Query 027198
Match_columns 226
No_of_seqs 95 out of 97
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:26:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027198.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027198hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02341 RcbX: RbcX protein; 100.0 2.1E-45 4.7E-50 293.4 12.7 102 110-212 8-109 (111)
2 cd00131 PAX Paired Box domain 77.5 7.2 0.00016 31.5 5.7 77 98-174 5-99 (128)
3 smart00351 PAX Paired Box doma 64.9 13 0.00028 29.8 4.5 58 114-171 25-96 (125)
4 PF12112 DUF3579: Protein of u 60.5 2.7 5.8E-05 33.5 -0.2 24 130-153 63-86 (92)
5 PRK07417 arogenate dehydrogena 52.0 1.2E+02 0.0025 26.8 8.7 99 110-213 171-271 (279)
6 COG4902 Uncharacterized protei 51.1 1E+02 0.0022 27.2 7.9 83 133-223 27-111 (189)
7 PF11985 DUF3486: Protein of u 42.0 1.5E+02 0.0033 24.9 7.5 45 167-213 60-104 (180)
8 PF12234 Rav1p_C: RAVE protein 41.9 55 0.0012 33.8 5.7 70 109-178 481-555 (631)
9 cd02518 GT2_SpsF SpsF is a gly 40.8 31 0.00067 29.0 3.2 29 123-151 196-225 (233)
10 TIGR02865 spore_II_E stage II 35.2 2.9E+02 0.0063 28.8 9.7 65 119-185 373-443 (764)
11 smart00674 CENPB Putative DNA- 34.9 1.3E+02 0.0029 20.6 5.2 17 137-153 47-63 (66)
12 cd08330 CARD_ASC_NALP1 Caspase 34.2 57 0.0012 24.6 3.4 38 135-172 43-80 (82)
13 TIGR01987 HI0074 nucleotidyltr 34.1 88 0.0019 25.5 4.7 65 105-175 34-105 (123)
14 PF09280 XPC-binding: XPC-bind 33.9 71 0.0015 23.1 3.7 31 125-163 24-54 (59)
15 PF14842 FliG_N: FliG N-termin 33.3 1.7E+02 0.0037 22.8 6.1 65 111-175 21-96 (108)
16 PF14677 FANCI_S3: FANCI solen 31.2 55 0.0012 29.1 3.4 25 138-163 191-215 (219)
17 PF03115 Astro_capsid: Astrovi 30.0 17 0.00038 38.2 0.0 52 1-75 147-198 (787)
18 cd06258 Peptidase_M3_like The 29.2 1.3E+02 0.0027 27.4 5.4 60 122-182 7-66 (365)
19 COG1536 FliG Flagellar motor s 25.7 2.7E+02 0.0058 26.6 7.0 61 111-171 205-269 (339)
20 TIGR00207 fliG flagellar motor 24.4 2.4E+02 0.0053 26.4 6.5 33 111-143 202-234 (338)
21 smart00302 GED Dynamin GTPase 22.1 1.2E+02 0.0027 23.0 3.4 14 159-172 58-71 (92)
22 PF02268 TFIIA_gamma_N: Transc 21.7 83 0.0018 22.4 2.2 18 159-176 19-39 (49)
23 PF02947 Flt3_lig: flt3 ligand 21.3 1.4E+02 0.0031 25.4 3.8 36 156-204 41-79 (135)
24 KOG4436 Predicted GTPase activ 21.2 4.6E+02 0.01 28.7 8.2 12 170-181 779-790 (948)
25 KOG1937 Uncharacterized conser 21.0 3.4E+02 0.0073 27.7 6.9 61 114-175 249-311 (521)
26 PF08740 BCS1_N: BCS1 N termin 21.0 1.4E+02 0.0031 24.5 3.8 20 136-155 34-53 (187)
No 1
>PF02341 RcbX: RbcX protein; InterPro: IPR003435 The RbcX protein has been identified as having a possible chaperonin-like function []. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RubisCO in Anabaena sp. (strain CA / ATCC 33047). RbcX has been shown to possess a chaperonin-like function assisting correct folding of RubisCO in Escherichia coli expression studies and is needed for RubisCO to reach its maximal activity [].; PDB: 2PEM_B 2PEI_L 2PEK_A 2Z46_E 2Z44_A 2PEJ_F 2PEN_D 2PEQ_B 2Z45_A 3Q20_A ....
