Query 024302
Match_columns 269
No_of_seqs 244 out of 1330
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:34:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1403 McrA Restriction endon 99.7 3.7E-17 8E-22 131.4 8.4 125 107-233 1-134 (146)
2 PF13395 HNH_4: HNH endonuclea 99.4 1.6E-13 3.5E-18 98.3 1.8 45 172-216 1-53 (54)
3 cd00085 HNHc HNH nucleases; HN 99.3 1.7E-12 3.7E-17 89.3 3.9 52 160-212 3-57 (57)
4 TIGR01865 cas_Csn1 CRISPR-asso 99.2 5.4E-12 1.2E-16 131.5 5.4 62 158-219 570-640 (805)
5 smart00507 HNHc HNH nucleases. 99.2 4.3E-12 9.3E-17 85.8 2.3 49 160-209 2-52 (52)
6 PF01844 HNH: HNH endonuclease 99.1 1.8E-12 3.8E-17 88.4 -3.0 43 172-214 1-47 (47)
7 PRK11295 hypothetical protein; 99.0 3.2E-10 7E-15 93.3 2.7 61 158-218 13-79 (113)
8 TIGR02646 conserved hypothetic 98.9 1.1E-09 2.4E-14 92.3 4.5 74 158-232 13-100 (144)
9 PF14279 HNH_5: HNH endonuclea 97.4 6.4E-05 1.4E-09 57.3 1.4 45 172-219 1-48 (71)
10 COG3513 Predicted CRISPR-assoc 96.5 0.0011 2.4E-08 70.0 1.7 60 160-219 562-630 (1088)
11 PHA02565 49 recombination endo 95.4 0.012 2.5E-07 51.4 2.6 55 158-215 9-69 (157)
12 COG3183 Predicted restriction 95.4 0.01 2.2E-07 55.7 2.4 59 157-215 183-255 (272)
13 smart00782 PhnA_Zn_Ribbon PhnA 95.3 0.0078 1.7E-07 42.7 1.3 44 164-210 2-45 (47)
14 PF05766 NinG: Bacteriophage L 94.4 0.057 1.2E-06 48.5 4.4 58 158-215 75-137 (189)
15 COG3440 Predicted restriction 93.8 0.027 5.8E-07 53.6 1.2 55 156-210 179-240 (301)
16 PF13391 HNH_2: HNH endonuclea 93.7 0.013 2.8E-07 42.0 -0.8 39 172-210 1-57 (66)
17 TIGR02986 restrict_Alw26I type 93.4 0.036 7.8E-07 54.7 1.4 49 170-219 245-294 (424)
18 PF06147 DUF968: Protein of un 91.3 0.2 4.3E-06 44.9 3.3 51 168-220 126-179 (200)
19 TIGR03031 cas_csx12 CRISPR-ass 90.3 0.14 3E-06 53.3 1.5 38 164-201 755-800 (802)
20 PF09665 RE_Alw26IDE: Type II 88.6 0.15 3.3E-06 51.4 0.4 49 175-224 250-299 (511)
21 PF05315 ICEA: ICEA Protein; 71.4 2.1 4.5E-05 39.4 1.3 57 156-212 83-151 (230)
22 PF02945 Endonuclease_7: Recom 64.5 3.2 7E-05 32.5 0.9 50 158-214 11-65 (81)
23 PF05198 IF3_N: Translation in 63.3 30 0.00064 26.6 6.1 52 94-148 9-63 (76)
24 PF08595 RXT2_N: RXT2-like, N- 58.9 8.7 0.00019 33.4 2.7 20 5-24 1-20 (149)
25 PF14239 RRXRR: RRXRR protein 43.8 38 0.00083 30.3 4.4 42 100-145 1-42 (176)
26 PF09257 BCMA-Tall_bind: BCMA, 34.0 5.3 0.00011 27.3 -1.9 20 197-216 7-26 (39)
27 TIGR00168 infC translation ini 33.4 1.1E+02 0.0023 26.9 5.5 54 94-150 4-60 (165)
28 PF07510 DUF1524: Protein of u 31.3 16 0.00034 29.2 -0.0 37 183-219 54-106 (142)
29 PRK00028 infC translation init 30.3 1.3E+02 0.0029 26.5 5.6 52 94-148 16-70 (177)
30 PF14255 Cys_rich_CPXG: Cystei 28.5 20 0.00043 26.0 0.1 32 171-206 2-33 (52)
31 COG3058 FdhE Uncharacterized p 27.8 46 0.00099 32.2 2.4 47 168-214 184-238 (308)
32 COG1435 Tdk Thymidine kinase [ 24.0 21 0.00046 32.6 -0.6 52 162-214 138-195 (201)
33 CHL00199 infC translation init 23.6 2.1E+02 0.0045 25.8 5.6 53 94-149 21-76 (182)
34 PF13966 zf-RVT: zinc-binding 21.6 1.4E+02 0.003 22.5 3.6 20 168-188 58-77 (86)
35 PF05605 zf-Di19: Drought indu 21.3 47 0.001 23.3 0.9 38 168-210 1-40 (54)
36 PTZ00293 thymidine kinase; Pro 20.7 37 0.00081 30.9 0.3 57 170-230 138-198 (211)
37 COG3303 NrfA Formate-dependent 20.3 49 0.0011 33.4 1.0 49 161-215 290-344 (501)
No 1
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=99.70 E-value=3.7e-17 Score=131.43 Aligned_cols=125 Identities=30% Similarity=0.556 Sum_probs=107.9
Q ss_pred cceeeeecHHHHHHHHhhCce--------eecCCceeecceEEEEeeceecccccccCCHHHHHHHHHHCCCccccCCCC
Q 024302 107 YRPVNVVCWKRAICLEFMEKT--------INSPNGSFYIPAVLRVRHLLQVVKRRRIKNNLSRKNLMYRDNFTCQYCSSR 178 (269)
Q Consensus 107 y~Pl~~~s~qrAv~l~~~~k~--------v~s~s~~~~vPsVIrL~~yv~~p~r~~v~~~~~R~~Vl~RD~~~C~YCG~~ 178 (269)
