Query 021122
Match_columns 317
No_of_seqs 250 out of 1655
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 07:46:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021122hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00368 universal minicircle 99.9 4.1E-27 9E-32 202.7 10.1 133 181-316 1-145 (148)
2 PTZ00368 universal minicircle 99.8 5.8E-21 1.2E-25 164.5 8.7 109 179-289 26-142 (148)
3 COG5082 AIR1 Arginine methyltr 99.8 3.2E-21 6.9E-26 171.3 6.7 122 178-313 58-189 (190)
4 COG5082 AIR1 Arginine methyltr 99.7 4.2E-18 9.2E-23 151.4 6.0 101 202-316 59-170 (190)
5 KOG4400 E3 ubiquitin ligase in 99.5 3.1E-14 6.8E-19 133.3 8.0 99 180-289 72-177 (261)
6 KOG4400 E3 ubiquitin ligase in 99.5 1.2E-13 2.5E-18 129.5 7.8 131 180-317 92-239 (261)
7 KOG0119 Splicing factor 1/bran 98.8 5E-10 1.1E-14 111.5 -0.7 133 87-221 155-303 (554)
8 PF00098 zf-CCHC: Zinc knuckle 97.8 1.1E-05 2.4E-10 45.9 1.4 17 182-198 2-18 (18)
9 PF00098 zf-CCHC: Zinc knuckle 97.7 2.5E-05 5.3E-10 44.5 2.0 16 251-266 2-17 (18)
10 PF13696 zf-CCHC_2: Zinc knuck 96.2 0.002 4.3E-08 42.0 1.1 21 247-267 6-26 (32)
11 PF13696 zf-CCHC_2: Zinc knuck 95.2 0.0095 2.1E-07 38.8 1.1 22 220-241 6-27 (32)
12 PF13917 zf-CCHC_3: Zinc knuck 94.8 0.013 2.8E-07 40.6 1.0 19 180-198 4-22 (42)
13 PF13917 zf-CCHC_3: Zinc knuck 93.0 0.053 1.1E-06 37.5 1.3 19 249-267 4-22 (42)
14 smart00343 ZnF_C2HC zinc finge 92.8 0.045 9.8E-07 33.4 0.8 17 182-198 1-17 (26)
15 KOG0119 Splicing factor 1/bran 92.7 0.082 1.8E-06 53.9 2.8 43 223-268 262-304 (554)
16 smart00343 ZnF_C2HC zinc finge 91.6 0.091 2E-06 32.1 1.1 17 251-267 1-17 (26)
17 KOG0109 RNA-binding protein LA 89.6 0.091 2E-06 50.5 -0.3 36 165-200 144-180 (346)
18 KOG0314 Predicted E3 ubiquitin 88.8 0.62 1.3E-05 47.4 4.8 69 171-241 103-177 (448)
19 KOG0314 Predicted E3 ubiquitin 86.9 0.73 1.6E-05 46.8 4.1 61 205-267 114-176 (448)
20 PF15288 zf-CCHC_6: Zinc knuck 86.6 0.31 6.8E-06 33.3 0.9 18 181-198 2-21 (40)
21 COG5222 Uncharacterized conser 86.5 0.28 6.2E-06 47.3 0.9 22 247-268 174-195 (427)
22 COG5222 Uncharacterized conser 86.3 0.34 7.4E-06 46.8 1.3 24 176-199 172-195 (427)
23 COG5176 MSL5 Splicing factor ( 85.2 0.23 4.9E-06 45.7 -0.4 127 38-169 119-258 (269)
24 PF14392 zf-CCHC_4: Zinc knuck 84.0 0.37 8.1E-06 33.9 0.3 17 181-197 32-48 (49)
25 KOG0109 RNA-binding protein LA 83.8 0.57 1.2E-05 45.1 1.6 23 248-270 159-181 (346)
26 PF14392 zf-CCHC_4: Zinc knuck 82.9 0.48 1E-05 33.4 0.5 18 249-266 31-48 (49)
27 PF14787 zf-CCHC_5: GAG-polypr 81.7 0.7 1.5E-05 30.9 0.9 19 181-199 3-21 (36)
28 PF15288 zf-CCHC_6: Zinc knuck 79.9 0.93 2E-05 31.0 1.1 13 277-289 2-14 (40)
29 PF14787 zf-CCHC_5: GAG-polypr 77.6 1.6 3.6E-05 29.1 1.7 20 250-269 3-22 (36)
30 smart00816 Amb_V_allergen Amb 70.9 2.9 6.2E-05 28.8 1.6 25 281-305 11-35 (45)
31 KOG3116 Predicted C3H1-type Zn 67.1 1.7 3.6E-05 38.1 -0.2 20 180-199 27-46 (177)
32 PF03913 Amb_V_allergen: Amb V 57.2 5 0.00011 27.5 0.8 25 281-305 10-34 (44)
33 PF10083 DUF2321: Uncharacteri 55.7 3 6.6E-05 36.7 -0.6 60 232-309 13-77 (158)
34 KOG2044 5'-3' exonuclease HKE1 46.3 13 0.00029 40.5 2.2 40 248-288 259-298 (931)
35 KOG3116 Predicted C3H1-type Zn 42.5 7.2 0.00016 34.3 -0.4 22 221-242 26-47 (177)
36 COG1198 PriA Primosomal protei 38.0 37 0.00081 36.9 4.0 48 247-309 433-484 (730)
37 PF07708 Tash_PEST: Tash prote 36.7 16 0.00034 21.1 0.5 15 21-35 4-18 (19)
38 PF13240 zinc_ribbon_2: zinc-r 35.2 25 0.00054 21.0 1.3 9 300-308 13-21 (23)
39 COG1107 Archaea-specific RecJ- 34.5 27 0.00059 37.1 2.2 86 181-287 3-106 (715)
40 KOG2813 Predicted molecular ch 34.3 61 0.0013 32.0 4.5 34 275-310 233-266 (406)
41 KOG1059 Vesicle coat complex A 32.4 38 0.00082 36.8 2.9 24 104-127 837-860 (877)
42 PRK14289 chaperone protein Dna 32.3 33 0.00073 34.1 2.5 23 39-61 16-38 (386)
43 PF12353 eIF3g: Eukaryotic tra 31.4 22 0.00048 30.2 0.9 19 180-199 106-124 (128)
44 PLN03086 PRLI-interacting fact 31.4 25 0.00054 37.1 1.4 21 259-286 494-514 (567)
45 COG0484 DnaJ DnaJ-class molecu 30.4 21 0.00045 35.8 0.6 19 43-61 19-37 (371)
46 KOG1244 Predicted transcriptio 30.4 24 0.00052 34.0 1.0 14 277-290 247-260 (336)
47 PF04216 FdhE: Protein involve 29.4 5.8 0.00013 37.8 -3.3 49 181-234 173-223 (290)
48 PRK14298 chaperone protein Dna 28.2 48 0.001 33.0 2.8 23 39-61 16-38 (377)
49 TIGR02349 DnaJ_bact chaperone 28.2 48 0.0011 32.4 2.8 23 39-61 11-33 (354)
50 PF12773 DZR: Double zinc ribb 27.4 93 0.002 21.3 3.4 10 276-285 29-38 (50)
51 TIGR00595 priA primosomal prot 27.1 60 0.0013 33.6 3.3 23 276-309 240-262 (505)
52 PRK14296 chaperone protein Dna 27.0 43 0.00094 33.2 2.2 67 223-310 150-216 (372)
53 KOG0066 eIF2-interacting prote 26.5 33 0.00072 35.6 1.3 56 13-75 86-142 (807)
54 PF12353 eIF3g: Eukaryotic tra 26.4 34 0.00075 29.0 1.2 19 248-267 105-123 (128)
55 smart00249 PHD PHD zinc finger 25.8 77 0.0017 20.3 2.7 19 276-294 14-32 (47)
56 KOG2813 Predicted molecular ch 25.4 1.2E+02 0.0026 30.1 4.8 36 248-288 233-268 (406)
57 COG0484 DnaJ DnaJ-class molecu 25.0 45 0.00098 33.4 1.9 15 139-153 44-58 (371)
58 PRK14285 chaperone protein Dna 24.6 77 0.0017 31.3 3.5 63 223-310 147-209 (365)
59 PRK14287 chaperone protein Dna 24.6 49 0.0011 32.8 2.1 22 39-60 15-36 (371)
60 PRK14286 chaperone protein Dna 24.6 47 0.001 32.9 2.0 63 223-310 151-213 (372)
61 PRK14276 chaperone protein Dna 23.9 52 0.0011 32.7 2.1 23 39-61 15-37 (380)
62 KOG2044 5'-3' exonuclease HKE1 23.9 34 0.00074 37.5 0.8 20 180-199 260-279 (931)
63 PRK14280 chaperone protein Dna 23.7 52 0.0011 32.6 2.1 22 39-60 15-36 (376)
64 PRK14278 chaperone protein Dna 23.7 49 0.0011 32.9 1.9 23 39-61 14-36 (378)
65 KOG2673 Uncharacterized conser 23.7 36 0.00078 34.9 0.9 18 182-199 130-147 (485)
66 PF00684 DnaJ_CXXCXGXG: DnaJ c 23.7 63 0.0014 23.8 2.1 38 250-288 16-53 (66)
67 PRK14301 chaperone protein Dna 23.5 52 0.0011 32.7 2.0 65 223-312 145-209 (373)
68 PRK03564 formate dehydrogenase 23.2 76 0.0016 31.0 3.0 72 223-309 188-261 (309)
69 PRK04023 DNA polymerase II lar 22.9 68 0.0015 36.2 2.9 12 179-190 625-636 (1121)
70 KOG2673 Uncharacterized conser 22.4 47 0.001 34.1 1.5 19 251-269 130-148 (485)
71 KOG0107 Alternative splicing f 22.3 43 0.00094 30.4 1.1 14 303-316 103-116 (195)
72 TIGR01562 FdhE formate dehydro 22.0 57 0.0012 31.8 2.0 49 181-234 185-236 (305)
73 PRK03564 formate dehydrogenase 21.9 65 0.0014 31.5 2.3 73 180-258 187-261 (309)
74 PRK14279 chaperone protein Dna 21.7 54 0.0012 32.8 1.8 65 223-312 174-238 (392)
75 KOG2879 Predicted E3 ubiquitin 21.6 70 0.0015 30.9 2.4 56 239-311 229-287 (298)
76 PRK14559 putative protein seri 21.6 1.1E+02 0.0024 32.9 4.1 7 205-211 3-9 (645)
77 COG3058 FdhE Uncharacterized p 21.6 19 0.00041 34.8 -1.4 15 301-315 226-240 (308)
78 PRK14282 chaperone protein Dna 20.7 83 0.0018 31.1 2.8 23 39-61 15-37 (369)
79 TIGR01562 FdhE formate dehydro 20.4 96 0.0021 30.2 3.1 71 223-309 185-261 (305)
80 PF08271 TF_Zn_Ribbon: TFIIB z 20.2 31 0.00067 23.3 -0.2 9 300-308 19-27 (43)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.94 E-value=4.1e-27 Score=202.68 Aligned_cols=133 Identities=32% Similarity=0.824 Sum_probs=111.8
Q ss_pred cccccccccCccccccccc----ccCCCCcccccCCCCCcccCCCC------ccccccccCCCCCCCCCCCCCCCCCCCc
Q 021122 181 QTCYNCGEEGHMAVNCRSA----VKRKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~----~~~~~~C~~CG~~GH~a~~Cp~~------~~C~~C~~~GH~ar~Cp~~~~~~~~~~~ 250 (317)
+.||+|++.||++++||.. ......||+|+..||++++||.. ..|++|++.||++++||+.... ....
