Query 046730
Match_columns 214
No_of_seqs 272 out of 1639
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 03:56:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046730hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3623 Homeobox transcription 98.8 6.2E-10 1.3E-14 108.1 0.8 77 46-128 904-980 (1007)
2 KOG2462 C2H2-type Zn-finger pr 98.7 4.5E-09 9.8E-14 92.4 1.1 85 20-109 159-255 (279)
3 KOG2462 C2H2-type Zn-finger pr 98.6 1.9E-08 4.1E-13 88.5 2.4 61 42-109 167-227 (279)
4 KOG3623 Homeobox transcription 98.3 1.6E-07 3.5E-12 91.7 0.5 68 42-109 246-321 (1007)
5 KOG3576 Ovo and related transc 98.2 9.6E-07 2.1E-11 75.3 2.3 56 49-109 130-185 (267)
6 PF13465 zf-H2C2_2: Zinc-finge 98.1 1.6E-06 3.4E-11 50.4 1.7 26 51-81 1-26 (26)
7 KOG1074 Transcriptional repres 97.8 7.1E-06 1.5E-10 81.3 1.7 46 48-98 617-662 (958)
8 KOG1074 Transcriptional repres 97.7 1.5E-05 3.3E-10 79.1 1.3 55 42-101 885-939 (958)
9 PHA02768 hypothetical protein; 97.5 2.1E-05 4.5E-10 53.8 -0.1 36 69-106 5-40 (55)
10 KOG3576 Ovo and related transc 97.4 6.8E-05 1.5E-09 64.2 1.6 78 16-98 111-203 (267)
11 PHA00616 hypothetical protein 97.4 4.1E-05 8.9E-10 50.1 0.0 32 69-100 1-32 (44)
12 PF00096 zf-C2H2: Zinc finger, 96.7 0.00047 1E-08 38.1 0.4 23 70-92 1-23 (23)
13 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0011 2.4E-08 38.0 0.4 25 69-93 1-25 (27)
14 PHA02768 hypothetical protein; 96.2 0.0037 8E-08 42.8 2.3 34 46-86 15-48 (55)
15 PHA00733 hypothetical protein 95.9 0.0028 6.1E-08 50.3 0.8 54 47-108 57-110 (128)
16 PF13894 zf-C2H2_4: C2H2-type 95.9 0.0034 7.3E-08 34.2 0.8 23 70-92 1-23 (24)
17 PHA00733 hypothetical protein 95.7 0.013 2.8E-07 46.5 3.9 52 20-92 71-122 (128)
18 smart00355 ZnF_C2H2 zinc finge 95.3 0.0098 2.1E-07 32.5 1.4 24 70-93 1-24 (26)
19 PF13465 zf-H2C2_2: Zinc-finge 94.7 0.003 6.5E-08 36.4 -1.9 23 84-106 1-23 (26)
20 KOG3608 Zn finger proteins [Ge 94.1 0.028 6.1E-07 51.8 2.0 49 47-101 274-323 (467)
21 PF09237 GAGA: GAGA factor; I 93.7 0.043 9.3E-07 37.1 1.7 32 66-97 21-52 (54)
22 KOG3608 Zn finger proteins [Ge 93.4 0.071 1.5E-06 49.3 3.2 65 40-109 183-249 (467)
23 PF12874 zf-met: Zinc-finger o 93.1 0.027 5.9E-07 31.5 0.0 23 70-92 1-23 (25)
24 PHA00732 hypothetical protein 93.0 0.033 7.2E-07 40.7 0.4 22 69-90 1-22 (79)
25 KOG2893 Zn finger protein [Gen 92.6 0.36 7.8E-06 42.6 6.3 33 51-92 25-58 (341)
26 PLN03086 PRLI-interacting fact 92.6 0.052 1.1E-06 53.0 1.3 52 48-105 488-549 (567)
27 PHA00732 hypothetical protein 91.5 0.2 4.4E-06 36.6 3.0 37 46-93 11-48 (79)
28 PF12171 zf-C2H2_jaz: Zinc-fin 91.3 0.077 1.7E-06 30.5 0.5 22 70-91 2-23 (27)
29 COG5189 SFP1 Putative transcri 90.5 0.14 3E-06 46.8 1.5 25 66-90 395-419 (423)
30 PLN03086 PRLI-interacting fact 87.7 0.29 6.3E-06 47.9 1.7 50 49-107 465-514 (567)
31 PF13913 zf-C2HC_2: zinc-finge 87.0 0.32 6.9E-06 27.8 1.0 21 70-91 3-23 (25)
32 PRK04860 hypothetical protein; 86.2 0.21 4.6E-06 41.1 -0.1 36 68-107 118-153 (160)
33 smart00451 ZnF_U1 U1-like zinc 83.8 0.52 1.1E-05 28.1 0.9 23 69-91 3-25 (35)
34 PF13909 zf-H2C2_5: C2H2-type 82.9 0.5 1.1E-05 26.1 0.5 22 70-92 1-22 (24)
35 PRK04860 hypothetical protein; 79.6 1 2.3E-05 37.1 1.5 30 49-83 128-157 (160)
36 PF05605 zf-Di19: Drought indu 79.4 2.3 5E-05 28.3 2.9 40 48-92 13-52 (54)
37 COG5048 FOG: Zn-finger [Genera 74.2 1.3 2.8E-05 39.1 0.7 54 43-101 296-355 (467)
38 PF12756 zf-C2H2_2: C2H2 type 73.2 1.7 3.6E-05 31.2 1.0 24 69-92 50-73 (100)
39 KOG3993 Transcription factor ( 67.5 1.3 2.9E-05 41.8 -0.7 27 68-94 355-381 (500)
