Query 032480
Match_columns 140
No_of_seqs 108 out of 151
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 14:37:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032480.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032480hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06487 SAP18: Sin3 associate 100.0 1.5E-48 3.2E-53 293.7 8.2 98 35-136 2-100 (120)
2 KOG3391 Transcriptional co-rep 100.0 4.2E-44 9E-49 277.7 8.5 99 35-137 16-116 (151)
3 PF12078 DUF3557: Domain of un 53.7 36 0.00077 24.9 4.9 40 68-108 113-152 (154)
4 PLN03132 NADH dehydrogenase (u 52.4 13 0.00029 34.1 2.9 33 58-94 50-82 (461)
5 cd05992 PB1 The PB1 domain is 43.9 51 0.0011 21.5 4.0 33 79-116 19-51 (81)
6 KOG0476 Cl- channel CLC-2 and 34.7 26 0.00057 34.8 2.0 53 34-93 563-617 (931)
7 cd04910 ACT_AK-Ectoine_1 ACT d 26.9 61 0.0013 22.4 2.3 31 68-98 37-68 (71)
8 PF12327 FtsZ_C: FtsZ family, 26.5 1.5E+02 0.0033 21.0 4.4 39 73-112 41-79 (95)
9 smart00666 PB1 PB1 domain. Pho 26.1 1.3E+02 0.0028 19.7 3.8 34 79-117 19-52 (81)
10 cd01764 Urm1 Urm1-like ubuitin 26.0 98 0.0021 22.0 3.3 41 74-114 22-67 (94)
11 PF00564 PB1: PB1 domain; Int 24.8 41 0.0009 22.1 1.1 33 79-116 20-52 (84)
12 PF08620 RPAP1_C: RPAP1-like, 23.8 35 0.00075 24.0 0.6 19 80-98 38-56 (73)
13 PF04967 HTH_10: HTH DNA bindi 23.7 61 0.0013 21.3 1.7 15 76-90 18-33 (53)
14 PF08731 AFT: Transcription fa 23.4 65 0.0014 24.5 2.1 21 32-52 72-92 (111)
15 PF13511 DUF4124: Domain of un 23.0 35 0.00076 21.6 0.5 10 72-81 12-21 (60)
16 KOG1924 RhoA GTPase effector D 22.4 71 0.0015 32.3 2.6 22 12-33 567-588 (1102)
17 PF05320 Pox_RNA_Pol_19: Poxvi 21.8 37 0.0008 27.6 0.5 24 40-66 126-149 (167)
18 TIGR01687 moaD_arch MoaD famil 21.6 1.5E+02 0.0032 19.9 3.4 34 79-112 23-61 (88)
19 cd06401 PB1_TFG The PB1 domain 20.1 1.7E+02 0.0038 21.1 3.6 37 79-117 19-55 (81)
No 1
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=100.00 E-value=1.5e-48 Score=293.75 Aligned_cols=98 Identities=55% Similarity=0.980 Sum_probs=78.8
Q ss_pred CCCCccCCCCcEEEEecccCCCCCCcccccCCCCCCCCeeeeecCCCCHHHHHHHHHHhCccccCCCceEEEEEEecCCC
Q 032480 35 EPVDREKTCPLLLRVFTKIGGHHSREDFAVRGKEPKDEVQIYTWKDATLRELTDLVKEVAPAARRRDARLSFAFVYPDKN 114 (140)
Q Consensus 35 ~~iDRektcPFLLRVF~~~g~hH~l~eF~~~g~lP~~ElQIYTW~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~~ 114 (140)
