Query psy17507
Match_columns 1121
No_of_seqs 487 out of 897
Neff 5.8
Searched_HMMs 46136
Date Sat Aug 17 00:20:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04096 Nucleoporin2: Nucleop 100.0 7E-50 1.5E-54 400.5 15.5 137 550-693 1-141 (141)
2 PF12110 Nup96: Nuclear protei 99.8 6.6E-22 1.4E-26 221.9 6.9 96 1026-1121 1-96 (290)
3 KOG0845|consensus 99.6 1.1E-13 2.5E-18 177.4 35.4 114 575-696 790-903 (903)
4 KOG3091|consensus 98.5 1.6E-06 3.5E-11 101.0 15.4 8 360-367 219-226 (508)
5 KOG3091|consensus 98.3 4.8E-06 1E-10 97.2 13.9 17 202-220 52-68 (508)
6 KOG0845|consensus 98.2 0.0019 4.1E-08 84.1 35.3 163 540-705 644-806 (903)
7 PF13634 Nucleoporin_FG: Nucle 97.7 0.00025 5.3E-09 69.7 9.8 7 247-253 86-92 (113)
8 PF13634 Nucleoporin_FG: Nucle 97.2 0.0016 3.5E-08 64.0 8.9 6 247-252 108-113 (113)
9 PF12931 Sec16_C: Sec23-bindin 90.6 0.21 4.7E-06 56.7 3.6 72 1030-1104 1-76 (284)
10 KOG0307|consensus 80.4 1.6 3.5E-05 56.6 4.2 136 973-1121 420-571 (1049)
11 PF07575 Nucleopor_Nup85: Nup8 57.3 12 0.00026 46.8 4.7 122 976-1104 95-252 (566)
12 KOG1428|consensus 57.0 2.9 6.4E-05 55.1 -0.7 26 8-33 2065-2090(3738)
13 PF04121 Nup84_Nup100: Nuclear 56.7 11 0.00024 48.3 4.4 85 1027-1120 136-238 (697)
14 cd03420 SirA_RHOD_Pry_redox Si 50.8 23 0.00049 31.7 4.1 31 661-691 38-68 (69)
15 PRK11018 hypothetical protein; 49.8 24 0.00053 32.5 4.2 31 662-692 48-78 (78)
16 PF12234 Rav1p_C: RAVE protein 45.5 29 0.00062 44.0 5.2 55 1022-1076 463-521 (631)
17 KOG1964|consensus 37.2 56 0.0012 41.5 5.8 75 1027-1104 223-313 (800)
18 PRK00299 sulfur transfer prote 34.3 58 0.0013 30.2 4.2 31 661-691 48-78 (81)
19 cd03422 YedF YedF is a bacteri 33.7 62 0.0013 29.0 4.2 30 662-691 39-68 (69)
20 cd03423 SirA SirA (also known 33.7 59 0.0013 29.0 4.0 30 662-691 39-68 (69)
21 cd00291 SirA_YedF_YeeD SirA, Y 27.1 91 0.002 27.2 4.1 31 662-692 39-69 (69)
No 1
>PF04096 Nucleoporin2: Nucleoporin autopeptidase; InterPro: IPR007230 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of autocatalytic serine endopeptidases belong to MEROPS peptidase family S59 (clan SP). The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 50 unique proteins, collectively known as nucleoporins. A number of the peptides are synthesised as precursors and undergo self-catalyzed cleavage. The proteolytic cleavage site of yeast Nup145p has been mapped upstream of an evolutionary conserved serine residue. Cleavage occurs at the same site when a precursor is artificially expressed in Escherichia coli. A hydroxyl-containing residue is critical for the reaction, although a thiol-containing residue offers an acceptable replacement. In vitro kinetics experiments using a purified precursor molecule demonstrate that the cleavage is self-catalyzed and that the catalytic domain lies within the N-terminal moiety. Taken altogether, the data are consistent with a proteolytic mechanism involving an N>O acyl rearrangement and a subsequent ester intermediate uncovered in other self-processing proteins []. Nup98 is a component of the nuclear pore that plays its primary role in the export of RNAs. Nup98 is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-terminal domain reveals a novel protein fold, and thus a new class of autocatalytic proteases. The structure further reveals that the suggested nucleoporin RNA binding motif is unlikely to bind to RNA []. The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [, ]: Vertebrate Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs. Yeast Nup100, plays an important role in several nuclear export and import pathways including poly(A)+ RNA and protein transport. Yeast Nup116, involved in mRNA export and protein transport. Yeast Nup145, involved in nuclear poly(A)+ RNA and tRNA export. The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore [, ]. The NUP C-terminal domain adopts a predominantly beta-strand structure. The molecule consists of a six-stranded beta-sheet sandwiched against a two-stranded beta-sheet and flanked by alpha-helical regions. The N-terminal helical region consists of two short helices, whereas the stretch on the opposite side of molecule consists of a single, longer helix [, ].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3PBP_E 2AIV_A 1KO6_A 2Q5X_A 2Q5Y_C 3KEP_A 3KES_A 3NF5_B 3TKN_I.
