Query 022473
Match_columns 296
No_of_seqs 57 out of 59
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 03:47:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022473hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1571 Predicted E3 ubiquitin 99.9 1E-23 2.2E-28 201.1 -3.5 243 3-250 12-255 (355)
2 PF12937 F-box-like: F-box-lik 98.8 3E-09 6.4E-14 72.9 2.3 44 25-70 3-47 (47)
3 PF00646 F-box: F-box domain; 98.3 9.4E-07 2E-11 59.9 4.7 43 25-69 5-48 (48)
4 smart00256 FBOX A Receptor for 98.2 1.2E-06 2.7E-11 56.5 3.6 39 26-66 1-40 (41)
5 KOG2997 F-box protein FBX9 [Ge 98.2 1.3E-06 2.8E-11 84.7 4.1 72 24-95 108-183 (366)
6 KOG2120 SCF ubiquitin ligase, 86.7 0.43 9.3E-06 47.6 2.3 41 24-66 99-140 (419)
7 KOG3926 F-box proteins [Amino 73.1 6 0.00013 38.9 4.9 79 23-105 202-283 (332)
8 PF06881 Elongin_A: RNA polyme 71.3 5.3 0.00012 32.3 3.5 67 22-96 3-69 (109)
9 PLN03215 ascorbic acid mannose 70.8 4.2 9E-05 40.4 3.3 35 25-60 6-40 (373)
10 PRK14892 putative transcriptio 55.6 3.2 6.8E-05 34.4 -0.5 47 178-224 8-54 (99)
11 PF04606 Ogr_Delta: Ogr/Delta- 53.2 10 0.00022 26.8 1.8 30 193-232 1-30 (47)
12 PF13408 Zn_ribbon_recom: Reco 51.0 7.3 0.00016 27.0 0.8 44 188-246 2-46 (58)
13 PF12660 zf-TFIIIC: Putative z 49.8 7.9 0.00017 31.4 0.9 40 190-248 13-54 (99)
14 KOG4408 Putative Mg2+ and Co2+ 47.4 2.9 6.4E-05 41.8 -2.2 47 24-72 9-56 (386)
15 KOG0281 Beta-TrCP (transducin 47.2 29 0.00063 35.6 4.5 41 28-70 84-125 (499)
16 PF11672 DUF3268: Protein of u 45.5 15 0.00033 30.6 2.0 33 192-232 3-36 (102)
17 PRK11088 rrmA 23S rRNA methylt 44.5 19 0.00041 32.6 2.6 34 192-245 3-41 (272)
18 COG1996 RPC10 DNA-directed RNA 42.3 12 0.00026 27.8 0.8 13 189-201 22-34 (49)
19 KOG4341 F-box protein containi 40.5 27 0.00058 36.3 3.2 87 19-107 68-168 (483)
20 PF10083 DUF2321: Uncharacteri 39.8 9.4 0.0002 34.4 -0.1 11 227-237 7-17 (158)
21 PF03115 Astro_capsid: Astrovi 37.2 12 0.00025 40.8 0.1 18 209-226 643-660 (787)
22 smart00746 TRASH metallochaper 37.1 30 0.00064 20.0 1.9 11 194-204 1-11 (39)
23 PRK09710 lar restriction allev 36.8 27 0.0006 27.3 2.1 28 189-231 4-31 (64)
24 COG4391 Uncharacterized protei 36.6 14 0.00031 28.8 0.5 10 191-200 48-57 (62)
25 PF11793 FANCL_C: FANCL C-term 36.2 16 0.00035 27.7 0.8 20 185-204 48-69 (70)
26 cd00350 rubredoxin_like Rubred 35.8 28 0.0006 23.0 1.7 11 190-200 16-26 (33)
27 KOG4264 Nucleo-cytoplasmic pro 34.7 25 0.00053 37.5 2.0 25 237-261 79-103 (694)
28 PF04871 Uso1_p115_C: Uso1 / p 34.4 29 0.00064 29.7 2.1 8 243-250 113-120 (136)
29 PRK13130 H/ACA RNA-protein com 33.2 11 0.00024 28.5 -0.6 37 173-211 1-37 (56)
30 KOG4364 Chromatin assembly fac 33.1 28 0.00061 37.8 2.1 31 243-273 535-565 (811)
31 PF10276 zf-CHCC: Zinc-finger 32.9 15 0.00033 26.0 0.1 9 192-200 30-38 (40)
32 PRK09678 DNA-binding transcrip 32.6 24 0.00052 27.8 1.2 33 192-234 2-34 (72)
33 PRK00398 rpoP DNA-directed RNA 32.1 20 0.00044 24.9 0.6 11 191-201 21-31 (46)
34 KOG0274 Cdc4 and related F-box 31.1 23 0.00049 36.5 1.1 48 24-73 109-157 (537)
35 COG4888 Uncharacterized Zn rib 30.7 18 0.00038 30.8 0.2 60 177-248 8-67 (104)
36 PF13013 F-box-like_2: F-box-l 30.2 1.2E+02 0.0027 25.4 5.1 44 10-57 11-54 (109)
37 smart00659 RPOLCX RNA polymera 30.2 24 0.00051 25.2 0.7 12 190-201 18-29 (44)
38 PF01096 TFIIS_C: Transcriptio 29.0 55 0.0012 22.5 2.3 30 193-232 2-33 (39)
39 COG1594 RPB9 DNA-directed RNA 28.9 90 0.0019 26.1 4.0 97 126-235 3-109 (113)
40 PF03604 DNA_RNApol_7kD: DNA d 28.8 30 0.00065 23.4 1.0 12 190-201 16-27 (32)
41 PF01698 FLO_LFY: Floricaula / 28.3 21 0.00045 36.1 0.2 13 276-289 226-238 (386)
42 PF04216 FdhE: Protein involve 28.0 35 0.00076 31.8 1.6 31 191-234 211-245 (290)
43 TIGR01384 TFS_arch transcripti 27.7 1.2E+02 0.0025 24.0 4.3 73 145-232 16-95 (104)
44 PF14354 Lar_restr_allev: Rest 27.5 28 0.0006 25.0 0.7 10 193-202 5-14 (61)
45 PF01607 CBM_14: Chitin bindin 27.5 48 0.001 22.0 1.9 15 222-236 13-27 (53)
46 smart00440 ZnF_C2C2 C2C2 Zinc 26.3 63 0.0014 22.4 2.3 29 193-232 2-33 (40)
47 KOG3241 Uncharacterized conser 26.0 27 0.0006 32.7 0.6 37 212-248 154-192 (227)
48 TIGR03655 anti_R_Lar restricti 25.3 32 0.00069 24.7 0.7 8 193-200 3-10 (53)
49 KOG2110 Uncharacterized conser 24.7 2.6E+02 0.0057 28.6 7.0 111 161-287 261-389 (391)
50 KOG0402 60S ribosomal protein 24.2 38 0.00083 28.2 1.0 24 173-200 22-45 (92)
51 KOG1832 HIV-1 Vpr-binding prot 24.2 46 0.001 37.9 1.9 44 51-94 1036-1083(1516)
52 PF06524 NOA36: NOA36 protein; 23.4 62 0.0014 31.9 2.4 10 191-200 209-218 (314)
53 PF09026 CENP-B_dimeris: Centr 22.4 29 0.00063 29.4 0.0 10 245-254 14-23 (101)
54 PF03066 Nucleoplasmin: Nucleo 22.4 48 0.001 28.9 1.4 21 225-245 88-111 (149)
55 PF14255 Cys_rich_CPXG: Cystei 22.3 41 0.00088 25.0 0.8 9 192-200 1-9 (52)
56 PF13248 zf-ribbon_3: zinc-rib 21.6 33 0.00072 21.6 0.1 11 191-201 16-26 (26)
57 PF05129 Elf1: Transcription e 21.1 40 0.00086 26.7 0.5 20 180-199 11-30 (81)
58 PTZ00415 transmission-blocking 21.0 63 0.0014 39.1 2.2 34 246-279 154-187 (2849)
59 KOG0943 Predicted ubiquitin-pr 20.4 64 0.0014 38.1 2.1 36 4-39 1282-1329(3015)
No 1
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.86 E-value=1e-23 Score=201.11 Aligned_cols=243 Identities=32% Similarity=0.379 Sum_probs=224.2
Q ss_pred CCcCcccCCCCCCCCCCcCCCCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHHHHhHHHHHHhhhchhHHHhhcC
Q 022473 3 GNANKRLRPNPPSQVPESGDSGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAERLLWRKLCECRAPRMIETLANG 82 (296)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~larrvLWRe~C~~raP~mv~dL~~~ 82 (296)
+|.+.+|.++++++.|..+..|+-.+.++...+.+..|+-.-...++=.-.++...++...|+..|+.+.|.|++.+...
