Query 023061
Match_columns 288
No_of_seqs 136 out of 254
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:09:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023061.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023061hhsearch_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 9E-105 2E-109 726.0 19.6 268 1-288 1-269 (295)
2 PF03986 Autophagy_N: Autophag 100.0 4.1E-57 8.8E-62 386.8 -1.2 108 7-116 2-109 (145)
3 PF03987 Autophagy_act_C: Auto 99.9 1.9E-25 4.2E-30 165.4 4.4 62 204-265 1-62 (62)
4 KOG4741 Uncharacterized conser 99.6 7.6E-17 1.7E-21 140.1 3.3 79 197-275 61-142 (173)
5 TIGR01209 RNA ligase, Pab1020 48.6 36 0.00077 34.1 5.4 70 203-283 145-219 (374)
6 cd08587 PI-PLCXDc_like Catalyt 46.8 74 0.0016 29.7 7.1 75 197-276 64-141 (288)
7 smart00258 SAND SAND domain. 36.7 15 0.00033 28.7 0.6 23 29-53 31-53 (73)
8 TIGR03829 YokU_near_AblA uncha 36.0 23 0.00049 28.7 1.6 18 66-83 21-38 (89)
9 KOG3558 Hypoxia-inducible fact 35.2 23 0.00049 38.2 1.9 42 217-274 131-181 (768)
10 PF13833 EF-hand_8: EF-hand do 32.3 21 0.00044 24.5 0.7 13 29-41 1-13 (54)
11 PF09693 Phage_XkdX: Phage unc 30.2 22 0.00047 24.4 0.5 14 26-39 20-33 (40)
12 PF09851 SHOCT: Short C-termin 30.0 22 0.00049 22.9 0.5 15 27-41 11-25 (31)
13 PF00036 EF-hand_1: EF hand; 26.1 30 0.00066 21.8 0.6 13 29-41 13-25 (29)
14 TIGR01669 phage_XkdX phage unc 25.7 32 0.0007 24.3 0.8 14 26-39 25-38 (45)
15 COG1866 PckA Phosphoenolpyruva 24.5 67 0.0014 33.4 3.0 57 222-278 348-418 (529)
16 PF07500 TFIIS_M: Transcriptio 22.7 31 0.00068 28.0 0.2 43 6-58 55-97 (115)
17 PF13405 EF-hand_6: EF-hand do 21.3 43 0.00093 20.7 0.6 13 29-41 13-25 (31)
18 PF08769 Spo0A_C: Sporulation 20.7 49 0.0011 27.2 1.0 40 2-41 60-100 (106)
19 PF01342 SAND: SAND domain; I 20.4 49 0.0011 26.0 0.9 23 29-53 40-62 (82)
No 1
>KOG2981 consensus Protein involved in autophagocytosis during starvation [General function prediction only]
Probab=100.00 E-value=9.4e-105 Score=726.04 Aligned_cols=268 Identities=48% Similarity=0.784 Sum_probs=225.3
Q ss_pred ChhHHHHHHHHhhhhhhhccCCCCCccccccccChHHHHHhcccccccCCccccCCCCCCCCCCCCCCCCeeEEeCCCch
Q 023061 1 MELQQKFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPC 80 (288)
Q Consensus 1 ~~~~~~~~s~~~~v~e~ltPv~~~S~F~etG~LTPeEFV~AGD~LV~k~PTW~W~~gd~~k~k~yLP~dKQfLiTRnVPC 80 (288)
+|+-++|+|+|++||||||||+++|+|++||||||||||+||||||||||||||++|+++|+|+|||+||||||||||||
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 023061 81 LRRAASVEEEYEGAGGEILVDNEDNDGWLATHGKPKAKCDEDEDDNLPSMEAVEISKNNNVRAISTYFGGEEEEEEDIPD 160 (288)
Q Consensus 81 ~~R~~~~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~D 160 (288)
+|||+|| +|..+.+.++. .++++|||+||...... +.+ ............+.+ +..+++++|++|
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------EYI---GKETIHSQDTPAAAP---ESSDEDDDELID 145 (295)
T ss_pred HHHHhhh--hcccccceEEe-ccCCCccccccchhhcc------ccc---chhhcccCCCCcCCc---cccccccccccc
Confidence 9999999 67777666664 45558999999643221 111 111111000111111 236678899999
Q ss_pred ccccCCCCCCccCCCCCCCCCCcccccCCCCCCCcceeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhcc
Q 023061 161 MAEYNEPDSIIENETDPATLPSTYLVAHEPDDDNILRTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQD 240 (288)
