 103 ~~v~~~v~e~r~~-----~~~~Ig~~~~~~~~~q~~l~~f~dst~y~~v~~~l~i~s~~ei~i~~~~~a~~~skl~~~~~ 177 (867)
T KOG0220|consen 103 PSVIVAVVEGRGL-----ARGEIGMASIDLKNPQIILSQFADSTTYAKVITKLKILSPLEIIISNTACAVGNSKLLFTLI 177 (867)
T ss_pred CceEEEEEecCCc-----ccceeEEEEecCCCCceehhhhhccchhHHHHhHhhccChhheeecccccccchHHHHHHHH
Confidence 4578899987653 46789999999999999999999999999999999999999999998776554444433211
Q ss_pred --CCCccccccCCccccChhhhHHHHHHHHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHH
Q 001977 532 --RNPLVNDLVPLSEFWDAETTVLEIKNIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALG 609 (987)
Q Consensus 532 --~~~~~~~l~p~~~f~d~~~~~~~l~~~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~Alg 609 (987)
..+-++-..-...+|+.+.+++.+..++....+ -++.+++ +..++++|+|
T Consensus 178 ~e~~~~v~~~~~s~k~fns~~gl~~i~~~~~~~~s------------------------~vle~i~----~k~~al~a~a 229 (867)
T KOG0220|consen 178 TENFKNVNFTTISRKYFNSTKGLEYIEQLCIAEFS------------------------TVLEEIQ----SKTYALGAAA 229 (867)
T ss_pred hhcccccceeehhhhhcCchhhHHHHHHHHhhhhH------------------------HHHHHHH----HHHHHHHHHH
Confidence 001111011124677888898888877653211 1344443 3589999999
Q ss_pred HHHHHHHHhcchhhhhcccccccccCCCccccCCCCeeecCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHH
Q 001977 610 GTLFYLKKSFLDETLLRFAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLR 689 (987)
Q Consensus 610 alL~YL~~~~ld~~ll~~~~f~~~~~~~~~~~~~~~~M~LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr 689 (987)
+++.|+..... .+....+ + .+......+.|.||..+.++|||+.+.. -+...+|++++|+|.|++|.|.||
T Consensus 230 ~llky~~~~~~--~~~~~~s---l---ri~~~gs~nT~~id~~~~~~lelV~~~~-~kn~~~l~~vl~~T~t~~g~r~lR 300 (867)
T KOG0220|consen 230 ALLKYVEEIQS--SVYAPKS---L---RICFQGSENTAMIDSSSAQSLELVINNQ-YKNNHTLFGVLNYTKTPGGYRRLR 300 (867)
T ss_pred HHHHHHHHHHH--hhhccce---e---EEEeecccceeeeecccccceEEechhh-hhcccceeeeeeeeecccchhhHH
Confidence 99999998765 2222211 1 2344567889999999999999998863 333559999999999999999999
Q ss_pred HHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcCCCCCHHHHHHHHhcCccc-cCcCCcchhhhHHHHHHHHHHH
Q 001977 690 TWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRLPDMERLLARLFASSEA-NGRNSNKVVLYEDAAKKQLQEF 768 (987)
Q Consensus 690 ~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk~lpDLERll~Ri~~~~~~-~~r~~~~~ilye~~~~~~L~~~ 768 (987)
..+++||+|...|+.|++++++|.. +.++...+|..+++.+|++++++++..-..+ ..+.....+ ..+..+
T Consensus 301 ssilqpl~d~~ti~~rleaiqeL~a-~~~L~~~Lr~~~k~~~dld~~~s~~~~~~~~~~i~~~~s~I-------~~~~~L 372 (867)
T KOG0220|consen 301 SSILQPLTDIETINMRLEAIQELLA-DEELFFGLRSVIKRFLDLDQLLSVLVQIPTQDTVNAAESKI-------NNLIYL 372 (867)
T ss_pred hhhcccccchhhhhHHHHHHHHHhc-CchHhhhhHHHHhhhhhHHHHHHHHHhhhhHHhhhcchhHH-------HHHHHH
Confidence 9999999999999999999999998 5678888999999999999999988532210 000000111 123344
Q ss_pred HHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCchhHHHHHHHHHhhcchhh--------hcCCCCeeeCCCCCH
Q 001977 769 ISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVE--------ANNSGRIIPHGGVDM 840 (987)
Q Consensus 769 ~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~~--------a~~~g~iipk~G~d~ 840 (987)
..+|+.+..+..++ .+..+.++....... ..+.+..+.+-|.++||... ..++.++.++.+.+.
T Consensus 373 k~tL~lv~~~~~al-------~~~~s~~~~e~~~~~-~~~r~~~i~~~i~e~I~dd~l~a~~~l~~~~qkcyAvks~i~~ 444 (867)
T KOG0220|consen 373 KHTLELVDPLKIAL-------KNCNSNLLREYYGSF-KDKRFGIILEKIKEVINDDALYAKGCLNLRTQKCYAVKSNING 444 (867)
T ss_pred HHHHHHHHHHHHHH-------hhchhHHHHHHHHHh-cchHHHHHHHHHHHHhhHHHHhccchhhhhccceeeecccccH
Confidence 44444443333222 112234444433211 12444455555566666421 224556777999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCeeEEEEecccc----cCCCCCCeEEEEeecCeEEEEChhHH
Q 001977 841 DYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVPESL----RGSVPRDYELRSSKKGFFRYWTPNIK 916 (987)
Q Consensus 841 eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~gY~IeVp~~~----~~kvP~~~~~~ss~kg~~rf~tpel~ 916 (987)
.||.+|+.+.++..+..+...++...+ ...+.+....-.||++.++... ...+|..|+..+..+++.+|+|..+.
T Consensus 445 ~LDiaR~ty~ei~~~~~~~i~~l~E~~-~~nl~~~f~sarGF~~ri~~~~~~~~~~~lP~~fi~~~~~~~~~~~~s~~~i 523 (867)
T KOG0220|consen 445 FLDIARRTYTEIVDDIAGMISQLGEKF-SLNLRLSFSSARGFFIRITTDCIALPSDTLPSEFIKISKVKNSYSFTSADLI 523 (867)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc-CccccccccccccEEEEeeccccccccccCchhhhhhhhhcceeeechHHHH
Confidence 999999999999998888777777766 3334433333468888888762 35789999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceecccC
Q 001977 917 KLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 917 eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~in 987 (987)
+++.++.+...++.-+...++..+...+.+|.+.+..+.++++-||+|+|| |.+....+||||+++
T Consensus 524 k~N~Rlk~~~~E~~l~te~~v~~lld~i~~~I~~L~~iae~~~~lD~l~sf-----a~~~~~~~y~~P~fT 589 (867)
T KOG0220|consen 524 KMNERLKEVLREIFLMTEMIVCKLLDEIYEHISCLYKLAEAVSMLDMLCSF-----AHACTLSDYVRPEFT 589 (867)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH-----HHhhccccccccccC
Confidence 999999999999999999999999999999999999999999999999999 777777899999985
No 9
>KOG0221 consensus Mismatch repair ATPase MSH5 (MutS family) [Replication, recombination and repair]
Probab=100.00 E-value=2.7e-31 Score=297.38 Aligned_cols=357 Identities=19% Similarity=0.256 Sum_probs=296.9
Q ss_pred chHHHHHHHHHHHHHHHhcchhhhhcccccccccCCCccccCCCCeeecCHHHHHhccCcccCCC------CCCcc-hhh
Q 001977 601 GSQVLSALGGTLFYLKKSFLDETLLRFAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRS------GDSSG-TLY 673 (987)
Q Consensus 601 ~~lal~AlgalL~YL~~~~ld~~ll~~~~f~~~~~~~~~~~~~~~~M~LD~~TL~nLEI~~n~~~------g~~~g-SL~ 673 (987)
...++.|+|+++.+|.+..+...+.. -+|+ -|+.+++.+...+.|.||.+|+++|+||+..+. |-..| |||
T Consensus 193 i~~~~r~~g~ll~fl~~~rigv~l~~-~~v~-~pI~gik~f~l~~lv~iD~nTisaL~Ifp~e~~~~~~k~~~~~g~Slf 270 (849)
T KOG0221|consen 193 IEAVVRALGGLLKFLGRRRIGVELED-YNVS-VPILGIKKFMLTHLVNIDQNTISALQIFPSESHPSKVKSGLKEGLSLF 270 (849)
T ss_pred hHHHHHhhhhHHhhcccceeeeeecc-cccc-ccccceeEEeecceeeeccchHHHHHhcccccccchhhhhhhcchhHH
Confidence 35778999999999998877644332 2332 245566777888899999999999999987653 12233 999
Q ss_pred hhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcC-ChHHHHHHHHhcCCCCCHHHHHHHHhcCccccCcCCc
Q 001977 674 AQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGV-NQPFALEFRKALSRLPDMERLLARLFASSEANGRNSN 752 (987)
Q Consensus 674 ~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~-n~~l~~~lr~~Lk~lpDLERll~Ri~~~~~~~~r~~~ 752 (987)
+++|+|.+.-|+|+||.|+.+|++|..+|..||++|.+|+.. |.++...+...|++++|+--++.|++.+...
T Consensus 271 ~l~n~c~s~~g~k~Lr~Wf~nPttd~~~l~sR~~~i~~fl~~qNa~~~~~Ls~~lgr~k~~~~~~~~~~sg~t~------ 344 (849)
T KOG0221|consen 271 GLLNRCHSKWGEKLLRLWFTNPTTDLGELSSRLDVIQFFLLPQNADMAQMLSRLLGRIKNVPLILKRMKSGHTK------ 344 (849)
T ss_pred HHHHHHhhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhcchhhHHHHHHHHHHhhcccHHHHHHHHhcCCce------
Confidence 999999999999999999999999999999999999999863 6778888999999999999999999865421
Q ss_pred chhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCchhHHHHHHHHHhhcchhhhcCCCCe
Q 001977 753 KVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRI 832 (987)
Q Consensus 753 ~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~lp~l~~ll~~i~~~iD~~~a~~~g~i 832 (987)
..+|..|++++...-.|.++|.+++. +..+.+.++. ..+.++.+++..+..+||+..+..++++
T Consensus 345 ---------l~~W~~~~stv~~~~~i~~~~rslp~------s~~~~~~~~~-~~~~~l~eia~~~g~vIdF~~S~~~~r~ 408 (849)
T KOG0221|consen 345 ---------LSDWQVLYSTVYSALGIRDACRSLPQ------SIQLFRDIAQ-EFSDDLHEIASLIGKVIDFEGSLAENRF 408 (849)
T ss_pred ---------echHHHHHHHHHHHHHHHHHHHhCcc------chhhhhHHHH-HHHHHHHHHHHHhhheeccccccccceE
Confidence 24788889999888888888877642 1122222211 1246778888888999999998889999
Q ss_pred eeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCC--CCeeEEEEcCeeEEEEecccccCCCCC----CeEEEEeecC
Q 001977 833 IPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGD--TSITYVTIGKDLYLLEVPESLRGSVPR----DYELRSSKKG 906 (987)
Q Consensus 833 ipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~--~~iky~~~~k~gY~IeVp~~~~~kvP~----~~~~~ss~kg 906 (987)
.+.+|+|++||+.|..|..++.-|.+...+....++. +++..+.++..||++.||.-..-...+ .|..+..+..
