Query 037858
Match_columns 119
No_of_seqs 81 out of 83
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:03:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037858.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037858hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08378 NERD: Nuclease-relate 99.6 4.6E-16 9.9E-21 107.2 6.9 76 40-117 4-83 (115)
2 cd00523 archeal_HJR Holliday j 94.4 0.097 2.1E-06 38.5 5.0 49 42-94 9-57 (123)
3 PF01870 Hjc: Archaeal hollida 93.4 0.1 2.2E-06 36.4 3.4 43 47-94 4-46 (88)
4 PRK14684 hypothetical protein; 93.1 0.33 7.2E-06 35.5 5.7 43 44-93 15-58 (120)
5 PRK14686 hypothetical protein; 93.0 0.27 5.8E-06 35.7 5.2 43 45-94 15-58 (119)
6 TIGR00252 conserved hypothetic 92.8 0.36 7.8E-06 35.2 5.6 43 45-94 16-59 (119)
7 PRK14677 hypothetical protein; 92.7 0.41 8.9E-06 34.4 5.7 40 45-91 10-50 (107)
8 PRK14676 hypothetical protein; 92.6 0.36 7.8E-06 35.1 5.4 39 45-90 17-56 (117)
9 PRK14679 hypothetical protein; 92.5 0.38 8.2E-06 35.6 5.5 43 45-94 25-68 (128)
10 PRK14688 hypothetical protein; 92.2 0.49 1.1E-05 34.7 5.7 44 44-94 15-59 (121)
11 PRK14675 hypothetical protein; 92.1 0.58 1.3E-05 34.3 6.0 49 43-98 16-65 (125)
12 PRK14689 hypothetical protein; 92.0 0.36 7.9E-06 35.7 4.8 43 44-93 17-60 (124)
13 PRK14674 hypothetical protein; 91.9 0.52 1.1E-05 35.1 5.6 43 44-93 14-57 (133)
14 PRK12497 hypothetical protein; 91.8 0.5 1.1E-05 34.1 5.2 45 44-95 15-60 (119)
15 PRK14680 hypothetical protein; 91.4 0.61 1.3E-05 34.8 5.5 44 45-95 16-60 (134)
16 PRK14685 hypothetical protein; 91.3 0.55 1.2E-05 37.0 5.4 35 53-93 59-94 (177)
17 PRK14678 hypothetical protein; 91.2 0.59 1.3E-05 34.1 5.2 43 45-94 16-59 (120)
18 PHA01753 Holliday junction res 91.1 0.42 9E-06 35.5 4.3 52 39-94 8-59 (121)
19 COG1591 Holliday junction reso 91.0 0.37 8E-06 36.7 4.0 58 42-99 6-64 (137)
20 PRK14681 hypothetical protein; 90.9 0.76 1.6E-05 35.3 5.7 43 45-94 53-97 (158)
21 PF13635 DUF4143: Domain of un 90.7 0.44 9.5E-06 32.0 3.8 48 39-90 41-88 (90)
22 PRK14682 hypothetical protein; 90.3 1.1 2.3E-05 32.6 5.8 45 44-95 13-59 (117)
23 PRK14683 hypothetical protein; 89.2 0.54 1.2E-05 34.7 3.6 40 45-91 23-63 (122)
24 PF02021 UPF0102: Uncharacteri 88.6 2.4 5.1E-05 29.4 6.3 46 45-97 6-52 (93)
25 PRK14673 hypothetical protein; 87.3 0.61 1.3E-05 35.1 2.9 43 45-94 36-80 (137)
26 COG0792 Predicted endonuclease 87.2 0.64 1.4E-05 34.1 2.8 25 71-95 32-56 (114)
27 PF04471 Mrr_cat: Restriction 85.8 1.6 3.4E-05 28.9 4.0 39 57-97 21-62 (115)
28 PRK14687 hypothetical protein; 84.8 1.1 2.4E-05 35.2 3.3 46 42-93 37-87 (173)
29 PF08011 DUF1703: Protein of u 84.3 1.3 2.8E-05 30.7 3.2 21 70-90 29-53 (105)
30 PF03008 DUF234: Archaea bacte 82.7 1.6 3.5E-05 30.1 3.1 23 71-93 67-91 (100)
31 PF08774 VRR_NUC: VRR-NUC doma 76.0 3.1 6.6E-05 28.2 2.8 36 70-106 45-84 (100)
32 PF14281 PDDEXK_4: PD-(D/E)XK 62.1 10 0.00022 27.8 3.2 25 70-94 73-98 (179)
33 PF08000 bPH_1: Bacterial PH d 60.9 42 0.00091 24.7 6.2 42 45-95 19-62 (124)
34 PHA02552 4 head completion pro 60.3 25 0.00055 26.9 5.1 60 37-96 24-90 (151)
35 PF07788 DUF1626: Protein of u 57.7 16 0.00034 24.8 3.2 19 73-92 4-22 (70)
36 TIGR00372 cas4 CRISPR-associat 57.7 48 0.001 23.9 6.1 42 51-92 48-89 (178)
37 PF09002 DUF1887: Domain of un 57.4 20 0.00043 30.4 4.5 21 71-91 289-309 (381)
38 PF11466 Doppel: Prion-like pr 51.7 16 0.00034 21.3 2.1 21 1-21 1-21 (30)
39 PRK04247 hypothetical protein; 51.6 33 0.00071 28.1 4.8 26 71-96 159-185 (238)
40 cd01424 MGS_CPS_II Methylglyox 51.3 41 0.00089 22.9 4.6 26 34-60 7-32 (110)
41 PHA00159 endonuclease I 50.4 31 0.00067 26.7 4.2 49 37-90 15-67 (148)
42 PF10926 DUF2800: Protein of u 49.9 24 0.00053 30.4 4.0 27 73-99 117-144 (372)
43 PF06319 DUF1052: Protein of u 49.7 28 0.00061 27.1 3.9 51 39-94 18-72 (157)
44 PF14082 DUF4263: Domain of un 47.9 33 0.00071 25.2 3.9 37 63-99 36-74 (164)
45 PF13588 HSDR_N_2: Type I rest 45.2 21 0.00046 24.3 2.4 47 47-95 11-64 (112)
46 cd01037 Restriction_endonuclea 44.1 24 0.00052 20.8 2.3 21 69-91 26-46 (80)
47 PF04556 DpnII: DpnII restrict 42.6 30 0.00066 29.1 3.3 26 69-94 193-218 (286)
48 PF01930 Cas_Cas4: Domain of u 40.5 45 0.00098 24.0 3.6 32 59-95 47-78 (162)
49 PRK14758 hypothetical protein; 40.5 21 0.00045 20.3 1.4 12 10-21 13-24 (27)
50 CHL00105 psaJ photosystem I su 39.4 29 0.00064 21.6 2.1 22 5-28 14-35 (42)
51 PF03749 SfsA: Sugar fermentat 38.7 55 0.0012 26.1 4.1 61 29-91 63-123 (215)
52 PRK02733 photosystem I reactio 38.3 30 0.00066 21.5 2.1 22 5-28 14-35 (42)
53 PF08722 Tn7_Tnp_TnsA_N: TnsA 38.1 44 0.00095 22.1 3.0 51 30-91 2-56 (88)
54 PRK14535 cysS cysteinyl-tRNA s 35.9 41 0.00089 31.7 3.4 24 70-93 60-83 (699)
55 cd05563 PTS_IIB_ascorbate PTS_ 35.5 65 0.0014 20.8 3.5 43 37-82 8-54 (86)
56 PF11817 Foie-gras_1: Foie gra 35.2 26 0.00057 27.6 1.8 20 12-31 7-26 (247)
57 KOG4771 Nucleolar protein (NOP 34.5 22 0.00049 28.6 1.3 26 29-54 121-146 (210)
58 cd06926 RNAP_II_RPB11 RPB11 su 33.9 98 0.0021 21.5 4.3 48 31-82 20-67 (93)
59 PF14986 DUF4514: Domain of un 33.4 45 0.00098 22.1 2.4 30 7-36 28-59 (61)
60 PF02655 ATP-grasp_3: ATP-gras 31.2 78 0.0017 23.1 3.7 39 39-91 117-156 (161)
61 PF14899 DUF4492: Domain of un 31.0 67 0.0015 21.6 3.0 45 6-51 19-64 (64)
62 PF04313 HSDR_N: Type I restri 30.5 69 0.0015 24.0 3.3 23 70-92 120-143 (194)
63 PF05367 Phage_endo_I: Phage e 29.7 27 0.00058 27.0 1.0 52 37-91 15-68 (149)
64 cd00251 Mth_Ecto The ectodomai 29.2 56 0.0012 25.4 2.7 40 53-96 17-56 (176)
65 PF12705 PDDEXK_1: PD-(D/E)XK 27.8 74 0.0016 22.8 3.0 24 70-93 131-155 (257)
66 PF05585 DUF1758: Putative pep 26.4 26 0.00057 25.6 0.4 61 55-115 97-161 (164)
67 TIGR01213 conserved hypothetic 26.0 52 0.0011 28.8 2.2 41 46-92 192-232 (388)
68 COG4998 Predicted endonuclease 25.9 1.6E+02 0.0035 23.7 4.8 46 45-91 9-54 (209)
69 COG3788 Uncharacterized relati 24.7 60 0.0013 24.6 2.1 22 1-22 2-23 (131)
70 COG5002 VicK Signal transducti 24.6 62 0.0013 29.0 2.4 42 19-60 392-433 (459)
71 PF11396 DUF2874: Protein of u 24.5 1.5E+02 0.0032 17.9 3.5 52 40-105 7-61 (61)
72 PF01939 DUF91: Protein of unk 24.3 1.8E+02 0.0039 23.6 4.9 23 72-94 136-159 (228)
73 PF08443 RimK: RimK-like ATP-g 24.1 1.1E+02 0.0023 22.9 3.3 23 72-95 149-171 (190)
74 cd07029 RNAP_I_III_AC19 AC19 s 23.9 1.7E+02 0.0037 19.9 4.1 48 31-82 12-59 (85)
75 KOG2364 Predicted pseudouridyl 23.9 65 0.0014 28.7 2.4 45 45-95 240-284 (433)
76 PF08393 DHC_N2: Dynein heavy 23.6 19 0.00041 29.8 -0.9 41 20-63 309-351 (408)
77 PRK01146 DNA-directed RNA poly 22.8 2E+02 0.0044 19.6 4.3 48 31-82 14-61 (85)
78 COG1258 Predicted pseudouridyl 22.3 70 0.0015 28.3 2.3 23 70-92 216-238 (398)
79 PF13131 DUF3951: Protein of u 21.7 84 0.0018 20.5 2.0 19 6-24 11-29 (53)
80 PF01646 Herpes_UL24: Herpes v 20.4 1.6E+02 0.0034 23.1 3.7 33 54-92 49-88 (179)
81 KOG1610 Corticosteroid 11-beta 20.3 1.6E+02 0.0035 25.4 4.0 55 9-64 2-63 (322)
82 PRK03298 hypothetical protein; 20.1 2.2E+02 0.0048 23.3 4.6 25 72-97 135-160 (224)
83 COG3660 Predicted nucleoside-d 20.1 2.2E+02 0.0048 24.6 4.8 76 4-82 41-118 (329)
No 1
>PF08378 NERD: Nuclease-related domain; InterPro: IPR011528 The nuclease-related domain (NERD) is found in a broad range of bacterial, as well as single archaeal and plant proteins. Most NERD-containing proteins have a single domain, sometimes with additional (predicted) transmembrane helices. In a few instances, proteins containing NERD domains have additional domains (mostly involved in DNA processing), such as the HRDC, the UvrD/REP helicase, the DNA-binding C4 zinc finger, or the serine/threonine and tyrosine protein kinases. In all cases in which a NERD domain is present in multidomain proteins, it is found at the N terminus. The NERD domain is predicted to function in DNA processing, and may have a nuclease function [].
