Query psy15735
Match_columns 574
No_of_seqs 511 out of 1559
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 20:04:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15735hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2890|consensus 100.0 8.7E-52 1.9E-56 413.1 13.1 224 347-574 68-300 (326)
2 KOG1555|consensus 100.0 6.6E-39 1.4E-43 325.6 9.9 154 7-162 160-314 (316)
3 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 7.9E-30 1.7E-34 260.3 14.1 128 181-310 2-131 (268)
4 KOG1555|consensus 100.0 1.1E-29 2.4E-34 258.4 12.1 205 162-367 3-312 (316)
5 KOG1554|consensus 99.9 5.9E-28 1.3E-32 238.9 9.6 159 150-312 16-177 (347)
6 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 2E-26 4.3E-31 223.3 16.5 121 188-312 4-132 (187)
7 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 1.5E-26 3.2E-31 236.4 16.0 153 189-344 1-163 (266)
8 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 1.9E-24 4.2E-29 216.1 15.4 123 188-310 1-133 (244)
9 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 4.2E-24 9.1E-29 192.9 12.7 105 196-310 1-109 (119)
10 KOG1560|consensus 99.9 3.2E-24 7E-29 211.9 12.5 160 185-347 9-185 (339)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 3.5E-24 7.6E-29 191.4 11.4 113 187-299 2-114 (114)
12 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 3.8E-24 8.2E-29 218.6 7.2 131 7-142 133-268 (268)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 1.8E-21 3.9E-26 177.5 16.1 121 190-311 1-121 (135)
14 cd08066 MPN_AMSH_like Mov34/MP 99.8 3E-20 6.6E-25 178.2 15.7 114 189-308 2-117 (173)
15 cd08057 MPN_euk_non_mb Mpr1p, 99.8 1E-19 2.2E-24 172.1 14.6 117 191-309 1-120 (157)
16 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.8 2.4E-19 5.1E-24 184.3 14.8 122 189-315 1-127 (280)
17 cd08070 MPN_like Mpr1p, Pad1p 99.8 1.1E-19 2.3E-24 166.1 9.9 119 196-326 2-121 (128)
18 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 8.5E-19 1.8E-23 156.0 13.9 107 199-311 2-108 (116)
19 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.8 5.3E-18 1.1E-22 173.5 13.6 119 191-315 1-123 (265)
20 PLN03246 26S proteasome regula 99.7 2.4E-17 5.1E-22 171.0 14.4 125 185-314 2-131 (303)
21 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.7 3.7E-16 8E-21 161.7 13.1 117 190-310 2-124 (288)
22 PF08551 DUF1751: Eukaryotic i 99.7 3E-17 6.5E-22 143.7 3.4 86 341-430 6-99 (99)
23 KOG1556|consensus 99.6 5.9E-15 1.3E-19 144.4 12.0 131 186-321 6-142 (309)
24 cd08072 MPN_archaeal Mov34/MPN 99.6 1.3E-14 2.8E-19 130.9 11.6 97 193-309 1-97 (117)
25 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.6 8.3E-15 1.8E-19 130.4 9.7 95 197-309 2-97 (108)
26 cd08060 MPN_UPF0172 Mov34/MPN/ 99.5 1.5E-13 3.3E-18 133.0 13.9 112 193-311 1-116 (182)
27 COG1310 Predicted metal-depend 99.5 8.3E-14 1.8E-18 128.4 11.6 104 191-307 2-106 (134)
28 KOG2975|consensus 99.5 3.8E-14 8.3E-19 140.3 7.5 129 187-321 19-150 (288)
29 PF14464 Prok-JAB: Prokaryotic 99.3 6.5E-12 1.4E-16 110.0 10.4 93 195-307 2-96 (104)
30 KOG2880|consensus 99.3 1.1E-12 2.4E-17 134.5 4.5 122 188-315 251-377 (424)
31 PF13012 MitMem_reg: Maintenan 99.2 1.2E-12 2.6E-17 117.3 -0.3 109 28-151 1-115 (115)
32 COG0705 Membrane associated se 99.2 2.5E-11 5.5E-16 121.2 9.0 137 342-492 67-212 (228)
33 TIGR03735 PRTRC_A PRTRC system 99.1 8.5E-11 1.9E-15 113.8 8.0 100 192-310 74-173 (192)
34 cd08059 MPN_prok_mb Mpr1p, Pad 99.0 1.3E-09 2.7E-14 95.5 10.2 92 197-308 2-93 (101)
35 PTZ00101 rhomboid-1 protease; 98.9 3E-09 6.4E-14 109.5 8.3 132 341-492 100-241 (278)
36 PF03665 UPF0172: Uncharacteri 98.9 2.6E-08 5.6E-13 97.8 13.8 115 190-311 3-122 (196)
37 TIGR02256 ICE_VC0181 integrati 98.8 1.4E-07 3.1E-12 86.6 13.4 109 198-307 3-114 (131)
38 KOG3050|consensus 98.6 8.2E-08 1.8E-12 94.7 7.9 122 184-311 4-131 (299)
39 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.6 5.3E-07 1.2E-11 91.2 13.6 126 189-323 36-173 (252)
40 PRK10907 intramembrane serine 98.6 2.1E-07 4.5E-12 96.0 10.5 126 341-491 133-270 (276)
41 PF01694 Rhomboid: Rhomboid fa 98.6 1.7E-08 3.7E-13 93.0 1.2 133 341-493 4-144 (145)
42 KOG2632|consensus 98.4 1.9E-06 4E-11 86.9 10.5 138 341-487 48-194 (258)
43 KOG3289|consensus 98.3 1.2E-05 2.7E-10 76.2 12.4 112 190-308 3-119 (199)
44 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.0 0.00018 3.8E-09 74.3 15.9 135 186-322 8-165 (274)
45 KOG2290|consensus 97.6 6.9E-05 1.5E-09 80.2 5.1 157 339-529 444-611 (652)
46 KOG2289|consensus 97.5 5.7E-05 1.2E-09 79.0 2.8 76 338-429 114-197 (316)
47 PF05021 NPL4: NPL4 family; I 96.7 0.02 4.4E-07 60.1 12.6 107 214-322 2-148 (306)
48 cd08065 MPN_eIF3h Mpr1p, Pad1p 96.6 0.0065 1.4E-07 62.7 7.8 67 7-82 123-189 (266)
49 PF04511 DER1: Der1-like famil 96.2 0.027 5.8E-07 55.5 9.4 102 368-486 73-177 (197)
50 KOG1554|consensus 94.5 0.047 1E-06 55.9 4.7 72 8-87 178-252 (347)
51 KOG0858|consensus 91.9 0.46 1E-05 47.9 7.0 64 418-488 121-184 (239)
52 COG5291 Predicted membrane pro 90.4 0.19 4.1E-06 50.7 2.6 39 422-460 133-171 (313)
53 KOG2834|consensus 85.6 5.9 0.00013 43.5 10.3 111 187-301 173-306 (510)
54 KOG2980|consensus 77.7 3.5 7.6E-05 43.1 5.0 37 412-448 221-257 (310)
55 PRK10862 SoxR reducing system 70.4 7.2 0.00016 37.1 4.8 43 450-492 84-127 (154)
56 KOG4463|consensus 64.8 2.7 5.8E-05 43.1 0.7 100 349-454 54-160 (323)
57 PF04246 RseC_MucC: Positive r 64.5 10 0.00022 34.8 4.5 43 450-492 77-120 (135)
58 PF15027 DUF4525: Domain of un 57.0 50 0.0011 30.5 7.2 67 97-167 40-106 (138)
59 cd08071 MPN_DUF2466 Mov34/MPN/ 50.1 1.9E+02 0.0041 25.8 11.2 77 207-294 12-88 (113)
60 PF04002 RadC: RadC-like JAB d 48.8 2.1E+02 0.0045 25.9 10.7 89 196-295 6-94 (123)
61 COG3086 RseC Positive regulato 40.3 48 0.001 31.3 4.6 43 450-492 84-127 (150)
62 PF02654 CobS: Cobalamin-5-pho 36.3 1.2E+02 0.0027 30.5 7.4 30 471-500 190-219 (235)
63 PF05814 DUF843: Baculovirus p 35.2 26 0.00056 29.9 1.8 32 121-152 50-81 (83)
64 PF11744 ALMT: Aluminium activ 33.2 2.6E+02 0.0055 30.9 9.6 72 358-435 41-116 (406)
65 COG1029 FwdB Formylmethanofura 33.0 53 0.0012 35.5 4.2 103 262-373 138-261 (429)
66 PF15659 Toxin-JAB1: JAB-like 32.9 44 0.00095 32.2 3.2 37 265-303 115-151 (162)
67 COG4956 Integral membrane prot 32.2 1.3E+02 0.0029 31.9 6.8 22 412-433 80-101 (356)
68 PF11309 DUF3112: Protein of u 31.9 1.4E+02 0.0031 28.5 6.6 35 415-449 58-95 (160)
69 PF06946 Phage_holin_5: Phage 30.5 90 0.002 27.3 4.4 20 445-464 31-50 (93)
70 PF13295 DUF4077: Domain of un 30.1 2E+02 0.0044 26.2 6.7 124 374-515 18-143 (175)
71 PF14220 DUF4329: Domain of un 29.1 47 0.001 30.5 2.6 25 266-290 59-88 (123)
72 TIGR00608 radc DNA repair prot 28.8 6.1E+02 0.013 25.5 11.0 90 194-294 99-188 (218)
73 KOG3142|consensus 26.5 89 0.0019 30.8 4.2 20 474-493 93-112 (187)
74 KOG3869|consensus 26.1 82 0.0018 34.6 4.2 45 75-121 5-50 (450)
75 COG2246 Predicted membrane pro 23.3 1E+02 0.0022 28.7 3.9 51 373-429 9-59 (139)
76 PF12073 DUF3553: Protein of u 23.1 43 0.00093 26.2 1.0 14 4-17 31-44 (52)
77 PF14778 ODR4-like: Olfactory 20.1 1.2E+02 0.0027 32.7 4.2 60 215-277 1-74 (362)
78 PF03739 YjgP_YjgQ: Predicted 20.0 2.2E+02 0.0049 29.8 6.2 42 413-455 57-101 (354)
No 1
>KOG2890|consensus
Probab=100.00 E-value=8.7e-52 Score=413.08 Aligned_cols=224 Identities=40% Similarity=0.693 Sum_probs=204.2
Q ss_pred hHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChh
Q psy15735 347 LEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLT 418 (574)
Q Consensus 347 Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~ 418 (574)
++...+.|++.|+|..+.+.+ +||.||+.|++|||.++|.+++++.++.+++.|++|.+..+++ .+++|+.
T Consensus 68 WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~-~~i~G~~ 146 (326)
T KOG2890|consen 68 WTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLY-IPIHGTT 146 (326)
T ss_pred HHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEE-EEeccch
Confidence 455569999999999876544 7999999999999999999999999999999999999988775 6799999
Q ss_pred HHHHHHHHHHHhhcCCceeeccccccccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHhhccCC-CCcc
Q psy15735 419 GYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRFYQYHT-NGTR 497 (574)
Q Consensus 419 g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLRf~q~~~-~~~r 497 (574)
|+++|++||+||++||+.|+-.+..++.+|++|++.++++++++++.+....++....+|+++||+||||||+|+ +..|
T Consensus 147 gilaGilVa~kQllpd~~il~~~~~r~~~~~lP~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRfyq~h~~~~~r 226 (326)
T KOG2890|consen 147 GILAGILVAWKQLLPDTIILELKSGRFLYAHLPLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLRFYQRHPTDELR 226 (326)
T ss_pred HHHHHHHHHHHHHcCceeEEeccchhhhhhhCCHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhheecccCCccccc
Confidence 999999999999999999998888999999999999999999999888877888889999999999999999997 4589
Q ss_pred CCcccCccccccCCccCcchhHhhhhHHHHHHHHHcccccccccccCCCCCCCCcccCCCCCCchhhhhhhhhhccC
Q psy15735 498 GDMADNFNFANFFPTIIQPPIAVVCNTIHEFLVRIGLCRKMVRKFDMSVAPSSGITITLPGIDPNDAERRSSVYCKE 574 (574)
Q Consensus 498 GD~Sd~Faf~~FFP~~~~p~i~~i~~~~~~~lv~~~lc~~~~~~~d~~~~~~~~~~~~lPg~~~~eAeRRR~~a~~~ 574 (574)
||+||+|+|++|||+.+||++.+|+|.+|++|++.|.|++..+ |.+ ++.++..+++||+|++|||||||+|||+
T Consensus 227 GD~Sd~F~fvsFFP~v~qp~~~li~n~~~~~l~~~~~~~~~~~--d~~-~~~~s~~~~lpg~d~~d~eRRRQ~alka 300 (326)
T KOG2890|consen 227 GDCSDSFTFVSFFPEVLQPFFHLIANTIYRILVRMGVVKKPHV--DID-LDSGSVGANLPGLDPKDAERRRQLALKA 300 (326)
T ss_pred CCchhceehhhhchhhhhHHHHHHHHHHHHHHHHhccccccce--ecc-cCcccccccCCCCChhHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999655 444 3345567899999999999999999984
No 2
>KOG1555|consensus
Probab=100.00 E-value=6.6e-39 Score=325.56 Aligned_cols=154 Identities=44% Similarity=0.585 Sum_probs=151.5
Q ss_pred CcCcEEEecccccCccccccCCCCcccccccCccCc-chHHHHHhhcCCcceeeEEeeeCCHHHHHHHhhcccCCccCCC
Q psy15735 7 QLGKVVIDAFRLINPNMMVLGQEPRQTTSNLGHLQK-HSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGL 85 (574)
Q Consensus 7 ~kgkvvidafr~i~~~~~~~~~eprqttsn~g~l~k-p~~~a~~~gl~r~yys~~i~~~~~~~e~~ml~~l~k~~w~~~l 85 (574)
.||||||||||+|||+.++.|+||||||||+||+++ ||+|+.+|||| ||||+.|+||++++|++|++|+||++|.++
T Consensus 160 ~~g~vv~d~f~~In~~~~~~~~eprqtts~~~~m~~~~s~q~~~~g~n-~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~- 237 (316)
T KOG1555|consen 160 PYGKVVPDAFSSINPQWISPGGEPRQTTSNGGHMDMQESLQEDIHGLN-RYYRIEIPLHVLPYEQLMLLNVPLKSWKSL- 237 (316)
T ss_pred CCCCccCChhhhcCcccccCCCCCccccccccccccchhHHhHhhccC-ceEEEEeeEEechhhhhchhccchhhhhhc-
Confidence 589999999999999999999999999999999999 99999999999 999999999999999999999999999999
Q ss_pred CccChHHHhhhhHHHHHHHHHHHHHHHHHHHHHhcCCHhHHhhhhcCCCChhhhHHHHHHHHhhhhhHHHHhhHHHH
Q psy15735 86 SLQDYNEHCKLNEGTVNDMLELAKHYNKALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMTANIIQCLDRNMER 162 (574)
Q Consensus 86 ~~~~~~~~~~~n~~~~~~~~~l~~~y~~~~~ee~~~~~~~~~~~~vgk~d~k~hl~~~~~~~~~~ni~q~l~~ml~~ 162 (574)
+..+|+++.+.|+..+++|.+|++.|||.+++|+.+++++++|.++|++|||+||++.+.+.+.+||+|+|++|.++
T Consensus 238 ~~~~y~e~~k~~~~~~~~~~sL~~~~N~~~~~~k~~~~~~~~i~d~~~~~~kq~l~~~v~~~~~~nl~~~l~~~~~~ 314 (316)
T KOG1555|consen 238 QDVLYEEKLKAYLQSVPSMKSLSKVYNKVCDVCKQMSDFLLMIEDVGEQNPKQHLKEAVTELLSENLVQELGSMERR 314 (316)
T ss_pred chhhHHHHHHHhhhhhhHHHhHHHHHHHHHHHHhhccHHHHHHHHhhhhhHHHHhHHHhhhhcccchhhcchhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999875
No 3
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.96 E-value=7.9e-30 Score=260.30 Aligned_cols=128 Identities=65% Similarity=1.027 Sum_probs=120.3
Q ss_pred CCCCCCCccEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHH--H
Q psy15735 181 DGPVVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLD--M 258 (574)
Q Consensus 181 ~~~~~~~~~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~--~ 258 (574)
|.+.++++++|+|++.|+++|++||+++.|.||||+|+|... +++++|++|||+|+.+++.+++ .++++|..|.+ +
T Consensus 2 ~~~~~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~-~~~v~Vt~~fp~p~~~t~~~v~-~~~e~~~~m~~~~~ 79 (268)
T cd08069 2 WKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVD-DYTIIVVDVFALPVEGTETRVN-AQDEFQEYMVQYEM 79 (268)
T ss_pred CCCCCCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeec-CCeEEEEEEEECCcCCCCCcee-ccHHHHHHHHHHHH
Confidence 788999999999999999999999999999999999999964 4699999999999988887776 56689999999 9
Q ss_pred HHhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCC
Q psy15735 259 LKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS 310 (574)
Q Consensus 259 lr~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s 310 (574)
+++.++++++||||||||+++||||..|+++|..||+..+++|+|||||.++
T Consensus 80 ~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t 131 (268)
T cd08069 80 LKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRS 131 (268)
T ss_pred HHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCcc
Confidence 9999999999999999999999999999999999999999999999999888
No 4
>KOG1555|consensus
Probab=99.96 E-value=1.1e-29 Score=258.39 Aligned_cols=205 Identities=65% Similarity=0.997 Sum_probs=182.6
Q ss_pred HHhhhcCCCCCC--CCCCCCCCCCCCCCccEEEECHHHHHHHHHHHhcCCCce-EEEEe-ee---EEcCCceEEEEEEEe
Q psy15735 162 RLLRLGSGMPGL--SQAPPVSDGPVVDTAEQVYISSLALLKMLKHGRAGVPME-VMGLM-LG---EFVDEYTVRVIDVFA 234 (574)
Q Consensus 162 ~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~V~Is~~vllkIl~Ha~~~~p~E-v~GlL-lG---~~~~~~~l~Vt~~fp 234 (574)
++.|+.+..+.. ++ .+.+|.+..+..++|+|+..++++|.+|.|.+.|.| ++|+| +| .+.++.++.|.++|.
