Query 041564
Match_columns 151
No_of_seqs 30 out of 32
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 08:26:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1293 Proteins containing ar 99.2 2E-11 4.3E-16 113.8 4.2 80 16-95 26-126 (678)
2 PF00514 Arm: Armadillo/beta-c 97.9 2.8E-05 6.1E-10 46.8 4.2 36 58-93 5-40 (41)
3 cd00020 ARM Armadillo/beta-cat 97.3 0.0011 2.3E-08 43.7 6.3 78 15-92 23-118 (120)
4 smart00185 ARM Armadillo/beta- 97.1 0.0013 2.9E-08 37.6 4.7 36 58-93 5-40 (41)
5 cd00020 ARM Armadillo/beta-cat 97.0 0.001 2.3E-08 43.7 3.9 49 46-94 29-78 (120)
6 PLN03200 cellulose synthase-in 96.1 0.0096 2.1E-07 62.3 5.7 82 13-94 418-517 (2102)
7 PLN03200 cellulose synthase-in 94.2 0.086 1.9E-06 55.6 5.8 77 16-92 463-557 (2102)
8 PF13513 HEAT_EZ: HEAT-like re 93.6 0.083 1.8E-06 32.7 2.8 44 46-90 9-53 (55)
9 KOG0166 Karyopherin (importin) 93.5 0.12 2.6E-06 48.0 4.8 73 18-90 298-389 (514)
10 KOG0166 Karyopherin (importin) 92.9 0.24 5.2E-06 46.1 5.9 73 19-91 342-433 (514)
11 PF02985 HEAT: HEAT repeat; I 92.2 0.27 5.8E-06 28.3 3.5 27 66-92 1-27 (31)
12 COG5064 SRP1 Karyopherin (impo 91.9 0.058 1.2E-06 49.9 0.6 44 47-90 138-182 (526)
13 COG5064 SRP1 Karyopherin (impo 90.3 0.32 6.9E-06 45.2 3.7 73 17-89 303-394 (526)
14 KOG4224 Armadillo repeat prote 85.6 1.3 2.9E-05 41.5 4.7 47 47-93 274-320 (550)
15 PF10508 Proteasom_PSMB: Prote 76.8 3.5 7.5E-05 36.8 4.0 49 47-95 100-149 (503)
16 PF13646 HEAT_2: HEAT repeats; 71.2 3.2 7E-05 26.6 1.8 28 66-93 32-59 (88)
17 KOG0547 Translocase of outer m 60.8 6.3 0.00014 37.9 2.3 54 78-141 319-372 (606)
18 PF13646 HEAT_2: HEAT repeats; 56.4 13 0.00028 23.8 2.6 25 67-91 1-26 (88)
19 PF05804 KAP: Kinesin-associat 54.0 19 0.00042 34.7 4.3 53 47-99 313-365 (708)
20 PF12348 CLASP_N: CLASP N term 51.1 15 0.00032 28.0 2.5 115 14-139 22-159 (228)
21 KOG4077 Cytochrome c oxidase, 49.9 13 0.00029 30.3 2.2 19 77-95 82-100 (149)
22 KOG1048 Neural adherens juncti 47.8 37 0.00081 33.3 5.2 74 20-94 519-595 (717)
23 PF09759 Atx10homo_assoc: Spin 47.4 31 0.00066 25.8 3.7 46 47-92 9-57 (102)
24 PF04064 DUF384: Domain of unk 44.6 59 0.0013 22.2 4.4 40 53-92 6-47 (58)
25 PF06012 DUF908: Domain of Unk 43.0 48 0.0011 28.1 4.6 31 64-94 25-55 (329)
26 PF06371 Drf_GBD: Diaphanous G 42.5 31 0.00066 25.4 3.0 36 58-93 100-144 (187)
27 PF14663 RasGEF_N_2: Rapamycin 41.8 32 0.00069 25.3 3.0 31 66-96 9-39 (115)
28 PF15007 CEP44: Centrosomal sp 39.5 31 0.00067 27.1 2.7 50 38-92 27-80 (131)
29 PF13155 Toprim_2: Toprim-like 37.4 45 0.00097 22.3 3.0 74 35-109 10-90 (96)
30 PF04826 Arm_2: Armadillo-like 34.5 75 0.0016 26.6 4.4 51 47-98 36-87 (254)
31 PF11698 V-ATPase_H_C: V-ATPas 32.9 29 0.00062 26.8 1.6 45 47-91 67-112 (119)
32 PF02284 COX5A: Cytochrome c o 32.8 35 0.00076 26.5 2.0 19 77-95 43-61 (108)
33 PF05804 KAP: Kinesin-associat 32.6 71 0.0015 31.0 4.5 51 47-97 272-322 (708)
34 cd00923 Cyt_c_Oxidase_Va Cytoc 32.3 36 0.00078 26.3 2.0 19 77-95 40-58 (103)
35 PF10274 ParcG: Parkin co-regu 30.2 62 0.0013 26.6 3.2 27 66-92 81-107 (183)
36 KOG2160 Armadillo/beta-catenin 29.0 35 0.00075 30.7 1.7 43 37-79 120-180 (342)
37 TIGR02156 PA_CoA_Oxy1 phenylac 28.8 32 0.0007 29.9 1.5 39 70-109 127-167 (289)
38 KOG3036 Protein involved in ce 28.7 32 0.0007 30.6 1.4 31 47-77 148-180 (293)
39 KOG1061 Vesicle coat complex A 28.6 48 0.001 32.8 2.7 37 62-98 157-193 (734)
40 PF08389 Xpo1: Exportin 1-like 28.5 36 0.00079 23.6 1.4 30 58-89 119-148 (148)
41 TIGR02765 crypto_DASH cryptoch 28.3 36 0.00078 29.3 1.6 21 80-100 332-352 (429)
42 KOG1240 Protein kinase contain 28.1 47 0.001 35.0 2.7 34 62-95 653-686 (1431)
43 PRK13778 paaA phenylacetate-Co 26.9 43 0.00094 29.6 1.9 43 67-110 142-186 (314)
44 COG3580 Uncharacterized protei 26.9 32 0.00069 31.4 1.1 45 47-91 278-328 (351)
45 PF08216 CTNNBL: Catenin-beta- 26.2 56 0.0012 25.0 2.2 35 47-82 69-104 (108)
46 KOG4413 26S proteasome regulat 26.1 97 0.0021 29.3 4.1 42 58-99 121-162 (524)
47 PF04826 Arm_2: Armadillo-like 24.7 1.4E+02 0.0031 25.0 4.5 77 15-93 70-162 (254)
48 PF03224 V-ATPase_H_N: V-ATPas 24.5 89 0.0019 25.8 3.2 35 58-92 232-267 (312)
49 PF12717 Cnd1: non-SMC mitotic 23.8 88 0.0019 23.8 2.9 27 68-94 66-92 (178)
50 TIGR02766 crypt_chrom_pln cryp 23.5 46 0.00099 29.3 1.4 22 81-102 329-350 (475)
51 PF10508 Proteasom_PSMB: Prote 23.5 86 0.0019 28.2 3.1 48 47-94 183-231 (503)
52 KOG4199 Uncharacterized conser 22.8 1.3E+02 0.0028 28.4 4.2 43 53-95 315-360 (461)
53 KOG4646 Uncharacterized conser 22.2 74 0.0016 26.5 2.3 45 47-91 78-125 (173)
54 KOG3678 SARM protein (with ste 21.6 86 0.0019 30.9 2.9 46 47-92 245-291 (832)
55 PF11791 Aconitase_B_N: Aconit 21.0 68 0.0015 26.2 1.8 30 67-96 96-125 (154)
56 KOG4500 Rho/Rac GTPase guanine 21.0 73 0.0016 30.8 2.3 46 47-92 338-388 (604)
57 PF12783 Sec7_N: Guanine nucle 20.8 92 0.002 23.3 2.4 47 47-93 52-101 (168)
58 KOG4224 Armadillo repeat prote 20.6 61 0.0013 30.9 1.7 75 18-92 353-444 (550)
No 1
>KOG1293 consensus Proteins containing armadillo/beta-catenin-like repeat [General function prediction only]
Probab=99.16 E-value=2e-11 Score=113.78 Aligned_cols=80 Identities=21% Similarity=0.137 Sum_probs=73.4
Q ss_pred chhHHhhhhhhhcccchhHhHHHHhh--hhhh-h----------------cccccccChHH-HHHHHhcCChHHHHhhhc
Q 041564 16 SSRLNNRLKNQIIGSQTKKLSFLKKL--YRLI-L----------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIFS 75 (151)
Q Consensus 16 s~rAlr~IKNqIIGNntKKlsfI~lG--PrlI-L----------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs 75 (151)
-+||+...||++||++++|..+|+.| |++. | ++||+++|.++ ++++++++.+|+|+++|+
T Consensus 26 lvrai~~~kN~vig~~~~K~~~ik~GAv~~Ll~L~s~e~~s~~~k~~~~~llns~f~~eqd~v~svL~~~~ll~Ll~LLs 105 (678)
T KOG1293|consen 26 LVRAIYMSKNLVIGFTDNKETNIKLGAVELLLALLSLEDGSTELKNGFAVLLNSLFLGEQDKVDSVLRIIELLKLLQLLS 105 (678)
T ss_pred HHHHHHHhcchhhcCCCccchhhhhcchHHHHhhccccCCchhhhhhHHHHHHhHHhhccchHHHHHHHhhHHHHHHHhc
Confidence 47999999999999999999999999 5422 2 99999999999 999999999999999999
Q ss_pred cCC-HHHHHHHHHHHHHhccc
Q 041564 76 RRD-EQVADTMLLCKAEAGGM 95 (151)
Q Consensus 76 ~~D-~KVVEAcLRcLr~~~~~ 95 (151)
.+| .+++|+++||+|..=-+
T Consensus 106 ~sD~~~~le~~l~~lR~Ifet 126 (678)
T KOG1293|consen 106 ESDSLNVLEKTLRCLRTIFET 126 (678)
T ss_pred CcchHhHHHHHHHHHHHHHhc
