Query 043421
Match_columns 326
No_of_seqs 60 out of 62
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 04:53:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12937 F-box-like: F-box-lik 98.9 1.1E-09 2.4E-14 76.0 2.9 45 7-53 2-47 (47)
2 KOG2997 F-box protein FBX9 [Ge 98.9 1.4E-09 3.1E-14 105.9 3.6 74 6-79 107-185 (366)
3 KOG1571 Predicted E3 ubiquitin 98.6 1E-08 2.2E-13 100.2 0.9 204 11-325 37-250 (355)
4 PF00646 F-box: F-box domain; 98.4 2.6E-07 5.6E-12 63.4 3.3 44 6-51 3-47 (48)
5 smart00256 FBOX A Receptor for 98.4 3.9E-07 8.5E-12 59.6 3.3 39 9-49 1-40 (41)
6 KOG2120 SCF ubiquitin ligase, 91.3 0.15 3.2E-06 51.3 2.7 42 6-49 98-140 (419)
7 PLN03215 ascorbic acid mannose 82.4 1.3 2.8E-05 44.4 3.5 38 6-44 4-41 (373)
8 PF11672 DUF3268: Protein of u 80.5 1 2.2E-05 38.0 1.7 38 272-319 3-40 (102)
9 KOG3926 F-box proteins [Amino 74.0 9 0.00019 38.2 6.3 70 6-78 202-274 (332)
10 PF11781 RRN7: RNA polymerase 70.8 3.2 7E-05 28.9 1.8 28 270-316 7-35 (36)
11 KOG4408 Putative Mg2+ and Co2+ 70.6 0.75 1.6E-05 46.4 -1.8 48 6-55 8-56 (386)
12 PF06881 Elongin_A: RNA polyme 64.8 11 0.00024 30.9 4.2 66 7-79 5-70 (109)
13 TIGR01562 FdhE formate dehydro 60.3 6.3 0.00014 38.7 2.3 14 301-314 246-259 (305)
14 KOG4341 F-box protein containi 58.9 7.8 0.00017 40.5 2.7 84 5-90 71-169 (483)
15 COG1594 RPB9 DNA-directed RNA 58.7 17 0.00036 30.8 4.3 99 207-315 3-109 (113)
16 KOG0281 Beta-TrCP (transducin 55.6 13 0.00029 38.3 3.7 45 6-52 75-124 (499)
17 TIGR03655 anti_R_Lar restricti 55.0 7.7 0.00017 28.3 1.5 35 272-317 2-36 (53)
18 TIGR01384 TFS_arch transcripti 53.9 19 0.0004 28.9 3.7 87 209-312 3-95 (104)
19 PF04216 FdhE: Protein involve 47.8 8.9 0.00019 36.1 1.1 41 272-314 198-245 (290)
20 KOG0274 Cdc4 and related F-box 41.5 12 0.00027 38.9 1.0 50 5-56 107-157 (537)
21 PF04606 Ogr_Delta: Ogr/Delta- 37.1 22 0.00047 25.5 1.5 34 273-316 1-37 (47)
22 PF12660 zf-TFIIIC: Putative z 35.6 14 0.00029 30.5 0.2 41 266-325 9-51 (99)
23 PRK03564 formate dehydrogenase 32.8 26 0.00055 34.7 1.7 41 272-314 213-259 (309)
24 PF14354 Lar_restr_allev: Rest 32.0 21 0.00045 25.9 0.7 11 272-282 4-14 (61)
25 PRK09678 DNA-binding transcrip 29.7 24 0.00052 28.2 0.7 33 272-314 2-34 (72)
26 KOG2691 RNA polymerase II subu 24.8 1.5E+02 0.0033 25.9 4.8 96 207-312 5-106 (113)
27 PF03811 Zn_Tnp_IS1: InsA N-te 24.8 34 0.00074 24.0 0.7 12 269-280 3-14 (36)
28 PF03478 DUF295: Protein of un 23.6 97 0.0021 22.3 2.9 24 220-246 29-52 (54)
29 PHA03399 pif3 per os infectivi 21.3 44 0.00095 31.4 0.9 17 297-315 131-147 (200)
30 PRK09710 lar restriction allev 21.0 52 0.0011 26.1 1.2 11 270-280 5-15 (64)
31 PF13408 Zn_ribbon_recom: Reco 20.5 67 0.0014 22.5 1.5 36 270-320 4-40 (58)
No 1
>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=98.88 E-value=1.1e-09 Score=75.98 Aligned_cols=45 Identities=36% Similarity=0.794 Sum_probs=39.1
Q ss_pred ccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHhh
Q 043421 7 SKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCSK 53 (326)
Q Consensus 7 ~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~~ 53 (326)
..||+||+.+||+.| ||++++++++|||+|+.++.. .+||..|.+
T Consensus 2 ~~LP~Eil~~If~~L--~~~dl~~~~~vcr~w~~~~~~~~lW~~~~~r 47 (47)
T PF12937_consen 2 SSLPDEILLEIFSYL--DPRDLLRLSLVCRRWRRIANDNSLWRRLCLR 47 (47)
T ss_dssp CCS-HHHHHHHHTTS---HHHHHHHTTSSHHHHHHHTCCCHHHHHC--
T ss_pred hHhHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHCChhhhhhhccC
Confidence 579999999999999 599999999999999999976 999999864
