Query 028245
Match_columns 211
No_of_seqs 128 out of 180
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:31:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09348 DUF1990: Domain of un 100.0 1.8E-60 3.8E-65 392.9 19.7 157 30-204 1-158 (158)
2 COG4762 Uncharacterized protei 100.0 5.9E-51 1.3E-55 331.7 15.1 159 26-205 8-167 (168)
3 PF10604 Polyketide_cyc2: Poly 87.8 9.5 0.00021 28.4 15.2 81 117-208 58-138 (139)
4 TIGR02266 gmx_TIGR02266 Myxoco 75.5 20 0.00044 25.8 7.3 62 61-128 5-68 (96)
5 cd08865 SRPBCC_10 Ligand-bindi 73.1 34 0.00075 25.1 17.2 100 96-209 39-139 (140)
6 cd07822 SRPBCC_4 Ligand-bindin 68.3 46 0.00099 24.6 15.8 99 99-208 40-140 (141)
7 cd08862 SRPBCC_Smu440-like Lig 42.2 1.4E+02 0.003 22.0 16.1 131 61-209 4-137 (138)
8 cd07824 SRPBCC_6 Ligand-bindin 38.5 1.8E+02 0.004 22.3 16.1 98 97-207 43-145 (146)
9 PF07238 PilZ: PilZ domain; I 36.0 1.5E+02 0.0032 20.5 5.8 40 89-128 35-75 (102)
10 cd08876 START_1 Uncharacterize 29.9 2.7E+02 0.0058 22.5 7.1 50 156-208 145-194 (195)
11 PF06094 AIG2: AIG2-like famil 27.7 25 0.00054 25.6 0.5 7 140-146 2-8 (102)
12 PHA02102 hypothetical protein 26.8 39 0.00084 24.5 1.3 16 153-170 54-69 (72)
13 COG4894 Uncharacterized conser 26.7 1.1E+02 0.0023 25.8 4.0 45 152-197 16-64 (159)
14 PF12357 PLD_C: Phospholipase 25.7 44 0.00096 24.7 1.5 21 143-168 34-54 (74)
15 cd07820 SRPBCC_3 Ligand-bindin 24.4 3.2E+02 0.0069 20.7 13.0 83 96-188 41-123 (137)
16 PF01139 RtcB: tRNA-splicing l 23.9 3.2E+02 0.0068 26.1 7.3 34 140-177 153-200 (420)
17 TIGR02588 conserved hypothetic 22.8 4.1E+02 0.0089 21.4 8.7 59 115-177 63-122 (122)
18 cd06661 GGCT_like GGCT-like do 21.3 43 0.00093 23.9 0.7 17 159-175 44-60 (99)
No 1
>PF09348 DUF1990: Domain of unknown function (DUF1990); InterPro: IPR018960 This entry represents proteins that are functionally uncharacterised.
Probab=100.00 E-value=1.8e-60 Score=392.94 Aligned_cols=157 Identities=36% Similarity=0.627 Sum_probs=150.3
Q ss_pred CCCCCCCCcccCCccccccCCCCCCCCceeeeeEEEecCchhHHHHHHHHHhcccccCceeeEe-cCCCCCCCCcEEEEE
Q 028245 30 NYDTKYKGATAKPVACLKEDQGLSKDGFLLNHARVLVGSGLETYEKGKTALKTWRHFGLNWAFV-DPKTPIQNGVKFCVC 108 (211)
Q Consensus 30 tY~~~~vGaT~~~~~~~~~~~~~~p~Gy~~~~~~~~lG~G~~~F~~A~~aL~~W~~~~~~g~~V-~~~~p~~~G~~v~v~ 108 (211)
||++ ||||+. +.+|+||+|++++++||+|+++|++|+++|++|+||+.+|++| .+++|+.+|++|+++
T Consensus 1 tY~e--vgat~~---------~~~p~Gy~~~~~~~~lG~G~~~f~~A~~al~~W~~~~~~g~~v~~~~~~~~~G~~v~l~ 69 (158)
T PF09348_consen 1 TYPE--VGATRQ---------GELPAGYRHVRRRVRLGSGEAVFERAAAALLSWRMHRRAGVRVRASDPPAAPGRTVVLR 69 (158)
T ss_pred Cccc--ccccCC---------CCCCCCceEEEEEEEccCCchHHHHHHHHHhccCCCCCcEEEEECCCCccCCCCEEEEE
Confidence 8999 999983 4479999999999999999999999999999999999999999 566788999999999
Q ss_pred eeeccceeeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEEEEEecCCchhhhhhhhh
Q 028245 109 VKEFLPWVTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEIVSFSKPADFLSFIGYPY 188 (211)
Q Consensus 109 ~~~~~~~~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I~AFSRPa~~~~rlg~P~ 188 (211)
