Query psy13939
Match_columns 86
No_of_seqs 139 out of 595
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 15:27:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13939hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3573|consensus 99.9 6.1E-22 1.3E-26 147.4 5.1 74 7-86 208-285 (300)
2 smart00115 CASc Caspase, inter 99.8 4E-21 8.6E-26 139.5 6.8 63 8-70 150-216 (241)
3 cd00032 CASc Caspase, interleu 99.8 6.2E-20 1.3E-24 133.0 5.7 63 8-70 154-220 (243)
4 PF00656 Peptidase_C14: Caspas 98.0 1E-05 2.2E-10 56.7 5.2 56 12-67 163-230 (248)
5 PF03500 Cellsynth_D: Cellulos 81.9 1.3 2.8E-05 30.8 2.3 35 36-70 2-36 (144)
6 cd00512 MM_CoA_mutase Coenzyme 81.5 0.78 1.7E-05 36.3 1.3 21 31-51 319-339 (399)
7 cd03677 MM_CoA_mutase_beta Coe 80.9 0.84 1.8E-05 36.3 1.3 21 31-51 344-364 (424)
8 cd03679 MM_CoA_mutase_alpha_li 77.1 1.3 2.8E-05 36.4 1.3 22 30-51 384-405 (536)
9 PF01642 MM_CoA_mutase: Methyl 76.7 1.2 2.6E-05 36.3 1.0 22 30-51 363-384 (516)
10 TIGR00642 mmCoA_mut_beta methy 76.6 1.3 2.9E-05 36.8 1.3 21 31-51 380-400 (619)
11 PRK09426 methylmalonyl-CoA mut 76.5 1.4 2.9E-05 37.3 1.3 21 31-51 391-411 (714)
12 TIGR00641 acid_CoA_mut_N methy 76.0 1.4 3.1E-05 36.1 1.3 22 30-51 368-389 (528)
13 cd03681 MM_CoA_mutase_MeaA Coe 75.4 1.5 3.3E-05 34.9 1.3 22 30-51 326-347 (407)
14 cd03680 MM_CoA_mutase_ICM_like 74.5 1.6 3.6E-05 35.8 1.3 22 30-51 388-409 (538)
15 cd03678 MM_CoA_mutase_1 Coenzy 73.0 1.9 4.1E-05 35.2 1.3 22 30-51 414-435 (495)
16 COG1884 Sbm Methylmalonyl-CoA 62.7 3.7 7.9E-05 34.0 1.0 21 31-51 391-411 (548)
17 PF09003 Phage_integ_N: Bacter 55.0 2.1 4.5E-05 26.7 -1.3 15 24-38 26-40 (75)
18 PF12109 CXCR4_N: CXCR4 Chemok 51.6 10 0.00022 20.2 1.2 19 2-20 13-31 (33)
19 PF08388 GIIM: Group II intron 44.5 61 0.0013 18.9 4.1 29 39-67 5-33 (80)
20 cd07357 HN_L-whirlin_R2_like S 43.8 16 0.00034 23.1 1.4 27 37-67 40-66 (81)
21 PF12475 Amdo_NSP: Amdovirus n 42.0 20 0.00043 20.6 1.5 14 36-49 16-29 (48)
22 PF05066 HARE-HTH: HB1, ASXL, 41.5 45 0.00097 19.4 3.2 37 38-74 3-39 (72)
23 cd08326 CARD_CASP9 Caspase act 40.1 36 0.00078 21.1 2.7 26 33-59 58-83 (84)
24 KOG2424|consensus 34.4 57 0.0012 23.8 3.2 29 32-60 148-178 (195)
25 PF04819 DUF716: Family of unk 34.0 18 0.00039 24.3 0.6 15 34-48 73-87 (137)
26 PF12993 DUF3877: Domain of un 32.6 64 0.0014 23.1 3.2 28 33-60 91-119 (175)
27 PF00806 PUF: Pumilio-family R 30.7 46 0.001 16.5 1.7 13 33-45 13-25 (35)
28 COG1955 FlaJ Archaeal flagella 28.1 68 0.0015 26.7 3.1 39 23-61 351-395 (527)
29 smart00025 Pumilio Pumilio-lik 27.0 50 0.0011 15.6 1.5 15 33-47 13-27 (36)
30 PF15463 ECM11: Extracellular 25.9 76 0.0017 21.2 2.6 35 33-67 76-111 (139)
31 PF04895 DUF651: Archaeal prot 25.3 1.3E+02 0.0028 19.9 3.5 42 22-67 42-85 (110)
32 PF12887 SICA_alpha: SICA extr 25.0 1.9E+02 0.0042 20.2 4.6 41 33-73 109-152 (184)
33 PF12221 HflK_N: Bacterial mem 21.8 98 0.0021 17.0 2.1 18 51-68 19-36 (42)
34 PRK05883 acyl carrier protein; 21.1 1.3E+02 0.0028 18.6 2.8 24 24-47 1-28 (91)
35 cd08332 CARD_CASP2 Caspase act 21.1 87 0.0019 19.5 2.0 27 34-61 63-89 (90)
36 cd08802 Death_UNC5B Death doma 20.9 1E+02 0.0022 19.4 2.2 19 39-57 63-81 (84)
37 PF12022 DUF3510: Domain of un 20.4 1.8E+02 0.0038 19.1 3.5 42 31-72 29-77 (125)
38 KOG4417|consensus 20.2 57 0.0012 24.5 1.2 24 22-48 87-110 (261)
39 PHA02593 62 clamp loader small 20.2 98 0.0021 22.5 2.3 37 24-63 14-50 (191)
No 1
>KOG3573|consensus
Probab=99.85 E-value=6.1e-22 Score=147.44 Aligned_cols=74 Identities=35% Similarity=0.614 Sum_probs=64.0
Q ss_pred ccccccCCCCCCccc----cCCCccccCCCCCchHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHhhhhccCCCcccccc
Q psy13939 7 LSKMYYKFDEEDDDD----VFVSFYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQ 82 (86)
Q Consensus 7 ~~~~~~~iP~~aD~L----T~~g~~s~R~~~~GSwFIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va~~~~s~~~~~~~~~~ 82 (86)
.....+.||.+|||| |+|||+||||+..||||||+||++|.++++. ||++||++||++|.. ... -+..++
T Consensus 208 ~~~~~~~ips~aD~L~~~st~~g~~s~R~~~~gsw~Iq~Lc~~~~~~~~~-~l~~ll~~v~~~~~~--~~~---~~~~~~ 281 (300)
