Query 030644
Match_columns 174
No_of_seqs 120 out of 1109
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 02:26:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030644.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030644hhsearch_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 1.7E-39 3.6E-44 248.8 15.3 125 32-157 2-126 (127)
2 TIGR01999 iscU FeS cluster ass 100.0 4.4E-39 9.4E-44 245.4 15.0 123 33-156 1-123 (124)
3 TIGR03419 NifU_clost FeS clust 100.0 5.7E-38 1.2E-42 238.4 14.9 120 33-157 1-121 (121)
4 COG0822 IscU NifU homolog invo 100.0 1E-36 2.2E-41 239.7 13.8 129 27-159 1-148 (150)
5 PF01592 NifU_N: NifU-like N t 100.0 3.9E-36 8.6E-41 229.3 15.2 123 32-156 1-124 (126)
6 TIGR01994 SUF_scaf_2 SUF syste 100.0 9.8E-36 2.1E-40 230.5 14.2 117 29-150 1-137 (137)
7 cd06664 IscU_like Iron-sulfur 100.0 4.7E-35 1E-39 221.4 13.2 112 32-148 1-123 (123)
8 KOG3361 Iron binding protein i 100.0 9E-35 1.9E-39 222.7 13.9 130 30-160 26-155 (157)
9 TIGR02000 NifU_proper Fe-S clu 100.0 2.2E-34 4.7E-39 247.2 15.0 125 30-158 2-127 (290)
10 PF02657 SufE: Fe-S metabolism 93.5 2.4 5.1E-05 32.3 11.4 108 28-146 9-121 (125)
11 PRK15019 CsdA-binding activato 90.2 7.8 0.00017 30.5 11.9 107 30-146 30-141 (147)
12 PRK09296 cysteine desufuration 89.4 8.6 0.00019 29.9 12.4 107 30-146 20-131 (138)
13 TIGR03391 FeS_syn_CsdE cystein 88.3 10 0.00022 29.4 11.5 100 30-139 25-129 (138)
14 PLN02673 quinolinate synthetas 86.0 24 0.00052 34.5 13.4 85 65-152 127-215 (724)
15 TIGR01038 L22_arch ribosomal p 84.3 4.6 0.0001 31.9 6.6 68 92-159 17-106 (150)
16 PF12637 TSCPD: TSCPD domain; 83.3 12 0.00025 27.1 8.0 46 67-117 7-61 (95)
17 PTZ00178 60S ribosomal protein 83.2 4.5 9.8E-05 33.0 6.3 64 96-159 24-109 (181)
18 PRK04223 rpl22p 50S ribosomal 82.5 5.9 0.00013 31.4 6.6 60 99-158 28-107 (153)
19 COG2166 sufE Cysteine desulfur 81.7 24 0.00052 27.8 10.6 78 65-146 54-136 (144)
20 PF10437 Lip_prot_lig_C: Bacte 79.5 2.9 6.4E-05 29.1 3.6 50 68-121 15-66 (86)
21 cd00336 Ribosomal_L22 Ribosoma 76.7 7.5 0.00016 28.3 5.2 47 102-158 16-62 (105)
22 COG0351 ThiD Hydroxymethylpyri 75.8 5 0.00011 34.6 4.6 45 82-129 200-244 (263)
23 PRK00565 rplV 50S ribosomal pr 74.5 13 0.00028 27.6 6.1 45 100-154 16-60 (112)
24 PF00237 Ribosomal_L22: Riboso 73.2 15 0.00032 26.7 6.1 50 101-160 13-63 (105)
25 TIGR01044 rplV_bact ribosomal 73.2 14 0.0003 27.2 5.8 43 101-153 13-55 (103)
26 CHL00034 rpl22 ribosomal prote 68.1 23 0.00049 26.7 6.2 43 101-153 24-66 (117)
27 PTZ00493 phosphomethylpyrimidi 64.2 10 0.00022 33.4 4.2 44 82-128 240-283 (321)
28 PF04205 FMN_bind: FMN-binding 62.5 11 0.00024 25.5 3.3 72 69-153 4-78 (81)
29 COG0091 RplV Ribosomal protein 57.2 34 0.00074 26.1 5.4 49 101-159 25-74 (120)
30 PRK12279 50S ribosomal protein 55.5 30 0.00065 30.6 5.5 44 100-153 16-59 (311)
31 PF08543 Phos_pyr_kin: Phospho 53.5 14 0.00031 30.6 3.1 43 83-128 190-232 (246)
32 TIGR00545 lipoyltrans lipoyltr 47.7 31 0.00067 30.3 4.4 44 68-115 257-300 (324)
33 PF02593 dTMP_synthase: Thymid 46.9 59 0.0013 27.2 5.7 123 15-149 77-216 (217)
34 PF01466 Skp1: Skp1 family, di 46.5 30 0.00065 23.8 3.4 24 98-121 33-56 (78)
35 PRK03822 lplA lipoate-protein 43.5 58 0.0013 28.8 5.5 43 68-114 262-304 (338)
36 PRK14061 unknown domain/lipoat 36.5 73 0.0016 30.4 5.2 44 67-114 485-528 (562)
37 PRK12413 phosphomethylpyrimidi 33.0 49 0.0011 27.0 3.2 42 84-128 199-240 (253)
38 PRK08176 pdxK pyridoxal-pyrido 30.9 56 0.0012 27.6 3.3 40 86-128 225-264 (281)
39 cd01169 HMPP_kinase 4-amino-5- 29.8 92 0.002 25.0 4.3 43 83-128 197-239 (242)
40 PRK12616 pyridoxal kinase; Rev 29.5 83 0.0018 26.3 4.1 37 89-128 211-247 (270)
41 PF14410 GH-E: HNH/ENDO VII su 29.4 55 0.0012 22.4 2.4 21 33-54 42-62 (70)
42 cd01173 pyridoxal_pyridoxamine 29.3 61 0.0013 26.4 3.2 39 87-128 211-249 (254)
43 PRK12412 pyridoxal kinase; Rev 29.3 87 0.0019 26.1 4.1 36 90-128 209-244 (268)
44 PRK05756 pyridoxamine kinase; 28.1 98 0.0021 25.9 4.3 39 87-128 215-253 (286)
45 PLN02978 pyridoxal kinase 27.6 1E+02 0.0023 26.4 4.4 42 83-128 223-265 (308)
46 PTZ00347 phosphomethylpyrimidi 25.5 1E+02 0.0023 28.3 4.3 44 82-128 433-476 (504)
47 TIGR00097 HMP-P_kinase phospho 24.7 1.1E+02 0.0025 25.0 4.0 43 83-128 196-238 (254)
48 TIGR00778 ahpD_dom alkylhydrop 24.6 1.5E+02 0.0033 17.8 3.7 29 91-120 18-46 (50)
49 PF03450 CO_deh_flav_C: CO deh 23.8 2E+02 0.0044 20.2 4.7 44 71-115 18-61 (103)
50 PRK06427 bifunctional hydroxy- 23.4 1.2E+02 0.0026 24.8 4.0 43 83-128 204-246 (266)
51 TIGR02870 spore_II_D stage II 22.7 1.8E+02 0.0039 25.9 5.0 43 74-119 286-328 (338)
52 PF00227 Proteasome: Proteasom 22.1 3.6E+02 0.0079 20.6 6.5 56 70-127 118-174 (190)
53 PF15076 DUF4543: Domain of un 21.7 94 0.002 21.5 2.4 20 29-48 46-65 (75)
54 TIGR02669 SpoIID_LytB SpoIID/L 21.2 1.7E+02 0.0037 24.9 4.5 36 82-119 223-258 (267)
No 1
>PRK11325 scaffold protein; Provisional
Probab=100.00 E-value=1.7e-39 Score=248.80 Aligned_cols=125 Identities=74% Similarity=1.198 Sum_probs=117.0
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCC
Q 030644 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (174)
Q Consensus 32 lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GK 111 (174)
+|+++||+||.||+|.|.+++++...+.+..+||+|||+|+|||+|+++ |+|+|++|+++||++++||+|+|+++++||
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 6999999999999999999998754456678999999999999999732 899999999999999999999999999999
Q ss_pred CHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHHhcC
Q 030644 112 QMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRT 157 (174)
Q Consensus 112 tl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~~~~ 157 (174)
|++|+..|+.+++.+.||+|++|++|++|+|+||++++++|..++.
