Query 008500
Match_columns 563
No_of_seqs 156 out of 238
Neff 5.2
Searched_HMMs 46136
Date Thu Mar 28 12:56:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2379 Endonuclease MUS81 [Re 99.9 5.8E-26 1.3E-30 243.1 19.6 232 283-540 249-498 (501)
2 PF02732 ERCC4: ERCC4 domain; 99.7 1.8E-16 3.9E-21 143.8 11.8 143 268-426 1-143 (143)
3 COG1948 MUS81 ERCC4-type nucle 99.4 3.5E-11 7.6E-16 121.6 20.1 216 262-546 26-241 (254)
4 PRK13766 Hef nuclease; Provisi 98.9 7.9E-08 1.7E-12 110.8 20.7 211 260-541 559-769 (773)
5 TIGR00596 rad1 DNA repair prot 98.8 1.3E-06 2.7E-11 101.8 25.4 224 260-542 583-811 (814)
6 KOG2841 Structure-specific end 93.2 5.4 0.00012 41.0 16.4 111 395-541 137-249 (254)
7 KOG0442 Structure-specific end 93.2 7.4 0.00016 46.2 19.7 235 259-553 648-886 (892)
8 PF12826 HHH_2: Helix-hairpin- 90.9 0.32 7E-06 39.6 4.0 51 472-541 7-57 (64)
9 KOG4364 Chromatin assembly fac 88.7 0.45 9.8E-06 54.4 4.2 34 209-242 303-336 (811)
10 KOG4364 Chromatin assembly fac 83.5 0.98 2.1E-05 51.8 3.5 40 214-253 297-336 (811)
11 PF14520 HHH_5: Helix-hairpin- 81.1 4.1 8.8E-05 32.4 5.3 53 468-539 5-58 (60)
12 PRK00247 putative inner membra 72.5 3.9 8.5E-05 45.3 4.0 11 151-161 275-285 (429)
13 PF07946 DUF1682: Protein of u 68.9 9 0.0002 40.7 5.7 8 215-222 261-268 (321)
14 PRK13901 ruvA Holliday junctio 67.1 12 0.00026 37.5 5.7 59 463-537 67-125 (196)
15 PRK14605 ruvA Holliday junctio 65.6 13 0.00028 36.9 5.6 36 463-499 68-103 (194)
16 KOG1029 Endocytic adaptor prot 64.5 9.9 0.00021 44.8 5.1 19 205-223 347-365 (1118)
17 PF15437 PGBA_C: Plasminogen-b 64.4 25 0.00054 30.6 6.3 21 212-232 36-56 (86)
18 PRK14601 ruvA Holliday junctio 62.7 16 0.00034 36.1 5.6 61 463-539 68-128 (183)
19 PF00633 HHH: Helix-hairpin-he 62.3 8.9 0.00019 27.0 2.7 20 467-486 10-29 (30)
20 PRK14603 ruvA Holliday junctio 61.8 14 0.00031 36.7 5.2 58 463-536 67-124 (197)
21 PRK14606 ruvA Holliday junctio 61.1 16 0.00034 36.2 5.3 61 463-539 68-128 (188)
22 PRK14600 ruvA Holliday junctio 59.8 15 0.00033 36.2 4.9 36 463-499 68-103 (186)
23 PRK14604 ruvA Holliday junctio 59.8 16 0.00035 36.3 5.2 60 463-538 68-127 (195)
24 KOG3654 Uncharacterized CH dom 59.1 1.5E+02 0.0032 33.9 12.7 34 17-54 226-260 (708)
25 KOG1144 Translation initiation 58.8 17 0.00036 43.2 5.6 12 418-429 677-688 (1064)
26 PRK14602 ruvA Holliday junctio 58.8 20 0.00043 35.8 5.6 58 463-536 69-126 (203)
27 PTZ00399 cysteinyl-tRNA-synthe 55.2 21 0.00047 41.6 5.9 31 209-239 546-576 (651)
28 KOG2412 Nuclear-export-signal 54.5 18 0.00039 41.2 4.9 13 243-255 263-275 (591)
29 PRK12766 50S ribosomal protein 54.2 26 0.00057 36.0 5.6 62 469-549 4-66 (232)
30 KOG0112 Large RNA-binding prot 53.9 12 0.00025 44.8 3.4 42 181-222 700-741 (975)
31 TIGR00084 ruvA Holliday juncti 52.2 31 0.00068 34.1 5.7 59 463-537 67-125 (191)
32 KOG4819 Uncharacterized conser 50.3 66 0.0014 29.0 6.7 38 209-246 31-69 (106)
33 PRK00116 ruvA Holliday junctio 49.1 42 0.00091 33.1 6.1 63 466-544 71-133 (192)
34 KOG1924 RhoA GTPase effector D 47.9 37 0.00081 40.4 6.2 30 265-296 1030-1059(1102)
35 KOG2412 Nuclear-export-signal 46.4 42 0.00091 38.3 6.1 6 493-498 536-541 (591)
36 PRK13482 DNA integrity scannin 46.1 18 0.00039 39.2 3.2 32 467-498 286-317 (352)
37 PRK14671 uvrC excinuclease ABC 44.5 41 0.00089 39.2 6.0 57 463-540 564-620 (621)
38 PRK02515 psbU photosystem II c 44.4 28 0.00061 32.8 3.8 34 463-496 56-91 (132)
39 KOG0163 Myosin class VI heavy 42.8 24 0.00052 41.8 3.6 14 524-537 1216-1229(1259)
40 COG1948 MUS81 ERCC4-type nucle 42.6 17 0.00036 37.8 2.2 36 468-503 214-249 (254)
41 PF15437 PGBA_C: Plasminogen-b 41.5 64 0.0014 28.1 5.2 30 216-245 33-62 (86)
42 KOG3054 Uncharacterized conser 40.0 54 0.0012 34.1 5.3 11 202-212 100-110 (299)
43 KOG2357 Uncharacterized conser 38.7 34 0.00074 37.8 3.9 8 70-77 110-117 (440)
44 KOG1029 Endocytic adaptor prot 37.2 50 0.0011 39.3 5.1 6 103-108 177-182 (1118)
45 PF06975 DUF1299: Protein of u 36.2 21 0.00046 27.3 1.3 26 4-29 13-38 (47)
46 PF12836 HHH_3: Helix-hairpin- 35.4 35 0.00076 27.6 2.6 21 467-487 13-33 (65)
47 PTZ00399 cysteinyl-tRNA-synthe 34.9 33 0.00072 40.1 3.3 6 253-258 585-590 (651)
48 cd00080 HhH2_motif Helix-hairp 34.5 50 0.0011 27.7 3.5 29 471-499 25-53 (75)
49 KOG3925 Uncharacterized conser 34.0 1.3E+02 0.0028 32.9 7.2 17 423-439 262-278 (371)
50 smart00278 HhH1 Helix-hairpin- 33.3 44 0.00096 22.3 2.4 19 469-487 2-20 (26)
51 PRK14666 uvrC excinuclease ABC 33.2 94 0.002 36.8 6.5 58 464-540 633-690 (694)
52 PF15236 CCDC66: Coiled-coil d 32.3 1.1E+02 0.0024 29.7 5.8 20 223-242 90-109 (157)
53 PRK00558 uvrC excinuclease ABC 30.5 94 0.002 36.1 6.0 59 463-540 538-596 (598)
54 PRK14669 uvrC excinuclease ABC 29.7 90 0.0019 36.5 5.6 57 463-540 547-603 (624)
55 TIGR01259 comE comEA protein. 28.3 73 0.0016 29.1 3.8 23 467-489 67-89 (120)
56 PLN02381 valyl-tRNA synthetase 27.7 68 0.0015 39.7 4.5 33 209-242 20-52 (1066)
57 PF04568 IATP: Mitochondrial A 27.1 1.8E+02 0.0038 26.3 5.8 10 240-249 88-97 (100)
58 KOG2751 Beclin-like protein [S 26.4 1.3E+02 0.0028 33.7 5.8 52 205-256 182-233 (447)
59 KOG2891 Surface glycoprotein [ 26.1 65 0.0014 34.1 3.3 8 157-164 268-275 (445)
60 PF09831 DUF2058: Uncharacteri 25.6 84 0.0018 31.1 3.8 17 207-223 13-29 (177)
61 PLN02858 fructose-bisphosphate 25.5 40 0.00087 42.8 2.0 33 277-309 1030-1064(1378)
62 COG0632 RuvA Holliday junction 25.2 1.6E+02 0.0035 29.6 5.8 64 463-542 68-131 (201)
63 KOG2689 Predicted ubiquitin re 24.6 1.4E+02 0.0029 31.7 5.3 38 209-246 134-171 (290)
64 PF06936 Selenoprotein_S: Sele 24.2 2.2E+02 0.0048 28.4 6.6 15 233-247 105-119 (190)
65 TIGR00426 competence protein C 24.2 1.6E+02 0.0036 23.7 4.8 22 467-488 15-37 (69)
66 PF08690 GET2: GET complex sub 24.0 53 0.0011 35.0 2.3 17 211-227 2-18 (302)
67 KOG2072 Translation initiation 24.0 1.3E+02 0.0028 36.3 5.5 31 218-248 805-835 (988)
68 PF06546 Vert_HS_TF: Vertebrat 23.7 1.2E+02 0.0027 31.8 4.8 76 1-78 14-95 (265)
69 KOG3223 Uncharacterized conser 23.3 87 0.0019 31.5 3.4 26 225-250 46-71 (221)
70 KOG2507 Ubiquitin regulatory p 23.0 63 0.0014 36.1 2.7 16 34-49 77-92 (506)
71 KOG2357 Uncharacterized conser 22.8 1.7E+02 0.0037 32.7 5.8 9 192-200 359-367 (440)
72 PF09726 Macoilin: Transmembra 22.2 1.1E+02 0.0024 36.2 4.7 55 201-255 493-565 (697)
73 PF09756 DDRGK: DDRGK domain; 22.1 30 0.00064 34.5 0.0 8 334-341 102-109 (188)
74 KOG2072 Translation initiation 22.1 1E+02 0.0023 37.0 4.3 6 304-309 903-908 (988)
75 cd03489 Topoisomer_IB_N_Ldtopo 21.2 60 0.0013 32.9 1.9 22 207-228 97-118 (212)
76 cd00660 Topoisomer_IB_N Topois 21.1 59 0.0013 33.0 1.9 25 270-295 143-171 (215)
77 cd03488 Topoisomer_IB_N_htopoI 21.0 61 0.0013 32.9 1.9 22 207-228 100-121 (215)
78 cd03490 Topoisomer_IB_N_1 Topo 20.9 60 0.0013 33.0 1.9 22 207-228 99-120 (217)
79 PF02371 Transposase_20: Trans 20.6 77 0.0017 27.0 2.2 28 468-495 2-35 (87)
80 PF03760 LEA_1: Late embryogen 20.3 2.2E+02 0.0047 24.4 4.8 34 212-245 37-70 (73)
81 PF12757 DUF3812: Protein of u 20.2 1.5E+02 0.0032 27.5 4.2 23 223-245 103-125 (126)
82 KOG2891 Surface glycoprotein [ 20.2 1.7E+02 0.0036 31.2 4.9 9 223-231 344-352 (445)
No 1
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=99.94 E-value=5.8e-26 Score=243.11 Aligned_cols=232 Identities=16% Similarity=0.228 Sum_probs=178.8
Q ss_pred HHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHHHHhcCchhHHHHHHHhhCCCCcEE
Q 008500 283 LTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCNLVLNESLMDHVSLVRRHYPSHTIC 362 (563)
Q Consensus 283 l~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~lI~d~~L~e~v~rLk~~~P~~kli 362 (563)
...+.-.||+++|+.+.+ |++.|.++-... +.+...++||.+.+.+||+.+|.||+|++|+.||++++. .++|
T Consensus 249 ~~~~~~~~v~~evR~L~v-GD~lWVa~~k~~-----g~E~VLd~IVERKr~DDl~SSIrDgRf~EQK~RLq~sGi-k~~i 321 (501)
T KOG2379|consen 249 GEYFELEGVKHEVRSLEV-GDFLWVARHKYD-----GTELVLDFIVERKRLDDLVSSIRDGRFKEQKNRLQRSGI-KRII 321 (501)
T ss_pred hhhhhhccceeeEEEecc-cceEEEecccCC-----CceEeeeeheeecchHHHHHHHhccchHHHHHHHHhcCc-ceEE
Confidence 344666799999999998 999999984222 344567899999999999999999999999999999988 6899
Q ss_pred EEeccchHHHHHHhhhhhcCCCCCCCCCCCcHHHHHHHHHHhhceeEEEEcCCHHHHHHHHHHHHHHHHhc---------
Q 008500 363 YLTNRLMAHISKKEKERYKNPANNSGWRRPPVEEVLAKLTTHFFRVHSRQCIDEAEVAEHVVGLTSSLASC--------- 433 (563)
Q Consensus 363 yLVEGL~~ylrKr~~~qyk~~~~~~~~~rp~VEeALlqLQl~~~~Vh~~~~~d~~Eta~~I~~lTKaIA~~--------- 433 (563)
|||||...- | + +.-...+.+|+.-.|+.. ++++..+.+..|++.+|..+|+.+-..