No 2
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=98.86 E-value=1.4e-09 Score=105.89 Aligned_cols=74 Identities=24% Similarity=0.363 Sum_probs=64.5
Q ss_pred cccccHHHHHHHHHhcC---CChHHHHHHhhchHhHHHHHHH-HhhhHHHhhhhhHHHHhhcCCC-CCCCCCchhhhhh
Q 043421 6 FSKLSDDVVLNIFFKLE---DDPRNWARLACVCVKFSSLVRN-ICWKTKCSKSIPAVVADLISPN-SGVPPGGWSSLHK 79 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn---~dPr~LaraACVCRkfr~lar~-vLWRe~C~~raP~Mv~dL~~~~-s~~~~GsW~AL~K 79 (326)
++.||||||+.||+.+= -|-|.|.++|||||.|...+|+ .+||.+|++.|++|+-.|-..- .+.+.++|+.|--
T Consensus 107 ~~~LPdEvLm~I~~~vv~~~~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~s~~~ln~~~~~sky~~SWR~Mfl 185 (366)
T KOG2997|consen 107 ISVLPDEVLMRIFRWVVSSLLDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQRSCIKLNPKILQSKYYTSWREMFL 185 (366)
T ss_pred hhhCCHHHHHHHHHHHHhhhcchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHHhhhccchhhhhhHHHhHHHHHHh
Confidence 38999999999999985 1339999999999999999999 9999999999999888877532 4889999997753
No 3
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.60 E-value=1e-08 Score=100.25 Aligned_cols=204 Identities=18% Similarity=0.213 Sum_probs=150.0
Q ss_pred HHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHHHhhhHHHhhhhhHHHHhhcCC-CCCCCCCchhhhhhhhcccCCccc
Q 043421 11 DDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRNICWKTKCSKSIPAVVADLISP-NSGVPPGGWSSLHKLSVCCPGLLH 89 (326)
Q Consensus 11 EDVLllIF~rLn~dPr~LaraACVCRkfr~lar~vLWRe~C~~raP~Mv~dL~~~-~s~~~~GsW~AL~KL~vcCpG~~~ 89 (326)
+.++...+.+..|+-.-...++=.-.++...++...|+..|+.+.|+|+..+..- +..+.++.|...+++++.|+|--
T Consensus 37 ~k~~~~~d~~~~~~~~~~~~I~~l~~~~~~~~~~~~~~~~~v~~v~gvv~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~- 115 (355)
T KOG1571|consen 37 EKVLVLVDLKSSWDIAPEKKIPYLVIRGCAIARKETLRSLCVSNVPGVVQALTLEEPKGRRDGGGHWNANSKIFHEGGN- 115 (355)
T ss_pred cceecchhhhhhhhhccccchHHHHHhhcccccccchHHhhcccCCceEEEeeeccceeeeccceeeccceeeccCCCc-
Confidence 3444556666666655555666666777788888999999999999999988753 24666789999999999999873
Q ss_pred cCccccccccccccccCCCCCCCCCCcCCCCCCCCCcccccccCCCCCcCCCcccccccccccccccCCCCCCCCCCCCC
Q 043421 90 AGVLLENSDFGLERELGPDSDYQSCSTSAIQPTSTTTTAEACSSNLNSVTDCSWSLFDDLYYDTVYDKSESHDDDGGGDG 169 (326)
Q Consensus 90 agvl~e~~dfgle~~lgpd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wsl~ddly~dt~y~~~~~~~~~~~~~~ 169 (326)
...| ...+|+
T Consensus 116 ------~~~~----------~l~~q~------------------------------------------------------ 125 (355)
T KOG1571|consen 116 ------EVPF----------FLRSQT------------------------------------------------------ 125 (355)
T ss_pred ------ccce----------eeccCC------------------------------------------------------
Confidence 3333 000000
Q ss_pred cccccccccccccccccchhhhhhccccccccccccceeehhccccccccccCCceEEeeCCCCccccc--ccccceeee
Q 043421 170 SLVVEDVDKCEVKVGGESAKKRKICRSFRSHLASGVWNLCREQGNKLLASRFRGDCLYICDWPGCLHTE--EKRNYMLFR 247 (326)
Q Consensus 170 ~~~~~G~~~~~~~~~~~~~k~r~~~~~~~~Hlasgsw~~SReqG~klLa~rfR~D~LYvcDwPgC~H~e--e~r~y~lFR 247 (326)
+..+|+ + ++|+++|.-+|+-+.++|.+|-+| ||+|.. -....++++
T Consensus 126 -----~~~~~~--~-----------------------~~s~~~~~~~l~l~~~~d~f~~s~--p~s~~~~~~~~~sg~~~ 173 (355)
T KOG1571|consen 126 -----TGFACE--V-----------------------RVSKTLGRLFLPLNVVYDLFEPSD--PCSLVDVGGGYHSGVRR 173 (355)
T ss_pred -----cceeee--e-----------------------eeecceeeeeecceeeeccccccC--cceeeecccccccceee
Confidence 111222 2 889999999999999999999999 999996 556779999
