Query 031815
Match_columns 152
No_of_seqs 202 out of 1166
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:44:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031815.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031815hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00191 60S ribosomal protein 100.0 2.4E-62 5.3E-67 381.7 14.5 142 10-152 4-145 (145)
2 KOG1751 60s ribosomal protein 100.0 2.3E-62 5.1E-67 385.5 11.3 146 7-152 10-157 (157)
3 PRK14548 50S ribosomal protein 100.0 1.7E-35 3.7E-40 212.6 9.6 84 69-152 1-84 (84)
4 TIGR03636 L23_arch archaeal ri 100.0 2.2E-33 4.7E-38 198.8 9.5 77 76-152 1-77 (77)
5 PRK05738 rplW 50S ribosomal pr 99.9 2.7E-28 5.8E-33 177.2 7.4 77 70-147 1-90 (92)
6 CHL00030 rpl23 ribosomal prote 99.9 2.2E-27 4.8E-32 173.4 7.6 76 70-147 1-89 (93)
7 COG0089 RplW Ribosomal protein 99.9 1.7E-27 3.7E-32 174.5 5.9 83 69-151 1-86 (94)
8 PRK12280 rplW 50S ribosomal pr 99.9 1.6E-26 3.5E-31 182.8 7.5 79 67-147 1-92 (158)
9 PF00276 Ribosomal_L23: Riboso 99.9 2.9E-26 6.3E-31 165.8 7.6 78 70-148 1-91 (91)
10 PF03939 Ribosomal_L23eN: Ribo 99.8 2.4E-21 5.3E-26 129.3 -0.8 53 12-64 2-54 (54)
11 KOG4089 Predicted mitochondria 97.2 0.00038 8.3E-09 55.9 4.3 49 72-127 27-75 (165)
12 PF08777 RRM_3: RNA binding mo 76.1 8.8 0.00019 28.2 5.4 52 92-148 4-56 (105)
13 COG0089 RplW Ribosomal protein 73.8 1.3 2.8E-05 32.7 0.5 22 125-147 71-92 (94)
14 cd04929 ACT_TPH ACT domain of 67.0 11 0.00024 26.0 3.9 41 66-114 25-65 (74)
15 PF03780 Asp23: Asp23 family; 60.6 13 0.00028 26.2 3.5 24 102-125 82-105 (108)
16 cd04904 ACT_AAAH ACT domain of 50.0 33 0.00072 23.0 4.0 42 65-114 24-65 (74)
17 cd01769 UBL Ubiquitin-like dom 49.5 43 0.00093 20.9 4.3 35 88-122 6-40 (69)
18 PLN02817 glutathione dehydroge 48.9 15 0.00033 30.8 2.6 39 111-149 24-62 (265)
19 cd04931 ACT_PAH ACT domain of 48.3 27 0.00058 25.0 3.4 41 65-113 38-79 (90)
20 PF00076 RRM_1: RNA recognitio 47.3 51 0.0011 20.3 4.3 53 95-147 5-57 (70)
21 PF10298 WhiA_N: WhiA N-termin 45.1 33 0.00072 23.8 3.4 62 89-152 22-86 (86)
22 PRK01178 rps24e 30S ribosomal 45.1 1.2E+02 0.0027 22.3 6.7 69 77-149 5-81 (99)
23 PF14560 Ubiquitin_2: Ubiquiti 44.0 52 0.0011 22.6 4.3 53 91-143 15-67 (87)
24 PF00240 ubiquitin: Ubiquitin 42.7 59 0.0013 20.8 4.2 36 89-124 5-40 (69)
25 cd04930 ACT_TH ACT domain of t 41.2 45 0.00097 24.9 3.8 42 65-114 65-106 (115)
26 PF14259 RRM_6: RNA recognitio 39.3 45 0.00098 21.1 3.2 52 96-149 6-59 (70)
27 cd01796 DDI1_N DNA damage indu 39.0 56 0.0012 21.8 3.7 34 88-121 8-41 (71)
28 PF01282 Ribosomal_S24e: Ribos 36.9 1.1E+02 0.0023 21.7 5.0 48 98-148 11-62 (84)
29 PLN03134 glycine-rich RNA-bind 35.7 1E+02 0.0022 23.4 5.2 56 91-148 37-95 (144)
30 PTZ00044 ubiquitin; Provisiona 35.3 84 0.0018 20.6 4.1 36 88-123 9-44 (76)
31 TIGR02830 spore_III_AG stage I 34.3 46 0.00099 27.3 3.1 31 93-123 149-183 (186)
32 cd01809 Scythe_N Ubiquitin-lik 33.6 98 0.0021 19.7 4.1 35 89-123 10-44 (72)
33 smart00213 UBQ Ubiquitin homol 32.9 95 0.0021 19.0 3.9 35 90-124 10-44 (64)
34 cd01798 parkin_N amino-termina 32.4 88 0.0019 20.4 3.8 33 89-121 8-40 (70)
35 PF02075 RuvC: Crossover junct 30.9 39 0.00085 26.0 2.1 19 99-117 114-132 (149)
36 PF09581 Spore_III_AF: Stage I 29.8 1.4E+02 0.003 23.2 5.1 41 100-140 87-133 (188)
37 PRK04046 translation initiatio 28.6 1.2E+02 0.0025 25.3 4.7 51 70-121 66-137 (222)
38 cd01806 Nedd8 Nebb8-like ubiq 28.4 1.5E+02 0.0033 19.0 4.4 35 89-123 10-44 (76)
39 KOG3279 Uncharacterized conser 28.3 6.3 0.00014 33.7 -2.9 61 22-96 90-150 (283)
40 cd01812 BAG1_N Ubiquitin-like 27.3 1E+02 0.0022 19.7 3.4 35 90-124 10-44 (71)
41 cd01803 Ubiquitin Ubiquitin. U 27.3 1.4E+02 0.003 19.2 4.1 35 89-123 10-44 (76)
42 cd01789 Alp11_N Ubiquitin-like 27.0 1.3E+02 0.0029 20.7 4.1 37 92-128 15-51 (84)
43 cd01805 RAD23_N Ubiquitin-like 26.7 1.6E+02 0.0035 19.2 4.3 35 89-123 10-46 (77)
44 PHA01813 hypothetical protein 26.5 46 0.001 22.5 1.6 24 94-118 11-35 (58)
45 PF02824 TGS: TGS domain; Int 26.5 99 0.0021 20.1 3.2 22 126-150 6-27 (60)
46 cd01800 SF3a120_C Ubiquitin-li 26.1 1.3E+02 0.0029 20.0 3.9 34 90-123 8-41 (76)
47 KOG3424 40S ribosomal protein 25.9 1.9E+02 0.004 22.7 5.0 46 99-149 34-85 (132)
48 cd04905 ACT_CM-PDT C-terminal 25.1 88 0.0019 20.8 2.9 41 66-114 26-68 (80)
49 TIGR01659 sex-lethal sex-letha 25.1 1.6E+02 0.0035 25.8 5.2 55 90-146 107-166 (346)
50 KOG0107 Alternative splicing f 25.1 2E+02 0.0043 24.0 5.3 52 91-146 13-64 (195)
51 TIGR00323 eIF-6 translation in 24.2 1.5E+02 0.0033 24.6 4.6 49 70-120 104-175 (215)
52 cd01807 GDX_N ubiquitin-like d 24.0 1.6E+02 0.0034 19.5 3.9 35 89-123 10-44 (74)
53 cd04880 ACT_AAAH-PDT-like ACT 23.8 1.4E+02 0.003 19.5 3.6 41 66-114 24-66 (75)
54 PF09439 SRPRB: Signal recogni 23.2 55 0.0012 26.4 1.8 30 86-115 73-102 (181)
55 cd01799 Hoil1_N Ubiquitin-like 22.8 1.6E+02 0.0034 20.1 3.8 35 88-122 11-45 (75)
56 cd06407 PB1_NLP A PB1 domain i 22.1 2.1E+02 0.0046 20.0 4.4 56 90-147 10-65 (82)
57 cd00529 RuvC_resolvase Hollida 21.9 82 0.0018 24.2 2.4 19 99-117 115-133 (154)
58 PF01250 Ribosomal_S6: Ribosom 21.1 1.5E+02 0.0032 20.5 3.4 33 91-123 4-42 (92)
59 PRK00039 ruvC Holliday junctio 20.3 91 0.002 24.6 2.4 29 88-116 95-134 (164)