|.|....+|++++..+..++. ..+.+.....|.+..+..+.+.+... .++.+|..++.+|++.|+||+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~r~~~~~~d~~~c~~c~~~ 78 (146)
T COG1403 1 YNPLESKSIRPALDRLVSQRAKHVAEYPCLASESKDLRRPSVTDLTGESKRPSEK--RPAKTRRAVLLRDNGLCQYCGSV 78 (146)
T ss_pred CccccccchhHHHHHHhhcccccccCcceecceecccccCccceeeeeecccCCC--CchHHHHHHHccccccccccCCc
Confidence 578889999999999998772 33334566789999999887666443 36889999999999999999987
Q ss_pred C-CCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHhccccccCCCCCCcc
Q 024302 179 E-NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKAPKDY 233 (269)
Q Consensus 179 ~-~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~gm~Ll~~P~~P~~~ 233 (269)
. .+++|||+|++.||.+.|+||+++|..||.+|+++.+.+++|.....|..|...
T Consensus 79 ~~~~~~dHiip~~~g~~~~~~Nl~~lc~~c~~~k~~~~~~~~~~~~~~~~~~~~~~ 134 (146)
T COG1403 79 GTDLEVDHIVPLSRGGASAWENLETLCERCHNKKGSRLPGKAGMKLRVKPRKPEVE 134 (146)
T ss_pred CCCCceeeEeecccCCcchHHHHHHHHHhhcccccccchhhccCcccccccCCchh
Confidence 3 789999999999999999999999999999999999999999999999988743
No 2
>PF13395 HNH_4: HNH endonuclease
Probab=99.37 E-value=1.6e-13 Score=98.35 Aligned_cols=45 Identities=49% Similarity=0.949 Sum_probs=42.0
Q ss_pred cccCCCC---C-----CCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCH
Q 024302 172 CQYCSSR---E-----NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTL 216 (269)
Q Consensus 172 C~YCG~~---~-----~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtp 216 (269)
|.|||+. . ..++|||+|+|.++.+++.|+|++|+.||+.|++++|
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 2799999999999999999999999999999999986
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=99.31 E-value=1.7e-12 Score=89.28 Aligned_cols=52 Identities=42% Similarity=0.797 Sum_probs=47.5
Q ss_pred HHHHHHHHCCCccccCCCC---CCCccceeeecCCCCCcchhhHHHhchhhhcCcC
Q 024302 160 SRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKG 212 (269)
Q Consensus 160 ~R~~Vl~RD~~~C~YCG~~---~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg 212 (269)
.|..+++++ ++|+||+.. ..+++|||+|.+.||.++++||+++|..||..|+
T Consensus 3 ~r~~~~~~~-~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~~ 57 (57)
T cd00085 3 HRLVLLARD-GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57 (57)
T ss_pred HHHHHHHhC-CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHHHHHhhccC
Confidence 678889998 899999974 6789999999999999999999999999999874
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=5.4e-12 Score=131.53 Aligned_cols=62 Identities=32% Similarity=0.432 Sum_probs=56.7
Q ss_pred HHHHHHHHHHCCCccccCCCC---C------CCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHh
Q 024302 158 NLSRKNLMYRDNFTCQYCSSR---E------NLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 219 (269)
Q Consensus 158 ~~~R~~Vl~RD~~~C~YCG~~---~------~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~ 219 (269)
...|..++.+++++|+|||.+ . .+++|||+|+|.||+|+|+|+|++|..||+.|++++|.++
T Consensus 570 ~~~k~~L~~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~~~N~~K~~~tp~e~ 640 (805)
T TIGR01865 570 NILKLRLYYQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEA 640 (805)
T ss_pred HHHHHHHHHHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhHHHHhhccCCCHHHH
Confidence 346788999999999999987 2 4789999999999999999999999999999999999995
No 5
>smart00507 HNHc HNH nucleases.
Probab=99.22 E-value=4.3e-12 Score=85.77 Aligned_cols=49 Identities=41% Similarity=0.788 Sum_probs=45.0
Q ss_pred HHHHHHHHCCCccccCCCCC--CCccceeeecCCCCCcchhhHHHhchhhhc
Q 024302 160 SRKNLMYRDNFTCQYCSSRE--NLTIDHVVPASRGGEWKWENLVAACFKCNS 209 (269)
Q Consensus 160 ~R~~Vl~RD~~~C~YCG~~~--~ltVDHIiP~S~GG~~tweNLV~aC~~CN~ 209 (269)
.|..++.|| +.|++||... .+++|||+|.+.||.++++||+++|..||.