Q ss_pred eccccchhhhhHHHHhc-CCCCCCccccCCCCccccch-hhhhhh-----hhhhhcccCCCCceEEEEEeecCceeeeee
Q 043421 248 GIFKNFKRSRVWRTIND-GNRSKIDVNCAFCNCKETWD-LHSAFC-----LRRVFGYHDDGEPVVRAYVCENGHVSGAWT 320 (326)
Q Consensus 248 GVFk~F~rSrvrr~l~d-~~r~~~~~~C~fC~~~~~Wd-l~sAfc-----lrr~~gyhddGEpvvrayVCeNGHv~Gawt 320 (326)
|.|+.++++.- +-. .++....+.|.||+-+ +|+ |..++- +.++..=..| ..-++|.|+|++|.++
T Consensus 174 ~~~~~~~~~l~---~~~~~t~l~e~v~d~~~~~r-~~~~~~g~~~v~~s~~d~LIsr~g~----~s~~~kv~~~~~~~~~ 245 (355)
T KOG1571|consen 174 GGFRETERVLP---LGTRLTALGELVRDGYCGVR-VQPPMQGPLYVTKSAADRLISREGD----LSFFVKVNGMVFGTLG 245 (355)
T ss_pred ecccceEEeec---cccceeeeehheecCCCceE-ecCCccCcceeeccchhhHHHhhcc----ceeeeeecceeeeeee
Confidence 99999998765 322 5566777999999997 999 543322 3333333233 6789999999999999
Q ss_pred cccCC
Q 043421 321 DLPLY 325 (326)
Q Consensus 321 ~~PLy 325 (326)
.++|+
T Consensus 246 ~ills 250 (355)
T KOG1571|consen 246 VILLS 250 (355)
T ss_pred EEeeh
Confidence 99886
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=98.40 E-value=2.6e-07 Score=63.41 Aligned_cols=44 Identities=32% Similarity=0.576 Sum_probs=38.4
Q ss_pred cccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHH
Q 043421 6 FSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKC 51 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C 51 (326)
+..||+|++.+||.+|+ +.+++++++|||+|+.++++ .+|+..|
T Consensus 3 ~~~LP~~il~~Il~~l~--~~~~~~l~~vsk~~~~~~~~~~~~~~~~ 47 (48)
T PF00646_consen 3 LSDLPDEILQEILSYLD--PKDLLRLSLVSKRWRSLVDSPRLWKKII 47 (48)
T ss_dssp HHHS-HHHHHHHHHTS---HHHHHHHCTT-HHHHHHHTTHHHHHHHH
T ss_pred HHHCCHHHHHHHHHHCc--HHHHHHHHHHhhHHHHHHcCCCccHHHh
Confidence 56799999999999997 99999999999999999998 8998876
No 5
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=98.36 E-value=3.9e-07 Score=59.65 Aligned_cols=39 Identities=31% Similarity=0.552 Sum_probs=36.5
Q ss_pred ccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhH
Q 043421 9 LSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKT 49 (326)
Q Consensus 9 LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe 49 (326)
||+|++.+||.+|+ |.+++++++|||+|+.+++. .+|++
T Consensus 1 lP~~ll~~I~~~l~--~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 1 LPDEILEEILSKLP--PKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CCHHHHHHHHHcCC--HHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 79999999999996 99999999999999999988 88875
No 6
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=91.28 E-value=0.15 Score=51.34 Aligned_cols=42 Identities=29% Similarity=0.621 Sum_probs=38.5
Q ss_pred cccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhH
Q 043421 6 FSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKT 49 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe 49 (326)
+..|||||++.||+-|- -.+|=+++-||+||--+++. .+|-.
T Consensus 98 ~~slpDEill~IFs~L~--kk~LL~~~~VC~Rfyr~~~de~lW~~ 140 (419)
T KOG2120|consen 98 WDSLPDEILLGIFSCLC--KKELLKVSGVCKRFYRLASDESLWQT 140 (419)
T ss_pred cccCCHHHHHHHHHhcc--HHHHHHHHHHHHHHhhccccccceee
Confidence 56899999999999997 78999999999999999998 89964
No 7
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=82.40 E-value=1.3 Score=44.40 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=33.0
Q ss_pred cccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH
Q 043421 6 FSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN 44 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~ 44 (326)
-+.||+|+|.+|..+|. ..-++.|...|||-||+.+..
