Query 020822
Match_columns 321
No_of_seqs 324 out of 1325
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:26:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020822.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020822hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2632 Rhomboid family protei 99.9 1.7E-24 3.7E-29 200.1 11.1 138 1-144 73-211 (258)
2 PTZ00101 rhomboid-1 protease; 99.4 1.1E-12 2.4E-17 124.4 10.6 119 1-137 122-247 (278)
3 COG0705 Membrane associated se 99.4 2.3E-12 5E-17 117.8 11.0 117 1-130 88-211 (228)
4 PRK10907 intramembrane serine 99.3 5.2E-12 1.1E-16 119.8 10.3 109 1-127 155-267 (276)
5 PF01694 Rhomboid: Rhomboid fa 99.3 1.4E-12 3E-17 110.1 5.2 115 1-131 26-143 (145)
6 PF00627 UBA: UBA/TS-N domain; 99.2 9E-12 2E-16 83.3 4.5 36 282-317 2-37 (37)
7 smart00165 UBA Ubiquitin assoc 99.1 1.5E-10 3.2E-15 77.0 5.2 36 282-317 1-36 (37)
8 cd00194 UBA Ubiquitin Associat 99.1 2.9E-10 6.2E-15 76.0 5.2 36 282-317 1-36 (38)
9 KOG2289 Rhomboid family protei 98.6 3.5E-09 7.6E-14 101.9 -1.6 108 1-128 139-252 (316)
10 TIGR00601 rad23 UV excision re 98.4 2.5E-07 5.5E-12 91.4 4.9 36 282-317 156-191 (378)
11 KOG0011 Nucleotide excision re 98.0 1.2E-05 2.7E-10 77.2 5.8 37 281-317 134-170 (340)
12 PF04511 DER1: Der1-like famil 97.9 5.3E-05 1.2E-09 68.4 8.3 120 2-136 64-186 (197)
13 KOG0944 Ubiquitin-specific pro 97.8 2E-05 4.3E-10 81.7 4.4 38 280-317 633-670 (763)
14 TIGR00601 rad23 UV excision re 97.7 3.9E-05 8.4E-10 76.1 5.4 43 277-319 332-375 (378)
15 KOG2290 Rhomboid family protei 97.6 2.1E-05 4.5E-10 78.6 0.8 115 5-136 475-591 (652)
16 KOG0011 Nucleotide excision re 97.5 0.00012 2.5E-09 70.7 5.0 41 279-319 295-336 (340)
17 KOG0418 Ubiquitin-protein liga 97.5 9.4E-05 2E-09 66.0 3.8 36 282-317 162-197 (200)
18 PF14555 UBA_4: UBA-like domai 96.9 0.002 4.3E-08 44.3 4.9 35 283-317 1-36 (43)
19 KOG2561 Adaptor protein NUB1, 96.8 0.0013 2.8E-08 65.9 4.1 38 280-317 301-338 (568)
20 KOG0858 Predicted membrane pro 96.7 0.0054 1.2E-07 57.0 7.5 114 1-135 74-190 (239)
21 PF02845 CUE: CUE domain; Int 96.6 0.0056 1.2E-07 41.7 4.9 35 283-317 2-38 (42)
22 COG5207 UBP14 Isopeptidase T [ 96.6 0.0016 3.5E-08 66.2 3.1 38 280-317 619-656 (749)
23 PF08551 DUF1751: Eukaryotic i 96.4 0.0025 5.4E-08 51.7 2.9 68 3-72 30-97 (99)
24 smart00546 CUE Domain that may 96.1 0.013 2.8E-07 40.0 4.9 36 282-317 2-39 (43)
25 PRK06369 nac nascent polypepti 95.9 0.018 3.9E-07 48.1 5.6 39 280-318 74-113 (115)
26 COG5207 UBP14 Isopeptidase T [ 95.7 0.013 2.8E-07 59.8 4.7 39 281-319 557-596 (749)
27 KOG2561 Adaptor protein NUB1, 95.6 0.014 2.9E-07 58.8 4.5 38 280-317 427-464 (568)
28 TIGR00264 alpha-NAC-related pr 95.5 0.03 6.5E-07 46.8 5.3 38 280-317 76-114 (116)
29 KOG0944 Ubiquitin-specific pro 95.4 0.022 4.7E-07 59.8 5.2 39 279-317 568-607 (763)
30 PF09288 UBA_3: Fungal ubiquit 95.4 0.018 3.8E-07 42.0 3.3 26 282-307 9-34 (55)
31 KOG2890 Predicted membrane pro 95.1 0.064 1.4E-06 51.6 6.9 124 3-134 89-219 (326)
32 COG1308 EGD2 Transcription fac 94.3 0.097 2.1E-06 44.0 5.3 38 280-317 82-120 (122)
33 COG5291 Predicted membrane pro 93.9 0.051 1.1E-06 51.0 3.2 46 76-122 143-188 (313)
34 KOG2980 Integral membrane prot 93.1 0.097 2.1E-06 50.4 3.8 73 55-127 220-298 (310)
35 KOG0010 Ubiquitin-like protein 93.0 0.11 2.4E-06 53.0 4.2 38 280-317 452-490 (493)
36 COG4008 Predicted metal-bindin 90.2 0.64 1.4E-05 39.5 5.1 37 280-317 112-148 (153)
37 PF11626 Rap1_C: TRF2-interact 88.6 0.62 1.3E-05 36.7 3.8 32 286-317 1-32 (87)
38 PF11547 E3_UbLigase_EDD: E3 u 88.2 1.2 2.7E-05 31.6 4.6 40 280-319 7-49 (53)
39 smart00804 TAP_C C-terminal do 87.9 1.1 2.4E-05 33.5 4.6 36 282-317 12-48 (63)
40 PF00641 zf-RanBP: Zn-finger i 87.4 0.25 5.4E-06 31.1 0.7 29 225-253 2-30 (30)
41 PF03943 TAP_C: TAP C-terminal 86.9 0.54 1.2E-05 33.6 2.3 35 283-317 1-36 (51)
42 PF06972 DUF1296: Protein of u 85.3 2 4.3E-05 31.8 4.6 37 283-319 6-45 (60)
43 KOG1071 Mitochondrial translat 84.3 1.8 3.9E-05 42.2 5.1 36 282-317 46-82 (340)
44 KOG4463 Uncharacterized conser 80.2 0.27 5.7E-06 46.7 -2.0 119 4-130 73-204 (323)
45 PF07499 RuvA_C: RuvA, C-termi 80.1 2.6 5.7E-05 29.3 3.5 26 282-307 3-28 (47)
46 PF07223 DUF1421: Protein of u 79.9 1.7 3.6E-05 43.2 3.3 23 282-304 321-343 (358)
47 PF02954 HTH_8: Bacterial regu 78.3 1.8 3.9E-05 29.3 2.1 24 294-317 5-28 (42)
48 KOG0943 Predicted ubiquitin-pr 78.2 7.7 0.00017 44.2 7.8 46 274-319 181-229 (3015)
49 smart00547 ZnF_RBZ Zinc finger 73.6 1.5 3.3E-05 26.3 0.7 25 226-250 1-25 (26)
50 PF08587 UBA_2: Ubiquitin asso 73.3 0.66 1.4E-05 32.6 -1.1 26 282-307 2-28 (46)
51 PF08938 HBS1_N: HBS1 N-termin 72.2 2 4.3E-05 33.3 1.2 25 295-319 45-70 (79)
52 PF03474 DMA: DMRTA motif; In 70.3 6.4 0.00014 26.7 3.2 22 296-317 17-38 (39)
53 PF11372 DUF3173: Domain of un 64.5 7.4 0.00016 28.8 2.8 20 287-306 7-26 (59)
54 KOG3763 mRNA export factor TAP 64.0 16 0.00034 38.4 6.0 36 282-317 535-571 (585)
55 KOG2239 Transcription factor c 55.4 18 0.00038 33.2 4.1 36 282-317 171-207 (209)
56 PRK14606 ruvA Holliday junctio 49.3 30 0.00066 31.2 4.7 26 282-307 143-168 (188)
57 PRK14603 ruvA Holliday junctio 49.0 32 0.0007 31.2 4.9 25 282-306 152-176 (197)
58 PRK14602 ruvA Holliday junctio 48.8 31 0.00067 31.5 4.7 25 282-306 155-179 (203)
59 PRK14604 ruvA Holliday junctio 48.2 32 0.00069 31.2 4.7 26 282-307 149-174 (195)
60 PF10440 WIYLD: Ubiquitin-bind 47.0 24 0.00052 26.6 3.1 24 282-305 11-34 (65)
61 PRK14601 ruvA Holliday junctio 46.4 23 0.0005 31.9 3.5 26 282-307 142-167 (183)
62 PRK14600 ruvA Holliday junctio 45.7 24 0.00052 31.8 3.5 26 282-307 145-170 (186)
63 smart00553 SEP Domain present 43.3 15 0.00032 29.6 1.6 16 208-223 74-89 (93)
64 PRK13901 ruvA Holliday junctio 43.2 29 0.00063 31.6 3.6 27 282-308 144-170 (196)
65 PRK07993 DNA polymerase III su 41.5 42 0.00091 32.8 4.8 36 282-317 168-205 (334)
66 TIGR00084 ruvA Holliday juncti 41.3 53 0.0012 29.6 5.1 26 282-307 147-172 (191)
67 COG0632 RuvA Holliday junction 40.5 41 0.00089 30.8 4.2 27 282-308 156-182 (201)
68 PRK08769 DNA polymerase III su 39.4 54 0.0012 32.0 5.1 37 282-318 174-210 (319)
69 PF04695 Pex14_N: Peroxisomal 38.5 38 0.00083 28.8 3.5 29 282-310 23-51 (136)
70 PRK00523 hypothetical protein; 38.1 67 0.0015 24.7 4.3 18 114-131 15-32 (72)
71 PF03765 CRAL_TRIO_N: CRAL/TRI 37.7 46 0.001 23.3 3.3 28 290-317 25-52 (55)
72 TIGR00834 ae anion exchange pr 36.6 1.8E+02 0.0038 32.7 9.0 72 56-130 425-504 (900)
73 KOG3450 Huntingtin interacting 32.9 63 0.0014 26.8 3.7 38 280-317 78-116 (119)
74 PRK01844 hypothetical protein; 32.5 91 0.002 24.0 4.3 19 113-131 13-31 (72)
75 PF03701 UPF0181: Uncharacteri 31.8 50 0.0011 23.7 2.5 21 283-303 17-37 (51)
