Query 031835
Match_columns 152
No_of_seqs 117 out of 1112
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:01:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031835hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11325 scaffold protein; Pro 100.0 1.9E-37 4.2E-42 232.1 14.0 119 32-151 2-121 (127)
2 TIGR01999 iscU FeS cluster ass 100.0 5.3E-37 1.1E-41 228.7 14.0 118 33-151 1-119 (124)
3 TIGR03419 NifU_clost FeS clust 100.0 4.5E-36 9.8E-41 222.9 13.9 114 33-151 1-116 (121)
4 PF01592 NifU_N: NifU-like N t 100.0 7.2E-36 1.6E-40 222.7 14.3 118 32-151 1-120 (126)
5 KOG3361 Iron binding protein i 100.0 4.7E-35 1E-39 220.2 12.1 119 31-150 27-146 (157)
6 COG0822 IscU NifU homolog invo 100.0 3.9E-33 8.4E-38 214.6 12.5 119 28-150 2-140 (150)
7 TIGR02000 NifU_proper Fe-S clu 100.0 8.3E-33 1.8E-37 232.0 14.3 117 32-151 3-121 (290)
8 cd06664 IscU_like Iron-sulfur 100.0 1.6E-32 3.4E-37 202.8 12.7 111 32-147 1-123 (123)
9 TIGR01994 SUF_scaf_2 SUF syste 100.0 1.2E-31 2.6E-36 203.0 14.3 114 30-149 2-137 (137)
10 PF12637 TSCPD: TSCPD domain; 92.8 0.85 1.8E-05 32.3 7.5 69 67-148 7-95 (95)
11 PF02657 SufE: Fe-S metabolism 88.7 7 0.00015 29.0 9.3 92 30-132 11-103 (125)
12 PF10437 Lip_prot_lig_C: Bacte 76.0 4.6 9.9E-05 27.5 3.7 43 68-114 15-57 (86)
13 COG0351 ThiD Hydroxymethylpyri 73.8 9.3 0.0002 32.2 5.6 45 82-129 200-244 (263)
14 PRK09296 cysteine desufuration 72.7 39 0.00085 25.6 9.5 65 64-132 48-113 (138)
15 PRK15019 CsdA-binding activato 71.3 44 0.00096 25.6 9.2 64 65-132 59-123 (147)
16 TIGR03391 FeS_syn_CsdE cystein 70.2 45 0.00097 25.3 9.2 64 65-132 54-118 (138)
17 COG2166 sufE Cysteine desulfur 70.1 26 0.00057 27.0 6.9 64 65-132 54-118 (144)
18 PRK03822 lplA lipoate-protein 66.3 28 0.0006 30.1 7.1 44 68-115 262-305 (338)
19 PLN02673 quinolinate synthetas 65.1 74 0.0016 30.6 10.1 60 65-128 127-186 (724)
20 PF02593 dTMP_synthase: Thymid 63.0 33 0.00072 28.1 6.6 121 15-148 77-216 (217)
21 PTZ00493 phosphomethylpyrimidi 62.2 14 0.00029 31.9 4.4 46 82-130 240-285 (321)
22 PF08543 Phos_pyr_kin: Phospho 57.5 13 0.00028 30.0 3.4 44 83-129 190-233 (246)
23 PF01466 Skp1: Skp1 family, di 49.7 25 0.00054 23.6 3.3 22 98-119 33-54 (78)
24 PRK14061 unknown domain/lipoat 46.8 54 0.0012 30.6 5.9 46 66-115 484-529 (562)
25 TIGR00545 lipoyltrans lipoyltr 45.0 36 0.00078 29.1 4.3 44 68-115 257-300 (324)
26 TIGR03295 frhA coenzyme F420 h 44.4 1.3E+02 0.0028 26.5 7.8 63 71-144 17-81 (411)
27 cd01169 HMPP_kinase 4-amino-5- 44.2 48 0.001 26.0 4.7 44 83-129 197-240 (242)
28 PF04205 FMN_bind: FMN-binding 38.0 51 0.0011 21.6 3.4 25 69-94 4-28 (81)
29 PRK12413 phosphomethylpyrimidi 36.5 45 0.00099 26.5 3.5 42 86-130 201-242 (253)
30 PF00227 Proteasome: Proteasom 36.5 1.7E+02 0.0037 21.9 6.5 58 70-129 118-176 (190)
31 cd03313 enolase Enolase: Enola 35.3 2.8E+02 0.006 24.4 8.5 62 88-151 53-120 (408)
32 PRK08176 pdxK pyridoxal-pyrido 34.1 51 0.0011 27.1 3.5 44 86-132 225-268 (281)
33 cd01173 pyridoxal_pyridoxamine 34.1 52 0.0011 26.1 3.4 40 87-129 211-250 (254)
34 COG3259 FrhA Coenzyme F420-red 33.3 1.9E+02 0.004 26.3 7.0 40 72-119 18-57 (441)
35 PRK05756 pyridoxamine kinase; 33.0 83 0.0018 25.7 4.5 40 88-130 216-255 (286)
36 PRK12616 pyridoxal kinase; Rev 32.1 83 0.0018 25.7 4.4 38 90-130 212-249 (270)
37 PLN02978 pyridoxal kinase 32.1 88 0.0019 26.2 4.6 44 86-132 225-269 (308)
38 PF02575 YbaB_DNA_bd: YbaB/Ebf 31.1 1.1E+02 0.0025 20.7 4.3 59 70-131 31-90 (93)
39 PRK08573 phosphomethylpyrimidi 29.7 84 0.0018 27.9 4.3 44 83-129 200-243 (448)
40 PRK00077 eno enolase; Provisio 29.5 3.6E+02 0.0079 23.8 8.2 43 88-132 58-101 (425)
41 PRK04223 rpl22p 50S ribosomal 29.2 1.6E+02 0.0035 22.8 5.3 22 101-122 30-51 (153)
42 cd00336 Ribosomal_L22 Ribosoma 29.1 1.2E+02 0.0026 21.3 4.3 20 102-121 16-35 (105)
43 TIGR01044 rplV_bact ribosomal 28.9 1.7E+02 0.0036 20.8 5.0 39 102-149 14-52 (103)
44 cd03752 proteasome_alpha_type_ 28.0 1.9E+02 0.0041 22.6 5.7 56 72-129 144-199 (213)
45 TIGR00778 ahpD_dom alkylhydrop 27.8 1.1E+02 0.0024 18.0 3.5 29 91-120 18-46 (50)
46 PF00237 Ribosomal_L22: Riboso 27.6 1.7E+02 0.0036 20.6 4.8 39 102-149 14-52 (105)
47 PRK06427 bifunctional hydroxy- 27.1 1.1E+02 0.0024 24.5 4.3 44 83-129 204-247 (266)
48 PTZ00347 phosphomethylpyrimidi 26.6 97 0.0021 27.8 4.2 45 82-129 433-477 (504)
49 PF11604 CusF_Ec: Copper bindi 26.5 1.1E+02 0.0024 20.2 3.4 25 64-88 42-67 (70)
50 COG4259 Uncharacterized protei 25.7 66 0.0014 23.9 2.4 21 23-44 26-46 (121)
51 cd03755 proteasome_alpha_type_ 25.4 2.5E+02 0.0055 21.8 5.9 57 71-129 140-196 (207)
52 COG0091 RplV Ribosomal protein 25.3 2.1E+02 0.0045 21.3 5.1 20 101-120 25-44 (120)
53 PLN02898 HMP-P kinase/thiamin- 25.1 1.5E+02 0.0032 26.6 5.1 44 84-130 210-253 (502)
54 PF03450 CO_deh_flav_C: CO deh 24.9 1.9E+02 0.0042 19.8 4.7 43 72-115 19-61 (103)
55 cd03756 proteasome_alpha_arche 24.7 3E+02 0.0064 21.5 6.2 57 71-129 140-196 (211)
56 TIGR01038 L22_arch ribosomal p 24.3 2.3E+02 0.005 21.8 5.3 27 96-122 21-47 (150)
57 TIGR00097 HMP-P_kinase phospho 24.0 1.2E+02 0.0027 24.2 4.0 44 83-129 196-239 (254)
58 COG0638 PRE1 20S proteasome, a 23.5 2.6E+02 0.0056 22.6 5.8 96 20-129 100-197 (236)
59 KOG1724 SCF ubiquitin ligase, 23.4 1.1E+02 0.0023 24.0 3.3 24 96-119 115-138 (162)
60 PF04879 Molybdop_Fe4S4: Molyb 23.3 1.3E+02 0.0029 18.3 3.2 24 65-90 9-32 (55)
61 PRK12412 pyridoxal kinase; Rev 23.1 1.4E+02 0.0031 24.2 4.3 37 91-130 210-246 (268)
62 PRK07105 pyridoxamine kinase; 22.9 1.6E+02 0.0034 24.0 4.5 40 87-129 215-254 (284)
63 cd03751 proteasome_alpha_type_ 22.2 3.3E+02 0.0072 21.4 6.1 57 71-129 142-198 (212)
64 PRK00565 rplV 50S ribosomal pr 21.8 2.2E+02 0.0049 20.5 4.6 21 101-121 17-37 (112)
65 TIGR02870 spore_II_D stage II 21.4 1.8E+02 0.004 25.2 4.7 43 73-118 285-327 (338)
66 PRK07217 replication factor A; 21.0 2.7E+02 0.0059 24.1 5.6 43 70-124 216-258 (311)
67 PF02563 Poly_export: Polysacc 20.7 65 0.0014 21.6 1.5 25 107-131 50-74 (82)
68 cd04451 S1_IF1 S1_IF1: Transla 20.2 1E+02 0.0023 19.6 2.3 14 64-77 40-53 (64)
No 1
>PRK11325 scaffold protein; Provisional
Probab=100.00 E-value=1.9e-37 Score=232.10 Aligned_cols=119 Identities=61% Similarity=0.923 Sum_probs=110.8
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCC
Q 031835 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (152)
Q Consensus 32 lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gk 111 (152)
+|+++|++||.||+|+|.+++++...++++.+||.|||+|+||++++++ |+|+|++|+++||++++||+|+|+++++||
T Consensus 2 ~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 2 AYSEKVIDHYENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVNDE-GIIEDAKFKTYGCGSAIASSSLVTEWVKGK 80 (127)
T ss_pred ccHHHHHHHHhCcCCCCCCCCCccccceEEecCCCCccEEEEEEEECCC-CeEEEEEEEeeCCHHHHHHHHHHHHHHcCC
Confidence 7999999999999999999998854456678999999999999999732 899999999999999999999999999999
Q ss_pred CHHHHHchhHHHHHhhhcCcH-HHHHHHHHHHHHHHHHhhh
Q 031835 112 QMQEVLSIKNTGVAGKLQNIF-LYHLLNCIAACLLKMLSRL 151 (152)
Q Consensus 112 tl~EA~~l~~~~I~~~Lg~~p-~~hca~~a~~~l~~~~~~~ 151 (152)
|++||..|+.++|.++||.+| ..||+.|+..||+++|.+.
