Query 026518
Match_columns 237
No_of_seqs 176 out of 378
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:04:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026518.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026518hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04855 SNF5: SNF5 / SMARCB1 100.0 1.7E-66 3.8E-71 462.0 22.7 207 15-237 4-244 (244)
2 KOG1649 SWI-SNF chromatin remo 100.0 4E-64 8.6E-69 462.3 17.9 200 13-237 170-371 (397)
3 PF04855 SNF5: SNF5 / SMARCB1 99.7 1.2E-17 2.5E-22 149.2 9.0 72 91-162 5-77 (244)
4 KOG1649 SWI-SNF chromatin remo 99.7 6.3E-18 1.4E-22 156.9 6.4 70 90-159 172-241 (397)
5 PF09070 PFU: PFU (PLAA family 88.5 1.3 2.8E-05 35.8 5.6 38 38-78 73-110 (116)
6 PF05402 PqqD: Coenzyme PQQ sy 73.1 3.7 8E-05 28.7 2.7 44 37-80 20-63 (68)
7 TIGR03859 PQQ_PqqD coenzyme PQ 40.2 29 0.00063 25.7 2.7 35 37-71 34-68 (81)
8 PF07531 TAFH: NHR1 homology t 39.6 33 0.00071 26.9 2.9 40 41-80 35-79 (96)
9 COG1405 SUA7 Transcription ini 37.0 94 0.002 28.7 6.0 37 45-82 190-226 (285)
10 PF02022 Integrase_Zn: Integra 36.1 45 0.00098 21.9 2.8 21 53-73 12-32 (40)
11 TIGR02877 spore_yhbH sporulati 32.0 30 0.00066 33.2 2.0 21 44-64 111-131 (371)
12 PRK05325 hypothetical protein; 32.0 31 0.00067 33.5 2.1 21 44-64 99-119 (401)
13 COG1405 SUA7 Transcription ini 31.8 99 0.0022 28.6 5.3 28 120-149 190-217 (285)
14 PF09070 PFU: PFU (PLAA family 29.8 94 0.002 25.1 4.2 54 94-153 56-109 (116)
15 TIGR01795 CM_mono_cladeE monof 28.6 91 0.002 23.9 3.8 40 122-162 45-90 (94)
16 PF05402 PqqD: Coenzyme PQQ sy 24.5 74 0.0016 21.9 2.5 28 111-138 19-46 (68)
17 PF10392 COG5: Golgi transport 23.1 1.3E+02 0.0028 24.2 3.9 48 117-165 3-64 (132)
18 PF13591 MerR_2: MerR HTH fami 22.8 2.2E+02 0.0047 21.1 4.8 45 115-161 35-79 (84)
19 PTZ00202 tuzin; Provisional 22.8 1.7E+02 0.0038 29.5 5.4 38 123-160 321-358 (550)
20 smart00549 TAFH TAF homology. 21.9 90 0.002 24.3 2.6 23 42-64 35-57 (92)
21 cd04752 Commd4 COMM_Domain con 21.2 2.2E+02 0.0047 24.1 5.1 36 121-158 59-94 (174)
22 PRK09239 chorismate mutase; Pr 20.9 2.1E+02 0.0045 22.4 4.5 33 129-162 65-97 (104)
23 PRK00423 tfb transcription ini 20.5 2E+02 0.0043 26.5 5.1 35 42-77 212-246 (310)
24 TIGR02849 spore_III_AD stage I 20.2 73 0.0016 25.1 1.8 20 125-150 55-74 (101)
No 1
>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=1.7e-66 Score=461.99 Aligned_cols=207 Identities=36% Similarity=0.556 Sum_probs=179.9
Q ss_pred CCCceeeeeEEEeee-CCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCChH-HHHHHHHHHHHHHHHhhcccCCcc---
Q 026518 15 PTADNLVPIRLDIET-EGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPPQ-FITQIAQSIQTQLTEFRSYEGQDM--- 89 (237)
Q Consensus 15 ~~~e~LVPIrLd~e~-~~~rlrD~F~WNlne~~itpe~FA~~lc~Dl~lp~~-~~~~I~~sI~~Qi~ey~~~~~~~~--- 89 (237)
..++.|||||||||+ +|+||||+|+||+||+++|||+||++||+||+||+. |+++|++||++||++|+.+...++