T Consensus 12 ~~v~l~l~~~~~g~~~~~s~~~~~a~k~~~~~d~~~~~~~~~~~~I~~l~~~~~~~~~~~~~~~~~v~~v~gvv~~~~~~ 91 (355)
T KOG1571|consen 12 TNVALRLLFRQYGRLPRVSKVGKEAEKVLVLVDLKSSWDIAPEKKIPYLVIRGCAIARKETLRSLCVSNVPGVVQALTLE 91 (355)
T ss_pred hHHHHHhhhhhcccchhhHHHhhhccceecchhhhhhhhhccccchHHHHHhhcccccccchHHhhcccCCceEEEeeec
Confidence 46788999999999999998999999999999999999999888888888999999999999999999999999999998
Q ss_pred CCCCCCCCchhHhHHHhhccCCCCCCCCcccccCCCCceeeccccccccCCcccccccCCceeeecCCCCCCCCCCCCce
Q 022473 83 APNGRINGGWHALAKLMFHCCGCESTRNFKVSKASPAHFVQASRFSKTSGRSFLTKKCRGDLLYVSDPCEHPMGNKEDDL 162 (296)
Q Consensus 83 ~~~~~i~GgW~AL~KLl~~C~G~~~~~~F~~s~~~pgHf~~~srfSRtsG~sfL~~rcR~D~LYVsDpCeH~~~ge~~d~ 162 (296)
.+-.+.+++|...++++|+|.|.....-|..+++ .| |+...++|+++|.-+|+-.++.|.+|-|+||+|.+.+-....
T Consensus 92 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~~l~~q~-~~-~~~~~~~s~~~~~~~l~l~~~~d~f~~s~p~s~~~~~~~~~s 169 (355)
T KOG1571|consen 92 EPKGRRDGGGHWNANSKIFHEGGNEVPFFLRSQT-TG-FACEVRVSKTLGRLFLPLNVVYDLFEPSDPCSLVDVGGGYHS 169 (355)
T ss_pred cceeeeccceeeccceeeccCCCcccceeeccCC-cc-eeeeeeeecceeeeeecceeeeccccccCcceeeeccccccc
Confidence 7778888999999999999999988765655333 34 888999999999999999999999999999999998888899
Q ss_pred eeeeeeccccchhhHHHHHhhccccccccccCCCCCcccch-hhhcccccccccccccccCCceeEEEeecCceeeeeee
Q 022473 163 GIFRGVFRGFLKSTTRACLIRRRVELEERVKCPYCGARVWS-MTAARLVPKSAARRLGSHDGGLEYFVCINGHLHGSCWL 241 (296)
Q Consensus 163 glfRGVFk~F~~Srvr~~Li~~~~~l~~~~~CpyC~ar~Ws-m~~A~~lp~sa~rrlG~~edgveyyVC~NGHv~G~ctl 241 (296)
|+++|.|+.++++.. |-.....|.+.++|+||+-++|+ |..+..+++|+..+|++.+++...++|+|+|++|.+|.
T Consensus 170 g~~~~~~~~~~~~l~---~~~~~t~l~e~v~d~~~~~r~~~~~~g~~~v~~s~~d~LIsr~g~~s~~~kv~~~~~~~~~~ 246 (355)
T KOG1571|consen 170 GVRRGGFRETERVLP---LGTRLTALGELVRDGYCGVRVQPPMQGPLYVTKSAADRLISREGDLSFFVKVNGMVFGTLGV 246 (355)
T ss_pred ceeeecccceEEeec---cccceeeeehheecCCCceEecCCccCcceeeccchhhHHHhhccceeeeeecceeeeeeeE
Confidence 999999999998855 66788899999999999999999 99999999999999999999999999999999999999
Q ss_pred eecCCCccc
Q 022473 242 VPLSSEEDA 250 (296)
Q Consensus 242 ~PLs~se~~ 250 (296)
++||.-+.+
T Consensus 247 ills~~~~d 255 (355)
T KOG1571|consen 247 ILLSFIVKD 255 (355)
T ss_pred EeehHHHHH
Confidence 999987644
No 2
>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=98.79 E-value=3e-09 Score=72.95 Aligned_cols=44 Identities=32% Similarity=0.502 Sum_probs=38.3
Q ss_pred ccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHh
Q 022473 25 IFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCEC 70 (296)
Q Consensus 25 ~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~ 70 (296)
.||+||+..||..|+ |++++++++|||+|+.++. +.+||.+|.+
T Consensus 3 ~LP~Eil~~If~~L~--~~dl~~~~~vcr~w~~~~~~~~lW~~~~~r 47 (47)
T PF12937_consen 3 SLPDEILLEIFSYLD--PRDLLRLSLVCRRWRRIANDNSLWRRLCLR 47 (47)
T ss_dssp CS-HHHHHHHHTTS---HHHHHHHTTSSHHHHHHHTCCCHHHHHC--
T ss_pred HhHHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHHCChhhhhhhccC
Confidence 699999999999996 9999999999999999997 5999999864
No 3
>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=98.32 E-value=9.4e-07 Score=59.86 Aligned_cols=43 Identities=16% Similarity=0.343 Sum_probs=36.8
Q ss_pred ccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHH
Q 022473 25 IFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCE 69 (296)
Q Consensus 25 ~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~ 69 (296)
.||+|++.+||.+|+ |.+++++++|||+|+.+++ ..+|+..|.
