Query 005036
Match_columns 717
No_of_seqs 101 out of 124
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 17:00:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07227 DUF1423: Protein of u 100.0 2E-165 5E-170 1311.8 34.9 438 260-706 1-446 (446)
2 smart00249 PHD PHD zinc finger 96.2 0.0059 1.3E-07 45.2 3.5 47 389-448 1-47 (47)
3 PF00628 PHD: PHD-finger; Int 89.5 0.15 3.2E-06 40.0 0.8 48 390-449 2-49 (51)
4 PRK08404 V-type ATP synthase s 78.1 20 0.00043 33.1 9.4 84 617-711 3-87 (103)
5 PRK01194 V-type ATP synthase s 75.2 40 0.00087 33.9 11.4 59 616-679 3-63 (185)
6 KOG0994 Extracellular matrix g 72.0 38 0.00083 43.1 12.0 108 605-715 1522-1634(1758)
7 PF02841 GBP_C: Guanylate-bind 70.2 50 0.0011 35.1 11.4 75 630-705 209-296 (297)
8 PF04156 IncA: IncA protein; 69.0 41 0.0009 32.9 9.8 95 611-709 95-191 (191)
9 TIGR00570 cdk7 CDK-activating 66.9 84 0.0018 34.7 12.3 99 389-510 5-112 (309)
10 PF11781 RRN7: RNA polymerase 62.6 3.5 7.7E-05 31.8 0.8 17 437-453 20-36 (36)
11 cd07674 F-BAR_FCHO1 The F-BAR 62.5 1.1E+02 0.0025 32.0 12.0 79 614-692 110-201 (261)
12 KOG1829 Uncharacterized conser 61.6 5 0.00011 47.0 2.2 46 373-426 502-552 (580)
13 TIGR03825 FliH_bacil flagellar 58.6 1.4E+02 0.0031 31.1 11.9 87 614-707 51-143 (255)
14 PF11793 FANCL_C: FANCL C-term 56.8 4.1 8.8E-05 35.0 0.3 59 389-451 4-64 (70)
15 COG1842 PspA Phage shock prote 55.5 1.2E+02 0.0026 31.8 10.8 81 625-713 52-133 (225)
16 PF01807 zf-CHC2: CHC2 zinc fi 52.5 17 0.00037 32.8 3.6 22 441-462 53-74 (97)
17 cd07652 F-BAR_Rgd1 The F-BAR ( 51.3 64 0.0014 33.5 7.9 66 651-716 30-109 (234)
18 PF12037 DUF3523: Domain of un 50.7 2.5E+02 0.0055 30.7 12.4 91 614-704 64-158 (276)
19 PF00611 FCH: Fes/CIP4, and EF 50.4 33 0.00072 29.0 4.9 40 631-671 15-54 (91)
20 PF09755 DUF2046: Uncharacteri 50.3 2.4E+02 0.0051 31.4 12.2 67 613-679 29-97 (310)
21 smart00109 C1 Protein kinase C 49.2 12 0.00026 28.2 1.8 32 390-423 14-45 (49)
22 smart00055 FCH Fes/CIP4 homolo 49.0 40 0.00087 28.8 5.2 37 632-669 16-52 (87)
23 cd00029 C1 Protein kinase C co 47.6 11 0.00025 28.7 1.5 33 390-423 14-46 (50)
24 KOG1556 26S proteasome regulat 47.4 68 0.0015 34.9 7.4 73 252-324 173-253 (309)
25 PRK13665 hypothetical protein; 47.1 41 0.00088 36.8 5.9 69 620-699 234-307 (316)
26 TIGR02499 HrpE_YscL_not type I 46.7 1.6E+02 0.0035 27.9 9.3 23 634-656 19-41 (166)
27 KOG0804 Cytoplasmic Zn-finger 46.2 59 0.0013 37.7 7.2 135 383-551 171-307 (493)
28 cd07649 F-BAR_GAS7 The F-BAR ( 45.9 3.2E+02 0.007 28.6 12.1 59 649-709 160-220 (233)
29 PF10168 Nup88: Nuclear pore c 45.5 1.9E+02 0.0041 35.2 11.6 55 660-715 595-661 (717)
30 PF11932 DUF3450: Protein of u 45.3 3.6E+02 0.0079 28.0 12.3 95 612-707 22-119 (251)
31 KOG0955 PHD finger protein BR1 43.9 16 0.00036 45.6 2.8 46 390-450 222-268 (1051)
32 cd07653 F-BAR_CIP4-like The F- 43.5 1.6E+02 0.0035 30.1 9.3 19 697-715 116-134 (251)
33 KOG0163 Myosin class VI heavy 41.2 69 0.0015 39.4 7.0 72 608-685 915-988 (1259)
34 PF10147 CR6_interact: Growth 40.3 1.7E+02 0.0036 31.0 8.9 61 636-696 115-179 (217)
35 PRK15422 septal ring assembly 39.9 76 0.0017 28.9 5.6 49 663-711 22-78 (79)
36 cd07648 F-BAR_FCHO The F-BAR ( 39.6 3E+02 0.0066 28.5 10.8 45 648-692 155-201 (261)
37 PF07649 C1_3: C1-like domain; 38.9 23 0.0005 25.7 1.8 18 403-420 13-30 (30)
38 PTZ00121 MAEBL; Provisional 38.1 1.1E+02 0.0023 40.4 8.2 22 632-653 1563-1584(2084)
39 cd07673 F-BAR_FCHO2 The F-BAR 37.3 3E+02 0.0065 29.3 10.4 16 653-668 39-54 (269)
40 cd07651 F-BAR_PombeCdc15_like 36.9 3.9E+02 0.0084 27.4 10.9 63 653-715 32-104 (236)
41 COG4864 Uncharacterized protei 36.7 1E+02 0.0022 33.1 6.8 78 619-707 232-316 (328)
42 PF04111 APG6: Autophagy prote 35.9 1E+02 0.0022 33.6 6.9 18 697-714 110-127 (314)
43 PRK00409 recombination and DNA 35.4 3.1E+02 0.0066 33.6 11.3 59 627-685 532-596 (782)
44 COG5141 PHD zinc finger-contai 35.0 17 0.00038 42.2 1.0 28 384-421 236-275 (669)
45 COG4396 Mu-like prophage host- 34.0 51 0.0011 33.1 3.8 47 621-667 5-60 (170)
46 PF13832 zf-HC5HC2H_2: PHD-zin 33.3 16 0.00035 32.8 0.4 61 389-455 2-68 (110)
47 KOG3091 Nuclear pore complex, 33.2 2.5E+02 0.0054 33.1 9.6 22 668-689 409-430 (508)
48 PRK12705 hypothetical protein; 32.7 4E+02 0.0087 31.4 11.3 8 655-662 68-75 (508)
49 PF13639 zf-RING_2: Ring finge 32.3 20 0.00044 27.4 0.7 31 389-423 2-33 (44)
50 PF01196 Ribosomal_L17: Riboso 32.0 55 0.0012 30.3 3.6 47 632-684 20-66 (97)
51 PF12127 YdfA_immunity: SigmaW 31.7 70 0.0015 35.2 4.8 66 620-696 229-299 (316)
52 PRK03963 V-type ATP synthase s 31.7 3.9E+02 0.0084 26.5 9.7 11 635-645 24-34 (198)
53 PRK10698 phage shock protein P 31.2 4.8E+02 0.01 27.2 10.5 81 624-712 51-132 (222)
54 PF07282 OrfB_Zn_ribbon: Putat 31.0 25 0.00055 29.2 1.1 29 390-418 31-59 (69)
55 PF11690 DUF3287: Protein of u 30.8 65 0.0014 30.8 3.9 28 628-655 27-54 (109)
56 cd07673 F-BAR_FCHO2 The F-BAR 30.6 2.4E+02 0.0052 30.0 8.5 44 649-692 163-208 (269)
57 PRK14471 F0F1 ATP synthase sub 29.9 4.5E+02 0.0098 25.5 9.6 54 630-683 65-125 (164)
58 KOG0957 PHD finger protein [Ge 29.6 26 0.00057 41.0 1.3 33 378-421 166-210 (707)
59 PRK14475 F0F1 ATP synthase sub 29.4 5.3E+02 0.011 25.3 10.0 25 630-654 67-91 (167)
60 PF00130 C1_1: Phorbol esters/ 29.4 27 0.00059 27.5 1.0 35 389-424 13-47 (53)
61 KOG0309 Conserved WD40 repeat- 29.2 26 0.00057 42.6 1.3 21 406-426 1043-1063(1081)
62 KOG0250 DNA repair protein RAD 28.6 3.6E+02 0.0078 34.6 10.4 89 598-686 676-768 (1074)
63 TIGR01069 mutS2 MutS2 family p 28.5 4E+02 0.0087 32.6 10.8 61 624-684 524-590 (771)
64 PTZ00266 NIMA-related protein 28.5 4.9E+02 0.011 33.3 11.7 24 466-489 224-247 (1021)
65 PF10083 DUF2321: Uncharacteri 28.4 1.1E+02 0.0023 31.1 5.0 105 408-522 31-146 (158)
66 PHA02562 46 endonuclease subun 28.0 8.4E+02 0.018 27.6 12.6 24 634-657 332-355 (562)
67 KOG2072 Translation initiation 27.6 3.8E+02 0.0082 33.7 10.1 100 605-710 727-848 (988)
68 PF00430 ATP-synt_B: ATP synth 27.5 4.1E+02 0.0089 24.1 8.4 24 629-652 55-78 (132)
69 cd07648 F-BAR_FCHO The F-BAR ( 27.3 6E+02 0.013 26.4 10.5 22 627-648 25-46 (261)
70 PF08112 ATP-synt_E_2: ATP syn 27.0 1.1E+02 0.0024 26.2 4.2 27 653-680 29-55 (56)
71 KOG3280 Mitochondrial/chloropl 26.7 1.7E+02 0.0036 30.1 6.1 57 623-682 37-93 (171)
72 KOG4323 Polycomb-like PHD Zn-f 26.5 46 0.001 38.5 2.5 57 390-455 171-228 (464)
73 PF04810 zf-Sec23_Sec24: Sec23 26.5 39 0.00084 26.3 1.4 32 383-415 3-34 (40)
74 KOG3654 Uncharacterized CH dom 26.5 1E+02 0.0022 36.4 5.2 44 611-662 400-443 (708)
75 smart00400 ZnF_CHCC zinc finge 26.4 76 0.0016 25.7 3.1 23 441-463 22-44 (55)
76 KOG3859 Septins (P-loop GTPase 25.4 2.4E+02 0.0052 31.7 7.4 34 628-661 344-377 (406)
77 PF11944 DUF3461: Protein of u 25.3 1.2E+02 0.0025 29.9 4.5 44 611-658 78-121 (125)
78 PHA02540 61 DNA primase; Provi 25.0 88 0.0019 34.8 4.2 22 440-461 53-74 (337)
79 PRK12402 replication factor C 24.9 3.3E+02 0.0072 28.2 8.2 82 256-339 242-327 (337)
80 TIGR02977 phageshock_pspA phag 24.8 7.2E+02 0.016 25.5 10.5 41 624-664 51-91 (219)
81 PRK14474 F0F1 ATP synthase sub 24.7 3.7E+02 0.008 28.4 8.5 15 669-683 108-122 (250)
82 KOG4691 Uncharacterized conser 24.2 8.1E+02 0.018 26.1 10.6 87 618-707 97-189 (227)
83 KOG3799 Rab3 effector RIM1 and 24.2 31 0.00067 34.4 0.6 20 389-417 67-86 (169)
84 PLN03188 kinesin-12 family pro 24.0 1E+02 0.0022 39.7 5.0 30 617-646 1201-1232(1320)
85 PF02841 GBP_C: Guanylate-bind 23.8 4.3E+02 0.0094 28.2 9.0 26 634-659 195-220 (297)
86 PF03962 Mnd1: Mnd1 family; I 23.7 7.9E+02 0.017 25.0 11.0 45 661-707 105-149 (188)
87 PF09538 FYDLN_acid: Protein o 23.6 38 0.00083 31.9 1.0 33 390-425 12-46 (108)
88 TIGR01069 mutS2 MutS2 family p 23.5 7.6E+02 0.017 30.4 11.9 21 477-497 404-424 (771)
89 TIGR01562 FdhE formate dehydro 23.2 47 0.001 36.3 1.8 18 400-417 205-222 (305)
90 PRK03564 formate dehydrogenase 23.0 49 0.0011 36.3 1.8 18 400-417 207-224 (309)
91 TIGR03321 alt_F1F0_F0_B altern 22.9 7.2E+02 0.016 25.9 10.1 22 662-683 101-122 (246)
92 cd07672 F-BAR_PSTPIP2 The F-BA 22.7 7E+02 0.015 26.3 10.1 32 635-667 15-46 (240)
93 TIGR01147 V_ATP_synt_G vacuola 22.6 2.7E+02 0.0058 26.7 6.4 53 617-684 28-86 (113)
94 PRK00420 hypothetical protein; 22.6 1.8E+02 0.004 27.8 5.3 30 494-525 72-101 (112)
95 PF00170 bZIP_1: bZIP transcri 22.5 80 0.0017 26.3 2.6 43 605-647 20-62 (64)
96 PRK00409 recombination and DNA 22.2 8.7E+02 0.019 29.9 12.0 43 451-498 388-430 (782)
97 PF06548 Kinesin-related: Kine 22.1 2.5E+02 0.0054 32.9 7.0 30 617-646 431-462 (488)
98 KOG3990 Uncharacterized conser 22.0 2E+02 0.0044 31.4 6.0 27 683-713 266-294 (305)
99 PF12171 zf-C2H2_jaz: Zinc-fin 21.8 33 0.00072 24.0 0.2 10 442-451 1-10 (27)
100 KOG1962 B-cell receptor-associ 21.7 5.8E+02 0.013 27.2 9.1 40 628-668 122-162 (216)
101 KOG1973 Chromatin remodeling p 21.7 28 0.00061 37.0 -0.2 36 404-452 231-269 (274)
102 PF07496 zf-CW: CW-type Zinc F 21.5 40 0.00086 27.4 0.6 15 404-418 2-16 (50)
103 TIGR02926 AhaH ATP synthase ar 21.4 5.7E+02 0.012 22.5 8.6 53 621-682 3-55 (85)
104 PRK02224 chromosome segregatio 21.4 1.2E+03 0.025 28.3 12.8 29 681-710 573-602 (880)
105 PF04003 Utp12: Dip2/Utp12 Fam 21.3 3.8E+02 0.0083 23.8 6.9 32 260-291 11-42 (110)
106 PRK09098 type III secretion sy 21.2 9.8E+02 0.021 25.2 12.1 49 614-662 22-73 (233)
107 PRK05667 dnaG DNA primase; Val 21.1 1E+02 0.0022 36.3 4.0 21 441-461 56-76 (580)
108 PRK06231 F0F1 ATP synthase sub 20.9 9.2E+02 0.02 24.8 10.3 28 630-657 105-132 (205)
No 1
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=100.00 E-value=2.2e-165 Score=1311.79 Aligned_cols=438 Identities=51% Similarity=0.887 Sum_probs=417.2
Q ss_pred HhccHHHHHHHHHhhhHHHHHHHHHHHHHhhcCchhhHHHHHHHHHhhhcCCCCHHHHhhhhhhHHHHHHHHHhcccccc
Q 005036 260 VSEAIPIMAQIIQELSDETLESVKEYLKNLFLMSEKREELMALKKRLERRSDLSKETLSKCHKDQLAILVAVKMGLGSFL 339 (717)
Q Consensus 260 vse~v~v~a~~~~em~~e~le~lKe~lr~il~~~dkr~e~~~LQk~lq~RsDLT~e~L~kahr~QLEILVAikTGi~~Fl 339 (717)
+||||++||++||+||+|+||+||++||+||++||||+||++||++||+|+|||++||++||||||||||||||||++||
T Consensus 1 ~~e~v~~~a~~~~~~~~e~l~~lk~~lr~i~~~~~~r~e~~~lQ~~l~~RsDLt~~~L~~~hr~QLEilVAiktG~~~fl 80 (446)
T PF07227_consen 1 ASESVPVMAEKMQEMPEESLEELKEYLREILEGPEKREEFVALQKLLQRRSDLTSETLSKAHRVQLEILVAIKTGIQAFL 80 (446)
T ss_pred CCCcHHHHHHHHHHchHHHHHHHHHHHHHHHhCcchHHHHHHHHHHHhccccCCHHHHhHhHHHHHHHHHHHhhCcHHHh
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcchhHHHhhhccccccccccCCCCCCCCcccccCCCCCCCCCcccccccccCCCCccceEecCCcchHHhHHh
Q 005036 340 SAKIQLPVNKLVEIFLYMRCRNVNCQSILPVDDCDCKICSTNKGFCSSCMCPVCLNFDCANNTCSWVGCDVCSHWCHAAC 419 (717)
Q Consensus 340 ~~~~~i~~s~LvEiFl~~rCRN~aCrs~Lp~dDc~C~IC~~~~GFCr~CsC~IC~KFD~nkdtc~WIgCd~CgHwcHldC 419 (717)
||+++||+++|||||+|+||||++|+++||++||+|+|||+++|||++||||||+|||+|+|||+|||||+||||||+||
T Consensus 81 ~~~~~~~~~~LveiFl~~rCrN~aC~s~LP~ddc~C~iC~~~~gFC~~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dC 160 (446)
T PF07227_consen 81 HPSISISQSELVEIFLYKRCRNLACRSQLPVDDCDCKICCSEPGFCRRCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDC 160 (446)
T ss_pred CCCCCcChHHHHHHHHHHhcCCHHhhccCCccccCcchhcCCCCccccCCccccCCcccCCCCeeEEeccCCCceehhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCcccCCCCCCCCCCCccceEEeccCCCccchhhhHHHHHhhhhhcchhhhHHHhhhhhhhhcccCCCcchhHHHHH
Q 005036 420 GIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHASEMFGFVKDVFLHCAKDWGLDTFVKELDCVTKIFKGSNDFKGKELQKK 499 (717)
Q Consensus 420 ALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~SeLlG~VKkvf~~ca~~w~~d~L~keL~lv~rIfrGSed~rGK~L~~~ 499 (717)
|||+++|++|++.+|+.|++||+|||++|||+||||||||+||++||++|++|+|++||+||+|||+||+|++||+||++
T Consensus 161 ALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk~vf~~ca~~~~~d~L~~eL~l~~rIf~GSed~rgk~L~~~ 240 (446)
T PF07227_consen 161 ALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVKKVFQTCAKAWRVDVLCKELDLVRRIFRGSEDYRGKELHEK 240 (446)
T ss_pred hcccccccCCccCCCCCccCceEEEccCCCChhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhCccchhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCchhHHHHHHHHhhccCCCccccccCccccccccccccc-cCCCCCCCCCCCCCCcccc------cc
Q 005036 500 AAELVSKLENKVMSPSEACNFIIRFFNNADSMSDFTASGTSLNDLIVTQASV-QKDAIPIPPATSLPPKYTI------YN 572 (717)
Q Consensus 500 veeal~KLe~~~v~~~d~~~~Il~ffk~~~gi~~~l~~g~~~~~L~~~q~~~-~~~a~~~~~~~~~~~k~~i------~~ 572 (717)
+++|++||++|+++++++||+||+||+++++.......+ +..++++||++| ++++.+++.++ .++++ ..
