Query 020931
Match_columns 319
No_of_seqs 154 out of 265
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:17:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2981 Protein involved in au 100.0 7E-117 2E-121 815.0 21.7 294 1-314 1-295 (295)
2 PF03986 Autophagy_N: Autophag 100.0 3.8E-56 8.2E-61 386.0 -1.2 108 7-116 2-109 (145)
3 PF03987 Autophagy_act_C: Auto 99.9 3.1E-25 6.7E-30 166.6 3.9 62 204-265 1-62 (62)
4 KOG4741 Uncharacterized conser 99.7 1.4E-18 2.9E-23 152.8 4.0 95 197-301 61-158 (173)
5 PF10381 Autophagy_Cterm: Auto 99.5 3.2E-15 6.9E-20 93.9 1.9 25 286-310 1-25 (25)
6 cd08587 PI-PLCXDc_like Catalyt 41.2 97 0.0021 29.4 7.1 75 197-276 64-141 (288)
7 COG1866 PckA Phosphoenolpyruva 32.2 28 0.00061 36.5 1.9 53 226-278 357-418 (529)
8 smart00258 SAND SAND domain. 31.0 22 0.00048 28.1 0.8 23 29-53 31-53 (73)
9 TIGR03829 YokU_near_AblA uncha 29.6 33 0.00072 28.1 1.6 29 54-82 4-37 (89)
10 PF13833 EF-hand_8: EF-hand do 29.5 24 0.00052 24.5 0.7 13 29-41 1-13 (54)
11 PF09693 Phage_XkdX: Phage unc 26.9 26 0.00057 24.3 0.5 14 26-39 20-33 (40)
12 PF09851 SHOCT: Short C-termin 25.6 34 0.00073 22.4 0.8 15 27-41 11-25 (31)
13 PF00036 EF-hand_1: EF hand; 23.9 35 0.00077 21.8 0.6 13 29-41 13-25 (29)
14 TIGR01669 phage_XkdX phage unc 22.5 41 0.00088 24.1 0.8 14 26-39 25-38 (45)
15 PRK15460 cpsB mannose-1-phosph 20.3 40 0.00087 35.1 0.5 29 21-57 175-204 (478)
No 1
>KOG2981 consensus Protein involved in autophagocytosis during starvation [General function prediction only]
Probab=100.00 E-value=7.1e-117 Score=814.96 Aligned_cols=294 Identities=51% Similarity=0.822 Sum_probs=249.2
Q ss_pred ChhHHHHHHHHhhhhhhcccCCCcCccccccccChHHHHHhcccccccCCccccCCCCCCCCCCCCCCCCeeEEeCCCcc
Q 020931 1 MELQQKFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPC 80 (319)
Q Consensus 1 ~~~~~~~~s~~~~~~e~ltpv~~~S~F~etG~LTPeEFV~AGD~LV~k~PTW~W~~g~~~k~r~yLP~dKQfLvTRnVPC 80 (319)
+|+-++|+|+|++||||||||+|+|+|++||+|||||||+||||||||||||||++|+++|+|+|||+||||||||||||
T Consensus 1 q~~~n~l~sa~l~~~E~lTpv~k~S~F~etGvitpeEFV~AGD~Lvh~cPTW~W~~gd~~k~r~fLPkdKQfLItRnVpC 80 (295)
T KOG2981|consen 1 QNLANTLKSAALNWREYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWSWAEGDESKIRPFLPKDKQFLITRNVPC 80 (295)
T ss_pred CcHHHHHHHHHHhHHHhcccccchhhhhhcCccCHHHHHhccchhhhcCCccccccCCcccccccCCCCceEEEeccChH
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhccCCcccccCCCCCceeecCCCCCCCCCCCccCCCCCchhhhhhcccccccccCCCCCCCCCcCCccC
Q 020931 81 LRRAASVEEEYEGAGGEILVDNEDNDGWLATHGKPKAKCDEDEDDNLPSMEAVEISKNNNVRAISTYFGGEEEEEEDIPD 160 (319)
Q Consensus 81 ~~R~~~~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~D 160 (319)