Confidence 999 99999999999987544
No 2
>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=97.87 E-value=2.8e-05 Score=46.76 Aligned_cols=36 Identities=22% Similarity=0.334 Sum_probs=33.8
Q ss_pred HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhc
Q 041564 58 IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAG 93 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~ 93 (151)
.+.++++|++|.|+++|.++|+.+.+.|+.+|+.++
T Consensus 5 ~~~i~~~g~i~~Lv~ll~~~~~~v~~~a~~al~nl~ 40 (41)
T PF00514_consen 5 KQAIVEAGGIPPLVQLLKSPDPEVQEEAAWALGNLA 40 (41)
T ss_dssp HHHHHHTTHHHHHHHHTTSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHcccHHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 899999999999999999999999999999998653
No 3
>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=97.31 E-value=0.0011 Score=43.66 Aligned_cols=78 Identities=17% Similarity=0.180 Sum_probs=65.9
Q ss_pred cchhHHhhhhhhhcccchhHhHHHHhh--hhhh--h-------------cccccccChHH-HHHHHhcCChHHHHhhhcc
Q 041564 15 SSSRLNNRLKNQIIGSQTKKLSFLKKL--YRLI--L-------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSR 76 (151)
Q Consensus 15 ~s~rAlr~IKNqIIGNntKKlsfI~lG--PrlI--L-------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~ 76 (151)
-+..|+..+.|...++...+..+++.| |..+ | +|+.++.+.++ .+.+.+.|++|.|+..|..
T Consensus 23 ~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~~~~~~~~g~l~~l~~~l~~ 102 (120)
T cd00020 23 VQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIVLEAGGVPKLVNLLDS 102 (120)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHHHHHHHHCCChHHHHHHHhc
Confidence 345678899999999888888999877 5522 2 89999998877 8888999999999999999
Q ss_pred CCHHHHHHHHHHHHHh
Q 041564 77 RDEQVADTMLLCKAEA 92 (151)
Q Consensus 77 ~D~KVVEAcLRcLr~~ 92 (151)
.+.++.+.++.+++-+
T Consensus 103 ~~~~~~~~a~~~l~~l 118 (120)
T cd00020 103 SNEDIQKNATGALSNL 118 (120)
T ss_pred CCHHHHHHHHHHHHHh
Confidence 9999999999988754
No 4
>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=97.14 E-value=0.0013 Score=37.60 Aligned_cols=36 Identities=28% Similarity=0.383 Sum_probs=32.9
Q ss_pred HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhc
Q 041564 58 IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAG 93 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~ 93 (151)
.+.+.++|++|.|+.+|.++|+++++.++.+|+-++
T Consensus 5 ~~~i~~~g~i~~L~~ll~~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 5 KQAVVDAGGLPALVELLKSEDEEVVKEAAWALSNLS 40 (41)
T ss_pred HHHHHHCCCHHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 677889999999999999999999999999998654
No 5
>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=97.02 E-value=0.001 Score=43.73 Aligned_cols=49 Identities=27% Similarity=0.404 Sum_probs=45.1
Q ss_pred hcccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhcc
Q 041564 46 LPPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 46 LVLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~ 94 (151)
..+++++.+.++ .+.+++.|++|.|+.+|.++|+++.+.|+.+|+....
T Consensus 29 ~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~ 78 (120)
T cd00020 29 WALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAA 78 (120)
T ss_pred HHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHcc
Confidence 489999999888 9999999999999999999999999999999998853
No 6
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=96.10 E-value=0.0096 Score=62.32 Aligned_cols=82 Identities=15% Similarity=0.039 Sum_probs=71.3
Q ss_pred cccchhHHhhhhhhhcccchhHhHHHHhh--hhhh--h-------------cccccccChHH-HHHHHhcCChHHHHhhh
Q 041564 13 KTSSSRLNNRLKNQIIGSQTKKLSFLKKL--YRLI--L-------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIF 74 (151)
Q Consensus 13 ~~~s~rAlr~IKNqIIGNntKKlsfI~lG--PrlI--L-------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lL 74 (151)
.....++...|+|.-.|++.....+++.| |+++ | ++|-++.|.++ -++++++|++|.|+++|
T Consensus 418 ~evQ~~Av~aL~~L~~~~~e~~~aIi~~ggIp~LV~LL~s~s~~iQ~~A~~~L~nLa~~ndenr~aIieaGaIP~LV~LL 497 (2102)
T PLN03200 418 ADVQEELIRALSSLCCGKGGLWEALGGREGVQLLISLLGLSSEQQQEYAVALLAILTDEVDESKWAITAAGGIPPLVQLL 497 (2102)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHcCcHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHCCCHHHHHHHH
Confidence 33456678889999999999999999998 7755 3 78999999988 88999999999999999
Q ss_pred ccCCHHHHHHHHHHHHHhcc
Q 041564 75 SRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 75 s~~D~KVVEAcLRcLr~~~~ 94 (151)
++++.++-|.|+.+|--++.
T Consensus 498 ~s~~~~iqeeAawAL~NLa~ 517 (2102)
T PLN03200 498 ETGSQKAKEDSATVLWNLCC 517 (2102)
T ss_pred cCCCHHHHHHHHHHHHHHhC
Confidence 99999999999999987766
No 7
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=94.22 E-value=0.086 Score=55.58 Aligned_cols=77 Identities=16% Similarity=0.091 Sum_probs=65.6
Q ss_pred chhHHhhhhhhhcccchhHhHHHHhh--hhhh--h-------------cccccccChHHHHHHH-hcCChHHHHhhhccC
Q 041564 16 SSRLNNRLKNQIIGSQTKKLSFLKKL--YRLI--L-------------PPSRFTCGFEAIQAML-DAGLFPDLSLIFSRR 77 (151)
Q Consensus 16 s~rAlr~IKNqIIGNntKKlsfI~lG--PrlI--L-------------VLGSFAcG~EaVkaLL-daGvvP~Ll~lLs~~ 77 (151)
...|++.|.|-.-||..++..+++.| |.++ | +||-+++..++.+.++ ++|++|.|+.+|.+.
T Consensus 463 Q~~A~~~L~nLa~~ndenr~aIieaGaIP~LV~LL~s~~~~iqeeAawAL~NLa~~~~qir~iV~~aGAIppLV~LL~sg 542 (2102)
T PLN03200 463 QEYAVALLAILTDEVDESKWAITAAGGIPPLVQLLETGSQKAKEDSATVLWNLCCHSEDIRACVESAGAVPALLWLLKNG 542 (2102)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhCCcHHHHHHHHHCCCHHHHHHHHhCC
Confidence 34678889999999999999999999 7644 3 8999998766678777 789999999999999
Q ss_pred CHHHHHHHHHHHHHh
Q 041564 78 DEQVADTMLLCKAEA 92 (151)
Q Consensus 78 D~KVVEAcLRcLr~~ 92 (151)
+.+..+-++.+|..+
T Consensus 543 d~~~q~~Aa~AL~nL 557 (2102)
T PLN03200 543 GPKGQEIAAKTLTKL 557 (2102)
T ss_pred CHHHHHHHHHHHHHH
Confidence 999999999988776
No 8
>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=93.58 E-value=0.083 Score=32.71 Aligned_cols=44 Identities=18% Similarity=0.253 Sum_probs=37.3
Q ss_pred hcccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHH
Q 041564 46 LPPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKA 90 (151)
Q Consensus 46 LVLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr 90 (151)
.+||.++-+..+ .+. .-..++|.|+.+|.++++.|-++++.||.