T Consensus 241 ~e~al~KL~~~~~~~~~a~~~il~ff~~~d~~~~~~~~~-~~~k~i~~q~a~~~~ia~~~~ea~---~~~e~v~~e~~~~ 316 (446)
T PF07227_consen 241 VEEALAKLENGVIDSSEACKAILQFFQELDSSKSFENSG-ESGKEIPPQEACPNRIAEVVQEAV---RKMESVAEEKMRM 316 (446)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHhcccccccccccc-cccccccccccccCCCCCcchhhc---ccchhhhhcchhh
Confidence 999999999997777799999999999987766655444 566677999999 77766665544 23322 45
Q ss_pred cccCCccccccchhhhhhhccccchhhhhhhhccccCCCCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhh
Q 005036 573 MTSSSGRRDSMSNDLFKKDLIGDLKVEDEIRFGKLSKNDGFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCART 652 (717)
Q Consensus 573 ~k~~~~~~~~~~~el~~~~~~~~~~~~~El~~~~~~Kk~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~ 652 (717)
+++++..+++++++|.+ ++++++|+++++++||++|||||||||||||||+|||.||||||||||||||||+||+
T Consensus 317 ~kka~~~~~~~~~~l~~-----k~k~~~e~~~~~~~kk~~~eeLESIVRiKqAEA~MFQ~kAdEARrEAE~LqrI~~aK~ 391 (446)
T PF07227_consen 317 LKKARLALETCDRELED-----KAKEVAELQFERQRKKPQIEELESIVRIKQAEAKMFQLKADEARREAEGLQRIALAKS 391 (446)
T ss_pred hhhhhhhhhhhhhHHHh-----hhhhhhhhhHHhhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 78999999999888665 7799999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhhcchHHHH-HHHHHHHHHH
Q 005036 653 EKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSHCDYLKMK-RMQAEIAGLL 706 (717)
Q Consensus 653 eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mk-rM~~~I~~LL 706 (717)
+|+|||||++|+||||+||||+|||||||||+||++|++|++|| ||+++|+|||
T Consensus 392 ~k~EEEYas~~~kl~l~eaee~r~~~~eelk~~e~s~~~~~~mk~rM~~~I~~LL 446 (446)
T PF07227_consen 392 EKIEEEYASRYLKLRLNEAEEERKKKFEELKVLENSHRDYDNMKMRMQSEIQDLL 446 (446)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999 9999999997
No 2
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=89.46 E-value=0.15 Score=39.95 Aligned_cols=48 Identities=25% Similarity=0.706 Sum_probs=34.0
Q ss_pred ccccccccCCCCccceEecCCcchHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCC
Q 005036 390 CPVCLNFDCANNTCSWVGCDVCSHWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCG 449 (717)
Q Consensus 390 C~IC~KFD~nkdtc~WIgCd~CgHwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCg 449 (717)
|.||.+ ..+.-.||.||.|+.|-|+.|.--.... ....+..|+|..|-
T Consensus 2 C~vC~~---~~~~~~~i~C~~C~~~~H~~C~~~~~~~---------~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQ---SDDDGDMIQCDSCNRWYHQECVGPPEKA---------EEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTS---SCTTSSEEEBSTTSCEEETTTSTSSHSH---------HSHHSSSBSSHHHH
T ss_pred CcCCCC---cCCCCCeEEcCCCChhhCcccCCCChhh---------ccCCCCcEECcCCc
Confidence 778888 4567889999999999999997544431 01112278887763
No 4
>PRK08404 V-type ATP synthase subunit H; Validated
Probab=78.08 E-value=20 Score=33.11 Aligned_cols=84 Identities=24% Similarity=0.313 Sum_probs=50.5
Q ss_pred hHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhhcchHHHH
Q 005036 617 ESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSHCDYLKMK 696 (717)
Q Consensus 617 EsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mk 696 (717)
|.|-+||+||++ |+....+|+.||..+-.=|....+++.+ --+.+|.++-.+++++-+. ..-.+--.+.
T Consensus 3 e~i~~ik~aE~~-~e~~L~~A~~Ea~~Ii~~Ak~~A~k~~~--------eii~eA~~eA~~ile~Ak~--eie~Ek~~a~ 71 (103)
T PRK08404 3 DVIKEIVKAEKE-AEERIEKAKEEAKKIIRKAKEEAKKIEE--------EIIKKAEEEAQKLIEKKKK--EGEEEAKKIL 71 (103)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Confidence 578899999987 7888899999998876655554444332 2345555555555554432 1111222233
Q ss_pred -HHHHHHHHHHHHHHH
Q 005036 697 -RMQAEIAGLLERMEA 711 (717)
Q Consensus 697 -rM~~~I~~LL~~MEa 711 (717)
.+..+|.+|...-+.
T Consensus 72 ~elk~eia~L~~~a~~ 87 (103)
T PRK08404 72 EEGEKEIEELKVKAEE 87 (103)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 566677776654443
No 5
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=75.17 E-value=40 Score=33.86 Aligned_cols=59 Identities=19% Similarity=0.364 Sum_probs=39.9
Q ss_pred hhHHHH--hhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhH
Q 005036 616 LESVVR--IKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKL 679 (717)
Q Consensus 616 LEsIVR--lKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~ 679 (717)
||.||. +++|+++. +.--++|++||+.+..-+.++.+++-++|..+.- .|++..+++..
T Consensus 3 le~i~~~I~~ea~~~a-~~I~~eA~~~aeei~~ea~~~a~~~~~~~~~k~~----~e~~~~~~rii 63 (185)
T PRK01194 3 LEDVIKDIEKSREEKK-KEINDEYSKRIEKLEKECDSKIQSIKEYYEKKMR----AEISRLKKSII 63 (185)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence 566663 34455443 4456789999999999999999998888877765 34444444444
No 6
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=71.97 E-value=38 Score=43.09 Aligned_cols=108 Identities=21% Similarity=0.265 Sum_probs=57.8
Q ss_pred ccccCCCCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHH-HHHHHhhhhhhhHHHHHHH---HhHH
Q 005036 605 GKLSKNDGFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEE-EYAHKLSKLCLRETEERRR---KKLE 680 (717)
Q Consensus 605 ~~~~Kk~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EE-EYas~~~Kl~l~EaEe~r~---~~~E 680 (717)
+++.+-+.+|.+=+=-+=.-|.|+|.|..|..||.+||.++.-|-.=.|.+|| +-|-..++=-|++|.+.-+ ++++
T Consensus 1522 e~v~sL~nVd~IL~~T~~di~ra~~L~s~A~~a~~~A~~v~~~ae~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~ 1601 (1758)
T KOG0994|consen 1522 ERVASLPNVDAILSRTKGDIARAENLQSEAERARSRAEDVKGQAEDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLA 1601 (1758)
T ss_pred HHHHhcccHHHHHHhhhhhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 35555555555544444455778888888888888888877655544444443 2333344445555544433 2333
Q ss_pred HHHHHHhhhcchHHHH-HHHHHHHHHHHHHHHhhhh
Q 005036 681 ELKVLEDSHCDYLKMK-RMQAEIAGLLERMEATKQQ 715 (717)
Q Consensus 681 elk~~E~s~~d~~~mk-rM~~~I~~LL~~MEatK~~ 715 (717)
+++. .... --... .|-..|.+|-.+||+.|.+
T Consensus 1602 kv~~--~t~~-aE~~~~~a~q~~~eL~~~~e~lk~~ 1634 (1758)
T KOG0994|consen 1602 KVQE--ETAA-AEKLATSATQQLGELETRMEELKHK 1634 (1758)
T ss_pred HHHH--HHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3321 1110 00111 4556677777777777653
No 7
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=70.18 E-value=50 Score=35.05 Aligned_cols=75 Identities=25% Similarity=0.365 Sum_probs=40.9
Q ss_pred HHhhHHHHHHHHHhhhHHHHh---hhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhhc--------c-hHHHH-
Q 005036 630 FQNKADEARREADEYKRMVCA---RTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSHC--------D-YLKMK- 696 (717)
Q Consensus 630 FQ~kAdeARrEAE~lqrI~~a---K~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~--------d-~~~mk- 696 (717)
-+.++..|++|.+.++..... ..+.-+..|..++..|. +..+++|+.+.+|...+-..+. + |-+.-
T Consensus 209 ~~~k~e~~e~e~~~l~e~~~~~~~~le~~~~~~ee~~~~L~-ekme~e~~~~~~e~e~~l~~k~~eq~~~l~e~~~~~~~ 287 (297)
T PF02841_consen 209 EQAKAEAAEKEKEKLEEKQKEQEQMLEQQERSYEEHIKQLK-EKMEEEREQLLQEQERLLEQKLQEQEELLKEGFQEEAE 287 (297)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-HHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777777777776654433 33444455655555554 4566666655554443322111 1 22222
Q ss_pred HHHHHHHHH
Q 005036 697 RMQAEIAGL 705 (717)
Q Consensus 697 rM~~~I~~L 705 (717)
+|+.+|++|
T Consensus 288 ~l~~ei~~L 296 (297)
T PF02841_consen 288 KLQKEIQDL 296 (297)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHc
Confidence 788888887
No 8
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=69.00 E-value=41 Score=32.89 Aligned_cols=95 Identities=21% Similarity=0.269 Sum_probs=58.4
Q ss_pred CCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhh--hHHHHHHHHhHHHHHHHHhh
Q 005036 611 DGFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCL--RETEERRRKKLEELKVLEDS 688 (717)
Q Consensus 611 ~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l--~EaEe~r~~~~Eelk~~E~s 688 (717)
.++++++..+.=.+.+..-. .+...+...+.+-+..+.+.+++.|.......+- ++..+.+.+.-+..+.+++.
T Consensus 95 ~el~~l~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~ 170 (191)
T PF04156_consen 95 EELDQLQERIQELESELEKL----KEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERL 170 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHH----HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555544444443322 2333334466666777777777777666554432 34556666666666667777
Q ss_pred hcchHHHHHHHHHHHHHHHHH
Q 005036 689 HCDYLKMKRMQAEIAGLLERM 709 (717)
Q Consensus 689 ~~d~~~mkrM~~~I~~LL~~M 709 (717)
..+|.....|..+.+.++++|
T Consensus 171 ~~~~~~l~~~~~~~~~l~~~~ 191 (191)
T PF04156_consen 171 QENLQQLEEKIQELQELLEQL 191 (191)
T ss_pred HHHHHHHHHHHHHHHHHHhhC
Confidence 777777778888889888876
No 9
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.89 E-value=84 Score=34.72 Aligned_cols=99 Identities=21% Similarity=0.337 Sum_probs=55.2
Q ss_pred ccccccccc-CCCCccceEecCCcchHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCCCccchhhhHHHHHhhhhh
Q 005036 389 MCPVCLNFD-CANNTCSWVGCDVCSHWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHASEMFGFVKDVFLHCAK 467 (717)
Q Consensus 389 sC~IC~KFD-~nkdtc~WIgCd~CgHwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~SeLlG~VKkvf~~ca~ 467 (717)
+|++|..-. .|.+--..|. .|||.-=-.|.-+.... | ...|..|+++-.--.+...+
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~l~~~--~------------~~~CP~C~~~lrk~~fr~q~------ 62 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDLLFVR--G------------SGSCPECDTPLRKNNFRVQL------ 62 (309)
T ss_pred CCCcCCCCCccCcccccccC--CCCCcccHHHHHHHhcC--C------------CCCCCCCCCccchhhccccc------
Confidence 688886631 2333334555 78888777888776532 1 12799999875544433323
Q ss_pred cchhhhHHHhhhhhhhhc---ccC-CCcch----hHHHHHHHHHHHHHhcC
Q 005036 468 DWGLDTFVKELDCVTKIF---KGS-NDFKG----KELQKKAAELVSKLENK 510 (717)
Q Consensus 468 ~w~~d~L~keL~lv~rIf---rGS-ed~rG----K~L~~~veeal~KLe~~ 510 (717)
+.-..+.+++++=.||+ .-+ +||.- =.-++.+|+++=.|-+|
T Consensus 63 -F~D~~vekEV~iRkrv~~i~Nk~e~dF~~l~~yNdYLE~vEdii~nL~~~ 112 (309)
T TIGR00570 63 -FEDPTVEKEVDIRKRVLKIYNKREEDFPSLREYNDYLEEVEDIVYNLTNN 112 (309)
T ss_pred -cccHHHHHHHHHHHHHHHHHccchhccCCHHHHHHHHHHHHHHHHHhhcC
Confidence 33355667777766554 222 22321 12234555555555555
No 10
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=62.57 E-value=3.5 Score=31.77 Aligned_cols=17 Identities=35% Similarity=0.665 Sum_probs=14.3
Q ss_pred CCccceEEeccCCCccc
Q 005036 437 GTSEMQFHCIGCGHASE 453 (717)
Q Consensus 437 ~~lDm~F~C~aCgk~Se 453 (717)
...||.|||..||++.|
T Consensus 20 ~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 20 YSDDGFYYCDRCGHQSE 36 (36)
T ss_pred EccCCEEEhhhCceEcC
Confidence 46788999999999864
No 11
>cd07674 F-BAR_FCHO1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 1 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH domain Only 1 (FCHO1) may be involved in clathrin-coated vesicle formation. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO2 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=62.53 E-value=1.1e+02 Score=31.96 Aligned_cols=79 Identities=15% Similarity=0.245 Sum_probs=51.2
Q ss_pred hhhhHHHHhhHHHHHHHHhhHH--HHHHHHHhhhH---------HHHhhhhhhHHHHHHHhhhhhh--hHHHHHHHHhHH
Q 005036 614 DSLESVVRIKEAEARMFQNKAD--EARREADEYKR---------MVCARTEKLEEEYAHKLSKLCL--RETEERRRKKLE 680 (717)
Q Consensus 614 eeLEsIVRlKqAEA~MFQ~kAd--eARrEAE~lqr---------I~~aK~eK~EEEYas~~~Kl~l--~EaEe~r~~~~E 680 (717)
+.++.+=.++..++.|--.|.. .|-+|+|+++. =+..|.+|.+++|+...-|+.- ..-++.=-..|+
T Consensus 110 ~~~~~~q~~q~~~~~l~kaK~~Y~~~cke~e~a~~~~~s~k~leK~~~K~~ka~~~y~~~~~ky~~~~~~~~~~m~~~~~ 189 (261)
T cd07674 110 GTLEAVQSLQVQSQHLQKSRENYHSKCVEQERLRREGVPQKELEKAELKTKKAAESLRGSVEKYNRARGDFEQKMLESAQ 189 (261)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555566667666665653 56666666642 2447788999999886555421 223444456689
Q ss_pred HHHHHHhhhcch
Q 005036 681 ELKVLEDSHCDY 692 (717)
Q Consensus 681 elk~~E~s~~d~ 692 (717)
.+|.+|..|.+|
T Consensus 190 ~~Q~~Ee~Ri~~ 201 (261)
T cd07674 190 KFQDIEETHLRH 201 (261)
T ss_pred HHHHHHHHHHHH
Confidence 999999988876
No 12
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=61.61 E-value=5 Score=47.05 Aligned_cols=46 Identities=17% Similarity=0.512 Sum_probs=34.9
Q ss_pred CCcccccCCCCCCCCCcccccccccCCCCccce-----EecCCcchHHhHHhhhhcCcc
Q 005036 373 CDCKICSTNKGFCSSCMCPVCLNFDCANNTCSW-----VGCDVCSHWCHAACGIQRNLI 426 (717)
Q Consensus 373 c~C~IC~~~~GFCr~CsC~IC~KFD~nkdtc~W-----IgCd~CgHwcHldCALr~~~i 426 (717)
..|+.|..+--+|-.| +.+.-.|=| ..|+.||++.|-.|-=+....
