Query 011182
Match_columns 491
No_of_seqs 343 out of 1840
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:01:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011182hhsearch_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 5.3E-25 1.1E-29 202.0 10.2 138 181-354 1-148 (148)
2 PTZ00368 universal minicircle 99.8 2.4E-19 5.3E-24 164.5 8.1 114 179-325 26-147 (148)
3 COG5082 AIR1 Arginine methyltr 99.8 3.8E-19 8.2E-24 167.4 7.1 84 178-271 58-142 (190)
4 COG5082 AIR1 Arginine methyltr 99.6 1.9E-16 4.1E-21 149.2 6.5 136 161-357 34-176 (190)
5 KOG4400 E3 ubiquitin ligase in 99.6 2E-15 4.3E-20 150.9 9.6 158 178-358 22-187 (261)
6 KOG4400 E3 ubiquitin ligase in 99.5 1.8E-13 3.8E-18 136.9 9.7 154 181-356 55-217 (261)
7 KOG0119 Splicing factor 1/bran 98.9 1.4E-10 3E-15 122.1 -1.2 120 99-220 165-302 (554)
8 KOG0335 ATP-dependent RNA heli 97.8 2.2E-05 4.7E-10 84.3 5.0 111 335-455 3-113 (482)
9 PF00098 zf-CCHC: Zinc knuckle 97.7 2.7E-05 5.9E-10 46.9 1.9 17 337-353 2-18 (18)
10 PF00098 zf-CCHC: Zinc knuckle 97.6 2.6E-05 5.7E-10 47.0 1.2 17 182-198 2-18 (18)
11 PF13696 zf-CCHC_2: Zinc knuck 94.7 0.016 3.5E-07 40.0 1.4 21 334-354 7-27 (32)
12 PF13696 zf-CCHC_2: Zinc knuck 94.7 0.014 2.9E-07 40.4 0.9 19 222-240 8-26 (32)
13 KOG0119 Splicing factor 1/bran 92.7 0.076 1.7E-06 57.3 2.8 45 301-356 262-306 (554)
14 PF13917 zf-CCHC_3: Zinc knuck 92.5 0.054 1.2E-06 39.8 0.9 19 180-198 4-22 (42)
15 PF13917 zf-CCHC_3: Zinc knuck 91.9 0.097 2.1E-06 38.4 1.6 19 335-353 4-22 (42)
16 smart00343 ZnF_C2HC zinc finge 90.9 0.12 2.6E-06 33.6 1.1 18 337-354 1-18 (26)
17 smart00343 ZnF_C2HC zinc finge 90.4 0.11 2.5E-06 33.7 0.7 17 182-198 1-17 (26)
18 PF14392 zf-CCHC_4: Zinc knuck 85.3 0.34 7.4E-06 36.4 0.7 21 333-353 29-49 (49)
19 KOG0314 Predicted E3 ubiquitin 81.6 1.6 3.4E-05 47.3 4.0 63 178-242 110-178 (448)
20 PF14392 zf-CCHC_4: Zinc knuck 81.2 0.54 1.2E-05 35.3 0.3 18 180-197 31-48 (49)
21 PF15288 zf-CCHC_6: Zinc knuck 79.3 0.87 1.9E-05 33.1 0.8 18 181-198 2-21 (40)
22 KOG0109 RNA-binding protein LA 77.9 1.2 2.6E-05 45.6 1.6 25 333-357 158-182 (346)
23 KOG0109 RNA-binding protein LA 77.0 1 2.2E-05 46.1 0.8 20 180-199 160-179 (346)
24 KOG0314 Predicted E3 ubiquitin 73.8 4.1 8.9E-05 44.2 4.4 64 203-268 112-177 (448)
25 COG5222 Uncharacterized conser 72.9 1.7 3.7E-05 44.5 1.2 21 179-199 175-195 (427)
26 COG5222 Uncharacterized conser 71.6 2.1 4.6E-05 43.9 1.5 23 334-356 175-197 (427)
27 PF14787 zf-CCHC_5: GAG-polypr 69.0 2.4 5.1E-05 30.2 0.9 19 181-199 3-21 (36)
28 PF14787 zf-CCHC_5: GAG-polypr 66.1 3.5 7.5E-05 29.3 1.2 23 335-357 2-24 (36)
29 KOG0334 RNA helicase [RNA proc 65.6 1.4 3E-05 51.7 -1.2 51 400-455 354-404 (997)
30 PF15288 zf-CCHC_6: Zinc knuck 65.0 4 8.7E-05 29.7 1.4 20 336-355 2-23 (40)
31 KOG0337 ATP-dependent RNA heli 63.6 1.9 4.1E-05 46.5 -0.7 44 413-458 20-63 (529)
32 KOG0336 ATP-dependent RNA heli 63.5 1.4 3.1E-05 47.3 -1.6 41 416-458 219-262 (629)
33 PLN00206 DEAD-box ATP-dependen 63.4 0.37 8E-06 53.1 -6.3 51 401-456 111-161 (518)
34 PF10083 DUF2321: Uncharacteri 49.4 4.3 9.3E-05 38.0 -0.7 12 333-344 66-77 (158)
35 COG1107 Archaea-specific RecJ- 49.0 10 0.00022 42.5 1.9 21 302-325 97-117 (715)
36 COG5176 MSL5 Splicing factor ( 46.4 3.6 7.8E-05 40.3 -1.8 126 37-169 118-258 (269)
37 COG5593 Nucleic-acid-binding p 43.6 11 0.00023 41.9 1.0 32 4-35 670-709 (821)
38 COG1107 Archaea-specific RecJ- 43.1 18 0.00038 40.7 2.6 63 276-355 53-119 (715)
39 KOG3116 Predicted C3H1-type Zn 36.1 9.6 0.00021 35.5 -0.6 24 220-243 25-48 (177)
40 smart00816 Amb_V_allergen Amb 33.4 28 0.0006 25.5 1.5 25 281-305 11-35 (45)
41 KOG3116 Predicted C3H1-type Zn 32.9 13 0.00029 34.6 -0.2 20 180-199 27-46 (177)
42 PF04931 DNA_pol_phi: DNA poly 31.9 20 0.00044 41.7 1.0 10 97-106 737-746 (784)
43 smart00249 PHD PHD zinc finger 30.6 51 0.0011 22.8 2.6 16 276-291 14-29 (47)
44 PTZ00110 helicase; Provisional 30.4 6.6 0.00014 43.7 -3.2 49 403-456 122-170 (545)
45 KOG2044 5'-3' exonuclease HKE1 28.1 27 0.00058 40.6 1.0 29 328-356 253-281 (931)
46 KOG0066 eIF2-interacting prote 27.5 34 0.00073 37.6 1.6 56 12-74 85-141 (807)
47 PF04216 FdhE: Protein involve 26.0 9.2 0.0002 39.0 -2.8 50 180-234 172-223 (290)
48 PRK04023 DNA polymerase II lar 22.6 64 0.0014 38.7 2.8 32 178-220 624-655 (1121)
49 COG5179 TAF1 Transcription ini 22.5 42 0.00091 38.0 1.2 18 178-195 935-952 (968)
50 KOG0107 Alternative splicing f 22.2 46 0.001 32.1 1.3 18 336-353 101-118 (195)
51 PF12353 eIF3g: Eukaryotic tra 21.0 43 0.00093 30.4 0.8 19 178-197 104-122 (128)
52 PRK14298 chaperone protein Dna 20.7 91 0.002 33.2 3.3 15 139-153 44-58 (377)
53 PF03913 Amb_V_allergen: Amb V 20.5 57 0.0012 23.8 1.2 25 281-305 10-34 (44)
54 TIGR02349 DnaJ_bact chaperone 20.4 85 0.0018 32.9 3.0 13 250-262 161-173 (354)
55 PRK14296 chaperone protein Dna 20.4 73 0.0016 33.9 2.5 15 139-153 43-57 (372)
56 PRK14298 chaperone protein Dna 20.4 83 0.0018 33.5 2.9 19 41-59 18-36 (377)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.92 E-value=5.3e-25 Score=201.99 Aligned_cols=138 Identities=32% Similarity=0.872 Sum_probs=100.7
Q ss_pred cccccccccCccccccccc----ccCCCCcceeecCCCCcccCCCC------ccccccccCCCCCCCCCCccCCCCcCCc
Q 011182 181 QTCYNCGEEGHMAVNCRSA----VKRKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (491)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~----~~~~~~C~~CG~~GH~a~~Cp~~------~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~ 250 (491)
++||+|++.||++++||.. ......|++|+..||++++||.. ..||+|++.||++++||..... ....
