Query 001634
Match_columns 1041
No_of_seqs 204 out of 379
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 05:38:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001634hhsearch_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 3E-68 6.6E-73 591.8 19.7 280 572-861 1-290 (290)
2 PF04096 Nucleoporin2: Nucleop 100.0 1.9E-45 4.1E-50 363.5 14.6 131 48-184 1-141 (141)
3 PF07575 Nucleopor_Nup85: Nup8 98.2 9.1E-06 2E-10 99.7 13.5 315 571-931 149-506 (566)
4 PF12931 Sec16_C: Sec23-bindin 93.3 0.072 1.6E-06 59.9 3.8 97 576-676 1-115 (284)
5 PF04121 Nup84_Nup100: Nuclear 92.3 0.24 5.3E-06 62.7 7.0 94 573-668 136-245 (697)
6 KOG0845 Nuclear pore complex, 91.1 0.17 3.6E-06 66.1 3.8 108 75-187 790-903 (903)
7 KOG1964 Nuclear pore complex, 72.1 2.8E+02 0.006 35.1 22.0 223 574-808 224-477 (800)
8 PF04097 Nic96: Nup93/Nic96; 52.0 3.2E+02 0.0069 34.5 15.9 306 570-907 111-481 (613)
9 KOG0307 Vesicle coat complex C 49.6 55 0.0012 42.7 8.6 94 571-673 488-582 (1049)
10 PRK11018 hypothetical protein; 48.6 29 0.00063 31.2 4.5 31 152-182 47-77 (78)
11 cd03420 SirA_RHOD_Pry_redox Si 48.3 29 0.00063 30.3 4.4 31 152-182 38-68 (69)
12 KOG2168 Cullins [Cell cycle co 47.4 5.3E+02 0.012 33.4 16.4 74 574-649 329-408 (835)
13 cd03422 YedF YedF is a bacteri 34.0 67 0.0015 28.1 4.4 31 152-182 38-68 (69)
14 cd03423 SirA SirA (also known 33.2 68 0.0015 28.0 4.3 31 152-182 38-68 (69)
15 PRK00299 sulfur transfer prote 33.2 69 0.0015 29.1 4.4 31 152-182 48-78 (81)
16 KOG4507 Uncharacterized conser 32.6 1.5E+02 0.0032 36.5 8.1 36 841-876 206-242 (886)
17 PF08796 DUF1797: Protein of u 24.2 1.3E+02 0.0028 26.6 4.2 29 153-181 2-44 (67)
18 cd00291 SirA_YedF_YeeD SirA, Y 22.9 1.4E+02 0.0029 25.6 4.4 30 153-182 39-68 (69)
19 PF12234 Rav1p_C: RAVE protein 20.1 1.9E+02 0.0042 36.4 6.3 42 569-610 464-506 (631)
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=3e-68 Score=591.77 Aligned_cols=280 Identities=39% Similarity=0.672 Sum_probs=213.8
Q ss_pred cHHHHHHHHHhcCCHHHHHHHHHHcCCCchhhHHhhcCCCchhHHHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCcc
Q 001634 572 NYLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSRSDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHIH 651 (1041)
Q Consensus 572 ~~~e~if~lL~g~~I~eAc~lAi~sgd~rLA~LLsq~gs~~~~r~~l~~QL~~W~~~~~d~~~I~~~r~kIY~LLAG~~~ 651 (1041)
+|+|+||.|||||||++||++|+++||+|||+||||+|+++.+|.++++||+.|+++|++ ++|++.++|||+||||+++
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 479999999999999999999999999999999999999999999999999999999998 8999999999999999998
Q ss_pred cccCC------CCCCHHHHHHHHHhccCCCCCCHHHHHHHHHHHhcCCCCCCCCCccccCCCCCCCCCCCCCCCCChhHH
Q 001634 652 SSLND------VTIDWKRFLGLLMWYQLPPETSLAIVFQTYQHLLDDGKAPLPVPIYVDEGPIDEPIDWSGNERNDLSYY 725 (1041)
Q Consensus 652 ~~~~~------~~LdW~ralgL~LWYg~~~~~si~~av~~y~~~~~~~~~~~P~P~y~~~~~~~~~~~~~~~~~~D~~~~ 725 (1041)
..... ++|||+|+||||||||++++.||++||+.|++++.++++++|.|||+++... .......+.+|++|+
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 66443 5699999999999999999999999999999999999999999999987651 111235678999999
Q ss_pred HHHhcccCCCcccchhhhhcccCCCCCCCCcchhHHHHHHHHHcCCCCC--chhhHhHHHHHHHHHhCCCchhHHHHHhc
Q 001634 726 LMLLHASGESKFGSLKTMFNALSSTYDPLDYHMIWHQREVLAAVGVISS--NDLQILDMGLVSQLLCQGKCHWAIYVVLH 803 (1041)
Q Consensus 726 LLkL~~~~~~~~~~L~~~l~P~~~s~~~lD~rLsW~l~~iL~a~g~~~~--~~~~~lt~~fA~QLe~~glw~wAifVllH 803 (1041)
|||||++++. .++++|.|.+++++||||||+|||+++|+++|+.+. ...++||++||+|||+.|+|+|||||+||
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 9999998776 499999999999999999999999999999998654 35689999999999999999999999999
