Query 025771
Match_columns 248
No_of_seqs 61 out of 63
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:20:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2997 F-box protein FBX9 [Ge 99.7 1.4E-17 3E-22 156.1 6.2 139 20-200 108-271 (366)
2 KOG1571 Predicted E3 ubiquitin 99.7 6E-18 1.3E-22 159.0 -1.0 219 20-242 33-253 (355)
3 PF12937 F-box-like: F-box-lik 98.8 4.2E-09 9.2E-14 71.0 3.0 45 20-66 2-47 (47)
4 PF00646 F-box: F-box domain; 98.3 8.1E-07 1.8E-11 59.2 4.1 42 21-64 5-47 (48)
5 smart00256 FBOX A Receptor for 98.2 1.3E-06 2.8E-11 55.6 3.0 39 22-62 1-40 (41)
6 KOG2120 SCF ubiquitin ligase, 88.4 0.28 6.2E-06 47.8 2.1 41 20-62 99-140 (419)
7 KOG3926 F-box proteins [Amino 78.1 6.8 0.00015 37.7 6.5 78 20-100 203-283 (332)
8 PF06881 Elongin_A: RNA polyme 77.5 5.9 0.00013 31.4 5.1 65 20-91 5-69 (109)
9 PLN03215 ascorbic acid mannose 72.0 3.6 7.8E-05 40.0 3.1 37 20-57 5-41 (373)
10 PF01096 TFIIS_C: Transcriptio 66.9 7.7 0.00017 26.0 3.0 33 186-226 1-33 (39)
11 COG1594 RPB9 DNA-directed RNA 62.4 7.5 0.00016 31.7 2.7 94 124-229 7-109 (113)
12 TIGR01384 TFS_arch transcripti 61.2 17 0.00036 28.2 4.4 34 183-226 60-95 (104)
13 PF04606 Ogr_Delta: Ogr/Delta- 57.9 9.1 0.0002 26.4 2.2 30 187-226 1-30 (47)
14 KOG4408 Putative Mg2+ and Co2+ 56.5 2 4.2E-05 42.1 -1.8 46 21-68 10-56 (386)
15 PF13408 Zn_ribbon_recom: Reco 55.3 5.5 0.00012 27.1 0.7 42 184-240 4-46 (58)
16 KOG0281 Beta-TrCP (transducin 41.8 30 0.00064 34.7 3.6 44 20-65 76-124 (499)
17 smart00440 ZnF_C2C2 C2C2 Zinc 37.3 43 0.00094 22.5 2.9 30 187-226 2-33 (40)
18 TIGR03655 anti_R_Lar restricti 35.6 35 0.00075 23.9 2.3 32 186-228 2-33 (53)
19 KOG4341 F-box protein containi 32.8 42 0.0009 34.1 3.1 82 18-101 71-167 (483)
20 PF01607 CBM_14: Chitin bindin 30.7 44 0.00095 21.7 2.1 15 216-230 13-27 (53)
21 KOG2691 RNA polymerase II subu 30.5 1.4E+02 0.0031 25.1 5.4 97 120-226 5-106 (113)
22 COG1996 RPC10 DNA-directed RNA 29.5 28 0.00061 25.2 1.0 14 183-196 22-35 (49)
23 KOG0274 Cdc4 and related F-box 27.5 29 0.00062 35.2 1.0 48 20-69 109-157 (537)
24 PRK14892 putative transcriptio 26.3 14 0.0003 30.0 -1.2 43 173-215 9-51 (99)
25 PRK09710 lar restriction allev 25.1 42 0.00092 25.6 1.3 17 184-200 5-21 (64)
26 PF15153 CYTL1: Cytokine-like 24.7 47 0.001 28.6 1.6 21 129-149 98-118 (132)
27 PRK09678 DNA-binding transcrip 24.4 47 0.001 25.5 1.5 32 186-227 2-33 (72)
28 COG4888 Uncharacterized Zn rib 24.1 20 0.00043 29.7 -0.6 30 168-197 5-34 (104)
29 PF14354 Lar_restr_allev: Rest 23.5 46 0.00099 23.3 1.2 15 186-200 4-18 (61)
30 PTZ00255 60S ribosomal protein 21.9 82 0.0018 25.4 2.4 24 166-193 21-44 (90)
31 PF13397 DUF4109: Domain of un 21.3 66 0.0014 26.6 1.9 18 221-242 28-45 (105)
32 KOG0402 60S ribosomal protein 21.2 54 0.0012 26.6 1.3 26 166-195 21-46 (92)
33 TIGR00280 L37a ribosomal prote 21.2 84 0.0018 25.4 2.4 24 166-193 20-43 (91)