40 COG5189 SFP1 Putative transcri 64.2 3.3 7.2E-05 38.1 1.1 44 66-109 346-410 (423)
41 KOG3993 Transcription factor ( 60.9 4 8.7E-05 38.7 1.1 26 68-93 294-319 (500)
42 PHA00616 hypothetical protein 58.7 4.8 0.0001 26.3 0.9 26 44-74 9-34 (44)
43 KOG4167 Predicted DNA-binding 46.2 4 8.6E-05 41.2 -1.5 28 67-94 790-817 (907)
44 PF05443 ROS_MUCR: ROS/MUCR tr 46.1 13 0.00028 29.8 1.6 29 68-99 71-99 (132)
45 KOG2186 Cell growth-regulating 45.3 13 0.00029 33.0 1.7 47 22-90 3-49 (276)
46 COG4049 Uncharacterized protei 44.5 7.3 0.00016 27.0 -0.0 26 66-91 14-39 (65)
47 KOG3408 U1-like Zn-finger-cont 44.1 13 0.00027 29.6 1.3 34 65-102 53-86 (129)
48 smart00614 ZnF_BED BED zinc fi 41.9 16 0.00035 23.7 1.3 25 69-93 18-48 (50)
49 PF02892 zf-BED: BED zinc fing 40.4 15 0.00032 23.0 1.0 24 66-89 13-40 (45)
50 KOG2893 Zn finger protein [Gen 38.1 10 0.00022 33.7 -0.1 21 71-91 12-32 (341)
51 COG5112 UFD2 U1-like Zn-finger 31.9 20 0.00043 27.9 0.6 35 65-103 51-85 (126)
52 PF04959 ARS2: Arsenite-resist 31.8 21 0.00046 30.8 0.8 31 66-96 74-104 (214)
53 KOG2071 mRNA cleavage and poly 31.6 23 0.0005 34.9 1.1 31 66-96 415-445 (579)
54 COG4957 Predicted transcriptio 28.3 33 0.00072 27.8 1.3 27 70-99 77-103 (148)
55 KOG3352 Cytochrome c oxidase, 22.0 30 0.00065 28.4 0.0 15 66-80 130-144 (153)
56 PF07055 Eno-Rase_FAD_bd: Enoy 21.0 34 0.00074 24.1 0.1 13 20-32 49-61 (65)
No 1
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.85 E-value=6.2e-10 Score=108.11 Aligned_cols=77 Identities=25% Similarity=0.316 Sum_probs=69.3
Q ss_pred cCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHhhhhhccccCCCCCCCCCC
Q 046730 46 SDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQATRHLVSSHYQHYHPMLSNL 125 (214)
Q Consensus 46 s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~~~~~~s~~~~~~p~~s~~ 125 (214)
....+.|.+|.--|+ |.|||+|.+|.|.|+...+|..|+|.|.|||||.|..|++++.. ..||.+|.|+.++.+
T Consensus 904 FqKqSSLaRHKYEHs-----GqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSH-SGSYSQHMNHRYSYC 977 (1007)
T KOG3623|consen 904 FQKQSSLARHKYEHS-----GQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSH-SGSYSQHMNHRYSYC 977 (1007)
T ss_pred HHhhHHHHHhhhhhc-----CCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccc-ccchHhhhccchhcc
Confidence 445667999999999 99999999999999999999999999999999999999999888 678888999988877
Q ss_pred CCC
Q 046730 126 SPR 128 (214)
Q Consensus 126 ~p~ 128 (214)
-+-
T Consensus 978 Kpy 980 (1007)
T KOG3623|consen 978 KPY 980 (1007)
T ss_pred cch
Confidence 553
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.69 E-value=4.5e-09 Score=92.43 Aligned_cols=85 Identities=14% Similarity=0.153 Sum_probs=61.4
Q ss_pred ceeeccccCCCCCCCCCC------------ccCcCccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhh
Q 046730 20 LKLFGFNISEDHNKNTDS------------FATSKTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGG 87 (214)
Q Consensus 20 ~k~fg~~~~~~~~~~~~~------------~~~~~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~ 87 (214)
-|-|-|++|+-.+..... .-.-+........-|.-|+|+|| |||||.|..|+|.|....+|+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHT-----GEKPF~C~hC~kAFADRSNLRA 233 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHT-----GEKPFSCPHCGKAFADRSNLRA 233 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccccccc-----CCCCccCCcccchhcchHHHHH
Confidence 566777777554332211 00224555555666777888888 8999999999999998889999
Q ss_pred hhhhccCCcchhHHHHHHHhhh
Q 046730 88 HQNAHKKERQLLKRAQLQATRH 109 (214)
Q Consensus 88 Hqr~H~gERpf~~r~~~~~~~~ 109 (214)
|+++|.+.|.|.|..+.+.+..
