Query 017840
Match_columns 365
No_of_seqs 342 out of 1037
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:53:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017840.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017840hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03144 Carbon catabolite rep 100.0 3.1E-97 7E-102 772.9 33.0 361 1-363 1-392 (606)
2 KOG2738 Putative methionine am 100.0 3.7E-34 8.1E-39 272.6 -2.3 162 63-230 7-199 (369)
3 PLN03158 methionine aminopepti 99.9 8.5E-28 1.9E-32 242.1 1.0 164 63-228 10-218 (396)
4 COG5239 CCR4 mRNA deadenylase, 99.9 1.8E-24 3.9E-29 211.5 9.0 110 253-363 30-170 (378)
5 KOG2338 Transcriptional effect 99.8 8.3E-20 1.8E-24 185.0 6.9 96 252-348 115-219 (495)
6 KOG0620 Glucose-repressible al 99.8 2.3E-19 5E-24 179.0 6.9 127 224-364 2-149 (361)
7 smart00476 DNaseIc deoxyribonu 98.8 1.6E-08 3.5E-13 98.1 7.3 97 251-361 15-128 (276)
8 TIGR03395 sphingomy sphingomye 98.4 5.8E-07 1.3E-11 87.4 7.1 65 254-326 1-66 (283)
9 PRK11756 exonuclease III; Prov 98.2 2.8E-06 6.1E-11 80.9 6.8 61 254-333 1-61 (268)
10 PF03372 Exo_endo_phos: Endonu 98.0 1.6E-05 3.6E-10 71.0 6.7 55 257-329 1-62 (249)
11 TIGR00195 exoDNase_III exodeox 97.9 2.6E-05 5.6E-10 73.6 7.2 68 254-340 1-72 (254)
12 TIGR00633 xth exodeoxyribonucl 97.9 1.5E-05 3.4E-10 74.3 5.3 58 254-330 1-59 (255)
13 PRK05421 hypothetical protein; 97.6 5.5E-05 1.2E-09 72.5 3.8 41 251-309 41-81 (263)
14 COG0708 XthA Exonuclease III [ 97.3 0.00028 6.1E-09 68.1 5.2 54 254-328 1-56 (261)
15 KOG2756 Predicted Mg2+-depende 97.3 0.00067 1.5E-08 65.6 7.3 69 250-334 96-164 (349)
16 COG3568 ElsH Metal-dependent h 97.2 0.0002 4.4E-09 69.0 3.2 44 253-308 9-52 (259)
17 PF01753 zf-MYND: MYND finger; 96.8 0.00091 2E-08 45.5 2.2 34 67-107 2-35 (37)
18 PTZ00297 pantothenate kinase; 96.7 0.0034 7.3E-08 73.3 7.8 63 250-325 7-81 (1452)
19 PRK13911 exodeoxyribonuclease 96.5 0.0035 7.6E-08 60.0 5.1 53 254-328 1-54 (250)
20 KOG1710 MYND Zn-finger and ank 90.9 0.14 3E-06 50.5 2.1 47 51-110 313-360 (396)
21 COG2374 Predicted extracellula 81.6 3.4 7.4E-05 45.5 6.5 97 249-347 459-586 (798)
22 PRK15251 cytolethal distending 77.6 3.1 6.6E-05 40.7 4.3 46 250-308 21-67 (271)
23 PF09889 DUF2116: Uncharacteri 73.7 2.7 5.8E-05 31.9 2.2 33 76-110 5-37 (59)
24 KOG3873 Sphingomyelinase famil 72.7 3 6.5E-05 42.5 2.9 44 252-306 7-50 (422)
25 PRK00418 DNA gyrase inhibitor; 72.3 2.1 4.6E-05 32.8 1.3 29 73-101 5-36 (62)
26 PRK01343 zinc-binding protein; 65.8 3.4 7.3E-05 31.2 1.2 27 74-101 9-35 (57)
27 PF03884 DUF329: Domain of unk 62.9 2.6 5.7E-05 31.7 0.2 28 74-101 2-32 (57)
28 PF04438 zf-HIT: HIT zinc fing 59.4 7.2 0.00016 25.5 1.8 28 63-99 3-30 (30)
29 smart00128 IPPc Inositol polyp 57.0 34 0.00074 33.8 6.9 11 296-306 37-49 (310)
30 COG3350 Uncharacterized conser 56.5 5.2 0.00011 29.7 0.8 10 90-99 28-37 (53)
31 COG0024 Map Methionine aminope 46.3 0.7 1.5E-05 44.8 -6.7 61 163-224 16-82 (255)
32 COG3024 Uncharacterized protei 44.6 11 0.00025 29.0 1.0 26 74-99 7-35 (65)
33 KOG3612 PHD Zn-finger protein 43.3 7.5 0.00016 41.4 -0.1 37 67-112 531-567 (588)
34 PF06467 zf-FCS: MYM-type Zinc 34.1 27 0.00058 23.7 1.5 12 89-100 31-42 (43)
35 PF13824 zf-Mss51: Zinc-finger 30.9 56 0.0012 24.5 2.8 29 73-108 13-41 (55)
36 KOG4745 Metalloproteinase inhi 29.0 52 0.0011 29.1 2.7 12 50-61 125-136 (141)
37 PF04181 RPAP2_Rtr1: Rtr1/RPAP 24.7 35 0.00076 26.8 0.9 12 90-101 59-70 (79)
38 KOG0808 Carbon-nitrogen hydrol 22.8 77 0.0017 31.3 3.0 24 283-306 99-122 (387)
39 KOG2857 Predicted MYND Zn-fing 22.7 37 0.00079 30.3 0.7 29 63-100 6-35 (157)
40 COG4306 Uncharacterized protei 20.0 29 0.00062 30.5 -0.5 19 63-82 29-47 (160)
41 PF04945 YHS: YHS domain; Int 20.0 46 0.001 23.3 0.6 11 90-100 25-35 (47)
No 1
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=100.00 E-value=3.1e-97 Score=772.90 Aligned_cols=361 Identities=80% Similarity=1.324 Sum_probs=326.9
Q ss_pred CccEEEEecCCCCceeceeeceEEEEecCCCCCCCCCCCCCCCCCCceeEEEEeeecCCcccccccCCCCcccccccchh
Q 017840 1 MLSVLRVHLPSDIPIVGCELTPYVLLRRPDNAVTTEDVPESAPIDGHFLRYKWYRIQSDRKVAVCSVHPSEQATLQCLGC 80 (365)
Q Consensus 1 ~~~~~~~~l~~~~Pi~gc~l~p~v~~r~~d~~~~~~~v~~~~~~~~~~~~~~w~r~~~~~~~~~C~~~c~~~a~lqCp~C 80 (365)
||+|||||||+|||||||||+|||++||+||+++++||||++|++|+||||||||+|+++++++|++|++++|+||||+|
T Consensus 1 ~~~~~~~~l~~~~pi~g~~~~p~v~~~~~~~~~~~~d~~~~~~~~~~~~~~~w~r~~~~~~~~~c~~h~~~~a~lqCp~C 80 (606)
T PLN03144 1 MLSVVRVHLPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQSDRKVAVCSVHPSEPATLQCVGC 80 (606)
T ss_pred CeeEEEEEcCCCCCeeeeeeEEEEEEEcCCCCcCcccCcccCCCCcceEEEEEEecCCCccceeEeecCCCcccccCccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCcceecChhhhhHhHHHHHHhhhhhhcccccCCCCccccccCCCcCCCcccccccCCCccccccCCCCccccC
Q 017840 81 VKAKIPVAKSYHCSPKCFSDAWQHHRVLHDRAASAVNENGNEEEELFGRFNSTGSGVINASLSGSASNSSLTNGSTPLYP 160 (365)
