Query 040083
Match_columns 635
No_of_seqs 216 out of 695
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:57:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1844 PHD Zn-finger proteins 99.9 1.1E-27 2.3E-32 261.3 4.8 173 73-280 13-188 (508)
2 PF00628 PHD: PHD-finger; Int 98.6 1E-08 2.2E-13 79.9 0.3 48 579-627 1-51 (51)
3 smart00249 PHD PHD zinc finger 98.4 2.2E-07 4.9E-12 69.1 3.4 44 580-624 2-47 (47)
4 KOG1844 PHD Zn-finger proteins 98.3 3.1E-07 6.6E-12 101.3 2.6 57 574-632 83-140 (508)
5 KOG1973 Chromatin remodeling p 98.2 8.6E-07 1.9E-11 92.1 3.1 52 574-629 216-270 (274)
6 COG5034 TNG2 Chromatin remodel 97.9 8E-06 1.7E-10 84.0 3.8 55 569-627 213-270 (271)
7 KOG4323 Polycomb-like PHD Zn-f 96.9 0.00038 8.3E-09 77.2 1.9 57 577-634 171-231 (464)
8 PF13831 PHD_2: PHD-finger; PD 96.7 0.00038 8.3E-09 52.1 -0.2 34 591-625 3-36 (36)
9 KOG0954 PHD finger protein [Ge 94.8 0.014 3E-07 67.9 1.9 50 576-627 270-321 (893)
10 KOG0825 PHD Zn-finger protein 94.7 0.016 3.5E-07 67.6 2.3 55 573-628 211-267 (1134)
11 KOG0957 PHD finger protein [Ge 94.7 0.025 5.4E-07 63.5 3.4 59 568-626 111-178 (707)
12 KOG1632 Uncharacterized PHD Zn 93.2 0.036 7.7E-07 60.1 1.1 50 579-628 62-114 (345)
13 KOG1512 PHD Zn-finger protein 91.9 0.062 1.3E-06 56.9 0.9 48 581-632 319-368 (381)
14 KOG1632 Uncharacterized PHD Zn 90.8 0.03 6.5E-07 60.7 -2.8 55 573-627 235-295 (345)
15 PF10407 Cytokin_check_N: Cdc1 90.1 0.92 2E-05 39.4 6.1 59 496-554 6-67 (73)
16 KOG1244 Predicted transcriptio 89.8 0.19 4.2E-06 53.0 2.2 46 581-627 286-331 (336)
17 KOG0955 PHD finger protein BR1 88.2 0.36 7.8E-06 59.0 3.2 54 572-628 215-270 (1051)
18 COG5141 PHD zinc finger-contai 84.5 0.37 7.9E-06 54.5 0.7 47 579-628 195-244 (669)
19 PF07227 DUF1423: Protein of u 83.4 1 2.2E-05 50.5 3.5 49 580-628 132-193 (446)
20 PF07496 zf-CW: CW-type Zinc F 81.1 0.92 2E-05 36.2 1.6 32 591-623 2-34 (50)
21 KOG0956 PHD finger protein AF1 79.1 1 2.2E-05 52.8 1.7 46 578-627 7-57 (900)
22 KOG4443 Putative transcription 78.6 0.43 9.3E-06 55.4 -1.4 51 578-628 146-203 (694)
23 KOG2752 Uncharacterized conser 77.6 1.6 3.4E-05 47.2 2.5 36 575-610 126-167 (345)
24 KOG0957 PHD finger protein [Ge 76.8 1.5 3.3E-05 49.8 2.2 52 575-627 542-598 (707)
25 KOG1245 Chromatin remodeling c 75.9 0.64 1.4E-05 58.7 -1.1 54 574-628 1105-1159(1404)
26 PF05207 zf-CSL: CSL zinc fing 71.7 2 4.3E-05 35.1 1.1 38 567-604 8-52 (55)
27 KOG4299 PHD Zn-finger protein 67.7 2.9 6.3E-05 48.6 1.8 57 577-634 253-312 (613)
28 PF14446 Prok-RING_1: Prokaryo 67.6 3.2 6.8E-05 34.3 1.5 33 576-608 4-37 (54)
29 KOG0383 Predicted helicase [Ge 62.4 3.6 7.8E-05 48.8 1.2 46 578-627 49-94 (696)
30 PF07649 C1_3: C1-like domain; 58.7 3.4 7.3E-05 29.4 0.1 26 581-607 5-30 (30)
31 PF13832 zf-HC5HC2H_2: PHD-zin 50.7 6.7 0.00014 35.1 0.7 33 575-610 53-88 (110)
32 cd01801 Tsc13_N Ubiquitin-like 44.8 17 0.00037 30.8 2.2 18 500-517 20-37 (77)
33 TIGR00311 aIF-2beta translatio 43.6 13 0.00028 35.7 1.4 98 490-601 24-127 (133)
34 KOG2626 Histone H3 (Lys4) meth 43.2 18 0.00039 41.7 2.8 55 574-628 17-77 (544)
35 cd01791 Ubl5 UBL5 ubiquitin-li 43.1 23 0.0005 30.2 2.8 26 497-523 16-41 (73)
36 PRK03988 translation initiatio 43.0 12 0.00025 36.2 1.1 99 490-602 29-133 (138)
37 cd01804 midnolin_N Ubiquitin-l 42.1 22 0.00048 30.3 2.6 20 497-516 16-35 (78)
38 smart00653 eIF2B_5 domain pres 40.1 12 0.00025 34.8 0.6 98 490-600 5-109 (110)
39 TIGR03853 matur_matur probable 36.3 49 0.0011 29.3 3.8 41 313-356 7-61 (77)
40 PRK09706 transcriptional repre 35.2 1.2E+02 0.0025 28.3 6.4 86 160-260 3-102 (135)
41 cd01792 ISG15_repeat1 ISG15 ub 33.8 36 0.00079 29.0 2.6 20 498-517 18-37 (80)
42 cd00730 rubredoxin Rubredoxin; 33.4 20 0.00044 29.0 0.9 19 613-631 29-47 (50)
43 cd01769 UBL Ubiquitin-like dom 32.1 47 0.001 26.2 2.8 21 497-517 12-32 (69)
44 cd05030 calgranulins Calgranul 31.0 84 0.0018 27.3 4.4 48 305-352 2-61 (88)
45 PF06377 Adipokin_hormo: Adipo 29.2 32 0.00069 28.0 1.3 20 410-445 29-48 (48)
46 PF00301 Rubredoxin: Rubredoxi 28.7 43 0.00093 26.8 2.0 17 613-629 29-45 (47)
47 PRK12336 translation initiatio 27.9 32 0.00069 34.9 1.5 102 490-605 25-132 (201)
48 smart00213 UBQ Ubiquitin homol 27.5 64 0.0014 25.1 2.9 20 497-516 14-33 (64)
49 cd01666 TGS_DRG_C TGS_DRG_C: 27.2 90 0.0019 27.1 3.9 25 491-515 13-37 (75)
50 PLN02400 cellulose synthase 27.1 43 0.00094 41.9 2.6 47 579-628 38-88 (1085)
51 KOG2266 Chromatin-associated p 26.8 86 0.0019 36.3 4.6 81 180-274 211-304 (594)
52 PLN02436 cellulose synthase A 26.6 40 0.00086 42.2 2.2 47 579-628 38-88 (1094)
53 PLN02560 enoyl-CoA reductase 26.4 60 0.0013 35.1 3.3 33 495-527 16-48 (308)
54 PF01506 HCV_NS5a: Hepatitis C 26.3 29 0.00062 24.2 0.6 13 160-172 4-16 (23)
55 KOG4443 Putative transcription 26.2 45 0.00097 39.6 2.4 46 578-625 69-116 (694)
56 PF04675 DNA_ligase_A_N: DNA l 25.8 70 0.0015 30.7 3.3 67 210-277 55-125 (177)
57 TIGR00043 metalloprotein, YbeY 25.7 17 0.00038 33.5 -0.8 14 130-143 77-90 (110)
58 PF03107 C1_2: C1 domain; Int 25.2 62 0.0013 23.2 2.1 25 581-607 5-30 (30)
59 PF04216 FdhE: Protein involve 25.1 38 0.00081 35.8 1.4 11 616-626 236-246 (290)
60 smart00342 HTH_ARAC helix_turn 24.7 51 0.0011 26.4 1.9 78 175-260 1-81 (84)
61 PF13922 PHD_3: PHD domain of 24.4 13 0.00027 32.1 -1.8 32 574-610 30-61 (69)
62 cd01812 BAG1_N Ubiquitin-like 24.3 73 0.0016 25.8 2.7 20 497-516 14-33 (71)
63 PRK08154 anaerobic benzoate ca 24.1 1.6E+02 0.0034 31.4 5.9 100 165-279 31-130 (309)
64 PF04714 BCL_N: BCL7, N-termin 23.9 78 0.0017 26.2 2.7 33 299-343 10-42 (52)
65 PLN02638 cellulose synthase A 23.7 47 0.001 41.5 2.1 47 579-628 19-69 (1079)
66 cd05025 S-100A1 S-100A1: S-100 23.4 1.4E+02 0.0031 25.7 4.5 49 304-352 2-62 (92)
67 KOG2320 RAS effector RIN1 (con 23.1 5.8E+02 0.013 30.6 10.3 127 213-368 257-389 (651)
68 cd01808 hPLIC_N Ubiquitin-like 23.0 86 0.0019 25.9 2.9 21 496-516 13-33 (71)
69 PF13771 zf-HC5HC2H: PHD-like 22.9 40 0.00087 28.9 1.0 34 575-611 34-70 (90)
70 PF14569 zf-UDP: Zinc-binding 22.5 17 0.00038 32.2 -1.3 46 580-628 12-61 (80)
71 COG1120 FepC ABC-type cobalami 21.9 48 0.001 35.2 1.5 97 127-238 26-133 (258)
72 PF04192 Utp21: Utp21 specific 21.5 90 0.002 32.5 3.4 87 215-336 120-209 (237)
73 cd00196 UBQ Ubiquitin-like pro 21.5 1E+02 0.0023 21.8 2.8 25 493-517 8-32 (69)
74 PF13901 DUF4206: Domain of un 20.9 64 0.0014 32.6 2.1 28 591-627 171-198 (202)
75 PF10767 DUF2593: Protein of u 20.1 39 0.00085 33.0 0.4 22 187-209 60-81 (144)
76 PF00240 ubiquitin: Ubiquitin 20.1 1.1E+02 0.0023 24.8 2.9 21 497-517 10-30 (69)
No 1
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=99.94 E-value=1.1e-27 Score=261.29 Aligned_cols=173 Identities=31% Similarity=0.444 Sum_probs=159.2
Q ss_pred CCCCcceEecCCCCcccCcceEEEeeCCchhhhhhccCCCCCCcccccccccccccccccceecccCccceEEecccccC
Q 040083 73 HQCKHCRYVGWGHHMVCIKKYHFILPSKNMAAAYLNFQGNEGEDAGMLSNLMQLQGHAMHGVFHSNGFGHLLCVNGVETG 152 (635)
Q Consensus 73 ~~Cd~Cr~vGW~~H~V~~krYHFIip~~~~~~~~~~c~~c~~~~~~~~~~~l~~~~HlLHGviH~NGfGHLl~vnGregg 152 (635)
++|++|++.||+.|.+|+++||||||++..+ .. +....+++.++|.+||.+|+||+||++++||+|.|
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~---~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 80 (508)
T KOG1844|consen 13 PRCSHCCKFGWSPHLVANKKYEHIIPADAEL---------FE---ESTSQSNEPSTASPHGTAHEPGKGVLLSLNGSEAG 80 (508)
T ss_pred cccccccccCCcccccccccccccccCCccc---------cc---CCchhhccccccccccccccCCCCccccccccccc
Confidence 8999999999999999999999999999876 33 45557899999999999999999999999999999
Q ss_pred CCCcchhhhhhHHHHhhccceeeeeeeeccccccchhhhhhhhhcCCcccccccccccCcccccCH-HHHHHHHHHHhCC
Q 040083 153 SDLTGHQIMDFWDRLCSGLQARKVSLYDISRKKGMELRLLHVVAYSQSWFGHWGYKFGRGSFGVTQ-PMYQKAIEAIQGM 231 (635)
Q Consensus 153 S~lsG~~iM~~WDrlC~~L~~RkVSv~DvSkK~gmelRLLh~Va~G~sWyG~WGY~Fg~Gsfgvt~-~~Y~~Aie~Lss~ 231 (635)
+. +++++..|.+.+..| |+++.+++|+++|+|+|+-|+|+++. +.|..++...+++
T Consensus 81 ~~------------------~~~~~~c~c~~~~~~-----~g~~i~c~~c~~Wqh~~C~g~~~~~~p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 81 SE------------------AREISRCDCGLEDDM-----EGLMIQCDWCGRWQHKICCGSFKSTKPDKYVCEICTPRNK 137 (508)
T ss_pred cC------------------cCcccccccccccCC-----CceeeCCcccCcccCceeeeecCCCCchhceeeeeccccc
