Query 025314
Match_columns 254
No_of_seqs 114 out of 214
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:36:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025314.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025314hhsearch_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 1.3E-99 3E-104 679.4 15.6 234 1-254 1-234 (295)
2 PF03986 Autophagy_N: Autophag 100.0 7.6E-59 1.6E-63 390.3 -0.7 108 7-116 2-109 (145)
3 PF03987 Autophagy_act_C: Auto 99.7 9.4E-19 2E-23 127.3 2.5 51 204-254 1-51 (62)
4 KOG4741 Uncharacterized conser 75.2 2.8 6.1E-05 36.7 2.9 53 202-254 66-121 (173)
5 TIGR03829 YokU_near_AblA uncha 44.9 14 0.00031 29.2 1.7 21 66-87 21-41 (89)
6 smart00258 SAND SAND domain. 42.8 11 0.00024 28.7 0.7 23 29-53 31-53 (73)
7 PF13833 EF-hand_8: EF-hand do 37.0 16 0.00034 24.6 0.7 13 29-41 1-13 (54)
8 PF09851 SHOCT: Short C-termin 36.3 16 0.00034 23.1 0.5 15 27-41 11-25 (31)
9 PF09693 Phage_XkdX: Phage unc 34.1 17 0.00037 24.3 0.5 14 26-39 20-33 (40)
10 PF00036 EF-hand_1: EF hand; 30.4 23 0.00049 21.8 0.6 13 29-41 13-25 (29)
11 TIGR01669 phage_XkdX phage unc 29.9 25 0.00054 24.3 0.8 14 26-39 25-38 (45)
12 PF07500 TFIIS_M: Transcriptio 28.6 20 0.00042 28.6 0.1 45 4-58 53-97 (115)
13 PF08769 Spo0A_C: Sporulation 28.1 30 0.00064 27.8 1.1 40 2-41 60-100 (106)
14 PF13405 EF-hand_6: EF-hand do 24.8 34 0.00073 20.7 0.6 13 29-41 13-25 (31)
15 PF12990 DUF3874: Domain of un 24.1 40 0.00086 25.6 1.0 29 210-243 13-41 (73)
16 TIGR01385 TFSII transcription 23.9 27 0.00059 33.0 0.1 46 3-58 185-230 (299)
17 PF13085 Fer2_3: 2Fe-2S iron-s 22.4 28 0.00061 28.3 -0.1 33 221-254 62-95 (110)
18 PF09066 B2-adapt-app_C: Beta2 21.0 51 0.0011 25.8 1.1 15 27-41 1-15 (114)
19 PF01342 SAND: SAND domain; I 20.8 42 0.00091 25.8 0.6 20 29-48 40-59 (82)
No 1
>KOG2981 consensus Protein involved in autophagocytosis during starvation [General function prediction only]
Probab=100.00 E-value=1.3e-99 Score=679.41 Aligned_cols=234 Identities=46% Similarity=0.721 Sum_probs=192.7
Q ss_pred ChhHHHHHHHHhhhhhhcccCCCCCccccccccCHHHHHHhcccccccCCceecCCCCCCCCCCCCCCCCeeEEecCCCc
Q 025314 1 MELQQKFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPC 80 (254)
Q Consensus 1 ~~~~~~~~s~~~~~~e~ltPv~~~S~F~etG~lTPeEFV~AGD~LV~k~PTW~W~~g~~~k~r~yLP~dKQfLvTRnVPC 80 (254)
+||-++|+|+|++||||||||+++|+|++||||||||||+||||||||||||||++|+++|+|+|||+||||||||||||
