Query 023513
Match_columns 281
No_of_seqs 122 out of 209
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:36:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00228 ruvC crossover junct 100.0 1.1E-43 2.4E-48 306.3 15.8 151 90-253 1-153 (156)
2 COG0817 RuvC Holliday junction 100.0 3.5E-43 7.5E-48 303.4 11.7 149 91-251 1-151 (160)
3 PRK00039 ruvC Holliday junctio 100.0 3E-41 6.6E-46 292.0 16.4 154 88-252 2-157 (164)
4 PF02075 RuvC: Crossover junct 100.0 2.1E-41 4.5E-46 287.9 12.5 147 90-247 1-149 (149)
5 cd00529 RuvC_resolvase Hollida 100.0 1.9E-37 4.2E-42 263.8 13.5 150 89-249 1-152 (154)
6 PF04848 Pox_A22: Poxvirus A22 98.7 2.4E-07 5.3E-12 79.7 12.1 135 88-247 1-139 (143)
7 PF07066 DUF3882: Lactococcus 98.7 1.6E-08 3.4E-13 87.5 4.1 143 90-247 4-157 (159)
8 smart00732 YqgFc Likely ribonu 97.1 0.0035 7.5E-08 48.2 7.9 87 89-193 2-90 (99)
9 PF04312 DUF460: Protein of un 97.0 0.001 2.3E-08 57.2 4.6 75 85-180 29-103 (138)
10 COG2433 Uncharacterized conser 96.9 0.0054 1.2E-07 63.5 9.9 53 88-156 244-296 (652)
11 PF01548 DEDD_Tnp_IS110: Trans 95.9 0.022 4.7E-07 46.8 5.9 107 90-249 1-108 (144)
12 PRK00109 Holliday junction res 95.7 0.5 1.1E-05 40.1 13.6 93 87-194 3-96 (138)
13 PF03652 UPF0081: Uncharacteri 95.4 0.19 4.2E-06 42.5 10.1 99 88-202 1-106 (135)
14 COG0816 Predicted endonuclease 93.2 3.6 7.8E-05 35.6 13.2 95 88-196 2-97 (141)
15 COG2410 Predicted nuclease (RN 92.5 3.7 7.9E-05 37.0 12.5 66 181-261 94-165 (178)
16 PF11215 DUF3010: Protein of u 90.5 2.1 4.6E-05 37.1 8.7 109 88-204 1-111 (138)
17 TIGR00250 RNAse_H_YqgF RNAse H 90.4 1.5 3.2E-05 36.9 7.6 89 91-194 1-90 (130)
18 PF03237 Terminase_6: Terminas 89.1 0.47 1E-05 42.9 3.9 65 84-158 222-292 (384)
19 PF09159 Ydc2-catalyt: Mitocho 88.4 2.2 4.8E-05 40.1 8.0 133 90-224 1-191 (274)
20 COG2183 Tex Transcriptional ac 83.8 2.1 4.5E-05 46.1 5.8 38 84-121 326-366 (780)
21 PF14239 RRXRR: RRXRR protein 81.5 1.7 3.6E-05 39.1 3.5 22 86-107 49-71 (176)
22 PF07318 DUF1464: Protein of u 74.6 5.5 0.00012 39.2 5.1 54 92-157 1-55 (343)
23 PTZ00340 O-sialoglycoprotein e 63.4 55 0.0012 32.2 9.4 100 88-196 1-110 (345)
24 PF04250 DUF429: Protein of un 61.2 1.2E+02 0.0025 26.8 12.3 67 183-249 109-187 (209)
25 COG2433 Uncharacterized conser 60.6 1.1E+02 0.0025 32.6 11.5 94 87-222 1-103 (652)
26 TIGR01630 psiM2_ORF9 phage unc 57.9 71 0.0015 26.3 8.0 84 148-247 42-139 (142)
27 COG2441 Predicted butyrate kin 53.2 14 0.00031 36.1 3.4 31 91-123 1-33 (374)
28 PF14639 YqgF: Holliday-juncti 51.3 33 0.00071 29.7 5.0 58 90-155 7-69 (150)
29 COG1214 Inactive homolog of me 49.7 32 0.0007 31.3 5.0 100 88-201 1-103 (220)
30 PRK09604 UGMP family protein; 49.5 77 0.0017 30.4 7.7 101 88-197 1-113 (332)
31 COG4020 Uncharacterized protei 38.0 82 0.0018 30.6 5.9 24 86-109 1-25 (332)
32 TIGR01865 cas_Csn1 CRISPR-asso 35.9 60 0.0013 35.3 5.2 19 90-108 3-22 (805)
33 PRK09605 bifunctional UGMP fam 33.9 1.8E+02 0.004 29.3 8.0 99 88-195 1-108 (535)
34 TIGR03725 bact_YeaZ universal 33.5 1.5E+02 0.0031 26.2 6.5 94 90-199 1-97 (202)
35 KOG1111 N-acetylglucosaminyltr 32.8 1.1E+02 0.0023 31.2 5.9 61 171-251 279-339 (426)
36 COG3547 Transposase and inacti 30.3 94 0.002 28.2 4.9 23 181-203 52-74 (303)
37 COG3513 Predicted CRISPR-assoc 28.5 28 0.00061 38.4 1.2 21 89-109 5-26 (1088)
38 COG1940 NagC Transcriptional r 27.4 1.5E+02 0.0033 27.3 5.8 25 85-109 3-28 (314)
39 COG0533 QRI7 Metal-dependent p 27.4 4.2E+02 0.0092 26.3 9.0 92 88-193 1-108 (342)
40 PF01385 OrfB_IS605: Probable 26.3 53 0.0011 28.2 2.4 32 62-99 104-135 (227)
41 PF11071 DUF2872: Protein of u 25.9 1.3E+02 0.0028 26.3 4.6 62 211-278 11-73 (141)
42 TIGR03646 YtoQ_fam YtoQ family 25.6 1.3E+02 0.0029 26.4 4.6 44 231-278 33-76 (144)
43 PLN03229 acetyl-coenzyme A car 25.3 2.4E+02 0.0053 30.9 7.4 92 90-193 182-286 (762)
44 PHA02535 P terminase ATPase su 24.0 1.6E+02 0.0036 31.1 5.8 89 88-202 403-499 (581)
45 PRK15080 ethanolamine utilizat 22.8 1.8E+02 0.0039 26.8 5.4 94 86-195 22-123 (267)
46 COG3426 Butyrate kinase [Energ 22.6 85 0.0018 31.0 3.2 107 90-201 5-136 (358)
47 PHA02533 17 large terminase pr 22.3 1.6E+02 0.0035 30.5 5.3 22 233-254 464-485 (534)
48 TIGR01766 tspaseT_teng_C trans 22.1 3.3E+02 0.0072 20.1 6.4 47 150-196 24-79 (82)
No 1
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=100.00 E-value=1.1e-43 Score=306.30 Aligned_cols=151 Identities=17% Similarity=0.109 Sum_probs=136.5
Q ss_pred EEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCch
Q 023513 90 ALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQ 167 (281)
Q Consensus 90 ILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvq 167 (281)
|||||||++. |||||+.+++ .+.++++|++++. +.++.+|| ..|++.|.+++. |+||+++||++| |++|++
T Consensus 1 ILGIDPGl~~tG~gvi~~~~~--~~~~v~~G~I~t~-~~~~~~RL--~~I~~~l~~~i~~y~P~~~aiE~~F--~~~N~~ 73 (156)
T TIGR00228 1 ILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTK-VDDLPSRL--KLIYAGVTEIITQFQPNYFAIEQVF--MAKNAD 73 (156)
T ss_pred CEeECcccccccEEEEEecCC--eEEEEEeeEEECC-CCCHHHHH--HHHHHHHHHHHHHhCCCEEEEeHHh--hccCHH
Confidence 6999999995 9999999888 8899999999876 45788866 899999999998 999999999987 999999
Q ss_pred hhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHc
Q 023513 168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYG 247 (281)
Q Consensus 168 SA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g 247 (281)
|++++|++|||++++++.+||||+||+|++|||+++|+ |+|+|+||++||+++|+..+ .|+ +|+|||||||+||
T Consensus 74 sa~~lg~arGvilla~~~~~ipv~Ey~P~~vKkavtG~-G~A~KeQV~~mV~~lL~l~~----~p~-~DaaDALAiAi~h 147 (156)
T TIGR00228 74 SALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRRLLKLPA----NPQ-ADAADALAIAITH 147 (156)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHcCCCC----CCC-CCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999776 99999999999999997654 245 7899999999999
Q ss_pred cccccC
Q 023513 248 KGLKLD 253 (281)
Q Consensus 248 ~~~~~~ 253 (281)
....+.
T Consensus 148 ~~~~~~ 153 (156)
T TIGR00228 148 AHVSQN 153 (156)
T ss_pred hcccCc
Confidence 865443
No 2
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.5e-43 Score=303.42 Aligned_cols=149 Identities=17% Similarity=0.132 Sum_probs=139.1
Q ss_pred EEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCchh
Q 023513 91 LGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQG 168 (281)
Q Consensus 91 LGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvqS 168 (281)
||||||++. |||||+.+++ ++..+++|+++++...++..|| +.|++.|.+++. |+||++|||++| +.+|++|
T Consensus 1 lGIDPGl~~~G~gvI~~~~~--~l~~v~~G~I~t~~~~~l~~RL--~~l~~~l~~vl~~~~P~~~AIE~~F--~~kN~~s 74 (160)
T COG0817 1 LGIDPGLRRTGYGVIEVEGR--QLSYLASGVIRTSSDAPLAERL--KQLYDGLSEVLDEYQPDEVAIEQVF--VNKNADS 74 (160)
T ss_pred CCcCCCccccceEEEEccCC--eEEEEeeeEEecCCCccHHHHH--HHHHHHHHHHHHHhCCCeeehhHHH--HhcChHH
Confidence 699999995 9999999998 9999999999998889999966 999999999999 999999999987 9999999
Q ss_pred hhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHcc
Q 023513 169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGK 248 (281)
Q Consensus 169 A~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~ 248 (281)
++++||||||+++++++.|+||+||+|+++||+|.|+ |+|+|+||+.||++||+... ++++|+|||||||+||.
T Consensus 75 ~lklgQARGv~~la~~~~~l~v~eY~p~~VKkavvG~-G~A~K~QVq~MV~~lL~~~~-----~~~~DaADALAiAitHa 148 (160)
T COG0817 75 ALKLGQARGVALLAAARRGLPVFEYTPNQVKKAVVGN-GKADKEQVQHMVKRLLGLEE-----PPPADAADALAIAITHA 148 (160)
T ss_pred HHHHHHHHHHHHHHHHHcCCChhhccHHHHHHHhhcC-CcccHHHHHHHHHHHhCCCC-----CCCccHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999665 99999999999999998332 67888999999999998
Q ss_pred ccc
Q 023513 249 GLK 251 (281)
Q Consensus 249 ~~~ 251 (281)
...
