Query 023698
Match_columns 278
No_of_seqs 247 out of 1332
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:58:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023698.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023698hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1403 McrA Restriction endon 99.8 1.3E-18 2.9E-23 140.5 8.1 133 107-242 1-134 (146)
2 PF13395 HNH_4: HNH endonuclea 99.4 1.5E-13 3.2E-18 99.0 1.7 45 181-225 1-53 (54)
3 cd00085 HNHc HNH nucleases; HN 99.3 1.5E-12 3.2E-17 90.1 4.1 53 168-221 2-57 (57)
4 TIGR01865 cas_Csn1 CRISPR-asso 99.3 5E-12 1.1E-16 132.4 5.5 61 168-228 571-640 (805)
5 smart00507 HNHc HNH nucleases. 99.2 2.9E-12 6.4E-17 87.0 2.4 49 169-218 2-52 (52)
6 PF01844 HNH: HNH endonuclease 99.2 1.3E-12 2.8E-17 89.4 -2.9 43 181-223 1-47 (47)
7 TIGR02646 conserved hypothetic 99.0 3.5E-10 7.6E-15 95.8 5.2 77 167-244 13-103 (144)
8 PRK11295 hypothetical protein; 98.9 5.7E-10 1.2E-14 92.3 2.9 61 167-227 13-79 (113)
9 PF14279 HNH_5: HNH endonuclea 97.3 0.00011 2.4E-09 56.2 1.4 44 181-227 1-47 (71)
10 COG3513 Predicted CRISPR-assoc 96.4 0.0013 2.7E-08 69.9 1.5 60 169-228 562-630 (1088)
11 PHA02565 49 recombination endo 95.8 0.0068 1.5E-07 53.1 2.7 55 167-224 9-69 (157)
12 smart00782 PhnA_Zn_Ribbon PhnA 95.3 0.011 2.3E-07 42.2 1.8 44 173-219 2-45 (47)
13 COG3183 Predicted restriction 95.3 0.011 2.4E-07 55.7 2.4 58 166-223 183-254 (272)
14 PF13391 HNH_2: HNH endonuclea 94.1 0.01 2.2E-07 42.8 -0.8 39 181-219 1-57 (66)
15 COG3440 Predicted restriction 93.8 0.026 5.6E-07 54.0 1.2 54 166-219 180-240 (301)
16 PF05766 NinG: Bacteriophage L 93.8 0.085 1.8E-06 47.6 4.4 57 168-224 76-137 (189)
17 TIGR02986 restrict_Alw26I type 92.2 0.066 1.4E-06 53.1 1.4 54 179-233 245-299 (424)
18 PF06147 DUF968: Protein of un 91.7 0.096 2.1E-06 47.2 1.8 51 177-229 126-179 (200)
19 TIGR03031 cas_csx12 CRISPR-ass 91.2 0.1 2.2E-06 54.5 1.5 39 172-210 754-800 (802)
20 PF09665 RE_Alw26IDE: Type II 85.4 0.29 6.2E-06 49.7 0.3 55 179-234 243-300 (511)
21 PF05315 ICEA: ICEA Protein; 82.7 0.38 8.2E-06 44.2 -0.1 69 149-221 71-151 (230)
22 PF14239 RRXRR: RRXRR protein 79.0 2.7 5.8E-05 37.7 4.0 33 100-132 1-33 (176)
23 PF05198 IF3_N: Translation in 75.4 15 0.00033 28.4 6.8 57 94-159 9-65 (76)
24 PF02945 Endonuclease_7: Recom 65.2 3 6.5E-05 32.8 0.9 48 168-222 12-64 (81)
25 PF08595 RXT2_N: RXT2-like, N- 55.1 11 0.00024 32.9 2.7 20 5-24 1-20 (149)
26 TIGR00168 infC translation ini 41.7 74 0.0016 28.0 5.8 57 94-159 4-60 (165)
27 CHL00199 infC translation init 36.1 1.1E+02 0.0023 27.7 6.0 56 94-158 21-76 (182)
28 PF09257 BCMA-Tall_bind: BCMA, 33.6 5.3 0.00011 27.4 -2.0 20 206-225 7-26 (39)
29 PRK00028 infC translation init 31.0 1.4E+02 0.003 26.6 5.9 56 94-158 16-71 (177)
30 PF14255 Cys_rich_CPXG: Cystei 30.9 17 0.00037 26.4 0.1 32 180-215 2-33 (52)
31 COG3058 FdhE Uncharacterized p 30.5 38 0.00082 32.9 2.3 47 177-223 184-238 (308)
32 PF07510 DUF1524: Protein of u 28.5 18 0.0004 28.9 -0.1 37 192-228 54-106 (142)
33 PF05605 zf-Di19: Drought indu 25.4 35 0.00076 24.0 0.9 38 177-219 1-40 (54)
34 KOG4768 Mitochondrial mRNA mat 23.9 17 0.00036 38.8 -1.4 44 179-222 735-788 (796)
35 PTZ00293 thymidine kinase; Pro 23.5 31 0.00068 31.6 0.4 58 179-240 138-199 (211)
36 COG1435 Tdk Thymidine kinase [ 21.2 27 0.00058 32.1 -0.5 51 172-223 139-195 (201)
No 1
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=99.76 E-value=1.3e-18 Score=140.54 Aligned_cols=133 Identities=29% Similarity=0.538 Sum_probs=117.8
Q ss_pred cceeeeeeHHHHHHHHHcCceeEEeecCCeeecCCcceecceEEEEeccchhhhhcccCCHHHHHHHHHHCCCccccCCC
Q 023698 107 YRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQVVKRRRIKNNLSRKNLMYRDNFTCQYCSS 186 (278)
Q Consensus 107 y~Pl~~vs~qrAv~l~~~gkAevl~~~~~~v~S~s~~~~vPsVIrL~~yv~~p~r~~~~~~~~R~~Vl~RD~~~C~YCG~ 186 (278)
|.|....+|++++..+..++|..+..+. -+++.+....+|.+..+..+...+... .+..+|..++.+|++.|+||+.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~r~~~~~~d~~~c~~c~~ 77 (146)
T COG1403 1 YNPLESKSIRPALDRLVSQRAKHVAEYP-CLASESKDLRRPSVTDLTGESKRPSEK--RPAKTRRAVLLRDNGLCQYCGS 77 (146)
T ss_pred CccccccchhHHHHHHhhcccccccCcc-eecceecccccCccceeeeeecccCCC--CchHHHHHHHccccccccccCC
Confidence 5688899999999999999999887654 455677788899999999887766543 4678999999999999999998
Q ss_pred CC-CCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHHHhcccccCCCCCCcc
Q 023698 187 RE-NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKAPKDY 242 (278)
Q Consensus 187 ~~-~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpeeagm~Ll~~P~~P~~~ 242 (278)
.. .+++|||+|++.||.+.|+||+++|..||.+|+++.+.+++|.....|..|...