T Consensus 234 HmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 234 HMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred HHHhhcCCccccCcchhhHHHH
Confidence 9999988888888888876654
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.60 E-value=1.9e-08 Score=88.54 Aligned_cols=61 Identities=21% Similarity=0.268 Sum_probs=54.6
Q ss_pred CccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHhhh
Q 046730 42 KTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQATRH 109 (214)
Q Consensus 42 ~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~~~ 109 (214)
+..+-+.--.|+.|+|+|+ -+++|.+|||.|.+..-|++|+|+|+|||||.|..+.+++..
T Consensus 167 C~K~YvSmpALkMHirTH~-------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 167 CGKVYVSMPALKMHIRTHT-------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred CCceeeehHHHhhHhhccC-------CCcccccccccccchHHhhcccccccCCCCccCCcccchhcc
Confidence 5666677778999999998 689999999999999999999999999999999988877754
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.29 E-value=1.6e-07 Score=91.68 Aligned_cols=68 Identities=19% Similarity=0.307 Sum_probs=57.9
Q ss_pred CccccCChhHHHHHhhhccCCC--------CCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHhhh
Q 046730 42 KTHLSDEALELETHISFQSNDN--------TNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQATRH 109 (214)
Q Consensus 42 ~~~~s~~ss~L~~H~r~ht~~~--------~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~~~ 109 (214)
++-+...+..|.+|+.+|..+. +...|.|+|..|+|.|+...+|..|.|+|.|||||.|.-|.+++..
T Consensus 246 CsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 246 CSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSH 321 (1007)
T ss_pred hhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccccccc
Confidence 3556678899999999886332 2245899999999999999999999999999999999999988876
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.16 E-value=9.6e-07 Score=75.33 Aligned_cols=56 Identities=20% Similarity=0.308 Sum_probs=49.8
Q ss_pred hhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHhhh
Q 046730 49 ALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQATRH 109 (214)
Q Consensus 49 ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~~~ 109 (214)
---|.+|++.|. ..|.+.|.+|+|.|...-.|.+|.|+|+|-|||+|..+.+++.+
T Consensus 130 QRmlnrh~kch~-----~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 130 QRMLNRHLKCHS-----DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred HHHHHHHhhhcc-----HHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 344778999998 88999999999999999999999999999999999999887765
No 6
>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=98.10 E-value=1.6e-06 Score=50.40 Aligned_cols=26 Identities=31% Similarity=0.818 Sum_probs=23.8
Q ss_pred HHHHHhhhccCCCCCCCcccccCccCCccCC
Q 046730 51 ELETHISFQSNDNTNITRKYECQYCCREFAN 81 (214)
Q Consensus 51 ~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~ 81 (214)
+|.+|+++|+ ++|+|.|.+|++.|.+
T Consensus 1 ~l~~H~~~H~-----~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHT-----GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHS-----SSSSEEESSSSEEESS
T ss_pred CHHHHhhhcC-----CCCCCCCCCCcCeeCc
Confidence 4889999999 9999999999999864
No 7
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.82 E-value=7.1e-06 Score=81.35 Aligned_cols=46 Identities=24% Similarity=0.452 Sum_probs=41.6
Q ss_pred ChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcch
Q 046730 48 EALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQL 98 (214)
Q Consensus 48 ~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf 98 (214)
=++.|+.|.|+|+ |||||+|.+|+|.|..+.+|+.|+-+|+..-++
T Consensus 617 C~saLqmHyrtHt-----GERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 617 CPSALQMHYRTHT-----GERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred chhhhhhhhhccc-----CcCccccccccchhccccchhhcccccccCccc
Confidence 3678999999999 999999999999999999999999999865443
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.67 E-value=1.5e-05 Score=79.10 Aligned_cols=55 Identities=18% Similarity=0.305 Sum_probs=49.5
Q ss_pred CccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHH
Q 046730 42 KTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKR 101 (214)
Q Consensus 42 ~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r 101 (214)
+......+..|..|+|+|+ ++|||.|.+|++.|.....|+.||.+|.+..++.+|
T Consensus 885 Cgk~FsSSsALqiH~rTHt-----g~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 885 CGKQFSSSAALEIHMRTHT-----GPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred chhcccchHHHHHhhhcCC-----CCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 4556677888999999999 999999999999999999999999999999888887
No 9
>PHA02768 hypothetical protein; Provisional
Probab=97.51 E-value=2.1e-05 Score=53.81 Aligned_cols=36 Identities=19% Similarity=0.371 Sum_probs=29.2
Q ss_pred ccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHH
Q 046730 69 KYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQA 106 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~ 106 (214)
-|+|+.|++.|.+.++|..|+++|+ ++++|-.+...