T Consensus 81 tl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~~~~~ 126 (127)
T PRK11325 81 TLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQA 126 (127)
T ss_pred CHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999987764
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=4.4e-39 Score=245.39 Aligned_cols=123 Identities=76% Similarity=1.192 Sum_probs=115.7
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCC
Q 030644 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (174)
Q Consensus 33 Y~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKt 112 (174)
|+++|++||.||+|.|.+++++..++.|+.+||+|||.|+|||+|+++ ++|+|++|+++||++++||+|+|+++++|||
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 899999999999999999998754456778999999999999999754 7999999999999999999999999999999
Q ss_pred HHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHHhc
Q 030644 113 MQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKR 156 (174)
Q Consensus 113 l~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~~~ 156 (174)
++|+..|+.+++.+.||+||+|+||++|+|+||++|+.+|..++
T Consensus 80 l~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~~~~ 123 (124)
T TIGR01999 80 LEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQ 123 (124)
T ss_pred HHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999998764
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=5.7e-38 Score=238.43 Aligned_cols=120 Identities=55% Similarity=0.958 Sum_probs=113.4
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCC
Q 030644 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (174)
Q Consensus 33 Y~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKt 112 (174)
|+++||+||.||+|+|.+++++. .++.+||+|||.|+|||++++ ++|+|++|+++||++|+||+|+|+++++|||
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 89999999999999999999874 467899999999999999987 8999999999999999999999999999999
Q ss_pred HHHHHhhhHHHHHhhcC-CCCchhHHHHHHHHHHHHHHHHHHHhcC
Q 030644 113 MQEVLSIKNTEIAKHLS-LPPVKLHCSMLAEDAIKAAVKDYEAKRT 157 (174)
Q Consensus 113 l~ea~~i~~~~i~e~L~-~~~~R~~CA~L~~~AL~~AL~~~~~~~~ 157 (174)
++|+..|..+++.+.|+ +|++|++|++|+|+||++++++|..+++
T Consensus 76 l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~~~~ 121 (121)
T TIGR03419 76 LEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 (121)
T ss_pred HHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHhccC
Confidence 99999999988888885 8999999999999999999999988753
No 4
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=100.00 E-value=1e-36 Score=239.73 Aligned_cols=129 Identities=54% Similarity=0.936 Sum_probs=115.9
Q ss_pred chhhhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHH
Q 030644 27 AAMPRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATE 106 (174)
Q Consensus 27 ~~~~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~e 106 (174)
+.+|.+|+++|++||.||+|.|.+++++. ..+..++|+|||.|+|||++++ |+|+|++|+++||+++|||+|+|++
T Consensus 1 ~~~~~~y~~~Ildh~~np~~~g~l~~~~~--~~~~~~~~~CGD~i~l~lkv~~--~~I~d~~F~~~GC~is~ASss~~te 76 (150)
T COG0822 1 SNLDDLYSEKILDHYKNPRNVGVLDDADV--GVGHVGAPACGDVITLYLKVDN--GVIEDAKFKGFGCAISIASSSMMTE 76 (150)
T ss_pred CcHHHHHHHHHHHHhcCCCcCCccCccch--hccccCCCCccceEEEEEEEcC--CEEEEEEeeecCcHHHHHHHHHHHH
Confidence 35799999999999999999999999874 3456678999999999999997 9999999999999999999999999
Q ss_pred HHcCCCHHHHHhhhHH--HHHhhcC-----------------CCCchhHHHHHHHHHHHHHHHHHHHhcCCC
Q 030644 107 WVKGKQMQEVLSIKNT--EIAKHLS-----------------LPPVKLHCSMLAEDAIKAAVKDYEAKRTKP 159 (174)
Q Consensus 107 l~~GKtl~ea~~i~~~--~i~e~L~-----------------~~~~R~~CA~L~~~AL~~AL~~~~~~~~~~ 159 (174)
+++|||++||.+|+.. ++.+.++ ++|.|++|++|+|+||++++++|..++...
T Consensus 77 ~v~Gkti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~~ai~~~~~~~~~~ 148 (150)
T COG0822 77 LVKGKTLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALKAAIKDYKGKAEEA 148 (150)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhHhhhhhccccccccchhccHHHHHHHHHHhhcccccc
Confidence 9999999999999955 4445443 899999999999999999999999886643
No 5
>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=3.9e-36 Score=229.30 Aligned_cols=123 Identities=48% Similarity=0.918 Sum_probs=115.3
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCC
Q 030644 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (174)
Q Consensus 32 lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GK 111 (174)
+|+++|++||.||+|+|.++++++ ++++.+||+|||+|+|||+|++++|+|+|++|+++||++++||+|+|+++++||
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 699999999999999999999885 246778999999999999999866899999999999999999999999999999
Q ss_pred CHHHHHhhhHHHHHhhcC-CCCchhHHHHHHHHHHHHHHHHHHHhc
Q 030644 112 QMQEVLSIKNTEIAKHLS-LPPVKLHCSMLAEDAIKAAVKDYEAKR 156 (174)
Q Consensus 112 tl~ea~~i~~~~i~e~L~-~~~~R~~CA~L~~~AL~~AL~~~~~~~ 156 (174)
|++||.+|+.+++.+.|+ +|+.|.+|+.|++.||++++++|..++
T Consensus 79 ~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~r~ 124 (126)
T PF01592_consen 79 TLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPARH 124 (126)
T ss_dssp BHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999999996 899999999999999999999999875
No 6
>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=100.00 E-value=9.8e-36 Score=230.52 Aligned_cols=117 Identities=33% Similarity=0.602 Sum_probs=104.2
Q ss_pred hhhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHH
Q 030644 29 MPRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWV 108 (174)
Q Consensus 29 ~~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~ 108 (174)
++++|+++|++||.||+|+|.+++++. .++.+||+|||+|+||++|++ ++|++++|+++||++|+||+|+|++++
T Consensus 1 ~~~lY~~~Ileh~~~p~n~g~l~~~~~---~~~~~np~CGD~i~l~l~v~~--~~I~d~~f~~~GCais~Asas~~~e~i 75 (137)
T TIGR01994 1 LDSLYRQVILDHYKNPRHRGKLEDATV---QERGHNPTCGDEITLTVKLEG--DRIEDIAFEGEGCSISQASASMMTELI 75 (137)
T ss_pred ChHHHHHHHHHHHhCCCCCCCCCCCCe---eEEeCCCCCCcEEEEEEEEcC--CeEEEEEEEecccHHHHHHHHHHHHHH
Confidence 367999999999999999999998874 457789999999999999987 899999999999999999999999999
Q ss_pred cCCCHHHHHhhhHHHH---H--------hhc---------CCCCchhHHHHHHHHHHHHHHH
Q 030644 109 KGKQMQEVLSIKNTEI---A--------KHL---------SLPPVKLHCSMLAEDAIKAAVK 150 (174)
Q Consensus 109 ~GKtl~ea~~i~~~~i---~--------e~L---------~~~~~R~~CA~L~~~AL~~AL~ 150 (174)
+|||++|+..+..++. . +.| ..+|+|++|++|+|+||++||+
T Consensus 76 ~Gk~~~ea~~l~~~~~~ml~~~~~~~~~~~l~dl~~l~~v~~~p~R~~Ca~L~~~al~~al~ 137 (137)
T TIGR01994 76 KGKTVEEALSLVEAFSEMIQGQETDEDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137 (137)
T ss_pred cCCCHHHHHHHHHHHHHHHhcCCCCccccccchHHHhhccccCcchHHHHHHHHHHHHHHhC
Confidence 9999999999998632 1 011 3589999999999999999973
No 7
>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=4.7e-35 Score=221.35 Aligned_cols=112 Identities=52% Similarity=0.921 Sum_probs=104.3
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCC
Q 030644 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (174)
Q Consensus 32 lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GK 111 (174)
+|+++|++||.||+|.|.+++++. .++.+||+|||+|+||+++++ ++|++++|+++||++++||+|+|+++++||
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 699999999999999999998864 467899999999999999988 899999999999999999999999999999
Q ss_pred CHHHHHhhhHHHHHhh-----------cCCCCchhHHHHHHHHHHHHH
Q 030644 112 QMQEVLSIKNTEIAKH-----------LSLPPVKLHCSMLAEDAIKAA 148 (174)
Q Consensus 112 tl~ea~~i~~~~i~e~-----------L~~~~~R~~CA~L~~~AL~~A 148 (174)
|++|+..|+.+++... .+.||+|++|++|+|+||+++
T Consensus 76 ~~~ea~~i~~~~~~~~~~~~~l~~~~~~~~~~~R~~Ca~L~~~Al~~a 123 (123)
T cd06664 76 TLDEALKLLNKDIAMLDGKEELAALAGVGLPPARIHCALLAWKALKAA 123 (123)
T ss_pred cHHHHHHHHHHHHHHhcCchhHHHhcccccCcccchHHHHHHHHHHhC
Confidence 9999999999987654 368999999999999999874
No 8
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=100.00 E-value=9e-35 Score=222.74 Aligned_cols=130 Identities=82% Similarity=1.253 Sum_probs=126.1
Q ss_pred hhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHc
Q 030644 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (174)
Q Consensus 30 ~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~ 109 (174)
..+|++.+++||.||||.|.++..+.++|+|..|-|.|||.++|+++|+++ |+|+|++|.++||+..|||+|+++||++
T Consensus 26 ~rlYh~~VidHy~nPRNVGSldK~dpnVGtGlVGAPACGDVMkLqIkvd~~-g~I~dakFKTFGCGSAIASSS~aTewvk 104 (157)
T KOG3361|consen 26 SRLYHENVIDHYENPRNVGSLDKNDPNVGTGLVGAPACGDVMKLQIKVDDS-GVIEDAKFKTFGCGSAIASSSLATEWVK 104 (157)
T ss_pred hhhcchhhhhcccCccccCccCCCCCCcccccccCccccceeeEEEEECCC-CcEEEeeeeecccchHhhhhHHHHHHHc
Confidence 389999999999999999999999999999999999999999999999875 9999999999999999999999999999
Q ss_pred CCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHHhcCCCC
Q 030644 110 GKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTKPS 160 (174)
Q Consensus 110 GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~~~~~~~ 160 (174)
|||++|+.+|...+|.++|.+||.++||.+|+.+|++.|+.+|+.++..+.