T Consensus 78 ~~~~~~~dHiip~~~g~~~~~~Nl~~lc~~c~~~k~~~~~~~~~~~~~~~~~~~~~~ 134 (146)
T COG1403 78 VGTDLEVDHIVPLSRGGASAWENLETLCERCHNKKGSRLPGKAGMKLRVKPRKPEVE 134 (146)
T ss_pred cCCCCceeeEeecccCCcchHHHHHHHHHhhcccccccchhhccCcccccccCCchh
Confidence 73 799999999999999999999999999999999999999999999999998753
No 2
>PF13395 HNH_4: HNH endonuclease
Probab=99.37 E-value=1.5e-13 Score=98.99 Aligned_cols=45 Identities=49% Similarity=0.949 Sum_probs=42.1
Q ss_pred cccCCCC---C-----CCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCH
Q 023698 181 CQYCSSR---E-----NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTL 225 (278)
Q Consensus 181 C~YCG~~---~-----~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtp 225 (278)
|.|||++ . ..++|||+|+|.++.+++.|||++|+.||+.|++++|
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s~~Nlvl~~~~~N~~K~~k~P 53 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDSFWNLVLCCKECNRSKGNKTP 53 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCCcchhheECHHHhhcccccCC
Confidence 9999987 2 3799999999999999999999999999999999986
No 3
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=99.32 E-value=1.5e-12 Score=90.08 Aligned_cols=53 Identities=42% Similarity=0.769 Sum_probs=48.1
Q ss_pred HHHHHHHHHCCCccccCCCC---CCCccceeeecCCCCCCchhhHHHhchhhhcCcC
Q 023698 168 LSRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKG 221 (278)
Q Consensus 168 ~~R~~Vl~RD~~~C~YCG~~---~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg 221 (278)
..|..+++++ ++|+||+.. ..+++|||+|.+.||.++++||+++|..||..|+
T Consensus 2 ~~r~~~~~~~-~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~~ 57 (57)
T cd00085 2 SHRLVLLARD-GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57 (57)
T ss_pred hHHHHHHHhC-CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHHHHHhhccC
Confidence 3678889998 899999984 6799999999999999999999999999999874
No 4
>TIGR01865 cas_Csn1 CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.
Probab=99.25 E-value=5e-12 Score=132.43 Aligned_cols=61 Identities=31% Similarity=0.418 Sum_probs=56.4
Q ss_pred HHHHHHHHHCCCccccCCCC---C------CCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHHH
Q 023698 168 LSRKNLMYRDNFTCQYCSSR---E------NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 228 (278)
Q Consensus 168 ~~R~~Vl~RD~~~C~YCG~~---~------~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpeea 228 (278)
..|..++.+++++|+|||.+ . .+++|||+|+|+||.|+|+|+|++|..||+.|++++|.+|
T Consensus 571 ~~k~~L~~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~~~N~~K~~~tp~e~ 640 (805)
T TIGR01865 571 ILKLRLYYQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEA 640 (805)
T ss_pred HHHHHHHHHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhHHHHhhccCCCHHHH
Confidence 45778999999999999987 2 4789999999999999999999999999999999999996
No 5
>smart00507 HNHc HNH nucleases.
Probab=99.25 E-value=2.9e-12 Score=87.02 Aligned_cols=49 Identities=41% Similarity=0.788 Sum_probs=45.1
Q ss_pred HHHHHHHHCCCccccCCCCC--CCccceeeecCCCCCCchhhHHHhchhhhc
Q 023698 169 SRKNLMYRDNFTCQYCSSRE--NLTIDHVVPASRGGEWKWENLVAACFKCNS 218 (278)
Q Consensus 169 ~R~~Vl~RD~~~C~YCG~~~--~ltvDHIiP~S~GG~~tweNLv~aC~~CN~ 218 (278)
.|..++.|| +.|++||.+. .+++|||+|.+.||.++++||+++|..||.