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 3699999999999999983 12345788888888888888753 2577777777777777765432 1345
Q ss_pred ccccCCCCCcCCCCCCCCCCCCccccccccccCCCCcccccCcCCCCCCCcccccCCCCCCCCcccccccccccccCCCC
Q 011182 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGET 330 (491)
Q Consensus 251 ~C~~Cg~~GH~~~dCp~~~~~~~~~~~~C~~Cg~~GHl~c~~~~~~~~~~~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~ 330 (491)
.|++|++.||++.+|++.+. .....+.||+|++.||+++ +|++...
T Consensus 79 ~C~~Cg~~GH~~~~C~~~~~-------------------------~~~~~~~C~~Cg~~gH~~~-------~C~~~~~-- 124 (148)
T PTZ00368 79 SCYNCGQTGHISRECPNRAK-------------------------GGAARRACYNCGGEGHISR-------DCPNAGK-- 124 (148)
T ss_pred ccCcCCCCCcccccCCCccc-------------------------ccccchhhcccCcCCcchh-------cCCCccc--
Confidence 67777777777777776421 1123468999999999999 9987421
Q ss_pred CCCCCCCcccCCCCCCCcCcCCCc
Q 011182 331 VEASPSSCYNCGAEGHFARECVSS 354 (491)
Q Consensus 331 ~~~~~~~Cy~Cg~~GH~ardCp~~ 354 (491)
.+.....||+|++.|||+++||.+
T Consensus 125 ~~~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 125 RPGGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred cCCCCCccccCCCcCcccccCCCC
Confidence 224568999999999999999974
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.78 E-value=2.4e-19 Score=164.48 Aligned_cols=114 Identities=34% Similarity=0.863 Sum_probs=93.5
Q ss_pred CccccccccccCccccccccccc--CCCCcceeecCCCCcccCCCC------ccccccccCCCCCCCCCCccCCCCcCCc
Q 011182 179 GWQTCYNCGEEGHMAVNCRSAVK--RKKPCFVCGSLEHGVRQCSKA------QDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (491)
Q Consensus 179 ~~~~C~~CG~~GH~a~~Cp~~~~--~~~~C~~CG~~GH~a~~Cp~~------~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~ 250 (491)
....||+|++.||++++||.+.. ....|++|++.||++++||.. ..|++|++.||++++||+.... .....
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 35789999999999999998621 345799999999999999974 3799999999999999997643 23457
Q ss_pred ccccCCCCCcCCCCCCCCCCCCccccccccccCCCCcccccCcCCCCCCCcccccCCCCCCCCcccccccccccc
Q 011182 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACAR 325 (491)
Q Consensus 251 ~C~~Cg~~GH~~~dCp~~~~~~~~~~~~C~~Cg~~GHl~c~~~~~~~~~~~~C~~Cg~~GH~~~~~~~~~~~C~~ 325 (491)
.||+|++.||++.+||+.+.. ....+.||+|++.||++. +||.
T Consensus 105 ~C~~Cg~~gH~~~~C~~~~~~-------------------------~~~~~~C~~Cg~~gH~~~-------dCp~ 147 (148)
T PTZ00368 105 ACYNCGGEGHISRDCPNAGKR-------------------------PGGDKTCYNCGQTGHLSR-------DCPD 147 (148)
T ss_pred hhcccCcCCcchhcCCCcccc-------------------------CCCCCccccCCCcCcccc-------cCCC
Confidence 899999999999999985321 113368999999999999 8875
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.77 E-value=3.8e-19 Score=167.38 Aligned_cols=84 Identities=29% Similarity=0.832 Sum_probs=74.4
Q ss_pred cCccccccccccCcccccccccccCCCCcceeecCCCCcccCCCCccccccccCCCCCCCC-CCccCCCCcCCcccccCC
Q 011182 178 RGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDC-PDKHKSGFQNAQVCLKCG 256 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~Cg~~GH~a~~C-p~~~~~~~~~~~~C~~Cg 256 (491)
.....||+||+.||++++||. .+|++|...||.+..||....|++|++.||++++| |.++. ...|+.|.
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 346789999999999999995 59999977999999999888999999999999999 56543 56999999
Q ss_pred CCCcCCCCCCCCCCC
Q 011182 257 DSGHDMFSCRNSYSL 271 (491)
Q Consensus 257 ~~GH~~~dCp~~~~~ 271 (491)
..+|.+.+||..|..
T Consensus 128 s~~H~s~~Cp~~~k~ 142 (190)
T COG5082 128 STRHSSEDCPSIWKH 142 (190)
T ss_pred CCccccccCcccccc
Confidence 999999999998854
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.64 E-value=1.9e-16 Score=149.25 Aligned_cols=136 Identities=30% Similarity=0.667 Sum_probs=98.4
Q ss_pred HHHHHhhCCCCCCCCCCcCccccccccccCcccccccccccCCCCcceeecCCCCcccCCCCccccccccCCCCCCCCCC
Q 011182 161 IVLRKLLRGPRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPD 240 (491)
Q Consensus 161 ~~~r~~lr~~Ryf~~~~~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~~~~C~~Cg~~GH~a~~Cp~ 240 (491)
.+++.+.-.-||++......- +..+. ..+|++||+.||..++|| ..+|++|...||.+..||.
T Consensus 34 ~~~~~~~~~~~~~~~~~~d~~-----------~~~~~-----~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~ 96 (190)
T COG5082 34 NELRSLRSSGRYEDRSVEDVS-----------AIREE-----NPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPK 96 (190)
T ss_pred cceeeccceeeeecccccccc-----------ccccc-----ccccchhcccCcccccCC-hhHhhhcCCCCcccccCCc
Confidence 344455555677766532222 33333 359999999999999999 7999999889999999998
Q ss_pred ccCCCCcCCcccccCCCCCcCCCCC-CCCCCCCccccccccccCCCCcccccCcCCCCCCCcccccCCCCCCCCcccccc
Q 011182 241 KHKSGFQNAQVCLKCGDSGHDMFSC-RNSYSLDDLKEVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSC 319 (491)
Q Consensus 241 ~~~~~~~~~~~C~~Cg~~GH~~~dC-p~~~~~~~~~~~~C~~Cg~~GHl~c~~~~~~~~~~~~C~~Cg~~GH~~~~~~~~ 319 (491)
+ +.|++||..||++++| |..|. . ..|+.|...+|++.
