Query psy8855
Match_columns 200
No_of_seqs 216 out of 2222
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 21:05:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8855.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8855hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0316 sufA Fe-S cluster asse 100.0 1.4E-35 3.1E-40 215.9 11.6 105 96-200 4-110 (110)
2 PRK09502 iscA iron-sulfur clus 100.0 4E-34 8.7E-39 209.2 11.5 104 97-200 3-107 (107)
3 TIGR02011 IscA iron-sulfur clu 100.0 9E-34 2E-38 206.7 11.4 102 99-200 4-105 (105)
4 PRK13623 iron-sulfur cluster i 100.0 9.5E-34 2.1E-38 209.8 10.5 108 93-200 6-115 (115)
5 PRK09504 sufA iron-sulfur clus 100.0 1.7E-33 3.8E-38 210.1 11.3 105 96-200 17-122 (122)
6 TIGR01997 sufA_proteo FeS asse 100.0 3E-33 6.5E-38 204.6 11.7 104 97-200 3-107 (107)
7 PLN03082 Iron-sulfur cluster a 100.0 1.1E-32 2.3E-37 214.3 10.5 105 96-200 54-162 (163)
8 TIGR00049 Iron-sulfur cluster 100.0 1.8E-31 3.9E-36 194.4 11.8 102 99-200 3-105 (105)
9 PRK11325 scaffold protein; Pro 100.0 7E-32 1.5E-36 202.9 9.3 103 1-103 1-103 (127)
10 KOG1120|consensus 100.0 8.3E-32 1.8E-36 196.2 8.7 106 95-200 28-134 (134)
11 TIGR01999 iscU FeS cluster ass 100.0 2.1E-30 4.6E-35 194.1 9.0 101 3-103 1-101 (124)
12 TIGR03419 NifU_clost FeS clust 100.0 2.7E-30 5.9E-35 192.7 9.4 97 3-103 1-98 (121)
13 PF01592 NifU_N: NifU-like N t 100.0 1.5E-29 3.3E-34 190.1 7.6 100 2-103 1-102 (126)
14 TIGR01994 SUF_scaf_2 SUF syste 99.9 6.7E-28 1.5E-32 183.5 8.9 92 2-98 4-95 (137)
15 cd06664 IscU_like Iron-sulfur 99.9 1.2E-27 2.5E-32 179.0 9.0 93 2-98 1-93 (123)
16 COG0822 IscU NifU homolog invo 99.9 1.3E-27 2.8E-32 183.9 6.8 95 1-98 5-101 (150)
17 KOG3361|consensus 99.9 3.7E-27 8.1E-32 173.3 7.9 100 2-101 28-127 (157)
18 TIGR02000 NifU_proper Fe-S clu 99.9 1.8E-26 4E-31 195.0 9.7 99 2-103 3-103 (290)
19 KOG1119|consensus 99.9 7E-25 1.5E-29 169.3 8.6 100 99-200 97-197 (199)
20 PRK11190 Fe/S biogenesis prote 99.9 2.2E-24 4.8E-29 172.2 10.7 94 97-190 2-98 (192)
21 TIGR03341 YhgI_GntY IscR-regul 99.9 1.5E-23 3.3E-28 167.3 11.2 92 99-190 4-97 (190)
22 TIGR01911 HesB_rel_seleno HesB 99.9 1.2E-23 2.7E-28 149.5 8.4 88 96-184 3-92 (92)
23 PF01521 Fe-S_biosyn: Iron-sul 99.8 1.3E-20 2.8E-25 138.5 8.4 96 99-196 6-112 (112)
24 COG4841 Uncharacterized protei 99.3 3.3E-12 7.1E-17 87.9 6.2 84 99-183 6-94 (95)
25 COG4918 Uncharacterized protei 98.4 9.8E-07 2.1E-11 62.5 6.4 86 99-186 6-94 (114)
26 COG3564 Uncharacterized protei 94.7 0.21 4.5E-06 35.5 7.0 86 98-188 9-100 (116)
27 PF05610 DUF779: Protein of un 94.4 0.18 3.8E-06 35.7 6.1 78 106-188 3-86 (95)
28 PF10437 Lip_prot_lig_C: Bacte 86.8 3.7 8E-05 28.1 6.5 42 39-83 16-57 (86)
29 PF02657 SufE: Fe-S metabolism 83.2 11 0.00024 28.0 8.0 84 5-98 16-100 (125)
30 COG3259 FrhA Coenzyme F420-red 82.8 3.9 8.4E-05 36.8 6.2 65 42-113 18-99 (441)
31 PRK09296 cysteine desufuration 82.6 5.6 0.00012 30.2 6.3 61 35-98 49-110 (138)
32 PRK15019 CsdA-binding activato 81.3 6.4 0.00014 30.2 6.2 61 35-98 59-120 (147)
33 TIGR03391 FeS_syn_CsdE cystein 81.3 6.6 0.00014 29.8 6.2 61 35-98 54-115 (138)
34 PLN02673 quinolinate synthetas 73.5 8.8 0.00019 36.6 5.9 60 35-97 127-186 (724)
35 COG4647 AcxC Acetone carboxyla 69.3 2.6 5.6E-05 31.7 1.2 21 179-199 59-80 (165)
36 COG0351 ThiD Hydroxymethylpyri 67.9 3.7 8.1E-05 34.6 2.0 37 51-90 200-236 (263)
37 TIGR03295 frhA coenzyme F420 h 62.2 33 0.00071 30.7 7.1 64 41-110 17-97 (411)
38 PF00919 UPF0004: Uncharacteri 56.8 4 8.7E-05 29.0 0.3 76 56-133 2-82 (98)
39 PF04205 FMN_bind: FMN-binding 56.4 21 0.00046 23.7 3.9 43 39-81 4-49 (81)
40 KOG3348|consensus 53.4 42 0.00091 23.3 4.8 38 102-140 4-41 (85)
41 PF10571 UPF0547: Uncharacteri 52.7 7.9 0.00017 20.7 0.9 14 186-199 11-25 (26)
42 COG2166 sufE Cysteine desulfur 52.3 45 0.00097 25.6 5.3 61 35-98 54-115 (144)
43 PTZ00493 phosphomethylpyrimidi 51.7 8.3 0.00018 33.4 1.4 45 51-98 240-284 (321)
44 cd01234 PH_CADPS CADPS (Ca2+-d 40.2 21 0.00046 25.9 1.8 20 158-177 45-64 (117)
45 PRK10334 mechanosensitive chan 39.8 44 0.00096 28.4 4.1 97 37-137 132-239 (286)
46 PRK03822 lplA lipoate-protein 39.6 1.3E+02 0.0028 26.3 6.9 44 38-84 262-305 (338)
47 COG0091 RplV Ribosomal protein 39.1 37 0.00079 25.2 3.0 36 70-112 25-61 (120)
48 PF00325 Crp: Bacterial regula 38.8 46 0.001 18.6 2.7 26 88-113 3-29 (32)
49 PF08543 Phos_pyr_kin: Phospho 37.0 7.2 0.00016 32.1 -1.2 43 52-97 190-232 (246)
50 PF07610 DUF1573: Protein of u 36.2 17 0.00036 21.8 0.7 7 189-195 18-24 (45)
51 PF14356 DUF4403: Domain of un 36.1 1.3E+02 0.0028 27.0 6.7 90 52-159 329-418 (427)
52 KOG4777|consensus 35.5 33 0.00072 29.2 2.5 39 150-188 114-152 (361)
53 PF01466 Skp1: Skp1 family, di 33.5 24 0.00053 23.7 1.2 22 68-89 34-55 (78)
54 COG5134 Uncharacterized conser 33.1 74 0.0016 26.1 4.1 51 105-158 60-112 (272)
55 TIGR00545 lipoyltrans lipoyltr 32.6 78 0.0017 27.4 4.5 44 38-84 257-300 (324)
56 TIGR01044 rplV_bact ribosomal 32.4 54 0.0012 23.4 2.9 20 71-90 14-33 (103)
57 cd00336 Ribosomal_L22 Ribosoma 32.1 51 0.0011 23.3 2.8 20 71-90 16-35 (105)
58 PRK12540 RNA polymerase sigma 32.0 80 0.0017 24.4 4.1 49 76-124 124-178 (182)
59 PF11604 CusF_Ec: Copper bindi 30.1 85 0.0018 20.6 3.4 24 34-57 42-67 (70)
60 smart00704 ZnF_CDGSH CDGSH-typ 30.0 22 0.00047 20.8 0.4 20 180-199 5-24 (38)
61 PF03952 Enolase_N: Enolase, N 29.7 1.7E+02 0.0036 21.9 5.3 69 37-112 14-94 (132)
62 COG2345 Predicted transcriptio 27.2 1.4E+02 0.0031 24.5 4.8 47 89-139 27-75 (218)
63 PRK10170 hydrogenase 1 large s 26.8 2.3E+02 0.0049 26.9 6.7 42 41-89 31-72 (597)
64 PF12637 TSCPD: TSCPD domain; 26.8 1.8E+02 0.0039 20.3 4.8 47 36-87 6-62 (95)
65 PRK14061 unknown domain/lipoat 26.5 4.5E+02 0.0098 24.8 8.5 44 38-84 486-529 (562)
66 PF03450 CO_deh_flav_C: CO deh 26.1 2.3E+02 0.0049 19.6 5.6 43 42-84 19-61 (103)
67 COG0537 Hit Diadenosine tetrap 26.0 2.8E+02 0.0061 20.6 6.6 57 80-140 44-104 (138)
68 PF02593 dTMP_synthase: Thymid 25.9 1E+02 0.0022 25.2 3.8 44 42-90 134-178 (217)
69 cd04482 RPA2_OBF_like RPA2_OBF 25.6 1.9E+02 0.0042 19.9 4.7 39 140-187 47-86 (91)
70 PF13103 TonB_2: TonB C termin 25.3 1.3E+02 0.0028 19.8 3.8 22 39-60 26-47 (85)
71 PRK09642 RNA polymerase sigma 24.6 1.1E+02 0.0024 22.7 3.6 35 78-112 121-156 (160)
72 TIGR02588 conserved hypothetic 24.5 3E+02 0.0065 20.5 7.2 27 162-188 80-109 (122)
73 cd03063 TRX_Fd_FDH_beta TRX-li 24.5 48 0.001 23.3 1.4 24 104-131 21-44 (92)
74 PF03544 TonB_C: Gram-negative 24.4 1.1E+02 0.0025 19.6 3.3 20 40-59 17-36 (79)
75 TIGR01962 NuoD NADH dehydrogen 24.3 3.1E+02 0.0068 24.3 6.9 18 41-59 18-35 (386)
76 PRK08176 pdxK pyridoxal-pyrido 24.1 48 0.001 27.7 1.7 41 55-98 225-265 (281)
77 PF09012 FeoC: FeoC like trans 23.9 1.2E+02 0.0026 19.6 3.2 28 87-114 14-42 (69)
78 PRK06075 NADH dehydrogenase su 23.8 3.2E+02 0.007 24.3 6.9 18 41-59 22-39 (392)
79 PF10083 DUF2321: Uncharacteri 23.6 94 0.002 24.1 3.0 76 35-114 43-135 (158)
80 cd01169 HMPP_kinase 4-amino-5- 23.1 48 0.001 26.6 1.4 41 53-96 198-238 (242)
81 PRK12412 pyridoxal kinase; Rev 23.0 48 0.001 27.5 1.4 36 59-97 209-244 (268)
82 PRK07217 replication factor A; 22.7 4.5E+02 0.0098 22.8 7.3 62 40-121 216-278 (311)
83 COG3369 Zinc finger domain con 22.7 32 0.0007 23.4 0.3 10 190-199 32-41 (78)
84 PRK09645 RNA polymerase sigma 22.5 1.3E+02 0.0028 22.6 3.7 36 77-112 132-168 (173)
85 TIGR03829 YokU_near_AblA uncha 22.5 1.2E+02 0.0027 21.2 3.2 19 179-198 26-45 (89)
86 PRK10467 hydrogenase 2 large s 21.8 3.2E+02 0.007 25.8 6.7 41 40-88 16-56 (567)
87 PF02575 YbaB_DNA_bd: YbaB/Ebf 21.3 95 0.0021 21.2 2.5 22 40-63 31-52 (93)
88 PF14410 GH-E: HNH/ENDO VII su 21.1 76 0.0017 21.0 1.8 20 4-24 43-62 (70)
89 PRK05756 pyridoxamine kinase; 21.0 46 0.001 27.8 1.0 39 57-98 216-254 (286)
90 PRK09643 RNA polymerase sigma 20.8 1.5E+02 0.0032 23.1 3.8 38 77-114 148-186 (192)
91 PF11720 Inhibitor_I78: Peptid 20.7 1E+02 0.0022 19.6 2.3 17 39-57 42-58 (60)
92 PRK12511 RNA polymerase sigma 20.6 2.1E+02 0.0046 22.1 4.6 45 77-121 125-173 (182)
93 PRK12616 pyridoxal kinase; Rev 20.5 57 0.0012 27.1 1.4 37 59-98 212-248 (270)
94 PF03852 Vsr: DNA mismatch end 20.3 71 0.0015 21.7 1.6 29 131-159 36-64 (75)
95 TIGR01566 ZF_HD_prot_N ZF-HD h 20.3 42 0.00092 21.0 0.4 10 190-199 40-49 (53)
No 1
>COG0316 sufA Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-35 Score=215.86 Aligned_cols=105 Identities=43% Similarity=0.843 Sum_probs=100.3
Q ss_pred HHh-hhhhHHHHHHhhhhc-CcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeE
Q psy8855 96 ELV-TKKAAKYINKYIQKR-GKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFE 173 (200)
Q Consensus 96 ~l~-~~~a~~~i~~~l~~~-~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~ 173 (200)
.+. |++|+++++++++++ +++.+|||+|+++||+|++|.|.|++++.++|.+++.+|++|+||+++++||.|++|||+
T Consensus 4 ~itlT~~Aa~~v~~ll~~~~~~~~~lRv~V~~gGCsG~~Y~~~~~~~~~~~D~v~e~~g~~v~vD~~S~~~L~G~~IDyv 83 (110)
T COG0316 4 MITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDDEINEDDTVFEQDGVKVVVDPKSLPYLEGTEIDYV 83 (110)
T ss_pred ceeeCHHHHHHHHHHHHhccCCCceEEEEEeCCCCCCcEeEEEEcCCCCCCCEEEEeCCEEEEEChhhhhhhcCCEEEEE
Confidence 355 899999999999998 457899999999999999999999998999999999999999999999999999999999
Q ss_pred ecCCccceEEeCCCCCCCccCCCCCCC
Q psy8855 174 FDGLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 174 ~~~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
++.++++|+|+|||++++||||+||++
T Consensus 84 ~~~~g~~F~~~NPNA~~~CgCg~Sf~v 110 (110)
T COG0316 84 EDLLGSGFTFKNPNAKSSCGCGESFSV 110 (110)
T ss_pred EcCcCCceEEECCCCCccccCCCCCCC
Confidence 999999999999999999999999986
No 2
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=100.00 E-value=4e-34 Score=209.19 Aligned_cols=104 Identities=50% Similarity=1.020 Sum_probs=98.4
Q ss_pred Hh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEec
Q psy8855 97 LV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFD 175 (200)
Q Consensus 97 l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~ 175 (200)
+. ||+|+++|++++++++++.+|||+++++||+|++|.|.|+++++++|.+++.+|++|+||+.++.||+|++|||+++
T Consensus 3 i~iT~~A~~~i~~l~~~~~~~~~LRi~v~~~GCsG~~Y~l~~~~~~~~~D~~~~~~g~~v~id~~s~~~l~g~~IDy~~~ 82 (107)
T PRK09502 3 ITLSDSAAARVNTFLANRGKGFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKVVVDGKSLQFLDGTQLDFVKE 82 (107)
T ss_pred EEECHHHHHHHHHHHhCcCCCceEEEEEECCCcCCeeeEeeecCCCCCCCEEEEcCCeEEEEeHHHHhHhCCCEEEEeeC
Confidence 45 89999999999987665668999999999999999999988899999999999999999999999999999999999
Q ss_pred CCccceEEeCCCCCCCccCCCCCCC
Q psy8855 176 GLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 176 ~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
..+++|+|+|||++++||||+||++
T Consensus 83 ~~~~~F~f~NPna~~~CgCG~Sf~~ 107 (107)
T PRK09502 83 GLNEGFKFTNPNVKDECGCGESFHV 107 (107)
T ss_pred CCCceEEEECCCCCCccCCCCCeeC
Confidence 9999999999999999999999985
No 3
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=100.00 E-value=9e-34 Score=206.68 Aligned_cols=102 Identities=54% Similarity=1.044 Sum_probs=97.4
Q ss_pred hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEecCCc
Q psy8855 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFDGLN 178 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~~~~ 178 (200)
||+|+++|++++++++++.+|||+++.+||+|++|.|.|+++++++|.+++.+|++|+||+.++.||+|++|||+++..+
T Consensus 4 T~~A~~~i~~~~~~~~~~~~lRi~v~~~GCsG~~y~l~l~~~~~~~D~v~~~~g~~v~id~~s~~~l~g~~IDy~~~~~~ 83 (105)
