Query 022798
Match_columns 292
No_of_seqs 200 out of 1009
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 06:12:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022798.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022798hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1161 Protein involved in va 100.0 1.6E-47 3.5E-52 354.5 20.9 254 1-283 1-260 (310)
2 KOG1162 Predicted small molecu 100.0 8.8E-33 1.9E-37 276.8 17.3 187 1-205 1-212 (617)
3 PF03105 SPX: SPX domain; Int 100.0 1.1E-32 2.4E-37 249.8 16.1 165 1-169 1-274 (275)
4 COG5036 SPX domain-containing 99.9 2.3E-24 5E-29 205.2 14.2 167 1-201 1-170 (509)
5 COG5408 SPX domain-containing 99.7 4.3E-17 9.3E-22 151.4 13.0 52 118-170 241-292 (296)
6 PF10146 zf-C4H2: Zinc finger- 63.7 83 0.0018 28.8 10.1 93 15-139 3-98 (230)
7 PF10112 Halogen_Hydrol: 5-bro 56.1 1.4E+02 0.003 26.1 11.6 69 124-196 117-185 (199)
8 PF07889 DUF1664: Protein of u 48.3 1.5E+02 0.0033 24.7 8.3 67 69-135 39-109 (126)
9 KOG4460 Nuclear pore complex, 38.5 4.3E+02 0.0093 27.7 11.3 72 76-155 605-687 (741)
10 PF10524 NfI_DNAbd_pre-N: Nucl 31.0 94 0.002 21.0 3.6 21 135-155 24-44 (44)
11 PF09763 Sec3_C: Exocyst compl 30.3 6.7E+02 0.015 26.4 16.3 122 71-196 3-135 (701)
12 COG5127 Vacuolar H+-ATPase V1 28.9 33 0.00071 33.0 1.6 21 259-279 30-50 (383)
13 PF01544 CorA: CorA-like Mg2+ 26.0 3.1E+02 0.0067 24.6 7.6 64 82-151 116-179 (292)
14 PF10498 IFT57: Intra-flagella 24.1 6.6E+02 0.014 24.5 9.7 20 16-35 216-235 (359)
15 PF10805 DUF2730: Protein of u 23.8 3.5E+02 0.0075 21.5 6.5 40 95-135 46-85 (106)
16 smart00526 H15 Domain in histo 22.3 46 0.00099 23.9 1.0 21 246-267 10-30 (66)
17 PF10267 Tmemb_cc2: Predicted 22.0 6.5E+02 0.014 25.1 9.3 38 72-109 225-269 (395)
18 PF12176 MtaB: Methanol-cobala 20.9 66 0.0014 32.2 2.1 25 237-261 384-408 (461)
No 1
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.6e-47 Score=354.49 Aligned_cols=254 Identities=43% Similarity=0.584 Sum_probs=207.1
Q ss_pred CcchhHHhHhhhhhcchhhhhcCChHhHHHHHhhhcCCCCCCCCCCCCCCCccccccccccccccccchhHHHHHHHHHH
Q 022798 1 MKFGKSLSNQIEETLPEWRDKFLSYKDLKKRLKLVEPYKGGDRPSKRPRFDESAVAGEDVKATDGYMSREEIDFISLLED 80 (292)
Q Consensus 1 MKFGk~L~~~ie~~vPEW~~~YidYk~LKklIK~~~~~~~~~~~~kr~~~d~~~~~~ed~~~~~~~~~~~e~~F~~~L~~ 80 (292)
|||||.|+.. .+|||+++||+|+.|||+||+.........+. ...+..|++.|+.
