Query 008492
Match_columns 563
No_of_seqs 275 out of 883
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 12:51:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008492hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00479 RAP Superfamily; Prov 100.0 9.9E-42 2.1E-46 350.8 27.5 338 152-545 55-395 (435)
2 PF08373 RAP: RAP domain; Int 99.8 1.8E-19 3.8E-24 140.3 5.0 58 484-541 1-58 (58)
3 PRK09169 hypothetical protein; 99.7 1E-16 2.2E-21 191.3 17.5 210 153-372 284-516 (2316)
4 PRK09169 hypothetical protein; 99.7 1.5E-16 3.4E-21 189.8 16.3 207 152-371 325-557 (2316)
5 PTZ00479 RAP Superfamily; Prov 99.5 2.2E-12 4.7E-17 134.4 17.7 147 199-382 53-199 (435)
6 PRK14707 hypothetical protein; 98.8 5.1E-08 1.1E-12 116.3 14.0 209 153-371 704-935 (2710)
7 PRK14707 hypothetical protein; 98.8 5.9E-08 1.3E-12 115.7 14.5 176 152-369 661-849 (2710)
8 PF04480 DUF559: Protein of un 98.8 4.7E-08 1E-12 85.8 10.3 93 443-542 12-107 (108)
9 cd01038 Endonuclease_DUF559 Do 98.7 1E-07 2.2E-12 83.7 10.7 80 442-526 11-93 (108)
10 PRK09767 hypothetical protein; 98.5 6.8E-07 1.5E-11 79.4 10.5 93 445-544 17-112 (117)
11 cd00221 Vsr Very Short Patch R 98.4 5.4E-07 1.2E-11 79.9 7.4 83 443-525 16-115 (115)
12 COG2852 Very-short-patch-repai 98.2 1.9E-06 4.2E-11 75.7 6.0 63 459-526 44-106 (129)
13 PF06743 FAST_1: FAST kinase-l 98.1 6.5E-06 1.4E-10 66.7 6.6 59 248-306 1-62 (71)
14 TIGR00632 vsr DNA mismatch end 98.1 8.2E-06 1.8E-10 72.1 7.3 74 448-521 24-114 (117)
15 PF06743 FAST_1: FAST kinase-l 98.0 3.1E-05 6.7E-10 62.7 7.4 62 209-270 1-63 (71)
16 PF08368 FAST_2: FAST kinase-l 97.2 0.0012 2.5E-08 56.4 7.2 74 403-477 5-83 (93)
17 cd01037 Restriction_endonuclea 96.7 0.0083 1.8E-07 47.7 7.6 73 449-521 4-79 (80)
18 PF10881 DUF2726: Protein of u 94.5 0.055 1.2E-06 48.6 4.7 56 468-526 53-113 (126)
19 COG3727 Vsr DNA G:T-mismatch r 93.3 1 2.3E-05 40.5 10.3 100 445-548 22-138 (150)
20 PF07671 DUF1601: Protein of u 92.2 0.065 1.4E-06 37.5 1.0 25 189-213 13-37 (37)
21 KOG0166 Karyopherin (importin) 90.4 31 0.00066 38.5 19.7 139 157-305 127-274 (514)
22 PF07671 DUF1601: Protein of u 90.2 0.16 3.6E-06 35.5 1.4 23 230-252 15-37 (37)
23 PF03852 Vsr: DNA mismatch end 89.1 0.56 1.2E-05 38.2 3.9 45 445-490 21-66 (75)
24 KOG2422 Uncharacterized conser 77.3 0.91 2E-05 50.3 0.6 32 264-295 340-374 (665)
25 PHA00159 endonuclease I 76.3 3.7 8.1E-05 37.3 4.1 47 443-490 15-70 (148)
26 KOG2422 Uncharacterized conser 64.8 2.7 5.9E-05 46.7 0.8 15 204-218 302-316 (665)
27 PF05367 Phage_endo_I: Phage e 60.6 17 0.00037 33.3 4.9 46 444-490 16-70 (149)
28 COG5064 SRP1 Karyopherin (impo 56.9 2.7E+02 0.0058 29.7 14.3 174 103-306 95-281 (526)
29 KOG0166 Karyopherin (importin) 56.6 1.5E+02 0.0033 33.1 12.4 89 206-294 209-305 (514)
30 cd00020 ARM Armadillo/beta-cat 44.9 1.8E+02 0.004 24.2 9.7 98 198-295 13-118 (120)
31 PF07862 Nif11: Nitrogen fixat 35.3 1.1E+02 0.0024 22.4 5.1 34 100-142 6-39 (49)
32 PF14851 FAM176: FAM176 family 33.8 19 0.0004 33.7 0.9 21 95-115 123-143 (153)
33 PF08597 eIF3_subunit: Transla 30.4 27 0.00059 35.1 1.5 26 11-36 177-202 (245)
34 KOG2548 SWAP mRNA splicing reg 29.0 24 0.00052 38.9 0.8 17 24-40 145-161 (653)
35 KOG2768 Translation initiation 28.8 26 0.00057 34.3 1.0 26 69-101 73-98 (231)
36 COG3414 SgaB Phosphotransferas 28.4 85 0.0018 26.8 3.9 66 447-512 18-90 (93)
37 cd00671 ArgRS_core catalytic c 27.9 92 0.002 30.4 4.7 47 481-527 1-51 (212)
38 PF13764 E3_UbLigase_R4: E3 ub 27.6 1.1E+03 0.024 28.1 14.1 166 100-277 86-275 (802)
39 PF03343 SART-1: SART-1 family 26.8 21 0.00046 40.8 0.0 17 25-41 279-295 (613)
40 KOG2141 Protein involved in hi 24.9 1.2E+03 0.025 27.5 14.2 63 245-307 421-487 (822)
41 TIGR00990 3a0801s09 mitochondr 24.9 2.9E+02 0.0063 31.4 8.8 34 127-171 171-204 (615)
42 PF04147 Nop14: Nop14-like fam 24.5 4.2E+02 0.009 31.8 10.1 35 125-172 421-455 (840)
43 KOG4727 U1-like Zn-finger prot 23.2 54 0.0012 31.0 1.9 11 62-72 176-186 (193)
44 PRK09687 putative lyase; Provi 23.2 8.1E+02 0.018 25.0 17.7 169 201-382 63-232 (280)
45 COG5064 SRP1 Karyopherin (impo 22.5 6.4E+02 0.014 27.0 9.6 64 207-270 216-282 (526)
46 PF13513 HEAT_EZ: HEAT-like re 22.4 3.1E+02 0.0068 19.9 5.9 45 250-294 6-54 (55)
47 PF13366 PDDEXK_3: PD-(D/E)XK 21.8 1.8E+02 0.004 25.9 4.9 45 445-490 25-79 (118)
48 KOG3962 Predicted actin-bundli 21.6 9.1 0.0002 37.6 -3.6 20 72-92 49-68 (246)
49 PF07789 DUF1627: Protein of u 20.8 84 0.0018 29.2 2.6 36 93-132 88-131 (155)
50 PF00750 tRNA-synt_1d: tRNA sy 20.6 1.3E+02 0.0028 32.0 4.4 38 478-522 18-65 (354)
No 1
>PTZ00479 RAP Superfamily; Provisional
Probab=100.00 E-value=9.9e-42 Score=350.80 Aligned_cols=338 Identities=16% Similarity=0.194 Sum_probs=267.4
Q ss_pred CCCCChhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHHHhhCCCCCHHHHHHHHHHHHHcCCCcCCHHHHHH
Q 008492 152 PSPLSPLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIAMTALPECSAQGISNIAWALSKIGGELLYLSEMDR 231 (563)
Q Consensus 152 ~~~fn~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~~~~l~~~~~q~LsNilWAlakLg~~~~~~~~l~~ 231 (563)
|.-+++.-+|.+...-|.+-.. ..+.+.....++.+.++.++||+|++|+|+|||+++-.. ..+++
T Consensus 55 ~~~md~~~is~~vqkaat~rkh------------D~~Lw~~f~~Rilel~dtL~Pqqig~Ilyg~gKsr~~~~--efy~~ 120 (435)
T PTZ00479 55 PDLMDGWYLSACVQKAATLRKH------------DLELWHGFTNRLLELSDTLTPQQIGYIFYGYGKSRFLNP--EFYEK 120 (435)
T ss_pred hhhcCHHHHHHHHHHHHhhhhc------------hHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhccCH--HHHHH
Confidence 4566777777666666654211 123456677788899999999999999999999998642 45789
Q ss_pred HHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHcCCCChhHHHHHHHHhh
Q 008492 232 VAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELAKRASDIVHTFQEQELAQVLWAFASLYEPADPLLESLDNAFK 311 (563)
Q Consensus 232 la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala~~v~~~l~~f~~qeLanilwAfA~l~~~~~~L~~al~~~~~ 311 (563)
+.+.+...+++|++++|++++|||++|+++++.++++++.++..+..+|+++++++++.|+|+||+.+..+.+.+.+.+.
