Query 033315
Match_columns 122
No_of_seqs 113 out of 1101
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:24:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033315hhsearch_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 2.3E-30 4.9E-35 185.2 11.2 89 32-121 2-90 (127)
2 TIGR01994 SUF_scaf_2 SUF syste 100.0 6.7E-30 1.5E-34 184.7 11.2 87 30-121 2-88 (137)
3 TIGR01999 iscU FeS cluster ass 100.0 6.9E-30 1.5E-34 181.8 11.0 88 33-121 1-88 (124)
4 PF01592 NifU_N: NifU-like N t 100.0 1.1E-29 2.3E-34 180.9 11.3 87 32-120 1-87 (126)
5 COG0822 IscU NifU homolog invo 100.0 8E-30 1.7E-34 187.3 10.3 90 27-120 1-90 (150)
6 TIGR03419 NifU_clost FeS clust 100.0 2.6E-29 5.7E-34 178.2 10.7 84 33-121 1-84 (121)
7 cd06664 IscU_like Iron-sulfur 100.0 1.2E-28 2.6E-33 173.8 10.3 85 32-121 1-85 (123)
8 KOG3361 Iron binding protein i 99.9 6.5E-28 1.4E-32 173.7 9.4 91 30-121 26-116 (157)
9 TIGR02000 NifU_proper Fe-S clu 99.9 1.8E-26 3.8E-31 184.7 11.3 87 32-121 3-89 (290)
10 PF02657 SufE: Fe-S metabolism 89.3 6 0.00013 28.0 9.7 81 30-120 11-92 (125)
11 PF10437 Lip_prot_lig_C: Bacte 84.0 2.2 4.8E-05 27.7 4.1 41 68-112 15-55 (86)
12 PF12637 TSCPD: TSCPD domain; 71.0 25 0.00053 23.6 6.3 49 66-119 6-63 (95)
13 PLN02673 quinolinate synthetas 65.3 58 0.0013 29.8 9.0 54 64-120 126-179 (724)
14 PRK09296 cysteine desufuration 65.2 49 0.0011 23.9 8.9 81 30-120 20-101 (138)
15 COG0351 ThiD Hydroxymethylpyri 61.4 11 0.00024 30.2 3.5 34 82-118 200-233 (263)
16 TIGR00545 lipoyltrans lipoyltr 61.1 18 0.00038 29.6 4.7 42 68-113 257-298 (324)
17 PF01466 Skp1: Skp1 family, di 60.1 12 0.00026 24.0 3.0 24 97-120 32-55 (78)
18 PRK03822 lplA lipoate-protein 59.4 32 0.00068 28.4 5.9 41 68-112 262-302 (338)
19 TIGR03391 FeS_syn_CsdE cystein 56.5 73 0.0016 23.0 8.5 53 64-120 53-106 (138)
20 PRK15019 CsdA-binding activato 55.6 79 0.0017 23.1 8.8 81 30-120 30-111 (147)
21 PF04205 FMN_bind: FMN-binding 51.2 30 0.00065 21.7 3.7 43 69-112 4-49 (81)
22 PRK14061 unknown domain/lipoat 50.2 44 0.00095 29.7 5.6 41 68-112 486-526 (562)
23 PF02593 dTMP_synthase: Thymid 50.0 32 0.0007 26.8 4.3 93 15-119 77-176 (217)
24 cd00336 Ribosomal_L22 Ribosoma 38.3 25 0.00055 23.7 1.9 19 102-120 16-34 (105)
25 COG2166 sufE Cysteine desulfur 37.9 1.6E+02 0.0035 21.6 7.8 54 64-121 53-107 (144)
26 TIGR02870 spore_II_D stage II 35.3 84 0.0018 26.0 4.8 43 73-118 285-327 (338)
27 COG3259 FrhA Coenzyme F420-red 35.1 66 0.0014 27.8 4.3 42 71-120 17-58 (441)
28 TIGR00778 ahpD_dom alkylhydrop 34.4 68 0.0015 18.1 3.1 29 91-120 18-46 (50)
29 PF11604 CusF_Ec: Copper bindi 32.2 92 0.002 19.5 3.7 24 65-88 43-67 (70)
30 TIGR02669 SpoIID_LytB SpoIID/L 31.7 84 0.0018 24.9 4.2 35 82-118 223-257 (267)
31 KOG1724 SCF ubiquitin ligase, 31.6 44 0.00095 24.9 2.4 27 95-121 114-140 (162)
32 PRK00565 rplV 50S ribosomal pr 30.5 40 0.00086 23.3 1.9 23 98-120 14-36 (112)
33 COG0091 RplV Ribosomal protein 30.1 40 0.00087 24.0 1.9 21 101-121 25-45 (120)
34 TIGR03295 frhA coenzyme F420 h 29.8 1.2E+02 0.0025 25.5 4.9 45 70-121 16-60 (411)
35 PF10976 DUF2790: Protein of u 29.5 1.1E+02 0.0024 20.0 3.8 31 64-95 45-77 (78)
36 PTZ00493 phosphomethylpyrimidi 29.1 40 0.00087 27.7 2.0 35 82-119 240-274 (321)
37 COG5201 SKP1 SCF ubiquitin lig 28.1 58 0.0012 24.0 2.4 84 33-121 50-135 (158)
38 PRK04223 rpl22p 50S ribosomal 27.8 45 0.00099 24.6 1.9 25 97-121 26-50 (153)
39 TIGR01038 L22_arch ribosomal p 27.1 48 0.001 24.4 1.9 31 91-121 16-46 (150)
40 CHL00034 rpl22 ribosomal prote 26.9 49 0.0011 23.2 1.9 20 101-120 24-43 (117)
41 PF13905 Thioredoxin_8: Thiore 26.5 1.5E+02 0.0033 18.4 4.1 28 82-109 1-28 (95)
42 PF08543 Phos_pyr_kin: Phospho 26.4 28 0.00062 26.7 0.6 34 83-119 190-223 (246)
43 PRK14887 KEOPS complex Pcc1-li 26.0 2E+02 0.0043 18.9 5.6 38 69-109 35-72 (84)
44 PF04879 Molybdop_Fe4S4: Molyb 26.0 1.4E+02 0.003 17.3 3.5 25 64-90 8-32 (55)