T Consensus 3 ~~~rl~~l~~~~s~~~-~~~~d~~~~~~~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~a 81 (316)
T KOG1555|consen 3 TLLRLTQLVHALSIMG-ELLGDEPHSDEKETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFA 81 (316)
T ss_pred hHHhhhccCCcccccc-cccCccccccCcceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeec
Confidence 555665543322 12 234689999999999999999999999999999999 99999 99 777888999999999
Q ss_pred CCcccCCCC--cccccHHHHHHHHHHHHhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCch
Q psy15735 235 MPQTGTGVS--VEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVK 312 (574)
Q Consensus 235 ~p~~~~~~~--~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~ 312 (574)
+|++++..+ ++.+||.+|.+|++++++.|+.+.|||||||||+|+||||..|+++|++||.+.+..++.++||+.+..
T Consensus 82 m~~sg~~is~~~e~~d~V~q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~ 161 (316)
T KOG1555|consen 82 MPQSGTGISKFVEAVDPVFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPY 161 (316)
T ss_pred cccccceecccchhccHHHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCC
Confidence 999999888 678999999999999999999999999999999999999999999999999999999999999988865
Q ss_pred --------------------------------------------------------------------------------
Q psy15735 313 -------------------------------------------------------------------------------- 312 (574)
Q Consensus 313 -------------------------------------------------------------------------------- 312 (574)
T Consensus 162 g~vv~d~f~~In~~~~~~~~eprqtts~~~~m~~~~s~q~~~~g~n~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~~~~~ 241 (316)
T KOG1555|consen 162 GKVVPDAFSSINPQWISPGGEPRQTTSNGGHMDMQESLQEDIHGLNRYYRIEIPLHVLPYEQLMLLNVPLKSWKSLQDVL 241 (316)
T ss_pred CCccCChhhhcCcccccCCCCCccccccccccccchhHHhHhhccCceEEEEeeEEechhhhhchhccchhhhhhcchhh
Confidence
Q ss_pred ----------------hHHHHHHHHhhhccCCCccchhcccccCCccchhhHHHHHHhhhhhHHHHHhhcc
Q psy15735 313 ----------------ELAKHYNKALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMTANIIQCLGGKL 367 (574)
Q Consensus 313 ----------------rLs~~y~~~~~ee~~ft~EeL~v~~vg~~DP~~~Le~~v~~fm~~nI~~~l~~mL 367 (574)
+|++.|++.+.++.+.+++.+.+.+++..||+||+++.+.+.+.+|+++.++.|.
T Consensus 242 y~e~~k~~~~~~~~~~sL~~~~N~~~~~~k~~~~~~~~i~d~~~~~~kq~l~~~v~~~~~~nl~~~l~~~~ 312 (316)
T KOG1555|consen 242 YEEKLKAYLQSVPSMKSLSKVYNKVCDVCKQMSDFLLMIEDVGEQNPKQHLKEAVTELLSENLVQELGSME 312 (316)
T ss_pred HHHHHHHhhhhhhHHHhHHHHHHHHHHHHhhccHHHHHHHHhhhhhHHHHhHHHhhhhcccchhhcchhhh
Confidence 5778888777667777888888999999999999999999999999999999886
No 5
>KOG1554|consensus
Probab=99.95 E-value=5.9e-28 Score=238.93 Aligned_cols=159 Identities=40% Similarity=0.659 Sum_probs=134.2
Q ss_pred hhhHHHHhhHHHHHhhhcCCCC-CCCCCCCCCCCCCCCCccEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEE
Q psy15735 150 ANIIQCLDRNMERLLRLGSGMP-GLSQAPPVSDGPVVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVR 228 (574)
Q Consensus 150 ~ni~q~l~~ml~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~ 228 (574)
+|-+|.+-. -|.+.++++..+ ..-.++| |..++..++.|.|++++++||..||++|.+.|+||+|.|...+ .++.
T Consensus 16 en~~~~~~~-~deif~yd~~sq~~~~~~kp--w~~Dp~~fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g-~t~I 91 (347)
T KOG1554|consen 16 ENNIQSVES-EDEIFRYDQKSQRKIILEKP--WSTDPHYFKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDG-DTII 91 (347)
T ss_pred hhhhccCcc-chhhhhcCHHHHHHHHhcCc--ccCCCchhhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccC-CeEE
Confidence 344444444 566777775321 1222345 7889999999999999999999999999999999999999754 5899
Q ss_pred EEEEEeCCcccCCCCcccccH--HHHHHHHHHHHhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEc
Q psy15735 229 VIDVFAMPQTGTGVSVEAVDP--VFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVD 306 (574)
Q Consensus 229 Vt~~fp~p~~~~~~~~~~idp--~~q~~ml~~lr~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvD 306 (574)
|.|||++|.++|++++.+.+. +|..+..+.++.+|+.+++||||||||+++||+|.+|+.||..-|++..++|++|+|
T Consensus 92 vmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViD 171 (347)
T KOG1554|consen 92 VMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVID 171 (347)
T ss_pred EEeccccccccccceechHHHHHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEec
Confidence 999999999999999876544 456777889999999999999999999999999999999999999999999999999
Q ss_pred CCCCch
Q psy15735 307 PIQSVK 312 (574)
Q Consensus 307 p~~s~~ 312 (574)
|.++..
T Consensus 172 P~Rtls 177 (347)
T KOG1554|consen 172 PTRTLS 177 (347)
T ss_pred Cccccc
Confidence 998863
No 6
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.94 E-value=2e-26 Score=223.29 Aligned_cols=121 Identities=31% Similarity=0.462 Sum_probs=108.9
Q ss_pred ccEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcC-CceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCC
Q psy15735 188 AEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD-EYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPE 266 (574)
Q Consensus 188 ~~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~-~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~ 266 (574)
+.+|+|++.|+++|++||+.+. .||||+|+|...+ ++.++|+++||+|+..+..+++ +||++|.+|.+.+++.| +
T Consensus 4 pf~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e-~dp~~q~e~~~~l~~~g--l 79 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCE-MDPVSETEIRESLESRG--L 79 (187)
T ss_pred CEEEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccc-cCHHHHHHHHHHHHHcC--C
Confidence 3699999999999999999987 9999999999653 4689999999999977655654 89999999999999877 5
Q ss_pred cEEEEEccCCCCCCcCCHHHHHHHHHHHhcCC-------CeEEEEEcCCCCch
Q psy15735 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSE-------RAVAVVVDPIQSVK 312 (574)
Q Consensus 267 ~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p-------~~V~LIvDp~~s~~ 312 (574)
++||||||||.++++||.+|+++|..||.+.+ ++|++||||..+.+
T Consensus 80 ~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~ 132 (187)
T cd08067 80 SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRN 132 (187)
T ss_pred EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCC
Confidence 99999999999999999999999999999766 79999999988643
No 7
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.94 E-value=1.5e-26 Score=236.40 Aligned_cols=153 Identities=27% Similarity=0.427 Sum_probs=133.3
Q ss_pred cEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCC--cccccHHHHHHHHHHHHhcCCCC
Q psy15735 189 EQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVS--VEAVDPVFQAKMLDMLKQTGRPE 266 (574)
Q Consensus 189 ~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~--~~~idp~~q~~ml~~lr~~g~~~ 266 (574)
++|+|++.|+++|++||+++.|.+|||+|+|...+ ++++||||||+|+..++.+ ....+.+||.+|+++++++|.++
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~-~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e 79 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVG-GTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH 79 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcC-CEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence 47999999999999999999999999999999865 6999999999999876554 23345599999999999999999
Q ss_pred cEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCch--------hHHHHHHHHhhhccCCCccchhcccc
Q psy15735 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVK--------ELAKHYNKALEEEEKMSPEQLAIKNV 338 (574)
Q Consensus 267 ~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~--------rLs~~y~~~~~ee~~ft~EeL~v~~v 338 (574)
++|||||||| ++++.|..++++++.||...+++|+||+||.++.+ ++++.++..+ .+++|+++.++..++
T Consensus 80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~-~~~~~~~~~l~~~~~ 157 (266)
T cd08065 80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELY-KEGKFSTESLREANL 157 (266)
T ss_pred cEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHh-hcCCcCHHHHHHhcC
Confidence 9999999999 99999999999999999888999999999986432 7889999887 478999999988777
Q ss_pred cCCccc
Q psy15735 339 GKQDPK 344 (574)
Q Consensus 339 g~~DP~ 344 (574)
++.+..
T Consensus 158 ~~~~if 163 (266)
T cd08065 158 TFSNIF 163 (266)
T ss_pred chhcEE
Confidence 754433
No 8
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.92 E-value=1.9e-24 Score=216.06 Aligned_cols=123 Identities=28% Similarity=0.447 Sum_probs=102.7
Q ss_pred ccEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcC------CceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHH--
Q psy15735 188 AEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD------EYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDML-- 259 (574)
Q Consensus 188 ~~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~------~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~l-- 259 (574)
+++|.|++.++.+|++||++++|.||||+|+|...+ +..+.|+..+++++.......+++||+.+.++.+.+
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~~ 80 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAER 80 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHHH
Confidence 368999999999999999999999999999998742 335566666666665544445579999886655444
Q ss_pred --HhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCC
Q psy15735 260 --KQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS 310 (574)
Q Consensus 260 --r~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s 310 (574)
+..|+++.+||||||||+++|+||.+|+++|..||++.|+++|+|+|+.+.
T Consensus 81 ~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~ 133 (244)
T cd08068 81 LTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNE 133 (244)
T ss_pred HHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCC
Confidence 447788999999999999999999999999999999999999999998765
No 9
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.91 E-value=4.2e-24 Score=192.90 Aligned_cols=105 Identities=45% Similarity=0.675 Sum_probs=88.2
Q ss_pred HHHHHHHHHHhcCCCceEEEEeeeEEcC----CceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEE
Q psy15735 196 LALLKMLKHGRAGVPMEVMGLMLGEFVD----EYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGW 271 (574)
Q Consensus 196 ~vllkIl~Ha~~~~p~Ev~GlLlG~~~~----~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGW 271 (574)
+++++|++||+++.|.|+||+|+|...+ +.+++|+++||.|.. .|+..|. ..+.+..++++++|||
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~--------~~~~~~~--~~~~~~~~~g~~~vG~ 70 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDS--------CTGENVE--ELFNVQTGRPLLVVGW 70 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCC--------chhHHHH--HHHHHHhCCCCeEEEE
Confidence 4789999999999999999999998753 345789999998862 3444443 3444455667899999
Q ss_pred EccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCC
Q psy15735 272 YHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS 310 (574)
Q Consensus 272 YHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s 310 (574)
|||||+++++||..|+++|++||++.|++++||+||.++
T Consensus 71 YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~ 109 (119)
T cd08058 71 YHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR 109 (119)
T ss_pred EecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC
Confidence 999999999999999999999999999999999999875
No 10
>KOG1560|consensus
Probab=99.91 E-value=3.2e-24 Score=211.94 Aligned_cols=160 Identities=27% Similarity=0.439 Sum_probs=138.1
Q ss_pred CCCccEEEECHHHHHHHHHHHhcCCCc--eEEEEeeeEEcCCceEEEEEEEeCCccc--CCCCcc--cccH---HHHHHH
Q psy15735 185 VDTAEQVYISSLALLKMLKHGRAGVPM--EVMGLMLGEFVDEYTVRVIDVFAMPQTG--TGVSVE--AVDP---VFQAKM 255 (574)
Q Consensus 185 ~~~~~~V~Is~~vllkIl~Ha~~~~p~--Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~--~~~~~~--~idp---~~q~~m 255 (574)
..++++|.|++++++||++||++..|. -+.|+|+|...| ++++||||||.|... .++.+. .+|+ .||.+|
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd-~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~m 87 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVD-GRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAM 87 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeec-ceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHH
Confidence 456899999999999999999997766 468999999886 599999999999754 222221 2343 478899
Q ss_pred HHHHHhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCch--------hHHHHHHHHhhhccC
Q psy15735 256 LDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVK--------ELAKHYNKALEEEEK 327 (574)
Q Consensus 256 l~~lr~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~--------rLs~~y~~~~~ee~~ 327 (574)
++.+|.+|.|..+||||+|| .++++.|..-+++|+.||...|+.|.+|+||.++.+ ||+++++..+ ++++
T Consensus 88 lrrlr~vnid~~hVGwYqs~-~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~-kekd 165 (339)
T KOG1560|consen 88 LRRLRYVNIDHLHVGWYQSA-YVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAH-KEKD 165 (339)
T ss_pred HHHhhhcCccceeeeeeeee-hhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHH-hcCC
Confidence 99999999999999999999 689999999999999999999999999999999987 9999999998 5889
Q ss_pred CCccchhcccccCCccchhh
Q psy15735 328 MSPEQLAIKNVGKQDPKRHL 347 (574)
Q Consensus 328 ft~EeL~v~~vg~~DP~~~L 347 (574)
|+||.+..+++++.+-...+
T Consensus 166 wtpealk~~nltyenmfeEl 185 (339)
T KOG1560|consen 166 WTPEALKSANLTYENMFEEL 185 (339)
T ss_pred CCHHHHHhcCCCHHHHHhhc
Confidence 99999999999986655443
No 11
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.91 E-value=3.5e-24 Score=191.41 Aligned_cols=113 Identities=35% Similarity=0.658 Sum_probs=97.3
Q ss_pred CccEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCC
Q psy15735 187 TAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPE 266 (574)
Q Consensus 187 ~~~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~ 266 (574)
++.+|.|+++|+++|++||.+..+.||||+|+|...++++++|++||++|+..++..+...+..+..+|.+++++.+.++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNL 81 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTS
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccc
Confidence 46899999999999999998887889999999998764499999999999988776665556666679999999998889
Q ss_pred cEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCC
Q psy15735 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSER 299 (574)
Q Consensus 267 ~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~ 299 (574)
.+||||||||.++|+||..|+++|+.||++.|+
T Consensus 82 ~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 82 EIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp EEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred eEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 999999999999999999999999999998764
No 12
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.90 E-value=3.8e-24 Score=218.62 Aligned_cols=131 Identities=50% Similarity=0.761 Sum_probs=126.0
Q ss_pred CcCcEEEecccccCccccccCCCCcccccccCccCcchHHHHHhhcCCcceeeEEeeeCCHHHHHHHhhcccCCccCCCC
Q psy15735 7 QLGKVVIDAFRLINPNMMVLGQEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLS 86 (574)
Q Consensus 7 ~kgkvvidafr~i~~~~~~~~~eprqttsn~g~l~kp~~~a~~~gl~r~yys~~i~~~~~~~e~~ml~~l~k~~w~~~l~ 86 (574)
.+|||.|+|||++++...++ |||+||||.|++.+|+++ ..++++++||+|+|+||++++|+.||.+|+++.|.++|+
T Consensus 133 ~~g~~~i~Afr~~~~~~~~~--~~~~~~s~~~~~~~~~~~-~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~~~l~ 209 (268)
T cd08069 133 VKGKVVIGAFRTIPPGYKPL--EPRQTTSNIGHLPKPKIE-DFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVNTLS 209 (268)
T ss_pred cCCcceeeEEEEECcccccc--CcccCccccCccCcHHHH-HhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHHHHhh
Confidence 68999999999999987765 999999999999999999 999999999999999999999999999999999999999
Q ss_pred ccChHHHhhhhHHHHHHHHHHHHHHHHHHHHHhcCCHhHHhhhhcCCCC-----hhhhHHH
Q psy15735 87 LQDYNEHCKLNEGTVNDMLELAKHYNKALEEEEKMSPEQLAIKNVGKQD-----PKRHLEE 142 (574)
Q Consensus 87 ~~~~~~~~~~n~~~~~~~~~l~~~y~~~~~ee~~~~~~~~~~~~vgk~d-----~k~hl~~ 142 (574)
+.++.+++ |+..++.|.+|+++|++.+.+|..++++++..+++||+| ||+|+++
T Consensus 210 ~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 268 (268)
T cd08069 210 LSPLLENS--NEYTIKQILDLAEKLEKAEQQEERLTGEELDIANVGKLDKARDSSKIHLEE 268 (268)
T ss_pred CCchhhhh--hHHHHHHHHHHHHHHHHHHhhhhccChhhhcccchhhhhhccccchhhhcC
Confidence 99998877 999999999999999999999999999999999999999 9999974
No 13
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.87 E-value=1.8e-21 Score=177.48 Aligned_cols=121 Identities=36% Similarity=0.533 Sum_probs=108.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEE
Q psy15735 190 QVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVV 269 (574)
Q Consensus 190 ~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vV 269 (574)
.|.|++.++++|++|+.++.|.|+||+|+|...+ ++++|+++|++|+...+.++...+.+++.+|.+..++.+.++++|
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~-~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 79 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNK-DRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIV 79 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcC-CEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEE
Confidence 4789999999999999999999999999999754 489999999999987665543467788889999989999999999
Q ss_pred EEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCc
Q psy15735 270 GWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311 (574)
Q Consensus 270 GWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~ 311 (574)
|||||||..+++||..|+++|..|+...+.++.+++|+..+.