Probab=99.64 E-value=4.6e-16 Score=107.23 Aligned_cols=76 Identities=29% Similarity=0.458 Sum_probs=62.1
Q ss_pred cchhhHHHHH-hhccC--ceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEEEcCCCCeEEecC-CcCCCC
Q 037858 40 TVTVSVANRL-EELYG--GTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSINNDGSWVCMGE-AVHPNP 115 (119)
Q Consensus 40 ~~~~~v~~~L-ekl~~--~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~~~~dg~W~q~~~-~~~~nP 115 (119)
.++-.++++| +.+.. +.+|+|+++|+ ..+...|||+|++|+++|+|||+|||+|.|+.+.+++|.|. + ..++||
T Consensus 4 ~gE~~~~~~L~~~l~~~~~~v~~~i~~~~-~~~~~~eiD~lvi~~~gi~viE~K~~~g~i~~~~~~~w~~~-~~~~~~nP 81 (115)
T PF08378_consen 4 AGEQRVAERLEKHLPDDEYHVFHNIRLPD-PQGGTREIDHLVITPKGIFVIEVKNWSGKIYGDEDGQWFQE-NKKEFKNP 81 (115)
T ss_pred HHHHHHHHHHHhhCCcCcEEEEeceEEec-cCCCCceeEEEEEeCCEEEEEEEecccceEEEcCCCcEEEc-CCeecCCH
Confidence 4566788889 44444 47999999987 45567899999999999999999999999998776689997 4 478888
Q ss_pred CC
Q 037858 116 VS 117 (119)
Q Consensus 116 V~ 117 (119)
+.
T Consensus 82 ~~ 83 (115)
T PF08378_consen 82 LE 83 (115)
T ss_pred HH
Confidence 74
No 2
>cd00523 archeal_HJR 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 eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=94.41 E-value=0.097 Score=38.49 Aligned_cols=49 Identities=27% Similarity=0.289 Sum_probs=33.9
Q ss_pred hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
+=.+++-|++ .| |.=+|.|...++...|||+|..-++.++.||||-.++
T Consensus 9 E~~a~~~L~~-~G---~~vlR~~~sG~~~~~eiDIIA~~~~~lvfVEVK~r~~ 57 (123)
T cd00523 9 ERELVKILEE-KG---FAVVRAPGSGGGPRPLPDIVAGNGGTYLAIEVKSTKK 57 (123)
T ss_pred HHHHHHHHHh-CC---CEEEEEcCCCCCCCCceeEEEecCCEEEEEEEEecCC
Confidence 3345555665 34 4444776543333459999999999999999997665
No 3
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=93.44 E-value=0.1 Score=36.40 Aligned_cols=43 Identities=23% Similarity=0.277 Sum_probs=31.9
Q ss_pred HHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 47 NRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 47 ~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
++|.++.-.++|+-+|.|...+. |+|-+-++.+++||+|..+.
T Consensus 4 rel~~~L~~~Gf~v~R~~~Sg~~-----DiiA~~~~~~l~IEvKs~~~ 46 (88)
T PF01870_consen 4 RELVKILWERGFAVVRAAGSGGG-----DIIAGKGGRYLAIEVKSTSK 46 (88)
T ss_dssp HHHHHHHHHTT-EEEEBSCCSSS-----SEEEEETTEEEEEEEEEESS
T ss_pred HHHHHHHHhCCcEEEEecCCCCc-----CEEEECCCEEEEEEEeeccC
Confidence 34444444578999999875432 99999999999999997663
No 4
>PRK14684 hypothetical protein; Provisional
Probab=93.06 E-value=0.33 Score=35.49 Aligned_cols=43 Identities=19% Similarity=0.256 Sum_probs=30.9
Q ss_pred hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858 44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS 93 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS 93 (119)
.++.-|++ .|+.+.+ |.|-| .+|||+|....+.+..||||--+
T Consensus 15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~ 58 (120)
T PRK14684 15 TACRYLQK-QGLSFITKNFRYK------QGEIDLIMSDQSMLVFIEVRYRR 58 (120)
T ss_pred HHHHHHHH-CCCEEEEEEecCC------CCeEEEEEEeCCEEEEEEEeEcC
Confidence 34444544 5666644 77763 35999999999999999999544
No 5
>PRK14686 hypothetical protein; Provisional
Probab=93.05 E-value=0.27 Score=35.73 Aligned_cols=43 Identities=28% Similarity=0.258 Sum_probs=31.4
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
++.-|++ .|+++.. |.|-+ .+|||+|..-.+.+..||||--++
T Consensus 15 A~~~L~~-~Gy~il~rN~r~~------~GEIDlIa~~~~~lvFVEVKtR~~ 58 (119)
T PRK14686 15 AVEFLIK-KGYTILERNYRFQ------KAEIDIIAQKGNILVIVEVKTRSS 58 (119)
T ss_pred HHHHHHH-CCCEEEEEEecCC------CCcEEEEECcCCEEEEEEEEecCC
Confidence 3444444 5676654 77763 359999999999999999996543
No 6
>TIGR00252 conserved hypothetical protein TIGR00252. the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment
Probab=92.78 E-value=0.36 Score=35.20 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=31.0
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
++.-|++ .|+.+.+ |.|-| .+|||+|....+.+..||||--++
T Consensus 16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~~ 59 (119)
T TIGR00252 16 ARAWLEQ-KGLKFIAANWNSP------WGEIDLIMHDTKTIAFVEVRTRSG 59 (119)
T ss_pred HHHHHHH-CCCEEeEEEecCC------CCcEEEEEeeCCEEEEEEEEecCC
Confidence 4444444 5666654 67763 359999999999999999996543
No 7
>PRK14677 hypothetical protein; Provisional
Probab=92.74 E-value=0.41 Score=34.35 Aligned_cols=40 Identities=28% Similarity=0.287 Sum_probs=29.6
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
++.-|++ .|+.+.. |.|-| .+|||+|....+.+..||||-
T Consensus 10 A~~~L~~-~Gy~Il~rN~r~~------~GEIDlIa~~~~~lvFVEVK~ 50 (107)
T PRK14677 10 ACKFLKK-KGYKILERNYRTK------YGEIDIVARDGREIVFVEVKS 50 (107)
T ss_pred HHHHHHH-CCCEEEEEEecCC------CceeeEEEEECCEEEEEEEec
Confidence 4444544 5666644 67764 259999999999999999994
No 8
>PRK14676 hypothetical protein; Provisional
Probab=92.64 E-value=0.36 Score=35.12 Aligned_cols=39 Identities=26% Similarity=0.278 Sum_probs=29.4
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEec
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVK 90 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvK 90 (119)
++.-|++ .|+.+.. |.|-| .+|||+|....+.+..||||
T Consensus 17 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK 56 (117)
T PRK14676 17 VARIYDR-SGRPVAARRWRGV------SGEIDLIAREGAEVIFIEVK 56 (117)
T ss_pred HHHHHHH-CCCEEeeeecCCC------CCeEEEEEeeCCEEEEEEEe
Confidence 4444554 5676654 67764 35999999999999999999
No 9
>PRK14679 hypothetical protein; Provisional
Probab=92.53 E-value=0.38 Score=35.65 Aligned_cols=43 Identities=16% Similarity=0.139 Sum_probs=30.5
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
++.-|+ ..|+.+.. |.|-+ .+|||+|.--.+.+..||||--++
T Consensus 25 A~~~L~-~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR~~ 68 (128)
T PRK14679 25 ALLALM-LKGYRPLARRFAAA------GGEIDLIVRRGRTIAFVEVKARAT 68 (128)
T ss_pred HHHHHH-HCCCEEEeeeccCC------CCeEEEEEEeCCEEEEEEEEecCC
Confidence 344444 35666643 66653 359999999999999999996543
No 10
>PRK14688 hypothetical protein; Provisional
Probab=92.22 E-value=0.49 Score=34.66 Aligned_cols=44 Identities=27% Similarity=0.233 Sum_probs=31.7
Q ss_pred hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
.++.-|++ .|+.+.. |.|-| .+|||+|.-..+.+..||||--++
T Consensus 15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK~R~~ 59 (121)
T PRK14688 15 LAAEYLKG-MGYSIIQTNCRLP------EGEIDIVGQDGEYLVFIEVRTKRR 59 (121)
T ss_pred HHHHHHHH-CCCEEEEEEeeCC------CCcEeEEEeeCCEEEEEEEEecCC
Confidence 34444544 5666654 77764 359999999999999999995443
No 11
>PRK14675 hypothetical protein; Provisional
Probab=92.14 E-value=0.58 Score=34.32 Aligned_cols=49 Identities=16% Similarity=0.068 Sum_probs=35.6
Q ss_pred hhHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEEE
Q 037858 43 VSVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVSI 98 (119)
Q Consensus 43 ~~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~~ 98 (119)
-.++.-|++ .|+++.. |.|.| .+|||+|..-.+.+.+||||-.++.-..
T Consensus 16 ~~A~~~L~~-~G~~il~rn~r~~------~GEIDlIa~d~~~lvFVEVK~R~~~~~g 65 (125)
T PRK14675 16 SIAVTYLKG-LRYKIVERNFRCR------CGEIDIIARDGKTLVFVEVKTRKNYAYG 65 (125)
T ss_pred HHHHHHHHH-CCCEEEEEEEeCC------CCeEEEEEEeCCEEEEEEEEeccCCCCc
Confidence 344555555 5666654 67774 3599999999999999999987765443
No 12
>PRK14689 hypothetical protein; Provisional
Probab=92.04 E-value=0.36 Score=35.75 Aligned_cols=43 Identities=23% Similarity=0.217 Sum_probs=31.0
Q ss_pred hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858 44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS 93 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS 93 (119)
.++.-|++ .|+.+.+ |.|-+ .+|||+|..-.+.+..||||--+
T Consensus 17 ~Aa~~L~~-~Gy~Il~rN~r~~------~GEIDIIa~~~~~lVFVEVKtR~ 60 (124)
T PRK14689 17 RVLRLLQR-RGWRLLDRNWSCR------WGELDLVLEKQQRLLVVEVKGRR 60 (124)
T ss_pred HHHHHHHH-CCCEEEEEecCCC------CCcccEEeeeCCEEEEEEEEECC
Confidence 34455554 5666654 67763 35999999999999999999543
No 13
>PRK14674 hypothetical protein; Provisional
Probab=91.92 E-value=0.52 Score=35.15 Aligned_cols=43 Identities=14% Similarity=0.172 Sum_probs=31.7
Q ss_pred hHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858 44 SVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS 93 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS 93 (119)
.++.-|++ .|+++.. |.|-| .+|||+|.-..+.+..||||--+
T Consensus 14 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~LVFVEVK~R~ 57 (133)
T PRK14674 14 TALKLLKE-QNYEWVASNYHSR------RGEVDLIVKRGNELIFVEVKARG 57 (133)
T ss_pred HHHHHHHH-CCCEEeEEeeecC------CCCEeEEEEeCCEEEEEEEEecC
Confidence 34444444 6777765 78763 35999999999999999999544
No 14
>PRK12497 hypothetical protein; Reviewed
Probab=91.76 E-value=0.5 Score=34.06 Aligned_cols=45 Identities=22% Similarity=0.203 Sum_probs=32.7
Q ss_pred hHHHHHhhccCceeE-EEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 44 SVANRLEELYGGTAY-VGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy-~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
-++.-|++ .|+.+. .|.|-| .+|||+|..-.+.+..||||-.++.