Q Consensus 161 m~~~~~~~~l~~~edD~~~~~~~~~~~~~~~~~~i~~~rtYd~~ItYd~~YqtP~l~l~gy~~~g~pL~~~~~~edi~~d 240 (288)
|++++++|++ +|+++++.. +.....++++|+++|||||||+||||||||||||+|||++|+|||+++|+||||+|
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 9999998864 456666542 22333456679999999999999999999999999999999999999999999999
Q ss_pred ccCcceeecCCCCC-CCCceEEecCCcHHHHHHHHHHHHhCCCCCccCC
Q 023061 241 HARKTVTIEDHPHL-TGKHASIHPCRHGAVMKKIIDVLVSRGVEPEVDK 288 (288)
Q Consensus 241 ~~~ktvT~e~HP~l-~~~~~siHPCkha~vMk~l~~~~~~~g~e~~v~~ 288 (288)
|++||||||.|||| +.+|+||||||||+|||+||++++++|++|+|||
T Consensus 221 ha~KTvTiE~hPh~~~~~m~SVHPCkHa~vMkklI~~~~e~g~~l~Vd~ 269 (295)
T KOG2981|consen 221 HAKKTVTIEKHPHLPGPNMASVHPCKHAEVMKKLIDQVRERGDELGVDQ 269 (295)
T ss_pred hccCeEEeccCCCCCCCCccccccchhHHHHHHHHHHHHhcCCCcceeh
Confidence 99999999999999 5569999999999999999999999999999996
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=4.1e-57 Score=386.84 Aligned_cols=108 Identities=52% Similarity=0.924 Sum_probs=43.9
Q ss_pred HHHHHhhhhhhhccCCCCCccccccccChHHHHHhcccccccCCccccCCCCCCCCCCCCCCCCeeEEeCCCchhhhhhh
Q 023061 7 FYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPCLRRAAS 86 (288)
Q Consensus 7 ~~s~~~~v~e~ltPv~~~S~F~etG~LTPeEFV~AGD~LV~k~PTW~W~~gd~~k~k~yLP~dKQfLiTRnVPC~~R~~~ 86 (288)
|+|+|++||||||||+|+|+|++||+|||||||+||||||||||||||++|+++|+|+|||+||||||||||||++||++
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 023061 87 VEEEYEGAGGEILVDNEDNDGWLATHGKPK 116 (288)
Q Consensus 87 ~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~ 116 (288)
+ ++....+.+++++++++|||.||+...
T Consensus 82 ~--~~~~~~e~~~~~~~~ddgWv~t~~~~~ 109 (145)
T PF03986_consen 82 M--EYSEEDEEIVEDDDDDDGWVDTHHNQT 109 (145)
T ss_dssp ------------------------------
T ss_pred c--cccccccceeccCCCCCCeEccCCccc
Confidence 9 455566667777778999999998653
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=1.9e-25 Score=165.44 Aligned_cols=62 Identities=45% Similarity=0.697 Sum_probs=52.3
Q ss_pred EEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhccccCcceeecCCCCCCCCceEEecCC
Q 023061 204 SITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDHARKTVTIEDHPHLTGKHASIHPCR 265 (288)
Q Consensus 204 ~ItYd~~YqtP~l~l~gy~~~g~pL~~~~~~edi~~d~~~ktvT~e~HP~l~~~~~siHPCk 265 (288)
||+||++||||+|||+||+++|+||++++|+++++.+++.++||+++||++|.||++||||+
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=99.64 E-value=7.6e-17 Score=140.13 Aligned_cols=79 Identities=23% Similarity=0.423 Sum_probs=68.3
Q ss_pred eeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhhccc---cCcceeecCCCCCCCCceEEecCCcHHHHHHH
Q 023061 197 RTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDH---ARKTVTIEDHPHLTGKHASIHPCRHGAVMKKI 273 (288)
Q Consensus 197 ~~rtYd~~ItYd~~YqtP~l~l~gy~~~g~pL~~~~~~edi~~d~---~~ktvT~e~HP~l~~~~~siHPCkha~vMk~l 273 (288)
++.++..||.|+..||+|+|||+.|-.+|+||...+|.|..-.+- ..-+||+.+||+||+||+.||||+|+++||.+
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 556778999999999999999999999999999998777543321 12699999999999999999999999999987
Q ss_pred HH
Q 023061 274 ID 275 (288)
Q Consensus 274 ~~ 275 (288)
..