Q Consensus 81 ~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~~~~~~~~~~~~~~~~~f~~f~~tg~~rp~r~vpg~~se~~~~~~~i~~~~ 160 (365)
+|+||++..||||||+|||++|++||.+|+.++++..+++++++++|++|+.+|++--.....|..++.+..++++++++
T Consensus 81 ~k~~~~~~~s~fCsq~CFk~~w~~Hk~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (606)
T PLN03144 81 VKAKLPVSKSYHCSPKCFSDAWRHHRVLHERAASAVRENGNEEDELFGRFNSSGSGVLSTSDSGSASSASLTNGSVPLYP 160 (606)
T ss_pred hhcCCCcCcceeeCHHHHHHHHHHHHHHHHHhhhhhcccCccccccccccCCCccccccccccccccccccccCcccccc
Confidence 99999878899999999999999999999999877788999999999999999986433222233344445778888888
Q ss_pred ccc--ccCCC-cceeEeccceecCCChhccCcEEEEEEEeecCCCCCCCCCcceeeeccccCCCCCCCCceeeeCCCCCC
Q 017840 161 AAV--TRSGG-ETWFEVGRSKTYTPSADDIGHVLKFECVVVDAETKLPVGHPNTLLTSRVIPAPSPSPRRLFPVNGSDMN 237 (365)
Q Consensus 161 ~~~--~~~~g-e~w~~vg~~~~YtPt~eDIG~llklecl~~dg~~~~plg~~~sv~Ts~Vip~P~P~~R~~i~~~~~~~~ 237 (365)
... .+..| ++|++||++++||||+||||+.|+|||+++++..+.+.+.+.+++|++|+++|.|++|+|+++.. .+
T Consensus 161 ~~~~~~~~~~~~~w~~vg~~~~y~p~~~d~g~~lk~~~~~~~~~~~~~~~~~~~~~t~~v~~~p~p~~R~~~~~~~--~~ 238 (606)
T PLN03144 161 SGIEQKTQVGGETWIEVGRSKTYTPTADDVGHVLKFECVVVDAETGLPVGHPQSILTSRVIPAPSPTPRRLIQVNG--LD 238 (606)
T ss_pred cccccccCCCCCceEEeCCCccccCChhhCCceEEEEEEEcccccCCCCccceeecccceecCCCCCCcceEEecc--cc
Confidence 763 33334 99999999999999999999999999999999877788888999999999999999999999875 34
Q ss_pred cccccCCCCCCCCCCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHh
Q 017840 238 MMGHIDSDGRISSTGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAP 317 (365)
Q Consensus 238 ~~~~~~~~~~~~~~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~ 317 (365)
.++|++++++..+.++|||||||||||.|+++++|+|||+++|+|+||+++|++||..|+|||||||||+.++|++||.+
T Consensus 239 ~~~~~~~~~~~~~~~~frVmSYNILAd~ya~~dly~ycp~~aL~W~yRk~lIl~EI~~~~aDIICLQEV~~~~~~d~~~p 318 (606)
T PLN03144 239 GMGHLDLDGRTSSAGTFTVLSYNILSDLYATSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAP 318 (606)
T ss_pred cccccccccccCCCCCEEEEEeeeccccccCcccccCCCccccCHHHHHHHHHHHHHhcCCCEEEEeecCHHHHHHHHHh
Confidence 46778888888889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCceEEEeccCCe-------------EEEecccccccccc---------------CCChhhHhhhccccc
Q 017840 318 ELDKHGYQALYKRKTNE-------------VEFNKAAQSLTDAI---------------LPSAQKKNALNRLVK 363 (365)
Q Consensus 318 ~L~~~gY~g~~~~K~g~-------------i~fn~~~~~l~e~~---------------~~~~~~~~~~~r~~~ 363 (365)
.|.++||.|+|.+|+++ |||++++|++++.. .++.+|+++++||||
T Consensus 319 ~L~~~GY~Gv~~~Kt~~~~~~~~~~~DGcAIFyr~drFeLv~~~~ief~~~~lslt~~~~~s~~~~~~l~Rl~k 392 (606)
T PLN03144 319 ELDKHGYQALYKKKTTEVYTGNTYVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLTEALIPSAQKKAALNRLLK 392 (606)
T ss_pred hhhhcCceEEEeCCCCccccccccCCceeEEEEECcceEEEEeeeeeccchhhccCccccccccchhhhhhhcc
Confidence 99999999999988641 99999999999752 356679999999875
No 2
>KOG2738 consensus Putative methionine aminopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.7e-34 Score=272.65 Aligned_cols=162 Identities=22% Similarity=0.341 Sum_probs=145.3
Q ss_pred cccc-CCCCcccccccchhhhcCCCCCcceecChhhhhHhHHHHHHhhhhhhcccccCCCCccccccCCCcCCCcccc--
Q 017840 63 AVCS-VHPSEQATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVLHDRAASAVNENGNEEEELFGRFNSTGSGVIN-- 139 (365)
Q Consensus 63 ~~C~-~~c~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~~~~~~~~~~~~~~~~~f~~f~~tg~~rp~-- 139 (365)
+.|. .+|+++|+||||+|+|+|++ .+|||+|+|||.+|..||.+|..+.. ......+|||+.|+|||+|||.
T Consensus 7 ~~c~~~~c~~~a~l~Cp~c~~~~i~--~~~fc~q~cf~~~w~~hK~~h~~~~~---~~~~g~~~p~p~~~~~g~Lr~~pv 81 (369)
T KOG2738|consen 7 ISCEGLQCGSEASLQCPTCLKLGIK--SAYFCAQECFKNSWLSHKKLHRKALR---IRKEGQYNPWPKFRFTGPLRPGPV 81 (369)
T ss_pred ceeeccccCChhhccCchhhhcCCC--cccccCchhhhcchhhhhhhcccchh---hhhhccCCCCccccccCCccccCC
Confidence 5676 99999999999999999998 48999999999999999999986521 1234567899999999999997
Q ss_pred ---cccC-----------C-Ccccccc-CCCCccccCcc------cccCCC-cceeEeccceecCCChhccCcEEEEEEE
Q 017840 140 ---ASLS-----------G-SASNSSL-TNGSTPLYPAA------VTRSGG-ETWFEVGRSKTYTPSADDIGHVLKFECV 196 (365)
Q Consensus 140 ---r~vp-----------g-~~se~~~-~~~~i~~~~~~------~~~~~g-e~w~~vg~~~~YtPt~eDIG~llklecl 196 (365)
|.|| | |.||+.. +++.|++++++ ++|+|| |+++++|+...+++||||||+.+|..++
T Consensus 82 sprr~VP~hI~rPdya~~g~s~se~~~~~s~~i~i~~~e~ie~mR~ac~LarevLd~Aa~~v~PgvTTdEiD~~VH~a~I 161 (369)
T KOG2738|consen 82 SPRRPVPDHIPRPDYADSGVSLSEQPEISSNEIKILDPEGIEGMRKACRLAREVLDYAATLVRPGVTTDEIDRAVHNAII 161 (369)
T ss_pred CCCCcCCccCCCCchhhcCCcccccccccccceeccCHHHHHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHH
Confidence 8888 5 7788887 66689999987 899999 9999999999999999999999999999
Q ss_pred eecCCCCCCCCC---cceeeecc--ccCCCCCCCCceee
Q 017840 197 VVDAETKLPVGH---PNTLLTSR--VIPAPSPSPRRLFP 230 (365)
Q Consensus 197 ~~dg~~~~plg~---~~sv~Ts~--Vip~P~P~~R~~i~ 230 (365)
..++ |++|+|| |||+|||+ ||||++|+.|.+..
