Query 020522
Match_columns 325
No_of_seqs 197 out of 1274
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 03:04:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020522.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020522hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 3.1E-45 6.7E-50 365.6 21.6 252 1-254 304-623 (846)
2 PF00872 Transposase_mut: Tran 99.8 7.7E-23 1.7E-27 192.3 -0.1 159 1-162 185-350 (381)
3 PF10551 MULE: MULE transposas 99.8 5.1E-21 1.1E-25 144.5 8.6 78 3-83 16-93 (93)
4 COG3328 Transposase and inacti 99.6 1.7E-15 3.6E-20 140.4 8.7 157 1-161 165-328 (379)
5 smart00575 ZnF_PMZ plant mutat 99.1 2.4E-11 5.2E-16 69.7 2.1 27 212-238 1-27 (28)
6 PF04434 SWIM: SWIM zinc finge 98.5 7.8E-08 1.7E-12 60.3 3.0 30 207-236 10-39 (40)
7 PF06782 UPF0236: Uncharacteri 96.1 0.029 6.2E-07 54.7 8.6 94 22-116 234-328 (470)
8 PF13610 DDE_Tnp_IS240: DDE do 95.8 0.002 4.4E-08 52.1 -0.4 60 5-69 22-81 (140)
9 PF01610 DDE_Tnp_ISL3: Transpo 94.9 0.022 4.8E-07 50.4 3.3 66 18-86 30-96 (249)
10 PF15288 zf-CCHC_6: Zinc knuck 92.4 0.062 1.3E-06 33.0 0.9 25 299-323 2-26 (40)
11 COG3316 Transposase and inacti 87.0 1.6 3.5E-05 37.6 5.6 62 6-73 92-153 (215)
12 PF02178 AT_hook: AT hook moti 86.0 0.31 6.8E-06 22.4 0.4 10 285-294 2-11 (13)
13 COG4888 Uncharacterized Zn rib 85.9 0.74 1.6E-05 34.3 2.6 25 298-322 22-55 (104)
14 PRK14892 putative transcriptio 83.5 1.1 2.4E-05 33.7 2.7 25 297-322 20-51 (99)
15 PF00098 zf-CCHC: Zinc knuckle 82.1 0.61 1.3E-05 23.5 0.6 13 300-312 2-14 (18)
16 COG5431 Uncharacterized metal- 80.8 1.3 2.8E-05 33.3 2.1 52 195-248 35-91 (117)
17 smart00384 AT_hook DNA binding 79.8 1.1 2.4E-05 24.6 1.1 14 284-297 1-14 (26)
18 PF05129 Elf1: Transcription e 78.4 1.7 3.7E-05 31.5 2.1 28 295-322 19-55 (81)
19 COG4279 Uncharacterized conser 78.0 1.3 2.8E-05 38.8 1.6 23 212-237 125-147 (266)
20 PF09297 zf-NADH-PPase: NADH p 75.8 1.6 3.6E-05 25.3 1.2 26 299-324 4-32 (32)
21 TIGR02642 phage_xxxx uncharact 75.5 1.6 3.4E-05 37.0 1.4 27 298-324 99-126 (186)
22 PF03050 DDE_Tnp_IS66: Transpo 74.3 1.5 3.2E-05 39.4 1.1 35 48-87 121-155 (271)
23 PF10122 Mu-like_Com: Mu-like 73.3 2.4 5.1E-05 27.6 1.5 23 299-321 5-32 (51)
24 PHA00626 hypothetical protein 72.8 2.7 5.8E-05 27.8 1.7 22 300-321 2-31 (59)
25 PRK14890 putative Zn-ribbon RN 71.3 1.5 3.3E-05 29.4 0.3 22 299-323 37-58 (59)
26 COG2888 Predicted Zn-ribbon RN 65.0 2.3 5.1E-05 28.5 0.2 21 300-323 40-60 (61)
27 COG2126 RPL37A Ribosomal prote 64.5 3.7 8.1E-05 27.4 1.1 27 296-322 14-40 (61)
28 COG4715 Uncharacterized conser 62.7 25 0.00053 34.8 6.7 38 201-240 56-99 (587)
29 PF13877 RPAP3_C: Potential Mo 62.7 15 0.00032 27.1 4.3 36 102-137 5-40 (94)
30 PRK09335 30S ribosomal protein 59.8 6.6 0.00014 29.1 1.8 26 281-306 2-28 (95)
31 PF04438 zf-HIT: HIT zinc fing 58.0 6 0.00013 22.7 1.1 18 300-321 4-21 (30)
32 PF06827 zf-FPG_IleRS: Zinc fi 56.4 13 0.00027 21.1 2.3 21 300-320 3-28 (30)
33 PRK00432 30S ribosomal protein 55.7 5.4 0.00012 25.9 0.7 26 299-325 21-49 (50)
34 PRK00398 rpoP DNA-directed RNA 55.6 6.8 0.00015 24.8 1.2 25 298-322 3-30 (46)
35 PF12760 Zn_Tnp_IS1595: Transp 54.9 15 0.00032 23.2 2.7 29 293-321 13-45 (46)
36 COG5179 TAF1 Transcription ini 54.5 5.5 0.00012 39.5 0.8 27 294-320 933-959 (968)
37 PF13248 zf-ribbon_3: zinc-rib 54.3 5.8 0.00012 21.8 0.6 23 299-322 3-25 (26)
38 PF13696 zf-CCHC_2: Zinc knuck 54.1 5.8 0.00012 23.2 0.6 17 296-312 6-22 (32)
39 PLN00186 ribosomal protein S26 54.0 9.6 0.00021 28.9 1.9 26 281-306 2-28 (109)
40 KOG3214 Uncharacterized Zn rib 53.9 8.9 0.00019 28.6 1.6 25 298-322 23-56 (109)
41 PHA02517 putative transposase 53.4 54 0.0012 29.2 7.1 42 14-57 139-180 (277)
42 PF04937 DUF659: Protein of un 53.4 81 0.0017 25.7 7.4 61 25-87 74-137 (153)
43 PRK05978 hypothetical protein; 53.0 6.1 0.00013 32.1 0.8 24 298-322 33-61 (148)
44 PTZ00172 40S ribosomal protein 52.3 10 0.00022 28.8 1.8 26 281-306 2-28 (108)
45 PF07754 DUF1610: Domain of un 51.4 11 0.00023 20.5 1.3 10 311-320 14-23 (24)
46 COG1996 RPC10 DNA-directed RNA 51.0 6.5 0.00014 25.4 0.5 23 299-321 7-32 (49)
47 PF07282 OrfB_Zn_ribbon: Putat 49.7 13 0.00027 25.6 1.9 25 298-322 28-55 (69)
48 PF10058 DUF2296: Predicted in 49.0 11 0.00023 25.0 1.3 22 298-321 22-52 (54)
49 PF03811 Zn_Tnp_IS1: InsA N-te 47.9 16 0.00035 21.9 1.9 23 298-320 5-36 (36)
50 PRK04351 hypothetical protein; 47.4 9.4 0.0002 31.1 1.0 24 298-321 112-140 (149)
51 PF08792 A2L_zn_ribbon: A2L zi 47.0 15 0.00032 21.6 1.5 26 298-323 3-31 (33)
52 PRK12286 rpmF 50S ribosomal pr 46.8 17 0.00037 24.3 2.0 38 281-320 4-47 (57)
53 PF00665 rve: Integrase core d 46.7 58 0.0013 24.4 5.5 55 3-60 27-81 (120)
54 TIGR02098 MJ0042_CXXC MJ0042 f 44.6 14 0.0003 22.1 1.2 24 299-322 3-34 (38)
55 PF07649 C1_3: C1-like domain; 44.1 14 0.00031 20.9 1.2 21 300-320 2-22 (30)
56 PRK04179 rpl37e 50S ribosomal 43.7 12 0.00026 25.4 0.9 25 297-321 16-40 (62)
57 PF10571 UPF0547: Uncharacteri 43.1 11 0.00024 20.9 0.6 22 300-322 2-23 (26)
58 PF00684 DnaJ_CXXCXGXG: DnaJ c 42.9 12 0.00027 25.7 0.9 24 298-321 41-64 (66)
59 TIGR02159 PA_CoA_Oxy4 phenylac 42.0 17 0.00037 29.4 1.8 25 298-322 105-139 (146)
60 PF13453 zf-TFIIB: Transcripti 41.8 25 0.00054 21.5 2.1 21 300-320 1-26 (41)
61 PF12172 DUF35_N: Rubredoxin-l 40.7 13 0.00029 22.1 0.8 25 299-324 12-36 (37)
62 PRK12380 hydrogenase nickel in 39.6 13 0.00029 28.6 0.8 31 293-323 65-96 (113)
63 COG4830 RPS26B Ribosomal prote 37.5 19 0.00042 26.7 1.3 26 281-306 2-28 (108)
64 PHA02942 putative transposase; 37.4 20 0.00044 34.0 1.7 25 298-322 325-351 (383)
65 COG1096 Predicted RNA-binding 37.0 21 0.00045 30.1 1.5 25 299-323 150-175 (188)
66 PF12017 Tnp_P_element: Transp 35.0 72 0.0016 28.1 4.7 50 11-64 180-229 (236)
67 TIGR00100 hypA hydrogenase nic 34.4 18 0.00038 28.0 0.7 27 296-322 68-95 (115)
68 COG1998 RPS31 Ribosomal protei 34.0 23 0.0005 22.9 1.0 25 299-324 20-48 (51)
69 PRK09409 IS2 transposase TnpB; 33.3 3.4E+02 0.0073 24.7 9.0 53 4-57 147-202 (301)
70 COG1107 Archaea-specific RecJ- 33.1 28 0.00061 34.6 1.9 26 299-324 54-79 (715)
71 PF13717 zinc_ribbon_4: zinc-r 33.0 31 0.00066 20.6 1.4 8 313-320 25-32 (36)
72 PRK14702 insertion element IS2 33.0 3.5E+02 0.0076 24.0 9.4 53 4-57 108-163 (262)
73 PF13719 zinc_ribbon_5: zinc-r 32.1 32 0.0007 20.6 1.5 9 312-320 24-32 (37)
74 PRK04023 DNA polymerase II lar 32.0 28 0.00061 36.9 1.9 12 25-36 264-275 (1121)
75 COG0675 Transposase and inacti 31.9 28 0.00061 31.8 1.8 23 298-322 309-331 (364)
76 PF01907 Ribosomal_L37e: Ribos 31.9 15 0.00032 24.4 -0.1 26 297-322 14-39 (55)
77 PF01283 Ribosomal_S26e: Ribos 31.5 24 0.00053 27.1 1.0 26 281-306 2-28 (113)
78 PF13824 zf-Mss51: Zinc-finger 30.9 25 0.00054 23.4 0.8 24 301-324 2-25 (55)
79 PF08271 TF_Zn_Ribbon: TFIIB z 30.6 45 0.00097 20.6 2.0 22 300-321 2-27 (43)
80 PLN00209 ribosomal protein S27 30.3 21 0.00046 25.9 0.5 24 298-321 36-63 (86)
81 PF06397 Desulfoferrod_N: Desu 30.3 27 0.00059 21.0 0.9 10 312-321 5-14 (36)
82 smart00659 RPOLCX RNA polymera 29.9 30 0.00066 21.8 1.1 23 299-321 3-27 (44)
83 PF13240 zinc_ribbon_2: zinc-r 29.8 24 0.00052 18.8 0.5 20 301-321 2-21 (23)
84 PRK03681 hypA hydrogenase nick 29.7 25 0.00054 27.2 0.8 28 295-322 67-96 (114)
85 PTZ00073 60S ribosomal protein 29.5 29 0.00063 25.5 1.1 26 296-321 14-39 (91)
86 PRK00564 hypA hydrogenase nick 29.0 23 0.00049 27.5 0.5 28 295-322 68-97 (117)
87 TIGR01031 rpmF_bact ribosomal 28.0 60 0.0013 21.5 2.3 21 298-320 26-46 (55)
88 COG0484 DnaJ DnaJ-class molecu 27.8 30 0.00065 32.6 1.1 39 285-324 166-208 (371)
89 COG4049 Uncharacterized protei 27.6 26 0.00056 23.2 0.5 10 312-321 16-25 (65)
90 PTZ00083 40S ribosomal protein 27.4 21 0.00045 25.9 0.1 24 298-321 35-62 (85)
91 PF05418 Apo-VLDL-II: Apovitel 27.3 2.3E+02 0.0049 20.0 5.1 48 110-174 22-71 (82)
92 PRK13130 H/ACA RNA-protein com 27.2 31 0.00067 23.0 0.8 22 298-322 5-26 (56)
93 COG3464 Transposase and inacti 26.6 1.2E+02 0.0025 29.1 5.0 70 2-80 169-238 (402)
94 cd02339 ZZ_Mind_bomb Zinc fing 26.0 53 0.0011 20.8 1.7 22 300-321 2-23 (45)
95 cd02345 ZZ_dah Zinc finger, ZZ 25.1 74 0.0016 20.4 2.3 22 300-321 2-23 (49)
96 smart00661 RPOL9 RNA polymeras 24.9 46 0.001 21.2 1.4 10 313-322 20-29 (52)
97 TIGR00757 RNaseEG ribonuclease 24.6 42 0.00092 32.2 1.6 47 170-217 254-301 (414)
98 PRK14714 DNA polymerase II lar 24.1 42 0.00091 36.6 1.5 13 25-37 266-278 (1337)
99 KOG2703 C4-type Zn-finger prot 24.0 61 0.0013 30.7 2.4 43 12-57 370-412 (460)
100 smart00343 ZnF_C2HC zinc finge 24.0 31 0.00068 18.6 0.3 13 300-312 1-13 (26)
101 KOG2879 Predicted E3 ubiquitin 23.6 51 0.0011 29.5 1.8 14 298-311 239-252 (298)