Q ss_pred ccCCCCchhHHHHHHHHHHHhhcccCCChh-HHHHHHH-HhCCCHHHHHHHHHHHHHHcC
Q 001634 804 MPRCDDYPYLQATLIREILFQYCESWSSEE-SQRKFIE-ALGVPSEWLHEAMAVYYNYYG 861 (1041)
Q Consensus 804 l~~~~~~~~~R~~avr~lL~r~~~~~~~~~-~~~~fL~-~L~IP~~WI~eAkAl~a~~~g 861 (1041)
|+|+. .|+.+||++|.||+..+..++ ..+.||. +|+||++|||||||++|+|+|
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 999999999999999999987
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=1.9e-45 Score=363.52 Aligned_cols=131 Identities=47% Similarity=0.743 Sum_probs=114.8
Q ss_pred CeeecCCHHHHhccccCCCCCccccCCcEEeccceEEEEeccccccCCCCcc----ceEEEeccEEEEecCCCCCCCCCC
Q 001634 48 DYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLD----QIVKFGRHEIVVYEDESSKPEVGQ 123 (1041)
Q Consensus 48 ~Y~~~Ps~~~l~~~~~~~~~~l~~V~~F~vgr~g~G~i~f~~~vdl~~~~ld----~iV~~~~~~v~vYpd~~~kP~~G~ 123 (1041)
||||+||+++|++|+..+ |++|+||+|||+|||+|+|++||||+++||| +||.|++++|+||||+..|||+|+
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 001634 124 GLNKAAEVTLFLQGRYLSLKLKEGDS------DDFVKKMKERTERQGARFVSFDPVSGEWKFLVVHF 184 (1041)
Q Consensus 124 gLN~~A~itl~~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~HF 184 (1041)
||||||+|||+ +++| .++.+++. .+|.++|++.|+++||+||+||++||+|+|+|+||
T Consensus 78 GLN~~A~ItL~-~~~p--~~~~~~~~i~d~~~~~~~~~l~~~~~~~~~~FvsYd~~tG~W~F~V~HF 141 (141)
T PF04096_consen 78 GLNVPAIITLE-NCWP--KDKSTREPIKDPSKPRFEKKLKRLTEKMGAEFVSYDPETGTWVFRVEHF 141 (141)
T ss_dssp TTCS-EEEEES-S-----BBTTTTCB--STTCHHHHHHHHHHHHCTTSEEEEEETTTTEEEEEESS-
T ss_pred CcCCCEEEEEE-eeEe--cCCCCCccccCccHHHHHHHHHHHHhcCCCEEEEEeCCCcEEEEEEecC
Confidence 99999999995 5555 77777542 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=98.22 E-value=9.1e-06 Score=99.71 Aligned_cols=315 Identities=18% Similarity=0.199 Sum_probs=145.8
Q ss_pred CcHHHHHHHHHhcCCHHHHHHHHHHcCCCc----------hhhHHhhcCCCc----hhHHHHHHHHHHHHHcC-------
Q 001634 571 SNYLKHIFLLLTGRQLDSSVELAASRGDVR----------LACLLSQAGGST----VSRSDIAHQLDLWRVNG------- 629 (1041)
Q Consensus 571 ~~~~e~if~lL~g~~I~eAc~lAi~sgd~r----------LA~LLsq~gs~~----~~r~~l~~QL~~W~~~~------- 629 (1041)
.++...|..++..|+++.|+++....++++ +..||..+..-. ....+...|...|+..-
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 467889999999999999999996666644 345555554211 12345666777776321
Q ss_pred -CCccc-ChHHHHHHHHHhhCCcccccCCCCCCHHHHHHHHHhccCCCC--CC-HHHHHHHHHHHhcCCCCCCCCCcccc
Q 001634 630 -LDFKF-IEKDRIRLYELLAGHIHSSLNDVTIDWKRFLGLLMWYQLPPE--TS-LAIVFQTYQHLLDDGKAPLPVPIYVD 704 (1041)
Q Consensus 630 -~d~~~-I~~~r~kIY~LLAG~~~~~~~~~~LdW~ralgL~LWYg~~~~--~s-i~~av~~y~~~~~~~~~~~P~P~y~~ 704 (1041)
.+..+ +.+...-|+++|+|+.....+. .=+|..+++-++-|-.|.. .. +....+.-.+.+ ++.
T Consensus 229 ~~~~~~~~~~~L~~l~~Il~G~~~~i~~~-~~~WyE~~~a~~ly~~P~~~~~e~l~~~a~~~~~~~------~~~----- 296 (566)
T PF07575_consen 229 LQDGPFEIRENLEDLLKILLGDEDTILEY-SQDWYEALVALLLYVDPTCKPFELLHEYAQSCLEEF------PPD----- 296 (566)
T ss_dssp ---S-HHHHHHHHHHHHHHHT-HHHHHHT--SSHHHHHHHHHHHT------TTTHHHHHHHHHHHS--------------
T ss_pred hccCchhhHHHHHHHHHHHCCCHHHHHHH-hCcHHHHHHHhheeeCCCcchhhhHHHHHHHHHhcC------CCC-----
Confidence 11111 5677789999999997533222 2289999999998887642 22 333222222211 000
Q ss_pred CCCCCCCCCCCCCCCCChhHHHHHhcccCCCcccchhhhhcccCCCCCCC--CcchhHHHHHHHHHcCCCCC--------
Q 001634 705 EGPIDEPIDWSGNERNDLSYYLMLLHASGESKFGSLKTMFNALSSTYDPL--DYHMIWHQREVLAAVGVISS-------- 774 (1041)
Q Consensus 705 ~~~~~~~~~~~~~~~~D~~~~LLkL~~~~~~~~~~L~~~l~P~~~s~~~l--D~rLsW~l~~iL~a~g~~~~-------- 774 (1041)
...+...++..++. .... ..|+.+ ..+ |..+.=|+..+|...|.+..