45 PF13103 TonB_2: TonB C termin 25.8 1.4E+02 0.0031 18.5 3.8 22 69-91 26-47 (85)
46 PF09341 Pcc1: Transcription f 25.6 1.8E+02 0.0038 18.2 4.6 38 68-108 30-67 (76)
47 PF03544 TonB_C: Gram-negative 25.3 1.3E+02 0.0029 18.1 3.6 34 70-104 17-52 (79)
48 PF15076 DUF4543: Domain of un 24.7 82 0.0018 20.4 2.4 17 32-48 49-65 (75)
49 PF00227 Proteasome: Proteasom 24.1 2.3E+02 0.005 20.1 5.1 49 70-120 118-167 (190)
50 PF00919 UPF0004: Uncharacteri 23.2 60 0.0013 21.8 1.7 27 87-113 2-28 (98)
51 PTZ00178 60S ribosomal protein 22.8 62 0.0013 24.6 1.9 29 93-121 21-49 (181)
52 PF01294 Ribosomal_L13e: Ribos 22.3 71 0.0015 24.4 2.1 19 6-25 28-46 (179)
53 TIGR00412 redox_disulf_2 small 22.0 1.1E+02 0.0024 19.0 2.7 25 87-111 3-27 (76)
54 cd02973 TRX_GRX_like Thioredox 21.2 75 0.0016 18.7 1.7 21 88-108 5-25 (67)
55 PRK07218 replication factor A; 21.2 2E+02 0.0043 24.6 4.8 39 70-120 323-361 (423)
56 PTZ00192 60S ribosomal protein 20.9 76 0.0017 24.9 2.0 19 6-25 39-57 (218)
57 cd04466 S1_YloQ_GTPase S1_YloQ 20.9 95 0.0021 18.5 2.2 23 64-87 37-59 (68)
58 cd04451 S1_IF1 S1_IF1: Transla 20.8 1.1E+02 0.0023 18.6 2.4 13 65-77 41-53 (64)
59 PF02852 Pyr_redox_dim: Pyridi 20.6 2.6E+02 0.0057 18.3 7.2 49 69-119 47-95 (110)
No 1
>PRK11325 scaffold protein; Provisional
Probab=99.97 E-value=2.3e-30 Score=185.16 Aligned_cols=89 Identities=76% Similarity=1.231 Sum_probs=81.6
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCC
Q 033315 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (122)
Q Consensus 32 ~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GK 111 (122)
+|+++|++||.||+|.|.+++++...+++..+||.|||+|+|||+|+++ |+|+|++|+++||++++||||+|+++++||
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 6999999999999999999988754445677899999999999999732 899999999999999999999999999999
Q ss_pred CHHHHhcccc
Q 033315 112 QMQEVLSIKN 121 (122)
Q Consensus 112 tleeA~~i~~ 121 (122)
|++||..|++
T Consensus 81 tl~ea~~i~~ 90 (127)
T PRK11325 81 TLDEALAIKN 90 (127)
T ss_pred CHHHHHhcCH
Confidence 9999999875
No 2
>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=99.97 E-value=6.7e-30 Score=184.70 Aligned_cols=87 Identities=37% Similarity=0.669 Sum_probs=81.1
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHc
Q 033315 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (122)
Q Consensus 30 ~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~ 109 (122)
.++|+++|+|||.||+|+|.+++++. +++.+||+|||+|++|++|++ ++|++++|+++||++++||+|+|+++++
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 57999999999999999999998875 346789999999999999987 8999999999999999999999999999
Q ss_pred CCCHHHHhcccc
Q 033315 110 GKQMQEVLSIKN 121 (122)
Q Consensus 110 GKtleeA~~i~~ 121 (122)
|||++|+..+.+
T Consensus 77 Gk~~~ea~~l~~ 88 (137)
T TIGR01994 77 GKTVEEALSLVE 88 (137)
T ss_pred CCCHHHHHHHHH
Confidence 999999998764
No 3
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=99.97 E-value=6.9e-30 Score=181.80 Aligned_cols=88 Identities=74% Similarity=1.177 Sum_probs=80.9
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCC
Q 033315 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (122)
Q Consensus 33 Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKt 112 (122)
|+++|++||.||+|.|.+++++..+++|..+||.|||+|+|||+|+++ ++|+|++|+++||++++||+|+|+++++|||
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 899999999999999999998754445677899999999999999654 7999999999999999999999999999999
Q ss_pred HHHHhcccc
Q 033315 113 MQEVLSIKN 121 (122)
Q Consensus 113 leeA~~i~~ 121 (122)
++||..|.+
T Consensus 80 l~ea~~i~~ 88 (124)
T TIGR01999 80 LEEALKIKN 88 (124)
T ss_pred HHHHHhccH
Confidence 999999874
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=99.96 E-value=1.1e-29 Score=180.91 Aligned_cols=87 Identities=47% Similarity=0.938 Sum_probs=81.0
