Query psy353
Match_columns 1363
No_of_seqs 442 out of 701
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 19:00:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy353.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/353hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1140|consensus 100.0 2E-112 3E-117 1086.1 43.4 846 114-1008 11-940 (1738)
2 smart00396 ZnF_UBR1 Putative z 99.8 4.1E-21 9E-26 174.7 5.7 71 117-187 1-71 (71)
3 PF02207 zf-UBR: Putative zinc 99.8 2.7E-19 5.9E-24 163.2 4.1 71 117-187 1-71 (71)
4 KOG1140|consensus 99.7 3.7E-19 8E-24 231.2 -7.6 753 12-912 60-990 (1738)
5 PF02617 ClpS: ATP-dependent C 99.4 1.1E-13 2.4E-18 130.1 6.3 78 299-377 5-82 (82)
6 KOG1139|consensus 99.4 5.8E-13 1.3E-17 160.7 7.6 448 721-1194 205-769 (784)
7 PRK00033 clpS ATP-dependent Cl 98.7 2.8E-08 6.1E-13 96.4 8.4 73 299-378 26-98 (100)
8 PRK13019 clpS ATP-dependent Cl 98.4 5.5E-07 1.2E-11 86.6 7.4 64 299-362 20-84 (94)
9 KOG1139|consensus 97.1 1.9E-05 4E-10 97.1 -6.9 130 1056-1191 115-244 (784)
10 PF10390 ELL: RNA polymerase I 96.9 0.00042 9E-09 80.2 2.1 80 848-933 196-278 (284)
11 COG2127 Uncharacterized conser 94.8 0.066 1.4E-06 52.9 6.4 54 299-352 27-80 (107)
12 KOG1777|consensus 93.2 0.054 1.2E-06 64.1 2.6 54 121-176 553-606 (625)
13 KOG0943|consensus 85.3 0.26 5.6E-06 63.9 -0.0 56 116-172 1240-1299(3015)
14 cd02340 ZZ_NBR1_like Zinc fing 83.9 0.9 2E-05 37.9 2.6 37 118-159 5-41 (43)
15 PF09538 FYDLN_acid: Protein o 83.6 0.59 1.3E-05 46.7 1.7 29 1073-1101 8-39 (108)
16 cd02249 ZZ Zinc finger, ZZ typ 82.1 1.1 2.4E-05 37.7 2.5 37 118-159 5-44 (46)
17 KOG2752|consensus 81.4 1.9 4.1E-05 49.9 4.7 58 116-174 40-100 (345)
18 KOG4796|consensus 81.1 1.6 3.4E-05 53.6 4.2 74 849-929 210-286 (604)
19 cd02335 ZZ_ADA2 Zinc finger, Z 78.8 1.6 3.5E-05 37.4 2.5 39 118-160 5-48 (49)
20 cd02344 ZZ_HERC2 Zinc finger, 78.0 1.9 4E-05 36.5 2.5 37 119-159 6-43 (45)
21 cd02338 ZZ_PCMF_like Zinc fing 76.5 2.2 4.7E-05 36.6 2.6 38 118-160 5-48 (49)
22 TIGR02300 FYDLN_acid conserved 75.6 1.5 3.2E-05 44.7 1.6 28 1073-1100 8-38 (129)
23 PF00643 zf-B_box: B-box zinc 75.3 1.4 3.1E-05 36.0 1.2 28 127-159 13-40 (42)
24 PF13240 zinc_ribbon_2: zinc-r 74.5 1.7 3.8E-05 31.5 1.2 23 1076-1098 1-23 (23)
25 PF10571 UPF0547: Uncharacteri 72.2 2 4.2E-05 32.2 1.1 23 1076-1098 2-24 (26)
26 PF13248 zf-ribbon_3: zinc-rib 71.5 2.3 4.9E-05 31.7 1.3 25 1074-1098 2-26 (26)
27 KOG2905|consensus 67.8 3.4 7.5E-05 46.3 2.3 59 852-912 184-244 (254)
28 PRK00415 rps27e 30S ribosomal 67.7 1.9 4.1E-05 38.4 0.2 28 1073-1100 10-42 (59)
29 cd02339 ZZ_Mind_bomb Zinc fing 66.5 4.1 8.8E-05 34.5 2.0 30 127-159 13-43 (45)
30 cd02336 ZZ_RSC8 Zinc finger, Z 63.3 2.5 5.4E-05 35.7 0.1 30 119-153 6-35 (45)
31 PLN00209 ribosomal protein S27 60.1 2.5 5.4E-05 40.3 -0.5 39 1056-1100 24-67 (86)
32 PTZ00083 40S ribosomal protein 59.4 2.6 5.7E-05 40.0 -0.4 40 1056-1101 23-67 (85)
33 cd00021 BBOX B-Box-type zinc f 54.7 9.2 0.0002 30.4 2.1 28 127-159 10-37 (39)
34 smart00336 BBOX B-Box-type zin 54.1 10 0.00022 30.6 2.3 29 126-159 12-40 (42)
35 COG2051 RPS27A Ribosomal prote 53.4 7 0.00015 35.6 1.2 28 1074-1101 19-51 (67)
36 cd02341 ZZ_ZZZ3 Zinc finger, Z 52.4 11 0.00024 32.4 2.2 38 118-158 5-45 (48)
37 PF01667 Ribosomal_S27e: Ribos 52.4 7.4 0.00016 34.4 1.2 28 1073-1100 6-38 (55)
38 cd02343 ZZ_EF Zinc finger, ZZ 51.5 8.2 0.00018 33.2 1.3 35 118-157 5-40 (48)
39 cd02337 ZZ_CBP Zinc finger, ZZ 51.2 8.6 0.00019 31.9 1.4 32 117-154 4-35 (41)
40 PF14446 Prok-RING_1: Prokaryo 49.4 9 0.00019 33.7 1.2 47 1073-1130 4-52 (54)
41 PF02148 zf-UBP: Zn-finger in 47.4 10 0.00022 34.1 1.4 48 1077-1138 1-48 (63)
42 PF02270 TFIIF_beta: Transcrip 46.2 11 0.00023 44.0 1.7 43 865-912 232-274 (275)
43 PF00569 ZZ: Zinc finger, ZZ t 40.9 7.7 0.00017 32.8 -0.4 36 118-157 9-45 (46)
44 smart00291 ZnF_ZZ Zinc-binding 39.8 19 0.00042 30.1 1.8 33 117-154 8-40 (44)
45 cd02334 ZZ_dystrophin Zinc fin 38.9 18 0.00039 31.2 1.5 32 118-153 5-36 (49)
46 cd02345 ZZ_dah Zinc finger, ZZ 37.8 21 0.00046 30.7 1.7 30 118-152 5-35 (49)
47 PF08271 TF_Zn_Ribbon: TFIIB z 32.1 29 0.00062 28.9 1.6 26 1076-1101 2-32 (43)
48 smart00290 ZnF_UBP Ubiquitin C 30.2 32 0.0007 29.1 1.7 24 1076-1101 1-24 (50)
49 COG4530 Uncharacterized protei 28.5 29 0.00063 34.6 1.2 26 1073-1098 8-36 (129)
50 PRK14559 putative protein seri 24.3 58 0.0013 42.5 3.2 24 1076-1099 3-26 (645)
51 PF05191 ADK_lid: Adenylate ki 23.7 29 0.00064 28.0 0.3 24 1075-1098 2-31 (36)
52 PF15616 TerY-C: TerY-C metal 22.4 48 0.001 34.5 1.6 25 1075-1102 78-102 (131)
53 PF12773 DZR: Double zinc ribb 21.6 45 0.00098 28.3 1.0 23 1077-1099 1-23 (50)
54 PF07649 C1_3: C1-like domain; 21.1 53 0.0012 25.1 1.2 21 117-138 4-24 (30)
55 PRK02935 hypothetical protein; 20.8 46 0.00099 33.2 1.0 28 1075-1102 71-100 (110)
56 COG5090 TFG2 Transcription ini 20.4 72 0.0016 36.0 2.5 63 851-916 192-257 (297)
57 KOG0944|consensus 20.2 76 0.0016 40.9 2.9 65 120-188 13-92 (763)
No 1
>KOG1140|consensus
Probab=100.00 E-value=1.5e-112 Score=1086.15 Aligned_cols=846 Identities=27% Similarity=0.404 Sum_probs=618.2
Q ss_pred CCccccccccccCccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccCCCccccCCCCCCCcCCCCCcCc
Q psy353 114 NPPSVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEAWKKEPYCDVHIIGTQKR 193 (1363)
Q Consensus 114 ~~~~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCGD~eawk~~~fC~~H~~~~~~~ 193 (1363)
..+..|||||++||++|+|.+|+.|+||++|..||+...|+-|.+.|++..++|.|||||++||..+..|+.|....++.
T Consensus 11 ~~g~~c~~~~~~~e~~y~c~~c~~~~~~~~c~~c~~~~~~~~~~~~v~~~~~~~~c~cgd~da~n~~~~~~~~~~~~~~~ 90 (1738)
T KOG1140|consen 11 HTGRNCGRVFKIGEPTYRCHECGTDDTCVLCIHCPEVHVNHSVCTKVHTEFTSGICDCGDEDAWNSPLHCKAEEQEDDIS 90 (1738)
T ss_pred hcccccccccccCCceEEEEecCCCcchhHHHhcchhhhhhhhcceeEecccccccCCCChhhccCcchHHHHhcccccc
Confidence 35789999999999999999999999999999997766666666788988899999999999999999999998776543
Q ss_pred CCC-CCCC---CHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC-CCCCCCcccchhcccCCCccccccccccccchhhh
Q psy353 194 HES-GSIL---PPDLAQRARLTFSSVLRYAYQLLTTDYGPSIPL-DLKVPPEDVLQITYSHNSDNFCTVLYNDEFHTFEQ 268 (1363)
Q Consensus 194 ~~~-~~~l---p~~l~~~~~~~~~~vl~y~~d~l~~~~~~~LP~-~L~~~~k~~~~~~~~~~~~~~~~vl~~de~~~~s~ 268 (1363)
... ...+ -++.+.. .....+++|..|++.-.+. .+|. +...+.+ .+..+.......+....+++...+
T Consensus 91 ~~~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~--~~~~~~~~~~~e~~~~~~~~~~~~-- 163 (1738)
T KOG1140|consen 91 ETNAAIKEEDVENDSVNI--ALVELVLDYFIDVFNQNIE-PLPTIQKDITNE--LREMTQQGYMYERAQFENDLKYEN-- 163 (1738)
T ss_pred hhhccchhhhhhhHHHHh--hccHHHHHHHHHHhhccch-hccccCccccch--HHHHhhhhhhhhhhhhhccccccc--
Confidence 210 0111 1111111 1223345777777763211 1121 1111100 000011111111122222222100
Q ss_pred cccccCCCCC------CCCCCCCCcchhhhcccCCCCceEEEEecCCCCCHHHHHHHHHHHhcCCHHHHHHHHHhhcccC
Q psy353 269 LLTTDYGPSI------PLDLKVPPEDVLQITYSHNSDNFCTVLYNDEFHTFEQVINTLVRSLKCSQKDAIEFVTNIDREG 342 (1363)
Q Consensus 269 l~~~~yg~~~------~~d~~~~~~~~~~~~~~~~~~~y~vvL~NDE~HtfdqVi~~L~~a~~~s~~~A~~~A~~ID~~G 342 (1363)
.... .|-+. +.+ .+.++++ ..+.+.++-++++.|.|.++++..+.....+ ..+.+-...||-+|
T Consensus 164 ~~~~-~~~~~~~~~~~~~~-~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 233 (1738)
T KOG1140|consen 164 DYMF-DGKTTAKTSPSNSP-EASPSLA-------KPENYTVITYIDNYVNYSQATTAARQGVPDN-VHIDLSTSRIDGEG 233 (1738)
T ss_pred cccc-CCcchhhccccccc-ccChhhc-------ccccccceEEeccchhhhhcchHHhcCCCcc-ceeccccceecchh
Confidence 0000 00000 000 0000111 0245778889999999999998887776544 33556666778888
Q ss_pred CeEEEccCcccchhHHHHHhhhcccCCCCCcEEEEEehHHHHHHHHHHHHHHHHHHHhcc-----ChhHHHHHhhhhc--
Q psy353 343 RAAVKCSNFSHCEDLKSEIERFTSRHGNRPIKVAVVNSVVIAHQIYAMRLLTWLQKVLGY-----SESFRMLFSEVCL-- 415 (1363)
Q Consensus 343 RavVk~~~~~~c~~~k~~I~~f~~~~~s~~L~v~v~~~~~~~~q~~~~~ll~WL~~~~~~-----s~~fR~i~c~~ll-- 415 (1363)
+ .+.+. .-.++.+.+-+..+.+|..+++.+..+.+++.+..+..| ...+ .-.++.-..+...