T Consensus 1 MkFGk~L~~~---~l~ew~~~yinYk~LKK~lK~~~~~~~~~~~~----------------------~~~e~dFv~~Ld~ 55 (310)
T KOG1161|consen 1 MKFGKYLKEE---LLPEWKDKYINYKELKKLLKQYSIQTADSSPD----------------------SRDESDFVRLLDA 55 (310)
T ss_pred CchhHHHHHh---hhhhHhhhhcCHHHHHHHHHHhccccccCCcc----------------------cchHHHHHHHHHH
Confidence 9999999964 69999999999999999999976543211110 1158899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc---cCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhhhHHHHHHHHHhhc
Q 022798 81 EMDKFNSFFVEKEEEYIIRLKELQDRVANA---NDSNEELIKIRKEIVDLHGEMVLLENYSALNYTAGLVKILKKYDKRT 157 (292)
Q Consensus 81 EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~---~~s~~~~~~l~~~~~el~~el~~L~~f~~LN~t~gf~KILKK~DK~t 157 (292)
||+||+.||.++++++.+|+++|+++++.. .++..++..|++++.+|++||++|.+|++||+| ||+||||||||+|
T Consensus 56 ELEKv~~F~lek~~el~~Rl~~L~e~~~~~~~~~~~~~~~~~lr~~l~~~~~em~~L~~fs~LN~t-Gf~KILKK~DKrt 134 (310)
T KOG1161|consen 56 ELEKVNGFQLEKESELIIRLKELEEKIDALSLEPPSAEEMKELREELVDFHGEMVLLENFSRLNYT-GFAKILKKHDKRT 134 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhHH-HHHHHHHHHhccc
Confidence 999999999999999999999999999742 235678899999999999999999999999999 9999999999999
Q ss_pred CCcccHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccchhcccCCCCCCcCcccccCCccccCchhhHHHH
Q 022798 158 GALIRLPFIQRVLQQPFFTTDLIYRLVKQCEKMLDGLFPKSEKPASTEAAEEGSEPTTSTTTKETSGDILQMPKELAEIE 237 (292)
Q Consensus 158 g~~lr~~f~~~V~~qpF~~~~~l~~Lv~~~E~l~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (292)
|..++.+|.++|..+|||+.+.+++|+.+|+.+|+.+++.+.... . ..+ ++....-.+++.--.....+|...-.+.
T Consensus 135 g~~l~~~f~~~l~~~Pf~~~e~~~~Lv~e~~~l~~~l~~~~~~~~-s-~~~-~~~~~~~~t~k~wvH~~n~~e~k~~~~~ 211 (310)
T KOG1161|consen 135 GYRLRPYFQVRLLHQPFFTTEQLFRLVYEISILLDLLRPSNRNGE-S-KES-NDSDFVRRTTKYWVHEDNVNEVKTYILR 211 (310)
T ss_pred ccccccHHHHHHHhCCCchhhhHHHHHHHHHHHHHHhcccccccc-c-ccc-cchhhhhhccccccCccccchhHHHHhc
Confidence 999999999999999999999999999999999999999887621 1 111 1111111122221222223445566677
Q ss_pred HhhhhHHHh-HHHHHHHHHHHhcCCccccccCCCCCCCCCCC--Ccccc
Q 022798 238 YMESLYMKS-TISALRALKEIRSGSSTVSVFSLPPLQISGLD--DSWKN 283 (292)
Q Consensus 238 ~~~~~~~~~-t~~al~~~~~~~~~sst~~~~s~~~~~~~~~~--~~~~~ 283 (292)
++..+++.+ |++||.++...++||+||+.||+||+..++.+ |.|+.
T Consensus 212 ~lpvL~~~~~~d~ait~~~~~n~~~~~y~~~l~~~~~a~~~rl~w~~~~ 260 (310)
T KOG1161|consen 212 HLPVLVFNSPTDAAITTLYFDNSGSDLYSQFLLKSLLAEALRLRWYGKL 260 (310)
T ss_pred cCcceecCCcchHHHHHHHHhccchHHHHHHhcccccchhhhhhhhcCC
Confidence 778888666 99999999999999999999999999999984 55554
No 2
>KOG1162 consensus Predicted small molecule transporter [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.8e-33 Score=276.77 Aligned_cols=187 Identities=30% Similarity=0.413 Sum_probs=160.2
Q ss_pred CcchhHHhHhhhhhcchhhhhcCChHhHHHHHhhhcCCCCCCCCCCCCCCCccccccccccccccccchhHHHHHHHHHH
Q 022798 1 MKFGKSLSNQIEETLPEWRDKFLSYKDLKKRLKLVEPYKGGDRPSKRPRFDESAVAGEDVKATDGYMSREEIDFISLLED 80 (292)
Q Consensus 1 MKFGk~L~~~ie~~vPEW~~~YidYk~LKklIK~~~~~~~~~~~~kr~~~d~~~~~~ed~~~~~~~~~~~e~~F~~~L~~ 80 (292)
|||||.|..|+ +|||++.||||+.||++||.+....++..++. .... .+...+.+..||+.|+.
