Query 001904
Match_columns 997
No_of_seqs 288 out of 1941
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 12:01:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.8 2.8E-21 6.1E-26 206.0 6.6 135 847-987 125-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.7 1.3E-18 2.9E-23 185.7 5.8 110 877-996 127-244 (279)
3 KOG1074 Transcriptional repres 99.4 5.6E-14 1.2E-18 166.2 1.5 77 851-929 604-692 (958)
4 KOG1074 Transcriptional repres 99.3 4.6E-13 1E-17 158.6 4.3 76 908-987 608-690 (958)
5 KOG3623 Homeobox transcription 99.2 1.4E-12 3E-17 152.3 1.0 78 905-986 894-971 (1007)
6 KOG3623 Homeobox transcription 99.2 2.1E-12 4.5E-17 150.9 2.0 103 879-987 209-331 (1007)
7 KOG3608 Zn finger proteins [Ge 99.1 4.2E-11 9.1E-16 131.6 5.4 135 853-993 180-348 (467)
8 KOG3576 Ovo and related transc 99.1 3.1E-11 6.7E-16 124.9 2.9 106 877-988 114-235 (267)
9 KOG3576 Ovo and related transc 99.1 2.1E-11 4.5E-16 126.2 -0.5 79 905-987 117-195 (267)
10 KOG3608 Zn finger proteins [Ge 98.8 2.3E-09 5E-14 118.2 3.3 138 852-997 237-383 (467)
11 PHA00733 hypothetical protein 98.5 9.6E-08 2.1E-12 94.0 3.9 89 874-988 34-122 (128)
12 PLN03086 PRLI-interacting fact 98.3 8.2E-07 1.8E-11 105.3 7.9 99 879-988 452-563 (567)
13 PLN03086 PRLI-interacting fact 98.3 1E-06 2.2E-11 104.5 7.7 119 854-988 409-537 (567)
14 PHA02768 hypothetical protein; 98.1 1.8E-06 3.8E-11 73.7 2.3 44 933-982 5-48 (55)
15 PF13465 zf-H2C2_2: Zinc-finge 97.9 8.2E-06 1.8E-10 59.4 2.3 26 950-977 1-26 (26)
16 PHA02768 hypothetical protein; 97.7 1.6E-05 3.4E-10 68.0 2.4 43 906-952 6-48 (55)
17 KOG3993 Transcription factor ( 97.7 6.3E-06 1.4E-10 93.5 -0.8 133 851-989 266-482 (500)
18 KOG3993 Transcription factor ( 97.6 1.6E-05 3.4E-10 90.4 -0.4 109 881-994 268-384 (500)
19 PHA00733 hypothetical protein 97.4 0.00017 3.7E-09 71.3 4.5 79 851-959 39-123 (128)
20 PF13465 zf-H2C2_2: Zinc-finge 97.2 0.00016 3.5E-09 52.7 1.4 26 920-947 1-26 (26)
21 PHA00732 hypothetical protein 96.9 0.00077 1.7E-08 61.7 3.2 20 907-926 3-22 (79)
22 PHA00616 hypothetical protein 96.9 0.00048 1E-08 56.6 1.6 34 933-968 1-34 (44)
23 COG5189 SFP1 Putative transcri 96.3 0.0016 3.4E-08 72.4 1.5 54 931-986 347-419 (423)
24 PHA00732 hypothetical protein 96.1 0.005 1.1E-07 56.4 3.3 45 933-987 1-46 (79)
25 COG5189 SFP1 Putative transcri 95.9 0.0018 3.9E-08 71.9 -0.6 73 878-956 347-419 (423)
26 PHA00616 hypothetical protein 95.8 0.0038 8.2E-08 51.5 1.1 29 963-995 1-29 (44)
27 PF12756 zf-C2H2_2: C2H2 type 95.7 0.0077 1.7E-07 54.7 2.8 75 908-992 2-77 (100)
28 PF05605 zf-Di19: Drought indu 95.5 0.019 4E-07 48.6 4.2 49 933-988 2-52 (54)
29 PF00096 zf-C2H2: Zinc finger, 95.0 0.014 3.1E-07 40.6 1.7 22 964-987 1-22 (23)
30 COG5048 FOG: Zn-finger [Genera 94.6 0.019 4.2E-07 63.1 2.4 137 851-987 288-440 (467)
31 PF13912 zf-C2H2_6: C2H2-type 94.2 0.032 6.8E-07 40.4 1.9 24 963-988 1-24 (27)
32 PF13894 zf-C2H2_4: C2H2-type 93.8 0.045 9.7E-07 37.5 2.1 23 964-988 1-23 (24)
33 PF05605 zf-Di19: Drought indu 93.6 0.12 2.7E-06 43.7 4.8 49 906-959 3-53 (54)
34 PF00096 zf-C2H2: Zinc finger, 93.5 0.032 7E-07 38.8 1.0 23 934-958 1-23 (23)
35 PRK04860 hypothetical protein; 91.6 0.1 2.2E-06 53.9 2.0 39 932-978 118-156 (160)
36 COG5048 FOG: Zn-finger [Genera 91.1 0.068 1.5E-06 58.9 0.2 75 905-979 289-367 (467)
37 PF12756 zf-C2H2_2: C2H2 type 90.5 0.14 3.1E-06 46.3 1.7 72 882-958 1-73 (100)
38 smart00355 ZnF_C2H2 zinc finge 89.8 0.22 4.8E-06 34.2 1.8 23 964-988 1-23 (26)
39 PF13912 zf-C2H2_6: C2H2-type 89.7 0.15 3.3E-06 36.8 0.9 25 933-959 1-25 (27)
40 smart00355 ZnF_C2H2 zinc finge 88.4 0.48 1E-05 32.5 2.7 24 934-959 1-24 (26)
41 PF13894 zf-C2H2_4: C2H2-type 88.0 0.33 7.1E-06 33.2 1.7 23 934-958 1-23 (24)
42 PF12874 zf-met: Zinc-finger o 83.5 0.49 1.1E-05 33.5 0.7 24 964-989 1-24 (25)
43 PRK04860 hypothetical protein; 82.1 0.75 1.6E-05 47.6 1.8 39 904-948 118-156 (160)
44 PF09237 GAGA: GAGA factor; I 77.2 1.7 3.7E-05 37.4 2.1 27 960-988 21-47 (54)
45 PF12171 zf-C2H2_jaz: Zinc-fin 77.2 0.9 1.9E-05 33.2 0.4 24 964-989 2-25 (27)
46 PF09237 GAGA: GAGA factor; I 75.3 2.1 4.5E-05 36.9 2.1 40 922-963 12-52 (54)
47 KOG2231 Predicted E3 ubiquitin 67.8 6.8 0.00015 48.7 5.0 17 941-957 188-204 (669)
48 PF13909 zf-H2C2_5: C2H2-type 67.2 3.5 7.6E-05 29.1 1.5 22 964-988 1-22 (24)
49 KOG4173 Alpha-SNAP protein [In 66.3 1.5 3.2E-05 47.1 -0.8 81 878-958 77-170 (253)
50 KOG1146 Homeobox protein [Gene 63.0 2.1 4.5E-05 56.0 -0.6 93 881-992 1261-1355(1406)
51 KOG1146 Homeobox protein [Gene 61.4 2.7 5.8E-05 55.1 -0.0 90 888-991 442-544 (1406)
52 PF12874 zf-met: Zinc-finger o 60.9 3.8 8.2E-05 29.0 0.7 23 934-958 1-23 (25)
53 KOG4377 Zn-finger protein [Gen 59.8 3.6 7.9E-05 48.1 0.7 107 879-988 270-426 (480)
54 KOG2231 Predicted E3 ubiquitin 57.7 11 0.00025 46.9 4.4 119 855-986 118-260 (669)
55 smart00451 ZnF_U1 U1-like zinc 55.3 6.9 0.00015 29.6 1.3 26 963-990 3-28 (35)
56 PF12171 zf-C2H2_jaz: Zinc-fin 52.2 5.7 0.00012 29.0 0.4 22 934-957 2-23 (27)
57 KOG2893 Zn finger protein [Gen 51.5 4.6 0.0001 44.3 -0.2 42 888-929 16-59 (341)
58 PF13909 zf-H2C2_5: C2H2-type 49.5 8.9 0.00019 27.0 1.1 22 934-958 1-22 (24)
59 KOG4173 Alpha-SNAP protein [In 48.7 5.6 0.00012 43.0 -0.1 79 905-988 81-169 (253)
60 PF13913 zf-C2HC_2: zinc-finge 44.0 16 0.00036 26.7 1.7 20 965-987 4-23 (25)
61 COG5236 Uncharacterized conser 38.4 15 0.00032 42.5 1.1 85 893-987 199-303 (493)
62 PF14597 Lactamase_B_5: Metall 34.0 24 0.00053 37.9 1.8 39 149-190 43-81 (199)
63 COG4049 Uncharacterized protei 31.3 22 0.00048 31.4 0.9 27 959-987 13-39 (65)
64 COG5236 Uncharacterized conser 28.9 47 0.001 38.6 3.1 90 862-957 198-303 (493)
65 smart00451 ZnF_U1 U1-like zinc 26.9 42 0.00091 25.3 1.6 23 933-957 3-25 (35)
66 KOG2893 Zn finger protein [Gen 25.2 26 0.00056 38.8 0.3 38 941-984 16-53 (341)
67 cd04864 LigD_Pol_like_1 LigD_P 24.7 1.1E+02 0.0023 34.0 4.8 59 130-189 103-174 (228)
68 cd04861 LigD_Pol_like LigD_Pol 23.4 1.1E+02 0.0025 33.8 4.7 63 128-190 99-174 (227)
69 cd04862 PaeLigD_Pol_like PaeLi 23.0 1.2E+02 0.0025 33.7 4.7 63 127-189 98-173 (227)
70 PF04273 DUF442: Putative phos 22.9 77 0.0017 31.0 3.0 59 154-214 21-84 (110)
71 cd04865 LigD_Pol_like_2 LigD_P 22.5 1.2E+02 0.0026 33.6 4.7 63 128-190 100-175 (228)
72 cd04866 LigD_Pol_like_3 LigD_P 22.3 1.4E+02 0.0031 32.9 5.2 63 127-189 93-169 (223)
73 TIGR00622 ssl1 transcription f 22.0 1E+02 0.0022 30.8 3.6 83 878-974 13-112 (112)
74 TIGR02778 ligD_pol DNA polymer 21.9 1.3E+02 0.0027 33.8 4.7 63 127-189 114-189 (245)
75 cd04863 MtLigD_Pol_like MtLigD 21.2 1.1E+02 0.0025 33.8 4.2 63 127-189 102-177 (231)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.83 E-value=2.8e-21 Score=206.02 Aligned_cols=135 Identities=21% Similarity=0.436 Sum_probs=125.8
Q ss_pred CCCCCccccccCCcccccCcccccccccccC---CCcccccCCCCCCcccChhHHhhhhccc---cCCCCCCCccCChHH
Q 001904 847 KEKNPAAKKKVKNASVVKAPAGLNNAKIKDE---EAGYHCDMEGCTMSFGTKQELVLHKKNI---CPVKGCGKKFFSHKY 920 (997)
Q Consensus 847 k~k~p~~kc~vc~ksf~kk~~L~~H~rtHtg---eKpyqC~iegCGKsFssksnLk~Hkr~h---CpCkeCgKsFsskss 920 (997)
....+...|..|++.+.....|..|..+|.. .+.+.|.+ ||+.|.+...|..|+++| |.|..|||.|...+.