Confidence 98 889999999999999 99999999999999999999999999 9999999999999
Q ss_pred chh--hHhcccCCCCCChhHHHHHhhcccchhhhcHHHHHHHHHhhhhcCC
Q 040083 232 PLC--LLLNHLGHLNPDIPLIFTRYQTLSDHFLATLGDLFHFLLDLKSRLP 280 (635)
Q Consensus 232 pL~--~~~~~~~~~~~~l~~ii~~Yq~lS~~~L~Tl~dL~~fmL~l~~~~p 280 (635)
+++ .+.+.-+.....+..+.++|++++..++.+..+++++|+.+.+..+
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (508)
T KOG1844|consen 138 EVERALALKRQSIEPEVLEPIRSTYRSLSQDSLDTTSDLKSFMLALISLST 188 (508)
T ss_pred cchhhhhcccccccccccCccchhhhhhcccCCCchHHHHHHHhhccccCc
Confidence 999 4444444555688889999999999999999999999999998774
No 2
>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=98.59 E-value=1e-08 Score=79.91 Aligned_cols=48 Identities=35% Similarity=0.938 Sum_probs=38.5
Q ss_pred Ee-ecCCCCCCCcceeeccccCceeeccccccCCC--CCCCCceecCCCccc
Q 040083 579 EC-ACGADEDDGERMVSCDICEVWQHTRCARIPNN--EEIPHIFLCNRCEQE 627 (635)
Q Consensus 579 rC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~--~~vP~~y~C~~C~~~ 627 (635)
+| +||..++++ .||+||.|+.|+|..|++++.. ......|+|+.|.++
T Consensus 1 ~C~vC~~~~~~~-~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~~ 51 (51)
T PF00628_consen 1 YCPVCGQSDDDG-DMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRPK 51 (51)
T ss_dssp EBTTTTSSCTTS-SEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHHC
T ss_pred eCcCCCCcCCCC-CeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcCc
Confidence 58 999965555 9999999999999999999864 222348999999753
No 3
>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 KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=98.29 E-value=3.1e-07 Score=101.33 Aligned_cols=57 Identities=28% Similarity=0.801 Sum_probs=50.7
Q ss_pred CCceEEeecCCCCC-CCcceeeccccCceeeccccccCCCCCCCCceecCCCcccccCCC
Q 040083 574 VNCVVECACGADED-DGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEIVHLS 632 (635)
Q Consensus 574 e~~~VrCiCG~~dD-DGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~~~~~ 632 (635)
..+.++|+||..++ +| +||+|+.|..|||..|+|+..... |+.|+|..|.++...+.
T Consensus 83 ~~~~~~c~c~~~~~~~g-~~i~c~~c~~Wqh~~C~g~~~~~~-p~~y~c~~c~~~~~~~~ 140 (508)
T KOG1844|consen 83 AREISRCDCGLEDDMEG-LMIQCDWCGRWQHKICCGSFKSTK-PDKYVCEICTPRNKEVE 140 (508)
T ss_pred cCcccccccccccCCCc-eeeCCcccCcccCceeeeecCCCC-chhceeeeeccccccch
Confidence 46899999999998 87 999999999999999999987554 99999999999886543
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.19 E-value=8.6e-07 Score=92.15 Aligned_cols=52 Identities=27% Similarity=0.675 Sum_probs=43.1
Q ss_pred CCceEEeecCCCCCCCcceeeccc--cC-ceeeccccccCCCCCCCCceecCCCccccc
Q 040083 574 VNCVVECACGADEDDGERMVSCDI--CE-VWQHTRCARIPNNEEIPHIFLCNRCEQEIV 629 (635)
Q Consensus 574 e~~~VrCiCG~~dDDGe~MI~CD~--C~-vWQH~~CvgI~~~~~vP~~y~C~~C~~~~~ 629 (635)
.+...+|+|. ...-| -||.||. |. .|+|..||||.. .....|+|+.|.....
T Consensus 216 ~~e~~yC~Cn-qvsyg-~Mi~CDn~~C~~eWFH~~CVGL~~--~PkgkWyC~~C~~~~~ 270 (274)
T KOG1973|consen 216 PDEPTYCICN-QVSYG-KMIGCDNPGCPIEWFHFTCVGLKT--KPKGKWYCPRCKAENK 270 (274)
T ss_pred CCCCEEEEec-ccccc-cccccCCCCCCcceEEEecccccc--CCCCcccchhhhhhhh
Confidence 5678999999 44566 9999998 99 999999999985 3346799999987653
No 6
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.91 E-value=8e-06 Score=83.99 Aligned_cols=55 Identities=25% Similarity=0.622 Sum_probs=43.6
Q ss_pred cccCCCCceEEeecCCCCCCCcceeeccc--cCc-eeeccccccCCCCCCCCceecCCCccc
Q 040083 569 YENGMVNCVVECACGADEDDGERMVSCDI--CEV-WQHTRCARIPNNEEIPHIFLCNRCEQE 627 (635)
Q Consensus 569 ~e~g~e~~~VrCiCG~~dDDGe~MI~CD~--C~v-WQH~~CvgI~~~~~vP~~y~C~~C~~~ 627 (635)
.++.++...++|-|... --| .||+||. |+. |+|..|||+... .-..|+|+.|...
T Consensus 213 s~d~se~e~lYCfCqqv-SyG-qMVaCDn~nCkrEWFH~~CVGLk~p--PKG~WYC~eCk~~ 270 (271)
T COG5034 213 SEDNSEGEELYCFCQQV-SYG-QMVACDNANCKREWFHLECVGLKEP--PKGKWYCPECKKA 270 (271)
T ss_pred ccccccCceeEEEeccc-ccc-cceecCCCCCchhheeccccccCCC--CCCcEeCHHhHhc
Confidence 34445778999999975 677 8999995 964 999999999852 2368999999753
No 7
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.92 E-value=0.00038 Score=77.23 Aligned_cols=57 Identities=26% Similarity=0.644 Sum_probs=45.3
Q ss_pred eEEeecCCCCCCCcceeeccccCceeeccccccCCCCC----CCCceecCCCcccccCCCCC
Q 040083 577 VVECACGADEDDGERMVSCDICEVWQHTRCARIPNNEE----IPHIFLCNRCEQEIVHLSSL 634 (635)
Q Consensus 577 ~VrCiCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~----vP~~y~C~~C~~~~~~~~~~ 634 (635)
-..|-||....-. +|++|++|+.|+|..|..-...++ .--.|+|..|......++-+
T Consensus 171 c~vC~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~ 231 (464)
T KOG4323|consen 171 CSVCYCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRL 231 (464)
T ss_pred eeeeecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhcccc
Confidence 6778888876665 999999999999999998654322 23479999999998777655
No 8
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.69 E-value=0.00038 Score=52.11 Aligned_cols=34 Identities=32% Similarity=0.717 Sum_probs=19.6
Q ss_pred ceeeccccCceeeccccccCCCCCCCCceecCCCc
Q 040083 591 RMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCE 625 (635)
Q Consensus 591 ~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~ 625 (635)
.||.|+.|++..|..|+||... +..+.|+|..|+
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~~-~~~~~W~C~~C~ 36 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSEV-PDGDDWLCDRCE 36 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS---SS-----HHH-
T ss_pred ceEEeCCCCCcCChhhCCcccC-CCCCcEECCcCC
Confidence 7999999999999999999864 334459999884
No 9
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=94.79 E-value=0.014 Score=67.86 Aligned_cols=50 Identities=30% Similarity=0.672 Sum_probs=41.0
Q ss_pred ceEEe-ecCCCC-CCCcceeeccccCceeeccccccCCCCCCCCceecCCCccc
Q 040083 576 CVVEC-ACGADE-DDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQE 627 (635)
Q Consensus 576 ~~VrC-iCG~~d-DDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~ 627 (635)
+.|-| +|...| +++.-||-||.|++-.|..|+||..-++ ..|.|..|..-
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~--gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE--GPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC--CCeeehhcccc
Confidence 55778 999886 5677999999999999999999985322 67999988754
No 10
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.74 E-value=0.016 Score=67.61 Aligned_cols=55 Identities=20% Similarity=0.484 Sum_probs=43.4
Q ss_pred CCCceEEe-ecCCCCCCCcceeeccccCce-eeccccccCCCCCCCCceecCCCcccc
Q 040083 573 MVNCVVEC-ACGADEDDGERMVSCDICEVW-QHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 573 ~e~~~VrC-iCG~~dDDGe~MI~CD~C~vW-QH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
..+..+.| ||+..|-. +.||-||.|+.- +|+-|...+-.+--...|+|..|....
T Consensus 211 ~~~E~~~C~IC~~~DpE-dVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 211 LSQEEVKCDICTVHDPE-DVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE 267 (1134)
T ss_pred cccccccceeeccCChH-HhheeecccccceeeccccCcccccccccceecCcchhhh
Confidence 35678999 99998655 499999999987 999999865332234789999997654
No 11
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.66 E-value=0.025 Score=63.46 Aligned_cols=59 Identities=24% Similarity=0.568 Sum_probs=43.7
Q ss_pred ccccCCCCceEEeec-CCCCCCCcceeeccccCceeeccccccCCCCCC--------CCceecCCCcc
Q 040083 568 IYENGMVNCVVECAC-GADEDDGERMVSCDICEVWQHTRCARIPNNEEI--------PHIFLCNRCEQ 626 (635)
Q Consensus 568 r~e~g~e~~~VrCiC-G~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~v--------P~~y~C~~C~~ 626 (635)
+.-+.+..|.+-|+| |..-+|-.-.||||.|++-.|-.|+|..+...+ .+.|+|+-|.-
T Consensus 111 ~~~Sapkk~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 111 RTPSAPKKAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY 178 (707)
T ss_pred cccCccccceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence 334445788899999 333334338999999999999999999864433 36799988864
No 12
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=93.18 E-value=0.036 Score=60.08 Aligned_cols=50 Identities=26% Similarity=0.666 Sum_probs=40.7
Q ss_pred EeecCCCCCCCcceeeccccCceeeccc--cccCCC-CCCCCceecCCCcccc
Q 040083 579 ECACGADEDDGERMVSCDICEVWQHTRC--ARIPNN-EEIPHIFLCNRCEQEI 628 (635)
Q Consensus 579 rCiCG~~dDDGe~MI~CD~C~vWQH~~C--vgI~~~-~~vP~~y~C~~C~~~~ 628 (635)
.|.|-...+-..+|++||.|..|+|+.| ++++.. ...++.|+|..|....