T Consensus 149 ~~~ 151 (160)
T COG0817 149 HRA 151 (160)
T ss_pred HHH
Confidence 765
No 3
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=100.00 E-value=3e-41 Score=292.01 Aligned_cols=154 Identities=19% Similarity=0.140 Sum_probs=140.4
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCC
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDG 165 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqN 165 (281)
|+|||||||++ .||||++.+++ .+.++++|+++++...++..|+ ..|++.|.+++. |+||.++||++| |++|
T Consensus 2 m~iLGIDPgl~~tG~avi~~~~~--~~~~~~~G~i~t~~~~~~~~Rl--~~I~~~l~~~i~~~~Pd~vaiE~~f--~~~n 75 (164)
T PRK00039 2 MRILGIDPGLRRTGYGVIEVEGR--RLSYVASGVIRTPSDLDLPERL--KQIYDGLSELIDEYQPDEVAIEEVF--FNKN 75 (164)
T ss_pred CEEEEEccccCceeEEEEEecCC--eEEEEEeeEEECCCCCCHHHHH--HHHHHHHHHHHHHhCCCEEEEehhh--hccC
Confidence 78999999998 59999999887 7899999999887777887865 999999999998 999999999987 8999
Q ss_pred chhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHH
Q 023513 166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAA 245 (281)
Q Consensus 166 vqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~ 245 (281)
.+|++++|++||++++++..+||||+||+|++|||+++|+ |+|+|+||+.||+++|+... .|++||+|||||||+
T Consensus 76 ~~sa~~l~~arGvi~la~~~~~ipv~ey~P~~VKk~vtG~-G~A~K~qV~~mv~~~l~l~~----~~~~~D~aDAlAiA~ 150 (164)
T PRK00039 76 PQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGY-GRADKEQVQHMVKRLLNLPE----IPKPDDAADALAIAI 150 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHhhhhhcCC-CCCCHHHHHHHHHHHhCCCC----CCCCCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999776 99999999999999997654 267789999999999
Q ss_pred Hcccccc
Q 023513 246 YGKGLKL 252 (281)
Q Consensus 246 ~g~~~~~ 252 (281)
||.....
T Consensus 151 ~h~~~~~ 157 (164)
T PRK00039 151 CHAHRRQ 157 (164)
T ss_pred HHHhhcc
Confidence 9987543
No 4
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=100.00 E-value=2.1e-41 Score=287.92 Aligned_cols=147 Identities=21% Similarity=0.187 Sum_probs=115.5
Q ss_pred EEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCch
Q 023513 90 ALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQ 167 (281)
Q Consensus 90 ILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvq 167 (281)
|||||||++ +||||++.+++ .+.++++|++++....++.+|+ ..|++.|.+++. |+||.++||++| |++|.+
T Consensus 1 ILGIDPgl~~tG~avi~~~~~--~~~~i~~G~I~t~~~~~~~~Rl--~~I~~~l~~li~~~~P~~vaiE~~f--~~~n~~ 74 (149)
T PF02075_consen 1 ILGIDPGLSNTGYAVIEEDGG--KLRLIDYGTIKTSSKDSLPERL--KEIYEELEELIEEYNPDEVAIEEIF--FGKNPK 74 (149)
T ss_dssp EEEEE--SSEEEEEEEEEETT--EEEEEEEEEEE---S--HHHHH--HHHHHHHHHHHHHH--SEEEEEE-S------HH
T ss_pred CEEECCCCCCeeEEEEEeeCC--EEEEEEeCeEECCCCCCHHHHH--HHHHHHHHHHHHhhCCCEEEeehhh--hccCHH
Confidence 799999999 59999999888 8999999999988887888866 889999999888 999999999986 899999
Q ss_pred hhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHc
Q 023513 168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYG 247 (281)
Q Consensus 168 SA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g 247 (281)
|++++|++|||+++++..+||||+||+|++|||+++|+ |+|+|+||+.||+++|+... .++++|+|||||||+||
T Consensus 75 s~~~l~~arGvi~l~~~~~~i~v~~y~P~~vKk~vtG~-G~A~KeqV~~mv~~ll~l~~----~~~~~d~aDAlAiA~~H 149 (149)
T PF02075_consen 75 SALKLGQARGVILLAAAQRGIPVFEYTPSEVKKAVTGN-GRASKEQVAFMVRKLLGLDE----KPKPDDAADALAIALCH 149 (149)
T ss_dssp HHHHHHHHHHHHHHHHHTTT--EEEEEHHHHHHHHTSS-TT--HHHHHHHHHHHTT--------SS-S-THHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCeEEEECHHHHHHHhhCC-CccCHHHHHHHHHHHhCCCC----CCCccchHhhHhhhhcC
Confidence 99999999999999999999999999999999999666 99999999999999997654 25668899999999998
No 5
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=100.00 E-value=1.9e-37 Score=263.84 Aligned_cols=150 Identities=17% Similarity=0.118 Sum_probs=136.1
Q ss_pred eEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCc
Q 023513 89 WALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGK 166 (281)
Q Consensus 89 iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNv 166 (281)
.|||||||++. ||||++.+++ .+.++++|++++..+.++..|+ ..|++.|.+++. |+||.++||++| |++|.
T Consensus 1 rILGIDPGl~~~G~av~~~~~~--~~~~~~~g~i~t~~~~~~~~rl--~~I~~~l~~~i~~~~Pd~vaiE~~~--~~~n~ 74 (154)
T cd00529 1 RILGIDPGSRNTGYGVIEQEGR--KLIYLASGVIRTSSDAPLPSRL--KTIYDGLNEVIDQFQPDVVAIERVF--FAKNP 74 (154)
T ss_pred CEEEEccCcCceEEEEEEeeCC--eEEEEEeeEEECCCCCCHHHHH--HHHHHHHHHHHHHhCCCEEEEEEhh--cccCh
Confidence 38999999995 9999998887 8999999999887777777755 889999999988 999999999987 89999
Q ss_pred hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHH
Q 023513 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAY 246 (281)
Q Consensus 167 qSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~ 246 (281)
+|++++|++||++++++..+|+||+||+|++||++++|+ |+|+|+||++||+++|+... .|++||+|||||||+|
T Consensus 75 ~s~~~l~~~~Gvi~~~~~~~~i~v~e~~P~~vKk~~tG~-G~A~KeqV~~mv~~~l~~~~----~~~~~d~aDAlaiA~~ 149 (154)
T cd00529 75 DSALKLGQARGALILALANRNLPVFEYTPNQVKKAVTGY-GKADKDQVQHMVKRLLNLSE----IPKPDDAADALAVAIT 149 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCEEEEccCeeEEEEECC-CCCCHHHHHHHHHHHhCCCC----CCCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999776 99999999999999997543 2577889999999999
Q ss_pred ccc
Q 023513 247 GKG 249 (281)
Q Consensus 247 g~~ 249 (281)
|..
T Consensus 150 ~~~ 152 (154)
T cd00529 150 HAH 152 (154)
T ss_pred HHh
Confidence 864
No 6
>PF04848 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 This family, representing the Poxvirus A22 protein, is a Holliday junction resolvase, it specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products. ; GO: 0000287 magnesium ion binding, 0000400 four-way junction DNA binding, 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination
Probab=98.70 E-value=2.4e-07 Score=79.69 Aligned_cols=135 Identities=18% Similarity=0.118 Sum_probs=91.0
Q ss_pred ceEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513 88 QWALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (281)
Q Consensus 88 ~iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv 166 (281)
|+|++||+|... ||.+++.+++ .+.+++....+.+ . +..+..++++..+..|.+.||++ +.+|+
T Consensus 1 mii~sIDiGikNlA~~iie~~~~--~i~~~~i~~~~~~--~--------~~~~~~~~dl~~~~~d~VlIErQ---~~r~~ 65 (143)
T PF04848_consen 1 MIILSIDIGIKNLAYCIIEFEGN--KIRVIDISKVDWS--R--------DWEYRILKDLLKYEADTVLIERQ---PPRNP 65 (143)
T ss_pred CeEEEEecCCCceeEEEEEcCCC--eEEEEEeccCCcc--c--------chHHHHHHHHhhccCCEEEEecC---CCCCc
Confidence 689999999996 9999999887 7888888876533 1 11222233333366899999998 46675
Q ss_pred hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCccc--ccc-cCCCCCCHHHHHHH
Q 023513 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLC--SQL-KRKKDHGKADAVLI 243 (281)
Q Consensus 167 qSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~--~~L-~~kk~ddaADALAI 243 (281)
.. + -.+-+.+-+...+..|..++|. +++..=+.-|+.+.+.++.++..-. ..+ ..+|-||.|||+++
T Consensus 66 ~~--~---i~~fI~~~f~~~~~kv~~v~p~-----~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~~~ 135 (143)
T PF04848_consen 66 NV--K---IVHFIHGYFYIKNTKVICVSPK-----MKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAFCQ 135 (143)
T ss_pred ch--h---HHHHHHHHhccCCceEEEECcc-----cccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHHHH
Confidence 32 2 2235555666689999999999 5221123458888888888853311 011 22566789999999
Q ss_pred HHHc
Q 023513 244 AAYG 247 (281)
Q Consensus 244 A~~g 247 (281)
|+..
T Consensus 136 al~~ 139 (143)
T PF04848_consen 136 ALAY 139 (143)
T ss_pred HHHH
Confidence 9854
No 7
>PF07066 DUF3882: Lactococcus phage M3 protein; InterPro: IPR009773 This family consists of several Lactococcus bacteriophage 712, middle-3 (M3) proteins of around 160 residues in length. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The function of this family is unknown.
Probab=98.68 E-value=1.6e-08 Score=87.55 Aligned_cols=143 Identities=21% Similarity=0.216 Sum_probs=92.1
Q ss_pred EEEEcCCCC------ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC---CCCCEEEEccccC
Q 023513 90 ALGIDPDLS------GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA---PIGTTAYVEQSIP 160 (281)
Q Consensus 90 ILGIDPGl~------gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~---~~Pd~aaVE~vf~ 160 (281)
+|.||=.++ +|||+.+ ++ +++-.+...-++++..-+ +.+.+.+.|+.++. -.-...+||+.
