Query 030945
Match_columns 168
No_of_seqs 206 out of 1149
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:55:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030945.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030945hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1751 60s ribosomal protein 100.0 3E-62 6.4E-67 392.1 11.2 146 23-168 10-157 (157)
2 PTZ00191 60S ribosomal protein 100.0 2.1E-61 4.6E-66 383.4 14.7 141 27-168 5-145 (145)
3 PRK14548 50S ribosomal protein 100.0 1.5E-34 3.3E-39 211.5 9.8 84 85-168 1-84 (84)
4 TIGR03636 L23_arch archaeal ri 100.0 1.3E-32 2.9E-37 198.3 9.7 77 92-168 1-77 (77)
5 PRK05738 rplW 50S ribosomal pr 99.9 1.2E-27 2.6E-32 176.8 7.7 77 86-163 1-90 (92)
6 CHL00030 rpl23 ribosomal prote 99.9 1.2E-26 2.7E-31 172.5 7.9 76 86-163 1-89 (93)
7 COG0089 RplW Ribosomal protein 99.9 7.2E-27 1.6E-31 174.4 6.2 83 85-167 1-86 (94)
8 PRK12280 rplW 50S ribosomal pr 99.9 1E-25 2.2E-30 181.5 7.5 79 83-163 1-92 (158)
9 PF00276 Ribosomal_L23: Riboso 99.9 1.6E-25 3.5E-30 164.6 7.8 78 86-164 1-91 (91)
10 PF03939 Ribosomal_L23eN: Ribo 99.8 4.8E-21 1.1E-25 130.4 -1.0 52 29-80 3-54 (54)
11 KOG4089 Predicted mitochondria 96.8 0.0017 3.8E-08 53.2 4.2 61 89-156 28-108 (165)
12 PF08777 RRM_3: RNA binding mo 73.0 12 0.00025 28.1 5.5 51 108-163 4-55 (105)
13 COG0089 RplW Ribosomal protein 68.9 2.2 4.9E-05 32.2 0.8 22 141-163 71-92 (94)
14 PLN02817 glutathione dehydroge 54.5 11 0.00024 32.3 2.6 39 127-165 24-62 (265)
15 cd04929 ACT_TPH ACT domain of 54.5 22 0.00048 24.9 3.7 40 82-129 25-64 (74)
16 PF03780 Asp23: Asp23 family; 52.6 20 0.00044 25.7 3.4 24 118-141 82-105 (108)
17 PF00076 RRM_1: RNA recognitio 46.3 50 0.0011 20.7 4.2 53 111-163 5-57 (70)
18 cd01769 UBL Ubiquitin-like dom 45.7 52 0.0011 20.9 4.2 35 104-138 6-40 (69)
19 PF10298 WhiA_N: WhiA N-termin 44.5 33 0.00072 24.3 3.4 62 105-168 22-86 (86)
20 PF14259 RRM_6: RNA recognitio 41.5 37 0.0008 21.9 3.1 51 112-164 6-58 (70)
21 PF14560 Ubiquitin_2: Ubiquiti 37.3 52 0.0011 23.1 3.5 53 107-159 15-67 (87)
22 PF00240 ubiquitin: Ubiquitin 37.2 72 0.0016 20.8 4.0 36 105-140 5-40 (69)
23 PRK01178 rps24e 30S ribosomal 36.8 1.7E+02 0.0037 22.0 6.4 68 94-165 6-81 (99)
24 cd04931 ACT_PAH ACT domain of 35.6 50 0.0011 24.1 3.2 41 81-129 38-79 (90)
25 cd04904 ACT_AAAH ACT domain of 35.0 81 0.0018 21.5 4.1 41 82-130 25-65 (74)
26 cd01796 DDI1_N DNA damage indu 35.0 66 0.0014 21.8 3.6 34 104-137 8-41 (71)
27 PF01282 Ribosomal_S24e: Ribos 34.2 1.4E+02 0.003 21.6 5.3 49 114-165 11-63 (84)
28 PLN03134 glycine-rich RNA-bind 34.0 1.2E+02 0.0026 23.6 5.4 55 107-163 37-94 (144)
29 KOG0107 Alternative splicing f 30.8 1.4E+02 0.003 25.4 5.5 52 107-162 13-64 (195)
30 PTZ00044 ubiquitin; Provisiona 30.3 1.1E+02 0.0024 20.4 4.1 36 104-139 9-44 (76)
31 TIGR02830 spore_III_AG stage I 29.9 58 0.0013 27.2 3.1 31 109-139 149-183 (186)
32 smart00213 UBQ Ubiquitin homol 29.6 1.1E+02 0.0024 19.0 3.9 35 106-140 10-44 (64)
33 PRK04046 translation initiatio 29.3 1.2E+02 0.0026 25.7 5.0 51 86-137 66-137 (222)
34 PF02075 RuvC: Crossover junct 28.7 44 0.00095 26.2 2.1 19 115-133 114-132 (149)
35 cd04930 ACT_TH ACT domain of t 28.4 99 0.0021 23.5 3.9 42 81-130 65-106 (115)
36 cd01809 Scythe_N Ubiquitin-lik 28.1 1.3E+02 0.0029 19.5 4.1 35 105-139 10-44 (72)
37 cd01798 parkin_N amino-termina 28.0 1.1E+02 0.0024 20.3 3.8 33 105-137 8-40 (70)
38 TIGR00323 eIF-6 translation in 27.9 1.2E+02 0.0027 25.6 4.8 51 86-139 104-177 (215)
39 PF09581 Spore_III_AF: Stage I 24.8 1.9E+02 0.0042 22.8 5.2 41 116-156 87-133 (188)
40 KOG3424 40S ribosomal protein 24.6 1.9E+02 0.0041 23.2 4.9 46 115-165 34-85 (132)
41 PF02824 TGS: TGS domain; Int 24.2 1.1E+02 0.0025 20.3 3.2 22 142-166 6-27 (60)
42 cd01806 Nedd8 Nebb8-like ubiq 24.0 2E+02 0.0043 18.8 4.4 35 105-139 10-44 (76)
43 TIGR01659 sex-lethal sex-letha 23.9 1.7E+02 0.0037 26.2 5.2 55 106-162 107-166 (346)
44 cd01805 RAD23_N Ubiquitin-like 23.6 1.9E+02 0.0042 19.2 4.3 35 105-139 10-46 (77)
45 cd01803 Ubiquitin Ubiquitin. U 23.3 1.8E+02 0.0038 19.1 4.1 35 105-139 10-44 (76)
46 PHA01813 hypothetical protein 23.0 57 0.0012 22.6 1.5 17 117-134 19-35 (58)
47 cd01812 BAG1_N Ubiquitin-like 23.0 1.3E+02 0.0029 19.5 3.4 35 106-140 10-44 (71)
48 cd06407 PB1_NLP A PB1 domain i 22.4 1.9E+02 0.0042 20.7 4.3 55 106-162 10-64 (82)
49 cd01800 SF3a120_C Ubiquitin-li 22.0 1.7E+02 0.0038 19.9 3.9 34 106-139 8-41 (76)
50 TIGR01661 ELAV_HUD_SF ELAV/HuD 21.6 2.4E+02 0.0053 23.9 5.5 57 105-165 270-331 (352)
51 PF01250 Ribosomal_S6: Ribosom 21.5 1.4E+02 0.0031 21.0 3.5 33 107-139 4-42 (92)
52 cd01789 Alp11_N Ubiquitin-like 21.1 2E+02 0.0043 20.3 4.1 47 110-157 17-63 (84)
53 cd04905 ACT_CM-PDT C-terminal 20.6 1.2E+02 0.0026 20.6 2.8 26 105-130 41-68 (80)
54 cd00529 RuvC_resolvase Hollida 20.5 88 0.0019 24.4 2.4 19 115-133 115-133 (154)
55 cd01807 GDX_N ubiquitin-like d 20.1 2E+02 0.0043 19.3 3.9 35 105-139 10-44 (74)
No 1
>KOG1751 consensus 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-62 Score=392.12 Aligned_cols=146 Identities=70% Similarity=0.972 Sum_probs=142.4
Q ss_pred CCCCCChhHHHHHHHHhhhcccCccccee-eeccccccCCCccCCCCCCCCCCCCCCCCCCCCcccc-ccccccchhhhh