T Consensus 80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~ 121 (135)
T smart00232 80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSF 121 (135)
T ss_pred EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccc
Confidence 999999999999999999999999999999999999998764
No 14
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.84 E-value=3e-20 Score=178.25 Aligned_cols=114 Identities=25% Similarity=0.491 Sum_probs=98.7
Q ss_pred cEEEECHHHHHHHHHHHhcCC--CceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCC
Q psy15735 189 EQVYISSLALLKMLKHGRAGV--PMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPE 266 (574)
Q Consensus 189 ~~V~Is~~vllkIl~Ha~~~~--p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~ 266 (574)
..+.|+..++.+|+.||+++. |.|+||+|+|...+ +..+|++++..|+.+++.+++.+|+. ++++.++..| +
T Consensus 2 ~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~-~~~~I~~i~~~~q~~~~~~~~~~~~~---e~~~~~~~~g--l 75 (173)
T cd08066 2 RQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSN-NAFFITHLIIPKQSGTSDSCQTTNEE---ELFDFQDQHD--L 75 (173)
T ss_pred eEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCC-CeEEEEEEEeccccCCCceecCCCHH---HHHHHHHhCC--C
Confidence 478999999999999999984 59999999998654 57889999888888877766656653 4666777655 7
Q ss_pred cEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCC
Q psy15735 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPI 308 (574)
Q Consensus 267 ~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~ 308 (574)
++||||||||+.+++||..|+++|.+||++.|++++||+||.
T Consensus 76 e~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~ 117 (173)
T cd08066 76 ITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK 117 (173)
T ss_pred eeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC
Confidence 999999999999999999999999999999999999999995
No 15
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.82 E-value=1e-19 Score=172.11 Aligned_cols=117 Identities=23% Similarity=0.369 Sum_probs=103.7
Q ss_pred EEECHHHHHHHHHHHhcCC--CceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcE
Q psy15735 191 VYISSLALLKMLKHGRAGV--PMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMV 268 (574)
Q Consensus 191 V~Is~~vllkIl~Ha~~~~--p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~v 268 (574)
|+|+|+|+++|++|+.+.. +.+|+|+|+|... +++++|+||||+|...++.+. .+|++|+.+|.++++++++++.+
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~-~~~veV~nsF~lp~~~~~~~~-~~d~~y~~~m~~~~~~v~~~~~v 78 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVD-GDKIEVTNSFELPFDEEEESI-FIDTEYLEKRYNLHKKVYPQEKI 78 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEe-CCEEEEEEeEEccccCCCcch-hhhHHHHHHHHHHHHHhCCCCCE
Confidence 6899999999999997766 8899999999986 469999999999997665553 47999999999999999999999
Q ss_pred EEEEccCCCCCCcCCHHHHHHHHHHHhc-CCCeEEEEEcCCC
Q psy15735 269 VGWYHSHPGFGCWLSGVDINTQQSFEAL-SERAVAVVVDPIQ 309 (574)
Q Consensus 269 VGWYHSHP~~~~~pS~~Di~tq~~yQ~~-~p~~V~LIvDp~~ 309 (574)
||||||||..++.++..|...+..|... .+++++|++||..
T Consensus 79 VGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~ 120 (157)
T cd08057 79 VGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSL 120 (157)
T ss_pred EEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCc
Confidence 9999999988778888888888877665 7889999999976
No 16
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.81 E-value=2.4e-19 Score=184.35 Aligned_cols=122 Identities=26% Similarity=0.454 Sum_probs=105.1
Q ss_pred cEEEECHHHHHHHHHHHhc---CCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCC--cccccHHHHHHHHHHHHhcC
Q psy15735 189 EQVYISSLALLKMLKHGRA---GVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVS--VEAVDPVFQAKMLDMLKQTG 263 (574)
Q Consensus 189 ~~V~Is~~vllkIl~Ha~~---~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~--~~~idp~~q~~ml~~lr~~g 263 (574)
++|.|+|+|+++|++|+.+ +.+.+|+|.|+|...+ ++++|+|||++|...++++ ...+|.+|+.+|.+++++++
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~-~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~ 79 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKK-GVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVN 79 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeC-CEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhC
Confidence 4799999999999999865 3467899999999865 6999999999999766544 24589999999999999999
Q ss_pred CCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCchhHH
Q psy15735 264 RPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKELA 315 (574)
Q Consensus 264 ~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~rLs 315 (574)
+++.+||||||||+ ++..|+.+|..|++.++++|+|++||..+..+++
T Consensus 80 ~~e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lp 127 (280)
T cd08062 80 AKEKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLP 127 (280)
T ss_pred CCCCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCc
Confidence 99999999999996 4667888899999999999999999987554443
No 17
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.80 E-value=1.1e-19 Score=166.12 Aligned_cols=119 Identities=24% Similarity=0.247 Sum_probs=98.5
Q ss_pred HHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCC-CcccccHHHHHHHHHHHHhcCCCCcEEEEEcc
Q psy15735 196 LALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGV-SVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHS 274 (574)
Q Consensus 196 ~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~-~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHS 274 (574)
.++.+|++||+++.|.|+||+|+|...+. ...|++++|+||...++ ..+.+||.++.++.+.+++.| +.+||||||
T Consensus 2 ~~~~~il~ha~~~~P~E~cGlL~G~~~~~-~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g--~~~vG~~HS 78 (128)
T cd08070 2 ELLEAILAHAEAEYPEECCGLLLGKGGGV-TAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERG--LEVVGIYHS 78 (128)
T ss_pred HHHHHHHHHHHhCCCCceEEEEEeecCCC-CceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCC--CeEEEEEeC
Confidence 46889999999999999999999997543 44678999999988777 567799999999999999876 799999999
Q ss_pred CCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCchhHHHHHHHHhhhcc
Q psy15735 275 HPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKELAKHYNKALEEEE 326 (574)
Q Consensus 275 HP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~rLs~~y~~~~~ee~ 326 (574)
||+.+++||..|++.+ ..++.+++|+++..+. ..++.|..+++
T Consensus 79 HP~~~~~PS~~D~~~~-----~~~~~~~lIv~~~~~~----~~~~~~~~~~~ 121 (128)
T cd08070 79 HPDGPARPSETDLRLA-----WPPGVSYLIVSLAGGA----PELRAWRLEGG 121 (128)
T ss_pred CCCCCCCCCHHHHHhc-----cCCCCeEEEEECCCCC----cEEEEEEEcCC
Confidence 9999999999999865 2457999999987653 34555544333
No 18
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.80 E-value=8.5e-19 Score=156.04 Aligned_cols=107 Identities=27% Similarity=0.396 Sum_probs=88.0
Q ss_pred HHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEccCCCC
Q psy15735 199 LKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGF 278 (574)
Q Consensus 199 lkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSHP~~ 278 (574)
.+|++||+.+.|.|+||+|+|...+ ++++|+++|++|+..++.. .+...+ |....+..+.++++||||||||..
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~-~~~~i~~~~~~~~~~~~~~---~~~~~~--~~~~~~~~~~~~~iVGwyhshp~~ 75 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTK-KVLDVDEVIAVPFDEGDKD---DNVWFL--MYLDFKKLNAGLRIVGWYHTHPKP 75 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcC-CEEEEEEEEecccCCCCCc---cHHHHH--HHHHHHHhcCCCeEEEEEEcCCCC
Confidence 5899999999999999999999865 4889999999998654322 222222 344444556779999999999999
Q ss_pred CCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCc
Q psy15735 279 GCWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311 (574)
Q Consensus 279 ~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~ 311 (574)
+++||..|+.+|..||+..+++++||+|+....
T Consensus 76 ~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~ 108 (116)
T cd07767 76 SCFLSPNDLATHELFQRYFPEKVMIIVDVKPKD 108 (116)
T ss_pred CCccCHHHHHHHHHHHHhCCCCEEEEEECCCcc
Confidence 999999999999999998999999999997753
No 19
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.76 E-value=5.3e-18 Score=173.47 Aligned_cols=119 Identities=19% Similarity=0.365 Sum_probs=97.7
Q ss_pred EEECHHHHHHHHHHHhc--CCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcE
Q psy15735 191 VYISSLALLKMLKHGRA--GVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMV 268 (574)
Q Consensus 191 V~Is~~vllkIl~Ha~~--~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~v 268 (574)
|.|+|+|+++|++|+.+ ..+.+|+|.|+|...+ ++++||||||+|+..+++.. .+|.+|+.+|.++++++++++.+
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~-~~veItnsF~~p~~~~~~~~-~~d~~y~~~m~~~~kkv~~~~~v 78 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSE-GEVEITNCFAVPHNESEDQV-AVDMEYHRTMYELHQKVNPKEVI 78 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeC-CEEEEEeCeecceeCCCCeE-EEcHHHHHHHHHHHHHhCCCCcE
Confidence 68999999999999865 5678999999999865 69999999999997766554 48999999999999999999999
Q ss_pred EEEEccCCCCCCcCCHHHHHHHHHHHhcCC--CeEEEEEcCCCCchhHH
Q psy15735 269 VGWYHSHPGFGCWLSGVDINTQQSFEALSE--RAVAVVVDPIQSVKELA 315 (574)
Q Consensus 269 VGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p--~~V~LIvDp~~s~~rLs 315 (574)
||||||+|. ++..|...|..|+...+ ++|+|++||..+.++++
T Consensus 79 VGWY~tg~~----~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~ 123 (265)
T cd08064 79 VGWYATGSE----ITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMS 123 (265)
T ss_pred EeeeeCCCC----CCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcc
Confidence 999999983 44344445555555555 89999999987655443
No 20
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.73 E-value=2.4e-17 Score=170.97 Aligned_cols=125 Identities=26% Similarity=0.408 Sum_probs=104.9
Q ss_pred CCCccEEEECHHHHHHHHHHHhcCC---CceEEEEeeeEEcCCceEEEEEEEeCCcccCCCC--cccccHHHHHHHHHHH
Q psy15735 185 VDTAEQVYISSLALLKMLKHGRAGV---PMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVS--VEAVDPVFQAKMLDML 259 (574)
Q Consensus 185 ~~~~~~V~Is~~vllkIl~Ha~~~~---p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~--~~~idp~~q~~ml~~l 259 (574)
++++.+|.|+|+|+++|++|+.+.. +..|+|.|+|...+ +.++|+|||++|....++. ...+|.+|+.+|++++
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~-~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~ 80 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFR-GRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMF 80 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecC-CEEEEEeccccCcccCCCCccceeecHHHHHHHHHHH
Confidence 5678999999999999999997654 45699999999854 6999999999998654332 2348999999999999
Q ss_pred HhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCchhH
Q psy15735 260 KQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKEL 314 (574)
Q Consensus 260 r~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~rL 314 (574)
++++.++.+||||+|.|. ++..|+..|..|...++.+++|++|+.....++
T Consensus 81 k~V~~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~l 131 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGI 131 (303)
T ss_pred HHhCCCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCC
Confidence 999999999999999985 445678888889888999999999986654444
No 21
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.67 E-value=3.7e-16 Score=161.70 Aligned_cols=117 Identities=23% Similarity=0.396 Sum_probs=99.2
Q ss_pred EEEECHHHHHHHHHHHhc----CC--CceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcC
Q psy15735 190 QVYISSLALLKMLKHGRA----GV--PMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTG 263 (574)
Q Consensus 190 ~V~Is~~vllkIl~Ha~~----~~--p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g 263 (574)
+|.|+|+|+++|++|+.+ .. |..|+|.|+|... +++++|+|||++|...+++....+|.+|+.+|.+++++++
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~-~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~ 80 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQD-GREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVF 80 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEc-CCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhc
Confidence 689999999999999966 22 6889999999874 4689999999999876653334589999999999999999
Q ss_pred CCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCC
Q psy15735 264 RPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS 310 (574)
Q Consensus 264 ~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s 310 (574)
+++.+||||+|+|. + +...|...|..|...++.+|+|++||..+
T Consensus 81 ~~~~vVGWY~tg~~-~--~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~ 124 (288)
T cd08063 81 KDLDFVGWYTTGPG-G--PTESDLPIHKQILEINESPVLLLLDPEAN 124 (288)
T ss_pred cCCceEEEEecCCC-C--CCHHHHHHHHHHHhhCCCcEEEEEccccc
Confidence 99999999999986 3 55666666777777788899999999873
No 22
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=99.66 E-value=3e-17 Score=143.74 Aligned_cols=86 Identities=38% Similarity=0.629 Sum_probs=80.5
Q ss_pred CccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchh
Q psy15735 341 QDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFV 412 (574)
Q Consensus 341 ~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~ 412 (574)
..||+.++ +.|+|.|++.++.+.+ +||.||+|||+||++++++++++++++.+++.|.++++.++++ +
T Consensus 6 ~~pWtl~T---~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~~l~-~ 81 (99)
T PF08551_consen 6 PYPWTLFT---AGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYAITGNESYLF-V 81 (99)
T ss_pred eehHHHHH---HHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCceeE-E
Confidence 37888887 9999999999986655 7999999999999999999999999999999999999999877 9
Q ss_pred hccChhHHHHHHHHHHHh
Q psy15735 413 RIHGLTGYISGVLVAVKQ 430 (574)
Q Consensus 413 ~i~G~~g~i~G~LVA~kQ 430 (574)
+++|++|+++|++||+||
T Consensus 82 ~i~G~~~~~~g~lVa~kQ 99 (99)
T PF08551_consen 82 PISGFMGVLAGFLVAFKQ 99 (99)
T ss_pred EecCcHHhHhheEEEEeC
Confidence 999999999999999998
No 23
>KOG1556|consensus
Probab=99.60 E-value=5.9e-15 Score=144.39 Aligned_cols=131 Identities=27% Similarity=0.422 Sum_probs=107.6
Q ss_pred CCccEEEECHHHHHHHHHHHhcC---CCceEEEEeeeEEcCCceEEEEEEEeCCcccCC--CCcccccHHHHHHHHHHHH
Q psy15735 186 DTAEQVYISSLALLKMLKHGRAG---VPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTG--VSVEAVDPVFQAKMLDMLK 260 (574)
Q Consensus 186 ~~~~~V~Is~~vllkIl~Ha~~~---~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~--~~~~~idp~~q~~ml~~lr 260 (574)
.+.++|.++|+|++..++|..+. ...+|.|+|+|.... .++.|+|+|++|..+.+ .++..+|..|...|..+++
T Consensus 6 ~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~-~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfk 84 (309)
T KOG1556|consen 6 LTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNG-DVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFK 84 (309)
T ss_pred cccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCC-CeEEeecceeccccccCCCCceEEeccHHHHHHHHHHH
Confidence 45789999999999999998653 347999999999865 48999999999997654 4577799999999999999
Q ss_pred hcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCchhH-HHHHHHH
Q psy15735 261 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKEL-AKHYNKA 321 (574)
Q Consensus 261 ~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~rL-s~~y~~~ 321 (574)
+++..+.+||||||.|.. ..+ |++....+..++|+++.+|+|.....--| +++|.+.