Probab=100.00 E-value=7e-50 Score=400.47 Aligned_cols=137 Identities=53% Similarity=0.915 Sum_probs=123.2
Q ss_pred CeeecCCHHHHHhcccCCCCceeccceEeeceeEEEEECccccccCCCccCcc----ceEEEecceEEEccCCCCCCCCC
Q psy17507 550 GYFVSPTLNELKQLKTKNGPCIVEGFTIGHEEFGSICFLESIDISELNNVDLD----SIVEFRFKEVVLYPDDANKPPVG 625 (1121)
Q Consensus 550 ~Y~~~Ps~~~L~~m~~~~gl~~V~~F~Igr~gyG~I~f~~pvDL~~~~~~~ld----~iV~~~~k~v~VYpd~~~kPp~G 625 (1121)
||||+|||+||++|+.+| |++|+||+|||+|||+|+|++||||++|| || +||+|++++|+||||+..|||+|
T Consensus 1 ~Y~~~Psl~eL~~m~~~~-l~~V~~F~Vgr~g~G~I~f~~pVDl~~ld---ld~~~~~iV~~~~~~v~VYpd~~~kPp~G 76 (141)
T PF04096_consen 1 GYWTSPSLEELQKMSDEE-LKRVENFTVGREGYGSIEFLGPVDLSGLD---LDDIFGKIVIFEPKEVTVYPDESEKPPVG 76 (141)
T ss_dssp TEEEES-HHHHHHSSCTT-CCSBESEEEEETTTEEEEESSEBE-TTSB---CGCTBTTTEEEETTEEEESSSSSS--STT
T ss_pred CceEcCCHHHHHhcCHHh-hCccCCeEEEeccEEEEEECCceeccccc---chhccCCEEEEecCEEEEECCCCCCCCCC
Confidence 799999999999999999 99999999999999999999999999999 88 99999999999999999999999
Q ss_pred CCCCcceEEEecccccCCCCCcccccchhhhhhhhHHHHHHHHhhcCCCEEEEEeCCCCEEEEEeCce
Q psy17507 626 TALNRPAKVTLLKVWPKDKSTGELIKDVQKIKNMNYEAIVIRACTRMNVEFVSYQPETGSWCFKVQHF 693 (1121)
Q Consensus 626 ~GLN~~A~ItL~~~~p~dk~t~~~i~d~~~~~~~~~~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~HF 693 (1121)
+||||||+|||+||||++|.++++|+||+++. |+++|+|+|+++|++||+||++||+|+|+|+||
T Consensus 77 ~GLN~~A~ItL~~~~p~~~~~~~~i~d~~~~~---~~~~l~~~~~~~~~~FvsYd~~tG~W~F~V~HF 141 (141)
T PF04096_consen 77 EGLNVPAIITLENCWPKDKSTREPIKDPSKPR---FEKKLKRLTEKMGAEFVSYDPETGTWVFRVEHF 141 (141)
T ss_dssp STTCS-EEEEESS---BBTTTTCB--STTCHH---HHHHHHHHHHCTTSEEEEEETTTTEEEEEESS-
T ss_pred CCcCCCEEEEEEeeEecCCCCCccccCccHHH---HHHHHHHHHhcCCCEEEEEeCCCcEEEEEEecC
Confidence 99999999999999999999999999999864 899999999999999999999999999999999
No 2
>PF12110 Nup96: Nuclear protein 96; InterPro: IPR021967 Nup96 (often known by the name of its yeast homologue Nup145C) is part of the Nup84 heptameric complex in the nuclear pore complex. Nup96 complexes with Sec13 in the middle of the heptamer. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96 is predicted to be an alpha helical solenoid. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex [], [].; PDB: 3BG1_C 3BG0_F 3IKO_B.