T Consensus 322 YlvE~~~~~-----n-~--------~~~~eslktA~~~t~v~~-GF~V~RT~~l~et~s~l~y~tr~~~~~~~~~~~~~~ 386 (501)
T KOG2379|consen 322 YLVEEDGNP-----N-Q--------SKPAESLKTAVTNTLVLE-GFDVIRTRDLGETVSKLAYLTRGLLQIYASLLLDKE 386 (501)
T ss_pred EEEeccCCc-----c-c--------ccHHHHHHHHHHHHhhhc-ceEEEEecChhHHHHHHHHHhHHHHHHHHHhhcccc
Confidence 999997510 0 0 001135677888888876 666666667889999999999999864
Q ss_pred cccccccccc---cccCCceeccCcc------ccCCCchHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcC
Q 008500 434 QFRKKLTRLS---VNANGSLISKDSV------DKNLIKKSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKS 504 (563)
Q Consensus 434 PyKk~~~~~s---~~~~g~~v~k~~V------~kg~~l~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~S 504 (563)
+|+...+.+. -...+.|+..+++ .++.++.++|.+|||||+|||.++|+||+.+||||.+|+.||+.| .+
T Consensus 387 d~~~~~~q~~~~~~~p~~~~~~f~~F~~~~~K~~~~TV~evf~~qLMqvkg~S~erAiAI~d~YpTl~sLl~AY~~s-~~ 465 (501)
T KOG2379|consen 387 DYRERDDQLKGAMTVPSETELSFSAFQERLSKGKALTVGEVFARQLMQVKGMSLERAIAIADRYPTLRSLLSAYEVS-AD 465 (501)
T ss_pred ccccchhhhhcccCCCCcccccHHHHHHHhhhcccccHHHHHHHHHHhccCccHHHHHHHHHhccCHHHHHHHHhcc-Cc
Confidence 3333222211 1122333433332 346789999999999999999999999999999999999999744 57
Q ss_pred hHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHh
Q 008500 505 VHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILI 540 (563)
Q Consensus 505 e~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vft 540 (563)
++++.++|..+++. . +.|+|||+||..||.+|.
T Consensus 466 ~k~~~l~ln~~~~~-~--~~rn~~~~Ls~~l~~~F~ 498 (501)
T KOG2379|consen 466 DKLRLLLLNPIKCG-P--GSRNIGPALSAKLYEFFL 498 (501)
T ss_pred HHHHhccccccccc-c--ccccccHHHHHHHHHhhh
Confidence 77888888888763 1 469999999999999885
No 2
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=99.69 E-value=1.8e-16 Score=143.82 Aligned_cols=143 Identities=17% Similarity=0.272 Sum_probs=111.7
Q ss_pred EcccccccCCchHHHHHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHHHHhcCchhH
Q 008500 268 IDAKVVELGSVGGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCNLVLNESLMD 347 (563)
Q Consensus 268 ID~~lle~~s~GgqLl~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~lI~d~~L~e 347 (563)
||++.++ +++|++|+..|+..||++.++.+|+ |++.|.+. . ........+++|...+..+|+.++.+++|.+
T Consensus 1 VD~re~~-~~~~~~l~~~l~~~gv~~~~~~l~~-gd~~~~~~---~---~~~~e~~~~~iverk~~~dl~~si~~~rl~~ 72 (143)
T PF02732_consen 1 VDSRELR-SSGGEQLLEALRELGVKVEVRQLPV-GDYIWWRI---N---QISEETMVPVIVERKTLDDLVASIKDGRLEE 72 (143)
T ss_dssp EEGGGCT-SSCHHHHHHHHHCTTSEEEEE--SS-SSEEEEES----------BESSECEEEEEEEHHHHHHHHHTTHHHH
T ss_pred CCchHhC-cccHHHHHHHHHHCCCEEEEEECCC-CCEEEECC---C---CCccccceEEEEEhhHHHHHHhhhcCCchHH
Confidence 7999987 5569999999999999999999997 88888761 1 0111223388999999999999999999999
Q ss_pred HHHHHHhhCCCCcEEEEeccchHHHHHHhhhhhcCCCCCCCCCCCcHHHHHHHHHHhhceeEEEEcCCHHHHHHHHHHH
Q 008500 348 HVSLVRRHYPSHTICYLTNRLMAHISKKEKERYKNPANNSGWRRPPVEEVLAKLTTHFFRVHSRQCIDEAEVAEHVVGL 426 (563)
Q Consensus 348 ~v~rLk~~~P~~kliyLVEGL~~ylrKr~~~qyk~~~~~~~~~rp~VEeALlqLQl~~~~Vh~~~~~d~~Eta~~I~~l 426 (563)
|+.+|++.++.++++|||||+..|++++.+.... .....++.+|+.||+++ ++++..+.+++|+|+||++|
T Consensus 73 q~~rl~~~~~~~~~~~lVEg~~~~~~~~~~~~~~-------~~~~~i~~~L~~lq~~~-~~~v~~~~~~~et~~~l~~f 143 (143)
T PF02732_consen 73 QVQRLKRASPFKRVILLVEGLDSYLRKNKNYRRQ-------QSPSAIEEALVELQLRY-GISVIFTESWEETADWLASF 143 (143)
T ss_dssp HHHHHHCCHCSSEEEEEEESCSSTCCC-----HS-------STHHHHHHHHHHHHHCS-S-EEEEESSHHHHHHHHHHH
T ss_pred HHHHHhhcCCCCeEEEEEEccCccccccchhccc-------CCHHHHHHHHHHHHHHc-CeEEEEECCHHHHHHHhhhC
Confidence 9999997778888999999999988753321100 11137899999999997 88888999999999999987
No 3
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=99.38 E-value=3.5e-11 Score=121.58 Aligned_cols=216 Identities=18% Similarity=0.226 Sum_probs=164.9
Q ss_pred ceEEEEEcccccccCCchHHHHHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHHHHh
Q 008500 262 DSIVTEIDAKVVELGSVGGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCNLVL 341 (563)
Q Consensus 262 K~mvVvID~~lle~~s~GgqLl~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~lI~ 341 (563)
..++|++|.+-+. ..+-..|..+|+++.++.+.+ |++.|... .+|.+.+.+||+++|.
T Consensus 26 ~~~~viVD~RE~r-----s~v~~~L~~~gv~v~~~~Lev-GDYvvs~~----------------v~VERKs~~Dfv~Si~ 83 (254)
T COG1948 26 FEVVVIVDSRELR-----SEVPRLLKRLGVKVEVRTLEV-GDYVVSDD----------------VIVERKSISDFVSSII 83 (254)
T ss_pred cceEEEEecchhc-----ccchHHHHhCCCeEEEEeccc-ccEEeecC----------------eeEEeccHHHHHHHHh
Confidence 6889999999876 345566679999999999998 99999985 3688999999999999
Q ss_pred cCchhHHHHHHHhhCCCCcEEEEeccchHHHHHHhhhhhcCCCCCCCCCCCcHHHHHHHHHHhhceeEEEEcCCHHHHHH
Q 008500 342 NESLMDHVSLVRRHYPSHTICYLTNRLMAHISKKEKERYKNPANNSGWRRPPVEEVLAKLTTHFFRVHSRQCIDEAEVAE 421 (563)
Q Consensus 342 d~~L~e~v~rLk~~~P~~kliyLVEGL~~ylrKr~~~qyk~~~~~~~~~rp~VEeALlqLQl~~~~Vh~~~~~d~~Eta~ 421 (563)
||+|.+|+.+|+..|+ . .+++|||=..+.+.. + .....|-.||+.+++.| ++++....+..+||.
T Consensus 84 dgRlfeQ~~rL~~~y~-r-pvliVegd~~~~~~~-----~-------i~~~av~~al~s~~vdf-g~~vi~t~~~~~Ta~ 148 (254)
T COG1948 84 DGRLFEQAKRLKKSYE-R-PVLIVEGDDSFSRRP-----K-------IHPNAVRGALASLAVDF-GLPVIWTRSPEETAE 148 (254)
T ss_pred cchHHHHHHHHHhcCC-c-cEEEEEccccccccc-----c-------cCHHHHHHHHHHHHhhc-CceEEEeCCHHHHHH
Confidence 9999999999999998 3 455555533332210 0 11235778999999985 788888888999999
Q ss_pred HHHHHHHHHHhccccccccccccccCCceeccCccccCCCchHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCC
Q 008500 422 HVVGLTSSLASCQFRKKLTRLSVNANGSLISKDSVDKNLIKKSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDP 501 (563)
Q Consensus 422 ~I~~lTKaIA~~PyKk~~~~~s~~~~g~~v~k~~V~kg~~l~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~c 501 (563)
.|..+++-... .+.+. ... . .-.+..++.+.=..+|.-||||+...|..+-.+|.|+..++.|=
T Consensus 149 ~i~~la~req~---e~~r~-v~~--------~-~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas--- 212 (254)
T COG1948 149 LIHELARREQE---ERKRS-VNP--------H-GKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTAS--- 212 (254)
T ss_pred HHHHHHHHHHH---hcccc-ccc--------c-ccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcC---
Confidence 99999999886 22222 111 1 11334667888888889999999999999999999999999874
Q ss_pred CcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhcCCCCc
Q 008500 502 SKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIAQSGSI 546 (563)
Q Consensus 502 s~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts~Dp~l 546 (563)
+ .-|.- + .-||+..+++||.+|++.....
