Query 020340
Match_columns 327
No_of_seqs 196 out of 392
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:58:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04502 DUF572: Family of unk 100.0 5.4E-84 1.2E-88 617.5 22.1 314 1-327 1-324 (324)
2 KOG2989 Uncharacterized conser 100.0 1.5E-69 3.2E-74 501.0 14.6 209 1-216 1-209 (253)
3 KOG2990 C2C2-type Zn-finger pr 100.0 1E-57 2.2E-62 430.1 9.8 210 1-214 1-223 (317)
4 COG5134 Uncharacterized conser 100.0 3.3E-36 7.2E-41 276.7 11.6 172 7-182 1-181 (272)
5 PF05907 DUF866: Eukaryotic pr 92.5 0.12 2.5E-06 46.3 3.3 64 35-102 25-90 (161)
6 PF04502 DUF572: Family of unk 91.6 0.87 1.9E-05 44.7 8.4 49 148-196 145-193 (324)
7 COG4332 Uncharacterized protei 86.4 0.43 9.2E-06 44.4 1.9 43 38-89 15-61 (203)
8 KOG2989 Uncharacterized conser 84.0 0.24 5.1E-06 47.7 -0.9 95 79-174 3-101 (253)
9 PF10122 Mu-like_Com: Mu-like 79.8 1.5 3.2E-05 33.1 2.2 35 39-90 3-37 (51)
10 PF08271 TF_Zn_Ribbon: TFIIB z 79.8 1.2 2.6E-05 31.2 1.7 24 78-102 1-24 (43)
11 PRK00564 hypA hydrogenase nick 76.3 1.4 3E-05 37.4 1.3 31 36-86 67-97 (117)
12 COG4416 Com Mu-like prophage p 75.5 1.2 2.6E-05 34.3 0.7 42 40-100 4-47 (60)
13 PRK12380 hydrogenase nickel in 75.3 1.5 3.1E-05 37.1 1.2 15 35-49 65-79 (113)
14 PRK03681 hypA hydrogenase nick 71.1 2 4.4E-05 36.3 1.1 14 35-48 65-78 (114)
15 PF06107 DUF951: Bacterial pro 68.8 3.8 8.3E-05 31.5 2.1 46 15-60 2-52 (57)
16 PF11931 DUF3449: Domain of un 68.3 1.7 3.6E-05 40.6 0.0 30 42-72 103-137 (196)
17 smart00834 CxxC_CXXC_SSSS Puta 68.3 5.2 0.00011 26.9 2.5 20 72-93 2-21 (41)
18 TIGR02098 MJ0042_CXXC MJ0042 f 67.6 4.3 9.3E-05 27.4 1.9 13 77-89 25-37 (38)
19 COG1996 RPC10 DNA-directed RNA 67.3 6.1 0.00013 29.5 2.8 36 40-94 6-41 (49)
20 KOG2990 C2C2-type Zn-finger pr 65.8 3.1 6.6E-05 41.2 1.3 28 5-54 74-101 (317)
21 PF11331 DUF3133: Protein of u 64.7 5.5 0.00012 29.4 2.1 41 37-90 4-44 (46)
22 TIGR00100 hypA hydrogenase nic 64.6 3.7 8E-05 34.7 1.4 30 36-86 66-95 (115)
23 PF13240 zinc_ribbon_2: zinc-r 63.7 3.4 7.3E-05 26.0 0.7 15 42-56 1-15 (23)
24 PRK00762 hypA hydrogenase nick 61.7 3.5 7.5E-05 35.3 0.7 14 35-49 65-78 (124)
25 cd00730 rubredoxin Rubredoxin; 61.4 4.5 9.7E-05 30.0 1.2 42 41-86 2-43 (50)
26 COG3091 SprT Zn-dependent meta 60.0 9 0.0002 34.8 3.1 41 39-93 116-156 (156)
27 COG0375 HybF Zn finger protein 58.2 6.4 0.00014 34.0 1.7 29 36-85 66-94 (115)
28 PF14353 CpXC: CpXC protein 55.6 3.8 8.3E-05 34.4 -0.0 47 41-89 2-50 (128)
29 PF05876 Terminase_GpA: Phage 53.7 7.9 0.00017 40.7 1.9 38 40-88 200-240 (557)
30 PF09723 Zn-ribbon_8: Zinc rib 52.9 14 0.00031 25.9 2.5 19 72-92 2-20 (42)
31 PF10263 SprT-like: SprT-like 52.5 13 0.00028 31.6 2.7 34 39-89 122-155 (157)
32 TIGR02605 CxxC_CxxC_SSSS putat 51.1 13 0.00028 26.6 2.1 18 72-91 2-19 (52)
33 KOG3794 CBF1-interacting corep 50.9 9.6 0.00021 39.4 1.9 14 5-18 66-81 (453)
34 PF13005 zf-IS66: zinc-finger 49.4 19 0.00042 25.1 2.8 43 42-84 4-47 (47)
35 PRK03824 hypA hydrogenase nick 48.6 11 0.00025 32.6 1.8 48 36-86 66-116 (135)
36 COG2888 Predicted Zn-ribbon RN 46.6 21 0.00046 27.9 2.8 32 40-90 9-40 (61)
37 PF05876 Terminase_GpA: Phage 44.7 11 0.00023 39.7 1.3 36 67-102 190-234 (557)
38 smart00731 SprT SprT homologue 43.3 26 0.00057 30.2 3.2 37 37-89 109-145 (146)
39 PF13248 zf-ribbon_3: zinc-rib 42.6 13 0.00027 23.7 0.9 18 39-56 1-18 (26)
40 PF01921 tRNA-synt_1f: tRNA sy 42.3 13 0.00028 37.7 1.4 40 37-89 171-211 (360)
41 PF06044 DRP: Dam-replacing fa 41.8 15 0.00032 35.8 1.6 51 40-106 31-82 (254)
42 PF13717 zinc_ribbon_4: zinc-r 41.4 30 0.00065 23.7 2.6 35 39-87 1-35 (36)
43 PF13790 DUF4182: Domain of un 41.0 34 0.00073 24.5 2.9 30 40-84 3-32 (38)
44 PRK00464 nrdR transcriptional 40.5 22 0.00047 32.0 2.3 55 41-106 1-58 (154)
45 KOG2636 Splicing factor 3a, su 40.1 9.8 0.00021 39.9 0.1 31 40-71 401-436 (497)
46 PRK14890 putative Zn-ribbon RN 38.2 41 0.00089 26.2 3.2 16 36-51 3-18 (59)
47 PRK00398 rpoP DNA-directed RNA 37.0 30 0.00065 24.4 2.2 18 77-94 21-38 (46)
48 PRK04351 hypothetical protein; 36.2 29 0.00062 30.9 2.4 37 37-90 109-145 (149)
49 PRK00750 lysK lysyl-tRNA synth 35.8 25 0.00053 36.8 2.2 27 37-63 172-199 (510)
50 cd00729 rubredoxin_SM Rubredox 35.5 18 0.00039 24.6 0.8 13 41-54 3-15 (34)
51 PF07255 Benyvirus_14KDa: Beny 35.1 28 0.00061 30.1 2.1 73 32-111 25-99 (123)
52 PRK04016 DNA-directed RNA poly 34.6 19 0.00042 28.1 0.9 13 39-51 3-15 (62)
53 PF04606 Ogr_Delta: Ogr/Delta- 34.3 57 0.0012 23.3 3.3 38 42-90 1-40 (47)
54 smart00132 LIM Zinc-binding do 34.3 21 0.00046 22.7 1.0 12 42-53 1-12 (39)
55 KOG1296 Uncharacterized conser 34.2 13 0.00027 33.9 -0.2 60 38-102 28-90 (161)
56 PF01155 HypA: Hydrogenase exp 33.6 17 0.00038 30.4 0.6 15 36-50 66-80 (113)
57 KOG2407 GPI transamidase compl 31.6 17 0.00037 38.7 0.3 17 32-48 490-506 (575)
58 cd02340 ZZ_NBR1_like Zinc fing 31.3 24 0.00052 25.1 0.9 19 41-60 1-19 (43)
59 COG1644 RPB10 DNA-directed RNA 30.8 22 0.00047 28.0 0.7 22 39-62 3-24 (63)
60 PF04690 YABBY: YABBY protein; 30.5 33 0.00071 31.6 1.8 37 41-90 13-49 (170)
61 PRK00807 50S ribosomal protein 30.2 16 0.00035 27.2 -0.1 45 42-98 3-49 (52)
62 KOG2846 Predicted membrane pro 29.7 28 0.00061 35.0 1.4 42 39-95 219-260 (328)
63 TIGR01206 lysW lysine biosynth 29.1 29 0.00063 26.2 1.1 18 77-94 2-19 (54)
64 smart00659 RPOLCX RNA polymera 29.1 54 0.0012 23.6 2.4 18 77-94 19-36 (44)
65 KOG3368 Transport protein part 28.6 74 0.0016 28.6 3.6 32 67-98 62-93 (140)
66 TIGR00467 lysS_arch lysyl-tRNA 28.5 46 0.001 35.1 2.8 24 37-60 165-188 (515)
67 TIGR01385 TFSII transcription 27.8 63 0.0014 31.9 3.5 41 40-89 258-298 (299)
68 PF11793 FANCL_C: FANCL C-term 27.8 31 0.00067 26.7 1.0 16 77-92 55-70 (70)
69 PRK08271 anaerobic ribonucleos 27.0 47 0.001 36.0 2.6 21 29-51 556-576 (623)
70 PF02146 SIR2: Sir2 family; I 26.9 28 0.00062 30.6 0.8 14 39-52 104-117 (178)
71 KOG3214 Uncharacterized Zn rib 26.0 39 0.00085 29.0 1.4 36 43-93 26-61 (109)
72 COG4481 Uncharacterized protei 25.6 53 0.0011 25.5 1.9 34 22-55 12-49 (60)
73 COG0068 HypF Hydrogenase matur 25.3 34 0.00075 37.8 1.2 65 33-112 117-183 (750)
74 PF01194 RNA_pol_N: RNA polyme 25.2 32 0.0007 26.7 0.7 13 39-51 3-15 (60)
75 PLN00032 DNA-directed RNA poly 25.2 36 0.00077 27.4 1.0 13 39-51 3-15 (71)
76 PF04810 zf-Sec23_Sec24: Sec23 25.2 77 0.0017 22.0 2.6 34 41-89 3-36 (40)
77 PF09855 DUF2082: Nucleic-acid 25.1 57 0.0012 25.4 2.1 43 42-86 2-45 (64)
78 PF14255 Cys_rich_CPXG: Cystei 24.3 57 0.0012 24.5 1.9 22 78-99 1-22 (52)
79 cd00674 LysRS_core_class_I cat 23.5 63 0.0014 32.5 2.6 14 37-51 166-179 (353)
80 COG5525 Bacteriophage tail ass 23.3 60 0.0013 35.3 2.5 52 39-107 226-286 (611)
81 TIGR03830 CxxCG_CxxCG_HTH puta 23.3 1E+02 0.0022 25.1 3.4 39 43-86 1-40 (127)
82 COG2816 NPY1 NTP pyrophosphohy 22.9 54 0.0012 32.3 2.0 49 41-108 112-166 (279)
83 PF06750 DiS_P_DiS: Bacterial 22.6 15 0.00033 30.0 -1.6 34 41-89 34-70 (92)
84 PRK09678 DNA-binding transcrip 22.5 72 0.0016 25.4 2.3 38 41-89 2-41 (72)
85 PRK05978 hypothetical protein; 22.5 36 0.00079 30.5 0.6 34 39-90 32-65 (148)
86 cd02338 ZZ_PCMF_like Zinc fing 22.2 36 0.00079 24.7 0.5 7 41-47 1-7 (49)
87 PF10058 DUF2296: Predicted in 22.1 88 0.0019 23.5 2.5 34 37-85 19-52 (54)
88 COG1405 SUA7 Transcription ini 21.9 42 0.0009 32.9 0.9 24 78-102 2-25 (285)
89 PF12855 Ecl1: Life-span regul 21.4 22 0.00047 25.8 -0.8 13 38-50 4-16 (43)
90 cd02339 ZZ_Mind_bomb Zinc fing 21.3 47 0.001 24.0 0.9 19 41-59 1-19 (45)
91 PF05864 Chordopox_RPO7: Chord 21.2 43 0.00094 26.2 0.7 15 37-51 1-15 (63)
92 TIGR00357 methionine-R-sulfoxi 21.1 85 0.0018 27.9 2.6 68 41-110 41-125 (134)
93 PRK05778 2-oxoglutarate ferred 21.0 36 0.00079 33.4 0.4 25 34-58 12-36 (301)
94 PF04113 Gpi16: Gpi16 subunit, 20.7 23 0.0005 37.8 -1.2 32 31-62 504-536 (564)