Probab=100.00 E-value=2.1e-45 Score=293.41 Aligned_cols=102 Identities=43% Similarity=0.685 Sum_probs=98.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHhccChhhHHHHHHHHHHHHHHHHHhcc
Q 027198 110 EDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVKQDLAERVMITRLHLYGKWVKKCD 189 (226)
Q Consensus 110 ~DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlRIMeVRehla~EW~~~l~ 189 (226)
.|||++|+|||||+||||||+||+|||||.|.||+||+++|||+|||+||++||+|+|+||+|||+||+|||+++.|+|+
T Consensus 8 kdtak~L~~yfTy~Avr~Vl~QL~etnp~~~~wL~~F~~~~~~~DGd~fl~~L~~e~~~LA~RIM~vR~~la~~~~d~l~ 87 (111)
T PF02341_consen 8 KDTAKVLQSYFTYQAVRTVLAQLYETNPPAYIWLYNFLSRNPLQDGDAFLEALMRENQELALRIMEVREHLAEEVFDFLP 87 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHSTCSSHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHGGGHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCccHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHhH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhh
Q 027198 190 HAQMYKAISDENLELMRERLIET 212 (226)
Q Consensus 190 ~~m~~~~I~e~N~elMRe~L~eT 212 (226)
+|++++|+++|+++||+||.+.
T Consensus 88 -em~~~~I~~~N~e~~R~~L~r~ 109 (111)
T PF02341_consen 88 -EMVREGIQQANMELMRQYLERM 109 (111)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHH
T ss_pred -HHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999875
No 2
>cd00131 PAX Paired Box domain
Probab=77.52 E-value=7.2 Score=31.49 Aligned_cols=77 Identities=12% Similarity=0.026 Sum_probs=51.7
Q ss_pred ecCCCCCc--cc--chHHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCC--------------HHHHH
Q 027198 98 VNEVGGQY--ED--SFEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGD--------------GKHFI 159 (226)
Q Consensus 98 ~~~~GGq~--ed--~f~DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~D--------------GD~fL 159 (226)
+|.+||.| +- +-+.=++++.-|-.=...+.+..+|.=.-+..+.|+..|-++..+.. -+.||
T Consensus 5 ~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i 84 (128)
T cd00131 5 VNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKI 84 (128)
T ss_pred ccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHH
Confidence 45677776 12 22344555555555556777777777777899999999997755421 35778
Q ss_pred HHHhccChhhHHHHH
Q 027198 160 RILGKVKQDLAERVM 174 (226)
Q Consensus 160 ~aLmrE~~eLAlRIM 174 (226)
.++.+++|++-++=|
T Consensus 85 ~~~v~~~p~~Tl~El 99 (128)
T cd00131 85 EIYKQENPGMFAWEI 99 (128)
T ss_pred HHHHHHCCCCCHHHH
Confidence 888888988755544
No 3
>smart00351 PAX Paired Box domain.
Probab=64.88 E-value=13 Score=29.76 Aligned_cols=58 Identities=9% Similarity=-0.069 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCC----H----------HHHHHHHhccChhhHH
Q 027198 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGD----G----------KHFIRILGKVKQDLAE 171 (226)
Q Consensus 114 k~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~D----G----------D~fL~aLmrE~~eLAl 171 (226)
+++.-|-.=...+.+..+|.=.-+..|.|+..|-++..+.. | +.||.++.+++|++-+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~ 96 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFA 96 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCH
Confidence 33333333334566666666666789999999987755543 3 5577777777776643
No 4
>PF12112 DUF3579: Protein of unknown function (DUF3579); InterPro: IPR021969 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif. ; PDB: 2L9D_A.
