Query 031052
Match_columns 166
No_of_seqs 143 out of 378
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:31:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031052.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031052hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1649 SWI-SNF chromatin remo 100.0 7.9E-57 1.7E-61 392.5 14.9 152 10-162 164-316 (397)
2 PF04855 SNF5: SNF5 / SMARCB1 100.0 1.8E-55 3.9E-60 369.4 18.6 146 16-162 2-178 (244)
3 KOG1649 SWI-SNF chromatin remo 99.8 1.2E-20 2.6E-25 165.7 7.0 73 93-165 172-244 (397)
4 PF04855 SNF5: SNF5 / SMARCB1 99.8 6.7E-20 1.4E-24 154.3 8.9 71 93-163 4-75 (244)
5 PF09070 PFU: PFU (PLAA family 89.1 0.99 2.2E-05 34.4 5.1 51 26-81 60-110 (116)
6 PF05402 PqqD: Coenzyme PQQ sy 75.4 3.3 7.1E-05 27.3 2.8 44 40-83 20-63 (68)
7 PF09070 PFU: PFU (PLAA family 68.4 20 0.00044 27.3 5.9 53 99-157 58-110 (116)
8 PF07531 TAFH: NHR1 homology t 49.8 18 0.00039 26.8 2.8 39 44-82 35-78 (96)
9 COG1405 SUA7 Transcription ini 48.6 39 0.00085 29.4 5.1 38 48-86 190-227 (285)
10 PF02022 Integrase_Zn: Integra 45.1 27 0.00058 21.7 2.6 21 56-76 12-32 (40)
11 TIGR03859 PQQ_PqqD coenzyme PQ 43.2 26 0.00057 24.4 2.7 38 40-77 34-71 (81)
12 COG1405 SUA7 Transcription ini 41.3 62 0.0013 28.1 5.2 33 123-157 190-222 (285)
13 TIGR02877 spore_yhbH sporulati 40.4 13 0.00029 33.6 1.0 21 47-67 111-131 (371)
14 PRK05325 hypothetical protein; 37.9 23 0.0005 32.4 2.1 21 47-67 99-119 (401)
15 PF03701 UPF0181: Uncharacteri 35.9 23 0.0005 23.4 1.3 20 139-158 27-46 (51)
16 PF04358 DsrC: DsrC like prote 35.7 85 0.0018 23.5 4.6 48 115-165 15-62 (109)
17 PRK05114 hypothetical protein; 34.5 25 0.00053 23.9 1.3 20 139-158 27-46 (59)
18 PF05402 PqqD: Coenzyme PQQ sy 34.3 42 0.00092 21.8 2.5 28 114-141 19-46 (68)
19 smart00549 TAFH TAF homology. 33.3 68 0.0015 23.6 3.6 23 45-67 35-57 (92)
20 TIGR02849 spore_III_AD stage I 32.4 35 0.00077 25.4 2.0 13 129-141 56-68 (101)
21 PTZ00202 tuzin; Provisional 31.5 86 0.0019 29.9 4.8 37 126-162 321-357 (550)
22 cd04752 Commd4 COMM_Domain con 30.8 92 0.002 24.7 4.3 32 125-158 60-91 (174)
23 PRK07075 isochorismate-pyruvat 27.5 1E+02 0.0023 22.4 3.8 31 57-87 62-97 (101)
24 TIGR02384 RelB_DinJ addiction 27.2 1.3E+02 0.0028 21.2 4.1 12 130-141 16-27 (83)
25 PRK00423 tfb transcription ini 27.2 1.4E+02 0.0031 25.8 5.2 35 122-158 214-248 (310)
26 PRK00423 tfb transcription ini 26.0 1.5E+02 0.0032 25.7 5.1 37 45-82 212-248 (310)
27 PF15494 SRCR_2: Scavenger rec 23.6 61 0.0013 23.0 1.9 18 124-142 23-40 (98)
28 PF01418 HTH_6: Helix-turn-hel 22.7 72 0.0016 21.7 2.1 24 57-80 52-77 (77)
29 PRK05325 hypothetical protein; 22.6 61 0.0013 29.7 2.1 19 124-142 101-119 (401)
30 cd04752 Commd4 COMM_Domain con 22.2 2.2E+02 0.0047 22.6 5.0 30 49-79 59-88 (174)
31 COG3140 Uncharacterized protei 22.1 72 0.0016 21.6 1.8 19 139-157 27-45 (60)
32 COG2127 Uncharacterized conser 21.4 1.3E+02 0.0027 22.7 3.3 31 123-154 36-67 (107)
33 PHA01623 hypothetical protein 21.3 1.8E+02 0.004 19.0 3.7 27 132-161 29-55 (56)
34 PF04221 RelB: RelB antitoxin; 21.1 1.9E+02 0.004 20.1 4.0 12 130-141 15-26 (83)
35 PTZ00202 tuzin; Provisional 20.7 3.4E+02 0.0073 26.0 6.5 36 51-86 321-357 (550)
36 TIGR03515 GldC gliding motilit 20.6 96 0.0021 23.5 2.5 28 26-53 5-32 (108)
37 PRK11235 bifunctional antitoxi 20.3 2.2E+02 0.0048 20.2 4.2 12 130-141 15-26 (80)
No 1
>KOG1649 consensus SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=7.9e-57 Score=392.51 Aligned_cols=152 Identities=45% Similarity=0.722 Sum_probs=146.5
Q ss_pred cccccccCCCCceeeeeEEEeeeCCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCCh-HHHHHHHHHHHHHHHHhhccc
Q 031052 10 KAPVKFRMPTADNLVPIRLDIETEGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPP-QFITQIAQSIQTQLTEFRSYE 88 (166)