T Consensus 4 Ws~Lp~dll~~i~~~l~-~~~d~~~~~~vC~sWr~a~~~ 41 (373)
T PLN03215 4 WSTLPEELLHMIAGRLF-SNVELKRFRSICRSWRSSVSG 41 (373)
T ss_pred hhhCCHHHHHHHHhhCC-cHHHHHHHHhhhhhHHHhccc
Confidence 46799999999999995 466999999999999976653
No 8
>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=80.51 E-value=1 Score=38.03 Aligned_cols=38 Identities=24% Similarity=0.667 Sum_probs=26.3
Q ss_pred cccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeecCceeeee
Q 043421 272 VNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCENGHVSGAW 319 (326)
Q Consensus 272 ~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeNGHv~Gaw 319 (326)
+.||||+.+-.. .++ ...+|+..|..|.+ |+|.+ .+||
T Consensus 3 ~~CpYCg~~~~l--~~~---~~iYg~~~~~~~~~--y~C~~---C~Ay 40 (102)
T PF11672_consen 3 IICPYCGGPAEL--VDG---SEIYGHRYDDGPYL--YVCTP---CDAY 40 (102)
T ss_pred cccCCCCCeeEE--ccc---chhcCccCCCCcee--EECCC---CCce
Confidence 689999997332 332 46788765555755 99998 5655
No 9
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=74.02 E-value=9 Score=38.19 Aligned_cols=70 Identities=26% Similarity=0.450 Sum_probs=53.3
Q ss_pred cccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHhhhhh--HHHHhhcCCCCCCCCCchhhhh
Q 043421 6 FSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCSKSIP--AVVADLISPNSGVPPGGWSSLH 78 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~~raP--~Mv~dL~~~~s~~~~GsW~AL~ 78 (326)
|.-||++++.+|..+|. |=++|-.+|=|=.-+..++.. .+||++|..-+. .+-..|..+-.+. -.|+.|.
T Consensus 202 l~dLP~e~vl~Il~rls-Dh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~erQi~~~l~l~k~~q--~dWkqmy 274 (332)
T KOG3926|consen 202 LHDLPLECVLNILLRLS-DHRDLESLAQAWETLAKLSEERRIWKKLCQFHFNERQIHTILILSKKGQ--KDWKQMY 274 (332)
T ss_pred cccchHHHHHHHHHHcc-CcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhhhccccc--hhHHHHH
Confidence 78899999999999998 778888888887777777766 999999998887 2223444322333 4598875
No 10
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=70.77 E-value=3.2 Score=28.88 Aligned_cols=28 Identities=39% Similarity=0.871 Sum_probs=21.6
Q ss_pred CccccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEe-ecCcee
Q 043421 270 IDVNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVC-ENGHVS 316 (326)
Q Consensus 270 ~~~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVC-eNGHv~ 316 (326)
+...|+-|+.+ +.+-+|| .|+| ..||+.
T Consensus 7 ~~~~C~~C~~~--------------~~~~~dG-----~~yC~~cG~~~ 35 (36)
T PF11781_consen 7 PNEPCPVCGSR--------------WFYSDDG-----FYYCDRCGHQS 35 (36)
T ss_pred CCCcCCCCCCe--------------EeEccCC-----EEEhhhCceEc
Confidence 34569998884 4467898 8999 999984
No 11
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=70.57 E-value=0.75 Score=46.39 Aligned_cols=48 Identities=21% Similarity=0.278 Sum_probs=44.1
Q ss_pred cccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHhhhh
Q 043421 6 FSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCSKSI 55 (326)
Q Consensus 6 ~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~~ra 55 (326)
+..++.++|..|..++- ++++++-|||.+++..+.++ -+|...|.+-+
T Consensus 8 le~~~~~~l~~vls~~~--~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l 56 (386)
T KOG4408|consen 8 LEWLPRDPLHLVLSFLL--YRDLINCAYVSRRLKELGSHLPLWNRPCKKYL 56 (386)
T ss_pred hhhcccccceeeecccc--hhhhhcceeechHHhhhhhccccccccccccc
Confidence 67789999999999996 99999999999999999999 99999996654
No 12
>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=64.83 E-value=11 Score=30.86 Aligned_cols=66 Identities=15% Similarity=0.231 Sum_probs=48.8
Q ss_pred ccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHHHhhhHHHhhhhhHHHHhhcCCCCCCCCCchhhhhh
Q 043421 7 SKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRNICWKTKCSKSIPAVVADLISPNSGVPPGGWSSLHK 79 (326)
Q Consensus 7 ~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~vLWRe~C~~raP~Mv~dL~~~~s~~~~GsW~AL~K 79 (326)
-.+|-++|-.|+.+++ |..|.++-=-|..+... -..||+.+|.+-||.-+.+-. -.-+.+|+.|+-
T Consensus 5 G~~py~ll~piL~~~~--~~QL~~iE~~np~l~~~-tdeLW~~~i~rdFp~~~~~~~----~~~~~~Wr~~Y~ 70 (109)
T PF06881_consen 5 GDVPYHLLRPILEKCS--PEQLRRIEDNNPHLIED-TDELWKKLIKRDFPEESKRQK----PKEPESWRELYE 70 (109)
T ss_pred CCCCHHHHHHHHccCC--HHHHHHHHHhCCCcchh-hHHHHHHHHHhHCcChhhccc----ccccchHHHHHH
Confidence 3578899999999995 99999999988665533 349999999999996222222 122348998864
No 13
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=60.26 E-value=6.3 Score=38.67 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=11.5
Q ss_pred CCceEEEEEeecCc
Q 043421 301 GEPVVRAYVCENGH 314 (326)
Q Consensus 301 GEpvvrayVCeNGH 314 (326)
+|+-+|++||++=|
T Consensus 246 ~~~~~r~e~C~~C~ 259 (305)
T TIGR01562 246 EKAVLKAETCDSCQ 259 (305)
T ss_pred CCcceEEeeccccc
Confidence 67899999998644
No 14
>KOG4341 consensus F-box protein containing LRR [General function prediction only]
Probab=58.86 E-value=7.8 Score=40.46 Aligned_cols=84 Identities=27% Similarity=0.493 Sum_probs=66.7
Q ss_pred ccccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHhhhhh-----HHHHhhcCC---------CCCC
Q 043421 5 LFSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCSKSIP-----AVVADLISP---------NSGV 69 (326)
Q Consensus 5 ~~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~~raP-----~Mv~dL~~~---------~s~~ 69 (326)
.-+.||.|++..||+.| |-..++|+|=+|+-|.-+|-. .+|-.-=+..+| ++|++...- ..+.