T KOG3573|consen 208 DDDATYKIPSEADFLVSYSTTPGYVSWRDPTKGSWFIQSLCEVLQEYAKS-DLLDLLTEVNRKVSF--SFD---VPGGNA 281 (300)
T ss_pred ccchhccCccccceeEeeecCCCceeeecCCCceeeHHHHHHHHHHhcch-hHHHHHHHHHHhhhc--ccc---cccccc
Confidence 345678899999999 9999999999999999999999999999998 999999999999642 121 157788
Q ss_pred ccCC
Q psy13939 83 QKQI 86 (86)
Q Consensus 83 ~KQm 86 (86)
.|||
T Consensus 282 ~kq~ 285 (300)
T KOG3573|consen 282 QKQM 285 (300)
T ss_pred cccC
Confidence 8886
No 2
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=99.84 E-value=4e-21 Score=139.54 Aligned_cols=63 Identities=43% Similarity=0.764 Sum_probs=58.0
Q ss_pred cccccCCCCCCccc----cCCCccccCCCCCchHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHhhh
Q psy13939 8 SKMYYKFDEEDDDD----VFVSFYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDM 70 (86)
Q Consensus 8 ~~~~~~iP~~aD~L----T~~g~~s~R~~~~GSwFIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va~~~ 70 (86)
+....++|.++|+| |+|||+|||++..||||||+||++|.+++++.||++|||+||++|+...
T Consensus 150 ~~~~~~~p~~~D~li~ysT~pG~va~r~~~~gS~fi~~L~~~l~~~~~~~~l~~ilt~V~~~V~~~~ 216 (241)
T smart00115 150 DDAIYKIPVEADFLAAYSTTPGYVSWRNPTRGSWFIQSLCQVLKEYARSLDLLDILTEVNRKVAVKF 216 (241)
T ss_pred ccccccCCCcCcEEEEEeCCCCeEeecCCCCCchHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhh
Confidence 34556899999999 9999999999999999999999999999999999999999999998643
No 3
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=99.80 E-value=6.2e-20 Score=132.98 Aligned_cols=63 Identities=38% Similarity=0.653 Sum_probs=58.1
Q ss_pred cccccCCCCCCccc----cCCCccccCCCCCchHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHhhh
Q psy13939 8 SKMYYKFDEEDDDD----VFVSFYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDM 70 (86)
Q Consensus 8 ~~~~~~iP~~aD~L----T~~g~~s~R~~~~GSwFIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va~~~ 70 (86)
......+|.++|+| |.|||+|||++..||||||+||++|.+++++.+|++||++||++|+...
T Consensus 154 ~~~~~~~p~~~d~lv~ysT~pG~~a~r~~~~gS~fi~~l~~~l~~~~~~~~l~~il~~V~~~V~~~~ 220 (243)
T cd00032 154 DDAVQTIPVEADFLVAYSTVPGYVSWRNTKKGSWFIQSLCQVLRKYAHSLDLLDILTKVNRKVAEKF 220 (243)
T ss_pred cccccCCCCcccEEEEecCCCCeEeecCCCCCCEeHHHHHHHHHHhCCCCcHHHHHHHHHHHHhhhh
Confidence 34567899999999 9999999999999999999999999999999999999999999998643
No 4
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=98.03 E-value=1e-05 Score=56.68 Aligned_cols=56 Identities=20% Similarity=0.195 Sum_probs=47.1
Q ss_pred cCCCCCCccc----cCCCccccCC-CCCchHHHHHHHHHHHhcCC-------CChHHHHHHHHHHHHH
Q psy13939 12 YKFDEEDDDD----VFVSFYSWRH-PENGTWFIQCLCQELADSGT-------KLDLLSIMTRVSRRVA 67 (86)
Q Consensus 12 ~~iP~~aD~L----T~~g~~s~R~-~~~GSwFIq~Lc~vl~~~~~-------~~dl~~ilt~Vn~~Va 67 (86)
...|..++++ |.+|.+||+. +..||||+++||+.|+++++ ...|.+|++.|+++|+
T Consensus 163 ~~~~~~~~~~~~~as~~~~~s~e~~~~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~~~v~~~~~ 230 (248)
T PF00656_consen 163 SDVPSPSGFIVLSASRPGQTSYEDSPGSGGLFTYALLEALKGNAADDPNQSWDELLEELLTEVNQKVA 230 (248)
T ss_dssp EEEETTTSEEEEESSSTTBCEEEECTTTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHHHHHHHHHH
T ss_pred ccccCCCCcEEEEeccccceeecccCccCHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHhHCC
Confidence 3444556655 9999999999 78999999999999987743 4789999999999996
No 5
>PF03500 Cellsynth_D: Cellulose synthase subunit D; InterPro: IPR022798 Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium spp. More correctly designated as "cellulose synthase catalytic subunits", plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity []. An operon encoding 4 proteins required for bacterial cellulose biosynthesis (bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementation with strains lacking cellulose synthase activity []. Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum. The calculated molecular mass of the protein encoded by bcsD is 17.3kDa []. The function of BcsD is unknown. This entry represents the D subunit from bacterial cellulose synthase.; PDB: 3AJ1_B 3AJ2_A 3A8E_A.
