Query 015442
Match_columns 406
No_of_seqs 174 out of 191
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 06:21:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015442hhsearch_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 9.7E-70 2.1E-74 531.4 24.3 333 1-406 2-348 (348)
2 PF03153 TFIIA: Transcription 100.0 2.5E-65 5.5E-70 496.3 11.5 324 8-406 1-375 (375)
3 COG5149 TOA1 Transcription ini 100.0 4.9E-40 1.1E-44 311.7 18.7 58 1-58 1-59 (293)
4 KOG1924 RhoA GTPase effector D 93.3 1.3 2.8E-05 50.2 13.1 14 8-21 422-435 (1102)
5 KOG1924 RhoA GTPase effector D 83.1 5.9 0.00013 45.2 9.1 7 13-19 459-465 (1102)
6 KOG2652 RNA polymerase II tran 81.6 2 4.3E-05 44.4 4.5 90 232-348 211-300 (348)
7 PF09211 DUF1958: Domain of un 74.4 3.3 7.2E-05 33.6 2.9 29 368-396 23-52 (65)
8 COG5013 NarG Nitrate reductase 65.3 4 8.6E-05 47.2 2.2 27 367-393 41-75 (1227)
9 PF09026 CENP-B_dimeris: Centr 58.5 2.8 6E-05 36.7 -0.4 7 363-369 40-46 (101)
10 PF04584 Pox_A28: Poxvirus A28 46.5 9.5 0.00021 35.2 1.0 16 372-387 65-80 (140)
11 PF01690 PLRV_ORF5: Potato lea 44.8 18 0.0004 38.8 2.9 8 240-247 220-227 (465)
12 KOG0943 Predicted ubiquitin-pr 42.9 41 0.00089 40.9 5.4 10 68-77 1380-1389(3015)
13 KOG0307 Vesicle coat complex C 33.9 9.1E+02 0.02 29.1 15.2 46 7-52 634-681 (1049)
14 PF04931 DNA_pol_phi: DNA poly 31.0 31 0.00068 38.4 2.2 13 7-19 350-362 (784)
15 PF12139 APS-reductase_C: Aden 31.0 34 0.00074 29.2 1.9 16 379-398 25-40 (83)
16 KOG1832 HIV-1 Vpr-binding prot 30.7 26 0.00057 41.1 1.5 37 7-51 835-871 (1516)
17 PF03153 TFIIA: Transcription 30.3 35 0.00076 34.2 2.2 18 375-393 330-347 (375)
18 KOG0119 Splicing factor 1/bran 25.2 1E+03 0.022 26.7 12.1 12 140-151 495-506 (554)
19 PHA03378 EBNA-3B; Provisional 24.5 6.2E+02 0.013 29.6 10.4 13 232-244 856-868 (991)
20 PTZ00486 apyrase Superfamily; 23.5 76 0.0016 33.2 3.2 29 365-393 60-90 (352)
21 PRK09719 hypothetical protein; 23.5 24 0.00051 29.7 -0.3 12 365-376 57-68 (89)
22 PHA03247 large tegument protei 21.5 1.8E+03 0.038 30.0 14.2 13 186-198 2965-2977(3151)
23 KOG1984 Vesicle coat complex C 21.2 1.5E+03 0.032 27.2 13.9 28 365-392 347-374 (1007)
24 KOG0943 Predicted ubiquitin-pr 20.9 54 0.0012 40.0 1.7 16 285-300 1699-1714(3015)
25 PF14480 DNA_pol3_a_NI: DNA po 20.2 72 0.0016 24.8 1.8 13 372-384 31-43 (76)
26 PF01473 CW_binding_1: Putativ 20.1 1.3E+02 0.0029 18.2 2.6 18 385-403 1-18 (19)
27 PF03115 Astro_capsid: Astrovi 20.0 35 0.00075 38.9 0.0 20 6-25 319-338 (787)
No 1
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=100.00 E-value=9.7e-70 Score=531.45 Aligned_cols=333 Identities=35% Similarity=0.559 Sum_probs=264.6
Q ss_pred CCCcchhhhhHHHHHHHHHHhHHHhhhCCCChhHHHHHHHHHHHHHHHhccc-ccCCCCCCC-CCCCCCCCCcccCCCCC
Q 015442 1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI-IDRTSAPKQ-PAPGGPITPVHDLNVPY 78 (406)
Q Consensus 1 MsNs~V~~VY~sVIeDVIn~vReDFed~GVDEsVLqELK~lWq~KLsqsgva-~~~~~a~~~-~~p~g~~~pvhdlnvpy 78 (406)
|+++.|++||++||+|||+.||++|+++||||+||+|||++||.||+|+||+ ++|.....+ |.++. +.| ++||
T Consensus 2 ~~~~~v~kvY~~VIeDVI~~vRe~F~~~GiDeqvL~eLk~lWe~Kl~qs~~~~~~~d~~s~~~p~~~~---q~~--~~~~ 76 (348)
T KOG2652|consen 2 ASTNTVSKVYESVIEDVINNVREDFLENGIDEQVLSELKNLWETKLIQSGVATFPWDRESNQRPPPGV---QLH--HVPL 76 (348)
T ss_pred CcccchHHHHHHHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHhhcccccCcccccccCCCCcc---ccc--Cccc
Confidence 6788999999999999999999999999999999999999999999999999 666544444 23333 444 8999
Q ss_pred CC-CCCCcCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCccCCCCCCCCCC--CCCCCCCCCc
Q 015442 79 EG-TEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPG-TADNSTYNIPTGSSDYPT--PASDSGGNTE 154 (406)
Q Consensus 79 e~-teey~tptAeilfPpTpl~t~~~tplP~~~~~~~~~~~p~~~~~~g-~~~~~~y~~ptg~~~~p~--~~~~~g~~~~ 154 (406)
++ |++|+||+ +||.++.+++..+++| | .++.+||||+.+.+.+++ |......|.