T Consensus 5 ~LP~~il~~Il~~l~--~~~~~~l~~vsk~~~~~~~~~~~~~~~~r 48 (48)
T PF00646_consen 5 DLPDEILQEILSYLD--PKDLLRLSLVSKRWRSLVDSPRLWKKIIR 48 (48)
T ss_dssp HS-HHHHHHHHHTS---HHHHHHHCTT-HHHHHHHTTHHHHHHHH-
T ss_pred HCCHHHHHHHHHHCc--HHHHHHHHHHhhHHHHHHcCCCccHHHhC
Confidence 489999999999999 9999999999999999999 699998873
No 4
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=98.24 E-value=1.2e-06 Score=56.51 Aligned_cols=39 Identities=18% Similarity=0.329 Sum_probs=36.3
Q ss_pred cchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHH
Q 022473 26 FNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRK 66 (296)
Q Consensus 26 LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe 66 (296)
|++|++..||.+|+ |++++++++|||+|+.+++ ..+|++
T Consensus 1 lP~~ll~~I~~~l~--~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 1 LPDEILEEILSKLP--PKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CCHHHHHHHHHcCC--HHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 68999999999998 9999999999999999999 688875
No 5
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=98.19 E-value=1.3e-06 Score=84.66 Aligned_cols=72 Identities=21% Similarity=0.296 Sum_probs=60.8
Q ss_pred CccchHHHHHHHHHcC---CChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhchhHHHhhcCCCCCCCCCchhHh
Q 022473 24 GIFNERILLLVFESVG---WDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAPRMIETLANGAPNGRINGGWHAL 95 (296)
Q Consensus 24 g~LsEdVLllVF~~Ln---wdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP~mv~dL~~~~~~~~i~GgW~AL 95 (296)
..||+|||+.||+.+= -|-|.|.++|||||.|...+| +-+||.+|.+.|-+|+-.|-.--...-..+.|..+
T Consensus 108 ~~LPdEvLm~I~~~vv~~~~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~s~~~ln~~~~~sky~~SWR~M 183 (366)
T KOG2997|consen 108 SVLPDEVLMRIFRWVVSSLLDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQRSCIKLNPKILQSKYYTSWREM 183 (366)
T ss_pred hhCCHHHHHHHHHHHHhhhcchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHHhhhccchhhhhhHHHhHHHHH
Confidence 6899999999999987 233999999999999999999 79999999999999998886643224457889853
No 6
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=86.74 E-value=0.43 Score=47.58 Aligned_cols=41 Identities=20% Similarity=0.374 Sum_probs=37.5
Q ss_pred CccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHH
Q 022473 24 GIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRK 66 (296)
Q Consensus 24 g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe 66 (296)
-.|+|+|++.||+-|- -.+|-+++-||+||-.+++ .-+|-.
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 5689999999999999 8999999999999999999 488854
No 7
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=73.10 E-value=6 Score=38.92 Aligned_cols=79 Identities=19% Similarity=0.274 Sum_probs=54.4
Q ss_pred CCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhch--hHHHhhcCCCCCCCCCchhHhHHHh
Q 022473 23 SGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAPR--MIETLANGAPNGRINGGWHALAKLM 99 (296)
Q Consensus 23 ~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP~--mv~dL~~~~~~~~i~GgW~AL~KLl 99 (296)
---||++++++|..+|. |-++|-.+|=|=.-+..+++ +-+||++|..-+-. +-..|..+.. +- -.|+.+.==|
T Consensus 202 l~dLP~e~vl~Il~rls-Dh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~erQi~~~l~l~k~-~q--~dWkqmyf~L 277 (332)
T KOG3926|consen 202 LHDLPLECVLNILLRLS-DHRDLESLAQAWETLAKLSEERRIWKKLCQFHFNERQIHTILILSKK-GQ--KDWKQMYFQL 277 (332)
T ss_pred cccchHHHHHHHHHHcc-CcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhhhccc-cc--hhHHHHHHHH
Confidence 35699999999999998 67788888877777887777 89999999876642 2223444433 22 3587654444
Q ss_pred hccCCC
Q 022473 100 FHCCGC 105 (296)
Q Consensus 100 ~~C~G~ 105 (296)
.-|.|+
T Consensus 278 ~r~yg~ 283 (332)
T KOG3926|consen 278 RRTYGV 283 (332)
T ss_pred HHhcCh
Confidence 444444
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=71.35 E-value=5.3 Score=32.31 Aligned_cols=67 Identities=21% Similarity=0.276 Sum_probs=49.1
Q ss_pred CCCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHHHHhHHHHHHhhhchhHHHhhcCCCCCCCCCchhHhH
Q 022473 22 DSGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAERLLWRKLCECRAPRMIETLANGAPNGRINGGWHALA 96 (296)
Q Consensus 22 ~~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~larrvLWRe~C~~raP~mv~dL~~~~~~~~i~GgW~AL~ 96 (296)
+-|.++-++|.-|+.+++ |..|.++-=-|.-+... -+-||+.+|.+-+|. ......+ .. +-.|..+.
T Consensus 3 dvG~~py~ll~piL~~~~--~~QL~~iE~~np~l~~~-tdeLW~~~i~rdFp~---~~~~~~~-~~-~~~Wr~~Y 69 (109)
T PF06881_consen 3 DVGDVPYHLLRPILEKCS--PEQLRRIEDNNPHLIED-TDELWKKLIKRDFPE---ESKRQKP-KE-PESWRELY 69 (109)
T ss_pred ccCCCCHHHHHHHHccCC--HHHHHHHHHhCCCcchh-hHHHHHHHHHhHCcC---hhhcccc-cc-cchHHHHH
Confidence 468899999999999996 99999998888544321 269999999999996 1111121 11 34888765
No 9
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=70.76 E-value=4.2 Score=40.41 Aligned_cols=35 Identities=17% Similarity=0.083 Sum_probs=30.9
Q ss_pred ccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH
Q 022473 25 IFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE 60 (296)
Q Consensus 25 ~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar 60 (296)
.|++|+|.+|..+|. ..-++.|.+.|||-||+-+.
T Consensus 6 ~Lp~dll~~i~~~l~-~~~d~~~~~~vC~sWr~a~~ 40 (373)
T PLN03215 6 TLPEELLHMIAGRLF-SNVELKRFRSICRSWRSSVS 40 (373)
T ss_pred hCCHHHHHHHHhhCC-cHHHHHHHHhhhhhHHHhcc
Confidence 599999999999994 36699999999999997655
No 10
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=55.56 E-value=3.2 Score=34.37 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=28.8
Q ss_pred HHHHhhccccccccccCCCCCcccchhhhcccccccccccccccCCc
Q 022473 178 RACLIRRRVELEERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGG 224 (296)
Q Consensus 178 r~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edg 224 (296)
++.++....++..-..||+|+...=++---+.++.-++..-|+|-+.
T Consensus 8 ~k~~~k~k~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 8 RKKIIRPKPKLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCCCcccccCCCcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 34556667888888999999964222111124556666667776443
No 11
>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=53.20 E-value=10 Score=26.85 Aligned_cols=30 Identities=33% Similarity=0.668 Sum_probs=17.0
Q ss_pred cCCCCCcccchhhhcccccccccccccccCCceeEEEeec
Q 022473 193 KCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCIN 232 (296)
Q Consensus 193 ~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~N 232 (296)
.||.|+++.==-.+-.+-+ +-.--||+|.|
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~----------~~~~~Y~qC~N 30 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSP----------LTRELYCQCTN 30 (47)
T ss_pred CcCCCCCeeEEEEchhhCc----------ceEEEEEEECC
Confidence 5999999731111222222 11247999999
No 12
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=51.04 E-value=7.3 Score=27.04 Aligned_cols=44 Identities=25% Similarity=0.634 Sum_probs=29.5
Q ss_pred ccccccCCCCCcccchhhhcccccccccccccccCCceeEEEeecCceee-eeeeeecCC
Q 022473 188 LEERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCINGHLHG-SCWLVPLSS 246 (296)
Q Consensus 188 l~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~NGHv~G-~ctl~PLs~ 246 (296)
|...+.|+.||.+++- +. +. .+..||+|-|..-.| .|.-..++.
T Consensus 2 l~g~l~C~~CG~~m~~--------~~--~~-----~~~~yy~C~~~~~~~~~C~~~~i~~ 46 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTR--------RK--RK-----GKYRYYRCSNRRRKGKGCPNKSIRE 46 (58)
T ss_pred CCCcEEcccCCcEeEE--------EE--CC-----CCceEEEcCCCcCCCCCCCCCEeCH
Confidence 3456899999988544 11 11 233899999999888 666554443
No 13
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=49.75 E-value=7.9 Score=31.40 Aligned_cols=40 Identities=35% Similarity=0.779 Sum_probs=13.8
Q ss_pred ccccCCCCCcccchhhhcccccccccccccccCCceeEEEeecCceeeee--eeeecCCCc
Q 022473 190 ERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCINGHLHGSC--WLVPLSSEE 248 (296)
Q Consensus 190 ~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~NGHv~G~c--tl~PLs~se 248 (296)
..|.|++|++.+ | + +..+.-+|.|||+-.-| |++|+.+..