T Consensus 141 ~k 142 (173)
T KOG4741|consen 141 PK 142 (173)
T ss_pred CC
Confidence 53
No 5
>TIGR01209 RNA ligase, Pab1020 family. Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity.
Probab=48.56 E-value=36 Score=34.11 Aligned_cols=70 Identities=16% Similarity=-0.003 Sum_probs=49.9
Q ss_pred EEEEEeCCCCCceeEEeeec----CCCCCCCHHHHHHhhhccccCcceeecCCCCCCCCceEEecCCcHH-HHHHHHHHH
Q 023061 203 ISITYDKYYQTPRVWLTGYD----ESRMLLKTELILEDVSQDHARKTVTIEDHPHLTGKHASIHPCRHGA-VMKKIIDVL 277 (288)
Q Consensus 203 ~~ItYd~~YqtP~l~l~gy~----~~g~pL~~~~~~edi~~d~~~ktvT~e~HP~l~~~~~siHPCkha~-vMk~l~~~~ 277 (288)
.+..|+-+|..--.||+.|| ..|++|+.++..+-+ +.+++-.+|.+.+++=.-+. -++.+|+.+
T Consensus 145 pY~~hs~~y~~l~~~FfvFDI~d~~t~~~L~~~er~~l~-----------e~yglp~Vpvlg~~~~~~~~~~~~eii~~L 213 (374)
T TIGR01209 145 PYTPEYYPEVKEDLGFFLFDIREGKTNRSLPVEERLELA-----------EKYGLPHVEILGVYTADEAVEEIYEIIERL 213 (374)
T ss_pred CCcccCccccCCCceEEEEEEEECCCCccCCHHHHHHHH-----------HHCCCCccceeeEEcHHHHHHHHHHHHHHh
Confidence 45667777777678888887 568999999876532 33344455666667766655 789999999
Q ss_pred HhCCCC
Q 023061 278 VSRGVE 283 (288)
Q Consensus 278 ~~~g~e 283 (288)
.+.|+|
T Consensus 214 ~~~gRE 219 (374)
T TIGR01209 214 NKEGRE 219 (374)
T ss_pred hhcCcc
Confidence 888864
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=46.85 E-value=74 Score=29.73 Aligned_cols=75 Identities=17% Similarity=0.313 Sum_probs=51.8
Q ss_pred eeEEEEEEEEEeCCCCCceeEEeeecCCCCCCCHHHHHHhhh---ccccCcceeecCCCCCCCCceEEecCCcHHHHHHH
Q 023061 197 RTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVS---QDHARKTVTIEDHPHLTGKHASIHPCRHGAVMKKI 273 (288)
Q Consensus 197 ~~rtYd~~ItYd~~YqtP~l~l~gy~~~g~pL~~~~~~edi~---~d~~~ktvT~e~HP~l~~~~~siHPCkha~vMk~l 273 (288)
-+|++||.+.|... ....||+.-.--.+ .++++++++|. ..|.+.+|.+.-+-+.+..-. .++.|..+++.|
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 37999999999765 45678877533333 67788888655 578888888875555432221 678899998776
Q ss_pred HHH
Q 023061 274 IDV 276 (288)
Q Consensus 274 ~~~ 276 (288)
.+.
T Consensus 139 ~~~ 141 (288)
T cd08587 139 EDI 141 (288)
T ss_pred HHH
Confidence 644
No 7
>smart00258 SAND SAND domain.