T Consensus 105 gkt~dea~kIkNteIAKeL~LPPVKLHCSMLAEDAIKaAikdyk~Kq~~~~ 155 (157)
T KOG3361|consen 105 GKTLDEALKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKDYKEKQNKPN 155 (157)
T ss_pred cccHHHHHhcccHHHHHhccCCchhhhhHHHHHHHHHHHHHHHHHhccCCC
Confidence 999999999999999999999999999999999999999999999988765
No 9
>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=2.2e-34 Score=247.24 Aligned_cols=125 Identities=46% Similarity=0.831 Sum_probs=115.8
Q ss_pred hhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHc
Q 030644 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (174)
Q Consensus 30 ~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~ 109 (174)
|. |+++||+||.||+|+|.+++++. .++.+||+|||.|+|||+|++++++|+|++|+++||++++||+|+|+++++
T Consensus 2 ~~-Ys~~Ildh~~nP~n~G~L~~~~~---~g~~~np~CGD~i~l~l~vd~~~~~I~d~~F~~~GCais~ASAs~~~eli~ 77 (290)
T TIGR02000 2 WD-YTDKVKEHFYNPKNAGVVEDANA---VGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIK 77 (290)
T ss_pred cc-hHHHHHHHHhCcCCCCCCCCCCc---EEEeCCCCCcceEEEEEEEcCCCCeEEEEEEEecCcHHHHHHHHHHHHHHc
Confidence 44 99999999999999999999874 467899999999999999984348999999999999999999999999999
Q ss_pred CCCHHHHHhhhHHHHHhhcC-CCCchhHHHHHHHHHHHHHHHHHHHhcCC
Q 030644 110 GKQMQEVLSIKNTEIAKHLS-LPPVKLHCSMLAEDAIKAAVKDYEAKRTK 158 (174)
Q Consensus 110 GKtl~ea~~i~~~~i~e~L~-~~~~R~~CA~L~~~AL~~AL~~~~~~~~~ 158 (174)
|||++||..|+.+++.++|+ +||+|+||+.|+|+||++||++|..+.+.
T Consensus 78 Gktv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~kp~~ 127 (290)
T TIGR02000 78 GLTLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLE 127 (290)
T ss_pred CCCHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhcCccc
Confidence 99999999999999999885 99999999999999999999999877554
No 10
>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=93.53 E-value=2.4 Score=32.29 Aligned_cols=108 Identities=18% Similarity=0.210 Sum_probs=67.1
Q ss_pred hhhhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCc-hhHHHHHHHHHH
Q 030644 28 AMPRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATE 106 (174)
Q Consensus 28 ~~~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GC-ais~ASasil~e 106 (174)
+-|+..-+.|+++.++......-...+.+ . -+.|-..|=|+....++ |++ .|.++.= .+...-.+++.+
T Consensus 9 ~~~~~ry~~Li~lgk~lp~l~~~~~~~~~----~--V~GC~S~vWl~~~~~~~-g~~---~f~adSda~ivkGl~all~~ 78 (125)
T PF02657_consen 9 DDWEERYRYLIDLGKKLPPLPEELRTDEN----L--VHGCQSQVWLHVEEDED-GKV---HFRADSDARIVKGLLALLLE 78 (125)
T ss_dssp SSHHHHHHHHHHHHHTS----CCCCSCCE----E--ETSSSS-EEEEEEEETT-SEE---EEEEEESSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhcCCCCCHHHhcccc----c--CCCCccceeEeeeeccC-CEE---EEEecCccHHHHHHHHHHHH
Confidence 34666777889999887765433322222 1 24599988775444432 765 6666543 477788999999
Q ss_pred HHcCCCHHHHHhhhHHHHHhhcC----CCCchhHHHHHHHHHHH
Q 030644 107 WVKGKQMQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIK 146 (174)
Q Consensus 107 l~~GKtl~ea~~i~~~~i~e~L~----~~~~R~~CA~L~~~AL~ 146 (174)
.+.|+|.+|+..+..+ +.+.+| +.|+|..=..-.++-++
T Consensus 79 ~~~g~t~~eI~~~~~~-fl~~lgl~~~Ls~sR~nGl~~~~~~ik 121 (125)
T PF02657_consen 79 VLNGQTPEEILAFDPD-FLEQLGLSQHLSPSRSNGLLAMLQRIK 121 (125)
T ss_dssp HTTT-BHHHHHHS-TH-HHHHHTSCCCSTHHHHHHHHHHHHHHH
T ss_pred HHcCCCHHHHHhCCHH-HHHHcCcccccCchHHHHHHHHHHHHH
Confidence 9999999999999999 455554 57888764444444433
No 11
>PRK15019 CsdA-binding activator; Provisional
Probab=90.16 E-value=7.8 Score=30.50 Aligned_cols=107 Identities=15% Similarity=0.035 Sum_probs=69.1
Q ss_pred hhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCc-hhHHHHHHHHHHHH
Q 030644 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATEWV 108 (174)
Q Consensus 30 ~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GC-ais~ASasil~el~ 108 (174)
|+.--+.|+++.+.-.- +++... . -...-+-|-..|=|...++++ | .+.|.++.= .|...-++++.+.+
T Consensus 30 weeRy~~LI~lgk~Lp~---lpe~~r-~--~~~~V~GCqS~VWL~~~~~~d-g---~~~f~~dSDA~IvkGl~alL~~~~ 99 (147)
T PRK15019 30 WEDKYRQLIMLGKQLPA---LPDELK-A--QAKEIAGCENRVWLGYTVAEN-G---KMHFFGDSEGRIVRGLLAVLLTAV 99 (147)
T ss_pred HHHHHHHHHHHHhhCCC---CChHHc-C--ccCcCCCcccceeeeeeecCC-C---EEEEEeeCccHHHHHHHHHHHHHH
Confidence 44444556777765443 332211 0 011234588888776666432 5 466766543 46778889999999
Q ss_pred cCCCHHHHHhhhHHHHHhhcC----CCCchhHHHHHHHHHHH
Q 030644 109 KGKQMQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIK 146 (174)
Q Consensus 109 ~GKtl~ea~~i~~~~i~e~L~----~~~~R~~CA~L~~~AL~ 146 (174)
.|+|.+|+..++.+++.+.|| +.|+|..=..-.++.++
T Consensus 100 ~g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~NGl~ami~~I~ 141 (147)
T PRK15019 100 EGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAII 141 (147)
T ss_pred cCCCHHHHHhcCHHHHHHHCCchhhcCccHHHHHHHHHHHHH
Confidence 999999999999977777776 67999874444444433
No 12
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=89.36 E-value=8.6 Score=29.86 Aligned_cols=107 Identities=10% Similarity=0.011 Sum_probs=68.2
Q ss_pred hhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecCc-hhHHHHHHHHHHHH
Q 030644 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATEWV 108 (174)