++|||||||||||||||++|+||+++||+. |.+|.||||||||+|||||||++|||+++|++|++||+|+|++||||.+
T Consensus 2 ~~idRektcPfLLRvF~~~g~~h~~~dF~~-~~~P~~elqIYtW~d~TLrEL~~Lik~~~~~~r~~~tr~~F~~VypD~~ 80 (120)
T PF06487_consen 2 KPIDREKTCPFLLRVFYRNGRHHRLDDFSR-GSLPRNELQIYTWMDATLRELADLIKDVNPPARRRGTRLSFRLVYPDTR 80 (120)
T ss_dssp ----CCCS--EEEEEEESSSS---GGGCGC-CS-TTTEEEEEE-TT-BHHHHHHHHHHH-HHHHSTT-EEEEEEEEECTT
T ss_pred CCcccCCCCCeEEEEEEecCCCCCHHHccC-CCCCcCeeEEEEcccCCHHHHHHHHHHhCcccCCCCCEEEEEEEeecCC
Confidence 579999999999999999999999999995 9999999999999999999999999999999999999999999999965
Q ss_pred -CCcceeccCCcceEEecCCccc
Q 032480 115 -GRFMVREVSHSSLTVSYLGHDQ 136 (140)
Q Consensus 115 -grf~~rdLG~~~~v~s~~~~~~ 136 (140)
|+|.+|||| +|++|+++.+
T Consensus 81 ~~r~~~kdlG---sv~~g~~~~d 100 (120)
T PF06487_consen 81 SGRYVSKDLG---SVVSGRKGPD 100 (120)
T ss_dssp TTCEEEEEEE---EEETTB--TT
T ss_pred CCceeeecCC---eEECCCCCCC
Confidence 999999999 9999988554
No 2
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=100.00 E-value=4.2e-44 Score=277.70 Aligned_cols=99 Identities=56% Similarity=0.906 Sum_probs=94.3
Q ss_pred CCCCccCCCCcEEEEecc-cCCCCCCcccccCCCCCCCCeeeeecCCCCHHHHHHHHHHhCccccCCCceEEEEEEecCC
Q 032480 35 EPVDREKTCPLLLRVFTK-IGGHHSREDFAVRGKEPKDEVQIYTWKDATLRELTDLVKEVAPAARRRDARLSFAFVYPDK 113 (140)
Q Consensus 35 ~~iDRektcPFLLRVF~~-~g~hH~l~eF~~~g~lP~~ElQIYTW~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~ 113 (140)
++||||||||||||||++ +|+||.+|||+. |++|++||||||||||||+||+.||||++|++|++||.|+|++||+|.
T Consensus 16 ~piDrektCPlLlrVf~~~~g~hH~~def~~-g~vPs~elQiYtW~datL~ELtsLvkevnpeaR~kgt~f~fa~Vf~d~ 94 (151)
T KOG3391|consen 16 KPIDREKTCPLLLRVFTQFNGRHHVMDEFED-GNVPSSELQIYTWMDATLRELTSLVKEVNPEARKKGTSFDFAVVFPDK 94 (151)
T ss_pred CcccccccCcceeeeeeecCCCCcchhhhhc-CCCCchheeEeehhhhhHHHHHHHHHHcCHHHhccCceEEEEEEeccC
Confidence 689999999999999999 999999999994 999999999999999999999999999999999999999999999998
Q ss_pred C-CCcceeccCCcceEEecCCcccc
Q 032480 114 N-GRFMVREVSHSSLTVSYLGHDQS 137 (140)
Q Consensus 114 ~-grf~~rdLG~~~~v~s~~~~~~~ 137 (140)
+ .+|.+|||| +||+|++.-|.
T Consensus 95 ~~~~y~~RevG---~t~~g~Kg~dd 116 (151)
T KOG3391|consen 95 KSPRYIVREVG---TTCLGRKGIDD 116 (151)
T ss_pred CCCCceeeeec---ccccCcccCCc
Confidence 6 599999999 99999987554
No 3
>PF12078 DUF3557: Domain of unknown function (DUF3557); InterPro: IPR021942 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length.