T Consensus 15 ~A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~~~ 60 (119)
T PRK12497 15 LAARYLES-KGLRILARNFRCR------FGEIDLIARDGDTLVFVEVKTRRSD 60 (119)
T ss_pred HHHHHHHH-CCCEEEcceecCC------CCcEeeeEEeCCEEEEEEEEeccCC
Confidence 34444543 566665 477764 3599999999999999999977654
No 15
>PRK14680 hypothetical protein; Provisional
Probab=91.44 E-value=0.61 Score=34.76 Aligned_cols=44 Identities=23% Similarity=0.185 Sum_probs=31.4
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
++.-|++ .|+.+.. |.|-| .+|||+|......+..||||-.++.
T Consensus 16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR~~~ 60 (134)
T PRK14680 16 AAALLQR-TGHRILARNWRHG------GLELDIVCEDGDTIVFVEVKTRAAH 60 (134)
T ss_pred HHHHHHH-CCCEEEEeecCCC------CCeEEEEEEeCCEEEEEEEEecCCC
Confidence 3444443 5666644 67763 3599999999999999999976654
No 16
>PRK14685 hypothetical protein; Provisional
Probab=91.28 E-value=0.55 Score=37.00 Aligned_cols=35 Identities=20% Similarity=0.254 Sum_probs=26.9
Q ss_pred cCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCc
Q 037858 53 YGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFS 93 (119)
Q Consensus 53 ~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwS 93 (119)
.|+.|.. |.|-| .+|||+|.-..+.+..||||--+
T Consensus 59 ~Gy~IL~RN~R~~------~GEIDIIA~dg~~LVFVEVKtR~ 94 (177)
T PRK14685 59 QGLRPLARNLRCR------AGEIDLAMRDGEVLVLVEVRARA 94 (177)
T ss_pred CCCEEeEeeecCC------CCcEEEEEecCCEEEEEEEeECC
Confidence 4666644 67764 35999999999999999999543
No 17
>PRK14678 hypothetical protein; Provisional
Probab=91.23 E-value=0.59 Score=34.11 Aligned_cols=43 Identities=28% Similarity=0.283 Sum_probs=30.7
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
++.-|++ .|+.+.. |.|-| .+|||+|..-.+.+..||||--++
T Consensus 16 A~~~L~~-~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVKtR~~ 59 (120)
T PRK14678 16 AAAYLER-CGYTIIARNWRCR------AGEIDIVAREGDQLVFVEVRTRRD 59 (120)
T ss_pred HHHHHHH-CCCEEeeeeecCC------CCCEeeeEEeCCEEEEEEEEECCC
Confidence 3444444 5666643 67763 359999999999999999995543
No 18
>PHA01753 Holliday junction resolvase
Probab=91.10 E-value=0.42 Score=35.54 Aligned_cols=52 Identities=29% Similarity=0.262 Sum_probs=35.5
Q ss_pred CcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCce
Q 037858 39 HTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
+..+-.+++-|++ ++|+=++-|-...+...|||+|....+.++.||||--++
T Consensus 8 ~~~E~~a~~~L~~----~G~~il~rn~~~~~~~GEiDIIA~~~~~lvfVEVKtR~~ 59 (121)
T PHA01753 8 KYYEYKTLEILES----NGFKALRIPVSGTGKQALPDIIATKNNTIYPIEVKSTSK 59 (121)
T ss_pred HHHHHHHHHHHHH----CCCEEEEeccccCCCCCCccEEEeeCCEEEEEEEEeCCC
Confidence 3344445556655 456666665443223579999999999999999996554
No 19
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=91.04 E-value=0.37 Score=36.70 Aligned_cols=58 Identities=17% Similarity=0.173 Sum_probs=43.7
Q ss_pred hhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee-EEEc
Q 037858 42 TVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL-VSIN 99 (119)
Q Consensus 42 ~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~-I~~~ 99 (119)
+-+..++|-+..-.++|+-+|.|....+++-..|+|-..+..+++||+|--++. |..+
T Consensus 6 G~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~kiYl~ 64 (137)
T COG1591 6 GSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRETKIYLD 64 (137)
T ss_pred cchHHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCCcEEEc
Confidence 344556666665568999999998763455579999999999999999965543 6654
No 20
>PRK14681 hypothetical protein; Provisional
Probab=90.86 E-value=0.76 Score=35.33 Aligned_cols=43 Identities=28% Similarity=0.250 Sum_probs=29.9
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeC-CeEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKN-GEEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~-~~IlVIEvKNwSG 94 (119)
++.-|++ .|+++.. |.|-| .+|||+|..-. +.+..||||--++
T Consensus 53 Aa~~L~~-~Gy~IL~rN~R~~------~GEIDIIa~d~~~~LVFVEVKtR~~ 97 (158)
T PRK14681 53 AAAWLEE-HGWTTLSRNWHCR------YGELDIVALNPEYTIVFVEVKTRRS 97 (158)
T ss_pred HHHHHHH-CCCEEEEEEEeCC------CCcEEEEEEcCCceEEEEEEEeccC
Confidence 3444443 5666654 77763 35999999886 5899999996543
No 21
>PF13635 DUF4143: Domain of unknown function (DUF4143)
Probab=90.69 E-value=0.44 Score=32.03 Aligned_cols=48 Identities=25% Similarity=0.266 Sum_probs=30.4
Q ss_pred CcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEec
Q 037858 39 HTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVK 90 (119)
Q Consensus 39 ~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvK 90 (119)
.-.+--|+.+|.+.... .+. +..=. +..+ .|||+|+-+.+.++.||||
T Consensus 41 ~l~En~V~~eL~~~~~~-~~~-l~y~r-~~~~-~EVDfv~~~~~~~~~IEVK 88 (90)
T PF13635_consen 41 ALFENFVAQELLKRLRE-GYE-LYYWR-DKSG-QEVDFVIENGGRIIPIEVK 88 (90)
T ss_pred HHHHHHHHHHHHHhcCC-Cce-EEEEE-CCCC-CEEEEEEEeCCEEEEEEEE
Confidence 33445678888877411 111 22211 1123 3999999999999999999
No 22
>PRK14682 hypothetical protein; Provisional
Probab=90.30 E-value=1.1 Score=32.62 Aligned_cols=45 Identities=22% Similarity=0.269 Sum_probs=32.8
Q ss_pred hHHHHHhhccCceeEE-EEE-ecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 44 SVANRLEELYGGTAYV-GLR-IPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 44 ~v~~~Lekl~~~kiy~-gLR-IPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
.++.-|++ .|+.+.. |.| .| .+|||+|..-.+.+..||||-.++.
T Consensus 13 ~A~~~L~~-~Gy~Il~rN~r~~~------~GEIDiIa~~~~~lvFVEVKtR~~~ 59 (117)
T PRK14682 13 QACKFLHT-QALEILAHNFKALP------YGEIDIIALDKDTLVFIEVKYRSKT 59 (117)
T ss_pred HHHHHHHH-CCCEEeeeeEECCC------CCcEEEEEeeCCEEEEEEEEecCCC
Confidence 44555555 5666654 777 44 2599999999999999999976643
No 23
>PRK14683 hypothetical protein; Provisional
Probab=89.22 E-value=0.54 Score=34.66 Aligned_cols=40 Identities=30% Similarity=0.183 Sum_probs=28.1
Q ss_pred HHHHHhhccCcee-EEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858 45 VANRLEELYGGTA-YVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 45 v~~~Lekl~~~ki-y~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
++.-|++ .|+.+ =.|.|- +.+|||+|.--.+.+..||||-
T Consensus 23 A~~~L~~-~Gy~Il~rN~r~------~~GEIDIIa~~~~~lVFVEVKt 63 (122)
T PRK14683 23 IILFLKC-KLYHIIKHRYRC------PLGEIDIIAHKNKQLVFIEVKT 63 (122)
T ss_pred HHHHHHH-CCCEEEeeecCC------CCCcEEEEEEeCCEEEEEEEee
Confidence 3444444 45544 344554 3469999999999999999994
No 24
>PF02021 UPF0102: Uncharacterised protein family UPF0102; InterPro: IPR003509 The proteins in this entry are functionally uncharacterised.; PDB: 3FOV_A.
Probab=88.61 E-value=2.4 Score=29.35 Aligned_cols=46 Identities=26% Similarity=0.175 Sum_probs=30.1
Q ss_pred HHHHHhhccCcee-EEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeEE
Q 037858 45 VANRLEELYGGTA-YVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLVS 97 (119)
Q Consensus 45 v~~~Lekl~~~ki-y~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I~ 97 (119)
++.-|++ .|+.+ =.|.|-|. +|||+|....+.+..||||=.++.-.
T Consensus 6 A~~~L~~-~G~~IL~rN~r~~~------GEIDiIa~~~~~lvfVEVK~R~~~~~ 52 (93)
T PF02021_consen 6 AARYLER-KGYRILERNWRCRR------GEIDIIARDGDTLVFVEVKTRSSSSF 52 (93)
T ss_dssp HHHHHHH-TT-EEEEEEEEETT------EEEEEEEEETTEEEEEEEEE------
T ss_pred HHHHHHH-CCCEEeeeeecCCC------CcEeEEEEEcccEEEEEEEEeecccc
Confidence 3444554 56655 56788843 59999999999999999998776544
No 25
>PRK14673 hypothetical protein; Provisional
Probab=87.35 E-value=0.61 Score=35.09 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=29.7
Q ss_pred HHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCC-eEEEEEecCCce
Q 037858 45 VANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNG-EEVVISVKNFSG 94 (119)
Q Consensus 45 v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~-~IlVIEvKNwSG 94 (119)
++.-|++ .|+.+.. |.|-| .+|||+|.--++ .+..||||--++
T Consensus 36 A~~~L~~-~Gy~IL~rN~r~~------~GEIDLIa~~~~~~lVFVEVKtR~~ 80 (137)
T PRK14673 36 ALAFLQR-AGLALVARNYRCR------GGEIDLVMRERDGTLVFVEVRARAS 80 (137)
T ss_pred HHHHHHH-CCCEEeEeEecCC------CCccCHHHccCCcEEEEEEEEeCCC
Confidence 3444443 5666654 67763 359999988766 888999996543
No 26
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=87.15 E-value=0.64 Score=34.14 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=21.6
Q ss_pred ceeeeEEEEeCCeEEEEEecCCcee
Q 037858 71 LQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 71 ~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
.+|||+|.--.+-|..||||--++.
T Consensus 32 ~GEIDlIa~~~~~ivFVEVK~R~~~ 56 (114)
T COG0792 32 YGEIDLIARDGDTVVFVEVKYRRND 56 (114)
T ss_pred CCceEEEEecCCEEEEEEEEeeccC
Confidence 3599999999999999999976654
No 27
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=85.81 E-value=1.6 Score=28.89 Aligned_cols=39 Identities=21% Similarity=0.409 Sum_probs=22.7
Q ss_pred eEEEEEecCCCCCCceeeeEEEEeCC---eEEEEEecCCceeEE
Q 037858 57 AYVGLRIPDPETRSLQNIDIVLVKNG---EEVVISVKNFSGLVS 97 (119)
Q Consensus 57 iy~gLRIPd~~~~~~~EIDlVIVT~~---~IlVIEvKNwSG~I~ 97 (119)
.|.+++.... ++...+|+++-... .-++||.|+|++.+.
