Query 025008
Match_columns 259
No_of_seqs 168 out of 374
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:12:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025008hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2990 C2C2-type Zn-finger pr 100.0 2.7E-71 5.8E-76 504.1 12.4 253 1-257 49-308 (317)
2 PF04502 DUF572: Family of unk 100.0 2.3E-57 5.1E-62 423.8 14.7 175 1-178 37-214 (324)
3 KOG2989 Uncharacterized conser 100.0 9.4E-35 2E-39 260.3 7.6 128 1-131 37-166 (253)
4 COG5134 Uncharacterized conser 100.0 3.2E-34 6.8E-39 253.9 10.3 168 1-170 39-212 (272)
5 PF05907 DUF866: Eukaryotic pr 90.4 0.26 5.7E-06 42.5 3.1 62 2-65 28-91 (161)
6 PF10122 Mu-like_Com: Mu-like 88.8 0.43 9.4E-06 34.1 2.7 37 1-52 1-37 (51)
7 PF08271 TF_Zn_Ribbon: TFIIB z 88.3 0.3 6.5E-06 32.9 1.6 24 40-64 1-24 (43)
8 smart00834 CxxC_CXXC_SSSS Puta 82.2 1.1 2.5E-05 29.0 2.1 21 33-55 1-21 (41)
9 PRK03681 hypA hydrogenase nick 82.1 0.69 1.5E-05 37.6 1.2 30 1-48 67-96 (114)
10 COG0375 HybF Zn finger protein 79.7 1.6 3.5E-05 36.1 2.6 27 2-47 68-94 (115)
11 PF13240 zinc_ribbon_2: zinc-r 78.2 1 2.2E-05 26.9 0.8 15 6-20 1-15 (23)
12 PRK12380 hydrogenase nickel in 77.2 1.2 2.6E-05 36.2 1.2 12 1-12 67-78 (113)
13 PRK00564 hypA hydrogenase nick 76.2 1.3 2.9E-05 36.1 1.2 29 2-48 69-97 (117)
14 TIGR02605 CxxC_CxxC_SSSS putat 74.8 2.3 5E-05 29.3 1.9 18 33-52 1-18 (52)
15 PF09855 DUF2082: Nucleic-acid 69.9 4.5 9.7E-05 30.1 2.6 47 6-52 2-49 (64)
16 TIGR00100 hypA hydrogenase nic 66.8 3.2 6.9E-05 33.7 1.4 28 2-48 68-95 (115)
17 COG4332 Uncharacterized protei 64.7 3.3 7.2E-05 37.0 1.2 39 4-49 17-59 (203)
18 PF07754 DUF1610: Domain of un 62.6 6.2 0.00013 24.1 1.7 11 7-17 1-11 (24)
19 PRK03824 hypA hydrogenase nick 62.2 4.4 9.5E-05 33.9 1.4 43 2-48 68-116 (135)
20 COG2888 Predicted Zn-ribbon RN 61.2 7.1 0.00015 28.9 2.2 32 4-52 9-40 (61)
21 PRK04016 DNA-directed RNA poly 57.7 5.4 0.00012 29.6 1.1 16 1-16 1-16 (62)
22 PF05876 Terminase_GpA: Phage 57.2 6.2 0.00014 40.2 1.8 36 29-64 190-234 (557)
23 PRK00762 hypA hydrogenase nick 56.6 5 0.00011 33.0 0.9 12 1-13 67-78 (124)
24 PF01921 tRNA-synt_1f: tRNA sy 56.3 6.7 0.00015 38.2 1.8 41 1-52 171-212 (360)
25 COG1644 RPB10 DNA-directed RNA 54.9 5.7 0.00012 29.6 0.8 24 1-26 1-24 (63)
26 PF04502 DUF572: Family of unk 53.2 7.1 0.00015 37.1 1.4 20 32-51 29-52 (324)
27 PRK14890 putative Zn-ribbon RN 52.7 16 0.00035 26.9 2.8 18 3-20 6-26 (59)
28 PF11931 DUF3449: Domain of un 52.2 4.7 0.0001 36.2 0.0 32 6-43 103-134 (196)
29 cd02340 ZZ_NBR1_like Zinc fing 52.1 6.9 0.00015 26.6 0.8 17 5-22 1-17 (43)
30 PRK00398 rpoP DNA-directed RNA 51.9 13 0.00028 25.2 2.1 18 39-56 21-38 (46)
31 PRK00750 lysK lysyl-tRNA synth 51.6 11 0.00023 38.1 2.4 39 1-51 172-211 (510)
32 PF13005 zf-IS66: zinc-finger 51.5 26 0.00056 23.4 3.6 41 6-46 4-47 (47)
33 KOG2407 GPI transamidase compl 50.4 6 0.00013 40.3 0.4 12 1-12 495-506 (575)
34 KOG3368 Transport protein part 49.1 23 0.00051 30.2 3.7 32 29-60 62-93 (140)
35 PF01155 HypA: Hydrogenase exp 48.0 8.8 0.00019 31.0 0.9 11 2-12 68-78 (113)
36 PF05876 Terminase_GpA: Phage 47.6 9.1 0.0002 39.0 1.2 39 3-50 199-240 (557)
37 PLN00032 DNA-directed RNA poly 47.5 10 0.00022 29.0 1.1 15 1-15 1-15 (71)
38 PF05973 Gp49: Phage derived p 47.5 35 0.00075 25.8 4.2 46 29-75 34-80 (91)
39 COG1405 SUA7 Transcription ini 45.9 11 0.00023 35.6 1.3 26 40-66 2-27 (285)
40 PF01194 RNA_pol_N: RNA polyme 43.2 10 0.00022 28.0 0.6 15 1-15 1-15 (60)
41 TIGR02098 MJ0042_CXXC MJ0042 f 42.6 13 0.00029 23.9 1.0 18 39-56 2-19 (38)
42 TIGR01206 lysW lysine biosynth 42.3 18 0.00039 26.0 1.7 12 41-52 4-15 (54)
43 PF01396 zf-C4_Topoisom: Topoi 42.3 23 0.00049 23.5 2.1 18 40-57 2-19 (39)
44 TIGR00467 lysS_arch lysyl-tRNA 39.7 24 0.00052 35.9 2.8 38 1-51 165-202 (515)
45 PF13248 zf-ribbon_3: zinc-rib 39.6 15 0.00032 22.2 0.8 17 4-20 2-18 (26)
46 PF14255 Cys_rich_CPXG: Cystei 39.1 27 0.00058 24.9 2.2 24 41-64 2-25 (52)
47 PRK09628 oorB 2-oxoglutarate-a 38.4 14 0.00031 34.5 0.9 19 4-22 16-34 (277)
48 PF09723 Zn-ribbon_8: Zinc rib 37.7 31 0.00066 23.1 2.2 19 33-53 1-19 (42)
49 smart00659 RPOLCX RNA polymera 37.3 31 0.00067 23.6 2.2 19 38-56 18-36 (44)
50 PHA02998 RNA polymerase subuni 36.9 22 0.00047 31.9 1.7 54 14-67 115-179 (195)
51 PF02150 RNA_POL_M_15KD: RNA p 36.9 34 0.00073 22.2 2.2 16 42-57 4-19 (35)
52 cd02338 ZZ_PCMF_like Zinc fing 35.6 16 0.00034 25.4 0.5 13 34-46 10-22 (49)
53 cd02339 ZZ_Mind_bomb Zinc fing 35.2 18 0.00039 24.9 0.8 17 5-21 1-17 (45)
54 PF14205 Cys_rich_KTR: Cystein 35.2 39 0.00084 24.6 2.5 38 5-53 5-42 (55)
55 PF10058 DUF2296: Predicted in 34.9 31 0.00067 24.7 2.0 34 2-48 20-53 (54)
56 PF06107 DUF951: Bacterial pro 34.9 34 0.00073 25.1 2.2 14 38-51 30-43 (57)
57 PF06750 DiS_P_DiS: Bacterial 34.5 6.7 0.00015 30.8 -1.6 33 6-51 35-70 (92)
58 COG4416 Com Mu-like prophage p 34.2 25 0.00053 25.8 1.4 44 2-62 2-47 (60)
59 PRK05778 2-oxoglutarate ferred 34.1 15 0.00033 34.7 0.4 13 4-16 18-30 (301)
60 KOG2846 Predicted membrane pro 33.4 21 0.00046 34.4 1.2 42 3-57 219-260 (328)
61 COG2093 DNA-directed RNA polym 32.7 24 0.00051 26.4 1.1 19 42-60 21-47 (64)
62 PF00569 ZZ: Zinc finger, ZZ t 32.2 22 0.00048 24.2 0.8 20 3-22 3-22 (46)
63 cd00674 LysRS_core_class_I cat 32.0 36 0.00078 33.0 2.5 38 1-51 166-204 (353)
64 COG1996 RPC10 DNA-directed RNA 31.7 42 0.00092 23.8 2.2 19 39-57 24-42 (49)
65 COG2816 NPY1 NTP pyrophosphohy 31.3 32 0.0007 32.5 2.0 33 38-70 128-166 (279)
66 PF01485 IBR: IBR domain; Int 31.2 28 0.00061 23.9 1.3 18 5-22 19-38 (64)
67 PF04606 Ogr_Delta: Ogr/Delta- 30.4 30 0.00065 23.7 1.2 19 41-59 1-19 (47)
68 PF05864 Chordopox_RPO7: Chord 30.2 23 0.00051 26.2 0.7 15 1-15 1-15 (63)
69 smart00661 RPOL9 RNA polymeras 29.7 31 0.00068 23.3 1.3 10 6-15 2-11 (52)
70 PRK11869 2-oxoacid ferredoxin 28.7 20 0.00044 33.6 0.2 11 4-14 8-18 (280)
71 COG0484 DnaJ DnaJ-class molecu 28.7 76 0.0016 31.2 4.1 53 2-57 140-201 (371)
72 PRK09678 DNA-binding transcrip 28.5 29 0.00062 26.4 1.0 16 40-55 2-17 (72)
73 COG5134 Uncharacterized conser 28.0 22 0.00048 32.8 0.4 13 38-50 41-53 (272)
74 PF05207 zf-CSL: CSL zinc fing 27.7 52 0.0011 23.4 2.1 15 37-52 16-30 (55)
75 PF01258 zf-dskA_traR: Prokary 27.3 30 0.00065 22.2 0.8 14 3-17 3-16 (36)
76 COG0846 SIR2 NAD-dependent pro 26.7 30 0.00065 32.0 0.9 16 3-18 121-136 (250)
77 TIGR02177 PorB_KorB 2-oxoacid: 26.5 25 0.00054 33.1 0.4 11 4-14 1-11 (287)
78 PF02146 SIR2: Sir2 family; I 26.3 29 0.00063 29.5 0.7 12 3-14 104-115 (178)
79 PHA03082 DNA-dependent RNA pol 26.1 30 0.00065 25.6 0.7 15 1-15 1-15 (63)
80 cd02344 ZZ_HERC2 Zinc finger, 26.1 32 0.0007 23.8 0.8 16 5-20 1-16 (45)
81 COG1779 C4-type Zn-finger prot 26.0 49 0.0011 29.9 2.1 27 34-60 9-35 (201)
82 cd02343 ZZ_EF Zinc finger, ZZ 26.0 33 0.0007 24.2 0.8 14 5-19 1-14 (48)
83 smart00132 LIM Zinc-binding do 25.9 27 0.00059 21.3 0.4 12 6-17 1-12 (39)
84 KOG3497 DNA-directed RNA polym 25.6 31 0.00067 25.8 0.7 13 3-15 3-15 (69)
85 PF00645 zf-PARP: Poly(ADP-rib 25.4 33 0.00072 25.5 0.8 13 6-18 9-21 (82)
86 PF11793 FANCL_C: FANCL C-term 25.3 42 0.00092 24.8 1.4 16 39-54 55-70 (70)
87 PRK00423 tfb transcription ini 25.3 35 0.00077 32.0 1.2 26 40-66 12-37 (310)
88 PF03604 DNA_RNApol_7kD: DNA d 24.9 32 0.00069 22.2 0.6 13 40-52 18-30 (32)
89 PF14353 CpXC: CpXC protein 24.6 42 0.0009 27.1 1.3 45 5-51 2-50 (128)
90 PRK03954 ribonuclease P protei 24.0 87 0.0019 26.1 3.1 44 5-54 65-108 (121)
91 COG5188 PRP9 Splicing factor 3 23.5 24 0.00052 34.8 -0.3 14 6-19 376-389 (470)
92 PRK11639 zinc uptake transcrip 23.4 61 0.0013 27.7 2.2 46 3-48 99-149 (169)
93 TIGR02652 conserved hypothetic 23.1 34 0.00073 29.6 0.5 35 34-68 4-53 (163)
94 KOG1296 Uncharacterized conser 23.1 27 0.00058 30.4 -0.1 47 3-52 29-77 (161)
95 PF13790 DUF4182: Domain of un 22.9 1E+02 0.0023 20.8 2.7 30 4-46 3-32 (38)
96 KOG4582 Uncharacterized conser 22.6 51 0.0011 30.8 1.7 16 5-20 153-168 (278)
97 PF04810 zf-Sec23_Sec24: Sec23 22.5 39 0.00084 22.4 0.6 35 5-52 3-37 (40)