95 PHA02998 RNA polymerase subuni 20.7 85 0.0018 29.5 2.7 60 37-102 108-176 (195)
96 PF01096 TFIIS_C: Transcriptio 20.6 1.3E+02 0.0029 20.8 3.0 38 41-87 1-38 (39)
97 cd00350 rubredoxin_like Rubred 20.5 54 0.0012 21.9 1.0 14 41-55 2-15 (33)
98 PF00569 ZZ: Zinc finger, ZZ t 20.4 52 0.0011 23.4 1.0 21 39-59 3-23 (46)
99 PF05973 Gp49: Phage derived p 20.3 2.1E+02 0.0046 22.3 4.6 42 67-109 34-76 (91)
No 1
>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=5.4e-84 Score=617.49 Aligned_cols=314 Identities=42% Similarity=0.661 Sum_probs=246.0
Q ss_pred CCcccCCCcccCCCCCCCCCcccCCCCCCccEEEEecccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEc
Q 020340 1 MGERKVLNKYYPPDFDPSKLPRIRRPKNQQIKVRMMLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKC 80 (327)
Q Consensus 1 MsERKvlNKYYPPDfDPsKipR~Kk~k~~~~~VRfm~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC 80 (327)
|||||||||||||||||++||+++++++++++|||||||+|||++||+|||+||||||+|++|.+|+|||||||||||||
T Consensus 1 M~ERK~~nkYyPPD~d~~k~~~~kr~k~~~~~VRf~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC 80 (324)
T PF04502_consen 1 MSERKVLNKYYPPDFDPSKHPLRKRAKQGILTVRFMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKC 80 (324)
T ss_pred CcccccCCCccCCCCCcccccccccCcCcceEEEEcCCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999988999999999999999
Q ss_pred CCCCceEEEeeCCCCCccccccCceecCCCCccchhhhHHHHHHHhhhhcCChhHHHHhhhhhhHHHHHHHHHHHHHHHH
Q 020340 81 TKCSAELTIKTDPQNSDYIVESGASRNYEPWRAEDEAVDEEKKRRDAEEMGDAMKALENRTLDSKREMDILAALDEMKSM 160 (327)
Q Consensus 81 ~~C~~eI~fkTDPkN~dY~~esGA~Rn~e~~~~~~~~~~~e~~~~e~ee~~D~M~~LE~rt~Dsk~Eme~~~~LeELk~l 160 (327)
|.|+++|+|+|||+|+||+|++||+|+|++|...+........++++++..|||++||+++.|++++|+++++|++|+++
T Consensus 81 ~~C~~~i~~kTDPkn~dY~~~~Ga~R~~~~~~~~~~~~~~~~~~~~~~~~~d~m~~LE~~~~d~~~~~~~~~~LeeL~~~ 160 (324)
T PF04502_consen 81 PRCSNEIEFKTDPKNTDYVVESGARRNFEPDKEEEEQEEREDKEEEEEEEEDPMKALEKRTEDSKREMEALERLEELQEL 160 (324)
T ss_pred CCCCCEEeeecCCCCCCeeeecCeeecCCcchhhhhhhhhhhHHHhhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999997765555444445555677999999999999999999999999999999
Q ss_pred HhhccCCCHHHHHHHHhhchHHHHHhhcHHHHHHHHHHhc--CCccceeccccCCCCCccchhhhhcccccCCccccccc
Q 020340 161 KSRHASVSVDAMLEALQSTAPEKEKRLEEEDEALIRSIFQ--KPREVVRRISDEDLDDDGDLFQFASERNEGSSNNLKKR 238 (327)
Q Consensus 161 n~R~~~vd~~~~L~~lr~~~~e~~~~~eeEDe~~~k~~~~--~~~~~~rrl~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (327)
|+|++.++.+++|+++++.++++++.++++|+++++.+.. ...+..+++.++|...+... .......
T Consensus 161 ~~r~d~~~~n~~Lr~~~r~~~k~~~~~~~~d~~~~~~~~~~~~~~~~~r~~~~~d~~~~~~~-----------~~~~~~~ 229 (324)
T PF04502_consen 161 NARKDDYDANQMLRKRFREEKKERERQEEEDEALKKKISLGPESEEDKRLAADEDSEEEDEK-----------NSNTSSK 229 (324)
T ss_pred HhccCchhhHHHHHHHHHHHHHHHHHhHHHHHHHHHhhccCcchhhhhhhhcchhhhhhhhc-----------ccccccc
Confidence 9999999999999999888888888889999999999844 33333444555443332100 0111112
Q ss_pred cCCCCCCCCCcccccccCCCCCCCCCCCCCCcccccCCCCCCCCCceeEEEeecCCCCcccccc-----h---hcccccc
Q 020340 239 KLSEDVPSKPTDALTEASFSDSTSNGENPTVSKTESDTKVPRKSSSIQIQVIKKPATVSATKVI-----A---KSENKSE 310 (327)
Q Consensus 239 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~v~kk~~~~~~~~~~-----~---~~e~k~~ 310 (327)
+........+++|++......... ......+..+.+....+..+.+++++||.+..+..... . .......
T Consensus 230 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~k~~~~~~~~~Kk~~~~~~~~~~~~~~~~~~~~~~~~~~ 307 (324)
T PF04502_consen 230 SSKSSSSKKPTSILSKSKAKKSRE--KSSSSIKLNSSSSSKKKSALSSIVKKKKKAPESSKSKSVQESSAKPTTSSPSST 307 (324)
T ss_pred ccccccCCCchhhhcccccccccc--cccccccccccccccccccccccccccCCCCCCCCCCcccccccCCCCCCCCCC
Confidence 233455677888888765532222 11222233345667788899999888885554443311 1 1111124
Q ss_pred cchhhhhhhhhcCCCCC
Q 020340 311 ERTGLQSLCQNYDSDDE 327 (327)
Q Consensus 311 ~~t~l~sl~qny~sd~~ 327 (327)
...+|+.|+++|||||+
T Consensus 308 ~~~sl~~l~~y~dSd~s 324 (324)
T PF04502_consen 308 GSSSLSLLGDYSDSDDS 324 (324)
T ss_pred CCcchhhccccCCcCCC
Confidence 44559999999999986
No 2
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.5e-69 Score=500.98 Aligned_cols=209 Identities=56% Similarity=0.944 Sum_probs=194.9
Q ss_pred CCcccCCCcccCCCCCCCCCcccCCCCCCccEEEEecccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEc
Q 020340 1 MGERKVLNKYYPPDFDPSKLPRIRRPKNQQIKVRMMLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKC 80 (327)
Q Consensus 1 MsERKvlNKYYPPDfDPsKipR~Kk~k~~~~~VRfm~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC 80 (327)
|+||||+||||||||||+++||++++++++++||+|+||+|+|++||+|||+|+|||++++.|+|++||||+||||||+|
T Consensus 1 m~Erk~lnkyyppdfDP~ki~r~k~~k~~q~~~Rlm~Pf~~rC~tCgeyi~kg~kfN~r~E~~~~e~yLgiki~Rf~i~C 80 (253)
T KOG2989|consen 1 MSERKVLNKYYPPDFDPKKIPRAKEPKNRQLKIRLMTPFRLRCNTCGEYIYKGKKFNAREEDVIEETYLGIKIFRFYIKC 80 (253)
T ss_pred CcccccccccCCCCCChhhhhhhhccchhhcceeecccceeecccccchhhcCCCcchhHHhhhccccccceeeeeeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEEeeCCCCCccccccCceecCCCCccchhhhHHHHHHHhhhhcCChhHHHHhhhhhhHHHHHHHHHHHHHHHH
Q 020340 81 TKCSAELTIKTDPQNSDYIVESGASRNYEPWRAEDEAVDEEKKRRDAEEMGDAMKALENRTLDSKREMDILAALDEMKSM 160 (327)
Q Consensus 81 ~~C~~eI~fkTDPkN~dY~~esGA~Rn~e~~~~~~~~~~~e~~~~e~ee~~D~M~~LE~rt~Dsk~Eme~~~~LeELk~l 160 (327)
++|+++|+|||||+|+||++++||+|+|++|...+++.....++ +++.|+|..||++|.+|+++|.++.+|++|+.+
T Consensus 81 t~cl~el~~rTDp~N~dY~~E~Ga~r~y~~~~~~eeek~k~~~~---~d~~d~m~~lekrt~~S~~e~~~~~~ldel~~~ 157 (253)
T KOG2989|consen 81 TRCLRELSFRTDPKNSDYVIESGATRNYEPIEEEEEEKRKFEEE---EDMKDEIKRLEKRTFQSKDEEIIRRALDELKVL 157 (253)
T ss_pred cchHhhhhhhcCCcchHHHHHhcchhcccccchhHHHHHHHHhh---hhhhhHHHHHHHHhhhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998766554333222 678999999999999999999999999999999
Q ss_pred HhhccCCCHHHHHHHHhhchHHHHHhhcHHHHHHHHHHhcCCccceeccccCCCCC
Q 020340 161 KSRHASVSVDAMLEALQSTAPEKEKRLEEEDEALIRSIFQKPREVVRRISDEDLDD 216 (327)
Q Consensus 161 n~R~~~vd~~~~L~~lr~~~~e~~~~~eeEDe~~~k~~~~~~~~~~rrl~d~~~~~ 216 (327)
+.|++.||.++||.++....+++.++.++|++.+++++++... ||.+++.++
T Consensus 158 k~r~~~id~~~~l~~~~~~~~k~~~~~eee~~~liks~~~~~~----ri~~ee~~~ 209 (253)
T KOG2989|consen 158 KERPAPIDLVSELLATNERPRKYAKRKEEEKKVLIKSIKFGQK----RIVDEELDN 209 (253)
T ss_pred hcccCcccHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccc----ccccccccc
Confidence 9999999999999999777788888899999999999999653 888888776
No 3
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=100.00 E-value=1e-57 Score=430.09 Aligned_cols=210 Identities=30% Similarity=0.510 Sum_probs=174.0
Q ss_pred CCcccCCCcccCCCCCCCCC------------cccCCCCCCccEEEEecccceecCCCCCccccCccccccccccCCCcc
Q 020340 1 MGERKVLNKYYPPDFDPSKL------------PRIRRPKNQQIKVRMMLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETY 68 (327)
Q Consensus 1 MsERKvlNKYYPPDfDPsKi------------pR~Kk~k~~~~~VRfm~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Y 68 (327)
|||||+.||||||||+|.+. .|+||...+++||||+|||||||++|.+||++||||||+|++| | +|
T Consensus 1 mgerkg~nkYyPPd~~p~~gsln~~~g~h~lrerarKi~~gilvIRFEMPynIWC~gC~nhIgmGvRyNAeKkkv-G-nY 78 (317)
T KOG2990|consen 1 MGERKGQNKYYPPDFNPKHGSLNKYHGTHALRERARKIDQGILVIRFEMPYNIWCDGCKNHIGMGVRYNAEKKKV-G-NY 78 (317)
T ss_pred CcccccCCcccCCCCCcccCcccccccchhHHHHHHhhccceEEEEEecccchhhccHHHhhhccceechhhhhc-c-cc
Confidence 99999999999999999432 2788899999999999999999999999999999999999997 8 89
Q ss_pred cceeeEEEEEEcCCCCceEEEeeCCCCCccccccCceecCCCCccchhhhHHHHHHHhhh-hcCChhHHHHhhhhhhHHH
Q 020340 69 LGIQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASRNYEPWRAEDEAVDEEKKRRDAE-EMGDAMKALENRTLDSKRE 147 (327)
Q Consensus 69 lgi~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~Rn~e~~~~~~~~~~~e~~~~e~e-e~~D~M~~LE~rt~Dsk~E 147 (327)
|+||||+|.||||.|.+.|+|+|||+|+||||.+||.|..++|++++.++.+...+.... ...|||++|||+..|.+..