T Consensus 4 ~~~e~LVPIRLdie~~~~~klrD~FlWNlne~~itpe~FA~~lc~Dl~lp~~~~~~~I~~sI~~Qi~e~~~~a~~~l~~~ 83 (244)
T PF04855_consen 4 ELPENLVPIRLDIEIRDGYKLRDTFLWNLNEPLITPEEFAEILCEDLDLPPSFFVQQIANSIREQIEEYASVAAHPLFQN 83 (244)
T ss_pred cCCceeeeEEEEeecCCCceEEEEEEeeCCCCCCCHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHhhhhhhhccc
Confidence 678999999999999 999999999999999999999999999999999986 699999999999999998744322
Q ss_pred --------------------------CCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChH
Q 026518 90 --------------------------YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVG 143 (237)
Q Consensus 90 --------------------------~~~e~~v~I~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~lc~DLgL~~~ef~ 143 (237)
..++++|+|+|||++|++.|+|+|||||+++.++||+||+++|+||||+ +||+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rv~I~LdI~ig~~~l~DqFEWDL~~~~~~PE~FA~~~c~dLgL~-~Ef~ 162 (244)
T PF04855_consen 84 PEMEPSEKRLDPEDPYTAFADSSLGSPDDDLRVIIKLDITIGNHLLVDQFEWDLSNPPNSPEEFARVLCADLGLP-GEFV 162 (244)
T ss_pred cccccccccccccccccccccccccCCCCceEEEEEEEEEECCEEEEEEEEecCCCCCCCHHHHHHHHHHHcCCc-HHHH
Confidence 1258999999999999999999999999999999999999999999999 5999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHhhhhhccCCCCCccccCcCCCCchhhhhhh--hcccccccc-CccccCcccceeeec
Q 026518 144 PAVAFAIREQLYEIAIQSVASAREIKISKKGRRGAEHAISSKGGGNALDLMKL--FRYNSSVVR-KRKEWYVYEPIVDIL 220 (237)
Q Consensus 144 ~aIa~sIreQl~~~~~~~~~~~~~~~i~~~g~~g~~~~~~~~~~~~~~d~~~~--~~~~~~v~r-~~~e~~~w~P~le~L 220 (237)
|||||||||||++|||+++..| .. +.... ....++... ++++.+++| +..++++|+|+|++|
T Consensus 163 ~aIahsIrEq~~~~kK~~~~~g---------~~---~~~~~---~~~~~~~~~~~~~~~~~~~r~~~~~~~~w~P~le~L 227 (244)
T PF04855_consen 163 PAIAHSIREQLLKYKKELCESG---------YL---FDGSP---VEDDEIRNAFLPGPLAGVRRDPDNEADEWTPRLEEL 227 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc---------cc---cCCCC---cccchhhhhcccccccceeecCccchhhcCCchhhC
Confidence 9999999999999999998643 11 11100 011122222 356888999 778899999999999
Q ss_pred CHHHHHHhhhhhhhccC
Q 026518 221 SNEEVDALEAREDRNTR 237 (237)
Q Consensus 221 s~~Eier~e~e~eR~~R 237 (237)
|.+||||+|+||||++|
T Consensus 228 s~eEier~e~ereR~~R 244 (244)
T PF04855_consen 228 SPEEIERREKERERESR 244 (244)
T ss_pred CHHHHHHHHHHhhhhcC
Confidence 99999999999999998
No 2
>KOG1649 consensus SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=4e-64 Score=462.25 Aligned_cols=200 Identities=40% Similarity=0.604 Sum_probs=181.8
Q ss_pred CCCCCceeeeeEEEeeeCCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCCh-HHHHHHHHHHHHHHHHhhcccCCccCC
Q 026518 13 VKPTADNLVPIRLDIETEGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPP-QFITQIAQSIQTQLTEFRSYEGQDMYT 91 (237)
Q Consensus 13 ~~~~~e~LVPIrLd~e~~~~rlrD~F~WNlne~~itpe~FA~~lc~Dl~lp~-~~~~~I~~sI~~Qi~ey~~~~~~~~~~ 91 (237)
..++++.|||||||||.+|+||||+|+||+||++||||+||+++|+||+||+ .|+++|++||++||++|+..++.+|..
