Query 028424
Match_columns 209
No_of_seqs 107 out of 286
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 11:19:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028424.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028424hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3151 26S proteasome regulat 100.0 4.3E-69 9.3E-74 455.5 19.0 207 1-209 53-260 (260)
2 KOG1861 Leucine permease trans 100.0 4.5E-33 9.8E-38 254.6 15.0 170 2-179 346-517 (540)
3 PF10075 PCI_Csn8: COP9 signal 100.0 3.6E-30 7.9E-35 205.1 8.8 130 47-179 3-134 (143)
4 PF03399 SAC3_GANP: SAC3/GANP/ 100.0 2.7E-29 5.9E-34 208.7 10.9 147 3-151 55-204 (204)
5 KOG4414 COP9 signalosome, subu 99.7 7.4E-17 1.6E-21 129.4 11.4 134 40-180 33-172 (197)
6 KOG1860 Nuclear protein export 98.1 0.00011 2.4E-09 73.3 15.7 172 2-178 215-424 (927)
7 COG5079 SAC3 Nuclear protein e 97.7 0.0017 3.7E-08 61.7 15.0 161 3-171 181-377 (646)
8 KOG3252 Uncharacterized conser 97.5 0.00095 2.1E-08 55.9 10.0 129 48-180 62-191 (217)
9 PF01399 PCI: PCI domain; Int 97.4 0.0027 5.9E-08 46.4 10.4 73 89-162 5-82 (105)
10 smart00088 PINT motif in prote 96.0 0.036 7.9E-07 39.8 7.0 62 117-179 2-69 (88)
11 smart00753 PAM PCI/PINT associ 96.0 0.036 7.9E-07 39.8 7.0 62 117-179 2-69 (88)
12 KOG0687 26S proteasome regulat 91.3 12 0.00026 34.5 14.8 170 9-183 146-365 (393)
13 KOG2582 COP9 signalosome, subu 90.4 1.8 3.9E-05 40.2 8.6 77 117-198 295-374 (422)
14 COG5187 RPN7 26S proteasome re 89.2 17 0.00037 33.2 14.6 173 5-182 153-378 (412)
15 KOG2581 26S proteasome regulat 88.4 3.6 7.7E-05 38.8 9.1 75 83-161 317-399 (493)
16 KOG1076 Translation initiation 75.6 16 0.00034 36.8 8.5 111 66-179 633-763 (843)
17 PF14559 TPR_19: Tetratricopep 70.6 23 0.00049 23.1 6.1 61 21-88 5-65 (68)
18 PF03374 ANT: Phage antirepres 65.9 14 0.00031 27.4 4.8 37 132-171 17-53 (111)
19 PF01399 PCI: PCI domain; Int 59.2 9.3 0.0002 27.3 2.6 83 54-136 5-88 (105)
20 KOG3389 NADH:ubiquinone oxidor 57.6 4.4 9.4E-05 33.0 0.6 31 139-171 119-149 (178)
21 cd02677 MIT_SNX15 MIT: domain 57.4 40 0.00088 23.9 5.6 47 83-136 9-63 (75)
22 PF12833 HTH_18: Helix-turn-he 55.1 49 0.0011 22.7 5.7 59 97-162 10-68 (81)
23 COG2522 Predicted transcriptio 54.8 38 0.00082 26.5 5.4 45 118-167 3-48 (119)
24 PLN00156 histone H2AX; Provisi 49.7 56 0.0012 26.2 5.8 81 82-175 26-112 (139)
25 PF09976 TPR_21: Tetratricopep 47.7 1.2E+02 0.0027 23.1 11.8 110 5-124 13-126 (145)
26 PF10668 Phage_terminase: Phag 42.7 60 0.0013 22.3 4.3 31 138-171 21-51 (60)
27 PF09339 HTH_IclR: IclR helix- 40.6 70 0.0015 20.4 4.3 44 128-172 7-51 (52)
28 PF06627 DUF1153: Protein of u 39.2 96 0.0021 23.1 5.2 39 124-163 34-72 (90)
29 KOG2908 26S proteasome regulat 39.0 3.3E+02 0.0071 25.4 14.0 135 38-179 189-339 (380)
30 PF10098 DUF2336: Uncharacteri 38.6 93 0.002 26.6 6.0 90 54-151 167-260 (262)
31 PF12728 HTH_17: Helix-turn-he 36.7 1E+02 0.0022 19.3 4.6 22 140-162 2-23 (51)
32 smart00342 HTH_ARAC helix_turn 35.6 1.3E+02 0.0028 19.8 5.3 30 139-169 50-79 (84)
33 KOG1464 COP9 signalosome, subu 34.1 3.7E+02 0.0081 24.6 12.4 133 21-162 245-386 (440)
34 PF00165 HTH_AraC: Bacterial r 34.0 69 0.0015 19.4 3.3 33 135-169 3-36 (42)
35 KOG0104 Molecular chaperones G 33.7 1E+02 0.0022 31.6 5.9 80 122-205 66-149 (902)
36 KOG1498 26S proteasome regulat 33.2 94 0.002 29.4 5.3 50 112-162 326-375 (439)
37 KOG2758 Translation initiation 32.3 4E+02 0.0086 24.9 9.0 127 50-180 249-395 (432)
38 PF10255 Paf67: RNA polymerase 32.3 1.1E+02 0.0024 28.8 5.7 46 116-162 298-343 (404)
39 KOG2072 Translation initiation 31.8 3.2E+02 0.0068 28.4 9.0 95 112-206 420-529 (988)
40 PF05687 DUF822: Plant protein 31.8 43 0.00093 27.2 2.5 50 121-178 17-71 (150)
41 KOG2495 NADH-dehydrogenase (ub 31.5 53 0.0011 31.5 3.4 63 108-170 174-250 (491)
42 PF04800 ETC_C1_NDUFA4: ETC co 31.3 28 0.00061 26.4 1.4 23 147-171 51-73 (101)
43 KOG3250 COP9 signalosome, subu 30.4 88 0.0019 27.3 4.3 52 53-104 63-141 (258)
44 PF12840 HTH_20: Helix-turn-he 30.2 1.5E+02 0.0034 19.3 4.8 44 117-162 3-46 (61)
45 PF13986 DUF4224: Domain of un 29.7 1.4E+02 0.0031 19.2 4.3 36 139-176 2-40 (47)
46 TIGR00540 hemY_coli hemY prote 29.6 4.3E+02 0.0094 24.0 10.2 95 5-106 188-286 (409)
47 PF05843 Suf: Suppressor of fo 29.5 3.5E+02 0.0076 23.4 8.2 63 5-78 36-100 (280)
48 PF03683 UPF0175: Uncharacteri 29.3 1.4E+02 0.003 21.0 4.6 38 121-162 17-56 (76)
49 PLN00157 histone H2A; Provisio 28.7 2.3E+02 0.0049 22.6 6.1 80 83-175 24-109 (132)
50 TIGR01764 excise DNA binding d 28.1 1.4E+02 0.003 17.8 4.5 22 140-162 2-23 (49)
51 PRK09210 RNA polymerase sigma 28.1 4.6E+02 0.01 23.9 10.0 105 56-162 120-254 (367)
52 KOG0686 COP9 signalosome, subu 27.3 5.6E+02 0.012 24.5 9.6 91 89-179 310-409 (466)
53 PLN00153 histone H2A; Provisio 27.3 1.8E+02 0.0038 23.1 5.2 81 83-176 22-108 (129)
54 PF04801 Sin_N: Sin-like prote 26.5 64 0.0014 29.9 3.1 107 54-171 274-388 (421)
55 PTZ00017 histone H2A; Provisio 24.0 3.1E+02 0.0067 21.9 6.1 80 83-175 25-110 (134)
56 KOG2753 Uncharacterized conser 23.9 2.4E+02 0.0053 26.2 6.1 66 95-162 251-316 (378)
57 cd04762 HTH_MerR-trunc Helix-T 23.8 1.7E+02 0.0036 17.3 4.1 22 140-162 1-22 (49)
58 PRK13503 transcriptional activ 23.4 1.6E+02 0.0035 24.8 4.9 40 122-162 220-259 (278)
59 cd00074 H2A Histone 2A; H2A is 23.4 1.8E+02 0.004 22.4 4.6 80 83-175 18-103 (115)
60 PRK15121 right oriC-binding tr 23.3 1.7E+02 0.0037 25.3 5.1 62 93-162 32-93 (289)
61 smart00414 H2A Histone 2A. 23.0 3E+02 0.0066 20.8 5.7 81 83-176 7-93 (106)
62 cd02681 MIT_calpain7_1 MIT: do 22.6 1.8E+02 0.0039 20.7 4.2 47 83-136 9-64 (76)
63 TIGR02297 HpaA 4-hydroxyphenyl 22.6 2.1E+02 0.0046 24.2 5.4 40 122-162 235-274 (287)
64 PF04212 MIT: MIT (microtubule 22.5 2.5E+02 0.0054 18.8 4.8 49 81-136 6-62 (69)
65 smart00745 MIT Microtubule Int 22.2 2.6E+02 0.0057 19.0 5.4 48 82-136 10-65 (77)
66 PF13412 HTH_24: Winged helix- 22.0 2E+02 0.0044 17.6 5.2 39 122-162 1-39 (48)
67 cd07977 TFIIE_beta_winged_heli 21.8 1.6E+02 0.0034 20.9 3.7 42 138-179 24-70 (75)
68 PF08564 CDC37_C: Cdc37 C term 21.8 66 0.0014 24.3 1.8 41 83-123 21-61 (99)
69 PF08858 IDEAL: IDEAL domain; 21.7 90 0.002 19.1 2.1 18 13-30 20-37 (37)
70 PHA01082 putative transcriptio 21.4 2E+02 0.0043 22.8 4.4 74 135-209 25-133 (133)
71 cd02684 MIT_2 MIT: domain cont 21.1 2E+02 0.0044 20.2 4.2 37 96-136 19-63 (75)
72 COG5071 RPN5 26S proteasome re 20.8 1.9E+02 0.0042 26.7 4.8 47 115-162 329-375 (439)
73 COG3357 Predicted transcriptio 20.7 1.7E+02 0.0036 22.0 3.7 39 123-161 2-40 (97)
74 PF09035 Tn916-Xis: Excisionas 20.7 2.7E+02 0.0058 19.4 4.6 40 139-179 13-54 (67)
75 PF10771 DUF2582: Protein of u 20.5 74 0.0016 22.1 1.7 38 137-180 20-57 (65)
76 PF05584 Sulfolobus_pRN: Sulfo 20.4 3.3E+02 0.0071 19.4 5.7 47 124-173 5-57 (72)
77 PF10602 RPN7: 26S proteasome 20.4 3.7E+02 0.0079 21.8 6.2 57 11-71 80-136 (177)
78 PF02042 RWP-RK: RWP-RK domain 20.1 1.8E+02 0.0038 19.4 3.4 27 135-162 11-37 (52)
No 1
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-69 Score=455.54 Aligned_cols=207 Identities=57% Similarity=0.873 Sum_probs=196.0
Q ss_pred ChHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhh-
Q 028424 1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL- 79 (209)
Q Consensus 1 ~~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~- 79 (209)
++||+|||+||++||.++|+++|+|||+||+|||+|+...+|+|+++++++||||||||||||+++||++||+||...+
T Consensus 53 ~~aR~ilEi~vl~SI~t~D~~sFerY~~Qlk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNRiaeFHteLe~lp~~~l~ 132 (260)
T KOG3151|consen 53 IIARDILEIGVLLSILTKDFESFERYMNQLKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNRIAEFHTELELLPKKILQ 132 (260)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHhcchhcccccccCcchhhhHHHHHHHHHHHHhccHHHHHHHHHhccHHHhh
Confidence 3799999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHH
Q 028424 80 ENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE 159 (209)
Q Consensus 80 ~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~ 159 (209)
.||||+||++|||++|||+|+|||.+++++|++.|++|||+|++|||+|||.|+||||..||+++|+.||+|++++++..