T Consensus 21 g~~~v~~~~~--~~d~giDi~~~~~~~~~~~~~vqcK~~~~~v~ 62 (115)
T PF04471_consen 21 GYTDVEVTGG--SGDGGIDIIAEKDDLGKERILVQCKRYKKKVD 62 (115)
T ss_dssp T-EEEEEE-S--SSEEEEEEEEEETT---EEEEEEE---S-EE-
T ss_pred CCccEEEecc--CCCCCEEEEEEEcccCceEEEEEEEEeccccc
Confidence 3446666432 24468999988754 688999999987655
No 28
>PRK14687 hypothetical protein; Provisional
Probab=84.82 E-value=1.1 Score=35.18 Aligned_cols=46 Identities=20% Similarity=0.301 Sum_probs=29.2
Q ss_pred hhhHHHHHhhccCceeEE-EEEecCCCCCCceeeeEEEEeCC----eEEEEEecCCc
Q 037858 42 TVSVANRLEELYGGTAYV-GLRIPDPETRSLQNIDIVLVKNG----EEVVISVKNFS 93 (119)
Q Consensus 42 ~~~v~~~Lekl~~~kiy~-gLRIPd~~~~~~~EIDlVIVT~~----~IlVIEvKNwS 93 (119)
+--++.-|++ .|+.+.+ |.|-+ ..+|||+|...++ .+..||||--+
T Consensus 37 E~~Aa~~L~~-kGy~IL~RN~R~~-----r~GEIDIIA~d~~~~~~~LVFVEVKtR~ 87 (173)
T PRK14687 37 EQLACEFLQE-QGLILIARNWQQP-----KVGELDLVMLEKGQAWSTLVFAEVRQRK 87 (173)
T ss_pred HHHHHHHHHH-CCCEEeeecccCC-----CCccEEEEEecCCCCCCEEEEEEEeECC
Confidence 3334444544 4555543 56642 2359999998774 89999999544
No 29
>PF08011 DUF1703: Protein of unknown function (DUF1703); InterPro: IPR012547 This family contains many hypothetical bacterial proteins.
Probab=84.26 E-value=1.3 Score=30.72 Aligned_cols=21 Identities=29% Similarity=0.295 Sum_probs=18.9
Q ss_pred CceeeeEEEE----eCCeEEEEEec
Q 037858 70 SLQNIDIVLV----KNGEEVVISVK 90 (119)
Q Consensus 70 ~~~EIDlVIV----T~~~IlVIEvK 90 (119)
+.+-+|+++. +...++|+|+|
T Consensus 29 ~~Gr~Dl~l~~~~~~~~~~~IiElK 53 (105)
T PF08011_consen 29 GKGRIDLVLEPPKPTPKYIYIIELK 53 (105)
T ss_pred CCCeEEEEEEEccCCCCeEEEEEEE
Confidence 4457999999 99999999999
No 30
>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) [].
Probab=82.73 E-value=1.6 Score=30.10 Aligned_cols=23 Identities=26% Similarity=0.173 Sum_probs=19.8
Q ss_pred ceeeeEEEEeCCe--EEEEEecCCc
Q 037858 71 LQNIDIVLVKNGE--EVVISVKNFS 93 (119)
Q Consensus 71 ~~EIDlVIVT~~~--IlVIEvKNwS 93 (119)
..|||+|.+..++ +++.|+|--+
T Consensus 67 ~~EIDiva~~~~~~~~~~gEcKw~~ 91 (100)
T PF03008_consen 67 NEEIDIVAVDEDGKRILFGECKWTN 91 (100)
T ss_pred CccEEEEEECCCCCEEEEEEEEeCC
Confidence 3499999999999 9999999543
No 31
>PF08774 VRR_NUC: VRR-NUC domain; InterPro: IPR014883 This entry contains proteins with the VRR-NUC domain. It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI: (P40815 from SWISSPROT).; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=76.00 E-value=3.1 Score=28.20 Aligned_cols=36 Identities=22% Similarity=0.243 Sum_probs=28.4
Q ss_pred CceeeeEEEEeCCe----EEEEEecCCceeEEEcCCCCeEE
Q 037858 70 SLQNIDIVLVKNGE----EVVISVKNFSGLVSINNDGSWVC 106 (119)
Q Consensus 70 ~~~EIDlVIVT~~~----IlVIEvKNwSG~I~~~~dg~W~q 106 (119)
..+-.|++++.+.+ .++||+|.=.|+++-. +-.|+.
T Consensus 45 ~~G~PDl~~~~~~~~~~~~~~iEvK~p~~~ls~~-Q~~~~~ 84 (100)
T PF08774_consen 45 RSGFPDLILWRPRGKRDIFLFIEVKGPGDRLSPN-QKEWID 84 (100)
T ss_pred CCCCCcEEEEecCCCccEEEEEEEcCCCCCcCHH-HHHHHH
Confidence 45689999999766 8999999999998853 345654
No 32
>PF14281 PDDEXK_4: PD-(D/E)XK nuclease superfamily
Probab=62.13 E-value=10 Score=27.76 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.1
Q ss_pred CceeeeEEE-EeCCeEEEEEecCCce
Q 037858 70 SLQNIDIVL-VKNGEEVVISVKNFSG 94 (119)
Q Consensus 70 ~~~EIDlVI-VT~~~IlVIEvKNwSG 94 (119)
....||++| -..+.+++||.|=+++
T Consensus 73 ~~~riDi~i~~~~~~~iiIEnKi~a~ 98 (179)
T PF14281_consen 73 SGGRIDILIDENDKFVIIIENKIYAS 98 (179)
T ss_pred CCCCccEEEEeCCCEEEEEEEcCCCC
Confidence 345899999 8999999999997754
No 33
>PF08000 bPH_1: Bacterial PH domain; InterPro: IPR012544 This family contains many bacterial hypothetical proteins.; PDB: 3DCX_E 3HSA_C 3B77_D.
Probab=60.85 E-value=42 Score=24.69 Aligned_cols=42 Identities=14% Similarity=0.278 Sum_probs=31.3
Q ss_pred HHHHHhh--ccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 45 VANRLEE--LYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 45 v~~~Lek--l~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
+.++++. +.|..+++.++.- =|.+++|..++++++....+|+
T Consensus 19 ~~~~~~~~L~~gE~I~~ayk~i---------RD~~vFTnkRlI~vD~QG~TGk 62 (124)
T PF08000_consen 19 IQKEYEPLLLDGEEIEAAYKLI---------RDEIVFTNKRLILVDKQGITGK 62 (124)
T ss_dssp HHHHHGGGSSTT--EEEEEEES---------SEEEEEESSEEEEEEEESSSSS
T ss_pred HHHHHHHhcCCCCeeeeeehhh---------ceeEEEecChheEEecccCccc
Confidence 3444444 4566888888873 2899999999999999999987
No 34
>PHA02552 4 head completion protein; Provisional
Probab=60.25 E-value=25 Score=26.91 Aligned_cols=60 Identities=12% Similarity=0.008 Sum_probs=39.2
Q ss_pred cCCcchhhHHHHHhhccCceeEEE--EEe----cCCCCCCceeeeEEEEeCCe-EEEEEecCCceeE
Q 037858 37 SDHTVTVSVANRLEELYGGTAYVG--LRI----PDPETRSLQNIDIVLVKNGE-EVVISVKNFSGLV 96 (119)
Q Consensus 37 s~~~~~~~v~~~Lekl~~~kiy~g--LRI----Pd~~~~~~~EIDlVIVT~~~-IlVIEvKNwSG~I 96 (119)
-+|+.+...+..|+.-..-.-|+. ++| |+....++--.|+++...++ .++||||--+-.-
T Consensus 24 yeS~lE~d~~~~le~dp~V~~~~sqp~~I~Y~~~~~Gk~r~Y~PDFLV~~~dG~~~lvEVKp~~~~~ 90 (151)
T PHA02552 24 YRSSWERWFMKWLDKNPSVIKWGSEEVVIPYFSNADGKRRRYFMDFYVKVDNGQKFLIEVKPKKETQ 90 (151)
T ss_pred ECCHHHHHHHHHhhcCCCeeEEecCCEEEEEEecCCCCeeeEcCcEEEEEeCCCEEEEEEccHHHcc
Confidence 356677777777777555433432 666 43333345688998877765 9999999765443
No 35
>PF07788 DUF1626: Protein of unknown function (DUF1626); InterPro: IPR012431 This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaea. One member (Q9YCN7 from SWISSPROT) is thought to be similar to tropomyosin [].
Probab=57.69 E-value=16 Score=24.81 Aligned_cols=19 Identities=21% Similarity=0.707 Sum_probs=15.7
Q ss_pred eeeEEEEeCCeEEEEEecCC
Q 037858 73 NIDIVLVKNGEEVVISVKNF 92 (119)
Q Consensus 73 EIDlVIVT~~~IlVIEvKNw 92 (119)
|+|+ ++..+.++++|+|.-
T Consensus 4 ElDv-vikdg~~ilvEikSs 22 (70)
T PF07788_consen 4 ELDV-VIKDGKVILVEIKSS 22 (70)
T ss_pred EEEE-EEECCeEEEEEEEcc
Confidence 7887 678888999999963
No 36
>TIGR00372 cas4 CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Probab=57.69 E-value=48 Score=23.94 Aligned_cols=42 Identities=26% Similarity=0.211 Sum_probs=27.9
Q ss_pred hccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCC
Q 037858 51 ELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNF 92 (119)
Q Consensus 51 kl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNw 92 (119)
++.+......+.+-....+-.+-||+|...++++.++|.|.=
T Consensus 48 ~~~~~~~~~~v~l~~~~~~l~G~iD~i~~~~~~~~ive~Ktg 89 (178)
T TIGR00372 48 SLGGVREEKEVPLKSKKLGLKGVIDVVLEADGELVPVEVKSG 89 (178)
T ss_pred ccCCEEEEEeeEeEcccCCcEEEEEEEEEECCeEEEEEEecC
Confidence 333333444555543333445689999999999999999953
No 37
>PF09002 DUF1887: Domain of unknown function (DUF1887); InterPro: IPR015093 This entry represents a set of hypothetical bacterial and archaeal proteins. ; PDB: 1XMX_A.
Probab=57.40 E-value=20 Score=30.42 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=19.6
Q ss_pred ceeeeEEEEeCCeEEEEEecC
Q 037858 71 LQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 71 ~~EIDlVIVT~~~IlVIEvKN 91 (119)
..|+|++++..+.+++||-|-
T Consensus 289 ~NElDV~~~~~~~L~~iECKt 309 (381)
T PF09002_consen 289 KNELDVAFMKGNKLYIIECKT 309 (381)
T ss_dssp EEEEEEEEEETTEEEEEEEES
T ss_pred CcceEEEEEeCCEEEEEEcCC
Confidence 469999999999999999996
No 38
>PF11466 Doppel: Prion-like protein Doppel; InterPro: IPR021566 Dpl is a homologue related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% alpha-helical structure however in aqueous solution it consists of a random coil. The alpha helical segment can adopt a transmembrane localisation also in a membrane. The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane. ; PDB: 1Z65_A.