T Consensus 170 ~~~~~e~lVPIRLDie~dg~klrDtFtWN~ndk~itpe~FAei~c~Dldl~~~~~v~qIa~sIq~Qied~~~~~~~~~~~ 249 (397)
T KOG1649|consen 170 NAETPEVLVPIRLDIELDGQKLRDTFTWNKNDKLITPEMFAEILCKDLDLPPATFVTQIAQSIQQQIEDYEPDPAIEMNS 249 (397)
T ss_pred hCCCCceeeeEEEeeecccchhhhhcccccCCccCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHhcCCCCcccccC
Confidence 3489999999999999999999999999999999999999999999999976 899999999999999999999999989
Q ss_pred CceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHhhhhh
Q 026518 92 AEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSVASAREIKIS 171 (237)
Q Consensus 92 ~e~~v~I~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~~~~~~~~~~i~ 171 (237)
++.+|+|||||++|+..|.|||||||+++.++||+||..+|.||||+ |||+|||||||||||++++|.++.+
T Consensus 250 ~d~rviikLdi~vg~~~l~DQFeWdls~~~~~PEEFA~~lC~dLGL~-gEf~taIA~SIreql~~~~k~~~~~------- 321 (397)
T KOG1649|consen 250 GDLRVIIKLDINVGNLSLVDQFEWDLSNPENSPEEFATSLCQDLGLG-GEFVTAIAYSIREQLLWIKKTYAFS------- 321 (397)
T ss_pred CceEEEEEEEEEeccceehhhheeccCCCCCCHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHHHHHHHHHhc-------
Confidence 99999999999999999999999999999999999999999999999 5999999999999999999999853
Q ss_pred ccCCCCCccccCcCCCCchhhhhhhhccc-cccccCccccCcccceeeecCHHHHHHhhhhhhhccC
Q 026518 172 KKGRRGAEHAISSKGGGNALDLMKLFRYN-SSVVRKRKEWYVYEPIVDILSNEEVDALEAREDRNTR 237 (237)
Q Consensus 172 ~~g~~g~~~~~~~~~~~~~~d~~~~~~~~-~~v~r~~~e~~~w~P~le~Ls~~Eier~e~e~eR~~R 237 (237)
.|.+.+ .+ ++++ ....|...+++.|||+|++||.+||||+++++||++|
T Consensus 322 ----D~~~~d---~~----------p~~~~~~~~r~~~~~s~w~P~letlt~ae~ek~~~~~dR~~R 371 (397)
T KOG1649|consen 322 ----DGSPID---AA----------PLPTSDIRRRNDSEGSAWCPFLETLTDAEMEKKERDQDRNTR 371 (397)
T ss_pred ----cCcccc---cc----------cccccCccccCcchhhhccchhhhccHHHHHHHhhhhHHHHH
Confidence 233221 11 2333 3356667788899999999999999999999999987
No 3
>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=99.72 E-value=1.2e-17 Score=149.17 Aligned_cols=72 Identities=36% Similarity=0.631 Sum_probs=66.6
Q ss_pred CCceeeeeEEEEEe-CCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 026518 91 TAEKIVPIKLDLRV-NHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSV 162 (237)
Q Consensus 91 ~~e~~v~I~Ldi~~-~~~~l~D~FeWdL~~~~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~~~ 162 (237)
..+.+|||+|||.+ ++++|+|+|.||+|++.+|||+||.+||.||+||...|+++|+.+|++||.+|+..+.
