Query 017931
Match_columns 363
No_of_seqs 112 out of 152
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 04:40:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2652 RNA polymerase II tran 100.0 3E-56 6.5E-61 428.1 17.3 289 1-363 45-348 (348)
2 PF03153 TFIIA: Transcription 100.0 2.4E-49 5.2E-54 371.7 4.2 293 1-363 37-375 (375)
3 COG5149 TOA1 Transcription ini 99.9 2.8E-23 6E-28 195.1 6.2 47 317-363 246-292 (293)
4 PF09211 DUF1958: Domain of un 76.8 2.9 6.4E-05 33.4 3.2 29 325-353 23-52 (65)
5 KOG2652 RNA polymerase II tran 67.6 8 0.00017 39.3 4.6 61 226-306 241-301 (348)
6 KOG1924 RhoA GTPase effector D 66.4 29 0.00064 39.3 8.8 20 64-83 545-565 (1102)
7 COG5013 NarG Nitrate reductase 62.7 4.6 9.9E-05 45.9 2.0 27 324-350 41-75 (1227)
8 PF09026 CENP-B_dimeris: Centr 60.8 2.8 6E-05 36.2 0.0 7 320-326 40-46 (101)
9 PF04584 Pox_A28: Poxvirus A28 51.3 7.4 0.00016 35.3 1.1 16 329-344 65-80 (140)
10 KOG1999 RNA polymerase II tran 50.9 1.3E+02 0.0029 34.7 10.6 34 9-44 749-783 (1024)
11 KOG1832 HIV-1 Vpr-binding prot 41.5 14 0.0003 42.5 1.5 10 37-46 929-938 (1516)
12 PF08629 PDE8: PDE8 phosphodie 35.2 24 0.00053 27.4 1.5 30 4-33 10-45 (52)
13 KOG0943 Predicted ubiquitin-pr 34.1 39 0.00084 40.5 3.5 10 25-34 1380-1389(3015)
14 PRK09719 hypothetical protein; 32.4 13 0.00029 30.9 -0.3 12 322-333 57-68 (89)
15 PF14812 PBP1_TM: Transmembran 30.4 17 0.00037 30.2 0.0 7 330-336 61-67 (81)
16 PF03153 TFIIA: Transcription 30.1 20 0.00043 34.8 0.4 13 189-201 270-282 (375)
17 PF15471 TMEM171: Transmembran 26.5 1.2E+02 0.0026 30.8 5.0 57 29-91 186-254 (319)
18 PF12139 APS-reductase_C: Aden 25.7 50 0.0011 27.9 1.9 16 336-355 25-40 (83)
19 KOG0943 Predicted ubiquitin-pr 25.4 39 0.00084 40.5 1.7 9 262-270 1716-1724(3015)
20 KOG1924 RhoA GTPase effector D 25.0 4.1E+02 0.0089 30.9 9.1 9 60-68 547-555 (1102)
21 PF10382 DUF2439: Protein of u 23.8 93 0.002 25.1 3.1 31 322-356 4-38 (83)
22 KOG3130 Uncharacterized conser 22.8 47 0.001 35.2 1.6 13 321-333 310-322 (514)
23 PTZ00486 apyrase Superfamily; 22.4 83 0.0018 32.3 3.2 30 322-351 60-91 (352)
24 KOG4672 Uncharacterized conser 21.6 1.9E+02 0.0041 30.9 5.6 9 140-148 403-411 (487)
25 cd06477 ACD_HspB3_Like Alpha c 21.4 53 0.0011 26.5 1.3 32 320-351 46-83 (83)
26 PF03115 Astro_capsid: Astrovi 21.3 31 0.00068 38.4 0.0 11 334-344 745-755 (787)
27 PF14480 DNA_pol3_a_NI: DNA po 20.9 68 0.0015 24.2 1.8 13 329-341 31-43 (76)
28 PF01473 CW_binding_1: Putativ 20.2 1.2E+02 0.0027 18.0 2.4 17 343-360 2-18 (19)
No 1
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=100.00 E-value=3e-56 Score=428.08 Aligned_cols=289 Identities=34% Similarity=0.520 Sum_probs=242.0
Q ss_pred Ccceeceee---eecCCCCCCCCCCCCCCcccccCCCCCC-cccccCCCceeccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 017931 1 MKMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEG-TEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLP 76 (363)
Q Consensus 1 ~km~q~g~i---ier~~a~~~~~p~gp~tpvhDLNvPyeg-tEEyeTPtaemLFpPtPlqtp~qTPlp~~~~~~~~~~~~ 76 (363)
.||||+||. ++|.+++.+ .+|+. .| ||||++ |.+|+||+ +||.+++|++..++||