T Consensus 409 Tv~~giD~elDE~r~~y~~lp~~Lt~vAr~e~~~L~~~~psv~~VYIPliGfllsiprl~~~~~~~d~~~~~~~mf~s~E 488 (849)
T KOG0221|consen 409 TVLPGIDPELDEKRRRYMGLPSFLTEVARKELENLDSRIPSVSVVYIPLIGFLLSIPRLPSMVEASDFENGLDFMFLSEE 488 (849)
T ss_pred EecCCCChHHHHHHHHHccchHHHHHHHHHHHHhhCCCCCceeEEEeeceeeEEecccccchhhcCCcccchHHHhcccc
Confidence 9999999999999999999999999999887777764 466666677899999999864211122 4788888889
Q ss_pred eEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhhhhcccCCceeccc
Q 001977 907 FFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLILLDGSLLHAFLILQSNSCSSEM 986 (987)
Q Consensus 907 ~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~Sla~l~kA~~A~~~~yvRP~i 986 (987)
..+|++...++|.+.++++.-++.+.+..|+-.|..++......+.+....+++||+|+|| |..|.+++|+||.+
T Consensus 489 ~l~~rnart~eLD~~~GDIy~~i~D~et~i~~~Lq~qvl~rk~~lt~~l~laSrldvLls~-----a~~aa~~gy~~P~l 563 (849)
T KOG0221|consen 489 KLHYRNARTKELDALLGDIYCEIRDQETLIMYQLQCQVLARKAVLTRVLDLASRLDVLLSL-----ASAAADYGYSRPRL 563 (849)
T ss_pred eeEeecccHHhHHHHhhhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHhcCCCCCcc
Confidence 9999999999999999999999999999999999999999999999999999999999999 88999999999986
No 10
>PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....
Probab=99.97 E-value=9.5e-32 Score=256.15 Aligned_cols=107 Identities=37% Similarity=0.683 Sum_probs=92.2
Q ss_pred CHHHHHHHHHHhhCCCeEEEEeeCCeEEEechhHHHHHHhccceecc----CC--CCccccCcccHHHHHHHHHHcCCeE
Q 001977 328 SEGQKQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK----GE--QPHCGFPERNFSMNVEKLARKGYRV 401 (987)
Q Consensus 328 TP~~~Qyw~iK~~~~D~Vlffk~GkFYEly~~DA~i~~~~L~l~~~~----~~--~~~~GfPe~s~~~~~~~Lv~~GykV 401 (987)
|||++|||+||++|+|+|+||++|+|||+|++||+.+++.|+++++. ++ .||||||.++++.|+++|+++||||
T Consensus 1 Tp~~~~y~~lk~k~~d~i~lf~~G~fYe~y~~DA~~~a~~l~~~~~~~~~~~~~~~~~~gfp~~~l~~~l~~Ll~~G~~V 80 (113)
T PF01624_consen 1 TPFEQQYWELKEKYPDTIVLFQVGDFYEAYGEDAEFVAEILGLKLSKRKTGGGKSVPMAGFPKSQLDKYLKKLLEAGYRV 80 (113)
T ss_dssp -HHHHHHHHHHCTSTTSEEEEEETTEEEEECHHHHHHHHHHTSSSEEEECSSSECEEEEEEEGGGHHHHHHHHHHTT-EE
T ss_pred ChHHHHHHHHHhhCCCeEEEEEcCCEEEEEccCHHHHHHhccceeeeccccccccccEecccHHHHHHHHHHHHHcCCEE
Confidence 89999999999999999999999999999999999999999999873 22 6999999999999999999999999
Q ss_pred EEEeccCChHHHHHhhhhcCCCCCeeEEEEEEEEecCcccccc
Q 001977 402 LVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGE 444 (987)
Q Consensus 402 avveQ~Et~~~~~~R~k~~g~k~kvv~Rev~~V~TpGTl~d~~ 444 (987)
+||||+|++... +++++|+|++|+||||+++++
T Consensus 81 ~i~~q~~~~~~~----------~~~~~R~v~~i~TpGt~~~~~ 113 (113)
T PF01624_consen 81 AIYEQVETPSET----------KGLIEREVTRIYTPGTLIDDE 113 (113)
T ss_dssp EEEEE-S-HHHH----------SSS--EEEEEEEBTTS-TST-
T ss_pred EEEEecCCcccc----------CCCccEEEEEEECcCeecCcC
Confidence 999999998752 358999999999999999864
No 11
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=99.95 E-value=1.4e-26 Score=285.52 Aligned_cols=291 Identities=14% Similarity=0.173 Sum_probs=242.5
Q ss_pred CHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcCC
Q 001977 650 DAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSR 729 (987)
Q Consensus 650 D~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk~ 729 (987)
+..|++.||+-. -+-.+.++|.|++|+|+|++ ++|++|++.|++||+.|++++. .+.......|++
T Consensus 2 ~~~~~~~Le~~~---------i~~~l~~~~~t~~Gk~~l~~--l~P~~~~~~i~~~l~~~~e~~~---~~~~~~~~~l~~ 67 (782)
T PRK00409 2 QEKTLRVLEFNK---------IKEQLKTFAASELGKEKVLQ--LDPETDFEEVEELLEETDEAAK---LLRLKGLPPFEG 67 (782)
T ss_pred ChhhHhhCCHHH---------HHHHHHhHcCCHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHH---HHHhcCCCCCCC
Confidence 456777888643 23456679999999999999 6999999999999999999974 234445668999
Q ss_pred CCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCchh
Q 001977 730 LPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGLPA 809 (987)
Q Consensus 730 lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~lp~ 809 (987)
++||++++.|+..++.+ .+.+|.+|..+|..+..+...+.... +....+.|..++.. +++
T Consensus 68 ~~Di~~~l~r~~~g~~l--------------~~~eL~~i~~~l~~~~~l~~~l~~~~---~~~~~~~L~~~~~~---l~~ 127 (782)
T PRK00409 68 VKDIDDALKRAEKGGVL--------------SGDELLEIAKTLRYFRQLKRFIEDLE---EEEELPILEEWVAK---IRT 127 (782)
T ss_pred CccHHHHHHHHhCCCCC--------------CHHHHHHHHHHHHHHHHHHHHHHhcc---cccchhHHHHHHHc---CcC
Confidence 99999999999865433 24689999999999888877654320 00134677777653 556
Q ss_pred HHHHHHHHHhhcchhhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-Ce--eEEEEcCeeEEEEe
Q 001977 810 IVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDT-SI--TYVTIGKDLYLLEV 886 (987)
Q Consensus 810 l~~ll~~i~~~iD~~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~-~i--ky~~~~k~gY~IeV 886 (987)
+.++++.|..+||. +| .+ ++|+|++|+.+|+.+++++.++++.++++.+..+.. .+ .+++.++++|+|+|
T Consensus 128 ~~~l~~~i~~~id~-----~g-~i-~d~aS~eL~~iR~~~~~~~~~i~~~l~~~~~~~~~~~~L~d~~it~r~~r~~i~v 200 (782)
T PRK00409 128 LPELEQEIHNCIDE-----EG-EV-KDSASEKLRGIRRQLRRKKSRIREKLESIIRSKSLQKYLQDTIITIRNDRYVLPV 200 (782)
T ss_pred cHHHHHHHHHHhCC-----CC-EE-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccceEEEECCEEEEEe
Confidence 66788888899983 44 44 899999999999999999999999999987765432 23 57788899999999
Q ss_pred cccccCCCCCCeEEEEeecCeEEEEChh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 887 PESLRGSVPRDYELRSSKKGFFRYWTPN-IKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLIL 965 (987)
Q Consensus 887 p~~~~~kvP~~~~~~ss~kg~~rf~tpe-l~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~ 965 (987)
+....+.+|+ +++..+.+|.++|++|. +++|++++.+++.++.+++.+|+++|+..+.+|...|..+.+++++|||++
T Consensus 201 k~~~~~~~~g-~v~~~s~sg~t~y~ep~~~~~ln~~l~~l~~~~~~~~~~il~~l~~~i~~~~~~l~~~~~~l~~lD~l~ 279 (782)
T PRK00409 201 KAEYKHAIKG-IVHDQSSSGATLYIEPQSVVELNNEIRELRNKEEQEIERILKELSAKVAKNLDFLKFLNKIFDELDFIF 279 (782)
T ss_pred chhhhccCCC-ceeeEECCCCEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9998888886 78888999999999996 999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhhhhcccCCceecccC
Q 001977 966 LDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 966 Sla~l~kA~~A~~~~yvRP~in 987 (987)
|+ |.+|..++||+|+|+
T Consensus 280 a~-----a~~a~~~~~~~P~~~ 296 (782)
T PRK00409 280 AR-----ARYAKALKATFPLFN 296 (782)
T ss_pred HH-----HHHHHHCCCccceEc
Confidence 98 899999999999984
No 12
>PF05192 MutS_III: MutS domain III C-terminus.; InterPro: IPR007696 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the core domain (domain 3) found in proteins of the MutS family. The core domain of MutS adopts a multi-helical structure comprised of two subdomains, which are interrupted by the clamp domain. Two of the helices in the core domain comprise the levers that extend towards the DNA. This domain is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 1FW6_A ....
Probab=99.93 E-value=5.2e-25 Score=231.32 Aligned_cols=199 Identities=32% Similarity=0.496 Sum_probs=157.1
Q ss_pred HHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcCCC
Q 001977 651 APALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRL 730 (987)
Q Consensus 651 ~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk~l 730 (987)
++|+++||||++..+|+..||||++||+|+|++|+|+|++||++|++|+++|+.||++|++|++ |+.+...++..|+++
T Consensus 1 ~~Tl~~L~i~~~~~~~~~~~sL~~~ln~t~T~~Gkr~L~~~l~~P~~d~~~I~~R~~~v~~~~~-n~~~~~~~~~~l~~~ 79 (204)
T PF05192_consen 1 ANTLKSLEIFENSRSGKKKGSLFSLLNRTSTPMGKRLLRSWLLQPLTDIEEIEKRQDAVEEFLQ-NEELREELRSILKKI 79 (204)
T ss_dssp HHHHHHTTSSSBTTTSSSSTSHHHHH---SSHHHHHHHHHHHHS-BS-HHHHHHHHHHHHHHHH-THHHHHHHHHHHTTC
T ss_pred ChhHHhccCCCCCCCCCCCCcHHHHHhcCCChHHHHHHHHHHhCccchHHHHHHHHHHHHHHHH-hhhHhhhhhhhhhcc
Confidence 5899999999998888899999999999999999999999999999999999999999999997 677888999999999
Q ss_pred CCHHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcCh-HHHHHhhcCCCCchh
Q 001977 731 PDMERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTES-RQLHHILTPGKGLPA 809 (987)
Q Consensus 731 pDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s-~lL~~l~~~~~~lp~ 809 (987)
+|+++++.++..+.. +..+|..+..++..+..+.+.+.. ...+ +.|..+.. .+++
T Consensus 80 ~di~~~l~~l~~~~~---------------~~~~~~~l~~~l~~~~~i~~~~~~------~~~~~~~L~~l~~---~l~~ 135 (204)
T PF05192_consen 80 PDIERILKRLRSGRA---------------SPQDLLKLYKTLRSIIEIKKLLSE------RLESSPLLRKLLS---SLPD 135 (204)
T ss_dssp -SHHHHHHHHHTTHH---------------HHHHHHHHHHHHHHHHHHHHHHHC------TSSSTHHHHHHHH---HHCS
T ss_pred chHHHHHHHHHHhhc---------------ChHHHHHHHHHHHHHHHHHHHHHh------hcccHHHHHHHHH---hccc
Confidence 999999999976421 346788888888777776554221 1222 56777764 2445
Q ss_pred HHHHHHHHHhhcchhh--hcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCeeEEEEec
Q 001977 810 IVSILKHFKDAFDWVE--ANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVP 887 (987)
Q Consensus 810 l~~ll~~i~~~iD~~~--a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~gY~IeVp 887 (987)
+..+.+.|+.+||... +.+.+.+| ++
T Consensus 136 ~~~l~~~i~~~id~~~~~~~~~~~~I-~~--------------------------------------------------- 163 (204)
T PF05192_consen 136 FSELLDEIESTIDEDKSLAIREQDII-RD--------------------------------------------------- 163 (204)
T ss_dssp HHHHHHHHHHHBHTS-CCHCTTSSSB-ST---------------------------------------------------
T ss_pred HHHHHHHHHHHHhcCcHHHHhcccHH-HH---------------------------------------------------
Confidence 7778888888888621 22233333 22
Q ss_pred ccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Q 001977 888 ESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLILLD 967 (987)
Q Consensus 888 ~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~Sl 967 (987)
+..++..++++|+..+.+|.+.|..++++||+||||+||
T Consensus 164 -----------------------------------------~~~~~~~i~~~L~~~i~~~~~~l~~~~~~i~eLD~l~s~ 202 (204)
T PF05192_consen 164 -----------------------------------------INDEEQRILRELTNEIRKYSPELRELSEAIAELDVLISF 202 (204)
T ss_dssp -----------------------------------------HHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred -----------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 778899999999999999999999999999999999998
No 13
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=99.93 E-value=5.7e-24 Score=261.65 Aligned_cols=286 Identities=18% Similarity=0.170 Sum_probs=238.3
Q ss_pred cCHHHHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcC
Q 001977 649 LDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALS 728 (987)
Q Consensus 649 LD~~TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk 728 (987)
|+..|++.||+-. -+=.+.++|.|++|++++++ +.|+.+.++|++||+.|+++... .. ...|.