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~ 40 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRI 40 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccce
Confidence 3899999999999999999999998 45655444443
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=97.40 E-value=6.8e-05 Score=64.19 Aligned_cols=78 Identities=18% Similarity=0.299 Sum_probs=58.7
Q ss_pred CCCCceeeccccCCCCCCCC--------------CCccCcCccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCC
Q 046730 16 TRSTLKLFGFNISEDHNKNT--------------DSFATSKTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFAN 81 (214)
Q Consensus 16 ~~~~~k~fg~~~~~~~~~~~--------------~~~~~~~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~ 81 (214)
+.++--+|-|.||.-.-... .---+-+..+..+--.|++|+|+|+ |.|||+|..|+|.|.+
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht-----gvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT-----GVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc-----CccccchhhhhHHHHh
Confidence 55667788888887532111 0001347788889999999999999 9999999999999999
Q ss_pred cchhhhhhh-hccCCcch
Q 046730 82 SQALGGHQN-AHKKERQL 98 (214)
Q Consensus 82 s~aL~~Hqr-~H~gERpf 98 (214)
...|..|.+ +|.-...|
T Consensus 186 rcsleshl~kvhgv~~~y 203 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQHQY 203 (267)
T ss_pred hccHHHHHHHHcCchHHH
Confidence 999999985 56443333
No 11
>PHA00616 hypothetical protein
Probab=97.37 E-value=4.1e-05 Score=50.08 Aligned_cols=32 Identities=22% Similarity=0.373 Sum_probs=29.8
Q ss_pred ccccCccCCccCCcchhhhhhhhccCCcchhH
Q 046730 69 KYECQYCCREFANSQALGGHQNAHKKERQLLK 100 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~ 100 (214)
+|.|..|++.|.+.+.|..|++.|++++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 58999999999999999999999999998865
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=96.72 E-value=0.00047 Score=38.11 Aligned_cols=23 Identities=30% Similarity=0.777 Sum_probs=21.3
Q ss_pred cccCccCCccCCcchhhhhhhhc
Q 046730 70 YECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
|.|..|++.|.+...|..|++.|
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 13
>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=96.36 E-value=0.0011 Score=38.00 Aligned_cols=25 Identities=32% Similarity=0.716 Sum_probs=23.1
Q ss_pred ccccCccCCccCCcchhhhhhhhcc
Q 046730 69 KYECQYCCREFANSQALGGHQNAHK 93 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr~H~ 93 (214)
+|+|..|++.|.....|..|++.|.
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 5899999999999999999998875
No 14
>PHA02768 hypothetical protein; Provisional
Probab=96.20 E-value=0.0037 Score=42.78 Aligned_cols=34 Identities=12% Similarity=0.052 Sum_probs=29.0
Q ss_pred cCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhh
Q 046730 46 SDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALG 86 (214)
Q Consensus 46 s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~ 86 (214)
...+++|..|+++|+ ++|+|..|+|.|.+...|.
T Consensus 15 Fs~~~~L~~H~r~H~-------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 15 YIKRKSMITHLRKHN-------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred eccHHHHHHHHHhcC-------CcccCCcccceecccceeE
Confidence 446678999999997 6899999999999877665
No 15
>PHA00733 hypothetical protein
Probab=95.91 E-value=0.0028 Score=50.28 Aligned_cols=54 Identities=22% Similarity=0.266 Sum_probs=39.3
Q ss_pred CChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHhh
Q 046730 47 DEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQATR 108 (214)
Q Consensus 47 ~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~~ 108 (214)
...+.|.+|+..+ ++++|.|..|++.|.....|..|++.| +++|.|..+...+.
T Consensus 57 ~~~~~l~~~~~~~------~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~ 110 (128)
T PHA00733 57 DESSYLYKLLTSK------AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFR 110 (128)
T ss_pred cchHHHHhhcccC------CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccC
Confidence 3444466664433 578999999999999999999999976 34677776655443
No 16
>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=95.88 E-value=0.0034 Score=34.18 Aligned_cols=23 Identities=26% Similarity=0.743 Sum_probs=19.4
Q ss_pred cccCccCCccCCcchhhhhhhhc
Q 046730 70 YECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
|.|.+|++.|.+...|..|++.|
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 68999999999999999999875
No 17
>PHA00733 hypothetical protein
Probab=95.74 E-value=0.013 Score=46.51 Aligned_cols=52 Identities=17% Similarity=0.330 Sum_probs=40.2
Q ss_pred ceeeccccCCCCCCCCCCccCcCccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhc
Q 046730 20 LKLFGFNISEDHNKNTDSFATSKTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 20 ~k~fg~~~~~~~~~~~~~~~~~~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
.+.|-|+.|+ ........|..|++++. ++|.|..|++.|.....|..|+...
T Consensus 71 ~kPy~C~~Cg--------------k~Fss~s~L~~H~r~h~-------~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 71 VSPYVCPLCL--------------MPFSSSVSLKQHIRYTE-------HSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCCccCCCCC--------------CcCCCHHHHHHHHhcCC-------cCccCCCCCCccCCHHHHHHHHHHh
Confidence 4567666663 33556778999998764 4699999999999999999998643
No 18
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.31 E-value=0.0098 Score=32.55 Aligned_cols=24 Identities=33% Similarity=0.703 Sum_probs=21.7
Q ss_pred cccCccCCccCCcchhhhhhhhcc
Q 046730 70 YECQYCCREFANSQALGGHQNAHK 93 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H~ 93 (214)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 19
>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=94.72 E-value=0.003 Score=36.42 Aligned_cols=23 Identities=17% Similarity=0.096 Sum_probs=19.3
Q ss_pred hhhhhhhhccCCcchhHHHHHHH
Q 046730 84 ALGGHQNAHKKERQLLKRAQLQA 106 (214)
Q Consensus 84 aL~~Hqr~H~gERpf~~r~~~~~ 106 (214)
+|..|+++|++||+|.|..+...