T Consensus 85 KvNakekivGWYhTGPkl--~~n--Dl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aV 142 (309)
T KOG1556|consen 85 KVNAKEKVVGWYHTGPKL--REN--DLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAV 142 (309)
T ss_pred HhcchhheeeeeccCCcc--ccc--hhhHHHHHhhcCCCceEEEEecccccCCCCchheeee
Confidence 999999999999999964 445 44445667788999999999987665434 4677654
No 24
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.58 E-value=1.3e-14 Score=130.89 Aligned_cols=97 Identities=22% Similarity=0.235 Sum_probs=76.4
Q ss_pred ECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEE
Q psy15735 193 ISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWY 272 (574)
Q Consensus 193 Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWY 272 (574)
|+..++.+|++||++++|.|+||+|+|.. + .|++++++||...++..+.++.+ +++. +++++|.|
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~--~---~v~~~~~~~n~~~~~~~~~f~~~--------~~~~--g~~ivgi~ 65 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKD--G---VITELLILPGTESGEVSAVFPLL--------MLPL--DMSIVGSV 65 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeec--c---EEEEEEECCCCCCCCcceeechH--------HhcC--CCeEEEEE
Confidence 46788999999999999999999999974 2 58999999987654333223331 2333 47999999
Q ss_pred ccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCC
Q psy15735 273 HSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQ 309 (574)
Q Consensus 273 HSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~ 309 (574)
||||+.+++||..|++.+ ..++.+++|+++..
T Consensus 66 HSHP~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~ 97 (117)
T cd08072 66 HSHPSGSPRPSDADLSFF-----SKTGLVHIIVGYPY 97 (117)
T ss_pred EcCCCCCCCCCHHHHHhh-----hcCCCEEEEEECcC
Confidence 999999999999998743 35889999999643
No 25
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.57 E-value=8.3e-15 Score=130.38 Aligned_cols=95 Identities=22% Similarity=0.163 Sum_probs=77.8
Q ss_pred HHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCC-CcccccHHHHHHHHHHHHhcCCCCcEEEEEccC
Q psy15735 197 ALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGV-SVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSH 275 (574)
Q Consensus 197 vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~-~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSH 275 (574)
++.+|++||+++.|.|+||+|+|.. .++.++|++|...++ ..+.+||+++.++.+ .+ .+||.||||
T Consensus 2 i~~~i~~ha~~~~P~E~CGll~g~~------~~~~~~p~~N~~~~p~~~F~idp~e~~~a~~----~~---~ivgi~HSH 68 (108)
T cd08073 2 LEDAILAHAKAEYPREACGLVVRKG------RKLRYIPCRNIAADPEEHFEISPEDYAAAED----EG---EIVAVVHSH 68 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecC------CceEEEECccCCCCccceEEeCHHHHHHHhc----CC---CEEEEEEcC
Confidence 5678999999999999999999963 256779999887665 457799988876552 23 899999999
Q ss_pred CCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCC
Q psy15735 276 PGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQ 309 (574)
Q Consensus 276 P~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~ 309 (574)
|+.++.||..|++.+ ..++.+++|++...
T Consensus 69 P~~~a~PS~~D~~~~-----~~~~~~~iIvs~~~ 97 (108)
T cd08073 69 PDGSPAPSEADRAQQ-----EATGLPWIIVSWPE 97 (108)
T ss_pred CCCCCCCCHHHHHHh-----hcCCCcEEEEEcCC
Confidence 999999999999732 35789999999753
No 26
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.52 E-value=1.5e-13 Score=132.96 Aligned_cols=112 Identities=24% Similarity=0.298 Sum_probs=94.9
Q ss_pred ECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHH---HHHHHHHHHhcCCCCcEE
Q psy15735 193 ISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVF---QAKMLDMLKQTGRPEMVV 269 (574)
Q Consensus 193 Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~---q~~ml~~lr~~g~~~~vV 269 (574)
|+..++.||+.||.+..|.||||+|+|....+.++.|++++|+.+.. +.++|.. +.++.+.+++.| +.+|
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~-----~~l~P~~Eval~~ve~~~~~~g--l~Iv 73 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHSC-----LALAPMLEVALALVDAYCKSSG--LVIV 73 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCCc-----cccCHHHHHHHHHHHHHHHHCC--CEEE
Confidence 57889999999999988889999999997534578999999999842 4688985 778889999866 6999
Q ss_pred EEEccCCCCC-CcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCc
Q psy15735 270 GWYHSHPGFG-CWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311 (574)
Q Consensus 270 GWYHSHP~~~-~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~ 311 (574)
|+|||||.++ ..|+.+-.......+...+.++.+++|-.+-.
T Consensus 74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~ 116 (182)
T cd08060 74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLT 116 (182)
T ss_pred EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcccc
Confidence 9999999875 57888888888888888899999999986653
No 27
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.52 E-value=8.3e-14 Score=128.36 Aligned_cols=104 Identities=30% Similarity=0.435 Sum_probs=78.2
Q ss_pred EEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCC-cccccHHHHHHHHHHHHhcCCCCcEE
Q psy15735 191 VYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVS-VEAVDPVFQAKMLDMLKQTGRPEMVV 269 (574)
Q Consensus 191 V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~-~~~idp~~q~~ml~~lr~~g~~~~vV 269 (574)
+.|+..++..|+.||++++|.|+||+|.|.... ...+++++...+.. .+.+++++.. +...++..| +.+|
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~------~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~g--~~vv 72 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG------ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDAG--EVVV 72 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc------ceeeccccccCCcceeEeeCHHHHH-HHHHHhhCC--CEEE
Confidence 568899999999999999999999999998642 55667777655433 2456777665 666666655 8999
Q ss_pred EEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcC
Q psy15735 270 GWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDP 307 (574)
Q Consensus 270 GWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp 307 (574)
|||||||+.+++||..|++. +...+....||+.+
T Consensus 73 g~yHSHP~~~~~pS~~D~~~----~~~~~~~~~iv~~~ 106 (134)
T COG1310 73 GWYHSHPGGPPYPSEADRRL----SKLGPLPWLIVSVP 106 (134)
T ss_pred EEEcCCCCCCCCcCHHHHhh----ccccCCCEEEEEcC
Confidence 99999999999999999982 33344434444443
No 28
>KOG2975|consensus
Probab=99.49 E-value=3.8e-14 Score=140.25 Aligned_cols=129 Identities=22% Similarity=0.356 Sum_probs=110.0
Q ss_pred CccEEEECHHHHHHHHHHHhc--CCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCC
Q psy15735 187 TAEQVYISSLALLKMLKHGRA--GVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGR 264 (574)
Q Consensus 187 ~~~~V~Is~~vllkIl~Ha~~--~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~ 264 (574)
..-+|.|+|.++.+|++|..+ .....|+|.|+|... ++.++|||||++|+.+.+++++ +|.+|..+|++..++++.
T Consensus 19 s~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~-~g~ieitNCFaVPhnEssdqve-vdm~y~~~M~~l~~k~np 96 (288)
T KOG2975|consen 19 SNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVD-KGSVEVTNCFAVPHNESSDQVE-VDMEYAKNMYELHKKVNP 96 (288)
T ss_pred CCceEEEcceEEeEeehhhhcCCccchhhhhheeeccc-CCeEEEEEeeeccCccccccce-eeHHHHHHHHHHhcccCC
Confidence 345899999999999999743 345689999999985 5799999999999998888886 899999999999999999
Q ss_pred CCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCchhHH-HHHHHH
Q psy15735 265 PEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKELA-KHYNKA 321 (574)
Q Consensus 265 ~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~rLs-~~y~~~ 321 (574)
++.+||||-+.++.+...|-+ |..|-+-.+++|+|.+|..-+.+|++ +.|.+.
T Consensus 97 nE~vvGWyaTg~dvt~~ssli----hdyYare~~~pvhLtVDT~~~n~rm~ikaYvss 150 (288)
T KOG2975|consen 97 NELVVGWYATGHDVTEHSSLI----HDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSS 150 (288)
T ss_pred CceeEEEEecCCCcccchhHH----HHHhhccCCCCeEEEEeccccCCccceeEEEEe
Confidence 999999999999887766653 77888889999999999988877665 555543
No 29
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.34 E-value=6.5e-12 Score=110.00 Aligned_cols=93 Identities=27% Similarity=0.360 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHH-HHHhcCCCCcEEEEEc
Q psy15735 195 SLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLD-MLKQTGRPEMVVGWYH 273 (574)
Q Consensus 195 ~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~-~lr~~g~~~~vVGWYH 273 (574)
..++.+|++|++++.|.|+||+|+|...+ ....++...+ .+|..+.++.. .+.+.+ ..+||+||
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~-~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~--~~~vg~~H 66 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDD-QRFIVVPNVN------------PDPRDSFRRERFEARERG--LEIVGIWH 66 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEEC-CEEEEEEEEE--------------HHCHHHHHH-HHHHHT---EEEEEEE
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecC-CEEEEEeCCC------------CCcHHHHHHHhhhhhccc--ceeeEEEE
Confidence 46889999999999999999999999743 3555555443 34555555555 555544 69999999
Q ss_pred cCCCCCCcCCHHHHHHHHHHHhcCC-CeEEEEEcC
Q psy15735 274 SHPGFGCWLSGVDINTQQSFEALSE-RAVAVVVDP 307 (574)
Q Consensus 274 SHP~~~~~pS~~Di~tq~~yQ~~~p-~~V~LIvDp 307 (574)
|||+.+++||.+|++.+. .. ..++||+..
T Consensus 67 SHP~~~a~pS~~D~~~~~-----~~~~~~~iI~~~ 96 (104)
T PF14464_consen 67 SHPSGPAFPSSTDIRSMR-----DLAPPSYIIVGN 96 (104)
T ss_dssp EESSSSSS--HHHHHTHC-----CS-SCEEEEEEE
T ss_pred cCCCCCCCCCHHHHHhhh-----ccCCeEEEEEeC
Confidence 999999999999998642 22 788888875
No 30
>KOG2880|consensus
Probab=99.31 E-value=1.1e-12 Score=134.50 Aligned_cols=122 Identities=21% Similarity=0.388 Sum_probs=101.9
Q ss_pred ccEEEECHHHHHHHHHHHhcC--CCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCC
Q psy15735 188 AEQVYISSLALLKMLKHGRAG--VPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRP 265 (574)
Q Consensus 188 ~~~V~Is~~vllkIl~Ha~~~--~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~ 265 (574)
...|+|+.......++-|+++ ...|.||+|.|.... +.+.||++..-.++++++.|..+++++..++. .+ .+
T Consensus 251 lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~-n~f~IThliiPkQeatsd~C~t~neeelF~vQ---dq--~~ 324 (424)
T KOG2880|consen 251 LRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLER-NEFYITHLIIPKQEATSDSCNTMNEEELFEVQ---DQ--HE 324 (424)
T ss_pred ceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhc-CcEEEEEEEeecccCCCccccccCHHHHheec---cc--cc
Confidence 677999999999999999875 456999999998754 47899999877788888888877775443333 23 34
Q ss_pred CcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCch---hHH
Q psy15735 266 EMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVK---ELA 315 (574)
Q Consensus 266 ~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~~---rLs 315 (574)
+-.+||-|+||..+||.|++|++||++||.|.|+++++|++|..... ||+
T Consensus 325 L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~~tGiFrLt 377 (424)
T KOG2880|consen 325 LLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSKTTGIFRLT 377 (424)
T ss_pred ceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccCCcceEEec
Confidence 78999999999999999999999999999999999999999975543 665
No 31
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.23 E-value=1.2e-12 Score=117.33 Aligned_cols=109 Identities=29% Similarity=0.386 Sum_probs=13.2
Q ss_pred CCCcccccccCccCcchHHHHHhhcCCcceeeEEeeeCCHHHHHHHhhcccCCccCCCCccCh----HHHhhhhHHHHHH
Q psy15735 28 QEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDY----NEHCKLNEGTVND 103 (574)
Q Consensus 28 ~eprqttsn~g~l~kp~~~a~~~gl~r~yys~~i~~~~~~~e~~ml~~l~k~~w~~~l~~~~~----~~~~~~n~~~~~~ 103 (574)
+||||+ ++.+++||++++||| +|. ++.+-+++||.+||++.|..+.-++++ .+.+..+...+.+
T Consensus 1 eEaEri----------gv~~l~~~~~~~~~s-~~~-~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~ 68 (115)
T PF13012_consen 1 EEAERI----------GVDHLARGLGDHYYS-SLS-SQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQD 68 (115)
T ss_dssp SHHHHH----------HHHHHHHH--S-----------------------------------------------------
T ss_pred CchHHH----------HHHHHHccCCCcccc-HHH-HHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHH
Confidence 478888 899999999999999 999 999999999999999999999999999 7888888999999
Q ss_pred HHHHHHHH-HHHHHHHhcC-CHhHHhhhhcCCCChhhhHHHHHHHHhhhh
Q psy15735 104 MLELAKHY-NKALEEEEKM-SPEQLAIKNVGKQDPKRHLEEKVDTLMTAN 151 (574)
Q Consensus 104 ~~~l~~~y-~~~~~ee~~~-~~~~~~~~~vgk~d~k~hl~~~~~~~~~~n 151 (574)
++.++..| .+.+++|... +.+++.+.++|+++++.| .+.+++++|
T Consensus 69 l~~~lp~~~~~~~~~~~~~~~~D~l~v~yL~~l~k~~~---~l~e~l~~~ 115 (115)
T PF13012_consen 69 LLSSLPKYDPEEFEEEFNSEINDVLMVSYLAKLTKKQH---ALNELLNNN 115 (115)
T ss_dssp --------------------------------------------------
T ss_pred HHHhcccccHHHHHHHHHhhchHHHHHHHHHHHhHHHH---HHHHHHhcC
Confidence 99999999 9999888877 789999999999999999 566776655
No 32
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.23 E-value=2.5e-11 Score=121.16 Aligned_cols=137 Identities=18% Similarity=0.138 Sum_probs=103.3
Q ss_pred ccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhh
Q psy15735 342 DPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVR 413 (574)
Q Consensus 342 DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~ 413 (574)
.+|+.++ ++|+|.|++|+++||+ +|+.+|+++|+.||+++++++++.+..+.. . + .++
T Consensus 67 ~~w~lit---~~FlH~~~~Hll~N~~~l~~fg~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~-------~-~---~~~ 132 (228)
T COG0705 67 QLWRLIT---AIFLHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGP-------K-G---GAP 132 (228)
T ss_pred chHHHHH---HHHHHhhHHHHHHHHHHHHHhhHHHHHHhchhHHHHHHHHHHHHHHHHHHHHcc-------c-c---cCc
Confidence 6777777 9999999999999999 899999999999999999999888444321 1 1 157
Q ss_pred ccChhHHHHHHHHHHHhhcCCceeecccc-ccccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHhhccC
Q psy15735 414 IHGLTGYISGVLVAVKQIMPDHVILNTGL-GKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRFYQYH 492 (574)
Q Consensus 414 i~G~~g~i~G~LVA~kQl~Pd~~il~~~~-~~ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLRf~q~~ 492 (574)
..|+||+++|++-|+-.+.|...+....+ ++..+..+-.+.++.+++....+...++++++|++|++.|++|..++.+.
T Consensus 133 ~~GASG~i~gllga~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~~ 212 (228)
T COG0705 133 SLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSRK 212 (228)
T ss_pred ccchhHHHHHHHHHHHHHccccchhhhhccCchhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 88999999999999999999987654433 34444333333333333333222223689999999999999999888764
No 33
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=99.15 E-value=8.5e-11 Score=113.78 Aligned_cols=100 Identities=17% Similarity=0.113 Sum_probs=77.9
Q ss_pred EECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEE
Q psy15735 192 YISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGW 271 (574)
Q Consensus 192 ~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGW 271 (574)
.|+...+.+|+.||+++.|.|+||++.|.. ++ .+..++|+.|...++..+.+|+..+ ..++.+|+.
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~-~~---~~~r~~p~~N~~~Sp~~~~~d~~~~----------~~ge~lV~i 139 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNS-ET---GSLRLAALESIEASPGHIDYRRPRL----------DDGEHLVVD 139 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcC-CC---CEEEEEeccccccCCceEEEcchHH----------hCCCeEEEE
Confidence 789999999999999999999999999963 22 2456799999887777777888621 346899999
Q ss_pred EccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCC
Q psy15735 272 YHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS 310 (574)
Q Consensus 272 YHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s 310 (574)
|||||..+++||.+|++.= ...-.++.|+-...+
T Consensus 140 yHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~~ 173 (192)
T TIGR03735 140 LHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLDQ 173 (192)
T ss_pred EcCCCCCCCCCCcccchhh-----cCceEEEEEEEecCC
Confidence 9999999999999999741 122345666654433
No 34
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.04 E-value=1.3e-09 Score=95.54 Aligned_cols=92 Identities=25% Similarity=0.272 Sum_probs=70.1
Q ss_pred HHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEccCC
Q psy15735 197 ALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHP 276 (574)
Q Consensus 197 vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSHP 276 (574)
++..|..|++..+|.|+||+|+|... + .++++.++|+..- .+++.+ .+.+.+.| ..+||.|||||
T Consensus 2 ~~~~i~~~~~~~~p~E~~gll~~~~~-~---~~~~~~~~~~~~~-----~~~~~~----~~~a~~~~--~~~v~i~HsHP 66 (101)
T cd08059 2 LLKTILVHAKDAHPDEFCGFLSGSKD-N---VMDELIFLPFVSG-----SVSAVI----DLAALEIG--MKVVGLVHSHP 66 (101)
T ss_pred HHHHHHHHHHhcCChhhheeeecCCC-C---eEEEEEeCCCcCC-----ccChHH----HHHHhhCC--CcEEEEEecCc
Confidence 57789999999999999999999642 1 6788888886431 355654 34444444 58999999999
Q ss_pred CCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCC
Q psy15735 277 GFGCWLSGVDINTQQSFEALSERAVAVVVDPI 308 (574)
Q Consensus 277 ~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~ 308 (574)
+.++.||..|++... .+...++|++..