T TIGR02011 4 TDSAAARVNTFLANRGKGFGLRLGVKTSGCSGMAYVLEFVDEPTPDDIVFEDKGVKIVIDGKSLQYLDGTQLDFVKEGLN 83 (105)
T ss_pred CHHHHHHHHHHHhccCCCceEEEEEeCCCCCCEEEEeeecCCCCCCCEEEEcCCEEEEEcHHHhHHhCCCEEEEecCCCc
Confidence 89999999999987765668999999999999999999988899999999999999999999999999999999999999
Q ss_pred cceEEeCCCCCCCccCCCCCCC
Q psy8855 179 KGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 179 ~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
++|+|+|||++++||||+||++
T Consensus 84 ~~F~~~nPna~~~CgCg~Sf~~ 105 (105)
T TIGR02011 84 EGFKFTNPNVKDECGCGESFHV 105 (105)
T ss_pred ceEEEECCCCCccCCCCCCccC
Confidence 9999999999999999999985
No 4
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=100.00 E-value=9.5e-34 Score=209.77 Aligned_cols=108 Identities=32% Similarity=0.635 Sum_probs=99.9
Q ss_pred hHHHHh-hhhhHHHHHHhhhhcC-cceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEE
Q psy8855 93 IAEELV-TKKAAKYINKYIQKRG-KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIEL 170 (200)
Q Consensus 93 i~~~l~-~~~a~~~i~~~l~~~~-~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~I 170 (200)
....+. ||+|+++|+++++.++ ++.+|||+++++||+|++|.|.+++++.++|.+++.+|++|+||+++++||+|++|
T Consensus 6 ~~~~i~iT~~A~~~i~~~~~~~~~~~~~LRi~v~~~GCsG~~y~l~l~~~~~~~D~v~e~~gv~v~id~~s~~~l~g~~I 85 (115)
T PRK13623 6 VPLPLVFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTFDEQVNEDDTTIEKQGVTLVVDPMSLQYLVGAEV 85 (115)
T ss_pred cCcceEECHHHHHHHHHHHhhCCCCceEEEEEEeCCCCCCcEEEEEECCCCCCCCEEEEcCCEEEEEcHHHHHHhCCCEE
Confidence 344567 9999999999997654 35679999999999999999999887899999999999999999999999999999
Q ss_pred EeEecCCccceEEeCCCCCCCccCCCCCCC
Q psy8855 171 DFEFDGLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 171 Dy~~~~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
||+++..+++|+|+|||++++||||+||++
T Consensus 86 Dy~~~~~~~~F~f~NPn~~~~CgCg~SF~~ 115 (115)
T PRK13623 86 DYTEGLEGSRFVIKNPNAKTTCGCGSSFSI 115 (115)
T ss_pred EeecCCCcceEEEECCCCCcCCCCCcCccC
Confidence 999999999999999999999999999986
No 5
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=100.00 E-value=1.7e-33 Score=210.14 Aligned_cols=105 Identities=40% Similarity=0.778 Sum_probs=99.2
Q ss_pred HHh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEe
Q psy8855 96 ELV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEF 174 (200)
Q Consensus 96 ~l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~ 174 (200)
.+. ||+|+++|+++++++++..+|||+++++||+|++|.|.+++++.++|.+++.+|++|+||+.++.||+|++|||++
T Consensus 17 ~I~iT~~A~~~i~~l~~~~~~~~~LRi~v~~gGCsG~~Y~~~l~~e~~~~D~v~e~~g~~v~Id~~s~~~L~g~~IDy~~ 96 (122)
T PRK09504 17 GLTLTPAAAAHIRELMAKQPGMKGVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEHDGAKLFVPLQAMPFIDGTEVDYVR 96 (122)
T ss_pred CEEECHHHHHHHHHHHhcCCCCceEEEEEECCCCCceEEEeeecCCCCCCCEEEEeCCEEEEEcHHHHHhhCCcEEEeec
Confidence 456 9999999999998766556899999999999999999998899999999999999999999999999999999999
Q ss_pred cCCccceEEeCCCCCCCccCCCCCCC
Q psy8855 175 DGLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 175 ~~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
+..+++|+|+|||++++||||+||++
T Consensus 97 ~~~~~gF~f~NPna~~~CgCG~SF~v 122 (122)
T PRK09504 97 EGLNQIFKFHNPKAQNECGCGESFGV 122 (122)
T ss_pred CCCcceEEEECCCCCCCcCCCCCeeC
Confidence 99999999999999999999999986
No 6
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=100.00 E-value=3e-33 Score=204.58 Aligned_cols=104 Identities=38% Similarity=0.836 Sum_probs=98.5
Q ss_pred Hh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEec
Q psy8855 97 LV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFD 175 (200)
Q Consensus 97 l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~ 175 (200)
+. ||+|+++|+++++++++..+|||+++++||+|++|.|.++++++++|.+++.+|++|+||+.++.||+|++|||+++
T Consensus 3 i~iT~~A~~~i~~l~~~~~~~~~lRi~v~~~GC~G~~y~~~l~~~~~~~D~v~~~~g~~v~id~~s~~~l~g~~IDy~~~ 82 (107)
T TIGR01997 3 ITLTDAAAIHIRELVAKRPEAVGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEHDGAKVFVAPEAVLFILGTQVDFVRT 82 (107)
T ss_pred EEECHHHHHHHHHHHhcCCCCcEEEEEEECCCCCCcEEEeeecCCCCCCCEEEecCCEEEEEcHHHHhhhCCCEEEEEEc
Confidence 45 89999999999987765668999999999999999999988899999999999999999999999999999999999
Q ss_pred CCccceEEeCCCCCCCccCCCCCCC
Q psy8855 176 GLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 176 ~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
..+++|+|+|||++++||||+||+.
T Consensus 83 ~~~~~F~~~NPn~~~~CgCG~Sf~~ 107 (107)
T TIGR01997 83 TLRQGFKFNNPNATSACGCGESFEL 107 (107)
T ss_pred CCcceEEEECCCCCCccCCCCCccC
Confidence 9999999999999999999999974
No 7
>PLN03082 Iron-sulfur cluster assembly; Provisional
Probab=100.00 E-value=1.1e-32 Score=214.34 Aligned_cols=105 Identities=25% Similarity=0.517 Sum_probs=98.6
Q ss_pred HHh-hhhhHHHHHHhhhhcC--cceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEe
Q psy8855 96 ELV-TKKAAKYINKYIQKRG--KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDF 172 (200)
Q Consensus 96 ~l~-~~~a~~~i~~~l~~~~--~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy 172 (200)
.+. ||+|+++|++++++++ ++.+|||+|+++||+|++|.|.|+++++++|.+++.+|++|+||+.+++||+|++|||
T Consensus 54 ~I~lTd~A~~~ik~l~~~~~~~~~~~LRl~V~~gGCSG~~Y~~~ld~~~~~~D~v~e~~Gv~vvVD~~s~~~L~Gs~IDY 133 (163)
T PLN03082 54 AVHMTDNCIRRLKELQTSEPSAEDKMLRLSVETGGCSGFQYVFELDDKTNSDDRVFEKDGVKLVVDNISYDFVKGATVDY 133 (163)
T ss_pred ceEECHHHHHHHHHHHHhCCCCCCceEEEEEecCCCCCceeeeEEccCCCCCCEEEecCCeEEEECHHHHHHhCCCEEEe
Confidence 366 9999999999998865 3568999999999999999999988888999999999999999999999999999999
Q ss_pred EecCCccceEE-eCCCCCCCccCCCCCCC
Q psy8855 173 EFDGLNKGFKF-KNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 173 ~~~~~~~~F~i-~nP~~~~~C~CG~sf~~ 200 (200)
+++..+++|+| +|||++++||||+||++
T Consensus 134 ve~l~~~gF~f~~NPna~~~CgCG~SF~v 162 (163)
T PLN03082 134 VEELIRSAFVVSTNPSAVGGCSCKSSFMV 162 (163)
T ss_pred ecCCCCCeeEEecCCCCCCCcCCCCCEeC
Confidence 99999999999 99999999999999986
No 8
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=99.97 E-value=1.8e-31 Score=194.43 Aligned_cols=102 Identities=46% Similarity=0.892 Sum_probs=96.5
Q ss_pred hhhhHHHHHHhhhhcC-cceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEecCC
Q psy8855 99 TKKAAKYINKYIQKRG-KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFDGL 177 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~-~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~~~ 177 (200)
||+|+++|+++++.++ ++.+|||+++.+||+|++|.|.|+++++++|++++.+|++|+||+++++||+|++|||+++..
T Consensus 3 T~~A~~~l~~~~~~~~~~~~~lRi~~~~~Gc~G~~~~l~l~~~~~~~D~~~~~~gi~~~id~~~~~~l~~~~IDy~~~~~ 82 (105)
T TIGR00049 3 TDSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQDGVKVVVDPKSLPYLDGSEIDYVEELL 82 (105)
T ss_pred CHHHHHHHHHHHhcCCCCceEEEEEEecCCCCCeEEEEeecCCCCCCCEEEEcCCEEEEEeHHHHhhhCCCEEEEeecCC
Confidence 7899999999998765 346899999999999999999998778899999999999999999999999999999999999
Q ss_pred ccceEEeCCCCCCCccCCCCCCC
Q psy8855 178 NKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 178 ~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
+++|+|+|||++++||||+||++
T Consensus 83 ~~~f~i~nPn~~~~c~cg~sf~~ 105 (105)
T TIGR00049 83 GSGFTFTNPNAKGTCGCGKSFSV 105 (105)
T ss_pred cceEEEECCCCCccCCCCcCccC
Confidence 99999999999999999999986
No 9
>PRK11325 scaffold protein; Provisional
Probab=99.97 E-value=7e-32 Score=202.87 Aligned_cols=103 Identities=83% Similarity=1.252 Sum_probs=94.2
Q ss_pred CcchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCC
Q psy8855 1 MSYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGK 80 (200)
Q Consensus 1 ~~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk 80 (200)
|+|+++||+||+||+|.|.|++|+...++++.+||.|||+|+|||+++++++|++++|+++||++++||||+|+++++||
T Consensus 1 ~~Y~~~il~h~~~P~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~~~~I~d~~f~~~GC~is~Asas~~~e~~~Gk 80 (127)
T PRK11325 1 MAYSEKVIDHYENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVNDEGIIEDAKFKTYGCGSAIASSSLVTEWVKGK 80 (127)
T ss_pred CccHHHHHHHHhCcCCCCCCCCCccccceEEecCCCCccEEEEEEEECCCCeEEEEEEEeeCCHHHHHHHHHHHHHHcCC
Confidence 89999999999999999999988643356778999999999999999744899999999999999999999999999999
Q ss_pred ChhHHhhhhhhhhHHHHhhhhhH
Q psy8855 81 TLDEAMSIKNTDIAEELVTKKAA 103 (200)
Q Consensus 81 ~~~ea~~l~~~~i~~~l~~~~a~ 103 (200)
|++||..|+.+++.++||+|+.+
T Consensus 81 tl~ea~~i~~~~i~~~lg~p~~r 103 (127)
T PRK11325 81 TLDEALAIKNTDIAEELALPPVK 103 (127)
T ss_pred CHHHHHhcCHHHHHHHcCCCccc
Confidence 99999999999999999866543
No 10
>KOG1120|consensus
Probab=99.97 E-value=8.3e-32 Score=196.23 Aligned_cols=106 Identities=44% Similarity=0.795 Sum_probs=101.8
Q ss_pred HHHh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeE
Q psy8855 95 EELV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFE 173 (200)
Q Consensus 95 ~~l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~ 173 (200)
..|. ||.|.++|+.+++++++...|||.|+..||+|++|.|.+..++...|.+++.+|++|+|||+++..+-|+++||+
T Consensus 28 ~~ltLTp~Av~~ik~ll~~~~e~~~lrigVk~rGCnGlsYtleY~~~kgkfDE~VeqdGv~I~ie~KA~l~liGteMDyv 107 (134)
T KOG1120|consen 28 AALTLTPSAVNHIKQLLSDKPEDVCLRIGVKQRGCNGLSYTLEYTKTKGKFDEVVEQDGVRIFIEPKALLTLIGTEMDYV 107 (134)
T ss_pred cccccCHHHHHHHHHHHHhCCcCceeEEEEecCCcCcceeeeeeeccCCCCcceeeecCcEEEEcccceeeeccceehhh
Confidence 4677 999999999999988888899999999999999999999988999999999999999999999999999999999
Q ss_pred ecCCccceEEeCCCCCCCccCCCCCCC
Q psy8855 174 FDGLNKGFKFKNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 174 ~~~~~~~F~i~nP~~~~~C~CG~sf~~ 200 (200)
++.++++|+|.|||++++||||+||++
T Consensus 108 ddkL~Sefvf~npna~gtcGcgeSf~~ 134 (134)
T KOG1120|consen 108 DDKLSSEFVFSNPNAKGTCGCGESFSV 134 (134)
T ss_pred hhhhcCceEeeCCCccccccccccccC
Confidence 999999999999999999999999985
No 11
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=99.97 E-value=2.1e-30 Score=194.14 Aligned_cols=101 Identities=73% Similarity=1.145 Sum_probs=92.5
Q ss_pred chHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCCh
Q psy8855 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTL 82 (200)
Q Consensus 3 Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~ 82 (200)
|+++|++||+||+|.|.|++|+...++++.+||.|||+|+|+|+++++++|++++|+++||++++||+|+|+++++|||+
T Consensus 1 Y~~~il~~~~~p~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~~~~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl 80 (124)
T TIGR01999 1 YSEKVLDHYENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSL 80 (124)
T ss_pred CcHHHHHHHhCCCCCCCCCCCccccceEEeCCCCCccEEEEEEEECCCCeEEEEEEEecCcHHHHHHHHHHHHHHcCCCH
Confidence 99999999999999999998864334778899999999999999975579999999999999999999999999999999
Q ss_pred hHHhhhhhhhhHHHHhhhhhH
Q psy8855 83 DEAMSIKNTDIAEELVTKKAA 103 (200)
Q Consensus 83 ~ea~~l~~~~i~~~l~~~~a~ 103 (200)
+||..|+.+++.++||+|+.+
T Consensus 81 ~ea~~i~~~~i~~~lg~p~~r 101 (124)
T TIGR01999 81 EEALKIKNTEIAKELSLPPVK 101 (124)
T ss_pred HHHHhccHHHHHHHcCCCccc
Confidence 999999999999999866544
No 12
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=99.97 E-value=2.7e-30 Score=192.74 Aligned_cols=97 Identities=57% Similarity=0.940 Sum_probs=92.2
Q ss_pred chHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCCh
Q psy8855 3 YSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTL 82 (200)
Q Consensus 3 Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~ 82 (200)