Q Consensus 10 ~~~~~~~~~~~e~LVPIrLdle~~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~-~f~~~I~~sI~~Qi~ey~~~~ 88 (166)
+...+..++++|.|||||||+|.+|+||||+|+||+||+.||||+||+++|+||+||+ .|+++|++||++||++|..++
T Consensus 164 ~~~~~~~~~~~e~lVPIRLDie~dg~klrDtFtWN~ndk~itpe~FAei~c~Dldl~~~~~v~qIa~sIq~Qied~~~~~ 243 (397)
T KOG1649|consen 164 KEPKKANAETPEVLVPIRLDIELDGQKLRDTFTWNKNDKLITPEMFAEILCKDLDLPPATFVTQIAQSIQQQIEDYEPDP 243 (397)
T ss_pred HHHHHhhCCCCceeeeEEEeeecccchhhhhcccccCCccCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHhcCCCC
Confidence 4466788999999999999999999999999999999999999999999999999976 899999999999999999999
Q ss_pred CCCcCCCceeeeeEEEEEeCCeeeeeeeeecCCCCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHhhc
Q 031052 89 GQDMYTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEVMI 162 (166)
Q Consensus 89 ~~~~~~~e~lvpI~Ldi~~~~~~l~D~FeWdl~~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~~ 162 (166)
+.++.++|.+|+|+|||++|+..|.|||+|||+++.++||+||..+|.||||+ |||+|+|||||||||..+++
T Consensus 244 ~~~~~~~d~rviikLdi~vg~~~l~DQFeWdls~~~~~PEEFA~~lC~dLGL~-gEf~taIA~SIreql~~~~k 316 (397)
T KOG1649|consen 244 AIEMNSGDLRVIIKLDINVGNLSLVDQFEWDLSNPENSPEEFATSLCQDLGLG-GEFVTAIAYSIREQLLWIKK 316 (397)
T ss_pred cccccCCceEEEEEEEEEeccceehhhheeccCCCCCCHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999 59999999999999999875
No 2
>PF04855 SNF5: SNF5 / SMARCB1 / INI1; InterPro: IPR006939 SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far []. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].; GO: 0006338 chromatin remodeling, 0000228 nuclear chromosome
Probab=100.00 E-value=1.8e-55 Score=369.40 Aligned_cols=146 Identities=42% Similarity=0.719 Sum_probs=135.8
Q ss_pred cCCCCceeeeeEEEeee-CCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCChH-HHHHHHHHHHHHHHHhhcccCCCc-
Q 031052 16 RMPTADNLVPIRLDIET-EGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPPQ-FITQIAQSIQTQLTEFRSYEGQDM- 92 (166)
Q Consensus 16 ~~~~~e~LVPIrLdle~-~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~~-f~~~I~~sI~~Qi~ey~~~~~~~~- 92 (166)
++..++.|||||||+|+ +|+||||+|+||+||+.+|||+||++||+||+||+. |.++|++||++||++|+....+++
T Consensus 2 qa~~~e~LVPIRLdie~~~~~klrD~FlWNlne~~itpe~FA~~lc~Dl~lp~~~~~~~I~~sI~~Qi~e~~~~a~~~l~ 81 (244)
T PF04855_consen 2 QAELPENLVPIRLDIEIRDGYKLRDTFLWNLNEPLITPEEFAEILCEDLDLPPSFFVQQIANSIREQIEEYASVAAHPLF 81 (244)
T ss_pred CccCCceeeeEEEEeecCCCceEEEEEEeeCCCCCCCHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHhhhhhhhc
Confidence 56678999999999999 999999999999999999999999999999999996 699999999999999998743221
Q ss_pred ----------------------------CCCceeeeeEEEEEeCCeeeeeeeeecCCCCCCCHHHHHHHHHHHcCCCCCc
Q 031052 93 ----------------------------YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPE 144 (166)
Q Consensus 93 ----------------------------~~~e~lvpI~Ldi~~~~~~l~D~FeWdl~~~~~tPE~FA~~lc~DLgL~~~e 144 (166)
..++.+|+|+|||++|++.|+|+|||||+++.++||+||+++|+||||+ +|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rv~I~LdI~ig~~~l~DqFEWDL~~~~~~PE~FA~~~c~dLgL~-~E 160 (244)
T PF04855_consen 82 QNPEMEPSEKRLDPEDPYTAFADSSLGSPDDDLRVIIKLDITIGNHLLVDQFEWDLSNPPNSPEEFARVLCADLGLP-GE 160 (244)
T ss_pred cccccccccccccccccccccccccccCCCCceEEEEEEEEEECCEEEEEEEEecCCCCCCCHHHHHHHHHHHcCCc-HH
Confidence 1257899999999999999999999999999999999999999999999 69
Q ss_pred hHHHHHHHHHHHHHHhhc
Q 031052 145 VGPAVAFAIREQLYEVMI 162 (166)
Q Consensus 145 f~~~Ia~sIreQl~~~~~ 162 (166)
|++||||||||||.+|++
T Consensus 161 f~~aIahsIrEq~~~~kK 178 (244)
T PF04855_consen 161 FVPAIAHSIREQLLKYKK 178 (244)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999986
No 3
>KOG1649 consensus SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics; Transcription]
Probab=99.82 E-value=1.2e-20 Score=165.73 Aligned_cols=73 Identities=29% Similarity=0.540 Sum_probs=69.4
