Query psy13328
Match_columns 68
No_of_seqs 74 out of 76
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 16:40:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13328.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13328hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0946|consensus 99.8 4.8E-19 1E-23 148.0 4.1 58 10-68 96-153 (970)
2 PF02985 HEAT: HEAT repeat; I 94.7 0.073 1.6E-06 27.1 3.5 29 39-67 2-30 (31)
3 PF12755 Vac14_Fab1_bd: Vacuol 93.2 0.11 2.3E-06 33.2 2.9 31 37-67 27-57 (97)
4 PF03810 IBN_N: Importin-beta 92.7 0.48 1E-05 27.0 4.9 40 28-67 4-46 (77)
5 PF08569 Mo25: Mo25-like; Int 88.9 1.2 2.5E-05 34.2 5.2 50 18-68 58-107 (335)
6 PF06371 Drf_GBD: Diaphanous G 86.8 1.4 3.1E-05 28.8 4.1 37 29-65 150-186 (187)
7 cd00020 ARM Armadillo/beta-cat 86.5 1.7 3.8E-05 25.2 4.0 32 34-65 88-119 (120)
8 smart00185 ARM Armadillo/beta- 86.2 2 4.3E-05 21.4 3.6 33 33-65 8-40 (41)
9 PF13646 HEAT_2: HEAT repeats; 86.1 1.1 2.3E-05 25.6 2.9 24 39-62 1-25 (88)
10 cd00020 ARM Armadillo/beta-cat 85.2 1.9 4.2E-05 25.0 3.7 33 35-67 47-79 (120)
11 PF00514 Arm: Armadillo/beta-c 84.9 2.9 6.2E-05 21.8 4.0 33 33-65 8-40 (41)
12 PF12717 Cnd1: non-SMC mitotic 81.6 4.7 0.0001 27.1 4.9 41 27-67 11-55 (178)
13 PF10363 DUF2435: Protein of u 81.1 2.2 4.8E-05 27.0 3.0 28 39-66 45-72 (92)
14 PF13646 HEAT_2: HEAT repeats; 74.4 3.2 6.9E-05 23.6 2.1 30 34-63 28-57 (88)
15 PF03224 V-ATPase_H_N: V-ATPas 69.2 8.9 0.00019 27.8 3.9 31 38-68 106-136 (312)
16 PRK09687 putative lyase; Provi 67.7 5.8 0.00013 29.0 2.8 41 22-64 10-50 (280)
17 PF10521 DUF2454: Protein of u 64.4 8.6 0.00019 27.9 3.1 29 39-67 121-149 (282)
18 PF13513 HEAT_EZ: HEAT-like re 61.8 10 0.00022 20.4 2.4 30 35-64 26-55 (55)
19 PF13251 DUF4042: Domain of un 59.1 10 0.00022 26.8 2.6 34 34-67 37-70 (182)
20 PF06012 DUF908: Domain of Unk 57.0 20 0.00044 26.7 4.0 41 28-68 256-299 (329)
21 PF06062 UPF0231: Uncharacteri 55.8 9.7 0.00021 25.6 2.0 27 22-48 23-49 (121)
22 PRK09687 putative lyase; Provi 54.1 9.9 0.00022 27.8 1.9 32 32-63 154-185 (280)
23 PF03637 Mob1_phocein: Mob1/ph 51.3 20 0.00042 25.1 3.0 32 18-49 19-50 (175)
24 PF10363 DUF2435: Protein of u 50.5 23 0.00049 22.4 2.9 32 37-68 3-34 (92)
25 COG5098 Chromosome condensatio 50.4 15 0.00032 32.8 2.7 33 34-66 383-415 (1128)
26 PF08569 Mo25: Mo25-like; Int 49.1 21 0.00045 27.4 3.0 30 39-68 211-240 (335)
27 PF08167 RIX1: rRNA processing 48.8 23 0.0005 23.8 3.0 28 39-66 27-54 (165)
28 PF14228 MOR2-PAG1_mid: Cell m 47.5 30 0.00065 31.0 4.1 39 27-65 526-571 (1120)
29 PF11707 Npa1: Ribosome 60S bi 47.4 48 0.001 24.6 4.7 44 21-66 42-85 (330)
30 KOG0414|consensus 46.2 18 0.00038 33.1 2.6 33 35-67 397-429 (1251)
31 PF04826 Arm_2: Armadillo-like 42.5 34 0.00073 25.1 3.2 43 25-67 42-84 (254)
32 PF06012 DUF908: Domain of Unk 39.9 73 0.0016 23.8 4.7 42 25-66 8-55 (329)
33 PF09450 DUF2019: Domain of un 39.8 51 0.0011 22.0 3.4 37 22-58 32-68 (106)
34 KOG2160|consensus 38.1 81 0.0018 24.9 4.8 49 19-67 97-154 (342)
35 cd06561 AlkD_like A new struct 37.2 1.2E+02 0.0026 19.8 4.9 43 22-64 90-132 (197)
36 KOG3879|consensus 36.5 29 0.00063 26.8 2.1 28 5-36 216-243 (267)
37 PF11698 V-ATPase_H_C: V-ATPas 36.2 48 0.0011 22.3 3.0 33 35-67 84-116 (119)
38 KOG1403|consensus 36.2 15 0.00033 29.9 0.6 26 16-41 109-134 (452)
39 PF10508 Proteasom_PSMB: Prote 35.2 58 0.0013 25.7 3.7 35 32-66 197-231 (503)
40 PF09060 L27_N: L27_N; InterP 32.3 20 0.00044 21.4 0.6 20 34-53 20-39 (49)
41 PF12095 DUF3571: Protein of u 31.4 14 0.00031 23.9 -0.2 46 14-60 16-82 (83)
42 KOG3392|consensus 30.3 8.6 0.00019 27.2 -1.5 10 48-57 3-12 (147)
43 cd07064 AlkD_like_1 A new stru 30.1 96 0.0021 21.7 3.8 37 23-59 100-137 (208)
44 PF08389 Xpo1: Exportin 1-like 30.1 1.3E+02 0.0029 18.2 4.9 42 23-65 7-53 (148)
45 KOG1824|consensus 29.1 60 0.0013 29.8 3.1 32 37-68 1007-1038(1233)
46 PF00283 Cytochrom_B559: Cytoc 28.3 42 0.00092 18.1 1.3 14 49-62 8-21 (29)
47 PRK05248 hypothetical protein; 27.3 54 0.0012 22.3 2.0 26 22-47 22-47 (121)
48 KOG2099|consensus 27.2 64 0.0014 28.3 2.9 44 17-60 498-541 (843)
49 PHA03256 BDLF3; Provisional 25.8 35 0.00076 22.1 0.9 15 33-47 55-69 (77)
50 PF12830 Nipped-B_C: Sister ch 25.7 96 0.0021 21.2 3.1 26 41-66 12-37 (187)
51 COG1413 FOG: HEAT repeat [Ener 24.6 1.4E+02 0.003 21.2 3.8 26 34-59 71-96 (335)
52 PF08713 DNA_alkylation: DNA a 24.5 91 0.002 20.6 2.7 38 26-63 108-146 (213)
53 PF15002 ERK-JNK_inhib: ERK an 24.2 2.5E+02 0.0053 20.6 5.1 52 10-61 4-56 (207)
54 KOG2417|consensus 24.1 86 0.0019 25.9 2.9 28 38-66 416-443 (462)
55 TIGR03060 PS_II_psb29 photosys 23.7 1.1E+02 0.0024 22.6 3.3 20 47-66 132-152 (214)
56 COG1320 MnhG Multisubunit Na+/ 23.3 49 0.0011 22.1 1.2 16 43-58 24-39 (113)
57 cd03572 ENTH_epsin_related ENT 23.0 96 0.0021 20.8 2.6 29 39-67 40-68 (122)
58 KOG1058|consensus 22.3 80 0.0017 28.3 2.6 33 36-68 316-348 (948)
59 PF14225 MOR2-PAG1_C: Cell mor 21.8 1.3E+02 0.0027 22.3 3.2 44 24-67 173-218 (262)
60 PF01602 Adaptin_N: Adaptin N 21.4 1.1E+02 0.0023 22.9 2.8 28 39-66 269-296 (526)
61 PF03334 PhaG_MnhG_YufB: Na+/H 21.3 92 0.002 19.1 2.1 21 42-62 13-33 (81)
62 PF04499 SAPS: SIT4 phosphatas 21.2 2.4E+02 0.0052 22.7 4.9 44 18-66 48-92 (475)
63 PF01047 MarR: MarR family; I 21.2 45 0.00098 18.0 0.6 29 27-55 22-50 (59)
64 PF12765 Cohesin_HEAT: HEAT re 21.0 95 0.0021 16.8 1.9 25 37-61 18-42 (42)
65 PF10508 Proteasom_PSMB: Prote 20.0 1.7E+02 0.0036 23.2 3.8 36 32-67 114-149 (503)
66 PF05918 API5: Apoptosis inhib 20.0 1.5E+02 0.0032 24.9 3.6 45 22-66 39-88 (556)
No 1
>KOG0946|consensus
Probab=99.75 E-value=4.8e-19 Score=147.99 Aligned_cols=58 Identities=40% Similarity=0.627 Sum_probs=54.1
Q ss_pred CCCCCCCCCCcchhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 10 TTKLPEGAIHREISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 10 ~~~~~e~s~~~~deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
.++|.++|. +++|+|+||||+|||+++||++||.++|+|||||||||||||++|+++|
T Consensus 96 ~~~v~dds~-qsdd~g~~iae~fik~qd~I~lll~~~e~~DF~VR~~aIqLlsalls~r 153 (970)
T KOG0946|consen 96 SPEVMDDST-QSDDLGLWIAEQFIKNQDNITLLLQSLEEFDFHVRLYAIQLLSALLSCR 153 (970)
T ss_pred chhhcccch-hhhHHHHHHHHHHHcCchhHHHHHHHHHhhchhhhhHHHHHHHHHHhcC
Confidence 456666666 9999999999999999999999999999999999999999999999987
No 2
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=94.65 E-value=0.073 Score=27.09 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=25.0
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