Probab=53.65 E-value=36 Score=24.89 Aligned_cols=40 Identities=13% Similarity=0.188 Sum_probs=31.6
Q ss_pred CCCCCeeeeecCCCCHHHHHHHHHHhCccccCCCceEEEEE
Q 032480 68 EPKDEVQIYTWKDATLRELTDLVKEVAPAARRRDARLSFAF 108 (140)
Q Consensus 68 lP~~ElQIYTW~DaTLrELa~LIk~~~P~ar~~gtrlsFr~ 108 (140)
++..++++- ...-+..|+..+|+.=.-.-|..||+|+|.+
T Consensus 113 l~n~~v~~~-~~~~~~~~~~~li~~W~~~~r~IGt~~sf~~ 152 (154)
T PF12078_consen 113 LRNKRVHLK-NDEFSWDDFLRLIENWIENGRPIGTCFSFGI 152 (154)
T ss_pred CCCCEEEEE-ecCCCHHHHHHHHHHHHhcCCCCcEEEEEEE
Confidence 443355555 5777889999999998778899999999975
No 4
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=52.38 E-value=13 Score=34.09 Aligned_cols=33 Identities=9% Similarity=-0.110 Sum_probs=22.2
Q ss_pred CCcccccCCCCCCCCeeeeecCCCCHHHHHHHHHHhC
Q 032480 58 SREDFAVRGKEPKDEVQIYTWKDATLRELTDLVKEVA 94 (140)
Q Consensus 58 ~l~eF~~~g~lP~~ElQIYTW~DaTLrELa~LIk~~~ 94 (140)
++++|-.+|- .-.+=.|...+-.||.+.|+++-
T Consensus 50 ~l~~y~~~gg----y~~l~~~~~~~p~~ii~~V~~sG 82 (461)
T PLN03132 50 FLKGAMKRGD----WHRTKDLVLKGPDWIVNEMKKSG 82 (461)
T ss_pred CHHHHHHcCC----HHHHHHHHhCCHHHHHHHHHHhC
Confidence 6888875542 11233445678899999999974
No 5
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=43.87 E-value=51 Score=21.53 Aligned_cols=33 Identities=24% Similarity=0.511 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHHHHhCccccCCCceEEEEEEecCCCCC
Q 032480 79 KDATLRELTDLVKEVAPAARRRDARLSFAFVYPDKNGR 116 (140)
Q Consensus 79 ~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~~gr 116 (140)
.++|+.||...|.+.++... ..|.+-|.|..|-
T Consensus 19 ~~~s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~d 51 (81)
T cd05992 19 RSISFEDLRSKIAEKFGLDA-----VSFKLKYPDEDGD 51 (81)
T ss_pred CCCCHHHHHHHHHHHhCCCC-----CcEEEEeeCCCCC
Confidence 68999999999999887653 6778889998763
No 6
>KOG0476 consensus Cl- channel CLC-2 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism]
Probab=34.67 E-value=26 Score=34.84 Aligned_cols=53 Identities=26% Similarity=0.350 Sum_probs=43.5
Q ss_pred CCCCCccCCCCcEEEEecccCCCCC--CcccccCCCCCCCCeeeeecCCCCHHHHHHHHHHh
Q 032480 34 FEPVDREKTCPLLLRVFTKIGGHHS--REDFAVRGKEPKDEVQIYTWKDATLRELTDLVKEV 93 (140)
Q Consensus 34 ~~~iDRektcPFLLRVF~~~g~hH~--l~eF~~~g~lP~~ElQIYTW~DaTLrELa~LIk~~ 93 (140)
-+.|=|-|.-|||=.+=.++...|+ +|+|-.+. + +|.|+|+|.+||-..|+..
T Consensus 563 YDSII~IKklPYLPDlpps~~~~h~v~VE~iMV~d-v------~yI~k~~Ty~elre~l~~~ 617 (931)
T KOG0476|consen 563 YDSIIRIKKLPYLPDLPPSRSSVHTVKVEHIMVTD-V------KYITKDTTYRELREALQTT 617 (931)
T ss_pred hhheeeeccCCcCCCCCCcccceeEEEeeeecccc-c------eeeeccCcHHHHHHHHHhC
Confidence 3567789999999999998888886 67887632 3 3999999999999988875
No 7
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=26.90 E-value=61 Score=22.41 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=26.9
Q ss_pred CCCCCeeeeecCCC-CHHHHHHHHHHhCcccc
Q 032480 68 EPKDEVQIYTWKDA-TLRELTDLVKEVAPAAR 98 (140)
Q Consensus 68 lP~~ElQIYTW~Da-TLrELa~LIk~~~P~ar 98 (140)
...|++-+|-|-+. +++.+...|++.+|++.
