Query 031794
Match_columns 153
No_of_seqs 213 out of 1149
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:26:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031794.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031794hhsearch_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 3.3E-63 7.1E-68 390.7 11.7 146 8-153 11-157 (157)
2 PTZ00191 60S ribosomal protein 100.0 1.8E-62 4E-67 382.8 14.6 142 10-153 4-145 (145)
3 PRK14548 50S ribosomal protein 100.0 2.4E-35 5.2E-40 212.1 9.5 84 70-153 1-84 (84)
4 TIGR03636 L23_arch archaeal ri 100.0 2.4E-33 5.2E-38 198.8 9.4 77 77-153 1-77 (77)
5 PRK05738 rplW 50S ribosomal pr 99.9 3.7E-28 7.9E-33 176.7 7.0 77 71-148 1-90 (92)
6 CHL00030 rpl23 ribosomal prote 99.9 3.3E-27 7.2E-32 172.6 7.2 76 71-148 1-89 (93)
7 COG0089 RplW Ribosomal protein 99.9 2.9E-27 6.3E-32 173.4 5.6 83 70-152 1-86 (94)
8 PRK12280 rplW 50S ribosomal pr 99.9 2.1E-26 4.5E-31 182.3 7.8 79 68-148 1-92 (158)
9 PF00276 Ribosomal_L23: Riboso 99.9 3.9E-26 8.5E-31 165.2 7.6 78 71-149 1-91 (91)
10 PF03939 Ribosomal_L23eN: Ribo 99.8 2.6E-21 5.6E-26 129.3 -0.4 53 12-65 2-54 (54)
11 KOG4089 Predicted mitochondria 97.1 0.00086 1.9E-08 54.0 4.8 49 73-128 27-75 (165)
12 PF08777 RRM_3: RNA binding mo 82.8 3.9 8.4E-05 30.1 5.4 52 93-149 4-56 (105)
13 COG0089 RplW Ribosomal protein 73.7 1.2 2.7E-05 32.9 0.3 21 127-148 72-92 (94)
14 PF03780 Asp23: Asp23 family; 59.2 14 0.00031 26.0 3.5 24 103-126 82-105 (108)
15 PLN02817 glutathione dehydroge 57.0 9.6 0.00021 32.1 2.6 39 112-150 24-62 (265)
16 cd04929 ACT_TPH ACT domain of 52.2 22 0.00048 24.5 3.4 25 91-115 41-65 (74)
17 PF00076 RRM_1: RNA recognitio 51.3 38 0.00083 20.9 4.2 54 95-148 4-57 (70)
18 cd01769 UBL Ubiquitin-like dom 49.1 48 0.001 20.7 4.5 35 89-123 6-40 (69)
19 PRK01178 rps24e 30S ribosomal 44.9 73 0.0016 23.6 5.4 69 78-150 5-81 (99)
20 PF10298 WhiA_N: WhiA N-termin 44.4 33 0.00073 23.8 3.4 62 90-153 22-86 (86)
21 KOG0107 Alternative splicing f 44.2 67 0.0014 26.8 5.5 53 91-147 12-64 (195)
22 PF00240 ubiquitin: Ubiquitin 43.5 63 0.0014 20.7 4.4 36 90-125 5-40 (69)
23 PF14560 Ubiquitin_2: Ubiquiti 42.3 58 0.0013 22.4 4.3 51 92-142 15-65 (87)
24 PF14259 RRM_6: RNA recognitio 41.5 39 0.00085 21.4 3.1 52 97-150 6-59 (70)
25 cd01796 DDI1_N DNA damage indu 40.2 55 0.0012 21.8 3.8 34 89-122 8-41 (71)
26 PLN03134 glycine-rich RNA-bind 39.5 84 0.0018 24.0 5.2 56 91-148 36-94 (144)
27 PF01282 Ribosomal_S24e: Ribos 36.3 1.2E+02 0.0026 21.5 5.2 49 99-150 11-63 (84)
28 PTZ00044 ubiquitin; Provisiona 35.5 92 0.002 20.4 4.3 36 89-124 9-44 (76)
29 cd01809 Scythe_N Ubiquitin-lik 34.1 1.1E+02 0.0023 19.6 4.4 36 90-125 10-45 (72)
30 smart00213 UBQ Ubiquitin homol 33.2 1E+02 0.0022 18.9 4.1 35 91-125 10-44 (64)
31 cd01798 parkin_N amino-termina 33.1 88 0.0019 20.4 3.9 33 90-122 8-40 (70)
32 TIGR02830 spore_III_AG stage I 31.8 54 0.0012 26.9 3.2 31 94-124 149-183 (186)
33 cd04904 ACT_AAAH ACT domain of 29.2 85 0.0019 21.0 3.4 40 68-115 26-65 (74)
34 PF02075 RuvC: Crossover junct 29.0 45 0.00097 25.7 2.1 19 100-118 114-132 (149)
35 cd04931 ACT_PAH ACT domain of 28.3 70 0.0015 22.9 2.9 40 67-114 39-79 (90)
36 PF09581 Spore_III_AF: Stage I 28.3 1.4E+02 0.0031 23.1 5.0 41 101-141 87-133 (188)
37 TIGR01659 sex-lethal sex-letha 27.7 1.4E+02 0.0031 26.2 5.3 55 91-147 107-166 (346)
38 cd01812 BAG1_N Ubiquitin-like 27.6 1.1E+02 0.0023 19.7 3.5 35 91-125 10-44 (71)
39 PF02824 TGS: TGS domain; Int 27.3 98 0.0021 20.2 3.3 22 127-151 6-27 (60)
40 cd04930 ACT_TH ACT domain of t 27.3 81 0.0018 23.5 3.2 26 90-115 81-106 (115)
41 PLN03121 nucleic acid binding 27.0 2E+02 0.0044 24.7 5.9 55 92-149 8-62 (243)
42 cd01806 Nedd8 Nebb8-like ubiq 27.0 1.8E+02 0.0039 18.7 4.6 35 90-124 10-44 (76)
43 cd01803 Ubiquitin Ubiquitin. U 26.9 1.6E+02 0.0034 19.0 4.3 35 90-124 10-44 (76)
44 cd01805 RAD23_N Ubiquitin-like 26.1 1.8E+02 0.0039 19.0 4.5 35 90-124 10-46 (77)
45 PRK04046 translation initiatio 26.1 1.1E+02 0.0024 25.4 4.1 50 72-122 67-137 (222)
46 cd01800 SF3a120_C Ubiquitin-li 25.9 1.5E+02 0.0033 19.8 4.1 34 91-124 8-41 (76)
47 cd01807 GDX_N ubiquitin-like d 24.2 1.6E+02 0.0035 19.4 4.0 35 90-124 10-44 (74)
48 cd06407 PB1_NLP A PB1 domain i 24.1 2E+02 0.0043 20.2 4.6 56 91-148 10-65 (82)
49 PF01206 TusA: Sulfurtransfera 24.0 2.1E+02 0.0046 18.5 5.6 44 79-123 16-59 (70)
50 TIGR01661 ELAV_HUD_SF ELAV/HuD 24.0 2.1E+02 0.0047 23.8 5.5 57 90-150 270-331 (352)
51 cd01799 Hoil1_N Ubiquitin-like 23.8 1.6E+02 0.0034 20.1 4.0 35 89-123 11-45 (75)
52 cd04905 ACT_CM-PDT C-terminal 23.6 1E+02 0.0022 20.5 2.9 26 90-115 41-68 (80)
53 cd03423 SirA SirA (also known 23.2 2.3E+02 0.005 18.7 6.1 53 79-135 15-67 (69)
54 cd01789 Alp11_N Ubiquitin-like 22.7 2.4E+02 0.0052 19.4 4.8 37 93-129 15-51 (84)
55 PF01250 Ribosomal_S6: Ribosom 22.3 1.4E+02 0.003 20.6 3.5 32 92-123 4-41 (92)
56 PHA01813 hypothetical protein 22.1 64 0.0014 21.8 1.6 25 94-119 10-35 (58)
57 cd03422 YedF YedF is a bacteri 22.1 2.5E+02 0.0053 18.6 5.9 45 78-123 14-58 (69)
58 cd03420 SirA_RHOD_Pry_redox Si 21.8 2.5E+02 0.0054 18.5 6.0 53 79-135 15-67 (69)