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKS 23 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCe
Confidence 48899999999999999766543
No 20
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=94.13 E-value=0.028 Score=51.85 Aligned_cols=49 Identities=22% Similarity=0.412 Sum_probs=40.2
Q ss_pred CChhHHHHHhhh-ccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHH
Q 046730 47 DEALELETHISF-QSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKR 101 (214)
Q Consensus 47 ~~ss~L~~H~r~-ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r 101 (214)
...+.|.+|++. |. ..|||+|+.|.+.|.+...|.+|..+|. +-.|.|.
T Consensus 274 ~~~ssL~~H~r~rHs-----~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~ 323 (467)
T KOG3608|consen 274 SSASSLTTHIRYRHS-----KDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCE 323 (467)
T ss_pred CChHHHHHHHHhhhc-----cCCCccccchhhhhccHHHHHHHHHhcc-ccceecC
Confidence 356779999998 55 7899999999999999999999999887 4344443
No 21
>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=93.67 E-value=0.043 Score=37.10 Aligned_cols=32 Identities=16% Similarity=0.282 Sum_probs=23.4
Q ss_pred CCcccccCccCCccCCcchhhhhhhhccCCcc
Q 046730 66 ITRKYECQYCCREFANSQALGGHQNAHKKERQ 97 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERp 97 (214)
.+.|-.|.+|+..+.++.+|.+|+.++.+.|+
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 67899999999999999999999988776654
No 22
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=93.39 E-value=0.071 Score=49.27 Aligned_cols=65 Identities=15% Similarity=0.166 Sum_probs=54.3
Q ss_pred CcCccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhcc--CCcchhHHHHHHHhhh
Q 046730 40 TSKTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHK--KERQLLKRAQLQATRH 109 (214)
Q Consensus 40 ~~~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~--gERpf~~r~~~~~~~~ 109 (214)
..+..+..++..|..|+|.|+ ++|...|..|++-|.+...|--|.+..+ ...+|.|..+.+++..
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs-----~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaT 249 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHS-----NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFAT 249 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcC-----CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhH
Confidence 457778899999999999999 9999999999999999999999987543 3457888877665543
No 23
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.05 E-value=0.027 Score=31.45 Aligned_cols=23 Identities=22% Similarity=0.668 Sum_probs=20.8
Q ss_pred cccCccCCccCCcchhhhhhhhc
Q 046730 70 YECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
|.|..|.+.|.+...|..|++.+
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 67999999999999999998754
No 24
>PHA00732 hypothetical protein
Probab=92.99 E-value=0.033 Score=40.70 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=14.1
Q ss_pred ccccCccCCccCCcchhhhhhh
Q 046730 69 KYECQYCCREFANSQALGGHQN 90 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr 90 (214)
||.|..|++.|.+...|..|++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhh
Confidence 3566666666666666666665
No 25
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.64 E-value=0.36 Score=42.61 Aligned_cols=33 Identities=21% Similarity=0.484 Sum_probs=23.9
Q ss_pred HHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhh-hhc
Q 046730 51 ELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQ-NAH 92 (214)
Q Consensus 51 ~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hq-r~H 92 (214)
-|..|++. |-|+|.+|.|++.+.-.|..|. ++|
T Consensus 25 iliqhqka---------khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 25 ILIQHQKA---------KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred hhhhhhhh---------ccceeeeehhhhccCCCceeehhhhh
Confidence 46677755 4499999999888777777663 444
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=92.64 E-value=0.052 Score=52.97 Aligned_cols=52 Identities=13% Similarity=0.195 Sum_probs=30.4
Q ss_pred ChhHHHHHhhhccCCCCCCCcccccCccCCccCC----------cchhhhhhhhccCCcchhHHHHHH
Q 046730 48 EALELETHISFQSNDNTNITRKYECQYCCREFAN----------SQALGGHQNAHKKERQLLKRAQLQ 105 (214)
Q Consensus 48 ~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~----------s~aL~~Hqr~H~gERpf~~r~~~~ 105 (214)
.+..|..|+++|. ++|++.|.+|++.|.. ...|..|..++ +.|++.|..|.+
T Consensus 488 ~R~~L~~H~~thC-----p~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk 549 (567)
T PLN03086 488 EKEQMVQHQASTC-----PLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGR 549 (567)
T ss_pred chhHHHhhhhccC-----CCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCC
Confidence 4455666666666 6666666666666632 12566666654 566666655543
No 27
>PHA00732 hypothetical protein
Probab=91.48 E-value=0.2 Score=36.55 Aligned_cols=37 Identities=16% Similarity=0.392 Sum_probs=27.7
Q ss_pred cCChhHHHHHhhh-ccCCCCCCCcccccCccCCccCCcchhhhhhhhcc
Q 046730 46 SDEALELETHISF-QSNDNTNITRKYECQYCCREFANSQALGGHQNAHK 93 (214)
Q Consensus 46 s~~ss~L~~H~r~-ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~ 93 (214)
......|..|++. |. + +.|..|++.|. .|..|...+.
T Consensus 11 F~s~s~Lk~H~r~~H~-----~---~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 11 TVTLFALKQHARRNHT-----L---TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred cCCHHHHHHHhhcccC-----C---CccCCCCCEeC---ChhhhhcccC
Confidence 4567789999985 55 3 58999999998 4777775443
No 28
>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=91.33 E-value=0.077 Score=30.46 Aligned_cols=22 Identities=23% Similarity=0.597 Sum_probs=20.1
Q ss_pred cccCccCCccCCcchhhhhhhh
Q 046730 70 YECQYCCREFANSQALGGHQNA 91 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~ 91 (214)
|.|..|++.|.+...+..|++.