T Consensus 121 ~~~~v~~~L~~fssh~L~~i~wALsrL~Ird~~fL~~~ak~vl~r~~~~r~~dl~k~~nslakLg~~~~~l~k~l~~~~~ 200 (435)
T PTZ00479 121 MLKFVQPLLPNFYSHSLMCIAWALNRVQIRDEAFLSRFAKEVGEKFDDIRTTDLIKICNSLAKLGGYTNNLKKFLSEKMV 200 (435)
T ss_pred HHHHHHHHhhhcCccHHHHHHHHHHhcCCCcHHHHHHHHHHHHhhccccCchhHHHHHHHHHHhcCCcHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888777665332
Q ss_pred hcchhhhhHHHHhhhhhccCCCCCCCCcccchhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhhHHHHhh
Q 008492 312 DATQFTCCLNKALSNCNENGGVKSSGDADSEGSLSSPVLSFNRDQLGNIAWSYAVLGQMDRIFFSDIWKTISRFEEQRIS 391 (563)
Q Consensus 312 ~~~~f~~~l~~~vs~~~~a~~~~~~~~L~~~~~~~~~l~~f~~qeLanilWSLA~Lg~~d~~lf~~l~~~L~~~~~~~ls 391 (563)
..++.|+++++-|.+-..+.++.++.+.--.++..... -.+
T Consensus 201 -----------------------------------~rle~~~~~~~r~~i~~it~~~Lf~d~m~~~~ler~s~---~~~- 241 (435)
T PTZ00479 201 -----------------------------------EKLESLFAQDFRNVVNDVTLIHLYDDNTQIYILERFSK---MFI- 241 (435)
T ss_pred -----------------------------------HHHhhhcccchhhhcChhhHHHHhhhHHHHHHHHHccc---cce-
Confidence 23456777777777777777777777643333322100 000
Q ss_pred HhhHHhhHHHHHHHHHHHHhhhhCCCcccccchHHHHHHHHhcccccc-CCCCCCHHHHHHHHHHHhcCCcceeeccccc
Q 008492 392 EQYREDIMFASQVHLVNQCLKLEHPHLQLALSSVLEEKIASAGKTKRF-NQKVTSSFQKEVARLLVSTGLNWIREYAVDG 470 (563)
Q Consensus 392 e~~~~~l~~~~QL~~~n~~l~lE~p~~~~~l~~~l~~~l~~a~~~~~~-~~~~~S~lq~~V~~~L~~lG~~~~~E~~~~G 470 (563)
-.|.. .+.|+|....++.+.+|+....++.+...++.+......- ....+|.+|++|+++|..||+.|+.|+..||
T Consensus 242 c~r~~---hl~~~y~~aly~rl~~p~v~~~Ls~~~r~Fl~r~s~r~i~~~~~~~S~~h~dVS~~L~~mGI~H~ne~~~Gp 318 (435)
T PTZ00479 242 CARPQ---HLQQAYKSAVAVRVLLPHVWFQLSKSVKSFYTRLSMRRIPQSLRKPSPFQWDVSNCLAKLGISHRNTFYWGC 318 (435)
T ss_pred ecccH---HHHHHHhhhhhheeechHHHHhcCHHHHHHHHHHhhccccccCCCCcHHHHHHHHHHHHhCCchhhheeecC
Confidence 01111 1223443334567788988778888888888776432111 1367999999999999999999999999999
Q ss_pred eeeeEeeC-CCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEehhhHHhhcCh-HHHHHHHHHHHHHH
Q 008492 471 YTVDAVLV-DKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLSHQEWEELQGS-FEQLDYLRVILKDY 545 (563)
Q Consensus 471 ~~vDi~~~-~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vpy~EW~~l~~~-~ek~~YLr~~L~~~ 545 (563)
|.|||+.+ +++++||||||+||++|+...+|.+.+|+|+|..+||+|++|||+||.++.++ ++|++||++.++.-
T Consensus 319 f~iDI~~~~~k~~~IeVdGPshFY~ns~~~Ta~skLkHriL~~lGw~V~~Ipy~eW~~L~~d~e~K~eYLrk~~e~~ 395 (435)
T PTZ00479 319 FWIDIGEIDDKRNCWFIDGPSCFYTSTNEYTESVKLQHRILSNLGWNIRRVVWIDWVQLGDDTEAKVQYVRKLRESE 395 (435)
T ss_pred eEEEEeccCCcceEEEEcCcchhhccchhhHHHHHHHHHHHHHCCCeEEEeeHHHHhhhCcCHHHHHHHHHHHhhcC
Confidence 99999965 68899999999999999999999999999999999999999999999999876 57999999998764
No 2
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=99.78 E-value=1.8e-19 Score=140.35 Aligned_cols=58 Identities=38% Similarity=0.723 Sum_probs=56.0
Q ss_pred EEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEehhhHHhhcChHHHHHHHHHH
Q 008492 484 FEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLSHQEWEELQGSFEQLDYLRVI 541 (563)
Q Consensus 484 IEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vpy~EW~~l~~~~ek~~YLr~~ 541 (563)
||||||+|||+|+..++|.+.||+|+|+++||+||+|||+||.++.+.++|++||+++
T Consensus 1 IevdGp~hy~~~~~~~~g~t~lk~r~L~~~G~~Vi~Ip~~eW~~l~~~~~k~~YL~~~ 58 (58)
T PF08373_consen 1 IEVDGPSHYYRNSNNLTGSTKLKHRHLKALGYKVISIPYYEWNKLKSREEKIEYLKKK 58 (58)
T ss_pred CEECCcHHhhCCCCccchHHHHHHHHHHHCCCEEEEecHHHHHhcCCHHHHHHHHhcC
Confidence 7999999999999999999999999999999999999999999999889999999874
No 3
>PRK09169 hypothetical protein; Validated
Probab=99.71 E-value=1e-16 Score=191.26 Aligned_cols=210 Identities=17% Similarity=0.124 Sum_probs=139.7
Q ss_pred CCCChhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHHHhhCCCCCHHHHHHHHHHHHHcCCCcCCHHHHHHH
Q 008492 153 SPLSPLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIAMTALPECSAQGISNIAWALSKIGGELLYLSEMDRV 232 (563)
Q Consensus 153 ~~fn~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~~~~l~~~~~q~LsNilWAlakLg~~~~~~~~l~~l 232 (563)
..||++++|++|+.|+|+.... ..+. +-...-..|.... .....|+||+|||++|||+|+............|
T Consensus 284 ~~~~~Q~vAN~LNALSKwp~~~---~cr~---aa~~LA~rL~~~~-~l~~~~~aQ~vAN~LNALSKWp~~~~c~~Aa~~L 356 (2316)
T PRK09169 284 LALDPQGVANALNALSKWPDTE---ACRQ---AAEALAERLAQER-GLLQAMNAQAVANALNALSKWPDEEACRAAAEAL 356 (2316)
T ss_pred hhcCHHHHHHHHHHHHhCCCch---HHHH---HHHHHHHHHHhCh-hhhhhCCHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence 4699999999999999985431 0110 1111112333333 3688999999999999999998654333334566
Q ss_pred HHHHH---HhhCCCChHHHHHHHHHHHHCCCCCH--HHHHHHHHHHhhh---hcCCCHHHHHHHHHHHHHcCCCC--hhH
Q 008492 233 AEVAL---TKVGEFNSQNVANVAGAFASMQHSAP--DLFSELAKRASDI---VHTFQEQELAQVLWAFASLYEPA--DPL 302 (563)
Q Consensus 233 a~~a~---~~~~~f~~q~LanilwAlA~L~~~~~--~L~~ala~~v~~~---l~~f~~qeLanilwAfA~l~~~~--~~L 302 (563)
+.++. .....||||+|||++|||+|+..... ..-.+++.++... .+.|++|+|+|++|||+|+...+ ...
T Consensus 357 A~rL~~~~~l~~~~npQelANaLnALSKwp~~~~cr~AA~aLA~rL~~~~~l~~~fnaQ~vANaLnALsKWp~~~~c~~a 436 (2316)
T PRK09169 357 AARLARDAGLRRALNAQELANALNALSKWPDEEACRAAAEALAARLARDAGLRAALNAQGVANALNALSKWPGAEACRQA 436 (2316)
T ss_pred HHHHHhChhhhhhCCHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHhchhhhhhcChHHHHHHHHHHhcCCCchHHHHH
Confidence 66553 34589999999999999999987643 4455666666543 46799999999999999998654 234
Q ss_pred HHHHHHHhhhc----chhhhhHHHHhhhhhccCCCCCCCC--cc----cchhc---cCCCCCCCHHHHHHHHHHHHhcCC
Q 008492 303 LESLDNAFKDA----TQFTCCLNKALSNCNENGGVKSSGD--AD----SEGSL---SSPVLSFNRDQLGNIAWSYAVLGQ 369 (563)
Q Consensus 303 ~~al~~~~~~~----~~f~~~l~~~vs~~~~a~~~~~~~~--L~----~~~~~---~~~l~~f~~qeLanilWSLA~Lg~ 369 (563)
..+|+..+... ..|+ ++.++|..+++++.+... .. +...+ ......|++|+|+|++|+|++++.
T Consensus 437 a~aLA~rl~~~a~lr~~fn---~QeLaN~LnALsKWp~~~~c~~aa~~LA~rl~~~~~l~~af~~Q~lAN~LnALsKwp~ 513 (2316)
T PRK09169 437 ALALAARLAADARLRNALS---AQELANALNALSKWPDEAACRRAAEALAARLAGDAELRQALDAQGLANALNALSKWPD 513 (2316)
T ss_pred HHHHHHHHhhchhhhhhCC---HHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhcChhhhhhcChHHHHHHHHHHhcCCc
Confidence 55565554443 2333 455666666555422111 00 11111 123578999999999999999997
Q ss_pred CCH
Q 008492 370 MDR 372 (563)
Q Consensus 370 ~d~ 372 (563)
.+.
T Consensus 514 ~~~ 516 (2316)
T PRK09169 514 SDA 516 (2316)
T ss_pred cHH
Confidence 665
No 4
>PRK09169 hypothetical protein; Validated
Probab=99.70 E-value=1.5e-16 Score=189.79 Aligned_cols=207 Identities=19% Similarity=0.150 Sum_probs=137.1
Q ss_pred CCCCChhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHHH---hhCCCCCHHHHHHHHHHHHHcCCCcCCHHH
Q 008492 152 PSPLSPLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIAM---TALPECSAQGISNIAWALSKIGGELLYLSE 228 (563)
Q Consensus 152 ~~~fn~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~~---~~l~~~~~q~LsNilWAlakLg~~~~~~~~ 228 (563)
...||++++|++|+.|+|+.... ..+. ....|...+. .....|+||+|||++|||+|++....+...
T Consensus 325 ~~~~~aQ~vAN~LNALSKWp~~~---~c~~-------Aa~~LA~rL~~~~~l~~~~npQelANaLnALSKwp~~~~cr~A 394 (2316)
T PRK09169 325 LQAMNAQAVANALNALSKWPDEE---ACRA-------AAEALAARLARDAGLRRALNAQELANALNALSKWPDEEACRAA 394 (2316)
T ss_pred hhhCCHHHHHHHHHHHhcCCCcH---HHHH-------HHHHHHHHHHhChhhhhhCCHHHHHHHHHHHHcCCCchHHHHH
Confidence 35799999999999999975331 0000 1123333332 345799999999999999999865443333
Q ss_pred HHHHHHHHHH---hhCCCChHHHHHHHHHHHHCCCCC--HHHHHHHHHHHhhh---hcCCCHHHHHHHHHHHHHcCCCCh
Q 008492 229 MDRVAEVALT---KVGEFNSQNVANVAGAFASMQHSA--PDLFSELAKRASDI---VHTFQEQELAQVLWAFASLYEPAD 300 (563)
Q Consensus 229 l~~la~~a~~---~~~~f~~q~LanilwAlA~L~~~~--~~L~~ala~~v~~~---l~~f~~qeLanilwAfA~l~~~~~ 300 (563)
.++|+.++.. ....||+|+|||++|||+|+...+ .....+++.++... ...|++|+|+|++|||+++...+.
T Consensus 395 A~aLA~rL~~~~~l~~~fnaQ~vANaLnALsKWp~~~~c~~aa~aLA~rl~~~a~lr~~fn~QeLaN~LnALsKWp~~~~ 474 (2316)
T PRK09169 395 AEALAARLARDAGLRAALNAQGVANALNALSKWPGAEACRQAALALAARLAADARLRNALSAQELANALNALSKWPDEAA 474 (2316)
T ss_pred HHHHHHHHHhchhhhhhcChHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhchhhhhhCCHHHHHHHHHHHhcCCchHH
Confidence 4566665543 246799999999999999998765 35677777776643 389999999999999999875431
Q ss_pred --hHHHHHHHHhhhcc----hhhhhHHHHhhhhhccCCCCCCCCc--cc----chhc---cCCCCCCCHHHHHHHHHHHH
Q 008492 301 --PLLESLDNAFKDAT----QFTCCLNKALSNCNENGGVKSSGDA--DS----EGSL---SSPVLSFNRDQLGNIAWSYA 365 (563)
Q Consensus 301 --~L~~al~~~~~~~~----~f~~~l~~~vs~~~~a~~~~~~~~L--~~----~~~~---~~~l~~f~~qeLanilWSLA 365 (563)
.....|+.++...+ .|. ++-++|..+++++.+.... .+ ...+ ...+..|+||+|+|++|+|+
T Consensus 475 c~~aa~~LA~rl~~~~~l~~af~---~Q~lAN~LnALsKwp~~~~c~~aA~aLA~rla~~~~l~~afnpQ~lAN~LnALS 551 (2316)
T PRK09169 475 CRRAAEALAARLAGDAELRQALD---AQGLANALNALSKWPDSDACRAAAEALADRLAQDPALLQAMDAQGLANTLNALS 551 (2316)
T ss_pred HHHHHHHHHHHHhcChhhhhhcC---hHHHHHHHHHHhcCCccHHHHHHHHHHHHHHhcChhhhhhcCHHHHHHHHHHHH
Confidence 12344455554432 233 3445555555443221110 01 1111 23568999999999999999
Q ss_pred hcCCCC
Q 008492 366 VLGQMD 371 (563)
Q Consensus 366 ~Lg~~d 371 (563)
+++..+
T Consensus 552 KWP~~~ 557 (2316)
T PRK09169 552 KWPEEP 557 (2316)
T ss_pred cCCCch
Confidence 998744
No 5
>PTZ00479 RAP Superfamily; Provisional
Probab=99.46 E-value=2.2e-12 Score=134.36 Aligned_cols=147 Identities=12% Similarity=0.139 Sum_probs=129.9
Q ss_pred hhCCCCCHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhhc
Q 008492 199 TALPECSAQGISNIAWALSKIGGELLYLSEMDRVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELAKRASDIVH 278 (563)
Q Consensus 199 ~~l~~~~~q~LsNilWAlakLg~~~~~~~~l~~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala~~v~~~l~ 278 (563)
...+-|+++.||+++=--|.+.-+.. ..+..+..++...++..+||++++++||||++++.+++||.++...+...++
T Consensus 53 ~~~~~md~~~is~~vqkaat~rkhD~--~Lw~~f~~Rilel~dtL~Pqqig~Ilyg~gKsr~~~~efy~~~~~~v~~~L~ 130 (435)
T PTZ00479 53 SPPDLMDGWYLSACVQKAATLRKHDL--ELWHGFTNRLLELSDTLTPQQIGYIFYGYGKSRFLNPEFYEKMLKFVQPLLP 130 (435)
T ss_pred cChhhcCHHHHHHHHHHHHhhhhchH--HHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhh
Confidence 35567999999999999999987653 5578899999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHcCCCChhHHHHHHHHhhhcchhhhhHHHHhhhhhccCCCCCCCCcccchhccCCCCCCCHHHHH
Q 008492 279 TFQEQELAQVLWAFASLYEPADPLLESLDNAFKDATQFTCCLNKALSNCNENGGVKSSGDADSEGSLSSPVLSFNRDQLG 358 (563)
Q Consensus 279 ~f~~qeLanilwAfA~l~~~~~~L~~al~~~~~~~~~f~~~l~~~vs~~~~a~~~~~~~~L~~~~~~~~~l~~f~~qeLa 358 (563)
.|+++++++++||++++++.++.++.+++..+. ...++|++++++
T Consensus 131 ~fssh~L~~i~wALsrL~Ird~~fL~~~ak~vl-----------------------------------~r~~~~r~~dl~ 175 (435)
T PTZ00479 131 NFYSHSLMCIAWALNRVQIRDEAFLSRFAKEVG-----------------------------------EKFDDIRTTDLI 175 (435)
T ss_pred hcCccHHHHHHHHHHhcCCCcHHHHHHHHHHHH-----------------------------------hhccccCchhHH
Confidence 999999999999999999999999988776332 334668999999
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHH
Q 008492 359 NIAWSYAVLGQMDRIFFSDIWKTI 382 (563)
Q Consensus 359 nilWSLA~Lg~~d~~lf~~l~~~L 382 (563)
+++.|+|+||..+..+...+-..+
T Consensus 176 k~~nslakLg~~~~~l~k~l~~~~ 199 (435)
T PTZ00479 176 KICNSLAKLGGYTNNLKKFLSEKM 199 (435)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHH
Confidence 999999999999997666665544
No 6
>PRK14707 hypothetical protein; Provisional
Probab=98.78 E-value=5.1e-08 Score=116.27 Aligned_cols=209 Identities=17% Similarity=0.143 Sum_probs=131.9
Q ss_pred CCCChhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHH---HhhCCCCCHHHHHHHHHHHHHcCCCcCCHHHH
Q 008492 153 SPLSPLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIA---MTALPECSAQGISNIAWALSKIGGELLYLSEM 229 (563)
Q Consensus 153 ~~fn~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~---~~~l~~~~~q~LsNilWAlakLg~~~~~~~~l 229 (563)
..||++++|++|+.|.|..... .. ++. -..|...+ .+....|++|+|+|++.||+|.-..+......