34 PF03604 DNA_RNApol_7kD: DNA d 20.6 70 0.0015 21.0 1.5 12 184-195 16-27 (32)
No 1
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=99.70 E-value=1.4e-17 Score=156.08 Aligned_cols=139 Identities=21% Similarity=0.294 Sum_probs=122.2
Q ss_pred CcCcHHHHHHHHHhcC---CChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhhhhHHhhhhcC-CCCCCCcHHHHHhhh
Q 025771 20 GHLSEDVIFLVFQHMN---WNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAPKMMVDLQSSG-SHSVDGNWRALGKLL 94 (248)
Q Consensus 20 g~L~EdvL~~VF~~ln---wdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP~mv~~L~~~~-~~~~~G~W~aL~KLl 94 (248)
..||||||+.||+.+= -|-+.|.++|||||.|...+|+ -+||.+|.+.|.+|+-.|-... .+.+.++|+.|+
T Consensus 108 ~~LPdEvLm~I~~~vv~~~~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~s~~~ln~~~~~sky~~SWR~Mf--- 184 (366)
T KOG2997|consen 108 SVLPDEVLMRIFRWVVSSLLDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQRSCIKLNPKILQSKYYTSWREMF--- 184 (366)
T ss_pred hhCCHHHHHHHHHHHHhhhcchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHHhhhccchhhhhhHHHhHHHHHH---
Confidence 6899999999999986 1339999999999999999999 9999999999999988777532 388899999999
Q ss_pred hcccCCCCCCcccccccCCceeccceeecccCCccccccccCCeeEeeC---------------CCcccCCCCCceeeee
Q 025771 95 IYCSGCKKGGLFNSIQIPGHFVNKTRFSRTSGKSFLLPQCRTDVLYVSD---------------PCEHLDQGEEGDVGFF 159 (248)
Q Consensus 95 ~~C~G~~~~~~f~~~~~pgHf~~~srfSrtsG~s~L~~rcR~D~LYVsD---------------~CeH~~~~e~r~~g~F 159 (248)
+.+||.|+|++|||. .++|++. |+||++||
T Consensus 185 ----------------------------------l~RpRvrFdG~YIS~~tYiR~G~~~~~~~~~PVHlV~-YYRYiRFy 229 (366)
T KOG2997|consen 185 ----------------------------------LERPRVRFDGVYISKTTYIRQGENSLDSFYRPVHLVE-YYRYIRFY 229 (366)
T ss_pred ----------------------------------hhCcceeecceEEEEEeEeecCchhhhhhcCcceeeE-EEEEEEec
Confidence 999999999999998 8999998 99999999
Q ss_pred c-ccc--c--chhHHHHHHHHHHhccCCCCCCCCCCccceeccccc
Q 025771 160 R-GVF--K--SFQMSKVRKMLIKRGAQLHPTEACPYCKAKLWSMLQ 200 (248)
Q Consensus 160 R-GvF--K--~F~~S~vrr~L~~r~a~~~~~~~CpfCg~~~Wsm~~ 200 (248)
+ |-| + +-.-+.|.+-|.-+..+ ..-++||.++.++..
T Consensus 230 P~G~~l~~~SsdEP~dvVk~~s~~Nt~----~~s~~~g~y~ls~~d 271 (366)
T KOG2997|consen 230 PDGHVLMLTSSDEPQDVVKRLSTRNTR----RDSILLGHYRLSQSD 271 (366)
T ss_pred CCCcEEEEeCCcChHHHHHhhhhccCc----chhhhcccccccCCc
Confidence 9 988 3 37888999999886666 456899998877766
No 2
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.66 E-value=6e-18 Score=159.00 Aligned_cols=219 Identities=24% Similarity=0.306 Sum_probs=196.0
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHHhhhHHHHHhhhhhhHHhhhhcCC-CCCCCcHHHHHhhhhccc
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKRVLWKEFCRTRAPKMMVDLQSSGS-HSVDGNWRALGKLLIYCS 98 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~vlWr~~C~~raP~mv~~L~~~~~-~~~~G~W~aL~KLl~~C~ 98 (248)
++-.+.++...+.+..|+-.-...++=.-.++...++...|+..|+.+.|+|+..+....+ .+.+++|.+.++++|+|.