T Consensus 1 MKFgk~~~~q~---~pEW~~ay~dY~~lK~~l~~i~~~~~~~~~t~----------~~~~---~~~~~~~~~~Ff~~ld~ 64 (617)
T KOG1162|consen 1 MKFGKELESQL---VPEWRQAYIDYKYLKKLLKEIIENKPSSEETT----------FLMV---SEEGGEFEEVFFRRLDE 64 (617)
T ss_pred CcchHHHHHhc---CHHHHHHhhhHHHHHHHHHHHHhcCCCcCccH----------HHHH---HHhhhhhHHHHHHHHHH
Confidence 99999999995 99999999999999999999877544321110 0000 13346789999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC--------------------C-----HHHHHHHHHHHHHHHHHHHHhh
Q 022798 81 EMDKFNSFFVEKEEEYIIRLKELQDRVANAND--------------------S-----NEELIKIRKEIVDLHGEMVLLE 135 (292)
Q Consensus 81 EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~~~--------------------s-----~~~~~~l~~~~~el~~el~~L~ 135 (292)
|++|||.||.++++|+.++.+.|++|+....+ . ...-++++.+|.|||.-+.+|+
T Consensus 65 el~Kvn~Fy~~k~~e~~~~~~~L~~ql~~~~~~r~~~~~~~~~~~~~~~~~~~f~~~~~~~e~~lk~af~Efy~~L~llk 144 (617)
T KOG1162|consen 65 ELNKVNKFYKEKVKEAREEAEELNKQLDALIALRVKSRSSVDISDRAARLRGKFTKVLRKAEEKLKLAFSEFYLKLRLLK 144 (617)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999865420 0 1123568899999999999999
Q ss_pred hHHHhhhhhhHHHHHHHHHhhcCCcccHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCccch
Q 022798 136 NYSALNYTAGLVKILKKYDKRTGALIRLPFIQRVLQQPFFTTDLIYRLVKQCEKMLDGLFPKSEKPASTE 205 (292)
Q Consensus 136 ~f~~LN~t~gf~KILKK~DK~tg~~lr~~f~~~V~~qpF~~~~~l~~Lv~~~E~l~~~lF~~~~~~~~~~ 205 (292)
+|+.||.+ ||+||+|||||.++.+. ..|++.|...+|.+.+.++.|+.+||++|.++|++||+.++..
T Consensus 145 ~y~~lN~~-~f~KI~KKyDK~~~~~~-~~~~~~v~~s~f~~~~~i~~l~~~Ve~~f~~~fan~nr~~~m~ 212 (617)
T KOG1162|consen 145 NYQFLNVT-AFRKILKKYDKITSRDA-KRYVKMVDKSYFTSSDEITRLMLEVEETFTKHFANGNRRKAMK 212 (617)
T ss_pred HHHHHHHH-HHHHHHHHHHhhcccch-HHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhCCChhHhhh
Confidence 99999999 99999999999999999 8899999999999999999999999999999999999987753
No 3
>PF03105 SPX: SPX domain; InterPro: IPR004331 The SPX domain is named after SYG1/Pho81/XPR1 proteins. This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal [] suggesting that all the members of this family are involved in G-protein associated signal transduction. The C-terminal of these proteins often have an EXS domain (IPR004342 from INTERPRO) []. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family [, ]. NUC-2 contains several ankyrin repeats (IPR002110 from INTERPRO). Several members of this family are the XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with Murine leukemia virus (MLV) []. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae [, ]. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction [, , ] and may itself function as a phosphate sensor [].
Probab=100.00 E-value=1.1e-32 Score=249.83 Aligned_cols=165 Identities=35% Similarity=0.567 Sum_probs=125.2
Q ss_pred CcchhHHhHhhhhhcchhhhhcCChHhHHHHHhhhcCCCCCCCCC----------------CCCC------CCccccccc
Q 022798 1 MKFGKSLSNQIEETLPEWRDKFLSYKDLKKRLKLVEPYKGGDRPS----------------KRPR------FDESAVAGE 58 (292)
Q Consensus 1 MKFGk~L~~~ie~~vPEW~~~YidYk~LKklIK~~~~~~~~~~~~----------------kr~~------~d~~~~~~e 58 (292)
||||+.|+.+ ++|||+++||||+.|||+||.+.......... .... ...+.....
T Consensus 1 MKFgk~L~~~---~vpEW~~~YidYk~LKk~ik~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (275)
T PF03105_consen 1 MKFGKQLQEN---AVPEWRDKYIDYKQLKKLIKRIQNEKESLGLSAETLSSISISSSSSSSSRSSSNSFESTSPSSSNTS 77 (275)
T ss_pred CCchHHHHHh---cCHHHHHHhCCHHHHHHHHHHHHhhhhcccccccccchhhhhhhhhccccccccccccccccccccc
Confidence 9999999997 59999999999999999999987764322000 0000 000000000
Q ss_pred cc---cccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC----------C------------
Q 022798 59 DV---KATDGYMSREEIDFISLLEDEMDKFNSFFVEKEEEYIIRLKELQDRVANAND----------S------------ 113 (292)
Q Consensus 59 d~---~~~~~~~~~~e~~F~~~L~~EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~~~----------s------------ 113 (292)
.. ..........+..|+..|+.||+||+.||.+++.++..+++.|+.++..+.. .