T Consensus 13 i~E~C~~C~~~i---------~------~----~~~~~~~C~~GH~w~RC~lT~l~i~~~~ 54 (99)
T PF12660_consen 13 IFEKCPICGAPI---------P------F----DDLDEAQCENGHVWPRCALTFLPIQTPG 54 (99)
T ss_dssp -----------------------------------SSEEE-TTS-EEEB-SSS-SBS-SS-
T ss_pred cccccccccccc---------c------c----CCcCEeECCCCCEEeeeeeeeeeeccCC
Confidence 339999998753 2 0 11345789999998866 678887766
No 14
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=47.44 E-value=2.9 Score=41.82 Aligned_cols=47 Identities=21% Similarity=0.292 Sum_probs=41.5
Q ss_pred CccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhh
Q 022473 24 GIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRA 72 (296)
Q Consensus 24 g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~ra 72 (296)
.-++.++|..|...+. |+++++-|||.+++..+++ .-+|...|.+-+
T Consensus 9 e~~~~~~l~~vls~~~--~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l 56 (386)
T KOG4408|consen 9 EWLPRDPLHLVLSFLL--YRDLINCAYVSRRLKELGSHLPLWNRPCKKYL 56 (386)
T ss_pred hhcccccceeeecccc--hhhhhcceeechHHhhhhhccccccccccccc
Confidence 4567889999999999 9999999999999999999 699999996543
No 15
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=47.16 E-value=29 Score=35.58 Aligned_cols=41 Identities=20% Similarity=0.400 Sum_probs=35.5
Q ss_pred hHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHh
Q 022473 28 ERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCEC 70 (296)
Q Consensus 28 EdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~ 70 (296)
|+|.++||+.|+ -..||..--|||+|+.+.. .-+||.+-.+
T Consensus 84 ~hi~e~ilsyld--~~sLc~celv~k~W~r~l~dg~~WKkLie~ 125 (499)
T KOG0281|consen 84 DHIAENILSYLD--ALSLCACELVCKEWKRVLSDGMLWKKLIER 125 (499)
T ss_pred HHHHHHHHHhcc--hhhhhHHHHHHHHHHHHhccchHHHHHHHH
Confidence 899999999999 8899999999999987666 6888877654
No 16
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=45.54 E-value=15 Score=30.63 Aligned_cols=33 Identities=36% Similarity=0.851 Sum_probs=20.1
Q ss_pred ccCCCCCcccchhhhccccccccccccccc-CCceeEEEeec
Q 022473 192 VKCPYCGARVWSMTAARLVPKSAARRLGSH-DGGLEYFVCIN 232 (296)
Q Consensus 192 ~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~-edgveyyVC~N 232 (296)
+.||||+.++ .+++ ++.-+|.. +++--+|||.+
T Consensus 3 ~~CpYCg~~~------~l~~--~~~iYg~~~~~~~~~y~C~~ 36 (102)
T PF11672_consen 3 IICPYCGGPA------ELVD--GSEIYGHRYDDGPYLYVCTP 36 (102)
T ss_pred cccCCCCCee------EEcc--cchhcCccCCCCceeEECCC
Confidence 7899999973 2233 23445533 23434499998
No 17
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=44.45 E-value=19 Score=32.61 Aligned_cols=34 Identities=26% Similarity=0.698 Sum_probs=25.3
Q ss_pred ccCCCCCcccchhhhcccccccccccccccCCceeEEEeecCcee-----eeeeeeecC
Q 022473 192 VKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCINGHLH-----GSCWLVPLS 245 (296)
Q Consensus 192 ~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~NGHv~-----G~ctl~PLs 245 (296)
..||-|+..+ +. .+ +-|+|.|||-. |.+.|+|-.
T Consensus 3 ~~CP~C~~~l---~~--------------~~---~~~~C~~~h~fd~a~~Gy~~ll~~~ 41 (272)
T PRK11088 3 YQCPLCHQPL---TL--------------EE---NSWICPQNHQFDCAKEGYVNLLPVQ 41 (272)
T ss_pred ccCCCCCcch---hc--------------CC---CEEEcCCCCCCccccCceEEecccc
Confidence 5799999864 11 01 34999999987 999999843
No 18
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.30 E-value=12 Score=27.78 Aligned_cols=13 Identities=46% Similarity=1.510 Sum_probs=10.9
Q ss_pred cccccCCCCCccc
Q 022473 189 EERVKCPYCGARV 201 (296)
Q Consensus 189 ~~~~~CpyC~ar~ 201 (296)
.+.++||||+.|+
T Consensus 22 ~~~irCp~Cg~rI 34 (49)
T COG1996 22 TRGIRCPYCGSRI 34 (49)
T ss_pred cCceeCCCCCcEE
Confidence 4668999999984
No 19
>KOG4341 consensus F-box protein containing LRR [General function prediction only]
Probab=40.53 E-value=27 Score=36.25 Aligned_cols=87 Identities=20% Similarity=0.233 Sum_probs=62.0
Q ss_pred CcCCCCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhchh-----HHHhhcCC-------C-
Q 022473 19 ESGDSGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAPRM-----IETLANGA-------P- 84 (296)
Q Consensus 19 ~~~~~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP~m-----v~dL~~~~-------~- 84 (296)
+-.....|+.+++.+||+.|. -..+++.|=+|+-|.-+|- +.+|-..=...+|+- |+-+.... +
T Consensus 68 ~~~~~~~LPpEl~lkvFS~LD--tksl~r~a~~c~~~n~~AlD~~~~q~idL~t~~rDv~g~VV~~~~~Rcgg~lk~LSl 145 (483)
T KOG4341|consen 68 NNSISRSLPPELLLKVFSMLD--TKSLCRAAQCCTMWNKLALDGSCWQHIDLFTFQRDVDGGVVENMISRCGGFLKELSL 145 (483)
T ss_pred cccccccCCHHHHHHHHHHHh--HHHHHHHHHHHHHhhhhhhccccceeeehhcchhcCCCcceehHhhhhccccccccc
Confidence 344568899999999999998 9999999999999999888 699988777777652 22222110 0
Q ss_pred CCCCCCchhHhHHHhhccCCCCC
Q 022473 85 NGRINGGWHALAKLMFHCCGCES 107 (296)
Q Consensus 85 ~~~i~GgW~AL~KLl~~C~G~~~ 107 (296)
-|..+-+-.+|.-+...||-.++
T Consensus 146 rG~r~v~~sslrt~~~~CpnIeh 168 (483)
T KOG4341|consen 146 RGCRAVGDSSLRTFASNCPNIEH 168 (483)
T ss_pred cccccCCcchhhHHhhhCCchhh
Confidence 13444455667777777776655
No 20
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=39.84 E-value=9.4 Score=34.38 Aligned_cols=11 Identities=36% Similarity=0.833 Sum_probs=8.6
Q ss_pred EEEeecCceee
Q 022473 227 YFVCINGHLHG 237 (296)
Q Consensus 227 yyVC~NGHv~G 237 (296)
+=||+|||+.-
T Consensus 7 aqiC~NGH~~t 17 (158)
T PF10083_consen 7 AQICLNGHVIT 17 (158)
T ss_pred HHHccCccccc
Confidence 34899999963
No 21
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=37.16 E-value=12 Score=40.79 Aligned_cols=18 Identities=17% Similarity=0.309 Sum_probs=0.4
Q ss_pred cccccccccccccCCcee
Q 022473 209 LVPKSAARRLGSHDGGLE 226 (296)
Q Consensus 209 ~lp~sa~rrlG~~edgve 226 (296)
.||++.....+..|+-++
T Consensus 643 ~lP~~~~~~~~~~e~~~~ 660 (787)
T PF03115_consen 643 SLPQSSSSSSGLWEDATS 660 (787)
T ss_dssp S-----------------
T ss_pred cccccccccccccccccc
Confidence 477666666666655543
No 22
>smart00746 TRASH metallochaperone-like domain.