+|||++| +|..+.+.++. +++++|||+||...... +.+...+.... ....+.+ +..+++++|++|
T Consensus 81 ~kR~~q~--~~~ee~e~iv~-~Edg~gwvdT~~~ed~l------e~~~~e~ih~~---~t~~~~~---e~~~edddE~~d 145 (295)
T KOG2981|consen 81 YKRCKQM--EYVEELEVIVD-EEDGGGWVDTHNEEDTL------EYIGKETIHSQ---DTPAAAP---ESSDEDDDELID 145 (295)
T ss_pred HHHHhhh--hcccccceEEe-ccCCCccccccchhhcc------cccchhhcccC---CCCcCCc---cccccccccccc
Confidence 9999999 56766555554 45558999999643211 11110000000 0011111 236678899999
Q ss_pred cccCCCCCCCccCCCCCCCCCCcccccCCCCCCCcceeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhhh
Q 020931 161 MAEYNEPDSIIENETDPATLPSTYLVAHEPDDDNILRTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQD 240 (319)
Q Consensus 161 m~~~~~~~~l~~~edD~~~~~~~~~~~~~~~~~~i~~~rtYD~~ItYs~~YqvPrLyl~gy~~~g~PLt~ee~~eDi~~d 240 (319)
|++++++|++ +|++.++.. ......++++|+++|||||||+||+|||||||||+||+++|+||++++||||||+|
T Consensus 146 ~~e~~e~d~~----edp~~~~s~-~~~~~~dd~gil~tRtYDL~I~YdkyYqtPRl~l~Gyde~r~pLt~E~myEDvS~D 220 (295)
T KOG2981|consen 146 MEELEESDEE----EDPATFVSK-AVAGLADDSGILQTRTYDLYITYDKYYQTPRLWLVGYDENRQPLTVEQMYEDVSQD 220 (295)
T ss_pred cccccccccc----cCHHHHhhh-hccccccccccceeeEEEEEEEeeccccCceEEEEEecCCCCcCCHHHHHHHhhhh
Confidence 9999988864 456665442 22333446679999999999999999999999999999999999999999999999
Q ss_pred ccCcceeccCCCCC-CCCceEEecCCcHHHHHHHHHHHHhCCCCCccchhHHHHHHHhhhcccceeecccceeec
Q 020931 241 HARKTVTIEDHPHL-TGKHASIHPCRHGAVMKKIIDVLVSRGVEPEVDKYLFLFLKFVASVIPTIEYDYTMDFDL 314 (319)
Q Consensus 241 ~~~ktVT~e~HP~l-g~~~~sIHPCkha~vMk~l~~~~~~~~~~~~v~~YL~ifLkFi~sViPTIEyDyT~~~~~ 314 (319)
|++||||||.|||+ +.+++||||||||+|||+||++++++|.+++|||||++|||||++|||||||||||+|.|
T Consensus 221 ha~KTvTiE~hPh~~~~~m~SVHPCkHa~vMkklI~~~~e~g~~l~Vd~YL~lFLKFv~sViPtiEyDYT~~~~l 295 (295)
T KOG2981|consen 221 HAKKTVTIEKHPHLPGPNMASVHPCKHAEVMKKLIDQVRERGDELGVDQYLILFLKFVQSVIPTIEYDYTMEFWL 295 (295)
T ss_pred hccCeEEeccCCCCCCCCccccccchhHHHHHHHHHHHHhcCCCcceehhHHHHHHHHHhhccceEeeeeeeccC
Confidence 99999999999999 556999999999999999999999999999999999999999999999999999999875
No 2
>PF03986 Autophagy_N: Autophagocytosis associated protein (Atg3), N-terminal domain ; InterPro: IPR007134 Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes. Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. Atg3 is the E2 enzyme for the LC3 lipidation process []. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A []. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme []. It catalyses the conjugation of Atg8 and phosphatidylethanolamine []. This domain is the N-terminal of Atg3 while the C-terminal is represented by IPR007135 from INTERPRO.; PDB: 3T7G_C 2DYT_A.
