Query 024593
Match_columns 265
No_of_seqs 174 out of 394
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 05:52:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08378 NERD: Nuclease-relate 99.8 1.7E-20 3.7E-25 148.4 13.6 108 31-147 2-115 (115)
2 PRK14687 hypothetical protein; 94.3 1.3 2.8E-05 38.1 12.2 49 31-84 33-85 (173)
3 cd00523 archeal_HJR Holliday j 94.1 0.19 4.1E-06 40.9 6.5 52 30-85 4-55 (123)
4 PRK14688 hypothetical protein; 93.2 1.7 3.6E-05 35.3 10.6 48 31-84 9-56 (121)
5 PRK14675 hypothetical protein; 93.1 2.3 5.1E-05 34.5 11.4 83 29-133 9-92 (125)
6 PRK14677 hypothetical protein; 92.6 0.41 8.8E-06 38.0 6.2 48 30-83 2-49 (107)
7 PRK14674 hypothetical protein; 92.1 4.2 9.2E-05 33.5 11.7 48 30-84 7-55 (133)
8 PRK14681 hypothetical protein; 91.8 3.7 8E-05 34.8 11.4 48 31-84 46-94 (158)
9 PRK12497 hypothetical protein; 91.8 0.41 8.9E-06 38.5 5.4 49 31-86 9-58 (119)
10 PF02021 UPF0102: Uncharacteri 91.3 0.71 1.5E-05 35.5 6.0 49 34-88 2-50 (93)
11 PRK14684 hypothetical protein; 91.3 0.62 1.3E-05 37.7 5.9 48 31-84 9-56 (120)
12 PRK14680 hypothetical protein; 90.9 0.59 1.3E-05 38.5 5.6 49 31-85 9-57 (134)
13 PRK14676 hypothetical protein; 90.9 0.59 1.3E-05 37.6 5.4 47 31-83 10-56 (117)
14 PRK14685 hypothetical protein; 90.5 0.66 1.4E-05 40.0 5.6 47 32-84 46-92 (177)
15 TIGR00252 conserved hypothetic 90.4 0.85 1.8E-05 36.8 5.9 48 31-84 9-56 (119)
16 PRK14682 hypothetical protein; 90.2 0.94 2E-05 36.4 6.1 50 31-86 7-57 (117)
17 PRK14679 hypothetical protein; 89.9 0.83 1.8E-05 37.4 5.5 47 32-85 19-66 (128)
18 PRK14686 hypothetical protein; 89.8 0.8 1.7E-05 36.9 5.3 48 31-84 8-55 (119)
19 PRK14689 hypothetical protein; 89.7 0.77 1.7E-05 37.4 5.2 48 30-84 10-58 (124)
20 PRK14683 hypothetical protein; 89.0 1.1 2.4E-05 36.4 5.6 49 30-84 15-63 (122)
21 PRK14678 hypothetical protein; 87.8 1.5 3.1E-05 35.5 5.6 49 31-85 9-57 (120)
22 PHA01753 Holliday junction res 86.9 1.8 4E-05 35.1 5.6 53 29-85 5-57 (121)
23 COG1591 Holliday junction reso 86.0 2.7 5.7E-05 34.8 6.2 76 30-133 5-80 (137)
24 PF13635 DUF4143: Domain of un 84.9 2.9 6.3E-05 31.4 5.6 49 30-83 39-88 (90)
25 COG0792 Predicted endonuclease 84.2 7.9 0.00017 31.1 8.0 51 31-87 5-55 (114)
26 PRK14673 hypothetical protein; 83.6 1.3 2.8E-05 36.7 3.4 49 31-85 29-78 (137)
27 PF04471 Mrr_cat: Restriction 80.0 5.6 0.00012 30.1 5.7 52 30-87 5-59 (115)
28 PF01870 Hjc: Archaeal hollida 77.0 9.5 0.00021 29.1 6.0 42 34-84 2-43 (88)
29 PF08011 DUF1703: Protein of u 75.2 16 0.00035 28.2 7.1 70 64-154 30-103 (105)
30 PF06129 Chordopox_G3: Chordop 70.0 27 0.00059 27.9 7.2 82 1-83 1-84 (109)
31 COG4998 Predicted endonuclease 68.1 11 0.00025 32.3 5.0 59 31-92 2-60 (209)
32 PF06319 DUF1052: Protein of u 67.6 3.8 8.1E-05 34.7 2.0 42 37-84 27-69 (157)
33 PF03008 DUF234: Archaea bacte 64.7 7.5 0.00016 29.9 3.1 20 64-83 67-88 (100)
34 PF14986 DUF4514: Domain of un 64.5 7.5 0.00016 27.1 2.6 27 3-29 31-59 (61)
35 PHA00159 endonuclease I 62.7 17 0.00036 30.3 4.8 50 31-83 16-67 (148)
36 PF14899 DUF4492: Domain of un 62.6 19 0.0004 26.0 4.5 41 2-43 22-63 (64)
37 PF14281 PDDEXK_4: PD-(D/E)XK 62.5 23 0.0005 29.6 5.9 33 52-84 61-95 (179)
38 PF08774 VRR_NUC: VRR-NUC doma 61.3 26 0.00056 26.6 5.5 23 64-86 46-72 (100)
39 PF05367 Phage_endo_I: Phage e 59.4 11 0.00023 31.6 3.2 114 31-188 16-134 (149)
40 PF09002 DUF1887: Domain of un 59.1 14 0.0003 35.5 4.4 25 63-89 288-312 (381)
41 PRK04247 hypothetical protein; 59.0 23 0.00051 32.0 5.6 51 29-83 128-179 (238)
42 PF03749 SfsA: Sugar fermentat 57.4 77 0.0017 28.1 8.6 50 66-130 105-155 (215)
43 TIGR00372 cas4 CRISPR-associat 48.2 54 0.0012 27.1 5.9 35 49-83 53-87 (178)
44 PHA02691 hypothetical protein; 45.8 1.5E+02 0.0033 23.6 7.5 86 2-88 3-90 (110)
45 COG5321 Uncharacterized protei 42.5 30 0.00065 28.8 3.2 32 47-83 36-68 (164)
46 PRK14535 cysS cysteinyl-tRNA s 38.9 29 0.00062 36.2 3.2 30 55-86 54-83 (699)
47 PHA02552 4 head completion pro 38.2 95 0.0021 26.1 5.7 106 22-135 19-134 (151)
48 PF07788 DUF1626: Protein of u 38.1 41 0.0009 24.7 3.1 18 66-84 4-21 (70)
49 PF01939 DUF91: Protein of unk 36.3 88 0.0019 28.1 5.5 49 32-84 107-156 (228)
50 cd06168 LSm9 The eukaryotic Sm 35.7 38 0.00083 24.9 2.7 23 211-233 10-32 (75)
51 cd01730 LSm3 The eukaryotic Sm 33.4 43 0.00093 24.9 2.7 20 214-233 14-33 (82)
52 cd01717 Sm_B The eukaryotic Sm 32.6 46 0.001 24.4 2.7 21 213-233 12-32 (79)
53 PF01423 LSM: LSM domain ; In 32.5 45 0.00097 23.2 2.5 23 211-233 8-30 (67)
54 cd01731 archaeal_Sm1 The archa 32.5 48 0.001 23.5 2.7 23 211-233 10-32 (68)
55 PF04556 DpnII: DpnII restrict 31.9 52 0.0011 30.6 3.5 51 35-87 154-218 (286)
56 smart00651 Sm snRNP Sm protein 31.1 53 0.0011 22.8 2.7 23 211-233 8-30 (67)
57 cd01721 Sm_D3 The eukaryotic S 30.2 55 0.0012 23.5 2.7 25 210-234 9-33 (70)
58 PRK13258 7-cyano-7-deazaguanin 30.1 2.2E+02 0.0049 22.7 6.4 44 161-217 48-93 (114)
59 PF08814 XisH: XisH protein; 29.9 54 0.0012 27.2 2.9 48 36-86 9-63 (135)
60 cd01726 LSm6 The eukaryotic Sm 29.5 57 0.0012 23.2 2.6 23 211-233 10-32 (67)
61 PF13588 HSDR_N_2: Type I rest 27.4 57 0.0012 25.0 2.6 34 49-84 23-60 (112)
62 cd00600 Sm_like The eukaryotic 27.2 70 0.0015 21.8 2.7 22 213-234 8-29 (63)
63 PRK03298 hypothetical protein; 26.6 4.3E+02 0.0094 23.7 8.2 45 35-83 109-154 (224)
64 PF08907 DUF1853: Domain of un 26.4 2.9E+02 0.0062 25.4 7.4 55 32-87 62-121 (284)
65 PRK00737 small nuclear ribonuc 26.0 71 0.0015 23.1 2.7 20 214-233 17-36 (72)
66 cd01719 Sm_G The eukaryotic Sm 25.8 75 0.0016 23.1 2.8 20 214-233 13-32 (72)
67 cd01729 LSm7 The eukaryotic Sm 25.7 71 0.0015 23.7 2.7 22 212-233 13-34 (81)
68 cd01722 Sm_F The eukaryotic Sm 25.6 75 0.0016 22.6 2.7 23 211-233 11-33 (68)
69 cd01723 LSm4 The eukaryotic Sm 25.1 75 0.0016 23.2 2.7 23 211-233 11-33 (76)
70 COG4811 Predicted membrane pro 25.0 1.8E+02 0.0039 24.2 5.1 33 47-85 97-129 (152)
71 PRK00347 putative DNA-binding 24.8 4.2E+02 0.0092 23.7 8.0 49 66-129 118-168 (234)
72 COG4902 Uncharacterized protei 24.8 57 0.0012 27.6 2.2 43 109-152 79-121 (189)
73 cd01728 LSm1 The eukaryotic Sm 24.6 84 0.0018 23.0 2.8 22 212-233 13-34 (74)
74 PF11466 Doppel: Prion-like pr 23.9 55 0.0012 20.0 1.4 10 2-11 9-18 (30)
75 COG1958 LSM1 Small nuclear rib 23.7 80 0.0017 23.1 2.6 19 215-233 21-39 (79)
76 PF15516 BpuSI_N: BpuSI N-term 22.8 2.5E+02 0.0054 23.5 5.5 20 65-84 43-65 (159)
77 PF08722 Tn7_Tnp_TnsA_N: TnsA 22.7 96 0.0021 22.9 2.9 46 65-134 33-82 (88)
78 PRK02913 hypothetical protein; 22.7 1.9E+02 0.0041 24.4 4.8 33 46-84 94-126 (150)
79 PRK10877 protein disulfide iso 21.7 5.6E+02 0.012 22.6 8.3 32 66-99 36-68 (232)
80 COG5309 Exo-beta-1,3-glucanase 21.4 2.5E+02 0.0053 26.3 5.7 104 110-214 147-273 (305)
81 PF10717 ODV-E18: Occlusion-de 21.2 86 0.0019 23.9 2.3 19 2-20 27-45 (85)
82 cd01720 Sm_D2 The eukaryotic S 20.4 1E+02 0.0023 23.3 2.7 23 211-233 14-36 (87)
83 PF05371 Phage_Coat_Gp8: Phage 20.1 1.1E+02 0.0023 21.2 2.4 18 3-20 33-50 (52)
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=99.85 E-value=1.7e-20 Score=148.39 Aligned_cols=108 Identities=31% Similarity=0.524 Sum_probs=88.9
Q ss_pred cchhHHHHHHHH-hcCCC--ceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccceeEEECCCCcEEEEecCCccc
Q 024593 31 DSNAIFSVAARL-EKLYK--GKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRS 107 (265)
Q Consensus 31 ~~~~~~~v~~~L-~~l~~--~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~ 107 (265)
+..+|..+.+.| +.+++ +++|+|+++|+ ......|||+|++|++||||||+|||+|.|+++.++.|++. . .