T Consensus 9 ~aLg~l~~~~~~~~~~-~~~~~~~~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 9 WALGRLAEGCPELLQP-YLPELLPALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHCTTTTTHHHHHH-HHHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHhhHhcccHHHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 478998877777 555 67789999999999999999999999885
No 9
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.46 E-value=0.12 Score=47.99 Aligned_cols=73 Identities=21% Similarity=0.231 Sum_probs=62.9
Q ss_pred hHHhhhhhhhcccchhHhHHHHhh--hh--hhh--------------cccccccChHH-HHHHHhcCChHHHHhhhccCC
Q 041564 18 RLNNRLKNQIIGSQTKKLSFLKKL--YR--LIL--------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRD 78 (151)
Q Consensus 18 rAlr~IKNqIIGNntKKlsfI~lG--Pr--lIL--------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D 78 (151)
=|+|.|=|-+=||--|=-..|..| |. .+| +|+=.+.|..+ +++++|+|++|.|+.+|+..|
T Consensus 298 PaLRaiGNIvtG~d~QTq~vi~~~~L~~l~~ll~~s~~~~ikkEAcW~iSNItAG~~~qiqaVida~l~p~Li~~l~~~e 377 (514)
T KOG0166|consen 298 PALRAIGNIVTGSDEQTQVVINSGALPVLSNLLSSSPKESIKKEACWTISNITAGNQEQIQAVIDANLIPVLINLLQTAE 377 (514)
T ss_pred HHHhhccceeeccHHHHHHHHhcChHHHHHHHhccCcchhHHHHHHHHHHHhhcCCHHHHHHHHHcccHHHHHHHHhccc
Confidence 489999999999999999999998 54 112 78888899999 999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 041564 79 EQVADTMLLCKA 90 (151)
Q Consensus 79 ~KVVEAcLRcLr 90 (151)
-+.=-.|+-++.
T Consensus 378 f~~rKEAawaIs 389 (514)
T KOG0166|consen 378 FDIRKEAAWAIS 389 (514)
T ss_pred hHHHHHHHHHHH
Confidence 887777777765
No 10
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.91 E-value=0.24 Score=46.07 Aligned_cols=73 Identities=19% Similarity=0.197 Sum_probs=62.5
Q ss_pred HHhhhhhhhcccchhHhHHHHhh--hhhh--h-------------cccccc-cChHH-HHHHHhcCChHHHHhhhccCCH
Q 041564 19 LNNRLKNQIIGSQTKKLSFLKKL--YRLI--L-------------PPSRFT-CGFEA-IQAMLDAGLFPDLSLIFSRRDE 79 (151)
Q Consensus 19 Alr~IKNqIIGNntKKlsfI~lG--PrlI--L-------------VLGSFA-cG~Ea-VkaLLdaGvvP~Ll~lLs~~D~ 79 (151)
|.-.|-|-.=||..|.-.+|..| |.++ | +|+=.+ -|+++ ++-|++.|.+++|-.+|...|.
T Consensus 342 AcW~iSNItAG~~~qiqaVida~l~p~Li~~l~~~ef~~rKEAawaIsN~ts~g~~~qi~yLv~~giI~plcdlL~~~D~ 421 (514)
T KOG0166|consen 342 ACWTISNITAGNQEQIQAVIDANLIPVLINLLQTAEFDIRKEAAWAISNLTSSGTPEQIKYLVEQGIIKPLCDLLTCPDV 421 (514)
T ss_pred HHHHHHHhhcCCHHHHHHHHHcccHHHHHHHHhccchHHHHHHHHHHHhhcccCCHHHHHHHHHcCCchhhhhcccCCCh
Confidence 56678898889999999999999 7644 3 555444 77788 9999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 041564 80 QVADTMLLCKAE 91 (151)
Q Consensus 80 KVVEAcLRcLr~ 91 (151)
+++..++-++.-
T Consensus 422 ~ii~v~Ld~l~n 433 (514)
T KOG0166|consen 422 KIILVALDGLEN 433 (514)
T ss_pred HHHHHHHHHHHH
Confidence 999999988754
No 11
>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=92.24 E-value=0.27 Score=28.30 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=23.5
Q ss_pred ChHHHHhhhccCCHHHHHHHHHHHHHh
Q 041564 66 LFPDLSLIFSRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 66 vvP~Ll~lLs~~D~KVVEAcLRcLr~~ 92 (151)
++|.++++|++++++|=++++.||...
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~~i 27 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLGAI 27 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 379999999999999999999999764
No 12
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=91.91 E-value=0.058 Score=49.93 Aligned_cols=44 Identities=16% Similarity=0.323 Sum_probs=41.1
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHH
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKA 90 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr 90 (151)
+|--.|.|+.+ -+-++|+|+||.++++|+.++..|-|-+.-+|-
T Consensus 138 alTNiaSGtt~QTkvVvd~~AVPlfiqlL~s~~~~V~eQavWALG 182 (526)
T COG5064 138 ALTNIASGTTQQTKVVVDAGAVPLFIQLLSSTEDDVREQAVWALG 182 (526)
T ss_pred HHhhhccCcccceEEEEeCCchHHHHHHHcCchHHHHHHHHHHhc
Confidence 88889999999 999999999999999999999999999888875
No 13
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=90.26 E-value=0.32 Score=45.22 Aligned_cols=73 Identities=22% Similarity=0.277 Sum_probs=61.2
Q ss_pred hhHHhhhhhhhcccchhHhHHHHhh--hh--hhh-------------cccccccChHH-HHHHHhcCChHHHHhhhccCC
Q 041564 17 SRLNNRLKNQIIGSQTKKLSFLKKL--YR--LIL-------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRD 78 (151)
Q Consensus 17 ~rAlr~IKNqIIGNntKKlsfI~lG--Pr--lIL-------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D 78 (151)
.-|+|-+-|-|-|+.-|-.-.|..| +. .+| .|.-.+.|..+ +++++|++.+|.|+.+|+..|
T Consensus 303 tPalR~vGNIVTG~D~QTqviI~~G~L~a~~~lLs~~ke~irKEaCWTiSNITAGnteqiqavid~nliPpLi~lls~ae 382 (526)
T COG5064 303 TPALRSVGNIVTGSDDQTQVIINCGALKAFRSLLSSPKENIRKEACWTISNITAGNTEQIQAVIDANLIPPLIHLLSSAE 382 (526)
T ss_pred CHHHHhhcCeeecCccceehheecccHHHHHHHhcChhhhhhhhhheeecccccCCHHHHHHHHhcccchHHHHHHHHHH
Confidence 3578999999999999999999999 32 333 88889999999 999999999999999999988
Q ss_pred HHHH-HHHHHHH
Q 041564 79 EQVA-DTMLLCK 89 (151)
Q Consensus 79 ~KVV-EAcLRcL 89 (151)
-|.- |||---.
T Consensus 383 ~k~kKEACWAis 394 (526)
T COG5064 383 YKIKKEACWAIS 394 (526)
T ss_pred HHHHHHHHHHHH
Confidence 8774 5664433
No 14
>KOG4224 consensus Armadillo repeat protein VAC8 required for vacuole fusion, inheritance and cytosol-to-vacuole protein targeting [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.61 E-value=1.3 Score=41.49 Aligned_cols=47 Identities=13% Similarity=0.182 Sum_probs=42.6
Q ss_pred cccccccChHHHHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhc
Q 041564 47 PPSRFTCGFEAIQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAG 93 (151)
Q Consensus 47 VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~ 93 (151)
+||-+|.-++=.+.++++|.+|+|+.+|+++-.+++-|..-|+|-.+
T Consensus 274 ALrnlasdt~Yq~eiv~ag~lP~lv~Llqs~~~plilasVaCIrnis 320 (550)
T KOG4224|consen 274 ALRNLASDTEYQREIVEAGSLPLLVELLQSPMGPLILASVACIRNIS 320 (550)
T ss_pred HHhhhcccchhhhHHHhcCCchHHHHHHhCcchhHHHHHHHHHhhcc
Confidence 88888887777999999999999999999999999999999998765
No 15
>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=76.80 E-value=3.5 Score=36.82 Aligned_cols=49 Identities=18% Similarity=0.178 Sum_probs=44.5
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhccc
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~ 95 (151)
.||..+...++ ++.+.+.+++|.++.+|.++|..|.++|..+|+..+..
