Query 026309
Match_columns 240
No_of_seqs 184 out of 380
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:21:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026309.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026309hhsearch_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 1.6E-67 3.4E-72 469.8 23.0 211 16-240 2-244 (244)
2 KOG1649 SWI-SNF chromatin remo 100.0 1.2E-65 2.6E-70 473.6 17.5 206 10-240 164-371 (397)
3 PF04855 SNF5: SNF5 / SMARCB1 99.7 1E-17 2.2E-22 149.9 9.2 72 94-165 5-77 (244)
4 KOG1649 SWI-SNF chromatin remo 99.7 4.2E-18 9.2E-23 158.4 6.4 70 93-162 172-241 (397)
5 PF09070 PFU: PFU (PLAA family 88.3 1.1 2.3E-05 36.4 5.0 51 26-81 60-110 (116)
6 PF05402 PqqD: Coenzyme PQQ sy 64.1 7.2 0.00016 27.3 2.6 44 40-83 20-63 (68)
7 COG1405 SUA7 Transcription ini 44.5 45 0.00097 30.9 5.1 39 48-87 190-228 (285)
8 PF07531 TAFH: NHR1 homology t 39.1 34 0.00073 26.9 2.9 40 44-83 35-79 (96)
9 PF02022 Integrase_Zn: Integra 36.9 41 0.00089 22.2 2.7 21 56-76 12-32 (40)
10 TIGR03859 PQQ_PqqD coenzyme PQ 35.9 36 0.00078 25.2 2.6 38 40-77 34-71 (81)
11 TIGR02877 spore_yhbH sporulati 32.1 23 0.0005 34.2 1.2 21 47-67 111-131 (371)
12 TIGR01795 CM_mono_cladeE monof 31.3 77 0.0017 24.4 3.8 42 124-166 44-91 (94)
13 PRK05325 hypothetical protein; 30.7 34 0.00074 33.3 2.1 21 47-67 99-119 (401)
14 COG1405 SUA7 Transcription ini 30.0 1.1E+02 0.0024 28.3 5.3 19 123-141 190-208 (285)
15 PRK09239 chorismate mutase; Pr 29.9 1.1E+02 0.0024 24.0 4.6 33 132-165 65-97 (104)
16 PF09070 PFU: PFU (PLAA family 28.1 1E+02 0.0023 24.9 4.2 52 99-156 58-109 (116)
17 PTZ00202 tuzin; Provisional 23.9 1.6E+02 0.0034 29.9 5.3 38 126-163 321-358 (550)
18 smart00549 TAFH TAF homology. 23.9 1.2E+02 0.0025 23.8 3.6 23 45-67 35-57 (92)
19 PRK00423 tfb transcription ini 22.9 1.7E+02 0.0036 27.1 5.1 36 45-81 212-247 (310)
20 KOG1597 Transcription initiati 20.9 94 0.002 29.3 3.0 73 58-153 156-228 (308)
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=1.6e-67 Score=469.79 Aligned_cols=211 Identities=36% Similarity=0.559 Sum_probs=180.7
Q ss_pred cCCCCceeeeeEEEeee-CCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCChH-HHHHHHHHHHHHHHHhhcccCCcc-
Q 026309 16 RMPTADNLVPIRLDIET-EGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPPQ-FITQIAQSIQTQLTEFRSYEGQDM- 92 (240)
Q Consensus 16 ~~~~~e~LVPIrLd~e~-~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~~-f~~~I~~sI~~Ql~ey~~~~~~~~- 92 (240)
++..++.|||||||||+ +|+||||+|+||+||+++|||+||++||+||+||+. |+++|++||++||++|++++..++
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 55678899999999999 999999999999999999999999999999999985 799999999999999998744322
Q ss_pred ----------------------------cCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCC
Q 026309 93 ----------------------------YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPE 144 (240)
Q Consensus 93 ----------------------------~~~e~~vpI~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~~c~DLgL~~~e 144 (240)
..++++|+|+|||++|++.|+|+|||||+++.++||+||+++|+||||+ +|
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 1258999999999999999999999999999999999999999999999 59
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCCCCccccCcCCCCCchhhhhhhcccccccc-CccccCcccceeeec
Q 026309 145 VGPAVAFAIREQLYEIAIQSVASAREIKISKKGRRGAEHAISSKGGGNALDLMKLFRYNSSVVR-KRKEWYVYEPIVDIL 223 (240)