T Consensus 1 m~~~~l~~Lef~~---------i~~~l~~~~~t~~gk~~~~~--l~P~~~~~~i~~~l~~~~e~~~~----~~--~~~l~ 63 (771)
T TIGR01069 1 MREKDLIKLEFDK---------VKENLLKQTFTPLGKEDAIG--LKPPKSVEESKEIIIKLTALGSI----EN--NVRFF 63 (771)
T ss_pred CChhhHHhcCHHH---------HHHHHHHHcCCHHHHHHHhc--CCCCCCHHHHHHHHHHHHHHHHh----hc--cCCcC
Confidence 3567888888743 24467789999999999999 89999999999999999999862 11 55799
Q ss_pred CCCCHHHHHHHHhcCccccCcCCcchhhhHHHHHHH-HHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCc
Q 001977 729 RLPDMERLLARLFASSEANGRNSNKVVLYEDAAKKQ-LQEFISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGL 807 (987)
Q Consensus 729 ~lpDLERll~Ri~~~~~~~~r~~~~~ilye~~~~~~-L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~l 807 (987)
+++|+++++.|+..++.+. +.+ |..+..+|..+..+...+... ...+.|..++.. +
T Consensus 64 ~~~di~~~l~r~~~g~~l~--------------~~e~l~~i~~~l~~~~~l~~~l~~~------~~~~~L~~~~~~---l 120 (771)
T TIGR01069 64 GFEDIRELLKRAELGGIVK--------------GLEYILVIQNALKTVKHLKVLSEHV------LDLEILFHLRLN---L 120 (771)
T ss_pred CCccHHHHHHHHhcCCcCC--------------hHHHHHHHHHHHHHHHHHHHHHhcc------ccchHHHHHHhc---C
Confidence 9999999999998654332 334 888888888888777655321 134677777653 4
Q ss_pred hhHHHHHHHHHhhcchhhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-C--eeEEEEcCeeEEE
Q 001977 808 PAIVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDT-S--ITYVTIGKDLYLL 884 (987)
Q Consensus 808 p~l~~ll~~i~~~iD~~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~-~--iky~~~~k~gY~I 884 (987)
+++.++++.|.++||. +|. + +++++++|+.+|++++.++.++++.++++.+..+.. . -.++++++++|+|
T Consensus 121 ~~~~~l~~~i~~~id~-----~g~-i-~d~aS~~L~~ir~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~it~r~~r~vi 193 (771)
T TIGR01069 121 ITLPPLENDIIACIDD-----DGK-V-KDGASEELDAIRESLKALEEEVVKRLHKIIRSKELAKYLSDTIVTIRNGRYVL 193 (771)
T ss_pred CCcHHHHHHHHHHhCC-----CCE-E-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhhhhcCceEEEECCEEEE
Confidence 4566677888899982 454 4 899999999999999999999999999876654321 1 2478888999999
Q ss_pred EecccccCCCCCCeEEEEeecCeEEEEChh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 885 EVPESLRGSVPRDYELRSSKKGFFRYWTPN-IKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTL 963 (987)
Q Consensus 885 eVp~~~~~kvP~~~~~~ss~kg~~rf~tpe-l~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~ 963 (987)
+|+.+..+++|+ +++..|.+|.++|++|+ +++|++++.+++.++.+++.+|+.+|+..|.++.+.|..+++++++|||
T Consensus 194 pvk~~~~~~i~g-~v~~~S~sg~t~~~ep~~~~~ln~~l~~l~~~~~~e~~~il~~L~~~i~~~~~~l~~~~~~l~~lD~ 272 (771)
T TIGR01069 194 PLKSGFKGKIKG-IVHDTSSSGETFYIEPQAIVKLNNKLAQLKNEEECEIEKILRTLSEKVQEYLLELKFLFKEFDFLDS 272 (771)
T ss_pred EeeHHHhhcCCC-eEEEEeCCCCEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999998888986 88889999999999996 9999999999999999999999999999999999999999999999999
Q ss_pred HHcccchhhhhhcccCCceecccC
Q 001977 964 ILLDGSLLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 964 L~Sla~l~kA~~A~~~~yvRP~in 987 (987)
++|+ |.+|...+||+|.++
T Consensus 273 l~a~-----a~~a~~~~~~~P~~~ 291 (771)
T TIGR01069 273 LQAR-----ARYAKAVKGEFPMPS 291 (771)
T ss_pred HHHH-----HHHHHHCCCeeceec
Confidence 9997 899999999999863
No 14
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=99.52 E-value=1.6e-13 Score=125.71 Aligned_cols=92 Identities=41% Similarity=0.554 Sum_probs=87.7
Q ss_pred CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHH
Q 001977 837 GVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIK 916 (987)
Q Consensus 837 G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~ 916 (987)
|+|++||.+++.+++++++|+++++++++.++++.++|..+++.||+|+||.+...++|++|+..+++++..||+|++|+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~~~~~~~~~~~lk~~~~~~~gy~i~v~~~~~~~~p~~~~~~~~~k~~~rf~t~~l~ 80 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLEEIRKKLGIPSLKLVYIPKRGYLIEVPKSDEKKLPKDFIIVSSTKSGVRFTTPELK 80 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-TTBEEEEETTTEEEEEEETCCGGGSTTTEEEEEEESSEEEEECHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEEEEEcCceEEEEEEEccccccCCCceEEEEEEcCcEEEECHHHH
Confidence 79999999999999999999999999999999999999999999999999999988899999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 001977 917 KLLGELSQAESE 928 (987)
Q Consensus 917 eL~~el~~~~~~ 928 (987)
+|+.++.+++++
T Consensus 81 ~L~~~~~~~~ee 92 (92)
T PF05190_consen 81 ELNEELKEAEEE 92 (92)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcC
Confidence 999999999864
No 15
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=99.52 E-value=4.3e-13 Score=163.14 Aligned_cols=283 Identities=18% Similarity=0.212 Sum_probs=223.6
Q ss_pred HHHhccCcccCCCCCCcchhhhhhhccCChHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHcCChHHHHHHHHhcCCCCC
Q 001977 653 ALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRLPD 732 (987)
Q Consensus 653 TL~nLEI~~n~~~g~~~gSL~~lLn~c~T~~GkRLLr~WL~~PL~d~~~I~~RldaVe~L~~~n~~l~~~lr~~Lk~lpD 732 (987)
||..||...- .-.++.++.|+.|+.+|++ +.|..+.+.|+..++.++++... +...--..+.++.|
T Consensus 3 ~l~~le~~k~---------k~~~~~~~~s~~g~~~~~~--l~p~~~~~~i~~~~~e~~~~~~~---~~~~g~~~~~~l~~ 68 (753)
T COG1193 3 TLEMLEFDKI---------KELLASYAQSSLGLEELKN--LKPRTDLELIEEELSETAEALDI---LEDEGLPPLGGLND 68 (753)
T ss_pred hHhhccchHH---------HHHHHHhccCHHHHHHHHh--cCccccHHHHHHHHHHHHHHHHH---HhccCCCCchhhhh
Confidence 5666665431 2245689999999999999 99999999999999999998751 11111236888999
Q ss_pred HHHHHHHHhcCccccCcCCcchhhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhcChHHHHHhhcCCCCchhHHH
Q 001977 733 MERLLARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVS 812 (987)
Q Consensus 733 LERll~Ri~~~~~~~~r~~~~~ilye~~~~~~L~~~~~~L~~~~~i~~~~~~l~~~l~~~~s~lL~~l~~~~~~lp~l~~ 812 (987)
+.-.+.++..++.+ ...+|..+...|+++..+..++..+... . ..+.. .++.+..
T Consensus 69 i~~~l~~~e~g~~l--------------~~~el~~i~~~l~~~~~lkr~~~~~e~~----~----~~~~~---~~~~~~~ 123 (753)
T COG1193 69 VSEALGRLEKGGRL--------------HVEELLEISDFLRGFRALKRAIKKLERI----K----RTLAL---ALIELSD 123 (753)
T ss_pred hHHHHHHHhhcccC--------------CHHHHHHHHHHHHHHHHHHHHHHHhhhH----H----HHHHH---hhhcchH
Confidence 99999999754432 2568889999999998888776554321 1 11111 2455566
Q ss_pred HHHHHHhhcchhhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCe--eEEEEcCeeEEEEecccc
Q 001977 813 ILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSI--TYVTIGKDLYLLEVPESL 890 (987)
Q Consensus 813 ll~~i~~~iD~~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~i--ky~~~~k~gY~IeVp~~~ 890 (987)
+...+...|| ..|.+ .+.++++|+.+|..++.+..++.+.++.+.+.-....+ .+++.+.++|+|+|+..+
T Consensus 124 l~~~i~~~id-----~~g~i--~d~as~~l~~ir~~lr~~~~~i~~~l~~~~~~~~~~~L~e~~v~~r~~r~vlpvk~~f 196 (753)
T COG1193 124 LELEINIPID-----DDGLI--KDRASFELDAIRRQLRDLEEEIRDKLESLIRSKEAKYLQDRIVTTRDGREVLPVKAEF 196 (753)
T ss_pred HHHHHhhhhc-----ccccc--cccccHHHHHHHhhhHHHHHHHHHHHHHHHhhhhhHhhhhceEeccCCeEEeHHHHHh
Confidence 6666677776 23444 79999999999999998988888888776443211222 377888999999999999
Q ss_pred cCCCCCCeEEEEeecCeEEEECh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Q 001977 891 RGSVPRDYELRSSKKGFFRYWTP-NIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLILLDGS 969 (987)
Q Consensus 891 ~~kvP~~~~~~ss~kg~~rf~tp-el~eL~~el~~~~~~~~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L~Sla~ 969 (987)
++.+++ .++..+..|.+.|..| .++.|++++..+..+...++..|++.|++.+.++...+..+...+++||++.+.
T Consensus 197 k~~i~g-iv~d~sssg~tl~ieP~~vv~l~n~~~~l~~eE~~e~e~il~~lsa~v~~~~~~l~~~~~~~~~lD~i~Ak-- 273 (753)
T COG1193 197 KGAIKG-IVHDTSSSGATLYIEPRSVVKLNNELRALLVEEDEEEERILRELSALVAPVIPELEILLEIIGELDFIEAK-- 273 (753)
T ss_pred hhhcCc-eEeecccccCeeeecchHHHhhccHhhhhhccchHhHHHHHHHHHHHHhhhhHHHHHHHHHhhhhHHHHHH--
Confidence 999987 7888888999999999 599999999999999999999999999999999999999999999999999995
Q ss_pred hhhhhhcccCCceecccC
Q 001977 970 LLHAFLILQSNSCSSEMN 987 (987)
Q Consensus 970 l~kA~~A~~~~yvRP~in 987 (987)
++++....++.|.++
T Consensus 274 ---~~~~~~~~~v~P~~~ 288 (753)
T COG1193 274 ---VRYAKALKGVKPDFS 288 (753)
T ss_pred ---HHHHHhhccCCCccC
Confidence 899999999999874
No 16
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=99.42 E-value=1.9e-12 Score=127.19 Aligned_cols=130 Identities=27% Similarity=0.401 Sum_probs=85.9
Q ss_pred cEEEEEEecCCCCCCCCCCCEEEEEEEeCCCCeEEEEEEcCcchHHHHHHHHHhcCCcEEEecCCCCChHHHHHHHhhcC
Q 001977 453 SYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQVMDDLDCSVLCCLLSELRPVEIIKPANMLSPETERAILRHTR 532 (987)
Q Consensus 453 ~yLlaI~e~~~~~~~~~~~~~~Gva~vD~sTG~f~l~qf~Dd~~~s~L~tlL~~~~P~EIl~~~~~ls~~t~~~l~~~~~ 532 (987)
|||+||.++. ....||+||+|++||+|++++|.| +++|.+.|.+++|+|||++.+..+......+.....