T Consensus 79 YtTpiw~FrmKchlC~n~i~iqTDP~NceYvI~SGaqRKeer~D~~d~Eq~~~t~~e~k~KLa~DamyrLEHqe~D~~k~ 158 (317)
T KOG2990|consen 79 YTTPIWSFRMKCHLCDNYIVIQTDPKNCEYVITSGAQRKEERYDAEDAEQMEPTAEEEKGKLASDAMYRLEHQEVDLKKK 158 (317)
T ss_pred ccCcccchhhcccccCCceeeecCCCCceEEEeccccccccccCchhhhhccchhhhhcccccccHHHHHHhHHHhHhhh
Confidence 999999999999999999999999999999999999999999999887755443333323 3469999999999999999
Q ss_pred HHHHHHHHHHHHHHhhccCCCHHHHHHHHhhchHHHHHhhcHHHHHHHHHHhcCCccceeccccCCC
Q 020340 148 MDILAALDEMKSMKSRHASVSVDAMLEALQSTAPEKEKRLEEEDEALIRSIFQKPREVVRRISDEDL 214 (327)
Q Consensus 148 me~~~~LeELk~ln~R~~~vd~~~~L~~lr~~~~e~~~~~eeEDe~~~k~~~~~~~~~~rrl~d~~~ 214 (327)
......|.-|++.|++.|. |.......||+.++++++..+++. +.-.++|.+....+.+|-...+
T Consensus 159 k~aep~l~~l~e~~~~rw~-Ddf~~ns~LRaqfR~~kK~~~e~~-~~D~~l~~r~sl~I~lLPeTe~ 223 (317)
T KOG2990|consen 159 KAAEPVLVRLQEVNDARWA-DDFQANSRLRAQFREEKKLINEQE-ARDLDLFARASLDILLLPETEE 223 (317)
T ss_pred hccchHHHHHHHHHHHHhc-cchhhhHHHHHHHHHHHHHhhhhh-hhhHHHHHhhhcCcccCCCchh
Confidence 9999999999999888887 666778888988888777554442 2223333322223555544433
No 4
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.3e-36 Score=276.67 Aligned_cols=172 Identities=30% Similarity=0.567 Sum_probs=130.3
Q ss_pred CCcccCCCCCCCCC---c-----ccCCCCCCccEEEEecccceecCCCCCccccCccccccccccCCCcccceeeEEEEE
Q 020340 7 LNKYYPPDFDPSKL---P-----RIRRPKNQQIKVRMMLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYF 78 (327)
Q Consensus 7 lNKYYPPDfDPsKi---p-----R~Kk~k~~~~~VRfm~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyi 78 (327)
+|+|||||+.|--. . ++|......+-||+|.||+|+|+.|++|||||+||||-||-+.+..||||.||||.|
T Consensus 1 ~~ky~pp~~NrvlAqpL~~~~~~KlK~arprglSiRL~TPF~~RCL~C~~YI~K~~rfNavkE~~~dK~y~~~kiYRf~I 80 (272)
T COG5134 1 MGKYIPPEGNRVLAQPLAKRKFDKLKNARPRGLSIRLETPFPVRCLNCENYIQKGTRFNAVKEEIGDKSYYTTKIYRFSI 80 (272)
T ss_pred CCCCcCCCCchhhcchhHHHHHHHhcccCcccceEEeccCcceeecchhhhhhcccchhHHHHHhcccccceeEEEEEEE
Confidence 58999999998433 2 334445678999999999999999999999999999999988777788999999999
Q ss_pred EcCCCCceEEEeeCCCCCccccccCceecCCCCccchhhhHH-HHHHHhhhhcCChhHHHHhhhhhhHHHHHHHHHHHHH
Q 020340 79 KCTKCSAELTIKTDPQNSDYIVESGASRNYEPWRAEDEAVDE-EKKRRDAEEMGDAMKALENRTLDSKREMDILAALDEM 157 (327)
Q Consensus 79 KC~~C~~eI~fkTDPkN~dY~~esGA~Rn~e~~~~~~~~~~~-e~~~~e~ee~~D~M~~LE~rt~Dsk~Eme~~~~LeEL 157 (327)
.||.|++.|.|+|||+|++||+|+|+.|+++|....++.... ..+.. .+.|...++|+...+...+----.+.+-+
T Consensus 81 ~C~~C~n~i~~RTDPkN~~YV~EsGg~R~i~pq~~n~D~~k~~~Ve~~---~Esd~~~~~eK~~~Q~~~~~~~ssA~n~~ 157 (272)
T COG5134 81 KCHLCSNPIDVRTDPKNTEYVVESGGRRKIEPQDINEDPAKAENVEKV---PESDAIEALEKQLTQQKSEKHNSSAINFI 157 (272)
T ss_pred EccCCCCceeeecCCCCceEEEecCceeecCccccccChhhhhhhhcC---chhHHHHHHHHHHHHhhcccchhhhhhHH
Confidence 999999999999999999999999999999998876544322 11211 23577778888766555433333455666
Q ss_pred HHHHhhccCCCHHHHHHHHhhchHH
Q 020340 158 KSMKSRHASVSVDAMLEALQSTAPE 182 (327)
Q Consensus 158 k~ln~R~~~vd~~~~L~~lr~~~~e 182 (327)
-.|+.|.|.+-+. -.+.++..+.+
T Consensus 158 D~L~Krl~~~~~~-~~~~~~~~~~~ 181 (272)
T COG5134 158 DELNKRLWSDPFV-SSQRLRKQFRE 181 (272)
T ss_pred HHHHHHhhcCchh-hhHHHHHHHHH
Confidence 6678898874332 23334444443
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=92.55 E-value=0.12 Score=46.30 Aligned_cols=64 Identities=23% Similarity=0.422 Sum_probs=36.2
Q ss_pred EecccceecCCCCCccccCcccccccc-ccCCCcccceeeEEEEEEcCCCCceEEEeeCCC-CCcccccc
Q 020340 35 MMLPMSIRCNTCGNYIYKGTKFNSRKE-DAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQ-NSDYIVES 102 (327)
Q Consensus 35 fm~PF~i~C~~Cg~yI~kG~KFNArKe-~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPk-N~dY~~es 102 (327)
|...|.+.|+.||+-.-+.+-+|..-+ .+.| |---=.|.+||..|..+.+|.--|. ..-|.++.
T Consensus 25 ~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~g----srG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 90 (161)
T PF05907_consen 25 FEWFFKVKCTSCGEVHPKWVYINRFEKHEIPG----SRGTANFVMKCKFCKRESSIDIIPGKGKPYTAED 90 (161)
T ss_dssp --EEEEEEETTSS--EEEEEEE-TT-BEE-TT----SS-EESEEE--SSSS--EEEEEE--TTTEEEGGG
T ss_pred CEEEEEEEECCCCCccCcceEeecceEEecCC----CccceEeEecCcCcCCccEEEEEecCcccccccc
Confidence 446789999999998888887885433 3334 3233489999999999988854443 45677653
No 6
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=91.65 E-value=0.87 Score=44.65 Aligned_cols=49 Identities=16% Similarity=0.153 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHhhccCCCHHHHHHHHhhchHHHHHhhcHHHHHHHH
Q 020340 148 MDILAALDEMKSMKSRHASVSVDAMLEALQSTAPEKEKRLEEEDEALIR 196 (327)
Q Consensus 148 me~~~~LeELk~ln~R~~~vd~~~~L~~lr~~~~e~~~~~eeEDe~~~k 196 (327)
...++.++.|.+|..++...+.......||+.++.+++..+.++++...
T Consensus 145 ~~~~~~~~~LeeL~~~~~r~d~~~~n~~Lr~~~r~~~k~~~~~~~~d~~ 193 (324)
T PF04502_consen 145 KREMEALERLEELQELNARKDDYDANQMLRKRFREEKKERERQEEEDEA 193 (324)
T ss_pred HHHHHHHHHHHHHHHHHhccCchhhHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 3567899999999999999888899999999988877766665544433
No 7
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.38 E-value=0.43 Score=44.45 Aligned_cols=43 Identities=33% Similarity=0.794 Sum_probs=32.3
Q ss_pred ccceecCCCC---CccccCc-cccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 38 PMSIRCNTCG---NYIYKGT-KFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 38 PF~i~C~~Cg---~yI~kG~-KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
|--..|++|| +|+.-|. |.||.++. | .+|..| ||+.|.....|
T Consensus 15 q~~k~C~~Cg~kr~f~cSg~fRvNAq~K~------L--DvWlIY-kC~~Cd~tWN~ 61 (203)
T COG4332 15 QPAKRCNSCGVKRAFTCSGKFRVNAQGKV------L--DVWLIY-KCTHCDYTWNI 61 (203)
T ss_pred hhhhhCcccCCcceeeecCcEEEcCCCcE------E--EEEEEE-EeeccCCccch
Confidence 3456899998 6899998 89998853 2 466666 89999875443
No 8
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=83.98 E-value=0.24 Score=47.68 Aligned_cols=95 Identities=11% Similarity=-0.016 Sum_probs=70.3
Q ss_pred EcCCCCceEEEeeCCCCCccccccCceecC-CCCccchh---hhHHHHHHHhhhhcCChhHHHHhhhhhhHHHHHHHHHH
Q 020340 79 KCTKCSAELTIKTDPQNSDYIVESGASRNY-EPWRAEDE---AVDEEKKRRDAEEMGDAMKALENRTLDSKREMDILAAL 154 (327)
Q Consensus 79 KC~~C~~eI~fkTDPkN~dY~~esGA~Rn~-e~~~~~~~---~~~~e~~~~e~ee~~D~M~~LE~rt~Dsk~Eme~~~~L 154 (327)
.|+.|...+.+-+||+..+|.-..|+++++ ..|.+-.- .-.+..-+ -..=..+-|.+++...++.+..|-....+
T Consensus 3 Erk~lnkyyppdfDP~ki~r~k~~k~~q~~~Rlm~Pf~~rC~tCgeyi~k-g~kfN~r~E~~~~e~yLgiki~Rf~i~Ct 81 (253)
T KOG2989|consen 3 ERKVLNKYYPPDFDPKKIPRAKEPKNRQLKIRLMTPFRLRCNTCGEYIYK-GKKFNAREEDVIEETYLGIKIFRFYIKCT 81 (253)
T ss_pred ccccccccCCCCCChhhhhhhhccchhhcceeecccceeecccccchhhc-CCCcchhHHhhhccccccceeeeeeeecc
Confidence 699999999999999999999999999987 67765311 10000000 00112356778899999999999999999
Q ss_pred HHHHHHHhhccCCCHHHHHH
Q 020340 155 DEMKSMKSRHASVSVDAMLE 174 (327)
Q Consensus 155 eELk~ln~R~~~vd~~~~L~ 174 (327)
..|+++..|...++.+...+
T Consensus 82 ~cl~el~~rTDp~N~dY~~E 101 (253)
T KOG2989|consen 82 RCLRELSFRTDPKNSDYVIE 101 (253)
T ss_pred chHhhhhhhcCCcchHHHHH
Confidence 99999999988777665544
No 9
>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=79.84 E-value=1.5 Score=33.08 Aligned_cols=35 Identities=26% Similarity=0.710 Sum_probs=25.8
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
=.+||.+|+..++++ | .|- .+.|||++|..--.|+
T Consensus 3 ~eiRC~~CnklLa~~-----------g-~~~-----~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKA-----------G-EVI-----ELEIKCPRCKTINHVR 37 (51)
T ss_pred cceeccchhHHHhhh-----------c-Ccc-----EEEEECCCCCccceEe
Confidence 368999999999875 2 222 3589999999865554
No 10
>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=79.82 E-value=1.2 Score=31.21 Aligned_cols=24 Identities=25% Similarity=0.689 Sum_probs=20.2
Q ss_pred EEcCCCCceEEEeeCCCCCcccccc
Q 020340 78 FKCTKCSAELTIKTDPQNSDYIVES 102 (327)
Q Consensus 78 iKC~~C~~eI~fkTDPkN~dY~~es 102 (327)
|+|+.|++.- |-+|+.+.+|++..
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 6899999976 88899999888765
No 11
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.27 E-value=1.4 Score=37.42 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=21.5
Q ss_pred ecccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCce
Q 020340 36 MLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAE 86 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~e 86 (327)
..|...+|..||.+..- . .| ++++||.|.+.