T Consensus 81 tl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y 121 (127)
T PRK11325 81 TLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADY 121 (127)
T ss_pred CHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHH
Confidence 999999999999999998777 9999999999999999764
No 2
>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=100.00 E-value=5.3e-37 Score=228.68 Aligned_cols=118 Identities=58% Similarity=0.877 Sum_probs=110.2
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCC
Q 031835 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (152)
Q Consensus 33 Ys~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gkt 112 (152)
||++|++||.||+|+|.+++++..+++|+.+||.|||.|+||++++++ ++|+|++|+++||++++||+|+|+++++|||
T Consensus 1 Y~~~il~~~~~p~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~~-~~I~d~~f~~~GC~~s~Asas~~~e~i~Gkt 79 (124)
T TIGR01999 1 YSEKVLDHYENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDD-GIIEDAKFKTFGCGSAIASSSLATELIKGKS 79 (124)
T ss_pred CcHHHHHHHhCCCCCCCCCCCccccceEEeCCCCCccEEEEEEEECCC-CeEEEEEEEecCcHHHHHHHHHHHHHHcCCC
Confidence 899999999999999999998854456778999999999999999654 7999999999999999999999999999999
Q ss_pred HHHHHchhHHHHHhhhcCcH-HHHHHHHHHHHHHHHHhhh
Q 031835 113 MQEVLSIKNTGVAGKLQNIF-LYHLLNCIAACLLKMLSRL 151 (152)
Q Consensus 113 l~EA~~l~~~~I~~~Lg~~p-~~hca~~a~~~l~~~~~~~ 151 (152)
++|+..|+.++|.++||.+| +.||+.|+..||++||.+.
T Consensus 80 l~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y 119 (124)
T TIGR01999 80 LEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDY 119 (124)
T ss_pred HHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHH
Confidence 99999999999999998777 9999999999999999864
No 3
>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=100.00 E-value=4.5e-36 Score=222.94 Aligned_cols=114 Identities=46% Similarity=0.750 Sum_probs=108.1
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCC
Q 031835 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (152)
Q Consensus 33 Ys~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gkt 112 (152)
|+++|++||.||+|+|.+++++. ++..+||.|||+|+||+++++ ++|+|++|+++||++|+||+|+|+++++|||
T Consensus 1 Y~~~il~~~~np~~~g~l~~~~~---~~~~~np~CGD~i~l~l~i~~--~~I~d~~f~~~GC~is~Asas~~~e~i~Gk~ 75 (121)
T TIGR03419 1 YSEKVMDHFMNPRNVGEIENADG---VGEVGNPKCGDIMKIFLKVED--DIIKDVKFKTFGCGAAIASSSMATEMIKGKT 75 (121)
T ss_pred ChHHHHHHHhCCCCCCCCCCCCe---EEEeCCCCCccEEEEEEEEcC--CEEEEEEEEEeccHHHHHHHHHHHHHHcCCC
Confidence 89999999999999999999884 467899999999999999987 8999999999999999999999999999999
Q ss_pred HHHHHchhHHHHHhhhcCcH--HHHHHHHHHHHHHHHHhhh
Q 031835 113 MQEVLSIKNTGVAGKLQNIF--LYHLLNCIAACLLKMLSRL 151 (152)
Q Consensus 113 l~EA~~l~~~~I~~~Lg~~p--~~hca~~a~~~l~~~~~~~ 151 (152)
++|+..|+.+++.++|+++| ..||+.|++.||++|+.+.
T Consensus 76 l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y 116 (121)
T TIGR03419 76 LEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDY 116 (121)
T ss_pred HHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999766 9999999999999998764
No 4
>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=100.00 E-value=7.2e-36 Score=222.71 Aligned_cols=118 Identities=37% Similarity=0.707 Sum_probs=110.3
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCC
Q 031835 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (152)
Q Consensus 32 lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gk 111 (152)
+|+++|++||.||+|+|.++++++ +++..+||.|||+|+||++|++++|+|+|++|+++||++++||+|+++++++||
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 699999999999999999999985 346779999999999999999866899999999999999999999999999999
Q ss_pred CHHHHHchhHHHHHhhhcCcH--HHHHHHHHHHHHHHHHhhh
Q 031835 112 QMQEVLSIKNTGVAGKLQNIF--LYHLLNCIAACLLKMLSRL 151 (152)
Q Consensus 112 tl~EA~~l~~~~I~~~Lg~~p--~~hca~~a~~~l~~~~~~~ 151 (152)
|++||..|+.++|.++|++.| +.||+.++..||++++++.
T Consensus 79 ~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y 120 (126)
T PF01592_consen 79 TLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADY 120 (126)
T ss_dssp BHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHH
Confidence 999999999999999999866 9999999999999999864
No 5
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=100.00 E-value=4.7e-35 Score=220.21 Aligned_cols=119 Identities=66% Similarity=0.972 Sum_probs=115.5
Q ss_pred HhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcC
Q 031835 31 RLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKG 110 (152)
Q Consensus 31 ~lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~G 110 (152)
.+|.+.++|||.||||.|.|+..|+.||+|..|-|.|||.+.++++++++ |+|+|++|.+|||+..|||+|+++||++|
T Consensus 27 rlYh~~VidHy~nPRNVGSldK~dpnVGtGlVGAPACGDVMkLqIkvd~~-g~I~dakFKTFGCGSAIASSS~aTewvkg 105 (157)
T KOG3361|consen 27 RLYHENVIDHYENPRNVGSLDKNDPNVGTGLVGAPACGDVMKLQIKVDDS-GVIEDAKFKTFGCGSAIASSSLATEWVKG 105 (157)
T ss_pred hhcchhhhhcccCccccCccCCCCCCcccccccCccccceeeEEEEECCC-CcEEEeeeeecccchHhhhhHHHHHHHcc
Confidence 88999999999999999999999999999999999999999999999864 99999999999999999999999999999
Q ss_pred CCHHHHHchhHHHHHhhhcCcH-HHHHHHHHHHHHHHHHhh
Q 031835 111 KQMQEVLSIKNTGVAGKLQNIF-LYHLLNCIAACLLKMLSR 150 (152)
Q Consensus 111 ktl~EA~~l~~~~I~~~Lg~~p-~~hca~~a~~~l~~~~~~ 150 (152)
||+||+..|.+.+|.+.|..+| +.||++||+-|.+-|+..
T Consensus 106 kt~dea~kIkNteIAKeL~LPPVKLHCSMLAEDAIKaAikd 146 (157)
T KOG3361|consen 106 KTLDEALKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKD 146 (157)
T ss_pred ccHHHHHhcccHHHHHhccCCchhhhhHHHHHHHHHHHHHH
Confidence 9999999999999999999999 999999999999988753
No 6
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=100.00 E-value=3.9e-33 Score=214.56 Aligned_cols=119 Identities=45% Similarity=0.662 Sum_probs=109.9
Q ss_pred hhhHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHH
Q 031835 28 AMPRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEW 107 (152)
Q Consensus 28 ~~~~lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~el 107 (152)
.+|++|+++|++||.||+|.|.+++++.. .+..++|.|||.|++||++++ |+|+|++|+++||++++||+|+|+++
T Consensus 2 ~~~~~y~~~Ildh~~np~~~g~l~~~~~~--~~~~~~~~CGD~i~l~lkv~~--~~I~d~~F~~~GC~is~ASss~~te~ 77 (150)
T COG0822 2 NLDDLYSEKILDHYKNPRNVGVLDDADVG--VGHVGAPACGDVITLYLKVDN--GVIEDAKFKGFGCAISIASSSMMTEL 77 (150)
T ss_pred cHHHHHHHHHHHHhcCCCcCCccCccchh--ccccCCCCccceEEEEEEEcC--CEEEEEEeeecCcHHHHHHHHHHHHH
Confidence 57999999999999999999999999843 456678999999999999997 99999999999999999999999999
Q ss_pred HcCCCHHHHHchh--HHHHHhhhc-----------------CcH-HHHHHHHHHHHHHHHHhh
Q 031835 108 VKGKQMQEVLSIK--NTGVAGKLQ-----------------NIF-LYHLLNCIAACLLKMLSR 150 (152)
Q Consensus 108 i~Gktl~EA~~l~--~~~I~~~Lg-----------------~~p-~~hca~~a~~~l~~~~~~ 150 (152)
++|||++||++++ ..+|.+.+| .+| .+||+.|+..||+.++.+
T Consensus 78 v~Gkti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~~ai~~ 140 (150)
T COG0822 78 VKGKTLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALKAAIKD 140 (150)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhHhhhhhccccccccchhccHHHHHHHHHH
Confidence 9999999999999 888999888 455 899999999999999864
No 7
>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=100.00 E-value=8.3e-33 Score=231.99 Aligned_cols=117 Identities=41% Similarity=0.647 Sum_probs=109.2
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCC
Q 031835 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (152)
Q Consensus 32 lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gk 111 (152)
+|+++|++||.||+|+|.+++++. +++.+||.|||.|+||+++++++++|+|++|+++||++++||+|+|+++++||
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 DYTDKVKEHFYNPKNAGVVEDANA---VGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIKGL 79 (290)
T ss_pred chHHHHHHHHhCcCCCCCCCCCCc---EEEeCCCCCcceEEEEEEEcCCCCeEEEEEEEecCcHHHHHHHHHHHHHHcCC
Confidence 499999999999999999999884 46789999999999999997444999999999999999999999999999999
Q ss_pred CHHHHHchhHHHHHhhhcCcH--HHHHHHHHHHHHHHHHhhh
Q 031835 112 QMQEVLSIKNTGVAGKLQNIF--LYHLLNCIAACLLKMLSRL 151 (152)
Q Consensus 112 tl~EA~~l~~~~I~~~Lg~~p--~~hca~~a~~~l~~~~~~~ 151 (152)
|++||+.++.++|.++|+++| .+||+.|+..||++||.+.
