Query 045251
Match_columns 163
No_of_seqs 291 out of 1136
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 11:21:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045251.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045251hhsearch_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 99.3 1.4E-12 3E-17 105.3 3.4 63 32-97 186-253 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.1 2.5E-11 5.5E-16 98.1 2.0 53 25-77 207-264 (279)
3 KOG3623 Homeobox transcription 98.7 7.5E-09 1.6E-13 93.0 1.9 61 30-93 891-956 (1007)
4 KOG1074 Transcriptional repres 98.5 4.3E-08 9.4E-13 89.1 3.2 60 32-91 604-669 (958)
5 KOG3576 Ovo and related transc 98.4 7.6E-08 1.7E-12 75.3 0.4 51 32-82 116-171 (267)
6 PHA02768 hypothetical protein; 98.3 2.3E-07 5E-12 58.2 1.9 41 33-73 5-48 (55)
7 KOG3623 Homeobox transcription 98.3 1.2E-07 2.6E-12 85.4 0.7 52 27-78 916-972 (1007)
8 KOG3576 Ovo and related transc 98.3 3.4E-07 7.4E-12 71.7 1.8 58 25-82 137-199 (267)
9 KOG1074 Transcriptional repres 98.3 5.4E-07 1.2E-11 82.2 3.3 52 33-84 879-935 (958)
10 PHA00616 hypothetical protein 98.1 1.1E-06 2.4E-11 52.6 1.1 30 33-62 1-30 (44)
11 PHA00733 hypothetical protein 97.9 1.4E-05 3E-10 58.7 4.7 52 28-81 68-124 (128)
12 PF00096 zf-C2H2: Zinc finger, 97.7 1.5E-05 3.2E-10 40.8 1.3 23 34-56 1-23 (23)
13 PF13465 zf-H2C2_2: Zinc-finge 97.5 2.4E-05 5.2E-10 41.6 0.4 19 27-45 8-26 (26)
14 PF13912 zf-C2H2_6: C2H2-type 97.4 7.1E-05 1.5E-09 39.7 1.4 26 33-58 1-26 (27)
15 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00021 4.5E-09 36.2 1.8 23 34-56 1-23 (24)
16 KOG3608 Zn finger proteins [Ge 97.1 0.00033 7.1E-09 59.2 2.3 69 27-96 286-361 (467)
17 PHA00732 hypothetical protein 97.0 0.00054 1.2E-08 46.2 2.8 45 33-80 1-48 (79)
18 smart00355 ZnF_C2H2 zinc finge 96.9 0.00082 1.8E-08 34.3 2.0 24 34-57 1-24 (26)
19 PF09237 GAGA: GAGA factor; I 96.9 0.0013 2.8E-08 40.6 3.0 35 27-61 18-52 (54)
20 PF13465 zf-H2C2_2: Zinc-finge 96.3 0.0021 4.5E-08 34.0 1.3 20 48-67 1-25 (26)
21 KOG3993 Transcription factor ( 96.0 0.0038 8.3E-08 53.9 2.0 50 33-82 295-382 (500)
22 PF12874 zf-met: Zinc-finger o 95.7 0.0055 1.2E-07 31.6 1.1 23 34-56 1-23 (25)
23 PF12171 zf-C2H2_jaz: Zinc-fin 95.2 0.0078 1.7E-07 31.9 0.7 22 34-55 2-23 (27)
24 KOG3608 Zn finger proteins [Ge 95.0 0.0093 2E-07 50.6 0.9 56 25-80 199-261 (467)
25 PF05605 zf-Di19: Drought indu 94.6 0.064 1.4E-06 33.1 3.7 45 33-80 2-53 (54)
26 PHA00733 hypothetical protein 94.2 0.029 6.3E-07 41.0 1.9 49 31-79 38-96 (128)
27 PF13909 zf-H2C2_5: C2H2-type 94.1 0.032 7E-07 28.5 1.4 23 34-57 1-23 (24)
28 PF13913 zf-C2HC_2: zinc-finge 93.3 0.062 1.4E-06 28.1 1.6 21 34-55 3-23 (25)
29 PLN03086 PRLI-interacting fact 93.2 0.16 3.4E-06 45.9 5.0 55 31-92 451-509 (567)
30 smart00451 ZnF_U1 U1-like zinc 92.5 0.097 2.1E-06 28.9 1.8 22 33-54 3-24 (35)
31 COG5189 SFP1 Putative transcri 91.7 0.067 1.5E-06 44.9 0.7 24 31-54 347-372 (423)
32 PHA02768 hypothetical protein; 90.7 0.29 6.2E-06 30.7 2.7 18 63-80 12-29 (55)
33 PF12756 zf-C2H2_2: C2H2 type 90.5 0.19 4.2E-06 33.7 2.0 25 33-57 50-74 (100)
34 COG5189 SFP1 Putative transcri 89.7 0.1 2.3E-06 43.8 0.1 23 31-53 396-418 (423)
35 PLN03086 PRLI-interacting fact 88.8 0.45 9.7E-06 43.0 3.5 46 32-79 477-537 (567)
36 PF12756 zf-C2H2_2: C2H2 type 88.4 0.25 5.4E-06 33.2 1.3 46 35-80 1-74 (100)
37 PRK04860 hypothetical protein; 86.6 0.49 1.1E-05 35.9 2.1 27 32-62 118-144 (160)
38 PHA00616 hypothetical protein 85.8 0.43 9.2E-06 28.5 1.1 20 63-82 8-27 (44)
39 COG4049 Uncharacterized protei 81.5 0.67 1.5E-05 29.2 0.7 28 28-55 12-39 (65)
40 KOG3993 Transcription factor ( 79.0 0.9 1.9E-05 39.6 0.9 26 32-57 355-380 (500)
41 PF05443 ROS_MUCR: ROS/MUCR tr 75.7 1.5 3.3E-05 32.3 1.2 28 31-61 70-97 (132)
42 COG5048 FOG: Zn-finger [Genera 75.0 0.83 1.8E-05 37.8 -0.4 52 32-83 288-350 (467)
43 PF02892 zf-BED: BED zinc fing 72.7 3.1 6.6E-05 24.1 1.9 24 30-53 13-40 (45)
44 smart00614 ZnF_BED BED zinc fi 68.1 4.3 9.3E-05 24.4 1.8 23 32-54 17-44 (50)
45 PF04959 ARS2: Arsenite-resist 66.4 3.7 8.1E-05 32.7 1.6 26 31-56 75-100 (214)
46 COG5048 FOG: Zn-finger [Genera 60.5 6.2 0.00013 32.5 2.0 52 31-82 31-89 (467)
47 PF08790 zf-LYAR: LYAR-type C2 57.4 4 8.6E-05 22.0 0.2 26 34-60 1-26 (28)
48 COG4957 Predicted transcriptio 56.7 5.4 0.00012 29.6 0.9 26 33-61 76-101 (148)
49 KOG4167 Predicted DNA-binding 53.5 2.5 5.4E-05 39.4 -1.5 27 32-58 791-817 (907)
50 PF09845 DUF2072: Zn-ribbon co 50.6 7 0.00015 28.7 0.7 15 33-47 1-15 (131)
51 KOG3408 U1-like Zn-finger-cont 49.2 9.4 0.0002 27.8 1.1 26 30-55 54-79 (129)
52 KOG2071 mRNA cleavage and poly 46.7 12 0.00026 34.1 1.6 28 30-57 415-442 (579)