T Consensus 78 ~~~~~~~~~~~~~~~~~~F~~~L~~El~KVn~Fy~~k~~el~~~~~~L~~ql~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (275)
T PF03105_consen 78 PSSSNSEQNEDNEESEEEFFELLDEELEKVNDFYKEKEKELRERLEELQKQLEELREQRSKSSDKYNWNQSSQLSSSSNI 157 (275)
T ss_pred ccccccchhhhhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccccccchhhcccccc
Confidence 00 0001223457899999999999999999999999999999999988754320 0
Q ss_pred --------------------------------------------------------------HHHHHHHHHHHHHHHHHH
Q 022798 114 --------------------------------------------------------------NEELIKIRKEIVDLHGEM 131 (292)
Q Consensus 114 --------------------------------------------------------------~~~~~~l~~~~~el~~el 131 (292)
......++.+|.++|.++
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~e~y~~l 237 (275)
T PF03105_consen 158 FSSSSSASAGSSNSSSASRRSQRFSSESSKQSSNSESDAESDNNRGDRSSDKPFLSSSQKSLKKARKQLKKAFIELYREL 237 (275)
T ss_pred ccCccccccCCccccccccccccchhhhhhccCCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHHH
Confidence 012356889999999999
Q ss_pred HHhhhHHHhhhhhhHHHHHHHHHhhcCCcccHHHHHHh
Q 022798 132 VLLENYSALNYTAGLVKILKKYDKRTGALIRLPFIQRV 169 (292)
Q Consensus 132 ~~L~~f~~LN~t~gf~KILKK~DK~tg~~lr~~f~~~V 169 (292)
.+|++|+.||+| ||+||||||||++|..++..||+.|
T Consensus 238 ~~Lk~f~~LN~t-af~KIlKK~DK~~~~~~~~~y~~~v 274 (275)
T PF03105_consen 238 ELLKSFVELNRT-AFRKILKKYDKVTGTSLSDDYMEEV 274 (275)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHhccccchHhhhhcc
Confidence 999999999999 9999999999999999999999865
No 4
>COG5036 SPX domain-containing protein involved in vacuolar polyphosphate accumulation [Inorganic ion transport and metabolism]
Probab=99.92 E-value=2.3e-24 Score=205.18 Aligned_cols=167 Identities=31% Similarity=0.489 Sum_probs=140.4
Q ss_pred CcchhHHhHhhhhhcchhhhhcCChHhHHHHHhhhcCCCCCCCCCCCCCCCccccccccccccccccchhHHHHHHHHHH
Q 022798 1 MKFGKSLSNQIEETLPEWRDKFLSYKDLKKRLKLVEPYKGGDRPSKRPRFDESAVAGEDVKATDGYMSREEIDFISLLED 80 (292)
Q Consensus 1 MKFGk~L~~~ie~~vPEW~~~YidYk~LKklIK~~~~~~~~~~~~kr~~~d~~~~~~ed~~~~~~~~~~~e~~F~~~L~~ 80 (292)
|+||+.|.+.+ .|+|++.||+|..||++||.-... ..|.+..+.+|++.|+.
