Query 023983
Match_columns 274
No_of_seqs 151 out of 194
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 08:05:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023983hhsearch_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 1.4E-36 3E-41 292.8 11.2 251 12-265 87-349 (432)
2 cd02642 R3H_encore_like R3H do 99.8 2E-21 4.3E-26 143.8 7.1 63 34-101 1-63 (63)
3 PF12752 SUZ: SUZ domain; Int 99.5 1.8E-14 3.9E-19 105.7 5.0 50 127-176 2-59 (59)
4 PF01424 R3H: R3H domain; Int 99.4 1.1E-12 2.4E-17 95.7 6.4 63 34-101 1-63 (63)
5 cd02325 R3H R3H domain. The na 99.3 1E-11 2.2E-16 86.7 5.9 59 38-100 1-59 (59)
6 smart00393 R3H Putative single 99.2 1.3E-11 2.9E-16 94.3 4.9 74 23-101 5-79 (79)
7 cd02641 R3H_Smubp-2_like R3H d 99.0 4.2E-10 9.2E-15 83.0 6.3 58 39-100 2-60 (60)
8 cd06006 R3H_unknown_2 R3H doma 99.0 5.2E-10 1.1E-14 82.7 6.5 57 40-100 3-59 (59)
9 cd02646 R3H_G-patch R3H domain 99.0 5.2E-10 1.1E-14 81.6 5.7 57 39-100 2-58 (58)
10 cd02636 R3H_sperm-antigen R3H 98.7 4.8E-08 1E-12 72.8 6.0 58 40-100 3-60 (61)
11 cd02640 R3H_NRF R3H domain of 98.7 4.9E-08 1.1E-12 72.3 6.1 57 40-100 3-60 (60)
12 cd06007 R3H_DEXH_helicase R3H 98.7 4.6E-08 9.9E-13 72.3 5.8 57 39-100 2-59 (59)
13 cd02643 R3H_NF-X1 R3H domain o 98.6 6E-08 1.3E-12 74.2 5.6 63 33-99 6-73 (74)
14 cd02644 R3H_jag R3H domain fou 97.5 0.00041 8.9E-09 52.3 6.7 61 35-100 5-66 (67)
15 cd02639 R3H_RRM R3H domain of 97.2 0.00013 2.8E-09 54.2 1.3 59 39-100 2-60 (60)
16 cd02645 R3H_AAA R3H domain of 96.8 0.0038 8.3E-08 46.3 5.8 51 44-99 9-59 (60)
17 cd02638 R3H_unknown_1 R3H doma 95.7 0.032 6.8E-07 42.0 5.5 55 41-99 4-60 (62)
18 cd02637 R3H_PARN R3H domain of 92.3 0.2 4.4E-06 37.7 3.8 37 41-79 4-40 (65)
19 COG1847 Jag Predicted RNA-bind 78.7 7.3 0.00016 35.8 6.7 60 36-100 147-207 (208)
20 KOG1952 Transcription factor N 65.4 5.3 0.00012 43.4 3.0 80 33-116 817-903 (950)
21 PF12206 DUF3599: Domain of un 52.0 2.5 5.3E-05 35.6 -1.7 19 65-84 2-20 (117)
22 KOG2953 mRNA-binding protein E 37.4 5 0.00011 40.4 -2.4 52 31-84 24-75 (432)
23 PF06262 DUF1025: Possibl zinc 36.7 19 0.00041 29.1 1.2 16 67-82 74-89 (97)
24 cd01611 GABARAP Ubiquitin doma 31.1 45 0.00098 27.5 2.6 18 153-170 3-20 (112)
25 KOG4060 Uncharacterized conser 28.6 28 0.0006 30.9 1.0 26 55-82 60-85 (176)
26 PF05572 Peptidase_M43: Pregna 28.6 31 0.00067 29.7 1.3 23 64-86 67-89 (154)
27 PF06755 DUF1219: Protein of u 27.9 41 0.00089 28.3 1.8 18 64-81 20-37 (114)
28 cd07311 terB_like_1 tellurium 23.7 2.3E+02 0.0049 24.4 5.8 21 64-84 106-126 (150)
29 PTZ00380 microtubule-associate 23.0 72 0.0016 27.0 2.5 19 152-170 5-23 (121)
30 PF09851 SHOCT: Short C-termin 21.8 67 0.0015 20.5 1.6 12 161-172 19-30 (31)
31 PF10788 DUF2603: Protein of u 20.5 96 0.0021 26.9 2.8 26 23-48 62-87 (137)
No 1
>KOG2953 consensus mRNA-binding protein Encore [RNA processing and modification]
Probab=100.00 E-value=1.4e-36 Score=292.81 Aligned_cols=251 Identities=45% Similarity=0.587 Sum_probs=221.9
Q ss_pred hhcccCCCCchHHHHHHhcCchhHHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecC---C