T Consensus 162 erg~-YPSPLnYy~FPKS~CTSVNEviCHGIPD~RpLed 199 (369)
T KOG2738|consen 162 ERGA-YPSPLNYYGFPKSVCTSVNEVICHGIPDSRPLED 199 (369)
T ss_pred hcCC-cCCCcccCCCchhhhcchhheeecCCCCcCcCCC
Confidence 9988 9999998 99999998 89999999998875
No 3
>PLN03158 methionine aminopeptidase; Provisional
Probab=99.93 E-value=8.5e-28 Score=242.05 Aligned_cols=164 Identities=24% Similarity=0.367 Sum_probs=129.0
Q ss_pred ccccCCCCcccccccchhhhcCCCCCcceecChhhhhHhHHHHHHhhhhhhcc----c----c-------cCCCCccccc
Q 017840 63 AVCSVHPSEQATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVLHDRAASA----V----N-------ENGNEEEELF 127 (365)
Q Consensus 63 ~~C~~~c~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~~~~~~----~----~-------~~~~~~~~~f 127 (365)
.+|+ +|+++|+||||+|+|+|+++..||||||+|||++|++||.+|+.++.. . . +.+...+++|
T Consensus 10 ~~c~-~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (396)
T PLN03158 10 LACA-RCSKPAHLQCPKCLELKLPREGASFCSQDCFKAAWSSHKSVHTKAKLSSIGQNSDAPAEGWLYCLKKGQARTSKL 88 (396)
T ss_pred cccc-CCCCcccccCccchhcCCCCCCceeECHHHHHHHHHHHHHHHHhhhhcccccccccccccccccccccccccCCC
Confidence 4485 999999999999999999877899999999999999999999875421 0 0 0111237899
Q ss_pred cCCCcCCCcccc-----cccC-----------C-Ccccccc-CCCCccccCcc------cccCCC-cceeEeccceecCC
Q 017840 128 GRFNSTGSGVIN-----ASLS-----------G-SASNSSL-TNGSTPLYPAA------VTRSGG-ETWFEVGRSKTYTP 182 (365)
Q Consensus 128 ~~f~~tg~~rp~-----r~vp-----------g-~~se~~~-~~~~i~~~~~~------~~~~~g-e~w~~vg~~~~YtP 182 (365)
++|+|||+|||. |.|| | |.++... ..+.+.|++++ ++|+++ +.++.+......+.
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~p~~i~~p~y~~~~~~~~~~~~~~~~~~~IKsp~EIe~mR~A~~ia~~al~~a~~~irpGv 168 (396)
T PLN03158 89 PDFDWTGPLRPYPISPRRVVPDHIPKPDWALDGTPKIEPNSDLQHSVEIKTPEQIQRMRETCRIAREVLDAAARAIKPGV 168 (396)
T ss_pred CCCCCCcccccCCCCCCCCCCccCCCCccccCCCCccccccccccceeeCCHHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 999999999997 7787 3 5444432 33456777776 788888 88999999999999
Q ss_pred ChhccCcEEEEEEEeecCCCCCCCCC---cceeeecc--ccCCCCCCCCce
Q 017840 183 SADDIGHVLKFECVVVDAETKLPVGH---PNTLLTSR--VIPAPSPSPRRL 228 (365)
Q Consensus 183 t~eDIG~llklecl~~dg~~~~plg~---~~sv~Ts~--Vip~P~P~~R~~ 228 (365)
|++||+..++-.++..++ +++++++ |+++|++. +++|+.|..|.+
T Consensus 169 Te~EI~~~v~~~~~~~Ga-~ps~l~y~~fp~svcts~N~~i~Hgip~~r~L 218 (396)
T PLN03158 169 TTDEIDRVVHEATIAAGG-YPSPLNYHFFPKSCCTSVNEVICHGIPDARKL 218 (396)
T ss_pred CHHHHHHHHHHHHHHcCC-ccccccccCCCceeeecccccccCCCCCCccC
Confidence 999999998877766555 6777664 78899876 778888876654
No 4
>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification]
Probab=99.91 E-value=1.8e-24 Score=211.47 Aligned_cols=110 Identities=37% Similarity=0.739 Sum_probs=96.9
Q ss_pred ceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEEeccC
Q 017840 253 TFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYKRKT 332 (365)
Q Consensus 253 ~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~~~K~ 332 (365)
.|+|||||+||+.|+++++|+|. .|+|+|+||+.+|++||..|+|||||||||+...|++||++.|...||+|+|.+|+
T Consensus 30 ~ftimTYN~Laq~y~~r~~y~~s-~~aL~W~~R~~~L~~EL~~Yn~Di~CLQEvd~~~~~~fw~~~l~~~gY~~if~~k~ 108 (378)
T COG5239 30 DFTIMTYNVLAQTYATRKMYPYS-GWALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLGKLGYDGIFIPKE 108 (378)
T ss_pred eeEEEehhhhhhhhccccccCCc-hhhhhhHHHHHHHHHHHhccCCceeeeehhhhhHHHHHHHHHhcccccceEEecCC
Confidence 79999999999999999999998 89999999999999999999999999999999999999999999999999999998
Q ss_pred Ce----------------EEEec----ccccccccc-----------CCChhhHhhhccccc
Q 017840 333 NE----------------VEFNK----AAQSLTDAI-----------LPSAQKKNALNRLVK 363 (365)
Q Consensus 333 g~----------------i~fn~----~~~~l~e~~-----------~~~~~~~~~~~r~~~ 363 (365)
|. |||+. .++-++-++ -.-+|-..++||+++
T Consensus 109 ~k~~~m~~~d~t~~dGc~if~k~~~~~sk~~li~~~~~~f~~p~~~~er~r~t~~~lnri~e 170 (378)
T COG5239 109 RKVKWMIDYDTTKVDGCAIFLKRFIDSSKLGLILAVTHLFWHPYGYYERFRQTYILLNRIGE 170 (378)
T ss_pred CcccccccccccccceEEEEEEeccccchhhhhhhhhHhhcccceeehhhhHHHHHHHHHhh
Confidence 82 88887 443344443 224556788888876
No 5
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription]
Probab=99.79 E-value=8.3e-20 Score=185.02 Aligned_cols=96 Identities=40% Similarity=0.667 Sum_probs=89.0
Q ss_pred CceEEEeeccccCcc---cCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEE
Q 017840 252 GTFSVLSYNILSDVY---ATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALY 328 (365)
Q Consensus 252 ~~frVmSYNILa~~y---a~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~ 328 (365)
..|+|||||||||.+ .++.+|+ ++..+|+|.+|.+.|+.||..|+|||||||||+.++|..++++.|..+||.++|
T Consensus 115 f~ftvmSYNILAQ~l~~~~~r~~~~-~s~~~L~W~~R~~~Ll~EL~~~dpDIlCLQEVq~d~~~~~~~~~~~~lGy~~~~ 193 (495)
T KOG2338|consen 115 FDFTVMSYNILAQDLLRDIRRLYFP-ESGPALKWLRRSQNLLNELKHYDPDVLCLQEVQEDHYPEFWQPLLGKLGYTGFF 193 (495)
T ss_pred cceEEEEehHhHHHHHHHhHHhhcc-CChhhcchhHHhHHHHHHHhhcCCCeeeehhhhhhhhHHHHHHHHhhcCceEEE
Confidence 489999999999999 4556777 899999999999999999999999999999999999999999999999999999
Q ss_pred eccCCe------EEEecccccccccc
Q 017840 329 KRKTNE------VEFNKAAQSLTDAI 348 (365)
Q Consensus 329 ~~K~g~------i~fn~~~~~l~e~~ 348 (365)
..+++. |+|++++|+++...