T Consensus 5 ~~e~LVPIRLdie~~~~~klrD~FlWNlne~~itpe~FA~~lc~Dl~lp~~~~~~~I~~sI~~Qi~e~~~~a~ 77 (244)
T PF04855_consen 5 LPENLVPIRLDIEIRDGYKLRDTFLWNLNEPLITPEEFAEILCEDLDLPPSFFVQQIANSIREQIEEYASVAA 77 (244)
T ss_pred CCceeeeEEEEeecCCCceEEEEEEeeCCCCCCCHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHhhhh
Confidence 46789999999999 9999999999999999999999999999999999634799999999999999987654
No 4
>KOG1649 consensus SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics; Transcription]
Probab=99.72 E-value=6.3e-18 Score=156.86 Aligned_cols=70 Identities=29% Similarity=0.554 Sum_probs=65.6
Q ss_pred CCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHH
Q 026518 90 YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAI 159 (237)
Q Consensus 90 ~~~e~~v~I~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~ 159 (237)
++.+.+|||+|||+++|++|+|+|.||.|++.+|||+||+++|+||+|+...|+++||.+|++||..|..
T Consensus 172 ~~~e~lVPIRLDie~dg~klrDtFtWN~ndk~itpe~FAei~c~Dldl~~~~~v~qIa~sIq~Qied~~~ 241 (397)
T KOG1649|consen 172 ETPEVLVPIRLDIELDGQKLRDTFTWNKNDKLITPEMFAEILCKDLDLPPATFVTQIAQSIQQQIEDYEP 241 (397)
T ss_pred CCCceeeeEEEeeecccchhhhhcccccCCccCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHhcCC
Confidence 3578999999999999999999999999999999999999999999997569999999999999998753
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=88.50 E-value=1.3 Score=35.80 Aligned_cols=38 Identities=24% Similarity=0.367 Sum_probs=30.2
Q ss_pred EEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Q 026518 38 FTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQL 78 (237)
Q Consensus 38 F~WNlne~~itpe~FA~~lc~Dl~lp~~~~~~I~~sI~~Qi 78 (237)
.-.|.+| .|..-|+.+|.+.+||..|..+|++-|.+..
T Consensus 73 LpyN~~d---nP~~aAq~Fi~~n~Lp~~yl~qI~~FI~~N~ 110 (116)
T PF09070_consen 73 LPYNKGD---NPYEAAQKFIERNNLPQSYLDQIANFIIQNT 110 (116)
T ss_dssp EEE-TTS----HHHHHHHHHHHHT--CCHHHHHHHHHHHHH
T ss_pred CCccCCC---CHHHHHHHHHHHcCCCHHHHHHHHHHHHHcC
Confidence 4567777 7999999999999999999999999998864
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=73.07 E-value=3.7 Score=28.73 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=28.9
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHH
Q 026518 37 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTE 80 (237)
Q Consensus 37 ~F~WNlne~~itpe~FA~~lc~Dl~lp~~~~~~I~~sI~~Qi~e 80 (237)
.|+|++-+...|+++.++.+|+.++.++.-+..-+.+.-+||.+
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 47899888889999999999999999885444444444444544
No 7
>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=40.21 E-value=29 Score=25.67 Aligned_cols=35 Identities=3% Similarity=0.030 Sum_probs=27.4
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHH
Q 026518 37 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIA 71 (237)
Q Consensus 37 ~F~WNlne~~itpe~FA~~lc~Dl~lp~~~~~~I~ 71 (237)
+|+|.+=+.-.|+++.+..||+.|+.+......+.
T Consensus 34 ~~Iw~lldg~~tv~eI~~~L~~~Y~~~e~~~~dV~ 68 (81)
T TIGR03859 34 GEILELCDGKRSLAEIIQELAQRFPAAEEIEDDVI 68 (81)
T ss_pred HHHHHHccCCCcHHHHHHHHHHHcCChhhHHHHHH
Confidence 58899888888999999999999998433433333
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=39.63 E-value=33 Score=26.92 Aligned_cols=40 Identities=20% Similarity=0.366 Sum_probs=27.3
Q ss_pred cCCCCCCCHHHHHHHHHHHcCCCh-----HHHHHHHHHHHHHHHH
Q 026518 41 NPSDPDSEVVVFAKRTVRDLKLPP-----QFITQIAQSIQTQLTE 80 (237)
Q Consensus 41 Nlne~~itpe~FA~~lc~Dl~lp~-----~~~~~I~~sI~~Qi~e 80 (237)
++.+..|++|+|...|=++++.|+ .|...-.-+.|+.+..
