Query psy14675
Match_columns 105
No_of_seqs 132 out of 1016
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 17:44:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14675.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14675hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2154 Pterin-4a-carbinolamin 100.0 1.2E-38 2.6E-43 209.7 12.8 98 5-104 2-99 (101)
2 PRK00823 phhB pterin-4-alpha-c 100.0 1.2E-37 2.7E-42 204.0 13.5 96 5-102 2-97 (97)
3 PF01329 Pterin_4a: Pterin 4 a 100.0 2.5E-37 5.5E-42 201.8 12.1 94 5-101 1-94 (95)
4 cd00914 PCD_DCoH_subfamily_b P 100.0 7.8E-33 1.7E-37 174.1 10.6 76 25-100 1-76 (76)
5 cd00913 PCD_DCoH_subfamily_a P 100.0 3.9E-32 8.5E-37 170.9 9.9 76 25-100 1-76 (76)
6 cd00488 PCD_DCoH PCD_DCoH: The 100.0 6.3E-32 1.4E-36 169.4 9.7 75 25-100 1-75 (75)
7 KOG4073|consensus 100.0 1E-31 2.2E-36 175.0 9.3 99 5-103 4-102 (104)
8 cd03527 RuBisCO_small Ribulose 80.4 0.88 1.9E-05 29.9 1.0 62 6-67 9-80 (99)
9 PF11548 Receptor_IA-2: Protei 70.5 22 0.00048 23.1 5.6 53 41-94 13-66 (91)
10 cd03074 PDI_b'_Calsequestrin_C 67.5 14 0.0003 25.0 4.3 64 26-90 15-94 (120)
11 CHL00130 rbcS ribulose-1,5-bis 66.9 3 6.5E-05 29.0 1.0 62 6-67 11-82 (138)
12 PF11987 IF-2: Translation-ini 65.4 1.1 2.4E-05 29.6 -1.3 28 72-99 42-69 (108)
13 PF00101 RuBisCO_small: Ribulo 64.9 1.9 4.2E-05 28.2 -0.2 25 5-29 7-31 (99)
14 PF01216 Calsequestrin: Calseq 61.2 14 0.0003 29.7 3.9 64 7-71 232-307 (383)
15 COG4451 RbcS Ribulose bisphosp 54.9 5.2 0.00011 27.3 0.5 81 5-85 15-108 (127)
16 PLN02289 ribulose-bisphosphate 54.3 5.2 0.00011 28.9 0.5 23 6-28 73-95 (176)
17 PF09840 DUF2067: Uncharacteri 49.0 67 0.0015 23.3 5.6 42 38-81 2-43 (190)
18 KOG1145|consensus 48.3 13 0.00028 31.8 2.0 30 71-100 496-525 (683)
19 TIGR02778 ligD_pol DNA polymer 43.4 1.4E+02 0.0031 22.6 6.8 67 14-82 139-215 (245)
20 PF12368 DUF3650: Protein of u 41.5 20 0.00043 18.3 1.3 14 8-21 15-28 (28)
21 PF13374 TPR_10: Tetratricopep 39.4 45 0.00097 16.5 2.6 26 41-66 15-42 (42)
22 cd04866 LigD_Pol_like_3 LigD_P 36.8 1.8E+02 0.0039 21.8 6.7 67 14-82 118-195 (223)
23 PF00125 Histone: Core histone 35.0 21 0.00047 21.1 1.0 13 86-98 63-75 (75)
24 CHL00189 infB translation init 34.3 35 0.00076 29.8 2.5 28 72-99 568-595 (742)
25 PF04800 ETC_C1_NDUFA4: ETC co 34.1 40 0.00086 22.1 2.2 28 24-53 38-67 (101)
26 PF12829 Mhr1: Transcriptional 34.0 1.2E+02 0.0026 19.5 4.5 55 6-65 21-82 (91)
27 TIGR02776 NHEJ_ligase_prk DNA 33.9 2.5E+02 0.0055 23.7 7.4 68 13-82 415-493 (552)
28 cd04863 MtLigD_Pol_like MtLigD 32.4 2.2E+02 0.0047 21.4 6.7 67 14-82 127-203 (231)
29 KOG1233|consensus 32.4 39 0.00085 28.0 2.4 20 38-57 347-366 (613)
30 COG3200 AroG 3-deoxy-D-arabino 31.9 63 0.0014 26.3 3.4 66 26-91 346-415 (445)
31 PF08047 His_leader: Histidine 31.9 3.9 8.5E-05 18.0 -1.9 6 61-66 11-16 (16)
32 PF07109 Mg-por_mtran_C: Magne 31.6 26 0.00057 22.9 1.1 39 5-50 57-95 (97)
33 PF00984 UDPG_MGDP_dh: UDP-glu 30.7 45 0.00097 21.3 2.1 17 46-62 17-33 (96)
34 PF14267 DUF4357: Domain of un 30.5 71 0.0015 18.5 2.7 21 32-52 16-36 (55)
35 PF14510 ABC_trans_N: ABC-tran 29.6 1.2E+02 0.0025 18.6 3.8 35 46-80 35-70 (85)
36 PF09559 Cas6: Cas6 Crispr; I 29.5 2.1E+02 0.0046 21.0 5.6 46 34-79 104-150 (195)
37 PF14097 SpoVAE: Stage V sporu 28.9 50 0.0011 24.0 2.2 21 1-21 30-50 (180)
38 COG0532 InfB Translation initi 28.7 56 0.0012 27.4 2.7 29 71-99 331-359 (509)
39 PF06864 PAP_PilO: Pilin acces 28.6 3E+02 0.0066 21.9 7.6 73 24-99 248-333 (414)
40 COG1724 Predicted RNA binding 28.0 1.2E+02 0.0026 18.5 3.4 34 5-42 3-36 (66)
41 cd01586 AcnA_IRP Aconitase A c 27.7 1.1E+02 0.0024 24.9 4.2 39 56-94 148-186 (404)
42 cd04862 PaeLigD_Pol_like PaeLi 27.7 2.7E+02 0.0057 20.9 6.8 68 13-82 122-199 (227)
43 PRK13798 putative OHCU decarbo 27.5 82 0.0018 22.3 3.1 86 8-101 13-105 (166)
44 PRK12466 isopropylmalate isome 27.3 1.6E+02 0.0034 24.5 5.1 39 56-94 150-188 (471)
45 PRK00402 3-isopropylmalate deh 26.8 1.5E+02 0.0033 24.2 4.9 39 56-94 141-179 (418)
46 PRK05306 infB translation init 26.8 39 0.00084 29.7 1.6 26 73-98 614-639 (787)
47 PF00330 Aconitase: Aconitase 26.6 1.4E+02 0.0031 24.6 4.8 40 56-95 149-188 (465)
48 PF08920 SF3b1: Splicing facto 26.5 44 0.00096 23.3 1.5 21 7-30 85-105 (144)
49 COG4004 Uncharacterized protei 26.1 72 0.0016 20.8 2.4 27 10-39 13-39 (96)
50 PF14814 UB2H: Bifunctional tr 25.6 84 0.0018 19.4 2.6 38 7-44 5-52 (85)
51 cd01583 IPMI 3-isopropylmalate 25.3 1.7E+02 0.0038 23.5 4.9 38 57-94 113-150 (382)
52 TIGR00170 leuC 3-isopropylmala 25.2 1.6E+02 0.0035 24.4 4.8 38 57-94 149-186 (465)
53 TIGR00487 IF-2 translation ini 25.1 53 0.0012 27.7 2.0 26 73-98 412-437 (587)
54 cd01585 AcnA_Bact Aconitase ca 25.1 1.7E+02 0.0036 23.7 4.7 39 56-94 110-148 (380)
55 PF13549 ATP-grasp_5: ATP-gras 24.4 78 0.0017 23.3 2.6 54 6-68 146-199 (222)
56 cd08871 START_STARD10-like Lip 24.2 87 0.0019 22.5 2.8 27 4-30 2-29 (222)
57 TIGR02083 LEU2 3-isopropylmala 24.0 1.8E+02 0.0038 23.9 4.7 38 58-95 143-180 (419)
58 cd01582 Homoaconitase Homoacon 23.7 1.8E+02 0.0038 23.4 4.6 30 65-94 119-148 (363)
59 PRK07229 aconitate hydratase; 23.5 1.8E+02 0.0038 25.1 4.8 39 56-94 139-177 (646)
60 TIGR01342 acon_putative aconit 23.4 1.6E+02 0.0036 25.4 4.7 40 56-95 136-175 (658)
61 COG4837 Uncharacterized protei 22.7 99 0.0022 20.4 2.5 48 42-99 23-70 (106)
62 PRK05478 isopropylmalate isome 22.5 1.9E+02 0.0041 24.0 4.7 39 56-94 148-186 (466)
63 PF13783 DUF4177: Domain of un 21.9 56 0.0012 18.8 1.2 22 9-30 17-38 (61)
64 PF11353 DUF3153: Protein of u 21.3 2.1E+02 0.0047 20.5 4.4 47 12-60 47-93 (209)
65 PF11203 DUF2984: Protein of u 21.2 1.2E+02 0.0025 19.5 2.7 36 6-41 55-97 (98)
66 TIGR01343 hacA_fam homoaconita 21.1 2.4E+02 0.0051 23.1 4.9 40 55-94 137-176 (412)
67 cd01584 AcnA_Mitochondrial Aco 21.1 2E+02 0.0044 23.4 4.5 34 61-94 123-156 (412)
68 PRK06703 flavodoxin; Provision 20.4 1.8E+02 0.0038 19.3 3.6 43 14-61 105-150 (151)
69 TIGR00139 h_aconitase homoacon 20.2 2.1E+02 0.0045 25.1 4.7 37 58-94 145-181 (712)
No 1
>COG2154 Pterin-4a-carbinolamine dehydratase [Coenzyme metabolism]
Probab=100.00 E-value=1.2e-38 Score=209.66 Aligned_cols=98 Identities=41% Similarity=0.728 Sum_probs=94.1
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCC
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCN 84 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 84 (105)
+++.|+++++...|.+| +||.+..++..|+|+|+|+||.+|+.||++||.+||+.||||+|.+.|++|+|+|+||++|
T Consensus 2 ~~~~lt~~~~~~~l~~l--~gW~l~~~~~~l~r~f~FknF~~a~~F~~~vA~~Ae~~~HHPdi~~~y~~V~vtltTHdag 79 (101)
T COG2154 2 RASKLTDEELAELLRAL--PGWELADDGAKLTRTFKFKNFKQAIAFVNRVAEIAEKLNHHPDIEVVYNRVTVTLTTHDAG 79 (101)
T ss_pred CccccCHHHHHHHhcCC--CCCEEecCcceEEEEEEcCCHHHHHHHHHHHHHHHHHhCCCCCeEEEeeeEEEEEEEccCC
Confidence 56789999999999999 9999998878999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHhhhc
Q psy14675 85 GLSNKDIKLASFMDTIIKAE 104 (105)
Q Consensus 85 glT~~D~~LA~~id~~~~~~ 104 (105)
|||++||+||++||+++...