T Consensus 97 ~--------~~C~~Cg~~GH~~~dC~P~~~~-----~------------------------~~C~~C~s~~H~s~----- 134 (190)
T COG5082 97 P--------KKCYNCGETGHLSRDCNPSKDQ-----Q------------------------KSCFDCNSTRHSSE----- 134 (190)
T ss_pred c--------cccccccccCccccccCccccc-----C------------------------cceeccCCCccccc-----
Confidence 4 7999999999999999 66542 2 34555555555555
Q ss_pred cccccccCCC------CCCCCCCCcccCCCCCCCcCcCCCcccc
Q 011182 320 MQACARSRGE------TVEASPSSCYNCGAEGHFARECVSSSKV 357 (491)
Q Consensus 320 ~~~C~~~~~~------~~~~~~~~Cy~Cg~~GH~ardCp~~~~~ 357 (491)
+||..+.. .+....++||.|+..+||+.+|+.+...
T Consensus 135 --~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s 176 (190)
T COG5082 135 --DCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSS 176 (190)
T ss_pred --cCcccccccccccCCCcceeeeccccCCccccCCCCCCCccc
Confidence 55543321 1113467999999999999999876643
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.60 E-value=2e-15 Score=150.91 Aligned_cols=158 Identities=28% Similarity=0.665 Sum_probs=125.5
Q ss_pred cCccccccccccCcccccccccccC-------CCCcceeecCCCCcccCCCCccccccccCCCCCCCCCCccCCCCcCCc
Q 011182 178 RGWQTCYNCGEEGHMAVNCRSAVKR-------KKPCFVCGSLEHGVRQCSKAQDCFICKKGGHRAKDCPDKHKSGFQNAQ 250 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~~~~-------~~~C~~CG~~GH~a~~Cp~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~ 250 (491)
.....|++|+..+|.+..|+..... ...+..+...+|....++ ...|+.|++.||....|+.. ..
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~c~~~g~~~~~~~~~~~~-------~~ 93 (261)
T KOG4400|consen 22 DSSPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECP-EVSCYICGEKGHLGRRCTRI-------AA 93 (261)
T ss_pred ccchhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCC-CceeeecCCCCchhhcCccc-------ch
Confidence 3456799999999999999875321 234555666778888888 68999999999999999972 57
Q ss_pred ccccCCCCCcCCCCCCCCCCCCccccccccccCCCCcccccCcC-CCCCCCcccccCCCCCCCCcccccccccccccCCC
Q 011182 251 VCLKCGDSGHDMFSCRNSYSLDDLKEVQCYICRCFGHLCCVNIS-DAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGE 329 (491)
Q Consensus 251 ~C~~Cg~~GH~~~dCp~~~~~~~~~~~~C~~Cg~~GHl~c~~~~-~~~~~~~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~ 329 (491)
.|++|++.||+..+|+..+.... ....||.|+..||+.|.+.. ...+..+.||+|++.||++. +|+..
T Consensus 94 ~c~~C~~~gH~~~~c~~~~~~~~-~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~-------~C~~~--- 162 (261)
T KOG4400|consen 94 ACFNCGEGGHIERDCPEAGKEGS-SETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISD-------DCPEN--- 162 (261)
T ss_pred hhhhCCCCccchhhCCcccCccc-ccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchh-------hCCCC---
Confidence 99999999999999999875433 56789999999999843322 12222278999999999999 99864
Q ss_pred CCCCCCCCcccCCCCCCCcCcCCCccccc
Q 011182 330 TVEASPSSCYNCGAEGHFARECVSSSKVR 358 (491)
Q Consensus 330 ~~~~~~~~Cy~Cg~~GH~ardCp~~~~~~ 358 (491)
....||+|+..||.+++||......
T Consensus 163 ----~~~~c~~c~~~~h~~~~C~~~~~~~ 187 (261)
T KOG4400|consen 163 ----KGGTCFRCGKVGHGSRDCPSKQKSK 187 (261)
T ss_pred ----CCCccccCCCcceecccCCcccccc
Confidence 2689999999999999999887663
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.46 E-value=1.8e-13 Score=136.88 Aligned_cols=154 Identities=32% Similarity=0.803 Sum_probs=115.8
Q ss_pred cccccccccCcccccccccccCCCCcceeecCCCCcccCCC-CccccccccCCCCCCCCCCccCCCCcCCcccccCCCCC
Q 011182 181 QTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK-AQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSG 259 (491)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~-~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~C~~Cg~~G 259 (491)
..+..+...+|+-..++.. .|+.||..+|....|+. ...|++|++.||++++||.++..+. ....||.|+..|
T Consensus 55 ~~~~~~~~~~~~~~~~~~~-----~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~-~~~~~~~c~~~g 128 (261)
T KOG4400|consen 55 PGCVSTSPNGPLKSECPEV-----SCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEGS-SETSCYSCGKTG 128 (261)
T ss_pred CcccccccCcccCCCCCCc-----eeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCccc-ccceeeccCCCc
Confidence 4455577778888888775 89999999999999985 7889999999999999999876432 456899999999
Q ss_pred cCCCCCCCCCCCC-ccccccccccCCCCcccccCcCCCCC--CCcccccCCCCCCCCcccccccccccccCCCCCC----
Q 011182 260 HDMFSCRNSYSLD-DLKEVQCYICRCFGHLCCVNISDAVP--GEVSCFRCGQLGHTGLHWNSCMQACARSRGETVE---- 332 (491)
Q Consensus 260 H~~~dCp~~~~~~-~~~~~~C~~Cg~~GHl~c~~~~~~~~--~~~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~~~---- 332 (491)
|.. |+...... ... +.||+|++.||+. ..|+ ....||.|++.||..+ +|+........
T Consensus 129 h~~--~~~~~~~~~~~~-~~Cy~Cg~~GH~s-----~~C~~~~~~~c~~c~~~~h~~~-------~C~~~~~~~~~~~~~ 193 (261)
T KOG4400|consen 129 HRG--CPDADPVDGPKP-AKCYSCGEQGHIS-----DDCPENKGGTCFRCGKVGHGSR-------DCPSKQKSKSKQGGQ 193 (261)
T ss_pred ccc--CcccccccCCCC-CccCCCCcCCcch-----hhCCCCCCCccccCCCcceecc-------cCCccccccccCccc
Confidence 999 43322211 223 7899999999996 5665 3689999999999999 99986543211
Q ss_pred -CCCCCcccCCCCCCCcCcCCCccc
Q 011182 333 -ASPSSCYNCGAEGHFARECVSSSK 356 (491)
Q Consensus 333 -~~~~~Cy~Cg~~GH~ardCp~~~~ 356 (491)
..-..|+ +...+|+.++|+....
T Consensus 194 ~~~~~~~~-~~~~~~~~~~~~~~~~ 217 (261)
T KOG4400|consen 194 RKGFGACY-DYPQGHKQRACGGSGP 217 (261)
T ss_pred ccccccCc-cccccccccccCCCCc
Confidence 1222344 5578888888876554
No 7
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.91 E-value=1.4e-10 Score=122.11 Aligned_cols=120 Identities=20% Similarity=0.313 Sum_probs=85.5
Q ss_pred chhhhhhhcchhhhHHHhhhhhhhhhhc------cccccccccccchhhhhhhcccccccc-------cccchhHHHHHH
Q 011182 99 DVIIEDVKSSDKKRIRVRKKKKKEADKI------EIEDQSVIVRKEEQKVETADNGDEGVT-------TVEISDNIVLRK 165 (491)
Q Consensus 99 ~~~~~~~k~~~~~~~r~K~~~k~~~~~~------~~e~~~v~~~~~ee~~E~~~~A~e~v~-------~~~~~~n~~~r~ 165 (491)
+-..-+.+|..|+.||||++|||++... .-++|.|+.+...+++|.+.+|.+.|+ .+++++|.+.+.
