Query 018220
Match_columns 359
No_of_seqs 145 out of 201
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:09:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2953 mRNA-binding protein E 100.0 6.5E-47 1.4E-51 376.7 15.7 326 11-357 86-424 (432)
2 cd02642 R3H_encore_like R3H do 99.8 3.9E-20 8.5E-25 141.9 7.2 63 34-101 1-63 (63)
3 PF12752 SUZ: SUZ domain; Int 99.5 6.4E-14 1.4E-18 106.6 5.2 50 127-176 2-59 (59)
4 PF01424 R3H: R3H domain; Int 99.3 8.7E-12 1.9E-16 94.3 6.6 63 34-101 1-63 (63)
5 cd02325 R3H R3H domain. The na 99.2 5.4E-11 1.2E-15 85.9 6.1 59 38-100 1-59 (59)
6 smart00393 R3H Putative single 99.1 7.4E-11 1.6E-15 93.6 5.1 74 23-101 5-79 (79)
7 cd02641 R3H_Smubp-2_like R3H d 98.9 2.2E-09 4.8E-14 82.2 6.5 58 39-100 2-60 (60)
8 cd06006 R3H_unknown_2 R3H doma 98.9 2.5E-09 5.5E-14 82.0 6.6 57 40-100 3-59 (59)
9 cd02646 R3H_G-patch R3H domain 98.9 2.4E-09 5.3E-14 81.0 5.9 57 39-100 2-58 (58)
10 cd02640 R3H_NRF R3H domain of 98.5 2E-07 4.4E-12 71.7 6.3 57 40-100 3-60 (60)
11 cd02636 R3H_sperm-antigen R3H 98.5 2.2E-07 4.9E-12 71.9 6.0 58 40-100 3-60 (61)
12 cd02643 R3H_NF-X1 R3H domain o 98.5 2E-07 4.3E-12 74.1 5.8 63 33-99 6-73 (74)
13 cd06007 R3H_DEXH_helicase R3H 98.5 2.4E-07 5.3E-12 71.1 6.0 57 39-100 2-59 (59)
14 cd02644 R3H_jag R3H domain fou 97.3 0.0012 2.5E-08 51.8 6.9 61 35-100 5-66 (67)
15 cd02639 R3H_RRM R3H domain of 96.9 0.00042 9.2E-09 53.5 1.6 59 39-100 2-60 (60)
16 cd02645 R3H_AAA R3H domain of 96.5 0.0086 1.9E-07 46.2 5.9 53 42-99 7-59 (60)
17 cd02638 R3H_unknown_1 R3H doma 95.1 0.061 1.3E-06 42.2 5.7 56 40-99 3-60 (62)
18 cd02637 R3H_PARN R3H domain of 88.7 0.61 1.3E-05 36.6 3.8 36 41-78 4-39 (65)
19 COG1847 Jag Predicted RNA-bind 75.7 9.9 0.00021 36.4 6.9 60 36-100 147-207 (208)
20 KOG1952 Transcription factor N 68.6 4 8.7E-05 45.9 3.0 80 33-116 817-903 (950)
21 PF12206 DUF3599: Domain of un 41.0 5 0.00011 35.1 -1.5 19 65-84 2-20 (117)
22 KOG2953 mRNA-binding protein E 32.9 6.8 0.00015 41.0 -2.4 54 30-85 23-76 (432)
23 PF07777 MFMR: G-box binding p 31.5 68 0.0015 30.4 4.2 36 291-335 60-95 (189)
24 cd01611 GABARAP Ubiquitin doma 30.1 46 0.001 28.6 2.6 18 153-170 3-20 (112)
25 PF06262 DUF1025: Possibl zinc 24.9 38 0.00083 28.5 1.2 17 67-83 74-90 (97)
26 PTZ00380 microtubule-associate 22.5 72 0.0016 28.2 2.5 19 152-170 5-23 (121)
27 KOG3248 Transcription factor T 21.6 1.4E+02 0.0031 31.0 4.6 65 270-334 54-127 (421)
28 PF05572 Peptidase_M43: Pregna 20.8 56 0.0012 29.2 1.5 22 64-85 67-88 (154)
29 PF10788 DUF2603: Protein of u 20.7 81 0.0018 28.5 2.5 27 23-49 62-88 (137)
30 PF09851 SHOCT: Short C-termin 20.4 73 0.0016 21.3 1.6 12 161-172 19-30 (31)
No 1
>KOG2953 consensus mRNA-binding protein Encore [RNA processing and modification]
Probab=100.00 E-value=6.5e-47 Score=376.67 Aligned_cols=326 Identities=41% Similarity=0.553 Sum_probs=289.1
Q ss_pred hhhhccCCCCchHHHHHHhcCchhHHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecc---
Q 018220 11 AAIVNERESMVDPFLVEALQNPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQEN--- 87 (359)
Q Consensus 11 ~~~~~~~~~~vd~~L~eAL~npkDRl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~--- 87 (359)
.+.+-+.+..+|.|++|||+|||+|++|+++|.+|.+|+++...++++|+++++||+|++.||||++|+|.+.+.+.