T Consensus 80 glT~~D~~lA~~id~~~~~~ 99 (101)
T COG2154 80 GLTDLDFKLAAKIDALAKTE 99 (101)
T ss_pred CccHHHHHHHHHHHHHHhhh
Confidence 99999999999999998753
No 2
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=100.00 E-value=1.2e-37 Score=204.02 Aligned_cols=96 Identities=52% Similarity=0.884 Sum_probs=91.9
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCC
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCN 84 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 84 (105)
++++|+++|+.++|.+| |||++.+++.+|+|+|+|+||.++++|+|+|+.+|+++||||+|+++|++|+|+|+||+++
T Consensus 2 ~~~~Ls~~ei~~~l~~l--~gW~~~~~~~~l~r~f~f~~f~~a~~f~~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 79 (97)
T PRK00823 2 MAEKLSDEEIAELLPQL--PGWTLVGDRDAIERTFKFKNFNEAFAFMNRVAEIAEEEDHHPDWFNVYNRVTVTLTTHDAG 79 (97)
T ss_pred CCCCCCHHHHHHHhhcC--CCCeEeCCcCeEEEEEEeCCHHHHHHHHHHHHHHHHHcCCCCCEEEEcCEEEEEEEeCCCC
Confidence 56899999999999999 8999987767899999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHhh
Q psy14675 85 GLSNKDIKLASFMDTIIK 102 (105)
Q Consensus 85 glT~~D~~LA~~id~~~~ 102 (105)
|||++||+||++||+++.
T Consensus 80 glT~~D~~lA~~id~~~~ 97 (97)
T PRK00823 80 GLTENDFILAAKIDALAG 97 (97)
T ss_pred CCCHHHHHHHHHHHHhhC
Confidence 999999999999999863
No 3
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=100.00 E-value=2.5e-37 Score=201.80 Aligned_cols=94 Identities=40% Similarity=0.642 Sum_probs=84.2
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCC
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCN 84 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 84 (105)
++++||++||.++|++| |||++.+ +..|+|+|+|+||.+|++|||+|+.+|++++|||+|+++|++|+|+|+||++|
T Consensus 1 ~~~~Ls~~ei~~~L~~l--~~W~~~~-~~~l~r~f~f~~f~~a~~f~~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 77 (95)
T PF01329_consen 1 DAPPLSEEEIAEALAEL--PGWKLDG-GGRLERTFKFKDFAEAVEFVNRVAALAEEENHHPDISLGYNRVTVTLTTHDAG 77 (95)
T ss_dssp S-SB-THHHHHHHHHTS--TTSEEET-SSEEEEEEE-SSHHHHHHHHHHHHHHHHHHT---EEEEETTEEEEEE-BTTTT
T ss_pred CCCCCCHHHHHHhhhcC--cCCEECC-CCcEEEEEEeCCHHHHHHHHHHHHHHHHHhCCCCCeEecCCcEEEEEEeCCCC
Confidence 46899999999999999 8999998 57999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHh
Q psy14675 85 GLSNKDIKLASFMDTII 101 (105)
Q Consensus 85 glT~~D~~LA~~id~~~ 101 (105)
|||++||+||++||+++
T Consensus 78 glT~~D~~lA~~id~~~ 94 (95)
T PF01329_consen 78 GLTEKDFILAARIDDLA 94 (95)
T ss_dssp BBBHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 99999999999999987
No 4
>cd00914 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon
Probab=100.00 E-value=7.8e-33 Score=174.14 Aligned_cols=76 Identities=68% Similarity=1.198 Sum_probs=73.2
Q ss_pred CCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHHHHHHH
Q psy14675 25 GWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLASFMDTI 100 (105)
Q Consensus 25 gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~~id~~ 100 (105)
||++.+++..|+|+|+|++|.+|++||++|+.+||++||||+|+++|++|+|.|+||++||||++||+||++||++
T Consensus 1 gW~~~~~~~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHPdi~~~~~~V~v~l~Thd~~glT~~D~~lA~~id~~ 76 (76)
T cd00914 1 GWTLVDGRDAIHKSFKFKDFNEAFGFMTRVALEAEKMNHHPEWFNVYNKVDITLTTHDAGGLTERDIKLAKFIEKA 76 (76)
T ss_pred CCeEeCCCCeEEEEEEeCCHHHHHHHHHHHHHHHHHhCCCCCEEEeccEEEEEEEeCCCCCcCHHHHHHHHHHhcC
Confidence 7999886668999999999999999999999999999999999999999999999999999999999999999975
No 5
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=99.98 E-value=3.9e-32 Score=170.88 Aligned_cols=76 Identities=34% Similarity=0.599 Sum_probs=73.2
Q ss_pred CCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHHHHHHH
Q psy14675 25 GWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLASFMDTI 100 (105)
Q Consensus 25 gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~~id~~ 100 (105)
||++.+++.+|+|+|+|++|.++++|+++||.+|++++|||+|+++|++|+|+|+||+++|||++||+||++||++
T Consensus 1 gW~~~~~~~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~lA~~id~l 76 (76)
T cd00913 1 GWELADDGLKLERTFRFKNFVEALEFVNAVGEIAEAEGHHPDLSLGWGRVRVTWWTHSIGGLSENDFIMAAKIDAL 76 (76)
T ss_pred CCcCcCCCCeEEEEEEcCCHHHHHHHHHHHHHHHHHcCCCCCEEEeccEEEEEEEeCCCCCCCHHHHHHHHHHhcC
Confidence 7999876678999999999999999999999999999999999999999999999999999999999999999974
No 6
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=99.97 E-value=6.3e-32 Score=169.42 Aligned_cols=75 Identities=49% Similarity=0.876 Sum_probs=72.0
Q ss_pred CCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHHHHHHH
Q psy14675 25 GWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLASFMDTI 100 (105)
Q Consensus 25 gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~~id~~ 100 (105)
||++.+ +.+|+|+|+|++|.+|++|+++|+.+||++||||+|+++|++|+|+|+||+++|||++||+||++||++
T Consensus 1 gW~~~~-~~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glt~~D~~lA~~id~~ 75 (75)
T cd00488 1 GWELAD-GDALERTFKFKDFKEAIAFVNRVAELAEALNHHPDISNVYNKVTVTLTTHDAGGLTENDFILAAKIDAL 75 (75)
T ss_pred CCcCCC-CCcEEEEEEcCCHHHHHHHHHHHHHHHHHcCCCCCEEEeeeEEEEEEEeCCCCCCCHHHHHHHHHHhcC
Confidence 799977 458999999999999999999999999999999999999999999999999999999999999999975
No 7
>KOG4073|consensus
Probab=99.97 E-value=1e-31 Score=175.03 Aligned_cols=99 Identities=59% Similarity=1.000 Sum_probs=89.2
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCC
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCN 84 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~ 84 (105)
++..|...|-...+..+...||.+..++.+|.|.|.|+||.+|+.|+.+||..||++||||+|.+.||+|.|+|+||++|
T Consensus 4 ~~~~~~~~er~~~ll~~~~agW~l~~~rd~i~kef~fKdF~~a~~FmtrVal~Ae~~~HHPew~nvynkV~itL~THd~g 83 (104)
T KOG4073|consen 4 KAHRLNESERKLKLLTLKAAGWDLVEGRDAIFKEFRFKDFNQAFGFMTRVALRAEKLGHHPEWFNVYNKVKITLSTHDIG 83 (104)
T ss_pred hhhhhhhhHHhccchhhhhcCCCcccCccceeeEEEeecHHHHHHHHHHHHHHHHHhcCCchhheeeeeeEEEEEecccC
Confidence 44566666666666555558999998889999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHhhh
Q psy14675 85 GLSNKDIKLASFMDTIIKA 103 (105)
Q Consensus 85 glT~~D~~LA~~id~~~~~ 103 (105)
|||++|++||.+||.++.+
T Consensus 84 gLse~Dv~lA~~Ie~~a~~ 102 (104)
T KOG4073|consen 84 GLSENDVKLAKFIESLAVE 102 (104)
T ss_pred CCCHHHHHHHHHHHHHHHh
Confidence 9999999999999998864
No 8
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=80.38 E-value=0.88 Score=29.93 Aligned_cols=62 Identities=11% Similarity=0.211 Sum_probs=41.0
Q ss_pred CCCCCHHHHHhhhcCCCCCCCEEec----CC---ccEEEEEEeCChH--HHHHHHHHHHHH-HHhcCCCcee
Q psy14675 6 SVKLSADERLSKLEPILKSGWKLVE----NR---DAIYKEYLFKNFN--EAFGFMTRTALL-AEKMDHHPEW 67 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~~~gW~~~~----~~---~~L~r~f~f~~f~--~a~~fv~~Va~~-ae~~~HHP~i 67 (105)
-++||++||.+.+..+...||.+-- .+ ..-..-|+.+-|. +..+.++.|.+. .+--|||-.+
T Consensus 9 lp~lt~~~i~~QI~yll~qG~~~~lE~ad~~~~~~~yW~mwklP~f~~~d~~~Vl~ei~~C~~~~p~~YVRl 80 (99)
T cd03527 9 LPPLTDEQIAKQIDYIISNGWAPCLEFTEPEHYDNRYWTMWKLPMFGCTDPAQVLREIEACRKAYPDHYVRV 80 (99)
T ss_pred CCCCCHHHHHHHHHHHHhCCCEEEEEcccCCCCCCCEEeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Confidence 5799999999999998889998752 11 2333344455552 456677777766 4445666554
No 9
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=70.49 E-value=22 Score=23.05 Aligned_cols=53 Identities=15% Similarity=0.080 Sum_probs=34.3
Q ss_pred eCChHHHHHHHHHHHHHHHhc-CCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 41 FKNFNEAFGFMTRTALLAEKM-DHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 41 f~~f~~a~~fv~~Va~~ae~~-~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+.++.++..+|+.|+++-.-. +-.-++.....-|++++..- ..++|..|+.=+
T Consensus 13 ~ls~~~G~~l~~~la~~l~l~s~~F~~i~V~g~avTFrv~~N-~~n~taadVa~~ 66 (91)
T PF11548_consen 13 PLSWDEGSRLMEKLAELLHLPSSSFINISVVGPAVTFRVRPN-NKNLTAADVAKQ 66 (91)
T ss_dssp T--HHHHHHHHHHHHHHHTS-GGGEEEEEEETTEEEEEE----TT---HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhCCCcccceeeeecCceEEEEeccC-cCCCCHHHHHHH
Confidence 457899999999888776533 44456778899999999544 488999998533
No 10
>cd03074 PDI_b'_Calsequestrin_C Protein Disulfide Isomerase (PDIb') family, Calsequestrin subfamily, C-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin
Probab=67.53 E-value=14 Score=25.00 Aligned_cols=64 Identities=9% Similarity=0.198 Sum_probs=43.6
Q ss_pred CEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeec--------------CEEEEEEEcCCCC--CCCHH
Q psy14675 26 WKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVY--------------NKVQVTLSTHDCN--GLSNK 89 (105)
Q Consensus 26 W~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~--------------~~V~v~l~Th~~~--glT~~ 89 (105)
|.-..++ .+..-|.=..-.++.+|+.-|..+|++..|+|++++-| +...|.|..+.+| .+|.+
T Consensus 15 wedd~~g-~~IvAFaee~dpdG~eFl~ilk~vA~~nt~np~LsiIWIDPD~FPllv~yWektF~IDl~~PqIGVV~vtda 93 (120)
T cd03074 15 WEDDLDG-IHIVAFAEEEDPDGYEFLEILKEVARDNTDNPDLSIIWIDPDDFPLLVPYWEKTFGIDLFRPQIGVVNVTDA 93 (120)
T ss_pred hhcccCC-ceEEEEeccCCccHHHHHHHHHHHHHhcCcCCCceEEEECCccCchhhHHHHhhcCcccCCCceeeEecccc
Confidence 7654443 34445655555799999999999999999999987642 2346666666665 34444
Q ss_pred H
Q psy14675 90 D 90 (105)
Q Consensus 90 D 90 (105)
|
T Consensus 94 d 94 (120)
T cd03074 94 D 94 (120)
T ss_pred c
Confidence 3
No 11
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=66.91 E-value=3 Score=29.02 Aligned_cols=62 Identities=10% Similarity=0.193 Sum_probs=38.7
Q ss_pred CCCCCHHHHHhhhcCCCCCCCEEe----cCC---ccEEEEEEeCCh--HHHHHHHHHHHHHHHhc-CCCcee
Q psy14675 6 SVKLSADERLSKLEPILKSGWKLV----ENR---DAIYKEYLFKNF--NEAFGFMTRTALLAEKM-DHHPEW 67 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~~~gW~~~----~~~---~~L~r~f~f~~f--~~a~~fv~~Va~~ae~~-~HHP~i 67 (105)
.++||++||...+.-+...||... +++ ..-.--|+.+=| .++...+..|.+.-+.- +||-.+
T Consensus 11 LPpLTdeqI~kQI~Y~i~~GW~p~iEft~~~~~~~~YW~MWkLPMFg~tD~~~Vl~Ei~~CrkayP~~yIRl 82 (138)
T CHL00130 11 LPDLTDQQIEKQIQYAISKGWALNVEWTDDPHPRNSYWELWGLPLFDVKDPAAVMFEINECRKQKPNGYIKV 82 (138)
T ss_pred CCCCCHHHHHHHHHHHHhcCCeEEEEecCCCCcCccEEeeeCCccCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence 579999999999988878999763 111 223333455545 45666777766654332 444333
No 12
>PF11987 IF-2: Translation-initiation factor 2; InterPro: IPR023115 Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 kDa that contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this group undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation. The function of IF-2 in facilitating the proper binding of initiator methionyl-tRNA to the ribosomal P site appears to be universally conserved, with an IF-2 homologue (aIF-2) present in archaea bacteria [] Methanopyrus kandleri. This entry represents the domain 3 of IF-2. It consists of a alpha/beta/alpha structure with a core formed by a parallel beta-sheet of 4 strands [].; PDB: 1Z9B_A 1ZO1_I 3IZY_P 1G7R_A 1G7S_A 1G7T_A.
Probab=65.41 E-value=1.1 Score=29.61 Aligned_cols=28 Identities=21% Similarity=0.396 Sum_probs=23.4
Q ss_pred CEEEEEEEcCCCCCCCHHHHHHHHHHHH
Q psy14675 72 NKVQVTLSTHDCNGLSNKDIKLASFMDT 99 (105)
Q Consensus 72 ~~V~v~l~Th~~~glT~~D~~LA~~id~ 99 (105)
..|.+.+-...+|.+|+.|+.||...+.
T Consensus 42 ~~v~i~Ii~~~VG~it~sDI~~A~~~~a 69 (108)
T PF11987_consen 42 DEVKIKIIHAGVGPITESDIELASASNA 69 (108)
T ss_dssp SSSCEEESEEEESSBHHHHHHHHHHHC-
T ss_pred ccccccEEEeeCCCCCHHHHHHHHhhCC
Confidence 3578888888899999999999998654
No 13
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=64.91 E-value=1.9 Score=28.24 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=17.7
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEe
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLV 29 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~ 29 (105)
..++||++||.+.+..+...||++-
T Consensus 7 ~lP~l~~~~i~~Qv~~ll~qG~~i~ 31 (99)
T PF00101_consen 7 YLPPLTDEEIAKQVRYLLSQGWIIG 31 (99)
T ss_dssp TSS---HHHHHHHHHHHHHTT-EEE
T ss_pred cCCCCCHHHHHHHHHhhhhcCceee
Confidence 3579999999999999888999874
No 14
>PF01216 Calsequestrin: Calsequestrin; InterPro: IPR001393 Calsequestrin is the principal calcium-binding protein present in the sarcoplasmic reticulum of cardiac and skeletal muscle []. It is a highly acidic protein that is able to bind over 40 calcium ions and acts as an internal calcium store in muscle. Sequence analysis has suggested that calcium is not bound in distinct pockets via EF-hand motifs, but rather via presentation of a charged protein surface. Two forms of calsequestrin have been identified. The cardiac form is present in cardiac and slow skeletal muscle and the fast skeletal form is found in fast skeletal muscle. The release of calsequestrin-bound calcium (through a a calcium release channel) triggers muscle contraction. The active protein is not highly structured, more than 50% of it adopting a random coil conformation []. When calcium binds there is a structural change whereby the alpha-helical content of the protein increases from 3 to 11% []. Both forms of calsequestrin are phosphorylated by casein kinase II, but the cardiac form is phosphorylated more rapidly and to a higher degree [].; GO: 0005509 calcium ion binding; PDB: 1SJI_B 2VAF_A 3UOM_C 1A8Y_A 3TRQ_A 3TRP_A 3US3_A.
Probab=61.25 E-value=14 Score=29.71 Aligned_cols=64 Identities=14% Similarity=0.193 Sum_probs=39.6
Q ss_pred CCCCHHHHHhhhcCCCCCC------------CEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEeec
Q psy14675 7 VKLSADERLSKLEPILKSG------------WKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVY 71 (105)
Q Consensus 7 ~~Lt~~ei~~~L~~l~~~g------------W~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~ 71 (105)
.|.|++|+.+.++.-..|- |.=.-++..|.+ |.=.+-.++.+|+.-+.++|+..-+||++++.|
T Consensus 232 ~p~~e~e~~~fi~~h~rptlrkl~~~~m~e~Wedd~~g~hIva-Faee~dpdG~efleilk~va~~nt~np~Lsivw 307 (383)
T PF01216_consen 232 KPYTEEELVEFIEEHKRPTLRKLRPEDMFETWEDDIDGIHIVA-FAEEEDPDGFEFLEILKQVARDNTDNPDLSIVW 307 (383)
T ss_dssp SS--HHHHHHHHHHT-S-SEEE--GGGHHHHHHSSSSSEEEEE-E--TTSHHHHHHHHHHHHHHHHCTT-TT--EEE
T ss_pred CCCCHHHHHHHHHHhchhHhhhCChhhhhhhhcccCCCceEEE-EecCCCCchHHHHHHHHHHHHhcCcCCceeEEE
Confidence 4789999988876532221 543333444443 555666899999999999999999999987654
No 15
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=54.85 E-value=5.2 Score=27.34 Aligned_cols=81 Identities=14% Similarity=0.124 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEec----CC---ccEEEEEEe--CChHHHHHHHHHHHH-HHHhcCCCceeE---eec
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVE----NR---DAIYKEYLF--KNFNEAFGFMTRTAL-LAEKMDHHPEWF---NVY 71 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~----~~---~~L~r~f~f--~~f~~a~~fv~~Va~-~ae~~~HHP~i~---~~~ 71 (105)
..++||+.||.+.+..|+..||++-- ++ ..-.-.+.. -.-..+-+.+..|.+ .++.-+++-.+. ...
T Consensus 15 ~lp~Ltd~qi~~QVrylL~QGykigvE~~d~rrprtgsWt~wg~p~f~~~~~~evlaele~Cr~dhp~eYIRliGfDp~g 94 (127)
T COG4451 15 SLPPLTDEQIAEQVRYLLSQGYKIGVEYVDDRRPRTGSWTMWGTPMFGAKTAGEVLAELEACRADHPGEYIRLIGFDPKG 94 (127)
T ss_pred cCCcCcHHHHHHHHHHHHhCCcccceeecccCCcccceeeecCCccccccchHHHHHHHHHHHHhCCCCeEEEEEecCCC
Confidence 45799999999999988889998641 11 111112221 111233344444333 355556665442 235
Q ss_pred CEEEEEEEcCCCCC
Q psy14675 72 NKVQVTLSTHDCNG 85 (105)
Q Consensus 72 ~~V~v~l~Th~~~g 85 (105)
.++++..--|-++|
T Consensus 95 krrv~sfIVhRPng 108 (127)
T COG4451 95 KRRVVSFIVHRPNG 108 (127)
T ss_pred ceEEEEEEEECCCC
Confidence 66777776676654
No 16
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=54.31 E-value=5.2 Score=28.88 Aligned_cols=23 Identities=17% Similarity=0.391 Sum_probs=20.3
Q ss_pred CCCCCHHHHHhhhcCCCCCCCEE
Q psy14675 6 SVKLSADERLSKLEPILKSGWKL 28 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~~~gW~~ 28 (105)
-++||++||...++-+...||..
T Consensus 73 LPpLtdeqI~kQVeYli~~GW~p 95 (176)
T PLN02289 73 LPDLTDEELAKEVDYLLRNKWVP 95 (176)
T ss_pred CCCCCHHHHHHHHHHHHhCCCee
Confidence 57999999999999888899965
No 17
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=49.01 E-value=67 Score=23.31 Aligned_cols=42 Identities=12% Similarity=0.142 Sum_probs=32.2
Q ss_pred EEEeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcC
Q psy14675 38 EYLFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTH 81 (105)
Q Consensus 38 ~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th 81 (105)
+|+|++-.++.+|+..|....... +-.+....++|.|.++=.