T Consensus 35 ~L~~~~i~~EeF~~~Lq~~lns~pqP~lvPFLK~~lp~Lr~~l~~ 79 (96)
T PF07531_consen 35 NLVDGKIEAEEFTSKLQEELNSSPQPYLVPFLKKSLPALRQELPN 79 (96)
T ss_dssp HHHTTSS-HHHHHHHHHHHCTSS--TTHHHHHHHHHHHHHHCHCH
T ss_pred HHHcCCCCHHHHHHHHHHHhcCCCCcchHHHHHHhHHHHHHHHHH
Confidence 466889999999999999999976 3444444445554433
No 9
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=37.03 E-value=94 Score=28.72 Aligned_cols=37 Identities=16% Similarity=0.190 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhh
Q 026518 45 PDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTEFR 82 (237)
Q Consensus 45 ~~itpe~FA~~lc~Dl~lp~~~~~~I~~sI~~Qi~ey~ 82 (237)
+.+.|..|...+|.+|+||.. +...|.-|-++..+..
T Consensus 190 ~~~~p~~yi~rf~s~L~l~~~-v~~~a~ei~~~~~~~g 226 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLSDE-VRRKAIEIVKKAKRAG 226 (285)
T ss_pred CCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhC
Confidence 347999999999999999963 3444444444444443
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=36.11 E-value=45 Score=21.88 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=15.0
Q ss_pred HHHHHHHcCCChHHHHHHHHH
Q 026518 53 AKRTVRDLKLPPQFITQIAQS 73 (237)
Q Consensus 53 A~~lc~Dl~lp~~~~~~I~~s 73 (237)
+..|..+++||...+.+|+++
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 578899999998777777754
No 11
>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=31.97 E-value=30 Score=33.23 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=18.4
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 026518 44 DPDSEVVVFAKRTVRDLKLPP 64 (237)
Q Consensus 44 e~~itpe~FA~~lc~Dl~lp~ 64 (237)
|-.+|.|+|+..|.+||.||.
T Consensus 111 e~e~s~eE~~~~lfEdLeLPn 131 (371)
T TIGR02877 111 ETEVTLEELFELLFEDLELPN 131 (371)
T ss_pred EEEecHHHHHHHHHhhccCCC
Confidence 346899999999999999984
No 12
>PRK05325 hypothetical protein; Provisional
Probab=31.96 E-value=31 Score=33.49 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=18.4
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 026518 44 DPDSEVVVFAKRTVRDLKLPP 64 (237)
Q Consensus 44 e~~itpe~FA~~lc~Dl~lp~ 64 (237)
|-.+|.|+|+..|.+||+||.
T Consensus 99 e~els~eE~~~~lfEdLeLPn 119 (401)
T PRK05325 99 EFEISLEELLDLLFEDLELPN 119 (401)
T ss_pred EEEecHHHHHHHHHhhcCCCC
Confidence 446899999999999999973
No 13
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=31.79 E-value=99 Score=28.56 Aligned_cols=28 Identities=21% Similarity=0.415 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHHcCCCCCChHHHHHHH
Q 026518 120 YESDPEEFARTFCNDMGIEDPEVGPAVAFA 149 (237)
Q Consensus 120 ~~~tPE~FA~~lc~DLgL~~~ef~~aIa~s 149 (237)
+...|+.|-..+|.+|||++ -+...|-.
T Consensus 190 ~~~~p~~yi~rf~s~L~l~~--~v~~~a~e 217 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLSD--EVRRKAIE 217 (285)
T ss_pred CCCCHHHHHHHHHHHcCCCH--HHHHHHHH
Confidence 34799999999999999993 34444433
No 14
>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=29.76 E-value=94 Score=25.05 Aligned_cols=54 Identities=15% Similarity=0.144 Sum_probs=32.6
Q ss_pred eeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHH
Q 026518 94 KIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQ 153 (237)
Q Consensus 94 ~~v~I~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQ 153 (237)
+-..+.+||.-|+..|. .-.|. .-+|-.=|+.+|.+.+|| ..|...|+.-|...
