Query 025662
Match_columns 249
No_of_seqs 79 out of 81
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 08:11:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025662hhsearch_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 2.8E-38 6.2E-43 268.2 12.4 145 90-248 1-148 (156)
2 PRK00039 ruvC Holliday junctio 100.0 2.5E-37 5.5E-42 263.0 13.4 149 88-248 2-153 (164)
3 PF02075 RuvC: Crossover junct 100.0 1.8E-37 3.9E-42 259.3 10.5 146 90-247 1-149 (149)
4 COG0817 RuvC Holliday junction 100.0 4.7E-37 1E-41 261.2 9.3 145 91-248 1-148 (160)
5 cd00529 RuvC_resolvase Hollida 100.0 4.8E-34 1E-38 238.8 12.2 148 89-248 1-151 (154)
6 PF07066 DUF3882: Lactococcus 98.9 9.7E-10 2.1E-14 93.5 5.3 144 89-247 3-157 (159)
7 PF04848 Pox_A22: Poxvirus A22 98.7 5.9E-08 1.3E-12 82.1 9.4 134 88-246 1-138 (143)
8 smart00732 YqgFc Likely ribonu 97.1 0.0036 7.9E-08 47.1 8.5 89 88-194 1-91 (99)
9 PF04312 DUF460: Protein of un 96.8 0.0034 7.4E-08 53.2 6.1 61 86-163 30-90 (138)
10 PF01548 DEDD_Tnp_IS110: Trans 96.6 0.0046 1E-07 49.8 5.6 105 90-223 1-108 (144)
11 PF11215 DUF3010: Protein of u 96.4 0.039 8.4E-07 46.9 9.9 106 88-205 1-112 (138)
12 COG2433 Uncharacterized conser 96.2 0.034 7.4E-07 56.9 10.3 59 88-163 244-302 (652)
13 PF03652 UPF0081: Uncharacteri 95.6 0.054 1.2E-06 45.0 7.4 92 88-194 1-94 (135)
14 PRK00109 Holliday junction res 95.2 0.53 1.1E-05 39.3 12.0 94 86-194 2-96 (138)
15 COG0816 Predicted endonuclease 93.1 0.99 2.1E-05 38.3 9.4 94 88-196 2-97 (141)
16 PF07318 DUF1464: Protein of u 89.1 4.6 0.0001 39.0 10.7 56 92-159 1-57 (343)
17 TIGR00250 RNAse_H_YqgF RNAse H 88.6 3.2 7E-05 34.2 8.2 88 91-194 1-90 (130)
18 COG2410 Predicted nuclease (RN 88.4 3.6 7.9E-05 36.4 8.7 53 181-248 94-147 (178)
19 PF03237 Terminase_6: Terminas 86.8 1.7 3.6E-05 38.5 5.9 66 84-159 222-293 (384)
20 PF14639 YqgF: Holliday-juncti 79.3 4.5 9.7E-05 34.4 5.3 111 89-228 6-128 (150)
21 PF04250 DUF429: Protein of un 76.1 36 0.00079 29.3 10.2 66 183-248 109-186 (209)
22 PRK09604 UGMP family protein; 75.5 8.8 0.00019 36.1 6.6 102 88-197 1-113 (332)
23 PF09159 Ydc2-catalyt: Mitocho 73.3 21 0.00045 33.0 8.3 131 90-224 1-191 (274)
24 COG3426 Butyrate kinase [Energ 69.9 7.9 0.00017 37.3 4.8 104 89-200 4-135 (358)
25 COG1214 Inactive homolog of me 68.9 9.6 0.00021 34.0 5.0 101 88-200 1-102 (220)
26 PTZ00340 O-sialoglycoprotein e 68.0 16 0.00035 35.2 6.6 101 88-197 1-111 (345)
27 COG4020 Uncharacterized protei 62.0 23 0.00051 33.7 6.2 95 86-194 1-116 (332)
28 PRK09605 bifunctional UGMP fam 59.8 29 0.00063 34.3 6.9 98 88-195 1-108 (535)
29 COG2183 Tex Transcriptional ac 59.0 23 0.0005 37.8 6.3 111 85-227 327-443 (780)
30 PRK03011 butyrate kinase; Prov 56.4 76 0.0016 30.6 8.9 21 88-108 2-23 (358)
31 PF14239 RRXRR: RRXRR protein 56.3 14 0.0003 32.7 3.6 60 38-108 12-72 (176)
32 PF00370 FGGY_N: FGGY family o 55.6 27 0.0006 30.4 5.4 20 90-109 2-22 (245)
33 TIGR03725 bact_YeaZ universal 55.6 23 0.0005 30.7 4.8 95 90-198 1-96 (202)
34 TIGR01630 psiM2_ORF9 phage unc 49.9 1.4E+02 0.0029 24.1 8.6 46 136-196 33-81 (142)
35 TIGR03723 bact_gcp putative gl 49.7 43 0.00094 31.3 6.0 103 90-198 1-112 (314)
36 PRK15080 ethanolamine utilizat 49.7 49 0.0011 30.0 6.2 97 86-195 22-123 (267)
37 COG1548 Predicted transcriptio 49.0 30 0.00066 33.1 4.8 92 86-195 1-96 (330)
38 COG2441 Predicted butyrate kin 47.9 37 0.0008 32.9 5.2 122 91-222 1-152 (374)
39 TIGR02261 benz_CoA_red_D benzo 46.9 69 0.0015 29.8 6.8 20 89-108 2-22 (262)
40 COG1433 Uncharacterized conser 44.9 1.8E+02 0.0039 24.1 8.4 84 93-203 16-102 (121)
41 COG2433 Uncharacterized conser 44.7 37 0.00079 35.6 4.9 55 87-162 1-63 (652)
42 COG3547 Transposase and inacti 44.5 29 0.00063 30.9 3.8 40 180-219 51-90 (303)
43 TIGR01766 tspaseT_teng_C trans 42.7 71 0.0015 23.3 5.1 48 149-196 23-79 (82)
44 PRK00047 glpK glycerol kinase; 40.4 79 0.0017 31.0 6.4 31 88-120 5-38 (498)
45 TIGR01315 5C_CHO_kinase FGGY-f 40.1 64 0.0014 32.2 5.8 20 90-109 2-22 (541)
46 PF01385 OrfB_IS605: Probable 38.1 26 0.00056 29.5 2.4 41 62-108 104-144 (227)
47 PTZ00294 glycerol kinase-like 36.9 81 0.0018 31.0 5.9 21 89-109 3-24 (504)
48 COG1924 Activator of 2-hydroxy 36.2 70 0.0015 31.8 5.2 24 85-108 132-156 (396)
49 TIGR03192 benz_CoA_bzdQ benzoy 35.6 1.2E+02 0.0026 28.8 6.6 19 88-106 32-51 (293)
50 PLN02683 pyruvate dehydrogenas 34.2 1.3E+02 0.0028 28.9 6.6 36 111-159 255-290 (356)
51 CHL00144 odpB pyruvate dehydro 33.6 1.3E+02 0.0028 28.4 6.5 36 111-159 228-263 (327)
52 PLN02295 glycerol kinase 32.6 92 0.002 30.7 5.5 21 89-109 1-22 (512)
53 TIGR01314 gntK_FGGY gluconate 32.3 1.1E+02 0.0024 30.1 5.9 20 90-109 2-22 (505)
54 TIGR01175 pilM type IV pilus a 32.3 87 0.0019 28.7 5.0 55 89-145 4-64 (348)
55 PRK10939 autoinducer-2 (AI-2) 31.8 1.8E+02 0.0039 28.7 7.4 21 89-109 4-25 (520)
56 COG1940 NagC Transcriptional r 31.2 2.2E+02 0.0048 25.7 7.4 26 84-109 2-28 (314)
57 PRK10331 L-fuculokinase; Provi 30.7 1.2E+02 0.0026 29.4 6.0 29 89-119 3-32 (470)
58 cd00652 TBP_TLF TATA box bindi 28.2 1.9E+02 0.004 25.1 6.1 114 104-226 41-173 (174)
59 COG1070 XylB Sugar (pentulose 28.1 1.4E+02 0.0031 29.5 6.0 22 87-108 3-25 (502)
60 PRK15027 xylulokinase; Provisi 26.1 1.4E+02 0.003 29.2 5.4 20 90-109 2-22 (484)
61 TIGR01311 glycerol_kin glycero 25.7 2.4E+02 0.0053 27.5 7.1 21 89-109 2-23 (493)
62 PRK14101 bifunctional glucokin 25.6 2.7E+02 0.0059 28.4 7.6 33 86-120 16-49 (638)
63 TIGR00241 CoA_E_activ CoA-subs 24.9 1.9E+02 0.0041 25.7 5.7 18 90-108 2-20 (248)
64 COG2971 Predicted N-acetylgluc 24.6 2.9E+02 0.0062 26.6 7.0 23 85-107 2-24 (301)
65 TIGR00329 gcp_kae1 metallohydr 24.5 1.8E+02 0.0038 27.0 5.6 100 91-198 1-111 (305)
66 PF12682 Flavodoxin_4: Flavodo 24.2 17 0.00036 30.7 -1.1 24 17-40 91-120 (156)
67 PRK00976 hypothetical protein; 24.1 89 0.0019 30.1 3.6 117 88-222 1-146 (326)
68 cd04517 TLF TBP-like factors ( 23.5 2.3E+02 0.005 24.6 5.8 124 92-226 31-173 (174)
69 cd01403 Cyt_c_Oxidase_VIIb Cyt 22.6 23 0.00049 25.5 -0.5 27 174-200 20-51 (51)
70 COG4972 PilM Tfp pilus assembl 22.4 1.2E+02 0.0025 29.8 4.0 73 89-163 11-96 (354)
71 PF01869 BcrAD_BadFG: BadF/Bad 22.3 1.5E+02 0.0033 26.2 4.6 57 91-149 1-59 (271)
72 COG2403 Predicted GTPase [Gene 21.9 3E+02 0.0066 27.7 6.8 78 133-224 69-153 (449)
73 PHA02533 17 large terminase pr 21.9 2.4E+02 0.0051 28.8 6.3 63 86-159 313-381 (534)
74 TIGR00204 dxs 1-deoxy-D-xylulo 21.7 4.1E+02 0.009 27.4 8.1 36 111-159 522-557 (617)
75 PRK04123 ribulokinase; Provisi 20.4 3.8E+02 0.0082 26.6 7.3 22 88-109 3-26 (548)
76 TIGR00215 lpxB lipid-A-disacch 20.3 2.5E+02 0.0053 26.6 5.8 55 129-200 72-127 (385)
77 PRK05444 1-deoxy-D-xylulose-5- 20.2 3.9E+02 0.0085 27.1 7.5 35 112-159 487-521 (580)
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=2.8e-38 Score=268.25 Aligned_cols=145 Identities=14% Similarity=0.113 Sum_probs=136.6
Q ss_pred EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|||||||++.+ |||++..++ .++++|+++|++.. .. .|+..++++|.++|++| +|+.++||++| +++|+
T Consensus 1 ILGIDPGl~~tG~gvi~~~~~--~~~~v~~G~I~t~~-~~~~~RL~~I~~~l~~~i~~y---~P~~~aiE~~F--~~~N~ 72 (156)
T TIGR00228 1 ILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTKV-DDLPSRLKLIYAGVTEIITQF---QPNYFAIEQVF--MAKNA 72 (156)
T ss_pred CEeECcccccccEEEEEecCC--eEEEEEeeEEECCC-CCHHHHHHHHHHHHHHHHHHh---CCCEEEEeHHh--hccCH
Confidence 69999999999 999998776 89999999999864 34 99999999999999999 99999999999 99999
Q ss_pred cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhh
Q 025662 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILY 246 (249)
Q Consensus 167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~ 246 (249)
+|++++|++||+++.+++..||||+||+|.+|||+++|+ |+|+|+|++.|++++|+..+. ++ +|.|||||||+|
T Consensus 73 ~sa~~lg~arGvilla~~~~~ipv~Ey~P~~vKkavtG~-G~A~KeQV~~mV~~lL~l~~~----p~-~DaaDALAiAi~ 146 (156)
T TIGR00228 73 DSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRRLLKLPAN----PQ-ADAADALAIAIT 146 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHcCCCCC----CC-CCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999 999999999999999987654 55 899999999999
Q ss_pred cc
Q 025662 247 HH 248 (249)
Q Consensus 247 h~ 248 (249)
|+
T Consensus 147 h~ 148 (156)
T TIGR00228 147 HA 148 (156)
T ss_pred Hh
Confidence 96
No 2
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=100.00 E-value=2.5e-37 Score=263.03 Aligned_cols=149 Identities=15% Similarity=0.113 Sum_probs=140.4
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q 164 (249)
|+|||||||++.+ |||++.+++ .++++|+++|++..+.. .|+..+++.|.++|++| +|+.++||++| +++
T Consensus 2 m~iLGIDPgl~~tG~avi~~~~~--~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~---~Pd~vaiE~~f--~~~ 74 (164)
T PRK00039 2 MRILGIDPGLRRTGYGVIEVEGR--RLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEY---QPDEVAIEEVF--FNK 74 (164)
T ss_pred CEEEEEccccCceeEEEEEecCC--eEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh---CCCEEEEehhh--hcc
Confidence 7899999999999 999998865 79999999999876555 99999999999999999 99999999988 999
Q ss_pred CccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHH
Q 025662 165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCI 244 (249)
Q Consensus 165 gvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA 244 (249)
|.+|++++|+++|+++++|...||||+||+|++|||+++|+ |+|+|+|++.|++++|+.... ++++|.|||||||
T Consensus 75 n~~sa~~l~~arGvi~la~~~~~ipv~ey~P~~VKk~vtG~-G~A~K~qV~~mv~~~l~l~~~----~~~~D~aDAlAiA 149 (164)
T PRK00039 75 NPQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGY-GRADKEQVQHMVKRLLNLPEI----PKPDDAADALAIA 149 (164)
T ss_pred ChHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHhhhhhcCC-CCCCHHHHHHHHHHHhCCCCC----CCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999 999999999999999987754 6689999999999
Q ss_pred hhcc
Q 025662 245 LYHH 248 (249)
Q Consensus 245 ~~h~ 248 (249)
+||+
T Consensus 150 ~~h~ 153 (164)
T PRK00039 150 ICHA 153 (164)
T ss_pred HHHH
Confidence 9996
No 3
>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=1.8e-37 Score=259.26 Aligned_cols=146 Identities=17% Similarity=0.141 Sum_probs=118.0
Q ss_pred EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|||||||++.+ |||++.++. .++++|+++|++..... .|+..++++|.++|++| +|+.++||++| +++|.