T Consensus 234 ~--~~~~~------~~~~~~~~~~~~~~~~l~~el~~~~e~~~~ea~~~~~~~---~~~~~d~~~~~~~~~~~~~~~~~~ 302 (1738)
T KOG1140|consen 234 R--LKQNQ------DISLLLGGFFAVDTNGLTDELTSWSEYLHQEACKYIINR---CLNIPDSSFQTTSRNMVGKTLCSE 302 (1738)
T ss_pred h--hhhcc------chhhhhcchhhhhcccchhhhHHHHHHHHHHhhhhhhhh---hhcccchHHHHHHHHHhccccCcc
Confidence 7 23222 222222222222445899999999999999999999999 2221 1112211111110
Q ss_pred -------c------CCC---------------------------------C-------ChhHHHHHhhhcccchHHHHHH
Q psy353 416 -------E------EKA---------------------------------P-------DLSIVEGILVKDSQLWKAARLH 442 (1363)
Q Consensus 416 -------~------~~p---------------------------------~-------~~s~l~~Lll~D~rlWK~~R~~ 442 (1363)
+ .++ + ...++++++++|.++||+.|.+
T Consensus 303 ~~~~~l~~~~~~~~~d~d~~~~~~~~~~~~~d~~~~~~~~~~~~~~~a~~~~~~~~l~~~~~~~~il~~d~~~~kr~r~~ 382 (1738)
T KOG1140|consen 303 YLNATLCGDMTPVVEDYDSNKFDKNDPENYIDLSILADGNNAPLRHHALSPSSSHSLSPFIRLQHILLFDNRYWKRLRKD 382 (1738)
T ss_pred cccccccCCccccccCchhhhccccchhhcccHHHHhhhhcccchhhhcCCCchhccchhHHHHHHHHHHHHHHHHHHHH
Confidence 0 000 0 1258999999999999999999
Q ss_pred HHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHhccCCCCCccceeEEEeccchhHHHHHHhhhCHHHHH---HHHHH
Q psy353 443 WHRLFISGMLMEYESKKSFARVFTKKYGSIMKDFIKDDHDHSFSIGSMSVQIYTVPTLAHYLIAHEDVLFIL---LSTFI 519 (1363)
Q Consensus 443 l~~L~i~tLl~~~e~K~~fa~~F~~~Y~~L~~~fl~dD~e~~~SI~~LSVQLFTvPSla~~Lv~~~nll~~l---l~t~~ 519 (1363)
++.++++++.++.++|+.||.+|+.+|..+.++|+.+||+++.+++.++||+||||++|..+++...+...+ +++|+
T Consensus 383 l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~~~vi~~~vqf~t~~~~a~~~~~~~~~~~l~~~~~~~~~ 462 (1738)
T KOG1140|consen 383 LQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPDLSVIELSVQFFTCPSLAKNIVENQSFLDIVWSIIDIFK 462 (1738)
T ss_pred HhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhheeeeecCcHHHHHhhhhccchHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999998899999999999999999998855554 34555
Q ss_pred HHhhhhccCCCceeeeec--CCc-----ccccchhHhhhchhhhccCCCCCCChHHHhhhhhhHHHHHHHHHHhcCCCce
Q psy353 520 SECTRKLNKKKKLEFERN--IPN-----ASFKRAQYILYDLRYLLGVPPDTWTPELRKGFAHGLQFLLDLLSYMQGMDEV 592 (1363)
Q Consensus 520 ~~~~~~~~~~g~l~f~~~--~~~-----~~frR~~~i~~DLrYlLs~~~~~~~~~lr~~fl~~~~~~L~lL~l~QGm~p~ 592 (1363)
.+.. ..++...++.. +.. .++||.++.|.|+ +.+.++ | +..|.++|..++.+++.||||+|+
T Consensus 463 ~~~~---~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~---~----~~~~~~~~~~~l~~~~v~qg~~~l 531 (1738)
T KOG1140|consen 463 EFNK---VEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDP---N----IPLRPKEFISLLLLLKVFQGVDPL 531 (1738)
T ss_pred Hhcc---cccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCc---c----ccccHHHHHHHHHHHHHhCCccHH
Confidence 5432 12333333332 222 1456777777777 665543 3 556778999999999999999999
Q ss_pred eccccccccccccchhhhHHHHhHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhhccCCCCCCccceeeeCCccceeeee
Q psy353 593 TRQVGQHMEYEPEWESAFNLHIKLAPVITLFLQWCGTDKEILIKAYRATMKTLCADEGIDLGQLGEVREVGDHSVACLHY 672 (1363)
Q Consensus 593 ~R~~geHVEyE~eW~~aF~l~~~l~~ii~~~~~~~~~d~~~L~~ai~~~l~~L~~~~~~~~~~~~~~~~l~~~s~~ii~f 672 (1363)
+|+.++||++|.+|+.+|.+.++++.+++++++||.+++.+...+.+.+..+++.....-...+....++++++.+++.|
T Consensus 532 kr~~~ehv~~e~~~~~~~~~v~~~t~~~s~i~~~~~~~ep~~~~~~~~l~~~~~r~~~s~~~~~~l~~~i~~~S~e~i~f 611 (1738)
T KOG1140|consen 532 KREELEHVEVEKEWENFFSLVEYLTAIYSMIQSLVKTSEPVKDSVYKKLLEAAIRIHPSLTGSESLTYTICGESHETINF 611 (1738)
T ss_pred HHHHhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHhhcccccCccceeeehhhhhhHhHhhh
Confidence 99999999999999999999999999999999999988777667777776666532211111122345678999999999
Q ss_pred eecCCceeeechHHHHHHHHHHHHhhcccchhhhhhhccccCCCCCC-hhhhhhhhHHHHHHHhhhhhcccccccHhHHH
Q psy353 673 DVSTQPVSIHLPLSRFLAGLYIHLDKFNLSFYSRELLSDNCFFSRLT-PEQLIEPVLRTQVMISQVHAGMWRRNGYSLLN 751 (1363)
Q Consensus 673 dVs~~~VSfH~PLhr~LA~L~~~l~~~~~~~~~~el~~~~~~~~~~~-~~~L~e~PLR~~Vl~AQI~AGmWvRNG~sl~~ 751 (1363)
+|+.++||||+|+.|+|++++ .+....+.....+.. +..+.+ ..+|.|||||++|++|||.+|||||||+|+.+
T Consensus 612 ~v~~~~~sv~~p~~~~l~~l~-~~~~s~v~~~~d~~~----~~~~~~n~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~ 686 (1738)
T KOG1140|consen 612 SVSQERVSVSNPVSRLLAFLI-ELSCSSVVSLKDAYE----RLEDCSNFLAISEHSLRVLVLCAQIDVGFWVRNGFSILH 686 (1738)
T ss_pred ccccccceeeccHHHHhhhhh-hcccchhhhcchhhh----hHhhhccchhhcccchhheeeeeecceeeEeecCcchhh
Confidence 999999999999999999986 333222222222221 122222 77999999999999999999999999999999
Q ss_pred HHHHcccCccccchhhhhHHHHHHHhhccChHHHHHHHHHhccccccccccccCCCCCCchhhHHhhhHHHHHHHHHHHH
Q psy353 752 QIYFYHNVKCRNEMLDKDIILLQIGASLIESNEFLIHVLNKFNLINWVYVNFESNSLKNPEEESIRQTISLVEEFLHLLI 831 (1363)
Q Consensus 752 Q~~~Y~~~~~r~~~~d~DI~LLQi~a~l~dp~~fL~~iL~RF~L~~W~~~~~~~~~~~~~~eD~~~q~~~l~EefL~lLI 831 (1363)
|+++|++.+||+++||+||+++|.++++.||++|+.++++||+|.+|+++.++... .|..++...|+|+|+.+||
T Consensus 687 q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~w~~g~~~~~~-----~d~~~~i~~~~ee~l~lii 761 (1738)
T KOG1140|consen 687 QAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLDWFTGEVDYQS-----NDTEDTISFMIEEFLALII 761 (1738)
T ss_pred hhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCcccc-----ccHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999865543 2445688899999999999
Q ss_pred HHhccccCCCCCCCCcHHHHHHHHHHHHhcCCCChHHHhhhCCCCCCCcchHHHHHHHhhcccCCCcCCCCceeeecccc
Q psy353 832 LITGERYMPGIGRVASDDCIKKEIIQQLCIKPLPHSELNKALPDDSNHETGLERVINEIADFKKPTQSSGKGVYELKPEF 911 (1363)
Q Consensus 832 ~LlteR~~~g~~~~t~~~~irreIIh~Lc~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~ 911 (1363)
.|++||...|++.+..++.+|++|||+||++|++||+|.+++|++++.+..||.++++||+|++|.|..+.|+|+||+|+
T Consensus 762 ~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~~ 841 (1738)
T KOG1140|consen 762 LLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKESY 841 (1738)
T ss_pred HHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechhh
Confidence 99999988899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCcccccCChHHHHHHHHHHHH-HHHhccCCccCCCCCCCCCCCcchhhhhhhhhHHHHHHHHHHHHHhhcccCCCC
Q psy353 912 YDGYNVFFYHYSREEVSRSEEEQRK-RRKAAKELECVPPPKLPPLLPPFSMVTNLLQCDVMLHVMSLVLERSINLRARSF 990 (1363)
Q Consensus 912 ~~e~DPyf~hYsr~~~~~Ae~~~kk-~~K~~~~~~~~ppP~lp~~~~~F~~l~~il~s~~f~~ii~~vL~~al~~~~~~~ 990 (1363)
|++|||||+||++++|++++..+++ +.++++...+.+||.+|.+...|+...++|-+.+...+...++++++...-...
T Consensus 842 ~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~~~~~~~ 921 (1738)
T KOG1140|consen 842 YDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLEHCLFME 921 (1738)
T ss_pred hhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999865 444443333555566666666665555555555555555555555554322235
Q ss_pred CHHHHHHHH-HHHHhhhcc
Q psy353 991 SEAQLHKIL-HLIGYALHE 1008 (1363)
Q Consensus 991 sE~~L~~~L-HLi~lal~e 1008 (1363)
++++++.++ |++++|+++
T Consensus 922 s~~~l~~~~~~ihG~~~~~ 940 (1738)
T KOG1140|consen 922 SSTLLSKVLHLIHGIALNE 940 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 899999999 555666654
No 2
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=99.83 E-value=4.1e-21 Score=174.65 Aligned_cols=71 Identities=48% Similarity=1.118 Sum_probs=68.1
Q ss_pred cccccccccCccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccCCCccccCCCCCCCcCC
Q psy353 117 SVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEAWKKEPYCDVHI 187 (1363)
Q Consensus 117 ~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCGD~eawk~~~fC~~H~ 187 (1363)
..||++|+.||++|+|+||+.++++++|..||+++.|+||+|.++.+.+||.|||||++|||+++||++|.