T Consensus 1 Nyl~aI~~~~-------~~~~~gla~~D~sTGe~~~~~~~d---~~~L~~~L~~~~P~EIi~~~~~~~~~~~~~~~~~~~ 70 (137)
T PF05188_consen 1 NYLAAIYEKN-------DEDSYGLAYIDLSTGEFYVTEFED---YSELKSELARLSPREIIIPEGFSSSDISALLSSLKN 70 (137)
T ss_dssp -EEEEEEEET-------CSSEEEEEEEETTTTEEEEEEEEC---HHHHHHHHHHH-ESEEEEETTCSHHHHHHHHHCCTT
T ss_pred CEEEEEEEec-------CCCEEEEEEEECCCCEEEEEEeCC---HHHHHHHHHhcCCeEEEEcCCCcccccchhhhhhcc
Confidence 6999999851 245699999999999999999998 899999999999999999998765432111111111
Q ss_pred CCccccccCCccccChhhhHHHHHHHHhhhccccccccccccccccccCCCCCCcchhhhhhhccCCCchHHHHHHHHHH
Q 001977 533 NPLVNDLVPLSEFWDAETTVLEIKNIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTL 612 (987)
Q Consensus 533 ~~~~~~l~p~~~f~d~~~~~~~l~~~~~~~~~~~~~k~d~~~~~~~~~~~~~~~~p~~l~~l~~~~~~~~lal~AlgalL 612 (987)
........+ ..+++.....+.+...|..... .+.+. ....+++++|+|+||
T Consensus 71 ~~~~~~~~~-~~~~~~~~~~~~i~~~~~~~~~---------------~~~~~-------------~~~~~~~~~Al~all 121 (137)
T PF05188_consen 71 SFFKVTETP-SWYFDSEFASEDIEEQFGVADL---------------DGFGL-------------EEDKELALSALGALL 121 (137)
T ss_dssp TCCEEEEET-CGGGSHHHHHHHHHHHCTSSST---------------CCCTT-------------GGGGHHHHHHHHHHH
T ss_pred ccceeeecc-hhhhhhHHHHHHHHHhhccccc---------------cccCc-------------cCCCHHHHHHHHHHH
Confidence 111111122 2345566666767766642211 11110 023578999999999
Q ss_pred HHHHHhcch
Q 001977 613 FYLKKSFLD 621 (987)
Q Consensus 613 ~YL~~~~ld 621 (987)
.||+.++..
T Consensus 122 ~Yl~~t~~~ 130 (137)
T PF05188_consen 122 KYLEETQKS 130 (137)
T ss_dssp HHHHHTTTC
T ss_pred HHHHHHCcc
Confidence 999998765
No 17
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=99.16 E-value=6.3e-11 Score=94.75 Aligned_cols=43 Identities=33% Similarity=0.628 Sum_probs=36.0
Q ss_pred cccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceee
Q 001977 105 VLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELL 147 (987)
Q Consensus 105 ~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l 147 (987)
-.|.+|.+|||+++.||+|.|++||..+..|+|.|+||++..|
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEe
Confidence 4899999999999999999999999999999999999999444
No 18
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=97.44 E-value=0.00022 Score=59.13 Aligned_cols=44 Identities=23% Similarity=0.474 Sum_probs=39.8
Q ss_pred cccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccC-CCceeeecC
Q 001977 105 VLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDD-GEDELLDLG 150 (987)
Q Consensus 105 ~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Ydd-g~~e~l~l~ 150 (987)
-+|..|.+.| .|+.||.|+|+++++. +.+.|.|.| |..|++...
T Consensus 4 ~~G~~~~a~~-~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~~~ 48 (57)
T smart00333 4 KVGDKVAARW-EDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVPPS 48 (57)
T ss_pred CCCCEEEEEe-CCCCEEEEEEEEECCC-CEEEEEEECCCccEEEeHH
Confidence 4899999999 9999999999999988 889999977 999988643
No 19
>KOG4675 consensus Uncharacterized conserved protein, contains ENT domain [General function prediction only]
Probab=97.40 E-value=8.6e-05 Score=79.12 Aligned_cols=84 Identities=25% Similarity=0.467 Sum_probs=54.8
Q ss_pred CCCCCCCCCCCCCCCCCcccccccc-ccCCCCCCCcccccccCCccccceEEEEcCCCCceEEEEEEeeeC-CCCeEEEE
Q 001977 61 PSPSPSPTTPSPLQSNPKKSRLVIG-QTPSPPPSTPAAAKSYGEDVLRKRIRVYWPLDKAWYEGCVKSFDK-ECNKHLVQ 138 (987)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~vg~rv~v~wp~d~~~y~g~v~~~~~-~~~~h~v~ 138 (987)
++|++.||++-. +. ++....+ ..|+|.++- .+..++.+||++|..-||++..||++.|+.|+. ...+|.+.
T Consensus 122 ~~ps~~~t~~~~-~~---~~a~pss~s~~~p~~~~---~n~pp~slvgr~v~~k~pdk~~~te~iit~~~~~~E~~~~l~ 194 (273)
T KOG4675|consen 122 VLPSPIPTGPLT-FN---NTATPSSFSVPSPVSSW---GNVPPESLVGRKVWIKWPDKRKFTEAIITQYDAEKEGHHLLV 194 (273)
T ss_pred CCCCccccCCcc-cC---cccccccccCCCCCCcc---ccCCchhhccccccccCcccccccccccccchhhhhhhhhcc
Confidence 466666666544 11 2222222 233443333 566677799999999999999999999999554 55577777
Q ss_pred ccCCCceeeecCcceEEEE
Q 001977 139 YDDGEDELLDLGKEKIEWV 157 (987)
Q Consensus 139 Yddg~~e~l~l~~e~~~~~ 157 (987)
|| +.-.++-|+|+
T Consensus 195 ~~------~~~~~~p~~wv 207 (273)
T KOG4675|consen 195 PD------INDCNDPWEWV 207 (273)
T ss_pred cc------cccccCCcccc
Confidence 77 44445555665
No 20
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=97.26 E-value=0.00053 Score=57.82 Aligned_cols=36 Identities=25% Similarity=0.389 Sum_probs=33.5
Q ss_pred cccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccC
Q 001977 105 VLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDD 141 (987)
Q Consensus 105 ~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Ydd 141 (987)
-+|..|.|+|+.++.||.|+|+.++. .++|.|.|++
T Consensus 4 ~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~ 39 (61)
T smart00743 4 KKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLT 39 (61)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECC
Confidence 48999999999999999999999998 6789999987
No 21
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=97.24 E-value=0.00054 Score=54.67 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=38.5
Q ss_pred cceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccC-CCceeeecC
Q 001977 107 RKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDD-GEDELLDLG 150 (987)
Q Consensus 107 g~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Ydd-g~~e~l~l~ 150 (987)
|..|-+.|++|+.||.|+|.+.++ .+.-.|.|.| |..|.+.+.
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~-~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS-DGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC-CCcEEEEEEcCCCcEEEeHH
Confidence 678999999999999999999998 7789999977 999988654
No 22
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=96.45 E-value=0.006 Score=57.65 Aligned_cols=45 Identities=31% Similarity=0.492 Sum_probs=35.7
Q ss_pred CCccccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceee
Q 001977 102 GEDVLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELL 147 (987)
Q Consensus 102 ~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l 147 (987)
|.++||.||---|-+++-||.|+|+. +....+.+|.+|||.+-.|
T Consensus 1 ~~~~iG~rV~AkWS~n~yyY~G~I~~-~~~~~kykv~FdDG~~~~v 45 (122)
T PF09038_consen 1 GSSFIGLRVFAKWSDNGYYYPGKITS-DKGKNKYKVLFDDGYECRV 45 (122)
T ss_dssp ---STT-EEEEESSTTSEEEEEEEEE-EETTTEEEEEETTS-EEEE
T ss_pred CCcccccEEEEEEccCCcccCceEee-cCCCCeEEEEecCCcccee
Confidence 56799999999999888889999999 5777899999999997554
No 23
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=93.34 E-value=0.14 Score=56.33 Aligned_cols=49 Identities=18% Similarity=0.330 Sum_probs=39.6
Q ss_pred CCccccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEcc-CCCceeeecC
Q 001977 102 GEDVLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYD-DGEDELLDLG 150 (987)
Q Consensus 102 ~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yd-dg~~e~l~l~ 150 (987)
..+-||-+|...|-.|+.||.++|++.+...+...|.|+ -|..|.+.|.
T Consensus 67 ~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp T---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGG
T ss_pred cCCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehh
Confidence 457799999999999999999999999999999999995 5778877765
No 24
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=88.35 E-value=0.29 Score=51.96 Aligned_cols=7 Identities=29% Similarity=0.729 Sum_probs=3.4
Q ss_pred hhhhccc
Q 001977 164 LKRLRRD 170 (987)
Q Consensus 164 ~~~~~~~ 170 (987)
|.||+-|
T Consensus 167 m~RLk~G 173 (303)
T KOG3064|consen 167 MERLKSG 173 (303)
T ss_pred HHHHhcC
Confidence 5555443
No 25
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=87.26 E-value=2.1 Score=50.14 Aligned_cols=39 Identities=15% Similarity=0.202 Sum_probs=32.2
Q ss_pred cccceEEEEcCCCCceEEEEEEeeeCCC------CeEEEEccCCC
Q 001977 105 VLRKRIRVYWPLDKAWYEGCVKSFDKEC------NKHLVQYDDGE 143 (987)
Q Consensus 105 ~vg~rv~v~wp~d~~~y~g~v~~~~~~~------~~h~v~Yddg~ 143 (987)
-||.+|.++|..|..||.++|....... ....|.|..=+
T Consensus 55 ~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~n 99 (450)
T PLN00104 55 EVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTEFN 99 (450)
T ss_pred ccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEecCC
Confidence 3999999999999999999999988633 36788886433
No 26
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=85.66 E-value=2.8 Score=34.63 Aligned_cols=43 Identities=19% Similarity=0.394 Sum_probs=34.5
Q ss_pred ccceEEEEcCCCCceEEEEEEeeeCCCC--eEEEEccCCC---ceeeec
Q 001977 106 LRKRIRVYWPLDKAWYEGCVKSFDKECN--KHLVQYDDGE---DELLDL 149 (987)
Q Consensus 106 vg~rv~v~wp~d~~~y~g~v~~~~~~~~--~h~v~Yddg~---~e~l~l 149 (987)
||.+|.+.| .++.||.++|..-....+ ...|.|..=+ .||+..