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 9999999874 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=99.14 E-value=1.8e-12 Score=88.37 Aligned_cols=43 Identities=42% Similarity=0.930 Sum_probs=31.6
Q ss_pred cccCCCC----CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCC
Q 024302 172 CQYCSSR----ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKK 214 (269)
Q Consensus 172 C~YCG~~----~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~r 214 (269)
|+|||.. ..+++|||+|++.||.++++||+++|..||+.|+++
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
>PRK11295 hypothetical protein; Provisional
Probab=98.96 E-value=3.2e-10 Score=93.34 Aligned_cols=61 Identities=20% Similarity=0.312 Sum_probs=53.1
Q ss_pred HHHHHHHHHHCCCccccCCCC------CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHH
Q 024302 158 NLSRKNLMYRDNFTCQYCSSR------ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEE 218 (269)
Q Consensus 158 ~~~R~~Vl~RD~~~C~YCG~~------~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee 218 (269)
.-.|+.++.++++.|+.|++. ..++||||+|...|+.++.+||+++|..||.+|+.+..+.
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 568999999999999999985 3569999999998988889999999999999997665433
No 8
>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=98.91 E-value=1.1e-09 Score=92.30 Aligned_cols=74 Identities=22% Similarity=0.377 Sum_probs=58.7
Q ss_pred HHHHHHHHHHCCCccccCCCC---CCCccceeeecCCCCC--cchhhHHHhchh---------hhcCcCCCCHHHhcccc
Q 024302 158 NLSRKNLMYRDNFTCQYCSSR---ENLTIDHVVPASRGGE--WKWENLVAACFK---------CNSRKGKKTLEEANMQL 223 (269)
Q Consensus 158 ~~~R~~Vl~RD~~~C~YCG~~---~~ltVDHIiP~S~GG~--~tweNLV~aC~~---------CN~~Kg~rtpee~gm~L 223 (269)
..+|..++...+++|+||+.. ..++|||++|++..+. .+|+||+.+|.. ||..|++..... ...+
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 568999999999999999984 5689999999998875 689999999999 888886554322 2344
Q ss_pred ccCCCCCCc
Q 024302 224 SRVPKAPKD 232 (269)
Q Consensus 224 l~~P~~P~~ 232 (269)
+..|..+..
T Consensus 92 ~i~P~~~~~ 100 (144)
T TIGR02646 92 LIDPLADDC 100 (144)
T ss_pred ccCCCCCCh
Confidence 556777754
No 9
>PF14279 HNH_5: HNH endonuclease
Probab=97.40 E-value=6.4e-05 Score=57.27 Aligned_cols=45 Identities=40% Similarity=0.826 Sum_probs=37.1
Q ss_pred cccCCCC---CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHh
Q 024302 172 CQYCSSR---ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 219 (269)
Q Consensus 172 C~YCG~~---~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~ 219 (269)
|.||.+. ...+.+||+|-|-||...+.| .|..||+.-|...-.+.
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~---vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN---VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc---hhHHHhHHHhHHHHHHH
Confidence 8999976 345689999999999888877 89999998876654443
No 10
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=96.51 E-value=0.0011 Score=69.96 Aligned_cols=60 Identities=32% Similarity=0.406 Sum_probs=53.3
Q ss_pred HHHHHHHHCCCccccCCCC------CC---CccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHh
Q 024302 160 SRKNLMYRDNFTCQYCSSR------EN---LTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 219 (269)
Q Consensus 160 ~R~~Vl~RD~~~C~YCG~~------~~---ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~ 219 (269)
.+-.++.-++++|.|.|.. .+ .+||||+|.|+--+|+.+|.|..-..-|+-|+|.+|.|+
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 4556778889999999986 23 899999999999999999999999999999999998774
No 11
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=95.36 E-value=0.012 Score=51.44 Aligned_cols=55 Identities=18% Similarity=0.308 Sum_probs=42.2
Q ss_pred HHHHHHHHHHCCCccccCCCC-----CCCccceeeecCCCCCcchhh-HHHhchhhhcCcCCCC
Q 024302 158 NLSRKNLMYRDNFTCQYCSSR-----ENLTIDHVVPASRGGEWKWEN-LVAACFKCNSRKGKKT 215 (269)
Q Consensus 158 ~~~R~~Vl~RD~~~C~YCG~~-----~~ltVDHIiP~S~GG~~tweN-LV~aC~~CN~~Kg~rt 215 (269)
+..++.+++.++++|+.|+.+ ..+++||.-|.+... + .+ --.+|..||...|.-.
