Query 011601
Match_columns 481
No_of_seqs 111 out of 141
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:10:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011601.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011601hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11891 DUF3411: Domain of un 100.0 4.2E-66 9.1E-71 481.5 12.4 169 245-415 1-179 (180)
2 PF06524 NOA36: NOA36 protein; 88.5 0.44 9.5E-06 48.8 3.6 11 103-113 219-229 (314)
3 PF02084 Bindin: Bindin; Inte 79.4 1.8 3.9E-05 43.5 3.2 30 181-210 104-133 (238)
4 PF14812 PBP1_TM: Transmembran 79.2 0.61 1.3E-05 40.0 0.0 14 148-161 35-48 (81)
5 PF02979 NHase_alpha: Nitrile 71.6 2.6 5.7E-05 41.2 2.1 48 205-255 17-68 (188)
6 PLN03138 Protein TOC75; Provis 69.0 8.2 0.00018 44.8 5.6 9 407-415 458-466 (796)
7 KOG0943 Predicted ubiquitin-pr 66.8 1.6 3.5E-05 52.6 -0.5 71 177-265 1796-1868(3015)
8 COG4907 Predicted membrane pro 63.4 5.1 0.00011 44.2 2.5 22 113-134 562-583 (595)
9 PF02957 TT_ORF2: TT viral ORF 58.8 7.4 0.00016 34.5 2.3 9 63-71 30-38 (122)
10 PLN00151 potassium transporter 54.2 16 0.00034 42.8 4.5 23 348-370 220-242 (852)
11 KOG3540 Beta amyloid precursor 54.1 15 0.00032 40.9 4.0 21 171-192 255-275 (615)
12 PF11705 RNA_pol_3_Rpc31: DNA- 53.4 8.1 0.00018 37.7 1.8 7 66-72 90-96 (233)
13 TIGR02877 spore_yhbH sporulati 50.9 16 0.00034 39.1 3.6 7 119-125 60-66 (371)
14 PF09849 DUF2076: Uncharacteri 49.5 19 0.00041 36.4 3.7 10 67-76 156-165 (247)
15 TIGR01323 nitrile_alph nitrile 39.2 34 0.00074 33.6 3.6 46 205-253 11-60 (185)
16 PF14812 PBP1_TM: Transmembran 39.1 10 0.00022 32.8 0.0 12 150-161 33-44 (81)
17 PF10446 DUF2457: Protein of u 39.1 17 0.00036 39.9 1.6 14 321-334 294-307 (458)
18 PLN03138 Protein TOC75; Provis 38.6 22 0.00048 41.4 2.6 12 199-210 189-200 (796)
19 PF02957 TT_ORF2: TT viral ORF 38.1 17 0.00037 32.2 1.3 11 118-128 75-85 (122)
20 PHA03249 DNA packaging tegumen 35.0 1.2E+02 0.0026 34.9 7.3 23 158-180 171-195 (653)
21 KOG0943 Predicted ubiquitin-pr 34.9 21 0.00045 43.9 1.6 7 441-447 2027-2033(3015)
22 PF09026 CENP-B_dimeris: Centr 34.8 13 0.00028 33.3 0.0 18 185-202 51-68 (101)
23 PRK05325 hypothetical protein; 33.6 58 0.0013 35.3 4.5 9 119-127 48-56 (401)
24 KOG3074 Transcriptional regula 32.7 26 0.00057 35.8 1.8 19 198-216 91-109 (263)
25 PF11705 RNA_pol_3_Rpc31: DNA- 32.0 28 0.00061 34.0 1.8 8 152-159 213-220 (233)
26 KOG0921 Dosage compensation co 31.6 59 0.0013 39.1 4.5 9 27-35 1116-1124(1282)
27 COG1512 Beta-propeller domains 31.2 59 0.0013 33.4 4.0 16 93-108 220-235 (271)
28 PF04931 DNA_pol_phi: DNA poly 30.5 48 0.0011 37.9 3.6 6 69-74 559-564 (784)
29 PHA00458 single-stranded DNA-b 29.3 57 0.0012 33.1 3.4 8 69-76 59-66 (233)
30 PF04858 TH1: TH1 protein; In 29.2 1.1E+02 0.0024 34.7 5.9 50 185-235 36-95 (584)
31 COG2818 Tag 3-methyladenine DN 27.2 37 0.00081 33.4 1.7 125 167-300 50-177 (188)
32 KOG2023 Nuclear transport rece 26.9 35 0.00075 39.6 1.6 39 89-127 302-343 (885)
33 PF08595 RXT2_N: RXT2-like, N- 24.1 41 0.00089 31.8 1.3 6 222-227 104-109 (149)
34 PLN03083 E3 UFM1-protein ligas 23.4 1.2E+02 0.0027 35.6 5.1 35 176-210 484-522 (803)
35 COG3685 Uncharacterized protei 23.3 54 0.0012 31.8 2.0 53 173-227 57-119 (167)
36 PF04931 DNA_pol_phi: DNA poly 22.7 48 0.001 38.0 1.8 10 65-74 559-568 (784)
37 KOG3973 Uncharacterized conser 21.6 69 0.0015 34.7 2.5 9 102-110 340-348 (465)
38 PRK05325 hypothetical protein; 21.4 71 0.0015 34.6 2.6 8 280-287 202-209 (401)
39 KOG3241 Uncharacterized conser 20.9 70 0.0015 31.9 2.2 7 134-140 182-188 (227)
40 PF06946 Phage_holin_5: Phage 20.9 2.4E+02 0.0053 25.2 5.3 27 339-376 57-83 (93)
41 PF04871 Uso1_p115_C: Uso1 / p 20.7 71 0.0015 29.4 2.1 21 141-161 116-136 (136)
42 KOG2023 Nuclear transport rece 20.5 99 0.0021 36.2 3.6 34 222-260 445-480 (885)
No 1
>PF11891 DUF3411: Domain of unknown function (DUF3411); InterPro: IPR021825 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 168 to 186 amino acids in length. This domain has a conserved RYQ sequence motif.