T Consensus 45 ~Kl~qs~~~~~~~d~~s~~~p-~~~~q---~~--~~~~~~~~~~~~~Pa---~~~~~~q~~~~~~~l~------------ 103 (348)
T KOG2652|consen 45 TKLIQSGVATFPWDRESNQRP-PPGVQ---LH--HVPLQSATANLATPA---VFPGAPQQTPAGVPLP------------ 103 (348)
T ss_pred HHHHhhcccccCcccccccCC-CCccc---cc--CcccccccccccCCc---cccccccccCcCccCc------------
Confidence 389999999 999999987 55553 45 899999 79999999 8999999999999999
Q ss_pred CCCCCCC-CCCCCcccCCCCCCCCC--CCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCcccceeeeeecCc----
Q 017931 77 GSTPLPG-TADNSTYNIPTGSSDYP--TPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR---- 149 (363)
Q Consensus 77 ~~~~~~g-~~~~~myniptg~s~yp--~~~~d~g~~~d~k~~~grps~ym~~~pspw~~~~~~l~vdVnvAYvegr---- 149 (363)
| .+..|||||+.+.+.|+ .|......|. -++.|+|.| .|.|.++|+. ++ ||.+|
T Consensus 104 ------~~~~~~s~~~i~~~~t~~~~~~P~~q~~~N~------~q~~p~~~p-~s~~~~~q~s----~~--~v~~~~~ip 164 (348)
T KOG2652|consen 104 ------GLSGHLSKANIPLPSTATNGQHPSQQVNVNS------TQPVPALSP-WSLQLNTQKS----QQ--TVLQQSAIP 164 (348)
T ss_pred ------cccccccccCccccccccCCcCccccccccc------cCCCcCcCc-cccccccccc----cc--ccccccccc
Confidence 7 77899999999999998 6777766666 478899999 9999985554 33 99999
Q ss_pred -cccccCCCCCCCccceecccccccccccCCcCCCCCCcccccCCCCCCCcccceeeeecCCCCccccccccchhhhhhh
Q 017931 150 -DEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANL 228 (363)
Q Consensus 150 -de~drg~s~q~lTqdfftmsSGKRKRdD~~~qy~~gg~~iPQQDGa~D~~~e~~~~e~~~~~~~~~~~~~~~~~~~~~~ 228 (363)
..+.+|..+++.||+-|.-++| |+.+.-.+|.+++ |||++|+++...+... ..+.++....|...+.+
T Consensus 165 ~~~p~~~~~~~~~tqq~~~~~~g--~~pq~~~~~~~~~--~~q~~~s~nd~~~~~~-------~~~a~~~~~~~~~~~~~ 233 (348)
T KOG2652|consen 165 PSGPVDGNHNQPVTQQILVPPGG--KSPQSSFHYINLN--IPQVDGSENDVEQIDG-------TDLAIHILKDRMVPRDS 233 (348)
T ss_pred ccCcccccccCccccccccCCCC--CCcccccceeccC--Cccccccccccccccc-------ccccccccccccccccc
Confidence 8999999999999999988888 8888888888888 8999999999888765 23667888888888888
Q ss_pred hcccccccCCCCCCCCCCCCcCCCCcccccCCcccccccccCCCCCCCcccCCCcccccCCcCCCCCCCCCCCCCCC--C
Q 017931 229 ASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDD--E 306 (363)
Q Consensus 229 ~~~~~~IPQlDGp~pdpydd~~~tpniy~yqGv~~Edyn~~~~~a~~e~~ast~~~~~~~~~~de~eEdpLNSdDDd--d 306 (363)
.....+|.|+||++.. +++.++|-+++ .||=||-. ..+ ...+++|+.+|+|||| +
T Consensus 234 ~s~~~~i~qv~~~~~~-----~~Q~Dg~~~~~--eE~e~Eee---------------~~~-~~~~~dee~~n~Dd~D~~E 290 (348)
T KOG2652|consen 234 VSEKDKIAQVDLSLRK-----ILQVDGTGDTS--EEDENEEE---------------DDD-PDPDEDEELGNSDDDDGVE 290 (348)
T ss_pred cchhhhhhhhcccccc-----eeecccccccc--cccccccc---------------ccC-cccchhhhcccccccCccc
Confidence 8899999999999984 78899999988 56444411 111 1123566777777755 5
Q ss_pred CcccccccCCC-CCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931 307 LDDVDQGEELN-TQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363 (363)
Q Consensus 307 ~dD~Dd~Ed~~-t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw 363 (363)
++++++++|.. |+||||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus 291 eeplnsedDvsdt~nvVvCqyDKV~RsKnKWKc~LKDGIM~ingkDY~F~KA~GeaEW 348 (348)
T KOG2652|consen 291 EEPLNSEDDVSDTQNVVVCQYDKVNRSKNKWKCYLKDGVMHINGKDYVFQKAQGEAEW 348 (348)