Probab=60.53 E-value=2.7 Score=33.45 Aligned_cols=24 Identities=21% Similarity=0.474 Sum_probs=20.8
Q ss_pred HHhhccCcchHHHHHhhhhcCCCC
Q 027198 130 HQLYEMNPTQYMWFYNFVATNKPG 153 (226)
Q Consensus 130 ~QL~EtNP~~y~WL~~Fls~npl~ 153 (226)
.+|++.||.+|..+++|...|.++
T Consensus 63 ~~L~~~~P~af~fvm~FA~dN~L~ 86 (92)
T PF12112_consen 63 ERLRDIEPMAFDFVMNFAKDNDLQ 86 (92)
T ss_dssp THHHHH-HHHHHHHHHHHHHHTEE
T ss_pred cHhhhcChHHHHHHHHHHHHCCCe
Confidence 578999999999999999999875
No 5
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=52.01 E-value=1.2e+02 Score=26.84 Aligned_cols=99 Identities=15% Similarity=0.116 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHhccChhhHHHH-HHHHHHHHHHHHHhc
Q 027198 110 EDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVKQDLAERV-MITRLHLYGKWVKKC 188 (226)
Q Consensus 110 ~DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlRI-MeVRehla~EW~~~l 188 (226)
+.+.+...++..|.|.-.+...+.+.++..-.....|.. .-.+| +..+...+|+|=.-| +..|+.+.+..++|.
T Consensus 171 D~~~a~~shlp~~~a~~l~~~~~~~~~~~~~~~~~~~~~-~gfrd----~tRia~~~p~~w~~i~~~N~~~i~~~l~~~~ 245 (279)
T PRK07417 171 DRAVALISHLPVMVSAALIQTCGTEKDPSVLKLAQNLAS-SGFAD----TSRVGGGNPELGVMMAEYNRAALLRSLASYR 245 (279)
T ss_pred HHHHHHHcchHHHHHHHHHHHHhhcccchhhHHhhhhcc-Ccccc----cccccCCChHHHHHHHHHhHHHHHHHHHHHH
Confidence 445555555555666555444444334332222233443 45554 333444566663333 355655544333332
Q ss_pred c-hHHHHHHHHHHHHHHHHHHHHhhc
Q 027198 189 D-HAQMYKAISDENLELMRERLIETV 213 (226)
Q Consensus 189 ~-~~m~~~~I~e~N~elMRe~L~eT~ 213 (226)
. =..+++.|+++|-+-+++.+.++-
T Consensus 246 ~~l~~~~~~l~~~d~~~l~~~~~~~~ 271 (279)
T PRK07417 246 QSLDQLEELIEQENWSALEQKLEQTQ 271 (279)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 2 013667788788777777776653
No 6
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.07 E-value=1e+02 Score=27.24 Aligned_cols=83 Identities=20% Similarity=0.168 Sum_probs=62.5
Q ss_pred hccCcchHHHHHhhhhcCCCCCHHHHHHHHhccChhhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHH--HHH
Q 027198 133 YEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVKQDLAERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRE--RLI 210 (226)
Q Consensus 133 ~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlRIMeVRehla~EW~~~l~~~m~~~~I~e~N~elMRe--~L~ 210 (226)
++||.|.-.-+-.-+...|+.|-+.=----|+|..-||.- |=..+|.+|. ++ +++.|+++--+||-. .|.