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 01223344555553 2211 123332 123 44566677788888787651
Q ss_pred -chhhHhHHHHHHHHHhC-CCchhHHHHHhcccCCCCchhHHHHHHHHHHHhhcccCCChhHHHHHH---HHhCCCHH--
Q 001634 775 -NDLQILDMGLVSQLLCQ-GKCHWAIYVVLHMPRCDDYPYLQATLIREILFQYCESWSSEESQRKFI---EALGVPSE-- 847 (1041)
Q Consensus 775 -~~~~~lt~~fA~QLe~~-glw~wAifVllHl~~~~~~~~~R~~avr~lL~r~~~~~~~~~~~~~fL---~~L~IP~~-- 847 (1041)
.-.+-+-+.||..|-+. ++|+-|+=+|.+.++.. ..++.++|.|. +. .+++.-.+.+ .+++.+..
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-PL-DTNDDAEKLLEICAELGLEDVAR 425 (566)
T ss_dssp S-HHHHHHHHHHHHHHT-TTTHHHHHHHHHS-SSS-------HHHHHHHGGG------SHHHHHHHHHHHHHHT-HHHHH
T ss_pred ccHHHHHHHHHHHHHhcCcchHHHHHHHHHHCChhh------HHHHHHHHhhC-CC-CchHHHHHHHHHHHHCCCHHHHH
Confidence 11345678999999765 99999999999987533 46677777654 32 2333223333 38888874
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHccCHHHHHHHHHHhhcccccccCChhHHHHHHHhccccCCccccccchhhHHHHH
Q 001634 848 WLHEAMAVYYNYYGELSKALEHFLECANWQKAHSIFVTSVAHTLFLSANHSDVWTLATSMESHKSEIENWDLGAGMYIVF 927 (1041)
Q Consensus 848 WI~eAkAl~a~~~gd~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II~~d~~~L~~Ll~~fe~~~~~I~~W~~GG~VY~dY 927 (1041)
=|++-.|.++..+|++..++.++++||++...+++.=.-+ -+.+.++ .....+++..+.+.. .++.==.+...|-+|
T Consensus 426 ~I~~~~~~~~~~~~~~g~AL~~~~ra~d~~~v~~i~~~ll-~~~~~~~-~~~~~~ll~~i~~~~-~~~~~L~fla~yreF 502 (566)
T PF07575_consen 426 EICKILGQRLLKEGRYGEALSWFIRAGDYSLVTRIADRLL-EEYCNNG-EPLDDDLLDNIGSPM-LLSQRLSFLAKYREF 502 (566)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------------------------
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHH-HHHhcCC-CcccHHHHHHhcchh-hhhhhhHHHHHHHHH
Confidence 4555567777789999999999999999988877654433 2222222 222234444443321 222222456778888
Q ss_pred HHhh
Q 001634 928 YLIR 931 (1041)
Q Consensus 928 l~l~ 931 (1041)
.++.
T Consensus 503 ~~~~ 506 (566)
T PF07575_consen 503 YELY 506 (566)
T ss_dssp ----
T ss_pred HHHH
Confidence 8863
No 4
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=93.26 E-value=0.072 Score=59.93 Aligned_cols=97 Identities=20% Similarity=0.292 Sum_probs=59.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHcCCCchhhHHhhcCCCchhH----HHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCcc
Q 001634 576 HIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSR----SDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHIH 651 (1041)
Q Consensus 576 ~if~lL~g~~I~eAc~lAi~sgd~rLA~LLsq~gs~~~~r----~~l~~QL~~W~~~~~d~~~I~~~r~kIY~LLAG~~~ 651 (1041)
+|..+|..|+.++|++.|++.|+.-.|+|||..+|.+..+ +.+++++. ..... ..+.....-+|++++|+..