T ss_pred cccccCcccccccceeEEEeeeeeccccceeeEEeecceEEeCCceeEeeecccccCC
Confidence 66666655663 8999999999999999999999999999999999999999999999
No 2
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=100.00 E-value=2.4e-49 Score=371.69 Aligned_cols=293 Identities=33% Similarity=0.476 Sum_probs=55.3
Q ss_pred Ccceeceee---eecCCCCCCCCCCCCCCcccccCCCCCCcccccCCCceeccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 017931 1 MKMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPG 77 (363)
Q Consensus 1 ~km~q~g~i---ier~~a~~~~~p~gp~tpvhDLNvPyegtEEyeTPtaemLFpPtPlqtp~qTPlp~~~~~~~~~~~~~ 77 (363)
.||+|+||+ .+...++.++.+..|..+ +.||+++++++ +++++
T Consensus 37 ~KL~qs~v~~~~~d~~~~~~~~~~~~p~~~--------------------~~~~~~~~~~~-~~~~~------------- 82 (375)
T PF03153_consen 37 SKLSQSGVADFPWDPPPAPPPPPPQQPQPP--------------------QSTPPSPSQQP-QAPQA------------- 82 (375)
T ss_dssp HHHHHH-SS--TTGGGG---------------------------------------------------------------
T ss_pred HHHHhcCCccCCCCcccCCCcccccCCCCc--------------------ccCCCCCCCCc-ccccc-------------
Confidence 389999999 555555444233333212 78888888888 77776
Q ss_pred CCCCCC-CCCCCcccCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCcccceeeeeecCccccccCC
Q 017931 78 STPLPG-TADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGT 156 (363)
Q Consensus 78 ~~~~~g-~~~~~myniptg~s~yp~~~~d~g~~~d~k~~~grps~ym~~~pspw~~~~~~l~vdVnvAYvegrde~drg~ 156 (363)
. ...+.++++|++.+.+..+......+. +. +++.++|++ |..|++.+.|..+..+.++..++....+..
T Consensus 83 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~iq~~-pG~~~~~~~P~~~~~~~~~~~~~~~~aqq~ 152 (375)
T PF03153_consen 83 -----IPQGQSQQQNQPSSMSNSNPPATFSTPPG--QV--PAPPTIQQP-PGQQYQVQVPSMNNQPPGNQQIAQQPAQQR 152 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred -----cCCCCccccccccccCcCCCcccccCCCc--cc--CCCCCccCC-CccccCcccCCccCCccccccccccccccc
Confidence 3 455778888888777633322221111 33 578888888 999999999998999999999999999999
Q ss_pred CCCCCccceecccccccc-----------cccCCcCCCCCCc-ccccCCCCCCCcc----cceeeeec-CC---------
Q 017931 157 SHQPLTQDFFTMSAGKRK-----------REDFPAQYHNGGY-NIPQQDGAGDAMS----EIFELEVS-EF--------- 210 (363)
Q Consensus 157 s~q~lTqdfftmsSGKRK-----------RdD~~~qy~~gg~-~iPQQDGa~D~~~----e~~~~e~~-~~--------- 210 (363)
..+++++.|+.+++.+++ +.....++..|.. .++|.||+++... +..+.... ..
T Consensus 153 ~~qq~~q~~g~~aa~q~~~~~qq~q~~~~~~~~~~~~~~~~~~~~~Qtdga~d~~~~~~~~~~~~~~~~~~~~~d~~L~~ 232 (375)
T PF03153_consen 153 AAQQLQQPYGQPAAQQISQQQQQQQPQQQQQQQQQQQQPGQQVQQQQTDGAGDSESNSQPRRLEAAVPLQRNEIDQVLRS 232 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccccccccccCCccccccccccccccccccccCCCccCCCcccCCCCcccchhccccccccccccccccccccc
Confidence 999999999999999999 5666666766665 3588999999852 11111111 00
Q ss_pred -----------CCccccccccchhhhh--hhhcccccccCCCCCCCCCCCCcCCCCcccccCCcccccccccCCCCCCCc
Q 017931 211 -----------PGRQDSVTTANREIFA--NLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDI 277 (363)
Q Consensus 211 -----------~~~~~~~~~~~~~~~~--~~~~~~~~IPQlDGp~pdpydd~~~tpniy~yqGv~~Edyn~~~~~a~~e~ 277 (363)
...+............ ...+...+|+|+||+.++..++.+. +..+.+||+.+.