|+++||+||+||+|.|.|++|+ ++++.+||.|||+|+|+|++++ ++|++++|+++||++++||||+|+++++|||+
T Consensus 1 Y~~~il~~~~np~~~g~l~~~~---~~~~~~np~CGD~i~l~l~i~~-~~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l 76 (121)
T TIGR03419 1 YSEKVMDHFMNPRNVGEIENAD---GVGEVGNPKCGDIMKIFLKVED-DIIKDVKFKTFGCGAAIASSSMATEMIKGKTL 76 (121)
T ss_pred ChHHHHHHHhCCCCCCCCCCCC---eEEEeCCCCCccEEEEEEEEcC-CEEEEEEEEEeccHHHHHHHHHHHHHHcCCCH
Confidence 9999999999999999999887 6789999999999999999986 79999999999999999999999999999999
Q ss_pred hHHhhhhhhhhHHHHh-hhhhH
Q psy8855 83 DEAMSIKNTDIAEELV-TKKAA 103 (200)
Q Consensus 83 ~ea~~l~~~~i~~~l~-~~~a~ 103 (200)
+||..+..+++.++|+ +|+.+
T Consensus 77 ~ea~~i~~~~i~~~l~~l~~~r 98 (121)
T TIGR03419 77 EEAWELTNKAVAEALDGLPPVK 98 (121)
T ss_pred HHHHHhhhHHHHHHHcCCCccc
Confidence 9999999999999999 88654
No 13
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=99.96 E-value=1.5e-29 Score=190.11 Aligned_cols=100 Identities=48% Similarity=0.867 Sum_probs=92.2
Q ss_pred cchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccC-CcEEEEEEEecCccceeechhhhhhhhcCC
Q psy8855 2 SYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKN-GVITDAKFKTYGCGSAIASSSLVTEWVKGK 80 (200)
Q Consensus 2 ~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~-~~I~~~~f~~~GC~~~~Asas~~~~~i~gk 80 (200)
+|+++|++||+||+|.|.+++++. ++++.+||+|||.|+|+|+|+++ ++|++++|+++||++++||+|+|+++++||
T Consensus 1 ~Y~~~i~~~~~nP~~~g~l~~~~~--~~~~~~n~~CGD~i~i~l~i~~~~~~I~d~~f~~~GC~~~~Asas~~~~~i~gk 78 (126)
T PF01592_consen 1 MYSDKILDHYRNPRNYGKLEDADA--GTGEAGNPSCGDEIRIYLKIDDDGGRIKDAKFQGFGCAISIASASMMCELIKGK 78 (126)
T ss_dssp HHHHHHHHHHHSTSSBSSSTTTSS--EEEEEEETTTTEEEEEEEEESSSTSBEEEEEEEEESSHHHHHHHHHHHHHHTTS
T ss_pred CchHHHHHHHhCCCCCCCCCCCCc--ceeeecCCCCCCEEEEEEEEecCCCeEEEEEEEeecChHHHHHHHHHHHHHcCC
Confidence 599999999999999999998873 37889999999999999999975 799999999999999999999999999999
Q ss_pred ChhHHhhhhhhhhHHHHh-hhhhH
Q psy8855 81 TLDEAMSIKNTDIAEELV-TKKAA 103 (200)
Q Consensus 81 ~~~ea~~l~~~~i~~~l~-~~~a~ 103 (200)
|++||..|+.++|.++|+ +|..+
T Consensus 79 ~l~ea~~i~~~~i~~~l~~~~~~~ 102 (126)
T PF01592_consen 79 TLEEALKITAEDIEEALGGLPPER 102 (126)
T ss_dssp BHHHHHCHHHHHHHHHHTC-CGTC
T ss_pred CHHHHHHHHHHHHHHHHhccccCc
Confidence 999999999999999999 77644
No 14
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=99.95 E-value=6.7e-28 Score=183.51 Aligned_cols=92 Identities=37% Similarity=0.639 Sum_probs=84.7
Q ss_pred cchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCC
Q psy8855 2 SYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKT 81 (200)
Q Consensus 2 ~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~ 81 (200)
+|+++|++||+||+|+|.+++|+ ++++.+||.|||+|+|+|++++ ++|++++|+++||++++||||+|+++++||+
T Consensus 4 lY~~~Ileh~~~p~n~g~l~~~~---~~~~~~np~CGD~i~l~l~v~~-~~I~d~~f~~~GCais~Asas~~~e~i~Gk~ 79 (137)
T TIGR01994 4 LYRQVILDHYKNPRHRGKLEDAT---VQERGHNPTCGDEITLTVKLEG-DRIEDIAFEGEGCSISQASASMMTELIKGKT 79 (137)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCC---eeEEeCCCCCCcEEEEEEEEcC-CeEEEEEEEecccHHHHHHHHHHHHHHcCCC
Confidence 79999999999999999999887 5788999999999999999985 7999999999999999999999999999999
Q ss_pred hhHHhhhhhhhhHHHHh
Q psy8855 82 LDEAMSIKNTDIAEELV 98 (200)
Q Consensus 82 ~~ea~~l~~~~i~~~l~ 98 (200)
++|+..+... +..+|.
T Consensus 80 ~~ea~~l~~~-~~~ml~ 95 (137)
T TIGR01994 80 VEEALSLVEA-FSEMIQ 95 (137)
T ss_pred HHHHHHHHHH-HHHHHh
Confidence 9999999774 445553
No 15
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=99.95 E-value=1.2e-27 Score=179.03 Aligned_cols=93 Identities=59% Similarity=0.913 Sum_probs=87.2
Q ss_pred cchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCC
Q psy8855 2 SYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKT 81 (200)
Q Consensus 2 ~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~ 81 (200)
+|+++|++||++|+|.|.+++|+ ++++.+||.|||+|+|++++++ ++|++++|+++||++++||||+|+++++||+
T Consensus 1 ~y~~~il~~~~~p~~~g~l~~~~---~~~~~~n~~CGD~v~l~l~i~~-~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~ 76 (123)
T cd06664 1 LYSEIILDHYRNPRNVGRLEDAD---GTGEVGNPLCGDEITLYLKVED-GRITDAKFQGFGCAISIASASLLTELIKGKT 76 (123)
T ss_pred CcHHHHHHHhhCCCCCCCCCCCC---eEEEcCCCCCCceEEEEEEEcC-CEEEEEEEEecCcHHHHHHHHHHHHHHcCCc
Confidence 69999999999999999999876 6889999999999999999986 8999999999999999999999999999999
Q ss_pred hhHHhhhhhhhhHHHHh
Q psy8855 82 LDEAMSIKNTDIAEELV 98 (200)
Q Consensus 82 ~~ea~~l~~~~i~~~l~ 98 (200)
++|+..++.+.+....+
T Consensus 77 ~~ea~~i~~~~~~~~~~ 93 (123)
T cd06664 77 LDEALKLLNKDIAMLDG 93 (123)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999987776644
No 16
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.94 E-value=1.3e-27 Score=183.92 Aligned_cols=95 Identities=65% Similarity=1.021 Sum_probs=86.9
Q ss_pred CcchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCC
Q psy8855 1 MSYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGK 80 (200)
Q Consensus 1 ~~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk 80 (200)
++|+++|++||.||+|.|.+++++. ..++.++|.|||.|+++|++++ ++|+|++|+++||++++||+|+|+++++||
T Consensus 5 ~~y~~~Ildh~~np~~~g~l~~~~~--~~~~~~~~~CGD~i~l~lkv~~-~~I~d~~F~~~GC~is~ASss~~te~v~Gk 81 (150)
T COG0822 5 DLYSEKILDHYKNPRNVGVLDDADV--GVGHVGAPACGDVITLYLKVDN-GVIEDAKFKGFGCAISIASSSMMTELVKGK 81 (150)
T ss_pred HHHHHHHHHHhcCCCcCCccCccch--hccccCCCCccceEEEEEEEcC-CEEEEEEeeecCcHHHHHHHHHHHHHHcCC
Confidence 4799999999999999999998862 4556777999999999999995 899999999999999999999999999999
Q ss_pred ChhHHhhhh--hhhhHHHHh
Q psy8855 81 TLDEAMSIK--NTDIAEELV 98 (200)
Q Consensus 81 ~~~ea~~l~--~~~i~~~l~ 98 (200)
|++||..++ ..++.+.++
T Consensus 82 ti~EAl~i~~~~~~m~~~~~ 101 (150)
T COG0822 82 TLDEALKITEAFTDMAKELG 101 (150)
T ss_pred CHHHHHHHHHHHHHHHHHcC
Confidence 999999999 777777777
No 17
>KOG3361|consensus
Probab=99.94 E-value=3.7e-27 Score=173.29 Aligned_cols=100 Identities=76% Similarity=1.182 Sum_probs=96.3
Q ss_pred cchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCC
Q psy8855 2 SYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKT 81 (200)
Q Consensus 2 ~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~ 81 (200)
+|++.++|||.||||.|.|+..++.+++|-++-|.|||.|+++++++++|+|+|++|.++||...+||.|+++||++|||
T Consensus 28 lYh~~VidHy~nPRNVGSldK~dpnVGtGlVGAPACGDVMkLqIkvd~~g~I~dakFKTFGCGSAIASSS~aTewvkgkt 107 (157)
T KOG3361|consen 28 LYHENVIDHYENPRNVGSLDKNDPNVGTGLVGAPACGDVMKLQIKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVKGKT 107 (157)
T ss_pred hcchhhhhcccCccccCccCCCCCCcccccccCccccceeeEEEEECCCCcEEEeeeeecccchHhhhhHHHHHHHcccc
Confidence 69999999999999999999888889999999999999999999999889999999999999999999999999999999
Q ss_pred hhHHhhhhhhhhHHHHhhhh
Q psy8855 82 LDEAMSIKNTDIAEELVTKK 101 (200)
Q Consensus 82 ~~ea~~l~~~~i~~~l~~~~ 101 (200)
++||..|.+.+|+..|.+|+
T Consensus 108 ~dea~kIkNteIAKeL~LPP 127 (157)
T KOG3361|consen 108 LDEALKIKNTEIAKELSLPP 127 (157)
T ss_pred HHHHHhcccHHHHHhccCCc
Confidence 99999999999999888665
No 18
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=99.93 E-value=1.8e-26 Score=194.97 Aligned_cols=99 Identities=48% Similarity=0.806 Sum_probs=92.7
Q ss_pred cchHHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEcc-CCcEEEEEEEecCccceeechhhhhhhhcCC
Q psy8855 2 SYSEKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNK-NGVITDAKFKTYGCGSAIASSSLVTEWVKGK 80 (200)
Q Consensus 2 ~Y~~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~-~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk 80 (200)
+|+++||+||+||+|.|.|++|+ ++++.+||.|||+|+|+|++++ +++|++++|+++||++++||||+|+++++||
T Consensus 3 ~Ys~~Ildh~~nP~n~G~L~~~~---~~g~~~np~CGD~i~l~l~vd~~~~~I~d~~F~~~GCais~ASAs~~~eli~Gk 79 (290)
T TIGR02000 3 DYTDKVKEHFYNPKNAGVVEDAN---AVGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIKGL 79 (290)
T ss_pred chHHHHHHHHhCcCCCCCCCCCC---cEEEeCCCCCcceEEEEEEEcCCCCeEEEEEEEecCcHHHHHHHHHHHHHHcCC
Confidence 59999999999999999999887 5789999999999999999973 5899999999999999999999999999999
Q ss_pred ChhHHhhhhhhhhHHHHh-hhhhH
Q psy8855 81 TLDEAMSIKNTDIAEELV-TKKAA 103 (200)
Q Consensus 81 ~~~ea~~l~~~~i~~~l~-~~~a~ 103 (200)
|++||..++.+++.++|+ +|+.+
T Consensus 80 tv~ea~~i~~~di~~~L~~lpp~r 103 (290)
T TIGR02000 80 TLDEALKVSNQDIADYLGGLPPEK 103 (290)
T ss_pred CHHHHHHhhHHHHHHHHcCCChhh
Confidence 999999999999999998 77654
No 19
>KOG1119|consensus
Probab=99.92 E-value=7e-25 Score=169.29 Aligned_cols=100 Identities=29% Similarity=0.600 Sum_probs=91.6
Q ss_pred hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEecCCc
Q psy8855 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFDGLN 178 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~~~~ 178 (200)
++.+.++++++.+..+ ..|||.|+++||+||+|.|.++....++|.+++.+|.+|+||..++.+++|+||||.++.++
T Consensus 97 sds~~krl~EI~~~~p--e~LRl~VegGGCsGFQYkf~LD~~in~dD~vf~e~~arVVvD~~SL~~~kGatvdy~~ELIr 174 (199)
T KOG1119|consen 97 SDSCSKRLKEIYENSP--EFLRLTVEGGGCSGFQYKFRLDNKINNDDRVFVENGARVVVDNVSLNLLKGATVDYTNELIR 174 (199)
T ss_pred hhHHHHHHHHHHhCCc--ceEEEEEecCCccceEEEEEecCCCCCcceEEeeCCcEEEEeccchhhccCceeehHHHHhh
Confidence 4566778888876654 58999999999999999999998888999999999999999999999999999999999999
Q ss_pred cceEE-eCCCCCCCccCCCCCCC
Q psy8855 179 KGFKF-KNPNIKNKCGCGKSFQI 200 (200)
Q Consensus 179 ~~F~i-~nP~~~~~C~CG~sf~~ 200 (200)
+.|.+ .||.++++||||.||.|
T Consensus 175 SsF~ivnNP~A~~gCsCgSSF~i 197 (199)
T KOG1119|consen 175 SSFRIVNNPSAKQGCSCGSSFDI 197 (199)
T ss_pred hhheeecCcccccCCCCCccccc
Confidence 99997 58999999999999986
No 20
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.91 E-value=2.2e-24 Score=172.21 Aligned_cols=94 Identities=23% Similarity=0.417 Sum_probs=87.8
Q ss_pred Hh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEE--ecccCCCcEEEEeCCEEEEEecccccccCCcEEEeE
Q psy8855 97 LV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEY--VDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFE 173 (200)
Q Consensus 97 l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l--~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~ 173 (200)
+. ||+|+++|++++++++.+.+|||+|+++||+|++|+|.| ++++.++|.+++.+|++|+||+.+++||+|++|||+
T Consensus 2 i~iTd~A~~~i~~ll~~~~~~~~LRI~V~~gGCsG~~Y~~~~~~~~~~~~~D~v~e~~gv~v~Vd~~S~~~L~G~~IDyv 81 (192)
T PRK11190 2 ITISDAAQAHFAKLLANQEEGTQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKFDGFSAYVDELSAPFLEDAEIDFV 81 (192)
T ss_pred cEECHHHHHHHHHHHhcCCCCceEEEEEECCCcCCceeeeEEeecCCCCCCCEEEEeCCEEEEECcchHhHhCCCEEEEe
Confidence 45 899999999999877655689999999999999999999 677889999999999999999999999999999999
Q ss_pred ecCCccceEEeCCCCCC
Q psy8855 174 FDGLNKGFKFKNPNIKN 190 (200)
Q Consensus 174 ~~~~~~~F~i~nP~~~~ 190 (200)
++..+++|+|+|||+++
T Consensus 82 e~~~g~gF~f~NPNa~~ 98 (192)
T PRK11190 82 TDQLGSQLTLKAPNAKM 98 (192)
T ss_pred ecCCCCceEEECCCCCC
Confidence 99999999999999875
No 21
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=99.90 E-value=1.5e-23 Score=167.35 Aligned_cols=92 Identities=26% Similarity=0.446 Sum_probs=86.1
Q ss_pred hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEE--ecccCCCcEEEEeCCEEEEEecccccccCCcEEEeEecC
Q psy8855 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEY--VDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFDG 176 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l--~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~~ 176 (200)
||+|+++|++++++++++.+|||+|+++||+|++|+|.| .+++.++|.+++.+|++|+||+.+++||+|++|||+++.