T Consensus 194 ~r~t~~KthG~ai~w~~~~F~lv~~~ 219 (495)
T KOG2338|consen 194 KRRTGTKTHGVAILWHSAKFKLVNHS 219 (495)
T ss_pred EeccCCCCceEEEEEecccceecccc
Confidence 888754 99999999998865
No 6
>KOG0620 consensus Glucose-repressible alcohol dehydrogenase transcriptional effector CCR4 and related proteins [Transcription]
Probab=99.78 E-value=2.3e-19 Score=178.96 Aligned_cols=127 Identities=49% Similarity=0.855 Sum_probs=105.0
Q ss_pred CCCceeeeCCCCCCcccccCCCCCCCCCCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEE
Q 017840 224 SPRRLFPVNGSDMNMMGHIDSDGRISSTGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCL 303 (365)
Q Consensus 224 ~~R~~i~~~~~~~~~~~~~~~~~~~~~~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCL 303 (365)
..|.|+.++.+ ...+...|+|||||||++.|+.+..|.|||.|++.|.||++.|++||..++||||||
T Consensus 2 ~~~~~~~~~~~------------~~~~~~~~~v~s~n~l~~~~~~~~~~~~~~~~~~~w~~r~~~~~~ei~~~~ad~icL 69 (361)
T KOG0620|consen 2 FWRDLISVSGK------------DVPQGETFTVLSYNILSQLYATSKLYMYCPSWALSWEYRRQLLLEEILNYNADILCL 69 (361)
T ss_pred ChhheeeccCC------------CccCCceEEeechhhhhhhhcccCCCcccchhhccHHHHHHHHHHHHhCCCcceeec
Confidence 34777777652 223445899999999999999999999999999999999999999999999999999
Q ss_pred eccChhhHHHHHHhhhhcCCceEEEeccC------Ce------EEEecccccccccc-CC--------ChhhHhhhcccc
Q 017840 304 QEVQNDHFEEFFAPELDKHGYQALYKRKT------NE------VEFNKAAQSLTDAI-LP--------SAQKKNALNRLV 362 (365)
Q Consensus 304 QEV~~~~~~~~~~~~L~~~gY~g~~~~K~------g~------i~fn~~~~~l~e~~-~~--------~~~~~~~~~r~~ 362 (365)
||| ++|++||.+.|...||.|+|.+|+ .+ |||+.++|+++... +- .....++++|+|
T Consensus 70 qev--~~~~~~~~p~l~~~gY~g~~~~k~~~~~~~~~~~dGcaiffk~s~f~li~~~~i~~n~~~~~~~~~~~~~~~~~~ 147 (361)
T KOG0620|consen 70 QEV--DRYHDFFSPELEASGYSGIFIEKTRMGEVELEKIDGCAIFFKPSLFQLIHSSAIELNQLALSRLPPNIAQLNRLT 147 (361)
T ss_pred chh--hHHHHHccchhhhcCCcceeecccccchhhcccCceeeeeecchHHhhhhhhhhhhHHHHHhhcchhHHHHHhhh
Confidence 999 889999999999889999999975 22 99999999998643 10 112346777777
Q ss_pred cC
Q 017840 363 KV 364 (365)
Q Consensus 363 ~~ 364 (365)
+.
T Consensus 148 ~~ 149 (361)
T KOG0620|consen 148 TL 149 (361)
T ss_pred cc
Confidence 64
No 7
>smart00476 DNaseIc deoxyribonuclease I. Deoxyribonuclease I catalyzes the endonucleolytic cleavage of double-stranded DNA. The enzyme is secreted outside the cell and also involved in apoptosis in the nucleus.
Probab=98.76 E-value=1.6e-08 Score=98.14 Aligned_cols=97 Identities=19% Similarity=0.271 Sum_probs=69.3
Q ss_pred CCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhh---c---CCc
Q 017840 251 TGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELD---K---HGY 324 (365)
Q Consensus 251 ~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~---~---~gY 324 (365)
...++||||||+. |+ +....|..|++.|.+.|. ++|||++|||...+..+ +...|. . .+|
T Consensus 15 ~~~l~I~SfNIr~--------fg---d~k~~~~~r~~~i~~il~--~~DIiglQEV~d~q~~~-l~~ll~~Ln~~~~~~Y 80 (276)
T smart00476 15 AASLRICAFNIQS--------FG---DSKMSNATLMSIIVKILS--RYDIALVQEVRDSDLSA-VPKLMDQLNSDSPNTY 80 (276)
T ss_pred CCcEEEEEEECcc--------cC---CccccHHHHHHHHHHHhc--cCCEEEEEEeecchhHH-HHHHHHHHhhcCCCCc
Confidence 3479999999972 22 234679999999999998 77999999997666544 444342 1 256
Q ss_pred eEEEeccC-----Ce---EEEeccccccccccCCCh---hhHhhhccc
Q 017840 325 QALYKRKT-----NE---VEFNKAAQSLTDAILPSA---QKKNALNRL 361 (365)
Q Consensus 325 ~g~~~~K~-----g~---i~fn~~~~~l~e~~~~~~---~~~~~~~r~ 361 (365)
.-+...+. +| ++|+++++++++...=.. +|++++.|.
T Consensus 81 ~~v~s~r~gr~~~~E~~a~~Yr~drv~v~~~~~f~d~~~~~~~~F~Re 128 (276)
T smart00476 81 SYVSSEPLGRNSYKEQYLFLYRSDLVSVLDSYLYDDGCECGNDVFSRE 128 (276)
T ss_pred eEEecCCCCCCCCCEEEEEEEecceEEEcccceecCCCCCcccccccc
Confidence 65554432 34 999999999998763222 488999885
No 8
>TIGR03395 sphingomy sphingomyelin phosphodiesterase. Members of this family are bacterial proteins that act as sphingomyelin phosphodiesterase (EC 3.1.4.12), also called sphingomyelinase. Some members of this family have been shown to act as hemolysins.
Probab=98.40 E-value=5.8e-07 Score=87.36 Aligned_cols=65 Identities=18% Similarity=0.078 Sum_probs=46.7
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhh-hcCCceE
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPEL-DKHGYQA 326 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L-~~~gY~g 326 (365)
|+||||||..- ++--.+...|+.|..+|.+.+...++||||||||...+..+.+...| ..++|..
T Consensus 1 lkVmtyNv~~l--------~~~~~~~~g~~~R~~~i~~~~~~~~~DVV~LQEv~~~~~~~~l~~~L~~~yp~~~ 66 (283)
T TIGR03395 1 IKILSHNVYML--------STNLYPNWGQMERADLIASADYIKNQDVVILNEAFDTSASKRLLDNLREEYPYQT 66 (283)
T ss_pred CeEEEEEeeee--------cccccCCccHhHHHHHHHHhhcccCCCEEEEecccchHHHHHHHHHHHhhCCceE
Confidence 68999999741 11112244689999999999999999999999997555444355556 3566655
No 9
>PRK11756 exonuclease III; Provisional
Probab=98.20 E-value=2.8e-06 Score=80.89 Aligned_cols=61 Identities=26% Similarity=0.391 Sum_probs=42.3
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEEeccCC
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYKRKTN 333 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~~~K~g 333 (365)
+|||||||.. +..|...|.+.|...+||||||||+.... +.+-...+...||...|..+.+
T Consensus 1 mri~T~Nv~g------------------~~~~~~~i~~~i~~~~pDIi~LQE~~~~~-~~~~~~~~~~~gy~~~~~~~~~ 61 (268)
T PRK11756 1 MKFVSFNING------------------LRARPHQLEAIIEKHQPDVIGLQETKVHD-EMFPLEEVEALGYHVFYHGQKG 61 (268)
T ss_pred CEEEEEEcCC------------------HHHHHHHHHHHHHhcCCCEEEEEeccccc-ccCCHHHHHhcCCEEEEeCCCC
Confidence 5899999952 34567789999999999999999985221 1111223456789877654433
No 10
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []. Proteins this domain is found in include: AP endonuclease proteins (4.2.99.18 from EC), DNase I proteins (3.1.21.1 from EC), Synaptojanin an inositol-1,4,5-trisphosphate phosphatase (3.1.3.56 from EC) and Sphingomyelinase (3.1.4.12 from EC).; PDB: 2J63_A 2JC4_A 3TEB_B 3MTC_A 3N9V_B 1ZWX_A 2F1N_A 1Y21_A 1NTF_A 2IMQ_X ....