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 4678899999999999999999999999999998865433 23333331 11101 1123345579999999974
Q ss_pred cccCC---C-----------CCCHHHHHHHHHhccCCCC
Q 001634 652 SSLND---V-----------TIDWKRFLGLLMWYQLPPE 676 (1041)
Q Consensus 652 ~~~~~---~-----------~LdW~ralgL~LWYg~~~~ 676 (1041)
..+.. . --+|+..+++-|=|..+.+
T Consensus 77 ~~v~~l~~~~~~~~~~~~~~~~~Wre~lA~il~N~~~~~ 115 (284)
T PF12931_consen 77 EAVDELVPNSAAPPLEGEWDLDNWRETLAIILSNRTPED 115 (284)
T ss_dssp HHHHHHHH-----HHHHHHHHHSHHHHHHHHHHTS---S
T ss_pred HHHHHhccccccccccccchhcCHHHHHHHHHhCCCccc
Confidence 33211 0 1169999999999987654
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=92.29 E-value=0.24 Score=62.68 Aligned_cols=94 Identities=22% Similarity=0.349 Sum_probs=53.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHcCCCchhhHHhhcCC--CchhHHHHH---------HHHHHHHHc-----CCCcccCh
Q 001634 573 YLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGG--STVSRSDIA---------HQLDLWRVN-----GLDFKFIE 636 (1041)
Q Consensus 573 ~~e~if~lL~g~~I~eAc~lAi~sgd~rLA~LLsq~gs--~~~~r~~l~---------~QL~~W~~~-----~~d~~~I~ 636 (1041)
.+..||.+|-+|++++|.+++.+.|++=+|..|.=... ++..-..+. .--..|+.. . +.. ++
T Consensus 136 ~~~~i~~llR~G~~~eA~~lc~~~gq~wrAasL~G~~~~~dp~~~~~~~~~~~~~~G~~~r~LWk~~c~~ls~-~~~-~~ 213 (697)
T PF04121_consen 136 LLKYIFELLRAGRIEEAQELCRERGQPWRAASLCGWQLYHDPNLDPELSDEDERMEGNRSRALWKRACYKLSQ-NPN-LD 213 (697)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHTTSB-B-TTTSGGGTTT-SS-BSBTTHHHHHHHHHHHHH-TSS-S-
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHcCccccCCcccccccccccccccCChhHHHHHHHHHHHHh-CCC-CC
Confidence 47789999999999999999999999999998883211 110000000 001234321 1 112 33
Q ss_pred HHHHHHHHHhhCCcccccCCCCCCHHHHHHHH
Q 001634 637 KDRIRLYELLAGHIHSSLNDVTIDWKRFLGLL 668 (1041)
Q Consensus 637 ~~r~kIY~LLAG~~~~~~~~~~LdW~ralgL~ 668 (1041)
+.=++||.+|||++...+..-.-+|--.|=++
T Consensus 214 ~yEraiY~~L~G~~~~~l~~~~~sWeD~lwa~ 245 (697)
T PF04121_consen 214 PYERAIYGALSGDLSSVLPVCSSSWEDYLWAY 245 (697)
T ss_dssp HHHHHHHHHHHTS---HHHHTT-SHHHHHHHH
T ss_pred HHHHHHHHHHhcccHhhhhhccCCHHHHHHHH
Confidence 44449999999998765432213898876543
No 6
>KOG0845 consensus Nuclear pore complex, Nup98 component (sc Nup145/Nup100/Nup116) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=91.10 E-value=0.17 Score=66.09 Aligned_cols=108 Identities=19% Similarity=0.248 Sum_probs=72.6
Q ss_pred cEEeccceEEEEeccccccCCCCccceEEEeccEEEEecCCCCCCCCCCCCcccEEEEEecccccccCCCCCCCh-----
Q 001634 75 FTVGRLGYGYVKFLGNTDVRWLDLDQIVKFGRHEIVVYEDESSKPEVGQGLNKAAEVTLFLQGRYLSLKLKEGDS----- 149 (1041)
Q Consensus 75 F~vgr~g~G~i~f~~~vdl~~~~ld~iV~~~~~~v~vYpd~~~kP~~G~gLN~~A~itl~~~~~~~~~~~~~~~~----- 149 (1041)
-+.++..++...+.+.+-+...=.+.++......+..+.+......-| ++|+.+.++++..+ .+++.+.+.
T Consensus 790 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~---~~~~~~~~~~~d~~ 865 (903)
T KOG0845|consen 790 VNPGTSKFGETKSPGERELAPSKVSTKKPFTSNAVKLSTTEPEYSNDG-PSNRDAGVTLEQVS---NLDKSTKEEIRDLM 865 (903)
T ss_pred ccccceeecccccccceeccccccccccccccccccccccccccCCcc-ccccccceeeeeee---ccccccchhhHHHH
Confidence 334445566666666666555545555555555555665544433344 99999999996333 367776542
Q ss_pred -HHHHHHHHHHhhhcCCEEEEEecCCcEEEEEECCcccc
Q 001634 150 -DDFVKKMKERTERQGARFVSFDPVSGEWKFLVVHFSRF 187 (1041)
Q Consensus 150 -~~~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~HFSkY 187 (1041)
.......++.+ +++..|..|+++|+.|.|.++|++.|
T Consensus 866 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 903 (903)
T KOG0845|consen 866 KLETEFSIRSVV-RPSEGFAPFRAETGSWSFRLDSESSY 903 (903)
T ss_pred HHhhccchhhhc-cccccccccccccceEEEeecccccC
Confidence 12233346677 89999999999999999999999987
No 7
>KOG1964 consensus Nuclear pore complex, rNup107 component (sc Nup84) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=72.05 E-value=2.8e+02 Score=35.11 Aligned_cols=223 Identities=14% Similarity=0.103 Sum_probs=119.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHcCCCchhhHHhhcC----------------CCchhHHHHHHHHHHHHHcCCCcccChH
Q 001634 574 LKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAG----------------GSTVSRSDIAHQLDLWRVNGLDFKFIEK 637 (1041)
Q Consensus 574 ~e~if~lL~g~~I~eAc~lAi~sgd~rLA~LLsq~g----------------s~~~~r~~l~~QL~~W~~~~~d~~~I~~ 637 (1041)
...||.+...|.+++|-++|+..||.--|..|--+- .+++.|+..+ -.-|+-.+. +-+++
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 455899999999999999999999988777664221 0123343333 233433331 23555
Q ss_pred HHHHHHHHhhCCcccccCCCCCCHHHHHHHHHhccCCCCCCHHHHHHHHHHHhcC-CCCCCC----CCccccCCCCCCCC
Q 001634 638 DRIRLYELLAGHIHSSLNDVTIDWKRFLGLLMWYQLPPETSLAIVFQTYQHLLDD-GKAPLP----VPIYVDEGPIDEPI 712 (1041)
Q Consensus 638 ~r~kIY~LLAG~~~~~~~~~~LdW~ralgL~LWYg~~~~~si~~av~~y~~~~~~-~~~~~P----~P~y~~~~~~~~~~ 712 (1041)
.-++||.+|+|+.....---.=+|--.+=.|+= . =+-.-|..|...... ...+.| .|++--+...++..