53 smart00734 ZnF_Rad18 Rad18-lik 45.7 17 0.00036 18.9 1.5 20 34-54 2-21 (26)
54 smart00834 CxxC_CXXC_SSSS Puta 45.4 10 0.00022 21.3 0.7 14 33-46 5-18 (41)
55 PF12013 DUF3505: Protein of u 45.2 16 0.00035 25.4 1.8 26 33-58 80-109 (109)
56 PF07754 DUF1610: Domain of un 41.5 14 0.00031 19.1 0.8 10 32-41 15-24 (24)
57 cd00924 Cyt_c_Oxidase_Vb Cytoc 41.0 14 0.0003 25.7 1.0 15 31-45 77-91 (97)
58 smart00154 ZnF_AN1 AN1-like Zi 40.6 15 0.00033 21.0 0.9 14 33-46 12-25 (39)
59 PF10571 UPF0547: Uncharacteri 40.3 15 0.00033 19.2 0.8 10 35-44 16-25 (26)
60 COG5112 UFD2 U1-like Zn-finger 39.8 14 0.0003 26.4 0.8 26 29-54 51-76 (126)
61 PF09986 DUF2225: Uncharacteri 38.2 7.6 0.00017 30.7 -0.8 24 31-54 3-26 (214)
62 PF09723 Zn-ribbon_8: Zinc rib 37.9 15 0.00032 21.3 0.6 15 33-47 5-19 (42)
63 KOG2482 Predicted C2H2-type Zn 36.7 19 0.00042 30.8 1.3 23 33-55 195-217 (423)
64 TIGR02605 CxxC_CxxC_SSSS putat 35.9 17 0.00037 21.7 0.7 14 33-46 5-18 (52)
65 PLN02294 cytochrome c oxidase 35.2 20 0.00042 27.7 1.0 15 31-45 139-153 (174)
66 COG3364 Zn-ribbon containing p 34.7 20 0.00044 25.3 1.0 15 33-47 2-16 (112)
67 KOG0717 Molecular chaperone (D 34.5 21 0.00047 31.7 1.3 21 34-54 293-313 (508)
68 KOG1146 Homeobox protein [Gene 33.1 30 0.00065 34.6 2.1 28 28-55 460-487 (1406)
69 PF01428 zf-AN1: AN1-like Zinc 32.9 18 0.00039 21.0 0.4 15 32-46 12-26 (43)
70 KOG2893 Zn finger protein [Gen 32.2 12 0.00025 30.7 -0.7 23 31-54 9-31 (341)
71 KOG2893 Zn finger protein [Gen 32.1 17 0.00037 29.7 0.3 33 25-57 26-59 (341)
72 PF13451 zf-trcl: Probable zin 29.7 26 0.00056 21.4 0.7 18 31-48 2-19 (49)
73 PF04423 Rad50_zn_hook: Rad50 29.5 20 0.00044 21.7 0.2 12 35-46 22-33 (54)
74 PF10276 zf-CHCC: Zinc-finger 29.0 23 0.00051 20.5 0.4 12 32-43 28-39 (40)
75 PF06220 zf-U1: U1 zinc finger 27.7 41 0.00089 19.1 1.3 22 32-53 2-25 (38)
76 PHA00626 hypothetical protein 27.4 33 0.00072 21.6 0.9 14 32-45 22-35 (59)
77 PF10013 DUF2256: Uncharacteri 26.4 37 0.00081 20.0 1.0 16 35-50 10-25 (42)
78 KOG2636 Splicing factor 3a, su 25.3 46 0.00099 29.5 1.7 27 28-54 396-423 (497)
79 PF13878 zf-C2H2_3: zinc-finge 25.1 54 0.0012 18.9 1.5 24 34-57 14-39 (41)
80 KOG2785 C2H2-type Zn-finger pr 25.1 72 0.0016 27.7 2.8 48 31-78 164-242 (390)
81 PRK00464 nrdR transcriptional 25.0 30 0.00064 26.1 0.5 20 31-50 26-45 (154)
82 COG1773 Rubredoxin [Energy pro 24.2 33 0.00071 21.4 0.5 14 32-45 2-15 (55)
83 PF06397 Desulfoferrod_N: Desu 22.8 39 0.00085 19.2 0.6 12 32-43 5-16 (36)
84 PF09538 FYDLN_acid: Protein o 22.6 47 0.001 23.5 1.1 15 32-46 25-39 (108)
85 PF15269 zf-C2H2_7: Zinc-finge 22.0 58 0.0013 19.6 1.2 22 34-55 21-42 (54)
86 PF14077 WD40_alt: Alternative 21.8 23 0.0005 21.3 -0.5 11 152-162 32-42 (48)
87 PF01927 Mut7-C: Mut7-C RNAse 21.5 72 0.0016 23.4 2.0 21 31-51 122-142 (147)
88 cd00729 rubredoxin_SM Rubredox 21.2 52 0.0011 18.1 0.9 12 33-44 2-13 (34)
89 PF07975 C1_4: TFIIH C1-like d 21.2 35 0.00075 20.9 0.2 27 31-57 19-45 (51)
90 COG5188 PRP9 Splicing factor 3 20.6 74 0.0016 27.5 2.1 43 11-53 347-395 (470)
91 cd00350 rubredoxin_like Rubred 20.6 50 0.0011 17.9 0.7 11 34-44 2-12 (33)
92 COG4391 Uncharacterized protei 20.5 39 0.00084 21.6 0.3 13 32-44 47-59 (62)
93 PF11931 DUF3449: Domain of un 20.3 34 0.00074 26.9 0.0 23 31-53 99-122 (196)
94 PLN02748 tRNA dimethylallyltra 20.1 66 0.0014 28.7 1.7 24 31-54 416-440 (468)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.30 E-value=1.4e-12 Score=105.30 Aligned_cols=63 Identities=16% Similarity=0.337 Sum_probs=55.7
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCCCCCCCCCCCCCCcCc
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANPSIEAPNIVSEDRGAV 97 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e~~~~p~~~~~~~~~~ 97 (163)
-+++|.+|||.|.+..-|+.|+|+|+||||| +|+|..+++|..||++|.+. +++.|..+...+
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~---K~~qC~~C~KsF 253 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV---KKHQCPRCGKSF 253 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCC---ccccCcchhhHH
Confidence 6899999999999999999999999999999 99999999999999999887 455565555443
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.11 E-value=2.5e-11 Score=98.07 Aligned_cols=53 Identities=19% Similarity=0.416 Sum_probs=50.6
Q ss_pred CCCCCCCcceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHH
Q 045251 25 SSDSGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIA 77 (163)
Q Consensus 25 ~~~htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r 77 (163)
.++|||||||.|.+|+|+|..+++|+.||++|.+.|+| +|.|..++.|.+|..