T Consensus 1 ~~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~~~~~~~~~~~CDCG~~~~~~~~~~C~~h~ 71 (71)
T smart00396 1 DVCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDYSLKTSRGSGICDCGDKEAWNEDLKCKAHE 71 (71)
T ss_pred CCCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCEEEEEecCCEEECCCChhccCCCccccccC
Confidence 36999999999999999999999999999999999999999999988877999999999999999999994
No 3
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=99.76 E-value=2.7e-19 Score=163.22 Aligned_cols=71 Identities=42% Similarity=0.981 Sum_probs=54.7
Q ss_pred cccccccccCccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccCCCccccCCCCCCCcCC
Q psy353 117 SVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEAWKKEPYCDVHI 187 (1363)
Q Consensus 117 ~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCGD~eawk~~~fC~~H~ 187 (1363)
+.|+++|.+++++|+|+||+.|++.++|.+||.++.|+||++.+..+.++|.|||||+++||+++||+.|+
T Consensus 1 ~~C~~~~~~~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~~~~~CDCG~~~~~k~~~~C~~H~ 71 (71)
T PF02207_consen 1 KKCTYVWTSGQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSSSGGCCDCGDPEAWKKEGFCKKHK 71 (71)
T ss_dssp -SS--B--TT-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--SCEBB-TT-GGGBSS--S-TTT-
T ss_pred CcCCCCCcCCCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeCCCeEEeCCCCccccCCCCCCCCC
Confidence 36999999999999999999999999999999999999999999887779999999999999999999995
No 4
>KOG1140|consensus
Probab=99.69 E-value=3.7e-19 Score=231.18 Aligned_cols=753 Identities=8% Similarity=-0.136 Sum_probs=443.2
Q ss_pred cccccCCCccccccccccccccchhHHHHHHHHHhcCCCCHHHHHHHHHHhcCccccCCCCCCCCCCccchHHHHHHHHH
Q psy353 12 MDDSIGSDMDVEQQLPVFIQCSSTNVVNDWKQKFQQGTLSITDFKEHWKVWVPHLLSPEPKSSCLDWSFDENKVQNILFD 91 (1363)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~vp~~~~~~~~~~~~~~~~~~~~~~~~ll~ 91 (1363)
++.+.+.+-+..+. --.|+.+.+.-++|.+.. .+...+++..+|++++...+. +-...+++++.
T Consensus 60 ~~~~~~c~cgd~da--~n~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~-------~~l~~~~~~~~ 123 (1738)
T KOG1140|consen 60 EFTSGICDCGDEDA--WNSPLHCKAEEQEDDISE-------TNAAIKEEDVENDSVNIALVE-------LVLDYFIDVFN 123 (1738)
T ss_pred cccccccCCCChhh--ccCcchHHHHhcccccch-------hhccchhhhhhhHHHHhhccH-------HHHHHHHHHhh
Confidence 34444444443333 225677788888886655 557888999999999988666 33488999999
Q ss_pred HHHHHHcCCChHHHHHHhhcCCCCccccccccccCccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccC
Q psy353 92 SLEEFICDGSPEEIFQKVSQMDNPPSVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDC 171 (1363)
Q Consensus 92 ~l~~~l~g~~p~~~~~~l~~~~~~~~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDC 171 (1363)
+..|.+.++.|...+++....+.....|+++|.+++.++.|+.|..++|+..|..|+....|..|+ ..+.+++.|+|
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 200 (1738)
T KOG1140|consen 124 QNIEPLPTIQKDITNELREMTQQGYMYERAQFENDLKYENDYMFDGKTTAKTSPSNSPEASPSLAK---PENYTVITYID 200 (1738)
T ss_pred ccchhccccCccccchHHHHhhhhhhhhhhhhhcccccccccccCCcchhhcccccccccChhhcc---cccccceEEec
Confidence 999999999998888877766677888999999999999999999999999999999999999999 55667899999
Q ss_pred CCccccCCCCCCCcCCCCCcCcCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcccchhcccCC
Q psy353 172 GDVEAWKKEPYCDVHIIGTQKRHE-SGSILPPDLAQRARLTFSSVLRYAYQLLTTDYGPSIPLDLKVPPEDVLQITYSHN 250 (1363)
Q Consensus 172 GD~eawk~~~fC~~H~~~~~~~~~-~~~~lp~~l~~~~~~~~~~vl~y~~d~l~~~~~~~LP~~L~~~~k~~~~~~~~~~ 250 (1363)
|| .+|+....|..|...++.... ..+.+.-+..++-...|..++.+..++..+..+.+|++.+...
T Consensus 201 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~el~~~~e~~------------ 267 (1738)
T KOG1140|consen 201 NY-VNYSQATTAARQGVPDNVHIDLSTSRIDGEGRLKQNQDISLLLGGFFAVDTNGLTDELTSWSEYL------------ 267 (1738)
T ss_pred cc-hhhhhcchHHhcCCCccceeccccceecchhhhhhccchhhhhcchhhhhcccchhhhHHHHHHH------------
Confidence 99 899999999999876543221 1122222222556667777888888888876554444422110
Q ss_pred CccccccccccccchhhhcccccCCCCCCCCCCCCCcchhhhcccCCCCceEEEEecCCCCCHHHHHHHHHHHhcCCHHH
Q psy353 251 SDNFCTVLYNDEFHTFEQLLTTDYGPSIPLDLKVPPEDVLQITYSHNSDNFCTVLYNDEFHTFEQVINTLVRSLKCSQKD 330 (1363)
Q Consensus 251 ~~~~~~vl~~de~~~~s~l~~~~yg~~~~~d~~~~~~~~~~~~~~~~~~~y~vvL~NDE~HtfdqVi~~L~~a~~~s~~~ 330 (1363)
.+| ...|+ ++| .+++.++..+......+....
T Consensus 268 ---------~~e-----------------------------------a~~~~-~~~---~~~~~d~~~~~~~~~~~~~~~ 299 (1738)
T KOG1140|consen 268 ---------HQE-----------------------------------ACKYI-INR---CLNIPDSSFQTTSRNMVGKTL 299 (1738)
T ss_pred ---------HHH-----------------------------------hhhhh-hhh---hhcccchHHHHHHHHHhcccc
Confidence 000 01233 666 888999999988888888888
Q ss_pred HHHHHHhhcccCCeEEEccCcccchhHHHHHhhhcccCCCCCcEEEEEehHHHHHHHHHHHHHHHHHHHhccChhHHHHH
Q psy353 331 AIEFVTNIDREGRAAVKCSNFSHCEDLKSEIERFTSRHGNRPIKVAVVNSVVIAHQIYAMRLLTWLQKVLGYSESFRMLF 410 (1363)
Q Consensus 331 A~~~A~~ID~~GRavVk~~~~~~c~~~k~~I~~f~~~~~s~~L~v~v~~~~~~~~q~~~~~ll~WL~~~~~~s~~fR~i~ 410 (1363)
+...++ ++..||-.+...++..+...+..+++...... ..+.+.+..... +++.....-+.|+.-
T Consensus 300 ~~~~~~-~~l~~~~~~~~~d~d~~~~~~~~~~~~~d~~~-~~~~~~~~~~~~-a~~~~~~~~l~~~~~------------ 364 (1738)
T KOG1140|consen 300 CSEYLN-ATLCGDMTPVVEDYDSNKFDKNDPENYIDLSI-LADGNNAPLRHH-ALSPSSSHSLSPFIR------------ 364 (1738)
T ss_pred Cccccc-ccccCCccccccCchhhhccccchhhcccHHH-Hhhhhcccchhh-hcCCCchhccchhHH------------
Confidence 888899 99999999999887766666655554322111 022222222222 444433344444431
Q ss_pred hhhhccCCCCChhHHHHHhhhcccchHHHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcccee
Q psy353 411 SEVCLEEKAPDLSIVEGILVKDSQLWKAARLHWHRLFISGMLMEYESKKSFARVFTKKYGSIMKDFIKDDHDHSFSIGSM 490 (1363)
Q Consensus 411 c~~ll~~~p~~~s~l~~Lll~D~rlWK~~R~~l~~L~i~tLl~~~e~K~~fa~~F~~~Y~~L~~~fl~dD~e~~~SI~~L 490 (1363)
++-. -.+-+++..+.+..|||.++--++..++...++...|+..++..+...|..-.+.....+ +...+.+..
T Consensus 365 ~~~i------l~~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~~~vi-~~~vqf~t~ 437 (1738)
T KOG1140|consen 365 LQHI------LLFDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPDLSVI-ELSVQFFTC 437 (1738)
T ss_pred HHHH------HHHHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcchhhH-hheeeeecC
Confidence 1111 013456778888899999999999999999999999999999999988887666555555 444444444
Q ss_pred EEEeccchhHHHH----------HHhh-----------------------------------------------------
Q psy353 491 SVQIYTVPTLAHY----------LIAH----------------------------------------------------- 507 (1363)
Q Consensus 491 SVQLFTvPSla~~----------Lv~~----------------------------------------------------- 507 (1363)
.++.++.+..... +++.
T Consensus 438 ~~~a~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l~~~~~~~~~~~~~~~~~ 517 (1738)
T KOG1140|consen 438 PSLAKNIVENQSFLDIVWSIIDIFKEFNKVEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDLSKVHDPNIPLRPKEFIS 517 (1738)
T ss_pred cHHHHHhhhhccchHHHHHHHHHHHHhcccccceecceeeeechhhhHHHHHHHHHHHHHHHhhccCCccccccHHHHHH
Confidence 4444443332210 0000
Q ss_pred ----------------------------hCHHHHHH--HHHHHHhhh-------------------------hccC----
Q psy353 508 ----------------------------EDVLFILL--STFISECTR-------------------------KLNK---- 528 (1363)
Q Consensus 508 ----------------------------~nll~~ll--~t~~~~~~~-------------------------~~~~---- 528 (1363)
++++.+++ ..+++.+.. .+..
T Consensus 518 ~l~~~~v~qg~~~lkr~~~ehv~~e~~~~~~~~~v~~~t~~~s~i~~~~~~~ep~~~~~~~~l~~~~~r~~~s~~~~~~l 597 (1738)
T KOG1140|consen 518 LLLLLKVFQGVDPLKREELEHVEVEKEWENFFSLVEYLTAIYSMIQSLVKTSEPVKDSVYKKLLEAAIRIHPSLTGSESL 597 (1738)
T ss_pred HHHHHHHhCCccHHHHHHhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHhhcccccCcccee
Confidence 00000000 000000000 0000
Q ss_pred --------CCceeeeecCCccc-cc---chhHh------------------hh----------------------chhhh
Q psy353 529 --------KKKLEFERNIPNAS-FK---RAQYI------------------LY----------------------DLRYL 556 (1363)
Q Consensus 529 --------~g~l~f~~~~~~~~-fr---R~~~i------------------~~----------------------DLrYl 556 (1363)
....+|+....... +. |.+.+ +. |.+|.
T Consensus 598 ~~~i~~~S~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~v~~~~d~~~~~~~~~n~~~i~e~~lr~~Vl~aqid~~~w 677 (1738)
T KOG1140|consen 598 TYTICGESHETINFSVSQERVSVSNPVSRLLAFLIELSCSSVVSLKDAYERLEDCSNFLAISEHSLRVLVLCAQIDVGFW 677 (1738)
T ss_pred eehhhhhhHhHhhhccccccceeeccHHHHhhhhhhcccchhhhcchhhhhHhhhccchhhcccchhheeeeeecceeeE
Confidence 01112221110000 01 11111 11 11122
Q ss_pred ccCCCCCCChHHHhhhhhhHHHHHHHHHHhcCCCceeccccccccccccchhhhHHHHhHHHHHHHHHhhhcCC-HHHHH
Q psy353 557 LGVPPDTWTPELRKGFAHGLQFLLDLLSYMQGMDEVTRQVGQHMEYEPEWESAFNLHIKLAPVITLFLQWCGTD-KEILI 635 (1363)
Q Consensus 557 Ls~~~~~~~~~lr~~fl~~~~~~L~lL~l~QGm~p~~R~~geHVEyE~eW~~aF~l~~~l~~ii~~~~~~~~~d-~~~L~ 635 (1363)
...++..|. +.+-.|...++.++--...++++-.+.+. +|.+.-..|.+.|-+...++.. .+.-..| ...+.