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 556999999999753321111148776533321 1 122234444433100 111111 22110000000000
Q ss_pred CC--------CCCCCCChhHHHHH-hcccCCCcccchhhhhcccCCCCCCCCcchhHHHHHHHHHcCCC-CCchhhHhHH
Q 001634 713 DW--------SGNERNDLSYYLML-LHASGESKFGSLKTMFNALSSTYDPLDYHMIWHQREVLAAVGVI-SSNDLQILDM 782 (1041)
Q Consensus 713 ~~--------~~~~~~D~~~~LLk-L~~~~~~~~~~L~~~l~P~~~s~~~lD~rLsW~l~~iL~a~g~~-~~~~~~~lt~ 782 (1041)
.. ...+..++.=|++. ++..--.. ..+-+..-.+.+..|.=-|+-.||.-+|+.+|.. .......+-.
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 NEADARVEEEAQHPIDILQNHLILDLIKELIES--VVEWLEKDRNGQVPPHLLRIMTHLVLFLRISGLEVNEDGSAKIIL 451 (800)
T ss_pred HHhhhcchhhhhchHHHHHHHHHHHHHHHHHHH--HHHHHHhcccCCCChHHHHHHHHHHHHHHHhCCCccccchHHHHH
Confidence 00 01122222222221 11110000 0111222233455677788899999999998843 2344668889
Q ss_pred HHHHHHHhCCCchhHHHHHhcccCCC
Q 001634 783 GLVSQLLCQGKCHWAIYVVLHMPRCD 808 (1041)
Q Consensus 783 ~fA~QLe~~glw~wAifVllHl~~~~ 808 (1041)
.|..-|...|+.+-+.|-..||+.+-
T Consensus 452 ~YieLL~~~g~~~lia~Yt~~L~e~l 477 (800)
T KOG1964|consen 452 TYIELLARSGHKNLIAFYTRFLPEDL 477 (800)
T ss_pred HHHHHHHhcCCcchhHHHHHhCCchh
Confidence 99999999999999999999998653
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=52.02 E-value=3.2e+02 Score=34.45 Aligned_cols=306 Identities=15% Similarity=0.149 Sum_probs=140.1
Q ss_pred CCcHHHHHHHHHhcCCHHHHHHHHHHcCC------CchhhHHhhcCCC--chhHHHHHHHH-HHHHHcCCCcccC--hHH
Q 001634 570 ESNYLKHIFLLLTGRQLDSSVELAASRGD------VRLACLLSQAGGS--TVSRSDIAHQL-DLWRVNGLDFKFI--EKD 638 (1041)
Q Consensus 570 ~~~~~e~if~lL~g~~I~eAc~lAi~sgd------~rLA~LLsq~gs~--~~~r~~l~~QL-~~W~~~~~d~~~I--~~~ 638 (1041)
+...+..||.+|-+|++++|.+.|.++++ ..++..+.-.-.+ ...-..++.+| ..|++.--. .. ||.
T Consensus 111 ~~p~Wa~Iyy~LR~G~~~~A~~~~~~~~~~~~~~~~~f~~~l~~~~~s~~~~l~~~~~~~l~~ey~~~~r~--~~~~Dpy 188 (613)
T PF04097_consen 111 GDPIWALIYYCLRCGDYDEALEVANENRNQFQKIERSFPTYLKAYASSPDRRLPPELRDKLKLEYNQRIRN--STDGDPY 188 (613)
T ss_dssp TEEHHHHHHHHHTTT-HHHHHHHHHHTGGGS-TTTTHHHHHHHHCTTTTSS---TCCCHHHHHHHHHHTTT---TTS-HH
T ss_pred CCccHHHHHHHHhcCCHHHHHHHHHHhhhhhcchhHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhcC--CCCCChH
Confidence 34569999999999999999999943332 3344444433222 11222333333 567653321 23 999
Q ss_pred HHHHHHHhhCCcccccC-------C-CCCCHH--HHHHHHHhccCCCCCCHHHHHHHHHHHhcC-CCCCCCCCccccCCC
Q 001634 639 RIRLYELLAGHIHSSLN-------D-VTIDWK--RFLGLLMWYQLPPETSLAIVFQTYQHLLDD-GKAPLPVPIYVDEGP 707 (1041)
Q Consensus 639 r~kIY~LLAG~~~~~~~-------~-~~LdW~--ralgL~LWYg~~~~~si~~av~~y~~~~~~-~~~~~P~P~y~~~~~ 707 (1041)
+.++|.+|.+. ..... . + ||+ +---++-=-.......=.-.+...+..+.+ |.. |-.