T Consensus 77 ~~~~~~~~~Pa---~~~~~~q~~~~~~~l~------------------~~~~~~s~~~i~~~~t~~~~~~P~~q~~~N~- 134 (348)
T KOG2652|consen 77 QSATANLATPA---VFPGAPQQTPAGVPLP------------------GLSGHLSKANIPLPSTATNGQHPSQQVNVNS- 134 (348)
T ss_pred ccccccccCCc---cccccccccCcCccCc------------------cccccccccCccccccccCCcCccccccccc-
Confidence 88 79998888 8999999998888887 7 678999999999999975 444444444
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCCCcccccchhcccc-----cccccCCCCCCcchhhhccccccccCcCCCCCCCCCC
Q 015442 155 AKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR-----DEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGG 229 (406)
Q Consensus 155 ~K~~~g~p~p~m~~~psp~~~q~~~l~vdvnvay~~~r-----~~~~~~~s~~~ltqd~~~~~sGkrkr~~~~~~~~~gg 229 (406)
-++.|+|+| .|.|++.|.- +.|+-+| .+..+++.+++.||+.|.-|+| |+++.-.+|.+++
T Consensus 135 -----~q~~p~~~p-~s~~~~~q~s------~~~v~~~~~ip~~~p~~~~~~~~~tqq~~~~~~g--~~pq~~~~~~~~~ 200 (348)
T KOG2652|consen 135 -----TQPVPALSP-WSLQLNTQKS------QQTVLQQSAIPPSGPVDGNHNQPVTQQILVPPGG--KSPQSSFHYINLN 200 (348)
T ss_pred -----cCCCcCcCc-cccccccccc------cccccccccccccCcccccccCccccccccCCCC--CCcccccceeccC
Confidence 266688988 9999986665 4489999 8899999999999998866766 8888888888887
Q ss_pred CCCcCCCCCCCccchhhhhhhcCCCCcccchhhhhhhhhhhhhcccccccccCCCCCCCCCCcCCCCCccccCccccccc
Q 015442 230 YNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDY 309 (406)
Q Consensus 230 y~~~QqDGa~D~~~e~~~~ev~~~~~~~~~~~~~~r~~~~~~~~~~~~ipQlDG~~~~P~dd~~s~~n~~~~~g~~~Edy 309 (406)
|+|.+|+++.+.+... ..++.+....|.....+..+..+|.|++|.+.. ....+|+-+.+ .||=
T Consensus 201 --~~q~~~s~nd~~~~~~-------~~~a~~~~~~~~~~~~~~s~~~~i~qv~~~~~~-----~~Q~Dg~~~~~--eE~e 264 (348)
T KOG2652|consen 201 --IPQVDGSENDVEQIDG-------TDLAIHILKDRMVPRDSVSEKDKIAQVDLSLRK-----ILQVDGTGDTS--EEDE 264 (348)
T ss_pred --Cccccccccccccccc-------ccccccccccccccccccchhhhhhhhcccccc-----eeecccccccc--cccc
Confidence 8999999988877655 124566667776666666777788888887764 55677777775 4433
Q ss_pred cccCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC--CCcccccCCCC-CCCCeEEEEeeeeeecCCceeEEeece
Q 015442 310 NIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDD--ELDDVDQGEEL-NTQHLVLAQFDKVTRTKSRWKCALKDG 386 (406)