T Consensus 100 ~l~~~~~~~~~~~~~~~~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~ 149 (503)
T PF10508_consen 100 QLGRIARHSEGAAQLLVDNELLPLIIQCLRDPDLSVAKAAIKALKKLASH 149 (503)
T ss_pred HHHHHhcCCHHHHHHhcCccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCC
Confidence 57787777777 99999999999999999999999999999999999863
No 16
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=71.16 E-value=3.2 Score=26.63 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=24.9
Q ss_pred ChHHHHhhhccCCHHHHHHHHHHHHHhc
Q 041564 66 LFPDLSLIFSRRDEQVADTMLLCKAEAG 93 (151)
Q Consensus 66 vvP~Ll~lLs~~D~KVVEAcLRcLr~~~ 93 (151)
++|.|+.+|.++|+.|..+++.+|...|
T Consensus 32 ~~~~L~~~l~d~~~~vr~~a~~aL~~i~ 59 (88)
T PF13646_consen 32 AIPALIELLKDEDPMVRRAAARALGRIG 59 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHCCH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence 4889999999999999999999998664
No 17
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.81 E-value=6.3 Score=37.86 Aligned_cols=54 Identities=28% Similarity=0.433 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHHHHhcccccccccceecCCCCCCCCccccccCCCCCccccchhHHHHHHHHHH
Q 041564 78 DEQVADTMLLCKAEAGGMHMRQSSNVEVPNGSDHDYDSVVPLDPSKNSLNNECGIIYLSLILAE 141 (151)
Q Consensus 78 D~KVVEAcLRcLr~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (151)
|.++ |-++++|...|.||--..+ ++|+..|+|.++-|||..|+| .|+++++.+.
T Consensus 319 d~~l-e~~A~al~~~gtF~fL~g~----~~~a~~d~~~~I~l~~~~~~l-----yI~~a~~y~d 372 (606)
T KOG0547|consen 319 DAEL-EYMAEALLLRGTFHFLKGD----SLGAQEDFDAAIKLDPAFNSL-----YIKRAAAYAD 372 (606)
T ss_pred chhH-HHHHHHHHHhhhhhhhcCC----chhhhhhHHHHHhcCcccchH-----HHHHHHHHhh
Confidence 6777 8899999999999987654 679999999999999999998 7888887763
No 18
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=56.42 E-value=13 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=22.0
Q ss_pred hHHHHhhh-ccCCHHHHHHHHHHHHH
Q 041564 67 FPDLSLIF-SRRDEQVADTMLLCKAE 91 (151)
Q Consensus 67 vP~Ll~lL-s~~D~KVVEAcLRcLr~ 91 (151)
+|.|++.| .++|+.+-..++++|..
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~~ 26 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALGE 26 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHC
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 68899998 88899999999999883
No 19
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=54.04 E-value=19 Score=34.73 Aligned_cols=53 Identities=11% Similarity=0.055 Sum_probs=44.7
Q ss_pred cccccccChHHHHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhccccccc
Q 041564 47 PPSRFTCGFEAIQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGMHMRQ 99 (151)
Q Consensus 47 VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~~ 99 (151)
.|-.++.-.|+-..+.+.|++|.|.++|.++++.+++.++|.|.-+|--....
T Consensus 313 fLkkLSi~~ENK~~m~~~giV~kL~kLl~s~~~~l~~~aLrlL~NLSfd~~~R 365 (708)
T PF05804_consen 313 FLKKLSIFKENKDEMAESGIVEKLLKLLPSENEDLVNVALRLLFNLSFDPELR 365 (708)
T ss_pred HHHHHcCCHHHHHHHHHcCCHHHHHHHhcCCCHHHHHHHHHHHHHhCcCHHHH
Confidence 66677777777888899999999999999999999999999999888654443
No 20
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=51.06 E-value=15 Score=27.99 Aligned_cols=115 Identities=15% Similarity=0.084 Sum_probs=59.6
Q ss_pred ccchhHHhhhhhhhccc--chhHhHHHHh------h-------hhhh------hcccccccChHH-HHHHHhcCChHHHH
Q 041564 14 TSSSRLNNRLKNQIIGS--QTKKLSFLKK------L-------YRLI------LPPSRFTCGFEA-IQAMLDAGLFPDLS 71 (151)
Q Consensus 14 ~~s~rAlr~IKNqIIGN--ntKKlsfI~l------G-------PrlI------LVLGSFAcG~Ea-VkaLLdaGvvP~Ll 71 (151)
+.+..|+..++.-+.|+ ......|+.. + .|.. .+++.++..... .+.. -...+|.|+
T Consensus 22 ~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~-~~~~l~~Ll 100 (228)
T PF12348_consen 22 EERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPY-ADILLPPLL 100 (228)
T ss_dssp HHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHH-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHH-HHHHHHHHH
Confidence 35678999999999999 2222222221 1 2311 166666655555 5544 334678999
Q ss_pred hhhccCCHHHHHHHHHHHHHhccccccc-ccceecCCCCCCCCccccccCCCCCccccchhHHHHHHHH
Q 041564 72 LIFSRRDEQVADTMLLCKAEAGGMHMRQ-SSNVEVPNGSDHDYDSVVPLDPSKNSLNNECGIIYLSLIL 139 (151)
Q Consensus 72 ~lLs~~D~KVVEAcLRcLr~~~~~h~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 (151)
..+.++..-+.+++..||...-.. -. .+.+. .....+.-.+||..-.++-..|+..++
T Consensus 101 ~~~~~~~~~i~~~a~~~L~~i~~~--~~~~~~~~--------~~~l~~~~~~Kn~~vR~~~~~~l~~~l 159 (228)
T PF12348_consen 101 KKLGDSKKFIREAANNALDAIIES--CSYSPKIL--------LEILSQGLKSKNPQVREECAEWLAIIL 159 (228)
T ss_dssp HGGG---HHHHHHHHHHHHHHHTT--S-H--HHH--------HHHHHHHTT-S-HHHHHHHHHHHHHHH
T ss_pred HHHccccHHHHHHHHHHHHHHHHH--CCcHHHHH--------HHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 989988888899999888764321 11 11111 122334445666655555555555544
No 21
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=49.86 E-value=13 Score=30.27 Aligned_cols=19 Identities=11% Similarity=0.130 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHHHHhccc
Q 041564 77 RDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 77 ~D~KVVEAcLRcLr~~~~~ 95 (151)
+++||+||+||+-|-+.-|
T Consensus 82 P~pkvIEaaLRA~RRvNDf 100 (149)
T KOG4077|consen 82 PSPKVIEAALRACRRVNDF 100 (149)
T ss_pred CChHHHHHHHHHHHHhccH
Confidence 5899999999999877655
No 22
>KOG1048 consensus Neural adherens junction protein Plakophilin and related Armadillo repeat proteins [Signal transduction mechanisms; Extracellular structures]
Probab=47.75 E-value=37 Score=33.30 Aligned_cols=74 Identities=14% Similarity=-0.013 Sum_probs=53.0
Q ss_pred HhhhhhhhcccchhHhHHHHh--hhhhhhcccccccChHHHHHH-HhcCChHHHHhhhccCCHHHHHHHHHHHHHhcc
Q 041564 20 NNRLKNQIIGSQTKKLSFLKK--LYRLILPPSRFTCGFEAIQAM-LDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 20 lr~IKNqIIGNntKKlsfI~l--GPrlILVLGSFAcG~EaVkaL-LdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~ 94 (151)
++.+++.-|+ ..||..-++. |....|..|++.....-...+ ....+.|+|..+|.++|..||.+++-+||-++.
T Consensus 519 vVr~Yl~Ll~-~s~n~~TlEasaGaLQNltA~~~~~~~~~~~~v~~kekgl~~l~~ll~~~~~~vv~s~a~~LrNls~ 595 (717)
T KOG1048|consen 519 VVRPYLLLLA-LSKNDNTLEASAGALQNLTAGLWTWSEYMRGAVFRKEKGLPPLVELLRNDDSDVVRSAAGALRNLSR 595 (717)
T ss_pred HHHHHHHHHH-HhcchHHHHHhhhhHhhhhccCCcchhHHHhhhhhhccCccHHHHHHhcCCchHHHHHHHHHhhhcc
Confidence 5566666666 5555555443 233446777776655445555 678899999999999999999999999998764
No 23
>PF09759 Atx10homo_assoc: Spinocerebellar ataxia type 10 protein domain; InterPro: IPR019156 This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region [].