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 57899999999999999999999999999999999999 999999999999964
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.67 E-value=7.5e-09 Score=92.95 Aligned_cols=61 Identities=18% Similarity=0.310 Sum_probs=50.1
Q ss_pred CCcceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCCCCCCCCCCCCC
Q 045251 30 HVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANPSIEAPNIVSED 93 (163)
Q Consensus 30 gekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e~~~~p~~~~~~ 93 (163)
.+.+|.|+.|+|.|.-.+.|.+|.--|+|.+|| .|+|..+..|..|+|.|.|| +|+.|..+
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGE---KPfQCdKC 956 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGE---KPFQCDKC 956 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCC---Ccchhhhh
Confidence 356888999999998888899998889999998 78899898999999999888 55555433
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.55 E-value=4.3e-08 Score=89.15 Aligned_cols=60 Identities=20% Similarity=0.263 Sum_probs=47.8
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCC-CCCCCCCCC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANP-SIEAPNIVS 91 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e-~~~~p~~~~ 91 (163)
.|-+|.+|-|..+..++|+.|.|+|+||||| +++|..+.+|+.|+-+|... +++.+..|+
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP 669 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCP 669 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCC
Confidence 4778888988888888899998999999888 88888888898888888654 444444444
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.38 E-value=7.6e-08 Score=75.33 Aligned_cols=51 Identities=20% Similarity=0.371 Sum_probs=24.3
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANP 82 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e 82 (163)
..|.|.+|+|.|.....|.+|+++|...|.| ||.|...-.|++|+|+|+|-
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgv 171 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGV 171 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCc
Confidence 3444555555554444444444444444433 44444444444444444444
No 6
>PHA02768 hypothetical protein; Provisional
Probab=98.34 E-value=2.3e-07 Score=58.15 Aligned_cols=41 Identities=15% Similarity=0.279 Sum_probs=33.9
Q ss_pred ceeCCccCcccCCchHHHHHhhhcC-CCCCC--CccCCCchHHH
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHR-KDRAK--LRQFSEENLLS 73 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Ht-gekpy--~k~F~~~s~L~ 73 (163)
-|.|+.||+.|....+|..|+++|+ +.+.. ++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 4799999999999999999999999 44333 88888776653
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.34 E-value=1.2e-07 Score=85.38 Aligned_cols=52 Identities=23% Similarity=0.551 Sum_probs=49.6
Q ss_pred CCCCCcceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHh
Q 045251 27 DSGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAK 78 (163)
Q Consensus 27 ~htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~ 78 (163)
-|+|.|||+|.+|.|+|.++..|..|+|.|.|+||| +|+|+....+..||..
T Consensus 916 EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMNH 972 (1007)
T KOG3623|consen 916 EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMNH 972 (1007)
T ss_pred hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhcc
Confidence 489999999999999999999999999999999999 8999999999999863
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.27 E-value=3.4e-07 Score=71.72 Aligned_cols=58 Identities=24% Similarity=0.398 Sum_probs=51.4
Q ss_pred CCCCCCCcceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCC
Q 045251 25 SSDSGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANP 82 (163)
Q Consensus 25 ~~~htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e 82 (163)
.+-|...|.|.|.+|||+|.....|++|+|+|+|.+|| +|+|.++..|..|++.-++.
T Consensus 137 ~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 137 LKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred hhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 35567788999999999999999999999999999999 89999999999998754343
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.27 E-value=5.4e-07 Score=82.18 Aligned_cols=52 Identities=21% Similarity=0.333 Sum_probs=48.5
Q ss_pred ceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcCCCC
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAANPSI 84 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~e~~ 84 (163)
.+.|.+||+.|....+|..|+|+|+|+||| ++.|..+.+|+.||.+|.....
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 478999999999999999999999999999 8999999999999999987644
No 10
>PHA00616 hypothetical protein
Probab=98.10 E-value=1.1e-06 Score=52.64 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=28.8
Q ss_pred ceeCCccCcccCCchHHHHHhhhcCCCCCC
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHRKDRAK 62 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Htgekpy 62 (163)
||+|..||+.|...+.|..|++.|+|++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 689999999999999999999999999987
No 11
>PHA00733 hypothetical protein
Probab=97.95 E-value=1.4e-05 Score=58.66 Aligned_cols=52 Identities=25% Similarity=0.436 Sum_probs=43.9
Q ss_pred CCCCcceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCCCchHHHHHHHhhcC
Q 045251 28 SGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFSEENLLSLDIAKAAN 81 (163)
Q Consensus 28 htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~~~s~L~~H~r~Ht~ 81 (163)
+.+++||.|..||+.|.....|..|++.|. .+| ++.|.....|..|+...++
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhcCC--cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 345789999999999999999999999763 345 8999999999999887544
No 12
>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=97.73 E-value=1.5e-05 Score=40.81 Aligned_cols=23 Identities=39% Similarity=0.868 Sum_probs=21.5
Q ss_pred eeCCccCcccCCchHHHHHhhhc
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIH 56 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~H 56 (163)
|+|..|++.|.....|..|++.|
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 78999999999999999999875
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=97.53 E-value=2.4e-05 Score=41.64 Aligned_cols=19 Identities=37% Similarity=0.882 Sum_probs=17.1
Q ss_pred CCCCCcceeCCccCcccCC
Q 045251 27 DSGHVKSYTCAFCKRGFSN 45 (163)
Q Consensus 27 ~htgekp~~C~~Cgk~F~~ 45 (163)
.|++++||.|++|++.|.+
T Consensus 8 ~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 8 THTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHSSSSSEEESSSSEEESS
T ss_pred hcCCCCCCCCCCCcCeeCc
Confidence 5899999999999999963
No 14
>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=97.42 E-value=7.1e-05 Score=39.73 Aligned_cols=26 Identities=31% Similarity=0.583 Sum_probs=23.8
Q ss_pred ceeCCccCcccCCchHHHHHhhhcCC
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHRK 58 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Htg 58 (163)
||.|..|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999988753
No 15
>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=97.24 E-value=0.00021 Score=36.23 Aligned_cols=23 Identities=30% Similarity=0.824 Sum_probs=19.5
Q ss_pred eeCCccCcccCCchHHHHHhhhc
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIH 56 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~H 56 (163)
|.|++|++.|.....|..|++.|
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 78999999999999999999876
No 16
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.07 E-value=0.00033 Score=59.18 Aligned_cols=69 Identities=9% Similarity=0.084 Sum_probs=53.6