T Consensus 62 ~~~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 62 YCKCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hhhcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence 7888877544349999999999999999 999863 3346889999998765
No 13
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=91.94 E-value=0.062 Score=56.95 Aligned_cols=48 Identities=23% Similarity=0.680 Sum_probs=38.5
Q ss_pred ecCCCCCCCcceeeccccCceeeccccccCCCCCCC-CceecC-CCcccccCCC
Q 040083 581 ACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP-HIFLCN-RCEQEIVHLS 632 (635)
Q Consensus 581 iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP-~~y~C~-~C~~~~~~~~ 632 (635)
||+.+.-.. -|+-||.|+.=+|+-|||+.+ +| ..|+|. .|....+.+|
T Consensus 319 IC~~P~~E~-E~~FCD~CDRG~HT~CVGL~~---lP~G~WICD~~C~~~~~~t~ 368 (381)
T KOG1512|consen 319 ICLGPVIES-EHLFCDVCDRGPHTLCVGLQD---LPRGEWICDMRCREATLNTT 368 (381)
T ss_pred ccCCcccch-heeccccccCCCCcccccccc---ccCccchhhhHHHHhcCCCC
Confidence 888876554 799999999999999999974 44 589998 4777766554
No 14
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=90.84 E-value=0.03 Score=60.67 Aligned_cols=55 Identities=25% Similarity=0.693 Sum_probs=42.6
Q ss_pred CCCceEEe-ecCCCCCCCcceeeccccCceeeccccccCCCC-CCCCc----eecCCCccc
Q 040083 573 MVNCVVEC-ACGADEDDGERMVSCDICEVWQHTRCARIPNNE-EIPHI----FLCNRCEQE 627 (635)
Q Consensus 573 ~e~~~VrC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~-~vP~~----y~C~~C~~~ 627 (635)
.+...+.| .||.++-...+||.|+.|..|+|+.|+.|.... ..+.. |+|+.|...
T Consensus 235 ~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 235 PDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred cccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 34556778 888765333799999999999999999998642 23455 999999873
No 15
>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].
Probab=90.07 E-value=0.92 Score=39.36 Aligned_cols=59 Identities=22% Similarity=0.278 Sum_probs=46.9
Q ss_pred eEeecCCCChHHHHHHHHHHHHHHHhhhhceeeecccccccCCCc---eeeeeeeeCceEEE
Q 040083 496 CVTIKNNATFDELKLEVQRNFRELYWGLRSFVIESIVNVNATGTD---LVCGFVEVGRRIVF 554 (635)
Q Consensus 496 lv~lp~~ATv~dLK~ea~rafrdtY~~~~~f~ve~l~~~~~~~~~---~~~g~v~sg~~v~V 554 (635)
|+..+++.|+++|+.|.+..|..+|=-.+.+.+..+.+-.+.+-+ .+.-...+|+.|+|
T Consensus 6 Lhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~cDLD~d~~V~DVf~~~~~vrv 67 (73)
T PF10407_consen 6 LHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGCDLDPDFLVKDVFNSNNVVRV 67 (73)
T ss_pred EEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCCCCCcccEeeeeeccCCEEEE
Confidence 456778999999999999999999999999999999987766554 44445555665554
No 16
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=89.81 E-value=0.19 Score=53.03 Aligned_cols=46 Identities=30% Similarity=0.640 Sum_probs=37.2
Q ss_pred ecCCCCCCCcceeeccccCceeeccccccCCCCCCCCceecCCCccc
Q 040083 581 ACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQE 627 (635)
Q Consensus 581 iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~ 627 (635)
|||.+++|. .++-||.|+.=+|+-|..-+-..+....|.|..|-..
T Consensus 286 icgtsendd-qllfcddcdrgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 286 ICGTSENDD-QLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred cccCcCCCc-eeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 899998886 8999999999999999987643333357999988643
No 17
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=88.21 E-value=0.36 Score=59.02 Aligned_cols=54 Identities=35% Similarity=0.626 Sum_probs=41.8
Q ss_pred CCCCceEEeecCCCCCC-CcceeeccccCceeeccccccCCCCCCC-CceecCCCcccc
Q 040083 572 GMVNCVVECACGADEDD-GERMVSCDICEVWQHTRCARIPNNEEIP-HIFLCNRCEQEI 628 (635)
Q Consensus 572 g~e~~~VrCiCG~~dDD-Ge~MI~CD~C~vWQH~~CvgI~~~~~vP-~~y~C~~C~~~~ 628 (635)
+.+...+-|||-..+-+ -..-+.||.|+.-.|..|+||+. +| -.|.|-.|-...
T Consensus 215 ~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~---ipeg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 215 LLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPF---IPEGQWLCRRCLQSP 270 (1051)
T ss_pred ccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCC---CCCCcEeehhhccCc
Confidence 34566778899876533 24899999999999999999873 44 479999997665
No 18
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=84.54 E-value=0.37 Score=54.46 Aligned_cols=47 Identities=30% Similarity=0.765 Sum_probs=36.4
Q ss_pred Ee-ecCCCCCC-CcceeeccccCceeeccccccCCCCCCCC-ceecCCCcccc
Q 040083 579 EC-ACGADEDD-GERMVSCDICEVWQHTRCARIPNNEEIPH-IFLCNRCEQEI 628 (635)
Q Consensus 579 rC-iCG~~dDD-Ge~MI~CD~C~vWQH~~CvgI~~~~~vP~-~y~C~~C~~~~ 628 (635)
.| +|..++.| -...|-||+|+.-.|-.|+||. -+|+ .|+|.+|--..
T Consensus 195 ~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~---f~peG~WlCrkCi~~~ 244 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQ---FLPEGFWLCRKCIYGE 244 (669)
T ss_pred hhHhccccccCCcceEEEecCcchhhhhhcccce---ecCcchhhhhhhcccc
Confidence 46 67666543 3589999999999999999998 4666 78888886543
No 19
>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=83.41 E-value=1 Score=50.50 Aligned_cols=49 Identities=27% Similarity=0.709 Sum_probs=34.8
Q ss_pred eecCCCCC--CCcceeeccccCceeeccccccCC--------CC---CCCCceecCCCcccc
Q 040083 580 CACGADED--DGERMVSCDICEVWQHTRCARIPN--------NE---EIPHIFLCNRCEQEI 628 (635)
Q Consensus 580 CiCG~~dD--DGe~MI~CD~C~vWQH~~CvgI~~--------~~---~vP~~y~C~~C~~~~ 628 (635)
|+|..-|+ |+-.+|.||.|+-|=|+.|.--.. .. ..--.|+|-.|....
T Consensus 132 ~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 132 CICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred cccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 47776432 456999999999999999964322 11 123479999998764
No 20
>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=81.14 E-value=0.92 Score=36.16 Aligned_cols=32 Identities=28% Similarity=0.711 Sum_probs=19.6
Q ss_pred ceeeccccCceeeccccccCC-CCCCCCceecCC
Q 040083 591 RMVSCDICEVWQHTRCARIPN-NEEIPHIFLCNR 623 (635)
Q Consensus 591 ~MI~CD~C~vWQH~~CvgI~~-~~~vP~~y~C~~ 623 (635)
..||||.|..|-... .++.. ...+|+.|+|..
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGG
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCC
Confidence 589999999999988 44443 245788999987
No 21
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=79.09 E-value=1 Score=52.75 Aligned_cols=46 Identities=30% Similarity=0.763 Sum_probs=34.3
Q ss_pred EEeecCCC--CCCCcceeecc--ccCceeeccccccCCCCCCC-CceecCCCccc
Q 040083 578 VECACGAD--EDDGERMVSCD--ICEVWQHTRCARIPNNEEIP-HIFLCNRCEQE 627 (635)
Q Consensus 578 VrCiCG~~--dDDGe~MI~CD--~C~vWQH~~CvgI~~~~~vP-~~y~C~~C~~~ 627 (635)
--|+|-.. ..+. ++|.|| .|.|-.|-.|+||-. +| -.|+|-+|...
T Consensus 7 GCCVCSDErGWaeN-PLVYCDG~nCsVAVHQaCYGIvq---VPtGpWfCrKCesq 57 (900)
T KOG0956|consen 7 GCCVCSDERGWAEN-PLVYCDGHNCSVAVHQACYGIVQ---VPTGPWFCRKCESQ 57 (900)
T ss_pred ceeeecCcCCCccC-ceeeecCCCceeeeehhcceeEe---cCCCchhhhhhhhh
Confidence 35899642 1233 999999 499999999999984 44 46888888653
No 22
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=78.62 E-value=0.43 Score=55.43 Aligned_cols=51 Identities=29% Similarity=0.700 Sum_probs=36.8
Q ss_pred EEe-ecCCCCCCC--cceeeccccCceeeccccccCCCC---CCCC-ceecCCCcccc
Q 040083 578 VEC-ACGADEDDG--ERMVSCDICEVWQHTRCARIPNNE---EIPH-IFLCNRCEQEI 628 (635)
Q Consensus 578 VrC-iCG~~dDDG--e~MI~CD~C~vWQH~~CvgI~~~~---~vP~-~y~C~~C~~~~ 628 (635)
-+| +|-..+-+. ..|++|+.|..|+|+.|-+|.+.. ...+ .|-|..|+..-
T Consensus 146 ~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR~es 203 (694)
T KOG4443|consen 146 SYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCRGES 203 (694)
T ss_pred ccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceeehhh
Confidence 345 355544443 478999999999999999998732 2244 89999998443
No 23
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=77.65 E-value=1.6 Score=47.21 Aligned_cols=36 Identities=31% Similarity=0.651 Sum_probs=28.4
Q ss_pred CceEEeecCCCCCC-----CcceeeccccCceee-ccccccC
Q 040083 575 NCVVECACGADEDD-----GERMVSCDICEVWQH-TRCARIP 610 (635)
Q Consensus 575 ~~~VrCiCG~~dDD-----Ge~MI~CD~C~vWQH-~~CvgI~ 610 (635)
-....|.|...++| +.-|+||..|.-|+| -.|+-..
T Consensus 126 fqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 126 FQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAK 167 (345)
T ss_pred hcceeEEecCCCCCccccccceeeeEEeccchhcccccCccc
Confidence 34678999998766 349999999999999 6676543
No 24
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=76.78 E-value=1.5 Score=49.81 Aligned_cols=52 Identities=21% Similarity=0.589 Sum_probs=39.0
Q ss_pred CceEEe-ecCCCCCCCcceeeccccCceeeccccccCCCC----CCCCceecCCCccc
Q 040083 575 NCVVEC-ACGADEDDGERMVSCDICEVWQHTRCARIPNNE----EIPHIFLCNRCEQE 627 (635)
Q Consensus 575 ~~~VrC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~----~vP~~y~C~~C~~~ 627 (635)
.-.+.| ||..+.|. ...++||.|+.-+|..|..-+-.. ...--|.|..|...
