Query 012141
Match_columns 470
No_of_seqs 255 out of 328
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 23:29:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10269 Tmemb_185A: Transmemb 100.0 1.2E-45 2.6E-50 358.7 8.7 235 28-314 1-238 (238)
2 KOG3879 Predicted membrane pro 100.0 1.9E-33 4.1E-38 270.0 8.1 189 80-359 9-201 (267)
3 KOG3879 Predicted membrane pro 99.8 4.8E-20 1E-24 177.9 7.1 129 8-159 55-195 (267)
4 PF10269 Tmemb_185A: Transmemb 99.6 8.8E-15 1.9E-19 142.9 11.6 172 12-190 48-238 (238)
5 KOG1101 Apoptosis inhibitor IA 98.6 5E-08 1.1E-12 90.0 5.8 59 352-423 50-108 (147)
6 KOG1100 Predicted E3 ubiquitin 98.4 1.3E-07 2.9E-12 91.5 2.3 151 300-469 37-188 (207)
7 PF13920 zf-C3HC4_3: Zinc fing 98.0 1.4E-06 3E-11 65.7 1.0 29 440-468 3-31 (50)
8 KOG4265 Predicted E3 ubiquitin 98.0 1.2E-06 2.6E-11 90.3 -0.5 35 435-469 286-320 (349)
9 KOG4275 Predicted E3 ubiquitin 98.0 1.6E-06 3.4E-11 87.6 0.2 30 440-469 301-330 (350)
10 KOG1571 Predicted E3 ubiquitin 97.5 3.5E-05 7.5E-10 79.8 0.7 31 439-469 305-335 (355)
11 smart00238 BIR Baculoviral inh 96.3 0.0019 4.1E-08 51.6 1.8 32 351-383 34-65 (71)
12 PF00653 BIR: Inhibitor of Apo 96.2 0.0018 3.8E-08 52.1 0.8 32 351-383 34-65 (70)
13 KOG4172 Predicted E3 ubiquitin 96.0 0.00048 1E-08 54.5 -3.1 28 441-468 9-36 (62)
14 cd00022 BIR Baculoviral inhibi 95.7 0.007 1.5E-07 48.1 2.4 32 351-383 32-63 (69)
15 PF13923 zf-C3HC4_2: Zinc fing 95.1 0.0071 1.5E-07 43.3 0.4 26 442-468 1-27 (39)
16 KOG4692 Predicted E3 ubiquitin 95.1 0.0059 1.3E-07 63.8 -0.1 28 438-466 421-448 (489)
17 smart00184 RING Ring finger. E 94.7 0.01 2.2E-07 40.0 0.3 25 442-467 1-25 (39)
18 PF13445 zf-RING_UBOX: RING-ty 92.9 0.037 8E-07 41.4 0.5 25 442-468 1-29 (43)
19 KOG1785 Tyrosine kinase negati 92.9 0.033 7.2E-07 59.2 0.3 28 440-468 370-397 (563)
20 PF00097 zf-C3HC4: Zinc finger 91.9 0.058 1.3E-06 38.5 0.5 26 442-468 1-27 (41)
21 KOG1814 Predicted E3 ubiquitin 91.7 0.061 1.3E-06 57.3 0.5 38 430-468 175-215 (445)
22 PF14447 Prok-RING_4: Prokaryo 89.0 0.17 3.8E-06 40.1 0.9 28 440-468 8-35 (55)
23 PF14634 zf-RING_5: zinc-RING 88.1 0.12 2.7E-06 38.0 -0.4 27 442-469 2-31 (44)
24 PF15227 zf-C3HC4_4: zinc fing 86.1 0.33 7.3E-06 35.8 0.9 25 442-467 1-25 (42)
25 cd00162 RING RING-finger (Real 84.9 0.34 7.4E-06 33.6 0.5 26 441-467 1-27 (45)
26 PHA02929 N1R/p28-like protein; 84.1 0.42 9E-06 47.9 0.8 27 440-467 175-209 (238)
27 PF13639 zf-RING_2: Ring finge 77.5 1 2.3E-05 32.7 0.8 26 441-467 2-30 (44)
28 COG5236 Uncharacterized conser 73.7 0.89 1.9E-05 48.0 -0.6 30 438-468 60-89 (493)
29 KOG0823 Predicted E3 ubiquitin 71.5 1.6 3.5E-05 43.6 0.6 27 439-466 47-73 (230)
30 PHA02926 zinc finger-like prot 71.4 1.4 3E-05 44.1 0.2 31 435-467 167-206 (242)
31 KOG0978 E3 ubiquitin ligase in 69.8 0.82 1.8E-05 52.0 -2.0 37 429-467 634-670 (698)
32 smart00504 Ubox Modified RING 68.6 2.1 4.6E-05 32.7 0.7 26 441-467 3-28 (63)
33 COG5243 HRD1 HRD ubiquitin lig 65.0 2.7 5.9E-05 44.9 0.8 29 433-461 281-322 (491)
34 KOG0317 Predicted E3 ubiquitin 62.4 1.4 3E-05 45.3 -1.8 26 440-466 240-265 (293)
35 COG5574 PEX10 RING-finger-cont 57.9 2.3 5.1E-05 43.3 -1.1 26 441-467 217-242 (271)
36 KOG3039 Uncharacterized conser 57.5 4.7 0.0001 41.0 1.0 32 437-469 219-254 (303)
37 KOG2164 Predicted E3 ubiquitin 45.0 9.6 0.00021 42.1 0.9 27 439-466 186-212 (513)
38 KOG0320 Predicted E3 ubiquitin 44.7 5.5 0.00012 38.7 -0.8 29 439-468 131-161 (187)
39 KOG4159 Predicted E3 ubiquitin 39.4 7.9 0.00017 41.6 -0.7 63 393-466 48-110 (398)
40 KOG0802 E3 ubiquitin ligase [P 36.8 11 0.00024 41.6 -0.1 31 435-466 287-322 (543)
41 COG5152 Uncharacterized conser 30.3 10 0.00022 37.6 -1.5 27 441-468 198-224 (259)
42 KOG2113 Predicted RNA binding 29.1 33 0.00071 36.3 1.8 31 439-469 136-166 (394)
43 PF10367 Vps39_2: Vacuolar sor 27.9 46 0.001 27.7 2.2 29 439-468 78-108 (109)
44 PF04710 Pellino: Pellino; In 26.7 21 0.00046 38.5 0.0 12 450-461 358-369 (416)
45 COG5540 RING-finger-containing 22.1 61 0.0013 34.2 2.3 23 439-461 323-348 (374)
46 KOG4628 Predicted E3 ubiquitin 21.9 49 0.0011 35.2 1.5 21 441-461 231-254 (348)
47 KOG1813 Predicted E3 ubiquitin 21.4 36 0.00078 35.6 0.4 27 442-469 244-270 (313)
48 KOG2113 Predicted RNA binding 20.1 55 0.0012 34.7 1.4 28 441-468 345-372 (394)
No 1
>PF10269 Tmemb_185A: Transmembrane Fragile-X-F protein ; InterPro: IPR019396 This entry represents conserved transmembrane proteins that in humans are expressed from a region upstream of the FragileXF site and appear to be intimately linked with Fragile-X syndrome. The absence of the human TMEM185A protein does not necessarily lead to developmental delay, but might, in combination with other, currently unknown, factors. Alternatively, the TMEM185A protein is either redundant, or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B [].