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~--~~~~ 78 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPG--SGPR 78 (148)
T ss_pred CcCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccC--CCCc
Confidence 4699999999999999973 12346899999999999999974 3699999999999999997643 2457
Q ss_pred ccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc--ccCCCCCCCCCccccCCCCCCcccCCC
Q 021122 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC--CVNISDAVPGEVSCFRCGQLGHTGLVS 316 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~--C~~~~~~~~~~~~C~~Cg~~GH~~~d~ 316 (317)
.||+|++.||++++||..+.. ......||+|++.||++ |+.........++||+|++.|||+.|+
T Consensus 79 ~C~~Cg~~GH~~~~C~~~~~~-~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dC 145 (148)
T PTZ00368 79 SCYNCGQTGHISRECPNRAKG-GAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDC 145 (148)
T ss_pred ccCcCCCCCcccccCCCcccc-cccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccC
Confidence 899999999999999997643 33567899999999999 776544455678999999999999986
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.84 E-value=5.8e-21 Score=164.48 Aligned_cols=109 Identities=34% Similarity=0.814 Sum_probs=92.2
Q ss_pred CccccccccccCccccccccccc--CCCCcccccCCCCCcccCCCC------ccccccccCCCCCCCCCCCCCCCCCCCc
Q 021122 179 GWQTCYNCGEEGHMAVNCRSAVK--RKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (317)
Q Consensus 179 ~~~~C~~CG~~GH~a~~Cp~~~~--~~~~C~~CG~~GH~a~~Cp~~------~~C~~C~~~GH~ar~Cp~~~~~~~~~~~ 250 (317)
+...||+|++.||++++||.+.. ....|++|+..||++++||.. ..|++|++.||++++||+.... .....
T Consensus 26 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~-~~~~~ 104 (148)
T PTZ00368 26 KARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKG-GAARR 104 (148)
T ss_pred CCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcccc-cccch
Confidence 45789999999999999998621 345799999999999999874 3799999999999999997643 33457
Q ss_pred ccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc
Q 021122 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC 289 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~ 289 (317)
.||+|++.||++++||..|.. ....++||+|++.|||+
T Consensus 105 ~C~~Cg~~gH~~~~C~~~~~~-~~~~~~C~~Cg~~gH~~ 142 (148)
T PTZ00368 105 ACYNCGGEGHISRDCPNAGKR-PGGDKTCYNCGQTGHLS 142 (148)
T ss_pred hhcccCcCCcchhcCCCcccc-CCCCCccccCCCcCccc
Confidence 899999999999999997643 23567999999999998
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.83 E-value=3.2e-21 Score=171.27 Aligned_cols=122 Identities=28% Similarity=0.749 Sum_probs=103.4
Q ss_pred cCccccccccccCcccccccccccCCCCcccccCCCCCcccCCCCccccccccCCCCCCCC-CCCCCCCCCCCcccCCCC
Q 021122 178 RGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDC-PDKHKSGFQNAQVCLKCG 256 (317)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~C-p~~~~~~~~~~~~C~~Cg 256 (317)
.....||+||+.||++++||. .+|++|...||.+..||....|++|++.||++++| |.++. ...|+.|+
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP~-----~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~-----~~~C~~C~ 127 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCPH-----SICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQ-----QKSCFDCN 127 (190)
T ss_pred ccccccchhcccCcccccCCh-----hHhhhcCCCCcccccCCcccccccccccCccccccCccccc-----CcceeccC
Confidence 345789999999999999995 48999977999999999988999999999999999 66654 56999999
Q ss_pred CCCcCCCCCCCCCCCCCcc-------CccccccCCCCcCc--ccCCCCCCCCCccccCCCCCCccc
Q 021122 257 DSGHDMFSCRNSYSLDDLK-------EVQCYICRCFGHLC--CVNISDAVPGEVSCFRCGQLGHTG 313 (317)
Q Consensus 257 ~~GH~a~dCp~~~~~~~~~-------~~~C~~Cg~~GHl~--C~~~~~~~~~~~~C~~Cg~~GH~~ 313 (317)
..+|.+.+||..|+.|.+. .+.||+|+..||++ |..++.. +-. |.|+..+|+.
T Consensus 128 s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s--~~~--~~~~~~~~~~ 189 (190)
T COG5082 128 STRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSS--RVP--YVCGKKGYVS 189 (190)
T ss_pred CCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCccc--ccc--ccccccccCC
Confidence 9999999999999988766 78899999999998 5433332 112 8888888764
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.72 E-value=4.2e-18 Score=151.41 Aligned_cols=101 Identities=32% Similarity=0.759 Sum_probs=88.5
Q ss_pred CCCCcccccCCCCCcccCCCCccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCC-CCCCCCCCccCcccc
Q 021122 202 RKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSC-RNSYSLDDLKEVQCY 280 (317)
Q Consensus 202 ~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dC-p~~~~~~~~~~~~C~ 280 (317)
....|++||+.||..++|| ..+|++|...||.+..||.. +.||+||+.||++++| |..|. ...|+
T Consensus 59 ~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~--------~~C~~Cg~~GH~~~dC~P~~~~-----~~~C~ 124 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKP--------KKCYNCGETGHLSRDCNPSKDQ-----QKSCF 124 (190)
T ss_pred cccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcc--------cccccccccCccccccCccccc-----Cccee
Confidence 3458999999999999999 69999999999999999983 7999999999999999 77664 35999
Q ss_pred ccCCCCcCc--ccCCCCCC--------CCCccccCCCCCCcccCCC
Q 021122 281 ICRCFGHLC--CVNISDAV--------PGEVSCFRCGQLGHTGLVS 316 (317)
Q Consensus 281 ~Cg~~GHl~--C~~~~~~~--------~~~~~C~~Cg~~GH~~~d~ 316 (317)
.|+..+|++ |+..++.+ +..+.||+|+..|||+.|+
T Consensus 125 ~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc 170 (190)
T COG5082 125 DCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDC 170 (190)
T ss_pred ccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCC
Confidence 999999999 77666543 2368999999999999986
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.51 E-value=3.1e-14 Score=133.34 Aligned_cols=99 Identities=36% Similarity=0.832 Sum_probs=65.8
Q ss_pred ccccccccccCcccccccccccCCCCcccccCCCCCcccCCCC-------ccccccccCCCCCCCCCCCCCCCCCCCccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKA-------QDCFICKKGGHRAKDCPDKHKSGFQNAQVC 252 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~-------~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C 252 (317)
...|+.|+..||.+..|+. ....|++|+..||+.++|+.. ..|+.|...||+. |+............|
T Consensus 72 ~~~c~~~g~~~~~~~~~~~---~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~--~~~~~~~~~~~~~~C 146 (261)
T KOG4400|consen 72 EVSCYICGEKGHLGRRCTR---IAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRG--CPDADPVDGPKPAKC 146 (261)
T ss_pred CceeeecCCCCchhhcCcc---cchhhhhCCCCccchhhCCcccCcccccceeeccCCCcccc--CcccccccCCCCCcc
Confidence 3568888888888777765 235678888888888887751 1467778888877 333221111222568
Q ss_pred CCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc
Q 021122 253 LKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC 289 (317)
Q Consensus 253 ~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~ 289 (317)
|+||+.||+.++||.. ....||.|+..||+.
