Query 040647
Match_columns 286
No_of_seqs 249 out of 1805
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 10:26:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040647hhsearch_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 99.7 9.7E-19 2.1E-23 159.8 3.9 94 18-114 134-247 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.6 2.2E-16 4.7E-21 144.5 1.6 74 18-102 191-264 (279)
3 KOG1074 Transcriptional repres 99.4 3.1E-13 6.7E-18 138.1 3.2 60 51-113 605-664 (958)
4 KOG3623 Homeobox transcription 99.4 1.4E-13 3E-18 138.8 0.7 87 18-115 898-984 (1007)
5 KOG3623 Homeobox transcription 99.3 1.1E-12 2.4E-17 132.4 1.5 84 17-102 243-330 (1007)
6 KOG1074 Transcriptional repres 99.2 1.1E-11 2.4E-16 127.0 4.4 60 51-113 879-938 (958)
7 KOG3576 Ovo and related transc 99.2 7.6E-13 1.6E-17 116.9 -3.9 83 18-111 121-203 (267)
8 PHA02768 hypothetical protein; 98.8 1.6E-09 3.5E-14 77.2 1.8 44 52-99 6-49 (55)
9 KOG3608 Zn finger proteins [Ge 98.8 2.9E-09 6.3E-14 100.8 2.1 87 17-106 182-316 (467)
10 KOG3608 Zn finger proteins [Ge 98.5 2.1E-08 4.5E-13 95.1 -0.5 85 18-107 241-347 (467)
11 KOG3576 Ovo and related transc 98.5 3.3E-08 7.1E-13 87.8 0.1 62 50-114 116-177 (267)
12 PHA00733 hypothetical protein 98.4 1.1E-07 2.4E-12 79.2 2.7 78 18-105 44-123 (128)
13 PF13465 zf-H2C2_2: Zinc-finge 98.3 2.5E-07 5.3E-12 56.2 1.5 25 66-92 1-25 (26)
14 PF13465 zf-H2C2_2: Zinc-finge 98.1 9.7E-07 2.1E-11 53.6 1.0 26 29-63 1-26 (26)
15 PLN03086 PRLI-interacting fact 98.0 2.5E-06 5.5E-11 86.4 3.2 78 18-113 457-544 (567)
16 PHA00616 hypothetical protein 98.0 1.3E-06 2.7E-11 59.7 0.4 34 51-84 1-34 (44)
17 PHA02768 hypothetical protein; 98.0 2.2E-06 4.7E-11 61.2 1.0 41 17-68 8-48 (55)
18 PHA00732 hypothetical protein 97.7 2.2E-05 4.8E-10 60.2 2.7 44 51-102 1-45 (79)
19 PLN03086 PRLI-interacting fact 97.5 7.4E-05 1.6E-09 75.9 3.1 57 50-114 452-508 (567)
20 PF00096 zf-C2H2: Zinc finger, 97.4 5.7E-05 1.2E-09 43.9 0.7 23 52-74 1-23 (23)
21 PHA00733 hypothetical protein 97.0 0.00029 6.4E-09 58.6 1.5 54 49-105 38-96 (128)
22 KOG3993 Transcription factor ( 97.0 0.00015 3.3E-09 70.6 -0.7 78 17-106 270-380 (500)
23 PF13912 zf-C2H2_6: C2H2-type 96.9 0.00046 1E-08 41.5 1.1 25 51-75 1-25 (27)
24 PHA00732 hypothetical protein 96.7 0.00077 1.7E-08 51.7 1.7 45 17-76 4-49 (79)
25 COG5189 SFP1 Putative transcri 96.6 0.001 2.2E-08 63.0 1.8 53 48-102 346-419 (423)
26 PF13894 zf-C2H2_4: C2H2-type 96.6 0.00089 1.9E-08 38.3 0.9 23 52-74 1-23 (24)
27 PHA00616 hypothetical protein 96.4 0.00058 1.3E-08 46.7 -0.8 32 79-113 1-32 (44)
28 smart00355 ZnF_C2H2 zinc finge 96.3 0.0022 4.8E-08 37.0 1.5 25 52-76 1-25 (26)
29 PRK04860 hypothetical protein; 96.3 0.0019 4.2E-08 55.8 1.7 36 51-92 119-154 (160)
30 PF05605 zf-Di19: Drought indu 96.0 0.0031 6.7E-08 44.5 1.3 47 51-102 2-50 (54)
31 PF09237 GAGA: GAGA factor; I 95.3 0.0087 1.9E-07 42.2 1.3 32 48-79 21-52 (54)
32 PF12756 zf-C2H2_2: C2H2 type 94.8 0.014 3E-07 44.7 1.4 57 18-74 3-73 (100)
33 PF12874 zf-met: Zinc-finger o 94.7 0.013 2.8E-07 34.4 0.7 23 52-74 1-23 (25)
34 COG5048 FOG: Zn-finger [Genera 94.4 0.026 5.6E-07 52.8 2.6 61 50-113 288-354 (467)
35 PF00096 zf-C2H2: Zinc finger, 94.3 0.0049 1.1E-07 35.5 -1.7 21 80-102 1-21 (23)
36 PF12171 zf-C2H2_jaz: Zinc-fin 93.7 0.03 6.6E-07 33.7 1.0 22 52-73 2-23 (27)
37 COG5189 SFP1 Putative transcri 93.7 0.031 6.7E-07 53.2 1.5 55 18-72 355-419 (423)
38 PF13912 zf-C2H2_6: C2H2-type 93.6 0.026 5.7E-07 33.7 0.6 25 79-106 1-25 (27)
39 COG5048 FOG: Zn-finger [Genera 93.4 0.046 1E-06 51.1 2.2 63 18-87 293-359 (467)
40 PF12756 zf-C2H2_2: C2H2 type 93.3 0.021 4.6E-07 43.6 -0.2 49 53-103 1-72 (100)
41 KOG3993 Transcription factor ( 92.6 0.029 6.4E-07 55.1 -0.5 53 51-106 267-319 (500)
42 PF09237 GAGA: GAGA factor; I 91.8 0.035 7.5E-07 39.2 -0.8 40 68-110 12-52 (54)
43 PF13894 zf-C2H2_4: C2H2-type 91.6 0.025 5.4E-07 32.1 -1.4 21 80-102 1-21 (24)
44 PF13913 zf-C2HC_2: zinc-finge 90.4 0.15 3.2E-06 30.5 1.2 21 52-73 3-23 (25)
45 PF13909 zf-H2C2_5: C2H2-type 90.3 0.12 2.7E-06 30.0 0.8 22 52-74 1-22 (24)
46 KOG2893 Zn finger protein [Gen 89.3 0.13 2.7E-06 47.4 0.3 52 12-76 8-60 (341)
47 PF05605 zf-Di19: Drought indu 89.3 0.26 5.5E-06 34.6 1.8 47 18-75 6-53 (54)
48 smart00355 ZnF_C2H2 zinc finge 88.4 0.14 3.1E-06 29.0 0.1 24 80-106 1-24 (26)
49 smart00451 ZnF_U1 U1-like zinc 87.1 0.34 7.4E-06 30.4 1.2 23 51-73 3-25 (35)
50 PRK04860 hypothetical protein; 85.6 0.4 8.6E-06 41.5 1.3 24 26-49 127-150 (160)
51 PF12171 zf-C2H2_jaz: Zinc-fin 80.3 1.2 2.7E-05 26.6 1.6 21 80-102 2-22 (27)
52 PF12874 zf-met: Zinc-finger o 77.5 0.76 1.6E-05 26.6 0.0 21 80-102 1-21 (25)
53 KOG1924 RhoA GTPase effector D 74.8 9.6 0.00021 40.8 7.2 12 54-65 439-450 (1102)
54 KOG1146 Homeobox protein [Gene 65.8 2.5 5.3E-05 47.2 0.7 51 50-102 464-539 (1406)
55 KOG1146 Homeobox protein [Gene 65.6 2.4 5.3E-05 47.2 0.6 67 7-73 457-540 (1406)
56 cd00350 rubredoxin_like Rubred 62.9 4.7 0.0001 25.5 1.3 24 52-87 2-25 (33)
57 KOG2893 Zn finger protein [Gen 62.8 2.8 6E-05 38.8 0.3 42 53-100 12-53 (341)
58 smart00451 ZnF_U1 U1-like zinc 60.3 4.1 8.9E-05 25.3 0.7 22 79-102 3-24 (35)
59 COG1198 PriA Primosomal protei 59.5 4.8 0.0001 42.8 1.5 45 43-87 436-483 (730)
60 smart00531 TFIIE Transcription 58.9 6 0.00013 33.4 1.7 43 49-95 97-139 (147)
61 TIGR00373 conserved hypothetic 58.9 5.6 0.00012 34.1 1.6 41 49-98 107-147 (158)
62 PRK06266 transcription initiat 58.3 5.8 0.00013 34.8 1.6 39 50-97 116-154 (178)
63 PF09986 DUF2225: Uncharacteri 57.7 4.4 9.6E-05 36.5 0.7 41 50-92 4-59 (214)
64 smart00614 ZnF_BED BED zinc fi 54.1 8.1 0.00018 26.5 1.4 24 52-75 19-48 (50)
65 TIGR02605 CxxC_CxxC_SSSS putat 51.7 6.3 0.00014 27.0 0.6 29 52-87 6-34 (52)
66 PRK00464 nrdR transcriptional 51.2 5.9 0.00013 34.1 0.5 17 80-98 29-45 (154)
67 PF02892 zf-BED: BED zinc fing 50.1 8.4 0.00018 25.4 1.0 21 51-71 16-40 (45)
68 PF12149 HSV_VP16_C: Herpes si 49.7 2.3 4.9E-05 26.2 -1.7 21 250-276 8-28 (30)
69 PF09538 FYDLN_acid: Protein o 48.8 13 0.00027 30.2 2.0 32 50-94 8-39 (108)
70 smart00834 CxxC_CXXC_SSSS Puta 46.2 8.6 0.00019 24.7 0.5 29 52-87 6-34 (41)
71 KOG4173 Alpha-SNAP protein [In 45.2 3.7 8E-05 37.2 -1.8 51 53-105 108-170 (253)
72 COG5236 Uncharacterized conser 45.1 14 0.0003 36.0 2.0 49 53-102 222-272 (493)
73 cd00729 rubredoxin_SM Rubredox 43.1 15 0.00033 23.4 1.3 25 51-87 2-26 (34)
74 PF09723 Zn-ribbon_8: Zinc rib 43.0 12 0.00026 24.9 0.8 29 52-87 6-34 (42)
75 COG1592 Rubrerythrin [Energy p 42.0 15 0.00033 32.0 1.6 26 49-87 132-157 (166)
76 PRK09678 DNA-binding transcrip 41.3 7.2 0.00016 29.4 -0.5 43 52-98 2-46 (72)
77 KOG2186 Cell growth-regulating 40.9 12 0.00025 34.9 0.7 46 52-102 4-49 (276)
78 PRK00398 rpoP DNA-directed RNA 40.4 12 0.00026 25.2 0.6 35 51-95 3-37 (46)
79 KOG4167 Predicted DNA-binding 39.6 5 0.00011 42.4 -2.1 27 51-77 792-818 (907)
80 KOG1365 RNA-binding protein Fu 39.4 1.2E+02 0.0025 30.3 7.2 27 193-219 439-465 (508)
81 COG4049 Uncharacterized protei 39.0 11 0.00024 27.2 0.2 26 48-73 14-39 (65)
82 PRK05580 primosome assembly pr 37.9 17 0.00036 38.3 1.4 45 43-87 382-429 (679)
83 PF04959 ARS2: Arsenite-resist 36.7 18 0.00039 32.8 1.3 28 48-75 74-102 (214)
84 PF13719 zinc_ribbon_5: zinc-r 36.5 28 0.0006 22.5 1.8 33 53-92 4-36 (37)
85 TIGR00595 priA primosomal prot 36.4 18 0.00039 36.7 1.3 17 44-60 215-231 (505)
86 TIGR02300 FYDLN_acid conserved 36.2 30 0.00064 29.0 2.3 32 50-94 8-39 (129)
87 PRK14873 primosome assembly pr 35.1 16 0.00036 38.4 0.8 18 44-61 385-402 (665)
88 KOG2231 Predicted E3 ubiquitin 34.9 22 0.00047 37.5 1.6 22 52-73 183-204 (669)
89 KOG2071 mRNA cleavage and poly 33.6 19 0.00041 37.2 0.9 29 49-77 416-444 (579)
90 COG1997 RPL43A Ribosomal prote 32.2 29 0.00062 27.3 1.5 30 51-92 35-64 (89)
91 KOG4124 Putative transcription 32.0 16 0.00035 35.6 0.2 52 49-102 347-419 (442)
92 TIGR02098 MJ0042_CXXC MJ0042 f 31.2 35 0.00076 21.7 1.6 34 52-92 3-36 (38)
93 COG4957 Predicted transcriptio 31.1 26 0.00055 29.8 1.2 25 52-79 77-101 (148)
94 PF13717 zinc_ribbon_4: zinc-r 30.7 44 0.00094 21.5 2.0 33 52-91 3-35 (36)
95 PF05443 ROS_MUCR: ROS/MUCR tr 30.1 23 0.00051 29.7 0.8 27 50-79 71-97 (132)