76 PRK14605 ruvA Holliday junctio 31.4 85 0.0019 28.3 4.7 26 282-307 148-173 (194)
77 COG3140 Uncharacterized protei 30.8 41 0.00089 24.6 2.0 35 283-317 17-55 (60)
78 PF09527 ATPase_gene1: Putativ 27.9 1.3E+02 0.0029 21.1 4.4 29 5-33 18-47 (55)
79 KOG2086 Protein tyrosine phosp 27.1 49 0.0011 33.2 2.6 13 207-219 255-267 (380)
80 PRK01905 DNA-binding protein F 25.7 61 0.0013 24.7 2.4 24 294-317 37-60 (77)
81 COG3086 RseC Positive regulato 25.7 1.4E+02 0.0031 26.1 4.8 24 109-132 105-128 (150)
82 PF07848 PaaX: PaaX-like prote 25.1 57 0.0012 24.7 2.1 25 282-306 23-47 (70)
83 PRK05114 hypothetical protein; 24.5 78 0.0017 23.4 2.6 20 283-302 17-36 (59)
84 PRK00116 ruvA Holliday junctio 24.5 1.3E+02 0.0028 27.0 4.6 27 282-308 149-175 (192)
85 PF15520 Toxin_40: Putative to 23.8 36 0.00078 29.6 0.8 17 206-222 145-161 (178)
86 PF11990 DUF3487: Protein of u 23.1 4E+02 0.0086 22.4 7.0 31 130-162 77-109 (121)
87 PF11833 DUF3353: Protein of u 22.9 4.6E+02 0.0099 23.8 7.9 69 56-132 91-164 (194)
88 PF02536 mTERF: mTERF; InterP 22.0 87 0.0019 29.9 3.2 26 282-307 243-268 (345)
89 PRK00430 fis global DNA-bindin 21.8 78 0.0017 25.3 2.4 24 294-317 55-78 (95)
90 PF03672 UPF0154: Uncharacteri 21.5 1.2E+02 0.0025 22.9 3.1 20 112-131 5-24 (64)
91 PF14851 FAM176: FAM176 family 21.2 1.6E+02 0.0035 25.9 4.3 14 62-75 28-41 (153)
92 PRK05441 murQ N-acetylmuramic 20.8 98 0.0021 29.8 3.3 28 290-317 244-271 (299)
No 1
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.91 E-value=1.7e-24 Score=200.06 Aligned_cols=138 Identities=46% Similarity=0.743 Sum_probs=127.8
Q ss_pred CeeehhhhHHHHHhhC-hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCc
Q 020822 1 MLALVPLGSELERIMG-SVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQ 79 (321)
Q Consensus 1 MlaL~~~G~~lEr~~G-T~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~ 79 (321)
|++|+++|..+||.+| |.+++.++.+.++++|++|+++++++. .++.+++++++|+||+.||+++..+...|.+
T Consensus 73 mlaL~~~g~~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~-----~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r 147 (258)
T KOG2632|consen 73 MLALWPLGSQFERTHGTTVRILMFTVLLALFSGILYLLAYHVFL-----LSDLVYVEGAIGFSGVLFAMMAVLEVQSPVR 147 (258)
T ss_pred HHHHHhchhHHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHh-----hcchhhhcccccccHHHHHHHHHHhhcCccc
Confidence 7899999999999999 999999999999999999999998542 3334567889999999999999998888888
Q ss_pred cccccccccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhhhhcCCchhhHHHhhh
Q 020822 80 SRSVFGLFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGTSFYSAIES 144 (321)
Q Consensus 80 ~~~l~G~~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~l~p~~~~~~~iE~ 144 (321)
.+++||.+.||+++.||++++.+++++|+.||+||+||+++||.|.++.+ +++|..+.++.+|.
T Consensus 148 ~~~~fg~~siP~~l~Pw~lLi~~~~lvp~aSFlghl~GllvG~ay~~~~f-~lip~~~~~~~v~~ 211 (258)
T KOG2632|consen 148 SRSVFGLFSIPIVLAPWALLIATQILVPQASFLGHLCGLLVGYAYAFSSF-GLIPGIRNYRAVTE 211 (258)
T ss_pred chhhcccccccHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHHHhh-ccCCcchhHHHhhh
Confidence 88899999999999999999999999999999999999999999999988 99999999999996
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.41 E-value=1.1e-12 Score=124.35 Aligned_cols=119 Identities=21% Similarity=0.238 Sum_probs=79.9
Q ss_pred CeeehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCcc
Q 020822 1 MLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQS 80 (321)
Q Consensus 1 MlaL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~~ 80 (321)
|++++.+|..+|+.+|++||+.+|++++++++++.+++. + ...++||||++||+++++....-
T Consensus 122 m~~l~~~G~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~---------~-----~~~svGASgAifGLiGa~~~~li--- 184 (278)
T PTZ00101 122 VFFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVT---------Y-----CPIKVGASTSGMGLLGIVTSELI--- 184 (278)
T ss_pred HHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHc---------c-----CCcEEehhHHHHHHHHHHHHHHH---
Confidence 678999999999999999999999999999987643321 1 23689999999999998753210
Q ss_pred ccccccccchhHHHH----HHHH---HHHHHhcchhHHHHHHHHHHHHHHHHHHhhhhcCCchh
Q 020822 81 RSVFGLFNIPAKWYP----LILL---VLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGTS 137 (321)
Q Consensus 81 ~~l~G~~~IP~~~~p----~ilL---il~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~l~p~~~ 137 (321)
..+...+.+.+... ++++ +...+..|+++++||++|+++|++++.-+.+.+....+
T Consensus 185 -l~w~~~~~~~~~~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~~~l~~~~~ 247 (278)
T PTZ00101 185 -LLWHVIRHRERVVFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYNSQMENKPS 247 (278)
T ss_pred -HHHHhhccHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHhhhhhccc
Confidence 00000011222111 1111 11122347899999999999999999887665543333
No 3
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.39 E-value=2.3e-12 Score=117.83 Aligned_cols=117 Identities=26% Similarity=0.343 Sum_probs=85.1
Q ss_pred CeeehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCcc
Q 020822 1 MLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQS 80 (321)
Q Consensus 1 MlaL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~~ 80 (321)
|+.|+.+|..+|+.+|+.+|+.+|+++++++++.++++... .....+|+||++||++++++...|...
T Consensus 88 ~~~l~~fg~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~------------~~~~~~GASG~i~gllga~~~~~~~~~ 155 (228)
T COG0705 88 MLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPK------------GGAPSLGASGAIFGLLGAYFLLFPFAR 155 (228)
T ss_pred HHHHHHhhHHHHHHhchhHHHHHHHHHHHHHHHHHHHHccc------------ccCcccchhHHHHHHHHHHHHHccccc
Confidence 67899999999999999999999999999999875543211 125799999999999999999888654
Q ss_pred cccccc-ccchhHHHHHHHHHHHHHhc------chhHHHHHHHHHHHHHHHHHHhhh
Q 020822 81 RSVFGL-FNIPAKWYPLILLVLFQVLM------TNVSLLGHLCGILSGFAYTYGFFN 130 (321)
Q Consensus 81 ~~l~G~-~~IP~~~~p~ilLil~~ll~------p~~S~lgHL~Gil~G~ly~~g~l~ 130 (321)
...+.. ++.|..++..+. ++.+++. +++++.+|++|++.|.+++..+.+
T Consensus 156 ~~~~~~~~~~~~~~~i~~~-~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~ 211 (228)
T COG0705 156 ILLLFLSLPRPALILILIW-LLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSR 211 (228)
T ss_pred hhhhhccCchhHHHHHHHH-HHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 444432 223333222111 2222222 257899999999999999986544
No 4
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.34 E-value=5.2e-12 Score=119.76 Aligned_cols=109 Identities=20% Similarity=0.300 Sum_probs=78.7
Q ss_pred CeeehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCcc
Q 020822 1 MLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQS 80 (321)
Q Consensus 1 MlaL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~~ 80 (321)
|++||.+|+.+|+.+|+++++.+|++++++++++..++ . ....+|+||+|||++++.......
