Query 007176
Match_columns 614
No_of_seqs 168 out of 291
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 19:58:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007176.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007176hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00501 BRIGHT BRIGHT, ARID 99.9 5.2E-22 1.1E-26 170.3 7.9 90 438-540 1-91 (93)
2 PF01388 ARID: ARID/BRIGHT DNA 99.8 1E-20 2.2E-25 160.7 6.5 87 438-537 5-92 (92)
3 KOG2744 DNA-binding proteins B 99.7 1.3E-16 2.8E-21 174.1 8.1 91 438-541 162-254 (512)
4 KOG2510 SWI-SNF chromatin-remo 98.8 1.1E-08 2.4E-13 111.2 10.3 85 437-540 291-375 (532)
5 PF00628 PHD: PHD-finger; Int 98.4 6.4E-08 1.4E-12 74.4 0.5 49 547-600 1-50 (51)
6 smart00249 PHD PHD zinc finger 98.3 8.4E-07 1.8E-11 64.9 3.7 46 547-598 1-47 (47)
7 KOG1973 Chromatin remodeling p 97.9 3.2E-06 7E-11 86.6 1.9 51 546-606 220-273 (274)
8 KOG0825 PHD Zn-finger protein 97.5 3.7E-05 7.9E-10 88.0 1.9 50 546-602 216-267 (1134)
9 KOG1632 Uncharacterized PHD Zn 97.1 6E-05 1.3E-09 80.0 -2.7 57 544-607 238-301 (345)
10 KOG1244 Predicted transcriptio 96.9 0.00031 6.7E-09 73.0 1.3 49 546-601 282-331 (336)
11 KOG4299 PHD Zn-finger protein 96.6 0.00086 1.9E-08 75.6 1.8 49 546-599 254-303 (613)
12 KOG1512 PHD Zn-finger protein 96.1 0.0026 5.5E-08 66.8 1.7 71 517-602 292-364 (381)
13 KOG0957 PHD finger protein [Ge 95.6 0.0047 1E-07 68.7 1.4 50 545-598 544-595 (707)
14 KOG4443 Putative transcription 95.6 0.0051 1.1E-07 70.0 1.7 48 546-600 69-117 (694)
15 KOG1245 Chromatin remodeling c 95.3 0.0051 1.1E-07 75.6 0.5 52 545-603 1108-1160(1404)
16 PF07227 DUF1423: Protein of u 95.2 0.016 3.6E-07 63.8 3.7 53 548-600 131-191 (446)
17 KOG0383 Predicted helicase [Ge 95.0 0.0083 1.8E-07 69.2 0.8 46 545-599 47-92 (696)
18 COG5034 TNG2 Chromatin remodel 93.5 0.045 9.8E-07 56.8 2.3 42 550-600 225-269 (271)
19 KOG0955 PHD finger protein BR1 92.6 0.11 2.4E-06 62.6 4.2 50 543-601 217-269 (1051)
20 KOG1246 DNA-binding protein ju 92.5 0.11 2.4E-06 61.5 4.0 60 540-606 150-209 (904)
21 KOG4323 Polycomb-like PHD Zn-f 90.5 0.12 2.6E-06 57.6 1.3 50 547-600 170-223 (464)
22 COG5141 PHD zinc finger-contai 89.6 0.21 4.6E-06 56.1 2.4 49 546-603 194-245 (669)
23 KOG1632 Uncharacterized PHD Zn 83.5 0.47 1E-05 51.0 1.0 37 558-600 74-112 (345)
24 KOG1844 PHD Zn-finger proteins 82.9 0.68 1.5E-05 50.7 1.9 49 546-603 87-137 (508)
25 KOG0954 PHD finger protein [Ge 71.4 2.5 5.3E-05 49.9 2.2 67 526-601 236-321 (893)
26 PF14446 Prok-RING_1: Prokaryo 69.9 3.2 6.9E-05 34.4 1.9 34 545-578 5-40 (54)
27 PF13901 DUF4206: Domain of un 69.7 3.6 7.9E-05 41.0 2.7 43 545-603 152-200 (202)
28 KOG4443 Putative transcription 67.8 1.6 3.4E-05 50.7 -0.3 52 547-604 20-75 (694)
29 KOG1512 PHD Zn-finger protein 67.0 1.8 3.9E-05 46.3 -0.1 55 546-606 259-323 (381)
30 PF13831 PHD_2: PHD-finger; PD 61.2 2 4.3E-05 32.3 -0.7 33 558-598 3-35 (36)
31 PF11793 FANCL_C: FANCL C-term 61.1 1.9 4.1E-05 36.4 -0.9 51 547-601 4-64 (70)
32 PHA00689 hypothetical protein 59.6 5.6 0.00012 32.9 1.5 34 531-564 2-42 (62)
33 PF13639 zf-RING_2: Ring finge 58.6 2.1 4.6E-05 32.2 -1.0 41 547-599 2-44 (44)
34 PF00249 Myb_DNA-binding: Myb- 54.8 18 0.0004 27.7 3.6 39 481-533 10-48 (48)
35 PF02591 DUF164: Putative zinc 53.9 10 0.00022 30.4 2.1 43 526-568 2-55 (56)
36 KOG2752 Uncharacterized conser 52.0 6 0.00013 42.8 0.7 22 556-577 145-167 (345)
37 PF07496 zf-CW: CW-type Zinc F 48.0 7.7 0.00017 30.8 0.6 16 557-572 1-16 (50)
38 PHA02926 zinc finger-like prot 47.5 6.7 0.00015 40.8 0.3 67 530-601 155-228 (242)
39 KOG2846 Predicted membrane pro 47.4 12 0.00027 40.5 2.2 41 556-607 217-257 (328)
40 PF14205 Cys_rich_KTR: Cystein 45.7 16 0.00034 30.6 2.1 36 557-601 2-37 (55)
41 CHL00174 accD acetyl-CoA carbo 44.7 9.3 0.0002 40.8 0.8 32 554-599 33-64 (296)
42 TIGR00515 accD acetyl-CoA carb 42.7 9.1 0.0002 40.5 0.4 31 555-599 22-52 (285)
43 PRK14890 putative Zn-ribbon RN 42.6 25 0.00055 29.7 2.8 46 544-599 6-55 (59)
44 KOG1829 Uncharacterized conser 42.6 12 0.00026 43.3 1.3 33 545-577 511-549 (580)
45 KOG1473 Nucleosome remodeling 42.3 17 0.00037 45.1 2.5 45 546-599 345-389 (1414)
46 PF07649 C1_3: C1-like domain; 41.5 11 0.00024 26.8 0.5 28 547-574 2-30 (30)
47 KOG4299 PHD Zn-finger protein 41.4 21 0.00047 41.6 3.0 48 545-600 47-94 (613)
48 PRK05654 acetyl-CoA carboxylas 39.7 11 0.00023 40.1 0.3 31 555-599 23-53 (292)
49 PF15135 UPF0515: Uncharacteri 39.1 26 0.00057 37.1 3.0 63 528-601 90-164 (278)
50 PRK09140 2-dehydro-3-deoxy-6-p 39.0 11 0.00023 37.8 0.2 76 230-326 25-100 (206)
51 PF09855 DUF2082: Nucleic-acid 38.1 13 0.00028 31.6 0.5 18 593-610 1-18 (64)
52 KOG0957 PHD finger protein [Ge 37.5 21 0.00045 41.1 2.1 54 546-599 120-177 (707)
53 KOG0956 PHD finger protein AF1 36.0 17 0.00036 43.2 1.1 47 548-603 8-59 (900)
54 PF10367 Vps39_2: Vacuolar sor 34.8 66 0.0014 27.6 4.4 30 545-576 78-109 (109)
55 cd00730 rubredoxin Rubredoxin; 34.2 28 0.0006 28.2 1.8 36 561-601 3-43 (50)
56 PF13712 Glyco_tranf_2_5: Glyc 32.8 26 0.00055 35.1 1.7 90 184-280 2-96 (217)
57 TIGR00269 conserved hypothetic 32.4 55 0.0012 29.4 3.6 61 500-568 41-101 (104)
58 PF15446 zf-PHD-like: PHD/FYVE 32.4 45 0.00099 33.5 3.3 31 547-577 1-35 (175)
59 smart00531 TFIIE Transcription 31.5 36 0.00077 32.3 2.3 35 520-554 71-108 (147)
60 KOG3576 Ovo and related transc 31.5 6.5 0.00014 40.6 -2.7 74 529-602 129-222 (267)
61 PF10497 zf-4CXXC_R1: Zinc-fin 31.3 22 0.00047 32.5 0.8 57 541-600 3-69 (105)
62 PRK11823 DNA repair protein Ra 30.8 29 0.00063 38.5 1.9 28 544-571 6-33 (446)
63 PHA02929 N1R/p28-like protein; 30.8 30 0.00065 36.0 1.9 64 528-602 157-226 (238)
64 COG0777 AccD Acetyl-CoA carbox 29.8 22 0.00047 38.2 0.7 30 556-599 25-54 (294)
65 cd00167 SANT 'SWI3, ADA2, N-Co 29.1 90 0.002 22.0 3.6 37 482-533 9-45 (45)
66 cd01121 Sms Sms (bacterial rad 28.3 37 0.0008 37.0 2.1 28 546-573 1-28 (372)
67 PRK03988 translation initiatio 26.6 75 0.0016 30.6 3.6 38 523-569 89-133 (138)
68 PF13832 zf-HC5HC2H_2: PHD-zin 26.3 34 0.00073 30.2 1.2 33 545-578 55-89 (110)
69 PF14445 Prok-RING_2: Prokaryo 26.3 6.4 0.00014 32.6 -3.0 33 545-577 7-40 (57)
70 PF07754 DUF1610: Domain of un 25.5 42 0.00091 23.8 1.2 11 589-599 13-23 (24)
71 COG2888 Predicted Zn-ribbon RN 25.4 56 0.0012 27.9 2.2 45 545-599 9-57 (61)
72 TIGR01557 myb_SHAQKYF myb-like 24.6 1.4E+02 0.0031 24.6 4.4 45 479-536 9-57 (57)
73 PF10058 DUF2296: Predicted in 24.4 52 0.0011 27.0 1.8 32 559-601 22-53 (54)
74 PF04216 FdhE: Protein involve 23.6 96 0.0021 32.3 4.0 28 545-572 172-210 (290)
75 COG1190 LysU Lysyl-tRNA synthe 23.4 1.4E+02 0.003 34.5 5.5 111 417-538 143-286 (502)
76 TIGR00416 sms DNA repair prote 23.1 50 0.0011 36.9 1.9 29 544-572 6-34 (454)
77 smart00653 eIF2B_5 domain pres 22.9 93 0.002 28.8 3.3 37 522-567 66-109 (110)
78 PF09416 UPF1_Zn_bind: RNA hel 22.1 47 0.001 32.7 1.4 24 548-571 3-26 (152)
79 TIGR00311 aIF-2beta translatio 22.1 1E+02 0.0022 29.6 3.5 37 523-568 84-127 (133)
80 KOG4718 Non-SMC (structural ma 21.8 38 0.00083 35.2 0.7 84 479-599 138-223 (235)
81 KOG2824 Glutaredoxin-related p 21.6 1E+02 0.0022 33.2 3.7 28 543-577 227-254 (281)
82 PF13921 Myb_DNA-bind_6: Myb-l 21.5 1.3E+02 0.0029 23.6 3.6 26 500-534 19-44 (60)
No 1
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=99.86 E-value=5.2e-22 Score=170.30 Aligned_cols=90 Identities=30% Similarity=0.553 Sum_probs=81.0
Q ss_pred CCHHHHHHHHHHHHHHhCCccccCCCCCCCCCCcccCCeechHHHHHHHHhhcCceeeccC-CCCHHHHHHhccCCcCCC
Q 007176 438 CSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNG-INWKGQVFSKMRNHTLTN 516 (614)
Q Consensus 438 ~~eeeFL~dL~kFhe~RGtp~liP~g~~s~fP~PvV~GK~LDLykLYk~V~sRGGF~kVnk-kkWkgEV~~~Mgn~~~p~ 516 (614)
++.++|+++|++||+.+|+++.. .|+|+|++||||+||++|+++|||++|+. ++|. +|+++|+ ++.