T Consensus 233 ~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Q~DG~~d~~~~e~~~------~~~~~d~d~~~~-------- 298 (375)
T PF03153_consen 233 QIENRAMQLEGGGLMSPLSQASKASKQNKSSNSESSRIPQLDGAGDDSDDEEDD------DDDDDDEDDEDK-------- 298 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccccccchhhccchhhcccccccccccccccccccccccCCCCCccccccc------cccccccccccc--------
Confidence 0000000000000000 0111124699999999886655433 344566666100
Q ss_pred ccCCCcccccCCcCCCCCCCCCCCCCCCCCc---ccccccCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeee
Q 017931 278 QASTPAVVTQNDAAEDDDDEPLNENDDDELD---DVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILF 354 (363)
Q Consensus 278 ~ast~~~~~~~~~~de~eEdpLNSdDDdd~d---D~Dd~Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF 354 (363)
+.++++++.+|||+|+++| |+|.+++++++||||||||||+|+||||||+|||||||||||||||
T Consensus 299 ------------~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~c~~~kv~r~k~~wk~~lk~g~~~~~~~d~~f 366 (375)
T PF03153_consen 299 ------------DKDEDDEDAINSDLDDSDDDVSDEDDEDDFDTDNVVLCQYDKVTRVKNKWKCTLKDGIMHINGKDYVF 366 (375)
T ss_dssp ---------------------------------B-------STTS-EEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEE
T ss_pred ------------cccccccccccCCcCCccccccccccccccCcCCEEEEEeeccccccceeEEEeeeeEEEECCeEEEE
Confidence 1112234444444433222 3344457799999999999999999999999999999999999999
Q ss_pred ecccccccC
Q 017931 355 NKATGEFDF 363 (363)
Q Consensus 355 ~KatGEfEw 363 (363)
+||+|||||
T Consensus 367 ~~~~ge~~w 375 (375)
T PF03153_consen 367 QKATGEFEW 375 (375)
T ss_dssp EEEEEEEE-
T ss_pred eeeeeeecC
Confidence 999999999
No 3
>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]
Probab=99.88 E-value=2.8e-23 Score=195.06 Aligned_cols=47 Identities=45% Similarity=0.920 Sum_probs=45.5
Q ss_pred CCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931 317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363 (363)
Q Consensus 317 ~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw 363 (363)
...|+|||+||||+|+|+||||+|||||+.|||+||+|+||+|||||
T Consensus 246 ~~~n~mlCLYdKVn~~K~kWKCtfkdGvV~In~~Dy~F~kAqgE~EW 292 (293)
T COG5149 246 GSTNCMLCLYDKVNMSKGKWKCTFKDGVVSINNIDYVFNKAQGELEW 292 (293)
T ss_pred CCceEEEEEeeecccccceeeEEeecceEEecCceeEEeeccceEee
Confidence 45699999999999999999999999999999999999999999999
No 4
>PF09211 DUF1958: Domain of unknown function (DUF1958); InterPro: IPR015294 Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. Penicillin-binding protein 4 (PBP4) functions as a transpeptidase, and belongs to MEROPS peptidase family S11 (clan SE). PBP4 acts co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents []. This entry represents the C-terminal domain PBP4.; PDB: 1TVF_A 3HUN_A 3HUM_B.
Probab=76.83 E-value=2.9 Score=33.36 Aligned_cols=29 Identities=31% Similarity=0.597 Sum_probs=21.3
Q ss_pred EEeeeeccCCceeEEeecceeEE-CCeeee
Q 017931 325 QFDKVTRTKSRWKCALKDGIMHI-NNKDIL 353 (363)
Q Consensus 325 qYDKV~R~KNKWKc~LKDGIm~I-NGKDyv 353 (363)
+||=|-+-+++|++.++||.++| +++.|+
T Consensus 23 lYd~VpK~~~~~~~~v~dg~v~vd~~r~fl 52 (65)
T PF09211_consen 23 LYDVVPKGKKPYKLKVKDGKVHVDYGRQFL 52 (65)
T ss_dssp EEEEEETT--GSEEEEETTEEEEE-S--BS
T ss_pred hhhhccCCCccceEEEeCCEEEEeCCcccC
Confidence 68889999999999999999999 566654
No 5
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=67.63 E-value=8 Score=39.32 Aligned_cols=61 Identities=28% Similarity=0.304 Sum_probs=33.9
Q ss_pred hhhhcccccccCCCCCCCCCCCCcCCCCcccccCCcccccccccCCCCCCCcccCCCcccccCCcCCCCCCCCCCCCCCC
Q 017931 226 ANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDD 305 (363)
Q Consensus 226 ~~~~~~~~~IPQlDGp~pdpydd~~~tpniy~yqGv~~Edyn~~~~~a~~e~~ast~~~~~~~~~~de~eEdpLNSdDDd 305 (363)
+++..+-.+|-|+||-...= -..+|= .||++...+.+ + .....+++|.+|||+|||+||.