Probab=100.00 E-value=1.2e-45 Score=358.69 Aligned_cols=235 Identities=49% Similarity=0.834 Sum_probs=200.0
Q ss_pred HhcCCccccchhHHHHHHHHHHHHHHhhcccCCCCCCCCcccccchhhHHHHHHHHHHHHHHHHHhccccccccccccee
Q 012141 28 LKLDHVISYSWWIVFFPVWIFHAVVARGRFSLPAPSVPHNRHWAPCHAIVATPLLIAFELLLCIYLESIYEHGFEAVNLK 107 (470)
Q Consensus 28 LKLDg~I~WSWwvVFiPLWI~d~lv~~g~~~~~~~~~~~rr~wa~~~smv~l~LLl~FelLLClKLd~~~~~~~~~~~w~ 107 (470)
||+||.++||||.||+|+|++++++++|++........+++.++.+++....+++++||+|+|.||++... .+|.
T Consensus 1 LrlD~~i~wsww~VF~Plw~~~~iv~~g~~~~~~~~~~~~~~~~~~~~~~~~lll~~f~~llc~~L~~~~~-----~~w~ 75 (238)
T PF10269_consen 1 LRLDGVISWSWWIVFIPLWIWKAIVIVGAFVGIAVSRPRVDFKAMLISVVAHLLLLAFELLLCIKLEGGSS-----ISWS 75 (238)
T ss_pred CccCceeeccHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHheeecCCCCc-----ceee
Confidence 69999999999999999999999999988655444444556666666777778899999999999965555 7999
Q ss_pred eehhhHHHHHH---HHHHHHhhhhhccCCCCCCcchhHHHHhhhhhHHHHHHHHHHHHHHHHhhhhhcccccccceeeeh
Q 012141 108 IVFLPLLAFEI---TILIDNFRMCRALMPGDEESMNDEAIWEALPHFWVAISMVFFVAATVFTLLKLCGYVGALGWWDLF 184 (470)
Q Consensus 108 iVFiPL~il~~---~llV~~fr~C~~~~~g~~~sl~~ea~~~~~~~fw~aismlf~laa~VfL~LKLDg~~v~~~W~vVF 184 (470)
+||+|+|++.. ..+++++|+ ++++++++++++.+.+.+++|..+++++.++|++|+++|||+. ++|+||+||
T Consensus 76 ~VFiPL~~l~~~~I~~~i~~~r~----~~~~~e~~~~~~~~~~~~~~~~~l~~if~~~f~v~l~Lkld~~-i~~sW~~vF 150 (238)
T PF10269_consen 76 IVFIPLFVLSALSILICIWNFRH----MPGDGEEMSDRSIWFELPFFWNILSLIFFLAFTVFLALKLDGV-IDWSWWIVF 150 (238)
T ss_pred eeeechhhHHHHHHHHHHHhhcc----CcccccCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCc-ccccHHHHH
Confidence 99999987775 667788888 7898889999999999999999999999999999999999999 899999999
Q ss_pred hhHHHHHHHHHHhhcccCCccccCCCCCCCCCccchhheeecccccccccccccCCCCccccccccchhhHHHHHHHHHH
Q 012141 185 INFGIAECFAFLVCTKWSNPVIHRSPQTRPATSSSAITYLDWNSGLVVSAEEEQNPDGMCGLSDIGGHIMKVPVIGFQVL 264 (470)
Q Consensus 185 IPLwI~l~f~~lv~~~~~~p~i~~~~~~~~~~~~~~~~~~~w~~~~~~~~~e~~~q~~~~~~~~i~~~~~~ip~~~fqvL 264 (470)
+|+||.+++++++|.-.. ...++|.+|+++...+.++++.|.+.+. |++++++|+++||+|
T Consensus 151 iPl~i~~~~~~~~~~~~~---------------i~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~i~~l~F~vL 211 (238)
T PF10269_consen 151 IPLWIADGLAFLVCLYSI---------------IMSIRYLDRNPGLLPSQRRSSLQSRICW----GGLFLVIPLLVFQVL 211 (238)
T ss_pred HHHHHHHHHHHHHHHHHH---------------HHHHHHHhccCCCchhhHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 999999999999754322 2255677888777665555555544444 669999999999999
Q ss_pred hhhhcchhhhhhccccccchhhhhhcccCCCcccccccccchhhhhHHHH
Q 012141 265 LCMHLEVCVLLICDHFYGLVYLINISLFQGTPAGARNIALPVLFSPLFLL 314 (470)
Q Consensus 265 L~~~L~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~if~Pl~l~ 314 (470)
||+||| |++.+++++|+.++|+|||++
T Consensus 212 L~~kLe-----------------------~~~~~~~~~~~~~vf~PL~i~ 238 (238)
T PF10269_consen 212 LCMKLE-----------------------GTPWSAANIPISVVFIPLFIL 238 (238)
T ss_pred HHHHhc-----------------------CCccccccccHHHHHHHHHhC
Confidence 999999 999889999999999999984
No 2
>KOG3879 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=1.9e-33 Score=269.97 Aligned_cols=189 Identities=26% Similarity=0.431 Sum_probs=170.9
Q ss_pred HHHHHHHHHHHHHhcccccccccccceeeehhhHHHHHH---HHHHHHhhhhhccCCCCCCcchhHHHHhhhhhHHHHHH
Q 012141 80 PLLIAFELLLCIYLESIYEHGFEAVNLKIVFLPLLAFEI---TILIDNFRMCRALMPGDEESMNDEAIWEALPHFWVAIS 156 (470)
Q Consensus 80 ~LLl~FelLLClKLd~~~~~~~~~~~w~iVFiPL~il~~---~llV~~fr~C~~~~~g~~~sl~~ea~~~~~~~fw~ais 156 (470)
+++++||+|.|+|||.+++ -|.+||+|++..++ ++|+|++|| +++++.|.. ++++
T Consensus 9 l~llmfe~lvcdkle~~~h------fw~lvf~plff~s~vsvgacvw~~Rh--------d~a~ele~~--------~avn 66 (267)
T KOG3879|consen 9 LLLLMFEVLVCDKLERDYH------FWLLVFMPLFFVSPVSVGACVWGFRH--------DLAFELEFT--------WAVN 66 (267)
T ss_pred HHHHHHHHHHhhhhccCce------ehHHHHHHHHhcChhhhhhhhhhhhc--------chHHHHHHH--------HHHH
Confidence 7799999999999999998 69999999999875 889999999 888888777 8999
Q ss_pred HHHHHHHHHHhhhhhcccccccceeeehhhHHHHHHHHHHhhcccCCccccCCCCCCCCCccchhheeeccccccccccc
Q 012141 157 MVFFVAATVFTLLKLCGYVGALGWWDLFINFGIAECFAFLVCTKWSNPVIHRSPQTRPATSSSAITYLDWNSGLVVSAEE 236 (470)
Q Consensus 157 mlf~laa~VfL~LKLDg~~v~~~W~vVFIPLwI~l~f~~lv~~~~~~p~i~~~~~~~~~~~~~~~~~~~w~~~~~~~~~e 236 (470)
++| .||+++|||.. +.|+|-+||+|+||.+++.+++ ++||+.|+ ++..||.|
T Consensus 67 ilq----lIflaLKLD~~-v~WnW~VVFvPlWI~~sil~V~----------------------VLy~iv~s-~~~lrs~~ 118 (267)
T KOG3879|consen 67 ILQ----LIFLALKLDKI-VHWNWFVVFVPLWIFDSILLVV----------------------VLYKIVWS-VLFLRSRD 118 (267)
T ss_pred HHH----HHHHHHhcCcc-cCCceEEEeehHHHHHHHHHHH----------------------HHHHHHHH-HHhccccc
Confidence 999 99999999999 8999999999999999999999 99999999 99999999
Q ss_pred -ccCCCCccccccccchhhHHHHHHHHHHhhhhcchhhhhhccccccchhhhhhcccCCCcccccccccchhhhhHHHHH
Q 012141 237 -EQNPDGMCGLSDIGGHIMKVPVIGFQVLLCMHLEVCVLLICDHFYGLVYLINISLFQGTPAGARNIALPVLFSPLFLLQ 315 (470)
Q Consensus 237 -~~~q~~~~~~~~i~~~~~~ip~~~fqvLL~~~L~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~if~Pl~l~~ 315 (470)
+.+|+|.|..+++++...++|.++||++||.||| |. ...++|.++|+||+++
T Consensus 119 v~p~~rr~~l~~ai~~i~~Vlp~Laf~VlLc~KLd-----------------------g~---~t~~sy~~vfaPLwls- 171 (267)
T KOG3879|consen 119 VIPEQRRTHLTMAIWNITIVLPLLAFQVLLCHKLD-----------------------GH---NTTFSYIVVFAPLWLS- 171 (267)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----------------------Cc---cccceEEEEHHHHHHH-
Confidence 9999999999999999999999999999999999 83 2389999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHhhcCCCCceEEEEeeccccceeeeee
Q 012141 316 GVGVVFSTTRLVEKIVILLRSGAGTGIYFRISSRAHDCFGFLHR 359 (470)
Q Consensus 316 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 359 (470)
+..-+....+ ++|+.+-|-++ +||..|+-.