Probab=100.00 E-value=3.8e-56 Score=385.98 Aligned_cols=108 Identities=52% Similarity=0.924 Sum_probs=43.8
Q ss_pred HHHHHhhhhhhcccCCCcCccccccccChHHHHHhcccccccCCccccCCCCCCCCCCCCCCCCeeEEeCCCcchhhhhh
Q 020931 7 FYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPCLRRAAS 86 (319)
Q Consensus 7 ~~s~~~~~~e~ltpv~~~S~F~etG~LTPeEFV~AGD~LV~k~PTW~W~~g~~~k~r~yLP~dKQfLvTRnVPC~~R~~~ 86 (319)
|+++|++||||||||+|+|+|++||+|||||||+||||||||||||||++|+++++|+|||+||||||||||||++||++
T Consensus 2 l~s~~~~~~e~ltPv~~~S~F~etG~iTPeEFV~AGD~LV~k~PTW~W~~g~~~k~k~yLP~dKQfLvtRnVPC~~R~~~ 81 (145)
T PF03986_consen 2 LRSTFSSVREYLTPVLHESKFKETGVITPEEFVAAGDYLVHKFPTWQWSAGDPSKRKDYLPKDKQFLVTRNVPCYRRAKD 81 (145)
T ss_dssp --------------------HHHHS---HHHHHHHHHHHHHH-TT-EE---TTB---TTS-TT-S-EEEEEEEE-S-TTT
T ss_pred hHHHHHHHHHHhcCCCCcccccccceeCHHHHHHhhhHHHhhCCcceeccCCccccCCCCCCCCeEEEecCcccHHhhhh
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhccCCcccccCCCCCceeecCCCCC
Q 020931 87 VEEEYEGAGGEILVDNEDNDGWLATHGKPK 116 (319)
Q Consensus 87 ~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~ 116 (319)
+. +....+.+++++++++|||.||+...
T Consensus 82 ~~--~~~~~e~~~~~~~~ddgWv~t~~~~~ 109 (145)
T PF03986_consen 82 ME--YSEEDEEIVEDDDDDDGWVDTHHNQT 109 (145)
T ss_dssp ------------------------------
T ss_pred cc--ccccccceeccCCCCCCeEccCCccc
Confidence 94 45555667777788999999998643
No 3
>PF03987 Autophagy_act_C: Autophagocytosis associated protein, active-site domain ; InterPro: IPR007135 Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes. Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. Atg3 is the E2 enzyme for the LC3 lipidation process []. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A []. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [].; PDB: 2DYT_A.
Probab=99.91 E-value=3.1e-25 Score=166.63 Aligned_cols=62 Identities=45% Similarity=0.697 Sum_probs=52.3
Q ss_pred EEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhhhccCcceeccCCCCCCCCceEEecCC
Q 020931 204 SITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDHARKTVTIEDHPHLTGKHASIHPCR 265 (319)
Q Consensus 204 ~ItYs~~YqvPrLyl~gy~~~g~PLt~ee~~eDi~~d~~~ktVT~e~HP~lg~~~~sIHPCk 265 (319)
||+||++||||+|||+||+++|+||++++|+++++++++.++||+++||++|.|+++||||+
T Consensus 1 ~I~Ys~~YqvP~L~f~~~~~~g~~l~~~~~~~~~~~~~~~~~it~~~HP~l~~p~~~iHPC~ 62 (62)
T PF03987_consen 1 HITYSPSYQVPVLYFRGYDEDGSPLSLEEVYEDLSPDSADSTITQEEHPILGIPWYSIHPCD 62 (62)
T ss_dssp EEEEETTTTEEEEEEEEEETT--B--HHHHHTTS-TTTHHHHEEEEE-TTBSS-EEEE-S-S
T ss_pred CEEecCccCCCEEEEEEECCCCCCCCHHHHHHhhccccccceeecccCCCCCCceEEEcCCC
Confidence 79999999999999999999999999999999999999999999999999999999999997
No 4
>KOG4741 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.73 E-value=1.4e-18 Score=152.75 Aligned_cols=95 Identities=20% Similarity=0.404 Sum_probs=81.2
Q ss_pred eeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhhhc---cCcceeccCCCCCCCCceEEecCCcHHHHHHH
Q 020931 197 RTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDH---ARKTVTIEDHPHLTGKHASIHPCRHGAVMKKI 273 (319)