Q ss_pred CCCceeeeeEEEEEeCCeeeeeeeeecCCCCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHhhcCCC
Q 031052 93 YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEVMIIPP 165 (166)
Q Consensus 93 ~~~e~lvpI~Ldi~~~~~~l~D~FeWdl~~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~~~~~ 165 (166)
.+++.+|||||||+++|++|+|+|.||.|++.+|||+||+++|+||+|+...|+++||.+|++||++|...|+
T Consensus 172 ~~~e~lVPIRLDie~dg~klrDtFtWN~ndk~itpe~FAei~c~Dldl~~~~~v~qIa~sIq~Qied~~~~~~ 244 (397)
T KOG1649|consen 172 ETPEVLVPIRLDIELDGQKLRDTFTWNKNDKLITPEMFAEILCKDLDLPPATFVTQIAQSIQQQIEDYEPDPA 244 (397)
T ss_pred CCCceeeeEEEeeecccchhhhhcccccCCccCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHhcCCCCc
Confidence 4578899999999999999999999999999999999999999999997569999999999999999999886
No 4
>PF04855 SNF5: SNF5 / SMARCB1 / INI1; InterPro: IPR006939 SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far []. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].; GO: 0006338 chromatin remodeling, 0000228 nuclear chromosome
Probab=99.81 E-value=6.7e-20 Score=154.29 Aligned_cols=71 Identities=35% Similarity=0.627 Sum_probs=66.1
Q ss_pred CCCceeeeeEEEEEe-CCeeeeeeeeecCCCCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHhhcC
Q 031052 93 YTAEKIVPIKLDLRV-NHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEVMII 163 (166)
Q Consensus 93 ~~~e~lvpI~Ldi~~-~~~~l~D~FeWdl~~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~~~ 163 (166)
...+.+||||||+++ +|++|+|+|.||+|++.+|||+||++||.|||||...|.++|+.+|++||.+|+..
T Consensus 4 ~~~e~LVPIRLdie~~~~~klrD~FlWNlne~~itpe~FA~~lc~Dl~lp~~~~~~~I~~sI~~Qi~e~~~~ 75 (244)
T PF04855_consen 4 ELPENLVPIRLDIEIRDGYKLRDTFLWNLNEPLITPEEFAEILCEDLDLPPSFFVQQIANSIREQIEEYASV 75 (244)
T ss_pred cCCceeeeEEEEeecCCCceEEEEEEeeCCCCCCCHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHhh
Confidence 346889999999999 99999999999999999999999999999999995347999999999999999965
No 5
>PF09070 PFU: PFU (PLAA family ubiquitin binding); InterPro: IPR015155 The PFU (for PLAA family ubiquitin binding domain) is an ubiquitin binding domain with no homology to several known ubiquitin binding domains (e.g., UIM, NZF, UBA, UEV, UBP, or CUE domains). The PFU domain appears to be unique to the PLAA family of proteins. A single member of this family of proteins exists in every eukaryotic species examined. Each of these homologues possesses identical domain structure: an N-terminal domain containing seven WD40 repeats, a central PFU domain, and a C-terminal PUL domain, which directly binds to Cdc48, a member of the AAA-ATPase family of molecular chaperone []. In addition to ubiquitin, the PFU domain of DOA1 has been shown to bind to the SH3 domain []. Secondary structure predictions of the PFU domain suggest the presence of an extensive length of beta-sheet, N-terminal to an alpha-helical region []. Some proteins known to contain a PFU domain include: Saccharomyces cerevisiae DOA1 (UFD3, ZZZ4), involved in the ubiquitin conjugation pathway. DOA1 participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. Schizosaccharomyces pombe ubiquitin homeostasis protein Lub1, acts as a negative regulator of vacuole-dependent ubiquitin degradation. Mammalian phospholipase A-2-activating protein (PLA2P, PLAA), the homologue of DOA1. PLA2P plays an important role in the regulation of specific inflammatory disease processes. ; PDB: 2K8B_B 2K8A_A 2K8C_B 2K89_A 3L3F_X 3PST_A 3PSP_A.
Probab=89.15 E-value=0.99 Score=34.42 Aligned_cols=51 Identities=27% Similarity=0.422 Sum_probs=33.8
Q ss_pred eEEEeeeCCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Q 031052 26 IRLDIETEGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQL 81 (166)
Q Consensus 26 IrLdle~~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Qi 81 (166)
+.+|++-++-.++ .-.|.+| .|..=|+.+|.+.+||..|..+|++-|.+-.