T Consensus 133 ~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~ 212 (260)
T KOG3151|consen 133 HNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKK 212 (260)
T ss_pred ccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHH
Confidence 77999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCceeeCCeEEEecCCCCCCCCCCChHHHHHHHHhHHHHhhhcC
Q 028424 160 YVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV 209 (209)
Q Consensus 160 f~~~~~~gW~~~~~~i~f~~~~~~~~~~~~~~~~li~~~l~Ya~elE~IV 209 (209)
|+ .+|+|.++.+.++++...+.+...++|+.+++.++|+||+|||+||
T Consensus 213 ~~--~~r~W~l~~~~~~~~~~~~~~p~~~~ps~~la~qtlsYar~LE~Iv 260 (260)
T KOG3151|consen 213 FA--TERQWPLDEKGVFSFASKETAPYEEIPSTELAEQTLSYARELEMIV 260 (260)
T ss_pred HH--HhcCCcccccccccchhhccCchhccCcHHHHHHHHHHHHHHHhcC
Confidence 96 4789999966666665545555568999999999999999999998
No 2
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=100.00 E-value=4.5e-33 Score=254.61 Aligned_cols=170 Identities=19% Similarity=0.349 Sum_probs=156.5
Q ss_pred hHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcC
Q 028424 2 VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALEN 81 (209)
Q Consensus 2 ~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~ 81 (209)
++.+|||+||+||+++||++|||||++|||.+|..+ +|+. ..+|+||+|||++.+.|..+..++|..|+.|+|+|
T Consensus 346 FTveVYEtHARIALEkGD~~EfNQCQtQLk~LY~eg---ipg~--~~EF~AYriLY~i~tkN~~di~sll~~lt~E~ked 420 (540)
T KOG1861|consen 346 FTVEVYETHARIALEKGDLEEFNQCQTQLKALYSEG---IPGA--YLEFTAYRILYYIFTKNYPDILSLLRDLTEEDKED 420 (540)
T ss_pred eeeeeehhhhHHHHhcCCHHHHHHHHHHHHHHHccC---CCCc--hhhHHHHHHHHHHHhcCchHHHHHHHhccHhhccC
Confidence 356899999999999999999999999999999654 6654 79999999999888777789999999999999999
Q ss_pred chhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccC-CccHHHHHHhhCCCCHHHHHHH
Q 028424 82 PCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYD-YLSIKDAGQMLLFTSDQELLEY 160 (209)
Q Consensus 82 ~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~-sl~l~~a~~lL~f~~~~e~~~f 160 (209)
++|.|+++|+.++..|||++||+++.++|. |.+|+||.|++++|..++..|+|||+ +||++++++.|.|++.++|..|
T Consensus 421 ~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~-M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~ 499 (540)
T KOG1861|consen 421 EAVAHALEVRSAVTLGNYHKFFRLYLTAPN-MSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCVNF 499 (540)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHHHhhccc-chhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHH
Confidence 999999999999999999999999999998 79999999999999999999999999 9999999999999999999999
Q ss_pred HhhhCCCceee-CCeEEEec
Q 028424 161 VKEEHPEWEMK-DGFVFFQK 179 (209)
Q Consensus 161 ~~~~~~gW~~~-~~~i~f~~ 179 (209)
.. +.+|+-+ .|..+..+
T Consensus 500 l~--~~~~~~~~~g~~~~~~ 517 (540)
T KOG1861|consen 500 LN--EQNLTYDSLGPQILDK 517 (540)
T ss_pred Hh--ccCccccccCCccccc
Confidence 74 6789887 55555444
No 3
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=99.96 E-value=3.6e-30 Score=205.10 Aligned_cols=130 Identities=28% Similarity=0.444 Sum_probs=104.7
Q ss_pred hhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhc-CchhhhHHHHHHHHHhcChHHHHHHhh-cCCCcchHHHHHHHHHH
Q 028424 47 EYMILGLNLLRLLVQNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQ-NVPNETYGYFMDLLAKT 124 (209)
Q Consensus 47 ~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~-~~~I~~~~~leq~L~eGnY~kv~~~~~-~~P~~~~~~fm~~L~~t 124 (209)
...+.|++|+.+|.+|++++||.+|++||+++++ ||+|+.+|.|+|+||+|+|+++|...+ +.|++.+.+||..|.++
T Consensus 3 ~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 82 (143)
T PF10075_consen 3 NPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDT 82 (143)
T ss_dssp -HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHH
T ss_pred chhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHH
Confidence 4689999999999999999999999999999995 799999999999999999999999654 56788999999999999
Q ss_pred HHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceeeCCeEEEec
Q 028424 125 VRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK 179 (209)
Q Consensus 125 iR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~~~~i~f~~ 179 (209)
+|++|+.||++||++|++++++++||++ ++|+.+|++ ++||+++++.++|+.
T Consensus 83 iR~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~--~~gW~~d~~~~~~~~ 134 (143)
T PF10075_consen 83 IRERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK--SRGWTVDGDGVLFPP 134 (143)
T ss_dssp HHHHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH--HHT-EE-----EE--
T ss_pred HHHHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH--HcCCEECCCccEEec
Confidence 9999999999999999999999999999 999999985 469999966655553
No 4
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=99.96 E-value=2.7e-29 Score=208.68 Aligned_cols=147 Identities=34% Similarity=0.546 Sum_probs=127.9
Q ss_pred HHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCc
Q 028424 3 SGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENP 82 (209)
Q Consensus 3 ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~ 82 (209)
+++|||.+|+++|..+|.++|++|++||+.+|.+. ...++++++.+|+|++||++|++|+.++||..+..+|++.++||
T Consensus 55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~-~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~ 133 (204)
T PF03399_consen 55 AIKVYERIARFAIESGDLEQFNQCLSQLKELYDDL-RDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSP 133 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSH
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhh-ccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCH
Confidence 78999999999999999999999999999999986 33577899999999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHHHhcChHHHHHHh--hcCCCcchHHHHHHHHHHHHHHHHHHHHhccCC-ccHHHHHHhhCC
Q 028424 83 CIKHAVELEQSFMEGAYNRVLSAK--QNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDY-LSIKDAGQMLLF 151 (209)
Q Consensus 83 ~I~~~~~leq~L~eGnY~kv~~~~--~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~s-l~l~~a~~lL~f 151 (209)
.|+++++|.+++++|||.++|+.. .++| ..++.+|+.+++++|..++.++++||.+ +|++.++++|+|
T Consensus 134 ~i~~al~l~~a~~~gny~~ff~l~~~~~~~-~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 134 YIQFALELCRALMEGNYVRFFRLYRSKSAP-YLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHHHHHHH--TTHHHHHHHHT-TTS--HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHhccCCC-hHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 999999999999999999999988 5654 5799999999999999999999999998 999999999997
No 5
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.71 E-value=7.4e-17 Score=129.39 Aligned_cols=134 Identities=11% Similarity=0.124 Sum_probs=119.0
Q ss_pred CCCCCc--chhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhh-cCchhhhHHHHHHHHHhcChHHHHHHhhcCC-CcchH
Q 028424 40 RLPPSP--NEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL-ENPCIKHAVELEQSFMEGAYNRVLSAKQNVP-NETYG 115 (209)
Q Consensus 40 ~l~~s~--~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~-~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P-~~~~~ 115 (209)
|+...+ -+...++.|+| -|+..+...+|+|||+.+| .+|++.-+|.++|.+|..+|..||.+.+... |++..
T Consensus 33 GIa~~~dw~Ya~~L~~Yf~----~dD~dnARfLWKRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak 108 (197)
T KOG4414|consen 33 GIATHDDWPYAIHLAGYFL----HDDCDNARFLWKRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAK 108 (197)
T ss_pred CccCCCcchHHHHHHHHHH----hccchhHHHHHHhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHH
Confidence 565555 56777777777 8999999999999999999 9999999999999999999999999987655 88999
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEE-EecC
Q 028424 116 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVF-FQKA 180 (209)
Q Consensus 116 ~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~-f~~~ 180 (209)
.+|..|-|..|.+....+..||+||..++++..||+. +++....+- +.||++| .+++. .+++
T Consensus 109 ~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~il--EnGWqaDaasqMasl~kk 172 (197)
T KOG4414|consen 109 DIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKGIL--ENGWQADAASQMASLKKK 172 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHHH--HcccchhhHHHHhhccch
Confidence 9999999999999999999999999999999999999 888888874 6799999 55665 5543
No 6
>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]
Probab=98.10 E-value=0.00011 Score=73.28 Aligned_cols=172 Identities=18% Similarity=0.287 Sum_probs=131.8
Q ss_pred hHHHHHHHHHHHHhhh----cCh-HHH---------HHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHH
Q 028424 2 VSGDIYEHAVLLSVKV----EDQ-DAF---------ERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEF 67 (209)
Q Consensus 2 ~ar~vlEi~a~~sl~~----~D~-~~F---------~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~ef 67 (209)
.|..++|-.|+.=|.. .|. +.| ..|..-|..+|.|+..+-.+.++..+|-|||+| |+-|+ .+.
T Consensus 215 ~Av~llE~i~RfhI~~~h~Lce~~~~Fda~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vL--l~Lgd-~~~ 291 (927)
T KOG1860|consen 215 EAVELLERIARFHILFRHRLCEEPEQFDAQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVL--LSLGD-PQV 291 (927)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCcccCChhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHH--HhcCC-chH
Confidence 4677888777765543 233 344 445566778898886555668999999999977 55565 355
Q ss_pred HHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHH-----------------HhhcCC-C-cchHHHHHHHHHHHHHH
Q 028424 68 HTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLS-----------------AKQNVP-N-ETYGYFMDLLAKTVRDE 128 (209)
Q Consensus 68 h~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~-----------------~~~~~P-~-~~~~~fm~~L~~tiR~~ 128 (209)
-.....+|+++..++.+++++.+.++...|||..+++ .....| . ..-..++..+..-+|.-
T Consensus 292 ~~~iq~~~~evr~~~~Vk~al~~~~a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~ 371 (927)
T KOG1860|consen 292 VRDIQAWPDEVRQDSEVKLALCLRRAFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWA 371 (927)
T ss_pred HHHHHhcCcccccchhHHHHHHHHHHhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHH
Confidence 6677889999999999999999999999999998863 122334 1 13466788889999999
Q ss_pred HHHHHHhccC----CccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEEEe
Q 028424 129 IAGCSEKAYD----YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQ 178 (209)
Q Consensus 129 ia~~iekAY~----sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~f~ 178 (209)
+...++.+|. .+|+.+...+|+|+++++...+.. .+|-+++ +..+..+
T Consensus 372 al~~~~~~~~~~~~~vp~~~l~~~l~f~~~e~~~~~~~--~y~Leis~~~~~~~~ 424 (927)
T KOG1860|consen 372 ALRAMSHAYNSKHVPVPLGKLDRILLFDGEEELKVVCN--YYGLEISVDDKIVLS 424 (927)
T ss_pred HHHHHHHHHhccCCCcchhHHHHHHhcCChhhhHhhhh--heeeEeecccccccc
Confidence 9999999996 599999999999999999999974 6888887 3334433
No 7
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=97.68 E-value=0.0017 Score=61.70 Aligned_cols=161 Identities=19% Similarity=0.233 Sum_probs=119.5
Q ss_pred HHHHHHHHHHHHhhh----cChHHHHHHHH--hh-------HHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHH
Q 028424 3 SGDIYEHAVLLSVKV----EDQDAFERDFF--QL-------KPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHT 69 (209)
Q Consensus 3 ar~vlEi~a~~sl~~----~D~~~F~~~~~--qL-------k~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~ 69 (209)
|.++.|..|++-|.. .|...|++=|. || -.+|.++..+-...+|..+|-+|-+|- +-+| ...-.
T Consensus 181 AV~c~EriaRfhIl~lh~L~~~p~Fs~qqeleQL~ksL~sL~elYdd~r~~~~~cpneaEFraYaiL~--slgD-p~yv~ 257 (646)
T COG5079 181 AVECHERIARFHILFLHLLHDHPHFSKQQELEQLKKSLASLIELYDDGRAGKKECPNEAEFRAYAILA--SLGD-PRYVA 257 (646)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccHHhHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHH--HhCC-chhhh
Confidence 667788888766543 45577765543 55 468999877778889999999998873 3332 23444
Q ss_pred HHHhccHhhhcCchhhhHHHHHHHHHhcCh---------------HHHHHHhhcCCCcchHHHHHHHHH----HHHHHHH
Q 028424 70 ELELLSSTALENPCIKHAVELEQSFMEGAY---------------NRVLSAKQNVPNETYGYFMDLLAK----TVRDEIA 130 (209)
Q Consensus 70 ~Le~l~~~~~~~~~I~~~~~leq~L~eGnY---------------~kv~~~~~~~P~~~~~~fm~~L~~----tiR~~ia 130 (209)
-...+|..+..++-++-++.+.|-...||| .++|+..+. | ...|||..|++ .+|.-++
T Consensus 258 ~iq~wp~~if~d~~vq~alkl~~laq~nn~r~~~~rnteac~nlytrFfkl~qS-p--sv~~lmg~lle~h~~sir~~aL 334 (646)
T COG5079 258 GIQGWPGGIFCDLPVQIALKLMQLAQSNNFRLLGRRNTEACFNLYTRFFKLIQS-P--SVQYLMGCLLEKHNISIRGGAL 334 (646)
T ss_pred ccccCCccccccchHHHHHHHHHHhhccCeeeccccchhhhhHHHHHHHHHHhC-c--cHHHHHHHHHHHhhHHHHHHHH
Confidence 566788888899999999999999888875 455665544 4 46777776655 5788888
Q ss_pred HHHHhcc----CCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee
Q 028424 131 GCSEKAY----DYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK 171 (209)
Q Consensus 131 ~~iekAY----~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~ 171 (209)
..++++| ..+|.-+...+|.|++.+|..+|++ --|-++.
T Consensus 335 kAm~k~~~sahk~ipf~~l~~il~f~~~~e~~efck--yy~lei~ 377 (646)
T COG5079 335 KAMEKEIESAHKNIPFVDLSGILDFEEKGEGEEFCK--YYGLEIR 377 (646)
T ss_pred HHHHHHHHHhhcCCCeehhhhhccccccchhHHHhh--hcceeee
Confidence 7555555 5799999999999999999999975 4577764
No 8
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.53 E-value=0.00095 Score=55.93 Aligned_cols=129 Identities=13% Similarity=0.146 Sum_probs=104.6
Q ss_pred hHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 028424 48 YMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRD 127 (209)
Q Consensus 48 ~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~ 127 (209)
..+++==||.-|..=--+||-...=.||+....+..++.++.|...|-.|+|..+|.....-|. +... |.=|-|.||.