T Consensus 1 ILGIDPgl~~tG~avi~~~~~--~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~---~P~~vaiE~~f--~~~n~ 73 (149)
T PF02075_consen 1 ILGIDPGLSNTGYAVIEEDGG--KLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEY---NPDEVAIEEIF--FGKNP 73 (149)
T ss_dssp EEEEE--SSEEEEEEEEEETT--EEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH-----SEEEEEE-S------H
T ss_pred CEEECCCCCCeeEEEEEeeCC--EEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhh---CCCEEEeehhh--hccCH
Confidence 79999999999 999999765 89999999999887655 99999999999999999 99999999988 99999
Q ss_pred cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhh
Q 025662 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILY 246 (249)
Q Consensus 167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~ 246 (249)
+|++++|+++|++++++...||||++|+|++|||+++|+ |+|+|+|++.|++++|+..+. ++++|.|||||||+|
T Consensus 74 ~s~~~l~~arGvi~l~~~~~~i~v~~y~P~~vKk~vtG~-G~A~KeqV~~mv~~ll~l~~~----~~~~d~aDAlAiA~~ 148 (149)
T PF02075_consen 74 KSALKLGQARGVILLAAAQRGIPVFEYTPSEVKKAVTGN-GRASKEQVAFMVRKLLGLDEK----PKPDDAADALAIALC 148 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHTTT--EEEEEHHHHHHHHTSS-TT--HHHHHHHHHHHTT--------SS-S-THHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCeEEEECHHHHHHHhhCC-CccCHHHHHHHHHHHhCCCCC----CCccchHhhHhhhhc
Confidence 999999999999999999999999999999999999999 899999999999999998865 667999999999999
Q ss_pred c
Q 025662 247 H 247 (249)
Q Consensus 247 h 247 (249)
|
T Consensus 149 H 149 (149)
T PF02075_consen 149 H 149 (149)
T ss_dssp H
T ss_pred C
Confidence 8
No 4
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.7e-37 Score=261.23 Aligned_cols=145 Identities=14% Similarity=0.127 Sum_probs=138.5
Q ss_pred EEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCcc
Q 025662 91 LGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ 167 (249)
Q Consensus 91 LGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvq 167 (249)
||||||++.+ |||++.+++ ++..+++++|+++.... .|+..+++.+.++|++| +|+.++||++| +.+|++
T Consensus 1 lGIDPGl~~~G~gvI~~~~~--~l~~v~~G~I~t~~~~~l~~RL~~l~~~l~~vl~~~---~P~~~AIE~~F--~~kN~~ 73 (160)
T COG0817 1 LGIDPGLRRTGYGVIEVEGR--QLSYLASGVIRTSSDAPLAERLKQLYDGLSEVLDEY---QPDEVAIEQVF--VNKNAD 73 (160)
T ss_pred CCcCCCccccceEEEEccCC--eEEEEeeeEEecCCCccHHHHHHHHHHHHHHHHHHh---CCCeeehhHHH--HhcChH
Confidence 6999999999 999999987 99999999999886666 99999999999999999 99999999999 999999
Q ss_pred ceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhhc
Q 025662 168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYH 247 (249)
Q Consensus 168 Saf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~h 247 (249)
|++++|++||+++++++..++||.||+|++.||+++|+ |+++|+|++.|+++||+ .+. ++++|+|||||||+||
T Consensus 74 s~lklgQARGv~~la~~~~~l~v~eY~p~~VKkavvG~-G~A~K~QVq~MV~~lL~-~~~----~~~~DaADALAiAitH 147 (160)
T COG0817 74 SALKLGQARGVALLAAARRGLPVFEYTPNQVKKAVVGN-GKADKEQVQHMVKRLLG-LEE----PPPADAADALAIAITH 147 (160)
T ss_pred HHHHHHHHHHHHHHHHHHcCCChhhccHHHHHHHhhcC-CcccHHHHHHHHHHHhC-CCC----CCCccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999 99999999999999999 444 7799999999999999
Q ss_pred c
Q 025662 248 H 248 (249)
Q Consensus 248 ~ 248 (249)
+
T Consensus 148 a 148 (160)
T COG0817 148 A 148 (160)
T ss_pred H
Confidence 6
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=4.8e-34 Score=238.77 Aligned_cols=148 Identities=14% Similarity=0.095 Sum_probs=138.3
Q ss_pred eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG 165 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg 165 (249)
+|||||||++.+ ||+++..++ ..+++++++|++..+.. .|+..+++.|.++|..| +|+.++||++| +++|
T Consensus 1 rILGIDPGl~~~G~av~~~~~~--~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~---~Pd~vaiE~~~--~~~n 73 (154)
T cd00529 1 RILGIDPGSRNTGYGVIEQEGR--KLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQF---QPDVVAIERVF--FAKN 73 (154)
T ss_pred CEEEEccCcCceEEEEEEeeCC--eEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh---CCCEEEEEEhh--cccC
Confidence 489999999999 999998775 89999999999875555 99999999999999999 89999999998 9999
Q ss_pred ccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHh
Q 025662 166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCIL 245 (249)
Q Consensus 166 vqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~ 245 (249)
.+|++++|+.+|+++++|...|+||++|+|++||++++|+ |+++|+|++.|++++|..... +++||.|||||||+
T Consensus 74 ~~s~~~l~~~~Gvi~~~~~~~~i~v~e~~P~~vKk~~tG~-G~A~KeqV~~mv~~~l~~~~~----~~~~d~aDAlaiA~ 148 (154)
T cd00529 74 PDSALKLGQARGALILALANRNLPVFEYTPNQVKKAVTGY-GKADKDQVQHMVKRLLNLSEI----PKPDDAADALAVAI 148 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCEEEEccCeeEEEEECC-CCCCHHHHHHHHHHHhCCCCC----CCCCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999 899999999999999987653 57899999999999
Q ss_pred hcc
Q 025662 246 YHH 248 (249)
Q Consensus 246 ~h~ 248 (249)
||.
T Consensus 149 ~~~ 151 (154)
T cd00529 149 THA 151 (154)
T ss_pred HHH
Confidence 995
No 6
>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=98.95 E-value=9.7e-10 Score=93.52 Aligned_cols=144 Identities=19% Similarity=0.175 Sum_probs=102.9
Q ss_pred eEEEEcCCCCc-----e-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccC
Q 025662 89 WALGIDPDLSG-----A-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIP 160 (249)
Q Consensus 89 ~ILGIDPGl~G-----a-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~ 160 (249)
.+|.||=.+++ + ||+.+.... ++...... ...+. +|-+.++.+|..+|.+|+-+ .-..+||+..
T Consensus 3 ~~LslD~STs~~~~~gTG~A~~~~~~~-----~~~si~~~-~k~Ks~~ER~k~ias~Lk~ii~~~d~~-~y~i~IE~~v- 74 (159)
T PF07066_consen 3 KVLSLDFSTSSKKGEGTGWAFFKGSDL-----VVGSIKAK-HKSKSFFERAKSIASELKTIIQKYDLK-FYIIVIEKPV- 74 (159)
T ss_pred eeEEEEEecccCCCCCceeEEecCCeE-----EEeeeeec-CcccCHHHHHHHHHHHHHHHHHHhCCC-cceEEEeccc-
Confidence 48999999985 7 999974321 12221111 11222 99999999999999999754 5678999954
Q ss_pred CCCCCccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCC-CCChHHH--HHHHHHhCCcccccccCCCCCCc
Q 025662 161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGG-TSTKDDS--RRVASTLFPSLCSQLKRKKDHGT 237 (249)
Q Consensus 161 ~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G-~AsKd~s--r~ma~~LfP~~~~~l~rkKdhgr 237 (249)
-|.|.||++++|...|.++|.+-..-=.++.|.|++|.+...-+|. ++.|.++ +..+..+.+ ..-++||.
T Consensus 75 -mg~Nqqs~i~l~~~~G~iLG~l~~~~n~~~fIn~s~W~kY~lis~K~rsrK~~sl~~l~a~~i~~------~k~~~DDe 147 (159)
T PF07066_consen 75 -MGPNQQSSIKLGIATGIILGRLINRANGYYFINVSTWRKYWLISYKDRSRKSMSLELLKASEIVD------NKVKDDDE 147 (159)
T ss_pred -ccccccceEEEEEEeEEEeeeeecccCcEEEecHHHhhhheeeeechhhhhhhhHHHHHHhcccc------ccccccch
Confidence 8889999999999999999997644227999999999999875422 3334444 233333333 23568999
Q ss_pred ccHHHHHhhc
Q 025662 238 ISSPYCILYH 247 (249)
Q Consensus 238 ADALaIA~~h 247 (249)
|||++|-.|-
T Consensus 148 ADAi~IgsY~ 157 (159)
T PF07066_consen 148 ADAILIGSYC 157 (159)
T ss_pred hhhhhhhhhh
Confidence 9999998773
No 7
>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=98.74 E-value=5.9e-08 Score=82.06 Aligned_cols=134 Identities=13% Similarity=0.035 Sum_probs=95.2
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|+|++||+|...- |++++..++ .+++++..-.+.+.+. .......+.+ + ..+.+.||++. .+|+
T Consensus 1 mii~sIDiGikNlA~~iie~~~~--~i~~~~i~~~~~~~~~---~~~~~~dl~~----~---~~d~VlIErQ~---~r~~ 65 (143)
T PF04848_consen 1 MIILSIDIGIKNLAYCIIEFEGN--KIRVIDISKVDWSRDW---EYRILKDLLK----Y---EADTVLIERQP---PRNP 65 (143)
T ss_pred CeEEEEecCCCceeEEEEEcCCC--eEEEEEeccCCcccch---HHHHHHHHhh----c---cCCEEEEecCC---CCCc
Confidence 7899999999999 999999776 6888988877765322 1222233333 5 78999999994 4454
Q ss_pred cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccc--c-ccCCCCCCcccHHHH
Q 025662 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCS--Q-LKRKKDHGTISSPYC 243 (249)
Q Consensus 167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~--~-l~rkKdhgrADALaI 243 (249)
.. + -.+.+.+.+.-.+..|..|+|. +++.+=+.-|+.|...+..++-.... . -+++|-||-|||+++
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 22 2 2346677777889999999999 55432356688888888877755321 1 233677999999998
Q ss_pred Hhh
Q 025662 244 ILY 246 (249)
Q Consensus 244 A~~ 246 (249)
|+.
T Consensus 136 al~ 138 (143)
T PF04848_consen 136 ALA 138 (143)
T ss_pred HHH
Confidence 864
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=97.13 E-value=0.0036 Score=47.12 Aligned_cols=89 Identities=17% Similarity=0.185 Sum_probs=56.3
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|.+||||+|.+.. +|+++.++. ..+....++. . +...+.+.+.++++++ .+..+.|+-.+.. +|.
T Consensus 1 ~~ilgiD~Ggt~i~~a~~d~~g~--~~~~~~~~~~---~----~~~~~~~~l~~~i~~~---~~~~i~Ig~pg~v--~g~ 66 (99)
T smart00732 1 KRVLGLDPGRKGIGVAVVDETGK--LADPLEVIPR---T----NKEADAARLKKLIKKY---QPDLIVIGLPLNM--NGT 66 (99)
T ss_pred CcEEEEccCCCeEEEEEECCCCC--EecCEEEEEe---c----CcchHHHHHHHHHHHh---CCCEEEEeCCcCC--CCC
Confidence 4689999998888 999987764 4443343332 1 3456789999999998 7888998876533 333
Q ss_pred cc-eeechhhhHHHHHHHHHcCCceeEeC
Q 025662 167 QG-WWSGGFGYGLWIGILVASGFSVVPIP 194 (249)
Q Consensus 167 qS-af~~G~a~Gv~~gvLaa~gIPV~eVt 194 (249)
.+ .|. +-+...+-...++||+.+.
T Consensus 67 ~~~~~~----~~l~~~l~~~~~~pv~~~n 91 (99)
T smart00732 67 ASRETE----EAFAELLKERFNLPVVLVD 91 (99)
T ss_pred cCHHHH----HHHHHHHHHhhCCcEEEEe
Confidence 21 121 2222222345678887653
No 9
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=96.78 E-value=0.0034 Score=53.22 Aligned_cols=61 Identities=16% Similarity=0.290 Sum_probs=44.0
Q ss_pred CCceEEEEcCCCCceEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662 86 DSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ 163 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~ 163 (249)
....|+|||||++-++|+|+.+|. .+.+... +.++..++.++|.++. .|-+++ =.+.++|.
T Consensus 30 ~~~lIVGiDPG~ttgiAildL~G~--~l~l~S~------------R~~~~~evi~~I~~~G--~PviVA-tDV~p~P~ 90 (138)
T PF04312_consen 30 RRYLIVGIDPGTTTGIAILDLDGE--LLDLKSS------------RNMSRSEVIEWISEYG--KPVIVA-TDVSPPPE 90 (138)
T ss_pred CCCEEEEECCCceeEEEEEecCCc--EEEEEee------------cCCCHHHHHHHHHHcC--CEEEEE-ecCCCCcH
Confidence 456799999999999999999985 4443333 4566788999999995 444433 44555654
No 10
>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=96.61 E-value=0.0046 Score=49.83 Aligned_cols=105 Identities=21% Similarity=0.229 Sum_probs=72.3
Q ss_pred EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccc
Q 025662 90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG 168 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqS 168 (249)
++|||-+..-- .+++...+. ......+++-+ -...++.+.|..+ .+..+++|.-.