98 PRK00807 50S ribosomal protein 22.2 27 0.0006 24.7 -0.1 43 6-58 3-47 (52)
99 PRK04023 DNA polymerase II lar 21.9 43 0.00094 37.0 1.2 8 6-13 628-635 (1121)
100 PF14447 Prok-RING_4: Prokaryo 21.8 49 0.0011 24.1 1.1 10 42-51 42-51 (55)
101 COG2023 RPR2 RNase P subunit R 21.4 1.3E+02 0.0027 24.7 3.5 38 5-51 57-94 (105)
102 PF10263 SprT-like: SprT-like 21.3 98 0.0021 25.3 3.0 27 36-62 120-146 (157)
103 PF01927 Mut7-C: Mut7-C RNAse 21.3 77 0.0017 26.5 2.4 46 2-49 89-134 (147)
104 PF04828 GFA: Glutathione-depe 21.0 1.1E+02 0.0023 22.3 2.8 40 26-67 35-75 (92)
105 COG1013 PorB Pyruvate:ferredox 20.5 36 0.00079 32.1 0.2 18 5-22 16-33 (294)
106 TIGR03830 CxxCG_CxxCG_HTH puta 20.5 1.5E+02 0.0033 23.2 3.8 8 41-48 33-40 (127)
107 PF07255 Benyvirus_14KDa: Beny 20.5 39 0.00084 27.8 0.4 42 33-74 59-100 (123)
108 PRK00464 nrdR transcriptional 20.2 60 0.0013 28.0 1.5 24 40-63 1-26 (154)
No 1
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=100.00 E-value=2.7e-71 Score=504.14 Aligned_cols=253 Identities=49% Similarity=0.755 Sum_probs=210.9
Q ss_pred CCcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCChhhhhc
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFDVEDAET 80 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~~~~~e~ 80 (259)
|||||||++|.+||||||||||+|++||+||+||||+|+||||+|.|+|+|+|||+||||||+|||+|+.++||++|+|+
T Consensus 49 MPynIWC~gC~nhIgmGvRyNAeKkkvGnYYtTpiw~FrmKchlC~n~i~iqTDP~NceYvI~SGaqRKeer~D~~d~Eq 128 (317)
T KOG2990|consen 49 MPYNIWCDGCKNHIGMGVRYNAEKKKVGNYYTTPIWSFRMKCHLCDNYIVIQTDPKNCEYVITSGAQRKEERYDAEDAEQ 128 (317)
T ss_pred cccchhhccHHHhhhccceechhhhhccccccCcccchhhcccccCCceeeecCCCCceEEEeccccccccccCchhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCchhhhcCCC-ChhHHhhhhHHHHHHHHHHhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHH----HH
Q 025008 81 LELPADEERGKLS-DPFYRLEHQEADLQKKKEAEPRLVQIQRISDGRFSDDYALNKALRAKLRSQRKRVTEEEA----AS 155 (259)
Q Consensus 81 ~~~~~~ee~~~~~-dpm~~LE~~~~D~~~~~~~~~~LeeL~~~~~~~~~Ddy~~N~~LR~~fR~~kk~~~~~e~----~~ 155 (259)
++..+.++.+++. |||++|||+..|.++.+.+.+.|..|++.++++|.|||.+|+.||++||++||..+++++ ..
T Consensus 129 ~~~t~~e~k~KLa~DamyrLEHqe~D~~k~k~aep~l~~l~e~~~~rw~Ddf~~ns~LRaqfR~~kK~~~e~~~~D~~l~ 208 (317)
T KOG2990|consen 129 MEPTAEEEKGKLASDAMYRLEHQEVDLKKKKAAEPVLVRLQEVNDARWADDFQANSRLRAQFREEKKLINEQEARDLDLF 208 (317)
T ss_pred ccchhhhhcccccccHHHHHHhHHHhHhhhhccchHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhhhhhhhhHHHH
Confidence 9888888888885 999999999999999999999999999999999999999999999999999999987644 34
Q ss_pred HhhCCCCCCCCCChHHHHHhcccCcchhhhhh-hH-HHHHhhhhcCCCCCCCCCcchhHHHHHHhhhcchhhhhhhhcCC
Q 025008 156 RKLGLGLRLLPSTKEDACAAAHVKFSSKFEKN-RK-DKRALINAASIFSGSSISSSKQLELEAKRRKINAGAASNMLTGA 233 (259)
Q Consensus 156 ~k~gl~i~Ll~e~eeD~~~A~~v~f~~~~~~~-~~-~kr~~i~~~siF~~~~~s~k~~~~~~~~r~k~~~~~a~~~l~~~ 233 (259)
.+.+|+|.|||++++|+..|.+++|.....+. +. ..|..|.++ ++...+.|.+ ...+. |.++.+..+++.+-|.
T Consensus 209 ~r~sl~I~lLPeTe~Dr~~A~llk~~~~~~kedr~~~~r~~i~sr-p~~~~S~sts-~g~l~--r~~~a~~~~~~~~lg~ 284 (317)
T KOG2990|consen 209 ARASLDILLLPETEEDRKIASLLKFNTKKRKEDRENNRRLEIKSR-PSRTGSTSTS-SGSLK--RDPFARKFLPSEDLGI 284 (317)
T ss_pred HhhhcCcccCCCchhhHHHHHHHhhcccchhhhHHhhhhhhhccC-CCCCCCcccc-ccccc--cchhhhcccchhhhhh
Confidence 57788999999999999999999997543332 23 344445444 4444343322 22333 8888888888888888
Q ss_pred CcCCcccCCCCCCccccCCccccc
Q 025008 234 FKPSSWSQSSVPSSRHKRSSVSAR 257 (259)
Q Consensus 234 ~k~~~~~~~~~~~~~~~~~~~~~~ 257 (259)
.+..+.+............+|..|
T Consensus 285 ~~~k~~st~~a~~~~~~~~~v~~~ 308 (317)
T KOG2990|consen 285 RRRKIESTSNAAGEKLPDSSVSDR 308 (317)
T ss_pred hhhhccCCcccCCCcCccchhccc
Confidence 887764443333333445555444
No 2
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=100.00 E-value=2.3e-57 Score=423.79 Aligned_cols=175 Identities=41% Similarity=0.670 Sum_probs=152.3
Q ss_pred CCcceecCCCCccccccccccceeeccCc--eeeeeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCChhhh
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVGN--YYSTKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFDVEDA 78 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg~--Y~st~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~~~~~ 78 (259)
|||+|||++|++|||+||||||+|++||+ |||||||+||||||.|+++|+|+|||+|+||||++||+|+++.|...+
T Consensus 37 ~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPkn~dY~~~~Ga~R~~~~~~~~~- 115 (324)
T PF04502_consen 37 MPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPKNTDYVVESGARRNFEPDKEEE- 115 (324)
T ss_pred CCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecCCCCCCeeeecCeeecCCcchhhh-
Confidence 89999999999999999999999999998 999999999999999999999999999999999999999777665443
Q ss_pred hccccCch-hhhcCCCChhHHhhhhHHHHHHHHHHhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025008 79 ETLELPAD-EERGKLSDPFYRLEHQEADLQKKKEAEPRLVQIQRISDGRFSDDYALNKALRAKLRSQRKRVTEEEAASRK 157 (259)
Q Consensus 79 e~~~~~~~-ee~~~~~dpm~~LE~~~~D~~~~~~~~~~LeeL~~~~~~~~~Ddy~~N~~LR~~fR~~kk~~~~~e~~~~k 157 (259)
+++...+. ++.+...|||++||+++.|+++++++.++|++|++++.+ .|||+.|++||+.||.++++++.+++....
T Consensus 116 ~~~~~~~~~~~~~~~~d~m~~LE~~~~d~~~~~~~~~~LeeL~~~~~r--~d~~~~n~~Lr~~~r~~~k~~~~~~~~d~~ 193 (324)
T PF04502_consen 116 EQEEREDKEEEEEEEEDPMKALEKRTEDSKREMEALERLEELQELNAR--KDDYDANQMLRKRFREEKKERERQEEEDEA 193 (324)
T ss_pred hhhhhhhHHHhhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--cCchhhHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 33333333 333456899999999999999999999999999999987 899999999999999999998876665555
Q ss_pred hCCCCCCCCCChHHHHHhccc
Q 025008 158 LGLGLRLLPSTKEDACAAAHV 178 (259)
Q Consensus 158 ~gl~i~Ll~e~eeD~~~A~~v 178 (259)
+...+.|.|++++|...+...
T Consensus 194 ~~~~~~~~~~~~~~~r~~~~~ 214 (324)
T PF04502_consen 194 LKKKISLGPESEEDKRLAADE 214 (324)
T ss_pred HHHhhccCcchhhhhhhhcch
Confidence 555555668899998887763
No 3
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=9.4e-35 Score=260.33 Aligned_cols=128 Identities=31% Similarity=0.562 Sum_probs=115.2
Q ss_pred CCcceecCCCCccccccccccceeecc-C-ceeeeeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCChhhh
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQV-G-NYYSTKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFDVEDA 78 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~v-g-~Y~st~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~~~~~ 78 (259)
.||+|+|++||+|||+|++||+.++.| | .||||+||+|||+|+.|+++|+|+|||+|+|||+++||.|++++|...+.
T Consensus 37 ~Pf~~rC~tCgeyi~kg~kfN~r~E~~~~e~yLgiki~Rf~i~Ct~cl~el~~rTDp~N~dY~~E~Ga~r~y~~~~~~ee 116 (253)
T KOG2989|consen 37 TPFRLRCNTCGEYIYKGKKFNAREEDVIEETYLGIKIFRFYIKCTRCLRELSFRTDPKNSDYVIESGATRNYEPIEEEEE 116 (253)
T ss_pred ccceeecccccchhhcCCCcchhHHhhhccccccceeeeeeeeccchHhhhhhhcCCcchHHHHHhcchhcccccchhHH
Confidence 599999999999999999999999998 3 89999999999999999999999999999999999999999999987665
Q ss_pred hccccCchhhhcCCCChhHHhhhhHHHHHHHHHHhHHHHHHHHHHhcccCCHH
Q 025008 79 ETLELPADEERGKLSDPFYRLEHQEADLQKKKEAEPRLVQIQRISDGRFSDDY 131 (259)
Q Consensus 79 e~~~~~~~ee~~~~~dpm~~LE~~~~D~~~~~~~~~~LeeL~~~~~~~~~Ddy 131 (259)
+.-.. .++ +...|||..||+++.+++.++.....|++|..++.++...|+
T Consensus 117 ek~k~--~~~-~d~~d~m~~lekrt~~S~~e~~~~~~ldel~~~k~r~~~id~ 166 (253)
T KOG2989|consen 117 EKRKF--EEE-EDMKDEIKRLEKRTFQSKDEEIIRRALDELKVLKERPAPIDL 166 (253)
T ss_pred HHHHH--Hhh-hhhhhHHHHHHHHhhhhhhHHHHHHHHHHHHHHhcccCcccH
Confidence 43211 122 456799999999999999999999999999999999877777
No 4
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.2e-34 Score=253.90 Aligned_cols=168 Identities=33% Similarity=0.596 Sum_probs=130.6
Q ss_pred CCcceecCCCCccccccccccceeeccC--ceeeeeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCChhhh
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVG--NYYSTKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFDVEDA 78 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg--~Y~st~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~~~~~ 78 (259)
.||+|+|+.|++||++|+||||.|+-++ .||||+||||.|+||.|++.|-|+|||+|++||+++|++|++++-++.+.