T Consensus 542 a~~ysCgiCkks~dQ-Hll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~ 598 (707)
T KOG0957|consen 542 AMNYSCGICKKSTDQ-HLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKN 598 (707)
T ss_pred ccceeeeeeccchhh-HHHhhcchhhceeeccccCCccccCcccccCcceeecccccc
Confidence 456778 99987655 599999999999999999866321 11345999999443
No 25
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=75.89 E-value=0.64 Score=58.69 Aligned_cols=54 Identities=28% Similarity=0.552 Sum_probs=45.2
Q ss_pred CCceEEe-ecCCCCCCCcceeeccccCceeeccccccCCCCCCCCceecCCCcccc
Q 040083 574 VNCVVEC-ACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 574 e~~~VrC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
......| +|....++ +.|+-||.|..|.|.-|....-..-.+..|.|+.|+...
T Consensus 1105 s~~~~~c~~cr~k~~~-~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQD-EKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred ccchhhhhhhhhcccc-hhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 5567889 99998777 499999999999999999977554456789999998765
No 26
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=71.71 E-value=2 Score=35.12 Aligned_cols=38 Identities=26% Similarity=0.723 Sum_probs=27.4
Q ss_pred cccccCCCCceEEeecCCCC-------CCCcceeeccccCceeec
Q 040083 567 QIYENGMVNCVVECACGADE-------DDGERMVSCDICEVWQHT 604 (635)
Q Consensus 567 ~r~e~g~e~~~VrCiCG~~d-------DDGe~MI~CD~C~vWQH~ 604 (635)
+..+.+.+.+...|.||... .+|+..++|+.|..|-..
T Consensus 8 ~~~~~~~~~~~y~CRCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 8 MEFDEEEGVYSYPCRCGGEFEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp SEEETTTTEEEEEETTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred ceecCCCCEEEEcCCCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence 34444556789999999863 456789999999999754
No 27
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.69 E-value=2.9 Score=48.60 Aligned_cols=57 Identities=26% Similarity=0.519 Sum_probs=42.7
Q ss_pred eEEe-ecCCCCCCCcceeeccccCceeeccccccCC-CCCC-CCceecCCCcccccCCCCC
Q 040083 577 VVEC-ACGADEDDGERMVSCDICEVWQHTRCARIPN-NEEI-PHIFLCNRCEQEIVHLSSL 634 (635)
Q Consensus 577 ~VrC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~-~~~v-P~~y~C~~C~~~~~~~~~~ 634 (635)
...| .|+.+..= -..|+||.|..=+|..|..-+- ..++ +.-|+|+.|..+....|.+
T Consensus 253 ~~fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in~~~ 312 (613)
T KOG4299|consen 253 EDFCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPKM 312 (613)
T ss_pred HHHHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccch
Confidence 3468 88876422 1359999999999999998662 2334 4689999999988777765
No 28
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.59 E-value=3.2 Score=34.30 Aligned_cols=33 Identities=30% Similarity=0.666 Sum_probs=27.8
Q ss_pred ceEEe-ecCCCCCCCcceeeccccCceeeccccc
Q 040083 576 CVVEC-ACGADEDDGERMVSCDICEVWQHTRCAR 608 (635)
Q Consensus 576 ~~VrC-iCG~~dDDGe~MI~CD~C~vWQH~~Cvg 608 (635)
...+| +||.+.-+++.-+.|..|+.-+|-.|..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 34568 8999876666889999999999999984
No 29
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=62.42 E-value=3.6 Score=48.81 Aligned_cols=46 Identities=28% Similarity=0.592 Sum_probs=33.3
Q ss_pred EEeecCCCCCCCcceeeccccCceeeccccccCCCCCCCCceecCCCccc
Q 040083 578 VECACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQE 627 (635)
Q Consensus 578 VrCiCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~ 627 (635)
--|+|+ |.| -.+.||.|-.|+|..|.+.+-.+.....|+|++|...
T Consensus 49 ~c~ic~---~~g-~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 49 ACRICA---DGG-ELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred hhhhhc---CCC-cEEEeccccHHHHHHccCCCCCcCCccceeeeeeccC
Confidence 334777 445 6788999999999999997753322233999999443
No 30
>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=58.69 E-value=3.4 Score=29.42 Aligned_cols=26 Identities=35% Similarity=0.723 Sum_probs=11.8
Q ss_pred ecCCCCCCCcceeeccccCceeecccc
Q 040083 581 ACGADEDDGERMVSCDICEVWQHTRCA 607 (635)
Q Consensus 581 iCG~~dDDGe~MI~CD~C~vWQH~~Cv 607 (635)
.||.+.+. .....|+.|+...|..|+
T Consensus 5 ~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 5 ACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp TTS----S---EEE-TTT-----HHHH
T ss_pred cCCCcCCC-CceEECccCCCccChhcC
Confidence 68876555 589999999999999984
No 31
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=50.73 E-value=6.7 Score=35.12 Aligned_cols=33 Identities=30% Similarity=0.769 Sum_probs=27.4
Q ss_pred CceEEe-ecCCCCCCCcceeeccc--cCceeeccccccC
Q 040083 575 NCVVEC-ACGADEDDGERMVSCDI--CEVWQHTRCARIP 610 (635)
Q Consensus 575 ~~~VrC-iCG~~dDDGe~MI~CD~--C~vWQH~~CvgI~ 610 (635)
.+...| +|+.+ .| ..|+|.. |..++|..|....
T Consensus 53 ~~~~~C~iC~~~--~G-~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 53 RFKLKCSICGKS--GG-ACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred hcCCcCcCCCCC--Cc-eeEEcCCCCCCcCCCHHHHHHC
Confidence 356667 99986 66 8999998 9999999998654
No 32
>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.
Probab=44.77 E-value=17 Score=30.83 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=15.9
Q ss_pred cCCCChHHHHHHHHHHHH
Q 040083 500 KNNATFDELKLEVQRNFR 517 (635)
Q Consensus 500 p~~ATv~dLK~ea~rafr 517 (635)
|++|||.|||.+.++.++
T Consensus 20 ~~~aTV~dlk~~i~~~~~ 37 (77)
T cd01801 20 SGDATIADLKKLIAKSSP 37 (77)
T ss_pred CCCccHHHHHHHHHHHcC
Confidence 899999999999888754
No 33
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=43.65 E-value=13 Score=35.71 Aligned_cols=98 Identities=15% Similarity=0.264 Sum_probs=51.5
Q ss_pred CCCCCceEeecCCCChHHHHHHHHHHHHHHHhhhhceeeecccccccCCCceeeeeeeeCceEEEeccccCCCccccccc
Q 040083 490 AMQPYECVTIKNNATFDELKLEVQRNFRELYWGLRSFVIESIVNVNATGTDLVCGFVEVGRRIVFEGSNSERGIVYGQIY 569 (635)
Q Consensus 490 ~~pP~Elv~lp~~ATv~dLK~ea~rafrdtY~~~~~f~ve~l~~~~~~~~~~~~g~v~sg~~v~V~G~~~~~d~~~~~r~ 569 (635)
.+|||++.+--....+.-++.-|...=|+--..++=| ..+ ++.. |.++ |+.+.++|+.....++..++
T Consensus 24 ~mP~~~v~~eG~kTvi~Nf~~Ia~~L~R~~~~v~ky~-~~E---Lgt~------g~i~-~~rlii~G~~~~~~i~~~L~- 91 (133)
T TIGR00311 24 EVPKAYIVIEGNRTIIQNFREVAKALNRDEQHLLKYL-LKE---LGTA------GNLE-GGRLILQGKFTHFLLNERIE- 91 (133)
T ss_pred cCCCceEEEEcCcEEEecHHHHHHHHCCCHHHHHHHH-HHH---hCCC------ceec-CCEEEEEeecCHHHHHHHHH-
Confidence 3899999888765444344444443333333333222 111 2222 2233 46789999873322222111
Q ss_pred ccCCCCceEEe-ecCCCC-----CCCcceeeccccCce
Q 040083 570 ENGMVNCVVEC-ACGADE-----DDGERMVSCDICEVW 601 (635)
Q Consensus 570 e~g~e~~~VrC-iCG~~d-----DDGe~MI~CD~C~vW 601 (635)
..=..-|-| .|+.+| ++.-.|+.|+.|+..
T Consensus 92 --~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 92 --DYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred --HHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 011345889 899876 334357899999864
No 34
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=43.20 E-value=18 Score=41.74 Aligned_cols=55 Identities=18% Similarity=0.421 Sum_probs=42.0
Q ss_pred CCceEEeecCCCCCCCcceeeccccCceeeccccccCC--C----CCCCCceecCCCcccc
Q 040083 574 VNCVVECACGADEDDGERMVSCDICEVWQHTRCARIPN--N----EEIPHIFLCNRCEQEI 628 (635)
Q Consensus 574 e~~~VrCiCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~--~----~~vP~~y~C~~C~~~~ 628 (635)
..-.+.|.|+....-+..-+||-.|..|.|+.|+--.. . ...-..|+|..|.+..
T Consensus 17 ~~~~~~~y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~~ 77 (544)
T KOG2626|consen 17 MKQATVCYCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPSG 77 (544)
T ss_pred ccCccccccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCcc
Confidence 34578899999887788999999999999987665432 1 1223579999999873
No 35
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=43.13 E-value=23 Score=30.23 Aligned_cols=26 Identities=15% Similarity=0.026 Sum_probs=20.2
Q ss_pred EeecCCCChHHHHHHHHHHHHHHHhhh
Q 040083 497 VTIKNNATFDELKLEVQRNFRELYWGL 523 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~rafrdtY~~~ 523 (635)
+-+++.+||+|||...+..+ .++.--
T Consensus 16 ~~v~~~~TV~~LK~~I~~~~-~~~~~~ 41 (73)
T cd01791 16 VKCNPDDTIGDLKKLIAAQT-GTRPEK 41 (73)
T ss_pred EEeCCCCcHHHHHHHHHHHh-CCChHH
Confidence 46789999999999998887 344443
No 36
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=42.96 E-value=12 Score=36.19 Aligned_cols=99 Identities=20% Similarity=0.282 Sum_probs=52.0
Q ss_pred CCCCCceEeecCCCChHHHHHHHHHHHHHHHhhhhceeeecccccccCCCceeeeeeeeCceEEEeccccCCCccccccc
Q 040083 490 AMQPYECVTIKNNATFDELKLEVQRNFRELYWGLRSFVIESIVNVNATGTDLVCGFVEVGRRIVFEGSNSERGIVYGQIY 569 (635)
Q Consensus 490 ~~pP~Elv~lp~~ATv~dLK~ea~rafrdtY~~~~~f~ve~l~~~~~~~~~~~~g~v~sg~~v~V~G~~~~~d~~~~~r~ 569 (635)
.+|||++..--....+ ..|.|+-..|+|- .+-+..|-+.+- -.-|.+ .|+.+.++|+....+++..++-
T Consensus 29 ~~p~~~v~~eG~kTvi--------~Nf~~I~~~L~R~-~~hv~ky~~~EL-gt~g~i-~~~~lii~G~~~~~~i~~~L~~ 97 (138)
T PRK03988 29 EVPKPDVRIEGNRTII--------RNFKEIADRLNRD-PKHVAKFLLKEL-GTAGNI-EGGRLILQGKFSPRVINEKIDR 97 (138)
T ss_pred eCCCCeEEEEcCcEEE--------ecHHHHHHHHCCC-HHHHHHHHHHHh-CCceee-cCCEEEEEEeeCHHHHHHHHHH
Confidence 3899999888754223 2345554444331 111111111000 012334 3578999998733233222210
Q ss_pred ccCCCCceEEe-ecCCCC-----CCCcceeeccccCcee
Q 040083 570 ENGMVNCVVEC-ACGADE-----DDGERMVSCDICEVWQ 602 (635)
Q Consensus 570 e~g~e~~~VrC-iCG~~d-----DDGe~MI~CD~C~vWQ 602 (635)
.=..-|-| .||.+| ++.-.++.|+.|+...
