Query psy13400
Match_columns 79
No_of_seqs 105 out of 213
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 18:30:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0477|consensus 99.6 1.5E-15 3.3E-20 120.4 4.5 74 6-79 173-246 (854)
2 PF14551 MCM_N: MCM N-terminal 99.4 5.6E-14 1.2E-18 88.3 2.7 59 11-69 15-73 (121)
3 PTZ00111 DNA replication licen 98.9 5.9E-09 1.3E-13 85.5 7.0 60 9-68 118-187 (915)
4 KOG0481|consensus 98.7 3.7E-08 8.1E-13 77.8 5.5 58 11-68 44-101 (729)
5 COG1241 MCM2 Predicted ATPase 98.3 2.2E-06 4.8E-11 68.9 6.7 65 11-76 16-80 (682)
6 KOG0479|consensus 97.9 3.7E-05 8E-10 61.9 6.6 68 10-77 26-93 (818)
7 KOG0480|consensus 97.6 0.00017 3.6E-09 58.4 5.8 60 9-68 40-100 (764)
8 KOG0478|consensus 97.1 0.00044 9.4E-09 56.3 3.0 62 11-72 151-212 (804)
9 KOG0482|consensus 95.7 0.031 6.6E-07 45.0 5.9 58 10-67 29-88 (721)
10 PF09280 XPC-binding: XPC-bind 95.0 0.018 4E-07 33.2 1.9 48 14-61 9-56 (59)
11 PF11310 DUF3113: Protein of u 92.8 0.1 2.2E-06 30.1 2.1 27 31-57 22-48 (60)
12 PF14213 DUF4325: Domain of un 87.6 1.1 2.5E-05 26.1 3.6 33 8-42 1-33 (74)
13 TIGR01568 A_thal_3678 uncharac 86.7 2.6 5.7E-05 24.9 4.7 53 13-70 13-65 (66)
14 PF04844 Ovate: Transcriptiona 84.9 4.3 9.4E-05 23.4 5.0 51 13-69 7-57 (59)
15 TIGR00601 rad23 UV excision re 83.9 0.47 1E-05 36.2 0.9 48 15-62 257-304 (378)
16 KOG0011|consensus 64.2 3 6.5E-05 31.7 0.7 50 14-63 224-273 (340)
17 TIGR00526 folB_dom FolB domain 54.8 21 0.00045 22.2 3.3 42 30-74 50-91 (118)
18 TIGR00525 folB dihydroneopteri 54.7 26 0.00057 21.7 3.8 40 31-73 50-89 (116)
19 smart00204 TGFB Transforming g 53.1 7.2 0.00016 24.2 0.9 12 26-37 3-14 (102)
20 cd00534 DHNA_DHNTPE Dihydroneo 52.2 30 0.00066 21.5 3.7 41 30-73 50-90 (118)
21 PF01418 HTH_6: Helix-turn-hel 51.4 13 0.00028 21.6 1.8 22 34-55 12-33 (77)
22 PRK11593 folB bifunctional dih 45.6 31 0.00067 21.6 3.0 30 42-71 59-88 (119)
23 PRK09162 hypoxanthine-guanine 44.6 32 0.0007 23.1 3.2 32 17-50 5-36 (181)
24 PF11693 DUF2990: Protein of u 42.1 13 0.00028 21.8 0.8 17 33-49 15-31 (64)
25 PF04358 DsrC: DsrC like prote 40.4 25 0.00054 22.4 2.0 33 21-53 1-37 (109)
26 COG4860 Uncharacterized protei 40.0 52 0.0011 22.6 3.5 39 11-50 113-151 (170)
27 PF03755 YicC_N: YicC-like fam 39.8 57 0.0012 21.5 3.7 62 6-67 79-147 (159)
28 COG1539 FolB Dihydroneopterin 39.1 61 0.0013 20.8 3.7 43 30-75 51-93 (121)
29 PF00156 Pribosyltran: Phospho 39.0 31 0.00067 20.8 2.2 27 27-53 1-27 (125)
30 PF04712 Radial_spoke: Radial 34.7 48 0.001 26.2 3.2 43 23-71 17-59 (491)
31 PF00019 TGF_beta: Transformin 33.6 20 0.00044 21.9 0.7 12 26-37 6-17 (105)
32 PRK11557 putative DNA-binding 31.8 34 0.00073 24.0 1.7 23 33-55 7-29 (278)
33 PRK11302 DNA-binding transcrip 30.9 57 0.0012 22.8 2.8 23 34-56 12-34 (284)
34 PF14367 DUF4411: Domain of un 29.8 93 0.002 20.5 3.5 40 13-52 23-63 (162)
35 PF08110 Antimicrobial15: Ocel 29.7 42 0.00091 15.1 1.2 13 54-66 1-13 (19)
36 PRK11337 DNA-binding transcrip 29.6 62 0.0014 22.9 2.8 30 34-63 24-54 (292)
37 PRK15482 transcriptional regul 29.3 39 0.00085 23.9 1.7 23 33-55 11-33 (285)
38 KOG0961|consensus 29.1 90 0.002 26.8 3.9 54 9-63 685-740 (1022)
39 COG1737 RpiR Transcriptional r 28.3 40 0.00086 24.2 1.6 23 34-56 14-36 (281)
40 PF13466 STAS_2: STAS domain 28.2 1.1E+02 0.0023 17.1 3.2 29 12-41 13-41 (80)
41 PRK09121 5-methyltetrahydropte 27.6 1.7E+02 0.0038 21.7 5.0 43 13-62 157-199 (339)
42 PF14164 YqzH: YqzH-like prote 27.3 1.3E+02 0.0028 17.6 3.4 42 25-66 20-62 (64)
43 KOG0912|consensus 27.3 1.3E+02 0.0029 23.1 4.3 43 18-72 6-48 (375)
44 cd07043 STAS_anti-anti-sigma_f 26.8 1.1E+02 0.0025 17.1 3.2 36 14-49 26-61 (99)
45 PF01133 ER: Enhancer of rudim 26.1 29 0.00063 22.1 0.5 32 13-45 35-66 (102)
46 PF03869 Arc: Arc-like DNA bin 25.5 43 0.00093 18.2 1.1 17 14-30 15-31 (50)
47 PF10223 DUF2181: Uncharacteri 24.9 1.6E+02 0.0035 21.3 4.2 40 3-45 51-90 (244)
48 PF02152 FolB: Dihydroneopteri 24.7 41 0.00089 20.5 1.0 41 31-74 48-88 (113)
49 PF01267 F-actin_cap_A: F-acti 23.6 79 0.0017 23.0 2.5 49 25-73 81-129 (271)
50 PF13167 GTP-bdg_N: GTP-bindin 23.0 75 0.0016 19.7 2.0 45 14-58 45-94 (95)
51 PRK11245 folX D-erythro-7,8-di 22.9 1.3E+02 0.0029 18.7 3.2 29 42-71 63-91 (120)
52 PF00452 Bcl-2: Apoptosis regu 22.8 42 0.00092 20.0 0.8 26 50-75 27-52 (101)
53 PF14510 ABC_trans_N: ABC-tran 22.8 1.5E+02 0.0033 17.3 3.2 30 11-40 36-68 (85)
54 PF02667 SCFA_trans: Short cha 22.3 43 0.00094 26.5 0.9 35 42-76 288-324 (453)
55 PF07533 BRK: BRK domain; Int 22.2 31 0.00067 18.7 0.1 14 39-52 26-39 (46)
56 PRK13386 fliH flagellar assemb 22.0 1.2E+02 0.0027 21.4 3.2 24 42-65 135-158 (236)
57 TIGR02697 WPE_wolbac Wolbachia 21.7 1.2E+02 0.0026 15.8 2.3 21 10-32 11-31 (36)
58 PF10386 DUF2441: Protein of u 21.5 1.6E+02 0.0034 19.8 3.4 33 42-74 38-71 (141)
59 PF11372 DUF3173: Domain of un 20.5 1.7E+02 0.0038 16.7 3.0 38 30-75 3-40 (59)
60 cd06845 Bcl-2_like Apoptosis r 20.5 1.2E+02 0.0025 19.4 2.6 56 14-76 35-90 (144)
61 cd03819 GT1_WavL_like This fam 20.5 3E+02 0.0064 18.9 5.7 51 19-70 300-350 (355)
62 PF01740 STAS: STAS domain; I 20.1 2.1E+02 0.0045 17.0 3.6 37 11-47 24-69 (117)
63 KOG0158|consensus 20.1 1.3E+02 0.0029 23.9 3.2 40 12-71 329-368 (499)
No 1
>KOG0477|consensus
Probab=99.58 E-value=1.5e-15 Score=120.39 Aligned_cols=74 Identities=45% Similarity=0.798 Sum_probs=71.0
Q ss_pred cccchhhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchhhccC
Q psy13400 6 DETVSQYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYERVFLK 79 (79)
Q Consensus 6 ~d~~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~I~~~ 79 (79)
.|++|+.+|.++|+.||.+|..||+|+|.||......||+||.++|.++|++|++|+.++|+.+||+|++||.+
T Consensus 173 ~d~~~~~~~~~ri~~~~~~n~esl~v~y~dla~~~~~la~fl~~ap~e~l~I~dr~a~~~v~~~~p~yeri~~~ 246 (854)
T KOG0477|consen 173 VDENGHNVYIERIRRMCEENRESLEVNYTDLAESEHVLAYFLPEAPEEMLEIFDRAALEVVLLHYPNYERIHNE 246 (854)
T ss_pred hcccccchHHHHHHHHHhhchHHHHHHHHHHHHhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhCCChhhcccc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999864
No 2
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=99.44 E-value=5.6e-14 Score=88.34 Aligned_cols=59 Identities=24% Similarity=0.412 Sum_probs=54.1
Q ss_pred hhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhh
Q psy13400 11 QYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSM 69 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~ 69 (79)
..+|+++|++|+..+++||+|||.||.+|++.||.+|.++|.+++++|++|+.+++...