Q ss_pred CCCCCcceeCCccCcccCCchHHHHHhhhcCCCCCC-------CccCCCchHHHHHHHhhcCCCCCCCCCCCCCCcC
Q 045251 27 DSGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-------LRQFSEENLLSLDIAKAANPSIEAPNIVSEDRGA 96 (163)
Q Consensus 27 ~htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-------~k~F~~~s~L~~H~r~Ht~e~~~~p~~~~~~~~~ 96 (163)
.|...|||+|+.|.+.|.+...|.+|..+|. +..| ...|++...|.+|++.+..-.-+.+++|-.++.-
T Consensus 286 rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ 361 (467)
T KOG3608|consen 286 RHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRF 361 (467)
T ss_pred hhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhh
Confidence 4777899999999999999999999999998 4444 4567788899999887654444477776654443
No 17
>PHA00732 hypothetical protein
Probab=97.04 E-value=0.00054 Score=46.16 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=35.2
Q ss_pred ceeCCccCcccCCchHHHHHhhh-cCCCCC-C-CccCCCchHHHHHHHhhc
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNI-HRKDRA-K-LRQFSEENLLSLDIAKAA 80 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~-Htgekp-y-~k~F~~~s~L~~H~r~Ht 80 (163)
||.|..|++.|.....|..|++. |.+.+- . ++.|. .|..|.+.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---ChhhhhcccC
Confidence 68999999999999999999984 665321 1 88887 5788886553
No 18
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.87 E-value=0.00082 Score=34.29 Aligned_cols=24 Identities=38% Similarity=0.740 Sum_probs=21.8
Q ss_pred eeCCccCcccCCchHHHHHhhhcC
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 679999999999999999998775
No 19
>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=96.85 E-value=0.0013 Score=40.56 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=25.2
Q ss_pred CCCCCcceeCCccCcccCCchHHHHHhhhcCCCCC
Q 045251 27 DSGHVKSYTCAFCKRGFSNAQALGGHMNIHRKDRA 61 (163)
Q Consensus 27 ~htgekp~~C~~Cgk~F~~~~~L~~H~r~Htgekp 61 (163)
.+..+.|..|++|+..+.+..+|++|+.++.+.||
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34567899999999999999999999988887775
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=96.33 E-value=0.0021 Score=34.03 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=14.7
Q ss_pred HHHHHhhhcCCCCCC-----CccCC
Q 045251 48 ALGGHMNIHRKDRAK-----LRQFS 67 (163)
Q Consensus 48 ~L~~H~r~Htgekpy-----~k~F~ 67 (163)
+|..|+++|+|++|| ++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 477888888888887 56654
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.00 E-value=0.0038 Score=53.85 Aligned_cols=50 Identities=20% Similarity=0.357 Sum_probs=41.8
Q ss_pred ceeCCccCcccCCchHHHHHhhhcC--------CCCC-------------------------C-----CccCCCchHHHH
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHR--------KDRA-------------------------K-----LRQFSEENLLSL 74 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Ht--------gekp-------------------------y-----~k~F~~~s~L~~ 74 (163)
-|+|..|+|.|+...+|..|.|.|. +..| | +|.|.+...|.+
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 4899999999999999999999984 2222 2 789999999999
Q ss_pred HHHhhcCC
Q 045251 75 DIAKAANP 82 (163)
Q Consensus 75 H~r~Ht~e 82 (163)
|+-+|...
T Consensus 375 Hqlthq~~ 382 (500)
T KOG3993|consen 375 HQLTHQRA 382 (500)
T ss_pred hHHhhhcc
Confidence 98888654
No 22
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.70 E-value=0.0055 Score=31.61 Aligned_cols=23 Identities=26% Similarity=0.762 Sum_probs=20.8
Q ss_pred eeCCccCcccCCchHHHHHhhhc
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIH 56 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~H 56 (163)
|.|.+|++.|.....|..|++.+
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 68999999999999999998754
No 23
>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=95.22 E-value=0.0078 Score=31.88 Aligned_cols=22 Identities=32% Similarity=0.676 Sum_probs=20.2
Q ss_pred eeCCccCcccCCchHHHHHhhh
Q 045251 34 YTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
|.|..|++.|.....+..|++.
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 7899999999999999999864
No 24
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=94.98 E-value=0.0093 Score=50.59 Aligned_cols=56 Identities=18% Similarity=0.355 Sum_probs=40.8
Q ss_pred CCCCCCCcceeCCccCcccCCchHHHHHhhhcC--CCCCC-----CccCCCchHHHHHHHhhc
Q 045251 25 SSDSGHVKSYTCAFCKRGFSNAQALGGHMNIHR--KDRAK-----LRQFSEENLLSLDIAKAA 80 (163)
Q Consensus 25 ~~~htgekp~~C~~Cgk~F~~~~~L~~H~r~Ht--gekpy-----~k~F~~~s~L~~H~r~Ht 80 (163)
++.|+++|-..|++||.-|++...|-.|.+..+ ...+| .|+|.....|..|++.|-
T Consensus 199 ~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv 261 (467)
T KOG3608|consen 199 IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV 261 (467)
T ss_pred HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh
Confidence 678889999899999999999888888876443 33455 566666666666666553
No 25
>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=94.56 E-value=0.064 Score=33.12 Aligned_cols=45 Identities=22% Similarity=0.451 Sum_probs=30.9
Q ss_pred ceeCCccCcccCCchHHHHHhh-hcCCCC-CC-----CccCCCchHHHHHHHhhc
Q 045251 33 SYTCAFCKRGFSNAQALGGHMN-IHRKDR-AK-----LRQFSEENLLSLDIAKAA 80 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r-~Htgek-py-----~k~F~~~s~L~~H~r~Ht 80 (163)
.|.|++|++. .....|..|.. .|..+. .+ ...+ ..+|..|+..+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~--~~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRV--TDNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhh--hhHHHHHHHHhc
Confidence 4899999995 55688999964 566543 23 3333 348889988754
No 26
>PHA00733 hypothetical protein
Probab=94.22 E-value=0.029 Score=41.03 Aligned_cols=49 Identities=22% Similarity=0.123 Sum_probs=39.5
Q ss_pred CcceeCCccCcccCCchHHHHH--hh---hcCCCCCC-----CccCCCchHHHHHHHhh
Q 045251 31 VKSYTCAFCKRGFSNAQALGGH--MN---IHRKDRAK-----LRQFSEENLLSLDIAKA 79 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H--~r---~Htgekpy-----~k~F~~~s~L~~H~r~H 79 (163)
.+++.|.+|.+.|.....|..+ ++ .+.+.+|| ++.|.....|..|++.|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 5789999999999888777766 22 23457787 89999999999999976
No 27
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.08 E-value=0.032 Score=28.47 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=17.6
Q ss_pred eeCCccCcccCCchHHHHHhhhcC
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
|+|..|..... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999998887 889999988753
No 28
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.27 E-value=0.062 Score=28.09 Aligned_cols=21 Identities=38% Similarity=0.763 Sum_probs=17.3
Q ss_pred eeCCccCcccCCchHHHHHhhh
Q 045251 34 YTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
..|..||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 57788888763
No 29
>PLN03086 PRLI-interacting factor K; Provisional
Probab=93.18 E-value=0.16 Score=45.89 Aligned_cols=55 Identities=13% Similarity=0.155 Sum_probs=40.4
Q ss_pred CcceeCCccCcccCCchHHHHHhhhcCCCCCC----CccCCCchHHHHHHHhhcCCCCCCCCCCCC
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK----LRQFSEENLLSLDIAKAANPSIEAPNIVSE 92 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy----~k~F~~~s~L~~H~r~Ht~e~~~~p~~~~~ 92 (163)
++.+.|.+|++.|. ...|..|+++|+ +++ ++.| .+..|..|+++|... .|..|+.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~CpCg~~~-~R~~L~~H~~thCp~---Kpi~C~f 509 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCPCGVVL-EKEQMVQHQASTCPL---RLITCRF 509 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCCCCCCc-chhHHHhhhhccCCC---CceeCCC
Confidence 45678999999996 678999999875 555 5444 568899999888666 4444443
No 30
>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=92.46 E-value=0.097 Score=28.89 Aligned_cols=22 Identities=18% Similarity=0.711 Sum_probs=19.9