T Consensus 241 ~qv~~~~~~~~Q~Dg~~~~~----eE~e~E-------ee~~~~~~~~d--e-------e~~n~Dd~D~~EeeplnsedDv 300 (348)
T KOG2652|consen 241 AQVDLSLRKILQVDGTGDTS----EEDENE-------EEDDDPDPDED--E-------ELGNSDDDDGVEEEPLNSEDDV 300 (348)
T ss_pred hhhcccccceeecccccccc----cccccc-------ccccCcccchh--h-------hcccccccCccccccccCcccc
Confidence 45555556699999966542 122332 55565555443 1 1222333333489999999875
Q ss_pred C
Q 017931 306 E 306 (363)
Q Consensus 306 d 306 (363)
.
T Consensus 301 s 301 (348)
T KOG2652|consen 301 S 301 (348)
T ss_pred c
Confidence 4
No 6
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=66.40 E-value=29 Score=39.34 Aligned_cols=20 Identities=50% Similarity=1.027 Sum_probs=8.9
Q ss_pred CCCCCCCCCCCCCC-CCCCCC
Q 017931 64 PGSTPLPGSTPLPG-STPLPG 83 (363)
Q Consensus 64 p~~~~~~~~~~~~~-~~~~~g 83 (363)
|+..||||..++|- ..||||
T Consensus 545 PppPPlpggag~PPPPpplPg 565 (1102)
T KOG1924|consen 545 PPPPPLPGGAGPPPPPPPLPG 565 (1102)
T ss_pred CCCCCCCCCCCCCccCCCCCc
Confidence 33445555544332 234555
No 7
>COG5013 NarG Nitrate reductase alpha subunit [Energy production and conversion]
Probab=62.75 E-value=4.6 Score=45.88 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=23.4
Q ss_pred EEEeeeeccC--------CceeEEeecceeEECCe
Q 017931 324 AQFDKVTRTK--------SRWKCALKDGIMHINNK 350 (363)
Q Consensus 324 CqYDKV~R~K--------NKWKc~LKDGIm~INGK 350 (363)
-|||||-|+- ..||++.|||||+-..+
T Consensus 41 WqhDKvVRSTHGVNCTGSCSWkIYVKdGiITWEtQ 75 (1227)
T COG5013 41 WQHDKVVRSTHGVNCTGSCSWKIYVKNGLITWETQ 75 (1227)
T ss_pred hcccceeeccCCccccceeeEEEEEeCCEEEEeec
Confidence 5899999975 57999999999997765
No 8
>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=60.83 E-value=2.8 Score=36.17 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=0.5
Q ss_pred CEEEEEE
Q 017931 320 HLVLAQF 326 (363)
Q Consensus 320 NvvLCqY 326 (363)
-+.+|-|
T Consensus 40 e~p~p~f 46 (101)
T PF09026_consen 40 EVPVPEF 46 (101)
T ss_dssp ------H
T ss_pred cccchhH
Confidence 4555554
No 9
>PF04584 Pox_A28: Poxvirus A28 family; InterPro: IPR007664 The poxvirus A28 protein is expressed at late times during the virus replication cycle and is a membrane component of the intracellular mature virion. Repression of A28 inhibits cell-to-cell spread, suggesting that all poxviruses use a common A28-dependent mechanism of cell penetration []. An N-terminal hydrophobic sequence, present in all poxvirus A28 orthologues, anchors the protein in the virion surface membrane so that most of it is exposed to the cytoplasm [].; GO: 0016032 viral reproduction, 0019031 viral envelope
Probab=51.27 E-value=7.4 Score=35.27 Aligned_cols=16 Identities=25% Similarity=0.777 Sum_probs=12.9
Q ss_pred eeccCCceeEEeecce
Q 017931 329 VTRTKSRWKCALKDGI 344 (363)
Q Consensus 329 V~R~KNKWKc~LKDGI 344 (363)
|.-+|.||||++.+++
T Consensus 65 ~~DvkqKWRCv~~~~~ 80 (140)
T PF04584_consen 65 VYDVKQKWRCVKYNNV 80 (140)
T ss_pred ccChhhceEEEeeCCe
Confidence 4557999999998865
No 10
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=50.86 E-value=1.3e+02 Score=34.67 Aligned_cols=34 Identities=24% Similarity=0.199 Sum_probs=22.9
Q ss_pred eeecCCCCCCCC-CCCCCCcccccCCCCCCcccccCC
Q 017931 9 IIDRTSAPKQPA-PGGPITPVHDLNVPYEGTEEYETP 44 (363)
Q Consensus 9 iier~~a~~~~~-p~gp~tpvhDLNvPyegtEEyeTP 44 (363)
++.|-.+..+.- -.|+.||.|+-|+|--| -+-||
T Consensus 749 ~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~--~s~tp 783 (1024)
T KOG1999|consen 749 RTPGYGRVTPARYGMGSSTPMYGSNTPLWG--GSRTP 783 (1024)
T ss_pred ccccccccCccccCCCCcCccCCCCCCCCC--cccCc
Confidence 344444444411 37889999999999988 36666
No 11
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=41.45 E-value=14 Score=42.52 Aligned_cols=10 Identities=30% Similarity=0.192 Sum_probs=4.2
Q ss_pred CcccccCCCc
Q 017931 37 GTEEYETPTA 46 (363)
Q Consensus 37 gtEEyeTPta 46 (363)
+|-|-..++|
T Consensus 929 ~~Se~~a~~a 938 (1516)
T KOG1832|consen 929 DTSETAAELA 938 (1516)
T ss_pred ccccccchhc
Confidence 4444333333
No 12
>PF08629 PDE8: PDE8 phosphodiesterase; InterPro: IPR013938 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This region is found at the N terminus of members of PDE8 phosphodiesterase family []. Phosphodiesterase 8 (PDE8) regulates chemotaxis of activated lymphocytes [].