T Consensus 1 ~~~~~F~~~L~~F~~~~g~~~~~---------~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~-~Va~~lg---~~~ 67 (93)
T smart00501 1 RERVLFLDRLYKFMEERGSPLKK---------IPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWK-EIARELG---IPD 67 (93)
T ss_pred CcHHHHHHHHHHHHHHcCCcCCc---------CCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHH-HHHHHhC---CCc
Confidence 35789999999999999998533 47999999999999999999999999965 5799 9999998 566
Q ss_pred ccccHHHHHHHHHHHhhhhhhccc
Q 007176 517 RMTGVGNTLKRHYETYLLEYELAH 540 (614)
Q Consensus 517 t~Tsag~~LK~hYERyLleYE~ah 540 (614)
+++++++.||++|+|||++||..+
T Consensus 68 ~~~~~~~~lk~~Y~k~L~~yE~~~ 91 (93)
T smart00501 68 TSTSAASSLRKHYERYLLPFERFL 91 (93)
T ss_pred ccchHHHHHHHHHHHHhHHHHHHh
Confidence 689999999999999999999864
No 2
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=99.82 E-value=1e-20 Score=160.74 Aligned_cols=87 Identities=32% Similarity=0.625 Sum_probs=75.2
Q ss_pred CCHHHHHHHHHHHHHHhCCccccCCCCCCCCCCcccCCeechHHHHHHHHhhcCceeeccC-CCCHHHHHHhccCCcCCC
Q 007176 438 CSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNG-INWKGQVFSKMRNHTLTN 516 (614)
Q Consensus 438 ~~eeeFL~dL~kFhe~RGtp~liP~g~~s~fP~PvV~GK~LDLykLYk~V~sRGGF~kVnk-kkWkgEV~~~Mgn~~~p~ 516 (614)
..+++|+++|++||+++|+++. +.|.++|++||||+||++|+++|||++|+. ++|. +|+++|+ ++.
T Consensus 5 ~~~~~F~~~L~~f~~~~g~~~~---------~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~-~va~~lg---~~~ 71 (92)
T PF01388_consen 5 REREQFLEQLREFHESRGTPID---------RPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWR-EVARKLG---FPP 71 (92)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSS---------S-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHH-HHHHHTT---S-T
T ss_pred hHHHHHHHHHHHHHHHcCCCCC---------CCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHH-HHHHHhC---CCC
Confidence 3578999999999999999953 357999999999999999999999999955 5799 9999998 555
Q ss_pred ccccHHHHHHHHHHHhhhhhh
Q 007176 517 RMTGVGNTLKRHYETYLLEYE 537 (614)
Q Consensus 517 t~Tsag~~LK~hYERyLleYE 537 (614)
..++.++.||++|++||++||
T Consensus 72 ~~~~~~~~L~~~Y~~~L~~fE 92 (92)
T PF01388_consen 72 SSTSAAQQLRQHYEKYLLPFE 92 (92)
T ss_dssp TSCHHHHHHHHHHHHHTHHHH
T ss_pred CCCcHHHHHHHHHHHHhHhhC
Confidence 556668999999999999998
No 3
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.66 E-value=1.3e-16 Score=174.11 Aligned_cols=91 Identities=33% Similarity=0.542 Sum_probs=83.6
Q ss_pred CCHHHHHHHHHHHHHHhCCccccCCCCCCCCCCcccCCeechHHHHHHHHhhcCceeec-cCCCCHHHHHHhccCCcCCC
Q 007176 438 CSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVG-NGINWKGQVFSKMRNHTLTN 516 (614)
Q Consensus 438 ~~eeeFL~dL~kFhe~RGtp~liP~g~~s~fP~PvV~GK~LDLykLYk~V~sRGGF~kV-nkkkWkgEV~~~Mgn~~~p~ 516 (614)
.+.|+||+||+.||++||+++. +.|+|+|++||||.||.+|+++||+++| +++.|+ +|...+. ++.
T Consensus 162 ~~~eeF~~dl~~f~~~~~~~~~---------~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wr-ev~~~l~---~pt 228 (512)
T KOG2744|consen 162 KSSEEFMEDLRRFMKKRGTKVK---------SIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWR-EVIDGLN---FPT 228 (512)
T ss_pred ccHHHHHHHHHHHHHHhCCcce---------eccccCCCcchHHHHHHHHhcCCchhHhhhhhhHH-HHhcccc---CCC
Confidence 4889999999999999999965 2469999999999999999999999999 677899 9999886 677
Q ss_pred -ccccHHHHHHHHHHHhhhhhhcccc
Q 007176 517 -RMTGVGNTLKRHYETYLLEYELAHD 541 (614)
Q Consensus 517 -t~Tsag~~LK~hYERyLleYE~ahd 541 (614)
++|+++++||++|.|||++||..|.
T Consensus 229 ~tiTsaaf~lr~~y~K~L~~ye~~~~ 254 (512)
T KOG2744|consen 229 PTITSAAFTLRKQYLKLLFEYECEFE 254 (512)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999775
No 4
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=98.84 E-value=1.1e-08 Score=111.20 Aligned_cols=85 Identities=24% Similarity=0.398 Sum_probs=74.9
Q ss_pred CCCHHHHHHHHHHHHHHhCCccccCCCCCCCCCCcccCCeechHHHHHHHHhhcCceeeccCCCCHHHHHHhccCCcCCC
Q 007176 437 VCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTN 516 (614)
Q Consensus 437 ~~~eeeFL~dL~kFhe~RGtp~liP~g~~s~fP~PvV~GK~LDLykLYk~V~sRGGF~kVnkkkWkgEV~~~Mgn~~~p~ 516 (614)
....++.++.|+.|++.|.+++.. + |.++.|+||||+||..|+++||+..|++.+ + |++..++
T Consensus 291 qp~r~~wvDR~raF~ee~~Sp~t~-------~--p~~gakPldl~rlYvsvke~gg~~~v~knk-r-d~a~~lg------ 353 (532)
T KOG2510|consen 291 QPERKEWVDRLRAFTEERASPMTN-------L--PAVGAKPLDLYRLYVSVKEIGGLTQVNKNK-R-DLATNLG------ 353 (532)
T ss_pred CcchhhHHHHHHHHHHhhcCcccc-------c--ccccccchhHHHHHHHHHHhccceeeccch-h-hhhhccc------
Confidence 456788999999999999998533 2 589999999999999999999999998877 6 8888765
Q ss_pred ccccHHHHHHHHHHHhhhhhhccc
Q 007176 517 RMTGVGNTLKRHYETYLLEYELAH 540 (614)
Q Consensus 517 t~Tsag~~LK~hYERyLleYE~ah 540 (614)
.++++.||++|.+||+.||+..
T Consensus 354 --ssaa~~l~k~y~~~lf~fec~f 375 (532)
T KOG2510|consen 354 --SSAASSLKKQYIQYLFAFECKF 375 (532)
T ss_pred --hHHHHHHHHHHHHHHHhhceee
Confidence 5789999999999999999866
No 5
>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=98.40 E-value=6.4e-08 Score=74.43 Aligned_cols=49 Identities=27% Similarity=0.700 Sum_probs=37.5
Q ss_pred cccccCCC-CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCccc
Q 007176 547 CCLLCHSS-AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSV 600 (614)
Q Consensus 547 ~C~~C~~~-~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~ 600 (614)
+|..|+.. +++.||.||.|++|||..|+.++.. .....+ ..|.||.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~----~~~~~~-~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK----AEEIPS-GDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS----HHSHHS-SSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh----hccCCC-CcEECcCCcC
Confidence 48889886 4889999999999999999999852 111111 1699999964
No 6
>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 KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.95 E-value=3.2e-06 Score=86.58 Aligned_cols=51 Identities=33% Similarity=0.835 Sum_probs=43.5
Q ss_pred ccccccCCCCCCCeEecCC--CC-CccccCcccCCCCCcccCccccCCceeecCCcccccccCC
Q 007176 546 ECCLLCHSSAAGDWVNCGI--CG-EWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNFKKK 606 (614)
Q Consensus 546 ~~C~~C~~~~~~~wi~CD~--C~-~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~~k~ 606 (614)
..| .|...+.+.||.||. |. +|||+.|+.++. .+|+. |.||.|..+..++.
T Consensus 220 ~yC-~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~------~Pkgk---WyC~~C~~~~~~~~ 273 (274)
T KOG1973|consen 220 TYC-ICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKT------KPKGK---WYCPRCKAENKKKG 273 (274)
T ss_pred EEE-EecccccccccccCCCCCCcceEEEecccccc------CCCCc---ccchhhhhhhhccC
Confidence 455 466667899999999 99 999999998874 78887 99999999887764
No 8
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.52 E-value=3.7e-05 Score=88.04 Aligned_cols=50 Identities=18% Similarity=0.431 Sum_probs=42.3
Q ss_pred ccccccCCCC-CCCeEecCCCCCc-cccCcccCCCCCcccCccccCCceeecCCccccc
Q 007176 546 ECCLLCHSSA-AGDWVNCGICGEW-AHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTN 602 (614)
Q Consensus 546 ~~C~~C~~~~-~~~wi~CD~C~~w-yH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~ 602 (614)
.-|.+|+..+ ++.+|+||+|++- ||.+|+-+++. +.+.++ |.|++|+..+
T Consensus 216 ~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~----eiP~~e---WYC~NC~dL~ 267 (1134)
T KOG0825|consen 216 VKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLS----ESPVNE---WYCTNCSLLE 267 (1134)
T ss_pred ccceeeccCChHHhheeecccccceeeccccCcccc----cccccc---eecCcchhhh
Confidence 5799999998 8899999999999 99999999862 445554 9999998543
No 9
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.06 E-value=6e-05 Score=80.02 Aligned_cols=57 Identities=30% Similarity=0.548 Sum_probs=48.2
Q ss_pred ccccccccCCCC--CCCeEecCCCCCccccCcccCCCCCcccCccccCCc-e----eecCCcccccccCCC
Q 007176 544 DGECCLLCHSSA--AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGL-E----YVCPQCSVTNFKKKS 607 (614)
Q Consensus 544 d~~~C~~C~~~~--~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~-~----Y~CP~Cs~~~~~k~~ 607 (614)
.+++|..|+-++ ..+|++||.|+.|||+.|+.+. .++..++ . |+||+|...++.|+.
