Query 002180
Match_columns 955
No_of_seqs 166 out of 371
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 18:20:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12110 Nup96: Nuclear protei 100.0 5.1E-68 1.1E-72 583.9 19.3 280 572-861 1-290 (290)
2 PF04096 Nucleoporin2: Nucleop 100.0 4.7E-46 1E-50 364.1 14.6 131 48-184 1-141 (141)
3 PF07575 Nucleopor_Nup85: Nup8 98.1 9.9E-06 2.2E-10 98.3 11.2 317 571-933 149-508 (566)
4 PF12931 Sec16_C: Sec23-bindin 93.3 0.067 1.5E-06 59.5 3.5 98 576-677 1-116 (284)
5 PF04121 Nup84_Nup100: Nuclear 92.0 0.36 7.9E-06 60.4 8.0 95 573-668 136-245 (697)
6 KOG0845 Nuclear pore complex, 91.2 0.17 3.6E-06 65.4 3.9 109 74-187 789-903 (903)
7 KOG1964 Nuclear pore complex, 79.0 1.8E+02 0.0039 36.3 22.4 223 574-808 224-477 (800)
8 PF04097 Nic96: Nup93/Nic96; 57.9 2.2E+02 0.0048 35.4 15.7 148 759-907 291-481 (613)
9 KOG2168 Cullins [Cell cycle co 53.5 2.5E+02 0.0054 35.8 14.7 294 574-908 329-687 (835)
10 cd03420 SirA_RHOD_Pry_redox Si 49.9 27 0.00059 30.1 4.4 31 152-182 38-68 (69)
11 PRK11018 hypothetical protein; 49.7 28 0.00061 31.0 4.5 31 152-182 47-77 (78)
12 KOG0307 Vesicle coat complex C 39.5 1E+02 0.0022 40.0 8.6 94 571-673 488-582 (1049)
13 cd03422 YedF YedF is a bacteri 35.7 62 0.0014 27.9 4.4 31 152-182 38-68 (69)
14 cd03423 SirA SirA (also known 34.7 63 0.0014 27.8 4.3 31 152-182 38-68 (69)
15 PRK00299 sulfur transfer prote 33.8 67 0.0015 28.7 4.5 32 151-182 47-78 (81)
16 PF08796 DUF1797: Protein of u 26.0 1.2E+02 0.0025 26.5 4.3 29 153-181 2-44 (67)
17 KOG3616 Selective LIM binding 24.8 2E+02 0.0043 35.9 7.3 104 785-893 1162-1271(1636)
18 PF13838 Clathrin_H_link: Clat 23.7 1.9E+02 0.004 25.2 5.1 39 863-904 9-47 (66)
19 cd00291 SirA_YedF_YeeD SirA, Y 23.3 1.4E+02 0.0029 25.3 4.4 30 153-182 39-68 (69)
20 KOG1920 IkappaB kinase complex 23.1 4.8E+02 0.01 34.6 10.6 99 779-886 940-1052(1265)
No 1
>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=100.00 E-value=5.1e-68 Score=583.92 Aligned_cols=280 Identities=39% Similarity=0.672 Sum_probs=213.2
Q ss_pred cHHHHHHHHHhcCCHHHHHHHHHHcCCCchhhhhhhcCCCchhHHHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCcc
Q 002180 572 NYLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSRSDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHIH 651 (955)
Q Consensus 572 ~~~e~if~lL~g~~V~~Ac~~Ai~s~n~rLAtLlsq~gs~~~~r~~l~~QL~~W~~~~~d~~~i~~~~~kIY~LLAG~~~ 651 (955)
+|+++||.|||||||++||++|+++||+|||+||||+|+++.+|.++++||+.|+++|++ .+|++.++|||+||||+++
T Consensus 1 ~~le~if~~L~~~~i~~A~~~A~~~~n~~LA~Llsq~~~~~~~r~~~~~QL~~W~~~~~~-~~I~~~~~~iY~LLAG~~~ 79 (290)
T PF12110_consen 1 SPLEKIFLLLSGHDIEEACELAIDSGNPHLATLLSQIGGDPAVRSLAKQQLEDWRESGAD-SFIDEPRRKIYELLAGNVF 79 (290)
T ss_dssp -HHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHTS--HHHHHHHHHHHHHTTSSSS---SS-HHHHHHHHHHHS-SS
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHCCCchHHHHHHHhcCCHHHHHHHHHHHHHHHhCCCC-eecCHHHHHHHHHhcCCCc
Confidence 479999999999999999999999999999999999998999999999999999999997 6999999999999999998
Q ss_pred cccCC------CCCCHHHHHHHHhhccCCCCCCHHHHHHHHHHHhcCCCCCCCCCccccCCCCCCCCCCCCCCCCChhHH
Q 002180 652 SSLND------VTIDWKRFLGLLMWYQLPPETSLAIVFQTYQHLLDDGKAPLPVPIYVDEGPIDEPIDWSGNERNDLSYY 725 (955)
Q Consensus 652 ~~~~~------~~LdW~rafgL~LWYg~~~~~~i~~ai~~y~~~~~~~~~~~P~P~y~~~~~~~~~~~~~~~~~~D~~~~ 725 (955)
..... ++|||+|+||||||||++++.+|+++|+.|++++.++++++|.|+|+++... .......+.+|++|+
T Consensus 80 ~~~~~~~~~~~~~LdW~~~lgl~lwY~~~~~~sl~~~v~~y~~~~~~~~~~~P~P~y~~~~~~--~~~~~~~~~~D~~~~ 157 (290)
T PF12110_consen 80 WSSGNKGINICEGLDWKRALGLHLWYGDPPDASLEDAVQSYEEAFSKGEAAPPLPPYAERNSS--WDDSNSEPREDLLYH 157 (290)
T ss_dssp SSTT-SGGG-GGTS-HHHHHHHHHHTTTTSSS-HHHHHHHHHHHS----------------------------TT-HHHH
T ss_pred ccccccccccCCCCCHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhhhccchhhhhhhcccc--cccccCCCCcCHHHH
Confidence 66432 4699999999999999999999999999999999999999999999987751 111235578999999