Probab=47.37 E-value=31 Score=25.81 Aligned_cols=46 Identities=4% Similarity=0.015 Sum_probs=37.4
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhh--hccCCHHHHHHHHHHHHHh
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLI--FSRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~l--Ls~~D~KVVEAcLRcLr~~ 92 (151)
+||.++..-.. -..+.+.|++|.+++. +-..||-+-|-+.-|+|-+
T Consensus 9 lianl~~~~~~~Qd~vr~~~Gi~liL~~c~iD~~nP~irEwai~aiRnL 57 (102)
T PF09759_consen 9 LIANLCYKNKEVQDLVRELGGIPLILSCCNIDDHNPFIREWAIFAIRNL 57 (102)
T ss_pred HHHHHHhCCHHHHHHHHHcCChHHHHHhcCCCcccHHHHHHHHHHHHHH
Confidence 78888888778 5667789999999987 3555999999988888754
No 24
>PF04064 DUF384: Domain of unknown function (DUF384); InterPro: IPR007206 This is a protein of unknown function. It is found C-terminal to another domain of unknown function (IPR007205 from INTERPRO).
Probab=44.59 E-value=59 Score=22.19 Aligned_cols=40 Identities=13% Similarity=0.003 Sum_probs=29.2
Q ss_pred cChHHHHHHHhcCChHHHHhhh--ccCCHHHHHHHHHHHHHh
Q 041564 53 CGFEAIQAMLDAGLFPDLSLIF--SRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 53 cG~EaVkaLLdaGvvP~Ll~lL--s~~D~KVVEAcLRcLr~~ 92 (151)
|.++.-|..+....++.+++-+ ...|++|.|+|-|..-++
T Consensus 6 ~~T~~GR~~lR~~~vY~IlRe~h~~E~d~~V~e~~erlV~iL 47 (58)
T PF04064_consen 6 CATREGREYLREKGVYPILRELHKWEEDEEVQEACERLVQIL 47 (58)
T ss_pred hccHHHHHHHHHcCchHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence 5666666666666777777776 667999999999865543
No 25
>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=43.00 E-value=48 Score=28.11 Aligned_cols=31 Identities=13% Similarity=-0.020 Sum_probs=27.8
Q ss_pred cCChHHHHhhhccCCHHHHHHHHHHHHHhcc
Q 041564 64 AGLFPDLSLIFSRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 64 aGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~ 94 (151)
++-.++|..+|..+|..|+.++++-+...+-
T Consensus 25 YsS~e~L~~LL~s~~~dVl~~aL~ll~~l~q 55 (329)
T PF06012_consen 25 YSSSEHLNSLLNSTDLDVLLAALRLLLRLAQ 55 (329)
T ss_pred cccHHHHHHHHcCCCHHHHHHHHHHHHHHHh
Confidence 7889999999999999999999998877554
No 26
>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=42.54 E-value=31 Score=25.44 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=28.2
Q ss_pred HHHHHhcCChHHHHhhhcc---------CCHHHHHHHHHHHHHhc
Q 041564 58 IQAMLDAGLFPDLSLIFSR---------RDEQVADTMLLCKAEAG 93 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lLs~---------~D~KVVEAcLRcLr~~~ 93 (151)
|+.-++.|++..|+.+|.. .+..+...|+||+|..-
T Consensus 100 v~~Fl~~~G~~~L~~~L~~~~~~~~~~~~~~~~~~~~l~Clkal~ 144 (187)
T PF06371_consen 100 VQEFLELGGLEALLNVLSKLNKKKEKSEEDIDIEHECLRCLKALM 144 (187)
T ss_dssp HHHH-HHHHHHHHHHHHHHHHTHHCTCTTCHHHHHHHHHHHHHHT
T ss_pred HHHhccCCCHHHHHHHHHHhhhhhhhcchhHHHHHHHHHHHHHHH
Confidence 8888899999999998732 34567888999999854
No 27
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=41.80 E-value=32 Score=25.28 Aligned_cols=31 Identities=16% Similarity=-0.057 Sum_probs=26.1
Q ss_pred ChHHHHhhhccCCHHHHHHHHHHHHHhcccc
Q 041564 66 LFPDLSLIFSRRDEQVADTMLLCKAEAGGMH 96 (151)
Q Consensus 66 vvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h 96 (151)
+++-|++-|..++++|+.+|++.|-++-.-+
T Consensus 9 ~i~lLv~QL~D~~~~V~~~A~~iL~e~c~~~ 39 (115)
T PF14663_consen 9 GIELLVTQLYDPSPEVVAAALEILEEACEDK 39 (115)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHhch
Confidence 4677888899999999999999999886544
No 28
>PF15007 CEP44: Centrosomal spindle body, CEP44
Probab=39.48 E-value=31 Score=27.14 Aligned_cols=50 Identities=14% Similarity=0.289 Sum_probs=33.6
Q ss_pred HHhh-hhhhhcccccc-cChHH--HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHh
Q 041564 38 LKKL-YRLILPPSRFT-CGFEA--IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 38 I~lG-PrlILVLGSFA-cG~Ea--VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~ 92 (151)
+..| |...|.+=+++ |+... -+.|++.|.- ++..+|.+++|++-|-||..
T Consensus 27 l~~G~p~afLpil~~~L~~yS~~va~~l~~~g~e-----L~~k~D~RF~E~vyk~LRde 80 (131)
T PF15007_consen 27 LYKGDPSAFLPILHYALLSYSTHVARLLVDRGYE-----LYGKNDLRFVESVYKLLRDE 80 (131)
T ss_pred HhcCCHHHHHHHHHHHHHcCCHHHHHHHHHcCch-----hhcCChHHHHHHHHHHHHHH
Confidence 4456 66554333333 55554 5566666643 57889999999999999975
No 29
>PF13155 Toprim_2: Toprim-like
Probab=37.37 E-value=45 Score=22.27 Aligned_cols=74 Identities=18% Similarity=0.157 Sum_probs=38.2
Q ss_pred hHHHHhhhhhh----hcccccccChHH-HHHHHhcCChHHHHhhhccC--CHHHHHHHHHHHHHhcccccccccceecCC
Q 041564 35 LSFLKKLYRLI----LPPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRR--DEQVADTMLLCKAEAGGMHMRQSSNVEVPN 107 (151)
Q Consensus 35 lsfI~lGPrlI----LVLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~--D~KVVEAcLRcLr~~~~~h~~~~~~~~~~~ 107 (151)
+||.++++... +++.+.++..+. +..++.......++-.+-++ ..+.++...+-+...+ +-.++......|+
T Consensus 10 LS~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~-~~~~~~~~~~~~~ 88 (96)
T PF13155_consen 10 LSYYQLGKENIKDNSLSLAGGGTLSEKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEG-FPNIKVRIEDPPD 88 (96)
T ss_pred HHHHHhCchhcCCceEEEECCchHHHHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhC-CCcceeeecCCCC
Confidence 57777775432 567777766555 66666433334444334443 4455555554444433 2334444445566
Q ss_pred CC
Q 041564 108 GS 109 (151)
Q Consensus 108 ~~ 109 (151)
|.
T Consensus 89 ~K 90 (96)
T PF13155_consen 89 GK 90 (96)
T ss_pred Cc
Confidence 64
No 30
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=34.53 E-value=75 Score=26.59 Aligned_cols=51 Identities=10% Similarity=0.051 Sum_probs=40.3
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhcccccc
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGMHMR 98 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~ 98 (151)
++|=. .++.. =..+-+.|+++.+..+|..+++++-+-++.||.-.+.-...
T Consensus 36 al~n~-aaf~~nq~~Ir~~Ggi~lI~~lL~~p~~~vr~~AL~aL~Nls~~~en 87 (254)
T PF04826_consen 36 ALGNS-AAFPFNQDIIRDLGGISLIGSLLNDPNPSVREKALNALNNLSVNDEN 87 (254)
T ss_pred HHHhh-ccChhHHHHHHHcCCHHHHHHHcCCCChHHHHHHHHHHHhcCCChhh
Confidence 55554 45555 66777899999999999999999999999999866654433
No 31
>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=32.86 E-value=29 Score=26.76 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=35.5
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHH
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAE 91 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~ 91 (151)
=||-|..=.++ .+.+-+.|+=+.+.++++|+|+.|-.-||.|+..
T Consensus 67 Dig~~vr~~p~gr~ii~~lg~K~~vM~Lm~h~d~eVr~eAL~avQk 112 (119)
T PF11698_consen 67 DIGEFVRHYPNGRNIIEKLGAKERVMELMNHEDPEVRYEALLAVQK 112 (119)
T ss_dssp HHHHHHHH-GGGHHHHHHHSHHHHHHHHTS-SSHHHHHHHHHHHHH
T ss_pred chHHHHHHChhHHHHHHhcChHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 56777776777 5555578999999999999999999999999864
No 32
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=32.75 E-value=35 Score=26.52 Aligned_cols=19 Identities=5% Similarity=0.163 Sum_probs=14.0
Q ss_pred CCHHHHHHHHHHHHHhccc
Q 041564 77 RDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 77 ~D~KVVEAcLRcLr~~~~~ 95 (151)
++|++++||||+-|-+.-|
T Consensus 43 P~P~ii~aALrAcRRvND~ 61 (108)
T PF02284_consen 43 PEPKIIEAALRACRRVNDF 61 (108)
T ss_dssp --HHHHHHHHHHHHHTT-H
T ss_pred CChHHHHHHHHHHHHhhhH
Confidence 5999999999998876544
No 33
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=32.64 E-value=71 Score=30.99 Aligned_cols=51 Identities=10% Similarity=0.016 Sum_probs=42.3
Q ss_pred cccccccChHHHHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhccccc
Q 041564 47 PPSRFTCGFEAIQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGMHM 97 (151)
Q Consensus 47 VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~ 97 (151)
.|.=+|--...-.++...|.|+.|+.+|.+.+..+.-.++.+|+-+|.|..