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 hhhhhhhhhhhhccCCcccccCCCCCceeecCCCCCCCCCCCccCCCCCchhhhhccccccccccCCCCCCCCCcCCccC
Q 025314 81 LRRAASVEEEYEGAGGEILVDNEDNDGWLATHGKPKAKCDEDEDDNLPSMEAVEISKNNNVRAISTYFGGEEEEEEDIPD 160 (254)
Q Consensus 81 ~~R~~~~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~D 160 (254)
+|||+|| +|..+.+.++. .++++|||+||...... ..+............+.+ +..+++++|++|
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---------EYIGKETIHSQDTPAAAP---ESSDEDDDELID 145 (295)
T ss_pred HHHHhhh--hcccccceEEe-ccCCCccccccchhhcc---------cccchhhcccCCCCcCCc---cccccccccccc
Confidence 9999999 67777666664 45558999999632211 111111111000001111 246678899999
Q ss_pred ccccCCCCCCccCCCCCCCCCCcccccCCCCCCCccceeEEEEEEEeeCCCCCceeEEeeecCCCCCCChhhHhhhhccc
Q 025314 161 MAEYNEPDSIIENETDPATLPSTYLVAHEPDDDNILRTRTYDISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQD 240 (254)
Q Consensus 161 m~~~~~~~~l~~~edD~~~~~~~~~~~~~~~~~~i~~~RtYDL~ITYDkyYqTPRlwL~GYde~~~PLt~~emfEDIs~D 240 (254)
|++++++|++ +|+++++. .++....++.+|+++||||||||||||||||||||+||||+|+|||++|||||||+|
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----EDPATFVS-KAVAGLADDSGILQTRTYDLYITYDKYYQTPRLWLVGYDENRQPLTVEQMYEDVSQD 220 (295)
T ss_pred cccccccccc----cCHHHHhh-hhccccccccccceeeEEEEEEEeeccccCceEEEEEecCCCCcCCHHHHHHHhhhh
Confidence 9999998864 45666654 222333456679999999999999999999999999999999999999999999999
Q ss_pred ccCCceecccCCCC
Q 025314 241 HARKTVRGVLYVHL 254 (254)
Q Consensus 241 ya~KTVTiE~hPhl 254 (254)
||+||||||+||||
T Consensus 221 ha~KTvTiE~hPh~ 234 (295)
T KOG2981|consen 221 HAKKTVTIEKHPHL 234 (295)
T ss_pred hccCeEEeccCCCC
Confidence 99999999999997
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=7.6e-59 Score=390.26 Aligned_cols=108 Identities=52% Similarity=0.924 Sum_probs=43.9
Q ss_pred HHHHHhhhhhhcccCCCCCccccccccCHHHHHHhcccccccCCceecCCCCCCCCCCCCCCCCeeEEecCCCchhhhhh
Q 025314 7 FYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGEPSKRKSYLPADKQFLITRNVPCLRRAAS 86 (254)
Q Consensus 7 ~~s~~~~~~e~ltPv~~~S~F~etG~lTPeEFV~AGD~LV~k~PTW~W~~g~~~k~r~yLP~dKQfLvTRnVPC~~R~~~ 86 (254)
|+|+|++||||||||+|+|+|++||+|||||||+||||||||||||||++|+++|+|+|||++|||||||||||++||++
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 025314 87 VEEEYEGAGGEILVDNEDNDGWLATHGKPK 116 (254)
Q Consensus 87 ~~~e~~~~~~~~~~~~~~ddgWv~t~~~~~ 116 (254)
+ ++....+.+++++++++|||.||+...