60 cd01802 AN1_N ubiquitin-like d 20.3 1.9E+02 0.004 21.0 3.9 34 89-122 37-70 (103)
61 cd06257 DnaJ DnaJ domain or J- 20.2 64 0.0014 19.5 1.3 20 94-113 6-25 (55)
62 TIGR00228 ruvC crossover junct 20.2 92 0.002 24.7 2.4 29 88-116 91-130 (156)
No 1
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=100.00 E-value=2.4e-62 Score=381.70 Aligned_cols=142 Identities=65% Similarity=0.965 Sum_probs=137.9
Q ss_pred CCChhHHHHHHHHhhhcccCcccceeeeccccccCCCccCCCCCCCCCCCCCCCCCCCCccccccccccchhhhhhhhcC
Q 031815 10 KADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDN 89 (152)
Q Consensus 10 ~~~~~aka~kakkavlkg~~~~~~~k~~~s~~f~~pktl~~~r~pky~rk~~p~~~kld~~~IIk~Pl~TEkamk~~E~~ 89 (152)
...++++|++|++++++|+|+ +++|+|+|++|+||+||+|+|+|+|||+|.|++++||+|+||++|++||+||+++|++
T Consensus 4 ~~~~~~ka~~a~k~~~~g~~~-~~~k~r~~~~f~rpktl~l~r~pky~r~~~~~~~~md~~~IIk~Pl~TEKa~~~~E~~ 82 (145)
T PTZ00191 4 AKKAKKKAKKAAKAAKKGVKV-KKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDKYSIIKYPLTTEKAMKKIEDN 82 (145)
T ss_pred cchHHHHHHHHHHHHhccccc-ceeEeeecceecCCccccCCCCCCCcccccCCCCCCchhhhhhcccccHHHHHHHhhC
Confidence 345688999999999999998 6799999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 031815 90 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 152 (152)
Q Consensus 90 NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvankigii 152 (152)
|+|+|+||++|||+|||+|||+||||+|.+|||+|+|+|||||||+|++|||||||||+||||
T Consensus 83 N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~g~KKA~V~L~~~~~aidva~kiGi~ 145 (145)
T PTZ00191 83 NTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKAYIRLSPDVDALDVANKIGII 145 (145)
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG1751 consensus 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-62 Score=385.49 Aligned_cols=146 Identities=70% Similarity=0.972 Sum_probs=142.6
Q ss_pred CCCCCChhHHHHHHHHhhhcccCccccee-eeccccccCCCccCCCCCCCCCCCCCCCCCCCCcccc-ccccccchhhhh
Q 031815 7 ETKKADPKVQALKTAKAVKSGRTFKKAKK-IRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQI-LKYPLTTESAMK 84 (152)
Q Consensus 7 ~~~~~~~~aka~kakkavlkg~~~~~~~k-~~~s~~f~~pktl~~~r~pky~rk~~p~~~kld~~~I-Ik~Pl~TEkamk 84 (152)
+||+++++++||+|+|||++|+|||++++ ++++++|++|.+++++|+|+|||+|.|+||+||+|.+ |++||+||++|+
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 69999999999999999999999998765 9999999999999999999999999999999999777 899999999999
Q ss_pred hhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 031815 85 KIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 152 (152)
Q Consensus 85 ~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvankigii 152 (152)
.+||||||||+||.+||||||||||++|||++|++|||||+|+|+|||||+|++|||||||||+||||
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 3
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=100.00 E-value=1.7e-35 Score=212.60 Aligned_cols=84 Identities=52% Similarity=0.864 Sum_probs=82.0
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHh
Q 031815 69 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANK 148 (152)
Q Consensus 69 ~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvank 148 (152)
.|+||++|++||+++.++|++|+|+|+||++|||.|||+|||++|||+|.+|||++.++|||||||+|.+|++|+|+|++
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 031815 149 IGII 152 (152)
Q Consensus 149 igii 152 (152)
||++
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=100.00 E-value=2.2e-33 Score=198.79 Aligned_cols=77 Identities=51% Similarity=0.808 Sum_probs=75.7
Q ss_pred cccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhhcCC
Q 031815 76 PLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 152 (152)
Q Consensus 76 Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvankigii 152 (152)
|++||++|.++|++|+|+|+||++|||+|||+|||++|||+|.+|||++.++|||||||+|.+|++|+|||++||++
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=99.95 E-value=2.7e-28 Score=177.22 Aligned_cols=77 Identities=35% Similarity=0.481 Sum_probs=73.1
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCC-------------CCeeeEEEEc
Q 031815 70 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP-------------DGTKKAYVRL 136 (152)
Q Consensus 70 ~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~-------------~g~KKAyV~L 136 (152)
|+||++|++||+||.++|++|+|+|.||++|||+|||+|||++|||+|.+|||++.+ .+||||||+|
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 031815 137 TPDSDALDVAN 147 (152)
Q Consensus 137 ~~d~daldvan 147 (152)
.+|++ +|+.+
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=99.94 E-value=2.2e-27 Score=173.35 Aligned_cols=76 Identities=24% Similarity=0.409 Sum_probs=71.4
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCC-------------eeeEEEEc
Q 031815 70 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDG-------------TKKAYVRL 136 (152)
Q Consensus 70 ~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g-------------~KKAyV~L 136 (152)
++||++|++||+|+.++| +|+|+|+||++|||.|||+|||++|||+|.+|||++.+++ ||||||+|
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 5999999999999999999999999999999999999975 99999999
Q ss_pred CCCCcHHHHHH
Q 031815 137 TPDSDALDVAN 147 (152)
Q Consensus 137 ~~d~daldvan 147 (152)
.+|++ ||++.