T Consensus 2 ~~~~~~~~E~~~fle~l~~~~~~~--~~~v~~k~n~l~I~i~G~ 43 (190)
T PF09840_consen 2 SFKFRDDEECEEFLERLSKMVKSI--YIYVEVKGNSLKIEIQGY 43 (190)
T ss_pred eEEcCChHHHHHHHHHHHhhccCc--EEEEEEeCCEEEEEEecC
Confidence 589999999999999997763322 335667789999998643
No 18
>KOG1145|consensus
Probab=48.34 E-value=13 Score=31.80 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=25.8
Q ss_pred cCEEEEEEEcCCCCCCCHHHHHHHHHHHHH
Q psy14675 71 YNKVQVTLSTHDCNGLSNKDIKLASFMDTI 100 (105)
Q Consensus 71 ~~~V~v~l~Th~~~glT~~D~~LA~~id~~ 100 (105)
...|++.+-...+|.+|+.|+.||+..+.+
T Consensus 496 ~~~v~l~~v~~gVG~vtesDlelA~~~dai 525 (683)
T KOG1145|consen 496 SEQVKLNVVHSGVGPVTESDLELAQASDAI 525 (683)
T ss_pred CCceEEEEEEeccCCCCcchhHHHHhcCcE
Confidence 346899998888899999999999988765
No 19
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=43.44 E-value=1.4e+02 Score=22.60 Aligned_cols=67 Identities=13% Similarity=0.133 Sum_probs=46.9
Q ss_pred HHhhhcCCCCCCCEEecCCccEEEEEEeC---ChHHHHHHHHHHHHHHHhcCCCceeE-------eecCEEEEEEEcCC
Q psy14675 14 RLSKLEPILKSGWKLVENRDAIYKEYLFK---NFNEAFGFMTRTALLAEKMDHHPEWF-------NVYNKVQVTLSTHD 82 (105)
Q Consensus 14 i~~~L~~l~~~gW~~~~~~~~L~r~f~f~---~f~~a~~fv~~Va~~ae~~~HHP~i~-------~~~~~V~v~l~Th~ 82 (105)
+.+.|..+.-++|-...|+.+|+=-..+. +|.++..|...||...++. ||++. .+.++|.|.+.-+.
T Consensus 139 ~r~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~--~Pd~~t~~~~k~~R~gkvfiDylqN~ 215 (245)
T TIGR02778 139 IRELLDELGLESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQ--MPDRFTAEMSKKNRVGKIFVDYLRNA 215 (245)
T ss_pred HHHHHHHcCCccceEccCCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHH--CchhhhhHhhHHhCCCCEEEECccCC
Confidence 45556555337787777777776555444 4899999999999988776 89874 24677888765444
No 20
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=41.46 E-value=20 Score=18.29 Aligned_cols=14 Identities=36% Similarity=0.463 Sum_probs=11.7
Q ss_pred CCCHHHHHhhhcCC
Q psy14675 8 KLSADERLSKLEPI 21 (105)
Q Consensus 8 ~Lt~~ei~~~L~~l 21 (105)
-||++|+.+.|+.+
T Consensus 15 ~ls~ee~~~RL~~i 28 (28)
T PF12368_consen 15 GLSEEEVAERLAAI 28 (28)
T ss_pred CCCHHHHHHHHHcC
Confidence 59999999998754
No 21
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=39.41 E-value=45 Score=16.51 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=14.4
Q ss_pred eCChHHHHHHHHHHHHHHHhc--CCCce
Q psy14675 41 FKNFNEAFGFMTRTALLAEKM--DHHPE 66 (105)
Q Consensus 41 f~~f~~a~~fv~~Va~~ae~~--~HHP~ 66 (105)
-..|.+|..+..++-.+.+.. ..|||
T Consensus 15 ~g~~~~A~~~~~~al~~~~~~~G~~Hpd 42 (42)
T PF13374_consen 15 QGRYEEALELLEEALEIRERLLGPDHPD 42 (42)
T ss_dssp CT-HHHHHHHHHHHHHHH----------
T ss_pred hhhcchhhHHHHHHHHHHHHHhcccccC
Confidence 357899999999988887765 56664
No 22
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=36.80 E-value=1.8e+02 Score=21.77 Aligned_cols=67 Identities=15% Similarity=0.145 Sum_probs=47.3
Q ss_pred HHhhhcCCCCCCCEEecCCccEEEEEEeC----ChHHHHHHHHHHHHHHHhcCCCceeE-------eecCEEEEEEEcCC
Q psy14675 14 RLSKLEPILKSGWKLVENRDAIYKEYLFK----NFNEAFGFMTRTALLAEKMDHHPEWF-------NVYNKVQVTLSTHD 82 (105)
Q Consensus 14 i~~~L~~l~~~gW~~~~~~~~L~r~f~f~----~f~~a~~fv~~Va~~ae~~~HHP~i~-------~~~~~V~v~l~Th~ 82 (105)
+.+.|+.+.-.+|-...|+.+|+=-.... +|.++..|...||...++. ||+.. .+.++|.|.+.-..
T Consensus 118 vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~~--~P~~~t~~~~k~~R~gkVfiDylqN~ 195 (223)
T cd04866 118 LKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQQ--FPELFTTERLKKNRHNRLYLDYVQHA 195 (223)
T ss_pred HHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHH--CchhhhHHhhHHhCCCCEEEECccCC
Confidence 45556655337887777777776665555 4899999999999988776 89864 24677888764443
No 23
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=35.03 E-value=21 Score=21.13 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=10.7
Q ss_pred CCHHHHHHHHHHH
Q psy14675 86 LSNKDIKLASFMD 98 (105)
Q Consensus 86 lT~~D~~LA~~id 98 (105)
||.+|+.+|.+++
T Consensus 63 I~~~DI~~A~r~~ 75 (75)
T PF00125_consen 63 ITPRDIQLAVRID 75 (75)
T ss_dssp EGHHHHHHHHHHT
T ss_pred ecHHHHHHHHhcC
Confidence 6779999998875
No 24
>CHL00189 infB translation initiation factor 2; Provisional
Probab=34.32 E-value=35 Score=29.82 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=24.1
Q ss_pred CEEEEEEEcCCCCCCCHHHHHHHHHHHH
Q psy14675 72 NKVQVTLSTHDCNGLSNKDIKLASFMDT 99 (105)
Q Consensus 72 ~~V~v~l~Th~~~glT~~D~~LA~~id~ 99 (105)
..|.+.+-...+|++|+.|+.||...+.
T Consensus 568 ~~v~i~i~~~~vG~it~~Dv~lA~~~~a 595 (742)
T CHL00189 568 KKVQLNILYASLGEVTETDVEFASTTNA 595 (742)
T ss_pred CcEEEEEEEeecCCCCHHHHHHHHhcCC
Confidence 3588999999999999999999987653
No 25
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=34.09 E-value=40 Score=22.13 Aligned_cols=28 Identities=18% Similarity=0.444 Sum_probs=19.4
Q ss_pred CCCEEecCCccEE--EEEEeCChHHHHHHHHH
Q psy14675 24 SGWKLVENRDAIY--KEYLFKNFNEAFGFMTR 53 (105)
Q Consensus 24 ~gW~~~~~~~~L~--r~f~f~~f~~a~~fv~~ 53 (105)
-||+-.++ .+. -...|++-++|++|..+
T Consensus 38 MGWtss~D--~~~q~v~l~F~skE~Ai~yaer 67 (101)
T PF04800_consen 38 MGWTSSGD--PLSQSVRLKFDSKEDAIAYAER 67 (101)
T ss_dssp T-SSSS----SEEE-CEEEESSHHHHHHHHHH
T ss_pred cCCCCCCC--hhhCeeEeeeCCHHHHHHHHHH
Confidence 58887766 454 57899999999988654
No 26
>PF12829 Mhr1: Transcriptional regulation of mitochondrial recombination; InterPro: IPR024629 These proteins are involved in regulation of RNA polymerase II-dependent transcription. They are also involved in regulation of mitochondrial DNA recombination, maintenance, repair, and generation of homoplasmic cells [, , , ].
Probab=33.96 E-value=1.2e+02 Score=19.53 Aligned_cols=55 Identities=13% Similarity=0.076 Sum_probs=38.2
Q ss_pred CCCCCHHHHHhhhcCCCCCCCEEecCCccE-------EEEEEeCChHHHHHHHHHHHHHHHhcCCCc
Q psy14675 6 SVKLSADERLSKLEPILKSGWKLVENRDAI-------YKEYLFKNFNEAFGFMTRTALLAEKMDHHP 65 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L-------~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP 65 (105)
.+.|+..+|...+.- +||+-..- +| -....|+++..|......+-++....+..+
T Consensus 21 ~p~l~~~~i~~Q~~~---~gkk~~pp--~lRkD~W~pm~vv~f~~~~~g~~~yq~Lrelr~~r~l~~ 82 (91)
T PF12829_consen 21 TPNLDNNQILKQFPF---PGKKNKPP--SLRKDYWRPMCVVNFPNYEVGVSAYQKLRELRKLRELSW 82 (91)
T ss_pred CcccChhHHHHhccC---CCcccCCc--hhccccceEeEEEECCChHHHHHHHHHHHHHHHHHhccC
Confidence 356777777766643 79987642 34 345689999999988888887766554443
No 27
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=33.87 E-value=2.5e+02 Score=23.66 Aligned_cols=68 Identities=10% Similarity=0.090 Sum_probs=47.2
Q ss_pred HHHhhhcCCCCCCCEEecCCccEEEEEEeCC----hHHHHHHHHHHHHHHHhcCCCceeEe-------ecCEEEEEEEcC
Q psy14675 13 ERLSKLEPILKSGWKLVENRDAIYKEYLFKN----FNEAFGFMTRTALLAEKMDHHPEWFN-------VYNKVQVTLSTH 81 (105)
Q Consensus 13 ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~----f~~a~~fv~~Va~~ae~~~HHP~i~~-------~~~~V~v~l~Th 81 (105)
.+.+.|..+.-.+|-...|+.+|+=...... |.++..|...||...++. ||+... +.++|.|.+.-+
T Consensus 415 ~~r~~L~~~gl~~~~KtSG~kGlhv~vPl~~~~~~~~~~~~fa~~~a~~~~~~--~P~~~t~~~~k~~R~grv~iDy~qn 492 (552)
T TIGR02776 415 LMKQLLDELGLVSFVKTSGGKGLHVVVPLRPNTFTWDETKLFAKAIAEYLARQ--FPERFTTEMGKKNRVGRIFIDYLRN 492 (552)
T ss_pred HHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHH--CcceehhhhhHhhCCCCEEEEcccC
Confidence 3555666654478977777777876665554 899999999999987765 888642 356677765443
Q ss_pred C
Q psy14675 82 D 82 (105)
Q Consensus 82 ~ 82 (105)
.