Probab=99.85 E-value=6.6e-22 Score=221.90 Aligned_cols=96 Identities=33% Similarity=0.521 Sum_probs=82.2
Q ss_pred ChHHHHHHHHcccCHHHHHHHHHHcCCceeehhhhhhcCChHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccc
Q psy17507 1026 DPEQNIFQLVTQHKLHEAIVSAQQSDNFYLSGALSMLGCSEIGQAFMQAQLSHYVNATSDSFINKDILKLMLLTSGQPLY 1105 (1121)
Q Consensus 1026 ~~~e~If~lLs~~~I~eA~~lA~~~~d~~LA~LlsQi~~~~~vR~l~~~QL~~W~~~~~d~~I~~~~lkIY~LLAG~~~~ 1105 (1121)
+++|+||.|||+|||++||++|+++||+|||+||+|+++|+.+|.+|++||+.|++.++|++|+++++|||+||||++.+
T Consensus 1 ~~le~if~~L~~~~i~~A~~~A~~~~n~~LA~Llsq~~~~~~~r~~~~~QL~~W~~~~~~~~I~~~~~~iY~LLAG~~~~ 80 (290)
T PF12110_consen 1 SPLEKIFLLLSGHDIEEACELAIDSGNPHLATLLSQIGGDPAVRSLAKQQLEDWRESGADSFIDEPRRKIYELLAGNVFW 80 (290)
T ss_dssp -HHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHTS--HHHHHHHHHHHHHTTSSSS--SS-HHHHHHHHHHHS-SSS
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHCCCchHHHHHHHhcCCHHHHHHHHHHHHHHHhCCCCeecCHHHHHHHHHhcCCCcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccccccCCCCC
Q psy17507 1106 DGSNGIINVCESLDWK 1121 (1121)
Q Consensus 1106 ~~s~~~Inv~e~LdWk 1121 (1121)
......+++|++|||+
T Consensus 81 ~~~~~~~~~~~~LdW~ 96 (290)
T PF12110_consen 81 SSGNKGINICEGLDWK 96 (290)
T ss_dssp STT-SGGG-GGTS-HH
T ss_pred cccccccccCCCCCHH
Confidence 9888888999999996
No 3
>KOG0845|consensus
Probab=99.65 E-value=1.1e-13 Score=177.41 Aligned_cols=114 Identities=29% Similarity=0.385 Sum_probs=88.4
Q ss_pred ceEeeceeEEEEECccccccCCCccCccceEEEecceEEEccCCCCCCCCCCCCCcceEEEecccccCCCCCcccccchh
Q psy17507 575 FTIGHEEFGSICFLESIDISELNNVDLDSIVEFRFKEVVLYPDDANKPPVGTALNRPAKVTLLKVWPKDKSTGELIKDVQ 654 (1121)
Q Consensus 575 F~Igr~gyG~I~f~~pvDL~~~~~~~ld~iV~~~~k~v~VYpd~~~kPp~G~GLN~~A~ItL~~~~p~dk~t~~~i~d~~ 654 (1121)
.+..+..|+...|...+-+..+- .+.++.....++.+|.+......-| .+|+.|+++||.||+.+|.++++|+|..
T Consensus 790 ~~~~~~~~~~~~~~~~~e~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~d~~ 865 (903)
T KOG0845|consen 790 VNPGTSKFGETKSPGERELAPSK---VSTKKPFTSNAVKLSTTEPEYSNDG-PSNRDAGVTLEQVSNLDKSTKEEIRDLM 865 (903)
T ss_pred ccccceeecccccccceeccccc---cccccccccccccccccccccCCcc-ccccccceeeeeeeccccccchhhHHHH
Confidence 33344456666666666666655 5555555555555555544433333 9999999999999999999999999998
Q ss_pred hhhhhhHHHHHHHHhhcCCCEEEEEeCCCCEEEEEeCceeee
Q psy17507 655 KIKNMNYEAIVIRACTRMNVEFVSYQPETGSWCFKVQHFSKY 696 (1121)
Q Consensus 655 ~~~~~~~~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~HFs~y 696 (1121)
++. ++..+++.+ ++...|+.|+++++.|+|.++|++.|
T Consensus 866 ~~~---~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 903 (903)
T KOG0845|consen 866 KLE---TEFSIRSVV-RPSEGFAPFRAETGSWSFRLDSESSY 903 (903)
T ss_pred HHh---hccchhhhc-cccccccccccccceEEEeecccccC
Confidence 875 666888888 99999999999999999999999987
No 4
>KOG3091|consensus
Probab=98.50 E-value=1.6e-06 Score=101.01 Aligned_cols=8 Identities=13% Similarity=0.032 Sum_probs=4.7
Q ss_pred cCCCCCcc
Q psy17507 360 SLPYFSAP 367 (1121)
Q Consensus 360 ~~pyG~~p 367 (1121)
.+.+|..|
T Consensus 219 ~~~lg~~p 226 (508)
T KOG3091|consen 219 HSSLGGQP 226 (508)
T ss_pred hhhhcCCC
Confidence 44566666
No 5
>KOG3091|consensus
Probab=98.34 E-value=4.8e-06 Score=97.16 Aligned_cols=17 Identities=35% Similarity=0.522 Sum_probs=9.1
Q ss_pred cccCCCCCCCCCcCCCCCC
Q psy17507 202 GFGTNTATNNTSLFGQKPA 220 (1121)
Q Consensus 202 ~FG~~~~~~~~~lFG~~~~ 220 (1121)
+||.+.+ .+++||.+++
T Consensus 52 ~fG~~~~--g~~~fG~~~~ 68 (508)
T KOG3091|consen 52 LFGANQA--GGTGFGTAST 68 (508)
T ss_pred ccccccC--CCCCccCCCC
Confidence 4665332 4566666654
No 6
>KOG0845|consensus
Probab=98.21 E-value=0.0019 Score=84.07 Aligned_cols=163 Identities=17% Similarity=0.069 Sum_probs=126.5
Q ss_pred CCCCceecCCCeeecCCHHHHHhcccCCCCceeccceEeeceeEEEEECccccccCCCccCccceEEEecceEEEccCCC
Q psy17507 540 DTFDFKLTRKGYFVSPTLNELKQLKTKNGPCIVEGFTIGHEEFGSICFLESIDISELNNVDLDSIVEFRFKEVVLYPDDA 619 (1121)
Q Consensus 540 ~~~~~~l~~~~Y~~~Ps~~~L~~m~~~~gl~~V~~F~Igr~gyG~I~f~~pvDL~~~~~~~ld~iV~~~~k~v~VYpd~~ 619 (1121)
++.+.......++..|.+++......++.++.|...++..+.++.+.|..++-...+. +..++.+..+....|.++.