Q 023983 12 AIVNERESMVDPFLVEALQNPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQEN---G 88 (274)
Q Consensus 12 ~~~~~~~~~vd~~L~eAL~nprDR~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~---~ 88 (274)
+.+-.....+|.|++|||+||+.|++|+++|.+|.+|+++...++++|+++|+||+|++.||+|++|+|.+.+.+. +
T Consensus 87 ~~~~p~e~~~dy~~ve~~qnpR~~~~lsR~El~~~~~~Q~~~~qqt~~q~~~ts~~~~~~~rvaq~y~l~T~~~p~~~~~ 166 (432)
T KOG2953|consen 87 ANKIPNEQAVDYFLVEALQNPRHRLTLSRKELDIQCQFQGPVQQQTEFQNYPTSYLRLAAHRVAQHYGLATTGEPSYISG 166 (432)
T ss_pred cccCchhhcccHHHHhhhhcchhhhhhhcccchhhhhhcCcccccccCCCccccchhhhhcccccccccccccccccccc
Confidence 4456678889999999999999999999999999999999999999999999999999999999999999998776 5
Q ss_pred cCCCccEEEEEecCCCCCCcccccccccCCCCcCchhhhhhhheeeCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHH
Q 023983 89 IEGLGNRILVRKTAESKYPAVRLSEIPAKQSEESDKLEKIKIAIRRRPNAGCVNG-ANETGTKRSPVRSVEERKEEYDRA 167 (274)
Q Consensus 89 ~dgs~~~Iiv~KT~~triP~vrLsdi~~~~~~~~~~~~~~k~~ImrR~~~~s~~~-~s~~~~k~~~~kS~EEREeeY~rA 167 (274)
.++...+|++.|+.+++.|.+++++++.+.+.+++.++..|+.|.-|+.++++.. .++.+.......|+|||+++|..|
T Consensus 167 ~~p~eqR~l~~k~~~s~~P~~~~~~~P~ssp~~~~~~~~~~~~~sp~p~~g~G~~~~~p~~~~~~~~~S~~~~kq~yd~~ 246 (432)
T KOG2953|consen 167 IDPYEQRILVTKTGESRFPGVSLSEIPVSSPSSNGWSEQRKGDISPRPTSGGGVSLSSPSNPQVTLLRSVEERKQEYDKA 246 (432)
T ss_pred cCchhccccccccccccCCchhhccccccCccccccccccccccCCCCCCCCcccccCCcCCCccccccchhhhhhhhhh
Confidence 7888899999999999999999999999766657888888999999998775443 233333445788999999999999
Q ss_pred HHhhcCCCCCCCCCCccccccCC---CCC--CCCCchhhHhhhc-chhhhhhhcccCCCCCCCceEEecCcccCCCCCCc
Q 023983 168 RARIFSGPSSPNSEDTLTQVSTD---MKN--IGFNRDEREIVRN-SITDAEKIISIRDGAGLSRVAIFRDREKDRTDPDY 241 (274)
Q Consensus 168 ReRIF~~~~~~d~~~~~~~~~~~---~~~--~~~~r~~~~~~~~-~~~~~ek~~~~~~~~~~~rvai~rdre~dr~dPDy 241 (274)
|+|||+.....++.|.+...++. ..+ ++++|.+.....| .++.-+++.+.|+.++.+||||+||||+||+||||
T Consensus 247 r~r~g~~~~~~~s~Dss~q~~p~~~~~~~g~~~~~~~~~p~~~N~~Pv~~~~~g~~~~~gps~~v~~nr~rr~~ry~p~~ 326 (432)
T KOG2953|consen 247 RGRIGSKPVTNDSKDSSSQQPPQNYQSGNGDPRLSRLEQPVSYNSPPLMHGPNGITRESGPSPRVAGNRDRRPDRYDPDY 326 (432)
T ss_pred hccccCccccccCcccccccCCccccCCCCccccccCCcccccCCCcccccCCCcccCCCCCcccccccccchhhcCccc
Confidence 99999999999999998876665 444 5799999988877 78899999999999999999999999999999999
Q ss_pred ccc--cccccccCCCCCCCCcccCCC
Q 023983 242 DRS--YESTILVFPNSVRSQGLKLPS 265 (274)
Q Consensus 242 dr~--y~ry~~~~~~g~~~~g~~~~~ 265 (274)
||+ .-|||..+||| +-|+--.
T Consensus 327 dr~~~~~~yv~~~Pp~---q~~~~~~ 349 (432)
T KOG2953|consen 327 DRSCGFVRYVTMLPPG---QTFMQYQ 349 (432)
T ss_pred ccCCCCcceeccCCCc---ccccccc
Confidence 999 88999999999 7766433
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=99.85 E-value=2e-21 Score=143.82 Aligned_cols=63 Identities=41% Similarity=0.711 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEec
Q 023983 34 HRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (274)
Q Consensus 34 DR~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~KT 101 (274)
||++||+||++|++||+++..+.++|||| |||+|||+|+||+||||.|++++.+ +.+|+|+||