T Consensus 3 vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~g~nkR~DeWV~~ 50 (55)
T PF11717_consen 3 VGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQGWNKRLDEWVPE 50 (55)
T ss_dssp TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEETTSTGCC-EEEET
T ss_pred cCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcCCCCCCceeeecH
Confidence 899999999 899999999999988654 7889997555 455543
No 27
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=84.91 E-value=1.8 Score=37.43 Aligned_cols=35 Identities=29% Similarity=0.394 Sum_probs=26.9
Q ss_pred ccceEEEEcCC---CCceEEEEEEeeeCCCCeEEEEccC
Q 001977 106 LRKRIRVYWPL---DKAWYEGCVKSFDKECNKHLVQYDD 141 (987)
Q Consensus 106 vg~rv~v~wp~---d~~~y~g~v~~~~~~~~~h~v~Ydd 141 (987)
.|.+|.|.--. ..+||.|+|.+..... +..|+|+|
T Consensus 3 ~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~ 40 (68)
T PF05641_consen 3 KGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDD 40 (68)
T ss_dssp TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT
T ss_pred CCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECC
Confidence 68899999866 4699999999998887 99999964
No 28
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=81.63 E-value=3 Score=40.58 Aligned_cols=41 Identities=24% Similarity=0.443 Sum_probs=35.7
Q ss_pred cceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceeee
Q 001977 107 RKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELLD 148 (987)
Q Consensus 107 g~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l~ 148 (987)
|.+|=..|+.|+-||.|+|.+.- ..+...|.+++|+.+.+.
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~-~~~~~lV~f~~~~~~~v~ 41 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV-SSGQFLVEFDDGDTQEVP 41 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc-CCCEEEEEECCCCEEEeC
Confidence 78899999999999999999987 677888999888877663
No 29
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=78.07 E-value=2.5 Score=51.94 Aligned_cols=47 Identities=34% Similarity=0.635 Sum_probs=37.4
Q ss_pred CccccceEEEEcCC----CCceEEEEEEeeeCCC--------CeEEEEccCCCceeeec
Q 001977 103 EDVLRKRIRVYWPL----DKAWYEGCVKSFDKEC--------NKHLVQYDDGEDELLDL 149 (987)
Q Consensus 103 ~~~vg~rv~v~wp~----d~~~y~g~v~~~~~~~--------~~h~v~Yddg~~e~l~l 149 (987)
++-.+-+|||||-+ |++|++|+|.+..+.+ .++.|+||.++.|.+.=
T Consensus 978 nW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~e~~~~sp 1036 (1113)
T KOG0644|consen 978 NWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNTETELHSP 1036 (1113)
T ss_pred ccccccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCCcccccCc
Confidence 34478999999986 5789999999976654 37899999997666543
No 30
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=73.09 E-value=2.7 Score=49.41 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=22.5
Q ss_pred cccCCccccceEEEEcCCCCceEEEEE
Q 001977 99 KSYGEDVLRKRIRVYWPLDKAWYEGCV 125 (987)
Q Consensus 99 ~~~~~~~vg~rv~v~wp~d~~~y~g~v 125 (987)
.-+|..+-|+.|.|=|..++.=|+++-
T Consensus 177 ~~N~~~i~gR~VAVDWAV~Kd~ye~ta 203 (678)
T KOG0127|consen 177 FFNGNKIDGRPVAVDWAVDKDTYEDTA 203 (678)
T ss_pred hccCceecCceeEEeeecccccccccc
Confidence 345778899999999999999888764
No 31
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=72.98 E-value=7.1 Score=36.53 Aligned_cols=52 Identities=19% Similarity=0.239 Sum_probs=40.7
Q ss_pred CccccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEc-cCCCceeeecCcceEEEE
Q 001977 103 EDVLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQY-DDGEDELLDLGKEKIEWV 157 (987)
Q Consensus 103 ~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Y-ddg~~e~l~l~~e~~~~~ 157 (987)
...+|..+-+.-+.|+.||.|.| ..+...+.-.|.| |-|..+.+... +++.+
T Consensus 51 ~~~~~~~~~~~~~~~~~w~Ra~I-~~~~~~~~~~V~~iD~G~~~~v~~~--~l~~l 103 (121)
T PF00567_consen 51 ESNPGEGCLCVVSEDGRWYRAVI-TVDIDENQYKVFLIDYGNTEKVSAS--DLRPL 103 (121)
T ss_dssp T--TTEEEEEEETTTSEEEEEEE-EEEECTTEEEEEETTTTEEEEEEGG--GEEE-
T ss_pred ccccCCEEEEEEecCCceeeEEE-EEecccceeEEEEEecCceEEEcHH--Hhhhh
Confidence 34478888888899999999999 7778888999999 99999997654 45544
No 32
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=63.44 E-value=12 Score=39.75 Aligned_cols=39 Identities=5% Similarity=0.102 Sum_probs=33.0
Q ss_pred CCccccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEcc
Q 001977 102 GEDVLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYD 140 (987)
Q Consensus 102 ~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yd 140 (987)
+.+=||.+|.+-|++|..||.++|....+..+.--|.++
T Consensus 89 ~~w~vg~K~~A~~~ddg~~y~AtIe~ita~~~~~ai~f~ 127 (262)
T KOG3026|consen 89 VGWKVGDKVQAVFSDDGQIYDATIEHITAMEGTVAIIFA 127 (262)
T ss_pred cccccCCEEEEeecCCCceEEeehhhccCCCCceeEEEe
Confidence 356699999999999999999999999997666666553
No 33
>PF15449 Retinal: Retinal protein
Probab=61.48 E-value=32 Score=44.02 Aligned_cols=24 Identities=13% Similarity=0.266 Sum_probs=20.2
Q ss_pred CccccceEEEEcCCCCceEEEEEE
Q 001977 103 EDVLRKRIRVYWPLDKAWYEGCVK 126 (987)
Q Consensus 103 ~~~vg~rv~v~wp~d~~~y~g~v~ 126 (987)
..+.|.-+.||||.-...|++...
T Consensus 1136 aK~~~Nt~SIFCPAtSSLFEAKsp 1159 (1287)
T PF15449_consen 1136 AKVSGNTCSIFCPATSSLFEAKSP 1159 (1287)
T ss_pred ccccCCccceecccchhhhhccCC
Confidence 356888999999999999998854
No 34
>PLN02782 Branched-chain amino acid aminotransferase
Probab=56.79 E-value=36 Score=40.02 Aligned_cols=71 Identities=15% Similarity=0.117 Sum_probs=54.0
Q ss_pred ccCCccccceEEEEcCCCCceEEEEEEeeeCCC---CeEEEEccCCCceeeecC---cceEEEEecchhhhhhhcccc
Q 001977 100 SYGEDVLRKRIRVYWPLDKAWYEGCVKSFDKEC---NKHLVQYDDGEDELLDLG---KEKIEWVQESVSLLKRLRRDS 171 (987)
Q Consensus 100 ~~~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~---~~h~v~Yddg~~e~l~l~---~e~~~~~~~~~~~~~~~~~~~ 171 (987)
..|....-.-+.+-|-.|+.|..|+++.|+..+ .-+-+.|-||--|.+..- +-++.+. -+++-++|++++.
T Consensus 76 ~fg~~~td~m~~~~~~~~~~w~ng~ivp~~~~~i~~~d~gl~YGdgvFEg~kayr~~~G~i~lF-r~d~H~~RL~~SA 152 (403)
T PLN02782 76 GFGLVPTDYMYIMKCNRDGEFSKGELQRFGNIELSPSAGVLNYGQGLFEGLKAYRKEDGNILLF-RPEENAIRMRNGA 152 (403)
T ss_pred CCCccccCceEEEEECCCCcEeCCEEEECCCCEeChhhhHHhhhhhhhheEEEEEcCCCcEeee-ChHHHHHHHHHHH
Confidence 346666777888999888999999999988754 367789999999988763 4456555 5666777887655
No 35
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=54.83 E-value=38 Score=42.00 Aligned_cols=19 Identities=16% Similarity=0.287 Sum_probs=12.0
Q ss_pred HHHhcCCCCCHHHHHHHHh
Q 001977 723 FRKALSRLPDMERLLARLF 741 (987)
Q Consensus 723 lr~~Lk~lpDLERll~Ri~ 741 (987)
++..-..+.+|||.+....
T Consensus 903 ~~~m~~~ik~Le~dlk~~~ 921 (1102)
T KOG1924|consen 903 LQQMENQIKKLERDLKNFK 921 (1102)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 4444556678888886554
No 36
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=52.78 E-value=0.85 Score=59.73 Aligned_cols=59 Identities=8% Similarity=-0.053 Sum_probs=53.1
Q ss_pred cccCCccccceEEEEcCCCCceEEE-EEEeeeCCCCeEEEEccCCCceeeecCcceEEEE
Q 001977 99 KSYGEDVLRKRIRVYWPLDKAWYEG-CVKSFDKECNKHLVQYDDGEDELLDLGKEKIEWV 157 (987)
Q Consensus 99 ~~~~~~~vg~rv~v~wp~d~~~y~g-~v~~~~~~~~~h~v~Yddg~~e~l~l~~e~~~~~ 157 (987)
...+.++||.++..||+.|..||.| .|..++...+.|.+.|++++.+..++....|+-.
T Consensus 982 ~~~~~e~V~~~~~~~la~d~~~~~~edv~~l~~~ke~~~~vl~~l~~~~~n~~~~~~~~~ 1041 (1266)
T KOG1525|consen 982 LAHLPEYVGSYVIHLLAHDPDFVKAEDVDSLSDLKECLWFVLEDLDEENENNQHKFWKRE 1041 (1266)
T ss_pred hhhhhHHhhhhhhhhhccCccccccchhhhHHHHHHhHHHHHhhhhhhhccchhHHHHHH
Confidence 4467999999999999999999999 7888888889999999999999999988877654
No 37
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=51.87 E-value=29 Score=34.18 Aligned_cols=45 Identities=13% Similarity=0.446 Sum_probs=35.4
Q ss_pred eEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceeeecCcceEEEEe
Q 001977 109 RIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELLDLGKEKIEWVQ 158 (987)
Q Consensus 109 rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l~l~~e~~~~~~ 158 (987)
.|...| ...||.|++.+.+....+..|+++||. ..+.++.++.++
T Consensus 15 avW~~~--~~~yYPa~~~~~~~~~~~~~V~Fedg~---~~i~~~dv~~LD 59 (131)
T PF08605_consen 15 AVWAGY--NLKYYPATCVGSGVDRDRSLVRFEDGT---YEIKNEDVKYLD 59 (131)
T ss_pred ceeecC--CCeEeeEEEEeecCCCCeEEEEEecCc---eEeCcccEeeee
Confidence 444545 789999999999888778999999999 445566677776
No 38
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=50.14 E-value=10 Score=44.82 Aligned_cols=22 Identities=18% Similarity=0.504 Sum_probs=14.9
Q ss_pred cCCccccceEE----EEcCCCCceEE
Q 001977 101 YGEDVLRKRIR----VYWPLDKAWYE 122 (987)
Q Consensus 101 ~~~~~vg~rv~----v~wp~d~~~y~ 122 (987)
.|...|+|-.+ +..|+|+.|.-
T Consensus 338 ~g~~av~CS~KAneG~LYPLekgFlF 363 (615)
T KOG0526|consen 338 SGTAAVKCSFKANEGLLYPLEKGFLF 363 (615)
T ss_pred CCCceeeeeecccCceEeecccceEe
Confidence 35555655555 68899998874
No 39
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=49.61 E-value=49 Score=39.47 Aligned_cols=19 Identities=21% Similarity=0.461 Sum_probs=10.6
Q ss_pred CCCCCCccccccccccCCC
Q 001977 72 PLQSNPKKSRLVIGQTPSP 90 (987)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~~ 90 (987)
+.++|++.+..++|+..+.