T Consensus 4 T~~A~~~l~~ll~~~~~~~~LRv~V~~gGCsG~~Y~l~~~~~~~~~~~D~v~e~~g~~v~Vd~~s~~~L~g~~IDyve~~ 83 (190)
T TIGR03341 4 TEAAQAYLAKLLAKQNEGTGIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEFNGFSAYVDALSAPFLEDAVIDFVTDR 83 (190)
T ss_pred CHHHHHHHHHHHhhCCCCceEEEEEECCccCCceeeeEEcccCCCCCCCEEEEeCCEEEEEccchhhHhCCCEEEEeecC
Confidence 899999999999876655689999999999999999999 567889999999999999999999999999999999999
Q ss_pred CccceEEeCCCCCC
Q psy8855 177 LNKGFKFKNPNIKN 190 (200)
Q Consensus 177 ~~~~F~i~nP~~~~ 190 (200)
.+++|+|+|||+++
T Consensus 84 ~g~gF~f~NPna~~ 97 (190)
T TIGR03341 84 MGGQLTLKAPNAKM 97 (190)
T ss_pred CCceeEEeCCccCC
Confidence 99999999999864
No 22
>TIGR01911 HesB_rel_seleno HesB-like selenoprotein. This model represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and pfam01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model.
Probab=99.90 E-value=1.2e-23 Score=149.49 Aligned_cols=88 Identities=15% Similarity=0.363 Sum_probs=80.7
Q ss_pred HHh-hhhhHHHHHHhhhhcCc-ceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEecccccccCCcEEEeE
Q psy8855 96 ELV-TKKAAKYINKYIQKRGK-GIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFE 173 (200)
Q Consensus 96 ~l~-~~~a~~~i~~~l~~~~~-~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~ 173 (200)
++. ||+|+++|++++++++. ..+|||+|+++||+|++|.|.+++ ++++|.+++.+|++|+||+.+++||.|++|||+
T Consensus 3 ~i~lT~~A~~~i~~ll~~~~~~~~~LRi~v~~gGCsG~~Y~~~ld~-~~~~D~v~~~~gv~v~vD~~s~~~l~G~~iDy~ 81 (92)
T TIGR01911 3 IVAMSDDAYEEFKDFLKENDIDNDVIRIHFAGMGCMGPMFNLIADE-EKEGDEIEKIHDLTFLIDKNLIDQFGGFSIECA 81 (92)
T ss_pred ceEECHHHHHHHHHHHHhCCCCCceEEEEEeCCCccCcccceEecC-CCCCCEEEEeCCEEEEECHHHHHHhCCCEEEEe
Confidence 355 89999999999987753 357999999999999999999975 689999999999999999999999999999999
Q ss_pred ecCCccceEEe
Q psy8855 174 FDGLNKGFKFK 184 (200)
Q Consensus 174 ~~~~~~~F~i~ 184 (200)
++..+++|+|+
T Consensus 82 ~~~~g~gF~~~ 92 (92)
T TIGR01911 82 EENFGAGFSLD 92 (92)
T ss_pred cCCCCCcEEeC
Confidence 99999999984
No 23
>PF01521 Fe-S_biosyn: Iron-sulphur cluster biosynthesis; InterPro: IPR000361 The proteins in this entry are variously annotated as iron-sulphur cluster insertion protein or Fe/S biogenesis protein. They appear to be involved in Fe-S cluster biogenesis. This family includes IscA, HesB, YadR and YfhF-like proteins. The hesB gene is expressed only under nitrogen fixation conditions []. IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulphur proteins. IscA is able to bind at least 2 iron ions per dimer []. Other members of this family include various hypothetical proteins that also contain the NifU-like domain (IPR001075 from INTERPRO) suggesting that they too are able to bind iron and are involved in Fe-S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens (Human) and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions []. ; PDB: 2D2A_A 1X0G_D 1NWB_A 2K4Z_A 1R94_B 1R95_A 1S98_B 2P2E_A 2QGO_A 2APN_A.
Probab=99.83 E-value=1.3e-20 Score=138.54 Aligned_cols=96 Identities=39% Similarity=0.703 Sum_probs=89.4
Q ss_pred hhhhHHHHHHhhhhcCcceeEEEEEecCC--------CC-CceEEEEEeccc-CCCcEEEEeCCEEEEEeccccccc-CC
Q psy8855 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRG--------CS-GLSYKLEYVDEK-RKEDQVFKLNGVQIFINEKDLLYF-NG 167 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~~~~~lRi~v~~~G--------C~-G~~~~l~l~~~~-~~~D~v~e~~gi~v~id~~~~~~l-~g 167 (200)
||+|+++|++++.+++.. |||++..+| |+ |++|.|.+++++ .+.|.+++.+|++|+|++.+.+|| ++
T Consensus 6 T~~A~~~l~~~~~~~~~~--irl~~~~gg~p~~~~~~C~~g~~y~l~~~~~~~~~~D~~~~~~~~~i~i~~~~~~~l~~~ 83 (112)
T PF01521_consen 6 TDAAAERLKQLLKEDPKK--IRLFVDDGGSPYSREGCCSIGFSYSLALVDKPDEEYDIVIESNGFTIYIDKYSLWYLDEG 83 (112)
T ss_dssp -HHHHHHHHHHHHCTTES--EEEEEEEESSCCGGSS-TTSEEEEEEEEESSTSTTSCEEEEETTEEEEEEGGGHHHH-TT
T ss_pred CHHHHHHHHHHHhcCCCE--EEEEEECCCcccccCCCCCCCcEEeEEEeecccccceEEEeeeEEEEEEeccHhhhhhCC
Confidence 899999999999887533 999999999 99 999999998877 899999999999999999999999 99
Q ss_pred cEEEeEecCCccceEEeCCCCCCCccCCC
Q psy8855 168 IELDFEFDGLNKGFKFKNPNIKNKCGCGK 196 (200)
Q Consensus 168 ~~IDy~~~~~~~~F~i~nP~~~~~C~CG~ 196 (200)
++|||.++..+.+|++.||+..+.|+||+
T Consensus 84 ~~iD~~~~~~~~~f~~~~~~~~~~~~~~~ 112 (112)
T PF01521_consen 84 LTIDYVEDLGGFGFKSDNPNLDSNCGCGD 112 (112)
T ss_dssp EEEEEEEETTEEEEEEETTTEEEEECECE
T ss_pred CEEEEEEccCccEEEECCCCcCceeccCC
Confidence 99999999999999999999999999984
No 24
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.33 E-value=3.3e-12 Score=87.90 Aligned_cols=84 Identities=26% Similarity=0.467 Sum_probs=68.4
Q ss_pred hhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEE---ecccCCCcEEEEeCCEEEEEecccccccCC--cEEEeE
Q psy8855 99 TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEY---VDEKRKEDQVFKLNGVQIFINEKDLLYFNG--IELDFE 173 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l---~~~~~~~D~v~e~~gi~v~id~~~~~~l~g--~~IDy~ 173 (200)
|++|.+|+++.+.-.. +..||++++.+||+..+-+|++ .+.|+|--...+.+|++|||+.+++||+++ ++|||.
T Consensus 6 td~A~~wfk~E~~l~~-g~~vrffvRyGG~~~~~~GFS~gv~~e~PkE~g~~q~~Dgltffiee~DlWYF~d~d~~v~y~ 84 (95)
T COG4841 6 TDQALKWFKEELDLEE-GNKVRFFVRYGGCSSLQQGFSLGVAKEVPKEIGYKQEYDGLTFFIEEKDLWYFDDHDLKVDYS 84 (95)
T ss_pred cHHHHHHHHHhcCCCC-CCEEEEEEEEcCcccccCCcceeeeccCchhhchheeecCeEEEEecCceEEEcCCcEEEecc
Confidence 8899999999997663 5589999999999744444443 134777777788999999999999999999 899999
Q ss_pred ecCCccceEE
Q psy8855 174 FDGLNKGFKF 183 (200)
Q Consensus 174 ~~~~~~~F~i 183 (200)
++.....|+.
T Consensus 85 ~~~Dei~fs~ 94 (95)
T COG4841 85 PDTDEISFSY 94 (95)
T ss_pred CCCCcceeec
Confidence 8876666654
No 25
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.40 E-value=9.8e-07 Score=62.55 Aligned_cols=86 Identities=20% Similarity=0.189 Sum_probs=69.2
Q ss_pred hhhhHHHHHHhhhhcC-cceeEEEEEecCCCCC-ceEEEEEecccCCCcEEEEeCCEEEEEecccccccCC-cEEEeEec
Q psy8855 99 TKKAAKYINKYIQKRG-KGIGLRLGVYNRGCSG-LSYKLEYVDEKRKEDQVFKLNGVQIFINEKDLLYFNG-IELDFEFD 175 (200)
Q Consensus 99 ~~~a~~~i~~~l~~~~-~~~~lRi~v~~~GC~G-~~~~l~l~~~~~~~D~v~e~~gi~v~id~~~~~~l~g-~~IDy~~~ 175 (200)
|++|+++|+..+..+. ....+|+..+++||.| -.+.+.++.+.+..|..+++|+.+++|.....-||++ ++|||.+.
T Consensus 6 td~a~~~l~~a~d~nl~~~~hl~ydtEgc~Ca~SGi~t~rlvae~tg~d~~idsn~gPiyik~~~~~Ff~D~mtidyN~~ 85 (114)
T COG4918 6 TDKAADKLKAAGDVNLVFDDHLLYDTEGCACAGSGISTYRLVAEETGFDASIDSNFGPIYIKDYGSYFFQDEMTIDYNPS 85 (114)
T ss_pred cHHHHHHHHHhhccCcCccceEEEeccccccccCCcceEEEEEeccCcccccccCCCcEEEEecceeEecceeeeecCCc
Confidence 7889999998887653 4578999999999965 4666667666778999999999999999988888887 79999776
Q ss_pred CCccceEEeCC
Q psy8855 176 GLNKGFKFKNP 186 (200)
Q Consensus 176 ~~~~~F~i~nP 186 (200)
. +.+.+++|
T Consensus 86 ~--ktl~LkS~ 94 (114)
T COG4918 86 Y--KTLELKST 94 (114)
T ss_pred c--ceEEEcCh
Confidence 5 55666544
No 26
>COG3564 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.74 E-value=0.21 Score=35.49 Aligned_cols=86 Identities=19% Similarity=0.284 Sum_probs=58.9
Q ss_pred hhhhhHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEec---ccCCCcEEE-EeCCEEEEEecccccccCC--cEEE
Q psy8855 98 VTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVD---EKRKEDQVF-KLNGVQIFINEKDLLYFNG--IELD 171 (200)
Q Consensus 98 ~~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~---~~~~~D~v~-e~~gi~v~id~~~~~~l~g--~~ID 171 (200)
.||+|..-|.++..++++ | +|-..+||+.-+--|-+.. -..++|+.. +++|++|+|.......-+- +.||
T Consensus 9 aT~aAl~Li~~l~~~hgp---v-mFHQSGGCCDGSsPMCYP~~~fivGd~DvlLG~i~gvPvyIs~~QyeaWKHTqLIID 84 (116)
T COG3564 9 ATPAALDLIAELQAEHGP---V-MFHQSGGCCDGSSPMCYPRADFIVGDNDVLLGEIDGVPVYISGPQYEAWKHTQLIID 84 (116)
T ss_pred cCHHHHHHHHHHHHhcCC---E-EEeccCCccCCCCCccccccceeecCCceEEeeeCCEEEEecCcHHhhhhccEEEEE
Confidence 389999999998877753 3 4556788852232233310 124667655 6899999999988877666 5889
Q ss_pred eEecCCccceEEeCCCC
Q psy8855 172 FEFDGLNKGFKFKNPNI 188 (200)
Q Consensus 172 y~~~~~~~~F~i~nP~~ 188 (200)
-+ ...|..|.+.|-..
T Consensus 85 VV-pGRGGmFSLdng~E 100 (116)
T COG3564 85 VV-PGRGGMFSLDNGRE 100 (116)
T ss_pred Ee-cCCCceeEccCCcc
Confidence 87 45678999987543
No 27
>PF05610 DUF779: Protein of unknown function (DUF779); InterPro: IPR008497 This family consists of several bacterial proteins of unknown function.
Probab=94.45 E-value=0.18 Score=35.74 Aligned_cols=78 Identities=22% Similarity=0.431 Sum_probs=53.2
Q ss_pred HHHhhhhcCcceeEEEEEecCCCCCceEEEEEec---ccCCCcEEE-EeCCEEEEEecccccccCC--cEEEeEecCCcc
Q psy8855 106 INKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVD---EKRKEDQVF-KLNGVQIFINEKDLLYFNG--IELDFEFDGLNK 179 (200)
Q Consensus 106 i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~---~~~~~D~v~-e~~gi~v~id~~~~~~l~g--~~IDy~~~~~~~ 179 (200)
|.++.++++ .| ++-..+||..-+-=+=+.. ...+.|+.. +..|++|+|.+....|.+. ++||-++ ..+.
T Consensus 3 i~~L~~~HG---~l-mFhQSGGCCDGSaPmC~p~gef~~g~~DV~LG~i~g~~fym~~~qfeywkht~L~iDVv~-GrG~ 77 (95)
T PF05610_consen 3 IRRLKAKHG---PL-MFHQSGGCCDGSAPMCYPAGEFRVGDSDVLLGEIGGVPFYMSKDQFEYWKHTQLTIDVVP-GRGG 77 (95)
T ss_pred HHHHHHhcC---CE-EEEeCCCCCCCCcceeEeCCceecCCCcEEEEEecCeEEEEchHHHHHhhCcEEEEEEEe-cCCC
Confidence 445555554 23 3445778853333343421 134667654 7899999999999999999 5999874 6689
Q ss_pred ceEEeCCCC
Q psy8855 180 GFKFKNPNI 188 (200)
Q Consensus 180 ~F~i~nP~~ 188 (200)
+|.+.+|.-
T Consensus 78 ~FSLE~~~G 86 (95)
T PF05610_consen 78 GFSLEAPEG 86 (95)
T ss_pred eeeccCCCC
Confidence 999999864
No 28
>PF10437 Lip_prot_lig_C: Bacterial lipoate protein ligase C-terminus; InterPro: IPR019491 This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with IPR004143 from INTERPRO, further upstream. This C-terminal domain is more stable than IPR004143 from INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues. ; PDB: 1X2G_A 3A7R_A 3A7A_A 1X2H_C 1VQZ_A 3R07_C.