102 PRK03824 hypA hydrogenase nick 23.5 50 0.0011 26.3 1.5 12 298-309 70-81 (135)
103 COG1997 RPL43A Ribosomal prote 23.4 61 0.0013 23.7 1.8 25 298-322 35-62 (89)
104 PF01096 TFIIS_C: Transcriptio 23.4 99 0.0022 18.7 2.5 12 300-311 2-13 (39)
105 PF14787 zf-CCHC_5: GAG-polypr 22.7 28 0.00061 20.9 -0.0 13 300-312 4-16 (36)
106 PRK02935 hypothetical protein; 22.0 49 0.0011 25.1 1.1 25 298-322 70-95 (110)
107 PF13390 DUF4108: Protein of u 22.0 51 0.0011 25.5 1.2 24 7-30 35-58 (136)
108 PTZ00473 Plasmodium Vir superf 21.4 2E+02 0.0044 27.3 5.2 47 245-291 199-252 (420)
109 TIGR00334 5S_RNA_mat_M5 ribonu 21.1 1.5E+02 0.0032 24.8 3.9 45 32-79 37-84 (174)
110 TIGR02605 CxxC_CxxC_SSSS putat 20.4 70 0.0015 20.5 1.5 6 316-321 29-34 (52)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.1e-45 Score=365.62 Aligned_cols=252 Identities=12% Similarity=0.157 Sum_probs=217.3
Q ss_pred CeEEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHH
Q 020522 1 MLTAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYE 80 (325)
Q Consensus 1 ll~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~ 80 (325)
|..++|+|+|++++++|+||+.+|+.|+|.|+|++|+++|++. .|.+||||++.+|.+||++|||++.||+|+|||++
T Consensus 304 fa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk--~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~ 381 (846)
T PLN03097 304 LALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQ--APKVIITDQDKAMKSVISEVFPNAHHCFFLWHILG 381 (846)
T ss_pred EEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCC--CCceEEecCCHHHHHHHHHHCCCceehhhHHHHHH
Confidence 4679999999999999999999999999999999999999987 69999999999999999999999999999999999
Q ss_pred HHHhhCC-----CchhHHHHHhhhc-ccChHHHHHHHHHH-HhhhhHhhHHHHhc--ccchhhhcccCCCccccccccch
Q 020522 81 RMKAKFP-----SNILWQLFWGACR-STNATEFYRHLDEI-KVLDERCYEWLMES--KWERWALHCMPAWAKCTHVTNKM 151 (325)
Q Consensus 81 n~~~~~~-----~~~~~~~~~~~~~-a~t~~eF~~~~~~l-~~~~~~~~~~L~~~--~~~~W~~~~~~~~~~~~~~t~N~ 151 (325)
|+.+++. .+.+.+.|.++.+ +.+++||+..|..| .+++.+..+||..+ .+++|+++|+++.+..|+.||++
T Consensus 382 ~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqR 461 (846)
T PLN03097 382 KVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQR 461 (846)
T ss_pred HHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccc
Confidence 9999875 3578889998776 67999999999986 57899999999997 89999999999999999999999
Q ss_pred hHHHHHHHHHhh--hhhhHHHHHHH----------------------------------------------HHHHHHhcc
Q 020522 152 GKKFFFWMHEYF--AQSITRRMEAI----------------------------------------------VNNAIEAAR 183 (325)
Q Consensus 152 ~Es~N~~i~~~r--~~pi~~~~e~i----------------------------------------------l~~~~~~a~ 183 (325)
+||+|++|++.. ..+|..+++.+ +|+++..+.
T Consensus 462 SES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~ 541 (846)
T PLN03097 462 SESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAV 541 (846)
T ss_pred cccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhh
Confidence 999999998743 34455544443 677788777
Q ss_pred ccEEEEeC----CceEEEEEec-ceEEEEEcc----CccccccccccCCCCchhHHHHHHhcC--CccccccCccchHHH
Q 020522 184 EMNVEATE----GQVMHVLENG-ISRVSVDIK----KQCCDCGSWQLSGIPCAHASKCILNVG--REVDDFVDPLLTKDR 252 (325)
Q Consensus 184 ~~~v~~~~----~~~~~V~~~~-~~~~~V~l~----~~~CsC~~~~~~giPC~Halav~~~~~--~~~~~~v~~~yt~~~ 252 (325)
.|.+...+ ...|.|.+.. ...|.|..+ ..+|+|++|+..||||+|||.|+.+.+ ..|+.||.++||.++
T Consensus 542 ~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdA 621 (846)
T PLN03097 542 ACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDA 621 (846)
T ss_pred heEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhh
Confidence 77766542 2367787533 356878554 579999999999999999999999988 479999999999887
Q ss_pred HH
Q 020522 253 YL 254 (325)
Q Consensus 253 ~~ 254 (325)
-.
T Consensus 622 K~ 623 (846)
T PLN03097 622 KS 623 (846)
T ss_pred hh
Confidence 54
No 2
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.85 E-value=7.7e-23 Score=192.30 Aligned_cols=159 Identities=18% Similarity=0.217 Sum_probs=142.0
Q ss_pred CeEEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHH
Q 020522 1 MLTAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYE 80 (325)
Q Consensus 1 ll~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~ 80 (325)
+++|+|+|.+|+..+||+.+.+.|+.++|.-||+.|+++ |.. .+..||+|+++||.+||.++||++.++.|.+|+++
T Consensus 185 ~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~--~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~R 261 (381)
T PF00872_consen 185 VYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLK--DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMR 261 (381)
T ss_pred hhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-ccc--ccceeeccccccccccccccccchhhhhheechhh
Confidence 578999999999999999999999999999999999999 877 49999999999999999999999999999999999
Q ss_pred HHHhhCCC---chhHHHHHhhhcccChHHHHHHHHHH----HhhhhHhhHHHHhcccchhhhcccCCCccccccccchhH
Q 020522 81 RMKAKFPS---NILWQLFWGACRSTNATEFYRHLDEI----KVLDERCYEWLMESKWERWALHCMPAWAKCTHVTNKMGK 153 (325)
Q Consensus 81 n~~~~~~~---~~~~~~~~~~~~a~t~~eF~~~~~~l----~~~~~~~~~~L~~~~~~~W~~~~~~~~~~~~~~t~N~~E 153 (325)
|+.++++. +.+.+.+..+..+.+.++....++++ ....|++.++|++...+.|+..-|+...+--+.|||.+|
T Consensus 262 Nv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iE 341 (381)
T PF00872_consen 262 NVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIE 341 (381)
T ss_pred hhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhcc
Confidence 99998864 36777888888888887777777775 456899999999988888998888887666778999999
Q ss_pred HHHHHHHHh
Q 020522 154 KFFFWMHEY 162 (325)
Q Consensus 154 s~N~~i~~~ 162 (325)
|+|+.|++.
T Consensus 342 sln~~irrr 350 (381)
T PF00872_consen 342 SLNKEIRRR 350 (381)
T ss_pred ccccchhhh
Confidence 999999873
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.84 E-value=5.1e-21 Score=144.50 Aligned_cols=78 Identities=31% Similarity=0.400 Sum_probs=74.6
Q ss_pred EEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHHHH
Q 020522 3 TAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYERM 82 (325)
Q Consensus 3 ~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~n~ 82 (325)
+++|+|++|+.+|+||+++++|+.++|.|||+.+++.++. . |.+||||++.|+.+|++++||++.|++|.||+.+|+
T Consensus 16 ~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~--~-p~~ii~D~~~~~~~Ai~~vfP~~~~~~C~~H~~~n~ 92 (93)
T PF10551_consen 16 IAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ--K-PKVIISDFDKALINAIKEVFPDARHQLCLFHILRNI 92 (93)
T ss_pred eEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc--C-ceeeeccccHHHHHHHHHHCCCceEehhHHHHHHhh
Confidence 5999999999999999999999999999999999999876 2 999999999999999999999999999999999998
Q ss_pred H
Q 020522 83 K 83 (325)
Q Consensus 83 ~ 83 (325)
+
T Consensus 93 k 93 (93)
T PF10551_consen 93 K 93 (93)
T ss_pred C
Confidence 5
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.61 E-value=1.7e-15 Score=140.43 Aligned_cols=157 Identities=15% Similarity=0.193 Sum_probs=130.8
Q ss_pred CeEEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHH
Q 020522 1 MLTAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYE 80 (325)
Q Consensus 1 ll~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~ 80 (325)
+++|+|+|.+|+..+|++.+.+.|+ ..|.-||..|+.+ |.. ....+++|+++|+.+||.++||.+.++.|..|+.+
T Consensus 165 ~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~--~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~R 240 (379)
T COG3328 165 VYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLS--DVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVR 240 (379)
T ss_pred eeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-ccc--ceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHh
Confidence 5789999999999999999999999 9999999999998 666 47888889999999999999999999999999999
Q ss_pred HHHhhCCCc---hhHHHHHhhhcccChHH----HHHHHHHHHhhhhHhhHHHHhcccchhhhcccCCCccccccccchhH
Q 020522 81 RMKAKFPSN---ILWQLFWGACRSTNATE----FYRHLDEIKVLDERCYEWLMESKWERWALHCMPAWAKCTHVTNKMGK 153 (325)
Q Consensus 81 n~~~~~~~~---~~~~~~~~~~~a~t~~e----F~~~~~~l~~~~~~~~~~L~~~~~~~W~~~~~~~~~~~~~~t~N~~E 153 (325)
|+..+...+ .....+..+..+.+.++ |+...+.+....|....|+.+...+.|....|+...+--+.|||.+|
T Consensus 241 nll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE 320 (379)
T COG3328 241 NLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIE 320 (379)
T ss_pred hhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHH
Confidence 999887654 34444555555555554 44444445567788999999988888888888877566788999999
Q ss_pred HHHHHHHH
Q 020522 154 KFFFWMHE 161 (325)
Q Consensus 154 s~N~~i~~ 161 (325)
++|+.++.