96 COG2888 Predicted Zn-ribbon RN 30.0 28 0.0006 25.4 1.0 32 51-87 27-58 (61)
97 KOG2785 C2H2-type Zn-finger pr 29.4 27 0.00059 34.3 1.2 50 51-102 166-241 (390)
98 TIGR00280 L37a ribosomal prote 29.3 31 0.00068 27.2 1.3 12 79-92 53-64 (91)
99 PTZ00255 60S ribosomal protein 29.3 32 0.0007 27.1 1.4 30 51-92 36-65 (90)
100 KOG2675 Adenylate cyclase-asso 28.2 71 0.0015 32.1 3.8 12 95-106 197-208 (480)
101 smart00659 RPOLCX RNA polymera 28.1 39 0.00085 22.9 1.5 29 52-91 3-31 (44)
102 COG3091 SprT Zn-dependent meta 27.5 33 0.00072 29.6 1.3 37 51-92 117-153 (156)
103 KOG2482 Predicted C2H2-type Zn 27.2 55 0.0012 32.0 2.8 80 20-101 201-354 (423)
104 PF08790 zf-LYAR: LYAR-type C2 26.2 27 0.00059 21.6 0.4 20 52-72 1-20 (28)
105 PF10571 UPF0547: Uncharacteri 26.0 55 0.0012 19.7 1.7 9 53-61 16-24 (26)
106 PF15135 UPF0515: Uncharacteri 25.8 40 0.00086 31.5 1.6 58 28-92 93-166 (278)
107 PF01780 Ribosomal_L37ae: Ribo 25.8 23 0.00049 27.9 -0.0 30 51-92 35-64 (90)
108 COG3364 Zn-ribbon containing p 25.7 40 0.00087 27.3 1.4 27 51-87 2-28 (112)
109 COG1996 RPC10 DNA-directed RNA 25.1 37 0.0008 23.8 0.9 28 50-87 5-32 (49)
110 PRK03976 rpl37ae 50S ribosomal 24.6 43 0.00094 26.4 1.3 12 79-92 54-65 (90)
111 KOG2593 Transcription initiati 23.2 41 0.00089 33.6 1.2 35 50-87 127-161 (436)
112 PF15471 TMEM171: Transmembran 23.0 3.2E+02 0.0069 26.0 6.9 25 196-220 264-289 (319)
113 COG5152 Uncharacterized conser 22.8 29 0.00063 31.4 0.1 41 41-87 195-238 (259)
114 PF02176 zf-TRAF: TRAF-type zi 22.4 62 0.0013 22.3 1.7 46 51-100 9-60 (60)
115 COG4049 Uncharacterized protei 22.2 21 0.00046 25.8 -0.7 32 73-106 11-42 (65)
116 KOG2231 Predicted E3 ubiquitin 22.2 42 0.0009 35.5 1.1 72 26-105 126-206 (669)
117 PF12013 DUF3505: Protein of u 22.1 48 0.001 26.2 1.2 25 51-75 80-108 (109)
118 smart00734 ZnF_Rad18 Rad18-lik 21.3 58 0.0013 19.5 1.2 19 53-72 3-21 (26)
119 PRK14890 putative Zn-ribbon RN 21.2 57 0.0012 23.7 1.3 11 77-87 46-56 (59)
120 COG5236 Uncharacterized conser 21.1 27 0.00058 34.2 -0.5 81 19-106 158-245 (493)
121 PF01363 FYVE: FYVE zinc finge 21.1 56 0.0012 23.4 1.3 27 52-92 10-36 (69)
122 PF03811 Zn_Tnp_IS1: InsA N-te 21.0 50 0.0011 21.5 0.9 29 53-85 7-35 (36)
123 PF10263 SprT-like: SprT-like 20.9 38 0.00083 28.1 0.4 29 51-87 123-151 (157)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.74 E-value=9.7e-19 Score=159.79 Aligned_cols=94 Identities=20% Similarity=0.306 Sum_probs=87.7
Q ss_pred hhcccccCCCchhhhhhhccC---CCCccCCCCCCc-----------------ccccCcCCcccCCchhhhhhhhhcCCC
Q 040647 18 KQVLDESSSTGAGAGHRKKKS---GAKDGKDDECGK-----------------VYECRFCSLKFCKSQALGGHMNRHRQE 77 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~Ht---GeKpf~C~~~eK-----------------Py~C~~Cgk~F~~ss~L~~H~r~Htge 77 (286)
..|+|.+.+.++|.+|+.+|. ..|.+.|+.|+| +++|.+|||.|.+.--|+.|+|+||||
T Consensus 134 ~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGE 213 (279)
T KOG2462|consen 134 PECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGE 213 (279)
T ss_pred cccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCC
Confidence 789999999999999999884 467899999986 899999999999999999999999999
Q ss_pred cccccCCCCcccccCCchhhhhcCCCCCCCCCCCCCC
Q 040647 78 RETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTPG 114 (286)
Q Consensus 78 KPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~~ 114 (286)
|||.|..|+| +|..+++|+.|++ +|.+.|.|.|.
T Consensus 214 KPF~C~hC~k--AFADRSNLRAHmQ-THS~~K~~qC~ 247 (279)
T KOG2462|consen 214 KPFSCPHCGK--AFADRSNLRAHMQ-THSDVKKHQCP 247 (279)
T ss_pred CCccCCcccc--hhcchHHHHHHHH-hhcCCccccCc
Confidence 9999999999 9999999999999 99999999863
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.59 E-value=2.2e-16 Score=144.47 Aligned_cols=74 Identities=19% Similarity=0.307 Sum_probs=61.7
Q ss_pred hhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhh
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNL 97 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L 97 (286)
..|+|.|.+..-|+.|+|+|||| |||.|..|+|+|..+++|+.||++|.+.|+|+|..|+| +|...+-|
T Consensus 191 ~iCGKaFSRPWLLQGHiRTHTGE---------KPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~K--sFsl~SyL 259 (279)
T KOG2462|consen 191 GICGKAFSRPWLLQGHIRTHTGE---------KPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGK--SFALKSYL 259 (279)
T ss_pred ccccccccchHHhhcccccccCC---------CCccCCcccchhcchHHHHHHHHhhcCCccccCcchhh--HHHHHHHH
Confidence 45555555555555555555554 46788899999999999999999999999999999999 99999999
Q ss_pred hhcCC
Q 040647 98 AVQGP 102 (286)
Q Consensus 98 ~~H~r 102 (286)
.+|..
T Consensus 260 nKH~E 264 (279)
T KOG2462|consen 260 NKHSE 264 (279)
T ss_pred HHhhh
Confidence 99987
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.35 E-value=3.1e-13 Score=138.08 Aligned_cols=60 Identities=23% Similarity=0.264 Sum_probs=57.0
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCCCCCCCCCCCCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTP 113 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~ 113 (286)
|-+|.+|-|...-.++|+.|.|+|||||||+|++|+| .|+++.+|+.|+. +|....+++.
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgR--AFtTkGNLkaH~~-vHka~p~~R~ 664 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGR--AFTTKGNLKAHMS-VHKAKPPARV 664 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccc--hhccccchhhccc-ccccCccccc
Confidence 8899999999999999999999999999999999999 9999999999999 9988777764
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.35 E-value=1.4e-13 Score=138.80 Aligned_cols=87 Identities=20% Similarity=0.287 Sum_probs=77.9
Q ss_pred hhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhh
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNL 97 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L 97 (286)
++|+|.|...+.|.+|.--|+|.+ ||+|.+|.|+|+.+.+|..|+|+|.|||||+|+.|+| +|++..+.
T Consensus 898 DqCDK~FqKqSSLaRHKYEHsGqR---------PyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClK--RFSHSGSY 966 (1007)
T KOG3623|consen 898 DQCDKAFQKQSSLARHKYEHSGQR---------PYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLK--RFSHSGSY 966 (1007)
T ss_pred HHHHHHHHhhHHHHHhhhhhcCCC---------CcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhh--hcccccch
Confidence 899999999999999999999976 5788899999999999999999999999999999999 99999999
Q ss_pred hhcCCCCCCCCCCCCCCC
Q 040647 98 AVQGPPPHLGCHPMTPGS 115 (286)
Q Consensus 98 ~~H~r~~H~g~kP~~~~~ 115 (286)
..||.-...-+|+|+-..
T Consensus 967 SQHMNHRYSYCKpyrEer 984 (1007)
T KOG3623|consen 967 SQHMNHRYSYCKPYREER 984 (1007)
T ss_pred Hhhhccchhcccchhhcc
Confidence 999982234577776433
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.27 E-value=1.1e-12 Score=132.42 Aligned_cols=84 Identities=15% Similarity=0.163 Sum_probs=72.7
Q ss_pred hhhcccccCCCchhhhhhhccCCCCccC----CCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 17 SKQVLDESSSTGAGAGHRKKKSGAKDGK----DDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 17 ~~~C~k~F~~~s~L~~H~r~HtGeKpf~----C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
|-.|.-.|..+..|.+||.+|.--.+-. =..|-|.|+|.+|+|+|+.+.+|+.|+|+|.|||||+|+.|.| +|+
T Consensus 243 C~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkK--RFS 320 (1007)
T KOG3623|consen 243 CMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKK--RFS 320 (1007)
T ss_pred chhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccc--ccc
Confidence 4789999999999999999986432211 1125689999999999999999999999999999999999999 999
Q ss_pred CchhhhhcCC
Q 040647 93 HNDNLAVQGP 102 (286)
Q Consensus 93 ~~s~L~~H~r 102 (286)
+..+...|+.
T Consensus 321 HSGSySSHmS 330 (1007)
T KOG3623|consen 321 HSGSYSSHMS 330 (1007)
T ss_pred cCCccccccc
Confidence 9999998876
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.19 E-value=1.1e-11 Score=126.95 Aligned_cols=60 Identities=25% Similarity=0.326 Sum_probs=56.5
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCCCCCCCCCCCCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTP 113 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~ 113 (286)
.+.|.+|+|.|..+++|++|||+|+++|||.|..|++ .|+.+.+|+.||. +|....+...