Q ss_pred HHhhcccCCCcccchhhhhcccCCCCCCCCcchhHHHHHHHHhcCCCCC--chhhHHHHHHHHHHHhCCCchhHHHHHhc
Q 002180 726 LMLLHASGESKFGSLKTMFNALSSTYDPLDYHMIWHQREVLAAVGVISS--NDLQILDMGLVSQLLCQGKCHWAIYVVLH 803 (955)
Q Consensus 726 LLkL~~~~~~~~~~l~~~l~p~~~s~~~lD~rLsW~l~~iL~a~g~~~~--~~~~~Lt~~fA~QLe~~glw~wAifVllH 803 (955)
|||||++++. +++.+|.|.+++++++||||+|||+++|+++|+... ...++||++||+|||+.|+|+|||||+||
T Consensus 158 LLkly~~~~~---~l~~~L~p~~~s~~~lD~~l~W~l~~~L~~~~~~~~~~~~~d~lt~~fa~QLe~~glw~~AlfVllh 234 (290)
T PF12110_consen 158 LLKLYADRSH---SLEQVLNPLSSSPSPLDYRLSWHLYQVLRALGYRHDSEDRADQLTLSFASQLESLGLWEWALFVLLH 234 (290)
T ss_dssp HHHHH-HSGT---THHHHHHHHHTT-SSS-HHHHHHHHHHHHTTSSS---HHHHHHHHHHHHHHHHHTT-HHHHHHHHHT
T ss_pred HHHhhcCCCC---CHHHHhChhccCCCccCChhHhHHHHHHHHcCCCccCccHHHHHHHHHHHHHHhCCccHHHHHHHhc
Confidence 9999988764 799999999999999999999999999999998654 35689999999999999999999999999
Q ss_pred ccCCCCchHHHHHHHHHHHHhhcccCCChh-HHHHHHH-HhCCCHHHHHHHHHHHHHhcC
Q 002180 804 MPRCDDYPYLQATLIREILFQYCESWSSEE-SQRKFIE-ALGVPSEWLHEAMAVYYNYYG 861 (955)
Q Consensus 804 l~d~~~~~~~R~~~vr~lL~r~~~~~~~~~-~~~~fL~-~L~IP~~WI~eAkAl~a~~~~ 861 (955)
|+|+. .|+.+||++|.||+..+.+++ ..+.||. +|+||++|||||||++|||+|
T Consensus 235 l~d~~----~r~~~ir~ll~r~~~~~~~~~~~~~~~l~~~L~IP~~wI~eA~Al~a~y~g 290 (290)
T PF12110_consen 235 LSDDS----SREQAIRELLARHIPELSSDDDEKEKFLLEKLKIPESWIHEAKALYARYEG 290 (290)
T ss_dssp -S-HH----HHHHHHHHHHHHCTGGGST---TTTSHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred CCCHH----HHHHHHHHHHHHhcccccccchhhHHHHHHHcCcCHHHHHHHHHHHHHccC
Confidence 98754 499999999999998876542 2345655 999999999999999999986
No 2
>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=4.7e-46 Score=364.14 Aligned_cols=131 Identities=47% Similarity=0.758 Sum_probs=115.3
Q ss_pred CeeecCCHHHHhccccCCCCCccccCCcEEeccceEEEEeccccccCCCCcc----ceEEEeccEEEEecCCCCCCCCCC
Q 002180 48 DYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLD----QIVKFGRHEIVVYEDESSKPEVGQ 123 (955)
Q Consensus 48 ~Y~~~Ps~~~L~~~~~~~~~~l~~v~~f~vgr~g~G~i~f~~~vdl~~~~ld----~iV~~~~~~v~vYp~~~~kPp~G~ 123 (955)
||||+||+++|++|+..+ |++|+||+|||+|||+|+|++||||+++||| +||.|++++|+||||+..|||+|+
T Consensus 1 ~Y~~~Psl~eL~~m~~~~---l~~V~~F~Vgr~g~G~I~f~~pVDl~~ldld~~~~~iV~~~~~~v~VYpd~~~kPp~G~ 77 (141)
T PF04096_consen 1 GYWTSPSLEELQKMSDEE---LKRVENFTVGREGYGSIEFLGPVDLSGLDLDDIFGKIVIFEPKEVTVYPDESEKPPVGE 77 (141)
T ss_dssp TEEEES-HHHHHHSSCTT---CCSBESEEEEETTTEEEEESSEBE-TTSBCGCTBTTTEEEETTEEEESSSSSS--STTS
T ss_pred CceEcCCHHHHHhcCHHh---hCccCCeEEEeccEEEEEECCceecccccchhccCCEEEEecCEEEEECCCCCCCCCCC
Confidence 799999999999999766 9999999999999999999999999999999 999999999999999999999999
Q ss_pred CCcccEEEEEecccccccCCCCCCCh------HHHHHHHHHHhhhcCCEEEEEecCCcEEEEEECCc
Q 002180 124 GLNKAAEVTLFLQGRYLSLKLKEGDS------DDFVKKMKERTERQGARFVSFDPVSGEWKFLVVHF 184 (955)
Q Consensus 124 gLN~~a~itl~~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~HF 184 (955)
||||||+|||+ + |||.++.+++. .+|.++|+++|+++|++||+||++||+|+|+|+||
T Consensus 78 GLN~~A~ItL~-~--~~p~~~~~~~~i~d~~~~~~~~~l~~~~~~~~~~FvsYd~~tG~W~F~V~HF 141 (141)
T PF04096_consen 78 GLNVPAIITLE-N--CWPKDKSTREPIKDPSKPRFEKKLKRLTEKMGAEFVSYDPETGTWVFRVEHF 141 (141)
T ss_dssp TTCS-EEEEES-S-----BBTTTTCB--STTCHHHHHHHHHHHHCTTSEEEEEETTTTEEEEEESS-
T ss_pred CcCCCEEEEEE-e--eEecCCCCCccccCccHHHHHHHHHHHHhcCCCEEEEEeCCCcEEEEEEecC
Confidence 99999999994 4 55588887652 35999999999999999999999999999999999
No 3
>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=98.13 E-value=9.9e-06 Score=98.30 Aligned_cols=317 Identities=18% Similarity=0.185 Sum_probs=144.2
Q ss_pred ccHHHHHHHHHhcCCHHHHHHHHHHcCCCc----------hhhhhhhcCCC----chhHHHHHHHHHHHHHcCC------
Q 002180 571 SNYLKHIFLLLTGRQLDSSVELAASRGDVR----------LACLLSQAGGS----TVSRSDIAHQLDLWRVNGL------ 630 (955)
Q Consensus 571 ~~~~e~if~lL~g~~V~~Ac~~Ai~s~n~r----------LAtLlsq~gs~----~~~r~~l~~QL~~W~~~~~------ 630 (955)
..+-..|..++..|+++.|+++....++++ +..||..+..- .....+...|...|+..-.