T Consensus 2 G~~gE~~~~~~L~~~l~~~~~~v~~~i~~~~-~~~~~~eiD~lvi~~~gi~viE~K~~~g~i~~~~~~~w~~~-~----~ 75 (115)
T PF08378_consen 2 GAAGEQRVAERLEKHLPDDEYHVFHNIRLPD-PQGGTREIDHLVITPKGIFVIEVKNWSGKIYGDEDGQWFQE-N----K 75 (115)
T ss_pred cHHHHHHHHHHHHhhCCcCcEEEEeceEEec-cCCCCceeEEEEEeCCEEEEEEEecccceEEEcCCCcEEEc-C----C
Confidence 567899999999 55554 57999999986 34445699999999999999999999999998865589984 2 3
Q ss_pred ccCCChHHHHHHHHHHHHHHHHH---cCCCCCCCceeEEEEEe
Q 024593 108 AAHPDPVAEAKKQASILESYLEQ---RGVALPEGYLSYKVIIP 147 (265)
Q Consensus 108 ~~~~nPv~Q~~r~~~~L~~~L~~---~g~~lp~~~i~~~VVf~ 147 (265)
..++||+.|+++++++|+++|+. .+...| |.++||||
T Consensus 76 ~~~~nP~~q~~~~~~~l~~~L~~~~~~~~~~~---v~~vVVf~ 115 (115)
T PF08378_consen 76 KEFKNPLEQVRRQAQALKNLLKKRKEKGPNVP---VHPVVVFP 115 (115)
T ss_pred eecCCHHHHHHHHHHHHHHHhhhhhccCCCce---EEEEEEEC
Confidence 56999999999999999999832 233456 99999996
No 2
>PRK14687 hypothetical protein; Provisional
Probab=94.25 E-value=1.3 Score=38.09 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=33.5
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC----eEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG----EAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~----gI~VIEVKn 84 (265)
+..+|...+..|+......+=+|.|-+ + ..|||+|....+ .++.||||-
T Consensus 33 Gr~gE~~Aa~~L~~kGy~IL~RN~R~~-r----~GEIDIIA~d~~~~~~~LVFVEVKt 85 (173)
T PRK14687 33 GGGFEQLACEFLQEQGLILIARNWQQP-K----VGELDLVMLEKGQAWSTLVFAEVRQ 85 (173)
T ss_pred hHHHHHHHHHHHHHCCCEEeeecccCC-C----CccEEEEEecCCCCCCEEEEEEEeE
Confidence 456788888888874333334456532 1 239999987664 899999994
No 3
>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=94.06 E-value=0.19 Score=40.88 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=39.3
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
.+..+|..+++.|+. .|..++ |.|..+.+...|||+|..-.+.+++||||.-
T Consensus 4 ~G~~~E~~a~~~L~~-~G~~vl---R~~~sG~~~~~eiDIIA~~~~~lvfVEVK~r 55 (123)
T cd00523 4 KGSRAERELVKILEE-KGFAVV---RAPGSGGGPRPLPDIVAGNGGTYLAIEVKST 55 (123)
T ss_pred hHHHHHHHHHHHHHh-CCCEEE---EEcCCCCCCCCceeEEEecCCEEEEEEEEec
Confidence 356689999999988 455566 6654433334599999999999999999943
No 4
>PRK14688 hypothetical protein; Provisional
Probab=93.17 E-value=1.7 Score=35.25 Aligned_cols=48 Identities=23% Similarity=0.137 Sum_probs=35.8
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|.--...++.||||-
T Consensus 9 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK~ 56 (121)
T PRK14688 9 GEFGEKLAAEYLKGMGYSIIQTNCRLP------EGEIDIVGQDGEYLVFIEVRT 56 (121)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEeeCC------CCcEeEEEeeCCEEEEEEEEe
Confidence 566788888999874333344466643 239999999989999999993
No 5
>PRK14675 hypothetical protein; Provisional
Probab=93.09 E-value=2.3 Score=34.52 Aligned_cols=83 Identities=14% Similarity=0.143 Sum_probs=51.4
Q ss_pred cccchhHHHHHHHHhcCCCceEE-eeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccceeEEECCCCcEEEEecCCccc
Q 024593 29 TSDSNAIFSVAARLEKLYKGKAY-VGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRS 107 (265)
Q Consensus 29 ~~~~~~~~~v~~~L~~l~~~~vl-~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~ 107 (265)
.-+..+|...+..|+.. |..|+ .|.+.+ ..|||+|..-...+++||||-.++.-++.+
T Consensus 9 ~~G~~gE~~A~~~L~~~-G~~il~rn~r~~------~GEIDlIa~d~~~lvFVEVK~R~~~~~g~~-------------- 67 (125)
T PRK14675 9 SLGEIGESIAVTYLKGL-RYKIVERNFRCR------CGEIDIIARDGKTLVFVEVKTRKNYAYGVP-------------- 67 (125)
T ss_pred HHhHHHHHHHHHHHHHC-CCEEEEEEEeCC------CCeEEEEEEeCCEEEEEEEEeccCCCCcCh--------------
Confidence 34566788888888874 44444 456543 229999999999999999995544322221
Q ss_pred ccCCChHHHHHHHHHHHHHHHHHcCC
Q 024593 108 AAHPDPVAEAKKQASILESYLEQRGV 133 (265)
Q Consensus 108 ~~~~nPv~Q~~r~~~~L~~~L~~~g~ 133 (265)
..--+|-.| ++=.++-+.||.+++.
T Consensus 68 ~~aV~~~K~-~ri~~~A~~yL~~~~~ 92 (125)
T PRK14675 68 QLAVTPFKQ-RQISKAALTWLAKKKL 92 (125)
T ss_pred HHcCCHHHH-HHHHHHHHHHHHHCCC
Confidence 111233223 2444555678888764
No 6
>PRK14677 hypothetical protein; Provisional
Probab=92.64 E-value=0.41 Score=37.98 Aligned_cols=48 Identities=25% Similarity=0.042 Sum_probs=35.6
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEee
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVK 83 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVK 83 (265)
.+..+|...+..|+......+=.|.|-+. .|||+|.--...++.||||
T Consensus 2 ~G~~~E~~A~~~L~~~Gy~Il~rN~r~~~------GEIDlIa~~~~~lvFVEVK 49 (107)
T PRK14677 2 DWKEAEELACKFLKKKGYKILERNYRTKY------GEIDIVARDGREIVFVEVK 49 (107)
T ss_pred ChHHHHHHHHHHHHHCCCEEEEEEecCCC------ceeeEEEEECCEEEEEEEe
Confidence 35678888889998743333444666432 3999999999999999999
No 7
>PRK14674 hypothetical protein; Provisional
Probab=92.08 E-value=4.2 Score=33.47 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=35.9
Q ss_pred ccchhHHHHHHHHhcCCCceEE-eeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 30 SDSNAIFSVAARLEKLYKGKAY-VGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl-~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
.+..+|...++.|+.. |+.|+ .|.|-+ ..|||+|.--...++.||||-
T Consensus 7 ~G~~gE~~A~~~L~~~-Gy~Il~rN~r~~------~GEIDiIa~~~~~LVFVEVK~ 55 (133)
T PRK14674 7 LGQWAEQTALKLLKEQ-NYEWVASNYHSR------RGEVDLIVKRGNELIFVEVKA 55 (133)
T ss_pred hhHHHHHHHHHHHHHC-CCEEeEEeeecC------CCCEeEEEEeCCEEEEEEEEe
Confidence 3566788888999874 44444 466643 239999998888999999993
No 8
>PRK14681 hypothetical protein; Provisional
Probab=91.84 E-value=3.7 Score=34.83 Aligned_cols=48 Identities=21% Similarity=0.071 Sum_probs=34.5
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeC-CeEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITK-GEAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~-~gI~VIEVKn 84 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|..-+ +.++.||||-
T Consensus 46 G~~gE~~Aa~~L~~~Gy~IL~rN~R~~------~GEIDIIa~d~~~~LVFVEVKt 94 (158)
T PRK14681 46 GALGEQYAAAWLEEHGWTTLSRNWHCR------YGELDIVALNPEYTIVFVEVKT 94 (158)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEeCC------CCcEEEEEEcCCceEEEEEEEe
Confidence 556788888888774333344467743 23999999876 4899999994
No 9
>PRK12497 hypothetical protein; Reviewed
Probab=91.76 E-value=0.41 Score=38.47 Aligned_cols=49 Identities=18% Similarity=0.099 Sum_probs=36.0
Q ss_pred cchhHHHHHHHHhcCCCceEE-eeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccc
Q 024593 31 DSNAIFSVAARLEKLYKGKAY-VGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLS 86 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl-~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~s 86 (265)
+..+|...+..|+.. |..|+ .|.|-+ ..|||+|..-...++.||||-.+
T Consensus 9 G~~gE~~A~~~L~~~-Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~R~ 58 (119)
T PRK12497 9 GAAGEDLAARYLESK-GLRILARNFRCR------FGEIDLIARDGDTLVFVEVKTRR 58 (119)
T ss_pred HHHHHHHHHHHHHHC-CCEEEcceecCC------CCcEeeeEEeCCEEEEEEEEecc
Confidence 456788888889864 44444 566653 22999999998899999999433
No 10
>PF02021 UPF0102: Uncharacterised protein family UPF0102; InterPro: IPR003509 The proteins in this entry are functionally uncharacterised.; PDB: 3FOV_A.
Probab=91.31 E-value=0.71 Score=35.49 Aligned_cols=49 Identities=22% Similarity=0.060 Sum_probs=33.4
Q ss_pred hHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecccee
Q 024593 34 AIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSGF 88 (265)
Q Consensus 34 ~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG~ 88 (265)
+|...+..|+......+=.|.|-+. .|||+|..-...++.||||-.++.