T Consensus 4 ~LslD~STs~~~~~gTG~A~~~--~~----~~~~~si~~~~k~Ks~~E--R~k~ias~Lk~ii~~~d~~~y~i~IE~~-- 73 (159)
T PF07066_consen 4 VLSLDFSTSSKKGEGTGWAFFK--GS----DLVVGSIKAKHKSKSFFE--RAKSIASELKTIIQKYDLKFYIIVIEKP-- 73 (159)
T ss_pred eEEEEEecccCCCCCceeEEec--CC----eEEEeeeeecCcccCHHH--HHHHHHHHHHHHHHHhCCCcceEEEecc--
Confidence 788888777 4999986 32 333222211123444434 23555555554433 33557899994
Q ss_pred CCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHh--cCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHH
Q 023513 161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWY--GLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKA 238 (281)
Q Consensus 161 ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaV--g~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaA 238 (281)
+-+.|.+|++++|.++|.+++.+-..-=.++.+.|++|.+.- .+. -++-|+|+.+..+.. .... ..-++||.|
T Consensus 74 vmg~Nqqs~i~l~~~~G~iLG~l~~~~n~~~fIn~s~W~kY~lis~K-~rsrK~~sl~~l~a~-~i~~---~k~~~DDeA 148 (159)
T PF07066_consen 74 VMGPNQQSSIKLGIATGIILGRLINRANGYYFINVSTWRKYWLISYK-DRSRKSMSLELLKAS-EIVD---NKVKDDDEA 148 (159)
T ss_pred cccccccceEEEEEEeEEEeeeeecccCcEEEecHHHhhhheeeeec-hhhhhhhhHHHHHHh-cccc---ccccccchh
Confidence 489999999999999999999876442279999999999987 332 345566664432222 1111 124577899
Q ss_pred HHHHHHHHc
Q 023513 239 DAVLIAAYG 247 (281)
Q Consensus 239 DALAIA~~g 247 (281)
||++|.-|-
T Consensus 149 DAi~IgsY~ 157 (159)
T PF07066_consen 149 DAILIGSYC 157 (159)
T ss_pred hhhhhhhhh
Confidence 999998763
No 8
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=97.07 E-value=0.0035 Score=48.15 Aligned_cols=87 Identities=16% Similarity=0.145 Sum_probs=47.9
Q ss_pred eEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCch
Q 023513 89 WALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ 167 (281)
Q Consensus 89 iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvq 167 (281)
.+||||||.+. ++|+++.+|. .......++ .. +... ..+.+.+++.+ ++|+.++|+-.+ +-++..
T Consensus 2 ~ilgiD~Ggt~i~~a~~d~~g~--~~~~~~~~~---~~--~~~~--~~~~l~~~i~~---~~~~~i~Ig~pg--~v~g~~ 67 (99)
T smart00732 2 RVLGLDPGRKGIGVAVVDETGK--LADPLEVIP---RT--NKEA--DAARLKKLIKK---YQPDLIVIGLPL--NMNGTA 67 (99)
T ss_pred cEEEEccCCCeEEEEEECCCCC--EecCEEEEE---ec--Ccch--HHHHHHHHHHH---hCCCEEEEeCCc--CCCCCc
Confidence 48999999884 9999987774 222222211 11 1111 33555566655 459999999754 223322
Q ss_pred h-hhHHHhhHHHHHHHHHHcCCceeee
Q 023513 168 G-WWSGGFGYGLWIGILVASGFSVVPI 193 (281)
Q Consensus 168 S-A~~vG~ArGVillala~~GIPV~Ey 193 (281)
+ .+ . +-+.-..-...++||+..
T Consensus 68 ~~~~---~-~~l~~~l~~~~~~pv~~~ 90 (99)
T smart00732 68 SRET---E-EAFAELLKERFNLPVVLV 90 (99)
T ss_pred CHHH---H-HHHHHHHHHhhCCcEEEE
Confidence 1 12 1 222223344568888754
No 9
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=96.98 E-value=0.001 Score=57.23 Aligned_cols=75 Identities=13% Similarity=0.173 Sum_probs=47.4
Q ss_pred CCCceEEEEcCCCCceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCC
Q 023513 85 ADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164 (281)
Q Consensus 85 ~~~~iILGIDPGl~gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgq 164 (281)
-...+|+|||||+++|+|+|+-+|+ +++....+ .++...+.++|.++- .|-.+|--. .++
T Consensus 29 ~~~~lIVGiDPG~ttgiAildL~G~-----~l~l~S~R---------~~~~~evi~~I~~~G--~PviVAtDV-~p~--- 88 (138)
T PF04312_consen 29 SRRYLIVGIDPGTTTGIAILDLDGE-----LLDLKSSR---------NMSRSEVIEWISEYG--KPVIVATDV-SPP--- 88 (138)
T ss_pred CCCCEEEEECCCceeEEEEEecCCc-----EEEEEeec---------CCCHHHHHHHHHHcC--CEEEEEecC-CCC---
Confidence 3556899999999999999999994 44443332 224467888888774 355555433 222
Q ss_pred CchhhhHHHhhHHHHH
Q 023513 165 GKQGWWSGGFGYGLWI 180 (281)
Q Consensus 165 NvqSA~~vG~ArGVil 180 (281)
..+.-++...+|+.+
T Consensus 89 -P~~V~Kia~~f~A~l 103 (138)
T PF04312_consen 89 -PETVKKIARSFNAVL 103 (138)
T ss_pred -cHHHHHHHHHhCCcc
Confidence 334555555555443
No 10
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=96.91 E-value=0.0054 Score=63.51 Aligned_cols=53 Identities=25% Similarity=0.409 Sum_probs=39.6
Q ss_pred ceEEEEcCCCCceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEc
Q 023513 88 QWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVE 156 (281)
Q Consensus 88 ~iILGIDPGl~gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE 156 (281)
.+|+|||||+++|+|+|+-+| .++++-... .++...+.++|.++- +|-.+|.-
T Consensus 244 ~lIVGIDPGiTtgiAvldldG-----evl~~~S~r---------~~~~~eVve~I~~lG--~PvvVAtD 296 (652)
T COG2433 244 SLIVGIDPGITTGIAVLDLDG-----EVLDLESRR---------GIDRSEVVEFISELG--KPVVVATD 296 (652)
T ss_pred ceEEEeCCCceeeEEEEecCC-----cEEeeeccc---------cCCHHHHHHHHHHcC--CceEEEcc
Confidence 479999999999999999999 566655443 335577888888874 46555543
No 11
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition. This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=95.86 E-value=0.022 Score=46.80 Aligned_cols=107 Identities=22% Similarity=0.227 Sum_probs=67.1
Q ss_pred EEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCchh
Q 023513 90 ALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG 168 (281)
Q Consensus 90 ILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvqS 168 (281)
++|||=|-.. -.+++...+. .......+..+ . .+..+.++|..+. +..+++|.-.. ++
T Consensus 1 ~vGiDv~k~~~~v~v~~~~~~--~~~~~~~~~~~--------~--~~~~l~~~l~~~~---~~~v~~E~tg~-y~----- 59 (144)
T PF01548_consen 1 FVGIDVSKDTHDVCVIDPNGE--KLRRFKFENDP--------A--GLEKLLDWLASLG---PVLVVMEATGG-YW----- 59 (144)
T ss_pred eEEEEcccCeEEEEEEcCCCc--EEEEEEEeccc--------c--chhHHhhhhcccc---ccccccccccc-cc-----
Confidence 6899999995 7777877663 22222222211 0 2245566666552 77888998431 11
Q ss_pred hhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHcc
Q 023513 169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGK 248 (281)
Q Consensus 169 A~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~ 248 (281)
+ -+.-.|...|++|+.+.|.++|..-... | .+.| .|..||..||.+..
T Consensus 60 -------~-~l~~~L~~~g~~v~~vnp~~~~~~~~~~-~----------------------~~~K-tD~~DA~~ia~~~~ 107 (144)
T PF01548_consen 60 -------R-PLADFLQDAGIEVVVVNPLQVKRFRKSL-G----------------------RRAK-TDKIDARAIARLLR 107 (144)
T ss_pred -------h-hhhhheeccccccccccccccccccccc-c----------------------cccc-ccccchHHHHHHHh
Confidence 1 2334567789999999999999987431 0 1123 34888888888777
Q ss_pred c
Q 023513 249 G 249 (281)
Q Consensus 249 ~ 249 (281)
.
T Consensus 108 ~ 108 (144)
T PF01548_consen 108 R 108 (144)
T ss_pred c
Confidence 6
No 12
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=95.68 E-value=0.5 Score=40.10 Aligned_cols=93 Identities=17% Similarity=0.099 Sum_probs=50.6
Q ss_pred CceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCC
Q 023513 87 SQWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG 165 (281)
Q Consensus 87 ~~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqN 165 (281)
+|.|||||||.. +|+|+-+..+. +..|...+..... .. +.+.|.++++++. ++..+|=-.. .-+|
T Consensus 3 ~~~iLalD~G~kriGvAv~d~~~~------~a~pl~~i~~~~~-~~--~~~~l~~~i~~~~---i~~iVvGlP~--~~~G 68 (138)
T PRK00109 3 SGRILGLDVGTKRIGVAVSDPLGG------TAQPLETIKRNNG-TP--DWDRLEKLIKEWQ---PDGLVVGLPL--NMDG 68 (138)
T ss_pred CCcEEEEEeCCCEEEEEEecCCCC------EEcCEEEEEcCCC-ch--HHHHHHHHHHHhC---CCEEEEeccC--CCCC
Confidence 567999999999 59998876543 2233221111111 11 3466666666654 7777776532 2233
Q ss_pred chhhhHHHhhHHHHHHHHHHcCCceeeeC
Q 023513 166 KQGWWSGGFGYGLWIGILVASGFSVVPIP 194 (281)
Q Consensus 166 vqSA~~vG~ArGVillala~~GIPV~Eyt 194 (281)
..+.. .-..+-.+-......++||+.+.
T Consensus 69 ~~~~~-~~~v~~f~~~L~~~~~~~v~~~D 96 (138)
T PRK00109 69 TEGPR-TERARKFANRLEGRFGLPVVLVD 96 (138)
T ss_pred CcCHH-HHHHHHHHHHHHHHhCCCEEEEc
Confidence 33221 12223333333445599998875
No 13
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=95.39 E-value=0.19 Score=42.48 Aligned_cols=99 Identities=14% Similarity=0.042 Sum_probs=57.7
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCc-ceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCC
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG 165 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~-~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqN 165 (281)
|.+||||+|.. +|+||-+..+.- ..+.++..... .. +...|.++++++. ++.++|=-.. .-+|
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~--------~~--~~~~l~~li~~~~---i~~iVvGlP~--~~~G 65 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNR--------EK--DIEELKKLIEEYQ---IDGIVVGLPL--NMDG 65 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCC--------CC--CHHHHHHHHHHCC---ECEEEEEEEB--BCTS
T ss_pred CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCC--------ch--HHHHHHHHHHHhC---CCEEEEeCCc--ccCC
Confidence 67999999999 599999876631 02344432211 11 4577778887765 8888887754 3233
Q ss_pred chhhhHHHhhHHHHHHHHHHc-CCceeee----ChhhHHHHh
Q 023513 166 KQGWWSGGFGYGLWIGILVAS-GFSVVPI----PSLTWKNWY 202 (281)
Q Consensus 166 vqSA~~vG~ArGVillala~~-GIPV~Ey----tP~qwKkaV 202 (281)
..+.. .-..+-.+-...... ++||+.+ |..+.+..+
T Consensus 66 ~~~~~-~~~v~~f~~~L~~~~~~ipV~~~DEr~TT~~A~~~l 106 (135)
T PF03652_consen 66 SESEQ-ARRVRKFAEELKKRFPGIPVILVDERLTTKEAERRL 106 (135)
T ss_dssp SC-CC-HHHHHHHHHHHHHHH-TSEEEEEECSCSHHCCHCCH
T ss_pred CccHH-HHHHHHHHHHHHHhcCCCcEEEECCChhHHHHHHHH
Confidence 22211 113344444445555 9999975 444444444
No 14
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=93.18 E-value=3.6 Score=35.58 Aligned_cols=95 Identities=15% Similarity=0.098 Sum_probs=59.2
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv 166 (281)
|.+||+|-|+. +|.|+-+..+. +..|.-.+....... ++...|.+++.++. |+.++|=-...| +|.