T Consensus 321 ~~n~~ir~ 328 (379)
T COG3328 321 SLNKLIRR 328 (379)
T ss_pred HHHHHHHH
Confidence 99997775
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=99.13 E-value=2.4e-11 Score=69.69 Aligned_cols=27 Identities=44% Similarity=1.015 Sum_probs=24.9
Q ss_pred ccccccccccCCCCchhHHHHHHhcCC
Q 020522 212 QCCDCGSWQLSGIPCAHASKCILNVGR 238 (325)
Q Consensus 212 ~~CsC~~~~~~giPC~Halav~~~~~~ 238 (325)
.+|||++||..||||+|+|+|+...+.
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998764
No 6
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.52 E-value=7.8e-08 Score=60.27 Aligned_cols=30 Identities=33% Similarity=0.794 Sum_probs=27.2
Q ss_pred EEccCccccccccccCCCCchhHHHHHHhc
Q 020522 207 VDIKKQCCDCGSWQLSGIPCAHASKCILNV 236 (325)
Q Consensus 207 V~l~~~~CsC~~~~~~giPC~Halav~~~~ 236 (325)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667789999999999999999999998764
No 7
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=96.05 E-value=0.029 Score=54.67 Aligned_cols=94 Identities=15% Similarity=0.188 Sum_probs=77.7
Q ss_pred eccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHHHHHhhCC-CchhHHHHHhhhc
Q 020522 22 EEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYERMKAKFP-SNILWQLFWGACR 100 (325)
Q Consensus 22 ~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~n~~~~~~-~~~~~~~~~~~~~ 100 (325)
...+.+.|.-+.+.+.+.....+...+.+.+|+...|..++. .+|++.|.+..+|+.+.+.+.++ .+.+.+.++++.+
T Consensus 234 ~~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~ 312 (470)
T PF06782_consen 234 GESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALK 312 (470)
T ss_pred ccchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHH
Confidence 356678899999988888765543367889999999998887 99999999999999999998885 4567777888888
Q ss_pred ccChHHHHHHHHHHHh
Q 020522 101 STNATEFYRHLDEIKV 116 (325)
Q Consensus 101 a~t~~eF~~~~~~l~~ 116 (325)
.....+++..++.+..
T Consensus 313 ~~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 313 KGDKKKLETVLDTAES 328 (470)
T ss_pred hcCHHHHHHHHHHHHH
Confidence 8888888888888764
No 8
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=95.80 E-value=0.002 Score=52.05 Aligned_cols=60 Identities=18% Similarity=0.153 Sum_probs=53.2
Q ss_pred EEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhcccc
Q 020522 5 VGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRA 69 (325)
Q Consensus 5 ~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a 69 (325)
.++|.+++ +|++-|-+.-+...=..||+.+.+..+. .|..|+||+..+...|++++.+..
T Consensus 22 ~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~---~p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 22 RAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRG---EPRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred Eeeccccc--chhhhhhhhcccccceeeccccceeecc---ccceeecccCCccchhhhhccccc
Confidence 57899999 8999999999999999999999888653 599999999999999999998763
No 9
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.94 E-value=0.022 Score=50.44 Aligned_cols=66 Identities=15% Similarity=0.049 Sum_probs=56.0
Q ss_pred EEEeeccccchHHHHHHHH-hhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHHHHHhhC
Q 020522 18 VYEVEEESNSTWYNFLLKL-GEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYERMKAKF 86 (325)
Q Consensus 18 ~aiv~~E~~~~w~wfl~~l-~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~n~~~~~ 86 (325)
++++++-+.++..-||+.+ -.... . ...+|++|...+...|+++.||+|.+..-.+|+++++.+.+
T Consensus 30 l~i~~~r~~~~l~~~~~~~~~~~~~-~--~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 30 LDILPGRDKETLKDFFRSLYPEEER-K--NVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred EEEcCCccHHHHHHHHHHhCccccc-c--ceEEEEcCCCccccccccccccccccccccchhhhhhhhcc
Confidence 4688999999999999877 43312 1 58899999999999999999999999999999999987644
No 10
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=92.37 E-value=0.062 Score=33.04 Aligned_cols=25 Identities=8% Similarity=-0.035 Sum_probs=21.5
Q ss_pred ccCCCccccceeeeEEeecCCCCCC
Q 020522 299 LCCSKVKQVSVVMSLYLIQPCGLSE 323 (325)
Q Consensus 299 ~~c~~c~~~gh~~~~~~~~~~~~~~ 323 (325)
.+|++|+++||..+.-.|++-+..+
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~~ 26 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWSG 26 (40)
T ss_pred ccccccccccccccCccCCCCCCCC
Confidence 5899999999999999999866543
No 11
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.99 E-value=1.6 Score=37.60 Aligned_cols=62 Identities=26% Similarity=0.236 Sum_probs=51.2
Q ss_pred EEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhcccccccc
Q 020522 6 GIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRI 73 (325)
Q Consensus 6 g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~ 73 (325)
++|.+|+ +|-+-|...-|...=.-||..+.+.-| .|.+|+||+.+....|+.++-+...|+.
T Consensus 92 Aid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~g----~p~v~vtDka~s~~~A~~~l~~~~ehr~ 153 (215)
T COG3316 92 AIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKHG----EPRVFVTDKAPSYTAALRKLGSEVEHRT 153 (215)
T ss_pred hhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhcC----CCceEEecCccchHHHHHhcCcchheec
Confidence 4566654 889999999999888999998877753 4999999999999999999988655543
No 12
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=86.01 E-value=0.31 Score=22.40 Aligned_cols=10 Identities=10% Similarity=-0.034 Sum_probs=3.5
Q ss_pred CCCCCCcccc
Q 020522 285 NTPDLTIHKA 294 (325)
Q Consensus 285 r~~GRPk~~R 294 (325)
|++|||+|.-
T Consensus 2 r~RGRP~k~~ 11 (13)
T PF02178_consen 2 RKRGRPRKNA 11 (13)
T ss_dssp --SS--TT--
T ss_pred CcCCCCcccc
Confidence 6789998753
No 13
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=85.87 E-value=0.74 Score=34.31 Aligned_cols=25 Identities=24% Similarity=0.523 Sum_probs=19.7
Q ss_pred CccCCCcccccee---------eeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVV---------MSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~---------~~~~~~~~~~~~ 322 (325)
...|++|+....+ ...--|.-||++
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcce
Confidence 5899999877666 366779999985
No 14
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.50 E-value=1.1 Score=33.69 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=17.5
Q ss_pred CCccCCCccccceee-------eEEeecCCCCC
Q 020522 297 SELCCSKVKQVSVVM-------SLYLIQPCGLS 322 (325)
Q Consensus 297 ~~~~c~~c~~~gh~~-------~~~~~~~~~~~ 322 (325)
....|+.|+.. .+. ....|+-||..
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCc
Confidence 35899999942 221 47889999963
No 15
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=82.11 E-value=0.61 Score=23.46 Aligned_cols=13 Identities=8% Similarity=0.158 Sum_probs=11.4
Q ss_pred cCCCccccceeee
Q 020522 300 CCSKVKQVSVVMS 312 (325)
Q Consensus 300 ~c~~c~~~gh~~~ 312 (325)
+|-+|++.||+.+
T Consensus 2 ~C~~C~~~GH~~~ 14 (18)
T PF00098_consen 2 KCFNCGEPGHIAR 14 (18)
T ss_dssp BCTTTSCSSSCGC
T ss_pred cCcCCCCcCcccc
Confidence 6999999999864
No 16
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=80.84 E-value=1.3 Score=33.31 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=31.8
Q ss_pred EEEEEecceEEEEEccCcccccccccc-----CCCCchhHHHHHHhcCCccccccCccc
Q 020522 195 MHVLENGISRVSVDIKKQCCDCGSWQL-----SGIPCAHASKCILNVGREVDDFVDPLL 248 (325)
Q Consensus 195 ~~V~~~~~~~~~V~l~~~~CsC~~~~~-----~giPC~Halav~~~~~~~~~~~v~~~y 248 (325)
|.|.-...+.|+++.+ -|||..|-. -.-||.|+++.-...-..-.++|+-+|
T Consensus 35 ~fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~ 91 (117)
T COG5431 35 FFVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYY 91 (117)
T ss_pred EEEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEec
Confidence 4454423457888776 899998762 235799999865443333345555444
No 17
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=79.80 E-value=1.1 Score=24.64 Aligned_cols=14 Identities=7% Similarity=0.031 Sum_probs=10.8
Q ss_pred CCCCCCCcccccCC
Q 020522 284 ANTPDLTIHKAKNS 297 (325)
Q Consensus 284 ~r~~GRPk~~R~~~ 297 (325)
.|++|||+|.....
T Consensus 1 kRkRGRPrK~~~~~ 14 (26)
T smart00384 1 KRKRGRPRKAPKDX 14 (26)
T ss_pred CCCCCCCCCCCCcc
Confidence 47899999887554
No 18
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=78.43 E-value=1.7 Score=31.45 Aligned_cols=28 Identities=21% Similarity=0.320 Sum_probs=12.6
Q ss_pred cCCCccCCCcc-ccceee--------eEEeecCCCCC
Q 020522 295 KNSELCCSKVK-QVSVVM--------SLYLIQPCGLS 322 (325)
Q Consensus 295 ~~~~~~c~~c~-~~gh~~--------~~~~~~~~~~~ 322 (325)
++....|+.|+ ..++.. +...|.-||++
T Consensus 19 l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGES 55 (81)
T ss_dssp -SS----TTT--SS-EEEEEETTTTEEEEEESSS--E
T ss_pred CCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCe
Confidence 34478999999 444433 56779999864
No 19
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=77.97 E-value=1.3 Score=38.78 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=19.4
Q ss_pred ccccccccccCCCCchhHHHHHHhcC
Q 020522 212 QCCDCGSWQLSGIPCAHASKCILNVG 237 (325)
Q Consensus 212 ~~CsC~~~~~~giPC~Halav~~~~~ 237 (325)
..|||..|.. ||.|+.||....+
T Consensus 125 ~dCSCPD~an---PCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYAN---PCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCccc---chHHHHHHHHHHH
Confidence 5799998865 9999999998754
No 20
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=75.78 E-value=1.6 Score=25.35 Aligned_cols=26 Identities=15% Similarity=0.271 Sum_probs=14.8
Q ss_pred ccCCCccccceee---eEEeecCCCCCCC
Q 020522 299 LCCSKVKQVSVVM---SLYLIQPCGLSEY 324 (325)
Q Consensus 299 ~~c~~c~~~gh~~---~~~~~~~~~~~~~ 324 (325)
.-|++|+..-+.. ..-+|+.||.+.|
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~~y 32 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHEHY 32 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-EE-
T ss_pred cccCcCCccccCCCCcCEeECCCCcCEeC
Confidence 4589998876655 5678999998876
No 21
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=75.49 E-value=1.6 Score=36.95 Aligned_cols=27 Identities=7% Similarity=0.206 Sum_probs=22.6
Q ss_pred CccCCCccccceeee-EEeecCCCCCCC
Q 020522 298 ELCCSKVKQVSVVMS-LYLIQPCGLSEY 324 (325)
Q Consensus 298 ~~~c~~c~~~gh~~~-~~~~~~~~~~~~ 324 (325)
...|++|++.|.+.. ...|+.|+-.++
T Consensus 99 ~~~C~~C~G~G~~i~~~~~C~~C~G~G~ 126 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQRECDTCAGTGR 126 (186)
T ss_pred CCcCCCCCCeeEEecCCCCCCCCCCccE
Confidence 677999999998886 468999998776
No 22
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=74.30 E-value=1.5 Score=39.35 Aligned_cols=35 Identities=11% Similarity=0.210 Sum_probs=28.0
Q ss_pred eEEEeCCchhHHHHHHhhccccccccchHHHHHHHHhhCC
Q 020522 48 FCFISDGENGVEDALEALMCRAEIRICAQTVYERMKAKFP 87 (325)
Q Consensus 48 ~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~n~~~~~~ 87 (325)
=+++||+..+=.. +....|+.|..|+.+.+.+-..