T Consensus 272 lLlNLAed~~ve~kM~~~~iV~~Lv~~Ldr~n~ellil~v~fLkkLSi~~E 322 (708)
T PF05804_consen 272 LLLNLAEDPRVELKMVNKGIVSLLVKCLDRENEELLILAVTFLKKLSIFKE 322 (708)
T ss_pred HHHHHhcChHHHHHHHhcCCHHHHHHHHcCCCHHHHHHHHHHHHHHcCCHH
Confidence 445555444447788899999999999999999999999999999998854
No 34
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=32.32 E-value=36 Score=26.29 Aligned_cols=19 Identities=11% Similarity=0.169 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHHHHhccc
Q 041564 77 RDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 77 ~D~KVVEAcLRcLr~~~~~ 95 (151)
++|++++||||+-|-+.-|
T Consensus 40 P~P~ii~aaLrAcRRvND~ 58 (103)
T cd00923 40 PEPKVIEAALRACRRVNDF 58 (103)
T ss_pred CCcHHHHHHHHHHHHhhhH
Confidence 6999999999998877544
No 35
>PF10274 ParcG: Parkin co-regulated protein; InterPro: IPR019399 This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system []. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Probab=30.19 E-value=62 Score=26.58 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=23.1
Q ss_pred ChHHHHhhhccCCHHHHHHHHHHHHHh
Q 041564 66 LFPDLSLIFSRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 66 vvP~Ll~lLs~~D~KVVEAcLRcLr~~ 92 (151)
.++.|-+.|+..|+.|+.++|.+|+.+
T Consensus 81 LI~plk~AL~tr~~~V~~~~L~~Lq~L 107 (183)
T PF10274_consen 81 LIIPLKRALNTRDPEVFCATLKALQQL 107 (183)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 456666778999999999999999877
No 36
>KOG2160 consensus Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.98 E-value=35 Score=30.69 Aligned_cols=43 Identities=14% Similarity=0.094 Sum_probs=0.0
Q ss_pred HHHhh--hhhhh---------------cccccccChHH-HHHHHhcCChHHHHhhhccCCH
Q 041564 37 FLKKL--YRLIL---------------PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDE 79 (151)
Q Consensus 37 fI~lG--PrlIL---------------VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~ 79 (151)
|+++| +.++. |||+.+-.-.. ...+++.|+++.|+.+|+.+++
T Consensus 120 l~~~ggl~~ll~~l~~~~~~lR~~Aa~Vigt~~qNNP~~Qe~v~E~~~L~~Ll~~ls~~~~ 180 (342)
T KOG2160|consen 120 LISLGGLVPLLGYLENSDAELRELAARVIGTAVQNNPKSQEQVIELGALSKLLKILSSDDP 180 (342)
T ss_pred HhhccCHHHHHHHhcCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHcccHHHHHHHHccCCC
No 37
>TIGR02156 PA_CoA_Oxy1 phenylacetate-CoA oxygenase, PaaG subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=28.84 E-value=32 Score=29.86 Aligned_cols=39 Identities=15% Similarity=0.191 Sum_probs=29.5
Q ss_pred HHhhhccCCHHHHHHHHHHHHHhccccccccccee--cCCCC
Q 041564 70 LSLIFSRRDEQVADTMLLCKAEAGGMHMRQSSNVE--VPNGS 109 (151)
Q Consensus 70 Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~~~~~~~--~~~~~ 109 (151)
+..+..++++.+.+++.+.++|.+ ||+|++...- .-+|+
T Consensus 127 ~~~L~~SSy~plA~ia~Ki~KEe~-yH~rh~~~wl~rL~~GT 167 (289)
T TIGR02156 127 QTPLCRCSYGPYSRAMVRICKEES-FHQRQGYEIMLTLARGT 167 (289)
T ss_pred HHHHhcCCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHcCC
Confidence 334447779999999999999986 8999987643 34444
No 38
>KOG3036 consensus Protein involved in cell differentiation/sexual development [General function prediction only]
Probab=28.67 E-value=32 Score=30.65 Aligned_cols=31 Identities=13% Similarity=0.089 Sum_probs=26.3
Q ss_pred cccccccChHH--HHHHHhcCChHHHHhhhccC
Q 041564 47 PPSRFTCGFEA--IQAMLDAGLFPDLSLIFSRR 77 (151)
Q Consensus 47 VLGSFAcG~Ea--VkaLLdaGvvP~Ll~lLs~~ 77 (151)
|||++.+-.|. ++-|+..++||..+++....
T Consensus 148 VIgaLvk~dd~eVi~fLl~TeIVPlCLrime~G 180 (293)
T KOG3036|consen 148 VIGALVKNDDQEVIRFLLTTEIVPLCLRIMESG 180 (293)
T ss_pred HHHHHHhcCcHHHHHHHHHhhhHHHHHHHHhcc
Confidence 99999976665 99999999999999987443
No 39
>KOG1061 consensus Vesicle coat complex AP-1/AP-2/AP-4, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.62 E-value=48 Score=32.75 Aligned_cols=37 Identities=24% Similarity=0.253 Sum_probs=32.9
Q ss_pred HhcCChHHHHhhhccCCHHHHHHHHHHHHHhcccccc
Q 041564 62 LDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGMHMR 98 (151)
Q Consensus 62 LdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~ 98 (151)
.+.|.++.|-.++..+|+-||-.|+++|.+..-.|+-
T Consensus 157 ~~~gl~~~L~~ll~D~~p~VVAnAlaaL~eI~e~~~~ 193 (734)
T KOG1061|consen 157 EDSGLVDALKDLLSDSNPMVVANALAALSEIHESHPS 193 (734)
T ss_pred cccchhHHHHHHhcCCCchHHHHHHHHHHHHHHhCCC
Confidence 3489999999999999999999999999998877764
No 40
>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=28.53 E-value=36 Score=23.55 Aligned_cols=30 Identities=10% Similarity=0.321 Sum_probs=23.0
Q ss_pred HHHHHhcCChHHHHhhhccCCHHHHHHHHHHH
Q 041564 58 IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCK 89 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcL 89 (151)
+..+.+.+.++.++++|.+++ +.++|+.||
T Consensus 119 ~~~i~~~~~l~~~~~~l~~~~--~~~~A~~cl 148 (148)
T PF08389_consen 119 IELIINSNLLNLIFQLLQSPE--LREAAAECL 148 (148)
T ss_dssp HHHHHSSSHHHHHHHHTTSCC--CHHHHHHHH
T ss_pred HHHhccHHHHHHHHHHcCCHH--HHHHHHHhC
Confidence 556667889999999895444 488888886
No 41
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=28.27 E-value=36 Score=29.29 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHhcccccccc
Q 041564 80 QVADTMLLCKAEAGGMHMRQS 100 (151)
Q Consensus 80 KVVEAcLRcLr~~~~~h~~~~ 100 (151)
-+||||-|+|+.-|-||.|.-
T Consensus 332 PivDAamrqL~~TG~mhnr~R 352 (429)
T TIGR02765 332 PLVDANMRELNATGFMSNRGR 352 (429)
T ss_pred hhhhHHHHHHHHhCCCCHHHH
Confidence 389999999999999998764
No 42
>KOG1240 consensus Protein kinase containing WD40 repeats [Signal transduction mechanisms]
Probab=28.15 E-value=47 Score=35.02 Aligned_cols=34 Identities=18% Similarity=0.069 Sum_probs=29.3
Q ss_pred HhcCChHHHHhhhccCCHHHHHHHHHHHHHhccc
Q 041564 62 LDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 62 LdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~ 95 (151)
++...+|.|.+.|+.++|-|++.+|+|+.++=-.