Probab=86.76 E-value=3.7 Score=28.11 Aligned_cols=42 Identities=21% Similarity=0.299 Sum_probs=30.8
Q ss_pred cEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChh
Q psy8855 39 DVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLD 83 (200)
Q Consensus 39 D~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ 83 (200)
-.|++++.|++ |+|+++++.|+-=.. .-...+.+.++|...+
T Consensus 16 G~v~v~~~V~~-G~I~~i~i~gDf~~~--~~i~~le~~L~G~~~~ 57 (86)
T PF10437_consen 16 GTVEVHLNVKN-GIIKDIKIYGDFFGP--EDIEELEEALIGCPYD 57 (86)
T ss_dssp EEEEEEEEEET-TEEEEEEEEECBS-C--CCHHHHHHHHTTCBSS
T ss_pred ceEEEEEEEEC-CEEEEEEEECCCCCc--hHHHHHHHHHHhcCCC
Confidence 45999999986 999999999873222 3356777778888543
No 29
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=83.16 E-value=11 Score=28.01 Aligned_cols=84 Identities=15% Similarity=0.251 Sum_probs=52.0
Q ss_pred HHHHHHHcCCCCCCCCCCCCCceeeEEecCCCcccEEEEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChh
Q psy8855 5 EKVLDHYENPRNVGVFEKNDNTVGTGMVGAPACGDVMKLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLD 83 (200)
Q Consensus 5 ~~il~~~~~p~~~g~l~~~~~~~~~~~~~~~~CGD~i~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ 83 (200)
+.|+++.+..... ++.... .... =+.|-..|=++....++|++ .|.++. -.+...-++++.+.+.|+|++
T Consensus 16 ~~Li~lgk~lp~l---~~~~~~--~~~~-V~GC~S~vWl~~~~~~~g~~---~f~adSda~ivkGl~all~~~~~g~t~~ 86 (125)
T PF02657_consen 16 RYLIDLGKKLPPL---PEELRT--DENL-VHGCQSQVWLHVEEDEDGKV---HFRADSDARIVKGLLALLLEVLNGQTPE 86 (125)
T ss_dssp HHHHHHHHTS-------CCCCS--CCEE-ETSSSS-EEEEEEEETTSEE---EEEEEESSHHHHHHHHHHHHHTTT-BHH
T ss_pred HHHHHHHhcCCCC---CHHHhc--cccc-CCCCccceeEeeeeccCCEE---EEEecCccHHHHHHHHHHHHHHcCCCHH
Confidence 3578888777643 221100 0111 25699998775444445765 677663 456777889999999999999
Q ss_pred HHhhhhhhhhHHHHh
Q psy8855 84 EAMSIKNTDIAEELV 98 (200)
Q Consensus 84 ea~~l~~~~i~~~l~ 98 (200)
|+..+... ..+.+|
T Consensus 87 eI~~~~~~-fl~~lg 100 (125)
T PF02657_consen 87 EILAFDPD-FLEQLG 100 (125)
T ss_dssp HHHHS-TH-HHHHHT
T ss_pred HHHhCCHH-HHHHcC
Confidence 99999987 666666
No 30
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]
Probab=82.77 E-value=3.9 Score=36.75 Aligned_cols=65 Identities=23% Similarity=0.388 Sum_probs=47.2
Q ss_pred EEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhh---------------hhhhHHHHh--hhhhHH
Q psy8855 42 KLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIK---------------NTDIAEELV--TKKAAK 104 (200)
Q Consensus 42 ~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~---------------~~~i~~~l~--~~~a~~ 104 (200)
.+.+.++++|++++++|...+=-. +-.++.||++++|..+. .+++...|| .|.+.+
T Consensus 18 kv~i~vdd~G~V~~~~~~it~~Rg-------fEk~~~Gkp~EeaP~i~~RICgiC~~sH~LAs~eA~e~a~gveip~~~~ 90 (441)
T COG3259 18 KVTIEVDDDGIVEDARFHITEVRG-------FEKFVLGKPIEEAPRIVPRICGICPASHHLASVEAAEAALGVEIPEEAE 90 (441)
T ss_pred EEEEEEcCCCceeeeEEEecccch-------HHHHhcCCChHHhhHHhhhhhccChhHHHHHHHHHHHHhcCCcCChHHH
Confidence 455566767999999998654322 44677889998888774 456677888 678888
Q ss_pred HHHHhhhhc
Q psy8855 105 YINKYIQKR 113 (200)
Q Consensus 105 ~i~~~l~~~ 113 (200)
++++++.-.
T Consensus 91 ~LREl~~~g 99 (441)
T COG3259 91 KLRELLNIG 99 (441)
T ss_pred HHHHHHHHH
Confidence 888887543
No 31
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=82.63 E-value=5.6 Score=30.19 Aligned_cols=61 Identities=11% Similarity=0.119 Sum_probs=46.5
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
+.|-..|=+...++++| .+.|.++. -.+...-++++...+.|+|++|+..+......+.||
T Consensus 49 ~GCqS~VWl~~~~~~~g---~~~f~~dSDa~ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lG 110 (138)
T PRK09296 49 QGCQSQVWIVMRQNAQG---IIELQGDSDAAIVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLA 110 (138)
T ss_pred CCcccceeeeEeecCCC---EEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcC
Confidence 57999887776676545 46777763 456677788999999999999999998655556666
No 32
>PRK15019 CsdA-binding activator; Provisional
Probab=81.27 E-value=6.4 Score=30.24 Aligned_cols=61 Identities=21% Similarity=0.207 Sum_probs=47.3
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
+.|-..|=+....+++| .+.|.++. -.+...-++++...+.|+|++|+..+...+..+.+|
T Consensus 59 ~GCqS~VWL~~~~~~dg---~~~f~~dSDA~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lG 120 (147)
T PRK15019 59 AGCENRVWLGYTVAENG---KMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELG 120 (147)
T ss_pred CCcccceeeeeeecCCC---EEEEEeeCccHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCC
Confidence 57989887766664445 46777763 456677788999999999999999998877777777
No 33
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=81.25 E-value=6.6 Score=29.82 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=46.8
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
+.|-..|=+...+.+||+ +.|.++- -.+...-++++.....|+|++|+..++.......||
T Consensus 54 ~GCqS~VWl~~~~~~dg~---~~f~~dSDa~IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lG 115 (138)
T TIGR03391 54 TGCENRVWLGHQVLPDGT---LHFYGDSEGRIVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELG 115 (138)
T ss_pred CCcccceeeeeeecCCCE---EEEEecCccHHHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcC
Confidence 579888877655444463 6677763 456677788999999999999999998877777776
No 34
>PLN02673 quinolinate synthetase A
Probab=73.50 E-value=8.8 Score=36.58 Aligned_cols=60 Identities=15% Similarity=0.229 Sum_probs=47.7
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHH
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l 97 (200)
+.|-..|-|...++++|++ .+.+..++ .|...-++++...+.|++.+|+..+..+.+ ..|
T Consensus 127 ~GCQSqVWL~~eldddGkv-~F~ADSDA-~IVKGL~ALLl~~lsG~TpeEILavD~d~~-~~L 186 (724)
T PLN02673 127 MGCTAQVWLEAELDQDGKM-RFWADSDS-EITKGFCSCLIWVLDGASPEEVLELKTEDL-AAL 186 (724)
T ss_pred CCcccceEEEEEEcCCCEE-EEEEeCcc-HHHHHHHHHHHHHHcCCCHHHHHhCCHHHH-HHH
Confidence 5799988887777655653 35555566 888999999999999999999999998777 444
No 35
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=69.27 E-value=2.6 Score=31.66 Aligned_cols=21 Identities=29% Similarity=0.664 Sum_probs=14.7
Q ss_pred cceEEeCCCCC-CCccCCCCCC
Q psy8855 179 KGFKFKNPNIK-NKCGCGKSFQ 199 (200)
Q Consensus 179 ~~F~i~nP~~~-~~C~CG~sf~ 199 (200)
.-|+..+|..+ ..|.||.||.
T Consensus 59 hlfi~qs~~~rv~rcecghsf~ 80 (165)
T COG4647 59 HLFICQSAQKRVIRCECGHSFG 80 (165)
T ss_pred cEEEEecccccEEEEecccccc
Confidence 45666666543 3899999995
No 36
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=67.86 E-value=3.7 Score=34.58 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=27.6
Q ss_pred CcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhh
Q psy8855 51 GVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKN 90 (200)
Q Consensus 51 ~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~ 90 (200)
.+|..=.-.|.||++ |+++.+.+++|.++.||.+--.
T Consensus 200 ~ri~t~~tHGTGCTl---SaAIaa~LA~G~~l~~AV~~Ak 236 (263)
T COG0351 200 PRIPTKNTHGTGCTL---SAAIAANLAKGLSLEEAVKKAK 236 (263)
T ss_pred cccCCCCCCCccHHH---HHHHHHHHHcCCCHHHHHHHHH
Confidence 355544457789998 5677889999999999876433
No 37
>TIGR03295 frhA coenzyme F420 hydrogenase, subunit alpha. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein is a member of the Nickel-dependent hydrogenase superfamily represented by Pfam model, pfam00374.
Probab=62.16 E-value=33 Score=30.69 Aligned_cols=64 Identities=17% Similarity=0.218 Sum_probs=40.7
Q ss_pred EEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhh---------------hhhhHHHHh--hhhhH
Q psy8855 41 MKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIK---------------NTDIAEELV--TKKAA 103 (200)
Q Consensus 41 i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~---------------~~~i~~~l~--~~~a~ 103 (200)
++|.+.++++++|.+++|...--. -=+-.+++|++..++..+. ..+++.++| .|+.+
T Consensus 17 ~rl~l~vdge~vv~~~~~~~~~~~------RG~Ek~~egr~~~~~~~l~~Ricg~c~~ah~~a~~~AvE~a~gi~vp~ra 90 (411)
T TIGR03295 17 AKLVLEVDDEGIVEKGDYLSITPV------RGFEKLLVGKTAEFAPIIVSRICGICPIAHTLASVEAIEDSIDCEVPKDG 90 (411)
T ss_pred eEEEEEEeCCCcEEEEEEeccCcC------cHHHHHHcCCCHHHHHHHHhHHhhcCHHHHHHHHHHHHHHHhCCCCCHHH
Confidence 678888886688888866532111 2355777888888888775 344556667 45555
Q ss_pred HHHHHhh
Q psy8855 104 KYINKYI 110 (200)
Q Consensus 104 ~~i~~~l 110 (200)
++++.++
T Consensus 91 ~~lR~l~ 97 (411)
T TIGR03295 91 LLLRELT 97 (411)
T ss_pred HHHHHHH
Confidence 5555544
No 38
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=56.80 E-value=4 Score=28.98 Aligned_cols=76 Identities=18% Similarity=0.234 Sum_probs=46.0
Q ss_pred EEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh---hhhhHHHHHHhhhhcC--cceeEEEEEecCCCCC
Q psy8855 56 AKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV---TKKAAKYINKYIQKRG--KGIGLRLGVYNRGCSG 130 (200)
Q Consensus 56 ~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~---~~~a~~~i~~~l~~~~--~~~~lRi~v~~~GC~G 130 (200)
+.+.+.||..-++=++.|...+...-.+.+......++.-.-. +.+|.+++...+.+-. +....+|.+. ||-.
T Consensus 2 v~i~T~GC~~N~~Dse~i~~~l~~~G~~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~--GC~a 79 (98)
T PF00919_consen 2 VYIETLGCQMNQYDSERIASILQAAGYEIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVT--GCMA 79 (98)
T ss_pred EEEEECCCcccHHHHHHHHHHHHhcCCeeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEE--eCcc
Confidence 5688999999999999999999887665555543333332212 5566554444443211 0134677664 6754
Q ss_pred ceE
Q psy8855 131 LSY 133 (200)
Q Consensus 131 ~~~ 133 (200)
-.+
T Consensus 80 q~~ 82 (98)
T PF00919_consen 80 QRY 82 (98)
T ss_pred ccC
Confidence 333
No 39
>PF04205 FMN_bind: FMN-binding domain; InterPro: IPR007329 This conserved region includes the FMN-binding site of the NqrC protein [] as well as the NosR and NirI regulatory proteins.; GO: 0010181 FMN binding, 0016020 membrane; PDB: 3LWX_A 2KZX_A 3DCZ_A 3O6U_D.
Probab=56.44 E-value=21 Score=23.66 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=28.4
Q ss_pred cEEEEEEEEccCCcEEEEEEEecCccceee---chhhhhhhhcCCC
Q psy8855 39 DVMKLQIKVNKNGVITDAKFKTYGCGSAIA---SSSLVTEWVKGKT 81 (200)
Q Consensus 39 D~i~i~l~i~~~~~I~~~~f~~~GC~~~~A---sas~~~~~i~gk~ 81 (200)
..|++.+.++++|+|+++.+..+.-..... ...-+.+.+.|+.
T Consensus 4 g~i~v~v~i~~dg~I~~v~~~~~~et~~~~~~~~~~~~~~~~~g~~ 49 (81)
T PF04205_consen 4 GPITVTVTIDKDGKITDVKILEHNETPGYGKKAEIEEFFDQIVGKQ 49 (81)
T ss_dssp EEEEEEEEEETTTEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHC
T ss_pred ceEEEEEEEeCCCEEEEEEEeeccCCcchhhhccHHHHHHHHHhcc
Confidence 468888888866999999999975443333 1334444455554
No 40
>KOG3348|consensus
Probab=53.44 E-value=42 Score=23.26 Aligned_cols=38 Identities=8% Similarity=0.217 Sum_probs=27.8
Q ss_pred hHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEecc
Q psy8855 102 AAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVDE 140 (200)
Q Consensus 102 a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~~ 140 (200)
..+++.++|.+.=+...|+|.=..+||++ .|.+.++.+
T Consensus 4 ~e~~l~~~L~~~l~p~~v~V~D~SgGCG~-~F~v~IvS~ 41 (85)
T KOG3348|consen 4 TEERLEELLTEALEPEHVEVQDVSGGCGS-MFDVVIVSA 41 (85)
T ss_pred hHHHHHHHHHhhcCceEEEEEEcCCCccc-eEEEEEEcc
Confidence 45677777776544568888888899865 888887653
No 41
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=52.66 E-value=7.9 Score=20.67 Aligned_cols=14 Identities=36% Similarity=0.925 Sum_probs=10.1
Q ss_pred CCCCCCcc-CCCCCC
Q psy8855 186 PNIKNKCG-CGKSFQ 199 (200)
Q Consensus 186 P~~~~~C~-CG~sf~ 199 (200)
|.....|. ||.+|.
T Consensus 11 ~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 11 PESAKFCPHCGYDFE 25 (26)
T ss_pred hhhcCcCCCCCCCCc
Confidence 34445797 999995
No 42
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=52.31 E-value=45 Score=25.56 Aligned_cols=61 Identities=21% Similarity=0.231 Sum_probs=48.3
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
+.|-..|=+....+++ ..+.|.|+- -.|...-++++...+.|+|.+|+..+++...-+.||
T Consensus 54 ~GC~S~vwL~~~~~~~---~~~~F~gdSdA~ivrGL~aill~~~~G~t~~eI~~~~~~~~f~~LG 115 (144)
T COG2166 54 PGCQSQVWLVTEQNDD---GTLHFFGDSDARIVRGLLAILLAAYSGKTAAEILAFDPLDFFEELG 115 (144)
T ss_pred CccccceeEEEeecCC---ceEEEeccchhHHHHHHHHHHHHHHcCCCHHHHHcCCHHHHHHHhh
Confidence 5688877776666653 347888874 567777889999999999999999999977777777
No 43
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=51.69 E-value=8.3 Score=33.45 Aligned_cols=45 Identities=9% Similarity=0.073 Sum_probs=32.4
Q ss_pred CcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 51 GVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 51 ~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
.++..-.|.|.||.++ +++++.++.|.++++|...-.+.+...+.
T Consensus 240 ~ri~~~~~hGTGc~fA---SAIAa~LA~G~~l~~Av~~A~~fv~~aI~ 284 (321)
T PTZ00493 240 KRKPGKDIHGTGCTLS---TAIACYLAKKHNILQSCIESKKYIYNCIR 284 (321)
T ss_pred cccCCCCCCChHHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 4665566789999984 56677788999999998876555544443
No 44
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=40.17 E-value=21 Score=25.93 Aligned_cols=20 Identities=10% Similarity=0.355 Sum_probs=14.5
Q ss_pred ecccccccCCcEEEeEecCC
Q psy8855 158 NEKDLLYFNGIELDFEFDGL 177 (200)
Q Consensus 158 d~~~~~~l~g~~IDy~~~~~ 177 (200)
+|..+..|+|-||||-+...