Probab=51.67 E-value=16 Score=21.32 Aligned_cols=21 Identities=19% Similarity=0.436 Sum_probs=14.9
Q ss_pred CCCcchhhHHHHHHHHHHHhh
Q 037858 1 MKGSLTTLCVGFLCGLVIYKI 21 (119)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (119)
|+--|.+-|++|+|=|+.--|
T Consensus 1 Mrk~Lg~~~lAi~c~LL~s~L 21 (30)
T PF11466_consen 1 MRKHLGGWWLAIVCVLLFSHL 21 (30)
T ss_dssp --SS-SSHHHHHHHHHHHHHT
T ss_pred CccchhhHHHHHHHHHHHHHh
Confidence 677888999999999876543
No 39
>PRK04247 hypothetical protein; Provisional
Probab=51.56 E-value=33 Score=28.14 Aligned_cols=26 Identities=23% Similarity=0.158 Sum_probs=21.5
Q ss_pred ceeeeEEEEeCC-eEEEEEecCCceeE
Q 037858 71 LQNIDIVLVKNG-EEVVISVKNFSGLV 96 (119)
Q Consensus 71 ~~EIDlVIVT~~-~IlVIEvKNwSG~I 96 (119)
.++||++-..++ .+.+||+|.-++..
T Consensus 159 ~G~IDila~D~~G~lViVEvKrr~~~~ 185 (238)
T PRK04247 159 AGIIDILGRDKDGNLVVLELKRRRAGL 185 (238)
T ss_pred CCceeEEEECCCCCEEEEEEEEccCCh
Confidence 359999999986 79999999876543
No 40
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=51.28 E-value=41 Score=22.92 Aligned_cols=26 Identities=31% Similarity=0.365 Sum_probs=18.2
Q ss_pred ceecCCcchhhHHHHHhhccCceeEEE
Q 037858 34 AETSDHTVTVSVANRLEELYGGTAYVG 60 (119)
Q Consensus 34 ~~~s~~~~~~~v~~~Lekl~~~kiy~g 60 (119)
+..++......++++|.++ |.++|+-
T Consensus 7 ~~~~~k~~~~~~~~~l~~~-G~~l~aT 32 (110)
T cd01424 7 VADRDKPEAVEIAKRLAEL-GFKLVAT 32 (110)
T ss_pred EEcCcHhHHHHHHHHHHHC-CCEEEEc
Confidence 3344556677888888887 7788773
No 41
>PHA00159 endonuclease I
Probab=50.40 E-value=31 Score=26.66 Aligned_cols=49 Identities=18% Similarity=0.126 Sum_probs=34.6
Q ss_pred cCCcchhhHHHHHhhccCceeEEEEEecC----CCCCCceeeeEEEEeCCeEEEEEec
Q 037858 37 SDHTVTVSVANRLEELYGGTAYVGLRIPD----PETRSLQNIDIVLVKNGEEVVISVK 90 (119)
Q Consensus 37 s~~~~~~~v~~~Lekl~~~kiy~gLRIPd----~~~~~~~EIDlVIVT~~~IlVIEvK 90 (119)
=+|+.+-.+|++|++..=..=|.+..+|= ..+ .--.|.+ -++||+ ||+|
T Consensus 15 fRSgLE~k~ak~Le~~gv~~~yE~~ki~y~~pA~~~--~YTPDF~--LpnGii-iEvK 67 (148)
T PHA00159 15 FRSGLEDKVSKQLEKKGVKFDYELWKIPYVIPASDH--KYTPDFL--LPNGII-IETK 67 (148)
T ss_pred ccchHHHHHHHHHHhcCCCeEeeeeeeeeeccCCCC--eeCCcee--cCCCCE-EEec
Confidence 35888899999999976566677755443 333 2367887 446888 9999
No 42
>PF10926 DUF2800: Protein of unknown function (DUF2800); InterPro: IPR021229 This entry is represented by Bacteriophage APSE-1, protein 51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins.
Probab=49.87 E-value=24 Score=30.42 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=23.5
Q ss_pred eeeEEEEeCCeEEEEEecCCce-eEEEc
Q 037858 73 NIDIVLVKNGEEVVISVKNFSG-LVSIN 99 (119)
Q Consensus 73 EIDlVIVT~~~IlVIEvKNwSG-~I~~~ 99 (119)
--|+||++.+.+.||++|+=.| .|+..
T Consensus 117 T~D~vii~~~~L~IiDlKyG~GV~V~Ae 144 (372)
T PF10926_consen 117 TADCVIIADDTLHIIDLKYGKGVPVSAE 144 (372)
T ss_pred ceeEEEEeCCeEEEEECCCCCCCcccCC
Confidence 6799999999999999999999 45553
No 43
>PF06319 DUF1052: Protein of unknown function (DUF1052); InterPro: IPR009394 This entry is represented by Ralstonia phage RSL1, Orf212. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of unknown function.; PDB: 3DNX_A.
Probab=49.65 E-value=28 Score=27.10 Aligned_cols=51 Identities=12% Similarity=0.238 Sum_probs=24.5
Q ss_pred CcchhhHHHHHhhccCc---eeEEEEEecCCCCCCceeeeEEEEeCCe-EEEEEecCCce
Q 037858 39 HTVTVSVANRLEELYGG---TAYVGLRIPDPETRSLQNIDIVLVKNGE-EVVISVKNFSG 94 (119)
Q Consensus 39 ~~~~~~v~~~Lekl~~~---kiy~gLRIPd~~~~~~~EIDlVIVT~~~-IlVIEvKNwSG 94 (119)
|..-..|++-...+... -+..-+-+|. + +-.|++-+++++ |.+||+|-=.-
T Consensus 18 ~~~a~~v~RGv~R~l~~~g~~~l~E~~L~~----G-RRaDv~al~~kGeI~ivEIKSs~~ 72 (157)
T PF06319_consen 18 SETALAVARGVCRLLRSLGFACLPEVPLPN----G-RRADVMALGPKGEIWIVEIKSSRA 72 (157)
T ss_dssp ------HHHHHHHHHHHTT-EEEEEE-SST----T---EEEEEE-TT--EEEEEE-SSHH
T ss_pred hhHHHHHHHHHHHHHHHCCCeEEEEecCCC----C-CeEEEEEECCCCeEEEEEEEcCHH
Confidence 44444555555554444 3344455542 2 379999999965 99999994333
No 44
>PF14082 DUF4263: Domain of unknown function (DUF4263)
Probab=47.86 E-value=33 Score=25.21 Aligned_cols=37 Identities=8% Similarity=0.060 Sum_probs=28.4
Q ss_pred ecCCCCCCceeeeEEEEeCCeEE--EEEecCCceeEEEc
Q 037858 63 IPDPETRSLQNIDIVLVKNGEEV--VISVKNFSGLVSIN 99 (119)
Q Consensus 63 IPd~~~~~~~EIDlVIVT~~~Il--VIEvKNwSG~I~~~ 99 (119)
.|.-..++...+|.++++.+.-. +||+|.=+..|...
T Consensus 36 ~~~~~~~~~~~~Dfl~~~~~~~~~~lVEiK~p~~~l~~~ 74 (164)
T PF14082_consen 36 FSEFPGGGDYIPDFLLARGDSDNDVLVEIKRPNTNLFTK 74 (164)
T ss_pred cCCccCCCCCeeeEEEEeCCCCceEEEEEeCCCchhhhh
Confidence 34444455679999999998877 99999888777654
No 45
>PF13588 HSDR_N_2: Type I restriction enzyme R protein N terminus (HSDR_N); PDB: 3H1T_A.
Probab=45.19 E-value=21 Score=24.29 Aligned_cols=47 Identities=23% Similarity=0.174 Sum_probs=20.7
Q ss_pred HHHhhccCc---eeEEEEEecCCCCCCceeeeEEEEeCC----eEEEEEecCCcee
Q 037858 47 NRLEELYGG---TAYVGLRIPDPETRSLQNIDIVLVKNG----EEVVISVKNFSGL 95 (119)
Q Consensus 47 ~~Lekl~~~---kiy~gLRIPd~~~~~~~EIDlVIVT~~----~IlVIEvKNwSG~ 95 (119)
+.|-+..|+ .+.....++-. +.+..+|+++.... -+++||.|.-+-.
T Consensus 11 ~~L~~~lGy~~~~i~~e~~i~~~--~~~~r~Divv~~~~~~~~p~~iIE~K~~~~~ 64 (112)
T PF13588_consen 11 KPLLEELGYPKEDIEVEVPISIG--SKKKRADIVVFRDDKDNKPLIIIECKAPSVS 64 (112)
T ss_dssp -------------EEEETTE-EE------EEEEEEEEET--TEEEEEEEE--TTS-
T ss_pred cccccccccchhhEEEEEEEEEC--CCCeeeEEEEEeCCCCCCeEEEEEECCCCCC
Confidence 344444443 34444444322 33457999999888 7899999976544
No 46
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=44.07 E-value=24 Score=20.81 Aligned_cols=21 Identities=24% Similarity=0.177 Sum_probs=14.9
Q ss_pred CCceeeeEEEEeCCeEEEEEecC
Q 037858 69 RSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 69 ~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
.....+|+++. ..-++||+|-
T Consensus 26 ~~~~~pDf~~~--~~~~~ie~kg 46 (80)
T cd01037 26 IGSYIPDFVCP--SAKLVIELKG 46 (80)
T ss_pred CCCCccCEEcc--CCCEEEEEEC
Confidence 34558898887 5566788883
No 47
>PF04556 DpnII: DpnII restriction endonuclease; InterPro: IPR007637 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry is found in type II restriction enzymes such as DpmII (3.1.21.4 from EC), which recognises the double-stranded unmethylated sequence GATC and cleave before G-1 [], where it encompasess the full length of the protein. It is also found in a number of proteins of unknown function, where it is located adjacent to a DNA adenine-specific methyltransferase domain (IPR012327 from INTERPRO).; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=42.55 E-value=30 Score=29.09 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=22.3
Q ss_pred CCceeeeEEEEeCCeEEEEEecCCce
Q 037858 69 RSLQNIDIVLVKNGEEVVISVKNFSG 94 (119)
Q Consensus 69 ~~~~EIDlVIVT~~~IlVIEvKNwSG 94 (119)
...+.+|.||-|++.+++||+.-++|
T Consensus 193 k~~KrFDFvi~~~~k~y~IE~NFY~~ 218 (286)
T PF04556_consen 193 KSEKRFDFVIKTNKKIYLIETNFYGS 218 (286)
T ss_pred CCceEEEEEEEcCCEEEEEEEeeecC
Confidence 34568999999999999999987765
No 48
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=40.50 E-value=45 Score=24.05 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=25.1
Q ss_pred EEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 59 VGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 59 ~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
..+.+ +. .+.+|+|......+.++|+|.-+..
T Consensus 47 ~~v~v-s~----~G~iD~v~~~~~~~~~~E~K~~~~~ 78 (162)
T PF01930_consen 47 REVPV-SE----SGKIDIVEKGGGEIIPVEIKSGRKP 78 (162)
T ss_pred eeecc-CC----cEEEEEEEEeCCEEEEEEEecCCCC
Confidence 55666 33 5699999999999999999965443
No 49
>PRK14758 hypothetical protein; Provisional
Probab=40.45 E-value=21 Score=20.32 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=9.4
Q ss_pred HHHHHHHHHHhh
Q 037858 10 VGFLCGLVIYKI 21 (119)
Q Consensus 10 ~~~~~~~~~~~~ 21 (119)
+-|+||+++-+.
