Query gi|254780259|ref|YP_003064672.1| 50S ribosomal protein L23 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 110
No_of_seqs 117 out of 1550
Neff 5.4
Searched_HMMs 39220
Date Tue May 24 09:53:55 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780259.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12280 rplW 50S ribosomal pr 100.0 3.6E-36 9.3E-41 229.5 10.1 93 4-109 1-93 (160)
2 CHL00030 rpl23 ribosomal prote 100.0 4.6E-34 1.2E-38 217.3 9.7 90 7-109 1-90 (92)
3 pfam00276 Ribosomal_L23 Riboso 100.0 9.7E-33 2.5E-37 209.7 9.8 89 8-109 1-90 (90)
4 PRK05738 rplW 50S ribosomal pr 100.0 2.2E-32 5.7E-37 207.7 10.6 90 3-105 1-91 (91)
5 COG0089 RplW Ribosomal protein 100.0 4.2E-31 1.1E-35 200.3 9.8 93 6-110 1-94 (94)
6 PTZ00191 60S ribosomal protein 99.9 2.4E-22 6.2E-27 149.8 8.3 81 2-108 63-145 (150)
7 TIGR03636 L23_arch archaeal ri 99.9 1.2E-21 3E-26 145.9 8.9 70 13-108 1-72 (77)
8 KOG1751 consensus 99.7 8.9E-17 2.3E-21 117.8 6.5 82 2-109 69-153 (157)
9 KOG4089 consensus 98.0 1.4E-05 3.5E-10 53.3 5.5 77 24-107 36-113 (165)
10 cd01808 hPLIC_N hPLIC-1 and hP 78.6 4.2 0.00011 21.7 4.5 42 24-66 8-49 (71)
11 cd04929 ACT_TPH ACT domain of 70.5 6.3 0.00016 20.7 3.7 34 24-57 39-73 (74)
12 PRK01178 rps24e 30S ribosomal 56.9 18 0.00047 18.0 4.3 46 14-59 5-54 (102)
13 PRK10767 chaperone protein Dna 53.9 11 0.00028 19.3 2.5 10 1-10 1-10 (376)
14 cd04904 ACT_AAAH ACT domain of 51.4 16 0.00042 18.3 3.0 28 24-51 39-66 (74)
15 COG0484 DnaJ DnaJ-class molecu 50.4 14 0.00035 18.7 2.5 19 30-48 10-28 (371)
16 TIGR02349 DnaJ_bact chaperone 48.9 16 0.00041 18.4 2.7 20 29-48 5-24 (386)
17 TIGR02830 spore_III_AG stage I 46.2 18 0.00045 18.1 2.5 31 29-59 156-190 (193)
18 cd01812 BAG1_N BAG1_N N-termi 34.9 42 0.0011 16.0 4.1 41 25-66 9-49 (71)
19 TIGR01729 taurine_ABC_bnd taur 33.5 33 0.00084 16.6 2.3 32 34-65 111-142 (304)
20 smart00213 UBQ Ubiquitin homol 33.4 44 0.0011 15.8 4.4 39 26-65 10-48 (64)
21 pfam09439 SRPRB Signal recogni 32.7 40 0.001 16.1 2.6 28 26-53 77-104 (181)
22 cd01813 UBP_N The UBP (ubiquit 29.6 51 0.0013 15.5 4.4 37 26-62 10-46 (74)
23 TIGR02834 spo_ytxC putative sp 28.3 48 0.0012 15.6 2.4 47 3-54 236-282 (283)
24 KOG3424 consensus 23.0 68 0.0017 14.7 4.8 41 21-61 16-60 (132)
25 pfam00240 ubiquitin Ubiquitin 22.0 72 0.0018 14.6 3.8 40 25-65 5-44 (69)
26 cd04880 ACT_AAAH-PDT-like ACT 21.9 72 0.0018 14.6 2.7 28 24-51 38-67 (75)
27 PTZ00044 ubiquitin; Provisiona 21.4 74 0.0019 14.5 3.9 41 24-65 9-49 (76)
28 KOG0010 consensus 21.1 75 0.0019 14.5 3.2 40 25-65 24-63 (493)
29 cd01807 GDX_N GDX contains an 20.3 78 0.002 14.4 3.6 40 24-64 9-48 (74)
No 1
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=100.00 E-value=3.6e-36 Score=229.46 Aligned_cols=93 Identities=39% Similarity=0.540 Sum_probs=89.3
Q ss_pred CHHHHHHHHCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCC
Q ss_conf 25786760032079988886489099998887898899999999968743378998518963331122466443223454
Q gi|254780259|r 4 IRFYDTIISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRD 83 (110)
Q Consensus 4 ~~~~~vi~~P~~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~ 83 (110)
|+++|||++|++||||+.++|+|+|+|.|+++|||+||++|||.+|+|+|.+|||+|++||.||+||+.|.+
T Consensus 1 M~~~~VIk~PviTEKs~~l~e~nkYtF~V~~~AnK~eIK~AVE~iF~VkV~kVNt~nv~~K~KR~Gr~~G~~-------- 72 (160)
T PRK12280 1 MNLNEVIKYPILTEKSYQLMEKNVYTFKVDPKANKIEIKKAVEFIFNVKVEKVNIFNVDKKPKRLGRFKGFT-------- 72 (160)
T ss_pred CCHHHHHHCCCCCHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCCC--------
T ss_conf 987887451502586787887393899989989989999999998297688996243699871036335556--------
Q ss_pred CCCCCCCCEEEEEECCCCCEECCCCC
Q ss_conf 44345881389999589973133248
Q gi|254780259|r 84 MYVSRKDVKRAFVTLAKGYSIDISAG 109 (110)
Q Consensus 84 ~~~k~~~~KKAiVtL~~G~~I~~~~g 109 (110)
++||||||||++|++|+||+.