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 9999999999999999999997743 578999997
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=99.51 E-value=1.8e-14 Score=105.75 Aligned_cols=50 Identities=42% Similarity=0.677 Sum_probs=37.6
Q ss_pred hhhhheeeCCCCCCCCC--------CCCCCCCCCCCCCHHHHHHHHHHHHHhhcCCCC
Q 023983 127 KIKIAIRRRPNAGCVNG--------ANETGTKRSPVRSVEERKEEYDRARARIFSGPS 176 (274)
Q Consensus 127 ~~k~~ImrR~~~~s~~~--------~s~~~~k~~~~kS~EEREeeY~rAReRIF~~~~ 176 (274)
.++++||||+++++... ....+.+....+|+||||++|++||+|||++++
T Consensus 2 ~p~~~IlkRp~~~~~~~~~~~~~~~~~~~~~~~~~~kSlEERE~eY~~AR~RIFg~~~ 59 (59)
T PF12752_consen 2 KPKRKILKRPSKGSSSSDSGSSGSSPNSSSRKKRPSKSLEEREAEYAEARARIFGSSE 59 (59)
T ss_pred CCCCeEecCCCCCCCcccccccccCCCcccccccccCCHHHHHHHHHHHHHHHhCCCC
Confidence 35899999986553321 112234567899999999999999999999864
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=99.37 E-value=1.1e-12 Score=95.67 Aligned_cols=63 Identities=25% Similarity=0.471 Sum_probs=52.7
Q ss_pred hHHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEec
Q 023983 34 HRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (274)
Q Consensus 34 DR~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~KT 101 (274)
.|..|+++++++++|+.++.. .+.|+|| |+|+|+++|.+|+||||.|.+.+.+ ...+|+|+||
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 367899999999999976654 7999999 9999999999999999999997744 3467999886
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=99.26 E-value=1e-11 Score=86.66 Aligned_cols=59 Identities=22% Similarity=0.412 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 38 ILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 38 lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
++++|+.|.+|+.+.....++|+|| |+|+|+++|++|++|||.+.+.+.+ ...+|+|.+
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 9999999999999999999996643 345676653
No 6
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=99.21 E-value=1.3e-11 Score=94.33 Aligned_cols=74 Identities=30% Similarity=0.596 Sum_probs=63.0
Q ss_pred HHHHHHhc-CchhHHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEec
Q 023983 23 PFLVEALQ-NPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKT 101 (274)
Q Consensus 23 ~~L~eAL~-nprDR~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~KT 101 (274)
+++++.+. +++.+.+|++++.++.+|+.... ..+.|||| |+|+|.++|++|++|||.|.+.+.++ ..+|+|+++
T Consensus 5 ~~~~d~~~~~~~~~~~l~~~~~~~~~~v~~~~-~~~~~~pm-~~~~R~~iH~~a~~~~l~s~S~g~g~---~R~vvv~~~ 79 (79)
T smart00393 5 PVTLDALSYRPRRREELIELELEIARFVKSTK-ESVELPPM-NSYERKIVHELAEKYGLESESFGEGP---KRRVVISKK 79 (79)
T ss_pred eEEEECCccCHHHHHHHHHHHHHHHHHHhccC-CeEEcCCC-CHHHHHHHHHHHHHcCCEEEEEcCCC---CcEEEEEeC
Confidence 34555665 88999999999999999998775 56999999 99999999999999999999987553 357888764
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=99.05 E-value=4.2e-10 Score=82.99 Aligned_cols=58 Identities=24% Similarity=0.411 Sum_probs=49.9
Q ss_pred HHHHHHHHHHhcCCCccccccCC-CCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 39 LRMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
.++++.|.+||+++....++||| | |+++|.+||.||+.|||.|...+.| ....|+|.|