T Consensus 172 ----------l~t~i~~s~~-kggn~wwFGiR---k~fcqflle 201 (267)
T KOG3879|consen 172 ----------LLTAIATSGS-KGGNHWWFGIR---KDFCQFLLE 201 (267)
T ss_pred ----------HHHHHHHhcc-CCCceEEEEec---chHHHHHHH
Confidence 5555555555 66788888887 788776643
No 3
>KOG3879 consensus Predicted membrane protein [Function unknown]
Probab=99.80 E-value=4.8e-20 Score=177.89 Aligned_cols=129 Identities=25% Similarity=0.468 Sum_probs=104.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHHHHHHHHh---------hcccCCCCCCCCcccccchh---h
Q 012141 8 KSVQAVAAHSLLLTFTLLLVLKLDHVISYSWWIVFFPVWIFHAVVAR---------GRFSLPAPSVPHNRHWAPCH---A 75 (470)
Q Consensus 8 ~~~~~~~~~~~LLvFtILLaLKLDg~I~WSWwvVFiPLWI~d~lv~~---------g~~~~~~~~~~~rr~wa~~~---s 75 (470)
++++..++|+.-++|+|++|||||.+++|||.+||+||||+|++.++ +.+.|+++..++.+.-.... .
T Consensus 55 ~a~ele~~~avnilqlIflaLKLD~~v~WnW~VVFvPlWI~~sil~V~VLy~iv~s~~~lrs~~v~p~~rr~~l~~ai~~ 134 (267)
T KOG3879|consen 55 LAFELEFTWAVNILQLIFLALKLDKIVHWNWFVVFVPLWIFDSILLVVVLYKIVWSVLFLRSRDVIPEQRRTHLTMAIWN 134 (267)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCcccCCceEEEeehHHHHHHHHHHHHHHHHHHHHHhccccccCHHHHHHHHHHHHHH
Confidence 45678899999999999999999999999999999999999999884 22667666666644332222 2
Q ss_pred HHHHHHHHHHHHHHHHHhcccccccccccceeeehhhHHHHHHHHHHHHhhhhhccCCCCCCcchhHHHHhhhhhHHHHH
Q 012141 76 IVATPLLIAFELLLCIYLESIYEHGFEAVNLKIVFLPLLAFEITILIDNFRMCRALMPGDEESMNDEAIWEALPHFWVAI 155 (470)
Q Consensus 76 mv~l~LLl~FelLLClKLd~~~~~~~~~~~w~iVFiPL~il~~~llV~~fr~C~~~~~g~~~sl~~ea~~~~~~~fw~ai 155 (470)
++.++++++||++||.||||..+. ++++.||+|+|+++.++++...+. .+||||+++
T Consensus 135 i~~Vlp~Laf~VlLc~KLdg~~t~----~sy~~vfaPLwlsl~t~i~~s~~k-------------------ggn~wwFGi 191 (267)
T KOG3879|consen 135 ITIVLPLLAFQVLLCHKLDGHNTT----FSYIVVFAPLWLSLLTAIATSGSK-------------------GGNHWWFGI 191 (267)
T ss_pred HHHHHHHHHHHHHHHHHhcCcccc----ceEEEEHHHHHHHHHHHHHHhccC-------------------CCceEEEEe
Confidence 466688999999999999987742 899999999999999887755442 358999999
Q ss_pred HHHH
Q 012141 156 SMVF 159 (470)
Q Consensus 156 smlf 159 (470)
+-.+
T Consensus 192 Rk~f 195 (267)
T KOG3879|consen 192 RKDF 195 (267)
T ss_pred cchH
Confidence 8877
No 4
>PF10269 Tmemb_185A: Transmembrane Fragile-X-F protein ; InterPro: IPR019396 This entry represents conserved transmembrane proteins that in humans are expressed from a region upstream of the FragileXF site and appear to be intimately linked with Fragile-X syndrome. The absence of the human TMEM185A protein does not necessarily lead to developmental delay, but might, in combination with other, currently unknown, factors. Alternatively, the TMEM185A protein is either redundant, or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B [].
Probab=99.58 E-value=8.8e-15 Score=142.91 Aligned_cols=172 Identities=23% Similarity=0.298 Sum_probs=115.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCccccchhHHHHHHHHHHHHHHhhc---ccC---CCCCCCCcccccc-hhhH--HHHHHH
Q 012141 12 AVAAHSLLLTFTLLLVLKLDHVISYSWWIVFFPVWIFHAVVARGR---FSL---PAPSVPHNRHWAP-CHAI--VATPLL 82 (470)
Q Consensus 12 ~~~~~~~LLvFtILLaLKLDg~I~WSWwvVFiPLWI~d~lv~~g~---~~~---~~~~~~~rr~wa~-~~sm--v~l~LL 82 (470)
.+..+.+++.|.+++|.||++.-+.+|..||+|+|+..++.+... +.. +.+...++..|.. .+.. +.....