T Consensus 86 ~~~~~p~e~~~dy~~ve~~qnpR~~~~lsR~El~~~~~~Q~~~~qqt~~q~~~ts~~~~~~~rvaq~y~l~T~~~p~~~~ 165 (432)
T KOG2953|consen 86 QANKIPNEQAVDYFLVEALQNPRHRLTLSRKELDIQCQFQGPVQQQTEFQNYPTSYLRLAAHRVAQHYGLATTGEPSYIS 165 (432)
T ss_pred ccccCchhhcccHHHHhhhhcchhhhhhhcccchhhhhhcCcccccccCCCccccchhhhhccccccccccccccccccc
Confidence 35566788899999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred cccCCcceEEEEecCCCCCCccccccccccCCCccchhhhcceeeecCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHH
Q 018220 88 GIEGLGNRILVRKTAESKYPAVRLSEIPAKQSEESDKLEKIKIAIRRRPNAGCVNG-ANETGTKRSPVRSVEERKEEYDR 166 (359)
Q Consensus 88 ~~dgs~~~Ivv~KT~~tRiP~vrLSdl~~~~~~~s~~~~~~K~~ImkR~~k~s~~~-~s~~~~k~~~~kSlEEREeeY~r 166 (359)
+.++...+|+++|+.+++.|.++|++++.+.+.+++..+..|+.|.-|+.++++.. .+..+......+|+||||++|.+
T Consensus 166 ~~~p~eqR~l~~k~~~s~~P~~~~~~~P~ssp~~~~~~~~~~~~~sp~p~~g~G~~~~~p~~~~~~~~~S~~~~kq~yd~ 245 (432)
T KOG2953|consen 166 GIDPYEQRILVTKTGESRFPGVSLSEIPVSSPSSNGWSEQRKGDISPRPTSGGGVSLSSPSNPQVTLLRSVEERKQEYDK 245 (432)
T ss_pred ccCchhccccccccccccCCchhhccccccCccccccccccccccCCCCCCCCcccccCCcCCCccccccchhhhhhhhh
Confidence 57888899999999999999999999999766667889999999999998766544 22333344578999999999999
Q ss_pred HHHhhcCCCCCCCCccccccccCC---CCC--CCCCcchhhhhcc-ccchhhhcccccCCCCCcceEEeccccccCCCCC
Q 018220 167 ARARIFSGPSSPNSEDTLTQVSTD---MKN--IGFNRDEREIVRN-SITDAEKIISIRDGAGLSRVAIFRDREKDRTDPD 240 (359)
Q Consensus 167 AReRIF~~~~s~d~~d~~~~~~~~---~~~--~~~~r~e~~~~~~-~~~~~e~~~~~r~~~~~~rvAi~Rdrekdr~DPD 240 (359)
||+|||+.....+++|++...+++ ..+ ++++|.+.+...| .++.-+++.+.|+.|+.+||||+|||||||+|||
T Consensus 246 ~r~r~g~~~~~~~s~Dss~q~~p~~~~~~~g~~~~~~~~~p~~~N~~Pv~~~~~g~~~~~gps~~v~~nr~rr~~ry~p~ 325 (432)
T KOG2953|consen 246 ARGRIGSKPVTNDSKDSSSQQPPQNYQSGNGDPRLSRLEQPVSYNSPPLMHGPNGITRESGPSPRVAGNRDRRPDRYDPD 325 (432)
T ss_pred hhccccCccccccCcccccccCCccccCCCCccccccCCcccccCCCcccccCCCcccCCCCCcccccccccchhhcCcc
Confidence 999999999999999998887766 555 5799999999888 7888899999999999999999999999999999
Q ss_pred chhh--hhhhcccCCCCCCCCCCCCCccccCCCccccCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 018220 241 YDRS--YERYVRSLPTNQGFSLPPFNMQKVQLPFMQYDTGFPQFSQIPRTQASLSFRPPSSPVMSPYCAVGPNQTSVEAA 318 (359)
Q Consensus 241 ydR~--y~ry~~~~~~~~~~~~~~~~~q~~~~p~~~y~~~f~q~~~~~~~~~~~~~~~~~~~~m~p~~~~~~~~~~~~~~ 318 (359)
|||+ .-|||+.+|+|+.|+..++ .|.+|+ ++..|+...+ .+ . ++++.|+||.. -+|+
T Consensus 326 ~dr~~~~~~yv~~~Pp~q~~~~~~~---ql~~~~--~~i~~~~~pq---~~-~-----~~n~~~s~~s~-------~a~~ 384 (432)
T KOG2953|consen 326 YDRSCGFVRYVTMLPPGQTFMQYQK---QLHTPY--HKIPFPNDPQ---GN-G-----GDNPARSEASH-------LAAK 384 (432)
T ss_pred cccCCCCcceeccCCCccccccccc---ccCCcc--cccccCCCCc---CC-C-----CCCcccccccc-------cccc
Confidence 9999 7899999999999999997 466688 8899988443 33 1 67899999933 4899
Q ss_pred cccCC-CccccccCchhhhhcccccCCccCCCcccccccc
Q 018220 319 YMQWP-SAAMMYAHSYEQFRQAAFQVPFCQQPLSFDYSQN 357 (359)
Q Consensus 319 y~~~p-~~~m~y~h~~~~~~~~~~q~~~~~~p~sf~~~~~ 357 (359)
|+.|| .|.|+|+|.+..++..++++.|-..|+|++|..+
T Consensus 385 yt~~p~~p~~~~a~n~~~~~~~~~ras~~~~~~s~~yd~~ 424 (432)
T KOG2953|consen 385 YTVLPAFPSMSYASNANEKKNGNSRASFKGRPSSMNYDSV 424 (432)
T ss_pred eeeccccccchhccchhhhhcCceeeeccCCccchhhHHH
Confidence 99999 9999999999999999999999999999998654
No 2
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.81 E-value=3.9e-20 Score=141.88 Aligned_cols=63 Identities=41% Similarity=0.711 Sum_probs=58.5
Q ss_pred hHHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEec
Q 018220 34 HRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (359)
Q Consensus 34 DRl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~KT 101 (359)