.+.+++|+.+|||||||+|| ++++||+||||||||| +|||+|.||+|+||+|||+|+|||||++|++||++|+
T Consensus 70 ~~~~~~~~~~p~RVv~v~de------~~r~GF~ygTL~GHpe-~GEE~F~V~~~~dg~V~~~I~afSRP~~~~~rl~~P~ 142 (158)
T PF09348_consen 70 AGVGPLWIRAPCRVVYVVDE------PDRFGFAYGTLPGHPE-RGEERFSVERDDDGSVWFEIRAFSRPASWLARLGYPV 142 (158)
T ss_pred eeccceEEEeeEEEEEEEcC------CceEEEEEEeCCCChh-hcEEEEEEEECCCCeEEEEEEEEecccchHHHhhhHH
Confidence 99888999999999999995 6899999999999999 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 028245 189 VQLRQKYFAHQSVNAV 204 (211)
Q Consensus 189 ~r~~Qr~~~rry~~al 204 (211)
++++|++|+++|++||
T Consensus 143 ~r~~Q~~~~rry~~am 158 (158)
T PF09348_consen 143 ARRAQRRFARRYLRAM 158 (158)
T ss_pred HHHHHHHHHHHHHhhC
Confidence 9999999999999997
No 2
>COG4762 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=5.9e-51 Score=331.73 Aligned_cols=159 Identities=30% Similarity=0.460 Sum_probs=148.7
Q ss_pred cCCCCCCCCCCCcccCCccccccCCCCCCCCceeeeeEEEecCchhHHHHHHHHHhcccccCceeeEecCCCCCCCCcEE
Q 028245 26 SGVFNYDTKYKGATAKPVACLKEDQGLSKDGFLLNHARVLVGSGLETYEKGKTALKTWRHFGLNWAFVDPKTPIQNGVKF 105 (211)
Q Consensus 26 ~~~~tY~~~~vGaT~~~~~~~~~~~~~~p~Gy~~~~~~~~lG~G~~~F~~A~~aL~~W~~~~~~g~~V~~~~p~~~G~~v 105 (211)
+.+++||| +|++. .+.+|+||+|.+++.+||.|++||++|++||++|+||+..|++|..++++.+++.+
T Consensus 8 e~~~~~~e--~g~s~---------~gr~p~g~~~~~~~l~lG~GeacfenA~~aL~sw~~hr~aglrvh~s~s~vv~~~~ 76 (168)
T COG4762 8 ELPLTYPE--VGASA---------TGRLPAGYNHLDVSLQLGTGEACFENAADALMSWGMHRNAGLRVHASSSTVVLVSA 76 (168)
T ss_pred hcCCCccc--ccccc---------cCcCCccccceeEEEEecccHHHHHHHHHHHhcccccccccEEeeccCCceeeeee
Confidence 67899999 99997 36799999999999999999999999999999999999999999999988888666
Q ss_pred EEEeeeccce-eeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEEEEEecCCchhhhh
Q 028245 106 CVCVKEFLPW-VTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEIVSFSKPADFLSFI 184 (211)
Q Consensus 106 ~v~~~~~~~~-~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I~AFSRPa~~~~rl 184 (211)
++.. ++| +++||||+|++|| ++++||+|||||||++ +|||+|.||+|++|+|||+|.+|||||.|++++
T Consensus 77 vllv---g~w~~r~~cRVL~l~d~------~~~~gf~yGTL~ghv~-rgeErflierda~d~V~~~i~sfsr~Al~~skl 146 (168)
T COG4762 77 VLLV---GIWFLRAPCRVLYLIDE------PDVRGFGYGTLPGHVV-RGEERFLIERDAMDSVVFEILSFSRPALWASKL 146 (168)
T ss_pred eeee---eeeeeecccEEEEEecC------CceeEEeecccCCccc-cchhheeEEecCCCcEEEEeeccccchhhhhhh
Confidence 5545 466 8999999999995 7999999999999999 999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHHHHHHHHHHH
Q 028245 185 GYPYVQLRQKYFAHQSVNAVK 205 (211)
Q Consensus 185 g~P~~r~~Qr~~~rry~~al~ 205 (211)
+.|+++.+||+.+++|++.|+
T Consensus 147 a~plv~~vqrr~aq~Ylrgl~ 167 (168)
T COG4762 147 AGPLVAVVQRRIAQRYLRGLK 167 (168)
T ss_pred hhhHHHHHHHHHHHHHHhhcC
Confidence 999999999999999999885
No 3
>PF10604 Polyketide_cyc2: Polyketide cyclase / dehydrase and lipid transport; InterPro: IPR019587 This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily []. ; PDB: 3QRZ_C 3CNW_A 3P9V_A 3OQU_B 3NEF_B 3JRQ_B 3KAY_A 3JRS_A 3KDJ_A 3NMN_C ....