T Consensus 204 ~~~~Kkk~~~ftlGgSs~~ 222 (507)
T PF11702_consen 204 PVPPKKKGAMFTLGGSSSS 222 (507)
T ss_pred cccccccCCeEeecCCCCc
Confidence 3344444456777776554
No 40
>KOG1118 consensus Lysophosphatidic acid acyltransferase endophilin/SH3GL, involved in synaptic vesicle formation [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=48.84 E-value=47 Score=36.91 Aligned_cols=31 Identities=26% Similarity=0.388 Sum_probs=24.3
Q ss_pred ccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEc
Q 001977 106 LRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQY 139 (987)
Q Consensus 106 vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Y 139 (987)
-|--|.|.--.|..||.|++.+- +|-.-|-|
T Consensus 327 eGDlI~l~~QIdenWyeG~~~g~---sG~FPvnY 357 (366)
T KOG1118|consen 327 EGDLITLTNQIDENWYEGEKHGE---SGMFPVNY 357 (366)
T ss_pred cCceeeehhhcCcchhhheecCc---cCccccce
Confidence 57778888999999999999874 66555555
No 41
>PF10851 DUF2652: Protein of unknown function (DUF2652) ; InterPro: IPR020503 This entry contains proteins with no known function.
Probab=43.97 E-value=13 Score=35.20 Aligned_cols=29 Identities=24% Similarity=0.265 Sum_probs=26.1
Q ss_pred CCCeEEEEeeCCeEEEechhHHHHHHhcc
Q 001977 341 HMDKVIFFKMGKFYELFEMDAHVGAKELD 369 (987)
Q Consensus 341 ~~D~Vlffk~GkFYEly~~DA~i~~~~L~ 369 (987)
|+..|=+++||.|=+||+.|-.++|++|-
T Consensus 80 H~Ge~~~~~Vk~~~kL~G~dVI~aHrlLK 108 (116)
T PF10851_consen 80 HYGEVAQQKVKRFCKLAGKDVIEAHRLLK 108 (116)
T ss_pred EeeeeeeeeecccchhcCchhhHhHHHHc
Confidence 45678899999999999999999999984
No 42
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=43.48 E-value=63 Score=25.75 Aligned_cols=39 Identities=26% Similarity=0.355 Sum_probs=31.6
Q ss_pred ccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEccCCCceee
Q 001977 106 LRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQYDDGEDELL 147 (987)
Q Consensus 106 vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l 147 (987)
+|++|+|..+ +..+.|.+...|.. +.=.|+.+||..+.+
T Consensus 2 lG~~V~v~~~--~~~~~G~~~gId~~-G~L~v~~~~g~~~~i 40 (48)
T PF02237_consen 2 LGQEVRVETG--DGEIEGIAEGIDDD-GALLVRTEDGSIRTI 40 (48)
T ss_dssp TTSEEEEEET--SCEEEEEEEEEETT-SEEEEEETTEEEEEE
T ss_pred CCCEEEEEEC--CeEEEEEEEEECCC-CEEEEEECCCCEEEE
Confidence 6999999994 55679999999876 778888888855544
No 43
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=42.09 E-value=8.4 Score=35.24 Aligned_cols=9 Identities=33% Similarity=0.254 Sum_probs=0.0
Q ss_pred chhhhhhhc
Q 001977 218 DLVDEQENK 226 (987)
Q Consensus 218 ~~~~~~~~~ 226 (987)
|++|+++.|
T Consensus 34 ddee~de~p 42 (101)
T PF09026_consen 34 DDEEEDEVP 42 (101)
T ss_dssp ---------
T ss_pred ccccccccc
Confidence 333444444
No 44
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=41.10 E-value=19 Score=42.56 Aligned_cols=12 Identities=25% Similarity=0.684 Sum_probs=6.8
Q ss_pred CCCCCcchhhhc
Q 001977 193 DRSDSSDDDWNK 204 (987)
Q Consensus 193 ~~~~~~d~~~~~ 204 (987)
+++++-|+|+-.
T Consensus 463 de~~e~Dedf~~ 474 (615)
T KOG0526|consen 463 DEDEEEDEDFKP 474 (615)
T ss_pred ccchhhhhhccc
Confidence 445556666663
No 45
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=41.05 E-value=37 Score=43.74 Aligned_cols=39 Identities=28% Similarity=0.421 Sum_probs=29.1
Q ss_pred CCceEEEEEEeeeCCCCeEEEEccCCCceeeecCcceEEEE
Q 001977 117 DKAWYEGCVKSFDKECNKHLVQYDDGEDELLDLGKEKIEWV 157 (987)
Q Consensus 117 d~~~y~g~v~~~~~~~~~h~v~Yddg~~e~l~l~~e~~~~~ 157 (987)
|+.-+.|.+++||. +..+|+|.||+.|.+.-+.-+=.-.
T Consensus 54 d~~~~~~k~~s~d~--~~~rv~~e~~~~~~~~~s~v~~~~~ 92 (1414)
T KOG1473|consen 54 DKKVFLGKIVSYDT--GLYRVKYEDGDVESLEASTVRPLII 92 (1414)
T ss_pred chhhhhcccccccC--cceeEEeeccccccccccccccccc
Confidence 35667899999885 5689999999999886664433333
No 46
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=40.85 E-value=1.7e+02 Score=33.18 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=6.0
Q ss_pred ccccccCCCCCC
Q 001977 82 LVIGQTPSPPPS 93 (987)
Q Consensus 82 ~~~~~~~~~~~~ 93 (987)
.|.|..-.|+.+
T Consensus 156 ~v~~~~~ip~~~ 167 (348)
T KOG2652|consen 156 TVLQQSAIPPSG 167 (348)
T ss_pred cccccccccccC
Confidence 566654444333
No 47
>PF05616 Neisseria_TspB: Neisseria meningitidis TspB protein; InterPro: IPR008708 This family consists mainly of Neisseria meningitidis TspB virulence factor proteins.
Probab=39.78 E-value=94 Score=36.78 Aligned_cols=7 Identities=29% Similarity=0.264 Sum_probs=2.9
Q ss_pred ccccccc
Q 001977 20 QITSFFS 26 (987)
Q Consensus 20 ~~~~~~~ 26 (987)
||+.=|+
T Consensus 294 q~~~tF~ 300 (502)
T PF05616_consen 294 QTVITFG 300 (502)
T ss_pred EEEEEEe
Confidence 4443343
No 48
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=39.53 E-value=17 Score=38.20 Aligned_cols=24 Identities=42% Similarity=0.436 Sum_probs=13.9
Q ss_pred hhhhhhhcccccCCccCCCccCCC
Q 001977 219 LVDEQENKVLRGRKRKSSGVKKSK 242 (987)
Q Consensus 219 ~~~~~~~~~~~~~~~~~~~~~~~~ 242 (987)
++||+|..+-+.||||.-.+||.+
T Consensus 257 d~d~dednk~~~rkrk~~~a~ksr 280 (303)
T COG5129 257 DEDEDEDNKGKIRKRKTDDAKKSR 280 (303)
T ss_pred ccccccccccchhhcccCchhhcc
Confidence 344444444566777776666555
No 49
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=34.32 E-value=27 Score=44.92 Aligned_cols=18 Identities=6% Similarity=-0.047 Sum_probs=8.9
Q ss_pred eEEEECh-hHHHHHHHHHH
Q 001977 907 FFRYWTP-NIKKLLGELSQ 924 (987)
Q Consensus 907 ~~rf~tp-el~eL~~el~~ 924 (987)
.....++ .+.+...++.+
T Consensus 2838 deilVnkdNViEYV~KYAE 2856 (3015)
T KOG0943|consen 2838 DEILVNKDNVIEYVRKYAE 2856 (3015)
T ss_pred ceeeecchhHHHHHHHHHH
Confidence 3344444 35566555544
No 50
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=33.89 E-value=17 Score=42.21 Aligned_cols=28 Identities=21% Similarity=0.188 Sum_probs=15.0
Q ss_pred CCCCccCCCCcc--c----ccCCCHHHHHHHHHH
Q 001977 311 YYDPRTLYLPPD--F----LRNLSEGQKQWWEFK 338 (987)
Q Consensus 311 ~YDp~TL~iP~~--~----~~~~TP~~~Qyw~iK 338 (987)
.+-|.|--+|.+ | |-.--|++.-|....
T Consensus 181 ~~Rp~tP~LPDSTDFVCGTLDEDRPLE~AY~Scl 214 (458)
T PF10446_consen 181 KIRPGTPELPDSTDFVCGTLDEDRPLEAAYISCL 214 (458)
T ss_pred CCCCCCCCCCCcccccCCCcCCcchHHHHHHHHH
Confidence 444555555543 1 234567777776543
No 51
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=33.50 E-value=64 Score=36.84 Aligned_cols=27 Identities=37% Similarity=0.603 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCccccc
Q 001977 56 NSNRTPSPSPSPTTPSPLQSNPKKSRL 82 (987)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (987)
.++.+.+|.+++|||+++..|+|||+-
T Consensus 173 ~s~T~ts~asT~ttt~at~KKpRKPRq 199 (379)
T PF11593_consen 173 PSNTPTSPASTPTTTTATAKKPRKPRQ 199 (379)
T ss_pred cCCCcccccccccCCccccCCCCCCCC
Confidence 445566888899999999999998873
No 52
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=33.42 E-value=23 Score=44.35 Aligned_cols=6 Identities=0% Similarity=-0.446 Sum_probs=2.3
Q ss_pred CCCCCC
Q 001977 307 PGDVYY 312 (987)
Q Consensus 307 p~dp~Y 312 (987)
|.+|+|
T Consensus 1504 ~~~d~e 1509 (1516)
T KOG1832|consen 1504 GEEDDE 1509 (1516)
T ss_pred CCCchh
Confidence 333333
No 53
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=32.82 E-value=1.9e+02 Score=28.56 Aligned_cols=46 Identities=22% Similarity=0.147 Sum_probs=35.4
Q ss_pred CCCEEEEEEEeCCCCe-EEEEEEc---CcchHHHHHHHHHhcCCcEEEec
Q 001977 470 TDRCFGICVVDVATSR-IILGQVM---DDLDCSVLCCLLSELRPVEIIKP 515 (987)
Q Consensus 470 ~~~~~Gva~vD~sTG~-f~l~qf~---Dd~~~s~L~tlL~~~~P~EIl~~ 515 (987)
+...+|||+.|..+.- .-+..+. .......|..++.+++|..||+-
T Consensus 9 G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvG 58 (135)
T PF03652_consen 9 GTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVG 58 (135)
T ss_dssp CSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEE
T ss_pred CCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEe
Confidence 3578999999997653 3344443 24668899999999999999983
No 54
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=32.70 E-value=21 Score=44.36 Aligned_cols=12 Identities=25% Similarity=0.221 Sum_probs=6.7
Q ss_pred HHHHHHHHHhcC
Q 001977 497 CSVLCCLLSELR 508 (987)
Q Consensus 497 ~s~L~tlL~~~~ 508 (987)
..+|..+|+++.
T Consensus 336 ~krL~~lLAkMG 347 (622)
T PF02724_consen 336 RKRLHKLLAKMG 347 (622)
T ss_pred HHHHHHHHHHhC
Confidence 345666666554
No 55
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=32.69 E-value=1.1e+02 Score=38.28 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=5.1
Q ss_pred HHHHHHHHHHH
Q 001977 606 SALGGTLFYLK 616 (987)
Q Consensus 606 ~AlgalL~YL~ 616 (987)
+|+|.-|.||.