T Consensus 644 ~~~~~~~s~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 720 (903)
T KOG0845|consen 644 QPAGSVSSPTLPFDLPRISTTKGITSEDSLDNVSSTTILDKSKGPLSFKFFISPTNLL---LKAIVSIPSEILKTELDEP 720 (903)
T ss_pred CccccccccccccchhhhHHHHhhhcccccccccCcchhhccccccceecccCcccch---hhcccccchhccccccccc
Confidence 3444455556778888888887777777788999999999999999888755555555 7778889999999999999
Q ss_pred CCCCCCCCCCcceEEEecccccCCCCCcccccchhhhhhhhHHHHHHHHhhcCCCEEEEEeCCCCEEEEEeCceeeecCC
Q psy17507 620 NKPPVGTALNRPAKVTLLKVWPKDKSTGELIKDVQKIKNMNYEAIVIRACTRMNVEFVSYQPETGSWCFKVQHFSKYGLL 699 (1121)
Q Consensus 620 ~kPp~G~GLN~~A~ItL~~~~p~dk~t~~~i~d~~~~~~~~~~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~HFs~ygl~ 699 (1121)
..+...+++...+......+++....+...+.-+.......++.++....++.......++.....|...+.+.++|+..
T Consensus 721 ~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 (903)
T KOG0845|consen 721 TTPLPSEGLESVLSPDADSASPSLKNTISLIGKPSTESTSGLESTLEGISRPLEASTKILRISNKSLLGVNPGTSKFGET 800 (903)
T ss_pred ccccccccccccccccccccCcccccchhccccccceecccccccccccccccccccccccccccccccccccceeeccc
Confidence 99999999999999999999998887777666555444445555565555555566777888888888888999999888
Q ss_pred CCCccC
Q psy17507 700 ESDEEG 705 (1121)
Q Consensus 700 d~d~~~ 705 (1121)
..+.+.
T Consensus 801 ~~~~~~ 806 (903)
T KOG0845|consen 801 KSPGER 806 (903)
T ss_pred ccccce
Confidence 776554
No 7
>PF13634 Nucleoporin_FG: Nucleoporin FG repeat region
Probab=97.67 E-value=0.00025 Score=69.68 Aligned_cols=7 Identities=29% Similarity=0.591 Sum_probs=4.0
Q ss_pred CccccCC
Q psy17507 247 TSTLFNS 253 (1121)
Q Consensus 247 ~~~lFg~ 253 (1121)
+++|||+
T Consensus 86 ~~~lFG~ 92 (113)
T PF13634_consen 86 SGGLFGQ 92 (113)
T ss_pred CCcccCC
Confidence 4456665
No 8
>PF13634 Nucleoporin_FG: Nucleoporin FG repeat region
Probab=97.19 E-value=0.0016 Score=63.99 Aligned_cols=6 Identities=33% Similarity=0.678 Sum_probs=4.3
Q ss_pred CccccC
Q psy17507 247 TSTLFN 252 (1121)
Q Consensus 247 ~~~lFg 252 (1121)
.++|||
T Consensus 108 ~~~lFG 113 (113)
T PF13634_consen 108 SGGLFG 113 (113)
T ss_pred CCCCCC
Confidence 567886
No 9
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=90.57 E-value=0.21 Score=56.72 Aligned_cols=72 Identities=19% Similarity=0.146 Sum_probs=47.7
Q ss_pred HHHHHHcccCHHHHHHHHHHcCCceeehhhhhhcCChHHH----HHHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCcc
Q psy17507 1030 NIFQLVTQHKLHEAIVSAQQSDNFYLSGALSMLGCSEIGQ----AFMQAQLSHYVNATSDSFINKDILKLMLLTSGQPL 1104 (1121)
Q Consensus 1030 ~If~lLs~~~I~eA~~lA~~~~d~~LA~LlsQi~~~~~vR----~l~~~QL~~W~~~~~d~~I~~~~lkIY~LLAG~~~ 1104 (1121)