Q Consensus 145 f~~aIa~aIreQl~~~~~~~~~~~~~~~i~~~g~~g~~~~~~~~~~~~~~d~~~~~~~~~~v~r-~~~e~~~w~P~le~L 223 (240)
|+|||||||||||++|||++++.|. ..+|..+.+. ..+....++++.+++| +..++++|+|+|++|
T Consensus 161 f~~aIahsIrEq~~~~kK~~~~~g~----~~~~~~~~~~---------~~~~~~~~~~~~~~~r~~~~~~~~w~P~le~L 227 (244)
T PF04855_consen 161 FVPAIAHSIREQLLKYKKELCESGY----LFDGSPVEDD---------EIRNAFLPGPLAGVRRDPDNEADEWTPRLEEL 227 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccc----ccCCCCcccc---------hhhhhcccccccceeecCccchhhcCCchhhC
Confidence 9999999999999999999986431 0011111100 0111112356788998 778899999999999
Q ss_pred CHHHHHHhhhhhhhccC
Q 026309 224 SNEEVDALEAREDRNTR 240 (240)
Q Consensus 224 S~eEier~e~e~eR~~R 240 (240)
|.+||||+|+||||++|
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=1.2e-65 Score=473.57 Aligned_cols=206 Identities=40% Similarity=0.610 Sum_probs=187.3
Q ss_pred cccccccCCCCceeeeeEEEeeeCCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCCh-HHHHHHHHHHHHHHHHhhccc
Q 026309 10 KAPVKFRMPTADNLVPIRLDIETEGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPP-QFITQIAQSIQTQLTEFRSYE 88 (240)
Q Consensus 10 ~~~~~~~~~~~e~LVPIrLd~e~~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~-~f~~~I~~sI~~Ql~ey~~~~ 88 (240)
+..+++.++++|.|||||||||++|+||||+|+||+||++||||+||+++|+||+||+ .|+++|++||++||++|..++
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 4578899999999999999999999999999999999999999999999999999976 899999999999999999999
Q ss_pred CCcccCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHHHhh
Q 026309 89 GQDMYTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSVASA 168 (240)
Q Consensus 89 ~~~~~~~e~~vpI~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~~~~~~~ 168 (240)
+.++..++.+|+|||||++|+..|.|||||||+++.++||+||..+|.||||+ |||+|||||||||||++++|.++.+
T Consensus 244 ~~~~~~~d~rviikLdi~vg~~~l~DQFeWdls~~~~~PEEFA~~lC~dLGL~-gEf~taIA~SIreql~~~~k~~~~~- 321 (397)
T KOG1649|consen 244 AIEMNSGDLRVIIKLDINVGNLSLVDQFEWDLSNPENSPEEFATSLCQDLGLG-GEFVTAIAYSIREQLLWIKKTYAFS- 321 (397)
T ss_pred cccccCCceEEEEEEEEEeccceehhhheeccCCCCCCHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHHHHHHHHHhc-
Confidence 99998999999999999999999999999999999999999999999999999 5999999999999999999999853
Q ss_pred hhhhhhccCCCCCccccCcCCCCCchhhhhhhcccc-ccccCccccCcccceeeecCHHHHHHhhhhhhhccC
Q 026309 169 REIKISKKGRRGAEHAISSKGGGNALDLMKLFRYNS-SVVRKRKEWYVYEPIVDILSNEEVDALEAREDRNTR 240 (240)
Q Consensus 169 ~~~~i~~~g~~g~~~~~~~~~~~~~~d~~~~~~~~~-~v~r~~~e~~~w~P~le~LS~eEier~e~e~eR~~R 240 (240)
.|.+. +.+ ++++. ...|...+++.|+|.|++||.+||||+++++||++|
T Consensus 322 ----------D~~~~---d~~----------p~~~~~~~~r~~~~~s~w~P~letlt~ae~ek~~~~~dR~~R 371 (397)
T KOG1649|consen 322 ----------DGSPI---DAA----------PLPTSDIRRRNDSEGSAWCPFLETLTDAEMEKKERDQDRNTR 371 (397)
T ss_pred ----------cCccc---ccc----------cccccCccccCcchhhhccchhhhccHHHHHHHhhhhHHHHH
Confidence 12222 111 23333 356666788899999999999999999999999987
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=99.73 E-value=1e-17 Score=149.91 Aligned_cols=72 Identities=36% Similarity=0.631 Sum_probs=66.6
Q ss_pred CCceeeeeEEEEEe-CCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 026309 94 TAEKIVPIKLDLRV-NHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSV 165 (240)
Q Consensus 94 ~~e~~vpI~Ldi~~-~~~~l~D~FeWdL~~~~~tPE~FA~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~~~~ 165 (240)
.++.+|||+|||.+ ++++|+|.|.||+|++.+|||+||+++|.||+||...|+++|+.+|++||.+|+..+.