T Consensus 155 ml~l~~lG~~iE~~~G~~~~l~l~l~s~i~~~~~~~~~----~-----------~~~~gGaSGvVygL~g~~~~~~~~-- 217 (276)
T PRK10907 155 LLWWWYLGGAVEKRLGSGKLIVITLISALLSGWVQSKF----S-----------GPWFGGLSGVVYALMGYVWLRGER-- 217 (276)
T ss_pred HHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH----c-----------cchhhHHHHHHHHHHHHHHHHhcc--
Confidence 67899999999999999999999999999998764322 1 123679999999999976554211
Q ss_pred ccccccccchhHHHHHHH----HHHHHHhcchhHHHHHHHHHHHHHHHHHH
Q 020822 81 RSVFGLFNIPAKWYPLIL----LVLFQVLMTNVSLLGHLCGILSGFAYTYG 127 (321)
Q Consensus 81 ~~l~G~~~IP~~~~p~il----Lil~~ll~p~~S~lgHL~Gil~G~ly~~g 127 (321)
.+-.+ +.+|..+..+++ +.+..++.++++..+|++|+++|+++++.
T Consensus 218 ~p~~~-~~lp~~~~~f~llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~ 267 (276)
T PRK10907 218 DPQSG-IYLPRGLIAFALLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFW 267 (276)
T ss_pred ccccc-hhhhHHHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHH
Confidence 12222 235554433332 22345566889999999999999998763
No 5
>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=99.33 E-value=1.4e-12 Score=110.09 Aligned_cols=115 Identities=30% Similarity=0.444 Sum_probs=80.8
Q ss_pred CeeehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCcc
Q 020822 1 MLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQS 80 (321)
Q Consensus 1 MlaL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~~ 80 (321)
|++++.+|..+|+.+|++++..+|+++++.++++++++... ..+.+|+||+++|++++.....+...
T Consensus 26 ~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~~-------------~~~~~G~Sg~~~~l~~~~~~~~~~~~ 92 (145)
T PF01694_consen 26 LLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSPP-------------NQPYVGASGAVFGLLGAFLFLYPQNK 92 (145)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S------------------SSHHHHHHHHHHHHHHHHCCC
T ss_pred HHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhcccccccc-------------ccccCCCcccchHHHHHHHHHHhhcc
Confidence 46789999999999999999999999999999876655321 12799999999999999987766543
Q ss_pred cccc---ccccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhhhh
Q 020822 81 RSVF---GLFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNL 131 (321)
Q Consensus 81 ~~l~---G~~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~ 131 (321)
.... ..+.++..+.++.+++ ...|++++.+|++|+++|++++..++++
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 93 KRLRFIYLALVVPIIVLVIILLL---GFIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp CCS---HCCCCCCCCCCCHHHCT---SSSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred chhhcchHHHHHHHHHHHHHHHH---HHHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3222 1122333222222222 1278999999999999999999987653
No 6
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=99.24 E-value=9e-12 Score=83.30 Aligned_cols=36 Identities=39% Similarity=0.690 Sum_probs=34.0
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++++|++|++|||++++|++||++++||+++|++||
T Consensus 2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 689999999999999999999999999999999997
No 7
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=99.10 E-value=1.5e-10 Score=77.02 Aligned_cols=36 Identities=39% Similarity=0.652 Sum_probs=34.5
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++++|++|++|||++++|++||++++||+++|++||
T Consensus 1 ~~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 378999999999999999999999999999999997
No 8
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=99.06 E-value=2.9e-10 Score=76.01 Aligned_cols=36 Identities=33% Similarity=0.625 Sum_probs=34.5
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++++|++|++|||++++|++||++++||+++|++||
T Consensus 1 ~~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 1 DEEKLEQLLEMGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 368999999999999999999999999999999998
No 9
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=98.63 E-value=3.5e-09 Score=101.88 Aligned_cols=108 Identities=23% Similarity=0.331 Sum_probs=75.5
Q ss_pred CeeehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCcc
Q 020822 1 MLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQS 80 (321)
Q Consensus 1 MlaL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~~ 80 (321)
|+++.++|..+|..+|.+|+..+|+++++.++++-++. .+ +..+||+||++|||+++...---
T Consensus 139 ~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~---------d~-----~~~sVGASggvfaLlgA~Ls~l~--- 201 (316)
T KOG2289|consen 139 MLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLF---------DP-----NSISVGASGGVFALLGAHLSNLL--- 201 (316)
T ss_pred HHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHh---------cc-----CCceecccHHHHHHHHHHHHHHH---
Confidence 56788999999999999999999999999999863332 22 56799999999999998864311
Q ss_pred ccccccccchhHHHHHH---HH---HHHHHhcchhHHHHHHHHHHHHHHHHHHh
Q 020822 81 RSVFGLFNIPAKWYPLI---LL---VLFQVLMTNVSLLGHLCGILSGFAYTYGF 128 (321)
Q Consensus 81 ~~l~G~~~IP~~~~p~i---lL---il~~ll~p~~S~lgHL~Gil~G~ly~~g~ 128 (321)
.+ +. .++.|...+. ++ .+..-+.|.+.+++|++|+..|+.+++-.
T Consensus 202 ~N-w~--~m~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil 252 (316)
T KOG2289|consen 202 TN-WT--IMKNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFVL 252 (316)
T ss_pred hh-HH--HhcchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchhHHh
Confidence 00 01 1222222111 11 11222467788899999999999887753
No 10
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.40 E-value=2.5e-07 Score=91.42 Aligned_cols=36 Identities=36% Similarity=0.566 Sum_probs=35.2
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++.|++|+||||+|++|++||+++.||.+||||||
T Consensus 156 ~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL 191 (378)
T TIGR00601 156 RETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYL 191 (378)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHH
Confidence 588999999999999999999999999999999999
No 11
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.95 E-value=1.2e-05 Score=77.21 Aligned_cols=37 Identities=38% Similarity=0.545 Sum_probs=35.7
Q ss_pred CCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 281 VSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 281 ~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
..++.|+++++||++|+++++||+++.||.|||||||
T Consensus 134 ~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYL 170 (340)
T KOG0011|consen 134 EYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYL 170 (340)
T ss_pred hhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHH
Confidence 3699999999999999999999999999999999999
No 12
>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=97.88 E-value=5.3e-05 Score=68.41 Aligned_cols=120 Identities=28% Similarity=0.382 Sum_probs=77.9
Q ss_pred eeehhhhHHHHHhh--Ch-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCC
Q 020822 2 LALVPLGSELERIM--GS-VRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGA 78 (321)
Q Consensus 2 laL~~~G~~lEr~~--GT-~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~ 78 (321)
+.++..++.+|+.. |+ ..|+.+.+++++...+ ++.+... .. .+. ..-..+-+++++-..+...|+
T Consensus 64 ~~l~~~s~~LE~~~f~~~~ady~~~ll~~~~~i~~----~~~~~~~---~~----~~~-~~l~~~l~~~l~Y~wsr~np~ 131 (197)
T PF04511_consen 64 YFLYQYSSSLEEGHFQGRSADYLWFLLFGASLILI----LSLLIGP---YF----FNI-PFLGSSLSFALTYIWSRKNPN 131 (197)
T ss_pred HHHHHHhhHhccCCCCCCHHHHHHHHHHHHHHHHH----HHHhhcc---ch----hHH-HHHHHHHHHHHHHHHHHhCcc
Confidence 45778899999983 22 4566665544333222 2221100 00 011 222345667777777777898
Q ss_pred ccccccccccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhhhhcCCch
Q 020822 79 QSRSVFGLFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGT 136 (321)
Q Consensus 79 ~~~~l~G~~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~l~p~~ 136 (321)
.+.+++|.+++|.+++||+++++..++.. .+.+.++.|+++|.+|- +++...|..