Probab=87.77 E-value=9.5 Score=28.37 Aligned_cols=81 Identities=11% Similarity=0.147 Sum_probs=55.1
Q ss_pred eeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEEEEEecCCchhhhhhhhhHHHHHHHH
Q 028245 117 TLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEIVSFSKPADFLSFIGYPYVQLRQKYF 196 (211)
Q Consensus 117 ~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I~AFSRPa~~~~rlg~P~~r~~Qr~~ 196 (211)
..-++|+...+ ++..+.|.-. +.... .+.-+|.++-.++| ..++....-+| .+...+..|+.+..-+..
T Consensus 58 ~~~~~i~~~~~------~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~g-t~v~~~~~~~~-~~~~~~~~~~~~~~~~~~ 126 (139)
T PF10604_consen 58 TVREEITEYDP------EPRRITWRFV--PSGFT-NGTGRWRFEPVGDG-TRVTWTVEFEP-GLPGWLAGPLLRPAVKRI 126 (139)
T ss_dssp EEEEEEEEEET------TTTEEEEEEE--SSSSC-EEEEEEEEEEETTT-EEEEEEEEEEE-SCTTSCHHHHHHHHHHHH
T ss_pred ceeEEEEEecC------CCcEEEEEEE--eccee-EEEEEEEEEEcCCC-EEEEEEEEEEE-eccchhhHHHHHHHHHHH
Confidence 35567776665 2467776664 33334 57888999988888 55666555555 445666778787777888
Q ss_pred HHHHHHHHHHHh
Q 028245 197 AHQSVNAVKKHL 208 (211)
Q Consensus 197 ~rry~~al~~~v 208 (211)
.++.++.|++.+
T Consensus 127 ~~~~l~~l~~~~ 138 (139)
T PF10604_consen 127 VREALENLKRAA 138 (139)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHhccc
Confidence 888899888875
No 4
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=75.49 E-value=20 Score=25.81 Aligned_cols=62 Identities=13% Similarity=0.088 Sum_probs=41.8
Q ss_pred eeEEEecCchhHHHHHHHHHhcccccCceeeEecCCCCCCCCcEEEEEeeecc--ceeeeceEEEEEeec
Q 028245 61 HARVLVGSGLETYEKGKTALKTWRHFGLNWAFVDPKTPIQNGVKFCVCVKEFL--PWVTLPLQIVYVNES 128 (211)
Q Consensus 61 ~~~~~lG~G~~~F~~A~~aL~~W~~~~~~g~~V~~~~p~~~G~~v~v~~~~~~--~~~~~PcRVV~v~de 128 (211)
+..+.+.++...|+.-. .+ --.+|+++..+.+..+|+.|.+...... ..+...++|+|+.+.
T Consensus 5 ~~~~~~~~~~~~~~~~~---~d---iS~gG~~~~~~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~ 68 (96)
T TIGR02266 5 RLKVDFRTDSEFLRDYS---IN---LSKGGLFIRTRKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPA 68 (96)
T ss_pred EEEEEECChhhHHHHHh---hh---cCCceEEEecCCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCC
Confidence 45677777655443211 11 2336788888888899999988775332 247788999999974
No 5
>cd08865 SRPBCC_10 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.