T Consensus 2 ~~ilalD~G~KrIGvA~sd~~~~------~A~pl~~i~~~~~~~--~~~~~l~~li~~~~---~~~vVVGlP~~m--~g~ 68 (141)
T COG0816 2 MRILALDVGTKRIGVAVSDILGS------LASPLETIKRKNGKP--QDFNALLKLVKEYQ---VDTVVVGLPLNM--DGT 68 (141)
T ss_pred ceEEEEecCCceEEEEEecCCCc------cccchhhheeccccH--hhHHHHHHHHHHhC---CCEEEEecCcCC--CCC
Confidence 67999999999 59998876553 333332221222211 36677888887765 899988764322 222
Q ss_pred hhhhHHHhhHHHHHHHHHHcCCceeeeChh
Q 023513 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSL 196 (281)
Q Consensus 167 qSA~~vG~ArGVillala~~GIPV~EytP~ 196 (281)
.+- ..-.++-..-......++||+....+
T Consensus 69 ~~~-~~~~~~~f~~~L~~r~~lpv~l~DER 97 (141)
T COG0816 69 EGP-RAELARKFAERLKKRFNLPVVLWDER 97 (141)
T ss_pred cch-hHHHHHHHHHHHHHhcCCCEEEEcCc
Confidence 222 22244555556678889999998853
No 15
>COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=92.49 E-value=3.7 Score=37.00 Aligned_cols=66 Identities=21% Similarity=0.236 Sum_probs=44.2
Q ss_pred HHHHHcCCceeeeChhhH-HHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHccccccC-----C
Q 023513 181 GILVASGFSVVPIPSLTW-KNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLD-----S 254 (281)
Q Consensus 181 lala~~GIPV~EytP~qw-KkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~~~~~~-----~ 254 (281)
-.+...|+||+|.=|... +++++. ++.+-+. .+.... --+|.-||++.|.++...+.. -
T Consensus 94 r~l~~~gv~ViEthP~aa~~~~~~l--~r~~l~~-------~ie~~~------~~~~~~dAv~ag~~a~~y~~G~~i~~~ 158 (178)
T COG2410 94 RLLESEGVPVIETHPRAALAKAAGL--RRHDLDR-------IIEDVA------VSEDAVDAVLAGLAALLYSLGEAIERE 158 (178)
T ss_pred HHHHhcCCeEEEecchHHHHHHHhh--ccchhhh-------hhhhhh------hhhhHHHHHHHHHHHHHhCcchhhccc
Confidence 457788999999999999 888776 3343321 121111 135689999999887666654 5
Q ss_pred CCCCCcc
Q 023513 255 SHLSGEL 261 (281)
Q Consensus 255 ~~~~~~~ 261 (281)
+.++|.+
T Consensus 159 ~~~~G~i 165 (178)
T COG2410 159 RGLSGSI 165 (178)
T ss_pred cCCceeE
Confidence 6667765
No 16
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=90.49 E-value=2.1 Score=37.11 Aligned_cols=109 Identities=11% Similarity=0.028 Sum_probs=68.5
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCC
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDG 165 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqN 165 (281)
|.|+||+=-.+ .=++++..+++ .+++.|+-+.+....++.. .-..+.....+.++.+ |+.|.++|=+= +-=|+.
T Consensus 1 M~vCGVELkgneaii~ll~~~~~--~~~~pdcr~~k~~l~~~~~-~~~vr~Fq~~f~kl~~dy~Vd~VvIk~R-~~KGKf 76 (138)
T PF11215_consen 1 MKVCGVELKGNEAIICLLSLDDG--LFQLPDCRVRKFSLSDDNS-TEEVRKFQFTFAKLMEDYKVDKVVIKER-ATKGKF 76 (138)
T ss_pred CeEEEEEEecCeEEEEEEecCCC--ceECCccceeEEEcCCCcc-HHHHHHHHHHHHHHHHHcCCCEEEEEec-ccCCCc
Confidence 67888885444 24778887776 7777777777554444421 1133566667777777 88999888552 112333
Q ss_pred chhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcC
Q 023513 166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL 204 (281)
Q Consensus 166 vqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~ 204 (281)
..++. |+---.++ ....+++|..++|.++|.....
T Consensus 77 AGga~--~FKmEaaI--QL~~~~~V~lvs~~~ik~~lKr 111 (138)
T PF11215_consen 77 AGGAV--GFKMEAAI--QLIDDVEVELVSPATIKAQLKR 111 (138)
T ss_pred cCCch--hHHHHHHH--HhcCCCcEEEECHHHHHHHHhc
Confidence 33332 22222222 1226999999999999999954
No 17
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=90.40 E-value=1.5 Score=36.92 Aligned_cols=89 Identities=16% Similarity=0.006 Sum_probs=47.4
Q ss_pred EEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCchhh
Q 023513 91 LGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGW 169 (281)
Q Consensus 91 LGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvqSA 169 (281)
||||||.. +|+|+-+..+. +..|...+.... ... +...|.++++++. |+.++|=-.. .-+|..|.
T Consensus 1 laiD~G~kriGvA~~d~~~~------~a~pl~~i~~~~-~~~--~~~~l~~~i~~~~---~~~iVvGlP~--~~dG~~~~ 66 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGW------TAQGIPTIKAQD-GEP--DWSRIEELLKEWT---PDKIVVGLPL--NMDGTEGP 66 (130)
T ss_pred CeEccCCCeEEEEEECCCCC------EEeceEEEEecC-CcH--HHHHHHHHHHHcC---CCEEEEeccC--CCCcCcCH
Confidence 69999999 59998765442 222222111111 111 3356666666654 8777775432 22333322
Q ss_pred hHHHhhHHHHHHHHHHcCCceeeeC
Q 023513 170 WSGGFGYGLWIGILVASGFSVVPIP 194 (281)
Q Consensus 170 ~~vG~ArGVillala~~GIPV~Eyt 194 (281)
....++-.+--.....++||+.+.
T Consensus 67 -~a~~v~~f~~~L~~~~~~~v~~~D 90 (130)
T TIGR00250 67 -LTERAQKFANRLEGRFGVPVVLWD 90 (130)
T ss_pred -HHHHHHHHHHHHHHHhCCCEEEEc
Confidence 122333333334455699998764
No 18
>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []. The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.
Probab=89.14 E-value=0.47 Score=42.87 Aligned_cols=65 Identities=22% Similarity=0.259 Sum_probs=28.2
Q ss_pred CCCCceEEEEcCC--CCc---eEEEE-eeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEcc
Q 023513 84 NADSQWALGIDPD--LSG---ALAVL-KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQ 157 (281)
Q Consensus 84 ~~~~~iILGIDPG--l~g---GyaVL-e~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~ 157 (281)
+-+..+++|+||| ..+ ++.++ ...++ ...+++.-... +..... -...+.++... +.|..+++|.
T Consensus 222 ~~~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~--~~~~~~~~~~~---~~~~~~--~~~~i~~~~~~---~~~~~i~~d~ 291 (384)
T PF03237_consen 222 PPDWPIIIGVDPAGGKGGDYTAIVVWEIVDDD--GFYVVDDEYER---GMSPEE--WAERIRELYKK---YNPIKIYIDA 291 (384)
T ss_dssp -TT--EEEEEE--SSCTTB-EEEEEE-E-SSS--SEEEEEEEEES---SS-TTT--HHHHHHHHHHH---TTS--EEEEE
T ss_pred CCCceEEEEEECCCCCccCCEEEEEEcccccc--ceEEeeehhhc---CCCHHH--HHHHHHHHHhh---cCceEEEEcC
Confidence 3445678999999 443 44444 23343 44555433221 111111 22344444443 5589999999
Q ss_pred c
Q 023513 158 S 158 (281)
Q Consensus 158 v 158 (281)
.
T Consensus 292 ~ 292 (384)
T PF03237_consen 292 N 292 (384)
T ss_dssp S
T ss_pred C
Confidence 4
No 19
>PF09159 Ydc2-catalyt: Mitochondrial resolvase Ydc2 / RNA splicing MRS1; InterPro: IPR015242 This domain forms a ribonuclease H fold consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. They are capable of resolving Holliday junctions and cleave DNA after 5'-CT-3, and 5'-TT-3, sequences []. This entry also includes a domain found in the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [, ].; PDB: 1KCF_A.
Probab=88.39 E-value=2.2 Score=40.07 Aligned_cols=133 Identities=14% Similarity=0.106 Sum_probs=64.8
Q ss_pred EEEEcCCCCc-eEEEEee------CCCcceeEEeecCCcccc---------------------cccchhhhhcHHHHHHH
Q 023513 90 ALGIDPDLSG-ALAVLKS------DHNGCSAEVFDTPHLPVL---------------------VGKRVRKRLDAKSMIML 141 (281)
Q Consensus 90 ILGIDPGl~g-GyaVLe~------~g~~~~~~vvd~p~i~~~---------------------~~~~l~~rl~~~~I~~l 141 (281)
||+||-|++. +|+.+.. ....-...+.+-..+.+. ....+..+.-....+.+
T Consensus 1 ILSIDmGIkNfAy~~l~~~~~~~~~~~~~~p~L~~W~kl~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~a~~a~~L 80 (274)
T PF09159_consen 1 ILSIDMGIKNFAYCKLKVSSDSKKASSSSLPTLNAWDKLNLSSLFSSNWQTEPGKEYFPTEEKEKESFSPRYLAHLAYKL 80 (274)
T ss_dssp EEEEEE-STTEEEEEEEE--------TTS-EEEEEEEEE-TT-------------SS-TT--------SHHHHHHHHHHH
T ss_pred CceeecchhhhhhhhhhhcccccccCCCCCccccCCceeecccccccccccccccccCCCCcccCCCCCHHHHHHHHHHH
Confidence 7999999996 9999998 111101222222222111 11112222333445567
Q ss_pred HHhhcC-CCCCEEEEccccCCCCCCchh-----hhHHHhhHHHHHHHHHHc---------CCceeeeChhhHHHHh-cCC
Q 023513 142 LRSLDA-PIGTTAYVEQSIPYPQDGKQG-----WWSGGFGYGLWIGILVAS---------GFSVVPIPSLTWKNWY-GLS 205 (281)
Q Consensus 142 L~~l~~-~~Pd~aaVE~vf~ffgqNvqS-----A~~vG~ArGVillala~~---------GIPV~EytP~qwKkaV-g~s 205 (281)
+..+.. +.||++.||+.= |.-|-.+ .+.++-==|.+..++... +.-|..+.|+.+-..- ...