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCC
Q 033315 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (122)
Q Consensus 32 ~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GK 111 (122)
+|+++|++||.||+|+|.++++++ ++++.+||+|||.|+|||+|++++|+|+|++|+++||++++||+|+|+++++||
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 245678999999999999999866899999999999999999999999999999
Q ss_pred CHHHHhccc
Q 033315 112 QMQEVLSIK 120 (122)
Q Consensus 112 tleeA~~i~ 120 (122)
|++||+.|+
T Consensus 79 ~l~ea~~i~ 87 (126)
T PF01592_consen 79 TLEEALKIT 87 (126)
T ss_dssp BHHHHHCHH
T ss_pred CHHHHHHHH
Confidence 999998875
No 5
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.96 E-value=8e-30 Score=187.31 Aligned_cols=90 Identities=56% Similarity=0.930 Sum_probs=83.3
Q ss_pred chhhHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHH
Q 033315 27 AAMPRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATE 106 (122)
Q Consensus 27 ~~~~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e 106 (122)
+.++.+|+++|++||.||+|.|.+++++.. .+..++|.|||.|++||++++ |+|+|++|+++||++++||+|+|++
T Consensus 1 ~~~~~~y~~~Ildh~~np~~~g~l~~~~~~--~~~~~~~~CGD~i~l~lkv~~--~~I~d~~F~~~GC~is~ASss~~te 76 (150)
T COG0822 1 SNLDDLYSEKILDHYKNPRNVGVLDDADVG--VGHVGAPACGDVITLYLKVDN--GVIEDAKFKGFGCAISIASSSMMTE 76 (150)
T ss_pred CcHHHHHHHHHHHHhcCCCcCCccCccchh--ccccCCCCccceEEEEEEEcC--CEEEEEEeeecCcHHHHHHHHHHHH
Confidence 357899999999999999999999988843 455677999999999999997 9999999999999999999999999
Q ss_pred HHcCCCHHHHhccc
Q 033315 107 WVKGKQMQEVLSIK 120 (122)
Q Consensus 107 ~i~GKtleeA~~i~ 120 (122)
+++|||++||++|+
T Consensus 77 ~v~Gkti~EAl~i~ 90 (150)
T COG0822 77 LVKGKTLDEALKIT 90 (150)
T ss_pred HHcCCCHHHHHHHH
Confidence 99999999999986
No 6
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=99.96 E-value=2.6e-29 Score=178.25 Aligned_cols=84 Identities=56% Similarity=0.968 Sum_probs=79.2
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCC
Q 033315 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (122)
Q Consensus 33 Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKt 112 (122)
|+++|+|||+||+|+|.+++++. +++.+||.|||+|+|||++++ ++|+|++|+++||++|+||+|+|+++++|||
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 89999999999999999998875 456789999999999999987 8999999999999999999999999999999
Q ss_pred HHHHhcccc
Q 033315 113 MQEVLSIKN 121 (122)
Q Consensus 113 leeA~~i~~ 121 (122)
++||.+|.+
T Consensus 76 l~ea~~i~~ 84 (121)
T TIGR03419 76 LEEAWELTN 84 (121)
T ss_pred HHHHHHhhh
Confidence 999998864
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=99.96 E-value=1.2e-28 Score=173.82 Aligned_cols=85 Identities=53% Similarity=0.939 Sum_probs=79.9
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCC
Q 033315 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (122)
Q Consensus 32 ~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GK 111 (122)
+|+++|++||.+|+|.|.+++++. .+..+||.|||+|+||+++++ ++|+|++|+++||++++||||+|+++++||
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 599999999999999999998874 456789999999999999998 899999999999999999999999999999
Q ss_pred CHHHHhcccc
Q 033315 112 QMQEVLSIKN 121 (122)
Q Consensus 112 tleeA~~i~~ 121 (122)
|++|+..|++
T Consensus 76 ~~~ea~~i~~ 85 (123)
T cd06664 76 TLDEALKLLN 85 (123)
T ss_pred cHHHHHHHHH
Confidence 9999998874
No 8
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.95 E-value=6.5e-28 Score=173.67 Aligned_cols=91 Identities=81% Similarity=1.271 Sum_probs=87.6
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHc
Q 033315 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (122)
Q Consensus 30 ~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~ 109 (122)
..+|++.++|||.||||.|.++..+.++|+|..+-|.|||.++++++|+++ |+|+|++|.++||+..+||+|+++||++
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 388999999999999999999999999999999999999999999999874 9999999999999999999999999999