T Consensus 48 ~~~~~lll~~f~~llc~~L~~~~~~~w~~VFiPL~~l~~~~I~~~i~~~r~~~~~~e~~~~~~~~~~~~~~~~~l~~if~ 127 (238)
T PF10269_consen 48 SVVAHLLLLAFELLLCIKLEGGSSISWSIVFIPLFVLSALSILICIWNFRHMPGDGEEMSDRSIWFELPFFWNILSLIFF 127 (238)
T ss_pred HHHHHHHHHHHHHHheeecCCCCcceeeeeeechhhHHHHHHHHHHHhhccCcccccCCCCchhhhhhhHHHHHHHHHHH
Confidence 557788899999999999988899999999999998887776422 111 1122222333322 2222 333557
Q ss_pred HHHHHHHHHHhcccccccccccceeeehhhHHHHHHHHH----HHHhhhhhccCCCCCCcchhHHHHhhhhhHHH--HHH
Q 012141 83 IAFELLLCIYLESIYEHGFEAVNLKIVFLPLLAFEITIL----IDNFRMCRALMPGDEESMNDEAIWEALPHFWV--AIS 156 (470)
Q Consensus 83 l~FelLLClKLd~~~~~~~~~~~w~iVFiPL~il~~~ll----V~~fr~C~~~~~g~~~sl~~ea~~~~~~~fw~--ais 156 (470)
++|.+++++|||+... |+|..||+|+|+.+.... ......++......+...+++.- +.....+. ..-
T Consensus 128 ~~f~v~l~Lkld~~i~-----~sW~~vFiPl~i~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 201 (238)
T PF10269_consen 128 LAFTVFLALKLDGVID-----WSWWIVFIPLWIADGLAFLVCLYSIIMSIRYLDRNPGLLPSQRRS-SLQSRICWGGLFL 201 (238)
T ss_pred HHHHHHHHHhcCCccc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCchhhHHH-HHHHHHHHHHHHH
Confidence 7999999999999998 999999999999987332 23344554433322222221111 00111222 223
Q ss_pred HHHHHHHHHHhhhhhccccc----ccceeeehhhHHHH
Q 012141 157 MVFFVAATVFTLLKLCGYVG----ALGWWDLFINFGIA 190 (470)
Q Consensus 157 mlf~laa~VfL~LKLDg~~v----~~~W~vVFIPLwI~ 190 (470)
+..+++|++++|.||||+ . +.+...+|+|+|++
T Consensus 202 ~i~~l~F~vLL~~kLe~~-~~~~~~~~~~~vf~PL~i~ 238 (238)
T PF10269_consen 202 VIPLLVFQVLLCMKLEGT-PWSAANIPISVVFIPLFIL 238 (238)
T ss_pred HHHHHHHHHHHHHHhcCC-ccccccccHHHHHHHHHhC
Confidence 455688999999999999 7 79999999999984
No 5
>KOG1101 consensus Apoptosis inhibitor IAP1 and related BIR domain proteins [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=98.62 E-value=5e-08 Score=89.99 Aligned_cols=59 Identities=25% Similarity=0.365 Sum_probs=51.9
Q ss_pred cceeeeeeCcccCCcccCCCCChHHHhhhhhcCCCCCccccCCCccceeecCchhhhHHHHHHHhhhcCCcc
Q 012141 352 DCFGFLHRGSRLLGWWSIDEGSREDQARLVHENSSGYNTFCGYPPEVVKKMPKKELAEEVWRLQAALGQQSE 423 (470)
Q Consensus 352 ~~~~~~~~~~rl~~~W~~de~~wee~Ar~~~~~~~~~~~~c~~~p~~v~~~~~~~~~~e~~~~~~a~~~q~~ 423 (470)
|.+.=.+|+++|-+ |+++||||+|||+|+|. | +||+..|++|++-.++....++.++++
T Consensus 50 D~~~Cf~C~~~L~~-We~~DDPW~EH~k~~p~--------C----~F~~~~k~~e~~~~v~~~~~~~~~~~~ 108 (147)
T KOG1101|consen 50 DCVKCFFCSGGLDD-WEPGDDPWEEHAKWSPE--------C----EFLKLKKGREFLGTVQSTARALLALKE 108 (147)
T ss_pred CceECcccCccccc-CCCCCCcHHHHHhhCCC--------C----ceeecccchhhhhHHHHhHhhhhhccC
Confidence 99999999999999 99999999999999999 9 999999999999988766554444333
No 6
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.38 E-value=1.3e-07 Score=91.49 Aligned_cols=151 Identities=13% Similarity=0.105 Sum_probs=99.9
Q ss_pred cccccchhhhhHHHHHhhhHHHHHHHHHHHHHHHhhcCCCC-ceEEEEeeccccceeeeeeCcccCCcccCCCCChHHHh
Q 012141 300 RNIALPVLFSPLFLLQGVGVVFSTTRLVEKIVILLRSGAGT-GIYFRISSRAHDCFGFLHRGSRLLGWWSIDEGSREDQA 378 (470)
Q Consensus 300 ~~~~~~~if~Pl~l~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~~~~~~s~~~~~~~~~~~~~rl~~~W~~de~~wee~A 378 (470)
+-.....-+.|..+-..++.+...+..-.+..-.-....++ .+++.-..|...+-....+|=...++|..+.+.-..|.
T Consensus 37 ~l~~~~~~~~~~~~~~~l~~~e~~~~~~l~~k~~ei~~~~~~~~~l~~~~~~~~~e~~~w~~~a~~ne~~~~~l~~nl~q 116 (207)
T KOG1100|consen 37 QLRRELEENRQRELRNLLKAVEEALVKKLREKDEEIERIGNLNWELEERVKSLYVEAQIWRDRAQTNEATVNSLRTNLDQ 116 (207)
T ss_pred HHHHHHHHhChHHHHHHHHHHHHHHHHHhhcchhHHHhcccccceehhhhhhhhhhHHHHHHHHHhChHHHHHHHHHHHH
Confidence 34455567788888888887776655555554444444444 77888888888888888888888887777665444444
Q ss_pred hhhhcCCCCCccccCCCccceeecCchhhhHHHHHHHhhhcCCcccccccHHHHHHhhhcccccccccccceeEEEecCC
Q 012141 379 RLVHENSSGYNTFCGYPPEVVKKMPKKELAEEVWRLQAALGQQSEITNYSRQEFERLQNEKVLCRVCFEGDISVVLLPCR 458 (470)
Q Consensus 379 r~~~~~~~~~~~~c~~~p~~v~~~~~~~~~~e~~~~~~a~~~q~~~~k~~~~~~~~l~~e~~~CkiC~~~~~~vVflPCg 458 (470)
..+. | + +.++..++.+.....++...+ + .+...++.++..+++. |+.|.+++..|+++||+
T Consensus 117 -~~~~--------~--~-~~~~~~~~~~~~~g~~~~~~~-----~-s~~~~~~~~~~~~~~~-Cr~C~~~~~~VlllPCr 177 (207)
T KOG1100|consen 117 -VLAQ--------C--P-ASAPAEERGQKSCGDREADDG-----K-SSYVDPSVDNFKRMRS-CRKCGEREATVLLLPCR 177 (207)
T ss_pred -HHHh--------c--c-cccCchhhhccccCccccccc-----c-ccccchhhhhhhcccc-ceecCcCCceEEeeccc
Confidence 4444 1 1 233333333322333332222 1 1345666777777774 99999999999999999
Q ss_pred ceeecccccCC
Q 012141 459 HRILCRYDHLT 469 (470)
Q Consensus 459 H~v~C~~Ca~s 469 (470)
|++.|+.|+.+
T Consensus 178 Hl~lC~~C~~~ 188 (207)
T KOG1100|consen 178 HLCLCGICDES 188 (207)
T ss_pred ceEeccccccc
Confidence 99999999863
No 7
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.05 E-value=1.4e-06 Score=65.65 Aligned_cols=29 Identities=41% Similarity=0.792 Sum_probs=26.2
Q ss_pred cccccccccceeEEEecCCceeecccccC
Q 012141 440 VLCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 440 ~~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
..|.||+++..++++.||||.+.|.+|+.