Q Consensus 310 n~~~~pap~~~~~~tp~~~~q~d~~~~~eEdpLNsdDDd--d~~D~d~~ed~-~t~NvvlCqydKV~R~KnKWKc~LKdG 386 (406)
|+-.+ .+ ...+++|+.+|+|||| ++++++.++|. +|+||||||||||+|+||||||+||||
T Consensus 265 ~Eee~---------------~~-~~~~~dee~~n~Dd~D~~EeeplnsedDvsdt~nvVvCqyDKV~RsKnKWKc~LKDG 328 (348)
T KOG2652|consen 265 NEEED---------------DD-PDPDEDEELGNSDDDDGVEEEPLNSEDDVSDTQNVVVCQYDKVNRSKNKWKCYLKDG 328 (348)
T ss_pred ccccc---------------cC-cccchhhhcccccccCccccccccCcccccccceeEEEeeeeeccccceeeEEeecc
Confidence 33000 11 1133566677777655 56666666666 489999999999999999999999999
Q ss_pred eeEeCCeeeeeecccccccC
Q 015442 387 IMHINNKDILFNKATGEFDF 406 (406)
Q Consensus 387 Im~ingkDyvF~Ka~GEfE~ 406 (406)
|||||||||||+||+|||||
T Consensus 329 IM~ingkDY~F~KA~GeaEW 348 (348)
T KOG2652|consen 329 VMHINGKDYVFQKAQGEAEW 348 (348)
T ss_pred eEEeCCceeEeeecccccCC
Confidence 99999999999999999999
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=2.5e-65 Score=496.29 Aligned_cols=324 Identities=31% Similarity=0.489 Sum_probs=92.3
Q ss_pred hhhHHHHHHHHHHhHHHhhhCCCChhHHHHHHHHHHHHHHHhccc-ccCCCCCCCCCCCCCCCCcccCCCCCCCCCCCcC
Q 015442 8 MVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI-IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYET 86 (406)
Q Consensus 8 ~VY~sVIeDVIn~vReDFed~GVDEsVLqELK~lWq~KLsqsgva-~~~~~a~~~~~p~g~~~pvhdlnvpye~teey~t 86 (406)
|||++||+|||++||+||+++||||+||+|||++||+||+++||+ ++|++.+.++.+ +.+ ++.+
T Consensus 1 kvY~~VI~dVI~~vr~dF~~~Gvde~vL~eLk~~We~KL~qs~v~~~~~d~~~~~~~~-----~~~-~p~~--------- 65 (375)
T PF03153_consen 1 KVYESVIDDVINNVREDFEEEGVDEQVLQELKQLWESKLSQSGVADFPWDPPPAPPPP-----PPQ-QPQP--------- 65 (375)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH-SS--TTGGGG---------------------------
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCccCCCCcccCCCcc-----ccc-CCCC---------
Confidence 799999999999999999999999999999999999999999999 999877654221 111 1211
Q ss_pred CcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCC-CCCCCCCCCccccCCCCCCCC
Q 015442 87 PTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPT-PASDSGGNTEAKSGNGRPSSY 165 (406)
Q Consensus 87 ptAeilfPpTpl~t~~~tplP~~~~~~~~~~~p~~~~~~g~~~~~~y~~ptg~~~~p~-~~~~~g~~~~~K~~~g~p~p~ 165 (406)
.+.||+++.+++ +.+++.++ ....+|+++++.+.+.. +....... +. +++.+.