T Consensus 56 YDyVf~Vdi~dg~~~lk--LpyN~---~dnP~~aAq~Fi~~n~Lp-~~yl~qI~~FI~~N 109 (116)
T PF09070_consen 56 YDYVFDVDIEDGGPPLK--LPYNK---GDNPYEAAQKFIERNNLP-QSYLDQIANFIIQN 109 (116)
T ss_dssp ESEEEEE--STTSS-EE--EEE-T---TS-HHHHHHHHHHHHT---CCHHHHHHHHHHHH
T ss_pred ceEEEEEEecCCCccee--CCccC---CCCHHHHHHHHHHHcCCC-HHHHHHHHHHHHHc
Confidence 33445555554443332 22344 458999999999999999 69999999888553
No 15
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=28.63 E-value=91 Score=23.91 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=28.9
Q ss_pred CCHHHHH------HHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 026518 122 SDPEEFA------RTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSV 162 (237)
Q Consensus 122 ~tPE~FA------~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~~~ 162 (237)
..|+..+ ...+.++||+ ++|+..|-..|++...+....++
T Consensus 45 ~dp~Re~~vl~~~~~~a~~~gl~-p~~~e~i~~~i~~esir~q~~~~ 90 (94)
T TIGR01795 45 ADPAREDYQIARLRRLAIDAGLD-PEFAEKFLNFIVTEVIKHHERIA 90 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHh
Confidence 4565544 4567789999 59998888888887766655555
No 16
>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=24.50 E-value=74 Score=21.93 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=20.9
Q ss_pred eceeecCCCCCCCHHHHHHHHHHHcCCC
Q 026518 111 DHFLWDLNNYESDPEEFARTFCNDMGIE 138 (237)
Q Consensus 111 D~FeWdL~~~~~tPE~FA~~lc~DLgL~ 138 (237)
-.|.|++.+...|.++-++.+|+..+.+
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 3588999988899999999999999887
No 17
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=23.05 E-value=1.3e+02 Score=24.19 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=34.9
Q ss_pred CCCCCCCHHHHHHHHHH--------HcCCCCCCh------HHHHHHHHHHHHHHHHHHHHHhh
Q 026518 117 LNNYESDPEEFARTFCN--------DMGIEDPEV------GPAVAFAIREQLYEIAIQSVASA 165 (237)
Q Consensus 117 L~~~~~tPE~FA~~lc~--------DLgL~~~ef------~~aIa~sIreQl~~~~~~~~~~~ 165 (237)
..+++.+|..||..+.. .+++.. .. ...|-..|++++...+.+++.+.
T Consensus 3 fl~~dFd~~~fan~ll~~~~~~~~~~ld~~~-~l~kL~~~i~eld~~i~~~v~~~~~~LL~q~ 64 (132)
T PF10392_consen 3 FLSPDFDPVQFANDLLKSTNNNSDSELDIST-PLKKLNFDIQELDKRIRSQVTSNHEDLLSQA 64 (132)
T ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCcccHHH-HHHHHHHHHHHHHHHHHHHHHhCHHHHHHHH
Confidence 34678999999999999 777762 22 23667778888877777777644
No 18
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=22.81 E-value=2.2e+02 Score=21.09 Aligned_cols=45 Identities=16% Similarity=0.292 Sum_probs=30.6
Q ss_pred ecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHH
Q 026518 115 WDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQS 161 (237)
Q Consensus 115 WdL~~~~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~~ 161 (237)
|=++.....-=+.+..+..|||++. -.-+++...-+++....++.