T Consensus 80 tv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y 121 (290)
T TIGR02000 80 TLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANY 121 (290)
T ss_pred CHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHH
Confidence 999999999999999999766 9999999999999998764
No 8
>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=100.00 E-value=1.6e-32 Score=202.77 Aligned_cols=111 Identities=43% Similarity=0.653 Sum_probs=102.9
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCC
Q 031835 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (152)
Q Consensus 32 lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gk 111 (152)
+|+++|++||.||+|+|.+++++. +++.+||.|||+|+||+++++ ++|+|++|+++||++++||+|+|+++++||
T Consensus 1 ~y~~~il~~~~~p~~~g~l~~~~~---~~~~~n~~CGD~v~l~l~i~~--~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk 75 (123)
T cd06664 1 LYSEIILDHYRNPRNVGRLEDADG---TGEVGNPLCGDEITLYLKVED--GRITDAKFQGFGCAISIASASLLTELIKGK 75 (123)
T ss_pred CcHHHHHHHhhCCCCCCCCCCCCe---EEEcCCCCCCceEEEEEEEcC--CEEEEEEEEecCcHHHHHHHHHHHHHHcCC
Confidence 599999999999999999999874 467899999999999999988 899999999999999999999999999999
Q ss_pred CHHHHHchhHHHHHhh----------h-cCcH-HHHHHHHHHHHHHHH
Q 031835 112 QMQEVLSIKNTGVAGK----------L-QNIF-LYHLLNCIAACLLKM 147 (152)
Q Consensus 112 tl~EA~~l~~~~I~~~----------L-g~~p-~~hca~~a~~~l~~~ 147 (152)
|++|+..++.+++... + +.+| ..||+.|+..||+++
T Consensus 76 ~~~ea~~i~~~~~~~~~~~~~l~~~~~~~~~~~R~~Ca~L~~~Al~~a 123 (123)
T cd06664 76 TLDEALKLLNKDIAMLDGKEELAALAGVGLPPARIHCALLAWKALKAA 123 (123)
T ss_pred cHHHHHHHHHHHHHHhcCchhHHHhcccccCcccchHHHHHHHHHHhC
Confidence 9999999999999886 3 4455 999999999999874
No 9
>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=99.98 E-value=1.2e-31 Score=202.96 Aligned_cols=114 Identities=30% Similarity=0.506 Sum_probs=100.8
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHc
Q 031835 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (152)
Q Consensus 30 ~~lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~ 109 (152)
.++|+++|+|||.||+|+|.+++++. +++.+||.|||+|+||+++++ ++|++++|+++||++|+||+|+|+++++
T Consensus 2 ~~lY~~~Ileh~~~p~n~g~l~~~~~---~~~~~np~CGD~i~l~l~v~~--~~I~d~~f~~~GCais~Asas~~~e~i~ 76 (137)
T TIGR01994 2 DSLYRQVILDHYKNPRHRGKLEDATV---QERGHNPTCGDEITLTVKLEG--DRIEDIAFEGEGCSISQASASMMTELIK 76 (137)
T ss_pred hHHHHHHHHHHHhCCCCCCCCCCCCe---eEEeCCCCCCcEEEEEEEEcC--CeEEEEEEEecccHHHHHHHHHHHHHHc
Confidence 57999999999999999999999885 456799999999999999987 8999999999999999999999999999
Q ss_pred CCCHHHHHchhHHHHHhhh---------------------cCcH-HHHHHHHHHHHHHHHHh
Q 031835 110 GKQMQEVLSIKNTGVAGKL---------------------QNIF-LYHLLNCIAACLLKMLS 149 (152)
Q Consensus 110 Gktl~EA~~l~~~~I~~~L---------------------g~~p-~~hca~~a~~~l~~~~~ 149 (152)
|||++|+..+..+ +.+++ ...| -.+|+.|+..||++||.
T Consensus 77 Gk~~~ea~~l~~~-~~~ml~~~~~~~~~~~l~dl~~l~~v~~~p~R~~Ca~L~~~al~~al~ 137 (137)
T TIGR01994 77 GKTVEEALSLVEA-FSEMIQGQETDEDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137 (137)
T ss_pred CCCHHHHHHHHHH-HHHHHhcCCCCccccccchHHHhhccccCcchHHHHHHHHHHHHHHhC
Confidence 9999999999853 22222 1245 78999999999999974
No 10
>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=92.82 E-value=0.85 Score=32.33 Aligned_cols=69 Identities=22% Similarity=0.387 Sum_probs=44.3
Q ss_pred CCCEEEEEEEEeCCCC----cEeeeeeeeccchHHHHHHHHHHHHH-----cCCCHHHHHchhHHHHHhhhcCcH----H
Q 031835 67 CGDVMKLQIKVDEETG----QIVDACFKTFGCGSAIASSSVATEWV-----KGKQMQEVLSIKNTGVAGKLQNIF----L 133 (152)
Q Consensus 67 CGD~I~i~l~i~~~~g----~I~d~~F~~~GC~isiAsaS~l~eli-----~Gktl~EA~~l~~~~I~~~Lg~~p----~ 133 (152)
|| .+.|.+..++|+| ++.++++.+ || .+-...++.++ .|.++++ |.+.|.+.. -
T Consensus 7 ~g-~~yvtv~~d~d~g~p~Evf~~~~~~G-g~---~~~~~ai~rliS~~Lr~G~~~~~--------ii~~L~gi~~~~~~ 73 (95)
T PF12637_consen 7 CG-KLYVTVNFDEDNGRPFEVFINVGKAG-GC---SGNLEAIARLISLALRSGVPPEE--------IIDQLRGIRCGPSG 73 (95)
T ss_pred cc-ceEEEEEeeCCCCcceEEEEecCcCC-Cc---hHHHHHHHHHHHHHHHcCCCHHH--------HHHHhcCCCCCCCC
Confidence 55 3444444454334 666666655 66 66677788888 9999776 334444332 4
Q ss_pred H-------HHHHHHHHHHHHHH
Q 031835 134 Y-------HLLNCIAACLLKML 148 (152)
Q Consensus 134 ~-------hca~~a~~~l~~~~ 148 (152)
. .|++....+|++.|
T Consensus 74 ~~~~~~~~S~~D~Ia~~L~~~~ 95 (95)
T PF12637_consen 74 TVGGSRVTSCPDAIAKALEEHL 95 (95)
T ss_pred ccCCCccCcHHHHHHHHHHHhC
Confidence 4 79999999998865
No 11
>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=88.70 E-value=7 Score=29.03 Aligned_cols=92 Identities=15% Similarity=0.148 Sum_probs=58.2
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeecc-chHHHHHHHHHHHHH
Q 031835 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWV 108 (152)
Q Consensus 30 ~~lYs~~Ile~~~~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~G-C~isiAsaS~l~eli 108 (152)
|+.--+.++++.++......-...+.. .-+.|-..|-++...+++ |++ .|.++. -.+...-.+++.+.+
T Consensus 11 ~~~ry~~Li~lgk~lp~l~~~~~~~~~------~V~GC~S~vWl~~~~~~~-g~~---~f~adSda~ivkGl~all~~~~ 80 (125)
T PF02657_consen 11 WEERYRYLIDLGKKLPPLPEELRTDEN------LVHGCQSQVWLHVEEDED-GKV---HFRADSDARIVKGLLALLLEVL 80 (125)
T ss_dssp HHHHHHHHHHHHHTS----CCCCSCCE------EETSSSS-EEEEEEEETT-SEE---EEEEEESSHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhcCCCCCHHHhcccc------cCCCCccceeEeeeeccC-CEE---EEEecCccHHHHHHHHHHHHHH
Confidence 555556778999887654432222221 124599998885544332 765 666653 457788899999999
Q ss_pred cCCCHHHHHchhHHHHHhhhcCcH
Q 031835 109 KGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 109 ~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
.|+|.+|+..++.+ ..+.||...
T Consensus 81 ~g~t~~eI~~~~~~-fl~~lgl~~ 103 (125)
T PF02657_consen 81 NGQTPEEILAFDPD-FLEQLGLSQ 103 (125)
T ss_dssp TT-BHHHHHHS-TH-HHHHHTSCC
T ss_pred cCCCHHHHHhCCHH-HHHHcCccc
Confidence 99999999999998 666677644
No 12
>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=76.02 E-value=4.6 Score=27.51 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=31.3
Q ss_pred CCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHH
Q 031835 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQ 114 (152)
Q Consensus 68 GD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~ 114 (152)
|-.|.+++.|++ |+|++++|.++==.. .--.-+.+.++|...+
T Consensus 15 ~G~v~v~~~V~~--G~I~~i~i~gDf~~~--~~i~~le~~L~G~~~~ 57 (86)
T PF10437_consen 15 WGTVEVHLNVKN--GIIKDIKIYGDFFGP--EDIEELEEALIGCPYD 57 (86)
T ss_dssp TEEEEEEEEEET--TEEEEEEEEECBS-C--CCHHHHHHHHTTCBSS
T ss_pred CceEEEEEEEEC--CEEEEEEEECCCCCc--hHHHHHHHHHHhcCCC
Confidence 456999999998 999999999762211 2246677888888543
No 13
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=73.84 E-value=9.3 Score=32.20 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=36.9
Q ss_pred CcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 82 g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
.+|..=.-.+.||.+| +++.+++++|.++.||..-..+.+...+.