T Consensus 33 ~~~a~k~~~~~d~~~~~~~~~~~~I~~l~~~~~~~~~~~~~~~~~v~~v~gvv~~~~~~~~~~~~~~~~~~~~~~k~~~~ 112 (355)
T KOG1571|consen 33 GKEAEKVLVLVDLKSSWDIAPEKKIPYLVIRGCAIARKETLRSLCVSNVPGVVQALTLEEPKGRRDGGGHWNANSKIFHE 112 (355)
T ss_pred hhhccceecchhhhhhhhhccccchHHHHHhhcccccccchHHhhcccCCceEEEeeeccceeeeccceeeccceeeccC
Confidence 6677888899999999998888888888888888999999999999999999998885433 666789999999999999
Q ss_pred CCCCCCcccccccCCceeccceeecccCCccccccccCCeeEeeCCCcccCCCCCceeeeecccccchhHHHHHHHHHHh
Q 025771 99 GCKKGGLFNSIQIPGHFVNKTRFSRTSGKSFLLPQCRTDVLYVSDPCEHLDQGEEGDVGFFRGVFKSFQMSKVRKMLIKR 178 (248)
Q Consensus 99 G~~~~~~f~~~~~pgHf~~~srfSrtsG~s~L~~rcR~D~LYVsD~CeH~~~~e~r~~g~FRGvFK~F~~S~vrr~L~~r 178 (248)
|-.....|+-.+.-| |+...++|+++|.-+|+-+++.|.+|-|+||+|.+.+-....|+++|.|+.+++... +-.+
T Consensus 113 ~~~~~~~~l~~q~~~-~~~~~~~s~~~~~~~l~l~~~~d~f~~s~p~s~~~~~~~~~sg~~~~~~~~~~~~l~---~~~~ 188 (355)
T KOG1571|consen 113 GGNEVPFFLRSQTTG-FACEVRVSKTLGRLFLPLNVVYDLFEPSDPCSLVDVGGGYHSGVRRGGFRETERVLP---LGTR 188 (355)
T ss_pred CCcccceeeccCCcc-eeeeeeeecceeeeeecceeeeccccccCcceeeecccccccceeeecccceEEeec---cccc
Confidence 998876666555555 788899999999999999999999999999999998777888999999999887655 6677
Q ss_pred ccCCCCCCCCCCccceecc-cccccccccccccccCCccCceEEEEeeCCeeeeeeeeeccCCCC
Q 025771 179 GAQLHPTEACPYCKAKLWS-MLQAKMIPQSASCRLGAYEDCIEYYVCLNGHMLGICSLLPLSDSE 242 (248)
Q Consensus 179 ~a~~~~~~~CpfCg~~~Ws-m~~a~~~p~sa~rRl~~ye~~veyyVC~NGHv~G~~tl~pls~se 242 (248)
.+.+.+.+.|+||+-++|+ |+.+..+++|+..+|.+-++....++|+|+|++|.+|.++||.-+
T Consensus 189 ~t~l~e~v~d~~~~~r~~~~~~g~~~v~~s~~d~LIsr~g~~s~~~kv~~~~~~~~~~ills~~~ 253 (355)
T KOG1571|consen 189 LTALGELVRDGYCGVRVQPPMQGPLYVTKSAADRLISREGDLSFFVKVNGMVFGTLGVILLSFIV 253 (355)
T ss_pred eeeeehheecCCCceEecCCccCcceeeccchhhHHHhhccceeeeeecceeeeeeeEEeehHHH
Confidence 7889999999999999999 999999999999999999999999999999999999999999654
No 3
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=98.78 E-value=4.2e-09 Score=70.98 Aligned_cols=45 Identities=22% Similarity=0.718 Sum_probs=38.7
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHh
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRT 66 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~ 66 (248)
..||+||+.+||+.|+ |++++++++|||+|+.++.. .+|++.|.+
T Consensus 2 ~~LP~Eil~~If~~L~--~~dl~~~~~vcr~w~~~~~~~~lW~~~~~r 47 (47)
T PF12937_consen 2 SSLPDEILLEIFSYLD--PRDLLRLSLVCRRWRRIANDNSLWRRLCLR 47 (47)
T ss_dssp CCS-HHHHHHHHTTS---HHHHHHHTTSSHHHHHHHTCCCHHHHHC--
T ss_pred hHhHHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHHCChhhhhhhccC
Confidence 3699999999999995 99999999999999999976 999998864
No 4
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=98.31 E-value=8.1e-07 Score=59.21 Aligned_cols=42 Identities=24% Similarity=0.522 Sum_probs=36.7
Q ss_pred cCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHH
Q 025771 21 HLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFC 64 (248)
Q Consensus 21 ~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C 64 (248)
.||+|++.+||.+|+ |.+++++++||++|++++++ .+|+..|
T Consensus 5 ~LP~~il~~Il~~l~--~~~~~~l~~vsk~~~~~~~~~~~~~~~~ 47 (48)
T PF00646_consen 5 DLPDEILQEILSYLD--PKDLLRLSLVSKRWRSLVDSPRLWKKII 47 (48)
T ss_dssp HS-HHHHHHHHHTS---HHHHHHHCTT-HHHHHHHTTHHHHHHHH
T ss_pred HCCHHHHHHHHHHCc--HHHHHHHHHHhhHHHHHHcCCCccHHHh
Confidence 489999999999998 99999999999999999999 8888876
No 5
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=98.20 E-value=1.3e-06 Score=55.59 Aligned_cols=39 Identities=15% Similarity=0.422 Sum_probs=36.2
Q ss_pred CcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHH
Q 025771 22 LSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKE 62 (248)
Q Consensus 22 L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~ 62 (248)
||+|++..||..++ |.+++++++|||+|+.+++. .+|++
T Consensus 1 lP~~ll~~I~~~l~--~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 1 LPDEILEEILSKLP--PKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CCHHHHHHHHHcCC--HHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 68999999999997 99999999999999999988 88875
No 6
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=88.42 E-value=0.28 Score=47.76 Aligned_cols=41 Identities=27% Similarity=0.575 Sum_probs=37.7
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHH
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKE 62 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~ 62 (248)
-.|||++++.||+-|- -.+|-+++-||+||--++++ -+|-.