T Consensus 9 ~~~k~~l~e~Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~--T-G~VRGLLC~~CN~~lG~~~ 69 (157)
T PHA02565 9 KEEKQKLFEAQNGICPLCKRELDGDVSKNHLDHDHELNGPN--A-GRVRGLLCNLCNALEGQMK 69 (157)
T ss_pred HHHHHHHHHHhCCcCCCCCCccCCCccccccCCCCCCCCcc--c-ccccccCchhhhhhhhhhh
Confidence 567889999999999999975 347899998776311 1 23 3579999999887663
No 12
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=95.35 E-value=0.01 Score=55.69 Aligned_cols=59 Identities=15% Similarity=0.302 Sum_probs=47.4
Q ss_pred CHHHHHHHHHHCCCccccCCCC----------CCCccceeeecCCCC----CcchhhHHHhchhhhcCcCCCC
Q 024302 157 NNLSRKNLMYRDNFTCQYCSSR----------ENLTIDHVVPASRGG----EWKWENLVAACFKCNSRKGKKT 215 (269)
Q Consensus 157 ~~~~R~~Vl~RD~~~C~YCG~~----------~~ltVDHIiP~S~GG----~~tweNLV~aC~~CN~~Kg~rt 215 (269)
.+..|++.++-.+..|.-|+-. .-.+|+|++|.+.-+ .+...-|+++|+.||..-+.+.
T Consensus 183 na~~ra~~Ia~~G~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~mvHrr~ 255 (272)
T COG3183 183 NATLRAAAIAIHGTVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHKMVHRRR 255 (272)
T ss_pred ChHHHHHHHHHhCceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHHHHhccC
Confidence 4678888888889999999854 358999999998533 3678999999999998655443
No 13
>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=95.35 E-value=0.0078 Score=42.70 Aligned_cols=44 Identities=32% Similarity=0.523 Sum_probs=35.5
Q ss_pred HHHHCCCccccCCCCCCCccceeeecCCCCCcchhhHHHhchhhhcC
Q 024302 164 LMYRDNFTCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFKCNSR 210 (269)
Q Consensus 164 Vl~RD~~~C~YCG~~~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~ 210 (269)
++.|.+..|..|+....|.+-+|-|.+.| .-+|-+.+|..|+..
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~Vpp~~~~---~~d~~iliC~tC~~Q 45 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYAVPPSSDV---TADNSVMLCDTCHSQ 45 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEecCCCCCC---CccceeeechHHHHh
Confidence 67899999999998888988887665443 356779999999864
No 14
>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=94.35 E-value=0.057 Score=48.47 Aligned_cols=58 Identities=19% Similarity=0.349 Sum_probs=45.4
Q ss_pred HHHHHHHHHHC-CCccccCCCC--CCCccceeeecCCCC--CcchhhHHHhchhhhcCcCCCC
Q 024302 158 NLSRKNLMYRD-NFTCQYCSSR--ENLTIDHVVPASRGG--EWKWENLVAACFKCNSRKGKKT 215 (269)
Q Consensus 158 ~~~R~~Vl~RD-~~~C~YCG~~--~~ltVDHIiP~S~GG--~~tweNLV~aC~~CN~~Kg~rt 215 (269)
....+.|..|| +..|..||.. ..++.-|...+..-. ..+.+|+-..|..||..+++..
T Consensus 75 ~afn~~IR~RD~~~~CiSCG~~~~~~~dagHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~ 137 (189)
T PF05766_consen 75 KAFNKYIRLRDAGKPCISCGRKHGGQWDAGHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNI 137 (189)
T ss_pred HHHHHHHHHHhcCCCcccCCCcCCCCcccccccccccCcccccChhhHhHcCCccccccccCH
Confidence 35667788886 7799999987 568899997653223 3678999999999999997654
No 15
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=93.77 E-value=0.027 Score=53.64 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=46.8
Q ss_pred CCHHHHHHHHHHCCCccccCCCC-------CCCccceeeecCCCCCcchhhHHHhchhhhcC
Q 024302 156 KNNLSRKNLMYRDNFTCQYCSSR-------ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 210 (269)
Q Consensus 156 ~~~~~R~~Vl~RD~~~C~YCG~~-------~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~ 210 (269)
+....|+.|+.--+++|+.||.. .....-||.|.+++|.+...|-.++|+..|-.
T Consensus 179 rd~~fRk~V~~~Y~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~nHh~~ 240 (301)
T COG3440 179 RDGAFRKIVLRQYDYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCKNHHWA 240 (301)
T ss_pred hhHHHHHHHHHHhcchhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhchhhHHH
Confidence 34789999999999999999943 33566799999999999999999999877763
No 16
>PF13391 HNH_2: HNH endonuclease
Probab=93.72 E-value=0.013 Score=42.03 Aligned_cols=39 Identities=23% Similarity=0.135 Sum_probs=31.8
Q ss_pred cccCCCCC-----CCccceeeecCCC--CCc-----------chhhHHHhchhhhcC
Q 024302 172 CQYCSSRE-----NLTIDHVVPASRG--GEW-----------KWENLVAACFKCNSR 210 (269)
Q Consensus 172 C~YCG~~~-----~ltVDHIiP~S~G--G~~-----------tweNLV~aC~~CN~~ 210 (269)
|..||... .+++-||+|.+.+ +.+ +.+|..++|..+|..