T Consensus 678 ~rNG~si~~-q~~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~g~----~~~~~~d~~~~i~ 750 (1738)
T KOG1140|consen 678 VRNGFSILH-QAAYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFTGE----VDYQSNDTEDTIS 750 (1738)
T ss_pred eecCcchhh-hhHhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhcCC----CccccccHHHHHH
Confidence 222222232 33333322333444444445554444444 5555555555555553333221 1111112 22333
Q ss_pred HHHHHHHHHHhhccCCCCCCccceeeeCCccceeeeeeecCCceeeechHHHHHHHHHHHHhhcccchhhhhhhccccCC
Q psy353 636 KAYRATMKTLCADEGIDLGQLGEVREVGDHSVACLHYDVSTQPVSIHLPLSRFLAGLYIHLDKFNLSFYSRELLSDNCFF 715 (1363)
Q Consensus 636 ~ai~~~l~~L~~~~~~~~~~~~~~~~l~~~s~~ii~fdVs~~~VSfH~PLhr~LA~L~~~l~~~~~~~~~~el~~~~~~~ 715 (1363)
.++..++..++. .. .+ +... +..-+.+.+......+|+++-+-+|+........+.... .+ ..
T Consensus 751 ~~~ee~l~lii~-ll----~E---r~~~--~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~--~l-----~~ 813 (1738)
T KOG1140|consen 751 FMIEEFLALIIL-LL----TE---RSYF--GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTK--TL-----SF 813 (1738)
T ss_pred HHHHHHHHHHHH-HH----Hh---eeec--ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhh--cc-----cc
Confidence 333333333220 00 00 1111 122344556666788999999999875433222111110 00 00
Q ss_pred CC--CChhhhhhhhHHHHHHHhhhhhcccccccHhHHHHHHHcccCccccchhhhhHHHHHHHhhccChHHHHHHHHHhc
Q psy353 716 SR--LTPEQLIEPVLRTQVMISQVHAGMWRRNGYSLLNQIYFYHNVKCRNEMLDKDIILLQIGASLIESNEFLIHVLNKF 793 (1363)
Q Consensus 716 ~~--~~~~~L~e~PLR~~Vl~AQI~AGmWvRNG~sl~~Q~~~Y~~~~~r~~~~d~DI~LLQi~a~l~dp~~fL~~iL~RF 793 (1363)
+. ..+....++++++.+.++++|+++|.+++-...++...|+....+..+++|+.-+.+++|.+.+|..++..+++ .
T Consensus 814 d~~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~-~ 892 (1738)
T KOG1140|consen 814 DEALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLK-K 892 (1738)
T ss_pred hHHHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHH-H
Confidence 10 11235778999999999999999999999999999999999999999999999999999999999999988887 3
Q ss_pred cccccccccccCCCCCCchhhHHhhhHHHHHHHHHHHHHHhccccCCCCCCCCcHHHHHHHHHHHHhcCCCChHHHhhhC
Q psy353 794 NLINWVYVNFESNSLKNPEEESIRQTISLVEEFLHLLILITGERYMPGIGRVASDDCIKKEIIQQLCIKPLPHSELNKAL 873 (1363)
Q Consensus 794 ~L~~W~~~~~~~~~~~~~~eD~~~q~~~l~EefL~lLI~LlteR~~~g~~~~t~~~~irreIIh~Lc~~p~t~SeL~~~l 873 (1363)
+....+.. .... ..-+.+++++..+..+..-.|..-..++..|++..+..+.++ ++-++. .
T Consensus 893 ~~~~L~~~-t~~~----~~~~ii~r~~~~~~~~~s~~~l~~~~~~ihG~~~~~~l~~~~----------~~~~~~----~ 953 (1738)
T KOG1140|consen 893 GADILGAA-VRLT----VFGLIIYRTLEHCLFMESSTLLSKVLHLIHGIALNEELINMK----------FAFTQK----T 953 (1738)
T ss_pred HHHHHHHH-HHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc----------cccccc----c
Confidence 43332210 0000 011333444444444444344444444555543222222222 333333 4
Q ss_pred CCCCCCcchHHHHHHHhhcccCCCcCCCCceeeeccccc
Q psy353 874 PDDSNHETGLERVINEIADFKKPTQSSGKGVYELKPEFY 912 (1363)
Q Consensus 874 pe~~~~~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~ 912 (1363)
+ ...++.+..-.-.-|+.+..+ +..+.+.+.+|..--
T Consensus 954 e-~~~~e~gl~~~e~lv~~~~~~-~~~~~~~v~~~l~~~ 990 (1738)
T KOG1140|consen 954 E-SIAREKGLSLYESLVRKPDSL-VHGKIIEVIVELFES 990 (1738)
T ss_pred c-ccccccchhhHHHhhhcchhh-cCCcceeeeHHHHhh
Confidence 4 455667777777778887777 556778888877544
No 5
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=99.44 E-value=1.1e-13 Score=130.10 Aligned_cols=78 Identities=36% Similarity=0.645 Sum_probs=63.2
Q ss_pred CceEEEEecCCCCCHHHHHHHHHHHhcCCHHHHHHHHHhhcccCCeEEEccCcccchhHHHHHhhhcccCCCCCcEEEE
Q psy353 299 DNFCTVLYNDEFHTFEQVINTLVRSLKCSQKDAIEFVTNIDREGRAAVKCSNFSHCEDLKSEIERFTSRHGNRPIKVAV 377 (1363)
Q Consensus 299 ~~y~vvL~NDE~HtfdqVi~~L~~a~~~s~~~A~~~A~~ID~~GRavVk~~~~~~c~~~k~~I~~f~~~~~s~~L~v~v 377 (1363)
+.|.|+|||||+|||++||++|++++|++.++|.++|..||++||++|..++.+.|+...+.|.++. +....||+++|
T Consensus 5 ~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~~g-~~~~~PL~~ti 82 (82)
T PF02617_consen 5 DMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQRAG-RDSGHPLRATI 82 (82)
T ss_dssp -EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHHHH-HHTT---EEEE
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHHHh-hccCCCeEEeC
Confidence 5789999999999999999999999999999999999999999999999999999999999998754 33445999986
No 6
>KOG1139|consensus
Probab=99.37 E-value=5.8e-13 Score=160.67 Aligned_cols=448 Identities=14% Similarity=0.140 Sum_probs=284.4
Q ss_pred hhhhhhhHHHHHHHhhhhhcccccccHh--HHHHHH--HcccCccccchhhhhHHHHHHHhhccChHHHHHHHHHhcccc
Q psy353 721 EQLIEPVLRTQVMISQVHAGMWRRNGYS--LLNQIY--FYHNVKCRNEMLDKDIILLQIGASLIESNEFLIHVLNKFNLI 796 (1363)
Q Consensus 721 ~~L~e~PLR~~Vl~AQI~AGmWvRNG~s--l~~Q~~--~Y~~~~~r~~~~d~DI~LLQi~a~l~dp~~fL~~iL~RF~L~ 796 (1363)
..+.-+++++.|--.-++..||+|+|.- +..|.+ +|.++. .---+-..+=.++..+++..||..++-+|.+.
T Consensus 205 wg~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~----kkrhePdt~~~r~~hi~~slfl~e~la~~~~~ 280 (784)
T KOG1139|consen 205 WGLLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSA----KKRHEPDTIRFRAAHIDKSLFLKELLASFNIT 280 (784)
T ss_pred HHHHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhccc----ccCCCCchhccccccccHHHHHHHHHHHhhhh
Confidence 3678889999999999999999999955 444443 333332 11112234445778899999999999999887
Q ss_pred cccc----------ccc---cC--CC----C----------------------------C---------------C-chh
Q psy353 797 NWVY----------VNF---ES--NS----L----------------------------K---------------N-PEE 813 (1363)
Q Consensus 797 ~W~~----------~~~---~~--~~----~----------------------------~---------------~-~~e 813 (1363)
+--. +.+ .. .. + + . .++
T Consensus 281 ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s 360 (784)
T KOG1139|consen 281 ECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDPRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDS 360 (784)
T ss_pred hhhhhhccceeEeccccccchhhhhhhccccccCchhcccCcchhHHHHhhccccccccCchHHHHhhhccccccccchh
Confidence 6211 000 00 00 0 0 0 000
Q ss_pred hH--------HhhhHHHHHHHHHHHHHHhccccCCCCCCCCcHHHHHHHHHHHHhcCCCChHHHhhhCCCCC-CCcchHH
Q psy353 814 ES--------IRQTISLVEEFLHLLILITGERYMPGIGRVASDDCIKKEIIQQLCIKPLPHSELNKALPDDS-NHETGLE 884 (1363)
Q Consensus 814 D~--------~~q~~~l~EefL~lLI~LlteR~~~g~~~~t~~~~irreIIh~Lc~~p~t~SeL~~~lpe~~-~~~~~fe 884 (1363)
+. ......+...+|.++..+|.++.+.| ..+++..+-|+.|.-+++..++|-+...+.+.. ..++.|+
T Consensus 361 ~vlr~~~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~---ai~~~~~~~em~n~~a~~~~~~s~~~aS~~~~~~~~~~~f~ 437 (784)
T KOG1139|consen 361 EVLRTIVIREPEWIDPMFWGMFKLVAELVVVSVNSG---AIPEEHYRSEMVNCMAMGNVPYSRLRASISEKGSMIDKHFE 437 (784)
T ss_pred hhhHHhhhccccccchhhcchHHHHHHHhhhhcccc---cchHHHHHHHHHhHHHhcCCCcccccccccCCCcccccccc
Confidence 10 01245677788888888888876544 578899999999999999999999998776554 3578999
Q ss_pred HHHHHhhcccCCCcCCC---Cceeeeccccc-cccCcccccCChHHHHHHHHHHHH--HHHhc-cCCccCC-CCCCCCC-
Q psy353 885 RVINEIADFKKPTQSSG---KGVYELKPEFY-DGYNVFFYHYSREEVSRSEEEQRK--RRKAA-KELECVP-PPKLPPL- 955 (1363)
Q Consensus 885 ~iL~eVA~Fk~P~g~~d---~G~Y~LK~E~~-~e~DPyf~hYsr~~~~~Ae~~~kk--~~K~~-~~~~~~p-pP~lp~~- 955 (1363)
.|+.+..+|..|-..++ +|.|.||...| .+.-|-|...+..--..|-+.+.+ .++.+ ..+..+- -.....+
T Consensus 438 ~i~~~~~~~~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~~~~~~s~~~~~~v~~~~~~~a~k~s~d~~l~~~~~~ed~s 517 (784)
T KOG1139|consen 438 TILNEIGDFIEPIETTTPLMQGSYQLKTSIWDSEVCPVFFMMRSTSIKQAREVFAKMEIRAQKNSLDKDLEVAKIEEDFS 517 (784)
T ss_pred cccccccccccchhhcCccccchhhccccCCccccccchheeeeeeccchhHHHHHHHHhhccchhhhhccccchhHHHH
Confidence 99999999999976555 99999999999 477787654432221122222111 22222 1111100 0000011
Q ss_pred ----CCcchhhhhhhhhHHHHHHHHHHHHHhhcccCCCCCHHHHHHHHHHHHhhhccccccC--Cc---ccccccc-ccc
Q psy353 956 ----LPPFSMVTNLLQCDVMLHVMSLVLERSINLRARSFSEAQLHKILHLIGYALHEEESGN--YQ---FFTFTDR-AEK 1025 (1363)
Q Consensus 956 ----~~~F~~l~~il~s~~f~~ii~~vL~~al~~~~~~~sE~~L~~~LHLi~lal~e~~~~~--~~---~~~f~~k-~~~ 1025 (1363)
...-..+.+.+.+..|..+--+++.+-++. .....|.--+.+.++..+...-+-+.. ++ ..+|+-. ...