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~--aFttrgnLKvHMg-tH~w~q~~sr 938 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEE--AFTTRGNLKVHMG-THMWVQPPSR 938 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhh--hhhhhhhhhhhhc-cccccCCCcc
Confidence 4889999999999999999999999999999999999 9999999999999 8988777653
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.18 E-value=7.6e-13 Score=116.92 Aligned_cols=83 Identities=19% Similarity=0.139 Sum_probs=74.9
Q ss_pred hhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhh
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNL 97 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L 97 (286)
..|+|.|.-..-|.+|++-|...| .|.|.+|||.|...-+|++|+|+|||.|||+|..|++ +|+++.+|
T Consensus 121 rvCgK~F~lQRmlnrh~kch~~vk---------r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~k--aftqrcsl 189 (267)
T KOG3576|consen 121 RVCGKKFGLQRMLNRHLKCHSDVK---------RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEK--AFTQRCSL 189 (267)
T ss_pred ehhhhhhhHHHHHHHHhhhccHHH---------HHHHhhccCcccchhhhhhhhccccCccccchhhhhH--HHHhhccH
Confidence 899999998889999999887644 6889999999999999999999999999999999999 99999999
Q ss_pred hhcCCCCCCCCCCC
Q 040647 98 AVQGPPPHLGCHPM 111 (286)
Q Consensus 98 ~~H~r~~H~g~kP~ 111 (286)
..|.+++|.....|
T Consensus 190 eshl~kvhgv~~~y 203 (267)
T KOG3576|consen 190 ESHLKKVHGVQHQY 203 (267)
T ss_pred HHHHHHHcCchHHH
Confidence 99998888754433
No 8
>PHA02768 hypothetical protein; Provisional
Probab=98.81 E-value=1.6e-09 Score=77.25 Aligned_cols=44 Identities=20% Similarity=0.422 Sum_probs=40.8
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAV 99 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~ 99 (286)
|+|+.|||.|.+.++|++||++|+ ++++|..|++ .|.+.+.|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k--~f~~~s~l~~ 49 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKR--ISLRTGEYIE 49 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccc--eecccceeEE
Confidence 899999999999999999999999 7999999999 9998887753
No 9
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.76 E-value=2.9e-09 Score=100.83 Aligned_cols=87 Identities=17% Similarity=0.264 Sum_probs=69.6
Q ss_pred hhhcccccCCCchhhhhhhccCCCCccCCCCCC-----------------------------------------------
Q 040647 17 SKQVLDESSSTGAGAGHRKKKSGAKDGKDDECG----------------------------------------------- 49 (286)
Q Consensus 17 ~~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~e----------------------------------------------- 49 (286)
|..|-+.|.++..|++|.|.|++||...|..|+
T Consensus 182 W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv 261 (467)
T KOG3608|consen 182 WAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV 261 (467)
T ss_pred chhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh
Confidence 388999999999999999999999999888744
Q ss_pred cccccCcCCcccCCchhhhhhhh-hcCCCcccccCCCCcccccCCchhhhhcCCCCCC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMN-RHRQERETETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r-~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
.-|+|+.|+......+.|.+|+| .|...|||+|+.|.+ .|.+.+.|++|.. +|.
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~--~c~~esdL~kH~~-~HS 316 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDT--RCVRESDLAKHVQ-VHS 316 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhh--hhccHHHHHHHHH-hcc
Confidence 14677777777777777777766 377788888888888 7777888888877 665
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.48 E-value=2.1e-08 Score=95.12 Aligned_cols=85 Identities=14% Similarity=0.168 Sum_probs=66.4
Q ss_pred hhcccccCCCchhhhhhhccCCCCccCCCCCC--------------------cccccCcCCcccCCchhhhhhhhhcCCC
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAKDGKDDECG--------------------KVYECRFCSLKFCKSQALGGHMNRHRQE 77 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~e--------------------KPy~C~~Cgk~F~~ss~L~~H~r~Htge 77 (286)
++|.|.|.....|+.|++.|.. -|+|+.|. |||+|+.|++.|.+.+.|.+|..+|. +
T Consensus 241 ~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~ 317 (467)
T KOG3608|consen 241 AQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-K 317 (467)
T ss_pred HHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-c
Confidence 8999999999999999988854 56777643 78888888888888888888888887 6
Q ss_pred cccccCC--CCcccccCCchhhhhcCCCCCCC
Q 040647 78 RETETLN--KARQLVFQHNDNLAVQGPPPHLG 107 (286)
Q Consensus 78 KPy~C~~--Cgr~~sFs~~s~L~~H~r~~H~g 107 (286)
.-|+|.. |-. +|++...+++|.+.+|.+
T Consensus 318 ~~y~C~h~~C~~--s~r~~~q~~~H~~evhEg 347 (467)
T KOG3608|consen 318 TVYQCEHPDCHY--SVRTYTQMRRHFLEVHEG 347 (467)
T ss_pred cceecCCCCCcH--HHHHHHHHHHHHHHhccC
Confidence 6677766 665 667777777777666654
No 11
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.46 E-value=3.3e-08 Score=87.81 Aligned_cols=62 Identities=21% Similarity=0.374 Sum_probs=59.5
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCCCCCCCCCCCCCC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTPG 114 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~~ 114 (286)
..|.|++|+|.|.-...|.+|++.|...|.|.|..||+ .|...-.|++|+| +|+|.+||+|.
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgk--gfndtfdlkrh~r-thtgvrpykc~ 177 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGK--GFNDTFDLKRHTR-THTGVRPYKCS 177 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccC--cccchhhhhhhhc-cccCccccchh
Confidence 47999999999999999999999999999999999999 9999999999999 99999999973
No 12
>PHA00733 hypothetical protein
Probab=98.43 E-value=1.1e-07 Score=79.17 Aligned_cols=78 Identities=17% Similarity=0.135 Sum_probs=59.7
Q ss_pred hhcccccCCCchhhhh--hhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCch
Q 040647 18 KQVLDESSSTGAGAGH--RKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHND 95 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H--~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s 95 (286)
..|.+.|.....|..+ ++.|.-. ..++||+|+.|++.|.....|..|+++| +++|.|..|++ .|....
T Consensus 44 ~~~~~~~~~~~~l~~~~~l~~~~~~------~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK--~F~~~~ 113 (128)
T PHA00733 44 AVVKTLIYNPQLLDESSYLYKLLTS------KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGK--EFRNTD 113 (128)
T ss_pred HHHhhhccChhhhcchHHHHhhccc------CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCC--ccCCHH
Confidence 6777777776666555 2222110 1245788999999999999999999987 46899999999 999999
Q ss_pred hhhhcCCCCC
Q 040647 96 NLAVQGPPPH 105 (286)
Q Consensus 96 ~L~~H~r~~H 105 (286)
+|.+|+.+-|
T Consensus 114 sL~~H~~~~h 123 (128)
T PHA00733 114 STLDHVCKKH 123 (128)
T ss_pred HHHHHHHHhc
Confidence 9999987444
No 13
>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=98.32 E-value=2.5e-07 Score=56.23 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=18.8
Q ss_pred hhhhhhhhcCCCcccccCCCCcccccC
Q 040647 66 ALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 66 ~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
+|.+|+++|++||||+|..|++ .|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k--~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGK--SFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSE--EES
T ss_pred CHHHHhhhcCCCCCCCCCCCcC--eeC
Confidence 4677777777777777777777 665
No 14
>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=98.11 E-value=9.7e-07 Score=53.58 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=20.6
Q ss_pred hhhhhhhccCCCCccCCCCCCcccccCcCCcccCC
Q 040647 29 AGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCK 63 (286)
Q Consensus 29 ~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ 63 (286)
+|.+|+++|+|||| |+|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~---------~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP---------YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS---------EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC---------CCCCCCcCeeCc
Confidence 58899999999775 677778777753
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.05 E-value=2.5e-06 Score=86.35 Aligned_cols=78 Identities=12% Similarity=0.110 Sum_probs=53.5
Q ss_pred hhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC-----
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ----- 92 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs----- 92 (286)
+.|++.|. ...|..|+++|+ ++ +.|. |++.+ .+..|..|+++|..+|++.|..|++ .|.
T Consensus 457 ~~Cgk~f~-~s~LekH~~~~H--kp---------v~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~--~v~~g~~~ 520 (567)
T PLN03086 457 EKCGQAFQ-QGEMEKHMKVFH--EP---------LQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGD--MVQAGGSA 520 (567)
T ss_pred CCCCCccc-hHHHHHHHHhcC--CC---------ccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCC--ccccCccc
Confidence 78888885 577899988874 44 4555 77544 4567777877777778888888777 663
Q ss_pred -----CchhhhhcCCCCCCCCCCCCC
Q 040647 93 -----HNDNLAVQGPPPHLGCHPMTP 113 (286)
Q Consensus 93 -----~~s~L~~H~r~~H~g~kP~~~ 113 (286)
....|+.|.. + .+.+++.|
T Consensus 521 ~d~~d~~s~Lt~HE~-~-CG~rt~~C 544 (567)
T PLN03086 521 MDVRDRLRGMSEHES-I-CGSRTAPC 544 (567)
T ss_pred cchhhhhhhHHHHHH-h-cCCcceEc
Confidence 1246777776 3 36666654
No 16
>PHA00616 hypothetical protein
Probab=98.03 E-value=1.3e-06 Score=59.69 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=31.9
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLN 84 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~ 84 (286)
||+|..||+.|.+.+.|.+|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998864
No 17
>PHA02768 hypothetical protein; Provisional
Probab=97.99 E-value=2.2e-06 Score=61.24 Aligned_cols=41 Identities=7% Similarity=-0.069 Sum_probs=35.6
Q ss_pred hhhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhh
Q 040647 17 SKQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALG 68 (286)
Q Consensus 17 ~~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~ 68 (286)
++.|+|.|.+..+|..|||+|+ | +|+|..|+|.|.+.+.|.
T Consensus 8 C~~CGK~Fs~~~~L~~H~r~H~--k---------~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 8 CPICGEIYIKRKSMITHLRKHN--T---------NLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cchhCCeeccHHHHHHHHHhcC--C---------cccCCcccceecccceeE
Confidence 3799999999999999999998 3 577888999999887765
No 18
>PHA00732 hypothetical protein
Probab=97.72 E-value=2.2e-05 Score=60.20 Aligned_cols=44 Identities=18% Similarity=0.308 Sum_probs=37.6
Q ss_pred ccccCcCCcccCCchhhhhhhh-hcCCCcccccCCCCcccccCCchhhhhcCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMN-RHRQERETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r-~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
||.|+.|++.|.+..+|++|++ .|++ +.|..|++ .|. .|..|.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgK--sF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNK--SYR---RLNQHFY 45 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCC--EeC---Chhhhhc
Confidence 5889999999999999999998 4764 58999999 887 5777776
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.46 E-value=7.4e-05 Score=75.87 Aligned_cols=57 Identities=12% Similarity=0.189 Sum_probs=50.1
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCCCCCCCCCCCCCC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTPG 114 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~~ 114 (286)
+.+.|+.|++.|. ...|..|+++|+ +++.|. |++ .+. +..|..|++ +|..++++.|.
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~--~~~-R~~L~~H~~-thCp~Kpi~C~ 508 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGV--VLE-KEQMVQHQA-STCPLRLITCR 508 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCC--Ccc-hhHHHhhhh-ccCCCCceeCC
Confidence 6889999999996 578999999985 899999 998 664 689999998 89999999875
No 20
>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=97.38 E-value=5.7e-05 Score=43.86 Aligned_cols=23 Identities=39% Similarity=0.882 Sum_probs=20.5
Q ss_pred cccCcCCcccCCchhhhhhhhhc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRH 74 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~H 74 (286)
|+|+.|++.|.+...|.+|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999999875
No 21
>PHA00733 hypothetical protein
Probab=97.01 E-value=0.00029 Score=58.63 Aligned_cols=54 Identities=9% Similarity=-0.108 Sum_probs=43.8
Q ss_pred CcccccCcCCcccCCchhhhhh--hh---hcCCCcccccCCCCcccccCCchhhhhcCCCCC
Q 040647 49 GKVYECRFCSLKFCKSQALGGH--MN---RHRQERETETLNKARQLVFQHNDNLAVQGPPPH 105 (286)
Q Consensus 49 eKPy~C~~Cgk~F~~ss~L~~H--~r---~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H 105 (286)
.|++.|.+|.+.|.....|..| ++ .+.+++||.|..|++ .|....+|..|++ .|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk--~Fss~s~L~~H~r-~h 96 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLM--PFSSSVSLKQHIR-YT 96 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCC--cCCCHHHHHHHHh-cC
Confidence 3678999999988888777665 11 233589999999999 9999999999998 55
No 22
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.96 E-value=0.00015 Score=70.58 Aligned_cols=78 Identities=18% Similarity=0.183 Sum_probs=58.0
Q ss_pred hhhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcC--------CCc----------
Q 040647 17 SKQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHR--------QER---------- 78 (286)
Q Consensus 17 ~~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~Ht--------geK---------- 78 (286)
|..|...|...-.|.+|+....-.- -|+|.+|+|.|.-..+|..|+|-|. +..