T Consensus 15 ~~~Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~ 73 (121)
T PF14551_consen 15 EPKYMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKEL 73 (121)
T ss_dssp S-CCHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT
T ss_pred chHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999999999999999999999999874
No 3
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=98.87 E-value=5.9e-09 Score=85.51 Aligned_cols=60 Identities=22% Similarity=0.286 Sum_probs=54.5
Q ss_pred chhhhHHHHHHHHHHcCc----------ceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHh
Q psy13400 9 VSQYIYKEKIKKMCENNF----------SSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLS 68 (79)
Q Consensus 9 ~g~~~Y~e~I~~m~~~nk----------~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~ 68 (79)
.....|..+|.+|..+++ +||+|||.||..|++.||.||+++|.++|++|++|++++...
T Consensus 118 ~~~~~y~~~~~~~~~~~~~~~~~~~~~~~sl~Vd~~~l~~fd~~L~~~l~~~P~e~i~~~e~~l~~~~~~ 187 (915)
T PTZ00111 118 YTELYYLWKLMNFIKENLRDHSTGYSRILPFEVDLMHVYSFDKVLYKLLVTFPADCIAELDKVLVKLFNE 187 (915)
T ss_pred hhHHHHHHHHHHHHHHhhhcccccccCCceEEEEHHHHHhhhHHHHHHHHHCHHHHHHHHHHHHHHHHHH
Confidence 345689999999999874 899999999999999999999999999999999999987553
No 4
>KOG0481|consensus
Probab=98.67 E-value=3.7e-08 Score=77.77 Aligned_cols=58 Identities=24% Similarity=0.407 Sum_probs=54.6
Q ss_pred hhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHh
Q psy13400 11 QYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLS 68 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~ 68 (79)
.++|+++++........||+|+..||.+|+.+||+.|...|.+.||+|++||++|...
T Consensus 44 ~f~Yrd~L~~N~~~~~y~L~v~le~L~~fdedl~~~L~~~P~~~lp~fEeAa~~Vad~ 101 (729)
T KOG0481|consen 44 DFKYRDQLKRNYNLGEYSLEVELEDLISFDEDLADKLSKQPADHLPLFEEAAKEVADE 101 (729)
T ss_pred ccchHHHHHhcccccceEEEEEHHHhhccchHHHHHHHhChHhHHHHHHHHHHHHHhh
Confidence 4789999999988899999999999999999999999999999999999999998654
No 5
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=98.29 E-value=2.2e-06 Score=68.94 Aligned_cols=65 Identities=25% Similarity=0.409 Sum_probs=57.9
Q ss_pred hhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchhh
Q psy13400 11 QYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYERV 76 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~I 76 (79)
...|.+++ .|...+.+|++|+|.||..+++.||..|+++|.+++++|++|++++...++|+|...
T Consensus 16 ~~~~~~~~-~~~~~~~~s~~v~~~~~~~~~~~la~~l~~~p~~~i~~~~~~~~~~~~~~~~~~~~~ 80 (682)
T COG1241 16 ILEYAENI-ILDKIINRSLEVDLSDLEEYDPELAGLLLENPEEIIPLFEKALDEIALLLFPEVDRS 80 (682)
T ss_pred HHHHHHHh-hhhhccceEEEEEhHHhhcccHHHHHHHHhChHHHHHHHHHHHHHHHHhcCcccccc
Confidence 45677776 566666669999999999999999999999999999999999999999999999874
No 6
>KOG0479|consensus
Probab=97.90 E-value=3.7e-05 Score=61.88 Aligned_cols=68 Identities=24% Similarity=0.282 Sum_probs=63.1
Q ss_pred hhhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchhhc
Q psy13400 10 SQYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYERVF 77 (79)
Q Consensus 10 g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~I~ 77 (79)
...+|.+.|..|.+++..-|.|+.+||-.+++.+|.-|+.+|.+.++-|++|+++++-...|.|+..+
T Consensus 26 D~~iy~e~i~~~~~~~~~RlIvNv~dlr~~~~~~A~glL~~p~~~~~~f~~AL~~~~~~~d~~~~~~~ 93 (818)
T KOG0479|consen 26 DADIYQEAIKKLLNEGQHRLIVNVDDLREFNRERASGLLENPAEEVPPFEDALTDAASRIDDVYAKVK 93 (818)
T ss_pred hhhHHHHHHHHhhhcCcceEEEEhHHHHHhHHHHHHhHhhChHhhhhhHHHHHHHHHhcccchhhhhc
Confidence 34589999999999999999999999999999999999999999999999999999999888887643
No 7
>KOG0480|consensus
Probab=97.58 E-value=0.00017 Score=58.39 Aligned_cols=60 Identities=15% Similarity=0.215 Sum_probs=57.1
Q ss_pred chhhhHHHHHHHHHHcCcceEEEechhHhh-chHHHHHHhhhChHHHHHHHHHHHHHHHHh
Q psy13400 9 VSQYIYKEKIKKMCENNFSSFTVEFQILAN-KENALAYFLPDAPLEMIAIFDEVAKDLVLS 68 (79)
Q Consensus 9 ~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~-~~~~LA~~L~~~P~~~L~~~~eaa~evv~~ 68 (79)
.|..+|...|..+...++.+|+|||.||.. ++++||..|.++|.-+++.+..|+..++.+
T Consensus 40 ~~e~~~~~~i~~~~~~~~~tl~vd~~~l~~~~~~~la~~l~~~~~r~~p~m~~av~~~l~d 100 (764)
T KOG0480|consen 40 AGEKKYLQSIELLDRPERNTLLVDFQHLSKQYNQNLATALEENYYRVLPCMCRAVHKVLKD 100 (764)
T ss_pred ccchhhHHHHHhhccCCCceEEEEHHHHHhhhhHHHHHHHHHhhhhhHHHHHHHHHHHHHc
Confidence 567789999999999999999999999999 999999999999999999999999999987
No 8
>KOG0478|consensus
Probab=97.08 E-value=0.00044 Score=56.34 Aligned_cols=62 Identities=26% Similarity=0.289 Sum_probs=58.1
Q ss_pred hhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcC
Q psy13400 11 QYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPS 72 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~ 72 (79)
...|.+++.+|-.....-|.++-.||..++..|+..++-.|.+++++|+.++++++.+.||.
T Consensus 151 ~~~yi~~l~e~~~~~~~~ln~~~~hl~~~~~~Ly~ql~~ypqevip~~d~t~~~~~~e~~~~ 212 (804)
T KOG0478|consen 151 CPYYIKSLLELKELEPEFLNLDAEHLTDFDMDLYRQLVVYPQEVIPIFDETANEIVLERYVL 212 (804)
T ss_pred chHHHHHHHHHHHhhhhhhhhhhhccccccHHHHHhhhhchHhhcccchHHHHHHHHhhccc
Confidence 45699999999998999999999999999999999999999999999999999999999964
No 9
>KOG0482|consensus
Probab=95.75 E-value=0.031 Score=45.03 Aligned_cols=58 Identities=10% Similarity=0.267 Sum_probs=51.5
Q ss_pred hhhhHHHHHHHHHHcCcceEEEechhHhhch--HHHHHHhhhChHHHHHHHHHHHHHHHH
Q psy13400 10 SQYIYKEKIKKMCENNFSSFTVEFQILANKE--NALAYFLPDAPLEMIAIFDEVAKDLVL 67 (79)
Q Consensus 10 g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~--~~LA~~L~~~P~~~L~~~~eaa~evv~ 67 (79)
+..+|++++.+.+...+.+++||.+||..|+ ..|...+.++-.-...+|..|+.+++.