Q 030945 23 ETKKADPKVQALKTAKAVKSGRTFKKAKK-IRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQI-LKYPLTTESAMK 100 (168)
Q Consensus 23 ~~~ka~akakalkakkavlkg~~~~~~~k-~~~s~~f~~pktl~l~r~pkyprk~~p~~~kld~~~I-Ik~Pl~TEkamk 100 (168)
++|++++++|||+|+|+|++|+|||++++ ++++++|++|.+++++|+|+|||+|.|+||+||||.+ |++||+||+||+
T Consensus 10 a~pka~a~akAlkakkav~kgv~~~~~~~~~~t~~~~~rP~t~~~~r~pk~prks~p~~~kld~y~~iik~plTtEsamK 89 (157)
T KOG1751|consen 10 APPKAEAKAKALKAKKAVLKGVHSHKKKKKSRTSPTFRRPKTLDLTRAPKYPRKSPPRRPKLDHYAIIIKFPLTTESAMK 89 (157)
T ss_pred CCcchhhhHHHHHHHHHhhccccCCcccCCccccCCCCCCcccccccCccccccccCCCCcchhhhhHhccccchhhhhc
Confidence 68899999999999999999999998765 9999999999999999999999999999999999777 899999999999
Q ss_pred hhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 030945 101 KIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 168 (168)
Q Consensus 101 ~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAnkigii 168 (168)
++||||||||+||.+||||||||||++|||+||++|||||+|+|+|||||+|++|||||||||+||||
T Consensus 90 k~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~kkayv~la~dydaldvankig~i 157 (157)
T KOG1751|consen 90 KIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII 157 (157)
T ss_pred chhhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCceeEEEecCCchhHHHHhcccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999997
No 2
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=100.00 E-value=2.1e-61 Score=383.39 Aligned_cols=141 Identities=66% Similarity=0.972 Sum_probs=137.4
Q ss_pred CChhHHHHHHHHhhhcccCcccceeeeccccccCCCccCCCCCCCCCCCCCCCCCCCCccccccccccchhhhhhhhcCC
Q 030945 27 ADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDNN 106 (168)
Q Consensus 27 a~akakalkakkavlkg~~~~~~~k~~~s~~f~~pktl~l~r~pkyprk~~p~~~kld~~~IIk~Pl~TEkamk~~E~nN 106 (168)
..++++|++|+|+|++|+|+ +++|+|+|++|+||+||+|+|+|+|||+|.|++|+||+|+||++|++||+||+++|++|
T Consensus 5 ~~~~~ka~~a~k~~~~g~~~-~~~k~r~~~~f~rpktl~l~r~pky~r~~~~~~~~md~~~IIk~Pl~TEKa~~~~E~~N 83 (145)
T PTZ00191 5 KKAKKKAKKAAKAAKKGVKV-KKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDKYSIIKYPLTTEKAMKKIEDNN 83 (145)
T ss_pred chHHHHHHHHHHHHhccccc-ceeEeeecceecCCccccCCCCCCCcccccCCCCCCchhhhhhcccccHHHHHHHhhCC
Confidence 44688999999999999998 67999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 030945 107 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 168 (168)
Q Consensus 107 tlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAnkigii 168 (168)
+|+|+||++|||+|||+|||+||||+|.+|||||+|+|+|||||+|++||||||+||+||||
T Consensus 84 ~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~g~KKA~V~L~~~~~aidva~kiGi~ 145 (145)
T PTZ00191 84 TLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKAYIRLSPDVDALDVANKIGII 145 (145)
T ss_pred EEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999997
No 3
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=100.00 E-value=1.5e-34 Score=211.54 Aligned_cols=84 Identities=52% Similarity=0.864 Sum_probs=81.9
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHh
Q 030945 85 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANK 164 (168)
Q Consensus 85 ~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAnk 164 (168)
.|+||++|++||+++.++|++|+|+|+||++|||.|||+|||++|||+|.+|||++.++|||||||+|.+|++|+|+|++
T Consensus 1 ~~~iI~~PviTEK~~~~~e~~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~k 80 (84)
T PRK14548 1 PYSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIASR 80 (84)
T ss_pred CccchhccccCHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHHh
Confidence 37899999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCC
Q 030945 165 IGII 168 (168)
Q Consensus 165 igii 168 (168)
||++
T Consensus 81 ig~~ 84 (84)
T PRK14548 81 LGVF 84 (84)
T ss_pred hccC
Confidence 9986
No 4
>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=99.98 E-value=1.3e-32 Score=198.33 Aligned_cols=77 Identities=51% Similarity=0.808 Sum_probs=75.7
Q ss_pred cccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 030945 92 PLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 168 (168)
Q Consensus 92 Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAnkigii 168 (168)
|++||++|.++|++|+|+|+||++|||+|||+|||.+|||+|.+|||+|.|+|||||||+|.+|++|+|||++|||+
T Consensus 1 P~iTEKs~~~~e~~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~KKA~VtL~~g~~a~~va~k~g~~ 77 (77)
T TIGR03636 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVKLAEEYAAEEIASRLGVF 77 (77)
T ss_pred CcccHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 89999999999988999999999999999999999999999999999999999999999999999999999999986
No 5
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.94 E-value=1.2e-27 Score=176.85 Aligned_cols=77 Identities=35% Similarity=0.481 Sum_probs=73.1
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCC-------------CCeeeEEEEc
Q 030945 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP-------------DGTKKAYVRL 152 (168)
Q Consensus 86 ~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p-------------~g~KKAyV~L 152 (168)
|+||++|++||+||.++|++|+|+|+||++|||+|||+|||++|||+|.+|||++.+ .++|||||+|
T Consensus 1 ~~ii~~P~~TEKs~~~~e~~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~~~g~~~~~KKA~VtL 80 (92)
T PRK05738 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRIGKRSDWKKAIVTL 80 (92)
T ss_pred CccccccccCHHHHHhHHhCCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecccccccCCcEEEEEEc
Confidence 579999999999999999889999999999999999999999999999999999999 5899999999
Q ss_pred CCCCcHHHHHH
Q 030945 153 TPDSDALDVAN 163 (168)
Q Consensus 153 a~d~dAlDvAn 163 (168)
.+|++ +|+.+
T Consensus 81 ~~g~~-i~~~~ 90 (92)
T PRK05738 81 AEGQK-IDFFG 90 (92)
T ss_pred CCCCE-Eeccc
Confidence 99988 88764
No 6
>CHL00030 rpl23 ribosomal protein L23
Probab=99.93 E-value=1.2e-26 Score=172.51 Aligned_cols=76 Identities=24% Similarity=0.409 Sum_probs=71.4
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCC-------------eeeEEEEc
Q 030945 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDG-------------TKKAYVRL 152 (168)
Q Consensus 86 ~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g-------------~KKAyV~L 152 (168)
++||++|++||+++.++| +|+|+|+||++|||.|||+|||.+|||+|.+|||++.|++ ||||||+|
T Consensus 1 ~~iI~~PivTEKs~~l~e-~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~~G~~~~~KKAiVtL 79 (93)
T CHL00030 1 MDGIKYPVFTDKSIRLLE-KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITL 79 (93)
T ss_pred CceeccceeCHHHHHhhH-CCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCcccccCCcEEEEEEc
Confidence 579999999999999997 5999999999999999999999999999999999999985 89999999
Q ss_pred CCCCcHHHHHH
Q 030945 153 TPDSDALDVAN 163 (168)
Q Consensus 153 a~d~dAlDvAn 163 (168)
.+|++ ||++.
T Consensus 80 ~~g~~-I~~~~ 89 (93)
T CHL00030 80 QPGYS-IPLFR 89 (93)
T ss_pred CCcCE-ecccc
Confidence 99977 88864
No 7
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=7.2e-27 Score=174.44 Aligned_cols=83 Identities=41% Similarity=0.530 Sum_probs=75.3
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEE---cCCCCcHHHH
Q 030945 85 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVR---LTPDSDALDV 161 (168)
Q Consensus 85 ~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~---La~d~dAlDv 161 (168)
+|+||++|++||+||.++|+.|+|||+||++|||.|||+|||.||||+|.+|||||++++.|++++. +.+++++.+|
T Consensus 1 ~~dvI~~PvvTEKa~~l~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k~~G~~~~~kka~V 80 (94)
T COG0089 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYV 80 (94)
T ss_pred CcchhhcceecHHHHHhHhhCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEeccccccCcccceeEE
Confidence 4899999999999999998889999999999999999999999999999999999999987777776 7777777777
Q ss_pred HHhhcC
Q 030945 162 ANKIGI 167 (168)
Q Consensus 162 Ankigi 167 (168)
+.++|.
T Consensus 81 ~l~~G~ 86 (94)
T COG0089 81 TLKEGQ 86 (94)
T ss_pred EccCCC
Confidence 777764
No 8
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.92 E-value=1e-25 Score=181.48 Aligned_cols=79 Identities=30% Similarity=0.453 Sum_probs=74.6
Q ss_pred CCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCC-------------CeeeEE
Q 030945 83 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-------------GTKKAY 149 (168)
Q Consensus 83 ld~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~-------------g~KKAy 149 (168)
||+|+||++|++||+++.++|. |+|+|.||++|||+||++|||.+|||+|.+|||++.++ ||||||
T Consensus 1 Md~~~iIk~PviTEKs~~l~e~-N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g~~~G~~~~~KKAi 79 (158)
T PRK12280 1 MNINEVIKKPILTEKSYSLMSK-NVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRFPGFTNSYKKAY 79 (158)
T ss_pred CChHhhhhccccCHHHHhhhhC-CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccCCcccccCCcEEEE
Confidence 7999999999999999999985 89999999999999999999999999999999999987 799999
Q ss_pred EEcCCCCcHHHHHH
Q 030945 150 VRLTPDSDALDVAN 163 (168)
Q Consensus 150 V~La~d~dAlDvAn 163 (168)
|+|.+|+. ||+..
T Consensus 80 VtL~~g~~-I~~f~ 92 (158)
T PRK12280 80 VTLAEGYS-INLFP 92 (158)
T ss_pred EECCCCCE-eeccC
Confidence 99999976 88754
No 9
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=99.92 E-value=1.6e-25 Score=164.64 Aligned_cols=78 Identities=42% Similarity=0.638 Sum_probs=71.5
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCC-------------CeeeEEEEc
Q 030945 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-------------GTKKAYVRL 152 (168)
Q Consensus 86 ~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~-------------g~KKAyV~L 152 (168)
|+||++|++||+++.++|++|+|+|.||++|||+||++|||++|||+|.+|||++.++ ++|||||+|
T Consensus 1 ~~ii~~p~iTeKs~~~~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKaiVtL 80 (91)
T PF00276_consen 1 YDIIKKPVITEKSMKLLENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKAIVTL 80 (91)
T ss_dssp TTTEEEE--SHHHHHHHHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEEEEEE
T ss_pred CCEeecceecHhHHHhhhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEEEEEe
Confidence 7899999999999999999899999999999999999999999999999999999994 369999999
Q ss_pred CCCCcHHHHHHh
Q 030945 153 TPDSDALDVANK 164 (168)
Q Consensus 153 a~d~dAlDvAnk 164 (168)
.+| +.+|++++
T Consensus 81 ~~~-~~i~~~~~ 91 (91)
T PF00276_consen 81 KEG-DKIPLFEE 91 (91)
T ss_dssp STT-SCHHHHHT
T ss_pred CCC-CccccccC
Confidence 999 66999874
No 10
>PF03939 Ribosomal_L23eN: Ribosomal protein L23, N-terminal domain; InterPro: IPR005633 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a.; PDB: 3IZR_X 4A1E_R 4A1A_R 4A1C_R 4A17_R 3O5H_W 3IZS_X 3O58_W.