T Consensus 39 TPF~~RCL~C~~YI~K~~rfNavkE~~~dK~y~~~kiYRf~I~C~~C~n~i~~RTDPkN~~YV~EsGg~R~i~pq~~n~D 118 (272)
T COG5134 39 TPFPVRCLNCENYIQKGTRFNAVKEEIGDKSYYTTKIYRFSIKCHLCSNPIDVRTDPKNTEYVVESGGRRKIEPQDINED 118 (272)
T ss_pred cCcceeecchhhhhhcccchhHHHHHhcccccceeEEEEEEEEccCCCCceeeecCCCCceEEEecCceeecCccccccC
Confidence 4999999999999999999999999997 68999999999999999999999999999999999999999887665443
Q ss_pred hccccCchhhhcCCCChhHHhhhhHHHHHHHHHHhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHH---
Q 025008 79 ETLELPADEERGKLSDPFYRLEHQEADLQKKKEAEPRLVQIQRISDGRFSDDYALNKALRAKLRSQRKRVTEEEAAS--- 155 (259)
Q Consensus 79 e~~~~~~~ee~~~~~dpm~~LE~~~~D~~~~~~~~~~LeeL~~~~~~~~~Ddy~~N~~LR~~fR~~kk~~~~~e~~~--- 155 (259)
+.... .-+.-...|....+|+..++..........+..+-.+..+-|+|+|...+.+|.+|+..|+.+..+++..
T Consensus 119 ~~k~~--~Ve~~~Esd~~~~~eK~~~Q~~~~~~~ssA~n~~D~L~Krl~~~~~~~~~~~~~~~~~~k~~e~~q~a~~~~~ 196 (272)
T COG5134 119 PAKAE--NVEKVPESDAIEALEKQLTQQKSEKHNSSAINFIDELNKRLWSDPFVSSQRLRKQFRERKKIEKKQEAKDLSL 196 (272)
T ss_pred hhhhh--hhhcCchhHHHHHHHHHHHHhhcccchhhhhhHHHHHHHHhhcCchhhhHHHHHHHHHHhhhHHHHHHHHhhh
Confidence 21100 0011122466677777776666554444455566666778899999999999999999998886555432
Q ss_pred -HhhCCCCCCCCCChH
Q 025008 156 -RKLGLGLRLLPSTKE 170 (259)
Q Consensus 156 -~k~gl~i~Ll~e~ee 170 (259)
....+.+.++|.+.+
T Consensus 197 ~~~a~~~~~i~~~~~d 212 (272)
T COG5134 197 KNRAALDIDILPSSSD 212 (272)
T ss_pred hhhhhhhhccCCccch
Confidence 234568888887543
No 5
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=90.36 E-value=0.26 Score=42.53 Aligned_cols=62 Identities=27% Similarity=0.412 Sum_probs=35.0
Q ss_pred CcceecCCCCccccccccccc-eeeccCceeeeeeEEEEEEcCCCCceeEEecCCC-CCCeeeecC
Q 025008 2 PFNIWCGGCNSMIAKGVRFNA-EKKQVGNYYSTKIWSFTMKSPCCKHQIVIQTDPK-NCEYVIISG 65 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNA-eKk~vg~Y~st~I~~F~mkC~~C~~~i~ikTDPk-n~dYvv~~G 65 (259)
.|.|.|+.|++--.+.|-+|. ++..+.. |---=.|.|||..|..+..|.--|. ...|.++..
T Consensus 28 ~fkvkCt~CgE~~~k~V~i~~~e~~e~~g--srG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~ 91 (161)
T PF05907_consen 28 FFKVKCTSCGEVHPKWVYINRFEKHEIPG--SRGTANFVMKCKFCKRESSIDIIPGKGKPYTAEDS 91 (161)
T ss_dssp EEEEEETTSS--EEEEEEE-TT-BEE-TT--SS-EESEEE--SSSS--EEEEEE--TTTEEEGGGT
T ss_pred EEEEEECCCCCccCcceEeecceEEecCC--CccceEeEecCcCcCCccEEEEEecCccccccccc
Confidence 488999999998888888885 4444422 2222389999999999988854443 345665433
No 6
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=88.80 E-value=0.43 Score=34.13 Aligned_cols=37 Identities=32% Similarity=0.606 Sum_probs=28.0
Q ss_pred CCcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEe
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ik 52 (259)
|.=.|+|.+|+...+++. .|- ...||||.|..--.|+
T Consensus 1 m~~eiRC~~CnklLa~~g----------~~~-----~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 1 MLKEIRCGHCNKLLAKAG----------EVI-----ELEIKCPRCKTINHVR 37 (51)
T ss_pred CCcceeccchhHHHhhhc----------Ccc-----EEEEECCCCCccceEe
Confidence 445799999999998852 221 5789999999877764
No 7
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=88.32 E-value=0.3 Score=32.90 Aligned_cols=24 Identities=38% Similarity=0.538 Sum_probs=21.6
Q ss_pred EEcCCCCceeEEecCCCCCCeeeec
Q 025008 40 MKSPCCKHQIVIQTDPKNCEYVIIS 64 (259)
Q Consensus 40 mkC~~C~~~i~ikTDPkn~dYvv~~ 64 (259)
|+||.|++.- |-+|+.+.+||+..
T Consensus 1 m~Cp~Cg~~~-~~~D~~~g~~vC~~ 24 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDPERGELVCPN 24 (43)
T ss_dssp ESBTTTSSSE-EEEETTTTEEEETT
T ss_pred CCCcCCcCCc-eEEcCCCCeEECCC
Confidence 7899999988 89999999998865
No 8
>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=82.19 E-value=1.1 Score=29.00 Aligned_cols=21 Identities=14% Similarity=0.417 Sum_probs=16.4
Q ss_pred eeeEEEEEEcCCCCceeEEecCC
Q 025008 33 TKIWSFTMKSPCCKHQIVIQTDP 55 (259)
Q Consensus 33 t~I~~F~mkC~~C~~~i~ikTDP 55 (259)
.|||.| +|+.|+..|++-..-
T Consensus 1 Mp~Y~y--~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 1 MPIYEY--RCEDCGHTFEVLQKI 21 (41)
T ss_pred CCCEEE--EcCCCCCEEEEEEec
Confidence 377877 899999999876643
No 9
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=82.06 E-value=0.69 Score=37.62 Aligned_cols=30 Identities=20% Similarity=0.538 Sum_probs=19.8
Q ss_pred CCcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCce
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~ 48 (259)
.|-..||..|+. ++..+-+ |++.||.|++.
T Consensus 67 ~p~~~~C~~Cg~-----------------~~~~~~~-~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQ-----------------YVTLLTQ-RVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCC-----------------eeecCCc-cCCcCcCcCCC
Confidence 377889999985 3332222 33679999965
No 10
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=79.67 E-value=1.6 Score=36.06 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=21.7
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCc
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKH 47 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~ 47 (259)
|--+||..| +.++..-.|.|+ ||.|++
T Consensus 68 p~~~~C~~C-----------------~~~~~~e~~~~~--CP~C~s 94 (115)
T COG0375 68 PAECWCLDC-----------------GQEVELEELDYR--CPKCGS 94 (115)
T ss_pred ccEEEeccC-----------------CCeecchhheeE--CCCCCC
Confidence 556788888 677888888888 999984
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=78.19 E-value=1 Score=26.91 Aligned_cols=15 Identities=27% Similarity=0.884 Sum_probs=12.3
Q ss_pred ecCCCCccccccccc
Q 025008 6 WCGGCNSMIAKGVRF 20 (259)
Q Consensus 6 wC~~C~~~I~kGvRF 20 (259)
.|..||+.|-.+.+|
T Consensus 1 ~Cp~CG~~~~~~~~f 15 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF 15 (23)
T ss_pred CCcccCCCCCCcCcc
Confidence 388888888888887
No 12
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=77.19 E-value=1.2 Score=36.15 Aligned_cols=12 Identities=33% Similarity=1.060 Sum_probs=9.3
Q ss_pred CCcceecCCCCc
Q 025008 1 MPFNIWCGGCNS 12 (259)
Q Consensus 1 mPF~iwC~~C~~ 12 (259)
.|-.+||..|+.
T Consensus 67 vp~~~~C~~Cg~ 78 (113)
T PRK12380 67 KPAQAWCWDCSQ 78 (113)
T ss_pred eCcEEEcccCCC
Confidence 377789999984
No 13
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.18 E-value=1.3 Score=36.13 Aligned_cols=29 Identities=10% Similarity=0.240 Sum_probs=18.7
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCce
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~ 48 (259)
|.-+||..|+....-. =| ++++||.|++.
T Consensus 69 p~~~~C~~Cg~~~~~~-----------------~~-~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPN-----------------AL-DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccC-----------------Cc-cCCcCcCCCCC
Confidence 7778999998443221 11 33579999975
No 14
>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=74.82 E-value=2.3 Score=29.25 Aligned_cols=18 Identities=17% Similarity=0.632 Sum_probs=14.1
Q ss_pred eeeEEEEEEcCCCCceeEEe
Q 025008 33 TKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 33 t~I~~F~mkC~~C~~~i~ik 52 (259)
.|||.| +|..|+..|++-
T Consensus 1 MP~Yey--~C~~Cg~~fe~~ 18 (52)
T TIGR02605 1 MPIYEY--RCTACGHRFEVL 18 (52)
T ss_pred CCCEEE--EeCCCCCEeEEE
Confidence 377777 689999988875
No 15
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=69.88 E-value=4.5 Score=30.08 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=35.2
Q ss_pred ecCCCCccccccccccceeeccCceeeeeeEEEEEE-cCCCCceeEEe
Q 025008 6 WCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMK-SPCCKHQIVIQ 52 (259)
Q Consensus 6 wC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mk-C~~C~~~i~ik 52 (259)
.|.+|++..+.=..+.+.-..+++.+.+..-+|+.. |+.|+-.=-.+
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~ 49 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYK 49 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEe
Confidence 499999987777777776666667788877788765 99998763334
No 16
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=66.79 E-value=3.2 Score=33.75 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=17.9
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCce
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~ 48 (259)
|-.+||..|+....-. .+.+.||.|++.
T Consensus 68 p~~~~C~~Cg~~~~~~-------------------~~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPE-------------------IDLYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecC-------------------CcCccCcCCcCC
Confidence 6678888888432221 114679999874
No 17
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.70 E-value=3.3 Score=37.00 Aligned_cols=39 Identities=26% Similarity=0.540 Sum_probs=28.1
Q ss_pred ceecCCCC---ccccccc-cccceeeccCceeeeeeEEEEEEcCCCCcee
Q 025008 4 NIWCGGCN---SMIAKGV-RFNAEKKQVGNYYSTKIWSFTMKSPCCKHQI 49 (259)
Q Consensus 4 ~iwC~~C~---~~I~kGv-RFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i 49 (259)
-..|++|| +|+.-|. |-||.++.++.++ || ||..|++..
T Consensus 17 ~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWl---IY----kC~~Cd~tW 59 (203)
T COG4332 17 AKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWL---IY----KCTHCDYTW 59 (203)
T ss_pred hhhCcccCCcceeeecCcEEEcCCCcEEEEEE---EE----EeeccCCcc
Confidence 35799998 5788885 8899888776433 33 799887653
No 18
>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=62.59 E-value=6.2 Score=24.08 Aligned_cols=11 Identities=36% Similarity=0.754 Sum_probs=7.1
Q ss_pred cCCCCcccccc
Q 025008 7 CGGCNSMIAKG 17 (259)
Q Consensus 7 C~~C~~~I~kG 17 (259)
|..||..|.-.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 77787666533
No 19
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.23 E-value=4.4 Score=33.87 Aligned_cols=43 Identities=14% Similarity=0.299 Sum_probs=22.4
Q ss_pred CcceecCCCCccccccccccceeeccCc------eeeeeeEEEEEEcCCCCce
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGN------YYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~------Y~st~I~~F~mkC~~C~~~ 48 (259)
|--.||..||....-. ..+.+++- -|.--...+.++||.|++.