T Consensus 35 ~~f~~~~l~rl~~~~rL~~Dl~in~--~gi~lil~LLd~i~~L~~el 79 (84)
T PF13591_consen 35 WYFSEEDLARLRRIRRLHRDLGINL--EGIALILDLLDRIEQLRREL 79 (84)
T ss_pred eeECHHHHHHHHHHHHHHHHcCCCH--HHHHHHHHHHHHHHHHHHHH
Confidence 3333334444457889999999983 45567777778888877655
No 19
>PTZ00202 tuzin; Provisional
Probab=22.76 E-value=1.7e+02 Score=29.47 Aligned_cols=38 Identities=16% Similarity=0.141 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHH
Q 026518 123 DPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQ 160 (237)
Q Consensus 123 tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~ 160 (237)
+|++|-..++..||+++..-...+..+|.+.|++.+.+
T Consensus 321 g~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e 358 (550)
T PTZ00202 321 GTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKM 358 (550)
T ss_pred CHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHh
Confidence 79999999999999985333367888999988876654
No 20
>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=21.92 E-value=90 Score=24.33 Aligned_cols=23 Identities=17% Similarity=0.138 Sum_probs=20.4
Q ss_pred CCCCCCCHHHHHHHHHHHcCCCh
Q 026518 42 PSDPDSEVVVFAKRTVRDLKLPP 64 (237)
Q Consensus 42 lne~~itpe~FA~~lc~Dl~lp~ 64 (237)
+-+..+++|+|...|=+.+..|+
T Consensus 35 L~~~~i~~EeF~~~Lq~~lns~~ 57 (92)
T smart00549 35 LVNGTITAEEFTSRLQEALNSPL 57 (92)
T ss_pred HHhCCCCHHHHHHHHHHHHcCCC
Confidence 45678999999999999999986
No 21
>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=21.23 E-value=2.2e+02 Score=24.06 Aligned_cols=36 Identities=14% Similarity=0.306 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHH
Q 026518 121 ESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIA 158 (237)
Q Consensus 121 ~~tPE~FA~~lc~DLgL~~~ef~~aIa~sIreQl~~~~ 158 (237)
..+|+.|...+ .+|||| .|...+++....+.-....
T Consensus 59 n~~~~~l~~eL-~~lglp-~e~~~~l~~~~~~~~~~l~ 94 (174)
T cd04752 59 NVDGESLSSEL-QQLGLP-KEHATSLCRSYEEKQSKLQ 94 (174)
T ss_pred CCCHHHHHHHH-HHcCCC-HHHHHHHHHHHHHHHHHHH
Confidence 47899999988 889999 5999999887665544433
No 22
>PRK09239 chorismate mutase; Provisional
Probab=20.87 E-value=2.1e+02 Score=22.38 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=25.1
Q ss_pred HHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 026518 129 RTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSV 162 (237)
Q Consensus 129 ~~lc~DLgL~~~ef~~aIa~sIreQl~~~~~~~~ 162 (237)
...+.++||+ ++|+.+|-..|.+...++..+++
T Consensus 65 ~~~a~~~gl~-p~~~~~i~~~ii~esir~q~~i~ 97 (104)
T PRK09239 65 RQLAKDANLD-PDFAEKFLNFIIKEVIRHHERIA 97 (104)
T ss_pred HHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566789999 59998888888887766665554
No 23
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.49 E-value=2e+02 Score=26.53 Aligned_cols=35 Identities=17% Similarity=0.217 Sum_probs=24.7
Q ss_pred CCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Q 026518 42 PSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQ 77 (237)
Q Consensus 42 lne~~itpe~FA~~lc~Dl~lp~~~~~~I~~sI~~Q 77 (237)
++-+.++|+.|...+|..|+||.... ..|..|-++
T Consensus 212 ~~~~~~~p~~~i~r~~~~L~L~~~v~-~~A~~i~~~ 246 (310)
T PRK00423 212 LKLPPTDPIDYVPRFASELGLSGEVQ-KKAIEILQK 246 (310)
T ss_pred CCCCCCCHHHHHHHHHHHcCCCHHHH-HHHHHHHHH
Confidence 34566889999999999999997543 334334333
No 24
>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=20.23 E-value=73 Score=25.14 Aligned_cols=20 Identities=40% Similarity=0.700 Sum_probs=15.7
Q ss_pred HHHHHHHHHHcCCCCCChHHHHHHHH
Q 026518 125 EEFARTFCNDMGIEDPEVGPAVAFAI 150 (237)
Q Consensus 125 E~FA~~lc~DLgL~~~ef~~aIa~sI 150 (237)
-+||..+|+|-|-+ +||..|
T Consensus 55 aef~s~iCkDAG~~------aiAskI 74 (101)
T TIGR02849 55 AEFGSQICKDAGEK------AIASKI 74 (101)
T ss_pred HHHHHHHHHHcChH------HHHHHH
Confidence 35999999999986 366655
Done!