T Consensus 2 gE~~A~~~L~~~G~~IL~rN~r~~~------GEIDiIa~~~~~lvfVEVK~R~~~ 50 (93)
T PF02021_consen 2 GEELAARYLERKGYRILERNWRCRR------GEIDIIARDGDTLVFVEVKTRSSS 50 (93)
T ss_dssp HHHHHHHHHHHTT-EEEEEEEEETT------EEEEEEEEETTEEEEEEEEE----
T ss_pred HHHHHHHHHHHCCCEEeeeeecCCC------CcEeEEEEEcccEEEEEEEEeecc
Confidence 4666777888744444556677633 399999999889999999965543
No 11
>PRK14684 hypothetical protein; Provisional
Probab=91.25 E-value=0.62 Score=37.67 Aligned_cols=48 Identities=21% Similarity=0.176 Sum_probs=35.7
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|.-....++.||||-
T Consensus 9 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~ 56 (120)
T PRK14684 9 GFNAEKTACRYLQKQGLSFITKNFRYK------QGEIDLIMSDQSMLVFIEVRY 56 (120)
T ss_pred hHHHHHHHHHHHHHCCCEEEEEEecCC------CCeEEEEEEeCCEEEEEEEeE
Confidence 566788888999874333344466643 239999999988999999993
No 12
>PRK14680 hypothetical protein; Provisional
Probab=90.94 E-value=0.59 Score=38.55 Aligned_cols=49 Identities=20% Similarity=0.092 Sum_probs=35.5
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|......++.||||--
T Consensus 9 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR 57 (134)
T PRK14680 9 GQHGEDAAAALLQRTGHRILARNWRHG------GLELDIVCEDGDTIVFVEVKTR 57 (134)
T ss_pred HHHHHHHHHHHHHHCCCEEEEeecCCC------CCeEEEEEEeCCEEEEEEEEec
Confidence 456788888889874333344466643 2399999998889999999943
No 13
>PRK14676 hypothetical protein; Provisional
Probab=90.92 E-value=0.59 Score=37.63 Aligned_cols=47 Identities=23% Similarity=0.157 Sum_probs=34.8
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEee
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVK 83 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVK 83 (265)
+..+|...++.|+......+=.|.|-+ ..|||+|.--...++.||||
T Consensus 10 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVK 56 (117)
T PRK14676 10 GQTAEEAVARIYDRSGRPVAARRWRGV------SGEIDLIAREGAEVIFIEVK 56 (117)
T ss_pred HHHHHHHHHHHHHHCCCEEeeeecCCC------CCeEEEEEeeCCEEEEEEEe
Confidence 456788888899874333344466643 23999999998899999999
No 14
>PRK14685 hypothetical protein; Provisional
Probab=90.47 E-value=0.66 Score=40.01 Aligned_cols=47 Identities=15% Similarity=0.071 Sum_probs=34.1
Q ss_pred chhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 32 SNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 32 ~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
..+|...+..|+......+=.|.|-+ ..|||+|.-....++.||||-
T Consensus 46 ~~gE~~Aa~yL~~~Gy~IL~RN~R~~------~GEIDIIA~dg~~LVFVEVKt 92 (177)
T PRK14685 46 QAYESAALRWLARQGLRPLARNLRCR------AGEIDLAMRDGEVLVLVEVRA 92 (177)
T ss_pred HHHHHHHHHHHHHCCCEEeEeeecCC------CCcEEEEEecCCEEEEEEEeE
Confidence 44688888888874333444466643 229999988888999999994
No 15
>TIGR00252 conserved hypothetical protein TIGR00252. the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment
Probab=90.38 E-value=0.85 Score=36.82 Aligned_cols=48 Identities=15% Similarity=0.118 Sum_probs=35.2
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|.--.+.++.||||-
T Consensus 9 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVK~ 56 (119)
T TIGR00252 9 GQAGESQARAWLEQKGLKFIAANWNSP------WGEIDLIMHDTKTIAFVEVRT 56 (119)
T ss_pred hHHHHHHHHHHHHHCCCEEeEEEecCC------CCcEEEEEeeCCEEEEEEEEe
Confidence 566788888999874333334466643 229999998888999999994
No 16
>PRK14682 hypothetical protein; Provisional
Probab=90.23 E-value=0.94 Score=36.44 Aligned_cols=50 Identities=24% Similarity=0.224 Sum_probs=36.9
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEe-eCCCCCCccceeEEEEeCCeEEEEEeeccc
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRI-PDPDTGSRQNIDIVLITKGEAVVISVKNLS 86 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrl-p~~~~~~~~EID~Vivt~~gI~VIEVKn~s 86 (265)
+..+|...+..|+......+=.|.|- + ..|||+|..-...++.||||-.+
T Consensus 7 G~~gE~~A~~~L~~~Gy~Il~rN~r~~~------~GEIDiIa~~~~~lvFVEVKtR~ 57 (117)
T PRK14682 7 GNKAELQACKFLHTQALEILAHNFKALP------YGEIDIIALDKDTLVFIEVKYRS 57 (117)
T ss_pred HHHHHHHHHHHHHHCCCEEeeeeEECCC------CCcEEEEEeeCCEEEEEEEEecC
Confidence 55678888999987544444456763 3 22999999988899999999433
No 17
>PRK14679 hypothetical protein; Provisional
Probab=89.86 E-value=0.83 Score=37.40 Aligned_cols=47 Identities=13% Similarity=-0.019 Sum_probs=34.0
Q ss_pred chhHHHHHHHHhcCCCceE-EeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 32 SNAIFSVAARLEKLYKGKA-YVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 32 ~~~~~~v~~~L~~l~~~~v-l~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
..+|...+..|+.. |+.| =.|.|-+ ..|||+|.--...++.||||--
T Consensus 19 ~~gE~~A~~~L~~~-Gy~Il~rN~r~~------~GEIDiIa~~~~~lVFVEVKtR 66 (128)
T PRK14679 19 LSAEGLALLALMLK-GYRPLARRFAAA------GGEIDLIVRRGRTIAFVEVKAR 66 (128)
T ss_pred HHHHHHHHHHHHHC-CCEEEeeeccCC------CCeEEEEEEeCCEEEEEEEEec
Confidence 45688888888764 4444 3455532 3399999999889999999943
No 18
>PRK14686 hypothetical protein; Provisional
Probab=89.75 E-value=0.8 Score=36.88 Aligned_cols=48 Identities=19% Similarity=0.078 Sum_probs=35.7
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|.--...++.||||-
T Consensus 8 G~~gE~~A~~~L~~~Gy~il~rN~r~~------~GEIDlIa~~~~~lvFVEVKt 55 (119)
T PRK14686 8 GKEGEDLAVEFLIKKGYTILERNYRFQ------KAEIDIIAQKGNILVIVEVKT 55 (119)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEecCC------CCcEEEEECcCCEEEEEEEEe
Confidence 456788888999874333444467642 239999998888999999994
No 19
>PRK14689 hypothetical protein; Provisional
Probab=89.73 E-value=0.77 Score=37.41 Aligned_cols=48 Identities=19% Similarity=0.122 Sum_probs=35.6
Q ss_pred ccchhHHHHHHHHhcCCCceEE-eeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 30 SDSNAIFSVAARLEKLYKGKAY-VGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl-~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
.+..+|...+..|++. |..|+ .|.|-+ ..|||+|..-...+..||||-
T Consensus 10 ~G~~gE~~Aa~~L~~~-Gy~Il~rN~r~~------~GEIDIIa~~~~~lVFVEVKt 58 (124)
T PRK14689 10 LGAWAEERVLRLLQRR-GWRLLDRNWSCR------WGELDLVLEKQQRLLVVEVKG 58 (124)
T ss_pred HHHHHHHHHHHHHHHC-CCEEEEEecCCC------CCcccEEeeeCCEEEEEEEEE
Confidence 3566788889999874 44444 466542 239999999888999999994
No 20
>PRK14683 hypothetical protein; Provisional
Probab=88.95 E-value=1.1 Score=36.39 Aligned_cols=49 Identities=20% Similarity=0.084 Sum_probs=35.1
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
-+..+|...+..|+......+=.|.|-+ ..|||+|.--...++.||||-
T Consensus 15 lG~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDIIa~~~~~lVFVEVKt 63 (122)
T PRK14683 15 LGYLGEVLIILFLKCKLYHIIKHRYRCP------LGEIDIIAHKNKQLVFIEVKT 63 (122)
T ss_pred HHHHHHHHHHHHHHHCCCEEEeeecCCC------CCcEEEEEEeCCEEEEEEEee
Confidence 3566788888888874333334444432 339999999999999999993
No 21
>PRK14678 hypothetical protein; Provisional
Probab=87.81 E-value=1.5 Score=35.51 Aligned_cols=49 Identities=22% Similarity=0.095 Sum_probs=35.4
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|..-...++.||||--
T Consensus 9 G~~gE~~A~~~L~~~Gy~Il~rN~r~~------~GEIDiIa~~~~~lvFVEVKtR 57 (120)
T PRK14678 9 GDWGEQVAAAYLERCGYTIIARNWRCR------AGEIDIVAREGDQLVFVEVRTR 57 (120)
T ss_pred HHHHHHHHHHHHHHCCCEEeeeeecCC------CCCEeeeEEeCCEEEEEEEEEC
Confidence 456788888889874333334456542 2399999999899999999943
No 22
>PHA01753 Holliday junction resolvase
Probab=86.87 E-value=1.8 Score=35.11 Aligned_cols=53 Identities=28% Similarity=0.243 Sum_probs=37.4
Q ss_pred cccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 29 TSDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 29 ~~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
..++.+|...++.|+.. |..++ +-+........|||+|....+-++.||||.-
T Consensus 5 ~~G~~~E~~a~~~L~~~-G~~il---~rn~~~~~~~GEiDIIA~~~~~lvfVEVKtR 57 (121)
T PHA01753 5 QSGKYYEYKTLEILESN-GFKAL---RIPVSGTGKQALPDIIATKNNTIYPIEVKST 57 (121)
T ss_pred hhhHHHHHHHHHHHHHC-CCEEE---EeccccCCCCCCccEEEeeCCEEEEEEEEeC
Confidence 34778899999999883 43333 3343321124599999999999999999943
No 23
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=85.99 E-value=2.7 Score=34.79 Aligned_cols=76 Identities=21% Similarity=0.160 Sum_probs=53.9
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccceeEEECCCCcEEEEecCCccccc
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRSAA 109 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~~ 109 (265)
.++..|..+.+.|... -|+-+|.|..+.+.+-..|+|-..++-+++||+|.-++
T Consensus 5 kG~~~EReLv~~L~e~----GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~---------------------- 58 (137)
T COG1591 5 KGSRFERELVRILWER----GFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRE---------------------- 58 (137)
T ss_pred ccchHHHHHHHHHHhc----CceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccC----------------------
Confidence 4677889999999753 46778999887334447999999999999999994322
Q ss_pred CCChHHHHHHHHHHHHHHHHHcCC
Q 024593 110 HPDPVAEAKKQASILESYLEQRGV 133 (265)
Q Consensus 110 ~~nPv~Q~~r~~~~L~~~L~~~g~ 133 (265)
+|+--.+.++..|-.+.+..|-
T Consensus 59 --~kiYl~~e~ve~L~~FA~~fGg 80 (137)
T COG1591 59 --TKIYLDKEQVEKLVEFARRFGG 80 (137)
T ss_pred --CcEEEcHHHHHHHHHHHHHcCC
Confidence 2222233566677777777654
No 24
>PF13635 DUF4143: Domain of unknown function (DUF4143)
Probab=84.85 E-value=2.9 Score=31.42 Aligned_cols=49 Identities=27% Similarity=0.232 Sum_probs=32.7
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEe-eCCCCCCccceeEEEEeCCeEEEEEee
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRI-PDPDTGSRQNIDIVLITKGEAVVISVK 83 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrl-p~~~~~~~~EID~Vivt~~gI~VIEVK 83 (265)
.+.-.|..|...|.+.. .. -..+.. .+. .+. |||+|+-.++.++.||||
T Consensus 39 ~G~l~En~V~~eL~~~~-~~-~~~l~y~r~~-~~~--EVDfv~~~~~~~~~IEVK 88 (90)
T PF13635_consen 39 KGALFENFVAQELLKRL-RE-GYELYYWRDK-SGQ--EVDFVIENGGRIIPIEVK 88 (90)
T ss_pred HhHHHHHHHHHHHHHhc-CC-CceEEEEECC-CCC--EEEEEEEeCCEEEEEEEE
Confidence 44455888888888763 11 111222 222 223 999999999999999999
No 25
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=84.15 E-value=7.9 Score=31.11 Aligned_cols=51 Identities=18% Similarity=0.018 Sum_probs=33.9
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccce
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSG 87 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG 87 (265)
+..+|...+..|++..-..+=.|.|-+ ..|||+|.--.+-|..||||.-++
T Consensus 5 G~~~E~~A~~~L~~~G~~il~rN~r~r------~GEIDlIa~~~~~ivFVEVK~R~~ 55 (114)
T COG0792 5 GAAGEDLAARFLESKGLRILARNWRCR------YGEIDLIARDGDTVVFVEVKYRRN 55 (114)
T ss_pred HHHHHHHHHHHHHHcCcchhhhhccCC------CCceEEEEecCCEEEEEEEEeecc
Confidence 345677777888775333333344432 239999999988888999995443
No 26
>PRK14673 hypothetical protein; Provisional
Probab=83.56 E-value=1.3 Score=36.72 Aligned_cols=49 Identities=16% Similarity=0.096 Sum_probs=34.4
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEeecc
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVKNL 85 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVKn~ 85 (265)
+..+|...+..|+......+=.|.|-+ ..|||+|.--+. .++.||||--
T Consensus 29 G~~gE~~A~~~L~~~Gy~IL~rN~r~~------~GEIDLIa~~~~~~lVFVEVKtR 78 (137)
T PRK14673 29 GAAFEDRALAFLQRAGLALVARNYRCR------GGEIDLVMRERDGTLVFVEVRAR 78 (137)
T ss_pred HHHHHHHHHHHHHHCCCEEeEeEecCC------CCccCHHHccCCcEEEEEEEEeC
Confidence 456788888889874333334466643 239999987766 8999999943
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=80.03 E-value=5.6 Score=30.12 Aligned_cols=52 Identities=23% Similarity=0.275 Sum_probs=26.4
Q ss_pred ccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC---eEEEEEeeccce
Q 024593 30 SDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG---EAVVISVKNLSG 87 (265)
Q Consensus 30 ~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~---gI~VIEVKn~sG 87 (265)
++..=+..++..|+.. + |.+++...... .+.+|+++.... .-++||+|+|.+
T Consensus 5 ~~~~FE~l~~~ll~~~-g---~~~v~~~~~~~--d~giDi~~~~~~~~~~~~~vqcK~~~~ 59 (115)
T PF04471_consen 5 SGREFEELVAELLRKL-G---YTDVEVTGGSG--DGGIDIIAEKDDLGKERILVQCKRYKK 59 (115)
T ss_dssp ---------HHHHHTT-T----EEEEEE-SSS--EEEEEEEEEETT---EEEEEEE---S-
T ss_pred ccchHHHHHHHHHHHc-C---CccEEEeccCC--CCCEEEEEEEcccCceEEEEEEEEecc
Confidence 3444566777788775 3 22666655433 569999988754 689999998764
No 28
>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=76.95 E-value=9.5 Score=29.13 Aligned_cols=42 Identities=21% Similarity=0.213 Sum_probs=31.3
Q ss_pred hHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 34 AIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 34 ~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
.|..+.+.|.. .| |.=+|.|..+.+ |+|.+-++.+++||||.