T Consensus 200 ~ri~t~~tHGTGCTlS---aAIaa~LA~G~~l~~AV~~Ak~fv~~AI~ 244 (263)
T COG0351 200 PRIPTKNTHGTGCTLS---AAIAANLAKGLSLEEAVKKAKEFVTRAIR 244 (263)
T ss_pred cccCCCCCCCccHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence 4666655678899986 56778899999999999998888888877
No 14
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=72.65 E-value=39 Score=25.59 Aligned_cols=65 Identities=9% Similarity=0.031 Sum_probs=48.9
Q ss_pred CCCCCCEEEEEEEEeCCCCcEeeeeeeecc-chHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 64 APACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 64 np~CGD~I~i~l~i~~~~g~I~d~~F~~~G-C~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
-+.|-..|-+...++++ | .+.|.++. -.+...-++++...+.|+|.+|+..++..+..+.||...
T Consensus 48 V~GCqS~VWl~~~~~~~-g---~~~f~~dSDa~ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~ 113 (138)
T PRK09296 48 IQGCQSQVWIVMRQNAQ-G---IIELQGDSDAAIVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQ 113 (138)
T ss_pred CCCcccceeeeEeecCC-C---EEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCccc
Confidence 35688888777666653 4 46666663 356778889999999999999999999767667777543
No 15
>PRK15019 CsdA-binding activator; Provisional
Probab=71.33 E-value=44 Score=25.65 Aligned_cols=64 Identities=19% Similarity=0.116 Sum_probs=49.4
Q ss_pred CCCCCEEEEEEEEeCCCCcEeeeeeeecc-chHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 65 PACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 65 p~CGD~I~i~l~i~~~~g~I~d~~F~~~G-C~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
+.|-..|-+....+++ | .+.|.++. -.+...-++++.+.+.|+|.+|+..++.++..+.||...
T Consensus 59 ~GCqS~VWL~~~~~~d-g---~~~f~~dSDA~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~ 123 (147)
T PRK15019 59 AGCENRVWLGYTVAEN-G---KMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRA 123 (147)
T ss_pred CCcccceeeeeeecCC-C---EEEEEeeCccHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchh
Confidence 4688888776666432 5 46666663 356778889999999999999999999988888888544
No 16
>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=70.25 E-value=45 Score=25.27 Aligned_cols=64 Identities=17% Similarity=0.107 Sum_probs=48.8
Q ss_pred CCCCCEEEEEEEEeCCCCcEeeeeeeecc-chHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 65 PACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 65 p~CGD~I~i~l~i~~~~g~I~d~~F~~~G-C~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
+.|-..|-+...+.++ | .+.|.++. -.+...-.+++.+.+.|+|.+|+.+++.++..+.||...
T Consensus 54 ~GCqS~VWl~~~~~~d-g---~~~f~~dSDa~IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~ 118 (138)
T TIGR03391 54 TGCENRVWLGHQVLPD-G---TLHFYGDSEGRIVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRA 118 (138)
T ss_pred CCcccceeeeeeecCC-C---EEEEEecCccHHHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchh
Confidence 4588888776654332 5 35576663 457778889999999999999999999988888888554
No 17
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=70.15 E-value=26 Score=27.01 Aligned_cols=64 Identities=14% Similarity=0.080 Sum_probs=49.3
Q ss_pred CCCCCEEEEEEEEeCCCCcEeeeeeeeccc-hHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 65 PACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 65 p~CGD~I~i~l~i~~~~g~I~d~~F~~~GC-~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
+.|-..|-+....++ + -.+.|+++.= .|...-.+++.+.+.|+|.+|...++..+.-+.||...
T Consensus 54 ~GC~S~vwL~~~~~~--~--~~~~F~gdSdA~ivrGL~aill~~~~G~t~~eI~~~~~~~~f~~LGL~~ 118 (144)
T COG2166 54 PGCQSQVWLVTEQND--D--GTLHFFGDSDARIVRGLLAILLAAYSGKTAAEILAFDPLDFFEELGLAQ 118 (144)
T ss_pred CccccceeEEEeecC--C--ceEEEeccchhHHHHHHHHHHHHHHcCCCHHHHHcCCHHHHHHHhhHHH
Confidence 457777666666655 4 4567777743 46677889999999999999999999988888888744
No 18
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=66.31 E-value=28 Score=30.12 Aligned_cols=44 Identities=18% Similarity=0.141 Sum_probs=32.8
Q ss_pred CCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHH
Q 031835 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (152)
Q Consensus 68 GD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~E 115 (152)
+-.|++.+.+++ |+|+++++.++.-. ..--+-+.+.++|...++
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 456899999998 99999999987433 233456777788887543
No 19
>PLN02673 quinolinate synthetase A
Probab=65.09 E-value=74 Score=30.56 Aligned_cols=60 Identities=18% Similarity=0.217 Sum_probs=47.6
Q ss_pred CCCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhh
Q 031835 65 PACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKL 128 (152)
Q Consensus 65 p~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~L 128 (152)
+.|-..|-|...++++ | -..+.+..+. .|...-++++.+.+.|+|.+|++.++.+++ +.|
T Consensus 127 ~GCQSqVWL~~elddd-G-kv~F~ADSDA-~IVKGL~ALLl~~lsG~TpeEILavD~d~~-~~L 186 (724)
T PLN02673 127 MGCTAQVWLEAELDQD-G-KMRFWADSDS-EITKGFCSCLIWVLDGASPEEVLELKTEDL-AAL 186 (724)
T ss_pred CCcccceEEEEEEcCC-C-EEEEEEeCcc-HHHHHHHHHHHHHHcCCCHHHHHhCCHHHH-HHH
Confidence 4688888887777653 4 3444555556 889999999999999999999999999888 555
No 20
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=63.00 E-value=33 Score=28.07 Aligned_cols=121 Identities=21% Similarity=0.296 Sum_probs=68.6
Q ss_pred HhhhhCCCCCCCchhhHhHHHHHHH---HHhCCCCCCCCCCCC-Cc---eeeeeecCCCCCCEEEEEEEEeCCCCcEeee
Q 031835 15 AAAVAAPRPVQVAAMPRLYHENVID---HYNNPRNVGSFEKND-AT---VGTGLVGAPACGDVMKLQIKVDEETGQIVDA 87 (152)
Q Consensus 15 ~~~~~~~~~~~~~~~~~lYs~~Ile---~~~~Prn~G~l~~~d-~~---v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~ 87 (152)
.-++-.|..-....+.....++.-+ ++..|+-+=.|++.. .. ... ..|.| .+.+.+++ |+|+++
T Consensus 77 ~kavIvp~~~~~~g~~~~lk~~~e~~gi~~~~P~~~CsL~~~~~p~i~~F~~-~fGkP------~~ei~v~~--~~I~~V 147 (217)
T PF02593_consen 77 VKAVIVPSESPKPGLRRQLKKQLEEFGIEVEFPKPFCSLEENGNPQIDEFAE-YFGKP------KVEIEVEN--GKIKDV 147 (217)
T ss_pred CCEEEEecCCCccchHHHHHHHHHhcCceeecCccccccCCCCChhHHHHHH-HhCCc------eEEEEecC--CcEEEE
Confidence 3344444433334555556666655 355565554455321 10 000 13444 56666667 899998
Q ss_pred eee-eccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhh-----------hcCcHHHHHHHHHHHHHHHHH
Q 031835 88 CFK-TFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGK-----------LQNIFLYHLLNCIAACLLKML 148 (152)
Q Consensus 88 ~F~-~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~-----------Lg~~p~~hca~~a~~~l~~~~ 148 (152)
+-- +.=|+ |+..+++.++|++++++.......+..+ ++..+..--+.+...|+.+||
T Consensus 148 ~VlR~aPCG----sT~~vAk~l~G~~~~d~~~~~g~~~q~YPC~As~~~d~~~~d~~~h~Ag~i~~~Ave~Al 216 (217)
T PF02593_consen 148 KVLRSAPCG----STWFVAKRLIGKEVEDAPEKAGLAHQHYPCRASMGRDFELGDTILHKAGYIHKEAVEKAL 216 (217)
T ss_pred EEEecCCCc----cHHHHHHHhcCCccchhhhhhhhhheecccccccccccccccchhhhhHHHHHHHHHHhh
Confidence 765 33454 5688899999999999988775444332 122223344566677777765
No 21
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=62.19 E-value=14 Score=31.93 Aligned_cols=46 Identities=9% Similarity=0.052 Sum_probs=35.3
Q ss_pred CcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 82 g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
.+|..-.|.|.||.++- ++++.++.|.++.+|.....+.+.+.+..
T Consensus 240 ~ri~~~~~hGTGc~fAS---AIAa~LA~G~~l~~Av~~A~~fv~~aI~~ 285 (321)
T PTZ00493 240 KRKPGKDIHGTGCTLST---AIACYLAKKHNILQSCIESKKYIYNCIRY 285 (321)
T ss_pred cccCCCCCCChHHHHHH---HHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 46665678899998865 45666788999999999887777766653
No 22
>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=57.54 E-value=13 Score=30.02 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=34.7
Q ss_pred cEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 83 ~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
++..-+|.|.||.++- .+++.+++|+++++|.....+.+...+.