T Consensus 270 CqLCK~kYeD~F~LAQHrC~RIV~v---------EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 270 CQLCKEKYEDAFALAQHRCPRIVHV---------EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred HHHHHHhhhhHHHHhhccCCeeEEe---------eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh
Confidence 3778788877778888864221111 2778888888888889999988774 111
Q ss_pred ---------------ccccCCCCcccccCCchhhhhcCCCCCC
Q 040647 79 ---------------ETETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 79 ---------------Py~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
-|.|..|+| .|++..-|++|+. +|.
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C~K--kFrRqAYLrKHql-thq 380 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTCGK--KFRRQAYLRKHQL-THQ 380 (500)
T ss_pred hhhhccccCCcccCceeecHHhhh--hhHHHHHHHHhHH-hhh
Confidence 378999999 9999999999988 444
No 23
>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=96.86 E-value=0.00046 Score=41.51 Aligned_cols=25 Identities=32% Similarity=0.567 Sum_probs=21.2
Q ss_pred ccccCcCCcccCCchhhhhhhhhcC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHR 75 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~Ht 75 (286)
+|+|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5788899999999999999988774
No 24
>PHA00732 hypothetical protein
Probab=96.73 E-value=0.00077 Score=51.68 Aligned_cols=45 Identities=13% Similarity=0.162 Sum_probs=36.0
Q ss_pred hhhcccccCCCchhhhhhhc-cCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcCC
Q 040647 17 SKQVLDESSSTGAGAGHRKK-KSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQ 76 (286)
Q Consensus 17 ~~~C~k~F~~~s~L~~H~r~-HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~Htg 76 (286)
++.|++.|.+...|+.|++. |++ +.|+.|++.|. .|..|++++..
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~------------~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTL------------TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCC------------CccCCCCCEeC---ChhhhhcccCC
Confidence 37899999999999999984 653 46889999998 57888865443
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.59 E-value=0.001 Score=63.03 Aligned_cols=53 Identities=21% Similarity=0.386 Sum_probs=43.5
Q ss_pred CCcccccCc--CCcccCCchhhhhhhhh-c------------------CCCcccccCCCCcccccCCchhhhhcCC
Q 040647 48 CGKVYECRF--CSLKFCKSQALGGHMNR-H------------------RQERETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 48 ~eKPy~C~~--Cgk~F~~ss~L~~H~r~-H------------------tgeKPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
.||||+|++ |+|.+++..-|+-|+.- | ...|||.|.+|+| ++...--|+-|.+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~K--RYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDK--RYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccch--hhccCccceeccc
Confidence 458889887 99999999999999742 2 1348999999999 9998888888766
No 26
>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=96.57 E-value=0.00089 Score=38.33 Aligned_cols=23 Identities=30% Similarity=0.752 Sum_probs=18.5
Q ss_pred cccCcCCcccCCchhhhhhhhhc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRH 74 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~H 74 (286)
|.|++|++.|.+...|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 67999999999999999998876
No 27
>PHA00616 hypothetical protein
Probab=96.39 E-value=0.00058 Score=46.67 Aligned_cols=32 Identities=9% Similarity=0.033 Sum_probs=28.8
Q ss_pred ccccCCCCcccccCCchhhhhcCCCCCCCCCCCCC
Q 040647 79 ETETLNKARQLVFQHNDNLAVQGPPPHLGCHPMTP 113 (286)
Q Consensus 79 Py~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~ 113 (286)
||+|..||+ .|..+++|++|++ .|++++++.+
T Consensus 1 pYqC~~CG~--~F~~~s~l~~H~r-~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGG--IFRKKKEVIEHLL-SVHKQNKLTL 32 (44)
T ss_pred CCccchhhH--HHhhHHHHHHHHH-HhcCCCccce
Confidence 689999999 9999999999999 7888887763
No 28
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.31 E-value=0.0022 Score=36.99 Aligned_cols=25 Identities=36% Similarity=0.643 Sum_probs=21.0
Q ss_pred cccCcCCcccCCchhhhhhhhhcCC
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQ 76 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~Htg 76 (286)
|+|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5788899999999999999887753
No 29
>PRK04860 hypothetical protein; Provisional
Probab=96.29 E-value=0.0019 Score=55.82 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=32.2
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
+|.|. |++ ....+++|.++|+++++|.|..|++ .|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~--~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGE--TLV 154 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCc--eeE
Confidence 79998 998 6778899999999999999999999 554
No 30
>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=96.00 E-value=0.0031 Score=44.51 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=36.1
Q ss_pred ccccCcCCcccCCchhhhhhhh-hcCCC-cccccCCCCcccccCCchhhhhcCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMN-RHRQE-RETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r-~Htge-KPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
.|.|++|++. .....|..|.. .|..+ +.+.|++|.. .++ .+|.+|+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~--~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSS--RVT--DNLIRHLN 50 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchh--hhh--hHHHHHHH
Confidence 4889999995 44578999954 56664 6799999998 555 48888887
No 31
>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=95.28 E-value=0.0087 Score=42.20 Aligned_cols=32 Identities=16% Similarity=0.338 Sum_probs=21.7
Q ss_pred CCcccccCcCCcccCCchhhhhhhhhcCCCcc
Q 040647 48 CGKVYECRFCSLKFCKSQALGGHMNRHRQERE 79 (286)
Q Consensus 48 ~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKP 79 (286)
.++|..|++|+..+.+..+|++|+.++.+.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 35678889999999999999999988777775
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.81 E-value=0.014 Score=44.65 Aligned_cols=57 Identities=26% Similarity=0.321 Sum_probs=16.5
Q ss_pred hhcccccCCCchhhhhhhccCCCC-c---cCCCC----------CCcccccCcCCcccCCchhhhhhhhhc
Q 040647 18 KQVLDESSSTGAGAGHRKKKSGAK-D---GKDDE----------CGKVYECRFCSLKFCKSQALGGHMNRH 74 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~HtGeK-p---f~C~~----------~eKPy~C~~Cgk~F~~ss~L~~H~r~H 74 (286)
..|...|.....|..|+....+-. + ..... -...+.|..|++.|.....|..||+.+
T Consensus 3 ~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 3 LFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 358889999999999986433311 1 00000 112467777777777777777777654
No 33
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.67 E-value=0.013 Score=34.38 Aligned_cols=23 Identities=22% Similarity=0.663 Sum_probs=19.6
Q ss_pred cccCcCCcccCCchhhhhhhhhc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRH 74 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~H 74 (286)
|.|++|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57899999999999999998754
No 34
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.44 E-value=0.026 Score=52.83 Aligned_cols=61 Identities=21% Similarity=0.334 Sum_probs=55.1
Q ss_pred cccccCcCCcccCCchhhhhhhh--hcCCC--cccccC--CCCcccccCCchhhhhcCCCCCCCCCCCCC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMN--RHRQE--RETETL--NKARQLVFQHNDNLAVQGPPPHLGCHPMTP 113 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r--~Htge--KPy~C~--~Cgr~~sFs~~s~L~~H~r~~H~g~kP~~~ 113 (286)
+++.|..|.+.|.....|.+|.+ .|+++ +++.|. .|++ .|.+.+.+.+|.. +|...++...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~~ 354 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGK--LFSRNDALKRHIL-LHTSISPAKE 354 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCc--cccccccccCCcc-cccCCCcccc
Confidence 37899999999999999999999 89999 999999 7999 9999999999999 8887766553
No 35
>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=94.29 E-value=0.0049 Score=35.50 Aligned_cols=21 Identities=14% Similarity=0.059 Sum_probs=19.7
Q ss_pred cccCCCCcccccCCchhhhhcCC
Q 040647 80 TETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|+|..|++ .|.+...|.+|++
T Consensus 1 y~C~~C~~--~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGK--SFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTE--EESSHHHHHHHHH
T ss_pred CCCCCCCC--ccCCHHHHHHHHh
Confidence 68999999 9999999999986
No 36
>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=93.73 E-value=0.03 Score=33.73 Aligned_cols=22 Identities=27% Similarity=0.603 Sum_probs=18.6
Q ss_pred cccCcCCcccCCchhhhhhhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMNR 73 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~ 73 (286)
|.|..|+|.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788899999999888888764
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.71 E-value=0.031 Score=53.19 Aligned_cols=55 Identities=13% Similarity=0.159 Sum_probs=38.8
Q ss_pred hhcccccCCCchhhhhhhc-cC----CCCccC-----CCCCCcccccCcCCcccCCchhhhhhhh
Q 040647 18 KQVLDESSSTGAGAGHRKK-KS----GAKDGK-----DDECGKVYECRFCSLKFCKSQALGGHMN 72 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r~-Ht----GeKpf~-----C~~~eKPy~C~~Cgk~F~~ss~L~~H~r 72 (286)
+.|.|.++..-.|+-|+.- |- .|.|-. -....|||+|++|+|++++..-|+-|+.
T Consensus 355 ~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 355 EGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 7888888888888888642 21 111110 1115599999999999999999998853
No 38
>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=93.62 E-value=0.026 Score=33.68 Aligned_cols=25 Identities=16% Similarity=0.102 Sum_probs=22.4
Q ss_pred ccccCCCCcccccCCchhhhhcCCCCCC
Q 040647 79 ETETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 79 Py~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
+|+|..|++ .|.....|..|++ .|.
T Consensus 1 ~~~C~~C~~--~F~~~~~l~~H~~-~h~ 25 (27)
T PF13912_consen 1 PFECDECGK--TFSSLSALREHKR-SHC 25 (27)
T ss_dssp SEEETTTTE--EESSHHHHHHHHC-TTT
T ss_pred CCCCCccCC--ccCChhHHHHHhH-Hhc
Confidence 589999999 9999999999998 553
No 39
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.43 E-value=0.046 Score=51.12 Aligned_cols=63 Identities=22% Similarity=0.206 Sum_probs=53.7
Q ss_pred hhcccccCCCchhhhhhh--ccCCC--CccCCCCCCcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 18 KQVLDESSSTGAGAGHRK--KKSGA--KDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r--~HtGe--Kpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
..|.+.|.+...|..|.+ .|+++ +++.| ++. .|++.|.+...+.+|..+|++.++..|.....