T Consensus 81 v~~Ll~~~~P~~vlIERQR--~RS~g~savlEwtLrvn~lE~mLyA~L~~~~~~~~~~~~~~~V~~v~P~rv~~fW~~~~ 158 (274)
T PF09159_consen 81 VSSLLLPYKPDHVLIERQR--FRSGGSSAVLEWTLRVNILEGMLYAVLYTLRQESKGEQANYVVISVDPQRVTRFWCERF 158 (274)
T ss_dssp HHHHHHHH--SEEEEEE------T-TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEE-CCHHHHHHHH--
T ss_pred HHHHcccCCCCEEEEeecc--ccCCCCCccchhHHHHhHHHHHHHHHHHHHHhhcccCCCCeEEEEECHHHHHHHHhccc
Confidence 777766 779999999973 4333232 356665556655555544 3479999999987665 211
Q ss_pred --------------CCCCCHHHHHHHHHHhCCc
Q 023513 206 --------------GGTSTKDDSRRVASTLFPS 224 (281)
Q Consensus 206 --------------~G~A~KeQVq~MV~~LLp~ 224 (281)
.++.+|.-=..+|+.+|..
T Consensus 159 ~~~~~~~~~~~~~~~~~~~K~~ki~Lv~~wL~~ 191 (274)
T PF09159_consen 159 PIRDSLNEKKKKKKSSKNSKKIKIDLVRSWLSN 191 (274)
T ss_dssp ---------HH-----------HHHHHHHHHHT
T ss_pred ccchhhhhhhcccccchhhHHHHHHHHHHHHHc
Confidence 1334566667788888743
No 20
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=83.82 E-value=2.1 Score=46.10 Aligned_cols=38 Identities=24% Similarity=0.441 Sum_probs=25.6
Q ss_pred CCCCceEEEEcCCCCc--eEEEEeeCCCcc-eeEEeecCCc
Q 023513 84 NADSQWALGIDPDLSG--ALAVLKSDHNGC-SAEVFDTPHL 121 (281)
Q Consensus 84 ~~~~~iILGIDPGl~g--GyaVLe~~g~~~-~~~vvd~p~i 121 (281)
.++++.++|+|||.++ -.||++..|.-| ...++.++..
T Consensus 326 P~~~~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~ 366 (780)
T COG2183 326 PAKPKATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPV 366 (780)
T ss_pred CCCCcceeecCCccccccEEEEEcCCCceeceeEEEcCCCc
Confidence 4666679999999995 488898876422 3444444443
No 21
>PF14239 RRXRR: RRXRR protein
Probab=81.51 E-value=1.7 Score=39.09 Aligned_cols=22 Identities=32% Similarity=0.504 Sum_probs=17.5
Q ss_pred CCceEEEEcCCCCc-eEEEEeeC
Q 023513 86 DSQWALGIDPDLSG-ALAVLKSD 107 (281)
Q Consensus 86 ~~~iILGIDPGl~g-GyaVLe~~ 107 (281)
..-+.||||||+.. |+||+...
T Consensus 49 ~qpi~lgiDpGsk~tGiav~~~~ 71 (176)
T PF14239_consen 49 TQPIRLGIDPGSKTTGIAVVSEK 71 (176)
T ss_pred ccCEEEEECCCCCeEEEEEEeCC
Confidence 34468999999995 99998654
No 22
>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown.
Probab=74.61 E-value=5.5 Score=39.20 Aligned_cols=54 Identities=20% Similarity=0.187 Sum_probs=32.2
Q ss_pred EEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEcc
Q 023513 92 GIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQ 157 (281)
Q Consensus 92 GIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~ 157 (281)
|||||+.. .+++++..|+ -..-...|+..+. + +-..+.+.|+++ ..||.++.=.
T Consensus 1 GIDpGT~s~dv~~~dd~g~--v~~~~~ipt~~v~------~--~p~~iv~~l~~~--~~~dlIa~ps 55 (343)
T PF07318_consen 1 GIDPGTKSFDVCGLDDDGK--VIFYFSIPTEEVA------K--NPSIIVEELEEF--GDIDLIAGPS 55 (343)
T ss_pred CCCCCCCcEEEEEEccCCc--EEEEeeccHHHhh------h--CHHHHHHHHHhc--cCCCEEEeCC
Confidence 89999995 8888876563 2222333333321 1 224467777776 2488887644
No 23
>PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional
Probab=63.39 E-value=55 Score=32.21 Aligned_cols=100 Identities=16% Similarity=0.088 Sum_probs=50.5
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEE-----eec--CCcccccccchhhhhcHHHHHHHHHhhcC--CCCCEEEEcc
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEV-----FDT--PHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQ 157 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~v-----vd~--p~i~~~~~~~l~~rl~~~~I~~lL~~l~~--~~Pd~aaVE~ 157 (281)
|.|||||=-.. ++.||++.+++ +-..+ ..+ |..+........++| ...+.+.|.+... ...|.+++=.
T Consensus 1 ~~iLgIETScd~tsvAl~~~~~~-il~~~~~sq~~~~G~GvvP~~a~r~H~~~l-~~~i~~~l~~a~~~~~did~Iavt~ 78 (345)
T PTZ00340 1 FLALGIEGSANKLGVGIVTSDGE-ILSNVRETYITPPGTGFLPRETAQHHREHI-LSLVKEALEEAKITPSDISLICYTK 78 (345)
T ss_pred CeEEEEEccchhhEEEEEECCCc-EEEEEEeeccccCCCCcCchHHHHHHHHHH-HHHHHHHHHHcCCCHHHCCEEEEec
Confidence 56999998888 59999985542 11111 112 333321222222222 2333344443211 2235555543
Q ss_pred ccCCCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeChh
Q 023513 158 SIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSL 196 (281)
Q Consensus 158 vf~ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP~ 196 (281)
|-|.-+.+.+|-+.+ -+.+...|+|++.++=+
T Consensus 79 -----GPGl~~~LrVG~~~A--k~LA~a~~~PligV~Hl 110 (345)
T PTZ00340 79 -----GPGMGAPLSVGAVVA--RTLSLLWGKPLVGVNHC 110 (345)
T ss_pred -----CCCcHhhHHHHHHHH--HHHHHHcCCCEeecchH
Confidence 334556676665443 34467788888876543
No 24
>PF04250 DUF429: Protein of unknown function (DUF429); InterPro: IPR007362 This is a family of uncharacterised proteins.
Probab=61.25 E-value=1.2e+02 Score=26.75 Aligned_cols=67 Identities=15% Similarity=0.112 Sum_probs=41.5
Q ss_pred HHHcCCceeeeChhhHHHHhcCCCC-----CCCHHHHHHHHHHhCCccc-----c--cccCCCCCCHHHHHHHHHHccc
Q 023513 183 LVASGFSVVPIPSLTWKNWYGLSGG-----TSTKDDSRRVASTLFPSLC-----S--QLKRKKDHGKADAVLIAAYGKG 249 (281)
Q Consensus 183 la~~GIPV~EytP~qwKkaVg~s~G-----~A~KeQVq~MV~~LLp~~~-----~--~L~~kk~ddaADALAIA~~g~~ 249 (281)
....+..|+|+=|.-.-+.+++..- ....++-+++...+..... . ....+..||.-||+++|+.+..
T Consensus 109 ~~~~~~~v~Ev~P~~~~~~l~~~~~~~K~~~~~~~~R~~lL~~~~~~~~~~~~~~~~~~~~~~~~D~lDA~i~Al~A~~ 187 (209)
T PF04250_consen 109 PPSSGRRVIEVHPEAAFKALGGAPRYYKKTAEGRAERRELLARLGIDAIPELILAQHRRRLKASDDELDALICALTARR 187 (209)
T ss_pred ccccCceEEEECcHHHHHHhCCCcccccCCcchHHHHHHHHHHHHHhhhhhhhccccccccCcCcCHHHHHHHHHHHHH
Confidence 3578999999999999988864201 1123344444444432210 0 0013567889999999997765
No 25
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=60.62 E-value=1.1e+02 Score=32.64 Aligned_cols=94 Identities=15% Similarity=0.152 Sum_probs=52.1
Q ss_pred CceEEEEc-----CCCCc-eEEEEe-eCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEcccc
Q 023513 87 SQWALGID-----PDLSG-ALAVLK-SDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (281)
Q Consensus 87 ~~iILGID-----PGl~g-GyaVLe-~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf 159 (281)
+|+|+||| |+..- -|||+- .+|. ++....+ ....+.+++.+. +||.+||-.+|
T Consensus 1 ~~~I~GVDI~~g~p~~~~p~yAvv~~~dg~-----~~~k~~~------------s~~rllrli~~~---kpDIvAvDnvy 60 (652)
T COG2433 1 DMVIMGVDIVSGSPRGKAPLYAVVILEDGE-----IVEKGEV------------SLRRLLRLIWSY---KPDIVAVDNVY 60 (652)
T ss_pred CceEEEEeeecCCCCCcCcceeEEEEecCc-----EEeehhh------------hHHHHHHHHHhc---CCCEEEeccHH
Confidence 47899999 44442 356664 3442 2222221 124456666654 59999999986
Q ss_pred CCCCCCchhhhHHH-hhHHHHHHH-HHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhC
Q 023513 160 PYPQDGKQGWWSGG-FGYGLWIGI-LVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLF 222 (281)
Q Consensus 160 ~ffgqNvqSA~~vG-~ArGVilla-la~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LL 222 (281)
- +| ..++++-.+ ..=-|..++.|| + +.-.=++-...+++..
T Consensus 61 E-----------L~~~~~~li~il~~lP~~tkLVQVT---------g--~~g~~~sL~~lArr~G 103 (652)
T COG2433 61 E-----------LGADKRDLIRILKRLPEGTKLVQVT---------G--RPGEQESLWELARRHG 103 (652)
T ss_pred H-----------HhcChhHHHHHHHhCCCCceEEEEe---------C--CCCCcchHHHHHHHhC
Confidence 3 23 223333321 222456677776 1 3355667778888874
No 26
>TIGR01630 psiM2_ORF9 phage uncharacterized protein (putative large terminase), C-terminal domain. This model represents the C-terminal region of a set of phage proteins typically about 400-500 amino acids in length, although some members are considerably shorter. An article on Methanobacterium phage Psi-M2 (PubMed:9791169) calls the member from that phage, ORF9, a putative large terminase subunit, and ORF8 a candidate terminase small subunit. Most proteins in this family have an apparent P-loop nucleotide-binding sequence toward the N-terminus.
Probab=57.94 E-value=71 Score=26.32 Aligned_cols=84 Identities=18% Similarity=0.076 Sum_probs=42.3
Q ss_pred CCCCEEEEccccCCCCCCchhhhHHHhhHHHHHHHHHH--cCCceeeeChhhHHHHh--cCC----CCC----CCHHHHH
Q 023513 148 PIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVA--SGFSVVPIPSLTWKNWY--GLS----GGT----STKDDSR 215 (281)
Q Consensus 148 ~~Pd~aaVE~vf~ffgqNvqSA~~vG~ArGVillala~--~GIPV~EytP~qwKkaV--g~s----~G~----A~KeQVq 215 (281)
|.++.+.+|... +++ +.+.+++-. +.. ..+||..++|+.=|..= ..+ .|+ .+..-..