T Consensus 29 ~~~kY~~~L~eia~Re~~ai~vdldDi~~~d~~~~l~~~i~~Na~ry~~lf~~~vdellp 88 (721)
T KOG0482|consen 29 ELGKYMNQLQEIANREQNAIEVDLDDIAEYDDATELVGAIESNARRYVELFSDAVDELLP 88 (721)
T ss_pred chhHHHHHHHHHhcccceeEEEehHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3347999999999999999999999999997 379999999999999999999988654
No 10
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=95.02 E-value=0.018 Score=33.18 Aligned_cols=48 Identities=15% Similarity=0.288 Sum_probs=42.0
Q ss_pred HHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHH
Q psy13400 14 YKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEV 61 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~ea 61 (79)
-...||+++..|=.-|.-=...|...+|.|+..+.++|++++.++.+.
T Consensus 9 qf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~ 56 (59)
T PF09280_consen 9 QFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNPEEFLRLLNEP 56 (59)
T ss_dssp HHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTHHHHHHHHHST
T ss_pred HHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCHHHHHHHHcCC
Confidence 457899999999888887789999999999999999999999998764
No 11
>PF11310 DUF3113: Protein of unknown function (DUF3113); InterPro: IPR021461 This entry is represented by Bacteriophage 92, Orf93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=92.76 E-value=0.1 Score=30.10 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=21.4
Q ss_pred EechhHhhchHHHHHHhhhChHHHHHH
Q psy13400 31 VEFQILANKENALAYFLPDAPLEMIAI 57 (79)
Q Consensus 31 Vdf~dL~~~~~~LA~~L~~~P~~~L~~ 57 (79)
..|.|+......||++|-++|.++|+.
T Consensus 22 ~~~~~vD~eKe~LAdyLy~NP~eiLeY 48 (60)
T PF11310_consen 22 HHFDDVDKEKEALADYLYNNPDEILEY 48 (60)
T ss_pred cchhhhhhHHHHHHHHHhcCHHHHhhc
Confidence 345666666678999999999999875
No 12
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=87.55 E-value=1.1 Score=26.05 Aligned_cols=33 Identities=9% Similarity=0.152 Sum_probs=24.6
Q ss_pred cchhhhHHHHHHHHHHcCcceEEEechhHhhchHH
Q psy13400 8 TVSQYIYKEKIKKMCENNFSSFTVEFQILANKENA 42 (79)
Q Consensus 8 ~~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~ 42 (79)
++|..+|.+ |......++. ++|||..+..+.+.
T Consensus 1 e~G~~~~~~-i~~~l~~~~~-V~lDF~gv~~~~ss 33 (74)
T PF14213_consen 1 EDGERLRDE-IEPALKEGEK-VVLDFEGVESITSS 33 (74)
T ss_pred CChHHHHHH-HHHHHhcCCe-EEEECCCcccccHH
Confidence 467766666 8888776655 99999999777553
No 13
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=86.65 E-value=2.6 Score=24.87 Aligned_cols=53 Identities=15% Similarity=0.275 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhC
Q psy13400 13 IYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMY 70 (79)
Q Consensus 13 ~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~ 70 (79)
-+++.+.+|+.++. +.-++.+|.. -|+-+|.-|+.+.-+.+=.|..++....+
T Consensus 13 DFr~SM~EMI~~~~--i~~~w~~Lee---LL~cYL~LN~~~~H~~Iv~AF~dl~~~L~ 65 (66)
T TIGR01568 13 DFRRSMEEMIEERE--LEADWKELEE---LLACYLDLNPKKSHRFIVRAFVDILSALL 65 (66)
T ss_pred HHHHHHHHHHHHcC--CCCCHHHHHH---HHHHHHHhCCchhhhHHHHHHHHHHHHHh
Confidence 48999999999875 4456777765 69999999999999988888888876554
No 14
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=84.89 E-value=4.3 Score=23.38 Aligned_cols=51 Identities=22% Similarity=0.247 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhh
Q psy13400 13 IYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSM 69 (79)
Q Consensus 13 ~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~ 69 (79)
-+++.+.+|+.++.-. ++.+|.. -|+-+|.-|+.+.-+++=+|..++....
T Consensus 7 DFr~SM~EMI~~~~i~---~~~~Lee---LL~cYL~LN~~~~H~~Iv~aF~dv~~~l 57 (59)
T PF04844_consen 7 DFRESMVEMIEENGIR---DWDDLEE---LLACYLSLNSPEHHKFIVEAFVDVWVEL 57 (59)
T ss_pred HHHHHHHHHHHHcCCC---CHHHHHH---HHHHHHHhCChhhhhHHHHHHHHHHHHH
Confidence 3899999999987633 7777765 6999999999999888888888876654
No 15
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.89 E-value=0.47 Score=36.17 Aligned_cols=48 Identities=10% Similarity=0.248 Sum_probs=44.1
Q ss_pred HHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHH
Q psy13400 15 KEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVA 62 (79)
Q Consensus 15 ~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa 62 (79)
...||+|+..|=+-|.-=...|.+.+|.|+..+.++|+++|.++.+.+
T Consensus 257 f~~lR~~vq~NP~~L~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~ 304 (378)
T TIGR00601 257 FQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPV 304 (378)
T ss_pred HHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHHHHHCHHHHHHHhcCcc
Confidence 677999999998888888899999999999999999999999998875
No 16
>KOG0011|consensus
Probab=64.16 E-value=3 Score=31.67 Aligned_cols=50 Identities=12% Similarity=0.234 Sum_probs=43.8
Q ss_pred HHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHH
Q psy13400 14 YKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAK 63 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~ 63 (79)
=..++|+|++.|-.-|.==.+.|..-+|.|...+-+|++.+|..+++.+.
T Consensus 224 qf~~lR~~iqqNP~ll~~~Lqqlg~~nP~L~q~Iq~nqe~Fl~mlnep~~ 273 (340)
T KOG0011|consen 224 QFQQLRQMIQQNPELLHPLLQQLGKQNPQLLQLIQENQEAFLQLLNEPVE 273 (340)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHhhcccc
Confidence 34688999999988887777889899999999999999999999997765
No 17
>TIGR00526 folB_dom FolB domain. Two paralogous genes of E. coli, folB (dihydroneopterin aldolase) and folX (d-erythro-7,8-dihydroneopterin triphosphate epimerase) are homologous to each other and homo-octameric. In Pneumocystis carinii, a multifunctional enzyme of folate synthesis has an N-terminal region active as dihydroneopterin aldolase. This region consists of two tandem sequences each homologous to folB and forms tetramers.
Probab=54.79 E-value=21 Score=22.24 Aligned_cols=42 Identities=17% Similarity=0.471 Sum_probs=29.7
Q ss_pred EEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCch
Q psy13400 30 TVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYE 74 (79)
Q Consensus 30 ~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~ 74 (79)
.|||.++.. .+..++...+-..|+.+-+.+.+.++..||.-.
T Consensus 50 ti~Y~~l~~---~i~~~~~~~~~~llE~la~~ia~~i~~~~~~v~ 91 (118)
T TIGR00526 50 SLNYAEIAS---NITKFVEENPFKLIETLAKSVSEVVLDDYQKVT 91 (118)
T ss_pred ccCHHHHHH---HHHHHHhCCCcchHHHHHHHHHHHHHHhCCCce
Confidence 345555544 455666678888888888888888888886543
No 18
>TIGR00525 folB dihydroneopterin aldolase. This model describes a bacterial dihydroneopterin aldolase, shown to form homo-octamers in E. coli. The equivalent activity is catalyzed by domains of larger folate biosynthesis proteins in other systems. The closely related parologous enzyme in E. coli, dihydroneopterin triphosphate epimerase, which is also homo-octameric, and dihydroneopterin aldolase domains of larger proteins, score below the trusted cutoff but may score well above the noise cutoff.