Q ss_pred CCCHHHHhcccc
Q 033315 110 GKQMQEVLSIKN 121 (122)
Q Consensus 110 GKtleeA~~i~~ 121 (122)
|||+||+.+|-|
T Consensus 105 gkt~dea~kIkN 116 (157)
T KOG3361|consen 105 GKTLDEALKIKN 116 (157)
T ss_pred cccHHHHHhccc
Confidence 999999999875
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=99.94 E-value=1.8e-26 Score=184.72 Aligned_cols=87 Identities=51% Similarity=0.858 Sum_probs=80.6
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCC
Q 033315 32 LYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGK 111 (122)
Q Consensus 32 ~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GK 111 (122)
+|+++|++||++|+|+|.+++++. .++.+||+|||+|+|||++++++++|+|++|+++||++++||||+|+++++||
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 599999999999999999998875 46778999999999999998544899999999999999999999999999999
Q ss_pred CHHHHhcccc
Q 033315 112 QMQEVLSIKN 121 (122)
Q Consensus 112 tleeA~~i~~ 121 (122)
|++||++|++
T Consensus 80 tv~ea~~i~~ 89 (290)
T TIGR02000 80 TLDEALKVSN 89 (290)
T ss_pred CHHHHHHhhH
Confidence 9999998864
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=89.32 E-value=6 Score=28.00 Aligned_cols=81 Identities=16% Similarity=0.191 Sum_probs=51.5
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEecc-chHHHHHHHHHHHHH
Q 033315 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWV 108 (122)
Q Consensus 30 ~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~G-Cais~ASasi~~e~i 108 (122)
|+..-+.|+++.++......-...+.. .-+.|-..|-++...+++ |++ .|.++. -.+...-.+++.+.+
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 556667789999887664332222221 235699999995554432 765 566553 468889999999999
Q ss_pred cCCCHHHHhccc
Q 033315 109 KGKQMQEVLSIK 120 (122)
Q Consensus 109 ~GKtleeA~~i~ 120 (122)
.|+|.+|+..+.
T Consensus 81 ~g~t~~eI~~~~ 92 (125)
T PF02657_consen 81 NGQTPEEILAFD 92 (125)
T ss_dssp TT-BHHHHHHS-
T ss_pred cCCCHHHHHhCC
Confidence 999999998754
No 11
>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=84.03 E-value=2.2 Score=27.73 Aligned_cols=41 Identities=17% Similarity=0.097 Sum_probs=29.6
Q ss_pred CCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCC
Q 033315 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (122)
Q Consensus 68 GD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKt 112 (122)
+-.|.+++.|++ |+|.++++.++-=.. .--.-+.+.++|..
T Consensus 15 ~G~v~v~~~V~~--G~I~~i~i~gDf~~~--~~i~~le~~L~G~~ 55 (86)
T PF10437_consen 15 WGTVEVHLNVKN--GIIKDIKIYGDFFGP--EDIEELEEALIGCP 55 (86)
T ss_dssp TEEEEEEEEEET--TEEEEEEEEECBS-C--CCHHHHHHHHTTCB
T ss_pred CceEEEEEEEEC--CEEEEEEEECCCCCc--hHHHHHHHHHHhcC
Confidence 347999999998 999999999762221 22556667777764
No 12
>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=70.99 E-value=25 Score=23.61 Aligned_cols=49 Identities=18% Similarity=0.479 Sum_probs=31.8
Q ss_pred CCCCEEEEEEEEeCCCC----cEEeeEEEeccchHHHHHHHHHHHHH-----cCCCHHHHhcc
Q 033315 66 ACGDVMKLQIKVDEETG----QIVDACFKTFGCGSAIASSSVATEWV-----KGKQMQEVLSI 119 (122)
Q Consensus 66 ~CGD~i~l~l~vd~~~g----~I~di~f~~~GCais~ASasi~~e~i-----~GKtleeA~~i 119 (122)
.|| .+.+.+..++++| ++.++.+.+ || .+-++.++.++ .|.+++++.+-
T Consensus 6 ~~g-~~yvtv~~d~d~g~p~Evf~~~~~~G-g~---~~~~~ai~rliS~~Lr~G~~~~~ii~~ 63 (95)
T PF12637_consen 6 GCG-KLYVTVNFDEDNGRPFEVFINVGKAG-GC---SGNLEAIARLISLALRSGVPPEEIIDQ 63 (95)
T ss_pred ccc-ceEEEEEeeCCCCcceEEEEecCcCC-Cc---hHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 466 4455555554335 455544433 56 77788888888 99999998653
No 13
>PLN02673 quinolinate synthetase A
Probab=65.33 E-value=58 Score=29.84 Aligned_cols=54 Identities=19% Similarity=0.224 Sum_probs=43.6
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 64 APACGDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
-+-|-..|.|..+++++ |+ ..+.+..+. .|...-+.++...+.|+|.+|++.+.