T Consensus 71 ~~~~LPpEl~lkvFS~L--Dtksl~r~a~~c~~~n~~AlD~~~~q~idL~t~~rDv~g~VV~~~~~Rcgg~lk~LSlrG~ 148 (483)
T KOG4341|consen 71 ISRSLPPELLLKVFSML--DTKSLCRAAQCCTMWNKLALDGSCWQHIDLFTFQRDVDGGVVENMISRCGGFLKELSLRGC 148 (483)
T ss_pred ccccCCHHHHHHHHHHH--hHHHHHHHHHHHHHhhhhhhccccceeeehhcchhcCCCcceehHhhhhcccccccccccc
Confidence 35789999999999999 599999999999999988888 999888777777 455554431 1455
Q ss_pred CCCchhhhhhhhcccCCcccc
Q 043421 70 PPGGWSSLHKLSVCCPGLLHA 90 (326)
Q Consensus 70 ~~GsW~AL~KL~vcCpG~~~a 90 (326)
.+-+-++|.-+..-||-..|=
T Consensus 149 r~v~~sslrt~~~~CpnIehL 169 (483)
T KOG4341|consen 149 RAVGDSSLRTFASNCPNIEHL 169 (483)
T ss_pred ccCCcchhhHHhhhCCchhhh
Confidence 666678888888888877664
No 15
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=58.69 E-value=17 Score=30.79 Aligned_cols=99 Identities=23% Similarity=0.384 Sum_probs=65.0
Q ss_pred eeehhccccccccccCCceEEeeCCCCcccccccccceeeeeccccchhhh-hHHHHh--c--CCCCCC--ccccCCCCc
Q 043421 207 NLCREQGNKLLASRFRGDCLYICDWPGCLHTEEKRNYMLFRGIFKNFKRSR-VWRTIN--D--GNRSKI--DVNCAFCNC 279 (326)
Q Consensus 207 ~~SReqG~klLa~rfR~D~LYvcDwPgC~H~ee~r~y~lFRGVFk~F~rSr-vrr~l~--d--~~r~~~--~~~C~fC~~ 279 (326)
.|+-+-|+-|++++=-.|.+++|. -|.+.++...-.+++-..+...... .--..+ + +....+ .+.||=|+-
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~--kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~ 80 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCR--KCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGN 80 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECC--CCCcchhccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCCC
Confidence 577888999999887778899999 9999988887666665555444332 212211 2 333333 478999999
Q ss_pred cccchhhhhhhhhhhhcccCCCCceEEEEEe-ecCce
Q 043421 280 KETWDLHSAFCLRRVFGYHDDGEPVVRAYVC-ENGHV 315 (326)
Q Consensus 280 ~~~Wdl~sAfclrr~~gyhddGEpvvrayVC-eNGHv 315 (326)
+|++=-+ ++-+ . .| ||..+.|.| .=||+
T Consensus 81 ~ea~y~~----~QtR--s-aD-Ep~T~Fy~C~~Cg~~ 109 (113)
T COG1594 81 KEAYYWQ----LQTR--S-AD-EPETRFYKCTRCGYR 109 (113)
T ss_pred ceeEEEe----eehh--c-cC-CCceEEEEecccCCE
Confidence 8765221 1111 1 34 899999999 44664
No 16
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=55.60 E-value=13 Score=38.35 Aligned_cols=45 Identities=20% Similarity=0.429 Sum_probs=38.7
Q ss_pred ccccc----HHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHh
Q 043421 6 FSKLS----DDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCS 52 (326)
Q Consensus 6 ~~~Ls----EDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~ 52 (326)
.+.|| |+|..+||+.|+ -..||..--||++|+-+..+ -+||.+-.