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~--C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKY--CGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWL 202 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccccccccccCCC--CCceeeehHHHhhHhhccCCCcccccccccccchHH
Confidence 3456778899999999999999999999974 57799988 999999999999999976 899999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhh
Q 001904 921 LVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 921 L~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
|+-|+|+|||||||.| ..|+|+|...++|+.||++|.+.|+|+|.. |+|+|+..+.|.+|...
T Consensus 203 LQGHiRTHTGEKPF~C--~hC~kAFADRSNLRAHmQTHS~~K~~qC~~--C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSC--PHCGKAFADRSNLRAHMQTHSDVKKHQCPR--CGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcccccccCCCCccC--CcccchhcchHHHHHHHHhhcCCccccCcc--hhhHHHHHHHHHHhhhh
Confidence 9999999999999999 569999999999999999999999999988 99999999999999764
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.74 E-value=1.3e-18 Score=185.71 Aligned_cols=110 Identities=35% Similarity=0.664 Sum_probs=101.3
Q ss_pred CCCcccccCCCCCCcccChhHHhhhhccc--------cCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccCh
Q 001904 877 EEAGYHCDMEGCTMSFGTKQELVLHKKNI--------CPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWA 948 (997)
Q Consensus 877 geKpyqC~iegCGKsFssksnLk~Hkr~h--------CpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~k 948 (997)
....|+|.. ||+.|.+.++|.+|+.+| +.|+.|+|.|..-..|..|+++|+ -+++| .+|||.|...
T Consensus 127 ~~~r~~c~e--Cgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C--~iCGKaFSRP 200 (279)
T KOG2462|consen 127 KHPRYKCPE--CGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCEC--GICGKAFSRP 200 (279)
T ss_pred cCCceeccc--cccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCccc--ccccccccch
Confidence 345699986 999999999999998877 459999999999999999999998 67899 6799999999
Q ss_pred HHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhhhCCCCCCCC
Q 001904 949 WARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRKTGHSAKKSR 996 (997)
Q Consensus 949 S~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rth~HsgeK~~ 996 (997)
+-|..|+|+|||||||.|.. |+|+|+.+++|+.|+.| |++.|+|
T Consensus 201 WLLQGHiRTHTGEKPF~C~h--C~kAFADRSNLRAHmQT--HS~~K~~ 244 (279)
T KOG2462|consen 201 WLLQGHIRTHTGEKPFSCPH--CGKAFADRSNLRAHMQT--HSDVKKH 244 (279)
T ss_pred HHhhcccccccCCCCccCCc--ccchhcchHHHHHHHHh--hcCCccc
Confidence 99999999999999999988 99999999999999999 6777765
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.40 E-value=5.6e-14 Score=166.18 Aligned_cols=77 Identities=25% Similarity=0.299 Sum_probs=67.6
Q ss_pred CccccccCCcccccCcccccccccccCCCcccccCCCCCCcccChhHHhhhhccc---------cCCC---CCCCccCCh
Q 001904 851 PAAKKKVKNASVVKAPAGLNNAKIKDEEAGYHCDMEGCTMSFGTKQELVLHKKNI---------CPVK---GCGKKFFSH 918 (997)
Q Consensus 851 p~~kc~vc~ksf~kk~~L~~H~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr~h---------CpCk---eCgKsFssk 918 (997)
....|-+|.........|.-|.++|+|++||+|.+ ||+.|.++.+|+.|+-.| +.|+ .|-+.|...
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKi--CgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKI--CGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCcccccc--ccchhccccchhhcccccccCccccccccCCchhhhccccccc
Confidence 34468999999999999999999999999999999 999999999999997543 6677 788888888
Q ss_pred HHHHHHHHHhc
Q 001904 919 KYLVQHRRVHL 929 (997)
Q Consensus 919 ssL~~HqRvHt 929 (997)
-.|.+|+++|+
T Consensus 682 V~lpQhIriH~ 692 (958)
T KOG1074|consen 682 VTLPQHIRIHL 692 (958)
T ss_pred ccccceEEeec
Confidence 88888888876
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.34 E-value=4.6e-13 Score=158.57 Aligned_cols=76 Identities=26% Similarity=0.460 Sum_probs=66.2
Q ss_pred CCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCC----ceecC---CCCcCCcccChhH
Q 001904 908 VKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGAR----PYVCA---EPGCGQTFRFVSD 980 (997)
Q Consensus 908 CkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEK----PYkC~---epGCGKsFs~sSs 980 (997)
|-.|-+.+.-.+.|+.|+++|+|++||+| ++||++|.++.+|+.||-+|...- +|.|+ + |-+.|...-.
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERPFkC--KiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i--c~~kftn~V~ 683 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERPFKC--KICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI--CQKKFTNAVT 683 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCcccc--ccccchhccccchhhcccccccCccccccccCCchhh--hccccccccc
Confidence 66688888889999999999999999999 779999999999999999887543 47787 6 9999999999
Q ss_pred HHHhhhh
Q 001904 981 FSRHKRK 987 (997)
Q Consensus 981 LkrH~Rt 987 (997)
|..|+|+
T Consensus 684 lpQhIri 690 (958)
T KOG1074|consen 684 LPQHIRI 690 (958)
T ss_pred ccceEEe
Confidence 9999998
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.24 E-value=1.4e-12 Score=152.30 Aligned_cols=78 Identities=32% Similarity=0.680 Sum_probs=75.5
Q ss_pred ccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHh
Q 001904 905 ICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRH 984 (997)
Q Consensus 905 hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH 984 (997)
.|.|..|.|.|...+.|.+|...|+|.+||+| .+|.|+|.++.+|..|+|.|.|||||+|.. |+|+|+.+.++..|
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC--~iCkKAFKHKHHLtEHkRLHSGEKPfQCdK--ClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQC--IICKKAFKHKHHLTEHKRLHSGEKPFQCDK--CLKRFSHSGSYSQH 969 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCccc--chhhHhhhhhhhhhhhhhhccCCCcchhhh--hhhhcccccchHhh
Confidence 48899999999999999999999999999999 889999999999999999999999999998 99999999999999
Q ss_pred hh
Q 001904 985 KR 986 (997)
Q Consensus 985 ~R 986 (997)
|-
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 86
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.24 E-value=2.1e-12 Score=150.87 Aligned_cols=103 Identities=26% Similarity=0.538 Sum_probs=92.8
Q ss_pred CcccccCCCCCCcccChhHHhhhhcc-------ccCCCCCCCccCChHHHHHHHHHhcC-------------CCCCCCCC
Q 001904 879 AGYHCDMEGCTMSFGTKQELVLHKKN-------ICPVKGCGKKFFSHKYLVQHRRVHLD-------------DRPLKCPW 938 (997)
Q Consensus 879 KpyqC~iegCGKsFssksnLk~Hkr~-------hCpCkeCgKsFsskssL~~HqRvHtG-------------EKPykCp~ 938 (997)
...+|++ |.+.+.....|+.|+++ .++|..|..+|..+..|.+|+.+|.- -+.|+|
T Consensus 209 qlltcpy--cdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKC-- 284 (1007)
T KOG3623|consen 209 QLLTCPY--CDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKC-- 284 (1007)
T ss_pred hhhcchh--HHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccc--
Confidence 3467998 99999999999999764 38899999999999999999998842 378999
Q ss_pred CCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhh
Q 001904 939 KGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 939 ~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
.+|||+|..+.+|+.|+|||.|||||.|+. |+|+|+.+.++..||..
T Consensus 285 tECgKAFKfKHHLKEHlRIHSGEKPfeCpn--CkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 285 TECGKAFKFKHHLKEHLRIHSGEKPFECPN--CKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccchhhhhHHHHHhhheeecCCCCcCCcc--cccccccCCcccccccc
Confidence 789999999999999999999999999977 99999999999999865
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.13 E-value=4.2e-11 Score=131.64 Aligned_cols=135 Identities=22% Similarity=0.364 Sum_probs=103.6
Q ss_pred cccccCCcccccCcccccccccccCCCcccccCCCCCCcccChhHHhhhhc-----------------------------
Q 001904 853 AKKKVKNASVVKAPAGLNNAKIKDEEAGYHCDMEGCTMSFGTKQELVLHKK----------------------------- 903 (997)
Q Consensus 853 ~kc~vc~ksf~kk~~L~~H~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr----------------------------- 903 (997)
+.-..|...+..+..|..|.++|++++-..|+. ||..|..+..|.-|.+
T Consensus 180 C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~--Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 180 CNWAMCTKHMGNKYRLREHIRTHSNEKVVACPH--CGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred ccchhhhhhhccHHHHHHHHHhcCCCeEEecch--HHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH
Confidence 344567777777777778888887777777766 7777777666666633
Q ss_pred -c---ccCCCCCCCccCChHHHHHHHHH-hcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccCh
Q 001904 904 -N---ICPVKGCGKKFFSHKYLVQHRRV-HLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFV 978 (997)
Q Consensus 904 -~---hCpCkeCgKsFsskssL~~HqRv-HtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~s 978 (997)
+ +|.|+.|..+....+.|..|++. |...|||+| ..|.+.|...+.|..|..+|+ +-.|.|..|.|..+|.+.