T Consensus 99 ~slpDEill~IFs~L~--kk~LL~~~~VC~Rfyr~~~de~lW~~ 140 (419)
T KOG2120|consen 99 DSLPDEILLGIFSCLC--KKELLKVSGVCKRFYRLASDESLWQT 140 (419)
T ss_pred ccCCHHHHHHHHHhcc--HHHHHHHHHHHHHHhhccccccceee
Confidence 4799999999999998 88999999999999999998 88864
No 7
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=78.10 E-value=6.8 Score=37.67 Aligned_cols=78 Identities=14% Similarity=0.318 Sum_probs=56.1
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhh--hhHHhhhhcCCCCCCCcHHHHHhhhhc
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAP--KMMVDLQSSGSHSVDGNWRALGKLLIY 96 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP--~mv~~L~~~~~~~~~G~W~aL~KLl~~ 96 (248)
.-||++++.+|..+|. |-++|-.+|=|=.-+..++.. -+||++|..-+. ++-..|..+-.+. -.|+.|.==|.-
T Consensus 203 ~dLP~e~vl~Il~rls-Dh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~erQi~~~l~l~k~~q--~dWkqmyf~L~r 279 (332)
T KOG3926|consen 203 HDLPLECVLNILLRLS-DHRDLESLAQAWETLAKLSEERRIWKKLCQFHFNERQIHTILILSKKGQ--KDWKQMYFQLRR 279 (332)
T ss_pred ccchHHHHHHHHHHcc-CcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhhhccccc--hhHHHHHHHHHH
Confidence 6799999999999998 778888888777777766665 999999998887 3333344333333 458887655555
Q ss_pred ccCC
Q 025771 97 CSGC 100 (248)
Q Consensus 97 C~G~ 100 (248)
|-|+
T Consensus 280 ~yg~ 283 (332)
T KOG3926|consen 280 TYGV 283 (332)
T ss_pred hcCh
Confidence 5554
No 8
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=77.53 E-value=5.9 Score=31.40 Aligned_cols=65 Identities=14% Similarity=0.298 Sum_probs=49.5
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHHhhhHHHHHhhhhhhHHhhhhcCCCCCCCcHHHHH
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKRVLWKEFCRTRAPKMMVDLQSSGSHSVDGNWRALG 91 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~vlWr~~C~~raP~mv~~L~~~~~~~~~G~W~aL~ 91 (248)
|.+|-++|.-|+.+++ |..|.++-=-|.-+... -.-||+.+|.+-+|.-+.+-. ..-+.+|+.++
T Consensus 5 G~~py~ll~piL~~~~--~~QL~~iE~~np~l~~~-tdeLW~~~i~rdFp~~~~~~~----~~~~~~Wr~~Y 69 (109)
T PF06881_consen 5 GDVPYHLLRPILEKCS--PEQLRRIEDNNPHLIED-TDELWKKLIKRDFPEESKRQK----PKEPESWRELY 69 (109)
T ss_pred CCCCHHHHHHHHccCC--HHHHHHHHHhCCCcchh-hHHHHHHHHHhHCcChhhccc----ccccchHHHHH
Confidence 7799999999999996 99999999888665543 348999999999996211111 22245999887
No 9
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=72.00 E-value=3.6 Score=40.04 Aligned_cols=37 Identities=8% Similarity=0.283 Sum_probs=32.3
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR 57 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~ 57 (248)
+.|++|+|.+|..+|. ..-++.+.+.||+-||+-+..
T Consensus 5 s~Lp~dll~~i~~~l~-~~~d~~~~~~vC~sWr~a~~~ 41 (373)
T PLN03215 5 STLPEELLHMIAGRLF-SNVELKRFRSICRSWRSSVSG 41 (373)
T ss_pred hhCCHHHHHHHHhhCC-cHHHHHHHHhhhhhHHHhccc
Confidence 4699999999999995 366999999999999987664
No 10
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=66.86 E-value=7.7 Score=26.01 Aligned_cols=33 Identities=30% Similarity=0.504 Sum_probs=19.1
Q ss_pred CCCCCccceecccccccccccccccccCCccCceEEEEeeC
Q 025771 186 EACPYCKAKLWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 186 ~~CpfCg~~~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
..||.||.+..-..+... -.+-||...+|+|.|
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~--------rsaDE~~T~fy~C~~ 33 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQT--------RSADEPMTLFYVCCN 33 (39)
T ss_dssp S--SSS-SSEEEEEEESS--------SSSSSSSEEEEEESS
T ss_pred CCCcCCCCCeEEEEEeec--------cCCCCCCeEEEEeCC
Confidence 369999995332222222 134799999999976
No 11
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=62.37 E-value=7.5 Score=31.73 Aligned_cols=94 Identities=23% Similarity=0.358 Sum_probs=55.6
Q ss_pred ccCCccccccccCCeeEeeCCCcccCCCCCceeeeecccc-cchhHHHHHHHH---HHhccCCCCC--CCCCCccce--e
Q 025771 124 TSGKSFLLPQCRTDVLYVSDPCEHLDQGEEGDVGFFRGVF-KSFQMSKVRKML---IKRGAQLHPT--EACPYCKAK--L 195 (248)
Q Consensus 124 tsG~s~L~~rcR~D~LYVsD~CeH~~~~e~r~~g~FRGvF-K~F~~S~vrr~L---~~r~a~~~~~--~~CpfCg~~--~ 195 (248)
.-|+=+++++=-.|.+++|..|.+.. +...-.+++-.. .++..++..... ...+++..++ +.||=||.+ .