T Consensus 132 ~~v~~~g~~~i~a~ylP~~~~~~~~l~~~-~~~~~~l~Gi~~Ghly~--fl~~~~p~~ 186 (197)
T PF04511_consen 132 AQVSFFGLFTIKAKYLPWVLLAFSLLFGG-SSPIPDLLGILVGHLYY--FLKDIYPRL 186 (197)
T ss_pred cceeeEEEEEEChhhHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHH--HHHHhcccc
Confidence 88889998899999999999987766554 46779999999999876 455444443
No 13
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=2e-05 Score=81.73 Aligned_cols=38 Identities=34% Similarity=0.561 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+++++.|+.+++|||+++||++||+++|+|+|+|+||+
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWi 670 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWI 670 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHH
Confidence 56899999999999999999999999999999999998
No 14
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.74 E-value=3.9e-05 Score=76.06 Aligned_cols=43 Identities=35% Similarity=0.425 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 277 QGAVVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 277 ~~~~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
+-++-+.+.|++|++|||+|+.|++|..+||.|+|.|+||| ++
T Consensus 332 ~lT~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~ 375 (378)
T TIGR00601 332 QVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQ 375 (378)
T ss_pred ccCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence 44556788999999999999999999999999999999999 54
No 15
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=97.57 E-value=2.1e-05 Score=78.58 Aligned_cols=115 Identities=18% Similarity=0.238 Sum_probs=74.9
Q ss_pred hhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHh-cCCccccc
Q 020822 5 VPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSL-SGAQSRSV 83 (321)
Q Consensus 5 ~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~-~p~~~~~l 83 (321)
+.+.+.+|+..|+.|.+++|+++||.+++... + +.| +...||.||+-||++....+- +. ...+
T Consensus 475 m~vmrdlEkL~g~~riAIiy~~SGitGNLASA----I-----Flp-----Y~~eVgPa~sQ~Gila~l~vEl~q--s~~i 538 (652)
T KOG2290|consen 475 MTVMRDLEKLAGWHRIAIIYFLSGITGNLASA----I-----FLP-----YRAEVGPAGSQFGILACLFVELFQ--SWQI 538 (652)
T ss_pred HHHHHHHHHhhcchhhheeeecccccccchhe----e-----eec-----cccccCCcccccchHHHHHHHHHh--hhHh
Confidence 56788999999999999999999999886421 1 123 346899999999988655432 11 1223
Q ss_pred ccc-ccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhhhhcCCch
Q 020822 84 FGL-FNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGT 136 (321)
Q Consensus 84 ~G~-~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~l~p~~ 136 (321)
+.. ++.=.++++.+ |++..-++|=+..++|+.|.+.|++...-++-.++-++
T Consensus 539 l~~~w~a~~~Lia~~-L~L~iGliPWiDN~aHlfG~i~GLl~s~~~~PYi~Fg~ 591 (652)
T KOG2290|consen 539 LERPWRAFFHLIATL-LVLCIGLIPWIDNWAHLFGTIFGLLTSIIFLPYIDFGD 591 (652)
T ss_pred hhhHHHHHHHHHHHH-HHHHhccccchhhHHHHHHHHHHHHHHHHhhccccccc
Confidence 220 00001112222 22233578999999999999999998877554444333
No 16
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.51 E-value=0.00012 Score=70.66 Aligned_cols=41 Identities=29% Similarity=0.393 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 279 AVVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 279 ~~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
+.-..|.|.+|++|||+|..|++|.-+||.|+|.|+||| ++
T Consensus 295 tpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~ 336 (340)
T KOG0011|consen 295 TPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSH 336 (340)
T ss_pred CHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhh
Confidence 455678899999999999999999999999999999999 54
No 17
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.49 E-value=9.4e-05 Score=66.03 Aligned_cols=36 Identities=28% Similarity=0.488 Sum_probs=34.8
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+..||++|.+|||+|++++.+|+..+||.+.|.|.|
T Consensus 162 ~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~ 197 (200)
T KOG0418|consen 162 DKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQL 197 (200)
T ss_pred hHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhh
Confidence 688999999999999999999999999999999987
No 18
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.93 E-value=0.002 Score=44.26 Aligned_cols=35 Identities=34% Similarity=0.404 Sum_probs=29.1
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 283 DEEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 283 ~~~v~~L~~-MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+++|+++++ .|.+++.|+.-|+.+|||+++|++.-
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHH
Confidence 578888755 58999999999999999999999976
No 19
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.76 E-value=0.0013 Score=65.88 Aligned_cols=38 Identities=34% Similarity=0.710 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
...+++...+|+|||.+.+||.||++|+||++.|+.++
T Consensus 301 ki~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI 338 (568)
T KOG2561|consen 301 KINDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFI 338 (568)
T ss_pred eccchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHH
Confidence 34688999999999999999999999999999999998
No 20
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=96.71 E-value=0.0054 Score=57.04 Aligned_cols=114 Identities=22% Similarity=0.319 Sum_probs=76.3
Q ss_pred CeeehhhhHHHHHhh---ChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcC
Q 020822 1 MLALVPLGSELERIM---GSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSG 77 (321)
Q Consensus 1 MlaL~~~G~~lEr~~---GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p 77 (321)
|+.++--++.+|+-. -|..|+.++++++++-.++-+ ..... .. .++-++.+.-..+...|
T Consensus 74 ~~FlyrY~~~LE~g~f~~rtadf~~mllf~~~l~~~~~~-~~~~~---------------fL-g~~l~~~l~YvWs~~Np 136 (239)
T KOG0858|consen 74 LYFLYRYSSMLEEGSFRGRTADFLYMLLFGAVLLTLTGL-FVYIV---------------FL-GQSLVFMLVYVWSKRNP 136 (239)
T ss_pred HHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHHHHH-HHHHH---------------HH-HHHHHHHHHHHHHhhCC
Confidence 455677789999873 257888887766665443211 11110 11 12445666666677778
Q ss_pred CccccccccccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhhhhcCCc
Q 020822 78 AQSRSVFGLFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPG 135 (321)
Q Consensus 78 ~~~~~l~G~~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ly~~g~l~~l~p~ 135 (321)
+...+++|.++++.+|.||+++.+..++.- .+ +--+-|+++|.+|-. ++.+.|.
T Consensus 137 ~~~v~F~g~~~f~a~YlPwvll~fs~l~g~-~~-~~dllGi~~GHiy~f--l~~~~p~ 190 (239)
T KOG0858|consen 137 DVIVSFFGLITFKAPYLPWVLLGFSFLFGG-SI-LVDLLGIIVGHIYYF--LDDVYPR 190 (239)
T ss_pred CceEEEEEEecCccccchHHHHHHHHHhCC-ch-HHHHHhhhhheeEEE--EeeeccC
Confidence 888889999999999999999988766643 33 888999999976543 4444444
No 21
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.56 E-value=0.0056 Score=41.74 Aligned_cols=35 Identities=34% Similarity=0.639 Sum_probs=32.1
Q ss_pred HHHHHHHHhc--CCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 283 DEEIQKLVSM--GFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 283 ~~~v~~L~~M--Gf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+++|++|.+| .++++..+.+|++++||+|.|++.|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 6889999999 6889999999999999999999998
No 22
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0016 Score=66.20 Aligned_cols=38 Identities=18% Similarity=0.206 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+|+|++++.|.||||+..++|+||-..|+|.+|+|+|.
T Consensus 619 eVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~ 656 (749)
T COG5207 619 EVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVWC 656 (749)
T ss_pred cccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEEE
Confidence 88999999999999999999999999999999999998
No 23
>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=96.42 E-value=0.0025 Score=51.68 Aligned_cols=68 Identities=24% Similarity=0.286 Sum_probs=50.3
Q ss_pred eehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHH
Q 020822 3 ALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIE 72 (321)
Q Consensus 3 aL~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~ 72 (321)
.++..|+.+|+.+|+++++.++.+..++++++-++...+... ..++..+...+.-|..|.+-|+++++
T Consensus 30 ~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~--i~~~~~~l~~~i~G~~~~~~g~lVa~ 97 (99)
T PF08551_consen 30 TLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYA--ITGNESYLFVPISGFMGVLAGFLVAF 97 (99)
T ss_pred HHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHH--HhCCCceeEEEecCcHHhHhheEEEE
Confidence 467889999999999999999988888888766555544432 23333334477889999998887653
No 24
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.15 E-value=0.013 Score=40.04 Aligned_cols=36 Identities=25% Similarity=0.535 Sum_probs=31.8
Q ss_pred CHHHHHHHHhc--CCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKLVSM--GFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L~~M--Gf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++.|+.|.+| .++++.++.+|++++||++.|++.|
T Consensus 2 ~~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 2 NDEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999999 3458899999999999999999988
No 25
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=95.91 E-value=0.018 Score=48.09 Aligned_cols=39 Identities=31% Similarity=0.475 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHh-cCCCHHHHHHHHHHhCCCHHHHHHHhh
Q 020822 280 VVSDEEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEILS 318 (321)
Q Consensus 280 ~~~~~~v~~L~~-MGf~~~~a~~AL~~~~~d~~~A~e~L~ 318 (321)
.++++.|+.+++ -|.++++|++||.+||||+-.|+-+|+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~ 113 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLS 113 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHh
Confidence 458999999854 689999999999999999999999983
No 26
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=95.70 E-value=0.013 Score=59.84 Aligned_cols=39 Identities=31% Similarity=0.395 Sum_probs=35.3
Q ss_pred CCHHHHHHHHhcCCCHHHHHHHHHHhCC-CHHHHHHHhhc
Q 020822 281 VSDEEIQKLVSMGFDKTQVEVALAAADG-DLNVAVEILSQ 319 (321)
Q Consensus 281 ~~~~~v~~L~~MGf~~~~a~~AL~~~~~-d~~~A~e~L~~ 319 (321)
..+..|.||++|||+++.+.+||-.+++ |.|.|++||.|
T Consensus 557 ~Nqs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFq 596 (749)
T COG5207 557 DNQSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQ 596 (749)
T ss_pred chHHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHh
Confidence 3577899999999999999999999987 99999999954
No 27
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.64 E-value=0.014 Score=58.84 Aligned_cols=38 Identities=32% Similarity=0.480 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++++.+|.+|+.|||++..|+.||+..++|++.|.+.|
T Consensus 427 ~vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L 464 (568)
T KOG2561|consen 427 QVDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLL 464 (568)
T ss_pred ccchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHH
Confidence 56899999999999999999999999999999999998
No 28
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=95.47 E-value=0.03 Score=46.75 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=34.4
Q ss_pred CCCHHHHHHHH-hcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLV-SMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~-~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++++.|+.++ .-|.++++|++||.+||||+-.|+-+|
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L 114 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKL 114 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHh
Confidence 46899999985 468999999999999999999999887
No 29
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=95.41 E-value=0.022 Score=59.81 Aligned_cols=39 Identities=26% Similarity=0.308 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHhcCCCHHHHHHHHHHh-CCCHHHHHHHh
Q 020822 279 AVVSDEEIQKLVSMGFDKTQVEVALAAA-DGDLNVAVEIL 317 (321)
Q Consensus 279 ~~~~~~~v~~L~~MGf~~~~a~~AL~~~-~~d~~~A~e~L 317 (321)
...++..|.+|++|||.++.+++||=.+ |.|.|.|.+||
T Consensus 568 ~~~d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl 607 (763)
T KOG0944|consen 568 FAADRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWL 607 (763)
T ss_pred cchhHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHH
Confidence 3457889999999999999999999999 88999999999
No 30
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=95.41 E-value=0.018 Score=41.95 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=21.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
+.+.|+++++|||+++++++||++-+
T Consensus 9 ~~~lVd~F~~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 9 DKDLVDQFENMGFERDKVVEVLRRLG 34 (55)
T ss_dssp SHHHHHHHHHHT--HHHHHHHHHHS-
T ss_pred CHHHHHHHHHcCCcHHHHHHHHHHhC
Confidence 68899999999999999999999876
No 31
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=95.08 E-value=0.064 Score=51.63 Aligned_cols=124 Identities=16% Similarity=0.197 Sum_probs=71.1
Q ss_pred eehhhhHHHHHhhChHHHHHHHHHHHHHHHH---HHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCc
Q 020822 3 ALVPLGSELERIMGSVRMFYITILLATSNAI---LHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQ 79 (321)
Q Consensus 3 aL~~~G~~lEr~~GT~~fl~lyll~~i~~gl---ly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~ 79 (321)
.|..-|+.+|+.+|+..++.+|.+.-....+ +++++.+.+ +.+..+.+.+..|+.|.+-|+++++-...|+.