T Consensus 653 ~seyllPLl~Q~ltD~EE~Viv~aL~~ls~Lik~ 686 (1431)
T KOG1240|consen 653 VSEYLLPLLQQGLTDGEEAVIVSALGSLSILIKL 686 (1431)
T ss_pred HHHHHHHHHHHhccCcchhhHHHHHHHHHHHHHh
Confidence 4678899999999999999999999998876433
No 43
>PRK13778 paaA phenylacetate-CoA oxygenase subunit PaaA; Provisional
Probab=26.91 E-value=43 Score=29.56 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=31.7
Q ss_pred hHHHHhhhccCCHHHHHHHHHHHHHhccccccccccee--cCCCCC
Q 041564 67 FPDLSLIFSRRDEQVADTMLLCKAEAGGMHMRQSSNVE--VPNGSD 110 (151)
Q Consensus 67 vP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~~~~~~~--~~~~~~ 110 (151)
+..+..+..++++.+.+++.+.++|.+ ||+|++...- +-+|++
T Consensus 142 ~~~~~~L~~sSy~plA~~a~Ki~KEe~-yH~rhg~~wl~rL~~GT~ 186 (314)
T PRK13778 142 IMNQVPLCRCSYGPYARAMVRICKEES-FHQRQGEEILLALARGTP 186 (314)
T ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCCH
Confidence 333444457789999999999999986 9999987643 344544
No 44
>COG3580 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.89 E-value=32 Score=31.36 Aligned_cols=45 Identities=13% Similarity=0.141 Sum_probs=24.4
Q ss_pred cccccccChHH-HHHHHh----cCC-hHHHHhhhccCCHHHHHHHHHHHHH
Q 041564 47 PPSRFTCGFEA-IQAMLD----AGL-FPDLSLIFSRRDEQVADTMLLCKAE 91 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLd----aGv-vP~Ll~lLs~~D~KVVEAcLRcLr~ 91 (151)
-|-||+||.|+ +-.+++ ..- +=.++.+=.+++.-=++.=+|++.-
T Consensus 278 ~l~SFgCG~Davttd~i~eIl~~~nk~ytvlkIDE~tn~gai~iRlesl~a 328 (351)
T COG3580 278 QLVSFGCGLDAVTTDLIEEILEGHNKIYTVLKIDEGTNLGAIRIRLESLKA 328 (351)
T ss_pred EEeecccCcchhHHHHHHHHHHhCCCeeEEEEecCCCCcchhhhhHHHHHH
Confidence 78899999999 544443 222 1111222244555555555566554
No 45
>PF08216 CTNNBL: Catenin-beta-like, Arm-motif containing nuclear; InterPro: IPR013180 This domain is found in eukaryotic proteins. A human nuclear protein with this domain (Q8WYA6 from SWISSPROT) is thought to have a role in apoptosis [].
Probab=26.16 E-value=56 Score=25.03 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=26.1
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHH
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVA 82 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVV 82 (151)
-+.-+|- .++ -..+++.|+++.|+.+|+|.|.-++
T Consensus 69 ~l~~La~-~P~LYp~lv~l~~v~sL~~LL~HeN~DIa 104 (108)
T PF08216_consen 69 KLSVLAT-APELYPELVELGAVPSLLGLLSHENTDIA 104 (108)
T ss_pred HHHHccC-ChhHHHHHHHcCCHHHHHHHHCCCCccee
Confidence 3333443 446 8889999999999999999986543
No 46
>KOG4413 consensus 26S proteasome regulatory complex, subunit PSMD5 [Posttranslational modification, protein turnover, chaperones]
Probab=26.09 E-value=97 Score=29.31 Aligned_cols=42 Identities=12% Similarity=0.091 Sum_probs=37.1
Q ss_pred HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhccccccc
Q 041564 58 IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGGMHMRQ 99 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h~~~ 99 (151)
|.-++.+|.+|.++..+.+.|..|..|+-.+++-.++|.---
T Consensus 121 illvvNaeilklildcIggeddeVAkAAiesikrialfpaal 162 (524)
T KOG4413|consen 121 ILLVVNAEILKLILDCIGGEDDEVAKAAIESIKRIALFPAAL 162 (524)
T ss_pred HHHHhhhhHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcHHHH
Confidence 666679999999999999999999999999999999885443
No 47
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=24.72 E-value=1.4e+02 Score=24.96 Aligned_cols=77 Identities=19% Similarity=0.239 Sum_probs=48.4
Q ss_pred cchhHHhhhhhhhcc--cchhHhHHHHhhhhhh-------------h-cccccccChHHHHHHHhcCChHHHHhhhccCC
Q 041564 15 SSSRLNNRLKNQIIG--SQTKKLSFLKKLYRLI-------------L-PPSRFTCGFEAIQAMLDAGLFPDLSLIFSRRD 78 (151)
Q Consensus 15 ~s~rAlr~IKNqIIG--NntKKlsfI~lGPrlI-------------L-VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~~D 78 (151)
-+.+|+..+.|.-.. |..+=..||.+.-+.+ | .|.+++-= ++.+.++ ++.+|.|+++|+..+
T Consensus 70 vr~~AL~aL~Nls~~~en~~~Ik~~i~~Vc~~~~s~~lns~~Q~agLrlL~nLtv~-~~~~~~l-~~~i~~ll~LL~~G~ 147 (254)
T PF04826_consen 70 VREKALNALNNLSVNDENQEQIKMYIPQVCEETVSSPLNSEVQLAGLRLLTNLTVT-NDYHHML-ANYIPDLLSLLSSGS 147 (254)
T ss_pred HHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHccCCC-cchhhhH-HhhHHHHHHHHHcCC
Confidence 346788888865443 3344345665542211 2 67777622 2244555 457999999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 041564 79 EQVADTMLLCKAEAG 93 (151)
Q Consensus 79 ~KVVEAcLRcLr~~~ 93 (151)
.++=.-++++|--+|
T Consensus 148 ~~~k~~vLk~L~nLS 162 (254)
T PF04826_consen 148 EKTKVQVLKVLVNLS 162 (254)
T ss_pred hHHHHHHHHHHHHhc
Confidence 988777777775543
No 48
>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=24.53 E-value=89 Score=25.77 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=29.8
Q ss_pred HHHHHhcCChHHHHhhh-ccCCHHHHHHHHHHHHHh
Q 041564 58 IQAMLDAGLFPDLSLIF-SRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 58 VkaLLdaGvvP~Ll~lL-s~~D~KVVEAcLRcLr~~ 92 (151)
++.+.+.+.||.|..++ ...-+||+-=|+-++|-.
T Consensus 232 ~~~~~~~~~i~~L~~i~~~~~KEKvvRv~la~l~Nl 267 (312)
T PF03224_consen 232 AEELNKKYLIPLLADILKDSIKEKVVRVSLAILRNL 267 (312)
T ss_dssp HHHHHTTSHHHHHHHHHHH--SHHHHHHHHHHHHHT
T ss_pred HHHHhccchHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence 89999999999999998 445999999999998854
No 49
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=23.77 E-value=88 Score=23.82 Aligned_cols=27 Identities=4% Similarity=-0.039 Sum_probs=16.8
Q ss_pred HHHHhhhccCCHHHHHHHHHHHHHhcc
Q 041564 68 PDLSLIFSRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 68 P~Ll~lLs~~D~KVVEAcLRcLr~~~~ 94 (151)
..++..|..+|+.+.+.|..++.+.+.
T Consensus 66 ~~~l~~l~D~~~~Ir~~A~~~~~e~~~ 92 (178)
T PF12717_consen 66 SRILKLLVDENPEIRSLARSFFSELLK 92 (178)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 555555666666666666666666543
No 50
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=23.52 E-value=46 Score=29.28 Aligned_cols=22 Identities=18% Similarity=0.063 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHhcccccccccc
Q 041564 81 VADTMLLCKAEAGGMHMRQSSN 102 (151)
Q Consensus 81 VVEAcLRcLr~~~~~h~~~~~~ 102 (151)
+||||-|+|+.-|-||-|.--.
T Consensus 329 ~VDA~MRqL~~TGwmhnR~Rm~ 350 (475)
T TIGR02766 329 LVDAGMRELWATGWLHDRIRVV 350 (475)
T ss_pred chhHHHHHHHHHCCCcHHHHHH
Confidence 8999999999999999886443
No 51
>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=23.49 E-value=86 Score=28.15 Aligned_cols=48 Identities=17% Similarity=0.065 Sum_probs=42.4
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhcc
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAGG 94 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~~ 94 (151)
++..+++..++ .+.+.+.|.++.+++.|.++|.-|--.|+..+.+++.