T Consensus 7 ~Cgsll~p~~~~~~~~l~C~kCgye~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~ea~ 84 (113)
T COG1594 7 KCGSLLYPKKDDEGGKLVCRKCGYEE--EASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGNKEAY 84 (113)
T ss_pred CccCeeEEeEcCCCcEEECCCCCcch--hccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCCCceeE
Confidence 33444556555567799999999998 455544555333 333333222221 2334444444 689999993 4
Q ss_pred cccccccccccccccccCCccCceEEEEee-CCee
Q 025771 196 WSMLQAKMIPQSASCRLGAYEDCIEYYVCL-NGHM 229 (248)
Q Consensus 196 Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~-NGHv 229 (248)
|=+.|-+- +-||..+.|.|. =||.
T Consensus 85 y~~~QtRs----------aDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 85 YWQLQTRS----------ADEPETRFYKCTRCGYR 109 (113)
T ss_pred EEeeehhc----------cCCCceEEEEecccCCE
Confidence 54444322 269999999994 4664
No 12
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=61.23 E-value=17 Score=28.20 Aligned_cols=34 Identities=29% Similarity=0.593 Sum_probs=24.2
Q ss_pred CCCCCCCCccc-e-ecccccccccccccccccCCccCceEEEEeeC
Q 025771 183 HPTEACPYCKA-K-LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 183 ~~~~~CpfCg~-~-~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
...+.||-||. + +|-..|- |. +-||.-.+|+|.|
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~---------Rs-adE~~T~fy~C~~ 95 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQT---------RR-ADEPETRFYKCTK 95 (104)
T ss_pred cccCCCCCCCCCeeEEEEecc---------CC-CCCCcEEEEEeCC
Confidence 34689999998 3 3544431 21 4699999999987
No 13
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=57.92 E-value=9.1 Score=26.43 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=17.8
Q ss_pred CCCCccceecccccccccccccccccCCccCceEEEEeeC
Q 025771 187 ACPYCKAKLWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 187 ~CpfCg~~~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
.||.||++.=--.+..+- -+-.--||.|.|
T Consensus 1 ~CP~Cg~~a~ir~S~~~s----------~~~~~~Y~qC~N 30 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLS----------PLTRELYCQCTN 30 (47)
T ss_pred CcCCCCCeeEEEEchhhC----------cceEEEEEEECC
Confidence 499999954222233222 122348999999
No 14
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=56.47 E-value=2 Score=42.09 Aligned_cols=46 Identities=17% Similarity=0.407 Sum_probs=41.0
Q ss_pred cCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhh
Q 025771 21 HLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRA 68 (248)
Q Consensus 21 ~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~ra 68 (248)
-++.++|..|...+- |+++++-|||.+++..+++. -+|...|.+-+
T Consensus 10 ~~~~~~l~~vls~~~--~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l 56 (386)
T KOG4408|consen 10 WLPRDPLHLVLSFLL--YRDLINCAYVSRRLKELGSHLPLWNRPCKKYL 56 (386)
T ss_pred hcccccceeeecccc--hhhhhcceeechHHhhhhhccccccccccccc
Confidence 467889999999997 99999999999999999999 89999995443
No 15
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=55.28 E-value=5.5 Score=27.10 Aligned_cols=42 Identities=29% Similarity=0.516 Sum_probs=28.4
Q ss_pred CCCCCCCccceecccccccccccccccccCCccCceEEEEeeCCeeee-eeeeeccCC
Q 025771 184 PTEACPYCKAKLWSMLQAKMIPQSASCRLGAYEDCIEYYVCLNGHMLG-ICSLLPLSD 240 (248)
Q Consensus 184 ~~~~CpfCg~~~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~NGHv~G-~~tl~pls~ 240 (248)
-.+.|+.||..+.-. .+-+.| .||+|-|..-.| .|.-..++.
T Consensus 4 g~l~C~~CG~~m~~~-----------~~~~~~----~yy~C~~~~~~~~~C~~~~i~~ 46 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR-----------KRKGKY----RYYRCSNRRRKGKGCPNKSIRE 46 (58)
T ss_pred CcEEcccCCcEeEEE-----------ECCCCc----eEEEcCCCcCCCCCCCCCEeCH
Confidence 347899999875541 111334 899999999888 666554443
No 16
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=41.76 E-value=30 Score=34.71 Aligned_cols=44 Identities=16% Similarity=0.394 Sum_probs=37.2
Q ss_pred CcCc----HHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHH
Q 025771 20 GHLS----EDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCR 65 (248)
Q Consensus 20 g~L~----EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~ 65 (248)
..|| |+|..+||+-|+ -..|+..--|||+|.-+..+ -+||.+=.