T Consensus 68 p~~~~C~~CG~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK----EVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecc----cccccccccccccccccccccccCcCCcCCCCC
Confidence 6678999998321110 01222221 1222233566889999864
No 20
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=61.15 E-value=7.1 Score=28.93 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=24.0
Q ss_pred ceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEe
Q 025008 4 NIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 4 ~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ik 52 (259)
...|+.||.-|.-|.++= .|.||.|++.+.+|
T Consensus 9 ~~~CtSCg~~i~p~e~~v-----------------~F~CPnCGe~~I~R 40 (61)
T COG2888 9 PPVCTSCGREIAPGETAV-----------------KFPCPNCGEVEIYR 40 (61)
T ss_pred CceeccCCCEeccCCcee-----------------EeeCCCCCceeeeh
Confidence 457999999887766553 36899999777665
No 21
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=57.72 E-value=5.4 Score=29.64 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=13.0
Q ss_pred CCcceecCCCCccccc
Q 025008 1 MPFNIWCGGCNSMIAK 16 (259)
Q Consensus 1 mPF~iwC~~C~~~I~k 16 (259)
|=|+|+|-+||.-|+-
T Consensus 1 MiiPvRCFTCGkvi~~ 16 (62)
T PRK04016 1 MMIPVRCFTCGKVIAE 16 (62)
T ss_pred CCCCeEecCCCCChHH
Confidence 6688999999988753
No 22
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=57.21 E-value=6.2 Score=40.16 Aligned_cols=36 Identities=19% Similarity=0.434 Sum_probs=26.3
Q ss_pred ceeeeeeEEEEEEcCCCCceeEEe---------cCCCCCCeeeec
Q 025008 29 NYYSTKIWSFTMKSPCCKHQIVIQ---------TDPKNCEYVIIS 64 (259)
Q Consensus 29 ~Y~st~I~~F~mkC~~C~~~i~ik---------TDPkn~dYvv~~ 64 (259)
.|......+|+..||.|+.+.+++ .+|+.+-|+|.+
T Consensus 190 ~~~~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~ 234 (557)
T PF05876_consen 190 LYEESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH 234 (557)
T ss_pred HHHhCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCC
Confidence 455555668889999998887764 257888888854
No 23
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.63 E-value=5 Score=33.04 Aligned_cols=12 Identities=33% Similarity=0.819 Sum_probs=9.1
Q ss_pred CCcceecCCCCcc
Q 025008 1 MPFNIWCGGCNSM 13 (259)
Q Consensus 1 mPF~iwC~~C~~~ 13 (259)
.|-..|| .|+.+
T Consensus 67 vp~~~~C-~Cg~~ 78 (124)
T PRK00762 67 IPVEIEC-ECGYE 78 (124)
T ss_pred cCeeEEe-eCcCc
Confidence 3778899 99843
No 24
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=56.34 E-value=6.7 Score=38.22 Aligned_cols=41 Identities=22% Similarity=0.425 Sum_probs=22.2
Q ss_pred CCcceecCCCCc-cccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEe
Q 025008 1 MPFNIWCGGCNS-MIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 1 mPF~iwC~~C~~-~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ik 52 (259)
.||+..|..||. .--.=+.||++..+| +..|+.|+++.++.
T Consensus 171 ~Pf~piC~~cGri~tt~v~~~d~~~~~v-----------~Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 171 SPFLPICEKCGRIDTTEVTEYDPEGGTV-----------TYRCEECGHEGEVD 212 (360)
T ss_dssp -SEEEEETTTEE--EEEEEEE--SSSEE-----------EEE--TTS---EEE
T ss_pred eeeeeeccccCCcccceeeEeecCCCEE-----------EEEecCCCCEEEEe
Confidence 399999999997 333334555544444 46789999887753
No 25
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=54.91 E-value=5.7 Score=29.59 Aligned_cols=24 Identities=21% Similarity=0.529 Sum_probs=16.2
Q ss_pred CCcceecCCCCccccccccccceeec
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQ 26 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~ 26 (259)
|=++|+|-+||.-|| -.|+.=|+.
T Consensus 1 MiiPiRCFsCGkvi~--~~w~~y~~r 24 (63)
T COG1644 1 MIIPVRCFSCGKVIG--HKWEEYKRR 24 (63)
T ss_pred CCCceEeecCCCCHH--HHHHHHHHH
Confidence 568899999998874 344443333
No 26
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=53.18 E-value=7.1 Score=37.09 Aligned_cols=20 Identities=15% Similarity=0.159 Sum_probs=14.9
Q ss_pred eeeeEE----EEEEcCCCCceeEE
Q 025008 32 STKIWS----FTMKSPCCKHQIVI 51 (259)
Q Consensus 32 st~I~~----F~mkC~~C~~~i~i 51 (259)
++.+.| |.|.|..|+++|-.
T Consensus 29 ~~~~VRf~~Pf~i~C~~C~~~I~k 52 (324)
T PF04502_consen 29 GILTVRFMMPFNIWCNTCGEYIYK 52 (324)
T ss_pred cceEEEEcCCccCcCCCCcccccc
Confidence 455555 57899999999863
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=52.75 E-value=16 Score=26.92 Aligned_cols=18 Identities=39% Similarity=0.578 Sum_probs=12.3
Q ss_pred cceecCCCCcccc---ccccc
Q 025008 3 FNIWCGGCNSMIA---KGVRF 20 (259)
Q Consensus 3 F~iwC~~C~~~I~---kGvRF 20 (259)
....|+.||..|. +||+|
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F 26 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKF 26 (59)
T ss_pred cCccccCCCCcccCCCccCEe
Confidence 3457999998775 35554
No 28
>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=52.23 E-value=4.7 Score=36.17 Aligned_cols=32 Identities=13% Similarity=0.268 Sum_probs=0.0
Q ss_pred ecCCCCccccccccccceeeccCceeeeeeEEEEEEcC
Q 025008 6 WCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSP 43 (259)
Q Consensus 6 wC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~ 43 (259)
-|.=||+++|+|.| .-.+.|+-+-+.|-|+|=
T Consensus 103 ~CEICGN~~Y~Grk------aFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 103 KCEICGNQSYKGRK------AFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp --------------------------------------
T ss_pred eeEeCCCcceecHH------HHHHhcChhHHHccChhc
Confidence 49999999999954 445667777777777774
No 29
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=52.07 E-value=6.9 Score=26.57 Aligned_cols=17 Identities=41% Similarity=1.040 Sum_probs=11.5
Q ss_pred eecCCCCccccccccccc
Q 025008 5 IWCGGCNSMIAKGVRFNA 22 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNA 22 (259)
|.|.+|+..| .|.||--
T Consensus 1 v~Cd~C~~~i-~G~ry~C 17 (43)
T cd02340 1 VICDGCQGPI-VGVRYKC 17 (43)
T ss_pred CCCCCCCCcC-cCCeEEC
Confidence 5688888744 7776643
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=51.86 E-value=13 Score=25.16 Aligned_cols=18 Identities=22% Similarity=0.648 Sum_probs=14.5
Q ss_pred EEEcCCCCceeEEecCCC
Q 025008 39 TMKSPCCKHQIVIQTDPK 56 (259)
Q Consensus 39 ~mkC~~C~~~i~ikTDPk 56 (259)
.++||.|++.+.++-.|.
T Consensus 21 ~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 21 GVRCPYCGYRILFKERPP 38 (46)
T ss_pred ceECCCCCCeEEEccCCC
Confidence 478999999999876553
No 31
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=51.57 E-value=11 Score=38.14 Aligned_cols=39 Identities=28% Similarity=0.600 Sum_probs=26.9
Q ss_pred CCcceecCCCCccccccc-cccceeeccCceeeeeeEEEEEEcCCCCceeEE
Q 025008 1 MPFNIWCGGCNSMIAKGV-RFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVI 51 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGv-RFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~i 51 (259)
.||+..|..||..-.-.| -||++..+|. | .|. |+++.+.
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~~~v~-y----------~~~-cG~~~~~ 211 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEAGTVT-Y----------DCE-CGHEGEV 211 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCCCEEE-E----------EcC-CCCEEEE
Confidence 399999999997765555 6777766552 2 454 7776654
No 32
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=51.52 E-value=26 Score=23.37 Aligned_cols=41 Identities=17% Similarity=0.344 Sum_probs=27.3
Q ss_pred ecCCCCccccc-cccccceeecc--CceeeeeeEEEEEEcCCCC
Q 025008 6 WCGGCNSMIAK-GVRFNAEKKQV--GNYYSTKIWSFTMKSPCCK 46 (259)
Q Consensus 6 wC~~C~~~I~k-GvRFNAeKk~v--g~Y~st~I~~F~mkC~~C~ 46 (259)
-|..||..+.. |..+=.+.-.+ ..++=+.++++...|+.|+
T Consensus 4 ~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 4 ACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred cCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 48889875542 44432222222 3677899999999999995
No 33
>KOG2407 consensus GPI transamidase complex, GPI16/PIG-T component, involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=50.44 E-value=6 Score=40.32 Aligned_cols=12 Identities=42% Similarity=1.085 Sum_probs=10.9
Q ss_pred CCcceecCCCCc
Q 025008 1 MPFNIWCGGCNS 12 (259)
Q Consensus 1 mPF~iwC~~C~~ 12 (259)
|||||+|.+|--
T Consensus 495 MPYNVIcltcTv 506 (575)
T KOG2407|consen 495 MPYNVICLTCTV 506 (575)
T ss_pred CceeEEeeehhh
Confidence 999999999964
No 34
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.13 E-value=23 Score=30.17 Aligned_cols=32 Identities=22% Similarity=0.285 Sum_probs=30.3
Q ss_pred ceeeeeeEEEEEEcCCCCceeEEecCCCCCCe
Q 025008 29 NYYSTKIWSFTMKSPCCKHQIVIQTDPKNCEY 60 (259)
Q Consensus 29 ~Y~st~I~~F~mkC~~C~~~i~ikTDPkn~dY 60 (259)
.||+|--|...+-|+.-+=+|++-|||+..+|
T Consensus 62 ~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~i 93 (140)
T KOG3368|consen 62 LSYKTSKYKLHFYETPTGLKFVLNTDPKAGSI 93 (140)
T ss_pred eEEeeceeEEEEEEcCCCcEEEEecCCCcccH
Confidence 79999999999999999999999999998775
No 35
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=47.99 E-value=8.8 Score=30.99 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=6.4
Q ss_pred CcceecCCCCc
Q 025008 2 PFNIWCGGCNS 12 (259)
Q Consensus 2 PF~iwC~~C~~ 12 (259)
|...||..|+.
T Consensus 68 p~~~~C~~Cg~ 78 (113)
T PF01155_consen 68 PARARCRDCGH 78 (113)
T ss_dssp --EEEETTTS-
T ss_pred CCcEECCCCCC
Confidence 66778888874
No 36
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=47.64 E-value=9.1 Score=38.98 Aligned_cols=39 Identities=13% Similarity=0.308 Sum_probs=27.8
Q ss_pred cceecCCCCccc---cccccccceeeccCceeeeeeEEEEEEcCCCCceeE
Q 025008 3 FNIWCGGCNSMI---AKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIV 50 (259)
Q Consensus 3 F~iwC~~C~~~I---~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ 50 (259)
|.+-|.+|+++. ..+.+|+-.- .--.-++.|+.|+..|+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~---------~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGE---------APETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCccccccceeecCCC---------CccceEEECCCCcCCCC
Confidence 678899999763 3567774221 33456789999999986
No 37
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=47.51 E-value=10 Score=28.99 Aligned_cols=15 Identities=27% Similarity=0.592 Sum_probs=11.5
Q ss_pred CCcceecCCCCcccc
Q 025008 1 MPFNIWCGGCNSMIA 15 (259)
Q Consensus 1 mPF~iwC~~C~~~I~ 15 (259)
|=++|+|=+||..||
T Consensus 1 MiiPVRCFTCGkvig 15 (71)
T PLN00032 1 MIIPVRCFTCGKVIG 15 (71)
T ss_pred CCCceeecCCCCCcH
Confidence 557888888888774
No 38
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=47.50 E-value=35 Score=25.77 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=37.9
Q ss_pred ceee-eeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCCh
Q 025008 29 NYYS-TKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFDV 75 (259)
Q Consensus 29 ~Y~s-t~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~~ 75 (259)
.++. ..||.+++.+.....-+.+-.++.+ .+|+.+|..++.+....