T Consensus 80 ~~g~~-I~~~~ 89 (93)
T CHL00030 80 QPGYS-IPLFR 89 (93)
T ss_pred CCcCE-ecccc
Confidence 99987 88864
No 7
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.7e-27 Score=174.46 Aligned_cols=83 Identities=41% Similarity=0.530 Sum_probs=74.2
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEE---cCCCCcHHHH
Q 031815 69 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVR---LTPDSDALDV 145 (152)
Q Consensus 69 ~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~---L~~d~daldv 145 (152)
+|+||++|++||+||.++|++|+|||+||++|||.|||+|||+||||+|.+|||||++++.|++++. +.+++++.+|
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 4899999999999999998889999999999999999999999999999999999999977777775 7777777777
Q ss_pred HHhhcC
Q 031815 146 ANKIGI 151 (152)
Q Consensus 146 ankigi 151 (152)
+.++|.
T Consensus 81 ~l~~G~ 86 (94)
T COG0089 81 TLKEGQ 86 (94)
T ss_pred EccCCC
Confidence 766664
No 8
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.93 E-value=1.6e-26 Score=182.78 Aligned_cols=79 Identities=30% Similarity=0.453 Sum_probs=74.7
Q ss_pred CCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCC-------------CeeeEE
Q 031815 67 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-------------GTKKAY 133 (152)
Q Consensus 67 ld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~-------------g~KKAy 133 (152)
||+|+||++|++||+++.++|+ |+|+|.||++|||+||++|||.+|||+|.+|||+++++ +|||||
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 7999999999999999999885 89999999999999999999999999999999999997 799999
Q ss_pred EEcCCCCcHHHHHH
Q 031815 134 VRLTPDSDALDVAN 147 (152)
Q Consensus 134 V~L~~d~daldvan 147 (152)
|+|.+|++ ||+..
T Consensus 80 VtL~~g~~-I~~f~ 92 (158)
T PRK12280 80 VTLAEGYS-INLFP 92 (158)
T ss_pred EECCCCCE-eeccC
Confidence 99999986 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=99.93 E-value=2.9e-26 Score=165.78 Aligned_cols=78 Identities=42% Similarity=0.638 Sum_probs=71.5
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCC-------------CeeeEEEEc
Q 031815 70 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-------------GTKKAYVRL 136 (152)
Q Consensus 70 ~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~-------------g~KKAyV~L 136 (152)
|+||++|++||+++.++|++|+|+|+||++|||+|||+|||++|||+|.+|||++.++ +||||||+|
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 469999999
Q ss_pred CCCCcHHHHHHh
Q 031815 137 TPDSDALDVANK 148 (152)
Q Consensus 137 ~~d~daldvank 148 (152)
.+| +.+|++++
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=99.80 E-value=2.4e-21 Score=129.33 Aligned_cols=53 Identities=60% Similarity=0.833 Sum_probs=17.4
Q ss_pred ChhHHHHHHHHhhhcccCcccceeeeccccccCCCccCCCCCCCCCCCCCCCC
Q 031815 12 DPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPR 64 (152)
Q Consensus 12 ~~~aka~kakkavlkg~~~~~~~k~~~s~~f~~pktl~~~r~pky~rk~~p~~ 64 (152)
++++||++|+|+|++|+|+++.++||||++|+||+||+|+|+|+|||+|+|+|
T Consensus 2 ~a~~KA~kakKav~KG~~~~~~rKirts~~F~rPKTL~l~R~PKYprkS~p~r 54 (54)
T PF03939_consen 2 KAKAKALKAKKAVLKGVHSKKKRKIRTSVTFRRPKTLRLPRQPKYPRKSVPRR 54 (54)
T ss_dssp ----------------------HHHHHHHHHT-SS--------SS-SSS---S
T ss_pred chHHHHHHHHHHHhcCCCccccceeecCcccCCCcccccCCCCCCcccCCCCC
Confidence 35778999999999999999889999999999999999999999999999985
No 11
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=97.25 E-value=0.00038 Score=55.92 Aligned_cols=49 Identities=24% Similarity=0.398 Sum_probs=42.0
Q ss_pred cccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCC
Q 031815 72 ILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD 127 (152)
Q Consensus 72 IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~ 127 (152)
+|..|+.+. -.++.+|+|+..+||.+++++++.+||.+|.+|.|.+..+
T Consensus 27 ~l~rp~~~q-------~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~G 75 (165)
T KOG4089|consen 27 NLVRPLVTQ-------PPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHG 75 (165)
T ss_pred hhhcccccC-------CCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeec
Confidence 334476654 2479999999999999999999999999999999999876
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=76.15 E-value=8.8 Score=28.16 Aligned_cols=52 Identities=23% Similarity=0.407 Sum_probs=29.7
Q ss_pred EEEE-EecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHh
Q 031815 92 LVFI-VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANK 148 (152)
Q Consensus 92 lvF~-Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvank 148 (152)
|-|. ++...++.+||.++.. |+ +|.-|.- ..|...+||++....+|-.+..+
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yVD~---~~G~~~g~VRf~~~~~A~~a~~~ 56 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYVDF---SRGDTEGYVRFKTPEAAQKALEK 56 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEEE-----TT-SEEEEEESS---HHHHHHH
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceEEe---cCCCCEEEEEECCcchHHHHHHH
Confidence 4466 7788999999999998 55 5555543 45889999999988777655443
No 13
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=73.78 E-value=1.3 Score=32.72 Aligned_cols=22 Identities=32% Similarity=0.388 Sum_probs=18.3
Q ss_pred CCCCeeeEEEEcCCCCcHHHHHH
Q 031815 125 RPDGTKKAYVRLTPDSDALDVAN 147 (152)
Q Consensus 125 ~~~g~KKAyV~L~~d~daldvan 147 (152)
...+||+|||+|.+|+. ||++.