Probab=35.23 E-value=24 Score=27.39 Aligned_cols=30 Identities=33% Similarity=0.649 Sum_probs=20.6
Q ss_pred eeceeeeec----CCCCCC--CCCCCCCCcccccCC
Q 017931 4 IQAGVIIDR----TSAPKQ--PAPGGPITPVHDLNV 33 (363)
Q Consensus 4 ~q~g~iier----~~a~~~--~~p~gp~tpvhDLNv 33 (363)
-|.|||+-| ++.+.| .+.-||.+|||-|=|
T Consensus 10 SqSgVvy~res~es~sP~qTtt~SQg~~~pl~GLFi 45 (52)
T PF08629_consen 10 SQSGVVYCRESDESNSPRQTTTVSQGPAAPLPGLFI 45 (52)
T ss_pred cccceEEEeccccCCCCCcceeeecCCCCCccceEE
Confidence 488999554 444444 234789999998865
No 13
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=34.06 E-value=39 Score=40.49 Aligned_cols=10 Identities=50% Similarity=0.723 Sum_probs=7.7
Q ss_pred CCcccccCCC
Q 017931 25 ITPVHDLNVP 34 (363)
Q Consensus 25 ~tpvhDLNvP 34 (363)
-+|-||||-|
T Consensus 1380 ~~PdHdLePP 1389 (3015)
T KOG0943|consen 1380 DMPDHDLEPP 1389 (3015)
T ss_pred CCCccCCCCc
Confidence 4588999866
No 14
>PRK09719 hypothetical protein; Provisional
Probab=32.44 E-value=13 Score=30.92 Aligned_cols=12 Identities=33% Similarity=0.473 Sum_probs=10.0
Q ss_pred EEEEEeeeeccC
Q 017931 322 VLAQFDKVTRTK 333 (363)
Q Consensus 322 vLCqYDKV~R~K 333 (363)
--|||||.+|+-
T Consensus 57 wrcqydklhrvp 68 (89)
T PRK09719 57 WRCQYDKLHRVP 68 (89)
T ss_pred hhcchhhhhccc
Confidence 469999999975
No 15
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=30.39 E-value=17 Score=30.23 Aligned_cols=7 Identities=57% Similarity=1.275 Sum_probs=0.0
Q ss_pred eccCCce
Q 017931 330 TRTKSRW 336 (363)
Q Consensus 330 ~R~KNKW 336 (363)
.|.|-+|
T Consensus 61 ~rkKrrw 67 (81)
T PF14812_consen 61 PRKKRRW 67 (81)
T ss_dssp -------
T ss_pred ccccchh
Confidence 3444444
No 16
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=30.07 E-value=20 Score=34.84 Aligned_cols=13 Identities=62% Similarity=1.004 Sum_probs=0.0
Q ss_pred cccCCCCCCCccc
Q 017931 189 IPQQDGAGDAMSE 201 (363)
Q Consensus 189 iPQQDGa~D~~~e 201 (363)
|+|-||++|...+
T Consensus 270 ~~Q~DG~~d~~~~ 282 (375)
T PF03153_consen 270 IPQLDGAGDDSDD 282 (375)
T ss_dssp -------------
T ss_pred cccccCCCCCccc
Confidence 6666666665544
No 17
>PF15471 TMEM171: Transmembrane protein family 171
Probab=26.52 E-value=1.2e+02 Score=30.77 Aligned_cols=57 Identities=30% Similarity=0.522 Sum_probs=31.7
Q ss_pred cccCCCCCCc--ccccCCCce----------eccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 017931 29 HDLNVPYEGT--EEYETPTAE----------ILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYN 91 (363)
Q Consensus 29 hDLNvPyegt--EEyeTPtae----------mLFpPtPlqtp~qTPlp~~~~~~~~~~~~~~~~~~g~~~~~myn 91 (363)
|.||+-=+.+ ||=.|++-| |+|||-|-+-=...+ .++-|+-||+..||-..|..-|+
T Consensus 186 ~nln~~qd~se~Ee~~~qs~Ep~qVTVGDaViiFPPPPPPYF~ess------~~a~t~~~~~~~l~~senPPsY~ 254 (319)
T PF15471_consen 186 NNLNGSQDASESEEGQTQSTEPVQVTVGDAVIIFPPPPPPYFPESS------ASAVTRSPGANSLPPSENPPSYY 254 (319)
T ss_pred cCCCcccCccccccCCCCCCCCEEEEecCEEEEcCCccCCCCCCCC------cccccCCCCCCCCCCCCCCCCcc
Confidence 6788877777 454577654 899995533222222 22334555555555544444444