Probab=73.11 E-value=34 Score=25.13 Aligned_cols=100 Identities=13% Similarity=0.085 Sum_probs=55.9
Q ss_pred CCCCCCCcEEEEEeeeccceeeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCC-eEEEEEEEE
Q 028245 96 KTPIQNGVKFCVCVKEFLPWVTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNN-QVWYEIVSF 174 (211)
Q Consensus 96 ~~p~~~G~~v~v~~~~~~~~~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg-~V~~~I~AF 174 (211)
+.+..+|..+.+.....+..+..-++|+.... +.++- |.... .+. .++..|.++-.++| .|.+++..-
T Consensus 39 ~~~~~~g~~~~~~~~~~g~~~~~~~~v~~~~p-------~~~~~--~~~~~-~~~-~~~~~~~~~~~~~~t~v~~~~~~~ 107 (140)
T cd08865 39 DGPVGVGTRYHQVRKFLGRRIELTYEITEYEP-------GRRVV--FRGSS-GPF-PYEDTYTFEPVGGGTRVRYTAELE 107 (140)
T ss_pred CCCCcCccEEEEEEEecCceEEEEEEEEEecC-------CcEEE--EEecC-CCc-ceEEEEEEEEcCCceEEEEEEEEc
Confidence 34567888887765533333445566654332 34444 44443 377 89999999976665 354555433
Q ss_pred ecCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 028245 175 SKPADFLSFIGYPYVQLRQKYFAHQSVNAVKKHLT 209 (211)
Q Consensus 175 SRPa~~~~rlg~P~~r~~Qr~~~rry~~al~~~v~ 209 (211)
. ..+.++..+++...=+...++.+++|++.+.
T Consensus 108 ~---~~~~~~~~~~~~~~~~~~~~~~l~~lk~~~e 139 (140)
T cd08865 108 P---GGFARLLDPLMAPAFRRRARAALENLKALLE 139 (140)
T ss_pred c---chhHHHHHHHHHHHHhhhhHHHHHHHHHHhh
Confidence 2 2234454554444444444556677766553
No 6
>cd07822 SRPBCC_4 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.
Probab=68.26 E-value=46 Score=24.57 Aligned_cols=99 Identities=17% Similarity=0.116 Sum_probs=54.5
Q ss_pred CCCCcEEEEEeeecc-ceeeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEE-EEEec
Q 028245 99 IQNGVKFCVCVKEFL-PWVTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEI-VSFSK 176 (211)
Q Consensus 99 ~~~G~~v~v~~~~~~-~~~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I-~AFSR 176 (211)
..+|..+.......+ ......++|+.++. +.++.|....-+.-.. .++-.|.++-.++|...++. ..|+-
T Consensus 40 ~~~G~~~~~~~~~~~~~~~~~~~~v~~~~p-------~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~T~~~~~~~~~g 111 (141)
T cd07822 40 LALGARLRFVVKLPGGPPRSFKPRVTEVEP-------PRRLAWRGGLPFPGLL-DGEHSFELEPLGDGGTRFVHRETFSG 111 (141)
T ss_pred cCCCCEEEEEEeCCCCCcEEEEEEEEEEcC-------CCEeEEEecCCCCcEe-eEEEEEEEEEcCCCcEEEEEeeEEEE
Confidence 578999888665332 33556677765443 5788888655443344 57778888876444444443 34443
Q ss_pred CCchhhhhhhhhHHHHHHHHHHHHHHHHHHHh
Q 028245 177 PADFLSFIGYPYVQLRQKYFAHQSVNAVKKHL 208 (211)
Q Consensus 177 Pa~~~~rlg~P~~r~~Qr~~~rry~~al~~~v 208 (211)
+ ..++..++.+..-+.-.++.++.|++.+
T Consensus 112 ~---~~~~~~~~~~~~~~~~~~~~~~~L~~~~ 140 (141)
T cd07822 112 L---LAPLVLLGLGRDLRAGFEAMNEALKARA 140 (141)
T ss_pred E---EhHHhhhhhHHHHhHhHHHHHHHHHHhh
Confidence 2 2233333333333333444556665543
No 7
>cd08862 SRPBCC_Smu440-like Ligand-binding SRPBCC domain of Streptococcus mutans Smu.440 and related proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Streptococcus mutans Smu.440 and related proteins. This domain belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Streptococcus mutans is a dental pathogen, and the leading cause of dental caries. In this pathogen, the gene encoding Smu.440 is in the same operon as the gene encoding SMU.441, a member of the MarR protein family of transcriptional regulators involved in multiple antibiotic resistance. It has been suggested that SMU.440 is involved in polyketide-like antibiotic resistance.