T Consensus 190 ~~~~~~~~GTGd~fss---~laa~l~~g~~l~~Av~~A~~~v~~~i~ 233 (246)
T PF08543_consen 190 RIPTGSFHGTGDLFSS---ALAAFLAKGYSLEEAVEKAKNFVRRAIK 233 (246)
T ss_dssp EECTSGCTTHHHHHHH---HHHHHHHTTSSHHHHHHHHHHHHHHHHH
T ss_pred EEcCCCCCCchhHHHH---HHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 4555788899998864 5567788999999999998887777664
No 23
>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=49.67 E-value=25 Score=23.61 Aligned_cols=22 Identities=18% Similarity=0.205 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHch
Q 031835 98 IASSSVATEWVKGKQMQEVLSI 119 (152)
Q Consensus 98 iAsaS~l~eli~Gktl~EA~~l 119 (152)
..++-.++.+++|||.+|..++
T Consensus 33 ~~~~~~iA~~i~gks~eeir~~ 54 (78)
T PF01466_consen 33 DLCCKYIANMIKGKSPEEIRKY 54 (78)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHHH
Confidence 4566788999999999888776
No 24
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=46.76 E-value=54 Score=30.59 Aligned_cols=46 Identities=17% Similarity=0.134 Sum_probs=33.6
Q ss_pred CCCCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHH
Q 031835 66 ACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (152)
Q Consensus 66 ~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~E 115 (152)
.-+-.|++++.|++ |+|+++++.++--.. .--+-+.+.+.|...+.
T Consensus 484 f~~G~vei~l~V~~--G~I~~~ki~gDf~~~--~~i~~le~~L~G~~y~~ 529 (562)
T PRK14061 484 FSWGGVELHFDVEK--GHITRAQVFTDSLNP--APLEALAGRLQGCLYRA 529 (562)
T ss_pred cccccEEEEEEEeC--CEEEEEEEECCCCCc--ccHHHHHHHhCCCCcCH
Confidence 34567899999998 999999999874332 22355777788887543
No 25
>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=44.95 E-value=36 Score=29.14 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=33.0
Q ss_pred CCEEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHH
Q 031835 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (152)
Q Consensus 68 GD~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~E 115 (152)
+..|++++.|++ |+|+++++.++-...- --+-+.+.++|.+.+.
T Consensus 257 ~G~v~i~l~v~~--g~I~~~~i~gDf~~~~--~~~~l~~~L~G~~~~~ 300 (324)
T TIGR00545 257 AGGFELHVQVEK--GKIVDCKFFGDFLSVA--DITPVTNRLIGQKYDY 300 (324)
T ss_pred CCcEEEEEEEeC--CEEEEEEEECCCCCcc--cHHHHHHHhCCCccCH
Confidence 557899999998 9999999988743222 2466777788887554
No 26
>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=44.42 E-value=1.3e+02 Score=26.49 Aligned_cols=63 Identities=14% Similarity=-0.042 Sum_probs=39.1
Q ss_pred EEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH--HHHHHHHHHHHH
Q 031835 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF--LYHLLNCIAACL 144 (152)
Q Consensus 71 I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p--~~hca~~a~~~l 144 (152)
+++.+.++++ ++|.+.+|...--- =-+-.+++||++.|+..+++ ..=+.-+ |.+|.-.|++.+
T Consensus 17 ~rl~l~vdge-~vv~~~~~~~~~~~------RG~Ek~~egr~~~~~~~l~~----Ricg~c~~ah~~a~~~AvE~a 81 (411)
T TIGR03295 17 AKLVLEVDDE-GIVEKGDYLSITPV------RGFEKLLVGKTAEFAPIIVS----RICGICPIAHTLASVEAIEDS 81 (411)
T ss_pred eEEEEEEeCC-CcEEEEEEeccCcC------cHHHHHHcCCCHHHHHHHHh----HHhhcCHHHHHHHHHHHHHHH
Confidence 5777788753 78888867632211 23567889999999987654 2222233 556666666554
No 27
>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=44.21 E-value=48 Score=25.98 Aligned_cols=44 Identities=20% Similarity=0.300 Sum_probs=32.3
Q ss_pred cEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 83 ~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
++....+.+-||.++ +.+++.++.|++++||.+.....+.+.+.
T Consensus 197 ~~~~~~~~GaGD~f~---a~l~a~l~~g~~~~~A~~~A~~~~~~~i~ 240 (242)
T cd01169 197 RIDTKNTHGTGCTLS---SAIAANLAKGLSLEEAVREAKEYVTQAIR 240 (242)
T ss_pred eeCCCCCCChHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Confidence 344455567777765 45666778899999999999888877664
No 28
>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=37.95 E-value=51 Score=21.61 Aligned_cols=25 Identities=16% Similarity=0.372 Sum_probs=20.1
Q ss_pred CEEEEEEEEeCCCCcEeeeeeeeccc
Q 031835 69 DVMKLQIKVDEETGQIVDACFKTFGC 94 (152)
Q Consensus 69 D~I~i~l~i~~~~g~I~d~~F~~~GC 94 (152)
..|++.+.++++ |+|.+++|..+.-
T Consensus 4 g~i~v~v~i~~d-g~I~~v~~~~~~e 28 (81)
T PF04205_consen 4 GPITVTVTIDKD-GKITDVKILEHNE 28 (81)
T ss_dssp EEEEEEEEEETT-TEEEEEEEEECCC
T ss_pred ceEEEEEEEeCC-CEEEEEEEeeccC
Confidence 357888888865 9999999998654
No 29
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=36.52 E-value=45 Score=26.52 Aligned_cols=42 Identities=29% Similarity=0.293 Sum_probs=30.0
Q ss_pred eeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 86 DACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 86 d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
.+...+-||++ ++.+++.++.|.+++|+.++....+.+.|..
T Consensus 201 ~~~~~GaGDaf---~a~~~~~l~~g~~l~ea~~~A~~~~~~~l~~ 242 (253)
T PRK12413 201 EKNNIGAGCTF---ASSIASQLVKGKSPLEAVKNSKDFVYQAIQQ 242 (253)
T ss_pred CCCCCChHHHH---HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 34444555555 4577788889999999999887777766653
No 30
>PF00227 Proteasome: Proteasome subunit; InterPro: IPR001353 ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins. They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, clpXP) complex in other eubacteria. Genes homologous to eubacterial HslV (ClpQ) and HslU (ClpY, clpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa []. The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). The prokaryotic ATP-dependent proteasome is coded for by the heat-shock locus VU (HslVU). It consists of HslV, the protease (MEROPS peptidase subfamily T1B), and HslU, IPR004491 from INTERPRO, the ATPase and chaperone belonging to the AAA/Clp/Hsp100 family. The crystal structure of Thermotoga maritima HslV has been determined to 2.1-A resolution. The structure of the dodecameric enzyme is well conserved compared to those from Escherichia coli and Haemophilus influenzae [, ]. This entry contains threonine peptidases and non-peptidase homologs belong to MEROPS peptidase family T1 (proteasome family, clan PB(T)). The family consists of the protease components of the archaeal and bacterial proteasomes and the alpha and beta subunits of the eukaryotic proteasome. ; GO: 0004298 threonine-type endopeptidase activity, 0051603 proteolysis involved in cellular protein catabolic process, 0005839 proteasome core complex; PDB: 3KRD_1 3H6F_M 2FHH_F 3HF9_F 2FHG_D 3HFA_B 3H6I_K 3MI0_A 3MFE_1 3MKA_F ....
Probab=36.48 E-value=1.7e+02 Score=21.90 Aligned_cols=58 Identities=17% Similarity=0.324 Sum_probs=45.2
Q ss_pred EEEEEEEEeCCCCcEeee-eeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 70 VMKLQIKVDEETGQIVDA-CFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 70 ~I~i~l~i~~~~g~I~d~-~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
.-.+| .++.. |.+.+. .|.+.|.+...+-.-+=..+-.+.|.+||.++..+-+....+
T Consensus 118 ~~~l~-~vd~~-G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~~ea~~~~~~~l~~~~~ 176 (190)
T PF00227_consen 118 GPQLY-SVDPS-GSYIECKRFAAIGSGSQFAQPILEKLYKPDLSLEEAIELALKALKEAID 176 (190)
T ss_dssp EEEEE-EEETT-SEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHHHHH
T ss_pred cccee-eeccc-cccccccccccchhcchhhhHHHHhhccCCCCHHHHHHHHHHHHHHHHh
Confidence 45666 56654 899999 699999887777766666666899999999998877776654
No 31
>cd03313 enolase Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions.
Probab=35.34 E-value=2.8e+02 Score=24.42 Aligned_cols=62 Identities=10% Similarity=-0.004 Sum_probs=35.8
Q ss_pred eeeeccchHHHHHH-HHHHHHHcCCCHHHHHchhHHHHHhhhcCcH-HHH---HHHHHHH-HHHHHHhhh
Q 031835 88 CFKTFGCGSAIASS-SVATEWVKGKQMQEVLSIKNTGVAGKLQNIF-LYH---LLNCIAA-CLLKMLSRL 151 (152)
Q Consensus 88 ~F~~~GC~isiAsa-S~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p-~~h---ca~~a~~-~l~~~~~~~ 151 (152)
+|.++|-.-.+..- ..++..++|+++.+-..|+. .|.+ +++.+ .-. =+.+|++ |+.++.|+.
T Consensus 53 ~~~g~~v~~av~~i~~~iap~LiG~d~~dq~~id~-~l~~-~dgt~~~~~~G~nAi~avsiAl~da~A~~ 120 (408)
T cd03313 53 RYLGKGVLKAVKNVNEIIAPALIGMDVTDQRAIDK-LLIE-LDGTPNKSKLGANAILGVSLAVAKAAAAA 120 (408)
T ss_pred cccCCcHHHHHHHHHHHHHHHHcCCChhhHHHHHH-HHHH-hcCCCcccccchHHHHHHHHHHHHHHHHH
Confidence 35555555555544 46788999999988887664 4444 45554 111 1333333 566665553
No 32
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=34.14 E-value=51 Score=27.10 Aligned_cols=44 Identities=16% Similarity=0.134 Sum_probs=33.2
Q ss_pred eeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 86 DACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 86 d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
...+.|-||.++ +.+++.+++|++++|+.+...+.+.+.+....