Probab=99.79 E-value=4.8e-21 Score=130.37 Aligned_cols=52 Identities=62% Similarity=0.846 Sum_probs=17.4
Q ss_pred hhHHHHHHHHhhhcccCcccceeeeccccccCCCccCCCCCCCCCCCCCCCC
Q 030945 29 PKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPR 80 (168)
Q Consensus 29 akakalkakkavlkg~~~~~~~k~~~s~~f~~pktl~l~r~pkyprk~~p~~ 80 (168)
+++||++|+|+|++|+|+++.+|||||++|+||+||+|+|+|+|||+|+|+|
T Consensus 3 a~~KA~kakKav~KG~~~~~~rKirts~~F~rPKTL~l~R~PKYprkS~p~r 54 (54)
T PF03939_consen 3 AKAKALKAKKAVLKGVHSKKKRKIRTSVTFRRPKTLRLPRQPKYPRKSVPRR 54 (54)
T ss_dssp ---------------------HHHHHHHHHT-SS--------SS-SSS---S
T ss_pred hHHHHHHHHHHHhcCCCccccceeecCcccCCCcccccCCCCCCcccCCCCC
Confidence 5788999999999999999889999999999999999999999999999985
No 11
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=96.78 E-value=0.0017 Score=53.24 Aligned_cols=61 Identities=26% Similarity=0.392 Sum_probs=49.8
Q ss_pred ccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCC--------------------CeeeE
Q 030945 89 LKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD--------------------GTKKA 148 (168)
Q Consensus 89 Ik~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~--------------------g~KKA 148 (168)
|..|+.+. -.++.+|+|+...||.+++.+++.+||.+|.+|.|.+..+ .++=|
T Consensus 28 l~rp~~~q-------~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~~~~k~r~~~~k~i~kdmd~p~~ 100 (165)
T KOG4089|consen 28 LVRPLVTQ-------PPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDYKKTKKRLQSPKRIKKDMDEPVA 100 (165)
T ss_pred hhcccccC-------CCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeechhhhcceecccccceeeccccccee
Confidence 33376654 2479999999999999999999999999999999999776 46667
Q ss_pred EEEcCCCC
Q 030945 149 YVRLTPDS 156 (168)
Q Consensus 149 yV~La~d~ 156 (168)
||.++-+.
T Consensus 101 Yv~~pr~~ 108 (165)
T KOG4089|consen 101 YVEEPRGS 108 (165)
T ss_pred eecCCCCc
Confidence 77776553
No 12
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=73.04 E-value=12 Score=28.10 Aligned_cols=51 Identities=22% Similarity=0.394 Sum_probs=29.2
Q ss_pred EEEE-EecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHH
Q 030945 108 LVFI-VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVAN 163 (168)
Q Consensus 108 lvFi-Vd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAn 163 (168)
|-|. ++...++.+||.++.. |+ +|.-|.- ..|...+||++....+|-.+..
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yVD~---~~G~~~g~VRf~~~~~A~~a~~ 55 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYVDF---SRGDTEGYVRFKTPEAAQKALE 55 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEEE-----TT-SEEEEEESS---HHHHHH
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceEEe---cCCCCEEEEEECCcchHHHHHH
Confidence 4466 7888999999999998 56 5655543 4588999999998877655544
No 13
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=68.86 E-value=2.2 Score=32.16 Aligned_cols=22 Identities=32% Similarity=0.388 Sum_probs=18.3
Q ss_pred CCCCeeeEEEEcCCCCcHHHHHH
Q 030945 141 RPDGTKKAYVRLTPDSDALDVAN 163 (168)
Q Consensus 141 ~p~g~KKAyV~La~d~dAlDvAn 163 (168)
...++|+|||.|.+|+. ||+++
T Consensus 71 ~~~~~kka~V~l~~G~~-i~~~~ 92 (94)
T COG0089 71 LRKDYKKAYVTLKEGQS-IDFFG 92 (94)
T ss_pred cCcccceeEEEccCCCE-Eeecc
Confidence 34589999999999988 88764
No 14
>PLN02817 glutathione dehydrogenase (ascorbate)
Probab=54.50 E-value=11 Score=32.28 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=34.7
Q ss_pred hHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhh
Q 030945 127 KMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKI 165 (168)
Q Consensus 127 klydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAnki 165 (168)
.-|++.+..+|++.+++|.+++++++.+..+.+|++.|-
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (265)
T PLN02817 24 PRFGTSHGGAKGVKRVGGRRRKYLTAITMSSPLEVCVKA 62 (265)
T ss_pred ccccceeecccccccCCcccceeEEecCCCccHHHHHhc
Confidence 447888889999999999999999999999999998874
No 15
>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=54.49 E-value=22 Score=24.93 Aligned_cols=40 Identities=13% Similarity=0.252 Sum_probs=28.9
Q ss_pred CCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHc
Q 030945 82 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMY 129 (168)
Q Consensus 82 kld~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkkly 129 (168)
.++...|-..|..+ .+..|.|.||...+..+++++++.|=
T Consensus 25 ~inl~~IeSRP~~~--------~~~~y~F~id~e~~~~~i~~~l~~l~ 64 (74)
T cd04929 25 GINVVHIESRKSKR--------RSSEFEIFVDCECDQRRLDELVQLLK 64 (74)
T ss_pred CCCEEEEEeccCCC--------CCceEEEEEEEEcCHHHHHHHHHHHH
Confidence 34444555555443 23579999999999999999999874
No 16
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=52.64 E-value=20 Score=25.73 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=21.5
Q ss_pred HHHHHHHHHhHcCCceeeEEEeeC
Q 030945 118 KKKIKDAVKKMYDIQAKKVNTLIR 141 (168)
Q Consensus 118 K~qIKqAVkklydV~V~kVNTli~ 141 (168)
..+|+++|+.+-|++|..||..+.
T Consensus 82 q~~V~~~v~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 82 QEKVKEAVEEMTGIEVSEVNVHVE 105 (108)
T ss_pred HHHHHHHHHHHHCCeeEEEEEEEE
Confidence 678999999999999999998763
No 17
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=46.28 E-value=50 Score=20.67 Aligned_cols=53 Identities=15% Similarity=0.178 Sum_probs=33.7
Q ss_pred EEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHH
Q 030945 111 IVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVAN 163 (168)
Q Consensus 111 iVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvAn 163 (168)
-++...+..+|++.++..=++....+..-.......-|||++....+|..+..
T Consensus 5 nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~ 57 (70)
T PF00076_consen 5 NLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALE 57 (70)
T ss_dssp SETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHH
T ss_pred CCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHH
Confidence 36778999999999999444433343332111234568999987766655443
No 18
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=45.68 E-value=52 Score=20.91 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=30.8
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEE
Q 030945 104 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNT 138 (168)
Q Consensus 104 ~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNT 138 (168)
+...+.|.++..++=.++|+.+...+|+.+.....