T Consensus 502 ~~C~lC~~~gfiCe~C--------q~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~s~~ 552 (580)
T KOG1829|consen 502 KECDLCTGKGFICELC--------QHNDIIYPFETRNTRRCSTCLAVFHKKCLRRKSPC 552 (580)
T ss_pred hhchhhccCeeeeeec--------cCCCcccccccccceeHHHHHHHHHHHHHhccCCC
Confidence 4588888876666666 445555566 899999999999998777654
No 13
>TIGR03825 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Probab=58.58 E-value=1.4e+02 Score=31.14 Aligned_cols=87 Identities=17% Similarity=0.185 Sum_probs=51.7
Q ss_pred hhhhHHHHhhHHHHHHHHhhH----HHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHH-HHhh
Q 005036 614 DSLESVVRIKEAEARMFQNKA----DEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKV-LEDS 688 (717)
Q Consensus 614 eeLEsIVRlKqAEA~MFQ~kA----deARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~-~E~s 688 (717)
++-+.||.=.+++|+=....+ ++|+.|++.+. ..|+.+= |..=|.+ -..|+.++-...+.++.. ++..
T Consensus 51 ~eA~~Ii~~A~~~a~~~~~~~~~~~~~~~~e~e~~~--e~A~~eG----y~eG~~~-G~~e~~~~~~~~i~~a~~i~~~a 123 (255)
T TIGR03825 51 AEAAQIIEQAEAQAAAIREQIEQERAQWEEERERLI--QEAKQEG----YEAGFQA-GESEALSIYQSTIDEANAIVEEA 123 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHH----HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667766666666655444 67777777653 3333333 4333333 234555555555555543 5666
Q ss_pred hcchHHHH-HHHHHHHHHHH
Q 005036 689 HCDYLKMK-RMQAEIAGLLE 707 (717)
Q Consensus 689 ~~d~~~mk-rM~~~I~~LL~ 707 (717)
..+|.++. .|+.+|-+|-.
T Consensus 124 ~~~~~~~l~~~e~el~~La~ 143 (255)
T TIGR03825 124 KDDYEEKIESAQPLIIELAC 143 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 77777777 78888888754
No 14
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=56.75 E-value=4.1 Score=35.01 Aligned_cols=59 Identities=17% Similarity=0.284 Sum_probs=22.9
Q ss_pred cccccccccCCCCccceEecC--CcchHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCCCc
Q 005036 389 MCPVCLNFDCANNTCSWVGCD--VCSHWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHA 451 (717)
Q Consensus 389 sC~IC~KFD~nkdtc~WIgCd--~CgHwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~ 451 (717)
.|.||+.+-...+.-..+.|+ .|++..|+.|-.+-.+.-.+.- ..-+. +.=.|..|.++
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~--~~~~~--~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSR--QSFIP--IFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS---TTT----EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCC--eeecc--cccCCcCCCCe
Confidence 488998875555666689998 9999999999876654311111 11111 22349999876
No 15
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=55.54 E-value=1.2e+02 Score=31.82 Aligned_cols=81 Identities=16% Similarity=0.217 Sum_probs=54.7
Q ss_pred HHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhhcchHHHH-HHHHHHH
Q 005036 625 AEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSHCDYLKMK-RMQAEIA 703 (717)
Q Consensus 625 AEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mk-rM~~~I~ 703 (717)
|..+-|+.+.++++..++.|+.=|..=..+-+|+.|...+ ++++.+=+.++.++.+.-....+. +|...|.
T Consensus 52 a~~k~~e~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al--------~~~~~le~~~~~~~~~~~~~~~~~~~l~~~~~ 123 (225)
T COG1842 52 ARQKQLERKLEEAQARAEKLEEKAELALQAGNEDLAREAL--------EEKQSLEDLAKALEAELQQAEEQVEKLKKQLA 123 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667899999999999999998888877888888886543 444444445555555444444454 5555555
Q ss_pred HHHHHHHHhh
Q 005036 704 GLLERMEATK 713 (717)
Q Consensus 704 ~LL~~MEatK 713 (717)
.|=.|++.+|
T Consensus 124 ~Le~Ki~e~~ 133 (225)
T COG1842 124 ALEQKIAELR 133 (225)
T ss_pred HHHHHHHHHH
Confidence 5555555444
No 16
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=52.46 E-value=17 Score=32.77 Aligned_cols=22 Identities=32% Similarity=0.841 Sum_probs=16.5
Q ss_pred ceEEeccCCCccchhhhHHHHH
Q 005036 441 MQFHCIGCGHASEMFGFVKDVF 462 (717)
Q Consensus 441 m~F~C~aCgk~SeLlG~VKkvf 462 (717)
..|+|-+||+.-|.+.+|.++-
T Consensus 53 ~~~~Cf~Cg~~Gd~i~~v~~~~ 74 (97)
T PF01807_consen 53 NRFKCFGCGKGGDVIDFVMKYE 74 (97)
T ss_dssp TEEEETTT--EE-HHHHHHHHH
T ss_pred CeEEECCCCCCCcHHhHHHHHh
Confidence 4899999999999999998764
No 17
>cd07652 F-BAR_Rgd1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Saccharomyces cerevisiae Rho GTPase activating protein Rgd1 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Saccharomyces cerevisiae Rgd1 is a GTPase activating protein (GAP) with activity towards Rho3p and Rho4p, which are involved in bud growth and cytokinesis, respectively. At low pH, S. cerevisiae Rgd1 is required for cell survival and the activation of the protein kinase C pathway, which is important in cell integrity and the maintenance of cell shape. It contains an N-terminal F-BAR domain and a C-terminal Rho GAP domain. The F-BAR domain of S. cerevisiae Rgd1 binds to phosphoinositides and plays an important role in the localization of the protein to the bud tip/neck during the cell cycle. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that
Probab=51.34 E-value=64 Score=33.48 Aligned_cols=66 Identities=24% Similarity=0.318 Sum_probs=41.2
Q ss_pred hhhhhHHHHHHHhhhhhhhHHH-------------HHHHHhHHHHHHHHhhhcchHHHH-HHHHHHHHHHHHHHHhhhhc
Q 005036 651 RTEKLEEEYAHKLSKLCLRETE-------------ERRRKKLEELKVLEDSHCDYLKMK-RMQAEIAGLLERMEATKQQW 716 (717)
Q Consensus 651 K~eK~EEEYas~~~Kl~l~EaE-------------e~r~~~~Eelk~~E~s~~d~~~mk-rM~~~I~~LL~~MEatK~~~ 716 (717)
|-..||+|||.++.||.-.=.. .-=...+++...+=..|..|.+-. .|..++..|...||..+..|
T Consensus 30 kRa~iEeeYak~L~KLak~~~~~~~~~~~~~gs~~~a~~~il~~~e~lA~~h~~~a~~L~~~~~eL~~l~~~~e~~RK~~ 109 (234)
T cd07652 30 KRAAIEEEHARGLKKLARTTLDTYKRPDHKQGSFSNAYHSSLEFHEKLADNGLRFAKALNEMSDELSSLAKTVEKSRKSI 109 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577899999998887543211 111222333444445666666533 67888888888888877665
No 18
>PF12037 DUF3523: Domain of unknown function (DUF3523); InterPro: IPR021911 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with PF00004 from PFAM. This domain has a conserved LER sequence motif.
Probab=50.65 E-value=2.5e+02 Score=30.69 Aligned_cols=91 Identities=25% Similarity=0.346 Sum_probs=70.2
Q ss_pred hhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHH--hhhhhhHHHHHHHhhhhhhh-HHHHHHHHhHHHHHHHHhhhc
Q 005036 614 DSLESVVRIKEAEARMFQNKADEARREADEYKRMVC--ARTEKLEEEYAHKLSKLCLR-ETEERRRKKLEELKVLEDSHC 690 (717)
Q Consensus 614 eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~--aK~eK~EEEYas~~~Kl~l~-EaEe~r~~~~Eelk~~E~s~~ 690 (717)
--+|---++++.||-.=|.+++..|-+.|--++.+. ++.+..=..|...++.-|.+ +.+..|+..-|.+++||-|-.
T Consensus 64 kQ~E~~ak~~e~ea~~~q~~~e~~rv~~EE~Rkt~~~q~q~~~q~aqY~D~LaRkR~~~e~~~qr~~n~e~lk~QEes~~ 143 (276)
T PF12037_consen 64 KQAELQAKIAEYEAAQAQAEIERQRVEAEERRKTLQQQTQQKQQRAQYEDELARKRYQDELEQQRRRNEELLKMQEESVI 143 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555678888888889999999999888777665 55667778899999988875 677777777888999998777
Q ss_pred chHHHH-HHHHHHHH
Q 005036 691 DYLKMK-RMQAEIAG 704 (717)
Q Consensus 691 d~~~mk-rM~~~I~~ 704 (717)
---+|. .++.+|+.
T Consensus 144 rqE~~Rr~Te~~i~~ 158 (276)
T PF12037_consen 144 RQEQMRRATEEQILA 158 (276)
T ss_pred HHHHHHHHHHHHHHH
Confidence 666777 67666665
No 19
>PF00611 FCH: Fes/CIP4, and EFC/F-BAR homology domain; InterPro: IPR001060 The FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. Many proteins containing an FCH domain are involved in the regulation of cytoskeletal rearrangements, vesicular transport and endocytosis. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. Proteins containing an FCH domain can be divided in 3 classes []: A subfamily of protein kinases usually associated with an SH2 domain: Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells. Fes related protein (fer). It is an ubiquitously expressed homologue of Fes. Adaptor proteins usually associated with a C-terminal SH3 domain: Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability. CD2 cytoplasmic domain binding protein. Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton. Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport. A subfamily of Rho-GAP proteins: Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells. Yeast hypothetical protein YBR260C. Caenorhabditis elegans hypothetical protein ZK669.1. ; PDB: 2EFK_A 2EFL_A 2X3W_A 2X3X_C 2X3V_C 3I2W_A 3ABH_B 3Q0K_B 3HAJ_A 3ACO_B ....
Probab=50.38 E-value=33 Score=29.01 Aligned_cols=40 Identities=25% Similarity=0.318 Sum_probs=29.4
Q ss_pred HhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHH
Q 005036 631 QNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRET 671 (717)
Q Consensus 631 Q~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~Ea 671 (717)
+.+.+......+.|..+.. |-.++|++|+.++.||.-.-.
T Consensus 15 ~~~~~~~~~~~~~l~~~~k-eRa~lE~~Yak~L~kl~~~~~ 54 (91)
T PF00611_consen 15 FKRLKQGIKLLEELASFFK-ERASLEEEYAKSLQKLAKKFK 54 (91)
T ss_dssp HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 3456666777777777654 456899999999999975543
No 20
>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Probab=50.32 E-value=2.4e+02 Score=31.42 Aligned_cols=67 Identities=13% Similarity=0.179 Sum_probs=45.7
Q ss_pred chhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHH--hhhhhhHHHHHHHhhhhhhhHHHHHHHHhH
Q 005036 613 FDSLESVVRIKEAEARMFQNKADEARREADEYKRMVC--ARTEKLEEEYAHKLSKLCLRETEERRRKKL 679 (717)
Q Consensus 613 ~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~--aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~ 679 (717)
+++|+.=-+...+|.+++-.++..-..|.+.|+..+. +-..-.||||-++-+=-+|+.+..++..+.
T Consensus 29 ~~sL~qen~~Lk~El~~ek~~~~~L~~e~~~lr~~sv~~~~~aEqEEE~isN~LlKkl~~l~keKe~L~ 97 (310)
T PF09755_consen 29 IESLQQENRVLKRELETEKARCKHLQEENRALREASVRIQAKAEQEEEFISNTLLKKLQQLKKEKETLA 97 (310)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455554566667888888888877777777776543 334456788888877777777777766654
No 21
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=49.23 E-value=12 Score=28.25 Aligned_cols=32 Identities=25% Similarity=0.528 Sum_probs=22.4
Q ss_pred ccccccccCCCCccceEecCCcchHHhHHhhhhc
Q 005036 390 CPVCLNFDCANNTCSWVGCDVCSHWCHAACGIQR 423 (717)
Q Consensus 390 C~IC~KFD~nkdtc~WIgCd~CgHwcHldCALr~ 423 (717)
|.+|.++-.... -++.|..|+..+|-.|+-+-
T Consensus 14 C~~C~~~i~~~~--~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 14 CCVCRKSIWGSF--QGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred ccccccccCcCC--CCcCCCCCCchHHHHHHhhc
Confidence 455555432222 47899999999999998653
No 22
>smart00055 FCH Fes/CIP4 homology domain. Alignment extended from original report. Highly alpha-helical. Also known as the RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Probab=48.99 E-value=40 Score=28.75 Aligned_cols=37 Identities=35% Similarity=0.579 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhh
Q 005036 632 NKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLR 669 (717)
Q Consensus 632 ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~ 669 (717)
.+.+...+..+.+.....-+ .++|+||+.++.||.-.