T Consensus 67 ~g~~~PS~~D~~~~~-----~~~~~~iIv~~~ 93 (101)
T cd08059 67 SGSCRPSEADLSLFT-----RFGLYHVIVCYP 93 (101)
T ss_pred CCCCCCCHHHHHHHH-----hcCCeEEEEECC
Confidence 999999999998542 247788888654
No 35
>PTZ00101 rhomboid-1 protease; Provisional
Probab=98.91 E-value=3e-09 Score=109.45 Aligned_cols=132 Identities=17% Similarity=0.145 Sum_probs=93.4
Q ss_pred CccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchh
Q psy15735 341 QDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFV 412 (574)
Q Consensus 341 ~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~ 412 (574)
..+||.++ +.|+|.+++|+++||+ +|+.||+.+|+..|+++++++++++..+.. ..
T Consensus 100 gq~WRLiT---~~FlH~~~~HLl~Nm~~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~-------------~~ 163 (278)
T PTZ00101 100 GEIHRLIL---PIFLHANIFHTFFNVFFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVTY-------------CP 163 (278)
T ss_pred CCCHHHHH---HHHHccCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHcc-------------CC
Confidence 46788887 9999999999999988 899999999999999999999887755421 12
Q ss_pred hccChhHHHHHHHHHHHhhcCCceeeccccccccchhHHHHH--HHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHhhc
Q psy15735 413 RIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLV--ILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRFYQ 490 (574)
Q Consensus 413 ~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~--ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLRf~q 490 (574)
...|+||+++|++-|+...+ ++.+...+.|.+.++.+. +++.+++.+.....+++.++|++|++.|++.--+|.
T Consensus 164 ~svGASgAifGLiGa~~~~l----il~w~~~~~~~~~~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~ 239 (278)
T PTZ00101 164 IKVGASTSGMGLLGIVTSEL----ILLWHVIRHRERVVFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYN 239 (278)
T ss_pred cEEehhHHHHHHHHHHHHHH----HHHHHhhccHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHH
Confidence 35799999999999987432 112222333444443222 122222222222467889999999999998888887
Q ss_pred cC
Q psy15735 491 YH 492 (574)
Q Consensus 491 ~~ 492 (574)
++
T Consensus 240 ~~ 241 (278)
T PTZ00101 240 SQ 241 (278)
T ss_pred hh
Confidence 64
No 36
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.89 E-value=2.6e-08 Score=97.76 Aligned_cols=115 Identities=22% Similarity=0.268 Sum_probs=91.8
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcCCc-eEEEEEEEeCCcccCCCCcccccHHH---HHHHHHHHHhcCCC
Q psy15735 190 QVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEY-TVRVIDVFAMPQTGTGVSVEAVDPVF---QAKMLDMLKQTGRP 265 (574)
Q Consensus 190 ~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~-~l~Vt~~fp~p~~~~~~~~~~idp~~---q~~ml~~lr~~g~~ 265 (574)
+|.|+..++.||+-||.+.....|+|+|+|...+++ .+.|+||+|+-+... .+.|.- ..++..++++.|
T Consensus 3 ~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~-----~L~PmlEvAL~qvd~~~~~~g-- 75 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWL-----SLSPMLEVALAQVDAYAKSNG-- 75 (196)
T ss_pred eEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceecccccc-----CcchHHHHHHHHHHHHHhhCC--
Confidence 689999999999999998777899999999976544 399999999988543 244533 335556677655
Q ss_pred CcEEEEEccCCCCC-CcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCc
Q psy15735 266 EMVVGWYHSHPGFG-CWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311 (574)
Q Consensus 266 ~~vVGWYHSHP~~~-~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~ 311 (574)
+.|||+||....+. ..|+.+-.+.........+.++.+++|..+-.
T Consensus 76 l~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~ 122 (196)
T PF03665_consen 76 LVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLS 122 (196)
T ss_pred CEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccc
Confidence 79999999998654 67888888888777778999999999986554
No 37
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=98.76 E-value=1.4e-07 Score=86.56 Aligned_cols=109 Identities=14% Similarity=0.102 Sum_probs=71.5
Q ss_pred HHHHHHHHhc-CCCceEEEEeeeEEcCCceEEEEEEE-eCCcccCCCCccccc-HHHHHHHHHHHHhcCCCCcEEEEEcc
Q psy15735 198 LLKMLKHGRA-GVPMEVMGLMLGEFVDEYTVRVIDVF-AMPQTGTGVSVEAVD-PVFQAKMLDMLKQTGRPEMVVGWYHS 274 (574)
Q Consensus 198 llkIl~Ha~~-~~p~Ev~GlLlG~~~~~~~l~Vt~~f-p~p~~~~~~~~~~id-p~~q~~ml~~lr~~g~~~~vVGWYHS 274 (574)
+..|..|.+. ..|.|.||+|+|...+ ..+.|+++. |.|....+...+.-+ +..|....+..++.+.....||-|||
T Consensus 3 ~~~~~~~~Q~~~~~~EtGGiLiG~~~~-~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHt 81 (131)
T TIGR02256 3 VAMLKSYRQWHDLSTETGGVLIGERRG-AHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHT 81 (131)
T ss_pred HHHHHHHHhCcCCCCccceEEEEEEcC-CcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCc
Confidence 3344444443 4688999999999865 477777766 344322111122223 33455666666666655899999999
Q ss_pred CCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcC
Q psy15735 275 HPGFGCWLSGVDINTQQSFEALSERAVAVVVDP 307 (574)
Q Consensus 275 HP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp 307 (574)
||...+.||.+|..+....-+.....+.||+.-
T Consensus 82 HP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG~ 114 (131)
T TIGR02256 82 HPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVGR 114 (131)
T ss_pred CCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEcC
Confidence 999999999999998766544344556666654
No 38
>KOG3050|consensus
Probab=98.63 E-value=8.2e-08 Score=94.69 Aligned_cols=122 Identities=19% Similarity=0.334 Sum_probs=97.6
Q ss_pred CCCCccEEEECHHHHHHHHHHHh-----cCCCc-eEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHH
Q psy15735 184 VVDTAEQVYISSLALLKMLKHGR-----AGVPM-EVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLD 257 (574)
Q Consensus 184 ~~~~~~~V~Is~~vllkIl~Ha~-----~~~p~-Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~ 257 (574)
......+|.++|+|+++|.+|.. .+.|. .|.|.++|... +++++|.|+|.+.....+. .+.+|-+|..+-.+
T Consensus 4 s~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~-GR~vEi~NSFeL~~d~~~~-~~~~dke~l~kk~e 81 (299)
T KOG3050|consen 4 SSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQR-GRNVEIMNSFELKMDTEED-TETIDKEYLEKKEE 81 (299)
T ss_pred CCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheeccc-CceEEEeeeeEEEecchhh-hhhccHHHHHHHHH
Confidence 34456799999999999999973 36777 89999999875 5799999999987543322 23578899988899
Q ss_pred HHHhcCCCCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEEEEcCCCCc
Q psy15735 258 MLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSV 311 (574)
Q Consensus 258 ~lr~~g~~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~~s~ 311 (574)
..+++-+++.++|||.+.. .|...|+..|...-..++.+++|-.+|....
T Consensus 82 qykqVFpdl~vlGwYttG~----d~t~sd~~i~k~l~~i~esplflkLNp~t~~ 131 (299)
T KOG3050|consen 82 QYKQVFPDLYVLGWYTTGS----DPTPSDIHIHKQLMDINESPLFLKLNPATNH 131 (299)
T ss_pred HHHHhcccceEEEEeecCC----CCChhhhHHHHHHHhhhcCceEEEecchhcc
Confidence 9999999999999999874 3466678888777677888999999985543
No 39
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=98.61 E-value=5.3e-07 Score=91.20 Aligned_cols=126 Identities=17% Similarity=0.162 Sum_probs=97.2
Q ss_pred cEEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcC--CceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCC
Q psy15735 189 EQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD--EYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPE 266 (574)
Q Consensus 189 ~~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~--~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~ 266 (574)
.++.|+..++.|.+.-|.. ..++||.|.|.... ++..+|+.+.-.||.++.+.+...+...+ .+.+ .++
T Consensus 36 ~t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~~~---~~~l----~~L 106 (252)
T cd08056 36 YTYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQ---HEYL----EDL 106 (252)
T ss_pred CEEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccCcc---chhh----CCC
Confidence 5899999999999999865 45999999998543 24678998888999998877752221111 1111 247
Q ss_pred cEEEEEccCCCCCCcCCHHHHHHHHHHHhcCC-----CeEEEEEcCCCCch-----hHHHHHHHHhh
Q psy15735 267 MVVGWYHSHPGFGCWLSGVDINTQQSFEALSE-----RAVAVVVDPIQSVK-----ELAKHYNKALE 323 (574)
Q Consensus 267 ~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p-----~~V~LIvDp~~s~~-----rLs~~y~~~~~ 323 (574)
+.+||-|+||.-.+++|+.|+.+|+.||+..| ++|.++|++..+.- +|++.=.+|..
T Consensus 107 e~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT~~G~~wg~ 173 (252)
T cd08056 107 EPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLTPEGYEWGK 173 (252)
T ss_pred EeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecCHHHHHHHH
Confidence 99999999999889999999999999999887 79999999985432 77765566653
No 40
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=98.60 E-value=2.1e-07 Score=95.99 Aligned_cols=126 Identities=17% Similarity=0.138 Sum_probs=84.5
Q ss_pred CccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchh
Q psy15735 341 QDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFV 412 (574)
Q Consensus 341 ~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~ 412 (574)
..+||.++ ++|+|.++.|+++||+ +|+.+|++.|+.+|+++++++++++..+ . . .
T Consensus 133 ~q~WRl~T---~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~~~~~~-------~--~-----~ 195 (276)
T PRK10907 133 FELWRYFT---HALLHFSLLHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGWVQSKF-------S--G-----P 195 (276)
T ss_pred CCcHHHHh---HHHHhCCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH-------c--c-----c
Confidence 45677776 9999999999999999 7999999999999999999888775432 1 1 2
Q ss_pred hccChhHHHHHHHHHHH---hhcCCceeeccccccccchhHHHHHHHHHHHHHHHhh-cCchhHHHHHHHHHHHHHHHHh
Q psy15735 413 RIHGLTGYISGVLVAVK---QIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGL-VDSIRPTMTLFGTLVSWIYLRF 488 (574)
Q Consensus 413 ~i~G~~g~i~G~LVA~k---Ql~Pd~~il~~~~~~ir~K~lP~i~ll~~~~l~~~~~-~~~~a~~~~~~G~~~sWiYLRf 488 (574)
.+.|+||+++|++...- ...|+..+. ++... ++++++-+++++.++ ..+++.++|++|+++|.+.--+
T Consensus 196 ~~gGaSGvVygL~g~~~~~~~~~p~~~~~------lp~~~--~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~ 267 (276)
T PRK10907 196 WFGGLSGVVYALMGYVWLRGERDPQSGIY------LPRGL--IAFALLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFW 267 (276)
T ss_pred hhhHHHHHHHHHHHHHHHHhccccccchh------hhHHH--HHHHHHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHH
Confidence 35799999999887532 223332211 00111 111222222333332 3578999999999998876555
Q ss_pred hcc
Q psy15735 489 YQY 491 (574)
Q Consensus 489 ~q~ 491 (574)
..+
T Consensus 268 ~~~ 270 (276)
T PRK10907 268 DTR 270 (276)
T ss_pred hhh
Confidence 443
No 41
>PF01694 Rhomboid: Rhomboid family; InterPro: IPR022764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of proteins contain serine peptidases belonging to the MEROPS peptidase family S54 (Rhomboid, clan ST). They are integral membrane proteins related to the Drosophila melanogaster (Fruit fly) rhomboid protein P20350 from SWISSPROT. Members of this family are found in archaea, bacteria and eukaryotes. The D. melanogaster rhomboid protease cleaves type-1 transmembrane domains using a catalytic triad composed of serine, histidine and asparagine contributed by different transmembrane domains. It cleaves the transmembrane proteins Spitz, Gurken and Keren within their transmembrane domains to release a soluble TGFalpha-like growth factor. Cleavage occurs in the Golgi, following translocation of the substrates from the endoplasmic reticulum membrane by Star, another transmembrane protein. The growth factors are then able to activate the epidermal growth factor receptor [, ]. Few substrates of mammalian rhomboid homologues have been determined, but rhomboid-like protein 2 (MEROPS S54.002) has been shown to cleave ephrin B3 []. Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite. In Saccharomyces cerevisiae (Baker's yeast) the Pcp1 (MDM37) protein (MEROPS S54.007) is a mitochondrial endopeptidase required for the activation of cytochrome c peroxidase and for the processing of the mitochondrial dynamin-like protein Mgm1 [, ]. Mutations in Pcp1 result in cells have fragmented mitochondria, which have very few short tubulues []. This entry represents the 6 transmembrane helix rhomboid domain.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=98.57 E-value=1.7e-08 Score=92.98 Aligned_cols=133 Identities=20% Similarity=0.201 Sum_probs=88.0
Q ss_pred CccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchh
Q psy15735 341 QDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFV 412 (574)
Q Consensus 341 ~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~ 412 (574)
...||.++ +.|+|.|+.|++.|++ +|+.+|++.++..+++++++++++..++.-. ..
T Consensus 4 ~~~wrl~T---~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~~------------~~ 68 (145)
T PF01694_consen 4 GQWWRLFT---SPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSPP------------NQ 68 (145)
T ss_dssp C-TTHHHH---GGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S--------------
T ss_pred CcchhhhH---HHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhcccccccc------------cc
Confidence 34566665 9999999999999988 7999999999999998888887776555321 11
Q ss_pred hccChhHHHHHHHHHHHhhcCCceeeccccccccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHhhccC
Q psy15735 413 RIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRFYQYH 492 (574)
Q Consensus 413 ~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLRf~q~~ 492 (574)
+..|++|+++|++.++....|+....... +.....++.+++.+... .+....+++..|++|+++|+.|-..+.++
T Consensus 69 ~~~G~Sg~~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~---~~~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 69 PYVGASGAVFGLLGAFLFLYPQNKKRLRF--IYLALVVPIIVLVIILL---LGFIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp ---SSHHHHHHHHHHHHHHHHCCCCCS-----HCCCCCCCCCCCHHHC---TSSSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred ccCCCcccchHHHHHHHHHHhhccchhhc--chHHHHHHHHHHHHHHH---HHHHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 67899999999999999999998532211 11222222222222111 22245677888999999999988887765
Q ss_pred C
Q psy15735 493 T 493 (574)
Q Consensus 493 ~ 493 (574)
+
T Consensus 144 ~ 144 (145)
T PF01694_consen 144 P 144 (145)
T ss_dssp -
T ss_pred c
Confidence 3
No 42
>KOG2632|consensus
Probab=98.38 E-value=1.9e-06 Score=86.88 Aligned_cols=138 Identities=18% Similarity=0.196 Sum_probs=111.1
Q ss_pred CccchhhHHHHHHhhhhhHHHHHhhcc--------cccccc-cchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccch
Q psy15735 341 QDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWG-SMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFF 411 (574)
Q Consensus 341 ~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wG-s~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~ 411 (574)
.++||.....++.+.|.|..|+++||+ .|+..| +-.++-|..+.++.++++..+++.+. . -.++...