T Consensus 258 ~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKC--d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~ 334 (467)
T KOG3608|consen 258 VRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKC--DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTY 334 (467)
T ss_pred HHhhhcccccccccCCCChHHHHHHHHhhhccCCCccc--cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHH
Confidence 2 36788888888888888888875 888888998 778888888888888888887 666888887888888888
Q ss_pred hHHHHhhhhhCCCCC
Q 001904 979 SDFSRHKRKTGHSAK 993 (997)
Q Consensus 979 SsLkrH~Rth~Hsge 993 (997)
..+.+|++.+ |-|-
T Consensus 335 ~q~~~H~~ev-hEg~ 348 (467)
T KOG3608|consen 335 TQMRRHFLEV-HEGN 348 (467)
T ss_pred HHHHHHHHHh-ccCC
Confidence 8888888875 5443
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.10 E-value=3.1e-11 Score=124.89 Aligned_cols=106 Identities=30% Similarity=0.536 Sum_probs=94.6
Q ss_pred CCCcccccCCCCCCcccChhHHhhhhccc-----cCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHH
Q 001904 877 EEAGYHCDMEGCTMSFGTKQELVLHKKNI-----CPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWAR 951 (997)
Q Consensus 877 geKpyqC~iegCGKsFssksnLk~Hkr~h-----CpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~L 951 (997)
+...|.|.+ |++.|....-|.+|++.| +-|..||+.|.....|.+|.++|+|.+||+| ..|+|+|.+.-.|
T Consensus 114 d~d~ftCrv--CgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc--~~c~kaftqrcsl 189 (267)
T KOG3576|consen 114 DQDSFTCRV--CGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC--SLCEKAFTQRCSL 189 (267)
T ss_pred CCCeeeeeh--hhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccch--hhhhHHHHhhccH
Confidence 456799999 999999999999998865 4577799999999999999999999999999 7899999999999
Q ss_pred HHHHH-hhC----------CCCceecCCCCcCCcccChhHHHHhhhhh
Q 001904 952 TEHIR-VHT----------GARPYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 952 krH~R-iHT----------GEKPYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
..|.+ +|. .+|.|+|.. ||.+-.....+..|...|
T Consensus 190 eshl~kvhgv~~~yaykerr~kl~vced--cg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 190 ESHLKKVHGVQHQYAYKERRAKLYVCED--CGYTSERPEVYYLHLKLH 235 (267)
T ss_pred HHHHHHHcCchHHHHHHHhhhheeeecc--cCCCCCChhHHHHHHHhc
Confidence 99987 452 467899998 999999999999999985
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.06 E-value=2.1e-11 Score=126.20 Aligned_cols=79 Identities=32% Similarity=0.620 Sum_probs=75.2
Q ss_pred ccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHh
Q 001904 905 ICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRH 984 (997)
Q Consensus 905 hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH 984 (997)
.+.|..|+|.|.....|.+|++.|...+.|-|.+ |||.|.....|++|+|+|||.+||+|.. |+|+|+++.+|..|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~--cgkgfndtfdlkrh~rthtgvrpykc~~--c~kaftqrcslesh 192 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTF--CGKGFNDTFDLKRHTRTHTGVRPYKCSL--CEKAFTQRCSLESH 192 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhh--ccCcccchhhhhhhhccccCccccchhh--hhHHHHhhccHHHH
Confidence 4678999999999999999999999999999955 9999999999999999999999999988 99999999999999
Q ss_pred hhh
Q 001904 985 KRK 987 (997)
Q Consensus 985 ~Rt 987 (997)
.++
T Consensus 193 l~k 195 (267)
T KOG3576|consen 193 LKK 195 (267)
T ss_pred HHH
Confidence 886
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.80 E-value=2.3e-09 Score=118.23 Aligned_cols=138 Identities=18% Similarity=0.296 Sum_probs=117.2
Q ss_pred ccccccCCcccccCcccccccccccCCCcccccCCCCCCcccChhHHhhhhcc------ccCCCCCCCccCChHHHHHHH
Q 001904 852 AAKKKVKNASVVKAPAGLNNAKIKDEEAGYHCDMEGCTMSFGTKQELVLHKKN------ICPVKGCGKKFFSHKYLVQHR 925 (997)
Q Consensus 852 ~~kc~vc~ksf~kk~~L~~H~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr~------hCpCkeCgKsFsskssL~~Hq 925 (997)
.+.|..|.+.|.....|.-|+..|- .-|+|+. |.......+.|..|+++ ++.|..|.+.|.+.+.|..|.
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCpl--Cdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~ 312 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPL--CDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV 312 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhh--hcccccc--cccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH
Confidence 5667888888888888888877775 5688988 99999999999999874 588999999999999999999
Q ss_pred HHhcCCCCCCCCCCCCCCcccChHHHHHHHHh-hCCC--CceecCCCCcCCcccChhHHHHhhhhhCCCCCCCCC
Q 001904 926 RVHLDDRPLKCPWKGCKMTFKWAWARTEHIRV-HTGA--RPYVCAEPGCGQTFRFVSDFSRHKRKTGHSAKKSRG 997 (997)
Q Consensus 926 RvHtGEKPykCp~~eCGK~Fs~kS~LkrH~Ri-HTGE--KPYkC~epGCGKsFs~sSsLkrH~Rth~HsgeK~~g 997 (997)
.+|. +.-|.|.++.|...|.+...+.+|++- |.|. -+|.|.. |++.|+.-.+|..|.++. |.=.=|+|
T Consensus 313 ~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~--Cdr~ft~G~~L~~HL~kk-H~f~~PsG 383 (467)
T KOG3608|consen 313 QVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHC--CDRFFTSGKSLSAHLMKK-HGFRLPSG 383 (467)
T ss_pred Hhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeec--chhhhccchhHHHHHHHh-hcccCCCC
Confidence 9998 667999888899999999999999986 4454 5699999 999999999999998873 55444444
No 11
>PHA00733 hypothetical protein
Probab=98.48 E-value=9.6e-08 Score=93.99 Aligned_cols=89 Identities=24% Similarity=0.306 Sum_probs=68.3
Q ss_pred cccCCCcccccCCCCCCcccChhHHhhhhccccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHH
Q 001904 874 IKDEEAGYHCDMEGCTMSFGTKQELVLHKKNICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTE 953 (997)
Q Consensus 874 tHtgeKpyqC~iegCGKsFssksnLk~Hkr~hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~Lkr 953 (997)
+....+++.|.+ |.+.|.....|..| ..|..|+.+ .+.+||.| ..||+.|.....|..
T Consensus 34 ~~~~~~~~~~~~--~~~~~~~~~~l~~~-----------------~~l~~~~~~-~~~kPy~C--~~Cgk~Fss~s~L~~ 91 (128)
T PHA00733 34 LTPEQKRLIRAV--VKTLIYNPQLLDES-----------------SYLYKLLTS-KAVSPYVC--PLCLMPFSSSVSLKQ 91 (128)
T ss_pred CChhhhhHHHHH--HhhhccChhhhcch-----------------HHHHhhccc-CCCCCccC--CCCCCcCCCHHHHHH
Confidence 334456777776 66666554444332 335566444 45899999 679999999999999
Q ss_pred HHHhhCCCCceecCCCCcCCcccChhHHHHhhhhh
Q 001904 954 HIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 954 H~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
|+++| +.+|.|.. |++.|.....|..|+...
T Consensus 92 H~r~h--~~~~~C~~--CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 92 HIRYT--EHSKVCPV--CGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred HHhcC--CcCccCCC--CCCccCCHHHHHHHHHHh
Confidence 99987 46899988 999999999999999985
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.34 E-value=8.2e-07 Score=105.28 Aligned_cols=99 Identities=23% Similarity=0.467 Sum_probs=72.8
Q ss_pred CcccccCCCCCCcccChhHHhhhhcc---ccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccC--------
Q 001904 879 AGYHCDMEGCTMSFGTKQELVLHKKN---ICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKW-------- 947 (997)
Q Consensus 879 KpyqC~iegCGKsFssksnLk~Hkr~---hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~-------- 947 (997)
..+.|+. |++.|. ...|..|... ++.|+ |++.| ....|..|+.+|...+|+.|+| |++.|..
T Consensus 452 ~H~~C~~--Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~ 524 (567)
T PLN03086 452 NHVHCEK--CGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVR 524 (567)
T ss_pred cCccCCC--CCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCC--CCCccccCccccchh
Confidence 3457877 888885 5778888664 35576 88654 5678888888888888888865 8888842
Q ss_pred --hHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhhh
Q 001904 948 --AWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 948 --kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
...|..|+.++ |.+++.|.. ||+.|..+ .|..|+-..
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~C~~--Cgk~Vrlr-dm~~H~~~~ 563 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAPCDS--CGRSVMLK-EMDIHQIAV 563 (567)
T ss_pred hhhhhHHHHHHhc-CCcceEccc--cCCeeeeh-hHHHHHHHh
Confidence 35788888875 888888877 88887766 456776653
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.31 E-value=1e-06 Score=104.48 Aligned_cols=119 Identities=17% Similarity=0.287 Sum_probs=87.4
Q ss_pred ccccCCcccccCcccccccccccCCCcccccCCCCCCcccChhHHhhhhccccCCCCCCCccCChHHHHHHHHHhcCCCC
Q 001904 854 KKKVKNASVVKAPAGLNNAKIKDEEAGYHCDMEGCTMSFGTKQELVLHKKNICPVKGCGKKFFSHKYLVQHRRVHLDDRP 933 (997)
Q Consensus 854 kc~vc~ksf~kk~~L~~H~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr~hCpCkeCgKsFsskssL~~HqRvHtGEKP 933 (997)
.|..|....... .+..|.. +..-..-.|+..+||..|. ...+.. |..|..|++.|. ...|..|+.+|+ +|
T Consensus 409 ~C~NC~~~i~l~-~l~lHe~-~C~r~~V~Cp~~~Cg~v~~-r~el~~----H~~C~~Cgk~f~-~s~LekH~~~~H--kp 478 (567)
T PLN03086 409 ECRNCKHYIPSR-SIALHEA-YCSRHNVVCPHDGCGIVLR-VEEAKN----HVHCEKCGQAFQ-QGEMEKHMKVFH--EP 478 (567)
T ss_pred ECCCCCCccchh-HHHHHHh-hCCCcceeCCcccccceee-cccccc----CccCCCCCCccc-hHHHHHHHHhcC--CC
Confidence 466666655432 3334442 2223445687557999993 344444 456888999996 678999999975 89
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCccc----------ChhHHHHhhhhh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFR----------FVSDFSRHKRKT 988 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs----------~sSsLkrH~Rth 988 (997)
+.| + ||+.| ....|..|+.+|.+++|+.|.+ |++.|. ..+.|..|..++
T Consensus 479 v~C--p-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 479 LQC--P-CGVVL-EKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred ccC--C-CCCCc-chhHHHhhhhccCCCCceeCCC--CCCccccCccccchhhhhhhHHHHHHhc
Confidence 999 6 99765 6689999999999999999998 999995 246899999874
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.07 E-value=1.8e-06 Score=73.72 Aligned_cols=44 Identities=14% Similarity=0.255 Sum_probs=38.1
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHH
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFS 982 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLk 982 (997)
.|.| +.||+.|...++|..|+++|+ +||+|.. |++.|.+.+.|.