++.++.++...+-.||..|++-|..+..+
T Consensus 2 lp~l~~~l~D~~~~VR~~a~~~l~~i~~~ 30 (31)
T PF02985_consen 2 LPILLQLLNDPSPEVRQAAAECLGAIAEH 30 (31)
T ss_dssp HHHHHHHHT-SSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Confidence 57889999999999999999999988754
No 3
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=93.19 E-value=0.11 Score=33.19 Aligned_cols=31 Identities=29% Similarity=0.319 Sum_probs=27.2
Q ss_pred chHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 37 ENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 37 eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+-|..+|.+++..|..|||+|.+-|-.+.+.
T Consensus 27 ~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~ 57 (97)
T PF12755_consen 27 EILPPVLKCFDDQDSRVRYYACEALYNISKV 57 (97)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999999999888753
No 4
>PF03810 IBN_N: Importin-beta N-terminal domain; InterPro: IPR001494 Karyopherins are a group of proteins involved in transporting molecules through the pores of the nuclear envelope. Karyopherins, which may act as importins or exportins, are part of the Importin-beta super-family, which all share a similar three-dimensional structure. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well. This entry represents the N-terminal domain of karyopherins that is important for the binding of the Ran protein []. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport; PDB: 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 1IBR_D 1QGR_A 3LWW_A 1F59_A 2Q5D_A ....
Probab=92.65 E-value=0.48 Score=27.00 Aligned_cols=40 Identities=28% Similarity=0.190 Sum_probs=32.0
Q ss_pred HHHHHhhc-cchHHHHHhhh--hccchhHHHhHHHHHHHHhhc
Q psy13328 28 FTEIFIKN-HENVSLVLGYL--EEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 28 ftE~f~k~-~eNItLLL~lL--ee~DF~VR~~avqLLTaLL~n 67 (68)
.=..|-+. |+.+..++.++ ...+.++|..|..+|....+.
T Consensus 4 ~L~~~~~~~p~~~~~l~~il~~~~~~~~~R~~A~i~LKn~I~~ 46 (77)
T PF03810_consen 4 QLKQFQKQNPGFWQYLLQILSSNSQDPEVRQLAAILLKNLIKK 46 (77)
T ss_dssp HHHHHHHSCTCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHH
Confidence 33455666 89999999999 445999999999999887654
No 5
>PF08569 Mo25: Mo25-like; InterPro: IPR013878 Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site of cell division in a cell cycle dependent manner [, ]. ; PDB: 2WTK_A 1UPK_A 3GNI_A 1UPL_A.
Probab=88.88 E-value=1.2 Score=34.15 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=38.9
Q ss_pred CCcchhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 18 IHREISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 18 ~~~~deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
++...|...++|.++.+. +.+..|+..|...||-.|-.+.++.++|++.+
T Consensus 58 ~ep~~e~v~qLa~Ei~~~-dll~~Li~~L~~L~fEsrKdv~~if~~llr~~ 107 (335)
T PF08569_consen 58 PEPNPEQVAQLAQEIYRS-DLLYLLIRNLPKLDFESRKDVAQIFSNLLRRQ 107 (335)
T ss_dssp ----HHHHHHHHHHHHHH-THHHHHHHTGGGS-HHHHHHHHHHHHHHHT--
T ss_pred CCCCHHHHHHHHHHHHHh-CHHHHHHHHhhhCCCcccccHHHHHHHHHhhc
Confidence 345556688888888855 99999999999999999999999999999753
No 6
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=86.84 E-value=1.4 Score=28.76 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=32.0
Q ss_pred HHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 29 TEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 29 tE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
.+.+++.++.|..+...|...+..+|--+++||++|.
T Consensus 150 ~~~v~~~~~~v~~i~~~L~s~~~~~r~~~leiL~~lc 186 (187)
T PF06371_consen 150 LEAVLSHPDSVNLIALSLDSPNIKTRKLALEILAALC 186 (187)
T ss_dssp HHHHHCSSSHHHHHHHT--TTSHHHHHHHHHHHHHHH
T ss_pred HHHHHcCcHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 4577889999999999999999999999999999985
No 7
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=86.48 E-value=1.7 Score=25.17 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=28.6
Q ss_pred hccchHHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 34 KNHENVSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
.+.+-+..++.+|.+++..+|.+++.+|.+|.
T Consensus 88 ~~~g~l~~l~~~l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 88 LEAGGVPKLVNLLDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred HHCCChHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence 45568999999999999999999999999875
No 8
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=86.17 E-value=2 Score=21.37 Aligned_cols=33 Identities=18% Similarity=0.130 Sum_probs=28.7
Q ss_pred hhccchHHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 33 IKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 33 ~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
+....=|..|+.+|...|-.++..|+..|..|.
T Consensus 8 i~~~g~i~~L~~ll~~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 8 VVDAGGLPALVELLKSEDEEVVKEAAWALSNLS 40 (41)
T ss_pred HHHCCCHHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 445667899999999999999999999999875
No 9
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=86.07 E-value=1.1 Score=25.58 Aligned_cols=24 Identities=29% Similarity=0.347 Sum_probs=17.3
Q ss_pred HHHHHhhh-hccchhHHHhHHHHHH
Q psy13328 39 VSLVLGYL-EEFDFRVRWSAVKLLT 62 (68)
Q Consensus 39 ItLLL~lL-ee~DF~VR~~avqLLT 62 (68)
|..|+..| .+.+.+||+.+++.|.
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~ 25 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALG 25 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 34566666 7778888888877775
No 10
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=85.16 E-value=1.9 Score=24.98 Aligned_cols=33 Identities=18% Similarity=0.110 Sum_probs=29.4
Q ss_pred ccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 35 NHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 35 ~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+.+-|..++.+|...+..||.+|+..|..|..+
T Consensus 47 ~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~ 79 (120)
T cd00020 47 EAGGLPALVQLLKSEDEEVVKAALWALRNLAAG 79 (120)
T ss_pred HCCChHHHHHHHhCCCHHHHHHHHHHHHHHccC
Confidence 358899999999999999999999999998753
No 11
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=84.92 E-value=2.9 Score=21.81 Aligned_cols=33 Identities=21% Similarity=0.138 Sum_probs=29.0
Q ss_pred hhccchHHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 33 IKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 33 ~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
+-+.+=|..|+.+|...|..||..|+.-|..|.