Probab=100.00 E-value=4.2e-66 Score=481.55 Aligned_cols=169 Identities=41% Similarity=0.610 Sum_probs=162.3
Q ss_pred hhhccCchhHHHHHHHHHHhhhhhhhhhhhhcchhhhhHHHHHHHHHHHHHHhhHHHhhhcccccccCCccc----cchH
Q 011601 245 GRMLADPSFLYKLILEQAATIGCTVLWELENRKERIKQEWDLALINVLTVTACNAFVVWSLAPCRSYGNTFR----FDLQ 320 (481)
Q Consensus 245 ~RlLADP~FLfKL~iE~~I~i~~~~~aE~~~Rge~F~~ElDfV~sdvv~g~v~nfaLVwLLAPt~s~G~~~~----~~lq 320 (481)
|||||||+|||||++||+||++|+++|||++|||+||+|||||+||+++++|+||+||||||||++++++++ +.+|
T Consensus 1 ~RllADP~Fl~Kl~~E~~i~i~~~~~~e~~~R~e~f~~E~d~v~~d~v~~~i~n~~lv~llAPt~s~~~~~~~~~~~~~~ 80 (180)
T PF11891_consen 1 ERLLADPSFLFKLAIEEVIGIGCATAAEYAKRGERFWNELDFVFSDVVVGSIVNFALVWLLAPTRSFGSPAASSPGGGLQ 80 (180)
T ss_pred CcccccchHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHhccchHhhCcccccccchHHH
Confidence 799999999999999999999999999999999999999999999999999999999999999999999988 6899
Q ss_pred HHhccCCCccccccCCCCCcchhhhHHHHHhhchhhhhhHhHHHhhHHHHHHHHhh-c-cC----CCcccCCchhhhhhh
Q 011601 321 NTLQKLPNNIFERSYPFREFDLQKRIHSLFYKAAELCMVGLSAGAVQGSLSNYLAG-K-KD----RLSVTIPSVSTSALE 394 (481)
Q Consensus 321 k~l~~lP~N~Feks~pg~~fsl~qRiga~v~KGa~l~~VG~~aGlvG~glSN~L~~-k-K~----~~s~~vP~l~tsAl~ 394 (481)
+++++||+||||+++||++||++||++||+|||++|++|||+||++|+++||+|++ | +. ++++++|||++||+
T Consensus 81 ~~~~~~P~n~Fq~~~~g~~fsl~qR~~~~~~kg~~l~~VG~~ag~vg~~lsn~L~~~rk~~~~~~e~~~~~ppv~~ta~- 159 (180)
T PF11891_consen 81 KFLGSLPNNAFQKGYPGRSFSLAQRIGAFVYKGAKLAAVGFIAGLVGTGLSNALIAARKKVDPSFEPSVPVPPVLKTAL- 159 (180)
T ss_pred HHHHhChHHHhccCCCCCcccHHHHHHHHHHcchHhhhhHHHHHHHHHHHHHHHHHHHHhcCccccCCCCCCCHHHHHH-
Confidence 99999999999999999999999999999999999999999999999999999999 4 33 35778899999999
Q ss_pred hhhhhhhcccccchhhhhHHH
Q 011601 395 RSRLAWLGVEADPLLQSDDLL 415 (481)
Q Consensus 395 ~~w~~fmGvSAN~RyQ~~nll 415 (481)
+|++|||+|||+|||..|++
T Consensus 160 -~~g~fmGvSsNlRYQil~Gi 179 (180)
T PF11891_consen 160 -GWGAFMGVSSNLRYQILNGI 179 (180)
T ss_pred -HHHHHHhhhHhHHHHHHcCC
Confidence 69999999999999998876
No 2
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=88.52 E-value=0.44 Score=48.84 Aligned_cols=11 Identities=27% Similarity=0.286 Sum_probs=4.6
Q ss_pred eeeccccccee
Q 011601 103 TLEKGKLDTTQ 113 (481)
Q Consensus 103 tleks~l~~~q 113 (481)
|-|-.-|.+|-
T Consensus 219 t~eTkdLSmSt 229 (314)
T PF06524_consen 219 TQETKDLSMST 229 (314)
T ss_pred ccccccceeee
Confidence 33444444443
No 3
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=79.39 E-value=1.8 Score=43.50 Aligned_cols=30 Identities=27% Similarity=0.554 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhhccCchHHHHHHHHcCCc
Q 011601 181 KFVDAVLNEWMKTMMDLPAGFRQAYEMGLV 210 (481)
Q Consensus 181 ~~i~aVL~E~~rt~~sLPaDl~~A~e~Glv 210 (481)
|-.+.+.+-.+.|--+||-||-+=++.||+
T Consensus 104 Kvm~~ikavLgaTKiDLPVDINDPYDlGLL 133 (238)
T PF02084_consen 104 KVMEDIKAVLGATKIDLPVDINDPYDLGLL 133 (238)
T ss_pred HHHHHHHHHhcccccccccccCChhhHHHH
Confidence 333444444578999999999999998864
No 4
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=79.22 E-value=0.61 Score=40.04 Aligned_cols=14 Identities=71% Similarity=0.902 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCC
Q 011601 148 DDDDYFDDFDDGDE 161 (481)
Q Consensus 148 ddddy~d~~ddgd~ 161 (481)
++|||+||++++||
T Consensus 35 ~ddd~~DDD~dDde 48 (81)
T PF14812_consen 35 YDDDYEDDDDDDDE 48 (81)
T ss_dssp --------------
T ss_pred cccccccccccchh
Confidence 34444444444333
No 5
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=71.63 E-value=2.6 Score=41.18 Aligned_cols=48 Identities=27% Similarity=0.479 Sum_probs=35.5
Q ss_pred HHcCCcCHHHHHHHHHhccCc----chhHHHHhhcCcchhhhhhhhhccCchhHH
Q 011601 205 YEMGLVSSAQMVKFLAINARP----TTTRFISRSLPQGISRAFIGRMLADPSFLY 255 (481)
Q Consensus 205 ~e~Glvssa~L~rFl~L~~~P----~~~~~l~R~lp~~~srgfR~RlLADP~FLf 255 (481)
+|.|+|+++.+.++.+...+- +-++.+.|.+-. .+||.|||+||.=..