T Consensus 89 ~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~i-----t~n~v~L~~~i~G~~gilaGilVa~kQllpd~ 163 (326)
T KOG2890|consen 89 TLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMI-----TDNHVYLYIPIHGTTGILAGILVAWKQLLPDT 163 (326)
T ss_pred heeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHH-----hcCceEEEEEeccchHHHHHHHHHHHHHcCce
Confidence 4667899999999999999988654333332 233333322 22333345669999999999999998888865
Q ss_pred cccccccccchhHH---HHHHHHHHHHHhc-chhHHHHHHHHHHHHHHHHHHhhhhcCC
Q 020822 80 SRSVFGLFNIPAKW---YPLILLVLFQVLM-TNVSLLGHLCGILSGFAYTYGFFNLLMP 134 (321)
Q Consensus 80 ~~~l~G~~~IP~~~---~p~ilLil~~ll~-p~~S~lgHL~Gil~G~ly~~g~l~~l~p 134 (321)
... - .+.+..+ .|+..+++..++. -.--....+.-+..|.+.+|-|+++..+
T Consensus 164 ~il--~-~~~~r~~~~~lP~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRfyq~ 219 (326)
T KOG2890|consen 164 IIL--E-LKSGRFLYAHLPLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLRFYQR 219 (326)
T ss_pred eEE--e-ccchhhhhhhCCHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhheeccc
Confidence 221 1 1222223 4444433222110 0001123445566677777777766543
No 32
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=94.25 E-value=0.097 Score=44.04 Aligned_cols=38 Identities=32% Similarity=0.460 Sum_probs=33.9
Q ss_pred CCCHHHHHHHH-hcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLV-SMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~-~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++++.|+..+ .-|.+|++||+||.++|||+-.|+-.|
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L 120 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKL 120 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHh
Confidence 45899999975 479999999999999999999999776
No 33
>COG5291 Predicted membrane protein [Function unknown]
Probab=93.91 E-value=0.051 Score=51.03 Aligned_cols=46 Identities=24% Similarity=0.490 Sum_probs=31.1
Q ss_pred cCCccccccccccchhHHHHHHHHHHHHHhcchhHHHHHHHHHHHHH
Q 020822 76 SGAQSRSVFGLFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGF 122 (321)
Q Consensus 76 ~p~~~~~l~G~~~IP~~~~p~ilLil~~ll~p~~S~lgHL~Gil~G~ 122 (321)
.|+....+||.+++|.||+|++++.+..+...+.+ .--+-|+.+|.
T Consensus 143 N~~~~Iqf~g~i~v~gkYlP~Illgfsfl~~~g~~-i~~vlGf~~g~ 188 (313)
T COG5291 143 NPRAIIQFFGFISVPGKYLPFILLGFSFLSRRGIS-IDDVLGFVVGH 188 (313)
T ss_pred CCceEEEEEEeeecchhhhhHHHHHHHHHhcCCcc-ceeeeeeeecc
Confidence 45555678899999999999999987665543332 33344555553
No 34
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=93.13 E-value=0.097 Score=50.42 Aligned_cols=73 Identities=16% Similarity=0.288 Sum_probs=48.5
Q ss_pred ccccCChHHHHHHHHHHHHHhcCCccccccccccchhHH-HHHHHHHH---HHHhcc--hhHHHHHHHHHHHHHHHHHH
Q 020822 55 DECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKW-YPLILLVL---FQVLMT--NVSLLGHLCGILSGFAYTYG 127 (321)
Q Consensus 55 ~~~~vGaSGaIFaLl~~~~~~~p~~~~~l~G~~~IP~~~-~p~ilLil---~~ll~p--~~S~lgHL~Gil~G~ly~~g 127 (321)
..+..||||++|+++...+.++|+.+..++..+++|.-+ .++-.++. ..+.+. .-+..+|++|-+.|..++.-
T Consensus 220 ~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~~i~~~~~a~~~l~~~~~n~~Ah~~gsl~Gv~va~~ 298 (310)
T KOG2980|consen 220 AGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFKAIAAYDFAGLILGWGFFNHAAHLSGSLFGVVVATY 298 (310)
T ss_pred cccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHHHHHHhhhcceeeccccchhHhhhcchHHHHHHHHH
Confidence 456799999999999999999998766666556676632 22222211 111121 23445999999999888764
No 35
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=93.04 E-value=0.11 Score=52.97 Aligned_cols=38 Identities=37% Similarity=0.463 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHhcCCC-HHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFD-KTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~-~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+..+...++|-+|||. |++..+||.++++|+++|||.|
T Consensus 452 ~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverl 490 (493)
T KOG0010|consen 452 ERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERL 490 (493)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHH
Confidence 3467789999999985 8899999999999999999988
No 36
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=90.15 E-value=0.64 Score=39.51 Aligned_cols=37 Identities=30% Similarity=0.304 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
+++.+.|+-+++-+.++++||+||..++ |+-+|++.|
T Consensus 112 ~~~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l 148 (153)
T COG4008 112 EPPVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKIL 148 (153)
T ss_pred CCcHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHH
Confidence 3468889999999999999999999998 999999998
No 37
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=88.55 E-value=0.62 Score=36.69 Aligned_cols=32 Identities=28% Similarity=0.456 Sum_probs=28.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 286 IQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 286 v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
|+.+.+.|++++.+..||.+|.+|++.|..++
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~v 32 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFV 32 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHH
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 56789999999999999999999999999965
No 38
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=88.22 E-value=1.2 Score=31.57 Aligned_cols=40 Identities=28% Similarity=0.330 Sum_probs=32.0
Q ss_pred CCCHHHHHHH--HhcCCCHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 280 VVSDEEIQKL--VSMGFDKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 280 ~~~~~~v~~L--~~MGf~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
.++|+.|.+. +=-|=+|+-.++-|+.+|-|++.|++.| |.
T Consensus 7 ~vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR 49 (53)
T PF11547_consen 7 QVPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR 49 (53)
T ss_dssp GS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence 4568888875 5679999999999999999999999998 53
No 39
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=87.92 E-value=1.1 Score=33.49 Aligned_cols=36 Identities=17% Similarity=0.285 Sum_probs=31.2
Q ss_pred CHHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.+++|.++ .+-|.+.+=++++|+.+|||.++|+...
T Consensus 12 q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 12 QQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 46677776 6779999999999999999999999865
No 40
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=87.40 E-value=0.25 Score=31.13 Aligned_cols=29 Identities=7% Similarity=-0.051 Sum_probs=23.1
Q ss_pred cccccchhhcccCCCCCcccccccccccc
Q 020822 225 HVDSNLQARLLDNSSPENRSHMIVTETGD 253 (321)
Q Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (321)
..+|.|.+|++.|......|.+|++.|++
T Consensus 2 ~g~W~C~~C~~~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPASRSKCVACGAPRPG 30 (30)
T ss_dssp SSSEEETTTTEEEESSSSB-TTT--BTTB
T ss_pred CcCccCCCCcCCchHHhhhhhCcCCCCcC
Confidence 34799999999999999999999998863
No 41
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=86.92 E-value=0.54 Score=33.58 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=27.8
Q ss_pred HHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 283 DEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 283 ~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++.|.++ ..-|.+.+-+.+.|..++||.++|+...