T Consensus 37 ~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~ 68 (71)
T cd04910 37 TNANTITHYLAGSLKTIKRLTEDLENRFPNAE 68 (71)
T ss_pred cCCCeEEEEEEcCHHHHHHHHHHHHHhCccCc
Confidence 34789999999996 99999999999999763
No 8
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=26.48 E-value=1.5e+02 Score=20.96 Aligned_cols=39 Identities=21% Similarity=0.259 Sum_probs=27.0
Q ss_pred eeeeecCCCCHHHHHHHHHHhCccccCCCceEEEEEEecC
Q 032480 73 VQIYTWKDATLRELTDLVKEVAPAARRRDARLSFAFVYPD 112 (140)
Q Consensus 73 lQIYTW~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD 112 (140)
++|+.+.|.||.|+...+..+.-.. ...+...|-+++-+
T Consensus 41 vni~~~~d~~l~ev~~~~~~i~~~~-~~~a~ii~G~~id~ 79 (95)
T PF12327_consen 41 VNITGGPDLSLSEVNEAMEIIREKA-DPDANIIWGASIDE 79 (95)
T ss_dssp EEEEE-TTS-HHHHHHHHHHHHHHS-STTSEEEEEEEE-T
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHh-hcCceEEEEEEECC
Confidence 7899999999999988776654333 37778888776543
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=26.11 E-value=1.3e+02 Score=19.70 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHhCccccCCCceEEEEEEecCCCCCc
Q 032480 79 KDATLRELTDLVKEVAPAARRRDARLSFAFVYPDKNGRF 117 (140)
Q Consensus 79 ~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~~grf 117 (140)
.++|+.||...|.+.++... =.|.+=|-|..|-+
T Consensus 19 ~~~s~~dL~~~i~~~~~~~~-----~~~~l~Y~Dedgd~ 52 (81)
T smart00666 19 RDISFEDLRSKVAKRFGLDN-----QSFTLKYQDEDGDL 52 (81)
T ss_pred CCCCHHHHHHHHHHHhCCCC-----CCeEEEEECCCCCE
Confidence 38999999999999987432 24566677877643
No 10
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=26.05 E-value=98 Score=22.04 Aligned_cols=41 Identities=17% Similarity=0.050 Sum_probs=29.0
Q ss_pred eeeecCCCCHHHHHHHHHHhCccccC-----CCceEEEEEEecCCC
Q 032480 74 QIYTWKDATLRELTDLVKEVAPAARR-----RDARLSFAFVYPDKN 114 (140)
Q Consensus 74 QIYTW~DaTLrELa~LIk~~~P~ar~-----~gtrlsFr~VYpD~~ 114 (140)
++=.|..+|++||...|++.++..+. .+.--.|-+||.+.+
T Consensus 22 ~~~~~~~~tV~dll~~L~~~~~~~~~~lf~~~g~lr~~i~VlvN~~ 67 (94)
T cd01764 22 VLDGEKPVTVGDLLDYVASNLLEERPDLFIEGGSVRPGIIVLINDT 67 (94)
T ss_pred eccCCCCCcHHHHHHHHHHhCchhhhhhEecCCcccCCEEEEECCc
Confidence 33344679999999999999876542 344445778888754
No 11
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=24.76 E-value=41 Score=22.11 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHhCccccCCCceEEEEEEecCCCCC
Q 032480 79 KDATLRELTDLVKEVAPAARRRDARLSFAFVYPDKNGR 116 (140)
Q Consensus 79 ~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~~gr 116 (140)
.++|+.+|...|++.++.. .-.|.+-|.|..|-
T Consensus 20 ~~~s~~~L~~~i~~~~~~~-----~~~~~l~Y~D~dgD 52 (84)
T PF00564_consen 20 SDVSFDDLRSKIREKFGLL-----DEDFQLKYKDEDGD 52 (84)
T ss_dssp STSHHHHHHHHHHHHHTTS-----TSSEEEEEEETTSS
T ss_pred CCCCHHHHHHHHHHHhCCC-----CccEEEEeeCCCCC
Confidence 6789999999999988776 34577778887764
No 12
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=23.80 E-value=35 Score=24.00 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHHhCcccc
Q 032480 80 DATLRELTDLVKEVAPAAR 98 (140)
Q Consensus 80 DaTLrELa~LIk~~~P~ar 98 (140)
--||.||..|.+..+|.-|
T Consensus 38 GYTi~El~~L~RSsv~~QR 56 (73)
T PF08620_consen 38 GYTIQELFHLSRSSVPSQR 56 (73)
T ss_pred CcCHHHHHHHHhcCcHHHH
Confidence 4589999999999988754
No 13
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=23.72 E-value=61 Score=21.29 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=11.8
Q ss_pred eec-CCCCHHHHHHHH
Q 032480 76 YTW-KDATLRELTDLV 90 (140)
Q Consensus 76 YTW-~DaTLrELa~LI 90 (140)
|.| .++||.||+..|
T Consensus 18 fd~PR~~tl~elA~~l 33 (53)
T PF04967_consen 18 FDVPRRITLEELAEEL 33 (53)
T ss_pred CCCCCcCCHHHHHHHh
Confidence 444 489999999876
No 14
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=23.40 E-value=65 Score=24.55 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=17.6
Q ss_pred CCCCCCCccCCCCcEEEEecc
Q 032480 32 PRFEPVDREKTCPLLLRVFTK 52 (140)
Q Consensus 32 ~~~~~iDRektcPFLLRVF~~ 52 (140)
.....+.|.-+|||=+|-.|+
T Consensus 72 k~k~t~srk~~CPFriRA~yS 92 (111)
T PF08731_consen 72 KKKRTKSRKNTCPFRIRANYS 92 (111)
T ss_pred cCCcccccccCCCeEEEEEEE
Confidence 446678999999999999876
No 15
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=22.96 E-value=35 Score=21.59 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=7.5
Q ss_pred CeeeeecCCC
Q 032480 72 EVQIYTWKDA 81 (140)
Q Consensus 72 ElQIYTW~Da 81 (140)
.-+||.|.|.