Q Consensus 30 ~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~GC-ais~ASasil~el~ 108 (174)
|+---+.|+++.+.-.. +++... . ....-+-|-..|=|...++++ | .+.|.++.= .|...-++++...+
T Consensus 20 we~Ry~~LI~lgk~Lp~---lpe~~r-~--~~~~V~GCqS~VWl~~~~~~~-g---~~~f~~dSDa~ivkGl~alL~~~~ 89 (138)
T PRK09296 20 WEEKYLYIIELGQRLPP---LTDEDR-S--PQNLIQGCQSQVWIVMRQNAQ-G---IIELQGDSDAAIVKGLIAVVFILY 89 (138)
T ss_pred HHHHHHHHHHHHhhCCC---CCHHHc-C--ccccCCCcccceeeeEeecCC-C---EEEEEEecccHHHHHHHHHHHHHH
Confidence 54444566788775543 332211 0 111234588877776666553 5 466766543 46777889999999
Q ss_pred cCCCHHHHHhhhHHHHHhhcC----CCCchhHHHHHHHHHHH
Q 030644 109 KGKQMQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIK 146 (174)
Q Consensus 109 ~GKtl~ea~~i~~~~i~e~L~----~~~~R~~CA~L~~~AL~ 146 (174)
.|+|.+|+..++..++.+.|| +.|+|..=..-.++.++
T Consensus 90 ~g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~nGl~aml~~ik 131 (138)
T PRK09296 90 QQMTPQDIVNFDVRPWFEKLALTQHLTPSRSQGLEAMIRAIR 131 (138)
T ss_pred cCCCHHHHHhCChHHHHHHcCcccccCccHHHHHHHHHHHHH
Confidence 999999999999755556665 67899874433333333
No 13
>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=88.32 E-value=10 Score=29.43 Aligned_cols=100 Identities=13% Similarity=0.034 Sum_probs=64.1
Q ss_pred hhhHHHHHHHHHhCCCCCCCCCCCCCccceeeecCCCCCCEEEEEEEEeCCCCceeeeeeeecC-chhHHHHHHHHHHHH
Q 030644 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWV 108 (174)
Q Consensus 30 ~~lY~e~Ileh~~~Prn~g~l~~~~~~~~~g~~~npsCGD~I~l~l~v~~~~g~I~d~~F~~~G-Cais~ASasil~el~ 108 (174)
|+.--+.|+++.+.-. .+++... . -...-+-|-..|=|...+.++ | .+.|.++. -.|...-.+++.+.+
T Consensus 25 we~ry~~lI~lgk~Lp---~lpe~~r-~--~~~~V~GCqS~VWl~~~~~~d-g---~~~f~~dSDa~IvkGl~alL~~~~ 94 (138)
T TIGR03391 25 WEDRYRQLILLAKQLP---ALPEALK-T--QATELTGCENRVWLGHQVLPD-G---TLHFYGDSEGRIVRGLLAVLLTAV 94 (138)
T ss_pred HHHHHHHHHHHHhhCC---CCChHHc-C--hhhccCCcccceeeeeeecCC-C---EEEEEecCccHHHHHHHHHHHHHH
Confidence 3333345677776443 2333211 0 011234588887766554332 6 45576654 356778889999999
Q ss_pred cCCCHHHHHhhhHHHHHhhcC----CCCchhHHHH
Q 030644 109 KGKQMQEVLSIKNTEIAKHLS----LPPVKLHCSM 139 (174)
Q Consensus 109 ~GKtl~ea~~i~~~~i~e~L~----~~~~R~~CA~ 139 (174)
.|+|.+|+..++.+++.+.|| +.|+|..=..
T Consensus 95 ~g~tp~eI~~~d~~~~~~~lGL~~~LSpsR~NGl~ 129 (138)
T TIGR03391 95 EGKTPEQLLAQDPLALFDELGLRAQLSASRSNGLA 129 (138)
T ss_pred cCCCHHHHHHCCHHHHHHHcCchhccCccHHHHHH
Confidence 999999999999876777775 6788887433
No 14
>PLN02673 quinolinate synthetase A
Probab=86.02 E-value=24 Score=34.47 Aligned_cols=85 Identities=13% Similarity=0.142 Sum_probs=62.8
Q ss_pred CCCCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhh-cC---CCCchhHHHHH
Q 030644 65 PACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKH-LS---LPPVKLHCSML 140 (174)
Q Consensus 65 psCGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~-L~---~~~~R~~CA~L 140 (174)
+-|-..|=|...++++ |+ ..+.+..++ .|...-+.++...+.|+|.+|+..++.+++.+. || ..|+|..=..-
T Consensus 127 ~GCQSqVWL~~elddd-Gk-v~F~ADSDA-~IVKGL~ALLl~~lsG~TpeEILavD~d~~~~LGLGL~~~SPSRsNGL~n 203 (724)
T PLN02673 127 MGCTAQVWLEAELDQD-GK-MRFWADSDS-EITKGFCSCLIWVLDGASPEEVLELKTEDLAALNVGLPGGERSRVNTWHN 203 (724)
T ss_pred CCcccceEEEEEEcCC-CE-EEEEEeCcc-HHHHHHHHHHHHHHcCCCHHHHHhCCHHHHHHHhhhhcccCCchhHHHHH
Confidence 4688888777777653 53 345555566 788999999999999999999999999887432 13 37889886666
Q ss_pred HHHHHHHHHHHH
Q 030644 141 AEDAIKAAVKDY 152 (174)
Q Consensus 141 ~~~AL~~AL~~~ 152 (174)
..+.+++-+...
T Consensus 204 ML~~Iq~~Ar~l 215 (724)
T PLN02673 204 VLVSMQKRTRRL 215 (724)
T ss_pred HHHHHHHHHHHH
Confidence 666666665553
No 15
>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=84.29 E-value=4.6 Score=31.94 Aligned_cols=68 Identities=7% Similarity=0.061 Sum_probs=48.7
Q ss_pred cCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhcC--------------------CCC--chhHHHHHHHHHHHHHH
Q 030644 92 FGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHLS--------------------LPP--VKLHCSMLAEDAIKAAV 149 (174)
Q Consensus 92 ~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L~--------------------~~~--~R~~CA~L~~~AL~~AL 149 (174)
..--+|-==+-.++.+++||++++|..+....+...-- ... .-.+|+.+..+.|+.|.
T Consensus 17 ~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~i~klL~sA~ 96 (150)
T TIGR01038 17 RNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKFILKVLQNAE 96 (150)
T ss_pred CCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHHHHHHHHHHH
Confidence 33344444567889999999999999999986543221 111 24589999999999999
Q ss_pred HHHHHhcCCC
Q 030644 150 KDYEAKRTKP 159 (174)
Q Consensus 150 ~~~~~~~~~~ 159 (174)
.+.+.+..++
T Consensus 97 aNA~~~gld~ 106 (150)
T TIGR01038 97 ANAEYKGLDV 106 (150)
T ss_pred HHHHhcCCCh
Confidence 9987644443
No 16
>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=83.33 E-value=12 Score=27.09 Aligned_cols=46 Identities=20% Similarity=0.517 Sum_probs=28.9
Q ss_pred CCCEEEEEEEEeCCCC----ceeeeeeeecCchhHHHHHHHHHHHH-----cCCCHHHHH
Q 030644 67 CGDVMKLQIKVDEETG----QIVDACFKTFGCGSAIASSSVATEWV-----KGKQMQEVL 117 (174)
Q Consensus 67 CGD~I~l~l~v~~~~g----~I~d~~F~~~GCais~ASasil~el~-----~GKtl~ea~ 117 (174)
|| .+.+.+..++++| ++.++++.| || .+-.+.++.++ .|.+++++.