T Consensus 66 ---~~~~~~~~~~~~-~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~---~~--~~~~~i 119 (375)
T PF03153_consen 66 ---PQSTPPSPSQQP-QAPQAIPQ-----------------GQSQQQNQPSSMSNSNPPATFSTPPG---QV--PAPPTI 119 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ---cccCCCCCCCCc-ccccccCC-----------------CCccccccccccCcCCCcccccCCCc---cc--CCCCCc
Confidence 155666666555 44443222 22223334433332211 11100000 11 233344
Q ss_pred CCCCCCCCCCCCCCCcccccchhcccccccccCCCCCCcchhhhcccccccc-----------CcCCCCCCCCCC-CCCc
Q 015442 166 MPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRK-----------REDFPAQYHNGG-YNIP 233 (406)
Q Consensus 166 m~~~psp~~~q~~~l~vdvnvay~~~r~~~~~~~s~~~ltqd~~~~~sGkrk-----------r~~~~~~~~~gg-y~~~ 233 (406)
|++ |..|+..+.+..+..+..+..++-..++..+.++|.+.|+.+.+.+++ +.....++..|. ++++
T Consensus 120 q~~-pG~~~~~~~P~~~~~~~~~~~~~~~~aqq~~~qq~~q~~g~~aa~q~~~~~qq~q~~~~~~~~~~~~~~~~~~~~~ 198 (375)
T PF03153_consen 120 QQP-PGQQYQVQVPSMNNQPPGNQQIAQQPAQQRAAQQLQQPYGQPAAQQISQQQQQQQPQQQQQQQQQQQQPGQQVQQQ 198 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCC-CccccCcccCCccCCcccccccccccccccccccccccccccccccCCccccccccccccccccccccCCCccCCC
Confidence 444 566666666666667777778888888888999999999988888887 344445555554 4679
Q ss_pred CCCCCCCccchhhhhhhcCCCCcccchhhhhh---hhhhhhhccc----------------------------------c
Q 015442 234 QQDGAGDAMSEIFELEVSEFPGRQDSVTTANR---EIFANLASSS----------------------------------V 276 (406)
Q Consensus 234 QqDGa~D~~~e~~~~ev~~~~~~~~~~~~~~r---~~~~~~~~~~----------------------------------~ 276 (406)
|+||++|....... ++++++.. .-.++++++. .
T Consensus 199 Qtdga~d~~~~~~~----------~~~~~~~~~~~~~~d~~L~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 268 (375)
T PF03153_consen 199 QTDGAGDSESNSQP----------RRLEAAVPLQRNEIDQVLRSQIENRAMQLEGGGLMSPLSQASKASKQNKSSNSESS 268 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCCCCcccchhc----------cccccccccccccccccccccccccccccchhhccchhhccccccccccccccccc
Confidence 99999998622111 11111111 0001111111 2
Q ss_pred cccccCCCCCCCCCCcCCCCCccccCccccccccccCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCcccccC
Q 015442 277 KIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDDELDDVDQG 356 (406)
Q Consensus 277 ~ipQlDG~~~~P~dd~~s~~n~~~~~g~~~Edyn~~~~pap~~~~~~tp~~~~q~d~~~~~eEdpLNsdDDdd~~D~d~~ 356 (406)
+|+|+||+..+..+|... +.....||+.... ...+..+..+||+|||+|| ++|+|.+
T Consensus 269 ~~~Q~DG~~d~~~~e~~~------~~~~~d~d~~~~~---------------~~~~~~~~~~~~~~~~~dd--~~~~~~~ 325 (375)
T PF03153_consen 269 RIPQLDGAGDDSDDEEDD------DDDDDDEDDEDKD---------------KDEDDEDAINSDLDDSDDD--VSDEDDE 325 (375)
T ss_dssp --------------------------------------------------------------------------B-----
T ss_pred ccccccCCCCCccccccc------ccccccccccccc---------------ccccccccccCCcCCcccc--ccccccc
Confidence 577777766554333221 2223344440000 0000111233444444433 2234445
Q ss_pred CCCCCCCeEEEEeeeeeecCCceeEEeeceeeEeCCeeeeeecccccccC
Q 015442 357 EELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 406 (406)
Q Consensus 357 ed~~t~NvvlCqydKV~R~KnKWKc~LKdGIm~ingkDyvF~Ka~GEfE~ 406 (406)
++++++|||||+||||+|+||||||+|||||||||||||||+||+|||||
T Consensus 326 ~~~~~~~~~~c~~~kv~r~k~~wk~~lk~g~~~~~~~d~~f~~~~ge~~w 375 (375)
T PF03153_consen 326 DDFDTDNVVLCQYDKVTRVKNKWKCTLKDGIMHINGKDYVFQKATGEFEW 375 (375)
T ss_dssp --STTS-EEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEE-
T ss_pred cccCcCCEEEEEeeccccccceeEEEeeeeEEEECCeEEEEeeeeeeecC
Confidence 57799999999999999999999999999999999999999999999999
No 3
>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]