T Consensus 704 ~al~pQ~vAN~LNALSKWP~~~---~C------r~A-A~~LA~rL~~~p~l~~a~~aQevANaLNALSKWPd~~~C~~AA 773 (2710)
T PRK14707 704 KELNPVDVANALNALSKWPRTP---VC------AAV-ASALAARVVAEPRLRKAFDAQQVATALNALSKWPDNQACAAAA 773 (2710)
T ss_pred hhcCHHHHHHHHhhhhcCCCcH---HH------HHH-HHHHHHHHhcChhhhhhcCHHHHHHHHHHhhcCCCchHHHHHH
Confidence 4699999999999999985431 01 100 01122222 23457899999999999999998665444445
Q ss_pred HHHHHHHHH---hhCCCChHHHHHHHHHHHHCCCCCH--HHHHHHHHHHh---hhhcCCCHHHHHHHHHHHHHcCCCC--
Q 008492 230 DRVAEVALT---KVGEFNSQNVANVAGAFASMQHSAP--DLFSELAKRAS---DIVHTFQEQELAQVLWAFASLYEPA-- 299 (563)
Q Consensus 230 ~~la~~a~~---~~~~f~~q~LanilwAlA~L~~~~~--~L~~ala~~v~---~~l~~f~~qeLanilwAfA~l~~~~-- 299 (563)
.+|+.+..+ ....|+||+++|++.||+|.-..+. ..-..|+.++. +....|++|+|+|.|.||+|+--.+
T Consensus 774 ~aLA~rLa~~~~Lr~aL~pQ~vAn~LNALSKWPe~~~Cr~AA~~LA~rLa~dp~Lr~af~AQ~VANaLNALSKWPd~~~C 853 (2710)
T PRK14707 774 NTLAERQLREPDVRDVLKPREMTNALNALSKWPDTPACAAAASALAARVADDPRLREAFDVQHVATVLNAMSKWPDNAVC 853 (2710)
T ss_pred HHHHHHHhhCcchhhhcCHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHhcChhHHHhcCHHHHHHHHHHhccCCCchHH
Confidence 666666443 3467999999999999999987654 44455666655 3346799999999999999985433
Q ss_pred hhHHHHHHHHhhhcchhhhhH-HHHhhhhhccCCCCCCCC--cc----cchhc---cCCCCCCCHHHHHHHHHHHHhcCC
Q 008492 300 DPLLESLDNAFKDATQFTCCL-NKALSNCNENGGVKSSGD--AD----SEGSL---SSPVLSFNRDQLGNIAWSYAVLGQ 369 (563)
Q Consensus 300 ~~L~~al~~~~~~~~~f~~~l-~~~vs~~~~a~~~~~~~~--L~----~~~~~---~~~l~~f~~qeLanilWSLA~Lg~ 369 (563)
..--.+|+.++...+++...+ ++.+++..-++++.+... -. +...+ ......|++|+++|++.+|++...
T Consensus 854 r~AA~aLA~RLa~e~~LR~aL~~QevantLNALSKWPd~~~C~~AA~aLA~rL~~d~~Lrqal~aQ~VAN~LNALSKWPd 933 (2710)
T PRK14707 854 AAAAGAMAERLADEPELRHTLTAHGVVIVLNALSKWPNVPVCAAAASALAERLADEPELRKALSAHRVATALNALSKWPD 933 (2710)
T ss_pred HHHHHHHHHHHhcChhhhhccchHHHHHHHhhhccCCCcHHHHHHHHHHHHHHhcCHHHHhhccHHHHHHHHhhhccCCC
Confidence 223345555555544332211 233333332222211110 00 01111 123468999999999999998876
Q ss_pred CC
Q 008492 370 MD 371 (563)
Q Consensus 370 ~d 371 (563)
-+
T Consensus 934 ~~ 935 (2710)
T PRK14707 934 IP 935 (2710)
T ss_pred ch
Confidence 43
No 7
>PRK14707 hypothetical protein; Provisional
Probab=98.78 E-value=5.9e-08 Score=115.74 Aligned_cols=176 Identities=15% Similarity=0.137 Sum_probs=120.1
Q ss_pred CCCCChhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHH---HhhCCCCCHHHHHHHHHHHHHcCCCcCCHHH
Q 008492 152 PSPLSPLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIA---MTALPECSAQGISNIAWALSKIGGELLYLSE 228 (563)
Q Consensus 152 ~~~fn~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~---~~~l~~~~~q~LsNilWAlakLg~~~~~~~~ 228 (563)
...||+++++++|+.|.|..... ..++. ...|.+.+ ......|+||+|+|++.+|+|.-..+.....
T Consensus 661 ~~~fnaQ~vAn~LNALSKWPe~e---------~Cr~A-a~~LA~rLa~~~~Lr~al~pQ~vAN~LNALSKWP~~~~Cr~A 730 (2710)
T PRK14707 661 RKTFNSLDVANALNALSKWPDTP---------VCAAA-AGGMAERLAADPGLRKELNPVDVANALNALSKWPRTPVCAAV 730 (2710)
T ss_pred HhhcchHHHHHHHHhhhcCCCch---------HHHHH-HHHHHHHHhcChhhHhhcCHHHHHHHHhhhhcCCCcHHHHHH
Confidence 35899999999999999985431 11110 11222221 2344679999999999999999876654333
Q ss_pred HHHHHHHHH---HhhCCCChHHHHHHHHHHHHCCCCC--HHHHHHHHHHHhhh---hcCCCHHHHHHHHHHHHHcCCCCh
Q 008492 229 MDRVAEVAL---TKVGEFNSQNVANVAGAFASMQHSA--PDLFSELAKRASDI---VHTFQEQELAQVLWAFASLYEPAD 300 (563)
Q Consensus 229 l~~la~~a~---~~~~~f~~q~LanilwAlA~L~~~~--~~L~~ala~~v~~~---l~~f~~qeLanilwAfA~l~~~~~ 300 (563)
...|+.++. .....|++|+|+|.+.||+|.-..+ ..--.+++.++.+. ...|+||+++|+|.||+|+-..+.
T Consensus 731 A~~LA~rL~~~p~l~~a~~aQevANaLNALSKWPd~~~C~~AA~aLA~rLa~~~~Lr~aL~pQ~vAn~LNALSKWPe~~~ 810 (2710)
T PRK14707 731 ASALAARVVAEPRLRKAFDAQQVATALNALSKWPDNQACAAAANTLAERQLREPDVRDVLKPREMTNALNALSKWPDTPA 810 (2710)
T ss_pred HHHHHHHHhcChhhhhhcCHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHhhCcchhhhcCHHHHHHHHHHhhcCCCchH
Confidence 455666553 3457899999999999999988653 34556677666532 467999999999999999975431
Q ss_pred --hHHHHHHHHhhhcchhhhhHHHHhhhhhccCCCCCCCCcccchhccCCCCCCCHHHHHHHHHHHHhcCC
Q 008492 301 --PLLESLDNAFKDATQFTCCLNKALSNCNENGGVKSSGDADSEGSLSSPVLSFNRDQLGNIAWSYAVLGQ 369 (563)
Q Consensus 301 --~L~~al~~~~~~~~~f~~~l~~~vs~~~~a~~~~~~~~L~~~~~~~~~l~~f~~qeLanilWSLA~Lg~ 369 (563)
..-..|+.++... ......|++|+++|++.+|++..-
T Consensus 811 Cr~AA~~LA~rLa~d--------------------------------p~Lr~af~AQ~VANaLNALSKWPd 849 (2710)
T PRK14707 811 CAAAASALAARVADD--------------------------------PRLREAFDVQHVATVLNAMSKWPD 849 (2710)
T ss_pred HHHHHHHHHHHHhcC--------------------------------hhHHHhcCHHHHHHHHHHhccCCC
Confidence 1112222222211 112356999999999999999874
No 8
>PF04480 DUF559: Protein of unknown function (DUF559); InterPro: IPR007569 This entry represents a protein of unknown function, but is thought to be a DNA mismatch repair endonuclease. ; PDB: 3R3P_B 3HRL_A.
Probab=98.78 E-value=4.7e-08 Score=85.84 Aligned_cols=93 Identities=22% Similarity=0.390 Sum_probs=64.6
Q ss_pred CCCHHHHHHHHHHHhc---CCcceeeccccceeeeEeeCCCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEE
Q 008492 443 VTSSFQKEVARLLVST---GLNWIREYAVDGYTVDAVLVDKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVS 519 (563)
Q Consensus 443 ~~S~lq~~V~~~L~~l---G~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~ 519 (563)
..|.....+...|... |+.+...+.+++|.+|++.++.+||||+||+.|+.. ......|.+.|...||.|++
T Consensus 12 ~~s~~E~~Lw~~Lr~~~~~g~~f~~q~~ig~y~~Df~~~~~kl~IE~DG~~H~~~-----~~~D~~R~~~L~~~Gw~VlR 86 (108)
T PF04480_consen 12 NMSEAERKLWRELRRRRLGGYKFRRQVPIGRYRVDFACPEAKLAIEIDGRQHSTP-----RERDRRRDNWLEALGWTVLR 86 (108)
T ss_dssp ---HHHHHHHHHHGGGTTTT--EEEEEEETTEEEEEEETCTTEEEEEE-S-TT-------HHHHHHHHHHHHHTT-EEEE
T ss_pred CCCHHHHHHHHHHHhcCCCCceEEEecCCCCEEEeeccCcccEEEEEcCccccch-----HHhhHHHHHHHHHCCCEEEE
Confidence 3566666666767654 455566677899999999999999999999998764 55789999999999999999
Q ss_pred EehhhHHhhcChHHHHHHHHHHH
Q 008492 520 LSHQEWEELQGSFEQLDYLRVIL 542 (563)
Q Consensus 520 Vpy~EW~~l~~~~ek~~YLr~~L 542 (563)
++..+.. ...++-+..+...|
T Consensus 87 ~~~~~v~--~~~~~vv~~I~~~i 107 (108)
T PF04480_consen 87 FTAEDVR--EDPEAVVEQIRAAI 107 (108)
T ss_dssp EEHHHHH--HGHHHHHHHHHHHH
T ss_pred eeHHHHH--hCHHHHHHHHHHHh
Confidence 9888764 22234555555544
No 9
>cd01038 Endonuclease_DUF559 Domain of unknown function, appears to be related to a diverse group of endonucleases.