No 18
>PF12139 APS-reductase_C: Adenosine-5'-phosphosulfate reductase beta subunit; InterPro: IPR022738 This domain is found in bacteria and archaea and is typically between 112 to 142 amino acids in length. It is found in association with PF00037 from PFAM, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of 1.8.99.2 from EC. ; PDB: 1JNZ_B 2FJE_D 2FJD_B 1JNR_D 2FJB_B 2FJA_B 3GYX_J.
Probab=25.74 E-value=50 Score=27.87 Aligned_cols=16 Identities=25% Similarity=0.733 Sum_probs=11.8
Q ss_pred eeEEeecceeEECCeeeeee
Q 017931 336 WKCALKDGIMHINNKDILFN 355 (363)
Q Consensus 336 WKc~LKDGIm~INGKDyvF~ 355 (363)
|+|+|+||.| |+|.|-
T Consensus 25 WtikFRnG~~----KrFkfP 40 (83)
T PF12139_consen 25 WTIKFRNGTV----KRFKFP 40 (83)
T ss_dssp EEEE-TTS-E----EEEEEE
T ss_pred EEEEecCCce----eeeecc
Confidence 9999999965 677774
No 19
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=25.44 E-value=39 Score=40.51 Aligned_cols=9 Identities=22% Similarity=0.158 Sum_probs=4.2
Q ss_pred ccccccccC
Q 017931 262 VNEDYNIVN 270 (363)
Q Consensus 262 ~~Edyn~~~ 270 (363)
.++|..+.+
T Consensus 1716 tnaDnEEre 1724 (3015)
T KOG0943|consen 1716 TNADNEERE 1724 (3015)
T ss_pred cccchhhhc
Confidence 455544433
No 20
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=25.03 E-value=4.1e+02 Score=30.86 Aligned_cols=9 Identities=44% Similarity=0.929 Sum_probs=4.0
Q ss_pred CCCCCCCCC
Q 017931 60 QTPLPGSTP 68 (363)
Q Consensus 60 qTPlp~~~~ 68 (363)
+.||||..+
T Consensus 547 pPPlpggag 555 (1102)
T KOG1924|consen 547 PPPLPGGAG 555 (1102)
T ss_pred CCCCCCCCC
Confidence 344554443
No 21
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=23.85 E-value=93 Score=25.10 Aligned_cols=31 Identities=19% Similarity=0.560 Sum_probs=21.4
Q ss_pred EEEEEeeeeccCCc-eeEEeecceeEEC---Ceeeeeec
Q 017931 322 VLAQFDKVTRTKSR-WKCALKDGIMHIN---NKDILFNK 356 (363)
Q Consensus 322 vLCqYDKV~R~KNK-WKc~LKDGIm~IN---GKDyvF~K 356 (363)
.-|||-+=.|.|.| | .||++.+. +|=.||.-
T Consensus 4 y~~lYT~q~~kK~K~W----~DG~l~~~~~~~kv~Lyde 38 (83)
T PF10382_consen 4 YECLYTHQKTKKRKKW----HDGFLKYHSFNKKVMLYDE 38 (83)
T ss_pred EEEEEEccccccceee----ECCEEEEEeCCCEEEEEcC
Confidence 35999887777765 7 49999875 44555543
No 22
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.85 E-value=47 Score=35.18 Aligned_cols=13 Identities=8% Similarity=0.202 Sum_probs=6.7
Q ss_pred EEEEEEeeeeccC
Q 017931 321 LVLAQFDKVTRTK 333 (363)
Q Consensus 321 vvLCqYDKV~R~K 333 (363)
+-+.+-+|-+|+|
T Consensus 310 i~f~~~~ep~~~~ 322 (514)
T KOG3130|consen 310 IYFSHTVEPKRVR 322 (514)
T ss_pred cccccccCcccce
Confidence 3456666644443
No 23
>PTZ00486 apyrase Superfamily; Provisional
Probab=22.39 E-value=83 Score=32.30 Aligned_cols=30 Identities=17% Similarity=0.529 Sum_probs=21.0
Q ss_pred EEEEEeeeec--cCCceeEEeecceeEECCee
Q 017931 322 VLAQFDKVTR--TKSRWKCALKDGIMHINNKD 351 (363)
Q Consensus 322 vLCqYDKV~R--~KNKWKc~LKDGIm~INGKD 351 (363)
|+.=-||-.| .+++|++.||-|.+...++.