Probab=36.74 E-value=15 Score=28.69 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=18.3
Q ss_pred cccccChHHHHHhcccccccCCccc
Q 023061 29 EKGVLSVSEFVLAGDNLVSKCPTWS 53 (288)
Q Consensus 29 etG~LTPeEFV~AGD~LV~k~PTW~ 53 (288)
+...+||.||..-|-.--.| .|+
T Consensus 31 ~~~~~TP~eFe~~~g~~~~K--~WK 53 (73)
T smart00258 31 EDKWFTPKEFEIEGGKGKSK--DWK 53 (73)
T ss_pred CCEEEChHHHHhhcCCcccC--Ccc
Confidence 45679999999988877766 676
No 8
>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=35.99 E-value=23 Score=28.73 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=16.3
Q ss_pred CCCCCeeEEeCCCchhhh
Q 023061 66 LPADKQFLITRNVPCLRR 83 (288)
Q Consensus 66 LP~dKQfLiTRnVPC~~R 83 (288)
||++.+.+|.|||||..-
T Consensus 21 l~~G~~~IvIknVPa~~C 38 (89)
T TIGR03829 21 LPDGTKAIEIKETPSISC 38 (89)
T ss_pred ecCCceEEEEecCCcccc
Confidence 899999999999999763
No 9
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=35.21 E-value=23 Score=38.23 Aligned_cols=42 Identities=24% Similarity=0.418 Sum_probs=29.0
Q ss_pred EEeeecCCCCCCCHHHHHHhhhccccCcceeecCCCCCC---------CCceEEecCCcHHHHHHHH
Q 023061 217 WLTGYDESRMLLKTELILEDVSQDHARKTVTIEDHPHLT---------GKHASIHPCRHGAVMKKII 274 (288)
Q Consensus 217 ~l~gy~~~g~pL~~~~~~edi~~d~~~ktvT~e~HP~l~---------~~~~siHPCkha~vMk~l~ 274 (288)
|.+..+++|.-| |...||++ +|| .-|=+||||-|.|+-+.|-
T Consensus 131 FVm~l~~dG~~l------------YiSEtVS~----yLGLSQvELTG~SvFDfiHP~DheE~~eqL~ 181 (768)
T KOG3558|consen 131 FVMALTQDGDFL------------YISETVSI----YLGLSQVELTGSSVFDFIHPCDHEEIAEQLG 181 (768)
T ss_pred eEEEEccCCCEE------------EEechhHh----hhCccceeeecchhhhccCccCHHHHHHHhc
Confidence 455667888777 55555555 443 3466899999999877664
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=32.32 E-value=21 Score=24.49 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=9.6
Q ss_pred cccccChHHHHHh
Q 023061 29 EKGVLSVSEFVLA 41 (288)
Q Consensus 29 etG~LTPeEFV~A 41 (288)
++|.||++||..|
T Consensus 1 ~~G~i~~~~~~~~ 13 (54)
T PF13833_consen 1 KDGKITREEFRRA 13 (54)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CcCEECHHHHHHH
Confidence 4678888888765
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=30.18 E-value=22 Score=24.36 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=11.4
Q ss_pred ccccccccChHHHH
Q 023061 26 AFKEKGVLSVSEFV 39 (288)
Q Consensus 26 ~F~etG~LTPeEFV 39 (288)
.|-..|.||+|||-
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=29.97 E-value=22 Score=22.91 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=12.6
Q ss_pred cccccccChHHHHHh
Q 023061 27 FKEKGVLSVSEFVLA 41 (288)
Q Consensus 27 F~etG~LTPeEFV~A 41 (288)
....|.||.+||-++
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=26.14 E-value=30 Score=21.81 Aligned_cols=13 Identities=23% Similarity=0.350 Sum_probs=10.9
Q ss_pred cccccChHHHHHh
Q 023061 29 EKGVLSVSEFVLA 41 (288)
Q Consensus 29 etG~LTPeEFV~A 41 (288)
..|.|+.+||+.+
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=25.74 E-value=32 Score=24.26 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=11.3
Q ss_pred ccccccccChHHHH
Q 023061 26 AFKEKGVLSVSEFV 39 (288)
Q Consensus 26 ~F~etG~LTPeEFV 39 (288)
.|-+-|.||||||-
T Consensus 25 ~~V~~~~IT~eey~ 38 (45)
T TIGR01669 25 KFVEKKLITREQYK 38 (45)
T ss_pred HHhhcCccCHHHHH
Confidence 46677999999984
No 15
>COG1866 PckA Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion]
Probab=24.52 E-value=67 Score=33.42 Aligned_cols=57 Identities=19% Similarity=0.221 Sum_probs=42.7
Q ss_pred cCCC-----CCCCHHHHHHhhhccccCcceee-----cCCC----CCCCCceEEecCCcHHHHHHHHHHHH
Q 023061 222 DESR-----MLLKTELILEDVSQDHARKTVTI-----EDHP----HLTGKHASIHPCRHGAVMKKIIDVLV 278 (288)
Q Consensus 222 ~~~g-----~pL~~~~~~edi~~d~~~ktvT~-----e~HP----~l~~~~~siHPCkha~vMk~l~~~~~ 278 (288)
|..| .-||++|++=-+.+-|..|+.-- |+-| ++|-||+.+||-+=|+++.++|+...