T Consensus 62 t~itaqILlKaL~~lP~tDF~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~-mle~-itGFedsvr~ 139 (217)
T KOG3252|consen 62 TTITAQILLKALTNLPHTDFTLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENRD-MLEG-ITGFEDSVRK 139 (217)
T ss_pred hHHHHHHHHHHHhcCCCcchhHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccchH-HhcC-CCcHHHHHHH
Confidence 3455556666676667788999999999988888999999999999999999999986542221 2222 2336889999
Q ss_pred HHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEEEecC
Q 028424 128 EIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQKA 180 (209)
Q Consensus 128 ~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~f~~~ 180 (209)
=+--.+.-.|.+|+-.-++++||-.+..++..+++ +-||..+ .|.|+++..
T Consensus 140 yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~--~~GW~a~e~G~ifv~~q 191 (217)
T KOG3252|consen 140 YACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMT--KYGWIADESGQIFVASQ 191 (217)
T ss_pred HHHHheechHhhchHHHHHHhhCcccHHHHHHHHH--HccceecCCceEEEecc
Confidence 99999999999999999999999999999999985 6799999 777777654
No 9
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.42 E-value=0.0027 Score=46.36 Aligned_cols=73 Identities=16% Similarity=0.258 Sum_probs=55.3
Q ss_pred HHHHHHHhcChHHHHHHhhcC-----CCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 89 ELEQSFMEGAYNRVLSAKQNV-----PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 89 ~leq~L~eGnY~kv~~~~~~~-----P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++-+++-.|+|..+.+..... ..+.....++.+...+|......+.+.|++|+++.++++++++ .++++.++.
T Consensus 5 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~~l~ 82 (105)
T PF01399_consen 5 ELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVESILI 82 (105)
T ss_dssp HHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHHHHH
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHHHHH
Confidence 455566666666665544433 1334556889999999999999999999999999999999999 788888875
No 10
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=96.01 E-value=0.036 Score=39.78 Aligned_cols=62 Identities=18% Similarity=0.277 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEec
Q 028424 117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQK 179 (209)
Q Consensus 117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~ 179 (209)
..+.+...+|........+.|++|++++++..++++ .+++..++.. ..-..++| +|.+.|..
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 356789999999999999999999999999999998 5577777652 23367787 56666665
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=96.01 E-value=0.036 Score=39.78 Aligned_cols=62 Identities=18% Similarity=0.277 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEec
Q 028424 117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQK 179 (209)
Q Consensus 117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~ 179 (209)
..+.+...+|........+.|++|++++++..++++ .+++..++.. ..-..++| +|.+.|..
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 356789999999999999999999999999999998 5577777652 23367787 56666665
No 12
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=91.30 E-value=12 Score=34.51 Aligned_cols=170 Identities=13% Similarity=0.096 Sum_probs=118.0
Q ss_pred HHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHH-HHhcc------------
Q 028424 9 HAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTE-LELLS------------ 75 (209)
Q Consensus 9 i~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~-Le~l~------------ 75 (209)
.-+++.+--.|..=-++.+...|..|..+ ...++++.+-.++=+|..+-.|..++-.+ ++.+|
T Consensus 146 ~~iRlglfy~D~~lV~~~iekak~liE~G----gDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~El~~Y~~ 221 (393)
T KOG0687|consen 146 YKIRLGLFYLDHDLVTESIEKAKSLIEEG----GDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSYELMSYET 221 (393)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHHHHHhC----CChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHcccccceecccHHH
Confidence 34556666788888899999999999887 34578888999999999998888877655 34444
Q ss_pred ---------------Hhh--h--cCchhhh-------HHHHHHHHHhcChHHHHHHhh-----c-CCCcchHHHHHHHHH
Q 028424 76 ---------------STA--L--ENPCIKH-------AVELEQSFMEGAYNRVLSAKQ-----N-VPNETYGYFMDLLAK 123 (209)
Q Consensus 76 ---------------~~~--~--~~~~I~~-------~~~leq~L~eGnY~kv~~~~~-----~-~P~~~~~~fm~~L~~ 123 (209)
+++ | ..|+|.- ..++=-.|-+-+|..+|.... + -+.-..+++-+-++-
T Consensus 222 ~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvR 301 (393)
T KOG0687|consen 222 FVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVR 301 (393)
T ss_pred HHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHH
Confidence 111 1 3454433 334445677899999988542 1 123344555666677
Q ss_pred HHHHHHHHHHHhccCCccHHHHHHhhCCC---CHHHHHHHHhhhCCCcee-e-CCeEEEecCCCC
Q 028424 124 TVRDEIAGCSEKAYDYLSIKDAGQMLLFT---SDQELLEYVKEEHPEWEM-K-DGFVFFQKAKDS 183 (209)
Q Consensus 124 tiR~~ia~~iekAY~sl~l~~a~~lL~f~---~~~e~~~f~~~~~~gW~~-~-~~~i~f~~~~~~ 183 (209)
-.|.++-.-.--+|++++++..|+-.|.+ -+.|+..|+. ..|-|.. | =+.|+.-++|+.
T Consensus 302 EMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~-~grL~ckIDrVnGVVEtNrpD~ 365 (393)
T KOG0687|consen 302 EMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIA-AGRLHCKIDRVNGVVETNRPDE 365 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhc-cCceeeeeecccceeecCCccc
Confidence 78888888877899999999999999987 2358999995 4566765 4 234555554433
No 13
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=90.37 E-value=1.8 Score=40.19 Aligned_cols=77 Identities=17% Similarity=0.270 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh---hCCCceeeCCeEEEecCCCCCCCCCCChHH
Q 028424 117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE---EHPEWEMKDGFVFFQKAKDSAPCKEIPSLQ 193 (209)
Q Consensus 117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~---~~~gW~~~~~~i~f~~~~~~~~~~~~~~~~ 193 (209)
|....+...-.+-.....|.|.||+|++++++..+.+.+|+.+++-+ ..+-..+-||.|+|-..+. +.+|.+
T Consensus 295 l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~e-----~~~Spe 369 (422)
T KOG2582|consen 295 LAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNPE-----KYNSPE 369 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCcc-----cCCCHH
Confidence 44455555566666778899999999999999999999999888753 2334444488887776432 244555
Q ss_pred HHHHH
Q 028424 194 LINQT 198 (209)
Q Consensus 194 li~~~ 198 (209)
++.|-
T Consensus 370 M~~nk 374 (422)
T KOG2582|consen 370 MHENK 374 (422)
T ss_pred HHhhH
Confidence 55543
No 14
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=89.24 E-value=17 Score=33.17 Aligned_cols=173 Identities=14% Similarity=0.122 Sum_probs=118.8
Q ss_pred HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhc-c--------
Q 028424 5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELL-S-------- 75 (209)
Q Consensus 5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l-~-------- 75 (209)
+|+=.-+++.+--+|.---++-...+++.|.-+ ...++++.+..++=+++++-.+..++-.+|-.+ |
T Consensus 153 Dv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkG----gDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~ 228 (412)
T COG5187 153 DVFLCKIRLGLIYGDRKVVEESLEVADDIIEKG----GDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELI 228 (412)
T ss_pred hhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhC----CCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccccc
Confidence 344445666677788888888888888888765 234677777778878888877777776665322 2
Q ss_pred -----------------------------Hh---hh-cCchhhhHHHHHHHHHhcChHHHHHHhh------cCCCcchHH
Q 028424 76 -----------------------------ST---AL-ENPCIKHAVELEQSFMEGAYNRVLSAKQ------NVPNETYGY 116 (209)
Q Consensus 76 -----------------------------~~---~~-~~~~I~~~~~leq~L~eGnY~kv~~~~~------~~P~~~~~~ 116 (209)
++ +. ++.-++...++--.|-+-+|...|.... =.|.....-
T Consensus 229 sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~r 308 (412)
T COG5187 229 SYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGR 308 (412)
T ss_pred cHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHH
Confidence 11 11 3445566677777888888887765221 123445566
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCC---CHHHHHHHHhhhCCCceee--CCeEEEecCCC
Q 028424 117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFT---SDQELLEYVKEEHPEWEMK--DGFVFFQKAKD 182 (209)
Q Consensus 117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~---~~~e~~~f~~~~~~gW~~~--~~~i~f~~~~~ 182 (209)
+.|.++--.|.++-.-+-.+|+.++++..|.-.|.+ -+-++-+|+- ..+-|.+- =+.|++.++|+
T Consensus 309 h~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp-~~~LncvIDRvnGvVetnrpd 378 (412)
T COG5187 309 HVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIP-EGRLNCVIDRVNGVVETNRPD 378 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCC-CCceeeeeecccceEeccCcc
Confidence 778888889999988888899999999999999987 1237888985 45677764 23455555543
No 15
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=88.43 E-value=3.6 Score=38.82 Aligned_cols=75 Identities=16% Similarity=0.222 Sum_probs=51.3
Q ss_pred hhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHH----HHHHHHHHHH----HHHHHhccCCccHHHHHHhhCCCCH
Q 028424 83 CIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD----LLAKTVRDEI----AGCSEKAYDYLSIKDAGQMLLFTSD 154 (209)
Q Consensus 83 ~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~----~L~~tiR~~i----a~~iekAY~sl~l~~a~~lL~f~~~ 154 (209)
.+.+=..|-++.-.||-.|+=.-..+.- .-|+. .|.-|.|..+ ...|.-+|+.||+.|+|+-|+++|+
T Consensus 317 sL~~Yf~Lt~AVr~gdlkkF~~~leq~k----~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Se 392 (493)
T KOG2581|consen 317 SLRPYFKLTQAVRLGDLKKFNETLEQFK----DKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSE 392 (493)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHH----HHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCc
Confidence 6777778888888888888744332210 11111 2344555544 4688999999999999999999987
Q ss_pred HHHHHHH
Q 028424 155 QELLEYV 161 (209)
Q Consensus 155 ~e~~~f~ 161 (209)
+++.-.+
T Consensus 393 ed~EyiV 399 (493)
T KOG2581|consen 393 EDAEYIV 399 (493)
T ss_pred hhHHHHH
Confidence 7655444
No 16
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=75.63 E-value=16 Score=36.75 Aligned_cols=111 Identities=15% Similarity=0.327 Sum_probs=73.7
Q ss_pred HHHHHHHhccHhhh-cCch--hhhHHHHHHHHHhcChHHHHHHhhc-------CCCcchHHHHHHHHHHHHHHHHHH---
Q 028424 66 EFHTELELLSSTAL-ENPC--IKHAVELEQSFMEGAYNRVLSAKQN-------VPNETYGYFMDLLAKTVRDEIAGC--- 132 (209)
Q Consensus 66 efh~~Le~l~~~~~-~~~~--I~~~~~leq~L~eGnY~kv~~~~~~-------~P~~~~~~fm~~L~~tiR~~ia~~--- 132 (209)
.||-.||....... .=|+ =.|++.--++|..||+.+-+.-..+ .| .-.-+.++|.++|+.+.+..
T Consensus 633 ~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfp--n~d~V~~Ml~~rIqEEsLRTYLf 710 (843)
T KOG1076|consen 633 SFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFP--NADTVLDMLTERIQEESLRTYLF 710 (843)
T ss_pred HHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcc--cHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555655533222 2222 3577888899999999887762222 23 34668999999999999873
Q ss_pred -HHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCC--CceeeCCeEEEec
Q 028424 133 -SEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHP--EWEMKDGFVFFQK 179 (209)
Q Consensus 133 -iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~--gW~~~~~~i~f~~ 179 (209)
-...|.|+|+..+|.|.-++ +..+...+.. .+- .|.=..+.|+|..
T Consensus 711 tYss~Y~SvSl~~LA~mFdLp-~~~VhsIiSkmiineEl~AslDqpt~~iv~hr 763 (843)
T KOG1076|consen 711 TYSSVYDSVSLAKLADMFDLP-EPKVHSIISKMIINEELHASLDQPTQCIVMHR 763 (843)
T ss_pred HhhhhhhhccHHHHHHHhCCC-chhHHHHHHHHHHHHHhhhccCCCcceEEEee
Confidence 34568899999999999998 7777777641 222 4443244555554
No 17
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=70.56 E-value=23 Score=23.09 Aligned_cols=61 Identities=18% Similarity=0.109 Sum_probs=40.4
Q ss_pred HHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHH
Q 028424 21 DAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAV 88 (209)
Q Consensus 21 ~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~ 88 (209)
+.|.+....++...... |. ...+.-..--.++.+|+..++...|++++.....||.+...+
T Consensus 5 ~~~~~A~~~~~~~l~~~----p~---~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~ 65 (68)
T PF14559_consen 5 GDYDEAIELLEKALQRN----PD---NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLL 65 (68)
T ss_dssp THHHHHHHHHHHHHHHT----TT---SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHC----CC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 34666677777777654 32 234444444457789999999999999988776667766543
No 18
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=65.89 E-value=14 Score=27.40 Aligned_cols=37 Identities=14% Similarity=0.389 Sum_probs=30.4
Q ss_pred HHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee
Q 028424 132 CSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK 171 (209)
Q Consensus 132 ~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~ 171 (209)
.+..+=.++++.++|++|++. +..+.+|+. +.||-.+
T Consensus 17 ~~~~~~~~~ti~~~AK~L~i~-~~~l~~~Lr--~~g~l~~ 53 (111)
T PF03374_consen 17 AFVDSDGLYTIREAAKLLGIG-RNKLFQWLR--EKGWLYR 53 (111)
T ss_pred HHHcCCCCccHHHHHHHhCCC-HHHHHHHHH--hCCceEE
Confidence 333344789999999999999 999999994 5788887
No 19
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=59.24 E-value=9.3 Score=27.29 Aligned_cols=83 Identities=14% Similarity=0.211 Sum_probs=54.0
Q ss_pred HHHHHHhhCCHHHHHHHHHhccHhhhcCchhh-hHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHH
Q 028424 54 NLLRLLVQNRIAEFHTELELLSSTALENPCIK-HAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGC 132 (209)
Q Consensus 54 ~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~-~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~ 132 (209)
.|+..+.++++.+|+..++........++++. +.=.+.+.+...+..++...+++++-+..+-....-.+.+..-+++.