||++||+||++|++||+++....++|+|| |||+|||+|+||+||||.|++++.+ +.+|+|.||
T Consensus 1 dr~~~l~~E~~i~~Fi~~~~~~~~~f~pm-~sy~RllvH~la~~~gL~s~s~~~~----~r~vvv~kt 63 (63)
T cd02642 1 DRLFVLKLEKDLLAFIKDSTRQSLELPPM-NSYYRLLAHRVAQYYGLDHNVDNSG----GKCVIVNKT 63 (63)
T ss_pred CchHHHHHHHHHHHHHhCCCCCeeEcCCC-CcHHHHHHHHHHHHhCCeeEeecCC----ceEEEEEeC
Confidence 79999999999999999997788999999 9999999999999999999997643 578999987
No 3
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=99.46 E-value=6.4e-14 Score=106.62 Aligned_cols=50 Identities=42% Similarity=0.677 Sum_probs=37.6
Q ss_pred hcceeeecCCCCCCCCC--------CCCCCCCCCCCCCHHHHHHHHHHHHHhhcCCCC
Q 018220 127 KIKIAIRRRPNAGCVNG--------ANETGTKRSPVRSVEERKEEYDRARARIFSGPS 176 (359)
Q Consensus 127 ~~K~~ImkR~~k~s~~~--------~s~~~~k~~~~kSlEEREeeY~rAReRIF~~~~ 176 (359)
.++++||||+++++..+ .+..+.+....||+||||++|++||+|||++++
T Consensus 2 ~p~~~IlkRp~~~~~~~~~~~~~~~~~~~~~~~~~~kSlEERE~eY~~AR~RIFg~~~ 59 (59)
T PF12752_consen 2 KPKRKILKRPSKGSSSSDSGSSGSSPNSSSRKKRPSKSLEEREAEYAEARARIFGSSE 59 (59)
T ss_pred CCCCeEecCCCCCCCcccccccccCCCcccccccccCCHHHHHHHHHHHHHHHhCCCC
Confidence 35789999987654322 112233568899999999999999999999863
No 4
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=99.28 E-value=8.7e-12 Score=94.30 Aligned_cols=63 Identities=25% Similarity=0.471 Sum_probs=52.7
Q ss_pred hHHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEec
Q 018220 34 HRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (359)
Q Consensus 34 DRl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~KT 101 (359)
.|..|+++++++++|+.++.. .++|+|| |+|+|++||.+|++|||.|.+.+.+ ...+|+|+||
T Consensus 1 r~~~l~~~~~~~~~~~~~~~~-~~~f~pm-~~~~R~~iH~~a~~~gL~s~S~g~~---~~R~vvv~k~ 63 (63)
T PF01424_consen 1 RREELEKIEEKLIEFFLSSGE-SLEFPPM-NSFERKLIHELAEYYGLKSKSEGEG---PNRRVVVSKT 63 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHCSS-EEEEEC---SHHHHHHHHHHHHCTEEEEEESSS---SSSEEEEEES
T ss_pred ChHHHHHHHHHHHHHHHcCCC-EEEECCC-CHHHHHHHHHHHHHCCCEEEEecCC---CCeEEEEEeC
Confidence 367899999999999976665 7999999 9999999999999999999997643 4467999886
No 5
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.17 E-value=5.4e-11 Score=85.94 Aligned_cols=59 Identities=22% Similarity=0.412 Sum_probs=50.6
Q ss_pred HHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 38 ILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 38 lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
++++|+.|++|+.+.....++|+|| |+|+|+++|++|++|||.+...+.+ ...+|+|.+
T Consensus 1 ~~~~~~~l~~f~~~~~~~~~~~~p~-~~~~R~~vH~la~~~~L~s~s~g~~---~~r~v~i~~ 59 (59)
T cd02325 1 REEREEELEAFAKDAAGKSLELPPM-NSYERKLIHDLAEYYGLKSESEGEG---PNRRVVITK 59 (59)
T ss_pred ChHHHHHHHHHHHhhcCCeEEcCCC-CHHHHHHHHHHHHHCCCEEEEecCC---CCcEEEEeC
Confidence 4689999999999996678999999 9999999999999999999997643 445677654
No 6
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=99.12 E-value=7.4e-11 Score=93.57 Aligned_cols=74 Identities=30% Similarity=0.597 Sum_probs=62.7
Q ss_pred HHHHHHhc-CchhHHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEec
Q 018220 23 PFLVEALQ-NPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (359)
Q Consensus 23 ~~L~eAL~-npkDRl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~KT 101 (359)
+++++.+. +++.+..|++++.+|.+|+..... .++|+|| |+|+|.++|++|+.|||.|...+.| ...+|+|.|+
T Consensus 5 ~~~~d~~~~~~~~~~~l~~~~~~~~~~v~~~~~-~~~~~pm-~~~~R~~iH~~a~~~~l~s~S~g~g---~~R~vvv~~~ 79 (79)
T smart00393 5 PVTLDALSYRPRRREELIELELEIARFVKSTKE-SVELPPM-NSYERKIVHELAEKYGLESESFGEG---PKRRVVISKK 79 (79)
T ss_pred eEEEECCccCHHHHHHHHHHHHHHHHHHhccCC-eEEcCCC-CHHHHHHHHHHHHHcCCEEEEEcCC---CCcEEEEEeC