Probab=100.00 E-value=4.9e-40 Score=311.75 Aligned_cols=58 Identities=38% Similarity=0.644 Sum_probs=57.0
Q ss_pred CCCcchhhhhHHHHHHHHHHhHHHhhhCCCChhHHHHHHHHHHHHHHHhccc-ccCCCC
Q 015442 1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI-IDRTSA 58 (406)
Q Consensus 1 MsNs~V~~VY~sVIeDVIn~vReDFed~GVDEsVLqELK~lWq~KLsqsgva-~~~~~a 58 (406)
|||+.|+.||++||.+||+.||+|||++|||+++|+|||.+||+||.++.|+ |+|+.+
T Consensus 1 msns~~~~vy~~vi~~vi~~~r~dfe~~gvdd~tlrelqnlwq~kl~~t~vatf~w~~~ 59 (293)
T COG5149 1 MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFPWAQA 59 (293)
T ss_pred CCcchhhHHHHHHHHHHHHHhhhHHHhcCccHHHHHHHHHHHHHhhhhheeeecchhhc
Confidence 9999999999999999999999999999999999999999999999999999 999876
No 4
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=93.32 E-value=1.3 Score=50.22 Aligned_cols=14 Identities=36% Similarity=0.686 Sum_probs=7.8
Q ss_pred hhhHHHHHHHHHHh
Q 015442 8 MVYIRVIEDVISKV 21 (406)
Q Consensus 8 ~VY~sVIeDVIn~v 21 (406)
.-|-.+||+.|+.+
T Consensus 422 pqYykLIEecISqI 435 (1102)
T KOG1924|consen 422 PQYYKLIEECISQI 435 (1102)
T ss_pred HHHHHHHHHHHHHH
Confidence 34555666666554
No 5
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=83.07 E-value=5.9 Score=45.25 Aligned_cols=7 Identities=14% Similarity=0.676 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 015442 13 VIEDVIS 19 (406)
Q Consensus 13 VIeDVIn 19 (406)
+|+..|+
T Consensus 459 liD~~vd 465 (1102)
T KOG1924|consen 459 LIDKMVD 465 (1102)
T ss_pred HHHHHHH
Confidence 3444433
No 6
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=81.55 E-value=2 Score=44.36 Aligned_cols=90 Identities=24% Similarity=0.289 Sum_probs=45.3
Q ss_pred CcCCCCCCCccchhhhhhhcCCCCcccchhhhhhhhhhhhhcccccccccCCCCCCCCCCcCCCCCccccCccccccccc
Q 015442 232 IPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNI 311 (406)
Q Consensus 232 ~~QqDGa~D~~~e~~~~ev~~~~~~~~~~~~~~r~~~~~~~~~~~~ipQlDG~~~~P~dd~~s~~n~~~~~g~~~Edyn~ 311 (406)
++|.+|+.=++...+..-+. +.+. +.+..-.++..+..+|.|+||.+..= +|. .|- .|+++.
T Consensus 211 ~~~~~~~~~a~~~~~~~~~~------~~~~-s~~~~i~qv~~~~~~~~Q~Dg~~~~~-eE~---e~E-------ee~~~~ 272 (348)
T KOG2652|consen 211 VEQIDGTDLAIHILKDRMVP------RDSV-SEKDKIAQVDLSLRKILQVDGTGDTS-EED---ENE-------EEDDDP 272 (348)
T ss_pred cccccccccccccccccccc------cccc-chhhhhhhhcccccceeecccccccc-ccc---ccc-------ccccCc
Confidence 67778744444444432222 2222 22322345555666799999966542 332 121 344554
Q ss_pred cCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 015442 312 VNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDD 348 (406)
Q Consensus 312 ~~~pap~~~~~~tp~~~~q~d~~~~~eEdpLNsdDDd 348 (406)
-.+..- .....|.+|.+|||+|||+||.
T Consensus 273 ~~~~de---------e~~n~Dd~D~~EeeplnsedDv 300 (348)
T KOG2652|consen 273 DPDEDE---------ELGNSDDDDGVEEEPLNSEDDV 300 (348)
T ss_pred ccchhh---------hcccccccCccccccccCcccc
Confidence 444431 1112233333599999999963
No 7
>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=74.42 E-value=3.3 Score=33.63 Aligned_cols=29 Identities=31% Similarity=0.597 Sum_probs=21.0
Q ss_pred EeeeeeecCCceeEEeeceeeEe-CCeeee
Q 015442 368 QFDKVTRTKSRWKCALKDGIMHI-NNKDIL 396 (406)
Q Consensus 368 qydKV~R~KnKWKc~LKdGIm~i-ngkDyv 396 (406)
+||=|-+-+++|++.++||.++| +++.|+
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 58889999999999999999999 555554
No 8
>COG5013 NarG Nitrate reductase alpha subunit [Energy production and conversion]
Probab=65.34 E-value=4 Score=47.16 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=23.3