T Consensus 5 ~y~C--~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~--C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYEC--PICGEIYIKRKSMITHLRKHN--TNLKLSN--CKRISLRTGEYI 48 (55)
T ss_pred ccCc--chhCCeeccHHHHHHHHHhcC--CcccCCc--ccceecccceeE
Confidence 4789 679999999999999999998 7999977 999999887764
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.87 E-value=8.2e-06 Score=59.45 Aligned_cols=26 Identities=42% Similarity=0.977 Sum_probs=22.4
Q ss_pred HHHHHHHhhCCCCceecCCCCcCCcccC
Q 001904 950 ARTEHIRVHTGARPYVCAEPGCGQTFRF 977 (997)
Q Consensus 950 ~LkrH~RiHTGEKPYkC~epGCGKsFs~ 977 (997)
+|.+|+++|+|++||.|+. |+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~--C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPY--CGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESS--SSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCC--CcCeeCc
Confidence 4788999999999999988 9999864
No 16
>PHA02768 hypothetical protein; Provisional
Probab=97.74 E-value=1.6e-05 Score=68.01 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=38.5
Q ss_pred cCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHH
Q 001904 906 CPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWART 952 (997)
Q Consensus 906 CpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~Lk 952 (997)
|.|+.||+.|.....|..|+++|+ +||+| ..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc--~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKL--SNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccC--CcccceecccceeE
Confidence 578889999999999999999999 79999 77999999877664
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.70 E-value=6.3e-06 Score=93.51 Aligned_cols=133 Identities=20% Similarity=0.224 Sum_probs=96.4
Q ss_pred CccccccCCcccccCcccccccccccCCCcccccCCCCCCcccChhHHhhhhccc-------------------------
Q 001904 851 PAAKKKVKNASVVKAPAGLNNAKIKDEEAGYHCDMEGCTMSFGTKQELVLHKKNI------------------------- 905 (997)
Q Consensus 851 p~~kc~vc~ksf~kk~~L~~H~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr~h------------------------- 905 (997)
-.+.|.+|...+.....|.+|.-.-.-.-.|.|.. |+|.|.+..||-.|++.|
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPE--C~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPE--CDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCc--ccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 34679999999999999999976555556799986 999999999999997642
Q ss_pred -------------cCCCCCCCccCChHHHHHHHHHhcCC---C---C-----------C---------------------
Q 001904 906 -------------CPVKGCGKKFFSHKYLVQHRRVHLDD---R---P-----------L--------------------- 934 (997)
Q Consensus 906 -------------CpCkeCgKsFsskssL~~HqRvHtGE---K---P-----------y--------------------- 934 (997)
|.|..|+|.|.+...|+.|+.+|... + + +
T Consensus 344 ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~ 423 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLY 423 (500)
T ss_pred hccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceee
Confidence 56888999999988999888776431 0 0 0
Q ss_pred --------CCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhhhC
Q 001904 935 --------KCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRKTG 989 (997)
Q Consensus 935 --------kCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rth~ 989 (997)
.| ..||-.+..+..--.|.+.-..+.-|.|.. |--+|..+..|.+|...+|
T Consensus 424 ~a~sael~~p--p~~~~ppsss~~sgg~~rlg~~~q~f~~ky--~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 424 VAGSAELELP--PYDGSPPSSSGSSGGYGRLGIAEQGFTCKY--CPATFYSSPGLTRHINKCH 482 (500)
T ss_pred eeccccccCC--CCCCCCcccCCCCCccccccchhhcccccc--chHhhhcCcchHhHhhhcC
Confidence 12 124434443333333333333345578988 9999999999999998863
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.55 E-value=1.6e-05 Score=90.40 Aligned_cols=109 Identities=21% Similarity=0.314 Sum_probs=55.8
Q ss_pred ccccCCCCCCcccChhHHhhhhc-----cccCCCCCCCccCChHHHHHHHHHhcCCCCCC-CCCCCCCCcccChHHHHHH
Q 001904 881 YHCDMEGCTMSFGTKQELVLHKK-----NICPVKGCGKKFFSHKYLVQHRRVHLDDRPLK-CPWKGCKMTFKWAWARTEH 954 (997)
Q Consensus 881 yqC~iegCGKsFssksnLk~Hkr-----~hCpCkeCgKsFsskssL~~HqRvHtGEKPyk-Cp~~eCGK~Fs~kS~LkrH 954 (997)
|.|.. |...|.....|-.|+- .-|.|.+|+|.|.-..+|..|.|=|.-..--. -..+-=.+......-.+.-
T Consensus 268 yiCqL--CK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 268 YICQL--CKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHH--HHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 66766 7666666666666642 12556666666666666666655443111000 0000000000000000000
Q ss_pred HHh--hCCCCceecCCCCcCCcccChhHHHHhhhhhCCCCCC
Q 001904 955 IRV--HTGARPYVCAEPGCGQTFRFVSDFSRHKRKTGHSAKK 994 (997)
Q Consensus 955 ~Ri--HTGEKPYkC~epGCGKsFs~sSsLkrH~Rth~HsgeK 994 (997)
.|. -..+--|.|.. |+|+|.+...|++|+.+| |...+
T Consensus 346 ~rsg~dss~gi~~C~~--C~KkFrRqAYLrKHqlth-q~~~~ 384 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHT--CGKKFRRQAYLRKHQLTH-QRAPL 384 (500)
T ss_pred cccCCcccCceeecHH--hhhhhHHHHHHHHhHHhh-hcccc
Confidence 000 01123599988 999999999999999997 44433
No 19
>PHA00733 hypothetical protein
Probab=97.38 E-value=0.00017 Score=71.28 Aligned_cols=79 Identities=18% Similarity=0.229 Sum_probs=49.8
Q ss_pred CccccccCCcccccCcccccc------cccccCCCcccccCCCCCCcccChhHHhhhhccccCCCCCCCccCChHHHHHH
Q 001904 851 PAAKKKVKNASVVKAPAGLNN------AKIKDEEAGYHCDMEGCTMSFGTKQELVLHKKNICPVKGCGKKFFSHKYLVQH 924 (997)
Q Consensus 851 p~~kc~vc~ksf~kk~~L~~H------~rtHtgeKpyqC~iegCGKsFssksnLk~Hkr~hCpCkeCgKsFsskssL~~H 924 (997)
....|.+|...+.....+..+ +.+ .+.+||.|.. |++.|.....|..|
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~-~~~kPy~C~~-------------------------Cgk~Fss~s~L~~H 92 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTS-KAVSPYVCPL-------------------------CLMPFSSSVSLKQH 92 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhccc-CCCCCccCCC-------------------------CCCcCCCHHHHHHH
Confidence 344577777776655544433 222 2355666654 56666666666666
Q ss_pred HHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhC
Q 001904 925 RRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHT 959 (997)
Q Consensus 925 qRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHT 959 (997)
++.| ..+|.| ..|++.|.....|..|+....
T Consensus 93 ~r~h--~~~~~C--~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 93 IRYT--EHSKVC--PVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HhcC--CcCccC--CCCCCccCCHHHHHHHHHHhc
Confidence 6655 346888 568888888888888887543
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.19 E-value=0.00016 Score=52.73 Aligned_cols=26 Identities=35% Similarity=0.680 Sum_probs=23.3
Q ss_pred HHHHHHHHhcCCCCCCCCCCCCCCcccC
Q 001904 920 YLVQHRRVHLDDRPLKCPWKGCKMTFKW 947 (997)
Q Consensus 920 sL~~HqRvHtGEKPykCp~~eCGK~Fs~ 947 (997)
+|..|+++|+|++||.| +.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C--~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKC--PYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEE--SSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCC--CCCcCeeCc
Confidence 48899999999999999 669999964
No 21
>PHA00732 hypothetical protein
Probab=96.87 E-value=0.00077 Score=61.70 Aligned_cols=20 Identities=30% Similarity=0.273 Sum_probs=9.7
Q ss_pred CCCCCCCccCChHHHHHHHH
Q 001904 907 PVKGCGKKFFSHKYLVQHRR 926 (997)
Q Consensus 907 pCkeCgKsFsskssL~~HqR 926 (997)
.|..|++.|.....|..|++
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred cCCCCCCccCCHHHHHHHhh
Confidence 34445555544444554444
No 22
>PHA00616 hypothetical protein
Probab=96.87 E-value=0.00048 Score=56.64 Aligned_cols=34 Identities=15% Similarity=0.145 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCC
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAE 968 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~e 968 (997)
||.| ..||+.|...+.|..|++.|+|++|+.|..
T Consensus 1 pYqC--~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQC--LRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCcc--chhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6888 668888888888888888888888888864
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.32 E-value=0.0016 Score=72.44 Aligned_cols=54 Identities=26% Similarity=0.696 Sum_probs=40.0
Q ss_pred CCCCCCCCCCCCCcccChHHHHHHHHh-h------------------CCCCceecCCCCcCCcccChhHHHHhhh
Q 001904 931 DRPLKCPWKGCKMTFKWAWARTEHIRV-H------------------TGARPYVCAEPGCGQTFRFVSDFSRHKR 986 (997)
Q Consensus 931 EKPykCp~~eCGK~Fs~kS~LkrH~Ri-H------------------TGEKPYkC~epGCGKsFs~sSsLkrH~R 986 (997)
+|||+|++..|.|+|.....|+.|+.- | ...|||.|.. |+|+|.....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCev--C~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV--CDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccc--cchhhccCccceeccc
Confidence 466677666677777666666666642 2 2358999988 9999999999988865
No 24
>PHA00732 hypothetical protein
Probab=96.08 E-value=0.005 Score=56.44 Aligned_cols=45 Identities=29% Similarity=0.526 Sum_probs=35.1
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHh-hCCCCceecCCCCcCCcccChhHHHHhhhh
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRV-HTGARPYVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~Ri-HTGEKPYkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
||.| ..||+.|.....|..|++. |+ ++.|.. ||+.|. .|..|.++
T Consensus 1 py~C--~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~--CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKC--PICGFTTVTLFALKQHARRNHT---LTKCPV--CNKSYR---RLNQHFYS 46 (79)
T ss_pred CccC--CCCCCccCCHHHHHHHhhcccC---CCccCC--CCCEeC---Chhhhhcc
Confidence 6788 6688888888888888874 65 357877 888887 47777765
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.88 E-value=0.0018 Score=71.94 Aligned_cols=73 Identities=19% Similarity=0.371 Sum_probs=50.5
Q ss_pred CCcccccCCCCCCcccChhHHhhhhccccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHH
Q 001904 878 EAGYHCDMEGCTMSFGTKQELVLHKKNICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIR 956 (997)
Q Consensus 878 eKpyqC~iegCGKsFssksnLk~Hkr~hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~R 956 (997)
++||.|++++|.|.|.....|+.|+..-+ |.........-..|...-...|||.| ..|+|+|.....|+.|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH----~~~~~~~~p~p~~~~~F~~~~KPYrC--evC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGH----QNQKLHENPSPEKMNIFSAKDKPYRC--EVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccc----cCcccCCCCCccccccccccCCceec--cccchhhccCccceeccc
Confidence 59999999999999999999999976321 11111111111111122345699999 569999999999999954
No 26
>PHA00616 hypothetical protein
Probab=95.80 E-value=0.0038 Score=51.48 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=24.9
Q ss_pred ceecCCCCcCCcccChhHHHHhhhhhCCCCCCC
Q 001904 963 PYVCAEPGCGQTFRFVSDFSRHKRKTGHSAKKS 995 (997)
Q Consensus 963 PYkC~epGCGKsFs~sSsLkrH~Rth~HsgeK~ 995 (997)
||+|.. ||+.|.+.+.|.+|+++ |.|+++
T Consensus 1 pYqC~~--CG~~F~~~s~l~~H~r~--~hg~~~ 29 (44)
T PHA00616 1 MYQCLR--CGGIFRKKKEVIEHLLS--VHKQNK 29 (44)
T ss_pred CCccch--hhHHHhhHHHHHHHHHH--hcCCCc
Confidence 799988 99999999999999998 444454
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.68 E-value=0.0077 Score=54.66 Aligned_cols=75 Identities=23% Similarity=0.328 Sum_probs=21.7
Q ss_pred CCCCCCccCChHHHHHHHHHhcC-CCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhh
Q 001904 908 VKGCGKKFFSHKYLVQHRRVHLD-DRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKR 986 (997)
Q Consensus 908 CkeCgKsFsskssL~~HqRvHtG-EKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~R 986 (997)
|..|+..|.....|..|+...++ ..+ . ...+.....+..+.+.-. ...+.|.. |++.|.....|..|++
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~-~------~~~l~~~~~~~~~~~~~~-~~~~~C~~--C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP-D------QKYLVDPNRLLNYLRKKV-KESFRCPY--CNKTFRSREALQEHMR 71 (100)
T ss_dssp -------------------------------------------------------SSEEBSS--SS-EESSHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccc-c------cccccccccccccccccc-CCCCCCCc--cCCCCcCHHHHHHHHc
Confidence 55577777777777777654222 211 0 111122333333433221 22678877 8888888888888888
Q ss_pred hhCCCC
Q 001904 987 KTGHSA 992 (997)
Q Consensus 987 th~Hsg 992 (997)
.++|..