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
>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=67.03 E-value=11 Score=25.96 Aligned_cols=41 Identities=12% Similarity=0.243 Sum_probs=30.7
Q ss_pred CCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhC
Q 031815 66 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYD 114 (152)
Q Consensus 66 kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~ 114 (152)
.++...|-.+|.-. .+..|.|.||...+..+++++++.|=.
T Consensus 25 ~inl~~IeSRP~~~--------~~~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 25 GINVVHIESRKSKR--------RSSEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred CCCEEEEEeccCCC--------CCceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 45555666666543 235799999999999999999998743
No 15
>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=60.56 E-value=13 Score=26.25 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=21.7
Q ss_pred HHHHHHHHHhHhCCceeeEEEeeC
Q 031815 102 KKKIKDAVKKMYDIQAKKVNTLIR 125 (152)
Q Consensus 102 K~qIKqAvekly~VkV~kVNTli~ 125 (152)
+.+|+++|+.+-|++|..||..+.
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 16
>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=49.96 E-value=33 Score=23.01 Aligned_cols=42 Identities=14% Similarity=0.250 Sum_probs=31.9
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhC
Q 031815 65 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYD 114 (152)
Q Consensus 65 ~kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~ 114 (152)
..++...|--+|.-.+ ...|.|.||......+++++++.|-.
T Consensus 24 ~~iNlt~IeSRP~~~~--------~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 24 FGVNLTHIESRPSRRN--------GSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred CCCcEEEEECCCCCCC--------CceEEEEEEEEcChHHHHHHHHHHHH
Confidence 4556667777776542 35799999999988899999998754
No 17
>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=49.49 E-value=43 Score=20.90 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=30.8
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEE
Q 031815 88 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNT 122 (152)
Q Consensus 88 ~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNT 122 (152)
+...+.|.++..++=.++|+.+.+.+++.+.....
T Consensus 6 ~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l 40 (69)
T cd01769 6 TGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL 40 (69)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEE
Confidence 35688899999999999999999999998887766
No 18
>PLN02817 glutathione dehydrogenase (ascorbate)
Probab=48.90 E-value=15 Score=30.81 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=34.5
Q ss_pred hHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHHhh
Q 031815 111 KMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKI 149 (152)
Q Consensus 111 kly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvanki 149 (152)
.-|++.+..+|++.++++.+++++++.+..+.+|++.|-
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (265)
T PLN02817 24 PRFGTSHGGAKGVKRVGGRRRKYLTAITMSSPLEVCVKA 62 (265)
T ss_pred ccccceeecccccccCCcccceeEEecCCCccHHHHHhc
Confidence 347788889999999999999999999999999999874
No 19
>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=48.33 E-value=27 Score=25.01 Aligned_cols=41 Identities=10% Similarity=0.268 Sum_probs=31.5
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEecCCC-HHHHHHHHHhHh
Q 031815 65 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRAD-KKKIKDAVKKMY 113 (152)
Q Consensus 65 ~kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAn-K~qIKqAvekly 113 (152)
..++...|--+|.-++ ...|.|.||.... ...++++++.|-
T Consensus 38 ~~INLt~IeSRP~~~~--------~~~Y~FfVDieg~~~~~~~~~l~~L~ 79 (90)
T cd04931 38 KDINLTHIESRPSRLN--------KDEYEFFINLDKKSAPALDPIIKSLR 79 (90)
T ss_pred CCCCEEEEEeccCCCC--------CceEEEEEEEEcCCCHHHHHHHHHHH
Confidence 4667777888886542 3589999999986 788889988874
No 20
>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=47.28 E-value=51 Score=20.25 Aligned_cols=53 Identities=15% Similarity=0.178 Sum_probs=34.4
Q ss_pred EEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHH
Q 031815 95 IVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVAN 147 (152)
Q Consensus 95 ~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvan 147 (152)
-++...+..+|++.++..=++.-..+..-.......=|||++....+|..+..