T Consensus 45 ~P~e~~qldGyTvDy~~~~~ 64 (117)
T cd01234 45 EPTEFIQLDGYTVDYMPESD 64 (117)
T ss_pred CchhheeecceEEeccCCCC
Confidence 45566788888999986543
No 45
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=39.84 E-value=44 Score=28.36 Aligned_cols=97 Identities=12% Similarity=0.185 Sum_probs=60.4
Q ss_pred cccEEEEEEEEccCCcEEEEEEEe------cCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh--hhhhHHHHHH
Q psy8855 37 CGDVMKLQIKVNKNGVITDAKFKT------YGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV--TKKAAKYINK 108 (200)
Q Consensus 37 CGD~i~i~l~i~~~~~I~~~~f~~------~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~--~~~a~~~i~~ 108 (200)
=||.|++. .. .|+|+++++.. +|-.+.+-=..++...+.+.|.+...++.-. +.=..+ .+++++.+++
T Consensus 132 vGD~I~i~-~~--~G~V~~I~~r~T~i~t~d~~~v~IPNs~~~~~~i~N~s~~~~rr~~~~-v~V~y~~d~~~~~~il~~ 207 (286)
T PRK10334 132 AGEYVDLG-GV--AGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSREPVRRNEFI-IGVAYDSDIDQVKQILTN 207 (286)
T ss_pred CCCEEEEC-CE--EEEEEEEEeEEEEEEcCCCCEEEEcchHhcCCeeEEcCCCCeEEEEEE-EEecCCCCHHHHHHHHHH
Confidence 47877764 22 26888888765 6888888888888888888886654433210 111111 3455666666
Q ss_pred hhhhcC---cceeEEEEEecCCCCCceEEEEE
Q psy8855 109 YIQKRG---KGIGLRLGVYNRGCSGLSYKLEY 137 (200)
Q Consensus 109 ~l~~~~---~~~~lRi~v~~~GC~G~~~~l~l 137 (200)
.+++.+ ++....+.+...|-++..|.+.+
T Consensus 208 ~~~~~~~vl~~p~p~v~~~~~~dssi~~~v~~ 239 (286)
T PRK10334 208 IIQSEDRILKDREMTVRLNELGASSINFVVRV 239 (286)
T ss_pred HHHhCCceecCCCCEEEEEeeeCceEEEEEEE
Confidence 665543 12234566778888888877776
No 46
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=39.56 E-value=1.3e+02 Score=26.31 Aligned_cols=44 Identities=23% Similarity=0.182 Sum_probs=32.4
Q ss_pred ccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhH
Q psy8855 38 GDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDE 84 (200)
Q Consensus 38 GD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~e 84 (200)
+-.|++.+.+++ |+|+++++.++.-. ..-...+.+.++|...+.
T Consensus 262 ~G~v~i~~~v~~-g~I~~~~i~gD~~~--~~~~~~l~~~L~G~~~~~ 305 (338)
T PRK03822 262 WGGVELHFDVEK-GHITRAQIFTDSLN--PAPLEALAGRLQGCLYRA 305 (338)
T ss_pred CCcEEEEEEEEC-CEEEEEEEECCCCC--cccHHHHHHHhCCCCCCH
Confidence 456899999986 99999999998422 344566777778887543
No 47
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=39.10 E-value=37 Score=25.19 Aligned_cols=36 Identities=33% Similarity=0.554 Sum_probs=26.0
Q ss_pred hhhhhhhhcCCChhHHhhhhhhhhHHHHhhh-hhHHHHHHhhhh
Q psy8855 70 SSLVTEWVKGKTLDEAMSIKNTDIAEELVTK-KAAKYINKYIQK 112 (200)
Q Consensus 70 as~~~~~i~gk~~~ea~~l~~~~i~~~l~~~-~a~~~i~~~l~~ 112 (200)
+.+++.+|.|+++++|..+... +| +|+..++++|+.
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~~-------~pkKaa~~v~KvL~s 61 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILEF-------VPKKAAKLVKKVLES 61 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHHh-------ChHHHHHHHHHHHHH
Confidence 4678999999999999876432 34 466667777643
No 48
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=38.76 E-value=46 Score=18.63 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=15.9
Q ss_pred hhhhhhHHHHh-hhhhHHHHHHhhhhc
Q psy8855 88 IKNTDIAEELV-TKKAAKYINKYIQKR 113 (200)
Q Consensus 88 l~~~~i~~~l~-~~~a~~~i~~~l~~~ 113 (200)
++.++|++++| +++-...+-.-++++
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 56788999999 777665555554443
No 49
>PF08543 Phos_pyr_kin: Phosphomethylpyrimidine kinase; InterPro: IPR013749 This enzyme 2.7.4.7 from EC is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes []. ; PDB: 2DDW_B 2DDO_B 2DDM_A 3IBQ_A 3H74_A 3HYO_A 1UB0_A 1VI9_D 1TD2_B 2PHP_D ....
Probab=36.97 E-value=7.2 Score=32.10 Aligned_cols=43 Identities=26% Similarity=0.257 Sum_probs=30.5
Q ss_pred cEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHH
Q psy8855 52 VITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97 (200)
Q Consensus 52 ~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l 97 (200)
++...+|.|.||.+ |+.+++.+++|+++++|.....+.+...+
T Consensus 190 ~~~~~~~~GTGd~f---ss~laa~l~~g~~l~~Av~~A~~~v~~~i 232 (246)
T PF08543_consen 190 RIPTGSFHGTGDLF---SSALAAFLAKGYSLEEAVEKAKNFVRRAI 232 (246)
T ss_dssp EECTSGCTTHHHHH---HHHHHHHHHTTSSHHHHHHHHHHHHHHHH
T ss_pred EEcCCCCCCchhHH---HHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 34335677788887 45677788999999999887655554444
No 50
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=36.19 E-value=17 Score=21.78 Aligned_cols=7 Identities=43% Similarity=1.455 Sum_probs=5.0
Q ss_pred CCCccCC
Q psy8855 189 KNKCGCG 195 (200)
Q Consensus 189 ~~~C~CG 195 (200)
..+|||=
T Consensus 18 ~tsCgCt 24 (45)
T PF07610_consen 18 QTSCGCT 24 (45)
T ss_pred eEccCCE
Confidence 4589993
No 51
>PF14356 DUF4403: Domain of unknown function (DUF4403)
Probab=36.10 E-value=1.3e+02 Score=26.96 Aligned_cols=90 Identities=18% Similarity=0.192 Sum_probs=55.1
Q ss_pred cEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHhhhhhHHHHHHhhhhcCcceeEEEEEecCCCCCc
Q psy8855 52 VITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELVTKKAAKYINKYIQKRGKGIGLRLGVYNRGCSGL 131 (200)
Q Consensus 52 ~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~ 131 (200)
+++|+.|..+-=.....+|+++..--.=+.+++...+.=. +. +.++++.+...+.+.....++|+..+
T Consensus 329 ~l~dld~~~~t~~~l~~~a~wl~~~~i~~~i~~~~~~~l~---~~--l~~~~~~i~~~l~~~~~~~gv~l~g~------- 396 (427)
T PF14356_consen 329 RLEDLDFDLDTKNFLLKTAAWLLHGRIRKAIEEKLVFDLG---PQ--LEEAKKKINAALANYKPAPGVRLNGK------- 396 (427)
T ss_pred EEEeeEEEecccchHHHHHHHHHHHHHHHHHHHHhCCChH---HH--HHHHHHHHHHHHhcCCCCCCEEEEEE-------
Confidence 4788899887555667777777755555555555443211 11 56777888888888434556777654
Q ss_pred eEEEEEecccCCCcEEEEeCCEEEEEec
Q psy8855 132 SYKLEYVDEKRKEDQVFKLNGVQIFINE 159 (200)
Q Consensus 132 ~~~l~l~~~~~~~D~v~e~~gi~v~id~ 159 (200)
...| .-.++.+..+++.+.+..
T Consensus 397 ~~~l------~~~~i~~~~~~l~~~~~a 418 (427)
T PF14356_consen 397 VDSL------RLDDIQVTPDGLVVQVNA 418 (427)
T ss_pred Ecee------EEeeEEEcCCEEEEEEEE
Confidence 1222 234666667777776654
No 52
>KOG4777|consensus
Probab=35.55 E-value=33 Score=29.18 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=33.1
Q ss_pred eCCEEEEEecccccccCCcEEEeEecCCccceEEeCCCC
Q psy8855 150 LNGVQIFINEKDLLYFNGIELDFEFDGLNKGFKFKNPNI 188 (200)
Q Consensus 150 ~~gi~v~id~~~~~~l~g~~IDy~~~~~~~~F~i~nP~~ 188 (200)
.+|++++|..---.-|+++..-..+...++||+|.|||-
T Consensus 114 e~~VPLvvP~VNpehld~ik~~~~~~k~~~G~iI~nsNC 152 (361)
T KOG4777|consen 114 EDGVPLVVPEVNPEHLDGIKVGLDTGKMGKGAIIANSNC 152 (361)
T ss_pred CCCCceEecccCHHHhhhheeccccCCCCCceEEecCCC
Confidence 367888888777788899888888888999999999994
No 53
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=33.47 E-value=24 Score=23.66 Aligned_cols=22 Identities=18% Similarity=0.273 Sum_probs=15.8
Q ss_pred echhhhhhhhcCCChhHHhhhh
Q psy8855 68 ASSSLVTEWVKGKTLDEAMSIK 89 (200)
Q Consensus 68 Asas~~~~~i~gk~~~ea~~l~ 89 (200)
.++-.++.+++|||++|+..+-
T Consensus 34 ~~~~~iA~~i~gks~eeir~~f 55 (78)
T PF01466_consen 34 LCCKYIANMIKGKSPEEIRKYF 55 (78)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHhcCCCHHHHHHHc
Confidence 3456778999999998877654
No 54
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=33.11 E-value=74 Score=26.11 Aligned_cols=51 Identities=12% Similarity=0.188 Sum_probs=34.3
Q ss_pred HHHHhhhhcC--cceeEEEEEecCCCCCceEEEEEecccCCCcEEEEeCCEEEEEe
Q psy8855 105 YINKYIQKRG--KGIGLRLGVYNRGCSGLSYKLEYVDEKRKEDQVFKLNGVQIFIN 158 (200)
Q Consensus 105 ~i~~~l~~~~--~~~~lRi~v~~~GC~G~~~~l~l~~~~~~~D~v~e~~gi~v~id 158 (200)
..++++.+.. .-..-|+.+.-.||+. .+.+-..|...|.|+|++|++=+..
T Consensus 60 avkE~~~dK~y~~~kiYRf~I~C~~C~n---~i~~RTDPkN~~YV~EsGg~R~i~p 112 (272)
T COG5134 60 AVKEEIGDKSYYTTKIYRFSIKCHLCSN---PIDVRTDPKNTEYVVESGGRRKIEP 112 (272)
T ss_pred HHHHHhcccccceeEEEEEEEEccCCCC---ceeeecCCCCceEEEecCceeecCc
Confidence 4455554442 1234688888888876 3455455889999999999985543
No 55
>TIGR00545 lipoyltrans lipoyltransferase and lipoate-protein ligase. One member of this group of proteins is bovine lipoyltransferase, which transfers the lipoyl group from lipoyl-AMP to the specific Lys of lipoate-dependent enzymes. However, it does not first activate lipoic acid with ATP to create lipoyl-AMP and pyrophosphate. Another member of this group, lipoate-protein ligase A from E. coli, catalyzes both the activation and the transfer of lipoate. Homology between the two is full-length, except for the bovine mitochondrial targeting signal, but is strongest toward the N-terminus.
Probab=32.56 E-value=78 Score=27.39 Aligned_cols=44 Identities=30% Similarity=0.324 Sum_probs=31.8
Q ss_pred ccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhH
Q psy8855 38 GDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDE 84 (200)
Q Consensus 38 GD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~e 84 (200)
+..|++++.|++ |+|+++++.++--.. --..-+.+.++|...+.
T Consensus 257 ~G~v~i~l~v~~-g~I~~~~i~gDf~~~--~~~~~l~~~L~G~~~~~ 300 (324)
T TIGR00545 257 AGGFELHVQVEK-GKIVDCKFFGDFLSV--ADITPVTNRLIGQKYDY 300 (324)
T ss_pred CCcEEEEEEEeC-CEEEEEEEECCCCCc--ccHHHHHHHhCCCccCH
Confidence 457999999986 899999999875322 22456666677776544
No 56
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=32.39 E-value=54 Score=23.40 Aligned_cols=20 Identities=30% Similarity=0.647 Sum_probs=16.6
Q ss_pred hhhhhhhcCCChhHHhhhhh
Q psy8855 71 SLVTEWVKGKTLDEAMSIKN 90 (200)
Q Consensus 71 s~~~~~i~gk~~~ea~~l~~ 90 (200)
-.++.+|.|+++++|..+..
T Consensus 14 ~~va~~IrG~~v~~A~~~L~ 33 (103)
T TIGR01044 14 RLVADLIRGKSVSQALDILR 33 (103)
T ss_pred HHHHHHHcCCcHHHHHHHHh
Confidence 46789999999999987643
No 57
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=32.07 E-value=51 Score=23.35 Aligned_cols=20 Identities=30% Similarity=0.556 Sum_probs=16.5
Q ss_pred hhhhhhhcCCChhHHhhhhh
Q psy8855 71 SLVTEWVKGKTLDEAMSIKN 90 (200)
Q Consensus 71 s~~~~~i~gk~~~ea~~l~~ 90 (200)
-.++.+|.|++++||..+..
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~ 35 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLE 35 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHH
Confidence 45789999999999987654
No 58
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=32.00 E-value=80 Score=24.44 Aligned_cols=49 Identities=12% Similarity=0.109 Sum_probs=26.7
Q ss_pred hhcCCChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhhcC-----cceeEEEEEe
Q psy8855 76 WVKGKTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQKRG-----KGIGLRLGVY 124 (200)
Q Consensus 76 ~i~gk~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~~~-----~~~~lRi~v~ 124 (200)
.+.|++.+|+.....-.....-. +-.|+++|++.+.... .+..+|-.+.
T Consensus 124 ~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~~~~~~~~~~~~~~~ 178 (182)
T PRK12540 124 GASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGAEDFGPDDTVRAVIG 178 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccccccCCCcccccccC
Confidence 34566665555544433333333 4567788888887542 3345665443
No 59
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=30.07 E-value=85 Score=20.60 Aligned_cols=24 Identities=25% Similarity=0.426 Sum_probs=16.7
Q ss_pred CCCcccEEEEEEEEccCC--cEEEEE
Q psy8855 34 APACGDVMKLQIKVNKNG--VITDAK 57 (200)
Q Consensus 34 ~~~CGD~i~i~l~i~~~~--~I~~~~ 57 (200)
.-.=||.|++.+...+++ +|++++
T Consensus 42 ~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 42 GLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp S-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred cCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 345799999999987666 677664
No 60
>smart00704 ZnF_CDGSH CDGSH-type zinc finger. Function unknown.
Probab=29.95 E-value=22 Score=20.76 Aligned_cols=20 Identities=20% Similarity=0.449 Sum_probs=12.5
Q ss_pred ceEEeCCCCCCCccCCCCCC
Q psy8855 180 GFKFKNPNIKNKCGCGKSFQ 199 (200)
Q Consensus 180 ~F~i~nP~~~~~C~CG~sf~ 199 (200)
.|.++....-.-|.||.|=+
T Consensus 5 ~~~~e~~~~~~lC~C~~S~~ 24 (38)
T smart00704 5 EVEVEKREKYALCRCGRSKN 24 (38)
T ss_pred EEEecCCCEEEEeeCCCCCC
Confidence 45555444445899998843
No 61
>PF03952 Enolase_N: Enolase, N-terminal domain; InterPro: IPR020811 Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [, ]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer []. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [] to be evolutionary related to enolase. Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.; GO: 0000287 magnesium ion binding, 0004634 phosphopyruvate hydratase activity, 0006096 glycolysis, 0000015 phosphopyruvate hydratase complex; PDB: 2FYM_D 3H8A_C 1E9I_D 3OTR_F 3QTP_A 1PDY_A 1PDZ_A 3TQP_B 2PTZ_A 2PTW_A ....