T Consensus 72 ~~~H~~ 77 (100)
T PF12756_consen 72 SKHHKK 77 (100)
T ss_dssp HTTTTC
T ss_pred CccCCC
Confidence 777765
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=95.48 E-value=0.019 Score=48.63 Aligned_cols=49 Identities=22% Similarity=0.489 Sum_probs=32.8
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHh-hCCC-CceecCCCCcCCcccChhHHHHhhhhh
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRV-HTGA-RPYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~Ri-HTGE-KPYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
.|.||| |++. .....|..|... |..+ +.+.|+. |...+. .+|..|+..+
T Consensus 2 ~f~CP~--C~~~-~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPY--CGKG-FSESSLVEHCEDEHRSESKNVVCPI--CSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCC--CCCc-cCHHHHHHHHHhHCcCCCCCccCCC--chhhhh--hHHHHHHHHh
Confidence 377866 8884 445678888664 5543 4678866 887655 3788888764
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=95.01 E-value=0.014 Score=40.63 Aligned_cols=22 Identities=41% Similarity=0.936 Sum_probs=16.6
Q ss_pred eecCCCCcCCcccChhHHHHhhhh
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
|+|+. |++.|...+.|..|++.
T Consensus 1 y~C~~--C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPI--CGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETT--TTEEESSHHHHHHHHHH
T ss_pred CCCCC--CCCccCCHHHHHHHHhH
Confidence 56766 77777777777777776
No 30
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.59 E-value=0.019 Score=63.13 Aligned_cols=137 Identities=21% Similarity=0.269 Sum_probs=86.8
Q ss_pred CccccccCCcccccCcccccccc--cccCC--CcccccCCCCCCcccChhHHhhhhccc-------cCCCCCCCccCChH
Q 001904 851 PAAKKKVKNASVVKAPAGLNNAK--IKDEE--AGYHCDMEGCTMSFGTKQELVLHKKNI-------CPVKGCGKKFFSHK 919 (997)
Q Consensus 851 p~~kc~vc~ksf~kk~~L~~H~r--tHtge--KpyqC~iegCGKsFssksnLk~Hkr~h-------CpCkeCgKsFssks 919 (997)
....|..|...+.....+..|.. .|.++ +++.|.+..|++.|.....+..|...+ +....|...+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 45678889999999999999999 89999 999999444999999999988886543 22223333333222
Q ss_pred HH-----HHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHhhhh
Q 001904 920 YL-----VQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 920 sL-----~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
.- ......-.....+.|.+..|-..+.....+..|...|....++.|..++|.+.|.....+..|++.
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKI 440 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccc
Confidence 21 111111222334444444466666666666666666666665555555566666666666666665
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=94.15 E-value=0.032 Score=40.36 Aligned_cols=24 Identities=46% Similarity=0.989 Sum_probs=20.4
Q ss_pred ceecCCCCcCCcccChhHHHHhhhhh
Q 001904 963 PYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 963 PYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
||.|.. |++.|.....|..|++.|
T Consensus 1 ~~~C~~--C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDE--CGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETT--TTEEESSHHHHHHHHCTT
T ss_pred CCCCCc--cCCccCChhHHHHHhHHh
Confidence 688888 999999999999998875
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=93.82 E-value=0.045 Score=37.52 Aligned_cols=23 Identities=35% Similarity=0.844 Sum_probs=16.7
Q ss_pred eecCCCCcCCcccChhHHHHhhhhh
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
|.|+. |++.|.....|..|+++|
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHH
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhh
Confidence 67877 888888888888888875
No 33
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=93.59 E-value=0.12 Score=43.67 Aligned_cols=49 Identities=24% Similarity=0.379 Sum_probs=36.9
Q ss_pred cCCCCCCCccCChHHHHHHHHH-hcCC-CCCCCCCCCCCCcccChHHHHHHHHhhC
Q 001904 906 CPVKGCGKKFFSHKYLVQHRRV-HLDD-RPLKCPWKGCKMTFKWAWARTEHIRVHT 959 (997)
Q Consensus 906 CpCkeCgKsFsskssL~~HqRv-HtGE-KPykCp~~eCGK~Fs~kS~LkrH~RiHT 959 (997)
|.|+.|++ ......|..|... |..+ +.+.| +.|...+. .+|..|+..+.
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~C--PiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVC--PICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccC--CCchhhhh--hHHHHHHHHhc
Confidence 56778999 5567789999765 6654 57999 56998655 48999998754
No 34
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.52 E-value=0.032 Score=38.82 Aligned_cols=23 Identities=30% Similarity=0.514 Sum_probs=16.0
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
|.| ..|++.|.....|..|++.|
T Consensus 1 y~C--~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKC--PICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEE--TTTTEEESSHHHHHHHHHHH
T ss_pred CCC--CCCCCccCCHHHHHHHHhHC
Confidence 456 45777777777777777664
No 35
>PRK04860 hypothetical protein; Provisional
Probab=91.59 E-value=0.1 Score=53.93 Aligned_cols=39 Identities=36% Similarity=0.751 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccCh
Q 001904 932 RPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFV 978 (997)
Q Consensus 932 KPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~s 978 (997)
-+|.| . |++ ....+.+|.++|+|+++|.|.. |+..|...
T Consensus 118 ~~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~--C~~~l~~~ 156 (160)
T PRK04860 118 FPYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRR--CGETLVFK 156 (160)
T ss_pred EEEEc--C-CCC---eeCHHHHHHHHhcCCccEECCC--CCceeEEe
Confidence 36899 5 987 6677999999999999999988 99998764
No 36
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.10 E-value=0.068 Score=58.90 Aligned_cols=75 Identities=25% Similarity=0.367 Sum_probs=55.7
Q ss_pred ccCCCCCCCccCChHHHHHHHH--HhcCC--CCCCCCCCCCCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChh
Q 001904 905 ICPVKGCGKKFFSHKYLVQHRR--VHLDD--RPLKCPWKGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVS 979 (997)
Q Consensus 905 hCpCkeCgKsFsskssL~~HqR--vHtGE--KPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sS 979 (997)
.+.|..|...|.....|..|.+ .|+++ +|+.|++..|++.|.+...+..|..+|++.+++.|....|...+....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 4556677788888888888877 78888 888885446888888888888888888888877776655655555443
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.48 E-value=0.14 Score=46.34 Aligned_cols=72 Identities=25% Similarity=0.391 Sum_probs=20.1
Q ss_pred cccCCCCCCcccChhHHhhhhccccCCC-CCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhh
Q 001904 882 HCDMEGCTMSFGTKQELVLHKKNICPVK-GCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 882 qC~iegCGKsFssksnLk~Hkr~hCpCk-eCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
+|.+ |+..|.....|..|+...+... .....+.....+..+.+.. -...+.| ..|++.|.....|..|++.+
T Consensus 1 ~C~~--C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~C--~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLF--CDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKK-VKESFRC--PYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEB--SSSS-EESSHHHHHHHHHHT
T ss_pred Cccc--cccccccccccccccccccccccccccccccccccccccccc-cCCCCCC--CccCCCCcCHHHHHHHHcCc
Confidence 4776 8888888888888876433211 1122222333333333321 2226889 55999999999999999864
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=89.77 E-value=0.22 Score=34.24 Aligned_cols=23 Identities=39% Similarity=0.862 Sum_probs=17.9
Q ss_pred eecCCCCcCCcccChhHHHHhhhhh
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
|.|.. |++.|.....|..|++.|
T Consensus 1 ~~C~~--C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPE--CGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCC--CcchhCCHHHHHHHHHHh
Confidence 56777 888888888888888753
No 39
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=89.67 E-value=0.15 Score=36.81 Aligned_cols=25 Identities=40% Similarity=0.660 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHhhC
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRVHT 959 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~RiHT 959 (997)
||.| ..|++.|.....|..|++.|.
T Consensus 1 ~~~C--~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFEC--DECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEE--TTTTEEESSHHHHHHHHCTTT
T ss_pred CCCC--CccCCccCChhHHHHHhHHhc
Confidence 5778 668888888888888887764
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.39 E-value=0.48 Score=32.52 Aligned_cols=24 Identities=38% Similarity=0.618 Sum_probs=17.1
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhhC
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVHT 959 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiHT 959 (997)
|.| ..|++.|.....|..|++.|.
T Consensus 1 ~~C--~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRC--PECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCC--CCCcchhCCHHHHHHHHHHhc
Confidence 467 457777777777777777664
No 41
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=88.02 E-value=0.33 Score=33.17 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=13.8
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
|.| ..|++.|.....|..|+++|
T Consensus 1 ~~C--~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQC--PICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE---SSTS-EESSHHHHHHHHHHH
T ss_pred CCC--cCCCCcCCcHHHHHHHHHhh
Confidence 456 44777777777777776654
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=83.45 E-value=0.49 Score=33.52 Aligned_cols=24 Identities=21% Similarity=0.582 Sum_probs=18.0
Q ss_pred eecCCCCcCCcccChhHHHHhhhhhC
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRKTG 989 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rth~ 989 (997)
|.|.. |++.|.....|..|++.+.