T Consensus 213 ---~----~eL~~--v-------~gig~k~A~~I~~~~~t~~~~~ 241 (254)
T COG1948 213 ---E----EELMK--V-------KGIGEKKAREIYRFLRTEYKLI 241 (254)
T ss_pred ---H----HHHHH--h-------cCccHHHHHHHHHHHhchhhhh
Confidence 1 11211 2 2588999999999998766543
No 4
>PRK13766 Hef nuclease; Provisional
Probab=98.90 E-value=7.9e-08 Score=110.83 Aligned_cols=211 Identities=16% Similarity=0.231 Sum_probs=150.4
Q ss_pred ccceEEEEEcccccccCCchHHHHHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHHH
Q 008500 260 AQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCNL 339 (563)
Q Consensus 260 ~lK~mvVvID~~lle~~s~GgqLl~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~l 339 (563)
....++|++|.+-+. ..+...|...|+++.+..+++ |++.+.- .++|.+.+.+||+.+
T Consensus 559 ~~~~~~i~vD~RE~~-----~~~~~~l~~~g~~~~~~~L~~-gDy~~~~----------------~~~vERK~~~Dl~~s 616 (773)
T PRK13766 559 EPEGPKIIVDSRELR-----SNVARHLKRLGAEVELKTLEV-GDYVVSD----------------RVAVERKTAEDFVDS 616 (773)
T ss_pred CCCCcEEEEeCCCcc-----chhhHHHHhCCCEEEEEecCC-CCEEccC----------------CeEEEeCcHHHHHHH
Confidence 447889999999764 237888899999999999998 8875321 257889999999999
Q ss_pred HhcCchhHHHHHHHhhCCCCcEEEEeccchHHHHHHhhhhhcCCCCCCCCCCCcHHHHHHHHHHhhceeEEEEcCCHHHH
Q 008500 340 VLNESLMDHVSLVRRHYPSHTICYLTNRLMAHISKKEKERYKNPANNSGWRRPPVEEVLAKLTTHFFRVHSRQCIDEAEV 419 (563)
Q Consensus 340 I~d~~L~e~v~rLk~~~P~~kliyLVEGL~~ylrKr~~~qyk~~~~~~~~~rp~VEeALlqLQl~~~~Vh~~~~~d~~Et 419 (563)
+.+|+|.+|+.+|+++|. +.+|||||-..|.+ ++ ....+-.+|+.|++++ ++....+.+.+|+
T Consensus 617 ~~~~r~~~q~~~l~~~~~--~~~lliE~~~~~~~-----~~---------~~~~i~~~l~~l~~~~-~~~ii~~~~~~et 679 (773)
T PRK13766 617 IIDRRLFEQVKDLKRAYE--RPVLIIEGDLYTIR-----NI---------HPNAIRGALASIAVDF-GIPILFTRDEEET 679 (773)
T ss_pred hhcCcHHHHHHHHHhcCC--CcEEEEEcCchhhc-----cc---------CHHHHHHHHHHHHHHc-CceEEEeCCHHHH
Confidence 999999999999999986 46889999421211 10 1125677899999986 6666677789999
Q ss_pred HHHHHHHHHHHHhccccccccccccccCCceeccCccccCCCchHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhc
Q 008500 420 AEHVVGLTSSLASCQFRKKLTRLSVNANGSLISKDSVDKNLIKKSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYM 499 (563)
Q Consensus 420 a~~I~~lTKaIA~~PyKk~~~~~s~~~~g~~v~k~~V~kg~~l~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~ 499 (563)
|.+|..+++.-..-|.+. ... ..+ .+..+..+.+.-.|..||||++..|..|.++|.|+..++.|=
T Consensus 680 a~~l~~l~~~~~~~~~~~----~~~-------~~~--~~~~~~~~~~~~~L~~ipgig~~~a~~Ll~~fgs~~~i~~as- 745 (773)
T PRK13766 680 ADLLKVIAKREQEEEKRE----VSV-------HGE--KKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEAVMTAS- 745 (773)
T ss_pred HHHHHHHHhhccccCCCC----ccc-------ccC--CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC-
Confidence 999999986543222111 000 000 011223333333489999999999999999999988887532
Q ss_pred CCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhc
Q 008500 500 DPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIA 541 (563)
Q Consensus 500 ~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts 541 (563)
.+ . |+.++ -+|+...++||.+|..
T Consensus 746 -----~~---~-L~~i~---------Gig~~~a~~i~~~~~~ 769 (773)
T PRK13766 746 -----EE---E-LMEVE---------GIGEKTAKRIREVVTS 769 (773)
T ss_pred -----HH---H-HHhCC---------CCCHHHHHHHHHHHhh
Confidence 21 1 33331 3789999999998864
No 5
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=98.79 E-value=1.3e-06 Score=101.81 Aligned_cols=224 Identities=16% Similarity=0.144 Sum_probs=156.0
Q ss_pred ccceEEEEEcccccccCCchHHHHHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHHH
Q 008500 260 AQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCNL 339 (563)
Q Consensus 260 ~lK~mvVvID~~lle~~s~GgqLl~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~l 339 (563)
....+.|++|.+-+.+ .|-..|...|+...+..+.| |+..=.. ..+|.+.+..||+++
T Consensus 583 ~~~~~~IiVD~REfrS-----~lp~~L~~~G~~v~p~tL~V-GDYilS~----------------~i~VERKSi~Dli~S 640 (814)
T TIGR00596 583 NLTQPKVIVDMREFRS-----SLPSLLHRRGIRVIPCMLTV-GDYILTP----------------DICVERKSISDLIGS 640 (814)
T ss_pred cCCCceEEEecCcccc-----hhHHHHHHCCCEEEEEecCc-ccEEecC----------------CeEEEeCcHHHHHHH
Confidence 5567789999998762 25577888899999999998 5544222 346889999999999
Q ss_pred HhcCchhHHHHHHHhhCCCCcEEEEeccch--HHHHHHhhhhhcCCCCCCCCCC--CcHHHHHHHHHHhhceeEEEEcCC
Q 008500 340 VLNESLMDHVSLVRRHYPSHTICYLTNRLM--AHISKKEKERYKNPANNSGWRR--PPVEEVLAKLTTHFFRVHSRQCID 415 (563)
Q Consensus 340 I~d~~L~e~v~rLk~~~P~~kliyLVEGL~--~ylrKr~~~qyk~~~~~~~~~r--p~VEeALlqLQl~~~~Vh~~~~~d 415 (563)
+.+|+|.+|+.+|.++|. ++++||||=. .| .-. .+... ...... ..+.-+|+.|.++|-++..-.+.+
T Consensus 641 l~~gRL~~Q~~~m~~~Y~--~PvLLIE~d~~~~f-~l~---~~~~~--~~~~~~~~~~i~~~L~~L~l~fP~l~IiwS~s 712 (814)
T TIGR00596 641 LNNGRLYNQCEKMLRYYA--YPVLLIEFDQNKSF-SLE---PRNDL--SQEISSVNNDIQQKLALLTLHFPKLRIIWSSS 712 (814)
T ss_pred HhcchHHHHHHHHHHhcC--CcEEEEEecCCccc-ccc---ccccc--ccccCccHHHHHHHHHHHHHhcCCceEEecCC
Confidence 999999999999999997 4899999833 11 100 00000 001112 366778899999865788777888
Q ss_pred HHHHHHHHHHHHHHHHhccccccccccccccCCceeccCccccCCCchHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHH
Q 008500 416 EAEVAEHVVGLTSSLASCQFRKKLTRLSVNANGSLISKDSVDKNLIKKSPWLKALVSIPKVQPRYAIAIWKKYPTMKALL 495 (563)
Q Consensus 416 ~~Eta~~I~~lTKaIA~~PyKk~~~~~s~~~~g~~v~k~~V~kg~~l~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv 495 (563)
..+||+++..|.+.-.+ |-.. ..... |. +.....++......++.+|+.||||++..|..|..+|.|+..|+
T Consensus 713 ~~~TA~i~~~Lk~~e~e-pd~~--~~v~i---~~--~~~~~~k~~~~~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~ 784 (814)
T TIGR00596 713 PYATAEIFEELKLGKEE-PDPA--TAAAL---GS--DENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELA 784 (814)
T ss_pred HHHHHHHHHHHHhcCCC-CCcc--cceec---Cc--ccccccccccccHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHH
Confidence 99999999888776332 3111 01111 10 11111122335677889999999999999999999999999999
Q ss_pred HHhcCCCcChHHHHhhhhcccccCCCCCccccc-HHHHHHHHHHHhcC
Q 008500 496 SIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLG-EVCSKRVYRILIAQ 542 (563)
Q Consensus 496 ~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIG-paLSrRIY~vfts~ 542 (563)
.|= .++ |+. -|| +...++||.+|...
T Consensus 785 ~as------~ee----L~~-----------~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 785 KLS------QNE----LNE-----------LIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred hCC------HHH----HHH-----------HhCCHHHHHHHHHHhccc
Confidence 853 221 211 166 89999999999875
No 6
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=93.24 E-value=5.4 Score=40.97 Aligned_cols=111 Identities=18% Similarity=0.134 Sum_probs=69.4
Q ss_pred HHHHHHHHHhhc--eeEEEEcCCHHHHHHHHHHHHHHHHhccccccccccccccCCceeccCccccCCCchHHHHHHHhh
Q 008500 395 EEVLAKLTTHFF--RVHSRQCIDEAEVAEHVVGLTSSLASCQFRKKLTRLSVNANGSLISKDSVDKNLIKKSPWLKALVS 472 (563)
Q Consensus 395 EeALlqLQl~~~--~Vh~~~~~d~~Eta~~I~~lTKaIA~~PyKk~~~~~s~~~~g~~v~k~~V~kg~~l~dvW~rqLqQ 472 (563)
..+|.+|..... .+-.....+.+|.|.||-.|-. --..|-.. .|. ++ ..++..--..-|++
T Consensus 137 ~~~l~el~k~~~l~~~Tl~lA~s~EeaaryIE~~k~-~ek~p~dl------------i~~--~~--~~d~ls~~~~~Lt~ 199 (254)
T KOG2841|consen 137 YKPLLELTKTCDLNDVTLVLAWSMEEAARYIETYKE-YEKKPIDL------------IME--RK--DRDLLSSLLGFLTT 199 (254)
T ss_pred HHHHHHHHHHHHhhceeeeeeccHHHHHHHHHHHHH-hhcCCchh------------hhh--cc--cccHHHHHHHHHHh
Confidence 456666554331 2222334577899988865422 11222111 111 00 12233355788999
Q ss_pred ccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhc
Q 008500 473 IPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIA 541 (563)
Q Consensus 473 I~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts 541 (563)
|++|.--.|..+..+|+|.+.+..|-+ . =|+.+. -+||+-.+|||.+|+.
T Consensus 200 i~~VnKtda~~LL~~FgsLq~~~~AS~------~----ele~~~---------G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 200 IPGVNKTDAQLLLQKFGSLQQISNASE------G----ELEQCP---------GLGPAKAKRLHKFLHQ 249 (254)
T ss_pred CCCCCcccHHHHHHhcccHHHHHhcCH------h----HHHhCc---------CcCHHHHHHHHHHHhc
Confidence 999999999999999999999998763 1 122232 3799999999999963
No 7
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=93.24 E-value=7.4 Score=46.23 Aligned_cols=235 Identities=14% Similarity=0.141 Sum_probs=138.9
Q ss_pred CccceEEEEEcccccccCCchHHHHHHHhhCCCeEEEeecCCCceEEEEccCCCCCCCCCCCccccCeEEEEecHHHHHH
Q 008500 259 FAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCN 338 (563)
Q Consensus 259 ~~lK~mvVvID~~lle~~s~GgqLl~~L~~lgv~~~I~s~pIp~sI~WrRkVp~~~~~~~~~~~eEp~VLv~l~aeeFv~ 338 (563)
...++..|++|..-+. -.|=..|...|++..+..+.| |+..=.- ..+|.+..-.|++.