T Consensus 42 ~~~~~~~~E~~~--~~~--------~~~~~l~~~-l~~~~~~~~i~~~~~~~~K~~Ri~~~~p~~e~G~V~~~~~~~~~~ 110 (142)
T TIGR01630 42 HRVNLAIIESNQ--EGK--------SFGRSLVKI-LKEKGIRTPARAVYPSGDKETRILSVAPWVEAGNVFPPNWAPWWP 110 (142)
T ss_pred cCCcceeeeccc--cch--------HHHHHHHHH-HHhhCCCCCceeeCCCCChHHhhhccHHHHHcCeEeCCCcchhHH
Confidence 558998999964 222 122333332 232 24678888886433210 000 011 0011133
Q ss_pred HHHHHh--CCcccccccCCCCCCHHHHHHHHHHc
Q 023513 216 RVASTL--FPSLCSQLKRKKDHGKADAVLIAAYG 247 (281)
Q Consensus 216 ~MV~~L--Lp~~~~~L~~kk~ddaADALAIA~~g 247 (281)
....+| ||.. ...|||..|||..|+..
T Consensus 111 ~l~~el~~Fp~~-----~~~hDD~~Dal~~a~~~ 139 (142)
T TIGR01630 111 DLIQALEAFPRE-----KAAHDDDPDAMTGAANS 139 (142)
T ss_pred HHHHHHHhcccc-----cccCCCchhhHHHHHHH
Confidence 344444 3321 14589999999999854
No 27
>COG2441 Predicted butyrate kinase [Energy production and conversion]
Probab=53.22 E-value=14 Score=36.14 Aligned_cols=31 Identities=23% Similarity=0.253 Sum_probs=20.5
Q ss_pred EEEcCCCC-c-eEEEEeeCCCcceeEEeecCCccc
Q 023513 91 LGIDPDLS-G-ALAVLKSDHNGCSAEVFDTPHLPV 123 (281)
Q Consensus 91 LGIDPGl~-g-GyaVLe~~g~~~~~~vvd~p~i~~ 123 (281)
+|||||+. . -+|+-+..|+ -+--+.-|+.++
T Consensus 1 ~GIDpGT~smdvfgfdDEsg~--vi~~~~I~rdeV 33 (374)
T COG2441 1 IGIDPGTGSMDVFGFDDESGN--VIVDVAIPRDEV 33 (374)
T ss_pred CCcCCCCCceeEEEEecCCCC--EEEEEecCHHHh
Confidence 59999997 5 8898887776 333334444443
No 28
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=51.32 E-value=33 Score=29.67 Aligned_cols=58 Identities=21% Similarity=0.170 Sum_probs=29.5
Q ss_pred EEEEcCCCCc-----eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEE
Q 023513 90 ALGIDPDLSG-----ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYV 155 (281)
Q Consensus 90 ILGIDPGl~g-----GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaV 155 (281)
||+|-.|..- -+++|+.+| +++|+..+.-....+..+.-+.+.|.++|.++. |+.++|
T Consensus 7 Vla~~~g~g~~~~~~~~v~ld~~G-----~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~k---P~vI~v 69 (150)
T PF14639_consen 7 VLALSWGSGDGDDAVFCVVLDENG-----EVLDHLKLVYNERDRERKEEDMERLKKFIEKHK---PDVIAV 69 (150)
T ss_dssp EEEEE-TT--TTS-EEEEEE-TTS------EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH-----SEEEE
T ss_pred EEEEEcCCCCCCCCEEEEEECCCC-----cEEEEEEEcCCccchHHHHHHHHHHHHHHHHcC---CeEEEE
Confidence 7888777652 367788777 455655551111222222224466667777665 999999
No 29
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=49.68 E-value=32 Score=31.27 Aligned_cols=100 Identities=18% Similarity=0.153 Sum_probs=51.6
Q ss_pred ceEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513 88 QWALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (281)
Q Consensus 88 ~iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv 166 (281)
|.||.||=.+.. +.||+..+++ +++..-+.. .++.+.+++ ...+.+++.+.. .+.--++.+. +++|.
T Consensus 1 m~iLaiDTs~~~~s~ai~~~~~~----~vl~~~~~~--~~r~hse~l-~~~i~~ll~~~~---~~~~dld~ia--v~~GP 68 (220)
T COG1214 1 MKILAIDTSTSALSVALYLADDG----KVLAEHTEK--LKRNHAERL-MPMIDELLKEAG---LSLQDLDAIA--VAKGP 68 (220)
T ss_pred CcEEEEEcChhhhhhheeecCCC----cEEEEEEEe--ccccHHHHH-HHHHHHHHHHcC---CCHHHCCEEE--EccCC
Confidence 568999988884 8777766333 232222222 122223333 344555555542 2222333332 33333
Q ss_pred h--hhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHH
Q 023513 167 Q--GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNW 201 (281)
Q Consensus 167 q--SA~~vG~ArGVillala~~GIPV~EytP~qwKka 201 (281)
. |.+.+|-+ ++-+.+...|||++-|+..+.=..
T Consensus 69 GSFTGlRIG~~--~AkgLA~~l~iplvgvssL~~~A~ 103 (220)
T COG1214 69 GSFTGLRIGVA--FAKGLALALNIPLVGVSSLEALAQ 103 (220)
T ss_pred CcccchhhHHH--HHHHHHHHcCCCEEEeCHHHHHHH
Confidence 2 33333322 223346779999999988776553
No 30
>PRK09604 UGMP family protein; Validated
Probab=49.45 E-value=77 Score=30.40 Aligned_cols=101 Identities=15% Similarity=0.123 Sum_probs=48.0
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEEeec--------CCc-ccccccchhhhhcHHHHHHHHHhhcC--CCCCEEEE
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDT--------PHL-PVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYV 155 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~--------p~i-~~~~~~~l~~rl~~~~I~~lL~~l~~--~~Pd~aaV 155 (281)
|.|||||=... .+.|+++.+++ +-...... +-+ +........+ .....+.+.|.+..- ...|.+++
T Consensus 1 m~iLgIdTS~~~~sval~~~~~~-il~~~~~~~~~~~~~~~Gi~P~~a~~~H~~-~l~~~i~~~L~~~~~~~~did~iav 78 (332)
T PRK09604 1 MLILGIETSCDETSVAVVDDGRG-LLSNVVASQIDLHARYGGVVPELASRAHVE-NIVPLIEEALKEAGLTLEDIDAIAV 78 (332)
T ss_pred CeEEEEEccccceEEEEEECCCc-EEEEEEecchhcccccCCcCcchhHHHHHH-HHHHHHHHHHHHcCCCHHHCCEEEE
Confidence 57999999666 49999975432 11111111 111 1111111111 112233344443311 22345554
Q ss_pred ccccCCCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeChhh
Q 023513 156 EQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLT 197 (281)
Q Consensus 156 E~vf~ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP~q 197 (281)
=. |-|.-+.+.+|-+. +-+.+...++|++.++=.+
T Consensus 79 t~-----GPG~~tglrvg~~~--Ak~La~~~~ipl~~v~h~~ 113 (332)
T PRK09604 79 TA-----GPGLVGALLVGVSF--AKALALALNKPLIGVNHLE 113 (332)
T ss_pred ec-----CCCcHHhHHHHHHH--HHHHHHHhCCCEEeecCHH
Confidence 33 22334445555443 4455777889998886543
No 31
>COG4020 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.96 E-value=82 Score=30.65 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=20.3
Q ss_pred CCceEEEEcCCCCc-eEEEEeeCCC
Q 023513 86 DSQWALGIDPDLSG-ALAVLKSDHN 109 (281)
Q Consensus 86 ~~~iILGIDPGl~g-GyaVLe~~g~ 109 (281)
+.|+.+|||-|+++ -+++++.++.
T Consensus 1 ~~m~fVGiDHGTsgi~~ai~d~e~~ 25 (332)
T COG4020 1 MTMMFVGIDHGTSGIKFAIYDGEKD 25 (332)
T ss_pred CceEEEeecCCCcceEEEEEcCCCC
Confidence 36789999999997 9999987664
No 32
>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=35.86 E-value=60 Score=35.25 Aligned_cols=19 Identities=26% Similarity=0.469 Sum_probs=17.1
Q ss_pred EEEEcCCCC-ceEEEEeeCC
Q 023513 90 ALGIDPDLS-GALAVLKSDH 108 (281)
Q Consensus 90 ILGIDPGl~-gGyaVLe~~g 108 (281)
+||+|=|++ +||||++.+.
T Consensus 3 ~LGLDiGt~SvGWAVv~~d~ 22 (805)
T TIGR01865 3 ILGLDIGIASVGWAIVEDDY 22 (805)
T ss_pred eeEEeecccceeEEEEeccc
Confidence 799999999 6999998765
No 33
>PRK09605 bifunctional UGMP family protein/serine/threonine protein kinase; Validated
Probab=33.91 E-value=1.8e+02 Score=29.29 Aligned_cols=99 Identities=11% Similarity=0.024 Sum_probs=49.7
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeEEee-----cCCc-ccccccchhhhhcHHHHHHHHHhhcC--CCCCEEEEccc
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFD-----TPHL-PVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQS 158 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd-----~p~i-~~~~~~~l~~rl~~~~I~~lL~~l~~--~~Pd~aaVE~v 158 (281)
|.|||||=-.. ++.||++.++. +-..... +|-+ +........+.+ ...+.+.|.+... ...|.+++=.
T Consensus 1 m~il~iets~~~~s~a~~~~~~~-~~~~~~~~~~~~~gg~~p~~~~~~H~~~l-~~~i~~~l~~~~~~~~~id~iav~~- 77 (535)
T PRK09605 1 MIVLGIEGTAWKTSAGIVDSDGD-VLFNESDPYKPPSGGIHPREAAEHHAEAI-PKVIKEALEEAGLKPEDIDLVAFSQ- 77 (535)
T ss_pred CEEEEEEccccceEEEEEeCCCc-EEEEEEeeccCCcCCCChHHHHHHHHHHH-HHHHHHHHHHcCCCHhhCCEEEECC-
Confidence 67999998776 59999985442 1111111 1211 111111121111 1333344444221 2235555443
Q ss_pred cCCCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeCh
Q 023513 159 IPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPS 195 (281)
Q Consensus 159 f~ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP 195 (281)
+-|.-+.+.+|.+. +-+.+...|+|++.+.=
T Consensus 78 ----gPg~~~~l~vg~~~--ak~la~~~~~~~~~v~h 108 (535)
T PRK09605 78 ----GPGLGPCLRVVATA--ARALALSLDVPLIGVNH 108 (535)
T ss_pred ----CCCcHhhHHHHHHH--HHHHHHHhCCCeecccH
Confidence 33455667666553 44557788999987753
No 34
>TIGR03725 bact_YeaZ universal bacterial protein YeaZ. This family describes a protein family, YeaZ, that appears to be universal in bacteria, but whose function is unknown. This family is related to the gcp (glycoprotease) protein family, also universal in bacteria and unknown in function. In Gram-positive lineages, members of these two related families often belong to the same operon, along with the ribosomal-protein-alanine acetyltransferase gene. Members of this family may occur as fusions with gcp or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI.