T Consensus 1 ~vGiDv~k~~~~v~v~~~~~~--~~~~~~~~~~~----------~~~~~l~~~l~~~---~~~~v~~E~tg--------- 56 (144)
T PF01548_consen 1 FVGIDVSKDTHDVCVIDPNGE--KLRRFKFENDP----------AGLEKLLDWLASL---GPVLVVMEATG--------- 56 (144)
T ss_pred eEEEEcccCeEEEEEEcCCCc--EEEEEEEeccc----------cchhHHhhhhccc---ccccccccccc---------
Confidence 69999999887 777776663 33333443321 2235677777777 36788888743
Q ss_pred eeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcc--cCCCCChHHHHHHHHHhCC
Q 025662 169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL--SGGTSTKDDSRRVASTLFP 223 (249)
Q Consensus 169 af~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g--~~G~AsKd~sr~ma~~LfP 223 (249)
|+.+ -|.-.|...|++|+.+.|...|..-.. .....||.|++.+|..++-
T Consensus 57 ----~y~~-~l~~~L~~~g~~v~~vnp~~~~~~~~~~~~~~KtD~~DA~~ia~~~~~ 108 (144)
T PF01548_consen 57 ----GYWR-PLADFLQDAGIEVVVVNPLQVKRFRKSLGRRAKTDKIDARAIARLLRR 108 (144)
T ss_pred ----ccch-hhhhheeccccccccccccccccccccccccccccccchHHHHHHHhc
Confidence 1222 345677889999999999999988742 3357788888888877764
No 11
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=96.37 E-value=0.039 Score=46.91 Aligned_cols=106 Identities=11% Similarity=-0.020 Sum_probs=75.8
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc---hhhhhhHHHHHHHHHhcCCCCCCEEEE-ccccCCC
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR---VRKRLDAKSMIMLLRSLDAPIGTTAYV-EQSIPYP 162 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~---~R~r~d~~~L~~lL~~~~~p~p~~a~I-E~v~~~p 162 (249)
|+|+||+=-.+-+ +++|+.++. ..++.|+-+.+++-.+. .-.|-=..++..++++| ..+.++| |+.- -
T Consensus 1 M~vCGVELkgneaii~ll~~~~~--~~~~pdcr~~k~~l~~~~~~~~vr~Fq~~f~kl~~dy---~Vd~VvIk~R~~--K 73 (138)
T PF11215_consen 1 MKVCGVELKGNEAIICLLSLDDG--LFQLPDCRVRKFSLSDDNSTEEVRKFQFTFAKLMEDY---KVDKVVIKERAT--K 73 (138)
T ss_pred CeEEEEEEecCeEEEEEEecCCC--ceECCccceeEEEcCCCccHHHHHHHHHHHHHHHHHc---CCCEEEEEeccc--C
Confidence 7899999888888 999998876 78888888777655554 44555567788999999 5555555 5543 4
Q ss_pred CCCccceeechhhhHHHHHHHHHc-CCceeEeCchhhhhhhccc
Q 025662 163 QDGKQGWWSGGFGYGLWIGILVAS-GFSVVPIPSLTWKNWYGLS 205 (249)
Q Consensus 163 ~qgvqSaf~~G~a~Gv~~gvLaa~-gIPV~eVtP~~WKkav~g~ 205 (249)
|+.+.|+.+| -+.+++.+. +++|..++|+++|....-+
T Consensus 74 GKfAGga~~F-----KmEaaIQL~~~~~V~lvs~~~ik~~lKrn 112 (138)
T PF11215_consen 74 GKFAGGAVGF-----KMEAAIQLIDDVEVELVSPATIKAQLKRN 112 (138)
T ss_pred CCccCCchhH-----HHHHHHHhcCCCcEEEECHHHHHHHHhcC
Confidence 5544444432 233444444 9999999999999998654
No 12
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=96.23 E-value=0.034 Score=56.86 Aligned_cols=59 Identities=24% Similarity=0.436 Sum_probs=44.4
Q ss_pred ceEEEEcCCCCceEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662 88 QWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ 163 (249)
Q Consensus 88 m~ILGIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~ 163 (249)
-.|+|||||++-++|+|+.+|. ++|+-.. +-++...+.++|.++. +|-+++ =.|.|+|+
T Consensus 244 ~lIVGIDPGiTtgiAvldldGe-----vl~~~S~---------r~~~~~eVve~I~~lG--~PvvVA-tDVtp~P~ 302 (652)
T COG2433 244 SLIVGIDPGITTGIAVLDLDGE-----VLDLESR---------RGIDRSEVVEFISELG--KPVVVA-TDVTPAPE 302 (652)
T ss_pred ceEEEeCCCceeeEEEEecCCc-----EEeeecc---------ccCCHHHHHHHHHHcC--CceEEE-ccCCCChH
Confidence 4799999999999999999984 4444433 4577889999999995 444444 45676765
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=95.63 E-value=0.054 Score=45.03 Aligned_cols=92 Identities=14% Similarity=0.052 Sum_probs=58.9
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|+|||||+|..-. +|+-+..+. . ....++++... ...+.+.|.++++++ .++.++|=-...| +|.
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~--~--a~pl~~i~~~~-----~~~~~~~l~~li~~~---~i~~iVvGlP~~~--~G~ 66 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGI--I--ASPLETIPRRN-----REKDIEELKKLIEEY---QIDGIVVGLPLNM--DGS 66 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTS--S--EEEEEEEEECC-----CCCCHHHHHHHHHHC---CECEEEEEEEBBC--TSS
T ss_pred CeEEEEEeCCCeEEEEEecCCCC--e--EeeeEEEECCC-----CchHHHHHHHHHHHh---CCCEEEEeCCccc--CCC
Confidence 7899999999999 999988763 2 22344443111 257889999999999 7888888765533 333
Q ss_pred cceeechhhhHHHHHHHHHc-CCceeEeC
Q 025662 167 QGWWSGGFGYGLWIGILVAS-GFSVVPIP 194 (249)
Q Consensus 167 qSaf~~G~a~Gv~~gvLaa~-gIPV~eVt 194 (249)
.+... -..+-....+.... ++||+.+.
T Consensus 67 ~~~~~-~~v~~f~~~L~~~~~~ipV~~~D 94 (135)
T PF03652_consen 67 ESEQA-RRVRKFAEELKKRFPGIPVILVD 94 (135)
T ss_dssp C-CCH-HHHHHHHHHHHHHH-TSEEEEEE
T ss_pred ccHHH-HHHHHHHHHHHHhcCCCcEEEEC
Confidence 22221 12233333444454 99999874
No 14
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=95.21 E-value=0.53 Score=39.27 Aligned_cols=94 Identities=17% Similarity=0.096 Sum_probs=55.2
Q ss_pred CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662 86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q 164 (249)
.+|.|||||+|..-. +|+-+..+. +..|.-.+...+ ...+.+.|.++++++ .++.++|=-.. .-+
T Consensus 2 ~~~~iLalD~G~kriGvAv~d~~~~------~a~pl~~i~~~~---~~~~~~~l~~~i~~~---~i~~iVvGlP~--~~~ 67 (138)
T PRK00109 2 PSGRILGLDVGTKRIGVAVSDPLGG------TAQPLETIKRNN---GTPDWDRLEKLIKEW---QPDGLVVGLPL--NMD 67 (138)
T ss_pred CCCcEEEEEeCCCEEEEEEecCCCC------EEcCEEEEEcCC---CchHHHHHHHHHHHh---CCCEEEEeccC--CCC
Confidence 367899999999999 998876543 344543222211 124578899999999 67777775433 223
Q ss_pred CccceeechhhhHHHHHHHHHcCCceeEeC
Q 025662 165 GKQGWWSGGFGYGLWIGILVASGFSVVPIP 194 (249)
Q Consensus 165 gvqSaf~~G~a~Gv~~gvLaa~gIPV~eVt 194 (249)
|..|.-. -..+-....+-...++||+.+.
T Consensus 68 G~~~~~~-~~v~~f~~~L~~~~~~~v~~~D 96 (138)
T PRK00109 68 GTEGPRT-ERARKFANRLEGRFGLPVVLVD 96 (138)
T ss_pred CCcCHHH-HHHHHHHHHHHHHhCCCEEEEc
Confidence 3322110 0111112222234489999886
No 15
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=93.06 E-value=0.99 Score=38.34 Aligned_cols=94 Identities=14% Similarity=0.055 Sum_probs=62.9
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhh-hhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKR-LDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG 165 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r-~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg 165 (249)
|.+||+|-|+.-. +|+-+..+. -....++++... .. ++...|..++++| .++.++|=-...| +|
T Consensus 2 ~~ilalD~G~KrIGvA~sd~~~~----~A~pl~~i~~~~-----~~~~~~~~l~~li~~~---~~~~vVVGlP~~m--~g 67 (141)
T COG0816 2 MRILALDVGTKRIGVAVSDILGS----LASPLETIKRKN-----GKPQDFNALLKLVKEY---QVDTVVVGLPLNM--DG 67 (141)
T ss_pred ceEEEEecCCceEEEEEecCCCc----cccchhhheecc-----ccHhhHHHHHHHHHHh---CCCEEEEecCcCC--CC
Confidence 7899999999988 888876653 222333443211 12 7999999999999 8888888665433 33
Q ss_pred ccceeechhhhHHHHHHHHHcCCceeEeCch
Q 025662 166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSL 196 (249)
Q Consensus 166 vqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~ 196 (249)
-.+. ..-...-....+-...++||+.+..+
T Consensus 68 ~~~~-~~~~~~~f~~~L~~r~~lpv~l~DER 97 (141)
T COG0816 68 TEGP-RAELARKFAERLKKRFNLPVVLWDER 97 (141)
T ss_pred Ccch-hHHHHHHHHHHHHHhcCCCEEEEcCc
Confidence 3222 22234444555567788999999864
No 16
>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=89.09 E-value=4.6 Score=39.03 Aligned_cols=56 Identities=18% Similarity=0.138 Sum_probs=39.2
Q ss_pred EEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 92 GIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 92 GIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
|||||+++- +++++..+. .+.-+..|+-.+ ..+...+.++|+++ ..+++++.=..+
T Consensus 1 GIDpGT~s~dv~~~dd~g~--v~~~~~ipt~~v--------~~~p~~iv~~l~~~--~~~dlIa~psGy 57 (343)
T PF07318_consen 1 GIDPGTKSFDVCGLDDDGK--VIFYFSIPTEEV--------AKNPSIIVEELEEF--GDIDLIAGPSGY 57 (343)
T ss_pred CCCCCCCcEEEEEEccCCc--EEEEeeccHHHh--------hhCHHHHHHHHHhc--cCCCEEEeCCcC
Confidence 899999988 899987443 555566776654 34456688888887 366777665443
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=88.60 E-value=3.2 Score=34.21 Aligned_cols=88 Identities=16% Similarity=0.059 Sum_probs=50.7
Q ss_pred EEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccce
Q 025662 91 LGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGW 169 (249)
Q Consensus 91 LGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSa 169 (249)
||||+|..-. +|+-+..+. +..|.-.+... ....+.+.|.++++++ .++.++|=-.. ..+|..|.
T Consensus 1 laiD~G~kriGvA~~d~~~~------~a~pl~~i~~~---~~~~~~~~l~~~i~~~---~~~~iVvGlP~--~~dG~~~~ 66 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGW------TAQGIPTIKAQ---DGEPDWSRIEELLKEW---TPDKIVVGLPL--NMDGTEGP 66 (130)
T ss_pred CeEccCCCeEEEEEECCCCC------EEeceEEEEec---CCcHHHHHHHHHHHHc---CCCEEEEeccC--CCCcCcCH
Confidence 6999999999 997765543 23333222111 1235568899999999 67777765433 22333222
Q ss_pred e-echhhhHHHHHHHHHcCCceeEeC
Q 025662 170 W-SGGFGYGLWIGILVASGFSVVPIP 194 (249)
Q Consensus 170 f-~~G~a~Gv~~gvLaa~gIPV~eVt 194 (249)
- ..-+.|+-. +....++||+.+.
T Consensus 67 ~a~~v~~f~~~--L~~~~~~~v~~~D 90 (130)
T TIGR00250 67 LTERAQKFANR--LEGRFGVPVVLWD 90 (130)
T ss_pred HHHHHHHHHHH--HHHHhCCCEEEEc
Confidence 1 111233332 2344599999886
No 18
>COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=88.40 E-value=3.6 Score=36.41 Aligned_cols=53 Identities=13% Similarity=0.100 Sum_probs=35.3
Q ss_pred HHHHHcCCceeEeCchhh-hhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhhcc
Q 025662 181 GILVASGFSVVPIPSLTW-KNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHH 248 (249)
Q Consensus 181 gvLaa~gIPV~eVtP~~W-Kkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~h~ 248 (249)
-.|...|+||+|.-|.+- ++++.+. +.+-+.-.. +.+ -.++.-||++.|.|+.
T Consensus 94 r~l~~~gv~ViEthP~aa~~~~~~l~--r~~l~~~ie-------~~~------~~~~~~dAv~ag~~a~ 147 (178)
T COG2410 94 RLLESEGVPVIETHPRAALAKAAGLR--RHDLDRIIE-------DVA------VSEDAVDAVLAGLAAL 147 (178)
T ss_pred HHHHhcCCeEEEecchHHHHHHHhhc--cchhhhhhh-------hhh------hhhhHHHHHHHHHHHH
Confidence 568899999999999999 8888764 333332111 111 1457778888877753
No 19
>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=86.80 E-value=1.7 Score=38.48 Aligned_cols=66 Identities=20% Similarity=0.221 Sum_probs=30.5
Q ss_pred CCCCceEEEEcCC--CCce---EEEE-ecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcc
Q 025662 84 NADSQWALGIDPD--LSGA---LAVL-KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQ 157 (249)
Q Consensus 84 ~~~~m~ILGIDPG--l~Ga---~avL-~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~ 157 (249)
+-+..+++|+||| ..+- +.++ ...+. ...+++.-... +. -...-.+.+.++...+ .+..+++|.
T Consensus 222 ~~~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~--~~~~~~~~~~~---~~--~~~~~~~~i~~~~~~~---~~~~i~~d~ 291 (384)
T PF03237_consen 222 PPDWPIIIGVDPAGGKGGDYTAIVVWEIVDDD--GFYVVDDEYER---GM--SPEEWAERIRELYKKY---NPIKIYIDA 291 (384)
T ss_dssp -TT--EEEEEE--SSCTTB-EEEEEE-E-SSS--SEEEEEEEEES---SS---TTTHHHHHHHHHHHT---TS--EEEEE
T ss_pred CCCceEEEEEECCCCCccCCEEEEEEcccccc--ceEEeeehhhc---CC--CHHHHHHHHHHHHhhc---CceEEEEcC
Confidence 3445568999999 4444 3333 22232 34444433221 10 1233345566677777 778889998
Q ss_pred cc
Q 025662 158 SI 159 (249)
Q Consensus 158 v~ 159 (249)
..
T Consensus 292 ~~ 293 (384)
T PF03237_consen 292 NG 293 (384)
T ss_dssp SC
T ss_pred Cc
Confidence 54
No 20
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=79.31 E-value=4.5 Score=34.38 Aligned_cols=111 Identities=17% Similarity=0.121 Sum_probs=55.7
Q ss_pred eEEEEcCCCC----ce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662 89 WALGIDPDLS----GA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ 163 (249)
Q Consensus 89 ~ILGIDPGl~----Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~ 163 (249)
.|++|-.|.. ++ .++|+.+| +++|+-.+.-......+++-+.+.|..+|.+| +|++++| . |
T Consensus 6 rVla~~~g~g~~~~~~~~v~ld~~G-----~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~---kP~vI~v-~-----g 71 (150)
T PF14639_consen 6 RVLALSWGSGDGDDAVFCVVLDENG-----EVLDHLKLVYNERDRERKEEDMERLKKFIEKH---KPDVIAV-G-----G 71 (150)
T ss_dssp -EEEEE-TT--TTS-EEEEEE-TTS------EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH-----SEEEE--------
T ss_pred EEEEEEcCCCCCCCCEEEEEECCCC-----cEEEEEEEcCCccchHHHHHHHHHHHHHHHHc---CCeEEEE-c-----C
Confidence 4777777744 45 77888777 45565555212233367788889999999999 8999999 1 1
Q ss_pred CCccceeechhhhHHHHHHHHHc-------CCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCccccc
Q 025662 164 DGKQGWWSGGFGYGLWIGILVAS-------GFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQ 228 (249)
Q Consensus 164 qgvqSaf~~G~a~Gv~~gvLaa~-------gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~ 228 (249)
.|..+. +-+--+..++... .|+|+.|....-+-+-. ...|.+-||+....