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 36778999999999999544444444333112234568999987766655543
No 21
>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=45.14 E-value=33 Score=23.81 Aligned_cols=62 Identities=19% Similarity=0.385 Sum_probs=20.4
Q ss_pred CCeEEEEE--ecCCCHHHHHHHHHhHhCCceeeEEEeeCCC-CeeeEEEEcCCCCcHHHHHHhhcCC
Q 031815 89 NNTLVFIV--DIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-GTKKAYVRLTPDSDALDVANKIGII 152 (152)
Q Consensus 89 ~NtlvF~V--d~kAnK~qIKqAvekly~VkV~kVNTli~~~-g~KKAyV~L~~d~daldvankigii 152 (152)
++.+++.+ +-.+-=.-|-.-++++||+++ .|.+..... ..+..|.-.-++. +.+++.++|++
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 34555444 333444567788999999988 444443222 2234554443443 89999999975
No 22
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=45.08 E-value=1.2e+02 Score=22.31 Aligned_cols=69 Identities=17% Similarity=0.279 Sum_probs=42.8
Q ss_pred ccchhhhhhhhcCCeEEEEEe----cCCCHHHHHHHHHhHhCCceeeEEE--eeC-C-CCeeeEEEEcCCCCcHHHHHHh
Q 031815 77 LTTESAMKKIEDNNTLVFIVD----IRADKKKIKDAVKKMYDIQAKKVNT--LIR-P-DGTKKAYVRLTPDSDALDVANK 148 (152)
Q Consensus 77 l~TEkamk~~E~~NtlvF~Vd----~kAnK~qIKqAvekly~VkV~kVNT--li~-~-~g~KKAyV~L~~d~daldvank 148 (152)
++.|+...++.. ..++|.|. ..-+|.+|+..+-++|+.+..-|=. +.. - +|.=..|... ||.+|.|.+
T Consensus 5 I~~~~~N~LL~R-ke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv~~~~t~fG~g~s~G~a~I---Yds~e~~kk 80 (99)
T PRK01178 5 IISDKENPLLGR-REIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVRKIKTEYGMGKSKGYAKV---YDDKERARK 80 (99)
T ss_pred EEEeeecCCcCc-EEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEEEccCccCCCceEEEEEEE---ECCHHHHHh
Confidence 345566666654 57888875 3568999999999999976543311 111 1 2444555544 456776665
Q ss_pred h
Q 031815 149 I 149 (152)
Q Consensus 149 i 149 (152)
+
T Consensus 81 ~ 81 (99)
T PRK01178 81 I 81 (99)
T ss_pred h
Confidence 4
No 23
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=43.95 E-value=52 Score=22.63 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=38.4
Q ss_pred eEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHH
Q 031815 91 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDAL 143 (152)
Q Consensus 91 tlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~dal 143 (152)
...-.++...+=.|+|+-++.+||+.+.........+..-..+..|..|...|
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 45578899999999999999999999999999887332224555565554433
No 24
>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=42.66 E-value=59 Score=20.82 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=32.1
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEee
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 124 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli 124 (152)
..++.|.|+...+=.++|+.|+...++.+.....+-
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 25
>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=41.23 E-value=45 Score=24.92 Aligned_cols=42 Identities=7% Similarity=0.147 Sum_probs=32.2
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEecCCCHHHHHHHHHhHhC
Q 031815 65 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYD 114 (152)
Q Consensus 65 ~kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAnK~qIKqAvekly~ 114 (152)
..++...|--+|.-+ ....|.|.||...+..+++++++.|-.
T Consensus 65 ~gINLt~IESRP~~~--------~~~eY~FfIdieg~~~~~~~aL~~L~~ 106 (115)
T cd04930 65 FEAKIHHLESRPSRK--------EGGDLEVLVRCEVHRSDLLQLISSLRQ 106 (115)
T ss_pred CCCCEEEEECCcCCC--------CCceEEEEEEEEeCHHHHHHHHHHHHH
Confidence 456666777777544 236799999999999999999998743
No 26
>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=39.26 E-value=45 Score=21.06 Aligned_cols=52 Identities=13% Similarity=0.275 Sum_probs=36.7
Q ss_pred EecCCCHHHHHHHHHhHhCCceeeEEEeeCCC--CeeeEEEEcCCCCcHHHHHHhh
Q 031815 96 VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD--GTKKAYVRLTPDSDALDVANKI 149 (152)
Q Consensus 96 Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~--g~KKAyV~L~~d~daldvanki 149 (152)
+...++..+|.+.++.. | +|..|...-..+ +..-|||.+....+|..+.+..
T Consensus 6 lp~~~~~~~l~~~f~~~-g-~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~ 59 (70)
T PF14259_consen 6 LPPSTTEEDLRNFFSRF-G-PVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELL 59 (70)
T ss_dssp STTT--HHHHHHHCTTS-S-BEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHhc-C-CcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHC
Confidence 45678899999988885 4 577887776544 4678999999777776665543
No 27
>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=38.96 E-value=56 Score=21.76 Aligned_cols=34 Identities=18% Similarity=0.168 Sum_probs=29.7
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEE
Q 031815 88 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 121 (152)
Q Consensus 88 ~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVN 121 (152)
..+++.+.|+..++=.++|+.++..+|+.+..-.
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~ 41 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQ 41 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeE
Confidence 3568999999999999999999999999886643
No 28
>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=36.86 E-value=1.1e+02 Score=21.73 Aligned_cols=48 Identities=15% Similarity=0.317 Sum_probs=30.9
Q ss_pred cCCCHHHHHHHHHhHhCCceee--EEEeeCCC--CeeeEEEEcCCCCcHHHHHHh
Q 031815 98 IRADKKKIKDAVKKMYDIQAKK--VNTLIRPD--GTKKAYVRLTPDSDALDVANK 148 (152)
Q Consensus 98 ~kAnK~qIKqAvekly~VkV~k--VNTli~~~--g~KKAyV~L~~d~daldvank 148 (152)
...+|.||++.+-++|+++..- |+.+.+.- |.-.+|...- |..|.+.+
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~IY---d~~e~~kk 62 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKIY---DSAEALKK 62 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEEE---SSHHHHHH
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEEe---CCHHHHHH
Confidence 4568999999999999986544 35555443 4556666664 44555554
No 29
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=35.67 E-value=1e+02 Score=23.45 Aligned_cols=56 Identities=11% Similarity=0.260 Sum_probs=38.5
Q ss_pred eEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCC-C--eeeEEEEcCCCCcHHHHHHh
Q 031815 91 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-G--TKKAYVRLTPDSDALDVANK 148 (152)
Q Consensus 91 tlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~-g--~KKAyV~L~~d~daldvank 148 (152)
-+|=-++..++..+|++.+++ |+ .|..|.....+. | .-=|||++....+|....+.
T Consensus 37 lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~ 95 (144)
T PLN03134 37 LFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95 (144)
T ss_pred EEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence 444456778999999999988 66 677777665442 2 12499999977766555443
No 30
>PTZ00044 ubiquitin; Provisional
Probab=35.32 E-value=84 Score=20.60 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=31.8
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 88 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 88 ~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
+.+++++.|+...+=.++|+.++...|+.+......
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 346999999999999999999999999988777665
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=34.30 E-value=46 Score=27.25 Aligned_cols=31 Identities=39% Similarity=0.582 Sum_probs=25.2
Q ss_pred EEEEecCCC----HHHHHHHHHhHhCCceeeEEEe
Q 031815 93 VFIVDIRAD----KKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 93 vF~Vd~kAn----K~qIKqAvekly~VkV~kVNTl 123 (152)
|.+|.-.|. |.+|-+||..+|||...+|+.+
T Consensus 149 VlVVAeGa~~~~Vk~~I~~AV~~ll~v~~hkI~V~ 183 (186)
T TIGR02830 149 VLVVAEGAENPQIKYRIVEAVSRVLDVPAHKVSVL 183 (186)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHhCCCcceEEEE
Confidence 566666665 6677789999999999999976
No 32
>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=33.56 E-value=98 Score=19.75 Aligned_cols=35 Identities=14% Similarity=0.234 Sum_probs=30.7
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
.+++.|.|+...+=.++|+.++..+|+.+.....+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 44 (72)
T cd01809 10 SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI 44 (72)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE
Confidence 46899999999999999999999999988776554
No 33
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=32.87 E-value=95 Score=18.99 Aligned_cols=35 Identities=11% Similarity=0.238 Sum_probs=29.9
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEee
Q 031815 90 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 124 (152)
Q Consensus 90 NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli 124 (152)
.++.|.|+...+=.++|+.++..+++.+.....+.