T Consensus 2 ~Erel~~~L~~-~G---f~v~R~~~Sg~~-----DiiA~~~~~~l~IEvKs 43 (88)
T PF01870_consen 2 FERELVKILWE-RG---FAVVRAAGSGGG-----DIIAGKGGRYLAIEVKS 43 (88)
T ss_dssp HHHHHHHHHHH-TT----EEEEBSCCSSS-----SEEEEETTEEEEEEEEE
T ss_pred HHHHHHHHHHh-CC---cEEEEecCCCCc-----CEEEECCCEEEEEEEee
Confidence 35667777875 33 445588886442 99999999999999994
No 29
>PF08011 DUF1703: Protein of unknown function (DUF1703); InterPro: IPR012547 This family contains many hypothetical bacterial proteins.
Probab=75.21 E-value=16 Score=28.24 Aligned_cols=70 Identities=16% Similarity=0.292 Sum_probs=42.3
Q ss_pred ccceeEEEE----eCCeEEEEEeeccceeEEECCCCcEEEEecCCcccccCCChHHHHHHHHHHHHHHHHHcCCCCCCCc
Q 024593 64 RQNIDIVLI----TKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRSAAHPDPVAEAKKQASILESYLEQRGVALPEGY 139 (265)
Q Consensus 64 ~~EID~Viv----t~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~~~~nPv~Q~~r~~~~L~~~L~~~g~~lp~~~ 139 (265)
..-+|+++. ++...++||.|-....-..+ ..-.+-+.|.+++.+..+ ++..| ...
T Consensus 30 ~Gr~Dl~l~~~~~~~~~~~IiElK~~~~~~~~~---------------~~~~~Al~QI~~k~y~~~--~~~~~----~~i 88 (105)
T PF08011_consen 30 KGRIDLVLEPPKPTPKYIYIIELKYAKSKESLE---------------KSAEEALEQIKEKKYAEE--LKEKG----KKI 88 (105)
T ss_pred CCeEEEEEEEccCCCCeEEEEEEEEcccccccc---------------cccHHHHHHHHHhCccHH--HHhCC----CcE
Confidence 448999999 88999999999322111000 112256667766665543 23222 234
Q ss_pred eeEEEEEeCCCeeEe
Q 024593 140 LSYKVIIPNPKFRVI 154 (265)
Q Consensus 140 i~~~VVf~np~~~l~ 154 (265)
+.-.|+|...++.+.
T Consensus 89 ~~igi~f~~k~~~i~ 103 (105)
T PF08011_consen 89 IKIGIVFSGKERNIV 103 (105)
T ss_pred EEEEEEEECCEEEEE
Confidence 777788887666553
No 30
>PF06129 Chordopox_G3: Chordopoxvirus G3 protein; InterPro: IPR010367 This family consists of several poxvirus specific G3 proteins. The function of this family is unknown.
Probab=69.99 E-value=27 Score=27.86 Aligned_cols=82 Identities=12% Similarity=0.216 Sum_probs=53.5
Q ss_pred ChhhhHHHHHHHHHHHHHhc-C-CcccccccccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEE
Q 024593 1 MWVQILCGLVIYKICKKLFY-D-DDVLDVETSDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAV 78 (265)
Q Consensus 1 m~~~i~~~~~~~~l~~~~~~-~-~~~~~~~~~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~ 78 (265)
||+-.++.+++|.++-.||. . -+++++.......+..+..+-.... ...+..+.+++++.-...++.+=.=+..|.+
T Consensus 1 m~ll~l~ffi~Fl~~~Y~~~y~PTNK~ql~v~~~~~~~~i~k~~d~~~-~~~~~t~lF~~~~~~~~~~v~l~Yds~~~~V 79 (109)
T PF06129_consen 1 MWLLYLIFFILFLVLCYFFNYYPTNKMQLAVRELNYENAIIKQQDDNL-PKLLNTVLFLNPDKPVSSQVILYYDSRSGTV 79 (109)
T ss_pred CcHHHHHHHHHHHHHHHHHhhccchHHHHhhcccchhhHHHhcccccC-ccceeeEEecCCCcccccceEEEEccCCCeE
Confidence 89999999999998866665 3 3477777776666666655543322 2467777777775433334444444456888
Q ss_pred EEEee
Q 024593 79 VISVK 83 (265)
Q Consensus 79 VIEVK 83 (265)
+|..|
T Consensus 80 tv~~~ 84 (109)
T PF06129_consen 80 TVAYK 84 (109)
T ss_pred EEEEC
Confidence 88888
No 31
>COG4998 Predicted endonuclease (RecB family) [DNA replication, recombination, and repair]
Probab=68.12 E-value=11 Score=32.29 Aligned_cols=59 Identities=27% Similarity=0.249 Sum_probs=46.4
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccceeEEEC
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSGFVTVN 92 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG~I~~~ 92 (265)
++.++.-+++.|.+..-..+-.|.++.+.+- .-.|||.|-.-.+.=|-|||| .|.+-++
T Consensus 2 GksaEeiaasiLrkeGfevvArn~~ve~egv-eVgEiDIVAek~GerYavEVK--AG~vdi~ 60 (209)
T COG4998 2 GKSAEEIAASILRKEGFEVVARNMPVEDEGV-EVGEIDIVAEKGGERYAVEVK--AGMVDIN 60 (209)
T ss_pred CccHHHHHHHHHHhcCcEEEeecceeecCCe-EEEEEEEEEecCCcEEEEEEe--ccccchH
Confidence 3557778888998866566777888877643 345999999999999999999 7877665
No 32
>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=67.62 E-value=3.8 Score=34.70 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=24.7
Q ss_pred HHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEeec
Q 024593 37 SVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVKN 84 (265)
Q Consensus 37 ~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVKn 84 (265)
-|.+.|.. .+...+.-+.+|+. . -.|++-++++ .|.+||+|.