T Consensus 72 ~~~~s~----~l~~~v~~~v~~~~~~~~~~~i~V~~v~~~~A~lY~~-----------S~rA~~EFP~~p~~ 128 (150)
T PF14639_consen 72 NSRESR----KLYDDVRDIVEELDEDEQMPPIPVVIVDDEVARLYSN-----------SKRAAEEFPDYPPL 128 (150)
T ss_dssp SSTHHH----HHHHHHHHHHHHTTB-TTS-B--EEE---TTHHHHHT-----------SHHHHHHSTT--HH
T ss_pred CChhHH----HHHHHHHHHHHHhhhcccCCCceEEEECcHHHHHHhc-----------CHHHHHHCCCCCHH
Confidence 233222 2233344445544 48888877654443321 23567778887543
No 21
>PF04250 DUF429: Protein of unknown function (DUF429); InterPro: IPR007362 This is a family of uncharacterised proteins.
Probab=76.12 E-value=36 Score=29.35 Aligned_cols=66 Identities=14% Similarity=0.122 Sum_probs=39.8
Q ss_pred HHHcCCceeEeCchhhhhhhcccCC-----CCChHHHHHHHHHhCCccc-----c--cccCCCCCCcccHHHHHhhcc
Q 025662 183 LVASGFSVVPIPSLTWKNWYGLSGG-----TSTKDDSRRVASTLFPSLC-----S--QLKRKKDHGTISSPYCILYHH 248 (249)
Q Consensus 183 Laa~gIPV~eVtP~~WKkav~g~~G-----~AsKd~sr~ma~~LfP~~~-----~--~l~rkKdhgrADALaIA~~h~ 248 (249)
....+..|+|+=|..--+.+++... ....++-+.+...+..... . .-..+..+|.-||+++|+.+.
T Consensus 109 ~~~~~~~v~Ev~P~~~~~~l~~~~~~~K~~~~~~~~R~~lL~~~~~~~~~~~~~~~~~~~~~~~~D~lDA~i~Al~A~ 186 (209)
T PF04250_consen 109 PPSSGRRVIEVHPEAAFKALGGAPRYYKKTAEGRAERRELLARLGIDAIPELILAQHRRRLKASDDELDALICALTAR 186 (209)
T ss_pred ccccCceEEEECcHHHHHHhCCCcccccCCcchHHHHHHHHHHHHHhhhhhhhccccccccCcCcCHHHHHHHHHHHH
Confidence 3577999999999998888876411 1112223333333333210 0 011356899999999998753
No 22
>PRK09604 UGMP family protein; Validated
Probab=75.51 E-value=8.8 Score=36.10 Aligned_cols=102 Identities=15% Similarity=0.103 Sum_probs=52.5
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeC--------CCcccccccchhhhhhHHHHHHHHHhcCC--CCCCEEEEc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDT--------PHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVE 156 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~--------pti~v~~g~~~R~r~d~~~L~~lL~~~~~--p~p~~a~IE 156 (249)
|.|||||-...-+ +||++.++. ........ +-+........-.+.+...+.++|++... ...+.+++=
T Consensus 1 m~iLgIdTS~~~~sval~~~~~~-il~~~~~~~~~~~~~~~Gi~P~~a~~~H~~~l~~~i~~~L~~~~~~~~did~iavt 79 (332)
T PRK09604 1 MLILGIETSCDETSVAVVDDGRG-LLSNVVASQIDLHARYGGVVPELASRAHVENIVPLIEEALKEAGLTLEDIDAIAVT 79 (332)
T ss_pred CeEEEEEccccceEEEEEECCCc-EEEEEEecchhcccccCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEe
Confidence 7899999977766 999986522 11122211 11100001112234555556666666532 222333322
Q ss_pred cccCCCCCCccceeechhhhHHHHHHHHHcCCceeEeCchh
Q 025662 157 QSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLT 197 (249)
Q Consensus 157 ~v~~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~ 197 (249)
. . | |.-+.+. -+..+..++....++|++.|+-..
T Consensus 80 ~-G--P--G~~tglr--vg~~~Ak~La~~~~ipl~~v~h~~ 113 (332)
T PRK09604 80 A-G--P--GLVGALL--VGVSFAKALALALNKPLIGVNHLE 113 (332)
T ss_pred c-C--C--CcHHhHH--HHHHHHHHHHHHhCCCEEeecCHH
Confidence 1 1 2 2222233 334456778889999999987643
No 23
>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=73.30 E-value=21 Score=32.96 Aligned_cols=131 Identities=12% Similarity=0.104 Sum_probs=62.8
Q ss_pred EEEEcCCCCce-EEEEec------CCCCceeeeeeCCCcccc-------------------cccc------hhhhhhHHH
Q 025662 90 ALGIDPDLSGA-LAVLKS------DHNGCSAEVFDTPHLPVL-------------------VGKR------VRKRLDAKS 137 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~------~g~g~~~~v~D~pti~v~-------------------~g~~------~R~r~d~~~ 137 (249)
|+.||-|++.. ||.+.. ........+.+-..+.+. ...+ .=..+-|.=
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 79999999999 999998 111112333333333333 0000 111122233
Q ss_pred HHHHHHhcCCCCCCEEEEccccCCCCCCccc----eeechhhhHHHHHHHHHc---------CCceeEeCchhhhhhhcc
Q 025662 138 MIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG----WWSGGFGYGLWIGILVAS---------GFSVVPIPSLTWKNWYGL 204 (249)
Q Consensus 138 L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqS----af~~G~a~Gv~~gvLaa~---------gIPV~eVtP~~WKkav~g 204 (249)
+..++..+ .|+++.||++=.+.+ |-.+ .+..+-==|++..+|... +.-|..+.|+..-.+-..
T Consensus 81 v~~Ll~~~---~P~~vlIERQR~RS~-g~savlEwtLrvn~lE~mLyA~L~~~~~~~~~~~~~~~V~~v~P~rv~~fW~~ 156 (274)
T PF09159_consen 81 VSSLLLPY---KPDHVLIERQRFRSG-GSSAVLEWTLRVNILEGMLYAVLYTLRQESKGEQANYVVISVDPQRVTRFWCE 156 (274)
T ss_dssp HHHHHHHH-----SEEEEEE----T--TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEE-CCHHHHHHHH
T ss_pred HHHHcccC---CCCEEEEeeccccCC-CCCccchhHHHHhHHHHHHHHHHHHHHhhcccCCCCeEEEEECHHHHHHHHhc
Confidence 44455566 699999999842222 3333 455555556666666655 448999999988766532
Q ss_pred ---------------cCCCCChHHHHHHHHHhCCc
Q 025662 205 ---------------SGGTSTKDDSRRVASTLFPS 224 (249)
Q Consensus 205 ---------------~~G~AsKd~sr~ma~~LfP~ 224 (249)
..+..+|..=..+++++|-.
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~K~~ki~Lv~~wL~~ 191 (274)
T PF09159_consen 157 RFPIRDSLNEKKKKKKSSKNSKKIKIDLVRSWLSN 191 (274)
T ss_dssp -----------HH-----------HHHHHHHHHHT
T ss_pred ccccchhhhhhhcccccchhhHHHHHHHHHHHHHc
Confidence 11334455556677776644
No 24
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=69.88 E-value=7.9 Score=37.31 Aligned_cols=104 Identities=18% Similarity=0.204 Sum_probs=59.4
Q ss_pred eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhH-------HHHHHHHHhcC--------------
Q 025662 89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDA-------KSMIMLLRSLD-------------- 146 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~-------~~L~~lL~~~~-------------- 146 (249)
.|+-|.||++++ +||++.+.. +-.-+++.+..+-.|.+.+. +.+.+.|.+..
T Consensus 4 riltINPGststKlaVfe~ek~------ife~tlrhs~eEl~~f~~i~dQ~~fR~~~i~~~i~e~g~~i~~~dAvvgRGG 77 (358)
T COG3426 4 RILTINPGSTSTKLAVFEDEKE------IFEKTLRHSLEELEKFKRIPDQFEFRKDAILEFIDEQGYNISKFDAVVGRGG 77 (358)
T ss_pred eEEEecCCCccceEEEecCchH------hhHHHhhcCHHHHHHHhhhhHhHhHHHHHHHHHHHHhCCCcCCccceeecCc
Confidence 489999999999 999996542 11122222211112222222 33444444432
Q ss_pred ----CCCCCEEEEccccCCCCCCccceeechhhhHHHH--HHHHHcCCceeEeCchhhhh
Q 025662 147 ----APIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWI--GILVASGFSVVPIPSLTWKN 200 (249)
Q Consensus 147 ----~p~p~~a~IE~v~~~p~qgvqSaf~~G~a~Gv~~--gvLaa~gIPV~eVtP~~WKk 200 (249)
.|.++-++=|+....-..|+++--- .+-|.++ -+....|||-+.|.|+..-.
T Consensus 78 LL~pi~gGTY~Vn~~M~~~lk~~~~G~ha--SnLGaiiA~~ia~~~gvPayIVDPvvVDE 135 (358)
T COG3426 78 LLRPIPGGTYVVNEKMLKDLKNGVQGEHA--SNLGAIIANRIAKALGVPAYIVDPVVVDE 135 (358)
T ss_pred cccccCCceeEeCHHHHHHHHcCCCCcch--hhhhHHHHHHHhhhcCCCeeeeCceehhh
Confidence 2555666666654444444443332 3345444 57889999999999998754
No 25
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=68.92 E-value=9.6 Score=34.03 Aligned_cols=101 Identities=17% Similarity=0.142 Sum_probs=55.3
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK 166 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv 166 (249)
|+||.||-.+..+ .||+..+. + +++..=+.+...+. ..++...+.+++.+.+. +.-=|+.+. .++|+
T Consensus 1 m~iLaiDTs~~~~s~ai~~~~~-~---~vl~~~~~~~~r~h---se~l~~~i~~ll~~~~~---~~~dld~ia--v~~GP 68 (220)
T COG1214 1 MKILAIDTSTSALSVALYLADD-G---KVLAEHTEKLKRNH---AERLMPMIDELLKEAGL---SLQDLDAIA--VAKGP 68 (220)
T ss_pred CcEEEEEcChhhhhhheeecCC-C---cEEEEEEEeccccH---HHHHHHHHHHHHHHcCC---CHHHCCEEE--EccCC
Confidence 6899999999988 78877622 2 22222222222222 34445556666666522 111233333 33333
Q ss_pred cceeechhhhHHHHHHHHHcCCceeEeCchhhhh
Q 025662 167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKN 200 (249)
Q Consensus 167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKk 200 (249)
.|==.+==+.++..+...+.|||++-|+....-.
T Consensus 69 GSFTGlRIG~~~AkgLA~~l~iplvgvssL~~~A 102 (220)
T COG1214 69 GSFTGLRIGVAFAKGLALALNIPLVGVSSLEALA 102 (220)
T ss_pred CcccchhhHHHHHHHHHHHcCCCEEEeCHHHHHH
Confidence 3322222334555677889999999998765544
No 26
>PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional
Probab=67.99 E-value=16 Score=35.19 Aligned_cols=101 Identities=15% Similarity=0.057 Sum_probs=53.6
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeee-----eC--CCcccccccchhhhhhHHHHHHHHHhcCC--CCCCEEEEcc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVF-----DT--PHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQ 157 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~-----D~--pti~v~~g~~~R~r~d~~~L~~lL~~~~~--p~p~~a~IE~ 157 (249)
|.|||||-...-+ .||++.++. ...++. .+ |.+|.... +.=.+.+..-+.+++++... ...+.+++=.
T Consensus 1 ~~iLgIETScd~tsvAl~~~~~~-il~~~~~sq~~~~G~GvvP~~a~-r~H~~~l~~~i~~~l~~a~~~~~did~Iavt~ 78 (345)
T PTZ00340 1 FLALGIEGSANKLGVGIVTSDGE-ILSNVRETYITPPGTGFLPRETA-QHHREHILSLVKEALEEAKITPSDISLICYTK 78 (345)
T ss_pred CeEEEEEccchhhEEEEEECCCc-EEEEEEeeccccCCCCcCchHHH-HHHHHHHHHHHHHHHHHcCCCHHHCCEEEEec
Confidence 6799999998888 999985542 111221 11 33332111 11233444445555555321 1223333222
Q ss_pred ccCCCCCCccceeechhhhHHHHHHHHHcCCceeEeCchh
Q 025662 158 SIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLT 197 (249)
Q Consensus 158 v~~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~ 197 (249)
|.|--+.+. -+.+.+.+.+.+.++|++.|.=++
T Consensus 79 -----GPGl~~~Lr--VG~~~Ak~LA~a~~~PligV~Hle 111 (345)
T PTZ00340 79 -----GPGMGAPLS--VGAVVARTLSLLWGKPLVGVNHCV 111 (345)
T ss_pred -----CCCcHhhHH--HHHHHHHHHHHHcCCCEeecchHH
Confidence 222333344 344556777899999999987554
No 27
>COG4020 Uncharacterized protein conserved in archaea [Function unknown]
Probab=61.98 E-value=23 Score=33.71 Aligned_cols=95 Identities=20% Similarity=0.189 Sum_probs=55.5
Q ss_pred CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhc--CC-CCCCEEEE------
Q 025662 86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSL--DA-PIGTTAYV------ 155 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~--~~-p~p~~a~I------ 155 (249)
++|..+|||-|++|- +++++.++. ..|..+. ..++..-.+++++-|.+. ++ .+-+++++
T Consensus 1 ~~m~fVGiDHGTsgi~~ai~d~e~~----~~Fklgr-------ae~~~~~ek~~L~~l~de~~i~l~eidlialtYsMGD 69 (332)
T COG4020 1 MTMMFVGIDHGTSGIKFAIYDGEKD----PEFKLGR-------AELRKVAEKSLLRELEDEARIALEEIDLIALTYSMGD 69 (332)
T ss_pred CceEEEeecCCCcceEEEEEcCCCC----ceEEech-------hhhhhhhHHHHHHHhhHhhCCccccceEEEEeecccc
Confidence 368899999999999 999987753 2233322 234444455555555554 11 22333332
Q ss_pred --------ccccCCCCCCccceeechhhhHH---HHHHHHHcCCceeEeC
Q 025662 156 --------EQSIPYPQDGKQGWWSGGFGYGL---WIGILVASGFSVVPIP 194 (249)
Q Consensus 156 --------E~v~~~p~qgvqSaf~~G~a~Gv---~~gvLaa~gIPV~eVt 194 (249)
|++ -+.|.+|.=..|.-.|- +.--+..+|||-+..+
T Consensus 70 ais~ikpiekv---e~rGl~si~GAGk~~GgGtrv~dei~esgipa~liP 116 (332)
T COG4020 70 AISEIKPIEKV---EGRGLRSIEGAGKKTGGGTRVYDEISESGIPAYLIP 116 (332)
T ss_pred chhhcccHHHh---cCCceeeccCcccccCCceehHHHHHhcCCCeeecc
Confidence 333 25566665544443332 3345788899988765
No 28
>PRK09605 bifunctional UGMP family protein/serine/threonine protein kinase; Validated
Probab=59.79 E-value=29 Score=34.28 Aligned_cols=98 Identities=11% Similarity=-0.029 Sum_probs=50.6
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc-------hhhhhhHHHHHHHHHhcCC--CCCCEEEEcc
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR-------VRKRLDAKSMIMLLRSLDA--PIGTTAYVEQ 157 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~-------~R~r~d~~~L~~lL~~~~~--p~p~~a~IE~ 157 (249)
|.|||||--..-+ .||++.++. ...+.... ....-|+- .=.+.+...+.+++.+... ...+.+++=.