T Consensus 493 ~ 493 (552)
T TIGR02776 493 A 493 (552)
T ss_pred C
Confidence 3
No 28
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=32.41 E-value=2.2e+02 Score=21.43 Aligned_cols=67 Identities=16% Similarity=0.132 Sum_probs=46.8
Q ss_pred HHhhhcCCCCCCCEEecCCccEEEEEEeC---ChHHHHHHHHHHHHHHHhcCCCceeEe-------ecCEEEEEEEcCC
Q psy14675 14 RLSKLEPILKSGWKLVENRDAIYKEYLFK---NFNEAFGFMTRTALLAEKMDHHPEWFN-------VYNKVQVTLSTHD 82 (105)
Q Consensus 14 i~~~L~~l~~~gW~~~~~~~~L~r~f~f~---~f~~a~~fv~~Va~~ae~~~HHP~i~~-------~~~~V~v~l~Th~ 82 (105)
+.+.|.++.-.+|-...|+.+|+=-..+. +|.++..|...||...++. ||+... +.++|.|.+.-+.
T Consensus 127 ~r~~L~~lgL~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~~~--~P~~~t~~~~k~~R~grvfiDylqN~ 203 (231)
T cd04863 127 LRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELERE--HPDLVVSRMTKSLRAGKVFVDWSQND 203 (231)
T ss_pred HHHHHHHcCCccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH--CchhhhhHhhHhhCCCcEEEECccCC
Confidence 45556655337887777777776555443 5899999999999988876 898742 3567777764443
No 29
>KOG1233|consensus
Probab=32.40 E-value=39 Score=27.99 Aligned_cols=20 Identities=25% Similarity=0.622 Sum_probs=17.8
Q ss_pred EEEeCChHHHHHHHHHHHHH
Q psy14675 38 EYLFKNFNEAFGFMTRTALL 57 (105)
Q Consensus 38 ~f~f~~f~~a~~fv~~Va~~ 57 (105)
.|.|+||.+++.|+..||..
T Consensus 347 S~aFPNFEqGV~f~REvA~q 366 (613)
T KOG1233|consen 347 SFAFPNFEQGVNFFREVAIQ 366 (613)
T ss_pred ccccCcHHHHHHHHHHHHHH
Confidence 57999999999999998864
No 30
>COG3200 AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=31.94 E-value=63 Score=26.26 Aligned_cols=66 Identities=14% Similarity=0.197 Sum_probs=42.1
Q ss_pred CEEec-CCccEEEE--EEeCChHHHHHHHHHHHHHHHhcCCCce-eEeecCEEEEEEEcCCCCCCCHHHH
Q psy14675 26 WKLVE-NRDAIYKE--YLFKNFNEAFGFMTRTALLAEKMDHHPE-WFNVYNKVQVTLSTHDCNGLSNKDI 91 (105)
Q Consensus 26 W~~~~-~~~~L~r~--f~f~~f~~a~~fv~~Va~~ae~~~HHP~-i~~~~~~V~v~l~Th~~~glT~~D~ 91 (105)
|..+. .+..|+.. |+..-|..-++=|...-++...++-||- |.+.-..=.|+=.+..+.+||+.|+
T Consensus 346 Ws~DPMHGNTi~a~~gyKTR~fd~Il~EV~sFfeihraeG~hpgGiHlEmTg~dVTEC~gga~~it~~~L 415 (445)
T COG3200 346 WSSDPMHGNTIKASTGYKTRPFDRILDEVQSFFEIHRAEGTHPGGIHLEMTGEDVTECLGGARAITETDL 415 (445)
T ss_pred EecCCCCCceeecCCCCccccHHHHHHHHHHHHHHHHhccCCCCceEEEecCcchhhhccCccccccccc
Confidence 77653 23466655 8888999998888888999999999993 3332211122222334445777554
No 31
>PF08047 His_leader: Histidine operon leader peptide; InterPro: IPR012565 This family consists of the leader peptide of the histidine (his) operon. The his operon contains all the genes necessary for histidine biosynthesis. The region corresponding to the untranslated 5'-end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons [].; GO: 0000105 histidine biosynthetic process
Probab=31.90 E-value=3.9 Score=18.01 Aligned_cols=6 Identities=50% Similarity=1.187 Sum_probs=3.3
Q ss_pred cCCCce
Q psy14675 61 MDHHPE 66 (105)
Q Consensus 61 ~~HHP~ 66 (105)
..||||
T Consensus 11 hhhhpd 16 (16)
T PF08047_consen 11 HHHHPD 16 (16)
T ss_pred cccCCC
Confidence 456664
No 32
>PF07109 Mg-por_mtran_C: Magnesium-protoporphyrin IX methyltransferase C-terminus; InterPro: IPR010940 This entry represents the C terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase (2.1.1.11 from EC). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX metylester using S-adenosyl-L-methionine as a cofactor [].; GO: 0046406 magnesium protoporphyrin IX methyltransferase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process
Probab=31.62 E-value=26 Score=22.91 Aligned_cols=39 Identities=10% Similarity=0.287 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHH
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGF 50 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~f 50 (105)
...+..++++.+.|.. .||++... ..+..-|.| .+++++
T Consensus 57 ~i~~~~e~~l~~~l~~---~g~~~~r~-~ris~gFY~---S~llE~ 95 (97)
T PF07109_consen 57 RIYPHREEDLRRALAA---AGWRIGRT-ERISSGFYI---SQLLEA 95 (97)
T ss_pred cEEEeCHHHHHHHHHh---CCCeeeec-ccccCcChH---HHHhhc
Confidence 3458899999999987 49998643 366666655 445443
No 33
>PF00984 UDPG_MGDP_dh: UDP-glucose/GDP-mannose dehydrogenase family, central domain; InterPro: IPR014026 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents an alpha helical region that serves as the dimerisation interface for these enzymes [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 2O3J_A 3OJO_A 3OJL_A 3PLR_A 3PJG_A 3PID_A 3PLN_A 3PHL_A 3TDK_B 2Q3E_A ....
Probab=30.71 E-value=45 Score=21.33 Aligned_cols=17 Identities=29% Similarity=0.419 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHhcC
Q psy14675 46 EAFGFMTRTALLAEKMD 62 (105)
Q Consensus 46 ~a~~fv~~Va~~ae~~~ 62 (105)
.=+.|+|.++.+|++.+
T Consensus 17 ~~iaf~Nel~~lce~~g 33 (96)
T PF00984_consen 17 TKIAFANELARLCEKLG 33 (96)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 34789999999999875
No 34
>PF14267 DUF4357: Domain of unknown function (DUF4357)
Probab=30.54 E-value=71 Score=18.53 Aligned_cols=21 Identities=24% Similarity=0.350 Sum_probs=16.7
Q ss_pred CccEEEEEEeCChHHHHHHHH
Q psy14675 32 RDAIYKEYLFKNFNEAFGFMT 52 (105)
Q Consensus 32 ~~~L~r~f~f~~f~~a~~fv~ 52 (105)
...+.+.|.|.+...|..||-
T Consensus 16 ~~~f~~d~~F~SPS~AA~~v~ 36 (55)
T PF14267_consen 16 RLVFTQDYLFSSPSAAAAVVL 36 (55)
T ss_pred cEEEecCeEcCChHHHHHHHc
Confidence 346788999999999888763
No 35
>PF14510 ABC_trans_N: ABC-transporter extracellular N-terminal
Probab=29.58 E-value=1.2e+02 Score=18.59 Aligned_cols=35 Identities=11% Similarity=0.024 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHhcCCCc-eeEeecCEEEEEEEc
Q psy14675 46 EAFGFMTRTALLAEKMDHHP-EWFNVYNKVQVTLST 80 (105)
Q Consensus 46 ~a~~fv~~Va~~ae~~~HHP-~i~~~~~~V~v~l~T 80 (105)
+...|+..+-..+++.+.|| .+.+.|..++|.=.-
T Consensus 35 dl~~~lr~~~~~~~~~g~~~r~~GV~fknLtV~G~g 70 (85)
T PF14510_consen 35 DLRRWLRNFVRRAEEQGIKPRKAGVSFKNLTVYGVG 70 (85)
T ss_pred cHHHHHHHHHHHHHhCCCCCCeEEEEEeCCeEEEEe
Confidence 66778888888888887554 677888887776433
No 36
>PF09559 Cas6: Cas6 Crispr; InterPro: IPR014174 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this entry resemble the Cas6 proteins described by IPR010156 from INTERPRO in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis (strain ATCC 29413/PCC 7937), Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus (strain DK 1622). Oddly, an orphan member is found in Thiobacillus denitrificans (strain ATCC 25259), whose genome does not seem to contain other evidence of CRISPR repeats or cas genes.
Probab=29.50 E-value=2.1e+02 Score=20.97 Aligned_cols=46 Identities=7% Similarity=0.159 Sum_probs=35.6
Q ss_pred cEEEEE-EeCChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEE
Q psy14675 34 AIYKEY-LFKNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLS 79 (105)
Q Consensus 34 ~L~r~f-~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~ 79 (105)
.|..++ .++.+.+-..|+..++..-++.+-++...+-+++-+|...
T Consensus 104 ~L~aR~V~~~~~~de~~FL~~a~rqL~~l~I~~~~~l~G~r~tl~~~ 150 (195)
T PF09559_consen 104 TLFARLVVIKGYQDEESFLEAAQRQLEALGIQGRKALCGRRRTLKIP 150 (195)
T ss_pred ceeEEEEeccCCCCHHHHHHHHHHHHHhccCcceEeeccceeEEeeC
Confidence 454444 5888999999999999999999999987765555555443
No 37
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=28.87 E-value=50 Score=23.98 Aligned_cols=21 Identities=24% Similarity=0.275 Sum_probs=19.2
Q ss_pred CCCcCCCCCCHHHHHhhhcCC
Q psy14675 1 MSASASVKLSADERLSKLEPI 21 (105)
Q Consensus 1 ~~~~~~~~Lt~~ei~~~L~~l 21 (105)
+|.|.+++||-+|+-+++.+-
T Consensus 30 ~S~GNPT~lsG~elV~lIk~a 50 (180)
T PF14097_consen 30 QSAGNPTPLSGEELVELIKQA 50 (180)
T ss_pred ccCCCCCcCCHHHHHHHHHhC
Confidence 689999999999999999876
No 38
>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=28.66 E-value=56 Score=27.44 Aligned_cols=29 Identities=24% Similarity=0.440 Sum_probs=24.4
Q ss_pred cCEEEEEEEcCCCCCCCHHHHHHHHHHHH
Q psy14675 71 YNKVQVTLSTHDCNGLSNKDIKLASFMDT 99 (105)
Q Consensus 71 ~~~V~v~l~Th~~~glT~~D~~LA~~id~ 99 (105)
-..|.+++-.-.+|++|+.|+.||+..+.