T Consensus 147 y~Cg~~GH~s~~C~~~------~~~~c~~c~~~~h~~ 177 (261)
T KOG4400|consen 147 YSCGEQGHISDDCPEN------KGGTCFRCGKVGHGS 177 (261)
T ss_pred CCCCcCCcchhhCCCC------CCCccccCCCcceec
Confidence 8888888888888754 346788888888876
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.46 E-value=1.2e-13 Score=129.46 Aligned_cols=131 Identities=27% Similarity=0.598 Sum_probs=99.1
Q ss_pred ccccccccccCcccccccccccC---CCCcccccCCCCCc-ccCC-----CCccccccccCCCCCCCCCCCCCCCCCCCc
Q 021122 180 WQTCYNCGEEGHMAVNCRSAVKR---KKPCFVCGSLEHGV-RQCS-----KAQDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~~~~---~~~C~~CG~~GH~a-~~Cp-----~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~ 250 (317)
...||+|++.||++++||..... ...|+.|+..||.. .++. ....||.|++.||+.++||++ ...
T Consensus 92 ~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~------~~~ 165 (261)
T KOG4400|consen 92 AAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN------KGG 165 (261)
T ss_pred chhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC------CCC
Confidence 47899999999999999986321 34689999999999 3332 124699999999999999986 247
Q ss_pred ccCCCCCCCcCCCCCCCCCCCCCcc------CccccccCCCCcCc--ccCCCCCCCCCccccCCCCCCcccCCCC
Q 021122 251 VCLKCGDSGHDMFSCRNSYSLDDLK------EVQCYICRCFGHLC--CVNISDAVPGEVSCFRCGQLGHTGLVSW 317 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~~~~~~~~~------~~~C~~Cg~~GHl~--C~~~~~~~~~~~~C~~Cg~~GH~~~d~~ 317 (317)
.||.|++.||..++||..+...... .-.|+ +...+|+. +........-...||+++..+|.+.++|
T Consensus 166 ~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 (261)
T KOG4400|consen 166 TCFRCGKVGHGSRDCPSKQKSKSKQGGQRKGFGACY-DYPQGHKQRACGGSGPDDNFNDSCYNKLSSGKLDQDCK 239 (261)
T ss_pred ccccCCCcceecccCCccccccccCcccccccccCc-cccccccccccCCCCcccccccccccccccccccchhh
Confidence 9999999999999999987643221 22344 55788886 3222223335789999999999988775
No 7
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.82 E-value=5e-10 Score=111.48 Aligned_cols=133 Identities=23% Similarity=0.389 Sum_probs=93.0
Q ss_pred EeecCCCCCCCcchhhhhccchhhHHHHHHhhhhhhhhhhc------cccc--ceEEeec-hhhhhhhccCccccc----
Q 021122 87 EAVVPGPSGTTDDVIIEDVKSSDKKRIRVRKKKKKEADKIE------IEDQ--SVIVRKE-EQKVETADNGDEGVT---- 153 (317)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~k~~~~~~~~~kk~~k~~~~k~~------i~~q--~v~via~-ee~lee~~~A~e~v~---- 153 (317)
|.+--+|. -++.+--+++.++||.||||+++||++..++ -+++ +..|.|+ +|.++..+...+.|.
T Consensus 155 vGLiiGPR--G~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av 232 (554)
T KOG0119|consen 155 VGLIIGPR--GNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAV 232 (554)
T ss_pred eEEEecCC--ccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhc
Confidence 44555664 5678888899999999999999999985544 2333 4455555 444444333333332
Q ss_pred cccchhhHHHhhhcCCC-CCCCCC-CcCccccccccccCcccccccccc-cCCCCcccccCCCCCcccCCC
Q 021122 154 TVEISDNIVLRKLLRGP-RYFDPP-DRGWQTCYNCGEEGHMAVNCRSAV-KRKKPCFVCGSLEHGVRQCSK 221 (317)
Q Consensus 154 ~~~~~~n~~~R~~~r~~-r~f~~~-~~~~~~C~~CG~~GH~a~~Cp~~~-~~~~~C~~CG~~GH~a~~Cp~ 221 (317)
.++.++|.+.+.++++- +.++.. +.....|.+||..||...+||... .....|+.||..||++.+|..
T Consensus 233 ~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~ 303 (554)
T KOG0119|consen 233 SVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKV 303 (554)
T ss_pred cCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCC
Confidence 45667788888887773 444443 345589999999999999999862 122379999999999999975
No 8
>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=97.78 E-value=1.1e-05 Score=45.91 Aligned_cols=17 Identities=53% Similarity=1.372 Sum_probs=14.0
Q ss_pred ccccccccCcccccccc
Q 021122 182 TCYNCGEEGHMAVNCRS 198 (317)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~ 198 (317)
.||+|++.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 58888888888888874
No 9
>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=97.70 E-value=2.5e-05 Score=44.48 Aligned_cols=16 Identities=38% Similarity=1.037 Sum_probs=10.8
Q ss_pred ccCCCCCCCcCCCCCC
Q 021122 251 VCLKCGDSGHDMFSCR 266 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp 266 (317)
.||+|++.||++++||
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4666666666666666
No 10
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.24 E-value=0.002 Score=41.96 Aligned_cols=21 Identities=33% Similarity=0.816 Sum_probs=18.1
Q ss_pred CCCcccCCCCCCCcCCCCCCC
Q 021122 247 QNAQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 247 ~~~~~C~~Cg~~GH~a~dCp~ 267 (317)
.....|++|++.||+..+||.
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCCEeecCCCCCccHhHCCC
Confidence 346789999999999999997
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.17 E-value=0.0095 Score=38.80 Aligned_cols=22 Identities=32% Similarity=0.785 Sum_probs=17.2
Q ss_pred CCCccccccccCCCCCCCCCCC
Q 021122 220 SKAQDCFICKKGGHRAKDCPDK 241 (317)
Q Consensus 220 p~~~~C~~C~~~GH~ar~Cp~~ 241 (317)
|....|++|++.||+.++||..
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCCEeecCCCCCccHhHCCCC
Confidence 3456788888888888888874
No 12
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=94.77 E-value=0.013 Score=40.56 Aligned_cols=19 Identities=32% Similarity=0.908 Sum_probs=16.6
Q ss_pred ccccccccccCcccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRS 198 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~ 198 (317)
...|.+|++.|||.++|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4679999999999999994
No 13
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.97 E-value=0.053 Score=37.49 Aligned_cols=19 Identities=42% Similarity=0.957 Sum_probs=16.7
Q ss_pred CcccCCCCCCCcCCCCCCC
Q 021122 249 AQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 249 ~~~C~~Cg~~GH~a~dCp~ 267 (317)
...|.+|++.||+..+||+
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4689999999999999994
No 14
>smart00343 ZnF_C2HC zinc finger.
Probab=92.83 E-value=0.045 Score=33.42 Aligned_cols=17 Identities=59% Similarity=1.458 Sum_probs=13.8
Q ss_pred ccccccccCcccccccc
Q 021122 182 TCYNCGEEGHMAVNCRS 198 (317)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~ 198 (317)
.|++||+.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 38888888888888874
No 15
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.71 E-value=0.082 Score=53.86 Aligned_cols=43 Identities=33% Similarity=0.800 Sum_probs=33.3
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
..|.+|+..||...+||.... .....|..|+..||++.||+..
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~---~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIP---NTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCCccccccCCcccc---cccccccccCCcccccccCCCc
Confidence 578889999998889988621 1123899999999999999865
No 16
>smart00343 ZnF_C2HC zinc finger.
Probab=91.60 E-value=0.091 Score=32.05 Aligned_cols=17 Identities=35% Similarity=0.905 Sum_probs=14.2
Q ss_pred ccCCCCCCCcCCCCCCC
Q 021122 251 VCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~ 267 (317)
.|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48889999999999984
No 17
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=89.63 E-value=0.091 Score=50.46 Aligned_cols=36 Identities=31% Similarity=0.588 Sum_probs=25.2
Q ss_pred hhcCCCCCCCCC-CcCccccccccccCcccccccccc
Q 021122 165 KLLRGPRYFDPP-DRGWQTCYNCGEEGHMAVNCRSAV 200 (317)
Q Consensus 165 ~~~r~~r~f~~~-~~~~~~C~~CG~~GH~a~~Cp~~~ 200 (317)
.++...|....+ -++.-.||.||++|||+.+||...
T Consensus 144 vq~stsrlrtapgmgDq~~cyrcGkeghwskEcP~~~ 180 (346)
T KOG0109|consen 144 VQLSTSRLRTAPGMGDQSGCYRCGKEGHWSKECPVDR 180 (346)
T ss_pred eeeeccccccCCCCCCHHHheeccccccccccCCccC
Confidence 344444444333 344568999999999999999863
No 18
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.77 E-value=0.62 Score=47.36 Aligned_cols=69 Identities=25% Similarity=0.374 Sum_probs=44.9
Q ss_pred CCCCCCCcCccccccccccCcccccccccccCCCCcccccCCCCCcccCCC------CccccccccCCCCCCCCCCC
Q 021122 171 RYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK------AQDCFICKKGGHRAKDCPDK 241 (317)
Q Consensus 171 r~f~~~~~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~------~~~C~~C~~~GH~ar~Cp~~ 241 (317)
.|...+......++.++..||..+.+... ....|.+|-..+|+...|.. ...|++|...||+...||..