T Consensus 6 ~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l 40 (69)
T cd01769 6 TGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL 40 (69)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEE
Confidence 35688899999999999999999999998887765
No 19
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=44.53 E-value=33 Score=24.28 Aligned_cols=62 Identities=19% Similarity=0.385 Sum_probs=20.6
Q ss_pred CCeEEEEE--ecCCCHHHHHHHHHhHcCCceeeEEEeeCCC-CeeeEEEEcCCCCcHHHHHHhhcCC
Q 030945 105 NNTLVFIV--DIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-GTKKAYVRLTPDSDALDVANKIGII 168 (168)
Q Consensus 105 nNtlvFiV--d~kAnK~qIKqAVkklydV~V~kVNTli~p~-g~KKAyV~La~d~dAlDvAnkigii 168 (168)
++.+++.+ +.-+-=.-|-.-++++||+++ .|.+..... +.+..|.-.-++. +.++..++|++
T Consensus 22 ~~~~~l~~~ten~~vARri~~llk~~f~i~~-ei~v~~~~~l~k~~~Y~i~i~~~-~~~iL~~lgll 86 (86)
T PF10298_consen 22 NGRISLEISTENAAVARRIYSLLKKLFDIDP-EISVRRSRNLKKNNVYTIRIEDS-AKEILRDLGLL 86 (86)
T ss_dssp TTEEEE--EES-HHHHHHHHHHHHHTT--EE-EEEEEE-SSSBEEE---------------------
T ss_pred CCEEEEEEEeCCHHHHHHHHHHHHHHhCCCe-EEEEecCCCCCCCCccccccccc-cccccccccCC
Confidence 34455444 334444567778999999988 444443222 2334565444443 78899999975
No 20
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=41.52 E-value=37 Score=21.91 Aligned_cols=51 Identities=14% Similarity=0.262 Sum_probs=36.0
Q ss_pred EecCCCHHHHHHHHHhHcCCceeeEEEeeCCC--CeeeEEEEcCCCCcHHHHHHh
Q 030945 112 VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD--GTKKAYVRLTPDSDALDVANK 164 (168)
Q Consensus 112 Vd~kAnK~qIKqAVkklydV~V~kVNTli~p~--g~KKAyV~La~d~dAlDvAnk 164 (168)
++..++..+|...++.. | +|..|...-..+ +..-|||.+....+|..+.+.
T Consensus 6 lp~~~~~~~l~~~f~~~-g-~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~ 58 (70)
T PF14259_consen 6 LPPSTTEEDLRNFFSRF-G-PVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALEL 58 (70)
T ss_dssp STTT--HHHHHHHCTTS-S-BEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHhc-C-CcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHH
Confidence 45678889999988885 4 577887776554 467899999977776665543
No 21
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=37.29 E-value=52 Score=23.11 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=38.1
Q ss_pred eEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHH
Q 030945 107 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDAL 159 (168)
Q Consensus 107 tlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAl 159 (168)
...-.++...+=.|+|+-++.+||+.+........++..-..+..|..|...|
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L 67 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATL 67 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBC
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEe
Confidence 44567889999999999999999999999998887332224555565544433
No 22
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=37.23 E-value=72 Score=20.81 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=32.1
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEee
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli 140 (168)
..++.|.|+...+=.++|+.|+...|+.+.....+-
T Consensus 5 g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~ 40 (69)
T PF00240_consen 5 GKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY 40 (69)
T ss_dssp SEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE
T ss_pred CcEEEEEECCCCCHHHhhhhcccccccccccceeee
Confidence 358999999999999999999999999998887654
No 23
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=36.76 E-value=1.7e+02 Score=22.05 Aligned_cols=68 Identities=18% Similarity=0.287 Sum_probs=41.9
Q ss_pred cchhhhhhhhcCCeEEEEEe----cCCCHHHHHHHHHhHcCCceeeEEE--ee-CCC-CeeeEEEEcCCCCcHHHHHHhh
Q 030945 94 TTESAMKKIEDNNTLVFIVD----IRADKKKIKDAVKKMYDIQAKKVNT--LI-RPD-GTKKAYVRLTPDSDALDVANKI 165 (168)
Q Consensus 94 ~TEkamk~~E~nNtlvFiVd----~kAnK~qIKqAVkklydV~V~kVNT--li-~p~-g~KKAyV~La~d~dAlDvAnki 165 (168)
+.|+...++.. ..++|.|. ...+|.+|+..+-++|+.+..-|=. +. ..| |.=..|... ||.+|.|.++
T Consensus 6 ~~~~~N~LL~R-ke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv~~~~t~fG~g~s~G~a~I---Yds~e~~kk~ 81 (99)
T PRK01178 6 ISDKENPLLGR-REIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVRKIKTEYGMGKSKGYAKV---YDDKERARKI 81 (99)
T ss_pred EEeeecCCcCc-EEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEEEccCccCCCceEEEEEEE---ECCHHHHHhh
Confidence 34555556654 57888875 4568999999999999976543311 11 112 444555544 4557766654
No 24
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.62 E-value=50 Score=24.10 Aligned_cols=41 Identities=10% Similarity=0.268 Sum_probs=30.2
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEecCCC-HHHHHHHHHhHc
Q 030945 81 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRAD-KKKIKDAVKKMY 129 (168)
Q Consensus 81 ~kld~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAn-K~qIKqAVkkly 129 (168)
..++...|--.|..++ ...|.|.||...+ ...++++++.|-
T Consensus 38 ~~INLt~IeSRP~~~~--------~~~Y~FfVDieg~~~~~~~~~l~~L~ 79 (90)
T cd04931 38 KDINLTHIESRPSRLN--------KDEYEFFINLDKKSAPALDPIIKSLR 79 (90)
T ss_pred CCCCEEEEEeccCCCC--------CceEEEEEEEEcCCCHHHHHHHHHHH
Confidence 4556666777775442 3689999999986 788889888764
No 25
>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=35.03 E-value=81 Score=21.52 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=29.9
Q ss_pred CCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcC
Q 030945 82 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYD 130 (168)
Q Consensus 82 kld~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklyd 130 (168)
.++...|-..|...+ ...|.|.||......+++++++.|-.
T Consensus 25 ~iNlt~IeSRP~~~~--------~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 25 GVNLTHIESRPSRRN--------GSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred CCcEEEEECCCCCCC--------CceEEEEEEEEcChHHHHHHHHHHHH
Confidence 445555666665542 35799999999988899999988744
No 26
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=35.00 E-value=66 Score=21.84 Aligned_cols=34 Identities=18% Similarity=0.168 Sum_probs=29.8
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEE
Q 030945 104 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 137 (168)
Q Consensus 104 ~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVN 137 (168)
..+++.+.|+..++=.++|+.|+..+|+.+..-.