T Consensus 149 p~FW~~v~~lvlrG~~~~a~~lL~~~s~~~~~~~~~~~~~~~~LL~~~P~~~~~~~~s~~~f~~~~~~W~~~~~~l~~~~ 228 (566)
T PF07575_consen 149 PDFWDYVQRLVLRGLFDQARQLLRLHSSYQSYSLQSAFEALIQLLSSMPRYRPNSGQSESEFSSQWREWKSECRRLRSSS 228 (566)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHH-TTTTTTTHHHHHHHHHHHHHHTT------------SS-HHHHHHHHHHHHHHHHHS
T ss_pred hhHHHHHHHHHHcCCHHHHHHHHHhcccccchhHHHHHHHHHHHHHhCCCccccchhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 456778999999999999999996666644 34555555421 1123456667777763211
Q ss_pred --Cc-ccChHHHHHHHHHhhCCcccccCCCCCCHHHHHHHHhhccCCCC--CC-HHHHHHHHHHHhcCCCCCCCCCcccc
Q 002180 631 --DF-KFIEKDRIRLYELLAGHIHSSLNDVTIDWKRFLGLLMWYQLPPE--TS-LAIVFQTYQHLLDDGKAPLPVPIYVD 704 (955)
Q Consensus 631 --d~-~~i~~~~~kIY~LLAG~~~~~~~~~~LdW~rafgL~LWYg~~~~--~~-i~~ai~~y~~~~~~~~~~~P~P~y~~ 704 (955)
+. --+.+...-|+++|+|+.....+. .=+|..+++-++-|-.|.. .. +.+..+.-.+.+ |. +
T Consensus 229 ~~~~~~~~~~~L~~l~~Il~G~~~~i~~~-~~~WyE~~~a~~ly~~P~~~~~e~l~~~a~~~~~~~-------~~----~ 296 (566)
T PF07575_consen 229 LQDGPFEIRENLEDLLKILLGDEDTILEY-SQDWYEALVALLLYVDPTCKPFELLHEYAQSCLEEF-------PP----D 296 (566)
T ss_dssp ---S-HHHHHHHHHHHHHHHT-HHHHHHT--SSHHHHHHHHHHHT------TTTHHHHHHHHHHHS--------------
T ss_pred hccCchhhHHHHHHHHHHHCCCHHHHHHH-hCcHHHHHHHhheeeCCCcchhhhHHHHHHHHHhcC-------CC----C
Confidence 11 125677789999999997543332 2289999999998877642 22 333333322221 10 0
Q ss_pred CCCCCCCCCCCCCCCCChhHHHHhhcccCCCcccchhhhhcccCCCCCCC--CcchhHHHHHHHHhcCCCCC--------
Q 002180 705 EGPIDEPIDWSGNERNDLSYYLMLLHASGESKFGSLKTMFNALSSTYDPL--DYHMIWHQREVLAAVGVISS-------- 774 (955)
Q Consensus 705 ~~~~~~~~~~~~~~~~D~~~~LLkL~~~~~~~~~~l~~~l~p~~~s~~~l--D~rLsW~l~~iL~a~g~~~~-------- 774 (955)
...+...++..+|. .... ..++.+ ..+ |..++=|+..+|...|.+..
T Consensus 297 ----------~~~~~e~~~~~i~~---~d~~--~vL~~~--------~~~~~~~w~aahladLl~~~g~L~~~~~~~~~~ 353 (566)
T PF07575_consen 297 ----------STNPLEQILLAIFE---GDIE--SVLKEI--------SSLFDDWWFAAHLADLLEHKGLLEDSEQEDFGG 353 (566)
T ss_dssp ----------TTSTTHHHHHHHHT---S--G--GGHHHH--------HHH--HHHHHHHHHHHHHHTTSS--SS-----T
T ss_pred ----------CCCHHHHHHHHHHc---cCHH--HHHHHH--------HHHccchhHHHHHHHHHHhcCcccccccccccc
Confidence 01123344555553 2111 122222 112 44566677788877787651
Q ss_pred -chhhHHHHHHHHHHHhC-CCchhHHHHHhcccCCCCchHHHHHHHHHHHHhhcccCCChhHHHHHH---HHhCCCHH--
Q 002180 775 -NDLQILDMGLVSQLLCQ-GKCHWAIYVVLHMPRCDDYPYLQATLIREILFQYCESWSSEESQRKFI---EALGVPSE-- 847 (955)
Q Consensus 775 -~~~~~Lt~~fA~QLe~~-glw~wAifVllHl~d~~~~~~~R~~~vr~lL~r~~~~~~~~~~~~~fL---~~L~IP~~-- 847 (955)
...+-+-+.||..|-+. ++|+-|+=+|.+.++.. ..++.++|.|. +.- +++.-...| .+++.+..
T Consensus 354 ~~lre~~ll~YA~~L~s~~~lW~vai~yL~~c~~~g------~~~i~~lL~~~-p~~-t~~~~~k~l~iC~~~~L~~~a~ 425 (566)
T PF07575_consen 354 SSLREYLLLEYASSLMSHHSLWQVAIGYLSSCPDEG------RERIEELLPRV-PLD-TNDDAEKLLEICAELGLEDVAR 425 (566)
T ss_dssp S-HHHHHHHHHHHHHHT-TTTHHHHHHHHHS-SSS-------HHHHHHHGGG------SHHHHHHHHHHHHHHT-HHHHH
T ss_pred ccHHHHHHHHHHHHHhcCcchHHHHHHHHHHCChhh------HHHHHHHHhhC-CCC-chHHHHHHHHHHHHCCCHHHHH
Confidence 12345778999999765 99999999999987532 46667777643 322 222222333 38888764
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHhCcCHHHHHHHHHHhhccchhccCChHHHHHHHHhhccccCccccccchhhHHHHH
Q 002180 848 WLHEAMAVYYNYYGELSKALEHFLECANWQKAHSIFVTSVAHTLFLSANHSDVWTLATSMESHKSEIENWDLGAGMYIVF 927 (955)
Q Consensus 848 WI~eAkAl~a~~~~d~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II~~d~~~L~~Ll~~~~~~~~~I~~W~~GG~Vy~dY 927 (955)
=|++-.|.++..+|++..++.++++||++...+++.=.-+ -+.+.++. ....+++..+.+.. .++.==.+.+.|-+|
T Consensus 426 ~I~~~~~~~~~~~~~~g~AL~~~~ra~d~~~v~~i~~~ll-~~~~~~~~-~~~~~ll~~i~~~~-~~~~~L~fla~yreF 502 (566)
T PF07575_consen 426 EICKILGQRLLKEGRYGEALSWFIRAGDYSLVTRIADRLL-EEYCNNGE-PLDDDLLDNIGSPM-LLSQRLSFLAKYREF 502 (566)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------------------------
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHH-HHHhcCCC-cccHHHHHHhcchh-hhhhhhHHHHHHHHH
Confidence 4555557777789999999999999999988777654333 22222222 22334444443321 222223356678888
Q ss_pred HHHHhh
Q 002180 928 YLIRSS 933 (955)
Q Consensus 928 l~l~~~ 933 (955)
.++...
T Consensus 503 ~~~~~~ 508 (566)
T PF07575_consen 503 YELYDE 508 (566)
T ss_dssp ------
T ss_pred HHHHhh
Confidence 776433
No 4
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=93.27 E-value=0.067 Score=59.51 Aligned_cols=98 Identities=19% Similarity=0.294 Sum_probs=60.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHcCCCchhhhhhhcCCCchhH----HHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCcc
Q 002180 576 HIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSR----SDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHIH 651 (955)
Q Consensus 576 ~if~lL~g~~V~~Ac~~Ai~s~n~rLAtLlsq~gs~~~~r----~~l~~QL~~W~~~~~d~~~i~~~~~kIY~LLAG~~~ 651 (955)
+|..+|..|+.++|++.|++.|+.-.|+||+..++.+..+ +.+++++. ..... ..+.....-+|++++|+..