Probab=54.65 E-value=26 Score=21.71 Aligned_cols=40 Identities=18% Similarity=0.347 Sum_probs=30.0
Q ss_pred EechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCc
Q psy13400 31 VEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSY 73 (79)
Q Consensus 31 Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y 73 (79)
|||.++.. .+..++...+-..|+.+-+.+-+.++..||.-
T Consensus 50 idY~~v~~---~i~~~~~~~~~~llE~la~~Ia~~i~~~~~~v 89 (116)
T TIGR00525 50 VNYAELYS---AIEEIVAEKPRDLIETVAYRIADRLFADFPQV 89 (116)
T ss_pred cCHHHHHH---HHHHHHhCCChhHHHHHHHHHHHHHHHHCCCc
Confidence 45555544 56666777888999999999888899888843
No 19
>smart00204 TGFB Transforming growth factor-beta (TGF-beta) family. Family members are active as disulphide-linked homo- or heterodimers. TGFB is a multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types.
Probab=53.09 E-value=7.2 Score=24.19 Aligned_cols=12 Identities=25% Similarity=0.340 Sum_probs=10.1
Q ss_pred cceEEEechhHh
Q psy13400 26 FSSFTVEFQILA 37 (79)
Q Consensus 26 k~SL~Vdf~dL~ 37 (79)
+++|+|||+||-
T Consensus 3 r~~l~VdF~~iG 14 (102)
T smart00204 3 RRQLYVDFKDLG 14 (102)
T ss_pred eeEEEEEHhhcC
Confidence 578999999874
No 20
>cd00534 DHNA_DHNTPE Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is DHNA which catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. Though it is known that DHNTPE catalyzes the epimerization of dihydroneopterin triphosphate to dihydromonapterin triphosphate, the biological role of this enzyme is still unclear. It is hypothesized that it is not an essential protein since a folX knockout in E. coli has a normal phenoty
Probab=52.16 E-value=30 Score=21.45 Aligned_cols=41 Identities=22% Similarity=0.481 Sum_probs=30.6
Q ss_pred EEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCc
Q psy13400 30 TVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSY 73 (79)
Q Consensus 30 ~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y 73 (79)
.|||..|.. .+..++.+.+-..|+.+-+.+.+.++..||.-
T Consensus 50 tidY~~l~~---~i~~~~~~~~~~llE~La~~ia~~i~~~~~~v 90 (118)
T cd00534 50 TLNYAEVAK---LIKKIVEGSPFKLIETLAEEIADILLEDYPKV 90 (118)
T ss_pred ccCHHHHHH---HHHHHHhCCCHhHHHHHHHHHHHHHHHhCCCc
Confidence 456666654 56677777888999999888888888776643
No 21
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=51.42 E-value=13 Score=21.60 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=15.9
Q ss_pred hhHhhchHHHHHHhhhChHHHH
Q psy13400 34 QILANKENALAYFLPDAPLEMI 55 (79)
Q Consensus 34 ~dL~~~~~~LA~~L~~~P~~~L 55 (79)
..|...+..+|+|+.++|.++.
T Consensus 12 ~~ls~~e~~Ia~yil~~~~~~~ 33 (77)
T PF01418_consen 12 NSLSPTEKKIADYILENPDEIA 33 (77)
T ss_dssp GGS-HHHHHHHHHHHH-HHHHC
T ss_pred hhCCHHHHHHHHHHHhCHHHHH
Confidence 3455556789999999999875
No 22
>PRK11593 folB bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase; Provisional
Probab=45.56 E-value=31 Score=21.58 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=24.1
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHHHHhhCc
Q psy13400 42 ALAYFLPDAPLEMIAIFDEVAKDLVLSMYP 71 (79)
Q Consensus 42 ~LA~~L~~~P~~~L~~~~eaa~evv~~~~P 71 (79)
.+..++.+.+-..|+.+-+.+.+.++..||
T Consensus 59 ~I~~~~~~~~~~LlE~la~~ia~~i~~~~~ 88 (119)
T PRK11593 59 TVISHVEGARFALVERVAEEVAELLLARFN 88 (119)
T ss_pred HHHHHHhCCCcccHHHHHHHHHHHHHhhCC
Confidence 566777778888899888888888887776
No 23
>PRK09162 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=44.61 E-value=32 Score=23.14 Aligned_cols=32 Identities=9% Similarity=0.047 Sum_probs=25.8
Q ss_pred HHHHHHHcCcceEEEechhHhhchHHHHHHhhhC
Q psy13400 17 KIKKMCENNFSSFTVEFQILANKENALAYFLPDA 50 (79)
Q Consensus 17 ~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~ 50 (79)
++++|.+ +.++.+++.++...-..||.++.+.
T Consensus 5 ~~~~~~~--~~~~~~s~~~i~~~i~~la~~i~~~ 36 (181)
T PRK09162 5 EIRQVLA--EADCLVSAAEVEAAIDRMADEITAD 36 (181)
T ss_pred HHHHHHh--hCcEeecHHHHHHHHHHHHHHHHHH
Confidence 3556666 4499999999999999999999863
No 24
>PF11693 DUF2990: Protein of unknown function (DUF2990); InterPro: IPR021706 This family of proteins represents a fungal protein with unknown function.
Probab=42.07 E-value=13 Score=21.81 Aligned_cols=17 Identities=24% Similarity=0.309 Sum_probs=14.6
Q ss_pred chhHhhchHHHHHHhhh
Q psy13400 33 FQILANKENALAYFLPD 49 (79)
Q Consensus 33 f~dL~~~~~~LA~~L~~ 49 (79)
|+|++.|+.+||.|+..
T Consensus 15 fd~~Yd~S~dlaeFy~r 31 (64)
T PF11693_consen 15 FDNVYDYSDDLAEFYGR 31 (64)
T ss_pred hhccccCCHHHHHHHHH
Confidence 68899999999999864
No 25
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=40.42 E-value=25 Score=22.39 Aligned_cols=33 Identities=18% Similarity=0.044 Sum_probs=21.4
Q ss_pred HHHcCcceEEEe---c-hhHhhchHHHHHHhhhChHH
Q psy13400 21 MCENNFSSFTVE---F-QILANKENALAYFLPDAPLE 53 (79)
Q Consensus 21 m~~~nk~SL~Vd---f-~dL~~~~~~LA~~L~~~P~~ 53 (79)
|.+-|.+++++| | .|...+++++|..|+..=..
T Consensus 1 ~~~i~g~~i~~D~eGfL~~~~dW~eevA~~lA~~egI 37 (109)
T PF04358_consen 1 MIEINGKTIETDEEGFLVDPEDWNEEVAEALAKEEGI 37 (109)
T ss_dssp -EEETTEEEEEETTSEESSGGG--HHHHHHHHHCTT-
T ss_pred CeeECCEEeeeCCCcCcCChHhCCHHHHHHHHHHcCC
Confidence 445577788887 3 57778888999998887443
No 26
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.03 E-value=52 Score=22.55 Aligned_cols=39 Identities=21% Similarity=0.230 Sum_probs=30.1
Q ss_pred hhhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhC
Q psy13400 11 QYIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDA 50 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~ 50 (79)
..-|.++|..++.++..|+. +..+=.+-+|.+...++.+
T Consensus 113 v~ey~~ei~~l~e~g~ts~~-~vt~~Ln~~p~~iraiakR 151 (170)
T COG4860 113 VKEYEDEIKALMEEGNTSFL-DVTDTLNISPTLIRAIAKR 151 (170)
T ss_pred HHHHHHHHHHHHHcCCceEe-ehhhhcCCChHHHHHHHHH
Confidence 45699999999999888887 7666667777777666554
No 27
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=39.84 E-value=57 Score=21.53 Aligned_cols=62 Identities=13% Similarity=0.088 Sum_probs=40.6
Q ss_pred cccchhhhHHHHHHHHHHcCcceEEEechhHhhchHHHH-HH--hhhCh----HHHHHHHHHHHHHHHH
Q psy13400 6 DETVSQYIYKEKIKKMCENNFSSFTVEFQILANKENALA-YF--LPDAP----LEMIAIFDEVAKDLVL 67 (79)
Q Consensus 6 ~d~~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA-~~--L~~~P----~~~L~~~~eaa~evv~ 67 (79)
.|..--.-|.+.++++...-.-.-.+++.+|.++...+. .- =.+.. ..+++.+++|+.+++.
T Consensus 79 in~~l~~~y~~~l~~l~~~~~~~~~~~~~~ll~~p~v~~~~~~~~~~~~e~~~~~l~~~l~~AL~~l~~ 147 (159)
T PF03755_consen 79 INEELAKAYYEALKELAEELGLAGPISLDDLLRLPGVLKVEEEEDEEEEEELWEALLEALEEALDELIA 147 (159)
T ss_pred cCHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHcCCCcccccCCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 344444469999999988766666889999999876665 22 11122 2266777777776654
No 28
>COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism]
Probab=39.12 E-value=61 Score=20.85 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=33.6
Q ss_pred EEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchh
Q psy13400 30 TVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYER 75 (79)
Q Consensus 30 ~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~ 75 (79)
.|+|.++.. .+..++...|-..++.+-+.+-+.++..||.-..