T Consensus 60 f~Vdi~dg~~~lk--LpyN~~d---nP~~aAq~Fi~~n~Lp~~yl~qI~~FI~~N~ 110 (116)
T PF09070_consen 60 FDVDIEDGGPPLK--LPYNKGD---NPYEAAQKFIERNNLPQSYLDQIANFIIQNT 110 (116)
T ss_dssp EEE--STTSS-EE--EEE-TTS----HHHHHHHHHHHHT--CCHHHHHHHHHHHHH
T ss_pred EEEEecCCCccee--CCccCCC---CHHHHHHHHHHHcCCCHHHHHHHHHHHHHcC
Confidence 4555553333333 3457777 6999999999999999999999999998743
No 6
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=75.41 E-value=3.3 Score=27.26 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=28.5
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHH
Q 031052 40 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTE 83 (166)
Q Consensus 40 ~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Qi~e 83 (166)
.|+|++-+...|.++-++.+|+.++.++.-...-+.+.-+||.+
T Consensus 20 ~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 20 AFIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLRE 63 (68)
T ss_dssp HHHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 47899888889999999999999999985434444444444544
No 7
>PF09070 PFU: PFU (PLAA family ubiquitin binding); InterPro: IPR015155 The PFU (for PLAA family ubiquitin binding domain) is an ubiquitin binding domain with no homology to several known ubiquitin binding domains (e.g., UIM, NZF, UBA, UEV, UBP, or CUE domains). The PFU domain appears to be unique to the PLAA family of proteins. A single member of this family of proteins exists in every eukaryotic species examined. Each of these homologues possesses identical domain structure: an N-terminal domain containing seven WD40 repeats, a central PFU domain, and a C-terminal PUL domain, which directly binds to Cdc48, a member of the AAA-ATPase family of molecular chaperone []. In addition to ubiquitin, the PFU domain of DOA1 has been shown to bind to the SH3 domain []. Secondary structure predictions of the PFU domain suggest the presence of an extensive length of beta-sheet, N-terminal to an alpha-helical region []. Some proteins known to contain a PFU domain include: Saccharomyces cerevisiae DOA1 (UFD3, ZZZ4), involved in the ubiquitin conjugation pathway. DOA1 participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. Schizosaccharomyces pombe ubiquitin homeostasis protein Lub1, acts as a negative regulator of vacuole-dependent ubiquitin degradation. Mammalian phospholipase A-2-activating protein (PLA2P, PLAA), the homologue of DOA1. PLA2P plays an important role in the regulation of specific inflammatory disease processes. ; PDB: 2K8B_B 2K8A_A 2K8C_B 2K89_A 3L3F_X 3PST_A 3PSP_A.
Probab=68.38 E-value=20 Score=27.28 Aligned_cols=53 Identities=15% Similarity=0.183 Sum_probs=34.2
Q ss_pred eeeEEEEEeCCeeeeeeeeecCCCCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHH
Q 031052 99 VPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQL 157 (166)
Q Consensus 99 vpI~Ldi~~~~~~l~D~FeWdl~~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl 157 (166)
..+.+||.-|+..|. .-.|.+ -+|-.=|+.+|.+.+|| ..|..+|+.-|....
T Consensus 58 yVf~Vdi~dg~~~lk--LpyN~~---dnP~~aAq~Fi~~n~Lp-~~yl~qI~~FI~~N~ 110 (116)
T PF09070_consen 58 YVFDVDIEDGGPPLK--LPYNKG---DNPYEAAQKFIERNNLP-QSYLDQIANFIIQNT 110 (116)
T ss_dssp EEEEE--STTSS-EE--EEE-TT---S-HHHHHHHHHHHHT---CCHHHHHHHHHHHHH
T ss_pred EEEEEEecCCCccee--CCccCC---CCHHHHHHHHHHHcCCC-HHHHHHHHHHHHHcC
Confidence 446666665554443 334554 58999999999999999 699999999987654
No 8
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=49.84 E-value=18 Score=26.79 Aligned_cols=39 Identities=21% Similarity=0.367 Sum_probs=26.2
Q ss_pred cCCCCCCCHHHHHHHHHHHcCCCh-----HHHHHHHHHHHHHHH
Q 031052 44 NPSDPDSEVVVFAKRTVRDLKLPP-----QFITQIAQSIQTQLT 82 (166)
Q Consensus 44 Nlne~~itpE~FA~~lc~Dl~lp~-----~f~~~I~~sI~~Qi~ 82 (166)
++.+..|++|+|...|=++++.|+ .|...=.-+.|+.+.