T Consensus 648 ~~t~e~pVIVDmREf~-----SsLP~~Lh~~G~~Vip~tL~v-GDYIlSP----------------~icVERKSIsDLi~ 705 (892)
T KOG0442|consen 648 EATKETPVIVDMREFR-----SSLPSLLHRKGLRVIPCTLEV-GDYILSP----------------DICVERKSISDLIQ 705 (892)
T ss_pred ccccccceEeehHHHH-----hhchHHHHhCCceEEEEeecc-cCEEccc----------------cceeeeccHHHHHH
Confidence 3556666888888765 345567788899888888877 5443211 23567999999999
Q ss_pred HHhcCchhHHHHHHHhhCCCCcEEEEeccchHHHHHHhhhhhcCCCC---CCCCCCCcHHHHHHHHHHhhceeEEEEcCC
Q 008500 339 LVLNESLMDHVSLVRRHYPSHTICYLTNRLMAHISKKEKERYKNPAN---NSGWRRPPVEEVLAKLTTHFFRVHSRQCID 415 (563)
Q Consensus 339 lI~d~~L~e~v~rLk~~~P~~kliyLVEGL~~ylrKr~~~qyk~~~~---~~~~~rp~VEeALlqLQl~~~~Vh~~~~~d 415 (563)
++.+|+|..|+..|.+.|+ .+++|||-=. .+ .+.-... +...++-++.--|.-|.+++-.+....+.+
T Consensus 706 SLnsgRly~Q~~~M~~~Y~--~pvLLIEfd~------~k-~fs~~~~~~ls~e~sk~~i~skL~lLil~fP~LRilWS~S 776 (892)
T KOG0442|consen 706 SLNSGRLYNQCEMMQRYYE--RPVLLIEFDQ------EK-SFSLQPRSDLSQELSKNDIVSKLTLLILAFPKLRILWSSS 776 (892)
T ss_pred hhhcchHHHHHHHHHHhcc--CcEEEEEecC------CC-CcCCCCccchhhhhhHHHHHHHHHHHHhcCCceEEEecCc
Confidence 9999999999999999997 4788887311 00 1110000 011122345555566666653444445556
Q ss_pred HHHHHHHHHHHHHHHHhccccccccccccccCCceeccCccccCCCchHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHH
Q 008500 416 EAEVAEHVVGLTSSLASCQFRKKLTRLSVNANGSLISKDSVDKNLIKKSPWLKALVSIPKVQPRYAIAIWKKYPTMKALL 495 (563)
Q Consensus 416 ~~Eta~~I~~lTKaIA~~PyKk~~~~~s~~~~g~~v~k~~V~kg~~l~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv 495 (563)
.-.||+.+.-|- .-...| -...+..+.. .|.. + ....+....=..-|.-+||||---+..+..++.+.+.|.
T Consensus 777 p~~Ta~if~eLK-l~~~ep--D~~~Ai~lg~--~~~~--~-~~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La 848 (892)
T KOG0442|consen 777 PLATAEIFEELK-LSEPEP--DPARAISLGT--DEEG--N-SESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELA 848 (892)
T ss_pred hhHHHHHHHHHh-hcCCCC--Ccchheeecc--cccc--c-ccccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHH
Confidence 667877754431 111111 1001111111 0100 0 001122333355567899999999999999988888876
Q ss_pred HHhcCCCcChHHHHhhhhcccccCCCCCccccc-HHHHHHHHHHHhcCCCCcccccccc
Q 008500 496 SIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLG-EVCSKRVYRILIAQSGSIKTDDIED 553 (563)
Q Consensus 496 ~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIG-paLSrRIY~vfts~Dp~l~ld~~~~ 553 (563)
. .|.++ |+.+ +| ++.+++||.||-..=++...+...+
T Consensus 849 ~------sS~~e----l~el-----------~~~~~~a~~LYdFi~~~~~~~~~~~~~~ 886 (892)
T KOG0442|consen 849 N------SSQEE----LSEL-----------LGVHENAKLLYDFIHTEFADQEKENTGN 886 (892)
T ss_pred h------CcHHH----HHHH-----------hcchHHHHHHHHHHHHhhhhhhccCCcc
Confidence 4 23332 2222 22 5889999999998888777664443
No 8
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=90.93 E-value=0.32 Score=39.58 Aligned_cols=51 Identities=22% Similarity=0.382 Sum_probs=35.6
Q ss_pred hccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhc
Q 008500 472 SIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIA 541 (563)
Q Consensus 472 QI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts 541 (563)
-||+|....|..++++|+|...|+.|. .+ -|+.+ .-|||.+++.||.+|..
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a~------~e----~L~~i---------~gIG~~~A~si~~ff~~ 57 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNAS------VE----ELSAI---------PGIGPKIAQSIYEFFQD 57 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC--------HH----HHCTS---------TT--HHHHHHHHHHHH-
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHcC------HH----HHhcc---------CCcCHHHHHHHHHHHCC
Confidence 699999999999999999999888765 11 12222 26999999999999953
No 9
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=88.75 E-value=0.45 Score=54.43 Aligned_cols=34 Identities=38% Similarity=0.498 Sum_probs=22.9
Q ss_pred ccccHHHHHhhHHHHHHhHHHHHHHHHHHHHHHH
Q 008500 209 KKMTKEERMLFMEEKKKKKEEEKLRKAALKAEAA 242 (563)
Q Consensus 209 k~~~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~a 242 (563)
|..++++|+.++|||+.++|+|++.|+.+|..++
T Consensus 303 kd~KKqqkekEkeEKrrKdE~Ek~kKqeek~KR~ 336 (811)
T KOG4364|consen 303 KDIKKQQKEKEKEEKRRKDEQEKLKKQEEKQKRA 336 (811)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 4555566667777777777777777776666555
No 10
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=83.54 E-value=0.98 Score=51.82 Aligned_cols=40 Identities=30% Similarity=0.279 Sum_probs=22.5
Q ss_pred HHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008500 214 EERMLFMEEKKKKKEEEKLRKAALKAEAAESKKLQKEMQK 253 (563)
Q Consensus 214 ~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~ae~Kk~eke~~K 253 (563)
+|+..+++.|+++|+-||++|.+.+++++..|..++++++
T Consensus 297 ee~Klekd~KKqqkekEkeEKrrKdE~Ek~kKqeek~KR~ 336 (811)
T KOG4364|consen 297 EETKLEKDIKKQQKEKEKEEKRRKDEQEKLKKQEEKQKRA 336 (811)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 4444444455566666666666666666555555555543
No 11
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=81.06 E-value=4.1 Score=32.41 Aligned_cols=53 Identities=23% Similarity=0.403 Sum_probs=41.0
Q ss_pred HHHhhccCCCHHHHHHHHHh-CCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHH
Q 008500 468 KALVSIPKVQPRYAIAIWKK-YPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRIL 539 (563)
Q Consensus 468 rqLqQI~rVS~eiA~AIv~~-YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vf 539 (563)
+-|++||||++..|..+... |.|+..|..+= . +. |..++ .||+...++|...+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~------~---~~-L~~i~---------Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEAGIKTLEDLANAD------P---EE-LAEIP---------GIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSH------H---HH-HHTST---------TSSHHHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhcCCCcHHHHHcCC------H---HH-HhcCC---------CCCHHHHHHHHHHH
Confidence 56889999999999999999 99998887531 1 12 44443 48999999998754
No 12
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=72.54 E-value=3.9 Score=45.30 Aligned_cols=11 Identities=9% Similarity=-0.058 Sum_probs=4.2
Q ss_pred CCCCCCCCcch
Q 008500 151 GDSSSQPTCSE 161 (563)
Q Consensus 151 ~~~~~~~~~~~ 161 (563)
.--|-.+.+-+
T Consensus 275 ~~~P~~~~~~~ 285 (429)
T PRK00247 275 RKYPLTDEFKE 285 (429)
T ss_pred HhcCCCcchHH
Confidence 33343333333
No 13
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=68.92 E-value=9 Score=40.67 Aligned_cols=8 Identities=25% Similarity=0.036 Sum_probs=2.9
Q ss_pred HHHhhHHH
Q 008500 215 ERMLFMEE 222 (563)
Q Consensus 215 ek~r~~ee 222 (563)
.|.|+++.
T Consensus 261 ~k~R~~~~ 268 (321)
T PF07946_consen 261 KKNREEEE 268 (321)
T ss_pred HHHHHHHH
Confidence 33333333
No 14
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.09 E-value=12 Score=37.45 Aligned_cols=59 Identities=12% Similarity=0.260 Sum_probs=43.8
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYR 537 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~ 537 (563)
..-|-++|..++||.|-.|.+|.+.| +|..|.+|-.. +....|+.++ -||+..++||-.
T Consensus 67 Er~lF~~LisVsGIGPK~ALaILs~~-~~~el~~aI~~------~D~~~L~~vp---------GIGkKtAeRIIl 125 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVLSGI-KYNEFRDAIDR------EDIELISKVK---------GIGNKMAGKIFL 125 (196)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHh------CCHHHHhhCC---------CCCHHHHHHHHH
Confidence 45567888999999999999999998 89999999942 2335666664 255555555543
No 15
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.57 E-value=13 Score=36.88 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=31.7
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhc
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYM 499 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~ 499 (563)
..-|-++|..|+||-|-.|.+|...| +|..|++|-.