T Consensus 331 ~~~v~~~i~~~~VG~ite~DV~lA~as~a 359 (509)
T COG0532 331 VDEVKVRIIHAGVGGITESDVMLAAASDA 359 (509)
T ss_pred CCceEEEEEEeecCCCChhhHHHHHhcCC
Confidence 35688888888999999999999987653
No 39
>PF06864 PAP_PilO: Pilin accessory protein (PilO); InterPro: IPR009663 This family consists of several enterobacterial PilO proteins. The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body []. This family does not seem to be related to IPR007445 from INTERPRO.
Probab=28.60 E-value=3e+02 Score=21.91 Aligned_cols=73 Identities=18% Similarity=0.226 Sum_probs=49.6
Q ss_pred CCCEEec---CCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeEe--ecC--EEEEEEEcCCC------CCCCHHH
Q psy14675 24 SGWKLVE---NRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWFN--VYN--KVQVTLSTHDC------NGLSNKD 90 (105)
Q Consensus 24 ~gW~~~~---~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~~--~~~--~V~v~l~Th~~------~glT~~D 90 (105)
.||++.. .+..++-+|.-..-....+|..+|..+- +.-|.+.+ +++ .|.+-++.... ..|-+.+
T Consensus 248 aGW~l~~a~C~~~~~~~~y~r~~g~Tv~dF~~~~~~l~---~~~p~f~~~~gg~~a~~~~p~~~~~~~~~~~de~l~~~~ 324 (414)
T PF06864_consen 248 AGWRLTSAECDPDGLRLTYSRTPGATVADFIRRVRELF---GDTPVFNLDDGGNQASVFLPFTFTAPPTPAGDEALPPAS 324 (414)
T ss_pred CCeeeeeEEEcCCcEEEEEecCCCCcHHHHHHHHHHHh---cCCCeEEecCCCceEEEEEeecccCCCCCCCCCCCCCHH
Confidence 7999985 2357899999988889999999988776 78898765 223 45555522221 1355566
Q ss_pred HHHHHHHHH
Q psy14675 91 IKLASFMDT 99 (105)
Q Consensus 91 ~~LA~~id~ 99 (105)
..|.+.++-
T Consensus 325 ~~l~~l~s~ 333 (414)
T PF06864_consen 325 EQLMRLTSH 333 (414)
T ss_pred HHHHHHHHH
Confidence 666666654
No 40
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=28.04 E-value=1.2e+02 Score=18.52 Aligned_cols=34 Identities=24% Similarity=0.396 Sum_probs=23.5
Q ss_pred CCCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeC
Q psy14675 5 ASVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFK 42 (105)
Q Consensus 5 ~~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~ 42 (105)
..++++..|+...|+.+ ||.+.... +=.+.|+-+
T Consensus 3 ~lp~~~~ke~ik~Le~~---Gf~~vrqk-GSH~q~kHp 36 (66)
T COG1724 3 KLPRMKAKEVIKALEKD---GFQLVRQK-GSHRQYKHP 36 (66)
T ss_pred cCCcCCHHHHHHHHHhC---CcEEEEee-cceeEEEcC
Confidence 35789999999999886 99886431 234445433
No 41
>cd01586 AcnA_IRP Aconitase A catalytic domain. Aconitase A catalytic domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydrolyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes.
Probab=27.72 E-value=1.1e+02 Score=24.92 Aligned_cols=39 Identities=21% Similarity=0.142 Sum_probs=30.0
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+---|-|......+.|+|+=.-..|+|.+|++|+
T Consensus 148 e~~~~ma~~~~~~~vP~~i~V~l~G~l~~gVtaKDviL~ 186 (404)
T cd01586 148 EAEAVMLGQPISMLLPEVVGVKLTGKLRPGVTATDLVLT 186 (404)
T ss_pred HHHHHHhCCccccCCCcEEEEEEEeecCCCcCHHHHHHH
Confidence 344445556666677889999997777789999999986
No 42
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=27.69 E-value=2.7e+02 Score=20.92 Aligned_cols=68 Identities=10% Similarity=0.110 Sum_probs=47.2
Q ss_pred HHHhhhcCCCCCCCEEecCCccEEEEEEeC---ChHHHHHHHHHHHHHHHhcCCCceeE-------eecCEEEEEEEcCC
Q psy14675 13 ERLSKLEPILKSGWKLVENRDAIYKEYLFK---NFNEAFGFMTRTALLAEKMDHHPEWF-------NVYNKVQVTLSTHD 82 (105)
Q Consensus 13 ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~---~f~~a~~fv~~Va~~ae~~~HHP~i~-------~~~~~V~v~l~Th~ 82 (105)
.+.+.|..+.-++|-...|+.+|+=-.... +|.++..|...||...++. ||+.. .+.++|.|.+.=+.
T Consensus 122 ~~r~~L~~lgL~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~--~P~~~t~~~~k~~R~gkvfiDylqN~ 199 (227)
T cd04862 122 LVRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLART--NPDRFVATMGKAKRVGKIFIDYLRNG 199 (227)
T ss_pred HHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH--CchhhhHHhhHHhCCCcEEEECccCC
Confidence 345566655337787777777776555544 5899999999999988776 89864 24677877774433
No 43
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=27.45 E-value=82 Score=22.25 Aligned_cols=86 Identities=13% Similarity=0.156 Sum_probs=50.5
Q ss_pred CCCHHHHHhhhcCCC-CCCCEEecCCccEEEEEEeCChHHHHHHHHHH------HHHHHhcCCCceeEeecCEEEEEEEc
Q psy14675 8 KLSADERLSKLEPIL-KSGWKLVENRDAIYKEYLFKNFNEAFGFMTRT------ALLAEKMDHHPEWFNVYNKVQVTLST 80 (105)
Q Consensus 8 ~Lt~~ei~~~L~~l~-~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~V------a~~ae~~~HHP~i~~~~~~V~v~l~T 80 (105)
.|+.++....|..+- .+-| .. .+...=.|.|+.+-..-+..+ ....+...+||+|.-.-.... .+
T Consensus 13 ~l~~~~f~~~l~~~~e~~~W-a~----~~~~~RPf~s~~~L~~a~~~~~~~~~~~~~~~~l~~HP~lg~~~~~~~---S~ 84 (166)
T PRK13798 13 ALPERQAVHALFECCHSTAW-AR----RLAAARPFADHDALLAAADEALAGLSEADIDEALAGHPRIGERPASKA---SA 84 (166)
T ss_pred CCCHHHHHHHHHHHhcChHH-HH----HHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhCCcccCcccccc---CH
Confidence 677888777776652 2558 42 233334688887666555554 334556789999975321111 55
Q ss_pred CCCCCCCHHHHHHHHHHHHHh
Q psy14675 81 HDCNGLSNKDIKLASFMDTII 101 (105)
Q Consensus 81 h~~~glT~~D~~LA~~id~~~ 101 (105)
+...||...|-...+++.++.
T Consensus 85 ~EQ~gl~~l~~~~~~~l~~lN 105 (166)
T PRK13798 85 REQAGVADADEAVMAALAAGN 105 (166)
T ss_pred HHhcccccCCHHHHHHHHHHH
Confidence 555677666555555555544
No 44
>PRK12466 isopropylmalate isomerase large subunit; Provisional
Probab=27.32 E-value=1.6e+02 Score=24.46 Aligned_cols=39 Identities=15% Similarity=0.188 Sum_probs=31.3
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+---|-|......|.|+|+=.-..|+|.+|++|.
T Consensus 150 d~~~~l~tg~~~~~vPetv~V~l~G~l~~gV~aKDviL~ 188 (471)
T PRK12466 150 EVEHVLATQTLVYRKPKTMRVRVDGELPPGVTAKDLILA 188 (471)
T ss_pred HHHHHHhCCeEEeeCCcEEEEEEEcccCCCcCHHHHHHH
Confidence 445555566777778889999997777789999999986
No 45
>PRK00402 3-isopropylmalate dehydratase large subunit; Reviewed
Probab=26.78 E-value=1.5e+02 Score=24.16 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=30.3
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+--.+-|......|.|+|+=.-..|+|.+|++|.
T Consensus 141 d~~~~l~tg~~~~~vPe~v~V~l~G~l~~gV~akDviL~ 179 (418)
T PRK00402 141 DMAAAMATGKTWFKVPETIKVVLEGKLPPGVTAKDVILH 179 (418)
T ss_pred HHHHHHhcCcEEEcCCCEEEEEEEeecCCCcCHHHHHHH
Confidence 334444456777778899999997777789999999885
No 46
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=26.78 E-value=39 Score=29.72 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=22.4
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHHH
Q psy14675 73 KVQVTLSTHDCNGLSNKDIKLASFMD 98 (105)
Q Consensus 73 ~V~v~l~Th~~~glT~~D~~LA~~id 98 (105)
.|.+.+-...+|++|+.|+.||...+
T Consensus 614 ~v~~~i~~~~vG~it~~Dv~la~~~~ 639 (787)
T PRK05306 614 EVKVNIIHSGVGAITESDVTLAAASN 639 (787)
T ss_pred CCceEEEeeccCCCCHHHHHHHHhcC
Confidence 47788888889999999999998754
No 47
>PF00330 Aconitase: Aconitase family (aconitate hydratase); InterPro: IPR001030 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. 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family []. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [, ]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis []. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. This entry represents a region containing 3 domains, each with a 3-layer alpha/beta/alpha topology. This regions represents the [4Fe-4S] cluster-binding region found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB. This domain is also found in the large subunit of isopropylmalate dehydratase (LeuC). More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0008152 metabolic process; PDB: 1L5J_B 1B0M_A 1B0J_A 1B0K_A 7ACN_A 6ACN_A 5ACN_A 3SNP_B 3SN2_A 2B3Y_A ....