T Consensus 27 ~gt~~~s~~~~~~~l~~~plsdeE~nsLiyMrEEEKLARD---VYL~LYnkw~--l~---IF~nIA~SEQ~HmDAVk~Ll 98 (189)
T COG4902 27 EGTNSESTDTSGVTLQDSPLSDEEINSLIYMREEEKLARD---VYLYLYNKWN--LP---IFRNIAASEQEHMDAVKSLL 98 (189)
T ss_pred cCCCCCCccchhhcccCCCCChHHHhhHHHHHHHHHHHhh---HHhhhhhccC--cH---HHHHHHHhHHHHHHHHHHHH
Confidence 3688777766777777889998877666667888888864 3456788996 45 889999999888864 677
Q ss_pred hhccCCCCCCCCC
Q 027198 211 ETVIWPSDDSNTE 223 (226)
Q Consensus 211 eT~~~psd~~n~~ 223 (226)
+-.+.|..+++++
T Consensus 99 ekYnv~dP~~~~s 111 (189)
T COG4902 99 EKYNVQDPASTTS 111 (189)
T ss_pred HHcCCCCCCccCc
Confidence 7778887777654
No 7
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=42.01 E-value=1.5e+02 Score=24.90 Aligned_cols=45 Identities=13% Similarity=0.268 Sum_probs=36.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhhc
Q 027198 167 QDLAERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRERLIETV 213 (226)
Q Consensus 167 ~eLAlRIMeVRehla~EW~~~l~~~m~~~~I~e~N~elMRe~L~eT~ 213 (226)
.+.+.++-+.|+ .++-|.+.+. ..--..+.+.++++++..+.+.+
T Consensus 60 ~~~~~~lr~are-~a~al~~~~~-~~~~~~~~~al~~~~~~~~f~~l 104 (180)
T PF11985_consen 60 EEVLERLREARE-IAEALAEELG-DEPEDDVTEALIEMLQTLLFEAL 104 (180)
T ss_pred HHHHHHHHHHHH-HHHHHHHHhc-CCCcchHHHHHHHHHHHHHHHHH
Confidence 578899999999 8998987765 22345889999999999998876
No 8
>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=41.87 E-value=55 Score=33.77 Aligned_cols=70 Identities=14% Similarity=0.148 Sum_probs=53.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccC-cchHHHHH-hhhhcCCCCCHHHHHHHHhc---cChhhHHHHHHHHH
Q 027198 109 FEDVKKQIQNYFTYKAVRTVLHQLYEMN-PTQYMWFY-NFVATNKPGDGKHFIRILGK---VKQDLAERVMITRL 178 (226)
Q Consensus 109 f~DtAk~L~~yFTY~AVRtVL~QL~EtN-P~~y~WL~-~Fls~npl~DGD~fL~aLmr---E~~eLAlRIMeVRe 178 (226)
..||..++.+++-=.-.-+++.-|+|-+ .|.+.+|. +++--.-+.+||.|++...- .+.+.|.|.+....
T Consensus 481 l~dAv~V~~~~l~D~qLAi~i~Rl~e~d~gp~~~~ll~~~vLp~a~~~~d~wl~s~~~W~L~~~~~ai~~Li~~~ 555 (631)
T PF12234_consen 481 LKDAVNVCLRQLNDPQLAIAIARLYEGDNGPVLKKLLEEHVLPEAIKEGDRWLASWAFWMLGDYDEAIRALISPP 555 (631)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHcCCCchHHHHHHHHhhhccccccCCHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence 4689999999988888888888887754 66666655 56666667899999998764 57888888875543
No 9
>cd02518 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration.
Probab=40.79 E-value=31 Score=29.05 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=22.0
Q ss_pred HHHHHHHHHhhccCcc-hHHHHHhhhhcCC
Q 027198 123 KAVRTVLHQLYEMNPT-QYMWFYNFVATNK 151 (226)
Q Consensus 123 ~AVRtVL~QL~EtNP~-~y~WL~~Fls~np 151 (226)
..++.+..+|++.|++ -+.|+.+|+++||
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p 225 (233)
T cd02518 196 ELIKEIYEALYPKNPDFSLEDIIELLDKNP 225 (233)
T ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhCh
Confidence 4446666778888876 6899999998887
No 10
>TIGR02865 spore_II_E stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs.
Probab=35.17 E-value=2.9e+02 Score=28.83 Aligned_cols=65 Identities=14% Similarity=0.113 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHhc------cChhhHHHHHHHHHHHHHHHH
Q 027198 119 YFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK------VKQDLAERVMITRLHLYGKWV 185 (226)
Q Consensus 119 yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmr------E~~eLAlRIMeVRehla~EW~ 185 (226)
+-||++..-++.++++..... ..+-+.+..+= .-.++|++++-. .|...-.|+.|-|+.+++...