T Consensus 839 ~afgF~is~L~ 849 (1102)
T KOG1924|consen 839 QAFGFNISFLC 849 (1102)
T ss_pred hhhccchHHHH
Confidence 34444444444
No 56
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.80 E-value=1.1e+02 Score=39.78 Aligned_cols=31 Identities=35% Similarity=0.628 Sum_probs=14.1
Q ss_pred CCCCCCCCCCCCCC-CCCCCccccccccccCCCCCCC
Q 001977 59 RTPSPSPSPTTPSP-LQSNPKKSRLVIGQTPSPPPST 94 (987)
Q Consensus 59 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 94 (987)
.||.|...|++|.| +.+++. .+..|.+++++
T Consensus 808 stP~~~~~~~~P~~~~~~~~~-----~~~~~~~~~S~ 839 (1049)
T KOG0307|consen 808 STPTPPAFSFTPPPSSGAADQ-----YSQPPAAPPSF 839 (1049)
T ss_pred CCCCCCCcCCCCCCccccccc-----CCCCCCCCccC
Confidence 33444455555554 222222 23355555555
No 57
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=31.58 E-value=2.9e+02 Score=34.17 Aligned_cols=55 Identities=18% Similarity=0.278 Sum_probs=35.5
Q ss_pred cCCCCchhHHHHHHHHHhhcch-hhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHHH
Q 001977 802 TPGKGLPAIVSILKHFKDAFDW-VEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTKH 859 (987)
Q Consensus 802 ~~~~~lp~l~~ll~~i~~~iD~-~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~~ 859 (987)
..+..++.|..-|+.|+.-|+. .....+|.++ .+...|+.++..+..++..|.++
T Consensus 162 ~~G~a~~~le~~l~~~e~~f~~f~~l~~~Gd~~---~A~e~l~~l~~~~~~l~~~~~~i 217 (569)
T PRK04778 162 SFGPALDELEKQLENLEEEFSQFVELTESGDYV---EAREILDQLEEELAALEQIMEEI 217 (569)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHhcCCCHH---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677888888888877764 3344567665 35566777777766666655543
No 58
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=31.34 E-value=23 Score=47.33 Aligned_cols=12 Identities=42% Similarity=0.794 Sum_probs=5.9
Q ss_pred ccccCChhhhhc
Q 001977 174 KVVVEDDEEMEN 185 (987)
Q Consensus 174 ~~~~~~~~~~~~ 185 (987)
..|++|||++++
T Consensus 150 ~~~~d~~~~~~~ 161 (2849)
T PTZ00415 150 NFVIDDDDEDED 161 (2849)
T ss_pred ccccCCcccccc
Confidence 345555555543
No 59
>KOG3208 consensus SNARE protein GS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.43 E-value=6.8e+02 Score=26.88 Aligned_cols=96 Identities=17% Similarity=0.212 Sum_probs=61.8
Q ss_pred CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEE--Chh
Q 001977 837 GVDMDYDSACKKVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYW--TPN 914 (987)
Q Consensus 837 G~d~eLD~lr~~i~~ie~~L~~~l~~~~k~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~--tpe 914 (987)
|..+-.+.+|++-..+|.+|+..|..+.+.... ..+||.+.-+.- .+...-|. +.+
T Consensus 2 ~~~s~we~LRkqArslE~~ld~kL~syskl~as--------~~gg~~~~~s~~--------------~~~~~s~ks~~~e 59 (231)
T KOG3208|consen 2 GSSSSWEALRKQARSLENQLDSKLVSYSKLGAS--------THGGYDIDTSPL--------------SGSDRSFKSLENE 59 (231)
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHHHhcc--------cCCCCCCCcccc--------------cCcCcchhhhHHH
Confidence 455667999999999999999999988764321 346665422110 01122333 347
Q ss_pred HHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHH
Q 001977 915 IKKLLGELSQAESEKES----------------ALKSILQRLIGQFCEHHNKWRQM 954 (987)
Q Consensus 915 l~eL~~el~~~~~~~~~----------------~~~~il~~L~~~~~~~~~~l~~~ 954 (987)
+..|.+++.++-+.+.+ ..++|+++...+|......+.+.
T Consensus 60 ie~LLeql~~vndsm~~~~~s~a~~aa~~htL~RHrEILqdy~qef~rir~n~~a~ 115 (231)
T KOG3208|consen 60 IEGLLEQLQDVNDSMNDCASSPANSAAVMHTLQRHREILQDYTQEFRRIRSNIDAK 115 (231)
T ss_pred HHHHHHHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88888888888777766 44667777777766655544433
No 60
>KOG4327 consensus mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification]
Probab=28.07 E-value=48 Score=34.42 Aligned_cols=45 Identities=20% Similarity=0.323 Sum_probs=35.9
Q ss_pred cccceEEEEcCCCCceEEEEEEeeeCCCCeEEEEc-cCCCceeeec
Q 001977 105 VLRKRIRVYWPLDKAWYEGCVKSFDKECNKHLVQY-DDGEDELLDL 149 (987)
Q Consensus 105 ~vg~rv~v~wp~d~~~y~g~v~~~~~~~~~h~v~Y-ddg~~e~l~l 149 (987)
=||-.+.--|-.+.+.|.|+|.+.+-..+...|+| --|-.+.++|
T Consensus 69 KVgdkc~A~Y~e~g~~ypatidsi~~~~~tcvv~ylgygnr~Ev~l 114 (218)
T KOG4327|consen 69 KVGDKCSAIYSEDGCIYPATIDSIDFKRETCVVVYLGYGNREEVNL 114 (218)
T ss_pred eecceeeeeeecCcccccceecccccccCceEEEEEeecchhhhhH
Confidence 39999999999999999999999997777777777 3444444444
No 61
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=27.39 E-value=1.2e+02 Score=29.81 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=29.4
Q ss_pred ccceEEEEcCCCCceEEEEEEeee-CCCCeEEEEccCCCc
Q 001977 106 LRKRIRVYWPLDKAWYEGCVKSFD-KECNKHLVQYDDGED 144 (987)
Q Consensus 106 vg~rv~v~wp~d~~~y~g~v~~~~-~~~~~h~v~Yddg~~ 144 (987)
.|.+|=-.||.=-+||.|+|.+-- ...+...++++|-+.
T Consensus 74 ~g~~VLAlYP~TT~FY~A~V~~~p~~~~~~y~l~Fedd~~ 113 (130)
T PF07039_consen 74 KGTKVLALYPDTTCFYPATVVSPPKKKSGEYKLKFEDDED 113 (130)
T ss_dssp TT-EEEEE-TTSSEEEEEEEEEE-SSTTS-EEEEECTTTS
T ss_pred CCCEEEEECCCCceEEEEEEEeCCCCCCCcEEEEEeCCCC
Confidence 899999999999999999999973 355678888865554
No 62
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=27.34 E-value=1.1e+02 Score=35.85 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=17.4
Q ss_pred ccccccccCCCCCCCCccccCCCCC
Q 001977 20 QITSFFSKSNSPSPSPTISKLNPNK 44 (987)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (987)
|=..-|+-+.-|.|+|+++..-+|+
T Consensus 266 dPlaafglPchpkpmpSlpqleepg 290 (666)
T KOG4825|consen 266 DPLAAFGLPCHPKPMPSLPQLEEPG 290 (666)
T ss_pred ChhhhcCCCCCCCCCCccccccCCC
Confidence 3334456666688888888887776
No 63
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=27.17 E-value=48 Score=40.94 Aligned_cols=87 Identities=23% Similarity=0.406 Sum_probs=0.0
Q ss_pred CChhhhhccccccCCCCCCCcchhhhcccCCCCCCcccccchhhhhhhcccccCCccCCCccCCCCCCCCCCCCcccccc
Q 001977 178 EDDEEMENVEDEISDDRSDSSDDDWNKNVGKEDVSEDEEVDLVDEQENKVLRGRKRKSSGVKKSKSDGNAVNADFKSPII 257 (987)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 257 (987)
++-|+++.++++++++.+|+|-++--.-..++++.|+|+.+.+|+++++ ...
T Consensus 217 Ee~e~e~~e~~e~~~~~~~sgs~~~~e~e~e~~~~de~~e~~~~~~d~d----------------------------~i~ 268 (822)
T KOG2141|consen 217 EEFEDEESEDSESGDEEDDSGSEDEDESEDEKDSVDEEEESEEDNEDDD----------------------------GIS 268 (822)
T ss_pred cccccccccccccccccccccCcccchhhhhccchhhhhhhhhcccCCc----------------------------ccc
Q ss_pred CCccccCCCCCCCCCCCCCcccchhhhhhhccccccccCCCCCccCCCCCCCCCCCC----ccCCCCcccccCC
Q 001977 258 KPVKIFGSDKLSNGFDNPVMGDVSERFSAREADKFHFLGPDRRDAKRRRPGDVYYDP----RTLYLPPDFLRNL 327 (987)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fl~~~~rD~~~r~p~dp~YDp----~TL~iP~~~~~~~ 327 (987)
.|.. ..++|+.++.-.+|.|-+ ++=||||+.-++|
T Consensus 269 E~~~-----------------------------------~~i~~s~~~~~~e~~~~~~~~s~sKYvPPslRkkl 307 (822)
T KOG2141|consen 269 EISN-----------------------------------SEIRDSALKKSEEPEYLRKINSSSKYVPPSLRKKL 307 (822)
T ss_pred cccc-----------------------------------ccccCCccccCCCcccccccccccccCCHHHHHHh
No 64
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=27.12 E-value=49 Score=42.71 Aligned_cols=14 Identities=29% Similarity=0.330 Sum_probs=7.0
Q ss_pred cCcccHHHHHHHHH
Q 001977 382 FPERNFSMNVEKLA 395 (987)
Q Consensus 382 fPe~s~~~~~~~Lv 395 (987)
+|+.....+...|.
T Consensus 506 ~p~~~a~~~r~~L~ 519 (840)
T PF04147_consen 506 YPEEAAECFREVLK 519 (840)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555544443
No 65
>PRK14637 hypothetical protein; Provisional
Probab=27.06 E-value=73 Score=32.17 Aligned_cols=45 Identities=16% Similarity=0.313 Sum_probs=34.5
Q ss_pred CCCCCCCcccccccCCccccceEEEEcCCCCceEEEEEEeeeCCC
Q 001977 88 PSPPPSTPAAAKSYGEDVLRKRIRVYWPLDKAWYEGCVKSFDKEC 132 (987)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~vg~rv~v~wp~d~~~y~g~v~~~~~~~ 132 (987)
.||+-.+.+-....=..++|+.|+|.+...+.|+.|++.+++..+
T Consensus 79 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~ 123 (151)
T PRK14637 79 SSPGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADETC 123 (151)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCCE
Confidence 566666655555556677999999988667888899999997753
No 66
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=25.50 E-value=40 Score=41.71 Aligned_cols=15 Identities=20% Similarity=0.078 Sum_probs=6.7
Q ss_pred CCCCCCCCccccccc
Q 001977 70 PSPLQSNPKKSRLVI 84 (987)
Q Consensus 70 ~~~~~~~~~~~~~~~ 84 (987)
-|-++.-.+-|-.|+
T Consensus 767 s~cLV~LtE~P~~Vv 781 (960)
T KOG1189|consen 767 SSCLVNLTEWPFFVV 781 (960)
T ss_pred hhhhhccccCCceEE
Confidence 344444444444443
No 67
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=25.39 E-value=2.8e+02 Score=34.22 Aligned_cols=60 Identities=15% Similarity=0.258 Sum_probs=34.4
Q ss_pred HHHHhhcCCCCchhHHHHHHHHHhhcch-hhhcCCCCeeeCCCCCHhHHHHHHHHHHHHHHHHH
Q 001977 796 QLHHILTPGKGLPAIVSILKHFKDAFDW-VEANNSGRIIPHGGVDMDYDSACKKVKEIEASLTK 858 (987)
Q Consensus 796 lL~~l~~~~~~lp~l~~ll~~i~~~iD~-~~a~~~g~iipk~G~d~eLD~lr~~i~~ie~~L~~ 858 (987)
++..-...+..++.|...++.++..|+. .....+|.++ .+...|..++..+..++..|+.
T Consensus 152 ll~~~~~~G~a~~~Le~~L~~ie~~F~~f~~lt~~GD~~---~A~eil~~l~~~~~~l~~~~e~ 212 (560)
T PF06160_consen 152 LLAHSFSYGPAIEELEKQLENIEEEFSEFEELTENGDYL---EAREILEKLKEETDELEEIMED 212 (560)
T ss_pred HHHhhhhhchhHHHHHHHHHHHHHHHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333455677788888888777764 2233456654 3455666666666555554443
No 68
>PRK13335 superantigen-like protein; Reviewed
Probab=23.89 E-value=3.8e+02 Score=30.41 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=10.4
Q ss_pred CceEEEEEEeeeCCCC
Q 001977 118 KAWYEGCVKSFDKECN 133 (987)
Q Consensus 118 ~~~y~g~v~~~~~~~~ 133 (987)
..||.|.--.|--.+|
T Consensus 172 k~YYs~ps~E~kNvsG 187 (356)
T PRK13335 172 RAYYTKPSFEFEKQFG 187 (356)
T ss_pred HHhcccCcceeeccee
Confidence 5788876666555554
No 69
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=23.60 E-value=36 Score=43.24 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=13.9
Q ss_pred CCCCeeecCHHHHHhccCccc
Q 001977 642 AKKPYMVLDAPALENLEVFEN 662 (987)
Q Consensus 642 ~~~~~M~LD~~TL~nLEI~~n 662 (987)
......+++..|.++|.+|..