T Consensus 73 -----~~~KKAiVtL~~G~~I~lf~e 93 (160)
T PRK12280 73 -----NKYKKAYVTLAEGYKINLFEE 93 (160)
T ss_pred -----CCCEEEEEECCCCCEEEECCC
T ss_conf -----876589998589997776877
No 2
>CHL00030 rpl23 ribosomal protein L23
Probab=100.00 E-value=4.6e-34 Score=217.34 Aligned_cols=90 Identities=40% Similarity=0.535 Sum_probs=84.8
Q ss_pred HHHHHHCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 86760032079988886489099998887898899999999968743378998518963331122466443223454443
Q gi|254780259|r 7 YDTIISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDMYV 86 (110)
Q Consensus 7 ~~vi~~P~~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~~~ 86 (110)
+|+|++|++||||+.+.|+|+|+|.|+++|||+|||+|||.+|+|+|.+|||++.+||.+|+|+.. |
T Consensus 1 md~Ik~PviTEKs~~l~e~n~Y~F~V~~~a~K~eIK~aVE~~f~VkV~~Vnt~~~~gK~kr~g~~~-------------G 67 (92)
T CHL00030 1 MDGIKYPVFTDKSIRLLGKNQYTFNVDSGSTKTEIKHWIELFFGVKVIAMNSHRLPGKGRRMGPIL-------------G 67 (92)
T ss_pred CCCCCCCEECHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCEEEEEEEEECCCCCEEECCCC-------------E
T ss_conf 973233371486777777897999989999989999999987398799998187289744778944-------------4
Q ss_pred CCCCCEEEEEECCCCCEECCCCC
Q ss_conf 45881389999589973133248
Q gi|254780259|r 87 SRKDVKRAFVTLAKGYSIDISAG 109 (110)
Q Consensus 87 k~~~~KKAiVtL~~G~~I~~~~g 109 (110)
++++||||||||++|++||||++
T Consensus 68 ~~~~~KKAiVtL~~G~~I~~F~~ 90 (92)
T CHL00030 68 HTMHYKRMIITLQPGYSIPLFRK 90 (92)
T ss_pred ECCCCEEEEEEECCCCEECCCCC
T ss_conf 31798899999189798378878
No 3
>pfam00276 Ribosomal_L23 Ribosomal protein L23.
Probab=100.00 E-value=9.7e-33 Score=209.74 Aligned_cols=89 Identities=46% Similarity=0.571 Sum_probs=82.3
Q ss_pred HHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 67600320799888864-89099998887898899999999968743378998518963331122466443223454443
Q gi|254780259|r 8 DTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDMYV 86 (110)
Q Consensus 8 ~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~~~ 86 (110)
|+|++|++||||+.+.| .|+|+|.|+++|||+|||+|||.+|+|+|.+|||+|++||.+|+|+.. |
T Consensus 1 dii~~PviTEKs~~l~e~~n~y~F~V~~~anK~eIK~ave~~f~VkV~~Vnt~~~~gK~kR~g~~~-------------g 67 (90)
T pfam00276 1 DVIKYPIITEKAMNLLEKPNQYVFIVDKKANKTEIKDAVEHIFGVKVEKVNTLILPGKVKRNGQYL-------------G 67 (90)
T ss_pred CEECCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEEECCCCEEECCCC-------------E
T ss_conf 962465128888887886888999989999999999999998298678998898289735878833-------------3
Q ss_pred CCCCCEEEEEECCCCCEECCCCC
Q ss_conf 45881389999589973133248
Q gi|254780259|r 87 SRKDVKRAFVTLAKGYSIDISAG 109 (110)
Q Consensus 87 k~~~~KKAiVtL~~G~~I~~~~g 109 (110)
++++||||||||++||+||||+.