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 7899999999999999999874
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.50 E-value=0.14 Score=46.83 Aligned_cols=25 Identities=24% Similarity=0.620 Sum_probs=22.0
Q ss_pred CCcccccCccCCccCCcchhhhhhh
Q 046730 66 ITRKYECQYCCREFANSQALGGHQN 90 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s~aL~~Hqr 90 (214)
..|||.|.+|+|++++-..|..|..
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 5699999999999999999988853
No 30
>PLN03086 PRLI-interacting factor K; Provisional
Probab=87.68 E-value=0.29 Score=47.87 Aligned_cols=50 Identities=18% Similarity=0.225 Sum_probs=39.4
Q ss_pred hhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHh
Q 046730 49 ALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQAT 107 (214)
Q Consensus 49 ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~ 107 (214)
...|..|+++++ +++.|. |++.+ ....|..|++.|..+|++.|+-|....
T Consensus 465 ~s~LekH~~~~H-------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 465 QGEMEKHMKVFH-------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred hHHHHHHHHhcC-------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 466888988876 678998 98755 558899999999999999988665443
No 31
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.04 E-value=0.32 Score=27.76 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=17.6
Q ss_pred cccCccCCccCCcchhhhhhhh
Q 046730 70 YECQYCCREFANSQALGGHQNA 91 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~ 91 (214)
..|..|++.| ....|..|+++
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 67889999764
No 32
>PRK04860 hypothetical protein; Provisional
Probab=86.18 E-value=0.21 Score=41.14 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=29.5
Q ss_pred cccccCccCCccCCcchhhhhhhhccCCcchhHHHHHHHh
Q 046730 68 RKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQLQAT 107 (214)
Q Consensus 68 Kpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~~~~~ 107 (214)
-+|.|. |++ ....+.+|.++|+++++|.|+.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 468998 987 666789999999999999998876543
No 33
>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=83.78 E-value=0.52 Score=28.07 Aligned_cols=23 Identities=17% Similarity=0.556 Sum_probs=19.5
Q ss_pred ccccCccCCccCCcchhhhhhhh
Q 046730 69 KYECQYCCREFANSQALGGHQNA 91 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr~ 91 (214)
+|.|++|.+.|.....+..|.+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888753
No 34
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=82.95 E-value=0.5 Score=26.06 Aligned_cols=22 Identities=27% Similarity=0.599 Sum_probs=16.3
Q ss_pred cccCccCCccCCcchhhhhhhhc
Q 046730 70 YECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
|.|..|.-... ...|..|++.|
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 67999987776 77899998875
No 35
>PRK04860 hypothetical protein; Provisional
Probab=79.62 E-value=1 Score=37.08 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=25.5
Q ss_pred hhHHHHHhhhccCCCCCCCcccccCccCCccCCcc
Q 046730 49 ALELETHISFQSNDNTNITRKYECQYCCREFANSQ 83 (214)
Q Consensus 49 ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~ 83 (214)
...+.+|.++|+ ++++|.|..|++.|....
T Consensus 128 ~~~~rrH~ri~~-----g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 128 QLTVRRHNRVVR-----GEAVYRCRRCGETLVFKG 157 (160)
T ss_pred eCHHHHHHHHhc-----CCccEECCCCCceeEEec
Confidence 445889999999 999999999999887543
No 36
>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=79.36 E-value=2.3 Score=28.28 Aligned_cols=40 Identities=18% Similarity=0.298 Sum_probs=26.2
Q ss_pred ChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhhhc
Q 046730 48 EALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 48 ~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
+...|..|...... ...+.+.|.+|...+. ..|..|++.+
T Consensus 13 ~~~~L~~H~~~~H~---~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 13 SESSLVEHCEDEHR---SESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CHHHHHHHHHhHCc---CCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 44568888765330 1345788999987655 3788887754
No 37
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=74.22 E-value=1.3 Score=39.12 Aligned_cols=54 Identities=19% Similarity=0.292 Sum_probs=40.7
Q ss_pred ccccCChhHHHHHhh--hccCCCCCCC--cccccC--ccCCccCCcchhhhhhhhccCCcchhHH
Q 046730 43 THLSDEALELETHIS--FQSNDNTNIT--RKYECQ--YCCREFANSQALGGHQNAHKKERQLLKR 101 (214)
Q Consensus 43 ~~~s~~ss~L~~H~r--~ht~~~~~ge--Kpf~C~--~C~k~F~~s~aL~~Hqr~H~gERpf~~r 101 (214)
.........|.+|.+ .|+ ++ +++.|. .|++.|.+...+..|...|.+.+.+.+.
T Consensus 296 ~~~~s~~~~l~~~~~~~~h~-----~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 296 NISFSRSSPLTRHLRSVNHS-----GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCccccccccccccccccc-----cccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 344445666777877 787 77 888888 6888888888888888888877766554
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=73.16 E-value=1.7 Score=31.19 Aligned_cols=24 Identities=29% Similarity=0.797 Sum_probs=21.2
Q ss_pred ccccCccCCccCCcchhhhhhhhc
Q 046730 69 KYECQYCCREFANSQALGGHQNAH 92 (214)
Q Consensus 69 pf~C~~C~k~F~~s~aL~~Hqr~H 92 (214)
.+.|.+|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999864
No 39
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=67.51 E-value=1.3 Score=41.85 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=24.0
Q ss_pred cccccCccCCccCCcchhhhhhhhccC
Q 046730 68 RKYECQYCCREFANSQALGGHQNAHKK 94 (214)
Q Consensus 68 Kpf~C~~C~k~F~~s~aL~~Hqr~H~g 94 (214)
.-|.|.+|+|+|.+...|+.|+-+|..