T Consensus 51 tl~Y~~v~~---~i~~~v~~~~~~LiE~lA~~ia~~l~~~~~~v~~ 93 (121)
T COG1539 51 TLNYAEVSE---LIKEIVEGKRFALIETLAEEIADLLLARFPRVEL 93 (121)
T ss_pred eecHHHHHH---HHHHHHhCCccchHHHHHHHHHHHHHhhCCccEE
Confidence 455655544 6888999999999999988888889988875443
No 29
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=39.03 E-value=31 Score=20.78 Aligned_cols=27 Identities=7% Similarity=0.116 Sum_probs=21.0
Q ss_pred ceEEEechhHhhchHHHHHHhhhChHH
Q psy13400 27 SSFTVEFQILANKENALAYFLPDAPLE 53 (79)
Q Consensus 27 ~SL~Vdf~dL~~~~~~LA~~L~~~P~~ 53 (79)
|++.+||.++......||.+|.+...+
T Consensus 1 ~~i~~~~~~~~~~~~~la~~i~~~~~~ 27 (125)
T PF00156_consen 1 RKIILSPEQIEALAERLAEQIKESGFD 27 (125)
T ss_dssp -EEEEBHHHHHHHHHHHHHHHHHHTTT
T ss_pred CEEEEcHHHHHHHHHHHHHHHHHhCCC
Confidence 578899999998888888888765443
No 30
>PF04712 Radial_spoke: Radial spokehead-like protein
Probab=34.71 E-value=48 Score=26.17 Aligned_cols=43 Identities=21% Similarity=0.385 Sum_probs=34.8
Q ss_pred HcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCc
Q psy13400 23 ENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYP 71 (79)
Q Consensus 23 ~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P 71 (79)
..+..||+ .||.+ .|..-|.++|...+.+|++.-+.|=...|-
T Consensus 17 ~~~G~sLY---dHL~~---vL~kIL~ErP~na~d~fE~iS~~vK~~~f~ 59 (491)
T PF04712_consen 17 NKSGDSLY---DHLSD---VLTKILDERPENAVDIFEEISRQVKESKFV 59 (491)
T ss_pred CCCCCcHH---HHHHH---HHHHHHHhCCCcHHHHHHHHHHHHHHhccc
Confidence 34677775 88877 699999999999999999998887665554
No 31
>PF00019 TGF_beta: Transforming growth factor beta like domain; InterPro: IPR001839 Transforming growth factor-beta (TGF-beta) is a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. TGF-beta-1 is a peptide of 112 amino acid residues derived by proteolytic cleavage from the C-terminal of a precursor protein []. A number of proteins are known to be related to TGF-beta-1 [, ]. Proteins from the TGF-beta family are only active as homo- or heterodimer; the two chains being linked by a single disulphide bond. From X-ray studies of TGF-beta-2 [], it is known that all the other cysteines are involved in intrachain disulphide bonds. There are four disulphide bonds in the TGF-beta's and in inhibin beta chains, while the other members of this family lack the first bond. The regulatory cytokine TGFbeta exerts tumour-suppressive effects, but also modulates cell invasion and immune regulation []. Misregulation of the TGF-beta signalling pathway can result in tumour development. ; GO: 0008083 growth factor activity; PDB: 2QCQ_B 2QCW_B 2R53_A 2R52_A 1M4U_L 1BMP_A 1LX5_A 1LXI_A 3FUB_B 2V5E_B ....
Probab=33.64 E-value=20 Score=21.86 Aligned_cols=12 Identities=33% Similarity=0.346 Sum_probs=10.1
Q ss_pred cceEEEechhHh
Q psy13400 26 FSSFTVEFQILA 37 (79)
Q Consensus 26 k~SL~Vdf~dL~ 37 (79)
+++|+|+|.||-
T Consensus 6 ~~~~~v~F~~lG 17 (105)
T PF00019_consen 6 RRSLYVNFKDLG 17 (105)
T ss_dssp EEEEEEECTCTT
T ss_pred eEEEEEEhhhcC
Confidence 578999999885
No 32
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=31.82 E-value=34 Score=24.01 Aligned_cols=23 Identities=26% Similarity=0.245 Sum_probs=18.9
Q ss_pred chhHhhchHHHHHHhhhChHHHH
Q psy13400 33 FQILANKENALAYFLPDAPLEMI 55 (79)
Q Consensus 33 f~dL~~~~~~LA~~L~~~P~~~L 55 (79)
|..|......+|+++.++|.++.
T Consensus 7 ~~~Lt~~e~~ia~yil~n~~~v~ 29 (278)
T PRK11557 7 YPGLAQSDRKLADYLLLQPDTAR 29 (278)
T ss_pred hhhCCHHHHHHHHHHHhCHHHHH
Confidence 45566677799999999999875
No 33
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=30.93 E-value=57 Score=22.75 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=18.5
Q ss_pred hhHhhchHHHHHHhhhChHHHHH
Q psy13400 34 QILANKENALAYFLPDAPLEMIA 56 (79)
Q Consensus 34 ~dL~~~~~~LA~~L~~~P~~~L~ 56 (79)
.+|......+|+++.++|.++..
T Consensus 12 ~~Lt~~e~~Ia~yil~n~~~v~~ 34 (284)
T PRK11302 12 EHLSKSERKVAEVILASPQTAIH 34 (284)
T ss_pred hhCCHHHHHHHHHHHhCHHHHHh
Confidence 34556677999999999999765
No 34
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=29.82 E-value=93 Score=20.54 Aligned_cols=40 Identities=13% Similarity=0.181 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHcC-cceEEEechhHhhchHHHHHHhhhChH
Q psy13400 13 IYKEKIKKMCENN-FSSFTVEFQILANKENALAYFLPDAPL 52 (79)
Q Consensus 13 ~Y~e~I~~m~~~n-k~SL~Vdf~dL~~~~~~LA~~L~~~P~ 52 (79)
-|++.+.++...+ -.|...=+.+|..-+++|+.|+-+++.
T Consensus 23 ~fW~~L~~~~~~g~i~~~~~V~~El~~~~d~l~~W~k~~~~ 63 (162)
T PF14367_consen 23 SFWDWLEQLIESGRIISPDEVYDELERGDDELAKWAKNNEP 63 (162)
T ss_pred HHHHHHHHHHhCCeEeehHHHHHHHhhCChhHHHHHHhCCc
Confidence 4899999998863 456666678998888999999999988
No 35
>PF08110 Antimicrobial15: Ocellatin family; InterPro: IPR012518 This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus (Argus frog). The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3. These peptides present haemolytic activity against human erythrocytes and are also active against Escherichia coli [].; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region
Probab=29.70 E-value=42 Score=15.10 Aligned_cols=13 Identities=38% Similarity=0.667 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHH
Q psy13400 54 MIAIFDEVAKDLV 66 (79)
Q Consensus 54 ~L~~~~eaa~evv 66 (79)
++.|+..|++++.
T Consensus 1 VlDIlK~AaK~l~ 13 (19)
T PF08110_consen 1 VLDILKGAAKDLL 13 (19)
T ss_pred ChHHHHhHHHHHH
Confidence 4678888888864
No 36
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=29.59 E-value=62 Score=22.86 Aligned_cols=30 Identities=17% Similarity=0.104 Sum_probs=21.5
Q ss_pred hhHhhchHHHHHHhhhChHHHHHH-HHHHHH
Q psy13400 34 QILANKENALAYFLPDAPLEMIAI-FDEVAK 63 (79)
Q Consensus 34 ~dL~~~~~~LA~~L~~~P~~~L~~-~~eaa~ 63 (79)
..|......+|+++.++|.++... +.+.|.
T Consensus 24 ~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~ 54 (292)
T PRK11337 24 EGLTPLESRVVEWLLKPGDLSEATALKDIAE 54 (292)
T ss_pred hhcCHHHHHHHHHHHhCHHHHHhcCHHHHHH
Confidence 455566779999999999998654 344443
No 37
>PRK15482 transcriptional regulator MurR; Provisional
Probab=29.34 E-value=39 Score=23.90 Aligned_cols=23 Identities=22% Similarity=0.206 Sum_probs=18.6
Q ss_pred chhHhhchHHHHHHhhhChHHHH
Q psy13400 33 FQILANKENALAYFLPDAPLEMI 55 (79)
Q Consensus 33 f~dL~~~~~~LA~~L~~~P~~~L 55 (79)
|..|......+|+|+.++|.++.