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---AGSPS-SKITHLLRTLYQVFSGNSP 76 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHTS-HHHHHHHHHHHHH-----------T-HHHHHHHHHHHHHTTT-HH
T ss_pred CHHHHHhCCCHHHHHHHHHHCCChHHHHHHHHhcCHHHHHHHHHHHHHHhcc---CCCCc-chhhHHHHHHHHHHcCCcH
Confidence 4678899999999999999999999999999988865433 23333331 11101 1233445579999999974
Q ss_pred cccCC---C-----------CCCHHHHHHHHhhccCCCCC
Q 002180 652 SSLND---V-----------TIDWKRFLGLLMWYQLPPET 677 (955)
Q Consensus 652 ~~~~~---~-----------~LdW~rafgL~LWYg~~~~~ 677 (955)
..+.. . --+|+..+++-|=|..+.+.
T Consensus 77 ~~v~~l~~~~~~~~~~~~~~~~~Wre~lA~il~N~~~~~~ 116 (284)
T PF12931_consen 77 EAVDELVPNSAAPPLEGEWDLDNWRETLAIILSNRTPEDS 116 (284)
T ss_dssp HHHHHHHH-----HHHHHHHHHSHHHHHHHHHHTS---SS
T ss_pred HHHHHhccccccccccccchhcCHHHHHHHHHhCCCcccH
Confidence 33210 0 01699999999999876543
No 5
>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=91.98 E-value=0.36 Score=60.43 Aligned_cols=95 Identities=22% Similarity=0.350 Sum_probs=53.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHcCCCchhhhhhhcC--CCchhHHHHH---------HHHHHHHHcCC----CcccChH
Q 002180 573 YLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAG--GSTVSRSDIA---------HQLDLWRVNGL----DFKFIEK 637 (955)
Q Consensus 573 ~~e~if~lL~g~~V~~Ac~~Ai~s~n~rLAtLlsq~g--s~~~~r~~l~---------~QL~~W~~~~~----d~~~i~~ 637 (955)
-+..||.+|-+|++++|.++|.+.|++=+|..|.=.. .++..-..+. .--..|+..-. . .-+++
T Consensus 136 ~~~~i~~llR~G~~~eA~~lc~~~gq~wrAasL~G~~~~~dp~~~~~~~~~~~~~~G~~~r~LWk~~c~~ls~~-~~~~~ 214 (697)
T PF04121_consen 136 LLKYIFELLRAGRIEEAQELCRERGQPWRAASLCGWQLYHDPNLDPELSDEDERMEGNRSRALWKRACYKLSQN-PNLDP 214 (697)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHTTSB-B-TTTSGGGTTT-SS-BSBTTHHHHHHHHHHHHHT-SSS-H
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHcCccccCCcccccccccccccccCChhHHHHHHHHHHHHhC-CCCCH
Confidence 4778999999999999999999999999999888211 0110000000 00122442100 1 12445
Q ss_pred HHHHHHHHhhCCcccccCCCCCCHHHHHHHH
Q 002180 638 DRIRLYELLAGHIHSSLNDVTIDWKRFLGLL 668 (955)
Q Consensus 638 ~~~kIY~LLAG~~~~~~~~~~LdW~rafgL~ 668 (955)
.-++||.+|||++...+....-+|--.|=+|
T Consensus 215 yEraiY~~L~G~~~~~l~~~~~sWeD~lwa~ 245 (697)
T PF04121_consen 215 YERAIYGALSGDLSSVLPVCSSSWEDYLWAY 245 (697)
T ss_dssp HHHHHHHHHHTS---HHHHTT-SHHHHHHHH
T ss_pred HHHHHHHHHhcccHhhhhhccCCHHHHHHHH
Confidence 5569999999998766542213898876554
No 6
>KOG0845 consensus Nuclear pore complex, Nup98 component (sc Nup145/Nup100/Nup116) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=91.22 E-value=0.17 Score=65.40 Aligned_cols=109 Identities=18% Similarity=0.240 Sum_probs=72.5
Q ss_pred CcEEeccceEEEEeccccccCCCCccceEEEeccEEEEecCCCCCCCCCCCCcccEEEEEecccccccCCCCCCCh----
Q 002180 74 DFTVGRLGYGYVKFLGNTDVRWLDLDQIVKFGRHEIVVYEDESSKPEVGQGLNKAAEVTLFLQGRYLSLKLKEGDS---- 149 (955)
Q Consensus 74 ~f~vgr~g~G~i~f~~~vdl~~~~ld~iV~~~~~~v~vYp~~~~kPp~G~gLN~~a~itl~~~~~~~~~~~~~~~~---- 149 (955)
+.+.++..++...+.+-+-+...=.+.++......+..+.+......-| ++|+.+.++|+. +|++++.+++.
T Consensus 789 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~~~~d~ 864 (903)
T KOG0845|consen 789 GVNPGTSKFGETKSPGERELAPSKVSTKKPFTSNAVKLSTTEPEYSNDG-PSNRDAGVTLEQ---VSNLDKSTKEEIRDL 864 (903)
T ss_pred cccccceeecccccccceeccccccccccccccccccccccccccCCcc-ccccccceeeee---eeccccccchhhHHH
Confidence 3344444556665555555555444555555555555555544433344 999999999963 45588877552
Q ss_pred --HHHHHHHHHHhhhcCCEEEEEecCCcEEEEEECCcccc
Q 002180 150 --DDFVKKMKERTERQGARFVSFDPVSGEWKFLVVHFSRF 187 (955)
Q Consensus 150 --~~~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~HFskY 187 (955)
.......++.+ +++..|..|+++|+.|.|.++|++.|
T Consensus 865 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 903 (903)
T KOG0845|consen 865 MKLETEFSIRSVV-RPSEGFAPFRAETGSWSFRLDSESSY 903 (903)
T ss_pred HHHhhccchhhhc-cccccccccccccceEEEeecccccC
Confidence 12222346667 88999999999999999999999987
No 7
>KOG1964 consensus Nuclear pore complex, rNup107 component (sc Nup84) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=78.96 E-value=1.8e+02 Score=36.27 Aligned_cols=223 Identities=13% Similarity=0.080 Sum_probs=119.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHcCCCchhhhhhhcC----------------CCchhHHHHHHHHHHHHHcCCCcccChH
Q 002180 574 LKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAG----------------GSTVSRSDIAHQLDLWRVNGLDFKFIEK 637 (955)
Q Consensus 574 ~e~if~lL~g~~V~~Ac~~Ai~s~n~rLAtLlsq~g----------------s~~~~r~~l~~QL~~W~~~~~d~~~i~~ 637 (955)
...||.+.-+|.+++|.++|+..||.--|..|--+- .+++.|+..+ -..|+-... +-+++
T Consensus 224 ~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 224 FKYIFELIRAGETDEALELCKRLGNGWRAAILQGISEYRDPNLDIPLEASPQEGNKYKRLWR--RSCYQLTQE--KSQDS 299 (800)
T ss_pred HHHHHHHHHccchHHHHHHHHHhCcHHHHHHHHHHHHhhCCCccchhhhCcccCCcHHHHHH--HHHHHHHHh--hccCh
Confidence 456999999999999999999999987776664221 0122333322 123333321 34566
Q ss_pred HHHHHHHHhhCCcccccCCCCCCHHHHHHHHhhccCCCCCCHHHHHHHHHHHhcC-CCCC----CCCCccccCCCCCCCC
Q 002180 638 DRIRLYELLAGHIHSSLNDVTIDWKRFLGLLMWYQLPPETSLAIVFQTYQHLLDD-GKAP----LPVPIYVDEGPIDEPI 712 (955)
Q Consensus 638 ~~~kIY~LLAG~~~~~~~~~~LdW~rafgL~LWYg~~~~~~i~~ai~~y~~~~~~-~~~~----~P~P~y~~~~~~~~~~ 712 (955)
.-++||.+|||+.....--..=+|--.+=.|+= . -+-.-|+.|...... ...+ .+.|++--+...+++.