Probab=97.97 E-value=1.6e-05 Score=71.00 Aligned_cols=55 Identities=33% Similarity=0.645 Sum_probs=39.6
Q ss_pred EeeccccCcccCCCCCCCCCCccCChHHHHHH------HHHHHhhcCCcEEEEeccChhhHHHHHHhhhhc-CCceEEEe
Q 017840 257 LSYNILSDVYATSESYSYCPSWALSWAYRRQN------LLREIIGYRADIVCLQEVQNDHFEEFFAPELDK-HGYQALYK 329 (365)
Q Consensus 257 mSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~------Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~-~gY~g~~~ 329 (365)
|||||+. |.+|... |.+.|..++||||||||+..+.+.+.+...+.. .++.+.+.
T Consensus 1 ~T~Nv~~------------------~~~~~~~~~~~~~i~~~i~~~~~Dii~LQEv~~~~~~~~~~~~~~~~~~~~~~~~ 62 (249)
T PF03372_consen 1 MTWNVRG------------------WNYRSDNDRKRREIAQWIAELDPDIIALQEVRNDDLSELLEEQLRGYLGYYGSFW 62 (249)
T ss_dssp EEEEEST------------------HHHHHHHHHHHHHHHHHHHHHT-SEEEEEEEESHHHHHHHHHHHHTCTTHEEEEE
T ss_pred CeEEeCc------------------CcccccchhHHHHHHHHHHhcCCCEEEEecchhhhhhhhhhhhccccccccccee
Confidence 7999973 6555544 999999999999999999866666656666664 44455554
No 11
>TIGR00195 exoDNase_III exodeoxyribonuclease III. The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family
Probab=97.91 E-value=2.6e-05 Score=73.65 Aligned_cols=68 Identities=19% Similarity=0.347 Sum_probs=45.1
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEEeccCC
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYKRKTN 333 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~~~K~g 333 (365)
+||+||||.. ...+...++++|..++||||||||+..... .+....+...||..++....|
T Consensus 1 mri~t~Ni~g------------------~~~~~~~~~~~l~~~~~DIi~LQE~~~~~~-~~~~~~~~~~g~~~~~~~~~g 61 (254)
T TIGR00195 1 MKIISWNVNG------------------LRARLHKGLAWLKENQPDVLCLQETKVQDE-QFPLEPFHKEGYHVFFSGQKG 61 (254)
T ss_pred CEEEEEEcCc------------------HHHhHHHHHHHHHhcCCCEEEEEecccchh-hCCHHHhhcCCcEEEEecCCC
Confidence 5899999962 123344589999999999999999965431 222333456888877655433
Q ss_pred e----EEEecc
Q 017840 334 E----VEFNKA 340 (365)
Q Consensus 334 ~----i~fn~~ 340 (365)
. |+.+..
T Consensus 62 ~~Gvailsr~~ 72 (254)
T TIGR00195 62 YSGVAIFSKEE 72 (254)
T ss_pred cceEEEEEcCC
Confidence 3 555533
No 12
>TIGR00633 xth exodeoxyribonuclease III (xth). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.89 E-value=1.5e-05 Score=74.30 Aligned_cols=58 Identities=26% Similarity=0.479 Sum_probs=40.9
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHHHHH-HHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEEec
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNL-LREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYKR 330 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~I-l~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~~~ 330 (365)
+||+||||..- .-|.+.+ ++.|..++||||||||+.... ..+....+...||..+|..
T Consensus 1 lri~t~Nv~g~------------------~~~~~~~~~~~l~~~~~DIv~LQE~~~~~-~~~~~~~~~~~g~~~~~~~ 59 (255)
T TIGR00633 1 MKIISWNVNGL------------------RARLHKLFLDWLKEEQPDVLCLQETKVAD-EQFPAELFEELGYHVFFHG 59 (255)
T ss_pred CEEEEEecccH------------------HHHhhccHHHHHHhcCCCEEEEEeccCch-hhCCHhHhccCCceEEEee
Confidence 68999999631 1233445 899999999999999997543 2223334457899887754
No 13
>PRK05421 hypothetical protein; Provisional
Probab=97.58 E-value=5.5e-05 Score=72.48 Aligned_cols=41 Identities=29% Similarity=0.440 Sum_probs=29.6
Q ss_pred CCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChh
Q 017840 251 TGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQND 309 (365)
Q Consensus 251 ~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~ 309 (365)
+++||||||||.... . . +....++.| .+++||||||||+..
T Consensus 41 ~~~lri~t~NI~~~~-----------~--~----~~~~~l~~l-~~~~DiI~LQEv~~~ 81 (263)
T PRK05421 41 EERLRLLVWNIYKQQ-----------R--A----GWLSVLKNL-GKDADLVLLQEAQTT 81 (263)
T ss_pred CCceeEEEEEccccc-----------c--c----cHHHHHHHh-ccCCCEEEEEecccC
Confidence 578999999997421 0 0 233555556 999999999999743
No 14
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]
Probab=97.33 E-value=0.00028 Score=68.11 Aligned_cols=54 Identities=28% Similarity=0.565 Sum_probs=40.4
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccC--hhhHHHHHHhhhhcCCceEEE
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQ--NDHFEEFFAPELDKHGYQALY 328 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~--~~~~~~~~~~~L~~~gY~g~~ 328 (365)
+||+||||= .-.-|.+.+++.|..++||||||||.- .++|- ...++..||+.++
T Consensus 1 mkI~SwNVN------------------giRar~~~~~~~l~~~~pDVlclQEtK~~~~~fp---~~~~~~~GY~~~~ 56 (261)
T COG0708 1 MKIASWNVN------------------GLRARLKKLLDWLEEEQPDVLCLQETKAQDEQFP---REELEALGYHHVF 56 (261)
T ss_pred CeeEEEehh------------------hHHHHHHHHHHHHHHhCCCEEEEEecccCcccCC---HhHHhhCCceEEE
Confidence 589999993 244677779999999999999999974 33433 3456678996665
No 15
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms]
Probab=97.30 E-value=0.00067 Score=65.63 Aligned_cols=69 Identities=17% Similarity=0.240 Sum_probs=48.7
Q ss_pred CCCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEEe
Q 017840 250 STGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALYK 329 (365)
Q Consensus 250 ~~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~~ 329 (365)
.+..|++|||||= . -+-.+-.-|...|...|..|+|||||||||....| +++.+ + +..|..++.
T Consensus 96 ~g~~~S~~~Wnid--g-----------Ldln~l~~RMrAv~H~i~l~sPdiiflQEV~p~~y-~~~~K-~-~s~y~i~~~ 159 (349)
T KOG2756|consen 96 QGSMFSLITWNID--G-----------LDLNNLSERMRAVCHYLALYSPDVIFLQEVIPPYY-SYLKK-R-SSNYEIITG 159 (349)
T ss_pred cccEEEEEEeecc--c-----------cccchHHHHHHHHHHHHHhcCCCEEEEeecCchhh-HHHHH-h-hhheeEEEe
Confidence 3456899999993 1 11223458999999999999999999999986655 34554 2 345666666
Q ss_pred ccCCe
Q 017840 330 RKTNE 334 (365)
Q Consensus 330 ~K~g~ 334 (365)
.+.+.
T Consensus 160 ~~~~~ 164 (349)
T KOG2756|consen 160 HEEGY 164 (349)
T ss_pred cccee
Confidence 66554
No 16
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only]
Probab=97.25 E-value=0.0002 Score=69.00 Aligned_cols=44 Identities=36% Similarity=0.459 Sum_probs=36.3
Q ss_pred ceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEeccCh
Q 017840 253 TFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEVQN 308 (365)
Q Consensus 253 ~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~ 308 (365)
.++|+||||... -. ..++.++.+.|.+.|.+..+||||||||+.