T Consensus 48 l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~---~-~~d~~~~ 123 (258)
T KOG2632|consen 48 LINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTTVRILMFTVLLALFSGILYLLAYHVF---L-LSDLVYV 123 (258)
T ss_pred hhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccceehHHHHHHHHHHHHHHHHHHHHHHH---h-hcchhhh
Confidence 467888888889999999999999999 699999 77777777788888888887776521 1 1233334
Q ss_pred hhccChhHHHHHHHHHHHhhcCCceeeccccccccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHH
Q psy15735 412 VRIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLR 487 (574)
Q Consensus 412 ~~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLR 487 (574)
...+|.+|.++|.+++-.-.-|.....++|.+.+..++.|.+++....++ ....+++-|++|+++|+.|.-
T Consensus 124 ~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~Pw~lLi~~~~l-----vp~aSFlghl~GllvG~ay~~ 194 (258)
T KOG2632|consen 124 EGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAPWALLIATQIL-----VPQASFLGHLCGLLVGYAYAF 194 (258)
T ss_pred cccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHHHHHHHHHHHH-----ccCchHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999998888999999999999986433222 355778899999999999976
No 43
>KOG3289|consensus
Probab=98.27 E-value=1.2e-05 Score=76.25 Aligned_cols=112 Identities=23% Similarity=0.308 Sum_probs=85.8
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEeeeEEcC-CceEEEEEEEeCCcccCCCCcccccHHHH---HHHHHHHHhcCCC
Q psy15735 190 QVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD-EYTVRVIDVFAMPQTGTGVSVEAVDPVFQ---AKMLDMLKQTGRP 265 (574)
Q Consensus 190 ~V~Is~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~-~~~l~Vt~~fp~p~~~~~~~~~~idp~~q---~~ml~~lr~~g~~ 265 (574)
.|+|+..++.||+-||.+....-|.|+|+|...+ ++.++|++|.|+-++.. ++.|.-+ ..+.....+.|
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~~l-----aLaPmlEvAl~lId~~~~~~G-- 75 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHSHL-----ALAPMLEVALNLIDVWGAQAG-- 75 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhcccc-----ccccHHHHHHHHHHHHHHhcC--
Confidence 5899999999999999987667899999996532 35899999999987654 3444322 22234445555
Q ss_pred CcEEEEEccCCCCC-CcCCHHHHHHHHHHHhcCCCeEEEEEcCC
Q psy15735 266 EMVVGWYHSHPGFG-CWLSGVDINTQQSFEALSERAVAVVVDPI 308 (574)
Q Consensus 266 ~~vVGWYHSHP~~~-~~pS~~Di~tq~~yQ~~~p~~V~LIvDp~ 308 (574)
..++|+||+...+. ..|...-.+.....+...|.+..|++|..
T Consensus 76 lviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~ 119 (199)
T KOG3289|consen 76 LVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNK 119 (199)
T ss_pred eEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEecc
Confidence 69999999987755 56777777777778888999999999986
No 44
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.01 E-value=0.00018 Score=74.29 Aligned_cols=135 Identities=16% Similarity=0.248 Sum_probs=103.7
Q ss_pred CCccEEEECHHHHHHHHHH-HhcCCCceEEEEeeeEEcCC------ceEEEEEEEeCCcccCCCCcccccHHHHHHHHHH
Q psy15735 186 DTAEQVYISSLALLKMLKH-GRAGVPMEVMGLMLGEFVDE------YTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDM 258 (574)
Q Consensus 186 ~~~~~V~Is~~vllkIl~H-a~~~~p~Ev~GlLlG~~~~~------~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~ 258 (574)
+.+..|..+......-... ..+.....-||+|.|...++ ....|.-+|.-|+.++.+.+..++...+.++.+.
T Consensus 8 r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~i 87 (274)
T cd08061 8 RHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAI 87 (274)
T ss_pred CCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHH
Confidence 4567888887777766666 54555678899999998654 2578888889999888777664443444556667
Q ss_pred HHhcCCCCcEEEEEccCCCC----CCcCCHHHHHHHHHHHh------cCCCeEEEEEcCCCCch------hHHHHHHHHh
Q psy15735 259 LKQTGRPEMVVGWYHSHPGF----GCWLSGVDINTQQSFEA------LSERAVAVVVDPIQSVK------ELAKHYNKAL 322 (574)
Q Consensus 259 lr~~g~~~~vVGWYHSHP~~----~~~pS~~Di~tq~~yQ~------~~p~~V~LIvDp~~s~~------rLs~~y~~~~ 322 (574)
++..| ++.|||-.||+.- +.++|+.++..++.+|. ..+++|-+|+++..... .+|++-++.+
T Consensus 88 A~~lG--L~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSdq~~~lv 165 (274)
T cd08061 88 AAALG--LERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSDQAMALV 165 (274)
T ss_pred HHHcC--CeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecHHHHHHH
Confidence 77766 7999999999976 67999999999999995 56789999999975543 6788777776
No 45
>KOG2290|consensus
Probab=97.60 E-value=6.9e-05 Score=80.21 Aligned_cols=157 Identities=20% Similarity=0.315 Sum_probs=102.0
Q ss_pred cCCccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccc
Q psy15735 339 GKQDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLF 410 (574)
Q Consensus 339 g~~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~ 410 (574)
.-.+|.|..-+.++-|+|.+++|++.++. +|.+-|++.+.+.|+.+|+.+++.+.++ +.
T Consensus 444 n~e~PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAIF-------------lp 510 (652)
T KOG2290|consen 444 NPEVPDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAIF-------------LP 510 (652)
T ss_pred CCCChhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchheee-------------ec
Confidence 35678999888999999999999987766 7999999999999999999998876553 22
Q ss_pred hhhccChhHHHHHHHHHHH-hhcCCceeeccccccccchhHHHHHHHHH-HHHHHHhhcCchhHHHHHHHHHHHHHH-HH
Q psy15735 411 FVRIHGLTGYISGVLVAVK-QIMPDHVILNTGLGKMTNRNIPLLVILIA-SILWLIGLVDSIRPTMTLFGTLVSWIY-LR 487 (574)
Q Consensus 411 ~~~i~G~~g~i~G~LVA~k-Ql~Pd~~il~~~~~~ir~K~lP~i~ll~~-~~l~~~~~~~~~a~~~~~~G~~~sWiY-LR 487 (574)
+-+-+|-+|.++|+|.++- .++-.-.|+- -||--++-++.. ++|+ +|+...+.-|+|++|+++|-+. .-
T Consensus 511 Y~~eVgPa~sQ~Gila~l~vEl~qs~~il~-------~~w~a~~~Lia~~L~L~-iGliPWiDN~aHlfG~i~GLl~s~~ 582 (652)
T KOG2290|consen 511 YRAEVGPAGSQFGILACLFVELFQSWQILE-------RPWRAFFHLIATLLVLC-IGLIPWIDNWAHLFGTIFGLLTSII 582 (652)
T ss_pred cccccCCcccccchHHHHHHHHHhhhHhhh-------hHHHHHHHHHHHHHHHH-hccccchhhHHHHHHHHHHHHHHHH
Confidence 3456788899999887653 3443334331 134223332222 2333 4766666667778887777442 22
Q ss_pred hhccCCCCccCCcccCccccccCCccCcchhHhhhhHHHHHH
Q psy15735 488 FYQYHTNGTRGDMADNFNFANFFPTIIQPPIAVVCNTIHEFL 529 (574)
Q Consensus 488 f~q~~~~~~rGD~Sd~Faf~~FFP~~~~p~i~~i~~~~~~~l 529 (574)
||.+- .-||. |-.. +...-.||.++|..|
T Consensus 583 ~~PYi---~Fg~~-d~yr---------Kr~~ilIs~ivf~~L 611 (652)
T KOG2290|consen 583 FLPYI---DFGDF-DLYR---------KRFYILISQIVFSGL 611 (652)
T ss_pred hhccc---cccch-hhhh---------hHHHHHHHHHHHHHH
Confidence 23321 23441 1111 446677888888754
No 46
>KOG2289|consensus
Probab=97.49 E-value=5.7e-05 Score=79.00 Aligned_cols=76 Identities=21% Similarity=0.216 Sum_probs=64.2
Q ss_pred ccCCccchhhHHHHHHhhhhhHHHHHhhcc--------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCccc
Q psy15735 338 VGKQDPKRHLEEKVDTLMTANIIQCLGGKL--------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLL 409 (574)
Q Consensus 338 vg~~DP~~~Le~~v~~fm~~nI~~~l~~mL--------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l 409 (574)
+-..--||.++ ++++|.+++|+++||+ +|...|..++..-|++.+++.++++.++ +.
T Consensus 114 ~~r~E~WRllT---ym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~---------d~--- 178 (316)
T KOG2289|consen 114 VHRGELWRLLT---YMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLF---------DP--- 178 (316)
T ss_pred hhhchhHHHHH---HHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHh---------cc---
Confidence 34456688888 9999999999999998 7999999999999999999888888775 22
Q ss_pred chhhccChhHHHHHHHHHHH
Q psy15735 410 FFVRIHGLTGYISGVLVAVK 429 (574)
Q Consensus 410 ~~~~i~G~~g~i~G~LVA~k 429 (574)
..+.+|+||+++|++-|.-
T Consensus 179 -~~~sVGASggvfaLlgA~L 197 (316)
T KOG2289|consen 179 -NSISVGASGGVFALLGAHL 197 (316)
T ss_pred -CCceecccHHHHHHHHHHH
Confidence 2457899999999998864
No 47
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=96.70 E-value=0.02 Score=60.08 Aligned_cols=107 Identities=15% Similarity=0.236 Sum_probs=82.3
Q ss_pred EEEeeeEEcCCc------eEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEccCCC----------
Q psy15735 214 MGLMLGEFVDEY------TVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPG---------- 277 (574)
Q Consensus 214 ~GlLlG~~~~~~------~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSHP~---------- 277 (574)
+|+|.|...+.. ...|.-+|..|+.++.+.+.-.+......+.+.++..| ++.|||-=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lG--L~rVG~IfTdl~~~~~~~g~v~ 79 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALG--LERVGWIFTDLTDDGSGDGTVK 79 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCC--CEEEEEEEecCcccccCCCcee
Confidence 799999876533 46788888999988776665333345566777777766 799999999986
Q ss_pred -----CCCcCCHHHHHHHHHHHhcC-------------CCeEEEEEcCCCCch------hHHHHHHHHh
Q psy15735 278 -----FGCWLSGVDINTQQSFEALS-------------ERAVAVVVDPIQSVK------ELAKHYNKAL 322 (574)
Q Consensus 278 -----~~~~pS~~Di~tq~~yQ~~~-------------p~~V~LIvDp~~s~~------rLs~~y~~~~ 322 (574)
-+.++|+..+...+.+|... ..+|-+++++..+.. .+|.+.++.+
T Consensus 80 ~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~q~~~Lv 148 (306)
T PF05021_consen 80 CKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDEEGEIHFEAYQVSNQCVALV 148 (306)
T ss_pred eccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCCCCceeeEEeeehHHHHHHH
Confidence 55789999999999999743 457889999966544 6788888886
No 48
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=96.58 E-value=0.0065 Score=62.65 Aligned_cols=67 Identities=19% Similarity=0.294 Sum_probs=56.4
Q ss_pred CcCcEEEecccccCccccccCCCCcccccccCccCcchHHHHHhhcCCcceeeEEeeeCCHHHHHHHhhcccCCcc
Q psy15735 7 QLGKVVIDAFRLINPNMMVLGQEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWM 82 (574)
Q Consensus 7 ~kgkvvidafr~i~~~~~~~~~eprqttsn~g~l~kp~~~a~~~gl~r~yys~~i~~~~~~~e~~ml~~l~k~~w~ 82 (574)
..|++.|.|||+.+. .+.+- --|+++++++++.-.+.+..|+.|||..|.+.|++.||..|....=.
T Consensus 123 ~~g~l~lkAyrl~~~-~~~~~--------~~~~~~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~ 189 (266)
T cd08065 123 SQGSLSLKAYRLSEK-FMELY--------KEGKFSTESLREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPS 189 (266)
T ss_pred cccceeeEEEEEcHH-HHHHh--------hcCCcCHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCc
Confidence 369999999998554 33332 23899999999999999999999999999999999999999775443
No 49
>PF04511 DER1: Der1-like family; InterPro: IPR007599 The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER []. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Probab=96.19 E-value=0.027 Score=55.47 Aligned_cols=102 Identities=17% Similarity=0.240 Sum_probs=68.6
Q ss_pred cccc-ccc--chhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChhHHHHHHHHHHHhhcCCceeecccccc
Q psy15735 368 IEPL-WGS--MEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMPDHVILNTGLGK 444 (574)
Q Consensus 368 ~E~~-wGs--~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ 444 (574)
+|.. ++. .+|+.|++++++...+++.+.... .+..++. ..+....++=.+.+..|+.++-++|.++
T Consensus 73 LE~~~f~~~~ady~~~ll~~~~~i~~~~~~~~~~----------~~~~~~l-~~~l~~~l~Y~wsr~np~~~v~~~g~~~ 141 (197)
T PF04511_consen 73 LEEGHFQGRSADYLWFLLFGASLILILSLLIGPY----------FFNIPFL-GSSLSFALTYIWSRKNPNAQVSFFGLFT 141 (197)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHHhhccc----------hhHHHHH-HHHHHHHHHHHHHHhCcccceeeEEEEE
Confidence 4765 554 478888765554443333322110 0112232 3558888888999999999998888899
Q ss_pred ccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHH
Q psy15735 445 MTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYL 486 (574)
Q Consensus 445 ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYL 486 (574)
+|++|+|.+.++++.++ + + -+.+..+.|.++|-+|.