T Consensus 98 ---yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 98 ---YVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred ---HHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 11345889 899876 4444789999998654
No 37
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=42.11 E-value=22 Score=30.32 Aligned_cols=20 Identities=15% Similarity=0.404 Sum_probs=17.8
Q ss_pred EeecCCCChHHHHHHHHHHH
Q 040083 497 VTIKNNATFDELKLEVQRNF 516 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~raf 516 (635)
|-++++|||+|||.+.+..+
T Consensus 16 l~v~~~~TV~~LK~~I~~~~ 35 (78)
T cd01804 16 LSVPPDETVEGLKKRISQRL 35 (78)
T ss_pred EEECCcCHHHHHHHHHHHHh
Confidence 67789999999999998776
No 38
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=40.05 E-value=12 Score=34.82 Aligned_cols=98 Identities=15% Similarity=0.292 Sum_probs=51.5
Q ss_pred CCCCCceEeecCCCCh-HHHHHHHHHHHHHHHhhhhceeeecccccccCCCceeeeeeeeCceEEEeccccCCCcccccc
Q 040083 490 AMQPYECVTIKNNATF-DELKLEVQRNFRELYWGLRSFVIESIVNVNATGTDLVCGFVEVGRRIVFEGSNSERGIVYGQI 568 (635)
Q Consensus 490 ~~pP~Elv~lp~~ATv-~dLK~ea~rafrdtY~~~~~f~ve~l~~~~~~~~~~~~g~v~sg~~v~V~G~~~~~d~~~~~r 568 (635)
.+|||++..--...|+ .-++.-+...=|+--..++ |-..+| +.. |.+...+.+.++|+....+++..++
T Consensus 5 ~~p~~~v~~eG~~kTvi~Nf~~I~~~L~R~p~hv~k-yl~~EL---gt~------g~id~~~rlii~G~~~~~~i~~~l~ 74 (110)
T smart00653 5 KMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLK-FLLAEL---GTQ------GSIDGKGRLIVNGRFTPKKLQDLLR 74 (110)
T ss_pred ccCCCeEEEEcCCeEEEEcHHHHHHHHCCCHHHHHH-HHHHHh---CCc------eeECCCCeEEEEEeeCHHHHHHHHH
Confidence 3899999888875444 3333333333333222221 111111 111 2232226788899873323322221
Q ss_pred cccCCCCceEEe-ecCCCC-----CCCcceeeccccCc
Q 040083 569 YENGMVNCVVEC-ACGADE-----DDGERMVSCDICEV 600 (635)
Q Consensus 569 ~e~g~e~~~VrC-iCG~~d-----DDGe~MI~CD~C~v 600 (635)
..=..-|-| .|+.+| +++-.++.|+.|+.
T Consensus 75 ---~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 75 ---RYIKEYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred ---HHHHhcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 011345889 899986 45567888999974
No 39
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=36.31 E-value=49 Score=29.30 Aligned_cols=41 Identities=17% Similarity=0.385 Sum_probs=31.5
Q ss_pred HHHHHHhhcCCcccHHHHHHHHhcccCC--------------cchHHHHHHhcCCccc
Q 040083 313 IVESLKRAESRWVSRQEVRDVARSYVGD--------------TGLLDFVLKSLGNHIV 356 (635)
Q Consensus 313 ~v~vLr~~~~~wvsr~~LR~aar~~Igd--------------tgLLD~~LK~l~~~~v 356 (635)
++..|.+.| +.+|+++|+.++-...|. .+||+|+++. ||++
T Consensus 7 VL~mml~~~-~~~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~k--gKfi 61 (77)
T TIGR03853 7 VLNLMLASG-EPYTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKK--GKFI 61 (77)
T ss_pred HHHHHHHcC-CCcCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHC--CCEe
Confidence 445555655 888999999999988886 4799998863 6665
No 40
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=35.15 E-value=1.2e+02 Score=28.28 Aligned_cols=86 Identities=10% Similarity=0.011 Sum_probs=62.5
Q ss_pred hhhhHHHHhhccceeeeeeeeccccccchhhhhhhhhcCCcccccccccccCcccccCHHHHHHHHHHHhCCchhhHhcc
Q 040083 160 IMDFWDRLCSGLQARKVSLYDISRKKGMELRLLHVVAYSQSWFGHWGYKFGRGSFGVTQPMYQKAIEAIQGMPLCLLLNH 239 (635)
Q Consensus 160 iM~~WDrlC~~L~~RkVSv~DvSkK~gmelRLLh~Va~G~sWyG~WGY~Fg~Gsfgvt~~~Y~~Aie~Lss~pL~~~~~~ 239 (635)
.|.|-+||-.....+++|..+++++-|+...-+.-+-.| .-..+.+...+-.+++ +++++.|+..
T Consensus 3 ~~~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g--------------~~~p~~~~l~~la~~l-~vs~~~l~~g 67 (135)
T PRK09706 3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERD--------------ETEPTGKNLFALAKAL-QCSPTWLLFG 67 (135)
T ss_pred hhhHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC--------------CCCCCHHHHHHHHHHH-CcCHHHHhcC
Confidence 466889999888889999999999999998877755544 3346666666666665 5777777643
Q ss_pred cCCC--------------CCChhHHHHHhhcccch
Q 040083 240 LGHL--------------NPDIPLIFTRYQTLSDH 260 (635)
Q Consensus 240 ~~~~--------------~~~l~~ii~~Yq~lS~~ 260 (635)
.... ..+-+.++..|+.|++.
T Consensus 68 ~~~~~~~~~~~~~~~~~l~~~~~~ll~~~~~L~~~ 102 (135)
T PRK09706 68 DEDKQPTPPVPLNQPVELSEDQKELLELFDALPES 102 (135)
T ss_pred CCcCCCCCcccccCCCCCCHHHHHHHHHHHHCCHH
Confidence 3211 12457899999999975
No 41
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=33.79 E-value=36 Score=28.97 Aligned_cols=20 Identities=20% Similarity=0.478 Sum_probs=17.1
Q ss_pred eecCCCChHHHHHHHHHHHH
Q 040083 498 TIKNNATFDELKLEVQRNFR 517 (635)
Q Consensus 498 ~lp~~ATv~dLK~ea~rafr 517 (635)
-+++++||+|||.+.+..+.
T Consensus 18 ~v~~~~TV~~lK~~I~~~~~ 37 (80)
T cd01792 18 SLRDSMTVSELKQQIAQKIG 37 (80)
T ss_pred EcCCCCcHHHHHHHHHHHhC
Confidence 45789999999999998874
No 42
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=33.38 E-value=20 Score=29.00 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=15.2
Q ss_pred CCCCCceecCCCcccccCC
Q 040083 613 EEIPHIFLCNRCEQEIVHL 631 (635)
Q Consensus 613 ~~vP~~y~C~~C~~~~~~~ 631 (635)
+++|+.|.|+.|......|
T Consensus 29 ~~Lp~~w~CP~C~a~K~~F 47 (50)
T cd00730 29 EDLPDDWVCPVCGAGKDDF 47 (50)
T ss_pred hHCCCCCCCCCCCCcHHHc
Confidence 3589999999998776544
No 43
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=32.06 E-value=47 Score=26.19 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=17.6
Q ss_pred EeecCCCChHHHHHHHHHHHH
Q 040083 497 VTIKNNATFDELKLEVQRNFR 517 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~rafr 517 (635)
+-+|+++||++||...++.+.
T Consensus 12 ~~~~~~~ti~~lK~~i~~~~~ 32 (69)
T cd01769 12 LEVSPDDTVAELKAKIAAKEG 32 (69)
T ss_pred EEECCCChHHHHHHHHHHHHC
Confidence 567889999999999888763
No 44
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=30.97 E-value=84 Score=27.34 Aligned_cols=48 Identities=13% Similarity=0.260 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhhcC-----CcccHHHHHHHHhcccCC-------cchHHHHHHhcC
Q 040083 305 RVEMATRVIVESLKRAES-----RWVSRQEVRDVARSYVGD-------TGLLDFVLKSLG 352 (635)
Q Consensus 305 r~~~a~~~~v~vLr~~~~-----~wvsr~~LR~aar~~Igd-------tgLLD~~LK~l~ 352 (635)
++|.|-+.|+.+.++--+ ..|++.+||..+.+..|+ ..-+|.+++.++
T Consensus 2 ~~e~~i~~~~~~f~~y~~~~~~~~~Is~~El~~ll~~~~g~~~t~~~~~~~v~~i~~~~D 61 (88)
T cd05030 2 ELEKAIETIINVFHQYSVRKGHPDTLYKKEFKQLVEKELPNFLKKEKNQKAIDKIFEDLD 61 (88)
T ss_pred hHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHhhHhhccCCCHHHHHHHHHHcC
Confidence 678899999999865532 499999999999764443 466888887763
No 45
>PF06377 Adipokin_hormo: Adipokinetic hormone; InterPro: IPR010475 This family consists of several insect adipokinetic hormone as well as the related crustacean red pigment concentrating hormone (RPCH) []. Flight activity of insects comprises one of the most intense biochemical processes known in nature, and therefore provides an attractive model system to study the hormonal regulation of metabolism during physical exercise. In long-distance flying insects, such as the migratory locust, both carbohydrate and lipid reserves are utilised as fuels for sustained flight activity. The mobilisation of these energy stores in Locusta migratoria (Migratory locust) is mediated by three structurally related adipokinetic hormones (AKHs), which are all capable of stimulating the release of both carbohydrates and lipids from the fat body [].; GO: 0005179 hormone activity
Probab=29.24 E-value=32 Score=27.98 Aligned_cols=20 Identities=30% Similarity=0.496 Sum_probs=15.1
Q ss_pred HHHHHHhhccCCCCCccccccchHHHHHHHhhcccc
Q 040083 410 VRILYKLILHDQKPATSSGIFSGISVASRIILDTKY 445 (635)
Q Consensus 410 l~~LY~~~L~~~~~~~~~~~~~~~~~Aa~~iLD~K~ 445 (635)
|.+||+-|-. =||+|+||.+
T Consensus 29 l~~iy~~iQ~----------------EAqkl~~C~~ 48 (48)
T PF06377_consen 29 LLHIYKLIQN----------------EAQKLLDCQK 48 (48)
T ss_pred HHHHHHHHHH----------------HHHHHHhccC
Confidence 4578888554 4999999975
No 46
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.74 E-value=43 Score=26.85 Aligned_cols=17 Identities=24% Similarity=0.671 Sum_probs=11.0
Q ss_pred CCCCCceecCCCccccc
Q 040083 613 EEIPHIFLCNRCEQEIV 629 (635)
Q Consensus 613 ~~vP~~y~C~~C~~~~~ 629 (635)
+++|+.|.|+.|.....