T Consensus 75 i~~lP~~gl~hi~e~ilsyld--~~sLc~celv~k~W~r~l~dg~~WKkLie 124 (499)
T KOG0281|consen 75 ITALPEQGLDHIAENILSYLD--ALSLCACELVCKEWKRVLSDGMLWKKLIE 124 (499)
T ss_pred HHhcccccHHHHHHHHHHhcc--hhhhhHHHHHHHHHHHHhccchHHHHHHH
Confidence 46788 999999999996 88999999999999977777 88887644
No 17
>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=55.03 E-value=7.7 Score=28.28 Aligned_cols=35 Identities=31% Similarity=0.600 Sum_probs=19.3
Q ss_pred cccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeecCceee
Q 043421 272 VNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCENGHVSG 317 (326)
Q Consensus 272 ~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeNGHv~G 317 (326)
..||||+.+. ..+|+.+.- -| ...+|.|.+=...|
T Consensus 2 kPCPfCGg~~-------~~~~~~~~~-~~---~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGAD-------VYLRRGFDP-LD---LSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcc-------eeeEeccCC-CC---CEEEEECCCCCCCc
Confidence 3699999972 223333321 22 25667898644443
No 18
>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=53.92 E-value=19 Score=28.93 Aligned_cols=87 Identities=24% Similarity=0.426 Sum_probs=49.6
Q ss_pred ehhccccccccccCCceEEeeCCCCcccccccc--cceeeeeccccchhhhhHHH-Hh-c--CCCCCCccccCCCCcccc
Q 043421 209 CREQGNKLLASRFRGDCLYICDWPGCLHTEEKR--NYMLFRGIFKNFKRSRVWRT-IN-D--GNRSKIDVNCAFCNCKET 282 (326)
Q Consensus 209 SReqG~klLa~rfR~D~LYvcDwPgC~H~ee~r--~y~lFRGVFk~F~rSrvrr~-l~-d--~~r~~~~~~C~fC~~~~~ 282 (326)
...-|+-|... ++ .|+|. -|.+.+++. +.++++=.++. +..-.. +. + ....++++.||-|+-+++
T Consensus 3 C~~Cg~~l~~~---~~-~~~C~--~C~~~~~~~~~~~~v~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a 73 (104)
T TIGR01384 3 CPKCGSLMTPK---NG-VYVCP--SCGYEKEKKPEDDYKVTEKVKH---KIKETIIIREEDSETLPTTRVECPKCGHKEA 73 (104)
T ss_pred CcccCcccccC---CC-eEECc--CCCCccccccccccEEEEEecc---ccccceeeccccccCCCcccCCCCCCCCCee
Confidence 34446655442 34 57898 999987653 34566643332 211111 11 1 123456899999999875
Q ss_pred chhhhhhhhhhhhcccCCCCceEEEEEeec
Q 043421 283 WDLHSAFCLRRVFGYHDDGEPVVRAYVCEN 312 (326)
Q Consensus 283 Wdl~sAfclrr~~gyhddGEpvvrayVCeN 312 (326)
.=+.. . . |. .| ||.-..|+|.|
T Consensus 74 ~f~~~-Q-~-Rs----ad-E~~T~fy~C~~ 95 (104)
T TIGR01384 74 YYWLL-Q-T-RR----AD-EPETRFYKCTK 95 (104)
T ss_pred EEEEe-c-c-CC----CC-CCcEEEEEeCC
Confidence 32211 1 1 22 23 78999999987
No 19
>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=47.80 E-value=8.9 Score=36.14 Aligned_cols=41 Identities=29% Similarity=0.737 Sum_probs=17.7
Q ss_pred cccCCCCccccchhhhhhhh------hhhhccc-CCCCceEEEEEeecCc
Q 043421 272 VNCAFCNCKETWDLHSAFCL------RRVFGYH-DDGEPVVRAYVCENGH 314 (326)
Q Consensus 272 ~~C~fC~~~~~Wdl~sAfcl------rr~~gyh-ddGEpvvrayVCeNGH 314 (326)
+.|.+|+. .|.+.=..|. ...+.|. ++|||.+|++||++=|
T Consensus 198 L~Cs~C~t--~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 198 LHCSLCGT--EWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEETTT----EEE--TTS-TTT---SS-EEE--------SEEEEEETTTT
T ss_pred EEcCCCCC--eeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCccc
Confidence 45666665 4666544442 2333444 8999999999998743
No 20
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=41.45 E-value=12 Score=38.93 Aligned_cols=50 Identities=24% Similarity=0.479 Sum_probs=42.5
Q ss_pred ccccccHHHHHHHHHhcCCChHHHHHHhhchHhHHHHHHH-HhhhHHHhhhhh
Q 043421 5 LFSKLSDDVVLNIFFKLEDDPRNWARLACVCVKFSSLVRN-ICWKTKCSKSIP 56 (326)
Q Consensus 5 ~~~~LsEDVLllIF~rLn~dPr~LaraACVCRkfr~lar~-vLWRe~C~~raP 56 (326)
+++.||-++...||..|. ++.+..++-||+.|+.++.. ..|.+.|-.-..