T Consensus 1 m~il~iets~~~~s~a~~~~~~~-~~~~~~~~--~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~~ 77 (535)
T PRK09605 1 MIVLGIEGTAWKTSAGIVDSDGD-VLFNESDP--YKPPSGGIHPREAAEHHAEAIPKVIKEALEEAGLKPEDIDLVAFSQ 77 (535)
T ss_pred CEEEEEEccccceEEEEEeCCCc-EEEEEEee--ccCCcCCCChHHHHHHHHHHHHHHHHHHHHHcCCCHhhCCEEEECC
Confidence 7899999877777 999985432 12222221 11111211 1122333455556665432 1223333221
Q ss_pred ccCCCCCCccceeechhhhHHHHHHHHHcCCceeEeCc
Q 025662 158 SIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPS 195 (249)
Q Consensus 158 v~~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP 195 (249)
|.|.-+.+..|.+ ...+...+.++|++.|.-
T Consensus 78 -----gPg~~~~l~vg~~--~ak~la~~~~~~~~~v~h 108 (535)
T PRK09605 78 -----GPGLGPCLRVVAT--AARALALSLDVPLIGVNH 108 (535)
T ss_pred -----CCCcHhhHHHHHH--HHHHHHHHhCCCeecccH
Confidence 2233444444433 466778899999998863
No 29
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=58.99 E-value=23 Score=37.80 Aligned_cols=111 Identities=16% Similarity=0.196 Sum_probs=60.4
Q ss_pred CCCceEEEEcCCCCc-e-EEEEecCCCCce-eeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCC
Q 025662 85 ADSQWALGIDPDLSG-A-LAVLKSDHNGCS-AEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPY 161 (249)
Q Consensus 85 ~~~m~ILGIDPGl~G-a-~avL~~~g~g~~-~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~ 161 (249)
+++..++|+|||.+- + +||++..|.-|. ..++.+|-.. ..+.-.+.|..+++.| .-..++|
T Consensus 327 ~~~~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~-------~~~~~~~~l~~l~~~~---~Ve~iaI------ 390 (780)
T COG2183 327 AKPKATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVN-------QSDKAEATLKDLIRKY---KVELIAI------ 390 (780)
T ss_pred CCCcceeecCCccccccEEEEEcCCCceeceeEEEcCCCcc-------chHHHHHHHHHHHHHh---CceEEEE------
Confidence 555679999999986 4 999987753111 2333444321 1344556678888888 4444443
Q ss_pred CCCCccceeechhhhHHHHHHHHH---cCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccc
Q 025662 162 PQDGKQGWWSGGFGYGLWIGILVA---SGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCS 227 (249)
Q Consensus 162 p~qgvqSaf~~G~a~Gv~~gvLaa---~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~ 227 (249)
|.|..|--. +.-+. -++-. .++..+.|+- .+|+-=.+...|.+-||++..
T Consensus 391 -GngTaSret-e~fv~---~vl~~~~~~~~~~viVsE-----------agAsvYsaSe~A~~EFPdL~v 443 (780)
T COG2183 391 -GNGTASRET-EKFVA---DVLKELPKEKVLKVIVSE-----------AGASVYSASERAAEEFPDLDV 443 (780)
T ss_pred -ecCCcchhH-HHHHH---HHHHhccCCCCcEEEEcc-----------cccchhcccHHHHHHCCCCch
Confidence 222222211 11111 22333 4455555542 245555566777888888765
No 30
>PRK03011 butyrate kinase; Provisional
Probab=56.38 E-value=76 Score=30.55 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=18.8
Q ss_pred ceEEEEcCCCCce-EEEEecCC
Q 025662 88 QWALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g 108 (249)
+.||-|.||++.+ +|+++.+.
T Consensus 2 ~~il~inpgststk~a~~~~~~ 23 (358)
T PRK03011 2 MRILVINPGSTSTKIAVFEDEK 23 (358)
T ss_pred CEEEEEcCCCchheEEEEcCCc
Confidence 6799999999999 99998654
No 31
>PF14239 RRXRR: RRXRR protein
Probab=56.34 E-value=14 Score=32.70 Aligned_cols=60 Identities=22% Similarity=0.118 Sum_probs=35.8
Q ss_pred chhhhhhhhhccchhHHHHHHHhhhcccccccCCCCCCCcccccccCCCCceEEEEcCCCCce-EEEEecCC
Q 025662 38 GRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~m~ILGIDPGl~Ga-~avL~~~g 108 (249)
--|-++|||--.+..+|.+. ++.+.+.-..++ .. ++...-+.+|||||...+ +|+++.+.
T Consensus 12 mP~~p~rAR~LLk~GkA~V~------r~~PFtI~L~~~--~~---~~~~qpi~lgiDpGsk~tGiav~~~~~ 72 (176)
T PF14239_consen 12 MPCHPARARKLLKQGKAKVV------RRYPFTIQLKYE--PS---GSYTQPIRLGIDPGSKTTGIAVVSEKK 72 (176)
T ss_pred CCCCHHHHHHHHHCCCEEEE------ecCCeEEEEEec--cC---CCcccCEEEEECCCCCeEEEEEEeCCE
Confidence 33456777766666666662 244444333322 11 112334689999999888 99998763
No 32
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=55.64 E-value=27 Score=30.39 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=17.7
Q ss_pred EEEEcCCCCce-EEEEecCCC
Q 025662 90 ALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~ 109 (249)
+||||=|+++. .++++.++.
T Consensus 2 ~lgiDiGTts~K~~l~d~~g~ 22 (245)
T PF00370_consen 2 YLGIDIGTTSVKAVLFDEDGK 22 (245)
T ss_dssp EEEEEECSSEEEEEEEETTSC
T ss_pred EEEEEEcccceEEEEEeCCCC
Confidence 79999999999 999996664
No 33
>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=55.56 E-value=23 Score=30.72 Aligned_cols=95 Identities=17% Similarity=0.137 Sum_probs=50.8
Q ss_pred EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccc
Q 025662 90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG 168 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqS 168 (249)
||+||-....+ +|+++.+. .+.-.. .. ..+.-.+.+...+.+++.+....-. =|+.+. .+.|+.|
T Consensus 1 iLaidTs~~~~sval~~~~~---~~~~~~---~~---~~~~h~~~l~~~i~~~l~~~~~~~~---~i~~ia--v~~GPGS 66 (202)
T TIGR03725 1 ILAIDTSTEALSVALLDDGE---ILAERS---EE---AGRNHSEILLPMIEELLAEAGLSLQ---DLDAIA--VGVGPGS 66 (202)
T ss_pred CEEEECCCcceEEEEEECCE---EEEEEe---eh---hhHHHHHHHHHHHHHHHHHcCCCHH---HCCEEE--EecCCCh
Confidence 58899888777 89888432 221111 11 1112234555566666666532111 122222 2333333
Q ss_pred eeechhhhHHHHHHHHHcCCceeEeCchhh
Q 025662 169 WWSGGFGYGLWIGILVASGFSVVPIPSLTW 198 (249)
Q Consensus 169 af~~G~a~Gv~~gvLaa~gIPV~eVtP~~W 198 (249)
-=.+=-+..+..+.+.+.++|++-|+..+.
T Consensus 67 fTGlRig~~~akgla~~~~~p~~~vssL~~ 96 (202)
T TIGR03725 67 FTGLRIGLATAKGLALALGIPLVGVSSLEA 96 (202)
T ss_pred HHhHHHHHHHHHHHHHHhCCCEEecCHHHH
Confidence 222223455666778889999999998765
No 34
>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=49.90 E-value=1.4e+02 Score=24.13 Aligned_cols=46 Identities=20% Similarity=0.148 Sum_probs=28.1
Q ss_pred HHHHHHHHhcCCCCCCEEEEccccCCCCCCccceeechhhhHHHHH-HHHH--cCCceeEeCch
Q 025662 136 KSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIG-ILVA--SGFSVVPIPSL 196 (249)
Q Consensus 136 ~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSaf~~G~a~Gv~~g-vLaa--~gIPV~eVtP~ 196 (249)
+.+.++.++| .++.+++|... .|.++|..+. .+.. ..+||..++|.
T Consensus 33 ~~i~~~~~~~---~~~~~~~E~~~------------~~~~~~~~l~~~l~~~~~~~~i~~~~~~ 81 (142)
T TIGR01630 33 RLVIRLLNAH---RVNLAIIESNQ------------EGKSFGRSLVKILKEKGIRTPARAVYPS 81 (142)
T ss_pred HHHHHHHHHc---CCcceeeeccc------------cchHHHHHHHHHHHhhCCCCCceeeCCC
Confidence 4566777788 67788899875 2234443332 2332 24678888875
No 35
>TIGR03723 bact_gcp putative glycoprotease GCP. This model represents bacterial members of a protein family that is widely distributed. In a few pathogenic species, the protein is exported in a way that may represent an exceptional secondary function. This model plus companion (archaeal) model TIGR03722 together span the prokaryotic member sequences of TIGR00329, a protein family that appears universal in life, and whose broad function is unknown. A member of TIGR03722 has been characterized as a DNA-binding protein with apurinic endopeptidase activity. In contrast, the rare characterized members of the present family show O-sialoglycoprotein endopeptidase (EC. 3.4.24.57) activity after export. These include glycoprotease (gcp) from Pasteurella haemolytica A1 and a cohemolysin from Riemerella anatipestifer (GB|AAG39646.1). The member from Staphylococcus aureus is essential and is related to cell wall dynamics and the modulation of autolysis, but members are also found in the Mycoplasmas
Probab=49.74 E-value=43 Score=31.30 Aligned_cols=103 Identities=10% Similarity=0.045 Sum_probs=51.1
Q ss_pred EEEEcCCCCce-EEEEecCCCCceeeeee--------CCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccC
Q 025662 90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFD--------TPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIP 160 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D--------~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~ 160 (249)
|||||--..-+ +||++.++. ...+... ++-|..+...+.-.+.+...+.+++++...... -|+.+.
T Consensus 1 iLaIdTs~~~~sval~~~~~~-il~~~~~~~~~~~~~~gGi~p~~~~~~H~~~l~~~i~~~l~~~~~~~~---~id~ia- 75 (314)
T TIGR03723 1 ILGIETSCDETAVAIVDDGKG-LLSNIVASQIELHARYGGVVPELASRAHLEAIPPLIEEALAEAGLTLS---DIDAIA- 75 (314)
T ss_pred CEEEECcccceEEEEEECCce-EEEEEEeehhhhccCcCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHH---HCCEEE-
Confidence 68999988888 999985431 1112111 111111111112233444555566655321111 122222
Q ss_pred CCCCCccceeechhhhHHHHHHHHHcCCceeEeCchhh
Q 025662 161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTW 198 (249)
Q Consensus 161 ~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~W 198 (249)
.+.|+.|.-.+=-+..+..+++.+.++|++.|+-..-
T Consensus 76 -v~~GPGsftglrig~~~Ak~la~~~~~p~~~v~h~~a 112 (314)
T TIGR03723 76 -VTAGPGLIGALLVGVSFAKALALALNKPLIGVNHLEG 112 (314)
T ss_pred -EecCCChHHhHHHHHHHHHHHHHHhCCCEEecccHHH
Confidence 2223333333333445566778888999999986553
No 36
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=49.72 E-value=49 Score=30.01 Aligned_cols=97 Identities=21% Similarity=0.090 Sum_probs=53.2
Q ss_pred CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHH---hc-CCCCCCEEEEccccC
Q 025662 86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLR---SL-DAPIGTTAYVEQSIP 160 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~---~~-~~p~p~~a~IE~v~~ 160 (249)
.+..++|||=|++-- ..+++..+. .+.+.+.|.-.+..|.-.....-...|..+++ ++ ..+ ...+++ .+
T Consensus 22 ~~~~~~~iDiGSssi~~vv~~~~~~--~~~~~~~~~~~vr~G~i~di~~a~~~i~~~~~~ae~~~g~~-i~~v~~-~v-- 95 (267)
T PRK15080 22 ESPLKVGVDLGTANIVLAVLDEDGQ--PVAGALEWADVVRDGIVVDFIGAVTIVRRLKATLEEKLGRE-LTHAAT-AI-- 95 (267)
T ss_pred CCCEEEEEEccCceEEEEEEcCCCC--EEEEEeccccccCCCEEeeHHHHHHHHHHHHHHHHHHhCCC-cCeEEE-Ee--
Confidence 356799999999998 666665543 57777887766555433222222222333332 23 112 233443 22
Q ss_pred CCCCCccceeechhhhHHHHHHHHHcCCceeEeCc
Q 025662 161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPS 195 (249)
Q Consensus 161 ~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP 195 (249)
|.. ++.+ .+..+.-++...|+.+..+-+
T Consensus 96 -p~~-----~~~~-~~~~~~~~~~~aGl~~~~ii~ 123 (267)
T PRK15080 96 -PPG-----TSEG-DPRAIINVVESAGLEVTHVLD 123 (267)
T ss_pred -CCC-----CCch-hHHHHHHHHHHcCCceEEEec
Confidence 221 2222 344566888999998874433
No 37
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=49.03 E-value=30 Score=33.06 Aligned_cols=92 Identities=13% Similarity=0.010 Sum_probs=52.4
Q ss_pred CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662 86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q 164 (249)
++|.|+|||=|-..+ +|..+.+.. .++++-.|--+ |+....+.|.++..++ .++.|.|=- .+.
T Consensus 1 ~~~kilGiDIGGAntk~a~~DG~~~--~~d~~YlPMWk-------~k~rL~~~Lkei~~k~---~~~~vgvvM----TaE 64 (330)
T COG1548 1 MKMKILGIDIGGANTKIASSDGDNY--KIDHIYLPMWK-------KKDRLEETLKEIVHKD---NVDYVGVVM----TAE 64 (330)
T ss_pred CCceEEEeeccCccchhhhccCCee--eeeEEEecccc-------chhHHHHHHHHHhccC---CcceeEEEe----eHH
Confidence 468899999999998 888544432 45666666552 2345556677777666 444222211 110
Q ss_pred CccceeechhhhHH---HHHHHHHcCCceeEeCc
Q 025662 165 GKQGWWSGGFGYGL---WIGILVASGFSVVPIPS 195 (249)
Q Consensus 165 gvqSaf~~G~a~Gv---~~gvLaa~gIPV~eVtP 195 (249)
..-+|+. ..-|| +--+=.+++.||+.|+.