Probab=37.08 E-value=30 Score=19.99 Aligned_cols=11 Identities=27% Similarity=1.213 Sum_probs=8.2
Q ss_pred CCCCCcccchh
Q 022473 194 CPYCGARVWSM 204 (296)
Q Consensus 194 CpyC~ar~Wsm 204 (296)
||+|+..+++-
T Consensus 1 c~~C~~~~~~~ 11 (39)
T smart00746 1 CSFCGKDIYNP 11 (39)
T ss_pred CCCCCCCccCC
Confidence 88998877543
No 23
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=36.79 E-value=27 Score=27.32 Aligned_cols=28 Identities=25% Similarity=0.555 Sum_probs=18.8
Q ss_pred cccccCCCCCcccchhhhcccccccccccccccCCceeEEEee
Q 022473 189 EERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCI 231 (296)
Q Consensus 189 ~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~ 231 (296)
+.-..||||++.+=.+-+ .++-.+++|-
T Consensus 4 d~lKPCPFCG~~~~~v~~---------------~~g~~~v~C~ 31 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKA---------------ISGYYRAKCN 31 (64)
T ss_pred ccccCCCCCCCceeEEEe---------------cCceEEEEcC
Confidence 445679999998655442 3556677885
No 24
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.56 E-value=14 Score=28.79 Aligned_cols=10 Identities=60% Similarity=1.537 Sum_probs=8.3
Q ss_pred cccCCCCCcc
Q 022473 191 RVKCPYCGAR 200 (296)
Q Consensus 191 ~~~CpyC~ar 200 (296)
-+.||||+.+
T Consensus 48 ev~CPYC~t~ 57 (62)
T COG4391 48 EVVCPYCSTR 57 (62)
T ss_pred cEecCccccE
Confidence 3889999986
No 25
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=36.25 E-value=16 Score=27.74 Aligned_cols=20 Identities=35% Similarity=0.881 Sum_probs=11.5
Q ss_pred cccccc-cccCCCCCcc-cchh
Q 022473 185 RVELEE-RVKCPYCGAR-VWSM 204 (296)
Q Consensus 185 ~~~l~~-~~~CpyC~ar-~Wsm 204 (296)
|..+.+ .-.||||+.+ .|+|
T Consensus 48 ~~~~~~~~G~CP~C~~~i~~~~ 69 (70)
T PF11793_consen 48 RQSFIPIFGECPYCSSPISWSF 69 (70)
T ss_dssp S-TTT--EEE-TTT-SEEEGGG
T ss_pred CeeecccccCCcCCCCeeeEec
Confidence 333443 3579999998 8987
No 26
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.85 E-value=28 Score=22.99 Aligned_cols=11 Identities=45% Similarity=0.981 Sum_probs=9.1
Q ss_pred ccccCCCCCcc
Q 022473 190 ERVKCPYCGAR 200 (296)
Q Consensus 190 ~~~~CpyC~ar 200 (296)
+...||-|++.
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 55899999985
No 27
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=34.73 E-value=25 Score=37.47 Aligned_cols=25 Identities=24% Similarity=0.241 Sum_probs=15.3
Q ss_pred eeeeeeecCCCcccCCCCCCCCCCC
Q 022473 237 GSCWLVPLSSEEDACDEDDDEDGED 261 (296)
Q Consensus 237 G~ctl~PLs~se~~~~~~~~~~~~~ 261 (296)
++--.+-+||||++.|++++++.++
T Consensus 79 ~~~g~asgsdsEe~ed~~~Edge~~ 103 (694)
T KOG4264|consen 79 APAGKASGSDSEEKEDEAAEDGEED 103 (694)
T ss_pred ccccccccCCcccccccccccCccc
Confidence 3444567888888777555444433
No 28
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=34.42 E-value=29 Score=29.69 Aligned_cols=8 Identities=38% Similarity=0.671 Sum_probs=5.2
Q ss_pred ecCCCccc
Q 022473 243 PLSSEEDA 250 (296)
Q Consensus 243 PLs~se~~ 250 (296)
|+|+.|+.
T Consensus 113 eVSddE~~ 120 (136)
T PF04871_consen 113 EVSDDEDS 120 (136)
T ss_pred CccCCccc
Confidence 66777755
No 29
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.17 E-value=11 Score=28.50 Aligned_cols=37 Identities=30% Similarity=0.571 Sum_probs=27.6
Q ss_pred chhhHHHHHhhccccccccccCCCCCcccchhhhccccc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGARVWSMTAARLVP 211 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp 211 (296)
|+|+++++=.-..--| ...||-||..+-+-+-|+.=|
T Consensus 1 Mks~mr~C~~CgvYTL--k~~CP~CG~~t~~~~P~rfSp 37 (56)
T PRK13130 1 MKSKIRKCPKCGVYTL--KEICPVCGGKTKNPHPPRFSP 37 (56)
T ss_pred CCccceECCCCCCEEc--cccCcCCCCCCCCCCCCCCCC
Confidence 4566666665555555 589999999998888888776
No 30
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=33.09 E-value=28 Score=37.84 Aligned_cols=31 Identities=42% Similarity=0.501 Sum_probs=20.0
Q ss_pred ecCCCcccCCCCCCCCCCCCCCCCCCCCCcc
Q 022473 243 PLSSEEDACDEDDDEDGEDGEDGGDDPDGAY 273 (296)
Q Consensus 243 PLs~se~~~~~~~~~~~~~~~~~~~~~~~~~ 273 (296)
.||+||++.|++++++.+|.+|+-+-+.+.+
T Consensus 535 SlS~sEddedd~~eEd~edEdDgffVPhgyL 565 (811)
T KOG4364|consen 535 SLSDSEDDEDDSLEEDCEDEDDGFFVPHGYL 565 (811)
T ss_pred cccccccccccccccccccccCCeecCCccc
Confidence 4778887777666666666666655555443
No 31
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=32.92 E-value=15 Score=26.03 Aligned_cols=9 Identities=78% Similarity=1.922 Sum_probs=7.9
Q ss_pred ccCCCCCcc
Q 022473 192 VKCPYCGAR 200 (296)
Q Consensus 192 ~~CpyC~ar 200 (296)
+.||||+.+
T Consensus 30 ~~CpYCg~~ 38 (40)
T PF10276_consen 30 VVCPYCGTR 38 (40)
T ss_dssp EEETTTTEE
T ss_pred EECCCCCCE
Confidence 799999975
No 32
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=32.64 E-value=24 Score=27.79 Aligned_cols=33 Identities=24% Similarity=0.469 Sum_probs=19.8
Q ss_pred ccCCCCCcccchhhhcccccccccccccccCCceeEEEeecCc
Q 022473 192 VKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCINGH 234 (296)
Q Consensus 192 ~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~NGH 234 (296)
-.||+|+++. -|+.| |.+... ---+||.|.|-.