T Consensus 107 fi~~lp~el~~~il~~Ld--~~~l~~~~~v~~~w~~~~~~~~~~~~~~~~~~~ 157 (537)
T KOG0274|consen 107 FLSLLPSELSLHILSFLD--GRDLLAVRQVCRNWNKLLDDDKVWWRMCRELIG 157 (537)
T ss_pred hhhcccchhcccccccCC--HHHhhhhhhhcchhhhhhhccchhhhhhhhhcc
Confidence 467899999999999995 99999999999999999998 777766655443
No 21
>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=37.09 E-value=22 Score=25.49 Aligned_cols=34 Identities=26% Similarity=0.366 Sum_probs=19.4
Q ss_pred ccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeec---Ccee
Q 043421 273 NCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCEN---GHVS 316 (326)
Q Consensus 273 ~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeN---GHv~ 316 (326)
.||.|+++ |. +|+...=+++. .-.||.|.| ||-.
T Consensus 1 ~CP~Cg~~-------a~-ir~S~~~s~~~--~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSK-------AR-IRTSRQLSPLT--RELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCe-------eE-EEEchhhCcce--EEEEEEECCCcCCCEE
Confidence 49999996 11 12222222332 457999999 6643
No 22
>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=35.63 E-value=14 Score=30.48 Aligned_cols=41 Identities=34% Similarity=0.547 Sum_probs=10.8
Q ss_pred CCCCCccccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeecCceeeee--ecccCC
Q 043421 266 NRSKIDVNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCENGHVSGAW--TDLPLY 325 (326)
Q Consensus 266 ~r~~~~~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeNGHv~Gaw--t~~PLy 325 (326)
....+.+.|++|+..-. . +| .+.-+|+|||+-.-| |.+|+.
T Consensus 9 ~~~~i~E~C~~C~~~i~--------------~-~~----~~~~~C~~GH~w~RC~lT~l~i~ 51 (99)
T PF12660_consen 9 PGLPIFEKCPICGAPIP--------------F-DD----LDEAQCENGHVWPRCALTFLPIQ 51 (99)
T ss_dssp ---------------------------------------SSEEE-TTS-EEEB-SSS-SBS-
T ss_pred ccccccccccccccccc--------------c-CC----cCEeECCCCCEEeeeeeeeeeec
Confidence 34455699999988511 1 33 234689999998754 455553
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.84 E-value=26 Score=34.67 Aligned_cols=41 Identities=22% Similarity=0.606 Sum_probs=25.5
Q ss_pred cccCCCCccccchhhhhhhh----hhhhccc--CCCCceEEEEEeecCc
Q 043421 272 VNCAFCNCKETWDLHSAFCL----RRVFGYH--DDGEPVVRAYVCENGH 314 (326)
Q Consensus 272 ~~C~fC~~~~~Wdl~sAfcl----rr~~gyh--ddGEpvvrayVCeNGH 314 (326)
+.|.+|+. .|.+.=..|. -+...|+ |++++-+|++||+.=|
T Consensus 213 L~CslC~t--eW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~ 259 (309)
T PRK03564 213 LHCNLCES--EWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCG 259 (309)
T ss_pred EEcCCCCC--cccccCccCCCCCCCCceeeeeecCCCcceEeeeccccc
Confidence 55666665 3666544442 2345665 5556789999998643
No 24
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=32.02 E-value=21 Score=25.95 Aligned_cols=11 Identities=27% Similarity=0.924 Sum_probs=8.3
Q ss_pred cccCCCCcccc
Q 043421 272 VNCAFCNCKET 282 (326)
Q Consensus 272 ~~C~fC~~~~~ 282 (326)
..|||||...+
T Consensus 4 kPCPFCG~~~~ 14 (61)
T PF14354_consen 4 KPCPFCGSADV 14 (61)
T ss_pred cCCCCCCCcce
Confidence 35999998743
No 25
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.65 E-value=24 Score=28.19 Aligned_cols=33 Identities=27% Similarity=0.476 Sum_probs=20.4
Q ss_pred cccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeecCc
Q 043421 272 VNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCENGH 314 (326)
Q Consensus 272 ~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeNGH 314 (326)
..||+|+.+ |. + |---+.+++ -.-+||.|.|-.