Confidence 34455664 789999999999999999987765 6999999 9999999999999999999997754 3357888764
No 7
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=98.93 E-value=2.2e-09 Score=82.16 Aligned_cols=58 Identities=24% Similarity=0.411 Sum_probs=49.7
Q ss_pred HHHHHHHHHHhcCCCccceecCC-CCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 39 LRMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
.++|+.|.+||+++....++||| | |+++|.+||.||..|||.|...+.| ....|+|.|
T Consensus 2 ~~~~~~i~~F~~~~~~~~l~F~p~l-s~~eR~~vH~lA~~~gL~s~S~G~g---~~R~v~v~k 60 (60)
T cd02641 2 KHLKAMVKAFMKDPKATELEFPPTL-SSHDRLLVHELAEELGLRHESTGEG---SDRVITVSK 60 (60)
T ss_pred hhHHHHHHHHHcCCCcCcEECCCCC-CHHHHHHHHHHHHHcCCceEeeCCC---CceEEEeeC
Confidence 46899999999999877899999 9 9999999999999999999987643 334566654
No 8
>cd06006 R3H_unknown_2 R3H domain of a group of fungal proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.93 E-value=2.5e-09 Score=82.03 Aligned_cols=57 Identities=21% Similarity=0.463 Sum_probs=50.5
Q ss_pred HHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 40 RMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
++|+.|.+||+|.....+.|+|| |+++|-+||-||++|||.++..|.+++ .+|+|.|
T Consensus 3 ~~E~~l~~fv~d~~~~~~~f~pM-~~~~R~~vHdla~~~gl~SeS~d~Ep~---R~V~v~k 59 (59)
T cd06006 3 QIESTLRKFINDKSKRSLRFPPM-RSPQRAFIHELAKDYGLYSESQDPEPK---RSVFVKK 59 (59)
T ss_pred hHHHHHHHHHhCCCCCceeCCCC-CHHHHHHHHHHHHHcCCeeEecCCCCC---cEEEEeC
Confidence 79999999999987778999999 999999999999999999999886653 4677765
No 9
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.91 E-value=2.4e-09 Score=80.99 Aligned_cols=57 Identities=19% Similarity=0.311 Sum_probs=49.3
Q ss_pred HHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 39 LRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
-++|++|.+||.++. ..+.|||| +++.|.+||+||+.|||.+...+.| ....|+|+|
T Consensus 2 ~~i~~~i~~F~~~~~-~~~~fppm-~~~~R~~vH~lA~~~~L~S~S~G~g---~~R~v~v~k 58 (58)
T cd02646 2 EDIKDEIEAFLLDSR-DSLSFPPM-DKHGRKTIHKLANCYNLKSKSRGKG---KKRFVTVTK 58 (58)
T ss_pred hHHHHHHHHHHhCCC-ceEecCCC-CHHHHHHHHHHHHHcCCcccccccC---CceEEEEEC
Confidence 478999999999885 57999999 9999999999999999999987643 445788875
No 10
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.54 E-value=2e-07 Score=71.67 Aligned_cols=57 Identities=23% Similarity=0.374 Sum_probs=47.4
Q ss_pred HHHHHHHHHhcCCCccceecCC-CCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 40 RMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
.+++.|.+|+.+.....+.||| | ++++|.+||.||.-+||.|..... |....|+|+|
T Consensus 3 ~~~~~i~~F~~s~~~~~l~f~p~l-t~~eR~~vH~~a~~~gL~s~S~G~---g~~R~v~v~k 60 (60)
T cd02640 3 DYRQIIQNYAHSDDIRDMVFSPEF-SKEERALIHQIAQKYGLKSRSYGS---GNDRYLVISK 60 (60)
T ss_pred hHHHHHHHHHcCCccceEEcCCCC-CHHHHHHHHHHHHHcCCceeeEeC---CCCeEEEEeC
Confidence 5689999999998777899999 9 999999999999999999998653 2334566654
No 11
>cd02636 R3H_sperm-antigen R3H domain of a group of metazoan proteins that is related to the sperm-associated antigen 7. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.51 E-value=2.2e-07 Score=71.90 Aligned_cols=58 Identities=19% Similarity=0.359 Sum_probs=49.0
Q ss_pred HHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 40 RMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
++|+.+.+||+|...+..+|+|| |+|+|-+||-+|+.-||.+..... ++...+|+|.|
T Consensus 3 ~~e~~~~~f~~d~~~~~~~l~pM-~~~eRkivHDv~~~~Gl~S~S~Ge--ee~~R~VVv~~ 60 (61)
T cd02636 3 SMEKEVSKFIKDSVRTREKFQPM-DKVERSIVHDVAEVAGLTSFSFGE--DEVDRYVMIFK 60 (61)
T ss_pred hHHHHHHHHhhcccccccccCCC-CHHHHHHHHHHHHhcCceeEecCC--CCCceEEEEec
Confidence 68999999999988788899999 999999999999999999988543 22335677765