T Consensus 225 ~~~~~GaGD~fa---a~~~a~l~~g~~l~~Av~~A~~~v~~~i~~t~ 268 (281)
T PRK08176 225 DTDLKGTGDLFC---AELVSGLLKGKALTDAAHRAGLRVLEVMRYTQ 268 (281)
T ss_pred CCCCCChhHHHH---HHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345666677664 35667778999999999999999888776543
No 33
>cd01173 pyridoxal_pyridoxamine_kinase Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and require its precursors in the form of vitamin B6 (pyridoxal, pyridoxine, and pyridoxamine) from their diet. Pyridoxal kinase encoding genes are also found in many other species including yeast and bacteria.
Probab=34.09 E-value=52 Score=26.13 Aligned_cols=40 Identities=28% Similarity=0.218 Sum_probs=29.8
Q ss_pred eeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 87 ACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 87 ~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
+.+.|-||+++ +.+++.++.|++++++.++....+.+.+.
T Consensus 211 ~~~~GaGD~f~---a~~~~~l~~g~~~~~a~~~A~~~~~~~i~ 250 (254)
T cd01173 211 AYFNGTGDLFA---ALLLARLLKGKSLAEALEKALNFVHEVLE 250 (254)
T ss_pred CCcCChHHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 34445566554 46777888999999999999888877664
No 34
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]
Probab=33.28 E-value=1.9e+02 Score=26.34 Aligned_cols=40 Identities=33% Similarity=0.506 Sum_probs=25.1
Q ss_pred EEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHch
Q 031835 72 KLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (152)
Q Consensus 72 ~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l 119 (152)
.+.+.++++ |++++.+|...+==. +=.++.||+++||..|
T Consensus 18 kv~i~vdd~-G~V~~~~~~it~~Rg-------fEk~~~Gkp~EeaP~i 57 (441)
T COG3259 18 KVTIEVDDD-GIVEDARFHITEVRG-------FEKFVLGKPIEEAPRI 57 (441)
T ss_pred EEEEEEcCC-CceeeeEEEecccch-------HHHHhcCCChHHhhHH
Confidence 444556654 999999998654221 2345566666666665
No 35
>PRK05756 pyridoxamine kinase; Validated
Probab=32.96 E-value=83 Score=25.69 Aligned_cols=40 Identities=13% Similarity=0.114 Sum_probs=29.8
Q ss_pred eeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 88 CFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 88 ~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
.+.|-||+++ |.+++.++.|++++|+.+.....+.+.|..
T Consensus 216 ~~~GaGD~f~---a~~~a~l~~g~~~~~al~~A~~~~~~~i~~ 255 (286)
T PRK05756 216 QPVGVGDLTS---ALFLARLLQGGSLEEALEHTTAAVYEVMAR 255 (286)
T ss_pred CCCChHHHHH---HHHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 4555566554 466777889999999999988887777653
No 36
>PRK12616 pyridoxal kinase; Reviewed
Probab=32.12 E-value=83 Score=25.66 Aligned_cols=38 Identities=18% Similarity=0.395 Sum_probs=29.2
Q ss_pred eeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 90 KTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 90 ~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
.+-||+++ +.+++.++.|++++++.+.....+.+.+..
T Consensus 212 ~GaGD~fs---aalaa~l~~g~~l~~Av~~A~~~~~~~i~~ 249 (270)
T PRK12616 212 HGAGCTFS---AAVTAELAKGSEVKEAIYAAKEFITAAIKE 249 (270)
T ss_pred CcHHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence 56677664 456777789999999999988887777664
No 37
>PLN02978 pyridoxal kinase
Probab=32.09 E-value=88 Score=26.22 Aligned_cols=44 Identities=14% Similarity=0.049 Sum_probs=31.3
Q ss_pred eeeeeeccchHHHHHHHHHHHHHcC-CCHHHHHchhHHHHHhhhcCcH
Q 031835 86 DACFKTFGCGSAIASSSVATEWVKG-KQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 86 d~~F~~~GC~isiAsaS~l~eli~G-ktl~EA~~l~~~~I~~~Lg~~p 132 (152)
+..|.|.||.++- .+++.+..| .+++||.+...+.+.+.+...-
T Consensus 225 ~~~~~GtGD~fsA---~laa~l~~g~~~l~~A~~~A~~~v~~~i~~t~ 269 (308)
T PLN02978 225 PAYFTGTGDLMAA---LLLGWSHKYPDNLDKAAELAVSSLQAVLRRTL 269 (308)
T ss_pred CCCCCCchHHHHH---HHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4456677777665 366667777 7999999988888877776543
No 38
>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=31.05 E-value=1.1e+02 Score=20.68 Aligned_cols=59 Identities=7% Similarity=0.024 Sum_probs=32.2
Q ss_pred EEEEEEEEeCCCCcEeeeeeeeccch-HHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcCc
Q 031835 70 VMKLQIKVDEETGQIVDACFKTFGCG-SAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQNI 131 (152)
Q Consensus 70 ~I~i~l~i~~~~g~I~d~~F~~~GC~-isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~~ 131 (152)
.|++.+ +.. |.|.+++|...... .....-+-+.....+.-..++.....+.+.+++|+.
T Consensus 31 ~V~V~v--~g~-g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~a~~~~~~~~~~~~g~~ 90 (93)
T PF02575_consen 31 LVTVTV--NGN-GEVVDIEIDPSALRPLDPEELEDLIVEAVNDAQKKAREKAQEEMAELTGGL 90 (93)
T ss_dssp TEEEEE--ETT-S-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred EEEEEE--ecC-ceEEEEEEehHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 455554 433 89999999988774 333332333333344555566666666666666654
No 39
>PRK08573 phosphomethylpyrimidine kinase; Provisional
Probab=29.74 E-value=84 Score=27.86 Aligned_cols=44 Identities=16% Similarity=0.345 Sum_probs=31.7
Q ss_pred cEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 83 ~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
++.-....|-||+++- .+++.++.|++++|+..+....+...+.
T Consensus 200 ~v~~~dt~GAGDaFsA---a~aa~l~~G~~l~eAl~~A~~~~~~al~ 243 (448)
T PRK08573 200 RVESGCTHGTGCSFSA---AIAAGLAKGLDPEEAIKTAKKFITMAIK 243 (448)
T ss_pred CcCCCCCCChHHHHHH---HHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 3333445566777654 4566778999999999998877777776
No 40
>PRK00077 eno enolase; Provisional
Probab=29.46 E-value=3.6e+02 Score=23.84 Aligned_cols=43 Identities=12% Similarity=0.062 Sum_probs=28.2
Q ss_pred eeeeccchHHHHHH-HHHHHHHcCCCHHHHHchhHHHHHhhhcCcH
Q 031835 88 CFKTFGCGSAIASS-SVATEWVKGKQMQEVLSIKNTGVAGKLQNIF 132 (152)
Q Consensus 88 ~F~~~GC~isiAsa-S~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p 132 (152)
+|.++|-.-.++.. ..++..++|+++.+...+.. .|.+ +++.+
T Consensus 58 ~~~g~~v~~av~~v~~~iap~LiG~d~~d~~~id~-~l~~-ldgt~ 101 (425)
T PRK00077 58 RYLGKGVLKAVENVNEEIAPALIGLDALDQRAIDK-AMIE-LDGTP 101 (425)
T ss_pred ccCCcCHHHHHHHHHHHHHHHHcCCChhhHHHHHH-HHHH-hhCcc
Confidence 36666655555544 46788999999998888775 3433 34444
No 41
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=29.16 E-value=1.6e+02 Score=22.76 Aligned_cols=22 Identities=14% Similarity=0.187 Sum_probs=19.2
Q ss_pred HHHHHHHHcCCCHHHHHchhHH
Q 031835 101 SSVATEWVKGKQMQEVLSIKNT 122 (152)
Q Consensus 101 aS~l~eli~Gktl~EA~~l~~~ 122 (152)
+..++.+|+|+++++|..+-..
T Consensus 30 ~r~va~~IRG~~v~~A~~~L~~ 51 (153)
T PRK04223 30 SVEIAREIRGMKLDEAKAYLED 51 (153)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH
Confidence 4678999999999999998864
No 42
>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=29.12 E-value=1.2e+02 Score=21.31 Aligned_cols=20 Identities=15% Similarity=0.358 Sum_probs=16.6
Q ss_pred HHHHHHHcCCCHHHHHchhH
Q 031835 102 SVATEWVKGKQMQEVLSIKN 121 (152)
Q Consensus 102 S~l~eli~Gktl~EA~~l~~ 121 (152)
-.++.++.|++++||..+-.
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~ 35 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLE 35 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHH
Confidence 46789999999999987653
No 43
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=28.90 E-value=1.7e+02 Score=20.85 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=26.6
Q ss_pred HHHHHHHcCCCHHHHHchhHHHHHhhhcCcHHHHHHHHHHHHHHHHHh
Q 031835 102 SVATEWVKGKQMQEVLSIKNTGVAGKLQNIFLYHLLNCIAACLLKMLS 149 (152)
Q Consensus 102 S~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p~~hca~~a~~~l~~~~~ 149 (152)
-.++.+|.|++++||...-. ..|+. .+......|+.|.+
T Consensus 14 ~~va~~IrG~~v~~A~~~L~--------f~pkk-~a~~i~klL~sA~a 52 (103)
T TIGR01044 14 RLVADLIRGKSVSQALDILR--------FTPKK-AAPLIKKVLASAIA 52 (103)
T ss_pred HHHHHHHcCCcHHHHHHHHh--------hCCHh-HHHHHHHHHHHHHH
Confidence 46789999999999987653 24433 55555566666554
No 44
>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=27.96 E-value=1.9e+02 Score=22.64 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=44.8
Q ss_pred EEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 72 KLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 72 ~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
.+| .+|.. |.+....|.+.|.....+-.-+=..+-.+++.+|+.++..+-|.+..+
T Consensus 144 ~ly-~~d~~-G~~~~~~~~a~G~gs~~~~~~Le~~y~~~ms~eea~~l~~~al~~~~~ 199 (213)
T cd03752 144 QLY-QSDPS-GNYSGWKATAIGNNNQAAQSLLKQDYKDDMTLEEALALAVKVLSKTMD 199 (213)
T ss_pred EEE-EECCC-CCeeeeeEEEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHh
Confidence 455 45544 888899999999999888877777777889999999988877776665
No 45
>TIGR00778 ahpD_dom alkylhydroperoxidase AhpD family core domain. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity.