T Consensus 238 ~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~-------~a~~~~~~~~~~~~~c~~~~~~~~~k~~ 301 (345)
T KOG1632|consen 238 SKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIF-------EARKRLNEIRNEVYKCPHCTVLKFEKKR 301 (345)
T ss_pred ccccccccCcchHHHHHHHHHHHHHHHhcccccccc-------cchhhhhhhhccceecCceeecccchhh
Confidence 348999999863 5899999999999999999998 5666665 6 999999998887763
No 10
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.93 E-value=0.00031 Score=73.02 Aligned_cols=49 Identities=18% Similarity=0.430 Sum_probs=41.9
Q ss_pred ccccccCCC-CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 546 ECCLLCHSS-AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 546 ~~C~~C~~~-~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
..|-+||.+ +++.++-||-||+.||.+|+.|+. .+++.|- |.|.-|-.+
T Consensus 282 k~csicgtsenddqllfcddcdrgyhmyclsppm----~eppegs---wsc~KOG~~ 331 (336)
T KOG1244|consen 282 KYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPM----VEPPEGS---WSCHLCLEE 331 (336)
T ss_pred ceeccccCcCCCceeEeecccCCceeeEecCCCc----CCCCCCc---hhHHHHHHH
Confidence 468889888 488999999999999999999997 5788775 999998643
No 11
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.61 E-value=0.00086 Score=75.64 Aligned_cols=49 Identities=22% Similarity=0.540 Sum_probs=41.2
Q ss_pred ccccccCCCC-CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 546 ECCLLCHSSA-AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 546 ~~C~~C~~~~-~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
.+|-.|++.. --+.|+||+|.+.||+.|+.||+ .=.+.+.+. |.||.|.
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl--~~eniP~g~---W~C~ec~ 303 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPL--EPENIPPGS---WFCPECK 303 (613)
T ss_pred HHHHHhCCccccccceeecCCchHHHHhhcCCCC--CcccCCCCc---cccCCCe
Confidence 4999999885 46889999999999999999995 224667675 9999995
No 12
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.10 E-value=0.0026 Score=66.85 Aligned_cols=71 Identities=20% Similarity=0.516 Sum_probs=54.7
Q ss_pred ccccHHHHHHHHHHHhhhhhhccccccccccccccCCC-CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeec
Q 007176 517 RMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSS-AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVC 595 (614)
Q Consensus 517 t~Tsag~~LK~hYERyLleYE~ahdDed~~~C~~C~~~-~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~C 595 (614)
.|....-.|-..|..|.|.-- +-.+|.+|+.. .++-++-||.||+.||++|+.- ++.+.|+ |+|
T Consensus 292 ~Ci~M~~elv~~~KTY~W~C~------~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL------~~lP~G~---WIC 356 (381)
T KOG1512|consen 292 YCVAMIPELVGQYKTYFWKCS------SCELCRICLGPVIESEHLFCDVCDRGPHTLCVGL------QDLPRGE---WIC 356 (381)
T ss_pred cchhcCHHHHhHHhhcchhhc------ccHhhhccCCcccchheeccccccCCCCcccccc------ccccCcc---chh
Confidence 456666678888888877542 34679999888 4889999999999999999955 4678887 999
Q ss_pred C-Cccccc
Q 007176 596 P-QCSVTN 602 (614)
Q Consensus 596 P-~Cs~~~ 602 (614)
- .|..++
T Consensus 357 D~~C~~~~ 364 (381)
T KOG1512|consen 357 DMRCREAT 364 (381)
T ss_pred hhHHHHhc
Confidence 7 465443
No 13
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.63 E-value=0.0047 Score=68.71 Aligned_cols=50 Identities=22% Similarity=0.539 Sum_probs=42.3
Q ss_pred cccccccCCCC-CCCeEecCCCCCccccCcccCCCCCcccCccccCC-ceeecCCc
Q 007176 545 GECCLLCHSSA-AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDG-LEYVCPQC 598 (614)
Q Consensus 545 ~~~C~~C~~~~-~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg-~~Y~CP~C 598 (614)
.|.|++|..+. .-.++.||-|...||.+|+.||++ ..+|-.. --|.|-.|
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLT----R~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLT----RLPKKNKNFGWQCSEC 595 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccc----cCcccccCcceeeccc
Confidence 57999998885 669999999999999999999985 4555553 37999999
No 14
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=95.62 E-value=0.0051 Score=70.03 Aligned_cols=48 Identities=17% Similarity=0.545 Sum_probs=40.4
Q ss_pred ccccccCCC-CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCccc
Q 007176 546 ECCLLCHSS-AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSV 600 (614)
Q Consensus 546 ~~C~~C~~~-~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~ 600 (614)
..|..||.. +......|+.||..||.+|.+|++ +.+..+. |+|++|..
T Consensus 69 rvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~----~~v~sg~---~~ckk~~~ 117 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPN----DKVPSGP---WLCKKCTR 117 (694)
T ss_pred eeeeeccccCCcccccccccccccccccccCCcc----ccccCcc---cccHHHHh
Confidence 468888855 577889999999999999999997 5777776 99999963
No 15
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.34 E-value=0.0051 Score=75.59 Aligned_cols=52 Identities=21% Similarity=0.473 Sum_probs=45.6
Q ss_pred cccccccCCCC-CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccc
Q 007176 545 GECCLLCHSSA-AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF 603 (614)
Q Consensus 545 ~~~C~~C~~~~-~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~ 603 (614)
...|..|...+ ++.++.||.|..|||.+|+++.. ..++.++ |-||.|..+-.
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~----~~~~~~d---W~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPAL----SSVPPGD---WMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhh----ccCCcCC---ccCCccchhhh
Confidence 47999998875 77999999999999999999986 5788887 99999987663
No 16
>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=95.18 E-value=0.016 Score=63.75 Aligned_cols=53 Identities=28% Similarity=0.904 Sum_probs=36.9
Q ss_pred ccccCCC----CCCCeEecCCCCCccccCcccCCCC-CcccCccccCC---ceeecCCccc
Q 007176 548 CLLCHSS----AAGDWVNCGICGEWAHFGCDRRQGL-GAFKDYAKTDG---LEYVCPQCSV 600 (614)
Q Consensus 548 C~~C~~~----~~~~wi~CD~C~~wyH~~C~~~~~~-g~~kd~ak~eg---~~Y~CP~Cs~ 600 (614)
|.+|+.- +.-.||.||+|+-|-|.-|..+... |++....-+-| ++|.|-.|-.
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~ 191 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGK 191 (446)
T ss_pred ccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCC
Confidence 4445554 2459999999999999999999864 44433322222 3999999953
No 17
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=94.99 E-value=0.0083 Score=69.23 Aligned_cols=46 Identities=24% Similarity=0.652 Sum_probs=36.9
Q ss_pred cccccccCCCCCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 545 GECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 545 ~~~C~~C~~~~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
-..|.+|..+.+-.| ||.|-.|||.+|+.+++. +.+.++ |+|++|-
T Consensus 47 ~e~c~ic~~~g~~l~--c~tC~~s~h~~cl~~pl~----~~p~~~---~~c~Rc~ 92 (696)
T KOG0383|consen 47 QEACRICADGGELLW--CDTCPASFHASCLGPPLT----PQPNGE---FICPRCF 92 (696)
T ss_pred hhhhhhhcCCCcEEE--eccccHHHHHHccCCCCC----cCCccc---eeeeeec
Confidence 368999998865555 999999999999999973 444443 9999994
No 18
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=93.46 E-value=0.045 Score=56.83 Aligned_cols=42 Identities=33% Similarity=0.865 Sum_probs=36.4
Q ss_pred ccCCCCCCCeEecCC--CC-CccccCcccCCCCCcccCccccCCceeecCCccc
Q 007176 550 LCHSSAAGDWVNCGI--CG-EWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSV 600 (614)
Q Consensus 550 ~C~~~~~~~wi~CD~--C~-~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~ 600 (614)
-|...+.|.||.||+ |. +|||..|+.. |.+|||- |.||.|..
T Consensus 225 fCqqvSyGqMVaCDn~nCkrEWFH~~CVGL------k~pPKG~---WYC~eCk~ 269 (271)
T COG5034 225 FCQQVSYGQMVACDNANCKREWFHLECVGL------KEPPKGK---WYCPECKK 269 (271)
T ss_pred EecccccccceecCCCCCchhheecccccc------CCCCCCc---EeCHHhHh
Confidence 688899999999997 54 6999999966 5699997 99999964
No 19
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=92.59 E-value=0.11 Score=62.59 Aligned_cols=50 Identities=18% Similarity=0.436 Sum_probs=40.4
Q ss_pred cccccccccCCCC---CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 543 VDGECCLLCHSSA---AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 543 ed~~~C~~C~~~~---~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
+....|..|..+. -...+-||+|+..+|..|.-++- .+.+ +|-|-+|.-.
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~------ipeg---~WlCr~Cl~s 269 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPF------IPEG---QWLCRRCLQS 269 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCcchhhhhccCCCC------CCCC---cEeehhhccC
Confidence 4457999998874 37999999999999999998662 4555 4999999744
No 20
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=92.52 E-value=0.11 Score=61.45 Aligned_cols=60 Identities=23% Similarity=0.405 Sum_probs=47.8
Q ss_pred ccccccccccccCCCCCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccccCC
Q 007176 540 HDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNFKKK 606 (614)
Q Consensus 540 hdDed~~~C~~C~~~~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~~k~ 606 (614)
.+-.+...|..|..+.++..+.||+|++.||.+|..++. ...++++ |+|++|...+++++
T Consensus 150 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~---~~~~~~~~~~~~~~ 209 (904)
T KOG1246|consen 150 VEFIDYPQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPL----TRVPDGD---WRCPKCIPTPESKP 209 (904)
T ss_pred cccccchhhhccccCCCccceecccccCcccccccCCCC----CcCCcCc---ccCCcccccccCCc
Confidence 444567899999888644555999999999999999985 4555555 99999998877765
No 21
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=90.45 E-value=0.12 Score=57.59 Aligned_cols=50 Identities=28% Similarity=0.682 Sum_probs=37.4
Q ss_pred cccccCCC---CCCCeEecCCCCCccccCcccCCCCCcccCccccCCc-eeecCCccc
Q 007176 547 CCLLCHSS---AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGL-EYVCPQCSV 600 (614)
Q Consensus 547 ~C~~C~~~---~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~-~Y~CP~Cs~ 600 (614)
.|--|..+ .--.+|.||.|..|||.-|-.++- +|---+|-- +|.|-.|..