T Consensus 373 ~~Ty~~~~~l~~~~e~~~~~~-~~~p~~~~~~C-~r~~~~~~~~~~~~~~~~~n~~w~~rl~e~R~~va~Ql~ 443 (764)
T TIGR02865 373 DYTYSAMEELIENLEEKKDPN-SKLPDEFERKC-IKRKELINTTEDILNNYIINEMWRKRLEEGRRLVAEQLK 443 (764)
T ss_pred HHHHHHHHHHHHHHHhcCCch-hhhhHHHHHhC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 448999999999999977655 66666665333 345677776654 367889999999998887544
No 11
>smart00674 CENPB Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.
Probab=34.94 E-value=1.3e+02 Score=20.59 Aligned_cols=17 Identities=12% Similarity=0.212 Sum_probs=13.5
Q ss_pred cchHHHHHhhhhcCCCC
Q 027198 137 PTQYMWFYNFVATNKPG 153 (226)
Q Consensus 137 P~~y~WL~~Fls~npl~ 153 (226)
.....||.+|...+++.
T Consensus 47 ~~s~~Wl~rF~~Rh~~~ 63 (66)
T smart00674 47 KASNGWLTRFKKRHNIV 63 (66)
T ss_pred CCCHHHHHHHHHHcCCc
Confidence 46688999999888874
No 12
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=34.20 E-value=57 Score=24.56 Aligned_cols=38 Identities=21% Similarity=0.247 Sum_probs=32.3
Q ss_pred cCcchHHHHHhhhhcCCCCCHHHHHHHHhccChhhHHH
Q 027198 135 MNPTQYMWFYNFVATNKPGDGKHFIRILGKVKQDLAER 172 (226)
Q Consensus 135 tNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlR 172 (226)
|++..+.-|.+++.+-...-=+.|+.+|...+|.|+..
T Consensus 43 T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~p~L~~~ 80 (82)
T cd08330 43 TNQEKMRKLFSFVRSWGASCKDIFYQILREEEPYLVED 80 (82)
T ss_pred CcHHHHHHHHHHHHccCHHHHHHHHHHHHHhChHHHhH
Confidence 77888999999998877777789999997788998864
No 13
>TIGR01987 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909).
Probab=34.08 E-value=88 Score=25.50 Aligned_cols=65 Identities=17% Similarity=0.218 Sum_probs=38.0
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHhccC-------hhhHHHHHH
Q 027198 105 YEDSFEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVK-------QDLAERVMI 175 (226)
Q Consensus 105 ~ed~f~DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~-------~eLAlRIMe 175 (226)
+|=+|+=+=|+|..||.|+.+. ..+.++|.- =+....+.+-|.||+.|++.|-..| .+.|..|..
T Consensus 34 FE~t~ELaWK~lK~~L~~~G~~-----~~~~~spr~-~ir~A~~~glI~d~~~W~~ml~~RN~tsHtYde~~a~~i~~ 105 (123)
T TIGR01987 34 FEFTFELAWKLMKRYLAQEGIN-----DIGAYSPKD-VLKEAFRAGLIGDESLWIAMLDDRNITSHTYDQEKAREIYA 105 (123)
T ss_pred hhhHHHHHHHHHHHHHHHcCCc-----ccccCCHHH-HHHHHHHcCCcCCHHHHHHHHHHhCcccccCCHHHHHHHHH
Confidence 3445544556777776665531 101233222 1445555677899999999987765 456666653
No 14
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=33.93 E-value=71 Score=23.14 Aligned_cols=31 Identities=26% Similarity=0.463 Sum_probs=18.1
Q ss_pred HHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHh
Q 027198 125 VRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILG 163 (226)
Q Consensus 125 VRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLm 163 (226)
+.-+|.||.++||..+....+ |=++|++-|.