T Consensus 65 -LaD~f~t-k~eGVe~Ii~~v~~Af~~pv~~v~~ 96 (330)
T COG1548 65 -LADAFKT-KAEGVEDIIDTVEKAFNCPVYVVDV 96 (330)
T ss_pred -HHHHhhh-HHhHHHHHHHHHHHhcCCceEEEec
Confidence 0011111 23333 33667788999888763
No 38
>COG2441 Predicted butyrate kinase [Energy production and conversion]
Probab=47.89 E-value=37 Score=32.86 Aligned_cols=122 Identities=16% Similarity=0.191 Sum_probs=63.9
Q ss_pred EEEcCCCCce--EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCC--CEEEEccccCCCCCCc
Q 025662 91 LGIDPDLSGA--LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIG--TTAYVEQSIPYPQDGK 166 (249)
Q Consensus 91 LGIDPGl~Ga--~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p--~~a~IE~v~~~p~qgv 166 (249)
+|||||+... +|+-+..|+ .+--+..|+-.|..+ ..-+.++|+++.+..+ +.++-=.-+.+|-+..
T Consensus 1 ~GIDpGT~smdvfgfdDEsg~--vi~~~~I~rdeVtk~--------p~iiv~ii~e~~~e~g~~daivgpSGyGlPlk~a 70 (374)
T COG2441 1 IGIDPGTGSMDVFGFDDESGN--VIVDVAIPRDEVTKS--------PRIIVDIIEEVQAEVGGIDAIVGPSGYGLPLKRA 70 (374)
T ss_pred CCcCCCCCceeEEEEecCCCC--EEEEEecCHHHhccC--------chHHHHHHHHHhhhhccccceeccccCCCcccch
Confidence 5999999877 565554454 455456666554433 2335566666622122 2223333344454433
Q ss_pred c---------ceeechhh-------hHH---HHHHHHHcCCceeEeC-------chhhhhhhcccCCCCChHHHHHHHHH
Q 025662 167 Q---------GWWSGGFG-------YGL---WIGILVASGFSVVPIP-------SLTWKNWYGLSGGTSTKDDSRRVAST 220 (249)
Q Consensus 167 q---------Saf~~G~a-------~Gv---~~gvLaa~gIPV~eVt-------P~~WKkav~g~~G~AsKd~sr~ma~~ 220 (249)
. .+|.+--. -|+ ..+.-.+++++.+.++ =-.|.|.=...-|.++|=-+...+..
T Consensus 71 re~~~~eI~laTfi~~sd~~~~lrivglr~Lm~l~~~~~dln~yftPgVIhLpTvP~wRK~nrID~GTaDKl~tv~lai~ 150 (374)
T COG2441 71 REATNEEIALATFITKSDVERRLRIVGLRELMALMREASDLNIYFTPGVIHLPTVPEWRKVNRIDLGTADKLFTVVLAIV 150 (374)
T ss_pred hhCCchheeeeEeccchhhhhhhccccHHHHHHHHHHhhcCccccccceeecCCCCchhhcCcccccchhHHHHHHHHHH
Confidence 2 23332222 121 1122256777766543 24688887655477888776666554
Q ss_pred hC
Q 025662 221 LF 222 (249)
Q Consensus 221 Lf 222 (249)
-+
T Consensus 151 ~~ 152 (374)
T COG2441 151 RL 152 (374)
T ss_pred HH
Confidence 43
No 39
>TIGR02261 benz_CoA_red_D benzoyl-CoA reductase, bcr type, subunit D. This model describes the D subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This family shows sequence similarity to the A subunit (TIGR02259) and to the 2-hydroxyglutaryl-CoA dehydratase alpha chain.
Probab=46.90 E-value=69 Score=29.83 Aligned_cols=20 Identities=20% Similarity=0.257 Sum_probs=16.8
Q ss_pred eEEEEcCCCCce-EEEEecCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g 108 (249)
+.+|||=|++.+ ..+++.++
T Consensus 2 ~~~GIDiGStttK~Vlid~~~ 22 (262)
T TIGR02261 2 ITAGIDIGTGAIKTVLFEVDG 22 (262)
T ss_pred eEEEEEcCcccEEEEEEecCC
Confidence 378999999999 88888544
No 40
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=44.91 E-value=1.8e+02 Score=24.12 Aligned_cols=84 Identities=18% Similarity=0.190 Sum_probs=60.7
Q ss_pred EcCCCCce--EEEEecCCCC-ceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccce
Q 025662 93 IDPDLSGA--LAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGW 169 (249)
Q Consensus 93 IDPGl~Ga--~avL~~~g~g-~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSa 169 (249)
|.|...-| +.|++.++.. -.++++..|.-....| -.-.+.++|.++ ..+.+++.++. ++
T Consensus 16 vs~hFgrap~F~Ivd~e~g~i~~vev~~np~~~~~~g-------~G~~~a~~l~~~---gvdvvi~~~iG--~~------ 77 (121)
T COG1433 16 VSPHFGRAPYFTIVDVEDGEIKNVEVIENPAASAEKG-------AGIRIAELLVDE---GVDVVIASNIG--PN------ 77 (121)
T ss_pred ccCCccCCceEEEEEecCCcEEEEEEeecccccccCc-------chHHHHHHHHHc---CCCEEEECccC--HH------
Confidence 67777788 8999987431 3466777775433333 224588899999 77888888875 32
Q ss_pred eechhhhHHHHHHHHHcCCceeEeCchhhhhhhc
Q 025662 170 WSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYG 203 (249)
Q Consensus 170 f~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~ 203 (249)
.+.+|.+.||.|+...+.+...++.
T Consensus 78 ---------a~~~l~~~GIkv~~~~~~~V~e~i~ 102 (121)
T COG1433 78 ---------AYNALKAAGIKVYVAPGGTVEEAIK 102 (121)
T ss_pred ---------HHHHHHHcCcEEEecCCCCHHHHHH
Confidence 2456889999999999988888775
No 41
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=44.65 E-value=37 Score=35.56 Aligned_cols=55 Identities=18% Similarity=0.239 Sum_probs=35.8
Q ss_pred CceEEEEc-----CCCCce--EEEEec-CCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccc
Q 025662 87 SQWALGID-----PDLSGA--LAVLKS-DHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQS 158 (249)
Q Consensus 87 ~m~ILGID-----PGl~Ga--~avL~~-~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v 158 (249)
+|.|+||| |+.. + ||++-- +|. + +.. ..+-...|..++.++ +|++++|-.+
T Consensus 1 ~~~I~GVDI~~g~p~~~-~p~yAvv~~~dg~---~--~~k------------~~~s~~rllrli~~~---kpDIvAvDnv 59 (652)
T COG2433 1 DMVIMGVDIVSGSPRGK-APLYAVVILEDGE---I--VEK------------GEVSLRRLLRLIWSY---KPDIVAVDNV 59 (652)
T ss_pred CceEEEEeeecCCCCCc-CcceeEEEEecCc---E--Eee------------hhhhHHHHHHHHHhc---CCCEEEeccH
Confidence 47899999 6666 4 666653 332 1 111 123345688899998 8999999888
Q ss_pred cCCC
Q 025662 159 IPYP 162 (249)
Q Consensus 159 ~~~p 162 (249)
+..+
T Consensus 60 yEL~ 63 (652)
T COG2433 60 YELG 63 (652)
T ss_pred HHHh
Confidence 6444
No 42
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.50 E-value=29 Score=30.89 Aligned_cols=40 Identities=23% Similarity=0.140 Sum_probs=27.5
Q ss_pred HHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHH
Q 025662 180 IGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVAS 219 (249)
Q Consensus 180 ~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~ 219 (249)
.-.|...|++|..+.|...+..+.+.....+|.+....+.
T Consensus 51 ~~~l~~~g~~v~~i~p~~v~~~~~~~~~k~d~~Da~~~~~ 90 (303)
T COG3547 51 ARYLRAEGYPVRLINPRQVKKKARGKRAKTDKADALAIAV 90 (303)
T ss_pred HHHHHHcCCeeEEECHHHhHHHHhccccccchhhHHHHHH
Confidence 3567889999999999999996666423444444433333
No 43
>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=42.68 E-value=71 Score=23.34 Aligned_cols=48 Identities=15% Similarity=-0.015 Sum_probs=30.9
Q ss_pred CCCEEEEccccCCCC----CCc-----cceeechhhhHHHHHHHHHcCCceeEeCch
Q 025662 149 IGTTAYVEQSIPYPQ----DGK-----QGWWSGGFGYGLWIGILVASGFSVVPIPSL 196 (249)
Q Consensus 149 ~p~~a~IE~v~~~p~----qgv-----qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~ 196 (249)
..+.++||.+....+ .|. -+.|.+|+-+-.+.-.+...||+|++|.|.
T Consensus 23 ~~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yka~~~Gi~v~~v~~~ 79 (82)
T TIGR01766 23 NNGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPA 79 (82)
T ss_pred cCCEEEECCccchhhhcchhhHHHHHHHHhhhHHHHHHHHHHHHHHcCCeEEEeCcc
Confidence 457899999751111 111 133445555556667789999999999984
No 44
>PRK00047 glpK glycerol kinase; Provisional
Probab=40.38 E-value=79 Score=30.97 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=22.7
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeee--eeCCC
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEV--FDTPH 120 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v--~D~pt 120 (249)
..+||||=|+++. .++++.++. .+.. ..+|.
T Consensus 5 ~~~lgiD~GTts~Ka~l~d~~g~--~~~~~~~~~~~ 38 (498)
T PRK00047 5 KYILALDQGTTSSRAIIFDHDGN--IVSVAQKEFTQ 38 (498)
T ss_pred CEEEEEecCCCceEEEEECCCCC--EEEEEeeeccc
Confidence 4699999999999 888887764 4444 34443
No 45
>TIGR01315 5C_CHO_kinase FGGY-family pentulose kinase. This model represents a subfamily of the FGGY family of carbohydrate kinases. This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol (PubMed:9639934 and JW Lengeler, personal communication); its annotation in GenBank as ribitol kinase is imprecise and may have affected public annotation of related proteins.
Probab=40.08 E-value=64 Score=32.16 Aligned_cols=20 Identities=20% Similarity=0.400 Sum_probs=17.6
Q ss_pred EEEEcCCCCce-EEEEecCCC
Q 025662 90 ALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~ 109 (249)
+||||=|+++. .+|++.+|.
T Consensus 2 ~lgID~GTts~Ka~l~d~~G~ 22 (541)
T TIGR01315 2 YIGVDVGTGSARACIIDSTGD 22 (541)
T ss_pred EEEEEecCcCEEEEEEcCCCC
Confidence 79999999999 888887764
No 46
>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=38.07 E-value=26 Score=29.51 Aligned_cols=41 Identities=20% Similarity=0.270 Sum_probs=27.5
Q ss_pred hcccccccCCCCCCCcccccccCCCCceEEEEcCCCCceEEEEecCC
Q 025662 62 QNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDH 108 (249)
Q Consensus 62 ~~~l~~l~~~~~~~~~~~~~~~~~~~m~ILGIDPGl~Ga~avL~~~g 108 (249)
..|.-++++--+.. .....+..++|||+|......+...++
T Consensus 104 ~~~yl~i~~~~~~~------~~~~~~~~~vgVDlGi~~~a~~~~~~~ 144 (227)
T PF01385_consen 104 GKWYLSITVEVEVE------PPPPDTEKVVGVDLGIKNLATVSSGDG 144 (227)
T ss_pred hhcccccccccccc------ccccccceeeeeccccceeeccccccc
Confidence 67887777664422 123456679999999998866665554
No 47
>PTZ00294 glycerol kinase-like protein; Provisional
Probab=36.94 E-value=81 Score=30.97 Aligned_cols=21 Identities=14% Similarity=0.303 Sum_probs=18.4
Q ss_pred eEEEEcCCCCce-EEEEecCCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~ 109 (249)
.+||||=|+++. .+|++.++.
T Consensus 3 ~~lgiDiGTts~Ka~l~d~~G~ 24 (504)
T PTZ00294 3 YIGSIDQGTTSTRFIIFDEKGN 24 (504)
T ss_pred EEEEEecCCCceEEEEECCCCC
Confidence 589999999999 999987764
No 48
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=36.20 E-value=70 Score=31.76 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=19.7
Q ss_pred CCCceEEEEcCCCCce-EEEEecCC
Q 025662 85 ADSQWALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 85 ~~~m~ILGIDPGl~Ga-~avL~~~g 108 (249)
-..|..||||-|++-+ ..++++++
T Consensus 132 ~~~~~~LGID~GSTtTK~VLm~d~~ 156 (396)
T COG1924 132 YQGMYTLGIDSGSTTTKAVLMEDGK 156 (396)
T ss_pred hcCcEEEEEecCCcceeEEEEeCCC
Confidence 4567899999999999 77777664
No 49
>TIGR03192 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=35.59 E-value=1.2e+02 Score=28.76 Aligned_cols=19 Identities=16% Similarity=0.136 Sum_probs=17.4
Q ss_pred ceEEEEcCCCCce-EEEEec
Q 025662 88 QWALGIDPDLSGA-LAVLKS 106 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~ 106 (249)
|..+|||=|++.+ ++|++.
T Consensus 32 m~~~GIDiGStt~K~Vlld~ 51 (293)
T TIGR03192 32 IITCGIDVGSVSSQAVLVCD 51 (293)
T ss_pred cEEEEEEeCchhEEEEEEeC
Confidence 8899999999999 999983
No 50
>PLN02683 pyruvate dehydrogenase E1 component subunit beta
Probab=34.16 E-value=1.3e+02 Score=28.86 Aligned_cols=36 Identities=25% Similarity=0.270 Sum_probs=30.1
Q ss_pred ceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 111 CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 111 ~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
-+++|+|+++++ -+|.+.|.+.++++ +.+++||+-.
T Consensus 255 I~v~VId~~~ik---------PlD~~~l~~~~~~t----~~vvtvEE~~ 290 (356)
T PLN02683 255 ISAEVINLRSIR---------PLDRDTINASVRKT----NRLVTVEEGW 290 (356)
T ss_pred CCEEEEECCCCC---------ccCHHHHHHHHhhc----CeEEEEeCCC
Confidence 468999999994 67889999999987 4689999975
No 51
>CHL00144 odpB pyruvate dehydrogenase E1 component beta subunit; Validated
Probab=33.58 E-value=1.3e+02 Score=28.43 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=29.9
Q ss_pred ceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 111 CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 111 ~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
-+++|+|+.+++ -+|.+.|.+.++++ +.++++|+-.
T Consensus 228 i~~~VId~~~ik---------PlD~~~i~~~~~~t----~~vv~vEE~~ 263 (327)
T CHL00144 228 YDPEIIDLISLK---------PLDLGTISKSVKKT----HKVLIVEECM 263 (327)
T ss_pred CCEEEEecCcCC---------CCCHHHHHHHHHhh----CcEEEEECCC
Confidence 378999999994 56788899999887 5799999975
No 52
>PLN02295 glycerol kinase
Probab=32.63 E-value=92 Score=30.71 Aligned_cols=21 Identities=14% Similarity=0.294 Sum_probs=18.2
Q ss_pred eEEEEcCCCCce-EEEEecCCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~ 109 (249)
+|||||=|+++. .+|++.+|.