T Consensus 165 TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~ 244 (554)
T KOG0119|consen 165 TQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRL 244 (554)
T ss_pred HHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHH
Confidence 3455567799999999999999999443 348999999999999999999988665 456666655555
Q ss_pred hhCC----CCCCCCCCcCccccccccccCccccccccccc-CCCCcceeecCCCCcccCC
Q 011182 166 LLRG----PRYFDPPDRGWQTCYNCGEEGHMAVNCRSAVK-RKKPCFVCGSLEHGVRQCS 220 (491)
Q Consensus 166 ~lr~----~Ryf~~~~~~~~~C~~CG~~GH~a~~Cp~~~~-~~~~C~~CG~~GH~a~~Cp 220 (491)
+|+. .-.+.. ..+..|.+||..||...+||.... -..+|.+||..||++.+|+
T Consensus 245 Qlrela~lNgt~r~--~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~ 302 (554)
T KOG0119|consen 245 QLRELARLNGTLRD--DDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCK 302 (554)
T ss_pred HHHHHHHhCCCCCc--cccccccccCCCccccccCCcccccccccccccCCcccccccCC
Confidence 5444 333222 335889999999999999998511 1125666666555555555
No 8
>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.79 E-value=2.2e-05 Score=84.33 Aligned_cols=111 Identities=19% Similarity=0.206 Sum_probs=78.2
Q ss_pred CCCcccCCCCCCCcCcCCCccccccccCCCCCCCcCCCCCCCCCCCCCCCCCcCCccccccCCCccccCccccccccCCC
Q 011182 335 PSSCYNCGAEGHFARECVSSSKVRKRNIDASTPTFRPHRENKDHSGIKSAPHDLGKVHKRKKTQHEERGIMTSRKSKQRG 414 (491)
Q Consensus 335 ~~~Cy~Cg~~GH~ardCp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~k~~k~~k~~~~~~~~~~~~~~~srg 414 (491)
...|.+|++.||+...|.+.... + .....+..|.....+ ..+-....++.|+.++..+.++.+|...|..+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~-~---~~~k~~~~~~~~~~~-~~~~~~~~~~~nfd~~~~i~v~~~G~~~p~~i~--- 74 (482)
T KOG0335|consen 3 LRSGRNCGEGGPRPKHCGNSTME-E---EKQKGKKGPLKAYLE-QAFFLGISTGINFDKYNDIPVKVSGRDVPPHIP--- 74 (482)
T ss_pred CccccccCCCCCCCccccccccc-c---cccccccCCcccchh-hhhhhccchhhccCCccceeeeccCCccCCCcc---
Confidence 35677777777887777765311 0 000111111111111 111122577899999999999999999888877
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCC
Q 011182 415 GWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGH 455 (491)
Q Consensus 415 g~~~~~~~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~ 455 (491)
+|.+.++.+.+..|+++.+|..| ||+|+|+ ||+|..|.+
T Consensus 75 ~f~~~~l~~~l~~ni~~~~~~~p-tpvQk~s-ip~i~~Grd 113 (482)
T KOG0335|consen 75 TFDEAILGEALAGNIKRSGYTKP-TPVQKYS-IPIISGGRD 113 (482)
T ss_pred cccccchhHHHhhccccccccCC-Ccceeec-cceeecCCc
Confidence 47888889999999999999999 9999999 999998765
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=97.66 E-value=2.7e-05 Score=46.88 Aligned_cols=17 Identities=53% Similarity=1.396 Sum_probs=13.4
Q ss_pred CcccCCCCCCCcCcCCC
Q 011182 337 SCYNCGAEGHFARECVS 353 (491)
Q Consensus 337 ~Cy~Cg~~GH~ardCp~ 353 (491)
.||+|++.||++++||+
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 10
>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=97.60 E-value=2.6e-05 Score=46.96 Aligned_cols=17 Identities=53% Similarity=1.372 Sum_probs=13.6
Q ss_pred ccccccccCcccccccc
Q 011182 182 TCYNCGEEGHMAVNCRS 198 (491)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~ 198 (491)
.||+|++.||++++||+
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 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.73 E-value=0.016 Score=40.04 Aligned_cols=21 Identities=29% Similarity=0.893 Sum_probs=17.1
Q ss_pred CCCCcccCCCCCCCcCcCCCc
Q 011182 334 SPSSCYNCGAEGHFARECVSS 354 (491)
Q Consensus 334 ~~~~Cy~Cg~~GH~ardCp~~ 354 (491)
....|+.|++.|||..+||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 357888999999999999873
No 12
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.67 E-value=0.014 Score=40.38 Aligned_cols=19 Identities=37% Similarity=0.898 Sum_probs=10.6
Q ss_pred CccccccccCCCCCCCCCC
Q 011182 222 AQDCFICKKGGHRAKDCPD 240 (491)
Q Consensus 222 ~~~C~~Cg~~GH~a~~Cp~ 240 (491)
...|++|++.||+..+||.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 3455555555555555555
No 13
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.73 E-value=0.076 Score=57.30 Aligned_cols=45 Identities=27% Similarity=0.702 Sum_probs=36.9
Q ss_pred cccccCCCCCCCCcccccccccccccCCCCCCCCCCCcccCCCCCCCcCcCCCccc
Q 011182 301 VSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGHFARECVSSSK 356 (491)
Q Consensus 301 ~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~~~ 356 (491)
..|.+|+..||-.. +|+.. +... ...|.+|+..|||+++|+.+.+
T Consensus 262 ~~c~~cg~~~H~q~-------~cp~r---~~~~-~n~c~~cg~~gH~~~dc~~~~q 306 (554)
T KOG0119|consen 262 RACRNCGSTGHKQY-------DCPGR---IPNT-TNVCKICGPLGHISIDCKVNDQ 306 (554)
T ss_pred ccccccCCCccccc-------cCCcc---cccc-cccccccCCcccccccCCCccc
Confidence 68999999999988 99974 2222 2399999999999999998743
No 14
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.51 E-value=0.054 Score=39.78 Aligned_cols=19 Identities=32% Similarity=0.908 Sum_probs=16.2
Q ss_pred ccccccccccCcccccccc
Q 011182 180 WQTCYNCGEEGHMAVNCRS 198 (491)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~ 198 (491)
...|.+|++.||+..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4679999999999999984
No 15
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=91.87 E-value=0.097 Score=38.45 Aligned_cols=19 Identities=37% Similarity=0.996 Sum_probs=17.0
Q ss_pred CCCcccCCCCCCCcCcCCC
Q 011182 335 PSSCYNCGAEGHFARECVS 353 (491)
Q Consensus 335 ~~~Cy~Cg~~GH~ardCp~ 353 (491)
...|.+|++.||+..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5689999999999999995
No 16
>smart00343 ZnF_C2HC zinc finger.