T Consensus 16 ~~~~~~~~~~~~~~~f~~~R-a~iE~eYak~L~kL~~~ 52 (87)
T smart00055 16 SRLKNGLRLLEDLKKFIRER-AKIEEEYAKKLQKLSKK 52 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHh
Confidence 34455566677777766555 78999999999999543
No 23
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=47.61 E-value=11 Score=28.73 Aligned_cols=33 Identities=24% Similarity=0.467 Sum_probs=23.4
Q ss_pred ccccccccCCCCccceEecCCcchHHhHHhhhhc
Q 005036 390 CPVCLNFDCANNTCSWVGCDVCSHWCHAACGIQR 423 (717)
Q Consensus 390 C~IC~KFD~nkdtc~WIgCd~CgHwcHldCALr~ 423 (717)
|.+|.++--.. +--++.|+.|+..+|-.|+-+-
T Consensus 14 C~~C~~~i~~~-~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 14 CDVCRKSIWGL-FKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred hhhcchhhhcc-ccceeEcCCCCCchhhhhhccC
Confidence 55565543322 4577889999999999998653
No 24
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=47.37 E-value=68 Score=34.86 Aligned_cols=73 Identities=21% Similarity=0.314 Sum_probs=58.6
Q ss_pred hhHHHHHHHhccHHHHHHHHHhhh------HHHHHHHHHHHHHhhcC--chhhHHHHHHHHHhhhcCCCCHHHHhhhhhh
Q 005036 252 PERILREIVSEAIPIMAQIIQELS------DETLESVKEYLKNLFLM--SEKREELMALKKRLERRSDLSKETLSKCHKD 323 (717)
Q Consensus 252 ~erilr~Ivse~v~v~a~~~~em~------~e~le~lKe~lr~il~~--~dkr~e~~~LQk~lq~RsDLT~e~L~kahr~ 323 (717)
+|-+||||--..+..+|.++-..- ..-|.+++.||..++.+ |=..+-+..||..+.-=.||+...|.+|--|
T Consensus 173 VEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~lQdvfNllP~l~~~~~~~a~~v 252 (309)
T KOG1556|consen 173 VEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQLQDVFNLLPNLTRNELVKAFNV 252 (309)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHhhCccccchhhhhhhcc
Confidence 567799999999988888764322 23478899999999976 6666789999999999999999888888764
Q ss_pred H
Q 005036 324 Q 324 (717)
Q Consensus 324 Q 324 (717)
+
T Consensus 253 k 253 (309)
T KOG1556|consen 253 K 253 (309)
T ss_pred c
Confidence 4
No 25
>PRK13665 hypothetical protein; Provisional
Probab=47.15 E-value=41 Score=36.81 Aligned_cols=69 Identities=26% Similarity=0.350 Sum_probs=31.9
Q ss_pred HHhhHHHHHH--HHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhh---cchHH
Q 005036 620 VRIKEAEARM--FQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSH---CDYLK 694 (717)
Q Consensus 620 VRlKqAEA~M--FQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~---~d~~~ 694 (717)
...-||||++ -|.||.|-|. +|.|+-+.+--.-.+.-+ .+.|||++=-.-+- +.+.+.. .|||+
T Consensus 234 Lq~dQAEADk~iAqAkAEeRRA-------mAvA~EQEmkA~v~emrA--kvVeAeaeVP~Ama--~A~r~G~lGvmDYy~ 302 (316)
T PRK13665 234 LQTDQAEADKRIAQAKAEERRA-------MAVALEQEMKAKVQEMRA--KVVEAEAEVPLAMA--EALRSGNLGVMDYYN 302 (316)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH--HhhhhhhhchHHHH--HHHHcCCCchhhhhh
Confidence 4567888876 3444444443 444443322222122222 23455544332221 2233333 39999
Q ss_pred HHHHH
Q 005036 695 MKRMQ 699 (717)
Q Consensus 695 mkrM~ 699 (717)
||-.+
T Consensus 303 ~kNi~ 307 (316)
T PRK13665 303 MKNIQ 307 (316)
T ss_pred hhccc
Confidence 99433
No 26
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=46.69 E-value=1.6e+02 Score=27.91 Aligned_cols=23 Identities=17% Similarity=0.086 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhhHHHHhhhhhhH
Q 005036 634 ADEARREADEYKRMVCARTEKLE 656 (717)
Q Consensus 634 AdeARrEAE~lqrI~~aK~eK~E 656 (717)
-++||++|+.+..-|..+.+.+-
T Consensus 19 l~~A~~~a~~i~~~A~~~~e~~~ 41 (166)
T TIGR02499 19 LAAARQRAEAILADAEEEAEASR 41 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999888887766543
No 27
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=46.22 E-value=59 Score=37.66 Aligned_cols=135 Identities=16% Similarity=0.273 Sum_probs=70.5
Q ss_pred CCCCCCcccccc-cccCCCCccceEecCCcchHHhHHhhhhcCcc-cCCCCCCCCCCCccceEEeccCCCccchhhhHHH
Q 005036 383 GFCSSCMCPVCL-NFDCANNTCSWVGCDVCSHWCHAACGIQRNLI-KPGPSLKGPSGTSEMQFHCIGCGHASEMFGFVKD 460 (717)
Q Consensus 383 GFCr~CsC~IC~-KFD~nkdtc~WIgCd~CgHwcHldCALr~~~i-~~G~~~kG~s~~lDm~F~C~aCgk~SeLlG~VKk 460 (717)
|+=-.=.|+||- ..|...++-+=+- |-|+-|-.|-.+-... ++-+--. .+-...-+-.|-.||.+-||.-
T Consensus 171 ~~tELPTCpVCLERMD~s~~gi~t~~---c~Hsfh~~cl~~w~~~scpvcR~~-q~p~~ve~~~c~~c~~~~~Lwi---- 242 (493)
T KOG0804|consen 171 GLTELPTCPVCLERMDSSTTGILTIL---CNHSFHCSCLMKWWDSSCPVCRYC-QSPSVVESSLCLACGCTEDLWI---- 242 (493)
T ss_pred CcccCCCcchhHhhcCccccceeeee---cccccchHHHhhcccCcChhhhhh-cCcchhhhhhhhhhcccccEEE----
Confidence 444455789995 4799999988875 5677777777665421 1111000 0011222445556665555432
Q ss_pred HHhhhhhcchhhhHHHhhhhhhhhcccCCCcchhHHHHHHHHHHHHHhcCCCCchhHHHHHHHHhhccCCCccccccCcc
Q 005036 461 VFLHCAKDWGLDTFVKELDCVTKIFKGSNDFKGKELQKKAAELVSKLENKVMSPSEACNFIIRFFNNADSMSDFTASGTS 540 (717)
Q Consensus 461 vf~~ca~~w~~d~L~keL~lv~rIfrGSed~rGK~L~~~veeal~KLe~~~v~~~d~~~~Il~ffk~~~gi~~~l~~g~~ 540 (717)
+..|++-|--.|++..-...-++-----.-+ +...-||.| -+++-|.|+.....
T Consensus 243 -------------------cliCg~vgcgrY~eghA~rHweet~H~yale-l~tqrVWDY------AGDnYVhRl~~~~~ 296 (493)
T KOG0804|consen 243 -------------------CLICGNVGCGRYKEGHARRHWEETGHCYALE-LETQRVWDY------AGDNYVHRLPQSKT 296 (493)
T ss_pred -------------------EEEccceecccccchhHHHHHHhhcceEEEe-ecceeeeec------ccchhhhhccccCC
Confidence 2345566777775444333333322111111 223355631 23455677777777
Q ss_pred ccccccccccc
Q 005036 541 LNDLIVTQASV 551 (717)
Q Consensus 541 ~~~L~~~q~~~ 551 (717)
.++|...+..+
T Consensus 297 dGklve~~~~~ 307 (493)
T KOG0804|consen 297 DGKLVESSTEG 307 (493)
T ss_pred CCceEEecccc
Confidence 77777666554
No 28
>cd07649 F-BAR_GAS7 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Growth Arrest Specific protein 7. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Growth Arrest Specific protein 7 (GAS7) is mainly expressed in the brain and is required for neurite outgrowth. It may also play a role in the protection and migration of embryonic stem cells. Treatment-related acute myeloid leukemia (AML) has been reported resulting from mixed-lineage leukemia (MLL)-GAS7 translocations as a complication of primary cancer treatment. GAS7 contains an N-terminal SH3 domain, followed by a WW domain, and a central F-BAR domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=45.88 E-value=3.2e+02 Score=28.65 Aligned_cols=59 Identities=10% Similarity=0.071 Sum_probs=41.9
Q ss_pred HhhhhhhHHHHHHHhhhh--hhhHHHHHHHHhHHHHHHHHhhhcchHHHHHHHHHHHHHHHHH
Q 005036 649 CARTEKLEEEYAHKLSKL--CLRETEERRRKKLEELKVLEDSHCDYLKMKRMQAEIAGLLERM 709 (717)
Q Consensus 649 ~aK~eK~EEEYas~~~Kl--~l~EaEe~r~~~~Eelk~~E~s~~d~~~mkrM~~~I~~LL~~M 709 (717)
..|.+|.+++|....-++ ....-+++=...|+.+|.+|..|..| ||-+...+..++.-|
T Consensus 160 ~~K~~Ka~~e~~~~ve~y~~~r~~we~~m~~~~~~~Q~~Ee~Rl~~--lk~~L~~y~~~~~~~ 220 (233)
T cd07649 160 RRKSTQAGDDLMRCVDLYNQAQSKWFEEMVTTSLELERLEVERIEM--IRQHLCQYTQLRHET 220 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHhc
Confidence 456788888887655443 22455667778999999999999888 665666666666544
No 29
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=45.51 E-value=1.9e+02 Score=35.15 Aligned_cols=55 Identities=20% Similarity=0.344 Sum_probs=28.9
Q ss_pred HHHhhhhhhhHHHHHHHHhHHHHHHH-Hhh----------hcchHHHH-HHHHHHHHHHHHHHHhhhh
Q 005036 660 AHKLSKLCLRETEERRRKKLEELKVL-EDS----------HCDYLKMK-RMQAEIAGLLERMEATKQQ 715 (717)
Q Consensus 660 as~~~Kl~l~EaEe~r~~~~Eelk~~-E~s----------~~d~~~mk-rM~~~I~~LL~~MEatK~~ 715 (717)
|.+++. |+.++.++.+.+...++.+ ..- -.+|.+-. +|..+|++|=.+++..|..
T Consensus 595 ae~Lae-R~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~~si~~lk~k 661 (717)
T PF10168_consen 595 AEKLAE-RYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLKASIEQLKKK 661 (717)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444 5666666666665555532 111 11443333 6777777766666665543
No 30
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=45.34 E-value=3.6e+02 Score=27.98 Aligned_cols=95 Identities=17% Similarity=0.219 Sum_probs=58.0
Q ss_pred CchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhH--HHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhh
Q 005036 612 GFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLE--EEYAHKLSKLCLRETEERRRKKLEELKVLEDSH 689 (717)
Q Consensus 612 ~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~E--EEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~ 689 (717)
.++++...++=..+.+...|.+.|+-..|...|..=...-...+| +.|..++. -.+...+++...+=+++..++...
T Consensus 22 ~~~~~~~~~~~~~~~~~~sQ~~id~~~~e~~~L~~e~~~l~~e~e~L~~~~~~l~-~~v~~q~~el~~L~~qi~~~~~~~ 100 (251)
T PF11932_consen 22 TLDQAQQVQQQWVQAAQQSQKRIDQWDDEKQELLAEYRQLEREIENLEVYNEQLE-RQVASQEQELASLEQQIEQIEETR 100 (251)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555566555556666888887777766665543322222221 23544443 356677777777777777777777
Q ss_pred cchHHHH-HHHHHHHHHHH
Q 005036 690 CDYLKMK-RMQAEIAGLLE 707 (717)
Q Consensus 690 ~d~~~mk-rM~~~I~~LL~ 707 (717)
.+..-+. +|.+.++.++.
T Consensus 101 ~~l~p~m~~m~~~L~~~v~ 119 (251)
T PF11932_consen 101 QELVPLMEQMIDELEQFVE 119 (251)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 7776666 77777776554
No 31
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=43.88 E-value=16 Score=45.58 Aligned_cols=46 Identities=30% Similarity=0.486 Sum_probs=31.2
Q ss_pred cccccccc-CCCCccceEecCCcchHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCCC
Q 005036 390 CPVCLNFD-CANNTCSWVGCDVCSHWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCGH 450 (717)
Q Consensus 390 C~IC~KFD-~nkdtc~WIgCd~CgHwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk 450 (717)
|+||.+-+ +|.|. -|.||.|....|.+|-= -.--.|++.-|++|.-
T Consensus 222 C~iC~~~~~~n~n~--ivfCD~Cnl~VHq~Cyg-------------i~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 222 CCICLDGECQNSNV--IVFCDGCNLAVHQECYG-------------IPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred ceeecccccCCCce--EEEcCCCcchhhhhccC-------------CCCCCCCcEeehhhcc
Confidence 45555542 23333 57899999999999953 1245677888888864
No 32
>cd07653 F-BAR_CIP4-like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein 4 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. Members of this subfamily typically contain an N-terminal F-BAR domain and a C-terminal SH3 domain. In addition, some members such as FNBP1L contain a central Cdc42-binding HR1 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged l
Probab=43.48 E-value=1.6e+02 Score=30.06 Aligned_cols=19 Identities=16% Similarity=0.489 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 005036 697 RMQAEIAGLLERMEATKQQ 715 (717)
Q Consensus 697 rM~~~I~~LL~~MEatK~~ 715 (717)
+.+.++...+..|+.+|+.
T Consensus 116 kl~~~~~~~~~~l~kskk~ 134 (251)
T cd07653 116 KLQQKLESSIKQLEKSKKA 134 (251)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3555555566666665543
No 33
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=41.16 E-value=69 Score=39.44 Aligned_cols=72 Identities=28% Similarity=0.330 Sum_probs=0.0
Q ss_pred cCCCCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhH--HHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHH
Q 005036 608 SKNDGFDSLESVVRIKEAEARMFQNKADEARREADEYKR--MVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVL 685 (717)
Q Consensus 608 ~Kk~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqr--I~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~ 685 (717)
+++++++|||..-++.++ .-+..||||||.=+| +..-|-.|.|-|-..+....+-.--||.-+++.-+++.+
T Consensus 915 k~~q~~~e~er~rk~qE~------~E~ER~rrEaeek~rre~ee~k~~k~e~e~kRK~eEeqr~~qee~e~~l~~e~q~q 988 (1259)
T KOG0163|consen 915 KEQQQIEELERLRKIQEL------AEAERKRREAEEKRRREEEEKKRAKAEMETKRKAEEEQRKAQEEEERRLALELQEQ 988 (1259)
T ss_pred hHHHHHHHHHHHHHHHHH------HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
No 34
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=40.33 E-value=1.7e+02 Score=31.03 Aligned_cols=61 Identities=18% Similarity=0.229 Sum_probs=42.0
Q ss_pred HHHHHHHhhhHHH--HhhhhhhHHHHHHHhhhhh--hhHHHHHHHHhHHHHHHHHhhhcchHHHH
Q 005036 636 EARREADEYKRMV--CARTEKLEEEYAHKLSKLC--LRETEERRRKKLEELKVLEDSHCDYLKMK 696 (717)
Q Consensus 636 eARrEAE~lqrI~--~aK~eK~EEEYas~~~Kl~--l~EaEe~r~~~~Eelk~~E~s~~d~~~mk 696 (717)
+..+..++.+.|| ++|..++=.+|-.+..|.. ..+++++|.+++||++-.=.-..|....+
T Consensus 115 k~~k~~~Rek~Ia~nM~Kmpk~i~e~~~~~~kk~~~~~~~k~rkerl~eEvre~fGy~vDprdpr 179 (217)
T PF10147_consen 115 KEEKRLAREKEIAKNMAKMPKWIAEWKAKIAKKEAKAQAAKERKERLIEEVREHFGYKVDPRDPR 179 (217)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcCCCCChH
Confidence 4455566777787 6788888899999888765 45677788888988875433333444433
No 35
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=39.93 E-value=76 Score=28.92 Aligned_cols=49 Identities=22% Similarity=0.319 Sum_probs=32.0
Q ss_pred hhhhhhhHHHHHHHHhHHHHHHHHhhhc----chHHHH----HHHHHHHHHHHHHHH
Q 005036 663 LSKLCLRETEERRRKKLEELKVLEDSHC----DYLKMK----RMQAEIAGLLERMEA 711 (717)
Q Consensus 663 ~~Kl~l~EaEe~r~~~~Eelk~~E~s~~----d~~~mk----rM~~~I~~LL~~MEa 711 (717)
+++..+.|..++...+-+|.+.+-.++- +..++| --++.|++||.+||.
T Consensus 22 LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr~LLGkm~~ 78 (79)
T PRK15422 22 LLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALLGRMEE 78 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4566666666666666666665433322 444555 368899999999984
No 36
>cd07648 F-BAR_FCHO The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proteins in this group have been named FCH domain Only (FCHO) proteins. Vertebrates have two members, FCHO1 and FCHO2. These proteins contain an F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=39.63 E-value=3e+02 Score=28.54 Aligned_cols=45 Identities=20% Similarity=0.265 Sum_probs=32.7
Q ss_pred HHhhhhhhHHHHHHHhhhhhhh--HHHHHHHHhHHHHHHHHhhhcch
Q 005036 648 VCARTEKLEEEYAHKLSKLCLR--ETEERRRKKLEELKVLEDSHCDY 692 (717)
Q Consensus 648 ~~aK~eK~EEEYas~~~Kl~l~--EaEe~r~~~~Eelk~~E~s~~d~ 692 (717)
+.+|.+|++++|...+-++.-. +-+.+=...|+.+|.+|..|.+|
T Consensus 155 ~~~K~~ka~~~Y~~~v~~~~~~~~~~~~~m~~~~~~~Q~lEe~Ri~~ 201 (261)
T cd07648 155 AEAKLKKAQDEYKALVEKYNNIRADFETKMTDSCKRFQEIEESHLRQ 201 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457788999999888776321 23445557788999999988876
No 37
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.88 E-value=23 Score=25.66 Aligned_cols=18 Identities=22% Similarity=0.547 Sum_probs=8.6
Q ss_pred cceEecCCcchHHhHHhh
Q 005036 403 CSWVGCDVCSHWCHAACG 420 (717)
Q Consensus 403 c~WIgCd~CgHwcHldCA 420 (717)
-.+-.|..|...-|++||
T Consensus 13 ~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 13 GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --EEE-TTT-----HHHH
T ss_pred CceEECccCCCccChhcC
Confidence 467789999999999997
No 38
>PTZ00121 MAEBL; Provisional
Probab=38.09 E-value=1.1e+02 Score=40.35 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHhhhHHHHhhhh
Q 005036 632 NKADEARREADEYKRMVCARTE 653 (717)
Q Consensus 632 ~kAdeARrEAE~lqrI~~aK~e 653 (717)
.|+-+++|.||..++||++|.+
T Consensus 1563 ~kk~eekr~aeE~k~~a~rkae 1584 (2084)
T PTZ00121 1563 KKKAEEAKKAEEDKNMALRKAE 1584 (2084)
T ss_pred HHHHHHHHHHhhhhhhhhhhHH
Confidence 4556667777888888888754
No 39
>cd07673 F-BAR_FCHO2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 2 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. The specific function of FCH domain Only 2 (FCHO2) is still unknown. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO1 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=37.35 E-value=3e+02 Score=29.31 Aligned_cols=16 Identities=31% Similarity=0.617 Sum_probs=11.0
Q ss_pred hhhHHHHHHHhhhhhh
Q 005036 653 EKLEEEYAHKLSKLCL 668 (717)
Q Consensus 653 eK~EEEYas~~~Kl~l 668 (717)
..|||+||.++.||.-
T Consensus 39 a~iEe~Yak~L~kLak 54 (269)
T cd07673 39 ATIEEAYSRSMTKLAK 54 (269)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 5677777777777653
No 40
>cd07651 F-BAR_PombeCdc15_like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe Cdc15, and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Schizosaccharomyces pombe Cdc15 and Imp2, and similar proteins. These proteins contain an N-terminal F-BAR domain and a C-terminal SH3 domain. S. pombe Cdc15 and Imp2 play both distinct and overlapping roles in the maintenance and strengthening of the contractile ring at the division site, which is required in cell division. Cdc15 is a component of the actomyosin ring and is required in normal cytokinesis. Imp2 colocalizes with the medial ring during septation and is required for normal septation. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation
Probab=36.94 E-value=3.9e+02 Score=27.40 Aligned_cols=63 Identities=21% Similarity=0.338 Sum_probs=30.1
Q ss_pred hhhHHHHHHHhhhhhhh--------HHHHHHHHhHHHHHHHHhhhcchHHHH--HHHHHHHHHHHHHHHhhhh
Q 005036 653 EKLEEEYAHKLSKLCLR--------ETEERRRKKLEELKVLEDSHCDYLKMK--RMQAEIAGLLERMEATKQQ 715 (717)
Q Consensus 653 eK~EEEYas~~~Kl~l~--------EaEe~r~~~~Eelk~~E~s~~d~~~mk--rM~~~I~~LL~~MEatK~~ 715 (717)
..||++|+.++.||.-. ....-=..++.+...+=..|..+.+.- -+...|..+...|+..++.