T Consensus 126 V~GCQSqVWL~~elddd-Gk-v~F~ADSDA-~IVKGL~ALLl~~lsG~TpeEILavD 179 (724)
T PLN02673 126 VMGCTAQVWLEAELDQD-GK-MRFWADSDS-EITKGFCSCLIWVLDGASPEEVLELK 179 (724)
T ss_pred CCCcccceEEEEEEcCC-CE-EEEEEeCcc-HHHHHHHHHHHHHHcCCCHHHHHhCC
Confidence 35799999998887664 54 336666667 89999999999999999999988764
No 14
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=65.21 E-value=49 Score=23.86 Aligned_cols=81 Identities=7% Similarity=-0.004 Sum_probs=52.4
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEecc-chHHHHHHHHHHHHH
Q 033315 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWV 108 (122)
Q Consensus 30 ~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~G-Cais~ASasi~~e~i 108 (122)
|+.--+.|+++.+.... +++.... ....-+-|-..|.+...++++ | .+.|.++. -.|...-+.++...+
T Consensus 20 we~Ry~~LI~lgk~Lp~---lpe~~r~---~~~~V~GCqS~VWl~~~~~~~-g---~~~f~~dSDa~ivkGl~alL~~~~ 89 (138)
T PRK09296 20 WEEKYLYIIELGQRLPP---LTDEDRS---PQNLIQGCQSQVWIVMRQNAQ-G---IIELQGDSDAAIVKGLIAVVFILY 89 (138)
T ss_pred HHHHHHHHHHHHhhCCC---CCHHHcC---ccccCCCcccceeeeEeecCC-C---EEEEEEecccHHHHHHHHHHHHHH
Confidence 43333556777765433 3222110 111236799999888777653 5 35666553 467888899999999
Q ss_pred cCCCHHHHhccc
Q 033315 109 KGKQMQEVLSIK 120 (122)
Q Consensus 109 ~GKtleeA~~i~ 120 (122)
.|+|.+|+..+.
T Consensus 90 ~g~tp~eIl~~d 101 (138)
T PRK09296 90 QQMTPQDIVNFD 101 (138)
T ss_pred cCCCHHHHHhCC
Confidence 999999988764
No 15
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=61.44 E-value=11 Score=30.22 Aligned_cols=34 Identities=21% Similarity=0.370 Sum_probs=25.8
Q ss_pred CcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhc
Q 033315 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLS 118 (122)
Q Consensus 82 g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~ 118 (122)
.+|..-.-.|.||.+| +.+.+++++|.+++||.+
T Consensus 200 ~ri~t~~tHGTGCTlS---aAIaa~LA~G~~l~~AV~ 233 (263)
T COG0351 200 PRIPTKNTHGTGCTLS---AAIAANLAKGLSLEEAVK 233 (263)
T ss_pred cccCCCCCCCccHHHH---HHHHHHHHcCCCHHHHHH
Confidence 4555444568899985 557788899999999865
No 16
>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=61.09 E-value=18 Score=29.56 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=30.6
Q ss_pred CCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCH
Q 033315 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQM 113 (122)
Q Consensus 68 GD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtl 113 (122)
+..|++++.|++ |+|+++++.++-... --.+-+.+.++|.+.
T Consensus 257 ~G~v~i~l~v~~--g~I~~~~i~gDf~~~--~~~~~l~~~L~G~~~ 298 (324)
T TIGR00545 257 AGGFELHVQVEK--GKIVDCKFFGDFLSV--ADITPVTNRLIGQKY 298 (324)
T ss_pred CCcEEEEEEEeC--CEEEEEEEECCCCCc--ccHHHHHHHhCCCcc
Confidence 458999999998 999999998874322 224566666777663
No 17
>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=60.11 E-value=12 Score=24.02 Aligned_cols=24 Identities=17% Similarity=0.126 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHcCCCHHHHhccc
Q 033315 97 AIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 97 s~ASasi~~e~i~GKtleeA~~i~ 120 (122)
...++..++.++.|||.+|..++.
T Consensus 32 ~~~~~~~iA~~i~gks~eeir~~f 55 (78)
T PF01466_consen 32 LDLCCKYIANMIKGKSPEEIRKYF 55 (78)
T ss_dssp HHHHHHHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHc
Confidence 345677889999999999988764
No 18
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=59.39 E-value=32 Score=28.35 Aligned_cols=41 Identities=20% Similarity=0.140 Sum_probs=29.6
Q ss_pred CCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCC
Q 033315 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (122)
Q Consensus 68 GD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKt 112 (122)
+..|++.+.|++ |+|+++++.++.-. ..--+-+.+.++|..
T Consensus 262 ~G~v~i~~~v~~--g~I~~~~i~gD~~~--~~~~~~l~~~L~G~~ 302 (338)
T PRK03822 262 WGGVELHFDVEK--GHITRAQIFTDSLN--PAPLEALAGRLQGCL 302 (338)
T ss_pred CCcEEEEEEEEC--CEEEEEEEECCCCC--cccHHHHHHHhCCCC
Confidence 457999999998 99999999987322 233445666666765
No 19
>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=56.47 E-value=73 Score=22.97 Aligned_cols=53 Identities=19% Similarity=0.156 Sum_probs=40.1
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEeeEEEecc-chHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 64 APACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di~f~~~G-Cais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
-+-|-..|.+...+.++ |+ +.|.++. -.+...-..++.+.+.|+|.+|++.+.