T Consensus 13 vlIlCalia~~f 24 (27)
T PRK14758 13 ILILCALIAARF 24 (27)
T ss_pred HHHHHHHHHHHh
Confidence 568999998764
No 50
>CHL00105 psaJ photosystem I subunit IX
Probab=39.38 E-value=29 Score=21.57 Aligned_cols=22 Identities=50% Similarity=0.789 Sum_probs=17.4
Q ss_pred chhhHHHHHHHHHHHhhhhhhccC
Q 037858 5 LTTLCVGFLCGLVIYKIFKRIADD 28 (119)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~d 28 (119)
+.+.|.-+..|++| -+.|||-|
T Consensus 14 la~~w~~~tag~lI--EiNRffPD 35 (42)
T CHL00105 14 LSTLWFGFLAGLLI--EINRFFPD 35 (42)
T ss_pred HHHHHHHHHHHHHH--HHHHhCCh
Confidence 56899999999987 46777765
No 51
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=38.70 E-value=55 Score=26.07 Aligned_cols=61 Identities=20% Similarity=0.151 Sum_probs=35.0
Q ss_pred CceecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858 29 DVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 29 d~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
+...-|+++-....+.-+-+-..+.+...|..++= -...+.+ -||+.+-++.+=..||||+
T Consensus 63 ~~~V~int~~~N~lv~~~l~~~~i~~l~~~~~i~r-Ev~~g~s-R~Dfll~~~~~~~~vEVKs 123 (215)
T PF03749_consen 63 GVWVGINTQLPNRLVEEALENGLIPELSGYSEIRR-EVKYGNS-RFDFLLEDNGGKCYVEVKS 123 (215)
T ss_pred CeEEEEccchHHHHHHHHHHcCCCccccCcceEee-ceeeCCc-cEEEEEEcCCCCEEEEEee
Confidence 44555666555555544443223333344444432 1112222 3999999998899999997
No 52
>PRK02733 photosystem I reaction center subunit IX; Provisional
Probab=38.32 E-value=30 Score=21.52 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=17.3
Q ss_pred chhhHHHHHHHHHHHhhhhhhccC
Q 037858 5 LTTLCVGFLCGLVIYKIFKRIADD 28 (119)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~d 28 (119)
+.+.|.-+..|++| -+.|||-|
T Consensus 14 la~~w~~~tag~lI--EiNRffPD 35 (42)
T PRK02733 14 VAAIWLTLTAGILI--EFNRFFPD 35 (42)
T ss_pred HHHHHHHHHHHHHH--HHHHhCch
Confidence 56899999999987 46677765
No 53
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=38.05 E-value=44 Score=22.08 Aligned_cols=51 Identities=22% Similarity=0.254 Sum_probs=26.5
Q ss_pred ceecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCC----eEEEEEecC
Q 037858 30 VVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNG----EEVVISVKN 91 (119)
Q Consensus 30 ~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~----~IlVIEvKN 91 (119)
+|.++..- ...+..+..+.+..+.+ -.+| .-.-.|+++..++ ...++|+|.
T Consensus 2 ~V~~i~eQ--Pl~~~~~~~~g~~~~~~----~~~~-----~~yTpDFlv~~~~g~~~~~~~ieVK~ 56 (88)
T PF08722_consen 2 DVVDIREQ--PLTIEIADELGKKHPYY----TGVP-----IVYTPDFLVTYRDGNGKKPVAIEVKP 56 (88)
T ss_dssp TEEEEEEE--E-HHHHHHHHT----EE----TTEE--------EEEEEEEESSS--SSEEEEEE--
T ss_pred CEEEEECC--CCeeEhhHhcCCCCCCC----CCCc-----cEEeccEEEEEccCCcceEEEEEEcc
Confidence 44444443 34555665555443322 1222 1247899999999 899999996
No 54
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=35.87 E-value=41 Score=31.67 Aligned_cols=24 Identities=17% Similarity=0.397 Sum_probs=21.5
Q ss_pred CceeeeEEEEeCCeEEEEEecCCc
Q 037858 70 SLQNIDIVLVKNGEEVVISVKNFS 93 (119)
Q Consensus 70 ~~~EIDlVIVT~~~IlVIEvKNwS 93 (119)
+..-+|++.+..+-+++||+|++.
T Consensus 60 ~~~~~d~~~~~~~~~~~~e~kd~~ 83 (699)
T PRK14535 60 GSSGVDIIALHESTLWLIEIKDYY 83 (699)
T ss_pred CcceeeEEEEcCCcEEEEEechhh
Confidence 345899999999999999999997
No 55
>cd05563 PTS_IIB_ascorbate PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal to the IIA (SgaT) domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include ascorbate, chitobiose/lichenan, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=35.49 E-value=65 Score=20.78 Aligned_cols=43 Identities=9% Similarity=0.113 Sum_probs=24.6
Q ss_pred cCCcchhhHHHHHhhccCcee----EEEEEecCCCCCCceeeeEEEEeCC
Q 037858 37 SDHTVTVSVANRLEELYGGTA----YVGLRIPDPETRSLQNIDIVLVKNG 82 (119)
Q Consensus 37 s~~~~~~~v~~~Lekl~~~ki----y~gLRIPd~~~~~~~EIDlVIVT~~ 82 (119)
++-+-..-++++|++.++... +....+.. ....++|+++-|..
T Consensus 8 ~G~~tS~ll~~kl~~~f~~~~i~~~~~~~~~~~---~~~~~~DlIisT~~ 54 (86)
T cd05563 8 SGLGSSLMLKMNVEKVLKELGIEAEVEHTDLGS---AKASSADIIVTSKD 54 (86)
T ss_pred CCccHHHHHHHHHHHHHHHCCCcEEEEEecccc---cCCCCCCEEEEchh
Confidence 334445556788999886432 22233321 12358998888875
No 56
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=35.20 E-value=26 Score=27.58 Aligned_cols=20 Identities=15% Similarity=0.110 Sum_probs=17.1
Q ss_pred HHHHHHHHhhhhhhccCCce
Q 037858 12 FLCGLVIYKIFKRIADDDVV 31 (119)
Q Consensus 12 ~~~~~~~~~~~~~~~~dd~~ 31 (119)
.+.+.+.||++|+.|...++
T Consensus 7 ~lad~i~~ki~rl~l~~~~~ 26 (247)
T PF11817_consen 7 TLADFIAFKICRLYLWLNQP 26 (247)
T ss_pred HHHHhHHHHHHHHHHhCCCH
Confidence 48899999999999996553
No 57
>KOG4771 consensus Nucleolar protein (NOP16) involved in 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=34.55 E-value=22 Score=28.62 Aligned_cols=26 Identities=31% Similarity=0.349 Sum_probs=23.7
Q ss_pred CceecceecCCcchhhHHHHHhhccC
Q 037858 29 DVVSDAETSDHTVTVSVANRLEELYG 54 (119)
Q Consensus 29 d~~~~~~~s~~~~~~~v~~~Lekl~~ 54 (119)
|||++.|.++.++.++|.++||..-.
T Consensus 121 DDV~~~e~~~~~~kTevvkqlee~as 146 (210)
T KOG4771|consen 121 DDVSGSELEEDDLKTEVVKQLEEGAS 146 (210)
T ss_pred ccccccccccChHHHHHHHHHHhhcc
Confidence 69999999999999999999998644
No 58
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=33.86 E-value=98 Score=21.47 Aligned_cols=48 Identities=19% Similarity=0.383 Sum_probs=34.2
Q ss_pred eecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCC
Q 037858 31 VSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNG 82 (119)
Q Consensus 31 ~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~ 82 (119)
...++.-|++.+=.+..+|-+ .+.=.|+|.++|+|-. .++=+-|-|.+
T Consensus 20 ~~~i~~EdHTLgNlLr~~L~~-~~~V~fagY~vpHPl~---~~~~l~i~t~~ 67 (93)
T cd06926 20 TFTINKEDHTLGNLLRMQLLK-DPNVLFAGYKVPHPLE---HKIELRIQTDG 67 (93)
T ss_pred EEEEeCCCchHHHHHHHHHhc-CCCeeEEeeccCCCCC---CceEEEEEeCC
Confidence 455777888888889999988 4456699999999842 24545554443
No 59
>PF14986 DUF4514: Domain of unknown function (DUF4514)
Probab=33.39 E-value=45 Score=22.11 Aligned_cols=30 Identities=27% Similarity=0.355 Sum_probs=23.1
Q ss_pred hhHHHHHHHHHHHhh--hhhhccCCceeccee
Q 037858 7 TLCVGFLCGLVIYKI--FKRIADDDVVSDAET 36 (119)
Q Consensus 7 ~~~~~~~~~~~~~~~--~~~~~~dd~~~~~~~ 36 (119)
.+=+.|-.|.++.|+ +|+-.+|+|-.|+.+
T Consensus 28 alGvaisAgFLaLKicmIrkhlfD~dssdlrs 59 (61)
T PF14986_consen 28 ALGVAISAGFLALKICMIRKHLFDNDSSDLRS 59 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCchhhhcc
Confidence 345678889999887 577888888888765
No 60
>PF02655 ATP-grasp_3: ATP-grasp domain; InterPro: IPR003806 The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyze the formation of amide bonds, catalyzing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule []. This fold is found in many different enzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes []. This entry describes a type of ATP-grasp fold that is found in a set of proteins of unknown function.; GO: 0005524 ATP binding, 0046872 metal ion binding; PDB: 3DF7_A.
Probab=31.20 E-value=78 Score=23.07 Aligned_cols=39 Identities=28% Similarity=0.530 Sum_probs=22.4
Q ss_pred CcchhhHHHHHhhcc-CceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858 39 HTVTVSVANRLEELY-GGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 39 ~~~~~~v~~~Lekl~-~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
+.....++.++-+.. |-.+|. -||+| ++.++++|||+.-
T Consensus 117 ~~~~~~~~~~i~~~l~gl~G~~-------------giD~I-~~~~~~~viEINP 156 (161)
T PF02655_consen 117 KEEIIELARRIAEALPGLRGYV-------------GIDFI-LDDGGPYVIEINP 156 (161)
T ss_dssp HHHHHHHHHHHHTTSTT--EEE-------------EEEEE-ESS-SEEEEEEES
T ss_pred HHHHHHHHHHHHHHcCCCeeeE-------------eEEEE-EeCCcEEEEEEcC
Confidence 444555666665554 334454 45665 5668999999863
No 61
>PF14899 DUF4492: Domain of unknown function (DUF4492)
Probab=30.97 E-value=67 Score=21.59 Aligned_cols=45 Identities=20% Similarity=0.236 Sum_probs=31.3
Q ss_pred hhhHHHHHHHHHH-HhhhhhhccCCceecceecCCcchhhHHHHHhh
Q 037858 6 TTLCVGFLCGLVI-YKIFKRIADDDVVSDAETSDHTVTVSVANRLEE 51 (119)
Q Consensus 6 ~~~~~~~~~~~~~-~~~~~~~~~dd~~~~~~~s~~~~~~~v~~~Lek 51 (119)
.|+|.=|++=|.+ .-++|-||+++-+... .++.+..==|.++|-|
T Consensus 19 ktLW~IIliKLfImF~vLK~FfFp~~l~~~-~~~~~k~~~V~~~L~k 64 (64)
T PF14899_consen 19 KTLWLIILIKLFIMFAVLKLFFFPNFLNTK-KTDEEKSDFVSKELIK 64 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCcchhccC-CCchHHHHHHHHHhcC
Confidence 4889999988755 5566777788776666 6666665566666643
No 62
>PF04313 HSDR_N: Type I restriction enzyme R protein N terminus (HSDR_N); InterPro: IPR007409 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the N-terminal domain found in both the R subunit (HsdR) of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoRI, which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity [, , ]. This domain is often found adjacent to a methylase domain (IPR002052 from INTERPRO) in restriction endonucleases or methylases. In one of the proteins, Q97RD0 from SWISSPROT, it is adjacent to a helicase domain (IPR011545 from INTERPRO) in a putative restriction endonuclease.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0006304 DNA modification; PDB: 2Y3T_B 2W74_B 2W00_B.