T Consensus 103 ~~~~~~~p~~q~~~~~~~~~~~~~~~t~~--~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 103 GYGRGPPPLIQMNGRMGGRGFGMRRQTPP--PGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred ccCCCCcchhhhccccccCCcccccCCCc--ccceeeecccCccccccccccCCCCCCcceecCCCCCccceecccc
Confidence 44434444556899999999998888543 34567777777777777654 23566666666666666553
No 19
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.92 E-value=0.73 Score=46.83 Aligned_cols=61 Identities=21% Similarity=0.402 Sum_probs=33.5
Q ss_pred CcccccCCCCCcccCCC--CccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCC
Q 021122 205 PCFVCGSLEHGVRQCSK--AQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 205 ~C~~CG~~GH~a~~Cp~--~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~ 267 (317)
.+..++..||..+.+.. ...|..|...+|+...|..... +.-...|++|+..|||...||.
T Consensus 114 ~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~--Pppsy~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 114 MNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGS--PPPSYKCVKCPTPGPWIKACPT 176 (448)
T ss_pred hccccccCCcccccCCCcccceeeecccCccccccccccCC--CCCCcceecCCCCCccceeccc
Confidence 45555666666555543 2346666666666655554332 2334556666666666666654
No 20
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=86.57 E-value=0.31 Score=33.34 Aligned_cols=18 Identities=44% Similarity=0.927 Sum_probs=13.2
Q ss_pred cccccccccCccc--ccccc
Q 021122 181 QTCYNCGEEGHMA--VNCRS 198 (317)
Q Consensus 181 ~~C~~CG~~GH~a--~~Cp~ 198 (317)
++|.+||.+||.+ +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 4688888888886 44665
No 21
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.53 E-value=0.28 Score=47.32 Aligned_cols=22 Identities=32% Similarity=0.827 Sum_probs=18.8
Q ss_pred CCCcccCCCCCCCcCCCCCCCC
Q 021122 247 QNAQVCLKCGDSGHDMFSCRNS 268 (317)
Q Consensus 247 ~~~~~C~~Cg~~GH~a~dCp~~ 268 (317)
.....||+||+.|||...||..
T Consensus 174 PpgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 174 PPGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CCceeEEecCCCCchhhcCCCC
Confidence 3467899999999999999863
No 22
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.34 E-value=0.34 Score=46.78 Aligned_cols=24 Identities=38% Similarity=0.891 Sum_probs=20.0
Q ss_pred CCcCccccccccccCccccccccc
Q 021122 176 PDRGWQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 176 ~~~~~~~C~~CG~~GH~a~~Cp~~ 199 (317)
++..+-.||+||+.|||..+||..
T Consensus 172 ppPpgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 172 PPPPGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CCCCceeEEecCCCCchhhcCCCC
Confidence 334457899999999999999975
No 23
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=85.19 E-value=0.23 Score=45.75 Aligned_cols=127 Identities=16% Similarity=0.077 Sum_probs=72.5
Q ss_pred ccccHHHHHHHHHHhhhhcCCCCCCCceeecCCCCCCCCCCCCCCCCceEeecCCCCCCCcchhhhhccchhhHHHHHHh
Q 021122 38 EDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNTSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIRVRK 117 (317)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~kk 117 (317)
||--|+|+|.||.|-.--...||.-+--+. .+..---...--+.-.|.+--||... +..--+..|.+||+|||+.
T Consensus 119 eder~~l~era~k~lp~fv~p~dy~rpsk~---q~KiYIPV~eyPe~NFVGLliGPRG~--Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 119 EDERLWLKERAQKILPRFVLPNDYIRPSKY---QNKIYIPVQEYPESNFVGLLIGPRGS--TLKQLERISRAKIAIRGSG 193 (269)
T ss_pred hHHHHHHHHHHHHhcCcccCCccccCcccc---cceEEeehhhCcccceeEEEecCCcc--hHHHHHHHhCCeEEEeccc
Confidence 444599999998886555555554221000 00000000000134456677777644 4455667799999999999
Q ss_pred hhhhhhhhhcccc----c----ceEEeec-hhhhhhhccCccccc----cccchhhHHHhhhcCC
Q 021122 118 KKKKEADKIEIED----Q----SVIVRKE-EQKVETADNGDEGVT----TVEISDNIVLRKLLRG 169 (317)
Q Consensus 118 ~~k~~~~k~~i~~----q----~v~via~-ee~lee~~~A~e~v~----~~~~~~n~~~R~~~r~ 169 (317)
++|+.+...+... . +--|+++ ++.+.++++....+. ..|.++|.+.|.+++.
T Consensus 194 svKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~ 258 (269)
T COG5176 194 SVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRW 258 (269)
T ss_pred ccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhcCCcccchHHHHHHHH
Confidence 9998877766311 1 1123444 555555555544433 6677788887777653
No 24
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=84.02 E-value=0.37 Score=33.94 Aligned_cols=17 Identities=35% Similarity=1.050 Sum_probs=15.5
Q ss_pred cccccccccCccccccc
Q 021122 181 QTCYNCGEEGHMAVNCR 197 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp 197 (317)
..|++||..||...+||
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 45999999999999997
No 25
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=83.84 E-value=0.57 Score=45.15 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=18.3
Q ss_pred CCcccCCCCCCCcCCCCCCCCCC
Q 021122 248 NAQVCLKCGDSGHDMFSCRNSYS 270 (317)
Q Consensus 248 ~~~~C~~Cg~~GH~a~dCp~~~~ 270 (317)
....||+||+.|||+++||....
T Consensus 159 Dq~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred CHHHheeccccccccccCCccCC
Confidence 45678999999999999987654
No 26
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=82.91 E-value=0.48 Score=33.37 Aligned_cols=18 Identities=33% Similarity=0.918 Sum_probs=12.4
Q ss_pred CcccCCCCCCCcCCCCCC
Q 021122 249 AQVCLKCGDSGHDMFSCR 266 (317)
Q Consensus 249 ~~~C~~Cg~~GH~a~dCp 266 (317)
...|++||..||...+||
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 356777777777777776
No 27
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=81.72 E-value=0.7 Score=30.87 Aligned_cols=19 Identities=42% Similarity=0.789 Sum_probs=11.3
Q ss_pred cccccccccCccccccccc
Q 021122 181 QTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~ 199 (317)
..|++|++..||+.+|...
T Consensus 3 ~~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSK 21 (36)
T ss_dssp -C-TTTSSSCS-TTT---T
T ss_pred ccCcccCCCcchhhhhhhh
Confidence 4699999999999999764
No 28
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=79.91 E-value=0.93 Score=31.05 Aligned_cols=13 Identities=46% Similarity=1.094 Sum_probs=8.7
Q ss_pred ccccccCCCCcCc
Q 021122 277 VQCYICRCFGHLC 289 (317)
Q Consensus 277 ~~C~~Cg~~GHl~ 289 (317)
+.|.+||+.||..
T Consensus 2 ~kC~~CG~~GH~~ 14 (40)
T PF15288_consen 2 VKCKNCGAFGHMR 14 (40)
T ss_pred ccccccccccccc
Confidence 4577777777773
No 29
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=77.63 E-value=1.6 Score=29.13 Aligned_cols=20 Identities=30% Similarity=0.655 Sum_probs=12.0
Q ss_pred cccCCCCCCCcCCCCCCCCC
Q 021122 250 QVCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 250 ~~C~~Cg~~GH~a~dCp~~~ 269 (317)
..|.+|++..|++.+|...+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 47899999999999997654
No 30
>smart00816 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens.
Probab=70.87 E-value=2.9 Score=28.77 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=22.4
Q ss_pred ccCCCCcCcccCCCCCCCCCccccC
Q 021122 281 ICRCFGHLCCVNISDAVPGEVSCFR 305 (317)
Q Consensus 281 ~Cg~~GHl~C~~~~~~~~~~~~C~~ 305 (317)
+||+.+-+.|..|.+-||=+++||-
T Consensus 11 ~CGekr~YCcSdpGrYCpwqvVCYe 35 (45)
T smart00816 11 NCGEKRKYCCSDPGRYCPWQVVCYE 35 (45)
T ss_pred cccccCccccCCCcccCCceEEEee
Confidence 8999999999989888999999983
No 31
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=67.15 E-value=1.7 Score=38.10 Aligned_cols=20 Identities=25% Similarity=0.707 Sum_probs=18.0
Q ss_pred ccccccccccCccccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (317)
.++|.+|.+.|||.++|.+.
T Consensus 27 ~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred chhHHHHHhhccceeeecCc
Confidence 46899999999999999875
No 32
>PF03913 Amb_V_allergen: Amb V Allergen; InterPro: IPR005611 Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens [].; PDB: 2BBG_A 3BBG_A 1BBG_A.