T Consensus 67 ~vp~~~~C~~Cg~~~~~------------~-~~-------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKP------------N-AL-------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCcccc------------C-Cc-------cCCcCcCCCCC
Confidence 57999999999954321 1 01 34679999984
No 12
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=75.47 E-value=1.2 Score=34.28 Aligned_cols=42 Identities=36% Similarity=0.754 Sum_probs=28.3
Q ss_pred ceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCc--eEEEeeCCCCCcccc
Q 020340 40 SIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSA--ELTIKTDPQNSDYIV 100 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~--eI~fkTDPkN~dY~~ 100 (327)
+|||..|+..+.+ +.|.-||- +|||+|.. +|+++ -+.+.|+-
T Consensus 4 tiRC~~CnKlLa~----------a~~~~yle-------~KCPrCK~vN~~~~~--~e~~t~~~ 47 (60)
T COG4416 4 TIRCAKCNKLLAE----------AEGQAYLE-------KKCPRCKEVNEFYIK--EEATTQIH 47 (60)
T ss_pred eeehHHHhHHHHh----------cccceeee-------ecCCccceeeeeecc--cccchhhh
Confidence 7899999987763 33445764 69999975 44444 45555653
No 13
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=75.27 E-value=1.5 Score=37.07 Aligned_cols=15 Identities=20% Similarity=0.521 Sum_probs=12.4
Q ss_pred EecccceecCCCCCc
Q 020340 35 MMLPMSIRCNTCGNY 49 (327)
Q Consensus 35 fm~PF~i~C~~Cg~y 49 (327)
-..|-..||..||..
T Consensus 65 ~~vp~~~~C~~Cg~~ 79 (113)
T PRK12380 65 VYKPAQAWCWDCSQV 79 (113)
T ss_pred EeeCcEEEcccCCCE
Confidence 468999999999943
No 14
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=71.13 E-value=2 Score=36.27 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=12.1
Q ss_pred EecccceecCCCCC
Q 020340 35 MMLPMSIRCNTCGN 48 (327)
Q Consensus 35 fm~PF~i~C~~Cg~ 48 (327)
-..|-..||..||.
T Consensus 65 ~~~p~~~~C~~Cg~ 78 (114)
T PRK03681 65 EEQEAECWCETCQQ 78 (114)
T ss_pred EeeCcEEEcccCCC
Confidence 45799999999996
No 15
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=68.77 E-value=3.8 Score=31.52 Aligned_cols=46 Identities=22% Similarity=0.506 Sum_probs=31.7
Q ss_pred CCCCCCcccCCCCC----CccEEEEecccceecCCCCCccccCc-cccccc
Q 020340 15 FDPSKLPRIRRPKN----QQIKVRMMLPMSIRCNTCGNYIYKGT-KFNSRK 60 (327)
Q Consensus 15 fDPsKipR~Kk~k~----~~~~VRfm~PF~i~C~~Cg~yI~kG~-KFNArK 60 (327)
|..--+-+.||++. .=-++|+=|=|-++|.+||..|-.-. +|+.+-
T Consensus 2 ~~vgDiV~mKK~HPCG~~~Wei~R~GaDikikC~gCg~~imlpR~~feK~~ 52 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGSNEWEIIRIGADIKIKCLGCGRQIMLPRSKFEKRL 52 (57)
T ss_pred ccCCCEEEEcCCCCCCCCEEEEEEccCcEEEEECCCCCEEEEeHHHHHHHH
Confidence 33334556677653 34689999999999999999876544 455443
No 16
>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=68.32 E-value=1.7 Score=40.63 Aligned_cols=30 Identities=47% Similarity=0.912 Sum_probs=0.0
Q ss_pred ecCCCCCccccCcc-----ccccccccCCCccccee
Q 020340 42 RCNTCGNYIYKGTK-----FNSRKEDAIGETYLGIQ 72 (327)
Q Consensus 42 ~C~~Cg~yI~kG~K-----FNArKe~v~gE~Ylgi~ 72 (327)
.|--||+++|+|.| |+..+- +.|-.-||||
T Consensus 103 ~CEICGN~~Y~GrkaFekHF~E~rH-~~GlrcLGI~ 137 (196)
T PF11931_consen 103 KCEICGNQSYKGRKAFEKHFQEWRH-AYGLRCLGIP 137 (196)
T ss_dssp ------------------------------------
T ss_pred eeEeCCCcceecHHHHHHhcChhHH-HccChhcCCC
Confidence 69999999999987 888774 4576666665
No 17
>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=68.26 E-value=5.2 Score=26.93 Aligned_cols=20 Identities=15% Similarity=0.680 Sum_probs=15.3
Q ss_pred eeEEEEEEcCCCCceEEEeeCC
Q 020340 72 QIFRFYFKCTKCSAELTIKTDP 93 (327)
Q Consensus 72 ~I~rFyiKC~~C~~eI~fkTDP 93 (327)
|||.| +|+.|...+++-..-
T Consensus 2 p~Y~y--~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 2 PIYEY--RCEDCGHTFEVLQKI 21 (41)
T ss_pred CCEEE--EcCCCCCEEEEEEec
Confidence 67776 799999988876644
No 18
>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=67.64 E-value=4.3 Score=27.38 Aligned_cols=13 Identities=23% Similarity=0.516 Sum_probs=10.1
Q ss_pred EEEcCCCCceEEE
Q 020340 77 YFKCTKCSAELTI 89 (327)
Q Consensus 77 yiKC~~C~~eI~f 89 (327)
.++|++|.+.|..
T Consensus 25 ~v~C~~C~~~~~~ 37 (38)
T TIGR02098 25 KVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEe
Confidence 4679999988764
No 19
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.34 E-value=6.1 Score=29.52 Aligned_cols=36 Identities=22% Similarity=0.629 Sum_probs=25.5
Q ss_pred ceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCC
Q 020340 40 SIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQ 94 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPk 94 (327)
.-.|..||.-+ +.. +.|. .++|+.|+.-|-||-=|.
T Consensus 6 ~Y~C~~Cg~~~----------~~~--~~~~-------~irCp~Cg~rIl~K~R~~ 41 (49)
T COG1996 6 EYKCARCGREV----------ELD--QETR-------GIRCPYCGSRILVKERPK 41 (49)
T ss_pred EEEhhhcCCee----------ehh--hccC-------ceeCCCCCcEEEEeccCC
Confidence 45799998765 211 1232 579999999999997665
No 20
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=65.76 E-value=3.1 Score=41.23 Aligned_cols=28 Identities=39% Similarity=0.730 Sum_probs=23.0
Q ss_pred cCCCcccCCCCCCCCCcccCCCCCCccEEEEecccceecCCCCCccccCc
Q 020340 5 KVLNKYYPPDFDPSKLPRIRRPKNQQIKVRMMLPMSIRCNTCGNYIYKGT 54 (327)
Q Consensus 5 KvlNKYYPPDfDPsKipR~Kk~k~~~~~VRfm~PF~i~C~~Cg~yI~kG~ 54 (327)
||-|+|++|+|. |+|.|.-|.+||..-|
T Consensus 74 kvGnYYtTpiw~----------------------FrmKchlC~n~i~iqT 101 (317)
T KOG2990|consen 74 KVGNYYTTPIWS----------------------FRMKCHLCDNYIVIQT 101 (317)
T ss_pred hccccccCcccc----------------------hhhcccccCCceeeec
Confidence 678899999986 6689999999987543
No 21
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=64.73 E-value=5.5 Score=29.36 Aligned_cols=41 Identities=24% Similarity=0.551 Sum_probs=27.7
Q ss_pred cccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
+||- .|..|.+.+--=.+|=..++.+ -.++|..|+..|.|.
T Consensus 4 APFv-~C~~C~~lLqlP~~~~~~~k~~------------~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 4 APFV-VCSSCFELLQLPAKFSLSKKNQ------------QKLRCGACSEVLSFS 44 (46)
T ss_pred CCEe-ECccHHHHHcCCCccCCCccce------------eEEeCCCCceeEEEe
Confidence 5774 5999998776544443333221 267899999999885
No 22
>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=64.60 E-value=3.7 Score=34.68 Aligned_cols=30 Identities=20% Similarity=0.556 Sum_probs=21.0
Q ss_pred ecccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCce
Q 020340 36 MLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAE 86 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~e 86 (327)
..|-..+|..||....- . .+++.||.|.+.
T Consensus 66 ~~p~~~~C~~Cg~~~~~------------~---------~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSP------------E---------IDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEec------------C---------CcCccCcCCcCC
Confidence 57889999999944321 1 115679999984
No 23
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=63.68 E-value=3.4 Score=26.03 Aligned_cols=15 Identities=40% Similarity=0.824 Sum_probs=10.9
Q ss_pred ecCCCCCccccCccc
Q 020340 42 RCNTCGNYIYKGTKF 56 (327)
Q Consensus 42 ~C~~Cg~yI~kG~KF 56 (327)
.|..||..|-.+.+|
T Consensus 1 ~Cp~CG~~~~~~~~f 15 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF 15 (23)
T ss_pred CCcccCCCCCCcCcc
Confidence 478888887766666
No 24
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.73 E-value=3.5 Score=35.33 Aligned_cols=14 Identities=43% Similarity=1.054 Sum_probs=11.5
Q ss_pred EecccceecCCCCCc
Q 020340 35 MMLPMSIRCNTCGNY 49 (327)
Q Consensus 35 fm~PF~i~C~~Cg~y 49 (327)
-+.|-..|| .||.+
T Consensus 65 ~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 65 EMIPVEIEC-ECGYE 78 (124)
T ss_pred EecCeeEEe-eCcCc
Confidence 468999999 99943
No 25
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=61.40 E-value=4.5 Score=30.02 Aligned_cols=42 Identities=24% Similarity=0.564 Sum_probs=23.1
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCce
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAE 86 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~e 86 (327)
.+|..|| |||-..+-+..---..|-.+-.+|- ..+|+.|.+.
T Consensus 2 y~C~~Cg-yiYd~~~Gd~~~~i~pGt~f~~Lp~---~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICG-YIYDPAEGDPDEGIPPGTPFEDLPD---DWVCPVCGAG 43 (50)
T ss_pred cCCCCCC-eEECCCCCCcccCcCCCCCHhHCCC---CCCCCCCCCc
Confidence 4799999 8887444333222122322222332 4689999873
No 26
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=60.04 E-value=9 Score=34.82 Aligned_cols=41 Identities=27% Similarity=0.676 Sum_probs=32.4
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCC
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDP 93 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDP 93 (327)
|.-+|. |+.+--+=.|+|--+. ||. .+|..|.+.+.+++++
T Consensus 116 ~~Y~C~-C~q~~l~~RRhn~~~~---g~~----------YrC~~C~gkL~~~~~~ 156 (156)
T COG3091 116 YPYRCQ-CQQHYLRIRRHNTVRR---GEV----------YRCGKCGGKLVFKGQV 156 (156)
T ss_pred eeEEee-cCCccchhhhcccccc---cce----------EEeccCCceEEeccCC
Confidence 334899 9999888888988774 543 3699999999998864
No 27
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=58.21 E-value=6.4 Score=34.04 Aligned_cols=29 Identities=24% Similarity=0.680 Sum_probs=22.5
Q ss_pred ecccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCc
Q 020340 36 MLPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSA 85 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~ 85 (327)
..|-..||..|+ .++..-.|.|+ ||.|.+
T Consensus 66 ~~p~~~~C~~C~-------------------~~~~~e~~~~~--CP~C~s 94 (115)
T COG0375 66 EEPAECWCLDCG-------------------QEVELEELDYR--CPKCGS 94 (115)
T ss_pred EeccEEEeccCC-------------------CeecchhheeE--CCCCCC
Confidence 468899999992 35566777777 999996
No 28
>PF14353 CpXC: CpXC protein
Probab=55.64 E-value=3.8 Score=34.38 Aligned_cols=47 Identities=26% Similarity=0.599 Sum_probs=26.7
Q ss_pred eecCCCCCccccC--ccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 41 IRCNTCGNYIYKG--TKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 41 i~C~~Cg~yI~kG--~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
|.|.+||.....= +-.|+....-.-+.-|+-.+| .+.|+.|+..+.+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~--~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLF--SFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcC--EEECCCCCCceec
Confidence 6799999753322 346654321111222333343 5569999998876
No 29
>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=53.69 E-value=7.9 Score=40.71 Aligned_cols=38 Identities=21% Similarity=0.565 Sum_probs=20.6
Q ss_pred ceecCCCCCcc---ccCccccccccccCCCcccceeeEEEEEEcCCCCceEE
Q 020340 40 SIRCNTCGNYI---YKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELT 88 (327)
Q Consensus 40 ~i~C~~Cg~yI---~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~ 88 (327)
.+.|.+||++. +.+.+|+.. + .--.-++.|+.|...|+
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~------~-----~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKG------E-----APETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceeecCC------C-----CccceEEECCCCcCCCC
Confidence 44577787653 234555311 0 11223677888877664
No 30
>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=52.88 E-value=14 Score=25.92 Aligned_cols=19 Identities=21% Similarity=0.838 Sum_probs=14.5
Q ss_pred eeEEEEEEcCCCCceEEEeeC
Q 020340 72 QIFRFYFKCTKCSAELTIKTD 92 (327)
Q Consensus 72 ~I~rFyiKC~~C~~eI~fkTD 92 (327)
|||.| +|..|...|++..-
T Consensus 2 P~Yey--~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 2 PIYEY--RCEECGHEFEVLQS 20 (42)
T ss_pred CCEEE--EeCCCCCEEEEEEE
Confidence 66765 59999998887654
No 31
>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=52.52 E-value=13 Score=31.60 Aligned_cols=34 Identities=21% Similarity=0.639 Sum_probs=22.0
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
|...|..|+..+.+=.+.+.. ..+|..|.+.++.