Probab=33.51 E-value=1.5e+02 Score=26.24 Aligned_cols=94 Identities=20% Similarity=0.132 Sum_probs=46.9
Q ss_pred EEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC--CCCCEEEEccccCCCCCCc
Q 023513 90 ALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQSIPYPQDGK 166 (281)
Q Consensus 90 ILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~--~~Pd~aaVE~vf~ffgqNv 166 (281)
||+||=... .+.|+++ ++ +++..-... .+....+. ....|.+.|.+..- ..-|..++=. |-|-
T Consensus 1 iLaidTs~~~~sval~~-~~-----~~~~~~~~~--~~~~h~~~-l~~~i~~~l~~~~~~~~~i~~iav~~-----GPGS 66 (202)
T TIGR03725 1 ILAIDTSTEALSVALLD-DG-----EILAERSEE--AGRNHSEI-LLPMIEELLAEAGLSLQDLDAIAVGV-----GPGS 66 (202)
T ss_pred CEEEECCCcceEEEEEE-CC-----EEEEEEeeh--hhHHHHHH-HHHHHHHHHHHcCCCHHHCCEEEEec-----CCCh
Confidence 588998877 4899987 33 223221111 11122221 22344445544321 1123333322 2233
Q ss_pred hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHH
Q 023513 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWK 199 (281)
Q Consensus 167 qSA~~vG~ArGVillala~~GIPV~EytP~qwK 199 (281)
=|.+.+| -.++.+.+...|+|++-++-.+.=
T Consensus 67 fTGlRig--~~~akgla~~~~~p~~~vssL~~l 97 (202)
T TIGR03725 67 FTGLRIG--LATAKGLALALGIPLVGVSSLEAL 97 (202)
T ss_pred HHhHHHH--HHHHHHHHHHhCCCEEecCHHHHH
Confidence 3444444 233445566689999999988773
No 35
>KOG1111 consensus N-acetylglucosaminyltransferase complex, subunit PIG-A/SPT14, required for phosphatidylinositol biosynthesis/Sulfolipid synthase [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Lipid transport and metabolism]
Probab=32.76 E-value=1.1e+02 Score=31.20 Aligned_cols=61 Identities=18% Similarity=0.043 Sum_probs=44.6
Q ss_pred HHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHcccc
Q 023513 171 SGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGL 250 (281)
Q Consensus 171 ~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~~~ 250 (281)
++-+++|.++.=|+.+|++|+.=. ||| +-..||..-..+.++.++|-++|+.-|+.-+..
T Consensus 279 SlTEafc~~ivEAaScGL~VVsTr-------VGG-------------IpeVLP~d~i~~~~~~~~dl~~~v~~ai~~~~~ 338 (426)
T KOG1111|consen 279 SLTEAFCMVIVEAASCGLPVVSTR-------VGG-------------IPEVLPEDMITLGEPGPDDLVGAVEKAITKLRT 338 (426)
T ss_pred HHHHHHHHHHHHHHhCCCEEEEee-------cCC-------------ccccCCccceeccCCChHHHHHHHHHHHHHhcc
Confidence 345899999999999999998632 343 345676652224557788999999999976665
Q ss_pred c
Q 023513 251 K 251 (281)
Q Consensus 251 ~ 251 (281)
.
T Consensus 339 ~ 339 (426)
T KOG1111|consen 339 L 339 (426)
T ss_pred C
Confidence 5
No 36
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.35 E-value=94 Score=28.20 Aligned_cols=23 Identities=26% Similarity=0.149 Sum_probs=19.0
Q ss_pred HHHHHcCCceeeeChhhHHHHhc
Q 023513 181 GILVASGFSVVPIPSLTWKNWYG 203 (281)
Q Consensus 181 lala~~GIPV~EytP~qwKkaVg 203 (281)
-.+...|++|..+.|..+|....
T Consensus 52 ~~l~~~g~~v~~i~p~~v~~~~~ 74 (303)
T COG3547 52 RYLRAEGYPVRLINPRQVKKKAR 74 (303)
T ss_pred HHHHHcCCeeEEECHHHhHHHHh
Confidence 34677999999999999998443
No 37
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=28.51 E-value=28 Score=38.42 Aligned_cols=21 Identities=29% Similarity=0.567 Sum_probs=18.2
Q ss_pred eEEEEcCCCC-ceEEEEeeCCC
Q 023513 89 WALGIDPDLS-GALAVLKSDHN 109 (281)
Q Consensus 89 iILGIDPGl~-gGyaVLe~~g~ 109 (281)
-|||.|=|++ +||||++.+.+
T Consensus 5 yilglDIGi~SVGWAvve~de~ 26 (1088)
T COG3513 5 YILGLDIGINSVGWAVVEDDED 26 (1088)
T ss_pred eEEEeeccccceeeEEeecccc
Confidence 4899999999 59999988763
No 38
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=27.45 E-value=1.5e+02 Score=27.27 Aligned_cols=25 Identities=24% Similarity=0.302 Sum_probs=20.7
Q ss_pred CCCceEEEEcCCCCc-eEEEEeeCCC
Q 023513 85 ADSQWALGIDPDLSG-ALAVLKSDHN 109 (281)
Q Consensus 85 ~~~~iILGIDPGl~g-GyaVLe~~g~ 109 (281)
-+.+.+||||-|-+. -+++++.+++
T Consensus 3 ~~~~~~lgidIggt~i~~~l~d~~g~ 28 (314)
T COG1940 3 PEAMTVLGIDIGGTKIKVALVDLDGE 28 (314)
T ss_pred ccCcEEEEEEecCCEEEEEEECCCCc
Confidence 445679999999994 9999998885
No 39
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=4.2e+02 Score=26.34 Aligned_cols=92 Identities=15% Similarity=0.122 Sum_probs=53.0
Q ss_pred ceEEEEcCCCC-ceEEEEeeCCCcceeE--------Eeec-CCcccccccchhhhhcHHHHHHHHHhhc----C--CCCC
Q 023513 88 QWALGIDPDLS-GALAVLKSDHNGCSAE--------VFDT-PHLPVLVGKRVRKRLDAKSMIMLLRSLD----A--PIGT 151 (281)
Q Consensus 88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~--------vvd~-p~i~~~~~~~l~~rl~~~~I~~lL~~l~----~--~~Pd 151 (281)
|+||||.=..- +|.||++.++ +-.. .-.+ |+++- +..|-..+.|-..|++.. . ...|
T Consensus 1 m~iLGIEtScDeT~vaIv~~~~--ilan~~~sq~~~h~~~GGVvPe-----~Asr~H~e~i~~li~~al~eA~~~~~dID 73 (342)
T COG0533 1 MIILGIETSCDETGVAIVDEEK--ILANVVASQIELHARYGGVVPE-----LASRHHVENIPPLIEEALAEAGVSLEDID 73 (342)
T ss_pred CeEEEEEcccccceeEEEeccC--hhheehhhcccccCCCCCcCcc-----HHHHHHHHHHHHHHHHHHHHcCCCcccCC
Confidence 67999997777 6999998654 2111 2233 22221 111223333444443332 2 3456
Q ss_pred EEEEccccCCCCCCchhhhHHHhhHHHHHHHHHHcCCceeee
Q 023513 152 TAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPI 193 (281)
Q Consensus 152 ~aaVE~vf~ffgqNvqSA~~vG~ArGVillala~~GIPV~Ey 193 (281)
.+|+=. +-|.-.++.+|-..+=.+ +...++|++-|
T Consensus 74 ~IA~T~-----gPGL~gaL~VG~~~Ak~L--A~a~~kPli~V 108 (342)
T COG0533 74 AIAVTA-----GPGLGGALLVGATAAKAL--ALALNKPLIPV 108 (342)
T ss_pred EEEEec-----CCCchhHHHHHHHHHHHH--HHHhCCCEeec
Confidence 666544 567788888887666555 56788888765
No 40
>PF01385 OrfB_IS605: Probable transposase; InterPro: IPR001959 This entry represents a conserved region of a probable transposase family, which is found in a number of uncharacterised bacterial proteins. A novel insertion sequence (IS)-like element of the Bacillus PS3 (Thermophilic bacterium PS-3) that promotes expression of the alanine carrier protein-encoding gene belongs to this entry, including IS891 [], IS1136 [], and IS1341 []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=26.27 E-value=53 Score=28.19 Aligned_cols=32 Identities=19% Similarity=0.311 Sum_probs=21.1
Q ss_pred hcccccccCCCCCCCccccccCCCCCceEEEEcCCCCc
Q 023513 62 QNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSG 99 (281)
Q Consensus 62 ~~~l~~l~~~~~~~~~~~~~~~~~~~~iILGIDPGl~g 99 (281)
..|.-++++--+.. .....+.-++|||+|...
T Consensus 104 ~~~yl~i~~~~~~~------~~~~~~~~~vgVDlGi~~ 135 (227)
T PF01385_consen 104 GKWYLSITVEVEVE------PPPPDTEKVVGVDLGIKN 135 (227)
T ss_pred hhcccccccccccc------ccccccceeeeeccccce
Confidence 77887777764332 112334458999999996
No 41
>PF11071 DUF2872: Protein of unknown function (DUF2872); InterPro: IPR019884 This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=25.93 E-value=1.3e+02 Score=26.34 Aligned_cols=62 Identities=16% Similarity=0.212 Sum_probs=38.1
Q ss_pred HHHHHHHHHHh-CCcccccccCCCCCCHHHHHHHHHHccccccCCCCCCCcccccccccccHHHHhhhh
Q 023513 211 KDDSRRVASTL-FPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278 (281)
Q Consensus 211 KeQVq~MV~~L-Lp~~~~~L~~kk~ddaADALAIA~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (281)
++|+.+-++.. ||.. +..+-.+|+++|+...++.|.....+-|--.|. +-|-+-|.-|+++-
T Consensus 11 Re~I~~ga~~~~L~v~--F~~PvtdH~~SD~~G~~iLG~e~~~fw~D~k~a----~iN~iRT~~li~~a 73 (141)
T PF11071_consen 11 REEIKEGAKAAGLPVE--FTSPVTDHEASDDCGVDILGEEPNKFWRDHKGA----KINAIRTRTLIEKA 73 (141)
T ss_pred HHHHHHHHHHcCCCeE--EecCCCCchhhhhhhHHHhCCCCccccccchhh----hhhHHHHHHHHhhC
Confidence 44555555543 3221 113456899999999999998888776654444 34555566666654
No 42
>TIGR03646 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=25.63 E-value=1.3e+02 Score=26.36 Aligned_cols=44 Identities=18% Similarity=0.121 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHHHHccccccCCCCCCCcccccccccccHHHHhhhh
Q 023513 231 RKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278 (281)
Q Consensus 231 ~kk~ddaADALAIA~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (281)
+-.+|+++|+...++.|.....+-+--.|. +-|-+-|.-|+++-
T Consensus 33 pvtdH~aSD~~G~~iLG~e~~~fw~D~k~a----~iNaiRT~~li~~a 76 (144)
T TIGR03646 33 PVTDHEASDNIGEDILGKQPSNFWRDDAAA----SINNIRTRKLIEKA 76 (144)
T ss_pred CCCCCcchhhhhHHHhCCCCcccccccccc----chhhHHHHHHHhhC
Confidence 356899999999999999888876655554 34555566666654
No 43
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=25.31 E-value=2.4e+02 Score=30.87 Aligned_cols=92 Identities=14% Similarity=0.115 Sum_probs=48.4
Q ss_pred EEEEcCCCCceEEEEeeCCCcceeEEeecCCc-------ccccccc----hhhhhcHHHHHHHHHhhcCCCCCEEEEccc
Q 023513 90 ALGIDPDLSGALAVLKSDHNGCSAEVFDTPHL-------PVLVGKR----VRKRLDAKSMIMLLRSLDAPIGTTAYVEQS 158 (281)
Q Consensus 90 ILGIDPGl~gGyaVLe~~g~~~~~~vvd~p~i-------~~~~~~~----l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~v 158 (281)
..|-||+.-+|+|-| +|. .+.|+....- ....|.. .++- ..+.++-.++ .-|=+..|+..