+|..+|..|++++|+++|++.+++-.|++|+..++.+..+ +.+++++. .......+...++-||.+++|+.-
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~~~wa~ALlLAs~~g~e~~~~v~~~y~~~~~~---~~~~~~~~~~~L~~l~~v~~g~~~ 76 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDNGLWAHALLLASSLGPELWKKVVQEYFRREFS---AGSPSSKITHLLRTLYQVFSGNSP 76 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHTS-HHHHHHHHHHHHH-----------THHHHHHHHHHHHHTTT-HH
T ss_pred CHHHHHhCCCHHHHHHHHHHCCChHHHHHHHHhcCHHHHHHHHHHHHHHhcc---CCCCcchhhHHHHHHHHHHcCCcH
Confidence 5788999999999999999999999999999987644433 33333331 111123455668889999999763
No 10
>KOG0307|consensus
Probab=80.44 E-value=1.6 Score=56.59 Aligned_cols=136 Identities=14% Similarity=0.107 Sum_probs=78.2
Q ss_pred chhhhhHHHhHhhhcCCCCCC-Cchhh--HHHHHHHHHHHHHHHH------HhccC-c-----cc-cCCChHHHHHHHHc
Q psy17507 973 DSYDAQVWKLCVALWGTLDAK-NNSHD--INMKRKDNLTEWLESV------MEENP-K-----SI-ASKDPEQNIFQLVT 1036 (1121)
Q Consensus 973 ~~~e~~VW~L~saLfd~~~~~-~~~~~--~~~~Rr~~LS~WL~~~------V~~~v-~-----~~-~~~~~~e~If~lLs 1036 (1121)
+++|+.+|.|..+||...... -.+++ ..-.=.+...+|-+.. +++.+ . .. ...+....|-..|.
T Consensus 420 ~e~ek~~W~lLk~~~e~~sr~K~~~~Lgy~k~~~e~~~~~~~~~~~d~~~~~~q~~~~~~~~~~~s~~~d~d~~Is~ali 499 (1049)
T KOG0307|consen 420 SEEEKLNWGLLKALLERDSRTKLLSLLGYVKDDLEADQDKNVESGTDTSIFSEQFVPEPKGSGNISLDSDIDGLISEALI 499 (1049)
T ss_pred hhHHHHHHHHHHHHhccchhhHHHHHhccCccchhhhhhhcccccccccccchhhcccCCCCcccCCCCcHHHHHHHHHH
Confidence 468999999999999864200 00000 0000112223331111 11111 1 12 24567788889999
Q ss_pred ccCHHHHHHHHHHcCCceeehhhhhhcCChHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCcccccc
Q psy17507 1037 QHKLHEAIVSAQQSDNFYLSGALSMLGCSEIGQAFMQAQLSHYVNATSDSFINKDILKLMLLTSGQPLYDGSNGIINVCE 1116 (1121)
Q Consensus 1037 ~~~I~eA~~lA~~~~d~~LA~LlsQi~~~~~vR~l~~~QL~~W~~~~~d~~I~~~~lkIY~LLAG~~~~~~s~~~Inv~e 1116 (1121)
.+++.+|++++++++-+-.|++|++.++-+ .++..+.- --++.+ ++..+-||+|..-+.. ..|+.|+
T Consensus 500 tgd~~~aV~~cl~~~~~a~AliiA~~gg~e-l~~~t~~~--Y~~k~~-----~k~s~li~a~v~~d~~-----~~ve~~~ 566 (1049)
T KOG0307|consen 500 TGDFKSAVELCLEANKMADALIIAHAGGTE-LLESTRDK--YLAKSN-----SKLSRLIYAMVNRDLD-----DYVETCE 566 (1049)
T ss_pred hccHHHHHHHHHhhhHHHHHHHHHhcCCHH-HHHHHHHH--HHHHhC-----ChHHHHHHHHHhhhHH-----HHHhhcc
Confidence 999999999999999999999999998755 33333322 112222 1234556666554332 2566676
Q ss_pred CCCCC
Q psy17507 1117 SLDWK 1121 (1121)
Q Consensus 1117 ~LdWk 1121 (1121)
--.||
T Consensus 567 ~k~Wk 571 (1049)
T KOG0307|consen 567 VKQWK 571 (1049)
T ss_pred hhhHH
Confidence 66664
No 11
>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human. Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.