T Consensus 183 l~v~i~~~S~~~~~~~~~sgll~~ll~eL~~dDiLvqlnalell~~La~ 231 (503)
T PF10508_consen 183 LLVEIASHSPEAAEAVVNSGLLDLLLKELDSDDILVQLNALELLSELAE 231 (503)
T ss_pred HHHHHHhcCHHHHHHHHhccHHHHHHHHhcCccHHHHHHHHHHHHHHHc
Confidence 66677777788 9999999999999999999999998899999988865
No 52
>KOG4199 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.78 E-value=1.3e+02 Score=28.40 Aligned_cols=43 Identities=9% Similarity=0.145 Sum_probs=34.5
Q ss_pred cChHHHH-HHHhcCChHHHHhhh--ccCCHHHHHHHHHHHHHhccc
Q 041564 53 CGFEAIQ-AMLDAGLFPDLSLIF--SRRDEQVADTMLLCKAEAGGM 95 (151)
Q Consensus 53 cG~EaVk-aLLdaGvvP~Ll~lL--s~~D~KVVEAcLRcLr~~~~~ 95 (151)
.|.|+|| .+++.|+.|.++.++ -.+||.|++.+..|+.++-+-
T Consensus 315 AG~DsvKs~IV~~gg~~~ii~l~~~h~~~p~Vi~~~~a~i~~l~LR 360 (461)
T KOG4199|consen 315 AGSDSVKSTIVEKGGLDKIITLALRHSDDPLVIQEVMAIISILCLR 360 (461)
T ss_pred hCCCchHHHHHHhcChHHHHHHHHHcCCChHHHHHHHHHHHHHHhc
Confidence 4777744 578999999999985 345999999999999888763
No 53
>KOG4646 consensus Uncharacterized conserved protein, contains ARM repeats [Function unknown]
Probab=22.24 E-value=74 Score=26.54 Aligned_cols=45 Identities=13% Similarity=0.077 Sum_probs=37.7
Q ss_pred cccccc--cChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHH
Q 041564 47 PPSRFT--CGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAE 91 (151)
Q Consensus 47 VLGSFA--cG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~ 91 (151)
.||-+- |-... ++-+.+++.+|..|..|+++.+-+|-.++..+--
T Consensus 78 gIgglCNlC~d~~n~~~I~ea~g~plii~~lssp~e~tv~sa~~~l~~ 125 (173)
T KOG4646|consen 78 GIGGLCNLCLDKTNAKFIREALGLPLIIFVLSSPPEITVHSAALFLQL 125 (173)
T ss_pred hHHHHHhhccChHHHHHHHHhcCCceEEeecCCChHHHHHHHHHHHHH
Confidence 555553 77777 9999999999999999999999999999887644
No 54
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=21.64 E-value=86 Score=30.93 Aligned_cols=46 Identities=15% Similarity=0.078 Sum_probs=41.2
Q ss_pred cccccccChHH-HHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHh
Q 041564 47 PPSRFTCGFEA-IQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEA 92 (151)
Q Consensus 47 VLGSFAcG~Ea-VkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~ 92 (151)
+||-+-+-.|+ .++|+++|++.+.+.-.-..|+.+..-|+.+|.-.
T Consensus 245 il~~mFKHSeet~~~Lvaa~~lD~vl~~~rRt~P~lLRH~ALAL~N~ 291 (832)
T KOG3678|consen 245 ILEHMFKHSEETCQRLVAAGGLDAVLYWCRRTDPALLRHCALALGNC 291 (832)
T ss_pred HHHHHhhhhHHHHHHHHhhcccchheeecccCCHHHHHHHHHHhhhh
Confidence 77888888999 99999999999999888899999999999888643
No 55
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=21.02 E-value=68 Score=26.18 Aligned_cols=30 Identities=13% Similarity=0.047 Sum_probs=21.7
Q ss_pred hHHHHhhhccCCHHHHHHHHHHHHHhcccc
Q 041564 67 FPDLSLIFSRRDEQVADTMLLCKAEAGGMH 96 (151)
Q Consensus 67 vP~Ll~lLs~~D~KVVEAcLRcLr~~~~~h 96 (151)
|..|+.+|.++|+.+.+.++.+|+--=+++
T Consensus 96 V~~LI~~L~~~d~~lA~~Aa~aLk~TlLvy 125 (154)
T PF11791_consen 96 VQPLIDLLKSDDEELAEEAAEALKNTLLVY 125 (154)
T ss_dssp HHHHHHGG--G-TTTHHHHHHHHHT--TTC
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHhhHHHH
Confidence 688999999999999999999998654443
No 56
>KOG4500 consensus Rho/Rac GTPase guanine nucleotide exchange factor smgGDS/Vimar [Signal transduction mechanisms]
Probab=21.01 E-value=73 Score=30.81 Aligned_cols=46 Identities=7% Similarity=0.040 Sum_probs=39.6
Q ss_pred cccccccChHHHHHHHhcCChHHHHhhhcc-----CCHHHHHHHHHHHHHh
Q 041564 47 PPSRFTCGFEAIQAMLDAGLFPDLSLIFSR-----RDEQVADTMLLCKAEA 92 (151)
Q Consensus 47 VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~-----~D~KVVEAcLRcLr~~ 92 (151)
+||-||...+.-..+++.|.+.-|+.+|.. .|-.+.-||+-+||-+
T Consensus 338 aigNfaR~D~~ci~~v~~~~~nkL~~~l~~~~~vdgnV~~qhA~lsALRnl 388 (604)
T KOG4500|consen 338 AIGNFARRDDICIQLVQKDFLNKLISCLMQEKDVDGNVERQHACLSALRNL 388 (604)
T ss_pred HHHhhhccchHHHHHHHHHHHHHHHHHHHHhcCCCccchhHHHHHHHHHhc
Confidence 888898887777789999999999999954 3788999999999964
No 57
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=20.79 E-value=92 Score=23.28 Aligned_cols=47 Identities=15% Similarity=0.027 Sum_probs=36.9
Q ss_pred ccccccc---ChHHHHHHHhcCChHHHHhhhccCCHHHHHHHHHHHHHhc
Q 041564 47 PPSRFTC---GFEAIQAMLDAGLFPDLSLIFSRRDEQVADTMLLCKAEAG 93 (151)
Q Consensus 47 VLGSFAc---G~EaVkaLLdaGvvP~Ll~lLs~~D~KVVEAcLRcLr~~~ 93 (151)
.-|+.-+ .......++...+.|.|++.+.+++..+.+.++|.+..+-
T Consensus 52 ~~~~~f~~~~~~~~l~~~lk~~l~~~Ll~~~~~~~~~i~~~slri~~~l~ 101 (168)
T PF12783_consen 52 NHGSVFRSSEEHPSLINLLKDDLCPALLKNLSSSDFPIFSRSLRIFLTLL 101 (168)
T ss_pred hCHHHHhCCcchHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHH
Confidence 4455445 3346888999999999999998888999998888877654
No 58
>KOG4224 consensus Armadillo repeat protein VAC8 required for vacuole fusion, inheritance and cytosol-to-vacuole protein targeting [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.63 E-value=61 Score=30.87 Aligned_cols=75 Identities=19% Similarity=0.161 Sum_probs=53.1
Q ss_pred hHHhhhhhhhcccchhHhHHHHhh--hhhh---h------------cccccccChHHHHHHHhcCChHHHHhhhccCCHH
Q 041564 18 RLNNRLKNQIIGSQTKKLSFLKKL--YRLI---L------------PPSRFTCGFEAIQAMLDAGLFPDLSLIFSRRDEQ 80 (151)
Q Consensus 18 rAlr~IKNqIIGNntKKlsfI~lG--PrlI---L------------VLGSFAcG~EaVkaLLdaGvvP~Ll~lLs~~D~K 80 (151)
-|+-.+.|--=.+.+-|..|+..| |.++ + .+.=+|...+.=.+++|+|.+|.|+-++.+..+.
T Consensus 353 hAvstLrnLAasse~n~~~i~esgAi~kl~eL~lD~pvsvqseisac~a~Lal~d~~k~~lld~gi~~iLIp~t~s~s~E 432 (550)
T KOG4224|consen 353 HAVSTLRNLAASSEHNVSVIRESGAIPKLIELLLDGPVSVQSEISACIAQLALNDNDKEALLDSGIIPILIPWTGSESEE 432 (550)
T ss_pred hHHHHHHHHhhhhhhhhHHHhhcCchHHHHHHHhcCChhHHHHHHHHHHHHHhccccHHHHhhcCCcceeecccCccchh
Confidence 456666776666777788888888 6533 2 2333344433367899999999999999888888
Q ss_pred HHHHHHHHHHHh
Q 041564 81 VADTMLLCKAEA 92 (151)
Q Consensus 81 VVEAcLRcLr~~ 92 (151)
|-.-++.+|--.
T Consensus 433 v~gNaAaAL~Nl 444 (550)
T KOG4224|consen 433 VRGNAAAALINL 444 (550)
T ss_pred hcccHHHHHHhh
Confidence 888777777654
Done!