T Consensus 7 ~g-~~yvtv~~d~d~g~p~Evf~~~~~~G-g~---~~~~~ai~rliS~~Lr~G~~~~~ii 61 (95)
T PF12637_consen 7 CG-KLYVTVNFDEDNGRPFEVFINVGKAG-GC---SGNLEAIARLISLALRSGVPPEEII 61 (95)
T ss_pred cc-ceEEEEEeeCCCCcceEEEEecCcCC-Cc---hHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 65 3333334443324 667776665 66 66667788888 899988743
No 17
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=83.20 E-value=4.5 Score=33.02 Aligned_cols=64 Identities=14% Similarity=0.070 Sum_probs=46.8
Q ss_pred hHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc--------------------CCCCc--hhHHHHHHHHHHHHHHHHHH
Q 030644 96 SAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL--------------------SLPPV--KLHCSMLAEDAIKAAVKDYE 153 (174)
Q Consensus 96 is~ASasil~el~~GKtl~ea~~i~~~~i~e~L--------------------~~~~~--R~~CA~L~~~AL~~AL~~~~ 153 (174)
+|-==+-.++++|.||++++|..+....|...- +.+.. -.+++.+..+.|+.|..+.+
T Consensus 24 iSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~GR~P~KaA~~i~KlL~SA~aNAe 103 (181)
T PTZ00178 24 VHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQGRWPEKSVKFVLSLLKNAEANAE 103 (181)
T ss_pred cchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccccccccCcCcHHHHHHHHHHHHHHHHHHH
Confidence 444446788999999999999999998654321 11222 45899999999999999987
Q ss_pred HhcCCC
Q 030644 154 AKRTKP 159 (174)
Q Consensus 154 ~~~~~~ 159 (174)
....++
T Consensus 104 ~~gld~ 109 (181)
T PTZ00178 104 AKGLDV 109 (181)
T ss_pred hcCCCh
Confidence 544433
No 18
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=82.53 E-value=5.9 Score=31.43 Aligned_cols=60 Identities=15% Similarity=0.138 Sum_probs=44.9
Q ss_pred HHHHHHHHHHcCCCHHHHHhhhHHHHHhh--c----------------CCCC--chhHHHHHHHHHHHHHHHHHHHhcCC
Q 030644 99 ASSSVATEWVKGKQMQEVLSIKNTEIAKH--L----------------SLPP--VKLHCSMLAEDAIKAAVKDYEAKRTK 158 (174)
Q Consensus 99 ASasil~el~~GKtl~ea~~i~~~~i~e~--L----------------~~~~--~R~~CA~L~~~AL~~AL~~~~~~~~~ 158 (174)
==+..++.++.||++++|..+....+... + +.+. .-.+|+.+..+.|+.|..+++.+..+
T Consensus 28 kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~KlL~sA~aNA~~~gld 107 (153)
T PRK04223 28 KHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFLKLLENAEANAEYKGLD 107 (153)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34578899999999999999999865432 1 1122 23589999999999999998764333
No 19
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=81.70 E-value=24 Score=27.85 Aligned_cols=78 Identities=17% Similarity=0.158 Sum_probs=55.6
Q ss_pred CCCCCEEEEEEEEeCCCCceeeeeeeecCc-hhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhcC----CCCchhHHHH
Q 030644 65 PACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHLS----LPPVKLHCSM 139 (174)
Q Consensus 65 psCGD~I~l~l~v~~~~g~I~d~~F~~~GC-ais~ASasil~el~~GKtl~ea~~i~~~~i~e~L~----~~~~R~~CA~ 139 (174)
+-|-..|=|....++ + -.+.|.|+.= .|...-++++...+.|||.+|+..++..++.+.|| +.|.|..=..
T Consensus 54 ~GC~S~vwL~~~~~~--~--~~~~F~gdSdA~ivrGL~aill~~~~G~t~~eI~~~~~~~~f~~LGL~~~LSpsR~nGl~ 129 (144)
T COG2166 54 PGCQSQVWLVTEQND--D--GTLHFFGDSDARIVRGLLAILLAAYSGKTAAEILAFDPLDFFEELGLAQHLSPSRSNGLE 129 (144)
T ss_pred CccccceeEEEeecC--C--ceEEEeccchhHHHHHHHHHHHHHHcCCCHHHHHcCCHHHHHHHhhHHHhcChHHhhHHH
Confidence 457776655555555 3 3567887654 46677889999999999999999999976777775 6888887443
Q ss_pred HHHHHHH
Q 030644 140 LAEDAIK 146 (174)
Q Consensus 140 L~~~AL~ 146 (174)
--.+.++
T Consensus 130 am~~~i~ 136 (144)
T COG2166 130 AMLKRIK 136 (144)
T ss_pred HHHHHHH
Confidence 3333333
No 20
>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=79.52 E-value=2.9 Score=29.15 Aligned_cols=50 Identities=16% Similarity=0.094 Sum_probs=34.5
Q ss_pred CCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCC--HHHHHhhhH
Q 030644 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ--MQEVLSIKN 121 (174)
Q Consensus 68 GD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKt--l~ea~~i~~ 121 (174)
|-.|++++.|++ |+|++++|.|+-=.. .-..-+.+.++|.. .+.+.+...
T Consensus 15 ~G~v~v~~~V~~--G~I~~i~i~gDf~~~--~~i~~le~~L~G~~~~~~~i~~~l~ 66 (86)
T PF10437_consen 15 WGTVEVHLNVKN--GIIKDIKIYGDFFGP--EDIEELEEALIGCPYDREAIKEALN 66 (86)
T ss_dssp TEEEEEEEEEET--TEEEEEEEEECBS-C--CCHHHHHHHHTTCBSSHHHHHHHHH
T ss_pred CceEEEEEEEEC--CEEEEEEEECCCCCc--hHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 456999999998 999999999853222 22566777788883 444444433
No 21
>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=76.73 E-value=7.5 Score=28.27 Aligned_cols=47 Identities=13% Similarity=0.154 Sum_probs=38.4
Q ss_pred HHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHHhcCC
Q 030644 102 SVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 158 (174)
Q Consensus 102 sil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~~~~~ 158 (174)
-.++.++.|++++||..+..... .+++.+..++|+.|..++......
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~~~~----------kk~a~~i~k~l~sa~~nA~~~~~~ 62 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLEFVP----------KKAAKIILKLLKSAEANAENNGLD 62 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHHhCC----------HHHHHHHHHHHHHHHHhHHHcCCC
Confidence 46789999999999988776531 778899999999999998765544
No 22
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=75.85 E-value=5 Score=34.55 Aligned_cols=45 Identities=16% Similarity=0.299 Sum_probs=36.8
Q ss_pred CceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhcC
Q 030644 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHLS 129 (174)
Q Consensus 82 g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L~ 129 (174)
.+|..-.-.|.||.+| +++.+.+++|.++.||.+-..+++...+.
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 5676666789999985 56778889999999999999998876663
No 23
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=74.49 E-value=13 Score=27.64 Aligned_cols=45 Identities=20% Similarity=0.397 Sum_probs=37.3
Q ss_pred HHHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHH
Q 030644 100 SSSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA 154 (174)
Q Consensus 100 Sasil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~ 154 (174)
=+-.++.++.||++++|..+... ...+.+....+.|+.|..+++.