Probab=27.77 E-value=1.1e+02 Score=18.01 Aligned_cols=29 Identities=17% Similarity=0.302 Sum_probs=22.2
Q ss_pred eccchHHHHHHHHHHHHHcCCCHHHHHchh
Q 031835 91 TFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (152)
Q Consensus 91 ~~GC~isiAsaS~l~eli~Gktl~EA~~l~ 120 (152)
..||.+|+..=+..+.. .|.+.+|...+.
T Consensus 18 ~~~C~yc~~~H~~~a~~-~G~~~~ei~~v~ 46 (50)
T TIGR00778 18 INGCGYCLDAHTKLARK-AGVTAEELAEAL 46 (50)
T ss_pred HcCCHHHHHHHHHHHHH-cCCCHHHHHHHH
Confidence 57999999997766644 699988876643
No 46
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=27.59 E-value=1.7e+02 Score=20.61 Aligned_cols=39 Identities=13% Similarity=0.113 Sum_probs=26.3
Q ss_pred HHHHHHHcCCCHHHHHchhHHHHHhhhcCcHHHHHHHHHHHHHHHHHh
Q 031835 102 SVATEWVKGKQMQEVLSIKNTGVAGKLQNIFLYHLLNCIAACLLKMLS 149 (152)
Q Consensus 102 S~l~eli~Gktl~EA~~l~~~~I~~~Lg~~p~~hca~~a~~~l~~~~~ 149 (152)
-.++.++.|+++++|...-. ++ | ...+......|+.|.+
T Consensus 14 ~~v~~~Irg~~v~~A~~~L~-~~-------~-~k~a~~i~k~L~~a~~ 52 (105)
T PF00237_consen 14 REVARLIRGMSVDEAIAQLK-FV-------P-KKAAKFILKLLKSAIA 52 (105)
T ss_dssp HHHHHHHTTSBHHHHHHHHH-HH-------S-SHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH-hC-------c-HHHHHHHHhhHHHHHh
Confidence 46789999999999987654 22 3 2345555666666554
No 47
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=27.08 E-value=1.1e+02 Score=24.46 Aligned_cols=44 Identities=18% Similarity=0.307 Sum_probs=30.4
Q ss_pred cEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 83 ~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
++..+.+.+-||.++- .+++.++.|.++.|+.++....+...+.
T Consensus 204 ~~~~~~~~GaGD~f~a---~l~~~l~~g~~l~~A~~~A~~~~~~~i~ 247 (266)
T PRK06427 204 RIPTKNTHGTGCTLSA---AIAAELAKGASLLDAVQTAKDYVTRAIR 247 (266)
T ss_pred eECCCCCCChHHHHHH---HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Confidence 3333355666776654 4666778899999999988777666554
No 48
>PTZ00347 phosphomethylpyrimidine kinase; Provisional
Probab=26.65 E-value=97 Score=27.81 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=31.5
Q ss_pred CcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 82 g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
.+|.-..+.|-||+++-+ +++.++.|+++.|+.++....+...+.
T Consensus 433 ~~i~~~~~~GaGD~fsaa---iaa~la~G~~l~eAv~~A~~~v~~~i~ 477 (504)
T PTZ00347 433 NRIATINTHGTGCTLASA---ISSFLARGYTVPDAVERAIGYVHEAIV 477 (504)
T ss_pred eeECCCCCCChHHHHHHH---HHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence 345555667778887655 555667899999999987666665553
No 49
>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=26.46 E-value=1.1e+02 Score=20.17 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=16.6
Q ss_pred CCCCCCEEEEEEEEeCCC-CcEeeee
Q 031835 64 APACGDVMKLQIKVDEET-GQIVDAC 88 (152)
Q Consensus 64 np~CGD~I~i~l~i~~~~-g~I~d~~ 88 (152)
.-.-||.|+|.+...+++ =+|++++
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 335699999999987652 2777764
No 50
>COG4259 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.70 E-value=66 Score=23.87 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=16.2
Q ss_pred CCCCchhhHhHHHHHHHHHhCC
Q 031835 23 PVQVAAMPRLYHENVIDHYNNP 44 (152)
Q Consensus 23 ~~~~~~~~~lYs~~Ile~~~~P 44 (152)
|-+-+. |+.|++.|.|+|.+.
T Consensus 26 pKslY~-w~gYq~tvyEy~K~~ 46 (121)
T COG4259 26 PKSLYQ-WEGYQDTVYEYFKGD 46 (121)
T ss_pred Cccccc-cCCccHHHHHHHcCC
Confidence 333344 999999999999884
No 51
>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=25.39 E-value=2.5e+02 Score=21.82 Aligned_cols=57 Identities=11% Similarity=0.130 Sum_probs=43.8
Q ss_pred EEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 71 I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
-.+| .+|.. |.+.+..+.+.|.+...+-.-+=..+-.+++.+|+.++..+-|.+.++
T Consensus 140 p~Ly-~iD~~-G~~~~~~~~a~G~gs~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~ 196 (207)
T cd03755 140 PRLY-QTDPS-GTYSAWKANAIGRNSKTVREFLEKNYKEEMTRDDTIKLAIKALLEVVQ 196 (207)
T ss_pred eEEE-EECCC-cCEEcceEEEECCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhC
Confidence 4555 56654 889999999999887777766656666788999999998877777665
No 52
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=25.31 E-value=2.1e+02 Score=21.34 Aligned_cols=20 Identities=25% Similarity=0.577 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCCHHHHHchh
Q 031835 101 SSVATEWVKGKQMQEVLSIK 120 (152)
Q Consensus 101 aS~l~eli~Gktl~EA~~l~ 120 (152)
+..++.++.|+++++|..+-
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L 44 (120)
T COG0091 25 ARLVADLIRGKKVAEALAIL 44 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHH
Confidence 46789999999999999874
No 53
>PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase
Probab=25.07 E-value=1.5e+02 Score=26.59 Aligned_cols=44 Identities=27% Similarity=0.342 Sum_probs=32.1
Q ss_pred EeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 84 IVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 84 I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
+....+.|-||.++ +.+++.++.|++++|+.....+.+...+..
T Consensus 210 i~~~~t~GaGD~fs---aaiaa~l~~G~~l~eAv~~A~~~v~~ai~~ 253 (502)
T PLN02898 210 IKTRNTHGTGCTLA---SCIAAELAKGSDMLSAVKVAKRYVETALEY 253 (502)
T ss_pred eCCCCCCchhhhHH---HHHHHHHHcCCCHHHHHHHHHHHHHHHHHh
Confidence 44445567888765 456667778999999999888777776653
No 54
>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=24.90 E-value=1.9e+02 Score=19.78 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=29.5
Q ss_pred EEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHH
Q 031835 72 KLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (152)
Q Consensus 72 ~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~E 115 (152)
-+.+.++++ |+|++++--.-|-+..---+.-+-+.+.|+++++
T Consensus 19 a~~~~~~~~-~~i~~~ria~g~v~~~p~r~~~~E~~L~g~~~~~ 61 (103)
T PF03450_consen 19 AVLVSVDDD-GRIEDARIAVGGVAPTPVRAEEVEAALIGKPLSE 61 (103)
T ss_dssp EEEEEEETT-SEEEEEEEEEESSSSSTEE-HHHHHHTTTSBSSH
T ss_pred hheEEEecC-ceEEEEEEEEeccccceeehHHHHHHHhhcchhh
Confidence 445556653 4999999887776666666666777889976653
No 55
>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=24.71 E-value=3e+02 Score=21.45 Aligned_cols=57 Identities=14% Similarity=0.257 Sum_probs=42.4
Q ss_pred EEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 71 I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
-.+| .+|.. |......|.+.|-....+-.-+=..+=.+++.+|+.++..+-+....+
T Consensus 140 ~~ly-~vd~~-G~~~~~~~~a~G~g~~~~~~~Le~~~~~~m~~~ea~~l~~~~l~~~~~ 196 (211)
T cd03756 140 PRLF-ETDPS-GAYNEYKATAIGSGRQAVTEFLEKEYKEDMSLEEAIELALKALYAALE 196 (211)
T ss_pred CEEE-EECCC-CCeeeeEEEEECCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhc
Confidence 4555 55554 778889999999888777765555666789999999988777765544
No 56
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=24.26 E-value=2.3e+02 Score=21.81 Aligned_cols=27 Identities=4% Similarity=0.154 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHchhHH
Q 031835 96 SAIASSSVATEWVKGKQMQEVLSIKNT 122 (152)
Q Consensus 96 isiAsaS~l~eli~Gktl~EA~~l~~~ 122 (152)
+|-==+-.++.+|+|+++++|..+-..
T Consensus 21 iS~kk~r~va~~IrG~~v~~A~~~L~~ 47 (150)
T TIGR01038 21 VSFKNARETARAIRGMELDKARKYLED 47 (150)
T ss_pred ccHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 333445678999999999999998864
No 57
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase. This model represents phosphomethylpyrimidine kinase, the ThiD protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species.
Probab=24.00 E-value=1.2e+02 Score=24.17 Aligned_cols=44 Identities=20% Similarity=0.334 Sum_probs=30.2
Q ss_pred cEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 83 ~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
++......+-||.++- .+++.++.|.+++|+..+....+...+.
T Consensus 196 ~~~~~d~~GaGD~f~a---alaa~la~g~~l~eA~~~A~~~~~~~i~ 239 (254)
T TIGR00097 196 RIETKNTHGTGCTLSA---AIAANLAKGLSLKEAVKEAKEFVTGAIR 239 (254)
T ss_pred ccCCCCCCChHHHHHH---HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Confidence 3433345667777754 4556677899999999988776666654
No 58
>COG0638 PRE1 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]
Probab=23.52 E-value=2.6e+02 Score=22.63 Aligned_cols=96 Identities=18% Similarity=0.271 Sum_probs=64.9
Q ss_pred CCCCCCCchhhHhHHHHHHHHHh--CCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEeeeeeeeccchHH
Q 031835 20 APRPVQVAAMPRLYHENVIDHYN--NPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSA 97 (152)
Q Consensus 20 ~~~~~~~~~~~~lYs~~Ile~~~--~Prn~G~l~~~d~~v~~g~~~np~CGD~I~i~l~i~~~~g~I~d~~F~~~GC~is 97 (152)
--+|++...+-.+.++.+..+-. .|-..+. .+ .| .++ +.-++| .+|.. |.+.+.++.+-|.+..