Probab=81.87 E-value=1.3 Score=30.79 Aligned_cols=35 Identities=23% Similarity=0.472 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHhhh
Q psy13939 36 TWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDM 70 (86)
Q Consensus 36 SwFIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va~~~ 70 (86)
|-|+++|++.|...+....+..+|.+|-++++.+|
T Consensus 2 ~lFl~aLa~E~~~q~g~~e~~~fLr~mG~rlA~r~ 36 (144)
T PF03500_consen 2 SLFLRALAEEFEDQAGEEELRAFLRRMGERLAARH 36 (144)
T ss_dssp HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHCTTB
T ss_pred hHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhC
Confidence 67999999999999999999999999999888654
No 6
>cd00512 MM_CoA_mutase Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the
Probab=81.46 E-value=0.78 Score=36.25 Aligned_cols=21 Identities=24% Similarity=0.574 Sum_probs=19.1
Q ss_pred CCCCchHHHHHHHHHHHhcCC
Q psy13939 31 HPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
||..|||||.+|.+-|.+.++
T Consensus 319 DPa~GSyyiE~LT~~la~~Aw 339 (399)
T cd00512 319 DPLGGSYYVEELTDSLEDAAW 339 (399)
T ss_pred CcccCcHHHHHHHHHHHHHHH
Confidence 899999999999999988765
No 7
>cd03677 MM_CoA_mutase_beta Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta heterodimers. For P. shermanni MCM, it is known that only the alpha subunit binds coenzyme B12 and substrates. The role of the beta subunit is unclear. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversib
Probab=80.86 E-value=0.84 Score=36.28 Aligned_cols=21 Identities=29% Similarity=0.696 Sum_probs=18.9
Q ss_pred CCCCchHHHHHHHHHHHhcCC
Q psy13939 31 HPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
||..|||||.+|.+-|.+.++
T Consensus 344 DPagGSyyiE~LT~~la~~AW 364 (424)
T cd03677 344 DPAGGSYYIESLTDQLAEKAW 364 (424)
T ss_pred CcccCCHHHHHHHHHHHHHHH
Confidence 899999999999999988765
No 8
>cd03679 MM_CoA_mutase_alpha_like Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain an N-terminal MCM domain and a C-terminal coenzyme B12 binding domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with
Probab=77.14 E-value=1.3 Score=36.42 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=19.3
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||-.|||||.+|.+.|.+.++
T Consensus 384 ~DPagGSyyiE~LT~~la~~Aw 405 (536)
T cd03679 384 VDPWGGSYYMESLTDDLAEKAW 405 (536)
T ss_pred cCcccCCHHHHHHHHHHHHHHH
Confidence 3789999999999999988764
No 9
>PF01642 MM_CoA_mutase: Methylmalonyl-CoA mutase; InterPro: IPR006099 Methylmalonyl-CoA mutase (5.4.99.2 from EC) (MCM) [] is an adenosylcobalamin (vitamin B12) dependent enzyme that catalyzes the isomerization between methylmalonyl-CoA and succinyl-CoA. MCM is involved in various catabolic or biosynthetic pathways; for example in man it is involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle; while in some bacteria it is involved in the synthesis of propionate from tricarboxylic acid-cycle intermediates. Deficiency of MCM in man causes an often fatal disorder of organic acid metabolism termed methylmalonic acidemia. The sequences of eukaryotic and prokaryotic MCM are rather well conserved. In eukaryotes MCM is located in the mitochondrial matrix and is a homodimer of a polypeptide chain of about 710 amino acids. In bacteria MCM is a dimer of two non-identical, yet structurally related chains. This family also includes an Escherichia coli protein (gene sbm) whose function is not yet known. A small degree of similarity is said [] to exist between MCM and the large subunit of the adenosylcobalamin-dependent enzyme ethanolamine ammonia-lyase, but this similarity is so weak that these two type of enzymes can not be detected by a single pattern.; GO: 0016866 intramolecular transferase activity, 0031419 cobalamin binding, 0008152 metabolic process; PDB: 6REQ_C 4REQ_A 2REQ_A 1E1C_A 5REQ_A 3REQ_A 1REQ_A 7REQ_C 3BIC_A 2XIQ_A ....