T Consensus 8 i~~~g~i~~Lv~ll~~~~~~v~~~a~~al~nl~ 40 (41)
T PF00514_consen 8 IVEAGGIPPLVQLLKSPDPEVQEEAAWALGNLA 40 (41)
T ss_dssp HHHTTHHHHHHHHTTSSSHHHHHHHHHHHHHHH
T ss_pred HHHcccHHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 346677899999999999999999999998875
No 12
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=81.59 E-value=4.7 Score=27.12 Aligned_cols=41 Identities=22% Similarity=0.296 Sum_probs=31.2
Q ss_pred HHHHHHhhccc----hHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 27 QFTEIFIKNHE----NVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 27 ~ftE~f~k~~e----NItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
-++|.-++-+. .+..+...|...+-.||..|+..|+.|+.+
T Consensus 11 ~l~DL~~r~~~~ve~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~ 55 (178)
T PF12717_consen 11 ALGDLCIRYPNLVEPYLPNLYKCLRDEDPLVRKTALLVLSHLILE 55 (178)
T ss_pred HHHHHHHhCcHHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHc
Confidence 34444444443 355788999999999999999999999864
No 13
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=81.06 E-value=2.2 Score=27.03 Aligned_cols=28 Identities=32% Similarity=0.278 Sum_probs=24.4
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
+.++++.|...|-||=++|||.|++|..
T Consensus 45 l~l~l~~L~d~DsyVYL~aI~~L~~La~ 72 (92)
T PF10363_consen 45 LDLFLSQLKDEDSYVYLNAIKGLAALAD 72 (92)
T ss_pred HHHHHHHcCCCCchHHHHHHHHHHHHHH
Confidence 4567788899999999999999999864
No 14
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=74.35 E-value=3.2 Score=23.60 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=25.6
Q ss_pred hccchHHHHHhhhhccchhHHHhHHHHHHH
Q psy13328 34 KNHENVSLVLGYLEEFDFRVRWSAVKLLTG 63 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~VR~~avqLLTa 63 (68)
+.++-+..|..++...|..||..|++-|..
T Consensus 28 ~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~ 57 (88)
T PF13646_consen 28 GDPEAIPALIELLKDEDPMVRRAAARALGR 57 (88)
T ss_dssp THHHHHHHHHHHHTSSSHHHHHHHHHHHHC
T ss_pred CCHhHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 566789999999999999999999887653
No 15
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=69.22 E-value=8.9 Score=27.83 Aligned_cols=31 Identities=29% Similarity=0.239 Sum_probs=25.1
Q ss_pred hHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 38 NVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 38 NItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
.+..++.+++..|-++...|.++|+.|++.+
T Consensus 106 ~~~~fl~ll~~~D~~i~~~a~~iLt~Ll~~~ 136 (312)
T PF03224_consen 106 PYSPFLKLLDRNDSFIQLKAAFILTSLLSQG 136 (312)
T ss_dssp -HHHHHHH-S-SSHHHHHHHHHHHHHHHTST
T ss_pred hHHHHHHHhcCCCHHHHHHHHHHHHHHHHcC
Confidence 5777888999999999999999999998753
No 16
>PRK09687 putative lyase; Provisional
Probab=67.70 E-value=5.8 Score=29.05 Aligned_cols=41 Identities=17% Similarity=0.079 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHH
Q psy13328 22 ISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGL 64 (68)
Q Consensus 22 deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaL 64 (68)
.+.-..|.+-|.+. ++.-|+.+|+..|+.|||.|++-|..+
T Consensus 10 ~~~~~~~~~~~~~~--~~~~L~~~L~d~d~~vR~~A~~aL~~~ 50 (280)
T PRK09687 10 ASKEYSLYSQCKKL--NDDELFRLLDDHNSLKRISSIRVLQLR 50 (280)
T ss_pred hhHHHHHHHHHhhc--cHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 34455666777665 466788999999999999999887643
No 17
>PF10521 DUF2454: Protein of unknown function (DUF2454); InterPro: IPR018870 Putative protein of unknown function; subunit of the ASTRA complex which is part of the chromatin remodeling machinery; similar to Schizosaccharomyces pombe (Fission yeast) Tti2p; may interact with Rsm23p [].
Probab=64.41 E-value=8.6 Score=27.94 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=26.6
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
++-+|.++|.++=.+|..++++|..++.+
T Consensus 121 iP~iL~llDD~~~~~K~~G~~lL~~ll~~ 149 (282)
T PF10521_consen 121 IPPILNLLDDYSPEIKIQGCQLLHHLLEK 149 (282)
T ss_pred HhhHHHHhcCCCHHHHHHHHHHHHHHHHh
Confidence 67789999999999999999999999864
No 18
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=61.81 E-value=10 Score=20.42 Aligned_cols=30 Identities=27% Similarity=0.170 Sum_probs=23.1
Q ss_pred ccchHHHHHhhhhccchhHHHhHHHHHHHH
Q psy13328 35 NHENVSLVLGYLEEFDFRVRWSAVKLLTGL 64 (68)
Q Consensus 35 ~~eNItLLL~lLee~DF~VR~~avqLLTaL 64 (68)
-++-++.|..+|.+.+=.||..|..-|..|
T Consensus 26 ~~~~~~~L~~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 26 LPELLPALIPLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHHHHHHHHHTTSSSHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhcC
Confidence 345577888888777779999998877654
No 19
>PF13251 DUF4042: Domain of unknown function (DUF4042)
Probab=59.07 E-value=10 Score=26.84 Aligned_cols=34 Identities=26% Similarity=0.218 Sum_probs=29.6
Q ss_pred hccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 34 KNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
.++...+|+-.++-+++-.||-.|+++|++||.+
T Consensus 37 ~~~~~~sLlt~il~Dp~~kvR~aA~~~l~~lL~g 70 (182)
T PF13251_consen 37 GRPATPSLLTCILKDPSPKVRAAAASALAALLEG 70 (182)
T ss_pred CCCCCcchhHHHHcCCchhHHHHHHHHHHHHHHc
Confidence 3556778888999999999999999999999864
No 20
>PF06012 DUF908: Domain of Unknown Function (DUF908); InterPro: IPR010309 This is a domain of unknown function found at the N terminus of a family of E3 ubiquitin protein ligases, including yeast TOM1, many of which appear to play a role in mRNA transcription and processing. This domain is found in association with and immediately N-terminal to another domain of unknown function: IPR010314 from INTERPRO.
Probab=57.03 E-value=20 Score=26.71 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=31.8
Q ss_pred HHHHHhhccchHHHHHhhh---hccchhHHHhHHHHHHHHhhcC
Q psy13328 28 FTEIFIKNHENVSLVLGYL---EEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 28 ftE~f~k~~eNItLLL~lL---ee~DF~VR~~avqLLTaLL~nR 68 (68)
.+-.|..+|+-|.-|.+|+ +.-...+|..|++.|++|+..|
T Consensus 256 ~~~~l~~dp~l~~eL~eLi~~~~~v~~~i~~~Al~~L~ai~~~~ 299 (329)
T PF06012_consen 256 SSKLLEQDPELVNELVELISPEEKVPMDIQTAALRALEAISHKR 299 (329)
T ss_pred HHHHHhcChHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHhcc
Confidence 3456667777777777777 4556789999999999998765
No 21
>PF06062 UPF0231: Uncharacterised protein family (UPF0231); InterPro: IPR008249 The proteins in this entry are functionally uncharacterised.
Probab=55.80 E-value=9.7 Score=25.65 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHhhccchHHHHHhhhhc
Q psy13328 22 ISVGEQFTEIFIKNHENVSLVLGYLEE 48 (68)
Q Consensus 22 deig~~ftE~f~k~~eNItLLL~lLee 48 (68)
.=||.||.+++-++.+.|..+|+.++.