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=99.73 E-value=9.4e-19 Score=127.29 Aligned_cols=51 Identities=37% Similarity=0.507 Sum_probs=44.0
Q ss_pred EEEeeCCCCCceeEEeeecCCCCCCChhhHhhhhcccccCCceecccCCCC
Q 025314 204 SITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDHARKTVRGVLYVHL 254 (254)
Q Consensus 204 ~ITYDkyYqTPRlwL~GYde~~~PLt~~emfEDIs~Dya~KTVTiE~hPhl 254 (254)
+|+||++||||+|||.||+++|.||+.++|++|++.+++++|||++.||+|
T Consensus 1 ~I~Ys~~YqvP~L~f~~~~~~g~~l~~~~~~~~~~~~~~~~~it~~~HP~l 51 (62)
T PF03987_consen 1 HITYSPSYQVPVLYFRGYDEDGSPLSLEEVYEDLSPDSADSTITQEEHPIL 51 (62)
T ss_dssp EEEEETTTTEEEEEEEEEETT--B--HHHHHTTS-TTTHHHHEEEEE-TTB
T ss_pred CEEecCccCCCEEEEEEECCCCCCCCHHHHHHhhccccccceeecccCCCC
Confidence 799999999999999999999999999999999999999999999999986
No 4
>KOG4741 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.20 E-value=2.8 Score=36.66 Aligned_cols=53 Identities=17% Similarity=0.301 Sum_probs=39.4
Q ss_pred EEEEEeeCCCCCceeEEeeecCCCCCCChhhHhhhhcccccC---CceecccCCCC
Q 025314 202 DISITYDKYYQTPRVWLTGYDESRMLLKTELILEDVSQDHAR---KTVRGVLYVHL 254 (254)
Q Consensus 202 DL~ITYDkyYqTPRlwL~GYde~~~PLt~~emfEDIs~Dya~---KTVTiE~hPhl 254 (254)
--.|=|..-||+|-+|..=|--||.||+..+|-|=--.+--. -++|-=.||.|
T Consensus 66 e~hilyn~kyqvp~lwf~f~~~ngrpl~~r~v~Ei~~t~l~e~~~~~Itq~eHP~L 121 (173)
T KOG4741|consen 66 EAHFLYNRKYQVPELWFMFYCRNGRPLRVRQVAEILGTKLEENDAIVITQSEHPTL 121 (173)
T ss_pred hheEEEEeeecchhheeehhhcCCCchhhhhhHHhhcCccccCccceeeeccCCcc
Confidence 335667778999999999999999999999776632222111 37888889876
No 5
>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=44.92 E-value=14 Score=29.19 Aligned_cols=21 Identities=14% Similarity=0.406 Sum_probs=17.7
Q ss_pred CCCCCeeEEecCCCchhhhhhh
Q 025314 66 LPADKQFLITRNVPCLRRAASV 87 (254)
Q Consensus 66 LP~dKQfLvTRnVPC~~R~~~~ 87 (254)
||++.+.+|.|||||.. |.+-
T Consensus 21 l~~G~~~IvIknVPa~~-C~~C 41 (89)
T TIGR03829 21 LPDGTKAIEIKETPSIS-CSHC 41 (89)
T ss_pred ecCCceEEEEecCCccc-ccCC
Confidence 89999999999999986 3443
No 6
>smart00258 SAND SAND domain.
Probab=42.75 E-value=11 Score=28.74 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=18.1
Q ss_pred cccccCHHHHHHhcccccccCCcee
Q 025314 29 EKGVLSVSEFVLAGDNLVSKCPTWS 53 (254)
Q Consensus 29 etG~lTPeEFV~AGD~LV~k~PTW~ 53 (254)
+...+||.||..-|-.--.| .|+
T Consensus 31 ~~~~~TP~eFe~~~g~~~~K--~WK 53 (73)
T smart00258 31 EDKWFTPKEFEIEGGKGKSK--DWK 53 (73)
T ss_pred CCEEEChHHHHhhcCCcccC--Ccc
Confidence 45679999999988877666 665
No 7
>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=36.95 E-value=16 Score=24.55 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=10.0
Q ss_pred cccccCHHHHHHh
Q 025314 29 EKGVLSVSEFVLA 41 (254)
Q Consensus 29 etG~lTPeEFV~A 41 (254)
++|.||++||..|
T Consensus 1 ~~G~i~~~~~~~~ 13 (54)
T PF13833_consen 1 KDGKITREEFRRA 13 (54)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CcCEECHHHHHHH
Confidence 4688888888776
No 8
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=36.30 E-value=16 Score=23.08 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=12.6
Q ss_pred cccccccCHHHHHHh
Q 025314 27 FKEKGVLSVSEFVLA 41 (254)
Q Consensus 27 F~etG~lTPeEFV~A 41 (254)
....|.||.+||-++
T Consensus 11 l~~~G~IseeEy~~~ 25 (31)