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i----~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLI----KDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeeecCCcCccceeeeecccccHHHHHhccCCC----CHhhccCccceEeehhhcc
Confidence 48888654 223999999999999999999985 333334433 899999964
No 22
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=89.55 E-value=0.21 Score=56.05 Aligned_cols=49 Identities=22% Similarity=0.489 Sum_probs=39.9
Q ss_pred ccccccCCCC---CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccc
Q 007176 546 ECCLLCHSSA---AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF 603 (614)
Q Consensus 546 ~~C~~C~~~~---~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~ 603 (614)
+.|..|.+.. ....+-||+|+-..|..|-.|+- .+.|- |-|-+|.-.+.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f------~peG~---WlCrkCi~~~~ 245 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQF------LPEGF---WLCRKCIYGEY 245 (669)
T ss_pred hhhHhccccccCCcceEEEecCcchhhhhhccccee------cCcch---hhhhhhccccc
Confidence 6778887663 47899999999999999999983 68775 99999975543
No 23
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=83.52 E-value=0.47 Score=50.99 Aligned_cols=37 Identities=27% Similarity=0.596 Sum_probs=29.1
Q ss_pred CeEecCCCCCccccCc--ccCCCCCcccCccccCCceeecCCccc
Q 007176 558 DWVNCGICGEWAHFGC--DRRQGLGAFKDYAKTDGLEYVCPQCSV 600 (614)
Q Consensus 558 ~wi~CD~C~~wyH~~C--~~~~~~g~~kd~ak~eg~~Y~CP~Cs~ 600 (614)
+++.||.|.+|||+.| +.++- ++.++- .+|+|..|.-
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~----~e~p~~--~~~~c~~c~~ 112 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAE----KEAPKE--DPKVCDECKE 112 (345)
T ss_pred hhhccccccccccccccccCchh----hcCCcc--ccccccccch
Confidence 9999999999999999 88873 233322 3899999963
No 24
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=82.87 E-value=0.68 Score=50.71 Aligned_cols=49 Identities=29% Similarity=0.635 Sum_probs=36.1
Q ss_pred ccccccCCC-C-CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccc
Q 007176 546 ECCLLCHSS-A-AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF 603 (614)
Q Consensus 546 ~~C~~C~~~-~-~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~ 603 (614)
..| .|+.+ + +++++.|+.|..|=|..|..+.. ....- .|.|..|...++
T Consensus 87 ~~c-~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~-----~~~p~---~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 87 SRC-DCGLEDDMEGLMIQCDWCGRWQHKICCGSFK-----STKPD---KYVCEICTPRNK 137 (508)
T ss_pred ccc-ccccccCCCceeeCCcccCcccCceeeeecC-----CCCch---hceeeeeccccc
Confidence 444 46655 5 78999999999999999997764 22212 499999975544
No 25
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=71.39 E-value=2.5 Score=49.88 Aligned_cols=67 Identities=21% Similarity=0.442 Sum_probs=48.0
Q ss_pred HHHHHHhhhhhhccc---------ccc-------ccccccccCCCC---CCCeEecCCCCCccccCcccCCCCCcccCcc
Q 007176 526 KRHYETYLLEYELAH---------DDV-------DGECCLLCHSSA---AGDWVNCGICGEWAHFGCDRRQGLGAFKDYA 586 (614)
Q Consensus 526 K~hYERyLleYE~ah---------dDe-------d~~~C~~C~~~~---~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~a 586 (614)
-..++|.|.|.|.-- +++ ..-.|-.|-++| ...|+-||.|.--.|..|-.|. +++.
T Consensus 236 ~~~~eRiieelE~~c~kqi~~~l~~eeglgie~dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIl-----e~p~ 310 (893)
T KOG0954|consen 236 EGTFERIIEELERRCKKQINHALETEEGLGIEYDEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGIL-----EVPE 310 (893)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhhhhcccceeeccccceeceecCCCccccceeEEeccchhHHHHhhhcee-----ecCC
Confidence 345677777777621 111 234799998885 4589999999999999999887 3333
Q ss_pred ccCCceeecCCcccc
Q 007176 587 KTDGLEYVCPQCSVT 601 (614)
Q Consensus 587 k~eg~~Y~CP~Cs~~ 601 (614)
+ .|.|-.|.-.
T Consensus 311 -g---pWlCr~Calg 321 (893)
T KOG0954|consen 311 -G---PWLCRTCALG 321 (893)
T ss_pred -C---Ceeehhcccc
Confidence 3 4999999765
No 26
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.91 E-value=3.2 Score=34.35 Aligned_cols=34 Identities=32% Similarity=0.621 Sum_probs=29.6
Q ss_pred cccccccCCC--CCCCeEecCCCCCccccCcccCCC
Q 007176 545 GECCLLCHSS--AAGDWVNCGICGEWAHFGCDRRQG 578 (614)
Q Consensus 545 ~~~C~~C~~~--~~~~wi~CD~C~~wyH~~C~~~~~ 578 (614)
+..|..|+.. +.++.+.|..|+--||..|-..-+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g 40 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAG 40 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCC
Confidence 5789999998 489999999999999999986653
No 27
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.69 E-value=3.6 Score=40.96 Aligned_cols=43 Identities=30% Similarity=0.679 Sum_probs=33.8
Q ss_pred cccccccCCCC------CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccc
Q 007176 545 GECCLLCHSSA------AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF 603 (614)
Q Consensus 545 ~~~C~~C~~~~------~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~ 603 (614)
+.+|..|++.+ .+.-+.|+.|.--||..|.... .||+|..-+-
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~----------------~CpkC~R~~~ 200 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK----------------SCPKCARRQK 200 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC----------------CCCCcHhHhc
Confidence 57899998762 4578899999999999998531 3999975543
No 28
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=67.78 E-value=1.6 Score=50.71 Aligned_cols=52 Identities=31% Similarity=0.576 Sum_probs=35.7
Q ss_pred cccccCCC---CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCccc-cccc
Q 007176 547 CCLLCHSS---AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSV-TNFK 604 (614)
Q Consensus 547 ~C~~C~~~---~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~-~~~~ 604 (614)
.|-+|++. .++.++-|--|+.-||.+|+..-.. -.+..++ |+||.|+. +.|.
T Consensus 20 mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~--~~~l~~g----WrC~~crvCe~c~ 75 (694)
T KOG4443|consen 20 MCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQ--HAVLSGG----WRCPSCRVCEACG 75 (694)
T ss_pred hhhhhccccccccCcchhhhhhcccCCcchhhHHHh--HHHhcCC----cccCCceeeeecc
Confidence 45566554 4889999999999999999985321 0112333 99999973 4443
No 29
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.04 E-value=1.8 Score=46.32 Aligned_cols=55 Identities=18% Similarity=0.387 Sum_probs=40.7
Q ss_pred ccccccCCC-------CCCCeEecCCCCCccccCcccCCC--CCcccCccccCCceeecCCcc-cccccCC
Q 007176 546 ECCLLCHSS-------AAGDWVNCGICGEWAHFGCDRRQG--LGAFKDYAKTDGLEYVCPQCS-VTNFKKK 606 (614)
Q Consensus 546 ~~C~~C~~~-------~~~~wi~CD~C~~wyH~~C~~~~~--~g~~kd~ak~eg~~Y~CP~Cs-~~~~~k~ 606 (614)
..|+.|-.+ ..+.||+|--|...||-+|+-.+- -|.+|-|. |.|-.|. -.-|.+|
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~------W~C~~C~lC~IC~~P 323 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYF------WKCSSCELCRICLGP 323 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcc------hhhcccHhhhccCCc
Confidence 579999543 378999999999999999986553 35556564 9999995 2334444
No 30
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=61.15 E-value=2 Score=32.32 Aligned_cols=33 Identities=18% Similarity=0.491 Sum_probs=17.9
Q ss_pred CeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCc
Q 007176 558 DWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQC 598 (614)
Q Consensus 558 ~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~C 598 (614)
.+|.|+.|+-.+|..|-.+.. .+.+ ..|.|-.|
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~------~~~~--~~W~C~~C 35 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSE------VPDG--DDWLCDRC 35 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS--------SS-------HHH
T ss_pred ceEEeCCCCCcCChhhCCccc------CCCC--CcEECCcC
Confidence 578999999999999998873 3333 24999777
No 31
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=61.12 E-value=1.9 Score=36.36 Aligned_cols=51 Identities=27% Similarity=0.375 Sum_probs=21.7
Q ss_pred cccccCCC----CCCCeEecC--CCCCccccCcccCCCCCcccCccccC----CceeecCCcccc
Q 007176 547 CCLLCHSS----AAGDWVNCG--ICGEWAHFGCDRRQGLGAFKDYAKTD----GLEYVCPQCSVT 601 (614)
Q Consensus 547 ~C~~C~~~----~~~~wi~CD--~C~~wyH~~C~~~~~~g~~kd~ak~e----g~~Y~CP~Cs~~ 601 (614)
-|++|.+. ++.-.+.|+ .|..-||..|+.--+ .+..+.. -+.-.||.|...
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf----~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWF----LSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHH----HHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHH----HHcccCCeeecccccCCcCCCCe
Confidence 49999765 233578998 999999999997643 2222221 136789999754
No 32
>PHA00689 hypothetical protein
Probab=59.63 E-value=5.6 Score=32.90 Aligned_cols=34 Identities=32% Similarity=0.617 Sum_probs=26.2
Q ss_pred Hhhhhhhcccccccc-ccccccCCC------CCCCeEecCC
Q 007176 531 TYLLEYELAHDDVDG-ECCLLCHSS------AAGDWVNCGI 564 (614)
Q Consensus 531 RyLleYE~ahdDed~-~~C~~C~~~------~~~~wi~CD~ 564 (614)
.|+.||++.||.+.. -.|.-|+.. +.+.|++=.+
T Consensus 2 tyfdeydqdhdqepravtckrcgktglrweddggewvlmeg 42 (62)
T PHA00689 2 TYFDEYDQDHDQEPRAVTCKRCGKTGLRWEDDGGEWVLMEG 42 (62)
T ss_pred ccccccccccccCcceeehhhccccCceeecCCCcEEEEec
Confidence 478999999998877 689999775 2457776544
No 33
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=58.57 E-value=2.1 Score=32.16 Aligned_cols=41 Identities=27% Similarity=0.592 Sum_probs=29.7
Q ss_pred cccccCCC--CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 547 CCLLCHSS--AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 547 ~C~~C~~~--~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
.|.+|... +.+..+... |+-.||..|...- .+.. +.||-|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~--------~~~~---~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEW--------LKRN---NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHH--------HHHS---SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHH--------HHhC---CcCCccC
Confidence 58999887 356777777 9999999998654 3332 6999884
No 34
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=54.77 E-value=18 Score=27.65 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=27.5
Q ss_pred HHHHHHHhhcCceeeccCCCCHHHHHHhccCCcCCCccccHHHHHHHHHHHhh
Q 007176 481 FNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYL 533 (614)
Q Consensus 481 ykLYk~V~sRGGF~kVnkkkWkgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyL 533 (614)
-.|...|...|.- +|. .|...|+ ++ -.+.+++.+|.+||
T Consensus 10 ~~l~~~v~~~g~~------~W~-~Ia~~~~----~~---Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 10 EKLLEAVKKYGKD------NWK-KIAKRMP----GG---RTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSTTT------HHH-HHHHHHS----SS---STHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCc------HHH-HHHHHcC----CC---CCHHHHHHHHHhhC
Confidence 3456666655532 799 9999886 12 23779999999986
No 35
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=53.89 E-value=10 Score=30.41 Aligned_cols=43 Identities=28% Similarity=0.464 Sum_probs=29.6
Q ss_pred HHHHHHhhhh-hhccccccccccccccCCC----------CCCCeEecCCCCCc
Q 007176 526 KRHYETYLLE-YELAHDDVDGECCLLCHSS----------AAGDWVNCGICGEW 568 (614)
Q Consensus 526 K~hYERyLle-YE~ahdDed~~~C~~C~~~----------~~~~wi~CD~C~~w 568 (614)
.+.|++.... ...+--.++...|..|+-. ..+..+-|+.|++.