T Consensus 293 ~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~-----p~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 (467)
T COG5048 293 KQCNISFSRSSPLTRHLRSVNHSGESLKPFSC-----PYS--LCGKLFSRNDALKRHILLHTSISPAKEKLLNS 359 (467)
T ss_pred ccccCCccccccccccccccccccccCCceee-----ecc--CCCccccccccccCCcccccCCCccccccccC
Confidence 789999999999999999 89998 66555 233 79999999999999999999999888865443
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.34 E-value=0.021 Score=43.58 Aligned_cols=49 Identities=20% Similarity=0.371 Sum_probs=20.1
Q ss_pred ccCcCCcccCCchhhhhhhhh-cCC----------------------CcccccCCCCcccccCCchhhhhcCCC
Q 040647 53 ECRFCSLKFCKSQALGGHMNR-HRQ----------------------ERETETLNKARQLVFQHNDNLAVQGPP 103 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~-Htg----------------------eKPy~C~~Cgr~~sFs~~s~L~~H~r~ 103 (286)
+|.+|+..|.....|..|+.. |.- ...+.|..|++ .|.....|..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~--~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNK--TFRSREALQEHMRS 72 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS---EESSHHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCC--CCcCHHHHHHHHcC
Confidence 589999999999999999853 221 01488999999 99999999999983
No 41
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=92.60 E-value=0.029 Score=55.07 Aligned_cols=53 Identities=26% Similarity=0.305 Sum_probs=45.8
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCCCCCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
-|.|..|...|...-.|.+|+=.-.-...|+|.+|+| +|....+|..|.| .|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~K--VFsCPANLASHRR-WHK 319 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDK--VFSCPANLASHRR-WHK 319 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccc--cccCchhhhhhhc-ccC
Confidence 3899999999999999999964434446799999999 9999999999999 664
No 42
>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=91.79 E-value=0.035 Score=39.22 Aligned_cols=40 Identities=13% Similarity=0.004 Sum_probs=23.5
Q ss_pred hhhhhh-cCCCcccccCCCCcccccCCchhhhhcCCCCCCCCCC
Q 040647 68 GGHMNR-HRQERETETLNKARQLVFQHNDNLAVQGPPPHLGCHP 110 (286)
Q Consensus 68 ~~H~r~-HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~g~kP 110 (286)
..+.+. +..+.|-.|.+|+. .+++..+|++|+. ++.+.||
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a--~~~~srnLrRHle-~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGA--VIRQSRNLRRHLE-IRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT----EESSHHHHHHHHH-HHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchh--hccchhhHHHHHH-HHhcccC
Confidence 344433 44688999999999 9999999999997 5444443
No 43
>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=91.56 E-value=0.025 Score=32.07 Aligned_cols=21 Identities=10% Similarity=0.042 Sum_probs=17.7
Q ss_pred cccCCCCcccccCCchhhhhcCC
Q 040647 80 TETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|.|..|++ .|.....|..|++
T Consensus 1 ~~C~~C~~--~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGK--SFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS---EESSHHHHHHHHH
T ss_pred CCCcCCCC--cCCcHHHHHHHHH
Confidence 68999999 9999999999987
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.35 E-value=0.15 Score=30.52 Aligned_cols=21 Identities=29% Similarity=0.570 Sum_probs=15.8
Q ss_pred cccCcCCcccCCchhhhhhhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMNR 73 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~ 73 (286)
..|..|+|.| ..+.|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3688888888 66678888764
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.33 E-value=0.12 Score=29.97 Aligned_cols=22 Identities=36% Similarity=0.809 Sum_probs=16.4
Q ss_pred cccCcCCcccCCchhhhhhhhhc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRH 74 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~H 74 (286)
|+|+.|+.... ...|.+|+++|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 67889998887 77899998875
No 46
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=89.29 E-value=0.13 Score=47.42 Aligned_cols=52 Identities=21% Similarity=0.357 Sum_probs=38.9
Q ss_pred CCcchhhhcccccCCCchhhhhhhccCCCCccCCCCCCcccccCcCCcccCCchhhhhh-hhhcCC
Q 040647 12 LPEDYSKQVLDESSSTGAGAGHRKKKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGH-MNRHRQ 76 (286)
Q Consensus 12 l~~e~~~~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H-~r~Htg 76 (286)
+.+.||=-|.+.|-....|..|++. |-|+|.+|.|.....--|..| |++|..
T Consensus 8 ~~kpwcwycnrefddekiliqhqka-------------khfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 8 VDKPWCWYCNREFDDEKILIQHQKA-------------KHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred cCCceeeecccccchhhhhhhhhhh-------------ccceeeeehhhhccCCCceeehhhhhhh
Confidence 4467888999999999999999864 247777887776666667666 667653
No 47
>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=89.26 E-value=0.26 Score=34.62 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=32.8
Q ss_pred hhcccccCCCchhhhhhh-ccCCCCccCCCCCCcccccCcCCcccCCchhhhhhhhhcC
Q 040647 18 KQVLDESSSTGAGAGHRK-KKSGAKDGKDDECGKVYECRFCSLKFCKSQALGGHMNRHR 75 (286)
Q Consensus 18 ~~C~k~F~~~s~L~~H~r-~HtGeKpf~C~~~eKPy~C~~Cgk~F~~ss~L~~H~r~Ht 75 (286)
..|++. .+...|..|.. .|..++ +.+.|++|...+. .+|.+|++.+.
T Consensus 6 P~C~~~-~~~~~L~~H~~~~H~~~~--------~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 6 PYCGKG-FSESSLVEHCEDEHRSES--------KNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCCCc-cCHHHHHHHHHhHCcCCC--------CCccCCCchhhhh--hHHHHHHHHhc
Confidence 568884 45678999965 465532 3578888887655 38999987653
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.35 E-value=0.14 Score=29.03 Aligned_cols=24 Identities=17% Similarity=0.195 Sum_probs=21.1
Q ss_pred cccCCCCcccccCCchhhhhcCCCCCC
Q 040647 80 TETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
|+|..|++ .|.....|..|++ .|.
T Consensus 1 ~~C~~C~~--~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGK--VFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcc--hhCCHHHHHHHHH-Hhc
Confidence 57999999 9999999999988 554
No 49
>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=87.07 E-value=0.34 Score=30.37 Aligned_cols=23 Identities=17% Similarity=0.668 Sum_probs=19.2
Q ss_pred ccccCcCCcccCCchhhhhhhhh
Q 040647 51 VYECRFCSLKFCKSQALGGHMNR 73 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~ 73 (286)
+|.|+.|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47899999999988888888753
No 50
>PRK04860 hypothetical protein; Provisional
Probab=85.62 E-value=0.4 Score=41.52 Aligned_cols=24 Identities=17% Similarity=0.189 Sum_probs=18.1
Q ss_pred CCchhhhhhhccCCCCccCCCCCC
Q 040647 26 STGAGAGHRKKKSGAKDGKDDECG 49 (286)
Q Consensus 26 ~~s~L~~H~r~HtGeKpf~C~~~e 49 (286)
....+.+|.++|+++++|.|..|+
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~ 150 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCG 150 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCC
Confidence 677889999999998765554443
No 51
>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=80.32 E-value=1.2 Score=26.55 Aligned_cols=21 Identities=10% Similarity=-0.016 Sum_probs=19.7
Q ss_pred cccCCCCcccccCCchhhhhcCC
Q 040647 80 TETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|.|..|++ .|.....|..|++
T Consensus 2 ~~C~~C~k--~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDK--YFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTB--BBSSHHHHHCCTT
T ss_pred CCcccCCC--CcCCHHHHHHHHc
Confidence 68999999 9999999999987
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=77.50 E-value=0.76 Score=26.64 Aligned_cols=21 Identities=10% Similarity=-0.073 Sum_probs=19.4
Q ss_pred cccCCCCcccccCCchhhhhcCC
Q 040647 80 TETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|.|..|.+ .|.....|+.|++
T Consensus 1 ~~C~~C~~--~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNK--SFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTE--EESSHHHHHHHHT
T ss_pred CCCCCCCC--CcCCHHHHHHHHC
Confidence 67999999 9999999999987
No 53
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=74.84 E-value=9.6 Score=40.80 Aligned_cols=12 Identities=8% Similarity=-0.288 Sum_probs=5.5
Q ss_pred cCcCCcccCCch
Q 040647 54 CRFCSLKFCKSQ 65 (286)
Q Consensus 54 C~~Cgk~F~~ss 65 (286)
|..|+--|..+.
T Consensus 439 r~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 439 RTGMDPDFKYRF 450 (1102)
T ss_pred cCCCCCCcchhh
Confidence 344554444443
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=65.80 E-value=2.5 Score=47.20 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=43.7
Q ss_pred cccccCcCCcccCCchhhhhhhhh---------------cC----------CCcccccCCCCcccccCCchhhhhcCC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNR---------------HR----------QERETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~---------------Ht----------geKPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|-++|+.|+..|+..+.|..|||. |. +-++|.|..|.- .++.+.+|..|+.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~--stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNY--STTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeee--eeecchHHHHHHH
Confidence 678999999999999999999998 11 125899999999 9999999999976
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=65.56 E-value=2.4 Score=47.24 Aligned_cols=67 Identities=16% Similarity=0.189 Sum_probs=47.4
Q ss_pred CCCCCCCcchh-hhcccccCCCchhhhhhhccCCC-CccCCCC---------------CCcccccCcCCcccCCchhhhh
Q 040647 7 LDLNNLPEDYS-KQVLDESSSTGAGAGHRKKKSGA-KDGKDDE---------------CGKVYECRFCSLKFCKSQALGG 69 (286)
Q Consensus 7 ldl~nl~~e~~-~~C~k~F~~~s~L~~H~r~HtGe-Kpf~C~~---------------~eKPy~C~~Cgk~F~~ss~L~~ 69 (286)
.+|+...+.+. ..|...|+....|..|||..+-+ ..-.|.. ..++|.|..|...++...+|-+
T Consensus 457 ~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsi 536 (1406)
T KOG1146|consen 457 VVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSI 536 (1406)
T ss_pred eeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHH
Confidence 34444444443 78889999999999999972211 1122221 4479999999999999999999
Q ss_pred hhhh
Q 040647 70 HMNR 73 (286)
Q Consensus 70 H~r~ 73 (286)
|+..
T Consensus 537 hlqS 540 (1406)
T KOG1146|consen 537 HLQS 540 (1406)
T ss_pred HHHH
Confidence 9863
No 56
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=62.93 E-value=4.7 Score=25.46 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=16.8
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
|+|.+||..+.-. +.++.|..|+.
T Consensus 2 ~~C~~CGy~y~~~------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC------------cCCCcCcCCCC
Confidence 6788888655432 26888988885
No 57
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=62.76 E-value=2.8 Score=38.82 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=32.4
Q ss_pred ccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhc
Q 040647 53 ECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQ 100 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H 100 (286)
.|=.|+|.|.....|.+|++ .|-|+|-+|-| |.|+ -.-|..|
T Consensus 12 wcwycnrefddekiliqhqk----akhfkchichk-kl~s-gpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKHFKCHICHK-KLFS-GPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhh----hccceeeeehh-hhcc-CCCceee
Confidence 47789999999999999876 57899999987 2454 4455555
No 58
>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=60.34 E-value=4.1 Score=25.27 Aligned_cols=22 Identities=5% Similarity=-0.192 Sum_probs=19.7
Q ss_pred ccccCCCCcccccCCchhhhhcCC
Q 040647 79 ETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 79 Py~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
+|.|..|.+ .|.....+..|.+
T Consensus 3 ~~~C~~C~~--~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNV--TFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCC--ccCCHHHHHHHHC
Confidence 588999999 9999999998876
No 59
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=59.47 E-value=4.8 Score=42.76 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=30.0
Q ss_pred cCCCCCCcccccCcCCcccCCch---hhhhhhhhcCCCcccccCCCCc
Q 040647 43 GKDDECGKVYECRFCSLKFCKSQ---ALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 43 f~C~~~eKPy~C~~Cgk~F~~ss---~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
..|..|+-..+|+.|+-..+... .|..|.=-|....|..|..|+.
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGS 483 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCC
Confidence 46989999999999996543222 2444443344566777777775
No 60
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.95 E-value=6 Score=33.40 Aligned_cols=43 Identities=16% Similarity=0.159 Sum_probs=28.6
Q ss_pred CcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCch
Q 040647 49 GKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHND 95 (286)
Q Consensus 49 eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s 95 (286)
..-|.|+.|++.|....++..- +. +..|.|+.|+..+.....+
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEEEcCch
Confidence 3479999999999976554321 12 3449999999844444333
No 61
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=58.93 E-value=5.6 Score=34.13 Aligned_cols=41 Identities=12% Similarity=0.173 Sum_probs=31.5
Q ss_pred CcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhh
Q 040647 49 GKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLA 98 (286)
Q Consensus 49 eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~ 98 (286)
..-|.|+.|++.|+...++. --|.|+.||..+.+-.++.+.