T Consensus 142 i~a~ylP~~~~~~~~l~---~-~--~~~~~~l~Gi~~Ghly~ 177 (197)
T PF04511_consen 142 IKAKYLPWVLLAFSLLF---G-G--SSPIPDLLGILVGHLYY 177 (197)
T ss_pred EChhhHHHHHHHHHHHh---C-C--CcHHHHHHHHHHHHHHH
Confidence 99999999988766543 2 1 13447899999998887
No 50
>KOG1554|consensus
Probab=94.49 E-value=0.047 Score=55.86 Aligned_cols=72 Identities=32% Similarity=0.459 Sum_probs=50.3
Q ss_pred cCcEEEecccccCccccccCCCCcccccccCccCcchHHHHHhhcC---CcceeeEEeeeCCHHHHHHHhhcccCCccCC
Q psy15735 8 LGKVVIDAFRLINPNMMVLGQEPRQTTSNLGHLQKHSVQALIHGLN---RHYYSISINYRKNELEQKMLLNLHKKTWMDG 84 (574)
Q Consensus 8 kgkvvidafr~i~~~~~~~~~eprqttsn~g~l~kp~~~a~~~gl~---r~yys~~i~~~~~~~e~~ml~~l~k~~w~~~ 84 (574)
-|||=|+|||+++-- --|+.+-+-.=.... -.-|.-+| +.|||+.|+|=|..++.+.|--|--+.|..-
T Consensus 178 agkv~iGAFRTyp~g-----yk~~d~~~seyqtip---l~kied~gvHck~yysl~isyfks~ld~kll~~Lwnkywv~T 249 (347)
T KOG1554|consen 178 AGKVNIGAFRTYPKG-----YKPPDEPPSEYQTIP---LNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKYWVRT 249 (347)
T ss_pred cCceeeceeecccCC-----CCCCCCCchhhhccc---hhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhhhhhcc
Confidence 499999999999863 334433322111111 12233343 5699999999999999999999999999876
Q ss_pred CCc
Q psy15735 85 LSL 87 (574)
Q Consensus 85 l~~ 87 (574)
|.=
T Consensus 250 lss 252 (347)
T KOG1554|consen 250 LSS 252 (347)
T ss_pred ccc
Confidence 543
No 51
>KOG0858|consensus
Probab=91.91 E-value=0.46 Score=47.94 Aligned_cols=64 Identities=19% Similarity=0.312 Sum_probs=51.0
Q ss_pred hHHHHHHHHHHHhhcCCceeeccccccccchhHHHHHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHh
Q psy15735 418 TGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASILWLIGLVDSIRPTMTLFGTLVSWIYLRF 488 (574)
Q Consensus 418 ~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ll~~~~l~~~~~~~~~a~~~~~~G~~~sWiYLRf 488 (574)
.+..+.++=.+.|..|+..+-++|.++++++|||.+.++++.+. | .+ . +..+.|+++|-+|.=+
T Consensus 121 ~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a~YlPwvll~fs~l~---g--~~-~-~~dllGi~~GHiy~fl 184 (239)
T KOG0858|consen 121 QSLVFMLVYVWSKRNPDVIVSFFGLITFKAPYLPWVLLGFSFLF---G--GS-I-LVDLLGIIVGHIYYFL 184 (239)
T ss_pred HHHHHHHHHHHHhhCCCceEEEEEEecCccccchHHHHHHHHHh---C--Cc-h-HHHHHhhhhheeEEEE
Confidence 45667777888999999999999999999999999998876643 2 22 2 5688999999887544
No 52
>COG5291 Predicted membrane protein [Function unknown]
Probab=90.36 E-value=0.19 Score=50.67 Aligned_cols=39 Identities=10% Similarity=0.225 Sum_probs=30.3
Q ss_pred HHHHHHHHhhcCCceeeccccccccchhHHHHHHHHHHH
Q psy15735 422 SGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLVILIASI 460 (574)
Q Consensus 422 ~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ll~~~~ 460 (574)
+.+.--+...-|+..|.++|.+++..||||++.+.++++
T Consensus 133 a~ItY~WS~~N~~~~Iqf~g~i~v~gkYlP~Illgfsfl 171 (313)
T COG5291 133 ATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSFL 171 (313)
T ss_pred hheeeeeeecCCceEEEEEEeeecchhhhhHHHHHHHHH
Confidence 333334455668888899999999999999999887764
No 53
>KOG2834|consensus
Probab=85.61 E-value=5.9 Score=43.51 Aligned_cols=111 Identities=19% Similarity=0.298 Sum_probs=77.7
Q ss_pred CccEEEEC-HHHHHHHHHHHhcCCCceEEEEeeeEEcCCceE------EEEEEEeCCcccCCCCcccccHHHHHHHHHHH
Q psy15735 187 TAEQVYIS-SLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTV------RVIDVFAMPQTGTGVSVEAVDPVFQAKMLDML 259 (574)
Q Consensus 187 ~~~~V~Is-~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l------~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~l 259 (574)
-+..|..+ +.++...++..|.. ...-.|.|.|...+.+.+ +|.-+|.-|+.++.+...-++...+..+.+.+
T Consensus 173 hvD~VeFd~~~~v~~Fl~~wr~s-g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a 251 (510)
T KOG2834|consen 173 HVDHVEFDNAELVNHFLNEWRAS-GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIA 251 (510)
T ss_pred ecceEeecchHHHHHHHHHHHHh-hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHH
Confidence 34455554 45566666666653 456679999998765555 78888999999888777644444555666666
Q ss_pred HhcCCCCcEEEEEcc----------------CCCCCCcCCHHHHHHHHHHHhcCCCeE
Q psy15735 260 KQTGRPEMVVGWYHS----------------HPGFGCWLSGVDINTQQSFEALSERAV 301 (574)
Q Consensus 260 r~~g~~~~vVGWYHS----------------HP~~~~~pS~~Di~tq~~yQ~~~p~~V 301 (574)
...| ++.|||--+ | .-+.++|+.++.+.+.+|...|+.+
T Consensus 252 ~~lG--LrRVG~IFTDl~~~~s~egtV~~~rh-kdsyFLSseE~~~aa~~Q~~hpn~~ 306 (510)
T KOG2834|consen 252 EGLG--LRRVGWIFTDLVTADSAEGTVHYKRH-KDSYFLSSEECITAAMFQNKHPNIC 306 (510)
T ss_pred HhcC--ceeeEEEEeeeecccCccceEEeeec-cchhcccHHHHHHHhhhhhcCCchh
Confidence 6655 799999643 2 2346899999999999998765543
No 54
>KOG2980|consensus
Probab=77.74 E-value=3.5 Score=43.13 Aligned_cols=37 Identities=11% Similarity=0.070 Sum_probs=29.5
Q ss_pred hhccChhHHHHHHHHHHHhhcCCceeeccccccccch
Q psy15735 412 VRIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNR 448 (574)
Q Consensus 412 ~~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K 448 (574)
.|-.|++|++++++..+.-++|+++.++....+.++-
T Consensus 221 gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~g 257 (310)
T KOG2980|consen 221 GPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAG 257 (310)
T ss_pred ccccccchHHHHHHHHHhhcCcCcceeEEEeeccccc
Confidence 4567999999999999999999998755445555553
No 55
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=70.42 E-value=7.2 Score=37.06 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHH-HHhhcCchhHHHHHHHHHHHHHHHHhhccC
Q psy15735 450 IPLLVILIASILW-LIGLVDSIRPTMTLFGTLVSWIYLRFYQYH 492 (574)
Q Consensus 450 lP~i~ll~~~~l~-~~~~~~~~a~~~~~~G~~~sWiYLRf~q~~ 492 (574)
+|++.+++..+++ .++..+..+.+..+.|+.+||.+.|+|.++
T Consensus 84 lPLl~li~ga~l~~~~~~~e~~~~~~~~~g~~~g~~~~r~~~~~ 127 (154)
T PRK10862 84 TPLVGLFLGAALFQLLFGSDLAALCGALLGGVGGFLLARGLSRK 127 (154)
T ss_pred HHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7777765543332 222234455667788999999999999875
No 56
>KOG4463|consensus
Probab=64.78 E-value=2.7 Score=43.13 Aligned_cols=100 Identities=15% Similarity=0.120 Sum_probs=65.8
Q ss_pred HHHHHhhhhhHHHHHhhcc-------cccccccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChhHHH
Q psy15735 349 EKVDTLMTANIIQCLGGKL-------IEPLWGSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYI 421 (574)
Q Consensus 349 ~~v~~fm~~nI~~~l~~mL-------~E~~wGs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~g~i 421 (574)
...++|.-.|-...+...+ +|+..||-+|+.|++..++.+-++..++.+++-..+.+.++ .+-.|.+
T Consensus 54 lL~~qF~~~n~~e~~~~l~I~Y~fR~~ERlLGShky~~fiv~s~~~~~l~~~il~~l~~~~~~nl~~------~qp~~li 127 (323)
T KOG4463|consen 54 LLMSQFAFSNTPELMFGLYILYYFRVFERLLGSHKYSVFIVFSGTVSLLLEVILLSLLKDTTANLLT------SQPYGLI 127 (323)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHHhccccceeehhHHHHHHHHHHHHHHHHHHHHHhhhhh------cCCCcee
Confidence 3346666555444443333 79999999999999999998888888887776666666443 3444577
Q ss_pred HHHHHHHHhhcCCceeeccccccccchhHHHHH
Q psy15735 422 SGVLVAVKQIMPDHVILNTGLGKMTNRNIPLLV 454 (574)
Q Consensus 422 ~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i~ 454 (574)
++.++-|--.+|-...+-...+++.-|+.-+++
T Consensus 128 Fa~~~~~y~~ip~~~f~r~f~~~f~dkni~~i~ 160 (323)
T KOG4463|consen 128 FASFIPFYLDIPVSTFFRVFGVNFSDKNISFIY 160 (323)
T ss_pred eeeccceEEEecceeEEEeecccccccceeeec
Confidence 777777777777665433333566666543444
No 57
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=64.54 E-value=10 Score=34.78 Aligned_cols=43 Identities=21% Similarity=0.413 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHH-HhhcCchhHHHHHHHHHHHHHHHHhhccC
Q psy15735 450 IPLLVILIASILWL-IGLVDSIRPTMTLFGTLVSWIYLRFYQYH 492 (574)
Q Consensus 450 lP~i~ll~~~~l~~-~~~~~~~a~~~~~~G~~~sWiYLRf~q~~ 492 (574)
+|++.+++..++.. ++..+..+....+.|+..+|.++|+|.++
T Consensus 77 lPll~li~g~~l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~~~~ 120 (135)
T PF04246_consen 77 LPLLALIAGAVLGSYLGGSELWAILGGLLGLALGFLILRLFDRR 120 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 67776655443321 22235566677888999999999999875
No 58
>PF15027 DUF4525: Domain of unknown function (DUF4525)
Probab=56.97 E-value=50 Score=30.47 Aligned_cols=67 Identities=22% Similarity=0.266 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCHhHHhhhhcCCCChhhhHHHHHHHHhhhhhHHHHhhHHHHHhhhc
Q psy15735 97 NEGTVNDMLELAKHYNKALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMTANIIQCLDRNMERLLRLG 167 (574)
Q Consensus 97 n~~~~~~~~~l~~~y~~~~~ee~~~~~~~~~~~~vgk~d~k~hl~~~~~~~~~~ni~q~l~~ml~~l~~~~ 167 (574)
..+--+.+++|++.|-|++.||.+-..+- -+.|-+-.=.-|+... ..+-|+|.|.|+..=..+..+.
T Consensus 40 s~~LR~QILdLSkrYVKaLAeEn~~~~dg---p~~~smagYaDLKkti-AVLLddiLqRl~kLE~kvd~lv 106 (138)
T PF15027_consen 40 SAELREQILDLSKRYVKALAEENKNVVDG---PYGASMAGYADLKKTI-AVLLDDILQRLVKLESKVDNLV 106 (138)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCCCCC---CcchhhHHHHHHhhhh-hhhhhHHHHHHHHHHHHHHHHe
Confidence 34555789999999999999997533221 1222222222233322 3456789999987766666654
No 59
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=50.09 E-value=1.9e+02 Score=25.83 Aligned_cols=77 Identities=19% Similarity=0.155 Sum_probs=43.5
Q ss_pred cCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEccCCCCCCcCCHHH
Q psy15735 207 AGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVD 286 (574)
Q Consensus 207 ~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSHP~~~~~pS~~D 286 (574)
.+.+.|+..++.=.. ..+ +.....+.. ++-+++ .++|.. +++.+=..+ ..-|..-|.||+..+.||..|
T Consensus 12 ~~~~~E~~~vl~Ld~-~~~---li~~~~l~~-G~~~~~-~v~~R~---i~~~aL~~~--A~~vil~HNHPsG~~~PS~~D 80 (113)
T cd08071 12 GDLDQEEFVVLLLDT-KNR---LIAVETISV-GTLNSS-LVHPRE---IFKEALRHN--AAAIILAHNHPSGDPTPSRED 80 (113)
T ss_pred CCCCceEEEEEEecC-CCC---EEEEEEEee-cCCcce-ecCHHH---HHHHHHHHh--hheEEEEeeCCCCCCCCCHHH
Confidence 345778877764322 222 233332221 221222 366753 333222223 378899999999999999999
Q ss_pred HHHHHHHH
Q psy15735 287 INTQQSFE 294 (574)
Q Consensus 287 i~tq~~yQ 294 (574)
++.-...+
T Consensus 81 ~~~T~~l~ 88 (113)
T cd08071 81 IELTKRLK 88 (113)
T ss_pred HHHHHHHH
Confidence 98754443
No 60
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=48.77 E-value=2.1e+02 Score=25.89 Aligned_cols=89 Identities=19% Similarity=0.088 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEccC
Q psy15735 196 LALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSH 275 (574)
Q Consensus 196 ~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYHSH 275 (574)
..+...++..-.+.+.|+.-++.= +...+.+.+..++ .++-.++ .++|.. +++.+=+.+. .-|=..|-|
T Consensus 6 ~~v~~~l~~~l~~~~~E~~~~l~L-d~~~~li~~~~v~----~G~~~~~-~v~~R~---I~~~al~~~A--~~vIl~HNH 74 (123)
T PF04002_consen 6 EDVADYLRPKLQGLDQEQFRVLYL-DSKNRLIGDEVVS----EGTIDSA-PVDPRE---IFRRALRLNA--SSVILAHNH 74 (123)
T ss_dssp HHHHHHHTTTSS-TTS-EEEEEEE--TTSBEEEEEEEE----ESTT-GG-GCSHHH---HHHHHHHTT---SEEEEEEE-
T ss_pred HHHHHHHHHHhCCCCCeEEEEEEE-CCCCcEEEEEEec----ccCCCcc-cccHHH---HHHHHHhhCC--ceEEEEEEc
Confidence 334444443333456677665542 2222233333322 2222223 367753 3333333343 556778999
Q ss_pred CCCCCcCCHHHHHHHHHHHh
Q psy15735 276 PGFGCWLSGVDINTQQSFEA 295 (574)
Q Consensus 276 P~~~~~pS~~Di~tq~~yQ~ 295 (574)
|+..+.||..|++.-...++
T Consensus 75 PsG~~~PS~~D~~~T~~L~~ 94 (123)
T PF04002_consen 75 PSGDPEPSDADIALTRRLKK 94 (123)
T ss_dssp TTS--S--HHHHHHHHHHHH
T ss_pred CCCCCCCCHhHHHHHHHHHH
Confidence 99999999999976555443
No 61
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=40.33 E-value=48 Score=31.29 Aligned_cols=43 Identities=19% Similarity=0.334 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHH-HHHhhcCchhHHHHHHHHHHHHHHHHhhccC
Q psy15735 450 IPLLVILIASIL-WLIGLVDSIRPTMTLFGTLVSWIYLRFYQYH 492 (574)
Q Consensus 450 lP~i~ll~~~~l-~~~~~~~~~a~~~~~~G~~~sWiYLRf~q~~ 492 (574)
+|++.+++..++ -.+++.+.+..+..+.|...||+.+|=|.|+
T Consensus 84 ~PL~~l~v~~~La~~L~~~e~~~~~~~~lg~~l~fl~~r~ysRk 127 (150)
T COG3086 84 FPLVGLFLGAILAQYLFFSELIVIFGAFLGLALGFLLARRYSRK 127 (150)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666555544 2344455566667788888899988888764
No 62
>PF02654 CobS: Cobalamin-5-phosphate synthase; InterPro: IPR003805 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CobS protein, a cobalamin-5-phosphate synthase that catyalzes the reactions: Adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP Adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP The protein product from these catalyses is associated with a large complex of proteins and is induced by cobinamide. CobS is involved in part III of cobalamin biosynthesis, one of the late steps in adenosylcobalamin synthesis that, together with CobU, CobT, and CobC proteins, defines the nucleotide loop assembly pathway [, ].; GO: 0008818 cobalamin 5'-phosphate synthase activity, 0009236 cobalamin biosynthetic process
Probab=36.28 E-value=1.2e+02 Score=30.49 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHHHHhhccCCCCccCCc
Q psy15735 471 RPTMTLFGTLVSWIYLRFYQYHTNGTRGDM 500 (574)
Q Consensus 471 a~~~~~~G~~~sWiYLRf~q~~~~~~rGD~ 500 (574)
.......+++++|.+-|+.+|+=.|.-||.
T Consensus 190 ~~~~~~~~~~~~~~~~~~~~r~lGG~tGD~ 219 (235)
T PF02654_consen 190 GLLALLVALLLALLLARYARRRLGGITGDV 219 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcChHH
Confidence 344566778899999999999878889993
No 63
>PF05814 DUF843: Baculovirus protein of unknown function (DUF843); InterPro: IPR008561 This family consists of several unidentified baculovirus proteins of around 85 residues long with no known function.
Probab=35.19 E-value=26 Score=29.89 Aligned_cols=32 Identities=22% Similarity=0.443 Sum_probs=28.8
Q ss_pred CCHhHHhhhhcCCCChhhhHHHHHHHHhhhhh
Q psy15735 121 MSPEQLAIKNVGKQDPKRHLEEKVDTLMTANI 152 (574)
Q Consensus 121 ~~~~~~~~~~vgk~d~k~hl~~~~~~~~~~ni 152 (574)
-+++++...++-|++-||||++.-|.+++.|.
T Consensus 50 S~~~dL~t~k~K~~KKK~~ln~afDAiLNKN~ 81 (83)
T PF05814_consen 50 STPQDLQTEKAKSIKKKRDLNDAFDAILNKNT 81 (83)
T ss_pred CcHHHHhhhhhhhHHHHHHHHHHHHHHHhccC
Confidence 36899999999999999999999999998874
No 64
>PF11744 ALMT: Aluminium activated malate transporter; InterPro: IPR020966 This entry represents an malate transporter which has been is identified as being critical for aluminium tolerance in Arabidopsis thaliana [].; GO: 0010044 response to aluminum ion
Probab=33.18 E-value=2.6e+02 Score=30.95 Aligned_cols=72 Identities=14% Similarity=0.108 Sum_probs=42.4
Q ss_pred hHHHHHhhcc-cccccc---cchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChhHHHHHHHHHHHhhcC
Q psy15735 358 NIIQCLGGKL-IEPLWG---SMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMP 433 (574)
Q Consensus 358 nI~~~l~~mL-~E~~wG---s~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~g~i~G~LVA~kQl~P 433 (574)
.+|-++-..+ .|+.-| +|-|-+. +-++++|++.+++.++.- ..++ -+..-+.+.+-++.|++..|.+++|
T Consensus 41 ~~WavlTVvvvfe~tvGatl~KG~nR~--lGTl~aG~La~~~~~la~-~~g~---~~~~~~i~~~vFi~~~~atf~r~~P 114 (406)
T PF11744_consen 41 AMWAVLTVVVVFEPTVGATLSKGLNRG--LGTLLAGILAFGVSWLAS-LSGD---PGEPIVIGISVFIIGFIATFVRFIP 114 (406)
T ss_pred chHHHhhhHhhccccccHHHHHHHHHH--HHHHHHHHHHHHHHHHHH-hcCc---cchhHHHHHHHHHHHHHHHHHHhch
Confidence 4444444333 577777 4566654 345556666666655431 1122 1123356888889999999999888
Q ss_pred Cc
Q psy15735 434 DH 435 (574)
Q Consensus 434 d~ 435 (574)
.-
T Consensus 115 ~~ 116 (406)
T PF11744_consen 115 KI 116 (406)
T ss_pred hh
Confidence 63
No 65
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=33.05 E-value=53 Score=35.54 Aligned_cols=103 Identities=27% Similarity=0.358 Sum_probs=58.5
Q ss_pred cCCCCcEEEE----EccCCCCCCcCCHHHHHHHHHH-HhcCCCeEEEEEcCCCCch----------------hHHHHHHH
Q psy15735 262 TGRPEMVVGW----YHSHPGFGCWLSGVDINTQQSF-EALSERAVAVVVDPIQSVK----------------ELAKHYNK 320 (574)
Q Consensus 262 ~g~~~~vVGW----YHSHP~~~~~pS~~Di~tq~~y-Q~~~p~~V~LIvDp~~s~~----------------rLs~~y~~ 320 (574)
.|+..-+|=| +||||.+-..-|.. ..-.| ++-..+--.+++||.++.. .|-++++.