T Consensus 1 q~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F 36 (51)
T PF03943_consen 1 QEMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNF 36 (51)
T ss_dssp HHHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3556665 6779999999999999999999999865
No 42
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=85.32 E-value=2 Score=31.82 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=30.3
Q ss_pred HHHHHHHHhc-C-CCHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 283 DEEIQKLVSM-G-FDKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 283 ~~~v~~L~~M-G-f~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
...||.|.|. | .++++.-..|..||.|++.|++-| +|
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 4456776553 3 589999999999999999999999 76
No 43
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=84.27 E-value=1.8 Score=42.19 Aligned_cols=36 Identities=33% Similarity=0.379 Sum_probs=33.8
Q ss_pred CHHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
..+.|++| .+-|.+-..+++||..||||+..|.+||
T Consensus 46 ~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L 82 (340)
T KOG1071|consen 46 SKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWL 82 (340)
T ss_pred cHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHH
Confidence 57789999 7899999999999999999999999999
No 44
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.24 E-value=0.27 Score=46.72 Aligned_cols=119 Identities=19% Similarity=0.245 Sum_probs=68.0
Q ss_pred ehhhhHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCccccCChHHHHHHHHHHHHHhcCCc-ccc
Q 020822 4 LVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQ-SRS 82 (321)
Q Consensus 4 L~~~G~~lEr~~GT~~fl~lyll~~i~~glly~ll~~l~~~~~~~~~~~~~~~~~vGaSGaIFaLl~~~~~~~p~~-~~~ 82 (321)
+++..+.+||.+|+-||..+.+++++.+-+.-.++..+.. .++. +--.++--|.+|+.+..+.+..|.. ..+
T Consensus 73 I~Y~fR~~ERlLGShky~~fiv~s~~~~~l~~~il~~l~~--~~~~-----nl~~~qp~~liFa~~~~~y~~ip~~~f~r 145 (323)
T KOG4463|consen 73 ILYYFRVFERLLGSHKYSVFIVFSGTVSLLLEVILLSLLK--DTTA-----NLLTSQPYGLIFASFIPFYLDIPVSTFFR 145 (323)
T ss_pred HHHHHHHHHHHhccccceeehhHHHHHHHHHHHHHHHHHH--HHHh-----hhhhcCCCceeeeeccceEEEecceeEEE
Confidence 5677899999999999999887777766654433333221 0111 2234444457888775554444432 235
Q ss_pred ccccccchhHHHHHHHHHHHHHh-cch-----------hHHHHHHHHHHHHHHHHHHhhh
Q 020822 83 VFGLFNIPAKWYPLILLVLFQVL-MTN-----------VSLLGHLCGILSGFAYTYGFFN 130 (321)
Q Consensus 83 l~G~~~IP~~~~p~ilLil~~ll-~p~-----------~S~lgHL~Gil~G~ly~~g~l~ 130 (321)
+|+ +++.-|.+-++.++-.++. .|| .+..=-+||++.|.+|-.+...
T Consensus 146 ~f~-~~f~dkni~~i~~~G~a~sh~~NkredksaveWk~~i~f~~~gLi~~~~~~~~~ag 204 (323)
T KOG4463|consen 146 VFG-VNFSDKNISFIYLAGVALSHSSNKREDKSAVEWKRSIFFGICGLIAGSLYRLNIAG 204 (323)
T ss_pred eec-ccccccceeeecccchhhhcCcccccccccceeecccccccchhhhhhHhhccccc
Confidence 666 3565664444444332222 221 1112357899999988877443
No 45
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=80.10 E-value=2.6 Score=29.28 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=22.3
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.++.|..+||++.++.+|+++..
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 37889999999999999999999873
No 46
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=79.92 E-value=1.7 Score=43.18 Aligned_cols=23 Identities=39% Similarity=0.645 Sum_probs=20.2
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHH
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALA 304 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~ 304 (321)
.+|.|+|++.|||.||+||..-+
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v~ 343 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATVR 343 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHH
Confidence 58999999999999999986544
No 47
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=78.26 E-value=1.8 Score=29.28 Aligned_cols=24 Identities=29% Similarity=0.545 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 294 FDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 294 f~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
|+++-.+.||..++||..+|.+.|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 356678899999999999999988
No 48
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=78.16 E-value=7.7 Score=44.19 Aligned_cols=46 Identities=24% Similarity=0.227 Sum_probs=37.4
Q ss_pred CCCCCCCCCHHHHHHH--HhcCCCHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 274 AGQQGAVVSDEEIQKL--VSMGFDKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 274 ~~~~~~~~~~~~v~~L--~~MGf~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
|...+..++||.|.+. |=-|=+|+-.++-|+.++-|++.|||.| |.
T Consensus 181 PriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 181 PRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 3334456679988764 6689999999999999999999999998 53
No 49
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=73.57 E-value=1.5 Score=26.35 Aligned_cols=25 Identities=12% Similarity=-0.055 Sum_probs=22.3
Q ss_pred ccccchhhcccCCCCCccccccccc
Q 020822 226 VDSNLQARLLDNSSPENRSHMIVTE 250 (321)
Q Consensus 226 ~~~~~~~~~~~~~~~~~~~~~~~~~ 250 (321)
.+|.|.+|++.|......|.+|++.
T Consensus 1 g~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 1 GDWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CcccCCCCCCcChhhhccccccCCc
Confidence 3799999999999999999999763
No 50
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=73.28 E-value=0.66 Score=32.62 Aligned_cols=26 Identities=31% Similarity=0.638 Sum_probs=18.1
Q ss_pred CHHHHHHH-HhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKL-VSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L-~~MGf~~~~a~~AL~~~~ 307 (321)
+++.|.+| ..||+++++...||++..
T Consensus 2 de~vv~~Ls~tMGY~kdeI~eaL~~~~ 28 (46)
T PF08587_consen 2 DEDVVSKLSKTMGYDKDEIYEALESSE 28 (46)
T ss_dssp -HCCHHHHHCTT---HHHHHHHCCSSS
T ss_pred cHHHHHHHHHHhCCCHHHHHHHHHcCC
Confidence 45567888 789999999999999854
No 51
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=72.24 E-value=2 Score=33.27 Aligned_cols=25 Identities=28% Similarity=0.227 Sum_probs=21.2
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHh-hc
Q 020822 295 DKTQVEVALAAADGDLNVAVEIL-SQ 319 (321)
Q Consensus 295 ~~~~a~~AL~~~~~d~~~A~e~L-~~ 319 (321)
++.+.+.||-.++.|+++|++|| ++
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 78889999999999999999999 54
No 52
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=70.26 E-value=6.4 Score=26.75 Aligned_cols=22 Identities=27% Similarity=0.510 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhCCCHHHHHHHh
Q 020822 296 KTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 296 ~~~a~~AL~~~~~d~~~A~e~L 317 (321)
++.-...|+.|+||+-+|+|.+
T Consensus 17 r~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 17 RSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred hHHHHHHHHHcCCcHHHHHHHh
Confidence 4556679999999999999974
No 53
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=64.52 E-value=7.4 Score=28.82 Aligned_cols=20 Identities=20% Similarity=0.502 Sum_probs=17.7
Q ss_pred HHHHhcCCCHHHHHHHHHHh
Q 020822 287 QKLVSMGFDKTQVEVALAAA 306 (321)
Q Consensus 287 ~~L~~MGf~~~~a~~AL~~~ 306 (321)
+-|++|||++.+|++-++++
T Consensus 7 ~dLi~lGf~~~tA~~IIrqA 26 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQA 26 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHH
Confidence 45899999999999998876
No 54
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=63.97 E-value=16 Score=38.37 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=32.2
Q ss_pred CHHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.+|+|.++ .+-|..-+=+.+.|+.+|||.|+|+.-.
T Consensus 535 ~~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k~F 571 (585)
T KOG3763|consen 535 TDEKLLKFQEETGLNSEWSTMCLEQNNWDYERALKLF 571 (585)
T ss_pred HHHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHHHH
Confidence 48899988 5789999999999999999999998754
No 55
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=55.36 E-value=18 Score=33.17 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=29.6
Q ss_pred CHHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++.|+.+ ...+.+|.+|++||+.+++|+--|+=-|
T Consensus 171 e~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 171 EAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMEL 207 (209)
T ss_pred chhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHh
Confidence 45667775 5678999999999999999998887543
No 56
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.29 E-value=30 Score=31.17 Aligned_cols=26 Identities=27% Similarity=0.420 Sum_probs=23.6
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.++.|+.+||++.+|++|+++..
T Consensus 143 ~~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 143 YHESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 47789999999999999999999884
No 57
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.99 E-value=32 Score=31.20 Aligned_cols=25 Identities=24% Similarity=0.547 Sum_probs=23.0
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAA 306 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~ 306 (321)
.+|.+..|+.+||++.+|.+|+++.
T Consensus 152 ~~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 152 AEDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4778999999999999999999986
No 58
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.76 E-value=31 Score=31.47 Aligned_cols=25 Identities=12% Similarity=0.348 Sum_probs=23.2
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAA 306 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~ 306 (321)
.+|.++.|+.+||++.+|.+|+++.
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4788999999999999999999987
No 59
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.23 E-value=32 Score=31.20 Aligned_cols=26 Identities=27% Similarity=0.428 Sum_probs=23.2
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.+..|+.+||++.+|.+|+.+..
T Consensus 149 ~~e~~~aL~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 149 DRELSEILISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 37789999999999999999998873
No 60
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=46.99 E-value=24 Score=26.63 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=20.5
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHH
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAA 305 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~ 305 (321)
.+..++.+..|||++.+++..|..