Probab=90.86 E-value=0.12 Score=33.59 Aligned_cols=18 Identities=61% Similarity=1.448 Sum_probs=15.6
Q ss_pred CcccCCCCCCCcCcCCCc
Q 011182 337 SCYNCGAEGHFARECVSS 354 (491)
Q Consensus 337 ~Cy~Cg~~GH~ardCp~~ 354 (491)
.|++|++.||++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 489999999999999843
No 17
>smart00343 ZnF_C2HC zinc finger.
Probab=90.43 E-value=0.11 Score=33.69 Aligned_cols=17 Identities=59% Similarity=1.458 Sum_probs=13.5
Q ss_pred ccccccccCcccccccc
Q 011182 182 TCYNCGEEGHMAVNCRS 198 (491)
Q Consensus 182 ~C~~CG~~GH~a~~Cp~ 198 (491)
.|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 37888888888888874
No 18
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=85.33 E-value=0.34 Score=36.41 Aligned_cols=21 Identities=38% Similarity=0.953 Sum_probs=16.8
Q ss_pred CCCCCcccCCCCCCCcCcCCC
Q 011182 333 ASPSSCYNCGAEGHFARECVS 353 (491)
Q Consensus 333 ~~~~~Cy~Cg~~GH~ardCp~ 353 (491)
.-|.+|++||..||...+||.
T Consensus 29 ~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 29 RLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred CcChhhcCCCCcCcCHhHcCC
Confidence 346788888888888888873
No 19
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.57 E-value=1.6 Score=47.33 Aligned_cols=63 Identities=24% Similarity=0.374 Sum_probs=50.8
Q ss_pred cCccccccccccCcccccccccccCCCCcceeecCCCCcccCCC------CccccccccCCCCCCCCCCcc
Q 011182 178 RGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCSK------AQDCFICKKGGHRAKDCPDKH 242 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp~------~~~C~~Cg~~GH~a~~Cp~~~ 242 (491)
.....|+.|+..||..+.|..+ ...+|..|-..+|....|.. ...|++|...|||.+.||...
T Consensus 110 p~~q~~~~~~~~~~~~~~~t~~--~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~ 178 (448)
T KOG0314|consen 110 PLIQMNGRMGGRGFGMRRQTPP--PGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVS 178 (448)
T ss_pred chhhhccccccCCcccccCCCc--ccceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccC
Confidence 3456899999999999999553 55689999999998888865 467888888888888888753
No 20
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=81.23 E-value=0.54 Score=35.35 Aligned_cols=18 Identities=33% Similarity=0.899 Sum_probs=16.0
Q ss_pred ccccccccccCccccccc
Q 011182 180 WQTCYNCGEEGHMAVNCR 197 (491)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp 197 (491)
...|+.||..||...+||
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 456999999999999997
No 21
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=79.33 E-value=0.87 Score=33.14 Aligned_cols=18 Identities=44% Similarity=0.927 Sum_probs=11.7
Q ss_pred cccccccccCccc--ccccc
Q 011182 181 QTCYNCGEEGHMA--VNCRS 198 (491)
Q Consensus 181 ~~C~~CG~~GH~a--~~Cp~ 198 (491)
++|.+||..||.+ +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 4577777777776 34554
No 22
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=77.93 E-value=1.2 Score=45.59 Aligned_cols=25 Identities=40% Similarity=0.982 Sum_probs=20.9
Q ss_pred CCCCCcccCCCCCCCcCcCCCcccc
Q 011182 333 ASPSSCYNCGAEGHFARECVSSSKV 357 (491)
Q Consensus 333 ~~~~~Cy~Cg~~GH~ardCp~~~~~ 357 (491)
..+..||.||+.||++.+||.....
T Consensus 158 gDq~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 158 GDQSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred CCHHHheeccccccccccCCccCCC
Confidence 3456899999999999999988765
No 23
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=76.98 E-value=1 Score=46.13 Aligned_cols=20 Identities=40% Similarity=1.001 Sum_probs=18.4
Q ss_pred ccccccccccCccccccccc
Q 011182 180 WQTCYNCGEEGHMAVNCRSA 199 (491)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (491)
.-.||+||++|||+.+||..
T Consensus 160 q~~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVD 179 (346)
T ss_pred HHHheeccccccccccCCcc
Confidence 45799999999999999997
No 24
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.78 E-value=4.1 Score=44.25 Aligned_cols=64 Identities=20% Similarity=0.375 Sum_probs=54.0
Q ss_pred CCCcceeecCCCCcccCCC--CccccccccCCCCCCCCCCccCCCCcCCcccccCCCCCcCCCCCCCC
Q 011182 203 KKPCFVCGSLEHGVRQCSK--AQDCFICKKGGHRAKDCPDKHKSGFQNAQVCLKCGDSGHDMFSCRNS 268 (491)
Q Consensus 203 ~~~C~~CG~~GH~a~~Cp~--~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~ 268 (491)
...|..|+..||..+.|.. ...|..|...+|+...|..-.. ..-...|++|+..||+...||..
T Consensus 112 ~q~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~--Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 112 IQMNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGS--PPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred hhhccccccCCcccccCCCcccceeeecccCccccccccccCC--CCCCcceecCCCCCccceecccc
Confidence 3578999999999998864 5789999999999999987543 23468999999999999999964
No 25
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.95 E-value=1.7 Score=44.55 Aligned_cols=21 Identities=38% Similarity=0.923 Sum_probs=18.0
Q ss_pred CccccccccccCccccccccc
Q 011182 179 GWQTCYNCGEEGHMAVNCRSA 199 (491)
Q Consensus 179 ~~~~C~~CG~~GH~a~~Cp~~ 199 (491)
..-.||+||+.|||..+||..
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CceeEEecCCCCchhhcCCCC
Confidence 356799999999999999974
No 26
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=71.62 E-value=2.1 Score=43.90 Aligned_cols=23 Identities=30% Similarity=0.944 Sum_probs=17.8
Q ss_pred CCCCcccCCCCCCCcCcCCCccc
Q 011182 334 SPSSCYNCGAEGHFARECVSSSK 356 (491)
Q Consensus 334 ~~~~Cy~Cg~~GH~ardCp~~~~ 356 (491)
....||+||+.||+-..||.+..
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred CceeEEecCCCCchhhcCCCCCC
Confidence 35678888888888888886553
No 27
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=69.01 E-value=2.4 Score=30.17 Aligned_cols=19 Identities=42% Similarity=0.789 Sum_probs=11.3
Q ss_pred cccccccccCccccccccc
Q 011182 181 QTCYNCGEEGHMAVNCRSA 199 (491)
Q Consensus 181 ~~C~~CG~~GH~a~~Cp~~ 199 (491)
..|++|++..|++.+|...
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 4699999999999999774
No 28
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=66.12 E-value=3.5 Score=29.35 Aligned_cols=23 Identities=43% Similarity=0.853 Sum_probs=13.6
Q ss_pred CCCcccCCCCCCCcCcCCCcccc
Q 011182 335 PSSCYNCGAEGHFARECVSSSKV 357 (491)
Q Consensus 335 ~~~Cy~Cg~~GH~ardCp~~~~~ 357 (491)
+..|.+|++-.|++++|-.....