T Consensus 27 Gv~R~l~~-~g~~~l~E~~L~~G---R--RaDv~al~~kGeI~ivEIKS 69 (157)
T PF06319_consen 27 GVCRLLRS-LGFACLPEVPLPNG---R--RADVMALGPKGEIWIVEIKS 69 (157)
T ss_dssp HHHHHHHH-TT-EEEEEE-SSTT-------EEEEEE-TT--EEEEEE-S
T ss_pred HHHHHHHH-CCCeEEEEecCCCC---C--eEEEEEECCCCeEEEEEEEc
Confidence 34444444 35556777777732 2 8999999997 599999993
No 33
>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=64.72 E-value=7.5 Score=29.90 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=18.4
Q ss_pred ccceeEEEEeCCe--EEEEEee
Q 024593 64 RQNIDIVLITKGE--AVVISVK 83 (265)
Q Consensus 64 ~~EID~Vivt~~g--I~VIEVK 83 (265)
..|||+|.++..+ +++.|+|
T Consensus 67 ~~EIDiva~~~~~~~~~~gEcK 88 (100)
T PF03008_consen 67 NEEIDIVAVDEDGKRILFGECK 88 (100)
T ss_pred CccEEEEEECCCCCEEEEEEEE
Confidence 3499999999998 9999999
No 34
>PF14986 DUF4514: Domain of unknown function (DUF4514)
Probab=64.51 E-value=7.5 Score=27.12 Aligned_cols=27 Identities=37% Similarity=0.764 Sum_probs=19.4
Q ss_pred hhhHHHHHHHHHH--HHHhcCCccccccc
Q 024593 3 VQILCGLVIYKIC--KKLFYDDDVLDVET 29 (265)
Q Consensus 3 ~~i~~~~~~~~l~--~~~~~~~~~~~~~~ 29 (265)
++|-+|+++.|++ |++.+|+|..|+.+
T Consensus 31 vaisAgFLaLKicmIrkhlfD~dssdlrs 59 (61)
T PF14986_consen 31 VAISAGFLALKICMIRKHLFDNDSSDLRS 59 (61)
T ss_pred HHHHHHHHHHHHHHHHHhhccCchhhhcc
Confidence 5788999999875 55666776655554
No 35
>PHA00159 endonuclease I
Probab=62.68 E-value=17 Score=30.32 Aligned_cols=50 Identities=24% Similarity=0.220 Sum_probs=34.2
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeC--CCCCCccceeEEEEeCCeEEEEEee
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPD--PDTGSRQNIDIVLITKGEAVVISVK 83 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~--~~~~~~~EID~Vivt~~gI~VIEVK 83 (265)
+|..|.+++..|+...=..-|....++. +...+.--.|.+ -|+||+ +|||
T Consensus 16 RSgLE~k~ak~Le~~gv~~~yE~~ki~y~~pA~~~~YTPDF~--LpnGii-iEvK 67 (148)
T PHA00159 16 RSGLEDKVSKQLEKKGVKFDYELWKIPYVIPASDHKYTPDFL--LPNGII-IETK 67 (148)
T ss_pred cchHHHHHHHHHHhcCCCeEeeeeeeeeeccCCCCeeCCcee--cCCCCE-EEec
Confidence 4567899999999876455566655444 212223489998 567888 9999
No 36
>PF14899 DUF4492: Domain of unknown function (DUF4492)
Probab=62.61 E-value=19 Score=26.04 Aligned_cols=41 Identities=22% Similarity=0.476 Sum_probs=27.8
Q ss_pred hhhhHH-HHHHHHHHHHHhcCCcccccccccchhHHHHHHHHh
Q 024593 2 WVQILC-GLVIYKICKKLFYDDDVLDVETSDSNAIFSVAARLE 43 (265)
Q Consensus 2 ~~~i~~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~v~~~L~ 43 (265)
|.-|++ .+|+|.+++-||+ |+.+.=..++.+.+..|.+.|-
T Consensus 22 W~IIliKLfImF~vLK~FfF-p~~l~~~~~~~~k~~~V~~~L~ 63 (64)
T PF14899_consen 22 WLIILIKLFIMFAVLKLFFF-PNFLNTKKTDEEKSDFVSKELI 63 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHC-cchhccCCCchHHHHHHHHHhc
Confidence 666664 5567777777777 6666666666666777777663
No 37
>PF14281 PDDEXK_4: PD-(D/E)XK nuclease superfamily
Probab=62.49 E-value=23 Score=29.56 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=22.5
Q ss_pred eeeEeeCC-CCCCccceeEEE-EeCCeEEEEEeec
Q 024593 52 VGLRIPDP-DTGSRQNIDIVL-ITKGEAVVISVKN 84 (265)
Q Consensus 52 ~~lrlp~~-~~~~~~EID~Vi-vt~~gI~VIEVKn 84 (265)
.++.+... .......||+++ -....+++||-|=
T Consensus 61 ~~~~v~~E~~~~~~~riDi~i~~~~~~~iiIEnKi 95 (179)
T PF14281_consen 61 ESIEVEREVSTESGGRIDILIDENDKFVIIIENKI 95 (179)
T ss_pred CceEEEEeeccCCCCCccEEEEeCCCEEEEEEEcC
Confidence 44555443 222244899999 6677999999993
No 38
>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=61.33 E-value=26 Score=26.56 Aligned_cols=23 Identities=22% Similarity=0.179 Sum_probs=18.7
Q ss_pred ccceeEEEEeCCe----EEEEEeeccc
Q 024593 64 RQNIDIVLITKGE----AVVISVKNLS 86 (265)
Q Consensus 64 ~~EID~Vivt~~g----I~VIEVKn~s 86 (265)
..-.|++++.+.+ ++.||||.=+
T Consensus 46 ~G~PDl~~~~~~~~~~~~~~iEvK~p~ 72 (100)
T PF08774_consen 46 SGFPDLILWRPRGKRDIFLFIEVKGPG 72 (100)
T ss_pred CCCCcEEEEecCCCccEEEEEEEcCCC
Confidence 4479999999876 8999999533
No 39
>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=59.39 E-value=11 Score=31.57 Aligned_cols=114 Identities=23% Similarity=0.385 Sum_probs=56.6
Q ss_pred cchhHHHHHHHHhcCCCceEEeeeEeeCCC--CCCccceeEEEEeCCeEEEEEeeccceeEEECCCCcEEEEecCCcccc
Q 024593 31 DSNAIFSVAARLEKLYKGKAYVGLRIPDPD--TGSRQNIDIVLITKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRSA 108 (265)
Q Consensus 31 ~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~--~~~~~EID~Vivt~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~ 108 (265)
+|..|..|+..|.++.-..-|...++|..- ..+.-..|.++ |+| ++||+| |.|-
T Consensus 16 RSgLEekva~~L~~~gv~~~yE~~ki~Yvipa~~h~YtPDF~L--png-iiiEtK-----------G~f~---------- 71 (149)
T PF05367_consen 16 RSGLEEKVAKQLEKLGVKYEYESWKIPYVIPASEHKYTPDFVL--PNG-IIIETK-----------GRFD---------- 71 (149)
T ss_dssp --HHHHHHHHHHHHTT---EES-EEEEEEEEEEEEEE--SEE---TTS-EEEEEE-----------SS------------
T ss_pred chhHHHHHHHHHHHcCCCceeeeeeeeeEeeccccccCCCEEc--cCc-eEEEee-----------eccC----------
Confidence 366789999999987644556666655432 12244889998 777 789999 3442
Q ss_pred cCCChHHHHHHHHHHHHHHHHHcCCCCCCCceeEEEEEeCCCeeEecCCCCCCccccHhHHhH---hhhhhhhhhhhhhc
Q 024593 109 AHPDPVAEAKKQASILESYLEQRGVALPEGYLSYKVIIPNPKFRVINASYFPPEVISYDQWML---MKPENKSMLSGWIK 185 (265)
Q Consensus 109 ~~~nPv~Q~~r~~~~L~~~L~~~g~~lp~~~i~~~VVf~np~~~l~~~~~~~p~Vi~~~ql~~---~~~~~~~~~~~wi~ 185 (265)
.+-+++..++++- .|+ ++=..||.+|...+... .+ .++.+|-+ |.=..+-.+.+||+
T Consensus 72 ------~~DR~K~l~Ik~q-------~P~--LDIR~VFq~~~~Ki~K~---Sk--TTYa~Wc~K~Gf~~adk~IP~~WLk 131 (149)
T PF05367_consen 72 ------AEDRRKHLLIKEQ-------YPE--LDIRFVFQSSRTKIYKG---SK--TTYAEWCEKHGFPWADKLIPVDWLK 131 (149)
T ss_dssp ------HHHHHHHHHHHHH--------TT--SEEEEEES-TTSBSSTT----S--SBHHHHHHHCT-EEEESS--HHHHH
T ss_pred ------cchhHHHHHHHHh-------CCC--ccEEEEEecCCCcccCC---CC--ccHHHHHHHcCCccccccCCHHHHh
Confidence 1223333333322 343 56778999988776543 22 34555532 11112356667777
Q ss_pred ccc
Q 024593 186 GAF 188 (265)
Q Consensus 186 ~~~ 188 (265)
..-
T Consensus 132 E~~ 134 (149)
T PF05367_consen 132 EPK 134 (149)
T ss_dssp S--
T ss_pred Ccc
Confidence 543
No 40
>PF09002 DUF1887: Domain of unknown function (DUF1887); InterPro: IPR015093 This entry represents a set of hypothetical bacterial and archaeal proteins. ; PDB: 1XMX_A.
Probab=59.12 E-value=14 Score=35.46 Aligned_cols=25 Identities=16% Similarity=0.430 Sum_probs=20.5
Q ss_pred CccceeEEEEeCCeEEEEEeeccceeE
Q 024593 63 SRQNIDIVLITKGEAVVISVKNLSGFV 89 (265)
Q Consensus 63 ~~~EID~Vivt~~gI~VIEVKn~sG~I 89 (265)
...|+|++++..+-+++||+| +|..
T Consensus 288 ~~NElDV~~~~~~~L~~iECK--t~~~ 312 (381)
T PF09002_consen 288 VKNELDVAFMKGNKLYIIECK--TGKF 312 (381)
T ss_dssp EEEEEEEEEEETTEEEEEEEE--SS--
T ss_pred CCcceEEEEEeCCEEEEEEcC--CCCC
Confidence 357999999999999999999 4554
No 41
>PRK04247 hypothetical protein; Provisional
Probab=59.00 E-value=23 Score=32.01 Aligned_cols=51 Identities=22% Similarity=0.278 Sum_probs=30.4
Q ss_pred cccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEee
Q 024593 29 TSDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVK 83 (265)
Q Consensus 29 ~~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVK 83 (265)
.+.+.-...+++.+..+..+..+-.-..+.+ ..+||++...+. .+++||+|
T Consensus 128 g~E~~Lq~~l~~np~li~~G~~~l~rE~~t~----~G~IDila~D~~G~lViVEvK 179 (238)
T PRK04247 128 GSEADMVDRILENPDLIEEGFRPLAREYPTP----AGIIDILGRDKDGNLVVLELK 179 (238)
T ss_pred ccHHHHHHHHHhCHHHHcCCCEEEEEecccC----CCceeEEEECCCCCEEEEEEE
Confidence 3333344555555555533332223333333 339999999985 79999999
No 42
>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=57.42 E-value=77 Score=28.12 Aligned_cols=50 Identities=26% Similarity=0.401 Sum_probs=36.6
Q ss_pred ceeEEEEeCCeEEEEEeeccceeEEECCCCcEEEEecCCcccccCCC-hHHHHHHHHHHHHHHHHH
Q 024593 66 NIDIVLITKGEAVVISVKNLSGFVTVNADGSWVCEAVGRHRSAAHPD-PVAEAKKQASILESYLEQ 130 (265)
Q Consensus 66 EID~Vivt~~gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~~~~n-Pv~Q~~r~~~~L~~~L~~ 130 (265)
-||+++-++.+=..||||+- .+.. + +.-.||| |-....+|...|..++++
T Consensus 105 R~Dfll~~~~~~~~vEVKsv----------tL~~---~--~~a~FPDApT~RG~kHL~eL~~l~~~ 155 (215)
T PF03749_consen 105 RFDFLLEDNGGKCYVEVKSV----------TLVE---D--GIAMFPDAPTERGRKHLRELAELAEE 155 (215)
T ss_pred cEEEEEEcCCCCEEEEEeee----------Eecc---C--CcccCCCccchHHHHHHHHHHHHHhc
Confidence 59999999999999999941 1111 1 1134775 888889999999888774
No 43
>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=48.24 E-value=54 Score=27.09 Aligned_cols=35 Identities=29% Similarity=0.399 Sum_probs=26.3
Q ss_pred eEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEee
Q 024593 49 KAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVK 83 (265)
Q Consensus 49 ~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVK 83 (265)
.+-.++.+....-+-..-||.|...++++.++|+|
T Consensus 53 ~~~~~v~l~~~~~~l~G~iD~i~~~~~~~~ive~K 87 (178)
T TIGR00372 53 REEKEVPLKSKKLGLKGVIDVVLEADGELVPVEVK 87 (178)
T ss_pred EEEEeeEeEcccCCcEEEEEEEEEECCeEEEEEEe
Confidence 34556666665434455899999999999999999
No 44
>PHA02691 hypothetical protein; Provisional
Probab=45.76 E-value=1.5e+02 Score=23.60 Aligned_cols=86 Identities=7% Similarity=0.096 Sum_probs=52.9
Q ss_pred hhhhHHHHHHHHHHHHHhc-C-CcccccccccchhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCCeEEE
Q 024593 2 WVQILCGLVIYKICKKLFY-D-DDVLDVETSDSNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVV 79 (265)
Q Consensus 2 ~~~i~~~~~~~~l~~~~~~-~-~~~~~~~~~~~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~V 79 (265)
|.-=++-+|+|.++-.||. . -+++++.-.....++.+..+..... ..++..+.++++++....++.+=.=+..|.++
T Consensus 3 ~l~~l~fFi~FL~l~Y~~ny~PTNKlqlaV~~l~~e~~~~k~~d~~~-p~~l~s~iF~~~~~~~~~~v~~yYds~~g~Vt 81 (110)
T PHA02691 3 WALEVALFAAFLAAAYVLTFLPTNKMQLAVRELADARAWRQRTDAQL-DGVSESVLFPRPDAPQGSAVIASMDSRRARVT 81 (110)
T ss_pred hHHHHHHHHHHHHHHHHHhhccchhHHHhhhhhhhhhhHHhhccccC-cceeeEEEecCCCCccccceEEEEcCCCCeEE
Confidence 6544566667766645554 2 2355555444444454444433222 24788888888877655677777777789999
Q ss_pred EEeecccee
Q 024593 80 ISVKNLSGF 88 (265)
Q Consensus 80 IEVKn~sG~ 88 (265)
|+.||=.-.