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 47889999999999999999999999887665543
No 34
>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=32.42 E-value=88 Score=20.40 Aligned_cols=33 Identities=24% Similarity=0.343 Sum_probs=29.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEE
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 121 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVN 121 (152)
..++.+.|+...+=.++|+.++...|+.+....
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 35
>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=30.85 E-value=39 Score=25.99 Aligned_cols=19 Identities=26% Similarity=0.473 Sum_probs=13.6
Q ss_pred CCCHHHHHHHHHhHhCCce
Q 031815 99 RADKKKIKDAVKKMYDIQA 117 (152)
Q Consensus 99 kAnK~qIKqAvekly~VkV 117 (152)
+|+|.||.++|+++++.+.
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 8999999999999998764
No 36
>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=29.78 E-value=1.4e+02 Score=23.16 Aligned_cols=41 Identities=27% Similarity=0.362 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHhHhCCceeeEEEeeCCC------CeeeEEEEcCCCC
Q 031815 100 ADKKKIKDAVKKMYDIQAKKVNTLIRPD------GTKKAYVRLTPDS 140 (152)
Q Consensus 100 AnK~qIKqAvekly~VkV~kVNTli~~~------g~KKAyV~L~~d~ 140 (152)
.=+.||++.++..||+.+.+|..-+..+ .-++..|.|.++.
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 3467888999989999999999988776 3578889988854
No 37
>PRK04046 translation initiation factor IF-6; Provisional
Probab=28.62 E-value=1.2e+02 Score=25.27 Aligned_cols=51 Identities=10% Similarity=0.173 Sum_probs=39.1
Q ss_pred cccccccccchhhhhhhhcC---------------------CeEEEEEecCCCHHHHHHHHHhHhCCceeeEE
Q 031815 70 YQILKYPLTTESAMKKIEDN---------------------NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVN 121 (152)
Q Consensus 70 ~~IIk~Pl~TEkamk~~E~~---------------------NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVN 121 (152)
+-+|..|.++|...+.+++. |-..+.|++.++..+++ .+++.++|+|....
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 34566777777777777653 56678999999999998 68888899886654
No 38
>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=28.36 E-value=1.5e+02 Score=19.03 Aligned_cols=35 Identities=11% Similarity=0.222 Sum_probs=30.6
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
..+..|.|+...+=.++|+.++..+++.+.....+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~ 44 (76)
T cd01806 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI 44 (76)
T ss_pred CCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE
Confidence 35788999999999999999999999999876665
No 39
>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]
Probab=28.28 E-value=6.3 Score=33.73 Aligned_cols=61 Identities=26% Similarity=0.299 Sum_probs=40.1
Q ss_pred HhhhcccCcccceeeeccccccCCCccCCCCCCCCCCCCCCCCCCCCccccccccccchhhhhhhhcCCeEEEEE
Q 031815 22 KAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIV 96 (152)
Q Consensus 22 kavlkg~~~~~~~k~~~s~~f~~pktl~~~r~pky~rk~~p~~~kld~~~IIk~Pl~TEkamk~~E~~NtlvF~V 96 (152)
.+|.||-.....+|.+ -|+||-|+ -+.++-...-||.|- .-.+||.+|.+|++..-|-|.+
T Consensus 90 e~vikg~~~~~~tk~~-~p~~wvp~----------l~~~v~~s~ild~y~---~v~vteRtl~LIDE~~GLD~YI 150 (283)
T KOG3279|consen 90 EAVIKGFQKREQTKRR-VPHFWVPN----------LRRSVVHSHVLDCYM---SVVVTERTLELIDECHGLDHYI 150 (283)
T ss_pred HHHHHHHHHHHHHhhc-CCcccccc----------hhhHHHHHHHHhhhh---eeeehHHHHHHHHHhcCcceee
Confidence 4566774433223333 78899887 234455556677763 4468999999998877777765
No 40
>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=27.30 E-value=1e+02 Score=19.72 Aligned_cols=35 Identities=6% Similarity=0.155 Sum_probs=30.1
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEee
Q 031815 90 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 124 (152)
Q Consensus 90 NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli 124 (152)
.++.+.|+..++=.++|+.++..+|+.+.....+.
T Consensus 10 ~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 44 (71)
T cd01812 10 ESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIF 44 (71)
T ss_pred EEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEee
Confidence 46788899999999999999999999987766553
No 41
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=27.26 E-value=1.4e+02 Score=19.23 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=30.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
..++.|.|+...+=.++|+.+++.+++.+......
T Consensus 10 g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~ 44 (76)
T cd01803 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 44 (76)
T ss_pred CCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE
Confidence 35788999999999999999999999988776555
No 42
>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=26.99 E-value=1.3e+02 Score=20.73 Aligned_cols=37 Identities=5% Similarity=-0.036 Sum_probs=30.6
Q ss_pred EEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCC
Q 031815 92 LVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDG 128 (152)
Q Consensus 92 lvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g 128 (152)
..-.++...+=.|+|+-++.+||+.+.........++
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 3345889999999999999999999999888655543
No 43
>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=26.66 E-value=1.6e+02 Score=19.22 Aligned_cols=35 Identities=11% Similarity=0.180 Sum_probs=29.4
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCC--ceeeEEEe
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDI--QAKKVNTL 123 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~V--kV~kVNTl 123 (152)
.+++.|.|+...+=.++|+.+...+|+ .+.....+
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 66655444
No 44
>PHA01813 hypothetical protein
Probab=26.53 E-value=46 Score=22.46 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=16.4
Q ss_pred EEEecC-CCHHHHHHHHHhHhCCcee
Q 031815 94 FIVDIR-ADKKKIKDAVKKMYDIQAK 118 (152)
Q Consensus 94 F~Vd~k-AnK~qIKqAvekly~VkV~ 118 (152)
+-|..+ ---|||.+ +|++|+++|.