Q ss_pred ceeCCccCcccCCchHHHHHhh
Q 045251 33 SYTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r 54 (163)
+|.|..|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6889999999999999999975
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=91.72 E-value=0.067 Score=44.92 Aligned_cols=24 Identities=33% Similarity=0.697 Sum_probs=22.0
Q ss_pred CcceeCCc--cCcccCCchHHHHHhh
Q 045251 31 VKSYTCAF--CKRGFSNAQALGGHMN 54 (163)
Q Consensus 31 ekp~~C~~--Cgk~F~~~~~L~~H~r 54 (163)
+|||+|++ |.|.+.....|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhh
Confidence 59999998 9999999999999975
No 32
>PHA02768 hypothetical protein; Provisional
Probab=90.69 E-value=0.29 Score=30.67 Aligned_cols=18 Identities=6% Similarity=0.041 Sum_probs=17.4
Q ss_pred CccCCCchHHHHHHHhhc
Q 045251 63 LRQFSEENLLSLDIAKAA 80 (163)
Q Consensus 63 ~k~F~~~s~L~~H~r~Ht 80 (163)
|+.|.....|..|+++|+
T Consensus 12 GK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 12 GEIYIKRKSMITHLRKHN 29 (55)
T ss_pred CCeeccHHHHHHHHHhcC
Confidence 899999999999999998
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.47 E-value=0.19 Score=33.71 Aligned_cols=25 Identities=32% Similarity=0.817 Sum_probs=21.7
Q ss_pred ceeCCccCcccCCchHHHHHhhhcC
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
.+.|.+|++.|.....|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6999999999999999999998653
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=89.65 E-value=0.1 Score=43.81 Aligned_cols=23 Identities=30% Similarity=0.664 Sum_probs=21.3
Q ss_pred CcceeCCccCcccCCchHHHHHh
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHM 53 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~ 53 (163)
.|||+|.+|+|.+.....|+-|+
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CCceeccccchhhccCccceecc
Confidence 59999999999999999999885
No 35
>PLN03086 PRLI-interacting factor K; Provisional
Probab=88.83 E-value=0.45 Score=43.03 Aligned_cols=46 Identities=11% Similarity=0.044 Sum_probs=36.8
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCCCCCC-----CccCC----------CchHHHHHHHhh
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-----LRQFS----------EENLLSLDIAKA 79 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-----~k~F~----------~~s~L~~H~r~H 79 (163)
+++.|. ||+.| ....|..|++.|...+++ ++.|. ....|..|...+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc
Confidence 789999 99755 668999999999999987 55553 134788998886
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.41 E-value=0.25 Score=33.15 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=14.3
Q ss_pred eCCccCcccCCchHHHHHhhhcCC-CCC----------------------C-----CccCCCchHHHHHHHhhc
Q 045251 35 TCAFCKRGFSNAQALGGHMNIHRK-DRA----------------------K-----LRQFSEENLLSLDIAKAA 80 (163)
Q Consensus 35 ~C~~Cgk~F~~~~~L~~H~r~Htg-ekp----------------------y-----~k~F~~~s~L~~H~r~Ht 80 (163)
+|.+|+..|.....|..|+....+ ..+ + ++.|.....|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 599999999999999999854322 111 1 677888999999999753
No 37
>PRK04860 hypothetical protein; Provisional
Probab=86.60 E-value=0.49 Score=35.95 Aligned_cols=27 Identities=19% Similarity=0.469 Sum_probs=23.8
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCCCCCC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRKDRAK 62 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy 62 (163)
.+|.|. |++ ....+..|.++|+++++|
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~Y 144 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVY 144 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccE
Confidence 589998 998 667789999999999988
No 38
>PHA00616 hypothetical protein
Probab=85.83 E-value=0.43 Score=28.53 Aligned_cols=20 Identities=5% Similarity=-0.012 Sum_probs=19.0
Q ss_pred CccCCCchHHHHHHHhhcCC
Q 045251 63 LRQFSEENLLSLDIAKAANP 82 (163)
Q Consensus 63 ~k~F~~~s~L~~H~r~Ht~e 82 (163)
|+.|...+.|..|++.|+++
T Consensus 8 G~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred hHHHhhHHHHHHHHHHhcCC
Confidence 78999999999999999988
No 39
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=81.51 E-value=0.67 Score=29.18 Aligned_cols=28 Identities=18% Similarity=0.243 Sum_probs=24.4
Q ss_pred CCCCcceeCCccCcccCCchHHHHHhhh
Q 045251 28 SGHVKSYTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 28 htgekp~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
..||.-+.|+-||..|.......+|.+.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4567889999999999999999999764
No 40
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=78.96 E-value=0.9 Score=39.64 Aligned_cols=26 Identities=23% Similarity=0.507 Sum_probs=23.7
Q ss_pred cceeCCccCcccCCchHHHHHhhhcC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
.-|.|.+|+|.|.+..-|+.|+..|.
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 38999999999999999999988775
No 41
>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=75.72 E-value=1.5 Score=32.31 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=17.6
Q ss_pred CcceeCCccCcccCCchHHHHHhhhcCCCCC
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIHRKDRA 61 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~Htgekp 61 (163)
+.-..|-+||+.|.. |++|++.|.|-.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 445689999999975 6999999977554
No 42
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=74.96 E-value=0.83 Score=37.81 Aligned_cols=52 Identities=21% Similarity=0.277 Sum_probs=43.1
Q ss_pred cceeCCccCcccCCchHHHHHhh--hcCCC--CCC-------CccCCCchHHHHHHHhhcCCC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMN--IHRKD--RAK-------LRQFSEENLLSLDIAKAANPS 83 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r--~Htge--kpy-------~k~F~~~s~L~~H~r~Ht~e~ 83 (163)
.++.|..|...|.....|..|.+ .|.++ +++ ++.|.+...+..|..+|++..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 47888889999999999999988 78888 776 578888888888888887763
No 43
>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=72.68 E-value=3.1 Score=24.14 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=14.8
Q ss_pred CCcceeCCccCcccCCc----hHHHHHh
Q 045251 30 HVKSYTCAFCKRGFSNA----QALGGHM 53 (163)
Q Consensus 30 gekp~~C~~Cgk~F~~~----~~L~~H~ 53 (163)
+....+|.+|++.+... ..|..|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34567899999988764 5777776
No 44
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.12 E-value=4.3 Score=24.36 Aligned_cols=23 Identities=22% Similarity=0.638 Sum_probs=16.3
Q ss_pred cceeCCccCcccCCc-----hHHHHHhh
Q 045251 32 KSYTCAFCKRGFSNA-----QALGGHMN 54 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~-----~~L~~H~r 54 (163)
..-.|.+|++.+... +.|.+|++
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 345799999988654 46666665
No 45
>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=66.37 E-value=3.7 Score=32.67 Aligned_cols=26 Identities=15% Similarity=0.452 Sum_probs=20.7
Q ss_pred CcceeCCccCcccCCchHHHHHhhhc
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIH 56 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~H 56 (163)
+..|.|..|+|.|.-...+..|+..-
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhc
Confidence 45799999999999999999998643
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=60.53 E-value=6.2 Score=32.53 Aligned_cols=52 Identities=23% Similarity=0.381 Sum_probs=44.2
Q ss_pred CcceeCCccCcccCCchHHHHHhhhcCCCCCC-------CccCCCchHHHHHHHhhcCC
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIHRKDRAK-------LRQFSEENLLSLDIAKAANP 82 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~Htgekpy-------~k~F~~~s~L~~H~r~Ht~e 82 (163)
.+.+.|..|...|........|.+.|.+++++ ...|.....+..|.+.|...