T Consensus 24 L~~lLqql~~~nP~l~q~I~~--------n~e~Fl~ll~ 54 (59)
T PF09280_consen 24 LPPLLQQLGQSNPQLLQLIQQ--------NPEEFLRLLN 54 (59)
T ss_dssp HHHHHHHHHCCSHHHHHHHHH--------THHHHHHHHH
T ss_pred HHHHHHHHhccCHHHHHHHHH--------CHHHHHHHHc
Confidence 445667777777776655443 3355665543
No 15
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=33.25 E-value=1.7e+02 Score=22.78 Aligned_cols=65 Identities=12% Similarity=0.268 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccC---c----chHHHHHh-hh-hcCCCCCHHHHHHHHhcc--ChhhHHHHHH
Q 027198 111 DVKKQIQNYFTYKAVRTVLHQLYEMN---P----TQYMWFYN-FV-ATNKPGDGKHFIRILGKV--KQDLAERVMI 175 (226)
Q Consensus 111 DtAk~L~~yFTY~AVRtVL~QL~EtN---P----~~y~WL~~-Fl-s~npl~DGD~fL~aLmrE--~~eLAlRIMe 175 (226)
|+|..+..+|+-.-++-|...+..+. + .....|++ .. ....+..|..|++.|+.. .++-|..||.
T Consensus 21 e~Aa~vlk~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~alg~~~a~~il~ 96 (108)
T PF14842_consen 21 EAAAEVLKHLDEEEIERISREMAKLGSVSPEEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEKALGEEKAKEILD 96 (108)
T ss_dssp HHHHHHHHHS-HHHHHHHHHHHHT-----HHHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHHHS---HHHHH--
T ss_pred HHHHHHHccCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHccccccChHHHHHHHHHHHCCHHHHHHHHH
Confidence 55566666788777777765555544 3 23334444 22 344557899999999876 4777877774
No 16
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=31.23 E-value=55 Score=29.05 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=16.5
Q ss_pred chHHHHHhhhhcCCCCCHHHHHHHHh
Q 027198 138 TQYMWFYNFVATNKPGDGKHFIRILG 163 (226)
Q Consensus 138 ~~y~WL~~Fls~npl~DGD~fL~aLm 163 (226)
..|.|+.+|+.++++.|-. |+.+|+
T Consensus 191 q~~~W~~~~ck~~~l~d~~-~~k~ll 215 (219)
T PF14677_consen 191 QMLSWTLKFCKENSLEDSS-FCKGLL 215 (219)
T ss_dssp HHHHHHHHHHHS---S-HH-HHHHHH
T ss_pred HHHHHHHHHHHhcCCCcHH-HHHHHH
Confidence 6699999999999998754 666654
No 17
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=29.95 E-value=17 Score=38.22 Aligned_cols=52 Identities=29% Similarity=0.328 Sum_probs=0.0
Q ss_pred CCcceeeeccccccCCCCceeeeccCCCcccCCcceEEeecccccchhheecccccccccccccccchhhhhhhh
Q 027198 1 MVGALSVVGSSVMDSHAGPCLCLDALPTSVKGGGELVLRRNSSVKRKKVKVAARSLELGSSFVDSWDDWRLSSKV 75 (226)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~a~p~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~r~~~~~ 75 (226)
|||+-.|.|+.+. -+|-..+.|+...-+ -.|+|||+-|.||- ...|++.+|-
T Consensus 147 lvG~saV~Gtv~r-----~sln~~~~p~~tsws--------~lgARkH~dv~~G~----------~~~~~l~~r~ 198 (787)
T PF03115_consen 147 LVGASAVSGTVVR-----VSLNLTGTPSSTSWS--------GLGARKHVDVPVGR----------PAVFKLTARD 198 (787)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred ccCccccCceEEE-----EEecCCCCCCCCCcc--------ccCceeEEEEcCCC----------ceEEEECHHH
Confidence 7999999999864 345666777765433 47999999986664 2367765543
No 18
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=29.21 E-value=1.3e+02 Score=27.38 Aligned_cols=60 Identities=13% Similarity=0.021 Sum_probs=48.7
Q ss_pred HHHHHHHHHHhhccCcchHHHHHhhhhcCCCCCHHHHHHHHhccChhhHHHHHHHHHHHHH
Q 027198 122 YKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVKQDLAERVMITRLHLYG 182 (226)
Q Consensus 122 Y~AVRtVL~QL~EtNP~~y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlRIMeVRehla~ 182 (226)
++-+|.-++|+-+++...-.||.++... .+.+=++|++.|-+.-+.++.++++.....+.