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d~ 24 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTDV 24 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCCC
T ss_pred CccCcccCCCcchhhhhhhhhcc
Confidence 45799999999999999876543
No 29
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=65.59 E-value=1.4 Score=51.74 Aligned_cols=51 Identities=22% Similarity=0.310 Sum_probs=43.4
Q ss_pred cccCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCC
Q 011182 400 EERGIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGH 455 (491)
Q Consensus 400 ~~~~~~~~~~~~srgg~~~~~~~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~ 455 (491)
.+.|...|++.++ |..-.+.-+++...++-||.+| ||+|-.+ ||.||+|.+
T Consensus 354 ~v~g~~~pkpv~s---W~q~gl~~~il~tlkkl~y~k~-~~IQ~qA-iP~ImsGrd 404 (997)
T KOG0334|consen 354 KVKGKECPKPVTS---WTQCGLSSKILETLKKLGYEKP-TPIQAQA-IPAIMSGRD 404 (997)
T ss_pred eeccCCCCcccch---HhhCCchHHHHHHHHHhcCCCC-cchhhhh-cchhccCcc
Confidence 3445566677776 9998888888888899999999 9999999 999999986
No 30
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=65.04 E-value=4 Score=29.75 Aligned_cols=20 Identities=40% Similarity=0.820 Sum_probs=13.5
Q ss_pred CCcccCCCCCCCcC--cCCCcc
Q 011182 336 SSCYNCGAEGHFAR--ECVSSS 355 (491)
Q Consensus 336 ~~Cy~Cg~~GH~ar--dCp~~~ 355 (491)
+.|.+||..||+.. .||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 45777777777774 577655
No 31
>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=63.56 E-value=1.9 Score=46.45 Aligned_cols=44 Identities=18% Similarity=0.297 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCCCCC
Q 011182 413 RGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSS 458 (491)
Q Consensus 413 rgg~~~~~~~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~~~~ 458 (491)
-|||.++.+.-.++.+|.+.||+-| ||+|.-+ ||.|..|-+-.+
T Consensus 20 ~g~fqsmgL~~~v~raI~kkg~~~p-tpiqRKT-ipliLe~~dvv~ 63 (529)
T KOG0337|consen 20 SGGFQSMGLDYKVLRAIHKKGFNTP-TPIQRKT-IPLILEGRDVVG 63 (529)
T ss_pred CCCccccCCCHHHHHHHHHhhcCCC-Cchhccc-ccceeeccccce
Confidence 5899999999999999999999999 9999999 999998877544
No 32
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=63.51 E-value=1.4 Score=47.27 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=35.3
Q ss_pred CCCCCC---CCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCCCCC
Q 011182 416 WITDDP---GDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHFSS 458 (491)
Q Consensus 416 ~~~~~~---~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~~~~ 458 (491)
|+|+|+ ...++.|++|.|+.+| ||+|... -|++..|.+..+
T Consensus 219 ctFddAFq~~pevmenIkK~GFqKP-tPIqSQa-WPI~LQG~DliG 262 (629)
T KOG0336|consen 219 CTFDDAFQCYPEVMENIKKTGFQKP-TPIQSQA-WPILLQGIDLIG 262 (629)
T ss_pred CcHHHHHhhhHHHHHHHHhccCCCC-Ccchhcc-cceeecCcceEE
Confidence 788887 5567889999999999 9999998 899999988543
No 33
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=63.38 E-value=0.37 Score=53.07 Aligned_cols=51 Identities=16% Similarity=0.092 Sum_probs=40.9
Q ss_pred ccCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCCC
Q 011182 401 ERGIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHF 456 (491)
Q Consensus 401 ~~~~~~~~~~~srgg~~~~~~~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~~ 456 (491)
+.|...|.+..+ |....+.+.++.+.++.||..| ||+|... +|.+..|.+.
T Consensus 111 ~~g~~~p~pi~~---f~~~~l~~~l~~~L~~~g~~~p-tpiQ~~a-ip~il~g~dv 161 (518)
T PLN00206 111 VKGEAVPPPILS---FSSCGLPPKLLLNLETAGYEFP-TPIQMQA-IPAALSGRSL 161 (518)
T ss_pred ecCCCCCchhcC---HHhCCCCHHHHHHHHHcCCCCC-CHHHHHH-HHHHhcCCCE
Confidence 456666667776 6666667778889999999999 9999999 9999988763
No 34
>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=49.42 E-value=4.3 Score=38.02 Aligned_cols=12 Identities=50% Similarity=1.090 Sum_probs=9.6
Q ss_pred CCCCCcccCCCC
Q 011182 333 ASPSSCYNCGAE 344 (491)
Q Consensus 333 ~~~~~Cy~Cg~~ 344 (491)
..|.+|++||..
T Consensus 66 ~~PsYC~~CGkp 77 (158)
T PF10083_consen 66 EAPSYCHNCGKP 77 (158)
T ss_pred CCChhHHhCCCC
Confidence 458899999974
No 35
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=49.00 E-value=10 Score=42.54 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=14.2
Q ss_pred ccccCCCCCCCCcccccccccccc
Q 011182 302 SCFRCGQLGHTGLHWNSCMQACAR 325 (491)
Q Consensus 302 ~C~~Cg~~GH~~~~~~~~~~~C~~ 325 (491)
.|..|.+.+|....|.. .|..
T Consensus 97 lc~~c~~~~~~vy~l~~---~c~~ 117 (715)
T COG1107 97 LCPECRRKPKIVYVLDN---SCTM 117 (715)
T ss_pred cChhHhhCCceeEEecc---ccch
Confidence 68888888886655544 5654
No 36
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=46.45 E-value=3.6 Score=40.33 Aligned_cols=126 Identities=17% Similarity=0.068 Sum_probs=66.2
Q ss_pred cccccHHHHHHHHHHHhhcccCCCCCCcccccCCCCCC--CCCCCCCCCCCccccCCCCCCCCcchhhhhhhcchhhhHH
Q 011182 37 NEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTN--TSDNSNNKNGGVEAVVPGPSGTTDDVIIEDVKSSDKKRIR 114 (491)
Q Consensus 37 ~~~~s~~~~~~~~~~~~~~~~~~d~~~~~~~~~d~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~r 114 (491)
+||.-|.+++.++-+-....+.+|.-.--++ ++.. .-..++ +--.+++--+|.+.|- ..-+.+|..|+.||
T Consensus 118 Leder~~l~era~k~lp~fv~p~dy~rpsk~---q~KiYIPV~eyP--e~NFVGLliGPRG~Tl--k~le~~s~akIaIR 190 (269)
T COG5176 118 LEDERLWLKERAQKILPRFVLPNDYIRPSKY---QNKIYIPVQEYP--ESNFVGLLIGPRGSTL--KQLERISRAKIAIR 190 (269)
T ss_pred hhHHHHHHHHHHHHhcCcccCCccccCcccc---cceEEeehhhCc--ccceeEEEecCCcchH--HHHHHHhCCeEEEe
Confidence 4555577888887776666666665331111 0000 000000 1112233334443332 23344588999999
Q ss_pred Hhhhhhhhhhhccccc---------cccccccchhhhhhhcccccccc----cccchhHHHHHHhhCC
Q 011182 115 VRKKKKKEADKIEIED---------QSVIVRKEEQKVETADNGDEGVT----TVEISDNIVLRKLLRG 169 (491)
Q Consensus 115 ~K~~~k~~~~~~~~e~---------~~v~~~~~ee~~E~~~~A~e~v~----~~~~~~n~~~r~~lr~ 169 (491)
|+.|+|++...-+++. .-++.++.++++..+.+....+. ..|.++|.+.|.+++.