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 77787655 6899999999987 444 788999999999864
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=93.38 E-value=0.036 Score=54.67 Aligned_cols=49 Identities=24% Similarity=0.378 Sum_probs=39.3
Q ss_pred CccccCCCC-CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHh
Q 024302 170 FTCQYCSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEA 219 (269)
Q Consensus 170 ~~C~YCG~~-~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~ 219 (269)
..|+-|+.. ..+..|||-|.|.|=.+... .+++|..||+.|.+|.--..
T Consensus 245 ~~~~~~~~~p~~~saDHIGPISlGF~h~P~-Fqplc~~cNSaKnnR~~lsD 294 (424)
T TIGR02986 245 CSIPECCKHPEKISADHIGPISLGFVHDPR-FQPLCSSCNSAKNDRLTLSD 294 (424)
T ss_pred ccCcccccCCCCCCccccCCcccccccCcc-ccccccccccccccceeHHH
Confidence 356677765 67899999999999777664 49999999999999874443
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=91.25 E-value=0.2 Score=44.95 Aligned_cols=51 Identities=14% Similarity=0.271 Sum_probs=37.2
Q ss_pred CCCccccCCCCCCCccceeeecCCCC---CcchhhHHHhchhhhcCcCCCCHHHhc
Q 024302 168 DNFTCQYCSSRENLTIDHVVPASRGG---EWKWENLVAACFKCNSRKGKKTLEEAN 220 (269)
Q Consensus 168 D~~~C~YCG~~~~ltVDHIiP~S~GG---~~tweNLV~aC~~CN~~Kg~rtpee~g 220 (269)
-...|..||+.. -.++|++..-+|| ...-..++++|+.||+...+ -...+.
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 4889997665554 34557899999999998877 555443
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=90.27 E-value=0.14 Score=53.25 Aligned_cols=38 Identities=24% Similarity=0.269 Sum_probs=28.0
Q ss_pred HHHHCCCccccCCCC--CCCccceeeecCCCCC------cchhhHH
Q 024302 164 LMYRDNFTCQYCSSR--ENLTIDHVVPASRGGE------WKWENLV 201 (269)
Q Consensus 164 Vl~RD~~~C~YCG~~--~~ltVDHIiP~S~GG~------~tweNLV 201 (269)
|..-..+.|+|||.. ..-++|||+|+|.-+. ++..||+
T Consensus 755 Ik~fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k~ygtvFN~E~NLI 800 (802)
T TIGR03031 755 IKNFSMGICPYKGASIGGQGEIDHIYPRSHSKKHYGTIFNSEVNLI 800 (802)
T ss_pred HHHHhccCCCCCCCCCCCcccccccccccccccccceeecCcccee
Confidence 444456899999987 5679999999998654 4455654
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=88.57 E-value=0.15 Score=51.44 Aligned_cols=49 Identities=29% Similarity=0.419 Sum_probs=37.1
Q ss_pred CCCC-CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCCCHHHhccccc
Q 024302 175 CSSR-ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLS 224 (269)
Q Consensus 175 CG~~-~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rtpee~gm~Ll 224 (269)
|+.. .-+..|||-|.|.|=.+... .+++|..||+.|.+|.--..-..|+
T Consensus 250 ~~~~~~~~SaDHIGPISlGF~h~P~-Fqplc~~cNSaKnnR~~lsDV~~Li 299 (511)
T PF09665_consen 250 CGKEEECLSADHIGPISLGFVHRPR-FQPLCKSCNSAKNNRMYLSDVKKLI 299 (511)
T ss_pred hhhhccccCccccCCcccccccCcc-ccccccccccccccceeHHHHHHHH
Confidence 5544 55799999999999877664 4999999999999987544333333
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=71.41 E-value=2.1 Score=39.38 Aligned_cols=57 Identities=21% Similarity=0.368 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHC-CCccccCCCC-----CCCccceeeecCCCC------CcchhhHHHhchhhhcCcC
Q 024302 156 KNNLSRKNLMYRD-NFTCQYCSSR-----ENLTIDHVVPASRGG------EWKWENLVAACFKCNSRKG 212 (269)
Q Consensus 156 ~~~~~R~~Vl~RD-~~~C~YCG~~-----~~ltVDHIiP~S~GG------~~tweNLV~aC~~CN~~Kg 212 (269)
....+|+.|..-- +-.|++||.. ..+++||---+...- ..+.+-++++|..||..|.