T Consensus 23 eaig~Wl~eEv~~d~~~i~~vl~~i~~ 49 (121)
T PF06062_consen 23 EAIGRWLNEEVGGDLEKIDQVLAAIEQ 49 (121)
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence 458999999999999999999988754
No 22
>PRK09687 putative lyase; Provisional
Probab=54.06 E-value=9.9 Score=27.85 Aligned_cols=32 Identities=22% Similarity=0.258 Sum_probs=27.0
Q ss_pred HhhccchHHHHHhhhhccchhHHHhHHHHHHH
Q psy13328 32 FIKNHENVSLVLGYLEEFDFRVRWSAVKLLTG 63 (68)
Q Consensus 32 f~k~~eNItLLL~lLee~DF~VR~~avqLLTa 63 (68)
.++.++-|..|+.+|+..|..||..|+.-|-.
T Consensus 154 ~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~ 185 (280)
T PRK09687 154 VINDEAAIPLLINLLKDPNGDVRNWAAFALNS 185 (280)
T ss_pred ccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhc
Confidence 45678899999999999999999999876654
No 23
>PF03637 Mob1_phocein: Mob1/phocein family; InterPro: IPR005301 Mob1 is an essential Saccharomyces cerevisiae (Baker's yeast) protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature []. This family also includes phocein Q9QYW3 from SWISSPROT, a rat protein that by yeast two hybrid interacts with striatin [].; PDB: 2HJN_A 1PI1_A 1R3B_A.
Probab=51.35 E-value=20 Score=25.07 Aligned_cols=32 Identities=16% Similarity=0.345 Sum_probs=25.3
Q ss_pred CCcchhHHHHHHHHHhhccchHHHHHhhhhcc
Q psy13328 18 IHREISVGEQFTEIFIKNHENVSLVLGYLEEF 49 (68)
Q Consensus 18 ~~~~deig~~ftE~f~k~~eNItLLL~lLee~ 49 (68)
.++..|.++|+|.....=-.+|.++.+.+.++
T Consensus 19 lP~g~d~~eWla~~~~~f~~~in~l~~~v~e~ 50 (175)
T PF03637_consen 19 LPKGVDENEWLAVHTVDFFNEINLLYGVVSEF 50 (175)
T ss_dssp -STT--HHHHHHHHHHHHHHHHHHHHHHHGGG
T ss_pred CcCCCChhhHHHHhhHHHHHHHHHHHhhccCc
Confidence 46678999999999999999999999988763
No 24
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=50.47 E-value=23 Score=22.36 Aligned_cols=32 Identities=25% Similarity=0.203 Sum_probs=26.3
Q ss_pred chHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 37 ENVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 37 eNItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
+.....+..|..+.--||-.++.+|+.|+..|
T Consensus 3 ~~~~~al~~L~dp~~PvRa~gL~~L~~Li~~~ 34 (92)
T PF10363_consen 3 ETLQEALSDLNDPLPPVRAHGLVLLRKLIESK 34 (92)
T ss_pred HHHHHHHHHccCCCcchHHHHHHHHHHHHHcC
Confidence 34456777888899999999999999998764
No 25
>COG5098 Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=50.38 E-value=15 Score=32.84 Aligned_cols=33 Identities=36% Similarity=0.447 Sum_probs=30.1
Q ss_pred hccchHHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 34 KNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
+|++.+.++...|..---.||+.|++|++.||.
T Consensus 383 ~r~ev~~lv~r~lqDrss~VRrnaikl~SkLL~ 415 (1128)
T COG5098 383 RRHEVIRLVGRRLQDRSSVVRRNAIKLCSKLLM 415 (1128)
T ss_pred hHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHh
Confidence 578889999999999999999999999999885
No 26
>PF08569 Mo25: Mo25-like; InterPro: IPR013878 Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site of cell division in a cell cycle dependent manner [, ]. ; PDB: 2WTK_A 1UPK_A 3GNI_A 1UPL_A.
Probab=49.12 E-value=21 Score=27.42 Aligned_cols=30 Identities=30% Similarity=0.398 Sum_probs=24.1
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
+...-.||+...|..|+.|+|||..||..|
T Consensus 211 f~~~~~Ll~s~NYvtkrqslkLL~ellldr 240 (335)
T PF08569_consen 211 FQKYNKLLESSNYVTKRQSLKLLGELLLDR 240 (335)
T ss_dssp HHHHHHHCT-SSHHHHHHHHHHHHHHHHSG
T ss_pred HHHHHHHccCCCeEeehhhHHHHHHHHHch
Confidence 344556778899999999999999999765
No 27
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=48.83 E-value=23 Score=23.84 Aligned_cols=28 Identities=21% Similarity=0.278 Sum_probs=23.8
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
++.+.++|...+-+.||.++.|+.++..
T Consensus 27 ~~ri~~LL~s~~~~~rw~G~~Ll~~~~~ 54 (165)
T PF08167_consen 27 VTRINSLLQSKSAYSRWAGLCLLKVTVE 54 (165)
T ss_pred HHHHHHHhCCCChhhHHHHHHHHHHHHH
Confidence 3457889999999999999999988764
No 28
>PF14228 MOR2-PAG1_mid: Cell morphogenesis central region
Probab=47.49 E-value=30 Score=31.02 Aligned_cols=39 Identities=28% Similarity=0.324 Sum_probs=32.0
Q ss_pred HHHHHHhhccch-------HHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 27 QFTEIFIKNHEN-------VSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 27 ~ftE~f~k~~eN-------ItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
-++|.|+++... +.|.|--+-..+.-||-.|+|||..|-
T Consensus 526 vlaev~~~~~~~~~~~~~LL~L~Lfklg~~~~eIR~~A~qLL~~Le 571 (1120)
T PF14228_consen 526 VLAEVFSEREYPPCPFWELLNLVLFKLGDESSEIRSKAMQLLRALE 571 (1120)
T ss_pred HHHHHHHcCCCCCCCHHHhHHHHHHhhcCCcHHHHHHHHHHHHHHH
Confidence 678999877654 566666778899999999999999874
No 29
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=47.45 E-value=48 Score=24.64 Aligned_cols=44 Identities=23% Similarity=0.286 Sum_probs=37.6
Q ss_pred chhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 21 EISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 21 ~deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
-.+.|..++..++++. ...+-..|....-.+..++++||+++.+
T Consensus 42 ~~~~g~~l~~~iL~~~--~k~lyr~L~~~~~~~~~~~LrLL~~iv~ 85 (330)
T PF11707_consen 42 FQSYGLELIRSILQNH--LKLLYRSLSSSKPSLTNPALRLLTAIVS 85 (330)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHhCcCcHHHHHHHHHHHHHHHc
Confidence 4677889999999986 8889999988887777799999999876
No 30
>KOG0414|consensus
Probab=46.24 E-value=18 Score=33.10 Aligned_cols=33 Identities=36% Similarity=0.448 Sum_probs=28.7
Q ss_pred ccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 35 NHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 35 ~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+++-++++.+-|+.---.||++|+||+..+|.+
T Consensus 397 ~~eV~~la~grl~DkSslVRk~Ai~Ll~~~L~~ 429 (1251)
T KOG0414|consen 397 RTEVLELAIGRLEDKSSLVRKNAIQLLSSLLDR 429 (1251)
T ss_pred HHHHHHHHhcccccccHHHHHHHHHHHHHHHhc
Confidence 466778888889999999999999999998864
No 31
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=42.48 E-value=34 Score=25.13 Aligned_cols=43 Identities=26% Similarity=0.311 Sum_probs=38.3
Q ss_pred HHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 25 GEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 25 g~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+-.++..++.+-+=|.++.++|..++=.||-.|++.|-+|..+
T Consensus 42 af~~nq~~Ir~~Ggi~lI~~lL~~p~~~vr~~AL~aL~Nls~~ 84 (254)
T PF04826_consen 42 AFPFNQDIIRDLGGISLIGSLLNDPNPSVREKALNALNNLSVN 84 (254)
T ss_pred cChhHHHHHHHcCCHHHHHHHcCCCChHHHHHHHHHHHhcCCC
Confidence 4478899999999999999999999999999999998877543
No 32
>PF06012 DUF908: Domain of Unknown Function (DUF908); InterPro: IPR010309 This is a domain of unknown function found at the N terminus of a family of E3 ubiquitin protein ligases, including yeast TOM1, many of which appear to play a role in mRNA transcription and processing. This domain is found in association with and immediately N-terminal to another domain of unknown function: IPR010314 from INTERPRO.