Probab=42.23 E-value=1.4e+02 Score=22.05 Aligned_cols=131 Identities=15% Similarity=0.219 Sum_probs=67.8
Q ss_pred eeEEEecCc-hhHHHHHHHHHhcccccCceeeEecCCCCC-CCCcEEEEEeeeccceeeeceEEEEEeecccccCCcceE
Q 028245 61 HARVLVGSG-LETYEKGKTALKTWRHFGLNWAFVDPKTPI-QNGVKFCVCVKEFLPWVTLPLQIVYVNESIRKKKTAASF 138 (211)
Q Consensus 61 ~~~~~lG~G-~~~F~~A~~aL~~W~~~~~~g~~V~~~~p~-~~G~~v~v~~~~~~~~~~~PcRVV~v~de~~~~~~~~r~ 138 (211)
..++.|-.- +.+|+...+ +.+|.-.-..-..+....+. .+|..+.+.... . ...-.+|+... .+.++
T Consensus 4 ~~~~~i~Ap~~~Vw~~~~d-~~~~~~w~~~~~~~~~~~~~~~~G~~~~~~~~~-~--~~~~~~i~~~~-------p~~~~ 72 (138)
T cd08862 4 EATIVIDAPPERVWAVLTD-VENWPAWTPSVETVRLEGPPPAVGSSFKMKPPG-L--VRSTFTVTELR-------PGHSF 72 (138)
T ss_pred EEEEEEcCCHHHHHHHHHh-hhhcccccCcceEEEEecCCCCCCcEEEEecCC-C--CceEEEEEEec-------CCCEE
Confidence 344445433 245555554 55554211121223323333 778888765531 1 12223443222 24565
Q ss_pred EEEeecCCCCcccceeEEEEEEEcCCCeEEEEE-EEEecCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 028245 139 GFGSGTLQGHLLQAGEERFSIELDDNNQVWYEI-VSFSKPADFLSFIGYPYVQLRQKYFAHQSVNAVKKHLT 209 (211)
Q Consensus 139 GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I-~AFSRPa~~~~rlg~P~~r~~Qr~~~rry~~al~~~v~ 209 (211)
-|.. .-++ . .+.-.|.++-.++|.+.+++ ..|+.|. ..+..++....-+...++.++.|+..+.
T Consensus 73 ~~~~-~~~~--~-~~~~~~~~~~~~~~~t~l~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~lk~~~E 137 (138)
T cd08862 73 TWTG-PAPG--I-SAVHRHEFEAKPDGGVRVTTSESLSGPL---AFLFGLFVGKKLRALLPEWLEGLKAAAE 137 (138)
T ss_pred EEEe-cCCC--E-EEEEEEEEEEcCCCcEEEEEEEEeecch---HHHHHHHHHHHHHhhHHHHHHHHHHHhc
Confidence 5542 2222 4 56677888766545555543 3455553 3335677777677777788888888775
No 8
>cd07824 SRPBCC_6 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.
Probab=38.47 E-value=1.8e+02 Score=22.34 Aligned_cols=98 Identities=11% Similarity=0.230 Sum_probs=55.5
Q ss_pred CCCCCCcEEEEEeeeccce-eeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEEE-EE
Q 028245 97 TPIQNGVKFCVCVKEFLPW-VTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEIV-SF 174 (211)
Q Consensus 97 ~p~~~G~~v~v~~~~~~~~-~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I~-AF 174 (211)
.+...|..+.+......++ +..-++|..+ + .+.++.|. ..|+ . .|+-.|.++-.++| ..++.. .|
T Consensus 43 ~~~~~g~~~~~~~~~~~~~~~~~~~~v~~~--~-----p~~~~~~~---~~g~-~-~~~~~~~~~~~~~g-t~vt~~~~~ 109 (146)
T cd07824 43 DEAGIGARRRYTWRGLLPYRLRFELRVTRI--E-----PLSLLEVR---ASGD-L-EGVGRWTLAPDGSG-TVVRYDWEV 109 (146)
T ss_pred CCCCcceEEEEEEEecCCcEEEEEEEEEee--c-----CCcEEEEE---EEEe-e-eEEEEEEEEEcCCC-EEEEEEEEE
Confidence 3446777765432212222 3333444332 2 24566653 3454 5 67888999876665 445554 56
Q ss_pred ecCCc---hhhhhhhhhHHHHHHHHHHHHHHHHHHH
Q 028245 175 SKPAD---FLSFIGYPYVQLRQKYFAHQSVNAVKKH 207 (211)
Q Consensus 175 SRPa~---~~~rlg~P~~r~~Qr~~~rry~~al~~~ 207 (211)
+-+.. .++.+..|+.+..=+++.+.-+++|++.