T Consensus 16 K~~~v~~~IrG~~v~~A~~~L~~----------~pkk~a~~i~k~L~sA~aNA~~ 60 (112)
T PRK00565 16 KARLVADLIRGKKVEEALAILKF----------SPKKAARLVKKVLKSAIANAEN 60 (112)
T ss_pred HHHHHHHHHcCCcHHHHHHHHHH----------CcHhHHHHHHHHHHHHHHHHHh
Confidence 34678999999999999987766 4556688899999999999875
No 24
>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=73.19 E-value=15 Score=26.72 Aligned_cols=50 Identities=14% Similarity=0.209 Sum_probs=39.7
Q ss_pred HHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHH-HhcCCCC
Q 030644 101 SSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE-AKRTKPS 160 (174)
Q Consensus 101 asil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~-~~~~~~~ 160 (174)
+-.++.++.|+++++|....... ..+.+....+.|+.|+.+.+ ....+++
T Consensus 13 ~~~v~~~Irg~~v~~A~~~L~~~----------~~k~a~~i~k~L~~a~~nA~~~~g~d~~ 63 (105)
T PF00237_consen 13 LREVARLIRGMSVDEAIAQLKFV----------PKKAAKFILKLLKSAIANAENNKGLDPD 63 (105)
T ss_dssp HHHHHHHHTTSBHHHHHHHHHHH----------SSHHHHHHHHHHHHHHHHHHHHCTSTCG
T ss_pred HHHHHHHHcCCCHHHHHHHHHhC----------cHHHHHHHHhhHHHHHhhcccccccccC
Confidence 34678999999999999887764 45778899999999999988 5444443
No 25
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=73.15 E-value=14 Score=27.17 Aligned_cols=43 Identities=16% Similarity=0.372 Sum_probs=36.3
Q ss_pred HHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHH
Q 030644 101 SSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 153 (174)
Q Consensus 101 asil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~ 153 (174)
+-.++.++.|++++||..+.. + ...+++....+.|+.|..+++
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~--------f--~pkk~a~~i~klL~sA~aNA~ 55 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILR--------F--TPKKAAPLIKKVLASAIANAE 55 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHh--------h--CCHhHHHHHHHHHHHHHHHHH
Confidence 356889999999999988776 2 456799999999999999985
No 26
>CHL00034 rpl22 ribosomal protein L22
Probab=68.08 E-value=23 Score=26.73 Aligned_cols=43 Identities=12% Similarity=0.172 Sum_probs=36.5
Q ss_pred HHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHH
Q 030644 101 SSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 153 (174)
Q Consensus 101 asil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~ 153 (174)
+-.++.++.||++++|..+... ...+.+....+.|+.|+.+++
T Consensus 24 ~r~va~~IRG~~v~~A~~~L~~----------~pkk~a~~i~klL~sA~aNA~ 66 (117)
T CHL00034 24 ARRVIDQIRGRSYEEALMILEF----------MPYRACYPILKLVYSAAANAS 66 (117)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH----------CcHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999988774 227889999999999999884
No 27
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=64.24 E-value=10 Score=33.42 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=34.4
Q ss_pred CceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 82 g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
.+|..-.|.|.||.++-| +.+.++.|.++.+|.....+++.+.+
T Consensus 240 ~ri~~~~~hGTGc~fASA---IAa~LA~G~~l~~Av~~A~~fv~~aI 283 (321)
T PTZ00493 240 KRKPGKDIHGTGCTLSTA---IACYLAKKHNILQSCIESKKYIYNCI 283 (321)
T ss_pred cccCCCCCCChHHHHHHH---HHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 466667789999998654 55566999999999999998876544
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=62.51 E-value=11 Score=25.50 Aligned_cols=72 Identities=19% Similarity=0.212 Sum_probs=42.6
Q ss_pred CEEEEEEEEeCCCCceeeeeeeecCchhHHH---HHHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHH
Q 030644 69 DVMKLQIKVDEETGQIVDACFKTFGCGSAIA---SSSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAI 145 (174)
Q Consensus 69 D~I~l~l~v~~~~g~I~d~~F~~~GCais~A---Sasil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL 145 (174)
..|++.+.++++ |+|.++.|..+.-..... ...-+.+.+.|+.. ......-+-+-=|++.-+++
T Consensus 4 g~i~v~v~i~~d-g~I~~v~~~~~~et~~~~~~~~~~~~~~~~~g~~~------------~~~~~~vD~vSGAT~ss~a~ 70 (81)
T PF04205_consen 4 GPITVTVTIDKD-GKITDVKILEHNETPGYGKKAEIEEFFDQIVGKQI------------KKDSDDVDAVSGATISSKAI 70 (81)
T ss_dssp EEEEEEEEEETT-TEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCC------------TTTSCEETTCTTBHHHHHHH
T ss_pred ceEEEEEEEeCC-CEEEEEEEeeccCCcchhhhccHHHHHHHHHhccc------------cccCCCCCeeeCcchhHHHH
Confidence 468888888866 899999999865422211 12233333333332 01123344456678888888
Q ss_pred HHHHHHHH
Q 030644 146 KAAVKDYE 153 (174)
Q Consensus 146 ~~AL~~~~ 153 (174)
.+++.+..
T Consensus 71 ~~av~~Al 78 (81)
T PF04205_consen 71 KEAVQKAL 78 (81)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88887654
No 29
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=57.18 E-value=34 Score=26.10 Aligned_cols=49 Identities=20% Similarity=0.395 Sum_probs=37.7
Q ss_pred HHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHHH-hcCCC
Q 030644 101 SSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEA-KRTKP 159 (174)
Q Consensus 101 asil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~~-~~~~~ 159 (174)
+..++.++.||++++|..+.... -.+-+....+.|+.|+.+.+. +-.++
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~~~----------pkKaa~~v~KvL~sA~aNAe~n~gLd~ 74 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILEFV----------PKKAAKLVKKVLESAIANAENNKGLDP 74 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHHhC----------hHHHHHHHHHHHHHHHhhHHhccCCCh
Confidence 46789999999999999985553 556777788889999988776 33333
No 30
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=55.48 E-value=30 Score=30.57 Aligned_cols=44 Identities=14% Similarity=0.280 Sum_probs=38.7
Q ss_pred HHHHHHHHHcCCCHHHHHhhhHHHHHhhcCCCCchhHHHHHHHHHHHHHHHHHH
Q 030644 100 SSSVATEWVKGKQMQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 153 (174)
Q Consensus 100 Sasil~el~~GKtl~ea~~i~~~~i~e~L~~~~~R~~CA~L~~~AL~~AL~~~~ 153 (174)
=+-.++.++.||++++|..+.... ..+++.+..+.|+.|+.+++
T Consensus 16 K~R~Va~~IRGk~v~~Al~~L~~~----------PkKaA~~I~KlLkSA~ANAe 59 (311)
T PRK12279 16 KASLVIDLVRNKPVHEAIRILSNT----------PKKFAPIVLKLLNSAISNVQ 59 (311)
T ss_pred HHHHHHHHHcCCcHHHHHHHHHhC----------CHHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999887763 67899999999999999987
No 31
>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=53.47 E-value=14 Score=30.59 Aligned_cols=43 Identities=16% Similarity=0.201 Sum_probs=33.5
Q ss_pred ceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 83 ~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
++...+|.|.||.++- .+++.+++|+++++|.....+++...+
T Consensus 190 ~~~~~~~~GTGd~fss---~laa~l~~g~~l~~Av~~A~~~v~~~i 232 (246)
T PF08543_consen 190 RIPTGSFHGTGDLFSS---ALAAFLAKGYSLEEAVEKAKNFVRRAI 232 (246)
T ss_dssp EECTSGCTTHHHHHHH---HHHHHHHTTSSHHHHHHHHHHHHHHHH
T ss_pred EEcCCCCCCchhHHHH---HHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 4555789999998865 455667999999999999888765443
No 32
>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=47.73 E-value=31 Score=30.26 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=32.7
Q ss_pred CCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHHH
Q 030644 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (174)
Q Consensus 68 GD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~e 115 (174)
+..|++++.|++ |+|+++++.|+-...- -.+-+.+.++|...+.
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 567999999998 9999999988754332 2466777778876443
No 33
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=46.87 E-value=59 Score=27.22 Aligned_cols=123 Identities=19% Similarity=0.312 Sum_probs=73.2
Q ss_pred HhhhhCCCCccCchhhhhHHHHHHH---HHhCCCCCCCCCCCC-Cccc--eeeecCCCCCCEEEEEEEEeCCCCceeeee
Q 030644 15 AAAVAAPRPVQVAAMPRLYHENVID---HYNNPRNVGSFEKND-ATVG--TGLVGAPACGDVMKLQIKVDEETGQIVDAC 88 (174)
Q Consensus 15 ~~~~~~~~~~~~~~~~~lY~e~Ile---h~~~Prn~g~l~~~~-~~~~--~g~~~npsCGD~I~l~l~v~~~~g~I~d~~ 88 (174)
.-++-.|..-+...+.....+++-+ ++..|+-+=.|++.. ..+. ....|.| ++.+.+++ |+|++++
T Consensus 77 ~kavIvp~~~~~~g~~~~lk~~~e~~gi~~~~P~~~CsL~~~~~p~i~~F~~~fGkP------~~ei~v~~--~~I~~V~ 148 (217)
T PF02593_consen 77 VKAVIVPSESPKPGLRRQLKKQLEEFGIEVEFPKPFCSLEENGNPQIDEFAEYFGKP------KVEIEVEN--GKIKDVK 148 (217)
T ss_pred CCEEEEecCCCccchHHHHHHHHHhcCceeecCccccccCCCCChhHHHHHHHhCCc------eEEEEecC--CcEEEEE
Confidence 4455555555555556666666666 356666555555421 1000 0001222 45555666 8998887
Q ss_pred ee-ecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhh------cC----CCCchhHHHHHHHHHHHHHH
Q 030644 89 FK-TFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKH------LS----LPPVKLHCSMLAEDAIKAAV 149 (174)
Q Consensus 89 F~-~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~------L~----~~~~R~~CA~L~~~AL~~AL 149 (174)
-- +.=|+ |+..+++.++|++++++.......+... .. ...-.|..+.+-.+|+++||
T Consensus 149 VlR~aPCG----sT~~vAk~l~G~~~~d~~~~~g~~~q~YPC~As~~~d~~~~d~~~h~Ag~i~~~Ave~Al 216 (217)
T PF02593_consen 149 VLRSAPCG----STWFVAKRLIGKEVEDAPEKAGLAHQHYPCRASMGRDFELGDTILHKAGYIHKEAVEKAL 216 (217)
T ss_pred EEecCCCc----cHHHHHHHhcCCccchhhhhhhhhheecccccccccccccccchhhhhHHHHHHHHHHhh
Confidence 54 33343 6788999999999999998886544322 11 12345577788888888887
No 34
>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=46.54 E-value=30 Score=23.77 Aligned_cols=24 Identities=17% Similarity=0.148 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHhhhH
Q 030644 98 IASSSVATEWVKGKQMQEVLSIKN 121 (174)
Q Consensus 98 ~ASasil~el~~GKtl~ea~~i~~ 121 (174)
..++..++.+++|||.+|+..+..