T Consensus 2 m~CP~Cg~~a-------~irtS--r~~s~~-~~~~Y~qC~N~e 34 (72)
T PRK09678 2 FHCPLCQHAA-------HARTS--RYITDT-TKERYHQCQNVN 34 (72)
T ss_pred ccCCCCCCcc-------EEEEC--hhcChh-hheeeeecCCCC
Confidence 3699999863 34444 333211 125899998753
No 33
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=32.11 E-value=20 Score=24.90 Aligned_cols=11 Identities=64% Similarity=1.685 Sum_probs=9.2
Q ss_pred cccCCCCCccc
Q 022473 191 RVKCPYCGARV 201 (296)
Q Consensus 191 ~~~CpyC~ar~ 201 (296)
...||||+.++
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 47999999973
No 34
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=31.09 E-value=23 Score=36.52 Aligned_cols=48 Identities=10% Similarity=0.249 Sum_probs=40.5
Q ss_pred CccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhc
Q 022473 24 GIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAP 73 (296)
Q Consensus 24 g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP 73 (296)
+.|+-++...||..|. |+.++.++-||+.|+.++. ...|++.|..-.+
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 5677888888999998 9999999999999999999 5777777766554
No 35
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.66 E-value=18 Score=30.76 Aligned_cols=60 Identities=30% Similarity=0.378 Sum_probs=32.4
Q ss_pred HHHHHhhccccccccccCCCCCcccchhhhcccccccccccccccCCceeEEEeecCceeeeeeeeecCCCc
Q 022473 177 TRACLIRRRVELEERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFVCINGHLHGSCWLVPLSSEE 248 (296)
Q Consensus 177 vr~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~NGHv~G~ctl~PLs~se 248 (296)
.|+.+..++..|+.+-.||+|+...=+..+ |.+. +++-.-+|=|=-++=.|-.-+|+..-
T Consensus 8 rr~~ik~~~~~L~k~FtCp~Cghe~vs~ct---vkk~---------~~~g~~~Cg~CGls~e~ev~~l~~~v 67 (104)
T COG4888 8 RRKIIKRRPQVLPKTFTCPRCGHEKVSSCT---VKKT---------VNIGTAVCGNCGLSFECEVPELSEPV 67 (104)
T ss_pred ccccCcccCccCCceEecCccCCeeeeEEE---EEec---------CceeEEEcccCcceEEEeccccccch
Confidence 333333444449999999999996333111 2222 23344456555555555555555543
No 36
>PF13013 F-box-like_2: F-box-like domain
Probab=30.20 E-value=1.2e+02 Score=25.36 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=30.9
Q ss_pred CCCCCCCCCCcCCCCccchHHHHHHHHHcCCChHHHHHHhhccHHHHH
Q 022473 10 RPNPPSQVPESGDSGIFNERILLLVFESVGWDLHMLCLTASLDRKLRA 57 (296)
Q Consensus 10 ~~~~~~~~~~~~~~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~ 57 (296)
..++|+.+... ---|++||+..||..-+ +..+-.+.-.|+.++.
T Consensus 11 ~~kp~~~~~lt--l~DLP~ELl~~I~~~C~--~~~l~~l~~~~~~~r~ 54 (109)
T PF13013_consen 11 SPKPPNRQSLT--LLDLPWELLQLIFDYCN--DPILLALSRTCRAYRS 54 (109)
T ss_pred cCCCCCccccc--hhhChHHHHHHHHhhcC--cHHHHHHHHHHHHHHH
Confidence 44555555542 23399999999999999 7777777777775553
No 37
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.16 E-value=24 Score=25.21 Aligned_cols=12 Identities=42% Similarity=1.066 Sum_probs=10.1
Q ss_pred ccccCCCCCccc
Q 022473 190 ERVKCPYCGARV 201 (296)
Q Consensus 190 ~~~~CpyC~ar~ 201 (296)
..++||+||.|+
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 459999999984
No 38
>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=29.03 E-value=55 Score=22.48 Aligned_cols=30 Identities=33% Similarity=0.763 Sum_probs=15.9
Q ss_pred cCCCCCcc--cchhhhcccccccccccccccCCceeEEEeec
Q 022473 193 KCPYCGAR--VWSMTAARLVPKSAARRLGSHDGGLEYFVCIN 232 (296)
Q Consensus 193 ~CpyC~ar--~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~N 232 (296)
.||.|+.+ +|-+.|.+ .+-|.-..+|+|.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~r----------saDE~~T~fy~C~~ 33 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTR----------SADEPMTLFYVCCN 33 (39)
T ss_dssp --SSS-SSEEEEEEESSS----------SSSSSSEEEEEESS
T ss_pred CCcCCCCCeEEEEEeecc----------CCCCCCeEEEEeCC
Confidence 69999997 33322211 12334489999976
No 39
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.91 E-value=90 Score=26.07 Aligned_cols=97 Identities=19% Similarity=0.306 Sum_probs=57.6
Q ss_pred ccccccCCcccccccCCceeeecCCCCCCCCCCCCceeeeeeeccccchhhHHHHH----hhcccccccc--ccCCCCCc
Q 022473 126 RFSKTSGRSFLTKKCRGDLLYVSDPCEHPMGNKEDDLGIFRGVFRGFLKSTTRACL----IRRRVELEER--VKCPYCGA 199 (296)
Q Consensus 126 rfSRtsG~sfL~~rcR~D~LYVsDpCeH~~~ge~~d~glfRGVFk~F~~Srvr~~L----i~~~~~l~~~--~~CpyC~a 199 (296)
+|.-.-|+=+++++=-.+.+++|.-|.+..+ -..-.+++-..+..........+ ...++++.++ +.||=|+.
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~ 80 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEEE--ASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGN 80 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcchh--ccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCCC
Confidence 4566667677777766777999999999965 33334454444444333222112 2234444444 68999999
Q ss_pred c--cchhhhcccccccccccccccCCc-eeEEEee-cCce
Q 022473 200 R--VWSMTAARLVPKSAARRLGSHDGG-LEYFVCI-NGHL 235 (296)
Q Consensus 200 r--~Wsm~~A~~lp~sa~rrlG~~edg-veyyVC~-NGHv 235 (296)
+ .|=++|- .+-|.+ .+.|.|. =||.
T Consensus 81 ~ea~y~~~Qt-----------RsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 81 KEAYYWQLQT-----------RSADEPETRFYKCTRCGYR 109 (113)
T ss_pred ceeEEEeeeh-----------hccCCCceEEEEecccCCE
Confidence 6 5555443 233444 8889994 4553
No 40
>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=28.78 E-value=30 Score=23.42 Aligned_cols=12 Identities=42% Similarity=1.362 Sum_probs=8.8
Q ss_pred ccccCCCCCccc
Q 022473 190 ERVKCPYCGARV 201 (296)
Q Consensus 190 ~~~~CpyC~ar~ 201 (296)
..++||+||.|+
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 348999999984
No 41
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2VY1_A 2VY2_A.