T Consensus 2 ~~~~~~~r~-~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~ 52 (52)
T smart00507 2 LRRLLLHRD-GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52 (52)
T ss_pred HHHHHHHHC-CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCeecChhhCc
Confidence 467899999 9999999884 489999999999999999999999999995
No 6
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=99.16 E-value=1.3e-12 Score=89.45 Aligned_cols=43 Identities=42% Similarity=0.930 Sum_probs=31.6
Q ss_pred cccCCCC----CCCccceeeecCCCCCCchhhHHHhchhhhcCcCCC
Q 023698 181 CQYCSSR----ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKK 223 (278)
Q Consensus 181 C~YCG~~----~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~r 223 (278)
|++||.. ..+++|||+|++.||.++++||+++|..||+.|+++
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~k~~k 47 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRKKHDK 47 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHHHH--
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHHhcCC
Confidence 8999987 468999999999999999999999999999999764
No 7
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=99.01 E-value=3.5e-10 Score=95.75 Aligned_cols=77 Identities=21% Similarity=0.367 Sum_probs=60.5
Q ss_pred HHHHHHHHHHCCCccccCCCC---CCCccceeeecCCCCC--CchhhHHHhchh---------hhcCcCCCCHHHHhccc
Q 023698 167 NLSRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGE--WKWENLVAACFK---------CNSRKGKKTLEEANMQL 232 (278)
Q Consensus 167 ~~~R~~Vl~RD~~~C~YCG~~---~~ltvDHIiP~S~GG~--~tweNLv~aC~~---------CN~~Kg~rtpeeagm~L 232 (278)
..+|..++..++++|+||+.. ..++||||+|++..+. .+|+||+++|.. ||..|++..... ...+
T Consensus 13 ~~i~~~L~~~~~~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~~sC~~~n~~~~~~~Cn~~K~~~~~~~-~~~~ 91 (144)
T TIGR02646 13 DEVHNQLLQLQGGLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLFGSCHRESKQGNPLHCGRFKDNSCGSN-NFDE 91 (144)
T ss_pred HHHHHHHHHHhCCCcCccCCCcCCCCcceeeecccCCChhhhcChhhchhhccccCCCCCccccccccccccccc-cccc
Confidence 468999999999999999984 6689999999998875 589999999999 888886554322 2345
Q ss_pred ccCCCCCCcccc
Q 023698 233 SRVPKAPKDYDI 244 (278)
Q Consensus 233 l~~P~~P~~~~~ 244 (278)
+..|..+...+.
T Consensus 92 ~i~P~~~~~~~~ 103 (144)
T TIGR02646 92 LIDPLADDCEQL 103 (144)
T ss_pred ccCCCCCChHHh
Confidence 666887764333
No 8
>PRK11295 hypothetical protein; Provisional
Probab=98.92 E-value=5.7e-10 Score=92.28 Aligned_cols=61 Identities=20% Similarity=0.312 Sum_probs=53.3
Q ss_pred HHHHHHHHHHCCCccccCCCC------CCCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHH
Q 023698 167 NLSRKNLMYRDNFTCQYCSSR------ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEE 227 (278)
Q Consensus 167 ~~~R~~Vl~RD~~~C~YCG~~------~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpee 227 (278)
...|+.++.++.+.|+.|++. ..++||||+|...|+.++-+||+++|..||++|+.+....
T Consensus 13 ~~~R~~~L~r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC~~CHn~kh~R~~~~ 79 (113)
T PRK11295 13 SGYREKALKLYPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLCLYCHDHEHSKYTEA 79 (113)
T ss_pred HHHHHHHHHHCcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHhHHHHhHHHhhHHHh
Confidence 468999999999999999985 3579999999998988889999999999999998666543
No 9
>PF14279 HNH_5: HNH endonuclease
Probab=97.27 E-value=0.00011 Score=56.20 Aligned_cols=44 Identities=41% Similarity=0.854 Sum_probs=36.2
Q ss_pred cccCCCC---CCCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHH
Q 023698 181 CQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEE 227 (278)
Q Consensus 181 C~YCG~~---~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpee 227 (278)
|.||++. ...+.+||+|-|-||...+.| .|..||+.-+...-.+
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~---vC~~CN~~~g~~vD~~ 47 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN---VCDKCNNKFGSKVDAE 47 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc---hhHHHhHHHhHHHHHH
Confidence 8999987 345689999999999888877 8999999887555433
No 10
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=96.43 E-value=0.0013 Score=69.88 Aligned_cols=60 Identities=32% Similarity=0.406 Sum_probs=53.7
Q ss_pred HHHHHHHHCCCccccCCCC------CC---CccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHHH
Q 023698 169 SRKNLMYRDNFTCQYCSSR------EN---LTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 228 (278)
Q Consensus 169 ~R~~Vl~RD~~~C~YCG~~------~~---ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpeea 228 (278)
.+-.++.-++++|.|.|+. .+ .++|||+|.|+-..|+.+|.|+.-..=|+-|+|.+|-|+
T Consensus 562 lKLrLY~~Q~gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkVLv~s~~Nq~KgnqtP~e~ 630 (1088)
T COG3513 562 LKLRLYYLQNGKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKVLVLSSENQEKGNQTPYEE 630 (1088)
T ss_pred hHHHHHHHhcCcccccCcccchhhcccccceeeceeccccccccccccceeEEeccccccccCCCCHHH
Confidence 4457888899999999986 33 899999999999999999999999999999999998774
No 11
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=95.78 E-value=0.0068 Score=53.09 Aligned_cols=55 Identities=18% Similarity=0.310 Sum_probs=42.3
Q ss_pred HHHHHHHHHHCCCccccCCCC-----CCCccceeeecCCCCCCchhh-HHHhchhhhcCcCCCC
Q 023698 167 NLSRKNLMYRDNFTCQYCSSR-----ENLTIDHVVPASRGGEWKWEN-LVAACFKCNSRKGKKT 224 (278)
Q Consensus 167 ~~~R~~Vl~RD~~~C~YCG~~-----~~ltvDHIiP~S~GG~~tweN-Lv~aC~~CN~~Kg~rt 224 (278)
+..++.+++.++++|+.|+.+ ..+.+||..|.+.... .+ --++|..||...|...