Probab=98.72 E-value=1e-07 Score=83.69 Aligned_cols=80 Identities=19% Similarity=0.297 Sum_probs=69.8
Q ss_pred CCCCHHHHHHHHHHHhc---CCcceeeccccceeeeEeeCCCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEE
Q 008492 442 KVTSSFQKEVARLLVST---GLNWIREYAVDGYTVDAVLVDKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVV 518 (563)
Q Consensus 442 ~~~S~lq~~V~~~L~~l---G~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv 518 (563)
...|+....+...|... |+.+...+.+++|.+|+++++.+++||+||++|+... .....|...|+..||.|+
T Consensus 11 ~~~S~~E~~l~~~L~~~~~~g~~~~~q~~i~~~~vD~~~~~~kl~IE~DG~~H~~~~-----~~D~~R~~~L~~~Gw~vl 85 (108)
T cd01038 11 RNQTDAERLLWQELRRRRLNGFKFRRQAPIGRYIVDFACPEAKLVVELDGGQHDEQI-----AYDAERDAWLEARGFRVL 85 (108)
T ss_pred cCCCHHHHHHHHHHHhcccCCCceeeccCCCCcEeeeEccccCEEEEEeCcccCchH-----HHHHHHHHHHHHCCCEEE
Confidence 45789999999999987 7777777778889999999999999999999886532 689999999999999999
Q ss_pred EEehhhHH
Q 008492 519 SLSHQEWE 526 (563)
Q Consensus 519 ~Vpy~EW~ 526 (563)
.+.+.++.
T Consensus 86 R~~~~dv~ 93 (108)
T cd01038 86 RFWNNEVL 93 (108)
T ss_pred EEEHHHHh
Confidence 99998874
No 10
>PRK09767 hypothetical protein; Provisional
Probab=98.54 E-value=6.8e-07 Score=79.36 Aligned_cols=93 Identities=19% Similarity=0.323 Sum_probs=72.7
Q ss_pred CHHHHHHHHHHHh--c-CCcceeeccccceeeeEeeCCCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEe
Q 008492 445 SSFQKEVARLLVS--T-GLNWIREYAVDGYTVDAVLVDKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLS 521 (563)
Q Consensus 445 S~lq~~V~~~L~~--l-G~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vp 521 (563)
+.-.+.+-..|+. + |+.+...+.+++|.+||+.+..|+|||+||.+|... ......|...|+..||.|+.+.
T Consensus 17 T~aE~~LW~~lr~~~~~g~kFrRQ~pig~yi~DF~c~~~rLaIE~DG~~H~~~-----~~~D~~R~~~L~~~G~~VlRf~ 91 (117)
T PRK09767 17 TLQERKLWRYLRSRRFGDFKFRRQHPVGSYILDFACCSARVVVELDGGQHDLA-----VAYDTRRTSWLESQGWTVLRFW 91 (117)
T ss_pred CHHHHHHHHHHHhcccCCCeeEecccccCeeeceeccccCEEEEEeCcccchh-----HHHHHHHHHHHHHCCCEEEEEE
Confidence 3444455556665 3 788888999999999999999999999999999431 3679999999999999999998
Q ss_pred hhhHHhhcChHHHHHHHHHHHHH
Q 008492 522 HQEWEELQGSFEQLDYLRVILKD 544 (563)
Q Consensus 522 y~EW~~l~~~~ek~~YLr~~L~~ 544 (563)
..+-. .+.+.-++.+...|..
T Consensus 92 n~dV~--~~~~~Vl~~I~~~l~~ 112 (117)
T PRK09767 92 NNEID--CNEEAVLEIILQELNR 112 (117)
T ss_pred HHHHH--hCHHHHHHHHHHHHhc
Confidence 87754 3445667777666654
No 11
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=98.44 E-value=5.4e-07 Score=79.88 Aligned_cols=83 Identities=16% Similarity=0.123 Sum_probs=65.3
Q ss_pred CCCHHHHHHHHHHHhcCCcceeeccccceeeeEeeCCCceEEEEcCCC-CcccCC---C-------------CCccchHH
Q 008492 443 VTSSFQKEVARLLVSTGLNWIREYAVDGYTVDAVLVDKKVAFEIDGPT-HFSRNT---G-------------VPLGHTML 505 (563)
Q Consensus 443 ~~S~lq~~V~~~L~~lG~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~-Hf~~ns---~-------------~~lG~t~l 505 (563)
..|+....|...|...|+.+.......+|.+|+++|+.+|||||||.. |.+.-. . ...-....
T Consensus 16 ~~s~~E~~lr~~L~~~Gl~~r~~~~~~~~~~D~~~~~~klaIe~DG~~wH~~~~~~~~~~~~~~~~w~~k~~~~~~rD~~ 95 (115)
T cd00221 16 KDTKPERAVRSALWELGYRFRKQDKDLPGKPDIVVPGYRLAIFVDGCFWHGHPCHKRKPPPKNTEFWLEKIERNVERDRR 95 (115)
T ss_pred CCCHHHHHHHHHHHHCCCEEEeCCCCCCcccCEEecCCCEEEEEcCccccCCccccccCCCccHHHHHHHHHHHHHHHHH
Confidence 367888899999999999887776667899999999999999999986 554311 0 11235677
Q ss_pred HHHHHHHCCCEEEEEehhhH
Q 008492 506 KRRYIAAAGWNVVSLSHQEW 525 (563)
Q Consensus 506 K~RlL~~~Gy~Vv~Vpy~EW 525 (563)
+...|+.+||.|+.|.-.||
T Consensus 96 r~~~L~~~GW~ViRvw~~e~ 115 (115)
T cd00221 96 VQAALERLGWRVLRVWECEL 115 (115)
T ss_pred HHHHHHHCcCEEEEEeCCcC
Confidence 88889999999999966554
No 12
>COG2852 Very-short-patch-repair endonuclease [Replication, recombination, and repair]
Probab=98.24 E-value=1.9e-06 Score=75.74 Aligned_cols=63 Identities=22% Similarity=0.358 Sum_probs=55.6
Q ss_pred CCcceeeccccceeeeEeeCCCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEehhhHH
Q 008492 459 GLNWIREYAVDGYTVDAVLVDKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLSHQEWE 526 (563)
Q Consensus 459 G~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vpy~EW~ 526 (563)
|+.+.....+++|.|||+.++.|++||+||+.|- ..-+..+-|.+.|...||.|++++..|-.
T Consensus 44 g~KFrRQ~~ig~yivDF~c~~~klIvElDG~qH~-----~~~~~Da~Rd~~L~~~G~~VLRf~N~ev~ 106 (129)
T COG2852 44 GFKFRRQQPIGRYIVDFACRDAKLIVELDGGQHE-----EREEYDAERDAFLESQGFTVLRFWNDEVL 106 (129)
T ss_pred CeeEEEeeeccCEEEEEEcCCccEEEEecCccch-----hhhhhhHHHHHHHHhCCceEEEeccHHHH
Confidence 7888888899999999999999999999999992 23468999999999999999999876643
No 13
>PF06743 FAST_1: FAST kinase-like protein, subdomain 1; InterPro: IPR010622 This entry represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins.; GO: 0004672 protein kinase activity
Probab=98.13 E-value=6.5e-06 Score=66.67 Aligned_cols=59 Identities=22% Similarity=0.520 Sum_probs=46.1
Q ss_pred HHHHHHHHHHCCCCCH---HHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHcCCCChhHHHHH
Q 008492 248 VANVAGAFASMQHSAP---DLFSELAKRASDIVHTFQEQELAQVLWAFASLYEPADPLLESL 306 (563)
Q Consensus 248 LanilwAlA~L~~~~~---~L~~ala~~v~~~l~~f~~qeLanilwAfA~l~~~~~~L~~al 306 (563)
|++++|+||+|+|.++ ++|+.+...+.+.++.++|+++.+++|+++-+++.|..+++.+
T Consensus 1 i~~il~~fa~LNy~P~~~~~f~~~~~~~L~~~l~~~~p~~ll~~v~Sl~~l~~~p~~~l~~v 62 (71)
T PF06743_consen 1 IASILLPFARLNYQPPNAEEFFEKLIERLESYLDEFSPEDLLDLVWSLCLLQRFPEDLLNKV 62 (71)
T ss_pred CHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhhCCHHHHHHH
Confidence 4677888888887764 5778888888888888888888888888888888887776654
No 14
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=98.11 E-value=8.2e-06 Score=72.06 Aligned_cols=74 Identities=24% Similarity=0.273 Sum_probs=58.2
Q ss_pred HHHHHHHHHhcCCcceeeccccceeeeEeeCCCceEEEEcCCC---CcccCCCCC--------------ccchHHHHHHH
Q 008492 448 QKEVARLLVSTGLNWIREYAVDGYTVDAVLVDKKVAFEIDGPT---HFSRNTGVP--------------LGHTMLKRRYI 510 (563)
Q Consensus 448 q~~V~~~L~~lG~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp~---Hf~~ns~~~--------------lG~t~lK~RlL 510 (563)
-..|-..|..+|+.+...+...+|.+||++++.|+||||||-. |-|.....| .....-+...|
T Consensus 24 E~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~klaIfVDGcfWHgh~c~~~~~pk~n~~fW~~Ki~~n~~rD~~~~~~L 103 (117)
T TIGR00632 24 EKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKTRTDFWSPKIEKNVERDRRVNSRL 103 (117)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcccEEecCCCEEEEEcccccccCCcccccCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445567888999998888888899999999999999999973 335322111 24677888999
Q ss_pred HHCCCEEEEEe
Q 008492 511 AAAGWNVVSLS 521 (563)
Q Consensus 511 ~~~Gy~Vv~Vp 521 (563)
+.+||+|+.|.
T Consensus 104 ~~~Gw~Vlr~W 114 (117)
T TIGR00632 104 QELGWRVLRVW 114 (117)
T ss_pred HHCcCEEEEEe
Confidence 99999999984
No 15
>PF06743 FAST_1: FAST kinase-like protein, subdomain 1; InterPro: IPR010622 This entry represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins.; GO: 0004672 protein kinase activity
Probab=97.96 E-value=3.1e-05 Score=62.72 Aligned_cols=62 Identities=15% Similarity=0.281 Sum_probs=55.1
Q ss_pred HHHHHHHHHHcCCCcCCHHH-HHHHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHH
Q 008492 209 ISNIAWALSKIGGELLYLSE-MDRVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELA 270 (563)
Q Consensus 209 LsNilWAlakLg~~~~~~~~-l~~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala 270 (563)
|++++|+||+|++.|...++ ++.+.+....+++.++|+++.+++||++-+++.++++.+.+.