59 cd01802 AN1_N ubiquitin-like d 20.9 1.8E+02 0.004 21.1 4.0 34 90-123 37-70 (103)
60 PRK14837 undecaprenyl pyrophos 20.9 1.8E+02 0.0038 24.6 4.4 51 82-132 115-185 (230)
61 PF09439 SRPRB: Signal recogni 20.8 67 0.0015 25.9 1.8 29 88-116 74-102 (181)
62 PF08766 DEK_C: DEK C terminal 20.6 89 0.0019 20.0 2.0 19 101-119 21-39 (54)
63 KOG3424 40S ribosomal protein 20.5 2.9E+02 0.0063 21.7 5.1 46 100-150 34-85 (132)
64 cd00529 RuvC_resolvase Hollida 20.2 95 0.0021 23.8 2.5 19 100-118 115-133 (154)
No 1
>KOG1751 consensus 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-63 Score=390.71 Aligned_cols=146 Identities=70% Similarity=0.987 Sum_probs=143.1
Q ss_pred CCCCCchHHHHHHHHhhhcCCCCcccceeecccccccCCCccCcCCCCCCCCcCCCCCCCCChhhh-hhccccchhhhhh
Q 031794 8 SKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQI-LKYPLTTESAMKK 86 (153)
Q Consensus 8 ~~~~~~k~kalkakkavlkg~~~~~~~~k~~~~~~f~~pktl~~~r~pky~rk~~p~~~kld~~~I-Ik~Pl~TEkamk~ 86 (153)
||+++++++||+|+|||++|+|+|++.+.++++++|++|.+++++|+|+|||+|.|+||+||||.+ |++||+||++|+.
T Consensus 11 ~pka~a~akAlkakkav~kgv~~~~~~~~~~t~~~~~rP~t~~~~r~pk~prks~p~~~kld~y~~iik~plTtEsamKk 90 (157)
T KOG1751|consen 11 PPKAEAKAKALKAKKAVLKGVHSHKKKKKSRTSPTFRRPKTLDLTRAPKYPRKSPPRRPKLDHYAIIIKFPLTTESAMKK 90 (157)
T ss_pred CcchhhhHHHHHHHHHhhccccCCcccCCccccCCCCCCcccccccCccccccccCCCCcchhhhhHhccccchhhhhcc
Confidence 899999999999999999999999986779999999999999999999999999999999999777 8999999999999
Q ss_pred hccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhhccC
Q 031794 87 IEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153 (153)
Q Consensus 87 ~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvankigii 153 (153)
+||||||||+||.+||||||||||++|||++|++|||||+|+|+|||||+|++|||||||||+||||
T Consensus 91 ~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~kkayv~la~dydaldvankig~i 157 (157)
T KOG1751|consen 91 IEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII 157 (157)
T ss_pred hhhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCceeEEEecCCchhHHHHhcccccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999997
No 2
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=100.00 E-value=1.8e-62 Score=382.80 Aligned_cols=142 Identities=65% Similarity=0.970 Sum_probs=137.7
Q ss_pred CCCchHHHHHHHHhhhcCCCCcccceeecccccccCCCccCcCCCCCCCCcCCCCCCCCChhhhhhccccchhhhhhhcc
Q 031794 10 KGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIED 89 (153)
Q Consensus 10 ~~~~k~kalkakkavlkg~~~~~~~~k~~~~~~f~~pktl~~~r~pky~rk~~p~~~kld~~~IIk~Pl~TEkamk~~E~ 89 (153)
.+.++++|++|+++|++|+|+++ +|+|+|++|+||+||+|+|+|+|||+|.|++|+||+|+||++|++||+||+++|+
T Consensus 4 ~~~~~~ka~~a~k~~~~g~~~~~--~k~r~~~~f~rpktl~l~r~pky~r~~~~~~~~md~~~IIk~Pl~TEKa~~~~E~ 81 (145)
T PTZ00191 4 AKKAKKKAKKAAKAAKKGVKVKK--RKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDKYSIIKYPLTTEKAMKKIED 81 (145)
T ss_pred cchHHHHHHHHHHHHhcccccce--eEeeecceecCCccccCCCCCCCcccccCCCCCCchhhhhhcccccHHHHHHHhh
Confidence 45678899999999999999854 8999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhhccC
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvankigii 153 (153)
+|+|+|+||++|||+|||+|||+||||+|.+|||+|+|+|||||||+|++|||||||||+||||
T Consensus 82 ~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~g~KKA~V~L~~~~~aidva~kiGi~ 145 (145)
T PTZ00191 82 NNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKAYIRLSPDVDALDVANKIGII 145 (145)
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 9999999999999999999999999999999999999999999999999999999999999997
No 3
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=100.00 E-value=2.4e-35 Score=212.09 Aligned_cols=84 Identities=52% Similarity=0.893 Sum_probs=81.9
Q ss_pred hhhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q 031794 70 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANK 149 (153)
Q Consensus 70 ~~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvank 149 (153)
.|+||++|++||+++.++|++|+|+|+||++|||.|||+|||++|||+|.+|||++.++|||||||+|.+|++|+|||++
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 031794 150 IGII 153 (153)
Q Consensus 150 igii 153 (153)
||++
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=2.4e-33 Score=198.77 Aligned_cols=77 Identities=51% Similarity=0.842 Sum_probs=75.7
Q ss_pred cccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhhccC
Q 031794 77 PLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153 (153)
Q Consensus 77 Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvankigii 153 (153)
|++||+++.++|++|+|+|+||++|||+|||+|||++|||+|.+|||++.|+|||||||+|.+|++|+|||++|||+
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=3.7e-28 Score=176.71 Aligned_cols=77 Identities=35% Similarity=0.468 Sum_probs=73.0
Q ss_pred hhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCC-------------CCeeEEEEEc
Q 031794 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP-------------DGTKKAYVRL 137 (153)
Q Consensus 71 ~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p-------------~g~KKAyV~L 137 (153)
|+||++|++||+|+.++|++|+|+|.||++|||+|||+|||++|||+|.+|||++.+ .+||||||+|