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 46899999999999878899999 9 9999999999999999999997754 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=99.04 E-value=5.2e-10 Score=82.66 Aligned_cols=57 Identities=21% Similarity=0.463 Sum_probs=50.6
Q ss_pred HHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 40 RMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
++|+.|.+||+|.....+.|||| |+++|-+||-||++|||.++..|.+++ .+|+|.|
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 78999999999987778999999 999999999999999999999887653 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=99.02 E-value=5.2e-10 Score=81.58 Aligned_cols=57 Identities=19% Similarity=0.322 Sum_probs=49.3
Q ss_pred HHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 39 LRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
-.++++|.+|+.++ ...+.|||| ++++|.+||+||..|||.+...+.| ....|+|+|
T Consensus 2 ~~i~~~i~~F~~~~-~~~~~fppm-~~~~R~~vH~lA~~~~L~S~S~G~g---~~R~v~v~k 58 (58)
T cd02646 2 EDIKDEIEAFLLDS-RDSLSFPPM-DKHGRKTIHKLANCYNLKSKSRGKG---KKRFVTVTK 58 (58)
T ss_pred hHHHHHHHHHHhCC-CceEecCCC-CHHHHHHHHHHHHHcCCcccccccC---CceEEEEEC
Confidence 47899999999998 467999999 9999999999999999999987754 335688765
No 10
>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=98.68 E-value=4.8e-08 Score=72.82 Aligned_cols=58 Identities=19% Similarity=0.344 Sum_probs=49.2
Q ss_pred HHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 40 RMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
++|+.+.+||+|...+..+|+|| |+|+|-++|-+|+..||.+.....+ +...+|+|++
T Consensus 3 ~~e~~~~~f~~d~~~~~~~l~pM-~~~eRkivHDv~~~~Gl~S~S~Gee--e~~R~VVv~~ 60 (61)
T cd02636 3 SMEKEVSKFIKDSVRTREKFQPM-DKVERSIVHDVAEVAGLTSFSFGED--EVDRYVMIFK 60 (61)
T ss_pred hHHHHHHHHhhcccccccccCCC-CHHHHHHHHHHHHhcCceeEecCCC--CCceEEEEec
Confidence 68999999999987788899999 9999999999999999999885532 2235687765
No 11
>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=98.68 E-value=4.9e-08 Score=72.30 Aligned_cols=57 Identities=23% Similarity=0.374 Sum_probs=47.5
Q ss_pred HHHHHHHHHhcCCCccccccCC-CCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 40 RMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 40 rlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
.+++.|.+|+.+...+.+.||| | ++++|.+||.||+.+||.|.....+ ....|+|+|
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-SKEERALIHQIAQKYGLKSRSYGSG---NDRYLVISK 60 (60)
T ss_pred hHHHHHHHHHcCCccceEEcCCCC-CHHHHHHHHHHHHHcCCceeeEeCC---CCeEEEEeC
Confidence 4689999999998778899999 9 9999999999999999999986543 324565653
No 12
>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=98.67 E-value=4.6e-08 Score=72.27 Aligned_cols=57 Identities=23% Similarity=0.429 Sum_probs=47.5
Q ss_pred HHHHHHHHHHhcCCCccccccCC-CCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 39 LRMELDIQRFLQNPDQQHFEFQH-FPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~p-mpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
+.+++.|.+|+++. ...++||| | |+++|.++|.||+.+||.|..... |....|+|.|