T Consensus 11 ~~~Lt~~e~~Ia~yIl~n~~~v~ 33 (285)
T PRK15482 11 ESEFTENEQKIADFLRANVSELK 33 (285)
T ss_pred HhhcCHHHHHHHHHHHhCHHHHH
Confidence 34566667899999999999975
No 38
>KOG0961|consensus
Probab=29.13 E-value=90 Score=26.76 Aligned_cols=54 Identities=9% Similarity=0.185 Sum_probs=39.8
Q ss_pred chhhhHHHHHHHHHHcCcceEEEechhHhhch--HHHHHHhhhChHHHHHHHHHHHH
Q psy13400 9 VSQYIYKEKIKKMCENNFSSFTVEFQILANKE--NALAYFLPDAPLEMIAIFDEVAK 63 (79)
Q Consensus 9 ~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~--~~LA~~L~~~P~~~L~~~~eaa~ 63 (79)
+|..+-.-....|. .+++||-++|+.|..-. .++...+-++|..+|+-++..=+
T Consensus 685 dg~~vlss~~~~~l-Y~~~slk~s~d~L~~Ek~l~ei~~~v~n~~~~Il~~~e~mR~ 740 (1022)
T KOG0961|consen 685 DGCTVLSSAVASML-YGKNSLKISFDELVLEKLLEEISKDVMNNPEAILEKLEQMRS 740 (1022)
T ss_pred CccEehHHHHHHHH-hcccchhhcccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 44444333333333 48999999999997763 58999999999999999987654
No 39
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=28.27 E-value=40 Score=24.16 Aligned_cols=23 Identities=22% Similarity=0.325 Sum_probs=18.1
Q ss_pred hhHhhchHHHHHHhhhChHHHHH
Q psy13400 34 QILANKENALAYFLPDAPLEMIA 56 (79)
Q Consensus 34 ~dL~~~~~~LA~~L~~~P~~~L~ 56 (79)
.+|......+|+|++++|+++..
T Consensus 14 ~~Lt~~er~iA~yil~~~~~~~~ 36 (281)
T COG1737 14 DSLTKSERKIADYILANPDEVAL 36 (281)
T ss_pred hcCCHHHHHHHHHHHhCHHHHHH
Confidence 45556677899999999998753
No 40
>PF13466 STAS_2: STAS domain
Probab=28.20 E-value=1.1e+02 Score=17.10 Aligned_cols=29 Identities=0% Similarity=0.087 Sum_probs=23.0
Q ss_pred hhHHHHHHHHHHcCcceEEEechhHhhchH
Q psy13400 12 YIYKEKIKKMCENNFSSFTVEFQILANKEN 41 (79)
Q Consensus 12 ~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~ 41 (79)
.-..+.+.+++..+ +.++||+.++...+.
T Consensus 13 ~~l~~~l~~~~~~~-~~v~lDls~v~~iDs 41 (80)
T PF13466_consen 13 PELRQALQALLASG-RPVVLDLSGVEFIDS 41 (80)
T ss_pred HHHHHHHHHHHcCC-CeEEEECCCCCeecH
Confidence 34677788888666 899999999988775
No 41
>PRK09121 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=27.57 E-value=1.7e+02 Score=21.66 Aligned_cols=43 Identities=14% Similarity=0.211 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHH
Q psy13400 13 IYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVA 62 (79)
Q Consensus 13 ~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa 62 (79)
.|+++|+.+...+-+.|.|| +|.|+....+.-+...+.++.++
T Consensus 157 al~~Ei~~L~~aG~~~IQiD-------eP~l~~~~~~~~~~~v~~~n~~~ 199 (339)
T PRK09121 157 ILNQEAKELEAAGVDIIQFD-------EPAFNVFFDEVNDWGVAALERAI 199 (339)
T ss_pred HHHHHHHHHHHCCCCEEEec-------ccHHhhhhHHHHHHHHHHHHHHH
Confidence 58889998888888888887 45566443333334444444444
No 42
>PF14164 YqzH: YqzH-like protein
Probab=27.30 E-value=1.3e+02 Score=17.60 Aligned_cols=42 Identities=10% Similarity=0.144 Sum_probs=31.2
Q ss_pred CcceEEEechhHhhchHHHHHHhhhChH-HHHHHHHHHHHHHH
Q psy13400 25 NFSSFTVEFQILANKENALAYFLPDAPL-EMIAIFDEVAKDLV 66 (79)
Q Consensus 25 nk~SL~Vdf~dL~~~~~~LA~~L~~~P~-~~L~~~~eaa~evv 66 (79)
+.+|..+|=.+...-...+...--+.|+ ++-++.++++.+.|
T Consensus 20 d~~~~pls~~E~~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~yi 62 (64)
T PF14164_consen 20 DVECMPLSDEEWEELCKHIQERKNEEPDEDLHEIVEDVVYDYI 62 (64)
T ss_pred cccCCCCCHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHh
Confidence 4567777766666666677777788888 88888888887765
No 43
>KOG0912|consensus
Probab=27.28 E-value=1.3e+02 Score=23.14 Aligned_cols=43 Identities=19% Similarity=0.273 Sum_probs=28.5
Q ss_pred HHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcC
Q psy13400 18 IKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPS 72 (79)
Q Consensus 18 I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~ 72 (79)
+...|..|.=-++==|.|++.|+.. ..++|++||.. +...||+
T Consensus 6 ~~~il~s~elvfv~FyAdWCrFSq~-----------L~piF~EAa~~-~~~e~P~ 48 (375)
T KOG0912|consen 6 IDSILDSNELVFVNFYADWCRFSQM-----------LKPIFEEAAAK-FKQEFPE 48 (375)
T ss_pred HHHhhccceEEeeeeehhhchHHHH-----------HhHHHHHHHHH-HHHhCCC
Confidence 4455555554444445788888764 45899999865 5668887
No 44
>cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.
Probab=26.76 E-value=1.1e+02 Score=17.15 Aligned_cols=36 Identities=6% Similarity=0.075 Sum_probs=24.5
Q ss_pred HHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhh
Q psy13400 14 YKEKIKKMCENNFSSFTVEFQILANKENALAYFLPD 49 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~ 49 (79)
..+.+.+......+.+.+|+.++...+..-+..|..
T Consensus 26 ~~~~~~~~~~~~~~~viid~~~v~~iDs~g~~~L~~ 61 (99)
T cd07043 26 LREALEELLAEGPRRLVLDLSGVTFIDSSGLGVLLG 61 (99)
T ss_pred HHHHHHHHHHcCCCEEEEECCCCCEEcchhHHHHHH
Confidence 455566555544588999999998888755555443
No 45
>PF01133 ER: Enhancer of rudimentary; InterPro: IPR000781 The Drosophila protein 'enhancer of rudimentary' (gene (e(r)) is a small protein of 104 residues whose function is not yet clear. From an evolutionary point of view, it is highly conserved [] and has been found to exist in probably all multicellular eukaryotic organisms. It has been proposed that this protein plays a role in the cell cycle.; GO: 0007049 cell cycle; PDB: 1W9G_A 2NML_A 1WWQ_A 1WZ7_B.
Probab=26.10 E-value=29 Score=22.08 Aligned_cols=32 Identities=31% Similarity=0.370 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHcCcceEEEechhHhhchHHHHH
Q psy13400 13 IYKEKIKKMCENNFSSFTVEFQILANKENALAY 45 (79)
Q Consensus 13 ~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~ 45 (79)
+|.+.++++ +-+..|+.-|..||..|-..|++
T Consensus 35 ~YE~~LK~~-nP~~~~ItYdIs~Lf~fID~l~D 66 (102)
T PF01133_consen 35 IYEEHLKRK-NPNSPSITYDISDLFDFIDSLAD 66 (102)
T ss_dssp HHHHHHHHH-STT-SS----HHHHHHHHHHSSE
T ss_pred HHHHHHHHc-CCCCCcccccHHHHHHHHhhhhh
Confidence 588888876 34788899888999988665654
No 46
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=25.46 E-value=43 Score=18.21 Aligned_cols=17 Identities=41% Similarity=0.456 Sum_probs=13.7
Q ss_pred HHHHHHHHHHcCcceEE
Q psy13400 14 YKEKIKKMCENNFSSFT 30 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~ 30 (79)
-.++|++++..|.+|+.