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 369999999999999999999887753
No 40
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=64.21 E-value=3.3 Score=38.07 Aligned_cols=44 Identities=18% Similarity=0.350 Sum_probs=32.2
Q ss_pred CCcccccCc--cCCccCCcchhhhhhhh-c------------------cCCcchhHHHHHHHhhh
Q 046730 66 ITRKYECQY--CCREFANSQALGGHQNA-H------------------KKERQLLKRAQLQATRH 109 (214)
Q Consensus 66 geKpf~C~~--C~k~F~~s~aL~~Hqr~-H------------------~gERpf~~r~~~~~~~~ 109 (214)
++|||+|.+ |.|++++...|..|+.. | ...|||.|.-|.++-.+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhcc
Confidence 459999998 99999999999888642 3 12367777766655444
No 41
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=60.90 E-value=4 Score=38.75 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=23.7
Q ss_pred cccccCccCCccCCcchhhhhhhhcc
Q 046730 68 RKYECQYCCREFANSQALGGHQNAHK 93 (214)
Q Consensus 68 Kpf~C~~C~k~F~~s~aL~~Hqr~H~ 93 (214)
.-|+|..|.|.|.-..+|..|.|-|+
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccC
Confidence 35999999999999999999999885
No 42
>PHA00616 hypothetical protein
Probab=58.70 E-value=4.8 Score=26.27 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=22.1
Q ss_pred cccCChhHHHHHhhhccCCCCCCCcccccCc
Q 046730 44 HLSDEALELETHISFQSNDNTNITRKYECQY 74 (214)
Q Consensus 44 ~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~ 74 (214)
-....+.+|.+|++.|+ +++++.|++
T Consensus 9 ~~F~~~s~l~~H~r~~h-----g~~~~~~~~ 34 (44)
T PHA00616 9 GIFRKKKEVIEHLLSVH-----KQNKLTLEY 34 (44)
T ss_pred HHHhhHHHHHHHHHHhc-----CCCccceeE
Confidence 34557889999999999 999999986
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=46.21 E-value=4 Score=41.23 Aligned_cols=28 Identities=21% Similarity=0.551 Sum_probs=24.9
Q ss_pred CcccccCccCCccCCcchhhhhhhhccC
Q 046730 67 TRKYECQYCCREFANSQALGGHQNAHKK 94 (214)
Q Consensus 67 eKpf~C~~C~k~F~~s~aL~~Hqr~H~g 94 (214)
.--|.|.+|+|.|..-..+..||+.|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3569999999999999999999999963
No 44
>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=46.15 E-value=13 Score=29.82 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=18.0
Q ss_pred cccccCccCCccCCcchhhhhhhhccCCcchh
Q 046730 68 RKYECQYCCREFANSQALGGHQNAHKKERQLL 99 (214)
Q Consensus 68 Kpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~ 99 (214)
.-..|-+|||.|+. |.+|.+.|.|-.+-.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPEE 99 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HHH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHHH
Confidence 44679999999886 799999997765433
No 45
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=45.34 E-value=13 Score=33.02 Aligned_cols=47 Identities=19% Similarity=0.398 Sum_probs=34.8
Q ss_pred eeccccCCCCCCCCCCccCcCccccCChhHHHHHhhhccCCCCCCCcccccCccCCccCCcchhhhhhh
Q 046730 22 LFGFNISEDHNKNTDSFATSKTHLSDEALELETHISFQSNDNTNITRKYECQYCCREFANSQALGGHQN 90 (214)
Q Consensus 22 ~fg~~~~~~~~~~~~~~~~~~~~~s~~ss~L~~H~r~ht~~~~~geKpf~C~~C~k~F~~s~aL~~Hqr 90 (214)
.|-||+|++.. .+-.+.+|+...+ + .-|.|..|++.|.+ .....|..
T Consensus 3 ~FtCnvCgEsv---------------KKp~vekH~srCr-----n-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESV---------------KKPQVEKHMSRCR-----N-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhc---------------cccchHHHHHhcc-----C-CeeEEeeccccccc-chhhhhhh
Confidence 58899997752 3345677877665 4 67999999999998 56677754
No 46
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.52 E-value=7.3 Score=26.96 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.8
Q ss_pred CCcccccCccCCccCCcchhhhhhhh
Q 046730 66 ITRKYECQYCCREFANSQALGGHQNA 91 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s~aL~~Hqr~ 91 (214)
||.-+.|.-|+..|.......+|.+.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 78889999999999999999999874
No 47
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=44.11 E-value=13 Score=29.60 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=26.2
Q ss_pred CCCcccccCccCCccCCcchhhhhhhhccCCcchhHHH
Q 046730 65 NITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRA 102 (214)
Q Consensus 65 ~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~ 102 (214)
+|.-.|.|..|.|-|.....|..|.+. |.+++|.