T Consensus 17 ~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~D---p~FK~rLLaD~~aA~ 68 (188)
T PF02979_consen 17 IEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTD---PAFKARLLADPTAAI 68 (188)
T ss_dssp HHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH----HHHHHHHHHSHHHHH
T ss_pred HHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCC---HHHHHHHHHCHHHHH
Confidence 679999999999988876543 236777887644 699999999997433
No 6
>PLN03138 Protein TOC75; Provisional
Probab=69.01 E-value=8.2 Score=44.79 Aligned_cols=9 Identities=0% Similarity=0.102 Sum_probs=4.5
Q ss_pred chhhhhHHH
Q 011601 407 PLLQSDDLL 415 (481)
Q Consensus 407 ~RyQ~~nll 415 (481)
..||-.||+
T Consensus 458 vs~~~~NL~ 466 (796)
T PLN03138 458 VSFEHRNIQ 466 (796)
T ss_pred EEEeccccc
Confidence 445555554
No 7
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=66.79 E-value=1.6 Score=52.60 Aligned_cols=71 Identities=27% Similarity=0.152 Sum_probs=40.0
Q ss_pred hhcHHHHHHHHHHHHhhccCchHHHHHHHHcCCcCHHHHHHHHHhccCcchhHHHHhhcCcchhhhhhh--hhccCchhH
Q 011601 177 LFDRKFVDAVLNEWMKTMMDLPAGFRQAYEMGLVSSAQMVKFLAINARPTTTRFISRSLPQGISRAFIG--RMLADPSFL 254 (481)
Q Consensus 177 ~fdR~~i~aVL~E~~rt~~sLPaDl~~A~e~Glvssa~L~rFl~L~~~P~~~~~l~R~lp~~~srgfR~--RlLADP~FL 254 (481)
.=||-+|.++..|.++--+.+|+-+.+|--.-.-+. ++-+.+ -+ | +.+.++ =|+|||.-+
T Consensus 1796 ~~dRieVq~ataeSE~aaepV~~afe~adpqp~dpd------~dDnSS--------ds--Q--e~~a~e~aFmiad~ahp 1857 (3015)
T KOG0943|consen 1796 SGDRIEVQAATAESEAAAEPVPAAFEEADPQPNDPD------DDDNSS--------DS--Q--EDDAEEEAFMIADPAHP 1857 (3015)
T ss_pred ccceeEEeecccccccccCCcccccCcCCCCCCCCC------cccccc--------cc--c--cccccccceeecCCcch
Confidence 346677778888888888888876655532211111 000000 00 0 011111 189999999
Q ss_pred HHHHHHHHHhh
Q 011601 255 YKLILEQAATI 265 (481)
Q Consensus 255 fKL~iE~~I~i 265 (481)
..|+.|+-.-+
T Consensus 1858 leva~aqpaN~ 1868 (3015)
T KOG0943|consen 1858 LEVALAQPANS 1868 (3015)
T ss_pred hhHhhcccCCC
Confidence 99999986544
No 8
>COG4907 Predicted membrane protein [Function unknown]
Probab=63.45 E-value=5.1 Score=44.17 Aligned_cols=22 Identities=18% Similarity=0.222 Sum_probs=11.2
Q ss_pred ecccccCceeecCCCCCCCCCC
Q 011601 113 QQQSETTPELATGGGGGDIGKK 134 (481)
Q Consensus 113 q~~~~~~p~l~~GgGgG~~g~~ 134 (481)
+.-+...|.-.+|-+||++|+-
T Consensus 562 raysa~a~S~~~~~~GGG~G~~ 583 (595)
T COG4907 562 RAYSAIASSRRSSSSGGGGGFS 583 (595)
T ss_pred hhhhcccccccCCCCCCCCCcC
Confidence 3345555655555555544443
No 9
>PF02957 TT_ORF2: TT viral ORF2; InterPro: IPR004118 This entry represents the Gyroviral VP2 protein and TT viral ORF2. Torque teno virus (TTV) is a nonenveloped and single-stranded DNA virus that was initially isolated from a Japanese patient with hepatitis of unknown aetiology, and which has since been found to infect both healthy and diseased individuals []. Numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF2 is a 150 residue protein of unknown function. Gyroviruses are small circular single stranded viruses, such as the Chicken anaemia virus. The VP2 protein contains a set of conserved cysteine and histidine residues suggesting a zinc binding domain. VP2 may act as a scaffold protein in virion assembly and may also play a role in intracellular signaling during viral replication.