T Consensus 121 GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 121 GILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred eeeeccccccccc-----cccccccccccccccccccccc
Confidence 3889999988544 2288999999999999987654
No 23
>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=73.30 E-value=2.4 Score=27.58 Aligned_cols=23 Identities=13% Similarity=0.310 Sum_probs=12.0
Q ss_pred ccCCCcccc----c-eeeeEEeecCCCC
Q 020522 299 LCCSKVKQV----S-VVMSLYLIQPCGL 321 (325)
Q Consensus 299 ~~c~~c~~~----g-h~~~~~~~~~~~~ 321 (325)
.+|+.|++. | ...-.++|++||-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 456666543 2 2224566666663
No 24
>PHA00626 hypothetical protein
Probab=72.79 E-value=2.7 Score=27.82 Aligned_cols=22 Identities=23% Similarity=0.511 Sum_probs=16.6
Q ss_pred cCCCccccceee--------eEEeecCCCC
Q 020522 300 CCSKVKQVSVVM--------SLYLIQPCGL 321 (325)
Q Consensus 300 ~c~~c~~~gh~~--------~~~~~~~~~~ 321 (325)
.|++|+..-++. -.|.|+.||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCC
Confidence 488888765665 5799999984
No 25
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.27 E-value=1.5 Score=29.43 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=14.9
Q ss_pred ccCCCccccceeeeEEeecCCCCCC
Q 020522 299 LCCSKVKQVSVVMSLYLIQPCGLSE 323 (325)
Q Consensus 299 ~~c~~c~~~gh~~~~~~~~~~~~~~ 323 (325)
.+|.+|++.| ..|.|+-||-.+
T Consensus 37 ~RC~~CRk~~---~~Y~CP~CGF~G 58 (59)
T PRK14890 37 YRCEKCRKQS---NPYTCPKCGFEG 58 (59)
T ss_pred eechhHHhcC---CceECCCCCCcC
Confidence 3466666666 468888888654
No 26
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.96 E-value=2.3 Score=28.49 Aligned_cols=21 Identities=24% Similarity=0.615 Sum_probs=12.1
Q ss_pred cCCCccccceeeeEEeecCCCCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCGLSE 323 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~~~~ 323 (325)
+|.+|++.|+ .|+|+-||-++
T Consensus 40 Rc~~CRk~g~---~Y~Cp~CGF~G 60 (61)
T COG2888 40 RCAKCRKLGN---PYRCPKCGFEG 60 (61)
T ss_pred hhhhHHHcCC---ceECCCcCccC
Confidence 4555555554 46777776543
No 27
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=64.47 E-value=3.7 Score=27.35 Aligned_cols=27 Identities=15% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCCccCCCccccceeeeEEeecCCCCC
Q 020522 296 NSELCCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 296 ~~~~~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
++...|-||++.+-+...-.|+-||-.
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 567789999999999999999999964
No 28
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=62.70 E-value=25 Score=34.76 Aligned_cols=38 Identities=26% Similarity=0.498 Sum_probs=26.5
Q ss_pred cceEE--EEEcc----CccccccccccCCCCchhHHHHHHhcCCcc
Q 020522 201 GISRV--SVDIK----KQCCDCGSWQLSGIPCAHASKCILNVGREV 240 (325)
Q Consensus 201 ~~~~~--~V~l~----~~~CsC~~~~~~giPC~Halav~~~~~~~~ 240 (325)
|.+.| .|.+. +.+|||.. ...| -|+|++||+.-....|
T Consensus 56 Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~p 99 (587)
T COG4715 56 GSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDDP 99 (587)
T ss_pred ccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhcc
Confidence 66666 55662 57899997 4444 5999999998654333
No 29
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=62.67 E-value=15 Score=27.10 Aligned_cols=36 Identities=25% Similarity=0.231 Sum_probs=29.8
Q ss_pred cChHHHHHHHHHHHhhhhHhhHHHHhcccchhhhcc
Q 020522 102 TNATEFYRHLDEIKVLDERCYEWLMESKWERWALHC 137 (325)
Q Consensus 102 ~t~~eF~~~~~~l~~~~~~~~~~L~~~~~~~W~~~~ 137 (325)
.|..||+..|..+.......++||..++++....-+
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~if 40 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPKIF 40 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHHHH
Confidence 467899999999987767889999999888776544
No 30
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=59.81 E-value=6.6 Score=29.09 Aligned_cols=26 Identities=8% Similarity=0.170 Sum_probs=19.5
Q ss_pred CCCCCCCCCCcccccCC-CccCCCccc
Q 020522 281 PQNANTPDLTIHKAKNS-ELCCSKVKQ 306 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~~-~~~c~~c~~ 306 (325)
|..++..||-|+-|... ..+|.+|.+
T Consensus 2 ~kKRrn~GR~K~~rGhv~~V~C~nCgr 28 (95)
T PRK09335 2 PKKRENRGRRKGDKGHVGYVQCDNCGR 28 (95)
T ss_pred CcccccCCCCCCCCCCCccEEeCCCCC
Confidence 56788889998888665 467777765
No 31
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=57.96 E-value=6 Score=22.72 Aligned_cols=18 Identities=28% Similarity=0.501 Sum_probs=12.2
Q ss_pred cCCCccccceeeeEEeecCCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
.|+-|+. .+.|+|++||.
T Consensus 4 ~C~vC~~----~~kY~Cp~C~~ 21 (30)
T PF04438_consen 4 LCSVCGN----PAKYRCPRCGA 21 (30)
T ss_dssp EETSSSS----EESEE-TTT--
T ss_pred CCccCcC----CCEEECCCcCC
Confidence 5777776 78999999985
No 32
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=56.42 E-value=13 Score=21.11 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=11.7
Q ss_pred cCCCccccceee-----eEEeecCCC
Q 020522 300 CCSKVKQVSVVM-----SLYLIQPCG 320 (325)
Q Consensus 300 ~c~~c~~~gh~~-----~~~~~~~~~ 320 (325)
+|.||...---. +.+.|++|-
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 588888765444 559999984
No 33
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=55.75 E-value=5.4 Score=25.94 Aligned_cols=26 Identities=15% Similarity=0.448 Sum_probs=18.2
Q ss_pred ccCCCccc---cceeeeEEeecCCCCCCCC
Q 020522 299 LCCSKVKQ---VSVVMSLYLIQPCGLSEYL 325 (325)
Q Consensus 299 ~~c~~c~~---~gh~~~~~~~~~~~~~~~~ 325 (325)
.-|++|+. .-|. ..+.|..||..+|.
T Consensus 21 ~fCP~Cg~~~m~~~~-~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 21 KFCPRCGSGFMAEHL-DRWHCGKCGYTEFK 49 (50)
T ss_pred CcCcCCCcchheccC-CcEECCCcCCEEec
Confidence 36999975 1222 46789999988873
No 34
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=55.56 E-value=6.8 Score=24.79 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=17.6
Q ss_pred CccCCCccccceee---eEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVVM---SLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~~---~~~~~~~~~~~ 322 (325)
+++|++|+..=... ...+|+.||..
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 35799998754333 36899999964
No 35
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=54.87 E-value=15 Score=23.24 Aligned_cols=29 Identities=10% Similarity=0.168 Sum_probs=20.4
Q ss_pred cccCCCccCCCccccceee----eEEeecCCCC
Q 020522 293 KAKNSELCCSKVKQVSVVM----SLYLIQPCGL 321 (325)
Q Consensus 293 ~R~~~~~~c~~c~~~gh~~----~~~~~~~~~~ 321 (325)
.|.++...|++|+...+.. .+|+|..|+.
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 4555667799999763332 6889998874
No 36
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=54.47 E-value=5.5 Score=39.50 Aligned_cols=27 Identities=19% Similarity=0.179 Sum_probs=22.2
Q ss_pred ccCCCccCCCccccceeeeEEeecCCC
Q 020522 294 AKNSELCCSKVKQVSVVMSLYLIQPCG 320 (325)
Q Consensus 294 R~~~~~~c~~c~~~gh~~~~~~~~~~~ 320 (325)
|++..++|+.|+|+||+..---||.=+
T Consensus 933 RK~Ttr~C~nCGQvGHmkTNK~CP~f~ 959 (968)
T COG5179 933 RKNTTRTCGNCGQVGHMKTNKACPKFS 959 (968)
T ss_pred CCCcceecccccccccccccccCcccc
Confidence 455578999999999999888887644
No 37
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.29 E-value=5.8 Score=21.84 Aligned_cols=23 Identities=13% Similarity=0.369 Sum_probs=17.3
Q ss_pred ccCCCccccceeeeEEeecCCCCC
Q 020522 299 LCCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 299 ~~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
..|++|+. .+-..---|+-||..
T Consensus 3 ~~Cp~Cg~-~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGA-EIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCC-cCCcccccChhhCCC
Confidence 57999998 566666669998864
No 38
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=54.13 E-value=5.8 Score=23.20 Aligned_cols=17 Identities=12% Similarity=0.219 Sum_probs=13.8
Q ss_pred CCCccCCCccccceeee
Q 020522 296 NSELCCSKVKQVSVVMS 312 (325)
Q Consensus 296 ~~~~~c~~c~~~gh~~~ 312 (325)
++...|-+|++.||.+.