T Consensus 7 lv~lr~e~A~~lGy~~~~d~~l~~~~~~-~~e~v~~f~~~l~~~~~p~~~~~~~~l~~~~~ 66 (365)
T cd06258 7 LVSLRNQLARLLGYENFADYKLALQEAK-SPETVEGFFEELKRKLRPLLAKLREEISAAKQ 66 (365)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557788889989977888888888876 78899999999988878888888887765543
No 19
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=25.69 E-value=2.7e+02 Score=26.61 Aligned_cols=61 Identities=25% Similarity=0.187 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCcchHHHHHh--hhhcCCCCCHHHHHHHHhcc--ChhhHH
Q 027198 111 DVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYN--FVATNKPGDGKHFIRILGKV--KQDLAE 171 (226)
Q Consensus 111 DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL~~--Fls~npl~DGD~fL~aLmrE--~~eLAl 171 (226)
+++-.+.|++...-.+++++.|++-||+.+.-..+ |.-++=+.=-|..|..|+++ +.+||.
T Consensus 205 ~~~aeIlN~~d~~~e~~il~~l~~~~~~la~~I~~kmF~Fediv~ldd~~iq~lL~~v~~~~La~ 269 (339)
T COG1536 205 KAAAEILNLLDRGTEKTILESLEEEDPELAEEIKEKMFVFEDIVLLDDRSIQRLLREVDKEDLAI 269 (339)
T ss_pred hHHHHHHHhcchhHHHHHHHHHhhcCHHHHHHHHHHHhhHHHHHhccHHHHHHHHHHcCHHHHHH
Confidence 66777889999999999999999999988766554 44444445567788888876 344543
No 20
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=24.37 E-value=2.4e+02 Score=26.36 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCcchHHHH
Q 027198 111 DVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWF 143 (226)
Q Consensus 111 DtAk~L~~yFTY~AVRtVL~QL~EtNP~~y~WL 143 (226)
+.+..+.|.+-...-+.++..|++.||+.+.-.
T Consensus 202 ~~~a~ILN~~~~~~~~~il~~L~~~dp~la~~I 234 (338)
T TIGR00207 202 RAVAEIINLMDRKTEKTIITSLEEFDPELAEEI 234 (338)
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHhCHHHHHHH
Confidence 444456666666667788888888888665444
No 21
>smart00302 GED Dynamin GTPase effector domain.
Probab=22.07 E-value=1.2e+02 Score=22.98 Aligned_cols=14 Identities=14% Similarity=0.235 Sum_probs=11.6
Q ss_pred HHHHhccChhhHHH
Q 027198 159 IRILGKVKQDLAER 172 (226)
Q Consensus 159 L~aLmrE~~eLAlR 172 (226)
+..|+.|+|++|.|
T Consensus 58 ~~~LL~E~~~i~~k 71 (92)
T smart00302 58 LDELLEEDPEIASK 71 (92)
T ss_pred HHHHHcCCHHHHHH
Confidence 78899999988765
No 22
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=21.66 E-value=83 Score=22.35 Aligned_cols=18 Identities=22% Similarity=0.193 Sum_probs=12.7
Q ss_pred HHHHhcc---ChhhHHHHHHH
Q 027198 159 IRILGKV---KQDLAERVMIT 176 (226)
Q Consensus 159 L~aLmrE---~~eLAlRIMeV 176 (226)
|.+|..+ +|+||++||..
T Consensus 19 LDeli~~~~I~p~La~kVL~~ 39 (49)
T PF02268_consen 19 LDELIQEGKITPQLAMKVLEQ 39 (49)
T ss_dssp HHHHHHTTSS-HHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHH
Confidence 4555655 49999999964
No 23
>PF02947 Flt3_lig: flt3 ligand ; InterPro: IPR004213 The flt3 (fms-related tyrosine kinase 3) ligand is a short chain cytokine with a 4 helical bundle fold. It is a type I membrane protein which stimulates the proliferation of of early hematopoeitic cells, and synergises well with other colony stimulating factors and interleukins.; GO: 0005125 cytokine activity, 0016020 membrane; PDB: 3QS7_A 1ETE_C 3QS9_A.