T Consensus 300 YeRA~y~~lSG~l~nl~~l~~s~Wed~vWAy~n--~----~v~~~ie~~l~~a~~~~tq~~p~~~~~~~lT~e~ifeEL~ 373 (800)
T KOG1964|consen 300 YERAIYGALSGILGNLLPLLKSGWEDKVWAYLN--S----MVQARIEAYLGAAPLNETQETPSDLFNGPLTSELIFEELR 373 (800)
T ss_pred HHHHHHHHHhccccchhhHHhcchHHHHHHHHH--H----HHHHHHHHHHhhccccccCCChhhhcCCcCcHHHHHHHHH
Confidence 667999999999753321111148776544332 1 122234444433110 1111 1222110000000000
Q ss_pred CC--------CCCCCCChhHHHH-hhcccCCCcccchhhhhcccCCCCCCCCcchhHHHHHHHHhcCCC-CCchhhHHHH
Q 002180 713 DW--------SGNERNDLSYYLM-LLHASGESKFGSLKTMFNALSSTYDPLDYHMIWHQREVLAAVGVI-SSNDLQILDM 782 (955)
Q Consensus 713 ~~--------~~~~~~D~~~~LL-kL~~~~~~~~~~l~~~l~p~~~s~~~lD~rLsW~l~~iL~a~g~~-~~~~~~~Lt~ 782 (955)
.. ...+..++.=+++ -++.. -. ....+-+..-.+.+..|.=-|+-.||.-+|+.+|.. .....+.+-.
T Consensus 374 ~~~~a~v~~ea~~~i~ilq~~lIld~~~~-li-~s~~~~l~~~~ng~~~p~lLRimtHlvlfl~~~G~~~~E~~s~~II~ 451 (800)
T KOG1964|consen 374 NEADARVEEEAQHPIDILQNHLILDLIKE-LI-ESVVEWLEKDRNGQVPPHLLRIMTHLVLFLRISGLEVNEDGSAKIIL 451 (800)
T ss_pred HHhhhcchhhhhchHHHHHHHHHHHHHHH-HH-HHHHHHHHhcccCCCChHHHHHHHHHHHHHHHhCCCccccchHHHHH
Confidence 00 0111112222222 11110 00 000111111223345577778899999999988843 2345678899
Q ss_pred HHHHHHHhCCCchhHHHHHhcccCCC
Q 002180 783 GLVSQLLCQGKCHWAIYVVLHMPRCD 808 (955)
Q Consensus 783 ~fA~QLe~~glw~wAifVllHl~d~~ 808 (955)
.|..-|...|+.+-+.|-..||+++.
T Consensus 452 ~YieLL~~~g~~~lia~Yt~~L~e~l 477 (800)
T KOG1964|consen 452 TYIELLARSGHKNLIAFYTRFLPEDL 477 (800)
T ss_pred HHHHHHHhcCCcchhHHHHHhCCchh
Confidence 99999999999999999999998654
No 8
>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex. It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.
Probab=57.87 E-value=2.2e+02 Score=35.40 Aligned_cols=148 Identities=15% Similarity=0.130 Sum_probs=82.7
Q ss_pred hHHHHHHHHhcCCCCCc------------------hhhHHHHHHHHHHHhCCCchhHHHHHhcccCCCCc--hHHHHHHH
Q 002180 759 IWHQREVLAAVGVISSN------------------DLQILDMGLVSQLLCQGKCHWAIYVVLHMPRCDDY--PYLQATLI 818 (955)
Q Consensus 759 sW~l~~iL~a~g~~~~~------------------~~~~Lt~~fA~QLe~~glw~wAifVllHl~d~~~~--~~~R~~~v 818 (955)
.=|+...|...|.+..+ +..+|-..|+...+ ..--..|+--+..|.+..+. ..+-..++
T Consensus 291 AVH~AIaL~~~gLL~~~~~~~~~lls~~~~~~~~ln~arLI~~Y~~~F~-~td~~~Al~Y~~li~~~~~~~~~~l~~~~l 369 (613)
T PF04097_consen 291 AVHFAIALAYYGLLRVSDSSSAPLLSVDPGDPPPLNFARLIGQYTRSFE-ITDPREALQYLYLICLFKDPEQRNLFHECL 369 (613)
T ss_dssp HHHHHHHHHHTT------------------------HHHHHHHHHHTTT-TT-HHHHHHHHHGGGGS-SCCHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCCccccceeeecCCCCCCcCHHHHHHHHHHHHh-ccCHHHHHHHHHHHHHcCCchHHHHHHHHH
Confidence 56777777766553211 12456667777665 34567788777777655441 11334555
Q ss_pred HHHHHhhc------ccCCChh-HHHHHHHH------hCCCHHHH---HHHHHHHHHhcCCHHHHHHHHHhCcCHHHHHHH
Q 002180 819 REILFQYC------ESWSSEE-SQRKFIEA------LGVPSEWL---HEAMAVYYNYYGELSKALEHFLECANWQKAHSI 882 (955)
Q Consensus 819 r~lL~r~~------~~~~~~~-~~~~fL~~------L~IP~~WI---~eAkAl~a~~~~d~~~e~~~Ll~A~~~~eAH~v 882 (955)
++++-.-- ..+..+. .....|++ +..+..-+ -+..|..+..+|.+..++..+.-|++|+.|-++
T Consensus 370 ~eLvletref~~LLG~i~~dG~r~~G~i~~~~~Li~~~~~~~~~~~i~~~~A~~~e~~g~~~dAi~Ly~La~~~d~vl~l 449 (613)
T PF04097_consen 370 RELVLETREFDLLLGDINPDGSRTPGLIERRLSLIKFDDDEDFLREIIEQAAREAEERGRFEDAILLYHLAEEYDKVLSL 449 (613)
T ss_dssp HHHHHHH--HHHHHEEE-TTS-EEE-HHHHTGGGGT-SSSSHHHHHHHHHHHHHHHHCT-HHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHccCCHHHHCCCCCCCCccccceeeccccccCCCCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhhHHHHHHH
Confidence 55543211 0011111 11235655 55444333 344477788899999999999999999999999
Q ss_pred HHHhhccchhccCC-------hHHHHHHHHhh
Q 002180 883 FVTSVAHTLFLSAN-------HSDVWTLATSM 907 (955)
Q Consensus 883 ~i~~vaP~~II~~d-------~~~L~~Ll~~~ 907 (955)
+.+.|+.-.--... -+.|..+...+
T Consensus 450 ln~~Ls~~l~~~~~~~~~~s~~~~l~~la~~i 481 (613)
T PF04097_consen 450 LNRLLSQVLSQPSSSSLSDSERERLIELAKEI 481 (613)
T ss_dssp HHHHHHHHHHCSSTSSSSSTTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCccccccccchhhhHHHHHHHH
Confidence 99999875544333 35565554444
No 9
>KOG2168 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=53.46 E-value=2.5e+02 Score=35.83 Aligned_cols=294 Identities=17% Similarity=0.214 Sum_probs=148.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHcCCCc--hhhhhhhc-CC--CchhHHHHHHHH-HHHHHc-CCCcccChHHHHHHHHHh
Q 002180 574 LKHIFLLLTGRQLDSSVELAASRGDVR--LACLLSQA-GG--STVSRSDIAHQL-DLWRVN-GLDFKFIEKDRIRLYELL 646 (955)
Q Consensus 574 ~e~if~lL~g~~V~~Ac~~Ai~s~n~r--LAtLlsq~-gs--~~~~r~~l~~QL-~~W~~~-~~d~~~i~~~~~kIY~LL 646 (955)
.--||.+|-+|++++|.+..-+++++. ||.+++-. -+ .+. -..+..|| ..|+.. |. .--||..++||++|
T Consensus 329 W~~vyy~lR~G~lk~A~~~l~e~~~~~~~l~~~f~~y~~A~~~~~-~~~le~qlrl~~~~~l~~--~~~DpyK~AvY~ii 405 (835)
T KOG2168|consen 329 WPLVYYLLRCGDLKAASQFLNENKDFFEKLAELFPTYFNAYAKNL-SSKLEKQLRLRLRSELGR--NSTDPYKLAVYKII 405 (835)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcCC-CccccHHHHHHHHHHhcc--ccCChHHHHHHHHH
Confidence 456999999999999999999999999 99999872 11 111 01233454 355533 23 35789999999999
Q ss_pred hCCcc----cccC--CCCCCHHHHHHHHhhccCCCCCC----------HHHHHHHHHHHhcCCCCCCCCCccccCCCCCC
Q 002180 647 AGHIH----SSLN--DVTIDWKRFLGLLMWYQLPPETS----------LAIVFQTYQHLLDDGKAPLPVPIYVDEGPIDE 710 (955)
Q Consensus 647 AG~~~----~~~~--~~~LdW~rafgL~LWYg~~~~~~----------i~~ai~~y~~~~~~~~~~~P~P~y~~~~~~~~ 710 (955)
.|.=. +.+- -++.=|.+.--+|--=+. ..+ ....+.+| | |.|..
T Consensus 406 g~cd~~~~~~ev~~tiED~LW~kL~~ir~~~~~--sds~~~~~~~~~~~~~il~~Y------G------~sYFt------ 465 (835)
T KOG2168|consen 406 GGCDLRRDLPEVADTIEDFLWFKLSLIRVDDQG--SDSPTDELFLLEDQKDILEAY------G------ESYFT------ 465 (835)
T ss_pred hcCccccccHHHHhHHHHHHHHHHHheeecCCC--CcchHHhhhhHHHHHHHHHHh------H------HHhhc------
Confidence 99311 1110 122335554444332111 111 11223333 1 22321
Q ss_pred CCCCCCCCCCChhHHHHhhcccCCCcccchhhhhcccCCCCCCC--CcchhHHHHHHHHhcCCCCC-------------c
Q 002180 711 PIDWSGNERNDLSYYLMLLHASGESKFGSLKTMFNALSSTYDPL--DYHMIWHQREVLAAVGVISS-------------N 775 (955)
Q Consensus 711 ~~~~~~~~~~D~~~~LLkL~~~~~~~~~~l~~~l~p~~~s~~~l--D~rLsW~l~~iL~a~g~~~~-------------~ 775 (955)
+...++.++..-|.-++ .++..+.- .++..+. | +=|+...|..+|++.. .
T Consensus 466 ------~ng~~p~~Yf~~LlLsg-----qfe~AI~f-L~~~~~~~~d---AVH~AI~l~~lglL~~~~s~~~~ll~~d~~ 530 (835)
T KOG2168|consen 466 ------NNGSQPLLYFQVLLLSG-----QFERAIEF-LHREEPNRID---AVHVAIALAELGLLRTSSSTSQELLSIDPN 530 (835)
T ss_pred ------cCCCChHHHHHHHHHHH-----hHHHHHHH-HHhhcCCcch---hHHHHHHHHHhhhhccCCCCCCcccccCCC
Confidence 11134433222222221 12221110 1112222 3 4455555655544311 0
Q ss_pred --------hhhHHHHHHHHHHHhCCCchhHHHHHhcccCCCCchHHHH---HHHHHHHHhhccc-------CCC-hhHHH
Q 002180 776 --------DLQILDMGLVSQLLCQGKCHWAIYVVLHMPRCDDYPYLQA---TLIREILFQYCES-------WSS-EESQR 836 (955)
Q Consensus 776 --------~~~~Lt~~fA~QLe~~glw~wAifVllHl~d~~~~~~~R~---~~vr~lL~r~~~~-------~~~-~~~~~ 836 (955)
....|+..|-.-.|...- ..|+--+.-+....+ +..+. .++.+++-.-+.. +.. .+...