Probab=57.21 E-value=5 Score=27.48 Aligned_cols=25 Identities=28% Similarity=0.675 Sum_probs=15.8
Q ss_pred ccCCCCcCcccCCCCCCCCCccccC
Q 021122 281 ICRCFGHLCCVNISDAVPGEVSCFR 305 (317)
Q Consensus 281 ~Cg~~GHl~C~~~~~~~~~~~~C~~ 305 (317)
+||+.+-+.|..|.+-||=.++||-
T Consensus 10 ~CGekr~YCcSdpGrYCpwqvVCYe 34 (44)
T PF03913_consen 10 ICGEKRAYCCSDPGRYCPWQVVCYE 34 (44)
T ss_dssp TTS-TTSEEE-SSSSS-----EEES
T ss_pred cccccCCeecCCCcccccceeeeec
Confidence 7999999999888888999999984
No 33
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=55.71 E-value=3 Score=36.68 Aligned_cols=60 Identities=27% Similarity=0.516 Sum_probs=30.7
Q ss_pred CCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCC--CCcCcccC---CCCCCCCCccccCC
Q 021122 232 GHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRC--FGHLCCVN---ISDAVPGEVSCFRC 306 (317)
Q Consensus 232 GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~--~GHl~C~~---~~~~~~~~~~C~~C 306 (317)
||...+.-.... ......|..||... ... |.+|+. .|++-.+- .......|.+|++|
T Consensus 13 GH~~t~~~~~~p--~~~~~fC~kCG~~t--I~~--------------Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~C 74 (158)
T PF10083_consen 13 GHVITDSYDKNP--ELREKFCSKCGAKT--ITS--------------CPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNC 74 (158)
T ss_pred ccccccccccCc--hHHHHHHHHhhHHH--HHH--------------CcCCCCCCCCceecCCeeeeCCCCCCChhHHhC
Confidence 676666544321 12245677777752 233 444443 24432110 01233468999999
Q ss_pred CCC
Q 021122 307 GQL 309 (317)
Q Consensus 307 g~~ 309 (317)
|.+
T Consensus 75 Gkp 77 (158)
T PF10083_consen 75 GKP 77 (158)
T ss_pred CCC
Confidence 975
No 34
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=46.26 E-value=13 Score=40.46 Aligned_cols=40 Identities=20% Similarity=0.442 Sum_probs=27.3
Q ss_pred CCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcC
Q 021122 248 NAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHL 288 (317)
Q Consensus 248 ~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl 288 (317)
....|+.||+.||.+.+|....+........+.. ..+.||
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~-~~ek~f 298 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEGKPRLGETNELADVP-GVEKPF 298 (931)
T ss_pred CcccchhhcccCCcHhhcCCcCCcccccccccCc-ccccce
Confidence 3567999999999999998765544445555666 445555
No 35
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=42.54 E-value=7.2 Score=34.25 Aligned_cols=22 Identities=27% Similarity=0.727 Sum_probs=15.7
Q ss_pred CCccccccccCCCCCCCCCCCC
Q 021122 221 KAQDCFICKKGGHRAKDCPDKH 242 (317)
Q Consensus 221 ~~~~C~~C~~~GH~ar~Cp~~~ 242 (317)
..+.|..|.+.|||..+|.+++
T Consensus 26 ~~~rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 26 SSARCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred cchhHHHHHhhccceeeecCce
Confidence 3457777778888877777654
No 36
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.04 E-value=37 Score=36.94 Aligned_cols=48 Identities=25% Similarity=0.434 Sum_probs=24.8
Q ss_pred CCCcccCCCCCCCcCCCCCCCCCCC--C--CccCccccccCCCCcCcccCCCCCCCCCccccCCCCC
Q 021122 247 QNAQVCLKCGDSGHDMFSCRNSYSL--D--DLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQL 309 (317)
Q Consensus 247 ~~~~~C~~Cg~~GH~a~dCp~~~~~--~--~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~ 309 (317)
.....|..||-. ..||+-... + ......|..||.... .+..|.+||..
T Consensus 433 s~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~-----------~p~~Cp~Cgs~ 484 (730)
T COG1198 433 APLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQEP-----------IPQSCPECGSE 484 (730)
T ss_pred cceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCCCC-----------CCCCCCCCCCC
Confidence 344556666543 456653211 1 124556766665432 25667777766
No 37
>PF07708 Tash_PEST: Tash protein PEST motif; InterPro: IPR011695 The PEST motif is found in one or more copies in Tash AT-hook proteins from Theileria annulata. Tash proteins are transported to the host nucleus and are thought to be involved in pathogenesis []. The PEST motif is often found in conjunction with the (IPR007480 from INTERPRO), whose function is unknown. These repeats may be part of the PEST motif (a signal for rapid proteolytic degradation) [], though this is not proven. This motif is also found in other T. annulata proteins, which have no other known domains.
Probab=36.69 E-value=16 Score=21.14 Aligned_cols=15 Identities=33% Similarity=0.415 Sum_probs=11.6
Q ss_pred hhccceeeeecCccc
Q 021122 21 EKLKSAAAMSSDDEE 35 (317)
Q Consensus 21 ~~~~~~~~~~~~~~~ 35 (317)
++.+..++++||||+
T Consensus 4 ePEti~vEi~SDeee 18 (19)
T PF07708_consen 4 EPETIPVEIGSDEEE 18 (19)
T ss_pred CCceEEEEecccccC
Confidence 355778899998886
No 38
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.22 E-value=25 Score=20.97 Aligned_cols=9 Identities=33% Similarity=0.800 Sum_probs=4.5
Q ss_pred CccccCCCC
Q 021122 300 EVSCFRCGQ 308 (317)
Q Consensus 300 ~~~C~~Cg~ 308 (317)
..+|.+||.
T Consensus 13 ~~fC~~CG~ 21 (23)
T PF13240_consen 13 AKFCPNCGT 21 (23)
T ss_pred CcchhhhCC
Confidence 444555553
No 39
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=34.47 E-value=27 Score=37.06 Aligned_cols=86 Identities=27% Similarity=0.522 Sum_probs=46.4
Q ss_pred cccccccccCcccccccccccCCCCcccccCCCCCcccCCC----------------CccccccccCCCC--CCCCCCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK----------------AQDCFICKKGGHR--AKDCPDKH 242 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~----------------~~~C~~C~~~GH~--ar~Cp~~~ 242 (317)
..|..|+..||... ....|..|+..|.....-|. ..-|-.|...|-. ...||.-.
T Consensus 3 ~~C~~C~g~G~i~v-------~~e~c~vc~gtG~~~~~d~k~~~~~~~~~~D~~~~~~~pc~~c~gkG~V~v~~~c~~c~ 75 (715)
T COG1107 3 KKCPECGGKGKIVV-------GEEECPVCHGTGFSDDFDPKGVANLSRETVDLFASFEIPCPKCRGKGTVTVYDTCPECG 75 (715)
T ss_pred ccccccCCCceEee-------eeeecccccccccccccChhhhhhhhhccccccccCCCCCCeeccceeEEEEeecccCC
Confidence 46899999888722 23457778877766444331 2356667666642 23444422
Q ss_pred CCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCc
Q 021122 243 KSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGH 287 (317)
Q Consensus 243 ~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GH 287 (317)
|......|..||..=+- | .+..|..|...+|
T Consensus 76 --G~gkv~~c~~cG~~~~~-------~-----~~~lc~~c~~~~~ 106 (715)
T COG1107 76 --GTGKVLTCDICGDIIVP-------W-----EEGLCPECRRKPK 106 (715)
T ss_pred --CceeEEeeccccceecC-------c-----ccccChhHhhCCc
Confidence 12234455555554221 1 1125777777777
No 40
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=34.32 E-value=61 Score=32.04 Aligned_cols=34 Identities=26% Similarity=0.631 Sum_probs=20.8
Q ss_pred cCccccccCCCCcCcccCCCCCCCCCccccCCCCCC
Q 021122 275 KEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLG 310 (317)
Q Consensus 275 ~~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~G 310 (317)
....||+|...|-+-|+..... ..+.|..|...|
T Consensus 233 t~~~C~~C~G~G~~~C~tC~gr--G~k~C~TC~gtg 266 (406)
T KOG2813|consen 233 THDLCYMCHGRGIKECHTCKGR--GKKPCTTCSGTG 266 (406)
T ss_pred ccchhhhccCCCcccCCcccCC--CCcccccccCcc
Confidence 3456777777776655533332 456677776666
No 41
>KOG1059 consensus Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.36 E-value=38 Score=36.83 Aligned_cols=24 Identities=33% Similarity=0.344 Sum_probs=12.9
Q ss_pred hccchhhHHHHHHhhhhhhhhhhc
Q 021122 104 DVKSSDKKRIRVRKKKKKEADKIE 127 (317)
Q Consensus 104 ~~k~~~~~~~~~kk~~k~~~~k~~ 127 (317)
.+++..++.|+..|++++.++++.
T Consensus 837 ~~~~~~e~~i~~~KkKskk~~k~~ 860 (877)
T KOG1059|consen 837 DNLKDTEKVIVIVKKKSKKKNKKK 860 (877)
T ss_pred Hhhhcccccchhhhhhhcccchhh
Confidence 444455666666555555544443
No 42
>PRK14289 chaperone protein DnaJ; Provisional
Probab=32.29 E-value=33 Score=34.06 Aligned_cols=23 Identities=13% Similarity=0.218 Sum_probs=16.0
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|+.-+.+|.+..|.++-+|-|
T Consensus 16 ~a~~~eik~ayr~la~~~HpD~~ 38 (386)
T PRK14289 16 TATVDEIKKAYRKKAIQYHPDKN 38 (386)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCC
Confidence 45555688888888877766654
No 43
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=31.36 E-value=22 Score=30.16 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=16.2
Q ss_pred ccccccccccCccccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (317)
.+.|+.|+ ..||...||-.