T Consensus 68 ~~~~~KKAiVtL~~g~~I~~~sk 90 (90)
T pfam00276 68 RKKSYKKAIVTLEEGDILPFASR 90 (90)
T ss_pred ECCCCEEEEEECCCCCEECCCCC
T ss_conf 04896899999289899645269
No 4
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.98 E-value=2.2e-32 Score=207.66 Aligned_cols=90 Identities=58% Similarity=0.774 Sum_probs=83.8
Q ss_pred CCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCC
Q ss_conf 5257867600320799888864-890999988878988999999999687433789985189633311224664432234
Q gi|254780259|r 3 NIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSS 81 (110)
Q Consensus 3 ~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~ 81 (110)
.|++||+|++|++||||+.+.| +|+|+|.|+++|||+|||+|||.+|+|+|.+|||+|.+||.||+++..
T Consensus 1 ~m~~~~ii~~PivTEKs~~l~e~~n~y~F~V~~~AnK~~Ik~ave~~f~VkV~~Vnt~~~~~K~kr~~~~~--------- 71 (91)
T PRK05738 1 MMRLYDVIKRPVITEKATLLMEKENKYVFKVDPDATKTEIKAAVEELFGVKVESVNTLNVKGKTKRFGRRV--------- 71 (91)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEEEECCCCEEECCCC---------
T ss_conf 95188756216237888987886887999989989999999999997199750898898389615778944---------
Q ss_pred CCCCCCCCCCEEEEEECCCCCEEC
Q ss_conf 544434588138999958997313
Q gi|254780259|r 82 RDMYVSRKDVKRAFVTLAKGYSID 105 (110)
Q Consensus 82 r~~~~k~~~~KKAiVtL~~G~~I~ 105 (110)
|++++||||||||++|++||
T Consensus 72 ----G~~~~~KKAiVtL~~G~~Id 91 (91)
T PRK05738 72 ----GKRSDWKKAYVTLAEGQSID 91 (91)
T ss_pred ----CCCCCCEEEEEEECCCCCCC
T ss_conf ----32489789999918989179
No 5
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.2e-31 Score=200.32 Aligned_cols=93 Identities=53% Similarity=0.695 Sum_probs=85.3
Q ss_pred HHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCC
Q ss_conf 7867600320799888864-890999988878988999999999687433789985189633311224664432234544
Q gi|254780259|r 6 FYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDM 84 (110)
Q Consensus 6 ~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~ 84 (110)
++|+|++|++||||+.++| +|+|+|.|+++|||+|||+|||++|+|+|.+|||+|++|+.||+++ ..
T Consensus 1 ~~dvI~~PvvTEKa~~l~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~------------k~ 68 (94)
T COG0089 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGV------------KR 68 (94)
T ss_pred CCCHHHCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEEEEECCCCEEEEC------------CC
T ss_conf 922444350058789767557879999989899799999999985987788887872896038840------------35
Q ss_pred CCCCCCCEEEEEECCCCCEECCCCCC
Q ss_conf 43458813899995899731332489
Q gi|254780259|r 85 YVSRKDVKRAFVTLAKGYSIDISAGV 110 (110)
Q Consensus 85 ~~k~~~~KKAiVtL~~G~~I~~~~gi 110 (110)
.|.+++||+|||+|++|++||+|+|.
T Consensus 69 ~G~~~~~kka~V~l~~G~~i~~~~~~ 94 (94)
T COG0089 69 IGLRKDYKKAYVTLKEGQSIDFFGGA 94 (94)
T ss_pred CCCCCCCCEEEEECCCCCEEEECCCC
T ss_conf 66376342047982689687612369
No 6
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=99.87 E-value=2.4e-22 Score=149.81 Aligned_cols=81 Identities=33% Similarity=0.523 Sum_probs=71.4
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCC
Q ss_conf 85257867600320799888864-89099998887898899999999968743378998518963331122466443223
Q gi|254780259|r 2 INIRFYDTIISPVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRS 80 (110)
Q Consensus 2 ~~~~~~~vi~~P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~ 80 (110)
+.|++|+||++|++||+|+...| +|+++|.||.+|||+|||+|||++|+|+|.+|||++.+.