Probab=58.75 E-value=7.4 Score=34.46 Aligned_cols=9 Identities=11% Similarity=0.106 Sum_probs=4.4
Q ss_pred cchhhhhhh
Q 011601 63 DHSVVLLER 71 (481)
Q Consensus 63 ~~~~~~~er 71 (481)
++-+.+|-+
T Consensus 30 ~dp~~HL~~ 38 (122)
T PF02957_consen 30 GDPIAHLLA 38 (122)
T ss_pred CCHHHHHHH
Confidence 355555444
No 10
>PLN00151 potassium transporter; Provisional
Probab=54.23 E-value=16 Score=42.81 Aligned_cols=23 Identities=13% Similarity=-0.096 Sum_probs=9.6
Q ss_pred HHHhhchhhhhhHhHHHhhHHHH
Q 011601 348 SLFYKAAELCMVGLSAGAVQGSL 370 (481)
Q Consensus 348 a~v~KGa~l~~VG~~aGlvG~gl 370 (481)
.++-|-..+-.+=++.+++|+++
T Consensus 220 ~~lE~s~~~k~~ll~l~l~Gtam 242 (852)
T PLN00151 220 ERLETSSLLKKLLLLLVLAGTSM 242 (852)
T ss_pred HHhhhhHHHHHHHHHHHHHhHHH
Confidence 33333333333334445555553
No 11
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=54.05 E-value=15 Score=40.89 Aligned_cols=21 Identities=43% Similarity=0.664 Sum_probs=15.0
Q ss_pred hhHHHHhhcHHHHHHHHHHHHh
Q 011601 171 RKILEELFDRKFVDAVLNEWMK 192 (481)
Q Consensus 171 r~~~~e~fdR~~i~aVL~E~~r 192 (481)
+.-++| =-|+-++.||+||+.
T Consensus 255 kmrlee-khr~rmd~VmkEW~~ 275 (615)
T KOG3540|consen 255 KMRLEE-KHRKRMDKVMKEWEE 275 (615)
T ss_pred HHHHHH-HHHHHHHHHHHHHHH
Confidence 333443 357889999999973
No 12
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 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. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=53.39 E-value=8.1 Score=37.74 Aligned_cols=7 Identities=29% Similarity=0.183 Sum_probs=5.0
Q ss_pred hhhhhhh
Q 011601 66 VVLLERC 72 (481)
Q Consensus 66 ~~~~er~ 72 (481)
...+||+
T Consensus 90 ~~~ierY 96 (233)
T PF11705_consen 90 FDDIERY 96 (233)
T ss_pred cccHHHH
Confidence 5568887
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=50.93 E-value=16 Score=39.14 Aligned_cols=7 Identities=0% Similarity=-0.149 Sum_probs=3.6
Q ss_pred CceeecC
Q 011601 119 TPELATG 125 (481)
Q Consensus 119 ~p~l~~G 125 (481)
+|....|
T Consensus 60 Ep~F~~g 66 (371)
T TIGR02877 60 EYRFRYD 66 (371)
T ss_pred cceEEeC
Confidence 5555544
No 14
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=49.49 E-value=19 Score=36.41 Aligned_cols=10 Identities=10% Similarity=0.052 Sum_probs=4.8
Q ss_pred hhhhhhhcCC
Q 011601 67 VLLERCYKAP 76 (481)
Q Consensus 67 ~~~er~~~~~ 76 (481)
.+||=-|...
T Consensus 156 n~i~~lF~~~ 165 (247)
T PF09849_consen 156 NGIESLFGGH 165 (247)
T ss_pred HHHHHHhcCC
Confidence 3455555443
No 15
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=39.22 E-value=34 Score=33.60 Aligned_cols=46 Identities=13% Similarity=0.323 Sum_probs=35.2
Q ss_pred HHcCCcCHHHHHHHHHhccC---c-chhHHHHhhcCcchhhhhhhhhccCchh
Q 011601 205 YEMGLVSSAQMVKFLAINAR---P-TTTRFISRSLPQGISRAFIGRMLADPSF 253 (481)
Q Consensus 205 ~e~Glvssa~L~rFl~L~~~---P-~~~~~l~R~lp~~~srgfR~RlLADP~F 253 (481)
+|.|+|+++.+.+.++...+ | +-++.+.|.+-. ..||.|||+|..=
T Consensus 11 ~eKGli~~~~id~~i~~~~~~~gP~nGA~vVArAW~D---p~fk~~Ll~d~~a 60 (185)
T TIGR01323 11 KSKGLIPEGAVDQLTSLYENEWGPENGAKVVAKAWVD---PEFRALLLKDATA 60 (185)
T ss_pred HHcCCCCHHHHHHHHHHHHhccCCcchhhhhhHHhcC---HHHHHHHHhChHH
Confidence 67899999998888876543 2 236778888654 5999999999753
No 16
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=39.15 E-value=10 Score=32.79 Aligned_cols=12 Identities=58% Similarity=1.168 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCC
Q 011601 150 DDYFDDFDDGDE 161 (481)
Q Consensus 150 ddy~d~~ddgd~ 161 (481)
|||+||.+|+|+
T Consensus 33 DD~ddd~~DDD~ 44 (81)
T PF14812_consen 33 DDYDDDYEDDDD 44 (81)
T ss_dssp ------------
T ss_pred hccccccccccc
Confidence 344444334333
No 17
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=39.06 E-value=17 Score=39.88 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=7.3
Q ss_pred HHhccCCCcccccc
Q 011601 321 NTLQKLPNNIFERS 334 (481)
Q Consensus 321 k~l~~lP~N~Feks 334 (481)
+.++.=|-..|...