T Consensus 5 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~ 84 (105)
T PF01399_consen 5 ELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDL 84 (105)
T ss_dssp HHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHH
Confidence 46778889999999999999955566566654 56678888889999999887777653223222222234444445555
Q ss_pred HHhc
Q 028424 133 SEKA 136 (209)
Q Consensus 133 iekA 136 (209)
|...
T Consensus 85 I~~~ 88 (105)
T PF01399_consen 85 ISNG 88 (105)
T ss_dssp HHTT
T ss_pred HHCC
Confidence 5433
No 20
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=57.59 E-value=4.4 Score=32.96 Aligned_cols=31 Identities=16% Similarity=0.456 Sum_probs=26.8
Q ss_pred CccHHHHHHhhCCCCHHHHHHHHhhhCCCceee
Q 028424 139 YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK 171 (209)
Q Consensus 139 sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~ 171 (209)
-=|++++-.-|.|++.+++..|+ +..||..|
T Consensus 119 aDPlsNvgm~L~F~tkEdA~sFa--EkngW~yd 149 (178)
T KOG3389|consen 119 ADPLSNVGMALAFDTKEDAKSFA--EKNGWDYD 149 (178)
T ss_pred CCcccccceeeeeccHHHHHHHH--HHcCCccc
Confidence 35788888889999999999997 46899987
No 21
>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
Probab=57.40 E-value=40 Score=23.89 Aligned_cols=47 Identities=21% Similarity=0.296 Sum_probs=36.0
Q ss_pred hhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHH--------HHHHHHHHHHHHHHHhc
Q 028424 83 CIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD--------LLAKTVRDEIAGCSEKA 136 (209)
Q Consensus 83 ~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~--------~L~~tiR~~ia~~iekA 136 (209)
.|+.+++.++. |+|...+..+.+. ..+||. .-.+++|.++...+.+|
T Consensus 9 l~~~Ave~d~~---~~y~eA~~~Y~~~----i~~~~~~~k~e~~~~~k~~ir~K~~eYl~RA 63 (75)
T cd02677 9 LIRLALEKEEE---GDYEAAFEFYRAG----VDLLLKGVQGDSSPERREAVKRKIAEYLKRA 63 (75)
T ss_pred HHHHHHHHHHH---hhHHHHHHHHHHH----HHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Confidence 45566666665 9999999988763 466776 44788999999998887
No 22
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=55.08 E-value=49 Score=22.68 Aligned_cols=59 Identities=15% Similarity=0.110 Sum_probs=34.7
Q ss_pred cChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 97 GAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 97 GnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
....++|+.....+. .. ++...|.+.+.-.-..+...|+.+++..+||.|..-+....+
T Consensus 10 ~~l~~~f~~~~g~s~--~~-----~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk 68 (81)
T PF12833_consen 10 RYLSRIFKKETGMSF--KQ-----YLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFK 68 (81)
T ss_dssp HHHHHHHHHHHSS-H--HH-----HHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCH--HH-----HHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHH
Confidence 344556665444321 22 345556555544333367999999999999999988877664
No 23
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=54.77 E-value=38 Score=26.46 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHH-HHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCC
Q 028424 118 MDLLAKTVRDEIAG-CSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPE 167 (209)
Q Consensus 118 m~~L~~tiR~~ia~-~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~g 167 (209)
.+.++-.+|-.+|. .+++ -+|-..+|++||++ ...+.+|+. ..||
T Consensus 3 ~~~vlPaiRa~lA~~L~ee---G~Sq~~iA~LLGlt-qaAVS~Yls-~krg 48 (119)
T COG2522 3 VEEVLPAIRALLAKELIEE---GLSQYRIAKLLGLT-QAAVSQYLS-GKRG 48 (119)
T ss_pred hHHHHHHHHHHHHHHHHHc---CCcHHHHHHHhCCC-HHHHHHHHc-cCCc
Confidence 45678899999995 5554 78889999999998 999999996 3455
No 24
>PLN00156 histone H2AX; Provisional
Probab=49.70 E-value=56 Score=26.25 Aligned_cols=81 Identities=15% Similarity=0.260 Sum_probs=52.3
Q ss_pred chhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc-----CCccHHHHHHhhCCCCHH
Q 028424 82 PCIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAY-----DYLSIKDAGQMLLFTSDQ 155 (209)
Q Consensus 82 ~~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY-----~sl~l~~a~~lL~f~~~~ 155 (209)
.-++||+ .++++|.+|+|.+ .....+| .||...++-+=-||+.+...+= ..|+-..+. |.+.+.+
T Consensus 26 AgL~FPVgRi~R~Lk~g~ya~--RVga~Ap-----VYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~--lAIrnDe 96 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKYAE--RVGAGAP-----VYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ--LAVRNDE 96 (139)
T ss_pred cCcccchHHHHHHHhcCChhh--ccCCccH-----HHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHH--hhccCcH
Confidence 3578887 5999999999986 2323333 4555555555555554444332 246666654 5567889
Q ss_pred HHHHHHhhhCCCceeeCCeE
Q 028424 156 ELLEYVKEEHPEWEMKDGFV 175 (209)
Q Consensus 156 e~~~f~~~~~~gW~~~~~~i 175 (209)
|+..++ .+|++-.|.|
T Consensus 97 EL~~Ll----~~vTIa~GGV 112 (139)
T PLN00156 97 ELSKLL----GSVTIAAGGV 112 (139)
T ss_pred HHHHHH----CCCccCCCcc
Confidence 999997 3899985554
No 25
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=47.73 E-value=1.2e+02 Score=23.09 Aligned_cols=110 Identities=25% Similarity=0.359 Sum_probs=70.3
Q ss_pred HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHH-HHhhCCHHHHHHHHHhccHhhhcCch
Q 028424 5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLR-LLVQNRIAEFHTELELLSSTALENPC 83 (209)
Q Consensus 5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~-LL~~n~i~efh~~Le~l~~~~~~~~~ 83 (209)
.+|+- ++.++..+|...-.....+|..-| |.++ +..+-.|.|=. +..+|+..+....|+.+.... .|+.
T Consensus 13 ~~y~~-~~~~~~~~~~~~~~~~~~~l~~~~-------~~s~-ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~-~d~~ 82 (145)
T PF09976_consen 13 ALYEQ-ALQALQAGDPAKAEAAAEQLAKDY-------PSSP-YAALAALQLAKAAYEQGDYDEAKAALEKALANA-PDPE 82 (145)
T ss_pred HHHHH-HHHHHHCCCHHHHHHHHHHHHHHC-------CCCh-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-CCHH
Confidence 34443 334456888888766555555544 2222 33333333333 446899999999999987644 5666
Q ss_pred hhhHHHH---HHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHH
Q 028424 84 IKHAVEL---EQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKT 124 (209)
Q Consensus 84 I~~~~~l---eq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~t 124 (209)
++....+ .-.+.+|+|.+.......+|.+.|..+...+.+-
T Consensus 83 l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gd 126 (145)
T PF09976_consen 83 LKPLARLRLARILLQQGQYDEALATLQQIPDEAFKALAAELLGD 126 (145)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHH
Confidence 6655554 3447799999999988877776777766554433
No 26
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=42.68 E-value=60 Score=22.31 Aligned_cols=31 Identities=16% Similarity=0.454 Sum_probs=25.6
Q ss_pred CCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee
Q 028424 138 DYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK 171 (209)
Q Consensus 138 ~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~ 171 (209)
-.+++.++|..||.+ +..+..+ ...-.|.-.
T Consensus 21 g~i~lkdIA~~Lgvs-~~tIr~W--K~~dkW~~~ 51 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVS-ESTIRKW--KSRDKWDEK 51 (60)
T ss_pred CCccHHHHHHHHCCC-HHHHHHH--hhhcchhhH
Confidence 389999999999998 8888888 344588765
No 27
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=40.59 E-value=70 Score=20.41 Aligned_cols=44 Identities=9% Similarity=0.141 Sum_probs=32.2
Q ss_pred HHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh-hCCCceeeC
Q 028424 128 EIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE-EHPEWEMKD 172 (209)
Q Consensus 128 ~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~-~~~gW~~~~ 172 (209)
+|+.++..+=..+++.++++.+|++ ...+...++. .+.||...|
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLP-KSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCcCeecC
Confidence 5677887777789999999999998 6666666542 256887654
No 28
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=39.18 E-value=96 Score=23.11 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh
Q 028424 124 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE 163 (209)
Q Consensus 124 tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~ 163 (209)
++|.+++-...-.|--||.++|+..-+++ ++|+..|..+
T Consensus 34 va~RKAaVV~aV~~Glis~~EA~~rY~Ls-~eEf~~W~~a 72 (90)
T PF06627_consen 34 VARRKAAVVRAVRGGLISVEEACRRYGLS-EEEFESWQRA 72 (90)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHCTTSS-HHHHHHHHHH
T ss_pred hhhHHHHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHHH
Confidence 46778887777788899999999999998 9999999754
No 29
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=39.00 E-value=3.3e+02 Score=25.41 Aligned_cols=135 Identities=21% Similarity=0.182 Sum_probs=82.6
Q ss_pred CCCCCCCc--chhHHHHHHHHHHHhhCCHHHHHHHHHhccH-hhhcCchhhhHHHHHHHHHhcChHHHHHHhhcCC-Ccc
Q 028424 38 GKRLPPSP--NEYMILGLNLLRLLVQNRIAEFHTELELLSS-TALENPCIKHAVELEQSFMEGAYNRVLSAKQNVP-NET 113 (209)
Q Consensus 38 ~~~l~~s~--~~~~il~l~LL~LL~~n~i~efh~~Le~l~~-~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P-~~~ 113 (209)
.+.+|.|+ ...-.+|++ -||..| +=+|-.+|.. |. +-..+....+-.++=.++-.||..++.+...... -|.
T Consensus 189 ~~~l~~se~~~lA~~L~~a--ALLGe~-iyNfGELL~H-PilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~ 264 (380)
T KOG2908|consen 189 IDDLSESEKQDLAFDLSLA--ALLGEN-IYNFGELLAH-PILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQPD 264 (380)
T ss_pred ccccCHHHHHHHHHHHHHH--HHhccc-cccHHHHHhh-HHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCch
Confidence 45677777 444445544 455543 4466554432 32 2225677788888899999999999998765321 223
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhccC------CccHHHHHHhhCCCCHHHHHHHHh-hhCC---Cceee--CCeEEEec
Q 028424 114 YGYFMDLLAKTVRDEIAGCSEKAYD------YLSIKDAGQMLLFTSDQELLEYVK-EEHP---EWEMK--DGFVFFQK 179 (209)
Q Consensus 114 ~~~fm~~L~~tiR~~ia~~iekAY~------sl~l~~a~~lL~f~~~~e~~~f~~-~~~~---gW~~~--~~~i~f~~ 179 (209)
.+---+.|.+.+|- .+.||-++. ++|.+++++.+.++ .+|+.-.+- +-+. .|.+| +|.+++.-
T Consensus 265 L~~~e~~L~qKI~L--maLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVMKAlslgLikG~Idqv~~~v~~sw 339 (380)
T KOG2908|consen 265 LASNEDFLLQKIRL--LALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVMKALSLGLIKGSIDQVEGVVYMSW 339 (380)
T ss_pred HHHHHHHHHHHHHH--HHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHHHHHhccceeeeecccccEEEEec
Confidence 45555556666653 556666664 59999999999998 455433321 1111 45565 56676654
No 30
>PF10098 DUF2336: Uncharacterized protein conserved in bacteria (DUF2336); InterPro: IPR019285 Members of this family of hypothetical bacterial proteins have no known function.