T Consensus 1 M~Fg~~L~~~l---y~p~k~~YinYe~LK~~lK~~~~~-------------------------~~w~e~dEsdFVe~Ld~ 52 (509)
T COG5036 1 MRFGKKLKNNL---YPPYKYSYINYENLKKLLKESEEE-------------------------GSWSESDESDFVEELDK 52 (509)
T ss_pred CchhHHHHhcc---CcccccccCCHHHHHHHHhhcccc-------------------------CCCcccchHHHHHHHHH
Confidence 99999999976 999999999999999999982111 03556778999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---CCHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhhhHHHHHHHHHhhc
Q 022798 81 EMDKFNSFFVEKEEEYIIRLKELQDRVANAN---DSNEELIKIRKEIVDLHGEMVLLENYSALNYTAGLVKILKKYDKRT 157 (292)
Q Consensus 81 EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~~---~s~~~~~~l~~~~~el~~el~~L~~f~~LN~t~gf~KILKK~DK~t 157 (292)
||+||..|...++.++.+|+..|+++..... ++. ...+.+.+...++..|.+|..||+| ||.||+|||||++
T Consensus 53 eLeKVY~F~~~k~~ev~erl~~leeq~~~~i~~~ds~----~~~~~LeE~L~~v~~l~kF~RLN~t-GF~KIvKKHDK~~ 127 (509)
T COG5036 53 ELEKVYGFQLSKYSEVMERLRTLEEQTDEAIQELDSD----NFPKILEEELDTVHDLAKFSRLNFT-GFKKIVKKHDKHT 127 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccHHHhhcccCC----cchhHHHHHHHHHHHHHhhhhhhhH-HHHHHHHhhcCCC
Confidence 9999999999999999999999999876332 111 1222455555588899999999999 9999999999999
Q ss_pred CCcccHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022798 158 GALIRLPFIQRVLQQPFFTTDLIYRLVKQCEKMLDGLFPKSEKP 201 (292)
Q Consensus 158 g~~lr~~f~~~V~~qpF~~~~~l~~Lv~~~E~l~~~lF~~~~~~ 201 (292)
|..++..|--++...||+ .+..+.|+-++..+|.-+-..+++-
T Consensus 128 ~y~lkpvfqvrLk~~p~~-se~yd~Ll~kis~LY~~lR~~~~~i 170 (509)
T COG5036 128 GYSLKPVFQVRLKAKPFF-SEQYDPLLYKISSLYNILRSSLSPI 170 (509)
T ss_pred CceechhHHHHhccCCcc-hhhhcHHHHHHHHHHHHHHhcCCcc
Confidence 998988888889999996 6789999999999999887766643
No 5
>COG5408 SPX domain-containing protein [Signal transduction mechanisms]
Probab=99.72 E-value=4.3e-17 Score=151.43 Aligned_cols=52 Identities=35% Similarity=0.568 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHhhhhhhHHHHHHHHHhhcCCcccHHHHHHhh
Q 022798 118 IKIRKEIVDLHGEMVLLENYSALNYTAGLVKILKKYDKRTGALIRLPFIQRVL 170 (292)
Q Consensus 118 ~~l~~~~~el~~el~~L~~f~~LN~t~gf~KILKK~DK~tg~~lr~~f~~~V~ 170 (292)
..+++.+.++|..+..|+.|++||+| ||+||+|||||..+..++..|+....
T Consensus 241 ~~lkk~ii~~y~~l~~lksf~eLN~t-Gf~Ki~KK~DK~l~~~~~~~~~s~~~ 292 (296)
T COG5408 241 SLLKKRIIELYIQLHQLKSFIELNYT-GFSKITKKYDKTLHQNLRHEYMSRSV 292 (296)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhhhhHHHHHHHHHHhh
Confidence 35778999999999999999999999 99999999999999999999987643
No 6
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=63.67 E-value=83 Score=28.83 Aligned_cols=93 Identities=20% Similarity=0.184 Sum_probs=57.6
Q ss_pred cchhhhhcCChHhHHHHHhhhcCCCCCCCCCCCCCCCccccccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 022798 15 LPEWRDKFLSYKDLKKRLKLVEPYKGGDRPSKRPRFDESAVAGEDVKATDGYMSREEIDFISLLEDEMDKFNSFFVEKEE 94 (292)
Q Consensus 15 vPEW~~~YidYk~LKklIK~~~~~~~~~~~~kr~~~d~~~~~~ed~~~~~~~~~~~e~~F~~~L~~EL~KVn~Fy~~ke~ 94 (292)
+.+-+.+=..|..+|.-|..-... ...+..|+..+..|++.+..=+....+
T Consensus 3 i~~ir~K~~~lek~k~~i~~e~~~-----------------------------~e~ee~~L~e~~kE~~~L~~Er~~h~e 53 (230)
T PF10146_consen 3 IKEIRNKTLELEKLKNEILQEVES-----------------------------LENEEKCLEEYRKEMEELLQERMAHVE 53 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666777777666653221 234567888888888887665555544
Q ss_pred HH---HHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 022798 95 EY---IIRLKELQDRVANANDSNEELIKIRKEIVDLHGEMVLLENYSA 139 (292)
Q Consensus 95 el---~~rl~~L~~~i~~~~~s~~~~~~l~~~~~el~~el~~L~~f~~ 139 (292)
+| ..-++.|+.-+... ..+..+.+..+..+|+++.-|+..+.