T Consensus 294 k~~g~SPrrlf~sp 307 (458)
T PF10446_consen 294 KLRGRSPRRLFRSP 307 (458)
T ss_pred hccCCCCcccccCC
Confidence 34444466666543
No 18
>PLN03138 Protein TOC75; Provisional
Probab=38.56 E-value=22 Score=41.41 Aligned_cols=12 Identities=8% Similarity=0.185 Sum_probs=4.8
Q ss_pred HHHHHHHHcCCc
Q 011601 199 AGFRQAYEMGLV 210 (481)
Q Consensus 199 aDl~~A~e~Glv 210 (481)
+|+..-.+.|..
T Consensus 189 ~dv~~I~~tG~F 200 (796)
T PLN03138 189 KELETLASCGMF 200 (796)
T ss_pred HHHHHHHhcCCc
Confidence 333333344444
No 19
>PF02957 TT_ORF2: TT viral ORF2; InterPro: IPR004118 This entry represents the Gyroviral VP2 protein and TT viral ORF2. Torque teno virus (TTV) is a nonenveloped and single-stranded DNA virus that was initially isolated from a Japanese patient with hepatitis of unknown aetiology, and which has since been found to infect both healthy and diseased individuals []. Numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF2 is a 150 residue protein of unknown function. Gyroviruses are small circular single stranded viruses, such as the Chicken anaemia virus. The VP2 protein contains a set of conserved cysteine and histidine residues suggesting a zinc binding domain. VP2 may act as a scaffold protein in virion assembly and may also play a role in intracellular signaling during viral replication.
Probab=38.08 E-value=17 Score=32.22 Aligned_cols=11 Identities=36% Similarity=0.622 Sum_probs=4.8
Q ss_pred cCceeecCCCC
Q 011601 118 TTPELATGGGG 128 (481)
Q Consensus 118 ~~p~l~~GgGg 128 (481)
..|-+.+||+.
T Consensus 75 ~~~~~~~gg~~ 85 (122)
T PF02957_consen 75 RQPCPGGGGGE 85 (122)
T ss_pred cccCCCCCCCC
Confidence 34455444433
No 20
>PHA03249 DNA packaging tegument protein UL25; Provisional
Probab=35.03 E-value=1.2e+02 Score=34.87 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=11.2
Q ss_pred CCCCCCCCcchhh--hhHHHHhhcH
Q 011601 158 DGDEGDEGGLFRR--RKILEELFDR 180 (481)
Q Consensus 158 dgd~gd~~g~~r~--r~~~~e~fdR 180 (481)
+-+||+|+.|--+ ..+-+|||.|
T Consensus 171 ~~~~~~e~~~~~~~~~~f~~~~~~~ 195 (653)
T PHA03249 171 DLAEGHEFSFCDSDIEDFEQECFER 195 (653)
T ss_pred CcccccccccccccHHHHHHHHHHh
Confidence 3345566554433 3344556544
No 21
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=34.88 E-value=21 Score=43.94 Aligned_cols=7 Identities=29% Similarity=0.444 Sum_probs=3.8
Q ss_pred hhHhhhh
Q 011601 441 NAIVSGL 447 (481)
Q Consensus 441 ~~~~sgl 447 (481)
++|++|+
T Consensus 2027 ~lmragc 2033 (3015)
T KOG0943|consen 2027 NLMRAGC 2033 (3015)
T ss_pred HHHHHHH
Confidence 4555555
No 22
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=34.82 E-value=13 Score=33.34 Aligned_cols=18 Identities=11% Similarity=0.157 Sum_probs=8.8
Q ss_pred HHHHHHHhhccCchHHHH
Q 011601 185 AVLNEWMKTMMDLPAGFR 202 (481)
Q Consensus 185 aVL~E~~rt~~sLPaDl~ 202 (481)
+-|..-.|-+-|+|-|=+
T Consensus 51 ~~~~~v~rYltSf~id~~ 68 (101)
T PF09026_consen 51 AYFTMVKRYLTSFPIDDK 68 (101)
T ss_dssp HHHHHHHHHHCTS---HH
T ss_pred hhcchHhhhhhccchhHh
Confidence 445555566777776544
No 23
>PRK05325 hypothetical protein; Provisional
Probab=33.57 E-value=58 Score=35.29 Aligned_cols=9 Identities=33% Similarity=0.756 Sum_probs=5.6
Q ss_pred CceeecCCC
Q 011601 119 TPELATGGG 127 (481)
Q Consensus 119 ~p~l~~GgG 127 (481)
+|....|-+
T Consensus 48 Ep~F~~g~~ 56 (401)
T PRK05325 48 EPKFRYGRG 56 (401)
T ss_pred cceEEeCCC
Confidence 677766544
No 24
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=32.70 E-value=26 Score=35.79 Aligned_cols=19 Identities=16% Similarity=0.198 Sum_probs=8.3
Q ss_pred hHHHHHHHHcCCcCHHHHH
Q 011601 198 PAGFRQAYEMGLVSSAQMV 216 (481)