T Consensus 9 ~~~k~~l~e~Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~T---G~VRGLLC~~CN~~lG~~~ 69 (157)
T PHA02565 9 KEEKQKLFEAQNGICPLCKRELDGDVSKNHLDHDHELNGPNA---GRVRGLLCNLCNALEGQMK 69 (157)
T ss_pred HHHHHHHHHHhCCcCCCCCCccCCCccccccCCCCCCCCccc---ccccccCchhhhhhhhhhh
Confidence 467889999999999999976 3478999988763221 23 4579999999887653
No 12
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=95.29 E-value=0.011 Score=42.20 Aligned_cols=44 Identities=32% Similarity=0.528 Sum_probs=35.4
Q ss_pred HHHHCCCccccCCCCCCCccceeeecCCCCCCchhhHHHhchhhhcC
Q 023698 173 LMYRDNFTCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (278)
Q Consensus 173 Vl~RD~~~C~YCG~~~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (278)
++.|.+..|..||....|.+-+|-|.+. ..-+|-+.+|..|+..
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~Vpp~~~---~~~d~~iliC~tC~~Q 45 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYAVPPSSD---VTADNSVMLCDTCHSQ 45 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEecCCCCC---CCccceeeechHHHHh
Confidence 6789999999999888899888766544 3456679999999864
No 13
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=95.27 E-value=0.011 Score=55.66 Aligned_cols=58 Identities=16% Similarity=0.308 Sum_probs=46.7
Q ss_pred CHHHHHHHHHHCCCccccCCCC----------CCCccceeeecCCCC----CCchhhHHHhchhhhcCcCCC
Q 023698 166 NNLSRKNLMYRDNFTCQYCSSR----------ENLTIDHVVPASRGG----EWKWENLVAACFKCNSRKGKK 223 (278)
Q Consensus 166 ~~~~R~~Vl~RD~~~C~YCG~~----------~~ltvDHIiP~S~GG----~~tweNLv~aC~~CN~~Kg~r 223 (278)
.+..|++.+.-.+..|..|+.. .-.+|||++|.+.-+ .+...-|+++|+.||..-+-+
T Consensus 183 na~~ra~~Ia~~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~mvHrr 254 (272)
T COG3183 183 NATLRAAAIAIHGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHKMVHRR 254 (272)
T ss_pred ChHHHHHHHHHhCceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHHHHhcc
Confidence 4568888888888999999965 358999999998532 378899999999999865443
No 14
>PF13391 HNH_2: HNH endonuclease
Probab=94.08 E-value=0.01 Score=42.80 Aligned_cols=39 Identities=23% Similarity=0.135 Sum_probs=32.2
Q ss_pred cccCCCCC-----CCccceeeecCCC--CCC-----------chhhHHHhchhhhcC
Q 023698 181 CQYCSSRE-----NLTIDHVVPASRG--GEW-----------KWENLVAACFKCNSR 219 (278)
Q Consensus 181 C~YCG~~~-----~ltvDHIiP~S~G--G~~-----------tweNLv~aC~~CN~~ 219 (278)
|..||... .+++-||+|.+.+ +.+ +.+|..++|..+|..
T Consensus 1 C~itg~~~~~~~~~~eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~~~lH~~ 57 (66)
T PF13391_consen 1 CVITGIRDPSPWELLEAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLRPDLHKL 57 (66)
T ss_pred CcCCcCCcCCCCCcEEEEEcccCccCCCchhhhhhhhhccCCCccEEEEcCHhHHHH
Confidence 78888665 6899999999987 445 778999999999864
No 15
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=93.84 E-value=0.026 Score=53.95 Aligned_cols=54 Identities=17% Similarity=0.241 Sum_probs=46.5
Q ss_pred CHHHHHHHHHHCCCccccCCCC-------CCCccceeeecCCCCCCchhhHHHhchhhhcC
Q 023698 166 NNLSRKNLMYRDNFTCQYCSSR-------ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (278)
Q Consensus 166 ~~~~R~~Vl~RD~~~C~YCG~~-------~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (278)
....|+.|+.--+|+|+.||.. ..+..-||.|.+++|.+...|-.++|+..|..
T Consensus 180 d~~fRk~V~~~Y~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~nHh~~ 240 (301)
T COG3440 180 DGAFRKIVLRQYDYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCKNHHWA 240 (301)
T ss_pred hHHHHHHHHHHhcchhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhchhhHHH
Confidence 4579999999999999999943 34667799999999999999999999877763
No 16
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=93.81 E-value=0.085 Score=47.56 Aligned_cols=57 Identities=19% Similarity=0.351 Sum_probs=43.9
Q ss_pred HHHHHHHHHC-CCccccCCCC--CCCccceeeecCCCC--CCchhhHHHhchhhhcCcCCCC
Q 023698 168 LSRKNLMYRD-NFTCQYCSSR--ENLTIDHVVPASRGG--EWKWENLVAACFKCNSRKGKKT 224 (278)
Q Consensus 168 ~~R~~Vl~RD-~~~C~YCG~~--~~ltvDHIiP~S~GG--~~tweNLv~aC~~CN~~Kg~rt 224 (278)
...+.|..|| +..|..||.. ..++.-|...+..-. ..+.+|+-..|..||..+++-.