T Consensus 182 ~~~dD~aIVtGlGRI--dGr--pV~VIAndkg~~tke~~~rnfG~~~peGyRKA---lRlmkLAekf--gLPIVtLVDTp 252 (762)
T PLN03229 182 AGYDDPAIVTGIGTI--DGK--RYMFIGHQKGRNTKENIMRNFGMPTPHGYRKA---LRMMYYADHH--GFPIVTFIDTP 252 (762)
T ss_pred cCCCCCCeEEEEEEE--CCE--EEEEEEecCCccccccccccCCCCCHHHHHHH---HHHHHHHHHc--CCCEEEEEECC
Confidence 346789888899977 555 5666643321 0111111 2211 1222222222 34888899998
Q ss_pred cCCCCCCchhhhHHHhhH--HHHHHHHHHcCCceeee
Q 023513 159 IPYPQDGKQGWWSGGFGY--GLWIGILVASGFSVVPI 193 (281)
Q Consensus 159 f~ffgqNvqSA~~vG~Ar--GVillala~~GIPV~Ey 193 (281)
++|++.+.-. .|+++ .-.+.+++...+|++.+
T Consensus 253 GA~pG~~AEe---~Gq~~aIArnl~amasl~VP~ISV 286 (762)
T PLN03229 253 GAYADLKSEE---LGQGEAIAHNLRTMFGLKVPIVSI 286 (762)
T ss_pred CcCCCchhHH---HhHHHHHHHHHHHHhCCCCCEEEE
Confidence 7666544433 24433 33445556677777765
No 44
>PHA02535 P terminase ATPase subunit; Provisional
Probab=24.03 E-value=1.6e+02 Score=31.13 Aligned_cols=89 Identities=18% Similarity=0.169 Sum_probs=50.9
Q ss_pred ceEEEEcCCCCc---eEEEEe---eCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccC
Q 023513 88 QWALGIDPDLSG---ALAVLK---SDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIP 160 (281)
Q Consensus 88 ~iILGIDPGl~g---GyaVLe---~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ 160 (281)
.+.+|.|||-++ ++.|+. ..|+ .++++..-... .+++....+.|+++.. |.-..++|-.-
T Consensus 403 ~VwiG~D~sr~~D~t~lvVvapp~~~g~--kfrvler~~~~---------g~~f~~QA~~I~~l~~rynV~~I~ID~T-- 469 (581)
T PHA02535 403 EVWVGYDPAHTGDSAGLVVVAPPAVPGG--KFRVLERHQWR---------GLDFAEQAAEIRKLTEKYNVTYIGIDAT-- 469 (581)
T ss_pred eEEEeeCCCCCCCCeEEEEEecCcccCC--eEEEEEEEEEc---------CCCHHHHHHHHHHHHHHcCceEEEEcCC--
Confidence 357999999885 788885 4445 56666332222 3456666666766665 55556777662
Q ss_pred CCCCCchhhhHHHhhHHHHHHHHHHcC-CceeeeChhhHHHHh
Q 023513 161 YPQDGKQGWWSGGFGYGLWIGILVASG-FSVVPIPSLTWKNWY 202 (281)
Q Consensus 161 ffgqNvqSA~~vG~ArGVillala~~G-IPV~EytP~qwKkaV 202 (281)
|-+.||+-.+-...+ +--+.|+|. .|..+
T Consensus 470 ------------GiG~~v~e~v~~~~p~v~~i~ys~~-~K~~L 499 (581)
T PHA02535 470 ------------GIGAGVYQLVKKFFPAAVAINYSPE-VKTRL 499 (581)
T ss_pred ------------CCCHHHHHHHHHhcCCeeEEEeCHH-HHHHH
Confidence 344566666332222 223556653 34443
No 45
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=22.85 E-value=1.8e+02 Score=26.83 Aligned_cols=94 Identities=24% Similarity=0.205 Sum_probs=50.6
Q ss_pred CCceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhc-------CCCCCEEEEcc
Q 023513 86 DSQWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLD-------APIGTTAYVEQ 157 (281)
Q Consensus 86 ~~~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~-------~~~Pd~aaVE~ 157 (281)
.+.+++|||=|++ .-.-+.+..++ .+++.+.+...+..+.-. |++...+.|+++. ......+++ .
T Consensus 22 ~~~~~~~iDiGSssi~~vv~~~~~~--~~~~~~~~~~~vr~G~i~----di~~a~~~i~~~~~~ae~~~g~~i~~v~~-~ 94 (267)
T PRK15080 22 ESPLKVGVDLGTANIVLAVLDEDGQ--PVAGALEWADVVRDGIVV----DFIGAVTIVRRLKATLEEKLGRELTHAAT-A 94 (267)
T ss_pred CCCEEEEEEccCceEEEEEEcCCCC--EEEEEeccccccCCCEEe----eHHHHHHHHHHHHHHHHHHhCCCcCeEEE-E
Confidence 3568999999999 45556666665 567777766654333321 3333333333222 112344554 3
Q ss_pred ccCCCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeCh
Q 023513 158 SIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPS 195 (281)
Q Consensus 158 vf~ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP 195 (281)
+ +. + ++.+ .+..+.-++...|+.+..+-+
T Consensus 95 v---p~-~----~~~~-~~~~~~~~~~~aGl~~~~ii~ 123 (267)
T PRK15080 95 I---PP-G----TSEG-DPRAIINVVESAGLEVTHVLD 123 (267)
T ss_pred e---CC-C----CCch-hHHHHHHHHHHcCCceEEEec
Confidence 2 11 1 1122 244566788888988874433
No 46
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=22.57 E-value=85 Score=30.99 Aligned_cols=107 Identities=13% Similarity=0.102 Sum_probs=53.8
Q ss_pred EEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhh--cHHHHHHHHHhhcC--CCCCE------------
Q 023513 90 ALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRL--DAKSMIMLLRSLDA--PIGTT------------ 152 (281)
Q Consensus 90 ILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl--~~~~I~~lL~~l~~--~~Pd~------------ 152 (281)
||-|.||++. =+||++.+.. +.-..+.....+...-+++...+ +-+.|.+.|.+.-- ..+|.
T Consensus 5 iltINPGststKlaVfe~ek~-ife~tlrhs~eEl~~f~~i~dQ~~fR~~~i~~~i~e~g~~i~~~dAvvgRGGLL~pi~ 83 (358)
T COG3426 5 ILTINPGSTSTKLAVFEDEKE-IFEKTLRHSLEELEKFKRIPDQFEFRKDAILEFIDEQGYNISKFDAVVGRGGLLRPIP 83 (358)
T ss_pred EEEecCCCccceEEEecCchH-hhHHHhhcCHHHHHHHhhhhHhHhHHHHHHHHHHHHhCCCcCCccceeecCccccccC
Confidence 8999999995 8999984432 11111111112211112211111 22566666666522 33333
Q ss_pred ----EEEccccCCC--CCCchhhhHHHhhHHHHH--HHHHHcCCceeeeChhhHHHH
Q 023513 153 ----AYVEQSIPYP--QDGKQGWWSGGFGYGLWI--GILVASGFSVVPIPSLTWKNW 201 (281)
Q Consensus 153 ----aaVE~vf~ff--gqNvqSA~~vG~ArGVil--lala~~GIPV~EytP~qwKka 201 (281)
++=|++..+. +.+.+-+-+ -|.++ -++...|||-+.+.|..+---
T Consensus 84 gGTY~Vn~~M~~~lk~~~~G~haSn----LGaiiA~~ia~~~gvPayIVDPvvVDEm 136 (358)
T COG3426 84 GGTYVVNEKMLKDLKNGVQGEHASN----LGAIIANRIAKALGVPAYIVDPVVVDEM 136 (358)
T ss_pred CceeEeCHHHHHHHHcCCCCcchhh----hhHHHHHHHhhhcCCCeeeeCceehhhc
Confidence 2223321111 122223333 44444 467889999999999887643
No 47
>PHA02533 17 large terminase protein; Provisional
Probab=22.27 E-value=1.6e+02 Score=30.48 Aligned_cols=22 Identities=9% Similarity=-0.127 Sum_probs=14.7
Q ss_pred CCCCHHHHHHHHHHccccccCC
Q 023513 233 KDHGKADAVLIAAYGKGLKLDS 254 (281)
Q Consensus 233 k~ddaADALAIA~~g~~~~~~~ 254 (281)
.|||--=|||||.|...--.++
T Consensus 464 ~HDD~Vmalal~~~~~~~~~~~ 485 (534)
T PHA02533 464 FHDDLVMSLVIFAWLVTQEKFK 485 (534)
T ss_pred CchHHHHHHHHHHHHhhhHHHH
Confidence 4777888888888854433333
No 48
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.
Probab=22.10 E-value=3.3e+02 Score=20.11 Aligned_cols=47 Identities=15% Similarity=-0.002 Sum_probs=31.8
Q ss_pred CCEEEEccccCCC---C-CCch-----hhhHHHhhHHHHHHHHHHcCCceeeeChh
Q 023513 150 GTTAYVEQSIPYP---Q-DGKQ-----GWWSGGFGYGLWIGILVASGFSVVPIPSL 196 (281)
Q Consensus 150 Pd~aaVE~vf~ff---g-qNvq-----SA~~vG~ArGVillala~~GIPV~EytP~ 196 (281)
.+.++||.+.-.- . .|.. +-+..|+-+-.+.-.|...||+|+++.|.
T Consensus 24 ~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yka~~~Gi~v~~v~~~ 79 (82)
T TIGR01766 24 NGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPA 79 (82)
T ss_pred CCEEEECCccchhhhcchhhHHHHHHHHhhhHHHHHHHHHHHHHHcCCeEEEeCcc
Confidence 4799999974101 1 1111 33556666777778889999999999984
Done!