T Consensus 518 ~~lr~~g~s~l~~~l~~~~~~d~~dt~~~~~~~~-~~~c~~~~~~la~~~~tl~~e~~~s~~~~~~i~~~m~~I~~~pf~ 596 (784)
T KOG1139|consen 518 DQLRHRGISNLYNVLLTERFLDHCDTVLASEADE-TAKCHDGTYQLAVYLLTLGVEYAQSYVGDEKIKKQMIDIFHTPFQ 596 (784)
T ss_pred HHHHHhhhHHHhhhhhhhhhhcccchhhccccch-hhhHHHHHHHHHHHHHHHhhhhhhhhcCCcchhhhhhhccCCchh
Confidence 111245566666666666666666655543 234455555666666666553222111 00 1111100 001
Q ss_pred ccHHHHHHHHhcCCCcccC-------------------CCC--CCCcccccccccCCCchHHHHHHhhcccccCCCCCCC
Q psy353 1026 WNIEQHIEELCSSPRVEAH-------------------KVP--QDRKPLEINRLINLPDDYSELINTVSLFTCPNSDRED 1084 (1363)
Q Consensus 1026 ~~I~~lLe~L~s~P~~ea~-------------------kv~--~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~ 1084 (1363)
.++.+-++...+.|-++.. |++ .+-.|...+.+.++|--|+++..+... ..
T Consensus 597 l~~kq~~~~~~~i~~i~e~~~k~~e~~~~~~~r~~e~~k~~r~~~~k~~~~fa~~~~~~~~q~~a~~s~~--------~~ 668 (784)
T KOG1139|consen 597 LILKQTRKNGALIVVIKEGKLKREELRISKHSRNQEKMKAPRDPVKKAAKEFAKRRMEAIMQNSAKKSAQ--------TE 668 (784)
T ss_pred hhHHHHHhcccCCchhHHHhHHHHHHHHHHHHHHHHHhhcccchHHHHhHHHHHHHHHHHHHHHHHhhhc--------cc
Confidence 1233333333444433221 222 222356668889999989887764333 23
Q ss_pred CCCceeeccccccccc-CCcccccccccccccccccccccccCCCeeEEEEeccceEEEEeCCCCcccCCCCcccCcCCC
Q psy353 1085 SRNPALCLICGDMLCS-QSYCCQTELFFKMSVGACTYHSHFCGAGVGMFLRVRECEVLFLASPNRGCFMSPPYLDDYGET 1163 (1363)
Q Consensus 1085 ~~~paiCL~CG~~lC~-q~~cC~~~~~~~~~~G~c~~H~~~Cg~g~GiFl~i~~~~vl~l~~~~rg~~~~spYlD~~GE~ 1163 (1363)
..+|+.|+.||...=- ..+||.. .+ .+|..+||+++|+|++|++ +.|+..+..+..-||+||||..|++
T Consensus 669 g~ed~~~~~~~~~q~~~k~y~C~i--------cg-~n~p~T~~np~G~~~l~~~-~~I~~~r~~~~~~~p~p~l~~de~e 738 (784)
T KOG1139|consen 669 GMEDAEVNKVDPSQQNRKVYECPI--------CG-QNAPNTVENPFGMLALLST-NFICEERIDASINTPDPLLKFDEYE 738 (784)
T ss_pred CCChHHHhhhCcccCCccCCcCCc--------CC-CCCCcccCCCceEEEEEee-cchHHHHHhhccCCCChhhhcchhh
Confidence 4689999999984332 5678852 23 5799999999999999997 5666666677889999999999999
Q ss_pred CCCCCCCCCcccCHHHHHHHHHHHHhcCcch
Q psy353 1164 DQGLRRGNPLRLCKERYKKLQRLWLSHGIHE 1194 (1363)
Q Consensus 1164 D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~ 1194 (1363)
|.+.-||+-+|++..||.+|....=+|.+.+
T Consensus 739 ~~~~~Rl~~e~~rr~~~~~l~~~~es~~l~~ 769 (784)
T KOG1139|consen 739 HVSANRLQSETRRRFFSKRLQATFESQDLVK 769 (784)
T ss_pred hhHHHHHHHHHHHHHHHHHhhhcccccchhh
Confidence 9999999999999999999999888887754
No 7
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=98.74 E-value=2.8e-08 Score=96.43 Aligned_cols=73 Identities=16% Similarity=0.287 Sum_probs=62.8
Q ss_pred CceEEEEecCCCCCHHHHHHHHHHHhcCCHHHHHHHHHhhcccCCeEEEccCcccchhHHHHHhhhcccCCCCCcEEEEE
Q psy353 299 DNFCTVLYNDEFHTFEQVINTLVRSLKCSQKDAIEFVTNIDREGRAAVKCSNFSHCEDLKSEIERFTSRHGNRPIKVAVV 378 (1363)
Q Consensus 299 ~~y~vvL~NDE~HtfdqVi~~L~~a~~~s~~~A~~~A~~ID~~GRavVk~~~~~~c~~~k~~I~~f~~~~~s~~L~v~v~ 378 (1363)
..|-|+||||++|||+.|+..|+++++++.++|.+++.+||.+||++|..++++.++...+.+.+ .||+++|-
T Consensus 26 ~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l~~-------~~L~~~ie 98 (100)
T PRK00033 26 PMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQVHQ-------HGLLCTME 98 (100)
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHHHc-------CCCeEEEe
Confidence 46999999999999999999999999999999999999999999999999987655554444432 38888874
No 8
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=98.42 E-value=5.5e-07 Score=86.64 Aligned_cols=64 Identities=25% Similarity=0.383 Sum_probs=54.1
Q ss_pred CceEEEEecCCCCCHHHHHH-HHHHHhcCCHHHHHHHHHhhcccCCeEEEccCcccchhHHHHHh
Q psy353 299 DNFCTVLYNDEFHTFEQVIN-TLVRSLKCSQKDAIEFVTNIDREGRAAVKCSNFSHCEDLKSEIE 362 (1363)
Q Consensus 299 ~~y~vvL~NDE~HtfdqVi~-~L~~a~~~s~~~A~~~A~~ID~~GRavVk~~~~~~c~~~k~~I~ 362 (1363)
..|-|+||||++|||+.||+ .++...+++.++|.+++.+||.+|+++|..++.+.++...+.+.
T Consensus 20 ~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~ 84 (94)
T PRK13019 20 PLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLT 84 (94)
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHH
Confidence 46999999999999999995 55556899999999999999999999999999765554444443
No 9
>KOG1139|consensus
Probab=97.09 E-value=1.9e-05 Score=97.11 Aligned_cols=130 Identities=13% Similarity=0.011 Sum_probs=106.4
Q ss_pred ccccCCCchHHHHHHhhcccccCCCCCCCCCCceeecccccccccCCcccccccccccccccccccccccCCCeeEEEEe
Q psy353 1056 NRLINLPDDYSELINTVSLFTCPNSDREDSRNPALCLICGDMLCSQSYCCQTELFFKMSVGACTYHSHFCGAGVGMFLRV 1135 (1363)
Q Consensus 1056 ~~Li~LP~~y~~l~~~~~~~~C~~c~~~~~~~paiCL~CG~~lC~q~~cC~~~~~~~~~~G~c~~H~~~Cg~g~GiFl~i 1135 (1363)
+.+.-||..+-.-++......|..|.+ ++++|++|..|+.+.|.+..||.... + .-+|..|...|++|+++++.+
T Consensus 115 P~~~~L~eltrmdfQ~r~~~tcs~~Ns-v~k~ptlen~cp~frl~k~L~a~qqs--s--yD~fv~h~q~~~asTsi~hf~ 189 (784)
T KOG1139|consen 115 PYMKMLCELTRMDFQWRIISTCSQENS-VQKAPTLENECPAFRLFKILAAIQQS--S--YDRFVDHIQSQHASTSITHFT 189 (784)
T ss_pred cHHHHHHHHhccCccceecccchhccC-CCCCCcccccccceechhhccccccc--C--CCcceecccccccchhhHHHH
Confidence 456667777777677777778999997 47899999999999999999886542 1 367999999999999999999
Q ss_pred ccceEEEEeCCCCcccCCCCcccCcCCCCCCCCCCCCcccCHHHHHHHHHHHHhcC
Q psy353 1136 RECEVLFLASPNRGCFMSPPYLDDYGETDQGLRRGNPLRLCKERYKKLQRLWLSHG 1191 (1363)
Q Consensus 1136 ~~~~vl~l~~~~rg~~~~spYlD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~ 1191 (1363)
+.+ |.-...+.+-++|+..|++.++|++..+++|++.+-+..++.-+...|.+|.
T Consensus 190 ~ds-v~~r~l~eell~wg~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~ 244 (784)
T KOG1139|consen 190 EDS-VRSRLLNEELLIWGLLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWN 244 (784)
T ss_pred HHH-HHHHHHHHHHHHHHHHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccch
Confidence 862 2222224677899999999999999999999999999999999988885444
No 10
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=96.90 E-value=0.00042 Score=80.19 Aligned_cols=80 Identities=25% Similarity=0.414 Sum_probs=58.5
Q ss_pred HHHHHHHHHHHHhcCCCChHHHhhhCCCCCCC---cchHHHHHHHhhcccCCCcCCCCceeeeccccccccCcccccCCh
Q psy353 848 DDCIKKEIIQQLCIKPLPHSELNKALPDDSNH---ETGLERVINEIADFKKPTQSSGKGVYELKPEFYDGYNVFFYHYSR 924 (1363)
Q Consensus 848 ~~~irreIIh~Lc~~p~t~SeL~~~lpe~~~~---~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~~e~DPyf~hYsr 924 (1363)
..-+|.-|||+|+++|....||..+|..+... -..++.||+|||... ..+.|.||+.+|+++|.=++.||-
T Consensus 196 ~rplReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~------~~~~y~Lk~~~ykevq~dWP~yse 269 (284)
T PF10390_consen 196 KRPLRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLN------KDNSYTLKDHFYKEVQKDWPGYSE 269 (284)
T ss_dssp TS-HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEE------TTTEEEE-STHHHHS-TT-TT--T
T ss_pred cccccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccC------cCCeEEehHHHHhhhccCCCCCCH
Confidence 34699999999999999999999988654433 357999999999865 357999999999999988999998
Q ss_pred HHHHHHHHH
Q psy353 925 EEVSRSEEE 933 (1363)
Q Consensus 925 ~~~~~Ae~~ 933 (1363)
.|++-...+
T Consensus 270 ~erq~l~r~ 278 (284)
T PF10390_consen 270 EERQLLKRR 278 (284)
T ss_dssp CHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 888655433
No 11
>COG2127 Uncharacterized conserved protein [Function unknown]
Probab=94.84 E-value=0.066 Score=52.93 Aligned_cols=54 Identities=24% Similarity=0.410 Sum_probs=51.0
Q ss_pred CceEEEEecCCCCCHHHHHHHHHHHhcCCHHHHHHHHHhhcccCCeEEEccCcc
Q psy353 299 DNFCTVLYNDEFHTFEQVINTLVRSLKCSQKDAIEFVTNIDREGRAAVKCSNFS 352 (1363)
Q Consensus 299 ~~y~vvL~NDE~HtfdqVi~~L~~a~~~s~~~A~~~A~~ID~~GRavVk~~~~~ 352 (1363)
..|-|+|-||+...-+-|+..|++..+.+.++|.++.-.|+++|.+|+-+.+.+
T Consensus 27 ~~ykVillNDd~T~mefVv~vL~~~F~~s~e~A~~lMl~VH~~G~av~gv~t~e 80 (107)
T COG2127 27 KMYKVILLNDDYTPMEFVVYVLQKFFGMSEERATKLMLQVHREGKAVVGVYTRE 80 (107)
T ss_pred CceeEEEecCCCcHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCcEEEEEccHH
Confidence 569999999999999999999999999999999999999999999999988854
No 12
>KOG1777|consensus
Probab=93.17 E-value=0.054 Score=64.06 Aligned_cols=54 Identities=24% Similarity=0.509 Sum_probs=43.9
Q ss_pred cccccCccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccCCCccc
Q psy353 121 RVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEA 176 (1363)
Q Consensus 121 ~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCGD~ea 176 (1363)
+.+-+=.-+|||-||...+..++|..|-++ -|+||+|.+.. ...-+||||--.+
T Consensus 553 ~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir-~Drffcdcgagtl 606 (625)
T KOG1777|consen 553 YTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIR-HDRFFCDCGAGTL 606 (625)
T ss_pred CCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEe-eceEEEecCCcee
Confidence 333344568999999999999999999988 69999998865 3578999996544
No 13
>KOG0943|consensus
Probab=85.33 E-value=0.26 Score=63.87 Aligned_cols=56 Identities=21% Similarity=0.654 Sum_probs=46.6
Q ss_pred ccccccccccC----ccEEEeccccCCCCccccccccCCCCCCCceEEEEecCCCccccCC
Q psy353 116 PSVCGRVFKMG----EPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCG 172 (1363)
Q Consensus 116 ~~~Cg~vf~~g----e~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCG 172 (1363)
.-.|...|... +-.|.|+|||.-.+-+-|.+|-.- -|+||+.++-.++....|||=
T Consensus 1240 NDtCSFTWTGadHINQDIfECkTCGL~~SLCCCsECAlt-CHk~HDCkLKRTSPTAYCDCW 1299 (3015)
T KOG0943|consen 1240 NDTCSFTWTGADHINQDIFECKTCGLLESLCCCSECALT-CHKGHDCKLKRTSPTAYCDCW 1299 (3015)
T ss_pred cCccceeecchhhccchhhhhcccccchhhhhhHHHHHH-hccCCccceeccCCcceeehh
Confidence 35688888753 467999999999888889999765 799999999776668999993
No 14
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=83.94 E-value=0.9 Score=37.93 Aligned_cols=37 Identities=30% Similarity=0.616 Sum_probs=29.2
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCCCCCCceEE
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYK 159 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~ 159 (1363)
.|+..+ .| .-|+|.+|. ..-||.+||.++.|.+|.+.