T Consensus 34 k~l~~~~i~ElR~~~~~~~~Ri~y~~~~~~-~ivll~~f~Kkt~k~p~ 80 (91)
T PF05973_consen 34 KHLKGDGIYELRVRGGSNIYRILYFFDGGD-IIVLLHGFIKKTQKTPK 80 (91)
T ss_pred cccCcCCeEEEEEeecCCcceEEEEEcCcc-EEEEEEEEEeCCCCCCH
Confidence 4555 8999999999998888999998888 88999999888754433
No 39
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=45.85 E-value=11 Score=35.59 Aligned_cols=26 Identities=31% Similarity=0.337 Sum_probs=22.9
Q ss_pred EEcCCCCceeEEecCCCCCCeeeecCc
Q 025008 40 MKSPCCKHQIVIQTDPKNCEYVIISGA 66 (259)
Q Consensus 40 mkC~~C~~~i~ikTDPkn~dYvv~~Ga 66 (259)
|.||.|+.. .|-+|+++.+|||..=+
T Consensus 2 ~~CpeCg~~-~~~~d~~~ge~VC~~CG 27 (285)
T COG1405 2 MSCPECGST-NIITDYERGEIVCADCG 27 (285)
T ss_pred CCCCCCCCc-cceeeccCCeEEeccCC
Confidence 679999999 99999999999997633
No 40
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=43.24 E-value=10 Score=28.03 Aligned_cols=15 Identities=27% Similarity=0.592 Sum_probs=9.5
Q ss_pred CCcceecCCCCcccc
Q 025008 1 MPFNIWCGGCNSMIA 15 (259)
Q Consensus 1 mPF~iwC~~C~~~I~ 15 (259)
|=+.|+|-+||..|+
T Consensus 1 MiiPVRCFTCGkvi~ 15 (60)
T PF01194_consen 1 MIIPVRCFTCGKVIG 15 (60)
T ss_dssp ---SSS-STTTSBTC
T ss_pred CCCceecCCCCCChh
Confidence 457889999998875
No 41
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=42.58 E-value=13 Score=23.86 Aligned_cols=18 Identities=17% Similarity=0.429 Sum_probs=15.1
Q ss_pred EEEcCCCCceeEEecCCC
Q 025008 39 TMKSPCCKHQIVIQTDPK 56 (259)
Q Consensus 39 ~mkC~~C~~~i~ikTDPk 56 (259)
.+.||.|+..+.|..|+-
T Consensus 2 ~~~CP~C~~~~~v~~~~~ 19 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQL 19 (38)
T ss_pred EEECCCCCCEEEeCHHHc
Confidence 478999999999987754
No 42
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=42.34 E-value=18 Score=26.00 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=6.3
Q ss_pred EcCCCCceeEEe
Q 025008 41 KSPCCKHQIVIQ 52 (259)
Q Consensus 41 kC~~C~~~i~ik 52 (259)
+||.|+..|++.
T Consensus 4 ~CP~CG~~iev~ 15 (54)
T TIGR01206 4 ECPDCGAEIELE 15 (54)
T ss_pred CCCCCCCEEecC
Confidence 455555555553
No 43
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=42.29 E-value=23 Score=23.51 Aligned_cols=18 Identities=28% Similarity=0.525 Sum_probs=15.9
Q ss_pred EEcCCCCceeEEecCCCC
Q 025008 40 MKSPCCKHQIVIQTDPKN 57 (259)
Q Consensus 40 mkC~~C~~~i~ikTDPkn 57 (259)
.+|+.|++.+++++-...
T Consensus 2 ~~CP~Cg~~lv~r~~k~g 19 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG 19 (39)
T ss_pred cCCCCCCceeEEEECCCC
Confidence 369999999999998887
No 44
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=39.69 E-value=24 Score=35.90 Aligned_cols=38 Identities=18% Similarity=0.567 Sum_probs=25.9
Q ss_pred CCcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEE
Q 025008 1 MPFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVI 51 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~i 51 (259)
.||+..|..||..-..=|-||++. +| .| .|. |+++.+.
T Consensus 165 ~P~~pic~~cGrv~~~~~~~~~~~-~v-~Y----------~c~-cG~~g~~ 202 (515)
T TIGR00467 165 YPISVFCENCGRDTTTVNNYDNEY-SI-EY----------SCE-CGNQESV 202 (515)
T ss_pred eeeeeecCCcCccCceEEEecCCc-eE-EE----------EcC-CCCEEEE
Confidence 399999999998755555677655 33 11 364 8877664
No 45
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.64 E-value=15 Score=22.22 Aligned_cols=17 Identities=24% Similarity=0.810 Sum_probs=10.9
Q ss_pred ceecCCCCccccccccc
Q 025008 4 NIWCGGCNSMIAKGVRF 20 (259)
Q Consensus 4 ~iwC~~C~~~I~kGvRF 20 (259)
.+.|..||..|..+-+|
T Consensus 2 ~~~Cp~Cg~~~~~~~~f 18 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKF 18 (26)
T ss_pred cCCCcccCCcCCccccc
Confidence 45677777766666554
No 46
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=39.07 E-value=27 Score=24.95 Aligned_cols=24 Identities=29% Similarity=0.499 Sum_probs=16.2
Q ss_pred EcCCCCceeEEecCCCCCCeeeec
Q 025008 41 KSPCCKHQIVIQTDPKNCEYVIIS 64 (259)
Q Consensus 41 kC~~C~~~i~ikTDPkn~dYvv~~ 64 (259)
.||-|+.+|++--||...+-..++
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiE 25 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIE 25 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEe
Confidence 577788888777777766544443
No 47
>PRK09628 oorB 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed
Probab=38.44 E-value=14 Score=34.46 Aligned_cols=19 Identities=26% Similarity=0.700 Sum_probs=12.8
Q ss_pred ceecCCCCccccccccccc
Q 025008 4 NIWCGGCNSMIAKGVRFNA 22 (259)
Q Consensus 4 ~iwC~~C~~~I~kGvRFNA 22 (259)
++||.||++.|--..=+.+
T Consensus 16 ~~~CpGCg~~i~~~~v~~a 34 (277)
T PRK09628 16 TLWCWGCGDGVILKSIIRA 34 (277)
T ss_pred CCcCCCCCCchHHHHHHHH
Confidence 6899999975554444444
No 48
>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=37.71 E-value=31 Score=23.09 Aligned_cols=19 Identities=16% Similarity=0.530 Sum_probs=14.8
Q ss_pred eeeEEEEEEcCCCCceeEEec
Q 025008 33 TKIWSFTMKSPCCKHQIVIQT 53 (259)
Q Consensus 33 t~I~~F~mkC~~C~~~i~ikT 53 (259)
.|||.| +|..|++.|++..
T Consensus 1 MP~Yey--~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 1 MPIYEY--RCEECGHEFEVLQ 19 (42)
T ss_pred CCCEEE--EeCCCCCEEEEEE
Confidence 367776 6889999999764
No 49
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.27 E-value=31 Score=23.63 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=15.9
Q ss_pred EEEEcCCCCceeEEecCCC
Q 025008 38 FTMKSPCCKHQIVIQTDPK 56 (259)
Q Consensus 38 F~mkC~~C~~~i~ikTDPk 56 (259)
..++|+.|++.|.++-=|.
T Consensus 18 ~~irC~~CG~rIlyK~R~~ 36 (44)
T smart00659 18 DVVRCRECGYRILYKKRTK 36 (44)
T ss_pred CceECCCCCceEEEEeCCC
Confidence 5689999999999987654
No 50
>PHA02998 RNA polymerase subunit; Provisional
Probab=36.90 E-value=22 Score=31.88 Aligned_cols=54 Identities=24% Similarity=0.411 Sum_probs=38.6
Q ss_pred ccccccccceeecc---CceeeeeeEEEEEEcCCCCc----eeEEecC----CCCCCeeeecCcc
Q 025008 14 IAKGVRFNAEKKQV---GNYYSTKIWSFTMKSPCCKH----QIVIQTD----PKNCEYVIISGAQ 67 (259)
Q Consensus 14 I~kGvRFNAeKk~v---g~Y~st~I~~F~mkC~~C~~----~i~ikTD----Pkn~dYvv~~Gar 67 (259)
|.+||-||-+|-.- +.||.+-==.-..+|+.|++ ++.+||- |...-|.|..-+.
T Consensus 115 v~~~veydid~~~d~~y~~yfnvlpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~ 179 (195)
T PHA02998 115 IKKGVEYDIDKIPDVDYDDYFNVLDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKK 179 (195)
T ss_pred HhcCCccchhhcccccchhheeccCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCC
Confidence 67999999988653 47888533225589999997 4667887 5567788765443
No 51
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=36.88 E-value=34 Score=22.24 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=9.9
Q ss_pred cCCCCceeEEecCCCC
Q 025008 42 SPCCKHQIVIQTDPKN 57 (259)
Q Consensus 42 C~~C~~~i~ikTDPkn 57 (259)
|+.|+|-+..+.|..+
T Consensus 4 Cp~C~nlL~p~~~~~~ 19 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEK 19 (35)
T ss_dssp ETTTTSBEEEEEETTT
T ss_pred CCCCCccceEcCCCcc
Confidence 6666666666666554
No 52
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=35.61 E-value=16 Score=25.39 Aligned_cols=13 Identities=15% Similarity=0.115 Sum_probs=7.6
Q ss_pred eeEEEEEEcCCCC
Q 025008 34 KIWSFTMKSPCCK 46 (259)
Q Consensus 34 ~I~~F~mkC~~C~ 46 (259)
||..++++|..|.
T Consensus 10 ~i~g~R~~C~~C~ 22 (49)
T cd02338 10 NFTGRRYKCLICY 22 (49)
T ss_pred CcEEeeEEeCCCC
Confidence 4445566677664
No 53
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=35.21 E-value=18 Score=24.87 Aligned_cols=17 Identities=29% Similarity=0.686 Sum_probs=11.1
Q ss_pred eecCCCCcccccccccc
Q 025008 5 IWCGGCNSMIAKGVRFN 21 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFN 21 (259)
|.|.+|+...-.|+||-
T Consensus 1 i~Cd~C~~~~i~G~Ryk 17 (45)
T cd02339 1 IICDTCRKQGIIGIRWK 17 (45)
T ss_pred CCCCCCCCCCcccCeEE
Confidence 57888886555565553
No 54
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=35.21 E-value=39 Score=24.63 Aligned_cols=38 Identities=26% Similarity=0.506 Sum_probs=28.1
Q ss_pred eecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEec
Q 025008 5 IWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQT 53 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ikT 53 (259)
+.|-.||+ |..+.-.-.|-+--|-..||.|..+..|.-
T Consensus 5 i~CP~Cgn-----------KTR~kir~DT~LkNfPlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 5 ILCPICGN-----------KTRLKIREDTVLKNFPLYCPKCKQETLIDV 42 (55)
T ss_pred EECCCCCC-----------ccceeeecCceeccccccCCCCCceEEEEe
Confidence 56888876 444545556778888899999999877743
No 55
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=34.89 E-value=31 Score=24.68 Aligned_cols=34 Identities=18% Similarity=0.398 Sum_probs=21.9
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCce
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~ 48 (259)
.|.+.|..|..|-|+-- ++ ..-....+|+.|+..