Probab=26.57 E-value=1.4e+02 Score=24.55 Aligned_cols=40 Identities=30% Similarity=0.445 Sum_probs=26.3
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLAS 95 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~ 95 (105)
+++..+---|-|......|.|+|+=.-..|+|.+|++|+-
T Consensus 149 d~a~~l~tg~~~~~vPetv~V~l~G~l~~gV~aKDviL~i 188 (465)
T PF00330_consen 149 DVAAALATGPLWFRVPETVRVELTGKLPPGVTAKDVILHI 188 (465)
T ss_dssp HHHHHHCTSBEEEE--EEEEEEEES---TT--HHHHHHHH
T ss_pred HHHHHHHhhhhccccCceEEEEEEecCCCCccHHHHHHHH
Confidence 4555566678788889999999977777899999999864
No 48
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=26.54 E-value=44 Score=23.30 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=13.5
Q ss_pred CCCCHHHHHhhhcCCCCCCCEEec
Q psy14675 7 VKLSADERLSKLEPILKSGWKLVE 30 (105)
Q Consensus 7 ~~Lt~~ei~~~L~~l~~~gW~~~~ 30 (105)
.+||++|+...|.. .|.++..
T Consensus 85 rpLTDEELD~mLPs---eGYkIl~ 105 (144)
T PF08920_consen 85 RPLTDEELDAMLPS---EGYKILE 105 (144)
T ss_dssp S-S-HHHHHHTS-----SSEEE--
T ss_pred CcCCHHHHHHhCCc---CCcEEcC
Confidence 58999999999964 6998875
No 49
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.14 E-value=72 Score=20.82 Aligned_cols=27 Identities=26% Similarity=0.514 Sum_probs=20.4
Q ss_pred CHHHHHhhhcCCCCCCCEEecCCccEEEEE
Q psy14675 10 SADERLSKLEPILKSGWKLVENRDAIYKEY 39 (105)
Q Consensus 10 t~~ei~~~L~~l~~~gW~~~~~~~~L~r~f 39 (105)
+.+-|.+.|..+ ||.+...++.|...|
T Consensus 13 ~~dri~~~l~e~---g~~v~~eGD~ivas~ 39 (96)
T COG4004 13 DPDRIMRGLSEL---GWTVSEEGDRIVASS 39 (96)
T ss_pred CHHHHHHHHHHh---CeeEeecccEEEEec
Confidence 567789999887 899987666665544
No 50
>PF14814 UB2H: Bifunctional transglycosylase second domain; PDB: 3FWL_A 3VMA_A.
Probab=25.65 E-value=84 Score=19.43 Aligned_cols=38 Identities=21% Similarity=0.209 Sum_probs=19.5
Q ss_pred CCCCHHHHHhhhcCC--------CCCCC-EEecCC-ccEEEEEEeCCh
Q psy14675 7 VKLSADERLSKLEPI--------LKSGW-KLVENR-DAIYKEYLFKNF 44 (105)
Q Consensus 7 ~~Lt~~ei~~~L~~l--------~~~gW-~~~~~~-~~L~r~f~f~~f 44 (105)
.+||.+++...|+.| ..||+ ...++. .-.+|.|.|++-
T Consensus 5 ~~ls~~~l~~eL~~LgYR~v~~~~~pG~y~~~g~~i~i~~R~F~F~Dg 52 (85)
T PF14814_consen 5 APLSPAQLEQELELLGYRKVSNPDRPGEYSRSGNRIEIYTRGFDFPDG 52 (85)
T ss_dssp -S--HHHHHHHHHHTT-EE-SS--STTEEEEETTEEEEEE--EEETTC
T ss_pred cccCHHHHHHHHHHcCCCcCCCCCCCeEEEEECCEEEEEECCCCCCCC
Confidence 478999999998865 11332 222221 233899999874
No 51
>cd01583 IPMI 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate. Aconatase-like catalytic domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes.
Probab=25.33 E-value=1.7e+02 Score=23.53 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=29.7
Q ss_pred HHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 57 LAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 57 ~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
++..+---+-|.-....+.|+|+=.-..|+|.+|++|.
T Consensus 113 ~a~~latg~~w~~vPeti~v~l~G~l~~gV~aKDviL~ 150 (382)
T cd01583 113 VAHVLATGKLWFRVPETMRVNVEGKLPPGVTAKDVILY 150 (382)
T ss_pred HHHHHhcCCeeeeCCcEEEEEEEeecCCCcCHHHHHHH
Confidence 34444455667778899999997777789999999995
No 52
>TIGR00170 leuC 3-isopropylmalate dehydratase, large subunit. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are now described by a separate model of subfamily (rather than equivalog) homology type, and the priors and cutoffs for this model have been changed to focus this equivalog family more narrowly.
Probab=25.17 E-value=1.6e+02 Score=24.38 Aligned_cols=38 Identities=16% Similarity=0.193 Sum_probs=29.6
Q ss_pred HHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 57 LAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 57 ~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
++..+---|-|......|.|+|+=.-..|+|.+|++|+
T Consensus 149 ~~~~l~tg~~~~~vPe~v~V~l~G~l~~gV~aKDviL~ 186 (465)
T TIGR00170 149 VEHVLATQTLKQARAKTMKIEVDGKLAPGITAKDIILA 186 (465)
T ss_pred HHHHHhCCcEeccCCCEEEEEEEeecCCCcCHHHHHHH
Confidence 34444456667777889999997777789999999986
No 53
>TIGR00487 IF-2 translation initiation factor IF-2. This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.
Probab=25.08 E-value=53 Score=27.74 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=22.4
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHHH
Q psy14675 73 KVQVTLSTHDCNGLSNKDIKLASFMD 98 (105)
Q Consensus 73 ~V~v~l~Th~~~glT~~D~~LA~~id 98 (105)
.|.+.+-..++|.+|+.|+.||...+
T Consensus 412 ~~~~~v~~~~vG~i~~~Dv~~a~~~~ 437 (587)
T TIGR00487 412 EVKVKVIHSGVGGITETDISLASASN 437 (587)
T ss_pred CCeEEEEEeecCCCchhhHHHHHhcC
Confidence 46788888889999999999998764
No 54
>cd01585 AcnA_Bact Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Bacterial Aconitase-like catalytic domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This distinct subfamily is found only in bacteria and Archaea. Its exact characteristics are not known.
Probab=25.07 E-value=1.7e+02 Score=23.67 Aligned_cols=39 Identities=23% Similarity=0.181 Sum_probs=30.3
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+---+-|......|.|+++=.-..|+|.+|++|+
T Consensus 110 d~~~~latg~~~~~vPetv~V~l~G~l~~gV~aKDviL~ 148 (380)
T cd01585 110 DVALAMAGEPYYIPMPKVVGVRLTGELPPWVTAKDVILE 148 (380)
T ss_pred HHHHHHhCCeEeccCCcEEEEEEEccCCCCcCHHHHHHH
Confidence 344445556667777889999997777789999999984
No 55
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=24.42 E-value=78 Score=23.33 Aligned_cols=54 Identities=15% Similarity=0.191 Sum_probs=34.3
Q ss_pred CCCCCHHHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHhcCCCceeE
Q psy14675 6 SVKLSADERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEKMDHHPEWF 68 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~~~HHP~i~ 68 (105)
.+|||.+++.+.+..+ ..|++..+. |-..=.|...-.+.+.++++++.. +|+|.
T Consensus 146 l~Pl~~~~a~~mi~~l--~~~~lL~G~----RG~p~~d~~al~~~l~~ls~l~~~---~p~I~ 199 (222)
T PF13549_consen 146 LPPLSEADAREMIREL--RAYPLLRGY----RGRPPADLDALADLLVRLSQLAAD---LPEIA 199 (222)
T ss_dssp ESS--HHHHHHHHHTS--TTHHHHH-----------B-HHHHHHHHHHHHHHHHH---TTTEE
T ss_pred eCCCCHHHHHHHHHHH--HhHHhhccc----CCCCCcCHHHHHHHHHHHHHHHHh---CCCEE
Confidence 4699999999999998 788876531 222224567777888888888774 57763
No 56
>cd08871 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD10 (also known as CGI-52, PTCP-like, and SDCCAG28). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD10 binds phophatidylcholine and phosphatidylethanolamine. This protein is widely expressed and is synthesized constitutively in many organs. It may function in the liver in the export of phospholipids into bile. It is concentrated in the sperm flagellum, and may play a role in energy metabolism. In the mammary gland it may participate in the enrichment of lipids in milk, and be a potential marker of differentiation. Its expression is induced in this gland during gestation and lactation. It is overe
Probab=24.21 E-value=87 Score=22.46 Aligned_cols=27 Identities=15% Similarity=0.044 Sum_probs=20.9
Q ss_pred cCCCCCCHHHHHhhhcCCCC-CCCEEec
Q psy14675 4 SASVKLSADERLSKLEPILK-SGWKLVE 30 (105)
Q Consensus 4 ~~~~~Lt~~ei~~~L~~l~~-~gW~~~~ 30 (105)
|..+|.|+++.+.+++.+.. +||++..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~W~~~~ 29 (222)
T cd08871 2 GEVRLPTDADFEEFKKLCDSTDGWKLKY 29 (222)
T ss_pred CeecCCCHHHHHHHHHHhcCCCCcEEEE
Confidence 55679999999988877632 6899873
No 57
>TIGR02083 LEU2 3-isopropylmalate dehydratase, large subunit. This model along with TIGR00170 describe clades which consist only of LeuC sequences. Here, the genes from Pyrococcus furiosus, Clostridium acetobutylicum, Thermotoga maritima and others are gene clustered with related genes from the leucine biosynthesis pathway.
Probab=24.01 E-value=1.8e+02 Score=23.88 Aligned_cols=38 Identities=24% Similarity=0.297 Sum_probs=29.3
Q ss_pred HHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHH
Q psy14675 58 AEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLAS 95 (105)
Q Consensus 58 ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~ 95 (105)
+..+---+-|......|.|+++=.-..|+|.+|++|+-
T Consensus 143 a~~latg~~w~~vPetv~v~l~G~l~~gV~aKDviL~l 180 (419)
T TIGR02083 143 AVGMATGKAWFRVPEAIKFVLKGKLKPWVTGKDLILHI 180 (419)
T ss_pred HHHHhcCCeeecCCCEEEEEEEeecCCCcCHHHHHHHH
Confidence 33444456666778999999977778899999999864
No 58
>cd01582 Homoaconitase Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase catalytic domain. Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases.