T Consensus 15 l~~~lk~~A~~~gRS~N 31 (50)
T PF03869_consen 15 LKEKLKERAEENGRSMN 31 (50)
T ss_dssp HHHHHHHHHHHTTS-HH
T ss_pred HHHHHHHHHHHhCCChH
Confidence 56889999999999975
No 47
>PF10223 DUF2181: Uncharacterized conserved protein (DUF2181); InterPro: IPR019356 This is region of approximately 250 residues with no known function.
Probab=24.91 E-value=1.6e+02 Score=21.28 Aligned_cols=40 Identities=15% Similarity=0.344 Sum_probs=27.5
Q ss_pred CCCcccchhhhHHHHHHHHHHcCcceEEEechhHhhchHHHHH
Q psy13400 3 PPSDETVSQYIYKEKIKKMCENNFSSFTVEFQILANKENALAY 45 (79)
Q Consensus 3 ~~~~d~~g~~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~ 45 (79)
||..+++.. ..+=+.++. ....-+.+||+.+..+.|.|..
T Consensus 51 PP~~~Sdlt--Lee~L~~v~-~~~kGIKLDFKs~eav~pSl~~ 90 (244)
T PF10223_consen 51 PPATDSDLT--LEEWLDEVL-SSRKGIKLDFKSIEAVEPSLDL 90 (244)
T ss_pred CCCCCCcCc--HHHHHHHHh-ccCcEEEEeccCHHHHHHHHHH
Confidence 666665543 455555555 5566899999999999885543
No 48
>PF02152 FolB: Dihydroneopterin aldolase; InterPro: IPR006157 Dihydroneopterin aldolase catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. In the opportunistic pathogen Pneumocystis carinii, dihydroneopterin aldolase function is expressed as the N-terminal portion of the multifunctional folic acid synthesis protein (Fas). This region encompasses two domains, FasA and FasB, which are 27% amino acid identical. FasA and FasB also share significant amino acid sequence similarity with bacterial dihydroneopterin aldolases. This region consists of two tandem sequences each homologous to folB and which form tetramers [].; GO: 0004150 dihydroneopterin aldolase activity, 0006760 folic acid-containing compound metabolic process; PDB: 1SQL_P 2O90_A 1B9L_A 1RSI_A 2NM2_C 1RRY_A 1RRW_A 1RS2_A 2DHN_A 1DHN_A ....
Probab=24.73 E-value=41 Score=20.49 Aligned_cols=41 Identities=20% Similarity=0.442 Sum_probs=28.4
Q ss_pred EechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCch
Q psy13400 31 VEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYE 74 (79)
Q Consensus 31 Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~ 74 (79)
|||..|.. .+..++.+..-..|+.+-+.+-+.++..||.-.
T Consensus 48 vdY~~l~~---~i~~~~~~~~f~llE~la~~i~~~i~~~~~~v~ 88 (113)
T PF02152_consen 48 VDYAELAE---AIRELVENSHFNLLETLAERIADRILKEFPQVQ 88 (113)
T ss_dssp SHHHHHHH---HHHHHHHSSEESSHHHHHHHHHHHHHHHTTTES
T ss_pred cCHHHHHH---HHHHHHhcCCcccHHHHHHHHHHHHHHhCCCcc
Confidence 45555544 455556666668888888888888888887443
No 49
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=23.60 E-value=79 Score=22.99 Aligned_cols=49 Identities=16% Similarity=0.080 Sum_probs=31.4
Q ss_pred CcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCc
Q psy13400 25 NFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSY 73 (79)
Q Consensus 25 nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y 73 (79)
++.|+.||.......+..-.....+..+..-..+++++...|..+||+.
T Consensus 81 ~~~~F~~DHl~~~~~d~e~~~~~~~~~e~~R~~l~~~l~~Yv~~hy~~g 129 (271)
T PF01267_consen 81 SKKSFSVDHLKQKASDVEPYEPPDEELESYRDALDKALEKYVKEHYPSG 129 (271)
T ss_dssp TTEEEEEETTTTEEEEEEE-----TSSHHHHHHHHHHHHHHHHHHSTTE
T ss_pred cCcEEEEeeeccEEccCccccccccchHHHHHHHHHHHHHHHHHhccCc
Confidence 5667777655444444333333445666777888999999999999875
No 50
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=23.00 E-value=75 Score=19.69 Aligned_cols=45 Identities=24% Similarity=0.219 Sum_probs=33.0
Q ss_pred HHHHHHHHHHcCcceEEEechhHhhch-----HHHHHHhhhChHHHHHHH
Q psy13400 14 YKEKIKKMCENNFSSFTVEFQILANKE-----NALAYFLPDAPLEMIAIF 58 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~Vdf~dL~~~~-----~~LA~~L~~~P~~~L~~~ 58 (79)
-.++|++++....-.+.|-+.+|.-.- ..+.--+.|++.-+|+||
T Consensus 45 K~eei~~~~~~~~~d~vvfd~~Lsp~Q~rNLe~~~~~~V~DRt~LIL~IF 94 (95)
T PF13167_consen 45 KVEEIKELIEELDADLVVFDNELSPSQQRNLEKALGVKVIDRTQLILEIF 94 (95)
T ss_pred HHHHHHHHHhhcCCCEEEECCCCCHHHHHHHHHHHCCeeeccccHHHHHc
Confidence 368899999988888888887775442 244555678888888876
No 51
>PRK11245 folX D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional
Probab=22.87 E-value=1.3e+02 Score=18.75 Aligned_cols=29 Identities=7% Similarity=0.205 Sum_probs=22.1
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHHHHhhCc
Q psy13400 42 ALAYFLPDAPLEMIAIFDEVAKDLVLSMYP 71 (79)
Q Consensus 42 ~LA~~L~~~P~~~L~~~~eaa~evv~~~~P 71 (79)
.+..++...+-..|+.+-+.+.+.++. +|
T Consensus 63 ~i~~~v~~~~~~llE~la~~Ia~~i~~-~~ 91 (120)
T PRK11245 63 NIIQHVENNRFSLLEKLTQDVLDIARE-HP 91 (120)
T ss_pred HHHHHHhcCCcchHHHHHHHHHHHHHc-cC
Confidence 566777778888888888888887775 44
No 52
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=22.77 E-value=42 Score=19.95 Aligned_cols=26 Identities=27% Similarity=0.337 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHHHHHHHhhCcCchh
Q psy13400 50 APLEMIAIFDEVAKDLVLSMYPSYER 75 (79)
Q Consensus 50 ~P~~~L~~~~eaa~evv~~~~P~y~~ 75 (79)
.|....+.|.+++.++....-++..+
T Consensus 27 ~~~~~~~~f~~v~~~lf~d~~inWGR 52 (101)
T PF00452_consen 27 TPDNAYETFNEVAEELFEDGGINWGR 52 (101)
T ss_dssp STTTHHHHHHHHHHHHTTTSSTCHHH
T ss_pred CcchHHHHHHHHHHHHhccCCCCHHH
Confidence 55556666777776665543444444
No 53
>PF14510 ABC_trans_N: ABC-transporter extracellular N-terminal
Probab=22.75 E-value=1.5e+02 Score=17.27 Aligned_cols=30 Identities=13% Similarity=0.058 Sum_probs=22.6
Q ss_pred hhhHHHHHHHHHHc---CcceEEEechhHhhch
Q psy13400 11 QYIYKEKIKKMCEN---NFSSFTVEFQILANKE 40 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~---nk~SL~Vdf~dL~~~~ 40 (79)
-..|...+.++..+ ..+++-|.|++|.-+.
T Consensus 36 l~~~lr~~~~~~~~~g~~~r~~GV~fknLtV~G 68 (85)
T PF14510_consen 36 LRRWLRNFVRRAEEQGIKPRKAGVSFKNLTVYG 68 (85)
T ss_pred HHHHHHHHHHHHHhCCCCCCeEEEEEeCCeEEE
Confidence 34577777777766 4689999999997653
No 54
>PF02667 SCFA_trans: Short chain fatty acid transporter; InterPro: IPR006160 Members of this family may be short chain fatty acid transporters although there has been no experimental characterisation of this function.