T Consensus 189 K~AvY~ilg~c-D~~~~~~~~V~~tiE--D~LW~~L~~vr~~~~~~~~~~e~~~L~~LQ~~i~~~Ge~------~F~--- 256 (613)
T PF04097_consen 189 KRAVYKILGRC-DLSRRHLPEVARTIE--DWLWLQLSLVREDERSSSSAYERYTLEDLQKLILKYGES------HFN--- 256 (613)
T ss_dssp HHHHHHHHHT---CCC-S-TTC--SHH--HHHHHHHHH---TTSSSSSSS----HHHHHHHHHHH-GG------GCT---
T ss_pred HHHHHHHHhcC-CccccchHHHhCcHH--HHHHHHHHhhccCCCccccccccccHHHHHHHHHHhchh------hcc---
Confidence 99999999544 22110 1 2 453 222221111100000001123333333321 110 000
Q ss_pred CCCCCCCCCCCCCChhHHHHHhcccCCCcccchhhhhcccCCCCCCCCcchhHHHHHHHHHcCCCCCch-----------
Q 001634 708 IDEPIDWSGNERNDLSYYLMLLHASGESKFGSLKTMFNALSSTYDPLDYHMIWHQREVLAAVGVISSND----------- 776 (1041)
Q Consensus 708 ~~~~~~~~~~~~~D~~~~LLkL~~~~~~~~~~L~~~l~P~~~s~~~lD~rLsW~l~~iL~a~g~~~~~~----------- 776 (1041)
+ ...=.+|--+.+.+.. ++..+.-... .+...--.=|+...|...|.+....
T Consensus 257 --------~-~~~p~~Yf~~LlLtgq------FE~AI~~L~~--~~~~~~dAVH~AIaL~~~gLL~~~~~~~~~lls~~~ 319 (613)
T PF04097_consen 257 --------A-GSNPLLYFQVLLLTGQ------FEAAIEFLYR--NEFNRVDAVHFAIALAYYGLLRVSDSSSAPLLSVDP 319 (613)
T ss_dssp --------T-------HHHHHHHTT-------HHHHHHHHHT----T-HHHHHHHHHHHHHTT-----------------
T ss_pred --------c-chhHHHHHHHHHHHhh------HHHHHHHHHh--hccCcccHHHHHHHHHHcCCCCCCCccccceeeecC
Confidence 0 0011133223333321 2322221111 1122222557777777666532211
Q ss_pred -------hhHhHHHHHHHHHhCCCchhHHHHHhcccCCCCc--hhHHHHHHHHHHHhhc---cc---CCChh-HHHHHHH
Q 001634 777 -------LQILDMGLVSQLLCQGKCHWAIYVVLHMPRCDDY--PYLQATLIREILFQYC---ES---WSSEE-SQRKFIE 840 (1041)
Q Consensus 777 -------~~~lt~~fA~QLe~~glw~wAifVllHl~~~~~~--~~~R~~avr~lL~r~~---~~---~~~~~-~~~~fL~ 840 (1041)
..+|-..|+...+. .--..|+--+..|.+..+. ..+-..++++++-.-. .+ +..+. .....++
T Consensus 320 ~~~~~ln~arLI~~Y~~~F~~-td~~~Al~Y~~li~~~~~~~~~~l~~~~l~eLvletref~~LLG~i~~dG~r~~G~i~ 398 (613)
T PF04097_consen 320 GDPPPLNFARLIGQYTRSFEI-TDPREALQYLYLICLFKDPEQRNLFHECLRELVLETREFDLLLGDINPDGSRTPGLIE 398 (613)
T ss_dssp -------HHHHHHHHHHTTTT-T-HHHHHHHHHGGGGS-SCCHHHHHHHHHHHHHHHH--HHHHHEEE-TTS-EEE-HHH
T ss_pred CCCCCcCHHHHHHHHHHHHhc-cCHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHccCCHHHHCCCCCCCCccccceee
Confidence 13466677776653 3467787777777655441 1233445555543211 01 11111 1123555
Q ss_pred H------hCCCHHHHH---HHHHHHHHHcCCHHHHHHHHHHccCHHHHHHHHHHhhcccccccCC-------hhHHHHHH
Q 001634 841 A------LGVPSEWLH---EAMAVYYNYYGELSKALEHFLECANWQKAHSIFVTSVAHTLFLSAN-------HSDVWTLA 904 (1041)
Q Consensus 841 ~------L~IP~~WI~---eAkAl~a~~~gd~~~e~~~Ll~A~~~~eAH~v~i~~vaP~~II~~d-------~~~L~~Ll 904 (1041)
+ +..+..-++ +.-|..+..+|.+..++..+.-|++|+.|-+++.+.|+.-.--... -+.|..+.