T Consensus 83 fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~ieiDHKd~rk~d~rvsd~~~q~~~dFQ~Lck~~N~~KR 151 (230)
T PF05315_consen 83 FNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEIDHKDGRKDDLRVSDMNTQTFDDFQPLCKACNDQKR 151 (230)
T ss_pred hhhHHHHHHHHHHHhcCeeeecccCCCccceeeecccccccccchhcccchhhHHHHHHHHHHHhHHHH
Confidence 4456777765543 3489999974 567888873332221 1345889999999999884
No 22
>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=64.47 E-value=3.2 Score=32.45 Aligned_cols=50 Identities=24% Similarity=0.410 Sum_probs=31.1
Q ss_pred HHHHHHHHHHCCCccccCCC-----CCCCccceeeecCCCCCcchhhHHHhchhhhcCcCCC
Q 024302 158 NLSRKNLMYRDNFTCQYCSS-----RENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKK 214 (269)
Q Consensus 158 ~~~R~~Vl~RD~~~C~YCG~-----~~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~r 214 (269)
.....++++.++++|+.|+. ...+.+||=-. .| . .. -.+|..||..-|.-
T Consensus 11 ~~~~~~l~~~q~~~C~iC~~~~~~~~~~~~vDHdH~--tG-~--vR--GlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 11 PEEYEALLEEQGGRCAICGKPLPGESRKLVVDHDHK--TG-R--VR--GLLCRSCNTALGKV 65 (81)
T ss_dssp HHHHHCCHHHTTTE-TTT-SEEETTCGGCEEEE-TT--TT-B--EE--EEEEHHHHHHHHHC
T ss_pred HHHHHHHHHHhCCcCcCCCCCcccCCCcceecCCCC--CC-C--ch--hhhhhHHhhhhccc
Confidence 34556788999999999998 25678888541 11 1 00 15899999865443
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=63.28 E-value=30 Score=26.63 Aligned_cols=52 Identities=19% Similarity=0.215 Sum_probs=34.6
Q ss_pred ccccceEEEEcCCcceeeeecHHHHHHHHhhCc---eeecCCceeecceEEEEeecee
Q 024302 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEK---TINSPNGSFYIPAVLRVRHLLQ 148 (269)
Q Consensus 94 ~~~~~~vLvLnasy~Pl~~~s~qrAv~l~~~~k---~v~s~s~~~~vPsVIrL~~yv~ 148 (269)
.+....|.|+|..++.+.+++..+|+.+.-.-. +.-+++.. |-|.+|..|-+
T Consensus 9 ~I~~~~VrlI~~~g~~lGv~~~~eAl~~A~~~~lDLV~v~~~~~---PPVcKi~dy~k 63 (76)
T PF05198_consen 9 EIRAPEVRLIDEDGEQLGVMSLREALRLAKEKGLDLVEVSPNAD---PPVCKIMDYGK 63 (76)
T ss_dssp G---SEEEEE-TTS-EEEEEEHHHHHHHHHHTT-EEEEEETTSS---S-EEEEE-HHH
T ss_pred CcCCCEEEEECCCCcEeceEEHHHHHHHHHHcCCcEEEEcCCCC---CCeEEEechHH
Confidence 456678999999999999999999999877644 44444433 78888887643
No 24
>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=58.92 E-value=8.7 Score=33.35 Aligned_cols=20 Identities=20% Similarity=0.062 Sum_probs=11.9
Q ss_pred ccccceeeeecCCCCeeeec
Q 024302 5 TSQGGLNLLFNGDGSSFGVE 24 (269)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~ 24 (269)
||.-..||+.+.+.++-+-.
T Consensus 1 ttNRGnKL~~~a~~V~~g~L 20 (149)
T PF08595_consen 1 TTNRGNKLKQRAEFVHRGQL 20 (149)
T ss_pred CCCcchhcchhccceecccc
Confidence 34445667666666666555
No 25
>PF14239 RRXRR: RRXRR protein
Probab=43.82 E-value=38 Score=30.28 Aligned_cols=42 Identities=21% Similarity=0.097 Sum_probs=33.5
Q ss_pred EEEEcCCcceeeeecHHHHHHHHhhCceeecCCceeecceEEEEee
Q 024302 100 GLVLDISYRPVNVVCWKRAICLEFMEKTINSPNGSFYIPAVLRVRH 145 (269)
Q Consensus 100 vLvLnasy~Pl~~~s~qrAv~l~~~~k~v~s~s~~~~vPsVIrL~~ 145 (269)
|.|||.+..||.=+...+|-.|+=.||...-- .-|-+|.|..