No 12
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.51 E-value=2e-07 Score=74.09 Aligned_cols=63 Identities=11% Similarity=0.305 Sum_probs=52.2
Q ss_pred hhHHHHHHHHHHHHHHhcCCC-----ccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEE
Q 018220 33 RHRLTILRMELDIQRFLQNPD-----QQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVR 99 (359)
Q Consensus 33 kDRl~lLrlE~di~~FI~d~~-----~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~ 99 (359)
++-.|+.++|+.|..|+.+.. ...+.|+|| |+|+|-+||-+|++|||.+...+.++. .+|||+
T Consensus 6 ~~~~~~~~vE~~l~~la~~~~~~~~~~~~~~l~PM-~~~eR~iIH~la~~~~l~S~S~G~ep~---R~VvI~ 73 (74)
T cd02643 6 KDPKFVKDVEKDLIELVESVNKGKQTSRSHSFPPM-NREKRRIVHELAEHFGIESVSYDQEPK---RNVVAT 73 (74)
T ss_pred HCHHHHHHHHHHHHHHHHHHHhccccCCeeECCCC-CHHHHHHHHHHHhhCCCEEEecCCCCC---ceEEEe
Confidence 445699999999999999643 246899999 999999999999999999999875543 467774
No 13
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.51 E-value=2.4e-07 Score=71.05 Aligned_cols=57 Identities=23% Similarity=0.429 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhcCCCccceecCC-CCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 39 LRMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
+.+++.|.+|+++. ...++||| | |+++|.+||+||..+||.|..... |....|+|.|
T Consensus 2 i~i~~~i~~F~~~~-~~~l~Fpp~l-s~~eR~~vH~~a~~~gL~s~S~G~---g~~R~v~v~K 59 (59)
T cd06007 2 IAINKALEDFRASD-NEEYEFPSSL-TNHERAVIHRLCRKLGLKSKSKGK---GSNRRLSVYK 59 (59)
T ss_pred ccHHHHHHHHHcCc-ccEEEcCCCC-CHHHHHHHHHHHHHcCCCceeecC---CCCeEEEEeC
Confidence 45789999999988 67899999 8 999999999999999999997543 3334565654
No 14
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=97.25 E-value=0.0012 Score=51.81 Aligned_cols=61 Identities=13% Similarity=0.211 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhc-cceeeecccccCCcceEEEEe
Q 018220 35 RLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYG-LVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 35 Rl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yyg-L~h~v~d~~~dgs~~~Ivv~K 100 (359)
...|.+|-+.+.+.+..... .+.|+|| |+|+|-+||.++.-|+ |.+...+.| ...+|+|.+
T Consensus 5 ~~~L~~~A~~~a~~v~~tg~-~~~l~PM-~~~eRrivH~~~~~~~~l~T~S~G~~---~~R~vvI~~ 66 (67)
T cd02644 5 EETLIRLAERAAEKVRRTGK-PVKLEPM-NAYERRIIHDALANDEDVETESEGEG---PYRRVVISP 66 (67)
T ss_pred HHHHHHHHHHHHHHHHHHCC-eeEeCCC-CHHHHHHHHHHHHhCCCceEEeecCC---CCeEEEEEe
Confidence 34677788888888887775 5999999 9999999999999877 999987644 346788764
No 15
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=96.91 E-value=0.00042 Score=53.50 Aligned_cols=59 Identities=15% Similarity=0.228 Sum_probs=45.4
Q ss_pred HHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEe
Q 018220 39 LRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
|.+-.+|+-|..+.....+.|||--+.-+|.++|.||..+||.|.....| ....|+|+|
T Consensus 2 l~~YsqlllFkdd~~~~eL~Fp~~ls~~eRriih~la~~lGL~~~s~G~g---~~R~v~v~k 60 (60)
T cd02639 2 LEIYSQLLLFKDDRMRDELAFPSSLSPAERRIVHLLASRLGLNHVSDGTG---ERRQVQITK 60 (60)
T ss_pred ccceeeEEEEecCCCceEEEcCCCCCHHHHHHHHHHHHHcCCceEEeCCC---ceEEEeecC
Confidence 34445667788888888899998449999999999999999999986533 334566554
No 16
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=96.46 E-value=0.0086 Score=46.24 Aligned_cols=53 Identities=19% Similarity=0.312 Sum_probs=38.6
Q ss_pred HHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEE
Q 018220 42 ELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVR 99 (359)
Q Consensus 42 E~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~ 99 (359)
+..+.+-+ .+.....+|.|| |+|-|-++|.+.+.|||.+.....++ ..+|+|.