Probab=38.63 E-value=93 Score=26.60 Aligned_cols=90 Identities=26% Similarity=0.265 Sum_probs=66.0
Q ss_pred HHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHHHhh--cCCCcchHHHHHHHHHHHHH--HH
Q 028424 54 NLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQ--NVPNETYGYFMDLLAKTVRD--EI 129 (209)
Q Consensus 54 ~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~--~~P~~~~~~fm~~L~~tiR~--~i 129 (209)
-|+..+.+|+...|...|..+..-. +-.+++.|..++...+.-+.. .+|...|.-|...+...-+. .-
T Consensus 167 lL~~a~~~g~~~~f~aaLA~lsgl~--------~~~v~~il~d~~~~~L~~l~kaaGL~~~~~~~~~~~~~~~~~~~~~~ 238 (262)
T PF10098_consen 167 LLLRAACSGRLAFFAAALAELSGLP--------PARVRRILADGGGEALAALCKAAGLPWATFPAFLAALAPWRRISRGD 238 (262)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHCcC--------HHHHHHHHhCCCchHHHHHHHHcCCCHHHHHHHHHHHhhhcccCcch
Confidence 4567778999999999999885311 346888999999999877554 66666777777776655442 23
Q ss_pred HHHHHhccCCccHHHHHHhhCC
Q 028424 130 AGCSEKAYDYLSIKDAGQMLLF 151 (209)
Q Consensus 130 a~~iekAY~sl~l~~a~~lL~f 151 (209)
..-....|..|+.+.+..+|.+
T Consensus 239 ~~~~~~~y~~L~~~~A~~~L~~ 260 (262)
T PF10098_consen 239 LEEALALYDRLSPDAAQRVLRF 260 (262)
T ss_pred HHHHHHHHHcCCHHHHHHHHHH
Confidence 3446679999999999888743
No 31
>PF12728 HTH_17: Helix-turn-helix domain
Probab=36.68 E-value=1e+02 Score=19.30 Aligned_cols=22 Identities=18% Similarity=0.545 Sum_probs=19.6
Q ss_pred ccHHHHHHhhCCCCHHHHHHHHh
Q 028424 140 LSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 140 l~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++.+++|.+||++ ..-+..+++
T Consensus 2 lt~~e~a~~l~is-~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH
Confidence 6889999999997 888999985
No 32
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=35.62 E-value=1.3e+02 Score=19.77 Aligned_cols=30 Identities=17% Similarity=0.065 Sum_probs=23.4
Q ss_pred CccHHHHHHhhCCCCHHHHHHHHhhhCCCce
Q 028424 139 YLSIKDAGQMLLFTSDQELLEYVKEEHPEWE 169 (209)
Q Consensus 139 sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~ 169 (209)
.++++++|..+||.|..-+....++ ..|.+
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~-~~g~s 79 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKK-LFGVT 79 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHH-HHCcC
Confidence 7999999999999778888777643 34544
No 33
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=34.14 E-value=3.7e+02 Score=24.64 Aligned_cols=133 Identities=17% Similarity=0.247 Sum_probs=82.0
Q ss_pred HHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHH-HHHhhCCHHHHHHHHHhccHhh---hcCchhhhHHHHHHHHHh
Q 028424 21 DAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLL-RLLVQNRIAEFHTELELLSSTA---LENPCIKHAVELEQSFME 96 (209)
Q Consensus 21 ~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL-~LL~~n~i~efh~~Le~l~~~~---~~~~~I~~~~~leq~L~e 96 (209)
++|+...+-.-.-+..|. -.+|+++..-+-+-.| .+|-...+.-|-. .+. |.||+|-..-.+=++--.
T Consensus 245 g~fe~AhTDFFEAFKNYD--EsGspRRttCLKYLVLANMLmkS~iNPFDs------QEAKPyKNdPEIlAMTnlv~aYQ~ 316 (440)
T KOG1464|consen 245 GEFEKAHTDFFEAFKNYD--ESGSPRRTTCLKYLVLANMLMKSGINPFDS------QEAKPYKNDPEILAMTNLVAAYQN 316 (440)
T ss_pred chHHHHHhHHHHHHhccc--ccCCcchhHHHHHHHHHHHHHHcCCCCCcc------cccCCCCCCHHHHHHHHHHHHHhc
Confidence 356655554444444442 2456666655543333 1222222222211 122 378888877777777666
Q ss_pred cChH---HHHHHhh-cC-CCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 97 GAYN---RVLSAKQ-NV-PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 97 GnY~---kv~~~~~-~~-P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++-. ++.++-+ ++ ..|....-|+.|+..||-.++--.-|-|..|.+.++++-|..+ +.++...+-
T Consensus 317 NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~LLV 386 (440)
T KOG1464|consen 317 NDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESLLV 386 (440)
T ss_pred ccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHHHH
Confidence 6544 4444332 21 1333445567899999999998888999999999999999998 888877764
No 34
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=33.97 E-value=69 Score=19.39 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=19.6
Q ss_pred hccC-CccHHHHHHhhCCCCHHHHHHHHhhhCCCce
Q 028424 135 KAYD-YLSIKDAGQMLLFTSDQELLEYVKEEHPEWE 169 (209)
Q Consensus 135 kAY~-sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~ 169 (209)
.-|. +++++++|..+|| |+.-+..-.+ +.-|.+
T Consensus 3 ~~~~~~~~l~~iA~~~g~-S~~~f~r~Fk-~~~g~t 36 (42)
T PF00165_consen 3 ENLQQKLTLEDIAEQAGF-SPSYFSRLFK-KETGMT 36 (42)
T ss_dssp TTT-SS--HHHHHHHHTS--HHHHHHHHH-HHTSS-
T ss_pred ccccCCCCHHHHHHHHCC-CHHHHHHHHH-HHHCcC
Confidence 3454 7999999999999 5776665543 334544
No 35
>KOG0104 consensus Molecular chaperones GRP170/SIL1, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=33.73 E-value=1e+02 Score=31.57 Aligned_cols=80 Identities=19% Similarity=0.294 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-C---CeEEEecCCCCCCCCCCChHHHHHH
Q 028424 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-D---GFVFFQKAKDSAPCKEIPSLQLINQ 197 (209)
Q Consensus 122 ~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~---~~i~f~~~~~~~~~~~~~~~~li~~ 197 (209)
-+|+=-+.|..|.--|+.-++.++..|||=.-.+.+.++.+.+..+..+. | +.|.|+.. + ...-+-++|+.+
T Consensus 66 ~eR~fg~~A~~ma~r~P~~~~~~l~~llgk~~~~~~v~ly~~~~p~~e~v~d~~rstV~F~i~--d--~~~ysvEellAM 141 (902)
T KOG0104|consen 66 GERIFGEAAASMATRFPQSTYRQLKDLLGKSLDDPTVDLYQKRFPFFELVEDPQRSTVVFKIS--D--QEEYSVEELLAM 141 (902)
T ss_pred CceehhhhhhhhhhcCcHHHHHHHHHHhCcccCCcHHHHHHhcCCceeecccCccceEEEEeC--C--ccccCHHHHHHH
Confidence 34555688999999999999999999999775555888876556677775 3 46777763 2 346789999999
Q ss_pred HHhHHHHh
Q 028424 198 TLSYAREL 205 (209)
Q Consensus 198 ~l~Ya~el 205 (209)
.|.||+.+
T Consensus 142 il~~a~~~ 149 (902)
T KOG0104|consen 142 ILQYAKSL 149 (902)
T ss_pred HHHHHHHH
Confidence 99999875
No 36
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=33.18 E-value=94 Score=29.39 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=42.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 112 ETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 112 ~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++..--.+.|..||=+-=..-|++=|++||+.-.+.+|++. ++++.+|+.
T Consensus 326 ~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~-~ee~E~~LS 375 (439)
T KOG1498|consen 326 EEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP-VEEMEKFLS 375 (439)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC-HHHHHHHHH
Confidence 34556667777777777778999999999999999999998 999999986
No 37
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=32.30 E-value=4e+02 Score=24.91 Aligned_cols=127 Identities=13% Similarity=0.141 Sum_probs=79.0
Q ss_pred HHHHHHHHHHhh----C---CHHHHHHHHHhccHhhh--cCchhhhHHHHHHHHHhcChHHHHHHhh----cCCC-cchH
Q 028424 50 ILGLNLLRLLVQ----N---RIAEFHTELELLSSTAL--ENPCIKHAVELEQSFMEGAYNRVLSAKQ----NVPN-ETYG 115 (209)
Q Consensus 50 il~l~LL~LL~~----n---~i~efh~~Le~l~~~~~--~~~~I~~~~~leq~L~eGnY~kv~~~~~----~~P~-~~~~ 115 (209)
-.+=.||++|+. | +....+.+.+-|..|-- +||-..|.--| -..=+|.+.-+..+ -+-+ .-.-
T Consensus 249 t~cPhllRYLatAvvtnk~~rr~~lkdlvkVIqqE~ysYkDPiteFl~cl---yvn~DFdgAq~kl~eCeeVl~nDfFLv 325 (432)
T KOG2758|consen 249 TSCPHLLRYLATAVVTNKRRRRNRLKDLVKVIQQESYSYKDPITEFLECL---YVNYDFDGAQKKLRECEEVLVNDFFLV 325 (432)
T ss_pred hhCHHHHHHHHHHhhcchHhhHHHHHHHHHHHHHhccccCCcHHHHHHHH---hhccchHHHHHHHHHHHHHHhcchhHH
Confidence 344567888863 3 44457777777877643 78877775433 33444444433222 1111 1223
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCC----Cceee--CCeEEEecC
Q 028424 116 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHP----EWEMK--DGFVFFQKA 180 (209)
Q Consensus 116 ~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~----gW~~~--~~~i~f~~~ 180 (209)
...+.|++..|.=|+..-+|--..|+++-+|.-|.++ ++|+..|+..-=| .=++| -|.|+...+
T Consensus 326 a~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~ 395 (432)
T KOG2758|consen 326 ALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIVNLIRTARLDAKIDSKLGHVVMGHP 395 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHHHHHHHhhhhhhhccccCceeecCC
Confidence 4556777777877887777777899999999999999 8898888753211 22233 466666553
No 38
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=32.27 E-value=1.1e+02 Score=28.76 Aligned_cols=46 Identities=15% Similarity=0.210 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 116 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 116 ~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
.||+.+......-..++--|=|.+||++-+|++|..+ ++++...+-
T Consensus 298 ~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd-~~~lr~~Ll 343 (404)
T PF10255_consen 298 LFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVD-EEELRSQLL 343 (404)
T ss_pred HHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCC-HHHHHHHHH
Confidence 3555444444445556777888999999999999997 777665543
No 39
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=31.81 E-value=3.2e+02 Score=28.45 Aligned_cols=95 Identities=17% Similarity=0.203 Sum_probs=65.1
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhh--CC--Cceee--CCeEEEecC-----
Q 028424 112 ETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEE--HP--EWEMK--DGFVFFQKA----- 180 (209)
Q Consensus 112 ~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~--~~--gW~~~--~~~i~f~~~----- 180 (209)
++.+..+..|-+-+=.+.+.-+.+-|.||+.+.+.++--|=|.-++..++-+. +. .-.+| .+.|.|...
T Consensus 420 ~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~FgsDl~~s~ 499 (988)
T KOG2072|consen 420 PDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFGSDLFLSK 499 (988)
T ss_pred CCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeecccccccc
Confidence 45577777888888888899999999999999999998887788998887632 22 33344 567777741
Q ss_pred ----CCCCCCCCCChHHHHHHHHhHHHHhh
Q 028424 181 ----KDSAPCKEIPSLQLINQTLSYARELE 206 (209)
Q Consensus 181 ----~~~~~~~~~~~~~li~~~l~Ya~elE 206 (209)
++....+.+||+.+=++.-..|+-|.
T Consensus 500 ~~~~~eg~~lqs~~sE~ir~~L~~m~~~L~ 529 (988)
T KOG2072|consen 500 EEDEPEGPELQSMPSEGIRSQLTAMAESLS 529 (988)
T ss_pred ccccCCCchhhcCchHhHHHHHHHHHHHHH
Confidence 11222345777766555545554443
No 40
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=31.75 E-value=43 Score=27.19 Aligned_cols=50 Identities=18% Similarity=0.276 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHH---hccCCccHHHHHHhhCCCCHHHHH-HHHhhhCCCceee-CCeEEEe
Q 028424 121 LAKTVRDEIAGCSE---KAYDYLSIKDAGQMLLFTSDQELL-EYVKEEHPEWEMK-DGFVFFQ 178 (209)
Q Consensus 121 L~~tiR~~ia~~ie---kAY~sl~l~~a~~lL~f~~~~e~~-~f~~~~~~gW~~~-~~~i~f~ 178 (209)
.-++=|..|+.-|- ++|-.-.|.- +-+ ..|+. +.+ .+-||+|+ ||+.|-.