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 031794 138 TPDYDALDVAN 148 (153)
Q Consensus 138 ~~d~dAldvan 148 (153)
.+|++ +|+.+
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=3.3e-27 Score=172.59 Aligned_cols=76 Identities=25% Similarity=0.446 Sum_probs=71.3
Q ss_pred hhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCC-------------eeEEEEEc
Q 031794 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDG-------------TKKAYVRL 137 (153)
Q Consensus 71 ~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g-------------~KKAyV~L 137 (153)
++||++|++||+|+.++| +|+|+|.||++|||.|||+|||.+|||+|.+|||++.|++ ||||||+|
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 99999999
Q ss_pred CCCCcHHHHHH
Q 031794 138 TPDYDALDVAN 148 (153)
Q Consensus 138 ~~d~dAldvan 148 (153)
++|++ ||++.
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=2.9e-27 Score=173.44 Aligned_cols=83 Identities=42% Similarity=0.564 Sum_probs=73.7
Q ss_pred hhhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEE---cCCCCcHHHH
Q 031794 70 HYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVR---LTPDYDALDV 146 (153)
Q Consensus 70 ~~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~---L~~d~dAldv 146 (153)
+|+||+.|++||+||.++|++|+|||+||++|||.|||+|||.||||+|.+|||||++++.|++++. +.+++++.+|
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 6777777666
Q ss_pred HHhhcc
Q 031794 147 ANKIGI 152 (153)
Q Consensus 147 ankigi 152 (153)
+.++|.
T Consensus 81 ~l~~G~ 86 (94)
T COG0089 81 TLKEGQ 86 (94)
T ss_pred EccCCC
Confidence 666664
No 8
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.93 E-value=2.1e-26 Score=182.34 Aligned_cols=79 Identities=32% Similarity=0.495 Sum_probs=74.7
Q ss_pred CChhhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCC-------------CeeEEE
Q 031794 68 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD-------------GTKKAY 134 (153)
Q Consensus 68 ld~~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~-------------g~KKAy 134 (153)
||+|+||++|++||+++.++|+ |+|+|.||++|||+||++|||.+|||+|.+|||++.++ ||||||
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 89999999999999999999999999999999999997 799999
Q ss_pred EEcCCCCcHHHHHH
Q 031794 135 VRLTPDYDALDVAN 148 (153)
Q Consensus 135 V~L~~d~dAldvan 148 (153)
|+|.+|++ ||+..
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=3.9e-26 Score=165.25 Aligned_cols=78 Identities=42% Similarity=0.632 Sum_probs=71.6
Q ss_pred hhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCC-------------CeeEEEEEc
Q 031794 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD-------------GTKKAYVRL 137 (153)
Q Consensus 71 ~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~-------------g~KKAyV~L 137 (153)
|+||++|++||+++.++|++|+|+|.||++|||+||++|||++|||+|.+|||++.++ +||||||+|
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 031794 138 TPDYDALDVANK 149 (153)
Q Consensus 138 ~~d~dAldvank 149 (153)
.+| +.+|++++
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=2.6e-21 Score=129.31 Aligned_cols=53 Identities=60% Similarity=0.825 Sum_probs=17.4
Q ss_pred CchHHHHHHHHhhhcCCCCcccceeecccccccCCCccCcCCCCCCCCcCCCCC
Q 031794 12 DPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPR 65 (153)
Q Consensus 12 ~~k~kalkakkavlkg~~~~~~~~k~~~~~~f~~pktl~~~r~pky~rk~~p~~ 65 (153)
++++||++|+|+|++|+|+++. ++||||++|+||+||+|+|+|+|||+|+|+|
T Consensus 2 ~a~~KA~kakKav~KG~~~~~~-rKirts~~F~rPKTL~l~R~PKYprkS~p~r 54 (54)
T PF03939_consen 2 KAKAKALKAKKAVLKGVHSKKK-RKIRTSVTFRRPKTLRLPRQPKYPRKSVPRR 54 (54)
T ss_dssp -----------------------HHHHHHHHHT-SS--------SS-SSS---S
T ss_pred chHHHHHHHHHHHhcCCCcccc-ceeecCcccCCCcccccCCCCCCcccCCCCC
Confidence 3578899999999999999987 8999999999999999999999999999985
No 11
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.00086 Score=53.98 Aligned_cols=49 Identities=22% Similarity=0.384 Sum_probs=42.1
Q ss_pred hhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCC
Q 031794 73 ILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD 128 (153)
Q Consensus 73 IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~ 128 (153)
.|..|+.+. -.++.+|.|+...||.+++.+++.+||.+|.+|.|.+..+
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 334477664 2479999999999999999999999999999999999776
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=82.81 E-value=3.9 Score=30.10 Aligned_cols=52 Identities=23% Similarity=0.377 Sum_probs=30.1
Q ss_pred EEEE-EecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q 031794 93 LVFI-VDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANK 149 (153)
Q Consensus 93 lvF~-Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvank 149 (153)
|-|. ++...++.+||.++.. |+ +|.-|.- ..|...+||++....+|-.+..+
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 56 6666654 35888999999988777655443
No 13
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=73.72 E-value=1.2 Score=32.90 Aligned_cols=21 Identities=33% Similarity=0.411 Sum_probs=17.9
Q ss_pred CCCeeEEEEEcCCCCcHHHHHH
Q 031794 127 PDGTKKAYVRLTPDYDALDVAN 148 (153)
Q Consensus 127 p~g~KKAyV~L~~d~dAldvan 148 (153)
..+||+|||+|.+|++ ||++.