T Consensus 348 DafGVlPPvsrLTpeQamYhFlsG~TaK~agTE~Gvtep~pTFStCFGaPFmp~hp~~YA~~L~~~i~~~~ 418 (529)
T COG1866 348 DAFGVLPPVSRLTPEQAMYHFLSGYTAKLAGTERGVTEPEPTFSTCFGAPFMPLHPTRYAELLGKLIKAHG 418 (529)
T ss_pred cccCCCCcchhcCHHHHHHHHHcchhhhccccccCCCCCCcccccccCCcccCCChhHHHHHHHHHHHHcC
Confidence 5556 35899998888888787765411 2333 45899999999999999999887653
No 16
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=22.70 E-value=31 Score=28.00 Aligned_cols=43 Identities=19% Similarity=0.164 Sum_probs=25.0
Q ss_pred HHHHHHhhhhhhhccCCCCCccccccccChHHHHHhcccccccCCccccCCCC
Q 023061 6 KFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGE 58 (288)
Q Consensus 6 ~~~s~~~~v~e~ltPv~~~S~F~etG~LTPeEFV~AGD~LV~k~PTW~W~~gd 58 (288)
++++.+.++.+--.|.+...-+ +|.|+|++||. +..+.+++.+
T Consensus 55 k~Rsl~~NLkd~~N~~L~~~il--~g~i~p~~lv~--------ms~~Elas~e 97 (115)
T PF07500_consen 55 KFRSLMFNLKDPKNPDLRRRIL--SGEISPEELVT--------MSPEELASEE 97 (115)
T ss_dssp HHHHHHHHHCSSTTCCHHHHHH--HSSSTTCHHHH--------CTTTTTTTSC
T ss_pred HHHHHHHHhccCCcHHHHHHHH--cCCCCHHHHhc--------CCHHHhCCHH
Confidence 3444444444333355555544 79999999874 3446666543
No 17
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=21.33 E-value=43 Score=20.74 Aligned_cols=13 Identities=15% Similarity=0.299 Sum_probs=10.9
Q ss_pred cccccChHHHHHh
Q 023061 29 EKGVLSVSEFVLA 41 (288)
Q Consensus 29 etG~LTPeEFV~A 41 (288)
..|.||++||.++
T Consensus 13 ~dG~I~~~el~~~ 25 (31)
T PF13405_consen 13 GDGFIDFEELRAI 25 (31)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CCCcCcHHHHHHH
Confidence 4799999999764
No 18
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=20.68 E-value=49 Score=27.17 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=23.8
Q ss_pred hhHHHHHHHHh-hhhhhhccCCCCCccccccccChHHHHHh
Q 023061 2 ELQQKFYGIFK-GTVEKITSHRTVSAFKEKGVLSVSEFVLA 41 (288)
Q Consensus 2 ~~~~~~~s~~~-~v~e~ltPv~~~S~F~etG~LTPeEFV~A 41 (288)
++||++...+. +=.+.|.-+..-+-...+|.-|..||++.
T Consensus 60 aIR~aI~~~w~~g~~~~l~~i~g~~~~~~~~kPTnsEFI~~ 100 (106)
T PF08769_consen 60 AIRHAIEVAWTRGNPELLEKIFGYTINEEKGKPTNSEFIAM 100 (106)
T ss_dssp HHHHHHHHHHHCS-CCCCHHCC-HHHHT-SS---HHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHhCCCcccCCCCCCHHHHHHH
Confidence 46777776666 33556666666666677899999999874
No 19
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=20.41 E-value=49 Score=26.01 Aligned_cols=23 Identities=35% Similarity=0.440 Sum_probs=15.9
Q ss_pred cccccChHHHHHhcccccccCCccc
Q 023061 29 EKGVLSVSEFVLAGDNLVSKCPTWS 53 (288)
Q Consensus 29 etG~LTPeEFV~AGD~LV~k~PTW~ 53 (288)
+.-.+||.||+..|-.--.| -|+
T Consensus 40 ~g~~~TP~eFE~~~G~~~sK--~WK 62 (82)
T PF01342_consen 40 EGRWFTPSEFERHGGKGSSK--DWK 62 (82)
T ss_dssp TTEEE-HHHHHHHHTTCTCS---HH
T ss_pred CCcEECHHHHHhhcCcccCC--CCC
Confidence 36689999999998775555 454
Done!