T Consensus 29 ~~Lp~~w~CP~C~a~K~ 45 (47)
T PF00301_consen 29 EDLPDDWVCPVCGAPKS 45 (47)
T ss_dssp GGS-TT-B-TTTSSBGG
T ss_pred HHCCCCCcCcCCCCccc
Confidence 46899999999987653
No 47
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.95 E-value=32 Score=34.90 Aligned_cols=102 Identities=20% Similarity=0.326 Sum_probs=54.5
Q ss_pred CCCCCceEeecCCCChHHHHHHHHHHHHHHHhhhhceeeecccccccCCCceeeeeeeeCceEEEeccccCCCccccccc
Q 040083 490 AMQPYECVTIKNNATFDELKLEVQRNFRELYWGLRSFVIESIVNVNATGTDLVCGFVEVGRRIVFEGSNSERGIVYGQIY 569 (635)
Q Consensus 490 ~~pP~Elv~lp~~ATv~dLK~ea~rafrdtY~~~~~f~ve~l~~~~~~~~~~~~g~v~sg~~v~V~G~~~~~d~~~~~r~ 569 (635)
.+|||++.+--....+.-++.-+...=|+--..++=|. .+| +. -|.+. |+.+.+.|+.....++..++
T Consensus 25 ~~p~~~v~~eG~kT~i~N~~~i~~~l~R~~~~~~ky~~-~EL---gt------~~~~~-~~~~ii~G~~~~~~i~~~l~- 92 (201)
T PRK12336 25 SIPEPKIFIEGKTTILTNFGEIADALNRDPDHLMKFLQ-REL---GT------AGKIE-GGRAVFNGKFTEEDIQAAID- 92 (201)
T ss_pred ecCCceEEEEcCcEEEecHHHHHHHHCCCHHHHHHHHH-HHh---CC------cceec-CCEEEEEeeeCHHHHHHHHH-
Confidence 38999988877433333444444443333333332221 111 11 13333 35788999862222222221
Q ss_pred ccCCCCceEEe-ecCCCC-----CCCcceeeccccCceeecc
Q 040083 570 ENGMVNCVVEC-ACGADE-----DDGERMVSCDICEVWQHTR 605 (635)
Q Consensus 570 e~g~e~~~VrC-iCG~~d-----DDGe~MI~CD~C~vWQH~~ 605 (635)
..=..-|-| .|+.+| +++-.++.|+.|+...-..
T Consensus 93 --~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 93 --AYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred --HHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccc
Confidence 011346889 899876 4555688999998765444
No 48
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=27.52 E-value=64 Score=25.06 Aligned_cols=20 Identities=25% Similarity=0.303 Sum_probs=17.3
Q ss_pred EeecCCCChHHHHHHHHHHH
Q 040083 497 VTIKNNATFDELKLEVQRNF 516 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~raf 516 (635)
+-+++++||++||...+..+
T Consensus 14 ~~v~~~~tv~~lk~~i~~~~ 33 (64)
T smart00213 14 LEVKPSDTVSELKEKIAELT 33 (64)
T ss_pred EEECCCCcHHHHHHHHHHHH
Confidence 56889999999999988765
No 49
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.16 E-value=90 Score=27.10 Aligned_cols=25 Identities=12% Similarity=0.227 Sum_probs=19.4
Q ss_pred CCCCceEeecCCCChHHHHHHHHHH
Q 040083 491 MQPYECVTIKNNATFDELKLEVQRN 515 (635)
Q Consensus 491 ~pP~Elv~lp~~ATv~dLK~ea~ra 515 (635)
...+|.++||..|||.|+=...-+.
T Consensus 13 ~d~~~~liL~~GaTV~D~a~~iH~d 37 (75)
T cd01666 13 PDFDEPVILRRGSTVEDVCNKIHKD 37 (75)
T ss_pred CCCCCCEEECCCCCHHHHHHHHHHH
Confidence 3458999999999999976655433
No 50
>PLN02400 cellulose synthase
Probab=27.07 E-value=43 Score=41.88 Aligned_cols=47 Identities=23% Similarity=0.645 Sum_probs=36.6
Q ss_pred Ee-ecCCC---CCCCcceeeccccCceeeccccccCCCCCCCCceecCCCcccc
Q 040083 579 EC-ACGAD---EDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 579 rC-iCG~~---dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
-| |||.. ..|||+.|+|..|..--=-.|+-....+ ..=.|+.|+-+-
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERke---Gnq~CPQCkTrY 88 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKD---GTQCCPQCKTRY 88 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhheeccc---CCccCcccCCcc
Confidence 36 99974 4899999999999999999999765432 344799997653
No 51
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=26.84 E-value=86 Score=36.26 Aligned_cols=81 Identities=22% Similarity=0.328 Sum_probs=58.1
Q ss_pred eccccccch-hhhhhhhhcCCcc--------ccc-ccccccCcccccCHHHHHHHHHHHhCCchhhHhcccCCCCCChhH
Q 040083 180 DISRKKGME-LRLLHVVAYSQSW--------FGH-WGYKFGRGSFGVTQPMYQKAIEAIQGMPLCLLLNHLGHLNPDIPL 249 (635)
Q Consensus 180 DvSkK~gme-lRLLh~Va~G~sW--------yG~-WGY~Fg~Gsfgvt~~~Y~~Aie~Lss~pL~~~~~~~~~~~~~l~~ 249 (635)
-||||+.=+ |+|||.|-||..= .|+ =||.|.. --.-+|.+..|.|-.+-=..|+. +=.
T Consensus 211 klskkk~De~L~~LHtIlfGk~gKa~~lKkNi~~FSGF~w~~----~eekq~~K~kEkl~K~~kekL~~--------fCd 278 (594)
T KOG2266|consen 211 KLSKKKSDENLKLLHTILFGKKGKAQMLKKNIGQFSGFVWSK----EEEKQYAKKKEKLKKCDKEKLIS--------FCD 278 (594)
T ss_pred HhhhcccchHHHHHHHHHhCChhHHHHHHHhhhcccCccccc----chHHHHHHHHHHHHHHHHHHHHH--------HHh
Confidence 368999889 9999999998542 222 3777765 34678999999998877777766 667
Q ss_pred HHHHhhcccch---hhhcHHHHHHHHHh
Q 040083 250 IFTRYQTLSDH---FLATLGDLFHFLLD 274 (635)
Q Consensus 250 ii~~Yq~lS~~---~L~Tl~dL~~fmL~ 274 (635)
|+++-++-|.. .|+ --||.||+.
T Consensus 279 vLdi~~~kst~kkeelv--~rvleFL~~ 304 (594)
T KOG2266|consen 279 VLDIPRSKSTVKKEELV--VRVLEFLEK 304 (594)
T ss_pred hhccccccccchHHHHH--HHHHHHHhC
Confidence 77777777765 444 346666664
No 52
>PLN02436 cellulose synthase A
Probab=26.62 E-value=40 Score=42.17 Aligned_cols=47 Identities=28% Similarity=0.646 Sum_probs=36.7
Q ss_pred Ee-ecCCC---CCCCcceeeccccCceeeccccccCCCCCCCCceecCCCcccc
Q 040083 579 EC-ACGAD---EDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 579 rC-iCG~~---dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
-| |||.. ..|||+.|+|..|..--=-.|+.....+ ..=.|+.|+-+-
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~e---g~~~Cpqckt~Y 88 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERRE---GNQACPQCKTRY 88 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhc---CCccCcccCCch
Confidence 46 99985 5899999999999999999999655322 344799997654
No 53
>PLN02560 enoyl-CoA reductase
Probab=26.41 E-value=60 Score=35.12 Aligned_cols=33 Identities=15% Similarity=0.296 Sum_probs=23.8
Q ss_pred ceEeecCCCChHHHHHHHHHHHHHHHhhhhcee
Q 040083 495 ECVTIKNNATFDELKLEVQRNFRELYWGLRSFV 527 (635)
Q Consensus 495 Elv~lp~~ATv~dLK~ea~rafrdtY~~~~~f~ 527 (635)
+.|-+|++|||+|||.+.+++..-.+.--++..
T Consensus 16 ~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~ 48 (308)
T PLN02560 16 GGLEVPDSATVADLKKAIHKRKKKYYPSRQRLT 48 (308)
T ss_pred eeEEcCCCCcHHHHHHHHHHHcCCCChhheEEE
Confidence 557779999999999999998543333334444
No 54
>PF01506 HCV_NS5a: Hepatitis C virus non-structural 5a protein membrane anchor; InterPro: IPR002868 The molecular function of the non-structural 5a viral protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA-dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ].; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1R7F_A 1R7E_A 1R7C_A 1R7G_A 1R7D_A.
Probab=26.28 E-value=29 Score=24.19 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=11.0
Q ss_pred hhhhHHHHhhccc
Q 040083 160 IMDFWDRLCSGLQ 172 (635)
Q Consensus 160 iM~~WDrlC~~L~ 172 (635)
+-|+||-+|+.|+
T Consensus 4 l~diWdWvc~~l~ 16 (23)
T PF01506_consen 4 LWDIWDWVCRVLR 16 (23)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4589999999876
No 55
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=26.21 E-value=45 Score=39.61 Aligned_cols=46 Identities=35% Similarity=0.928 Sum_probs=33.5
Q ss_pred EEe-ecCCCCCCCcceeeccccCceeeccccccCCCCCCC-CceecCCCc
Q 040083 578 VEC-ACGADEDDGERMVSCDICEVWQHTRCARIPNNEEIP-HIFLCNRCE 625 (635)
Q Consensus 578 VrC-iCG~~dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP-~~y~C~~C~ 625 (635)
+-| .||...|-+ ....|+.|.+-+|+-|..-.. +.+| ..|+|..|-
T Consensus 69 rvCe~c~~~gD~~-kf~~Ck~cDvsyh~yc~~P~~-~~v~sg~~~ckk~~ 116 (694)
T KOG4443|consen 69 RVCEACGTTGDPK-KFLLCKRCDVSYHCYCQKPPN-DKVPSGPWLCKKCT 116 (694)
T ss_pred eeeeeccccCCcc-cccccccccccccccccCCcc-ccccCcccccHHHH
Confidence 445 788777777 677899999999999998654 3444 457776543
No 56
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=25.82 E-value=70 Score=30.72 Aligned_cols=67 Identities=19% Similarity=0.278 Sum_probs=40.2
Q ss_pred cCcccccCHHHHHHHHHHHhCCchhhHhcccCC---CCCChhHHHHHhhcc-cchhhhcHHHHHHHHHhhhh
Q 040083 210 GRGSFGVTQPMYQKAIEAIQGMPLCLLLNHLGH---LNPDIPLIFTRYQTL-SDHFLATLGDLFHFLLDLKS 277 (635)
Q Consensus 210 g~Gsfgvt~~~Y~~Aie~Lss~pL~~~~~~~~~---~~~~l~~ii~~Yq~l-S~~~L~Tl~dL~~fmL~l~~ 277 (635)
+| .||+....-.+|+-...++|-..+-..... .-.-+..++...+.. ...+-.|+.|+..+|-+|..
T Consensus 55 ~r-~~~i~~~~L~k~~~~~~~~~~~~~~~~~~~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~ 125 (177)
T PF04675_consen 55 GR-EYGIGEKLLAKAIAEALGLPEKSIDESYKKVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAA 125 (177)
T ss_dssp S----S--HHHHHHHHHHHHTS-HHHHHHHHHHHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH
T ss_pred hh-HhccchhHHHHHHHHHHcCCHHHHHHHHHhcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHH
Confidence 67 999999999999999999998888663211 112334444444433 23577899999999999885
No 57
>TIGR00043 metalloprotein, YbeY/UPF0054 family. This minimally protein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrates metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and somewhat more weakly to be a metalloproteinase.