T Consensus 35 ~L~~~~i~~EeF~~~Lq~~lns~pqP~lvPFLK~~lp~Lr~~l~ 78 (96)
T PF07531_consen 35 NLVDGKIEAEEFTSKLQEELNSSPQPYLVPFLKKSLPALRQELP 78 (96)
T ss_dssp HHHTTSS-HHHHHHHHHHHCTSS--TTHHHHHHHHHHHHHHCHC
T ss_pred HHHcCCCCHHHHHHHHHHHhcCCCCcchHHHHHHhHHHHHHHHH
Confidence 456789999999999999999986 344443444444333
No 9
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=48.57 E-value=39 Score=29.38 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhhc
Q 031052 48 PDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTEFRS 86 (166)
Q Consensus 48 ~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Qi~ey~~ 86 (166)
+.+.|+.|..++|.+|+||.. +...|.-|-++..+...
T Consensus 190 ~~~~p~~yi~rf~s~L~l~~~-v~~~a~ei~~~~~~~g~ 227 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLSDE-VRRKAIEIVKKAKRAGL 227 (285)
T ss_pred CCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhCc
Confidence 346999999999999999964 33444455555555433
No 10
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=45.07 E-value=27 Score=21.69 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=15.2
Q ss_pred HHHHHHHcCCChHHHHHHHHH
Q 031052 56 AKRTVRDLKLPPQFITQIAQS 76 (166)
Q Consensus 56 A~~lc~Dl~lp~~f~~~I~~s 76 (166)
++.|..++|||..-+.+|+++
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~ 32 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQ 32 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHH
Confidence 578999999999877777754
No 11
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=43.18 E-value=26 Score=24.40 Aligned_cols=38 Identities=3% Similarity=0.026 Sum_probs=29.3
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHH
Q 031052 40 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSI 77 (166)
Q Consensus 40 ~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI 77 (166)
.|+|.+=+..-|+++-+..||++|+.+......+.+-+
T Consensus 34 ~~Iw~lldg~~tv~eI~~~L~~~Y~~~e~~~~dV~~fL 71 (81)
T TIGR03859 34 GEILELCDGKRSLAEIIQELAQRFPAAEEIEDDVIAFL 71 (81)
T ss_pred HHHHHHccCCCcHHHHHHHHHHHcCChhhHHHHHHHHH
Confidence 58899888888999999999999999434444444433
No 12
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=41.35 E-value=62 Score=28.13 Aligned_cols=33 Identities=21% Similarity=0.389 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHH
Q 031052 123 YESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQL 157 (166)
Q Consensus 123 ~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl 157 (166)
+...|+.|-..+|.+|||+ .+ +...|..|-.+.
T Consensus 190 ~~~~p~~yi~rf~s~L~l~-~~-v~~~a~ei~~~~ 222 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLS-DE-VRRKAIEIVKKA 222 (285)
T ss_pred CCCCHHHHHHHHHHHcCCC-HH-HHHHHHHHHHHH
Confidence 3479999999999999998 34 444444443333
No 13
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=40.38 E-value=13 Score=33.58 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 031052 47 DPDSEVVVFAKRTVRDLKLPP 67 (166)
Q Consensus 47 e~~itpE~FA~~lc~Dl~lp~ 67 (166)
|-.+|.|+|+..|-+||+||.
T Consensus 111 e~e~s~eE~~~~lfEdLeLPn 131 (371)
T TIGR02877 111 ETEVTLEELFELLFEDLELPN 131 (371)
T ss_pred EEEecHHHHHHHHHhhccCCC
Confidence 456899999999999999974
No 14
>PRK05325 hypothetical protein; Provisional
Probab=37.89 E-value=23 Score=32.37 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 031052 47 DPDSEVVVFAKRTVRDLKLPP 67 (166)
Q Consensus 47 e~~itpE~FA~~lc~Dl~lp~ 67 (166)
|-.+|.|+|+..|-+||+||.
T Consensus 99 e~els~eE~~~~lfEdLeLPn 119 (401)
T PRK05325 99 EFEISLEELLDLLFEDLELPN 119 (401)
T ss_pred EEEecHHHHHHHHHhhcCCCC
Confidence 457899999999999999974
No 15
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=35.90 E-value=23 Score=23.38 Aligned_cols=20 Identities=35% Similarity=0.343 Sum_probs=17.0
Q ss_pred CCCCCchHHHHHHHHHHHHH
Q 031052 139 GIEDPEVGPAVAFAIREQLY 158 (166)
Q Consensus 139 gL~~~ef~~~Ia~sIreQl~ 158 (166)
|++.+|....+|..|||+-.
T Consensus 27 GmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 27 GMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred cccHHHHHHHHHHHHHHHHH
Confidence 77777999999999998754
No 16
>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=35.73 E-value=85 Score=23.47 Aligned_cols=48 Identities=25% Similarity=0.271 Sum_probs=31.4
Q ss_pred eeeecCCCCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHhhcCCC
Q 031052 115 HFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEVMIIPP 165 (166)
Q Consensus 115 ~FeWdl~~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~~~~~ 165 (166)
-|..|..+ +++| .|..+++..|+.-.+-+=.|-+-+|+.-.++..+|+
T Consensus 15 GfL~~~~d--W~ee-vA~~lA~~egI~Ltd~HW~vI~flR~~y~~~~~~P~ 62 (109)
T PF04358_consen 15 GFLVDPED--WNEE-VAEALAKEEGIELTDEHWEVIRFLRDYYQEYGVSPA 62 (109)
T ss_dssp SEESSGGG----HH-HHHHHHHCTT-S--HHHHHHHHHHHHHHHHHSS---
T ss_pred cCcCChHh--CCHH-HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHCCCCc
Confidence 37766653 5555 999999999987334455688999999999888875
No 17
>PRK05114 hypothetical protein; Provisional
Probab=34.49 E-value=25 Score=23.89 Aligned_cols=20 Identities=25% Similarity=0.218 Sum_probs=17.1
Q ss_pred CCCCCchHHHHHHHHHHHHH
Q 031052 139 GIEDPEVGPAVAFAIREQLY 158 (166)
Q Consensus 139 gL~~~ef~~~Ia~sIreQl~ 158 (166)
|++.||....||+.|||+-.