T Consensus 53 V~GCqS~VWl~~~~~~d-g~---~~f~~dSDa~IvkGl~alL~~~~~g~tp~eI~~~d 106 (138)
T TIGR03391 53 LTGCENRVWLGHQVLPD-GT---LHFYGDSEGRIVRGLLAVLLTAVEGKTPEQLLAQD 106 (138)
T ss_pred cCCcccceeeeeeecCC-CE---EEEEecCccHHHHHHHHHHHHHHcCCCHHHHHHCC
Confidence 35699999887765332 63 5566653 467888999999999999999988764
No 20
>PRK15019 CsdA-binding activator; Provisional
Probab=55.60 E-value=79 Score=23.11 Aligned_cols=81 Identities=15% Similarity=0.020 Sum_probs=51.5
Q ss_pred hHhHHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCCCcEEeeEEEecc-chHHHHHHHHHHHHH
Q 033315 30 PRLYHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEETGQIVDACFKTFG-CGSAIASSSVATEWV 108 (122)
Q Consensus 30 ~~~Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~g~I~di~f~~~G-Cais~ASasi~~e~i 108 (122)
|+.--+.|+++.+.-.- +++.... -...-+-|-..|.+...++++ | .+.|.++. -.|...-+.++.+.+
T Consensus 30 weeRy~~LI~lgk~Lp~---lpe~~r~---~~~~V~GCqS~VWL~~~~~~d-g---~~~f~~dSDA~IvkGl~alL~~~~ 99 (147)
T PRK15019 30 WEDKYRQLIMLGKQLPA---LPDELKA---QAKEIAGCENRVWLGYTVAEN-G---KMHFFGDSEGRIVRGLLAVLLTAV 99 (147)
T ss_pred HHHHHHHHHHHHhhCCC---CChHHcC---ccCcCCCcccceeeeeeecCC-C---EEEEEeeCccHHHHHHHHHHHHHH
Confidence 43333456777764433 3222110 111236799999887777442 6 35666653 467888899999999
Q ss_pred cCCCHHHHhccc
Q 033315 109 KGKQMQEVLSIK 120 (122)
Q Consensus 109 ~GKtleeA~~i~ 120 (122)
.|+|.+|++.+.
T Consensus 100 ~g~tp~eIl~~d 111 (147)
T PRK15019 100 EGKTAAELQAQS 111 (147)
T ss_pred cCCCHHHHHhcC
Confidence 999999998754
No 21
>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=51.16 E-value=30 Score=21.66 Aligned_cols=43 Identities=19% Similarity=0.276 Sum_probs=29.0
Q ss_pred CEEEEEEEEeCCCCcEEeeEEEeccchHHH---HHHHHHHHHHcCCC
Q 033315 69 DVMKLQIKVDEETGQIVDACFKTFGCGSAI---ASSSVATEWVKGKQ 112 (122)
Q Consensus 69 D~i~l~l~vd~~~g~I~di~f~~~GCais~---ASasi~~e~i~GKt 112 (122)
..|++.+.++++ |+|.++++..+.-.... +...-+.+.+.|+.
T Consensus 4 g~i~v~v~i~~d-g~I~~v~~~~~~et~~~~~~~~~~~~~~~~~g~~ 49 (81)
T PF04205_consen 4 GPITVTVTIDKD-GKITDVKILEHNETPGYGKKAEIEEFFDQIVGKQ 49 (81)
T ss_dssp EEEEEEEEEETT-TEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHC
T ss_pred ceEEEEEEEeCC-CEEEEEEEeeccCCcchhhhccHHHHHHHHHhcc
Confidence 468888888865 99999999986542222 22555666666655
No 22
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=50.16 E-value=44 Score=29.70 Aligned_cols=41 Identities=20% Similarity=0.157 Sum_probs=29.5
Q ss_pred CCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCC
Q 033315 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQ 112 (122)
Q Consensus 68 GD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKt 112 (122)
+..|++++.|++ |+|+++++.++--.. .--+-+.+.+.|..
T Consensus 486 ~G~vei~l~V~~--G~I~~~ki~gDf~~~--~~i~~le~~L~G~~ 526 (562)
T PRK14061 486 WGGVELHFDVEK--GHITRAQVFTDSLNP--APLEALAGRLQGCL 526 (562)
T ss_pred cccEEEEEEEeC--CEEEEEEEECCCCCc--ccHHHHHHHhCCCC
Confidence 457999999998 999999999873322 22344666666765
No 23
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=50.03 E-value=32 Score=26.83 Aligned_cols=93 Identities=22% Similarity=0.381 Sum_probs=52.1
Q ss_pred HhhhhCCCCCcCchhhHhHHHHHHH---HHhCCCCCCCCCCCCC-cee--eeeecCCCCCCEEEEEEEEeCCCCcEEeeE
Q 033315 15 AAAVAAPRPVQVAAMPRLYHENVID---HYNNPRNVGSFEKNDA-TVG--TGLVGAPACGDVMKLQIKVDEETGQIVDAC 88 (122)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~Y~~~Ile---~~~~P~n~g~l~~~~~-~~~--~g~~~np~CGD~i~l~l~vd~~~g~I~di~ 88 (122)
.-++-.|..-....+.....++.-+ ++..|+-+=.|++... .+. ....|.| ++.+.+++ |+|.+++
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 3344444333334555566666666 3556665555553211 000 0001222 44555556 8999998
Q ss_pred EE-eccchHHHHHHHHHHHHHcCCCHHHHhcc
Q 033315 89 FK-TFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (122)
Q Consensus 89 f~-~~GCais~ASasi~~e~i~GKtleeA~~i 119 (122)
-. +-=| .|+..+++.++|++++|+...