T Consensus 54 eLrqI~~DIn~lE~iIkqa---~~er~~~~~~i~r~~eey~~Lk~~in 98 (230)
T PF10146_consen 54 ELRQINQDINTLENIIKQA---ESERNKRQEKIQRLYEEYKPLKDEIN 98 (230)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44 33344444444432 45566778888899998888886443
No 7
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=56.10 E-value=1.4e+02 Score=26.12 Aligned_cols=69 Identities=19% Similarity=0.239 Sum_probs=45.1
Q ss_pred HHHHHHHHHHhhhHHHhhhhhhHHHHHHHHHhhcCCcccHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcC
Q 022798 124 IVDLHGEMVLLENYSALNYTAGLVKILKKYDKRTGALIRLPFIQRVLQQPFFTTDLIYRLVKQCEKMLDGLFP 196 (292)
Q Consensus 124 ~~el~~el~~L~~f~~LN~t~gf~KILKK~DK~tg~~lr~~f~~~V~~qpF~~~~~l~~Lv~~~E~l~~~lF~ 196 (292)
+.+==..+...+.|..-=.- +.+|++.||........+..-+...+.+ ....|..|....+..|.+++.
T Consensus 117 v~~~P~~l~~a~~Fl~~yLp-~~~~l~~kY~~l~~~~~~~~~~~~~l~e---~~~~L~~l~~~f~~~~~~l~~ 185 (199)
T PF10112_consen 117 VEKDPERLTQARKFLYYYLP-TAVKLLEKYAELESQPVKSEEIKQSLEE---IEETLDTLNQAFEKDLDKLLE 185 (199)
T ss_pred HHHCHHhHHHHHHHHHHHhh-HHHHHHHHHHHHHhccCCChhHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Confidence 33334556667777766667 9999999999887766544433222211 246777777888888887774
No 8
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=48.29 E-value=1.5e+02 Score=24.70 Aligned_cols=67 Identities=9% Similarity=0.332 Sum_probs=45.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC----CHHHHHHHHHHHHHHHHHHHHhh
Q 022798 69 REEIDFISLLEDEMDKFNSFFVEKEEEYIIRLKELQDRVANAND----SNEELIKIRKEIVDLHGEMVLLE 135 (292)
Q Consensus 69 ~~e~~F~~~L~~EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~~~----s~~~~~~l~~~~~el~~el~~L~ 135 (292)
.....+...+..+|+.|.+=....-.++..|++.|..+++.... ..+++..++..+..+..++..++
T Consensus 39 r~m~~A~~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~ 109 (126)
T PF07889_consen 39 RSMSDAVASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQ 109 (126)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 44677888899999999888888888888888888777765431 12334445555555555554444
No 9
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=38.52 E-value=4.3e+02 Score=27.72 Aligned_cols=72 Identities=18% Similarity=0.224 Sum_probs=45.1
Q ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhhccC--------CHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhh
Q 022798 76 SLLEDEMDKF---NSFFVEKEEEYIIRLKELQDRVANAND--------SNEELIKIRKEIVDLHGEMVLLENYSALNYTA 144 (292)
Q Consensus 76 ~~L~~EL~KV---n~Fy~~ke~el~~rl~~L~~~i~~~~~--------s~~~~~~l~~~~~el~~el~~L~~f~~LN~t~ 144 (292)
..++.|+++| ..|..++.+++..+.+.|...+.++.. ....-+..++++.-+-.++..|.+
T Consensus 605 ~~~~eer~~i~e~a~~La~R~eea~e~qe~L~~~~~~L~~~~~~~lp~l~~AErdFk~Elq~~~~~~~~L~~-------- 676 (741)
T KOG4460|consen 605 SYCREERKSLREMAERLADRYEEAKEKQEDLMNRMKKLLHSFHSELPVLSDAERDFKKELQLIPDQLRHLGN-------- 676 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcccccCCcchhHHHHHHHHHHHhHHHHHHHHH--------
Confidence 3455555555 456667777777777777666655431 122334466677667777777773
Q ss_pred hHHHHHHHHHh
Q 022798 145 GLVKILKKYDK 155 (292)
Q Consensus 145 gf~KILKK~DK 155 (292)
|+.-.-+|+||
T Consensus 677 ~iET~~~~~~K 687 (741)
T KOG4460|consen 677 AIETVTMKKDK 687 (741)
T ss_pred HHHHHHHHHHH
Confidence 77777777777
No 10
>PF10524 NfI_DNAbd_pre-N: Nuclear factor I protein pre-N-terminus; InterPro: IPR019548 Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF) [, ] (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. CTF/NF-I binding sites are present in viral and cellular promoters and in the origin of DNA replication of Human adenovirus 2 (HAdV-2). The CTF/NF-I proteins were first identified as nuclear factor I, a collection of proteins that activate the replication of several Adenovirus serotypes (together with NF-II and NF-III) []. The family of proteins was also identified as the CTF transcription factors, before the NFI and CTF families were found to be identical []. The CTF/NF-I proteins are individually capable of activating transcription and DNA replication. In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 []. This entry represents the N terminus, of which 200 residues contain the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication [].