T Consensus 72 ~~~~kka~V~l~~G~~-i~~~~ 92 (94)
T COG0089 72 RKDYKKAYVTLKEGQS-IDFFG 92 (94)
T ss_pred CcccceeEEEccCCCE-Eeecc
Confidence 4589999999999988 88764
No 14
>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=59.23 E-value=14 Score=26.05 Aligned_cols=24 Identities=33% Similarity=0.552 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhCCceeeEEEeeC
Q 031794 103 KRKIKDAVKKMYEIQTKKVNTLIR 126 (153)
Q Consensus 103 K~qIKqAvekly~V~V~kVNTli~ 126 (153)
..+|+++|+.+-|++|..||..+.
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 15
>PLN02817 glutathione dehydrogenase (ascorbate)
Probab=57.03 E-value=9.6 Score=32.07 Aligned_cols=39 Identities=15% Similarity=0.236 Sum_probs=34.7
Q ss_pred HHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q 031794 112 KMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANKI 150 (153)
Q Consensus 112 kly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvanki 150 (153)
.-|++.+..+|++.+++|.+++++++.+..+.+|++.|-
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (265)
T PLN02817 24 PRFGTSHGGAKGVKRVGGRRRKYLTAITMSSPLEVCVKA 62 (265)
T ss_pred ccccceeecccccccCCcccceeEEecCCCccHHHHHhc
Confidence 447788889999999999999999999999999999874
No 16
>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=52.24 E-value=22 Score=24.45 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=22.1
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhC
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYE 115 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~ 115 (153)
..|.|.||...+..+++++++.|=.
T Consensus 41 ~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 41 SEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred ceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 5799999999999999999998743
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=51.32 E-value=38 Score=20.87 Aligned_cols=54 Identities=15% Similarity=0.127 Sum_probs=34.7
Q ss_pred EEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHH
Q 031794 95 FIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVAN 148 (153)
Q Consensus 95 F~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvan 148 (153)
=-++...+..+|++.++..=++.-..+..-.......=|||++....+|..+..
T Consensus 4 ~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~ 57 (70)
T PF00076_consen 4 GNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALE 57 (70)
T ss_dssp ESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHH
T ss_pred cCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHH
Confidence 346778999999999999444434444332111234568999987766655543
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=49.13 E-value=48 Score=20.69 Aligned_cols=35 Identities=9% Similarity=0.084 Sum_probs=30.9
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEE
Q 031794 89 DNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123 (153)
Q Consensus 89 ~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNT 123 (153)
+...+.|.++..++=.++|+.+...+++.+.....
T Consensus 6 ~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l 40 (69)
T cd01769 6 TGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL 40 (69)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEE
Confidence 35688899999999999999999999998887766
No 19
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=44.95 E-value=73 Score=23.58 Aligned_cols=69 Identities=17% Similarity=0.319 Sum_probs=43.1
Q ss_pred ccchhhhhhhccCCeEEEEEe----cCCCHHHHHHHHHHHhCCceeeEEE--eeC-C-CCeeEEEEEcCCCCcHHHHHHh
Q 031794 78 LTTESAMKKIEDNNTLVFIVD----IRADKRKIKDAVKKMYEIQTKKVNT--LIR-P-DGTKKAYVRLTPDYDALDVANK 149 (153)
Q Consensus 78 l~TEkamk~~E~nNtlvF~Vd----~kAnK~qIKqAvekly~V~V~kVNT--li~-p-~g~KKAyV~L~~d~dAldvank 149 (153)
++.++...++.. .+++|.|. ...+|.+|+..+-++|+.+..-|=. +.+ - +|.=..|... ||.+|.|.+
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 345556666654 68888885 3568999999999999976533311 111 1 2444555544 566777765
Q ss_pred h
Q 031794 150 I 150 (153)
Q Consensus 150 i 150 (153)
+
T Consensus 81 ~ 81 (99)
T PRK01178 81 I 81 (99)
T ss_pred h
Confidence 4
No 20
>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=44.44 E-value=33 Score=23.81 Aligned_cols=62 Identities=18% Similarity=0.350 Sum_probs=21.4
Q ss_pred CCeEEE--EEecCCCHHHHHHHHHHHhCCceeeEEEeeCCC-CeeEEEEEcCCCCcHHHHHHhhccC
Q 031794 90 NNTLVF--IVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD-GTKKAYVRLTPDYDALDVANKIGII 153 (153)
Q Consensus 90 nNtlvF--~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~-g~KKAyV~L~~d~dAldvankigii 153 (153)
++.+++ ..+.-+-=.-|-.-++++||+++ .|.+..... +....|.-.-++. +.++..++|++
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 344544 44444455567788999999988 444443222 2234554443443 88999999975
No 21
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=44.17 E-value=67 Score=26.77 Aligned_cols=53 Identities=30% Similarity=0.362 Sum_probs=41.6
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHH
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVA 147 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldva 147 (153)
..||=....+|+|.||..+|-. || .+-.|-.-..|.|+ |||.+..--||.|-.
T Consensus 12 kVYVGnL~~~a~k~eLE~~F~~-yG-~lrsvWvArnPPGf--AFVEFed~RDA~DAv 64 (195)
T KOG0107|consen 12 KVYVGNLGSRATKRELERAFSK-YG-PLRSVWVARNPPGF--AFVEFEDPRDAEDAV 64 (195)
T ss_pred eEEeccCCCCcchHHHHHHHHh-cC-cceeEEEeecCCCc--eEEeccCcccHHHHH
Confidence 3566667789999999888765 55 56677777788897 999999888887753
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=43.54 E-value=63 Score=20.70 Aligned_cols=36 Identities=14% Similarity=0.187 Sum_probs=32.2
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEee
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLI 125 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli 125 (153)
...+.|.|+...+=.++|+.|+..+|+.+.....+-
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
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=42.34 E-value=58 Score=22.43 Aligned_cols=51 Identities=12% Similarity=0.133 Sum_probs=37.5
Q ss_pred eEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCc
Q 031794 92 TLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYD 142 (153)
Q Consensus 92 tlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~d 142 (153)
...-.++...+=.|+|+-++.+||+.+........++..-..+..|..|..