Probab=25.69 E-value=17 Score=33.45 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=12.7
Q ss_pred cccceecccCccce
Q 040083 130 AMHGVFHSNGFGHL 143 (635)
Q Consensus 130 lLHGviH~NGfGHL 143 (635)
+.||+.|..||-|-
T Consensus 77 ~iHG~LHLlGyDH~ 90 (110)
T TIGR00043 77 TVHGLLHLLGYDHE 90 (110)
T ss_pred HHHHHHHHcCCCCC
Confidence 67999999999995
No 58
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=25.22 E-value=62 Score=23.16 Aligned_cols=25 Identities=36% Similarity=0.700 Sum_probs=19.7
Q ss_pred ecCCCCCCCcc-eeeccccCceeecccc
Q 040083 581 ACGADEDDGER-MVSCDICEVWQHTRCA 607 (635)
Q Consensus 581 iCG~~dDDGe~-MI~CD~C~vWQH~~Cv 607 (635)
+|+.. -+| + +..|+.|..=.|.+|+
T Consensus 5 ~C~~~-~~~-~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 5 VCRRK-IDG-FYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCC-cCC-CEeEEeCCCCCeEcCccC
Confidence 67765 455 4 8999999999999885
No 59
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=25.05 E-value=38 Score=35.76 Aligned_cols=11 Identities=18% Similarity=0.655 Sum_probs=8.1
Q ss_pred CCceecCCCcc
Q 040083 616 PHIFLCNRCEQ 626 (635)
Q Consensus 616 P~~y~C~~C~~ 626 (635)
...++|..|..
T Consensus 236 ~rve~C~~C~~ 246 (290)
T PF04216_consen 236 YRVEVCESCGS 246 (290)
T ss_dssp EEEEEETTTTE
T ss_pred EEEEECCcccc
Confidence 35688999974
No 60
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=24.66 E-value=51 Score=26.37 Aligned_cols=78 Identities=13% Similarity=0.211 Sum_probs=50.3
Q ss_pred eeeeeeccccccchhhhhhhhhcCCcccccccccccCcccccCHHHHHHHHHHHhC--CchhhHhcccCC-CCCChhHHH
Q 040083 175 KVSLYDISRKKGMELRLLHVVAYSQSWFGHWGYKFGRGSFGVTQPMYQKAIEAIQG--MPLCLLLNHLGH-LNPDIPLIF 251 (635)
Q Consensus 175 kVSv~DvSkK~gmelRLLh~Va~G~sWyG~WGY~Fg~Gsfgvt~~~Y~~Aie~Lss--~pL~~~~~~~~~-~~~~l~~ii 251 (635)
++||.+|++..|+..+.|+-+-.-. +| ..+.. | +...-.++|++.|.. +++..+-...+- ...++-..+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~--~~---~s~~~--~-~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~F 72 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE--TG---TTPKQ--Y-LRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAF 72 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH--hC---cCHHH--H-HHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHH
Confidence 4688899999999999888775421 11 00000 0 223345678888775 788888877777 445777777
Q ss_pred HHhhcccch
Q 040083 252 TRYQTLSDH 260 (635)
Q Consensus 252 ~~Yq~lS~~ 260 (635)
..+-.+|..
T Consensus 73 k~~~g~sp~ 81 (84)
T smart00342 73 KKLFGVTPS 81 (84)
T ss_pred HHHHCcChh
Confidence 766666544
No 61
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=24.42 E-value=13 Score=32.12 Aligned_cols=32 Identities=25% Similarity=0.626 Sum_probs=28.2
Q ss_pred CCceEEeecCCCCCCCcceeeccccCceeeccccccC
Q 040083 574 VNCVVECACGADEDDGERMVSCDICEVWQHTRCARIP 610 (635)
Q Consensus 574 e~~~VrCiCG~~dDDGe~MI~CD~C~vWQH~~CvgI~ 610 (635)
++-...|.|..+ .||-|-+|+..=|-+|+|-.
T Consensus 30 ~~~~~~C~C~Lk-----AMi~Cq~CGAFCHDDCIgps 61 (69)
T PF13922_consen 30 ESTSNKCACSLK-----AMIMCQGCGAFCHDDCIGPS 61 (69)
T ss_pred cccccccccchH-----HHHHHhhccchhccccccHH
Confidence 455678999997 89999999999999999965
No 62
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=24.27 E-value=73 Score=25.78 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=16.7
Q ss_pred EeecCCCChHHHHHHHHHHH
Q 040083 497 VTIKNNATFDELKLEVQRNF 516 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~raf 516 (635)
+-+++++||+|||.+.+...
T Consensus 14 i~v~~~~tv~~lK~~i~~~~ 33 (71)
T cd01812 14 LSISSQATFGDLKKMLAPVT 33 (71)
T ss_pred EEECCCCcHHHHHHHHHHhh
Confidence 45789999999999887764
No 63
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=24.10 E-value=1.6e+02 Score=31.42 Aligned_cols=100 Identities=23% Similarity=0.245 Sum_probs=77.1
Q ss_pred HHHhhccceeeeeeeeccccccchhhhhhhhhcCCcccccccccccCcccccCHHHHHHHHHHHhCCchhhHhcccCCCC
Q 040083 165 DRLCSGLQARKVSLYDISRKKGMELRLLHVVAYSQSWFGHWGYKFGRGSFGVTQPMYQKAIEAIQGMPLCLLLNHLGHLN 244 (635)
Q Consensus 165 DrlC~~L~~RkVSv~DvSkK~gmelRLLh~Va~G~sWyG~WGY~Fg~Gsfgvt~~~Y~~Aie~Lss~pL~~~~~~~~~~~ 244 (635)
+||=..-..++.|..+++++-|+.-.-+.-+-+ |....+.++..+-.++| +++++.|+..-....
T Consensus 31 ~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~--------------g~~~ps~~~l~~ia~~l-~v~~~~l~~~~~~~~ 95 (309)
T PRK08154 31 ERVRTLRARRGMSRKVLAQASGVSERYLAQLES--------------GQGNVSILLLRRVARAL-GCSLADLLGDVDTSS 95 (309)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC--------------CCCCCCHHHHHHHHHHh-CCCHHHHhCCCCCCC
Confidence 344444445789999999999998776655544 44467778888877777 678999987665556
Q ss_pred CChhHHHHHhhcccchhhhcHHHHHHHHHhhhhcC
Q 040083 245 PDIPLIFTRYQTLSDHFLATLGDLFHFLLDLKSRL 279 (635)
Q Consensus 245 ~~l~~ii~~Yq~lS~~~L~Tl~dL~~fmL~l~~~~ 279 (635)
.++..+...++.+++.++.-+.+++.-|+.-..+.
T Consensus 96 ~~~~~l~~~l~~l~~~~~~~~~~~l~~~~~~~~~~ 130 (309)
T PRK08154 96 PDWLLIRELLEQASPAQLARVRDALSGMLGAGRRA 130 (309)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhhhhc
Confidence 67888999999999999999999999888866554
No 64
>PF04714 BCL_N: BCL7, N-terminal conserver region; InterPro: IPR006804 The members of this group of sequences contain a conserved N-terminal domain which is found in the BCL7 family. The function of BCL7 proteins is unknown, though they may be involved in early development. Notably, BCL7B is commonly hemizygously deleted in patients with Williams syndrome [].
Probab=23.90 E-value=78 Score=26.15 Aligned_cols=33 Identities=27% Similarity=0.492 Sum_probs=26.1
Q ss_pred CCcchHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHhcccCCcch
Q 040083 299 CRWSAKRVEMATRVIVESLKRAESRWVSRQEVRDVARSYVGDTGL 343 (635)
Q Consensus 299 ~rWs~~r~~~a~~~~v~vLr~~~~~wvsr~~LR~aar~~IgdtgL 343 (635)
-+.++++++++.+++=++ |.-+.+||+ +|||.|
T Consensus 10 Rsr~KddiKrv~~~iekV-r~wEKKWVt-----------v~dtsl 42 (52)
T PF04714_consen 10 RSRAKDDIKRVMASIEKV-RKWEKKWVT-----------VGDTSL 42 (52)
T ss_pred hcchhHHHHHHHHHHHHH-HHHhhceEE-----------eccceE
Confidence 356899999999999888 444558996 788876
No 65
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.68 E-value=47 Score=41.55 Aligned_cols=47 Identities=28% Similarity=0.685 Sum_probs=36.3
Q ss_pred Ee-ecCCC---CCCCcceeeccccCceeeccccccCCCCCCCCceecCCCcccc
Q 040083 579 EC-ACGAD---EDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 579 rC-iCG~~---dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
-| |||.. ..||++.|+|..|..--=-.|+-....+ ..=.|+.|+-+-
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~e---G~q~CPqCktrY 69 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKD---GNQSCPQCKTKY 69 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhc---CCccCCccCCch
Confidence 36 99975 4899999999999999999999765322 334799997653
No 66
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=23.36 E-value=1.4e+02 Score=25.69 Aligned_cols=49 Identities=18% Similarity=0.404 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHhhc---C-C-cccHHHHHHHHhcccC-------CcchHHHHHHhcC
Q 040083 304 KRVEMATRVIVESLKRAE---S-R-WVSRQEVRDVARSYVG-------DTGLLDFVLKSLG 352 (635)
Q Consensus 304 ~r~~~a~~~~v~vLr~~~---~-~-wvsr~~LR~aar~~Ig-------dtgLLD~~LK~l~ 352 (635)
.++|.|++.+.++.+.-- + . .|++.+||.+.++.+| +..-++-+++.++
T Consensus 2 ~~~e~~~~~l~~~F~~fDd~dg~G~~Is~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~D 62 (92)
T cd05025 2 SELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSDFLDAQKDADAVDKIMKELD 62 (92)
T ss_pred ChHHHHHHHHHHHHHHHhcccCCCCeECHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence 478999999999887552 2 3 5999999999987444 3566888887764
No 67
>KOG2320 consensus RAS effector RIN1 (contains VPS domain) [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.06 E-value=5.8e+02 Score=30.57 Aligned_cols=127 Identities=13% Similarity=0.079 Sum_probs=68.0
Q ss_pred ccccCHHHHHHHHHHHhCCchhhHhcccCCCCCChhHHHHHhhcc--cchh----hhcHHHHHHHHHhhhhcCCcccCCC
Q 040083 213 SFGVTQPMYQKAIEAIQGMPLCLLLNHLGHLNPDIPLIFTRYQTL--SDHF----LATLGDLFHFLLDLKSRLPKENCNF 286 (635)
Q Consensus 213 sfgvt~~~Y~~Aie~Lss~pL~~~~~~~~~~~~~l~~ii~~Yq~l--S~~~----L~Tl~dL~~fmL~l~~~~p~~~~~~ 286 (635)
||+-....|-|++..|..=+-..| -.-||+.|++|++. -.+. |.++|..+..|=++.+.-++...
T Consensus 257 s~~~~e~q~~ke~a~L~qd~~tyf-------G~lvqD~vs~~~d~~~~~td~a~mL~~iRq~lt~~k~yL~qs~e~~~-- 327 (651)
T KOG2320|consen 257 SFLGPERQHYKESAELEQDKMTYF-------GSLVQDYVSDYEDVWHRPTDSASMLQSIRQALTRRKNYLSQSPELDT-- 327 (651)
T ss_pred hhhhhHHHHHHHHHHHhcCcccHH-------HHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHhHHHHhhcCCCCC--
Confidence 455566666666666665444333 23699999999988 2333 77888777766666654443321
Q ss_pred CCCCCCCcccccCCcchHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHhcccCCcchHHHHHHhcCCccccccEEEEeec
Q 040083 287 GSYNPGILVETNCRWSAKRVEMATRVIVESLKRAESRWVSRQEVRDVARSYVGDTGLLDFVLKSLGNHIVGKYLVRRSLN 366 (635)
Q Consensus 287 ~~~~~~~~~~~~~rWs~~r~~~a~~~~v~vLr~~~~~wvsr~~LR~aar~~IgdtgLLD~~LK~l~~~~vg~~~vrrr~N 366 (635)
+ +..... |..++|.+.|+++-..--+..++.--.-|+....+ =|++++|+ .|..|-|..|
T Consensus 328 ----~-v~~~~~---s~~~leavlEs~Lhk~vLkPlkp~l~~~l~~~h~~-dGsl~~l~-----------en~~vvr~~~ 387 (651)
T KOG2320|consen 328 ----P-VQPSLL---SETPLEAVLESALHKSVLKPLKPNLSAQLPPVHSK-DGSLQQLK-----------ENQDVVRAAN 387 (651)
T ss_pred ----C-cccccc---CcchHHHHHHHHHHHhhccccchhHhhhcchhhhh-ccHHHHHh-----------cccceecccC
Confidence 1 111112 33788888776665432222232222222332222 24444332 4666667788
Q ss_pred CC
Q 040083 367 PV 368 (635)
Q Consensus 367 p~ 368 (635)
|.