T Consensus 1 i~~il~~fa~LNy~P~~~~~f~~~~~~~L~~~l~~~~p~~ll~~v~Sl~~l~~~p~~~l~~vf 63 (71)
T PF06743_consen 1 IASILLPFARLNYQPPNAEEFFEKLIERLESYLDEFSPEDLLDLVWSLCLLQRFPEDLLNKVF 63 (71)
T ss_pred CHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhhCCHHHHHHHc
Confidence 57899999999999886554 588888899999999999999999999999999998887653
No 16
>PF08368 FAST_2: FAST kinase-like protein, subdomain 2; InterPro: IPR013579 This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (2.7.1 from EC) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Probab=97.21 E-value=0.0012 Score=56.42 Aligned_cols=74 Identities=26% Similarity=0.285 Sum_probs=49.9
Q ss_pred HHHHHHHHhhhhCCCcccc-cchHHHHHHHHhccccccCCCCCCHHHHHHHHHHHhc-CCc-c-eee-ccccceeeeEee
Q 008492 403 QVHLVNQCLKLEHPHLQLA-LSSVLEEKIASAGKTKRFNQKVTSSFQKEVARLLVST-GLN-W-IRE-YAVDGYTVDAVL 477 (563)
Q Consensus 403 QL~~~n~~l~lE~p~~~~~-l~~~l~~~l~~a~~~~~~~~~~~S~lq~~V~~~L~~l-G~~-~-~~E-~~~~G~~vDi~~ 477 (563)
+|.++|.++++|+|++.++ +++.+........ ......+..|++|.+|.++|.++ |.+ + ... .++.||+||+.+
T Consensus 5 kL~~Ln~~v~LE~p~y~gp~L~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~~~L~~lLg~~~~~~~~v~tp~gy~iD~E~ 83 (93)
T PF08368_consen 5 KLLQLNAAVQLECPEYQGPRLPPRYQVKSFLVP-QSSKKEKQPSPLQQEVQEALKSLLGGENYFRSNVITPYGYTIDFEI 83 (93)
T ss_pred HHHHHHHHHhhcCCCCcCCCCChHHhhhhhhcc-ccccccCCCchHHHHHHHHHHHHhCCccceEEccccCCCceEEEEE
Confidence 6788999999999999876 5443321111110 01112356789999999999996 644 4 333 478999999987
No 17
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=96.67 E-value=0.0083 Score=47.71 Aligned_cols=73 Identities=21% Similarity=0.264 Sum_probs=51.2
Q ss_pred HHHHHHHHhcCCccee---eccccceeeeEeeCCCceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEe
Q 008492 449 KEVARLLVSTGLNWIR---EYAVDGYTVDAVLVDKKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLS 521 (563)
Q Consensus 449 ~~V~~~L~~lG~~~~~---E~~~~G~~vDi~~~~~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vp 521 (563)
..+...|...|..+.. .....++.+|++++..+++|||||..|.............-+...|...||+++.+.
T Consensus 4 ~~l~~~l~~~~~~~~~~~~~~~~~~~~pDf~~~~~~~~ie~kg~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~ 79 (80)
T cd01037 4 RLLWKLLRAKGLAVRRFRRQVPIGSYIPDFVCPSAKLVIELKGTFHDGLLRKLRTSEKQERIAFLEADGKKVLRFW 79 (80)
T ss_pred HHHHHHHHhCCCCcEEeecCCCCCCCccCEEccCCCEEEEEECccccCchhhhhhcchHHHHHHHHHCCCEEEEEe
Confidence 3456677777776543 445677999999999999999999987654321111111356778999999998873
No 18
>PF10881 DUF2726: Protein of unknown function (DUF2726); InterPro: IPR024402 This domain found in bacterial proteins has no known function.
Probab=94.48 E-value=0.055 Score=48.56 Aligned_cols=56 Identities=23% Similarity=0.331 Sum_probs=44.5
Q ss_pred ccceeeeEeeCC-----CceEEEEcCCCCcccCCCCCccchHHHHHHHHHCCCEEEEEehhhHH
Q 008492 468 VDGYTVDAVLVD-----KKVAFEIDGPTHFSRNTGVPLGHTMLKRRYIAAAGWNVVSLSHQEWE 526 (563)
Q Consensus 468 ~~G~~vDi~~~~-----~rVAIEvdGp~Hf~~ns~~~lG~t~lK~RlL~~~Gy~Vv~Vpy~EW~ 526 (563)
+.+..+|+++-+ -..|||+||++|... .......+|++.|+..|..+++++-.+..
T Consensus 53 ~~~~~vDFvv~d~~~~~p~~vIEld~~~h~~~---~~~~rD~~k~~~l~~agiplir~~~~~~~ 113 (126)
T PF10881_consen 53 INQKHVDFVVCDKRDGRPVAVIELDGSSHDQE---KRQERDEFKDRVLKKAGIPLIRISPKDSY 113 (126)
T ss_pred hcCCCccEEEEECCCCcEEEEEEecCccccch---hhHHHHHHHHHHHHHCCCCEEEEeCCCCC
Confidence 355678998853 469999999999843 34458999999999999999999776543
No 19
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=93.34 E-value=1 Score=40.51 Aligned_cols=100 Identities=19% Similarity=0.235 Sum_probs=61.8
Q ss_pred CHHHHHHHHHHHhcCCcceeeccccceeeeEeeCCCceEEEEcCC---CCcccCCCCC----------ccchHHHHH---
Q 008492 445 SSFQKEVARLLVSTGLNWIREYAVDGYTVDAVLVDKKVAFEIDGP---THFSRNTGVP----------LGHTMLKRR--- 508 (563)
Q Consensus 445 S~lq~~V~~~L~~lG~~~~~E~~~~G~~vDi~~~~~rVAIEvdGp---~Hf~~ns~~~----------lG~t~lK~R--- 508 (563)
+.-...+...|..+|+.+...-.--+=.-||++|+.+++|-|+|- +|-|...+.| .|+..-|++
T Consensus 22 TkpE~~lr~~L~~~G~rfR~~~~~lpGkPDiVl~~y~~viFvHGCFWh~H~c~~a~vPksnt~fWleKi~kNveRD~r~~ 101 (150)
T COG3727 22 TKPEKRLRSLLTGQGLRFRVQDKDLPGKPDIVLPKYRCVIFVHGCFWHGHHCYLAKVPKSNTEFWLEKIGKNVERDERDI 101 (150)
T ss_pred ccHHHHHHHHHhhcceEEEecCCCCCCCCCEeecCceEEEEEeeeeccCCccccccCCCcchHHHHHHHhhhhhhhHHHH
Confidence 344556777888899887654322222459999999999999995 3446554333 244444443
Q ss_pred -HHHHCCCEEEEEehhhHHhhcChHHHHHHHHHHHHHHhcc
Q 008492 509 -YIAAAGWNVVSLSHQEWEELQGSFEQLDYLRVILKDYIGG 548 (563)
Q Consensus 509 -lL~~~Gy~Vv~Vpy~EW~~l~~~~ek~~YLr~~L~~~~~~ 548 (563)
-|+.+||+|+.|--.+.. ......-+-+.|..++++
T Consensus 102 ~~L~~~GwrvlvVWEC~~r----~kas~a~~l~rl~~~~s~ 138 (150)
T COG3727 102 KRLQQLGWRVLVVWECALR----KKASDAARLERLEEWISG 138 (150)
T ss_pred HHHHHcCCeEEEEEeeech----HHHhHHHHHHHHHHHHhc
Confidence 488899999999444442 223334444455555444
No 20
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=92.25 E-value=0.065 Score=37.53 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=15.7
Q ss_pred hHHHHHHHHHhhCCCCCHHHHHHHH
Q 008492 189 EMSMLVAIAMTALPECSAQGISNIA 213 (563)
Q Consensus 189 ~~~~L~~~~~~~l~~~~~q~LsNil 213 (563)
.-..|+..+.+.+++|+||+|||++
T Consensus 13 L~~~L~~aV~~~a~~Fn~QeiaNtL 37 (37)
T PF07671_consen 13 LSDRLLDAVRRNAEQFNPQEIANTL 37 (37)
T ss_pred chHHHHHHHHHHHHHcCHHHHhhcC
Confidence 3455666666666667777776653
No 21
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.40 E-value=31 Score=38.46 Aligned_cols=139 Identities=17% Similarity=0.247 Sum_probs=83.8
Q ss_pred hhhHHHHHHHHHhcccccchhhhhhhhhccchhHHHHHHHHHhhCCCCCHHHHHHHHHHHHHcCCCcCC-HHHH--HHHH
Q 008492 157 PLNIATALHRIAKNMEKVSMMTTHRLAFTRQREMSMLVAIAMTALPECSAQGISNIAWALSKIGGELLY-LSEM--DRVA 233 (563)
Q Consensus 157 ~vn~atAL~RLak~~~~~s~~~~~r~~~ar~~~~~~L~~~~~~~l~~~~~q~LsNilWAlakLg~~~~~-~~~l--~~la 233 (563)
-+..|+||.-||...... ++.. ........| ...+..-+..=--..+||++.+-++++. .+.+ -.+.
T Consensus 127 q~eAAWaLTnIAsgtse~----T~~v--v~agavp~f----i~Ll~s~~~~v~eQavWALgNIagds~~~Rd~vl~~g~l 196 (514)
T KOG0166|consen 127 QFEAAWALTNIASGTSEQ----TKVV--VDAGAVPIF----IQLLSSPSADVREQAVWALGNIAGDSPDCRDYVLSCGAL 196 (514)
T ss_pred HHHHHHHHHHHhcCchhh----cccc--ccCCchHHH----HHHhcCCcHHHHHHHHHHHhccccCChHHHHHHHhhcch
Confidence 478999999999865432 2221 111111112 2333344444445779999999876532 1111 0111
Q ss_pred HHHHHhhCCCCh-HHHHHHHHHHHHCCCC--CH---HHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHcCCCChhHHHH
Q 008492 234 EVALTKVGEFNS-QNVANVAGAFASMQHS--AP---DLFSELAKRASDIVHTFQEQELAQVLWAFASLYEPADPLLES 305 (563)
Q Consensus 234 ~~a~~~~~~f~~-q~LanilwAlA~L~~~--~~---~L~~ala~~v~~~l~~f~~qeLanilwAfA~l~~~~~~L~~a 305 (563)
.-.+..+....+ .-+-|+.|++..|--. |+ +-...+...+...++.-++.-++.++||++.+--.+.+....
T Consensus 197 ~pLl~~l~~~~~~~~lRn~tW~LsNlcrgk~P~P~~~~v~~iLp~L~~ll~~~D~~Vl~Da~WAlsyLsdg~ne~iq~ 274 (514)
T KOG0166|consen 197 DPLLRLLNKSDKLSMLRNATWTLSNLCRGKNPSPPFDVVAPILPALLRLLHSTDEEVLTDACWALSYLTDGSNEKIQM 274 (514)
T ss_pred HHHHHHhccccchHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCChHHHHH
Confidence 222333444433 6788899999999643 32 445556667778889999999999999999996555444443
No 22
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=90.17 E-value=0.16 Score=35.55 Aligned_cols=23 Identities=30% Similarity=0.511 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhCCCChHHHHHHH
Q 008492 230 DRVAEVALTKVGEFNSQNVANVA 252 (563)
Q Consensus 230 ~~la~~a~~~~~~f~~q~Lanil 252 (563)
+.|..++..+++.|+||++||++
T Consensus 15 ~~L~~aV~~~a~~Fn~QeiaNtL 37 (37)
T PF07671_consen 15 DRLLDAVRRNAEQFNPQEIANTL 37 (37)
T ss_pred HHHHHHHHHHHHHcCHHHHhhcC
Confidence 55666677888899999999874
No 23
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=89.08 E-value=0.56 Score=38.18 Aligned_cols=45 Identities=24% Similarity=0.297 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHhcCCcceeec-cccceeeeEeeCCCceEEEEcCCC
Q 008492 445 SSFQKEVARLLVSTGLNWIREY-AVDGYTVDAVLVDKKVAFEIDGPT 490 (563)
Q Consensus 445 S~lq~~V~~~L~~lG~~~~~E~-~~~G~~vDi~~~~~rVAIEvdGp~ 490 (563)
+.--..|.+.|..+|+.+...+ .+.| ..||++++.++||.|||-.