T Consensus 68 Er~lF~~Li~V~GIGpK~Al~ILs~~-~~~~l~~aI~ 103 (194)
T PRK14605 68 ELSLFETLIDVSGIGPKLGLAMLSAM-NAEALASAII 103 (194)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhC-CHHHHHHHHH
Confidence 45667889999999999999999999 5999999884
No 16
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=64.47 E-value=9.9 Score=44.83 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=7.8
Q ss_pred hhccccccHHHHHhhHHHH
Q 008500 205 VGKKKKMTKEERMLFMEEK 223 (563)
Q Consensus 205 ~~~~k~~~~~ek~r~~eeK 223 (563)
+.+|-+...+.|+|+++|+
T Consensus 347 ~eqkEreE~ekkererqEq 365 (1118)
T KOG1029|consen 347 VEQKEREEEEKKERERQEQ 365 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333333344444444443
No 17
>PF15437 PGBA_C: Plasminogen-binding protein pgbA C-terminal
Probab=64.44 E-value=25 Score=30.59 Aligned_cols=21 Identities=48% Similarity=0.577 Sum_probs=14.6
Q ss_pred cHHHHHhhHHHHHHhHHHHHH
Q 008500 212 TKEERMLFMEEKKKKKEEEKL 232 (563)
Q Consensus 212 ~~~ek~r~~eeK~~~Ke~eK~ 232 (563)
.++||.|++++|+..|.+.++
T Consensus 36 ~kEekrrLkeEkKkAKAeqrA 56 (86)
T PF15437_consen 36 PKEEKRRLKEEKKKAKAEQRA 56 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 347888888887777665544
No 18
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.73 E-value=16 Score=36.11 Aligned_cols=61 Identities=16% Similarity=0.271 Sum_probs=45.1
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRIL 539 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vf 539 (563)
..-|-++|..++||-|-.|.+|.+.| +|..|.+|-.. +-...|..++ -||+..++||-.=+
T Consensus 68 Er~lF~~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~------~D~~~L~~vp---------GIGkKtAeRIilEL 128 (183)
T PRK14601 68 EQKMFEMLLKVNGIGANTAMAVCSSL-DVNSFYKALSL------GDESVLKKVP---------GIGPKSAKRIIAEL 128 (183)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHh------CCHHHHhhCC---------CCCHHHHHHHHHHH
Confidence 45667888999999999999999998 78999999942 2235666554 35666666665433
No 19
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=62.28 E-value=8.9 Score=26.99 Aligned_cols=20 Identities=30% Similarity=0.582 Sum_probs=17.2
Q ss_pred HHHHhhccCCCHHHHHHHHH
Q 008500 467 LKALVSIPKVQPRYAIAIWK 486 (563)
Q Consensus 467 ~rqLqQI~rVS~eiA~AIv~ 486 (563)
...|+++|||.+.+|.+|.+
T Consensus 10 ~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 10 IEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHHTSTT-SHHHHHHHHH
T ss_pred HHHHHhCCCcCHHHHHHHHh
Confidence 57899999999999999975
No 20
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.81 E-value=14 Score=36.67 Aligned_cols=58 Identities=17% Similarity=0.297 Sum_probs=43.4
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVY 536 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY 536 (563)
..-|-++|..++||-|-.|.+|.+.| +|..|.+|-.+ +-...|..++ -||+..++||-
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~------~D~~~L~kvp---------GIGkKtAerIi 124 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSAL-PPALLARALLE------GDARLLTSAS---------GVGKKLAERIA 124 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHh------CCHHHHhhCC---------CCCHHHHHHHH
Confidence 56677889999999999999999998 89999999942 2235666554 25555555554
No 21
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.06 E-value=16 Score=36.22 Aligned_cols=61 Identities=16% Similarity=0.265 Sum_probs=45.0
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRIL 539 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vf 539 (563)
..-|-++|..++||-|-+|.+|.+.| +|..|.+|-.+ +....|..++ -||+..++||-.=+
T Consensus 68 Er~lF~~Li~V~GIGpK~AL~iLs~~-~~~el~~aI~~------~D~~~L~~vp---------GIGkKtAerIilEL 128 (188)
T PRK14606 68 KKELFLSLTKVSRLGPKTALKIISNE-DAETLVTMIAS------QDVEGLSKLP---------GISKKTAERIVMEL 128 (188)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHh------CCHHHHhhCC---------CCCHHHHHHHHHHH
Confidence 45677888999999999999999998 88999999943 2235666554 35666666665433
No 22
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.82 E-value=15 Score=36.25 Aligned_cols=36 Identities=28% Similarity=0.366 Sum_probs=32.2
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhc
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYM 499 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~ 499 (563)
..-|-++|..++||-|-+|.+|.+.| +|..|.+|-.
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs~~-~~~~l~~aI~ 103 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILSKL-TPEQLFSAIV 103 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHccC-CHHHHHHHHH
Confidence 45567788999999999999999998 8999999994
No 23
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.81 E-value=16 Score=36.28 Aligned_cols=60 Identities=15% Similarity=0.195 Sum_probs=44.2
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRI 538 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~v 538 (563)
..-|-++|..++||-|-.|.+|...| +|..|.+|-.+ +-...|..++ =||+..++||-.=
T Consensus 68 Er~lF~~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~------~D~~~L~kvp---------GIGkKtAerIilE 127 (195)
T PRK14604 68 QRQLFELLIGVSGVGPKAALNLLSSG-TPDELQLAIAG------GDVARLARVP---------GIGKKTAERIVLE 127 (195)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHh------CCHHHHhhCC---------CCCHHHHHHHHHH
Confidence 56677889999999999999999987 89999999943 2235666554 2555555555433
No 24
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=59.13 E-value=1.5e+02 Score=33.93 Aligned_cols=34 Identities=26% Similarity=0.383 Sum_probs=18.7
Q ss_pred CCCCCCCcccccCCCCCC-CCeeEeeCCCCCCCCCCCCC
Q 008500 17 ETPIQCPYKKIRTGPHPV-APTVLILDDDPTPKKSGFAP 54 (563)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 54 (563)
..+.|.+-+|+-..++.. .|.-|+ |+|+-.-+++
T Consensus 226 ~p~~p~p~~k~~~q~g~~~ap~~fs----p~~p~~v~~~ 260 (708)
T KOG3654|consen 226 PPEAPGPAPKAWVQPGPTTAPKAFS----PSPPRRVPAT 260 (708)
T ss_pred CCCCCCCCCccccCCCCcCCCccCC----CCCCCCCccc
Confidence 345566666766655433 555565 6666544333
No 25
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=58.84 E-value=17 Score=43.16 Aligned_cols=12 Identities=25% Similarity=0.268 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHH
Q 008500 418 EVAEHVVGLTSS 429 (563)
Q Consensus 418 Eta~~I~~lTKa 429 (563)
++.-||..+|+.
T Consensus 677 dLl~llv~ltQk 688 (1064)
T KOG1144|consen 677 DLLLLLVQLTQK 688 (1064)
T ss_pred HHHHHHHHHHHH
Confidence 566777777754
No 26
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.77 E-value=20 Score=35.83 Aligned_cols=58 Identities=19% Similarity=0.338 Sum_probs=43.1
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVY 536 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY 536 (563)
..-|-++|..++||-|-.|.+|.+.| +|..|.+|-... -...|..++ -||+..++||-
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~-~~~~l~~aI~~~------D~~~L~~ip---------GIGkKtAerIi 126 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQF-RPDDLRRLVAEE------DVAALTRVS---------GIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhC-CHHHHHHHHHhC------CHHHHhcCC---------CcCHHHHHHHH
Confidence 55677899999999999999999998 788999999532 235565554 25555555554
No 27
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=55.18 E-value=21 Score=41.63 Aligned_cols=31 Identities=39% Similarity=0.313 Sum_probs=18.1
Q ss_pred ccccHHHHHhhHHHHHHhHHHHHHHHHHHHH
Q 008500 209 KKMTKEERMLFMEEKKKKKEEEKLRKAALKA 239 (563)
Q Consensus 209 k~~~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka 239 (563)
|...++|-.+++|+|++++++.+++|+++|+
T Consensus 546 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 576 (651)
T PTZ00399 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQE 576 (651)
T ss_pred EECCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677777777776655555555544443
No 28
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=54.49 E-value=18 Score=41.15 Aligned_cols=13 Identities=23% Similarity=0.289 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHhh
Q 008500 243 ESKKLQKEMQKWA 255 (563)
Q Consensus 243 e~Kk~eke~~K~~ 255 (563)
++|+.+..+.|..
T Consensus 263 e~ke~e~~~~k~~ 275 (591)
T KOG2412|consen 263 ERKEAEEQAEKEV 275 (591)
T ss_pred HHHHHHHHHHHHh
Confidence 3444444444444
No 29
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=54.19 E-value=26 Score=35.96 Aligned_cols=62 Identities=18% Similarity=0.187 Sum_probs=47.6
Q ss_pred HHhhccCCCHHHHHHHHHh-CCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhcCCCCcc
Q 008500 469 ALVSIPKVQPRYAIAIWKK-YPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIAQSGSIK 547 (563)
Q Consensus 469 qLqQI~rVS~eiA~AIv~~-YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts~Dp~l~ 547 (563)
.|..|+||.+..|..+..+ |.|+..|..|= .+ .| ..+ .-||+++..+||..|...+-+..
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS------~e---EL-~~V---------~GIg~k~AekI~e~l~~~~~~~~ 64 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAAD------QS---EL-AEV---------DGIGNALAARIKADVGGLEVSEE 64 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCC------HH---HH-HHc---------cCCCHHHHHHHHHHhcccccccc
Confidence 4789999999999999999 99999998753 11 22 222 24799999999999986665544
Q ss_pred cc
Q 008500 548 TD 549 (563)
Q Consensus 548 ld 549 (563)
.|
T Consensus 65 ~~ 66 (232)
T PRK12766 65 TE 66 (232)
T ss_pred cc
Confidence 44
No 30
>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=53.85 E-value=12 Score=44.83 Aligned_cols=42 Identities=24% Similarity=0.160 Sum_probs=31.1
Q ss_pred hhhhcccccccccccccccccchhhhccccccHHHHHhhHHH
Q 008500 181 MGNLLNTKRSLQVNADNRKSTDEAVGKKKKMTKEERMLFMEE 222 (563)
Q Consensus 181 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~ek~r~~ee 222 (563)
+-+.++..+...|.+.+....+.-+-+||+.+++|+...+|.
T Consensus 700 r~k~~n~~~k~k~~e~~~r~~~~~~~~kk~~td~e~rk~~e~ 741 (975)
T KOG0112|consen 700 RFKSKNKRSKKKLKEKPERIRDARREMKKKETDEEKRKEMER 741 (975)
T ss_pred hhccccccChhhhccccccCccchhhhhhccchhhhhhhHhh
Confidence 455667777778888777777766777788888887777666
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=52.17 E-value=31 Score=34.11 Aligned_cols=59 Identities=17% Similarity=0.280 Sum_probs=42.5
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYR 537 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~ 537 (563)
..-|-++|..|+||-|-.|.+|...| ++..|.+|-.+. -...|..++ -||+....||..
T Consensus 67 Er~lF~~L~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~------d~~~L~~ip---------GiGkKtAerIil 125 (191)
T TIGR00084 67 ERELFKELIKVNGVGPKLALAILSNM-SPEEFVYAIETE------EVKALVKIP---------GVGKKTAERLLL 125 (191)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHhcC-CHHHHHHHHHhC------CHHHHHhCC---------CCCHHHHHHHHH
Confidence 45566778899999999999999987 699999998421 224455554 356666666653
No 32
>KOG4819 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.28 E-value=66 Score=28.97 Aligned_cols=38 Identities=26% Similarity=0.254 Sum_probs=25.8
Q ss_pred ccccHHHHHhhHHHHHHhHHHHHHH-HHHHHHHHHHHHH
Q 008500 209 KKMTKEERMLFMEEKKKKKEEEKLR-KAALKAEAAESKK 246 (563)
Q Consensus 209 k~~~~~ek~r~~eeK~~~Ke~eK~~-K~a~Ka~~ae~Kk 246 (563)
+-.+.+++-+.+.+|+++|.+|+++ ++..-|+.++-|+
T Consensus 31 ~~qk~~~~~~~~qeK~a~k~~Ere~~r~~R~e~~~aykK 69 (106)
T KOG4819|consen 31 KPNKPEIRNMKRQEKAAQKAAEREKVRADRDEQVKAYKK 69 (106)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 4456688888888898888888887 4444444444443
No 33
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=49.12 E-value=42 Score=33.05 Aligned_cols=63 Identities=19% Similarity=0.314 Sum_probs=45.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhcCCC
Q 008500 466 WLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIAQSG 544 (563)
Q Consensus 466 W~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts~Dp 544 (563)
+...|..||||.+..|.+|...|.+ ..|.++-.+. +. .-|..++ -||+....+|+.-|...-.