T Consensus 6 P~~Y~C~~C~~~GH~i~ 22 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQ 22 (32)
T ss_pred CCCCEeecCCCCCccHh
Confidence 34688999999999764
No 39
>PLN00186 ribosomal protein S26; Provisional
Probab=53.98 E-value=9.6 Score=28.93 Aligned_cols=26 Identities=12% Similarity=0.215 Sum_probs=19.6
Q ss_pred CCCCCCCCCCcccccCC-CccCCCccc
Q 020522 281 PQNANTPDLTIHKAKNS-ELCCSKVKQ 306 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~~-~~~c~~c~~ 306 (325)
|..+|..||-|+-|... ..+|++|.+
T Consensus 2 ~kKRrN~GR~K~~rGhv~~V~C~nCgr 28 (109)
T PLN00186 2 TKKRRNGGRNKHGRGHVKRIRCSNCGK 28 (109)
T ss_pred CcccccCCCCCCCCCCCcceeeCCCcc
Confidence 56788889999888665 467777765
No 40
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=53.87 E-value=8.9 Score=28.62 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=18.0
Q ss_pred CccCCCccccc---------eeeeEEeecCCCCC
Q 020522 298 ELCCSKVKQVS---------VVMSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~g---------h~~~~~~~~~~~~~ 322 (325)
+..|.-|.... |+.+..-|+-|+++
T Consensus 23 ~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~es 56 (109)
T KOG3214|consen 23 QFNCLFCNHEKSVSCTLDKKHNIGKASCRICEES 56 (109)
T ss_pred eeccCccccccceeeeehhhcCcceeeeeehhhh
Confidence 57899887654 34467778888875
No 41
>PHA02517 putative transposase OrfB; Reviewed
Probab=53.44 E-value=54 Score=29.21 Aligned_cols=42 Identities=12% Similarity=-0.133 Sum_probs=23.6
Q ss_pred EEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchh
Q 020522 14 WPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENG 57 (325)
Q Consensus 14 ~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~g 57 (325)
+++|+.+...++.+.-.-+|+.+....|.. .++.|.||+...
T Consensus 139 ~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~--~~~i~~sD~G~~ 180 (277)
T PHA02517 139 RIVGWRVSSSMDTDFVLDALEQALWARGRP--GGLIHHSDKGSQ 180 (277)
T ss_pred eeeecccCCCCChHHHHHHHHHHHHhcCCC--cCcEeecccccc
Confidence 366777777777765444444443333322 245667888554
No 42
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=53.43 E-value=81 Score=25.71 Aligned_cols=61 Identities=11% Similarity=0.088 Sum_probs=44.2
Q ss_pred ccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHh---hccccccccchHHHHHHHHhhCC
Q 020522 25 SNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEA---LMCRAEIRICAQTVYERMKAKFP 87 (325)
Q Consensus 25 ~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~---vfP~a~h~~C~~Hi~~n~~~~~~ 87 (325)
+.+..--+|+...+-+|.. ..+.||||-...+.+|-+. -+|+..+-.|..|-+.-+.+.+.
T Consensus 74 ~a~~l~~ll~~vIeeVG~~--nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 74 TAEYLFELLDEVIEEVGEE--NVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred cHHHHHHHHHHHHHHhhhh--hhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 4444545555555556765 5889999999998888444 48999999999998877766544
No 43
>PRK05978 hypothetical protein; Provisional
Probab=53.00 E-value=6.1 Score=32.08 Aligned_cols=24 Identities=13% Similarity=0.242 Sum_probs=18.9
Q ss_pred CccCCCcccccee-----eeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVV-----MSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~-----~~~~~~~~~~~~ 322 (325)
..+|++|++ |+. .-.-.|+-||+.
T Consensus 33 ~grCP~CG~-G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 33 RGRCPACGE-GKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred cCcCCCCCC-CcccccccccCCCccccCCc
Confidence 578999997 777 455579999974
No 44
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=52.28 E-value=10 Score=28.79 Aligned_cols=26 Identities=12% Similarity=0.195 Sum_probs=19.6
Q ss_pred CCCCCCCCCCcccccCC-CccCCCccc
Q 020522 281 PQNANTPDLTIHKAKNS-ELCCSKVKQ 306 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~~-~~~c~~c~~ 306 (325)
|..+|..||-|+-|... ..+|.+|.+
T Consensus 2 ~kKRrN~GR~K~~rGhv~~V~C~nCgr 28 (108)
T PTZ00172 2 TSKRRNNGRSKHGRGHVKPVRCSNCGR 28 (108)
T ss_pred CcccccCCCCCCCCCCCccEEeCCccc
Confidence 56788889999888665 467777765
No 45
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=51.41 E-value=11 Score=20.54 Aligned_cols=10 Identities=20% Similarity=0.491 Sum_probs=7.3
Q ss_pred eeEEeecCCC
Q 020522 311 MSLYLIQPCG 320 (325)
Q Consensus 311 ~~~~~~~~~~ 320 (325)
...|.||-||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4567888887
No 46
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=51.01 E-value=6.5 Score=25.42 Aligned_cols=23 Identities=13% Similarity=0.143 Sum_probs=15.1
Q ss_pred ccCCCccccce---eeeEEeecCCCC
Q 020522 299 LCCSKVKQVSV---VMSLYLIQPCGL 321 (325)
Q Consensus 299 ~~c~~c~~~gh---~~~~~~~~~~~~ 321 (325)
..|.+|++.=- ....++|+.||-
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCc
Confidence 56777776543 336678888873
No 47
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=49.67 E-value=13 Score=25.65 Aligned_cols=25 Identities=12% Similarity=0.379 Sum_probs=16.9
Q ss_pred CccCCCcccccee---eeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVV---MSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~---~~~~~~~~~~~~ 322 (325)
...|+.|+..... .+.+.|+.||..
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCE
Confidence 3457777766554 477888888753
No 48
>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=49.03 E-value=11 Score=25.00 Aligned_cols=22 Identities=32% Similarity=0.360 Sum_probs=16.8
Q ss_pred CccCCCccccceee---------eEEeecCCCC
Q 020522 298 ELCCSKVKQVSVVM---------SLYLIQPCGL 321 (325)
Q Consensus 298 ~~~c~~c~~~gh~~---------~~~~~~~~~~ 321 (325)
..-|++|.. ||+ -.|+|+-||.
T Consensus 22 aLIC~~C~~--hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 22 ALICSKCFS--HNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred eEECcccch--hhcccccccCCceEEEcCCCCC
Confidence 467999974 665 4699999985
No 49
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=47.94 E-value=16 Score=21.92 Aligned_cols=23 Identities=17% Similarity=0.491 Sum_probs=15.3
Q ss_pred CccCCCccccc-eee--------eEEeecCCC
Q 020522 298 ELCCSKVKQVS-VVM--------SLYLIQPCG 320 (325)
Q Consensus 298 ~~~c~~c~~~g-h~~--------~~~~~~~~~ 320 (325)
...|++|.+.. .+. --|+|+.|+
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcCC
Confidence 35788888766 222 568888774
No 50
>PRK04351 hypothetical protein; Provisional
Probab=47.42 E-value=9.4 Score=31.07 Aligned_cols=24 Identities=17% Similarity=0.177 Sum_probs=19.5
Q ss_pred CccCCCccc-----cceeeeEEeecCCCC
Q 020522 298 ELCCSKVKQ-----VSVVMSLYLIQPCGL 321 (325)
Q Consensus 298 ~~~c~~c~~-----~gh~~~~~~~~~~~~ 321 (325)
...|.+|+. ..|+...|+|..||.
T Consensus 112 ~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g 140 (149)
T PRK04351 112 LYECQSCGQQYLRKRRINTKRYRCGKCRG 140 (149)
T ss_pred EEECCCCCCEeeeeeecCCCcEEeCCCCc
Confidence 578988876 567778899999984
No 51
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=46.98 E-value=15 Score=21.64 Aligned_cols=26 Identities=27% Similarity=0.206 Sum_probs=20.7
Q ss_pred CccCCCcccccee---eeEEeecCCCCCC
Q 020522 298 ELCCSKVKQVSVV---MSLYLIQPCGLSE 323 (325)
Q Consensus 298 ~~~c~~c~~~gh~---~~~~~~~~~~~~~ 323 (325)
...|+.|++-+.+ .+.+-|.-||.+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 3579999998877 3778899999763
No 52
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.75 E-value=17 Score=24.32 Aligned_cols=38 Identities=11% Similarity=0.305 Sum_probs=23.0
Q ss_pred CCCCCCCCCCcccccC------CCccCCCccccceeeeEEeecCCC
Q 020522 281 PQNANTPDLTIHKAKN------SELCCSKVKQVSVVMSLYLIQPCG 320 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~------~~~~c~~c~~~gh~~~~~~~~~~~ 320 (325)
|..+..+.|.+++|.. +...|+.|+. ...+-+.|+.||
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~--~~~~H~vC~~CG 47 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGE--PKLPHRVCPSCG 47 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCC--ccCCeEECCCCC
Confidence 5555556665555532 2367888874 344566778887
No 53
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=46.66 E-value=58 Score=24.39 Aligned_cols=55 Identities=15% Similarity=-0.034 Sum_probs=38.4
Q ss_pred EEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHH
Q 020522 3 TAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVED 60 (325)
Q Consensus 3 ~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~ 60 (325)
+.+.+|..-. +.+++.+-..++.+...-+|+......|.. .|.+|+||+......
T Consensus 27 ~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 27 LLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKRGGR--PPRVIRTDNGSEFTS 81 (120)
T ss_dssp EEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHHS-S--E-SEEEEESCHHHHS
T ss_pred EEEEEECCCC-cEEEEEeecccccccccccccccccccccc--cceeccccccccccc
Confidence 3455665544 466777887778888888888766665643 289999999988654
No 54
>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=44.57 E-value=14 Score=22.15 Aligned_cols=24 Identities=21% Similarity=0.250 Sum_probs=14.0
Q ss_pred ccCCCcccccee--------eeEEeecCCCCC
Q 020522 299 LCCSKVKQVSVV--------MSLYLIQPCGLS 322 (325)
Q Consensus 299 ~~c~~c~~~gh~--------~~~~~~~~~~~~ 322 (325)
.+|++|+..--+ ....+|+.||..
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 457777762222 235678888754
No 55
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=44.14 E-value=14 Score=20.88 Aligned_cols=21 Identities=14% Similarity=0.176 Sum_probs=9.9
Q ss_pred cCCCccccceeeeEEeecCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCG 320 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~ 320 (325)
.|.-|+..+.....|.|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECD 22 (30)
T ss_dssp --TTTS----S--EEE-TTT-
T ss_pred cCCcCCCcCCCCceEECccCC
Confidence 588899888888899999884
No 56
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=43.69 E-value=12 Score=25.35 Aligned_cols=25 Identities=16% Similarity=0.402 Sum_probs=22.2
Q ss_pred CCccCCCccccceeeeEEeecCCCC
Q 020522 297 SELCCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 297 ~~~~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
....|-||+..+-....-.|+-||-
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGF 40 (62)
T ss_pred ccchhcccCcccccccccchhhcCC
Confidence 5678999999999999999999985
No 57
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=43.10 E-value=11 Score=20.86 Aligned_cols=22 Identities=23% Similarity=0.428 Sum_probs=15.3
Q ss_pred cCCCccccceeeeEEeecCCCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
+|+.|.. -...+.-.|+.||-+
T Consensus 2 ~CP~C~~-~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGA-EVPESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcC-CchhhcCcCCCCCCC
Confidence 5788875 445567778888853
No 58
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=42.92 E-value=12 Score=25.67 Aligned_cols=24 Identities=13% Similarity=0.230 Sum_probs=14.7
Q ss_pred CccCCCccccceeeeEEeecCCCC
Q 020522 298 ELCCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 298 ~~~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
+..|+.|++.|.++....|+.|+-
T Consensus 41 ~~~C~~C~G~G~~i~~~~C~~C~G 64 (66)
T PF00684_consen 41 QQTCPKCGGTGKIIEKDPCKTCKG 64 (66)
T ss_dssp EEE-TTTSSSSEE-TSSB-SSSTT
T ss_pred EEECCCCcceeeEECCCCCCCCCC
Confidence 466777777777776667777764
No 59
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=42.03 E-value=17 Score=29.45 Aligned_cols=25 Identities=16% Similarity=0.478 Sum_probs=19.2
Q ss_pred CccCCCccccceee----------eEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVVM----------SLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~~----------~~~~~~~~~~~ 322 (325)
...|++|+..-... ++|+|.-|...