Probab=31.00 E-value=94 Score=21.01 Aligned_cols=21 Identities=33% Similarity=0.275 Sum_probs=17.7
Q ss_pred hhHHHhhhhhhHHHHHHHHHh
Q 022798 135 ENYSALNYTAGLVKILKKYDK 155 (292)
Q Consensus 135 ~~f~~LN~t~gf~KILKK~DK 155 (292)
-.|.-.|..|+=||-.|||||
T Consensus 24 fay~WfnLQA~KRk~~Kkhek 44 (44)
T PF10524_consen 24 FAYTWFNLQAAKRKHYKKHEK 44 (44)
T ss_pred HHHHHHhHHHHHHHHHHhccC
Confidence 367888888889999999986
No 11
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=30.29 E-value=6.7e+02 Score=26.42 Aligned_cols=122 Identities=15% Similarity=0.132 Sum_probs=74.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC-----------HHHHHHHHHHHHHHHHHHHHhhhHHH
Q 022798 71 EIDFISLLEDEMDKFNSFFVEKEEEYIIRLKELQDRVANANDS-----------NEELIKIRKEIVDLHGEMVLLENYSA 139 (292)
Q Consensus 71 e~~F~~~L~~EL~KVn~Fy~~ke~el~~rl~~L~~~i~~~~~s-----------~~~~~~l~~~~~el~~el~~L~~f~~ 139 (292)
-..|.+.|..||.+++.=.....-+...+++.|...+..+... ...+..++..+..+-..=..| .=..
T Consensus 3 ad~~~~~L~~eL~~le~~ni~~l~~s~~~v~~l~~~ld~a~~e~d~le~~l~~y~~~L~~~~~di~~IE~qn~~L-qvq~ 81 (701)
T PF09763_consen 3 ADAFEERLSKELSALEAANIHSLLESEKQVNSLMEYLDEALAECDELESWLSLYDVELNSVRDDIEYIESQNNGL-QVQS 81 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCch-hhHH
Confidence 4578899999999988777766666666666666655443211 112222333332222222222 2344
Q ss_pred hhhhhhHHHHHHHHHhhcCCcccHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcC
Q 022798 140 LNYTAGLVKILKKYDKRTGALIRLPFIQRVLQQPFFTTDLIYRLVKQCEKMLDGLFP 196 (292)
Q Consensus 140 LN~t~gf~KILKK~DK~tg~~lr~~f~~~V~~qpF~~~~~l~~Lv~~~E~l~~~lF~ 196 (292)
-|.. .+.+-|...-... .+....+..+.+.+|-+.+.|..+...+..+|..+-.
T Consensus 82 ~N~k-~L~~eL~~Ll~~l--~i~~~~l~~L~~~~l~~~~~l~~~e~a~~~L~~Al~~ 135 (701)
T PF09763_consen 82 ANQK-LLLNELENLLDTL--SIPEEHLEALRNASLSSPDGLEKIEEAAEALYKALKA 135 (701)
T ss_pred HHHH-HHHHHHHHHHHhc--CCCHHHHHHHhcCCCCCcccHHHHHHHHHHHHHHHHh
Confidence 5555 4444444433222 3566777888888998888899999999999988766
No 12
>COG5127 Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]
Probab=28.93 E-value=33 Score=33.01 Aligned_cols=21 Identities=48% Similarity=0.623 Sum_probs=18.2
Q ss_pred cCCccccccCCCCCCCCCCCC
Q 022798 259 SGSSTVSVFSLPPLQISGLDD 279 (292)
Q Consensus 259 ~~sst~~~~s~~~~~~~~~~~ 279 (292)
+|+||+|+|-+||+....+|.
T Consensus 30 ggrstvs~f~~P~Fk~~SLd~ 50 (383)
T COG5127 30 GGRSTVSRFLLPSFKGVSLDG 50 (383)
T ss_pred cCccccccccCCCccccchHH
Confidence 899999999999998776653
No 13
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=26.02 E-value=3.1e+02 Score=24.56 Aligned_cols=64 Identities=25% Similarity=0.304 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhhhHHHHHH
Q 022798 82 MDKFNSFFVEKEEEYIIRLKELQDRVANANDSNEELIKIRKEIVDLHGEMVLLENYSALNYTAGLVKILK 151 (292)
Q Consensus 82 L~KVn~Fy~~ke~el~~rl~~L~~~i~~~~~s~~~~~~l~~~~~el~~el~~L~~f~~LN~t~gf~KILK 151 (292)
++.+..-|.....++..++++++..+... .. ......+.++.+++..+++...-+.. .+.+++.