Q Consensus 198 PaDl~~A~e~Glvssa~L~ 216 (481)
|.+++...|...+-++.|+
T Consensus 91 ~~~~~~~~ee~~lkSe~L~ 109 (263)
T KOG3074|consen 91 PPELAAPSEEHELKSEELQ 109 (263)
T ss_pred CcccccchhhhhHHHHHHh
Confidence 3444444444433344443
No 25
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 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. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=32.03 E-value=28 Score=34.04 Aligned_cols=8 Identities=50% Similarity=0.999 Sum_probs=4.4
Q ss_pred CCCCCCCC
Q 011601 152 YFDDFDDG 159 (481)
Q Consensus 152 y~d~~ddg 159 (481)
|||++||+
T Consensus 213 YFDnGedD 220 (233)
T PF11705_consen 213 YFDNGEDD 220 (233)
T ss_pred cCCCCCcc
Confidence 36665543
No 26
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=31.55 E-value=59 Score=39.12 Aligned_cols=9 Identities=0% Similarity=-0.005 Sum_probs=4.3
Q ss_pred CCCCCCCCC
Q 011601 27 TLAAPRYST 35 (481)
Q Consensus 27 ~~~~~~~~~ 35 (481)
|.-|-+|-+
T Consensus 1116 PaiIsqLdp 1124 (1282)
T KOG0921|consen 1116 PAIISQLDP 1124 (1282)
T ss_pred hhHhhccCc
Confidence 334555554
No 27
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=31.22 E-value=59 Score=33.40 Aligned_cols=16 Identities=19% Similarity=0.167 Sum_probs=8.9
Q ss_pred CcccCcccceeeeccc
Q 011601 93 GGQYGAFGAVTLEKGK 108 (481)
Q Consensus 93 g~~~g~~ga~tleks~ 108 (481)
+.++..|+..++++..
T Consensus 220 ~~~~~~~~~~~~~~~~ 235 (271)
T COG1512 220 GRQPDRWLNGVLGRRR 235 (271)
T ss_pred ccccccccceeEEeee
Confidence 3355666666665554
No 28
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=30.49 E-value=48 Score=37.95 Aligned_cols=6 Identities=50% Similarity=1.320 Sum_probs=2.7
Q ss_pred hhhhhc
Q 011601 69 LERCYK 74 (481)
Q Consensus 69 ~er~~~ 74 (481)
|.-|+.
T Consensus 559 l~~c~~ 564 (784)
T PF04931_consen 559 LQICYE 564 (784)
T ss_pred HHHHHH
Confidence 444543
No 29
>PHA00458 single-stranded DNA-binding protein
Probab=29.31 E-value=57 Score=33.13 Aligned_cols=8 Identities=0% Similarity=0.094 Sum_probs=3.5
Q ss_pred hhhhhcCC
Q 011601 69 LERCYKAP 76 (481)
Q Consensus 69 ~er~~~~~ 76 (481)
|++|+...
T Consensus 59 I~~~hee~ 66 (233)
T PHA00458 59 IVKAHEEN 66 (233)
T ss_pred HHHHHHHH
Confidence 44444433
No 30
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=29.24 E-value=1.1e+02 Score=34.71 Aligned_cols=50 Identities=16% Similarity=0.333 Sum_probs=31.4
Q ss_pred HHHHHHHhhccCc-----h---HHHHHHHHcCCcCHHHHHHHHH--hccCcchhHHHHhhc
Q 011601 185 AVLNEWMKTMMDL-----P---AGFRQAYEMGLVSSAQMVKFLA--INARPTTTRFISRSL 235 (481)
Q Consensus 185 aVL~E~~rt~~sL-----P---aDl~~A~e~Glvssa~L~rFl~--L~~~P~~~~~l~R~l 235 (481)
.++.||.+.+..= | .+|.+=++.|.= +++++++|+ +.+.+.+..++..|+
T Consensus 36 ~~~~~~~~~l~~~D~Imep~i~~~i~~y~~~gG~-p~~vv~~Ls~~Y~g~aq~~~ll~~WL 95 (584)
T PF04858_consen 36 EVLEECLRRLSQPDAIMEPSIFDTIKRYFRAGGD-PEEVVELLSENYRGYAQMCNLLAEWL 95 (584)
T ss_pred HHHHHHHHhcCCCCeeeCchHHHHHHHHHHCCCC-HHHHHHHHHHhcccHHHHHHHHHHHH
Confidence 4666776664332 2 345555667774 667777775 456677777777776
No 31
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.15 E-value=37 Score=33.43 Aligned_cols=125 Identities=10% Similarity=0.028 Sum_probs=81.8
Q ss_pred chhhhhHHHHhhcHHHHHHHHHHHHhhccCchHHHHHHHHcCCcCHH--HHHHHHHhccC-cchhHHHHhhcCcchhhhh
Q 011601 167 LFRRRKILEELFDRKFVDAVLNEWMKTMMDLPAGFRQAYEMGLVSSA--QMVKFLAINAR-PTTTRFISRSLPQGISRAF 243 (481)
Q Consensus 167 ~~r~r~~~~e~fdR~~i~aVL~E~~rt~~sLPaDl~~A~e~Glvssa--~L~rFl~L~~~-P~~~~~l~R~lp~~~srgf 243 (481)
++++|...||.|..=+++.|.+.-..-++.|=+|-.=.--.|.|-+. -=+.+++|+.. .....|+--+.+. +.-
T Consensus 50 VL~KRe~freaF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf~~flWsf~~~---~~~ 126 (188)