T Consensus 106 ~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 106 KVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred eEEeCCCC-CCcccccCCcc
Confidence 47899996 78999999974
No 44
>PLN03086 PRLI-interacting factor K; Provisional
Probab=31.36 E-value=25 Score=37.14 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=14.2
Q ss_pred CcCCCCCCCCCCCCCccCccccccCCCC
Q 021122 259 GHDMFSCRNSYSLDDLKEVQCYICRCFG 286 (317)
Q Consensus 259 GH~a~dCp~~~~~~~~~~~~C~~Cg~~G 286 (317)
-|....||. +...|..|+...
T Consensus 494 ~H~~thCp~-------Kpi~C~fC~~~v 514 (567)
T PLN03086 494 QHQASTCPL-------RLITCRFCGDMV 514 (567)
T ss_pred hhhhccCCC-------CceeCCCCCCcc
Confidence 366667775 457888887654
No 45
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=30.41 E-value=21 Score=35.78 Aligned_cols=19 Identities=21% Similarity=0.176 Sum_probs=12.4
Q ss_pred HHHHHHHHHhhhhcCCCCC
Q 021122 43 KIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~ 61 (317)
.=+.||-|.-|.|.-+|.|
T Consensus 19 ~EIKkAYRkLA~kyHPD~n 37 (371)
T COG0484 19 EEIKKAYRKLAKKYHPDRN 37 (371)
T ss_pred HHHHHHHHHHHHHhCCCCC
Confidence 3456777777777766666
No 46
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=30.38 E-value=24 Score=33.99 Aligned_cols=14 Identities=43% Similarity=0.876 Sum_probs=8.0
Q ss_pred ccccccCCCCcCcc
Q 021122 277 VQCYICRCFGHLCC 290 (317)
Q Consensus 277 ~~C~~Cg~~GHl~C 290 (317)
+.|.-||..||-+|
T Consensus 247 vscsdcgrsghpsc 260 (336)
T KOG1244|consen 247 VSCSDCGRSGHPSC 260 (336)
T ss_pred cchhhcCCCCCcch
Confidence 45555555555554
No 47
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.45 E-value=5.8 Score=37.80 Aligned_cols=49 Identities=27% Similarity=0.421 Sum_probs=20.5
Q ss_pred cccccccccCccccccccc--ccCCCCcccccCCCCCcccCCCCccccccccCCCC
Q 021122 181 QTCYNCGEEGHMAVNCRSA--VKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHR 234 (317)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~--~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ 234 (317)
..|..||..=.++.--... +.+.-.|..|+..-|+. ...|..|+...|.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~-----R~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV-----RIKCPYCGNTDHE 223 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE-------TTS-TTT---SS-
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec-----CCCCcCCCCCCCc
Confidence 5799999876555544432 22444577887766663 3467778777764
No 48
>PRK14298 chaperone protein DnaJ; Provisional
Probab=28.24 E-value=48 Score=32.99 Aligned_cols=23 Identities=26% Similarity=0.245 Sum_probs=14.1
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|..-+.||.+..|.++-+|.|
T Consensus 16 ~a~~~eik~ayr~la~~~HPD~~ 38 (377)
T PRK14298 16 DASVEDIKKAYRKLAMKYHPDKN 38 (377)
T ss_pred CCCHHHHHHHHHHHHHHhCcccc
Confidence 33444567777777777665544
No 49
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=28.18 E-value=48 Score=32.41 Aligned_cols=23 Identities=26% Similarity=0.187 Sum_probs=15.7
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|...+.+|.+..|.++-+|-+
T Consensus 11 ~a~~~~ik~ayr~la~~~HPD~~ 33 (354)
T TIGR02349 11 DASEEEIKKAYRKLAKKYHPDRN 33 (354)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCC
Confidence 45667788887777777665544
No 50
>PF12773 DZR: Double zinc ribbon
Probab=27.36 E-value=93 Score=21.25 Aligned_cols=10 Identities=20% Similarity=0.345 Sum_probs=6.1
Q ss_pred CccccccCCC
Q 021122 276 EVQCYICRCF 285 (317)
Q Consensus 276 ~~~C~~Cg~~ 285 (317)
.++|.+|+..
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 4566677664
No 51
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.08 E-value=60 Score=33.57 Aligned_cols=23 Identities=26% Similarity=0.662 Sum_probs=14.0
Q ss_pred CccccccCCCCcCcccCCCCCCCCCccccCCCCC
Q 021122 276 EVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQL 309 (317)
Q Consensus 276 ~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~ 309 (317)
...|..||.. .+-+..|.+||..
T Consensus 240 ~l~Ch~Cg~~-----------~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 240 KLRCHYCGYQ-----------EPIPKTCPQCGSE 262 (505)
T ss_pred eEEcCCCcCc-----------CCCCCCCCCCCCC
Confidence 4567777642 2235678888763
No 52
>PRK14296 chaperone protein DnaJ; Provisional
Probab=26.96 E-value=43 Score=33.21 Aligned_cols=67 Identities=18% Similarity=0.512 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCcc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVS 302 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~ 302 (317)
..|..|...|-.....+. .|..|+..|.....-.... ..-.....|..|+..|-+. ...
T Consensus 150 ~~C~~C~G~G~~~~~~~~----------~C~~C~G~G~~~~~~~~g~-~~~q~~~~C~~C~G~G~~~----------~~~ 208 (372)
T PRK14296 150 TNCSKCFGSGAESNSDIH----------ICNNCHGTGEVLVQKNMGF-FQFQQSAKCNVCNGAGKII----------KNK 208 (372)
T ss_pred eccCCCCCCccCCCCCCc----------cCCCCCCCceEEEEEeccc-eEEEEEecCCCcCCcceee----------ccc
Q ss_pred ccCCCCCC
Q 021122 303 CFRCGQLG 310 (317)
Q Consensus 303 C~~Cg~~G 310 (317)
|..|...|
T Consensus 209 C~~C~G~g 216 (372)
T PRK14296 209 CKNCKGKG 216 (372)
T ss_pred ccCCCCce
No 53
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=26.52 E-value=33 Score=35.64 Aligned_cols=56 Identities=21% Similarity=0.286 Sum_probs=31.4
Q ss_pred cccchhhhhhccceeeeec-CcccccccccHHHHHHHHHHhhhhcCCCCCCCceeecCCCCCCC
Q 021122 13 HEENGEEEEKLKSAAAMSS-DDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTNT 75 (317)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 75 (317)
..+++|+.|++-+.--++. |||||.+-- +--.|.-|-..-.++++..|+|-+..++
T Consensus 86 ~~de~e~~e~~~~~~~l~~~~~de~~~~p-------~p~~k~~k~~k~~d~fs~~l~d~~~eed 142 (807)
T KOG0066|consen 86 WSDEDEKPEKSLPANDLDDEDDDEAAKKP-------QPSKKNKKNKKKNDDFSLDLDDLDNEED 142 (807)
T ss_pred CCccccchhhcCcccccCCCCchhhhcCC-------CCCccccccccCCCccceeccccccccc
Confidence 4444555667777777776 556652211 1123444556667888888866544443
No 54
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=26.35 E-value=34 Score=28.98 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=13.8
Q ss_pred CCcccCCCCCCCcCCCCCCC
Q 021122 248 NAQVCLKCGDSGHDMFSCRN 267 (317)
Q Consensus 248 ~~~~C~~Cg~~GH~a~dCp~ 267 (317)
....|+.|+ ..||...||.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPY 123 (128)
T ss_pred ceEEeCCCC-CCcccccCCc
Confidence 346788885 7788888874
No 55
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.43 E-value=1.2e+02 Score=30.09 Aligned_cols=36 Identities=22% Similarity=0.531 Sum_probs=23.9
Q ss_pred CCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcC
Q 021122 248 NAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHL 288 (317)
Q Consensus 248 ~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl 288 (317)
....|++|...|- +.|+.-... ....|..|...|-+
T Consensus 233 t~~~C~~C~G~G~--~~C~tC~gr---G~k~C~TC~gtgsl 268 (406)
T KOG2813|consen 233 THDLCYMCHGRGI--KECHTCKGR---GKKPCTTCSGTGSL 268 (406)
T ss_pred ccchhhhccCCCc--ccCCcccCC---CCcccccccCccce
Confidence 4568999988874 567654322 34678888887754
No 57
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.97 E-value=45 Score=33.41 Aligned_cols=15 Identities=20% Similarity=0.297 Sum_probs=9.9
Q ss_pred hhhhhhhccCccccc
Q 021122 139 EQKVETADNGDEGVT 153 (317)
Q Consensus 139 ee~lee~~~A~e~v~ 153 (317)
+|++.++..|-+++.
T Consensus 44 eeKFKEI~eAYEVLs 58 (371)
T COG0484 44 EEKFKEINEAYEVLS 58 (371)
T ss_pred HHHHHHHHHHHHHhC
Confidence 566666666666665
No 58
>PRK14285 chaperone protein DnaJ; Provisional
Probab=24.60 E-value=77 Score=31.34 Aligned_cols=63 Identities=22% Similarity=0.318 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCcc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVS 302 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~ 302 (317)
..|..|...|-....-+. .|..|+..|.... ..+.-.....|..|+..|-+ ....