Probab=39.91 E-value=73 Score=23.78 Aligned_cols=42 Identities=26% Similarity=0.316 Sum_probs=34.8
Q ss_pred HHHHHHHHhhccch------HHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 25 GEQFTEIFIKNHEN------VSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 25 g~~ftE~f~k~~eN------ItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
-++|+-+.+.+-.| ..-|.+||...|+-|...|++++..+..
T Consensus 8 IL~Ft~lLLEnc~NRslYsS~e~L~~LL~s~~~dVl~~aL~ll~~l~q 55 (329)
T PF06012_consen 8 ILRFTRLLLENCGNRSLYSSSEHLNSLLNSTDLDVLLAALRLLLRLAQ 55 (329)
T ss_pred HHHHHHHHHhccCCCCccccHHHHHHHHcCCCHHHHHHHHHHHHHHHh
Confidence 35788888888777 4568899999999999999999977643
No 33
>PF09450 DUF2019: Domain of unknown function (DUF2019); InterPro: IPR018568 Protein of unknown function found in bacteria. ; PDB: 2I9C_A.
Probab=39.76 E-value=51 Score=22.02 Aligned_cols=37 Identities=16% Similarity=0.170 Sum_probs=26.8
Q ss_pred hhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHH
Q psy13328 22 ISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAV 58 (68)
Q Consensus 22 deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~av 58 (68)
+.+..-+.+.-.+..+.-..|+.||+-++-+||..|=
T Consensus 32 ~k~~~~~~eLk~r~gd~r~aLl~LL~hpn~~VRl~AA 68 (106)
T PF09450_consen 32 DKMIRIYDELKSRGGDQRDALLPLLKHPNMQVRLWAA 68 (106)
T ss_dssp HHHHHHHHHHHHSTT-GGGGGGGGGGSS-HHHHHHHH
T ss_pred HHHHHHHHHHHhcCcchHHHHHHHHcCCChhHHHHHH
Confidence 3455556666666667889999999999999998764
No 34
>KOG2160|consensus
Probab=38.12 E-value=81 Score=24.94 Aligned_cols=49 Identities=22% Similarity=0.276 Sum_probs=36.8
Q ss_pred CcchhHHHHHHHHHhhccchH---------HHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 19 HREISVGEQFTEIFIKNHENV---------SLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 19 ~~~deig~~ftE~f~k~~eNI---------tLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
.++-+.+...=++++..-+|- ..|+.+|+..|=-+|+.|.+.|++...|
T Consensus 97 le~ke~ald~Le~lve~iDnAndl~~~ggl~~ll~~l~~~~~~lR~~Aa~Vigt~~qN 154 (342)
T KOG2160|consen 97 LEDKEDALDNLEELVEDIDNANDLISLGGLVPLLGYLENSDAELRELAARVIGTAVQN 154 (342)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHhHhhccCHHHHHHHhcCCcHHHHHHHHHHHHHHHhc
Confidence 344455666666676666653 3455699999999999999999999876
No 35
>cd06561 AlkD_like A new structural DNA glycosylase. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.
Probab=37.18 E-value=1.2e+02 Score=19.82 Aligned_cols=43 Identities=19% Similarity=0.177 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHHHHHH
Q psy13328 22 ISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGL 64 (68)
Q Consensus 22 deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqLLTaL 64 (68)
|-++..+.-.+....++..++.......+.++|+.|+-.+...
T Consensus 90 D~~~~~~~~~~~~~~~~~~~~~~w~~s~~~~~rR~~~~~~~~~ 132 (197)
T cd06561 90 DSLCANLLGKLLYAEPELDLLEEWAKSENEWVRRAAIVLLLRL 132 (197)
T ss_pred HHHHHHHHHHHHhcCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 3344444455555666666777777777777777777666544
No 36
>KOG3879|consensus
Probab=36.47 E-value=29 Score=26.81 Aligned_cols=28 Identities=18% Similarity=0.173 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q psy13328 5 TKDGSTTKLPEGAIHREISVGEQFTEIFIKNH 36 (68)
Q Consensus 5 ~~d~~~~~~~e~s~~~~deig~~ftE~f~k~~ 36 (68)
++.++||..||++.+++.++|. +|-|++
T Consensus 216 th~~d~e~~ee~~~~~~~~iaa----~f~k~~ 243 (267)
T KOG3879|consen 216 THHEDNEPEEETEVPEEPKIAA----EFRKKA 243 (267)
T ss_pred cccccCCCCcccCCCCCcchhH----HHhhhh
Confidence 7888999999999999999998 555543
No 37
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=36.22 E-value=48 Score=22.33 Aligned_cols=33 Identities=21% Similarity=0.278 Sum_probs=25.5
Q ss_pred ccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 35 NHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 35 ~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+-.=-..++.|+...|=-||+.|++-+..|+.+
T Consensus 84 ~lg~K~~vM~Lm~h~d~eVr~eAL~avQklm~~ 116 (119)
T PF11698_consen 84 KLGAKERVMELMNHEDPEVRYEALLAVQKLMVN 116 (119)
T ss_dssp HHSHHHHHHHHTS-SSHHHHHHHHHHHHHHHHH
T ss_pred hcChHHHHHHHhcCCCHHHHHHHHHHHHHHHHh
Confidence 333445788999999999999999998888764
No 38
>KOG1403|consensus
Probab=36.16 E-value=15 Score=29.89 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=21.8
Q ss_pred CCCCcchhHHHHHHHHHhhccchHHH
Q psy13328 16 GAIHREISVGEQFTEIFIKNHENVSL 41 (68)
Q Consensus 16 ~s~~~~deig~~ftE~f~k~~eNItL 41 (68)
||-.+..|+++++|..|+|.|+-|++
T Consensus 109 NSGSEANDLALRLAR~ftkhqDvItl 134 (452)
T KOG1403|consen 109 NSGSEANDLALRLARNFTKHQDVITL 134 (452)
T ss_pred cCCchhhHHHHHHHHhhcccCceEEE
Confidence 44455679999999999999998875
No 39
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=35.20 E-value=58 Score=25.68 Aligned_cols=35 Identities=29% Similarity=0.309 Sum_probs=29.9
Q ss_pred HhhccchHHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 32 FIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 32 f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
.+.+.+-+..++..|+.-|--||..++.+|+.|..
T Consensus 197 ~~~~sgll~~ll~eL~~dDiLvqlnalell~~La~ 231 (503)
T PF10508_consen 197 AVVNSGLLDLLLKELDSDDILVQLNALELLSELAE 231 (503)
T ss_pred HHHhccHHHHHHHHhcCccHHHHHHHHHHHHHHHc
Confidence 34455678999999999999999999999998854
No 40
>PF09060 L27_N: L27_N; InterPro: IPR015145 The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation []. ; PDB: 1Y76_B 3UIT_B 1VF6_C.