T COG2818 50 VLKKREAFREAFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSFSEFLWSFVGG---KPS 126 (188)
T ss_pred HHHhHHHHHHHHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhcCC---Ccc
Confidence 57888899999988777777765544444443332111113333121 23578888886 6666666555543 456
Q ss_pred hhhhccCchhHHHHHHHHHHhhhhhhhhhhhhcchhhhhHHHHHHHHHHHHHHhhHH
Q 011601 244 IGRMLADPSFLYKLILEQAATIGCTVLWELENRKERIKQEWDLALINVLTVTACNAF 300 (481)
Q Consensus 244 R~RlLADP~FLfKL~iE~~I~i~~~~~aE~~~Rge~F~~ElDfV~sdvv~g~v~nfa 300 (481)
+.....=+.|+.+ ..++.++..++++||-.|.-.-=.+.-...+|.|.|-+
T Consensus 127 ~~~~~~~~~~pa~------t~~S~~mskaLKkrGf~fvGpTt~yafmqA~G~vndH~ 177 (188)
T COG2818 127 RNQVNDGSEVPAS------TELSDAMSKALKKRGFKFVGPTTVYAFMQATGLVNDHA 177 (188)
T ss_pred cccccchhhcccc------chhHHHHHHHHHHccCeecCcHHHHHHHHHHcchHHHH
Confidence 6666666777777 33466788899999999988887777777888887654
No 32
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.88 E-value=35 Score=39.64 Aligned_cols=39 Identities=15% Similarity=0.347 Sum_probs=17.6
Q ss_pred CCccCc-ccCcccceeeecccccceecc--cccCceeecCCC
Q 011601 89 PLMKGG-QYGAFGAVTLEKGKLDTTQQQ--SETTPELATGGG 127 (481)
Q Consensus 89 ~~~~g~-~~g~~ga~tleks~l~~~q~~--~~~~p~l~~GgG 127 (481)
||.-++ .|.----+.|+.-.=|-++.- .+.+|..+.+--
T Consensus 302 PvLl~~M~Ysd~D~~LL~~~eeD~~vpDreeDIkPRfhksk~ 343 (885)
T KOG2023|consen 302 PVLLSGMVYSDDDIILLKNNEEDESVPDREEDIKPRFHKSKE 343 (885)
T ss_pred HHHHccCccccccHHHhcCccccccCCchhhhccchhhhchh
Confidence 555554 444333333331222333333 355787776543
No 33
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=24.13 E-value=41 Score=31.77 Aligned_cols=6 Identities=17% Similarity=0.440 Sum_probs=2.7
Q ss_pred ccCcch
Q 011601 222 NARPTT 227 (481)
Q Consensus 222 ~~~P~~ 227 (481)
-.+|.+
T Consensus 104 ~tHPai 109 (149)
T PF08595_consen 104 PTHPAI 109 (149)
T ss_pred cCCccc
Confidence 345544
No 34
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=23.39 E-value=1.2e+02 Score=35.64 Aligned_cols=35 Identities=14% Similarity=0.253 Sum_probs=23.3
Q ss_pred HhhcHHHHHHHHHHHHhhccC----chHHHHHHHHcCCc
Q 011601 176 ELFDRKFVDAVLNEWMKTMMD----LPAGFRQAYEMGLV 210 (481)
Q Consensus 176 e~fdR~~i~aVL~E~~rt~~s----LPaDl~~A~e~Glv 210 (481)
.+|.=++|..++.+|...+++ -|..|...+..-+.
T Consensus 484 ~i~~~e~i~~~l~~~~~d~~e~~~~~~~~ll~~lA~~l~ 522 (803)
T PLN03083 484 NIPPEEWVMKKILEWVPDLEEDGTEDPGSILKHLADHLR 522 (803)
T ss_pred ccccHHHHHHHHHHHcccchhcccccHHHHHHHHHHHHH
Confidence 334667888899988887544 66677766554444
No 35
>COG3685 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.32 E-value=54 Score=31.84 Aligned_cols=53 Identities=25% Similarity=0.421 Sum_probs=45.6
Q ss_pred HHHHhhcH----------HHHHHHHHHHHhhccCchHHHHHHHHcCCcCHHHHHHHHHhccCcch
Q 011601 173 ILEELFDR----------KFVDAVLNEWMKTMMDLPAGFRQAYEMGLVSSAQMVKFLAINARPTT 227 (481)
Q Consensus 173 ~~~e~fdR----------~~i~aVL~E~~rt~~sLPaDl~~A~e~Glvssa~L~rFl~L~~~P~~ 227 (481)
.++|||+| ..++-++.|...-++..|.+ ++++.|++.+++.+.-+++.-+.++
T Consensus 57 rLe~Vfe~~g~~~~~~~cda~~giiaegq~i~~~~~~~--evlda~L~~aaq~vEhyEIA~YgtL 119 (167)
T COG3685 57 RLEQVFERLGKKARRVTCDAMEGLIAEGQEIMEEFKSN--EVLDAGLIGAAQKVEHYEIACYGTL 119 (167)
T ss_pred HHHHHHHHhCcccccchHHHHHHHHHHHHHHHHhcccc--HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999 66778888888889999999 9999999999999999998876543
No 36
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=22.71 E-value=48 Score=37.98 Aligned_cols=10 Identities=10% Similarity=0.295 Sum_probs=4.3
Q ss_pred hhhhhhhhhc
Q 011601 65 SVVLLERCYK 74 (481)
Q Consensus 65 ~~~~~er~~~ 74 (481)
.....+|.+.