T Consensus 147 ~~C~~C~G~G~~~~~~~~----------~C~~C~G~G~~~~-----~~G~~~~~~~C~~C~G~G~~----------~~~~ 201 (365)
T PRK14285 147 MLCESCLGKKSEKGTSPS----------ICNMCNGSGRVMQ-----GGGFFRVTTTCPKCYGNGKI----------ISNP 201 (365)
T ss_pred ccCCCCCCcccCCCCCCc----------cCCCccCceeEEe-----cCceeEEeeecCCCCCcccc----------cCCC
Q ss_pred ccCCCCCC
Q 021122 303 CFRCGQLG 310 (317)
Q Consensus 303 C~~Cg~~G 310 (317)
|..|...|
T Consensus 202 C~~C~G~g 209 (365)
T PRK14285 202 CKSCKGKG 209 (365)
T ss_pred CCCCCCCC
No 59
>PRK14287 chaperone protein DnaJ; Provisional
Probab=24.56 E-value=49 Score=32.82 Aligned_cols=22 Identities=27% Similarity=0.166 Sum_probs=13.1
Q ss_pred cccHHHHHHHHHHhhhhcCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDD 60 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~ 60 (317)
+.|..-|.||.+..|.++-+|-
T Consensus 15 ~a~~~eik~ayr~la~~~HpD~ 36 (371)
T PRK14287 15 NASVDEVKKAYRKLARKYHPDV 36 (371)
T ss_pred CCCHHHHHHHHHHHHHHHCcCC
Confidence 3444456777777766665543
No 60
>PRK14286 chaperone protein DnaJ; Provisional
Probab=24.56 E-value=47 Score=32.93 Aligned_cols=63 Identities=27% Similarity=0.526 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCcc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVS 302 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~ 302 (317)
..|..|...|-.....+. .|..|+..|.....- ..-.....|..|...|.+. ...
T Consensus 151 ~~C~~C~G~G~~~~~~~~----------~C~~C~G~G~v~~~~-----G~~~~~~~C~~C~G~G~~~----------~~~ 205 (372)
T PRK14286 151 ESCVDCNGSGASKGSSPT----------TCPDCGGSGQIRRTQ-----GFFSVATTCPTCRGKGTVI----------SNP 205 (372)
T ss_pred ccCCCCcCCCcCCCCCCc----------cCCCCcCeEEEEEEe-----ceEEEEEeCCCCCceeeEe----------ccc
Q ss_pred ccCCCCCC
Q 021122 303 CFRCGQLG 310 (317)
Q Consensus 303 C~~Cg~~G 310 (317)
|..|...|
T Consensus 206 C~~C~G~g 213 (372)
T PRK14286 206 CKTCGGQG 213 (372)
T ss_pred CCCCCCCc
No 61
>PRK14276 chaperone protein DnaJ; Provisional
Probab=23.88 E-value=52 Score=32.69 Aligned_cols=23 Identities=22% Similarity=0.125 Sum_probs=14.6
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|..-+.+|.+..|.++-+|-|
T Consensus 15 ~a~~~eik~ayr~la~~~HpD~~ 37 (380)
T PRK14276 15 DASQDEIKKAYRKLSKKYHPDIN 37 (380)
T ss_pred CCCHHHHHHHHHHHHHHHCcCCC
Confidence 45556677777777777665544
No 62
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=23.86 E-value=34 Score=37.47 Aligned_cols=20 Identities=35% Similarity=0.916 Sum_probs=13.8
Q ss_pred ccccccccccCccccccccc
Q 021122 180 WQTCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (317)
...||.||+.||.+.+|...
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred cccchhhcccCCcHhhcCCc
Confidence 35577777777777777653
No 63
>PRK14280 chaperone protein DnaJ; Provisional
Probab=23.73 E-value=52 Score=32.62 Aligned_cols=22 Identities=18% Similarity=0.046 Sum_probs=13.8
Q ss_pred cccHHHHHHHHHHhhhhcCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDD 60 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~ 60 (317)
+.|..-+.+|.+..|.++-+|-
T Consensus 15 ~a~~~eik~ayr~la~~~HpD~ 36 (376)
T PRK14280 15 SASKDEIKKAYRKLSKKYHPDI 36 (376)
T ss_pred CCCHHHHHHHHHHHHHHHCcCC
Confidence 3455557777777776665554
No 64
>PRK14278 chaperone protein DnaJ; Provisional
Probab=23.70 E-value=49 Score=32.86 Aligned_cols=23 Identities=17% Similarity=0.092 Sum_probs=16.0
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|..-|.+|.+..|.++-+|-|
T Consensus 14 ~a~~~eik~ayr~la~~~hpD~~ 36 (378)
T PRK14278 14 NASDAEIKRAYRKLARELHPDVN 36 (378)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCC
Confidence 45666677887877777766654
No 65
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=23.67 E-value=36 Score=34.94 Aligned_cols=18 Identities=33% Similarity=0.933 Sum_probs=16.7
Q ss_pred ccccccccCccccccccc
Q 021122 182 TCYNCGEEGHMAVNCRSA 199 (317)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~~ 199 (317)
.|||||..-|.-++||.+
T Consensus 130 ~CFNC~g~~hsLrdC~rp 147 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRP 147 (485)
T ss_pred cccccCCCCCccccCCCc
Confidence 399999999999999987
No 66
>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=23.66 E-value=63 Score=23.81 Aligned_cols=38 Identities=18% Similarity=0.293 Sum_probs=16.0
Q ss_pred cccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcC
Q 021122 250 QVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHL 288 (317)
Q Consensus 250 ~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl 288 (317)
..|..|+..|.....=. .........+.|..|+..|.+
T Consensus 16 ~~C~~C~G~G~~~~~~~-~~~~~~~~~~~C~~C~G~G~~ 53 (66)
T PF00684_consen 16 KTCPQCNGSGQVTRRQQ-TPGGVFQMQQTCPKCGGTGKI 53 (66)
T ss_dssp EE-TTSSSSSEEEEEEE-SSSTTEEEEEE-TTTSSSSEE
T ss_pred cCCcCCCCeeEEEEEEe-CCCeEEEEEEECCCCcceeeE
Confidence 45666666555432211 001111234556666666665
No 67
>PRK14301 chaperone protein DnaJ; Provisional
Probab=23.53 E-value=52 Score=32.66 Aligned_cols=65 Identities=28% Similarity=0.478 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCcc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVS 302 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~ 302 (317)
..|..|...|-.....+. .|..|+..|.....- +.-.....|..|+..|-+. ...
T Consensus 145 ~~C~~C~G~G~~~~~~~~----------~C~~C~G~G~v~~~~-----G~~~~~~~C~~C~G~G~~~----------~~~ 199 (373)
T PRK14301 145 VTCDDCGGSGAAPGTSPE----------TCRHCGGSGQVRQSQ-----GFFQIAVPCPVCRGEGRVI----------THP 199 (373)
T ss_pred ccCCCCCCcccCCCCCCc----------ccCCccCeeEEEEEe-----eeEEEEEeCCCCCceeeec----------CCC
Q ss_pred ccCCCCCCcc
Q 021122 303 CFRCGQLGHT 312 (317)
Q Consensus 303 C~~Cg~~GH~ 312 (317)
|..|...|..
T Consensus 200 C~~C~G~g~v 209 (373)
T PRK14301 200 CPKCKGSGIV 209 (373)
T ss_pred CCCCCCCcee
No 68
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.24 E-value=76 Score=31.02 Aligned_cols=72 Identities=22% Similarity=0.305 Sum_probs=38.6
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCC--CCCCC
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISD--AVPGE 300 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~--~~~~~ 300 (317)
..|-.||..-..+--=..... ......|..|+..=|+. -+.|.+||+.+.+.=-.... ..-+-
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~--G~RyL~CslC~teW~~~-------------R~~C~~Cg~~~~l~y~~~~~~~~~~r~ 252 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQ--GLRYLHCNLCESEWHVV-------------RVKCSNCEQSGKLHYWSLDSEQAAVKA 252 (309)
T ss_pred CCCCCCCCcchhheeeccCCC--CceEEEcCCCCCccccc-------------CccCCCCCCCCceeeeeecCCCcceEe
Confidence 456678887654411000011 11245688887765543 36788899888765110111 12244
Q ss_pred ccccCCCCC
Q 021122 301 VSCFRCGQL 309 (317)
Q Consensus 301 ~~C~~Cg~~ 309 (317)
-+|..|+.+
T Consensus 253 e~C~~C~~Y 261 (309)
T PRK03564 253 ESCGDCGTY 261 (309)
T ss_pred eeccccccc
Confidence 678888764
No 69
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.86 E-value=68 Score=36.20 Aligned_cols=12 Identities=42% Similarity=1.046 Sum_probs=8.1
Q ss_pred CccccccccccC
Q 021122 179 GWQTCYNCGEEG 190 (317)
Q Consensus 179 ~~~~C~~CG~~G 190 (317)
+...|..||..+
T Consensus 625 g~RfCpsCG~~t 636 (1121)
T PRK04023 625 GRRKCPSCGKET 636 (1121)
T ss_pred cCccCCCCCCcC
Confidence 445677777765
No 70
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=22.39 E-value=47 Score=34.13 Aligned_cols=19 Identities=26% Similarity=0.940 Sum_probs=16.2
Q ss_pred ccCCCCCCCcCCCCCCCCC
Q 021122 251 VCLKCGDSGHDMFSCRNSY 269 (317)
Q Consensus 251 ~C~~Cg~~GH~a~dCp~~~ 269 (317)
.|++|+..-|..+|||.+.