T Consensus 12 aa~vYk~~D~ 21 (60)
T PF13511_consen 12 AAEVYKWVDE 21 (60)
T ss_pred hccEEEEECC
Confidence 3578999875
No 16
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=22.42 E-value=71 Score=32.26 Aligned_cols=22 Identities=45% Similarity=0.859 Sum_probs=0.0
Q ss_pred cCCCCCCCCCCCCCCCCCCCCC
Q 032480 12 AGRSRPLHPSGRGPPPPPPRPR 33 (140)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~ 33 (140)
+++++|.||||-|.+|||+.|.
T Consensus 567 aG~PPpPppppg~~gppPPPpp 588 (1102)
T KOG1924|consen 567 AGGPPPPPPPPGGGGPPPPPPP 588 (1102)
T ss_pred cCCCCccCCCCCCCCCCCcCCC
No 17
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.76 E-value=37 Score=27.62 Aligned_cols=24 Identities=42% Similarity=0.743 Sum_probs=20.2
Q ss_pred cCCCCcEEEEecccCCCCCCcccccCC
Q 032480 40 EKTCPLLLRVFTKIGGHHSREDFAVRG 66 (140)
Q Consensus 40 ektcPFLLRVF~~~g~hH~l~eF~~~g 66 (140)
|.|||..+ .|+|.+-++.||+..|
T Consensus 126 Eg~CPIVI---eKNGElLS~~DFD~~g 149 (167)
T PF05320_consen 126 EGTCPIVI---EKNGELLSINDFDKKG 149 (167)
T ss_pred cCCCcEEE---eeCCeEccccccCHHH
Confidence 67999865 6999999999999644
No 18
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=21.60 E-value=1.5e+02 Score=19.93 Aligned_cols=34 Identities=9% Similarity=0.061 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHHHhCccccC-----CCceEEEEEEecC
Q 032480 79 KDATLRELTDLVKEVAPAARR-----RDARLSFAFVYPD 112 (140)
Q Consensus 79 ~DaTLrELa~LIk~~~P~ar~-----~gtrlsFr~VYpD 112 (140)
..+|++||...|.+.+|.... .+.-..+-.|+.|
T Consensus 23 ~~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN 61 (88)
T TIGR01687 23 EGKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVN 61 (88)
T ss_pred CCCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEEC
Confidence 589999999999999886322 2333344455555
No 19
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=20.09 E-value=1.7e+02 Score=21.07 Aligned_cols=37 Identities=22% Similarity=0.302 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHhCccccCCCceEEEEEEecCCCCCc
Q 032480 79 KDATLRELTDLVKEVAPAARRRDARLSFAFVYPDKNGRF 117 (140)
Q Consensus 79 ~DaTLrELa~LIk~~~P~ar~~gtrlsFr~VYpD~~grf 117 (140)
.+||+.||.+.|+..+... -+.-=+|.+=|-|..|-.
T Consensus 19 ~~~t~~~L~~~v~~~F~~~--~~~~~~flIKYkD~dGDl 55 (81)
T cd06401 19 EDITYDELLLMMQRVFRGK--LGSSDDVLIKYKDEDGDL 55 (81)
T ss_pred ccccHHHHHHHHHHHhccc--cCCcccEEEEEECCCCCE
Confidence 5799999999999876622 122236788899987643
Done!