T Consensus 63 ~klD~y~IIk~PltTEkAmkkiEd~NtLvFiVd~kAnK~qIK~AVekLydV~V~kVNTli~p~----------------- 125 (150)
T PTZ00191 63 KKLDKFNIIRYPLTTEKAMKKIEENNTLVFIVDSRANKTQIKKAVSKLYEVKVVKVNTLITPD----------------- 125 (150)
T ss_pred CCCCCCEEEECCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEECEEEEEECCC-----------------
T ss_conf 788730255157568899999986587999978858989999999998398106686558689-----------------
Q ss_pred CCCCCCCCCCCEEEEEECCCCC-EECCCC
Q ss_conf 4544434588138999958997-313324
Q gi|254780259|r 81 SRDMYVSRKDVKRAFVTLAKGY-SIDISA 108 (110)
Q Consensus 81 ~r~~~~k~~~~KKAiVtL~~G~-~I~~~~ 108 (110)
+-|||||+|.+++ -+|+..
T Consensus 126 ---------G~KKAyV~L~~d~dAlDvAn 145 (150)
T PTZ00191 126 ---------GLKKAYIRLSPDHDALDVAN 145 (150)
T ss_pred ---------CCEEEEEECCCCCCHHHHHH
T ss_conf ---------97789997799998999988
No 7
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=99.86 E-value=1.2e-21 Score=145.86 Aligned_cols=70 Identities=43% Similarity=0.672 Sum_probs=63.0
Q ss_pred CCCCHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 320799888864-8909999888789889999999996874337899851896333112246644322345444345881
Q gi|254780259|r 13 PVIAEKSTLLAG-QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDMYVSRKDV 91 (110)
Q Consensus 13 P~~TEKs~~~~e-~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~~~k~~~~ 91 (110)
|++||||+.+.| +|+|+|.|+++|||+|||+|||++|+|+|.+|||++.+ .+|
T Consensus 1 P~iTEKa~~~~e~~N~~~F~V~~~AnK~eIK~AVE~lf~VkV~~VnT~~~~--------------------------~g~ 54 (77)
T TIGR03636 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP--------------------------RGE 54 (77)
T ss_pred CCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCEECEEEEEECC--------------------------CCC
T ss_conf 924789999898689799998897998999999999819852579844868--------------------------997
Q ss_pred EEEEEECCCCC-EECCCC
Q ss_conf 38999958997-313324
Q gi|254780259|r 92 KRAFVTLAKGY-SIDISA 108 (110)
Q Consensus 92 KKAiVtL~~G~-~I~~~~ 108 (110)
|||||+|++|+ .+|+.+
T Consensus 55 KKAyV~L~~~~~A~dva~ 72 (77)
T TIGR03636 55 KKAYVKLAEEYAAEEIAS 72 (77)
T ss_pred EEEEEECCCCCCHHHHHH
T ss_conf 789998599997999998
No 8
>KOG1751 consensus
Probab=99.67 E-value=8.9e-17 Score=117.77 Aligned_cols=82 Identities=34% Similarity=0.553 Sum_probs=68.8
Q ss_pred CCCHHHHH-HHHCCCCHHHHH-HHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCC
Q ss_conf 85257867-600320799888-8648909999888789889999999996874337899851896333112246644322
Q gi|254780259|r 2 INIRFYDT-IISPVIAEKSTL-LAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVR 79 (110)
Q Consensus 2 ~~~~~~~v-i~~P~~TEKs~~-~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~ 79 (110)
+++++|.+ |+.|+.||+++. .+++|+++|.||..|||+|||+||.+||+++|.+||||+.|
T Consensus 69 ~kld~y~~iIk~plTtEsamKk~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p----------------- 131 (157)
T KOG1751 69 PKLDHYAIIIKFPLTTESAMKKIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRP----------------- 131 (157)
T ss_pred CCCCCHHHHHCCCCCHHHHHCCHHHCCEEEEEEECCCCHHHHHHHHHHHCCCCHHHHEEEECC-----------------
T ss_conf 752005666507440033223550286579998335674899999999715630341244467-----------------
Q ss_pred CCCCCCCCCCCCEEEEEECCCCC-EECCCCC
Q ss_conf 34544434588138999958997-3133248
Q gi|254780259|r 80 SSRDMYVSRKDVKRAFVTLAKGY-SIDISAG 109 (110)
Q Consensus 80 ~~r~~~~k~~~~KKAiVtL~~G~-~I~~~~g 109 (110)
.+-|||||.|++++ -+|+.-+
T Consensus 132 ---------~g~kkAyv~la~dydaldvank 153 (157)
T KOG1751 132 ---------DGEKKAYVRLAPDYDALDVANK 153 (157)
T ss_pred ---------CCCEEEEEECCCCHHHHHHHCC