Probab=32.29 E-value=20 Score=21.39 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=16.8
Q ss_pred hccchHHHHHhhhhccchhH
Q psy13328 34 KNHENVSLVLGYLEEFDFRV 53 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~V 53 (68)
+.|+-|.++|.||-..||.-
T Consensus 20 qSQ~Dv~lllqLl~~~dFq~ 39 (49)
T PF09060_consen 20 QSQQDVELLLQLLQNSDFQN 39 (49)
T ss_dssp HHHHHHHHHHHHHH-HHHHH
T ss_pred hhHHhHHHHHHHHhhHhHHH
Confidence 67889999999999999963
No 41
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=31.41 E-value=14 Score=23.88 Aligned_cols=46 Identities=17% Similarity=0.261 Sum_probs=25.8
Q ss_pred CCCCCCc---chhHHHHHHHHHhhccchHHHHHhhh-----------h-------ccchhHHHhHHHH
Q psy13328 14 PEGAIHR---EISVGEQFTEIFIKNHENVSLVLGYL-----------E-------EFDFRVRWSAVKL 60 (68)
Q Consensus 14 ~e~s~~~---~deig~~ftE~f~k~~eNItLLL~lL-----------e-------e~DF~VR~~avqL 60 (68)
|++.+++ ..|+=.|+.+.+.+ +++++.=|.-+ + .+.+|+-||||+|
T Consensus 16 Ep~~~Eqflt~~Ell~~Lk~~L~~-~~~LP~dL~~~~s~~~qa~~Lldt~CeLeigpg~~lQWyaVRL 82 (83)
T PF12095_consen 16 EPGQPEQFLTPEELLEKLKEWLQN-QDDLPPDLAKFSSVEEQAQYLLDTACELEIGPGGYLQWYAVRL 82 (83)
T ss_dssp ESSS-SEEE-HHHHHHHHHHHHHH-TTTS-HHHHH---HHHHHHHHHHH---EEEETTEEEEEEE---
T ss_pred cCCCCcccCCHHHHHHHHHHHHHc-CCCCCHHHHhCCCHHHHHHHHHHhceeeecCCCCEEEEEEEec
Confidence 3445543 47888888888887 76665533222 1 2567788888775
No 42
>KOG3392|consensus
Probab=30.29 E-value=8.6 Score=27.21 Aligned_cols=10 Identities=30% Similarity=0.531 Sum_probs=8.1
Q ss_pred ccchhHHHhH
Q psy13328 48 EFDFRVRWSA 57 (68)
Q Consensus 48 e~DF~VR~~a 57 (68)
..|||||+|.
T Consensus 3 asdfy~ryyv 12 (147)
T KOG3392|consen 3 ASDFYLRYYV 12 (147)
T ss_pred ccceEEEEEe
Confidence 4689999984
No 43
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=30.13 E-value=96 Score=21.67 Aligned_cols=37 Identities=14% Similarity=0.258 Sum_probs=26.7
Q ss_pred hHHHHHHHHHhhccchH-HHHHhhhhccchhHHHhHHH
Q psy13328 23 SVGEQFTEIFIKNHENV-SLVLGYLEEFDFRVRWSAVK 59 (68)
Q Consensus 23 eig~~ftE~f~k~~eNI-tLLL~lLee~DF~VR~~avq 59 (68)
.++..+...|..++++. ..+.......++++|+.|+=
T Consensus 100 ~~~~~i~g~~~~~~~~~~~~l~~W~~s~~~W~rR~ai~ 137 (208)
T cd07064 100 SLAKVVGGILLADYPEFEPVMDEWSTDENFWLRRTAIL 137 (208)
T ss_pred HHHHHHhHHHHhCChhHHHHHHHHHcCCcHHHHHHHHH
Confidence 34444445556666664 78888889999999999973
No 44
>PF08389 Xpo1: Exportin 1-like protein; InterPro: IPR013598 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found close to the N terminus of yeast exportin 1 (Xpo1, Crm1, P14068 from SWISSPROT), as well as adjacent to the N-terminal domain of importin-beta (IPR001494 from INTERPRO). Exportin 1 is a nuclear export receptor that translocates proteins out of the nucleus; it interacts with leucine-rich nuclear export signal (NES) sequences in proteins to be transported, as well as with RanGTP [, ]. Importin-beta is a nuclear import receptor that translocates proteins into the nucleus; it interacts with RanGTP and importin-alpha, the latter binding with the nuclear localisation signal (NLS) sequences in proteins to be transported []. More information about these proteins can be found at Protein of the Month: Importins [].; PDB: 3IBV_A 3ICQ_U 3M1I_C 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 2XWU_B 2X19_B ....
Probab=30.10 E-value=1.3e+02 Score=18.23 Aligned_cols=42 Identities=14% Similarity=0.133 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhhc-----cchHHHHHhhhhccchhHHHhHHHHHHHHh
Q psy13328 23 SVGEQFTEIFIKN-----HENVSLVLGYLEEFDFRVRWSAVKLLTGLL 65 (68)
Q Consensus 23 eig~~ftE~f~k~-----~eNItLLL~lLee~DF~VR~~avqLLTaLL 65 (68)
-++.-+++++.+. |+.+.-++.++.. +...+...+.+|+.|.
T Consensus 7 kl~~~l~~i~~~~~P~~Wp~~l~~l~~~~~~-~~~~~~~~L~iL~~l~ 53 (148)
T PF08389_consen 7 KLAQVLAEIAKRDWPQQWPDFLEDLLQLLQS-SPQHLELVLRILRILP 53 (148)
T ss_dssp HHHHHHHHHHHHHTTTTSTTHHHHHHHHHHT-THHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHChhhCchHHHHHHHHhcc-chhHHHHHHHHHHHHH
Confidence 4666777777777 5666666666665 4555556666666553
No 45
>KOG1824|consensus
Probab=29.09 E-value=60 Score=29.81 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=27.1
Q ss_pred chHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 37 ENVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 37 eNItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
.+|...|-++..+|-.||+-|++-+.+-..||
T Consensus 1007 ~~ig~fl~~~~dpDl~VrrvaLvv~nSaahNK 1038 (1233)
T KOG1824|consen 1007 QQIGDFLKLLRDPDLEVRRVALVVLNSAAHNK 1038 (1233)
T ss_pred HHHHHHHHHHhCCchhHHHHHHHHHHHHHccC
Confidence 35677788999999999999999998877665
No 46
>PF00283 Cytochrom_B559: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits; InterPro: IPR013081 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. Cytochrome b559, which forms part of the reaction centre core of PSII is a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a haem cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly []. This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha sbunit it occurs together with a lumenal domain (IPR013082 from INTERPRO), while in the beta subunit it occurs on its own.; GO: 0046872 metal ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009536 plastid, 0009579 thylakoid, 0016021 integral to membrane; PDB: 3ARC_f 3A0H_f 3A0B_f 1W5C_K 1S5L_e 3BZ2_E 3PRQ_E 1IZL_P 2AXT_E 4FBY_R ....
Probab=28.33 E-value=42 Score=18.05 Aligned_cols=14 Identities=50% Similarity=0.705 Sum_probs=11.0
Q ss_pred cchhHHHhHHHHHH
Q psy13328 49 FDFRVRWSAVKLLT 62 (68)
Q Consensus 49 ~DF~VR~~avqLLT 62 (68)
.=|-|||-++--|+
T Consensus 8 pI~tvR~~~IH~l~ 21 (29)
T PF00283_consen 8 PIFTVRWWAIHALT 21 (29)
T ss_dssp HSSSHHHHHHHHHH
T ss_pred eeeeEeeeeeeecc
Confidence 34789999998776
No 47
>PRK05248 hypothetical protein; Provisional
Probab=27.29 E-value=54 Score=22.30 Aligned_cols=26 Identities=27% Similarity=0.254 Sum_probs=21.6
Q ss_pred hhHHHHHHHHHhhccchHHHHHhhhh
Q psy13328 22 ISVGEQFTEIFIKNHENVSLVLGYLE 47 (68)
Q Consensus 22 deig~~ftE~f~k~~eNItLLL~lLe 47 (68)
.=||.||.|+.-+++.-|..++..+.