Q Consensus 197 ~~rtYD~~ItYs~~YqvPrLyl~gy~~~g~PLt~ee~~eDi~~d~---~~ktVT~e~HP~lg~~~~sIHPCkha~vMk~l 273 (319)
++.+++.||.|+..||+|+|||..|-.+|+||...+|-|..-.+- -..+||+.+||+||+|++.||||+|+++||.+
T Consensus 61 ~vi~~e~hilyn~kyqvp~lwf~f~~~ngrpl~~r~v~Ei~~t~l~e~~~~~Itq~eHP~Lg~pyy~LHPC~Tse~mke~ 140 (173)
T KOG4741|consen 61 QVINREAHFLYNRKYQVPELWFMFYCRNGRPLRVRQVAEILGTKLEENDAIVITQSEHPTLGIPYYKLHPCDTSELMKEI 140 (173)
T ss_pred HHhhhhheEEEEeeecchhheeehhhcCCCchhhhhhHHhhcCccccCccceeeeccCCcccceeeeecCCcHHHHHhhc
Confidence 556788999999999999999999999999999997777544331 11599999999999999999999999999998
Q ss_pred HHHHHhCCCCCccchhHHHHHHHhhhcc
Q 020931 274 IDVLVSRGVEPEVDKYLFLFLKFVASVI 301 (319)
Q Consensus 274 ~~~~~~~~~~~~v~~YL~ifLkFi~sVi 301 (319)
.. ..+|++.|++..|.++
T Consensus 141 ~k----------~sNyilswiS~yGp~v 158 (173)
T KOG4741|consen 141 PK----------RSNYILSWISAYGPEV 158 (173)
T ss_pred CC----------chHHHHHHHHHhCchh
Confidence 63 2399999998887765
No 5
>PF10381 Autophagy_Cterm: Autophagocytosis associated protein C-terminal; InterPro: IPR019461 Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex []. It carries a highly characteristic conserved FLKF sequence motif. ; PDB: 2DYT_A.
Probab=99.53 E-value=3.2e-15 Score=93.94 Aligned_cols=25 Identities=80% Similarity=1.386 Sum_probs=20.5
Q ss_pred cchhHHHHHHHhhhcccceeecccc
Q 020931 286 VDKYLFLFLKFVASVIPTIEYDYTM 310 (319)
Q Consensus 286 v~~YL~ifLkFi~sViPTIEyDyT~ 310 (319)
|||||++|||||++|||||||||||
T Consensus 1 vd~yl~iFLKFi~sViPtIeyD~t~ 25 (25)
T PF10381_consen 1 VDQYLVIFLKFISSVIPTIEYDYTM 25 (25)
T ss_dssp GGGHHHHHHHHHHHHSTTB--TT--
T ss_pred CceeehhHHHHHhhcCCceeeeccC
Confidence 6899999999999999999999997
No 6
>cd08587 PI-PLCXDc_like Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins. This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs and their bacterial homologs contain a single TIM-barrel type catalytic domain, X domain, which is more closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be
Probab=41.23 E-value=97 Score=29.40 Aligned_cols=75 Identities=17% Similarity=0.313 Sum_probs=53.1
Q ss_pred eeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhh---hhccCcceeccCCCCCCCCceEEecCCcHHHHHHH
Q 020931 197 RTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVS---QDHARKTVTIEDHPHLTGKHASIHPCRHGAVMKKI 273 (319)
Q Consensus 197 ~~rtYD~~ItYs~~YqvPrLyl~gy~~~g~PLt~ee~~eDi~---~d~~~ktVT~e~HP~lg~~~~sIHPCkha~vMk~l 273 (319)
-+|..|+.+.|... ....||+....-.+ .++++++++|. ..|.+.+|.+.-+-+.+..-. .++.|..+++.|
T Consensus 64 GiR~fDlR~~~~~~-~~~~~~~~H~~~~~--~~~~~~l~~i~~fl~~~p~Evvil~~~~~~~~~~~--~~~~~~~l~~~l 138 (288)
T cd08587 64 GIRYFDLRVAYKPD-SENKLYFVHGLYSG--EPVDEVLEDVNDFLDEHPKEVVILDFNHFYGMDDK--SPEDHEKLVELL 138 (288)
T ss_pred CceEEEEEEeecCC-CCCeEEEEeecccc--cCHHHHHHHHHHHHHhCCCcEEEEEEEccccCCcc--cHHHHHHHHHHH
Confidence 47999999999765 56788888433222 67788887654 568888888876655533222 788899999877
Q ss_pred HHH
Q 020931 274 IDV 276 (319)
Q Consensus 274 ~~~ 276 (319)
.+.