T Consensus 7 ~~aa~~V~-~~~~~~veL~Pm-~~~eRri~H~~v~~~~l~s~S~G~ep---~RrvvI~ 59 (60)
T cd02645 7 RLAIEQVV-IPKGEPVELLPR-SAYIRRLQHDLVERYQLRSESFGSEP---NRRLRIL 59 (60)
T ss_pred HHHHHHHH-hcCCceEEcCCC-CHHHHHHHHHHHHHCCCeEEEecCCC---CcEEEEe
Confidence 33444444 344235899999 99999999999999999999976443 3467764
No 17
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=95.14 E-value=0.061 Score=42.16 Aligned_cols=56 Identities=21% Similarity=0.318 Sum_probs=40.3
Q ss_pred HHHHHHHHHhcCCCc-cceecCCCCChHHHHHHHHhhh-hhccceeeecccccCCcceEEEE
Q 018220 40 RMELDIQRFLQNPDQ-QHFEFQHFPTSYLRLAAHRVSQ-HYGLVTMVQENGIEGLGNRILVR 99 (359)
Q Consensus 40 rlE~di~~FI~d~~~-~~lef~pmpnSY~RLLvHRvA~-yygL~h~v~d~~~dgs~~~Ivv~ 99 (359)
...++|+-|++.... ..+.|+|| |+|.|-++|...+ +-++.+..+.. +...+|+|.
T Consensus 3 ~~~~~~~~f~~~~~~~r~v~LePM-~~~ERkIIH~~Lq~~~~v~T~S~G~---ep~RrVVI~ 60 (62)
T cd02638 3 RVSEELEIFLLSFQRYRVLLFPPL-NSRRRYLIHQTVENRFLLSTFSVGE---GWARRTVVC 60 (62)
T ss_pred hhHHHHHHHHHhcccCCeEecCCC-ChHHHHHHHHHHhcCCCceEEEccC---CCCcEEEEe
Confidence 356778888887633 46789999 9999999998655 66777776543 344567663
No 18
>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=88.69 E-value=0.61 Score=36.57 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhh
Q 018220 41 MELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHY 78 (359)
Q Consensus 41 lE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yy 78 (359)
+...|.+|+++. ...+++++| |+|+|-|++....+.
T Consensus 4 v~~~i~~fl~s~-~~~l~le~c-ngf~RkLiyq~l~~~ 39 (65)
T cd02637 4 VIERIEAFLESE-EDDLELEPC-NGFQRKLIYQTLEQK 39 (65)
T ss_pred HHHHHHHHHhcC-ccccccccc-ccHHHHHHHHHHHHH
Confidence 345678899887 567999999 999999999887765
No 19
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=75.74 E-value=9.9 Score=36.37 Aligned_cols=60 Identities=17% Similarity=0.276 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHh-hhhhccceeeecccccCCcceEEEEe
Q 018220 36 LTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRV-SQHYGLVTMVQENGIEGLGNRILVRK 100 (359)
Q Consensus 36 l~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRv-A~yygL~h~v~d~~~dgs~~~Ivv~K 100 (359)
-.|.+|-+.+-.=+....+ ..+|.|| ++|.|-+||.. .++=|+.+..+.. +...+|||.+
T Consensus 147 e~L~~LA~~~A~rV~~tg~-~v~L~pM-~~~ERkIVH~~l~~~~~V~T~SeG~---ep~R~vVV~~ 207 (208)
T COG1847 147 ETLIKLAERAAERVLETGR-SVELEPM-PPFERKIVHTALSANPGVETYSEGE---EPNRRVVVRP 207 (208)
T ss_pred HHHHHHHHHHHHHHHhhCC-eeecCCC-CHHHHHHHHHHHHhcCCcceeecCC---CCceEEEEec
Confidence 4555666666555554443 5899999 99999999984 6677888887643 3345777753
No 20
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=68.64 E-value=4 Score=45.95 Aligned_cols=80 Identities=13% Similarity=0.277 Sum_probs=59.1
Q ss_pred hhHHHHHHHHHHHHHHhcCCCc------cceecCCCCChHHHHHHHHhhhhhccceeeecccccCCcceEEEEecC-CCC
Q 018220 33 RHRLTILRMELDIQRFLQNPDQ------QHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKTA-ESK 105 (359)
Q Consensus 33 kDRl~lLrlE~di~~FI~d~~~------~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Ivv~KT~-~tR 105 (359)
++-.|+.-+|++++.|+..... -+..||+| +-..|-+||-+|+.|+|.....+..+.. .++|+.+- .+.