T Consensus 484 e~~~vi~~Sd~t~eel~Vf~~ 504 (1024)
T KOG1999|consen 484 EQGDVILLSDLTMEELKVFAR 504 (1024)
T ss_pred eCCeEEEEecCccceeeEEeh
Confidence 334456677777788877764
No 70
>smart00026 EPEND Ependymins. Ependymins are the predominant proteins in the cerebrospinal fluid (CSF) of teleost fish. They have been implicated in the neurochemistry of memory and neuronal regeneration. They are glycoproteins of about 200 amino acids that can bind calcium. Four cysteines are conserved that probably form disulfide bonds.
Probab=23.41 E-value=39 Score=35.36 Aligned_cols=19 Identities=42% Similarity=0.941 Sum_probs=16.6
Q ss_pred HhhCCCeEEEEeeCCeEEE
Q 001977 338 KSKHMDKVIFFKMGKFYEL 356 (987)
Q Consensus 338 K~~~~D~Vlffk~GkFYEl 356 (987)
|..|+|.|++|+.|.+|++
T Consensus 48 ~t~~~d~L~lf~eGv~Y~i 66 (191)
T smart00026 48 KTSHLDVLIHFEEGVFYDI 66 (191)
T ss_pred CceeeEEEEEecCCcEEEE
Confidence 3457899999999999987
No 71
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=21.82 E-value=3.4e+02 Score=26.56 Aligned_cols=45 Identities=22% Similarity=0.301 Sum_probs=31.9
Q ss_pred CCCEEEEEEEeCCCCeEE--EEEEc---CcchHHHHHHHHHhcCCcEEEec
Q 001977 470 TDRCFGICVVDVATSRII--LGQVM---DDLDCSVLCCLLSELRPVEIIKP 515 (987)
Q Consensus 470 ~~~~~Gva~vD~sTG~f~--l~qf~---Dd~~~s~L~tlL~~~~P~EIl~~ 515 (987)
+...+|||+.|. +|.+. ++.+. .......|..++.+++|.+||+-
T Consensus 6 G~kriGvA~~d~-~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iVvG 55 (130)
T TIGR00250 6 GTKSIGVAGQDI-TGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVG 55 (130)
T ss_pred CCCeEEEEEECC-CCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEEEEe
Confidence 457899999988 44332 12221 22446789999999999999986
No 72
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.45 E-value=1.7e+02 Score=32.04 Aligned_cols=11 Identities=36% Similarity=0.534 Sum_probs=5.7
Q ss_pred CCCCCCCCCCC
Q 001977 46 NSNPNPNPNSN 56 (987)
Q Consensus 46 ~~~~~~~~~~~ 56 (987)
.|||+|.++|.
T Consensus 248 ~nnP~p~ySst 258 (338)
T KOG0917|consen 248 ANNPAPVYSST 258 (338)
T ss_pred cCCCCCCCCCC
Confidence 34566655543
No 73
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=1.4e+02 Score=27.93 Aligned_cols=37 Identities=38% Similarity=0.680 Sum_probs=27.2
Q ss_pred eeccC--CCCccccCcccHHHHHHHHHHcC-CeEEEEeccCChH
Q 001977 371 QYMKG--EQPHCGFPERNFSMNVEKLARKG-YRVLVVEQTETPE 411 (987)
Q Consensus 371 ~~~~~--~~~~~GfPe~s~~~~~~~Lv~~G-ykVavveQ~Et~~ 411 (987)
-||+| .+|+|||.. .-+..|-..| -..+-|+=.++++
T Consensus 19 LFMKGtp~~P~CGFS~----~~vqiL~~~g~v~~~~vnVL~d~e 58 (105)
T COG0278 19 LFMKGTPEFPQCGFSA----QAVQILSACGVVDFAYVDVLQDPE 58 (105)
T ss_pred EEecCCCCCCCCCccH----HHHHHHHHcCCcceeEEeeccCHH
Confidence 36777 489999985 4455677889 6777788777764
No 74
>PF12946 EGF_MSP1_1: MSP1 EGF domain 1; InterPro: IPR024730 This EGF-like domain is found at the C terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite [].; PDB: 1N1I_C 2FLG_A 1CEJ_A 2NPR_A 1B9W_A 1OB1_F.
Probab=20.85 E-value=54 Score=24.95 Aligned_cols=18 Identities=33% Similarity=0.375 Sum_probs=14.2
Q ss_pred eEEEEccCCCceeeecCc
Q 001977 134 KHLVQYDDGEDELLDLGK 151 (987)
Q Consensus 134 ~h~v~Yddg~~e~l~l~~ 151 (987)
--.++|+||.+||..|..
T Consensus 11 A~C~~~~dG~eecrCllg 28 (37)
T PF12946_consen 11 AGCFRYDDGSEECRCLLG 28 (37)
T ss_dssp EEEEEETTSEEEEEE-TT
T ss_pred cccEEcCCCCEEEEeeCC
Confidence 457899999999998863
No 75
>PF06511 IpaD: Invasion plasmid antigen IpaD; InterPro: IPR009483 This family consists of several invasion plasmid antigen IpaD proteins. Entry of Shigella flexneri into epithelial cells and lysis of the phagosome involve the IpaB, IpaC, and IpaD proteins, which are secreted by type III secretion machinery, and appear to form a multi-protein complex capable of inducing the phagocytic event which internalizes the bacterium [].; GO: 0009405 pathogenesis; PDB: 3R9V_B 2JAA_B 2J0O_A 2J0N_B 2P7N_A 2YM9_A 3NZZ_A 3O02_A 3O00_A 2YM0_B ....
Probab=20.78 E-value=9e+02 Score=27.77 Aligned_cols=93 Identities=10% Similarity=0.091 Sum_probs=47.4
Q ss_pred HHHHHHhCCCCeeEEEEcCeeEEEEecccccCCCCCCeEEEEeecCeEEEEChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 861 KEQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTPNIKKLLGELSQAESEKESALKSILQRL 940 (987)
Q Consensus 861 ~~~~k~l~~~~iky~~~~k~gY~IeVp~~~~~kvP~~~~~~ss~kg~~rf~tpel~eL~~el~~~~~~~~~~~~~il~~L 940 (987)
....++++.+.... ....++|+|-+--....++...+-.. ..++.+-..+.+...+..-+...++.+... ++.|
T Consensus 231 ~~W~~eLg~~~~~v-k~~~g~~~I~~D~spL~~m~~sl~~~-~~~~~~~~~~a~~qaw~~~f~~~~~~~~~~----~q~~ 304 (337)
T PF06511_consen 231 EKWLKELGLPFFCV-KQSGGGIVISPDMSPLDKMIKSLDGL-GSNGDVELSTAEYQAWQAGFDAQKNNIQSN----VQSL 304 (337)
T ss_dssp HHHHHHHTTTGGGE-EEETTCEEEEE-THHHHHHHHHHHHT-TSTSCEEEEHHHHHHHHHHHHHHHHHHHHH----HHHH
T ss_pred HHHHHHhCCCCceE-EecCCceEEEeCchHHHHHHHhccCC-CCCCcccccHHHHHHHHHHHhHHHHHHHHH----HHHH
Confidence 34556677664333 34456788866544322111000000 112445555667777777777666555544 4555
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 001977 941 IGQFCEHHNKWRQMVAATA 959 (987)
Q Consensus 941 ~~~~~~~~~~l~~~~~~iA 959 (987)
.+++......+..++++|+
T Consensus 305 ~~kys~ans~~dnl~k~ls 323 (337)
T PF06511_consen 305 TQKYSQANSTFDNLIKVLS 323 (337)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhccchHHHHHHHHH
Confidence 5555555555555555544
No 76
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=20.75 E-value=8.2e+02 Score=24.13 Aligned_cols=53 Identities=19% Similarity=0.234 Sum_probs=35.9
Q ss_pred EEEEEEecCCCCCCCCCCCEEEEEEEeCCCCeE-EEEEE--c-CcchHHHHHHHHHhcCCcEEEec
Q 001977 454 YLMALTESNQSPASQSTDRCFGICVVDVATSRI-ILGQV--M-DDLDCSVLCCLLSELRPVEIIKP 515 (987)
Q Consensus 454 yLlaI~e~~~~~~~~~~~~~~Gva~vD~sTG~f-~l~qf--~-Dd~~~s~L~tlL~~~~P~EIl~~ 515 (987)
-++||-. +...+|||+.|....-- -++.+ . .......|..++.+++|..||+-
T Consensus 5 ~iLalD~---------G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~iVvG 61 (138)
T PRK00109 5 RILGLDV---------GTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVG 61 (138)
T ss_pred cEEEEEe---------CCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEEEEe
Confidence 3777765 35789999999843211 11122 2 22347889999999999999985
No 77
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=20.73 E-value=88 Score=28.78 Aligned_cols=25 Identities=40% Similarity=0.848 Sum_probs=20.1
Q ss_pred CccccCccc---HHHHHHHHHHcCCeEE
Q 001977 378 PHCGFPERN---FSMNVEKLARKGYRVL 402 (987)
Q Consensus 378 ~~~GfPe~s---~~~~~~~Lv~~GykVa 402 (987)
||.|.|+.+ |+.-+++|.++||.|.
T Consensus 6 PmtG~~~~N~~~f~~~a~~L~~~G~~vv 33 (92)
T PF14359_consen 6 PMTGLPDYNRPAFNAAAKRLRAKGYEVV 33 (92)
T ss_pred CcCCCcchHHHHHHHHHHHHHHCCCEEe
Confidence 899999874 5556788999998874
No 78
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=20.39 E-value=3.5e+02 Score=20.89 Aligned_cols=35 Identities=20% Similarity=0.213 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001977 930 ESALKSILQRLIGQFCEHHNKWRQMVAATAGLTLI 964 (987)
Q Consensus 930 ~~~~~~il~~L~~~~~~~~~~l~~~~~~iAeLD~L 964 (987)
.++.+.++-+|-..+.+-.+.++.+...|.++|-.
T Consensus 6 ieelkqll~rle~eirett~sl~ninksidq~dk~ 40 (46)
T PF08181_consen 6 IEELKQLLWRLENEIRETTDSLRNINKSIDQYDKY 40 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhch
Confidence 34566777778888888888899999999988854
No 79
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=20.04 E-value=1.1e+02 Score=30.25 Aligned_cols=53 Identities=17% Similarity=0.318 Sum_probs=31.1
Q ss_pred CCCCCCcccccccCCccccceEEEEc--CC-CCceEEEEEEeeeCCCCeEEEEccCCC
Q 001977 89 SPPPSTPAAAKSYGEDVLRKRIRVYW--PL-DKAWYEGCVKSFDKECNKHLVQYDDGE 143 (987)
Q Consensus 89 ~~~~~~~~~~~~~~~~~vg~rv~v~w--p~-d~~~y~g~v~~~~~~~~~h~v~Yddg~ 143 (987)
||+-.+.+.....=...+|+.|+|++ |. ...+|.|.+.+++. ....+.++++.
T Consensus 69 SPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~~~~ 124 (141)
T PF02576_consen 69 SPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITLEVEGKG 124 (141)
T ss_dssp --SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEEEEE-SS
T ss_pred CCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEEEECCcc
Confidence 45444433333333456999999998 33 45799999999988 56677776664
Done!