T Consensus 110 ~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~L~~~ 145 (146)
T cd07824 110 RTTKPWMNLLAPLARPVFRWNHRRVMRAGEKGLARR 145 (146)
T ss_pred EcCHHHHHhhhHhhhhHHHHhHHHHHHhHHHHHHhh
Confidence 66665 4666667777666666666777777654
No 9
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=35.96 E-value=1.5e+02 Score=20.54 Aligned_cols=40 Identities=8% Similarity=0.020 Sum_probs=26.9
Q ss_pred eeeEecCCCCCCCCcEEEEEeeeccce-eeeceEEEEEeec
Q 028245 89 NWAFVDPKTPIQNGVKFCVCVKEFLPW-VTLPLQIVYVNES 128 (211)
Q Consensus 89 ~g~~V~~~~p~~~G~~v~v~~~~~~~~-~~~PcRVV~v~de 128 (211)
+|+.+..+.+..+|..|.+.......- ....++|+++...
T Consensus 35 ~G~~~~~~~~~~~~~~v~l~~~~~~~~~~~~~~~V~~~~~~ 75 (102)
T PF07238_consen 35 GGCAFRSPKPLEPGDRVRLSFSLPGGGFPIVTGRVVRIQKD 75 (102)
T ss_dssp SEEEEEECTG--TTSEEEEEEECTTTSCEEEEEEEEEEEEE
T ss_pred cceEEEECCCCCCCCEEEEEEEeCCCCeeEEEEEEEEEECC
Confidence 567776666889999888776533322 2388999999984
No 10
>cd08876 START_1 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family. Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the START family (STARDs), it is known which lipids bind in this pocket; these include cholesterol (STARD1, -3, -4, and -5), 25-hydroxycholesterol (STARD5), phosphatidylcholine (STARD2, -7, and -10), phosphatidylethanolamine (STARD10) and ceramides (STARD11). Mammalian STARDs participate in the control of various cellular processes, including lipid trafficking between intracellular compartments, lipid metabolism, and modulation of signaling events. Mutation or altered expression of STARDs is linked to diseases such as cancer, genetic disorders, a
Probab=29.92 E-value=2.7e+02 Score=22.51 Aligned_cols=50 Identities=10% Similarity=0.117 Sum_probs=37.9
Q ss_pred EEEEEEcCCCeEEEEEEEEecCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHh
Q 028245 156 RFSIELDDNNQVWYEIVSFSKPADFLSFIGYPYVQLRQKYFAHQSVNAVKKHL 208 (211)
Q Consensus 156 ~F~Ve~~~dg~V~~~I~AFSRPa~~~~rlg~P~~r~~Qr~~~rry~~al~~~v 208 (211)
.|.++..+++...++..+++-|..|+ -..++..+.+.....-+++|++.+
T Consensus 145 ~~~i~~~~~~~t~vt~~~~~dp~g~i---P~~lv~~~~~~~~~~~l~~l~~~~ 194 (195)
T cd08876 145 QWTFTPLGNGKTRVTYQAYADPGGSI---PGWLANAFAKDAPYNTLENLRKQL 194 (195)
T ss_pred eEEEEECCCCeEEEEEEEEeCCCCCC---CHHHHHHHHHHHHHHHHHHHHHhh
Confidence 47788777888899999999998764 244566667777778888888764
No 11
>PF06094 AIG2: AIG2-like family; InterPro: IPR009288 AIG2 is an Arabidopsis protein that exhibit RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2 []. Its structure consists of a five-stranded beta-barrel surrounded by two alpha-helices and a small beta-sheet. A long flexible alpha-helix protrudes from the structure at the C-terminal end. Conserved residues in a hydrophilic cavity, which are able to bind small ligands, may act as an active site in AIG2-like proteins [].; PDB: 1XHS_A 2KL2_A 1VKB_A 3JUD_A 3JUB_A 3JUC_A 2JQV_A 2QIK_A 2G0Q_A 1V30_A.
Probab=27.68 E-value=25 Score=25.63 Aligned_cols=7 Identities=57% Similarity=0.662 Sum_probs=5.5
Q ss_pred EEeecCC
Q 028245 140 FGSGTLQ 146 (211)
Q Consensus 140 FaYGTLp 146 (211)
|.||||-
T Consensus 2 FvYGTL~ 8 (102)
T PF06094_consen 2 FVYGTLM 8 (102)
T ss_dssp EESSTTS
T ss_pred EEECCCC
Confidence 7888884
No 12
>PHA02102 hypothetical protein
Probab=26.75 E-value=39 Score=24.51 Aligned_cols=16 Identities=31% Similarity=0.721 Sum_probs=13.0
Q ss_pred eeEEEEEEEcCCCeEEEE
Q 028245 153 GEERFSIELDDNNQVWYE 170 (211)
Q Consensus 153 GEE~F~Ve~~~dg~V~~~ 170 (211)
|-|.|.++ .||+||+.