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (467)
T COG5048 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89 (467)
T ss_pred CchhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhccccccc
Confidence 46789999999999999999999999999997 56777777888888776544
No 47
>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=57.43 E-value=4 Score=21.99 Aligned_cols=26 Identities=15% Similarity=0.543 Sum_probs=14.1
Q ss_pred eeCCccCcccCCchHHHHHhhhcCCCC
Q 045251 34 YTCAFCKRGFSNAQALGGHMNIHRKDR 60 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~Htgek 60 (163)
|.|-.|++.| .....+.|...-+.+.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~CItE~e 26 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSCITEAE 26 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-----S---
T ss_pred CeeecCCCCc-CcCCcCCCCcccCccc
Confidence 5799999999 5566777776555443
No 48
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=56.75 E-value=5.4 Score=29.57 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=21.6
Q ss_pred ceeCCccCcccCCchHHHHHhhhcCCCCC
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNIHRKDRA 61 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~Htgekp 61 (163)
-..|-+|||.|. .|++|..+|.|--|
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCCCH
Confidence 457999999996 59999999987655
No 49
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=53.49 E-value=2.5 Score=39.36 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=24.1
Q ss_pred cceeCCccCcccCCchHHHHHhhhcCC
Q 045251 32 KSYTCAFCKRGFSNAQALGGHMNIHRK 58 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~~L~~H~r~Htg 58 (163)
..|.|..|+|.|.--..+..||+.|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 469999999999999999999999863
No 50
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=50.62 E-value=7 Score=28.75 Aligned_cols=15 Identities=27% Similarity=0.642 Sum_probs=13.2
Q ss_pred ceeCCccCcccCCch
Q 045251 33 SYTCAFCKRGFSNAQ 47 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~ 47 (163)
||+|..||+.|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 789999999998765
No 51
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=49.20 E-value=9.4 Score=27.78 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=22.5
Q ss_pred CCcceeCCccCcccCCchHHHHHhhh
Q 045251 30 HVKSYTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 30 gekp~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
|-..|.|-.|.+-|....+|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44579999999999999999999763
No 52
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=46.69 E-value=12 Score=34.07 Aligned_cols=28 Identities=25% Similarity=0.526 Sum_probs=24.1
Q ss_pred CCcceeCCccCcccCCchHHHHHhhhcC
Q 045251 30 HVKSYTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 30 gekp~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
..+|.+|..||.+|........||..|-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999999888888775
No 53
>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=45.69 E-value=17 Score=18.93 Aligned_cols=20 Identities=20% Similarity=0.604 Sum_probs=14.5
Q ss_pred eeCCccCcccCCchHHHHHhh
Q 045251 34 YTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r 54 (163)
..|++|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999988 4566667654
No 54
>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=45.42 E-value=10 Score=21.27 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=11.0
Q ss_pred ceeCCccCcccCCc
Q 045251 33 SYTCAFCKRGFSNA 46 (163)
Q Consensus 33 p~~C~~Cgk~F~~~ 46 (163)
-|+|..||+.|...
T Consensus 5 ~y~C~~Cg~~fe~~ 18 (41)
T smart00834 5 EYRCEDCGHTFEVL 18 (41)
T ss_pred EEEcCCCCCEEEEE
Confidence 48999999988643
No 55
>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=45.22 E-value=16 Score=25.39 Aligned_cols=26 Identities=15% Similarity=0.358 Sum_probs=22.1
Q ss_pred ceeC----CccCcccCCchHHHHHhhhcCC
Q 045251 33 SYTC----AFCKRGFSNAQALGGHMNIHRK 58 (163)
Q Consensus 33 p~~C----~~Cgk~F~~~~~L~~H~r~Htg 58 (163)
-|.| ..|+..+.+...+..|.+.+.|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3789 8999999999999999886653
No 56
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=41.52 E-value=14 Score=19.07 Aligned_cols=10 Identities=20% Similarity=0.660 Sum_probs=8.4
Q ss_pred cceeCCccCc
Q 045251 32 KSYTCAFCKR 41 (163)
Q Consensus 32 kp~~C~~Cgk 41 (163)
-+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4799999985
No 57
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=41.05 E-value=14 Score=25.75 Aligned_cols=15 Identities=27% Similarity=0.395 Sum_probs=12.5
Q ss_pred CcceeCCccCcccCC
Q 045251 31 VKSYTCAFCKRGFSN 45 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~ 45 (163)
.+|++|..||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 379999999998863
No 58
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=40.63 E-value=15 Score=21.01 Aligned_cols=14 Identities=21% Similarity=0.719 Sum_probs=11.9
Q ss_pred ceeCCccCcccCCc
Q 045251 33 SYTCAFCKRGFSNA 46 (163)
Q Consensus 33 p~~C~~Cgk~F~~~ 46 (163)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999988653
No 59
>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=40.26 E-value=15 Score=19.18 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=8.4
Q ss_pred eCCccCcccC
Q 045251 35 TCAFCKRGFS 44 (163)
Q Consensus 35 ~C~~Cgk~F~ 44 (163)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6999998885
No 60
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=39.82 E-value=14 Score=26.39 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.0
Q ss_pred CCCcceeCCccCcccCCchHHHHHhh
Q 045251 29 GHVKSYTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 29 tgekp~~C~~Cgk~F~~~~~L~~H~r 54 (163)
.|-..|.|-+|.+-|.+..+|..|.+
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhc
Confidence 34456899999999999999999875
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=38.25 E-value=7.6 Score=30.67 Aligned_cols=24 Identities=25% Similarity=0.603 Sum_probs=18.5
Q ss_pred CcceeCCccCcccCCchHHHHHhh
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r 54 (163)
+|...|++|++.|....-+....+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 467899999999998766655554
No 62
>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=37.88 E-value=15 Score=21.27 Aligned_cols=15 Identities=33% Similarity=0.713 Sum_probs=11.4
Q ss_pred ceeCCccCcccCCch
Q 045251 33 SYTCAFCKRGFSNAQ 47 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~ 47 (163)
-|+|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 488999998886543
No 63
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=36.68 E-value=19 Score=30.81 Aligned_cols=23 Identities=26% Similarity=0.673 Sum_probs=21.0
Q ss_pred ceeCCccCcccCCchHHHHHhhh
Q 045251 33 SYTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
.+.|-.|.+.|..+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 46899999999999999999974
No 64
>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=35.91 E-value=17 Score=21.66 Aligned_cols=14 Identities=29% Similarity=0.748 Sum_probs=11.1
Q ss_pred ceeCCccCcccCCc
Q 045251 33 SYTCAFCKRGFSNA 46 (163)
Q Consensus 33 p~~C~~Cgk~F~~~ 46 (163)
-|+|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 48899999988644
No 65
>PLN02294 cytochrome c oxidase subunit Vb
Probab=35.17 E-value=20 Score=27.66 Aligned_cols=15 Identities=33% Similarity=0.718 Sum_probs=12.7
Q ss_pred CcceeCCccCcccCC
Q 045251 31 VKSYTCAFCKRGFSN 45 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~ 45 (163)
.+|+.|.+||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 479999999998864
No 66
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=34.75 E-value=20 Score=25.29 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=13.1
Q ss_pred ceeCCccCcccCCch
Q 045251 33 SYTCAFCKRGFSNAQ 47 (163)
Q Consensus 33 p~~C~~Cgk~F~~~~ 47 (163)
||+|..||..|....