T Consensus 1 ~~C~~--C~~~f~s~~~~~~H~~s~~ 24 (25)
T PF12874_consen 1 FYCDI--CNKSFSSENSLRQHLRSKK 24 (25)
T ss_dssp EEETT--TTEEESSHHHHHHHHTTHH
T ss_pred CCCCC--CCCCcCCHHHHHHHHCcCC
Confidence 56777 8888888888888877643
No 43
>PRK04860 hypothetical protein; Provisional
Probab=82.11 E-value=0.75 Score=47.64 Aligned_cols=39 Identities=21% Similarity=0.403 Sum_probs=31.7
Q ss_pred cccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccCh
Q 001904 904 NICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWA 948 (997)
Q Consensus 904 ~hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~k 948 (997)
++|.|. |+. ....+..|.++|+++++|.| ..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC--~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRC--RRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEEC--CCCCceeEEe
Confidence 346665 776 56778999999999999999 6799988754
No 44
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=77.23 E-value=1.7 Score=37.39 Aligned_cols=27 Identities=26% Similarity=0.580 Sum_probs=15.0
Q ss_pred CCCceecCCCCcCCcccChhHHHHhhhhh
Q 001904 960 GARPYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 960 GEKPYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
.+.|..|++ |+..+.+..+|.+|+..+
T Consensus 21 S~~PatCP~--C~a~~~~srnLrRHle~~ 47 (54)
T PF09237_consen 21 SEQPATCPI--CGAVIRQSRNLRRHLEIR 47 (54)
T ss_dssp TS--EE-TT--T--EESSHHHHHHHHHHH
T ss_pred cCCCCCCCc--chhhccchhhHHHHHHHH
Confidence 456777765 777777777777777653
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=77.17 E-value=0.9 Score=33.21 Aligned_cols=24 Identities=17% Similarity=0.560 Sum_probs=18.0
Q ss_pred eecCCCCcCCcccChhHHHHhhhhhC
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRKTG 989 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rth~ 989 (997)
|.|.. |++.|.....|..|+++..
T Consensus 2 ~~C~~--C~k~f~~~~~~~~H~~sk~ 25 (27)
T PF12171_consen 2 FYCDA--CDKYFSSENQLKQHMKSKK 25 (27)
T ss_dssp CBBTT--TTBBBSSHHHHHCCTTSHH
T ss_pred CCccc--CCCCcCCHHHHHHHHccCC
Confidence 56777 8888888888888877643
No 46
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=75.35 E-value=2.1 Score=36.94 Aligned_cols=40 Identities=13% Similarity=0.367 Sum_probs=25.2
Q ss_pred HHHHHH-hcCCCCCCCCCCCCCCcccChHHHHHHHHhhCCCCc
Q 001904 922 VQHRRV-HLDDRPLKCPWKGCKMTFKWAWARTEHIRVHTGARP 963 (997)
Q Consensus 922 ~~HqRv-HtGEKPykCp~~eCGK~Fs~kS~LkrH~RiHTGEKP 963 (997)
..+.+. +..+.|-.| ++|+..+.+.-+|.+|+.++.+.||
T Consensus 12 ~~~~k~~~~S~~PatC--P~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATC--PICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE---TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCC--CcchhhccchhhHHHHHHHHhcccC
Confidence 344444 346778999 6699999999999999999888876
No 47
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.79 E-value=6.8 Score=48.73 Aligned_cols=17 Identities=24% Similarity=0.276 Sum_probs=8.9
Q ss_pred CCCcccChHHHHHHHHh
Q 001904 941 CKMTFKWAWARTEHIRV 957 (997)
Q Consensus 941 CGK~Fs~kS~LkrH~Ri 957 (997)
|...|.....|.+|++.
T Consensus 188 C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 188 CHERFLDDDELYRHLRF 204 (669)
T ss_pred hhhhhccHHHHHHhhcc
Confidence 55555555555555543
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=67.17 E-value=3.5 Score=29.09 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=15.0
Q ss_pred eecCCCCcCCcccChhHHHHhhhhh
Q 001904 964 YVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 964 YkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
|.|.. |+.... ...|..|+++|
T Consensus 1 y~C~~--C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPH--CSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SS--SS-EES-HHHHHHHHHHH
T ss_pred CCCCC--CCCcCC-HHHHHHHHHhh
Confidence 67777 887777 77888888774
No 49
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.26 E-value=1.5 Score=47.14 Aligned_cols=81 Identities=22% Similarity=0.429 Sum_probs=59.5
Q ss_pred CCcccccCCCCCCcccChhHHhhhhcc--ccCCCCCCCccCChHHHHHHHHH-h---------cCCCCCCCCCCCCCCcc
Q 001904 878 EAGYHCDMEGCTMSFGTKQELVLHKKN--ICPVKGCGKKFFSHKYLVQHRRV-H---------LDDRPLKCPWKGCKMTF 945 (997)
Q Consensus 878 eKpyqC~iegCGKsFssksnLk~Hkr~--hCpCkeCgKsFsskssL~~HqRv-H---------tGEKPykCp~~eCGK~F 945 (997)
...|.|++.+|...|......-.|... --.|..|.+.|.+...|-.|+.. | .|.--|.|-+.+|+..|
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 355889999999998776655555432 24688899999999999888753 3 34445788777888888
Q ss_pred cChHHHHHHHH-hh
Q 001904 946 KWAWARTEHIR-VH 958 (997)
Q Consensus 946 s~kS~LkrH~R-iH 958 (997)
.+.-....|+- +|
T Consensus 157 kT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhHHHHhc
Confidence 88877777764 45
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=62.97 E-value=2.1 Score=56.04 Aligned_cols=93 Identities=13% Similarity=0.106 Sum_probs=63.8
Q ss_pred ccccCCCCCCcccChhHHhhhhc--cccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHHhh
Q 001904 881 YHCDMEGCTMSFGTKQELVLHKK--NICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 881 yqC~iegCGKsFssksnLk~Hkr--~hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
+.|.. |.+.|.....+. |.- .+|.|..|...|.....|..|++ + |-+.|.....+.-|+..|
T Consensus 1261 ~~c~~--~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~--------k-----~~~~~~~~~~~~~~~l~~ 1324 (1406)
T KOG1146|consen 1261 GECGA--VDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQR--------K-----FCFAGRGSGGSMPPPLRV 1324 (1406)
T ss_pred chhhh--ccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHH--------H-----HHhccCccccCCCCcccC
Confidence 66765 777776665555 543 35667777777777777777762 2 223455555555565556
Q ss_pred CCCCceecCCCCcCCcccChhHHHHhhhhhCCCC
Q 001904 959 TGARPYVCAEPGCGQTFRFVSDFSRHKRKTGHSA 992 (997)
Q Consensus 959 TGEKPYkC~epGCGKsFs~sSsLkrH~Rth~Hsg 992 (997)
..-.+| |.. |...|.....|..|+|+.+|.-
T Consensus 1325 ~d~~~~-c~~--c~~~~~~~~alqihm~~~~~~~ 1355 (1406)
T KOG1146|consen 1325 PDCTYH-CLA--CEVLLSGREALQIHMRSSAHRR 1355 (1406)
T ss_pred cccccc-chH--HHhhcchhHHHHHHHHHhhhcc
Confidence 666778 988 9999999999999999866643
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=61.43 E-value=2.7 Score=55.10 Aligned_cols=90 Identities=19% Similarity=0.276 Sum_probs=52.6
Q ss_pred CCCcccChhHHhhhhc------cccCCCCCCCccCChHHHHHHHHH-hcCCCCCCCCCCCCCCcccChHHHHHHHH----
Q 001904 888 CTMSFGTKQELVLHKK------NICPVKGCGKKFFSHKYLVQHRRV-HLDDRPLKCPWKGCKMTFKWAWARTEHIR---- 956 (997)
Q Consensus 888 CGKsFssksnLk~Hkr------~hCpCkeCgKsFsskssL~~HqRv-HtGEKPykCp~~eCGK~Fs~kS~LkrH~R---- 956 (997)
|+..|..+..+-.|.. ..+.|+.|+..|.....|-.|+|+ |..-.--.|.+ ...|.+
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~------------gq~~~~~arg 509 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKA------------GQNHPRLARG 509 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHh------------cccccccccc
Confidence 4445544444444422 235666777777777777777665 32221122210 111111
Q ss_pred --hhCCCCceecCCCCcCCcccChhHHHHhhhhhCCC
Q 001904 957 --VHTGARPYVCAEPGCGQTFRFVSDFSRHKRKTGHS 991 (997)
Q Consensus 957 --iHTGEKPYkC~epGCGKsFs~sSsLkrH~Rth~Hs 991 (997)
.-.+.+||.|.. |...|....+|.+|+...-|.