Probab=76.72 E-value=1.2 Score=36.35 Aligned_cols=22 Identities=32% Similarity=0.669 Sum_probs=19.4
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||..|||||.+|.+.|.+.++
T Consensus 363 ~DPagGSyyiE~LT~~la~~Aw 384 (516)
T PF01642_consen 363 VDPAGGSYYIEALTDELAEKAW 384 (516)
T ss_dssp SSTTTTCHHHHHHHHHHHHHHH
T ss_pred CCcccCCHHHHHHHHHHHHHHH
Confidence 4889999999999999998654
No 10
>TIGR00642 mmCoA_mut_beta methylmalonyl-CoA mutase, heterodimeric type, beta chain. The adenosylcobalamin-binding, catalytic chain of methylmalonyl-CoA mutase may form homodimers, as in mitochondrion and E. coli, or heterodimers with a shorter, homologous chain that does not bind adenosylcobalamin. This model describes this non-catalytic beta chain, as found in the enzyme from Propionibacterium freudenreichii, for which the 3-dimensional structure has been solved.
Probab=76.65 E-value=1.3 Score=36.84 Aligned_cols=21 Identities=29% Similarity=0.715 Sum_probs=18.8
Q ss_pred CCCCchHHHHHHHHHHHhcCC
Q psy13939 31 HPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
||.-|||||.+|.+-|.+.++
T Consensus 380 DPagGSyyIE~LT~~La~~AW 400 (619)
T TIGR00642 380 DPAGGSYYVESLTRSLADAAW 400 (619)
T ss_pred CcCcCcHHHHHHHHHHHHHHH
Confidence 889999999999999988765
No 11
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=76.48 E-value=1.4 Score=37.33 Aligned_cols=21 Identities=29% Similarity=0.637 Sum_probs=18.8
Q ss_pred CCCCchHHHHHHHHHHHhcCC
Q psy13939 31 HPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
||..|||||.+|.+-|.+.++
T Consensus 391 DPagGSyyiE~LT~~la~~Aw 411 (714)
T PRK09426 391 DPWAGSYYVESLTHELAEKAW 411 (714)
T ss_pred CcccCCHHHHHHHHHHHHHHH
Confidence 789999999999999988765
No 12
>TIGR00641 acid_CoA_mut_N methylmalonyl-CoA mutase N-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 abd AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the N-terminal domain subfamily. In a neighbor-joining tree, AF2215 branches with a bacterial isobutyryl-CoA mutase, which is also the same length. Scoring between the noise and trusted cutoffs are the non-catalytic, partially homologous beta chains from certain heterodimeric examples of 5.4.99.2.
Probab=75.96 E-value=1.4 Score=36.07 Aligned_cols=22 Identities=18% Similarity=0.548 Sum_probs=19.3
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||-.|||||.+|.+.|.+.++
T Consensus 368 ~DPagGSyyIE~LT~~la~~Aw 389 (528)
T TIGR00641 368 IDPLGGSYYVEWLTDDIAERAW 389 (528)
T ss_pred cCcccCCHHHHHHHHHHHHHHH
Confidence 3789999999999999988765
No 13
>cd03681 MM_CoA_mutase_MeaA Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, MeaA-like subfamily; contains various methylmalonyl coenzyme A (CoA) mutase (MCM)-like proteins similar to the Streptomyces cinnamonensis MeaA, Methylobacterium extorquens MeaA and Streptomyces collinus B12-dependent mutase. Members of this subfamily contain an N-terminal MCM domain and a C-terminal coenzyme B12 binding domain. S. cinnamonensis MeaA is a putative B12-dependent mutase which provides methylmalonyl-CoA precursors for the biosynthesis of the monensin polyketide via an unknown pathway. S. collinus B12-dependent mutase may be involved in a pathway for acetate assimilation.
Probab=75.43 E-value=1.5 Score=34.91 Aligned_cols=22 Identities=9% Similarity=0.191 Sum_probs=19.5
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||-.|||||.+|.+.|.+.++
T Consensus 326 ~DP~~GSyyiE~LT~~la~~Aw 347 (407)
T cd03681 326 DDLFDGSKVVEAKVEALKEEAR 347 (407)
T ss_pred CCcccccHHHHHHHHHHHHHHH
Confidence 4889999999999999988764
No 14
>cd03680 MM_CoA_mutase_ICM_like Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA, intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis.
Probab=74.51 E-value=1.6 Score=35.80 Aligned_cols=22 Identities=18% Similarity=0.560 Sum_probs=19.3
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||-.|||||.+|.+.|.+.++
T Consensus 388 ~DPagGSyyvE~LT~~la~~Aw 409 (538)
T cd03680 388 VDPLGGSYYVEALTDEIEEEAW 409 (538)
T ss_pred cCcccCcHHHHHHHHHHHHHHH
Confidence 3789999999999999988764
No 15
>cd03678 MM_CoA_mutase_1 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Members of this subfamily also contain an N-terminal coenzyme B12 binding domain followed by a domain similar to the E. coli ArgK membrane ATPase.