T Consensus 100 ~~~~i~v~~la~~ls~~l~~~~~~~rP~gv~~------ii-aG--~d~---~~p~Ly-~~Dp~-G~~~~~~~~a~Gsgs~ 165 (236)
T COG0638 100 YGEPISVEALAKLLSNILQEYTQSGRPYGVSL------LV-AG--VDD---GGPRLY-STDPS-GSYNEYKATAIGSGSQ 165 (236)
T ss_pred hCCCCCHHHHHHHHHHHHHHhccCcccceEEE------EE-EE--EcC---CCCeEE-EECCC-CceeecCEEEEcCCcH
Confidence 34577777888888887766655 3332221 11 12 132 233555 55654 7888999999999988
Q ss_pred HHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 98 IASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 98 iAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
.|-.-+=-+.-.+++++|+..+.-+.|.+..+
T Consensus 166 ~a~~~Le~~y~~~m~~eeai~la~~al~~a~~ 197 (236)
T COG0638 166 FAYGFLEKEYREDLSLEEAIELAVKALRAAIE 197 (236)
T ss_pred HHHHHHHhhccCCCCHHHHHHHHHHHHHHHHh
Confidence 88766666666789999999998888877766
No 59
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=23.40 E-value=1.1e+02 Score=23.97 Aligned_cols=24 Identities=21% Similarity=0.253 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHch
Q 031835 96 SAIASSSVATEWVKGKQMQEVLSI 119 (152)
Q Consensus 96 isiAsaS~l~eli~Gktl~EA~~l 119 (152)
..-.++-.++++++|||.+|...+
T Consensus 115 Ll~~~ck~va~mikgktpeEir~~ 138 (162)
T KOG1724|consen 115 LLDLTCKTVANMIKGKTPEEIREI 138 (162)
T ss_pred HHHHHHHHHHHHHccCCHHHHHHH
Confidence 455667889999999999888776
No 60
>PF04879 Molybdop_Fe4S4: Molybdopterin oxidoreductase Fe4S4 domain; InterPro: IPR006963 The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2VPZ_A 2VPY_A 2VPW_A 2VPX_A 2NYA_A 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 ....
Probab=23.27 E-value=1.3e+02 Score=18.29 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=17.9
Q ss_pred CCCCCEEEEEEEEeCCCCcEeeeeee
Q 031835 65 PACGDVMKLQIKVDEETGQIVDACFK 90 (152)
Q Consensus 65 p~CGD~I~i~l~i~~~~g~I~d~~F~ 90 (152)
+.|+..-.|.+.+++ |+|..+.-.
T Consensus 9 ~~C~~gC~i~~~v~~--g~i~~v~g~ 32 (55)
T PF04879_consen 9 PYCSSGCGIDVYVKD--GKIVKVEGD 32 (55)
T ss_dssp SSCTT--EEEEEEET--TEEEEEEE-
T ss_pred cCCcCCCcEEEEEec--CceEEEECC
Confidence 579999899999988 999988664
No 61
>PRK12412 pyridoxal kinase; Reviewed
Probab=23.11 E-value=1.4e+02 Score=24.15 Aligned_cols=37 Identities=19% Similarity=0.407 Sum_probs=28.1
Q ss_pred eccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhcC
Q 031835 91 TFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQN 130 (152)
Q Consensus 91 ~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg~ 130 (152)
+-||.++ +.+++.++.|++++|+.+.....+.+.+..
T Consensus 210 GaGD~f~---aa~aa~l~~g~~l~eA~~~A~~~~~~~i~~ 246 (268)
T PRK12412 210 GAGCTYS---AAITAELAKGKPVKEAVKTAKEFITAAIRY 246 (268)
T ss_pred chHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence 5566554 466778889999999999988777776653
No 62
>PRK07105 pyridoxamine kinase; Validated
Probab=22.87 E-value=1.6e+02 Score=23.98 Aligned_cols=40 Identities=10% Similarity=0.072 Sum_probs=29.7
Q ss_pred eeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 87 ACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 87 ~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
..+.|-||+++- .+++.+++|.+++++.+.....+...+.
T Consensus 215 ~~~~GaGD~f~a---a~~~~l~~g~~l~~av~~A~~~~~~~i~ 254 (284)
T PRK07105 215 AHYPGTGDIFTS---VITGSLLQGDSLPIALDRAVQFIEKGIR 254 (284)
T ss_pred CCcCChhHHHHH---HHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence 455666777654 5566778999999999988777766665
No 63
>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=22.16 E-value=3.3e+02 Score=21.44 Aligned_cols=57 Identities=11% Similarity=-0.014 Sum_probs=43.2
Q ss_pred EEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHHHhhhc
Q 031835 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGVAGKLQ 129 (152)
Q Consensus 71 I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I~~~Lg 129 (152)
-.+| .+|.. |...+.+|.+.|.+-..|-.-+=-.+=.++|.+||.++.-+-|.+.++
T Consensus 142 p~Ly-~~D~~-Gs~~~~~~~a~G~g~~~a~~~Lek~~~~dms~eeai~l~~~~L~~~~~ 198 (212)
T cd03751 142 PQLY-MIEPS-GVSYGYFGCAIGKGKQAAKTELEKLKFSELTCREAVKEAAKIIYIVHD 198 (212)
T ss_pred CEEE-EECCC-CCEEeeEEEEECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhh
Confidence 4555 56654 889999999999988887766666667789999998877766666555
No 64
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=21.78 E-value=2.2e+02 Score=20.47 Aligned_cols=21 Identities=24% Similarity=0.593 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCCHHHHHchhH
Q 031835 101 SSVATEWVKGKQMQEVLSIKN 121 (152)
Q Consensus 101 aS~l~eli~Gktl~EA~~l~~ 121 (152)
.-.++.+|.|++++||..+-.
T Consensus 17 ~~~v~~~IrG~~v~~A~~~L~ 37 (112)
T PRK00565 17 ARLVADLIRGKKVEEALAILK 37 (112)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 457899999999999987643
No 65
>TIGR02870 spore_II_D stage II sporulation protein D. Stage II sporulation protein D (SpoIID) is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is one of three major proteins involved in engulfment of the forespore by the mother cell.
Probab=21.42 E-value=1.8e+02 Score=25.19 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=31.7
Q ss_pred EEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHc
Q 031835 73 LQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLS 118 (152)
Q Consensus 73 i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~ 118 (152)
|.++.+++ +.+..-+=.|+|-+.||=.|..|++ +|++.+|.++
T Consensus 285 F~i~~~~~-~~~~~g~G~GHGVGMSQ~GA~~mA~--~G~~y~eIL~ 327 (338)
T TIGR02870 285 FTWKVQGD-KIVITTIGYGHGVGMSQYGANAMAK--EGKTYDEILK 327 (338)
T ss_pred eEEEEcCC-EEEEEEeeecCCcCccHHHHHHHHH--cCCCHHHHHH
Confidence 44444442 4555555568899999999999998 6999998865
No 66
>PRK07217 replication factor A; Reviewed
Probab=21.04 E-value=2.7e+02 Score=24.12 Aligned_cols=43 Identities=16% Similarity=0.283 Sum_probs=31.6
Q ss_pred EEEEEEEEeCCCCcEeeeeeeeccchHHHHHHHHHHHHHcCCCHHHHHchhHHHH
Q 031835 70 VMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTGV 124 (152)
Q Consensus 70 ~I~i~l~i~~~~g~I~d~~F~~~GC~isiAsaS~l~eli~Gktl~EA~~l~~~~I 124 (152)
.+++...+||.++ ...+.|.- =+++.+.|.+++||+++..+.+
T Consensus 216 DLrik~vlDDGt~-~~~~~~~~-----------e~te~l~G~~l~eak~~a~dal 258 (311)
T PRK07217 216 DLRIKGVLDDGEE-VQEVIFNR-----------EATEELTGITLEEAKQMAMDAL 258 (311)
T ss_pred eeEEEEEEECCCC-eEEEEECh-----------HHhHHHhCCCHHHHHHHHHHhh
Confidence 4788888887434 55555553 3678889999999999886555
No 67
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=20.72 E-value=65 Score=21.59 Aligned_cols=25 Identities=12% Similarity=0.057 Sum_probs=16.5
Q ss_pred HHcCCCHHHHHchhHHHHHhhhcCc
Q 031835 107 WVKGKQMQEVLSIKNTGVAGKLQNI 131 (152)
Q Consensus 107 li~Gktl~EA~~l~~~~I~~~Lg~~ 131 (152)
.+.|+|++|+.+...+.+.+.+..+
T Consensus 50 ~v~G~T~~e~~~~I~~~l~~~~~~p 74 (82)
T PF02563_consen 50 KVAGLTLEEAEEEIKQRLQKYYRDP 74 (82)
T ss_dssp E-TT--HHHHHHHHHHHHTTTSSS-
T ss_pred EECCCCHHHHHHHHHHHHHHHhcCC
Confidence 3569999999998888887766543
No 68
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=20.16 E-value=1e+02 Score=19.57 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=11.5
Q ss_pred CCCCCCEEEEEEEE
Q 031835 64 APACGDVMKLQIKV 77 (152)
Q Consensus 64 np~CGD~I~i~l~i 77 (152)
.+.+||.|.+.+..
T Consensus 40 ~~~vGD~V~~~~~~ 53 (64)
T cd04451 40 RILPGDRVKVELSP 53 (64)
T ss_pred ccCCCCEEEEEEee
Confidence 37899999998754
Done!