T Consensus 510 ~~~~~~~~p~~C~~--C~~stttng~LsihlqS~~h~ 544 (1406)
T KOG1146|consen 510 EVYRCPGKPYPCRA--CNYSTTTNGNLSIHLQSDLHR 544 (1406)
T ss_pred ccccCCCCccccee--eeeeeecchHHHHHHHHHhhH
Confidence 122567899988 999999999999999875454
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=60.88 E-value=3.8 Score=28.98 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=16.2
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
|.| ..|++.|.....|..|++.+
T Consensus 1 ~~C--~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYC--DICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEE--TTTTEEESSHHHHHHHHTTH
T ss_pred CCC--CCCCCCcCCHHHHHHHHCcC
Confidence 456 56777777777777777643
No 53
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=59.79 E-value=3.6 Score=48.10 Aligned_cols=107 Identities=32% Similarity=0.547 Sum_probs=66.3
Q ss_pred CcccccCCCCCCcccChhHHhhhhc-------------------cccCCCCCCCccCChHHHHHHHHHhcCC-----C--
Q 001904 879 AGYHCDMEGCTMSFGTKQELVLHKK-------------------NICPVKGCGKKFFSHKYLVQHRRVHLDD-----R-- 932 (997)
Q Consensus 879 KpyqC~iegCGKsFssksnLk~Hkr-------------------~hCpCkeCgKsFsskssL~~HqRvHtGE-----K-- 932 (997)
--|.|.-+.|+-.+..+..+.+|.. ++|....|.+ ..+....|-..|+.. +
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrt 346 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRT 346 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecc
Confidence 3477877778888777777777733 1355567887 334556666666432 2
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHhhCCCC------------------------ceecCCCCcCCcccChhHHHHhhhhh
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRVHTGAR------------------------PYVCAEPGCGQTFRFVSDFSRHKRKT 988 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~RiHTGEK------------------------PYkC~epGCGKsFs~sSsLkrH~Rth 988 (997)
-|.|.-..|--+|.-..+-..|.+-+.++. .|-|.++||+.+|...+.+..|.|.|
T Consensus 347 hfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkh 426 (480)
T KOG4377|consen 347 HFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKH 426 (480)
T ss_pred eeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhhhh
Confidence 366733233355554333333443333221 14588899999999999999999985
No 54
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.68 E-value=11 Score=46.87 Aligned_cols=119 Identities=18% Similarity=0.173 Sum_probs=71.6
Q ss_pred cccCCcccccCcccccccc-cccCCCcccccCCC--------CCCcccChhHHhhhhcc----------ccCCCCCCCcc
Q 001904 855 KKVKNASVVKAPAGLNNAK-IKDEEAGYHCDMEG--------CTMSFGTKQELVLHKKN----------ICPVKGCGKKF 915 (997)
Q Consensus 855 c~vc~ksf~kk~~L~~H~r-tHtgeKpyqC~ieg--------CGKsFssksnLk~Hkr~----------hCpCkeCgKsF 915 (997)
|..| ..|.....|..|+. .|.. +-|.+-- |.+. .+...|..|+.. |-.|..|...|
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~f 192 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKL-YTRAELNLHLMFGDPDDESCRGHPLCKFCHERF 192 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeeh-ehHHHHHHHHhcCCCccccccCCccchhhhhhh
Confidence 4455 55556777788873 4432 2232200 2333 356778888664 23477899999
Q ss_pred CChHHHHHHHHHhcCCCCCCCCC----CCCCCcccChHHHHHHHHhhCCCCceecCCCCcC-CcccChhHHHHhhh
Q 001904 916 FSHKYLVQHRRVHLDDRPLKCPW----KGCKMTFKWAWARTEHIRVHTGARPYVCAEPGCG-QTFRFVSDFSRHKR 986 (997)
Q Consensus 916 sskssL~~HqRvHtGEKPykCp~----~eCGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCG-KsFs~sSsLkrH~R 986 (997)
.....|..|++.++ |.|.+ ..++..|.....|..|.|.+ .|.|...-|. +.|.....+..|++
T Consensus 193 ld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~----HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 193 LDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKG----HFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred ccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhc----CccccccccccceeeehhHHHHHHH
Confidence 99999999988644 34422 22456788889999999864 3777732365 34444433333333
No 55
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=55.30 E-value=6.9 Score=29.64 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=19.0
Q ss_pred ceecCCCCcCCcccChhHHHHhhhhhCC
Q 001904 963 PYVCAEPGCGQTFRFVSDFSRHKRKTGH 990 (997)
Q Consensus 963 PYkC~epGCGKsFs~sSsLkrH~Rth~H 990 (997)
+|.|.. |++.|.....+..|+....|
T Consensus 3 ~~~C~~--C~~~~~~~~~~~~H~~gk~H 28 (35)
T smart00451 3 GFYCKL--CNVTFTDEISVEAHLKGKKH 28 (35)
T ss_pred CeEccc--cCCccCCHHHHHHHHChHHH
Confidence 577877 88888888888888765433
No 56
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=52.22 E-value=5.7 Score=28.98 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=17.1
Q ss_pred CCCCCCCCCCcccChHHHHHHHHh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRV 957 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~Ri 957 (997)
|.| ..|++.|.....|..|++.
T Consensus 2 ~~C--~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYC--DACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBB--TTTTBBBSSHHHHHCCTTS
T ss_pred CCc--ccCCCCcCCHHHHHHHHcc
Confidence 677 5688888888888888764
No 57
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=51.50 E-value=4.6 Score=44.33 Aligned_cols=42 Identities=33% Similarity=0.501 Sum_probs=28.5
Q ss_pred CCCcccChhHHhhhhc-cccCCCCCCCccCChHHHHHH-HHHhc
Q 001904 888 CTMSFGTKQELVLHKK-NICPVKGCGKKFFSHKYLVQH-RRVHL 929 (997)
Q Consensus 888 CGKsFssksnLk~Hkr-~hCpCkeCgKsFsskssL~~H-qRvHt 929 (997)
|++.|-...-|..|++ .||.|..|-|.+.+--.|..| +.+|.
T Consensus 16 cnrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred cccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 7777777777777765 467777777776666666666 33453
No 58
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=49.53 E-value=8.9 Score=27.04 Aligned_cols=22 Identities=23% Similarity=0.505 Sum_probs=12.7
Q ss_pred CCCCCCCCCCcccChHHHHHHHHhh
Q 001904 934 LKCPWKGCKMTFKWAWARTEHIRVH 958 (997)
Q Consensus 934 ykCp~~eCGK~Fs~kS~LkrH~RiH 958 (997)
|.| ..|..... ...|..|++.|
T Consensus 1 y~C--~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKC--PHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE---SSSS-EES-HHHHHHHHHHH
T ss_pred CCC--CCCCCcCC-HHHHHHHHHhh
Confidence 456 44776666 66777777664
No 59
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.69 E-value=5.6 Score=42.97 Aligned_cols=79 Identities=27% Similarity=0.466 Sum_probs=62.9
Q ss_pred ccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCCcccChHHHHHHHH-hh---------CCCCceecCCCCcCCc
Q 001904 905 ICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKMTFKWAWARTEHIR-VH---------TGARPYVCAEPGCGQT 974 (997)
Q Consensus 905 hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK~Fs~kS~LkrH~R-iH---------TGEKPYkC~epGCGKs 974 (997)
.|+.-.|...|........|..+-++. .| ..|.+.|.+.--|..|+. .| .|.--|+|-..||+-.
T Consensus 81 ~cqvagc~~~~d~lD~~E~hY~~~h~~---sC--s~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 81 ACQVAGCCQVFDALDDYEHHYHTLHGN---SC--SFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccchHHHHhhhhhHHHhhhhcccc---hh--HHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 366677888998888788887653333 79 669999999999999986 24 3555699998899999
Q ss_pred ccChhHHHHhhhhh
Q 001904 975 FRFVSDFSRHKRKT 988 (997)
Q Consensus 975 Fs~sSsLkrH~Rth 988 (997)
|........|+-..
T Consensus 156 FkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRM 169 (253)
T ss_pred hhhhhhhhhHHHHh
Confidence 99999999998764
No 60
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=43.96 E-value=16 Score=26.72 Aligned_cols=20 Identities=25% Similarity=0.700 Sum_probs=11.3
Q ss_pred ecCCCCcCCcccChhHHHHhhhh
Q 001904 965 VCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 965 kC~epGCGKsFs~sSsLkrH~Rt 987 (997)
.|+. ||+.| ....|.+|+..
T Consensus 4 ~C~~--CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPI--CGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCC--CCCEE-CHHHHHHHHHh
Confidence 4544 66666 45556666543
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=38.37 E-value=15 Score=42.51 Aligned_cols=85 Identities=24% Similarity=0.359 Sum_probs=58.2
Q ss_pred cChhHHhhhhcc---------ccCCCCCCCccCChHHHHHHHHHhcCCCCCCCCCCCCCC-------cccChHHHHHHHH
Q 001904 893 GTKQELVLHKKN---------ICPVKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKGCKM-------TFKWAWARTEHIR 956 (997)
Q Consensus 893 ssksnLk~Hkr~---------hCpCkeCgKsFsskssL~~HqRvHtGEKPykCp~~eCGK-------~Fs~kS~LkrH~R 956 (997)
.++..|..|... |-.|..|..-|..-..|..|++..+. .| -+|++ -|..-..|-.|.+
T Consensus 199 F~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE----~C--hICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 199 FRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE----AC--HICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred eecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhhh----hh--hhhhccCccchhhhhCHHHHHHHhh
Confidence 356677778542 34578899999999999999886322 45 34553 4666677878876
Q ss_pred hhCCCCceecCCCCcC----CcccChhHHHHhhhh
Q 001904 957 VHTGARPYVCAEPGCG----QTFRFVSDFSRHKRK 987 (997)
Q Consensus 957 iHTGEKPYkC~epGCG----KsFs~sSsLkrH~Rt 987 (997)
. -.|.|.+..|. ..|.....|..|...
T Consensus 273 ~----~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 273 N----AHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred c----CceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 3 24777765553 357888888999765
No 62
>PF14597 Lactamase_B_5: Metallo-beta-lactamase superfamily; PDB: 2P97_B.
Probab=34.01 E-value=24 Score=37.88 Aligned_cols=39 Identities=26% Similarity=0.297 Sum_probs=29.0
Q ss_pred HHHHHHhhcccCCceEEEEeCCChhHHHHHHHHHHHHhCCcc
Q 001904 149 AVEVEQQLRPIGGVDIFLLCHPDYPKMVAEAKLVAEELGIDS 190 (997)
Q Consensus 149 a~e~~~~l~~~gg~~~~~~ch~~y~~~~~~a~~~a~e~~~~~ 190 (997)
+.+.++.|+++||+..|||.|.|-. +.|..+|+..|++.
T Consensus 43 s~~~~~~l~a~ggv~~IvLTn~dHv---R~A~~ya~~~~a~i 81 (199)
T PF14597_consen 43 SAHDWKHLDALGGVAWIVLTNRDHV---RAAEDYAEQTGAKI 81 (199)
T ss_dssp -HHHHHHHHHTT--SEEE-SSGGG----TTHHHHHHHS--EE
T ss_pred cHHHHHHHHhcCCceEEEEeCChhH---hHHHHHHHHhCCee
Confidence 5678899999999999999999974 67999999999876
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=31.30 E-value=22 Score=31.36 Aligned_cols=27 Identities=37% Similarity=0.711 Sum_probs=17.3
Q ss_pred CCCCceecCCCCcCCcccChhHHHHhhhh
Q 001904 959 TGARPYVCAEPGCGQTFRFVSDFSRHKRK 987 (997)
Q Consensus 959 TGEKPYkC~epGCGKsFs~sSsLkrH~Rt 987 (997)
.||--+.|+. ||..|...-++.+|.-.
T Consensus 13 DGE~~lrCPR--C~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPR--CGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCc--hhHHHHHhHHHHHHhhH
Confidence 3555666755 77777776666676554
No 64
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.88 E-value=47 Score=38.62 Aligned_cols=90 Identities=22% Similarity=0.353 Sum_probs=59.8
Q ss_pred cccCcccccccccccCCCcc----cccCCCCCCcccChhHHhhhhcc-ccCCCCCCCc-------cCChHHHHHHHHHhc
Q 001904 862 VVKAPAGLNNAKIKDEEAGY----HCDMEGCTMSFGTKQELVLHKKN-ICPVKGCGKK-------FFSHKYLVQHRRVHL 929 (997)
Q Consensus 862 f~kk~~L~~H~rtHtgeKpy----qC~iegCGKsFssksnLk~Hkr~-hCpCkeCgKs-------FsskssL~~HqRvHt 929 (997)
......|..|...-..+..| .|.+ |..-|..-..|..|++. |=.|..|.+. |.....|..|-+
T Consensus 198 lF~~~~Lr~H~~~G~~e~GFKGHP~C~F--C~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~--- 272 (493)
T COG5236 198 LFRSSTLRDHKNGGLEEEGFKGHPLCIF--CKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFR--- 272 (493)
T ss_pred eeecccccccccCCccccCcCCCchhhh--ccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhh---
Confidence 34445566665544433333 3988 99999999999999874 4456777664 444555666644
Q ss_pred CCCCCCCCCCCCC----CcccChHHHHHHHHh
Q 001904 930 DDRPLKCPWKGCK----MTFKWAWARTEHIRV 957 (997)
Q Consensus 930 GEKPykCp~~eCG----K~Fs~kS~LkrH~Ri 957 (997)
.-.|.|.+..|. .+|....-|..|+..