T Consensus 17 ~RERrRRAIaakIfaGLR~~Gny~Lp~-----~aD-~NeVLkALc--~eAGw~Ve~DGTtyr~ 71 (150)
T PF05687_consen 17 RRERRRRAIAAKIFAGLRAHGNYKLPK-----HAD-NNEVLKALC--REAGWTVEPDGTTYRK 71 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCC-----cCC-HHHHHHHHH--HhCCEEEccCCCeecc
Confidence 45666776776553 2332111110 113 44554 554 46899999 7777653
No 41
>KOG2495 consensus NADH-dehydrogenase (ubiquinone) [Energy production and conversion]
Probab=31.51 E-value=53 Score=31.46 Aligned_cols=63 Identities=24% Similarity=0.304 Sum_probs=48.5
Q ss_pred cCC-CcchHHHHHHH--HHHHHHHHHHHHHhccC-CccHHHHHHhhCC----------CCHHHHHHHHhhhCCCcee
Q 028424 108 NVP-NETYGYFMDLL--AKTVRDEIAGCSEKAYD-YLSIKDAGQMLLF----------TSDQELLEYVKEEHPEWEM 170 (209)
Q Consensus 108 ~~P-~~~~~~fm~~L--~~tiR~~ia~~iekAY~-sl~l~~a~~lL~f----------~~~~e~~~f~~~~~~gW~~ 170 (209)
++| -.++++|+... ...||.+++.|+|+|=. .++-.+-+++|+| +=..|+.+|+.+.-+.|--
T Consensus 174 gipGV~e~~~FLKEv~dAqeIR~~~~~~le~a~~~~l~~eerkRlLh~VVVGGGPTGVEFAaEL~Dfi~~Dl~k~yp 250 (491)
T KOG2495|consen 174 GIPGVEENAHFLKEVEDAQEIRRKVIDNLEKAELPGLSDEERKRLLHFVVVGGGPTGVEFAAELADFIPEDLRKIYP 250 (491)
T ss_pred CCCchhhchhhhhhhhHHHHHHHHHHHHHHHhhcCCCChHHhhheEEEEEECCCCcceeehHHHHHHHHHHHHHhhh
Confidence 344 45788899876 56799999999999986 8999999999987 2346899998754455543
No 42
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=31.28 E-value=28 Score=26.37 Aligned_cols=23 Identities=22% Similarity=0.585 Sum_probs=18.3
Q ss_pred HhhCCCCHHHHHHHHhhhCCCceee
Q 028424 147 QMLLFTSDQELLEYVKEEHPEWEMK 171 (209)
Q Consensus 147 ~lL~f~~~~e~~~f~~~~~~gW~~~ 171 (209)
.-|.|+|.+++++||+ ..||...
T Consensus 51 v~l~F~skE~Ai~yae--r~G~~Y~ 73 (101)
T PF04800_consen 51 VRLKFDSKEDAIAYAE--RNGWDYE 73 (101)
T ss_dssp CEEEESSHHHHHHHHH--HCT-EEE
T ss_pred eEeeeCCHHHHHHHHH--HcCCeEE
Confidence 4678999999999984 5799974
No 43
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=30.35 E-value=88 Score=27.29 Aligned_cols=52 Identities=25% Similarity=0.335 Sum_probs=38.9
Q ss_pred HHHHHHHhhCCHHHHHHHHHhccHh--------------------------h-hcCchhhhHHHHHHHHHhcChHHHHH
Q 028424 53 LNLLRLLVQNRIAEFHTELELLSST--------------------------A-LENPCIKHAVELEQSFMEGAYNRVLS 104 (209)
Q Consensus 53 l~LL~LL~~n~i~efh~~Le~l~~~--------------------------~-~~~~~I~~~~~leq~L~eGnY~kv~~ 104 (209)
++||.+.+-|.+.|...+|.++|.- . ...+.++..-+||-.+|+-=|+.|..
T Consensus 63 lrlL~lFa~Gt~~Dy~aea~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~Ilr 141 (258)
T KOG3250|consen 63 LRLLELFAYGTYRDYSAEALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILR 141 (258)
T ss_pred HHHHHHHhcCchhhhhhhhhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHH
Confidence 7888999999999999999999841 1 12344555667777777777777766
No 44
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=30.16 E-value=1.5e+02 Score=19.33 Aligned_cols=44 Identities=11% Similarity=0.118 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+.+.|.+-.|.+|...+ ..-...+..+++..|+++ ...+..-++
T Consensus 3 i~~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~-~~t~s~hL~ 46 (61)
T PF12840_consen 3 IFKALSDPTRLRILRLL-ASNGPMTVSELAEELGIS-QSTVSYHLK 46 (61)
T ss_dssp HHHHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS--HHHHHHHHH
T ss_pred HHHHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCC-HHHHHHHHH
Confidence 55677888999999999 677899999999999998 555555543
No 45
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=29.68 E-value=1.4e+02 Score=19.18 Aligned_cols=36 Identities=8% Similarity=0.252 Sum_probs=28.0
Q ss_pred CccHHHHHHhhCCCCHHHHHHHHhhhCCCceee---CCeEE
Q 028424 139 YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK---DGFVF 176 (209)
Q Consensus 139 sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~---~~~i~ 176 (209)
.|+-+++..+.|.+....-+++++ ..||.+. +|+.+
T Consensus 2 fLT~~El~elTG~k~~~~Q~~~L~--~~Gi~~~~~~~G~p~ 40 (47)
T PF13986_consen 2 FLTDEELQELTGYKRPSKQIRWLR--RNGIPFVVRADGRPI 40 (47)
T ss_pred CCCHHHHHHHHCCCCHHHHHHHHH--HCCCeeEECCCCCEE
Confidence 478889999999998888888885 4588875 55443
No 46
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=29.59 E-value=4.3e+02 Score=23.99 Aligned_cols=95 Identities=9% Similarity=-0.044 Sum_probs=61.8
Q ss_pred HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHH----hhCCHHHHHHHHHhccHhhhc
Q 028424 5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLL----VQNRIAEFHTELELLSSTALE 80 (209)
Q Consensus 5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL----~~n~i~efh~~Le~l~~~~~~ 80 (209)
.++..-+.+.+..||.++=.....+|+.. . ..++++...+-...-..+| .+..+..+...|+.+|...++
T Consensus 188 ~~l~ll~~~~~~~~d~~~a~~~l~~l~k~---~---~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~ 261 (409)
T TIGR00540 188 EVLKLAEEAYIRSGAWQALDDIIDNMAKA---G---LFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRH 261 (409)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHc---C---CCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhC
Confidence 56777788888888887666665555443 1 2222222121111111223 345567889999999998888
Q ss_pred CchhhhHHHHHHHHHhcChHHHHHHh
Q 028424 81 NPCIKHAVELEQSFMEGAYNRVLSAK 106 (209)
Q Consensus 81 ~~~I~~~~~leq~L~eGnY~kv~~~~ 106 (209)
++.+.....- ..+..|.+.+..+..
T Consensus 262 ~~~l~~~~a~-~l~~~g~~~~A~~~l 286 (409)
T TIGR00540 262 NIALKIALAE-HLIDCDDHDSAQEII 286 (409)
T ss_pred CHHHHHHHHH-HHHHCCChHHHHHHH
Confidence 8888777654 899999999998843
No 47
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=29.50 E-value=3.5e+02 Score=23.43 Aligned_cols=63 Identities=19% Similarity=0.031 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhh-hcChH-HHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhh
Q 028424 5 DIYEHAVLLSVK-VEDQD-AFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA 78 (209)
Q Consensus 5 ~vlEi~a~~sl~-~~D~~-~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~ 78 (209)
+||.-.|++=-. .+|.. +..=+-.-||.|-. ...++-.|+=+|+..|++.+...++|+.-..+
T Consensus 36 ~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~-----------~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l 100 (280)
T PF05843_consen 36 HVYVAYALMEYYCNKDPKRARKIFERGLKKFPS-----------DPDFWLEYLDFLIKLNDINNARALFERAISSL 100 (280)
T ss_dssp HHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT------------HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTS
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCC-----------CHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhc
Confidence 456666666555 45555 44444444554332 24688899999999999999999999986543
No 48
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=29.29 E-value=1.4e+02 Score=20.98 Aligned_cols=38 Identities=29% Similarity=0.480 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHhccC--CccHHHHHHhhCCCCHHHHHHHHh
Q 028424 121 LAKTVRDEIAGCSEKAYD--YLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 121 L~~tiR~~ia~~iekAY~--sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+...+|..+|- +-|. .||+..||+++|++ .-++.+++.
T Consensus 17 ~~~~~r~~~Ai---~lY~~g~iS~gkAAelag~s-~~eF~~~L~ 56 (76)
T PF03683_consen 17 FEQELREELAI---KLYEEGKISLGKAAELAGMS-RWEFLELLK 56 (76)
T ss_pred HHHHHHHHHHH---HHHHcCCCCHHHHHHHhCCC-HHHHHHHHH
Confidence 34455655553 4675 89999999999996 999999985
No 49
>PLN00157 histone H2A; Provisional
Probab=28.71 E-value=2.3e+02 Score=22.61 Aligned_cols=80 Identities=15% Similarity=0.249 Sum_probs=51.7
Q ss_pred hhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc-----CCccHHHHHHhhCCCCHHH
Q 028424 83 CIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAY-----DYLSIKDAGQMLLFTSDQE 156 (209)
Q Consensus 83 ~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY-----~sl~l~~a~~lL~f~~~~e 156 (209)
-++||+ .++++|.+|+|.+ .....+| .||...++-+=-||+.+...+= ..|+-..+. |.+.+.+|
T Consensus 24 gL~FPVgRi~R~Lk~g~~a~--RIg~~A~-----VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~--lAI~nDeE 94 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKYAT--RVGAGAP-----VYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQ--LAVRNDEE 94 (132)
T ss_pred CcccchHHHHHHHhcCchhh--hcCCCcH-----hHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHh--hcccCcHH
Confidence 577777 5899999999985 3323333 4555555555555555444432 145555543 56678899
Q ss_pred HHHHHhhhCCCceeeCCeE
Q 028424 157 LLEYVKEEHPEWEMKDGFV 175 (209)
Q Consensus 157 ~~~f~~~~~~gW~~~~~~i 175 (209)
+.+++ .++++..|.|
T Consensus 95 L~~Ll----~~vtIa~GGV 109 (132)
T PLN00157 95 LSKLL----GGVTIAAGGV 109 (132)
T ss_pred HHHHH----cCceecCCcc
Confidence 99997 3899985554
No 50
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=28.13 E-value=1.4e+02 Score=17.81 Aligned_cols=22 Identities=14% Similarity=0.385 Sum_probs=19.5
Q ss_pred ccHHHHHHhhCCCCHHHHHHHHh
Q 028424 140 LSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 140 l~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+++.++|++||++ ..-+..+++
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH
Confidence 6889999999998 889999975
No 51
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=28.12 E-value=4.6e+02 Score=23.86 Aligned_cols=105 Identities=9% Similarity=0.021 Sum_probs=65.0
Q ss_pred HHHHhhCCHHHHHHHHHhccHhhh--cCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHH
Q 028424 56 LRLLVQNRIAEFHTELELLSSTAL--ENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCS 133 (209)
Q Consensus 56 L~LL~~n~i~efh~~Le~l~~~~~--~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~i 133 (209)
+.....|+...|..+++.--+-+. ...+.......+--+.+| +-++|++..+........|.....-.||..|-.+|
T Consensus 120 ~~~~~~Gd~~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg-~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i 198 (367)
T PRK09210 120 AKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEG-NMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAI 198 (367)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHH-HHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHH
Confidence 344457777777777764333332 445555566677777788 66777776655422233455555666777776666
Q ss_pred HhccCC----------------------------ccHHHHHHhhCCCCHHHHHHHHh
Q 028424 134 EKAYDY----------------------------LSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 134 ekAY~s----------------------------l~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
...-++ -+...+|..||++ ++++.+...
T Consensus 199 ~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~-~~~v~~~~~ 254 (367)
T PRK09210 199 ADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMP-PEKVREILK 254 (367)
T ss_pred HHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcC-HHHHHHHHH
Confidence 554432 2456788888888 777777654
No 52
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=27.27 E-value=5.6e+02 Score=24.53 Aligned_cols=91 Identities=15% Similarity=0.197 Sum_probs=65.2
Q ss_pred HHHHHHHhcChHHHHHHhh-cCC----CcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCC---CHHHHHHH
Q 028424 89 ELEQSFMEGAYNRVLSAKQ-NVP----NETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFT---SDQELLEY 160 (209)
Q Consensus 89 ~leq~L~eGnY~kv~~~~~-~~P----~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~---~~~e~~~f 160 (209)
++=...-++.|..-++... .-| .+..++=.+.|-+.||++...---.-|.+++....|.-.+.+ -+.++.+.
T Consensus 310 ~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~L 389 (466)
T KOG0686|consen 310 EILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLEL 389 (466)
T ss_pred HHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHH
Confidence 3334555888888888544 333 344567778899999999998888899999999999988876 24577777
Q ss_pred HhhhCCCceee-CCeEEEec
Q 028424 161 VKEEHPEWEMK-DGFVFFQK 179 (209)
Q Consensus 161 ~~~~~~gW~~~-~~~i~f~~ 179 (209)
+.+.+-.=.+| ...+++-.
T Consensus 390 I~~~~i~~rIDs~~ki~~~~ 409 (466)
T KOG0686|consen 390 ILEGKISGRIDSHNKILYAR 409 (466)
T ss_pred HHccchheeeccccceeeec
Confidence 76555555666 45555554
No 53
>PLN00153 histone H2A; Provisional
Probab=27.26 E-value=1.8e+02 Score=23.13 Aligned_cols=81 Identities=16% Similarity=0.282 Sum_probs=51.8
Q ss_pred hhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc-----CCccHHHHHHhhCCCCHHH
Q 028424 83 CIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAY-----DYLSIKDAGQMLLFTSDQE 156 (209)
Q Consensus 83 ~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY-----~sl~l~~a~~lL~f~~~~e 156 (209)
-++||+ .++++|.+|+|.+ .....+| .||...++-+=-||+.+...+= ..|+-..+. |.+.+.+|
T Consensus 22 gL~FpVgRi~R~Lr~g~~a~--Rvga~A~-----VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~--lAI~nDeE 92 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYAE--RIGAGAP-----VYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQ--LAIRNDEE 92 (129)
T ss_pred CcccchHHHHHHHhcCchhh--ccCCCch-----HHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHH--hhccCcHH
Confidence 577777 5899999999986 2333343 3555555555555554444332 246666654 55678899
Q ss_pred HHHHHhhhCCCceeeCCeEE
Q 028424 157 LLEYVKEEHPEWEMKDGFVF 176 (209)
Q Consensus 157 ~~~f~~~~~~gW~~~~~~i~ 176 (209)
+.+++ .++++..|.+.