T Consensus 76 afn~~IR~RD~~~~CiSCG~~~~~~~dagHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~ 137 (189)
T PF05766_consen 76 AFNKYIRLRDAGKPCISCGRKHGGQWDAGHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNI 137 (189)
T ss_pred HHHHHHHHHhcCCCcccCCCcCCCCcccccccccccCcccccChhhHhHcCCccccccccCH
Confidence 4556777886 6799999987 568889997553222 3578999999999999997654
No 17
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=92.16 E-value=0.066 Score=53.09 Aligned_cols=54 Identities=24% Similarity=0.334 Sum_probs=41.6
Q ss_pred CccccCCCC-CCCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHHHhcccc
Q 023698 179 FTCQYCSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLS 233 (278)
Q Consensus 179 ~~C~YCG~~-~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpeeagm~Ll 233 (278)
..|+.|+.. ..+..|||-|.|-|=.+.. +++++|..||+.|.+|.--..-..|+
T Consensus 245 ~~~~~~~~~p~~~saDHIGPISlGF~h~P-~Fqplc~~cNSaKnnR~~lsDV~~Li 299 (424)
T TIGR02986 245 CSIPECCKHPEKISADHIGPISLGFVHDP-RFQPLCSSCNSAKNDRLTLSDVKTLI 299 (424)
T ss_pred ccCcccccCCCCCCccccCCcccccccCc-cccccccccccccccceeHHHHHHHH
Confidence 456778875 7799999999999876655 45999999999999997544333333
No 18
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=91.70 E-value=0.096 Score=47.21 Aligned_cols=51 Identities=14% Similarity=0.271 Sum_probs=37.8
Q ss_pred CCCccccCCCCCCCccceeeecCCCC---CCchhhHHHhchhhhcCcCCCCHHHHh
Q 023698 177 DNFTCQYCSSRENLTIDHVVPASRGG---EWKWENLVAACFKCNSRKGKKTLEEAN 229 (278)
Q Consensus 177 D~~~C~YCG~~~~ltvDHIiP~S~GG---~~tweNLv~aC~~CN~~Kg~rtpeeag 229 (278)
-.-.|..||++. -+++|++..-.|| ...-..++++|+.||+..++ -.+.+.
T Consensus 126 ~~~~C~iCGk~~-~d~hH~iG~g~~~~~~~~~d~~~ipLCr~hH~e~H~-g~~~Fe 179 (200)
T PF06147_consen 126 KSRPCVICGKPP-ADIHHIIGMGRGRMGIKHHDLFVIPLCREHHRELHR-GRKAFE 179 (200)
T ss_pred ccCccccCCCCc-cccceeeccccCccccccCCCeehhccHHHHHHHhC-CHHHHH
Confidence 345899999763 4899997665454 34567899999999998877 555554
No 19
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=91.24 E-value=0.1 Score=54.48 Aligned_cols=39 Identities=23% Similarity=0.265 Sum_probs=29.2
Q ss_pred HHHHHCCCccccCCCC--CCCccceeeecCCCCC------CchhhHH
Q 023698 172 NLMYRDNFTCQYCSSR--ENLTIDHVVPASRGGE------WKWENLV 210 (278)
Q Consensus 172 ~Vl~RD~~~C~YCG~~--~~ltvDHIiP~S~GG~------~tweNLv 210 (278)
.|..-..+-|+|||.. ..-++|||+|+|.-+. |+..||.
T Consensus 754 RIk~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k~ygtvFN~E~NLI 800 (802)
T TIGR03031 754 RIKNFSMGICPYKGASIGGQGEIDHIYPRSHSKKHYGTIFNSEVNLI 800 (802)
T ss_pred HHHHHhccCCCCCCCCCCCcccccccccccccccccceeecCcccee
Confidence 4455567899999987 5679999999998654 4555654
No 20
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=85.37 E-value=0.29 Score=49.70 Aligned_cols=55 Identities=27% Similarity=0.446 Sum_probs=40.0
Q ss_pred Ccccc--CCCC-CCCccceeeecCCCCCCchhhHHHhchhhhcCcCCCCHHHHhccccc
Q 023698 179 FTCQY--CSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSR 234 (278)
Q Consensus 179 ~~C~Y--CG~~-~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~rtpeeagm~Ll~ 234 (278)
+.|+. |++. .-+..|||-|.|-|=.+... ++++|..||+.|.+|.--..-..|+.
T Consensus 243 G~~~~~~~~~~~~~~SaDHIGPISlGF~h~P~-Fqplc~~cNSaKnnR~~lsDV~~Li~ 300 (511)
T PF09665_consen 243 GLCRFPNCGKEEECLSADHIGPISLGFVHRPR-FQPLCKSCNSAKNNRMYLSDVKKLIN 300 (511)
T ss_pred CcccCCchhhhccccCccccCCcccccccCcc-ccccccccccccccceeHHHHHHHHH
Confidence 45543 5554 55799999999998766654 49999999999999975444434443
No 21
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=82.74 E-value=0.38 Score=44.25 Aligned_cols=69 Identities=19% Similarity=0.367 Sum_probs=44.6
Q ss_pred EEEEeccchhhhhcccCCHHHHHHHHHHCC-CccccCCCC-----CCCccceeeecCCCC------CCchhhHHHhchhh
Q 023698 149 VLRVRHLLQVVKRRRIKNNLSRKNLMYRDN-FTCQYCSSR-----ENLTIDHVVPASRGG------EWKWENLVAACFKC 216 (278)
Q Consensus 149 VIrL~~yv~~p~r~~~~~~~~R~~Vl~RD~-~~C~YCG~~-----~~ltvDHIiP~S~GG------~~tweNLv~aC~~C 216 (278)
.|||..| .+.. +....+|+.|..-.. -.|.+||.. ..+++||-.-+...- ..+.+-++++|..|
T Consensus 71 ~IRLnG~--n~~~--~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~ieiDHKd~rk~d~rvsd~~~q~~~dFQ~Lck~~ 146 (230)
T PF05315_consen 71 RIRLNGF--NTEK--VFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEIDHKDGRKDDLRVSDMNTQTFDDFQPLCKAC 146 (230)
T ss_pred HHHHcCc--Cchh--hhhhHHHHHHHHHHHhcCeeeecccCCCccceeeecccccccccchhcccchhhHHHHHHHHHHH
Confidence 5677766 2222 234567776654432 479999974 568899974333221 12568899999999
Q ss_pred hcCcC
Q 023698 217 NSRKG 221 (278)
Q Consensus 217 N~~Kg 221 (278)
|..|.