T Consensus 21 TkpE~~lr~~L~~~G~RyR~~~~~lpG-~PDiv~~~~k~aIFVdGCF 66 (75)
T PF03852_consen 21 TKPELALRRALHALGLRYRLNRKDLPG-KPDIVFPKYKIAIFVDGCF 66 (75)
T ss_dssp -HHHHHHHHHHHHTT--EEES-TTSTT---SEEEGGGTEEEEEE-TT
T ss_pred ChHHHHHHHHHHhcCCEEEEccCcCCC-CCCEEECCCCEEEEEecce
Confidence 3455667888999999987765 3444 7799999999999999964
No 24
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.34 E-value=0.91 Score=50.28 Aligned_cols=32 Identities=9% Similarity=0.197 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhhhhcC---CCHHHHHHHHHHHHHc
Q 008492 264 DLFSELAKRASDIVHT---FQEQELAQVLWAFASL 295 (563)
Q Consensus 264 ~L~~ala~~v~~~l~~---f~~qeLanilwAfA~l 295 (563)
.||-+|-.++....+. =+.-+.|.++|+|--.
T Consensus 340 ~FyL~l~r~m~~l~~RGC~rTA~E~cKlllsLdp~ 374 (665)
T KOG2422|consen 340 QFYLALFRYMQSLAQRGCWRTALEWCKLLLSLDPS 374 (665)
T ss_pred HHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCc
Confidence 5666666655432221 2455666666666544
No 25
>PHA00159 endonuclease I
Probab=76.34 E-value=3.7 Score=37.28 Aligned_cols=47 Identities=23% Similarity=0.375 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHhcCCcceeec-----cc----cceeeeEeeCCCceEEEEcCCC
Q 008492 443 VTSSFQKEVARLLVSTGLNWIREY-----AV----DGYTVDAVLVDKKVAFEIDGPT 490 (563)
Q Consensus 443 ~~S~lq~~V~~~L~~lG~~~~~E~-----~~----~G~~vDi~~~~~rVAIEvdGp~ 490 (563)
-.|.++..|+..|...|+.+..|. ++ .-|+-||++|+ -|+||+-|-.
T Consensus 15 fRSgLE~k~ak~Le~~gv~~~yE~~ki~y~~pA~~~~YTPDF~Lpn-GiiiEvKG~w 70 (148)
T PHA00159 15 FRSGLEDKVSKQLEKKGVKFDYELWKIPYVIPASDHKYTPDFLLPN-GIIIETKGLW 70 (148)
T ss_pred ccchHHHHHHHHHHhcCCCeEeeeeeeeeeccCCCCeeCCceecCC-CCEEEecccC
Confidence 369999999999999999987773 22 23899999997 6779999854
No 26
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.78 E-value=2.7 Score=46.66 Aligned_cols=15 Identities=13% Similarity=0.164 Sum_probs=7.1
Q ss_pred CCHHHHHHHHHHHHH
Q 008492 204 CSAQGISNIAWALSK 218 (563)
Q Consensus 204 ~~~q~LsNilWAlak 218 (563)
+...-|.-.+|+|-.
T Consensus 302 ~aadLieR~Ly~~d~ 316 (665)
T KOG2422|consen 302 MAADLIERGLYVFDR 316 (665)
T ss_pred hHHHHHHHHHHHHHH
Confidence 334444455555544
No 27
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=60.58 E-value=17 Score=33.30 Aligned_cols=46 Identities=30% Similarity=0.502 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhcCCcceee-----ccc---c-ceeeeEeeCCCceEEEEcCCC
Q 008492 444 TSSFQKEVARLLVSTGLNWIRE-----YAV---D-GYTVDAVLVDKKVAFEIDGPT 490 (563)
Q Consensus 444 ~S~lq~~V~~~L~~lG~~~~~E-----~~~---~-G~~vDi~~~~~rVAIEvdGp~ 490 (563)
.|.|-.+|+..|..+|+.+..| |++ . -|+-|+++|+ -|.||.-|..
T Consensus 16 RSgLEekva~~L~~~gv~~~yE~~ki~Yvipa~~h~YtPDF~Lpn-giiiEtKG~f 70 (149)
T PF05367_consen 16 RSGLEEKVAKQLEKLGVKYEYESWKIPYVIPASEHKYTPDFVLPN-GIIIETKGRF 70 (149)
T ss_dssp --HHHHHHHHHHHHTT---EES-EEEEEEEEEEEEEE--SEE-TT-SEEEEEESS-
T ss_pred chhHHHHHHHHHHHcCCCceeeeeeeeeEeeccccccCCCEEccC-ceEEEeeecc
Confidence 6889999999999999887666 233 2 2888999997 4999999976
No 28
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=56.95 E-value=2.7e+02 Score=29.66 Aligned_cols=174 Identities=16% Similarity=0.277 Sum_probs=97.5
Q ss_pred HHHhhhhcCCCCchhhhhhHHHHHhcccCHHHHHHHHHHHHHhhcCCCCCCCCChhhHHHHHHHHHhcccccchhhhhhh
Q 008492 103 FVHRLSQFSGPSNRRKEINLNKDIVDAQTAQEVLEVIAEMITAVGKGLSPSPLSPLNIATALHRIAKNMEKVSMMTTHRL 182 (563)
Q Consensus 103 ~~~~~~~~~~ps~~~~~~~Ln~~i~~a~s~~evl~lv~~~~~~~~~~~~~~~fn~vn~atAL~RLak~~~~~s~~~~~r~ 182 (563)
|-+.||.=..|+.. ...+|.-+....+...++ ++ .+-....|+||.-+|.-.++ +++..
T Consensus 95 FR~~LS~E~~PPIq--------~VIdaGvVpRfvefm~~~----q~-----~mlqfEAaWalTNiaSGtt~----QTkvV 153 (526)
T COG5064 95 FRKLLSKETSPPIQ--------PVIDAGVVPRFVEFMDEI----QR-----DMLQFEAAWALTNIASGTTQ----QTKVV 153 (526)
T ss_pred HHHHhccccCCCch--------hHHhccccHHHHHHHHhc----ch-----hHHHHHHHHHHhhhccCccc----ceEEE
Confidence 55555555555543 344555555555555443 12 34445889999999986544 12221
Q ss_pred -hhccchhHHHHHHHHHhhCCCCCHHHHHHHHHHHHHcCCCcCC-HH------HHHHHHHHHHHhhCCCChHHHHHHHHH
Q 008492 183 -AFTRQREMSMLVAIAMTALPECSAQGISNIAWALSKIGGELLY-LS------EMDRVAEVALTKVGEFNSQNVANVAGA 254 (563)
Q Consensus 183 -~~ar~~~~~~L~~~~~~~l~~~~~q~LsNilWAlakLg~~~~~-~~------~l~~la~~a~~~~~~f~~q~LanilwA 254 (563)
.....|.| .+.+..-+-.-.-..+|||+.+.+++.- .+ .++-+........ -.-.=+-|..|.
T Consensus 154 vd~~AVPlf-------iqlL~s~~~~V~eQavWALGNiAGDS~~~RD~vL~~galeplL~ll~ss~--~~ismlRn~TWt 224 (526)
T COG5064 154 VDAGAVPLF-------IQLLSSTEDDVREQAVWALGNIAGDSEGCRDYVLQCGALEPLLGLLLSSA--IHISMLRNATWT 224 (526)
T ss_pred EeCCchHHH-------HHHHcCchHHHHHHHHHHhccccCCchhHHHHHHhcCchHHHHHHHHhcc--chHHHHHHhHHH
Confidence 11112233 2223333333344679999999876431 11 1233333222111 112456788999
Q ss_pred HHHCCCC--CHHHHHHHHHH---HhhhhcCCCHHHHHHHHHHHHHcCCCChhHHHHH
Q 008492 255 FASMQHS--APDLFSELAKR---ASDIVHTFQEQELAQVLWAFASLYEPADPLLESL 306 (563)
Q Consensus 255 lA~L~~~--~~~L~~ala~~---v~~~l~~f~~qeLanilwAfA~l~~~~~~L~~al 306 (563)
++.|.-. +|+=+..+... ....+...++.-++...||++.+--.+.+-..++
T Consensus 225 LSNlcRGknP~P~w~~isqalpiL~KLiys~D~evlvDA~WAiSYlsDg~~E~i~av 281 (526)
T COG5064 225 LSNLCRGKNPPPDWSNISQALPILAKLIYSRDPEVLVDACWAISYLSDGPNEKIQAV 281 (526)
T ss_pred HHHhhCCCCCCCchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHhccCcHHHHHHH
Confidence 9999643 44445544443 4467788999999999999999977665554444
No 29
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.64 E-value=1.5e+02 Score=33.12 Aligned_cols=89 Identities=11% Similarity=0.168 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHHcCCC--cC-CHHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHHH-----HHhhhh
Q 008492 206 AQGISNIAWALSKIGGE--LL-YLSEMDRVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELAK-----RASDIV 277 (563)
Q Consensus 206 ~q~LsNilWAlakLg~~--~~-~~~~l~~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala~-----~v~~~l 277 (563)
-.-+-|++|+++.+... |. ....+..+.......+..-++.-+++++||++.|--.+++..+.+.. +++..+
T Consensus 209 ~~~lRn~tW~LsNlcrgk~P~P~~~~v~~iLp~L~~ll~~~D~~Vl~Da~WAlsyLsdg~ne~iq~vi~~gvv~~LV~lL 288 (514)
T KOG0166|consen 209 LSMLRNATWTLSNLCRGKNPSPPFDVVAPILPALLRLLHSTDEEVLTDACWALSYLTDGSNEKIQMVIDAGVVPRLVDLL 288 (514)
T ss_pred hHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCChHHHHHHHHccchHHHHHHH
Confidence 35677899999999642 21 11335566677788899999999999999999998777766665543 455666
Q ss_pred cCCCHHHHHHHHHHHHH
Q 008492 278 HTFQEQELAQVLWAFAS 294 (563)
Q Consensus 278 ~~f~~qeLanilwAfA~ 294 (563)
...+++-.+-.+-+.+.
T Consensus 289 ~~~~~~v~~PaLRaiGN 305 (514)
T KOG0166|consen 289 GHSSPKVVTPALRAIGN 305 (514)
T ss_pred cCCCcccccHHHhhccc
Confidence 66666555444444444
No 30
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=44.86 E-value=1.8e+02 Score=24.17 Aligned_cols=98 Identities=12% Similarity=0.096 Sum_probs=60.6
Q ss_pred HhhCCCCCHHHHHHHHHHHHHcCCCc-CCHHHH-H-HHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHH-----H
Q 008492 198 MTALPECSAQGISNIAWALSKIGGEL-LYLSEM-D-RVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSE-----L 269 (563)
Q Consensus 198 ~~~l~~~~~q~LsNilWAlakLg~~~-~~~~~l-~-~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~a-----l 269 (563)
...+.+-++.-..+.+|+++.+.... .....+ + .+.......+...++.-....+|+++.+-...+..... +
T Consensus 13 ~~~l~~~~~~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~~~~~~~~g~ 92 (120)
T cd00020 13 VSLLSSSDENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIVLEAGG 92 (120)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHHHHHHHHCCC
Confidence 34444556888889999999987642 111111 1 22333444455667888888999999998776533222 3
Q ss_pred HHHHhhhhcCCCHHHHHHHHHHHHHc
Q 008492 270 AKRASDIVHTFQEQELAQVLWAFASL 295 (563)
Q Consensus 270 a~~v~~~l~~f~~qeLanilwAfA~l 295 (563)
...+...+.+.+..-.-..+|++..+
T Consensus 93 l~~l~~~l~~~~~~~~~~a~~~l~~l 118 (120)
T cd00020 93 VPKLVNLLDSSNEDIQKNATGALSNL 118 (120)
T ss_pred hHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence 34455666666777677777777654
No 31
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=35.33 E-value=1.1e+02 Score=22.40 Aligned_cols=34 Identities=21% Similarity=0.464 Sum_probs=25.3
Q ss_pred HHHHHHhhhhcCCCCchhhhhhHHHHHhcccCHHHHHHHHHHH
Q 008492 100 IEEFVHRLSQFSGPSNRRKEINLNKDIVDAQTAQEVLEVIAEM 142 (563)
Q Consensus 100 ~~~~~~~~~~~~~ps~~~~~~~Ln~~i~~a~s~~evl~lv~~~ 142 (563)
.+.|++.+. +.. .|...|..|.++++++.+..++
T Consensus 6 l~~Fl~~~~-----~d~----~l~~~l~~~~~~~e~~~lA~~~ 39 (49)
T PF07862_consen 6 LKAFLEKVK-----SDP----ELREQLKACQNPEEVVALAREA 39 (49)
T ss_pred HHHHHHHHh-----cCH----HHHHHHHhcCCHHHHHHHHHHc
Confidence 455666554 222 7889999999999999997654
No 32
>PF14851 FAM176: FAM176 family
Probab=33.77 E-value=19 Score=33.67 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=14.1
Q ss_pred HhhhhHHHHHHhhhhcCCCCc
Q 008492 95 KREKTIEEFVHRLSQFSGPSN 115 (563)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~ps~ 115 (563)
.|=--||+-+|-+|-=++|..