T Consensus 2 L~~Y~rl~~~~~g~~va~v~~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 2 LAEYERLRKRKGGVAVARVEGGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHHHHhhcCCcEEEEeeCCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 4567766655 3444445667799999764 24688999999874
No 36
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=51.96 E-value=6 Score=42.80 Aligned_cols=22 Identities=36% Similarity=1.028 Sum_probs=18.8
Q ss_pred CCCeEecCCCCCccc-cCcccCC
Q 007176 556 AGDWVNCGICGEWAH-FGCDRRQ 577 (614)
Q Consensus 556 ~~~wi~CD~C~~wyH-~~C~~~~ 577 (614)
++-++.|-+|++||| .+|..-.
T Consensus 145 e~~m~QC~iCEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 145 EGEMLQCVICEDWFHCEGCMQAK 167 (345)
T ss_pred cceeeeEEeccchhcccccCccc
Confidence 679999999999999 8886544
No 37
>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=47.96 E-value=7.7 Score=30.82 Aligned_cols=16 Identities=31% Similarity=1.005 Sum_probs=9.5
Q ss_pred CCeEecCCCCCccccC
Q 007176 557 GDWVNCGICGEWAHFG 572 (614)
Q Consensus 557 ~~wi~CD~C~~wyH~~ 572 (614)
+.|+.||.|.+|..--
T Consensus 1 ~~WVQCd~C~KWR~lp 16 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLP 16 (50)
T ss_dssp -EEEE-TTT--EEEE-
T ss_pred CeEEECCCCCceeeCC
Confidence 3699999999998643
No 38
>PHA02926 zinc finger-like protein; Provisional
Probab=47.46 E-value=6.7 Score=40.78 Aligned_cols=67 Identities=16% Similarity=0.213 Sum_probs=42.4
Q ss_pred HHhhhhhhccccccccccccccCCCC-------CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 530 ETYLLEYELAHDDVDGECCLLCHSSA-------AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 530 ERyLleYE~ahdDed~~~C~~C~~~~-------~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
-+.|.+||..+.-.....|++|-..- +-.--.=+.|+-.|...|.+.=. +..+..+....||-|+..
T Consensus 155 ~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr-----~~r~~~~~~rsCPiCR~~ 228 (242)
T PHA02926 155 IKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWH-----RTRRETGASDNCPICRTR 228 (242)
T ss_pred hHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHH-----HhccccCcCCcCCCCcce
Confidence 56789999888665557899997641 11111224677778888876542 111223456789999854
No 39
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=47.36 E-value=12 Score=40.54 Aligned_cols=41 Identities=32% Similarity=0.668 Sum_probs=29.1
Q ss_pred CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccccccCCC
Q 007176 556 AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNFKKKS 607 (614)
Q Consensus 556 ~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~~k~~ 607 (614)
.-.-+.|..|. .|-+|.... ++ +-|.|+||.|-+.+--||+
T Consensus 217 ~ryALIC~~C~--~HNGla~~e------e~---~yi~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 217 NRYALICSQCH--HHNGLARKE------EY---EYITFRCPHCNALNPAKKS 257 (328)
T ss_pred chhhhcchhhc--cccCcCChh------hc---CceEEECccccccCCCcCC
Confidence 33455666664 699999774 23 5567999999888777665
No 40
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=45.70 E-value=16 Score=30.57 Aligned_cols=36 Identities=25% Similarity=0.833 Sum_probs=22.3
Q ss_pred CCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 557 GDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 557 ~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
+.||.|-.|+.---.+=-.-| .-++.+ ..||+|..+
T Consensus 2 ~~Wi~CP~CgnKTR~kir~DT---~LkNfP------lyCpKCK~E 37 (55)
T PF14205_consen 2 SEWILCPICGNKTRLKIREDT---VLKNFP------LYCPKCKQE 37 (55)
T ss_pred CeEEECCCCCCccceeeecCc---eecccc------ccCCCCCce
Confidence 469999999964433222222 224454 789999754
No 41
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.74 E-value=9.3 Score=40.85 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=22.7
Q ss_pred CCCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 554 SAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 554 ~~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
-.++.|..|+.|++-.+.+=+ .+. .|+||+|.
T Consensus 33 ~p~~lw~kc~~C~~~~~~~~l-----------~~~---~~vcp~c~ 64 (296)
T CHL00174 33 KYKHLWVQCENCYGLNYKKFL-----------KSK---MNICEQCG 64 (296)
T ss_pred CCCCCeeECCCccchhhHHHH-----------HHc---CCCCCCCC
Confidence 457899999999987654332 222 38999994
No 42
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=42.72 E-value=9.1 Score=40.48 Aligned_cols=31 Identities=29% Similarity=0.651 Sum_probs=20.6
Q ss_pred CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 555 AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 555 ~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
.++.|..|+.|++-.+.+=+ .+ ..|+||+|.
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l-----------~~---~~~vc~~c~ 52 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKEL-----------ER---NLEVCPKCD 52 (285)
T ss_pred CCCCeeECCCCcchhhHHHH-----------Hh---hCCCCCCCC
Confidence 35689999999887654322 11 138899984
No 43
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.59 E-value=25 Score=29.72 Aligned_cols=46 Identities=26% Similarity=0.650 Sum_probs=30.3
Q ss_pred ccccccccCCC-C--C-CCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 544 DGECCLLCHSS-A--A-GDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 544 d~~~C~~C~~~-~--~-~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
....|-+|+.. . + .....|-.||+--=..|-+=- ..+..|+||+|-
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CR----------k~~~~Y~CP~CG 55 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCR----------KQSNPYTCPKCG 55 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHH----------hcCCceECCCCC
Confidence 34679999886 2 3 678899999875344454321 123459999994
No 44
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=42.58 E-value=12 Score=43.31 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=24.9
Q ss_pred cccccccCCCC------CCCeEecCCCCCccccCcccCC
Q 007176 545 GECCLLCHSSA------AGDWVNCGICGEWAHFGCDRRQ 577 (614)
Q Consensus 545 ~~~C~~C~~~~------~~~wi~CD~C~~wyH~~C~~~~ 577 (614)
+.+|.+|..++ .+.-.-|+.|+-+||-+|.++-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~ 549 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK 549 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc
Confidence 45777774432 3345899999999999999886
No 45
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=42.30 E-value=17 Score=45.10 Aligned_cols=45 Identities=24% Similarity=0.676 Sum_probs=37.2
Q ss_pred ccccccCCCCCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 546 ECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 546 ~~C~~C~~~~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
+.|..||. .++.+||..|.+-||..|+.+|.. +.++++ |-|--|.
T Consensus 345 dhcrf~~d--~~~~lc~Et~prvvhlEcv~hP~~----~~~s~~---~e~evc~ 389 (1414)
T KOG1473|consen 345 DHCRFCHD--LGDLLCCETCPRVVHLECVFHPRF----AVPSAF---WECEVCN 389 (1414)
T ss_pred ccccccCc--ccceeecccCCceEEeeecCCccc----cCCCcc---chhhhhh
Confidence 46999985 478999999999999999999973 566665 8887775
No 46
>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=41.55 E-value=11 Score=26.76 Aligned_cols=28 Identities=25% Similarity=0.487 Sum_probs=12.3
Q ss_pred cccccCCCCCC-CeEecCCCCCccccCcc
Q 007176 547 CCLLCHSSAAG-DWVNCGICGEWAHFGCD 574 (614)
Q Consensus 547 ~C~~C~~~~~~-~wi~CD~C~~wyH~~C~ 574 (614)
.|..|+....+ .+-.|..|+=..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 48888887655 88899999999998873
No 47
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=41.43 E-value=21 Score=41.55 Aligned_cols=48 Identities=27% Similarity=0.627 Sum_probs=36.5
Q ss_pred cccccccCCCCCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCccc
Q 007176 545 GECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSV 600 (614)
Q Consensus 545 ~~~C~~C~~~~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~ 600 (614)
.+.|++|.++ +..++|+.|...+|..|++..+. +|..- -++.|-.|..
T Consensus 47 ~ts~~~~~~~--gn~~~~~~~~~s~h~~~~~~~~s---p~~~~---~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSG--GNLLCCDHCPASFHLECDKPPLS---PDLKG---SEINCSRCPK 94 (613)
T ss_pred hhhcchhhhc--CCccccccCccccchhccCcccC---ccccc---ccccccCCCc
Confidence 4679999776 56789999999999999999974 33322 2578877753
No 48
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=39.68 E-value=11 Score=40.06 Aligned_cols=31 Identities=29% Similarity=0.611 Sum_probs=21.1
Q ss_pred CCCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 555 AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 555 ~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
.++.|+.|+.|+.-.+.+=+ .+ ..|+||+|-
T Consensus 23 ~~~~~~~c~~c~~~~~~~~l-----------~~---~~~vc~~c~ 53 (292)
T PRK05654 23 PEGLWTKCPSCGQVLYRKEL-----------EA---NLNVCPKCG 53 (292)
T ss_pred CCCCeeECCCccchhhHHHH-----------Hh---cCCCCCCCC
Confidence 36789999999987665322 21 137999994
No 49
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=39.14 E-value=26 Score=37.12 Aligned_cols=63 Identities=22% Similarity=0.436 Sum_probs=41.5
Q ss_pred HHHHhhhhhhcccccc-----ccccccccCCC------CCCCeEecCCCCCccccCcccCCCCCcccCccccCCc-eeec
Q 007176 528 HYETYLLEYELAHDDV-----DGECCLLCHSS------AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGL-EYVC 595 (614)
Q Consensus 528 hYERyLleYE~ahdDe-----d~~~C~~C~~~------~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~-~Y~C 595 (614)
.-|++|.-|..++++. -..-|..|--. .------|..|.+-| +.+|. .|--|+ +|.|
T Consensus 90 LTe~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rY----DPVP~-------dkmwG~aef~C 158 (278)
T PF15135_consen 90 LTEENLRMFDDAQENLIPSVDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRY----DPVPC-------DKMWGIAEFHC 158 (278)
T ss_pred chHHHHHHhhhhhhccccccceeeeccccchHHHhccCccccccccccccccc----CCCcc-------ccccceeeeec
Confidence 3477888888888774 23689999332 122334699998887 45552 344455 7999
Q ss_pred CCcccc
Q 007176 596 PQCSVT 601 (614)
Q Consensus 596 P~Cs~~ 601 (614)
|+|...