Probab=73.05 E-value=1.9 Score=35.24 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=19.5
Q ss_pred CCCCCchHHHHHHHHHHHhcCC
Q psy13939 30 RHPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 30 R~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
=||-.|||||.+|.+.|.+.++
T Consensus 414 ~DPagGSyyVE~LT~~la~~Aw 435 (495)
T cd03678 414 ENPLQGSFIIEELTDLVEEAVL 435 (495)
T ss_pred cCcCCCcHHHHHHHHHHHHHHH
Confidence 4889999999999999998765
No 16
>COG1884 Sbm Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism]
Probab=62.70 E-value=3.7 Score=34.05 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=19.1
Q ss_pred CCCCchHHHHHHHHHHHhcCC
Q psy13939 31 HPENGTWFIQCLCQELADSGT 51 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~~~ 51 (86)
||--|||||..|.+-|.+.++
T Consensus 391 DP~gGSyyVE~LTd~L~e~Aw 411 (548)
T COG1884 391 DPLGGSYYVEWLTDELEEAAW 411 (548)
T ss_pred CCCCCcchHHHHHHHHHHHHH
Confidence 889999999999999998764
No 17
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=55.00 E-value=2.1 Score=26.67 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=10.5
Q ss_pred CCccccCCCCCchHH
Q psy13939 24 VSFYSWRHPENGTWF 38 (86)
Q Consensus 24 ~g~~s~R~~~~GSwF 38 (86)
-||+.||||.+|.+|
T Consensus 26 k~Yy~Yr~P~tGk~~ 40 (75)
T PF09003_consen 26 KGYYQYRNPITGKEH 40 (75)
T ss_dssp -SEEEEE-TTTS-EE
T ss_pred eeEEEEecCCCCcee
Confidence 389999999998754
No 18
>PF12109 CXCR4_N: CXCR4 Chemokine receptor N terminal; InterPro: IPR022726 This entry represents the N-terminal region of the CXC type 4 chemokine receptor. CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of Human immunodeficiency virus 1, and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N-terminal domain of most chemokine receptors is the ligand binding domain and so the N-terminal domain of CXCR4 is the binding site for SDF-1 [].; PDB: 3OE9_B 3OE0_A 3ODU_A 2K03_D 3OE8_A 2K05_D 3OE6_A 2K04_B.
Probab=51.62 E-value=10 Score=20.17 Aligned_cols=19 Identities=37% Similarity=0.321 Sum_probs=9.6
Q ss_pred CCcccccccccCCCCCCcc
Q psy13939 2 SGDYELSKMYYKFDEEDDD 20 (86)
Q Consensus 2 ~~~~~~~~~~~~iP~~aD~ 20 (86)
||||+.-..+......+||
T Consensus 13 SGDy~~~kEpCf~~eNadF 31 (33)
T PF12109_consen 13 SGDYDSYKEPCFREENADF 31 (33)
T ss_dssp ---SSBS-S--SS-SSSST
T ss_pred CcccccccCcccccccccc
Confidence 6899988888777777776
No 19
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=44.50 E-value=61 Score=18.85 Aligned_cols=29 Identities=3% Similarity=0.008 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q psy13939 39 IQCLCQELADSGTKLDLLSIMTRVSRRVA 67 (86)
Q Consensus 39 Iq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va 67 (86)
.+.+-+++.......++.+++.++|..+.
T Consensus 5 ~~kik~~~~~~~~~~~~~~~i~~LN~~lr 33 (80)
T PF08388_consen 5 RRKIKEITRRRNRGKSLEELIKKLNPILR 33 (80)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Confidence 34455555444467899999999998884
No 20
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=43.80 E-value=16 Score=23.14 Aligned_cols=27 Identities=11% Similarity=0.284 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q psy13939 37 WFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67 (86)
Q Consensus 37 wFIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va 67 (86)
-|+++|++.|..+++ +++|++|...|+
T Consensus 40 alV~aL~elLnt~~K----~sLLsEiR~lI~ 66 (81)
T cd07357 40 ALVMALFELLNTHEK----FSLLSEIRELIS 66 (81)
T ss_pred HHHHHHHHHhccHHH----HHHHHHHHHhcC
Confidence 488899999988755 788888876665
No 21
>PF12475 Amdo_NSP: Amdovirus non-structural protein ; InterPro: IPR020960 This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the three types of Amdovirus non-structural protein [].
Probab=42.04 E-value=20 Score=20.57 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=11.5
Q ss_pred hHHHHHHHHHHHhc
Q psy13939 36 TWFIQCLCQELADS 49 (86)
Q Consensus 36 SwFIq~Lc~vl~~~ 49 (86)
+|||..+++-|+..