T ss_conf ---------8754678861883458987302
No 9
>KOG4089 consensus
Probab=97.99 E-value=1.4e-05 Score=53.29 Aligned_cols=77 Identities=19% Similarity=0.326 Sum_probs=59.4
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCC-CCEEEEEECCCCC
Q ss_conf 489099998887898899999999968743378998518963331122466443223454443458-8138999958997
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLSRISAARSRVRSSRDMYVSRK-DVKRAFVTLAKGY 102 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~Kr~~r~~g~k~~~~~~r~~~~k~~-~~KKAiVtL~~G~ 102 (110)
-.+...|.|+...||.+++++++.+|+.+|.+|.|..+-||.- +.++.+-......... +++-|||.++.|+
T Consensus 36 ~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~-------~~~k~r~~~~k~i~kdmd~p~~Yv~~pr~~ 108 (165)
T KOG4089 36 PPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDY-------KKTKKRLQSPKRIKKDMDEPVAYVEEPRGS 108 (165)
T ss_pred CCCEEEEECCHHHCCCCHHHHHHHHCCCCEEEEEEEEEECHHH-------HCCEECCCCCCEEECCCCCCEEEECCCCCC
T ss_conf 9851799716465221399999886488233112002204044-------304312456602302445642431378775
Q ss_pred EECCC
Q ss_conf 31332
Q gi|254780259|r 103 SIDIS 107 (110)
Q Consensus 103 ~I~~~ 107 (110)
+.-+-
T Consensus 109 ~~~~P 113 (165)
T KOG4089 109 KFSFP 113 (165)
T ss_pred CCCCC
T ss_conf 34577
No 10
>cd01808 hPLIC_N hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=78.61 E-value=4.2 Score=21.74 Aligned_cols=42 Identities=24% Similarity=0.336 Sum_probs=34.9
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE
Q ss_conf 4890999988878988999999999687433789985189633
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110)
.+++++|.|+++++=.|.|+.+.+-|++.+...+ |+..||.=
T Consensus 8 ~~~k~~i~v~~~~tV~~lKe~ia~~~~~~~~~qr-LIf~GkiL 49 (71)
T cd01808 8 PKDKEEIEIAEDASVKDFKEAVSKKFKANQEQLV-LIFAGKIL 49 (71)
T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEE-EEECCEEE
T ss_conf 9963899989999799999999988199968889-99878583
No 11
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=70.46 E-value=6.3 Score=20.69 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=27.1
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHH-CCCEEEEE
Q ss_conf 48909999888789889999999996-87433789
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALF-SVKVVSVN 57 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f-~V~V~~Vn 57 (110)
...+|.|.||.+.++..+.+|++.|= .+...+||
T Consensus 39 ~~~~Y~ffvD~e~~~~~l~~~l~~Lk~~~~~vkv~ 73 (74)
T cd04929 39 RSSEFEIFVDCECDQRRLDELVQLLKREVASVNMN 73 (74)
T ss_pred CCCEEEEEEEECCCHHHHHHHHHHHHHHCEEEEEC
T ss_conf 89718999990399799999999999852099714
No 12
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=56.90 E-value=18 Score=18.02 Aligned_cols=46 Identities=22% Similarity=0.361 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHCCEEEEEEC----CCCCHHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 20799888864890999988----87898899999999968743378998
Q gi|254780259|r 14 VIAEKSTLLAGQNQVVFNVK----KDSSKSEIKSAVEALFSVKVVSVNTL 59 (110)
Q Consensus 14 ~~TEKs~~~~e~n~y~F~V~----~~atK~eIK~ave~~f~V~V~~Vnt~ 59 (110)
++.++-..|+.-.++.|.|. +..++.+|+..+..+|++++.-|=+-
T Consensus 5 I~~~k~N~LL~R~Ei~~~v~h~g~~Tpsr~ei~~kla~~~~~~~~~vvv~ 54 (102)
T PRK01178 5 IIEDKENPLLNRREIKFKVKHEGSATPSRKDVKKKLAAMLNADKELVVVD 54 (102)
T ss_pred EEECCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf 88635587747689999997089999899999999999878898879997
No 13
>PRK10767 chaperone protein DnaJ; Provisional
Probab=53.86 E-value=11 Score=19.29 Aligned_cols=10 Identities=20% Similarity=0.664 Sum_probs=5.0
Q ss_pred CCCCHHHHHH
Q ss_conf 9852578676
Q gi|254780259|r 1 MINIRFYDTI 10 (110)