T Consensus 11 ~daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 11 IDAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467788999999999999887764
No 61
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.40 E-value=23 Score=31.88 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=23.5
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.++.|+.+||++.+|++|+++..
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~ 167 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQ 167 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcc
Confidence 37889999999999999999999873
No 62
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.73 E-value=24 Score=31.80 Aligned_cols=26 Identities=27% Similarity=0.546 Sum_probs=23.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.++.|+.+||++.+|++|+++..
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~ 170 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIK 170 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 47889999999999999999999875
No 63
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=43.33 E-value=15 Score=29.62 Aligned_cols=16 Identities=31% Similarity=0.572 Sum_probs=13.4
Q ss_pred CCcccccccccCCCCC
Q 020822 208 SRFPGRGRTLSSSQSP 223 (321)
Q Consensus 208 ~~f~G~Gr~LG~~~~~ 223 (321)
..|.|+||+||+...+
T Consensus 74 ~~F~G~G~~LGs~~p~ 89 (93)
T smart00553 74 KPFSGSGQKLGSPGPQ 89 (93)
T ss_pred cCCccCCccCCCCCCC
Confidence 5799999999987553
No 64
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.19 E-value=29 Score=31.64 Aligned_cols=27 Identities=33% Similarity=0.364 Sum_probs=23.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADG 308 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~ 308 (321)
.+|.++.|+.+||++.+|++|+++.-.
T Consensus 144 ~~ea~~AL~~LGy~~~ea~~al~~v~~ 170 (196)
T PRK13901 144 FKELEQSIVNMGFDRKLVNSAIKEIML 170 (196)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 378899999999999999999987643
No 65
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=41.52 E-value=42 Score=32.82 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=29.9
Q ss_pred CHHHHH-HHHhc-CCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 282 SDEEIQ-KLVSM-GFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 282 ~~~~v~-~L~~M-Gf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.++.+. -|.+- |.+++++..+++.++|++.+|.+++
T Consensus 168 ~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~ 205 (334)
T PRK07993 168 PEQYALTWLSREVTMSQDALLAALRLSAGAPGAALALL 205 (334)
T ss_pred CHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 345444 57665 9999999999999999999999998
No 66
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=41.32 E-value=53 Score=29.58 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=23.3
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.++.|+.+||++++|++|+.+..
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 37789999999999999999999874
No 67
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=40.46 E-value=41 Score=30.81 Aligned_cols=27 Identities=19% Similarity=0.447 Sum_probs=22.9
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADG 308 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~ 308 (321)
.++.|..|+.+||++.++++|+++..-
T Consensus 156 ~~~~v~AL~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 156 LEEAVEALVALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 344599999999999999999988764
No 68
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=39.37 E-value=54 Score=31.96 Aligned_cols=37 Identities=27% Similarity=0.377 Sum_probs=32.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHhh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEILS 318 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~~~A~e~L~ 318 (321)
.++.++-|.+-|.++++|..++..++|.+.+|.++++
T Consensus 174 ~~~~~~~L~~~~~~~~~a~~~~~l~~G~p~~A~~~~~ 210 (319)
T PRK08769 174 AHEALAWLLAQGVSERAAQEALDAARGHPGLAAQWLR 210 (319)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHcCCCHHHHHHHhc
Confidence 3666778888999999999999999999999999983
No 69
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=38.51 E-value=38 Score=28.76 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=23.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCCCH
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADGDL 310 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~d~ 310 (321)
.++||+-|..-|.++++..+||+.++.+.
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 59999999999999999999999998877
No 70
>PRK00523 hypothetical protein; Provisional
Probab=38.09 E-value=67 Score=24.75 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHhhhh
Q 020822 114 HLCGILSGFAYTYGFFNL 131 (321)
Q Consensus 114 HL~Gil~G~ly~~g~l~~ 131 (321)
-+.|++.||.++..++++
T Consensus 15 li~G~~~Gffiark~~~k 32 (72)
T PRK00523 15 LIVGGIIGYFVSKKMFKK 32 (72)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 457999999988887653
No 71
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=37.69 E-value=46 Score=23.28 Aligned_cols=28 Identities=21% Similarity=0.126 Sum_probs=22.1
Q ss_pred HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 290 VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 290 ~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.....+.....+=|++.+||++.|.+.|
T Consensus 25 ~~~~~~d~~llRFLRARkf~v~~A~~mL 52 (55)
T PF03765_consen 25 EKEDHDDNFLLRFLRARKFDVEKAFKML 52 (55)
T ss_dssp HTSS-SHHHHHHHHHHTTT-HHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence 4455577788999999999999999987
No 72
>TIGR00834 ae anion exchange protein. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
Probab=36.63 E-value=1.8e+02 Score=32.66 Aligned_cols=72 Identities=15% Similarity=0.191 Sum_probs=35.3
Q ss_pred cccCChHHHHHHHHHHHHHhcCCccccccccccchhHHHHHHHHHHHHHhcchhH--------HHHHHHHHHHHHHHHHH
Q 020822 56 ECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWYPLILLVLFQVLMTNVS--------LLGHLCGILSGFAYTYG 127 (321)
Q Consensus 56 ~~~vGaSGaIFaLl~~~~~~~p~~~~~l~G~~~IP~~~~p~ilLil~~ll~p~~S--------~lgHL~Gil~G~ly~~g 127 (321)
-+.+|.+|-+.-+.....-........+ +.+..|.-.|..++++.+..-+.| |..-+.|+++.++|.+.
T Consensus 425 L~IlG~TGPilvF~~~ly~~c~~~~~~y---l~~~~WigiW~~~~~~lla~~~~s~lvryiTRFTeEiFa~lIs~IFI~e 501 (900)
T TIGR00834 425 LLVVGFSGPLLVFEEAFFSFCESNGLEY---LVGRVWIGLWLVLLVLLLVATEGSFLVRYISRFTQEIFSFLISLIFIYE 501 (900)
T ss_pred eEEecCcccHHHHHHHHHHHHhhcCCch---HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3577777766554433322222111111 234445444544433332222333 45567788888888776
Q ss_pred hhh
Q 020822 128 FFN 130 (321)
Q Consensus 128 ~l~ 130 (321)
-++
T Consensus 502 ai~ 504 (900)
T TIGR00834 502 TFS 504 (900)
T ss_pred HHH
Confidence 443
No 73
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=32.88 E-value=63 Score=26.84 Aligned_cols=38 Identities=21% Similarity=0.348 Sum_probs=33.0
Q ss_pred CCCHHHHHHH-HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 280 VVSDEEIQKL-VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 280 ~~~~~~v~~L-~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
.+..+.|+.+ -||=.++..|++.|+.++||+-.|+.-|
T Consensus 78 ~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral 116 (119)
T KOG3450|consen 78 TIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRAL 116 (119)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence 4467777775 6899999999999999999999999877
No 74
>PRK01844 hypothetical protein; Provisional
Probab=32.53 E-value=91 Score=24.04 Aligned_cols=19 Identities=16% Similarity=0.301 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 020822 113 GHLCGILSGFAYTYGFFNL 131 (321)
Q Consensus 113 gHL~Gil~G~ly~~g~l~~ 131 (321)
+-+.|++.||.++..++++
T Consensus 13 ~li~G~~~Gff~ark~~~k 31 (72)
T PRK01844 13 ALVAGVALGFFIARKYMMN 31 (72)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3457999999988887653
No 75
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=31.76 E-value=50 Score=23.74 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=18.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHH
Q 020822 283 DEEIQKLVSMGFDKTQVEVAL 303 (321)
Q Consensus 283 ~~~v~~L~~MGf~~~~a~~AL 303 (321)
-|+|++|++-|.+..+|++-.
T Consensus 17 vE~Iq~LMaqGmSsgEAI~~V 37 (51)
T PF03701_consen 17 VERIQELMAQGMSSGEAIAIV 37 (51)
T ss_pred HHHHHHHHHhcccHHHHHHHH
Confidence 468999999999999998743
No 76
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.36 E-value=85 Score=28.34 Aligned_cols=26 Identities=12% Similarity=0.414 Sum_probs=23.5
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
.+|.+..|..+||++.+|.+|+.+..
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 47789999999999999999999884
No 77
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.80 E-value=41 Score=24.64 Aligned_cols=35 Identities=23% Similarity=0.233 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCCHHHHHH----HHHHhCCCHHHHHHHh
Q 020822 283 DEEIQKLVSMGFDKTQVEV----ALAAADGDLNVAVEIL 317 (321)
Q Consensus 283 ~~~v~~L~~MGf~~~~a~~----AL~~~~~d~~~A~e~L 317 (321)
-|+|++|++-|.+..+|+. .|+...-+.++++...