T Consensus 76 ~~lP~~gl~hi~e~ilsyld--~~sLc~celv~k~W~r~l~dg~~WKkLie 124 (499)
T KOG0281|consen 76 TALPEQGLDHIAENILSYLD--ALSLCACELVCKEWKRVLSDGMLWKKLIE 124 (499)
T ss_pred HhcccccHHHHHHHHHHhcc--hhhhhHHHHHHHHHHHHhccchHHHHHHH
Confidence 3567 999999999997 88999999999999877766 88887654
No 17
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=37.28 E-value=43 Score=22.54 Aligned_cols=30 Identities=37% Similarity=0.709 Sum_probs=20.6
Q ss_pred CCCCccce--ecccccccccccccccccCCccCceEEEEeeC
Q 025771 187 ACPYCKAK--LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 187 ~CpfCg~~--~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
.||-||.. +|-..| -|. +-||..-+|+|+|
T Consensus 2 ~Cp~C~~~~a~~~q~Q---------~Rs-aDE~mT~fy~C~~ 33 (40)
T smart00440 2 PCPKCGNREATFFQLQ---------TRS-ADEPMTVFYVCTK 33 (40)
T ss_pred cCCCCCCCeEEEEEEc---------ccC-CCCCCeEEEEeCC
Confidence 69999983 333322 122 4799999999998
No 18
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=35.63 E-value=35 Score=23.92 Aligned_cols=32 Identities=22% Similarity=0.408 Sum_probs=17.7
Q ss_pred CCCCCccceecccccccccccccccccCCccCceEEEEeeCCe
Q 025771 186 EACPYCKAKLWSMLQAKMIPQSASCRLGAYEDCIEYYVCLNGH 228 (248)
Q Consensus 186 ~~CpfCg~~~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~NGH 228 (248)
.+|||||.+. .++ ++.+.-.+.-.||.|-+=.
T Consensus 2 kPCPfCGg~~------~~~-----~~~~~~~~~~~~~~C~~Cg 33 (53)
T TIGR03655 2 KPCPFCGGAD------VYL-----RRGFDPLDLSHYFECSTCG 33 (53)
T ss_pred CCCCCCCCcc------eee-----EeccCCCCCEEEEECCCCC
Confidence 3799999842 222 2222233556677787533
No 19
>KOG4341 consensus F-box protein containing LRR [General function prediction only]
Probab=32.82 E-value=42 Score=34.14 Aligned_cols=82 Identities=13% Similarity=0.241 Sum_probs=60.4
Q ss_pred cCCcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhh-----hhHHhhhhcC---------CCC
Q 025771 18 TKGHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAP-----KMMVDLQSSG---------SHS 82 (248)
Q Consensus 18 ~~g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP-----~mv~~L~~~~---------~~~ 82 (248)
....||.+++..||+-|. -..+++.|=+|+-|.-+|-+ .+|-.-=..++| ++|++..... .+.
T Consensus 71 ~~~~LPpEl~lkvFS~LD--tksl~r~a~~c~~~n~~AlD~~~~q~idL~t~~rDv~g~VV~~~~~Rcgg~lk~LSlrG~ 148 (483)
T KOG4341|consen 71 ISRSLPPELLLKVFSMLD--TKSLCRAAQCCTMWNKLALDGSCWQHIDLFTFQRDVDGGVVENMISRCGGFLKELSLRGC 148 (483)
T ss_pred ccccCCHHHHHHHHHHHh--HHHHHHHHHHHHHhhhhhhccccceeeehhcchhcCCCcceehHhhhhcccccccccccc
Confidence 347899999999999996 99999999999999999888 889877777777 4555444321 134
Q ss_pred CCCcHHHHHhhhhcccCCC
Q 025771 83 VDGNWRALGKLLIYCSGCK 101 (248)
Q Consensus 83 ~~G~W~aL~KLl~~C~G~~ 101 (248)
.+-+-.+|.-+..-||-..
T Consensus 149 r~v~~sslrt~~~~CpnIe 167 (483)
T KOG4341|consen 149 RAVGDSSLRTFASNCPNIE 167 (483)
T ss_pred ccCCcchhhHHhhhCCchh
Confidence 4444566666666666553
No 20
>PF01607 CBM_14: Chitin binding Peritrophin-A domain; InterPro: IPR002557 This entry represents a chitin binding domain []. It is found in (amongst others) the Peritrophin-A chitin binding proteins, particularly the peritrophic matrix proteins of insects and animal chitinases [, , ]. Copies of the domain are also found in some baculoviruses. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains [].; GO: 0008061 chitin binding, 0006030 chitin metabolic process, 0005576 extracellular region; PDB: 1DQC_A.
Probab=30.70 E-value=44 Score=21.69 Aligned_cols=15 Identities=47% Similarity=1.283 Sum_probs=11.8
Q ss_pred cCceEEEEeeCCeee
Q 025771 216 EDCIEYYVCLNGHML 230 (248)
Q Consensus 216 e~~veyyVC~NGHv~ 230 (248)
++.-.||+|.||...