T Consensus 27 GmSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 27 GMSSGEAIALVAEELRANHQ 46 (59)
T ss_pred cccHHHHHHHHHHHHHHHHh
Confidence 77778999999999999654
No 18
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=34.35 E-value=42 Score=21.79 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=21.1
Q ss_pred eeeeecCCCCCCCHHHHHHHHHHHcCCC
Q 031052 114 DHFLWDLNNYESDPEEFARTFCNDMGIE 141 (166)
Q Consensus 114 D~FeWdl~~~~~tPE~FA~~lc~DLgL~ 141 (166)
-.|.|++.+...|.++-++.+|+..+.+
T Consensus 19 a~~Iw~~~~g~~t~~ei~~~l~~~y~~~ 46 (68)
T PF05402_consen 19 AAFIWELLDGPRTVEEIVDALAEEYDVD 46 (68)
T ss_dssp HHHHHHH--SSS-HHHHHHHHHHHTT--
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHcCCC
Confidence 4689999998899999999999999887
No 19
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=33.26 E-value=68 Score=23.63 Aligned_cols=23 Identities=17% Similarity=0.138 Sum_probs=20.3
Q ss_pred CCCCCCCHHHHHHHHHHHcCCCh
Q 031052 45 PSDPDSEVVVFAKRTVRDLKLPP 67 (166)
Q Consensus 45 lne~~itpE~FA~~lc~Dl~lp~ 67 (166)
+-+..+++|+|...|=+.++.|+
T Consensus 35 L~~~~i~~EeF~~~Lq~~lns~~ 57 (92)
T smart00549 35 LVNGTITAEEFTSRLQEALNSPL 57 (92)
T ss_pred HHhCCCCHHHHHHHHHHHHcCCC
Confidence 34678999999999999999986
No 20
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=32.40 E-value=35 Score=25.39 Aligned_cols=13 Identities=38% Similarity=0.853 Sum_probs=12.0
Q ss_pred HHHHHHHHHcCCC
Q 031052 129 EFARTFCNDMGIE 141 (166)
Q Consensus 129 ~FA~~lc~DLgL~ 141 (166)
+||..+|+|-|-+
T Consensus 56 ef~s~iCkDAG~~ 68 (101)
T TIGR02849 56 EFGSQICKDAGEK 68 (101)
T ss_pred HHHHHHHHHcChH
Confidence 6999999999986
No 21
>PTZ00202 tuzin; Provisional
Probab=31.45 E-value=86 Score=29.85 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHhhc
Q 031052 126 DPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEVMI 162 (166)
Q Consensus 126 tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~~ 162 (166)
+|++|-+.++..||+++.+....+-.+|.+.+.+.+.
T Consensus 321 g~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~ 357 (550)
T PTZ00202 321 GTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKK 357 (550)
T ss_pred CHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHH
Confidence 7899999999999998433445788889888887654
No 22
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=30.76 E-value=92 Score=24.73 Aligned_cols=32 Identities=16% Similarity=0.295 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHH
Q 031052 125 SDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLY 158 (166)
Q Consensus 125 ~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~ 158 (166)
.+++.|...+ .+|||| .|...+++..-.+.-.
T Consensus 60 ~~~~~l~~eL-~~lglp-~e~~~~l~~~~~~~~~ 91 (174)
T cd04752 60 VDGESLSSEL-QQLGLP-KEHATSLCRSYEEKQS 91 (174)
T ss_pred CCHHHHHHHH-HHcCCC-HHHHHHHHHHHHHHHH
Confidence 6799999988 899999 6999998886655443
No 23
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=27.47 E-value=1e+02 Score=22.41 Aligned_cols=31 Identities=23% Similarity=0.295 Sum_probs=22.4
Q ss_pred HHHHHHcCCChHH-----HHHHHHHHHHHHHHhhcc
Q 031052 57 KRTVRDLKLPPQF-----ITQIAQSIQTQLTEFRSY 87 (166)
Q Consensus 57 ~~lc~Dl~lp~~f-----~~~I~~sI~~Qi~ey~~~ 87 (166)
..++.++|+|+.+ ..-|..+|+.|..+|...