Q Consensus 1 m~~~~~~~vi 10 (110)
|+.-+||+||
T Consensus 1 ma~kDyY~iL 10 (376)
T PRK10767 1 MAKQDYYEIL 10 (376)
T ss_pred CCCCCCHHHC
T ss_conf 9978818871
No 14
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=51.39 E-value=16 Score=18.32 Aligned_cols=28 Identities=14% Similarity=0.272 Sum_probs=24.3
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf 4890999988878988999999999687
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSV 51 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V 51 (110)
....|.|.||...+..++++|++.+=.+
T Consensus 39 ~~~~y~FfvD~eg~~~~i~~al~~Lk~~ 66 (74)
T cd04904 39 NGSEYEFFVDCEVDRGDLDQLISSLRRV 66 (74)
T ss_pred CCCCEEEEEEEECCHHHHHHHHHHHHHH
T ss_conf 9975999999608989999999999974
No 15
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=50.41 E-value=14 Score=18.72 Aligned_cols=19 Identities=47% Similarity=0.609 Sum_probs=9.6
Q ss_pred EEECCCCCHHHHHHHHHHH
Q ss_conf 9988878988999999999
Q gi|254780259|r 30 FNVKKDSSKSEIKSAVEAL 48 (110)
Q Consensus 30 F~V~~~atK~eIK~ave~~ 48 (110)
+-|+.+|+..|||+|..+|
T Consensus 10 LGV~k~As~~EIKkAYRKL 28 (371)
T COG0484 10 LGVSKDASEEEIKKAYRKL 28 (371)
T ss_pred CCCCCCCCHHHHHHHHHHH
T ss_conf 0988899999999999999
No 16
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=48.88 E-value=16 Score=18.36 Aligned_cols=20 Identities=45% Similarity=0.630 Sum_probs=17.4
Q ss_pred EEEECCCCCHHHHHHHHHHH
Q ss_conf 99988878988999999999
Q gi|254780259|r 29 VFNVKKDSSKSEIKSAVEAL 48 (110)
Q Consensus 29 ~F~V~~~atK~eIK~ave~~ 48 (110)
+.-|+.+||.-|||+|-.+|
T Consensus 5 iLGVsK~A~~~EIKKAYRkL 24 (386)
T TIGR02349 5 ILGVSKDASEEEIKKAYRKL 24 (386)
T ss_pred EECCCCCCCHHHHHHHHHHH
T ss_conf 62427998989999999988
No 17
>TIGR02830 spore_III_AG stage III sporulation protein AG; InterPro: IPR014195 This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species..
Probab=46.19 E-value=18 Score=18.13 Aligned_cols=31 Identities=32% Similarity=0.412 Sum_probs=25.1
Q ss_pred EEEECCCCC----HHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 999888789----8899999999968743378998
Q gi|254780259|r 29 VFNVKKDSS----KSEIKSAVEALFSVKVVSVNTL 59 (110)
Q Consensus 29 ~F~V~~~at----K~eIK~ave~~f~V~V~~Vnt~ 59 (110)
|+.|+-.|. |.+|.+||-.+|+|..-+|+++
T Consensus 156 VlVVAeGA~n~~iK~~i~~AV~~~L~vP~hkV~V~ 190 (193)
T TIGR02830 156 VLVVAEGAENVQIKAEIVEAVSRVLDVPAHKVSVL 190 (193)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHHHCCCCHHEEEC
T ss_conf 89997748898999999999999865960034621
No 18
>cd01812 BAG1_N BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=34.91 E-value=42 Score=15.97 Aligned_cols=41 Identities=15% Similarity=0.214 Sum_probs=34.4
Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCEE
Q ss_conf 890999988878988999999999687433789985189633
Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVK 66 (110)
Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~K 66 (110)
.++|.+.|++++|=.+.|+.++...||.+..-+. +.+||..
T Consensus 9 ~~~~~v~v~~~~Tv~~lK~~l~~~tgvpp~~QrL-IfkGK~l 49 (71)
T cd01812 9 GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKL-IFKGKER 49 (71)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHHCCCCHHCEE-EECCCCC
T ss_conf 9889999899883999999999988889247189-9898175
No 19
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein; InterPro: IPR010068 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulphonates, and sulphate esters import sulphur when sulphate levels are low. The most closely related proteins outside this family are putative aliphatic sulphonate binding proteins..