T Consensus 33 ~~~~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 33 DLCCKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCHHHHHHHcC
Confidence 456678899999999999988765
No 35
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=43.47 E-value=58 Score=28.81 Aligned_cols=43 Identities=19% Similarity=0.144 Sum_probs=32.4
Q ss_pred CCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHH
Q 030644 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQ 114 (174)
Q Consensus 68 GD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~ 114 (174)
+..|++.+.|++ |+|+++++.++.-. ..--+-+.+.++|...+
T Consensus 262 ~G~v~i~~~v~~--g~I~~~~i~gD~~~--~~~~~~l~~~L~G~~~~ 304 (338)
T PRK03822 262 WGGVELHFDVEK--GHITRAQIFTDSLN--PAPLEALAGRLQGCLYR 304 (338)
T ss_pred CCcEEEEEEEEC--CEEEEEEEECCCCC--cccHHHHHHHhCCCCCC
Confidence 456999999998 99999999987433 23345677778887643
No 36
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=36.51 E-value=73 Score=30.43 Aligned_cols=44 Identities=18% Similarity=0.157 Sum_probs=32.3
Q ss_pred CCCEEEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHH
Q 030644 67 CGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQ 114 (174)
Q Consensus 67 CGD~I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~ 114 (174)
-+..|++++.|++ |+|+++++.|+--.. .-.+-+.+.+.|...+
T Consensus 485 ~~G~vei~l~V~~--G~I~~~ki~gDf~~~--~~i~~le~~L~G~~y~ 528 (562)
T PRK14061 485 SWGGVELHFDVEK--GHITRAQVFTDSLNP--APLEALAGRLQGCLYR 528 (562)
T ss_pred ccccEEEEEEEeC--CEEEEEEEECCCCCc--ccHHHHHHHhCCCCcC
Confidence 3567999999998 999999999874332 2235577777787643
No 37
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=32.98 E-value=49 Score=27.02 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=31.3
Q ss_pred eeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 84 IVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 84 I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
+..+...|-||++ ++.+++.+++|++++++.++...++.+.|
T Consensus 199 ~~~~~~~GaGDaf---~a~~~~~l~~g~~l~ea~~~A~~~~~~~l 240 (253)
T PRK12413 199 VLEKNNIGAGCTF---ASSIASQLVKGKSPLEAVKNSKDFVYQAI 240 (253)
T ss_pred ccCCCCCChHHHH---HHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 3455667777777 45677778899999999988887765544
No 38
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=30.85 E-value=56 Score=27.55 Aligned_cols=40 Identities=15% Similarity=0.180 Sum_probs=30.8
Q ss_pred eeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 86 DACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 86 d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
...+.|-||.++- .+++.+++|++++++.++..+++.+.+
T Consensus 225 ~~~~~GaGD~faa---~~~a~l~~g~~l~~Av~~A~~~v~~~i 264 (281)
T PRK08176 225 DTDLKGTGDLFCA---ELVSGLLKGKALTDAAHRAGLRVLEVM 264 (281)
T ss_pred CCCCCChhHHHHH---HHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 4567888888754 556667899999999999988776544
No 39
>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=29.85 E-value=92 Score=24.97 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=32.3
Q ss_pred ceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 83 ~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
++.-..+.|-||+++- .+++.++.|+++.++.++...++.+.+
T Consensus 197 ~~~~~~~~GaGD~f~a---~l~a~l~~g~~~~~A~~~A~~~~~~~i 239 (242)
T cd01169 197 RIDTKNTHGTGCTLSS---AIAANLAKGLSLEEAVREAKEYVTQAI 239 (242)
T ss_pred eeCCCCCCChHHHHHH---HHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 4445677788888764 456666899999999999988776544
No 40
>PRK12616 pyridoxal kinase; Reviewed
Probab=29.49 E-value=83 Score=26.29 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=28.7
Q ss_pred eeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 89 FKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 89 F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
..|-||+++ +.+++.++.|++++++.+....++.+.+
T Consensus 211 t~GaGD~fs---aalaa~l~~g~~l~~Av~~A~~~~~~~i 247 (270)
T PRK12616 211 THGAGCTFS---AAVTAELAKGSEVKEAIYAAKEFITAAI 247 (270)
T ss_pred CCcHHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 368888875 4566677899999999999988766554
No 41
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=29.43 E-value=55 Score=22.43 Aligned_cols=21 Identities=29% Similarity=0.586 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCCCCCCCCCCC
Q 030644 33 YHENVIDHYNNPRNVGSFEKND 54 (174)
Q Consensus 33 Y~e~Ileh~~~Prn~g~l~~~~ 54 (174)
=++.++++|.+|.|+ +++.+.
T Consensus 42 t~ke~~d~~n~p~ny-rlE~~s 62 (70)
T PF14410_consen 42 TRKEFLDWYNDPDNY-RLEDPS 62 (70)
T ss_pred CHHHHHHHHhCccce-eecCCc
Confidence 378899999999998 577654
No 42
>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=29.33 E-value=61 Score=26.40 Aligned_cols=39 Identities=26% Similarity=0.232 Sum_probs=30.2
Q ss_pred eeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 87 ACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 87 ~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
+.+.|-||+++ +.+++.++.|++++++.++...++.+.+
T Consensus 211 ~~~~GaGD~f~---a~~~~~l~~g~~~~~a~~~A~~~~~~~i 249 (254)
T cd01173 211 AYFNGTGDLFA---ALLLARLLKGKSLAEALEKALNFVHEVL 249 (254)
T ss_pred CCcCChHHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 55677788775 4567777899999999999988776554
No 43
>PRK12412 pyridoxal kinase; Reviewed
Probab=29.27 E-value=87 Score=26.10 Aligned_cols=36 Identities=22% Similarity=0.431 Sum_probs=27.9
Q ss_pred eecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 90 KTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 90 ~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
.|-||+++ +.+++.++.|++++++.++...++.+.+
T Consensus 209 ~GaGD~f~---aa~aa~l~~g~~l~eA~~~A~~~~~~~i 244 (268)
T PRK12412 209 HGAGCTYS---AAITAELAKGKPVKEAVKTAKEFITAAI 244 (268)
T ss_pred CchHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 57788775 4567777899999999999988765544
No 44
>PRK05756 pyridoxamine kinase; Validated
Probab=28.10 E-value=98 Score=25.90 Aligned_cols=39 Identities=10% Similarity=0.118 Sum_probs=29.9
Q ss_pred eeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 87 ACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 87 ~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
+.+.|-||+++ +.+++.+++|++++++.++...++.+.+
T Consensus 215 v~~~GaGD~f~---a~~~a~l~~g~~~~~al~~A~~~~~~~i 253 (286)
T PRK05756 215 RQPVGVGDLTS---ALFLARLLQGGSLEEALEHTTAAVYEVM 253 (286)
T ss_pred CCCCChHHHHH---HHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 36677788775 4566677899999999999988765544
No 45
>PLN02978 pyridoxal kinase
Probab=27.59 E-value=1e+02 Score=26.44 Aligned_cols=42 Identities=17% Similarity=0.073 Sum_probs=30.5
Q ss_pred ceeeeeeeecCchhHHHHHHHHHHHHcC-CCHHHHHhhhHHHHHhhc
Q 030644 83 QIVDACFKTFGCGSAIASSSVATEWVKG-KQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 83 ~I~d~~F~~~GCais~ASasil~el~~G-Ktl~ea~~i~~~~i~e~L 128 (174)
+| +..|.|.||.++-+ +++.+..| .+++++.+...+++.+.+
T Consensus 223 ~i-~~~~~GtGD~fsA~---laa~l~~g~~~l~~A~~~A~~~v~~~i 265 (308)
T PLN02978 223 KI-PAYFTGTGDLMAAL---LLGWSHKYPDNLDKAAELAVSSLQAVL 265 (308)
T ss_pred CC-CCCCCCchHHHHHH---HHHHHhcCCcCHHHHHHHHHHHHHHHH
Confidence 44 45578888887763 56666788 799999998888765444
No 46
>PTZ00347 phosphomethylpyrimidine kinase; Provisional
Probab=25.46 E-value=1e+02 Score=28.31 Aligned_cols=44 Identities=14% Similarity=0.207 Sum_probs=32.8
Q ss_pred CceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 82 g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
.+|.-..+.|.||+++-+ +++.+++|+++.++.++...++...+
T Consensus 433 ~~i~~~~~~GaGD~fsaa---iaa~la~G~~l~eAv~~A~~~v~~~i 476 (504)
T PTZ00347 433 NRIATINTHGTGCTLASA---ISSFLARGYTVPDAVERAIGYVHEAI 476 (504)
T ss_pred eeECCCCCCChHHHHHHH---HHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 345556778999988755 55556889999999999888765444
No 47
>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=24.75 E-value=1.1e+02 Score=25.00 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=30.7
Q ss_pred ceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 83 ~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
++......|-||+++-+ +++.++.|++++|+.++...++...+
T Consensus 196 ~~~~~d~~GaGD~f~aa---laa~la~g~~l~eA~~~A~~~~~~~i 238 (254)
T TIGR00097 196 RIETKNTHGTGCTLSAA---IAANLAKGLSLKEAVKEAKEFVTGAI 238 (254)
T ss_pred ccCCCCCCChHHHHHHH---HHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 44444467888888654 55556889999999998887665444
No 48
>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=24.59 E-value=1.5e+02 Score=17.80 Aligned_cols=29 Identities=17% Similarity=0.322 Sum_probs=22.5
Q ss_pred ecCchhHHHHHHHHHHHHcCCCHHHHHhhh
Q 030644 91 TFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (174)
Q Consensus 91 ~~GCais~ASasil~el~~GKtl~ea~~i~ 120 (174)
..||.+|+..=...+. -.|.+.+|+.++.