Probab=57.27 E-value=12 Score=46.77 Aligned_cols=122 Identities=16% Similarity=0.222 Sum_probs=68.5
Q ss_pred hhhHHHhHhhhcCCCCCCCchhhHHHHHHHHHHHHHHHH-------HhccCc-c---ccC-CChHHHHHHHHcccCHHHH
Q psy17507 976 DAQVWKLCVALWGTLDAKNNSHDINMKRKDNLTEWLESV-------MEENPK-S---IAS-KDPEQNIFQLVTQHKLHEA 1043 (1121)
Q Consensus 976 e~~VW~L~saLfd~~~~~~~~~~~~~~Rr~~LS~WL~~~-------V~~~v~-~---~~~-~~~~e~If~lLs~~~I~eA 1043 (1121)
-..+|.||.+||-+.. +... =-+.|-+|+-+. ...++. . ... .++=+.|..+++.|++++|
T Consensus 95 ~~~iw~L~eil~~~~~--~~~~-----v~~~Ll~WvNr~~~~~~~~~~~~vl~~~~p~~~~p~FW~~v~~lvlrG~~~~a 167 (566)
T PF07575_consen 95 LEAIWHLCEILYVDSQ--PRGP-----VPEQLLDWVNRFHFPPSEELAEEVLSSEPPYEHDPDFWDYVQRLVLRGLFDQA 167 (566)
T ss_dssp HHHHHSSSTT-S-TTT--THHH-----HHHHHHHHHHTTS--SHHHHHTTSCSS-HSCSGSHHHHHHHHHHHHTT-HHHH
T ss_pred HHHHHHHHHhhccCcc--cCCc-----hHHHHHHHHHHhCCCCchhHHHHHhccCCCCccchhHHHHHHHHHHcCCHHHH
Confidence 4689999999997632 1111 145688999322 122231 1 111 3556789999999999999
Q ss_pred HHHHHHcCCce----------eehhhhhhc--C--ChHHHHHHHHHHHHHHhcC----------CCCCCCHHHHHHHHHh
Q psy17507 1044 IVSAQQSDNFY----------LSGALSMLG--C--SEIGQAFMQAQLSHYVNAT----------SDSFINKDILKLMLLT 1099 (1121)
Q Consensus 1044 ~~lA~~~~d~~----------LA~LlsQi~--~--~~~vR~l~~~QL~~W~~~~----------~d~~I~~~~lkIY~LL 1099 (1121)
+++.....+++ +..||..+- . +......+..|..+||+.= ..-.+.+.+..|+.||
T Consensus 168 ~~lL~~~s~~~~~~~~~~~~~~~~LL~~~P~~~~~~~~s~~~f~~~~~~W~~~~~~l~~~~~~~~~~~~~~~L~~l~~Il 247 (566)
T PF07575_consen 168 RQLLRLHSSYQSYSLQSAFEALIQLLSSMPRYRPNSGQSESEFSSQWREWKSECRRLRSSSLQDGPFEIRENLEDLLKIL 247 (566)
T ss_dssp HHHH-TTTTTTTHHHHHHHHHHHHHHTT------------SS-HHHHHHHHHHHHHHHHHS---S-HHHHHHHHHHHHHH
T ss_pred HHHHHhcccccchhHHHHHHHHHHHHHhCCCccccchhhhHHHHHHHHHHHHHHHHHHHHhhccCchhhHHHHHHHHHHH
Confidence 99986655543 222333321 0 1123366778888886421 1223677899999999
Q ss_pred cCCcc
Q psy17507 1100 SGQPL 1104 (1121)
Q Consensus 1100 AG~~~ 1104 (1121)
+|+.-
T Consensus 248 ~G~~~ 252 (566)
T PF07575_consen 248 LGDED 252 (566)
T ss_dssp HT-HH
T ss_pred CCCHH
Confidence 99764
No 12
>KOG1428|consensus
Probab=57.03 E-value=2.9 Score=55.08 Aligned_cols=26 Identities=8% Similarity=-0.188 Sum_probs=23.2
Q ss_pred ceeeeeeccccccccCccchhhhhcc
Q psy17507 8 ILQKCTFIVREAEMHVPLPLILQKYV 33 (1121)
Q Consensus 8 ~~~~~I~~m~~y~~~s~eELR~edY~ 33 (1121)
++|..|+.|+-|++||+||||+.--.