T PF09851_consen 11 LYDKGEISEEEYEQK 25 (31)
T ss_pred HHHcCCCCHHHHHHH
Confidence 457899999999775
No 9
>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=34.08 E-value=17 Score=24.26 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=11.3
Q ss_pred ccccccccCHHHHH
Q 025314 26 AFKEKGVLSVSEFV 39 (254)
Q Consensus 26 ~F~etG~lTPeEFV 39 (254)
.|-..|.||+|||-
T Consensus 20 ~~V~~g~IT~eey~ 33 (40)
T PF09693_consen 20 NFVEAGWITKEEYK 33 (40)
T ss_pred HHhhcCeECHHHHH
Confidence 46678999999984
No 10
>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=30.39 E-value=23 Score=21.84 Aligned_cols=13 Identities=23% Similarity=0.350 Sum_probs=10.9
Q ss_pred cccccCHHHHHHh
Q 025314 29 EKGVLSVSEFVLA 41 (254)
Q Consensus 29 etG~lTPeEFV~A 41 (254)
-.|.|+.+||+.+
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 11
>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=29.86 E-value=25 Score=24.25 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=11.3
Q ss_pred ccccccccCHHHHH
Q 025314 26 AFKEKGVLSVSEFV 39 (254)
Q Consensus 26 ~F~etG~lTPeEFV 39 (254)
.|-+-|.||||||-
T Consensus 25 ~~V~~~~IT~eey~ 38 (45)
T TIGR01669 25 KFVEKKLITREQYK 38 (45)
T ss_pred HHhhcCccCHHHHH
Confidence 46677999999984
No 12
>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=28.60 E-value=20 Score=28.57 Aligned_cols=45 Identities=20% Similarity=0.188 Sum_probs=27.3
Q ss_pred HHHHHHHHhhhhhhcccCCCCCccccccccCHHHHHHhcccccccCCceecCCCC
Q 025314 4 QQKFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGE 58 (254)
Q Consensus 4 ~~~~~s~~~~~~e~ltPv~~~S~F~etG~lTPeEFV~AGD~LV~k~PTW~W~~g~ 58 (254)
+.++++.+.++.+--.|.|...-+ +|.|+|++||. +..+.+++.+
T Consensus 53 ~~k~Rsl~~NLkd~~N~~L~~~il--~g~i~p~~lv~--------ms~~Elas~e 97 (115)
T PF07500_consen 53 KQKFRSLMFNLKDPKNPDLRRRIL--SGEISPEELVT--------MSPEELASEE 97 (115)
T ss_dssp HHHHHHHHHHHCSSTTCCHHHHHH--HSSSTTCHHHH--------CTTTTTTTSC
T ss_pred HHHHHHHHHHhccCCcHHHHHHHH--cCCCCHHHHhc--------CCHHHhCCHH
Confidence 345555555555444466655544 79999999874 3446665543
No 13
>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=28.11 E-value=30 Score=27.79 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=25.3
Q ss_pred hhHHHHHHHHh-hhhhhcccCCCCCccccccccCHHHHHHh
Q 025314 2 ELQQKFYGIFK-GTVEKITSHRTVSAFKEKGVLSVSEFVLA 41 (254)
Q Consensus 2 ~~~~~~~s~~~-~~~e~ltPv~~~S~F~etG~lTPeEFV~A 41 (254)
++||++...+. +=.+.|.-+..-+-...+|.-|..||++.
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 57788877777 44666666666666778899999999874
No 14
>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=24.80 E-value=34 Score=20.72 Aligned_cols=13 Identities=15% Similarity=0.299 Sum_probs=10.9
Q ss_pred cccccCHHHHHHh
Q 025314 29 EKGVLSVSEFVLA 41 (254)
Q Consensus 29 etG~lTPeEFV~A 41 (254)
..|.||++||.++
T Consensus 13 ~dG~I~~~el~~~ 25 (31)
T PF13405_consen 13 GDGFIDFEELRAI 25 (31)
T ss_dssp SSSEEEHHHHHHH
T ss_pred CCCcCcHHHHHHH
Confidence 4799999999864
No 15
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=24.08 E-value=40 Score=25.61 Aligned_cols=29 Identities=14% Similarity=0.231 Sum_probs=24.5
Q ss_pred CCCCceeEEeeecCCCCCCChhhHhhhhcccccC
Q 025314 210 YYQTPRVWLTGYDESRMLLKTELILEDVSQDHAR 243 (254)
Q Consensus 210 yYqTPRlwL~GYde~~~PLt~~emfEDIs~Dya~ 243 (254)
||++|.- +|.|..|++-|||+-+...+..