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 35789999999998 77899999 8 999999999999999999998553 3334566654
No 13
>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=98.63 E-value=6e-08 Score=74.20 Aligned_cols=63 Identities=11% Similarity=0.312 Sum_probs=52.1
Q ss_pred hhHHHHHHHHHHHHHHhcCCCc-----cccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEE
Q 023983 33 RHRLTILRMELDIQRFLQNPDQ-----QHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVR 99 (274)
Q Consensus 33 rDR~~lLrlE~di~~FI~d~~~-----~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~ 99 (274)
++-.|+.++|+.|..|+.+... ..+.|+|| |+|+|-+||-+|++|||.+...+.++. .+|||+
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 3456999999999999996432 45789999 999999999999999999999886543 467774
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=97.49 E-value=0.00041 Score=52.25 Aligned_cols=61 Identities=13% Similarity=0.211 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhc-cceeeecCCcCCCccEEEEEe
Q 023983 35 RLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYG-LVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 35 R~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yyg-L~h~v~d~~~dgs~~~Iiv~K 100 (274)
.-.|.+|-+.+.+.+..... .+.|+|| |+|+|-+||.+++-|. |.+...+.+ ...+|+|.+
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 34577788888888888764 4999999 9999999999999877 999987754 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=97.23 E-value=0.00013 Score=54.24 Aligned_cols=59 Identities=15% Similarity=0.228 Sum_probs=45.3
Q ss_pred HHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEe
Q 023983 39 LRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 39 LrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
|.+-.+|+-|..+.....+.|||-.+.-+|.++|.||..+||.|.....| ....|+|+|
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 34445667788888888899999449999999999999999999985533 334565553
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=96.79 E-value=0.0038 Score=46.31 Aligned_cols=51 Identities=18% Similarity=0.295 Sum_probs=37.6
Q ss_pred HHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEE
Q 023983 44 DIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVR 99 (274)
Q Consensus 44 di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~ 99 (274)
.+..-+ .+.....+|.|| |+|-|-++|.+.+.|||.+.....++ -.+|+|.
T Consensus 9 aa~~V~-~~~~~~veL~Pm-~~~eRri~H~~v~~~~l~s~S~G~ep---~RrvvI~ 59 (60)
T cd02645 9 AIEQVV-IPKGEPVELLPR-SAYIRRLQHDLVERYQLRSESFGSEP---NRRLRIL 59 (60)
T ss_pred HHHHHH-hcCCceEEcCCC-CHHHHHHHHHHHHHCCCeEEEecCCC---CcEEEEe
Confidence 333333 444234899999 99999999999999999999976443 3467664
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=95.66 E-value=0.032 Score=42.03 Aligned_cols=55 Identities=20% Similarity=0.295 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCCc-cccccCCCCChHHHHHHHHHhh-hhccceeeecCCcCCCccEEEEE
Q 023983 41 MELDIQRFLQNPDQ-QHFEFQHFPTSYLRLAAHRVSQ-HYGLVTMVQENGIEGLGNRILVR 99 (274)
Q Consensus 41 lE~di~~FI~d~~~-~~lef~pmpnSY~RLLvHRvA~-yygL~h~v~d~~~dgs~~~Iiv~ 99 (274)
..++++-|++.... ..+.|+|| |+|.|-++|...+ +-++.+..+..+ ...+|+|.