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 789999999998754
No 67
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=34.47 E-value=21 Score=31.69 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=19.6
Q ss_pred eeCCccCcccCCchHHHHHhh
Q 045251 34 YTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r 54 (163)
+.|.+|.|.|.+..+|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999999999975
No 68
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=33.13 E-value=30 Score=34.60 Aligned_cols=28 Identities=32% Similarity=0.558 Sum_probs=24.7
Q ss_pred CCCCcceeCCccCcccCCchHHHHHhhh
Q 045251 28 SGHVKSYTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 28 htgekp~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
|.-.|.|+|+.|+..|.....|..|||.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccc
Confidence 3445889999999999999999999987
No 69
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=32.94 E-value=18 Score=20.99 Aligned_cols=15 Identities=20% Similarity=0.704 Sum_probs=9.9
Q ss_pred cceeCCccCcccCCc
Q 045251 32 KSYTCAFCKRGFSNA 46 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~ 46 (163)
-|+.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 589999999998653
No 70
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=32.24 E-value=12 Score=30.66 Aligned_cols=23 Identities=30% Similarity=0.596 Sum_probs=18.1
Q ss_pred CcceeCCccCcccCCchHHHHHhh
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMN 54 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r 54 (163)
.|| .|-+|++.|.....|..|++
T Consensus 9 ~kp-wcwycnrefddekiliqhqk 31 (341)
T KOG2893|consen 9 DKP-WCWYCNREFDDEKILIQHQK 31 (341)
T ss_pred CCc-eeeecccccchhhhhhhhhh
Confidence 344 58889999988888888875
No 71
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=32.13 E-value=17 Score=29.68 Aligned_cols=33 Identities=21% Similarity=0.543 Sum_probs=24.5
Q ss_pred CCCCCCCcceeCCccCcccCCchHHHHH-hhhcC
Q 045251 25 SSDSGHVKSYTCAFCKRGFSNAQALGGH-MNIHR 57 (163)
Q Consensus 25 ~~~htgekp~~C~~Cgk~F~~~~~L~~H-~r~Ht 57 (163)
...|...|-|+|-+|-|...+...|..| |++|.
T Consensus 26 liqhqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 26 LIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred hhhhhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 3457778899999998877776777776 55664
No 72
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.70 E-value=26 Score=21.36 Aligned_cols=18 Identities=28% Similarity=0.440 Sum_probs=14.0
Q ss_pred CcceeCCccCcccCCchH
Q 045251 31 VKSYTCAFCKRGFSNAQA 48 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~ 48 (163)
++.+.|..||..|.-...
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 468899999998875443
No 73
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=29.47 E-value=20 Score=21.72 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.6
Q ss_pred eCCccCcccCCc
Q 045251 35 TCAFCKRGFSNA 46 (163)
Q Consensus 35 ~C~~Cgk~F~~~ 46 (163)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999998754
No 74
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=28.98 E-value=23 Score=20.54 Aligned_cols=12 Identities=17% Similarity=0.816 Sum_probs=10.1
Q ss_pred cceeCCccCccc
Q 045251 32 KSYTCAFCKRGF 43 (163)
Q Consensus 32 kp~~C~~Cgk~F 43 (163)
++..|.+||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467999999877
No 75
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=27.73 E-value=41 Score=19.11 Aligned_cols=22 Identities=23% Similarity=0.581 Sum_probs=8.6
Q ss_pred cceeCCccCcccCCch--HHHHHh
Q 045251 32 KSYTCAFCKRGFSNAQ--ALGGHM 53 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~~--~L~~H~ 53 (163)
+.|-|++|...|..-. .-+.|.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT
T ss_pred cCeecccccceecCCChHHHHHhh
Confidence 3588999999884333 334554
No 76
>PHA00626 hypothetical protein
Probab=27.40 E-value=33 Score=21.57 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=12.0
Q ss_pred cceeCCccCcccCC
Q 045251 32 KSYTCAFCKRGFSN 45 (163)
Q Consensus 32 kp~~C~~Cgk~F~~ 45 (163)
..|+|..||..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 57999999998864
No 77
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.37 E-value=37 Score=19.99 Aligned_cols=16 Identities=25% Similarity=0.625 Sum_probs=12.4
Q ss_pred eCCccCcccCCchHHH
Q 045251 35 TCAFCKRGFSNAQALG 50 (163)
Q Consensus 35 ~C~~Cgk~F~~~~~L~ 50 (163)
.|.+||+.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5999999998765443
No 78
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=25.29 E-value=46 Score=29.54 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=21.5
Q ss_pred CCCCcceeCCccC-cccCCchHHHHHhh
Q 045251 28 SGHVKSYTCAFCK-RGFSNAQALGGHMN 54 (163)
Q Consensus 28 htgekp~~C~~Cg-k~F~~~~~L~~H~r 54 (163)
|--.+-|.|.+|| +++....++.+|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4446779999999 78888888888864
No 79
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.13 E-value=54 Score=18.87 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=17.1
Q ss_pred eeCCccCcccCCc--hHHHHHhhhcC
Q 045251 34 YTCAFCKRGFSNA--QALGGHMNIHR 57 (163)
Q Consensus 34 ~~C~~Cgk~F~~~--~~L~~H~r~Ht 57 (163)
-.|..||-.|... ..-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4899999877653 46667776664
No 80
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=25.09 E-value=72 Score=27.67 Aligned_cols=48 Identities=19% Similarity=0.224 Sum_probs=37.4
Q ss_pred CcceeCCccCcccCCchHHHHHhhhcCCC----CCC---------------------------CccCCCchHHHHHHHh
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIHRKD----RAK---------------------------LRQFSEENLLSLDIAK 78 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~Htge----kpy---------------------------~k~F~~~s~L~~H~r~ 78 (163)
..|-.|-+|++.|........||..+.|- +-| ++.|......+.||.-
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 34678999999999999999999877652 111 5778888888899874
No 81
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.99 E-value=30 Score=26.11 Aligned_cols=20 Identities=15% Similarity=0.459 Sum_probs=15.3
Q ss_pred CcceeCCccCcccCCchHHH
Q 045251 31 VKSYTCAFCKRGFSNAQALG 50 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~ 50 (163)
.+.++|..||+.|..-..+.