T Consensus 17 VE~Iq~lMaeGmSsGEAIa~VA~elRe~hk~~~~~~~~f 55 (60)
T COG3140 17 VERIQELMAEGMSSGEAIALVAQELRENHKGENRIVARF 55 (60)
T ss_pred HHHHHHHHHccccchhHHHHHHHHHHHHhcccccccccc
Confidence 4789999999999888765 5666666655555444
No 78
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=27.91 E-value=1.3e+02 Score=21.08 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=19.1
Q ss_pred hhhhHHHHHhhCh-HHHHHHHHHHHHHHHH
Q 020822 5 VPLGSELERIMGS-VRMFYITILLATSNAI 33 (321)
Q Consensus 5 ~~~G~~lEr~~GT-~~fl~lyll~~i~~gl 33 (321)
++.|..+++.+|| ..+..+.++.++.+++
T Consensus 18 ~~~G~~lD~~~~t~p~~~~~g~llG~~~g~ 47 (55)
T PF09527_consen 18 FFLGYWLDKWFGTSPWFTLIGLLLGIAAGF 47 (55)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHHHHHHH
Confidence 5677888888888 3444445666666665
No 79
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=27.09 E-value=49 Score=33.18 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=11.4
Q ss_pred CCCcccccccccC
Q 020822 207 DSRFPGRGRTLSS 219 (321)
Q Consensus 207 ~~~f~G~Gr~LG~ 219 (321)
-..|.|+||+||+
T Consensus 255 ~~pF~G~Gq~LGs 267 (380)
T KOG2086|consen 255 FKPFSGEGQRLGS 267 (380)
T ss_pred cCCCCCcCeecCC
Confidence 4579999999997
No 80
>PRK01905 DNA-binding protein Fis; Provisional
Probab=25.70 E-value=61 Score=24.66 Aligned_cols=24 Identities=33% Similarity=0.526 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 294 FDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 294 f~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
|+++..+++|..++||..+|.+.|
T Consensus 37 ~E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 37 VEKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467779999999999999999988
No 81
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=25.69 E-value=1.4e+02 Score=26.12 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhhc
Q 020822 109 VSLLGHLCGILSGFAYTYGFFNLL 132 (321)
Q Consensus 109 ~S~lgHL~Gil~G~ly~~g~l~~l 132 (321)
...++-+.|.+.||+...+|-+++
T Consensus 105 ~~~~~~~lg~~l~fl~~r~ysRkl 128 (150)
T COG3086 105 IVIFGAFLGLALGFLLARRYSRKL 128 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455778888889999888876543
No 82
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=25.06 E-value=57 Score=24.67 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=19.8
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHh
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAA 306 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~ 306 (321)
..+-|+-|.++|+++..+|.||+..
T Consensus 23 ~~~Li~ll~~~Gv~e~avR~alsRl 47 (70)
T PF07848_consen 23 VASLIRLLAAFGVSESAVRTALSRL 47 (70)
T ss_dssp HHHHHHHHCCTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHH
Confidence 3667899999999999999999864
No 83
>PRK05114 hypothetical protein; Provisional
Probab=24.49 E-value=78 Score=23.37 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=17.5
Q ss_pred HHHHHHHHhcCCCHHHHHHH
Q 020822 283 DEEIQKLVSMGFDKTQVEVA 302 (321)
Q Consensus 283 ~~~v~~L~~MGf~~~~a~~A 302 (321)
-|+|++|+.-|.+-.+|+.-
T Consensus 17 VErIq~LMaqGmSsgEAI~~ 36 (59)
T PRK05114 17 VERIQELMAQGMSSGEAIAL 36 (59)
T ss_pred HHHHHHHHHccccHHHHHHH
Confidence 57899999999999998864
No 84
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.47 E-value=1.3e+02 Score=27.01 Aligned_cols=27 Identities=22% Similarity=0.380 Sum_probs=24.1
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhCC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAADG 308 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~~ 308 (321)
.++.+..|+++||++.+|.+|+++...
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 378899999999999999999998853
No 85
>PF15520 Toxin_40: Putative toxin 40
Probab=23.82 E-value=36 Score=29.58 Aligned_cols=17 Identities=35% Similarity=0.732 Sum_probs=14.2
Q ss_pred CCCCcccccccccCCCC
Q 020822 206 QDSRFPGRGRTLSSSQS 222 (321)
Q Consensus 206 ~~~~f~G~Gr~LG~~~~ 222 (321)
.++-|.|.||+||+.+.
T Consensus 145 ~~pgfvg~grtlggare 161 (178)
T PF15520_consen 145 PNPGFVGKGRTLGGARE 161 (178)
T ss_pred CCCccccCCccccccee
Confidence 36789999999998754
No 86
>PF11990 DUF3487: Protein of unknown function (DUF3487); InterPro: IPR021877 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
Probab=23.11 E-value=4e+02 Score=22.37 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=21.8
Q ss_pred hhcCCchhhHHHhhhhhhhhhh--hcCCCeeEecC
Q 020822 130 NLLMPGTSFYSAIESSSLLSTC--IRQPKFILCTG 162 (321)
Q Consensus 130 ~~l~p~~~~~~~iE~~~~l~~~--~r~p~~v~~~g 162 (321)
|.-.|-.+.++++|. +++.. ...+.||...|
T Consensus 77 KRGKP~~yl~r~l~~--~l~~~g~l~~~~lI~~sg 109 (121)
T PF11990_consen 77 KRGKPEGYLYRRLQW--RLARRGPLGGSRLITRSG 109 (121)
T ss_pred HcCCchhHHHHHHHH--HHHHhcccCCCCcEEeeC
Confidence 555688899999996 56555 46677887443
No 87
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=22.94 E-value=4.6e+02 Score=23.77 Aligned_cols=69 Identities=17% Similarity=0.085 Sum_probs=39.5
Q ss_pred cccCChHHHHHHHHHHHHHhcCCccccccccccchhHHHHHHHHHHHHHhc-----chhHHHHHHHHHHHHHHHHHHhhh
Q 020822 56 ECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWYPLILLVLFQVLM-----TNVSLLGHLCGILSGFAYTYGFFN 130 (321)
Q Consensus 56 ~~~vGaSGaIFaLl~~~~~~~p~~~~~l~G~~~IP~~~~p~ilLil~~ll~-----p~~S~lgHL~Gil~G~ly~~g~l~ 130 (321)
...+.-.+++|++++......+.. ..|.....+.+...+.++. .+-+++--++|+++|++.+..+..
T Consensus 91 ~~~l~~~~~~f~~L~~~~~~~~~~--------~~~~l~Lal~~~~~iyfl~~K~~~~~rA~~~~~~~L~~G~~lGs~l~~ 162 (194)
T PF11833_consen 91 SQDLLIRAAAFGALGLWSLLFPAA--------SGPGLQLALGLGACIYFLNRKERKLGRAFLWTLGGLVVGLILGSLLAS 162 (194)
T ss_pred cchHHHHHHHHHHHHHHHHHHcCC--------CCcchHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 346778899999998888775411 2333333333333333332 233555567777777777665444
Q ss_pred hc
Q 020822 131 LL 132 (321)
Q Consensus 131 ~l 132 (321)
++
T Consensus 163 ~l 164 (194)
T PF11833_consen 163 WL 164 (194)
T ss_pred hc
Confidence 33
No 88
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=21.97 E-value=87 Score=29.91 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=20.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHhC
Q 020822 282 SDEEIQKLVSMGFDKTQVEVALAAAD 307 (321)
Q Consensus 282 ~~~~v~~L~~MGf~~~~a~~AL~~~~ 307 (321)
-+++++-|.++||+++++.+.+.++=
T Consensus 243 l~~~i~~L~~lG~s~~ei~~mv~~~P 268 (345)
T PF02536_consen 243 LKPKIEFLQSLGFSEEEIAKMVRRFP 268 (345)
T ss_dssp HHHHHHHHHTTT--HHHHHHHHHHSG
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHhCc
Confidence 36789999999999999999988763
No 89
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=21.77 E-value=78 Score=25.32 Aligned_cols=24 Identities=13% Similarity=0.275 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 294 FDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 294 f~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
|++...+.||..++||..+|.+.|
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 567779999999999999999988
No 90
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=21.53 E-value=1.2e+02 Score=22.92 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 020822 112 LGHLCGILSGFAYTYGFFNL 131 (321)
Q Consensus 112 lgHL~Gil~G~ly~~g~l~~ 131 (321)
++-+.|+++||.++..++++
T Consensus 5 lali~G~~~Gff~ar~~~~k 24 (64)
T PF03672_consen 5 LALIVGAVIGFFIARKYMEK 24 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34457899999988887653
No 91
>PF14851 FAM176: FAM176 family
Probab=21.17 E-value=1.6e+02 Score=25.89 Aligned_cols=14 Identities=36% Similarity=0.377 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHh
Q 020822 62 SGVIFSLIVIETSL 75 (321)
Q Consensus 62 SGaIFaLl~~~~~~ 75 (321)
+|+++||+...+.+
T Consensus 28 ~gVC~GLlLtLcll 41 (153)
T PF14851_consen 28 SGVCAGLLLTLCLL 41 (153)
T ss_pred HHHHHHHHHHHHHH
Confidence 35555555444443
No 92
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=20.79 E-value=98 Score=29.76 Aligned_cols=28 Identities=32% Similarity=0.598 Sum_probs=20.9
Q ss_pred HhcCCCHHHHHHHHHHhCCCHHHHHHHh
Q 020822 290 VSMGFDKTQVEVALAAADGDLNVAVEIL 317 (321)
Q Consensus 290 ~~MGf~~~~a~~AL~~~~~d~~~A~e~L 317 (321)
...|.++++|+++|.+++|++..|+-.+
T Consensus 244 ~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 244 EATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 3467888888888888888887777654
Done!