T Consensus 147 N~~KR 151 (230)
T PF05315_consen 147 NDQKR 151 (230)
T ss_pred hHHHH
Confidence 99884
No 22
>PF14239 RRXRR: RRXRR protein
Probab=79.02 E-value=2.7 Score=37.70 Aligned_cols=33 Identities=30% Similarity=0.152 Sum_probs=31.1
Q ss_pred EEEEcCCcceeeeeeHHHHHHHHHcCceeEEee
Q 023698 100 GLVLDISYRPVNVVCWKRAICLEFMEKADVLEY 132 (278)
Q Consensus 100 vLvLN~sy~Pl~~vs~qrAv~l~~~gkAevl~~ 132 (278)
|.|||.+..||.=++..+|-.|+-.|||.|+..
T Consensus 1 VfVld~~gkPLmP~~p~rAR~LLk~GkA~V~r~ 33 (176)
T PF14239_consen 1 VFVLDKNGKPLMPCHPARARKLLKQGKAKVVRR 33 (176)
T ss_pred CeEECCCCCcCCCCCHHHHHHHHHCCCEEEEec
Confidence 689999999999999999999999999998873
No 23
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=75.44 E-value=15 Score=28.36 Aligned_cols=57 Identities=19% Similarity=0.241 Sum_probs=38.8
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeecCCcceecceEEEEeccchhh
Q 023698 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQVV 159 (278)
Q Consensus 94 ~~~~~~vLvLN~sy~Pl~~vs~qrAv~l~~~gkAevl~~~~~~v~S~s~~~~vPsVIrL~~yv~~p 159 (278)
.+....|.|+|..++.+++++..+|+.+.-.-..++++.. +... |.|.+|..|-+..
T Consensus 9 ~I~~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~------~~~~---PPVcKi~dy~k~~ 65 (76)
T PF05198_consen 9 EIRAPEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVS------PNAD---PPVCKIMDYGKYK 65 (76)
T ss_dssp G---SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEE------TTSS---S-EEEEE-HHHHH
T ss_pred CcCCCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEc------CCCC---CCeEEEechHHHH
Confidence 3556789999999999999999999999888888888743 2333 7788888774443
No 24
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=65.20 E-value=3 Score=32.78 Aligned_cols=48 Identities=25% Similarity=0.427 Sum_probs=30.1
Q ss_pred HHHHHHHHHCCCccccCCCC-----CCCccceeeecCCCCCCchhhHHHhchhhhcCcCC
Q 023698 168 LSRKNLMYRDNFTCQYCSSR-----ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGK 222 (278)
Q Consensus 168 ~~R~~Vl~RD~~~C~YCG~~-----~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~Kg~ 222 (278)
....++++.++++|+.|+.+ ..+.+||=- ..| . . =-++|..||..-|.
T Consensus 12 ~~~~~l~~~q~~~C~iC~~~~~~~~~~~~vDHdH--~tG-~--v--RGlLC~~CN~~lG~ 64 (81)
T PF02945_consen 12 EEYEALLEEQGGRCAICGKPLPGESRKLVVDHDH--KTG-R--V--RGLLCRSCNTALGK 64 (81)
T ss_dssp HHHHCCHHHTTTE-TTT-SEEETTCGGCEEEE-T--TTT-B--E--EEEEEHHHHHHHHH
T ss_pred HHHHHHHHHhCCcCcCCCCCcccCCCcceecCCC--CCC-C--c--hhhhhhHHhhhhcc
Confidence 45567889999999999982 557788754 111 1 0 01589999986543
No 25
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=55.08 E-value=11 Score=32.87 Aligned_cols=20 Identities=20% Similarity=0.062 Sum_probs=12.0
Q ss_pred ccccceeeeecCCCCeeeec
Q 023698 5 TSQGGLNLLFNGDGSSFGVE 24 (278)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~ 24 (278)
||.-..||+.+.+.++-+-.
T Consensus 1 ttNRGnKL~~~a~~V~~g~L 20 (149)
T PF08595_consen 1 TTNRGNKLKQRAEFVHRGQL 20 (149)
T ss_pred CCCcchhcchhccceecccc
Confidence 34445677767666666555
No 26
>TIGR00168 infC translation initiation factor IF-3. render its expression particularly sensitive to excess of its gene product IF-3 thereby regulating its own expression
Probab=41.66 E-value=74 Score=28.04 Aligned_cols=57 Identities=14% Similarity=0.144 Sum_probs=43.6
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeecCCcceecceEEEEeccchhh
Q 023698 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQVV 159 (278)
Q Consensus 94 ~~~~~~vLvLN~sy~Pl~~vs~qrAv~l~~~gkAevl~~~~~~v~S~s~~~~vPsVIrL~~yv~~p 159 (278)
.+..+.|.+.|..++.+++++.++|+.+.-.-.-++++.. +.. -|.|-++-.|-+..