T Consensus 22 EaiG~Wl~eEv~~d~~~i~~il~~~~ 47 (121)
T PRK05248 22 EAIGRWFNEEVGKNLAKLDEVLAAAA 47 (121)
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHH
Confidence 45899999999999988888887543
No 48
>KOG2099|consensus
Probab=27.16 E-value=64 Score=28.33 Aligned_cols=44 Identities=16% Similarity=0.316 Sum_probs=39.8
Q ss_pred CCCcchhHHHHHHHHHhhccchHHHHHhhhhccchhHHHhHHHH
Q psy13328 17 AIHREISVGEQFTEIFIKNHENVSLVLGYLEEFDFRVRWSAVKL 60 (68)
Q Consensus 17 s~~~~deig~~ftE~f~k~~eNItLLL~lLee~DF~VR~~avqL 60 (68)
+|.-++=|.+|+-|.|+.+-+-++-|..+.+..+|..-|..+|+
T Consensus 498 nP~LadlI~e~ige~~i~dl~~l~~L~~~a~d~~f~~~~a~vK~ 541 (843)
T KOG2099|consen 498 NPGLADLITEKIGEEWITDLDQLTKLRKFADDEEFQREWAKVKQ 541 (843)
T ss_pred CchHHHHHHHHhhhHhhhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence 35556789999999999999999999999999999999999886
No 49
>PHA03256 BDLF3; Provisional
Probab=25.83 E-value=35 Score=22.07 Aligned_cols=15 Identities=20% Similarity=0.361 Sum_probs=12.9
Q ss_pred hhccchHHHHHhhhh
Q psy13328 33 IKNHENVSLVLGYLE 47 (68)
Q Consensus 33 ~k~~eNItLLL~lLe 47 (68)
.|+-|||.++|||.-
T Consensus 55 ~Q~lenI~llLDLvG 69 (77)
T PHA03256 55 VQRLENICTLLDLAG 69 (77)
T ss_pred hhhHHHHHHHHHhhc
Confidence 578899999999974
No 50
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=25.72 E-value=96 Score=21.20 Aligned_cols=26 Identities=27% Similarity=0.213 Sum_probs=21.1
Q ss_pred HHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 41 LVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 41 LLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
-+|.+.-..+-.||..|++++..+++
T Consensus 12 ~Il~~~~~~~~~vr~~Al~~l~~il~ 37 (187)
T PF12830_consen 12 NILELCLSSDDSVRLAALQVLELILR 37 (187)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 46667778888999999999988775
No 51
>COG1413 FOG: HEAT repeat [Energy production and conversion]
Probab=24.62 E-value=1.4e+02 Score=21.25 Aligned_cols=26 Identities=35% Similarity=0.331 Sum_probs=13.0
Q ss_pred hccchHHHHHhhhhccchhHHHhHHH
Q psy13328 34 KNHENVSLVLGYLEEFDFRVRWSAVK 59 (68)
Q Consensus 34 k~~eNItLLL~lLee~DF~VR~~avq 59 (68)
...+.+..+..+|...++.||+.|+.
T Consensus 71 ~~~~av~~l~~~l~d~~~~vr~~a~~ 96 (335)
T COG1413 71 GSEEAVPLLRELLSDEDPRVRDAAAD 96 (335)
T ss_pred chHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 33444455555555555555555544
No 52
>PF08713 DNA_alkylation: DNA alkylation repair enzyme; InterPro: IPR014825 These proteins are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein shows it to adopt a super coiled alpha helical structure. ; PDB: 3JY1_A 3JXY_A 3JX7_A 3JXZ_A 3BVS_A 2B6C_B 1T06_B 3L9T_A.
Probab=24.53 E-value=91 Score=20.62 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=27.1
Q ss_pred HHHHHHHhhc-cchHHHHHhhhhccchhHHHhHHHHHHH
Q psy13328 26 EQFTEIFIKN-HENVSLVLGYLEEFDFRVRWSAVKLLTG 63 (68)
Q Consensus 26 ~~ftE~f~k~-~eNItLLL~lLee~DF~VR~~avqLLTa 63 (68)
..+.-.++++ ++-..++.......+.++|+.|+.++..
T Consensus 108 ~~~~~~~~~~~~~~~~~~~~W~~s~~~w~rR~~~v~~~~ 146 (213)
T PF08713_consen 108 SKLLGPLLKKHPEALELLEKWAKSDNEWVRRAAIVMLLR 146 (213)
T ss_dssp HHHHHHHHHHHGGHHHHHHHHHHCSSHHHHHHHHHCTTT
T ss_pred HHHHHHHHHhhHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 3333333333 7888889999999999999999866543
No 53
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=24.16 E-value=2.5e+02 Score=20.59 Aligned_cols=52 Identities=19% Similarity=0.369 Sum_probs=40.2
Q ss_pred CCCCCCCCCCcchhHHHHHHHHH-hhccchHHHHHhhhhccchhHHHhHHHHH
Q psy13328 10 TTKLPEGAIHREISVGEQFTEIF-IKNHENVSLVLGYLEEFDFRVRWSAVKLL 61 (68)
Q Consensus 10 ~~~~~e~s~~~~deig~~ftE~f-~k~~eNItLLL~lLee~DF~VR~~avqLL 61 (68)
.++..+......++.-..|.+.| .||.+.+..|=.+++-.++-=|+--|++|
T Consensus 4 ~~~~~~~~~~~~~~~~k~y~k~F~~KR~eh~~ai~~l~~~~~~~k~~k~i~~l 56 (207)
T PF15002_consen 4 DTKLKTEEAPEHDDHEKLYKKLFELKRKEHLAAIKSLFEIDDYEKRYKLIEIL 56 (207)
T ss_pred cccCCccccCCCchHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 34455555666677888899998 48899999999999988887777777665
No 54
>KOG2417|consensus
Probab=24.07 E-value=86 Score=25.92 Aligned_cols=28 Identities=36% Similarity=0.530 Sum_probs=20.3
Q ss_pred hHHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 38 NVSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 38 NItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
-||-+|+ =-.|+||-||-.++.|.+.++
T Consensus 416 iit~VlG-dlqfnfyhRwfdviFl~Sa~~ 443 (462)
T KOG2417|consen 416 IITEVLG-DLQFNFYHRWFDVIFLVSALS 443 (462)
T ss_pred HHHHHhh-hhcchhHHHHHHHHHHHHHHH
Confidence 3555555 147999999999998876553
No 55
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=23.71 E-value=1.1e+02 Score=22.63 Aligned_cols=20 Identities=25% Similarity=0.157 Sum_probs=16.6
Q ss_pred hccch-hHHHhHHHHHHHHhh
Q psy13328 47 EEFDF-RVRWSAVKLLTGLLL 66 (68)
Q Consensus 47 ee~DF-~VR~~avqLLTaLL~ 66 (68)
....| |+|+-||-|.+-|-.
T Consensus 132 ~n~~f~YSRl~AIGL~~LLe~ 152 (214)
T TIGR03060 132 GRHKFKYSRLFAIGLYSLLEE 152 (214)
T ss_pred cCCCcchHHHHHHHHHHHHHh
Confidence 56778 999999999987754
No 56
>COG1320 MnhG Multisubunit Na+/H+ antiporter, MnhG subunit [Inorganic ion transport and metabolism]
Probab=23.27 E-value=49 Score=22.14 Aligned_cols=16 Identities=31% Similarity=0.322 Sum_probs=13.1
Q ss_pred HhhhhccchhHHHhHH
Q psy13328 43 LGYLEEFDFRVRWSAV 58 (68)
Q Consensus 43 L~lLee~DF~VR~~av 58 (68)
++++-=+|||.|++|-
T Consensus 24 iGl~R~PD~YtRlHaa 39 (113)
T COG1320 24 IGLLRFPDVYTRLHAA 39 (113)
T ss_pred HHHHHCchHHHHHHhc
Confidence 5667789999999874
No 57
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=23.04 E-value=96 Score=20.81 Aligned_cols=29 Identities=17% Similarity=0.236 Sum_probs=21.6
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
..-|+.-|....-||.+-++++|..|+.+
T Consensus 40 ~d~L~kRL~~~~~hVK~K~Lrilk~l~~~ 68 (122)
T cd03572 40 LEYLLKRLKRSSPHVKLKVLKIIKHLCEK 68 (122)
T ss_pred HHHHHHHhcCCCCcchHHHHHHHHHHHhh
Confidence 33444455678899999999999988753
No 58
>KOG1058|consensus
Probab=22.31 E-value=80 Score=28.30 Aligned_cols=33 Identities=24% Similarity=0.253 Sum_probs=27.4
Q ss_pred cchHHHHHhhhhccchhHHHhHHHHHHHHhhcC
Q psy13328 36 HENVSLVLGYLEEFDFRVRWSAVKLLTGLLLNR 68 (68)
Q Consensus 36 ~eNItLLL~lLee~DF~VR~~avqLLTaLL~nR 68 (68)
++=|.-+|.+|..+|+-||.-++.+-.-|.+.|
T Consensus 316 ~~l~mDvLrvLss~dldvr~Ktldi~ldLvssr 348 (948)
T KOG1058|consen 316 QGLIMDVLRVLSSPDLDVRSKTLDIALDLVSSR 348 (948)
T ss_pred HHHHHHHHHHcCcccccHHHHHHHHHHhhhhhc
Confidence 344667888899999999999999988887765
No 59
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=21.81 E-value=1.3e+02 Score=22.35 Aligned_cols=44 Identities=25% Similarity=0.349 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhc--cchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 24 VGEQFTEIFIKN--HENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 24 ig~~ftE~f~k~--~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
+..-+.|.|.-+ .+=++.|+++|+.--=-+|..++|+|..|+.+
T Consensus 173 v~~~l~~~f~P~~~~~~l~~Ll~lL~n~~~w~~~~~L~iL~~ll~~ 218 (262)
T PF14225_consen 173 VVSYLREAFFPDHEFQILTFLLGLLENGPPWLRRKTLQILKVLLPH 218 (262)
T ss_pred HHHHHHHHhCchhHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHhcc
Confidence 444566666533 44577888999877778899999999998864
No 60
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin 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 []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=21.39 E-value=1.1e+02 Score=22.89 Aligned_cols=28 Identities=25% Similarity=0.319 Sum_probs=18.7
Q ss_pred HHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 39 VSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 39 ItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
+..|..+|...|.-+|+.+++.|..|..