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~~C~~ 31 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCEECAE 31 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEHHHHH
T ss_pred CCCccCCccCCceEEeCCCChHHHHHHhH
Confidence 48999999999999999999999999975
No 8
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=1.2e-06 Score=90.29 Aligned_cols=35 Identities=29% Similarity=0.566 Sum_probs=30.9
Q ss_pred hhhcccccccccccceeEEEecCCceeecccccCC
Q 012141 435 LQNEKVLCRVCFEGDISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 435 l~~e~~~CkiC~~~~~~vVflPCgH~v~C~~Ca~s 469 (470)
.+++.+.|+||+.+-+|++.+||||+|+|+.||..
T Consensus 286 ~~~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~ 320 (349)
T KOG4265|consen 286 ESESGKECVICLSESRDTVVLPCRHLCLCSGCAKS 320 (349)
T ss_pred cccCCCeeEEEecCCcceEEecchhhehhHhHHHH
Confidence 34445689999999999999999999999999964
No 9
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=1.6e-06 Score=87.61 Aligned_cols=30 Identities=27% Similarity=0.639 Sum_probs=28.0
Q ss_pred cccccccccceeEEEecCCceeecccccCC
Q 012141 440 VLCRVCFEGDISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 440 ~~CkiC~~~~~~vVflPCgH~v~C~~Ca~s 469 (470)
.+|+||||..||.|||||||.|.|.+|...
T Consensus 301 ~LC~ICmDaP~DCvfLeCGHmVtCt~CGkr 330 (350)
T KOG4275|consen 301 RLCAICMDAPRDCVFLECGHMVTCTKCGKR 330 (350)
T ss_pred HHHHHHhcCCcceEEeecCcEEeehhhccc
Confidence 489999999999999999999999999754
No 10
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=3.5e-05 Score=79.81 Aligned_cols=31 Identities=32% Similarity=0.651 Sum_probs=28.5
Q ss_pred ccccccccccceeEEEecCCceeecccccCC
Q 012141 439 KVLCRVCFEGDISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 439 ~~~CkiC~~~~~~vVflPCgH~v~C~~Ca~s 469 (470)
+..|.||.+++.|++|+||||+|+|..|+..
T Consensus 305 p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~ 335 (355)
T KOG1571|consen 305 PDLCVVCLDEPKSAVFVPCGHVCCCTLCSKH 335 (355)
T ss_pred CCceEEecCCccceeeecCCcEEEchHHHhh
Confidence 4589999999999999999999999999864
No 11
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=96.34 E-value=0.0019 Score=51.57 Aligned_cols=32 Identities=16% Similarity=0.287 Sum_probs=28.8
Q ss_pred ccceeeeeeCcccCCcccCCCCChHHHhhhhhc
Q 012141 351 HDCFGFLHRGSRLLGWWSIDEGSREDQARLVHE 383 (470)
Q Consensus 351 ~~~~~~~~~~~rl~~~W~~de~~wee~Ar~~~~ 383 (470)
.|-+.=.+|+.++.+ |+++|+||+||+++.|+
T Consensus 34 ~d~v~C~~C~~~l~~-w~~~d~p~~~H~~~~p~ 65 (71)
T smart00238 34 GDEVKCFFCGGELDN-WEPGDDPWEEHKKWSPN 65 (71)
T ss_pred CCEEEeCCCCCCcCC-CCCCCCHHHHHhHhCcC
Confidence 555666789999999 99999999999999999
No 12
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=96.19 E-value=0.0018 Score=52.12 Aligned_cols=32 Identities=19% Similarity=0.279 Sum_probs=27.7
Q ss_pred ccceeeeeeCcccCCcccCCCCChHHHhhhhhc
Q 012141 351 HDCFGFLHRGSRLLGWWSIDEGSREDQARLVHE 383 (470)
Q Consensus 351 ~~~~~~~~~~~rl~~~W~~de~~wee~Ar~~~~ 383 (470)
.|-+.=.+|+..+.+ |+++||||+||.++.|+
T Consensus 34 ~d~v~C~~C~~~l~~-w~~~Ddp~~~H~~~sp~ 65 (70)
T PF00653_consen 34 GDRVRCFYCGLELDN-WEPNDDPWEEHKRHSPN 65 (70)
T ss_dssp TTEEEETTTTEEEES--STT--HHHHHHHHSTT
T ss_pred CCEEEEeccCCEEeC-CCCCCCHHHHHHHHCcC
Confidence 788999999999999 89999999999999999
No 13
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.00 E-value=0.00048 Score=54.48 Aligned_cols=28 Identities=32% Similarity=0.752 Sum_probs=26.6
Q ss_pred ccccccccceeEEEecCCceeecccccC
Q 012141 441 LCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 441 ~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
+|.||+|+.+|.|+--|||.+.|-.|+.
T Consensus 9 ECTICye~pvdsVlYtCGHMCmCy~Cg~ 36 (62)
T KOG4172|consen 9 ECTICYEHPVDSVLYTCGHMCMCYACGL 36 (62)
T ss_pred ceeeeccCcchHHHHHcchHHhHHHHHH
Confidence 6999999999999999999999999974
No 14
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=95.73 E-value=0.007 Score=48.06 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=29.6
Q ss_pred ccceeeeeeCcccCCcccCCCCChHHHhhhhhc
Q 012141 351 HDCFGFLHRGSRLLGWWSIDEGSREDQARLVHE 383 (470)
Q Consensus 351 ~~~~~~~~~~~rl~~~W~~de~~wee~Ar~~~~ 383 (470)
+|-+.=.+|+.++.+ |+++|+||+||+++.|+
T Consensus 32 ~d~v~C~~C~~~~~~-w~~~d~p~~~H~~~~p~ 63 (69)
T cd00022 32 GDEVKCFFCGLELKN-WEPGDDPWEEHKRWSPN 63 (69)
T ss_pred CCEEEeCCCCCCccC-CCCCCCHHHHHhHhCcC
Confidence 577777789999999 99999999999999999
No 15
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=95.09 E-value=0.0071 Score=43.33 Aligned_cols=26 Identities=27% Similarity=0.686 Sum_probs=22.2
Q ss_pred cccccccceeE-EEecCCceeecccccC
Q 012141 442 CRVCFEGDISV-VLLPCRHRILCRYDHL 468 (470)
Q Consensus 442 CkiC~~~~~~v-VflPCgH~v~C~~Ca~ 468 (470)
|.||++.-+|. ++.||||.. |.+|..
T Consensus 1 C~iC~~~~~~~~~~~~CGH~f-C~~C~~ 27 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSF-CKECIE 27 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEE-EHHHHH
T ss_pred CCCCCCcccCcCEECCCCCch-hHHHHH
Confidence 78999999999 799999995 999864
No 16
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.06 E-value=0.0059 Score=63.83 Aligned_cols=28 Identities=43% Similarity=0.971 Sum_probs=24.9
Q ss_pred cccccccccccceeEEEecCCceeecccc
Q 012141 438 EKVLCRVCFEGDISVVLLPCRHRILCRYD 466 (470)
Q Consensus 438 e~~~CkiC~~~~~~vVflPCgH~v~C~~C 466 (470)
|..+|.||+..++++||-||+|.. |..|
T Consensus 421 Ed~lCpICyA~pi~Avf~PC~H~S-C~~C 448 (489)
T KOG4692|consen 421 EDNLCPICYAGPINAVFAPCSHRS-CYGC 448 (489)
T ss_pred ccccCcceecccchhhccCCCCch-HHHH
Confidence 445999999999999999999997 7777
No 17
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=94.67 E-value=0.01 Score=39.97 Aligned_cols=25 Identities=40% Similarity=0.887 Sum_probs=22.4
Q ss_pred cccccccceeEEEecCCceeeccccc
Q 012141 442 CRVCFEGDISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 442 CkiC~~~~~~vVflPCgH~v~C~~Ca 467 (470)
|.||++...+.+.+||||. .|.+|.