T Consensus 4 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLVev~------~~a---~PPVckImdy~k~~ 60 (165)
T TIGR00168 4 RIRFNEVRLIDENGEQLGIVSREEALEIAEEAGLDLVLIS------PNA---KPPVCKIMDYGKYK 60 (165)
T ss_pred CcCCCEEEEECCCCcCCCcccHHHHHHHHHHcCCcEEEEC------CCC---CCCEEEEeeHHHHH
Confidence 3456789999999999999999999999887777777643 222 26788888775443
No 27
>CHL00199 infC translation initiation factor 3; Provisional
Probab=36.14 E-value=1.1e+02 Score=27.72 Aligned_cols=56 Identities=18% Similarity=0.140 Sum_probs=43.8
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeecCCcceecceEEEEeccchh
Q 023698 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (278)
Q Consensus 94 ~~~~~~vLvLN~sy~Pl~~vs~qrAv~l~~~gkAevl~~~~~~v~S~s~~~~vPsVIrL~~yv~~ 158 (278)
.+....|.|.|..++.+++++.++|+.+.-...-++|+.. +... |.|-++..|-+.
T Consensus 21 ~I~~~~VrlI~~~G~~lGv~~~~eAl~~A~~~~lDLVeVs------~~a~---PPVCKImdygK~ 76 (182)
T CHL00199 21 RIRFPKVRVIDDSGEQLGIFTSEQAIQLAANQGLDLVLVS------EKSD---PPVCRIIDYGKY 76 (182)
T ss_pred ccCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEEC------CCCC---CCeEEEeehHHH
Confidence 4566789999999999999999999999887777777743 2222 778888877544
No 28
>PF09257 BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IPR015337 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. Members of this entry, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 2KN1_A 1OQD_R 1XU2_T.
Probab=33.55 E-value=5.3 Score=27.39 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=16.7
Q ss_pred hhhHHHhchhhhcCcCCCCH
Q 023698 206 WENLVAACFKCNSRKGKKTL 225 (278)
Q Consensus 206 weNLv~aC~~CN~~Kg~rtp 225 (278)
++||..+|++||-+-++.+|
T Consensus 7 fD~LL~aCkPChLRCsn~tP 26 (39)
T PF09257_consen 7 FDRLLHACKPCHLRCSNNTP 26 (39)
T ss_dssp EETTTTEEEEHHHHHTSSS-
T ss_pred HHHHHHhcccceeecCCCCC
Confidence 58899999999999888664
No 29
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=31.02 E-value=1.4e+02 Score=26.59 Aligned_cols=56 Identities=16% Similarity=0.198 Sum_probs=42.6
Q ss_pred ccccceEEEEcCCcceeeeeeHHHHHHHHHcCceeEEeecCCeeecCCcceecceEEEEeccchh
Q 023698 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLLQV 158 (278)
Q Consensus 94 ~~~~~~vLvLN~sy~Pl~~vs~qrAv~l~~~gkAevl~~~~~~v~S~s~~~~vPsVIrL~~yv~~ 158 (278)
.+....|.|+|..++.+++++..+|+.+.-.-.-++|+.. +... |.|-++-.|-+.
T Consensus 16 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLV~v~------~~~~---PPVckI~dy~k~ 71 (177)
T PRK00028 16 QIRAREVRLIGDDGEQLGIVSTREALELAEEAGLDLVEIS------PNAK---PPVCKIMDYGKF 71 (177)
T ss_pred CcCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEEC------CCCC---CCEEEEEeHHHH
Confidence 3566789999999999999999999999776666776642 2333 678888777443
No 30
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=30.87 E-value=17 Score=26.44 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=22.9
Q ss_pred ccccCCCCCCCccceeeecCCCCCCchhhHHHhchh
Q 023698 180 TCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFK 215 (278)
Q Consensus 180 ~C~YCG~~~~ltvDHIiP~S~GG~~tweNLv~aC~~ 215 (278)
.|+|||....+.+| .|.|+..-++-....|++
T Consensus 2 ~CPyCge~~~~~iD----~s~~~Q~yiEDC~vCC~P 33 (52)
T PF14255_consen 2 QCPYCGEPIEILID----PSAGDQEYIEDCQVCCRP 33 (52)
T ss_pred CCCCCCCeeEEEEe----cCCCCeeEEeehhhcCCc
Confidence 69999977555554 455666778888888865
No 31
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=30.45 E-value=38 Score=32.86 Aligned_cols=47 Identities=17% Similarity=0.387 Sum_probs=33.4
Q ss_pred CCCccccCCCCCCCccceeeecCCCCC--------CchhhHHHhchhhhcCcCCC
Q 023698 177 DNFTCQYCSSRENLTIDHVVPASRGGE--------WKWENLVAACFKCNSRKGKK 223 (278)
Q Consensus 177 D~~~C~YCG~~~~ltvDHIiP~S~GG~--------~tweNLv~aC~~CN~~Kg~r 223 (278)
..+.|+.||......+=|+--...|=. +.|.-+..-|..|.+.|+..
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~l~ 238 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKKLH 238 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCCcc
Confidence 446899999874444445544444432 58999999999999988543
No 32
>PF07510 DUF1524: Protein of unknown function (DUF1524); InterPro: IPR011089 The family contains RloF from Campylobacter jejuni, its function and those of the other members are unknown.