T Consensus 269 ~~~L~~lL~s~~~nvr~~~L~~L~~l~~ 296 (526)
T PF01602_consen 269 INPLIKLLSSSDPNVRYIALDSLSQLAQ 296 (526)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHhhcccchhehhHHHHHHHhhc
Confidence 4556666677777777777777766654
No 61
>PF03334 PhaG_MnhG_YufB: Na+/H+ antiporter subunit; InterPro: IPR005133 This is a family of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti (Sinorhizobium meliloti), show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons. ; GO: 0005451 monovalent cation:hydrogen antiporter activity, 0015672 monovalent inorganic cation transport, 0015992 proton transport
Probab=21.32 E-value=92 Score=19.13 Aligned_cols=21 Identities=29% Similarity=0.306 Sum_probs=16.2
Q ss_pred HHhhhhccchhHHHhHHHHHH
Q psy13328 42 VLGYLEEFDFRVRWSAVKLLT 62 (68)
Q Consensus 42 LL~lLee~DF~VR~~avqLLT 62 (68)
.+.++.-+|||.|.++.-.-+
T Consensus 13 ~iGllR~pd~y~RlHa~s~~~ 33 (81)
T PF03334_consen 13 AIGLLRFPDFYTRLHAASKAD 33 (81)
T ss_pred HHHHHhCCcHHHHhhhhhHHH
Confidence 467788899999999875433
No 62
>PF04499 SAPS: SIT4 phosphatase-associated protein; InterPro: IPR007587 The SAPS family consists of proteins that associate with the SIT4 phosphatase protein []. This association is required for SIT4's role in G1 cyclin transcription and for bud formation in yeast.
Probab=21.20 E-value=2.4e+02 Score=22.68 Aligned_cols=44 Identities=14% Similarity=0.230 Sum_probs=35.2
Q ss_pred CCcchhHHHHHHHHHhhccchHHHHHhhhh-ccchhHHHhHHHHHHHHhh
Q psy13328 18 IHREISVGEQFTEIFIKNHENVSLVLGYLE-EFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 18 ~~~~deig~~ftE~f~k~~eNItLLL~lLe-e~DF~VR~~avqLLTaLL~ 66 (68)
++.+.++-.|+.+ +.-|..|+++|. +++=.+--.|-++|.+|.+
T Consensus 48 ~~~~~~ilewL~~-----q~LI~~Li~~L~p~~~~~~q~naa~~L~aII~ 92 (475)
T PF04499_consen 48 PESPTGILEWLAE-----QNLIPRLIDLLSPSYSSDVQSNAADFLKAIIR 92 (475)
T ss_pred ccchHHHHHHHHH-----hCHHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 5566788888877 789999999995 6777788888888888754
No 63
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=21.19 E-value=45 Score=17.99 Aligned_cols=29 Identities=17% Similarity=0.149 Sum_probs=23.8
Q ss_pred HHHHHHhhccchHHHHHhhhhccchhHHH
Q psy13328 27 QFTEIFIKNHENVSLVLGYLEEFDFRVRW 55 (68)
Q Consensus 27 ~ftE~f~k~~eNItLLL~lLee~DF~VR~ 55 (68)
.+|+.+--.+.+++-++.-|++.+|-.|.
T Consensus 22 ~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 22 ELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 67788888999999999999998887664
No 64
>PF12765 Cohesin_HEAT: HEAT repeat associated with sister chromatid cohesion
Probab=20.95 E-value=95 Score=16.82 Aligned_cols=25 Identities=32% Similarity=0.307 Sum_probs=19.4
Q ss_pred chHHHHHhhhhccchhHHHhHHHHH
Q psy13328 37 ENVSLVLGYLEEFDFRVRWSAVKLL 61 (68)
Q Consensus 37 eNItLLL~lLee~DF~VR~~avqLL 61 (68)
.-...+...|...+=.||-.||+||
T Consensus 18 ~v~~~i~~rl~D~s~~VR~aav~ll 42 (42)
T PF12765_consen 18 DVQSAIIRRLSDSSPSVREAAVDLL 42 (42)
T ss_pred HHHHHHHHHhcCCChHHHHHHHHHC
Confidence 3345666777888899999999985
No 65
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=20.04 E-value=1.7e+02 Score=23.15 Aligned_cols=36 Identities=25% Similarity=0.374 Sum_probs=31.6
Q ss_pred HhhccchHHHHHhhhhccchhHHHhHHHHHHHHhhc
Q psy13328 32 FIKNHENVSLVLGYLEEFDFRVRWSAVKLLTGLLLN 67 (68)
Q Consensus 32 f~k~~eNItLLL~lLee~DF~VR~~avqLLTaLL~n 67 (68)
.+.+.+=+.+++.+|...|-.|--.|+++|..|.++
T Consensus 114 ~~~~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~ 149 (503)
T PF10508_consen 114 LLVDNELLPLIIQCLRDPDLSVAKAAIKALKKLASH 149 (503)
T ss_pred HhcCccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCC
Confidence 345677789999999999999999999999999865
No 66
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=20.03 E-value=1.5e+02 Score=24.86 Aligned_cols=45 Identities=27% Similarity=0.319 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhhccc-----hHHHHHhhhhccchhHHHhHHHHHHHHhh
Q psy13328 22 ISVGEQFTEIFIKNHE-----NVSLVLGYLEEFDFRVRWSAVKLLTGLLL 66 (68)
Q Consensus 22 deig~~ftE~f~k~~e-----NItLLL~lLee~DF~VR~~avqLLTaLL~ 66 (68)
--++.||--.|.|.-. -|..++||.|+-|.-||-.|++=|-.+.+
T Consensus 39 K~Laaq~I~kffk~FP~l~~~Ai~a~~DLcEDed~~iR~~aik~lp~~ck 88 (556)
T PF05918_consen 39 KRLAAQFIPKFFKHFPDLQEEAINAQLDLCEDEDVQIRKQAIKGLPQLCK 88 (556)
T ss_dssp HHHHHHHHHHHHCC-GGGHHHHHHHHHHHHT-SSHHHHHHHHHHGGGG--
T ss_pred HHHHHHHHHHHHhhChhhHHHHHHHHHHHHhcccHHHHHHHHHhHHHHHH
Confidence 3466677777776644 47789999999999999999998776654
Done!