Probab=23.74 E-value=1.8e+02 Score=23.38 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=24.3
Q ss_pred ceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 65 PEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 65 P~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+-|......+.|+|+=.-..|+|.+|++|+
T Consensus 119 ~~w~~vPe~i~v~l~G~l~~gV~aKDviL~ 148 (363)
T cd01582 119 QTWWQIPPVAKVELKGQLPKGVTGKDVIVA 148 (363)
T ss_pred CeeecCCCEEEEEEecccCCCCCHHHHHHH
Confidence 335555789999997777789999999886
No 59
>PRK07229 aconitate hydratase; Validated
Probab=23.48 E-value=1.8e+02 Score=25.13 Aligned_cols=39 Identities=26% Similarity=0.199 Sum_probs=31.4
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+---|-|......|.|+|+=.-..|+|.+|++|+
T Consensus 139 d~~~~m~~g~~~~~vPe~v~V~l~G~l~~gV~akDviL~ 177 (646)
T PRK07229 139 DVALAMAGGPYYLKMPKVVGVKLTGKLPPWVSAKDVILE 177 (646)
T ss_pred HHHHHHhcCcEEccCCCEEEEEEEccCCCCcCHHHHHHH
Confidence 445556667777778899999997777779999999886
No 60
>TIGR01342 acon_putative aconitate hydratase, putative, Aquifex type. This model represents a small family of proteins homologous (and likely functionally equivalent to) aconitase 1. Members are found, so far in the anaerobe Clostridium acetobutylicum, in the microaerophilic, early-branching bacterium Aquifex aeolicus, and in the halophilic archaeon Halobacterium sp. NRC-1. No member is experimentally characterized.
Probab=23.37 E-value=1.6e+02 Score=25.41 Aligned_cols=40 Identities=23% Similarity=0.127 Sum_probs=31.6
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLAS 95 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~ 95 (105)
+++..+---|-|......|.|+|+=.-..|+|.+|++|+-
T Consensus 136 d~a~~matg~~~~~vPe~i~V~l~G~l~~gV~aKDviL~i 175 (658)
T TIGR01342 136 DIAAAMAGEAFYLEMPEIVGVHLEGELPEWATAKDIILEL 175 (658)
T ss_pred HHHHHHhCCcEEccCCcEEEEEEecccCCCcCHHHHHHHH
Confidence 4455555667777788999999977777899999999863
No 61
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.67 E-value=99 Score=20.39 Aligned_cols=48 Identities=15% Similarity=0.279 Sum_probs=33.2
Q ss_pred CChHHHHHHHHHHHHHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHHHHHHH
Q psy14675 42 KNFNEAFGFMTRTALLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLASFMDT 99 (105)
Q Consensus 42 ~~f~~a~~fv~~Va~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA~~id~ 99 (105)
++-.++.+++. |-.....|...+.+..|.|. -.-+++.|..+|.+|.+
T Consensus 23 PtsKdt~eWLe-----aalkRKyp~~~F~~~YiDI~-----n~~~e~~~~~~aekI~~ 70 (106)
T COG4837 23 PTSKDTYEWLE-----AALKRKYPNQPFKYTYIDIT-----NPPLEDHDLQFAEKIEQ 70 (106)
T ss_pred CcchhHHHHHH-----HHHhccCCCCCcEEEEEEcC-----CCccHHHHHHHHHHHhc
Confidence 33445555443 33456788888888888775 34689999999999863
No 62
>PRK05478 isopropylmalate isomerase large subunit; Validated
Probab=22.55 E-value=1.9e+02 Score=23.95 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=30.9
Q ss_pred HHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 56 LLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 56 ~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+++..+---|-|......|.|+|+=.-..|+|.+|++|.
T Consensus 148 d~a~~m~tg~~~~~vPe~i~V~l~G~l~~gV~aKDviL~ 186 (466)
T PRK05478 148 EVEHVLATQTLLQKKPKTMKIEVDGKLPPGVTAKDIILA 186 (466)
T ss_pred HHHHHHhCCcEeccCCCEEEEEEEeecCCCcCHHHHHHH
Confidence 344555567777778899999997777789999999986
No 63
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=21.93 E-value=56 Score=18.82 Aligned_cols=22 Identities=27% Similarity=0.522 Sum_probs=17.2
Q ss_pred CCHHHHHhhhcCCCCCCCEEec
Q psy14675 9 LSADERLSKLEPILKSGWKLVE 30 (105)
Q Consensus 9 Lt~~ei~~~L~~l~~~gW~~~~ 30 (105)
...+++++.|.++-..||++..
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~ 38 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVS 38 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEE
Confidence 4567788888887678999874
No 64
>PF11353 DUF3153: Protein of unknown function (DUF3153); InterPro: IPR021499 This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=21.31 E-value=2.1e+02 Score=20.53 Aligned_cols=47 Identities=11% Similarity=-0.041 Sum_probs=34.0
Q ss_pred HHHHhhhcCCCCCCCEEecCCccEEEEEEeCChHHHHHHHHHHHHHHHh
Q psy14675 12 DERLSKLEPILKSGWKLVENRDAIYKEYLFKNFNEAFGFMTRTALLAEK 60 (105)
Q Consensus 12 ~ei~~~L~~l~~~gW~~~~~~~~L~r~f~f~~f~~a~~fv~~Va~~ae~ 60 (105)
++++..++++. +.|+.... ..+.-++.|.++.++.+.++.....+..
T Consensus 47 ~~~~~~~~~~~-~~~~~~~~-~~~~v~~~~~~~~el~~~~~~~~~~~~~ 93 (209)
T PF11353_consen 47 ESLEQRLKELG-GKVQRDSD-GEQQVTIPFLNGQELQQLLNQFFNPAGE 93 (209)
T ss_pred hHHHHHHHHhc-CcceecCC-CeEEEEecCCCHHHHHHHHHHHhhhchh
Confidence 34556666664 66885443 4788889999999999999887666544
No 65
>PF11203 DUF2984: Protein of unknown function (DUF2984); InterPro: IPR021368 This entry represents the transmembrane protein EccE found in the Actinobacteria, which are part of type VII secretion system (T7SS) [].
Probab=21.23 E-value=1.2e+02 Score=19.47 Aligned_cols=36 Identities=19% Similarity=0.299 Sum_probs=24.6
Q ss_pred CCCCCHHHHHhhhcCCC-------CCCCEEecCCccEEEEEEe
Q psy14675 6 SVKLSADERLSKLEPIL-------KSGWKLVENRDAIYKEYLF 41 (105)
Q Consensus 6 ~~~Lt~~ei~~~L~~l~-------~~gW~~~~~~~~L~r~f~f 41 (105)
..+|+.+|+.+.+..+. ...|+...++..-...|.+
T Consensus 55 a~~l~a~el~~~~~~~~~~~~~~~~E~W~~~~~~~~~~t~Y~v 97 (98)
T PF11203_consen 55 ARVLTADELPAALAALADGLPPAPRETWRGWRGGGGYHTTYWV 97 (98)
T ss_pred ceecChhhhHHHHHHhhccCCCCCCCCcceEeeCCcEEEEEEe
Confidence 45788889888887664 3578866554556666654
No 66
>TIGR01343 hacA_fam homoaconitate hydratase family protein. This model represents a subfamily of proteins consisting of aconitase, homoaconitase, 3-isopropylmalate dehydratase, and uncharacterized proteins. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterized member is Thermus thermophilus homoaconitase, an enzyme of a non-aspartate pathway of Lys biosynthesis.
Probab=21.13 E-value=2.4e+02 Score=23.05 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=32.1
Q ss_pred HHHHHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 55 ALLAEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 55 a~~ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
.+++..+--.+-|......|.|+++=.-..|++.+|++|.
T Consensus 137 td~a~~~atg~~w~~vPe~i~v~l~G~l~~gV~akDviL~ 176 (412)
T TIGR01343 137 TDIAYAIATGKTWFRVPESMKVTLTGKLNPGVTAKDVILE 176 (412)
T ss_pred HHHHHHHhcCcEeecCCcEEEEEEEcccCCCcCHHHHHHH
Confidence 3455556667778778899999997777789999999996
No 67
>cd01584 AcnA_Mitochondrial Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Mitochondrial aconitase A catalytic domain. Aconitase (also known as aconitate hydratase and citrate hydro-lyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediary product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. This is the mitochondrial form. The mitochondrial product is coded by a nuclear gene. Most members of this subfamily are mitochondrial but there are some bacterial members.
Probab=21.12 E-value=2e+02 Score=23.45 Aligned_cols=34 Identities=24% Similarity=0.137 Sum_probs=27.4
Q ss_pred cCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 61 MDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 61 ~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+--.|.+......|.|+|+=.-..|+|.+|++|.
T Consensus 123 m~g~~~~~~vPe~i~v~l~G~l~~gV~aKDliL~ 156 (412)
T cd01584 123 MAGIPWELKCPKVIGVKLTGKLSGWTSPKDVILK 156 (412)
T ss_pred HhCCeeccCCCCEEEEEEEcccCCCcCHHHHHHH
Confidence 3355655677899999997777789999999885
No 68
>PRK06703 flavodoxin; Provisional
Probab=20.36 E-value=1.8e+02 Score=19.35 Aligned_cols=43 Identities=19% Similarity=0.123 Sum_probs=21.3
Q ss_pred HHhhhcCCCCCCCEEecCCccEEEEEEe---CChHHHHHHHHHHHHHHHhc
Q psy14675 14 RLSKLEPILKSGWKLVENRDAIYKEYLF---KNFNEAFGFMTRTALLAEKM 61 (105)
Q Consensus 14 i~~~L~~l~~~gW~~~~~~~~L~r~f~f---~~f~~a~~fv~~Va~~ae~~ 61 (105)
+...|+.+ |+++... .+.-.+.- .+..++.+|..+++....++
T Consensus 105 l~~~l~~~---G~~~~~~--~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 150 (151)
T PRK06703 105 FEERLVER---GAELVQE--GLKIELAPETDEDVEKCSNFAIAFAEKFAQM 150 (151)
T ss_pred HHHHHHHC---CCEEccc--CeEEecCCCchhHHHHHHHHHHHHHHHHHhc
Confidence 44455443 6665443 23333332 34455566666666554443
No 69
>TIGR00139 h_aconitase homoaconitase. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures, but 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble leuC and leuD over their lengths but are even closer to the respective domains of homoaconitase, and their identity is uncertain.
Probab=20.25 E-value=2.1e+02 Score=25.12 Aligned_cols=37 Identities=24% Similarity=0.331 Sum_probs=28.4
Q ss_pred HHhcCCCceeEeecCEEEEEEEcCCCCCCCHHHHHHH
Q psy14675 58 AEKMDHHPEWFNVYNKVQVTLSTHDCNGLSNKDIKLA 94 (105)
Q Consensus 58 ae~~~HHP~i~~~~~~V~v~l~Th~~~glT~~D~~LA 94 (105)
+-.+---+-|......|.|+|+=.-..|+|.+|++|+
T Consensus 145 a~amatg~~w~~vPe~v~V~ltG~L~~gV~aKDviL~ 181 (712)
T TIGR00139 145 AAIWATGKTWWQIPPVAKVEFKGQLPPGVSGKDIIVA 181 (712)
T ss_pred HHHHhhCCEeccCCCEEEEEEecccCCCCCHHHHHHH
Confidence 3334444566667889999997777789999999986
Done!