T Consensus 16 ~w~~k~~n~DLa~~ 29 (48)
T PF12475_consen 16 GWFLKTTNKDLALI 29 (48)
T ss_pred HHHHHHhhHHHHHH
Confidence 69999998888764
No 22
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=41.50 E-value=45 Score=19.42 Aligned_cols=37 Identities=14% Similarity=0.245 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHhhhhccC
Q psy13939 38 FIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYN 74 (86)
Q Consensus 38 FIq~Lc~vl~~~~~~~dl~~ilt~Vn~~Va~~~~s~~ 74 (86)
|+.+.-++|++.+...+.-+|..++..+--....+.+
T Consensus 3 ~~eaa~~vL~~~~~pm~~~eI~~~i~~~~~~~~~~k~ 39 (72)
T PF05066_consen 3 FKEAAYEVLEEAGRPMTFKEIWEEIQERGLYKKSGKT 39 (72)
T ss_dssp HHHHHHHHHHHH-S-EEHHHHHHHHHHHHTS---GGG
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCcccCC
Confidence 6778889999999999999999887766544433333
No 23
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=40.13 E-value=36 Score=21.10 Aligned_cols=26 Identities=19% Similarity=0.406 Sum_probs=20.2
Q ss_pred CCchHHHHHHHHHHHhcCCCChHHHHH
Q psy13939 33 ENGTWFIQCLCQELADSGTKLDLLSIM 59 (86)
Q Consensus 33 ~~GSwFIq~Lc~vl~~~~~~~dl~~il 59 (86)
..|..=-.+||++|++.+ ..+|.++|
T Consensus 58 ~RG~~AF~~F~~aL~~~~-~~~LA~lL 83 (84)
T cd08326 58 TRGKQAFPAFLSALRETG-QTDLAELL 83 (84)
T ss_pred hcCHHHHHHHHHHHHhcC-chHHHHHh
Confidence 577788888999998864 45888776
No 24
>KOG2424|consensus
Probab=34.42 E-value=57 Score=23.75 Aligned_cols=29 Identities=24% Similarity=0.361 Sum_probs=19.8
Q ss_pred CCCchHHHHHHHHHHHhcC--CCChHHHHHH
Q psy13939 32 PENGTWFIQCLCQELADSG--TKLDLLSIMT 60 (86)
Q Consensus 32 ~~~GSwFIq~Lc~vl~~~~--~~~dl~~ilt 60 (86)
..-|..+|-+||+.|.... .+.+|.+||+
T Consensus 148 A~~Gaf~I~elcq~l~~~s~d~Ed~ideil~ 178 (195)
T KOG2424|consen 148 ATLGAFLILELCQCLQAQSDDLEDNIDEILL 178 (195)
T ss_pred hhhhHHHHHHHHHHHHhccccHHHHHHHHHH
Confidence 3579999999999999622 2334555554
No 25
>PF04819 DUF716: Family of unknown function (DUF716) ; InterPro: IPR006904 These sequences are a family of uncharacterised hypothetical proteins restricted to eukaryotes. Q9SLW7 from SWISSPROT represents a sequence from Nicotiana tabacum (Common tobacco)which is up regulated in response to TMV infection.
Probab=33.97 E-value=18 Score=24.34 Aligned_cols=15 Identities=33% Similarity=0.457 Sum_probs=11.7
Q ss_pred CchHHHHHHHHHHHh
Q psy13939 34 NGTWFIQCLCQELAD 48 (86)
Q Consensus 34 ~GSwFIq~Lc~vl~~ 48 (86)
.|+||+|.-.-....
T Consensus 73 qGtWf~Q~g~~Ly~p 87 (137)
T PF04819_consen 73 QGTWFWQIGFILYPP 87 (137)
T ss_pred HHHHHHHHHHHhcCC
Confidence 699999987666555
No 26
>PF12993 DUF3877: Domain of unknown function, E. rectale Gene description (DUF3877); InterPro: IPR024539 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=32.59 E-value=64 Score=23.15 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=20.0
Q ss_pred CCchHHHHHHHHHHHhcCCCC-hHHHHHH
Q psy13939 33 ENGTWFIQCLCQELADSGTKL-DLLSIMT 60 (86)
Q Consensus 33 ~~GSwFIq~Lc~vl~~~~~~~-dl~~ilt 60 (86)
...+-||++|.+.+.+|+.+. +|.+++.
T Consensus 91 ~~~~eFik~lIe~v~~hgcT~e~I~~~F~ 119 (175)
T PF12993_consen 91 TKENEFIKELIELVGKHGCTLEDILELFH 119 (175)
T ss_pred CCCCHHHHHHHHHHhcCCcCHHHHHHHHH
Confidence 466889999999999976432 4555443
No 27
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=30.71 E-value=46 Score=16.55 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=11.7
Q ss_pred CCchHHHHHHHHH
Q psy13939 33 ENGTWFIQCLCQE 45 (86)
Q Consensus 33 ~~GSwFIq~Lc~v 45 (86)
..||+.||.+.+.