T Consensus 191 G~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~ 258 (269)
T COG5176 191 GSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRW 258 (269)
T ss_pred cccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHhcCCcccchHHHHHHHH
Confidence 9999999887765421 22345555555555444432111 5566777776766653
No 37
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=43.63 E-value=11 Score=41.92 Aligned_cols=32 Identities=25% Similarity=0.178 Sum_probs=20.2
Q ss_pred hhcccccccc-----ccchhhh---hhccceeeeecCccc
Q 011182 4 RQKLKGKLYH-----EENGEEE---EKLKSAAAMSSDDEE 35 (491)
Q Consensus 4 ~~~~~~~~~~-----~~~~~~~---~~~~~~~~~~~~d~e 35 (491)
+.+++.|++- ++|.|.| -+|++.++++|||+|
T Consensus 670 k~~k~~k~~~d~d~emde~eiw~alv~srp~~e~d~ddse 709 (821)
T COG5593 670 KGKKSNKASFDSDDEMDENEIWSALVKSRPDVEDDSDDSE 709 (821)
T ss_pred cccccccCCcCccccccHHHHHHHHhccCCccccCccccc
Confidence 4455556552 2234455 458999999988765
No 38
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=43.09 E-value=18 Score=40.69 Aligned_cols=63 Identities=22% Similarity=0.444 Sum_probs=31.8
Q ss_pred cccccccCCCCcccccCcCCCCCCCcccccCCCCCCCCcccccccccccccCCCCCCCCCCCcccCCCCCC----CcCcC
Q 011182 276 EVQCYICRCFGHLCCVNISDAVPGEVSCFRCGQLGHTGLHWNSCMQACARSRGETVEASPSSCYNCGAEGH----FAREC 351 (491)
Q Consensus 276 ~~~C~~Cg~~GHl~c~~~~~~~~~~~~C~~Cg~~GH~~~~~~~~~~~C~~~~~~~~~~~~~~Cy~Cg~~GH----~ardC 351 (491)
++.|..|...|-.. --..|..|+..|-... |..............|-.|.+..| +...|
T Consensus 53 ~~pc~~c~gkG~V~---------v~~~c~~c~G~gkv~~--------c~~cG~~~~~~~~~lc~~c~~~~~~vy~l~~~c 115 (715)
T COG1107 53 EIPCPKCRGKGTVT---------VYDTCPECGGTGKVLT--------CDICGDIIVPWEEGLCPECRRKPKIVYVLDNSC 115 (715)
T ss_pred CCCCCeeccceeEE---------EEeecccCCCceeEEe--------eccccceecCcccccChhHhhCCceeEEecccc
Confidence 45677777766542 1134455555554432 222222222223447888888888 33456
Q ss_pred CCcc
Q 011182 352 VSSS 355 (491)
Q Consensus 352 p~~~ 355 (491)
....
T Consensus 116 ~~~D 119 (715)
T COG1107 116 TMED 119 (715)
T ss_pred chhh
Confidence 5433
No 39
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=36.07 E-value=9.6 Score=35.50 Aligned_cols=24 Identities=29% Similarity=0.717 Sum_probs=18.5
Q ss_pred CCCccccccccCCCCCCCCCCccC
Q 011182 220 SKAQDCFICKKGGHRAKDCPDKHK 243 (491)
Q Consensus 220 p~~~~C~~Cg~~GH~a~~Cp~~~~ 243 (491)
+....|..|.+.|||..+|.++++
T Consensus 25 ~~~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 25 GSSARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred ccchhHHHHHhhccceeeecCcee
Confidence 345678888888888888888764
No 40
>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=33.36 E-value=28 Score=25.52 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=20.1
Q ss_pred ccCCCCcccccCcCCCCCCCccccc
Q 011182 281 ICRCFGHLCCVNISDAVPGEVSCFR 305 (491)
Q Consensus 281 ~Cg~~GHl~c~~~~~~~~~~~~C~~ 305 (491)
+||+.+-++|.++..-||-.+.||.
T Consensus 11 ~CGekr~YCcSdpGrYCpwqvVCYe 35 (45)
T smart00816 11 NCGEKRKYCCSDPGRYCPWQVVCYE 35 (45)
T ss_pred cccccCccccCCCcccCCceEEEee
Confidence 6777777778788888888888886
No 41
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=32.86 E-value=13 Score=34.58 Aligned_cols=20 Identities=25% Similarity=0.707 Sum_probs=17.7
Q ss_pred ccccccccccCccccccccc
Q 011182 180 WQTCYNCGEEGHMAVNCRSA 199 (491)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~ 199 (491)
.+.|..|.+.|||..+|.+.
T Consensus 27 ~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred chhHHHHHhhccceeeecCc
Confidence 46899999999999999884
No 42
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.93 E-value=20 Score=41.71 Aligned_cols=10 Identities=20% Similarity=0.205 Sum_probs=5.0
Q ss_pred Ccchhhhhhh
Q 011182 97 TDDVIIEDVK 106 (491)
Q Consensus 97 ~~~~~~~~~k 106 (491)
-|....+.-|
T Consensus 737 lD~~La~~Fk 746 (784)
T PF04931_consen 737 LDEQLAAIFK 746 (784)
T ss_pred HHHHHHHHHH
Confidence 3455555545
No 43
>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 PTZ00110 helicase; Provisional
Probab=30.44 E-value=6.6 Score=43.72 Aligned_cols=49 Identities=16% Similarity=0.127 Sum_probs=38.0
Q ss_pred CccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCcccCCCCCC
Q 011182 403 GIMTSRKSKQRGGWITDDPGDISYGKPKRNHWRSPGTPSSKAHKISAITSGGHF 456 (491)
Q Consensus 403 ~~~~~~~~~srgg~~~~~~~~~~~~~~~~~~~~~p~tp~~~~~~~~~~~~g~~~ 456 (491)
+...|.+..+ |......+.++...++.||..| ||+|... +|++++|.+.
T Consensus 122 g~~~p~p~~~---f~~~~l~~~l~~~l~~~g~~~p-t~iQ~~a-ip~~l~G~dv 170 (545)
T PTZ00110 122 GENVPKPVVS---FEYTSFPDYILKSLKNAGFTEP-TPIQVQG-WPIALSGRDM 170 (545)
T ss_pred CCCCCcccCC---HhhcCCCHHHHHHHHHCCCCCC-CHHHHHH-HHHHhcCCCE
Confidence 4555666665 5555556677788889999999 9999999 9999998763
No 45
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=28.08 E-value=27 Score=40.55 Aligned_cols=29 Identities=31% Similarity=0.785 Sum_probs=21.9
Q ss_pred CCCCCCCCCCcccCCCCCCCcCcCCCccc
Q 011182 328 GETVEASPSSCYNCGAEGHFARECVSSSK 356 (491)
Q Consensus 328 ~~~~~~~~~~Cy~Cg~~GH~ardCp~~~~ 356 (491)
...++..+..|+.||+.||++.+|.....