T Consensus 20 r~aLIC~~C~~hNGla~-----~~--------~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 20 RYALICSKCFSHNGLAP-----KE--------EFEEIQYRCPYCGAL 53 (54)
T ss_pred ceeEECcccchhhcccc-----cc--------cCCceEEEcCCCCCc
Confidence 47889999998877643 11 111235679999753
No 56
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=34.87 E-value=34 Score=25.09 Aligned_cols=14 Identities=29% Similarity=0.589 Sum_probs=11.9
Q ss_pred EEEEcCCCCceeEE
Q 025008 38 FTMKSPCCKHQIVI 51 (259)
Q Consensus 38 F~mkC~~C~~~i~i 51 (259)
|.++|..|+..|.+
T Consensus 30 ikikC~gCg~~iml 43 (57)
T PF06107_consen 30 IKIKCLGCGRQIML 43 (57)
T ss_pred EEEEECCCCCEEEE
Confidence 78889999988876
No 57
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=34.52 E-value=6.7 Score=30.77 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=24.4
Q ss_pred ecCCCCccccccccccceeeccCceeeeeeEEE---EEEcCCCCceeEE
Q 025008 6 WCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSF---TMKSPCCKHQIVI 51 (259)
Q Consensus 6 wC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F---~mkC~~C~~~i~i 51 (259)
.|.+|+.. +.-|.-+||++| +-||..|...|.+
T Consensus 35 ~C~~C~~~-------------L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 35 HCPHCGHP-------------LSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred cCcCCCCc-------------CcccccchHHHHHHhCCCCcccCCCCCh
Confidence 47777654 346677899887 5679999998854
No 58
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=34.19 E-value=25 Score=25.77 Aligned_cols=44 Identities=25% Similarity=0.489 Sum_probs=27.7
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCC--ceeEEecCCCCCCeee
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCK--HQIVIQTDPKNCEYVI 62 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~--~~i~ikTDPkn~dYvv 62 (259)
-=+|+|..|+..+.+.. ...|+ ..|||.|. |+|.|+ -+++.|+-
T Consensus 2 ~~tiRC~~CnKlLa~a~--------~~~yl-------e~KCPrCK~vN~~~~~--~e~~t~~~ 47 (60)
T COG4416 2 MQTIRCAKCNKLLAEAE--------GQAYL-------EKKCPRCKEVNEFYIK--EEATTQIH 47 (60)
T ss_pred ceeeehHHHhHHHHhcc--------cceee-------eecCCccceeeeeecc--cccchhhh
Confidence 34799999998765421 01354 57899997 455555 45666653
No 59
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=34.11 E-value=15 Score=34.67 Aligned_cols=13 Identities=31% Similarity=0.963 Sum_probs=10.1
Q ss_pred ceecCCCCccccc
Q 025008 4 NIWCGGCNSMIAK 16 (259)
Q Consensus 4 ~iwC~~C~~~I~k 16 (259)
++||.|||+.+-.
T Consensus 18 ~~~CpGCg~~~i~ 30 (301)
T PRK05778 18 TTWCPGCGNFGIL 30 (301)
T ss_pred CCCCCCCCChHHH
Confidence 4799999986543
No 60
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=33.44 E-value=21 Score=34.43 Aligned_cols=42 Identities=19% Similarity=0.532 Sum_probs=29.0
Q ss_pred cceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEecCCCC
Q 025008 3 FNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQTDPKN 57 (259)
Q Consensus 3 F~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ikTDPkn 57 (259)
|.++|..|..|=|+-.+ +.- .|- .+.|+.|.....=+-+|+|
T Consensus 219 yALIC~~C~~HNGla~~-----ee~-~yi-------~F~C~~Cn~LN~~~k~~e~ 260 (328)
T KOG2846|consen 219 YALICSQCHHHNGLARK-----EEY-EYI-------TFRCPHCNALNPAKKSPEN 260 (328)
T ss_pred hhhcchhhccccCcCCh-----hhc-Cce-------EEECccccccCCCcCCccc
Confidence 67899999999887654 111 111 3679999998876666555
No 61
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.66 E-value=24 Score=26.44 Aligned_cols=19 Identities=32% Similarity=0.725 Sum_probs=14.8
Q ss_pred cCCCCce--------eEEecCCCCCCe
Q 025008 42 SPCCKHQ--------IVIQTDPKNCEY 60 (259)
Q Consensus 42 C~~C~~~--------i~ikTDPkn~dY 60 (259)
||.|+.. +.|-+||++++-
T Consensus 21 CP~Cgs~~~te~W~G~~iIidpe~SeI 47 (64)
T COG2093 21 CPVCGSTDLTEEWFGLLIIIDPEKSEI 47 (64)
T ss_pred CCCCCCcccchhhccEEEEEcCcHHHH
Confidence 8999887 667888888653
No 62
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=32.22 E-value=22 Score=24.16 Aligned_cols=20 Identities=30% Similarity=0.679 Sum_probs=11.8
Q ss_pred cceecCCCCccccccccccc
Q 025008 3 FNIWCGGCNSMIAKGVRFNA 22 (259)
Q Consensus 3 F~iwC~~C~~~I~kGvRFNA 22 (259)
+.+.|.+|+...-.|+||--
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C 22 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHC 22 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEE
T ss_pred CCeECcCCCCCcCcCCeEEC
Confidence 46889999875445666643
No 63
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=32.00 E-value=36 Score=32.96 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=22.9
Q ss_pred CCcceecCCCCcccccc-ccccceeeccCceeeeeeEEEEEEcCCCCceeEE
Q 025008 1 MPFNIWCGGCNSMIAKG-VRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVI 51 (259)
Q Consensus 1 mPF~iwC~~C~~~I~kG-vRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~i 51 (259)
.||+..|..|| -|.-- +-||.+..+| .| .|. |+++.+.
T Consensus 166 ~P~~p~c~~cg-~~~~~v~~~d~~~~~v---------~y--~c~-cG~~g~~ 204 (353)
T cd00674 166 YPFMPYCEKCG-KDTTTVEAYDAKAGTV---------TY--KCE-CGHEETV 204 (353)
T ss_pred eeeeeecCCcC-cceeEEEEEeCCCCeE---------EE--EcC-CCCEEEE
Confidence 39999999999 33322 2456555444 12 463 7776654
No 64
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.69 E-value=42 Score=23.82 Aligned_cols=19 Identities=26% Similarity=0.730 Sum_probs=15.6
Q ss_pred EEEcCCCCceeEEecCCCC
Q 025008 39 TMKSPCCKHQIVIQTDPKN 57 (259)
Q Consensus 39 ~mkC~~C~~~i~ikTDPkn 57 (259)
.++|+.|+..|-|+-=|.-
T Consensus 24 ~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 24 GIRCPYCGSRILVKERPKV 42 (49)
T ss_pred ceeCCCCCcEEEEeccCCc
Confidence 3689999999999876654
No 65
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.30 E-value=32 Score=32.51 Aligned_cols=33 Identities=18% Similarity=0.392 Sum_probs=24.3
Q ss_pred EEEEcCCCCceeEEecCCC------CCCeeeecCcccCC
Q 025008 38 FTMKSPCCKHQIVIQTDPK------NCEYVIISGAQRKT 70 (259)
Q Consensus 38 F~mkC~~C~~~i~ikTDPk------n~dYvv~~GarR~~ 70 (259)
..+-|+.|++.+-=+|||- +.++++.-|-.|..
T Consensus 128 ~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~ 166 (279)
T COG2816 128 WARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHF 166 (279)
T ss_pred eeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCC
Confidence 4578999999999999994 45555555555544
No 66
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=31.19 E-value=28 Score=23.93 Aligned_cols=18 Identities=33% Similarity=0.789 Sum_probs=6.2
Q ss_pred eecCC--CCccccccccccc
Q 025008 5 IWCGG--CNSMIAKGVRFNA 22 (259)
Q Consensus 5 iwC~~--C~~~I~kGvRFNA 22 (259)
.||.+ |+..|.....-+.
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~ 38 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNS 38 (64)
T ss_dssp C--TTSST---ECS-SSTTS
T ss_pred cCCCCCCCcccEEecCCCCC
Confidence 46655 7666655544444
No 67
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=30.41 E-value=30 Score=23.67 Aligned_cols=19 Identities=21% Similarity=0.417 Sum_probs=15.5
Q ss_pred EcCCCCceeEEecCCCCCC
Q 025008 41 KSPCCKHQIVIQTDPKNCE 59 (259)
Q Consensus 41 kC~~C~~~i~ikTDPkn~d 59 (259)
+||.|++...|+|-..-++
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~ 19 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSP 19 (47)
T ss_pred CcCCCCCeeEEEEchhhCc
Confidence 5999999999998766544
No 68
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=30.19 E-value=23 Score=26.16 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=11.9
Q ss_pred CCcceecCCCCcccc
Q 025008 1 MPFNIWCGGCNSMIA 15 (259)
Q Consensus 1 mPF~iwC~~C~~~I~ 15 (259)
|-|.+.|.+||.-|.
T Consensus 1 MVf~lvCSTCGrDlS 15 (63)
T PF05864_consen 1 MVFQLVCSTCGRDLS 15 (63)
T ss_pred CeeeeeecccCCcch
Confidence 678899999986554
No 69
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.71 E-value=31 Score=23.26 Aligned_cols=10 Identities=30% Similarity=1.049 Sum_probs=6.3
Q ss_pred ecCCCCcccc
Q 025008 6 WCGGCNSMIA 15 (259)
Q Consensus 6 wC~~C~~~I~ 15 (259)
.|..||+.++
T Consensus 2 FCp~Cg~~l~ 11 (52)
T smart00661 2 FCPKCGNMLI 11 (52)
T ss_pred CCCCCCCccc
Confidence 3777777554
No 70
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=28.73 E-value=20 Score=33.57 Aligned_cols=11 Identities=36% Similarity=1.120 Sum_probs=9.0
Q ss_pred ceecCCCCccc
Q 025008 4 NIWCGGCNSMI 14 (259)
Q Consensus 4 ~iwC~~C~~~I 14 (259)
++||.|||+.+
T Consensus 8 ~~~CpGCg~~~ 18 (280)
T PRK11869 8 IAWCPGCGNFG 18 (280)
T ss_pred CCCCcCCCCHH
Confidence 57999999853
No 71
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=28.68 E-value=76 Score=31.23 Aligned_cols=53 Identities=25% Similarity=0.479 Sum_probs=33.2
Q ss_pred CcceecCCCCccccccccccceeecc------Cceee---eeeEEEEEEcCCCCceeEEecCCCC
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQV------GNYYS---TKIWSFTMKSPCCKHQIVIQTDPKN 57 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~v------g~Y~s---t~I~~F~mkC~~C~~~i~ikTDPkn 57 (259)
|-.+-|.+|+-. |.+-.+.-++- |.... |-+|++...|+.|.+.=.|-.||=.
T Consensus 140 ~~~~~C~~C~Gs---Gak~gt~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i~~pC~ 201 (371)
T COG0484 140 TRSVTCSTCHGS---GAKPGTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKIIKDPCG 201 (371)
T ss_pred ceeeECCcCCCC---CCCCCCCCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeECCCCCC
Confidence 556778888633 44444322222 11221 2678999999999998888888744
No 72
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=28.53 E-value=29 Score=26.40 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=13.4
Q ss_pred EEcCCCCceeEEecCC
Q 025008 40 MKSPCCKHQIVIQTDP 55 (259)
Q Consensus 40 mkC~~C~~~i~ikTDP 55 (259)
|+||.|++.-.|+|-=
T Consensus 2 m~CP~Cg~~a~irtSr 17 (72)
T PRK09678 2 FHCPLCQHAAHARTSR 17 (72)
T ss_pred ccCCCCCCccEEEECh
Confidence 8999999999887643
No 73
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=28.02 E-value=22 Score=32.76 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=12.1
Q ss_pred EEEEcCCCCceeE
Q 025008 38 FTMKSPCCKHQIV 50 (259)
Q Consensus 38 F~mkC~~C~~~i~ 50 (259)
|.|+|-.|+++|-
T Consensus 41 F~~RCL~C~~YI~ 53 (272)
T COG5134 41 FPVRCLNCENYIQ 53 (272)
T ss_pred cceeecchhhhhh
Confidence 9999999999994
No 74
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=27.72 E-value=52 Score=23.43 Aligned_cols=15 Identities=13% Similarity=0.372 Sum_probs=12.4
Q ss_pred EEEEEcCCCCceeEEe
Q 025008 37 SFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 37 ~F~mkC~~C~~~i~ik 52 (259)
.|++.| +|++.|.|-
T Consensus 16 ~~~y~C-RCG~~f~i~ 30 (55)
T PF05207_consen 16 VYSYPC-RCGGEFEIS 30 (55)
T ss_dssp EEEEEE-TTSSEEEEE
T ss_pred EEEEcC-CCCCEEEEc
Confidence 388899 999998874
No 75
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=27.30 E-value=30 Score=22.20 Aligned_cols=14 Identities=29% Similarity=0.826 Sum_probs=8.1
Q ss_pred cceecCCCCcccccc
Q 025008 3 FNIWCGGCNSMIAKG 17 (259)
Q Consensus 3 F~iwC~~C~~~I~kG 17 (259)
|.+ |..||+.|...