T Consensus 54 g~eaF~~~--SDGsvWm~ 69 (72)
T PHA02102 54 GGEAFVAR--SDGSVWMP 69 (72)
T ss_pred ccceeeec--cCCcEecc
Confidence 67899986 58999984
No 13
>COG4894 Uncharacterized conserved protein [Function unknown]
Probab=26.67 E-value=1.1e+02 Score=25.78 Aligned_cols=45 Identities=20% Similarity=0.274 Sum_probs=34.8
Q ss_pred ceeEEEEEEEcCCCeEEEEE--EEEecCCch--hhhhhhhhHHHHHHHHH
Q 028245 152 AGEERFSIELDDNNQVWYEI--VSFSKPADF--LSFIGYPYVQLRQKYFA 197 (211)
Q Consensus 152 ~GEE~F~Ve~~~dg~V~~~I--~AFSRPa~~--~~rlg~P~~r~~Qr~~~ 197 (211)
++-++|.|. |+||++.|.| ..||.|.+. .--.|-|+..+-|+..+
T Consensus 16 ~~gd~f~I~-d~dgE~af~VeGs~f~i~dtlti~Da~G~~l~~i~~kll~ 64 (159)
T COG4894 16 SFGDAFHIY-DRDGEEAFKVEGSFFSIGDTLTITDASGKTLVSIEQKLLS 64 (159)
T ss_pred hcccceEEE-CCCCcEEEEEeeeEEeeCceEEEEecCCCChHHHHHHHhh
Confidence 677889985 7899998877 789999883 34567788888887654
No 14
>PF12357 PLD_C: Phospholipase D C terminal ; InterPro: IPR024632 Phospholipase D (PLD) catalyses the hydrolysis of the phosphodiester bond of glycerophospholipids to generate phosphatidic acid and a free head group. Phospholipase D activities have been detected in simple to complex organisms from viruses and bacteria to yeast, plants, and mammals []. In higher organisms, PLD specifically catalyzes the hydrolysis of phosphatidylcholine (PC) to phosphatidic acid (PA) and choline and is activated in response to stimulators of vesicle transport, endocytosis, exocytosis, cell migration, and mitosis. This entry represents the C-terminal domain of eukaryotic phospholipase D. The domain is approximately 70 amino acids in length and contains a conserved FPD sequence motif.
Probab=25.70 E-value=44 Score=24.66 Aligned_cols=21 Identities=33% Similarity=0.738 Sum_probs=18.4
Q ss_pred ecCCCCcccceeEEEEEEEcCCCeEE
Q 028245 143 GTLQGHLLQAGEERFSIELDDNNQVW 168 (211)
Q Consensus 143 GTLpGHpe~~GEE~F~Ve~~~dg~V~ 168 (211)
.-||||+. +|=|+.+.||.|.
T Consensus 34 ~dl~GHLl-----~YPv~V~~dG~V~ 54 (74)
T PF12357_consen 34 TDLPGHLL-----KYPVQVDRDGKVT 54 (74)
T ss_pred ccCCCccc-----cCCeEEcCCCCEe
Confidence 66999999 7999999999885
No 15
>cd07820 SRPBCC_3 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.
Probab=24.43 E-value=3.2e+02 Score=20.71 Aligned_cols=83 Identities=14% Similarity=0.118 Sum_probs=45.2
Q ss_pred CCCCCCCcEEEEEeeeccceeeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEcCCCeEEEEEEEEe
Q 028245 96 KTPIQNGVKFCVCVKEFLPWVTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELDDNNQVWYEIVSFS 175 (211)
Q Consensus 96 ~~p~~~G~~v~v~~~~~~~~~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~~dg~V~~~I~AFS 175 (211)
+.++.+|+.+....+.++..+.-=++|+.... +.++.+. ...|=.. .-+-.+.++-.++|...=....|+
T Consensus 41 ~~~~~~G~~~~~~~~~~~~~~~w~~~it~~~p-------~~~f~~~--~~~G~~~-~w~h~~~f~~~~~gT~vt~~v~~~ 110 (137)
T cd07820 41 PGLIYGGARVTYRLRHFGIPQRWTTEITEVEP-------PRRFVDE--QVSGPFR-SWRHTHRFEAIGGGTLMTDRVEYR 110 (137)
T ss_pred CCcccCCcEEEEEEEecCCceEEEEEEEEEcC-------CCeEEEE--eccCCch-hCEEEEEEEECCCceEEEEEEEEe
Confidence 34567889988877755533344555553332 3455544 4445334 455555666555663322334566
Q ss_pred cCCchhhhhhhhh
Q 028245 176 KPADFLSFIGYPY 188 (211)
Q Consensus 176 RPa~~~~rlg~P~ 188 (211)
=|...+.++..|+
T Consensus 111 ~p~g~lg~~~~~~ 123 (137)
T cd07820 111 LPLGPLGRLAAPL 123 (137)
T ss_pred CCchhHHHHHHHH
Confidence 6776666665553
No 16
>PF01139 RtcB: tRNA-splicing ligase RtcB; InterPro: IPR001233 A number of uncharacterised proteins including Escherichia coli rtcB, Mycobacterium tuberculosis MtCY441.01., Caenorhabditis elegans F16A11.2 and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0682 belong to this family.; PDB: 2EPG_B 1UC2_B.