T Consensus 817 ~~~~f~~sv~~e~~~lv~~~~~~~~~~~k~~~~p~m-s~~~rr~vh~~~e~~~l~~~sa~~~pkr---~~v~t~ir~~s~ 892 (950)
T KOG1952|consen 817 KDLKFVKSVEKELEFLVELVKRGKNYSKKSHSFPPM-SRDKRRLVHELAEVFGLESVSADSEPKR---NVVVTAIRGKSV 892 (950)
T ss_pred hchhhhccchhhhHHHHHHHhhcccccccccccCch-hHHHHHHHHhhhhccCCcccccCCCccc---ceeeEeeccccc
Confidence 4566888888888888765433 24579999 9999999999999999999876644333 47777774 566
Q ss_pred CCccccccccc
Q 018220 106 YPAVRLSEIPA 116 (359)
Q Consensus 106 iP~vrLSdl~~ 116 (359)
+|.+.+.+++.
T Consensus 893 ~~~~~~~~~~~ 903 (950)
T KOG1952|consen 893 FPATTITGVLN 903 (950)
T ss_pred CchhhHHHHHH
Confidence 66666666654
No 21
>PF12206 DUF3599: Domain of unknown function (DUF3599); InterPro: IPR024556 This family of bacterial proteins includes phage-like element PBSX protein xkdH from Bacillus subtilis. The function of the family is unknown.; PDB: 3F3B_A.
Probab=41.04 E-value=5 Score=35.15 Aligned_cols=19 Identities=37% Similarity=0.525 Sum_probs=6.3
Q ss_pred hHHHHHHHHhhhhhccceee
Q 018220 65 SYLRLAAHRVSQHYGLVTMV 84 (359)
Q Consensus 65 SY~RLLvHRvA~yygL~h~v 84 (359)
||++||+||| +.|||+...
T Consensus 2 Syq~mL~hrC-DIYHl~~~e 20 (117)
T PF12206_consen 2 SYQRMLTHRC-DIYHLEQKE 20 (117)
T ss_dssp -------EEE-EEE--EEE-
T ss_pred CHHHhhhccc-cccchhhhc
Confidence 8999999986 678885543
No 22
>KOG2953 consensus mRNA-binding protein Encore [RNA processing and modification]
Probab=32.92 E-value=6.8 Score=41.04 Aligned_cols=54 Identities=13% Similarity=-0.020 Sum_probs=40.6
Q ss_pred cCchhHHHHHHHHHHHHHHhcCCCccceecCCCCChHHHHHHHHhhhhhccceeee
Q 018220 30 QNPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQ 85 (359)
Q Consensus 30 ~npkDRl~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~ 85 (359)
.++-++..||..+.-|...++....+.-++.- ||||++++-|+| .+|++++.+.
T Consensus 23 ~s~~~~~~~~~~~~~m~~~~~~~s~q~~~~~~-~ss~~~~~~~~c-v~f~~~~~q~ 76 (432)
T KOG2953|consen 23 VSFINSNQLLFQLRPMQPYYQLLSHQIAPGHY-PSSVLQYRPDSC-VLFKGENNQK 76 (432)
T ss_pred ccCCCcchhhhcccccCchhhcchhccCCccC-ccchhhccccce-eeeccccCcc
Confidence 46677788888888888888877765444444 488888888888 8888888774
No 23
>PF07777 MFMR: G-box binding protein MFMR; InterPro: IPR012900 This region is found to the N terminus of IPR011616 from INTERPRO, which is a transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain) [], whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C [], classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions []. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2 []. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=31.54 E-value=68 Score=30.39 Aligned_cols=36 Identities=28% Similarity=0.466 Sum_probs=21.9
Q ss_pred CcCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCccccccCchhh
Q 018220 291 SLSFRPPSSPVMSPYCAVGPNQTSVEAAYMQWPSAAMMYAHSYEQ 335 (359)
Q Consensus 291 ~~~~~~~~~~~m~p~~~~~~~~~~~~~~y~~~p~~~m~y~h~~~~ 335 (359)
.-=+|++- +||.||++.. .=.|+|.| +=.|+|+-=.
T Consensus 60 PYMWG~~q-~mmPPYGtP~----pY~A~Yph----GgvYAHP~mp 95 (189)
T PF07777_consen 60 PYMWGPQQ-PMMPPYGTPV----PYPAMYPH----GGVYAHPSMP 95 (189)
T ss_pred CcccCCCc-cccCCCCCCC----CCccccCC----CccccCCCCC
Confidence 34467554 9999998842 23567765 4455554433
No 24
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=30.07 E-value=46 Score=28.61 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=16.1
Q ss_pred CCCCHHHHHHHHHHHHHh
Q 018220 153 PVRSVEERKEEYDRARAR 170 (359)
Q Consensus 153 ~~kSlEEREeeY~rAReR 170 (359)
...|+|||.+++++.|++
T Consensus 3 ~~~s~e~R~~e~~~ir~k 20 (112)
T cd01611 3 ERHPFEKRKAEVERIRAK 20 (112)
T ss_pred cccCHHHHHHHHHHHHHH
Confidence 467999999999999986
No 25
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=24.87 E-value=38 Score=28.53 Aligned_cols=17 Identities=18% Similarity=0.479 Sum_probs=12.1
Q ss_pred HHHHHHHhhhhhcccee
Q 018220 67 LRLAAHRVSQHYGLVTM 83 (359)
Q Consensus 67 ~RLLvHRvA~yygL~h~ 83 (359)
+.-++|.||+|||+...