T Consensus 4 ~~~~~~~f~~~~~~~r~v~LePM-~~~ERkIIH~~Lq~~~~v~T~S~G~e---p~RrVVI~ 60 (62)
T cd02638 4 VSEELEIFLLSFQRYRVLLFPPL-NSRRRYLIHQTVENRFLLSTFSVGEG---WARRTVVC 60 (62)
T ss_pred hHHHHHHHHHhcccCCeEecCCC-ChHHHHHHHHHHhcCCCceEEEccCC---CCcEEEEe
Confidence 45677778887633 45789999 9999999998655 667777765533 33566663
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=92.31 E-value=0.2 Score=37.72 Aligned_cols=37 Identities=14% Similarity=0.213 Sum_probs=30.6
Q ss_pred HHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhc
Q 023983 41 MELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYG 79 (274)
Q Consensus 41 lE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yyg 79 (274)
+...|.+|+++. ...++++|| |+|+|-|+++...+.-
T Consensus 4 v~~~i~~fl~s~-~~~l~le~c-ngf~RkLiyq~l~~~~ 40 (65)
T cd02637 4 VIERIEAFLESE-EDDLELEPC-NGFQRKLIYQTLEQKY 40 (65)
T ss_pred HHHHHHHHHhcC-ccccccccc-ccHHHHHHHHHHHHHc
Confidence 345678899887 567999999 9999999999877653
No 19
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=78.67 E-value=7.3 Score=35.79 Aligned_cols=60 Identities=17% Similarity=0.276 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHH-hhhhccceeeecCCcCCCccEEEEEe
Q 023983 36 LTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRV-SQHYGLVTMVQENGIEGLGNRILVRK 100 (274)
Q Consensus 36 ~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRv-A~yygL~h~v~d~~~dgs~~~Iiv~K 100 (274)
-.|.+|-+.+-.=+.... ...+|.|| ++|.|-+||.. .++-|+.+..+..+ ...+|||.+
T Consensus 147 e~L~~LA~~~A~rV~~tg-~~v~L~pM-~~~ERkIVH~~l~~~~~V~T~SeG~e---p~R~vVV~~ 207 (208)
T COG1847 147 ETLIKLAERAAERVLETG-RSVELEPM-PPFERKIVHTALSANPGVETYSEGEE---PNRRVVVRP 207 (208)
T ss_pred HHHHHHHHHHHHHHHhhC-CeeecCCC-CHHHHHHHHHHHHhcCCcceeecCCC---CceEEEEec
Confidence 345555555555554444 45899999 99999999985 56778888775533 335677653
No 20
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=65.39 E-value=5.3 Score=43.40 Aligned_cols=80 Identities=13% Similarity=0.277 Sum_probs=57.5
Q ss_pred hhHHHHHHHHHHHHHHhcCCCc------cccccCCCCChHHHHHHHHHhhhhccceeeecCCcCCCccEEEEEecC-CCC
Q 023983 33 RHRLTILRMELDIQRFLQNPDQ------QHFEFQHFPTSYLRLAAHRVSQHYGLVTMVQENGIEGLGNRILVRKTA-ESK 105 (274)
Q Consensus 33 rDR~~lLrlE~di~~FI~d~~~------~~lef~pmpnSY~RLLvHRvA~yygL~h~v~d~~~dgs~~~Iiv~KT~-~tr 105 (274)
++-.|+.-+|++++.|+.-... .+..||+| +-..|-+||-+|+.|+|.....+..+.. .++++.+- .+.