T Consensus 1 C~iC~~~~~~~~~~~C~H~-~c~~C~ 25 (39)
T smart00184 1 CPICLEELKDPVVLPCGHT-FCRSCI 25 (39)
T ss_pred CCcCccCCCCcEEecCCCh-HHHHHH
Confidence 7899999999999999999 488875
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=92.91 E-value=0.037 Score=41.41 Aligned_cols=25 Identities=32% Similarity=0.721 Sum_probs=13.9
Q ss_pred ccccccccee----EEEecCCceeecccccC
Q 012141 442 CRVCFEGDIS----VVLLPCRHRILCRYDHL 468 (470)
Q Consensus 442 CkiC~~~~~~----vVflPCgH~v~C~~Ca~ 468 (470)
|.||+| ..+ -+.|||||.. |.+|..
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~-c~~cl~ 29 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVF-CKDCLQ 29 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EE-EHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHH-HHHHHH
Confidence 678887 555 6779999997 888753
No 19
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.86 E-value=0.033 Score=59.17 Aligned_cols=28 Identities=36% Similarity=0.776 Sum_probs=25.3
Q ss_pred cccccccccceeEEEecCCceeecccccC
Q 012141 440 VLCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 440 ~~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
.+||||-|++.||=.=||||+. |..|-.
T Consensus 370 eLCKICaendKdvkIEPCGHLl-Ct~CLa 397 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEPCGHLL-CTSCLA 397 (563)
T ss_pred HHHHHhhccCCCcccccccchH-HHHHHH
Confidence 3899999999999999999996 998853
No 20
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=91.91 E-value=0.058 Score=38.49 Aligned_cols=26 Identities=42% Similarity=0.809 Sum_probs=22.8
Q ss_pred cccccccceeEE-EecCCceeecccccC
Q 012141 442 CRVCFEGDISVV-LLPCRHRILCRYDHL 468 (470)
Q Consensus 442 CkiC~~~~~~vV-flPCgH~v~C~~Ca~ 468 (470)
|.||++.-.+-+ ++||||.. |.+|..
T Consensus 1 C~iC~~~~~~~~~~~~C~H~f-C~~C~~ 27 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSF-CRDCLR 27 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEE-EHHHHH
T ss_pred CCcCCccccCCCEEecCCCcc-hHHHHH
Confidence 789999999998 99999995 988853
No 21
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.69 E-value=0.061 Score=57.33 Aligned_cols=38 Identities=29% Similarity=0.635 Sum_probs=31.1
Q ss_pred HHHHHhhhcccccccccccc---eeEEEecCCceeecccccC
Q 012141 430 QEFERLQNEKVLCRVCFEGD---ISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 430 ~~~~~l~~e~~~CkiC~~~~---~~vVflPCgH~v~C~~Ca~ 468 (470)
+..+..++....|-|||+.+ .+++|+||+|+- |..|+.
T Consensus 175 a~~~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~-Ck~C~k 215 (445)
T KOG1814|consen 175 ATLEKFVNSLFDCCICFEEQMGQHCFKFLPCSHVF-CKSCLK 215 (445)
T ss_pred HHHHHHHhhcccceeeehhhcCcceeeecccchHH-HHHHHH
Confidence 34567777788999999976 569999999986 999974
No 22
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.03 E-value=0.17 Score=40.06 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=24.5
Q ss_pred cccccccccceeEEEecCCceeecccccC
Q 012141 440 VLCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 440 ~~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
..|..|......=+++||||++ |..|-+
T Consensus 8 ~~~~~~~~~~~~~~~~pCgH~I-~~~~f~ 35 (55)
T PF14447_consen 8 QPCVFCGFVGTKGTVLPCGHLI-CDNCFP 35 (55)
T ss_pred eeEEEcccccccccccccccee-eccccC
Confidence 4899999998899999999998 888853
No 23
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=88.13 E-value=0.12 Score=37.98 Aligned_cols=27 Identities=30% Similarity=0.588 Sum_probs=21.7
Q ss_pred cccccccc---eeEEEecCCceeecccccCC
Q 012141 442 CRVCFEGD---ISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 442 CkiC~~~~---~~vVflPCgH~v~C~~Ca~s 469 (470)
|.+|+++- +..++++|||.. |.+|...
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~-C~~C~~~ 31 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIF-CEKCLKK 31 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHH-HHHHHHh
Confidence 77787764 579999999996 9999754
No 24
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=86.11 E-value=0.33 Score=35.79 Aligned_cols=25 Identities=36% Similarity=0.760 Sum_probs=20.5
Q ss_pred cccccccceeEEEecCCceeeccccc
Q 012141 442 CRVCFEGDISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 442 CkiC~~~~~~vVflPCgH~v~C~~Ca 467 (470)
|-||++-=.+=|-++|||.. |..|-
T Consensus 1 CpiC~~~~~~Pv~l~CGH~F-C~~Cl 25 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSF-CRSCL 25 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEE-EHHHH
T ss_pred CCccchhhCCccccCCcCHH-HHHHH
Confidence 78999999999999999997 88874
No 25
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=84.87 E-value=0.34 Score=33.56 Aligned_cols=26 Identities=38% Similarity=0.768 Sum_probs=19.0
Q ss_pred ccccccccceeEEEe-cCCceeeccccc
Q 012141 441 LCRVCFEGDISVVLL-PCRHRILCRYDH 467 (470)
Q Consensus 441 ~CkiC~~~~~~vVfl-PCgH~v~C~~Ca 467 (470)
.|.||++.-.+.+.+ ||||.. |.+|.
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~-c~~C~ 27 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVF-CRSCI 27 (45)
T ss_pred CCCcCchhhhCceEecCCCChh-cHHHH
Confidence 488999987454444 599985 77775
No 26
>PHA02929 N1R/p28-like protein; Provisional
Probab=84.12 E-value=0.42 Score=47.86 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=20.3
Q ss_pred ccccccccccee--------EEEecCCceeeccccc
Q 012141 440 VLCRVCFEGDIS--------VVLLPCRHRILCRYDH 467 (470)
Q Consensus 440 ~~CkiC~~~~~~--------vVflPCgH~v~C~~Ca 467 (470)
..|.||+|.-.+ .++.||||.- |.+|-
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~F-C~~CI 209 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVF-CIECI 209 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcc-cHHHH
Confidence 479999996332 4677899975 88884
No 27
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=77.47 E-value=1 Score=32.73 Aligned_cols=26 Identities=38% Similarity=0.616 Sum_probs=21.0
Q ss_pred ccccccccc---eeEEEecCCceeeccccc
Q 012141 441 LCRVCFEGD---ISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 441 ~CkiC~~~~---~~vVflPCgH~v~C~~Ca 467 (470)
.|.||++.- ..++-+||||.. |.+|.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~f-h~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVF-HRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEE-EHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCee-CHHHH
Confidence 588998764 689999999976 87774
No 28
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.65 E-value=0.89 Score=48.01 Aligned_cols=30 Identities=27% Similarity=0.662 Sum_probs=26.2
Q ss_pred cccccccccccceeEEEecCCceeecccccC
Q 012141 438 EKVLCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 438 e~~~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
|...|.||-+.-.=+...||+|.. |--||.