T Consensus 9 ~~~v~TyNih~~-----------~~-~~d~r~~~~r~~~~i~~~~~Div~LQEv~~ 52 (259)
T COG3568 9 RFKVLTYNIHKG-----------FG-AFDRRFDLPRIAEVIREVGADIVALQEVDG 52 (259)
T ss_pred eeEEEEEEEEEc-----------cC-ccCceecHHHHHHHHHhhccCeeeeecccc
Confidence 389999999732 11 127888999999999999999999999984
No 17
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=96.77 E-value=0.00091 Score=45.47 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=28.1
Q ss_pred CCCCcccccccchhhhcCCCCCcceecChhhhhHhHHHHHH
Q 017840 67 VHPSEQATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRV 107 (365)
Q Consensus 67 ~~c~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~ 107 (365)
..|++++...|+.|. ..+|||.+|.+.+|..||.
T Consensus 2 ~~C~~~~~~~C~~C~-------~~~YCs~~Cq~~~w~~Hk~ 35 (37)
T PF01753_consen 2 AVCGKPALKRCSRCK-------SVYYCSEECQRADWPYHKF 35 (37)
T ss_dssp TTTSSCSSEEETTTS-------SSEESSHHHHHHHHHHHCC
T ss_pred cCCCCCcCCcCCCCC-------CEEecCHHHHHHHHHHHhh
Confidence 467887777899883 2789999999999999975
No 18
>PTZ00297 pantothenate kinase; Provisional
Probab=96.74 E-value=0.0034 Score=73.35 Aligned_cols=63 Identities=24% Similarity=0.337 Sum_probs=39.3
Q ss_pred CCCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhh-cCCcEEEEeccChhh-----------HHHHHHh
Q 017840 250 STGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIG-YRADIVCLQEVQNDH-----------FEEFFAP 317 (365)
Q Consensus 250 ~~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~-~~aDIiCLQEV~~~~-----------~~~~~~~ 317 (365)
...+||||||||. +|+ .+.-.| ..+.|...|.. .++||||||||.... |+.-+..
T Consensus 7 ~~~~l~VlTyNv~--------~~~---~~~~~~--~~~ri~~~i~~l~~~DIv~lQEvf~~~~~~~~~~~~~~~~~~~~~ 73 (1452)
T PTZ00297 7 GCAQARVLSYNFN--------ILP---RGCGGF--QHERIETFLASVDAYDVVLLQEVYAASVLPYFLQKQLCFQKMLVD 73 (1452)
T ss_pred CCCceEEEEEEcc--------ccC---CCcccc--cHHHHHHHHHhccCCCEEEEecccccccccccccccchhhHHHHH
Confidence 4457999999985 222 111123 24666666666 477999999997432 3333456
Q ss_pred hhhcCCce
Q 017840 318 ELDKHGYQ 325 (365)
Q Consensus 318 ~L~~~gY~ 325 (365)
.|++.||.
T Consensus 74 ~l~~~g~~ 81 (1452)
T PTZ00297 74 ELKARGFH 81 (1452)
T ss_pred HHHhcCCc
Confidence 67777874
No 19
>PRK13911 exodeoxyribonuclease III; Provisional
Probab=96.52 E-value=0.0035 Score=60.00 Aligned_cols=53 Identities=17% Similarity=0.345 Sum_probs=35.1
Q ss_pred eEEEeeccccCcccCCCCCCCCCCccCChHHHH-HHHHHHHhhcCCcEEEEeccChhhHHHHHHhhhhcCCceEEE
Q 017840 254 FSVLSYNILSDVYATSESYSYCPSWALSWAYRR-QNLLREIIGYRADIVCLQEVQNDHFEEFFAPELDKHGYQALY 328 (365)
Q Consensus 254 frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~-~~Il~eI~~~~aDIiCLQEV~~~~~~~~~~~~L~~~gY~g~~ 328 (365)
+||+||||=. ..-|. .-+++.|...+||||||||.-....+ + .+...||...+
T Consensus 1 mki~swNVNg------------------ir~~~~~~~~~~l~~~~~DIiclQEtK~~~~~-~---~~~~~gY~~~~ 54 (250)
T PRK13911 1 MKLISWNVNG------------------LRACMTKGFMDFFNSVDADVFCIQESKMQQEQ-N---TFEFKGYFDFW 54 (250)
T ss_pred CEEEEEEeCC------------------hhHhhhhhHHHHHHhcCCCEEEEEeecccccc-c---ccccCCceEEE
Confidence 5899999952 22333 24788999999999999998533221 1 13345776655
No 20
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=90.91 E-value=0.14 Score=50.48 Aligned_cols=47 Identities=17% Similarity=0.346 Sum_probs=35.0
Q ss_pred EEEeeecCCcccccccCCCCcc-cccccchhhhcCCCCCcceecChhhhhHhHHHHHHhhh
Q 017840 51 YKWYRIQSDRKVAVCSVHPSEQ-ATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVLHD 110 (365)
Q Consensus 51 ~~w~r~~~~~~~~~C~~~c~~~-a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~ 110 (365)
-||+-. +..| ..||.+ |+.+|-.|.- -.||+|+|-|-.|-.||.+-+
T Consensus 313 qr~~~d-----~~fC-stCG~~ga~KrCs~CKa-------v~YCdqeCQk~hWf~HKK~C~ 360 (396)
T KOG1710|consen 313 QRIAAD-----CQFC-STCGHPGAKKRCSQCKA-------VAYCDQECQKFHWFIHKKVCS 360 (396)
T ss_pred ceeEEe-----cccc-cccCCCCccchhhhhHH-------HHHHHHHHHHhhhHHHHHHHH
Confidence 356544 4456 577764 5688998864 458999999999999998764
No 21
>COG2374 Predicted extracellular nuclease [General function prediction only]
Probab=81.59 E-value=3.4 Score=45.50 Aligned_cols=97 Identities=20% Similarity=0.334 Sum_probs=60.6
Q ss_pred CCCCceEEEeeccccCcccC-CCCCCC-------C--CCccCChHHHHHHHHHHHhhcCCcEEEEeccChh--------h
Q 017840 249 SSTGTFSVLSYNILSDVYAT-SESYSY-------C--PSWALSWAYRRQNLLREIIGYRADIVCLQEVQND--------H 310 (365)
Q Consensus 249 ~~~~~frVmSYNILa~~ya~-~~~f~y-------~--p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV~~~--------~ 310 (365)
.-.+.|||.||||| .|-+ -+.+++ | +...-+.+.-+..|..-|...++||+.|=|++.+ .
T Consensus 459 ~v~G~LkiasfNVl--Nyf~~~~~~g~~~~~~~d~rga~~~~e~~~Q~~k~v~ai~~ldaDV~GL~Eien~~~~~~s~~a 536 (798)
T COG2374 459 DVGGSLKIASFNVL--NYFNKLSGDGGGASTFSDCRGANTTEEFARQRAKIVTAILTLDADVLGLMEIENNGYGTDSGDA 536 (798)
T ss_pred ccCceeeeeeeehh--hhhccCCCCCCCccccccccCccchhHHHHHHHHHHHHHhhcchhhheeeeeeccCCCCCcHHH
Confidence 34578999999999 4443 233322 2 1112233455678999999999999999999765 3
Q ss_pred HHHHHHhhhhcC----CceEEEeccC---Ce------EEEeccccccccc
Q 017840 311 FEEFFAPELDKH----GYQALYKRKT---NE------VEFNKAAQSLTDA 347 (365)
Q Consensus 311 ~~~~~~~~L~~~----gY~g~~~~K~---g~------i~fn~~~~~l~e~ 347 (365)
..+.+...-++. .|.-++-.+. |. +.|+..+.+++..
T Consensus 537 i~~lV~~lna~~G~~~~y~~v~p~~~~~lgtD~I~vg~iY~~~~V~~~g~ 586 (798)
T COG2374 537 IAQLVNALNAKAGAGTRYAFVAPGRNGGLGTDAIRVGFIYKPSAVSLVGK 586 (798)
T ss_pred HHHHHHHHHhhcCCCceEEEEecCccCCcCCCceeEEEEeccceEEeccc
Confidence 334232222222 3666665543 22 7899888888664
No 22
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional
Probab=77.63 E-value=3.1 Score=40.74 Aligned_cols=46 Identities=24% Similarity=0.400 Sum_probs=30.5
Q ss_pred CCCceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhc-CCcEEEEeccCh
Q 017840 250 STGTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGY-RADIVCLQEVQN 308 (365)
Q Consensus 250 ~~~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~-~aDIiCLQEV~~ 308 (365)
.-..++|.|||+-...+++ .-+|.- -+.+.|.++ ++||+.+||++.