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 9999999999999999999999999999999999634799999999999999987644
No 4
>KOG1649 consensus SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics; Transcription]
Probab=99.72 E-value=4.2e-18 Score=158.43 Aligned_cols=70 Identities=29% Similarity=0.554 Sum_probs=65.5
Q ss_pred cCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHH
Q 026309 93 YTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAI 162 (240)
Q Consensus 93 ~~~e~~vpI~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~ 162 (240)
++++.+|||+|||+++|++|+|+|+||.|++.+|||+||+++|+||+|+...|+++||.+|++||..|..
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 3578999999999999999999999999999999999999999999997579999999999999998753
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=88.33 E-value=1.1 Score=36.41 Aligned_cols=51 Identities=27% Similarity=0.422 Sum_probs=34.1
Q ss_pred eEEEeeeCCcEEEEEEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Q 026309 26 IRLDIETEGQRYKDAFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQL 81 (240)
Q Consensus 26 IrLd~e~~~~klrD~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Ql 81 (240)
+.+|++-++-.++ .-.|.+| .|..=|+.+|.+.+||..|..+|++-|.+..
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 4444443333332 3468888 7999999999999999999999999998754
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=64.13 E-value=7.2 Score=27.30 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=27.0
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHH
Q 026309 40 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTE 83 (240)
Q Consensus 40 ~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Ql~e 83 (240)
.|+|++-+...|+++.++.+|+.++.++.-...=+.+.-+||.+
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 37899888889999999999999999884333333333334433
No 7
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=44.54 E-value=45 Score=30.91 Aligned_cols=39 Identities=15% Similarity=0.121 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhhcc
Q 026309 48 PDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQLTEFRSY 87 (240)
Q Consensus 48 ~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Ql~ey~~~ 87 (240)
+.+.|..|..++|.+|+||+.. ...|.-|-++..+....
T Consensus 190 ~~~~p~~yi~rf~s~L~l~~~v-~~~a~ei~~~~~~~g~~ 228 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLSDEV-RRKAIEIVKKAKRAGLT 228 (285)
T ss_pred CCCCHHHHHHHHHHHcCCCHHH-HHHHHHHHHHHHHhCcc
Confidence 3469999999999999999643 44555555555554433
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=39.14 E-value=34 Score=26.94 Aligned_cols=40 Identities=20% Similarity=0.366 Sum_probs=27.4
Q ss_pred cCCCCCCCHHHHHHHHHHHcCCCh-----HHHHHHHHHHHHHHHH
Q 026309 44 NPSDPDSEVVVFAKRTVRDLKLPP-----QFITQIAQSIQTQLTE 83 (240)
Q Consensus 44 Nlne~~itpE~FA~~lc~Dl~lp~-----~f~~~I~~sI~~Ql~e 83 (240)
++-+..|++|+|...|=++++.|+ .|...=.-+.|+.+..
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 456789999999999999999975 3544444455554443
No 9
>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=36.92 E-value=41 Score=22.15 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=15.2
Q ss_pred HHHHHHHcCCChHHHHHHHHH
Q 026309 56 AKRTVRDLKLPPQFITQIAQS 76 (240)
Q Consensus 56 A~~lc~Dl~lp~~f~~~I~~s 76 (240)
++.|..+++||.....+|+++
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 567899999999887877754
No 10
>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=35.86 E-value=36 Score=25.24 Aligned_cols=38 Identities=3% Similarity=0.026 Sum_probs=29.4
Q ss_pred EEEecCCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHH
Q 026309 40 AFTWNPSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSI 77 (240)
Q Consensus 40 ~F~WNlne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI 77 (240)
.|+|.+=+...|+++-++.||+.|+.+......+.+-+
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 47899888888999999999999999444545544444
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=32.12 E-value=23 Score=34.16 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 026309 47 DPDSEVVVFAKRTVRDLKLPP 67 (240)
Q Consensus 47 e~~itpE~FA~~lc~Dl~lp~ 67 (240)
|..+|.|+|+..|-+||.||.