T Consensus 60 en~~C~ICA~~~TYs~~~PC~H~~-CH~Ca~ 89 (493)
T COG5236 60 ENMNCQICAGSTTYSARYPCGHQI-CHACAV 89 (493)
T ss_pred ccceeEEecCCceEEEeccCCchH-HHHHHH
Confidence 345899999999999999999997 888875
No 29
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.47 E-value=1.6 Score=43.62 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=23.7
Q ss_pred ccccccccccceeEEEecCCceeecccc
Q 012141 439 KVLCRVCFEGDISVVLLPCRHRILCRYD 466 (470)
Q Consensus 439 ~~~CkiC~~~~~~vVflPCgH~v~C~~C 466 (470)
.-.|-||+|...|-|+=+|||+- |=.|
T Consensus 47 ~FdCNICLd~akdPVvTlCGHLF-CWpC 73 (230)
T KOG0823|consen 47 FFDCNICLDLAKDPVVTLCGHLF-CWPC 73 (230)
T ss_pred ceeeeeeccccCCCEEeecccce-ehHH
Confidence 34799999999999999999997 6555
No 30
>PHA02926 zinc finger-like protein; Provisional
Probab=71.39 E-value=1.4 Score=44.12 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=22.5
Q ss_pred hhhcccccccccccc---------eeEEEecCCceeeccccc
Q 012141 435 LQNEKVLCRVCFEGD---------ISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 435 l~~e~~~CkiC~~~~---------~~vVflPCgH~v~C~~Ca 467 (470)
..+|+ +|.||+|.- +--++.||+|.- |-.|-
T Consensus 167 ~SkE~-eCgICmE~I~eK~~~~eRrFGIL~~CnHsF-Cl~CI 206 (242)
T PHA02926 167 VSKEK-ECGICYEVVYSKRLENDRYFGLLDSCNHIF-CITCI 206 (242)
T ss_pred ccCCC-CCccCccccccccccccccccccCCCCchH-HHHHH
Confidence 33444 899999863 225889999985 88773
No 31
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=69.79 E-value=0.82 Score=51.99 Aligned_cols=37 Identities=22% Similarity=0.428 Sum_probs=29.6
Q ss_pred HHHHHHhhhcccccccccccceeEEEecCCceeeccccc
Q 012141 429 RQEFERLQNEKVLCRVCFEGDISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 429 ~~~~~~l~~e~~~CkiC~~~~~~vVflPCgH~v~C~~Ca 467 (470)
.||+++-++ ...|.+|.+|..|+|+.-|||+- |.+|-
T Consensus 634 ~EElk~yK~-~LkCs~Cn~R~Kd~vI~kC~H~F-C~~Cv 670 (698)
T KOG0978|consen 634 AEELKEYKE-LLKCSVCNTRWKDAVITKCGHVF-CEECV 670 (698)
T ss_pred HHHHHHHHh-ceeCCCccCchhhHHHHhcchHH-HHHHH
Confidence 344444443 56899999999999999999997 88885
No 32
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=68.56 E-value=2.1 Score=32.73 Aligned_cols=26 Identities=27% Similarity=0.364 Sum_probs=22.4
Q ss_pred ccccccccceeEEEecCCceeeccccc
Q 012141 441 LCRVCFEGDISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 441 ~CkiC~~~~~~vVflPCgH~v~C~~Ca 467 (470)
.|.||++--.|=|..||||.. |.+|-
T Consensus 3 ~Cpi~~~~~~~Pv~~~~G~v~-~~~~i 28 (63)
T smart00504 3 LCPISLEVMKDPVILPSGQTY-ERRAI 28 (63)
T ss_pred CCcCCCCcCCCCEECCCCCEE-eHHHH
Confidence 699999999999999999886 77663
No 33
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=64.96 E-value=2.7 Score=44.92 Aligned_cols=29 Identities=31% Similarity=0.732 Sum_probs=20.3
Q ss_pred HHhhhccccccccccccee-----------E--EEecCCcee
Q 012141 433 ERLQNEKVLCRVCFEGDIS-----------V--VLLPCRHRI 461 (470)
Q Consensus 433 ~~l~~e~~~CkiC~~~~~~-----------v--VflPCgH~v 461 (470)
|++.+++..|.||||+-.. + ==+||||--
T Consensus 281 eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHil 322 (491)
T COG5243 281 EQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHIL 322 (491)
T ss_pred hhhcCCCCeEEEecccccCCCCccCcccccCCccccccccee
Confidence 5667777799999998111 1 238999963
No 34
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=62.39 E-value=1.4 Score=45.33 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=23.2
Q ss_pred cccccccccceeEEEecCCceeecccc
Q 012141 440 VLCRVCFEGDISVVLLPCRHRILCRYD 466 (470)
Q Consensus 440 ~~CkiC~~~~~~vVflPCgH~v~C~~C 466 (470)
..|.+|+|+..|=-.-||||.- |-.|
T Consensus 240 ~kC~LCLe~~~~pSaTpCGHiF-CWsC 265 (293)
T KOG0317|consen 240 RKCSLCLENRSNPSATPCGHIF-CWSC 265 (293)
T ss_pred CceEEEecCCCCCCcCcCcchH-HHHH
Confidence 3799999999999999999997 7666
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.87 E-value=2.3 Score=43.29 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=22.8
Q ss_pred ccccccccceeEEEecCCceeeccccc
Q 012141 441 LCRVCFEGDISVVLLPCRHRILCRYDH 467 (470)
Q Consensus 441 ~CkiC~~~~~~vVflPCgH~v~C~~Ca 467 (470)
.|.+|+|..-+-+-.||||+- |-.|-
T Consensus 217 kC~lC~e~~~~ps~t~CgHlF-C~~Cl 242 (271)
T COG5574 217 KCFLCLEEPEVPSCTPCGHLF-CLSCL 242 (271)
T ss_pred ceeeeecccCCcccccccchh-hHHHH
Confidence 699999999999999999997 55553
No 36
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.53 E-value=4.7 Score=41.03 Aligned_cols=32 Identities=19% Similarity=0.279 Sum_probs=26.2
Q ss_pred hccccccccccc----ceeEEEecCCceeecccccCC
Q 012141 437 NEKVLCRVCFEG----DISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 437 ~e~~~CkiC~~~----~~~vVflPCgH~v~C~~Ca~s 469 (470)
+++-.|.+|.+. -.++|+-||||+| |.+|+..
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv-~~ecvEk 254 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVV-TKECVEK 254 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEe-eHHHHHH
Confidence 367799999875 4568999999997 9999864
No 37
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.95 E-value=9.6 Score=42.12 Aligned_cols=27 Identities=26% Similarity=0.528 Sum_probs=23.6
Q ss_pred ccccccccccceeEEEecCCceeecccc
Q 012141 439 KVLCRVCFEGDISVVLLPCRHRILCRYD 466 (470)
Q Consensus 439 ~~~CkiC~~~~~~vVflPCgH~v~C~~C 466 (470)
...|-||++...-.+..-|||.- |-.|
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiF-C~~C 212 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIF-CGPC 212 (513)
T ss_pred CCcCCcccCCCCcccccccCcee-eHHH
Confidence 34899999999999999999997 6566
No 38
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.65 E-value=5.5 Score=38.68 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=23.0
Q ss_pred ccccccccccceeEE--EecCCceeecccccC
Q 012141 439 KVLCRVCFEGDISVV--LLPCRHRILCRYDHL 468 (470)
Q Consensus 439 ~~~CkiC~~~~~~vV--flPCgH~v~C~~Ca~ 468 (470)
..-|.||++....-+ ---|||+- |++|..