T Consensus 32 a~iE~eYak~L~kLakk~~~~~~~gsl~~a~~~i~~e~e~~a~~H~~~a~~L~~~v~~~l~~~~~~~~~~rK~ 104 (236)
T cd07651 32 ASIEEEYAKRLEKLSRKSLGGSEEGGLKNSLDTLRLETESMAKSHLKFAKQIRQDLEEKLAAFASSYTQKRKK 104 (236)
T ss_pred HHHHHHHHHHHHHHHccccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45777777777666421 111111222333333334555554433 3445566666666655443
No 41
>COG4864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.67 E-value=1e+02 Score=33.15 Aligned_cols=78 Identities=29% Similarity=0.340 Sum_probs=38.6
Q ss_pred HHHhhHHHHHH--HHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHh---hhcchH
Q 005036 619 VVRIKEAEARM--FQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLED---SHCDYL 693 (717)
Q Consensus 619 IVRlKqAEA~M--FQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~---s~~d~~ 693 (717)
.....||||+| -|.||.|-|.+|=.+.+=.+||-+ | .-+| ..|||++--.-+-+ .|+. +--|||
T Consensus 232 ~lqteqa~adk~iaqakaeerramava~eqemrarve---e----mrak--vveaeaevp~als~--alr~gnigvmdy~ 300 (328)
T COG4864 232 KLQTEQAEADKNIAQAKAEERRAMAVALEQEMRARVE---E----MRAK--VVEAEAEVPLALSE--ALREGNIGVMDYY 300 (328)
T ss_pred ccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH---H----HHHH--HHHhhccccHHHHH--HHHhCCchhhhhh
Confidence 44567899987 466666655555444333333322 1 1122 34555554333222 2332 334999
Q ss_pred HHHH--HHHHHHHHHH
Q 005036 694 KMKR--MQAEIAGLLE 707 (717)
Q Consensus 694 ~mkr--M~~~I~~LL~ 707 (717)
+||- --+.+++-+.
T Consensus 301 n~~nv~adt~mr~si~ 316 (328)
T COG4864 301 NMKNVQADTAMRDSIN 316 (328)
T ss_pred hhhcccccHHHHHHHh
Confidence 9992 2334444443
No 42
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=35.86 E-value=1e+02 Score=33.58 Aligned_cols=18 Identities=22% Similarity=0.241 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 005036 697 RMQAEIAGLLERMEATKQ 714 (717)
Q Consensus 697 rM~~~I~~LL~~MEatK~ 714 (717)
.++.+.+.|....+.+.+
T Consensus 110 ~~~~e~~sl~~q~~~~~~ 127 (314)
T PF04111_consen 110 EFQEERDSLKNQYEYASN 127 (314)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455666666666555543
No 43
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=35.43 E-value=3.1e+02 Score=33.64 Aligned_cols=59 Identities=24% Similarity=0.330 Sum_probs=37.7
Q ss_pred HHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhh------hhHHHHHHHHhHHHHHHH
Q 005036 627 ARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLC------LRETEERRRKKLEELKVL 685 (717)
Q Consensus 627 A~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~------l~EaEe~r~~~~Eelk~~ 685 (717)
.+--...+...++|++.+++=...+.++++++....+.+++ +.+|.++=+.++.+|+.+
T Consensus 532 ~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~~~~~a~~~l~~a~~~~~~~i~~lk~~ 596 (782)
T PRK00409 532 LEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQL 596 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445556667777788877777777777777766554443 445555555666677653
No 44
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=34.99 E-value=17 Score=42.23 Aligned_cols=28 Identities=25% Similarity=0.914 Sum_probs=0.0
Q ss_pred CCCCCcccccccccCCCCccceEecCCc------------chHHhHHhhh
Q 005036 384 FCSSCMCPVCLNFDCANNTCSWVGCDVC------------SHWCHAACGI 421 (717)
Q Consensus 384 FCr~CsC~IC~KFD~nkdtc~WIgCd~C------------gHwcHldCAL 421 (717)
||+.|+ ..++..+.|..| |.|||+-|||
T Consensus 236 lCrkCi----------~~~~~i~~C~fCps~dGaFkqT~dgrW~H~iCA~ 275 (669)
T COG5141 236 LCRKCI----------YGEYQIRCCSFCPSSDGAFKQTSDGRWGHVICAM 275 (669)
T ss_pred hhhhhc----------ccccceeEEEeccCCCCceeeccCCchHhHhHHH
No 45
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=34.01 E-value=51 Score=33.07 Aligned_cols=47 Identities=26% Similarity=0.383 Sum_probs=35.7
Q ss_pred HhhHHHHHHHHhh---------HHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhh
Q 005036 621 RIKEAEARMFQNK---------ADEARREADEYKRMVCARTEKLEEEYAHKLSKLC 667 (717)
Q Consensus 621 RlKqAEA~MFQ~k---------AdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~ 667 (717)
||||+--.-||.+ .-|-.||+.||.-=.--|...++|+||-++.-|+
T Consensus 5 kiK~~A~~a~q~~eeV~~~Ir~iGDlqRE~~RLeTemnDk~aai~e~Yapq~~~lk 60 (170)
T COG4396 5 KIKQPAIEAAQDKEEVTAFIRQIGDLQREVKRLETEMNDKKAAIEEEYAPQAAPLK 60 (170)
T ss_pred hhhhhHHhccccHHHHHHHHHHHHHHHHHHHHHHHHhcchHhHHHHHhhhhhHHHH
Confidence 4555544445544 4577899999988888899999999999987665
No 46
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=33.33 E-value=16 Score=32.83 Aligned_cols=61 Identities=20% Similarity=0.362 Sum_probs=0.0
Q ss_pred cccccccccCCCCccceEecCCcchHHhHHhhhhcCccc------CCCCCCCCCCCccceEEeccCCCccchh
Q 005036 389 MCPVCLNFDCANNTCSWVGCDVCSHWCHAACGIQRNLIK------PGPSLKGPSGTSEMQFHCIGCGHASEMF 455 (717)
Q Consensus 389 sC~IC~KFD~nkdtc~WIgCd~CgHwcHldCALr~~~i~------~G~~~kG~s~~lDm~F~C~aCgk~SeLl 455 (717)
.|++|.+.+.+.-+.. -+.|+|+-|||-...+. +.++.............|.-|++.....
T Consensus 2 ~C~lC~~~~Galk~t~------~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~~~C~iC~~~~G~~ 68 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTS------DGQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFKLKCSICGKSGGAC 68 (110)
T ss_pred ccEeCCCCCCcccCcc------CCcEEEeEccceeCccEEeechhcCcccceeecchhcCCcCcCCCCCCcee
No 47
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=33.21 E-value=2.5e+02 Score=33.09 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=11.9
Q ss_pred hhHHHHHHHHhHHHHHHHHhhh
Q 005036 668 LRETEERRRKKLEELKVLEDSH 689 (717)
Q Consensus 668 l~EaEe~r~~~~Eelk~~E~s~ 689 (717)
|.-.||+=+.||.-|..+=+.+
T Consensus 409 L~~~EE~Lr~Kldtll~~ln~P 430 (508)
T KOG3091|consen 409 LTPDEEELRAKLDTLLAQLNAP 430 (508)
T ss_pred CCccHHHHHHHHHHHHHHhcCh
Confidence 4445555555666555554444
No 48
>PRK12705 hypothetical protein; Provisional
Probab=32.72 E-value=4e+02 Score=31.36 Aligned_cols=8 Identities=13% Similarity=0.131 Sum_probs=3.1
Q ss_pred hHHHHHHH
Q 005036 655 LEEEYAHK 662 (717)
Q Consensus 655 ~EEEYas~ 662 (717)
+|+||..+
T Consensus 68 ~e~e~~~~ 75 (508)
T PRK12705 68 QRQEARRE 75 (508)
T ss_pred HHHHHHHH
Confidence 33444333
No 49
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=32.26 E-value=20 Score=27.42 Aligned_cols=31 Identities=32% Similarity=0.673 Sum_probs=21.1
Q ss_pred ccccccc-ccCCCCccceEecCCcchHHhHHhhhhc
Q 005036 389 MCPVCLN-FDCANNTCSWVGCDVCSHWCHAACGIQR 423 (717)
Q Consensus 389 sC~IC~K-FD~nkdtc~WIgCd~CgHwcHldCALr~ 423 (717)
.|.||.. |+. +-.++... |||.-|.+|..+-
T Consensus 2 ~C~IC~~~~~~---~~~~~~l~-C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 2 ECPICLEEFED---GEKVVKLP-CGHVFHRSCIKEW 33 (44)
T ss_dssp CETTTTCBHHT---TSCEEEET-TSEEEEHHHHHHH
T ss_pred CCcCCChhhcC---CCeEEEcc-CCCeeCHHHHHHH
Confidence 3788866 444 33444555 8999999996553
No 50
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=31.97 E-value=55 Score=30.28 Aligned_cols=47 Identities=28% Similarity=0.267 Sum_probs=32.2
Q ss_pred hhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHH
Q 005036 632 NKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKV 684 (717)
Q Consensus 632 ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~ 684 (717)
.||.|+|+-||+| |.+||... .++.+.+.-.|. -.+-.+++|++|--
T Consensus 20 ~KAke~r~~aErl--It~ak~~~---~~~~r~~~~~l~-~~~~v~KLf~~l~p 66 (97)
T PF01196_consen 20 AKAKELRPYAERL--ITLAKKGD---LHARRQALSWLR-DKELVKKLFKELAP 66 (97)
T ss_dssp HHHHHHHHHHHHH--HHHHTSST---HHHHHHHHHCSS-SHHHHHHHHTTHHH
T ss_pred HHHHHHHHHHHHH--HHHhccCc---HHHHHHHHHHhc-chHHHHHHHHHHHH
Confidence 5899999999998 66777554 344455554555 44566778887743
No 51
>PF12127 YdfA_immunity: SigmaW regulon antibacterial; InterPro: IPR022853 This entry represents the uncharacterised protein family UPF0365. Its function is not known. The proteins in this family are found in bacteria. They are about 330 amino acids in length and encoded by a gene located in an operon which confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.
Probab=31.72 E-value=70 Score=35.18 Aligned_cols=66 Identities=24% Similarity=0.308 Sum_probs=31.4
Q ss_pred HHhhHHHHHH--HHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhh---cchHH
Q 005036 620 VRIKEAEARM--FQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSH---CDYLK 694 (717)
Q Consensus 620 VRlKqAEA~M--FQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~---~d~~~ 694 (717)
...-||||++ .|.||.|-|-.|-...+=-.||.+. .-+| +.|||++=-.-+- +.+.+.. .|||+
T Consensus 229 Lq~dQAeADk~iAqAkAEeRRA~AvA~EQEm~A~vqe-------~rAk--vVeAeaevP~A~a--eAfr~G~lGvmDYy~ 297 (316)
T PF12127_consen 229 LQTDQAEADKRIAQAKAEERRAMAVAREQEMKAKVQE-------MRAK--VVEAEAEVPLAMA--EAFRSGNLGVMDYYN 297 (316)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHhH--heehhhhchHHHH--HHHHcCCCcchhhhh
Confidence 4567889875 4555555444443333333333322 2222 3444444322221 1233332 39999
Q ss_pred HH
Q 005036 695 MK 696 (717)
Q Consensus 695 mk 696 (717)
||
T Consensus 298 ~~ 299 (316)
T PF12127_consen 298 LK 299 (316)
T ss_pred hh
Confidence 99
No 52
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=31.67 E-value=3.9e+02 Score=26.50 Aligned_cols=11 Identities=45% Similarity=0.767 Sum_probs=4.4
Q ss_pred HHHHHHHHhhh
Q 005036 635 DEARREADEYK 645 (717)
Q Consensus 635 deARrEAE~lq 645 (717)
.+|+.||+.+.
T Consensus 24 ~~A~~~a~~i~ 34 (198)
T PRK03963 24 EEAQKEAEKIK 34 (198)
T ss_pred HHHHHHHHHHH
Confidence 34444444333
No 53
>PRK10698 phage shock protein PspA; Provisional
Probab=31.20 E-value=4.8e+02 Score=27.17 Aligned_cols=81 Identities=20% Similarity=0.214 Sum_probs=49.9
Q ss_pred HHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHHHHHHhhhcchHHHH-HHHHHH
Q 005036 624 EAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEELKVLEDSHCDYLKMK-RMQAEI 702 (717)
Q Consensus 624 qAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mk-rM~~~I 702 (717)
-|..++++.+.+++..+++.+.+=|..=.++=+|+-|.. |=++|+..-+.+..++..+-.-..+- .|+..|
T Consensus 51 ~A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~--------AL~~K~~~~~~~~~l~~~~~~~~~~~~~L~~~l 122 (222)
T PRK10698 51 LAEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARA--------ALIEKQKLTDLIATLEHEVTLVDETLARMKKEI 122 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888999999999888887777677777775543 22344444455555555554444443 455555
Q ss_pred HHHHHHHHHh
Q 005036 703 AGLLERMEAT 712 (717)
Q Consensus 703 ~~LL~~MEat 712 (717)
+.|=.+++.+
T Consensus 123 ~~L~~ki~ea 132 (222)
T PRK10698 123 GELENKLSET 132 (222)
T ss_pred HHHHHHHHHH
Confidence 5554444443
No 54
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.01 E-value=25 Score=29.24 Aligned_cols=29 Identities=17% Similarity=0.371 Sum_probs=17.4
Q ss_pred ccccccccCCCCccceEecCCcchHHhHH
Q 005036 390 CPVCLNFDCANNTCSWVGCDVCSHWCHAA 418 (717)
Q Consensus 390 C~IC~KFD~nkdtc~WIgCd~CgHwcHld 418 (717)
|..|+......-.-.+..|..||+..|-|
T Consensus 31 C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 31 CPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred ccCcccccccccccceEEcCCCCCEECcH
Confidence 55565554444455666777777766655
No 55
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=30.82 E-value=65 Score=30.80 Aligned_cols=28 Identities=14% Similarity=0.377 Sum_probs=16.6
Q ss_pred HHHHhhHHHHHHHHHhhhHHHHhhhhhh
Q 005036 628 RMFQNKADEARREADEYKRMVCARTEKL 655 (717)
Q Consensus 628 ~MFQ~kAdeARrEAE~lqrI~~aK~eK~ 655 (717)
.+|+.--++.++||+.+=.=+.-|..+.