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~ 41 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQ 41 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeE
Confidence 3578999999999999999999999999886643
No 27
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=34.19 E-value=1.4e+02 Score=21.64 Aligned_cols=49 Identities=12% Similarity=0.315 Sum_probs=31.3
Q ss_pred cCCCHHHHHHHHHhHcCCceeeE--EEeeCCC--CeeeEEEEcCCCCcHHHHHHhh
Q 030945 114 IRADKKKIKDAVKKMYDIQAKKV--NTLIRPD--GTKKAYVRLTPDSDALDVANKI 165 (168)
Q Consensus 114 ~kAnK~qIKqAVkklydV~V~kV--NTli~p~--g~KKAyV~La~d~dAlDvAnki 165 (168)
+..+|.||+..+-++||++..-| +.+...- |.-.+|...- |..|.+.++
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~IY---d~~e~~kk~ 63 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKIY---DSAEALKKF 63 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEEE---SSHHHHHHH
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEEe---CCHHHHHHh
Confidence 45789999999999999876543 5555443 4556676664 445555543
No 28
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=33.98 E-value=1.2e+02 Score=23.56 Aligned_cols=55 Identities=11% Similarity=0.257 Sum_probs=37.8
Q ss_pred eEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCC-C--eeeEEEEcCCCCcHHHHHH
Q 030945 107 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-G--TKKAYVRLTPDSDALDVAN 163 (168)
Q Consensus 107 tlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~-g--~KKAyV~La~d~dAlDvAn 163 (168)
-+|=-++..++..+|++.++. |+ +|..|.....+. | .-=|||++....+|....+
T Consensus 37 lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~ 94 (144)
T PLN03134 37 LFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94 (144)
T ss_pred EEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHH
Confidence 444556778999999999988 66 677777665442 2 1249999997766555443
No 29
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=30.83 E-value=1.4e+02 Score=25.43 Aligned_cols=52 Identities=29% Similarity=0.367 Sum_probs=38.8
Q ss_pred eEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHH
Q 030945 107 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVA 162 (168)
Q Consensus 107 tlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvA 162 (168)
.||=-...+|+|.||..+|-. || .+-.|=.--.|.|+ |||.+..--||-|..
T Consensus 13 VYVGnL~~~a~k~eLE~~F~~-yG-~lrsvWvArnPPGf--AFVEFed~RDA~DAv 64 (195)
T KOG0107|consen 13 VYVGNLGSRATKRELERAFSK-YG-PLRSVWVARNPPGF--AFVEFEDPRDAEDAV 64 (195)
T ss_pred EEeccCCCCcchHHHHHHHHh-cC-cceeEEEeecCCCc--eEEeccCcccHHHHH
Confidence 566667779999999888865 45 44455555578897 999999888877743
No 30
>PTZ00044 ubiquitin; Provisional
Probab=30.25 E-value=1.1e+02 Score=20.41 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=31.7
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 104 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 104 ~nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
+.+++++.|+...+=.++|+.++...|+.+......
T Consensus 9 ~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 44 (76)
T PTZ00044 9 TGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI 44 (76)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE
Confidence 347999999999999999999999999988776655
No 31
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=29.92 E-value=58 Score=27.23 Aligned_cols=31 Identities=39% Similarity=0.582 Sum_probs=25.0
Q ss_pred EEEEecCCC----HHHHHHHHHhHcCCceeeEEEe
Q 030945 109 VFIVDIRAD----KKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 109 vFiVd~kAn----K~qIKqAVkklydV~V~kVNTl 139 (168)
|.+|.-.|. |.+|-+||..+|||...+|+.+
T Consensus 149 VlVVAeGa~~~~Vk~~I~~AV~~ll~v~~hkI~V~ 183 (186)
T TIGR02830 149 VLVVAEGAENPQIKYRIVEAVSRVLDVPAHKVSVL 183 (186)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHhCCCcceEEEE
Confidence 566666655 6677789999999999999976
No 32
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=29.64 E-value=1.1e+02 Score=19.03 Aligned_cols=35 Identities=11% Similarity=0.238 Sum_probs=30.0
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEee
Q 030945 106 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140 (168)
Q Consensus 106 NtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli 140 (168)
.++.|.|+...+=.++|+.++..+|+.+.....+.
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 47889999999999999999999999887665543
No 33
>PRK04046 translation initiation factor IF-6; Provisional
Probab=29.30 E-value=1.2e+02 Score=25.65 Aligned_cols=51 Identities=10% Similarity=0.173 Sum_probs=39.4
Q ss_pred cccccccccchhhhhhhhcC---------------------CeEEEEEecCCCHHHHHHHHHhHcCCceeeEE
Q 030945 86 YQILKYPLTTESAMKKIEDN---------------------NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 137 (168)
Q Consensus 86 ~~IIk~Pl~TEkamk~~E~n---------------------NtlvFiVd~kAnK~qIKqAVkklydV~V~kVN 137 (168)
+-+|..|.++|...+.+++. |-..++|++.++..+++ .+++.+||+|....
T Consensus 66 ~g~lvp~~~~~~e~~~l~e~L~v~V~~~~~~~~~vGn~i~~N~~G~lv~p~~~~ee~~-~i~~~L~V~v~~~t 137 (222)
T PRK04046 66 NGILVPSIVLDEELELLKEALDLNVEVLPSKLTALGNLILANDKGALVHPELSDEARK-VIEDTLGVEVERGT 137 (222)
T ss_pred ceEEeCCCCCHHHHHHHHHhcCceEEEEeccccceEeEEEEcCcEEEECCCCCHHHHH-HHHHhhCceEEEEe
Confidence 34566777788877777653 56678999999999998 58888899886654
No 34
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=28.68 E-value=44 Score=26.23 Aligned_cols=19 Identities=26% Similarity=0.473 Sum_probs=13.6
Q ss_pred CCCHHHHHHHHHhHcCCce
Q 030945 115 RADKKKIKDAVKKMYDIQA 133 (168)
Q Consensus 115 kAnK~qIKqAVkklydV~V 133 (168)
+|+|.||.++|+++++.+.
T Consensus 114 ~A~KeqV~~mv~~ll~l~~ 132 (149)
T PF02075_consen 114 RASKEQVAFMVRKLLGLDE 132 (149)
T ss_dssp T--HHHHHHHHHHHTT---
T ss_pred ccCHHHHHHHHHHHhCCCC
Confidence 8999999999999998765
No 35
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.43 E-value=99 Score=23.54 Aligned_cols=42 Identities=7% Similarity=0.147 Sum_probs=31.1
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHcC
Q 030945 81 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYD 130 (168)
Q Consensus 81 ~kld~~~IIk~Pl~TEkamk~~E~nNtlvFiVd~kAnK~qIKqAVkklyd 130 (168)
..++...|--.|.-+ .+..|.|.||...+..+++++++.|-.
T Consensus 65 ~gINLt~IESRP~~~--------~~~eY~FfIdieg~~~~~~~aL~~L~~ 106 (115)
T cd04930 65 FEAKIHHLESRPSRK--------EGGDLEVLVRCEVHRSDLLQLISSLRQ 106 (115)
T ss_pred CCCCEEEEECCcCCC--------CCceEEEEEEEEeCHHHHHHHHHHHHH
Confidence 345555666667543 246899999999999999999988743
No 36
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=28.11 E-value=1.3e+02 Score=19.48 Aligned_cols=35 Identities=14% Similarity=0.234 Sum_probs=30.6
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
.+++.|.|+...+=.++|+.++..+|+.+......