T Consensus 1 ~vlgID~GTts~Ka~l~d~~G~ 22 (512)
T PLN02295 1 FVGAIDQGTTSTRFIIYDRDAR 22 (512)
T ss_pred CEEEEecCCCceEEEEECCCCC
Confidence 489999999999 889987764
No 53
>TIGR01314 gntK_FGGY gluconate kinase, FGGY type. Gluconate is derived from glucose in two steps. This model describes one form of gluconate kinase, belonging to the FGGY family of carbohydrate kinases. Gluconate kinase phosphoryates gluconate for entry into the Entner-Douderoff pathway.
Probab=32.30 E-value=1.1e+02 Score=30.06 Aligned_cols=20 Identities=10% Similarity=0.350 Sum_probs=17.6
Q ss_pred EEEEcCCCCce-EEEEecCCC
Q 025662 90 ALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~ 109 (249)
+||||=|+++. .++++.++.
T Consensus 2 ~lgiDiGtt~~K~~l~d~~g~ 22 (505)
T TIGR01314 2 MIGVDIGTTSTKAVLFEENGK 22 (505)
T ss_pred EEEEeccccceEEEEEcCCCC
Confidence 79999999999 889987654
No 54
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=32.27 E-value=87 Score=28.70 Aligned_cols=55 Identities=24% Similarity=0.228 Sum_probs=35.3
Q ss_pred eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc-----hhhhhhHHHHHHHHHhc
Q 025662 89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR-----VRKRLDAKSMIMLLRSL 145 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~-----~R~r~d~~~L~~lL~~~ 145 (249)
+++|||=|.++- ++.++..+. ..++..+..++++.+.- .-.....+.|.+++.+.
T Consensus 4 ~~vgiDIg~~~Ik~v~~~~~~~--~~~v~~~~~~~~p~~~i~~g~i~d~~~~~~~l~~~~~~~ 64 (348)
T TIGR01175 4 LLVGIDIGSTSVKVAQLKRSGD--RYKLEHYAVEPLPAGIFTEGHIVEYQAVAEALKELLSEL 64 (348)
T ss_pred cEEEEEeccCeEEEEEEEecCC--ceEEEEEEEEECCCCcccCCCccCHHHHHHHHHHHHHHc
Confidence 699999999999 888876554 57777777766543321 22233344555555554
No 55
>PRK10939 autoinducer-2 (AI-2) kinase; Provisional
Probab=31.84 E-value=1.8e+02 Score=28.74 Aligned_cols=21 Identities=10% Similarity=0.316 Sum_probs=18.6
Q ss_pred eEEEEcCCCCce-EEEEecCCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~ 109 (249)
.+||||=|++++ .++++.+|.
T Consensus 4 ~~lgID~GTts~Ka~l~d~~G~ 25 (520)
T PRK10939 4 YLMALDAGTGSIRAVIFDLNGN 25 (520)
T ss_pred EEEEEecCCCceEEEEECCCCC
Confidence 599999999999 999987764
No 56
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=31.19 E-value=2.2e+02 Score=25.67 Aligned_cols=26 Identities=27% Similarity=0.334 Sum_probs=22.1
Q ss_pred CCCCceEEEEcCCCCce-EEEEecCCC
Q 025662 84 NADSQWALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 84 ~~~~m~ILGIDPGl~Ga-~avL~~~g~ 109 (249)
|-+.+.+||||-|-+.. +++++.++.
T Consensus 2 ~~~~~~~lgidIggt~i~~~l~d~~g~ 28 (314)
T COG1940 2 NPEAMTVLGIDIGGTKIKVALVDLDGE 28 (314)
T ss_pred CccCcEEEEEEecCCEEEEEEECCCCc
Confidence 45567899999999999 999988875
No 57
>PRK10331 L-fuculokinase; Provisional
Probab=30.71 E-value=1.2e+02 Score=29.41 Aligned_cols=29 Identities=14% Similarity=0.091 Sum_probs=22.3
Q ss_pred eEEEEcCCCCce-EEEEecCCCCceeeeeeCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTP 119 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~p 119 (249)
.+||||=|+++. .++++.+|. .+.....+
T Consensus 3 ~~lgID~GTt~~Ka~l~d~~G~--~~~~~~~~ 32 (470)
T PRK10331 3 VILVLDCGATNVRAIAVDRQGK--IVARASTP 32 (470)
T ss_pred eEEEEecCCCceEEEEEcCCCc--EEEEEecc
Confidence 589999999999 889987765 54444444
No 58
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=28.25 E-value=1.9e+02 Score=25.08 Aligned_cols=114 Identities=15% Similarity=0.158 Sum_probs=67.4
Q ss_pred EecCCCCceeeeeeCCCcccccccc-hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccceeechhhhHHHHHH
Q 025662 104 LKSDHNGCSAEVFDTPHLPVLVGKR-VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGI 182 (249)
Q Consensus 104 L~~~g~g~~~~v~D~pti~v~~g~~-~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSaf~~G~a~Gv~~gv 182 (249)
++..+..|.+.++..|-|-+.-.+. .-.+.-.+.+...|++++-+. + +...+--+|+.+.+++|+.-=+-..+
T Consensus 41 ~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L~~~g~~~-----~-~~~~~~v~NIvas~~l~~~i~L~~la 114 (174)
T cd00652 41 MRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARILQKLGFPV-----E-KFPEFKVQNIVASCDLGFPIRLEELA 114 (174)
T ss_pred EEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHHHHcCCCc-----c-ccCceEEEEEEEEEECCCcccHHHHH
Confidence 3333334578888888775432222 445555677888888884221 1 22222347888999988775544443
Q ss_pred HHHcCCceeEeCchh----------hhhhh--------cccCCCCChHHHHHHHHHhCCccc
Q 025662 183 LVASGFSVVPIPSLT----------WKNWY--------GLSGGTSTKDDSRRVASTLFPSLC 226 (249)
Q Consensus 183 Laa~gIPV~eVtP~~----------WKkav--------~g~~G~AsKd~sr~ma~~LfP~~~ 226 (249)
.... +.++|.|.+ .|-.+ ..+ |..+-++.+.....++|.+.
T Consensus 115 ~~~~--~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvit-Gaks~~~~~~a~~~i~~~L~ 173 (174)
T cd00652 115 LKHP--ENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVIT-GAKSREDIYEAVEKIYPILK 173 (174)
T ss_pred hhhh--cccEECCccCceEEEEecCCcEEEEEEcCCEEEEE-ecCCHHHHHHHHHHHHHHHh
Confidence 3322 366666654 33322 124 45677889998999888763
No 59
>COG1070 XylB Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=28.05 E-value=1.4e+02 Score=29.47 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=18.4
Q ss_pred CceEEEEcCCCCce-EEEEecCC
Q 025662 87 SQWALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 87 ~m~ILGIDPGl~Ga-~avL~~~g 108 (249)
.+.+||||=|++++ ..+++.++
T Consensus 3 ~~~~lgIDiGTt~~Kavl~d~~~ 25 (502)
T COG1070 3 MKYVLGIDIGTTSVKAVLFDEDG 25 (502)
T ss_pred ccEEEEEEcCCCcEEEEEEeCCC
Confidence 34699999999999 88888773
No 60
>PRK15027 xylulokinase; Provisional
Probab=26.14 E-value=1.4e+02 Score=29.19 Aligned_cols=20 Identities=30% Similarity=0.493 Sum_probs=17.5
Q ss_pred EEEEcCCCCce-EEEEecCCC
Q 025662 90 ALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g~ 109 (249)
+||||=|++++ .++++.++.
T Consensus 2 ~lgID~GTts~Ka~l~d~~G~ 22 (484)
T PRK15027 2 YIGIDLGTSGVKVILLNEQGE 22 (484)
T ss_pred EEEEEecccceEEEEEcCCCC
Confidence 79999999999 888987664
No 61
>TIGR01311 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
Probab=25.72 E-value=2.4e+02 Score=27.53 Aligned_cols=21 Identities=29% Similarity=0.465 Sum_probs=18.4
Q ss_pred eEEEEcCCCCce-EEEEecCCC
Q 025662 89 WALGIDPDLSGA-LAVLKSDHN 109 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~ 109 (249)
.+||||=|+++. .++++.++.
T Consensus 2 ~~lgiDiGtt~iKa~l~d~~g~ 23 (493)
T TIGR01311 2 YILAIDQGTTSSRAIVFDKDGN 23 (493)
T ss_pred eEEEEecCCCceEEEEECCCCC
Confidence 489999999999 999987764
No 62
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=25.60 E-value=2.7e+02 Score=28.43 Aligned_cols=33 Identities=15% Similarity=0.001 Sum_probs=22.7
Q ss_pred CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCC
Q 025662 86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPH 120 (249)
Q Consensus 86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pt 120 (249)
.++++||||=|-+.. +|+++.++. ......+|+
T Consensus 16 ~~~~~L~iDIGGT~ir~al~~~~g~--i~~~~~~~t 49 (638)
T PRK14101 16 ADGPRLLADVGGTNARFALETGPGE--ITQIRVYPG 49 (638)
T ss_pred CCCCEEEEEcCchhheeeeecCCCc--ccceeEEec
Confidence 345699999999998 999965543 333344444
No 63
>TIGR00241 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase.
Probab=24.95 E-value=1.9e+02 Score=25.67 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=15.6
Q ss_pred EEEEcCCCCce-EEEEecCC
Q 025662 90 ALGIDPDLSGA-LAVLKSDH 108 (249)
Q Consensus 90 ILGIDPGl~Ga-~avL~~~g 108 (249)
+||||=|+++. .++++ ++
T Consensus 2 ~lGIDiGtts~K~vl~d-~g 20 (248)
T TIGR00241 2 SLGIDSGSTTTKMVLME-DG 20 (248)
T ss_pred EEEEEcChhheEEEEEc-CC
Confidence 79999999999 88886 44
No 64
>COG2971 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=24.61 E-value=2.9e+02 Score=26.57 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=19.4
Q ss_pred CCCceEEEEcCCCCceEEEEecC
Q 025662 85 ADSQWALGIDPDLSGALAVLKSD 107 (249)
Q Consensus 85 ~~~m~ILGIDPGl~Ga~avL~~~ 107 (249)
.+.+.+||||=|-+++-|+|...
T Consensus 2 ~~~~~~lGVDGGGTkt~a~l~~~ 24 (301)
T COG2971 2 EPMPYFLGVDGGGTKTRAVLADE 24 (301)
T ss_pred CCccEEEEEccCCcceEEEEEcC
Confidence 45677999999999998888873
No 65
>TIGR00329 gcp_kae1 metallohydrolase, glycoprotease/Kae1 family. This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this subfamily show unrelated activities as demonstrated in Pyrococcus abyssi: DNA binding, iron binding, apurinic endonuclease activity, genomic association with a kinase domain, and no glycoprotease activity. This family thus pulls together a set of proteins as a homology group that appears to be near-universal in life, yet heterogeneous in assayed function between bacteria and archaea.
Probab=24.51 E-value=1.8e+02 Score=26.99 Aligned_cols=100 Identities=13% Similarity=0.039 Sum_probs=49.7
Q ss_pred EEEcCCCCce-EEEEecCCCCceeeee-e-------CCCcccccccchhhhhhHHHHHHHHHhcCC--CCCCEEEEcccc
Q 025662 91 LGIDPDLSGA-LAVLKSDHNGCSAEVF-D-------TPHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQSI 159 (249)
Q Consensus 91 LGIDPGl~Ga-~avL~~~g~g~~~~v~-D-------~pti~v~~g~~~R~r~d~~~L~~lL~~~~~--p~p~~a~IE~v~ 159 (249)
||||-...-+ +||++.++. ...++. . ++-|......+.-.+.+...+.++|++... ..-+.+++=.
T Consensus 1 LaidTs~~~~sval~~~~~~-il~~~~~~~~~~~~~~gGi~p~~~~~~H~~~l~~~i~~~l~~~~~~~~did~iav~~-- 77 (305)
T TIGR00329 1 LGIETSCDDTGVAIVDEEGN-VLANIKISQIPLHAKYGGVVPEEASRHHAENIPPLLERALIESNVDKSEIDLIAYTQ-- 77 (305)
T ss_pred CEEecCccceEEEEEECCCc-EEEEEEecccccccccCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEec--
Confidence 5788777767 888875332 112221 1 222211111122344555556666655322 1223333322
Q ss_pred CCCCCCccceeechhhhHHHHHHHHHcCCceeEeCchhh
Q 025662 160 PYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTW 198 (249)
Q Consensus 160 ~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~W 198 (249)
|.|.-+.+..| .....+...+.++|++.|+-..-
T Consensus 78 ---GPG~~tglrvg--~~~Ak~la~~~~~p~~~v~hl~~ 111 (305)
T TIGR00329 78 ---GPGLGGSLRVG--ATFARSLALSLDKPLIGVNHLLG 111 (305)
T ss_pred ---CCCchhhHHHH--HHHHHHHHHHhCCCEeecccHHH
Confidence 12233334433 33466778899999999986654
No 66
>PF12682 Flavodoxin_4: Flavodoxin; PDB: 3EDO_B 3KLB_A.