T Consensus 123 ~rlEeRe~iirEIW~n~~~d~ 143 (153)
T PF14851_consen 123 QRLEERERIIREIWMNGQPDI 143 (153)
T ss_pred HHHHHHHHHHHHHHHhcCCCC
Confidence 344456777888887777654
No 33
>PF08597 eIF3_subunit: Translation initiation factor eIF3 subunit; InterPro: IPR013906 This shows protein subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae (Baker's yeast) protein Q05775 from SWISSPROT has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p []. ; PDB: 3BPJ_D 2KRB_B.
Probab=30.38 E-value=27 Score=35.07 Aligned_cols=26 Identities=31% Similarity=0.372 Sum_probs=19.4
Q ss_pred HHHhHHhhCcchhHHHhhhhhhhhhh
Q 008492 11 ALKSIEARGLASSMEDLIKVKKKKKK 36 (563)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 (563)
-|.+=+-|-++.+|..|.+-|.|.-|
T Consensus 177 ~L~~~~ikki~s~l~~l~nEK~K~EK 202 (245)
T PF08597_consen 177 NLTSEDIKKISSSLTVLANEKQKAEK 202 (245)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666778889999999998866555
No 34
>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]
Probab=29.04 E-value=24 Score=38.88 Aligned_cols=17 Identities=41% Similarity=0.386 Sum_probs=9.3
Q ss_pred HHHhhhhhhhhhhhhhh
Q 008492 24 MEDLIKVKKKKKKGKKK 40 (563)
Q Consensus 24 ~~~~~~~~~~~~~~~~~ 40 (563)
.|.-...+|||+|.||.
T Consensus 145 ~qr~~e~~KKk~kekks 161 (653)
T KOG2548|consen 145 TQRAQEPKKKKNKEKKS 161 (653)
T ss_pred cCccCCchhhhcccccc
Confidence 44445556666655554
No 35
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=28.78 E-value=26 Score=34.30 Aligned_cols=26 Identities=35% Similarity=0.371 Sum_probs=16.2
Q ss_pred ccCCCCCCchhHHHHHHHhhccchhHHhhhhHH
Q 008492 69 MGSGNGYDMNDLRRTVSMMAGGMFEEKREKTIE 101 (563)
Q Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (563)
.|..|.+.-++|=.||. .-=|++|.|
T Consensus 73 ~g~e~dy~Y~ElL~rvf-------~ilreknpe 98 (231)
T KOG2768|consen 73 VGSEPDYTYYELLSRVF-------NILREKNPE 98 (231)
T ss_pred cccCCCccHHHHHHHHH-------HHHHhcCch
Confidence 45666666667766653 334777766
No 36
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=28.39 E-value=85 Score=26.77 Aligned_cols=66 Identities=20% Similarity=0.287 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcCCcceeecc----ccce--eeeEeeCCCceEEEE-cCCCCcccCCCCCccchHHHHHHHHH
Q 008492 447 FQKEVARLLVSTGLNWIREYA----VDGY--TVDAVLVDKKVAFEI-DGPTHFSRNTGVPLGHTMLKRRYIAA 512 (563)
Q Consensus 447 lq~~V~~~L~~lG~~~~~E~~----~~G~--~vDi~~~~~rVAIEv-dGp~Hf~~ns~~~lG~t~lK~RlL~~ 512 (563)
.+..|-++|+++|+++..+.. ..++ ..|+.+...+++-|+ ++|.-+....+..+-...++..+++.
T Consensus 18 ik~kve~~l~~~gi~~~~~~~~v~~~~~~~~~aDiiv~s~~l~~~~~~~~~~~v~~~~~~~d~~ei~~~l~~~ 90 (93)
T COG3414 18 IKMKVEEVLKELGIDVDVEQCAVDEIKALTDGADIIVTSTKLADEFEDIPKGYVVITGNGMDIEEIKQKLLEI 90 (93)
T ss_pred HHHHHHHHHHHcCCCceeeeEEecccccCCCcccEEEEehHhhhhcCcCCCceEEEEcccCCHHHHHHHHHHH
Confidence 556888999999998765531 2222 349999999999999 55652222222223336666666543
No 37
>cd00671 ArgRS_core catalytic core domain of arginyl-tRNA synthetases. Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups of ArgRS. One type contains both characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The second subtype lacks the KMSKS motif; however, it has a lysine N-terminal to the HIGH motif, which serves as the functional counterpart to the second lysine of the KMSKS motif. A third group, which is found primarily in archaea and a few bacteria, lacks both the KMSKS motif and the HIGH loop lysine.
Probab=27.91 E-value=92 Score=30.36 Aligned_cols=47 Identities=15% Similarity=0.092 Sum_probs=28.5
Q ss_pred ceEEEEcCCCCcccCC-CCCc--cchHHHHHHHHHCCCEEEEEehh-hHHh
Q 008492 481 KVAFEIDGPTHFSRNT-GVPL--GHTMLKRRYIAAAGWNVVSLSHQ-EWEE 527 (563)
Q Consensus 481 rVAIEvdGp~Hf~~ns-~~~l--G~t~lK~RlL~~~Gy~Vv~Vpy~-EW~~ 527 (563)
+|.||..+|+=.-.-. ++.. -.--.=.|+|+..||+|+.+.|. +|..
T Consensus 1 ~v~ve~~spN~~~~~HiGH~R~~vigD~l~R~l~~~G~~V~~~~~~~D~G~ 51 (212)
T cd00671 1 KILVEFVSANPTGPLHVGHLRNAIIGDSLARILEFLGYDVTREYYINDWGR 51 (212)
T ss_pred CeEEEecCCCCCCCccccccHHHHHHHHHHHHHHHCCCcEEEEeccCCcHH
Confidence 5788887774321100 1111 12223468999999999999998 7743
No 38
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=27.60 E-value=1.1e+03 Score=28.14 Aligned_cols=166 Identities=16% Similarity=0.134 Sum_probs=83.9
Q ss_pred HHHHHHhhhhcCC-CCchhhhhhHHHHHhcccCHHHHHHHHHHHHHhhcCCCCCCCCChhhHHHHHHHHHhcccccchhh
Q 008492 100 IEEFVHRLSQFSG-PSNRRKEINLNKDIVDAQTAQEVLEVIAEMITAVGKGLSPSPLSPLNIATALHRIAKNMEKVSMMT 178 (563)
Q Consensus 100 ~~~~~~~~~~~~~-ps~~~~~~~Ln~~i~~a~s~~evl~lv~~~~~~~~~~~~~~~fn~vn~atAL~RLak~~~~~s~~~ 178 (563)
-|+||..+.+=.. ..+.-..+.|..-+..|.-.+.++..++.. . +.+..+.-...+-..|..+.|.-..
T Consensus 86 tE~~v~~l~~~~~~~~d~e~~~~~~~v~~~~gGL~~ll~~l~~~----~-~~~~~~~ll~~llkLL~~c~Kv~~N----- 155 (802)
T PF13764_consen 86 TEEFVESLEDDSEEEEDPEQEFKIASVLAECGGLEVLLSRLDSI----R-DFSRGRELLQVLLKLLRYCCKVKVN----- 155 (802)
T ss_pred chhhHhhccCccccccCHHHHHHHHHHhhcCCCHHHHHHHHHhh----c-cccCcHHHHHHHHHHHHHHHhhHHH-----
Confidence 4778887765332 233334679999999999999999998653 2 2223345555666666666665221
Q ss_pred hhhhhhccchhH-----------------------HHHHHHHHhhCCCCCHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Q 008492 179 THRLAFTRQREM-----------------------SMLVAIAMTALPECSAQGISNIAWALSKIGGELLYLSEMDRVAEV 235 (563)
Q Consensus 179 ~~r~~~ar~~~~-----------------------~~L~~~~~~~l~~~~~q~LsNilWAlakLg~~~~~~~~l~~la~~ 235 (563)
|+ .+..-... ..|+..+...+.+-+.+.+.+...+...-|.......-+..+.+.
T Consensus 156 -R~-~Ll~~~al~~LL~~L~~~l~~~~~~~~~~i~E~LL~IiE~ll~ea~~~~~~~~~~~~~~~~~~~~~~~~v~~lL~~ 233 (802)
T PF13764_consen 156 -RR-ALLELNALNRLLSVLNRALQANQNSSQAEIAEQLLEIIESLLSEANSSSSSESKSSSSLSGSEEQDKEQVEMLLER 233 (802)
T ss_pred -HH-HHHHcCCHHHHHHHHHHHHhCccccccchHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccHHHHHHHHHH
Confidence 21 11111111 222222222222222222222222211111000011224445555
Q ss_pred HHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhh
Q 008492 236 ALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELAKRASDIV 277 (563)
Q Consensus 236 a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala~~v~~~l 277 (563)
.......-+++-+..++--+..|-+.+++.++++.+++...+
T Consensus 234 l~s~~~r~~~~i~~~l~RiLP~Lt~G~~e~m~~Lv~~F~p~l 275 (802)
T PF13764_consen 234 LNSPFVRSNPQILQALARILPFLTYGNEEKMDALVEHFKPYL 275 (802)
T ss_pred hcCccccCCHHHHHHHHHHhhHHhcCCHHHHHHHHHHHHHhc
Confidence 444444456666666666666666777777777777665544
No 39
>PF03343 SART-1: SART-1 family; InterPro: IPR005011 This family of proteins appear to contain a leucine zipper [] and may therefore be a family of transcription factors.; PDB: 3PLV_C 3PLU_D.
Probab=26.82 E-value=21 Score=40.84 Aligned_cols=17 Identities=65% Similarity=0.749 Sum_probs=0.0
Q ss_pred HHhhhhhhhhhhhhhhH
Q 008492 25 EDLIKVKKKKKKGKKKL 41 (563)
Q Consensus 25 ~~~~~~~~~~~~~~~~~ 41 (563)
+.|+..||.|||++|++
T Consensus 279 ~Em~kfKK~KkKk~kk~ 295 (613)
T PF03343_consen 279 EEMIKFKKPKKKKKKKK 295 (613)
T ss_dssp -----------------
T ss_pred cccccccccccccchhh
Confidence 35677776666544433
No 40
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=24.95 E-value=1.2e+03 Score=27.48 Aligned_cols=63 Identities=6% Similarity=0.079 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHH---CCCCCHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHc-CCCChhHHHHHH
Q 008492 245 SQNVANVAGAFAS---MQHSAPDLFSELAKRASDIVHTFQEQELAQVLWAFASL-YEPADPLLESLD 307 (563)
Q Consensus 245 ~q~LanilwAlA~---L~~~~~~L~~ala~~v~~~l~~f~~qeLanilwAfA~l-~~~~~~L~~al~ 307 (563)
...+.|++.-++. +++..+.|.--+..-....+..++..-|-.|+-.++.. +-.++..+.-+.
T Consensus 421 ~K~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~l~e~~ve~ll~ii~~~G~~LRkDDp~alk~~i 487 (822)
T KOG2141|consen 421 DKSLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAENLNETNVEALLTIIANCGFSLRKDDPLALKDII 487 (822)
T ss_pred cchhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhchhhhhHHHHHHHHHHccchhcCCChHHHHHHH
Confidence 4445555554444 45666766666666666666666655555554444332 223344444443
No 41
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=24.94 E-value=2.9e+02 Score=31.39 Aligned_cols=34 Identities=24% Similarity=0.195 Sum_probs=19.1
Q ss_pred hcccCHHHHHHHHHHHHHhhcCCCCCCCCChhhHHHHHHHHHhcc
Q 008492 127 VDAQTAQEVLEVIAEMITAVGKGLSPSPLSPLNIATALHRIAKNM 171 (563)
Q Consensus 127 ~~a~s~~evl~lv~~~~~~~~~~~~~~~fn~vn~atAL~RLak~~ 171 (563)
.....+++.+....+-+ .++|-|. .++.|+|...