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 58899998654433 89999999863
No 60
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=41.78 E-value=25 Score=21.55 Aligned_cols=21 Identities=14% Similarity=0.379 Sum_probs=12.5
Q ss_pred cCCCcccccee-----eeEEeecCCC
Q 020522 300 CCSKVKQVSVV-----MSLYLIQPCG 320 (325)
Q Consensus 300 ~c~~c~~~gh~-----~~~~~~~~~~ 320 (325)
+|++|+..-.. ..++.|+.||
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCC
Confidence 47777653222 3667788776
No 61
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=40.74 E-value=13 Score=22.13 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=12.4
Q ss_pred ccCCCccccceeeeEEeecCCCCCCC
Q 020522 299 LCCSKVKQVSVVMSLYLIQPCGLSEY 324 (325)
Q Consensus 299 ~~c~~c~~~gh~~~~~~~~~~~~~~~ 324 (325)
.+|..|+.+-+-.+ ..|+.||-.++
T Consensus 12 ~rC~~Cg~~~~pPr-~~Cp~C~s~~l 36 (37)
T PF12172_consen 12 QRCRDCGRVQFPPR-PVCPHCGSDEL 36 (37)
T ss_dssp EE-TTT--EEES---SEETTTT----
T ss_pred EEcCCCCCEecCCC-cCCCCcCcccc
Confidence 46888888755555 77999986654
No 62
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.56 E-value=13 Score=28.61 Aligned_cols=31 Identities=16% Similarity=0.096 Sum_probs=20.6
Q ss_pred cccCCCccCCCccccceee-eEEeecCCCCCC
Q 020522 293 KAKNSELCCSKVKQVSVVM-SLYLIQPCGLSE 323 (325)
Q Consensus 293 ~R~~~~~~c~~c~~~gh~~-~~~~~~~~~~~~ 323 (325)
.+++...+|..|+...-.. ..+.||.||...
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQHDAQCPHCHGER 96 (113)
T ss_pred EeeCcEEEcccCCCEEecCCcCccCcCCCCCC
Confidence 3344467788888766663 556789888543
No 63
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=37.50 E-value=19 Score=26.74 Aligned_cols=26 Identities=8% Similarity=0.176 Sum_probs=19.3
Q ss_pred CCCCCCCCCCcccccCC-CccCCCccc
Q 020522 281 PQNANTPDLTIHKAKNS-ELCCSKVKQ 306 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~~-~~~c~~c~~ 306 (325)
|..++..||.|+-|..- -.+|-+|..
T Consensus 2 pkkR~N~GR~K~~rGhv~~v~CdnCg~ 28 (108)
T COG4830 2 PKKRRNRGRNKKGRGHVKYVRCDNCGK 28 (108)
T ss_pred cchhhhcCCCCCCCCCccceeeccccc
Confidence 67888999998887654 456777764
No 64
>PHA02942 putative transposase; Provisional
Probab=37.37 E-value=20 Score=34.03 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=18.8
Q ss_pred CccCCCcccccee--eeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVV--MSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~--~~~~~~~~~~~~ 322 (325)
...||.|+....- .+.|.|+.||-.
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 4679999876432 468999999964
No 65
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.98 E-value=21 Score=30.11 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=18.2
Q ss_pred ccCCCccccceee-eEEeecCCCCCC
Q 020522 299 LCCSKVKQVSVVM-SLYLIQPCGLSE 323 (325)
Q Consensus 299 ~~c~~c~~~gh~~-~~~~~~~~~~~~ 323 (325)
..||||++.=... -...||.||+.|
T Consensus 150 A~CsrC~~~L~~~~~~l~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVKKGNMLKCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEEcCcEEECCCCCCEE
Confidence 5799998754433 556799999865
No 66
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=35.00 E-value=72 Score=28.11 Aligned_cols=50 Identities=14% Similarity=0.009 Sum_probs=31.8
Q ss_pred CCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHh
Q 020522 11 DGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEA 64 (325)
Q Consensus 11 ~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~ 64 (325)
+...|++|++-..=+.+.-.-..+.|.++ |. ..+.++||...+=..+.++
T Consensus 180 ~WKQpi~~~f~t~m~~~~l~~iI~~l~~~-g~---~VvAivsD~g~~N~~~w~~ 229 (236)
T PF12017_consen 180 SWKQPIYFDFDTSMDADILKNIIEKLHEI-GY---NVVAIVSDMGSNNISLWRE 229 (236)
T ss_pred cCCccEEEEecCcCCHHHHHHHHHHHHHC-CC---EEEEEECCCCcchHHHHHH
Confidence 46789999994433333333334444444 54 4899999999876666554
No 67
>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=34.40 E-value=18 Score=28.03 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=17.2
Q ss_pred CCCccCCCccccceee-eEEeecCCCCC
Q 020522 296 NSELCCSKVKQVSVVM-SLYLIQPCGLS 322 (325)
Q Consensus 296 ~~~~~c~~c~~~gh~~-~~~~~~~~~~~ 322 (325)
+....|..|+...... ..+.||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 3346677787665553 45668888754
No 68
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=33.97 E-value=23 Score=22.88 Aligned_cols=25 Identities=24% Similarity=0.612 Sum_probs=15.9
Q ss_pred ccCCCccccceeee----EEeecCCCCCCC
Q 020522 299 LCCSKVKQVSVVMS----LYLIQPCGLSEY 324 (325)
Q Consensus 299 ~~c~~c~~~gh~~~----~~~~~~~~~~~~ 324 (325)
..|+||+- |+++. -+-|-+||--|+
T Consensus 20 ~~CPrCG~-gvfmA~H~dR~~CGkCgyTe~ 48 (51)
T COG1998 20 RFCPRCGP-GVFMADHKDRWACGKCGYTEF 48 (51)
T ss_pred ccCCCCCC-cchhhhcCceeEeccccceEe
Confidence 45999983 44442 334888887665
No 69
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=33.30 E-value=3.4e+02 Score=24.72 Aligned_cols=53 Identities=9% Similarity=0.038 Sum_probs=31.8
Q ss_pred EEEEcCCCCeEEEEEEEeec-cccchHHHHHHH-Hhhhccc-CCCCCeEEEeCCchh
Q 020522 4 AVGIDANDGIWPVAVYEVEE-ESNSTWYNFLLK-LGEMLRV-DNGEGFCFISDGENG 57 (325)
Q Consensus 4 a~g~D~~~~~~~la~aiv~~-E~~~~w~wfl~~-l~~~lg~-~~~~~~~iisD~~~g 57 (325)
++-+|.... .+||+++... .+.+.-.-.|+. +..+.|. ....++.|-||+..-
T Consensus 147 ~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 147 TFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred EEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcc
Confidence 444555555 5889999875 566665556654 4443332 112478888998544
No 70
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=33.13 E-value=28 Score=34.62 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=18.3
Q ss_pred ccCCCccccceeeeEEeecCCCCCCC
Q 020522 299 LCCSKVKQVSVVMSLYLIQPCGLSEY 324 (325)
Q Consensus 299 ~~c~~c~~~gh~~~~~~~~~~~~~~~ 324 (325)
.-|++|++.|.+...-.|+.||-.++
T Consensus 54 ~pc~~c~gkG~V~v~~~c~~c~G~gk 79 (715)
T COG1107 54 IPCPKCRGKGTVTVYDTCPECGGTGK 79 (715)
T ss_pred CCCCeeccceeEEEEeecccCCCcee
Confidence 45777777777777777777775543
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.98 E-value=31 Score=20.63 Aligned_cols=8 Identities=25% Similarity=0.467 Sum_probs=3.6
Q ss_pred EEeecCCC
Q 020522 313 LYLIQPCG 320 (325)
Q Consensus 313 ~~~~~~~~ 320 (325)
.-+|+.||
T Consensus 25 ~v~C~~C~ 32 (36)
T PF13717_consen 25 KVRCSKCG 32 (36)
T ss_pred EEECCCCC
Confidence 34444444
No 72
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=32.96 E-value=3.5e+02 Score=24.01 Aligned_cols=53 Identities=11% Similarity=0.023 Sum_probs=30.4
Q ss_pred EEEEcCCCCeEEEEEEEeec-cccchHHHHHHHHhhh-ccc-CCCCCeEEEeCCchh
Q 020522 4 AVGIDANDGIWPVAVYEVEE-ESNSTWYNFLLKLGEM-LRV-DNGEGFCFISDGENG 57 (325)
Q Consensus 4 a~g~D~~~~~~~la~aiv~~-E~~~~w~wfl~~l~~~-lg~-~~~~~~~iisD~~~g 57 (325)
++-+|.... .++|+++... .+.+.-.-.|+..... .|. ....+..|.||+..-
T Consensus 108 ~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 108 TFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred EEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 344555444 5888888874 5666655566543333 231 111478888998544
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.07 E-value=32 Score=20.61 Aligned_cols=9 Identities=22% Similarity=0.394 Sum_probs=4.3
Q ss_pred eEEeecCCC
Q 020522 312 SLYLIQPCG 320 (325)
Q Consensus 312 ~~~~~~~~~ 320 (325)
+.-+|+.||
T Consensus 24 ~~vrC~~C~ 32 (37)
T PF13719_consen 24 RKVRCPKCG 32 (37)
T ss_pred cEEECCCCC
Confidence 344455554
No 74
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.02 E-value=28 Score=36.90 Aligned_cols=12 Identities=8% Similarity=0.050 Sum_probs=7.0
Q ss_pred ccchHHHHHHHH
Q 020522 25 SNSTWYNFLLKL 36 (325)
Q Consensus 25 ~~~~w~wfl~~l 36 (325)
..+.|.|+=+..
T Consensus 264 ~~dgW~wL~~li 275 (1121)
T PRK04023 264 KIDGWEWLEELI 275 (1121)
T ss_pred CCCCcHHHHHHh
Confidence 456687754443
No 75
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.90 E-value=28 Score=31.77 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=18.8
Q ss_pred CccCCCccccceeeeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
...|+.|+. =..+++.|+.||..
T Consensus 309 S~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 309 SKTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred cccccccCC--ccceeEECCCCCCe
Confidence 478999998 34689999999964
No 76
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=31.88 E-value=15 Score=24.37 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=19.6
Q ss_pred CCccCCCccccceeeeEEeecCCCCC
Q 020522 297 SELCCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 297 ~~~~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
+...|-+|+..+-....-.|.-||-.