T Consensus 26 ~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 26 RRRRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeeeccccCCcceEeEecc
Confidence 34599999999998765443
No 82
>COG1773 Rubredoxin [Energy production and conversion]
Probab=24.19 E-value=33 Score=21.42 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=10.7
Q ss_pred cceeCCccCcccCC
Q 045251 32 KSYTCAFCKRGFSN 45 (163)
Q Consensus 32 kp~~C~~Cgk~F~~ 45 (163)
+.|+|..||..|.-
T Consensus 2 ~~~~C~~CG~vYd~ 15 (55)
T COG1773 2 KRWRCSVCGYVYDP 15 (55)
T ss_pred CceEecCCceEecc
Confidence 36899999987754
No 83
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.75 E-value=39 Score=19.17 Aligned_cols=12 Identities=25% Similarity=0.667 Sum_probs=7.0
Q ss_pred cceeCCccCccc
Q 045251 32 KSYTCAFCKRGF 43 (163)
Q Consensus 32 kp~~C~~Cgk~F 43 (163)
+-|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 579999999754
No 84
>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=22.61 E-value=47 Score=23.50 Aligned_cols=15 Identities=20% Similarity=0.547 Sum_probs=11.1
Q ss_pred cceeCCccCcccCCc
Q 045251 32 KSYTCAFCKRGFSNA 46 (163)
Q Consensus 32 kp~~C~~Cgk~F~~~ 46 (163)
.|-.|+.||..|...
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 466788888877654
No 85
>PF15269 zf-C2H2_7: Zinc-finger
Probab=21.99 E-value=58 Score=19.61 Aligned_cols=22 Identities=27% Similarity=0.466 Sum_probs=16.6
Q ss_pred eeCCccCcccCCchHHHHHhhh
Q 045251 34 YTCAFCKRGFSNAQALGGHMNI 55 (163)
Q Consensus 34 ~~C~~Cgk~F~~~~~L~~H~r~ 55 (163)
|+|-.|.-...-++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5687887777777888888763
No 86
>PF14077 WD40_alt: Alternative WD40 repeat motif
Probab=21.76 E-value=23 Score=21.30 Aligned_cols=11 Identities=36% Similarity=0.736 Sum_probs=6.8
Q ss_pred cchhcccccCC
Q 045251 152 RITKDLYRSSS 162 (163)
Q Consensus 152 ~~~~~~~~~~~ 162 (163)
-.-|+.|+||+
T Consensus 32 KINrdLfdFSt 42 (48)
T PF14077_consen 32 KINRDLFDFST 42 (48)
T ss_pred HHhHHHHhhhh
Confidence 34566777765
No 87
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.50 E-value=72 Score=23.44 Aligned_cols=21 Identities=10% Similarity=0.232 Sum_probs=16.1
Q ss_pred CcceeCCccCcccCCchHHHH
Q 045251 31 VKSYTCAFCKRGFSNAQALGG 51 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~ 51 (163)
+.-+.|+.||+.|...++..+
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 347889999999987666554
No 88
>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=21.21 E-value=52 Score=18.13 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=8.5
Q ss_pred ceeCCccCcccC
Q 045251 33 SYTCAFCKRGFS 44 (163)
Q Consensus 33 p~~C~~Cgk~F~ 44 (163)
.|+|..||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 478888887544
No 89
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=21.20 E-value=35 Score=20.93 Aligned_cols=27 Identities=26% Similarity=0.440 Sum_probs=15.9
Q ss_pred CcceeCCccCcccCCchHHHHHhhhcC
Q 045251 31 VKSYTCAFCKRGFSNAQALGGHMNIHR 57 (163)
Q Consensus 31 ekp~~C~~Cgk~F~~~~~L~~H~r~Ht 57 (163)
...|+|+.|...|-.--.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 468999999999987777777776664
No 90
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.62 E-value=74 Score=27.52 Aligned_cols=43 Identities=19% Similarity=0.325 Sum_probs=28.4
Q ss_pred CcccceecCCCCCC-----CCCCCCCcceeCCccC-cccCCchHHHHHh
Q 045251 11 EKSSQILWSSDDLD-----SSDSGHVKSYTCAFCK-RGFSNAQALGGHM 53 (163)
Q Consensus 11 ~~~~~~~~~~~~~~-----~~~htgekp~~C~~Cg-k~F~~~~~L~~H~ 53 (163)
.++.+.++.+|..+ -+-|--.+-|.|.+|| +.+.....+-+|.
T Consensus 347 ~k~fdmPLG~DG~PmP~WL~klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 347 GKSFDMPLGPDGLPMPRWLCKLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred cCcccCCCCCCCCCCchHHHHhcCCCcceeeeecccccccchHHHHhhh
Confidence 45555666666653 2334456789999999 6666667777664
No 91
>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=20.60 E-value=50 Score=17.93 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=8.2
Q ss_pred eeCCccCcccC
Q 045251 34 YTCAFCKRGFS 44 (163)
Q Consensus 34 ~~C~~Cgk~F~ 44 (163)
|+|..||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 67888887654
No 92
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.51 E-value=39 Score=21.60 Aligned_cols=13 Identities=15% Similarity=0.774 Sum_probs=10.2
Q ss_pred cceeCCccCcccC
Q 045251 32 KSYTCAFCKRGFS 44 (163)
Q Consensus 32 kp~~C~~Cgk~F~ 44 (163)
.--.|++|++.|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 3457999999886
No 93
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=20.31 E-value=34 Score=26.90 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=0.0
Q ss_pred CcceeCCccCc-ccCCchHHHHHh
Q 045251 31 VKSYTCAFCKR-GFSNAQALGGHM 53 (163)
Q Consensus 31 ekp~~C~~Cgk-~F~~~~~L~~H~ 53 (163)
.+-|.|.+||. .|.-+.++..|.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhc
Confidence 45689999995 344555555553
No 94
>PLN02748 tRNA dimethylallyltransferase
Probab=20.10 E-value=66 Score=28.65 Aligned_cols=24 Identities=21% Similarity=0.427 Sum_probs=20.3
Q ss_pred CcceeCCccCc-ccCCchHHHHHhh
Q 045251 31 VKSYTCAFCKR-GFSNAQALGGHMN 54 (163)
Q Consensus 31 ekp~~C~~Cgk-~F~~~~~L~~H~r 54 (163)
.+.|.|..|++ .+........|++
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhc
Confidence 47789999997 7888888888875
Done!