Probab=30.49 E-value=69 Score=23.97 Aligned_cols=23 Identities=35% Similarity=0.384 Sum_probs=14.1
Q ss_pred CceeeeEEEEeCCe-EEEEEecCC
Q 037858 70 SLQNIDIVLVKNGE-EVVISVKNF 92 (119)
Q Consensus 70 ~~~EIDlVIVT~~~-IlVIEvKNw 92 (119)
..+.+|+|+.-.+- +.+||+|+-
T Consensus 120 ~~~r~D~vLfvNGlPl~~iE~K~~ 143 (194)
T PF04313_consen 120 DKRRPDIVLFVNGLPLAIIELKSP 143 (194)
T ss_dssp ----EEEEEEETTEEEEEEEE--T
T ss_pred cCCcceEEEEECCeEEEEEEecCC
Confidence 44689999987654 788999997
No 63
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=29.66 E-value=27 Score=27.05 Aligned_cols=52 Identities=25% Similarity=0.266 Sum_probs=28.8
Q ss_pred cCCcchhhHHHHHhhccCceeEEEEEecCCC--CCCceeeeEEEEeCCeEEEEEecC
Q 037858 37 SDHTVTVSVANRLEELYGGTAYVGLRIPDPE--TRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 37 s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~--~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
=+|+.+=.||++|+++--..-|...+||=.. ....-..|.++ +++ ++||.|-
T Consensus 15 yRSgLEekva~~L~~~gv~~~yE~~ki~Yvipa~~h~YtPDF~L--png-iiiEtKG 68 (149)
T PF05367_consen 15 YRSGLEEKVAKQLEKLGVKYEYESWKIPYVIPASEHKYTPDFVL--PNG-IIIETKG 68 (149)
T ss_dssp ---HHHHHHHHHHHHTT---EES-EEEEEEEEEEEEEE--SEE---TTS-EEEEEES
T ss_pred cchhHHHHHHHHHHHcCCCceeeeeeeeeEeeccccccCCCEEc--cCc-eEEEeee
Confidence 3578888999999998554667666655322 12334789888 567 5589883
No 64
>cd00251 Mth_Ecto The ectodomain of Methuselah (Mth); Mth mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage; The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family; Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site.
Probab=29.22 E-value=56 Score=25.37 Aligned_cols=40 Identities=25% Similarity=0.451 Sum_probs=28.0
Q ss_pred cCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCceeE
Q 037858 53 YGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGLV 96 (119)
Q Consensus 53 ~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~I 96 (119)
.|...|.|+.||..- -+++|..++....-.-++ ||.+|-|
T Consensus 17 ngSy~y~gv~iP~~l---~~~ydy~~~~dg~~~~v~-~hlRgCv 56 (176)
T cd00251 17 NGSYLYEGIIIPAHL---TGEYDYVILPDGSREPVP-EHLRGCV 56 (176)
T ss_pred CCCEEECCEEEChHH---eEEEEEEEecCCcEEEcc-ccceeEe
Confidence 667999999999653 259999998633332233 7888854
No 65
>PF12705 PDDEXK_1: PD-(D/E)XK nuclease superfamily; PDB: 1W36_B 3K70_B 3U4Q_A 3U44_A.
Probab=27.79 E-value=74 Score=22.82 Aligned_cols=24 Identities=21% Similarity=0.148 Sum_probs=20.4
Q ss_pred CceeeeEEEEe-CCeEEEEEecCCc
Q 037858 70 SLQNIDIVLVK-NGEEVVISVKNFS 93 (119)
Q Consensus 70 ~~~EIDlVIVT-~~~IlVIEvKNwS 93 (119)
-++.||.|... .+++.||+.|--+
T Consensus 131 l~G~iD~i~~~~~g~~~IvDyKt~~ 155 (257)
T PF12705_consen 131 LRGRIDRIDRDKDGRVRIVDYKTGS 155 (257)
T ss_dssp EEEEEEEEEECESSTEEEEEEESSS
T ss_pred EEEEEeEEEEeCCCcEEEEEEcCCC
Confidence 45699999999 8899999999543
No 66
>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []. However, it seems likely that these proteins act as aspartic peptidases.
Probab=26.44 E-value=26 Score=25.58 Aligned_cols=61 Identities=21% Similarity=0.340 Sum_probs=35.0
Q ss_pred ceeEEEEEecCCCCCCceeeeEEEEeCCeEEEE---EecCCc-eeEEEcCCCCeEEecCCcCCCC
Q 037858 55 GTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVI---SVKNFS-GLVSINNDGSWVCMGEAVHPNP 115 (119)
Q Consensus 55 ~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVI---EvKNwS-G~I~~~~dg~W~q~~~~~~~nP 115 (119)
|..+.+|.+.|+.-....+||++|=....--++ ..|.-. |-+-.+-.-=|+-.++....+|
T Consensus 97 ~~~~~~l~lad~~f~~~~~iDiLIG~D~~~~ll~~~~i~~~~~~~~a~~T~~GWiisG~~~~~~~ 161 (164)
T PF05585_consen 97 WKHLNNLPLADPNFRESSPIDILIGADYFWQLLTGGQIKRLPGGPTAQETKFGWIISGKASEQKP 161 (164)
T ss_pred HhhhcCCccccccccCCCCCeEEEccchHHHHhCCceEecCCCCCEEEeCCeEeEEeCccCCccC
Confidence 566788999886666778999998665533222 134333 3233222346777655443333
No 67
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=25.98 E-value=52 Score=28.84 Aligned_cols=41 Identities=22% Similarity=0.346 Sum_probs=28.5
Q ss_pred HHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCC
Q 037858 46 ANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNF 92 (119)
Q Consensus 46 ~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNw 92 (119)
+.-+.+.+++. +..+- +.+|-.||+-++-..+=||+|+||-
T Consensus 192 ~~~v~~~~~~~---~~~Fh---~aGREDvDvRMLG~GRPFvlEi~~P 232 (388)
T TIGR01213 192 ASPFLKATGGT---DAYFH---GAGREDVDVRMLGTGRPFVLEVKEP 232 (388)
T ss_pred HHHHHHHhCCc---eeEEe---ccCccccceeeccCCCceEEEecCC
Confidence 33455566653 22231 2366799999999999999999954
No 68
>COG4998 Predicted endonuclease (RecB family) [DNA replication, recombination, and repair]
Probab=25.89 E-value=1.6e+02 Score=23.69 Aligned_cols=46 Identities=26% Similarity=0.260 Sum_probs=32.4
Q ss_pred HHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC
Q 037858 45 VANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN 91 (119)
Q Consensus 45 v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN 91 (119)
+|+-|.|.--.-+=.|+++-+.+- --.|||+|-.....=|-||+|-
T Consensus 9 aasiLrkeGfevvArn~~ve~egv-eVgEiDIVAek~GerYavEVKA 54 (209)
T COG4998 9 AASILRKEGFEVVARNMPVEDEGV-EVGEIDIVAEKGGERYAVEVKA 54 (209)
T ss_pred HHHHHHhcCcEEEeecceeecCCe-EEEEEEEEEecCCcEEEEEEec
Confidence 456666653334455666754432 4569999999999999999994
No 69
>COG3788 Uncharacterized relative of glutathione S-transferase, MAPEG superfamily [General function prediction only]
Probab=24.68 E-value=60 Score=24.64 Aligned_cols=22 Identities=27% Similarity=0.329 Sum_probs=19.2
Q ss_pred CCCcchhhHHHHHHHHHHHhhh
Q 037858 1 MKGSLTTLCVGFLCGLVIYKIF 22 (119)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~ 22 (119)
|||-.+|.|+-+.|++.++--|
T Consensus 2 ~kgmvstlyavl~~llll~LS~ 23 (131)
T COG3788 2 MKGMVSALYAVLNALLLLKLSF 23 (131)
T ss_pred ccchHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999887544
No 70
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=24.58 E-value=62 Score=28.96 Aligned_cols=42 Identities=19% Similarity=0.318 Sum_probs=34.1
Q ss_pred HhhhhhhccCCceecceecCCcchhhHHHHHhhccCceeEEE
Q 037858 19 YKIFKRIADDDVVSDAETSDHTVTVSVANRLEELYGGTAYVG 60 (119)
Q Consensus 19 ~~~~~~~~~dd~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~g 60 (119)
-|+|+||+-=|+--.=.--+++.++++|+.+=+..|+.+++.
T Consensus 392 ~~iFdrfyRvdkARsR~~gGTGLGLaIakeiV~~hgG~iWA~ 433 (459)
T COG5002 392 EKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAE 433 (459)
T ss_pred HHHHHHHhhhhhhhhhcCCCCchhHHHHHHHHHHhCCeEEEe
Confidence 489999998555444455669999999999999999999875
No 71
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=24.55 E-value=1.5e+02 Score=17.90 Aligned_cols=52 Identities=17% Similarity=0.330 Sum_probs=27.9
Q ss_pred cchhhHHHHHhhccCc-eeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecC--CceeEEEcCCCCeE
Q 037858 40 TVTVSVANRLEELYGG-TAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKN--FSGLVSINNDGSWV 105 (119)
Q Consensus 40 ~~~~~v~~~Lekl~~~-kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKN--wSG~I~~~~dg~W~ 105 (119)
..--.|.+-+++-|++ ++- +++..--.....|-||+++ -.-.|.++.+|+|+
T Consensus 7 ~lP~~v~~~i~~~yp~~~i~--------------~v~~~~~~~~~~Y~v~l~~~~~~~~v~fd~~G~~l 61 (61)
T PF11396_consen 7 ELPAAVKNAIKKNYPGAKIK--------------EVEKETDPGGKYYEVELKKGGNEYEVYFDANGNWL 61 (61)
T ss_dssp GS-HHHHHHHHHHSTTSEEE--------------EEEEEEETTEEEEEEEETETTTSEEEEEETTS-EE
T ss_pred HCCHHHHHHHHHHCCCCeEE--------------EEEEEEcCCCCEEEEEEEEeCCeEEEEEcCCCCCC
Confidence 3334566666666554 322 2333332233678888882 12238888899986
No 72
>PF01939 DUF91: Protein of unknown function DUF91; InterPro: IPR002793 The function of these prokaryotic proteins is unknown. Computational analysis suggests that they may form a restriction endonuclease-like fold, similar to that found in a variety of endonucleases and DNA repair enzymes [].; PDB: 2VLD_A.
Probab=24.34 E-value=1.8e+02 Score=23.63 Aligned_cols=23 Identities=30% Similarity=0.322 Sum_probs=17.0
Q ss_pred eeeeEEEEeCCe-EEEEEecCCce
Q 037858 72 QNIDIVLVKNGE-EVVISVKNFSG 94 (119)
Q Consensus 72 ~EIDlVIVT~~~-IlVIEvKNwSG 94 (119)
+-||++-..+++ .+|||+|.-.+
T Consensus 136 G~IDiL~~D~~G~~VVIElKR~~a 159 (228)
T PF01939_consen 136 GRIDILAKDKDGNLVVIELKRRRA 159 (228)
T ss_dssp EEEEEEEE-TTS-EEEEEE-SS-B
T ss_pred CceeEEEECCCCCEEEEEEEeccC
Confidence 479999999866 88999998744
No 73
>PF08443 RimK: RimK-like ATP-grasp domain; InterPro: IPR013651 This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK []. It has an unusual nucleotide-binding fold referred to as palmate, or ATP-grasp fold. This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis.; PDB: 1UC8_B 1UC9_A.