T Consensus 559 l~~c~~~~~~ 568 (784)
T PF04931_consen 559 LQICYEKAFG 568 (784)
T ss_pred HHHHHHHHhc
Confidence 3444444444
No 37
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=21.56 E-value=69 Score=34.73 Aligned_cols=9 Identities=22% Similarity=0.272 Sum_probs=4.6
Q ss_pred eeeeccccc
Q 011601 102 VTLEKGKLD 110 (481)
Q Consensus 102 ~tleks~l~ 110 (481)
-|.+++|--
T Consensus 340 g~f~~~~~~ 348 (465)
T KOG3973|consen 340 GTFDRPKTH 348 (465)
T ss_pred CCCcCcccc
Confidence 455555543
No 38
>PRK05325 hypothetical protein; Provisional
Probab=21.44 E-value=71 Score=34.64 Aligned_cols=8 Identities=25% Similarity=0.459 Sum_probs=4.1
Q ss_pred hhhHHHHH
Q 011601 280 IKQEWDLA 287 (481)
Q Consensus 280 F~~ElDfV 287 (481)
|++++|+-
T Consensus 202 f~d~~DlR 209 (401)
T PRK05325 202 FIDPFDLR 209 (401)
T ss_pred CCCccccc
Confidence 55555543
No 39
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.95 E-value=70 Score=31.87 Aligned_cols=7 Identities=43% Similarity=0.572 Sum_probs=3.0
Q ss_pred CCCCCCC
Q 011601 134 KINHGGG 140 (481)
Q Consensus 134 ~~~~GGG 140 (481)
-+++||-
T Consensus 182 ~i~~~~~ 188 (227)
T KOG3241|consen 182 IIGHGSV 188 (227)
T ss_pred hcccCCC
Confidence 3444443
No 40
>PF06946 Phage_holin_5: Phage holin; InterPro: IPR009708 This entry represents the Bacteriophage A118, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=20.93 E-value=2.4e+02 Score=25.15 Aligned_cols=27 Identities=19% Similarity=0.122 Sum_probs=20.6
Q ss_pred CcchhhhHHHHHhhchhhhhhHhHHHhhHHHHHHHHhh
Q 011601 339 EFDLQKRIHSLFYKAAELCMVGLSAGAVQGSLSNYLAG 376 (481)
Q Consensus 339 ~fsl~qRiga~v~KGa~l~~VG~~aGlvG~glSN~L~~ 376 (481)
++++.+++.+ |.+||+.+++|-...-+
T Consensus 57 ~~~l~~~~~a-----------G~laGlAaTGL~e~~t~ 83 (93)
T PF06946_consen 57 DGNLALMAWA-----------GGLAGLAATGLFEQFTN 83 (93)
T ss_pred CccHHHHHHH-----------HHHhhhhhhhHHHHHHh
Confidence 4566666544 88999999999888877
No 41
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=20.74 E-value=71 Score=29.42 Aligned_cols=21 Identities=43% Similarity=0.634 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCC
Q 011601 141 DGGDDDGDDDDYFDDFDDGDE 161 (481)
Q Consensus 141 gGgdddGddddy~d~~ddgd~ 161 (481)
++.++++++||.+|+++|+|+
T Consensus 116 ddE~~~d~~dd~edd~~deee 136 (136)
T PF04871_consen 116 DDEDSEDDEDDDEDDDEDEEE 136 (136)
T ss_pred CCccccccCCCCCCccCCCCC
No 42
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.50 E-value=99 Score=36.19 Aligned_cols=34 Identities=9% Similarity=0.304 Sum_probs=15.3
Q ss_pred ccCcchhHHHHhhcCcchhhhhhhhhccCch--hHHHHHHH
Q 011601 222 NARPTTTRFISRSLPQGISRAFIGRMLADPS--FLYKLILE 260 (481)
Q Consensus 222 ~~~P~~~~~l~R~lp~~~srgfR~RlLADP~--FLfKL~iE 260 (481)
++.|.+....||.|.. |-.-+.-||. |+-+|..+
T Consensus 445 DKkplVRsITCWTLsR-----ys~wv~~~~~~~~f~pvL~~ 480 (885)
T KOG2023|consen 445 DKKPLVRSITCWTLSR-----YSKWVVQDSRDEYFKPVLEG 480 (885)
T ss_pred cCccceeeeeeeeHhh-----hhhhHhcCChHhhhHHHHHH
Confidence 3446554444554432 2223444543 55555443
Done!