T Consensus 71 ~f~~L~~i~GIGpk~A~~il~~fg~-~~l~~~i~~~-----d~-~~L~~v~---------Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 71 LFRLLISVSGVGPKLALAILSGLSP-EELVQAIANG-----DV-KALTKVP---------GIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HHHHHhcCCCCCHHHHHHHHHhCCH-HHHHHHHHhC-----CH-HHHHhCC---------CCCHHHHHHHHHHHHHHhh
Confidence 3788999999999999999999976 4566655322 11 2233332 4888888999888876654
No 34
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=47.93 E-value=37 Score=40.43 Aligned_cols=30 Identities=23% Similarity=0.323 Sum_probs=17.6
Q ss_pred EEEEcccccccCCchHHHHHHHhhCCCeEEEe
Q 008500 265 VTEIDAKVVELGSVGGHLLTRFAEKRFKYRIA 296 (563)
Q Consensus 265 vVvID~~lle~~s~GgqLl~~L~~lgv~~~I~ 296 (563)
.++++..--+.| +.+.++++|++ |..|..+
T Consensus 1030 lIdm~a~~de~G-VmDslLeaLqs-gaafr~r 1059 (1102)
T KOG1924|consen 1030 LIDMNAEGDETG-VMDSLLEALQS-GAAFRTR 1059 (1102)
T ss_pred Hhccccccchhh-hHHHHHHHHHh-hccccCc
Confidence 345555444423 67789999986 4444443
No 35
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=46.40 E-value=42 Score=38.34 Aligned_cols=6 Identities=50% Similarity=0.783 Sum_probs=3.4
Q ss_pred HHHHHh
Q 008500 493 ALLSIY 498 (563)
Q Consensus 493 ~Lv~AY 498 (563)
.|++.|
T Consensus 536 ~L~q~Y 541 (591)
T KOG2412|consen 536 GLLQRY 541 (591)
T ss_pred HHHHHH
Confidence 455556
No 36
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=46.15 E-value=18 Score=39.22 Aligned_cols=32 Identities=16% Similarity=0.351 Sum_probs=30.4
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCHHHHHHHh
Q 008500 467 LKALVSIPKVQPRYAIAIWKKYPTMKALLSIY 498 (563)
Q Consensus 467 ~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY 498 (563)
-|.|..||||..++|..++++|.|.+.++.|=
T Consensus 286 yRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As 317 (352)
T PRK13482 286 YRLLSKIPRLPSAVIENLVEHFGSLQGLLAAS 317 (352)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCC
Confidence 79999999999999999999999999999865
No 37
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=44.53 E-value=41 Score=39.17 Aligned_cols=57 Identities=18% Similarity=0.290 Sum_probs=45.6
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHh
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILI 540 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vft 540 (563)
...+...|..|+||.+..|.+|..+|.|+..|..| +.++ |. +-||+.+..+|+.+|.
T Consensus 564 k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A------s~ee-------L~--------~vig~k~A~~I~~~~~ 620 (621)
T PRK14671 564 KRTLQTELTDIAGIGEKTAEKLLEHFGSVEKVAKA------SLEE-------LA--------AVAGPKTAETIYRYYH 620 (621)
T ss_pred HHHhhhhhhcCCCcCHHHHHHHHHHcCCHHHHHhC------CHHH-------HH--------HHhCHHHHHHHHHHhC
Confidence 45667889999999999999999999999998875 1221 11 1189999999999984
No 38
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=44.44 E-value=28 Score=32.81 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=26.2
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHH--hCCCHHHHHH
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWK--KYPTMKALLS 496 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~--~YPSP~~Lv~ 496 (563)
...=.+.|+++|||-|..|.+|++ -|-|+..|++
T Consensus 56 N~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 56 NNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 334478899999999999999997 3666666654
No 39
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=42.82 E-value=24 Score=41.81 Aligned_cols=14 Identities=21% Similarity=0.313 Sum_probs=7.2
Q ss_pred cccccHHHHHHHHH
Q 008500 524 NRKLGEVCSKRVYR 537 (563)
Q Consensus 524 ~RRIGpaLSrRIY~ 537 (563)
.|+-|.++|.+=|.
T Consensus 1216 ~rKrGAEI~~~eFe 1229 (1259)
T KOG0163|consen 1216 TRKRGAEILEHEFE 1229 (1259)
T ss_pred ccccccccChHHHH
Confidence 35556666554443
No 40
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=42.58 E-value=17 Score=37.81 Aligned_cols=36 Identities=17% Similarity=0.195 Sum_probs=33.8
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCc
Q 008500 468 KALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSK 503 (563)
Q Consensus 468 rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~ 503 (563)
..|+.+.||++..|..|...|+|+..+..+|..+..
T Consensus 214 ~eL~~v~gig~k~A~~I~~~~~t~~~~~~~~~~~~~ 249 (254)
T COG1948 214 EELMKVKGIGEKKAREIYRFLRTEYKLIEALETDSS 249 (254)
T ss_pred HHHHHhcCccHHHHHHHHHHHhchhhhhcccCCccc
Confidence 899999999999999999999999999999987753
No 41
>PF15437 PGBA_C: Plasminogen-binding protein pgbA C-terminal
Probab=41.50 E-value=64 Score=28.14 Aligned_cols=30 Identities=37% Similarity=0.420 Sum_probs=16.6
Q ss_pred HHhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 008500 216 RMLFMEEKKKKKEEEKLRKAALKAEAAESK 245 (563)
Q Consensus 216 k~r~~eeK~~~Ke~eK~~K~a~Ka~~ae~K 245 (563)
+---+|+|+..|++.|..|+..+|..-+++
T Consensus 33 kl~~kEekrrLkeEkKkAKAeqrA~EfEqR 62 (86)
T PF15437_consen 33 KLSPKEEKRRLKEEKKKAKAEQRAREFEQR 62 (86)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666666666666665555544433
No 42
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.96 E-value=54 Score=34.14 Aligned_cols=11 Identities=36% Similarity=0.619 Sum_probs=5.7
Q ss_pred chhhhcccccc
Q 008500 202 DEAVGKKKKMT 212 (563)
Q Consensus 202 ~~~~~~~k~~~ 212 (563)
+...||||..+
T Consensus 100 ~~kigkkK~aK 110 (299)
T KOG3054|consen 100 QAKIGKKKEAK 110 (299)
T ss_pred hhhhhhHHHHH
Confidence 34566644444
No 43
>KOG2357 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.75 E-value=34 Score=37.83 Aligned_cols=8 Identities=0% Similarity=0.360 Sum_probs=4.2
Q ss_pred ceeEEEec
Q 008500 70 DVCIIKCT 77 (563)
Q Consensus 70 ~~~~~~~~ 77 (563)
++++|-|-
T Consensus 110 E~~~v~~L 117 (440)
T KOG2357|consen 110 EIVMVAIL 117 (440)
T ss_pred HHHHHHHH
Confidence 45555554
No 44
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=37.17 E-value=50 Score=39.35 Aligned_cols=6 Identities=50% Similarity=0.534 Sum_probs=2.8
Q ss_pred EeecCC
Q 008500 103 CLESDN 108 (563)
Q Consensus 103 ~les~~ 108 (563)
.+||-|
T Consensus 177 ~~~s~~ 182 (1118)
T KOG1029|consen 177 SIESVN 182 (1118)
T ss_pred cchhhh
Confidence 445544
No 45
>PF06975 DUF1299: Protein of unknown function (DUF1299); InterPro: IPR010725 This entry represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many proteins contain multiple copies of this region.
Probab=36.19 E-value=21 Score=27.34 Aligned_cols=26 Identities=35% Similarity=0.376 Sum_probs=16.6
Q ss_pred ceeccCcccccCCCCCCCCCcccccC
Q 008500 4 PIILSDEEDQNALETPIQCPYKKIRT 29 (563)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (563)
-|||||+||...--|---+.|+|-.|
T Consensus 13 yvilsdde~ngtaptekesq~qkeet 38 (47)
T PF06975_consen 13 YVILSDDEDNGTAPTEKESQPQKEET 38 (47)
T ss_pred eeeccccccCCcCCcccccccchhhh
Confidence 48999999987333333455555554
No 46
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=35.41 E-value=35 Score=27.60 Aligned_cols=21 Identities=29% Similarity=0.426 Sum_probs=17.0
Q ss_pred HHHHhhccCCCHHHHHHHHHh
Q 008500 467 LKALVSIPKVQPRYAIAIWKK 487 (563)
Q Consensus 467 ~rqLqQI~rVS~eiA~AIv~~ 487 (563)
..+|+++||++...|.+|++.
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHH
Confidence 678999999999999999864
No 47
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=34.90 E-value=33 Score=40.11 Aligned_cols=6 Identities=50% Similarity=0.523 Sum_probs=2.6
Q ss_pred HhhccC
Q 008500 253 KWAKGK 258 (563)
Q Consensus 253 K~~k~k 258 (563)
|+++.+
T Consensus 585 ~~~~~~ 590 (651)
T PTZ00399 585 KLEKAK 590 (651)
T ss_pred HHHHcC
Confidence 344444
No 48
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=34.46 E-value=50 Score=27.68 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=26.5
Q ss_pred hhccCCCHHHHHHHHHhCCCHHHHHHHhc
Q 008500 471 VSIPKVQPRYAIAIWKKYPTMKALLSIYM 499 (563)
Q Consensus 471 qQI~rVS~eiA~AIv~~YPSP~~Lv~AY~ 499 (563)
.-||||-+-.|..|..+|+|...++++..
T Consensus 25 ~gv~giG~k~A~~ll~~~~~~~~~~~~~~ 53 (75)
T cd00080 25 PGVPGIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHHHH
Confidence 45899999999999999999999999883
No 49
>KOG3925 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.95 E-value=1.3e+02 Score=32.89 Aligned_cols=17 Identities=12% Similarity=0.294 Sum_probs=11.3
Q ss_pred HHHHHHHHHhccccccc
Q 008500 423 VVGLTSSLASCQFRKKL 439 (563)
Q Consensus 423 I~~lTKaIA~~PyKk~~ 439 (563)
-..|+.-.++.||+.--
T Consensus 262 assls~vf~~~P~~~GY 278 (371)
T KOG3925|consen 262 ASSLSEVFSESPFKGGY 278 (371)
T ss_pred hhhHHHHhhcCCccCCc
Confidence 34567777778887643
No 50
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=33.27 E-value=44 Score=22.29 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=17.1
Q ss_pred HHhhccCCCHHHHHHHHHh
Q 008500 469 ALVSIPKVQPRYAIAIWKK 487 (563)
Q Consensus 469 qLqQI~rVS~eiA~AIv~~ 487 (563)
.|++|+||....|..|...
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 5899999999999999874
No 51
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=33.19 E-value=94 Score=36.79 Aligned_cols=58 Identities=14% Similarity=0.266 Sum_probs=45.3
Q ss_pred HHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHh
Q 008500 464 SPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILI 540 (563)
Q Consensus 464 dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vft 540 (563)
.+..-.|..||||.+..+..+.++|.|+..+..|= .++ |+.+ .-||+.+.++||..|.
T Consensus 633 ~~~~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS------~eE----La~V---------~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 633 AALTGELQRVEGIGPATARLLWERFGSLQAMAAAG------EEG----LAAV---------PGIGPARAAALHEHLK 690 (694)
T ss_pred hhhHhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcC------HHH----HHhc---------CCcCHHHHHHHHHHHH
Confidence 44467899999999999999999999999998854 221 3333 2478899999998874
No 52
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=32.28 E-value=1.1e+02 Score=29.74 Aligned_cols=20 Identities=15% Similarity=0.297 Sum_probs=9.8
Q ss_pred HHHhHHHHHHHHHHHHHHHH
Q 008500 223 KKKKKEEEKLRKAALKAEAA 242 (563)
Q Consensus 223 K~~~Ke~eK~~K~a~Ka~~a 242 (563)
.++.++.+.++++.+.+..+
T Consensus 90 ~Rl~rere~~q~~~E~E~~~ 109 (157)
T PF15236_consen 90 ERLAREREELQRQFEEEQRK 109 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44455555555554444443
No 53
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=30.49 E-value=94 Score=36.06 Aligned_cols=59 Identities=25% Similarity=0.404 Sum_probs=45.2
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHh
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILI 540 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vft 540 (563)
+....--|..||||.+..|..+.++|+|+..+.+|= .++ |+.+. -||+.+.+.|+.+|.