T Consensus 82 v~~~~kK~~ 90 (110)
T PHA02691 82 VAHGREKST 90 (110)
T ss_pred EEeCCcEEE
Confidence 999864433
No 45
>COG5321 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.45 E-value=30 Score=28.76 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=25.2
Q ss_pred CceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEee
Q 024593 47 KGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVK 83 (265)
Q Consensus 47 ~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVK 83 (265)
+..++..|.++.. . ..|++-++++ .|.+||+|
T Consensus 36 g~a~LpEltLasG---R--RADLials~kGeiwIiEiK 68 (164)
T COG5321 36 GHAVLPELTLASG---R--RADLIALSPKGEIWIIEIK 68 (164)
T ss_pred ccccCccccccCC---c--ccceeeecCCCcEEEEEee
Confidence 3456777777653 2 7899999997 89999999
No 46
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=38.87 E-value=29 Score=36.17 Aligned_cols=30 Identities=20% Similarity=0.410 Sum_probs=23.7
Q ss_pred EeeCCCCCCccceeEEEEeCCeEEEEEeeccc
Q 024593 55 RIPDPDTGSRQNIDIVLITKGEAVVISVKNLS 86 (265)
Q Consensus 55 rlp~~~~~~~~EID~Vivt~~gI~VIEVKn~s 86 (265)
.+.+.++.. -+|+|++.++.+++||||.|.
T Consensus 54 ~~~~~~~~~--~~d~~~~~~~~~~~~e~kd~~ 83 (699)
T PRK14535 54 SVDDDNGSS--GVDIIALHESTLWLIEIKDYY 83 (699)
T ss_pred cccccCCcc--eeeEEEEcCCcEEEEEechhh
Confidence 344444434 899999999999999999876
No 47
>PHA02552 4 head completion protein; Provisional
Probab=38.23 E-value=95 Score=26.14 Aligned_cols=106 Identities=11% Similarity=0.011 Sum_probs=58.5
Q ss_pred CcccccccccchhHHHHHHHHhcCCCce--EEeeeEeeC----CCCCCccceeEEEEeCCe-EEEEEeeccceeEEECCC
Q 024593 22 DDVLDVETSDSNAIFSVAARLEKLYKGK--AYVGLRIPD----PDTGSRQNIDIVLITKGE-AVVISVKNLSGFVTVNAD 94 (265)
Q Consensus 22 ~~~~~~~~~~~~~~~~v~~~L~~l~~~~--vl~~lrlp~----~~~~~~~EID~Vivt~~g-I~VIEVKn~sG~I~~~~~ 94 (265)
++.+--+|+ .|......|+.-+.-. .=+.+.||. .+...+.-.|.+|....| .++||||..+=.-.....
T Consensus 19 ~~~V~yeS~---lE~d~~~~le~dp~V~~~~sqp~~I~Y~~~~~Gk~r~Y~PDFLV~~~dG~~~lvEVKp~~~~~~p~~~ 95 (151)
T PHA02552 19 PRKITYRSS---WERWFMKWLDKNPSVIKWGSEEVVIPYFSNADGKRRRYFMDFYVKVDNGQKFLIEVKPKKETQPPKKP 95 (151)
T ss_pred CCeEEECCH---HHHHHHHHhhcCCCeeEEecCCEEEEEEecCCCCeeeEcCcEEEEEeCCCEEEEEEccHHHccCcccc
Confidence 334444444 6777677777666532 334467744 444456789999987765 999999942211110000
Q ss_pred CcEEEEecCCcccccCCC---hHHHHHHHHHHHHHHHHHcCCCC
Q 024593 95 GSWVCEAVGRHRSAAHPD---PVAEAKKQASILESYLEQRGVAL 135 (265)
Q Consensus 95 ~~W~q~~~~~~~~~~~~n---Pv~Q~~r~~~~L~~~L~~~g~~l 135 (265)
. +..-..+..+.| =...++.+-++-+.+-+++|+.+
T Consensus 96 ~-----~~~~~~~~~~~~~~~~w~~~~~K~~Aa~~~a~~~Gw~F 134 (151)
T PHA02552 96 A-----KMTTAAKKRFINEVYTWSVNTDKWKAARALCEKKGWKF 134 (151)
T ss_pred c-----ccchhhhhhhhhhhhhHHHHHHHHHHHHHHHHHcCCEE
Confidence 0 000000122332 24567777777777778888763
No 48
>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=38.09 E-value=41 Score=24.68 Aligned_cols=18 Identities=22% Similarity=0.763 Sum_probs=14.5
Q ss_pred ceeEEEEeCCeEEEEEeec
Q 024593 66 NIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 66 EID~Vivt~~gI~VIEVKn 84 (265)
|+|+ ++..+.++++|+|+
T Consensus 4 ElDv-vikdg~~ilvEikS 21 (70)
T PF07788_consen 4 ELDV-VIKDGKVILVEIKS 21 (70)
T ss_pred EEEE-EEECCeEEEEEEEc
Confidence 6776 66777999999994
No 49
>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=36.28 E-value=88 Score=28.12 Aligned_cols=49 Identities=27% Similarity=0.306 Sum_probs=27.4
Q ss_pred chhHHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEeec
Q 024593 32 SNAIFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVKN 84 (265)
Q Consensus 32 ~~~~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVKn 84 (265)
+.-...+++..+.+..+..+-.-..+.+. .-||++...+. ..+|||+|.
T Consensus 107 ~dL~~~i~~~p~lie~g~~~i~rE~~t~~----G~IDiL~~D~~G~~VVIElKR 156 (228)
T PF01939_consen 107 ADLQDLIAENPELIEEGLRLIEREYPTPI----GRIDILAKDKDGNLVVIELKR 156 (228)
T ss_dssp HHHHHHHHH-GGGT-TT-EEEEEEEEETT----EEEEEEEE-TTS-EEEEEE-S
T ss_pred HHHHHHHHhCHHHhCCCCEEEEEEEeCCC----CceeEEEECCCCCEEEEEEEe
Confidence 33455666666666544433333344442 27999999997 599999994
No 50
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=35.75 E-value=38 Score=24.93 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=19.4
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
..==+|.+.+|+.+.|-|.+|..
T Consensus 10 ~~~v~V~l~dgR~~~G~l~~~D~ 32 (75)
T cd06168 10 GRTMRIHMTDGRTLVGVFLCTDR 32 (75)
T ss_pred CCeEEEEEcCCeEEEEEEEEEcC
Confidence 33457999999999999998876
No 51
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=33.40 E-value=43 Score=24.86 Aligned_cols=20 Identities=10% Similarity=0.383 Sum_probs=17.9
Q ss_pred eEEEEecCeEEeeeeeeccC
Q 024593 214 DRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 214 drv~l~gG~~~~Gd~~~~~~ 233 (265)
=.|.++||+.+.|-+++|..
T Consensus 14 V~V~l~~gr~~~G~L~~fD~ 33 (82)
T cd01730 14 VYVKLRGDRELRGRLHAYDQ 33 (82)
T ss_pred EEEEECCCCEEEEEEEEEcc
Confidence 46899999999999999887
No 52
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=32.64 E-value=46 Score=24.44 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=18.3
Q ss_pred eeEEEEecCeEEeeeeeeccC
Q 024593 213 WDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 213 wdrv~l~gG~~~~Gd~~~~~~ 233 (265)
==+|.+++|+.+.|-+.+|..
T Consensus 12 ~V~V~l~dgR~~~G~L~~~D~ 32 (79)
T cd01717 12 RLRVTLQDGRQFVGQFLAFDK 32 (79)
T ss_pred EEEEEECCCcEEEEEEEEEcC
Confidence 346899999999999999876
No 53
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=32.49 E-value=45 Score=23.24 Aligned_cols=23 Identities=22% Similarity=0.323 Sum_probs=19.9
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==+|++++|+.+.|-+.+|..
T Consensus 8 g~~V~V~l~~g~~~~G~L~~~D~ 30 (67)
T PF01423_consen 8 GKRVRVELKNGRTYRGTLVSFDQ 30 (67)
T ss_dssp TSEEEEEETTSEEEEEEEEEEET
T ss_pred CcEEEEEEeCCEEEEEEEEEeec
Confidence 44457999999999999999986
No 54
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=32.46 E-value=48 Score=23.54 Aligned_cols=23 Identities=22% Similarity=0.223 Sum_probs=19.4
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==.|+|++|+.+.|-+.+|..
T Consensus 10 ~~~V~V~l~~g~~~~G~L~~~D~ 32 (68)
T cd01731 10 NKPVLVKLKGGKEVRGRLKSYDQ 32 (68)
T ss_pred CCEEEEEECCCCEEEEEEEEECC
Confidence 34457899999999999999876
No 55
>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=31.92 E-value=52 Score=30.60 Aligned_cols=51 Identities=16% Similarity=0.160 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCC---CceEE-----------eeeEeeCCCCCCccceeEEEEeCCeEEEEEeeccce
Q 024593 35 IFSVAARLEKLY---KGKAY-----------VGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNLSG 87 (265)
Q Consensus 35 ~~~v~~~L~~l~---~~~vl-----------~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~sG 87 (265)
+..|+..+++.. +...+ -+..++.. ...+.+|.||-+++.+|+|||.-|+|
T Consensus 154 E~~ve~~i~~~~~~~~~~y~~q~~~~~i~~~~~~d~~~~--k~~KrFDFvi~~~~k~y~IE~NFY~~ 218 (286)
T PF04556_consen 154 ENLVENYIKKACFKKNINYFKQVYSSEIKEKWGIDLSVG--KSEKRFDFVIKTNKKIYLIETNFYGS 218 (286)
T ss_pred HHHHHHHHHHHHhhcCCcEEeecCHHHHHHHhCCcccCC--CCceEEEEEEEcCCEEEEEEEeeecC
Confidence 788888887752 11111 12334443 33558999999999999999997775
No 56
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=31.07 E-value=53 Score=22.82 Aligned_cols=23 Identities=17% Similarity=0.141 Sum_probs=19.7
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==+|+|++|+.+.|-+.+|..
T Consensus 8 ~~~V~V~l~~g~~~~G~L~~~D~ 30 (67)
T smart00651 8 GKRVLVELKNGREYRGTLKGFDQ 30 (67)
T ss_pred CcEEEEEECCCcEEEEEEEEECc
Confidence 44457899999999999999986
No 57
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=30.24 E-value=55 Score=23.55 Aligned_cols=25 Identities=16% Similarity=0.186 Sum_probs=20.9
Q ss_pred CCceeEEEEecCeEEeeeeeeccCc
Q 024593 210 APIWDRLEVKGNKYVLGEFLEFKGK 234 (265)
Q Consensus 210 ~~twdrv~l~gG~~~~Gd~~~~~~~ 234 (265)
.+.==.|||++|..+.|-+.+|.+-
T Consensus 9 ~g~~V~VeLk~g~~~~G~L~~~D~~ 33 (70)
T cd01721 9 EGHIVTVELKTGEVYRGKLIEAEDN 33 (70)
T ss_pred CCCEEEEEECCCcEEEEEEEEEcCC
Confidence 3555578999999999999999873
No 58
>PRK13258 7-cyano-7-deazaguanine reductase; Provisional
Probab=30.12 E-value=2.2e+02 Score=22.66 Aligned_cols=44 Identities=14% Similarity=0.119 Sum_probs=32.3
Q ss_pred CccccHhHHhHhhhhhhhhhhhhhcccccCCcccccHHHHHHHHHHhccC--CceeEEE
Q 024593 161 PEVISYDQWMLMKPENKSMLSGWIKGAFRGGKKEMQESIHQQLNFILSTA--PIWDRLE 217 (265)
Q Consensus 161 p~Vi~~~ql~~~~~~~~~~~~~wi~~~~~~~~~~~~d~~~~~~~~~L~~~--~twdrv~ 217 (265)
+.++-...|+.|+.++++.. ..+|+.+++++..|+.+ |.|=+|.