Probab=28.28 E-value=21 Score=36.10 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=1.4
Q ss_pred CCCCCCceeeeecc
Q 022473 276 DDNHEHRTVIKCEP 289 (296)
Q Consensus 276 ~~~~~~~~~~~~~~ 289 (296)
+-|||||-++| ||
T Consensus 226 ERQREHPFIVT-EP 238 (386)
T PF01698_consen 226 ERQREHPFIVT-EP 238 (386)
T ss_dssp -------B-----T
T ss_pred cccccCCceec-cc
Confidence 88999999888 54
No 42
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=28.01 E-value=35 Score=31.77 Aligned_cols=31 Identities=32% Similarity=0.703 Sum_probs=15.1
Q ss_pred cccCCCCCcccchhhhccccccccccccccc----CCceeEEEeecCc
Q 022473 191 RVKCPYCGARVWSMTAARLVPKSAARRLGSH----DGGLEYFVCINGH 234 (296)
Q Consensus 191 ~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~----edgveyyVC~NGH 234 (296)
+..||||+.. ....|.++ +++++.+||.+=|
T Consensus 211 R~~Cp~Cg~~-------------~~~~l~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 211 RIKCPYCGNT-------------DHEKLEYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp TTS-TTT----------------SS-EEE--------SEEEEEETTTT
T ss_pred CCCCcCCCCC-------------CCcceeeEecCCCCcEEEEECCccc
Confidence 3679999973 11223333 3459999998755
No 43
>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=27.68 E-value=1.2e+02 Score=23.98 Aligned_cols=73 Identities=18% Similarity=0.400 Sum_probs=39.1
Q ss_pred eeecCCCCCCCCCCCCceeeeeeeccccchhhHHHH-Hhhcc---ccccccccCCCCCcc--cchhhhcccccccccccc
Q 022473 145 LYVSDPCEHPMGNKEDDLGIFRGVFRGFLKSTTRAC-LIRRR---VELEERVKCPYCGAR--VWSMTAARLVPKSAARRL 218 (296)
Q Consensus 145 LYVsDpCeH~~~ge~~d~glfRGVFk~F~~Srvr~~-Li~~~---~~l~~~~~CpyC~ar--~Wsm~~A~~lp~sa~rrl 218 (296)
.|+|.-|.+.......+-.+++=.++ ++..-.. +.... .+ ...+.||-|+.+ +|-++| .
T Consensus 16 ~~~C~~C~~~~~~~~~~~~v~~~~~~---~~~~~~~~~~~~~~~~~~-~~~~~Cp~Cg~~~a~f~~~Q-----------~ 80 (104)
T TIGR01384 16 VYVCPSCGYEKEKKPEDDYKVTEKVK---HKIKETIIIREEDSETLP-TTRVECPKCGHKEAYYWLLQ-----------T 80 (104)
T ss_pred eEECcCCCCccccccccccEEEEEec---cccccceeeccccccCCC-cccCCCCCCCCCeeEEEEec-----------c
Confidence 67899999885422122234543332 2211122 22111 12 235899999996 565544 2
Q ss_pred cccCCc-eeEEEeec
Q 022473 219 GSHDGG-LEYFVCIN 232 (296)
Q Consensus 219 G~~edg-veyyVC~N 232 (296)
.+-|++ -.+|+|.|
T Consensus 81 RsadE~~T~fy~C~~ 95 (104)
T TIGR01384 81 RRADEPETRFYKCTK 95 (104)
T ss_pred CCCCCCcEEEEEeCC
Confidence 233444 89999987
No 44
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=27.50 E-value=28 Score=24.96 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=7.7
Q ss_pred cCCCCCcccc
Q 022473 193 KCPYCGARVW 202 (296)
Q Consensus 193 ~CpyC~ar~W 202 (296)
.|||||...-
T Consensus 5 PCPFCG~~~~ 14 (61)
T PF14354_consen 5 PCPFCGSADV 14 (61)
T ss_pred CCCCCCCcce
Confidence 5999998643
No 45
>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=27.46 E-value=48 Score=21.96 Aligned_cols=15 Identities=33% Similarity=0.804 Sum_probs=11.9
Q ss_pred CCceeEEEeecCcee
Q 022473 222 DGGLEYFVCINGHLH 236 (296)
Q Consensus 222 edgveyyVC~NGHv~ 236 (296)
++.=.||+|.||...
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 566899999999875
No 46
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=26.30 E-value=63 Score=22.36 Aligned_cols=29 Identities=31% Similarity=0.698 Sum_probs=19.2
Q ss_pred cCCCCCcc--cchhhhcccccccccccccccCCc-eeEEEeec
Q 022473 193 KCPYCGAR--VWSMTAARLVPKSAARRLGSHDGG-LEYFVCIN 232 (296)
Q Consensus 193 ~CpyC~ar--~Wsm~~A~~lp~sa~rrlG~~edg-veyyVC~N 232 (296)
.||-|+.+ +|=.+| ..+-|++ .-+|+|+|
T Consensus 2 ~Cp~C~~~~a~~~q~Q-----------~RsaDE~mT~fy~C~~ 33 (40)
T smart00440 2 PCPKCGNREATFFQLQ-----------TRSADEPMTVFYVCTK 33 (40)
T ss_pred cCCCCCCCeEEEEEEc-----------ccCCCCCCeEEEEeCC
Confidence 69999985 443333 2234445 88999998
No 47
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.02 E-value=27 Score=32.68 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=26.6
Q ss_pred ccccccccccCCc--eeEEEeecCceeeeeeeeecCCCc
Q 022473 212 KSAARRLGSHDGG--LEYFVCINGHLHGSCWLVPLSSEE 248 (296)
Q Consensus 212 ~sa~rrlG~~edg--veyyVC~NGHv~G~ctl~PLs~se 248 (296)
|+-+..+|.-+-. |+-|-=..|-++|+..+....|.+
T Consensus 154 ~~d~~~~~~~~~s~~~~~~~~~~~~~~~~i~~~~~~de~ 192 (227)
T KOG3241|consen 154 RSDSSKVGDVFPSTSLEEYANKSGRVSGIIGHGSVPDEA 192 (227)
T ss_pred hcchhhhcccccchhHHHHHhhhcchhhhcccCCCCccc
Confidence 3444567766555 888888999999998887665544
No 48
>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=25.28 E-value=32 Score=24.71 Aligned_cols=8 Identities=50% Similarity=1.730 Sum_probs=7.0
Q ss_pred cCCCCCcc
Q 022473 193 KCPYCGAR 200 (296)
Q Consensus 193 ~CpyC~ar 200 (296)
.||||+.+
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 69999986
No 49
>KOG2110 consensus Uncharacterized conserved protein, contains WD40 repeats [Function unknown]
Probab=24.68 E-value=2.6e+02 Score=28.63 Aligned_cols=111 Identities=23% Similarity=0.300 Sum_probs=61.2
Q ss_pred ceeeeeeeccccch---hhHHHHHhhccccccccccCCCCCcccchhhhcccccccccccccccCCceeEEE-eecCcee
Q 022473 161 DLGIFRGVFRGFLK---STTRACLIRRRVELEERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGGLEYFV-CINGHLH 236 (296)
Q Consensus 161 d~glfRGVFk~F~~---Srvr~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edgveyyV-C~NGHv~ 236 (296)
.-+.+.=+.|.+-. ++|.+++... +++-. ..=|+++ +...+-|+.++..-+.+| +-+||+.