T Consensus 14 tH~~CrRCG~~syH~qK~~CasCGyp 39 (55)
T PF01907_consen 14 THTLCRRCGRRSYHIQKKTCASCGYP 39 (55)
T ss_dssp SEEE-TTTSSEEEETTTTEETTTBTT
T ss_pred cEeeecccCCeeeecCCCcccccCCC
Confidence 45678999988888888888888843
No 77
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=31.49 E-value=24 Score=27.15 Aligned_cols=26 Identities=4% Similarity=0.121 Sum_probs=13.0
Q ss_pred CCCCCCCCCCcccccCC-CccCCCccc
Q 020522 281 PQNANTPDLTIHKAKNS-ELCCSKVKQ 306 (325)
Q Consensus 281 P~~~r~~GRPk~~R~~~-~~~c~~c~~ 306 (325)
|..+|..||-|+-|... ..+|.+|.+
T Consensus 2 ~~KRrN~Gr~KkgrGhv~~V~C~nCgr 28 (113)
T PF01283_consen 2 TKKRRNNGRSKKGRGHVQPVRCDNCGR 28 (113)
T ss_dssp ----TTTTSS-SSSS---EEE-TTTB-
T ss_pred CcccccCCCCCCCCCCCcCEeeCcccc
Confidence 56678888888877655 467777764
No 78
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=30.93 E-value=25 Score=23.38 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=12.9
Q ss_pred CCCccccceeeeEEeecCCCCCCC
Q 020522 301 CSKVKQVSVVMSLYLIQPCGLSEY 324 (325)
Q Consensus 301 c~~c~~~gh~~~~~~~~~~~~~~~ 324 (325)
|+-|+...-...-|.|+.||-.-|
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTH 25 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCc
Confidence 444444333445566777765543
No 79
>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=30.56 E-value=45 Score=20.61 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=14.3
Q ss_pred cCCCcccccee----eeEEeecCCCC
Q 020522 300 CCSKVKQVSVV----MSLYLIQPCGL 321 (325)
Q Consensus 300 ~c~~c~~~gh~----~~~~~~~~~~~ 321 (325)
+|+.|+...-+ ..-+-|+.||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 58888886521 25667888884
No 80
>PLN00209 ribosomal protein S27; Provisional
Probab=30.28 E-value=21 Score=25.91 Aligned_cols=24 Identities=13% Similarity=0.314 Sum_probs=20.1
Q ss_pred CccCCCcccc----ceeeeEEeecCCCC
Q 020522 298 ELCCSKVKQV----SVVMSLYLIQPCGL 321 (325)
Q Consensus 298 ~~~c~~c~~~----gh~~~~~~~~~~~~ 321 (325)
..+|+.|... ||..+.-.|.-||.
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~ 63 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQT 63 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCC
Confidence 4899999875 67778999999985
No 81
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=30.25 E-value=27 Score=21.00 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=6.0
Q ss_pred eEEeecCCCC
Q 020522 312 SLYLIQPCGL 321 (325)
Q Consensus 312 ~~~~~~~~~~ 321 (325)
-.|+|..||+
T Consensus 5 ~~YkC~~CGn 14 (36)
T PF06397_consen 5 EFYKCEHCGN 14 (36)
T ss_dssp EEEE-TTT--
T ss_pred cEEEccCCCC
Confidence 4799999997
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.86 E-value=30 Score=21.77 Aligned_cols=23 Identities=13% Similarity=0.410 Sum_probs=12.8
Q ss_pred ccCCCccccceee--eEEeecCCCC
Q 020522 299 LCCSKVKQVSVVM--SLYLIQPCGL 321 (325)
Q Consensus 299 ~~c~~c~~~gh~~--~~~~~~~~~~ 321 (325)
..|++|+..=-.. ...+|+-||-
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 3577776532222 4567777763
No 83
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.84 E-value=24 Score=18.83 Aligned_cols=20 Identities=15% Similarity=0.311 Sum_probs=11.0
Q ss_pred CCCccccceeeeEEeecCCCC
Q 020522 301 CSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 301 c~~c~~~gh~~~~~~~~~~~~ 321 (325)
|++|+..=-..+.| |+-||.
T Consensus 2 Cp~CG~~~~~~~~f-C~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKF-CPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcc-hhhhCC
Confidence 66666544333333 777764
No 84
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.68 E-value=25 Score=27.18 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=17.5
Q ss_pred cCCCccCCCccccceee--eEEeecCCCCC
Q 020522 295 KNSELCCSKVKQVSVVM--SLYLIQPCGLS 322 (325)
Q Consensus 295 ~~~~~~c~~c~~~gh~~--~~~~~~~~~~~ 322 (325)
.+....|..|+..--.. ..+.||.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 34456788888654332 23568888854
No 85
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=29.49 E-value=29 Score=25.46 Aligned_cols=26 Identities=15% Similarity=0.324 Sum_probs=22.0
Q ss_pred CCCccCCCccccceeeeEEeecCCCC
Q 020522 296 NSELCCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 296 ~~~~~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
+....|-+|+..+-....-.|+-||-
T Consensus 14 ktHtlCrRCG~~syH~qK~~CasCGy 39 (91)
T PTZ00073 14 KTHTLCRRCGKRSFHVQKKRCASCGY 39 (91)
T ss_pred cCcchhcccCccccccccccchhcCC
Confidence 45678999999998888888999985
No 86
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.99 E-value=23 Score=27.53 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=16.8
Q ss_pred cCCCccCCCccccceee-eEE-eecCCCCC
Q 020522 295 KNSELCCSKVKQVSVVM-SLY-LIQPCGLS 322 (325)
Q Consensus 295 ~~~~~~c~~c~~~gh~~-~~~-~~~~~~~~ 322 (325)
.+....|..|+...-.. ..+ +||.||..
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 34456677777665553 334 38888754
No 87
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.00 E-value=60 Score=21.50 Aligned_cols=21 Identities=14% Similarity=0.464 Sum_probs=14.4
Q ss_pred CccCCCccccceeeeEEeecCCC
Q 020522 298 ELCCSKVKQVSVVMSLYLIQPCG 320 (325)
Q Consensus 298 ~~~c~~c~~~gh~~~~~~~~~~~ 320 (325)
...|+.|+. -..+-+-|+.||
T Consensus 26 l~~C~~cG~--~~~~H~vc~~cG 46 (55)
T TIGR01031 26 LVVCPNCGE--FKLPHRVCPSCG 46 (55)
T ss_pred ceECCCCCC--cccCeeECCccC
Confidence 367888885 344556678887
No 88
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.77 E-value=30 Score=32.59 Aligned_cols=39 Identities=8% Similarity=0.012 Sum_probs=28.4
Q ss_pred CCCCCCcccc----cCCCccCCCccccceeeeEEeecCCCCCCC
Q 020522 285 NTPDLTIHKA----KNSELCCSKVKQVSVVMSLYLIQPCGLSEY 324 (325)
Q Consensus 285 r~~GRPk~~R----~~~~~~c~~c~~~gh~~~~~~~~~~~~~~~ 324 (325)
...|.-+..| ...+..|+.|++.|++. ...|+.|+=.++
T Consensus 166 ~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i-~~pC~~C~G~G~ 208 (371)
T COG0484 166 NGSGQVRTVQRTGFFSFQQTCPTCNGTGKII-KDPCGKCKGKGR 208 (371)
T ss_pred CCcCeEEEEEeeeEEEEEEECCCCccceeEC-CCCCCCCCCCCe
Confidence 3444434444 34478999999999999 788999987665
No 89
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=27.62 E-value=26 Score=23.23 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=6.7
Q ss_pred eEEeecCCCC
Q 020522 312 SLYLIQPCGL 321 (325)
Q Consensus 312 ~~~~~~~~~~ 321 (325)
-+.+||+||.
T Consensus 16 ~~lrCPRC~~ 25 (65)
T COG4049 16 EFLRCPRCGM 25 (65)
T ss_pred eeeeCCchhH
Confidence 4667777763
No 90
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=27.43 E-value=21 Score=25.91 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=20.0
Q ss_pred CccCCCcccc----ceeeeEEeecCCCC
Q 020522 298 ELCCSKVKQV----SVVMSLYLIQPCGL 321 (325)
Q Consensus 298 ~~~c~~c~~~----gh~~~~~~~~~~~~ 321 (325)
..+|+.|..+ ||..+.-.|.-||.
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~ 62 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSS 62 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCC
Confidence 4899999875 67778999999985
No 91
>PF05418 Apo-VLDL-II: Apovitellenin I (Apo-VLDL-II); InterPro: IPR008404 This family consists of several avian apovitellenin I sequences. As part of the avian reproductive effort, large quantities of triglyceride-rich very-low-density lipoprotein (VLDL) particles are transported by receptor-mediated endocytosis into the female germ cells. Although the oocytes are surrounded by a layer of granulosa cells harbouring high levels of active lipoprotein lipase, non-lipolysed VLDL is transported into the yolk. This is because VLDL particles from laying chickens (Gallus gallus) are protected from lipolysis by apolipoprotein (apo)-VLDL-II, a potent dimeric lipoprotein lipase inhibitor []. Apo-VLDL-II is produced in the liver and secreted into the blood stream when induced by estrogen production in female birds.; GO: 0004857 enzyme inhibitor activity, 0006629 lipid metabolic process, 0042627 chylomicron
Probab=27.30 E-value=2.3e+02 Score=20.00 Aligned_cols=48 Identities=19% Similarity=0.210 Sum_probs=30.4
Q ss_pred HHHHHHhhhhHhhHHHHhcccchhhhcccCCCccccccccchhHHHHHHHHHhhhhhhH--HHHHHH
Q 020522 110 HLDEIKVLDERCYEWLMESKWERWALHCMPAWAKCTHVTNKMGKKFFFWMHEYFAQSIT--RRMEAI 174 (325)
Q Consensus 110 ~~~~l~~~~~~~~~~L~~~~~~~W~~~~~~~~~~~~~~t~N~~Es~N~~i~~~r~~pi~--~~~e~i 174 (325)
..+.+.+.+|++.+||.+.- .|+-.++.-|-.|++...++|. +|+|.|
T Consensus 22 iYEavNkvsPr~~qfL~d~~-----------------Q~~vv~g~Rn~lirEt~k~sil~Eql~EKi 71 (82)
T PF05418_consen 22 IYEAVNKVSPRVGQFLLDAS-----------------QTPVVVGTRNFLIRETSKLSILAEQLVEKI 71 (82)
T ss_pred HHHHHHccChhHHHHHHHHh-----------------cccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666778899999998741 2333556667777777665543 344444
No 92
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.21 E-value=31 Score=23.04 Aligned_cols=22 Identities=18% Similarity=0.240 Sum_probs=16.6
Q ss_pred CccCCCccccceeeeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVVMSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~~~~~~~~~~~~~ 322 (325)
..+|++|+.+.- ...|+.||..