T Consensus 111 e~e~s~eE~~~~lfEdLeLPn 131 (371)
T TIGR02877 111 ETEVTLEELFELLFEDLELPN 131 (371)
T ss_pred EEEecHHHHHHHHHhhccCCC
Confidence 456899999999999999984
No 12
>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=31.30 E-value=77 Score=24.39 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=30.4
Q ss_pred CCCHHHHH------HHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHHH
Q 026309 124 ESDPEEFA------RTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSVA 166 (240)
Q Consensus 124 ~~tPE~FA------~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~~~~~ 166 (240)
...|+..+ ...+.++||+ ++|+..|-..|++...+...+++.
T Consensus 44 v~dp~Re~~vl~~~~~~a~~~gl~-p~~~e~i~~~i~~esir~q~~~~~ 91 (94)
T TIGR01795 44 PADPAREDYQIARLRRLAIDAGLD-PEFAEKFLNFIVTEVIKHHERIAD 91 (94)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34566544 4567789999 599988888888887776666653
No 13
>PRK05325 hypothetical protein; Provisional
Probab=30.71 E-value=34 Score=33.32 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHHcCCCh
Q 026309 47 DPDSEVVVFAKRTVRDLKLPP 67 (240)
Q Consensus 47 e~~itpE~FA~~lc~Dl~lp~ 67 (240)
|-.+|.|+|+..|-+||+||.
T Consensus 99 e~els~eE~~~~lfEdLeLPn 119 (401)
T PRK05325 99 EFEISLEELLDLLFEDLELPN 119 (401)
T ss_pred EEEecHHHHHHHHHhhcCCCC
Confidence 457899999999999999974
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=29.99 E-value=1.1e+02 Score=28.34 Aligned_cols=19 Identities=21% Similarity=0.616 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHHcCCC
Q 026309 123 YESDPEEFARTFCNDMGIE 141 (240)
Q Consensus 123 ~~~tPE~FA~~~c~DLgL~ 141 (240)
+...|+.|-..+|.+|||+
T Consensus 190 ~~~~p~~yi~rf~s~L~l~ 208 (285)
T COG1405 190 PPVDPSDYIPRFASKLGLS 208 (285)
T ss_pred CCCCHHHHHHHHHHHcCCC
Confidence 3479999999999999999
No 15
>PRK09239 chorismate mutase; Provisional
Probab=29.86 E-value=1.1e+02 Score=23.99 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=25.8
Q ss_pred HHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 026309 132 RTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQSV 165 (240)
Q Consensus 132 ~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~~~~ 165 (240)
...+.++||+ ++|+.+|-..|.+...++..+++
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 4456789999 59998888888888777766665
No 16
>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=28.09 E-value=1e+02 Score=24.87 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=31.7
Q ss_pred eeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHHcCCCCCChHHHHHHHHHHH
Q 026309 99 VPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCNDMGIEDPEVGPAVAFAIREQ 156 (240)
Q Consensus 99 vpI~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~~c~DLgL~~~ef~~aIa~aIreQ 156 (240)
..+.+||.-|+..|. .-.|. .-+|-.=|+.+|.+.+|| ..|..+|+.-|...