T Consensus 13 ~~Gn~VvQk~le~ 25 (35)
T PF00806_consen 13 QYGNYVVQKCLEH 25 (35)
T ss_dssp TTHHHHHHHHHHH
T ss_pred cccCHHHHHHHHH
Confidence 6899999999887
No 28
>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=28.05 E-value=68 Score=26.68 Aligned_cols=39 Identities=23% Similarity=0.424 Sum_probs=26.2
Q ss_pred CCCccccC--CCCCchHHHHHHHHHHHhc----CCCChHHHHHHH
Q psy13939 23 FVSFYSWR--HPENGTWFIQCLCQELADS----GTKLDLLSIMTR 61 (86)
Q Consensus 23 ~~g~~s~R--~~~~GSwFIq~Lc~vl~~~----~~~~dl~~ilt~ 61 (86)
..--.||| .-++|||.||-+.++|.+- |.-..+-++.-+
T Consensus 351 ids~~aW~~F~aeTGS~LI~~~S~if~d~i~lGGdp~~~GeiIS~ 395 (527)
T COG1955 351 IDSNKAWRLFSAETGSYLISKFSEIFTDAIDLGGDPDVVGEIISE 395 (527)
T ss_pred CCHHHHHHHhhcCchhHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34456777 4589999999999999873 344444444433
No 29
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=26.99 E-value=50 Score=15.64 Aligned_cols=15 Identities=20% Similarity=0.299 Sum_probs=12.0
Q ss_pred CCchHHHHHHHHHHH
Q psy13939 33 ENGTWFIQCLCQELA 47 (86)
Q Consensus 33 ~~GSwFIq~Lc~vl~ 47 (86)
..||+.||.+.+...
T Consensus 13 ~~g~~viqk~l~~~~ 27 (36)
T smart00025 13 QYGNRVVQKLLEHAS 27 (36)
T ss_pred chhhHHHHHHHHHCC
Confidence 689999999877544
No 30
>PF15463 ECM11: Extracellular mutant protein 11
Probab=25.90 E-value=76 Score=21.21 Aligned_cols=35 Identities=14% Similarity=0.372 Sum_probs=21.6
Q ss_pred CCchHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHH
Q psy13939 33 ENGTWFIQCLCQELADSG-TKLDLLSIMTRVSRRVA 67 (86)
Q Consensus 33 ~~GSwFIq~Lc~vl~~~~-~~~dl~~ilt~Vn~~Va 67 (86)
..|-|||+.+++++.+-- ....+-.++...+..|.
T Consensus 76 ~~Gd~~l~qf~~l~~kl~~~R~~~r~~~~~fe~eI~ 111 (139)
T PF15463_consen 76 EAGDWFLEQFSELMQKLKEARRKLRKKFAVFEDEIN 111 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 379999999999998753 22333344443344443
No 31
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=25.29 E-value=1.3e+02 Score=19.87 Aligned_cols=42 Identities=17% Similarity=0.273 Sum_probs=32.3
Q ss_pred cCCCccccCCCCCchHHHHHHHHHHHhcC--CCChHHHHHHHHHHHHH
Q psy13939 22 VFVSFYSWRHPENGTWFIQCLCQELADSG--TKLDLLSIMTRVSRRVA 67 (86)
Q Consensus 22 T~~g~~s~R~~~~GSwFIq~Lc~vl~~~~--~~~dl~~ilt~Vn~~Va 67 (86)
-.|||.+ --|-|+|.+-+...-+.. .-.+|.+-+..|+.++.
T Consensus 42 I~p~Y~~----PlGvW~VRE~vR~A~~~~p~~f~~l~eAl~~~~~~l~ 85 (110)
T PF04895_consen 42 ITPEYYA----PLGVWQVRENVRKAMKGKPEKFETLEEALEYVSSRLK 85 (110)
T ss_pred ecCCcee----eeeeehHHHHHHHHHhCCCcccCCHHHHHHHHHHHhC
Confidence 6778766 479999998887665443 45689999999988884
No 32
>PF12887 SICA_alpha: SICA extracellular alpha domain; InterPro: IPR024290 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-alpha domain.
Probab=24.96 E-value=1.9e+02 Score=20.22 Aligned_cols=41 Identities=15% Similarity=0.373 Sum_probs=27.3
Q ss_pred CCchHHHHHHHHHHHh---cCCCChHHHHHHHHHHHHHhhhhcc
Q psy13939 33 ENGTWFIQCLCQELAD---SGTKLDLLSIMTRVSRRVALDMESY 73 (86)
Q Consensus 33 ~~GSwFIq~Lc~vl~~---~~~~~dl~~ilt~Vn~~Va~~~~s~ 73 (86)
..--||+++++-.+.- ++..+++-+++..|...|...-...
T Consensus 109 ~~~~~Y~RCIVG~vaL~~iygdhC~~~~vi~~i~~~v~~~l~~~ 152 (184)
T PF12887_consen 109 DDWEAYLRCIVGAVALSEIYGDHCKLKKVIQKISDKVEEKLKGH 152 (184)
T ss_pred chHHhcchhHHhHHHHHHHHhccCCHHHHHHHHHHHHHHhcccC
Confidence 3456888877644332 4677888888888888886444333
No 33
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=21.83 E-value=98 Score=17.01 Aligned_cols=18 Identities=11% Similarity=0.189 Sum_probs=15.2
Q ss_pred CCChHHHHHHHHHHHHHh
Q psy13939 51 TKLDLLSIMTRVSRRVAL 68 (86)
Q Consensus 51 ~~~dl~~ilt~Vn~~Va~ 68 (86)
.--||.+|+...++++..