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeeeccCHHHH
Confidence 35699999999999998885 369999999855555555443
No 62
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=58.31 E-value=5.8 Score=34.82 Aligned_cols=39 Identities=18% Similarity=0.264 Sum_probs=30.4
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhh
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNL 97 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L 97 (286)
.-|.|+.|++.|+...++. --|.|+.||..+.+-.++.+
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~~dn~~~ 154 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEEYDNSEL 154 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCeecccHHH
Confidence 5699999999999988763 37999999986665555444
No 63
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=57.68 E-value=4.4 Score=36.46 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=28.8
Q ss_pred cccccCcCCcccCCchhhhhhhhh---cC-------CCcc-----cccCCCCcccccC
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNR---HR-------QERE-----TETLNKARQLVFQ 92 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~---Ht-------geKP-----y~C~~Cgr~~sFs 92 (286)
|..+|++|++.|.....+....++ .+ +..| ..|+.||- +|.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~Cgy--A~~ 59 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGY--AAF 59 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCC--ccc
Confidence 567899999999988777766654 11 2222 47999997 655
No 64
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=54.11 E-value=8.1 Score=26.48 Aligned_cols=24 Identities=29% Similarity=0.793 Sum_probs=15.7
Q ss_pred cccCcCCcccCCc-----hhhhhhhh-hcC
Q 040647 52 YECRFCSLKFCKS-----QALGGHMN-RHR 75 (286)
Q Consensus 52 y~C~~Cgk~F~~s-----s~L~~H~r-~Ht 75 (286)
-.|..|++.+... ++|.+|++ .|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 3577777776554 57888877 553
No 65
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=51.71 E-value=6.3 Score=26.99 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=18.8
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
|+|..|+..|...... +. +..-.|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 6788888877754322 11 34567888886
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=51.23 E-value=5.9 Score=34.09 Aligned_cols=17 Identities=18% Similarity=0.264 Sum_probs=13.1
Q ss_pred cccCCCCcccccCCchhhh
Q 040647 80 TETLNKARQLVFQHNDNLA 98 (286)
Q Consensus 80 y~C~~Cgr~~sFs~~s~L~ 98 (286)
++|+.|++ +|.+...+.
T Consensus 29 ~~c~~c~~--~f~~~e~~~ 45 (154)
T PRK00464 29 RECLACGK--RFTTFERVE 45 (154)
T ss_pred eeccccCC--cceEeEecc
Confidence 89999999 887655543
No 67
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=50.07 E-value=8.4 Score=25.41 Aligned_cols=21 Identities=24% Similarity=0.534 Sum_probs=12.6
Q ss_pred ccccCcCCcccCCc----hhhhhhh
Q 040647 51 VYECRFCSLKFCKS----QALGGHM 71 (286)
Q Consensus 51 Py~C~~Cgk~F~~s----s~L~~H~ 71 (286)
..+|..|++.+... ++|.+|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 46788888877764 5788887
No 68
>PF12149 HSV_VP16_C: Herpes simplex virus virion protein 16 C terminal; InterPro: IPR021051 This domain is about 30 amino acids in length. It is found in association with PF02232 from PFAM. This domain is found in the C-terminal region of the HSV virion protein 16 (alpha-TIF). This protein is a transcription promoter. The C-terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc. Alpha-TIF (VP16) from Herpes Simplex virus is an essential tegument protein involved in the transcriptional activation of viral immediate early (IE) promoters (alpha genes) during the lytic phase of viral infection. VP16 associates with cellular transcription factors to enhance transcription rates, including the general transcription factor TFIIB and the transcriptional coactivator PC4. The N-terminal residues of VP16 confer specificity for the IE genes, while the C-terminal residues are responsible for transcriptional activation. Within the C-terminal region are two activation regions that can independently and cooperatively activate transcription []. VP16 forms a transcriptional regulatory complex with two cellular proteins, the POU-domain transcription factor Oct-1 and the cell-proliferation factor HCF-1 []. VP16 is an alpha/beta protein with an unusual fold. Other transcription factors may have a similar topology.; PDB: 2K2U_B 2PHG_B 2PHE_C.
Probab=49.71 E-value=2.3 Score=26.20 Aligned_cols=21 Identities=43% Similarity=0.746 Sum_probs=16.5
Q ss_pred CCchhHHHHHHHHhhhccccccccccc
Q 040647 250 GDCCSFIFELMYTLSYFGFKPFGIDDY 276 (286)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 276 (286)
||...|-||-|+|- ..|||||
T Consensus 8 ld~adfefeqmftd------algid~f 28 (30)
T PF12149_consen 8 LDMADFEFEQMFTD------ALGIDEF 28 (30)
T ss_dssp CTCCCCCHHCCCCC------CCCTCCC
T ss_pred chhhhHHHHHHHhh------hhCcccc
Confidence 56677889999884 5688887
No 69
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=48.79 E-value=13 Score=30.21 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=24.6
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCc
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHN 94 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~ 94 (286)
....|..||++|.-. ...|-.|..||. .|.-.
T Consensus 8 tKR~Cp~CG~kFYDL-----------nk~PivCP~CG~--~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-----------NKDPIVCPKCGT--EFPPE 39 (108)
T ss_pred CcccCCCCcchhccC-----------CCCCccCCCCCC--ccCcc
Confidence 357899999999864 236888999999 77644
No 70
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=46.24 E-value=8.6 Score=24.72 Aligned_cols=29 Identities=17% Similarity=0.294 Sum_probs=18.3
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
|+|..|++.|....... . ...-.|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS------D-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecC------C-CCCCCCCCCCC
Confidence 67888888776543321 1 34557888876
No 71
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.23 E-value=3.7 Score=37.16 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=37.6
Q ss_pred ccCcCCcccCCchhhhhhhh----------hcCCCcccccCC--CCcccccCCchhhhhcCCCCC
Q 040647 53 ECRFCSLKFCKSQALGGHMN----------RHRQERETETLN--KARQLVFQHNDNLAVQGPPPH 105 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r----------~HtgeKPy~C~~--Cgr~~sFs~~s~L~~H~r~~H 105 (286)
.|.+|.|.|....-|..|+- +-.|.--|+|.+ |+- .|.+....+.|+-..|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~--KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE--KFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh--hhhhhhhhhhHHHHhc
Confidence 79999999999999988874 234555689964 555 8887777777765344
No 72
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=45.10 E-value=14 Score=36.04 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=30.6
Q ss_pred ccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcc--cccCCchhhhhcCC
Q 040647 53 ECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQ--LVFQHNDNLAVQGP 102 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~--~sFs~~s~L~~H~r 102 (286)
.|.+|.+.|-....|.+|+|.- -|+-|.|+.-++- --|..-..|-+|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~-HE~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR-HEACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hhhhccceecChHHHHHHHHhh-hhhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 5999999999999999998842 2333444332210 02555566666655
No 73
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=43.09 E-value=15 Score=23.42 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=16.9
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
.|+|.+||..+... +.|..|..|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 47888888554322 25778998885
No 74
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=42.97 E-value=12 Score=24.91 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=19.4
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
|+|..|+..|-.... +.. ...-.|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 778888887765533 222 45677888876
No 75
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=42.00 E-value=15 Score=32.05 Aligned_cols=26 Identities=27% Similarity=0.452 Sum_probs=20.7
Q ss_pred CcccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 49 GKVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 49 eKPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
++.|.|.+||. +|.++-|-+|++|+-
T Consensus 132 ~~~~vC~vCGy-------------~~~ge~P~~CPiCga 157 (166)
T COG1592 132 GKVWVCPVCGY-------------THEGEAPEVCPICGA 157 (166)
T ss_pred CCEEEcCCCCC-------------cccCCCCCcCCCCCC
Confidence 34799999984 356788999999993
No 76
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=41.29 E-value=7.2 Score=29.41 Aligned_cols=43 Identities=14% Similarity=0.213 Sum_probs=28.3
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccC--CCCcccccCCchhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETL--NKARQLVFQHNDNLA 98 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~--~Cgr~~sFs~~s~L~ 98 (286)
+.|+.|+..-.-..+-..+.. +.++-++|. .|+. +|.....+.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~--tF~t~es~s 46 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSA--TFITYESVQ 46 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCC--EEEEEEEEE
Confidence 468888866544433322222 567889998 9999 998665543
No 77
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=40.91 E-value=12 Score=34.94 Aligned_cols=46 Identities=17% Similarity=0.367 Sum_probs=27.8
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCchhhhhcCC
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
|.|..||-..... .+.+|+-..++ .-|.|--|++ .|.+ .....|.+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k--~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGK--TFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccc--cccc-chhhhhhh
Confidence 5666666655544 45556655555 5566777777 6664 55566655
No 78
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.39 E-value=12 Score=25.17 Aligned_cols=35 Identities=11% Similarity=0.211 Sum_probs=22.3
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCch
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHND 95 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~s 95 (286)
.|+|..|+..|...... ....|..||..+.+...+
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TGVRCPYCGYRILFKERP 37 (46)
T ss_pred EEECCCCCCEEEECCCC----------CceECCCCCCeEEEccCC
Confidence 57888898877654321 167899999744433333
No 79
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=39.62 E-value=5 Score=42.41 Aligned_cols=27 Identities=37% Similarity=0.778 Sum_probs=24.7
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQE 77 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~Htge 77 (286)
-|.|.+|+|.|-.-.++..||++|...
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 599999999999999999999999853
No 80
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=39.43 E-value=1.2e+02 Score=30.28 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=12.7
Q ss_pred CCCCCCCCCCCCCCCCcceecCccccC
Q 040647 193 SQYPHNQSNLNNFMDSSYTCIGAPVGH 219 (286)
Q Consensus 193 ~~~~~~~~~~~~~~~~~y~~~~~~~~~ 219 (286)
...+|.--++.---...-+|-|+|+--
T Consensus 439 ~~P~~s~~~V~f~~~Pt~~~~g~p~s~ 465 (508)
T KOG1365|consen 439 TTPEHSVDNVLFTRWPTHLCPGEPIST 465 (508)
T ss_pred CCCCCccceeeeecCccccCCCCchhh
Confidence 333343333322224455677777643
No 81
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=39.01 E-value=11 Score=27.24 Aligned_cols=26 Identities=19% Similarity=0.468 Sum_probs=21.4
Q ss_pred CCcccccCcCCcccCCchhhhhhhhh
Q 040647 48 CGKVYECRFCSLKFCKSQALGGHMNR 73 (286)
Q Consensus 48 ~eKPy~C~~Cgk~F~~ss~L~~H~r~ 73 (286)
+|--+.|+-|++.|....+..+|.+.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 34467889999999999999999764
No 82
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.93 E-value=17 Score=38.32 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=29.7
Q ss_pred cCCCCCCcccccCcCCcccC---CchhhhhhhhhcCCCcccccCCCCc
Q 040647 43 GKDDECGKVYECRFCSLKFC---KSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 43 f~C~~~eKPy~C~~Cgk~F~---~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
..|..|+...+|+.|+-... ....|..|.=-++...+..|..|+.
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGS 429 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcC
Confidence 46888999999999996543 2223444444444555777777765
No 83
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.74 E-value=18 Score=32.80 Aligned_cols=28 Identities=18% Similarity=0.394 Sum_probs=21.2
Q ss_pred CCcccccCcCCcccCCchhhhhhhhh-cC
Q 040647 48 CGKVYECRFCSLKFCKSQALGGHMNR-HR 75 (286)
Q Consensus 48 ~eKPy~C~~Cgk~F~~ss~L~~H~r~-Ht 75 (286)
.+..|.|..|+|.|.-.....+|+.. |.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 45679999999999999999999764 44
No 84
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=36.48 E-value=28 Score=22.51 Aligned_cols=33 Identities=18% Similarity=0.347 Sum_probs=22.6
Q ss_pred ccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 53 ECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
+|+.|+..|.-... ++-.+.+..+|..|+. .|.