T Consensus 3 yg~-C~~CGe~I~~~ 16 (36)
T PF01258_consen 3 YGI-CEDCGEPIPEE 16 (36)
T ss_dssp -SB--TTTSSBEEHH
T ss_pred CCC-ccccCChHHHH
Confidence 444 88888877654
No 76
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=26.67 E-value=30 Score=32.01 Aligned_cols=16 Identities=13% Similarity=0.314 Sum_probs=10.9
Q ss_pred cceecCCCCccccccc
Q 025008 3 FNIWCGGCNSMIAKGV 18 (259)
Q Consensus 3 F~iwC~~C~~~I~kGv 18 (259)
+...|..|++-.+...
T Consensus 121 ~~~~C~~C~~~~~~~~ 136 (250)
T COG0846 121 KRVRCSKCGNQYYDED 136 (250)
T ss_pred eeeEeCCCcCccchhh
Confidence 4578999987655443
No 77
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes.
Probab=26.47 E-value=25 Score=33.07 Aligned_cols=11 Identities=36% Similarity=1.075 Sum_probs=8.8
Q ss_pred ceecCCCCccc
Q 025008 4 NIWCGGCNSMI 14 (259)
Q Consensus 4 ~iwC~~C~~~I 14 (259)
.+||.|||+.+
T Consensus 1 ~~~CpGCg~~~ 11 (287)
T TIGR02177 1 PDWCPGCGDFG 11 (287)
T ss_pred CCcCCCCCChH
Confidence 37999999854
No 78
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=26.34 E-value=29 Score=29.50 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=8.1
Q ss_pred cceecCCCCccc
Q 025008 3 FNIWCGGCNSMI 14 (259)
Q Consensus 3 F~iwC~~C~~~I 14 (259)
+.+.|..|+...
T Consensus 104 ~~~~C~~C~~~~ 115 (178)
T PF02146_consen 104 FRLRCSKCGKEY 115 (178)
T ss_dssp EEEEETTTSBEE
T ss_pred ceeeecCCCccc
Confidence 456788887643
No 79
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=26.08 E-value=30 Score=25.61 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=11.7
Q ss_pred CCcceecCCCCcccc
Q 025008 1 MPFNIWCGGCNSMIA 15 (259)
Q Consensus 1 mPF~iwC~~C~~~I~ 15 (259)
|-|.+.|.+||.-|.
T Consensus 1 MVf~lVCsTCGrDlS 15 (63)
T PHA03082 1 MVFQLVCSTCGRDLS 15 (63)
T ss_pred CeeeeeecccCcchh
Confidence 678899999986543
No 80
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.05 E-value=32 Score=23.77 Aligned_cols=16 Identities=38% Similarity=0.918 Sum_probs=9.1
Q ss_pred eecCCCCccccccccc
Q 025008 5 IWCGGCNSMIAKGVRF 20 (259)
Q Consensus 5 iwC~~C~~~I~kGvRF 20 (259)
|.|.+|+...-.|.||
T Consensus 1 V~Cd~C~~~pI~G~Ry 16 (45)
T cd02344 1 VTCDGCQMFPINGPRF 16 (45)
T ss_pred CCCCCCCCCCCccCeE
Confidence 4577777654444444
No 81
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=26.01 E-value=49 Score=29.93 Aligned_cols=27 Identities=11% Similarity=0.269 Sum_probs=22.6
Q ss_pred eeEEEEEEcCCCCceeEEecCCCCCCe
Q 025008 34 KIWSFTMKSPCCKHQIVIQTDPKNCEY 60 (259)
Q Consensus 34 ~I~~F~mkC~~C~~~i~ikTDPkn~dY 60 (259)
.++.|.|-||.|++.+...+=+-|.-|
T Consensus 9 ~~~~~~~~CPvCg~~l~~~~~~~~IPy 35 (201)
T COG1779 9 EEFETRIDCPVCGGTLKAHMYLYDIPY 35 (201)
T ss_pred eeeeeeecCCcccceeeEEEeeecCCc
Confidence 578899999999999888887777555
No 82
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.99 E-value=33 Score=24.22 Aligned_cols=14 Identities=36% Similarity=0.776 Sum_probs=8.3
Q ss_pred eecCCCCcccccccc
Q 025008 5 IWCGGCNSMIAKGVR 19 (259)
Q Consensus 5 iwC~~C~~~I~kGvR 19 (259)
|-|.+|..+| .|+|
T Consensus 1 i~CdgC~~~~-~~~R 14 (48)
T cd02343 1 ISCDGCDEIA-PWHR 14 (48)
T ss_pred CCCCCCCCcC-CCce
Confidence 4588887754 3433
No 83
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=25.95 E-value=27 Score=21.31 Aligned_cols=12 Identities=42% Similarity=0.933 Sum_probs=9.9
Q ss_pred ecCCCCcccccc
Q 025008 6 WCGGCNSMIAKG 17 (259)
Q Consensus 6 wC~~C~~~I~kG 17 (259)
.|.+|+..|.-+
T Consensus 1 ~C~~C~~~i~~~ 12 (39)
T smart00132 1 KCAGCGKPIRGG 12 (39)
T ss_pred CccccCCcccCC
Confidence 488999988776
No 84
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=25.65 E-value=31 Score=25.84 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=7.5
Q ss_pred cceecCCCCcccc
Q 025008 3 FNIWCGGCNSMIA 15 (259)
Q Consensus 3 F~iwC~~C~~~I~ 15 (259)
.+|+|-+||.-||
T Consensus 3 iPiRCFtCGKvig 15 (69)
T KOG3497|consen 3 IPIRCFTCGKVIG 15 (69)
T ss_pred eeeEeeecccccc
Confidence 4566666665553
No 85
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=25.35 E-value=33 Score=25.52 Aligned_cols=13 Identities=54% Similarity=0.994 Sum_probs=10.7
Q ss_pred ecCCCCccccccc
Q 025008 6 WCGGCNSMIAKGV 18 (259)
Q Consensus 6 wC~~C~~~I~kGv 18 (259)
.|.+|+..|.+|.
T Consensus 9 ~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 9 KCKGCKKKIAKGE 21 (82)
T ss_dssp BETTTSCBE-TTS
T ss_pred cCcccCCcCCCCC
Confidence 6999999999985
No 86
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=25.31 E-value=42 Score=24.82 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=11.2
Q ss_pred EEEcCCCCceeEEecC
Q 025008 39 TMKSPCCKHQIVIQTD 54 (259)
Q Consensus 39 ~mkC~~C~~~i~ikTD 54 (259)
.-.||.|..+|.+++|
T Consensus 55 ~G~CP~C~~~i~~~~~ 70 (70)
T PF11793_consen 55 FGECPYCSSPISWSFS 70 (70)
T ss_dssp EEE-TTT-SEEEGGG-
T ss_pred ccCCcCCCCeeeEecC
Confidence 3579999999999886
No 87
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.26 E-value=35 Score=32.03 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=20.1
Q ss_pred EEcCCCCceeEEecCCCCCCeeeecCc
Q 025008 40 MKSPCCKHQIVIQTDPKNCEYVIISGA 66 (259)
Q Consensus 40 mkC~~C~~~i~ikTDPkn~dYvv~~Ga 66 (259)
.+||.|+. -.|-+|.++.++||..=+
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG 37 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGEIVCADCG 37 (310)
T ss_pred CcCcCCCC-CCeeEECCCCeEeecccC
Confidence 47999997 478888998888876544
No 88
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=24.95 E-value=32 Score=22.18 Aligned_cols=13 Identities=31% Similarity=0.881 Sum_probs=10.0
Q ss_pred EEcCCCCceeEEe
Q 025008 40 MKSPCCKHQIVIQ 52 (259)
Q Consensus 40 mkC~~C~~~i~ik 52 (259)
++|+.|+..|-++
T Consensus 18 irC~~CG~RIlyK 30 (32)
T PF03604_consen 18 IRCPECGHRILYK 30 (32)
T ss_dssp SSBSSSS-SEEBE
T ss_pred EECCcCCCeEEEe
Confidence 5899999988776
No 89
>PF14353 CpXC: CpXC protein
Probab=24.61 E-value=42 Score=27.10 Aligned_cols=45 Identities=20% Similarity=0.466 Sum_probs=24.5
Q ss_pred eecCCCCcccc--ccccccceeec--cCceeeeeeEEEEEEcCCCCceeEE
Q 025008 5 IWCGGCNSMIA--KGVRFNAEKKQ--VGNYYSTKIWSFTMKSPCCKHQIVI 51 (259)
Q Consensus 5 iwC~~C~~~I~--kGvRFNAeKk~--vg~Y~st~I~~F~mkC~~C~~~i~i 51 (259)
|-|.+|+.... -=.-.|+.... ...=++-.+ |.+.||.|+..+.+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l--~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSL--FSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCc--CEEECCCCCCceec
Confidence 67999986421 11344543221 111222222 45679999999986
No 90
>PRK03954 ribonuclease P protein component 4; Validated
Probab=23.96 E-value=87 Score=26.07 Aligned_cols=44 Identities=20% Similarity=0.362 Sum_probs=28.0
Q ss_pred eecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEecC
Q 025008 5 IWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQTD 54 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ikTD 54 (259)
.+|..|+.++-=|+ |+.-+.-+.=++ .+.+.|..|+..--|-.+
T Consensus 65 ~~CK~C~t~LiPG~--n~~vRi~~~~~~----~vvitCl~CG~~kR~P~~ 108 (121)
T PRK03954 65 RYCKRCHSFLVPGV--NARVRLRQKRMP----HVVITCLECGHIMRYPYL 108 (121)
T ss_pred HHhhcCCCeeecCC--ceEEEEecCCcc----eEEEECccCCCEEeeccc
Confidence 37999999987774 443222221111 268899999987766443
No 91
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.49 E-value=24 Score=34.77 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=12.4
Q ss_pred ecCCCCcccccccc
Q 025008 6 WCGGCNSMIAKGVR 19 (259)
Q Consensus 6 wC~~C~~~I~kGvR 19 (259)
.|.-||||+|.|.+
T Consensus 376 ~CEICgNyvy~GR~ 389 (470)
T COG5188 376 ECEICGNYVYYGRD 389 (470)
T ss_pred eeeecccccccchH
Confidence 49999999999964
No 92
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=23.38 E-value=61 Score=27.74 Aligned_cols=46 Identities=9% Similarity=0.148 Sum_probs=26.2
Q ss_pred cceecCCCCccccc-cccccceeecc----CceeeeeeEEEEEEcCCCCce
Q 025008 3 FNIWCGGCNSMIAK-GVRFNAEKKQV----GNYYSTKIWSFTMKSPCCKHQ 48 (259)
Q Consensus 3 F~iwC~~C~~~I~k-GvRFNAeKk~v----g~Y~st~I~~F~mkC~~C~~~ 48 (259)
+.+.|..||..|-- +.-+..--+.+ |.-....-..|+..|+.|.+.