T Consensus 62 ~~~a~~~gl~~~~i~~if~~Ii~~~i~~q~~~~~~~ 97 (101)
T PRK07075 62 RRWAEQAGLDADFVEKLFAQLIHWYIAQQIKHWRQQ 97 (101)
T ss_pred HHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4455678998854 344568999999999764
No 24
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=27.17 E-value=1.3e+02 Score=21.20 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=9.2
Q ss_pred HHHHHHHHcCCC
Q 031052 130 FARTFCNDMGIE 141 (166)
Q Consensus 130 FA~~lc~DLgL~ 141 (166)
=|..+|++|||+
T Consensus 16 ~a~~i~~~lGl~ 27 (83)
T TIGR02384 16 EAYAVFEELGLT 27 (83)
T ss_pred HHHHHHHHhCCC
Confidence 366788888887
No 25
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=27.15 E-value=1.4e+02 Score=25.78 Aligned_cols=35 Identities=20% Similarity=0.363 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHH
Q 031052 122 NYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLY 158 (166)
Q Consensus 122 ~~~~tPE~FA~~lc~DLgL~~~ef~~~Ia~sIreQl~ 158 (166)
-+..+|+.|...+|..|+|+. . +...|..|-....
T Consensus 214 ~~~~~p~~~i~r~~~~L~L~~-~-v~~~A~~i~~~a~ 248 (310)
T PRK00423 214 LPPTDPIDYVPRFASELGLSG-E-VQKKAIEILQKAK 248 (310)
T ss_pred CCCCCHHHHHHHHHHHcCCCH-H-HHHHHHHHHHHHH
Confidence 446789999999999999983 3 4445555555443
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.03 E-value=1.5e+02 Score=25.69 Aligned_cols=37 Identities=16% Similarity=0.196 Sum_probs=25.6
Q ss_pred CCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHH
Q 031052 45 PSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLT 82 (166)
Q Consensus 45 lne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Qi~ 82 (166)
++-+.++|+.|...+|..|+||.... ..|..|-++..
T Consensus 212 ~~~~~~~p~~~i~r~~~~L~L~~~v~-~~A~~i~~~a~ 248 (310)
T PRK00423 212 LKLPPTDPIDYVPRFASELGLSGEVQ-KKAIEILQKAK 248 (310)
T ss_pred CCCCCCCHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHH
Confidence 34556789999999999999997533 34444444333
No 27
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=23.56 E-value=61 Score=23.03 Aligned_cols=18 Identities=11% Similarity=0.480 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHHcCCCC
Q 031052 124 ESDPEEFARTFCNDMGIED 142 (166)
Q Consensus 124 ~~tPE~FA~~lc~DLgL~~ 142 (166)
..++ .+|+..|++||++.
T Consensus 23 ~W~~-~~s~~~C~qLGy~~ 40 (98)
T PF15494_consen 23 NWNE-ALSKAACQQLGYSS 40 (98)
T ss_pred ccCH-HHHHHHHHHhCCCC
Confidence 3444 59999999999973
No 28
>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=22.69 E-value=72 Score=21.68 Aligned_cols=24 Identities=25% Similarity=0.380 Sum_probs=18.3
Q ss_pred HHHHHHcCCCh--HHHHHHHHHHHHH
Q 031052 57 KRTVRDLKLPP--QFITQIAQSIQTQ 80 (166)
Q Consensus 57 ~~lc~Dl~lp~--~f~~~I~~sI~~Q 80 (166)
.++|+.||+.+ +|...+...+.+|
T Consensus 52 ~Rf~kkLG~~gf~efk~~l~~~~~~~ 77 (77)
T PF01418_consen 52 VRFCKKLGFSGFKEFKIALAQELSQQ 77 (77)
T ss_dssp HHHHHHCTTTCHHHHHHHHHCHHHS-
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence 67999999987 7877777766554
No 29
>PRK05325 hypothetical protein; Provisional
Probab=22.55 E-value=61 Score=29.68 Aligned_cols=19 Identities=21% Similarity=0.347 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHHHHcCCCC
Q 031052 124 ESDPEEFARTFCNDMGIED 142 (166)
Q Consensus 124 ~~tPE~FA~~lc~DLgL~~ 142 (166)
.+|.|+|++.|-+||+||+
T Consensus 101 els~eE~~~~lfEdLeLPn 119 (401)
T PRK05325 101 EISLEELLDLLFEDLELPN 119 (401)
T ss_pred EecHHHHHHHHHhhcCCCC
Confidence 4689999999999999974
No 30
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.23 E-value=2.2e+02 Score=22.57 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHHcCCChHHHHHHHHHHHH
Q 031052 49 DSEVVVFAKRTVRDLKLPPQFITQIAQSIQT 79 (166)
Q Consensus 49 ~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~ 79 (166)
.++++.|.+.| +++|||.+....+++.-.+
T Consensus 59 n~~~~~l~~eL-~~lglp~e~~~~l~~~~~~ 88 (174)
T cd04752 59 NVDGESLSSEL-QQLGLPKEHATSLCRSYEE 88 (174)