T Consensus 159 ~~C~h~ 164 (278)
T PF15135_consen 159 PKCRHN 164 (278)
T ss_pred cccccc
Confidence 999644
No 50
>PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed
Probab=38.96 E-value=11 Score=37.75 Aligned_cols=76 Identities=13% Similarity=0.162 Sum_probs=53.1
Q ss_pred CCCcccccccCCceEEEEEeehhhHHHHHHHhcCCCCchhhhhhhhhhcCCccccccchhhHHHHHhhhhccCCCCCCCC
Q 007176 230 EPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADHTEN 309 (614)
Q Consensus 230 epr~S~siA~Gasv~ev~~~~p~Wa~qvLrqLa~~~sYrsLvaLGia~v~g~~vasF~~~Da~rll~~~~~~~~~~~~~~ 309 (614)
.+.--+.++.|..++|+.++.|.|.. .|+.|+.+ |...+.+|.+.| ++.+|++..+- -+
T Consensus 25 ~~~~~a~~~gGi~~iEvt~~~~~~~~-~i~~l~~~--~~~~~~iGaGTV-------~~~~~~~~a~~-----------aG 83 (206)
T PRK09140 25 LAHVGALIEAGFRAIEIPLNSPDPFD-SIAALVKA--LGDRALIGAGTV-------LSPEQVDRLAD-----------AG 83 (206)
T ss_pred HHHHHHHHHCCCCEEEEeCCCccHHH-HHHHHHHH--cCCCcEEeEEec-------CCHHHHHHHHH-----------cC
Confidence 34455789999999999999999775 88888765 544578898887 56777776633 23
Q ss_pred CccCCCCCCCCCCCcCc
Q 007176 310 SVLTRPPSWLTSPAPSR 326 (614)
Q Consensus 310 ~~~~~~p~w~~~p~~~r 326 (614)
.-+.+.|.+.......+
T Consensus 84 A~fivsp~~~~~v~~~~ 100 (206)
T PRK09140 84 GRLIVTPNTDPEVIRRA 100 (206)
T ss_pred CCEEECCCCCHHHHHHH
Confidence 34556666655444443
No 51
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=38.10 E-value=13 Score=31.58 Aligned_cols=18 Identities=22% Similarity=0.824 Sum_probs=14.1
Q ss_pred eecCCcccccccCCCCCC
Q 007176 593 YVCPQCSVTNFKKKSQKT 610 (614)
Q Consensus 593 Y~CP~Cs~~~~~k~~~~~ 610 (614)
|+||+|-++++..+..+.
T Consensus 1 y~C~KCg~~~~e~~~v~~ 18 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRA 18 (64)
T ss_pred CCCCCCCCcceecceEEc
Confidence 899999999887775443
No 52
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=37.55 E-value=21 Score=41.08 Aligned_cols=54 Identities=22% Similarity=0.483 Sum_probs=34.5
Q ss_pred ccccccCCC---CCCCeEecCCCCCccccCcccCCCCCcccCccccCCc-eeecCCcc
Q 007176 546 ECCLLCHSS---AAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGL-EYVCPQCS 599 (614)
Q Consensus 546 ~~C~~C~~~---~~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~-~Y~CP~Cs 599 (614)
-.|..|-+. +.+..|.||.||-..|.+|-.....-....-+-.+++ -|-|-.|.
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence 379999443 6889999999999999999744310000001111222 69998885
No 53
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=36.03 E-value=17 Score=43.17 Aligned_cols=47 Identities=21% Similarity=0.509 Sum_probs=37.6
Q ss_pred ccccCCC---CCCCeEecCC--CCCccccCcccCCCCCcccCccccCCceeecCCcccccc
Q 007176 548 CLLCHSS---AAGDWVNCGI--CGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF 603 (614)
Q Consensus 548 C~~C~~~---~~~~wi~CD~--C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~~~ 603 (614)
|=.|... +|--+|-||| |.--+|..|--|. .++.|. |.|-||-..|.
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv------qVPtGp---WfCrKCesqer 59 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV------QVPTGP---WFCRKCESQER 59 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeE------ecCCCc---hhhhhhhhhhh
Confidence 4457543 5778999997 9999999999886 588887 99999965554
No 54
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=34.77 E-value=66 Score=27.55 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=22.1
Q ss_pred cccccccCCC--CCCCeEecCCCCCccccCcccC
Q 007176 545 GECCLLCHSS--AAGDWVNCGICGEWAHFGCDRR 576 (614)
Q Consensus 545 ~~~C~~C~~~--~~~~wi~CD~C~~wyH~~C~~~ 576 (614)
...|..|+.. ..-|.+..+ +.-||..|.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~--~~v~H~~C~~r 109 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPC--GHVVHYSCIKR 109 (109)
T ss_pred CCCccCcCCcCCCceEEEeCC--CeEEecccccC
Confidence 4689999987 344555544 58899999865
No 55
>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=34.15 E-value=28 Score=28.21 Aligned_cols=36 Identities=33% Similarity=0.751 Sum_probs=20.0
Q ss_pred ecCCCCCccccC-cc----cCCCCCcccCccccCCceeecCCcccc
Q 007176 561 NCGICGEWAHFG-CD----RRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 561 ~CD~C~~wyH~~-C~----~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
.|.+|+--|.-. -+ ++++. .|.|.+. .|+||.|.+.
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt-~f~~Lp~----~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGT-PFEDLPD----DWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCC-CHhHCCC----CCCCCCCCCc
Confidence 366676555532 11 22322 4555553 5999999754
No 56
>PF13712 Glyco_tranf_2_5: Glycosyltransferase like family; PDB: 2QGI_A 2NXV_B.
Probab=32.75 E-value=26 Score=35.11 Aligned_cols=90 Identities=18% Similarity=0.277 Sum_probs=48.0
Q ss_pred EEEeecCcccccchHHHHHHHHHHHhhccceEEeecCCCCCCCCCCCCCcccccccCCc--eE---EEEEeehhhHHHHH
Q 007176 184 SLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPPSEPRKSASIACGAS--VF---EVSMKVSTWASQVL 258 (614)
Q Consensus 184 sllvsgs~qtcf~d~llE~~ik~elie~~q~v~~~~~~e~~~~~~~epr~S~siA~Gas--v~---ev~~~~p~Wa~qvL 258 (614)
|+++-=+-+.-|+. +++ +|++..+-+..+|.++.... ..+.++----+.=.+-+- || ||.+.-+.|..++|
T Consensus 2 siI~c~n~~~~~~~-~~~-~i~~~~~~~~~~i~i~~~~~--~~s~~~~yN~a~~~a~~~ylvflHqDv~i~~~~~l~~il 77 (217)
T PF13712_consen 2 SIIICVNDEELYEE-CLR-SIKRLIGPPGELIEIDNVRN--AKSMAAAYNEAMEKAKAKYLVFLHQDVFIINENWLEDIL 77 (217)
T ss_dssp EEEEEES-HHHHHH-HHH-HHHHTT--TEEEEEEE-SSS---S-TTTHHHHHGGG--SSEEEEEETTEE-SSHHHHHHHH
T ss_pred EEEEEECCHHHHHH-HHH-HHHhhCCCCceEEEEeccCC--CcCHHHHHHHHHHhCCCCEEEEEeCCeEEcchhHHHHHH
Confidence 44433333444444 555 58888888888888865544 233333333333334444 33 78888899999999
Q ss_pred HHhcCCCCchhhhhhhhhhcCC
Q 007176 259 RQLAPDVSYRSLVMLGIASIQG 280 (614)
Q Consensus 259 rqLa~~~sYrsLvaLGia~v~g 280 (614)
+.|..+. .+-++|+||...
T Consensus 78 ~~~~~~~---~~G~iGvaG~~~ 96 (217)
T PF13712_consen 78 EIFEEDP---NIGMIGVAGSKR 96 (217)
T ss_dssp HHHHH-T---TEEEEESEEEES
T ss_pred HHHhhCC---CccEEEeecCCc
Confidence 9997664 344445555443
No 57
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=32.44 E-value=55 Score=29.38 Aligned_cols=61 Identities=18% Similarity=0.346 Sum_probs=38.1
Q ss_pred CCHHHHHHhccCCcCCCccccHHHHHHHHHHHhhhhhhccccccccccccccCCCCCCCeEecCCCCCc
Q 007176 500 NWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEW 568 (614)
Q Consensus 500 kWkgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyLleYE~ahdDed~~~C~~C~~~~~~~wi~CD~C~~w 568 (614)
.++ ++...|. ....++-..+.+.++++...|....++.+...|..||....+. .|-.|.-|
T Consensus 41 ~~k-~~L~~LE-----~~~P~~k~~i~~s~~~~~~~~~~~~~~~~~~~C~~CG~pss~~--iC~~C~l~ 101 (104)
T TIGR00269 41 RIR-DFLYDLE-----NKKPGVKFSVLRGFEKLIPLLKELSEQEDLRRCERCGEPTSGR--ICKACKFL 101 (104)
T ss_pred HHH-HHHHHHH-----HHCcChHHHHHHHHHHHHHHhhcccccccCCcCCcCcCcCCcc--ccHhhhhh
Confidence 466 7777765 2334566677777776665554333334567899999886554 57777543
No 58
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=32.38 E-value=45 Score=33.51 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=25.7
Q ss_pred cccccCC---C-CCCCeEecCCCCCccccCcccCC
Q 007176 547 CCLLCHS---S-AAGDWVNCGICGEWAHFGCDRRQ 577 (614)
Q Consensus 547 ~C~~C~~---~-~~~~wi~CD~C~~wyH~~C~~~~ 577 (614)
.|..|+. + .-|-+|-|-||-..||-.|+.+-
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~R 35 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPR 35 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCc
Confidence 4888853 2 36899999999999999999765
No 59
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.48 E-value=36 Score=32.28 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=21.5
Q ss_pred cHHHHHHHHHHHhhhhhhccccc---cccccccccCCC
Q 007176 520 GVGNTLKRHYETYLLEYELAHDD---VDGECCLLCHSS 554 (614)
Q Consensus 520 sag~~LK~hYERyLleYE~ahdD---ed~~~C~~C~~~ 554 (614)
.+-..+|.-..+.+...+..-+. ...+.|..|+..