T Consensus 1 VfVld~~gkPLmP~~p~rAR~LLk~GkA~V~r----~~PFtI~L~~ 42 (176)
T PF14239_consen 1 VFVLDKNGKPLMPCHPARARKLLKQGKAKVVR----RYPFTIQLKY 42 (176)
T ss_pred CeEECCCCCcCCCCCHHHHHHHHHCCCEEEEe----cCCeEEEEEe
Confidence 68999999999999999999999999942211 3466777764
No 26
>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=34.04 E-value=5.3 Score=27.27 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=16.8
Q ss_pred hhhHHHhchhhhcCcCCCCH
Q 024302 197 WENLVAACFKCNSRKGKKTL 216 (269)
Q Consensus 197 weNLV~aC~~CN~~Kg~rtp 216 (269)
+++|..+|+.||.+-++.+|
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 58999999999999888664
No 27
>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=33.37 E-value=1.1e+02 Score=26.90 Aligned_cols=54 Identities=15% Similarity=0.154 Sum_probs=40.9
Q ss_pred ccccceEEEEcCCcceeeeecHHHHHHHHhhCc---eeecCCceeecceEEEEeeceecc
Q 024302 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEK---TINSPNGSFYIPAVLRVRHLLQVV 150 (269)
Q Consensus 94 ~~~~~~vLvLnasy~Pl~~~s~qrAv~l~~~~k---~v~s~s~~~~vPsVIrL~~yv~~p 150 (269)
.+..+.|.+.|..++.+.+++.++|+.+.-... +.-++.. -|-|.++..|-+.-
T Consensus 4 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLVev~~~a---~PPVckImdy~k~~ 60 (165)
T TIGR00168 4 RIRFNEVRLIDENGEQLGIVSREEALEIAEEAGLDLVLISPNA---KPPVCKIMDYGKYK 60 (165)
T ss_pred CcCCCEEEEECCCCcCCCcccHHHHHHHHHHcCCcEEEECCCC---CCCEEEEeeHHHHH
Confidence 356678999999999999999999998877544 4444543 37788988875443
No 28
>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=31.29 E-value=16 Score=29.18 Aligned_cols=37 Identities=27% Similarity=0.272 Sum_probs=29.2
Q ss_pred cceeeecCCCCC----------------cchhhHHHhchhhhcCcCCCCHHHh
Q 024302 183 IDHVVPASRGGE----------------WKWENLVAACFKCNSRKGKKTLEEA 219 (269)
Q Consensus 183 VDHIiP~S~GG~----------------~tweNLV~aC~~CN~~Kg~rtpee~ 219 (269)
+|||.|.+.... +...||+.+=..=|..++++.+.+-
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 999999985442 5678899998888988888776553
No 29
>PRK00028 infC translation initiation factor IF-3; Reviewed
Probab=30.26 E-value=1.3e+02 Score=26.55 Aligned_cols=52 Identities=15% Similarity=0.139 Sum_probs=40.1
Q ss_pred ccccceEEEEcCCcceeeeecHHHHHHHHhhCc---eeecCCceeecceEEEEeecee
Q 024302 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEK---TINSPNGSFYIPAVLRVRHLLQ 148 (269)
Q Consensus 94 ~~~~~~vLvLnasy~Pl~~~s~qrAv~l~~~~k---~v~s~s~~~~vPsVIrL~~yv~ 148 (269)
.+....|.|+|..++.+.+++..+|+.+.-.-. +.-++... |.|-++..|-+
T Consensus 16 ~I~~~~Vrli~~dG~~lgv~~~~eAl~~A~~~~lDLV~v~~~~~---PPVckI~dy~k 70 (177)
T PRK00028 16 QIRAREVRLIGDDGEQLGIVSTREALELAEEAGLDLVEISPNAK---PPVCKIMDYGK 70 (177)
T ss_pred CcCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEECCCCC---CCEEEEEeHHH
Confidence 466788999999999999999999998766433 44455444 78888887754
No 30
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.52 E-value=20 Score=25.96 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=22.8
Q ss_pred ccccCCCCCCCccceeeecCCCCCcchhhHHHhchh
Q 024302 171 TCQYCSSRENLTIDHVVPASRGGEWKWENLVAACFK 206 (269)
Q Consensus 171 ~C~YCG~~~~ltVDHIiP~S~GG~~tweNLV~aC~~ 206 (269)
.|+|||....+.+| .|.|+..-++-....|++
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 69999976544444 456666778888888864
No 31
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=27.79 E-value=46 Score=32.15 Aligned_cols=47 Identities=17% Similarity=0.387 Sum_probs=32.8
Q ss_pred CCCccccCCCCCCCccceeeecCCCCC--------cchhhHHHhchhhhcCcCCC
Q 024302 168 DNFTCQYCSSRENLTIDHVVPASRGGE--------WKWENLVAACFKCNSRKGKK 214 (269)
Q Consensus 168 D~~~C~YCG~~~~ltVDHIiP~S~GG~--------~tweNLV~aC~~CN~~Kg~r 214 (269)
..+.|.-||......+=|+--...|=+ +.|.-+.+-|..|.+.|+..
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 345899999874334445543444433 68999999999999998654
No 32
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=23.98 E-value=21 Score=32.58 Aligned_cols=52 Identities=19% Similarity=0.268 Sum_probs=29.0
Q ss_pred HHHHHHCCCccccCCCCCCC---ccceeeecCCCCC---cchhhHHHhchhhhcCcCCC
Q 024302 162 KNLMYRDNFTCQYCSSRENL---TIDHVVPASRGGE---WKWENLVAACFKCNSRKGKK 214 (269)
Q Consensus 162 ~~Vl~RD~~~C~YCG~~~~l---tVDHIiP~S~GG~---~tweNLV~aC~~CN~~Kg~r 214 (269)
+.|.+-+ --|.+||++..+ .++..-+...|.. -.-++-++.|+.||...+..
T Consensus 138 Dkv~kL~-aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~~~~~~ 195 (201)
T COG1435 138 DKVTKLK-AICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHKEPGKE 195 (201)
T ss_pred HHHHHHH-HHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhhccccc
Confidence 3344433 479999987321 2232222222211 12578899999999877544
No 33
>CHL00199 infC translation initiation factor 3; Provisional
Probab=23.60 E-value=2.1e+02 Score=25.80 Aligned_cols=53 Identities=19% Similarity=0.157 Sum_probs=41.1
Q ss_pred ccccceEEEEcCCcceeeeecHHHHHHHHhhCc---eeecCCceeecceEEEEeeceec
Q 024302 94 ELACFRGLVLDISYRPVNVVCWKRAICLEFMEK---TINSPNGSFYIPAVLRVRHLLQV 149 (269)
Q Consensus 94 ~~~~~~vLvLnasy~Pl~~~s~qrAv~l~~~~k---~v~s~s~~~~vPsVIrL~~yv~~ 149 (269)
.+....|.|.|..++.+.+++.++|+.+.-... +.-++... |-|-++..|-+.