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~ 65 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDA 65 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSS
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCcc
Confidence 455788999999999999999999999999998883322245555654443
No 24
>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=39 Score=21.40 Aligned_cols=52 Identities=13% Similarity=0.245 Sum_probs=36.7
Q ss_pred EecCCCHHHHHHHHHHHhCCceeeEEEeeCCC--CeeEEEEEcCCCCcHHHHHHhh
Q 031794 97 VDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD--GTKKAYVRLTPDYDALDVANKI 150 (153)
Q Consensus 97 Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~--g~KKAyV~L~~d~dAldvanki 150 (153)
+...++..+|...++.. | .|..|-..-..+ +..-|||.+....+|..+.+..
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 4678999999877776665543
No 25
>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=40.18 E-value=55 Score=21.80 Aligned_cols=34 Identities=15% Similarity=0.134 Sum_probs=29.7
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEE
Q 031794 89 DNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVN 122 (153)
Q Consensus 89 ~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVN 122 (153)
..+++++.|+..++=.++|+.|+..+|+.+..-.
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 26
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=39.55 E-value=84 Score=23.97 Aligned_cols=56 Identities=11% Similarity=0.224 Sum_probs=38.9
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCC-C--eeEEEEEcCCCCcHHHHHH
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD-G--TKKAYVRLTPDYDALDVAN 148 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~-g--~KKAyV~L~~d~dAldvan 148 (153)
.-+|=-++..++..+|++.+++ |+ .|..|.....+. | .-=|||++....+|....+
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~ 94 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHH
Confidence 3455556778999999999988 66 677777765442 2 1249999997766655443
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=36.29 E-value=1.2e+02 Score=21.47 Aligned_cols=49 Identities=14% Similarity=0.369 Sum_probs=31.5
Q ss_pred cCCCHHHHHHHHHHHhCCceee--EEEeeCCC--CeeEEEEEcCCCCcHHHHHHhh
Q 031794 99 IRADKRKIKDAVKKMYEIQTKK--VNTLIRPD--GTKKAYVRLTPDYDALDVANKI 150 (153)
Q Consensus 99 ~kAnK~qIKqAvekly~V~V~k--VNTli~p~--g~KKAyV~L~~d~dAldvanki 150 (153)
...+|.||+..+-++|+++..- |+.+.+.- |.-.+|... ||..|.+.++
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~I---Yd~~e~~kk~ 63 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKI---YDSAEALKKF 63 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEE---ESSHHHHHHH
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEE---eCCHHHHHHh
Confidence 4578999999999999986544 45555553 455666666 4556655543
No 28
>PTZ00044 ubiquitin; Provisional
Probab=35.54 E-value=92 Score=20.43 Aligned_cols=36 Identities=14% Similarity=0.220 Sum_probs=31.8
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEe
Q 031794 89 DNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 89 ~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTl 124 (153)
+.+++++.|+...+=.++|+.++...|+.+......
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 346999999999999999999999999988877665
No 29
>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=34.11 E-value=1.1e+02 Score=19.61 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=31.1
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEee
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLI 125 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli 125 (153)
.+++.|.|+...+=.++|+.++..+|+.+.......
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 10 SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 468999999999999999999999999887765543
No 30
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=33.21 E-value=1e+02 Score=18.88 Aligned_cols=35 Identities=11% Similarity=0.226 Sum_probs=30.1
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEee
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLI 125 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli 125 (153)
.++.|.|+...+=.++|+.++..+++.+.....+.
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 47889999999999999999999999887666553
No 31
>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=33.15 E-value=88 Score=20.41 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=29.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEE
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVN 122 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVN 122 (153)
..++++.|+...+=.++|+.++...|+.+....
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 32
>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=31.80 E-value=54 Score=26.87 Aligned_cols=31 Identities=32% Similarity=0.545 Sum_probs=25.1
Q ss_pred EEEEecCCC----HHHHHHHHHHHhCCceeeEEEe
Q 031794 94 VFIVDIRAD----KRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 94 vF~Vd~kAn----K~qIKqAvekly~V~V~kVNTl 124 (153)
|.+|.-.|. |.+|-+||..+|||...+|+.+
T Consensus 149 VlVVAeGa~~~~Vk~~I~~AV~~ll~v~~hkI~V~ 183 (186)
T TIGR02830 149 VLVVAEGAENPQIKYRIVEAVSRVLDVPAHKVSVL 183 (186)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHhCCCcceEEEE
Confidence 566766665 6677789999999999999876
No 33
>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=29.19 E-value=85 Score=20.98 Aligned_cols=40 Identities=15% Similarity=0.315 Sum_probs=28.3
Q ss_pred CChhhhhhccccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhC
Q 031794 68 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYE 115 (153)
Q Consensus 68 ld~~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~ 115 (153)
++...|--+|... ....|.|.||......+++++++.|-.
T Consensus 26 iNlt~IeSRP~~~--------~~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 26 VNLTHIESRPSRR--------NGSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred CcEEEEECCCCCC--------CCceEEEEEEEEcChHHHHHHHHHHHH
Confidence 3444455555443 235799999999988899999988754
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=28.97 E-value=45 Score=25.71 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=13.5
Q ss_pred CCCHHHHHHHHHHHhCCce
Q 031794 100 RADKRKIKDAVKKMYEIQT 118 (153)
Q Consensus 100 kAnK~qIKqAvekly~V~V 118 (153)
+|+|.||.++|.++++.+.