T Consensus 58 yVf~Vdi~dg~~~lk--LpyN~---~dnP~~aAq~Fi~~n~Lp-~~yl~qI~~FI~~N 109 (116)
T PF09070_consen 58 YVFDVDIEDGGPPLK--LPYNK---GDNPYEAAQKFIERNNLP-QSYLDQIANFIIQN 109 (116)
T ss_dssp EEEEE--STTSS-EE--EEE-T---TS-HHHHHHHHHHHHT---CCHHHHHHHHHHHH
T ss_pred EEEEEEecCCCccee--CCccC---CCCHHHHHHHHHHHcCCC-HHHHHHHHHHHHHc
Confidence 345555554443332 22344 458999999999999999 59999999888543
No 17
>PTZ00202 tuzin; Provisional
Probab=23.94 E-value=1.6e+02 Score=29.90 Aligned_cols=38 Identities=16% Similarity=0.141 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHH
Q 026309 126 DPEEFARTFCNDMGIEDPEVGPAVAFAIREQLYEIAIQ 163 (240)
Q Consensus 126 tPE~FA~~~c~DLgL~~~ef~~aIa~aIreQl~~~~~~ 163 (240)
+|++|-..++..||+++.+-...+...|++.|++.+++
T Consensus 321 g~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e 358 (550)
T PTZ00202 321 GTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKM 358 (550)
T ss_pred CHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHh
Confidence 79999999999999985334467889999998887664
No 18
>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=23.91 E-value=1.2e+02 Score=23.82 Aligned_cols=23 Identities=17% Similarity=0.138 Sum_probs=20.2
Q ss_pred CCCCCCCHHHHHHHHHHHcCCCh
Q 026309 45 PSDPDSEVVVFAKRTVRDLKLPP 67 (240)
Q Consensus 45 lne~~itpE~FA~~lc~Dl~lp~ 67 (240)
+-+..+++|+|...|=+.+..|+
T Consensus 35 L~~~~i~~EeF~~~Lq~~lns~~ 57 (92)
T smart00549 35 LVNGTITAEEFTSRLQEALNSPL 57 (92)
T ss_pred HHhCCCCHHHHHHHHHHHHcCCC
Confidence 34678999999999999999986
No 19
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.88 E-value=1.7e+02 Score=27.08 Aligned_cols=36 Identities=17% Similarity=0.200 Sum_probs=25.4
Q ss_pred CCCCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Q 026309 45 PSDPDSEVVVFAKRTVRDLKLPPQFITQIAQSIQTQL 81 (240)
Q Consensus 45 lne~~itpE~FA~~lc~Dl~lp~~f~~~I~~sI~~Ql 81 (240)
++-+.++|+.|...+|..|+||.... ..|..|-++.
T Consensus 212 ~~~~~~~p~~~i~r~~~~L~L~~~v~-~~A~~i~~~a 247 (310)
T PRK00423 212 LKLPPTDPIDYVPRFASELGLSGEVQ-KKAIEILQKA 247 (310)
T ss_pred CCCCCCCHHHHHHHHHHHcCCCHHHH-HHHHHHHHHH
Confidence 34556789999999999999997543 3444444433
No 20
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.85 E-value=94 Score=29.27 Aligned_cols=73 Identities=14% Similarity=0.203 Sum_probs=41.6
Q ss_pred HHHHHcCCChHHHHHHHHHHHHHHHHhhcccCCcccCCceeeeeEEEEEeCCeeeeeceeecCCCCCCCHHHHHHHHHHH
Q 026309 58 RTVRDLKLPPQFITQIAQSIQTQLTEFRSYEGQDMYTAEKIVPIKLDLRVNHTLIKDHFLWDLNNYESDPEEFARTFCND 137 (240)
Q Consensus 58 ~lc~Dl~lp~~f~~~I~~sI~~Ql~ey~~~~~~~~~~~e~~vpI~Ldi~~~~~~l~D~FeWdL~~~~~tPE~FA~~~c~D 137 (240)
+-|++.+.|-+|. .|....+-|..|...+....... ..+++. |. .++.+.|-..+|..
T Consensus 156 iACRq~~~pRT~k-EI~~~anv~kKEIgr~~K~i~~~------l~~s~~-----------~~----s~~t~~~m~RFCs~ 213 (308)
T KOG1597|consen 156 IACRQEDVPRTFK-EISAVANVSKKEIGRCVKLIGEA------LETSVD-----------LI----SISTGDFMPRFCSN 213 (308)
T ss_pred HHHHhcCCCchHH-HHHHHHcCCHHHHHHHHHHHHHH------Hhccch-----------hh----hhhHHHHHHHHHHh
Confidence 4588888888763 35554445555554432211000 111111 11 46688999999999
Q ss_pred cCCCCCChHHHHHHHH
Q 026309 138 MGIEDPEVGPAVAFAI 153 (240)
Q Consensus 138 LgL~~~ef~~aIa~aI 153 (240)
|+||. ..+.|..|.-
T Consensus 214 L~L~~-~~q~aA~e~a 228 (308)
T KOG1597|consen 214 LGLPK-SAQEAATEIA 228 (308)
T ss_pred cCCCH-HHHHHHHHHH
Confidence 99994 5555554443
Done!