T Consensus 11 y~~~i~~~~~h~i~~-fe~~~~~kvi 35 (58)
T PHA01813 11 YCDEIKGHFPHQISM-FEDLYDAKVV 35 (58)
T ss_pred EehhhcccChhHHHH-HHhhhceeEE
Confidence 334443 23578876 8999999984
No 45
>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=26.50 E-value=99 Score=20.13 Aligned_cols=22 Identities=50% Similarity=0.656 Sum_probs=18.4
Q ss_pred CCCeeeEEEEcCCCCcHHHHHHhhc
Q 031815 126 PDGTKKAYVRLTPDSDALDVANKIG 150 (152)
Q Consensus 126 ~~g~KKAyV~L~~d~daldvankig 150 (152)
|+|.-+- |..|..++|+|..|+
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 8886543 889999999999986
No 46
>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=26.12 E-value=1.3e+02 Score=20.05 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=30.2
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 90 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 90 NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
.++.+.|+...+=.++|+-|+...|+.+..-..+
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 47
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=25.86 E-value=1.9e+02 Score=22.70 Aligned_cols=46 Identities=26% Similarity=0.376 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHhHhCCceeeEEEee---CCCCee---eEEEEcCCCCcHHHHHHhh
Q 031815 99 RADKKKIKDAVKKMYDIQAKKVNTLI---RPDGTK---KAYVRLTPDSDALDVANKI 149 (152)
Q Consensus 99 kAnK~qIKqAvekly~VkV~kVNTli---~~~g~K---KAyV~L~~d~daldvanki 149 (152)
..+|.||++-+-++|.++...|-..- .-||-| .|.| ||.+|+|.++
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 57899999999999988765554321 123322 2333 7899999875
No 48
>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=25.15 E-value=88 Score=20.82 Aligned_cols=41 Identities=15% Similarity=0.275 Sum_probs=27.6
Q ss_pred CCCccccccccccchhhhhhhhcCCeEEEEEecCCC--HHHHHHHHHhHhC
Q 031815 66 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRAD--KKKIKDAVKKMYD 114 (152)
Q Consensus 66 kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kAn--K~qIKqAvekly~ 114 (152)
..+...|..+|.-. ++..|+|.||...+ ..+++++++.|=+
T Consensus 26 ~ini~~i~s~p~~~--------~~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 26 GINLTKIESRPSKG--------GLWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CcCEEEEEEEEcCC--------CCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 44445555555421 34679999998875 8888888887644
No 49
>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=25.12 E-value=1.6e+02 Score=25.84 Aligned_cols=55 Identities=9% Similarity=0.160 Sum_probs=38.1
Q ss_pred CeEEEE--EecCCCHHHHHHHHHhHhCCceeeEEEeeCCC-Ceee--EEEEcCCCCcHHHHH
Q 031815 90 NTLVFI--VDIRADKKKIKDAVKKMYDIQAKKVNTLIRPD-GTKK--AYVRLTPDSDALDVA 146 (152)
Q Consensus 90 NtlvF~--Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~-g~KK--AyV~L~~d~daldva 146 (152)
++-+|+ ++..++..+|++.|+..-. |..|..+..+. |..+ |||.+....+|....
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 5778999999999998654 66666665432 3333 999998776765544
No 50
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=25.10 E-value=2e+02 Score=24.01 Aligned_cols=52 Identities=29% Similarity=0.367 Sum_probs=38.3
Q ss_pred eEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHH
Q 031815 91 TLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVA 146 (152)
Q Consensus 91 tlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldva 146 (152)
.||=....+|+|.|+..+|-. |+ .+-.|=.-..|.|+ |||.+..--||.|-.
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 555566778999999888766 45 44455555578886 999998888877743
No 51
>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=24.17 E-value=1.5e+02 Score=24.56 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=34.8
Q ss_pred cccccccccchhhhhhhhc-----------------------CCeEEEEEecCCCHHHHHHHHHhHhCCceeeE
Q 031815 70 YQILKYPLTTESAMKKIED-----------------------NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKV 120 (152)
Q Consensus 70 ~~IIk~Pl~TEkamk~~E~-----------------------~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kV 120 (152)
+-+|..|.+++...+.+++ +| ..-.|++.++..+++ .++.+++|+|..-
T Consensus 104 ~G~lv~~~~~~~e~~~i~~~L~v~V~~~~i~~~~~vG~~~v~nN-~G~lvhP~~s~ee~~-~i~d~LgV~v~~g 175 (215)
T TIGR00323 104 YGALASPELDRDTEELISDVLGVEVFRGTIAGLITVGSYAVVTN-RGGLVHPQTSVQEQE-ELSSLLGVELVAG 175 (215)
T ss_pred ceEEeCCCCCHHHHHHHHHhcCCcEEEEecccccccceEEEEeC-cEEEECCCCCHHHHH-HHHHHhCCcEEEE
Confidence 4566677777776665543 23 345788999999888 4888999987655
No 52
>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=24.04 E-value=1.6e+02 Score=19.45 Aligned_cols=35 Identities=11% Similarity=0.184 Sum_probs=30.5
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEe
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTL 123 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTl 123 (152)
.+++++.|+...+=.++|+.++...|+.+.....+
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 46889999999999999999999999988765553
No 53
>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=23.81 E-value=1.4e+02 Score=19.45 Aligned_cols=41 Identities=20% Similarity=0.303 Sum_probs=28.1
Q ss_pred CCCccccccccccchhhhhhhhcCCeEEEEEecCC--CHHHHHHHHHhHhC
Q 031815 66 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRA--DKKKIKDAVKKMYD 114 (152)
Q Consensus 66 kld~~~IIk~Pl~TEkamk~~E~~NtlvF~Vd~kA--nK~qIKqAvekly~ 114 (152)
..+...|--+|... ....|.|.||... +..+++++++.|=+
T Consensus 24 ~vni~~I~Srp~~~--------~~~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 24 GINLTKIESRPSRK--------GLWEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred CCCEEEEEeeecCC--------CCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 34445555555433 2468999999987 68888888888744
No 54
>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.