T Consensus 2065 aRYiaIt~M~vYeNYS~EElRf~~~~ 2090 (3738)
T KOG1428|consen 2065 ARYIAITMMKVYENYSFEELRFASPT 2090 (3738)
T ss_pred hhhhhhhhhhhhhcccHhhhcccCCC
Confidence 57899999999999999999997544
No 13
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=56.72 E-value=11 Score=48.27 Aligned_cols=85 Identities=15% Similarity=0.216 Sum_probs=52.8
Q ss_pred hHHHHHHHHcccCHHHHHHHHHHcCCceeehhhhhh--cCChH----------------HHHHHHHHHHHHHhcCCCCCC
Q psy17507 1027 PEQNIFQLVTQHKLHEAIVSAQQSDNFYLSGALSML--GCSEI----------------GQAFMQAQLSHYVNATSDSFI 1088 (1121)
Q Consensus 1027 ~~e~If~lLs~~~I~eA~~lA~~~~d~~LA~LlsQi--~~~~~----------------vR~l~~~QL~~W~~~~~d~~I 1088 (1121)
....||.+|-+|+++||.++|.+.|++=+|..|.=. -.|+. -|.+-++ ..|+-++ ...+
T Consensus 136 ~~~~i~~llR~G~~~eA~~lc~~~gq~wrAasL~G~~~~~dp~~~~~~~~~~~~~~G~~~r~LWk~--~c~~ls~-~~~~ 212 (697)
T PF04121_consen 136 LLKYIFELLRAGRIEEAQELCRERGQPWRAASLCGWQLYHDPNLDPELSDEDERMEGNRSRALWKR--ACYKLSQ-NPNL 212 (697)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHTTSB-B-TTTSGGGTTT-SS-BSBTTHHHHHH--HHHHHHH-TSSS
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHcCccccCCcccccccccccccccCChhHHHHHH--HHHHHHh-CCCC
Confidence 466799999999999999999999999888877621 11222 1222221 1222111 2578
Q ss_pred CHHHHHHHHHhcCCccccCCCCccccccCCCC
Q psy17507 1089 NKDILKLMLLTSGQPLYDGSNGIINVCESLDW 1120 (1121)
Q Consensus 1089 ~~~~lkIY~LLAG~~~~~~s~~~Inv~e~LdW 1120 (1121)
++.=+.||.+|||+.- ....+|. -+|
T Consensus 213 ~~yEraiY~~L~G~~~-----~~l~~~~-~sW 238 (697)
T PF04121_consen 213 DPYERAIYGALSGDLS-----SVLPVCS-SSW 238 (697)
T ss_dssp -HHHHHHHHHHHTS--------HHHHTT--SH
T ss_pred CHHHHHHHHHHhcccH-----hhhhhcc-CCH
Confidence 8999999999999776 3566663 255
No 14
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=50.79 E-value=23 Score=31.74 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=27.3
Q ss_pred HHHHHHHHhhcCCCEEEEEeCCCCEEEEEeC
Q psy17507 661 YEAIVIRACTRMNVEFVSYQPETGSWCFKVQ 691 (1121)
Q Consensus 661 ~~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~ 691 (1121)
..+-|.++|++.|.++++++...|.|.|.++
T Consensus 38 a~~di~~~~~~~G~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03420 38 FARDAQAWCKSTGNTLISLETEKGKVKAVIE 68 (69)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 3467899999999999999999999999874
No 15
>PRK11018 hypothetical protein; Provisional
Probab=49.77 E-value=24 Score=32.47 Aligned_cols=31 Identities=6% Similarity=0.022 Sum_probs=26.9
Q ss_pred HHHHHHHhhcCCCEEEEEeCCCCEEEEEeCc
Q psy17507 662 EAIVIRACTRMNVEFVSYQPETGSWCFKVQH 692 (1121)
Q Consensus 662 ~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~H 692 (1121)
.+.|.++|++.|-++++++.+.|.|.|.|..
T Consensus 48 ~~di~~~~~~~G~~v~~~~~~~g~~~~~I~k 78 (78)
T PRK11018 48 INNIPLDARNHGYTVLDIQQDGPTIRYLIQK 78 (78)
T ss_pred HHHHHHHHHHcCCEEEEEEecCCeEEEEEEC
Confidence 4578888999999999999889999999863
No 16
>PF12234 Rav1p_C: RAVE protein 1 C terminal; InterPro: IPR022033 This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C-terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Probab=45.52 E-value=29 Score=44.01 Aligned_cols=55 Identities=13% Similarity=0.115 Sum_probs=43.7
Q ss_pred ccCCChHHHHHHHHcccCHHHHHHHHH-HcCCceeehhhhhhc---CChHHHHHHHHHH
Q psy17507 1022 IASKDPEQNIFQLVTQHKLHEAIVSAQ-QSDNFYLSGALSMLG---CSEIGQAFMQAQL 1076 (1121)
Q Consensus 1022 ~~~~~~~e~If~lLs~~~I~eA~~lA~-~~~d~~LA~LlsQi~---~~~~vR~l~~~QL 1076 (1121)
..++.+..++--.|.++++.+||+++. .-+|+.||++|+-+- .++..++++++.+
T Consensus 463 lsk~Ry~~AAaFFLLag~l~dAv~V~~~~l~D~qLAi~i~Rl~e~d~gp~~~~ll~~~v 521 (631)
T PF12234_consen 463 LSKHRYEYAAAFFLLAGSLKDAVNVCLRQLNDPQLAIAIARLYEGDNGPVLKKLLEEHV 521 (631)