T Consensus 122 ~~~~C~~C~~~~~r~~~~~~~-----------------~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRSKRK-----------------RYRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeeeecccchh-----------------hEECCCCCCEEEE
Confidence 677899998776433333110 1679999988875
No 32
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=51.15 E-value=13 Score=26.56 Aligned_cols=18 Identities=22% Similarity=0.835 Sum_probs=12.7
Q ss_pred eeEEEEEEcCCCCceEEEee
Q 020340 72 QIFRFYFKCTKCSAELTIKT 91 (327)
Q Consensus 72 ~I~rFyiKC~~C~~eI~fkT 91 (327)
|||.| +|..|...+++..
T Consensus 2 P~Yey--~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 2 PIYEY--RCTACGHRFEVLQ 19 (52)
T ss_pred CCEEE--EeCCCCCEeEEEE
Confidence 56666 5888888777653
No 33
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=50.92 E-value=9.6 Score=39.38 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=11.1
Q ss_pred cCCCccc--CCCCCCC
Q 020340 5 KVLNKYY--PPDFDPS 18 (327)
Q Consensus 5 KvlNKYY--PPDfDPs 18 (327)
.++|+|| ||-+++.
T Consensus 66 ~~~sFMY~~PPG~~KE 81 (453)
T KOG3794|consen 66 NGLSFMYEAPPGAKKE 81 (453)
T ss_pred cccceeecCCCCCCch
Confidence 4678888 8888877
No 34
>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=49.37 E-value=19 Score=25.07 Aligned_cols=43 Identities=19% Similarity=0.341 Sum_probs=28.2
Q ss_pred ecCCCCCcccc-CccccccccccCCCcccceeeEEEEEEcCCCC
Q 020340 42 RCNTCGNYIYK-GTKFNSRKEDAIGETYLGIQIFRFYFKCTKCS 84 (327)
Q Consensus 42 ~C~~Cg~yI~k-G~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~ 84 (327)
.|..||..+.. |..+=.+.-.++--.+.=+.+.++...|+.|.
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 48889987664 55533333233333566688899999999995
No 35
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.57 E-value=11 Score=32.65 Aligned_cols=48 Identities=23% Similarity=0.549 Sum_probs=24.6
Q ss_pred ecccceecCCCCCccccC-cccc--ccccccCCCcccceeeEEEEEEcCCCCce
Q 020340 36 MLPMSIRCNTCGNYIYKG-TKFN--SRKEDAIGETYLGIQIFRFYFKCTKCSAE 86 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI~kG-~KFN--ArKe~v~gE~Ylgi~I~rFyiKC~~C~~e 86 (327)
..|-..||..||....-. .++- ..-...+ .|+. -...++++||.|.+.
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAI--HFIP-EVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccc--cccc-cccccCcCCcCCCCC
Confidence 567889999999432211 0110 0000000 1222 233566889999974
No 36
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=46.65 E-value=21 Score=27.93 Aligned_cols=32 Identities=31% Similarity=0.665 Sum_probs=22.5
Q ss_pred ceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 40 SIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
...|++||.-|.- +|.|. .|.|++|..++..+
T Consensus 9 ~~~CtSCg~~i~p------------~e~~v-------~F~CPnCGe~~I~R 40 (61)
T COG2888 9 PPVCTSCGREIAP------------GETAV-------KFPCPNCGEVEIYR 40 (61)
T ss_pred CceeccCCCEecc------------CCcee-------EeeCCCCCceeeeh
Confidence 6789999998863 44442 46799998665543
No 37
>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=44.70 E-value=11 Score=39.73 Aligned_cols=36 Identities=22% Similarity=0.598 Sum_probs=28.4
Q ss_pred cccceeeEEEEEEcCCCCceEEEe---------eCCCCCcccccc
Q 020340 67 TYLGIQIFRFYFKCTKCSAELTIK---------TDPQNSDYIVES 102 (327)
Q Consensus 67 ~Ylgi~I~rFyiKC~~C~~eI~fk---------TDPkN~dY~~es 102 (327)
.|..-.-.+|+..||+|..+..++ .+|+..-|+|.+
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 455556669999999999987765 258889999975
No 38
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=43.30 E-value=26 Score=30.18 Aligned_cols=37 Identities=24% Similarity=0.605 Sum_probs=26.9
Q ss_pred cccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
..|.-+|..|+..+++=+|.|.. =..+|..|.+.+.+
T Consensus 109 ~~~~y~C~~C~~~~~~~rr~~~~----------------~~y~C~~C~g~l~~ 145 (146)
T smart00731 109 KKYPYRCTGCGQRYLRVRRSNNV----------------SRYRCGKCGGKLIL 145 (146)
T ss_pred ceEEEECCCCCCCCceEccccCc----------------ceEEcCCCCCEEEe
Confidence 35788999999888655555432 14679999999876
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=42.62 E-value=13 Score=23.72 Aligned_cols=18 Identities=39% Similarity=0.768 Sum_probs=12.2
Q ss_pred cceecCCCCCccccCccc
Q 020340 39 MSIRCNTCGNYIYKGTKF 56 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KF 56 (327)
|.+.|..||..|-.+-+|
T Consensus 1 m~~~Cp~Cg~~~~~~~~f 18 (26)
T PF13248_consen 1 MEMFCPNCGAEIDPDAKF 18 (26)
T ss_pred CcCCCcccCCcCCccccc
Confidence 457788888877655444
No 40
>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=42.33 E-value=13 Score=37.67 Aligned_cols=40 Identities=20% Similarity=0.562 Sum_probs=21.5
Q ss_pred cccceecCCCCCc-cccCccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 37 LPMSIRCNTCGNY-IYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 37 ~PF~i~C~~Cg~y-I~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
.||...|..||.. --.=+.||....+| ..+|..|+.+.++
T Consensus 171 ~Pf~piC~~cGri~tt~v~~~d~~~~~v-------------~Y~c~~cG~~g~~ 211 (360)
T PF01921_consen 171 SPFLPICEKCGRIDTTEVTEYDPEGGTV-------------TYRCEECGHEGEV 211 (360)
T ss_dssp -SEEEEETTTEE--EEEEEEE--SSSEE-------------EEE--TTS---EE
T ss_pred eeeeeeccccCCcccceeeEeecCCCEE-------------EEEecCCCCEEEE
Confidence 5999999999973 33333555444433 5689999997654
No 41
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=41.81 E-value=15 Score=35.76 Aligned_cols=51 Identities=25% Similarity=0.658 Sum_probs=24.5
Q ss_pred ceecCCCCCc-cccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCCCccccccCcee
Q 020340 40 SIRCNTCGNY-IYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASR 106 (327)
Q Consensus 40 ~i~C~~Cg~y-I~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~R 106 (327)
++-|..||.. |. +|.+. .|+=-|| |+.|..++++|.-=++..=++..||-.
T Consensus 31 n~yCP~Cg~~~L~---~f~NN-----------~PVaDF~--C~~C~eeyELKSk~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 31 NMYCPNCGSKPLS---KFENN-----------RPVADFY--CPNCNEEYELKSKKKKLSNKINDGAYH 82 (254)
T ss_dssp H---TTT--SS-E---E-------------------EEE---TTT--EEEEEEEESS--SEEEEEEHH
T ss_pred CCcCCCCCChhHh---hccCC-----------CccceeE--CCCCchHHhhhhhccccCCcccCccHH
Confidence 6889999975 53 34333 3444444 999999999998777777788888744
No 42
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.43 E-value=30 Score=23.74 Aligned_cols=35 Identities=26% Similarity=0.575 Sum_probs=21.4
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceE
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAEL 87 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI 87 (327)
|.|.|..|+ ++|+-.-+++.+. ....+|+.|+..|
T Consensus 1 M~i~Cp~C~------~~y~i~d~~ip~~--------g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQ------AKYEIDDEKIPPK--------GRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCC------CEEeCCHHHCCCC--------CcEEECCCCCCEe
Confidence 457788885 3455444444331 2278899998865
No 43
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=40.98 E-value=34 Score=24.49 Aligned_cols=30 Identities=30% Similarity=0.605 Sum_probs=20.5
Q ss_pred ceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCC
Q 020340 40 SIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCS 84 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~ 84 (327)
.|.|.+|++.|. .+.. -++=-||..|..|-
T Consensus 3 tIvCq~C~~~Id----------~~e~-----ekV~~lYg~C~~~e 32 (38)
T PF13790_consen 3 TIVCQHCNETID----------HFET-----EKVTTLYGKCGKCE 32 (38)
T ss_pred EEEeccccceee----------eecC-----CcEEEEEEECCCCc
Confidence 478999998875 2322 35556788898764
No 44
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=40.49 E-value=22 Score=31.96 Aligned_cols=55 Identities=20% Similarity=0.309 Sum_probs=31.1
Q ss_pred eecCCCCCccccCccccccccccCCCcccce--eeEEEEEEcCCCCceE-EEeeCCCCCccccccCcee
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGI--QIFRFYFKCTKCSAEL-TIKTDPQNSDYIVESGASR 106 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi--~I~rFyiKC~~C~~eI-~fkTDPkN~dY~~esGA~R 106 (327)
|+|..||..-- ++ ....|++- -|=|| -+|+.|+..| ++.+=-...-||+-..+++
T Consensus 1 m~cp~c~~~~~-----~~-----~~s~~~~~~~~~~~~-~~c~~c~~~f~~~e~~~~~~i~VIKRDG~~ 58 (154)
T PRK00464 1 MRCPFCGHPDT-----RV-----IDSRPAEDGNAIRRR-RECLACGKRFTTFERVELVPLLVIKKDGRR 58 (154)
T ss_pred CcCCCCCCCCC-----Ee-----EeccccCCCCceeee-eeccccCCcceEeEeccCcccEEEecCCcC
Confidence 78999986210 11 22244442 57778 7899999854 3333333334565554444
No 45
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=40.11 E-value=9.8 Score=39.87 Aligned_cols=31 Identities=52% Similarity=1.033 Sum_probs=22.9
Q ss_pred ceecCCCCCccccCcc-----ccccccccCCCcccce
Q 020340 40 SIRCNTCGNYIYKGTK-----FNSRKEDAIGETYLGI 71 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~K-----FNArKe~v~gE~Ylgi 71 (327)
.-.|--||||.|+|.| ||--+- +-|..-|||
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~EwRH-~hGmrCLGI 436 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFNEWRH-AHGMRCLGI 436 (497)
T ss_pred ccceeeccCccccCcHHHHHHhHHHHH-hhcceecCC
Confidence 4469999999999986 887774 445544554
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=38.18 E-value=41 Score=26.16 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=12.1
Q ss_pred ecccceecCCCCCccc
Q 020340 36 MLPMSIRCNTCGNYIY 51 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI~ 51 (327)
++.....|.+||..|.
T Consensus 3 ~~~~~~~CtSCg~~i~ 18 (59)
T PRK14890 3 EMMEPPKCTSCGIEIA 18 (59)
T ss_pred ccccCccccCCCCccc
Confidence 4455568999998886
No 47
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.05 E-value=30 Score=24.41 Aligned_cols=18 Identities=22% Similarity=0.576 Sum_probs=14.9
Q ss_pred EEEcCCCCceEEEeeCCC
Q 020340 77 YFKCTKCSAELTIKTDPQ 94 (327)
Q Consensus 77 yiKC~~C~~eI~fkTDPk 94 (327)
.++|+.|++.+.++..+.
T Consensus 21 ~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 21 GVRCPYCGYRILFKERPP 38 (46)
T ss_pred ceECCCCCCeEEEccCCC
Confidence 579999999999876654
No 48
>PRK04351 hypothetical protein; Provisional
Probab=36.20 E-value=29 Score=30.87 Aligned_cols=37 Identities=22% Similarity=0.622 Sum_probs=27.6
Q ss_pred cccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
-.|--+|..||..+.+=.++|- -..+|..|.+.+.+.