Probab=21.29 E-value=1.4e+02 Score=25.43 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=23.9
Q ss_pred HHHHHHHhccChhhHHHHHHHHHHHHHHHHHhcc---hHHHHHHHHHHHHHH
Q 027198 156 KHFIRILGKVKQDLAERVMITRLHLYGKWVKKCD---HAQMYKAISDENLEL 204 (226)
Q Consensus 156 D~fL~aLmrE~~eLAlRIMeVRehla~EW~~~l~---~~m~~~~I~e~N~el 204 (226)
|+++.+| =|.++|++|.+.|. +..+.+-+..-|+|+
T Consensus 41 de~C~al-------------WhL~Laqr~m~rLk~VaGs~m~~lle~V~tei 79 (135)
T PF02947_consen 41 DELCGAL-------------WHLVLAQRWMERLKTVAGSKMQKLLEKVNTEI 79 (135)
T ss_dssp -TTTHHH-------------HHHHHHHHHHHHHHCTB-HHHHHHHHHHHHHH
T ss_pred HHHHHHH-------------HHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhe
Confidence 5677776 36678888887775 445677777777765
No 24
>KOG4436 consensus Predicted GTPase activator NB4S/EVI5 (contains TBC domain)/Calmodulin-binding protein Pollux (contains PTB and TBC domains) [General function prediction only]
Probab=21.15 E-value=4.6e+02 Score=28.68 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHH
Q 027198 170 AERVMITRLHLY 181 (226)
Q Consensus 170 AlRIMeVRehla 181 (226)
|+-+|.||+.+.
T Consensus 779 a~~llsv~k~~l 790 (948)
T KOG4436|consen 779 ALSLLSVHKQLL 790 (948)
T ss_pred HHHHHHhhHHHH
Confidence 777777775543
No 25
>KOG1937 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.99 E-value=3.4e+02 Score=27.73 Aligned_cols=61 Identities=18% Similarity=0.198 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCcch--HHHHHhhhhcCCCCCHHHHHHHHhccChhhHHHHHH
Q 027198 114 KQIQNYFTYKAVRTVLHQLYEMNPTQ--YMWFYNFVATNKPGDGKHFIRILGKVKQDLAERVMI 175 (226)
Q Consensus 114 k~L~~yFTY~AVRtVL~QL~EtNP~~--y~WL~~Fls~npl~DGD~fL~aLmrE~~eLAlRIMe 175 (226)
..=+..--|+|+.---.|+.+-|... ..-|..=+. .-+.||++||++|+..=.+++.+||+
T Consensus 249 e~kqh~v~~~ales~~sq~~e~~selE~llklkerl~-e~l~dgeayLaKL~~~l~~~~~~~~~ 311 (521)
T KOG1937|consen 249 EYKQHLVEYKALESKRSQFEEQNSELEKLLKLKERLI-EALDDGEAYLAKLMGKLAELNKQMEE 311 (521)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhHHHHH-HhcCChHhHHHHHHHHHHHHHHHHHH
Confidence 33334445666666667777777533 222333232 45689999999999876666666663
No 26
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=20.99 E-value=1.4e+02 Score=24.49 Aligned_cols=20 Identities=10% Similarity=0.443 Sum_probs=16.8
Q ss_pred CcchHHHHHhhhhcCCCCCH
Q 027198 136 NPTQYMWFYNFVATNKPGDG 155 (226)
Q Consensus 136 NP~~y~WL~~Fls~npl~DG 155 (226)
+-+.|.||+.+++++|....
T Consensus 34 ~D~~Y~~lm~Wls~q~~~~~ 53 (187)
T PF08740_consen 34 DDEAYDWLMRWLSSQPFSKR 53 (187)
T ss_pred CCHHHHHHHHHHhhCCcccc
Confidence 44799999999999998653
Done!