T Consensus 253 E~~~P~~~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 253 EEFFPNKPRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred eeecCCCcccchhhcccCCcHhhcCCcCC
Confidence 34445667789999999999999976643
No 46
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=27.51 E-value=34 Score=37.64 Aligned_cols=56 Identities=21% Similarity=0.270 Sum_probs=32.0
Q ss_pred ccccchhhhhhccceeeeec-CcccccccccHHHHHHHHHHHhhcccCCCCCCcccccCCCCCC
Q 011182 12 YHEENGEEEEKLKSAAAMSS-DDEEGNEDLSLKIVEKHMLMRAAKLDQDDSDSDVVLNDNTNTN 74 (491)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~-~d~e~~~~~s~~~~~~~~~~~~~~~~~~d~~~~~~~~~d~~~~ 74 (491)
|..+++|+.|.+-+.--++. ||+||.+-- +--.++.+...-.|+++..|+|-++.+
T Consensus 85 d~~de~e~~e~~~~~~~l~~~~~de~~~~p-------~p~~k~~k~~k~~d~fs~~l~d~~~ee 141 (807)
T KOG0066|consen 85 DWSDEDEKPEKSLPANDLDDEDDDEAAKKP-------QPSKKNKKNKKKNDDFSLDLDDLDNEE 141 (807)
T ss_pred CCCccccchhhcCcccccCCCCchhhhcCC-------CCCccccccccCCCccceecccccccc
Confidence 34455566677766666666 555552211 123467777777888876665444433
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=25.99 E-value=9.2 Score=39.03 Aligned_cols=50 Identities=28% Similarity=0.437 Sum_probs=20.5
Q ss_pred ccccccccccCccccccccc--ccCCCCcceeecCCCCcccCCCCccccccccCCCC
Q 011182 180 WQTCYNCGEEGHMAVNCRSA--VKRKKPCFVCGSLEHGVRQCSKAQDCFICKKGGHR 234 (491)
Q Consensus 180 ~~~C~~CG~~GH~a~~Cp~~--~~~~~~C~~CG~~GH~a~~Cp~~~~C~~Cg~~GH~ 234 (491)
...|-.||..=.++.--... ..+...|..|+..-|+.+ ..|..|+...|.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R-----~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR-----IKCPYCGNTDHE 223 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--T-----TS-TTT---SS-
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC-----CCCcCCCCCCCc
Confidence 36899999987766665543 234556777776655542 445666666554
No 48
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.59 E-value=64 Score=38.66 Aligned_cols=32 Identities=31% Similarity=0.740 Sum_probs=19.0
Q ss_pred cCccccccccccCcccccccccccCCCCcceeecCCCCcccCC
Q 011182 178 RGWQTCYNCGEEGHMAVNCRSAVKRKKPCFVCGSLEHGVRQCS 220 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp~~~~~~~~C~~CG~~GH~a~~Cp 220 (491)
.+...|..||..+ ... .|-.||......+.||
T Consensus 624 Vg~RfCpsCG~~t-~~f----------rCP~CG~~Te~i~fCP 655 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYR----------RCPFCGTHTEPVYRCP 655 (1121)
T ss_pred ccCccCCCCCCcC-Ccc----------cCCCCCCCCCcceeCc
Confidence 4457799999986 223 4555666544444444
No 49
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=22.46 E-value=42 Score=38.04 Aligned_cols=18 Identities=50% Similarity=0.911 Sum_probs=12.2
Q ss_pred cCccccccccccCccccc
Q 011182 178 RGWQTCYNCGEEGHMAVN 195 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~ 195 (491)
...++|.+||+.||+..+
T Consensus 935 ~Ttr~C~nCGQvGHmkTN 952 (968)
T COG5179 935 NTTRTCGNCGQVGHMKTN 952 (968)
T ss_pred Ccceeccccccccccccc
Confidence 345678888888777543
No 50
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=22.18 E-value=46 Score=32.10 Aligned_cols=18 Identities=44% Similarity=1.215 Sum_probs=12.8
Q ss_pred CCcccCCCCCCCcCcCCC
Q 011182 336 SSCYNCGAEGHFARECVS 353 (491)
Q Consensus 336 ~~Cy~Cg~~GH~ardCp~ 353 (491)
..||+||+.||+.+.|.+
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 347777777777777765
No 51
>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=21.04 E-value=43 Score=30.36 Aligned_cols=19 Identities=21% Similarity=0.541 Sum_probs=0.0
Q ss_pred cCccccccccccCccccccc
Q 011182 178 RGWQTCYNCGEEGHMAVNCR 197 (491)
Q Consensus 178 ~~~~~C~~CG~~GH~a~~Cp 197 (491)
...+.|+.|+ -.||...||
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CP 122 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCP 122 (128)
T ss_pred CceEEeCCCC-CCcccccCC
No 52
>PRK14298 chaperone protein DnaJ; Provisional
Probab=20.74 E-value=91 Score=33.19 Aligned_cols=15 Identities=13% Similarity=0.180 Sum_probs=7.4
Q ss_pred hhhhhhhcccccccc
Q 011182 139 EQKVETADNGDEGVT 153 (491)
Q Consensus 139 ee~~E~~~~A~e~v~ 153 (491)
++.+.+++.|-++++
T Consensus 44 ~~~f~~i~~Ay~vL~ 58 (377)
T PRK14298 44 EEKFKEISEAYAVLS 58 (377)
T ss_pred HHHHHHHHHHHHHhc
Confidence 344555555554443
No 53
>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=20.51 E-value=57 Score=23.83 Aligned_cols=25 Identities=28% Similarity=0.675 Sum_probs=14.5
Q ss_pred ccCCCCcccccCcCCCCCCCccccc
Q 011182 281 ICRCFGHLCCVNISDAVPGEVSCFR 305 (491)
Q Consensus 281 ~Cg~~GHl~c~~~~~~~~~~~~C~~ 305 (491)
+||+.+-++|.++..-||-.+.||.
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 6778888888888888888888885
No 54
>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=20.43 E-value=85 Score=32.93 Aligned_cols=13 Identities=31% Similarity=0.864 Sum_probs=6.8
Q ss_pred cccccCCCCCcCC
Q 011182 250 QVCLKCGDSGHDM 262 (491)
Q Consensus 250 ~~C~~Cg~~GH~~ 262 (491)
..|..|+..|...
T Consensus 161 ~~C~~C~G~G~~~ 173 (354)
T TIGR02349 161 KTCPTCGGTGQVR 173 (354)
T ss_pred ccCCCCCCeeEEE
Confidence 3455566555443
No 55
>PRK14296 chaperone protein DnaJ; Provisional
Probab=20.37 E-value=73 Score=33.88 Aligned_cols=15 Identities=7% Similarity=0.147 Sum_probs=8.1
Q ss_pred hhhhhhhcccccccc
Q 011182 139 EQKVETADNGDEGVT 153 (491)
Q Consensus 139 ee~~E~~~~A~e~v~ 153 (491)
++++.+++.|-++++
T Consensus 43 ~~~F~~i~~AyevLs 57 (372)
T PRK14296 43 HDKMVEINEAADVLL 57 (372)
T ss_pred HHHHHHHHHHHHHhc
Confidence 445555555555554
No 56
>PRK14298 chaperone protein DnaJ; Provisional
Probab=20.36 E-value=83 Score=33.52 Aligned_cols=19 Identities=26% Similarity=0.211 Sum_probs=9.3
Q ss_pred cHHHHHHHHHHHhhcccCC
Q 011182 41 SLKIVEKHMLMRAAKLDQD 59 (491)
Q Consensus 41 s~~~~~~~~~~~~~~~~~~ 59 (491)
+.+-|.++-+..|.+.-.|
T Consensus 18 ~~~eik~ayr~la~~~HPD 36 (377)
T PRK14298 18 SVEDIKKAYRKLAMKYHPD 36 (377)
T ss_pred CHHHHHHHHHHHHHHhCcc
Confidence 3334555555555555433
Done!