T Consensus 48 ~~iielkSLk~Yl~Sf~~~~-------------~~qE~lt~~I~~dL~~~l~p~~l~v~ 93 (114)
T PRK13258 48 KKCVELKSLKLYLFSFRNHG-------------IFHEDCTNRILDDLVALLDPRWLRVG 93 (114)
T ss_pred CCEEcHHHHHHHHHHHHCCC-------------chHHHHHHHHHHHHHHhhCCCEEEEE
Confidence 44777778888888876552 46788888888888876 7776663
No 59
>PF08814 XisH: XisH protein; InterPro: IPR014919 The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required []. ; PDB: 2OKF_A.
Probab=29.88 E-value=54 Score=27.17 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=23.9
Q ss_pred HHHHHHHhcCCCceEEee-eEeeCCCCCCccceeE----EEEe-C-CeEEEEEeeccc
Q 024593 36 FSVAARLEKLYKGKAYVG-LRIPDPDTGSRQNIDI----VLIT-K-GEAVVISVKNLS 86 (265)
Q Consensus 36 ~~v~~~L~~l~~~~vl~~-lrlp~~~~~~~~EID~----Vivt-~-~gI~VIEVKn~s 86 (265)
..|.++|.| +||.|=+| +++...+.. -+||+ ++.. + +.=+.||+|.+-
T Consensus 9 ~~Vk~AL~k-dgW~IT~DPl~l~~~~~~--~~iDLgAek~iaAek~~~kIAVEIKSF~ 63 (135)
T PF08814_consen 9 DAVKNALEK-DGWTITHDPLRLKYGGVD--LYIDLGAEKLIAAEKDGEKIAVEIKSFL 63 (135)
T ss_dssp HHHHHHHHH-TT-EEEESS---EETTEE------------EEEEETTEEEEEEE----
T ss_pred HHHHHHHHH-cCCEEECCCcEEEECcEE--EEeccchHHHHHhhccCceEEEEEeCCC
Confidence 457788888 78888888 788776543 38886 2332 2 367889999543
No 60
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=29.50 E-value=57 Score=23.15 Aligned_cols=23 Identities=9% Similarity=-0.062 Sum_probs=19.2
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==.|+|+||+.+.|-+.+|..
T Consensus 10 ~~~V~V~Lk~g~~~~G~L~~~D~ 32 (67)
T cd01726 10 GRPVVVKLNSGVDYRGILACLDG 32 (67)
T ss_pred CCeEEEEECCCCEEEEEEEEEcc
Confidence 33446899999999999998876
No 61
>PF13588 HSDR_N_2: Type I restriction enzyme R protein N terminus (HSDR_N); PDB: 3H1T_A.
Probab=27.40 E-value=57 Score=25.04 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=20.2
Q ss_pred eEEeeeEeeCCCCCCccceeEEEEeCC----eEEEEEeec
Q 024593 49 KAYVGLRIPDPDTGSRQNIDIVLITKG----EAVVISVKN 84 (265)
Q Consensus 49 ~vl~~lrlp~~~~~~~~EID~Vivt~~----gI~VIEVKn 84 (265)
.+.....++.... ...+|.+|..+. -+++||+|.
T Consensus 23 ~i~~e~~i~~~~~--~~r~Divv~~~~~~~~p~~iIE~K~ 60 (112)
T PF13588_consen 23 DIEVEVPISIGSK--KKRADIVVFRDDKDNKPLIIIECKA 60 (112)
T ss_dssp -EEEETTE-EE------EEEEEEEEET--TEEEEEEEE--
T ss_pred hEEEEEEEEECCC--CeeeEEEEEeCCCCCCeEEEEEECC
Confidence 4555555553323 347999999887 789999993
No 62
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=27.19 E-value=70 Score=21.77 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=19.0
Q ss_pred eeEEEEecCeEEeeeeeeccCc
Q 024593 213 WDRLEVKGNKYVLGEFLEFKGK 234 (265)
Q Consensus 213 wdrv~l~gG~~~~Gd~~~~~~~ 234 (265)
==+|++++|+.+.|-+.+|..-
T Consensus 8 ~V~V~l~~g~~~~G~L~~~D~~ 29 (63)
T cd00600 8 TVRVELKDGRVLEGVLVAFDKY 29 (63)
T ss_pred EEEEEECCCcEEEEEEEEECCC
Confidence 3468999999999999999864
No 63
>PRK03298 hypothetical protein; Provisional
Probab=26.60 E-value=4.3e+02 Score=23.74 Aligned_cols=45 Identities=20% Similarity=0.256 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCceEEeeeEeeCCCCCCccceeEEEEeCC-eEEEEEee
Q 024593 35 IFSVAARLEKLYKGKAYVGLRIPDPDTGSRQNIDIVLITKG-EAVVISVK 83 (265)
Q Consensus 35 ~~~v~~~L~~l~~~~vl~~lrlp~~~~~~~~EID~Vivt~~-gI~VIEVK 83 (265)
-..++...+.+..++-+-.--.|.+ ...||++---.. ..++||+|
T Consensus 109 q~~lae~p~~i~~G~~lv~rE~~t~----~G~IDil~rD~~G~~V~vEvK 154 (224)
T PRK03298 109 QELLAEHIETLGEGYTLVRREYPTA----IGPVDLLCRDADGGTVAVEIK 154 (224)
T ss_pred HHHHHhCHHHhcCCCEEEEEEecCC----CCceeEEEEcCCCCEEEEEEE
Confidence 3444444444554444433334444 239999999965 68999999
No 64
>PF08907 DUF1853: Domain of unknown function (DUF1853); InterPro: IPR015003 This group of proteins are functionally uncharacterised.
Probab=26.38 E-value=2.9e+02 Score=25.41 Aligned_cols=55 Identities=16% Similarity=0.040 Sum_probs=40.0
Q ss_pred chhHHHHHHHHhcCCCc-eEEeeeEeeCCCCCCccceeEEEE--eCCeEEEEEe--eccce
Q 024593 32 SNAIFSVAARLEKLYKG-KAYVGLRIPDPDTGSRQNIDIVLI--TKGEAVVISV--KNLSG 87 (265)
Q Consensus 32 ~~~~~~v~~~L~~l~~~-~vl~~lrlp~~~~~~~~EID~Viv--t~~gI~VIEV--Kn~sG 87 (265)
.++|.-++-.|+..+.. .+-+|+.|-..+. +-.|+|+|+- ..+.++=+|+ |=|-|
T Consensus 62 ~y~E~L~~f~l~~~p~~~lla~NlqI~~~~~-TlGElDfl~~~~~~~~~~H~ElAiKFYL~ 121 (284)
T PF08907_consen 62 FYFERLLSFWLEHAPHYRLLAENLQIRSGKR-TLGELDFLLRNRPNGQIEHWELAIKFYLG 121 (284)
T ss_pred HHHHHHHHHHHHhCCCcchhhcCCcEecCCe-EEEeeEEEEEecCCCCEEEEEEEeeeecc
Confidence 44577777778877765 5788999886543 4569999999 5568888886 55544
No 65
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=25.99 E-value=71 Score=23.05 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=18.1
Q ss_pred eEEEEecCeEEeeeeeeccC
Q 024593 214 DRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 214 drv~l~gG~~~~Gd~~~~~~ 233 (265)
=.|+|++|+.+.|-+.+|..
T Consensus 17 V~V~lk~g~~~~G~L~~~D~ 36 (72)
T PRK00737 17 VLVRLKGGREFRGELQGYDI 36 (72)
T ss_pred EEEEECCCCEEEEEEEEEcc
Confidence 56899999999999999876
No 66
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.81 E-value=75 Score=23.06 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=17.9
Q ss_pred eEEEEecCeEEeeeeeeccC
Q 024593 214 DRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 214 drv~l~gG~~~~Gd~~~~~~ 233 (265)
=+|.|++|+.+.|-+.+|..
T Consensus 13 V~V~L~~g~~~~G~L~~~D~ 32 (72)
T cd01719 13 LSLKLNGNRKVSGILRGFDP 32 (72)
T ss_pred EEEEECCCeEEEEEEEEEcc
Confidence 36899999999999999985
No 67
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.71 E-value=71 Score=23.73 Aligned_cols=22 Identities=18% Similarity=0.253 Sum_probs=18.3
Q ss_pred ceeEEEEecCeEEeeeeeeccC
Q 024593 212 IWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 212 twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
.==+|.|++|+.+.|-+++|..
T Consensus 13 k~V~V~l~~gr~~~G~L~~~D~ 34 (81)
T cd01729 13 KKIRVKFQGGREVTGILKGYDQ 34 (81)
T ss_pred CeEEEEECCCcEEEEEEEEEcC
Confidence 3347889999999999998765
No 68
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=25.63 E-value=75 Score=22.61 Aligned_cols=23 Identities=9% Similarity=-0.076 Sum_probs=19.2
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==.|+|++|+.+.|-+.+|..
T Consensus 11 g~~V~V~Lk~g~~~~G~L~~~D~ 33 (68)
T cd01722 11 GKPVIVKLKWGMEYKGTLVSVDS 33 (68)
T ss_pred CCEEEEEECCCcEEEEEEEEECC
Confidence 33346999999999999998876
No 69
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.13 E-value=75 Score=23.18 Aligned_cols=23 Identities=13% Similarity=0.073 Sum_probs=19.8
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
+.==.|+|++|..+.|-+.+|.+
T Consensus 11 g~~V~VeLkng~~~~G~L~~~D~ 33 (76)
T cd01723 11 NHPMLVELKNGETYNGHLVNCDN 33 (76)
T ss_pred CCEEEEEECCCCEEEEEEEEEcC
Confidence 44456899999999999999987
No 70
>COG4811 Predicted membrane protein [Function unknown]
Probab=24.96 E-value=1.8e+02 Score=24.19 Aligned_cols=33 Identities=18% Similarity=0.282 Sum_probs=27.2
Q ss_pred CceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeecc
Q 024593 47 KGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKNL 85 (265)
Q Consensus 47 ~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn~ 85 (265)
.+..|.|+-+|.. .|-.+=++++||+|+|.++-
T Consensus 97 ~Gfffan~~~~Ya------rI~~mNLsEdgvLVi~l~~r 129 (152)
T COG4811 97 KGFFFANVFIEYA------RIKAMNLSEDGVLVIQLEQR 129 (152)
T ss_pred cCeeEEEEEEehh------hhhhcCcCcCcEEEEEeccc
Confidence 4678999999986 45567789999999999963
No 71
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=24.79 E-value=4.2e+02 Score=23.71 Aligned_cols=49 Identities=20% Similarity=0.293 Sum_probs=33.0
Q ss_pred ceeEEEEeCC-eEEEEEeeccceeEEECCCCcEEEEecCCcccccCCC-hHHHHHHHHHHHHHHHH
Q 024593 66 NIDIVLITKG-EAVVISVKNLSGFVTVNADGSWVCEAVGRHRSAAHPD-PVAEAKKQASILESYLE 129 (265)
Q Consensus 66 EID~Vivt~~-gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~~~~n-Pv~Q~~r~~~~L~~~L~ 129 (265)
-||+++=... +-..||||+- .+. + + +.-.||| |-....+|...|..+.+
T Consensus 118 R~Dfll~~~~~~~~~vEVKsv--tL~-~-~-----------~~A~FPDapT~RG~kHl~eL~~l~~ 168 (234)
T PRK00347 118 RIDFLLTADDRPDCYVEVKSV--TLE-E-N-----------GLAMFPDAVTERGQKHLRELIELAK 168 (234)
T ss_pred cEEEEEecCCCCcEEEEEcCE--EeC-C-C-----------CEEECCCCCcHHHHHHHHHHHHHHH
Confidence 8999997654 5579999953 111 1 1 1233665 77788888888887665
No 72
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.78 E-value=57 Score=27.62 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=34.7
Q ss_pred cCCChHHHHHHHHHHHHHHHHHcCCCCCCCceeEEEEEeCCCee
Q 024593 109 AHPDPVAEAKKQASILESYLEQRGVALPEGYLSYKVIIPNPKFR 152 (265)
Q Consensus 109 ~~~nPv~Q~~r~~~~L~~~L~~~g~~lp~~~i~~~VVf~np~~~ 152 (265)
-|.|-..--++|..+.+.+|++-+++-|.+ -.+.-||+||++.