T Consensus 21 ~~~~~~~~twn~qg~s~~~----------~~kw~~---~v~~l~~~~~~~DIla~QEags 67 (271)
T PRK15251 21 NLEDYKVATWNLQGSSAST----------ESKWNV---NVRQLLSGENPADILMVQEAGS 67 (271)
T ss_pred ccccceEEEeecCCCCCCC----------hhhhhh---hHHHHhcCCCCCCEEEEEecCC
Confidence 4457999999997544332 224531 345556665 699999999963
No 23
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=73.70 E-value=2.7 Score=31.89 Aligned_cols=33 Identities=27% Similarity=0.654 Sum_probs=24.9
Q ss_pred ccchhhhcCCCCCcceecChhhhhHhHHHHHHhhh
Q 017840 76 QCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVLHD 110 (365)
Q Consensus 76 qCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~ 110 (365)
.||.|- ..|+ ...-|||++|=+..++.+|+..+
T Consensus 5 HC~~CG-~~Ip-~~~~fCS~~C~~~~~k~qk~~~~ 37 (59)
T PF09889_consen 5 HCPVCG-KPIP-PDESFCSPKCREEYRKRQKRMRK 37 (59)
T ss_pred cCCcCC-CcCC-cchhhhCHHHHHHHHHHHHHHHH
Confidence 477774 3444 35789999999999999888764
No 24
>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms]
Probab=72.74 E-value=3 Score=42.46 Aligned_cols=44 Identities=30% Similarity=0.341 Sum_probs=35.3
Q ss_pred CceEEEeeccccCcccCCCCCCCCCCccCChHHHHHHHHHHHhhcCCcEEEEecc
Q 017840 252 GTFSVLSYNILSDVYATSESYSYCPSWALSWAYRRQNLLREIIGYRADIVCLQEV 306 (365)
Q Consensus 252 ~~frVmSYNILa~~ya~~~~f~y~p~~~l~w~~R~~~Il~eI~~~~aDIiCLQEV 306 (365)
-++||++.|+-+--|+++ .-..|...|-+++.+-..||+.||||
T Consensus 7 ~~lriltlN~Wgip~~Sk-----------~R~~Rm~~~g~~l~~E~yDiv~LQEv 50 (422)
T KOG3873|consen 7 LELRILTLNIWGIPYVSK-----------DRRHRMDAIGDELASEKYDIVSLQEV 50 (422)
T ss_pred heeeeeEeeccccccccc-----------hhHHHHHHHhHHHhhcccchhhHHHH
Confidence 468999999987555433 23467778888999999999999999
No 25
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=72.31 E-value=2.1 Score=32.79 Aligned_cols=29 Identities=24% Similarity=0.324 Sum_probs=20.1
Q ss_pred cccccchhhhcCC---CCCcceecChhhhhHh
Q 017840 73 ATLQCLGCVKAKI---PVAKSYHCSPKCFSDA 101 (365)
Q Consensus 73 a~lqCp~C~k~~~---~~~~s~fCsq~CFk~~ 101 (365)
.+..||+|.|.-. ......|||+-|=.-.
T Consensus 5 ~~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ID 36 (62)
T PRK00418 5 ITVNCPTCGKPVEWGEISPFRPFCSKRCQLID 36 (62)
T ss_pred ccccCCCCCCcccccCCCCcCCcccHHHHhhh
Confidence 4578999999742 1125679999995544
No 26
>PRK01343 zinc-binding protein; Provisional
Probab=65.81 E-value=3.4 Score=31.19 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=20.2
Q ss_pred ccccchhhhcCCCCCcceecChhhhhHh
Q 017840 74 TLQCLGCVKAKIPVAKSYHCSPKCFSDA 101 (365)
Q Consensus 74 ~lqCp~C~k~~~~~~~s~fCsq~CFk~~ 101 (365)
...||+|.|.-.. ....|||+-|=.-.
T Consensus 9 ~~~CP~C~k~~~~-~~rPFCS~RC~~iD 35 (57)
T PRK01343 9 TRPCPECGKPSTR-EAYPFCSERCRDID 35 (57)
T ss_pred CCcCCCCCCcCcC-CCCcccCHHHhhhh
Confidence 4779999887663 46689999996544
No 27
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=62.94 E-value=2.6 Score=31.73 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=14.6
Q ss_pred ccccchhhhcCCC---CCcceecChhhhhHh
Q 017840 74 TLQCLGCVKAKIP---VAKSYHCSPKCFSDA 101 (365)
Q Consensus 74 ~lqCp~C~k~~~~---~~~s~fCsq~CFk~~ 101 (365)
+..||+|.|.-.. -....|||+-|=.-.
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iD 32 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCKLID 32 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHHHHH
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhcccC
Confidence 3568888876442 135669999995443
No 28
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=59.39 E-value=7.2 Score=25.47 Aligned_cols=28 Identities=25% Similarity=0.632 Sum_probs=19.5
Q ss_pred ccccCCCCcccccccchhhhcCCCCCcceecChhhhh
Q 017840 63 AVCSVHPSEQATLQCLGCVKAKIPVAKSYHCSPKCFS 99 (365)
Q Consensus 63 ~~C~~~c~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk 99 (365)
..| .-|+..+.-.||.|. ..+||-+|+|
T Consensus 3 ~~C-~vC~~~~kY~Cp~C~--------~~~CSl~C~k 30 (30)
T PF04438_consen 3 KLC-SVCGNPAKYRCPRCG--------ARYCSLACYK 30 (30)
T ss_dssp EEE-TSSSSEESEE-TTT----------EESSHHHHH
T ss_pred CCC-ccCcCCCEEECCCcC--------CceeCcEeEC
Confidence 356 348888889999763 4499999997
No 29
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
Probab=56.99 E-value=34 Score=33.78 Aligned_cols=11 Identities=55% Similarity=0.721 Sum_probs=9.7
Q ss_pred cCCcE--EEEecc
Q 017840 296 YRADI--VCLQEV 306 (365)
Q Consensus 296 ~~aDI--iCLQEV 306 (365)
.++|| |+|||+
T Consensus 37 ~~pDI~viglQEi 49 (310)
T smart00128 37 EKPDIYVIGLQEV 49 (310)
T ss_pred CCCCEEEEEeeee
Confidence 67998 789998
No 30
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=56.50 E-value=5.2 Score=29.70 Aligned_cols=10 Identities=40% Similarity=0.952 Sum_probs=8.2
Q ss_pred ceecChhhhh
Q 017840 90 SYHCSPKCFS 99 (365)
Q Consensus 90 s~fCsq~CFk 99 (365)
=|||||+|..
T Consensus 28 YYFcse~~~~ 37 (53)
T COG3350 28 YYFCSEECKE 37 (53)
T ss_pred EEEeCHHHHH
Confidence 6899999943
No 31
>COG0024 Map Methionine aminopeptidase [Translation, ribosomal structure and biogenesis]
Probab=46.34 E-value=0.7 Score=44.77 Aligned_cols=61 Identities=11% Similarity=-0.023 Sum_probs=49.2
Q ss_pred cccCCC-cceeEeccceecCCChhccCcEEEEEEEeecCCCCCCCCC---cceeeecc--ccCCCCCC
Q 017840 163 VTRSGG-ETWFEVGRSKTYTPSADDIGHVLKFECVVVDAETKLPVGH---PNTLLTSR--VIPAPSPS 224 (365)
Q Consensus 163 ~~~~~g-e~w~~vg~~~~YtPt~eDIG~llklecl~~dg~~~~plg~---~~sv~Ts~--Vip~P~P~ 224 (365)
+|+++. +++.++.....++.|+.||+.+.+-.+.. .+-+++++|+ |..+|+|. +++|..|.