T ss_pred CCCHHHHHHHH-HHcCCCHHHHHHHHHHHHH
Confidence 37899999987 8999999777666655444
No 31
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.12 E-value=72 Score=21.56 Aligned_cols=19 Identities=32% Similarity=0.345 Sum_probs=16.0
Q ss_pred CCCCCchHHHHHHHHHHHH
Q 031052 139 GIEDPEVGPAVAFAIREQL 157 (166)
Q Consensus 139 gL~~~ef~~~Ia~sIreQl 157 (166)
|++.||....+|..|||-=
T Consensus 27 GmSsGEAIa~VA~elRe~h 45 (60)
T COG3140 27 GMSSGEAIALVAQELRENH 45 (60)
T ss_pred cccchhHHHHHHHHHHHHh
Confidence 7777899999999999853
No 32
>COG2127 Uncharacterized conserved protein [Function unknown]
Probab=21.37 E-value=1.3e+02 Score=22.74 Aligned_cols=31 Identities=16% Similarity=0.313 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHHH-cCCCCCchHHHHHHHHH
Q 031052 123 YESDPEEFARTFCND-MGIEDPEVGPAVAFAIR 154 (166)
Q Consensus 123 ~~~tPE~FA~~lc~D-LgL~~~ef~~~Ia~sIr 154 (166)
.++||.+|...+... .|++ .+-+++|--++|
T Consensus 36 Dd~T~mefVv~vL~~~F~~s-~e~A~~lMl~VH 67 (107)
T COG2127 36 DDYTPMEFVVYVLQKFFGMS-EERATKLMLQVH 67 (107)
T ss_pred CCCcHHHHHHHHHHHHhccC-HHHHHHHHHHHH
Confidence 479999999999888 7888 577777777665
No 33
>PHA01623 hypothetical protein
Probab=21.30 E-value=1.8e+02 Score=19.00 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=19.2
Q ss_pred HHHHHHcCCCCCchHHHHHHHHHHHHHHhh
Q 031052 132 RTFCNDMGIEDPEVGPAVAFAIREQLYEVM 161 (166)
Q Consensus 132 ~~lc~DLgL~~~ef~~~Ia~sIreQl~~~~ 161 (166)
..+|.+.|++ -..+|..+|++-+.+..
T Consensus 29 d~y~~~~g~~---rSe~IreAI~~yL~~~~ 55 (56)
T PHA01623 29 KVYCAKNNLQ---LTQAIEEAIKEYLQKRE 55 (56)
T ss_pred HHHHHHcCCC---HHHHHHHHHHHHHHHcc
Confidence 4579999996 45667777777776543
No 34
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=21.13 E-value=1.9e+02 Score=20.05 Aligned_cols=12 Identities=17% Similarity=0.409 Sum_probs=7.8
Q ss_pred HHHHHHHHcCCC
Q 031052 130 FARTFCNDMGIE 141 (166)
Q Consensus 130 FA~~lc~DLgL~ 141 (166)
=|..+|+++||+
T Consensus 15 ~a~~il~~~Glt 26 (83)
T PF04221_consen 15 EAEAILEELGLT 26 (83)
T ss_dssp HHHHHHHHTT--
T ss_pred HHHHHHHHcCCC
Confidence 367788888887
No 35
>PTZ00202 tuzin; Provisional
Probab=20.70 E-value=3.4e+02 Score=26.01 Aligned_cols=36 Identities=11% Similarity=0.068 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHHcCCChHHH-HHHHHHHHHHHHHhhc
Q 031052 51 EVVVFAKRTVRDLKLPPQFI-TQIAQSIQTQLTEFRS 86 (166)
Q Consensus 51 tpE~FA~~lc~Dl~lp~~f~-~~I~~sI~~Qi~ey~~ 86 (166)
++++|-..++..||+++.+. ..+..+|.+.|.+...
T Consensus 321 g~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~ 357 (550)
T PTZ00202 321 GTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKK 357 (550)
T ss_pred CHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHH
Confidence 78999999999999987444 5677777777777554
No 36
>TIGR03515 GldC gliding motility-associated protein GldC. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldC do not abolish the gliding phenotype but do impair it. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=20.58 E-value=96 Score=23.49 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=23.7
Q ss_pred eEEEeeeCCcEEEEEEEecCCCCCCCHH
Q 031052 26 IRLDIETEGQRYKDAFTWNPSDPDSEVV 53 (166)
Q Consensus 26 IrLdle~~~~klrD~F~WNlne~~itpE 53 (166)
|++++++|..++-+...|+..+..+.-+
T Consensus 5 Ik~~V~LDen~vPE~i~W~A~Dg~~~~~ 32 (108)
T TIGR03515 5 IKFNVELDDNNVPEQILWEATDGPSQGQ 32 (108)
T ss_pred EEEEEEEcCCCCCcceeEecCCCCcCCc
Confidence 7888999999999999999888766544
No 37
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.29 E-value=2.2e+02 Score=20.18 Aligned_cols=12 Identities=17% Similarity=0.290 Sum_probs=9.5
Q ss_pred HHHHHHHHcCCC
Q 031052 130 FARTFCNDMGIE 141 (166)
Q Consensus 130 FA~~lc~DLgL~ 141 (166)
=|..+|++|||+
T Consensus 15 ~A~~vl~~lGls 26 (80)
T PRK11235 15 RAYAVLEKLGVT 26 (80)
T ss_pred HHHHHHHHhCCC
Confidence 467788888887
Done!