Q ss_pred EEeeeeeecC--------CceeEEeeceeeEeCCe
Q 015442 367 AQFDKVTRTK--------SRWKCALKDGIMHINNK 393 (406)
Q Consensus 367 CqydKV~R~K--------nKWKc~LKdGIm~ingk 393 (406)
-|||||-|+- +.||++.|||||+-..+
T Consensus 41 WqhDKvVRSTHGVNCTGSCSWkIYVKdGiITWEtQ 75 (1227)
T COG5013 41 WQHDKVVRSTHGVNCTGSCSWKIYVKNGLITWETQ 75 (1227)
T ss_pred hcccceeeccCCccccceeeEEEEEeCCEEEEeec
Confidence 5899999973 67999999999997765
No 9
>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=58.54 E-value=2.8 Score=36.71 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=0.5
Q ss_pred CeEEEEe
Q 015442 363 HLVLAQF 369 (406)
Q Consensus 363 NvvlCqy 369 (406)
-+.+|.|
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 4556654
No 10
>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=46.49 E-value=9.5 Score=35.17 Aligned_cols=16 Identities=25% Similarity=0.777 Sum_probs=13.2
Q ss_pred eeecCCceeEEeecee
Q 015442 372 VTRTKSRWKCALKDGI 387 (406)
Q Consensus 372 V~R~KnKWKc~LKdGI 387 (406)
|.-+|-||||.+.+++
T Consensus 65 ~~DvkqKWRCv~~~~~ 80 (140)
T PF04584_consen 65 VYDVKQKWRCVKYNNV 80 (140)
T ss_pred ccChhhceEEEeeCCe
Confidence 5568999999998865
No 11
>PF01690 PLRV_ORF5: Potato leaf roll virus readthrough protein; InterPro: IPR002929 This family consists mainly of the Potato leafroll virus (PLrV) read through protein otherwise known as the minor capsid protein. This is generated via a readthrough of open reading frame 3, the coat protein, allowing transcription of open reading frame 5 to give an extended coat protein with a large C-terminal addition or read through domain []. The read through protein is essential for the circulative aphid transmission of PLrV [] and Beet western yellows virus []. The N-terminal region of the luteovirus readthrough domain determines virus binding to Buchnera GroEL and is essential for virus persistence in the aphid [].; GO: 0019028 viral capsid
Probab=44.75 E-value=18 Score=38.85 Aligned_cols=8 Identities=25% Similarity=-0.018 Sum_probs=3.4
Q ss_pred Cccchhhh
Q 015442 240 DAMSEIFE 247 (406)
Q Consensus 240 D~~~e~~~ 247 (406)
|-..||-.
T Consensus 220 dk~mE~G~ 227 (465)
T PF01690_consen 220 DKDMEFGS 227 (465)
T ss_pred ccceeeee
Confidence 44444433
No 12
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=42.89 E-value=41 Score=40.92 Aligned_cols=10 Identities=50% Similarity=0.723 Sum_probs=7.8
Q ss_pred CCCcccCCCC
Q 015442 68 ITPVHDLNVP 77 (406)
Q Consensus 68 ~~pvhdlnvp 77 (406)
-+|-||||-|
T Consensus 1380 ~~PdHdLePP 1389 (3015)
T KOG0943|consen 1380 DMPDHDLEPP 1389 (3015)
T ss_pred CCCccCCCCc
Confidence 4689999955
No 13
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.93 E-value=9.1e+02 Score=29.09 Aligned_cols=46 Identities=15% Similarity=0.189 Sum_probs=33.9
Q ss_pred hhhhHHHHHHHHHHhHH--HhhhCCCChhHHHHHHHHHHHHHHHhccc
Q 015442 7 GMVYIRVIEDVISKVRD--EFVNNGPGESVLNELQGIWEMKMIQAGVI 52 (406)
Q Consensus 7 ~~VY~sVIeDVIn~vRe--DFed~GVDEsVLqELK~lWq~KLsqsgva 52 (406)
...|...+|+|+.-.+. -|-..+..-..|..+..-.-+-|...|..
T Consensus 634 ~~~y~~~~e~l~~~~~~l~~~~~~~~~s~~l~~~~~~yanllasQG~~ 681 (1049)
T KOG0307|consen 634 PTSYQDLAEDLMELTLKLAQFSANKTYSAGLAKKFSEYANLLASQGAL 681 (1049)
T ss_pred hHHHHHHHHHHHHHHhhhhhcccCccccHHHHHHHHHHHHHHHhcChH
Confidence 57899999999655544 36666677777777777777788888875
No 14
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.04 E-value=31 Score=38.38 Aligned_cols=13 Identities=8% Similarity=0.112 Sum_probs=5.2
Q ss_pred hhhhHHHHHHHHH
Q 015442 7 GMVYIRVIEDVIS 19 (406)
Q Consensus 7 ~~VY~sVIeDVIn 19 (406)
.++..+.+.+.|.