T Consensus 538 k~~~~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As------~ee----L~~v~---------Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 538 KARLTSALDDIPGIGPKRRKALLKHFGSLKAIKEAS------VEE----LAKVP---------GISKKLAEAIYEALH 596 (598)
T ss_pred cchhhhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCC------HHH----HhhcC---------CcCHHHHHHHHHHhc
Confidence 344566789999999999999999999999887742 221 33332 379999999999884
No 54
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=29.74 E-value=90 Score=36.52 Aligned_cols=57 Identities=12% Similarity=0.212 Sum_probs=45.9
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHh
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILI 540 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vft 540 (563)
+.+....|..||||.+..+.++.++|.|+..+..|= .+ .| . .-||+.+.++||.+|.
T Consensus 547 k~~~~S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As------~e---eL----~--------~vi~~k~A~~I~~~l~ 603 (624)
T PRK14669 547 TRDRTSELLEIPGVGAKTVQRLLKHFGSLERVRAAT------ET---QL----A--------AVVGRAAAEAIIAHFT 603 (624)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC------HH---HH----H--------HHhCHHHHHHHHHHhc
Confidence 455677899999999999999999999999998854 22 12 1 1288999999999996
No 55
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=28.27 E-value=73 Score=29.14 Aligned_cols=23 Identities=30% Similarity=0.390 Sum_probs=20.9
Q ss_pred HHHHhhccCCCHHHHHHHHHhCC
Q 008500 467 LKALVSIPKVQPRYAIAIWKKYP 489 (563)
Q Consensus 467 ~rqLqQI~rVS~eiA~AIv~~YP 489 (563)
..+|++||||++..|..|+..+.
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~R~ 89 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEYRE 89 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHH
Confidence 78899999999999999998864
No 56
>PLN02381 valyl-tRNA synthetase
Probab=27.66 E-value=68 Score=39.74 Aligned_cols=33 Identities=42% Similarity=0.365 Sum_probs=18.4
Q ss_pred ccccHHHHHhhHHHHHHhHHHHHHHHHHHHHHHH
Q 008500 209 KKMTKEERMLFMEEKKKKKEEEKLRKAALKAEAA 242 (563)
Q Consensus 209 k~~~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~a 242 (563)
+|.+++||+++||.|+++. ++|.+|++.+++++
T Consensus 20 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 52 (1066)
T PLN02381 20 RKKKKEEKAKEKELKKLKA-AQKEAKAKLQAQQA 52 (1066)
T ss_pred HHHhhhHHHHHHHHHHHHH-HHHHHHHHHHHHhc
Confidence 4556677777777776543 33444444444443
No 57
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=27.13 E-value=1.8e+02 Score=26.29 Aligned_cols=10 Identities=30% Similarity=0.395 Sum_probs=5.6
Q ss_pred HHHHHHHHHH
Q 008500 240 EAAESKKLQK 249 (563)
Q Consensus 240 ~~ae~Kk~ek 249 (563)
++++++.+++
T Consensus 88 ~~k~i~~le~ 97 (100)
T PF04568_consen 88 HRKEIDELEK 97 (100)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4555665554
No 58
>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]
Probab=26.36 E-value=1.3e+02 Score=33.66 Aligned_cols=52 Identities=23% Similarity=0.317 Sum_probs=42.6
Q ss_pred hhccccccHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 008500 205 VGKKKKMTKEERMLFMEEKKKKKEEEKLRKAALKAEAAESKKLQKEMQKWAK 256 (563)
Q Consensus 205 ~~~~k~~~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~ae~Kk~eke~~K~~k 256 (563)
+.++++.+.+|++...+-|+.+|+++.+.-+-.+.+.++....+++.+.|..
T Consensus 182 ~~e~~~l~~eE~~L~q~lk~le~~~~~l~~~l~e~~~~~~~~~e~~~~~~~e 233 (447)
T KOG2751|consen 182 LKELKNLKEEEERLLQQLEELEKEEAELDHQLKELEFKAERLNEEEDQYWRE 233 (447)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555788889999999999999999888877777777777778888887775
No 59
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=26.09 E-value=65 Score=34.14 Aligned_cols=8 Identities=25% Similarity=0.227 Sum_probs=3.8
Q ss_pred CCcchhhh
Q 008500 157 PTCSEYDM 164 (563)
Q Consensus 157 ~~~~~~~~ 164 (563)
-.||+.+|
T Consensus 268 rhlsevqi 275 (445)
T KOG2891|consen 268 RHLSEVQI 275 (445)
T ss_pred hhhhHHHH
Confidence 34555444
No 60
>PF09831 DUF2058: Uncharacterized protein conserved in bacteria (DUF2058); InterPro: IPR018636 This family, found in various prokaryotic proteins, has no known function.
Probab=25.59 E-value=84 Score=31.09 Aligned_cols=17 Identities=29% Similarity=0.261 Sum_probs=8.2
Q ss_pred ccccccHHHHHhhHHHH
Q 008500 207 KKKKMTKEERMLFMEEK 223 (563)
Q Consensus 207 ~~k~~~~~ek~r~~eeK 223 (563)
.|++++++.++..+..|
T Consensus 13 ~~kkakka~~~k~k~~k 29 (177)
T PF09831_consen 13 DKKKAKKAKKEKRKQRK 29 (177)
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 34555555555544443
No 61
>PLN02858 fructose-bisphosphate aldolase
Probab=25.52 E-value=40 Score=42.80 Aligned_cols=33 Identities=6% Similarity=0.091 Sum_probs=24.0
Q ss_pred CchHHHHHHH-hhCCCe-EEEeecCCCceEEEEcc
Q 008500 277 SVGGHLLTRF-AEKRFK-YRIASNPIERSIVWTMP 309 (563)
Q Consensus 277 s~GgqLl~~L-~~lgv~-~~I~s~pIp~sI~WrRk 309 (563)
.+|.-...-| ..+++. +++..+-.||...|+-.
T Consensus 1030 kGGdTs~~vl~~~L~~~~~~l~gei~pGvp~~~~~ 1064 (1378)
T PLN02858 1030 KGGITSSDLATKALEARRAKVVGQALAGVPLWKLG 1064 (1378)
T ss_pred CCchhHHHHHHhhcCcceeeeecccccCCceEEec
Confidence 3455555565 778887 44888889999999873
No 62
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=25.15 E-value=1.6e+02 Score=29.61 Aligned_cols=64 Identities=19% Similarity=0.315 Sum_probs=48.0
Q ss_pred hHHHHHHHhhccCCCHHHHHHHHHhCCCHHHHHHHhcCCCcChHHHHhhhhcccccCCCCCcccccHHHHHHHHHHHhcC
Q 008500 463 KSPWLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTVDGLLGDNRKLGEVCSKRVYRILIAQ 542 (563)
Q Consensus 463 ~dvW~rqLqQI~rVS~eiA~AIv~~YPSP~~Lv~AY~~cs~Se~Eke~LLadlki~g~~g~~RRIGpaLSrRIY~vfts~ 542 (563)
...|-+.|+.++||-|-.|.||.+-. ++..|.+|-.. +-...|..++ -||+...+||-.-+-++
T Consensus 68 ER~lF~~LisVnGIGpK~ALaiLs~~-~~~~l~~aI~~------~d~~~L~k~P---------GIGkKtAerivleLk~K 131 (201)
T COG0632 68 ERELFRLLISVNGIGPKLALAILSNL-DPEELAQAIAN------EDVKALSKIP---------GIGKKTAERIVLELKGK 131 (201)
T ss_pred HHHHHHHHHccCCccHHHHHHHHcCC-CHHHHHHHHHh------cChHhhhcCC---------CCCHHHHHHHHHHHhhh
Confidence 57788999999999999999999865 78899999842 2224555443 47777888877655444
No 63
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.57 E-value=1.4e+02 Score=31.69 Aligned_cols=38 Identities=11% Similarity=0.278 Sum_probs=20.5
Q ss_pred ccccHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 008500 209 KKMTKEERMLFMEEKKKKKEEEKLRKAALKAEAAESKK 246 (563)
Q Consensus 209 k~~~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~ae~Kk 246 (563)
+++...|+.++-++++++|.++.++.++-+++=.+-|+
T Consensus 134 ~r~q~~e~~~~~qkRrreK~e~~eaRqRV~~~Ie~DKa 171 (290)
T KOG2689|consen 134 RRLQDDEMRRAAQKRRREKAEDEEARQRVLRQIERDKA 171 (290)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhHH
Confidence 45555666665566666665555555555544444443
No 64
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=24.24 E-value=2.2e+02 Score=28.42 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHHHH
Q 008500 233 RKAALKAEAAESKKL 247 (563)
Q Consensus 233 ~K~a~Ka~~ae~Kk~ 247 (563)
+|+..++++|+++++
T Consensus 105 EKq~q~EEEKRrqki 119 (190)
T PF06936_consen 105 EKQKQEEEEKRRQKI 119 (190)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444444444
No 65
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=24.15 E-value=1.6e+02 Score=23.73 Aligned_cols=22 Identities=23% Similarity=0.051 Sum_probs=19.1
Q ss_pred HHHHhh-ccCCCHHHHHHHHHhC
Q 008500 467 LKALVS-IPKVQPRYAIAIWKKY 488 (563)
Q Consensus 467 ~rqLqQ-I~rVS~eiA~AIv~~Y 488 (563)
...|.+ +||+++..|.+|+...
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHH
Confidence 457888 9999999999999983
No 66
>PF08690 GET2: GET complex subunit GET2; InterPro: IPR014802 This family corresponds to the GET complex subunit GET2. The GET complex is involved in the retrieval of ER resident proteins from the Golgi []. ; PDB: 3SJD_D 3ZS9_C.
Probab=24.04 E-value=53 Score=34.97 Aligned_cols=17 Identities=18% Similarity=0.425 Sum_probs=10.3
Q ss_pred ccHHHHHhhHHHHHHhH
Q 008500 211 MTKEERMLFMEEKKKKK 227 (563)
Q Consensus 211 ~~~~ek~r~~eeK~~~K 227 (563)
++++||+|++.||+++|
T Consensus 2 ls~aEkrRLrRERReAK 18 (302)
T PF08690_consen 2 LSEAEKRRLRRERREAK 18 (302)
T ss_dssp --HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 57788888777665443
No 67
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=24.01 E-value=1.3e+02 Score=36.28 Aligned_cols=31 Identities=23% Similarity=0.350 Sum_probs=13.3
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 008500 218 LFMEEKKKKKEEEKLRKAALKAEAAESKKLQ 248 (563)
Q Consensus 218 r~~eeK~~~Ke~eK~~K~a~Ka~~ae~Kk~e 248 (563)
|+.||-++.|++|.+.+++.++++++.|+.+
T Consensus 805 re~EEEr~Rr~EEe~~ae~~ee~~e~akr~~ 835 (988)
T KOG2072|consen 805 REIEEERARREEEEANAERQEEAAERAKRTE 835 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444333444333
No 68
>PF06546 Vert_HS_TF: Vertebrate heat shock transcription factor; InterPro: IPR010542 This domain represents the C-terminal region of vertebrate heat shock transcription factors. Heat shock transcription factors regulate the expression of heat shock proteins - a set of proteins that protect the cell from damage caused by stress and aid the cell's recovery after the removal of stress []. This C-terminal region is found with the N-terminal IPR000232 from INTERPRO, and may contain a three-stranded coiled-coil trimerisation domain and a CE2 regulatory region, the latter of which is involved in sustained heat shock response [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.66 E-value=1.2e+02 Score=31.77 Aligned_cols=76 Identities=21% Similarity=0.211 Sum_probs=44.7
Q ss_pred CCCceeccCcccccCCCCCCCCCcccccCCCCCCCCeeEeeCCCCCCCCCCCCCCC------CCCCccccCCCCCceeEE
Q 008500 1 MSEPIILSDEEDQNALETPIQCPYKKIRTGPHPVAPTVLILDDDPTPKKSGFAPSS------SSTPSFVAETPMSDVCII 74 (563)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~ 74 (563)
+++-|||||--+ .+.-+|..+...-....+-...|.|.|-+..++|-- .+..+. ....+...+||||-+++|
T Consensus 14 ~s~gpIIsDiTE-~~~ssP~~s~~~~~d~~~~~~sp~v~ikEEp~sp~~-s~~~~~~~p~~~l~~~~~~~~~p~sP~~~i 91 (265)
T PF06546_consen 14 ISSGPIISDITE-LAPSSPEASEDSSSDESNLSSSPLVRIKEEPASPSQ-SPEASEASPAVSLSSGSSCVDPPESPASFI 91 (265)
T ss_pred cCCCCEEecCcC-CCCCCcccCCCcccccccccCCCceeeccCCCCCCC-CccccccCCcccccCCcccCCCcCChHHHh
Confidence 456788999874 345577776666555443445788888884444422 222222 122345677888876666
Q ss_pred Eecc
Q 008500 75 KCTS 78 (563)
Q Consensus 75 ~~~~ 78 (563)
-...