T Consensus 116 l~~~~~~~~~~l~~l~~~l~~le~~~~~~-~~----~~~~~~l~~l~~~l~~l~~~l~~~~~-~l~~~~~ 179 (292)
T PF01544_consen 116 LDEIVDDYFEVLEELEDELDELEDELDDR-PS----NELLRELFDLRRELSRLRRSLSPLRE-VLQRLLR 179 (292)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTHT-TT----HHHCCHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcccc-cc----hhhHHHHHHHHHHHHHHHHHhhhHHH-HHHHHHH
Confidence 45666666667777777888888877321 11 12233455566777777777777777 7777776
No 14
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=24.07 E-value=6.6e+02 Score=24.54 Aligned_cols=20 Identities=25% Similarity=0.529 Sum_probs=9.9
Q ss_pred chhhhhcCChHhHHHHHhhh
Q 022798 16 PEWRDKFLSYKDLKKRLKLV 35 (292)
Q Consensus 16 PEW~~~YidYk~LKklIK~~ 35 (292)
.+||-|+=.=+.+++-|...
T Consensus 216 kDWR~hleqm~~~~~~I~~~ 235 (359)
T PF10498_consen 216 KDWRSHLEQMKQHKKSIESA 235 (359)
T ss_pred chHHHHHHHHHHHHHHHHHh
Confidence 35555555544444444443
No 15
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=23.81 E-value=3.5e+02 Score=21.49 Aligned_cols=40 Identities=23% Similarity=0.425 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhh
Q 022798 95 EYIIRLKELQDRVANANDSNEELIKIRKEIVDLHGEMVLLE 135 (292)
Q Consensus 95 el~~rl~~L~~~i~~~~~s~~~~~~l~~~~~el~~el~~L~ 135 (292)
+...|+..++..++.+ |+.+++..|+..+.++-+++..|.
T Consensus 46 ~~~~Rl~~lE~~l~~L-Pt~~dv~~L~l~l~el~G~~~~l~ 85 (106)
T PF10805_consen 46 EHDRRLQALETKLEHL-PTRDDVHDLQLELAELRGELKELS 85 (106)
T ss_pred HHHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHhHHHHHH
Confidence 4466677777777665 466788888888888888887765
No 16
>smart00526 H15 Domain in histone families 1 and 5.
Probab=22.26 E-value=46 Score=23.87 Aligned_cols=21 Identities=43% Similarity=0.472 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHhcCCcccccc
Q 022798 246 STISALRALKEIRSGSSTVSVF 267 (292)
Q Consensus 246 ~t~~al~~~~~~~~~sst~~~~ 267 (292)
-.+.|+.++.| |+|||...+.
T Consensus 10 mI~eAI~~l~e-r~GsS~~aI~ 30 (66)
T smart00526 10 MITEAISALKE-RKGSSLQAIK 30 (66)
T ss_pred HHHHHHHHcCC-CCCCCHHHHH
Confidence 35689999999 9999876543
No 17
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=22.03 E-value=6.5e+02 Score=25.05 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHhh
Q 022798 72 IDFISLLEDEMDKFNS-------FFVEKEEEYIIRLKELQDRVAN 109 (292)
Q Consensus 72 ~~F~~~L~~EL~KVn~-------Fy~~ke~el~~rl~~L~~~i~~ 109 (292)
.+....|+.+++++.. |+.+...|-..|.+.|++++..
T Consensus 225 k~~~~~L~~~~e~Lk~~~~~e~~~~~~~LqEEr~R~erLEeqlNd 269 (395)
T PF10267_consen 225 KESQSRLEESIEKLKEQYQREYQFILEALQEERYRYERLEEQLND 269 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 3344455555555554 4444444445555556665544
No 18
>PF12176 MtaB: Methanol-cobalamin methyltransferase B subunit; InterPro: IPR021079 This entry represents a family of methanol-cobalamin methyltransferase B subunit (MtaB) proteins found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulphurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C-O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function []. ; PDB: 2I2X_E.
Probab=20.95 E-value=66 Score=32.22 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=20.9
Q ss_pred HHhhhhHHHhHHHHHHHHHHHhcCC
Q 022798 237 EYMESLYMKSTISALRALKEIRSGS 261 (292)
Q Consensus 237 ~~~~~~~~~~t~~al~~~~~~~~~s 261 (292)
+..+++|.|...||+.++++||.|.
T Consensus 384 k~~~d~ylRak~AA~~a~~~i~~~~ 408 (461)
T PF12176_consen 384 KNGDDIYLRAKAAALEAIEIIREGV 408 (461)
T ss_dssp TTTT-HHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCcHHHHHHHHHHHHHHHHHhhh
Confidence 4448899999999999999999864
Done!