T Consensus 350 ~~il~~~~~~~l~ 362 (784)
T PF04931_consen 350 EQILLSLDVDGLK 362 (784)
T ss_pred HHHHhccchHHHH
Confidence 3344444444433
No 15
>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=31.01 E-value=34 Score=29.22 Aligned_cols=16 Identities=25% Similarity=0.733 Sum_probs=11.8
Q ss_pred eeEEeeceeeEeCCeeeeee
Q 015442 379 WKCALKDGIMHINNKDILFN 398 (406)
Q Consensus 379 WKc~LKdGIm~ingkDyvF~ 398 (406)
|+|+|+||.| |+|.|-
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 16
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=30.69 E-value=26 Score=41.09 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=24.9
Q ss_pred hhhhHHHHHHHHHHhHHHhhhCCCChhHHHHHHHHHHHHHHHhcc
Q 015442 7 GMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51 (406)
Q Consensus 7 ~~VY~sVIeDVIn~vReDFed~GVDEsVLqELK~lWq~KLsqsgv 51 (406)
+..|+.--+.||...++-|-. .||-.+-.+.|..++.
T Consensus 835 ~~~~~~~~~~v~~~aq~sfp~--------~elL~li~~HL~ss~L 871 (1516)
T KOG1832|consen 835 SIAYSTTQEMVTPLAQESFPS--------NELLSLIKKHLASSTL 871 (1516)
T ss_pred hhhhhhHHhhhhhhhhccCCH--------HHHHHHHHHHHhhccc
Confidence 457887788999999998876 3444444455555544
No 17
>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=30.29 E-value=35 Score=34.25 Aligned_cols=18 Identities=28% Similarity=0.484 Sum_probs=9.3
Q ss_pred cCCceeEEeeceeeEeCCe
Q 015442 375 TKSRWKCALKDGIMHINNK 393 (406)
Q Consensus 375 ~KnKWKc~LKdGIm~ingk 393 (406)
..|-=-|.+ |=|-++.+|
T Consensus 330 ~~~~~~c~~-~kv~r~k~~ 347 (375)
T PF03153_consen 330 TDNVVLCQY-DKVTRVKNK 347 (375)
T ss_dssp TS-EEEEEE-EEEEEETTE
T ss_pred cCCEEEEEe-eccccccce
Confidence 445445544 346666666
No 18
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=25.19 E-value=1e+03 Score=26.74 Aligned_cols=12 Identities=17% Similarity=0.274 Sum_probs=5.5
Q ss_pred CCCCCCCCCCCC
Q 015442 140 SDYPTPASDSGG 151 (406)
Q Consensus 140 ~~~p~~~~~~g~ 151 (406)
.--|.++..+|+
T Consensus 495 ~a~Pg~p~~~~~ 506 (554)
T KOG0119|consen 495 AAPPGAPFHGGN 506 (554)
T ss_pred cCCCCCCCCCCC
Confidence 333444455544
No 19
>PHA03378 EBNA-3B; Provisional
Probab=24.49 E-value=6.2e+02 Score=29.57 Aligned_cols=13 Identities=15% Similarity=0.314 Sum_probs=7.1
Q ss_pred CcCCCCCCCccch
Q 015442 232 IPQQDGAGDAMSE 244 (406)
Q Consensus 232 ~~QqDGa~D~~~e 244 (406)
-.-+-|.+|-++.
T Consensus 856 p~p~~gt~~~~vq 868 (991)
T PHA03378 856 PSPGSGTSDKIVQ 868 (991)
T ss_pred CCCCCCCccceee
Confidence 4445566665543
No 20
>PTZ00486 apyrase Superfamily; Provisional
Probab=23.54 E-value=76 Score=33.25 Aligned_cols=29 Identities=17% Similarity=0.546 Sum_probs=20.5
Q ss_pred EEEEeeeeee--cCCceeEEeeceeeEeCCe
Q 015442 365 VLAQFDKVTR--TKSRWKCALKDGIMHINNK 393 (406)
Q Consensus 365 vlCqydKV~R--~KnKWKc~LKdGIm~ingk 393 (406)
||+=-||-.| .+++|+++||-|.+...++
T Consensus 60 iIaDlD~~S~~~~~~~w~S~~~~G~L~~~~~ 90 (352)
T PTZ00486 60 LVADLDKASKDKEGKKWRSKVIKGTIFRQGN 90 (352)
T ss_pred EEecCchhccccCCCceEEEEEEEEEEEcCC
Confidence 4444555555 4788999999999877664
No 21
>PRK09719 hypothetical protein; Provisional
Probab=23.49 E-value=24 Score=29.73 Aligned_cols=12 Identities=33% Similarity=0.473 Sum_probs=9.7
Q ss_pred EEEEeeeeeecC
Q 015442 365 VLAQFDKVTRTK 376 (406)
Q Consensus 365 vlCqydKV~R~K 376 (406)
--|||||.+|+-
T Consensus 57 wrcqydklhrvp 68 (89)
T PRK09719 57 WRCQYDKLHRVP 68 (89)
T ss_pred hhcchhhhhccc
Confidence 469999999874
No 22
>PHA03247 large tegument protein UL36; Provisional
Probab=21.53 E-value=1.8e+03 Score=30.00 Aligned_cols=13 Identities=38% Similarity=0.240 Sum_probs=7.2
Q ss_pred chhcccccccccC
Q 015442 186 VAYVEGRDEADRG 198 (406)
Q Consensus 186 vay~~~r~~~~~~ 198 (406)
-+-++||...-|.