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 44 (72)
T cd01809 10 SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI 44 (72)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE
Confidence 46899999999999999999999999988766554
No 37
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=28.01 E-value=1.1e+02 Score=20.31 Aligned_cols=33 Identities=24% Similarity=0.343 Sum_probs=29.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEE
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 137 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVN 137 (168)
.+++.+.|+...+=.++|+.++...|+++....
T Consensus 8 g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~ 40 (70)
T cd01798 8 GHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLR 40 (70)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCCCHHHeE
Confidence 468999999999999999999999999887653
No 38
>TIGR00323 eIF-6 translation initiation factor eIF-6, putative. This model finds translation initiation factor eIF-6 of eukaryotes, which is a ribosome dissociation factor. It also finds a set of apparent archaeal orthologs, slightly shorter proteins not yet shown to act as initiation factors; these probably should be designated as translation initiation factor aIF-6, putative.
Probab=27.93 E-value=1.2e+02 Score=25.63 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=36.5
Q ss_pred cccccccccchhhhhhhhc-----------------------CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 86 YQILKYPLTTESAMKKIED-----------------------NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 86 ~~IIk~Pl~TEkamk~~E~-----------------------nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
+-+|.+|.+++...+.+++ +| ..-+|++.++..+++. ++.++||+|..- |+
T Consensus 104 ~G~lv~~~~~~~e~~~i~~~L~v~V~~~~i~~~~~vG~~~v~nN-~G~lvhP~~s~ee~~~-i~d~LgV~v~~g-Ti 177 (215)
T TIGR00323 104 YGALASPELDRDTEELISDVLGVEVFRGTIAGLITVGSYAVVTN-RGGLVHPQTSVQEQEE-LSSLLGVELVAG-TV 177 (215)
T ss_pred ceEEeCCCCCHHHHHHHHHhcCCcEEEEecccccccceEEEEeC-cEEEECCCCCHHHHHH-HHHHhCCcEEEE-Ee
Confidence 4566777777777666643 33 3457889999999884 889999997655 44
No 39
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=24.81 E-value=1.9e+02 Score=22.81 Aligned_cols=41 Identities=27% Similarity=0.362 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHhHcCCceeeEEEeeCCC------CeeeEEEEcCCCC
Q 030945 116 ADKKKIKDAVKKMYDIQAKKVNTLIRPD------GTKKAYVRLTPDS 156 (168)
Q Consensus 116 AnK~qIKqAVkklydV~V~kVNTli~p~------g~KKAyV~La~d~ 156 (168)
.=+.||++.++..||+.+.+|..-+..+ .-++..|.|.++.
T Consensus 87 ~l~~~i~~~l~~~~g~~~~~V~v~~~~~~~~~~~~I~~I~v~l~~~~ 133 (188)
T PF09581_consen 87 QLEKQIKALLEDKYGVEVVKVEVEIDEDEESPDFEIKEIKVTLSEEE 133 (188)
T ss_pred HHHHHHHHHHhhhcCCceEEEEEEEEcCCCccccceeEEEEEEcCCC
Confidence 3467889999989999999999988766 3577888888754
No 40
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=24.59 E-value=1.9e+02 Score=23.18 Aligned_cols=46 Identities=26% Similarity=0.376 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHhHcCCceeeEEEee---CCCCee---eEEEEcCCCCcHHHHHHhh
Q 030945 115 RADKKKIKDAVKKMYDIQAKKVNTLI---RPDGTK---KAYVRLTPDSDALDVANKI 165 (168)
Q Consensus 115 kAnK~qIKqAVkklydV~V~kVNTli---~p~g~K---KAyV~La~d~dAlDvAnki 165 (168)
..+|.||++-+-++|.++...|-..- .-||-| .|-| ||.+|+|.++
T Consensus 34 ~vsK~EirEKla~mYkt~~d~V~vfgfrt~~GggkstgfalI-----Ydsve~akkf 85 (132)
T KOG3424|consen 34 NVSKTEIREKLAKMYKTTPDAVFVFGFRTHFGGGKSTGFALI-----YDSVEYAKKF 85 (132)
T ss_pred CCCHHHHHHHHHHHhcCCcceEEEEEeeeccCCcccceeeee-----eehHHHHHhc
Confidence 57899999999999988765554322 223322 2222 6889999875
No 41
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=24.19 E-value=1.1e+02 Score=20.27 Aligned_cols=22 Identities=50% Similarity=0.656 Sum_probs=18.4
Q ss_pred CCCeeeEEEEcCCCCcHHHHHHhhc
Q 030945 142 PDGTKKAYVRLTPDSDALDVANKIG 166 (168)
Q Consensus 142 p~g~KKAyV~La~d~dAlDvAnkig 166 (168)
|||.-+- |..|..++|+|..|+
T Consensus 6 pdG~~~~---~~~g~T~~d~A~~I~ 27 (60)
T PF02824_consen 6 PDGSIKE---LPEGSTVLDVAYSIH 27 (60)
T ss_dssp TTSCEEE---EETTBBHHHHHHHHS
T ss_pred CCCCeee---CCCCCCHHHHHHHHC
Confidence 8887543 889999999999986
No 42
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=24.04 E-value=2e+02 Score=18.85 Aligned_cols=35 Identities=11% Similarity=0.222 Sum_probs=30.4
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
..+..|.|+...+=.++|+.++..+|+.+.....+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~ 44 (76)
T cd01806 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI 44 (76)
T ss_pred CCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE
Confidence 45788999999999999999999999999876655
No 43
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=23.89 E-value=1.7e+02 Score=26.19 Aligned_cols=55 Identities=9% Similarity=0.160 Sum_probs=37.9
Q ss_pred CeEEEE--EecCCCHHHHHHHHHhHcCCceeeEEEeeCCC-Ceee--EEEEcCCCCcHHHHH
Q 030945 106 NTLVFI--VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-GTKK--AYVRLTPDSDALDVA 162 (168)
Q Consensus 106 NtlvFi--Vd~kAnK~qIKqAVkklydV~V~kVNTli~p~-g~KK--AyV~La~d~dAlDvA 162 (168)
++-+|+ ++..++..+|++.|+.... |..|..+..+. |..+ |||++....+|.+..