T Consensus 18 ~~~C~yc~~~H~~~a~-~~G~~~~ei~~v~ 46 (50)
T TIGR00778 18 INGCGYCLDAHTKLAR-KAGVTAEELAEAL 46 (50)
T ss_pred HcCCHHHHHHHHHHHH-HcCCCHHHHHHHH
Confidence 5799999999776664 3699999877654
No 49
>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=23.82 E-value=2e+02 Score=20.18 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=30.4
Q ss_pred EEEEEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHHH
Q 030644 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQE 115 (174)
Q Consensus 71 I~l~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~e 115 (174)
+-+.+.++++ |+|++++--.-|-+..---+.-+-+.+.|+.+.+
T Consensus 18 ~a~~~~~~~~-~~i~~~ria~g~v~~~p~r~~~~E~~L~g~~~~~ 61 (103)
T PF03450_consen 18 VAVLVSVDDD-GRIEDARIAVGGVAPTPVRAEEVEAALIGKPLSE 61 (103)
T ss_dssp EEEEEEEETT-SEEEEEEEEEESSSSSTEE-HHHHHHTTTSBSSH
T ss_pred hhheEEEecC-ceEEEEEEEEeccccceeehHHHHHHHhhcchhh
Confidence 3455566653 4999998887776666555666777889987764
No 50
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=23.40 E-value=1.2e+02 Score=24.85 Aligned_cols=43 Identities=19% Similarity=0.346 Sum_probs=31.2
Q ss_pred ceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhhc
Q 030644 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKHL 128 (174)
Q Consensus 83 ~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~L 128 (174)
++.-+.+.|-||.++-+ +++.++.|+++.++.++...++...+
T Consensus 204 ~~~~~~~~GaGD~f~a~---l~~~l~~g~~l~~A~~~A~~~~~~~i 246 (266)
T PRK06427 204 RIPTKNTHGTGCTLSAA---IAAELAKGASLLDAVQTAKDYVTRAI 246 (266)
T ss_pred eECCCCCCChHHHHHHH---HHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 44444677888887654 66666899999999998887655443
No 51
>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=22.72 E-value=1.8e+02 Score=25.86 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=32.7
Q ss_pred EEEEeCCCCceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhh
Q 030644 74 QIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (174)
Q Consensus 74 ~l~v~~~~g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i 119 (174)
.++.+++ +.+-.-+-.|+|-+.||--|..|++ .|++.+|+.+.
T Consensus 286 ~i~~~~~-~~~~~g~G~GHGVGMSQ~GA~~mA~--~G~~y~eIL~h 328 (338)
T TIGR02870 286 TWKVQGD-KIVITTIGYGHGVGMSQYGANAMAK--EGKTYDEILKH 328 (338)
T ss_pred EEEEcCC-EEEEEEeeecCCcCccHHHHHHHHH--cCCCHHHHHHH
Confidence 4444442 5566666778999999999999997 69999998754
No 52
>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=22.10 E-value=3.6e+02 Score=20.56 Aligned_cols=56 Identities=18% Similarity=0.326 Sum_probs=41.9
Q ss_pred EEEEEEEEeCCCCceeee-eeeecCchhHHHHHHHHHHHHcCCCHHHHHhhhHHHHHhh
Q 030644 70 VMKLQIKVDEETGQIVDA-CFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKNTEIAKH 127 (174)
Q Consensus 70 ~I~l~l~v~~~~g~I~d~-~F~~~GCais~ASasil~el~~GKtl~ea~~i~~~~i~e~ 127 (174)
.-.|| .++.. |.+.+. .|.+.|..-..+-.-+=..+-.+.|++|+.++..+-+...
T Consensus 118 ~~~l~-~vd~~-G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~~ea~~~~~~~l~~~ 174 (190)
T PF00227_consen 118 GPQLY-SVDPS-GSYIECKRFAAIGSGSQFAQPILEKLYKPDLSLEEAIELALKALKEA 174 (190)
T ss_dssp EEEEE-EEETT-SEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHHH
T ss_pred cccee-eeccc-cccccccccccchhcchhhhHHHHhhccCCCCHHHHHHHHHHHHHHH
Confidence 45666 56655 889999 6999998777666655555567999999999988765543
No 53
>PF15076 DUF4543: Domain of unknown function (DUF4543)
Probab=21.72 E-value=94 Score=21.54 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=15.6
Q ss_pred hhhhHHHHHHHHHhCCCCCC
Q 030644 29 MPRLYHENVIDHYNNPRNVG 48 (174)
Q Consensus 29 ~~~lY~e~Ileh~~~Prn~g 48 (174)
+++.-.+..|+|+.||.++.
T Consensus 46 LeqraeEqflEhWlNPHC~P 65 (75)
T PF15076_consen 46 LEQRAEEQFLEHWLNPHCKP 65 (75)
T ss_pred HHHHHHHHHHHHhcCCCCCC
Confidence 34556788999999998864
No 54
>TIGR02669 SpoIID_LytB SpoIID/LytB domain. This model describes a domain found typically in two or three proteins per genome in Cyanobacteria and Firmicutes, and sporadically in other genomes. One member is SpoIID of Bacillus subtilis. Another in B. subtilis is the C-terminal half of LytB, encoded immediately upstream of an amidase, the autolysin LytC, to which its N-terminus is homologous. Gene neighborhoods are not well conserved for members of this family, as many, such as SpoIID, are monocistronic. One early modelling-based study suggests a DNA-binding role for SpoIID, but the function of this domain is unknown.
Probab=21.17 E-value=1.7e+02 Score=24.94 Aligned_cols=36 Identities=17% Similarity=0.153 Sum_probs=29.8
Q ss_pred CceeeeeeeecCchhHHHHHHHHHHHHcCCCHHHHHhh
Q 030644 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (174)
Q Consensus 82 g~I~d~~F~~~GCais~ASasil~el~~GKtl~ea~~i 119 (174)
+.+-.-+-.|+|.+.||--|.-|++ .|++.+|++..
T Consensus 223 ~~~f~g~G~GHGvGmSQ~GA~~mA~--~G~~y~eIL~~ 258 (267)
T TIGR02669 223 AILFTGKGYGHGVGMSQWGANGLAK--LGKDYREILKH 258 (267)
T ss_pred EEEEEEeecccCccCCHHHHHHHHH--cCCCHHHHHHh
Confidence 4556666678999999999999998 59999998764
Done!