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt----K~HKrRv 86 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT----KVHKRRV 86 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc----cHHHHHH
Confidence 466679999999999999999888763 4455554
No 48
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=41.86 E-value=16 Score=23.74 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=18.5
Q ss_pred ccccCccCCccCCc-----chhhhhhh-hcc
Q 046730 69 KYECQYCCREFANS-----QALGGHQN-AHK 93 (214)
Q Consensus 69 pf~C~~C~k~F~~s-----~aL~~Hqr-~H~ 93 (214)
.-.|.+|++.+... ..|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45799999988665 47888876 453
No 49
>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=40.36 E-value=15 Score=22.99 Aligned_cols=24 Identities=29% Similarity=0.555 Sum_probs=14.9
Q ss_pred CCcccccCccCCccCCc----chhhhhh
Q 046730 66 ITRKYECQYCCREFANS----QALGGHQ 89 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s----~aL~~Hq 89 (214)
......|.+|++.+... ..|..|+
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 45667899999988764 5677776
No 50
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=38.13 E-value=10 Score=33.68 Aligned_cols=21 Identities=48% Similarity=0.802 Sum_probs=18.9
Q ss_pred ccCccCCccCCcchhhhhhhh
Q 046730 71 ECQYCCREFANSQALGGHQNA 91 (214)
Q Consensus 71 ~C~~C~k~F~~s~aL~~Hqr~ 91 (214)
.|=+|+|.|-....|.+||++
T Consensus 12 wcwycnrefddekiliqhqka 32 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA 32 (341)
T ss_pred eeeecccccchhhhhhhhhhh
Confidence 488999999999999999874
No 51
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=31.88 E-value=20 Score=27.94 Aligned_cols=35 Identities=26% Similarity=0.347 Sum_probs=26.1
Q ss_pred CCCcccccCccCCccCCcchhhhhhhhccCCcchhHHHH
Q 046730 65 NITRKYECQYCCREFANSQALGGHQNAHKKERQLLKRAQ 103 (214)
Q Consensus 65 ~geKpf~C~~C~k~F~~s~aL~~Hqr~H~gERpf~~r~~ 103 (214)
+|-..+-|..|.+-|....+|..|.+ .+++++|..
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkk----gkvHkRR~K 85 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKK----GKVHKRRAK 85 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhc----cchhHHHHH
Confidence 35566889999999999999988765 345555543
No 52
>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=31.82 E-value=21 Score=30.83 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=22.9
Q ss_pred CCcccccCccCCccCCcchhhhhhhhccCCc
Q 046730 66 ITRKYECQYCCREFANSQALGGHQNAHKKER 96 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s~aL~~Hqr~H~gER 96 (214)
.+..|.|..|+|.|.-..-..+|+..-..|+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 4567999999999999999999987544444
No 53
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=31.55 E-value=23 Score=34.93 Aligned_cols=31 Identities=19% Similarity=0.386 Sum_probs=27.0
Q ss_pred CCcccccCccCCccCCcchhhhhhhhccCCc
Q 046730 66 ITRKYECQYCCREFANSQALGGHQNAHKKER 96 (214)
Q Consensus 66 geKpf~C~~C~k~F~~s~aL~~Hqr~H~gER 96 (214)
..++..|..||.+|.+......||..|-..+
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~dwh 445 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDDWH 445 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhhhh
Confidence 4578899999999999999999999997543
No 54
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=28.31 E-value=33 Score=27.79 Aligned_cols=27 Identities=19% Similarity=0.128 Sum_probs=21.6
Q ss_pred cccCccCCccCCcchhhhhhhhccCCcchh
Q 046730 70 YECQYCCREFANSQALGGHQNAHKKERQLL 99 (214)
Q Consensus 70 f~C~~C~k~F~~s~aL~~Hqr~H~gERpf~ 99 (214)
..|-+|||.|++ |.+|..+|.+--|-.
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTPd~ 103 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTPDE 103 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCHHH
Confidence 469999999985 999999988765543
No 55
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=22.04 E-value=30 Score=28.43 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=11.3
Q ss_pred CCcccccCccCCccC
Q 046730 66 ITRKYECQYCCREFA 80 (214)
Q Consensus 66 geKpf~C~~C~k~F~ 80 (214)
..+.++|..|+.-|+
T Consensus 130 Kge~~rc~eCG~~fk 144 (153)
T KOG3352|consen 130 KGETQRCPECGHYFK 144 (153)
T ss_pred cCCcccCCcccceEE
Confidence 345678999998776
No 56
>PF07055 Eno-Rase_FAD_bd: Enoyl reductase FAD binding domain; InterPro: IPR010758 This family contains a number of bacterial putative reductases. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3S8M_A 3ZU5_A 3ZU3_A 3ZU4_A 3ZU2_A.
Probab=20.98 E-value=34 Score=24.15 Aligned_cols=13 Identities=38% Similarity=0.754 Sum_probs=7.8
Q ss_pred ceeeccccCCCCC
Q 046730 20 LKLFGFNISEDHN 32 (214)
Q Consensus 20 ~k~fg~~~~~~~~ 32 (214)
++||||+|.+-..
T Consensus 49 l~L~GF~~~gVDY 61 (65)
T PF07055_consen 49 LQLFGFGVDGVDY 61 (65)
T ss_dssp HHHTT-S-TTS-T
T ss_pred HHHcCCCCCCCCC
Confidence 6899999986543
Done!