T Consensus 92 dSIL 95 (265)
T PF06546_consen 92 DSIL 95 (265)
T ss_pred hhhh
Confidence 6433
No 69
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.27 E-value=87 Score=31.49 Aligned_cols=26 Identities=38% Similarity=0.548 Sum_probs=13.1
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008500 225 KKKEEEKLRKAALKAEAAESKKLQKE 250 (563)
Q Consensus 225 ~~Ke~eK~~K~a~Ka~~ae~Kk~eke 250 (563)
+.||++...++.+-++.++.++|..+
T Consensus 46 qrKEeee~KR~eal~RK~E~krL~ee 71 (221)
T KOG3223|consen 46 QRKEEEEEKRAEALERKAEAKRLAEE 71 (221)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555554444444455555555443
No 70
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=22.96 E-value=63 Score=36.06 Aligned_cols=16 Identities=19% Similarity=0.434 Sum_probs=11.5
Q ss_pred CCCeeEeeCCCCCCCC
Q 008500 34 VAPTVLILDDDPTPKK 49 (563)
Q Consensus 34 ~~~~~~~~~~~~~~~~ 49 (563)
+.|.+|.|++--||--
T Consensus 77 ~vPs~ffIg~sGtpLe 92 (506)
T KOG2507|consen 77 SVPSIFFIGFSGTPLE 92 (506)
T ss_pred cccceeeecCCCceeE
Confidence 3788888888666644
No 71
>KOG2357 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.83 E-value=1.7e+02 Score=32.67 Aligned_cols=9 Identities=11% Similarity=0.243 Sum_probs=3.8
Q ss_pred ccccccccc
Q 008500 192 QVNADNRKS 200 (563)
Q Consensus 192 ~~~~e~~~~ 200 (563)
.+|-+-+..
T Consensus 359 ~lS~~~k~k 367 (440)
T KOG2357|consen 359 FLSKDAKAK 367 (440)
T ss_pred hchHHHHhh
Confidence 444443333
No 72
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=22.21 E-value=1.1e+02 Score=36.24 Aligned_cols=55 Identities=27% Similarity=0.387 Sum_probs=0.0
Q ss_pred cchhhhccccccH-HHHHhhHHHHHHhHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHhh
Q 008500 201 TDEAVGKKKKMTK-EERMLFMEEKKKKKEEEKLRKA-----------------ALKAEAAESKKLQKEMQKWA 255 (563)
Q Consensus 201 ~~~~~~~~k~~~~-~ek~r~~eeK~~~Ke~eK~~K~-----------------a~Ka~~ae~Kk~eke~~K~~ 255 (563)
+.+..+.+++.+. .|+++..|+|+.++|+++..++ +.++...|.|+++.|-+..+
T Consensus 493 LEkrL~eE~~~R~~lEkQL~eErk~r~~ee~~aar~~~~~~~~r~e~~e~~r~r~~~lE~E~~~lr~elk~ke 565 (697)
T PF09726_consen 493 LEKRLAEERRQRASLEKQLQEERKARKEEEEKAARALAQAQATRQECAESCRQRRRQLESELKKLRRELKQKE 565 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhccccchhccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
No 73
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=22.13 E-value=30 Score=34.46 Aligned_cols=8 Identities=38% Similarity=0.667 Sum_probs=3.7
Q ss_pred HHHHHHHh
Q 008500 334 EEFCNLVL 341 (563)
Q Consensus 334 eeFv~lI~ 341 (563)
.+|++.|.
T Consensus 102 ~~Fi~yIK 109 (188)
T PF09756_consen 102 QEFINYIK 109 (188)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 34444444
No 74
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=22.13 E-value=1e+02 Score=37.02 Aligned_cols=6 Identities=17% Similarity=0.446 Sum_probs=2.6
Q ss_pred EEEEcc
Q 008500 304 IVWTMP 309 (563)
Q Consensus 304 I~WrRk 309 (563)
-.|+|-
T Consensus 903 ~~WrR~ 908 (988)
T KOG2072|consen 903 AEWRRG 908 (988)
T ss_pred hHHhhc
Confidence 345543
No 75
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=21.25 E-value=60 Score=32.91 Aligned_cols=22 Identities=55% Similarity=0.608 Sum_probs=0.0
Q ss_pred ccccccHHHHHhhHHHHHHhHH
Q 008500 207 KKKKMTKEERMLFMEEKKKKKE 228 (563)
Q Consensus 207 ~~k~~~~~ek~r~~eeK~~~Ke 228 (563)
+||.++++||.++|++|+++.+
T Consensus 97 ~kK~~tkeEKk~~K~ek~~~e~ 118 (212)
T cd03489 97 KKKSRTKEEKKALKEEKDKEAE 118 (212)
T ss_pred HHHhCCHHHHHHHHHHHHHhhc
No 76
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=21.12 E-value=59 Score=33.00 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=12.1
Q ss_pred ccccccCCc----hHHHHHHHhhCCCeEEE
Q 008500 270 AKVVELGSV----GGHLLTRFAEKRFKYRI 295 (563)
Q Consensus 270 ~~lle~~s~----GgqLl~~L~~lgv~~~I 295 (563)
|+|+. |.+ .|.|-.+..-.+|...+
T Consensus 143 PgLFr-GRG~HPK~G~lK~Rv~PedVtINi 171 (215)
T cd00660 143 PGLFR-GRGEHPKMGKLKRRIMPEDITINI 171 (215)
T ss_pred Ccccc-cCCCCCCCCccccccChhhEEEec
Confidence 46665 432 34444444444555544
No 77
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=20.99 E-value=61 Score=32.94 Aligned_cols=22 Identities=45% Similarity=0.561 Sum_probs=0.0
Q ss_pred ccccccHHHHHhhHHHHHHhHH
Q 008500 207 KKKKMTKEERMLFMEEKKKKKE 228 (563)
Q Consensus 207 ~~k~~~~~ek~r~~eeK~~~Ke 228 (563)
+||.++++||.++|++|++..+
T Consensus 100 ~kK~~tkeEKk~~K~ek~~~e~ 121 (215)
T cd03488 100 EKKAMSKEEKKAIKAEKEKLEE 121 (215)
T ss_pred HHHcCCHHHHHHHHHHHHhhhc
No 78
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=20.90 E-value=60 Score=33.01 Aligned_cols=22 Identities=36% Similarity=0.462 Sum_probs=0.0
Q ss_pred ccccccHHHHHhhHHHHHHhHH
Q 008500 207 KKKKMTKEERMLFMEEKKKKKE 228 (563)
Q Consensus 207 ~~k~~~~~ek~r~~eeK~~~Ke 228 (563)
+||.++++||.++|++|++..+
T Consensus 99 ~kK~~tkeEKk~~K~ek~~~e~ 120 (217)
T cd03490 99 KKKNLNKEEKEAKKKERAKREY 120 (217)
T ss_pred HHHhcCHHHHHHHHHHHHHhhc
No 79
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=20.64 E-value=77 Score=27.00 Aligned_cols=28 Identities=29% Similarity=0.475 Sum_probs=21.9
Q ss_pred HHHhhccCCCHHHHHHHHH------hCCCHHHHH
Q 008500 468 KALVSIPKVQPRYAIAIWK------KYPTMKALL 495 (563)
Q Consensus 468 rqLqQI~rVS~eiA~AIv~------~YPSP~~Lv 495 (563)
+-|++||||.+-.|..|+. +|++++.|.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~ 35 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLA 35 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhh
Confidence 3589999999999999987 455555554
No 80
>PF03760 LEA_1: Late embryogenesis abundant (LEA) group 1 ; InterPro: IPR005513 LEA proteins are late embryonic proteins abundant in higher plant seed embryos. They may play an essential role in seed survival and control of water exchanges during seed desiccation and imbibition. Family members are conserved along the entire coding region, especially within the hydrophobic internal 20 amino acid motif. This motif may be repeated.; GO: 0009790 embryo development
Probab=20.29 E-value=2.2e+02 Score=24.39 Aligned_cols=34 Identities=32% Similarity=0.393 Sum_probs=23.1
Q ss_pred cHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 008500 212 TKEERMLFMEEKKKKKEEEKLRKAALKAEAAESK 245 (563)
Q Consensus 212 ~~~ek~r~~eeK~~~Ke~eK~~K~a~Ka~~ae~K 245 (563)
+..||+..+|+|+.+..+.+.+|...|+.-+..|
T Consensus 37 ~~~eKe~A~erk~ak~a~Ae~~~h~aka~~aa~k 70 (73)
T PF03760_consen 37 DPEEKEMAHERKEAKEAQAEMDKHQAKAENAAEK 70 (73)
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 4467777777777777777777777776555443
No 81
>PF12757 DUF3812: Protein of unknown function (DUF3812); InterPro: IPR024527 This family of fungal proteins represents the eisosome 1 family. Eisosome protein 1 is required for normal formation of eisosomes, large cytoplasmic protein assemblies that localize to specialised domains on plasma membrane and mark the site of endocytosis [].
Probab=20.22 E-value=1.5e+02 Score=27.52 Aligned_cols=23 Identities=30% Similarity=0.284 Sum_probs=11.4
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHH
Q 008500 223 KKKKKEEEKLRKAALKAEAAESK 245 (563)
Q Consensus 223 K~~~Ke~eK~~K~a~Ka~~ae~K 245 (563)
++++.++.+...+..|+++++.|
T Consensus 103 ~k~~~~~~k~~~~~~k~re~e~k 125 (126)
T PF12757_consen 103 IKLDEEERKREHEEWKEREREKK 125 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 44444455555555555554443
No 82
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=20.15 E-value=1.7e+02 Score=31.17 Aligned_cols=9 Identities=44% Similarity=0.737 Sum_probs=3.3
Q ss_pred HHHhHHHHH
Q 008500 223 KKKKKEEEK 231 (563)
Q Consensus 223 K~~~Ke~eK 231 (563)
|+.++|++.
T Consensus 344 kkr~eeaee 352 (445)
T KOG2891|consen 344 KKREEEAEE 352 (445)
T ss_pred HHHHHHHHH
Confidence 333333333
Done!