Probab=28.50 E-value=18 Score=28.93 Aligned_cols=37 Identities=27% Similarity=0.272 Sum_probs=29.3
Q ss_pred cceeeecCCCCC----------------CchhhHHHhchhhhcCcCCCCHHHH
Q 023698 192 IDHVVPASRGGE----------------WKWENLVAACFKCNSRKGKKTLEEA 228 (278)
Q Consensus 192 vDHIiP~S~GG~----------------~tweNLv~aC~~CN~~Kg~rtpeea 228 (278)
+|||.|.+.... ++..||+++=..=|..++++.+.+-
T Consensus 54 iEHI~Pq~~~~~~~~~~~~~~~~~~~~~~~igNL~LL~~~~N~~~~n~~f~~K 106 (142)
T PF07510_consen 54 IEHIFPQNPKKESKSEKDWDEEEREIYLNSIGNLTLLSKSLNSSISNKPFLEK 106 (142)
T ss_pred eEeeccCCCCcccccccccCHHHHHHHhcccccEEEeccchhhccchhhhHHH
Confidence 999999986542 5678888888888988888776553
No 33
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=25.42 E-value=35 Score=24.05 Aligned_cols=38 Identities=34% Similarity=0.695 Sum_probs=20.8
Q ss_pred CCCccccCCCC--CCCccceeeecCCCCCCchhhHHHhchhhhcC
Q 023698 177 DNFTCQYCSSR--ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 219 (278)
Q Consensus 177 D~~~C~YCG~~--~~ltvDHIiP~S~GG~~tweNLv~aC~~CN~~ 219 (278)
+.+.|+||++. ..-=++|+.-.-.+... ...|.-|..+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~-----~v~CPiC~~~ 40 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESK-----NVVCPICSSR 40 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCC-----CccCCCchhh
Confidence 45899999984 11123455433222211 2578888753
No 34
>KOG4768 consensus Mitochondrial mRNA maturase [RNA processing and modification]
Probab=23.87 E-value=17 Score=38.84 Aligned_cols=44 Identities=16% Similarity=0.340 Sum_probs=30.6
Q ss_pred CccccCCCCCCCccceeeecCCCC--CCch--------hhHHHhchhhhcCcCC
Q 023698 179 FTCQYCSSRENLTIDHVVPASRGG--EWKW--------ENLVAACFKCNSRKGK 222 (278)
Q Consensus 179 ~~C~YCG~~~~ltvDHIiP~S~GG--~~tw--------eNLv~aC~~CN~~Kg~ 222 (278)
..|+.|+..-+++++||....+-- .+.. .--.++|+.||-+-+.
T Consensus 735 ~~c~ic~st~dvemhhvrql~nlk~~kdyl~grmikmnrkqiplck~ch~k~h~ 788 (796)
T KOG4768|consen 735 LQCAICQSTYDVEMHHVRQLKNLKPIKDYLDGRMIKMNRKQIPLCKSCHMKLHA 788 (796)
T ss_pred chhhhhcCccceehHHHHHHhcCCcccchhhhHHHhhccccCchhhhhhhhhhc
Confidence 689999999889999997664311 1111 1236899999987543
No 35
>PTZ00293 thymidine kinase; Provisional
Probab=23.50 E-value=31 Score=31.57 Aligned_cols=58 Identities=22% Similarity=0.397 Sum_probs=32.5
Q ss_pred CccccCCCCCCCccceeee---c-CCCCCCchhhHHHhchhhhcCcCCCCHHHHhcccccCCCCCC
Q 023698 179 FTCQYCSSRENLTIDHVVP---A-SRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKAPK 240 (278)
Q Consensus 179 ~~C~YCG~~~~ltvDHIiP---~-S~GG~~tweNLv~aC~~CN~~Kg~rtpeeagm~Ll~~P~~P~ 240 (278)
-.|..||.+..++.= ++. . --||.+ ...+.|+.|+..|.....+.-.-.....+..++
T Consensus 138 aiC~~CG~~A~~t~R-~~~~~~~v~IGg~e---~Y~a~CR~c~~~~~~~~~~~~~~~~~~~~~~~~ 199 (211)
T PTZ00293 138 AVCMFCGKEASFSKR-IVQSEQIELIGGED---KYIATCRKCFRTKQLAEKELEKQDLVEFADFSN 199 (211)
T ss_pred eEchhhCCcceeEEE-EcCCCCEEEECCcc---cEEehhhhhhhhhccchHhhhhchhhhhcccCc
Confidence 479999987322211 111 0 123433 578999999988877766444433333344443
No 36
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=21.25 E-value=27 Score=32.08 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=28.5
Q ss_pred HHHHHCCCccccCCCCCCC---ccceeeecCCCCC---CchhhHHHhchhhhcCcCCC
Q 023698 172 NLMYRDNFTCQYCSSRENL---TIDHVVPASRGGE---WKWENLVAACFKCNSRKGKK 223 (278)
Q Consensus 172 ~Vl~RD~~~C~YCG~~~~l---tvDHIiP~S~GG~---~tweNLv~aC~~CN~~Kg~r 223 (278)
.|.+-+ --|.+||++..+ .++..-+...|.. -.-++.++.|+.||...+..
T Consensus 139 kv~kL~-aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~~~~~~ 195 (201)
T COG1435 139 KVTKLK-AICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHKEPGKE 195 (201)
T ss_pred HHHHHH-HHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhhccccc
Confidence 344433 479999987321 2222222222211 12577889999999876544
Done!