T Consensus 79 IF~nIA~SEQ~HmDAVk~LlekYnv~dP~~-~~siGvF~Npelq 121 (189)
T COG4902 79 IFRNIAASEQEHMDAVKSLLEKYNVQDPAS-TTSIGVFTNPELQ 121 (189)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHcCCCCCCc-cCcceeecCHHHH
Confidence 366777777899999999999988876644 6788899998765
No 73
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=24.60 E-value=84 Score=23.03 Aligned_cols=22 Identities=9% Similarity=0.140 Sum_probs=18.8
Q ss_pred ceeEEEEecCeEEeeeeeeccC
Q 024593 212 IWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 212 twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
.==.|.+++|+.+.|-+++|..
T Consensus 13 k~v~V~l~~gr~~~G~L~~fD~ 34 (74)
T cd01728 13 KKVVVLLRDGRKLIGILRSFDQ 34 (74)
T ss_pred CEEEEEEcCCeEEEEEEEEECC
Confidence 3446899999999999999986
No 74
>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=23.88 E-value=55 Score=20.00 Aligned_cols=10 Identities=40% Similarity=1.218 Sum_probs=7.8
Q ss_pred hhhhHHHHHH
Q 024593 2 WVQILCGLVI 11 (265)
Q Consensus 2 ~~~i~~~~~~ 11 (265)
|+||.|-|++
T Consensus 9 ~lAi~c~LL~ 18 (30)
T PF11466_consen 9 WLAIVCVLLF 18 (30)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 7888887764
No 75
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=23.70 E-value=80 Score=23.08 Aligned_cols=19 Identities=16% Similarity=0.340 Sum_probs=17.4
Q ss_pred EEEEecCeEEeeeeeeccC
Q 024593 215 RLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 215 rv~l~gG~~~~Gd~~~~~~ 233 (265)
.|+|++|+.+.|-+.+|..
T Consensus 21 ~V~lk~g~~~~G~L~~~D~ 39 (79)
T COG1958 21 LVKLKNGREYRGTLVGFDQ 39 (79)
T ss_pred EEEECCCCEEEEEEEEEcc
Confidence 5799999999999999876
No 76
>PF15516 BpuSI_N: BpuSI N-terminal domain
Probab=22.78 E-value=2.5e+02 Score=23.52 Aligned_cols=20 Identities=35% Similarity=0.323 Sum_probs=16.8
Q ss_pred cceeEEEEeC---CeEEEEEeec
Q 024593 65 QNIDIVLITK---GEAVVISVKN 84 (265)
Q Consensus 65 ~EID~Vivt~---~gI~VIEVKn 84 (265)
-+.|.|+.-. .-+++||||.
T Consensus 43 i~~DFvl~~k~t~k~vL~iEvKR 65 (159)
T PF15516_consen 43 IVPDFVLRRKSTNKYVLIIEVKR 65 (159)
T ss_pred cccceEEEecCCceEEEEEEEec
Confidence 3999999976 4899999993
No 77
>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=22.72 E-value=96 Score=22.86 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=30.2
Q ss_pred cceeEEEEeCC----eEEEEEeeccceeEEECCCCcEEEEecCCcccccCCChHHHHHHHHHHHHHHHHHcCCC
Q 024593 65 QNIDIVLITKG----EAVVISVKNLSGFVTVNADGSWVCEAVGRHRSAAHPDPVAEAKKQASILESYLEQRGVA 134 (265)
Q Consensus 65 ~EID~Vivt~~----gI~VIEVKn~sG~I~~~~~~~W~q~~~~~~~~~~~~nPv~Q~~r~~~~L~~~L~~~g~~ 134 (265)
.-.|++|...+ ...++|||. . ....+ .....+..+-+.|.+++|++
T Consensus 33 yTpDFlv~~~~g~~~~~~~ieVK~-----------------~-----~~l~~--~~~~~k~~~~~~y~~~~g~~ 82 (88)
T PF08722_consen 33 YTPDFLVTYRDGNGKKPVAIEVKP-----------------S-----SELEK--PRTKEKLEIEREYWEEQGIP 82 (88)
T ss_dssp -EEEEEEEESSS--SSEEEEEE-------------------G-----GGGGS--HHHHHHHHHHHHHHHHCT--
T ss_pred EeccEEEEEccCCcceEEEEEEcc-----------------H-----HHhcC--hhHHHHHHHHHHHHHHcCCe
Confidence 47899999998 799999994 0 11223 44556666778899988865
No 78
>PRK02913 hypothetical protein; Provisional
Probab=22.70 E-value=1.9e+02 Score=24.39 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=27.1
Q ss_pred CCceEEeeeEeeCCCCCCccceeEEEEeCCeEEEEEeec
Q 024593 46 YKGKAYVGLRIPDPDTGSRQNIDIVLITKGEAVVISVKN 84 (265)
Q Consensus 46 ~~~~vl~~lrlp~~~~~~~~EID~Vivt~~gI~VIEVKn 84 (265)
..+..|.|+-+|.+ .|-.+=++++||+|++.++
T Consensus 94 ~~GFf~an~fi~Y~------~Ik~mNLSEDgiLVi~Le~ 126 (150)
T PRK02913 94 EKGFFYANVFIEYS------RIKAMNLSEDGILVIDLEQ 126 (150)
T ss_pred ccceEEeeeeeehH------HhhhcccccCCEEEEEecC
Confidence 35688999999887 4556668899999999997
No 79
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=21.75 E-value=5.6e+02 Score=22.59 Aligned_cols=32 Identities=13% Similarity=0.198 Sum_probs=23.5
Q ss_pred ceeEEEEeC-CeEEEEEeeccceeEEECCCCcEEE
Q 024593 66 NIDIVLITK-GEAVVISVKNLSGFVTVNADGSWVC 99 (265)
Q Consensus 66 EID~Vivt~-~gI~VIEVKn~sG~I~~~~~~~W~q 99 (265)
+++.|.-|| .|+|=|.+. +|.++.+++++.+.
T Consensus 36 ~v~~v~~sp~~Gl~ev~~~--~~i~Y~~~dg~y~i 68 (232)
T PRK10877 36 QSADIQPSPVAGMKTVLTE--SGVLYITDDGKHII 68 (232)
T ss_pred ceeEEccCCCCCeEEEEEC--CeEEEEcCCCCEEE
Confidence 667777778 588888774 56888888886653
No 80
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=21.39 E-value=2.5e+02 Score=26.26 Aligned_cols=104 Identities=9% Similarity=0.022 Sum_probs=59.9
Q ss_pred CCChHHHHHHHHHHHHHHHHHcCCCCCCCceeEEEEEeC-CCeeEecCC---CCCCc------------cccHhHHhHhh
Q 024593 110 HPDPVAEAKKQASILESYLEQRGVALPEGYLSYKVIIPN-PKFRVINAS---YFPPE------------VISYDQWMLMK 173 (265)
Q Consensus 110 ~~nPv~Q~~r~~~~L~~~L~~~g~~lp~~~i~~~VVf~n-p~~~l~~~~---~~~p~------------Vi~~~ql~~~~ 173 (265)
-.=|..|.-..+.-.|+.|++.|.+.|.+=+++.+++.| |+.+-...- +..|- ++ ..|+.+.-
T Consensus 147 ~~~tasql~~~I~~vrsav~~agy~gpV~T~dsw~~~~~np~l~~~SDfia~N~~aYwd~~~~a~~~~~f~-~~q~e~vq 225 (305)
T COG5309 147 NDLTASQLIEYIDDVRSAVKEAGYDGPVTTVDSWNVVINNPELCQASDFIAANAHAYWDGQTVANAAGTFL-LEQLERVQ 225 (305)
T ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCCceeecccceeeeCChHHhhhhhhhhcccchhccccchhhhhhHHH-HHHHHHHH
Confidence 344789999999999999999999888555666666663 433321110 00000 11 12222211
Q ss_pred hhhhhhhhhhhcccccCCc-------ccccHHHHHHHHHHhccCCcee
Q 024593 174 PENKSMLSGWIKGAFRGGK-------KEMQESIHQQLNFILSTAPIWD 214 (265)
Q Consensus 174 ~~~~~~~~~wi~~~~~~~~-------~~~~d~~~~~~~~~L~~~~twd 214 (265)
...-....-|+.....|++ ..-.+-|.+.+.+++..++.|.
T Consensus 226 sa~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~G 273 (305)
T COG5309 226 SACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSCG 273 (305)
T ss_pred HhcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhccC
Confidence 1111223457777777766 2234567777778888777664
No 81
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=21.23 E-value=86 Score=23.86 Aligned_cols=19 Identities=37% Similarity=0.355 Sum_probs=16.9
Q ss_pred hhhhHHHHHHHHHHHHHhc
Q 024593 2 WVQILCGLVIYKICKKLFY 20 (265)
Q Consensus 2 ~~~i~~~~~~~~l~~~~~~ 20 (265)
-+.||++|||.+|++-+|.
T Consensus 27 lMtILivLVIIiLlImlfq 45 (85)
T PF10717_consen 27 LMTILIVLVIIILLIMLFQ 45 (85)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 4689999999999988887
No 82
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.40 E-value=1e+02 Score=23.33 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=19.2
Q ss_pred CceeEEEEecCeEEeeeeeeccC
Q 024593 211 PIWDRLEVKGNKYVLGEFLEFKG 233 (265)
Q Consensus 211 ~twdrv~l~gG~~~~Gd~~~~~~ 233 (265)
++==+|.|++|+.+.|-+.+|..
T Consensus 14 ~~~V~V~lr~~r~~~G~L~~fD~ 36 (87)
T cd01720 14 NTQVLINCRNNKKLLGRVKAFDR 36 (87)
T ss_pred CCEEEEEEcCCCEEEEEEEEecC
Confidence 34446899999999999999876
No 83
>PF05371 Phage_Coat_Gp8: Phage major coat protein, Gp8; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 1IFK_A 2C0W_A 2HI5_A 1FDM_A 1IFJ_A 2C0X_A 1IFI_A 1IFD_A 1MZT_A 1IFL_A ....
Probab=20.13 E-value=1.1e+02 Score=21.22 Aligned_cols=18 Identities=17% Similarity=0.204 Sum_probs=13.7
Q ss_pred hhhHHHHHHHHHHHHHhc
Q 024593 3 VQILCGLVIYKICKKLFY 20 (265)
Q Consensus 3 ~~i~~~~~~~~l~~~~~~ 20 (265)
+.+..++|..+||++|++
T Consensus 33 v~v~gafigirlFKKf~s 50 (52)
T PF05371_consen 33 VLVTGAFIGIRLFKKFAS 50 (52)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 345678888899988875
Done!