Probab=24.06 E-value=1.1e+02 Score=22.87 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=17.3
Q ss_pred eeeeEEEEeCCeEEEEEecCCcee
Q 037858 72 QNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 72 ~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
.-|| ++-+.++-+|+|+....|+
T Consensus 149 ~giD-i~~~~~~~~v~EvN~~~~~ 171 (190)
T PF08443_consen 149 AGID-ILDTNDGPYVLEVNPNPGF 171 (190)
T ss_dssp EEEE-EEEETTEEEEEEEETT---
T ss_pred EEEE-EEecCCCeEEEEecCCchH
Confidence 3699 6789999999999987765
No 74
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=23.90 E-value=1.7e+02 Score=19.94 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=32.5
Q ss_pred eecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCC
Q 037858 31 VSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNG 82 (119)
Q Consensus 31 ~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~ 82 (119)
...++.-|++.+=.++..|-+ .+.=.|+|.++|+|-. ..+-+-|-|.+
T Consensus 12 ~~~i~~EdHTLgNlLr~~L~~-~p~V~fagY~vpHPl~---~~~~lriqT~~ 59 (85)
T cd07029 12 TFVFYGEDHTLGNSLRYVIMK-NPEVEFCGYSIPHPSE---NKINLRIQTKG 59 (85)
T ss_pred EEEEeCCCcchHHHHHHHHhh-CCCceEEeecccCCCC---CccEEEEEeCC
Confidence 344566678888788888877 4455699999999843 24555555544
No 75
>KOG2364 consensus Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=23.87 E-value=65 Score=28.69 Aligned_cols=45 Identities=16% Similarity=0.374 Sum_probs=32.3
Q ss_pred HHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCCeEEEEEecCCcee
Q 037858 45 VANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNGEEVVISVKNFSGL 95 (119)
Q Consensus 45 v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~IlVIEvKNwSG~ 95 (119)
+-+.|++-|+.+- +++- +.+|-++|+=++-+++=+|+|+||-.-.
T Consensus 240 i~dhl~~~F~a~d---~~F~---sSGREDvDVRmLG~GRPFvlEl~N~rr~ 284 (433)
T KOG2364|consen 240 IKDHLKEFFSADD---VVFI---SSGREDVDVRMLGTGRPFVLELKNPRRN 284 (433)
T ss_pred HHHHHHhhcCccc---eeec---cCCCcceeeEeccCCCceEEEcCCcccc
Confidence 4556666776643 2221 2366799999999999999999997543
No 76
>PF08393 DHC_N2: Dynein heavy chain, N-terminal region 2; InterPro: IPR013602 Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, where each heavy chain consists of a C-terminal globular head, a flexible microtubule-binding stalk, and a flexible N-terminal tail known as the cargo-binding domain []. The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains. This entry represents a region found C-terminal to the dynein heavy chain N-terminal region 1 (IPR013594 from INTERPRO) in many members of this family. No functions seem to have been attributed specifically to this region. ; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=23.61 E-value=19 Score=29.79 Aligned_cols=41 Identities=17% Similarity=0.257 Sum_probs=28.8
Q ss_pred hhhhhhcc--CCceecceecCCcchhhHHHHHhhccCceeEEEEEe
Q 037858 20 KIFKRIAD--DDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRI 63 (119)
Q Consensus 20 ~~~~~~~~--dd~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRI 63 (119)
..|=|||+ |||+++|-+..+ .-..+..-|.|+|++ ...+.+
T Consensus 309 ~~FPRfyFlsd~eLl~ils~~~-~~~~i~~~l~k~F~~--i~~l~~ 351 (408)
T PF08393_consen 309 EAFPRFYFLSDDELLEILSQSK-DPEQIQPHLKKCFPG--IKSLEF 351 (408)
T ss_dssp HHSCCHHHC-HHHHHHHHHTTT-TCHHHHHHHHHCCSS--EEEEEE
T ss_pred hhccceeecCcHHHHHHHHcCC-ChHHHHHHHHHHHHH--HHHHHh
Confidence 35656666 899999987654 356788899999875 334455
No 77
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=22.84 E-value=2e+02 Score=19.56 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=32.6
Q ss_pred eecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeCC
Q 037858 31 VSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKNG 82 (119)
Q Consensus 31 ~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~~ 82 (119)
...++.-|++.+=.+..+|-+- +.=.|||.++|+|-. .++=+.|=|..
T Consensus 14 ~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~vpHPl~---~~~~lrIqt~~ 61 (85)
T PRK01146 14 ELEIEGEDHTLMNLLKEELLED-PGVEAASYDIDHPLI---SNPVLKIKTDG 61 (85)
T ss_pred EEEEeCCCchHHHHHHHHHhcC-CCeeEEEeecCCCCC---CccEEEEEECC
Confidence 4456677788888888888763 344589999999842 25555555543
No 78
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=22.26 E-value=70 Score=28.33 Aligned_cols=23 Identities=22% Similarity=0.460 Sum_probs=21.3
Q ss_pred CceeeeEEEEeCCeEEEEEecCC
Q 037858 70 SLQNIDIVLVKNGEEVVISVKNF 92 (119)
Q Consensus 70 ~~~EIDlVIVT~~~IlVIEvKNw 92 (119)
+|-.+|+-|+-..+=+|+|+|+-
T Consensus 216 GREDvDvRMLG~GRPfVlEvk~P 238 (398)
T COG1258 216 GREDVDVRMLGTGRPFVLEVKEP 238 (398)
T ss_pred CCCccceeeecCCCceEEEecCc
Confidence 66799999999999999999987
No 79
>PF13131 DUF3951: Protein of unknown function (DUF3951)
Probab=21.72 E-value=84 Score=20.48 Aligned_cols=19 Identities=37% Similarity=0.749 Sum_probs=14.6
Q ss_pred hhhHHHHHHHHHHHhhhhh
Q 037858 6 TTLCVGFLCGLVIYKIFKR 24 (119)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~ 24 (119)
-+.-+-.|.|++.||+|..
T Consensus 11 ~~~~I~~lIgfity~mfV~ 29 (53)
T PF13131_consen 11 FTIFIFFLIGFITYKMFVK 29 (53)
T ss_pred HHHHHHHHHHHHHHHhhee
Confidence 4556667889999999864
No 80
>PF01646 Herpes_UL24: Herpes virus protein UL24; InterPro: IPR002580 This entry consists of the human herpes virus protein UL24 and its orthologues, which are universally present in avian, mammalian and reptilian herpes viruses. Though the functions of these proteins are not known, computational analysis suggests that they may belong to the restriction endonuclease-like fold superfamily, which contains a variety of endonucleases, DNA repair enzymes and exonucleases []. Proteins in this entry contain an absolutely conserved PD-(D/E)XK motif thought to be critical for nucleotide-cleaving activity.
Probab=20.42 E-value=1.6e+02 Score=23.11 Aligned_cols=33 Identities=15% Similarity=0.176 Sum_probs=23.6
Q ss_pred CceeEEEEEecCCCCCCceeeeEEEEeCCe-------EEEEEecCC
Q 037858 54 GGTAYVGLRIPDPETRSLQNIDIVLVKNGE-------EVVISVKNF 92 (119)
Q Consensus 54 ~~kiy~gLRIPd~~~~~~~EIDlVIVT~~~-------IlVIEvKNw 92 (119)
+-++|.-+.+ +++-.|.|++...+ =||||+|-=
T Consensus 49 ~~~l~FEV~L------G~R~PDCI~v~~~~~~~~~~vCyiiElKTc 88 (179)
T PF01646_consen 49 RFRLFFEVNL------GRRRPDCICVFSSESSGGKGVCYIIELKTC 88 (179)
T ss_pred cEEEEEEEec------CCCCCCEEEEEecCCCCcceEEEEEEeehh
Confidence 3466766666 55678888887766 589999954
No 81
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=20.30 E-value=1.6e+02 Score=25.36 Aligned_cols=55 Identities=15% Similarity=0.179 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhhhhhhcc-------CCceecceecCCcchhhHHHHHhhccCceeEEEEEec
Q 037858 9 CVGFLCGLVIYKIFKRIAD-------DDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIP 64 (119)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~-------dd~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIP 64 (119)
|.=++-++..|-+.+.++. .|-.+=|-+-||+-+..+|.+|.+. |-.+|++...+
T Consensus 2 ~l~l~~~~~l~~~~~~~~~~~~~~~~~~k~VlITGCDSGfG~~LA~~L~~~-Gf~V~Agcl~~ 63 (322)
T KOG1610|consen 2 WLPLAGLLLLYLLLRVRLERQVLDSLSDKAVLITGCDSGFGRLLAKKLDKK-GFRVFAGCLTE 63 (322)
T ss_pred eehHHHHHHHHHHHHHHHhhhcccccCCcEEEEecCCcHHHHHHHHHHHhc-CCEEEEEeecC
Confidence 4434444555666665554 2446778888999999999999987 45999999443
No 82
>PRK03298 hypothetical protein; Provisional
Probab=20.11 E-value=2.2e+02 Score=23.33 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=20.0
Q ss_pred eeeeEEEEe-CCeEEEEEecCCceeEE
Q 037858 72 QNIDIVLVK-NGEEVVISVKNFSGLVS 97 (119)
Q Consensus 72 ~EIDlVIVT-~~~IlVIEvKNwSG~I~ 97 (119)
++||++-.- .+...+||+|.- |.+.
T Consensus 135 G~IDil~rD~~G~~V~vEvKRr-~~id 160 (224)
T PRK03298 135 GPVDLLCRDADGGTVAVEIKRR-GEID 160 (224)
T ss_pred CceeEEEEcCCCCEEEEEEEec-CCcc
Confidence 499999999 455888999987 6554
No 83
>COG3660 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]
Probab=20.08 E-value=2.2e+02 Score=24.58 Aligned_cols=76 Identities=18% Similarity=0.270 Sum_probs=49.5
Q ss_pred cchhhHHHHHHHHHHHhhhhhhcc--CCceecceecCCcchhhHHHHHhhccCceeEEEEEecCCCCCCceeeeEEEEeC
Q 037858 4 SLTTLCVGFLCGLVIYKIFKRIAD--DDVVSDAETSDHTVTVSVANRLEELYGGTAYVGLRIPDPETRSLQNIDIVLVKN 81 (119)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~--dd~~~~~~~s~~~~~~~v~~~Lekl~~~kiy~gLRIPd~~~~~~~EIDlVIVT~ 81 (119)
-|...|....|+=+.-++|..-++ -|+.-|+..+---+.--++-.|+|-+++ ++ =+.|-||.--. ..+|+||+..
T Consensus 41 ~lP~~wl~~yp~~~~~~l~~~~~~r~p~~~Pdl~I~aGrrta~l~~~lkk~~~~-~~-vVqI~~Prlp~-~~fDlvivp~ 117 (329)
T COG3660 41 KLPNFWLAYYPIHILRELFGPRLSRKPEQRPDLIITAGRRTAPLAFYLKKKFGG-IK-VVQIQDPRLPY-NHFDLVIVPY 117 (329)
T ss_pred cCchhhhhcCccHhHHHhhcCccccCccCCCceEEecccchhHHHHHHHHhcCC-ce-EEEeeCCCCCc-ccceEEeccc
Confidence 455689999999888888887777 2555666665544444566788888888 21 12233332212 3799999975
Q ss_pred C
Q 037858 82 G 82 (119)
Q Consensus 82 ~ 82 (119)
.
T Consensus 118 H 118 (329)
T COG3660 118 H 118 (329)
T ss_pred h
Confidence 4
Done!