T Consensus 5 ~C~~~i-~G-~ry~C~~C~---d~dLC~~C~~~~~H~~H~f~ 41 (43)
T cd02340 5 GCQGPI-VG-VRYKCLVCP---DYDLCESCEAKGVHPEHAML 41 (43)
T ss_pred CCCCcC-cC-CeEECCCCC---CccchHHhhCcCCCCCCCEE
Confidence 377733 34 799999996 46799999999999888764
No 15
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.64 E-value=0.59 Score=46.74 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=23.6
Q ss_pred cccccCCCCCC---CCCCceeecccccccccC
Q psy353 1073 SLFTCPNSDRE---DSRNPALCLICGDMLCSQ 1101 (1363)
Q Consensus 1073 ~~~~C~~c~~~---~~~~paiCL~CG~~lC~q 1101 (1363)
++|.||+||+. ..++|++|-.||+.+=.-
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 47889999973 337999999999987654
No 16
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=82.12 E-value=1.1 Score=37.73 Aligned_cols=37 Identities=30% Similarity=0.759 Sum_probs=28.7
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCC--CCC-CceEE
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKS--THR-NHKYK 159 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s--~H~-~H~~~ 159 (1363)
.|++.+. | .-|+|.+|. ..-||.+||..+ .|. +|.+.
T Consensus 5 ~C~~~i~-g-~r~~C~~C~---d~dLC~~Cf~~~~~~H~~~H~~~ 44 (46)
T cd02249 5 GCLKPIV-G-VRYHCLVCE---DFDLCSSCYAKGKKGHPPDHSFT 44 (46)
T ss_pred CCCCCCc-C-CEEECCCCC---CCcCHHHHHCcCcCCCCCCCCEe
Confidence 4888444 5 899999996 567999999998 665 67654
No 17
>KOG2752|consensus
Probab=81.36 E-value=1.9 Score=49.87 Aligned_cols=58 Identities=24% Similarity=0.565 Sum_probs=44.6
Q ss_pred ccccccc--cccCccEEEeccccCCC-CccccccccCCCCCCCceEEEEecCCCccccCCCc
Q psy353 116 PSVCGRV--FKMGEPTYNCRECGMDA-TCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDV 174 (1363)
Q Consensus 116 ~~~Cg~v--f~~ge~~y~C~~C~~d~-tcvlC~~CF~~s~H~~H~~~~~~s~~gG~CDCGD~ 174 (1363)
+..|+.. .++-.+.|+|.||..++ ...+|..|=.. -|.||.-..-...+..-||||+.
T Consensus 40 ~~~CTy~~Gy~~rQ~l~sClTC~P~~~~agvC~~C~~~-CH~~H~lveL~tKR~FrCDCg~s 100 (345)
T KOG2752|consen 40 PDVCTYAKGYKKRQALFSCLTCTPAPEMAGVCYACSLS-CHDGHELVELYTKRNFRCDCGNS 100 (345)
T ss_pred CcccccccCcccccceeEeecccCChhhceeEEEeeee-ecCCceeeeccccCCcccccccc
Confidence 4567643 33347889999999999 77899998765 69999977644456789999985
No 18
>KOG4796|consensus
Probab=81.13 E-value=1.6 Score=53.64 Aligned_cols=74 Identities=19% Similarity=0.324 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHhcCCCChHHHhhhCCCCCCCc---chHHHHHHHhhcccCCCcCCCCceeeeccccccccCcccccCChH
Q psy353 849 DCIKKEIIQQLCIKPLPHSELNKALPDDSNHE---TGLERVINEIADFKKPTQSSGKGVYELKPEFYDGYNVFFYHYSRE 925 (1363)
Q Consensus 849 ~~irreIIh~Lc~~p~t~SeL~~~lpe~~~~~---~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~~e~DPyf~hYsr~ 925 (1363)
--||.-|||+|+.++...-||.++|-.+...+ ..+..||.+.. ....|+|.|++.+|+|+|-=++.|+-.
T Consensus 210 r~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~~~-------~~~~~t~~Lrd~~~~evdq~Wp~yse~ 282 (604)
T KOG4796|consen 210 RPIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQNS-------RSKDGTYTLRDSMLKEVDQNWPGYSEG 282 (604)
T ss_pred cchHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHhhc-------ccccccchHHHHhhhHHHhcCCCcchH
Confidence 35899999999999999999999987666543 45777888822 247899999999999999988999977
Q ss_pred HHHH
Q psy353 926 EVSR 929 (1363)
Q Consensus 926 ~~~~ 929 (1363)
|++.
T Consensus 283 d~~~ 286 (604)
T KOG4796|consen 283 DKQH 286 (604)
T ss_pred HHHH
Confidence 6643
No 19
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=78.84 E-value=1.6 Score=37.38 Aligned_cols=39 Identities=31% Similarity=0.830 Sum_probs=28.7
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCCC----CC-CceEEE
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKST----HR-NHKYKM 160 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~----H~-~H~~~~ 160 (1363)
.|++.... ..-|+|.+|. .--||.+||..+. |. .|.|.+
T Consensus 5 ~C~~~~~~-g~r~~C~~C~---d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 5 YCSKDITG-TIRIKCAECP---DFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CcCCCCCC-CcEEECCCCC---CcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 47776664 4899999995 3669999999884 42 466654
No 20
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=78.00 E-value=1.9 Score=36.51 Aligned_cols=37 Identities=32% Similarity=0.877 Sum_probs=28.9
Q ss_pred cccccccCccEEEeccccCCCCccccccccCCCCC-CCceEE
Q psy353 119 CGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTH-RNHKYK 159 (1363)
Q Consensus 119 Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H-~~H~~~ 159 (1363)
|+..--.| +-|+|.+|. ..-||..||....| .+|.+.
T Consensus 6 C~~~pI~G-~RykC~~C~---dyDLC~~Cf~~~~H~~~H~F~ 43 (45)
T cd02344 6 CQMFPING-PRFKCRNCD---DFDFCENCFKTRKHNTRHTFG 43 (45)
T ss_pred CCCCCCcc-CeEECCCCC---CccchHHhhCCCCcCCCCcee
Confidence 66544445 889999997 45699999999999 588764
No 21
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=76.54 E-value=2.2 Score=36.64 Aligned_cols=38 Identities=34% Similarity=0.822 Sum_probs=28.0
Q ss_pred ccc-cccccCccEEEeccccCCCCccccccccCCC----CCC-CceEEE
Q psy353 118 VCG-RVFKMGEPTYNCRECGMDATCVLCVDCFKKS----THR-NHKYKM 160 (1363)
Q Consensus 118 ~Cg-~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s----~H~-~H~~~~ 160 (1363)
.|+ ..+. | .-|+|..|. ..-+|.+||..+ .|. .|.+.+
T Consensus 5 ~C~~~~i~-g-~R~~C~~C~---d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 5 GCGKSNFT-G-RRYKCLICY---DYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCcCCCcE-E-eeEEeCCCC---CCccchhHHhCCCcCCCCCCCCCEEE
Confidence 377 4454 3 889999994 477999999988 665 676654
No 22
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=75.56 E-value=1.5 Score=44.70 Aligned_cols=28 Identities=25% Similarity=0.465 Sum_probs=22.5
Q ss_pred cccccCCCCCC---CCCCceeeccccccccc
Q psy353 1073 SLFTCPNSDRE---DSRNPALCLICGDMLCS 1100 (1363)
Q Consensus 1073 ~~~~C~~c~~~---~~~~paiCL~CG~~lC~ 1100 (1363)
.+|.||+||+. ..++|++|-.||+.+-.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 47889999973 33799999999998643
No 23
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=75.33 E-value=1.4 Score=35.98 Aligned_cols=28 Identities=29% Similarity=0.708 Sum_probs=24.9
Q ss_pred ccEEEeccccCCCCccccccccCCCCCCCceEE
Q psy353 127 EPTYNCRECGMDATCVLCVDCFKKSTHRNHKYK 159 (1363)
Q Consensus 127 e~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~ 159 (1363)
...|.|.+|.. .+|..|+... |.+|++.
T Consensus 13 ~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 13 PLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp BEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 38999999976 7999999998 9999975
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.52 E-value=1.7 Score=31.46 Aligned_cols=23 Identities=35% Similarity=0.732 Sum_probs=20.0
Q ss_pred ccCCCCCCCCCCceeeccccccc
Q psy353 1076 TCPNSDREDSRNPALCLICGDML 1098 (1363)
Q Consensus 1076 ~C~~c~~~~~~~paiCL~CG~~l 1098 (1363)
.||+||+..+.+...|--||+-|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCcC
Confidence 49999999888999999999743
No 25
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=72.18 E-value=2 Score=32.17 Aligned_cols=23 Identities=30% Similarity=0.691 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCCceeeccccccc
Q psy353 1076 TCPNSDREDSRNPALCLICGDML 1098 (1363)
Q Consensus 1076 ~C~~c~~~~~~~paiCL~CG~~l 1098 (1363)
+||.|++.+|.....|-.||..+
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 69999999999999999999764
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=71.49 E-value=2.3 Score=31.65 Aligned_cols=25 Identities=32% Similarity=0.659 Sum_probs=21.1
Q ss_pred ccccCCCCCCCCCCceeeccccccc
Q psy353 1074 LFTCPNSDREDSRNPALCLICGDML 1098 (1363)
Q Consensus 1074 ~~~C~~c~~~~~~~paiCL~CG~~l 1098 (1363)
...||+||+..+.+-..|-.||+-|
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3579999998788999999999753
No 27
>KOG2905|consensus
Probab=67.80 E-value=3.4 Score=46.33 Aligned_cols=59 Identities=25% Similarity=0.377 Sum_probs=39.6
Q ss_pred HHHHHHHHh--cCCCChHHHhhhCCCCCCCcchHHHHHHHhhcccCCCcCCCCceeeeccccc
Q psy353 852 KKEIIQQLC--IKPLPHSELNKALPDDSNHETGLERVINEIADFKKPTQSSGKGVYELKPEFY 912 (1363)
Q Consensus 852 rreIIh~Lc--~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~ 912 (1363)
|+||+-.|. |.-..|=-|...+-..-+...-+.+||++|++|.+- | ..+|+|+|||||-
T Consensus 184 k~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkK-g-~~k~tyeLKPEYK 244 (254)
T KOG2905|consen 184 KNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKK-G-PYKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhcc-C-cccCceecCHHHh
Confidence 566766663 554444334433333333456789999999999864 3 4799999999986
No 28
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=67.74 E-value=1.9 Score=38.44 Aligned_cols=28 Identities=29% Similarity=0.727 Sum_probs=23.1
Q ss_pred cccccCCCCCCC-----CCCceeeccccccccc
Q psy353 1073 SLFTCPNSDRED-----SRNPALCLICGDMLCS 1100 (1363)
Q Consensus 1073 ~~~~C~~c~~~~-----~~~paiCL~CG~~lC~ 1100 (1363)
.+.+||.|+... ++.++.|..||+.|+-
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 356899999753 5789999999999975
No 29
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=66.47 E-value=4.1 Score=34.48 Aligned_cols=30 Identities=27% Similarity=0.793 Sum_probs=24.3
Q ss_pred ccEEEeccccCCCCccccccccCCCCC-CCceEE
Q psy353 127 EPTYNCRECGMDATCVLCVDCFKKSTH-RNHKYK 159 (1363)
Q Consensus 127 e~~y~C~~C~~d~tcvlC~~CF~~s~H-~~H~~~ 159 (1363)
..-|+|.+|. .--||.+||....| .+|.+.