T Consensus 171 ~~l~~~~~Ai~~~~~al----------~l~p~~~-~a~~~~a~a~ 204 (615)
T TIGR00990 171 NALGDWEKVVEDTTAAL----------ELDPDYS-KALNRRANAY 204 (615)
T ss_pred HHhCCHHHHHHHHHHHH----------HcCCCCH-HHHHHHHHHH
Confidence 33466777776665533 3455443 4677777653
No 42
>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=24.50 E-value=4.2e+02 Score=31.81 Aligned_cols=35 Identities=26% Similarity=0.359 Sum_probs=27.1
Q ss_pred HHhcccCHHHHHHHHHHHHHhhcCCCCCCCCChhhHHHHHHHHHhccc
Q 008492 125 DIVDAQTAQEVLEVIAEMITAVGKGLSPSPLSPLNIATALHRIAKNME 172 (563)
Q Consensus 125 ~i~~a~s~~evl~lv~~~~~~~~~~~~~~~fn~vn~atAL~RLak~~~ 172 (563)
.+....|.++++.++. ..++-+..|.+.||-++..
T Consensus 421 tf~~P~s~eel~~lL~-------------~~~~~~~~~iI~RIrk~~h 455 (840)
T PF04147_consen 421 TFPCPSSHEELLELLD-------------GYSPEDQPTIIQRIRKCYH 455 (840)
T ss_pred eecCCCCHHHHHHHHh-------------cCCHHHHhHHHHHHHHhCC
Confidence 4445679999999984 3566789999999999753
No 43
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=23.24 E-value=54 Score=31.04 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=6.8
Q ss_pred cccccccccCC
Q 008492 62 DMKMDDIMGSG 72 (563)
Q Consensus 62 ~~~~~~~~~~~ 72 (563)
++++..+||-.
T Consensus 176 ~~~~~amMGFS 186 (193)
T KOG4727|consen 176 KDEMAAMMGFS 186 (193)
T ss_pred cHHHHHHhCcc
Confidence 46677777643
No 44
>PRK09687 putative lyase; Provisional
Probab=23.22 E-value=8.1e+02 Score=24.99 Aligned_cols=169 Identities=11% Similarity=0.013 Sum_probs=81.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCcCC-HHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhhcC
Q 008492 201 LPECSAQGISNIAWALSKIGGELLY-LSEMDRVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELAKRASDIVHT 279 (563)
Q Consensus 201 l~~~~~q~LsNilWAlakLg~~~~~-~~~l~~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala~~v~~~l~~ 279 (563)
+.+=++..=...+|+|+.+|....- ...+..|...+ ..+=++.--+..+.+++.++...+.....+.......+.+
T Consensus 63 l~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~---~~D~d~~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~D 139 (280)
T PRK09687 63 CSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLA---LEDKSACVRASAINATGHRCKKNPLYSPKIVEQSQITAFD 139 (280)
T ss_pred HhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHH---hcCCCHHHHHHHHHHHhcccccccccchHHHHHHHHHhhC
Confidence 3344566666778999999864310 01122222221 2344455566778888888654321111122222222333
Q ss_pred CCHHHHHHHHHHHHHcCCCChhHHHHHHHHhhhcchhhhhHHHHhhhhhccCCCCCCCCcccchhccCCCCCCCHHHHHH
Q 008492 280 FQEQELAQVLWAFASLYEPADPLLESLDNAFKDATQFTCCLNKALSNCNENGGVKSSGDADSEGSLSSPVLSFNRDQLGN 359 (563)
Q Consensus 280 f~~qeLanilwAfA~l~~~~~~L~~al~~~~~~~~~f~~~l~~~vs~~~~a~~~~~~~~L~~~~~~~~~l~~f~~qeLan 359 (563)
=+++-=...++|++.++ ++..++.|...+.+.+.. +..... .++|......-.+...+...+.+-++.-=..
T Consensus 140 ~~~~VR~~a~~aLg~~~--~~~ai~~L~~~L~d~~~~---VR~~A~---~aLg~~~~~~~~~~~~L~~~L~D~~~~VR~~ 211 (280)
T PRK09687 140 KSTNVRFAVAFALSVIN--DEAAIPLLINLLKDPNGD---VRNWAA---FALNSNKYDNPDIREAFVAMLQDKNEEIRIE 211 (280)
T ss_pred CCHHHHHHHHHHHhccC--CHHHHHHHHHHhcCCCHH---HHHHHH---HHHhcCCCCCHHHHHHHHHHhcCCChHHHHH
Confidence 35555567788887665 445566666655443211 111100 1111100000011112233344556666678
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHH
Q 008492 360 IAWSYAVLGQMDRIFFSDIWKTI 382 (563)
Q Consensus 360 ilWSLA~Lg~~d~~lf~~l~~~L 382 (563)
.+|+|+.++. +..+..+.+.+
T Consensus 212 A~~aLg~~~~--~~av~~Li~~L 232 (280)
T PRK09687 212 AIIGLALRKD--KRVLSVLIKEL 232 (280)
T ss_pred HHHHHHccCC--hhHHHHHHHHH
Confidence 8888888764 55566665554
No 45
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=22.52 E-value=6.4e+02 Score=26.97 Aligned_cols=64 Identities=9% Similarity=0.146 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHcCC---CcCCHHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHCCCCCHHHHHHHH
Q 008492 207 QGISNIAWALSKIGG---ELLYLSEMDRVAEVALTKVGEFNSQNVANVAGAFASMQHSAPDLFSELA 270 (563)
Q Consensus 207 q~LsNilWAlakLg~---~~~~~~~l~~la~~a~~~~~~f~~q~LanilwAlA~L~~~~~~L~~ala 270 (563)
.=|-|..|.|+.|.. +|+.-+.+..........+-..++.-++..+||++.+--.+-+-.+++.
T Consensus 216 smlRn~TWtLSNlcRGknP~P~w~~isqalpiL~KLiys~D~evlvDA~WAiSYlsDg~~E~i~avl 282 (526)
T COG5064 216 SMLRNATWTLSNLCRGKNPPPDWSNISQALPILAKLIYSRDPEVLVDACWAISYLSDGPNEKIQAVL 282 (526)
T ss_pred HHHHHhHHHHHHhhCCCCCCCchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHhccCcHHHHHHHH
Confidence 446799999999964 2222123444444445667888999999999999999776655555443
No 46
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=22.43 E-value=3.1e+02 Score=19.93 Aligned_cols=45 Identities=16% Similarity=0.296 Sum_probs=23.9
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHH----HhhhhcCCCHHHHHHHHHHHHH
Q 008492 250 NVAGAFASMQHSAPDLFSELAKR----ASDIVHTFQEQELAQVLWAFAS 294 (563)
Q Consensus 250 nilwAlA~L~~~~~~L~~ala~~----v~~~l~~f~~qeLanilwAfA~ 294 (563)
+.+|+++.+....++.+...... +...+.+=++.--.+.+||++.
T Consensus 6 ~A~~aLg~l~~~~~~~~~~~~~~~~~~L~~~L~d~~~~VR~~A~~aLg~ 54 (55)
T PF13513_consen 6 AAAWALGRLAEGCPELLQPYLPELLPALIPLLQDDDDSVRAAAAWALGN 54 (55)
T ss_dssp HHHHHHHCTTTTTHHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHHHC
T ss_pred HHHHHHhhHhcccHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 45677777665555544433333 3344444444445566666654
No 47
>PF13366 PDDEXK_3: PD-(D/E)XK nuclease superfamily
Probab=21.77 E-value=1.8e+02 Score=25.93 Aligned_cols=45 Identities=22% Similarity=0.407 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHHhcCCcceeec---------ccc-ceeeeEeeCCCceEEEEcCCC
Q 008492 445 SSFQKEVARLLVSTGLNWIREY---------AVD-GYTVDAVLVDKKVAFEIDGPT 490 (563)
Q Consensus 445 S~lq~~V~~~L~~lG~~~~~E~---------~~~-G~~vDi~~~~~rVAIEvdGp~ 490 (563)
|-+|.-...-|+.-|+++..+. .++ +|.+|+.+ +.+|+||+---.
T Consensus 25 ~vYe~aL~~EL~~~gi~~~~q~~l~v~Ykg~~l~~~~r~DllV-~~~vIvElKav~ 79 (118)
T PF13366_consen 25 SVYEEALEIELEKRGIPVERQVPLPVYYKGQPLGEGYRADLLV-ENKVIVELKAVE 79 (118)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeeeeeEECCEEeccceEeeEEE-cCeEEEEEeeHh
Confidence 4466667777888898887663 233 38999988 568999986543
No 48
>KOG3962 consensus Predicted actin-bundling protein [Cytoskeleton]
Probab=21.59 E-value=9.1 Score=37.64 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=10.9
Q ss_pred CCCCCchhHHHHHHHhhccch
Q 008492 72 GNGYDMNDLRRTVSMMAGGMF 92 (563)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~~~~ 92 (563)
...+.+|| +-++..+-.|-|
T Consensus 49 ~v~ie~~~-~~yl~a~dng~f 68 (246)
T KOG3962|consen 49 TVAIEIDD-GTYLGAMDNGLF 68 (246)
T ss_pred EEEEEecC-ceEEEEEecCce
Confidence 55566666 555555544443
No 49
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=20.84 E-value=84 Score=29.15 Aligned_cols=36 Identities=31% Similarity=0.527 Sum_probs=29.2
Q ss_pred hHHhhhhHHHHHHhhhhcC--------CCCchhhhhhHHHHHhcccCH
Q 008492 93 EEKREKTIEEFVHRLSQFS--------GPSNRRKEINLNKDIVDAQTA 132 (563)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~--------~ps~~~~~~~Ln~~i~~a~s~ 132 (563)
++-+.++.+++||-+..|. +||-+ ..|++|+.|++-
T Consensus 88 e~~kt~tv~~iV~~~Psfte~~~d~li~pslr----~a~rElRRak~k 131 (155)
T PF07789_consen 88 EEIKTETVAEIVQSIPSFTEKRADDLILPSLR----KANRELRRAKSK 131 (155)
T ss_pred ccCCCcchhhhccCCCCcccccCcceechhHH----HHHHHHHHHHHH
Confidence 4457889999999999999 56666 889999888653
No 50
>PF00750 tRNA-synt_1d: tRNA synthetases class I (R); InterPro: IPR015945 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the core region of arginyl-tRNA synthetase (6.1.1.19 from EC), which has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available []. ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1IQ0_A 1F7V_A 1F7U_A 1BS2_A 3GDZ_B.
Probab=20.62 E-value=1.3e+02 Score=32.00 Aligned_cols=38 Identities=37% Similarity=0.601 Sum_probs=26.3
Q ss_pred CCCceEEEEcCCCCcccCCCCCc----------cchHHHHHHHHHCCCEEEEEeh
Q 008492 478 VDKKVAFEIDGPTHFSRNTGVPL----------GHTMLKRRYIAAAGWNVVSLSH 522 (563)
Q Consensus 478 ~~~rVAIEvdGp~Hf~~ns~~~l----------G~t~lK~RlL~~~Gy~Vv~Vpy 522 (563)
.+++|.||+..| |+..|+ |.+. .|+|+..||+|+..-|
T Consensus 18 ~~~kv~VE~sSp-----Np~kplHvGHlR~~iiGd~l--aril~~~G~~V~r~ny 65 (354)
T PF00750_consen 18 KGKKVVVEFSSP-----NPTKPLHVGHLRNTIIGDSL--ARILEAAGYDVTRENY 65 (354)
T ss_dssp TSEEEEEEE--------BTTSS-BHHHHHHHHHHHHH--HHHHHHTTEEEEEEEE
T ss_pred CCCEEEEEecCC-----CCCCCCcCCcchhhhhhHHH--HHHHHHcCCeeeeEEE
Confidence 368999998876 555444 3333 5899999999999988
Done!