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 4566888888888888765432 34579999 9999999999999999998876644333 46677765 455
Q ss_pred CCccccccccc
Q 023983 106 YPAVRLSEIPA 116 (274)
Q Consensus 106 iP~vrLsdi~~ 116 (274)
+|.+.+..++.
T Consensus 893 ~~~~~~~~~~~ 903 (950)
T KOG1952|consen 893 FPATTITGVLN 903 (950)
T ss_pred CchhhHHHHHH
Confidence 56655555533
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=52.03 E-value=2.5 Score=35.59 Aligned_cols=19 Identities=37% Similarity=0.525 Sum_probs=6.3
Q ss_pred hHHHHHHHHHhhhhccceee
Q 023983 65 SYLRLAAHRVSQHYGLVTMV 84 (274)
Q Consensus 65 SY~RLLvHRvA~yygL~h~v 84 (274)
||++||+||| +.|||+...
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=37.45 E-value=5 Score=40.38 Aligned_cols=52 Identities=13% Similarity=-0.021 Sum_probs=26.2
Q ss_pred CchhHHHHHHHHHHHHHHhcCCCccccccCCCCChHHHHHHHHHhhhhccceee
Q 023983 31 NPRHRLTILRMELDIQRFLQNPDQQHFEFQHFPTSYLRLAAHRVSQHYGLVTMV 84 (274)
Q Consensus 31 nprDR~~lLrlE~di~~FI~d~~~~~lef~pmpnSY~RLLvHRvA~yygL~h~v 84 (274)
++-++..||..+.-|...++....+.-++.- ||||++++-|+| .+|++++.+
T Consensus 24 s~~~~~~~~~~~~~m~~~~~~~s~q~~~~~~-~ss~~~~~~~~c-v~f~~~~~q 75 (432)
T KOG2953|consen 24 SFINSNQLLFQLRPMQPYYQLLSHQIAPGHY-PSSVLQYRPDSC-VLFKGENNQ 75 (432)
T ss_pred cCCCcchhhhcccccCchhhcchhccCCccC-ccchhhccccce-eeeccccCc
Confidence 4445555555555555555555433222222 255555555555 555555544
No 23
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=36.70 E-value=19 Score=29.12 Aligned_cols=16 Identities=19% Similarity=0.551 Sum_probs=11.7
Q ss_pred HHHHHHHHhhhhccce
Q 023983 67 LRLAAHRVSQHYGLVT 82 (274)
Q Consensus 67 ~RLLvHRvA~yygL~h 82 (274)
+.-++|.||+|||+..
T Consensus 74 ~~tlvhEiah~fG~~~ 89 (97)
T PF06262_consen 74 RDTLVHEIAHHFGISD 89 (97)
T ss_dssp HHHHHHHHHHHTT--H
T ss_pred HHHHHHHHHHHcCCCH
Confidence 4567999999999964
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=31.06 E-value=45 Score=27.50 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=16.1
Q ss_pred CCCCHHHHHHHHHHHHHh
Q 023983 153 PVRSVEERKEEYDRARAR 170 (274)
Q Consensus 153 ~~kS~EEREeeY~rAReR 170 (274)
...|+|+|.+++++.|++
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
>KOG4060 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.62 E-value=28 Score=30.94 Aligned_cols=26 Identities=12% Similarity=0.376 Sum_probs=21.4
Q ss_pred cccccCCCCChHHHHHHHHHhhhhccce
Q 023983 55 QHFEFQHFPTSYLRLAAHRVSQHYGLVT 82 (274)
Q Consensus 55 ~~lef~pmpnSY~RLLvHRvA~yygL~h 82 (274)
+-++|+-+ .||++- +|.+|.+|+++-
T Consensus 60 ~gyD~~~l-EsYq~y-vH~la~~l~~~V 85 (176)
T KOG4060|consen 60 TGYDMTLL-ESYQQY-VHNLANSLSIKV 85 (176)
T ss_pred EecccchH-HHHHHH-HHHHHHHcCcee
Confidence 34678888 999985 799999999964
No 26
>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=28.59 E-value=31 Score=29.66 Aligned_cols=23 Identities=17% Similarity=0.262 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHhhhhccceeeec
Q 023983 64 TSYLRLAAHRVSQHYGLVTMVQE 86 (274)
Q Consensus 64 nSY~RLLvHRvA~yygL~h~v~d 86 (274)
.+..+.|+|-|..|+||-|...+
T Consensus 67 ~~~g~TltHEvGH~LGL~HtF~~ 89 (154)
T PF05572_consen 67 YNFGKTLTHEVGHWLGLYHTFGG 89 (154)
T ss_dssp S-SSHHHHHHHHHHTT---TT--
T ss_pred cccccchhhhhhhhhcccccccC
Confidence 66789999999999999998843
No 27
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=27.87 E-value=41 Score=28.28 Aligned_cols=18 Identities=33% Similarity=0.575 Sum_probs=16.8
Q ss_pred ChHHHHHHHHHhhhhccc
Q 023983 64 TSYLRLAAHRVSQHYGLV 81 (274)
Q Consensus 64 nSY~RLLvHRvA~yygL~ 81 (274)
.-+|+||.|=|.+||||.