T Consensus 60 iIaDlD~~S~~~~~~~w~S~~~~G~L~~~~~~ 91 (352)
T PTZ00486 60 LVADLDKASKDKEGKKWRSKVIKGTIFRQGNG 91 (352)
T ss_pred EEecCchhccccCCCceEEEEEEEEEEEcCCC
Confidence 4444555555 47889999999998777653
No 24
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=21.59 E-value=1.9e+02 Score=30.88 Aligned_cols=9 Identities=33% Similarity=0.475 Sum_probs=7.0
Q ss_pred ceeeeeecC
Q 017931 140 DVNVAYVEG 148 (363)
Q Consensus 140 dVnvAYveg 148 (363)
|.++|.+|-
T Consensus 403 d~s~a~ies 411 (487)
T KOG4672|consen 403 DMSRATIES 411 (487)
T ss_pred Ccccccccc
Confidence 668888887
No 25
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=21.36 E-value=53 Score=26.48 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=22.4
Q ss_pred CEEEEEEeeeecc-----CCceeEEe-ecceeEECCee
Q 017931 320 HLVLAQFDKVTRT-----KSRWKCAL-KDGIMHINNKD 351 (363)
Q Consensus 320 NvvLCqYDKV~R~-----KNKWKc~L-KDGIm~INGKD 351 (363)
+++-+.|-+..+- ..+=+..| +|||+.|.+||
T Consensus 46 ~~~~r~F~R~~~LP~~Vd~~~v~A~~~~dGvL~I~~~~ 83 (83)
T cd06477 46 GFISRSFTRQYQLPDGVEHKDLSAMLCHDGILVVETKD 83 (83)
T ss_pred CEEEEEEEEEEECCCCcchheEEEEEcCCCEEEEEecC
Confidence 3455566555543 26678887 89999999875
No 26
>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=21.34 E-value=31 Score=38.35 Aligned_cols=11 Identities=36% Similarity=0.561 Sum_probs=0.0
Q ss_pred CceeEEeecce
Q 017931 334 SRWKCALKDGI 344 (363)
Q Consensus 334 NKWKc~LKDGI 344 (363)
+-..+.|-||+
T Consensus 745 ~vy~d~LaDGl 755 (787)
T PF03115_consen 745 NVYMDALADGL 755 (787)
T ss_dssp -----------
T ss_pred hhHHhhhccCC
Confidence 44555555553
No 27
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=20.95 E-value=68 Score=24.21 Aligned_cols=13 Identities=23% Similarity=0.716 Sum_probs=10.8
Q ss_pred eeccCCceeEEee
Q 017931 329 VTRTKSRWKCALK 341 (363)
Q Consensus 329 V~R~KNKWKc~LK 341 (363)
|+|.+++|++.|+
T Consensus 31 v~k~~~~w~f~l~ 43 (76)
T PF14480_consen 31 VHKKSRKWRFHLS 43 (76)
T ss_pred EEccCCEEEEEEE
Confidence 5678899999986
No 28
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=20.22 E-value=1.2e+02 Score=18.04 Aligned_cols=17 Identities=24% Similarity=0.304 Sum_probs=11.7
Q ss_pred ceeEECCeeeeeeccccc
Q 017931 343 GIMHINNKDILFNKATGE 360 (363)
Q Consensus 343 GIm~INGKDyvF~KatGE 360 (363)
|-++++|+=|.| +..|+
T Consensus 2 ~W~~~~~~wYy~-~~~G~ 18 (19)
T PF01473_consen 2 GWVQDNGNWYYF-DSDGY 18 (19)
T ss_dssp EEEEETTEEEEE-TTTSB
T ss_pred cCEEECCEEEEe-CCCcc
Confidence 556778888777 55554
Done!