T Consensus 531 d~~k~~~lnf~rLi~~Ytk~fe~~d~-~~al~y~~~lr~~~d-~q~~~l~l~~v~~lVl~t~~~f~~iLG~i~~dG~r~~ 608 (835)
T KOG2168|consen 531 DPPKSRRLNFARLIIAYTKSFEYTDT-RVALQYYYLLRLNKD-PQGSNLFLKCVCELVLETEEEFDLILGKIKPDGSREP 608 (835)
T ss_pred CCcccccccHHHHHHHHHHHHHhccc-hhhhheeeeecccCC-hhHHHHHHHHHHHHHHhccccHHHHhcccCCCCCCCc
Confidence 124566666665554321 111111122222222 22222 3333333222111 111 11123
Q ss_pred HHHHHhC----CCHHHHHHHHHHHHHhcCCHHHHHHHHHhCcCHHHHHHHHHHhhccchhcc----CChHHHHHHHHhhc
Q 002180 837 KFIEALG----VPSEWLHEAMAVYYNYYGELSKALEHFLECANWQKAHSIFVTSVAHTLFLS----ANHSDVWTLATSME 908 (955)
Q Consensus 837 ~fL~~L~----IP~~WI~eAkAl~a~~~~d~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II~----~d~~~L~~Ll~~~~ 908 (955)
.+|.+.. -+...+.+| |-.+--.|.+...+..+..||.|+.|-.++.+.+++-..-. .+.+.+..|...+.
T Consensus 609 G~l~~f~~~~~~~~~i~~~v-A~~a~~~G~~~~sI~LY~lag~yd~al~link~LS~~l~~~~~~~~n~erl~~La~~~~ 687 (835)
T KOG2168|consen 609 GLLDEFLPLIEDLQKIILEV-ASEADEDGLFEDAILLYHLAGDYDKALELINKLLSQVLHSPTLGQSNKERLGDLALSMN 687 (835)
T ss_pred chHhhhccchhhHHHHHHHH-HHHHHhcCCHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhhcccCCcchhhHHHHHHHHH
Confidence 3555333 344555443 55677899999999999999999999999999888654332 25567777765543
No 10
>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=49.92 E-value=27 Score=30.15 Aligned_cols=31 Identities=16% Similarity=0.383 Sum_probs=27.5
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 152 ~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
..+-+.+.|++.|-++++++...|.|+|.++
T Consensus 38 a~~di~~~~~~~G~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03420 38 FARDAQAWCKSTGNTLISLETEKGKVKAVIE 68 (69)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 4577889999999999999999999999875
No 11
>PRK11018 hypothetical protein; Provisional
Probab=49.71 E-value=28 Score=30.96 Aligned_cols=31 Identities=6% Similarity=0.205 Sum_probs=27.0
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 152 ~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
-.+.+.+.+++.|-+|++.+...|.|.|.|.
T Consensus 47 a~~di~~~~~~~G~~v~~~~~~~g~~~~~I~ 77 (78)
T PRK11018 47 SINNIPLDARNHGYTVLDIQQDGPTIRYLIQ 77 (78)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCeEEEEEE
Confidence 3467888888899999999989999999986
No 12
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.46 E-value=1e+02 Score=39.99 Aligned_cols=94 Identities=18% Similarity=0.212 Sum_probs=63.4
Q ss_pred ccHHHHHHHHHhcCCHHHHHHHHHHcCCCchhhhhhhcCCCchhHHHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCc
Q 002180 571 SNYLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSRSDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHI 650 (955)
Q Consensus 571 ~~~~e~if~lL~g~~V~~Ac~~Ai~s~n~rLAtLlsq~gs~~~~r~~l~~QL~~W~~~~~d~~~i~~~~~kIY~LLAG~~ 650 (955)
.+....|-..|..|++.+|++..++++-+-.|++|+..|+.+ .+.. .|-+--.+.+. +.-+-||++..-+.
T Consensus 488 ~d~d~~Is~alitgd~~~aV~~cl~~~~~a~AliiA~~gg~e-l~~~--t~~~Y~~k~~~------k~s~li~a~v~~d~ 558 (1049)
T KOG0307|consen 488 SDIDGLISEALITGDFKSAVELCLEANKMADALIIAHAGGTE-LLES--TRDKYLAKSNS------KLSRLIYAMVNRDL 558 (1049)
T ss_pred CcHHHHHHHHHHhccHHHHHHHHHhhhHHHHHHHHHhcCCHH-HHHH--HHHHHHHHhCC------hHHHHHHHHHhhhH
Confidence 345666777788889999999999999999999999999966 2222 22222333332 13345788777765
Q ss_pred ccccCC-CCCCHHHHHHHHhhccC
Q 002180 651 HSSLND-VTIDWKRFLGLLMWYQL 673 (955)
Q Consensus 651 ~~~~~~-~~LdW~rafgL~LWYg~ 673 (955)
...++. .--.||-+|++-+=|..
T Consensus 559 ~~~ve~~~~k~Wke~la~i~t~~~ 582 (1049)
T KOG0307|consen 559 DDYVETCEVKQWKETLAAICTYAQ 582 (1049)
T ss_pred HHHHhhcchhhHHHHHHHHHHhcc
Confidence 433321 11249999988888765
No 13
>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=35.67 E-value=62 Score=27.92 Aligned_cols=31 Identities=6% Similarity=0.283 Sum_probs=26.6
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 152 ~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
-.+.+.+.+++.|-+++..+...|.|+|.|.
T Consensus 38 s~~ni~~~~~~~g~~v~~~~~~~~~~~~~i~ 68 (69)
T cd03422 38 SINNIPIDARNHGYKVLAIEQSGPTIRYLIQ 68 (69)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 4567888888899999998888999999985
No 14
>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=34.71 E-value=63 Score=27.82 Aligned_cols=31 Identities=6% Similarity=0.229 Sum_probs=26.4
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 152 ~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
..+-+.+.+++.|-++++.....|.|+|.|.
T Consensus 38 s~~di~~~~~~~g~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03423 38 TTRDIPKFCTFLGHELLAQETEDEPYRYLIR 68 (69)
T ss_pred hHHHHHHHHHHcCCEEEEEEEcCCEEEEEEE
Confidence 3467788888899999998889999999875
No 15
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=33.83 E-value=67 Score=28.74 Aligned_cols=32 Identities=3% Similarity=0.111 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 151 DFVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 151 ~~~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
...+-+.+.|++.|.++++...+.|.|+|.+.
T Consensus 47 ~~~~di~~~~~~~G~~~~~~~~~~g~~~~~I~ 78 (81)
T PRK00299 47 ATTRDIPSFCRFMDHELLAQETEQLPYRYLIR 78 (81)
T ss_pred cHHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 35577888888999999999999999999875
No 16
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=25.98 E-value=1.2e+02 Score=26.54 Aligned_cols=29 Identities=14% Similarity=0.371 Sum_probs=20.3
Q ss_pred HHHHHHHhhh------------cCC--EEEEEecCCcEEEEEE
Q 002180 153 VKKMKERTER------------QGA--RFVSFDPVSGEWKFLV 181 (955)
Q Consensus 153 ~~~l~~~~~~------------~~~--~fv~y~~~tg~w~F~V 181 (955)
++||+.+.+. .|. --|+||+.||+|+.+.