T Consensus 16 ~Ag~i~a~~l~~~~~~v~pGvtt~Eld~~~~~~i~~-~ga~pa~~gy~g~~~~~ciSvNe~v~HgiP~ 82 (255)
T COG0024 16 EAGKIAAKALKEVASLVKPGVTTLELDEIAEEFIRE-KGAYPAFLGYKGFPFPTCISVNEVVAHGIPG 82 (255)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH-cCceehhccCcCCCcceEeehhheeeecCCC
Confidence 677777 88999999999999999999987766655 3336677765 78999998 78898876
No 32
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.58 E-value=11 Score=29.03 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=17.9
Q ss_pred ccccchhhhcCCC---CCcceecChhhhh
Q 017840 74 TLQCLGCVKAKIP---VAKSYHCSPKCFS 99 (365)
Q Consensus 74 ~lqCp~C~k~~~~---~~~s~fCsq~CFk 99 (365)
+-.||+|-|.-.- -....|||+-|--
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCkl 35 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKL 35 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhh
Confidence 4678888775441 1467899999954
No 33
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=43.33 E-value=7.5 Score=41.36 Aligned_cols=37 Identities=24% Similarity=0.482 Sum_probs=26.0
Q ss_pred CCCCcccccccchhhhcCCCCCcceecChhhhhHhHHHHHHhhhhh
Q 017840 67 VHPSEQATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVLHDRA 112 (365)
Q Consensus 67 ~~c~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~H~~~ 112 (365)
.+|.++|-+-|= . ..-|||-+|-...|..|++.-...
T Consensus 531 ~nC~~EAiy~CC--------W-NTSYCsveCQQ~HW~~H~ksCrrk 567 (588)
T KOG3612|consen 531 YNCLDEAIYHCC--------W-NTSYCSVECQQGHWPEHRKSCRRK 567 (588)
T ss_pred HhhhHHHHHHhh--------c-cccccCcchhhccchhHhhhhccc
Confidence 566666655543 1 244699999999999998766543
No 34
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=34.10 E-value=27 Score=23.73 Aligned_cols=12 Identities=33% Similarity=0.741 Sum_probs=9.9
Q ss_pred cceecChhhhhH
Q 017840 89 KSYHCSPKCFSD 100 (365)
Q Consensus 89 ~s~fCsq~CFk~ 100 (365)
.-.|||+.|...
T Consensus 31 ~~~FCS~~C~~~ 42 (43)
T PF06467_consen 31 MKQFCSQSCLSS 42 (43)
T ss_dssp TSCCSSHHHHHH
T ss_pred ccChhCHHHHhh
Confidence 468999999864
No 35
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=30.90 E-value=56 Score=24.51 Aligned_cols=29 Identities=38% Similarity=0.924 Sum_probs=19.8
Q ss_pred cccccchhhhcCCCCCcceecChhhhhHhHHHHHHh
Q 017840 73 ATLQCLGCVKAKIPVAKSYHCSPKCFSDAWQHHRVL 108 (365)
Q Consensus 73 a~lqCp~C~k~~~~~~~s~fCsq~CFk~~W~~Hk~~ 108 (365)
....||.| ||| ++||.+=.++....|+.+
T Consensus 13 v~~~Cp~c---Gip----thcS~ehw~~D~e~H~~~ 41 (55)
T PF13824_consen 13 VNFECPDC---GIP----THCSEEHWEDDYEEHRQL 41 (55)
T ss_pred cCCcCCCC---CCc----CccCHHHHHHhHHHHHHH
Confidence 35778865 885 678887666666666653
No 36
>KOG4745 consensus Metalloproteinase inhibitor TIMP and related proteins [General function prediction only]
Probab=28.95 E-value=52 Score=29.14 Aligned_cols=12 Identities=50% Similarity=0.797 Sum_probs=9.4
Q ss_pred EEEEeeecCCcc
Q 017840 50 RYKWYRIQSDRK 61 (365)
Q Consensus 50 ~~~w~r~~~~~~ 61 (365)
+++|||+++..+
T Consensus 125 ~C~W~r~~~~~~ 136 (141)
T KOG4745|consen 125 RCSWYRGQLPPK 136 (141)
T ss_pred eeEEeeccCCch
Confidence 689999987544
No 37
>PF04181 RPAP2_Rtr1: Rtr1/RPAP2 family; InterPro: IPR007308 This entry represents a domain found in PAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 proteins. Its function is not known however it is thought to be a zinc finger.
Probab=24.70 E-value=35 Score=26.77 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=10.8
Q ss_pred ceecChhhhhHh
Q 017840 90 SYHCSPKCFSDA 101 (365)
Q Consensus 90 s~fCsq~CFk~~ 101 (365)
+.|||..||+.+
T Consensus 59 ~~fCS~~C~~~s 70 (79)
T PF04181_consen 59 SKFCSKDCYKAS 70 (79)
T ss_pred cCcCCHHHHHHH
Confidence 489999999986
No 38
>KOG0808 consensus Carbon-nitrogen hydrolase [Amino acid transport and metabolism]
Probab=22.81 E-value=77 Score=31.25 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHhhcCCcEEEEecc
Q 017840 283 AYRRQNLLREIIGYRADIVCLQEV 306 (365)
Q Consensus 283 ~~R~~~Il~eI~~~~aDIiCLQEV 306 (365)
-.|...|++--..-...||||||.
T Consensus 99 h~r~kaiieaaa~agvniiclqea 122 (387)
T KOG0808|consen 99 HDRLKAIIEAAAVAGVNIICLQEA 122 (387)
T ss_pred HHHHHHHHHHHHhcCccEEEeehh
Confidence 466777888777889999999997
No 39
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=22.68 E-value=37 Score=30.33 Aligned_cols=29 Identities=31% Similarity=0.599 Sum_probs=20.8
Q ss_pred ccccCCCCc-ccccccchhhhcCCCCCcceecChhhhhH
Q 017840 63 AVCSVHPSE-QATLQCLGCVKAKIPVAKSYHCSPKCFSD 100 (365)
Q Consensus 63 ~~C~~~c~~-~a~lqCp~C~k~~~~~~~s~fCsq~CFk~ 100 (365)
.+| .-|.+ +.+-+||.|. ..|||-.|||-
T Consensus 6 ~tC-~ic~e~~~KYKCpkC~--------vPYCSl~CfKi 35 (157)
T KOG2857|consen 6 TTC-VICLESEIKYKCPKCS--------VPYCSLPCFKI 35 (157)
T ss_pred eee-hhhhcchhhccCCCCC--------Cccccchhhhh
Confidence 456 66766 4578899874 34999999874
No 40
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.02 E-value=29 Score=30.46 Aligned_cols=19 Identities=32% Similarity=0.536 Sum_probs=15.1
Q ss_pred ccccCCCCcccccccchhhh
Q 017840 63 AVCSVHPSEQATLQCLGCVK 82 (365)
Q Consensus 63 ~~C~~~c~~~a~lqCp~C~k 82 (365)
+-| .+||..+-+|||+|-.
T Consensus 29 afc-skcgeati~qcp~csa 47 (160)
T COG4306 29 AFC-SKCGEATITQCPICSA 47 (160)
T ss_pred HHH-hhhchHHHhcCCccCC
Confidence 347 6888888899999964
No 41
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=20.01 E-value=46 Score=23.33 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=8.6
Q ss_pred ceecChhhhhH
Q 017840 90 SYHCSPKCFSD 100 (365)
Q Consensus 90 s~fCsq~CFk~ 100 (365)
=+|||++|-..
T Consensus 25 Y~FCS~~C~~~ 35 (47)
T PF04945_consen 25 YYFCSEGCKEK 35 (47)
T ss_dssp EEESSHHHHHH
T ss_pred EEEcCHHHHHH
Confidence 57999999443
Done!