T Consensus 27 ~~f~~~~~kd~~ea~~F~~kV~~qH~~~ 54 (109)
T PF11690_consen 27 AVFRHLPSKDKKEAYDFIDKVVDQHQRY 54 (109)
T ss_pred HHHccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566777777777655554444443
No 56
>cd07673 F-BAR_FCHO2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 2 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. The specific function of FCH domain Only 2 (FCHO2) is still unknown. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO1 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=30.58 E-value=2.4e+02 Score=29.99 Aligned_cols=44 Identities=18% Similarity=0.334 Sum_probs=32.3
Q ss_pred HhhhhhhHHHHHHHhhhhhhh--HHHHHHHHhHHHHHHHHhhhcch
Q 005036 649 CARTEKLEEEYAHKLSKLCLR--ETEERRRKKLEELKVLEDSHCDY 692 (717)
Q Consensus 649 ~aK~eK~EEEYas~~~Kl~l~--EaEe~r~~~~Eelk~~E~s~~d~ 692 (717)
.+|..|.+++|+..+-|+--. +=+++=...|+.+|.+|-.|.+|
T Consensus 163 ~~k~~ka~~~Y~~~v~~l~~~~~~~~~~m~~~~~~~Q~~Ee~Ri~~ 208 (269)
T cd07673 163 AVKSKKATESYKLYVEKYALAKADFEQKMTETAQKFQDIEETHLIR 208 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577889999999887776321 33455566778888888888776
No 57
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=29.90 E-value=4.5e+02 Score=25.48 Aligned_cols=54 Identities=20% Similarity=0.222 Sum_probs=23.3
Q ss_pred HHhhHHHHHHHHHhhhHHHHhhhhhhHHHH-------HHHhhhhhhhHHHHHHHHhHHHHH
Q 005036 630 FQNKADEARREADEYKRMVCARTEKLEEEY-------AHKLSKLCLRETEERRRKKLEELK 683 (717)
Q Consensus 630 FQ~kAdeARrEAE~lqrI~~aK~eK~EEEY-------as~~~Kl~l~EaEe~r~~~~Eelk 683 (717)
|+.+-.+||.||.....=|.+..+++.++. +.++...--.+.+.+|++.+.+|+
T Consensus 65 ~e~~l~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i~~ek~~a~~~l~ 125 (164)
T PRK14471 65 NERLLKEARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQAKASIESEKNAAMAEIK 125 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555555554444433333333222 333333333444555555554443
No 58
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=29.60 E-value=26 Score=40.96 Aligned_cols=33 Identities=36% Similarity=1.074 Sum_probs=0.0
Q ss_pred ccCCCCCCCCCcccccccccCCCCccceEecCCc------------chHHhHHhhh
Q 005036 378 CSTNKGFCSSCMCPVCLNFDCANNTCSWVGCDVC------------SHWCHAACGI 421 (717)
Q Consensus 378 C~~~~GFCr~CsC~IC~KFD~nkdtc~WIgCd~C------------gHwcHldCAL 421 (717)
|+.+|-||-.|-| +-++ --|+.| |.|.|+-|||
T Consensus 166 ~stepWfCeaC~~----------Gvs~-P~CElCPn~~GifKetDigrWvH~iCAL 210 (707)
T KOG0957|consen 166 CSTEPWFCEACLY----------GVSL-PHCELCPNRFGIFKETDIGRWVHAICAL 210 (707)
T ss_pred CCCCchhhhhHhc----------CCCC-CccccCCCcCCcccccchhhHHHHHHHh
No 59
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=29.38 E-value=5.3e+02 Score=25.32 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=13.6
Q ss_pred HHhhHHHHHHHHHhhhHHHHhhhhh
Q 005036 630 FQNKADEARREADEYKRMVCARTEK 654 (717)
Q Consensus 630 FQ~kAdeARrEAE~lqrI~~aK~eK 654 (717)
|+.+-.+||.||..+..=+.+..++
T Consensus 67 ~e~~L~~A~~ea~~Ii~~A~~~a~~ 91 (167)
T PRK14475 67 VKAEREEAERQAAAMLAAAKADARR 91 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455566666666655444444433
No 60
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=29.38 E-value=27 Score=27.53 Aligned_cols=35 Identities=26% Similarity=0.469 Sum_probs=23.4
Q ss_pred cccccccccCCCCccceEecCCcchHHhHHhhhhcC
Q 005036 389 MCPVCLNFDCANNTCSWVGCDVCSHWCHAACGIQRN 424 (717)
Q Consensus 389 sC~IC~KFD~nkdtc~WIgCd~CgHwcHldCALr~~ 424 (717)
.|.+|.++=.. ..-.-+.|..|+..+|-+|+-+-.
T Consensus 13 ~C~~C~~~i~g-~~~~g~~C~~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 13 YCDVCGKFIWG-LGKQGYRCSWCGLVCHKKCLSKVP 47 (53)
T ss_dssp B-TTSSSBECS-SSSCEEEETTTT-EEETTGGCTSS
T ss_pred CCcccCcccCC-CCCCeEEECCCCChHhhhhhhhcC
Confidence 35566665433 455678899999999999986544
No 61
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=29.24 E-value=26 Score=42.65 Aligned_cols=21 Identities=24% Similarity=0.476 Sum_probs=18.2
Q ss_pred EecCCcchHHhHHhhhhcCcc
Q 005036 406 VGCDVCSHWCHAACGIQRNLI 426 (717)
Q Consensus 406 IgCd~CgHwcHldCALr~~~i 426 (717)
+.|..|||.-|.+|+..=..+
T Consensus 1043 ~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1043 NFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred hhhccccccccHHHHHHHHhc
Confidence 568899999999999877765
No 62
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=28.62 E-value=3.6e+02 Score=34.56 Aligned_cols=89 Identities=21% Similarity=0.180 Sum_probs=53.2
Q ss_pred hhhhhhhccccCCCCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHH---HHhhhhhhHHHHHHHhhhhh-hhHHHH
Q 005036 598 VEDEIRFGKLSKNDGFDSLESVVRIKEAEARMFQNKADEARREADEYKRM---VCARTEKLEEEYAHKLSKLC-LRETEE 673 (717)
Q Consensus 598 ~~~El~~~~~~Kk~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI---~~aK~eK~EEEYas~~~Kl~-l~EaEe 673 (717)
+..+++..+-.=+-.++++++-++-.+-.-.=-+.+...+|.|.-.|+.+ -..++.+++++|-...-++. |.+-++
T Consensus 676 ~~~~l~~~~~~~e~~l~e~~~~~~~l~~~~~q~~~~~~~~~~em~el~n~~e~~~~~~~~~~~l~~ei~~~~~eIe~~~~ 755 (1074)
T KOG0250|consen 676 EILELENQRREAEKNLEELEKKLRELSEHIEQIKRRIRKKRAEMTELKNTAEEKQVDISKLEDLAREIKKKEKEIEEKEA 755 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcchhhhHHHHHHHHHHHHHHHHHHH
Confidence 34455555555556788888888877766666667777888888888874 33446666666665554443 333333
Q ss_pred HHHHhHHHHHHHH
Q 005036 674 RRRKKLEELKVLE 686 (717)
Q Consensus 674 ~r~~~~Eelk~~E 686 (717)
.+.++=+|++.++
T Consensus 756 ~~e~l~~e~e~~~ 768 (1074)
T KOG0250|consen 756 PLEKLKEELEHIE 768 (1074)
T ss_pred HHHHHHHHHHHHH
Confidence 3333334444333
No 63
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=28.47 E-value=4e+02 Score=32.64 Aligned_cols=61 Identities=21% Similarity=0.249 Sum_probs=40.6
Q ss_pred HHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhh------hhHHHHHHHHhHHHHHH
Q 005036 624 EAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLC------LRETEERRRKKLEELKV 684 (717)
Q Consensus 624 qAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~------l~EaEe~r~~~~Eelk~ 684 (717)
+.+.+.-...+...++|++.+++-...+.+++|++....+.+++ +.+|.++=+.++.+|+.
T Consensus 524 ~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~a~~ea~~~~~~a~~~~~~~i~~lk~ 590 (771)
T TIGR01069 524 EKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVESIIRELKE 590 (771)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34556666777788888888888888888888887776664433 34444444555555553
No 64
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=28.46 E-value=4.9e+02 Score=33.26 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=15.0
Q ss_pred hhcchhhhHHHhhhhhhhhcccCC
Q 005036 466 AKDWGLDTFVKELDCVTKIFKGSN 489 (717)
Q Consensus 466 a~~w~~d~L~keL~lv~rIfrGSe 489 (717)
.+.|+..++.++|-.+.-.|.+..
T Consensus 224 SDVWSLG~ILYELLTGk~PF~~~~ 247 (1021)
T PTZ00266 224 SDMWALGCIIYELCSGKTPFHKAN 247 (1021)
T ss_pred hHHHHHHHHHHHHHHCCCCCCcCC
Confidence 455777777777766665554433
No 65
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.36 E-value=1.1e+02 Score=31.14 Aligned_cols=105 Identities=18% Similarity=0.261 Sum_probs=0.0
Q ss_pred cCCcchHHhHHh-----hhhcCcccCCCCCCCCCCCccceEEeccCCCccchhhhHHHHHhhhhhcch-hhhH---HHhh
Q 005036 408 CDVCSHWCHAAC-----GIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHASEMFGFVKDVFLHCAKDWG-LDTF---VKEL 478 (717)
Q Consensus 408 Cd~CgHwcHldC-----ALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~SeLlG~VKkvf~~ca~~w~-~d~L---~keL 478 (717)
|+-||--+-+.| -||-.+--.|.. +=.++.+.-.||-.||++ +.|.+..+..+...-. .|.| .++.
T Consensus 31 C~kCG~~tI~~Cp~C~~~IrG~y~v~gv~--~~g~~~~~PsYC~~CGkp---yPWt~~~L~aa~el~ee~eeLs~deke~ 105 (158)
T PF10083_consen 31 CSKCGAKTITSCPNCSTPIRGDYHVEGVF--GLGGHYEAPSYCHNCGKP---YPWTENALEAANELIEEDEELSPDEKEQ 105 (158)
T ss_pred HHHhhHHHHHHCcCCCCCCCCceecCCee--eeCCCCCCChhHHhCCCC---CchHHHHHHHHHHHHHHhhcCCHHHHHH
Q ss_pred hhh--hhhcccCCCcchhHHHHHHHHHHHHHhcCCCCchhHHHHHH
Q 005036 479 DCV--TKIFKGSNDFKGKELQKKAAELVSKLENKVMSPSEACNFII 522 (717)
Q Consensus 479 ~lv--~rIfrGSed~rGK~L~~~veeal~KLe~~~v~~~d~~~~Il 522 (717)
... -.|+.-+-+. +.--.+...++.|+-.. ..++.+-||
T Consensus 106 ~~~sl~dL~~d~PkT--~vA~~rfKk~~~K~g~~---v~~~~~dIl 146 (158)
T PF10083_consen 106 FKESLPDLTKDTPKT--KVAATRFKKILSKAGSI---VGDAIRDIL 146 (158)
T ss_pred HHhhhHHHhhcCCcc--HHHHHHHHHHHHHHhHH---HHHHHHHHH
No 66
>PHA02562 46 endonuclease subunit; Provisional
Probab=28.01 E-value=8.4e+02 Score=27.64 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=12.2
Q ss_pred HHHHHHHHHhhhHHHHhhhhhhHH
Q 005036 634 ADEARREADEYKRMVCARTEKLEE 657 (717)
Q Consensus 634 AdeARrEAE~lqrI~~aK~eK~EE 657 (717)
.++++++.+.++.....+.+.+++
T Consensus 332 ~~~~~~~i~el~~~i~~~~~~i~~ 355 (562)
T PHA02562 332 FNEQSKKLLELKNKISTNKQSLIT 355 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555555554444433
No 67
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=27.58 E-value=3.8e+02 Score=33.72 Aligned_cols=100 Identities=28% Similarity=0.306 Sum_probs=60.5
Q ss_pred ccccCCCCchhhhHHHHhhHHHHHHHH------------------hh--HHHHHHHHHhhhHHHHhhhhhhHHHHHHHhh
Q 005036 605 GKLSKNDGFDSLESVVRIKEAEARMFQ------------------NK--ADEARREADEYKRMVCARTEKLEEEYAHKLS 664 (717)
Q Consensus 605 ~~~~Kk~~~eeLEsIVRlKqAEA~MFQ------------------~k--AdeARrEAE~lqrI~~aK~eK~EEEYas~~~ 664 (717)
+.++....+-|=|+-|..|.+=+.|+- .+ --+|+-|||+ .||+-.|.+.+||---.-
T Consensus 727 Ek~Ri~~~~ae~e~~vk~k~~l~rm~~d~~~f~e~vk~~rqs~~~e~~~~~ea~leaer-~rl~erk~~R~eerk~~~-- 803 (988)
T KOG2072|consen 727 EKQRIEAAIAERESAVKDKKRLSRMYDDRDKFKEHVKGERQSEYEEKLKQFEARLEAER-NRLAERKRARIEERKQAY-- 803 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHH--
Confidence 344444555566777777766666643 22 2367889999 999999988888754322
Q ss_pred hhhhhHHHHHHHHhHHHHHHHHhhhcchHHHH--HHHHHHHHHHHHHH
Q 005036 665 KLCLRETEERRRKKLEELKVLEDSHCDYLKMK--RMQAEIAGLLERME 710 (717)
Q Consensus 665 Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mk--rM~~~I~~LL~~ME 710 (717)
+-|.||+|.++-||+-.-|..-..--..| +=+.+|...-.+-|
T Consensus 804 ---~re~EEEr~Rr~EEe~~ae~~ee~~e~akr~~~eRe~e~~~ak~e 848 (988)
T KOG2072|consen 804 ---YREIEEERARREEEEANAERQEEAAERAKRTEEEREIENRVAKKE 848 (988)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 24678888888888766554332111233 44555555554444
No 68
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=27.52 E-value=4.1e+02 Score=24.14 Aligned_cols=24 Identities=29% Similarity=0.320 Sum_probs=13.6
Q ss_pred HHHhhHHHHHHHHHhhhHHHHhhh
Q 005036 629 MFQNKADEARREADEYKRMVCART 652 (717)
Q Consensus 629 MFQ~kAdeARrEAE~lqrI~~aK~ 652 (717)
-++.+..+||.||+.+..=+....
T Consensus 55 e~~~~l~~a~~ea~~i~~~a~~~a 78 (132)
T PF00430_consen 55 EYEEKLAEAREEAQEIIEEAKEEA 78 (132)
T ss_dssp HHHHHHHHHHHHHCHHHHHHCHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355666677777765554443333
No 69
>cd07648 F-BAR_FCHO The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proteins in this group have been named FCH domain Only (FCHO) proteins. Vertebrates have two members, FCHO1 and FCHO2. These proteins contain an F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=27.32 E-value=6e+02 Score=26.42 Aligned_cols=22 Identities=9% Similarity=0.244 Sum_probs=11.6
Q ss_pred HHHHHhhHHHHHHHHHhhhHHH
Q 005036 627 ARMFQNKADEARREADEYKRMV 648 (717)
Q Consensus 627 A~MFQ~kAdeARrEAE~lqrI~ 648 (717)
+++|+.||.==..=|.+|++++
T Consensus 25 ~~f~keRa~IEe~Yak~L~kLa 46 (261)
T cd07648 25 ADFLRERATIEETYSKALNKLA 46 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666654444444455444
No 70
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=26.99 E-value=1.1e+02 Score=26.19 Aligned_cols=27 Identities=41% Similarity=0.524 Sum_probs=22.0
Q ss_pred hhhHHHHHHHhhhhhhhHHHHHHHHhHH
Q 005036 653 EKLEEEYAHKLSKLCLRETEERRRKKLE 680 (717)
Q Consensus 653 eK~EEEYas~~~Kl~l~EaEe~r~~~~E 680 (717)
.++-.|| ++++|+|+.+.|+-||+.+.