T Consensus 93 L~~Ll----~~vTIa~GGV~ 108 (129)
T PLN00153 93 LGKLL----GEVTIASGGVL 108 (129)
T ss_pred HHHHH----CCCccCCCccC
Confidence 99997 38999865553
No 54
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=26.49 E-value=64 Score=29.94 Aligned_cols=107 Identities=20% Similarity=0.265 Sum_probs=70.8
Q ss_pred HHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHHHhhc--CCCcchHHHHHHHHHHHHHHHHH
Q 028424 54 NLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQN--VPNETYGYFMDLLAKTVRDEIAG 131 (209)
Q Consensus 54 ~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~~--~P~~~~~~fm~~L~~tiR~~ia~ 131 (209)
.|..+|...++..|-.+.+.+|....++..|=..+.---.|..|++. .++. .|. .-...+.+.|+-|+.
T Consensus 274 qi~~ll~~~~v~~Fs~L~~ll~~~~~~~~~lL~~L~~~AvLV~G~WV----~kS~ll~~~-----~~~e~~~~aRD~iL~ 344 (421)
T PF04801_consen 274 QIKALLKKARVISFSELRKLLPSNSDTDEELLRALQQVAVLVQGNWV----VKSELLYPD-----VPAEQLCRARDYILL 344 (421)
T ss_pred HHHHHHHhCCcccHHHHHHHhccccchHHHHHHHHHhheEEEeeeEE----EehhhccCC-----CcchhhhhhHHHHHH
Confidence 66777888888888888888876554223333344444445566542 1111 111 112367899999999
Q ss_pred HHHhccCCccHHHHHHhhCCCCHHHHHHHHh----hh--CCCceee
Q 028424 132 CSEKAYDYLSIKDAGQMLLFTSDQELLEYVK----EE--HPEWEMK 171 (209)
Q Consensus 132 ~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~----~~--~~gW~~~ 171 (209)
+..+. ..|+-+++....++. .+++.++++ .. .+||.+.
T Consensus 345 ~F~~~-~~v~r~~l~~~~~l~-~~~~~eiL~~~a~~~~~~~~W~lk 388 (421)
T PF04801_consen 345 LFTKS-RYVKRKELMSATKLP-PEDVKEILKEIAVLRPSNRGWKLK 388 (421)
T ss_pred HhcCC-CceeHHHhhhhcCCC-HHHHHHHHHHHhhccCCCCceEEc
Confidence 99887 789999999999997 666666654 23 6799985
No 55
>PTZ00017 histone H2A; Provisional
Probab=24.04 E-value=3.1e+02 Score=21.87 Aligned_cols=80 Identities=15% Similarity=0.289 Sum_probs=49.1
Q ss_pred hhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhc---cC--CccHHHHHHhhCCCCHHH
Q 028424 83 CIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKA---YD--YLSIKDAGQMLLFTSDQE 156 (209)
Q Consensus 83 ~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekA---Y~--sl~l~~a~~lL~f~~~~e 156 (209)
-++||+ .++++|.+|+|.+ .-...+| .|+...++-+=-||+.+...+ -. .|+-.++. |.+.+.+|
T Consensus 25 gL~FPVgRi~R~Lk~g~~a~--RV~a~A~-----VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~--lAI~nDeE 95 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRYAK--RVGAGAP-----VYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQ--LAIRNDEE 95 (134)
T ss_pred CcccchHHHHHHHhccchhc--cccccch-----hhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHH--hhccCcHH
Confidence 467776 5899999999987 2223444 344444444444444433332 22 45556554 55678899
Q ss_pred HHHHHhhhCCCceeeCCeE
Q 028424 157 LLEYVKEEHPEWEMKDGFV 175 (209)
Q Consensus 157 ~~~f~~~~~~gW~~~~~~i 175 (209)
+..++ .++++-.|.|
T Consensus 96 L~~Ll----~~vtIa~GGV 110 (134)
T PTZ00017 96 LNKLL----AGVTIASGGV 110 (134)
T ss_pred HHHHH----cCCcccCCcc
Confidence 99997 3889985554
No 56
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=23.86 E-value=2.4e+02 Score=26.16 Aligned_cols=66 Identities=14% Similarity=0.110 Sum_probs=45.8
Q ss_pred HhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 95 MEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 95 ~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+..+|.+++..-... ...++.-=+..+-.+|-=....+...-..||.+++++-|-+. ++|+..|+-
T Consensus 251 ~L~aYveF~~~N~~F-vqs~gl~~E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI 316 (378)
T KOG2753|consen 251 KLDAYVEFVAANSGF-VQSQGLVHEQNMAKMRLLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI 316 (378)
T ss_pred chHHHHHHHHhChHH-HHHhcccHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH
Confidence 445666666543221 223455556778888877666555555589999999999998 899999975
No 57
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=23.75 E-value=1.7e+02 Score=17.25 Aligned_cols=22 Identities=32% Similarity=0.481 Sum_probs=18.9
Q ss_pred ccHHHHHHhhCCCCHHHHHHHHh
Q 028424 140 LSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 140 l~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+++.++|++||.+ ...+..+++
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVK 22 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH
Confidence 4788999999998 888999974
No 58
>PRK13503 transcriptional activator RhaS; Provisional
Probab=23.45 E-value=1.6e+02 Score=24.75 Aligned_cols=40 Identities=13% Similarity=-0.017 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 122 ~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+...|-+.|... -...++|++++|..+||+|..-...+-+
T Consensus 220 i~~~Rl~~A~~L-L~~~~~sI~eIA~~~GF~~~s~F~r~FK 259 (278)
T PRK13503 220 LNRLRLLKARHL-LRHSDASVTDIAYRCGFGDSNHFSTLFR 259 (278)
T ss_pred HHHHHHHHHHHH-HHcCCCCHHHHHHHhCCCCHHHHHHHHH
Confidence 455666665433 2557899999999999999887776654
No 59
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=23.43 E-value=1.8e+02 Score=22.42 Aligned_cols=80 Identities=13% Similarity=0.211 Sum_probs=47.0
Q ss_pred hhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHH----hcc-CCccHHHHHHhhCCCCHHH
Q 028424 83 CIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSE----KAY-DYLSIKDAGQMLLFTSDQE 156 (209)
Q Consensus 83 ~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~ie----kAY-~sl~l~~a~~lL~f~~~~e 156 (209)
-++||+ .++++|.+|+|.. .-... ...+|...++-+=.||+.+.. .+= ..|+-.++. |.+.+.+|
T Consensus 18 gL~fPV~ri~R~Lk~~~~a~--RVs~~-----A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~--lAi~nD~E 88 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRYAE--RVGAG-----APVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQ--LAVRNDEE 88 (115)
T ss_pred CccCcHHHHHHHHHcCcccc--ccccc-----hHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHH--HHHhccHH
Confidence 456665 5889998898873 22222 333444444444444443322 222 267777774 45567889
Q ss_pred HHHHHhhhCCCceeeCCeE
Q 028424 157 LLEYVKEEHPEWEMKDGFV 175 (209)
Q Consensus 157 ~~~f~~~~~~gW~~~~~~i 175 (209)
+...+ .++++..|.+
T Consensus 89 L~~L~----~~vtI~~ggv 103 (115)
T cd00074 89 LNKLL----KGVTIASGGV 103 (115)
T ss_pred HHHHH----cCCcccCCcc
Confidence 99886 3788875554
No 60
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=23.34 E-value=1.7e+02 Score=25.28 Aligned_cols=62 Identities=15% Similarity=0.088 Sum_probs=41.5
Q ss_pred HHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 93 SFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 93 ~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
.+....++++|+.....+. .. .+.+.|.+-|.-.-+ +...++.++|..+||+|.+.+....+
T Consensus 32 ~~S~~~l~r~F~~~~g~s~--~~-----yi~~~Rl~~A~~~L~-~~~~~i~~iA~~~Gf~s~~~f~r~Fk 93 (289)
T PRK15121 32 GYSKWHLQRMFKDVTGHAI--GA-----YIRARRLSKAAVALR-LTSRPILDIALQYRFDSQQTFTRAFK 93 (289)
T ss_pred CcCHHHHHHHHHHHHCcCH--HH-----HHHHHHHHHHHHHHH-cCCCCHHHHHHHHCCCCHHHHHHHHH
Confidence 4555667777776544331 12 366677776654433 36899999999999998887755443
No 61
>smart00414 H2A Histone 2A.
Probab=22.97 E-value=3e+02 Score=20.85 Aligned_cols=81 Identities=14% Similarity=0.259 Sum_probs=48.5
Q ss_pred hhhhHH-HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhc---cC--CccHHHHHHhhCCCCHHH
Q 028424 83 CIKHAV-ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKA---YD--YLSIKDAGQMLLFTSDQE 156 (209)
Q Consensus 83 ~I~~~~-~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekA---Y~--sl~l~~a~~lL~f~~~~e 156 (209)
-++||+ .++++|.+|+|.+ .-...+ ..|+...++-+=.||+.+...+ -. .|+-.++. +.+.+.+|
T Consensus 7 gL~fPVgRi~r~Lk~~~~~~--Rv~~~A-----~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~--lAi~nD~E 77 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTYAK--RVGAGA-----PVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQ--LAIRNDEE 77 (106)
T ss_pred CccCchHHHHHHHHcCcccc--cccccc-----HHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHh--hhccCCHH
Confidence 456666 6899999999987 222233 3444444444444444433222 22 45555544 55678899
Q ss_pred HHHHHhhhCCCceeeCCeEE
Q 028424 157 LLEYVKEEHPEWEMKDGFVF 176 (209)
Q Consensus 157 ~~~f~~~~~~gW~~~~~~i~ 176 (209)
+.+.+ .|+++.+|.+.
T Consensus 78 L~~L~----~~vti~~ggv~ 93 (106)
T smart00414 78 LNKLL----KGVTIAQGGVL 93 (106)
T ss_pred HHHHH----cCcccCCCccC
Confidence 99886 37888765554
No 62
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=22.65 E-value=1.8e+02 Score=20.70 Aligned_cols=47 Identities=19% Similarity=0.255 Sum_probs=32.9
Q ss_pred hhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHH---------HHHHHHHHHHHHHHHhc
Q 028424 83 CIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD---------LLAKTVRDEIAGCSEKA 136 (209)
Q Consensus 83 ~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~---------~L~~tiR~~ia~~iekA 136 (209)
+++-+++..+ .|+|...+..+.+. ..+||. .-.+++|.++...+.||
T Consensus 9 ~a~~Ave~D~---~g~y~eA~~~Y~~a----ie~l~~~~~~~~~n~~~k~~ir~K~~eYl~RA 64 (76)
T cd02681 9 FARLAVQRDQ---EGRYSEAVFYYKEA----AQLLIYAEMAGTLNDSHLKTIQEKSNEYLDRA 64 (76)
T ss_pred HHHHHHHHHH---ccCHHHHHHHHHHH----HHHHHHHHHhcCCChHHHHHHHHHHHHHHHHH
Confidence 4455555554 69999999888764 355666 34567888888888876
No 63
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=22.64 E-value=2.1e+02 Score=24.24 Aligned_cols=40 Identities=10% Similarity=-0.030 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 122 ~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
+...|-+-|...- ..+..|+.++|..+||+|..-...+.+
T Consensus 235 i~~~Rl~~A~~lL-~~t~~sI~eIA~~~GF~s~s~Fsr~FK 274 (287)
T TIGR02297 235 IIERVMQEARRLL-LFTQHSINQIAYDLGYKDPAYFARFFQ 274 (287)
T ss_pred HHHHHHHHHHHHH-HcCCCCHHHHHHHhCCCCHHHHHHHHH
Confidence 3444555555432 367899999999999999888887765
No 64
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=22.48 E-value=2.5e+02 Score=18.81 Aligned_cols=49 Identities=29% Similarity=0.467 Sum_probs=32.9
Q ss_pred CchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHH--------HHHHHHHHHHHHhc
Q 028424 81 NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA--------KTVRDEIAGCSEKA 136 (209)
Q Consensus 81 ~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~--------~tiR~~ia~~iekA 136 (209)
-+.++-+++.++ .|+|...+..+.+. ..+||..+. +.+|.++-..+++|
T Consensus 6 ~~~~~~Av~~D~---~g~~~~A~~~Y~~a----i~~l~~~~~~~~~~~~~~~l~~k~~~yl~RA 62 (69)
T PF04212_consen 6 IELIKKAVEADE---AGNYEEALELYKEA----IEYLMQALKSESNPERRQALRQKMKEYLERA 62 (69)
T ss_dssp HHHHHHHHHHHH---TTSHHHHHHHHHHH----HHHHHHHHHHSTTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---CCCHHHHHHHHHHH----HHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Confidence 356777888888 89999999988652 355555443 33666666665554
No 65
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=22.22 E-value=2.6e+02 Score=19.00 Aligned_cols=48 Identities=19% Similarity=0.394 Sum_probs=31.8
Q ss_pred chhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHH--------HHHHHHHHHHHHHhc
Q 028424 82 PCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL--------AKTVRDEIAGCSEKA 136 (209)
Q Consensus 82 ~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L--------~~tiR~~ia~~iekA 136 (209)
..|+.+++.++ .|+|..-+..+.+. ...||..+ .+.+|.++...+.+|
T Consensus 10 ~li~~Av~~d~---~g~~~eAl~~Y~~a----~e~l~~~~~~~~~~~~~~~~~~k~~eyl~ra 65 (77)
T smart00745 10 ELISKALKADE---AGDYEEALELYKKA----IEYLLEGIKVESDSKRREAVKAKAAEYLDRA 65 (77)
T ss_pred HHHHHHHHHHH---cCCHHHHHHHHHHH----HHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Confidence 45667778887 69999887766542 23344433 677788887777664
No 66
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=22.01 E-value=2e+02 Score=17.62 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 122 ~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++..+.+|...+.+ =..++..+++..+|++ ...+...++
T Consensus 1 l~~~~~~Il~~l~~-~~~~t~~ela~~~~is-~~tv~~~l~ 39 (48)
T PF13412_consen 1 LDETQRKILNYLRE-NPRITQKELAEKLGIS-RSTVNRYLK 39 (48)
T ss_dssp --HHHHHHHHHHHH-CTTS-HHHHHHHHTS--HHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-cCCCCHHHHHHHhCCC-HHHHHHHHH
Confidence 35678889988876 4459999999999998 666666654
No 67
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=21.81 E-value=1.6e+02 Score=20.87 Aligned_cols=42 Identities=24% Similarity=0.319 Sum_probs=32.3
Q ss_pred CCccHHHHHHhhC-CCCHHHHHHHHhhhCC----CceeeCCeEEEec
Q 028424 138 DYLSIKDAGQMLL-FTSDQELLEYVKEEHP----EWEMKDGFVFFQK 179 (209)
Q Consensus 138 ~sl~l~~a~~lL~-f~~~~e~~~f~~~~~~----gW~~~~~~i~f~~ 179 (209)
.-+|++++...|. ++-...+.++++...+ .|...+|+..|..