T Consensus 20 ~vWQ~llt~LL~~HYGLt 37 (114)
T PF06755_consen 20 EVWQQLLTYLLEQHYGLT 37 (114)
T ss_pred HHHHHHHHHHHHHhcCCc
Confidence 679999999999999995
No 28
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=23.72 E-value=2.3e+02 Score=24.44 Aligned_cols=21 Identities=10% Similarity=0.012 Sum_probs=19.1
Q ss_pred ChHHHHHHHHHhhhhccceee
Q 023983 64 TSYLRLAAHRVSQHYGLVTMV 84 (274)
Q Consensus 64 nSY~RLLvHRvA~yygL~h~v 84 (274)
+.+.+-+++++|+++|+.|..
T Consensus 106 ~~~E~~lL~~iA~~LGis~~~ 126 (150)
T cd07311 106 SPGEVAAVRKAASLLGISEDE 126 (150)
T ss_pred CHHHHHHHHHHHHHcCCCHHH
Confidence 889999999999999998754
No 29
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=23.00 E-value=72 Score=27.00 Aligned_cols=19 Identities=32% Similarity=0.478 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHHHHh
Q 023983 152 SPVRSVEERKEEYDRARAR 170 (274)
Q Consensus 152 ~~~kS~EEREeeY~rAReR 170 (274)
+...|+|+|.+|+++.|++
T Consensus 5 K~~~s~e~R~~e~~~Ir~k 23 (121)
T PTZ00380 5 HSSNPVEARRAECARLQAK 23 (121)
T ss_pred hhcCCHHHHHHHHHHHHHH
Confidence 3567999999999999985
No 30
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=21.78 E-value=67 Score=20.53 Aligned_cols=12 Identities=42% Similarity=0.960 Sum_probs=9.7
Q ss_pred HHHHHHHHHhhc
Q 023983 161 KEEYDRARARIF 172 (274)
Q Consensus 161 EeeY~rAReRIF 172 (274)
++||.+++++|-
T Consensus 19 eeEy~~~k~~ll 30 (31)
T PF09851_consen 19 EEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHHHh
Confidence 578999998874
No 31
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=20.55 E-value=96 Score=26.86 Aligned_cols=26 Identities=31% Similarity=0.382 Sum_probs=20.9
Q ss_pred HHHHHHhcCchhHHHHHHHHHHHHHH
Q 023983 23 PFLVEALQNPRHRLTILRMELDIQRF 48 (274)
Q Consensus 23 ~~L~eAL~nprDR~~lLrlE~di~~F 48 (274)
..|+++|++.+.=-|.|+||++|..-
T Consensus 62 ~~Li~~~k~~~~E~f~lkLEk~I~q~ 87 (137)
T PF10788_consen 62 QNLIESLKNAQKENFELKLEKDILQQ 87 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45777778777778999999999753
Done!