T Consensus 2 m~CP~Cg~~-------a~-i-rtSr~~s~~-~~~~Y~qC~N~e 34 (72)
T PRK09678 2 FHCPLCQHA-------AH-A-RTSRYITDT-TKERYHQCQNVN 34 (72)
T ss_pred ccCCCCCCc-------cE-E-EEChhcChh-hheeeeecCCCC
Confidence 369999997 21 1 222244555 456899998743
No 26
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=24.84 E-value=1.5e+02 Score=25.95 Aligned_cols=96 Identities=21% Similarity=0.303 Sum_probs=61.2
Q ss_pred eeehhccccccccc--cCCceEEeeCCCCcccccccccceeeeeccc--cchhhhh-HHHHhc-CCCCCCccccCCCCcc
Q 043421 207 NLCREQGNKLLASR--FRGDCLYICDWPGCLHTEEKRNYMLFRGIFK--NFKRSRV-WRTIND-GNRSKIDVNCAFCNCK 280 (326)
Q Consensus 207 ~~SReqG~klLa~r--fR~D~LYvcDwPgC~H~ee~r~y~lFRGVFk--~F~rSrv-rr~l~d-~~r~~~~~~C~fC~~~ 280 (326)
+|.||-.|-|-++- +-.=+||-|- -|.|.+|-.+=.+|+-=+. .=-..++ .-...| +-+++.+..||-|+-+
T Consensus 5 rfC~eCNNmLYPkEDked~~L~laCr--nCd~ve~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~ 82 (113)
T KOG2691|consen 5 RFCRECNNMLYPKEDKEDRILLLACR--NCDYVEEADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHR 82 (113)
T ss_pred chhhhhhccccccccccccEEEEEec--CCcceEecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCc
Confidence 88999888877753 3344899999 9999999888888874322 1111222 222345 5556678999999998
Q ss_pred ccchhhhhhhhhhhhcccCCCCceEEEEEeec
Q 043421 281 ETWDLHSAFCLRRVFGYHDDGEPVVRAYVCEN 312 (326)
Q Consensus 281 ~~Wdl~sAfclrr~~gyhddGEpvvrayVCeN 312 (326)
|.==..+ ..+=-| |-+.=+|||.|
T Consensus 83 eavffQ~------~~~r~d--~~m~l~yvC~~ 106 (113)
T KOG2691|consen 83 EAVFFQA------QTRRAD--EAMRLFYVCCS 106 (113)
T ss_pred ceEEEec------cccccc--ceEEEEEEecc
Confidence 6421111 111112 44778999998
No 27
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.77 E-value=34 Score=23.95 Aligned_cols=12 Identities=50% Similarity=1.041 Sum_probs=10.7
Q ss_pred CCccccCCCCcc
Q 043421 269 KIDVNCAFCNCK 280 (326)
Q Consensus 269 ~~~~~C~fC~~~ 280 (326)
++++.||||...
T Consensus 3 ~i~v~CP~C~s~ 14 (36)
T PF03811_consen 3 KIDVHCPRCQST 14 (36)
T ss_pred cEeeeCCCCCCC
Confidence 678999999987
No 28
>PF03478 DUF295: Protein of unknown function (DUF295); InterPro: IPR005174 This family of proteins are found in plants. The function of the proteins is unknown.
Probab=23.61 E-value=97 Score=22.28 Aligned_cols=24 Identities=25% Similarity=0.701 Sum_probs=18.6
Q ss_pred ccCCceEEeeCCCCcccccccccceee
Q 043421 220 RFRGDCLYICDWPGCLHTEEKRNYMLF 246 (326)
Q Consensus 220 rfR~D~LYvcDwPgC~H~ee~r~y~lF 246 (326)
-+++|++|..| . .+.+..+++++|
T Consensus 29 g~~~n~IYf~~--~-~~~~~~~~~~Vy 52 (54)
T PF03478_consen 29 GLKGNCIYFLD--D-SSDESDRDIGVY 52 (54)
T ss_pred CccCCEEEEec--C-CCCCCCCCEEEE
Confidence 37899999999 4 555677777776
No 29
>PHA03399 pif3 per os infectivity factor 3; Provisional
Probab=21.27 E-value=44 Score=31.45 Aligned_cols=17 Identities=65% Similarity=1.251 Sum_probs=14.1
Q ss_pred ccCCCCceEEEEEeecCce
Q 043421 297 YHDDGEPVVRAYVCENGHV 315 (326)
Q Consensus 297 yhddGEpvvrayVCeNGHv 315 (326)
+.|+|| +|=|||+||-+
T Consensus 131 vdD~g~--lRPYvC~nG~l 147 (200)
T PHA03399 131 VDDDGE--LRPYVCENGTL 147 (200)
T ss_pred CCCCCC--cCceEecCCeE
Confidence 668884 79999999975
No 30
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=21.04 E-value=52 Score=26.14 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=8.8
Q ss_pred CccccCCCCcc
Q 043421 270 IDVNCAFCNCK 280 (326)
Q Consensus 270 ~~~~C~fC~~~ 280 (326)
.-..||||++.
T Consensus 5 ~lKPCPFCG~~ 15 (64)
T PRK09710 5 NVKPCPFCGCP 15 (64)
T ss_pred cccCCCCCCCc
Confidence 34679999996
No 31
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=20.50 E-value=67 Score=22.48 Aligned_cols=36 Identities=25% Similarity=0.529 Sum_probs=23.1
Q ss_pred CccccCCCCccccchhhhhhhhhhhhcccCCCCceEEEEEeecCceee-eee
Q 043421 270 IDVNCAFCNCKETWDLHSAFCLRRVFGYHDDGEPVVRAYVCENGHVSG-AWT 320 (326)
Q Consensus 270 ~~~~C~fC~~~~~Wdl~sAfclrr~~gyhddGEpvvrayVCeNGHv~G-awt 320 (326)
--+.|+.|+.+ |+. +. ...+ ..||+|.|.+-.| .|.
T Consensus 4 g~l~C~~CG~~----m~~----~~----~~~~---~~yy~C~~~~~~~~~C~ 40 (58)
T PF13408_consen 4 GLLRCGHCGSK----MTR----RK----RKGK---YRYYRCSNRRRKGKGCP 40 (58)
T ss_pred CcEEcccCCcE----eEE----EE----CCCC---ceEEEcCCCcCCCCCCC
Confidence 34789999996 222 11 1122 3889999998777 444
Done!