T Consensus 388 ~~ 389 (651)
T KOG2320|consen 388 PT 389 (651)
T ss_pred cc
Confidence 76
No 68
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=22.99 E-value=86 Score=25.89 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=18.0
Q ss_pred eEeecCCCChHHHHHHHHHHH
Q 040083 496 CVTIKNNATFDELKLEVQRNF 516 (635)
Q Consensus 496 lv~lp~~ATv~dLK~ea~raf 516 (635)
.+-+.+++||+|||.+.++.+
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~ 33 (71)
T cd01808 13 EIEIAEDASVKDFKEAVSKKF 33 (71)
T ss_pred EEEECCCChHHHHHHHHHHHh
Confidence 467789999999999998775
No 69
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.92 E-value=40 Score=28.92 Aligned_cols=34 Identities=26% Similarity=0.640 Sum_probs=27.1
Q ss_pred CceEEe-ecCCCCCCCcceeeccc--cCceeeccccccCC
Q 040083 575 NCVVEC-ACGADEDDGERMVSCDI--CEVWQHTRCARIPN 611 (635)
Q Consensus 575 ~~~VrC-iCG~~dDDGe~MI~CD~--C~vWQH~~CvgI~~ 611 (635)
.+...| +|+.+ .| ..|+|.. |...+|..|.....
T Consensus 34 ~~~~~C~~C~~~--~G-a~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 34 RRKLKCSICKKK--GG-ACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred HhCCCCcCCCCC--CC-eEEEEeCCCCCcEEChHHHccCC
Confidence 455567 88865 56 9999985 99999999987654
No 70
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.54 E-value=17 Score=32.21 Aligned_cols=46 Identities=28% Similarity=0.702 Sum_probs=21.4
Q ss_pred e-ecCCC---CCCCcceeeccccCceeeccccccCCCCCCCCceecCCCcccc
Q 040083 580 C-ACGAD---EDDGERMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQEI 628 (635)
Q Consensus 580 C-iCG~~---dDDGe~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~~ 628 (635)
| |||-. ..+|+..++|..|.+--=-.|+.....+ ..=.|+.|..+-
T Consensus 12 CqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErke---g~q~CpqCkt~y 61 (80)
T PF14569_consen 12 CQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKE---GNQVCPQCKTRY 61 (80)
T ss_dssp -SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHT---S-SB-TTT--B-
T ss_pred cccccCccccCCCCCEEEEEcccCCccchhHHHHHhhc---CcccccccCCCc
Confidence 5 88864 4789999999999999888888765321 334789997543
No 71
>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]
Probab=21.90 E-value=48 Score=35.16 Aligned_cols=97 Identities=23% Similarity=0.327 Sum_probs=73.1
Q ss_pred ccccccceecccCccc---eEEecc---cccCCC-CcchhhhhhHHHHhhccceeeeeeeeccccccchhhhhhhhhcC-
Q 040083 127 QGHAMHGVFHSNGFGH---LLCVNG---VETGSD-LTGHQIMDFWDRLCSGLQARKVSLYDISRKKGMELRLLHVVAYS- 198 (635)
Q Consensus 127 ~~HlLHGviH~NGfGH---Ll~vnG---reggS~-lsG~~iM~~WDrlC~~L~~RkVSv~DvSkK~gmelRLLh~Va~G- 198 (635)
+..=+=++|=-||-|. |.+++| ...|.= |.|+.|.++ =..=.||++++.-=+.-....+...-.|+.|
T Consensus 26 ~~G~i~~iiGpNG~GKSTLLk~l~g~l~p~~G~V~l~g~~i~~~----~~kelAk~ia~vpQ~~~~~~~~tV~d~V~~GR 101 (258)
T COG1120 26 PKGEITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIASL----SPKELAKKLAYVPQSPSAPFGLTVYELVLLGR 101 (258)
T ss_pred cCCcEEEEECCCCCCHHHHHHHHhccCCCCCCEEEECCCchhhc----CHHHHhhhEEEeccCCCCCCCcEEeehHhhcC
Confidence 3333457788888886 556666 345655 889888762 2233578999988888889999999999999
Q ss_pred ---CcccccccccccCcccccCHHHHHHHHHHHhCCchhhHhc
Q 040083 199 ---QSWFGHWGYKFGRGSFGVTQPMYQKAIEAIQGMPLCLLLN 238 (635)
Q Consensus 199 ---~sWyG~WGY~Fg~Gsfgvt~~~Y~~Aie~Lss~pL~~~~~ 238 (635)
.+||++| +++.++.+.++|..+-+..+..
T Consensus 102 ~p~~~~~~~~-----------~~~D~~~v~~aL~~~~~~~la~ 133 (258)
T COG1120 102 YPHLGLFGRP-----------SKEDEEIVEEALELLGLEHLAD 133 (258)
T ss_pred CcccccccCC-----------CHhHHHHHHHHHHHhCcHHHhc
Confidence 5677766 5778889999999999988855
No 72
>PF04192 Utp21: Utp21 specific WD40 associated putative domain ; InterPro: IPR007319 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. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=21.52 E-value=90 Score=32.53 Aligned_cols=87 Identities=15% Similarity=0.156 Sum_probs=54.4
Q ss_pred ccCHHHHHHHHHHHhCCchhhHhcccCCCCCChhHHHHHhhcccchhhhcHHHHHHHHHhhhhcCCcccCCCCCCCCCCc
Q 040083 215 GVTQPMYQKAIEAIQGMPLCLLLNHLGHLNPDIPLIFTRYQTLSDHFLATLGDLFHFLLDLKSRLPKENCNFGSYNPGIL 294 (635)
Q Consensus 215 gvt~~~Y~~Aie~Lss~pL~~~~~~~~~~~~~l~~ii~~Yq~lS~~~L~Tl~dL~~fmL~l~~~~p~~~~~~~~~~~~~~ 294 (635)
|.+...|..+++.|.+|+-|.+=..++... ..+..++..+.-+++||.....
T Consensus 120 ~~~~~dy~~~~~~LkslsPS~iDlEIRsL~-----------~~~~~~~~~l~~Fl~~l~~~L~----------------- 171 (237)
T PF04192_consen 120 ASESEDYSEFLEYLKSLSPSAIDLEIRSLS-----------PESGGSYEELVSFLRFLTYRLK----------------- 171 (237)
T ss_pred hcccccHHHHHHHHHhCChhHHHHHHHhcc-----------CccCCcHHHHHHHHHHHHHHHH-----------------
Confidence 556788999999999999988744333222 2334455555566666655331
Q ss_pred ccccCCcchHHHHHHHHHHHHHHHhhcCCcccH---HHHHHHHhc
Q 040083 295 VETNCRWSAKRVEMATRVIVESLKRAESRWVSR---QEVRDVARS 336 (635)
Q Consensus 295 ~~~~~rWs~~r~~~a~~~~v~vLr~~~~~wvsr---~~LR~aar~ 336 (635)
+++++|.++.-|--.||-+|.-=+.- .+||.++.+
T Consensus 172 -------~~~dfElvQa~l~vFLk~Hgd~i~~~~~~~~L~~~l~~ 209 (237)
T PF04192_consen 172 -------SRRDFELVQAYLSVFLKVHGDVIMESEEEEELREALEE 209 (237)
T ss_pred -------cCCCHHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHH
Confidence 45678888877777788887411111 346666554
No 73
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=21.48 E-value=1e+02 Score=21.84 Aligned_cols=25 Identities=12% Similarity=0.191 Sum_probs=20.3
Q ss_pred CCceEeecCCCChHHHHHHHHHHHH
Q 040083 493 PYECVTIKNNATFDELKLEVQRNFR 517 (635)
Q Consensus 493 P~Elv~lp~~ATv~dLK~ea~rafr 517 (635)
..+.+.+++++|+.|+|..+.+.+.
T Consensus 8 ~~~~~~~~~~~tv~~l~~~i~~~~~ 32 (69)
T cd00196 8 KTVELLVPSGTTVADLKEKLAKKLG 32 (69)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHHC
Confidence 3455677789999999999998873
No 74
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.89 E-value=64 Score=32.61 Aligned_cols=28 Identities=29% Similarity=0.723 Sum_probs=23.6
Q ss_pred ceeeccccCceeeccccccCCCCCCCCceecCCCccc
Q 040083 591 RMVSCDICEVWQHTRCARIPNNEEIPHIFLCNRCEQE 627 (635)
Q Consensus 591 ~MI~CD~C~vWQH~~CvgI~~~~~vP~~y~C~~C~~~ 627 (635)
.-+.|+.|+.-+|..|..- . .||+|.+.
T Consensus 171 ~~~~C~~C~~v~H~~C~~~-~--------~CpkC~R~ 198 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFRK-K--------SCPKCARR 198 (202)
T ss_pred CeeeCCcCccccchhhcCC-C--------CCCCcHhH
Confidence 6899999999999999983 1 39999764
No 75
>PF10767 DUF2593: Protein of unknown function (DUF2593); InterPro: IPR019703 This entry represents proteins that appear to be restricted to Enterobacteriaceae. Some members are annotated as YbjO, however there is currently no known function.
Probab=20.13 E-value=39 Score=32.97 Aligned_cols=22 Identities=36% Similarity=0.868 Sum_probs=18.2
Q ss_pred chhhhhhhhhcCCcccccccccc
Q 040083 187 MELRLLHVVAYSQSWFGHWGYKF 209 (635)
Q Consensus 187 melRLLh~Va~G~sWyG~WGY~F 209 (635)
+|+|==-+|.+|+.| |||||--
T Consensus 60 ~Ei~Cgfav~~g~nw-gRW~yl~ 81 (144)
T PF10767_consen 60 LEIRCGFAVMRGRNW-GRWGYLA 81 (144)
T ss_pred HHHHHHHHHhccCcc-hhHHHHH
Confidence 577777789999999 9999953
No 76
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=20.11 E-value=1.1e+02 Score=24.77 Aligned_cols=21 Identities=14% Similarity=0.305 Sum_probs=17.6
Q ss_pred EeecCCCChHHHHHHHHHHHH
Q 040083 497 VTIKNNATFDELKLEVQRNFR 517 (635)
Q Consensus 497 v~lp~~ATv~dLK~ea~rafr 517 (635)
+-++++.||.|||...+....
T Consensus 10 ~~v~~~~tV~~lK~~i~~~~~ 30 (69)
T PF00240_consen 10 LEVDPDDTVADLKQKIAEETG 30 (69)
T ss_dssp EEEETTSBHHHHHHHHHHHHT
T ss_pred EEECCCCCHHHhhhhcccccc
Confidence 557889999999998887665
Done!