T Consensus 130 ~CFNC~g~~hsLrdC~rp~ 148 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRPF 148 (485)
T ss_pred cccccCCCCCccccCCCcc
Confidence 3899999999999998765
No 71
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=22.30 E-value=43 Score=30.36 Aligned_cols=14 Identities=50% Similarity=1.265 Sum_probs=0.0
Q ss_pred ccCCCCCCcccCCC
Q 021122 303 CFRCGQLGHTGLVS 316 (317)
Q Consensus 303 C~~Cg~~GH~~~d~ 316 (317)
||+||+.||++..+
T Consensus 103 ~~r~G~rg~~~r~~ 116 (195)
T KOG0107|consen 103 CYRCGERGHIGRNC 116 (195)
T ss_pred cccCCCcccccccc
No 72
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.04 E-value=57 Score=31.76 Aligned_cols=49 Identities=22% Similarity=0.418 Sum_probs=30.7
Q ss_pred cccccccccCcccc--ccc-ccccCCCCcccccCCCCCcccCCCCccccccccCCCC
Q 021122 181 QTCYNCGEEGHMAV--NCR-SAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHR 234 (317)
Q Consensus 181 ~~C~~CG~~GH~a~--~Cp-~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ 234 (317)
..|..||..=+.+. .-. ....+.-.|..|+..-|+. ...|.+|+...++
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~-----R~~C~~Cg~~~~l 236 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV-----RVKCSHCEESKHL 236 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc-----CccCCCCCCCCce
Confidence 47999998765442 211 1123445688888877774 3567778776654
No 73
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.94 E-value=65 Score=31.47 Aligned_cols=73 Identities=26% Similarity=0.355 Sum_probs=38.9
Q ss_pred ccccccccccCcccc--cccccccCCCCcccccCCCCCcccCCCCccccccccCCCCCCCCCCCCCCCCCCCcccCCCCC
Q 021122 180 WQTCYNCGEEGHMAV--NCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGD 257 (317)
Q Consensus 180 ~~~C~~CG~~GH~a~--~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~ 257 (317)
...|..||..=..+. .-.....+.-.|..|+..-|+. ...|.+|+..+.+..-=.+. .........|..|+.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~-----R~~C~~Cg~~~~l~y~~~~~-~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-----RVKCSNCEQSGKLHYWSLDS-EQAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc-----CccCCCCCCCCceeeeeecC-CCcceEeeecccccc
Confidence 367999998754431 1111123445688888887774 35677788755432110010 000122356777776
Q ss_pred C
Q 021122 258 S 258 (317)
Q Consensus 258 ~ 258 (317)
+
T Consensus 261 Y 261 (309)
T PRK03564 261 Y 261 (309)
T ss_pred c
Confidence 5
No 74
>PRK14279 chaperone protein DnaJ; Provisional
Probab=21.74 E-value=54 Score=32.76 Aligned_cols=65 Identities=29% Similarity=0.476 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCcc
Q 021122 223 QDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVS 302 (317)
Q Consensus 223 ~~C~~C~~~GH~ar~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~ 302 (317)
..|-.|...|-.....+. .|..|+..|-.... ...-.....|..|+..|-+. ...
T Consensus 174 ~~C~~C~G~G~~~~~~~~----------~C~~C~G~G~~~~~-----~g~~~~~~~C~~C~G~G~~i----------~~~ 228 (392)
T PRK14279 174 APCTTCHGSGARPGTSPK----------VCPTCNGSGVISRN-----QGAFGFSEPCTDCRGTGSII----------EDP 228 (392)
T ss_pred ccCCCCccccccCCCCCC----------CCCCCcceEEEEEE-----ecceEEEEecCCCCceeEEe----------CCc
Q ss_pred ccCCCCCCcc
Q 021122 303 CFRCGQLGHT 312 (317)
Q Consensus 303 C~~Cg~~GH~ 312 (317)
|..|...|..
T Consensus 229 C~~C~G~g~v 238 (392)
T PRK14279 229 CEECKGTGVT 238 (392)
T ss_pred CCCCCCCeEE
No 75
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.64 E-value=70 Score=30.87 Aligned_cols=56 Identities=25% Similarity=0.517 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCcccCCCCCCC---cCCCCCCCCCCCCCccCccccccCCCCcCcccCCCCCCCCCccccCCCCCCc
Q 021122 239 PDKHKSGFQNAQVCLKCGDSG---HDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGH 311 (317)
Q Consensus 239 p~~~~~~~~~~~~C~~Cg~~G---H~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~C~~~~~~~~~~~~C~~Cg~~GH 311 (317)
|....+.......|-.||+.- |.+--|.. ++||.|-. .+..-..--.|.+||+.+|
T Consensus 229 p~~sss~~t~~~~C~~Cg~~PtiP~~~~~C~H---------iyCY~Ci~--------ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 229 PKFSSSTGTSDTECPVCGEPPTIPHVIGKCGH---------IYCYYCIA--------TSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCcccccccCCceeeccCCCCCCCeeeccccc---------eeehhhhh--------hhhcchhhcccCccCCCCc
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.64 E-value=1.1e+02 Score=32.94 Aligned_cols=7 Identities=29% Similarity=0.539 Sum_probs=4.0
Q ss_pred CcccccC
Q 021122 205 PCFVCGS 211 (317)
Q Consensus 205 ~C~~CG~ 211 (317)
.|..||.
T Consensus 3 ~Cp~Cg~ 9 (645)
T PRK14559 3 ICPQCQF 9 (645)
T ss_pred cCCCCCC
Confidence 4666654
No 77
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.64 E-value=19 Score=34.75 Aligned_cols=15 Identities=27% Similarity=0.401 Sum_probs=7.1
Q ss_pred ccccCCCCCCcccCC
Q 021122 301 VSCFRCGQLGHTGLV 315 (317)
Q Consensus 301 ~~C~~Cg~~GH~~~d 315 (317)
+.|-||++.+|+++.
T Consensus 226 ~KC~nC~~t~~l~y~ 240 (308)
T COG3058 226 VKCSNCEQSKKLHYW 240 (308)
T ss_pred HHhccccccCCccce
Confidence 444445554444443
No 78
>PRK14282 chaperone protein DnaJ; Provisional
Probab=20.70 E-value=83 Score=31.08 Aligned_cols=23 Identities=4% Similarity=0.060 Sum_probs=15.5
Q ss_pred cccHHHHHHHHHHhhhhcCCCCC
Q 021122 39 DLSLKIVEKHMLMRAAKLDQDDS 61 (317)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~ 61 (317)
+.|..-+.+|.+..|-++-+|-|
T Consensus 15 ~a~~~eik~ayr~la~~~HPD~~ 37 (369)
T PRK14282 15 NATQEEIKRAYKRLVKEWHPDRH 37 (369)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCC
Confidence 45566677787777777766654
No 79
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.44 E-value=96 Score=30.25 Aligned_cols=71 Identities=20% Similarity=0.291 Sum_probs=39.3
Q ss_pred ccccccccCCCCCC--CCCCCCCCCCCCCcccCCCCCCCcCCCCCCCCCCCCCccCccccccCCCCcCc-c-cCC--CCC
Q 021122 223 QDCFICKKGGHRAK--DCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLC-C-VNI--SDA 296 (317)
Q Consensus 223 ~~C~~C~~~GH~ar--~Cp~~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~~~~~~~~~C~~Cg~~GHl~-C-~~~--~~~ 296 (317)
..|-.||..-+.+. .-... . ......|..|+..=|+. -+.|.+||+..++. - ... ...
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~-~--G~RyL~CslC~teW~~~-------------R~~C~~Cg~~~~l~y~~~e~~~~~~ 248 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKE-T--GLRYLSCSLCATEWHYV-------------RVKCSHCEESKHLAYLSLEHDAEKA 248 (305)
T ss_pred CcCCCCCChhhhhhhcccCCC-C--CceEEEcCCCCCccccc-------------CccCCCCCCCCceeeEeecCCCCCc
Confidence 35667888765432 21100 0 11235688887765543 36888999988875 1 111 011
Q ss_pred CCCCccccCCCCC
Q 021122 297 VPGEVSCFRCGQL 309 (317)
Q Consensus 297 ~~~~~~C~~Cg~~ 309 (317)
.-+--+|..|+.+
T Consensus 249 ~~r~e~C~~C~~Y 261 (305)
T TIGR01562 249 VLKAETCDSCQGY 261 (305)
T ss_pred ceEEeeccccccc
Confidence 1234589888864
No 80
>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=20.23 E-value=31 Score=23.28 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=4.0
Q ss_pred CccccCCCC
Q 021122 300 EVSCFRCGQ 308 (317)
Q Consensus 300 ~~~C~~Cg~ 308 (317)
..+|.+||.
T Consensus 19 ~~vC~~CG~ 27 (43)
T PF08271_consen 19 ELVCPNCGL 27 (43)
T ss_dssp EEEETTT-B
T ss_pred eEECCCCCC
Confidence 445555543
Done!