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 7999999999999998765
No 35
>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=28.33 E-value=70 Score=22.87 Aligned_cols=40 Identities=10% Similarity=0.277 Sum_probs=28.2
Q ss_pred CCChhhhhhccccchhhhhhhccCCeEEEEEecCCC-HHHHHHHHHHHh
Q 031794 67 KLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRAD-KRKIKDAVKKMY 114 (153)
Q Consensus 67 kld~~~IIk~Pl~TEkamk~~E~nNtlvF~Vd~kAn-K~qIKqAvekly 114 (153)
.++...|--+|..+ ....|.|.||.... ...++++++.|-
T Consensus 39 ~INLt~IeSRP~~~--------~~~~Y~FfVDieg~~~~~~~~~l~~L~ 79 (90)
T cd04931 39 DINLTHIESRPSRL--------NKDEYEFFINLDKKSAPALDPIIKSLR 79 (90)
T ss_pred CCCEEEEEeccCCC--------CCceEEEEEEEEcCCCHHHHHHHHHHH
Confidence 44455555666433 23689999999986 788889888764
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=28.29 E-value=1.4e+02 Score=23.11 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhCCceeeEEEeeCCC------CeeEEEEEcCCCC
Q 031794 101 ADKRKIKDAVKKMYEIQTKKVNTLIRPD------GTKKAYVRLTPDY 141 (153)
Q Consensus 101 AnK~qIKqAvekly~V~V~kVNTli~p~------g~KKAyV~L~~d~ 141 (153)
.=..||++.++..||+.+.+|..-+..+ .-++..|.|.++.
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 3467888889989999999999988776 3577888888854
No 37
>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=27.70 E-value=1.4e+02 Score=26.24 Aligned_cols=55 Identities=11% Similarity=0.154 Sum_probs=37.9
Q ss_pred CeEEEE--EecCCCHHHHHHHHHHHhCCceeeEEEeeCCC-CeeE--EEEEcCCCCcHHHHH
Q 031794 91 NTLVFI--VDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD-GTKK--AYVRLTPDYDALDVA 147 (153)
Q Consensus 91 NtlvF~--Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~-g~KK--AyV~L~~d~dAldva 147 (153)
++-+|+ ++.+++..+|++.|+..-. |..|..+..+. |..+ |||++....+|....
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 344455 5778999999999998654 66676665443 3333 999998776765544
No 38
>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=27.60 E-value=1.1e+02 Score=19.66 Aligned_cols=35 Identities=6% Similarity=0.146 Sum_probs=30.3
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEee
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLI 125 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli 125 (153)
.++.+.|+..++=.++|+.++..+|+.+.....+.
T Consensus 10 ~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 44 (71)
T cd01812 10 ESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIF 44 (71)
T ss_pred EEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEee
Confidence 56788999999999999999999999987766654
No 39
>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=27.33 E-value=98 Score=20.17 Aligned_cols=22 Identities=45% Similarity=0.594 Sum_probs=18.4
Q ss_pred CCCeeEEEEEcCCCCcHHHHHHhhc
Q 031794 127 PDGTKKAYVRLTPDYDALDVANKIG 151 (153)
Q Consensus 127 p~g~KKAyV~L~~d~dAldvankig 151 (153)
|+|.-+- |+.|..++|+|..|+
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 40
>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=27.27 E-value=81 Score=23.55 Aligned_cols=26 Identities=8% Similarity=0.234 Sum_probs=22.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhC
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYE 115 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~ 115 (153)
+..|.|.||...+..+++++++.|-.
T Consensus 81 ~~eY~FfIdieg~~~~~~~aL~~L~~ 106 (115)
T cd04930 81 GGDLEVLVRCEVHRSDLLQLISSLRQ 106 (115)
T ss_pred CceEEEEEEEEeCHHHHHHHHHHHHH
Confidence 46899999999999999999988743
No 41
>PLN03121 nucleic acid binding protein; Provisional
Probab=27.05 E-value=2e+02 Score=24.67 Aligned_cols=55 Identities=18% Similarity=0.214 Sum_probs=38.3
Q ss_pred eEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q 031794 92 TLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVANK 149 (153)
Q Consensus 92 tlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvank 149 (153)
.+|-.++.+++..+|++-|.. || +|..|..+...+...-|||++...++ .+.|-.
T Consensus 8 V~V~NLS~~tTE~dLrefFS~-~G-~I~~V~I~~D~et~gfAfVtF~d~~a-aetAll 62 (243)
T PLN03121 8 AEVTNLSPKATEKDVYDFFSH-CG-AIEHVEIIRSGEYACTAYVTFKDAYA-LETAVL 62 (243)
T ss_pred EEEecCCCCCCHHHHHHHHHh-cC-CeEEEEEecCCCcceEEEEEECCHHH-HHHHHh
Confidence 455567889999999998877 55 56677754433223479999997755 466644
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=26.97 E-value=1.8e+02 Score=18.71 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=30.5
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEe
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTl 124 (153)
..+..|.|+...+=.++|+.++..+|+.+.....+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~ 44 (76)
T cd01806 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI 44 (76)
T ss_pred CCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE
Confidence 35788999999999999999999999998876665
No 43
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=26.86 E-value=1.6e+02 Score=18.98 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=30.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEe
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTl 124 (153)
..++.|.|+...+=.++|+.++..+++.+......
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 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=26.11 E-value=1.8e+02 Score=18.98 Aligned_cols=35 Identities=11% Similarity=0.168 Sum_probs=29.4
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCC--ceeeEEEe
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEI--QTKKVNTL 124 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V--~V~kVNTl 124 (153)
.+++.|.|+...+=.++|+.+...+|+ .+.....+
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 66655443
No 45
>PRK04046 translation initiation factor IF-6; Provisional
Probab=26.11 E-value=1.1e+02 Score=25.41 Aligned_cols=50 Identities=10% Similarity=0.174 Sum_probs=37.2
Q ss_pred hhhhccccchhhhhhhccC---------------------CeEEEEEecCCCHHHHHHHHHHHhCCceeeEE
Q 031794 72 QILKYPLTTESAMKKIEDN---------------------NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVN 122 (153)
Q Consensus 72 ~IIk~Pl~TEkamk~~E~n---------------------NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVN 122 (153)
-+|..|.+++...+.+++. |-..+.|.+.++..+++ .+++.+||+|....