T Consensus 149 VlR~aPC----GsT~~vAk~l~G~~~~d~~~~ 176 (217)
T PF02593_consen 149 VLRSAPC----GSTWFVAKRLIGKEVEDAPEK 176 (217)
T ss_pred EEecCCC----ccHHHHHHHhcCCccchhhhh
Confidence 65 2334 367889999999999998654
No 24
>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=38.29 E-value=25 Score=23.68 Aligned_cols=19 Identities=16% Similarity=0.361 Sum_probs=16.3
Q ss_pred HHHHHHHcCCCHHHHhccc
Q 033315 102 SVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 102 si~~e~i~GKtleeA~~i~ 120 (122)
-.++++|.|++++||..+.
T Consensus 16 ~~v~~~Irg~~v~~A~~~L 34 (105)
T cd00336 16 RLVARLIRGMSVDEALAQL 34 (105)
T ss_pred HHHHHHHcCCcHHHHHHHH
Confidence 4688999999999998764
No 25
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=37.90 E-value=1.6e+02 Score=21.60 Aligned_cols=54 Identities=15% Similarity=0.135 Sum_probs=41.7
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEeeEEEeccc-hHHHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 64 APACGDVMKLQIKVDEETGQIVDACFKTFGC-GSAIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di~f~~~GC-ais~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
-+-|-..|-+....++ + -.+.|.++-= .|...-+.++.+.+.|||.+|...+..
T Consensus 53 V~GC~S~vwL~~~~~~--~--~~~~F~gdSdA~ivrGL~aill~~~~G~t~~eI~~~~~ 107 (144)
T COG2166 53 VPGCQSQVWLVTEQND--D--GTLHFFGDSDARIVRGLLAILLAAYSGKTAAEILAFDP 107 (144)
T ss_pred CCccccceeEEEeecC--C--ceEEEeccchhHHHHHHHHHHHHHHcCCCHHHHHcCCH
Confidence 4668888888877766 4 3466777643 577788999999999999999987653
No 26
>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=35.34 E-value=84 Score=26.00 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=32.1
Q ss_pred EEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhc
Q 033315 73 LQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLS 118 (122)
Q Consensus 73 l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~ 118 (122)
|.++.+++ +.+...+=.|+|-+.||--|..|++ +|++.+|.+.
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 34444442 4555566668899999999999998 6999999864
No 27
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]
Probab=35.14 E-value=66 Score=27.80 Aligned_cols=42 Identities=31% Similarity=0.463 Sum_probs=25.9
Q ss_pred EEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 71 MKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 71 i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
-.+.+.|+++ |++++.+|...+==- +=.++.||+++||..|.
T Consensus 17 akv~i~vdd~-G~V~~~~~~it~~Rg-------fEk~~~Gkp~EeaP~i~ 58 (441)
T COG3259 17 AKVTIEVDDD-GIVEDARFHITEVRG-------FEKFVLGKPIEEAPRIV 58 (441)
T ss_pred eEEEEEEcCC-CceeeeEEEecccch-------HHHHhcCCChHHhhHHh
Confidence 3556667665 999999998654221 23345566666665543
No 28
>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=34.42 E-value=68 Score=18.10 Aligned_cols=29 Identities=17% Similarity=0.302 Sum_probs=23.0
Q ss_pred eccchHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 91 TFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 91 ~~GCais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
..||.+++..=..++.. .|.|.+|..++.
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 47999999998877754 699999877653
No 29
>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=32.18 E-value=92 Score=19.54 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=16.4
Q ss_pred CCCCCEEEEEEEEeCCC-CcEEeeE
Q 033315 65 PACGDVMKLQIKVDEET-GQIVDAC 88 (122)
Q Consensus 65 p~CGD~i~l~l~vd~~~-g~I~di~ 88 (122)
-.-||.|.|.+...++. =+|++++
T Consensus 43 l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 43 LKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp -STT-EEEEEEEEETTCEEEEEEEE
T ss_pred CCCCCEEEEEEEECCCCcEEEEEEE
Confidence 35699999999987652 2777764
No 30
>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=31.73 E-value=84 Score=24.95 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=28.7
Q ss_pred CcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhc
Q 033315 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLS 118 (122)
Q Consensus 82 g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~ 118 (122)
+.+...+=.|+|.+.||--|..|++ +|++.+|.+.