T Consensus 273 -~~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 273 -NAHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred -cCceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 334777766664 467888889999864
No 65
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=26.90 E-value=42 Score=25.31 Aligned_cols=23 Identities=26% Similarity=0.469 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHh
Q 001904 933 PLKCPWKGCKMTFKWAWARTEHIRV 957 (997)
Q Consensus 933 PykCp~~eCGK~Fs~kS~LkrH~Ri 957 (997)
+|.| ..|++.|.....+..|+..
T Consensus 3 ~~~C--~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYC--KLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEc--cccCCccCCHHHHHHHHCh
Confidence 5789 6799999988888888763
No 66
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=25.21 E-value=26 Score=38.78 Aligned_cols=38 Identities=21% Similarity=0.372 Sum_probs=20.1
Q ss_pred CCCcccChHHHHHHHHhhCCCCceecCCCCcCCcccChhHHHHh
Q 001904 941 CKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQTFRFVSDFSRH 984 (997)
Q Consensus 941 CGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKsFs~sSsLkrH 984 (997)
|.+-|....-|..|++ .|.|+|.+ |.|..-.--.|..|
T Consensus 16 cnrefddekiliqhqk----akhfkchi--chkkl~sgpglsih 53 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQK----AKHFKCHI--CHKKLFSGPGLSIH 53 (341)
T ss_pred cccccchhhhhhhhhh----hccceeee--ehhhhccCCCceee
Confidence 5555655555555554 33456655 65554444444444
No 67
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=24.74 E-value=1.1e+02 Score=34.02 Aligned_cols=59 Identities=17% Similarity=0.146 Sum_probs=45.8
Q ss_pred cccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCCC--hhHHHHHHHHHHHHhCCc
Q 001904 130 FAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHPD--YPKMVAEAKLVAEELGID 189 (997)
Q Consensus 130 ~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~~--y~~~~~~a~~~a~e~~~~ 189 (997)
++..-|.+. -.---|+|=|..+-+.|..+| |.||++=.-|. |..+.+-|+.||++|.-.
T Consensus 103 ~vfDLDP~~-~~f~~v~~~A~~~r~~L~~~gL~~f~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~~ 174 (228)
T cd04864 103 MVFDLDPSA-DDIEAVRTAALAVRELLDELGLPSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAKR 174 (228)
T ss_pred EEEecCCCC-CCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 344444442 255679999999999999988 88999988874 568888999999998654
No 68
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=23.37 E-value=1.1e+02 Score=33.77 Aligned_cols=63 Identities=21% Similarity=0.238 Sum_probs=51.0
Q ss_pred CCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCC--ChhHHHHHHHHHHHHhCCcc
Q 001904 128 MSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHP--DYPKMVAEAKLVAEELGIDS 190 (997)
Q Consensus 128 ~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~--~y~~~~~~a~~~a~e~~~~~ 190 (997)
.-++..-|.+.--.-.-|.|=|+.+-+.|..+| |.||++=..| +|..+.+-|+.||++|.-.+
T Consensus 99 D~lvfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~ 174 (227)
T cd04861 99 DRLVFDLDPGPGVPFEDVVEAALLLRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARRL 174 (227)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence 345555566656667789999999999999987 8899998887 56789999999999987543
No 69
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=22.96 E-value=1.2e+02 Score=33.65 Aligned_cols=63 Identities=21% Similarity=0.226 Sum_probs=50.9
Q ss_pred CCCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCC--ChhHHHHHHHHHHHHhCCc
Q 001904 127 EMSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHP--DYPKMVAEAKLVAEELGID 189 (997)
Q Consensus 127 ~~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~--~y~~~~~~a~~~a~e~~~~ 189 (997)
+.-++..-|.+.--.-.-|.|=|..+-+.|..+| |.||++=..| +|..+.+-|+.||++|.-.
T Consensus 98 PD~lvfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~ 173 (227)
T cd04862 98 PDRIVFDLDPGPGVPWKAVVEAALLVRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLART 173 (227)
T ss_pred CCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3445566666666677889999999999999988 8899998887 5678889999999998755
No 70
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=22.95 E-value=77 Score=31.04 Aligned_cols=59 Identities=31% Similarity=0.321 Sum_probs=35.3
Q ss_pred HhhcccCCceEEEEeCCC-----hhHHHHHHHHHHHHhCCccccccchhcccChhhHHHHHhhccc
Q 001904 154 QQLRPIGGVDIFLLCHPD-----YPKMVAEAKLVAEELGIDSLCDEISFRVATKEDEKRIHLSLDS 214 (997)
Q Consensus 154 ~~l~~~gg~~~~~~ch~~-----y~~~~~~a~~~a~e~~~~~~~~~~~~~~a~~~~~~~i~~~~~~ 214 (997)
++|...|=.+||-+. || -|.. +.-...|+++|+.|-+--|.+...+.++...+..+|+.
T Consensus 21 ~~la~~GfktVInlR-pd~E~~~qp~~-~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~ 84 (110)
T PF04273_consen 21 AQLAAQGFKTVINLR-PDGEEPGQPSS-AEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALES 84 (110)
T ss_dssp HHHHHCT--EEEE-S--TTSTTT-T-H-HCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHT
T ss_pred HHHHHCCCcEEEECC-CCCCCCCCCCH-HHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHh
Confidence 467777777776665 54 2322 23345789999999999999999999999999999985
No 71
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=22.46 E-value=1.2e+02 Score=33.59 Aligned_cols=63 Identities=21% Similarity=0.264 Sum_probs=50.0
Q ss_pred CCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCC--ChhHHHHHHHHHHHHhCCcc
Q 001904 128 MSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHP--DYPKMVAEAKLVAEELGIDS 190 (997)
Q Consensus 128 ~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~--~y~~~~~~a~~~a~e~~~~~ 190 (997)
.-++..-|.+.--.-.-|.|=|..+-+.|..+| |.||++=.-| +|..+.+-|+.||++|.-.+
T Consensus 100 D~lvfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~sf~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l~~~~ 175 (228)
T cd04865 100 DELVIDLDPQPGTSFEDVVEVALLVREVLDELGLRGYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREVERRL 175 (228)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence 334555555555566789999999999999988 8899998887 56788899999999987543
No 72
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=22.33 E-value=1.4e+02 Score=32.90 Aligned_cols=63 Identities=17% Similarity=0.229 Sum_probs=50.6
Q ss_pred CCCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeC-C--ChhHHHHHHHHHHHHhCCc
Q 001904 127 EMSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCH-P--DYPKMVAEAKLVAEELGID 189 (997)
Q Consensus 127 ~~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch-~--~y~~~~~~a~~~a~e~~~~ 189 (997)
+.-++..-|.+.--.-.-|.|=|+.+-+.|..+| |.||++=.. | +|..+.+-|+.||++|.-.
T Consensus 93 PD~lvfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~~ 169 (223)
T cd04866 93 PSEIVFDLDPPSRDHFSLAVEAANLLKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQQ 169 (223)
T ss_pred CCeEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3445555666555666789999999999999988 889999888 5 5789999999999998754
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.04 E-value=1e+02 Score=30.78 Aligned_cols=83 Identities=23% Similarity=0.405 Sum_probs=0.0
Q ss_pred CCcccccCCCCCCcccChhHHhhhhccccC-----------------CCCCCCccCChHHHHHHHHHhcCCCCCCCCCCC
Q 001904 878 EAGYHCDMEGCTMSFGTKQELVLHKKNICP-----------------VKGCGKKFFSHKYLVQHRRVHLDDRPLKCPWKG 940 (997)
Q Consensus 878 eKpyqC~iegCGKsFssksnLk~Hkr~hCp-----------------CkeCgKsFsskssL~~HqRvHtGEKPykCp~~e 940 (997)
+-|..|++ ||........|.+.....|+ |-.|...|........-. -.....|.| ..
T Consensus 13 ~LP~~Cpi--CgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~~~~y~C--~~ 86 (112)
T TIGR00622 13 ELPVECPI--CGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKDSHRYVC--AV 86 (112)
T ss_pred CCCCcCCc--CCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--cccccceeC--CC
Q ss_pred CCCcccChHHHHHHHHhhCCCCceecCCCCcCCc
Q 001904 941 CKMTFKWAWARTEHIRVHTGARPYVCAEPGCGQT 974 (997)
Q Consensus 941 CGK~Fs~kS~LkrH~RiHTGEKPYkC~epGCGKs 974 (997)
|...|-..-.+-.|...|. | |||...
T Consensus 87 C~~~FC~dCD~fiHe~Lh~------C--PGC~~~ 112 (112)
T TIGR00622 87 CKNVFCVDCDVFVHESLHC------C--PGCIHK 112 (112)
T ss_pred CCCccccccchhhhhhccC------C--cCCCCC
No 74
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=21.86 E-value=1.3e+02 Score=33.79 Aligned_cols=63 Identities=17% Similarity=0.265 Sum_probs=51.1
Q ss_pred CCCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCC--ChhHHHHHHHHHHHHhCCc
Q 001904 127 EMSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHP--DYPKMVAEAKLVAEELGID 189 (997)
Q Consensus 127 ~~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~--~y~~~~~~a~~~a~e~~~~ 189 (997)
+.-++..-|-+.-..-.-|.|=|+.+-+.|...| |.||++=.-| +|..+.+-|+.||++|.-.
T Consensus 114 PD~lvfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~ 189 (245)
T TIGR02778 114 PDRIVFDLDPGPGVAWKLVVEAAQLIRELLDELGLESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQ 189 (245)
T ss_pred CCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3445666666666677889999999999999987 8899998887 5678888999999998754
No 75
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=21.16 E-value=1.1e+02 Score=33.85 Aligned_cols=63 Identities=19% Similarity=0.206 Sum_probs=50.0
Q ss_pred CCCcccCCCCCCccceeehhhhHHHHHHhhcccC-----------CceEEEEeCCC--hhHHHHHHHHHHHHhCCc
Q 001904 127 EMSFAPRSDEDSSRMHVFCLEHAVEVEQQLRPIG-----------GVDIFLLCHPD--YPKMVAEAKLVAEELGID 189 (997)
Q Consensus 127 ~~~~~~~~~~~s~r~~vfcleha~e~~~~l~~~g-----------g~~~~~~ch~~--y~~~~~~a~~~a~e~~~~ 189 (997)
+.-++..-|.+.--.---|+|=|..+-+.|..+| |.||++=.-|. |..+.+-|+.||++|.-.
T Consensus 102 PD~~vfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~~~ 177 (231)
T cd04863 102 PDRLVFDLDPGEPAGLVECARVALWLRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELERE 177 (231)
T ss_pred CCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3444555555555666789999999999999988 88999988884 568888999999998765
Done!