T Consensus 67 g~lvp~~~~~~e~~~l~e~L~v~V~~~~~~~~~vGn~i~~N~~G~lv~p~~~~ee~~-~i~~~L~V~v~~~t 137 (222)
T PRK04046 67 GILVPSIVLDEELELLKEALDLNVEVLPSKLTALGNLILANDKGALVHPELSDEARK-VIEDTLGVEVERGT 137 (222)
T ss_pred eEEeCCCCCHHHHHHHHHhcCceEEEEeccccceEeEEEEcCcEEEECCCCCHHHHH-HHHHhhCceEEEEe
Confidence 3455566777766666543 56678999999999998 68888899886654
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=25.94 E-value=1.5e+02 Score=19.80 Aligned_cols=34 Identities=12% Similarity=0.133 Sum_probs=30.2
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEe
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTl 124 (153)
.++.+.|+...+=.++|+-|+...|+.+..-..+
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
>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=24.15 E-value=1.6e+02 Score=19.39 Aligned_cols=35 Identities=11% Similarity=0.168 Sum_probs=30.5
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEe
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTl 124 (153)
.+++++.|+...+=.++|+.++..+|+.+.....+
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 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=24.11 E-value=2e+02 Score=20.21 Aligned_cols=56 Identities=20% Similarity=0.227 Sum_probs=40.6
Q ss_pred CeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHH
Q 031794 91 NTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYVRLTPDYDALDVAN 148 (153)
Q Consensus 91 NtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV~L~~d~dAldvan 148 (153)
..+.|.+.+..+=.++.+.|.+.|++.-..-=+|-+.|.+ -=+|.|..|.| |+-|-
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 5889999999999999999999999863223334444443 34688888876 55443
No 49
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=24.00 E-value=2.1e+02 Score=18.49 Aligned_cols=44 Identities=18% Similarity=0.213 Sum_probs=35.8
Q ss_pred cchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEE
Q 031794 79 TTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123 (153)
Q Consensus 79 ~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNT 123 (153)
.+-++++.++.+..+.+++|-.....+|..+.+.. |..+..++.
T Consensus 16 ~~~~~l~~l~~G~~l~v~~d~~~~~~di~~~~~~~-g~~~~~~~~ 59 (70)
T PF01206_consen 16 KAKKALKELPPGEVLEVLVDDPAAVEDIPRWCEEN-GYEVVEVEE 59 (70)
T ss_dssp HHHHHHHTSGTT-EEEEEESSTTHHHHHHHHHHHH-TEEEEEEEE
T ss_pred HHHHHHHhcCCCCEEEEEECCccHHHHHHHHHHHC-CCEEEEEEE
Confidence 45677888877779999999999999999999885 777777766
No 50
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=23.98 E-value=2.1e+02 Score=23.79 Aligned_cols=57 Identities=12% Similarity=0.154 Sum_probs=0.0
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCC-----CCeeEEEEEcCCCCcHHHHHHhh
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP-----DGTKKAYVRLTPDYDALDVANKI 150 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p-----~g~KKAyV~L~~d~dAldvanki 150 (153)
.+-+|+.++...+-.++++.++. || .|..|+.+..+ .|+ |||.+..-.+|......+
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
>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=23.81 E-value=1.6e+02 Score=20.13 Aligned_cols=35 Identities=17% Similarity=0.078 Sum_probs=30.6
Q ss_pred cCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEE
Q 031794 89 DNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123 (153)
Q Consensus 89 ~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNT 123 (153)
...++++.|++..+=.++|+-++..+|+.+..-..
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 52
>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=23.58 E-value=1e+02 Score=20.54 Aligned_cols=26 Identities=15% Similarity=0.364 Sum_probs=20.7
Q ss_pred CCeEEEEEecCCC--HHHHHHHHHHHhC
Q 031794 90 NNTLVFIVDIRAD--KRKIKDAVKKMYE 115 (153)
Q Consensus 90 nNtlvF~Vd~kAn--K~qIKqAvekly~ 115 (153)
+..|+|.||...+ ..+++++++.|=+
T Consensus 41 ~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 41 LWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 4679999998875 8888888887644
No 53
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.22 E-value=2.3e+02 Score=18.66 Aligned_cols=53 Identities=13% Similarity=0.174 Sum_probs=40.8
Q ss_pred cchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEE
Q 031794 79 TTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYV 135 (153)
Q Consensus 79 ~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV 135 (153)
-+.++++.++....+..++|-.....+|..++++. |-++..+.. -+|.=..+|
T Consensus 15 ~~k~~l~~l~~G~~l~V~~dd~~s~~di~~~~~~~-g~~~~~~~~---~~~~~~~~I 67 (69)
T cd03423 15 MLHKKVRKMKPGDTLLVLATDPSTTRDIPKFCTFL-GHELLAQET---EDEPYRYLI 67 (69)
T ss_pred HHHHHHHcCCCCCEEEEEeCCCchHHHHHHHHHHc-CCEEEEEEE---cCCEEEEEE
Confidence 46788998887778999999999999999999864 777776654 244444554
No 54
>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=22.70 E-value=2.4e+02 Score=19.45 Aligned_cols=37 Identities=3% Similarity=-0.062 Sum_probs=30.5
Q ss_pred EEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCC
Q 031794 93 LVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDG 129 (153)
Q Consensus 93 lvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g 129 (153)
..-.++...+=.|+|+-++.+||+.+......+..++
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 3345889999999999999999999999888655443
No 55
>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=22.28 E-value=1.4e+02 Score=20.65 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=23.0
Q ss_pred eEEEEEecCCCHHHHHHHHHHHh------CCceeeEEE
Q 031794 92 TLVFIVDIRADKRKIKDAVKKMY------EIQTKKVNT 123 (153)
Q Consensus 92 tlvF~Vd~kAnK~qIKqAvekly------~V~V~kVNT 123 (153)
.++|++++..+..++++.++.+- |-.|.++..
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~ 41 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVEN 41 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEE
Confidence 46899999999999998877653 445555554
No 56
>PHA01813 hypothetical protein
Probab=22.14 E-value=64 Score=21.82 Aligned_cols=25 Identities=12% Similarity=0.335 Sum_probs=16.8
Q ss_pred EEEEecCC-CHHHHHHHHHHHhCCcee
Q 031794 94 VFIVDIRA-DKRKIKDAVKKMYEIQTK 119 (153)
Q Consensus 94 vF~Vd~kA-nK~qIKqAvekly~V~V~ 119 (153)
.+-|..+- --|||.+ +|++|+++|.
T Consensus 10 ly~~~i~~~~~h~i~~-fe~~~~~kvi 35 (58)
T PHA01813 10 LYCDEIKGHFPHQISM-FEDLYDAKVV 35 (58)
T ss_pred EEehhhcccChhHHHH-HHhhhceeEE
Confidence 34444442 3578876 8999999884
No 57
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.11 E-value=2.5e+02 Score=18.61 Aligned_cols=45 Identities=13% Similarity=0.161 Sum_probs=37.8
Q ss_pred ccchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEE
Q 031794 78 LTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123 (153)
Q Consensus 78 l~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNT 123 (153)
+-|.++++.++....+..++|-......|....+. .|-.|..++.