Probab=33.49 E-value=33 Score=16.56 Aligned_cols=32 Identities=16% Similarity=0.158 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE
Q ss_conf 87898899999999968743378998518963
Q gi|254780259|r 34 KDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110)
Q Consensus 34 ~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110)
...|-...=.|+|..-++++..||++|++|..
T Consensus 111 vSTtHysLLaaLk~vw~~dp~~V~IlNl~PP~ 142 (304)
T TIGR01729 111 VSTTHYSLLAALKHVWKVDPKEVEILNLKPPE 142 (304)
T ss_pred CCHHHHHHHHHHHHHHCCCCCEEEEEECCCHH
T ss_conf 11345899998887626787605786179657
No 20
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=33.39 E-value=44 Score=15.83 Aligned_cols=39 Identities=33% Similarity=0.473 Sum_probs=31.6
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE
Q ss_conf 9099998887898899999999968743378998518963
Q gi|254780259|r 26 NQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110)
Q Consensus 26 n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110)
+.+.+.|++..|=.++|+.++...++.+..- -+...|+.
T Consensus 10 ~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q-~Li~~Gk~ 48 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQ-RLIYKGKV 48 (64)
T ss_pred CEEEEEECCCCHHHHHHHHHHHHHCCCHHHE-EEEECCEE
T ss_conf 8399998997939999999999879596898-99989949
No 21
>pfam09439 SRPRB Signal recognition particle receptor beta subunit. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.
Probab=32.68 E-value=40 Score=16.10 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=24.4
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCE
Q ss_conf 9099998887898899999999968743
Q gi|254780259|r 26 NQVVFNVKKDSSKSEIKSAVEALFSVKV 53 (110)
Q Consensus 26 n~y~F~V~~~atK~eIK~ave~~f~V~V 53 (110)
.-++|.||..+...+++.+-|.||++=.
T Consensus 77 ~gIVfVVDS~~~~~~l~~~Ae~Ly~iL~ 104 (181)
T pfam09439 77 RGLVFVVDSTAFPKEVTDTAEFLYDILS 104 (181)
T ss_pred EEEEEEEECCCCHHHHHHHHHHHHHHHH
T ss_conf 4999999786656679999999999984
No 22
>cd01813 UBP_N The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=29.60 E-value=51 Score=15.45 Aligned_cols=37 Identities=14% Similarity=0.087 Sum_probs=34.2
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECC
Q ss_conf 9099998887898899999999968743378998518
Q gi|254780259|r 26 NQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRK 62 (110)
Q Consensus 26 n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~ 62 (110)
+.|...|+.++|=.+.|+.++++=+|.|.+--.++.+
T Consensus 10 k~y~v~v~~~~tv~~LK~~i~~lT~V~PeRQKlLglk 46 (74)
T cd01813 10 QEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLK 46 (74)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHHCCCCHHEEEECCC
T ss_conf 8887785798889999999999878994243763202
No 23
>TIGR02834 spo_ytxC putative sporulation protein YtxC; InterPro: IPR014199 This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtilis ..
Probab=28.33 E-value=48 Score=15.62 Aligned_cols=47 Identities=28% Similarity=0.481 Sum_probs=38.2
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCCEE
Q ss_conf 5257867600320799888864890999988878988999999999687433
Q gi|254780259|r 3 NIRFYDTIISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVV 54 (110)
Q Consensus 3 ~~~~~~vi~~P~~TEKs~~~~e~n~y~F~V~~~atK~eIK~ave~~f~V~V~ 54 (110)
.|+.-|.+++|++| ++=...+.+..++.-||-|+=..|..+|+=.|.
T Consensus 236 ~~~~~d~lISpLIs-----~aP~kI~~y~~~~~~n~dE~~~Ti~~VF~eRV~ 282 (283)
T TIGR02834 236 GLNIEDILISPLIS-----LAPEKIKIYTDDPDHNKDEIILTIQNVFQERVE 282 (283)
T ss_pred CCCHHHHHHHHHHH-----HCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 76387788879986-----288658995268998830357778987421037
No 24
>KOG3424 consensus
Probab=23.00 E-value=68 Score=14.74 Aligned_cols=41 Identities=22% Similarity=0.269 Sum_probs=30.6
Q ss_pred HHHHCCEEEEEEC----CCCCHHHHHHHHHHHHCCCEEEEEEEEC
Q ss_conf 8864890999988----8789889999999996874337899851
Q gi|254780259|r 21 LLAGQNQVVFNVK----KDSSKSEIKSAVEALFSVKVVSVNTLIR 61 (110)
Q Consensus 21 ~~~e~n~y~F~V~----~~atK~eIK~ave~~f~V~V~~Vnt~~~ 61 (110)
.|+...|.+..|- +..+|.||++-+.++|.+++..|-..-.