T Consensus 139 ~~~ 141 (288)
T cd08587 139 EDI 141 (288)
T ss_pred HHH
Confidence 654
No 7
>COG1866 PckA Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion]
Probab=32.19 E-value=28 Score=36.49 Aligned_cols=53 Identities=19% Similarity=0.165 Sum_probs=39.7
Q ss_pred CCCCHHHHHHhhhhhccCc------ceec---cCCCCCCCCceEEecCCcHHHHHHHHHHHH
Q 020931 226 MLLKTELILEDVSQDHARK------TVTI---EDHPHLTGKHASIHPCRHGAVMKKIIDVLV 278 (319)
Q Consensus 226 ~PLt~ee~~eDi~~d~~~k------tVT~---e~HP~lg~~~~sIHPCkha~vMk~l~~~~~ 278 (319)
.-||++|++=.+.+-|..| .||- ..-+.+|.||+..||-+=|+++.++|+...
T Consensus 357 srLTpeQamYhFlsG~TaK~agTE~Gvtep~pTFStCFGaPFmp~hp~~YA~~L~~~i~~~~ 418 (529)
T COG1866 357 SRLTPEQAMYHFLSGYTAKLAGTERGVTEPEPTFSTCFGAPFMPLHPTRYAELLGKLIKAHG 418 (529)
T ss_pred hhcCHHHHHHHHHcchhhhccccccCCCCCCcccccccCCcccCCChhHHHHHHHHHHHHcC
Confidence 4689999777777766554 4443 123455999999999999999999997643
No 8
>smart00258 SAND SAND domain.
Probab=30.95 E-value=22 Score=28.14 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=18.0
Q ss_pred cccccChHHHHHhcccccccCCccc
Q 020931 29 EKGVLSVSEFVLAGDNLVSKCPTWS 53 (319)
Q Consensus 29 etG~LTPeEFV~AGD~LV~k~PTW~ 53 (319)
+...+||.||..-|-.--.| .|+
T Consensus 31 ~~~~~TP~eFe~~~g~~~~K--~WK 53 (73)
T smart00258 31 EDKWFTPKEFEIEGGKGKSK--DWK 53 (73)
T ss_pred CCEEEChHHHHhhcCCcccC--Ccc
Confidence 45679999999888877666 666
No 9
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=29.55 E-value=33 Score=28.15 Aligned_cols=29 Identities=21% Similarity=0.510 Sum_probs=21.1
Q ss_pred cCCCCC---CCCCCC--CCCCCeeEEeCCCcchh
Q 020931 54 WESGEP---SKRKSY--LPADKQFLITRNVPCLR 82 (319)
Q Consensus 54 W~~g~~---~k~r~y--LP~dKQfLvTRnVPC~~ 82 (319)
|+++.. ++.--+ ||++.+.+|.|||||..