T Consensus 109 ~~y~Y~C~~Cg~~~~r~Rr~n~-----------------~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 109 KNYLYECQSCGQQYLRKRRINT-----------------KRYRCGKCRGKLKLI 145 (149)
T ss_pred ceEEEECCCCCCEeeeeeecCC-----------------CcEEeCCCCcEeeec
Confidence 3478899999987766556652 145799999998876
No 49
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=35.84 E-value=25 Score=36.77 Aligned_cols=27 Identities=15% Similarity=0.442 Sum_probs=20.8
Q ss_pred cccceecCCCCCccccCc-ccccccccc
Q 020340 37 LPMSIRCNTCGNYIYKGT-KFNSRKEDA 63 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~-KFNArKe~v 63 (327)
.||+..|..||.-....+ .||....+|
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~~~v 199 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEAGTV 199 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCCCEE
Confidence 499999999998776665 677776555
No 50
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.54 E-value=18 Score=24.58 Aligned_cols=13 Identities=46% Similarity=1.081 Sum_probs=10.6
Q ss_pred eecCCCCCccccCc
Q 020340 41 IRCNTCGNYIYKGT 54 (327)
Q Consensus 41 i~C~~Cg~yI~kG~ 54 (327)
-+|..|| ||+.|.
T Consensus 3 ~~C~~CG-~i~~g~ 15 (34)
T cd00729 3 WVCPVCG-YIHEGE 15 (34)
T ss_pred EECCCCC-CEeECC
Confidence 4799999 888775
No 51
>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=35.08 E-value=28 Score=30.06 Aligned_cols=73 Identities=21% Similarity=0.286 Sum_probs=52.2
Q ss_pred EEEEecccceecCCCCCc--cccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCCCccccccCceecCC
Q 020340 32 KVRMMLPMSIRCNTCGNY--IYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASRNYE 109 (327)
Q Consensus 32 ~VRfm~PF~i~C~~Cg~y--I~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~Rn~e 109 (327)
+-||-+-|+-||.-=..- -|+|. ..+|.+.. .+--..|.|+|..|+..++||..-+|.---+-.|-.|...
T Consensus 25 ~~~FSiK~~~W~LFT~~V~V~YR~~---~~~E~~~K----D~~RLHF~~~CV~C~~K~~~K~~Nk~H~~~~~~G~~R~~R 97 (123)
T PF07255_consen 25 CERFSIKFSEWKLFTTAVYVEYRQL---GEKECSLK----DVCRLHFNMSCVKCCRKLKCKKQNKNHSKHVQNGYLRKVR 97 (123)
T ss_pred eEEEEEecCCEEEEeeEEEEEEecc---CCccceeh----eeeeEEEeeehhhhcccceehhcCcchHHHhhcCeEEEec
Confidence 568889999999865431 23332 23444322 3556789999999999999999999888777888777554
Q ss_pred CC
Q 020340 110 PW 111 (327)
Q Consensus 110 ~~ 111 (327)
.+
T Consensus 98 NF 99 (123)
T PF07255_consen 98 NF 99 (123)
T ss_pred ce
Confidence 44
No 52
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=34.65 E-value=19 Score=28.14 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=10.9
Q ss_pred cceecCCCCCccc
Q 020340 39 MSIRCNTCGNYIY 51 (327)
Q Consensus 39 F~i~C~~Cg~yI~ 51 (327)
|.|+|-|||.-|+
T Consensus 3 iPvRCFTCGkvi~ 15 (62)
T PRK04016 3 IPVRCFTCGKVIA 15 (62)
T ss_pred CCeEecCCCCChH
Confidence 5689999998875
No 53
>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=34.34 E-value=57 Score=23.34 Aligned_cols=38 Identities=26% Similarity=0.544 Sum_probs=25.9
Q ss_pred ecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCC--CCceEEEe
Q 020340 42 RCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTK--CSAELTIK 90 (327)
Q Consensus 42 ~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~--C~~eI~fk 90 (327)
.|..||......+. .+++.-+-.+|..|++ |+..++..
T Consensus 1 ~CP~Cg~~a~ir~S-----------~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTS-----------RQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEc-----------hhhCcceEEEEEEECCCcCCCEEEEE
Confidence 48888875432211 3556667789999998 99877653
No 54
>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=34.32 E-value=21 Score=22.72 Aligned_cols=12 Identities=42% Similarity=1.007 Sum_probs=10.1
Q ss_pred ecCCCCCccccC
Q 020340 42 RCNTCGNYIYKG 53 (327)
Q Consensus 42 ~C~~Cg~yI~kG 53 (327)
+|..|+..|+-+
T Consensus 1 ~C~~C~~~i~~~ 12 (39)
T smart00132 1 KCAGCGKPIRGG 12 (39)
T ss_pred CccccCCcccCC
Confidence 588999998876
No 55
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.19 E-value=13 Score=33.92 Aligned_cols=60 Identities=25% Similarity=0.512 Sum_probs=33.8
Q ss_pred ccceecCCCCCccccCc--cccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCC-CCCcccccc
Q 020340 38 PMSIRCNTCGNYIYKGT--KFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDP-QNSDYIVES 102 (327)
Q Consensus 38 PF~i~C~~Cg~yI~kG~--KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDP-kN~dY~~es 102 (327)
-|.+.|..||+.--+=+ .-|-+-. +.|- =|+- .|-|||..|+.+-++.-=| ++.-|+.+.
T Consensus 28 ~~kLkCtnCgE~~dkw~~I~l~E~~~-~pg~--Rgta--~~v~KCK~C~Rensv~iv~~~~~pyt~ed 90 (161)
T KOG1296|consen 28 YLKLKCTNCGELSDKWQYITLNEEVA-MPGS--RGTA--SFVMKCKFCSRENSVTIVAFEDKPYTAED 90 (161)
T ss_pred EEEeccccccccCCceEEEEeeeeec-CCCC--cchh--hHhhhhhhhcccCcEEEecCCCCcccccc
Confidence 46789999998544333 2222221 2221 1232 7899999999876664322 344455444
No 56
>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=33.65 E-value=17 Score=30.44 Aligned_cols=15 Identities=33% Similarity=0.884 Sum_probs=9.8
Q ss_pred ecccceecCCCCCcc
Q 020340 36 MLPMSIRCNTCGNYI 50 (327)
Q Consensus 36 m~PF~i~C~~Cg~yI 50 (327)
..|...||..||...
T Consensus 66 ~~p~~~~C~~Cg~~~ 80 (113)
T PF01155_consen 66 EVPARARCRDCGHEF 80 (113)
T ss_dssp EE--EEEETTTS-EE
T ss_pred ecCCcEECCCCCCEE
Confidence 579999999998643
No 57
>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=31.57 E-value=17 Score=38.74 Aligned_cols=17 Identities=24% Similarity=0.573 Sum_probs=14.5
Q ss_pred EEEEecccceecCCCCC
Q 020340 32 KVRMMLPMSIRCNTCGN 48 (327)
Q Consensus 32 ~VRfm~PF~i~C~~Cg~ 48 (327)
+=-|-||||+.|.+|--
T Consensus 490 TPDFSMPYNVIcltcTv 506 (575)
T KOG2407|consen 490 TPDFSMPYNVICLTCTV 506 (575)
T ss_pred CCCCCCceeEEeeehhh
Confidence 45789999999999953
No 58
>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=31.27 E-value=24 Score=25.11 Aligned_cols=19 Identities=21% Similarity=0.611 Sum_probs=11.8
Q ss_pred eecCCCCCccccCccccccc
Q 020340 41 IRCNTCGNYIYKGTKFNSRK 60 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArK 60 (327)
+.|++|+..| .|.||--..
T Consensus 1 v~Cd~C~~~i-~G~ry~C~~ 19 (43)
T cd02340 1 VICDGCQGPI-VGVRYKCLV 19 (43)
T ss_pred CCCCCCCCcC-cCCeEECCC
Confidence 4688887744 666665443
No 59
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=30.80 E-value=22 Score=28.00 Aligned_cols=22 Identities=32% Similarity=0.720 Sum_probs=14.4
Q ss_pred cceecCCCCCccccCccccccccc
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKED 62 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~ 62 (327)
+.|||-+||.-|+ -+|+.=|+.
T Consensus 3 iPiRCFsCGkvi~--~~w~~y~~r 24 (63)
T COG1644 3 IPVRCFSCGKVIG--HKWEEYKRR 24 (63)
T ss_pred CceEeecCCCCHH--HHHHHHHHH
Confidence 5689999998774 344444443
No 60
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=30.52 E-value=33 Score=31.56 Aligned_cols=37 Identities=19% Similarity=0.521 Sum_probs=30.6
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
|.|+-|+..+.-|+-.++-=..| ..||..|.+-+.+-
T Consensus 13 VhCnFC~TiLaVsVP~ssL~~~V-------------TVRCGHCtNLLSVN 49 (170)
T PF04690_consen 13 VHCNFCNTILAVSVPCSSLLKTV-------------TVRCGHCTNLLSVN 49 (170)
T ss_pred EEcCCcCeEEEEecchhhhhhhh-------------ceeccCccceeeee
Confidence 68999999999999888766655 67999999987753
No 61
>PRK00807 50S ribosomal protein L24e; Validated
Probab=30.18 E-value=16 Score=27.17 Aligned_cols=45 Identities=27% Similarity=0.620 Sum_probs=30.6
Q ss_pred ecCCCCCccccC--ccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCCCcc
Q 020340 42 RCNTCGNYIYKG--TKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQNSDY 98 (327)
Q Consensus 42 ~C~~Cg~yI~kG--~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY 98 (327)
.|.-||.-||-| ..|=. ..| +| |||=|..|...+-.+.+|..-..
T Consensus 3 ~C~fcG~~I~pg~G~~~vr----~Dg------kv--~~Fcs~KC~~~f~~~~nprk~~W 49 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVK----KDG------TI--LYFCSSKCEKNYKLGRVPRKLKW 49 (52)
T ss_pred ccCCCCCeEcCCCCeEEEE----eCC------cE--EEEeCHHHHHHHHccCCCCcccc
Confidence 599999999954 44321 113 34 46667899998999999976443
No 62
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=29.70 E-value=28 Score=35.03 Aligned_cols=42 Identities=33% Similarity=0.661 Sum_probs=28.5
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCC
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQN 95 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN 95 (327)
|.++|..|..|-+.- +||.. .| | .|+|+.|.+...=+-+|+|
T Consensus 219 yALIC~~C~~HNGla-----~~ee~---~y--i-----~F~C~~Cn~LN~~~k~~e~ 260 (328)
T KOG2846|consen 219 YALICSQCHHHNGLA-----RKEEY---EY--I-----TFRCPHCNALNPAKKSPEN 260 (328)
T ss_pred hhhcchhhccccCcC-----Chhhc---Cc--e-----EEECccccccCCCcCCccc
Confidence 578999999988764 44432 23 2 5779999997655555443
No 63
>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=29.10 E-value=29 Score=26.23 Aligned_cols=18 Identities=28% Similarity=0.757 Sum_probs=14.6
Q ss_pred EEEcCCCCceEEEeeCCC
Q 020340 77 YFKCTKCSAELTIKTDPQ 94 (327)
Q Consensus 77 yiKC~~C~~eI~fkTDPk 94 (327)
.|+|+.|.++|++..+..
T Consensus 2 ~~~CP~CG~~iev~~~~~ 19 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL 19 (54)
T ss_pred ccCCCCCCCEEecCCCcc
Confidence 368999999999966554
No 64
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.09 E-value=54 Score=23.61 Aligned_cols=18 Identities=17% Similarity=0.551 Sum_probs=15.7
Q ss_pred EEEcCCCCceEEEeeCCC
Q 020340 77 YFKCTKCSAELTIKTDPQ 94 (327)
Q Consensus 77 yiKC~~C~~eI~fkTDPk 94 (327)
-++|+.|+..|-+|-=|+
T Consensus 19 ~irC~~CG~rIlyK~R~~ 36 (44)
T smart00659 19 VVRCRECGYRILYKKRTK 36 (44)
T ss_pred ceECCCCCceEEEEeCCC
Confidence 689999999999987665
No 65
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.59 E-value=74 Score=28.58 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=29.7
Q ss_pred cccceeeEEEEEEcCCCCceEEEeeCCCCCcc
Q 020340 67 TYLGIQIFRFYFKCTKCSAELTIKTDPQNSDY 98 (327)
Q Consensus 67 ~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY 98 (327)
.|+.|.-|+..+-|+--+=.|++-|||+-.+|
T Consensus 62 ~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~i 93 (140)
T KOG3368|consen 62 LSYKTSKYKLHFYETPTGLKFVLNTDPKAGSI 93 (140)
T ss_pred eEEeeceeEEEEEEcCCCcEEEEecCCCcccH
Confidence 68889999999999999999999999998775
No 66
>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=28.54 E-value=46 Score=35.09 Aligned_cols=24 Identities=21% Similarity=0.595 Sum_probs=17.5
Q ss_pred cccceecCCCCCccccCccccccc
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRK 60 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArK 60 (327)
.||+..|..||.-...=+.+|+..