T Consensus 13 ~FR~a~~-----~Ee~e~lsa~~If~~L~k~~~~ 41 (73)
T PF12990_consen 13 CFRPAEE-----GEEGEWLSAAEIFERLQKKSPA 41 (73)
T ss_pred HccCCCC-----CccceeecHHHHHHHHHHhCcc
Confidence 6788876 7999999999999999776654
No 16
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.95 E-value=27 Score=33.03 Aligned_cols=46 Identities=11% Similarity=0.201 Sum_probs=32.3
Q ss_pred hHHHHHHHHhhhhhhcccCCCCCccccccccCHHHHHHhcccccccCCceecCCCC
Q 025314 3 LQQKFYGIFKGTVEKITSHRTVSAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGE 58 (254)
Q Consensus 3 ~~~~~~s~~~~~~e~ltPv~~~S~F~etG~lTPeEFV~AGD~LV~k~PTW~W~~g~ 58 (254)
-|.++++.+.++.+.=+|-|+..=+ .|.|||++||. +..+.|++.+
T Consensus 185 Yk~k~Rsl~~NLKd~kNp~Lr~~vl--~G~i~p~~lv~--------Ms~eEmas~e 230 (299)
T TIGR01385 185 YKARYRSIYSNLRDKNNPDLRHNVL--TGEITPEKLAT--------MTAEEMASAE 230 (299)
T ss_pred HHHHHHHHHHHccCCCCHHHHHHHH--cCCCCHHHHhc--------CCHHHcCCHH
Confidence 3567777777777666666665533 89999999984 4567776643
No 17
>PF13085 Fer2_3: 2Fe-2S iron-sulfur cluster binding domain; PDB: 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N 1KF6_B 3P4P_N 3P4S_B 1L0V_B 1ZOY_B ....
Probab=22.41 E-value=28 Score=28.25 Aligned_cols=33 Identities=6% Similarity=0.023 Sum_probs=21.4
Q ss_pred ecCCCCC-CChhhHhhhhcccccCCceecccCCCC
Q 025314 221 YDESRML-LKTELILEDVSQDHARKTVRGVLYVHL 254 (254)
Q Consensus 221 Yde~~~P-Lt~~emfEDIs~Dya~KTVTiE~hPhl 254 (254)
..=||+| |.=..-..++...+- ++|||||+|++
T Consensus 62 m~ING~~~LAC~t~v~~~~~~~~-~~i~IePL~~f 95 (110)
T PF13085_consen 62 MRINGRPRLACKTQVDDLIEKFG-NVITIEPLPNF 95 (110)
T ss_dssp EEETTEEEEGGGSBGGGCTTSET-BEEEEEESTTS
T ss_pred EEECCceecceeeEchhccCCCc-ceEEEEECCCC
Confidence 3447776 555555555555444 78999999864
No 18
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=20.99 E-value=51 Score=25.81 Aligned_cols=15 Identities=33% Similarity=0.496 Sum_probs=8.4
Q ss_pred cccccccCHHHHHHh
Q 025314 27 FKEKGVLSVSEFVLA 41 (254)
Q Consensus 27 F~etG~lTPeEFV~A 41 (254)
|.+.|.|+|++|...
T Consensus 1 f~~d~~~~~~~F~~~ 15 (114)
T PF09066_consen 1 FVEDGSMDPEEFQEM 15 (114)
T ss_dssp B-TT----HHHHHHH
T ss_pred CCCCCccCHHHHHHH
Confidence 678999999999873
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=20.79 E-value=42 Score=25.78 Aligned_cols=20 Identities=35% Similarity=0.268 Sum_probs=14.6
Q ss_pred cccccCHHHHHHhccccccc
Q 025314 29 EKGVLSVSEFVLAGDNLVSK 48 (254)
Q Consensus 29 etG~lTPeEFV~AGD~LV~k 48 (254)
+...+||.||+..|-.--.|
T Consensus 40 ~g~~~TP~eFE~~~G~~~sK 59 (82)
T PF01342_consen 40 EGRWFTPSEFERHGGKGSSK 59 (82)
T ss_dssp TTEEE-HHHHHHHHTTCTCS
T ss_pred CCcEECHHHHHhhcCcccCC
Confidence 36689999999998775554
Done!