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~--~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGH--VFR 36 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCc--Eee
Confidence 68888888877654 2224455778988888 664
No 85
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.37 E-value=18 Score=36.68 Aligned_cols=17 Identities=24% Similarity=0.630 Sum_probs=14.7
Q ss_pred CCCCCCcccccCcCCcc
Q 040647 44 KDDECGKVYECRFCSLK 60 (286)
Q Consensus 44 ~C~~~eKPy~C~~Cgk~ 60 (286)
.|..|+...+|+.|+-.
T Consensus 215 ~C~~Cg~~~~C~~C~~~ 231 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVS 231 (505)
T ss_pred EhhhCcCccCCCCCCCc
Confidence 68889999999999844
No 86
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=36.16 E-value=30 Score=29.03 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=24.3
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccCCc
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQHN 94 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs~~ 94 (286)
....|..|+++|... ...|-.|..||. .|.-.
T Consensus 8 tKr~Cp~cg~kFYDL-----------nk~p~vcP~cg~--~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDL-----------NRRPAVSPYTGE--QFPPE 39 (129)
T ss_pred ccccCCCcCcccccc-----------CCCCccCCCcCC--ccCcc
Confidence 357899999999764 235889999999 76543
No 87
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.12 E-value=16 Score=38.39 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=15.5
Q ss_pred CCCCCCcccccCcCCccc
Q 040647 44 KDDECGKVYECRFCSLKF 61 (286)
Q Consensus 44 ~C~~~eKPy~C~~Cgk~F 61 (286)
.|..|+...+|+.|+-..
T Consensus 385 ~C~~Cg~~~~C~~C~~~L 402 (665)
T PRK14873 385 ACARCRTPARCRHCTGPL 402 (665)
T ss_pred EhhhCcCeeECCCCCCce
Confidence 798999999999998543
No 88
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.87 E-value=22 Score=37.52 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=17.4
Q ss_pred cccCcCCcccCCchhhhhhhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMNR 73 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~ 73 (286)
=.|.+|...|.....|.+|++.
T Consensus 183 p~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred ccchhhhhhhccHHHHHHhhcc
Confidence 3577888888888888888874
No 89
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=33.57 E-value=19 Score=37.23 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=24.2
Q ss_pred CcccccCcCCcccCCchhhhhhhhhcCCC
Q 040647 49 GKVYECRFCSLKFCKSQALGGHMNRHRQE 77 (286)
Q Consensus 49 eKPy~C~~Cgk~F~~ss~L~~H~r~Htge 77 (286)
.++.+|..||++|.+.....+||..|..+
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 36789999999999999988888887643
No 90
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=32.21 E-value=29 Score=27.25 Aligned_cols=30 Identities=13% Similarity=0.094 Sum_probs=18.1
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
.|.|++|++. .+.|+-+| -+.|..|+. .|.
T Consensus 35 ~~~Cp~C~~~--------~VkR~a~G--IW~C~kCg~--~fA 64 (89)
T COG1997 35 KHVCPFCGRT--------TVKRIATG--IWKCRKCGA--KFA 64 (89)
T ss_pred CCcCCCCCCc--------ceeeeccC--eEEcCCCCC--eec
Confidence 5777778764 22333333 467888887 665
No 91
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=32.03 E-value=16 Score=35.61 Aligned_cols=52 Identities=15% Similarity=0.310 Sum_probs=36.7
Q ss_pred CcccccCc--CCcccCCchhhhhhhhh---------------cCC----CcccccCCCCcccccCCchhhhhcCC
Q 040647 49 GKVYECRF--CSLKFCKSQALGGHMNR---------------HRQ----ERETETLNKARQLVFQHNDNLAVQGP 102 (286)
Q Consensus 49 eKPy~C~~--Cgk~F~~ss~L~~H~r~---------------Htg----eKPy~C~~Cgr~~sFs~~s~L~~H~r 102 (286)
.|+|+|.+ |.+.+++..-|+.|... |++ .|+|+|.+|.+ ++.-...|+-|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~--~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSK--RYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhh--hhccCCCCCceee
Confidence 37888876 88888887777766432 543 58999999998 7765555555533
No 92
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.19 E-value=35 Score=21.68 Aligned_cols=34 Identities=12% Similarity=0.149 Sum_probs=21.4
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
.+|+.|+..|.-..... .......+|..|+. .|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~--~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGH--VWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCC--EEE
Confidence 46888888877665432 12223578888887 553
No 93
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=31.15 E-value=26 Score=29.77 Aligned_cols=25 Identities=24% Similarity=0.219 Sum_probs=20.6
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERE 79 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKP 79 (286)
-.|-+|||.|+ +|++|..+|-+--|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 56888898887 68999999988665
No 94
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.65 E-value=44 Score=21.53 Aligned_cols=33 Identities=18% Similarity=0.275 Sum_probs=22.0
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCccccc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVF 91 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sF 91 (286)
.+|+.|+..|.-..... -...+..+|..|+. .|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~--~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGH--VF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCC--Ee
Confidence 36888888887766532 23345678888887 65
No 95
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=30.08 E-value=23 Score=29.71 Aligned_cols=27 Identities=26% Similarity=0.391 Sum_probs=16.7
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcc
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERE 79 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKP 79 (286)
..-.|-+|||.|.. |++|.+.|.|-.|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34678899998875 6999999977654
No 96
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.02 E-value=28 Score=25.44 Aligned_cols=32 Identities=6% Similarity=-0.021 Sum_probs=18.2
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
.|.|+.||+.-..+. .+.-....+|+|..||-
T Consensus 27 ~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 467777775443332 22222346888888874
No 97
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=29.43 E-value=27 Score=34.31 Aligned_cols=50 Identities=20% Similarity=0.204 Sum_probs=42.5
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCC----Cc-------------------ccccCCCC---cccccCCchhhhhcCC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQ----ER-------------------ETETLNKA---RQLVFQHNDNLAVQGP 102 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~Htg----eK-------------------Py~C~~Cg---r~~sFs~~s~L~~H~r 102 (286)
|-.|-+|++.|..-.....||..|.| ++ -+.|..|. + .|......+.||.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~--~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGR--PFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccC--cccccHHHHHHHh
Confidence 67899999999999999999988765 22 36788898 7 8999999999987
No 98
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=29.32 E-value=31 Score=27.21 Aligned_cols=12 Identities=8% Similarity=-0.163 Sum_probs=7.7
Q ss_pred ccccCCCCcccccC
Q 040647 79 ETETLNKARQLVFQ 92 (286)
Q Consensus 79 Py~C~~Cgr~~sFs 92 (286)
-++|..|++ .|.
T Consensus 53 IW~C~~C~~--~~A 64 (91)
T TIGR00280 53 IWTCRKCGA--KFA 64 (91)
T ss_pred EEEcCCCCC--EEe
Confidence 466777777 554
No 99
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.29 E-value=32 Score=27.07 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=17.1
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
.|.|++|++.-..+. ...-++|..|++ .|.
T Consensus 36 ~y~CpfCgk~~vkR~----------a~GIW~C~~C~~--~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQ----------AVGIWRCKGCKK--TVA 65 (90)
T ss_pred CccCCCCCCCceeee----------eeEEEEcCCCCC--EEe
Confidence 477777775422221 223567777877 664
No 100
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=28.22 E-value=71 Score=32.13 Aligned_cols=12 Identities=17% Similarity=-0.045 Sum_probs=6.8
Q ss_pred hhhhhcCCCCCC
Q 040647 95 DNLAVQGPPPHL 106 (286)
Q Consensus 95 s~L~~H~r~~H~ 106 (286)
..|+...+.+|+
T Consensus 197 ~eL~~YVk~hht 208 (480)
T KOG2675|consen 197 LELQAYVKEHHT 208 (480)
T ss_pred HHHHHHHHHhcc
Confidence 356666664443
No 101
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.11 E-value=39 Score=22.87 Aligned_cols=29 Identities=10% Similarity=0.225 Sum_probs=20.2
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCccccc
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVF 91 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sF 91 (286)
|.|..|+..|.-. ..-+.+|..||.+..|
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIly 31 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYRILY 31 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCceEEE
Confidence 7888898877644 2346789999974333
No 102
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=27.50 E-value=33 Score=29.62 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=26.1
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
+|.|. |+..|.+. ++|-.+-.|| .|.|..|+-.+.|.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL~~~ 153 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKLVFK 153 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCceEEec
Confidence 78899 99876654 4555555577 89999998744443
No 103
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=27.20 E-value=55 Score=31.98 Aligned_cols=80 Identities=15% Similarity=0.177 Sum_probs=0.0
Q ss_pred cccccCCCchhhhhhhccCCCCccCCCC---------------------------------------------CCccc--
Q 040647 20 VLDESSSTGAGAGHRKKKSGAKDGKDDE---------------------------------------------CGKVY-- 52 (286)
Q Consensus 20 C~k~F~~~s~L~~H~r~HtGeKpf~C~~---------------------------------------------~eKPy-- 52 (286)
|.|.|..+..|+.|||.....+--.-.- ..-+-
T Consensus 201 CekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v 280 (423)
T KOG2482|consen 201 CEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSV 280 (423)
T ss_pred eccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccce
Q ss_pred ccCcCCcccCCchhhhhhhhh---------------------------cCCCcccccCCCCcccccCCchhhhhcC
Q 040647 53 ECRFCSLKFCKSQALGGHMNR---------------------------HRQERETETLNKARQLVFQHNDNLAVQG 101 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~---------------------------HtgeKPy~C~~Cgr~~sFs~~s~L~~H~ 101 (286)
+|-+|.+..-+...|..||.+ -...+.-.|-.|.- .|.....|..|+
T Consensus 281 ~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~--~F~~e~~l~~hm 354 (423)
T KOG2482|consen 281 VCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDL--SFWKEPGLLIHM 354 (423)
T ss_pred EEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccc--cccCcchhhhhc
No 104
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=26.22 E-value=27 Score=21.63 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=9.5
Q ss_pred cccCcCCcccCCchhhhhhhh
Q 040647 52 YECRFCSLKFCKSQALGGHMN 72 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r 72 (286)
|.|-.|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 3566677776 3344555543
No 105
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=26.00 E-value=55 Score=19.70 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=4.0
Q ss_pred ccCcCCccc
Q 040647 53 ECRFCSLKF 61 (286)
Q Consensus 53 ~C~~Cgk~F 61 (286)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 344444444
No 106
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=25.84 E-value=40 Score=31.47 Aligned_cols=58 Identities=12% Similarity=0.161 Sum_probs=33.6
Q ss_pred chhhhhhhccCCC-----CccCCCCCC-----------cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCccccc
Q 040647 28 GAGAGHRKKKSGA-----KDGKDDECG-----------KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVF 91 (286)
Q Consensus 28 s~L~~H~r~HtGe-----Kpf~C~~~e-----------KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sF 91 (286)
.+|+...+.+... +.|.|..|. +.-.|..|.+.|----. ..-.|--.|.|..|++ .|
T Consensus 93 ~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h--~F 165 (278)
T PF15135_consen 93 ENLRMFDDAQENLIPSVDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRH--NF 165 (278)
T ss_pred HHHHHhhhhhhccccccceeeeccccchHHHhccCcccccccccccccccCCCcc-----ccccceeeeecccccc--cc
Confidence 3455554444333 677787765 24557777766543221 1123445789999999 77
Q ss_pred C
Q 040647 92 Q 92 (286)
Q Consensus 92 s 92 (286)
+
T Consensus 166 ~ 166 (278)
T PF15135_consen 166 R 166 (278)
T ss_pred h
Confidence 7
No 107
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=25.76 E-value=23 Score=27.93 Aligned_cols=30 Identities=20% Similarity=0.317 Sum_probs=16.7
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
.|.|++|++.-..+ .-+| -++|..|++ .|.