T Consensus 165 ~P~~pic~~cGrv~~~~~~~~~~~ 188 (515)
T TIGR00467 165 YPISVFCENCGRDTTTVNNYDNEY 188 (515)
T ss_pred eeeeeecCCcCccCceEEEecCCc
Confidence 699999999998755333455544
No 67
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=27.85 E-value=63 Score=31.87 Aligned_cols=41 Identities=17% Similarity=0.498 Sum_probs=22.9
Q ss_pred ceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 40 SIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 40 ~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
...|..||. +..-|..---.-.+| |.=.|| .|..|.+.+.|
T Consensus 258 ~~~C~~C~~---~~~~~~q~QtrsaDE-----pmT~f~-~C~~Cg~~w~f 298 (299)
T TIGR01385 258 LFTCGKCKQ---KKCTYYQLQTRSADE-----PMTTFV-TCEECGNRWKF 298 (299)
T ss_pred cccCCCCCC---ccceEEEecccCCCC-----CCeEEE-EcCCCCCeeee
Confidence 468999984 223332221112233 334455 49999998776
No 68
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=27.76 E-value=31 Score=26.71 Aligned_cols=16 Identities=19% Similarity=0.538 Sum_probs=11.7
Q ss_pred EEEcCCCCceEEEeeC
Q 020340 77 YFKCTKCSAELTIKTD 92 (327)
Q Consensus 77 yiKC~~C~~eI~fkTD 92 (327)
+..||.|...|++++|
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 6789999999999875
No 69
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.99 E-value=47 Score=35.98 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=14.1
Q ss_pred CccEEEEecccceecCCCCCccc
Q 020340 29 QQIKVRMMLPMSIRCNTCGNYIY 51 (327)
Q Consensus 29 ~~~~VRfm~PF~i~C~~Cg~yI~ 51 (327)
++.-.-+-.||++ |..|| |++
T Consensus 556 ~i~Yf~in~~~~i-C~~CG-~~~ 576 (623)
T PRK08271 556 GCNYFAFNVKITI-CNDCH-HID 576 (623)
T ss_pred CCceEEeCCCCcc-CCCCC-CcC
Confidence 3445666667775 99999 553
No 70
>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=26.91 E-value=28 Score=30.57 Aligned_cols=14 Identities=29% Similarity=0.876 Sum_probs=10.1
Q ss_pred cceecCCCCCcccc
Q 020340 39 MSIRCNTCGNYIYK 52 (327)
Q Consensus 39 F~i~C~~Cg~yI~k 52 (327)
+.++|..|+.....
T Consensus 104 ~~~~C~~C~~~~~~ 117 (178)
T PF02146_consen 104 FRLRCSKCGKEYDR 117 (178)
T ss_dssp EEEEETTTSBEEEG
T ss_pred ceeeecCCCccccc
Confidence 45799999985443
No 71
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=26.05 E-value=39 Score=29.04 Aligned_cols=36 Identities=22% Similarity=0.433 Sum_probs=22.1
Q ss_pred cCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCC
Q 020340 43 CNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDP 93 (327)
Q Consensus 43 C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDP 93 (327)
|..|+.-- -+--|-.|+..+| ++.|.-|... |.|+-
T Consensus 26 ClfcnHek--~v~~~~Dk~~~iG-----------~~sC~iC~es--Fqt~i 61 (109)
T KOG3214|consen 26 CLFCNHEK--SVSCTLDKKHNIG-----------KASCRICEES--FQTTI 61 (109)
T ss_pred cCcccccc--ceeeeehhhcCcc-----------eeeeeehhhh--hccch
Confidence 77787542 3344555555556 6778889874 55543
No 72
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.61 E-value=53 Score=25.52 Aligned_cols=34 Identities=21% Similarity=0.551 Sum_probs=26.1
Q ss_pred ccCCCC----CCccEEEEecccceecCCCCCccccCcc
Q 020340 22 RIRRPK----NQQIKVRMMLPMSIRCNTCGNYIYKGTK 55 (327)
Q Consensus 22 R~Kk~k----~~~~~VRfm~PF~i~C~~Cg~yI~kG~K 55 (327)
-.|||+ |+--+||+-+-..|.|.+||..|-.+..
T Consensus 12 EMKK~H~Cg~NrwkIiRvGaDIkikC~nC~h~vm~pR~ 49 (60)
T COG4481 12 EMKKPHACGTNRWKIIRVGADIKIKCENCGHSVMMPRY 49 (60)
T ss_pred eecCCCccccceEEEEEecCcEEEEecCCCcEEEecHH
Confidence 345554 3455899999999999999998877763
No 73
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.34 E-value=34 Score=37.79 Aligned_cols=65 Identities=23% Similarity=0.478 Sum_probs=46.1
Q ss_pred EEEecccceecCCCCCc--cccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCCCccccccCceecCCC
Q 020340 33 VRMMLPMSIRCNTCGNY--IYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASRNYEP 110 (327)
Q Consensus 33 VRfm~PF~i~C~~Cg~y--I~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~Rn~e~ 110 (327)
=|++.||.. |++||-. |-+.-.|-....+ .=.|- -|+.|..| -.||.|.-|-..--|=....|
T Consensus 117 rrY~YPF~~-CT~CGPRfTIi~alPYDR~nTs----------M~~F~-lC~~C~~E---Y~dP~nRRfHAQp~aCp~CGP 181 (750)
T COG0068 117 RRYLYPFIN-CTNCGPRFTIIEALPYDRENTS----------MADFP-LCPFCDKE---YKDPLNRRFHAQPIACPKCGP 181 (750)
T ss_pred cceeccccc-cCCCCcceeeeccCCCCcccCc----------cccCc-CCHHHHHH---hcCccccccccccccCcccCC
Confidence 489999975 9999953 5566555544422 22233 39999987 679999999888877777776
Q ss_pred Cc
Q 020340 111 WR 112 (327)
Q Consensus 111 ~~ 112 (327)
|-
T Consensus 182 ~~ 183 (750)
T COG0068 182 HL 183 (750)
T ss_pred Ce
Confidence 43
No 74
>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=25.17 E-value=32 Score=26.73 Aligned_cols=13 Identities=46% Similarity=1.009 Sum_probs=9.3
Q ss_pred cceecCCCCCccc
Q 020340 39 MSIRCNTCGNYIY 51 (327)
Q Consensus 39 F~i~C~~Cg~yI~ 51 (327)
+.|||-|||..|+
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 4689999998885
No 75
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=25.17 E-value=36 Score=27.40 Aligned_cols=13 Identities=46% Similarity=1.009 Sum_probs=9.5
Q ss_pred cceecCCCCCccc
Q 020340 39 MSIRCNTCGNYIY 51 (327)
Q Consensus 39 F~i~C~~Cg~yI~ 51 (327)
+.|||-|||.-|+
T Consensus 3 iPVRCFTCGkvig 15 (71)
T PLN00032 3 IPVRCFTCGKVIG 15 (71)
T ss_pred CceeecCCCCCcH
Confidence 4678888887664
No 76
>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=25.15 E-value=77 Score=22.02 Aligned_cols=34 Identities=21% Similarity=0.635 Sum_probs=18.4
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEE
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTI 89 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~f 89 (327)
++|..|+.||--=.+|+..-. ..+|..|...-.|
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~---------------~w~C~~C~~~N~l 36 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGK---------------TWICNFCGTKNPL 36 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTT---------------EEEETTT--EEE-
T ss_pred cccCCCCCEECCcceEcCCCC---------------EEECcCCCCcCCC
Confidence 689999999987777765321 4678888875443
No 77
>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=25.10 E-value=57 Score=25.45 Aligned_cols=43 Identities=23% Similarity=0.556 Sum_probs=29.1
Q ss_pred ecCCCCCccccCccccccccccCCCcccceeeEEEE-EEcCCCCce
Q 020340 42 RCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFY-FKCTKCSAE 86 (327)
Q Consensus 42 ~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFy-iKC~~C~~e 86 (327)
.|..||+..|.=..+-+.--.. + +.+.++.-+|+ +-|++|+-.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~-s-kiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGL-S-KIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCee-E-EEEEecCcEEEEEECCCCCCE
Confidence 4999999888777776655332 2 44555555565 469999874
No 78
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.27 E-value=57 Score=24.50 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=18.1
Q ss_pred EEcCCCCceEEEeeCCCCCccc
Q 020340 78 FKCTKCSAELTIKTDPQNSDYI 99 (327)
Q Consensus 78 iKC~~C~~eI~fkTDPkN~dY~ 99 (327)
+.||.|+..|.+--|+...+-.
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~ 22 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQE 22 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCee
Confidence 4699999999999999876433
No 79
>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=23.54 E-value=63 Score=32.50 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=11.8
Q ss_pred cccceecCCCCCccc
Q 020340 37 LPMSIRCNTCGNYIY 51 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~ 51 (327)
.||+..|..|| -|.
T Consensus 166 ~P~~p~c~~cg-~~~ 179 (353)
T cd00674 166 YPFMPYCEKCG-KDT 179 (353)
T ss_pred eeeeeecCCcC-cce
Confidence 79999999999 443
No 80
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=23.34 E-value=60 Score=35.27 Aligned_cols=52 Identities=21% Similarity=0.406 Sum_probs=0.0
Q ss_pred cceecCCCCCcc---------ccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCCCCccccccCceec
Q 020340 39 MSIRCNTCGNYI---------YKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASRN 107 (327)
Q Consensus 39 F~i~C~~Cg~yI---------~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~Rn 107 (327)
|-+-|.|||++- +.|.+.-+- +.+ ++.|++|...|.=+ -|..+++..-+-+.
T Consensus 226 ~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~-~~~-------------~~~c~h~~~~i~~~---~~~~gv~~~~g~~~ 286 (611)
T COG5525 226 FYVPCPHCGEEQQLKFGEKSGPRGLKDTPA-EAA-------------FIQCEHCGCVIRPK---LNGRGVCLRTGEWI 286 (611)
T ss_pred EEeeCCCCCchhhccccccCCCcCcccchh-hhh-------------hhhccccCceeeee---ccCccchhccCCcC
No 81
>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=23.26 E-value=1e+02 Score=25.10 Aligned_cols=39 Identities=28% Similarity=0.480 Sum_probs=19.6
Q ss_pred cCCCC-CccccCccccccccccCCCcccceeeEEEEEEcCCCCce
Q 020340 43 CNTCG-NYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAE 86 (327)
Q Consensus 43 C~~Cg-~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~e 86 (327)
|..|| ..+.++++=..-. .-|+ .+.|=.-...|+.|+.+
T Consensus 1 C~~C~~~~~~~~~~~~~~~--~~G~---~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYT--YKGE---SITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEE--EcCE---EEEEeeeeeECCCCCCE
Confidence 88888 4566665432211 1131 12222234468888775
No 82
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.92 E-value=54 Score=32.35 Aligned_cols=49 Identities=29% Similarity=0.541 Sum_probs=35.9
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEeeCCC------CCccccccCceecC
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIKTDPQ------NSDYIVESGASRNY 108 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fkTDPk------N~dY~~esGA~Rn~ 108 (327)
-+|..||..++. ..|+ .-+.|+.|.+++.=+|||- +.++++--|..|.+
T Consensus 112 RFCg~CG~~~~~----------~~~g---------~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~ 166 (279)
T COG2816 112 RFCGRCGTKTYP----------REGG---------WARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHF 166 (279)
T ss_pred cCCCCCCCcCcc----------ccCc---------eeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCC
Confidence 469999876653 1232 2678999999999999996 67777777766665
No 83
>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=22.57 E-value=15 Score=30.04 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=25.2
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEE---EEEcCCCCceEEE
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRF---YFKCTKCSAELTI 89 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rF---yiKC~~C~~eI~f 89 (327)
-.|.+|+..+. -|--|||++| ..||..|.+.|.+
T Consensus 34 S~C~~C~~~L~---------------~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 34 SHCPHCGHPLS---------------WWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CcCcCCCCcCc---------------ccccchHHHHHHhCCCCcccCCCCCh
Confidence 46999987653 3446888876 6799999987754
No 84
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=22.49 E-value=72 Score=25.44 Aligned_cols=38 Identities=24% Similarity=0.495 Sum_probs=26.8
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcC--CCCceEEE
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCT--KCSAELTI 89 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~--~C~~eI~f 89 (327)
|.|..||..- + |..-.|++-..-+.|..|+ .|+..|+.