T Consensus 2965 ~~~~~~~~~~pR~ 2977 (3151)
T PHA03247 2965 GALVPGRVAVPRF 2977 (3151)
T ss_pred cccCcccccCccc
Confidence 4445666665554
No 23
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.17 E-value=1.5e+03 Score=27.25 Aligned_cols=28 Identities=7% Similarity=0.239 Sum_probs=23.7
Q ss_pred EEEEeeeeeecCCceeEEeeceeeEeCC
Q 015442 365 VLAQFDKVTRTKSRWKCALKDGIMHINN 392 (406)
Q Consensus 365 vlCqydKV~R~KnKWKc~LKdGIm~ing 392 (406)
-+|-|=|..-.-.||.|.|+...+.+.+
T Consensus 347 YinPFmqF~~~gr~f~Cn~C~~~n~vp~ 374 (1007)
T KOG1984|consen 347 YINPFMQFIDGGRKFICNFCGSKNQVPD 374 (1007)
T ss_pred hcCcceEEecCCceEEecCCCccccCCh
Confidence 5788888888888999999998887754
No 24
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=20.91 E-value=54 Score=40.01 Aligned_cols=16 Identities=38% Similarity=0.453 Sum_probs=8.6
Q ss_pred CCCCCCCcCCCCCccc
Q 015442 285 IPDPYDDVLSTPNIYN 300 (406)
Q Consensus 285 ~~~P~dd~~s~~n~~~ 300 (406)
+|-|---++.+-|..|
T Consensus 1699 iptprrrrllsgnttn 1714 (3015)
T KOG0943|consen 1699 IPTPRRRRLLSGNTTN 1714 (3015)
T ss_pred CCCchhhhhccCCccC
Confidence 4445555555555544
No 25
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=20.23 E-value=72 Score=24.77 Aligned_cols=13 Identities=23% Similarity=0.716 Sum_probs=11.2
Q ss_pred eeecCCceeEEee
Q 015442 372 VTRTKSRWKCALK 384 (406)
Q Consensus 372 V~R~KnKWKc~LK 384 (406)
|+|.+++|+++|+
T Consensus 31 v~k~~~~w~f~l~ 43 (76)
T PF14480_consen 31 VHKKSRKWRFHLS 43 (76)
T ss_pred EEccCCEEEEEEE
Confidence 6788899999986
No 26
>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=20.15 E-value=1.3e+02 Score=18.18 Aligned_cols=18 Identities=22% Similarity=0.328 Sum_probs=12.3
Q ss_pred ceeeEeCCeeeeeeccccc
Q 015442 385 DGIMHINNKDILFNKATGE 403 (406)
Q Consensus 385 dGIm~ingkDyvF~Ka~GE 403 (406)
+|.++++|+-|.| +..|+
T Consensus 1 n~W~~~~~~wYy~-~~~G~ 18 (19)
T PF01473_consen 1 NGWVQDNGNWYYF-DSDGY 18 (19)
T ss_dssp SEEEEETTEEEEE-TTTSB
T ss_pred CcCEEECCEEEEe-CCCcc
Confidence 3567778888887 55554
No 27
>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=20.01 E-value=35 Score=38.93 Aligned_cols=20 Identities=5% Similarity=0.169 Sum_probs=0.0
Q ss_pred hhhhhHHHHHHHHHHhHHHh
Q 015442 6 TGMVYIRVIEDVISKVRDEF 25 (406)
Q Consensus 6 V~~VY~sVIeDVIn~vReDF 25 (406)
++.+.=.|.+.++..+...|
T Consensus 319 ~~e~iw~v~~~~v~~~~~~~ 338 (787)
T PF03115_consen 319 VSETIWQVVDTAVDAAASVL 338 (787)
T ss_dssp --------------------
T ss_pred ccceEEEEccchhhhhhhcC
Confidence 44444455555555444443
Done!