T Consensus 399 ~~~~Li~~~~~~~~~~~i~~~~A~~~e~~g~~~dAi~Ly~La~~~d~vl~lln~~Ls~~l~~~~~~~~~~s~~~~l~~la 478 (613)
T PF04097_consen 399 RRLSLIKFDDDEDFLREIIEQAAREAEERGRFEDAILLYHLAEEYDKVLSLLNRLLSQVLSQPSSSSLSDSERERLIELA 478 (613)
T ss_dssp HTGGGGT-SSSSHHHHHHHHHHHHHHHHCT-HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCSSTSSSSSTTTTSHHHHH
T ss_pred ccccccCCCCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCccccccccchhhhHHHHH
Confidence 5 554444333 4447778889999999999999999999999999998765433333 35555554
Q ss_pred Hhc
Q 001634 905 TSM 907 (1041)
Q Consensus 905 ~~f 907 (1041)
..+
T Consensus 479 ~~i 481 (613)
T PF04097_consen 479 KEI 481 (613)
T ss_dssp HHH
T ss_pred HHH
Confidence 444
No 9
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.55 E-value=55 Score=42.69 Aligned_cols=94 Identities=18% Similarity=0.203 Sum_probs=63.6
Q ss_pred CcHHHHHHHHHhcCCHHHHHHHHHHcCCCchhhHHhhcCCCchhHHHHHHHHHHHHHcCCCcccChHHHHHHHHHhhCCc
Q 001634 571 SNYLKHIFLLLTGRQLDSSVELAASRGDVRLACLLSQAGGSTVSRSDIAHQLDLWRVNGLDFKFIEKDRIRLYELLAGHI 650 (1041)
Q Consensus 571 ~~~~e~if~lL~g~~I~eAc~lAi~sgd~rLA~LLsq~gs~~~~r~~l~~QL~~W~~~~~d~~~I~~~r~kIY~LLAG~~ 650 (1041)
.+....|-..|..+++.+|+++.++++-+-.|++||..||.+ .+...+ -+--.+.+. +.-+-||++..-+.
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-LLESTR--DKYLAKSNS------KLSRLIYAMVNRDL 558 (1049)
T ss_pred CcHHHHHHHHHHhccHHHHHHHHHhhhHHHHHHHHHhcCCHH-HHHHHH--HHHHHHhCC------hHHHHHHHHHhhhH
Confidence 345666777788889999999999999999999999999966 222222 222223331 23335788877765
Q ss_pred ccccCC-CCCCHHHHHHHHHhccC
Q 001634 651 HSSLND-VTIDWKRFLGLLMWYQL 673 (1041)
Q Consensus 651 ~~~~~~-~~LdW~ralgL~LWYg~ 673 (1041)
...++. .--.||-+|++-+=|..
T Consensus 559 ~~~ve~~~~k~Wke~la~i~t~~~ 582 (1049)
T KOG0307|consen 559 DDYVETCEVKQWKETLAAICTYAQ 582 (1049)
T ss_pred HHHHhhcchhhHHHHHHHHHHhcc
Confidence 433221 11249999999988865
No 10
>PRK11018 hypothetical protein; Provisional
Probab=48.58 E-value=29 Score=31.23 Aligned_cols=31 Identities=6% Similarity=0.205 Sum_probs=27.2
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 152 ~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
-.+.+.+.+++.|-+|++.+...|.|.|.|.
T Consensus 47 a~~di~~~~~~~G~~v~~~~~~~g~~~~~I~ 77 (78)
T PRK11018 47 SINNIPLDARNHGYTVLDIQQDGPTIRYLIQ 77 (78)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCeEEEEEE
Confidence 3467888888999999999989999999986
No 11
>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=48.34 E-value=29 Score=30.35 Aligned_cols=31 Identities=16% Similarity=0.383 Sum_probs=27.6
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 152 ~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
..+-+.+.|++.|-++++++...|.|+|.++
T Consensus 38 a~~di~~~~~~~G~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03420 38 FARDAQAWCKSTGNTLISLETEKGKVKAVIE 68 (69)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 4577889999999999999999999999875
No 12
>KOG2168 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=47.39 E-value=5.3e+02 Score=33.39 Aligned_cols=74 Identities=19% Similarity=0.275 Sum_probs=52.9
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHcCCCc--hhhHHhhc-CCCchh-HHHHHHHH-HHHHH-cCCCcccChHHHHHHHHHhh
Q 001634 574 LKHIFLLLTGRQLDSSVELAASRGDVR--LACLLSQA-GGSTVS-RSDIAHQL-DLWRV-NGLDFKFIEKDRIRLYELLA 647 (1041)
Q Consensus 574 ~e~if~lL~g~~I~eAc~lAi~sgd~r--LA~LLsq~-gs~~~~-r~~l~~QL-~~W~~-~~~d~~~I~~~r~kIY~LLA 647 (1041)
+--||.+|-+|++++|.+..-+++++. ||.+++-. .+.... -.-+..|| ..|+. -|. .--||..++||.+|.
T Consensus 329 W~~vyy~lR~G~lk~A~~~l~e~~~~~~~l~~~f~~y~~A~~~~~~~~le~qlrl~~~~~l~~--~~~DpyK~AvY~iig 406 (835)
T KOG2168|consen 329 WPLVYYLLRCGDLKAASQFLNENKDFFEKLAELFPTYFNAYAKNLSSKLEKQLRLRLRSELGR--NSTDPYKLAVYKIIG 406 (835)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcCCCccccHHHHHHHHHHhcc--ccCChHHHHHHHHHh
Confidence 778999999999999999999999999 99998872 221100 01233444 34543 322 237899999999999
Q ss_pred CC
Q 001634 648 GH 649 (1041)
Q Consensus 648 G~ 649 (1041)
|.