T Consensus 107 ~~~LfVgnLp~~~te~~L~~lF~~~G~--V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai 166 (346)
T TIGR01659 107 GTNLIVNYLPQDMTDRELYALFRTIGP--INTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166 (346)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHhcCC--EEEEEEEecCCCCccCcEEEEEEccHHHHHHHH
Confidence 445555 5789999999999998654 66666665433 3333 999998776665543
No 44
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=23.63 E-value=1.9e+02 Score=19.19 Aligned_cols=35 Identities=11% Similarity=0.180 Sum_probs=29.5
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCC--ceeeEEEe
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDI--QAKKVNTL 139 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV--~V~kVNTl 139 (168)
.+++.|.|+...+=.++|+.+...+|+ .+.....+
T Consensus 10 g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~ 46 (77)
T cd01805 10 QQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI 46 (77)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEE
Confidence 468899999999999999999999998 76665443
No 45
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=23.29 E-value=1.8e+02 Score=19.09 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=30.2
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
..++.|.|+...+=.++|+.++..+|+.+......
T Consensus 10 g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~ 44 (76)
T cd01803 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 44 (76)
T ss_pred CCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE
Confidence 35788999999999999999999999988776554
No 46
>PHA01813 hypothetical protein
Probab=23.04 E-value=57 Score=22.57 Aligned_cols=17 Identities=18% Similarity=0.282 Sum_probs=13.8
Q ss_pred CHHHHHHHHHhHcCCcee
Q 030945 117 DKKKIKDAVKKMYDIQAK 134 (168)
Q Consensus 117 nK~qIKqAVkklydV~V~ 134 (168)
--|||.+ +|++|+++|.
T Consensus 19 ~~h~i~~-fe~~~~~kvi 35 (58)
T PHA01813 19 FPHQISM-FEDLYDAKVV 35 (58)
T ss_pred ChhHHHH-HHhhhceeEE
Confidence 3578886 8999999884
No 47
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. 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=22.99 E-value=1.3e+02 Score=19.54 Aligned_cols=35 Identities=6% Similarity=0.155 Sum_probs=30.0
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEee
Q 030945 106 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140 (168)
Q Consensus 106 NtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli 140 (168)
.++.+.|+..++=.++|+.++..+|+.+.....+.
T Consensus 10 ~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 44 (71)
T cd01812 10 ESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIF 44 (71)
T ss_pred EEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEee
Confidence 46778899999999999999999999987766553
No 48
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=22.42 E-value=1.9e+02 Score=20.70 Aligned_cols=55 Identities=20% Similarity=0.264 Sum_probs=40.6
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHH
Q 030945 106 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVA 162 (168)
Q Consensus 106 NtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~dAlDvA 162 (168)
..+.|.+.+..+=.++.+.|.+.|++.-..-=+|-+.|.+ -=+|.|..|.| |+-|
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dde-gd~v~ltsd~D-L~ea 64 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDD-EEWVLLTCDAD-LEEC 64 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCC-CCeEEeecHHH-HHHH
Confidence 5889999999999999999999999863223344444544 45688888876 5544
No 49
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=22.00 E-value=1.7e+02 Score=19.90 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=30.1
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 106 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 106 NtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
.++.+.|+...+=.++|+-|+...|+.+..-..+
T Consensus 8 ~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~ 41 (76)
T cd01800 8 QMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQ 41 (76)
T ss_pred eEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE
Confidence 5899999999999999999999999988776544
No 50
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=21.59 E-value=2.4e+02 Score=23.85 Aligned_cols=57 Identities=12% Similarity=0.181 Sum_probs=0.0
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEeeCC-----CCeeeEEEEcCCCCcHHHHHHhh
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP-----DGTKKAYVRLTPDSDALDVANKI 165 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTli~p-----~g~KKAyV~La~d~dAlDvAnki 165 (168)
.+.+|+-++...+-.+|++.++. || .|..|+.+..+ .|+ |||.+..-.+|......+
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~~-fG-~v~~v~i~~d~~t~~skG~--aFV~F~~~~~A~~Ai~~l 331 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFGP-FG-AVQNVKIIRDLTTNQCKGY--GFVSMTNYDEAAMAILSL 331 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHh-CC-CeEEEEEeEcCCCCCccce--EEEEECCHHHHHHHHHHh
No 51
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=21.54 E-value=1.4e+02 Score=21.01 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=23.5
Q ss_pred eEEEEEecCCCHHHHHHHHHhHc------CCceeeEEEe
Q 030945 107 TLVFIVDIRADKKKIKDAVKKMY------DIQAKKVNTL 139 (168)
Q Consensus 107 tlvFiVd~kAnK~qIKqAVkkly------dV~V~kVNTl 139 (168)
.++|++++..+..++++.++.+- |-.|.++..+
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~ 42 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENW 42 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEE
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEE
Confidence 36899999999999998877653 4456565553
No 52
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=21.05 E-value=2e+02 Score=20.27 Aligned_cols=47 Identities=11% Similarity=0.048 Sum_probs=33.8
Q ss_pred EEEecCCCHHHHHHHHHhHcCCceeeEEEeeCCCCeeeEEEEcCCCCc
Q 030945 110 FIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSD 157 (168)
Q Consensus 110 FiVd~kAnK~qIKqAVkklydV~V~kVNTli~p~g~KKAyV~La~d~d 157 (168)
-.++...+=.|+|+-++.++|+++.........++. .....|..|..
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~-~~~~~l~~d~~ 63 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDD-KLVSKLDDDDA 63 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCC-CeEeecCCCcc
Confidence 448889999999999999999999998886554432 12223554543
No 53
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=20.58 E-value=1.2e+02 Score=20.61 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=20.6
Q ss_pred CCeEEEEEecCCC--HHHHHHHHHhHcC
Q 030945 105 NNTLVFIVDIRAD--KKKIKDAVKKMYD 130 (168)
Q Consensus 105 nNtlvFiVd~kAn--K~qIKqAVkklyd 130 (168)
+..|+|.||...+ ..+++++++.|=+
T Consensus 41 ~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 41 LWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 4679999998875 8888888887643
No 54
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=20.50 E-value=88 Score=24.44 Aligned_cols=19 Identities=26% Similarity=0.642 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHhHcCCce
Q 030945 115 RADKKKIKDAVKKMYDIQA 133 (168)
Q Consensus 115 kAnK~qIKqAVkklydV~V 133 (168)
+|+|.|+.++|+.+++.+-
T Consensus 115 ~A~KeqV~~mv~~~l~~~~ 133 (154)
T cd00529 115 KADKDQVQHMVKRLLNLSE 133 (154)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 6999999999999998765
No 55
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=20.14 E-value=2e+02 Score=19.31 Aligned_cols=35 Identities=11% Similarity=0.184 Sum_probs=30.5
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHcCCceeeEEEe
Q 030945 105 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 139 (168)
Q Consensus 105 nNtlvFiVd~kAnK~qIKqAVkklydV~V~kVNTl 139 (168)
.+++++.|+...+=.++|+.++...|+.+.....+
T Consensus 10 G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~ 44 (74)
T cd01807 10 GRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLL 44 (74)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE
Confidence 47889999999999999999999999988765543
Done!