T Consensus 2 m~CP~Cg~~a--------~---irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAA--------H---ARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCcc--------E---EEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 7899998643 1 1122577766788999999 99986544
No 85
>PRK05978 hypothetical protein; Provisional
Probab=22.47 E-value=36 Score=30.52 Aligned_cols=34 Identities=29% Similarity=0.725 Sum_probs=24.3
Q ss_pred cceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceEEEe
Q 020340 39 MSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAELTIK 90 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI~fk 90 (327)
+..+|-.||+ |.=|. .||.+ .-+|+.|...+.+.
T Consensus 32 l~grCP~CG~----G~LF~---------g~Lkv-----~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGE----GKLFR---------AFLKP-----VDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCC----Ccccc---------ccccc-----CCCccccCCccccC
Confidence 5689999974 44332 36665 66899999988765
No 86
>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=22.16 E-value=36 Score=24.68 Aligned_cols=7 Identities=43% Similarity=1.597 Sum_probs=4.8
Q ss_pred eecCCCC
Q 020340 41 IRCNTCG 47 (327)
Q Consensus 41 i~C~~Cg 47 (327)
|.|++|+
T Consensus 1 i~C~~C~ 7 (49)
T cd02338 1 VSCDGCG 7 (49)
T ss_pred CCCCCCc
Confidence 4677776
No 87
>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=22.08 E-value=88 Score=23.47 Aligned_cols=34 Identities=24% Similarity=0.506 Sum_probs=22.4
Q ss_pred cccceecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCc
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSA 85 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~ 85 (327)
-.+.+.|..|..|-+.-- ++. |-.+ .++|+.|..
T Consensus 19 ~r~aLIC~~C~~hNGla~-----~~~-----~~~i-----~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAP-----KEE-----FEEI-----QYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccc-----ccc-----CCce-----EEEcCCCCC
Confidence 347789999998876543 221 2122 678999976
No 88
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=21.86 E-value=42 Score=32.91 Aligned_cols=24 Identities=21% Similarity=0.582 Sum_probs=19.6
Q ss_pred EEcCCCCceEEEeeCCCCCcccccc
Q 020340 78 FKCTKCSAELTIKTDPQNSDYIVES 102 (327)
Q Consensus 78 iKC~~C~~eI~fkTDPkN~dY~~es 102 (327)
+.|+.|... .|-+|++++++||..
T Consensus 2 ~~CpeCg~~-~~~~d~~~ge~VC~~ 25 (285)
T COG1405 2 MSCPECGST-NIITDYERGEIVCAD 25 (285)
T ss_pred CCCCCCCCc-cceeeccCCeEEecc
Confidence 468888888 888888888888765
No 89
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=21.35 E-value=22 Score=25.82 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=11.9
Q ss_pred ccceecCCCCCcc
Q 020340 38 PMSIRCNTCGNYI 50 (327)
Q Consensus 38 PF~i~C~~Cg~yI 50 (327)
+|+-+|..|+..|
T Consensus 4 ~F~~yC~~Cdk~~ 16 (43)
T PF12855_consen 4 AFNDYCIVCDKQI 16 (43)
T ss_pred hhhhHHHHhhccc
Confidence 8999999999888
No 90
>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=21.27 E-value=47 Score=24.00 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=12.8
Q ss_pred eecCCCCCccccCcccccc
Q 020340 41 IRCNTCGNYIYKGTKFNSR 59 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNAr 59 (327)
|.|.+|+...-.|.||--.
T Consensus 1 i~Cd~C~~~~i~G~RykC~ 19 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCA 19 (45)
T ss_pred CCCCCCCCCCcccCeEECC
Confidence 5688888766666666544
No 91
>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=21.23 E-value=43 Score=26.21 Aligned_cols=15 Identities=27% Similarity=0.778 Sum_probs=11.8
Q ss_pred cccceecCCCCCccc
Q 020340 37 LPMSIRCNTCGNYIY 51 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~ 51 (327)
|=|.+.|.+||.-|.
T Consensus 1 MVf~lvCSTCGrDlS 15 (63)
T PF05864_consen 1 MVFQLVCSTCGRDLS 15 (63)
T ss_pred CeeeeeecccCCcch
Confidence 458889999997664
No 92
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=21.15 E-value=85 Score=27.89 Aligned_cols=68 Identities=24% Similarity=0.428 Sum_probs=39.2
Q ss_pred eecCCCCCccccCc-cccccc-----------cccCC-CcccceeeEEEEEEcCCCCceE--EEeeCC--CCCccccccC
Q 020340 41 IRCNTCGNYIYKGT-KFNSRK-----------EDAIG-ETYLGIQIFRFYFKCTKCSAEL--TIKTDP--QNSDYIVESG 103 (327)
Q Consensus 41 i~C~~Cg~yI~kG~-KFNArK-----------e~v~g-E~Ylgi~I~rFyiKC~~C~~eI--~fkTDP--kN~dY~~esG 103 (327)
-.|..||+.+|... |||+-= ..|.- +++ +.-.-|--++|.+|.+++ +|.=-| .+.-|-|- |
T Consensus 41 Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~-s~gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCIN-s 118 (134)
T TIGR00357 41 YVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDE-SHGMIRTEVRCRNCDAHLGHVFDDGPEPTGLRYCIN-S 118 (134)
T ss_pred EEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecC-CCCcEEEEEEecCCCCccCcccCCCCCCCCceEeec-c
Confidence 35999999999887 888721 11100 011 122346789999999976 465333 44455443 4
Q ss_pred ceecCCC
Q 020340 104 ASRNYEP 110 (327)
Q Consensus 104 A~Rn~e~ 110 (327)
+.=.|.+
T Consensus 119 ~sL~F~p 125 (134)
T TIGR00357 119 AALKFIP 125 (134)
T ss_pred eeEeccc
Confidence 4444443
No 93
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=21.02 E-value=36 Score=33.36 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=15.4
Q ss_pred EEecccceecCCCCCccccCccccc
Q 020340 34 RMMLPMSIRCNTCGNYIYKGTKFNS 58 (327)
Q Consensus 34 Rfm~PF~i~C~~Cg~yI~kG~KFNA 58 (327)
|...-=++||.+||+++--..=..|
T Consensus 12 ~~~~~~~~~CpGCg~~~i~~~i~~a 36 (301)
T PRK05778 12 RYDGLPTTWCPGCGNFGILNAIIQA 36 (301)
T ss_pred ccCCCCCCCCCCCCChHHHHHHHHH
Confidence 4444345799999998654433333
No 94
>PF04113 Gpi16: Gpi16 subunit, GPI transamidase component; InterPro: IPR007245 GPI (glycosyl phosphatidyl inositol) transamidase is a multiprotein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif [].; GO: 0016021 integral to membrane, 0042765 GPI-anchor transamidase complex
Probab=20.73 E-value=23 Score=37.76 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=22.9
Q ss_pred cEEEEecccceecCCCCCc-cccCccccccccc
Q 020340 31 IKVRMMLPMSIRCNTCGNY-IYKGTKFNSRKED 62 (327)
Q Consensus 31 ~~VRfm~PF~i~C~~Cg~y-I~kG~KFNArKe~ 62 (327)
.+=-|-|||||.|.+|--. ++=|.-||.--++
T Consensus 504 ptPDFSMPyNVI~lt~Tv~Al~FG~i~nlltrr 536 (564)
T PF04113_consen 504 PTPDFSMPYNVIILTCTVMALAFGSIFNLLTRR 536 (564)
T ss_pred CCCCCCccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3556899999999999643 5667666654433
No 95
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.72 E-value=85 Score=29.54 Aligned_cols=60 Identities=22% Similarity=0.434 Sum_probs=39.0
Q ss_pred cccceecCCCCCccccCccccccccc-cCCCcccceeeEEEEEEcCCCCc----eEEEeeC----CCCCcccccc
Q 020340 37 LPMSIRCNTCGNYIYKGTKFNSRKED-AIGETYLGIQIFRFYFKCTKCSA----ELTIKTD----PQNSDYIVES 102 (327)
Q Consensus 37 ~PF~i~C~~Cg~yI~kG~KFNArKe~-v~gE~Ylgi~I~rFyiKC~~C~~----eI~fkTD----PkN~dY~~es 102 (327)
+=|.|.| |.+||.||-.+=. +.-..|+.+-==.-..+|+.|.+ .+.++|- |...-|.|..
T Consensus 108 ~lfgikc------v~~~veydid~~~d~~y~~yfnvlpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~ 176 (195)
T PHA02998 108 LLFGIKC------IKKGVEYDIDKIPDVDYDDYFNVLDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD 176 (195)
T ss_pred HHHHHHH------HhcCCccchhhcccccchhheeccCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC
Confidence 3488888 5689999988732 11145666322224578999987 4566776 5666777755
No 96
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.57 E-value=1.3e+02 Score=20.81 Aligned_cols=38 Identities=26% Similarity=0.667 Sum_probs=17.5
Q ss_pred eecCCCCCccccCccccccccccCCCcccceeeEEEEEEcCCCCceE
Q 020340 41 IRCNTCGNYIYKGTKFNSRKEDAIGETYLGIQIFRFYFKCTKCSAEL 87 (327)
Q Consensus 41 i~C~~Cg~yI~kG~KFNArKe~v~gE~Ylgi~I~rFyiKC~~C~~eI 87 (327)
+.|..||. +..-|...-.+..+| +.=.|| .|..|+..+
T Consensus 1 ~~Cp~Cg~---~~a~~~~~Q~rsaDE-----~~T~fy-~C~~C~~~w 38 (39)
T PF01096_consen 1 IKCPKCGH---NEAVFFQIQTRSADE-----PMTLFY-VCCNCGHRW 38 (39)
T ss_dssp S--SSS-S---SEEEEEEESSSSSSS-----SSEEEE-EESSSTEEE
T ss_pred CCCcCCCC---CeEEEEEeeccCCCC-----CCeEEE-EeCCCCCee
Confidence 46888886 333444332222243 222344 598998754
No 97
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.49 E-value=54 Score=21.87 Aligned_cols=14 Identities=50% Similarity=1.279 Sum_probs=10.3
Q ss_pred eecCCCCCccccCcc
Q 020340 41 IRCNTCGNYIYKGTK 55 (327)
Q Consensus 41 i~C~~Cg~yI~kG~K 55 (327)
-+|..|| |||.|.+
T Consensus 2 ~~C~~CG-y~y~~~~ 15 (33)
T cd00350 2 YVCPVCG-YIYDGEE 15 (33)
T ss_pred EECCCCC-CEECCCc
Confidence 3699999 7776654
No 98
>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=20.44 E-value=52 Score=23.40 Aligned_cols=21 Identities=19% Similarity=0.551 Sum_probs=12.0
Q ss_pred cceecCCCCCccccCcccccc
Q 020340 39 MSIRCNTCGNYIYKGTKFNSR 59 (327)
Q Consensus 39 F~i~C~~Cg~yI~kG~KFNAr 59 (327)
+.+.|++|+...-.|.||.-.
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~ 23 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCL 23 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEES
T ss_pred CCeECcCCCCCcCcCCeEECC
Confidence 457899998754456665544
No 99
>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=20.35 E-value=2.1e+02 Score=22.28 Aligned_cols=42 Identities=10% Similarity=0.025 Sum_probs=35.2
Q ss_pred cccc-eeeEEEEEEcCCCCceEEEeeCCCCCccccccCceecCC
Q 020340 67 TYLG-IQIFRFYFKCTKCSAELTIKTDPQNSDYIVESGASRNYE 109 (327)
Q Consensus 67 ~Ylg-i~I~rFyiKC~~C~~eI~fkTDPkN~dY~~esGA~Rn~e 109 (327)
.+|+ -.||.+++.+.....-|.|-.+..+ .+++.+|...+-+
T Consensus 34 k~l~~~~i~ElR~~~~~~~~Ri~y~~~~~~-~ivll~~f~Kkt~ 76 (91)
T PF05973_consen 34 KHLKGDGIYELRVRGGSNIYRILYFFDGGD-IIVLLHGFIKKTQ 76 (91)
T ss_pred cccCcCCeEEEEEeecCCcceEEEEEcCcc-EEEEEEEEEeCCC
Confidence 4666 8999999999998999999999888 6777888877654
Done!