Probab=24.20 E-value=17 Score=30.73 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=15.3
Q ss_pred hhhhhhhc------cccccccccCcccchh
Q 025662 17 SMNTFVSS------KIRTLCTYPFAQHGRT 40 (249)
Q Consensus 17 ~~~~~~~~------~~~~~~~~~~~~~~~~ 40 (249)
-|+||+.+ ++-+|||...+..+++
T Consensus 91 pv~tFL~~~~~~gK~v~~F~T~ggs~~~~~ 120 (156)
T PF12682_consen 91 PVRTFLEQYDFSGKTVIPFCTSGGSGFGNS 120 (156)
T ss_dssp HHHHHHHCTTTTTSEEEEEEE-SS--CHHH
T ss_pred HHHHHHHhcCCCCCcEEEEEeeCCCChhHH
Confidence 46777764 6889999988766655
No 67
>PRK00976 hypothetical protein; Provisional
Probab=24.07 E-value=89 Score=30.14 Aligned_cols=117 Identities=20% Similarity=0.215 Sum_probs=62.3
Q ss_pred ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCC-CCCCEEEE----------
Q 025662 88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYV---------- 155 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~-p~p~~a~I---------- 155 (249)
|..+|||-|++|- +|+++.+ ...++..|.-..... -...|.++ +.+++ .+-+.++|
T Consensus 1 ~~~~g~dhgt~~~~~~~~~~~----~~~~f~~~r~~~~~~-------~~~~~~~~-~~~~~~~~i~~~~~~ysmgd~~~~ 68 (326)
T PRK00976 1 MMFVGIDHGTTGIRFAIIEGG----KKSIFKLPRTEAKSM-------EKSALEEL-EKRVPLEDIELIAVTYSMGDGISK 68 (326)
T ss_pred CeEEeecCCCccEEEEEEcCC----ceeEEEeeHHHhhhc-------cHHHHHHH-hcCCChhheeEEEEeecccCChhh
Confidence 6789999999999 9999433 467777776543221 12233333 33322 22233333
Q ss_pred ----ccccCCCCCCccceeech----hhhHHHHHHHHHcCCceeEeCc------h---hhhhhhcccCCCCChHHHHHHH
Q 025662 156 ----EQSIPYPQDGKQGWWSGG----FGYGLWIGILVASGFSVVPIPS------L---TWKNWYGLSGGTSTKDDSRRVA 218 (249)
Q Consensus 156 ----E~v~~~p~qgvqSaf~~G----~a~Gv~~gvLaa~gIPV~eVtP------~---~WKkav~g~~G~AsKd~sr~ma 218 (249)
|++ -.+|++|.=-.| -..-| .-.+..++||++.++- . .|+ .+.=- +.++|=.+-..|
T Consensus 69 i~~i~~~---~~rg~~s~~gag~~~ggg~~v-~~~i~~s~ip~~~iPGvh~~~~t~~p~~r-~~sh~-~s~eK~~ia~~a 142 (326)
T PRK00976 69 ITPIEKV---KNRGVISIEGAGKKTGGGTRV-YDEIKESGIPAVVIPGLHRGSPTLDPRFR-VYSHI-ASPEKIGIAYNA 142 (326)
T ss_pred cccHhHh---ccCCeecccCCcceeccHHHH-HHHHHhCCCCEEEeCceecCCCCCCHHHH-HhccC-CCHHHHHHHHHH
Confidence 222 234454443333 33333 3456899999976642 2 355 23211 456666666666
Q ss_pred HHhC
Q 025662 219 STLF 222 (249)
Q Consensus 219 ~~Lf 222 (249)
...|
T Consensus 143 ~~~~ 146 (326)
T PRK00976 143 YKLF 146 (326)
T ss_pred Hhhc
Confidence 5544
No 68
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=23.53 E-value=2.3e+02 Score=24.57 Aligned_cols=124 Identities=14% Similarity=0.154 Sum_probs=74.7
Q ss_pred EEcCCCCceEEEEecCCCCceeeeeeCCCcccccccc-hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCcccee
Q 025662 92 GIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKR-VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWW 170 (249)
Q Consensus 92 GIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~-~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSaf 170 (249)
=-|| ..--.+++.....|.+.++..|-+-+.-.+. .-.+.-.+.+.++|++++-+. + +...|--+|+.+.+
T Consensus 31 eYeP--~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~~~g~~~-----~-~~~~f~v~nIvat~ 102 (174)
T cd04517 31 EYNP--RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQKLGFKV-----V-RFSNFRVVNVLATC 102 (174)
T ss_pred EEeC--CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHHcCCCc-----c-cCCceEEEEEEEEE
Confidence 3567 3333445555555788999999886543333 445555677888888874211 1 11122456778888
Q ss_pred echhhhHHHHHHHHHcCCceeEeCchh----------hhhhh--------cccCCCCChHHHHHHHHHhCCccc
Q 025662 171 SGGFGYGLWIGILVASGFSVVPIPSLT----------WKNWY--------GLSGGTSTKDDSRRVASTLFPSLC 226 (249)
Q Consensus 171 ~~G~a~Gv~~gvLaa~gIPV~eVtP~~----------WKkav--------~g~~G~AsKd~sr~ma~~LfP~~~ 226 (249)
.+|+.-= +--++....+..+|-|-+ +|-.+ ..+ |..+.++.+.....++|.+.
T Consensus 103 ~~~~~i~--L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivit-Gaks~~~~~~a~~~i~pil~ 173 (174)
T cd04517 103 SMPFPIR--LDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVT-GARSMEDVREAVEKIYPIVF 173 (174)
T ss_pred eCCCccc--HHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEE-ecCCHHHHHHHHHHHHHHHh
Confidence 8776544 444554455566666644 44333 123 55777999999999988763
No 69
>cd01403 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family.
Probab=22.57 E-value=23 Score=25.55 Aligned_cols=27 Identities=19% Similarity=0.601 Sum_probs=22.1
Q ss_pred hhhHHHHHHHHHcCC-----ceeEeCchhhhh
Q 025662 174 FGYGLWIGILVASGF-----SVVPIPSLTWKN 200 (249)
Q Consensus 174 ~a~Gv~~gvLaa~gI-----PV~eVtP~~WKk 200 (249)
+--.+|.-++.+.|| ||--|+|.+|++
T Consensus 20 Fc~avw~~v~TQ~GIeWnlSPVGrVtPkeWr~ 51 (51)
T cd01403 20 FCTAVWTYVMTQTGIEWNLSPVGRVTPKEWRE 51 (51)
T ss_pred hhhhhhhheeeecceeeccccccccCcccccC
Confidence 345678888889888 789999999984
No 70
>COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.45 E-value=1.2e+02 Score=29.85 Aligned_cols=73 Identities=21% Similarity=0.207 Sum_probs=49.3
Q ss_pred eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc-hhhhhhHHHHHHHHHhcCC-----------CCCCEEEE
Q 025662 89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR-VRKRLDAKSMIMLLRSLDA-----------PIGTTAYV 155 (249)
Q Consensus 89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~-~R~r~d~~~L~~lL~~~~~-----------p~p~~a~I 155 (249)
.++|||=|.+.- ..-|+..+. ..++..|-..+++.|-- .++-++++++.+.|++..+ .-|.-++|
T Consensus 11 ~~vGIdI~~~sVKvvqLs~~g~--~~kLe~y~~~~lp~~iv~dg~ivd~~av~~~Lk~ala~~gi~~k~aa~AVP~s~ai 88 (354)
T COG4972 11 AAVGIDIGSHSVKVVQLSRSGN--RYKLEKYASEPLPENIVADGKIVDYDAVASALKRALAKLGIKSKNAATAVPGSAAI 88 (354)
T ss_pred ceeeEeeccceEEEEEEcccCC--ceeeeeeeecccCccccccCCcccHHHHHHHHHHHHHhcCcchhhhhhhcCcccee
Confidence 589999999888 888886555 67777777777666544 6666777777776665431 33444555
Q ss_pred ccccCCCC
Q 025662 156 EQSIPYPQ 163 (249)
Q Consensus 156 E~v~~~p~ 163 (249)
=+..+||.
T Consensus 89 tk~i~vp~ 96 (354)
T COG4972 89 TKTIPVPD 96 (354)
T ss_pred eEEeccCC
Confidence 55555554
No 71
>PF01869 BcrAD_BadFG: BadF/BadG/BcrA/BcrD ATPase family; InterPro: IPR002731 This domain is found in the BadF (O07462 from SWISSPROT) and BadG (O07463 from SWISSPROT) proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase (P11568 from SWISSPROT). The hypothetical protein AQ_278 from Aquifex aeolicus O66634 from SWISSPROT contains two copies of this region suggesting that the family may structurally dimerise.; PDB: 2E2N_B 2E2Q_A 2E2P_B 2E2O_A 1ZBS_A 2CH6_A 2CH5_D 1ZC6_A 1HUX_A.
Probab=22.27 E-value=1.5e+02 Score=26.24 Aligned_cols=57 Identities=14% Similarity=-0.032 Sum_probs=29.7
Q ss_pred EEEcCCCCce-EEEEecCCCCcee-eeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCC
Q 025662 91 LGIDPDLSGA-LAVLKSDHNGCSA-EVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPI 149 (249)
Q Consensus 91 LGIDPGl~Ga-~avL~~~g~g~~~-~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~ 149 (249)
||||=|.+.+ ..+++.++. .+ +...-|+-.-..+...=.+.+.+.+.++++....+.
T Consensus 1 lGIDgGgTkt~~vl~d~~g~--il~~~~~~~~n~~~~~~~~~~~~i~~~i~~~~~~~~~~~ 59 (271)
T PF01869_consen 1 LGIDGGGTKTKAVLVDENGN--ILGRGKGGGANYNSVGFEEAMENIKEAIEEALSQAGLSP 59 (271)
T ss_dssp EEEEECSSEEEEEEEETTSE--EEEEEEES-TTHHHHHHHHHHHHHHHHHHHHHHHHTTST
T ss_pred CEEeeChheeeeEEEeCCCC--EEEEEEeCCCCCCCCCcchhhhHHHHHHHHHHHHcCCCc
Confidence 7999999999 666665553 22 233333321111111112344566677777765433
No 72
>COG2403 Predicted GTPase [General function prediction only]
Probab=21.95 E-value=3e+02 Score=27.72 Aligned_cols=78 Identities=10% Similarity=-0.061 Sum_probs=58.4
Q ss_pred hhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccceeechhhhHHHHHHHHHcCCceeEeCchhhhh-------hhccc
Q 025662 133 LDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKN-------WYGLS 205 (249)
Q Consensus 133 ~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKk-------av~g~ 205 (249)
-+|+.|..+|+++ .-+++++--+ + -.-..++-+.....+.|..+.+..|.+|-. +++++
T Consensus 69 k~~~~lek~ire~---~VD~~VlayS-----D------vs~e~v~~IaS~vLs~GA~f~~~gP~et~~~~ekPviaV~at 134 (449)
T COG2403 69 KDYDDLEKIIREK---DVDIVVLAYS-----D------VSYEHVFRIASRVLSAGADFKELGPKETMLKLEKPVIAVTAT 134 (449)
T ss_pred ccHHHHHHHHHHc---CCCeEEEEcc-----c------CCHHHHHHHHHHHHhCCceeEEeCccHHhhhhcCceEEEEEe
Confidence 3489999999999 4555554332 1 223667778888889999999999999987 34667
Q ss_pred CCCCChHHHHHHHHHhCCc
Q 025662 206 GGTSTKDDSRRVASTLFPS 224 (249)
Q Consensus 206 ~G~AsKd~sr~ma~~LfP~ 224 (249)
|.+..|-++...+.+++..
T Consensus 135 rtg~GKsaVS~~v~r~l~e 153 (449)
T COG2403 135 RTGVGKSAVSRYVARLLRE 153 (449)
T ss_pred ccccchhHHHHHHHHHHHH
Confidence 7899999987777776543
No 73
>PHA02533 17 large terminase protein; Provisional
Probab=21.86 E-value=2.4e+02 Score=28.75 Aligned_cols=63 Identities=16% Similarity=0.274 Sum_probs=34.1
Q ss_pred CCceEEEEcCCCC-ceEEEEecCCCCceeeeeeCCCcc---ccc--ccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 86 DSQWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLP---VLV--GKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 86 ~~m~ILGIDPGl~-Ga~avL~~~g~g~~~~v~D~pti~---v~~--g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
+..-++|+||+-+ +. +.+ .+.|+|.|..+ |.+ .+..-...-++.+.++.+.| -...+.||.-+
T Consensus 313 ~~~y~ig~D~a~G~~~------D~s--~~~V~~~~~~~~r~v~~~~~~~~~~~~~a~~I~~l~~~Y---n~a~i~id~tg 381 (534)
T PHA02533 313 GHKYIATLDVSEGRGQ------DYS--ALHIIDITEYPYKQVAVYHNNTISPLILPDIIVDYLMEY---NEAPVYIELNS 381 (534)
T ss_pred CceEEEEEECCCCCCC------cee--EEEEEccCCCCcEEEEEEecCCCCHHHHHHHHHHHHHHh---CceEEEEecCC
Confidence 3344899999963 22 111 34555544332 110 11122334556677788888 45568899854
No 74
>TIGR00204 dxs 1-deoxy-D-xylulose-5-phosphate synthase. DXP synthase is a thiamine diphosphate-dependent enzyme related to transketolase and the pyruvate dehydrogenase E1-beta subunit. By an acyloin condensation of pyruvate with glyceraldehyde 3-phosphate, it produces 1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine diphosphate (TPP), pyridoxal phosphate, and the isoprenoid building block isopentenyl diphosphate (IPP).
Probab=21.73 E-value=4.1e+02 Score=27.38 Aligned_cols=36 Identities=22% Similarity=0.251 Sum_probs=28.8
Q ss_pred ceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 111 CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 111 ~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
.+++|+|+.+++ -+|.+.+...++++ ..+++||+-.
T Consensus 522 i~~~VId~~~lk---------PlD~e~i~~~~~k~----~~vvtvEE~~ 557 (617)
T TIGR00204 522 IEATVVDARFVK---------PLDEELILEIAASH----EKLVTVEENA 557 (617)
T ss_pred CCEEEEecCcCC---------cCCHHHHHHHHhhc----CeEEEEECCC
Confidence 478999999984 46778888888876 4689999975
No 75
>PRK04123 ribulokinase; Provisional
Probab=20.43 E-value=3.8e+02 Score=26.61 Aligned_cols=22 Identities=9% Similarity=0.277 Sum_probs=18.1
Q ss_pred ceEEEEcCCCCce-EEEEec-CCC
Q 025662 88 QWALGIDPDLSGA-LAVLKS-DHN 109 (249)
Q Consensus 88 m~ILGIDPGl~Ga-~avL~~-~g~ 109 (249)
..+||||=|++++ .+|++. ++.
T Consensus 3 ~~~lgiD~GTts~Ka~l~d~~~g~ 26 (548)
T PRK04123 3 AYVIGLDFGTDSVRALLVDCATGE 26 (548)
T ss_pred cEEEEEecCCCceEEEEEECCCCc
Confidence 3599999999999 888884 653
No 76
>TIGR00215 lpxB lipid-A-disaccharide synthase. Lipid-A precursor biosynthesis producing lipid A disaccharide in a condensation reaction. transcribed as part of an operon including lpxA
Probab=20.34 E-value=2.5e+02 Score=26.65 Aligned_cols=55 Identities=11% Similarity=0.000 Sum_probs=34.1
Q ss_pred hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccceeechhhhHHHHHHHHHcCCceeEe-Cchhhhh
Q 025662 129 VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPI-PSLTWKN 200 (249)
Q Consensus 129 ~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eV-tP~~WKk 200 (249)
-+......++..+|++. .|+.++.=. + ++ |++ . +...+...|||++.| +|++|-.
T Consensus 72 ~~~~~~~~~~~~~l~~~---kPd~vi~~g-~--~~------~~~----~-~a~aa~~~gip~v~~i~P~~waw 127 (385)
T TIGR00215 72 GRLLKIRKEVVQLAKQA---KPDLLVGID-A--PD------FNL----T-KELKKKDPGIKIIYYISPQVWAW 127 (385)
T ss_pred HHHHHHHHHHHHHHHhc---CCCEEEEeC-C--CC------ccH----H-HHHHHhhCCCCEEEEeCCcHhhc
Confidence 34445566788889888 788776422 1 22 332 1 223556779999986 7787644
No 77
>PRK05444 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=20.23 E-value=3.9e+02 Score=27.07 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=27.0
Q ss_pred eeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662 112 SAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI 159 (249)
Q Consensus 112 ~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~ 159 (249)
+++|+|+++++ -+|.+.+.+++++. ..+++||+-.
T Consensus 487 ~~~VId~~~i~---------p~D~~~i~~~~~~~----~~vv~vEe~~ 521 (580)
T PRK05444 487 SATVVDARFVK---------PLDEELLLELAAKH----DLVVTVEEGA 521 (580)
T ss_pred CCEEEEeCcCC---------ccCHHHHHHHHhcC----CeEEEEECCC
Confidence 37889999884 45778888888776 4689999975
Done!