T Consensus 138 KNraDviVyWGtNP~~shPRhmSRYs~f---~RG~~~~rGr~dRtvIvVD~RkT~TAklad~~~qi~p~sDyelisAl~~ 214 (429)
T COG1029 138 KNRADVIVYWGTNPMHSHPRHMSRYSVF---PRGFFRPRGREDRTVIVVDPRKTATAKLADNHVQIKPNSDYELISALRA 214 (429)
T ss_pred cccccEEEEeCCCcccccchhhhhcccc---cccccccCCcccceEEEEecCcCchhhhhhheEecCCCCcHHHHHHHHH
Confidence 3555677777 79999753221111 00001 1123455679999988865 45555565
Q ss_pred HhhhccCCCccchhcccccCCccchhhHHHHHHhhhhhHHHHHhhcccccccc
Q psy15735 321 ALEEEEKMSPEQLAIKNVGKQDPKRHLEEKVDTLMTANIIQCLGGKLIEPLWG 373 (574)
Q Consensus 321 ~~~ee~~ft~EeL~v~~vg~~DP~~~Le~~v~~fm~~nI~~~l~~mL~E~~wG 373 (574)
.+.-.....+|++. -.|...+++.++++-+.++-.+++.|=+...-|
T Consensus 215 ~l~G~~~~~~eev~------gvp~~~i~e~a~~mKna~Fg~if~GlGlt~S~g 261 (429)
T COG1029 215 ALHGKEPHRSEEVA------GVPIEEIEELADMMKNAKFGAIFVGLGLTSSRG 261 (429)
T ss_pred HhcCCCCCCchhhc------CCCHHHHHHHHHHHhcCCcceEEEeeceeeccc
Confidence 54211111223333 468888888888888777777666665554444
No 66
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=32.90 E-value=44 Score=32.17 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=25.7
Q ss_pred CCcEEEEEccCCCCCCcCCHHHHHHHHHHHhcCCCeEEE
Q psy15735 265 PEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAV 303 (574)
Q Consensus 265 ~~~vVGWYHSHP~~~~~pS~~Di~tq~~yQ~~~p~~V~L 303 (574)
...++. .||||..+..||..|......... .|.++|.
T Consensus 115 ~~~iid-iHSHP~~~~~~S~~D~~~~~~~~~-i~~a~y~ 151 (162)
T PF15659_consen 115 GNKIID-IHSHPENSNGPSGNDMKNAKPRKN-IPYAIYS 151 (162)
T ss_pred CceEEE-eccCCCCCCCCCcchhhhhhhccc-ccceeeE
Confidence 357777 999998888999999986543321 3445543
No 67
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=32.22 E-value=1.3e+02 Score=31.92 Aligned_cols=22 Identities=36% Similarity=0.543 Sum_probs=18.5
Q ss_pred hhccChhHHHHHHHHHHHhhcC
Q psy15735 412 VRIHGLTGYISGVLVAVKQIMP 433 (574)
Q Consensus 412 ~~i~G~~g~i~G~LVA~kQl~P 433 (574)
.-+.|..|++.|+++|+-...|
T Consensus 80 ~ilf~tiGLiiGLlia~l~~~p 101 (356)
T COG4956 80 TILFGTIGLIIGLLIAVLLSSP 101 (356)
T ss_pred HHHHHHHHHHHHHHHHHHHhhH
Confidence 3457999999999999988774
No 68
>PF11309 DUF3112: Protein of unknown function (DUF3112); InterPro: IPR021460 This eukaryotic family of proteins has no known function.
Probab=31.93 E-value=1.4e+02 Score=28.53 Aligned_cols=35 Identities=20% Similarity=0.273 Sum_probs=25.1
Q ss_pred cChhHHHHHHHHHHHhhcCCc---eeeccccccccchh
Q psy15735 415 HGLTGYISGVLVAVKQIMPDH---VILNTGLGKMTNRN 449 (574)
Q Consensus 415 ~G~~g~i~G~LVA~kQl~Pd~---~il~~~~~~ir~K~ 449 (574)
.-..+..--.+++..-..|.. .+-.||..+++.|-
T Consensus 58 ~~v~a~~pi~lv~la~~~P~~~p~~iE~Fg~g~~~~k~ 95 (160)
T PF11309_consen 58 LAVYAFLPIPLVALAFFLPRRKPWWIESFGPGSHRTKI 95 (160)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCcccCCccchhHHH
Confidence 334455555677788899997 66668888999983
No 69
>PF06946 Phage_holin_5: Phage holin; InterPro: IPR009708 This entry represents the Bacteriophage A118, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=30.47 E-value=90 Score=27.29 Aligned_cols=20 Identities=30% Similarity=0.507 Sum_probs=15.7
Q ss_pred ccchhHHHHHHHHHHHHHHH
Q psy15735 445 MTNRNIPLLVILIASILWLI 464 (574)
Q Consensus 445 ir~K~lP~i~ll~~~~l~~~ 464 (574)
++.||+|++.+++-+++.++
T Consensus 31 v~~K~iPlIs~viGilLG~~ 50 (93)
T PF06946_consen 31 VPNKWIPLISVVIGILLGAA 50 (93)
T ss_pred CCcchhhHHHHHHHHHHHHH
Confidence 57899999998777766554
No 70
>PF13295 DUF4077: Domain of unknown function (DUF4077)
Probab=30.08 E-value=2e+02 Score=26.24 Aligned_cols=124 Identities=19% Similarity=0.262 Sum_probs=64.4
Q ss_pred cchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChhHHHHHHHHHHHhhcCCceeeccccccccchhHHHH
Q psy15735 374 SMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVKQIMPDHVILNTGLGKMTNRNIPLL 453 (574)
Q Consensus 374 s~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~g~i~G~LVA~kQl~Pd~~il~~~~~~ir~K~lP~i 453 (574)
...++.|+-+|.+.-+++....|- |..|... + ..-.+|.+-+++|-|.-|-.-+... .||+--+
T Consensus 18 knhlllfiticsfflgiiaigyyg--yiftera-i--afwvcgisvvvfgtlltfiesmeam-----------ykyimtf 81 (175)
T PF13295_consen 18 KNHLLLFITICSFFLGIIAIGYYG--YIFTERA-I--AFWVCGISVVVFGTLLTFIESMEAM-----------YKYIMTF 81 (175)
T ss_pred hCcEeeHHHHHHHHHHHHHHhhhh--eeehhHH-H--HHHhhchhhhhHhHHHHHHHHHHHH-----------HHHHHHH
Confidence 345677888888877777766542 3333221 1 1246899999999988775443211 3443222
Q ss_pred HHHHHHHHHHHhhcCchhHH-HHHHHHHHHHHHHHhhccCCCCccCCc-ccCccccccCCccCc
Q psy15735 454 VILIASILWLIGLVDSIRPT-MTLFGTLVSWIYLRFYQYHTNGTRGDM-ADNFNFANFFPTIIQ 515 (574)
Q Consensus 454 ~ll~~~~l~~~~~~~~~a~~-~~~~G~~~sWiYLRf~q~~~~~~rGD~-Sd~Faf~~FFP~~~~ 515 (574)
.++...+.....+..+-+.+ +..+-..+|.+||-= +.--...|-+ --+|-+-++.|+..-
T Consensus 82 mllmmsfimvqafnespavfqmvyftlavsliylse--rlvvilggvavvltfilcsywpeqff 143 (175)
T PF13295_consen 82 MLLMMSFIMVQAFNESPAVFQMVYFTLAVSLIYLSE--RLVVILGGVAVVLTFILCSYWPEQFF 143 (175)
T ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHh--HHHHhcccchheeehhhhhcChHHHH
Confidence 22222222223333333333 556666778888731 1000112222 346666677776544
No 71
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=29.08 E-value=47 Score=30.47 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=20.8
Q ss_pred CcEEEEEccCCCCC-----CcCCHHHHHHH
Q psy15735 266 EMVVGWYHSHPGFG-----CWLSGVDINTQ 290 (574)
Q Consensus 266 ~~vVGWYHSHP~~~-----~~pS~~Di~tq 290 (574)
..+|+-||||...+ -.||..|+..-
T Consensus 59 ~~~vA~yHTHG~~~~~y~~evfS~~D~~~~ 88 (123)
T PF14220_consen 59 STIVASYHTHGAYSDGYDNEVFSPQDIRGD 88 (123)
T ss_pred cceeeEeecccccCCCccccCCCHHHhhhh
Confidence 58999999998654 47999999875
No 72
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.80 E-value=6.1e+02 Score=25.46 Aligned_cols=90 Identities=20% Similarity=0.080 Sum_probs=49.4
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeeeEEcCCceEEEEEEEeCCcccCCCCcccccHHHHHHHHHHHHhcCCCCcEEEEEc
Q psy15735 194 SSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVIDVFAMPQTGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYH 273 (574)
Q Consensus 194 s~~vllkIl~Ha~~~~p~Ev~GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~~~~idp~~q~~ml~~lr~~g~~~~vVGWYH 273 (574)
++..+...+...-.+.+.|..-++.= +..++.+....++ .++-+++ .++|.+ +.+.+=+.+. .-|=.-|
T Consensus 99 s~~~v~~~l~~~l~~~~~E~f~vl~L-d~~n~li~~~~i~----~Gt~~~~-~v~pRe---I~~~Al~~~A--~~vIlaH 167 (218)
T TIGR00608 99 SPEAAAEFLHTDLAHETREHFMVLFL-DRKNRLIAKEVVF----IGTVNHV-PVHPRE---IFKEALKLSA--SALILAH 167 (218)
T ss_pred CHHHHHHHHHHHhcCCCceEEEEEEE-CCCCcEEEEEEee----cCCCCeE-EEcHHH---HHHHHHHhhC--CeEEEEe
Confidence 45556666655555667787766542 2222233333222 2332222 367753 3332222232 4455679
Q ss_pred cCCCCCCcCCHHHHHHHHHHH
Q psy15735 274 SHPGFGCWLSGVDINTQQSFE 294 (574)
Q Consensus 274 SHP~~~~~pS~~Di~tq~~yQ 294 (574)
=||++.+.||..|++.-....
T Consensus 168 NHPSG~~~PS~~Di~~T~~l~ 188 (218)
T TIGR00608 168 NHPSGEPSPSQEDILITERLR 188 (218)
T ss_pred ecCCCCCCCCHHHHHHHHHHH
Confidence 999999999999998654443
No 73
>KOG3142|consensus
Probab=26.51 E-value=89 Score=30.79 Aligned_cols=20 Identities=20% Similarity=0.687 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHhhccCC
Q psy15735 474 MTLFGTLVSWIYLRFYQYHT 493 (574)
Q Consensus 474 ~~~~G~~~sWiYLRf~q~~~ 493 (574)
..+.+.+.+|+||+|++-.|
T Consensus 93 ivl~~lv~~w~~LY~~rd~p 112 (187)
T KOG3142|consen 93 IVLLALVAAWLFLYFLRDEP 112 (187)
T ss_pred HHHHHHHHHHHheeeecCCC
Confidence 46778899999999999443
No 74
>KOG3869|consensus
Probab=26.09 E-value=82 Score=34.56 Aligned_cols=45 Identities=22% Similarity=0.408 Sum_probs=36.9
Q ss_pred hcc-cCCccCCCCccChHHHhhhhHHHHHHHHHHHHHHHHHHHHHhcC
Q psy15735 75 NLH-KKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYNKALEEEEKM 121 (574)
Q Consensus 75 ~l~-k~~w~~~l~~~~~~~~~~~n~~~~~~~~~l~~~y~~~~~ee~~~ 121 (574)
.|+ |++|.-++ |.+.+++-+..+....++.+| +.|.+.|+||...
T Consensus 5 DLNlkKsWhp~~-mkN~ekVWkaEq~~k~E~Kkl-E~lr~eI~eER~r 50 (450)
T KOG3869|consen 5 DLNLKKSWHPEL-MKNQEKVWKAEQKHKAEQKKL-EELRKEINEERAR 50 (450)
T ss_pred ccccccccChhh-hcchHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 466 99999665 777788888888888888888 8899999999765
No 75
>COG2246 Predicted membrane protein [Function unknown]
Probab=23.31 E-value=1e+02 Score=28.66 Aligned_cols=51 Identities=10% Similarity=0.104 Sum_probs=33.3
Q ss_pred ccchhhhhhhhHhhHHHHHHHHHHHHHHHHhcCCcccchhhccChhHHHHHHHHHHH
Q psy15735 373 GSMEMMTFFAIVNIGVAISSTLFYFFLYMCTFNTDLLFFVRIHGLTGYISGVLVAVK 429 (574)
Q Consensus 373 Gs~EflkF~~vv~v~~~il~~~~~~~~y~~t~~~~~l~~~~i~G~~g~i~G~LVA~k 429 (574)
-..+++||. +||+++.++.+++.++++... .. ...+.-..|..+|++++|-
T Consensus 9 ~~~~~lrF~-~VG~~~t~V~~~~~~ll~~~~-~~----~~~~A~~~a~~~~ii~sf~ 59 (139)
T COG2246 9 TLSRLLRFA-IVGGLGTLVDFAVLWLLVKAL-GV----PYALANAIAYEAAIIFSFV 59 (139)
T ss_pred HHHHHHHHH-hcchHHHHHHHHHHHHHHHhc-cc----chHHHHHHHHHHHHHHHHH
Confidence 357899984 688888888887776655441 11 1234556677777777763
No 76
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=23.12 E-value=43 Score=26.15 Aligned_cols=14 Identities=50% Similarity=0.665 Sum_probs=11.6
Q ss_pred CCCCcCcEEEeccc
Q psy15735 4 NLPQLGKVVIDAFR 17 (574)
Q Consensus 4 ~~~~kgkvvidafr 17 (574)
|-+.-||+|||+-|
T Consensus 31 nF~~aGK~vI~~~~ 44 (52)
T PF12073_consen 31 NFEHAGKKVIDGSR 44 (52)
T ss_pred eeccCCeEEEeccE
Confidence 45678999999977
No 77
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=20.11 E-value=1.2e+02 Score=32.68 Aligned_cols=60 Identities=18% Similarity=0.331 Sum_probs=35.9
Q ss_pred EEeeeEEcCCceEEEEEEEeCCcccCCCC----------cccccHHHHHHHHHHHHhcC----CCCcEEEEEccCCC
Q psy15735 215 GLMLGEFVDEYTVRVIDVFAMPQTGTGVS----------VEAVDPVFQAKMLDMLKQTG----RPEMVVGWYHSHPG 277 (574)
Q Consensus 215 GlLlG~~~~~~~l~Vt~~fp~p~~~~~~~----------~~~idp~~q~~ml~~lr~~g----~~~~vVGWYHSHP~ 277 (574)
|+|+|.....+.-.|.+..+.|...++.. ...+|.+. +.+.++++. -+..|||.|=.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~W---VaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEW---VAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHH---HHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 89999873333456888888887654332 11244432 222333321 15899999987764
No 78
>PF03739 YjgP_YjgQ: Predicted permease YjgP/YjgQ family; InterPro: IPR005495 Members of this family are predicted integral membrane proteins of unknown function. They are about 350 amino acids long, contain about 6 transmembrane regions and may be permeases, although there is no verification of this.; GO: 0016021 integral to membrane
Probab=20.05 E-value=2.2e+02 Score=29.77 Aligned_cols=42 Identities=10% Similarity=0.274 Sum_probs=28.5
Q ss_pred hccChhHHHHHHHHHHHhhcCCceeec---cccccccchhHHHHHH
Q psy15735 413 RIHGLTGYISGVLVAVKQIMPDHVILN---TGLGKMTNRNIPLLVI 455 (574)
Q Consensus 413 ~i~G~~g~i~G~LVA~kQl~Pd~~il~---~~~~~ir~K~lP~i~l 455 (574)
...--.+++.|++..+.++.-|.|+.. .|..+.+. ..|++.+
T Consensus 57 ~~~lP~~~lia~~~~l~~L~~~~El~a~~a~GiS~~~l-~~p~i~~ 101 (354)
T PF03739_consen 57 SLILPLAFLIAVLLTLGRLSRNNELVAMRASGISLKRL-LRPIIIF 101 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcchHHHHHHcCCCHHHH-HHHHHHH
Confidence 345567889999999999999999843 35433333 2455543
Done!