T Consensus 14 i~~kkal~~l~~G~~l~V~~d~~~s~~ni~~~~~~-~g~~v~~~~~ 58 (69)
T cd03422 14 IATLEALPSLKPGEILEVISDCPQSINNIPIDARN-HGYKVLAIEQ 58 (69)
T ss_pred HHHHHHHHcCCCCCEEEEEecCchHHHHHHHHHHH-cCCEEEEEEe
Confidence 35788999888777899999999999999999875 5888877664
No 58
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=21.83 E-value=2.5e+02 Score=18.54 Aligned_cols=53 Identities=17% Similarity=0.145 Sum_probs=40.9
Q ss_pred cchhhhhhhccCCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEE
Q 031794 79 TTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKKAYV 135 (153)
Q Consensus 79 ~TEkamk~~E~nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNTli~p~g~KKAyV 135 (153)
-|.++++.++....|..++|-.+...+|..+.+. .|-++..+.. .+|.=..+|
T Consensus 15 ~~kkal~~l~~G~~l~V~~d~~~a~~di~~~~~~-~G~~~~~~~~---~~~~~~~~I 67 (69)
T cd03420 15 KLKKEIDKLQDGEQLEVKASDPGFARDAQAWCKS-TGNTLISLET---EKGKVKAVI 67 (69)
T ss_pred HHHHHHHcCCCCCEEEEEECCccHHHHHHHHHHH-cCCEEEEEEe---cCCEEEEEE
Confidence 4789999988777899999999999999998876 4888876665 244434443
No 59
>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=20.92 E-value=1.8e+02 Score=21.08 Aligned_cols=34 Identities=9% Similarity=0.097 Sum_probs=29.3
Q ss_pred CCeEEEEEecCCCHHHHHHHHHHHhCCceeeEEE
Q 031794 90 NNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123 (153)
Q Consensus 90 nNtlvF~Vd~kAnK~qIKqAvekly~V~V~kVNT 123 (153)
..++++.|+...+=.+||+.|...+|+.+..-..
T Consensus 37 G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrL 70 (103)
T cd01802 37 GTCFELRVSPFETVISVKAKIQRLEGIPVAQQHL 70 (103)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE
Confidence 4689999999999999999999999988865443
No 60
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.86 E-value=1.8e+02 Score=24.61 Aligned_cols=51 Identities=25% Similarity=0.376 Sum_probs=33.8
Q ss_pred hhhhhhccCCeEEEEEecC-CCHHHHHHHHHHHhC-------------------CceeeEEEeeCCCCeeE
Q 031794 82 SAMKKIEDNNTLVFIVDIR-ADKRKIKDAVKKMYE-------------------IQTKKVNTLIRPDGTKK 132 (153)
Q Consensus 82 kamk~~E~nNtlvF~Vd~k-AnK~qIKqAvekly~-------------------V~V~kVNTli~p~g~KK 132 (153)
.++..+.+|+.+++.|-.. -.+.||-+|++++.. -+.-.|..+|+.+|+++
T Consensus 115 ~~e~~T~~n~~~~Lnia~~Yggr~EI~~A~~~~~~~~~~~~~i~e~~~~~~L~~~~~p~~DLlIRTsGE~R 185 (230)
T PRK14837 115 DAISFTKNFDGLVLNLAINYGGRNEIVRAVKKFLSSGLDLETLNENVFSKFLDNPELPDLDLLIRTGGDMR 185 (230)
T ss_pred HHHHHhcCCCCcEEEEEecCCCHHHHHHHHHHHHhcCCChhhCCHHHHHHhhccCCCCCCCEEEECCCccc
Confidence 4445556677777777665 789999999987642 12335667777777653
No 61
>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=20.80 E-value=67 Score=25.94 Aligned_cols=29 Identities=24% Similarity=0.706 Sum_probs=24.8
Q ss_pred ccCCeEEEEEecCCCHHHHHHHHHHHhCC
Q 031794 88 EDNNTLVFIVDIRADKRKIKDAVKKMYEI 116 (153)
Q Consensus 88 E~nNtlvF~Vd~kAnK~qIKqAvekly~V 116 (153)
+.-..++|.||--....+++++-|-||+|
T Consensus 74 ~~~k~IIfvvDSs~~~~~~~~~Ae~Ly~i 102 (181)
T PF09439_consen 74 SNAKGIIFVVDSSTDQKELRDVAEYLYDI 102 (181)
T ss_dssp GGEEEEEEEEETTTHHHHHHHHHHHHHHH
T ss_pred hhCCEEEEEEeCccchhhHHHHHHHHHHH
Confidence 33468999999877789999999999986
No 62
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=20.65 E-value=89 Score=19.99 Aligned_cols=19 Identities=5% Similarity=0.447 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHhCCcee
Q 031794 101 ADKRKIKDAVKKMYEIQTK 119 (153)
Q Consensus 101 AnK~qIKqAvekly~V~V~ 119 (153)
.+..+|+++++.-||++..
T Consensus 21 vT~k~vr~~Le~~~~~dL~ 39 (54)
T PF08766_consen 21 VTKKQVREQLEERFGVDLS 39 (54)
T ss_dssp --HHHHHHHHHHH-SS--S
T ss_pred hhHHHHHHHHHHHHCCCcH
Confidence 6899999999999999863
No 63
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=20.54 E-value=2.9e+02 Score=21.68 Aligned_cols=46 Identities=28% Similarity=0.447 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhCCceeeEEEee---CCCCee---EEEEEcCCCCcHHHHHHhh
Q 031794 100 RADKRKIKDAVKKMYEIQTKKVNTLI---RPDGTK---KAYVRLTPDYDALDVANKI 150 (153)
Q Consensus 100 kAnK~qIKqAvekly~V~V~kVNTli---~p~g~K---KAyV~L~~d~dAldvanki 150 (153)
..+|.||++-+-++|.++...|-..= .-||-| .|.| ||.+|+|.++
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 57899999999999988665543321 123322 2333 7899999875
No 64
>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=20.19 E-value=95 Score=23.82 Aligned_cols=19 Identities=26% Similarity=0.604 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHHHhCCce
Q 031794 100 RADKRKIKDAVKKMYEIQT 118 (153)
Q Consensus 100 kAnK~qIKqAvekly~V~V 118 (153)
+|+|.|+..+|+.+++.+-
T Consensus 115 ~A~KeqV~~mv~~~l~~~~ 133 (154)
T cd00529 115 KADKDQVQHMVKRLLNLSE 133 (154)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 6999999999999998765
Done!