T Consensus 13 G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~ 43 (45)
T cd02339 13 GIRWKCAECP---NYDLCTTCYHGDKHDLEHRFY 43 (45)
T ss_pred cCeEECCCCC---CccchHHHhCCCCCCCCCCEE
Confidence 4679999995 36699999999988 578764
No 30
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=63.26 E-value=2.5 Score=35.74 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=19.2
Q ss_pred cccccccCccEEEeccccCCCCccccccccCCCCC
Q psy353 119 CGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTH 153 (1363)
Q Consensus 119 Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H 153 (1363)
||.-.. .+-|+|..+. ...||..||..+.-
T Consensus 6 Cg~D~t--~vryh~~~~~---~~dLC~~CF~~G~f 35 (45)
T cd02336 6 CGNDCT--RVRYHNLKAK---KYDLCPSCYQEGRF 35 (45)
T ss_pred CCCccC--ceEEEecCCC---ccccChHHHhCcCC
Confidence 554443 3566666543 46699999988653
No 31
>PLN00209 ribosomal protein S27; Provisional
Probab=60.09 E-value=2.5 Score=40.28 Aligned_cols=39 Identities=23% Similarity=0.525 Sum_probs=31.0
Q ss_pred ccccCCCchHHHHHHhhcccccCCCCCC-----CCCCceeeccccccccc
Q psy353 1056 NRLINLPDDYSELINTVSLFTCPNSDRE-----DSRNPALCLICGDMLCS 1100 (1363)
Q Consensus 1056 ~~Li~LP~~y~~l~~~~~~~~C~~c~~~-----~~~~paiCL~CG~~lC~ 1100 (1363)
.+||+=|++|- .+.+||.|+.. ..+.++.|..||++||-
T Consensus 24 k~Lv~~PnS~F------m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 24 KRLVQSPNSFF------MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred eeeecCCCCEE------EEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 46888898864 36789999963 23678999999999985
No 32
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=59.42 E-value=2.6 Score=40.03 Aligned_cols=40 Identities=28% Similarity=0.610 Sum_probs=31.4
Q ss_pred ccccCCCchHHHHHHhhcccccCCCCCC-----CCCCceeecccccccccC
Q psy353 1056 NRLINLPDDYSELINTVSLFTCPNSDRE-----DSRNPALCLICGDMLCSQ 1101 (1363)
Q Consensus 1056 ~~Li~LP~~y~~l~~~~~~~~C~~c~~~-----~~~~paiCL~CG~~lC~q 1101 (1363)
.+||+-|++|- .+.+|+.|+.. ..+.++.|..||++||--
T Consensus 23 k~Lv~~PnS~F------m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 23 KRLVQGPNSYF------MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred eeEecCCCCeE------EEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 46888898864 36789999963 226789999999999853
No 33
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=54.71 E-value=9.2 Score=30.38 Aligned_cols=28 Identities=29% Similarity=0.516 Sum_probs=23.0
Q ss_pred ccEEEeccccCCCCccccccccCCCCCCCceEE
Q psy353 127 EPTYNCRECGMDATCVLCVDCFKKSTHRNHKYK 159 (1363)
Q Consensus 127 e~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~ 159 (1363)
...|.|.+|+. ++|..|-..+ |.+|.+.
T Consensus 10 ~~~~fC~~~~~----~iC~~C~~~~-H~~H~~~ 37 (39)
T cd00021 10 PLSLFCETDRA----LLCVDCDLSV-HSGHRRV 37 (39)
T ss_pred ceEEEeCccCh----hhhhhcChhh-cCCCCEe
Confidence 44788988864 7999999887 9999875
No 34
>smart00336 BBOX B-Box-type zinc finger.
Probab=54.06 E-value=10 Score=30.57 Aligned_cols=29 Identities=34% Similarity=0.818 Sum_probs=23.5
Q ss_pred CccEEEeccccCCCCccccccccCCCCCCCceEE
Q psy353 126 GEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYK 159 (1363)
Q Consensus 126 ge~~y~C~~C~~d~tcvlC~~CF~~s~H~~H~~~ 159 (1363)
....|.|.+|+. ++|..|... .|.+|.+.
T Consensus 12 ~~~~~~C~~c~~----~iC~~C~~~-~H~~H~~~ 40 (42)
T smart00336 12 EPAEFFCEECGA----LLCRTCDEA-EHRGHTVV 40 (42)
T ss_pred CceEEECCCCCc----ccccccChh-hcCCCcee
Confidence 344788988874 799999988 99999875
No 35
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=53.41 E-value=7 Score=35.60 Aligned_cols=28 Identities=32% Similarity=0.758 Sum_probs=22.1
Q ss_pred ccccCCCCCC-----CCCCceeecccccccccC
Q psy353 1074 LFTCPNSDRE-----DSRNPALCLICGDMLCSQ 1101 (1363)
Q Consensus 1074 ~~~C~~c~~~-----~~~~paiCL~CG~~lC~q 1101 (1363)
+.+||.|+-. .++..+-|+.||++++--
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 4589999952 346789999999999853
No 36
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=52.45 E-value=11 Score=32.41 Aligned_cols=38 Identities=34% Similarity=0.759 Sum_probs=26.1
Q ss_pred cccc-ccccCccEEEeccccCCCCccccccccCCC-CC-CCceE
Q psy353 118 VCGR-VFKMGEPTYNCRECGMDATCVLCVDCFKKS-TH-RNHKY 158 (1363)
Q Consensus 118 ~Cg~-vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s-~H-~~H~~ 158 (1363)
.|+. .+. -.-|+|.+|.- ...-+|.+||.++ .| .+|..
T Consensus 5 ~C~~~pI~--G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~ 45 (48)
T cd02341 5 SCGIEPIP--GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWL 45 (48)
T ss_pred CCCCCccc--cceEECCCCCC-CCCccCHHHHhCcCCCCCCCce
Confidence 3665 222 45699999963 2466999999999 66 35654
No 37
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=52.40 E-value=7.4 Score=34.39 Aligned_cols=28 Identities=21% Similarity=0.592 Sum_probs=18.2
Q ss_pred cccccCCCCCC-----CCCCceeeccccccccc
Q psy353 1073 SLFTCPNSDRE-----DSRNPALCLICGDMLCS 1100 (1363)
Q Consensus 1073 ~~~~C~~c~~~-----~~~~paiCL~CG~~lC~ 1100 (1363)
.+.+||.|+.. ..+-++.|..||++||-
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 45689999962 23789999999999985
No 38
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=51.51 E-value=8.2 Score=33.17 Aligned_cols=35 Identities=26% Similarity=0.627 Sum_probs=26.4
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCCCCC-Cce
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHR-NHK 157 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~-~H~ 157 (1363)
.|++... ..-|+|..|. ..-||..||..+.+. +|+
T Consensus 5 gC~~~~~--~~RykCl~C~---d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 5 GCDEIAP--WHRYRCLQCT---DMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCcCC--CceEECCCCC---CchhHHHHHhCCccCCCCC
Confidence 3777542 4799999996 477999999988874 344
No 39
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=51.16 E-value=8.6 Score=31.88 Aligned_cols=32 Identities=25% Similarity=0.750 Sum_probs=24.9
Q ss_pred cccccccccCccEEEeccccCCCCccccccccCCCCCC
Q psy353 117 SVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHR 154 (1363)
Q Consensus 117 ~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~ 154 (1363)
..|+++ +++-|+|.+|. .--+|..||.+..|.
T Consensus 4 ~~C~~~---~~~r~~C~~C~---dfDLC~~C~~~~~H~ 35 (41)
T cd02337 4 NECKHH---VETRWHCTVCE---DYDLCITCYNTKNHP 35 (41)
T ss_pred CCCCCc---CCCceECCCCc---chhhHHHHhCCCCCC
Confidence 357763 34999999996 356999999998883
No 40
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.36 E-value=9 Score=33.71 Aligned_cols=47 Identities=26% Similarity=0.587 Sum_probs=34.8
Q ss_pred cccccCCCCCCC--CCCceeecccccccccCCcccccccccccccccccccccccCCCee
Q psy353 1073 SLFTCPNSDRED--SRNPALCLICGDMLCSQSYCCQTELFFKMSVGACTYHSHFCGAGVG 1130 (1363)
Q Consensus 1073 ~~~~C~~c~~~~--~~~paiCL~CG~~lC~q~~cC~~~~~~~~~~G~c~~H~~~Cg~g~G 1130 (1363)
...+|+.||+.. ..|.++|--||+.-.-. | - ...|+|..+. ||++..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~--C-~------~~~g~C~~~~--c~~~~~ 52 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRD--C-W------EKAGGCINYS--CGTGFE 52 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHH--H-H------hhCCceEecc--CCCCcc
Confidence 456899999866 57899999999977543 3 1 2468898877 777653
No 41
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=47.42 E-value=10 Score=34.11 Aligned_cols=48 Identities=23% Similarity=0.382 Sum_probs=28.7
Q ss_pred cCCCCCCCCCCceeecccccccccCCcccccccccccccccccccccccCCCeeEEEEeccc
Q psy353 1077 CPNSDREDSRNPALCLICGDMLCSQSYCCQTELFFKMSVGACTYHSHFCGAGVGMFLRVREC 1138 (1363)
Q Consensus 1077 C~~c~~~~~~~paiCL~CG~~lC~q~~cC~~~~~~~~~~G~c~~H~~~Cg~g~GiFl~i~~~ 1138 (1363)
|..|+.. +.++-+||.||.+.|.... .|-...|+++= +=-+++.+.+-
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~~~-----------~~Ha~~H~~~~--~H~l~v~~~~~ 48 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGRYS-----------NGHALKHYKET--GHPLAVSLSTG 48 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETTTS-----------TSHHHHHHHHH--T--EEEETTTT
T ss_pred CCCCCCc-CCceEEeCCCCcccccCCc-----------CcHHHHhhccc--CCeEEEECCCC
Confidence 5667754 5689999999999998532 13345666643 34456666653
No 42
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=46.24 E-value=11 Score=43.99 Aligned_cols=43 Identities=30% Similarity=0.479 Sum_probs=20.3
Q ss_pred ChHHHhhhCCCCCCCcchHHHHHHHhhcccCCCcCCCCceeeeccccc
Q psy353 865 PHSELNKALPDDSNHETGLERVINEIADFKKPTQSSGKGVYELKPEFY 912 (1363)
Q Consensus 865 t~SeL~~~lpe~~~~~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~ 912 (1363)
+..+|..... +.+.-+-+||+|||+|.+- | ...|+|+|||||-
T Consensus 232 slK~L~~~t~---QP~~yLKeiL~eIa~~~k~-g-~~~~~w~LKpeyk 274 (275)
T PF02270_consen 232 SLKDLRQRTQ---QPEAYLKEILEEIAVLNKR-G-PHKNMWELKPEYK 274 (275)
T ss_dssp -HHHHHHH-----S-HHHHHHHHHHH--EE---T-T---EE----SS-
T ss_pred CHHHHHHHHC---CCHHHHHHHHHHHHHHhcc-C-CcCCcEecchHHc
Confidence 4555555442 2356789999999999875 4 4789999999984
No 43
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=40.87 E-value=7.7 Score=32.79 Aligned_cols=36 Identities=42% Similarity=0.828 Sum_probs=22.6
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCCC-CCCce
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKST-HRNHK 157 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~-H~~H~ 157 (1363)
.|+...-.| .-|+|..|. ..-||..||..+. +.+|+
T Consensus 9 ~C~~~~i~g-~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPIIG-VRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEES-SEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCcC-CeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 477632234 679999994 5779999999864 45664
No 44
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=39.84 E-value=19 Score=30.06 Aligned_cols=33 Identities=30% Similarity=0.755 Sum_probs=24.8
Q ss_pred cccccccccCccEEEeccccCCCCccccccccCCCCCC
Q psy353 117 SVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHR 154 (1363)
Q Consensus 117 ~~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H~ 154 (1363)
..|+..+. ..-|+|..|. ..-||.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 45888543 4578999993 577999999987664
No 45
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=38.92 E-value=18 Score=31.21 Aligned_cols=32 Identities=28% Similarity=0.644 Sum_probs=23.7
Q ss_pred ccccccccCccEEEeccccCCCCccccccccCCCCC
Q psy353 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTH 153 (1363)
Q Consensus 118 ~Cg~vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~H 153 (1363)
.|+..--.| .-|+|.+|. .--||..||..+.|
T Consensus 5 ~C~~~pi~g-~RykC~~C~---d~DLC~~Cf~~g~~ 36 (49)
T cd02334 5 ICKEFPITG-FRYRCLKCF---NYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCcee-eeEECCCCC---CcCchHHHHhCCCc
Confidence 466543334 789999996 46699999988865
No 46
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=37.81 E-value=21 Score=30.71 Aligned_cols=30 Identities=23% Similarity=0.774 Sum_probs=23.8
Q ss_pred cccc-ccccCccEEEeccccCCCCccccccccCCCC
Q psy353 118 VCGR-VFKMGEPTYNCRECGMDATCVLCVDCFKKST 152 (1363)
Q Consensus 118 ~Cg~-vf~~ge~~y~C~~C~~d~tcvlC~~CF~~s~ 152 (1363)
.|.+ .+. +.-|+|..|. .--||..||..+.