T Consensus 19 gPPDLdel~r~l~~kl~~ 36 (42)
T PF12221_consen 19 GPPDLDELFRKLQDKLGG 36 (42)
T ss_pred CCCCHHHHHHHHHHHHhc
Confidence 366999999999999864
No 34
>PRK05883 acyl carrier protein; Validated
Probab=21.13 E-value=1.3e+02 Score=18.62 Aligned_cols=24 Identities=13% Similarity=0.142 Sum_probs=17.3
Q ss_pred CCccccCCCCCc----hHHHHHHHHHHH
Q psy13939 24 VSFYSWRHPENG----TWFIQCLCQELA 47 (86)
Q Consensus 24 ~g~~s~R~~~~G----SwFIq~Lc~vl~ 47 (86)
||-.|||++..- .|++.-|++.|.
T Consensus 1 ~~~~~~~~~~~~~~I~~~l~~iia~~l~ 28 (91)
T PRK05883 1 PGVASFAMTSSPSTVSATLLSILRDDLN 28 (91)
T ss_pred CCcCccCCCCCHHHHHHHHHHHHHHHhC
Confidence 788899987654 466777777764
No 35
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=21.09 E-value=87 Score=19.47 Aligned_cols=27 Identities=15% Similarity=0.474 Sum_probs=18.2
Q ss_pred CchHHHHHHHHHHHhcCCCChHHHHHHH
Q psy13939 34 NGTWFIQCLCQELADSGTKLDLLSIMTR 61 (86)
Q Consensus 34 ~GSwFIq~Lc~vl~~~~~~~dl~~ilt~ 61 (86)
.|.-=-..||++|++.+ ..||.++|.+
T Consensus 63 RG~~AF~~F~~aL~~~~-~~~La~lL~~ 89 (90)
T cd08332 63 RGPRAFSAFCEALRETS-QEHLCDLLEK 89 (90)
T ss_pred hChhHHHHHHHHHHhcC-hHHHHHHHhh
Confidence 34444567899997643 4688888854
No 36
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=20.87 E-value=1e+02 Score=19.41 Aligned_cols=19 Identities=21% Similarity=0.342 Sum_probs=13.4
Q ss_pred HHHHHHHHHhcCCCChHHH
Q psy13939 39 IQCLCQELADSGTKLDLLS 57 (86)
Q Consensus 39 Iq~Lc~vl~~~~~~~dl~~ 57 (86)
|+.|+++|++.++..-+.-
T Consensus 63 v~~L~~~L~~mgR~D~~~~ 81 (84)
T cd08802 63 LNSLASALEEMGKSEMLVV 81 (84)
T ss_pred HHHHHHHHHHcCcchHHHH
Confidence 6888888888766555543
No 37
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=20.45 E-value=1.8e+02 Score=19.09 Aligned_cols=42 Identities=10% Similarity=0.059 Sum_probs=29.4
Q ss_pred CCCCchHHHHHHHHHHHhc-------CCCChHHHHHHHHHHHHHhhhhc
Q psy13939 31 HPENGTWFIQCLCQELADS-------GTKLDLLSIMTRVSRRVALDMES 72 (86)
Q Consensus 31 ~~~~GSwFIq~Lc~vl~~~-------~~~~dl~~ilt~Vn~~Va~~~~s 72 (86)
-|.+-||||..+..-|... .....+.+++..|-..|...|-.
T Consensus 29 ~Pt~~S~yV~~il~Pl~~F~~~~~~~~~~~~~~~~~~~v~~~v~~~y~~ 77 (125)
T PF12022_consen 29 VPTKPSPYVSSILRPLKSFLEEYSSYLSPEIIEEWLQKVITEVTERYYE 77 (125)
T ss_pred CCCCccHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899998887777653 23457777888777777766644
No 38
>KOG4417|consensus
Probab=20.23 E-value=57 Score=24.51 Aligned_cols=24 Identities=13% Similarity=0.308 Sum_probs=20.3
Q ss_pred cCCCccccCCCCCchHHHHHHHHHHHh
Q psy13939 22 VFVSFYSWRHPENGTWFIQCLCQELAD 48 (86)
Q Consensus 22 T~~g~~s~R~~~~GSwFIq~Lc~vl~~ 48 (86)
-+|||.|||.. -|+.+-|-.+..+
T Consensus 87 YvPgfLafREa---~v~l~~L~~v~~e 110 (261)
T KOG4417|consen 87 YVPGFLAFREA---EVMLDFLKSVITE 110 (261)
T ss_pred cCccceeeehh---HHHHHHHHhcccc
Confidence 79999999985 6999988888754
No 39
>PHA02593 62 clamp loader small subunit; Provisional
Probab=20.21 E-value=98 Score=22.50 Aligned_cols=37 Identities=16% Similarity=0.329 Sum_probs=27.9
Q ss_pred CCccccCCCCCchHHHHHHHHHHHhcCCCChHHHHHHHHH
Q psy13939 24 VSFYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVS 63 (86)
Q Consensus 24 ~g~~s~R~~~~GSwFIq~Lc~vl~~~~~~~dl~~ilt~Vn 63 (86)
+.-.|||+.. ===||+||+.|.+. .+..|..||..||
T Consensus 14 EHeiAW~skD--w~~V~elad~fke~-~en~lF~ii~~it 50 (191)
T PHA02593 14 EHEIAWRSKD--WDAVQELADSFKEK-AENELFAIIDDIT 50 (191)
T ss_pred HHHHHHhccC--HHHHHHHHHHhCcc-hhhHHHHHHHHHh
Confidence 3446888853 23699999999987 4568888988877
Done!