Probab=29.70 E-value=1.7e+02 Score=21.92 Aligned_cols=69 Identities=19% Similarity=0.200 Sum_probs=42.5
Q ss_pred ccc-EEEEEEEEccCCcEEEEEEEecCccceeechhhhh---------hhhcCCChhHHhhhhhhhhHHHHh--hhhhHH
Q psy8855 37 CGD-VMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVT---------EWVKGKTLDEAMSIKNTDIAEELV--TKKAAK 104 (200)
Q Consensus 37 CGD-~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~---------~~i~gk~~~ea~~l~~~~i~~~l~--~~~a~~ 104 (200)
.|. +|++.|..++ | +.+.+++.+-||...-- +.-.||.+..|.....+.|...|- -+..++
T Consensus 14 rG~PTVEveV~~~~-g------~~~ra~~PsGaStG~~Ea~elrD~~~~~~~gkgV~~Av~~vn~~i~~~L~g~~~~dQ~ 86 (132)
T PF03952_consen 14 RGNPTVEVEVFTSN-G------NVGRASVPSGASTGSHEAVELRDGDPERYGGKGVSKAVENVNEIIAPALIGLDPTDQE 86 (132)
T ss_dssp TS-EEEEEEEEETT-E------EEEEEE--B-SSSSSSS-B---B-STTSGGGTBHHHHHHHHHHTHHHHHTTSBTT-HH
T ss_pred CCCceEEEEEEECC-c------ccceeccccccCCCccccccccCCCcceecCcccchhhhhHHHHHHHHHHhcchhhHH
Confidence 444 4677766653 3 34466777666665432 344678899998888888877664 667777
Q ss_pred HHHHhhhh
Q psy8855 105 YINKYIQK 112 (200)
Q Consensus 105 ~i~~~l~~ 112 (200)
.|.++|.+
T Consensus 87 ~iD~~L~~ 94 (132)
T PF03952_consen 87 EIDQILIE 94 (132)
T ss_dssp HHHHHHHH
T ss_pred HhCcccee
Confidence 88877754
No 62
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=27.20 E-value=1.4e+02 Score=24.45 Aligned_cols=47 Identities=11% Similarity=0.103 Sum_probs=33.1
Q ss_pred hhhhhHHHHh-hhh-hHHHHHHhhhhcCcceeEEEEEecCCCCCceEEEEEec
Q psy8855 89 KNTDIAEELV-TKK-AAKYINKYIQKRGKGIGLRLGVYNRGCSGLSYKLEYVD 139 (200)
Q Consensus 89 ~~~~i~~~l~-~~~-a~~~i~~~l~~~~~~~~lRi~v~~~GC~G~~~~l~l~~ 139 (200)
+..++++.|| ++. ++.+|..+.++. .+......+|=+-|.+.+.+.+
T Consensus 27 sa~elA~~Lgis~~avR~HL~~Le~~G----lv~~~~~~~g~GRP~~~y~Lt~ 75 (218)
T COG2345 27 SADELAEELGISPMAVRRHLDDLEAEG----LVEVERQQGGRGRPAKLYRLTE 75 (218)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCc----ceeeeeccCCCCCCceeeeecc
Confidence 4688999999 654 455666555332 4666677788888999888853
No 63
>PRK10170 hydrogenase 1 large subunit; Provisional
Probab=26.82 E-value=2.3e+02 Score=26.94 Aligned_cols=42 Identities=19% Similarity=0.213 Sum_probs=23.6
Q ss_pred EEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhhh
Q psy8855 41 MKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIK 89 (200)
Q Consensus 41 i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~ 89 (200)
+++.+.++++++|.++...+.-= -=+-.+++|++..++..+.
T Consensus 31 lrv~v~vdge~vv~~a~~~g~~~-------RG~Ekil~GR~p~dal~iv 72 (597)
T PRK10170 31 MRCEVNINDQNVITNAVSCGTMF-------RGLEIILQGRDPRDAWAFV 72 (597)
T ss_pred EEEEEEEcCCcEEEEEEEecccc-------cHHHHHHcCCCHHHHHHHh
Confidence 56777776546777766555210 1133556666666666553
No 64
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=26.76 E-value=1.8e+02 Score=20.30 Aligned_cols=47 Identities=17% Similarity=0.485 Sum_probs=28.6
Q ss_pred CcccEEEEEEEEccC-C----cEEEEEEEecCccceeechhhhhhhh-----cCCChhHHhh
Q psy8855 36 ACGDVMKLQIKVNKN-G----VITDAKFKTYGCGSAIASSSLVTEWV-----KGKTLDEAMS 87 (200)
Q Consensus 36 ~CGD~i~i~l~i~~~-~----~I~~~~f~~~GC~~~~Asas~~~~~i-----~gk~~~ea~~ 87 (200)
.|| .+.|.+..++| | ++..+++.+ || .+-+..++.++ .|.+++++.+
T Consensus 6 ~~g-~~yvtv~~d~d~g~p~Evf~~~~~~G-g~---~~~~~ai~rliS~~Lr~G~~~~~ii~ 62 (95)
T PF12637_consen 6 GCG-KLYVTVNFDEDNGRPFEVFINVGKAG-GC---SGNLEAIARLISLALRSGVPPEEIID 62 (95)
T ss_pred ccc-ceEEEEEeeCCCCcceEEEEecCcCC-Cc---hHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 465 34444444433 5 444444444 56 56677788888 8999888654
No 65
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=26.52 E-value=4.5e+02 Score=24.78 Aligned_cols=44 Identities=23% Similarity=0.198 Sum_probs=32.2
Q ss_pred ccEEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhH
Q psy8855 38 GDVMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDE 84 (200)
Q Consensus 38 GD~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~e 84 (200)
+-.|++.+.|++ |+|+++++.++--.. .-...+.+.+.|...+.
T Consensus 486 ~G~vei~l~V~~-G~I~~~ki~gDf~~~--~~i~~le~~L~G~~y~~ 529 (562)
T PRK14061 486 WGGVELHFDVEK-GHITRAQVFTDSLNP--APLEALAGRLQGCLYRA 529 (562)
T ss_pred cccEEEEEEEeC-CEEEEEEEECCCCCc--ccHHHHHHHhCCCCcCH
Confidence 456899999986 999999999984332 22456777778877543
No 66
>PF03450 CO_deh_flav_C: CO dehydrogenase flavoprotein C-terminal domain; InterPro: IPR005107 Proteins containing this domain form structural complexes with other known families, such as IPR008274 from INTERPRO and IPR001041 from INTERPRO]. The carbon monoxide (CO) dehydrogenase of Oligotropha carboxidovorans is a heterotrimeric complex composed of a apoflavoprotein, a molybdoprotein, and an iron-sulphur protein. It can be dissociated with sodium dodecylsulphate []. CO dehydrogenase catalyzes the oxidation of CO according to the following equation []: CO + H2O = CO2 + 2e + 2H+ Subunit S represents the iron-sulphur protein of CO dehydrogenase and is clearly divided into a C- and an N-terminal domain, each binding a [2Fe-2S] cluster [].; PDB: 3EUB_K 3NS1_K 3NVV_B 1FO4_B 3AM9_A 3AX7_B 3BDJ_A 3ETR_B 3UNI_A 3AMZ_A ....
Probab=26.05 E-value=2.3e+02 Score=19.59 Aligned_cols=43 Identities=26% Similarity=0.370 Sum_probs=30.4
Q ss_pred EEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhH
Q psy8855 42 KLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDE 84 (200)
Q Consensus 42 ~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~e 84 (200)
-+.+.++++++|++++--.-|-+..---+.-+.+.+.|+.+.+
T Consensus 19 a~~~~~~~~~~i~~~ria~g~v~~~p~r~~~~E~~L~g~~~~~ 61 (103)
T PF03450_consen 19 AVLVSVDDDGRIEDARIAVGGVAPTPVRAEEVEAALIGKPLSE 61 (103)
T ss_dssp EEEEEEETTSEEEEEEEEEESSSSSTEE-HHHHHHTTTSBSSH
T ss_pred hheEEEecCceEEEEEEEEeccccceeehHHHHHHHhhcchhh
Confidence 3455666545999999888777666666666777889987765
No 67
>COG0537 Hit Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]
Probab=26.03 E-value=2.8e+02 Score=20.65 Aligned_cols=57 Identities=16% Similarity=0.360 Sum_probs=40.5
Q ss_pred CChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhhcCcceeEEEEEecCCCCC---ceEEEEEecc
Q psy8855 80 KTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQKRGKGIGLRLGVYNRGCSG---LSYKLEYVDE 140 (200)
Q Consensus 80 k~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~~~~~~~lRi~v~~~GC~G---~~~~l~l~~~ 140 (200)
+.+.+...++++.+.+++- +...++++++.+.. .++++....+-.+| +++.+.+.+.
T Consensus 44 ~h~~~l~~l~~~~~~~l~~~~~~ia~al~~~~~~----~g~ni~~N~g~~agq~V~HlH~HvIPr 104 (138)
T COG0537 44 RHVSDLEDLDPEELAELFLLAQKIAKALKEAFGA----DGYNIGINNGKAAGQEVFHLHIHIIPR 104 (138)
T ss_pred cchhhhhhCCHHHHHHHHHHHHHHHHHHHHHhCC----CceEEEEecCcccCcCcceEEEEEcCC
Confidence 6677777888877777777 77778888877752 25666665555555 8888888753
No 68
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=25.90 E-value=1e+02 Score=25.25 Aligned_cols=44 Identities=32% Similarity=0.525 Sum_probs=33.1
Q ss_pred EEEEEEccCCcEEEEEEEecC-ccceeechhhhhhhhcCCChhHHhhhhh
Q psy8855 42 KLQIKVNKNGVITDAKFKTYG-CGSAIASSSLVTEWVKGKTLDEAMSIKN 90 (200)
Q Consensus 42 ~i~l~i~~~~~I~~~~f~~~G-C~~~~Asas~~~~~i~gk~~~ea~~l~~ 90 (200)
.+.+.+++ ++|++|+-.-.. |. |+.-+++.++|++++++.....
T Consensus 134 ~~ei~v~~-~~I~~V~VlR~aPCG----sT~~vAk~l~G~~~~d~~~~~g 178 (217)
T PF02593_consen 134 KVEIEVEN-GKIKDVKVLRSAPCG----STWFVAKRLIGKEVEDAPEKAG 178 (217)
T ss_pred eEEEEecC-CcEEEEEEEecCCCc----cHHHHHHHhcCCccchhhhhhh
Confidence 35556665 799999877542 54 5678899999999999887653
No 69
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=25.56 E-value=1.9e+02 Score=19.86 Aligned_cols=39 Identities=18% Similarity=0.054 Sum_probs=22.3
Q ss_pred ccCCCcEEEEeCCEEEEEecccccccCCcEEEeEec-CCccceEEeCCC
Q psy8855 140 EKRKEDQVFKLNGVQIFINEKDLLYFNGIELDFEFD-GLNKGFKFKNPN 187 (200)
Q Consensus 140 ~~~~~D~v~e~~gi~v~id~~~~~~l~g~~IDy~~~-~~~~~F~i~nP~ 187 (200)
.+.++|.|.-..+++++- -+.+...+- .++......||.
T Consensus 47 ~l~~Gd~V~v~G~v~~y~---------ql~ve~l~~~glg~~~~~~np~ 86 (91)
T cd04482 47 LLIPGDEVTVYGSVRPGT---------TLNLEKLRVIRLARLYERENPV 86 (91)
T ss_pred CCCCCCEEEEEEEEecCC---------EEEEEEEEECCCcceEEEcCCc
Confidence 356778877777776664 234443332 234445556775
No 70
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=25.32 E-value=1.3e+02 Score=19.84 Aligned_cols=22 Identities=9% Similarity=0.317 Sum_probs=15.0
Q ss_pred cEEEEEEEEccCCcEEEEEEEe
Q psy8855 39 DVMKLQIKVNKNGVITDAKFKT 60 (200)
Q Consensus 39 D~i~i~l~i~~~~~I~~~~f~~ 60 (200)
-.++|.+.|+.+|+|.+++...
T Consensus 26 ~~~~V~i~i~~dG~v~~~~i~~ 47 (85)
T PF13103_consen 26 LSVTVRITIDPDGRVISVRIVK 47 (85)
T ss_dssp --EEEEEEE-TTSBEEEEEEEE
T ss_pred cEEEEEEEECCCCCEEEEEEec
Confidence 4577888888889998777654
No 71
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.56 E-value=1.1e+02 Score=22.71 Aligned_cols=35 Identities=17% Similarity=0.219 Sum_probs=16.2
Q ss_pred cCCChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhh
Q psy8855 78 KGKTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQK 112 (200)
Q Consensus 78 ~gk~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~ 112 (200)
.|.|.+|+..+..-.....-. +-.|+++|++.++.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 444444444433332222222 34456677776644
No 72
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=24.51 E-value=3e+02 Score=20.46 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=19.0
Q ss_pred ccccCCcEEEeEecCC--ccceEEe-CCCC
Q psy8855 162 LLYFNGIELDFEFDGL--NKGFKFK-NPNI 188 (200)
Q Consensus 162 ~~~l~g~~IDy~~~~~--~~~F~i~-nP~~ 188 (200)
..--...+|||..... ..+|+|. ||..
T Consensus 80 v~E~~e~tiDfl~g~e~~~G~~IF~~dP~~ 109 (122)
T TIGR02588 80 VVENAEVTIDYLASGSKENGTLIFRSDPRN 109 (122)
T ss_pred eeEEeeEEEEEcCCCCeEeEEEEEccCccc
Confidence 3344568999998775 3799996 5543
No 73
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=24.46 E-value=48 Score=23.29 Aligned_cols=24 Identities=25% Similarity=0.422 Sum_probs=16.2
Q ss_pred HHHHHhhhhcCcceeEEEEEecCCCCCc
Q psy8855 104 KYINKYIQKRGKGIGLRLGVYNRGCSGL 131 (200)
Q Consensus 104 ~~i~~~l~~~~~~~~lRi~v~~~GC~G~ 131 (200)
+.|++.+++++ |++.+...||-|+
T Consensus 21 ~al~~ei~~~g----l~v~v~~tGC~G~ 44 (92)
T cd03063 21 EAIEAEAAARG----LAATIVRNGSRGM 44 (92)
T ss_pred HHHHHHHHHcC----CeEEEEEecCcee
Confidence 45555555542 3788899999875
No 74
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=24.41 E-value=1.1e+02 Score=19.58 Aligned_cols=20 Identities=10% Similarity=0.436 Sum_probs=15.4
Q ss_pred EEEEEEEEccCCcEEEEEEE
Q psy8855 40 VMKLQIKVNKNGVITDAKFK 59 (200)
Q Consensus 40 ~i~i~l~i~~~~~I~~~~f~ 59 (200)
.+.+.+.|+.+|+|++++-.
T Consensus 17 ~v~v~~~I~~~G~v~~~~v~ 36 (79)
T PF03544_consen 17 TVVVEFTIDPDGRVSDVRVI 36 (79)
T ss_dssp EEEEEEEEETTTEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEEEE
Confidence 47788888878999987643
No 75
>TIGR01962 NuoD NADH dehydrogenase I, D subunit. This model recognizes specificially the D subunit of NADH dehydrogenase I complex. It excludes the related chain of NAD(P)H-quinone oxidoreductases from chloroplast and Synechocystis, where the quinone may be plastoquinone rather than ubiquinone. This subunit often appears as a C/D fusion.
Probab=24.28 E-value=3.1e+02 Score=24.31 Aligned_cols=18 Identities=11% Similarity=0.281 Sum_probs=13.3
Q ss_pred EEEEEEEccCCcEEEEEEE
Q psy8855 41 MKLQIKVNKNGVITDAKFK 59 (200)
Q Consensus 41 i~i~l~i~~~~~I~~~~f~ 59 (200)
+++.+.+++ ++|.++.+.
T Consensus 18 ~r~~l~~~g-e~I~~~~~~ 35 (386)
T TIGR01962 18 LRLILELDG-EYVVRADPH 35 (386)
T ss_pred eEEEEEEcC-CEEEEEEEe
Confidence 577777775 688887775
No 76
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=24.13 E-value=48 Score=27.74 Aligned_cols=41 Identities=27% Similarity=0.302 Sum_probs=31.1
Q ss_pred EEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 55 DAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 55 ~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
.+.+.|-||++ ++.+++.++.|+++++|.+.-.+.+...+.