T Consensus 5 mr~C~~CgvYTL---k~~CP~CG~~ 26 (56)
T PRK13130 5 IRKCPKCGVYTL---KEICPVCGGK 26 (56)
T ss_pred ceECCCCCCEEc---cccCcCCCCC
Confidence 357999987665 6678999864
No 93
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.64 E-value=1.2e+02 Score=29.09 Aligned_cols=70 Identities=16% Similarity=0.049 Sum_probs=54.4
Q ss_pred eEEEEEcCCCCeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchhHHHHHHhhccccccccchHHHHH
Q 020522 2 LTAVGIDANDGIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENGVEDALEALMCRAEIRICAQTVYE 80 (325)
Q Consensus 2 l~a~g~D~~~~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~gl~~Av~~vfP~a~h~~C~~Hi~~ 80 (325)
++++.+|++.... ..++++-+.++-.-+|+.. |.. +...+..|...+..+++++.+|++.+-+=.+|+.+
T Consensus 169 ~~~i~~D~~~~~~---i~i~~~r~~~ti~~~l~~~----g~~--~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 169 YQTIAVDLDTRKV---IDILEGRSVRTLRRYLRRG----GSE--QVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred EEEEEEcCCCCce---eeecCCccHHHHHHHHHhC----CCc--ceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 4677777775222 4678888888877777654 322 47888999999999999999999999998888865
No 94
>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=26.00 E-value=53 Score=20.76 Aligned_cols=22 Identities=9% Similarity=0.303 Sum_probs=18.9
Q ss_pred cCCCccccceeeeEEeecCCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
.|..|+...-++.-|+|..|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~d 23 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPN 23 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCC
Confidence 5889998888899999999975
No 95
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=25.07 E-value=74 Score=20.41 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=18.0
Q ss_pred cCCCccccceeeeEEeecCCCC
Q 020522 300 CCSKVKQVSVVMSLYLIQPCGL 321 (325)
Q Consensus 300 ~c~~c~~~gh~~~~~~~~~~~~ 321 (325)
.|+.|++..-.+--|+|..|.+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d 23 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRD 23 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCC
Confidence 5899998777777899999975
No 96
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.86 E-value=46 Score=21.19 Aligned_cols=10 Identities=20% Similarity=0.760 Sum_probs=4.7
Q ss_pred EEeecCCCCC
Q 020522 313 LYLIQPCGLS 322 (325)
Q Consensus 313 ~~~~~~~~~~ 322 (325)
.+-|+.||-.
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 3445555543
No 97
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=24.64 E-value=42 Score=32.22 Aligned_cols=47 Identities=15% Similarity=0.201 Sum_probs=30.3
Q ss_pred HHHHH-HHHHHHhccccEEEEeCCceEEEEEecceEEEEEccCcccccc
Q 020522 170 RMEAI-VNNAIEAAREMNVEATEGQVMHVLENGISRVSVDIKKQCCDCG 217 (325)
Q Consensus 170 ~~e~i-l~~~~~~a~~~~v~~~~~~~~~V~~~~~~~~~V~l~~~~CsC~ 217 (325)
+++.+ ++++++.+..-.|. -.+|.|-|.+...--.++|.+...++.+
T Consensus 254 lf~~y~ie~~i~~~l~~~V~-L~~Gg~lvIe~TEALtvIDVNsG~~~~~ 301 (414)
T TIGR00757 254 LFEGFQIEKQIDKATQRKVW-LPSGGYIVIDQTEALTTIDVNSGRFTGG 301 (414)
T ss_pred hhHhhCHHHHHHHhcCCcEE-CCCCeEEEEecCccEEEEEecCCCCCCC
Confidence 44444 77888877665444 4456688887444456888888776543
No 98
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.06 E-value=42 Score=36.58 Aligned_cols=13 Identities=8% Similarity=0.164 Sum_probs=8.6
Q ss_pred ccchHHHHHHHHh
Q 020522 25 SNSTWYNFLLKLG 37 (325)
Q Consensus 25 ~~~~w~wfl~~l~ 37 (325)
..+.|.|+=+.+.
T Consensus 266 ~~~gW~wL~~li~ 278 (1337)
T PRK14714 266 KEEGWDWLQELID 278 (1337)
T ss_pred CCCCcHHHHHHHh
Confidence 5678999755543
No 99
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=23.96 E-value=61 Score=30.66 Aligned_cols=43 Identities=21% Similarity=0.370 Sum_probs=33.2
Q ss_pred CeEEEEEEEeeccccchHHHHHHHHhhhcccCCCCCeEEEeCCchh
Q 020522 12 GIWPVAVYEVEEESNSTWYNFLLKLGEMLRVDNGEGFCFISDGENG 57 (325)
Q Consensus 12 ~~~~la~aiv~~E~~~~w~wfl~~l~~~lg~~~~~~~~iisD~~~g 57 (325)
+.|.++ -=++....+.|.-||.+|..++.+. .+.++|-|--.|
T Consensus 370 ~~f~~~-DS~~~~~~~~~~~F~~~l~~~i~~~--~~~tlIldDp~~ 412 (460)
T KOG2703|consen 370 RSFTFG-DSMDEGQKARWQEFLAKLDDIIAGK--LPATLILDDPLG 412 (460)
T ss_pred Cceecc-ccCCHHHHHHHHHHHHHHHHHHhcc--cceEEEeecCCc
Confidence 344444 4455677889999999999998877 599999887666
No 100
>smart00343 ZnF_C2HC zinc finger.
Probab=23.95 E-value=31 Score=18.62 Aligned_cols=13 Identities=8% Similarity=0.174 Sum_probs=10.6
Q ss_pred cCCCccccceeee
Q 020522 300 CCSKVKQVSVVMS 312 (325)
Q Consensus 300 ~c~~c~~~gh~~~ 312 (325)
.|.+|.+.||..+
T Consensus 1 ~C~~CG~~GH~~~ 13 (26)
T smart00343 1 KCYNCGKEGHIAR 13 (26)
T ss_pred CCccCCCCCcchh
Confidence 4889999999764
No 101
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.64 E-value=51 Score=29.52 Aligned_cols=14 Identities=7% Similarity=0.204 Sum_probs=9.7
Q ss_pred CccCCCccccceee
Q 020522 298 ELCCSKVKQVSVVM 311 (325)
Q Consensus 298 ~~~c~~c~~~gh~~ 311 (325)
...|+.|++...+.
T Consensus 239 ~~~C~~Cg~~PtiP 252 (298)
T KOG2879|consen 239 DTECPVCGEPPTIP 252 (298)
T ss_pred CceeeccCCCCCCC
Confidence 57888888765443
No 102
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.46 E-value=50 Score=26.34 Aligned_cols=12 Identities=17% Similarity=0.135 Sum_probs=7.0
Q ss_pred CccCCCccccce
Q 020522 298 ELCCSKVKQVSV 309 (325)
Q Consensus 298 ~~~c~~c~~~gh 309 (325)
...|..|+..--
T Consensus 70 ~~~C~~CG~~~~ 81 (135)
T PRK03824 70 VLKCRNCGNEWS 81 (135)
T ss_pred EEECCCCCCEEe
Confidence 456777765443
No 103
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.42 E-value=61 Score=23.69 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=18.9
Q ss_pred CccCCCccccceee---eEEeecCCCCC
Q 020522 298 ELCCSKVKQVSVVM---SLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh~~---~~~~~~~~~~~ 322 (325)
.+.|+.|+...|-. ....|+-||..
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAK 62 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCe
Confidence 68899999885544 56788888853
No 104
>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=23.41 E-value=99 Score=18.72 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=5.6
Q ss_pred cCCCccccceee
Q 020522 300 CCSKVKQVSVVM 311 (325)
Q Consensus 300 ~c~~c~~~gh~~ 311 (325)
+|++|+....+.
T Consensus 2 ~Cp~Cg~~~a~~ 13 (39)
T PF01096_consen 2 KCPKCGHNEAVF 13 (39)
T ss_dssp --SSS-SSEEEE
T ss_pred CCcCCCCCeEEE
Confidence 578887655544
No 105
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=22.72 E-value=28 Score=20.89 Aligned_cols=13 Identities=15% Similarity=0.112 Sum_probs=9.0
Q ss_pred cCCCccccceeee
Q 020522 300 CCSKVKQVSVVMS 312 (325)
Q Consensus 300 ~c~~c~~~gh~~~ 312 (325)
.|+||++-.|-.+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 5999999888763
No 106
>PRK02935 hypothetical protein; Provisional
Probab=21.99 E-value=49 Score=25.07 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=18.2
Q ss_pred CccCCCccccce-eeeEEeecCCCCC
Q 020522 298 ELCCSKVKQVSV-VMSLYLIQPCGLS 322 (325)
Q Consensus 298 ~~~c~~c~~~gh-~~~~~~~~~~~~~ 322 (325)
+..|+.|++.-. -++...|--|++.
T Consensus 70 qV~CP~C~K~TKmLGrvD~CM~C~~P 95 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVDACMHCNQP 95 (110)
T ss_pred eeECCCCCchhhhccceeecCcCCCc
Confidence 467888887654 4478888888864
No 107
>PF13390 DUF4108: Protein of unknown function (DUF4108)
Probab=21.97 E-value=51 Score=25.45 Aligned_cols=24 Identities=21% Similarity=0.019 Sum_probs=19.7
Q ss_pred EcCCCCeEEEEEEEeeccccchHH
Q 020522 7 IDANDGIWPVAVYEVEEESNSTWY 30 (325)
Q Consensus 7 ~D~~~~~~~la~aiv~~E~~~~w~ 30 (325)
.|+--.+-|++||++..|+..-|.
T Consensus 35 ~~~~~NI~Pv~FA~~~K~~ak~~d 58 (136)
T PF13390_consen 35 FKKKWNIKPVKFAFVTKEGAKFED 58 (136)
T ss_pred hcccccccceEEEEEcCCCCeeEE
Confidence 355667889999999999988773
No 108
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=21.37 E-value=2e+02 Score=27.30 Aligned_cols=47 Identities=2% Similarity=-0.114 Sum_probs=30.3
Q ss_pred CccchHHHHHhccCcccccCCCCCCCC------CCCCCcccCCC-CCCCCCCCc
Q 020522 245 DPLLTKDRYLSTYAVMMQLLPEEKCWP------SSKFESILPPQ-NANTPDLTI 291 (325)
Q Consensus 245 ~~~yt~~~~~~~y~~~i~pv~~~~~w~------~~~~~~~~PP~-~~r~~GRPk 291 (325)
.=|+-++.+...|..-++|-..-..|. .+|...+.|+. .+.-..+|=
T Consensus 199 t~C~EL~~F~D~Yd~~mYp~l~~r~~~i~~l~~~~d~arv~c~~~~~~yg~~pf 252 (420)
T PTZ00473 199 TICNELNNFFDKYKEHLYPPLKYRRILIESLGDGIDTARVQCKVCEREYGSNPF 252 (420)
T ss_pred HHHHHHHHHHHHHHhhcCcccchhhcceeecccCCCCceecccchhhhcCCCcc
Confidence 347788999999999888766434443 33556677765 344455553
No 109
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=21.08 E-value=1.5e+02 Score=24.82 Aligned_cols=45 Identities=9% Similarity=0.132 Sum_probs=33.0
Q ss_pred HHHHHhhhcccCCCCCeEEEeCCch---hHHHHHHhhccccccccchHHHH
Q 020522 32 FLLKLGEMLRVDNGEGFCFISDGEN---GVEDALEALMCRAEIRICAQTVY 79 (325)
Q Consensus 32 fl~~l~~~lg~~~~~~~~iisD~~~---gl~~Av~~vfP~a~h~~C~~Hi~ 79 (325)
.++.++.+.. . .++.|+||.+. =|..-+.+.+|++.|.+=.+.-.
T Consensus 37 ~i~~i~~~~~-~--rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a 84 (174)
T TIGR00334 37 TINLIKKAQK-K--QGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLA 84 (174)
T ss_pred HHHHHHHHhh-c--CCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhc
Confidence 4566666532 2 59999999986 47788888899999988655543
No 110
>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=20.42 E-value=70 Score=20.45 Aligned_cols=6 Identities=33% Similarity=0.661 Sum_probs=2.8
Q ss_pred ecCCCC
Q 020522 316 IQPCGL 321 (325)
Q Consensus 316 ~~~~~~ 321 (325)
|+.||.
T Consensus 29 CP~Cg~ 34 (52)
T TIGR02605 29 CPECGG 34 (52)
T ss_pred CCCCCC
Confidence 444443
Done!