T Consensus 5 ~C~~~~i~--g~R~~C~~C~---dydLC~~Cf~~~~ 35 (49)
T cd02345 5 ACRKQDIS--GIRFPCQVCR---DYSLCLGCYTKGR 35 (49)
T ss_pred CCCCCCce--EeeEECCCCC---CcCchHHHHhCCC
Confidence 4777 566 4889999994 5679999999774
No 47
>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=32.06 E-value=29 Score=28.86 Aligned_cols=26 Identities=31% Similarity=0.722 Sum_probs=17.3
Q ss_pred ccCCCCCCC-----CCCceeecccccccccC
Q psy353 1076 TCPNSDRED-----SRNPALCLICGDMLCSQ 1101 (1363)
Q Consensus 1076 ~C~~c~~~~-----~~~paiCL~CG~~lC~q 1101 (1363)
+||+||... .+.-.+|-.||.++--.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence 699999631 14556999999988543
No 48
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=30.21 E-value=32 Score=29.10 Aligned_cols=24 Identities=33% Similarity=0.744 Sum_probs=19.3
Q ss_pred ccCCCCCCCCCCceeecccccccccC
Q psy353 1076 TCPNSDREDSRNPALCLICGDMLCSQ 1101 (1363)
Q Consensus 1076 ~C~~c~~~~~~~paiCL~CG~~lC~q 1101 (1363)
+|..|+.. .+.-+||-||.+.|..
T Consensus 1 ~C~~C~~~--~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTI--ENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCc--CCeEEecCCCCcccCC
Confidence 58899964 4688999999988754
No 49
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.53 E-value=29 Score=34.62 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=21.3
Q ss_pred cccccCCCCCC---CCCCceeeccccccc
Q psy353 1073 SLFTCPNSDRE---DSRNPALCLICGDML 1098 (1363)
Q Consensus 1073 ~~~~C~~c~~~---~~~~paiCL~CG~~l 1098 (1363)
++|.||.||+. ...+|+||-.||+..
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCccccchhhccCCCccccCcccccc
Confidence 46789999973 347999999999865
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.28 E-value=58 Score=42.48 Aligned_cols=24 Identities=33% Similarity=0.775 Sum_probs=19.4
Q ss_pred ccCCCCCCCCCCceeecccccccc
Q psy353 1076 TCPNSDREDSRNPALCLICGDMLC 1099 (1363)
Q Consensus 1076 ~C~~c~~~~~~~paiCL~CG~~lC 1099 (1363)
.||.||...|.+.-.|--||..+=
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~ 26 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLT 26 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCC
Confidence 688888887777788888888773
No 51
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=23.72 E-value=29 Score=28.04 Aligned_cols=24 Identities=29% Similarity=0.678 Sum_probs=16.8
Q ss_pred cccCCCCC------CCCCCceeeccccccc
Q psy353 1075 FTCPNSDR------EDSRNPALCLICGDML 1098 (1363)
Q Consensus 1075 ~~C~~c~~------~~~~~paiCL~CG~~l 1098 (1363)
+.|+.||+ .+|+.+.+|-.||.-|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCee
Confidence 45888885 3467889999999744
No 52
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.45 E-value=48 Score=34.53 Aligned_cols=25 Identities=28% Similarity=0.764 Sum_probs=20.0
Q ss_pred cccCCCCCCCCCCceeecccccccccCC
Q psy353 1075 FTCPNSDREDSRNPALCLICGDMLCSQS 1102 (1363)
Q Consensus 1075 ~~C~~c~~~~~~~paiCL~CG~~lC~q~ 1102 (1363)
-.||.||-. ..-|+| -||+++|...
T Consensus 78 PgCP~CGn~--~~fa~C-~CGkl~Ci~g 102 (131)
T PF15616_consen 78 PGCPHCGNQ--YAFAVC-GCGKLFCIDG 102 (131)
T ss_pred CCCCCCcCh--hcEEEe-cCCCEEEeCC
Confidence 369999963 467888 8999999754
No 53
>PF12773 DZR: Double zinc ribbon
Probab=21.56 E-value=45 Score=28.29 Aligned_cols=23 Identities=26% Similarity=0.722 Sum_probs=12.4
Q ss_pred cCCCCCCCCCCceeecccccccc
Q psy353 1077 CPNSDREDSRNPALCLICGDMLC 1099 (1363)
Q Consensus 1077 C~~c~~~~~~~paiCL~CG~~lC 1099 (1363)
||+|++..+.+-..|.-||+.+=
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 45555555555555555555543
No 54
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.08 E-value=53 Score=25.11 Aligned_cols=21 Identities=33% Similarity=0.801 Sum_probs=9.0
Q ss_pred cccccccccCccEEEeccccCC
Q psy353 117 SVCGRVFKMGEPTYNCRECGMD 138 (1363)
Q Consensus 117 ~~Cg~vf~~ge~~y~C~~C~~d 138 (1363)
..||..... +..|+|.+|.++
T Consensus 4 ~~C~~~~~~-~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 4 DACGKPIDG-GWFYRCSECDFD 24 (30)
T ss_dssp TTTS----S---EEE-TTT---
T ss_pred CcCCCcCCC-CceEECccCCCc
Confidence 358877765 799999999875
No 55
>PRK02935 hypothetical protein; Provisional
Probab=20.76 E-value=46 Score=33.19 Aligned_cols=28 Identities=18% Similarity=0.539 Sum_probs=21.0
Q ss_pred cccCCCCCCCC--CCceeecccccccccCC
Q psy353 1075 FTCPNSDREDS--RNPALCLICGDMLCSQS 1102 (1363)
Q Consensus 1075 ~~C~~c~~~~~--~~paiCL~CG~~lC~q~ 1102 (1363)
..||+|+|... ...-.|..||+.+-..+
T Consensus 71 V~CP~C~K~TKmLGrvD~CM~C~~PLTLd~ 100 (110)
T PRK02935 71 VICPSCEKPTKMLGRVDACMHCNQPLTLDR 100 (110)
T ss_pred eECCCCCchhhhccceeecCcCCCcCCcCc
Confidence 37999998422 34569999999987754
No 56
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=20.43 E-value=72 Score=35.95 Aligned_cols=63 Identities=25% Similarity=0.408 Sum_probs=39.2
Q ss_pred HHHHHHHHH--hcCCCChHHHhhhCCCCC-CCcchHHHHHHHhhcccCCCcCCCCceeeeccccccccC
Q psy353 851 IKKEIIQQL--CIKPLPHSELNKALPDDS-NHETGLERVINEIADFKKPTQSSGKGVYELKPEFYDGYN 916 (1363)
Q Consensus 851 irreIIh~L--c~~p~t~SeL~~~lpe~~-~~~~~fe~iL~eVA~Fk~P~g~~d~G~Y~LK~E~~~e~D 916 (1363)
=|+||+-.| |+....|=-|.- |.|.. +.+.-+.+||+.||+..+- | -=.-+|+|||||-.-.|
T Consensus 192 pknEvlD~lFK~Fe~Y~yWtlKg-L~e~~~QPea~lkEild~iavLnKk-g-pya~kY~LrPEYK~~~d 257 (297)
T COG5090 192 PKNEVLDMLFKAFEKYPYWTLKG-LAEFCGQPEAFLKEILDDIAVLNKK-G-PYANKYELRPEYKQTMD 257 (297)
T ss_pred chhHHHHHHHHHhhcCCchhhhh-HHHHhcChHHHHHHHHHHHHhhhcc-C-cccceeecCHHHHhHHH
Confidence 367888777 355554444432 22222 2356789999999996543 1 12458999999875444
No 57
>KOG0944|consensus
Probab=20.19 E-value=76 Score=40.88 Aligned_cols=65 Identities=15% Similarity=0.220 Sum_probs=0.0
Q ss_pred ccccccCccEEE--eccccCCCCcc----ccccccCCCCC---------CCceEEEEecCCCccccCCCccccCCCCCCC
Q psy353 120 GRVFKMGEPTYN--CRECGMDATCV----LCVDCFKKSTH---------RNHKYKMGTSNAGGCCDCGDVEAWKKEPYCD 184 (1363)
Q Consensus 120 g~vf~~ge~~y~--C~~C~~d~tcv----lC~~CF~~s~H---------~~H~~~~~~s~~gG~CDCGD~eawk~~~fC~ 184 (1363)
+++-+.++++|+ |--|--+|..- +|+.||..--| +||.++++.-.+--.|+|| .|+ ..+|.
T Consensus 13 ~~vp~~~~~i~kdeC~ycf~sp~~e~glyicl~~f~afg~~~v~~~f~~tg~~~yl~i~r~~k~k~~~-~~~---~~p~~ 88 (763)
T KOG0944|consen 13 VVVPRASQVIYKDECAYCFDSPESEGGLYICLNCFLAFGREHVEEYFRKTGHSVYLHIARVKKIKEEG-AEG---AEPKR 88 (763)
T ss_pred eeecCCCCceehhhceeeccCCCCCCCEEeehhhhhhhhhHHHHHHHhhcCceEEEEeccccchhhcc-CcC---CCccc
Q ss_pred cCCC
Q psy353 185 VHII 188 (1363)
Q Consensus 185 ~H~~ 188 (1363)
+|+.
T Consensus 89 K~tk 92 (763)
T KOG0944|consen 89 KITK 92 (763)
T ss_pred ccee
Done!