T Consensus 4 ~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~ 37 (89)
T TIGR03829 4 WCEEEKAIARTTTVYWELPDGTKAIEIKETPSIS 37 (89)
T ss_pred ccCCCceecceEEEEEEecCCceEEEEecCCccc
Confidence 775432 233334 89999999999999976
No 10
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=29.54 E-value=24 Score=24.51 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=9.1
Q ss_pred cccccChHHHHHh
Q 020931 29 EKGVLSVSEFVLA 41 (319)
Q Consensus 29 etG~LTPeEFV~A 41 (319)
++|.||++||..|
T Consensus 1 ~~G~i~~~~~~~~ 13 (54)
T PF13833_consen 1 KDGKITREEFRRA 13 (54)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CcCEECHHHHHHH
Confidence 4677777777765
No 11
>PF09693 Phage_XkdX: Phage uncharacterised protein (Phage_XkdX); InterPro: IPR010022 This entry is represented by Bacteriophage 69, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=26.95 E-value=26 Score=24.26 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=11.3
Q ss_pred ccccccccChHHHH
Q 020931 26 AFKEKGVLSVSEFV 39 (319)
Q Consensus 26 ~F~etG~LTPeEFV 39 (319)
.|-..|.||+|||-
T Consensus 20 ~~V~~g~IT~eey~ 33 (40)
T PF09693_consen 20 NFVEAGWITKEEYK 33 (40)
T ss_pred HHhhcCeECHHHHH
Confidence 46678999999984
No 12
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=25.59 E-value=34 Score=22.38 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=12.5
Q ss_pred cccccccChHHHHHh
Q 020931 27 FKEKGVLSVSEFVLA 41 (319)
Q Consensus 27 F~etG~LTPeEFV~A 41 (319)
....|.||.+||-++
T Consensus 11 l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 11 LYDKGEISEEEYEQK 25 (31)
T ss_pred HHHcCCCCHHHHHHH
Confidence 457899999999775
No 13
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=23.87 E-value=35 Score=21.81 Aligned_cols=13 Identities=23% Similarity=0.350 Sum_probs=10.9
Q ss_pred cccccChHHHHHh
Q 020931 29 EKGVLSVSEFVLA 41 (319)
Q Consensus 29 etG~LTPeEFV~A 41 (319)
..|.|+.+||+.+
T Consensus 13 ~dG~I~~~Ef~~~ 25 (29)
T PF00036_consen 13 GDGKIDFEEFKEM 25 (29)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CCCcCCHHHHHHH
Confidence 3699999999874
No 14
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=22.53 E-value=41 Score=24.09 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=11.3
Q ss_pred ccccccccChHHHH
Q 020931 26 AFKEKGVLSVSEFV 39 (319)
Q Consensus 26 ~F~etG~LTPeEFV 39 (319)
.|-+-|.||||||-
T Consensus 25 ~~V~~~~IT~eey~ 38 (45)
T TIGR01669 25 KFVEKKLITREQYK 38 (45)
T ss_pred HHhhcCccCHHHHH
Confidence 46677999999984
No 15
>PRK15460 cpsB mannose-1-phosphate guanyltransferase; Provisional
Probab=20.28 E-value=40 Score=35.06 Aligned_cols=29 Identities=34% Similarity=0.627 Sum_probs=24.5
Q ss_pred CCCcCcccccccc-ChHHHHHhcccccccCCccccCCC
Q 020931 21 HRTVSAFKEKGVL-SVSEFVLAGDNLVSKCPTWSWESG 57 (319)
Q Consensus 21 v~~~S~F~etG~L-TPeEFV~AGD~LV~k~PTW~W~~g 57 (319)
+..-.+|.|+--+ |-++|++.|+|| |++|
T Consensus 175 ~~~V~~F~EKPd~~tA~~yl~~G~y~--------WNsG 204 (478)
T PRK15460 175 AFEVAQFVEKPNLETAQAYVASGEYY--------WNSG 204 (478)
T ss_pred ceEeeEEEeCCCHHHHHHHHHcCCEE--------Eecc
Confidence 3466889999777 899999999999 8887
Done!