T Consensus 261 ~~~~~~~~sk~~~sylps~V~~~~~~~-R~FAt-~~l~~s~-------------~~~~~~l~~~~~~~~v~vas~dG~~y 325 (391)
T KOG2110|consen 261 GTSWFGKVSKAATSYLPSQVSSVLDQS-RKFAT-AKLPESG-------------RKNICSLSSIQKIPRVLVASYDGHLY 325 (391)
T ss_pred CCcccchhhhhhhhhcchhhhhhhhhc-cceeE-EEccCCC-------------ccceEEeeccCCCCEEEEEEcCCeEE
Confidence 45666667776654 7888886533 33221 2223332 223456777777744443 7788874
Q ss_pred ---------eeeeeeecCCCcccCCCCCCCCCCCCCCCCC-----CCCCccccCCCCCCceeeee
Q 022473 237 ---------GSCWLVPLSSEEDACDEDDDEDGEDGEDGGD-----DPDGAYDLDDNHEHRTVIKC 287 (296)
Q Consensus 237 ---------G~ctl~PLs~se~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~ 287 (296)
|-|+|+--....+..|.+ .+.+..++-+++ ..+..+.+||.+++|.+|-+
T Consensus 326 ~y~l~~~~gGec~lik~h~~~~~~~t~-~a~~~~~~~~~~~~~~~s~~~~~~ld~e~~~pp~~~~ 389 (391)
T KOG2110|consen 326 SYRLPPKEGGECALIKRHFLDGSIDTS-AASGKTDDLGAVGGAVLSDEAALNLDDEREFPPMILT 389 (391)
T ss_pred EEEcCCCCCceeEEEEeeccCCccccc-cccccCCcccccccceeccccccCCCCccCCCCeeee
Confidence 778887633333333222 222222222221 22347889999999999876
No 50
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=24.18 E-value=38 Score=28.19 Aligned_cols=24 Identities=21% Similarity=0.693 Sum_probs=18.0
Q ss_pred chhhHHHHHhhccccccccccCCCCCcc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGAR 200 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~ar 200 (296)
-|.+|++++|.++++ -.|+||+.+
T Consensus 22 Lrk~vKkiei~Qhak----y~CsfCGK~ 45 (92)
T KOG0402|consen 22 LRKMVKKIEIQQHAK----YTCSFCGKK 45 (92)
T ss_pred HHHHHHHHHHHHhhh----hhhhhcchh
Confidence 356788888876665 679999974
No 51
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.17 E-value=46 Score=37.85 Aligned_cols=44 Identities=7% Similarity=-0.074 Sum_probs=28.9
Q ss_pred ccHHHHHHHHHHhHHHHHHhhhchhHHHhhcC----CCCCCCCCchhH
Q 022473 51 LDRKLRAIAERLLWRKLCECRAPRMIETLANG----APNGRINGGWHA 94 (296)
Q Consensus 51 VCrkfr~larrvLWRe~C~~raP~mv~dL~~~----~~~~~i~GgW~A 94 (296)
.|..|.-+.-.+|=...-..-+|.-|.--+.. ++-+.+.|||.-
T Consensus 1036 TcPPfSLf~pH~CPEpk~~~~ap~N~t~Rl~~rel~~~y~gV~g~~~d 1083 (1516)
T KOG1832|consen 1036 TCPPFSLFHPHVCPEPKRLLEAPLNMTGRLGTRELQSFYSGVHGNRRD 1083 (1516)
T ss_pred cCCChhhcCCccCCChHHHhhcchhhhhcccchhhcCcccccccCccc
Confidence 57777766666666666677788766544432 234778888854
No 52
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=23.44 E-value=62 Score=31.87 Aligned_cols=10 Identities=40% Similarity=1.162 Sum_probs=8.0
Q ss_pred cccCCCCCcc
Q 022473 191 RVKCPYCGAR 200 (296)
Q Consensus 191 ~~~CpyC~ar 200 (296)
...||-|+-.
T Consensus 209 ~~PCPKCg~e 218 (314)
T PF06524_consen 209 PIPCPKCGYE 218 (314)
T ss_pred CCCCCCCCCc
Confidence 3789999975
No 53
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=22.41 E-value=29 Score=29.38 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=0.0
Q ss_pred CCCcccCCCC
Q 022473 245 SSEEDACDED 254 (296)
Q Consensus 245 s~se~~~~~~ 254 (296)
++|+++.++|
T Consensus 14 ~dsdEdeeee 23 (101)
T PF09026_consen 14 SDSDEDEEEE 23 (101)
T ss_dssp ----------
T ss_pred cccccchhhh
Confidence 3444443333
No 54
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=22.39 E-value=48 Score=28.86 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=11.7
Q ss_pred eeEE-EeecC--ceeeeeeeeecC
Q 022473 225 LEYF-VCING--HLHGSCWLVPLS 245 (296)
Q Consensus 225 veyy-VC~NG--Hv~G~ctl~PLs 245 (296)
|... +|-+| ||+|--....-.
T Consensus 88 Vtf~L~~GsGPVhisG~~~~~~~~ 111 (149)
T PF03066_consen 88 VTFRLKCGSGPVHISGQHLVAMEE 111 (149)
T ss_dssp EEEEEEESSS-EEEEEEEEEE---
T ss_pred EEEEEEecCCCEEeeCcccccccc
Confidence 6665 57777 777766544433
No 55
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.28 E-value=41 Score=25.02 Aligned_cols=9 Identities=56% Similarity=1.800 Sum_probs=7.4
Q ss_pred ccCCCCCcc
Q 022473 192 VKCPYCGAR 200 (296)
Q Consensus 192 ~~CpyC~ar 200 (296)
..|||||..
T Consensus 1 i~CPyCge~ 9 (52)
T PF14255_consen 1 IQCPYCGEP 9 (52)
T ss_pred CCCCCCCCe
Confidence 369999996
No 56
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.64 E-value=33 Score=21.60 Aligned_cols=11 Identities=45% Similarity=1.123 Sum_probs=7.6
Q ss_pred cccCCCCCccc
Q 022473 191 RVKCPYCGARV 201 (296)
Q Consensus 191 ~~~CpyC~ar~ 201 (296)
...||+||+++
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45788888764
No 57
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.07 E-value=40 Score=26.72 Aligned_cols=20 Identities=20% Similarity=0.647 Sum_probs=4.8
Q ss_pred HHhhccccccccccCCCCCc
Q 022473 180 CLIRRRVELEERVKCPYCGA 199 (296)
Q Consensus 180 ~Li~~~~~l~~~~~CpyC~a 199 (296)
-...+..+|...-.||||+.
T Consensus 11 ~~kk~~~~l~~~F~CPfC~~ 30 (81)
T PF05129_consen 11 PKKKKKPKLPKVFDCPFCNH 30 (81)
T ss_dssp ---------SS----TTT--
T ss_pred CccCcCCCCCceEcCCcCCC
Confidence 34467788999999999994
No 58
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=20.97 E-value=63 Score=39.09 Aligned_cols=34 Identities=26% Similarity=0.602 Sum_probs=15.5
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCccccCCCC
Q 022473 246 SEEDACDEDDDEDGEDGEDGGDDPDGAYDLDDNH 279 (296)
Q Consensus 246 ~se~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 (296)
|.||+.++||+++++|++.+.......+-.||..
T Consensus 154 d~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~de~ 187 (2849)
T PTZ00415 154 DDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDED 187 (2849)
T ss_pred CCccccccccccccccccccccccccccCCCchh
Confidence 3344444444444444444444444455555543
No 59
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=20.38 E-value=64 Score=38.14 Aligned_cols=36 Identities=11% Similarity=0.246 Sum_probs=25.1
Q ss_pred CcCcccCCCCCCCCCCcCCC------------CccchHHHHHHHHHcC
Q 022473 4 NANKRLRPNPPSQVPESGDS------------GIFNERILLLVFESVG 39 (296)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~------------g~LsEdVLllVF~~Ln 39 (296)
|+.-|||-.+|.--|+|-+| ..+-||+|.+++..-|
T Consensus 1282 ~HDCkLKRTSPTAYCDCWEKssCkCKaLIAGnel~Re~LLseLLk~T~ 1329 (3015)
T KOG0943|consen 1282 GHDCKLKRTSPTAYCDCWEKSSCKCKALIAGNELAREDLLSELLKATN 1329 (3015)
T ss_pred CCccceeccCCcceeehhhcccccchhhhcchHHHHHHHHHHHHhhcc
Confidence 56678888888888887665 3456777777766544
Done!