Probab=23.94 E-value=3.2e+02 Score=26.11 Aligned_cols=34 Identities=44% Similarity=0.615 Sum_probs=18.4
Q ss_pred EEeecCCC--CcccceeEEEEEE------------EcCCCeEEEEEEEEecC
Q 028245 140 FGSGTLQG--HLLQAGEERFSIE------------LDDNNQVWYEIVSFSKP 177 (211)
Q Consensus 140 FaYGTLpG--Hpe~~GEE~F~Ve------------~~~dg~V~~~I~AFSRP 177 (211)
-..|||-| |-. |--.|+ ++.+|.||+-|++=||-
T Consensus 153 ~qLGTLGgGNHFi----Eiq~v~~v~~~~~a~~~gl~~~g~v~l~vHsGSRg 200 (420)
T PF01139_consen 153 KQLGTLGGGNHFI----EIQVVEEVFDKEAANALGLDENGQVWLMVHSGSRG 200 (420)
T ss_dssp GGTT---STT-EE----EEEEEEEES-HHHHHHCT--T-TEEEEEEEE--CC
T ss_pred hhcCCCCCCcceE----EeeeeehhcCHHHHhhcCccccceEEEEEecCCcH
Confidence 45799988 887 333444 56669999999999986
No 17
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=22.80 E-value=4.1e+02 Score=21.40 Aligned_cols=59 Identities=12% Similarity=0.085 Sum_probs=40.0
Q ss_pred eeeeceEEEEEeecccccCCcceEEEEeecCCCCcccceeEEEEEEEc-CCCeEEEEEEEEecC
Q 028245 115 WVTLPLQIVYVNESIRKKKTAASFGFGSGTLQGHLLQAGEERFSIELD-DNNQVWYEIVSFSKP 177 (211)
Q Consensus 115 ~~~~PcRVV~v~de~~~~~~~~r~GFaYGTLpGHpe~~GEE~F~Ve~~-~dg~V~~~I~AFSRP 177 (211)
--.+-++|+-......+.-|....=|.| ||||-+ + +=.|.-+.| .+|++..+|.+||-|
T Consensus 63 ~TAasV~V~geL~~~~~v~E~~e~tiDf--l~g~e~-~-~G~~IF~~dP~~g~L~irv~gY~~P 122 (122)
T TIGR02588 63 TTAAAVNIRGELRQAGAVVENAEVTIDY--LASGSK-E-NGTLIFRSDPRNGQLRLRVAGYKEP 122 (122)
T ss_pred cEEEEEEEEEEEccCCceeEEeeEEEEE--cCCCCe-E-eEEEEEccCcccCeEEEEEEeccCC
Confidence 3456778876665422111223344555 999988 3 567888888 478999999999987
No 18
>cd06661 GGCT_like GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avir
Probab=21.26 E-value=43 Score=23.88 Aligned_cols=17 Identities=18% Similarity=0.380 Sum_probs=10.8
Q ss_pred EEEcCCCeEEEEEEEEe
Q 028245 159 IELDDNNQVWYEIVSFS 175 (211)
Q Consensus 159 Ve~~~dg~V~~~I~AFS 175 (211)
+..++++.|+-+|...+
T Consensus 44 ~~~~~~~~v~G~v~~i~ 60 (99)
T cd06661 44 LVPGPGARVWGELYEVD 60 (99)
T ss_pred EEeCCCCEEEEEEEEEC
Confidence 44455667777777666
Done!