T Consensus 21 ~I~~~~VrlI~~~G~~lGv~~~~eAl~~A~~~~lDLVeVs~~a~---PPVCKImdygK~ 76 (182)
T CHL00199 21 RIRFPKVRVIDDSGEQLGIFTSEQAIQLAANQGLDLVLVSEKSD---PPVCRIIDYGKY 76 (182)
T ss_pred ccCCCEEEEECCCCcCCCceeHHHHHHHHHHcCCCEEEECCCCC---CCeEEEeehHHH
Confidence 466789999999999999999999998876543 45555433 788888887543
No 34
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=21.57 E-value=1.4e+02 Score=22.48 Aligned_cols=20 Identities=30% Similarity=0.620 Sum_probs=14.8
Q ss_pred CCCccccCCCCCCCccceeee
Q 024302 168 DNFTCQYCSSRENLTIDHVVP 188 (269)
Q Consensus 168 D~~~C~YCG~~~~ltVDHIiP 188 (269)
....|..|+...+ +++|+.=
T Consensus 58 ~~~~C~~C~~~~E-t~~Hlf~ 77 (86)
T PF13966_consen 58 VDPICPLCGNEEE-TIEHLFF 77 (86)
T ss_pred cCCccccCCCccc-cccceec
Confidence 3579999997533 8889863
No 35
>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=21.35 E-value=47 Score=23.27 Aligned_cols=38 Identities=34% Similarity=0.695 Sum_probs=21.2
Q ss_pred CCCccccCCCC--CCCccceeeecCCCCCcchhhHHHhchhhhcC
Q 024302 168 DNFTCQYCSSR--ENLTIDHVVPASRGGEWKWENLVAACFKCNSR 210 (269)
Q Consensus 168 D~~~C~YCG~~--~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~ 210 (269)
+.+.|+||++. ..-=++|+.-.-.+... ...|.-|...
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 35799999984 11123565543332211 2578888753
No 36
>PTZ00293 thymidine kinase; Provisional
Probab=20.68 E-value=37 Score=30.92 Aligned_cols=57 Identities=23% Similarity=0.445 Sum_probs=31.8
Q ss_pred CccccCCCCCCCccceeee---c-CCCCCcchhhHHHhchhhhcCcCCCCHHHhccccccCCCCC
Q 024302 170 FTCQYCSSRENLTIDHVVP---A-SRGGEWKWENLVAACFKCNSRKGKKTLEEANMQLSRVPKAP 230 (269)
Q Consensus 170 ~~C~YCG~~~~ltVDHIiP---~-S~GG~~tweNLV~aC~~CN~~Kg~rtpee~gm~Ll~~P~~P 230 (269)
-.|..||.+..++.- ++. . --||. +.-++.|+.|+..|.....+.-.......+..+
T Consensus 138 aiC~~CG~~A~~t~R-~~~~~~~v~IGg~---e~Y~a~CR~c~~~~~~~~~~~~~~~~~~~~~~~ 198 (211)
T PTZ00293 138 AVCMFCGKEASFSKR-IVQSEQIELIGGE---DKYIATCRKCFRTKQLAEKELEKQDLVEFADFS 198 (211)
T ss_pred eEchhhCCcceeEEE-EcCCCCEEEECCc---ccEEehhhhhhhhhccchHhhhhchhhhhcccC
Confidence 589999987332211 111 0 12332 357899999998887766544443333333333
No 37
>COG3303 NrfA Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit [Inorganic ion transport and metabolism]
Probab=20.28 E-value=49 Score=33.43 Aligned_cols=49 Identities=20% Similarity=0.468 Sum_probs=35.4
Q ss_pred HHHHHHHCCCccccCCCC------CCCccceeeecCCCCCcchhhHHHhchhhhcCcCCCC
Q 024302 161 RKNLMYRDNFTCQYCSSR------ENLTIDHVVPASRGGEWKWENLVAACFKCNSRKGKKT 215 (269)
Q Consensus 161 R~~Vl~RD~~~C~YCG~~------~~ltVDHIiP~S~GG~~tweNLV~aC~~CN~~Kg~rt 215 (269)
-.-|....+-+|.-|.-+ ..+..||-| .+-.+|+...|..||..-....
T Consensus 290 s~GvHgkNgVtCiDCHMPkVq~a~gK~yTdH~I------~nPf~~f~stCanCH~Qsk~~L 344 (501)
T COG3303 290 SAGVHGKNGVTCIDCHMPKVQNAEGKLYTDHKI------GNPFDNFASTCANCHTQSKAKL 344 (501)
T ss_pred hccccccCCceeEecCCccccCCCCceeecccc------CChhHHHHHHHhhhhhhhHHHH
Confidence 344666677799999754 345667776 3568999999999998755443
Done!