T ss_pred HhcccHHHHHHHHHhcccHHHHHHHHHHHccChhHHHHHHHHHcCCCchHHHHHHHHhh
Confidence 456778877777777888999998655 559999999999973 2678888888774
No 17
>KOG1964|consensus
Probab=37.18 E-value=56 Score=41.53 Aligned_cols=75 Identities=15% Similarity=0.038 Sum_probs=53.9
Q ss_pred hHHHHHHHHcccCHHHHHHHHHHcCCceeehhhhhhc--CCh--------------HHHHHHHHHHHHHHhcCCCCCCCH
Q psy17507 1027 PEQNIFQLVTQHKLHEAIVSAQQSDNFYLSGALSMLG--CSE--------------IGQAFMQAQLSHYVNATSDSFINK 1090 (1121)
Q Consensus 1027 ~~e~If~lLs~~~I~eA~~lA~~~~d~~LA~LlsQi~--~~~--------------~vR~l~~~QL~~W~~~~~d~~I~~ 1090 (1121)
....||.|+-+|.++||.++|+..|+.--|..|--+. .|| .-|.+-+ -..|+-.+ .+.+++
T Consensus 223 ~~k~~F~LIRaG~~deal~Lck~~G~~wr~A~LqG~~~y~dPnl~i~~E~~~~eGn~~k~lwr--rs~~~ltq-~k~~d~ 299 (800)
T KOG1964|consen 223 FFKYIFELIRAGETDEALELCKRLGNGWRAAILQGISEYRDPNLDIPLEASPQEGNKYKRLWR--RSCYQLTQ-EKSQDS 299 (800)
T ss_pred HHHHHHHHHHccchHHHHHHHHHhCcHHHHHHHHHHHHhhCCCccchhhhCcccCCcHHHHHH--HHHHHHHH-hhccCh
Confidence 3567999999999999999999999987666554332 344 1122322 23444444 578999
Q ss_pred HHHHHHHHhcCCcc
Q psy17507 1091 DILKLMLLTSGQPL 1104 (1121)
Q Consensus 1091 ~~lkIY~LLAG~~~ 1104 (1121)
.-|+||.+|+|+.-
T Consensus 300 YeRA~y~~lSG~l~ 313 (800)
T KOG1964|consen 300 YERAIYGALSGILG 313 (800)
T ss_pred HHHHHHHHHhcccc
Confidence 99999999999764
No 18
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=34.29 E-value=58 Score=30.21 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=27.2
Q ss_pred HHHHHHHHhhcCCCEEEEEeCCCCEEEEEeC
Q psy17507 661 YEAIVIRACTRMNVEFVSYQPETGSWCFKVQ 691 (1121)
Q Consensus 661 ~~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~ 691 (1121)
..+-|.++|+..|.++++.+.+.|.|+|.|.
T Consensus 48 ~~~di~~~~~~~G~~~~~~~~~~g~~~~~I~ 78 (81)
T PRK00299 48 TTRDIPSFCRFMDHELLAQETEQLPYRYLIR 78 (81)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 4567889999999999999989999999875
No 19
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=33.73 E-value=62 Score=28.97 Aligned_cols=30 Identities=3% Similarity=-0.004 Sum_probs=26.2
Q ss_pred HHHHHHHhhcCCCEEEEEeCCCCEEEEEeC
Q psy17507 662 EAIVIRACTRMNVEFVSYQPETGSWCFKVQ 691 (1121)
Q Consensus 662 ~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~ 691 (1121)
.+-|.++|+..|.+++..+.+.|.|+|.|.
T Consensus 39 ~~ni~~~~~~~g~~v~~~~~~~~~~~~~i~ 68 (69)
T cd03422 39 INNIPIDARNHGYKVLAIEQSGPTIRYLIQ 68 (69)
T ss_pred HHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 457889999999999998888899999875
No 20
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=33.70 E-value=59 Score=29.05 Aligned_cols=30 Identities=13% Similarity=0.331 Sum_probs=26.0
Q ss_pred HHHHHHHhhcCCCEEEEEeCCCCEEEEEeC
Q psy17507 662 EAIVIRACTRMNVEFVSYQPETGSWCFKVQ 691 (1121)
Q Consensus 662 ~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~ 691 (1121)
.+-|.++|+++|-++++.+.+.|.|.|.|.
T Consensus 39 ~~di~~~~~~~g~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03423 39 TRDIPKFCTFLGHELLAQETEDEPYRYLIR 68 (69)
T ss_pred HHHHHHHHHHcCCEEEEEEEcCCEEEEEEE
Confidence 456888899999999998878999999874
No 21
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=27.10 E-value=91 Score=27.24 Aligned_cols=31 Identities=10% Similarity=0.102 Sum_probs=26.0
Q ss_pred HHHHHHHhhcCCCEEEEEeCCCCEEEEEeCc
Q psy17507 662 EAIVIRACTRMNVEFVSYQPETGSWCFKVQH 692 (1121)
Q Consensus 662 ~~~l~~~~~~~~~~Fv~Yd~~tG~W~F~V~H 692 (1121)
.+-|.++++.+|.++++.+.+.|.|++.|++
T Consensus 39 ~~~i~~~~~~~g~~~~~~~~~~~~~~i~i~k 69 (69)
T cd00291 39 VEDIPAWAKETGHEVLEVEEEGGVYRILIRK 69 (69)
T ss_pred HHHHHHHHHHcCCEEEEEEEeCCEEEEEEEC
Confidence 3467788888999999999888999998753
Done!