T Consensus 13 ~~C~~Y~~C~~g~~~ 27 (53)
T PF01607_consen 13 DDCRKYYQCVNGQAV 27 (53)
T ss_dssp S-SSEEEEEETTEEE
T ss_pred CCCCEEEEeeCCcEE
Confidence 567789999999875
No 21
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=30.48 E-value=1.4e+02 Score=25.11 Aligned_cols=97 Identities=15% Similarity=0.289 Sum_probs=54.8
Q ss_pred eeecccCCccccccc--cCCeeEeeCCCcccCCCCCceeeeecccc--cchhHHHHHHHHH-HhccCCCCCCCCCCccce
Q 025771 120 RFSRTSGKSFLLPQC--RTDVLYVSDPCEHLDQGEEGDVGFFRGVF--KSFQMSKVRKMLI-KRGAQLHPTEACPYCKAK 194 (248)
Q Consensus 120 rfSrtsG~s~L~~rc--R~D~LYVsD~CeH~~~~e~r~~g~FRGvF--K~F~~S~vrr~L~-~r~a~~~~~~~CpfCg~~ 194 (248)
||-|+-.|-|-++-= -.=+||-|++|+|.. +-..=.+|+--+ +.=-...+-.-|. |--=+...+..||-||.+
T Consensus 5 rfC~eCNNmLYPkEDked~~L~laCrnCd~ve--~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~ 82 (113)
T KOG2691|consen 5 RFCRECNNMLYPKEDKEDRILLLACRNCDYVE--EADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHR 82 (113)
T ss_pred chhhhhhccccccccccccEEEEEecCCcceE--ecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCc
Confidence 566666665554322 222899999999999 777888888433 2222112222221 211133345789999984
Q ss_pred ecccccccccccccccccCCccCceEEEEeeC
Q 025771 195 LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 195 ~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
- +-|.- +-.+|. -|...=||||.|
T Consensus 83 e----avffQ--~~~~r~--d~~m~l~yvC~~ 106 (113)
T KOG2691|consen 83 E----AVFFQ--AQTRRA--DEAMRLFYVCCS 106 (113)
T ss_pred c----eEEEe--cccccc--cceEEEEEEecc
Confidence 1 11222 222332 367778999998
No 22
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.49 E-value=28 Score=25.18 Aligned_cols=14 Identities=29% Similarity=0.895 Sum_probs=11.2
Q ss_pred CCCCCCCCccceec
Q 025771 183 HPTEACPYCKAKLW 196 (248)
Q Consensus 183 ~~~~~CpfCg~~~W 196 (248)
.+.++|||||.++.
T Consensus 22 ~~~irCp~Cg~rIl 35 (49)
T COG1996 22 TRGIRCPYCGSRIL 35 (49)
T ss_pred cCceeCCCCCcEEE
Confidence 45689999999864
No 23
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=27.45 E-value=29 Score=35.15 Aligned_cols=48 Identities=15% Similarity=0.450 Sum_probs=40.4
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhh
Q 025771 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAP 69 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP 69 (248)
+.|+-++...||..|. |+.+..++-||+.|+.++.. ..|++.|..-..
T Consensus 109 ~~lp~el~~~il~~Ld--~~~l~~~~~v~~~w~~~~~~~~~~~~~~~~~~~ 157 (537)
T KOG0274|consen 109 SLLPSELSLHILSFLD--GRDLLAVRQVCRNWNKLLDDDKVWWRMCRELIG 157 (537)
T ss_pred hcccchhcccccccCC--HHHhhhhhhhcchhhhhhhccchhhhhhhhhcc
Confidence 5678888888999997 99999999999999999998 677766665444
No 24
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.33 E-value=14 Score=29.95 Aligned_cols=43 Identities=26% Similarity=0.329 Sum_probs=25.7
Q ss_pred HHHHHhccCCCCCCCCCCccceecccccccccccccccccCCc
Q 025771 173 KMLIKRGAQLHPTEACPYCKAKLWSMLQAKMIPQSASCRLGAY 215 (248)
Q Consensus 173 r~L~~r~a~~~~~~~CpfCg~~~Wsm~~a~~~p~sa~rRl~~y 215 (248)
+.++....++..-..||+|+..+-+..--+.+|.-.+..=|.|
T Consensus 9 k~~~k~k~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 9 KKIIRPKPKLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CCCcccccCCCcEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 3344445566667899999975444222234556566666655
No 25
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=25.07 E-value=42 Score=25.57 Aligned_cols=17 Identities=18% Similarity=0.612 Sum_probs=13.1
Q ss_pred CCCCCCCccceeccccc
Q 025771 184 PTEACPYCKAKLWSMLQ 200 (248)
Q Consensus 184 ~~~~CpfCg~~~Wsm~~ 200 (248)
.-.+|||||..+-.+.+
T Consensus 5 ~lKPCPFCG~~~~~v~~ 21 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA 21 (64)
T ss_pred cccCCCCCCCceeEEEe
Confidence 34689999998777664
No 26
>PF15153 CYTL1: Cytokine-like protein 1
Probab=24.66 E-value=47 Score=28.59 Aligned_cols=21 Identities=38% Similarity=0.904 Sum_probs=18.5
Q ss_pred cccccccCCeeEeeCCCcccC
Q 025771 129 FLLPQCRTDVLYVSDPCEHLD 149 (248)
Q Consensus 129 ~L~~rcR~D~LYVsD~CeH~~ 149 (248)
...+.||.|+.|.||.|+-++
T Consensus 98 Im~~~CrRDLVFlsDDC~ALe 118 (132)
T PF15153_consen 98 IMNSFCRRDLVFLSDDCEALE 118 (132)
T ss_pred HHHHHhhcceeeecCchHhhc