T Consensus 71 ~~~~vik~r~~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~ 108 (147)
T smart00531 71 TLLDVVKYKLDKMRKRLEDKLEDETNNAYYKCPNCQSK 108 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcEEECcCCCCE
Confidence 45667777777776666544322 234788888764
No 60
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=31.47 E-value=6.5 Score=40.64 Aligned_cols=74 Identities=23% Similarity=0.435 Sum_probs=51.9
Q ss_pred HHHhhhhhhccccccccccccccCCC-CCC-------------CeEecCCCCCccccCcccCCC----CCcccCccccCC
Q 007176 529 YETYLLEYELAHDDVDGECCLLCHSS-AAG-------------DWVNCGICGEWAHFGCDRRQG----LGAFKDYAKTDG 590 (614)
Q Consensus 529 YERyLleYE~ahdDed~~~C~~C~~~-~~~-------------~wi~CD~C~~wyH~~C~~~~~----~g~~kd~ak~eg 590 (614)
|+|.|..--..|.|+-.++|..||-+ .+. .---|..|++.|-..|-.-.- +|.-..||-.|.
T Consensus 129 lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayker 208 (267)
T KOG3576|consen 129 LQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKER 208 (267)
T ss_pred HHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHh
Confidence 45666666678999888999999887 232 234699999999999964321 455555665554
Q ss_pred c--eeecCCccccc
Q 007176 591 L--EYVCPQCSVTN 602 (614)
Q Consensus 591 ~--~Y~CP~Cs~~~ 602 (614)
. -|+|..|--..
T Consensus 209 r~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 209 RAKLYVCEDCGYTS 222 (267)
T ss_pred hhheeeecccCCCC
Confidence 4 79999996443
No 61
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=31.35 E-value=22 Score=32.54 Aligned_cols=57 Identities=25% Similarity=0.549 Sum_probs=35.5
Q ss_pred cccccccccccCCCCCCCeEec------CCC---CCccccCcccCCCCCcccCcccc-CCceeecCCccc
Q 007176 541 DDVDGECCLLCHSSAAGDWVNC------GIC---GEWAHFGCDRRQGLGAFKDYAKT-DGLEYVCPQCSV 600 (614)
Q Consensus 541 dDed~~~C~~C~~~~~~~wi~C------D~C---~~wyH~~C~~~~~~g~~kd~ak~-eg~~Y~CP~Cs~ 600 (614)
|.+-+..|..|..-..++-..| ..| ..-|=+.|+..-- | .++... +..+|+||+|..
T Consensus 3 d~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ry-g--e~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRY-G--ENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cCCCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHH-h--hhHHHHhcCCceECCCCCC
Confidence 4555688999987665555566 666 8888888876541 0 111100 123699999973
No 62
>PRK11823 DNA repair protein RadA; Provisional
Probab=30.83 E-value=29 Score=38.48 Aligned_cols=28 Identities=21% Similarity=0.579 Sum_probs=24.4
Q ss_pred ccccccccCCCCCCCeEecCCCCCcccc
Q 007176 544 DGECCLLCHSSAAGDWVNCGICGEWAHF 571 (614)
Q Consensus 544 d~~~C~~C~~~~~~~wi~CD~C~~wyH~ 571 (614)
..|.|..||-.....|-.|..|+.|=-.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~ 33 (446)
T PRK11823 6 TAYVCQECGAESPKWLGRCPECGAWNTL 33 (446)
T ss_pred CeEECCcCCCCCcccCeeCcCCCCccce
Confidence 4589999999999999999999999544
No 63
>PHA02929 N1R/p28-like protein; Provisional
Probab=30.80 E-value=30 Score=36.00 Aligned_cols=64 Identities=19% Similarity=0.312 Sum_probs=41.4
Q ss_pred HHHHhhhhhhccccccccccccccCCCC--CC----CeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 528 HYETYLLEYELAHDDVDGECCLLCHSSA--AG----DWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 528 hYERyLleYE~ahdDed~~~C~~C~~~~--~~----~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
..-+.|.+||...+......|..|...- .+ ....=..|+-.||..|...-+ +. +=.||-|+..
T Consensus 157 ~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl--------~~---~~tCPlCR~~ 225 (238)
T PHA02929 157 TIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWK--------KE---KNTCPVCRTP 225 (238)
T ss_pred hcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHH--------hc---CCCCCCCCCE
Confidence 3344667888776665567899998862 21 112224788899999986642 11 2379999865
Q ss_pred c
Q 007176 602 N 602 (614)
Q Consensus 602 ~ 602 (614)
-
T Consensus 226 ~ 226 (238)
T PHA02929 226 F 226 (238)
T ss_pred e
Confidence 3
No 64
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=29.83 E-value=22 Score=38.17 Aligned_cols=30 Identities=33% Similarity=0.698 Sum_probs=22.9
Q ss_pred CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 556 AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 556 ~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
++.|+-|..|+.--|.+=+ +...|+||+|.
T Consensus 25 e~lw~KCp~c~~~~y~~eL--------------~~n~~vcp~c~ 54 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKEL--------------ESNLKVCPKCG 54 (294)
T ss_pred CCceeECCCccceeeHHHH--------------HhhhhcccccC
Confidence 7899999999988765433 22249999995
No 65
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=29.08 E-value=90 Score=21.98 Aligned_cols=37 Identities=16% Similarity=0.349 Sum_probs=25.2
Q ss_pred HHHHHHhhcCceeeccCCCCHHHHHHhccCCcCCCccccHHHHHHHHHHHhh
Q 007176 482 NLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYL 533 (614)
Q Consensus 482 kLYk~V~sRGGF~kVnkkkWkgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyL 533 (614)
.|.+.|...|- .+|. .|+..|++ -.+..++++|.+++
T Consensus 9 ~l~~~~~~~g~------~~w~-~Ia~~~~~--------rs~~~~~~~~~~~~ 45 (45)
T cd00167 9 LLLEAVKKYGK------NNWE-KIAKELPG--------RTPKQCRERWRNLL 45 (45)
T ss_pred HHHHHHHHHCc------CCHH-HHHhHcCC--------CCHHHHHHHHHHhC
Confidence 35555555552 6799 99998862 23678899988764
No 66
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=28.31 E-value=37 Score=37.03 Aligned_cols=28 Identities=25% Similarity=0.491 Sum_probs=24.2
Q ss_pred ccccccCCCCCCCeEecCCCCCccccCc
Q 007176 546 ECCLLCHSSAAGDWVNCGICGEWAHFGC 573 (614)
Q Consensus 546 ~~C~~C~~~~~~~wi~CD~C~~wyH~~C 573 (614)
|.|..||-....-|-.|..|+.|=-..=
T Consensus 1 ~~c~~cg~~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCCccEECcCCCCceeeee
Confidence 5799999999888999999999966544
No 67
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=26.64 E-value=75 Score=30.59 Aligned_cols=38 Identities=24% Similarity=0.492 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhhhccccccccccccccCCCC-----C--CCeEecCCCCCcc
Q 007176 523 NTLKRHYETYLLEYELAHDDVDGECCLLCHSSA-----A--GDWVNCGICGEWA 569 (614)
Q Consensus 523 ~~LK~hYERyLleYE~ahdDed~~~C~~C~~~~-----~--~~wi~CD~C~~wy 569 (614)
..+.+...+|+.+|= .|..|++.+ + -..+.|+.||-..
T Consensus 89 ~~i~~~L~~yI~~yV---------lC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 89 RVINEKIDRYVKEYV---------ICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred HHHHHHHHHHHHhcE---------ECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 466777777777775 499999973 2 3678999999754
No 68
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=26.29 E-value=34 Score=30.25 Aligned_cols=33 Identities=30% Similarity=0.700 Sum_probs=29.1
Q ss_pred cccccccCCCCCCCeEecCC--CCCccccCcccCCC
Q 007176 545 GECCLLCHSSAAGDWVNCGI--CGEWAHFGCDRRQG 578 (614)
Q Consensus 545 ~~~C~~C~~~~~~~wi~CD~--C~~wyH~~C~~~~~ 578 (614)
...|..|+.. .|..+.|.. |..+||-.|....+
T Consensus 55 ~~~C~iC~~~-~G~~i~C~~~~C~~~fH~~CA~~~g 89 (110)
T PF13832_consen 55 KLKCSICGKS-GGACIKCSHPGCSTAFHPTCARKAG 89 (110)
T ss_pred CCcCcCCCCC-CceeEEcCCCCCCcCCCHHHHHHCC
Confidence 4689999987 677999999 99999999998875
No 69
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=26.28 E-value=6.4 Score=32.62 Aligned_cols=33 Identities=33% Similarity=0.766 Sum_probs=26.8
Q ss_pred cccccccCCCC-CCCeEecCCCCCccccCcccCC
Q 007176 545 GECCLLCHSSA-AGDWVNCGICGEWAHFGCDRRQ 577 (614)
Q Consensus 545 ~~~C~~C~~~~-~~~wi~CD~C~~wyH~~C~~~~ 577 (614)
.+.|-+|++.. -..+-.|-+|++|.-..|-.-.
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 37899999884 5678899999999988887443
No 70
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=25.50 E-value=42 Score=23.82 Aligned_cols=11 Identities=27% Similarity=1.141 Sum_probs=8.8
Q ss_pred CCceeecCCcc
Q 007176 589 DGLEYVCPQCS 599 (614)
Q Consensus 589 eg~~Y~CP~Cs 599 (614)
.+..|.||+|-
T Consensus 13 ~~v~f~CPnCG 23 (24)
T PF07754_consen 13 QAVPFPCPNCG 23 (24)
T ss_pred cCceEeCCCCC
Confidence 36689999993
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=25.37 E-value=56 Score=27.94 Aligned_cols=45 Identities=27% Similarity=0.653 Sum_probs=31.5
Q ss_pred cccccccCCC---C-CCCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 545 GECCLLCHSS---A-AGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 545 ~~~C~~C~~~---~-~~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
...|-+|+.. . -..-..|-.|++--=..|.+=-. -|..|+||+|-
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk----------~g~~Y~Cp~CG 57 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRK----------LGNPYRCPKCG 57 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHH----------cCCceECCCcC
Confidence 4689999886 2 34667899999877677765432 22359999994
No 72
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=24.64 E-value=1.4e+02 Score=24.60 Aligned_cols=45 Identities=24% Similarity=0.564 Sum_probs=28.1
Q ss_pred hHHHHHHHHh-hcCceeeccCCCC---HHHHHHhccCCcCCCccccHHHHHHHHHHHhhhhh
Q 007176 479 DLFNLYREVV-SRGGFHVGNGINW---KGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEY 536 (614)
Q Consensus 479 DLykLYk~V~-sRGGF~kVnkkkW---kgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyLleY 536 (614)
|++.+|-+.. ..|+ .+| + .|.+.|+ .+. . ...+++.|++||.+.+
T Consensus 9 eeh~~Fl~ai~~~G~------g~~a~pk-~I~~~~~---~~~-l--T~~qV~SH~QKy~~k~ 57 (57)
T TIGR01557 9 DLHDRFLQAVQKLGG------PDWATPK-RILELMV---VDG-L--TRDQVASHLQKYRLKQ 57 (57)
T ss_pred HHHHHHHHHHHHhCC------CcccchH-HHHHHcC---CCC-C--CHHHHHHHHHHHHccC
Confidence 4555665543 2222 357 7 8888886 221 1 3679999999998653
No 73
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=24.41 E-value=52 Score=27.00 Aligned_cols=32 Identities=25% Similarity=0.749 Sum_probs=18.9
Q ss_pred eEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcccc
Q 007176 559 WVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVT 601 (614)
Q Consensus 559 wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs~~ 601 (614)
-+.|--|. .|.++.... ++ +.++|+||.|...