Probab=23.20 E-value=55 Score=26.41 Aligned_cols=30 Identities=30% Similarity=0.741 Sum_probs=25.3
Q ss_pred hhcCCeEEEEEecCCCHHHHHHHHHhHhCC
Q 031815 86 IEDNNTLVFIVDIRADKKKIKDAVKKMYDI 115 (152)
Q Consensus 86 ~E~~NtlvF~Vd~kAnK~qIKqAvekly~V 115 (152)
.+.-..++|.||--....+++++-|-||+|
T Consensus 73 ~~~~k~IIfvvDSs~~~~~~~~~Ae~Ly~i 102 (181)
T PF09439_consen 73 LSNAKGIIFVVDSSTDQKELRDVAEYLYDI 102 (181)
T ss_dssp HGGEEEEEEEEETTTHHHHHHHHHHHHHHH
T ss_pred hhhCCEEEEEEeCccchhhHHHHHHHHHHH
Confidence 334468999999887889999999999986
No 55
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=22.81 E-value=1.6e+02 Score=20.09 Aligned_cols=35 Identities=17% Similarity=0.090 Sum_probs=30.6
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEE
Q 031815 88 DNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNT 122 (152)
Q Consensus 88 ~~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNT 122 (152)
...++++.|++..+=.++|+-++..+|+.+..-..
T Consensus 11 ~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL 45 (75)
T cd01799 11 HTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW 45 (75)
T ss_pred CCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE
Confidence 35799999999999999999999999998876544
No 56
>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=22.09 E-value=2.1e+02 Score=20.05 Aligned_cols=56 Identities=20% Similarity=0.243 Sum_probs=40.4
Q ss_pred CeEEEEEecCCCHHHHHHHHHhHhCCceeeEEEeeCCCCeeeEEEEcCCCCcHHHHHH
Q 031815 90 NTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVAN 147 (152)
Q Consensus 90 NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNTli~~~g~KKAyV~L~~d~daldvan 147 (152)
..+.|.+.+..+=.++.+.|.+.|++.-..-=+|-+.|.+ -=+|.|..|.| |+-|-
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dde-gd~v~ltsd~D-L~eai 65 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDD-EEWVLLTCDAD-LEECI 65 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCC-CCeEEeecHHH-HHHHH
Confidence 5889999999999999999999999863222334444433 34688888876 55543
No 57
>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=21.89 E-value=82 Score=24.15 Aligned_cols=19 Identities=26% Similarity=0.642 Sum_probs=17.2
Q ss_pred CCCHHHHHHHHHhHhCCce
Q 031815 99 RADKKKIKDAVKKMYDIQA 117 (152)
Q Consensus 99 kAnK~qIKqAvekly~VkV 117 (152)
+|+|.|+.++|+.+++.+-
T Consensus 115 ~A~KeqV~~mv~~~l~~~~ 133 (154)
T cd00529 115 KADKDQVQHMVKRLLNLSE 133 (154)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 6999999999999998765
No 58
>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=21.15 E-value=1.5e+02 Score=20.47 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=23.7
Q ss_pred eEEEEEecCCCHHHHHHHHHhHh------CCceeeEEEe
Q 031815 91 TLVFIVDIRADKKKIKDAVKKMY------DIQAKKVNTL 123 (152)
Q Consensus 91 tlvF~Vd~kAnK~qIKqAvekly------~VkV~kVNTl 123 (152)
.++|++++..+..++++.++.+- |-.|.++..+
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 46899999999999998877654 4455555554
No 59
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=20.35 E-value=91 Score=24.55 Aligned_cols=29 Identities=24% Similarity=0.365 Sum_probs=22.7
Q ss_pred cCCeEEEEEec-----------CCCHHHHHHHHHhHhCCc
Q 031815 88 DNNTLVFIVDI-----------RADKKKIKDAVKKMYDIQ 116 (152)
Q Consensus 88 ~~NtlvF~Vd~-----------kAnK~qIKqAvekly~Vk 116 (152)
..+--+|.+.+ +|+|.||..+|+.+++.+
T Consensus 95 ~~~ipv~ey~P~~VKk~vtG~G~A~K~qV~~mv~~~l~l~ 134 (164)
T PRK00039 95 QRGLPVAEYTPLQVKKAVVGYGRADKEQVQHMVKRLLNLP 134 (164)
T ss_pred HcCCCEEEECHHHhhhhhcCCCCCCHHHHHHHHHHHhCCC
Confidence 34555666665 599999999999999876
No 60
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=20.30 E-value=1.9e+02 Score=21.03 Aligned_cols=34 Identities=9% Similarity=0.110 Sum_probs=29.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHhHhCCceeeEEE
Q 031815 89 NNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNT 122 (152)
Q Consensus 89 ~NtlvF~Vd~kAnK~qIKqAvekly~VkV~kVNT 122 (152)
..++++.|+...+=.+||+.|+..+|+.+..-..
T Consensus 37 G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrL 70 (103)
T cd01802 37 GTCFELRVSPFETVISVKAKIQRLEGIPVAQQHL 70 (103)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE
Confidence 4689999999999999999999999988866443
No 61
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=20.23 E-value=64 Score=19.54 Aligned_cols=20 Identities=30% Similarity=0.311 Sum_probs=16.0
Q ss_pred EEEecCCCHHHHHHHHHhHh
Q 031815 94 FIVDIRADKKKIKDAVKKMY 113 (152)
Q Consensus 94 F~Vd~kAnK~qIKqAvekly 113 (152)
|-|+..++..+|+++...+.
T Consensus 6 Lgl~~~~~~~~ik~~y~~l~ 25 (55)
T cd06257 6 LGVPPDASDEEIKKAYRKLA 25 (55)
T ss_pred cCCCCCCCHHHHHHHHHHHH
Confidence 45667889999999988874
No 62
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=20.16 E-value=92 Score=24.74 Aligned_cols=29 Identities=17% Similarity=0.397 Sum_probs=23.0
Q ss_pred cCCeEEEEEec-----------CCCHHHHHHHHHhHhCCc
Q 031815 88 DNNTLVFIVDI-----------RADKKKIKDAVKKMYDIQ 116 (152)
Q Consensus 88 ~~NtlvF~Vd~-----------kAnK~qIKqAvekly~Vk 116 (152)
..+--+|...+ +|+|.||..+|+.+++.+
T Consensus 91 ~~~ipv~Ey~P~~vKkavtG~G~A~KeQV~~mV~~lL~l~ 130 (156)
T TIGR00228 91 NQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRRLLKLP 130 (156)
T ss_pred HcCCCEEEECHHHHHHHhcCCCCCCHHHHHHHHHHHcCCC
Confidence 34566676665 799999999999999865
Done!