T Consensus 35 ky~Cp~Cgk~~vkR--------~a~G--IW~C~~C~~--~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKR--------VATG--IWKCKKCGK--KFA 64 (90)
T ss_dssp -BEESSSSSSEEEE--------EETT--EEEETTTTE--EEE
T ss_pred CCcCCCCCCceeEE--------eeeE--EeecCCCCC--EEe
Confidence 47777777643222 2223 367777877 653
No 108
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.65 E-value=40 Score=27.27 Aligned_cols=27 Identities=11% Similarity=0.030 Sum_probs=19.6
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
||.|..||..|...+... ---|..||.
T Consensus 2 pH~CtrCG~vf~~g~~~i----------l~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEI----------LSGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHH----------HccCccccc
Confidence 688999999999864432 125888886
No 109
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=25.11 E-value=37 Score=23.78 Aligned_cols=28 Identities=14% Similarity=0.239 Sum_probs=19.6
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
.-|+|..|++.|..- .......|+.|+.
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCc
Confidence 358899999988211 2345678999986
No 110
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.59 E-value=43 Score=26.37 Aligned_cols=12 Identities=17% Similarity=-0.061 Sum_probs=7.5
Q ss_pred ccccCCCCcccccC
Q 040647 79 ETETLNKARQLVFQ 92 (286)
Q Consensus 79 Py~C~~Cgr~~sFs 92 (286)
-++|..|++ .|.
T Consensus 54 IW~C~~C~~--~~A 65 (90)
T PRK03976 54 IWECRKCGA--KFA 65 (90)
T ss_pred EEEcCCCCC--EEe
Confidence 466777776 554
No 111
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.23 E-value=41 Score=33.60 Aligned_cols=35 Identities=23% Similarity=0.262 Sum_probs=25.5
Q ss_pred cccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 50 KVYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 50 KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
+-|.|+.|.+.|+....++ -+-...-.|.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 4699999999998776654 2233345789999976
No 112
>PF15471 TMEM171: Transmembrane protein family 171
Probab=23.01 E-value=3.2e+02 Score=26.00 Aligned_cols=25 Identities=24% Similarity=0.299 Sum_probs=15.2
Q ss_pred CCCCCCC-CCCCCCcceecCccccCC
Q 040647 196 PHNQSNL-NNFMDSSYTCIGAPVGHG 220 (286)
Q Consensus 196 ~~~~~~~-~~~~~~~y~~~~~~~~~~ 220 (286)
+...+.+ ....|+.||=-|.-.-.+
T Consensus 264 ~e~q~~as~rd~esiYTIsg~~~~se 289 (319)
T PF15471_consen 264 PEGQGAASERDCESIYTISGTSSSSE 289 (319)
T ss_pred cccCCccccccCceEEEecCCCCccc
Confidence 4454555 567788898766544333
No 113
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=22.78 E-value=29 Score=31.39 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=25.9
Q ss_pred CccCCCCCCcccccCc---CCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 41 KDGKDDECGKVYECRF---CSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 41 Kpf~C~~~eKPy~C~~---Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
.||.|.+|.|-|+-++ ||-.|...-..++- .+--+|-+|++
T Consensus 195 IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y------~kg~~C~~Cgk 238 (259)
T COG5152 195 IPFLCGICKKDYESPVVTECGHSFCSLCAIRKY------QKGDECGVCGK 238 (259)
T ss_pred CceeehhchhhccchhhhhcchhHHHHHHHHHh------ccCCcceecch
Confidence 3677777777776654 77776665544433 23457888876
No 114
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=22.44 E-value=62 Score=22.31 Aligned_cols=46 Identities=13% Similarity=0.205 Sum_probs=25.0
Q ss_pred ccccCc--CCcccCCchhhhhhhhhcCCCcccccCC----CCcccccCCchhhhhc
Q 040647 51 VYECRF--CSLKFCKSQALGGHMNRHRQERETETLN----KARQLVFQHNDNLAVQ 100 (286)
Q Consensus 51 Py~C~~--Cgk~F~~ss~L~~H~r~HtgeKPy~C~~----Cgr~~sFs~~s~L~~H 100 (286)
+-.|+. |...+. +..|..|....=..++..|.. |.. .+. ...|..|
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~--~~~-~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKE--RVP-REDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S----EEE-HHHHHHC
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCC--ccc-hhHHhCC
Confidence 456766 444455 447888887555567778887 776 555 3445444
No 115
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.22 E-value=21 Score=25.84 Aligned_cols=32 Identities=13% Similarity=0.031 Sum_probs=26.8
Q ss_pred hcCCCcccccCCCCcccccCCchhhhhcCCCCCC
Q 040647 73 RHRQERETETLNKARQLVFQHNDNLAVQGPPPHL 106 (286)
Q Consensus 73 ~HtgeKPy~C~~Cgr~~sFs~~s~L~~H~r~~H~ 106 (286)
.-.||.-+.|+.|+. .|+......+|..+.|.
T Consensus 11 ~RDGE~~lrCPRC~~--~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGM--VFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhH--HHHHhHHHHHHhhHHhh
Confidence 345788899999999 99999999999875564
No 116
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.15 E-value=42 Score=35.46 Aligned_cols=72 Identities=14% Similarity=0.032 Sum_probs=44.5
Q ss_pred CCchhhhhh-hccCCCCccCCCCC---CcccccCcCCcccCCchhhhhhhhhcC-CCc---c-cccCCCCcccccCCchh
Q 040647 26 STGAGAGHR-KKKSGAKDGKDDEC---GKVYECRFCSLKFCKSQALGGHMNRHR-QER---E-TETLNKARQLVFQHNDN 96 (286)
Q Consensus 26 ~~s~L~~H~-r~HtGeKpf~C~~~---eKPy~C~~Cgk~F~~ss~L~~H~r~Ht-geK---P-y~C~~Cgr~~sFs~~s~ 96 (286)
....|+.|+ .+|.. +.|.+| .|-| ..|.|.+++. .|..|++.-- +++ - -.|..|.. .|-....
T Consensus 126 s~~~Lk~H~~~~H~~---~~c~lC~~~~kif--~~e~k~Yt~~-el~~h~~~gd~d~~s~rGhp~C~~C~~--~fld~~e 197 (669)
T KOG2231|consen 126 SVENLKNHMRDQHKL---HLCSLCLQNLKIF--INERKLYTRA-ELNLHLMFGDPDDESCRGHPLCKFCHE--RFLDDDE 197 (669)
T ss_pred HHHHHHHHHHHhhhh---hccccccccceee--eeeeehehHH-HHHHHHhcCCCccccccCCccchhhhh--hhccHHH
Confidence 556788887 35543 444444 3433 3355666555 4566655422 222 1 36888998 9999999
Q ss_pred hhhcCCCCC
Q 040647 97 LAVQGPPPH 105 (286)
Q Consensus 97 L~~H~r~~H 105 (286)
|.+|++..|
T Consensus 198 l~rH~~~~h 206 (669)
T KOG2231|consen 198 LYRHLRFDH 206 (669)
T ss_pred HHHhhccce
Confidence 999999444
No 117
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.10 E-value=48 Score=26.18 Aligned_cols=25 Identities=16% Similarity=0.438 Sum_probs=20.6
Q ss_pred cccc----CcCCcccCCchhhhhhhhhcC
Q 040647 51 VYEC----RFCSLKFCKSQALGGHMNRHR 75 (286)
Q Consensus 51 Py~C----~~Cgk~F~~ss~L~~H~r~Ht 75 (286)
=|.| ..|+....+...+++|.+.+.
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3788 889999999999999987654
No 118
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=21.27 E-value=58 Score=19.47 Aligned_cols=19 Identities=16% Similarity=0.595 Sum_probs=12.0
Q ss_pred ccCcCCcccCCchhhhhhhh
Q 040647 53 ECRFCSLKFCKSQALGGHMN 72 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r 72 (286)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577888777 4445566654
No 119
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.15 E-value=57 Score=23.71 Aligned_cols=11 Identities=0% Similarity=-0.284 Sum_probs=8.1
Q ss_pred CcccccCCCCc
Q 040647 77 ERETETLNKAR 87 (286)
Q Consensus 77 eKPy~C~~Cgr 87 (286)
..+|+|..||-
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 35788888874
No 120
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.13 E-value=27 Score=34.17 Aligned_cols=81 Identities=21% Similarity=0.129 Sum_probs=49.3
Q ss_pred hcccccCCCchhhhhhhccCCCCccCCCCCC---cccccCcCCcccCCchhhhhhhhhcCCCcc----cccCCCCccccc
Q 040647 19 QVLDESSSTGAGAGHRKKKSGAKDGKDDECG---KVYECRFCSLKFCKSQALGGHMNRHRQERE----TETLNKARQLVF 91 (286)
Q Consensus 19 ~C~k~F~~~s~L~~H~r~HtGeKpf~C~~~e---KPy~C~~Cgk~F~~ss~L~~H~r~HtgeKP----y~C~~Cgr~~sF 91 (286)
.|...-.....|+.|.++..+ -+-|.+|- |.|.|+. +.| ++..|+.|...-..+.- -.|..|.. .|
T Consensus 158 kc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~--~lF-~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~--~F 230 (493)
T COG5236 158 KCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEI--RLF-RSSTLRDHKNGGLEEEGFKGHPLCIFCKI--YF 230 (493)
T ss_pred hhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccce--eee-ecccccccccCCccccCcCCCchhhhccc--ee
Confidence 333333334567777765443 24565553 3444433 234 34468888776554422 26999998 99
Q ss_pred CCchhhhhcCCCCCC
Q 040647 92 QHNDNLAVQGPPPHL 106 (286)
Q Consensus 92 s~~s~L~~H~r~~H~ 106 (286)
-..+.|.+|+|..|.
T Consensus 231 YdDDEL~~HcR~~HE 245 (493)
T COG5236 231 YDDDELRRHCRLRHE 245 (493)
T ss_pred cChHHHHHHHHhhhh
Confidence 999999999884443
No 121
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=21.13 E-value=56 Score=23.39 Aligned_cols=27 Identities=30% Similarity=0.438 Sum_probs=11.9
Q ss_pred cccCcCCcccCCchhhhhhhhhcCCCcccccCCCCcccccC
Q 040647 52 YECRFCSLKFCKSQALGGHMNRHRQERETETLNKARQLVFQ 92 (286)
Q Consensus 52 y~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr~~sFs 92 (286)
-.|..|++.|.. -.+.+.|..||+ .|-
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~--~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGR--VVC 36 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT----EEE
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCC--EEC
Confidence 357778888843 134567888887 665
No 122
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.03 E-value=50 Score=21.45 Aligned_cols=29 Identities=7% Similarity=0.150 Sum_probs=18.5
Q ss_pred ccCcCCcccCCchhhhhhhhhcCCCcccccCCC
Q 040647 53 ECRFCSLKFCKSQALGGHMNRHRQERETETLNK 85 (286)
Q Consensus 53 ~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~C 85 (286)
.|+.|+.. ..+.+|-+...|...|.|..|
T Consensus 7 ~CP~C~s~----~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQST----EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCC----CcceeCCCCCCCCEeEecCcC
Confidence 46666522 225667666777777888777
No 123
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=20.89 E-value=38 Score=28.06 Aligned_cols=29 Identities=17% Similarity=0.365 Sum_probs=19.4
Q ss_pred ccccCcCCcccCCchhhhhhhhhcCCCcccccCCCCc
Q 040647 51 VYECRFCSLKFCKSQALGGHMNRHRQERETETLNKAR 87 (286)
Q Consensus 51 Py~C~~Cgk~F~~ss~L~~H~r~HtgeKPy~C~~Cgr 87 (286)
.|+|..|+..+. +|.++ ..+.|.|..|+.
T Consensus 123 ~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~ 151 (157)
T PF10263_consen 123 VYRCPSCGREYK------RHRRS--KRKRYRCGRCGG 151 (157)
T ss_pred EEEcCCCCCEee------eeccc--chhhEECCCCCC
Confidence 578888887663 33343 334488988887
Done!