T Consensus 22 aLIC~~C~--~hNGla~~~------~~---~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 22 ALICSKCF--SHNGLAPKE------EF---EEIQYRCPYCGAL 53 (54)
T ss_pred eEECcccc--hhhcccccc------cC---CceEEEcCCCCCc
Confidence 34455553 366666432 12 4458999999754
No 74
>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=23.55 E-value=96 Score=32.31 Aligned_cols=28 Identities=29% Similarity=0.767 Sum_probs=15.0
Q ss_pred cccccccCCC--------CC--C-CeEecCCCCCccccC
Q 007176 545 GECCLLCHSS--------AA--G-DWVNCGICGEWAHFG 572 (614)
Q Consensus 545 ~~~C~~C~~~--------~~--~-~wi~CD~C~~wyH~~ 572 (614)
...|-.||+. .+ | .++.|..|+--||+.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~ 210 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV 210 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec
Confidence 4699999985 22 3 899999999988863
No 75
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=23.38 E-value=1.4e+02 Score=34.48 Aligned_cols=111 Identities=32% Similarity=0.430 Sum_probs=62.1
Q ss_pred ccccCCCCccccCCCCCC--------CCCC---CHHHH------HHHHHHHHHHhC-----CccccCC-CCCCCCCCcc-
Q 007176 417 IISLNPLPLKKHGCGRAP--------IQVC---SEEEF------LRDVMQFLILRG-----HTRLVPQ-GGLAEFPDAI- 472 (614)
Q Consensus 417 ~~~~~P~p~k~h~~~RpP--------l~~~---~eeeF------L~dL~kFhe~RG-----tp~liP~-g~~s~fP~Pv- 472 (614)
.-++.|+|+|-|+-.=+- +... +.+.| ++.+++||+.|| ||++-+- |+.+-- |.
T Consensus 143 sKsL~pLPeK~hgL~D~E~RyR~RylDLi~N~e~r~~f~~Rs~ii~~iR~fl~~~gFlEVETP~lq~i~GGA~Ar--PF~ 220 (502)
T COG1190 143 SKSLRPLPEKFHGLTDKEIRYRQRYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPGGAAAR--PFI 220 (502)
T ss_pred cccCCCCChhhcCCccHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHCCCeEeccccccccCCCcccc--cce
Confidence 345889999999821100 0011 23334 567999999998 3433221 332221 23
Q ss_pred --cCCeechHHH-----HHHHHhhcCceeecc--CCCCHHHHHHhccCCcCCCccccHHHHHHHHHHHhhhhhhc
Q 007176 473 --LNAKRLDLFN-----LYREVVSRGGFHVGN--GINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEL 538 (614)
Q Consensus 473 --V~GK~LDLyk-----LYk~V~sRGGF~kVn--kkkWkgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyLleYE~ 538 (614)
.|--.+|||. ||-.=.-.|||++|- +++.+ .=| . ...-|.-+++...|+-|-.-.+.
T Consensus 221 ThhNald~dlyLRIApELyLKRliVGG~erVfEIgr~FR-----NEG---i-d~tHNPEFTmlE~Y~AYaDy~D~ 286 (502)
T COG1190 221 THHNALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFR-----NEG---I-DTTHNPEFTMLEFYQAYADYEDL 286 (502)
T ss_pred eeecccCCceEEeeccHHHHHHHHhcCchhheeeccccc-----cCC---C-ccccCcchhhHHHHHHHhHHHHH
Confidence 2445667763 565555569999993 34443 111 1 12236678888888887654433
No 76
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.06 E-value=50 Score=36.91 Aligned_cols=29 Identities=17% Similarity=0.436 Sum_probs=24.9
Q ss_pred ccccccccCCCCCCCeEecCCCCCccccC
Q 007176 544 DGECCLLCHSSAAGDWVNCGICGEWAHFG 572 (614)
Q Consensus 544 d~~~C~~C~~~~~~~wi~CD~C~~wyH~~ 572 (614)
..|.|..||-.....+-.|..|+.|=-..
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~ 34 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQGKCPACHAWNTIT 34 (454)
T ss_pred CeEECCcCCCCCccccEECcCCCCccccc
Confidence 35899999999988888999999996554
No 77
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=22.87 E-value=93 Score=28.85 Aligned_cols=37 Identities=30% Similarity=0.618 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhhhhhccccccccccccccCCCC------C-CCeEecCCCCC
Q 007176 522 GNTLKRHYETYLLEYELAHDDVDGECCLLCHSSA------A-GDWVNCGICGE 567 (614)
Q Consensus 522 g~~LK~hYERyLleYE~ahdDed~~~C~~C~~~~------~-~~wi~CD~C~~ 567 (614)
...+.+...+|+.+|=+ |..|++.+ . -..+.|+.||.
T Consensus 66 ~~~i~~~l~~yI~~yVl---------C~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRYIKEYVL---------CPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHHHhcEE---------CCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 45677777778877764 99999973 1 24567999985
No 78
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=22.12 E-value=47 Score=32.68 Aligned_cols=24 Identities=25% Similarity=0.682 Sum_probs=17.1
Q ss_pred ccccCCCCCCCeEecCCCCCcccc
Q 007176 548 CLLCHSSAAGDWVNCGICGEWAHF 571 (614)
Q Consensus 548 C~~C~~~~~~~wi~CD~C~~wyH~ 571 (614)
|.-||-.+.+-.+.|..|++||=-
T Consensus 3 C~YCG~~~p~~vv~C~~c~kWFCN 26 (152)
T PF09416_consen 3 CAYCGIHDPSCVVKCNTCNKWFCN 26 (152)
T ss_dssp -TTT----CCCEEEETTTTEEEES
T ss_pred ccccCCCCcccEeEcCCCCcEeec
Confidence 888998899999999999999843
No 79
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=22.09 E-value=1e+02 Score=29.56 Aligned_cols=37 Identities=27% Similarity=0.634 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhhhhhccccccccccccccCCCC-----CC--CeEecCCCCCc
Q 007176 523 NTLKRHYETYLLEYELAHDDVDGECCLLCHSSA-----AG--DWVNCGICGEW 568 (614)
Q Consensus 523 ~~LK~hYERyLleYE~ahdDed~~~C~~C~~~~-----~~--~wi~CD~C~~w 568 (614)
..+.+..++|+.+|= .|..|++.+ ++ .++.|+.||..
T Consensus 84 ~~i~~~L~~yI~~yV---------lC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 84 FLLNERIEDYVRKYV---------ICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHhheE---------ECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 356666667776665 499999973 22 35799999865
No 80
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=21.84 E-value=38 Score=35.21 Aligned_cols=84 Identities=26% Similarity=0.572 Sum_probs=49.6
Q ss_pred hHHHHHHHHhhcCceeeccCCCCHHHHHHhccCCcCC-CccccHHHHHHHHHHHhhhhhhccccccccccccccCCCC-C
Q 007176 479 DLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLT-NRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSA-A 556 (614)
Q Consensus 479 DLykLYk~V~sRGGF~kVnkkkWkgEV~~~Mgn~~~p-~t~Tsag~~LK~hYERyLleYE~ahdDed~~~C~~C~~~~-~ 556 (614)
+.=.|-+.-+..|.|..++++ |. +. ....-..+-|...|..+| ..|.+||.-. .
T Consensus 138 ~iE~lLqkf~q~gwf~e~eg~-ft-----------l~~ralaELe~YL~s~y~dnl------------k~Cn~Ch~LvIq 193 (235)
T KOG4718|consen 138 RIEELLQKFIQMGWFMEVEGR-FT-----------LGPRALAELEFYLSSNYADNL------------KNCNLCHCLVIQ 193 (235)
T ss_pred HHHHHHHHHHHhchhheecce-EE-----------EchHHHHHHHHHHHhhhHHHH------------HHHhHhHHHhhe
Confidence 344445555666777665442 22 22 222233445555555444 4599998763 2
Q ss_pred CCeEecCCCCCccccCcccCCCCCcccCccccCCceeecCCcc
Q 007176 557 GDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS 599 (614)
Q Consensus 557 ~~wi~CD~C~~wyH~~C~~~~~~g~~kd~ak~eg~~Y~CP~Cs 599 (614)
+ +.|+.|+--||-.|.--- -.. .-+||+|-
T Consensus 194 g--~rCg~c~i~~h~~c~qty--------~q~---~~~cphc~ 223 (235)
T KOG4718|consen 194 G--IRCGSCNIQYHRGCIQTY--------LQR---RDICPHCG 223 (235)
T ss_pred e--eccCcccchhhhHHHHHH--------hcc---cCcCCchh
Confidence 2 679999999999998443 222 36899984
No 81
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.61 E-value=1e+02 Score=33.22 Aligned_cols=28 Identities=25% Similarity=0.713 Sum_probs=19.4
Q ss_pred cccccccccCCCCCCCeEecCCCCCccccCcccCC
Q 007176 543 VDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQ 577 (614)
Q Consensus 543 ed~~~C~~C~~~~~~~wi~CD~C~~wyH~~C~~~~ 577 (614)
+....|..||+ -.|+-|..| ||.|-...
T Consensus 227 ~~~~~C~~CGg---~rFlpC~~C----~GS~kv~~ 254 (281)
T KOG2824|consen 227 EGGGVCESCGG---ARFLPCSNC----HGSCKVHE 254 (281)
T ss_pred CCCCcCCCcCC---cceEecCCC----CCceeeee
Confidence 34567888875 577888888 67776555
No 82
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=21.53 E-value=1.3e+02 Score=23.60 Aligned_cols=26 Identities=19% Similarity=0.500 Sum_probs=19.2
Q ss_pred CCHHHHHHhccCCcCCCccccHHHHHHHHHHHhhh
Q 007176 500 NWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLL 534 (614)
Q Consensus 500 kWkgEV~~~Mgn~~~p~t~Tsag~~LK~hYERyLl 534 (614)
+|. +|+..|+ ++ ...+++..|.++|.
T Consensus 19 ~W~-~Ia~~l~-----~R---t~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 19 DWK-KIAEHLG-----NR---TPKQCRNRWRNHLR 44 (60)
T ss_dssp -HH-HHHHHST-----TS----HHHHHHHHHHTTS
T ss_pred CHH-HHHHHHC-----cC---CHHHHHHHHHHHCc
Confidence 799 9999886 22 26799999999774
Done!