T Consensus 29 ~~ln~EY-~kiLk~r~~~lEevKrk~LK 55 (56)
T PF08112_consen 29 SNLNMEY-EKILKQRRKELEEVKRKALK 55 (56)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHhc
Confidence 4566788 47899999999999998764
No 71
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=26.74 E-value=1.7e+02 Score=30.11 Aligned_cols=57 Identities=23% Similarity=0.240 Sum_probs=41.0
Q ss_pred hHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHH
Q 005036 623 KEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEEL 682 (717)
Q Consensus 623 KqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eel 682 (717)
|.--++.+-.||+|||+=||.| |.++|.+----+|+.+++-.=|.|-. -=.++|++|
T Consensus 37 kHErIe~t~ara~Ear~~aEkl--It~~~k~g~~~~~~~~~a~~~l~ekd-li~KlF~vl 93 (171)
T KOG3280|consen 37 KHERIETTWARAKEARRYAEKL--ITLGKKAGSLHERTARMADGWLREKD-LLHKLFTVL 93 (171)
T ss_pred HhhhhhhHHHHHHHHHHHHHHH--HHHHHhcCcHhHHHHHHHhcccccch-HHHHHHHHh
Confidence 4445567899999999999988 77777666667777777766666654 334566655
No 72
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=26.51 E-value=46 Score=38.45 Aligned_cols=57 Identities=26% Similarity=0.563 Sum_probs=37.3
Q ss_pred ccccccc-cCCCCccceEecCCcchHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCCCccchh
Q 005036 390 CPVCLNF-DCANNTCSWVGCDVCSHWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHASEMF 455 (717)
Q Consensus 390 C~IC~KF-D~nkdtc~WIgCd~CgHwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~SeLl 455 (717)
||+|+.- --..| .-|.|+.|.-|-|-+|----.. .-. .+.-+..|+|-.|...-+-+
T Consensus 171 c~vC~~g~~~~~N--rmlqC~~C~~~fHq~Chqp~i~--~~l-----~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 171 CSVCYCGGPGAGN--RMLQCDKCRQWYHQACHQPLIK--DEL-----AGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred eeeeecCCcCccc--eeeeecccccHHHHHhccCCCC--Hhh-----ccCccceEeehhhccchhhc
Confidence 5566432 33334 8999999999999999632221 111 24467899999998875443
No 73
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=26.49 E-value=39 Score=26.29 Aligned_cols=32 Identities=16% Similarity=0.449 Sum_probs=15.2
Q ss_pred CCCCCCcccccccccCCCCccceEecCCcchHH
Q 005036 383 GFCSSCMCPVCLNFDCANNTCSWVGCDVCSHWC 415 (717)
Q Consensus 383 GFCr~CsC~IC~KFD~nkdtc~WIgCd~CgHwc 415 (717)
--|++|-..|.-..-.+.++-.|+ |.+|++.-
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~-C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWI-CNFCGTKN 34 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEE-ETTT--EE
T ss_pred cccCCCCCEECCcceEcCCCCEEE-CcCCCCcC
Confidence 457788888874443334566675 77777643
No 74
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=26.46 E-value=1e+02 Score=36.38 Aligned_cols=44 Identities=34% Similarity=0.343 Sum_probs=24.7
Q ss_pred CCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHH
Q 005036 611 DGFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHK 662 (717)
Q Consensus 611 ~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~ 662 (717)
++--+=|.-+|-.|-||+|=|.| +||||-||.= -.+.|||-|.|
T Consensus 400 qqrraeear~rkqqleae~e~kr-eearrkaeee-------r~~keee~arr 443 (708)
T KOG3654|consen 400 QQRRAEEARRRKQQLEAEKEQKR-EEARRKAEEE-------RAPKEEEVARR 443 (708)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhHhh-------hcchhhhhhHH
Confidence 34444566667777777776543 5666655543 23445555554
No 75
>smart00400 ZnF_CHCC zinc finger.
Probab=26.37 E-value=76 Score=25.73 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=20.3
Q ss_pred ceEEeccCCCccchhhhHHHHHh
Q 005036 441 MQFHCIGCGHASEMFGFVKDVFL 463 (717)
Q Consensus 441 m~F~C~aCgk~SeLlG~VKkvf~ 463 (717)
..|||-+||+.-|++.+|+++..
T Consensus 22 n~~~Cf~cg~gGd~i~fv~~~~~ 44 (55)
T smart00400 22 QFFHCFGCGAGGNVISFLMKYDK 44 (55)
T ss_pred CEEEEeCCCCCCCHHHHHHHHHC
Confidence 47999999999999999998753
No 76
>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]
Probab=25.35 E-value=2.4e+02 Score=31.66 Aligned_cols=34 Identities=18% Similarity=0.312 Sum_probs=18.0
Q ss_pred HHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHH
Q 005036 628 RMFQNKADEARREADEYKRMVCARTEKLEEEYAH 661 (717)
Q Consensus 628 ~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas 661 (717)
.||+.|.+|-..|...-.+=..+|-+.+.+.|..
T Consensus 344 qmFvqrvkekE~elke~Ekel~~kf~~lkr~h~e 377 (406)
T KOG3859|consen 344 QMFVQRVKEKEAELKEAEKELHEKFDRLKRLHQE 377 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5777777765544443333444455544444443
No 77
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=25.25 E-value=1.2e+02 Score=29.87 Aligned_cols=44 Identities=16% Similarity=0.305 Sum_probs=37.3
Q ss_pred CCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHH
Q 005036 611 DGFDSLESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEE 658 (717)
Q Consensus 611 ~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEE 658 (717)
..||||+.|+.-.++|.+.=|.-.+| .+.|.+++-.|.+.||..
T Consensus 78 ~vieELdqi~~~~~~~~d~K~kiL~d----L~HLE~Vv~~KIaEIe~d 121 (125)
T PF11944_consen 78 YVIEELDQITGREQAEVDLKQKILDD----LRHLEKVVNSKIAEIERD 121 (125)
T ss_pred HHHHHHHHHHcchhhhHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Confidence 45899999999999999988877765 557899999998888865
No 78
>PHA02540 61 DNA primase; Provisional
Probab=24.99 E-value=88 Score=34.77 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=19.9
Q ss_pred cceEEeccCCCccchhhhHHHH
Q 005036 440 EMQFHCIGCGHASEMFGFVKDV 461 (717)
Q Consensus 440 Dm~F~C~aCgk~SeLlG~VKkv 461 (717)
++.|||-+||+--|.+.|+++.
T Consensus 53 ~~~yhCFgCGa~Gd~i~Flme~ 74 (337)
T PHA02540 53 GGVFKCHNCGYHRPFGNFLKDY 74 (337)
T ss_pred ceEEEecCCCCCCCHHHHHHHh
Confidence 6799999999999999999853
No 79
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=24.91 E-value=3.3e+02 Score=28.23 Aligned_cols=82 Identities=12% Similarity=0.159 Sum_probs=50.0
Q ss_pred HHHHHhc-c-HHHHHHHHHhhhHHHHHHHHHHHHHhh--cCchhhHHHHHHHHHhhhcCCCCHHHHhhhhhhHHHHHHHH
Q 005036 256 LREIVSE-A-IPIMAQIIQELSDETLESVKEYLKNLF--LMSEKREELMALKKRLERRSDLSKETLSKCHKDQLAILVAV 331 (717)
Q Consensus 256 lr~Ivse-~-v~v~a~~~~em~~e~le~lKe~lr~il--~~~dkr~e~~~LQk~lq~RsDLT~e~L~kahr~QLEILVAi 331 (717)
+.+++.+ + -..|-+.+..+-..-.......+++++ .+....+=+..|-..++.| .+.+.|.++++.-.|+=+++
T Consensus 242 v~~~~~~~~~~~~i~~l~~ai~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~~~~~~--~~~~~l~~~~~~l~~~d~~l 319 (337)
T PRK12402 242 AYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARSR--YRGDNLARLHRLAADADARL 319 (337)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHH
Confidence 4555543 2 234444444444333455556666665 2322223334444456666 89999999999999999999
Q ss_pred Hhcccccc
Q 005036 332 KMGLGSFL 339 (717)
Q Consensus 332 kTGi~~Fl 339 (717)
|||..+.+
T Consensus 320 k~g~~~~~ 327 (337)
T PRK12402 320 TDGANDRI 327 (337)
T ss_pred HcCCCHHH
Confidence 99965543
No 80
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=24.82 E-value=7.2e+02 Score=25.49 Aligned_cols=41 Identities=10% Similarity=0.139 Sum_probs=29.1
Q ss_pred HHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhh
Q 005036 624 EAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLS 664 (717)
Q Consensus 624 qAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~ 664 (717)
-|..+++..+.+++...++.+..=|..=..+=+|+-|..-+
T Consensus 51 ~a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al 91 (219)
T TIGR02977 51 IADKKELERRVSRLEAQVADWQEKAELALSKGREDLARAAL 91 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 35667778888888888888877776666666777555443
No 81
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=24.70 E-value=3.7e+02 Score=28.41 Aligned_cols=15 Identities=13% Similarity=0.357 Sum_probs=6.6
Q ss_pred hHHHHHHHHhHHHHH
Q 005036 669 RETEERRRKKLEELK 683 (717)
Q Consensus 669 ~EaEe~r~~~~Eelk 683 (717)
.+.+.+|++.+.+|+
T Consensus 108 ~~ie~Ek~~a~~~L~ 122 (250)
T PRK14474 108 EQLEREKQEFFKALQ 122 (250)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444443
No 82
>KOG4691 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.25 E-value=8.1e+02 Score=26.11 Aligned_cols=87 Identities=20% Similarity=0.283 Sum_probs=46.2
Q ss_pred HHHHhhHHHHHHHHhh--HHHHHHHHHhhhHHHHhhhhhhHHHHHHHhh---hhhhhHHHHHHHHhHHH-HHHHHhhhcc
Q 005036 618 SVVRIKEAEARMFQNK--ADEARREADEYKRMVCARTEKLEEEYAHKLS---KLCLRETEERRRKKLEE-LKVLEDSHCD 691 (717)
Q Consensus 618 sIVRlKqAEA~MFQ~k--AdeARrEAE~lqrI~~aK~eK~EEEYas~~~---Kl~l~EaEe~r~~~~Ee-lk~~E~s~~d 691 (717)
-|++.+++||--||.- +|+|+.++-.=-||+ ...+-++|-.+.++ ...+.+-++.+++.=.| ++++|+|. +
T Consensus 97 ~ie~~~e~eaaE~~el~a~N~a~N~~~~~~R~~--Rla~~~~E~~~~i~ee~~~~~e~~~a~k~qae~eVl~~iersk-n 173 (227)
T KOG4691|consen 97 LIERKAEKEAAEHRELMAWNQAENRRLHELRIA--RLAQEEREQEQRIAEEQARKAEEVQAWKQQAEREVLQLIERSK-N 173 (227)
T ss_pred HHHhhhhhHHHHHHHHHHHhHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-h
Confidence 3899999999999865 455555544333333 22233333333332 22334444555554433 56677776 5
Q ss_pred hHHHHHHHHHHHHHHH
Q 005036 692 YLKMKRMQAEIAGLLE 707 (717)
Q Consensus 692 ~~~mkrM~~~I~~LL~ 707 (717)
|--=--+++.|-.-|.
T Consensus 174 fITReNLea~Ie~AL~ 189 (227)
T KOG4691|consen 174 FITRENLEARIEAALD 189 (227)
T ss_pred hhhHHhHHHHHHHHHc
Confidence 5222246666655543
No 83
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.22 E-value=31 Score=34.41 Aligned_cols=20 Identities=35% Similarity=0.791 Sum_probs=13.1
Q ss_pred cccccccccCCCCccceEecCCcchHHhH
Q 005036 389 MCPVCLNFDCANNTCSWVGCDVCSHWCHA 417 (717)
Q Consensus 389 sC~IC~KFD~nkdtc~WIgCd~CgHwcHl 417 (717)
.|-||+|.-|+ |.|||-||-
T Consensus 67 tC~IC~KTKFA---------DG~GH~C~Y 86 (169)
T KOG3799|consen 67 TCGICHKTKFA---------DGCGHNCSY 86 (169)
T ss_pred chhhhhhcccc---------cccCcccch
Confidence 35577776554 468888873
No 84
>PLN03188 kinesin-12 family protein; Provisional
Probab=23.95 E-value=1e+02 Score=39.69 Aligned_cols=30 Identities=43% Similarity=0.503 Sum_probs=24.7
Q ss_pred hHHHHhhHHH--HHHHHhhHHHHHHHHHhhhH
Q 005036 617 ESVVRIKEAE--ARMFQNKADEARREADEYKR 646 (717)
Q Consensus 617 EsIVRlKqAE--A~MFQ~kAdeARrEAE~lqr 646 (717)
|=+||||+|| +-.=|.||.+|..|+|.+++
T Consensus 1201 ellvrl~eaeea~~~a~~r~~~~eqe~~~~~k 1232 (1320)
T PLN03188 1201 ELLVRLKEAEEALTVAQKRAMDAEQEAAEAYK 1232 (1320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4489999998 34568899999999998876
No 85
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=23.76 E-value=4.3e+02 Score=28.18 Aligned_cols=26 Identities=27% Similarity=0.215 Sum_probs=10.5
Q ss_pred HHHHHHHHHhhhHHHHhhhhhhHHHH
Q 005036 634 ADEARREADEYKRMVCARTEKLEEEY 659 (717)
Q Consensus 634 AdeARrEAE~lqrI~~aK~eK~EEEY 659 (717)
+|.+-.+.|.-..-..+|.+.++.++
T Consensus 195 ~d~~L~~~ek~~~~~~~k~e~~e~e~ 220 (297)
T PF02841_consen 195 ADQQLTEKEKEIEEEQAKAEAAEKEK 220 (297)
T ss_dssp H-TTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34333333333333455555554443
No 86
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=23.71 E-value=7.9e+02 Score=25.05 Aligned_cols=45 Identities=20% Similarity=0.141 Sum_probs=27.2
Q ss_pred HHhhhhhhhHHHHHHHHhHHHHHHHHhhhcchHHHHHHHHHHHHHHH
Q 005036 661 HKLSKLCLRETEERRRKKLEELKVLEDSHCDYLKMKRMQAEIAGLLE 707 (717)
Q Consensus 661 s~~~Kl~l~EaEe~r~~~~Eelk~~E~s~~d~~~mkrM~~~I~~LL~ 707 (717)
..-+--+|++++++.+.+-.||+... ..|+-.+..|..+++.+..
T Consensus 105 R~~~l~~l~~l~~~~~~l~~el~~~~--~~Dp~~i~~~~~~~~~~~~ 149 (188)
T PF03962_consen 105 REELLEELEELKKELKELKKELEKYS--ENDPEKIEKLKEEIKIAKE 149 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--hcCHHHHHHHHHHHHHHHH
Confidence 33344466777777777777777433 3455556666666665543
No 87
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.55 E-value=38 Score=31.89 Aligned_cols=33 Identities=18% Similarity=0.487 Sum_probs=25.0
Q ss_pred cccccc--ccCCCCccceEecCCcchHHhHHhhhhcCc
Q 005036 390 CPVCLN--FDCANNTCSWVGCDVCSHWCHAACGIQRNL 425 (717)
Q Consensus 390 C~IC~K--FD~nkdtc~WIgCd~CgHwcHldCALr~~~ 425 (717)
|.-|.+ ||.|++| |.|-.||..-.++=.++...
T Consensus 12 Cp~CG~kFYDLnk~P---ivCP~CG~~~~~~~~~k~r~ 46 (108)
T PF09538_consen 12 CPSCGAKFYDLNKDP---IVCPKCGTEFPPEPPLKSRR 46 (108)
T ss_pred CCCCcchhccCCCCC---ccCCCCCCccCccccccccc
Confidence 567754 5999999 88999999998884444443
No 88
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=23.51 E-value=7.6e+02 Score=30.37 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=11.6
Q ss_pred hhhhhhhhcccCCCcchhHHH
Q 005036 477 ELDCVTKIFKGSNDFKGKELQ 497 (717)
Q Consensus 477 eL~lv~rIfrGSed~rGK~L~ 497 (717)
.|-+.--+++|+.-..|..|.
T Consensus 404 sLvLlDE~g~GtD~~eg~ala 424 (771)
T TIGR01069 404 SLVLFDELGAGTDPDEGSALA 424 (771)
T ss_pred cEEEecCCCCCCCHHHHHHHH
Confidence 344444456677666555554
No 89
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.24 E-value=47 Score=36.33 Aligned_cols=18 Identities=17% Similarity=0.547 Sum_probs=14.1
Q ss_pred CCccceEecCCcchHHhH
Q 005036 400 NNTCSWVGCDVCSHWCHA 417 (717)
Q Consensus 400 kdtc~WIgCd~CgHwcHl 417 (717)
.++-+|+.|..|++--|.
T Consensus 205 ~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 205 ETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCCceEEEcCCCCCcccc
Confidence 577888888888877664
No 90
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.96 E-value=49 Score=36.31 Aligned_cols=18 Identities=17% Similarity=0.569 Sum_probs=14.6
Q ss_pred CCccceEecCCcchHHhH
Q 005036 400 NNTCSWVGCDVCSHWCHA 417 (717)
Q Consensus 400 kdtc~WIgCd~CgHwcHl 417 (717)
.++-+|+.|..|++.-|.