T Consensus 2 i~RL~aM~~~~~~e~q~R~FE~~G~~~c~V~y~~~t~~F~l~~ 44 (67)
T PF08796_consen 2 IQRLEAMQEDTDGEVQVRRFEKEGVEVCTVTYDQETETFELEE 44 (67)
T ss_dssp HHHHHHHHHHHCTS-EEEEEEETTEEEEEEEEETTTTEEEEEE
T ss_pred hhHHHHHHhccCCCceEEEeecCCEEEEEEEEECCCCeEEEEE
Confidence 5677777653 232 2589999999887765
No 17
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=24.80 E-value=2e+02 Score=35.92 Aligned_cols=104 Identities=17% Similarity=0.173 Sum_probs=58.0
Q ss_pred HHHHHhCCCchhHHHHHhccc-CCCCchHHHHHHHHHHHHhhc----ccCCChhHHHHHHHHhC-CCHHHHHHHHHHHHH
Q 002180 785 VSQLLCQGKCHWAIYVVLHMP-RCDDYPYLQATLIREILFQYC----ESWSSEESQRKFIEALG-VPSEWLHEAMAVYYN 858 (955)
Q Consensus 785 A~QLe~~glw~wAifVllHl~-d~~~~~~~R~~~vr~lL~r~~----~~~~~~~~~~~fL~~L~-IP~~WI~eAkAl~a~ 858 (955)
|..-|+.|.|.-|+=.||-+. |..+.. .+++.+-..-+ ..+.++++.+.++..++ +-+.=-|+|.|-.-.
T Consensus 1162 ak~weq~gd~rkav~~~lkinrdst~nd----~l~e~~~~kaadl~ikfl~~d~nme~i~aa~~al~~~~~~e~aael~l 1237 (1636)
T KOG3616|consen 1162 AKEWEQAGDWRKAVDALLKINRDSTDND----ALAEHCTEKAADLSIKFLMGDENMEVIGAAGGALDEAGCHEAAAELLL 1237 (1636)
T ss_pred HHHHHhcccHHHHHHHHhhhccCCCCcH----HHHHHHHHHHHhhhhhhcCCccchhhHHhcchhhhcccccHHHHHHHH
Confidence 445689999999999999994 333321 22222211111 11223332222222111 111122455554444
Q ss_pred hcCCHHHHHHHHHhCcCHHHHHHHHHHhhccchhc
Q 002180 859 YYGELSKALEHFLECANWQKAHSIFVTSVAHTLFL 893 (955)
Q Consensus 859 ~~~d~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II 893 (955)
.-+-..+++..+++|..|+.|.+|. .++-|+.+=
T Consensus 1238 ~f~~~keaida~~~~eewakakqva-ke~~p~~~~ 1271 (1636)
T KOG3616|consen 1238 LFDLSKEAIDAFCEAEEWAKAKQVA-KELDPEMED 1271 (1636)
T ss_pred HhhhHHHHHHHHHhHHHHHHHHHHH-HHhCchhhH
Confidence 4566677889999999999998875 567787753
No 18
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=23.67 E-value=1.9e+02 Score=25.21 Aligned_cols=39 Identities=5% Similarity=0.147 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCcCHHHHHHHHHHhhccchhccCChHHHHHHH
Q 002180 863 LSKALEHFLECANWQKAHSIFVTSVAHTLFLSANHSDVWTLA 904 (955)
Q Consensus 863 ~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II~~d~~~L~~Ll 904 (955)
+..+++.|+..|+|++|-++..+ +|.-|+ +..+++.+|-
T Consensus 9 ~~~~F~~l~~~g~y~eAA~~AA~--sP~giL-Rt~~Ti~rFk 47 (66)
T PF13838_consen 9 YVQQFNELFSQGQYEEAAKVAAN--SPRGIL-RTPETINRFK 47 (66)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHH--SGGGTT--SHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHh--Cccchh-cCHHHHHHHH
Confidence 56789999999999999998776 688888 5568887654
No 19
>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=23.30 E-value=1.4e+02 Score=25.27 Aligned_cols=30 Identities=13% Similarity=0.382 Sum_probs=25.6
Q ss_pred HHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 002180 153 VKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (955)
Q Consensus 153 ~~~l~~~~~~~~~~fv~y~~~tg~w~F~V~ 182 (955)
.+-+.+.++.+|.++++...+.|.|+|.++
T Consensus 39 ~~~i~~~~~~~g~~~~~~~~~~~~~~i~i~ 68 (69)
T cd00291 39 VEDIPAWAKETGHEVLEVEEEGGVYRILIR 68 (69)
T ss_pred HHHHHHHHHHcCCEEEEEEEeCCEEEEEEE
Confidence 466777777899999999988999999875
No 20
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=23.15 E-value=4.8e+02 Score=34.64 Aligned_cols=99 Identities=11% Similarity=0.119 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcccCCCCchHHHHHHHHH---------HHHhhcccCCChhHHH----HHHH-HhCC
Q 002180 779 ILDMGLVSQLLCQGKCHWAIYVVLHMPRCDDYPYLQATLIRE---------ILFQYCESWSSEESQR----KFIE-ALGV 844 (955)
Q Consensus 779 ~Lt~~fA~QLe~~glw~wAifVllHl~d~~~~~~~R~~~vr~---------lL~r~~~~~~~~~~~~----~fL~-~L~I 844 (955)
.+...||.-|...++|..|.-.+.-.-. -++|++. .+.-+.. .+.+..+- .-|. +|.=
T Consensus 940 ~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk-------lekAl~a~~~~~dWr~~l~~a~q-l~~~~de~~~~a~~L~s~L~e 1011 (1265)
T KOG1920|consen 940 VIYEAYADHLREELMSDEAALMYERCGK-------LEKALKAYKECGDWREALSLAAQ-LSEGKDELVILAEELVSRLVE 1011 (1265)
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHhcc-------HHHHHHHHHHhccHHHHHHHHHh-hcCCHHHHHHHHHHHHHHHHH
Confidence 4667799999999999998877776643 2344332 2221111 11111000 0111 2211
Q ss_pred CHHHHHHHHHHHHHhcCCHHHHHHHHHhCcCHHHHHHHHHHh
Q 002180 845 PSEWLHEAMAVYYNYYGELSKALEHFLECANWQKAHSIFVTS 886 (955)
Q Consensus 845 P~~WI~eAkAl~a~~~~d~~~e~~~Ll~A~~~~eAH~v~i~~ 886 (955)
-..= .||--+...|-+|+.+++--|++|..|.+|-++....
T Consensus 1012 ~~kh-~eAa~il~e~~sd~~~av~ll~ka~~~~eAlrva~~~ 1052 (1265)
T KOG1920|consen 1012 QRKH-YEAAKILLEYLSDPEEAVALLCKAKEWEEALRVASKA 1052 (1265)
T ss_pred cccc-hhHHHHHHHHhcCHHHHHHHHhhHhHHHHHHHHHHhc
Confidence 1111 3455556679999999999999999999999886543
Done!