T Consensus 16 rLL~RKqmvvdvlHPG~a~vsK~EIrEKlA~mYkt~~d~V~vfgf 60 (132)
T KOG3424 16 RLLSRKQMVVDVLHPGKANVSKTEIREKLAKMYKTTPDAVFVFGF 60 (132)
T ss_pred HHHHHHHEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf 556422146888538989989899999999996478770899886
No 25
>pfam00240 ubiquitin Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
Probab=21.96 E-value=72 Score=14.61 Aligned_cols=40 Identities=23% Similarity=0.301 Sum_probs=32.7
Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE
Q ss_conf 89099998887898899999999968743378998518963
Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110)
Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110)
...+.+.|+++.|=.++|..|+...++.+..-+-+ ..|+.
T Consensus 5 g~~~~l~V~~~~TV~~lK~~i~~~~~ip~~~qrLi-~~Gk~ 44 (69)
T pfam00240 5 GKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLI-FSGKV 44 (69)
T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEEE-ECCEE
T ss_conf 96899998998949999999974678196897989-89989
No 26
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=21.92 E-value=72 Score=14.61 Aligned_cols=28 Identities=29% Similarity=0.359 Sum_probs=23.4
Q ss_pred HCCEEEEEECCCC--CHHHHHHHHHHHHCC
Q ss_conf 4890999988878--988999999999687
Q gi|254780259|r 24 GQNQVVFNVKKDS--SKSEIKSAVEALFSV 51 (110)
Q Consensus 24 e~n~y~F~V~~~a--tK~eIK~ave~~f~V 51 (110)
....|.|.||.+. ....+++|++.+-..
T Consensus 38 ~~~~y~F~id~eg~~~~~~~~~~l~~l~~~ 67 (75)
T cd04880 38 GLWEYEFFVDFEGHIDDPDVKEALEELKRV 67 (75)
T ss_pred CCCEEEEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 995699999971685978999999999984
No 27
>PTZ00044 ubiquitin; Provisional
Probab=21.42 E-value=74 Score=14.55 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=33.6
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE
Q ss_conf 489099998887898899999999968743378998518963
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110)
.-..+++.|+++.|=.++|..|+..-|+.+...+-+ ..||.
T Consensus 9 ~G~~~~l~v~~~dTV~~lK~~I~~k~gip~~qQrLI-f~Gk~ 49 (76)
T PTZ00044 9 TGKKQSFNFEPDNTIQQVKMALQEKEGIDAKQIRLI-YSGKQ 49 (76)
T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEEE-ECCEE
T ss_conf 998999997897969999999998759996897999-89869
No 28
>KOG0010 consensus
Probab=21.11 E-value=75 Score=14.51 Aligned_cols=40 Identities=25% Similarity=0.352 Sum_probs=33.5
Q ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCE
Q ss_conf 89099998887898899999999968743378998518963
Q gi|254780259|r 25 QNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 (110)
Q Consensus 25 ~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK~ 65 (110)
+++|.|.|+.+++=.|.|++|-..|++.++... ++..||.
T Consensus 24 ~dk~~~~V~~~ssV~qlKE~I~~~f~a~~dqlv-LIfaGrI 63 (493)
T KOG0010 24 KDKYEVNVASDSSVLQLKELIAQRFGAPPDQLV-LIYAGRI 63 (493)
T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHCCCHHHEE-EEECCCC
T ss_conf 850357425404799999999876079865735-4542732
No 29
>cd01807 GDX_N GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=20.33 E-value=78 Score=14.41 Aligned_cols=40 Identities=23% Similarity=0.239 Sum_probs=32.9
Q ss_pred HCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEECCCC
Q ss_conf 48909999888789889999999996874337899851896
Q gi|254780259|r 24 GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGK 64 (110)
Q Consensus 24 e~n~y~F~V~~~atK~eIK~ave~~f~V~V~~Vnt~~~~gK 64 (110)
.-..++|.|+++.+=.++|+-|++..|+.+..=+- +..||
T Consensus 9 ~Gk~~~~~v~~~~tV~~lK~~I~ek~gIP~~qQRL-If~Gk 48 (74)
T cd01807 9 QGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRL-LFKGK 48 (74)
T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHCCCHHHEEE-EECCC
T ss_conf 99789999799692999999999887979689488-86782
Done!