T Consensus 207 ~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 207 TQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCceEEEcCCCCCcccc
Confidence 578899999988887764
No 91
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=22.86 E-value=7.2e+02 Score=25.92 Aligned_cols=22 Identities=9% Similarity=0.152 Sum_probs=11.9
Q ss_pred HhhhhhhhHHHHHHHHhHHHHH
Q 005036 662 KLSKLCLRETEERRRKKLEELK 683 (717)
Q Consensus 662 ~~~Kl~l~EaEe~r~~~~Eelk 683 (717)
++.+--..+.+.+++..+++|+
T Consensus 101 ~~~~~a~~~ie~E~~~a~~~l~ 122 (246)
T TIGR03321 101 EIREKWQEALRREQAALSDELR 122 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444556666666666553
No 92
>cd07672 F-BAR_PSTPIP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 2 (PSTPIP2), also known as Macrophage Actin-associated tYrosine Phosphorylated protein (MAYP), is mostly expressed in hematopoietic cells but is also expressed in the brain. It is involved in regulating cell adhesion and motility. Mutations in the gene encoding murine PSTPIP2 can cause autoinflammatory disorders such as chronic multifocal osteomyelitis and macrophage autoinflammatory disease. PSTPIP2 contains an N-terminal F-BAR domain and lacks the PEST motifs and SH3 domain that are found in PSTPIP1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They ca
Probab=22.74 E-value=7e+02 Score=26.30 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=15.1
Q ss_pred HHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhh
Q 005036 635 DEARREADEYKRMVCARTEKLEEEYAHKLSKLC 667 (717)
Q Consensus 635 deARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~ 667 (717)
+++.+=.+.|...+.-+ ..||++||.++.||.
T Consensus 15 ~~g~~~~~el~~f~kER-A~IE~~YaK~L~kLs 46 (240)
T cd07672 15 NDGRKNCKEFEDFLKER-ASIEEKYGKELLNLS 46 (240)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 33333344444444333 455666666655554
No 93
>TIGR01147 V_ATP_synt_G vacuolar ATP synthase, subunit G. This model describes the vacuolar ATP synthase G subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. V-ATPases are multi-subunit enzymes composed of two functional domains: A transmembrane Vo domain and a peripheral catalytic domain V1. The G subunit is one of the subunits of the catalytic domain. V-ATPases are responsible for the acidification of endosomes and lysosomes, which are part of the central vacuolar system.
Probab=22.58 E-value=2.7e+02 Score=26.73 Aligned_cols=53 Identities=28% Similarity=0.479 Sum_probs=31.2
Q ss_pred hHHHHhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhh------hhhHHHHHHHHhHHHHHH
Q 005036 617 ESVVRIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKL------CLRETEERRRKKLEELKV 684 (717)
Q Consensus 617 EsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl------~l~EaEe~r~~~~Eelk~ 684 (717)
...-|||||. .||.+|++.|+. +.|+||....++. .-.+++.+=+.++.+|+.
T Consensus 28 ~r~~RLKqAK--------~EA~~EI~~yr~-------~kE~ef~~~ea~~~g~~~~~~~~l~~et~~ki~~ik~ 86 (113)
T TIGR01147 28 RKTKRLKQAK--------EEAQKEVEKYKQ-------QREKEFKEFEAKHLGGNGAAEEKAEAETQAKIREIKK 86 (113)
T ss_pred HHHHHHHHHH--------HHHHHHHHHHHH-------HHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHHHH
Confidence 3456777775 468888888764 5566776655542 234445555555555543
No 94
>PRK00420 hypothetical protein; Validated
Probab=22.57 E-value=1.8e+02 Score=27.84 Aligned_cols=30 Identities=30% Similarity=0.334 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCchhHHHHHHHHh
Q 005036 494 KELQKKAAELVSKLENKVMSPSEACNFIIRFF 525 (717)
Q Consensus 494 K~L~~~veeal~KLe~~~v~~~d~~~~Il~ff 525 (717)
+.|..++..+..||..+. ..+-.+.|+..+
T Consensus 72 ~il~~ki~~L~~kL~~e~--~~~ri~Ei~~~l 101 (112)
T PRK00420 72 EVLIEKINYLAKKLKEDE--DIERITEIIRYL 101 (112)
T ss_pred HHHHHHHHHHHHhCcccc--chhHHHHHHHHH
Confidence 689999999999998882 333344555544
No 95
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=22.46 E-value=80 Score=26.29 Aligned_cols=43 Identities=19% Similarity=0.276 Sum_probs=37.5
Q ss_pred ccccCCCCchhhhHHHHhhHHHHHHHHhhHHHHHHHHHhhhHH
Q 005036 605 GKLSKNDGFDSLESVVRIKEAEARMFQNKADEARREADEYKRM 647 (717)
Q Consensus 605 ~~~~Kk~~~eeLEsIVRlKqAEA~MFQ~kAdeARrEAE~lqrI 647 (717)
-|.+|+..+++||.=|.--++|-.......+..+.|...|+.-
T Consensus 20 ~R~RKk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 20 SRQRKKQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4678999999999999999999999998888888888888754
No 96
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=22.17 E-value=8.7e+02 Score=29.91 Aligned_cols=43 Identities=16% Similarity=0.132 Sum_probs=23.2
Q ss_pred ccchhhhHHHHHhhhhhcchhhhHHHhhhhhhhhcccCCCcchhHHHH
Q 005036 451 ASEMFGFVKDVFLHCAKDWGLDTFVKELDCVTKIFKGSNDFKGKELQK 498 (717)
Q Consensus 451 ~SeLlG~VKkvf~~ca~~w~~d~L~keL~lv~rIfrGSed~rGK~L~~ 498 (717)
.|.+.+..+....+..... ...|-+.--++.|+.-..|..|..
T Consensus 388 lStfS~~m~~~~~Il~~~~-----~~sLvLlDE~~~GtDp~eg~ala~ 430 (782)
T PRK00409 388 LSTFSGHMTNIVRILEKAD-----KNSLVLFDELGAGTDPDEGAALAI 430 (782)
T ss_pred hhHHHHHHHHHHHHHHhCC-----cCcEEEecCCCCCCCHHHHHHHHH
Confidence 3445566655544433321 124555556778887776666544
No 97
>PF06548 Kinesin-related: Kinesin-related; InterPro: IPR010544 This entry represents a domain within kinesin-related proteins from higher plants. Many proteins containing this domain also contain the IPR001752 from INTERPRO domain. Kinesins are ATP-driven microtubule motor proteins that produce directed force []. Some family members are associated with the phragmoplast, a structure composed mainly of microtubules that executes cytokinesis in higher plants [].
Probab=22.10 E-value=2.5e+02 Score=32.90 Aligned_cols=30 Identities=40% Similarity=0.574 Sum_probs=25.5
Q ss_pred hHHHHhhHHH--HHHHHhhHHHHHHHHHhhhH
Q 005036 617 ESVVRIKEAE--ARMFQNKADEARREADEYKR 646 (717)
Q Consensus 617 EsIVRlKqAE--A~MFQ~kAdeARrEAE~lqr 646 (717)
|=+||||+|| |-.-|.+|.+|..|++.+++
T Consensus 431 Ellvrl~eaeea~~~a~~r~~~~eqe~ek~~k 462 (488)
T PF06548_consen 431 ELLVRLREAEEAASVAQERAMDAEQENEKAKK 462 (488)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4489999999 45789999999999998765
No 98
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.98 E-value=2e+02 Score=31.42 Aligned_cols=27 Identities=26% Similarity=0.378 Sum_probs=20.0
Q ss_pred HHHHhhhcchHHHH--HHHHHHHHHHHHHHHhh
Q 005036 683 KVLEDSHCDYLKMK--RMQAEIAGLLERMEATK 713 (717)
Q Consensus 683 k~~E~s~~d~~~mk--rM~~~I~~LL~~MEatK 713 (717)
+.+|+.| .|+ -++.+|.++|+..++.+
T Consensus 266 ~~~ek~H----ke~v~qL~~k~~~~lk~~a~l~ 294 (305)
T KOG3990|consen 266 KELEKKH----KERVQQLQKKKEESLKAIAQLR 294 (305)
T ss_pred HHHHHHH----HHHHHHHHHHHHHHHHHHHHHh
Confidence 5567777 454 57888889998888765
No 99
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=21.81 E-value=33 Score=24.03 Aligned_cols=10 Identities=40% Similarity=0.856 Sum_probs=8.1
Q ss_pred eEEeccCCCc
Q 005036 442 QFHCIGCGHA 451 (717)
Q Consensus 442 ~F~C~aCgk~ 451 (717)
+|+|..||+.
T Consensus 1 q~~C~~C~k~ 10 (27)
T PF12171_consen 1 QFYCDACDKY 10 (27)
T ss_dssp -CBBTTTTBB
T ss_pred CCCcccCCCC
Confidence 6899999986
No 100
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=21.73 E-value=5.8e+02 Score=27.17 Aligned_cols=40 Identities=23% Similarity=0.270 Sum_probs=27.0
Q ss_pred HHHHhhH-HHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhh
Q 005036 628 RMFQNKA-DEARREADEYKRMVCARTEKLEEEYAHKLSKLCL 668 (717)
Q Consensus 628 ~MFQ~kA-deARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l 668 (717)
+++..++ ..|.+|++.++..+...+. .|||=++.-.++--
T Consensus 122 ~l~~l~~~~~~~~~~~~lk~~~~~~~~-~~~~~~~~~~~~~k 162 (216)
T KOG1962|consen 122 ELATLRANEKAMKENEALKKQLENSSK-LEEENDKLKADLEK 162 (216)
T ss_pred HHHHHHhhHHHHHHHHHHHHhhhcccc-hhhhHHHHHhhHHH
Confidence 3444444 5789999999999887665 66666665555443
No 101
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=21.73 E-value=28 Score=36.98 Aligned_cols=36 Identities=28% Similarity=0.776 Sum_probs=25.7
Q ss_pred ceEecCC--cc-hHHhHHhhhhcCcccCCCCCCCCCCCccceEEeccCCCcc
Q 005036 404 SWVGCDV--CS-HWCHAACGIQRNLIKPGPSLKGPSGTSEMQFHCIGCGHAS 452 (717)
Q Consensus 404 ~WIgCd~--Cg-HwcHldCALr~~~i~~G~~~kG~s~~lDm~F~C~aCgk~S 452 (717)
--|+||- |. -|-|+.|- |-. ...-+..||..|-...
T Consensus 231 ~Mi~CDn~~C~~eWFH~~CV--------GL~-----~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 231 KMIGCDNPGCPIEWFHFTCV--------GLK-----TKPKGKWYCPRCKAEN 269 (274)
T ss_pred cccccCCCCCCcceEEEecc--------ccc-----cCCCCcccchhhhhhh
Confidence 4589995 99 99999994 332 2233459999997653
No 102
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=21.52 E-value=40 Score=27.37 Aligned_cols=15 Identities=40% Similarity=1.145 Sum_probs=9.7
Q ss_pred ceEecCCcchHHhHH
Q 005036 404 SWVGCDVCSHWCHAA 418 (717)
Q Consensus 404 ~WIgCd~CgHwcHld 418 (717)
.||.||.|+.|=.|.
T Consensus 2 ~WVQCd~C~KWR~lp 16 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP 16 (50)
T ss_dssp EEEE-TTT--EEEE-
T ss_pred eEEECCCCCceeeCC
Confidence 499999999998776
No 103
>TIGR02926 AhaH ATP synthase archaeal, H subunit. he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes.
Probab=21.42 E-value=5.7e+02 Score=22.54 Aligned_cols=53 Identities=19% Similarity=0.184 Sum_probs=27.9
Q ss_pred HhhHHHHHHHHhhHHHHHHHHHhhhHHHHhhhhhhHHHHHHHhhhhhhhHHHHHHHHhHHHH
Q 005036 621 RIKEAEARMFQNKADEARREADEYKRMVCARTEKLEEEYAHKLSKLCLRETEERRRKKLEEL 682 (717)
Q Consensus 621 RlKqAEA~MFQ~kAdeARrEAE~lqrI~~aK~eK~EEEYas~~~Kl~l~EaEe~r~~~~Eel 682 (717)
.||.||++. .....+|+.||..+-.=|....++ +..--+++|+++..+++++-
T Consensus 3 ~ik~ae~~~-~~~l~~A~~ea~~Ii~~A~~~A~~--------~~~~a~~~A~~ea~~ii~~A 55 (85)
T TIGR02926 3 EIKKAEEDA-EELIEEAEEERKQRIAEAREEARE--------LLEEAEEEASKLGEEIIKEA 55 (85)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHH
Confidence 567777763 455667777777553333322222 22233455555555555543
No 104
>PRK02224 chromosome segregation protein; Provisional
Probab=21.37 E-value=1.2e+03 Score=28.35 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=13.1
Q ss_pred HHHHHHhhhcchHHHH-HHHHHHHHHHHHHH
Q 005036 681 ELKVLEDSHCDYLKMK-RMQAEIAGLLERME 710 (717)
Q Consensus 681 elk~~E~s~~d~~~mk-rM~~~I~~LL~~ME 710 (717)
++..++..--+..+=+ +++ ++.++...++
T Consensus 573 ~~~~~~~~~~~l~~~~~~le-~~~~~~~~i~ 602 (880)
T PRK02224 573 EVAELNSKLAELKERIESLE-RIRTLLAAIA 602 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 4444443333333333 455 4555555554
No 105
>PF04003 Utp12: Dip2/Utp12 Family; InterPro: IPR007148 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This domain is found at the C terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein. In yeast, these proteins are called Utp5, Utp1 or Pwp2, Utp12 or DIP2 Q12220 from SWISSPROT. They interact with snoRNA U3 and with MPP10 []. Pwp2 is an essential Saccharomyces cerevisiae (Baker's yeast) protein involved in cell separation.
Probab=21.30 E-value=3.8e+02 Score=23.82 Aligned_cols=32 Identities=9% Similarity=0.075 Sum_probs=23.8
Q ss_pred HhccHHHHHHHHHhhhHHHHHHHHHHHHHhhc
Q 005036 260 VSEAIPIMAQIIQELSDETLESVKEYLKNLFL 291 (717)
Q Consensus 260 vse~v~v~a~~~~em~~e~le~lKe~lr~il~ 291 (717)
-+-|...+....+.||..++..|=+.|-..+.
T Consensus 11 ~~~~~~~I~~tv~~Lp~~~~~~LL~~l~~~l~ 42 (110)
T PF04003_consen 11 ERIPPSDIENTVRSLPFSYAERLLQFLSERLQ 42 (110)
T ss_pred hhCCHHHHHHHHHhCCHHHHHHHHHHHHHHhc
Confidence 35677777777888888888887777777664
No 106
>PRK09098 type III secretion system protein HrpB; Validated
Probab=21.24 E-value=9.8e+02 Score=25.20 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=25.6
Q ss_pred hhhhHHHHhhHHHHHHHHhh---HHHHHHHHHhhhHHHHhhhhhhHHHHHHH
Q 005036 614 DSLESVVRIKEAEARMFQNK---ADEARREADEYKRMVCARTEKLEEEYAHK 662 (717)
Q Consensus 614 eeLEsIVRlKqAEA~MFQ~k---AdeARrEAE~lqrI~~aK~eK~EEEYas~ 662 (717)
+.|++||-|--|=|.+--.+ -..||.||+.+=-=|.++.++|.++....
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~ila~Ar~~A~~Il~~A~~~A~~I~~~A~~e 73 (233)
T PRK09098 22 EAFATVLALDAALAAVHAERDAVLAAARARAERIVAEARAQAEAILEAARRE 73 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666665555544332 23455555555555555555555544443
No 107
>PRK05667 dnaG DNA primase; Validated
Probab=21.12 E-value=1e+02 Score=36.32 Aligned_cols=21 Identities=29% Similarity=0.920 Sum_probs=19.0
Q ss_pred ceEEeccCCCccchhhhHHHH
Q 005036 441 MQFHCIGCGHASEMFGFVKDV 461 (717)
Q Consensus 441 m~F~C~aCgk~SeLlG~VKkv 461 (717)
..|||-+||..-|.+.||.+.
T Consensus 56 ~~~~CF~Cg~~Gd~i~fv~~~ 76 (580)
T PRK05667 56 QFYHCFGCGAGGDVIKFLMEY 76 (580)
T ss_pred CeEEECCCCCCCCHHHHHHHH
Confidence 479999999999999999876
No 108
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=20.91 E-value=9.2e+02 Score=24.78 Aligned_cols=28 Identities=14% Similarity=0.125 Sum_probs=16.6
Q ss_pred HHhhHHHHHHHHHhhhHHHHhhhhhhHH
Q 005036 630 FQNKADEARREADEYKRMVCARTEKLEE 657 (717)
Q Consensus 630 FQ~kAdeARrEAE~lqrI~~aK~eK~EE 657 (717)
|+.+..+||.||..+..=|.+..+++.+
T Consensus 105 ~e~~L~~A~~eA~~Ii~~A~~eAe~~~e 132 (205)
T PRK06231 105 AKQRHENALAQAKEIIDQANYEALQLKS 132 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556667777776666555555544433
Done!