T Consensus 74 ~~tlvhEiah~fG~~~e 90 (97)
T PF06262_consen 74 RDTLVHEIAHHFGISDE 90 (97)
T ss_dssp HHHHHHHHHHHTT--HH
T ss_pred HHHHHHHHHHHcCCCHH
Confidence 45679999999999653
No 26
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=22.49 E-value=72 Score=28.15 Aligned_cols=19 Identities=32% Similarity=0.478 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHHHHh
Q 018220 152 SPVRSVEERKEEYDRARAR 170 (359)
Q Consensus 152 ~~~kSlEEREeeY~rAReR 170 (359)
+...|+|+|.+|+++.|++
T Consensus 5 K~~~s~e~R~~e~~~Ir~k 23 (121)
T PTZ00380 5 HSSNPVEARRAECARLQAK 23 (121)
T ss_pred hhcCCHHHHHHHHHHHHHH
Confidence 3568999999999999985
No 27
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=21.59 E-value=1.4e+02 Score=31.01 Aligned_cols=65 Identities=23% Similarity=0.475 Sum_probs=40.2
Q ss_pred CCcccc-CCCCCCCCCCCCCC-----CCcCCCCCCCCCCCCCCCCCCCCCCCCcccccCC---CccccccCchh
Q 018220 270 LPFMQY-DTGFPQFSQIPRTQ-----ASLSFRPPSSPVMSPYCAVGPNQTSVEAAYMQWP---SAAMMYAHSYE 334 (359)
Q Consensus 270 ~p~~~y-~~~f~q~~~~~~~~-----~~~~~~~~~~~~m~p~~~~~~~~~~~~~~y~~~p---~~~m~y~h~~~ 334 (359)
+|.+.| |.-|+--.-|+-.+ -+=+|++|..++++||-+.-.|+.-...--|-|| .++-.|-|+|-
T Consensus 54 ~pli~ys~ehF~p~~pps~~p~dis~k~g~~r~~~~pd~~p~y~ls~gavgqip~~l~wp~y~~pt~~~~~p~p 127 (421)
T KOG3248|consen 54 TPLITYSNEHFSPGSPPSPLPADISPKQGIPRPPHPPDLSPFYPLSPGAVGQIPHPLGWPVYPIPTFGFRHPYP 127 (421)
T ss_pred CchhhhhhhhCCCCCCCCCCcccccccCCCCCCCCCccccccccCCccccccCCCccCCccccCCCCCCCCCCc
Confidence 355566 34565433222222 3447999999999999888777666666666774 45455555554
No 28
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=20.84 E-value=56 Score=29.24 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=15.7
Q ss_pred ChHHHHHHHHhhhhhccceeee
Q 018220 64 TSYLRLAAHRVSQHYGLVTMVQ 85 (359)
Q Consensus 64 nSY~RLLvHRvA~yygL~h~v~ 85 (359)
.+.-|.|+|-|..|+||.|...
T Consensus 67 ~~~g~TltHEvGH~LGL~HtF~ 88 (154)
T PF05572_consen 67 YNFGKTLTHEVGHWLGLYHTFG 88 (154)
T ss_dssp S-SSHHHHHHHHHHTT---TT-
T ss_pred cccccchhhhhhhhhccccccc
Confidence 6678999999999999999884
No 29
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=20.73 E-value=81 Score=28.47 Aligned_cols=27 Identities=30% Similarity=0.402 Sum_probs=21.4
Q ss_pred HHHHHHhcCchhHHHHHHHHHHHHHHh
Q 018220 23 PFLVEALQNPRHRLTILRMELDIQRFL 49 (359)
Q Consensus 23 ~~L~eAL~npkDRl~lLrlE~di~~FI 49 (359)
..|+++|++...=.|.|+||++|..-+
T Consensus 62 ~~Li~~~k~~~~E~f~lkLEk~I~q~~ 88 (137)
T PF10788_consen 62 QNLIESLKNAQKENFELKLEKDILQQM 88 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 457778888777789999999997643
No 30
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=20.38 E-value=73 Score=21.32 Aligned_cols=12 Identities=42% Similarity=0.960 Sum_probs=9.9
Q ss_pred HHHHHHHHHhhc
Q 018220 161 KEEYDRARARIF 172 (359)
Q Consensus 161 EeeY~rAReRIF 172 (359)
++||+++|++|-
T Consensus 19 eeEy~~~k~~ll 30 (31)
T PF09851_consen 19 EEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHHHh
Confidence 578999999884
Done!