T Consensus 24 ~Plt~~EIl~~ls~~d~~~~~~~~L~~~~~~~n~~~~~~~~tf~fkP 70 (75)
T cd07977 24 HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPKDGTFSFKP 70 (75)
T ss_pred CCccHHHHHHHHhccCccHHHHHHHHhhhhccCceeccCCCEEEecc
Confidence 6699999999999 8877788888874444 6887777766554
No 68
>PF08564 CDC37_C: Cdc37 C terminal domain; InterPro: IPR013873 Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain IPR013874 from INTERPRO and the N-terminal kinase binding domain of Cdc37 IPR013855 from INTERPRO []. ; PDB: 1US7_B.
Probab=21.81 E-value=66 Score=24.29 Aligned_cols=41 Identities=15% Similarity=0.223 Sum_probs=18.7
Q ss_pred hhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHH
Q 028424 83 CIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 123 (209)
Q Consensus 83 ~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~ 123 (209)
|=++|-.+..++..|+-++|=+-...+|.++..+.|+.|.+
T Consensus 21 FeslP~emq~Alet~~ld~vnkVl~~M~veeAE~~v~~~~e 61 (99)
T PF08564_consen 21 FESLPPEMQKALETGDLDEVNKVLGKMPVEEAEYHVERCIE 61 (99)
T ss_dssp HHHS-TT------------HHHHHT--SSSHHHHHHHHHHH
T ss_pred HHHCCHHHHHHHHcCCHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence 34667777788888888888887788887788888776654
No 69
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=21.66 E-value=90 Score=19.10 Aligned_cols=18 Identities=17% Similarity=0.073 Sum_probs=14.9
Q ss_pred HHhhhcChHHHHHHHHhh
Q 028424 13 LSVKVEDQDAFERDFFQL 30 (209)
Q Consensus 13 ~sl~~~D~~~F~~~~~qL 30 (209)
.|+..+|-+.|.+.-+||
T Consensus 20 ~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 20 EALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHTT-HHHHHHHHHHH
T ss_pred HHHHcCCHHHHHHHHhhC
Confidence 588999999999988876
No 70
>PHA01082 putative transcription regulator
Probab=21.35 E-value=2e+02 Score=22.80 Aligned_cols=74 Identities=22% Similarity=0.359 Sum_probs=46.3
Q ss_pred hccC-CccHHHHHHhhCCCCHHHHHHHHhh-----------------------hCCCceeeCCeEEEecCCCCC------
Q 028424 135 KAYD-YLSIKDAGQMLLFTSDQELLEYVKE-----------------------EHPEWEMKDGFVFFQKAKDSA------ 184 (209)
Q Consensus 135 kAY~-sl~l~~a~~lL~f~~~~e~~~f~~~-----------------------~~~gW~~~~~~i~f~~~~~~~------ 184 (209)
+-|. -||+.++|++- |+|.-.+.+|=+. .=.||.+..++..+|...-..
T Consensus 25 RefeCgLsveeaa~LC-fKsVrtVk~WD~G~~IPPeCkRLMr~~~gRELs~~e~W~~FrM~~~rLelPTGq~VtpQqILt 103 (133)
T PHA01082 25 REFECGLSVEEAAKLC-FKTVSEVKQWDAGEKIPPICKRLMRWHSRRELYYGDEWWGFRMEGGRLIFPTGDRVAPQQLLA 103 (133)
T ss_pred hhhccCccHHHHHHHH-HHhHHHHhhccCCCcCChHHHHHHHHhcccccccchhhhhhhhccCceecCCcCcccHHHHHH
Confidence 4454 57777777654 5556666555221 112888888899999863111
Q ss_pred -----CCCCCChHHHHHHHHhHHHHhhhcC
Q 028424 185 -----PCKEIPSLQLINQTLSYARELERIV 209 (209)
Q Consensus 185 -----~~~~~~~~~li~~~l~Ya~elE~IV 209 (209)
.-..-+.....++.|.||+-|-+|+
T Consensus 104 GiALLEIgAe~D~~~~~kiLKyAR~L~~i~ 133 (133)
T PHA01082 104 AIAILQIQAPDDAMTRSKLLKYARAMARIK 133 (133)
T ss_pred HhHhhhccCcchHHHHHHHHHHHHHHHhcC
Confidence 1122345667789999999998764
No 71
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=21.07 E-value=2e+02 Score=20.16 Aligned_cols=37 Identities=22% Similarity=0.338 Sum_probs=27.4
Q ss_pred hcChHHHHHHhhcCCCcchHHHHHHH--------HHHHHHHHHHHHHhc
Q 028424 96 EGAYNRVLSAKQNVPNETYGYFMDLL--------AKTVRDEIAGCSEKA 136 (209)
Q Consensus 96 eGnY~kv~~~~~~~P~~~~~~fm~~L--------~~tiR~~ia~~iekA 136 (209)
.|+|...+..+.+. ..+||..+ .+++|.++...+++|
T Consensus 19 ~g~y~eA~~lY~~a----le~~~~~~k~e~~~~~k~~lr~k~~eyl~RA 63 (75)
T cd02684 19 RGDAAAALSLYCSA----LQYFVPALHYETDAQRKEALRQKVLQYVSRA 63 (75)
T ss_pred hccHHHHHHHHHHH----HHHHHHHHhhCCCHHHHHHHHHHHHHHHHHH
Confidence 58899888887663 45566544 688899998888875
No 72
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=20.79 E-value=1.9e+02 Score=26.73 Aligned_cols=47 Identities=15% Similarity=0.135 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 115 GYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 115 ~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
..-.+-|..++=+--...|++-|++|++..+..+|.++ +++..+|+.
T Consensus 329 ~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~-~s~te~~IS 375 (439)
T COG5071 329 EKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMS-PSETEQFIS 375 (439)
T ss_pred hhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCC-HHHHHHHHH
Confidence 36677788888888889999999999999999999988 999999985
No 73
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.71 E-value=1.7e+02 Score=22.04 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHH
Q 028424 123 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYV 161 (209)
Q Consensus 123 ~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~ 161 (209)
.|.|++|.+.+..+=+-++++.+..+++-+.++++-+-+
T Consensus 2 ~t~rEkii~lL~e~~eplt~~ei~~~~~~~~~~~v~~~L 40 (97)
T COG3357 2 ETTREKIISLLLESDEPLTVAEIFELLNGEKEKEVYDHL 40 (97)
T ss_pred chHHHHHHHHHHcCCCcchHHHHHHHHcCCchHHHHHHH
Confidence 588999999888777789999999999998777665544
No 74
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=20.67 E-value=2.7e+02 Score=19.44 Aligned_cols=40 Identities=13% Similarity=0.220 Sum_probs=28.0
Q ss_pred CccHHHHHHhhCCCCHHHHHHHH-hhhCCCceee-CCeEEEec
Q 028424 139 YLSIKDAGQMLLFTSDQELLEYV-KEEHPEWEMK-DGFVFFQK 179 (209)
Q Consensus 139 sl~l~~a~~lL~f~~~~e~~~f~-~~~~~gW~~~-~~~i~f~~ 179 (209)
.|+++.|+.+.|+. ..-+.+.+ ....-+|.+- ++++.+..
T Consensus 13 ~LTi~EAa~Y~gIG-~~klr~l~~~~~~~~f~~~~G~r~lIkR 54 (67)
T PF09035_consen 13 TLTIEEAAEYFGIG-EKKLRELAEENPDCPFVLWIGNRRLIKR 54 (67)
T ss_dssp EEEHHHHHHHT-S--HHHHHHHHHH-TT-SSEEEETTEEEEES
T ss_pred ccCHHHHHHHhCcc-HHHHHHHHHhCCCCCEEEEECCEEEEeH
Confidence 68999999999999 99999998 3334578877 44555544
No 75
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=20.50 E-value=74 Score=22.12 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=28.0
Q ss_pred cCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceeeCCeEEEecC
Q 028424 137 YDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA 180 (209)
Q Consensus 137 Y~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~~~~i~f~~~ 180 (209)
-..+|++++++.+++++ .++..-+ ||-...|+|.|...
T Consensus 20 ~~~~s~~el~k~~~l~~-~~~~~Ai-----GWLarE~KI~~~~~ 57 (65)
T PF10771_consen 20 NGEWSVSELKKATGLSD-KEVYLAI-----GWLARENKIEFEEK 57 (65)
T ss_dssp SSSEEHHHHHHHCT-SC-HHHHHHH-----HHHHCTTSEEEEEE
T ss_pred CCCcCHHHHHHHhCcCH-HHHHHHH-----HHHhccCceeEEee
Confidence 45799999999999974 4444332 99999888887753
No 76
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.40 E-value=3.3e+02 Score=19.41 Aligned_cols=47 Identities=19% Similarity=0.278 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh------hCCCceeeCC
Q 028424 124 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE------EHPEWEMKDG 173 (209)
Q Consensus 124 tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~------~~~gW~~~~~ 173 (209)
|+.+.|..++.+. +.+++++.+-.|++ ..++.-++.. -.|+|..-+|
T Consensus 5 t~~~~IL~~ls~~--c~TLeeL~ekTgi~-k~~LlV~LsrL~k~GiI~Rkw~~~~g 57 (72)
T PF05584_consen 5 TVTQKILIILSKR--CCTLEELEEKTGIS-KNTLLVYLSRLAKRGIIERKWRKFGG 57 (72)
T ss_pred hHHHHHHHHHHhc--cCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeeeeeEEecC
Confidence 5778888888777 99999999999998 7777666542 1467877544
No 77
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=20.35 E-value=3.7e+02 Score=21.83 Aligned_cols=57 Identities=11% Similarity=0.004 Sum_probs=0.0
Q ss_pred HHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHH
Q 028424 11 VLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTEL 71 (209)
Q Consensus 11 a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~L 71 (209)
.++++.-+|......|+++.+..-..+ .....++++-++.=|+.|.+++...+-..+
T Consensus 80 irv~i~~~d~~~v~~~i~ka~~~~~~~----~d~~~~nrlk~~~gL~~l~~r~f~~AA~~f 136 (177)
T PF10602_consen 80 IRVAIFFGDWSHVEKYIEKAESLIEKG----GDWERRNRLKVYEGLANLAQRDFKEAAELF 136 (177)
T ss_pred HHHHHHhCCHHHHHHHHHHHHHHHhcc----chHHHHHHHHHHHHHHHHHhchHHHHHHHH
No 78
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=20.08 E-value=1.8e+02 Score=19.37 Aligned_cols=27 Identities=26% Similarity=0.237 Sum_probs=21.7
Q ss_pred hccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424 135 KAYDYLSIKDAGQMLLFTSDQELLEYVK 162 (209)
Q Consensus 135 kAY~sl~l~~a~~lL~f~~~~e~~~f~~ 162 (209)
++|=.+|+.+||+.||+. ...+..-+.
T Consensus 11 ~~~fhlp~~eAA~~Lgv~-~T~LKr~CR 37 (52)
T PF02042_consen 11 SQYFHLPIKEAAKELGVS-VTTLKRRCR 37 (52)
T ss_pred HHHhCCCHHHHHHHhCCC-HHHHHHHHH
Confidence 467789999999999998 777766663
Done!