T Consensus 225 ~~~~~GaGD~f---aa~~~a~l~~g~~l~~Av~~A~~~v~~~i~ 265 (281)
T PRK08176 225 DTDLKGTGDLF---CAELVSGLLKGKALTDAAHRAGLRVLEVMR 265 (281)
T ss_pred CCCCCChhHHH---HHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 35667778877 456777888999999999987777766665
No 77
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=23.85 E-value=1.2e+02 Score=19.57 Aligned_cols=28 Identities=14% Similarity=0.319 Sum_probs=20.7
Q ss_pred hhhhhhhHHHHh-hhhhHHHHHHhhhhcC
Q psy8855 87 SIKNTDIAEELV-TKKAAKYINKYIQKRG 114 (200)
Q Consensus 87 ~l~~~~i~~~l~-~~~a~~~i~~~l~~~~ 114 (200)
.++..+|+..|+ .|.+.+.+.+.+...+
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 345678888999 7888888888887764
No 78
>PRK06075 NADH dehydrogenase subunit D; Validated
Probab=23.78 E-value=3.2e+02 Score=24.30 Aligned_cols=18 Identities=17% Similarity=0.364 Sum_probs=13.0
Q ss_pred EEEEEEEccCCcEEEEEEE
Q psy8855 41 MKLQIKVNKNGVITDAKFK 59 (200)
Q Consensus 41 i~i~l~i~~~~~I~~~~f~ 59 (200)
+++.+.+++ ++|.++.+.
T Consensus 22 ~r~~l~~dg-e~I~~~~~~ 39 (392)
T PRK06075 22 LRLILELDG-EVVVRADPH 39 (392)
T ss_pred eEEEEEEcC-CEEEEEEEe
Confidence 677777775 688887764
No 79
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.63 E-value=94 Score=24.14 Aligned_cols=76 Identities=25% Similarity=0.344 Sum_probs=51.2
Q ss_pred CCcccEEEEEEEEccCCcEEEEEEEec------Ccc-------ceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh---
Q psy8855 35 PACGDVMKLQIKVNKNGVITDAKFKTY------GCG-------SAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV--- 98 (200)
Q Consensus 35 ~~CGD~i~i~l~i~~~~~I~~~~f~~~------GC~-------~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~--- 98 (200)
|.|+--|+=...++ |.+ .+++... -|. ..+.+|.-|++...+.+.+|-..+.. .+.+.+-
T Consensus 43 p~C~~~IrG~y~v~--gv~-~~g~~~~~PsYC~~CGkpyPWt~~~L~aa~el~ee~eeLs~deke~~~~-sl~dL~~d~P 118 (158)
T PF10083_consen 43 PNCSTPIRGDYHVE--GVF-GLGGHYEAPSYCHNCGKPYPWTENALEAANELIEEDEELSPDEKEQFKE-SLPDLTKDTP 118 (158)
T ss_pred cCCCCCCCCceecC--Cee-eeCCCCCCChhHHhCCCCCchHHHHHHHHHHHHHHhhcCCHHHHHHHHh-hhHHHhhcCC
Confidence 77877777666765 232 3333322 232 24677788888889999999888755 5666665
Q ss_pred -hhhhHHHHHHhhhhcC
Q psy8855 99 -TKKAAKYINKYIQKRG 114 (200)
Q Consensus 99 -~~~a~~~i~~~l~~~~ 114 (200)
|+-|..+||.++.+-+
T Consensus 119 kT~vA~~rfKk~~~K~g 135 (158)
T PF10083_consen 119 KTKVAATRFKKILSKAG 135 (158)
T ss_pred ccHHHHHHHHHHHHHHh
Confidence 5668889999987754
No 80
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=23.13 E-value=48 Score=26.61 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=28.8
Q ss_pred EEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHH
Q psy8855 53 ITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEE 96 (200)
Q Consensus 53 I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~ 96 (200)
+..+.+.|-||++ ++.+++.++.|+++++|.+.-...+...
T Consensus 198 ~~~~~~~GaGD~f---~a~l~a~l~~g~~~~~A~~~A~~~~~~~ 238 (242)
T cd01169 198 IDTKNTHGTGCTL---SSAIAANLAKGLSLEEAVREAKEYVTQA 238 (242)
T ss_pred eCCCCCCChHHHH---HHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 3345556778877 4567778889999999988766555443
No 81
>PRK12412 pyridoxal kinase; Reviewed
Probab=22.99 E-value=48 Score=27.49 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=25.9
Q ss_pred EecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHH
Q psy8855 59 KTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEEL 97 (200)
Q Consensus 59 ~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l 97 (200)
.|-||++ ++.+++.++.|+++++|.+.-...+.+.+
T Consensus 209 ~GaGD~f---~aa~aa~l~~g~~l~eA~~~A~~~~~~~i 244 (268)
T PRK12412 209 HGAGCTY---SAAITAELAKGKPVKEAVKTAKEFITAAI 244 (268)
T ss_pred CchHHHH---HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 4667777 45677888899999999887655444443
No 82
>PRK07217 replication factor A; Reviewed
Probab=22.70 E-value=4.5e+02 Score=22.79 Aligned_cols=62 Identities=21% Similarity=0.276 Sum_probs=37.5
Q ss_pred EEEEEEEEccCCc-EEEEEEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHhhhhhHHHHHHhhhhcCccee
Q psy8855 40 VMKLQIKVNKNGV-ITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELVTKKAAKYINKYIQKRGKGIG 118 (200)
Q Consensus 40 ~i~i~l~i~~~~~-I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~~~~a~~~i~~~l~~~~~~~~ 118 (200)
.+++...+++ |. ...+.|. .=+++.+.|.+++||+.+-. ++|++..-...|++.+ -|.+
T Consensus 216 DLrik~vlDD-Gt~~~~~~~~-----------~e~te~l~G~~l~eak~~a~----dald~~vv~~~i~~~l----lGr~ 275 (311)
T PRK07217 216 DLRIKGVLDD-GEEVQEVIFN-----------REATEELTGITLEEAKQMAM----DALDTGVVLDELKEKL----LGRY 275 (311)
T ss_pred eeEEEEEEEC-CCCeEEEEEC-----------hHHhHHHhCCCHHHHHHHHH----HhhchhhHHHHHHHhh----cCce
Confidence 4777777775 42 3344443 33578889999999988753 4455444445555544 3445
Q ss_pred EEE
Q psy8855 119 LRL 121 (200)
Q Consensus 119 lRi 121 (200)
+|+
T Consensus 276 ~~v 278 (311)
T PRK07217 276 YRV 278 (311)
T ss_pred EEE
Confidence 555
No 83
>COG3369 Zinc finger domain containing protein (CDGSH-type) [Function unknown]
Probab=22.67 E-value=32 Score=23.39 Aligned_cols=10 Identities=40% Similarity=0.860 Sum_probs=7.5
Q ss_pred CCccCCCCCC
Q psy8855 190 NKCGCGKSFQ 199 (200)
Q Consensus 190 ~~C~CG~sf~ 199 (200)
.-|.||.|=+
T Consensus 32 ~LCrCG~S~N 41 (78)
T COG3369 32 ALCRCGHSEN 41 (78)
T ss_pred EEEeccCcCC
Confidence 4799999843
No 84
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.53 E-value=1.3e+02 Score=22.65 Aligned_cols=36 Identities=8% Similarity=-0.032 Sum_probs=16.6
Q ss_pred hcCCChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhh
Q psy8855 77 VKGKTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQK 112 (200)
Q Consensus 77 i~gk~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~ 112 (200)
+.|++.+|+..+..-.....-. +-.|.++|++.+++
T Consensus 132 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 168 (173)
T PRK09645 132 YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQE 168 (173)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444444433322222222 34456677777654
No 85
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=22.50 E-value=1.2e+02 Score=21.19 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=13.7
Q ss_pred cceEEeCCCCCCCc-cCCCCC
Q psy8855 179 KGFKFKNPNIKNKC-GCGKSF 198 (200)
Q Consensus 179 ~~F~i~nP~~~~~C-~CG~sf 198 (200)
.-.+|+|=.+. .| .||++|
T Consensus 26 ~~IvIknVPa~-~C~~CGe~y 45 (89)
T TIGR03829 26 KAIEIKETPSI-SCSHCGMEY 45 (89)
T ss_pred eEEEEecCCcc-cccCCCcEe
Confidence 56778885554 68 599986
No 86
>PRK10467 hydrogenase 2 large subunit; Provisional
Probab=21.78 E-value=3.2e+02 Score=25.76 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=25.6
Q ss_pred EEEEEEEEccCCcEEEEEEEecCccceeechhhhhhhhcCCChhHHhhh
Q psy8855 40 VMKLQIKVNKNGVITDAKFKTYGCGSAIASSSLVTEWVKGKTLDEAMSI 88 (200)
Q Consensus 40 ~i~i~l~i~~~~~I~~~~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l 88 (200)
.++|.+.+++ ++|+++...+. - - ==+..+++|++..++..+
T Consensus 16 ~lri~v~vd~-g~V~~a~~~g~--~-~----RGiEkileGR~p~dal~l 56 (567)
T PRK10467 16 HLRIDCEIEN-GVVSKAWASGT--M-W----RGMEEIVKNRDPRDAWMI 56 (567)
T ss_pred EEEEEEEEEC-CEEEEEEEcCc--c-c----CcHHHHHcCCCHHHHHHH
Confidence 4788888885 79998875332 1 1 113456667777776544
No 87
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=21.33 E-value=95 Score=21.20 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=13.4
Q ss_pred EEEEEEEEccCCcEEEEEEEecCc
Q psy8855 40 VMKLQIKVNKNGVITDAKFKTYGC 63 (200)
Q Consensus 40 ~i~i~l~i~~~~~I~~~~f~~~GC 63 (200)
.|++. ++.+|.|.++.|.....
T Consensus 31 ~V~V~--v~g~g~v~~i~i~~~~~ 52 (93)
T PF02575_consen 31 LVTVT--VNGNGEVVDIEIDPSAL 52 (93)
T ss_dssp TEEEE--EETTS-EEEEEE-GGGG
T ss_pred EEEEE--EecCceEEEEEEehHhh
Confidence 45554 55568999999986543
No 88
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=21.14 E-value=76 Score=21.03 Aligned_cols=20 Identities=30% Similarity=0.581 Sum_probs=16.4
Q ss_pred hHHHHHHHcCCCCCCCCCCCC
Q psy8855 4 SEKVLDHYENPRNVGVFEKND 24 (200)
Q Consensus 4 ~~~il~~~~~p~~~g~l~~~~ 24 (200)
++.+++++.+|.|+ +|+.|.
T Consensus 43 ~ke~~d~~n~p~ny-rlE~~s 62 (70)
T PF14410_consen 43 RKEFLDWYNDPDNY-RLEDPS 62 (70)
T ss_pred HHHHHHHHhCccce-eecCCc
Confidence 56889999999998 577664
No 89
>PRK05756 pyridoxamine kinase; Validated
Probab=21.02 E-value=46 Score=27.76 Aligned_cols=39 Identities=18% Similarity=0.256 Sum_probs=29.6
Q ss_pred EEEecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 57 KFKTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 57 ~f~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
.+.|-||++ +|.+++.++.|++++++.+.-...+...|.
T Consensus 216 ~~~GaGD~f---~a~~~a~l~~g~~~~~al~~A~~~~~~~i~ 254 (286)
T PRK05756 216 QPVGVGDLT---SALFLARLLQGGSLEEALEHTTAAVYEVMA 254 (286)
T ss_pred CCCChHHHH---HHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 566677777 457778889999999999887766665555
No 90
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.79 E-value=1.5e+02 Score=23.05 Aligned_cols=38 Identities=5% Similarity=0.070 Sum_probs=22.3
Q ss_pred hcCCChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhhcC
Q psy8855 77 VKGKTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQKRG 114 (200)
Q Consensus 77 i~gk~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~~~ 114 (200)
+.|++.+|+..+..-.....-. +-.|+++|++.++.-+
T Consensus 148 ~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~ 186 (192)
T PRK09643 148 MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLR 186 (192)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566666655554444434444 5567788888887653
No 91
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=20.75 E-value=1e+02 Score=19.60 Aligned_cols=17 Identities=35% Similarity=0.728 Sum_probs=11.3
Q ss_pred cEEEEEEEEccCCcEEEEE
Q psy8855 39 DVMKLQIKVNKNGVITDAK 57 (200)
Q Consensus 39 D~i~i~l~i~~~~~I~~~~ 57 (200)
|++.|. ++++|+|++++
T Consensus 42 dRLnv~--~D~~g~I~~v~ 58 (60)
T PF11720_consen 42 DRLNVE--VDDDGVITRVR 58 (60)
T ss_pred CcEEEE--ECCCCcEEEEe
Confidence 555555 44568999876
No 92
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.63 E-value=2.1e+02 Score=22.07 Aligned_cols=45 Identities=18% Similarity=0.299 Sum_probs=23.5
Q ss_pred hcCCChhHHhhhhhhhhHHHHh-hhhhHHHHHHhhhhcCc---ceeEEE
Q psy8855 77 VKGKTLDEAMSIKNTDIAEELV-TKKAAKYINKYIQKRGK---GIGLRL 121 (200)
Q Consensus 77 i~gk~~~ea~~l~~~~i~~~l~-~~~a~~~i~~~l~~~~~---~~~lRi 121 (200)
+.|+|.+|+.....-.....-. +-.|.++|++++...++ ...+|+
T Consensus 125 ~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~~~~~~~~~~~ 173 (182)
T PRK12511 125 IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTGPARGRAHLRV 173 (182)
T ss_pred HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCceeeee
Confidence 3455555544443333322222 44567888888876542 335665
No 93
>PRK12616 pyridoxal kinase; Reviewed
Probab=20.49 E-value=57 Score=27.08 Aligned_cols=37 Identities=24% Similarity=0.368 Sum_probs=26.7
Q ss_pred EecCccceeechhhhhhhhcCCChhHHhhhhhhhhHHHHh
Q psy8855 59 KTYGCGSAIASSSLVTEWVKGKTLDEAMSIKNTDIAEELV 98 (200)
Q Consensus 59 ~~~GC~~~~Asas~~~~~i~gk~~~ea~~l~~~~i~~~l~ 98 (200)
.|-||++ ++.+++.++.|+++++|.+.-...+.+.|.
T Consensus 212 ~GaGD~f---saalaa~l~~g~~l~~Av~~A~~~~~~~i~ 248 (270)
T PRK12616 212 HGAGCTF---SAAVTAELAKGSEVKEAIYAAKEFITAAIK 248 (270)
T ss_pred CcHHHHH---HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Confidence 5667877 456777888999999998876655544443
No 94
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=20.34 E-value=71 Score=21.66 Aligned_cols=29 Identities=34% Similarity=0.519 Sum_probs=15.6
Q ss_pred ceEEEEEecccCCCcEEEEeCCEEEEEec
Q psy8855 131 LSYKLEYVDEKRKEDQVFKLNGVQIFINE 159 (200)
Q Consensus 131 ~~~~l~l~~~~~~~D~v~e~~gi~v~id~ 159 (200)
+.|.+...+-|..-|+++....+.||||-
T Consensus 36 ~RyR~~~~~lpG~PDiv~~~~k~aIFVdG 64 (75)
T PF03852_consen 36 LRYRLNRKDLPGKPDIVFPKYKIAIFVDG 64 (75)
T ss_dssp --EEES-TTSTT--SEEEGGGTEEEEEE-
T ss_pred CEEEEccCcCCCCCCEEECCCCEEEEEec
Confidence 34444333334456888888888888874
No 95
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=20.26 E-value=42 Score=21.00 Aligned_cols=10 Identities=40% Similarity=1.308 Sum_probs=8.0
Q ss_pred CCccCCCCCC
Q psy8855 190 NKCGCGKSFQ 199 (200)
Q Consensus 190 ~~C~CG~sf~ 199 (200)
..|||..+|+
T Consensus 40 aACgCHRnFH 49 (53)
T TIGR01566 40 AACGCHRNFH 49 (53)
T ss_pred eecCcccccc
Confidence 3789999886
Done!