Confidence 456789999999999999887
No 27
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=24.39 E-value=47 Score=25.52 Aligned_cols=32 Identities=22% Similarity=0.365 Sum_probs=18.1
Q ss_pred CCCCCccceecccccccccccccccccCCccCceEEEEeeCC
Q 025771 186 EACPYCKAKLWSMLQAKMIPQSASCRLGAYEDCIEYYVCLNG 227 (248)
Q Consensus 186 ~~CpfCg~~~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~NG 227 (248)
-.||+||.+. =...++-+ . -+-.-+||.|.|-
T Consensus 2 m~CP~Cg~~a-~irtSr~~--------s-~~~~~~Y~qC~N~ 33 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYI--------T-DTTKERYHQCQNV 33 (72)
T ss_pred ccCCCCCCcc-EEEEChhc--------C-hhhheeeeecCCC
Confidence 3699999864 22222222 2 1234479999874
No 28
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.07 E-value=20 Score=29.67 Aligned_cols=30 Identities=33% Similarity=0.463 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhccCCCCCCCCCCccceecc
Q 025771 168 MSKVRKMLIKRGAQLHPTEACPYCKAKLWS 197 (248)
Q Consensus 168 ~S~vrr~L~~r~a~~~~~~~CpfCg~~~Ws 197 (248)
+.+.++.+..++.+|+.+-.||+|+...-+
T Consensus 5 r~krr~~ik~~~~~L~k~FtCp~Cghe~vs 34 (104)
T COG4888 5 RRKRRKIIKRRPQVLPKTFTCPRCGHEKVS 34 (104)
T ss_pred cccccccCcccCccCCceEecCccCCeeee
Confidence 344555555656669999999999996555
No 29
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=23.46 E-value=46 Score=23.29 Aligned_cols=15 Identities=27% Similarity=0.691 Sum_probs=10.3
Q ss_pred CCCCCccceeccccc
Q 025771 186 EACPYCKAKLWSMLQ 200 (248)
Q Consensus 186 ~~CpfCg~~~Wsm~~ 200 (248)
..|||||.......+
T Consensus 4 kPCPFCG~~~~~~~~ 18 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ 18 (61)
T ss_pred cCCCCCCCcceEeec
Confidence 479999986544443
No 30
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.87 E-value=82 Score=25.37 Aligned_cols=24 Identities=25% Similarity=0.577 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc
Q 025771 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA 193 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~ 193 (248)
.-|.+|.+..+...++ -.||||+.
T Consensus 21 slRK~v~kie~~q~a~----y~CpfCgk 44 (90)
T PTZ00255 21 SLRKQIKKIEISQHAK----YFCPFCGK 44 (90)
T ss_pred HHHHHHHHHHHHHhCC----ccCCCCCC
Confidence 4566777777665554 69999986
No 31
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=21.35 E-value=66 Score=26.60 Aligned_cols=18 Identities=33% Similarity=0.704 Sum_probs=13.2
Q ss_pred EEEeeCCeeeeeeeeeccCCCC
Q 025771 221 YYVCLNGHMLGICSLLPLSDSE 242 (248)
Q Consensus 221 yyVC~NGHv~G~~tl~pls~se 242 (248)
-|.|-|||. |.+|++...
T Consensus 28 ~Y~C~~Gh~----~~v~Fa~eA 45 (105)
T PF13397_consen 28 SYWCPNGHE----TEVPFAAEA 45 (105)
T ss_pred EEECCCCCE----EeccccccC
Confidence 589999998 456666643
No 32
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=21.24 E-value=54 Score=26.58 Aligned_cols=26 Identities=27% Similarity=0.487 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCcccee
Q 025771 166 FQMSKVRKMLIKRGAQLHPTEACPYCKAKL 195 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~~~ 195 (248)
=-+.+|+++++...++ -.|+|||.++
T Consensus 21 SLrk~vKkiei~Qhak----y~CsfCGK~~ 46 (92)
T KOG0402|consen 21 SLRKMVKKIEIQQHAK----YTCSFCGKKT 46 (92)
T ss_pred HHHHHHHHHHHHHhhh----hhhhhcchhh
Confidence 3466888888875555 7999999754
No 33
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=21.16 E-value=84 Score=25.37 Aligned_cols=24 Identities=29% Similarity=0.627 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc
Q 025771 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA 193 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~ 193 (248)
.-|.+|.+..+...++ -.||||+.
T Consensus 20 slRK~v~kie~~q~a~----y~CpfCgk 43 (91)
T TIGR00280 20 KLRRQVKKIEIQQKAK----YVCPFCGK 43 (91)
T ss_pred HHHHHHHHHHHHHhcC----ccCCCCCC
Confidence 4566777777765554 69999975
No 34
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.61 E-value=70 Score=21.03 Aligned_cols=12 Identities=25% Similarity=0.767 Sum_probs=8.8
Q ss_pred CCCCCCCcccee
Q 025771 184 PTEACPYCKAKL 195 (248)
Q Consensus 184 ~~~~CpfCg~~~ 195 (248)
..+.|++||.++
T Consensus 16 ~~irC~~CG~RI 27 (32)
T PF03604_consen 16 DPIRCPECGHRI 27 (32)
T ss_dssp STSSBSSSS-SE
T ss_pred CcEECCcCCCeE
Confidence 348999999875
Done!