Probab=22.32 E-value=43 Score=26.46 Aligned_cols=35 Identities=20% Similarity=0.430 Sum_probs=31.9
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHH--HHhhCcCchhh
Q psy13400 42 ALAYFLPDAPLEMIAIFDEVAKDL--VLSMYPSYERV 76 (79)
Q Consensus 42 ~LA~~L~~~P~~~L~~~~eaa~ev--v~~~~P~y~~I 76 (79)
-|...|--.|..++..+.+|++.. ++..||=|+.|
T Consensus 288 ~lGllLh~tP~~y~~a~~~a~~~~~gIllQFPfYAGI 324 (453)
T PF02667_consen 288 FLGLLLHGTPRRYLRAVKEAVRSAAGILLQFPFYAGI 324 (453)
T ss_pred HHHHHHcCCHHHHHHHHHHHhccccceeeechHHHHH
Confidence 588899999999999999999998 78899999876
No 55
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=22.22 E-value=31 Score=18.69 Aligned_cols=14 Identities=29% Similarity=0.351 Sum_probs=10.3
Q ss_pred chHHHHHHhhhChH
Q psy13400 39 KENALAYFLPDAPL 52 (79)
Q Consensus 39 ~~~~LA~~L~~~P~ 52 (79)
+..+|..||.++|.
T Consensus 26 ~~~~L~~WL~~~P~ 39 (46)
T PF07533_consen 26 KLKELEEWLEEHPG 39 (46)
T ss_dssp BCCCHHHHHHH-TT
T ss_pred CHHHHHHHHHHCcC
Confidence 34589999999985
No 56
>PRK13386 fliH flagellar assembly protein H; Provisional
Probab=22.01 E-value=1.2e+02 Score=21.39 Aligned_cols=24 Identities=21% Similarity=0.342 Sum_probs=19.8
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHH
Q psy13400 42 ALAYFLPDAPLEMIAIFDEVAKDL 65 (79)
Q Consensus 42 ~LA~~L~~~P~~~L~~~~eaa~ev 65 (79)
.+...|..+|..++.++.+|+..+
T Consensus 135 vi~~el~~~p~~il~~v~eaL~~l 158 (236)
T PRK13386 135 VIRCELTLQPQQILALVEETLAAL 158 (236)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHhc
Confidence 455567889999999999999875
No 57
>TIGR02697 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode.
Probab=21.72 E-value=1.2e+02 Score=15.77 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=15.0
Q ss_pred hhhhHHHHHHHHHHcCcceEEEe
Q psy13400 10 SQYIYKEKIKKMCENNFSSFTVE 32 (79)
Q Consensus 10 g~~~Y~e~I~~m~~~nk~SL~Vd 32 (79)
++.++-+.+++|++.| .+-||
T Consensus 11 ~~li~n~~~~~l~nk~--WIPVS 31 (36)
T TIGR02697 11 ENLIANERIRQLYNKN--WIPVS 31 (36)
T ss_pred chhhhhHHHHHHhccC--ceeee
Confidence 3467888899998754 36665
No 58
>PF10386 DUF2441: Protein of unknown function (DUF2441); InterPro: IPR018840 This is a family of highly conserved predicted proteins primarily found in Bacillus species. Structurally they form homo-dimers, but their function is unknown. ; PDB: 2AUA_A.
Probab=21.55 E-value=1.6e+02 Score=19.83 Aligned_cols=33 Identities=18% Similarity=0.201 Sum_probs=24.1
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHHHH-hhCcCch
Q psy13400 42 ALAYFLPDAPLEMIAIFDEVAKDLVL-SMYPSYE 74 (79)
Q Consensus 42 ~LA~~L~~~P~~~L~~~~eaa~evv~-~~~P~y~ 74 (79)
+=|..+.+.-+.++..+.|.+.|.|. ..||+|-
T Consensus 38 e~~~~~~~y~~~t~~avRE~I~E~vRl~efP~~P 71 (141)
T PF10386_consen 38 ENAKVVMNYMDQTIRAVRETILEMVRLQEFPEYP 71 (141)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTS-
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHccCCc
Confidence 44666777778888888888888876 6899874
No 59
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.54 E-value=1.7e+02 Score=16.72 Aligned_cols=38 Identities=18% Similarity=0.082 Sum_probs=28.1
Q ss_pred EEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchh
Q psy13400 30 TVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYER 75 (79)
Q Consensus 30 ~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~ 75 (79)
.|+++||..-+- .|...-.++.+|=.-.|..-|+-|.+
T Consensus 3 tv~k~dLi~lGf--------~~~tA~~IIrqAK~~lV~~G~~~Y~n 40 (59)
T PF11372_consen 3 TVTKKDLIELGF--------SESTARDIIRQAKALLVQKGFSFYNN 40 (59)
T ss_pred ccCHHHHHHcCC--------CHHHHHHHHHHHHHHHHHcCCCcccC
Confidence 366677766432 56677778888888889999998876
No 60
>cd06845 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting
Probab=20.50 E-value=1.2e+02 Score=19.43 Aligned_cols=56 Identities=18% Similarity=0.287 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCcCchhh
Q psy13400 14 YKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYPSYERV 76 (79)
Q Consensus 14 Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P~y~~I 76 (79)
-...|++++.+ |+-.+.++.. .++.-|...|....+.|.+++.++...--++..+|
T Consensus 35 ~~~~Lr~~~de----le~~~~~~f~---~~~~~l~~~~~~~~~~f~~v~~~lf~dg~inWGRI 90 (144)
T cd06845 35 VAETLRRVGDE----LEEKHRRLFE---NMCRQLNISPDNAYEVFQEVARELFEDGGINWGRI 90 (144)
T ss_pred HHHHHHHHHHH----HHHHHHHHHH---HHHHHhCCCcchHHHHHHHHHHHHhccCCCChHHH
Confidence 44566666655 2223333322 46666667888889999999988877645565554
No 61
>cd03819 GT1_WavL_like This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
Probab=20.49 E-value=3e+02 Score=18.90 Aligned_cols=51 Identities=16% Similarity=0.114 Sum_probs=34.0
Q ss_pred HHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhC
Q psy13400 19 KKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMY 70 (79)
Q Consensus 19 ~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~ 70 (79)
.+.+..+...+.++..|.......|...+...|++.....+ .+++.+...|
T Consensus 300 ~e~i~~~~~g~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~-~a~~~~~~~f 350 (355)
T cd03819 300 RETVRPGETGLLVPPGDAEALAQALDQILSLLPEGRAKMFA-KARMCVETLF 350 (355)
T ss_pred HHHHhCCCceEEeCCCCHHHHHHHHHHHHhhCHHHHHHHHH-HHHHHHHHhh
Confidence 34445566778888888887777777777778886655544 4555555444
No 62
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=20.14 E-value=2.1e+02 Score=16.97 Aligned_cols=37 Identities=8% Similarity=0.188 Sum_probs=27.2
Q ss_pred hhhHHHHHHHHHHcCc---------ceEEEechhHhhchHHHHHHh
Q psy13400 11 QYIYKEKIKKMCENNF---------SSFTVEFQILANKENALAYFL 47 (79)
Q Consensus 11 ~~~Y~e~I~~m~~~nk---------~SL~Vdf~dL~~~~~~LA~~L 47 (79)
.....++|.+...... +.+.+|+..+...+..-+..|
T Consensus 24 ~~~~~~~i~~~~~~~~~~~~~~~~~~~vIlD~s~v~~iDssgi~~L 69 (117)
T PF01740_consen 24 AEEFRDRIRKLIDEDPERIKKRQTIKNVILDMSGVSFIDSSGIQAL 69 (117)
T ss_dssp HHHHHHHHHHHHCCSSS--HTSSSSSEEEEEETTESEESHHHHHHH
T ss_pred HHHHHHHHHHhhhcccccccccccceEEEEEEEeCCcCCHHHHHHH
Confidence 3457788888888765 899999999977776444443
No 63
>KOG0158|consensus
Probab=20.06 E-value=1.3e+02 Score=23.89 Aligned_cols=40 Identities=25% Similarity=0.492 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHHcCcceEEEechhHhhchHHHHHHhhhChHHHHHHHHHHHHHHHHhhCc
Q psy13400 12 YIYKEKIKKMCENNFSSFTVEFQILANKENALAYFLPDAPLEMIAIFDEVAKDLVLSMYP 71 (79)
Q Consensus 12 ~~Y~e~I~~m~~~nk~SL~Vdf~dL~~~~~~LA~~L~~~P~~~L~~~~eaa~evv~~~~P 71 (79)
.+-+++|++.|.+... ++|+.|.. |+.++-+++| ++++||
T Consensus 329 ~kLreEI~~~~~~~~~---ltyd~l~~----------------L~YLd~Vi~E-TLR~yP 368 (499)
T KOG0158|consen 329 DKLREEIDEVLEEKEG---LTYDSLSK----------------LKYLDMVIKE-TLRLYP 368 (499)
T ss_pred HHHHHHHHHHhcccCC---CCHHHHhC----------------CcHHHHHHHH-HHhhCC
Confidence 3466777777665443 77776654 5667777776 444555
Done!