T Consensus 407 ~c 408 (835)
T KOG2168|consen 407 GC 408 (835)
T ss_pred cC
Confidence 93
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=34.01 E-value=67 Score=28.08 Aligned_cols=31 Identities=6% Similarity=0.283 Sum_probs=26.8
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 152 ~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
-.+.+.+.+++.|-+++..+...|.|+|.|.
T Consensus 38 s~~ni~~~~~~~g~~v~~~~~~~~~~~~~i~ 68 (69)
T cd03422 38 SINNIPIDARNHGYKVLAIEQSGPTIRYLIQ 68 (69)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 3577888888999999998888999999975
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=33.21 E-value=68 Score=28.00 Aligned_cols=31 Identities=6% Similarity=0.229 Sum_probs=26.5
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 152 ~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
..+-+.+.++++|-++++...+.|.|.|.|.
T Consensus 38 s~~di~~~~~~~g~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03423 38 TTRDIPKFCTFLGHELLAQETEDEPYRYLIR 68 (69)
T ss_pred hHHHHHHHHHHcCCEEEEEEEcCCEEEEEEE
Confidence 3467888888999999998889999999875
No 15
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=33.18 E-value=69 Score=29.06 Aligned_cols=31 Identities=3% Similarity=0.118 Sum_probs=27.5
Q ss_pred HHHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 152 FVKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 152 ~~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
..+-+.+.|++.|-++++...+.|.|+|.+.
T Consensus 48 ~~~di~~~~~~~G~~~~~~~~~~g~~~~~I~ 78 (81)
T PRK00299 48 TTRDIPSFCRFMDHELLAQETEQLPYRYLIR 78 (81)
T ss_pred HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 5677888899999999999999999999875
No 16
>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]
Probab=32.60 E-value=1.5e+02 Score=36.53 Aligned_cols=36 Identities=22% Similarity=0.441 Sum_probs=27.8
Q ss_pred HhCCCHHHH-HHHHHHHHHHcCCHHHHHHHHHHccCH
Q 001634 841 ALGVPSEWL-HEAMAVYYNYYGELSKALEHFLECANW 876 (1041)
Q Consensus 841 ~L~IP~~WI-~eAkAl~a~~~gd~~~e~~~Ll~A~~~ 876 (1041)
.=++|.+|. |.+.|.|.|.+|+..+++.|...|-+|
T Consensus 206 lq~~~~sw~lH~~as~YWR~~G~~~~A~~Ca~~a~hf 242 (886)
T KOG4507|consen 206 LQKNTSSWVLHNMASFYWRIKGEPYQAVECAMRALHF 242 (886)
T ss_pred hhcCchhHHHHHHHHHHHHHcCChhhhhHHHHHHhhh
Confidence 457898885 667788899999999988886655444
No 17
>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=24.24 E-value=1.3e+02 Score=26.63 Aligned_cols=29 Identities=14% Similarity=0.401 Sum_probs=20.0
Q ss_pred HHHHHHHhhh------------cCCE--EEEEecCCcEEEEEE
Q 001634 153 VKKMKERTER------------QGAR--FVSFDPVSGEWKFLV 181 (1041)
Q Consensus 153 ~~~l~~~~~~------------~~~~--f~~y~~~tG~w~F~V 181 (1041)
++||+.+.+. .|.+ -|.||+.||+|+.+.
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 5677776653 2322 589999999887764
No 18
>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=22.94 E-value=1.4e+02 Score=25.61 Aligned_cols=30 Identities=13% Similarity=0.382 Sum_probs=25.9
Q ss_pred HHHHHHHhhhcCCEEEEEecCCcEEEEEEC
Q 001634 153 VKKMKERTERQGARFVSFDPVSGEWKFLVV 182 (1041)
Q Consensus 153 ~~~l~~~~~~~~~~f~~y~~~tG~w~F~V~ 182 (1041)
.+-+.+.++.+|-++++...+.|.|+|.++
T Consensus 39 ~~~i~~~~~~~g~~~~~~~~~~~~~~i~i~ 68 (69)
T cd00291 39 VEDIPAWAKETGHEVLEVEEEGGVYRILIR 68 (69)
T ss_pred HHHHHHHHHHcCCEEEEEEEeCCEEEEEEE
Confidence 466778888899999999989999999875
No 19
>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=20.14 E-value=1.9e+02 Score=36.36 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=30.3
Q ss_pred cCCcHHHHHHHHHhcCCHHHHHHHHHHc-CCCchhhHHhhcCC
Q 001634 569 DESNYLKHIFLLLTGRQLDSSVELAASR-GDVRLACLLSQAGG 610 (1041)
Q Consensus 569 ~~~~~~e~if~lL~g~~I~eAc~lAi~s-gd~rLA~LLsq~gs 610 (1041)
++..++..+--.|.++++.+||+++++. +|..||++|+-+-.
T Consensus 464 sk~Ry~~AAaFFLLag~l~dAv~V~~~~l~D~qLAi~i~Rl~e 506 (631)
T PF12234_consen 464 SKHRYEYAAAFFLLAGSLKDAVNVCLRQLNDPQLAIAIARLYE 506 (631)
T ss_pred hcccHHHHHHHHHhcccHHHHHHHHHHHccChhHHHHHHHHHc
Confidence 4456654444444455899999987665 99999999997743
Done!