T Consensus 131 ~~~CPiCl~~~sek~~vsTkCGHvF-C~~Cik 161 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVPVSTKCGHVF-CSQCIK 161 (187)
T ss_pred ccCCCceecchhhccccccccchhH-HHHHHH
Confidence 357999999877666 36999997 999963
No 39
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.37 E-value=7.9 Score=41.64 Aligned_cols=63 Identities=24% Similarity=0.403 Sum_probs=39.6
Q ss_pred CCCccceeecCchhhhHHHHHHHhhhcCCcccccccHHHHHHhhhcccccccccccceeEEEecCCceeecccc
Q 012141 393 GYPPEVVKKMPKKELAEEVWRLQAALGQQSEITNYSRQEFERLQNEKVLCRVCFEGDISVVLLPCRHRILCRYD 466 (470)
Q Consensus 393 ~~~p~~v~~~~~~~~~~e~~~~~~a~~~q~~~~k~~~~~~~~l~~e~~~CkiC~~~~~~vVflPCgH~v~C~~C 466 (470)
|+|++..+.-++++..+-... +++..-.+.+++. ..| -.|-||+.---+-|-.||||-- |..|
T Consensus 48 ~~p~~~~~~~~~~~~~e~~~~------~~~~~~~s~~~~~---~se-f~c~vc~~~l~~pv~tpcghs~-c~~C 110 (398)
T KOG4159|consen 48 GVPNRCINEDPGKSSEETMAD------STPKALLSGPEEI---RSE-FECCVCSRALYPPVVTPCGHSF-CLEC 110 (398)
T ss_pred cCCHHHHhcccchhhhhhhhh------hhhhhhhccCccc---cch-hhhhhhHhhcCCCccccccccc-cHHH
Confidence 678888777777774442221 2222111122222 333 3799999998888888999986 8877
No 40
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.77 E-value=11 Score=41.59 Aligned_cols=31 Identities=32% Similarity=0.457 Sum_probs=25.0
Q ss_pred hhhccccccccccccee-----EEEecCCceeecccc
Q 012141 435 LQNEKVLCRVCFEGDIS-----VVLLPCRHRILCRYD 466 (470)
Q Consensus 435 l~~e~~~CkiC~~~~~~-----vVflPCgH~v~C~~C 466 (470)
+.+....|.||.|.-.+ .--+||||.. |.+|
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hif-h~~C 322 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIF-HDSC 322 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccch-HHHH
Confidence 44445589999999998 7999999986 6665
No 41
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=30.26 E-value=10 Score=37.64 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=24.8
Q ss_pred ccccccccceeEEEecCCceeecccccC
Q 012141 441 LCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 441 ~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
.|.||.+.=.+-|.-.|||.- |+.||.
T Consensus 198 ~C~iCKkdy~spvvt~CGH~F-C~~Cai 224 (259)
T COG5152 198 LCGICKKDYESPVVTECGHSF-CSLCAI 224 (259)
T ss_pred eehhchhhccchhhhhcchhH-HHHHHH
Confidence 799999999999999999997 999984
No 42
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=29.09 E-value=33 Score=36.27 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=28.2
Q ss_pred ccccccccccceeEEEecCCceeecccccCC
Q 012141 439 KVLCRVCFEGDISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 439 ~~~CkiC~~~~~~vVflPCgH~v~C~~Ca~s 469 (470)
+..|.+|++++.-+-.+||||-|-|.+|++.
T Consensus 136 ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~ 166 (394)
T KOG2113|consen 136 TIKRIQQFTNTYIATPVRCGEPVFCVTGAPK 166 (394)
T ss_pred ccchheecccceEeeeccCCCceEEEecCCc
Confidence 4579999999999999999999999999864
No 43
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=27.88 E-value=46 Score=27.72 Aligned_cols=29 Identities=24% Similarity=0.367 Sum_probs=21.3
Q ss_pred ccccccccccc--eeEEEecCCceeecccccC
Q 012141 439 KVLCRVCFEGD--ISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 439 ~~~CkiC~~~~--~~vVflPCgH~v~C~~Ca~ 468 (470)
...|.+|..+= ...+.-||||.+ -..|+.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~-H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV-HYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE-eccccc
Confidence 34799998753 356677999876 888863
No 44
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=26.70 E-value=21 Score=38.51 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=0.0
Q ss_pred eeEEEecCCcee
Q 012141 450 ISVVLLPCRHRI 461 (470)
Q Consensus 450 ~~vVflPCgH~v 461 (470)
-.-+|-||||.+
T Consensus 358 pthaF~PCGHv~ 369 (416)
T PF04710_consen 358 PTHAFNPCGHVC 369 (416)
T ss_dssp ------------
T ss_pred Cceeeccccccc
Confidence 356999999997
No 45
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.14 E-value=61 Score=34.22 Aligned_cols=23 Identities=39% Similarity=0.907 Sum_probs=17.2
Q ss_pred ccccccccccce---eEEEecCCcee
Q 012141 439 KVLCRVCFEGDI---SVVLLPCRHRI 461 (470)
Q Consensus 439 ~~~CkiC~~~~~---~vVflPCgH~v 461 (470)
...|.|||++-+ -++.+||.|.-
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~F 348 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRF 348 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCcee
Confidence 368999998522 28899999863
No 46
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.90 E-value=49 Score=35.24 Aligned_cols=21 Identities=33% Similarity=0.975 Sum_probs=16.9
Q ss_pred cccccccc---ceeEEEecCCcee
Q 012141 441 LCRVCFEG---DISVVLLPCRHRI 461 (470)
Q Consensus 441 ~CkiC~~~---~~~vVflPCgH~v 461 (470)
+|-||+|. +-.+..|||+|--
T Consensus 231 ~CaIClEdY~~GdklRiLPC~H~F 254 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILPCSHKF 254 (348)
T ss_pred eEEEeecccccCCeeeEecCCCch
Confidence 79999874 4567889999963
No 47
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.40 E-value=36 Score=35.56 Aligned_cols=27 Identities=26% Similarity=0.489 Sum_probs=24.9
Q ss_pred cccccccceeEEEecCCceeecccccCC
Q 012141 442 CRVCFEGDISVVLLPCRHRILCRYDHLT 469 (470)
Q Consensus 442 CkiC~~~~~~vVflPCgH~v~C~~Ca~s 469 (470)
|-||..-=++=|.--|||.+ |+.||.+
T Consensus 244 c~icr~~f~~pVvt~c~h~f-c~~ca~~ 270 (313)
T KOG1813|consen 244 CFICRKYFYRPVVTKCGHYF-CEVCALK 270 (313)
T ss_pred ccccccccccchhhcCCcee-ehhhhcc
Confidence 99999999999999999998 9999964
No 48
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=20.12 E-value=55 Score=34.68 Aligned_cols=28 Identities=7% Similarity=-0.264 Sum_probs=26.8
Q ss_pred ccccccccceeEEEecCCceeecccccC
Q 012141 441 LCRVCFEGDISVVLLPCRHRILCRYDHL 468 (470)
Q Consensus 441 ~CkiC~~~~~~vVflPCgH~v~C~~Ca~ 468 (470)
.|-+|-++-....+.||||-.-|.+||.
T Consensus 345 ~~~~~~~~~~st~~~~~~~n~~~~~~a~ 372 (394)
T KOG2113|consen 345 KGTSAGFGLLSTIWSGGNMNLSPGSLAS 372 (394)
T ss_pred ccccccCceeeeEeecCCcccChhhhhh
Confidence 7999999999999999999999999985
Done!