T Consensus 99 ~H~iC~~CGki~~i~~~~l~~~~~~~~~~~gf~i~~~~l~~~GiC~~C~~~ 149 (169)
T PRK11639 99 AMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEV 149 (169)
T ss_pred CeEEeCCCCCEEEecccHHHHHHHHHHHHcCCEEeccEEEEEEEChhhcCc
Confidence 46899999975532 11122212223 333344556777889999665
No 93
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=23.14 E-value=34 Score=29.65 Aligned_cols=35 Identities=26% Similarity=0.606 Sum_probs=27.0
Q ss_pred eeEEEEEEcCCCCceeE---------------EecCCCCCCeeeecCccc
Q 025008 34 KIWSFTMKSPCCKHQIV---------------IQTDPKNCEYVIISGAQR 68 (259)
Q Consensus 34 ~I~~F~mkC~~C~~~i~---------------ikTDPkn~dYvv~~GarR 68 (259)
|||-=.|.||.|-..|. |.-||++.+-|-..-+|+
T Consensus 4 PIFGpei~CPhCRQ~ipALtLTDtYLC~rHGaFEAdP~t~eLVHLqSgR~ 53 (163)
T TIGR02652 4 PIFGPEIRCPHCRQNIPALTLTDTYLCNRHGAFEADPETGELVHLQSGRR 53 (163)
T ss_pred CccCCcCcCchhhcccchheecceeeccCCCccccCCCCCceEEeecCce
Confidence 67777777877777664 889999999987766654
No 94
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.13 E-value=27 Score=30.40 Aligned_cols=47 Identities=26% Similarity=0.420 Sum_probs=25.3
Q ss_pred cceecCCCCccccccccc--cceeeccCceeeeeeEEEEEEcCCCCceeEEe
Q 025008 3 FNIWCGGCNSMIAKGVRF--NAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 3 F~iwC~~C~~~I~kGvRF--NAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ik 52 (259)
|.+.|+.||+.--+=+=- |-+=..-| -=||- +|-|||..|+.+-.|-
T Consensus 29 ~kLkCtnCgE~~dkw~~I~l~E~~~~pg-~Rgta--~~v~KCK~C~Rensv~ 77 (161)
T KOG1296|consen 29 LKLKCTNCGELSDKWQYITLNEEVAMPG-SRGTA--SFVMKCKFCSRENSVT 77 (161)
T ss_pred EEeccccccccCCceEEEEeeeeecCCC-Ccchh--hHhhhhhhhcccCcEE
Confidence 457899999743322111 11100001 01222 8999999999876664
No 95
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=22.87 E-value=1e+02 Score=20.82 Aligned_cols=30 Identities=33% Similarity=0.609 Sum_probs=18.5
Q ss_pred ceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCC
Q 025008 4 NIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCK 46 (259)
Q Consensus 4 ~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~ 46 (259)
.|.|.+|+..|.- |-.+ ++=-||-.|..|.
T Consensus 3 tIvCq~C~~~Id~---~e~e----------kV~~lYg~C~~~e 32 (38)
T PF13790_consen 3 TIVCQHCNETIDH---FETE----------KVTTLYGKCGKCE 32 (38)
T ss_pred EEEeccccceeee---ecCC----------cEEEEEEECCCCc
Confidence 4789999988752 3332 3334566777654
No 96
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=22.58 E-value=51 Score=30.80 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=10.7
Q ss_pred eecCCCCccccccccc
Q 025008 5 IWCGGCNSMIAKGVRF 20 (259)
Q Consensus 5 iwC~~C~~~I~kGvRF 20 (259)
+-|.+|+.+.=-|.||
T Consensus 153 v~CD~C~~~~IvG~Ry 168 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARY 168 (278)
T ss_pred ccCCCccCCcccccee
Confidence 8888888765445444
No 97
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=22.50 E-value=39 Score=22.39 Aligned_cols=35 Identities=17% Similarity=0.377 Sum_probs=17.5
Q ss_pred eecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEEe
Q 025008 5 IWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQ 52 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ik 52 (259)
++|..|+.||--=+.|+-..+ ..+|..|+..-.|.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~-------------~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGK-------------TWICNFCGTKNPLP 37 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTT-------------EEEETTT--EEE--
T ss_pred cccCCCCCEECCcceEcCCCC-------------EEECcCCCCcCCCC
Confidence 789999999877777765211 24688887755543
No 98
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.24 E-value=27 Score=24.71 Aligned_cols=43 Identities=16% Similarity=0.315 Sum_probs=28.7
Q ss_pred ecCCCCcccc--ccccccceeeccCceeeeeeEEEEEEcCCCCceeEEecCCCCC
Q 025008 6 WCGGCNSMIA--KGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVIQTDPKNC 58 (259)
Q Consensus 6 wC~~C~~~I~--kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~ikTDPkn~ 58 (259)
.|.-||.-|+ .|..|=... -+ -|++=|..|...+-.+.+|..-
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~D--------gk--v~~Fcs~KC~~~f~~~~nprk~ 47 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKD--------GT--ILYFCSSKCEKNYKLGRVPRKL 47 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeC--------Cc--EEEEeCHHHHHHHHccCCCCcc
Confidence 4899998887 554432211 12 3566677888888899998754
No 99
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.88 E-value=43 Score=37.03 Aligned_cols=8 Identities=25% Similarity=0.701 Sum_probs=6.3
Q ss_pred ecCCCCcc
Q 025008 6 WCGGCNSM 13 (259)
Q Consensus 6 wC~~C~~~ 13 (259)
.|..||..
T Consensus 628 fCpsCG~~ 635 (1121)
T PRK04023 628 KCPSCGKE 635 (1121)
T ss_pred cCCCCCCc
Confidence 68888877
No 100
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.83 E-value=49 Score=24.06 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=8.5
Q ss_pred cCCCCceeEE
Q 025008 42 SPCCKHQIVI 51 (259)
Q Consensus 42 C~~C~~~i~i 51 (259)
||.|+..|+.
T Consensus 42 CPfC~~~~~~ 51 (55)
T PF14447_consen 42 CPFCGTPFEF 51 (55)
T ss_pred CCCCCCcccC
Confidence 9999988864
No 101
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.40 E-value=1.3e+02 Score=24.70 Aligned_cols=38 Identities=16% Similarity=0.217 Sum_probs=27.5
Q ss_pred eecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCceeEE
Q 025008 5 IWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQIVI 51 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i~i 51 (259)
..|.+|.....-|+ |++-+-.+.+ -.+.|..|+...-|
T Consensus 57 ~~CkkC~t~Lvpg~--n~rvR~~~~~-------v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGK--NARVRLRKGR-------VVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCc--ceEEEEcCCe-------EEEEecCCCcEEEe
Confidence 36999999877774 5655555555 56789999987665
No 102
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=21.33 E-value=98 Score=25.32 Aligned_cols=27 Identities=15% Similarity=0.332 Sum_probs=17.4
Q ss_pred EEEEEEcCCCCceeEEecCCCCCCeee
Q 025008 36 WSFTMKSPCCKHQIVIQTDPKNCEYVI 62 (259)
Q Consensus 36 ~~F~mkC~~C~~~i~ikTDPkn~dYvv 62 (259)
++|...|+.|+..+.-+..-+-..|.+
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C 146 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRC 146 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEEC
Confidence 567777777777776666554445554
No 103
>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=21.28 E-value=77 Score=26.45 Aligned_cols=46 Identities=20% Similarity=0.356 Sum_probs=20.8
Q ss_pred CcceecCCCCccccccccccceeeccCceeeeeeEEEEEEcCCCCcee
Q 025008 2 PFNIWCGGCNSMIAKGVRFNAEKKQVGNYYSTKIWSFTMKSPCCKHQI 49 (259)
Q Consensus 2 PF~iwC~~C~~~I~kGvRFNAeKk~vg~Y~st~I~~F~mkC~~C~~~i 49 (259)
|+--+|..||..+-.-.+ +.-+..|..|- ..-|.-...|+.|+.-+
T Consensus 89 ~~~sRC~~CN~~L~~v~~-~~v~~~vp~~v-~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRPVSK-EEVKDRVPPYV-YETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCCccCCCCcEeeechh-hccccccCccc-cccCCeEEECCCCCCEe
Confidence 345688888874433222 22222232211 01111145688887643
No 104
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=20.99 E-value=1.1e+02 Score=22.29 Aligned_cols=40 Identities=18% Similarity=0.291 Sum_probs=23.4
Q ss_pred ccCcee-eeeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcc
Q 025008 26 QVGNYY-STKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQ 67 (259)
Q Consensus 26 ~vg~Y~-st~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~Gar 67 (259)
.+..|- +.+--. +.-|+.|+..|-.. ++...+++.|..+.
T Consensus 35 ~l~~y~~s~~~~~-r~FC~~CGs~l~~~-~~~~~~~~~V~~g~ 75 (92)
T PF04828_consen 35 NLKEYQFSGKGVE-RYFCPTCGSPLFSE-DERDPDLVGVNAGT 75 (92)
T ss_dssp GEEEC--TTSSCE-EEEETTT--EEEEE-ESSTTTEEEEEGGG
T ss_pred cceEEEeCCCcCc-CcccCCCCCeeecc-cCCCCCEEEEEeEe
Confidence 444565 333333 37799999999988 55666666665554
No 105
>COG1013 PorB Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]
Probab=20.51 E-value=36 Score=32.08 Aligned_cols=18 Identities=33% Similarity=0.787 Sum_probs=12.8
Q ss_pred eecCCCCccccccccccc
Q 025008 5 IWCGGCNSMIAKGVRFNA 22 (259)
Q Consensus 5 iwC~~C~~~I~kGvRFNA 22 (259)
.||.|||+.++.-.=.+|
T Consensus 16 ~~CpGCG~~~~l~~i~~a 33 (294)
T COG1013 16 RWCPGCGEFIILKLLTQA 33 (294)
T ss_pred CcCCCCCchHHHHHHHHh
Confidence 699999997665444444
No 106
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.50 E-value=1.5e+02 Score=23.22 Aligned_cols=8 Identities=25% Similarity=0.775 Sum_probs=4.8
Q ss_pred EcCCCCce
Q 025008 41 KSPCCKHQ 48 (259)
Q Consensus 41 kC~~C~~~ 48 (259)
.|+.|+..
T Consensus 33 ~C~~CGe~ 40 (127)
T TIGR03830 33 YCPACGEE 40 (127)
T ss_pred ECCCCCCE
Confidence 46666654
No 107
>PF07255 Benyvirus_14KDa: Benyvirus 14KDa protein; InterPro: IPR009884 This family consists of several Benyvirus specific 14 kDa proteins of around 125 residues in length. Members of this family contain 9 conserved cysteine residues. The function of this family is unknown.
Probab=20.48 E-value=39 Score=27.76 Aligned_cols=42 Identities=21% Similarity=0.296 Sum_probs=34.0
Q ss_pred eeeEEEEEEcCCCCceeEEecCCCCCCeeeecCcccCCCcCC
Q 025008 33 TKIWSFTMKSPCCKHQIVIQTDPKNCEYVIISGAQRKTEEFD 74 (259)
Q Consensus 33 t~I~~F~mkC~~C~~~i~ikTDPkn~dYvv~~GarR~~e~~~ 74 (259)
+--.-|.|+|-.|...++++..-+|..--+-.|-.|....|.
T Consensus 59 ~~RLHF~~~CV~C~~K~~~K~~Nk~H~~~~~~G~~R~~RNFS 100 (123)
T PF07255_consen 59 VCRLHFNMSCVKCCRKLKCKKQNKNHSKHVQNGYLRKVRNFS 100 (123)
T ss_pred eeeEEEeeehhhhcccceehhcCcchHHHhhcCeEEEeccee
Confidence 334569999999999999999999988778888877765544
No 108
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.18 E-value=60 Score=27.96 Aligned_cols=24 Identities=33% Similarity=0.559 Sum_probs=14.4
Q ss_pred EEcCCCCcee--EEecCCCCCCeeee
Q 025008 40 MKSPCCKHQI--VIQTDPKNCEYVII 63 (259)
Q Consensus 40 mkC~~C~~~i--~ikTDPkn~dYvv~ 63 (259)
|+||.|+++. ++.+++-.-.|+|.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~ 26 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIR 26 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCcee
Confidence 7899999765 45555333344443
Done!