T Consensus 223 ~~~f~g~G~GHGvGmSQ~GA~~mA~--~G~~y~eIL~ 257 (267)
T TIGR02669 223 AILFTGKGYGHGVGMSQWGANGLAK--LGKDYREILK 257 (267)
T ss_pred EEEEEEeecccCccCCHHHHHHHHH--cCCCHHHHHH
Confidence 4455556668899999999999998 5999999875
No 31
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=31.60 E-value=44 Score=24.89 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=21.4
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 95 GSAIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 95 ais~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
++.--++-.++++++|||.+|...+.+
T Consensus 114 gLl~~~ck~va~mikgktpeEir~~f~ 140 (162)
T KOG1724|consen 114 GLLDLTCKTVANMIKGKTPEEIREIFN 140 (162)
T ss_pred HHHHHHHHHHHHHHccCCHHHHHHHcC
Confidence 355567788999999999999887643
No 32
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=30.53 E-value=40 Score=23.31 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHcCCCHHHHhccc
Q 033315 98 IASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 98 ~ASasi~~e~i~GKtleeA~~i~ 120 (122)
-==+-.++.+|.|++++||+.+.
T Consensus 14 pkK~~~v~~~IrG~~v~~A~~~L 36 (112)
T PRK00565 14 PRKARLVADLIRGKKVEEALAIL 36 (112)
T ss_pred HHHHHHHHHHHcCCcHHHHHHHH
Confidence 33356789999999999998764
No 33
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=30.13 E-value=40 Score=23.98 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCCHHHHhcccc
Q 033315 101 SSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 101 asi~~e~i~GKtleeA~~i~~ 121 (122)
+..++.+|.|+++++|..+.+
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~ 45 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILE 45 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 567899999999999988753
No 34
>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=29.78 E-value=1.2e+02 Score=25.52 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=30.4
Q ss_pred EEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 70 VMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 70 ~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
.+++.+.++++ ++|.+..|...-.- -=+-.+++||+..|+..+++
T Consensus 16 ~~rl~l~vdge-~vv~~~~~~~~~~~------RG~Ek~~egr~~~~~~~l~~ 60 (411)
T TIGR03295 16 HAKLVLEVDDE-GIVEKGDYLSITPV------RGFEKLLVGKTAEFAPIIVS 60 (411)
T ss_pred ceEEEEEEeCC-CcEEEEEEeccCcC------cHHHHHHcCCCHHHHHHHHh
Confidence 47888888854 78887766622111 23567788999998887654
No 35
>PF10976 DUF2790: Protein of unknown function (DUF2790); InterPro: IPR021245 This family of proteins with unknown function appear to be restricted to Pseudomonadaceae.
Probab=29.46 E-value=1.1e+02 Score=20.00 Aligned_cols=31 Identities=19% Similarity=0.669 Sum_probs=22.5
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEeeEEEec--cch
Q 033315 64 APACGDVMKLQIKVDEETGQIVDACFKTF--GCG 95 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di~f~~~--GCa 95 (122)
.+.|| .|...+.-+|..|+...+.|+.. ||.
T Consensus 45 ~~~C~-Vvpa~MtY~DS~G~~h~l~Y~~~g~~C~ 77 (78)
T PF10976_consen 45 PNVCG-VVPARMTYEDSQGELHTLEYRVMGTGCS 77 (78)
T ss_pred CCCCc-EEccEEEEECCCCCEEEEEeEeeccccC
Confidence 36786 77777776655599999999855 574
No 36
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=29.12 E-value=40 Score=27.69 Aligned_cols=35 Identities=14% Similarity=0.096 Sum_probs=26.0
Q ss_pred CcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhcc
Q 033315 82 GQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (122)
Q Consensus 82 g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i 119 (122)
.+|..-.|.|.||.++-| +.+.++.|.++++|.+.
T Consensus 240 ~ri~~~~~hGTGc~fASA---IAa~LA~G~~l~~Av~~ 274 (321)
T PTZ00493 240 KRKPGKDIHGTGCTLSTA---IACYLAKKHNILQSCIE 274 (321)
T ss_pred cccCCCCCCChHHHHHHH---HHHHHHcCCCHHHHHHH
Confidence 455555678999998654 55666789999998765
No 37
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=28.14 E-value=58 Score=24.00 Aligned_cols=84 Identities=17% Similarity=0.150 Sum_probs=45.5
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCceeeeeecCCCCCCEEEEEEEEeCCC--CcEEeeEEEeccchHHHHHHHHHHHHHcC
Q 033315 33 YHENVIDHYNNPRNVGSFEKNDATVGTGLVGAPACGDVMKLQIKVDEET--GQIVDACFKTFGCGSAIASSSVATEWVKG 110 (122)
Q Consensus 33 Y~~~Ile~~~~P~n~g~l~~~~~~~~~g~~~np~CGD~i~l~l~vd~~~--g~I~di~f~~~GCais~ASasi~~e~i~G 110 (122)
-=.+|+++..+-++.+.-+..+.... + ..| -...=++++++|.+. .++..+.|.-. =...-+++-++++++.|
T Consensus 50 vl~kv~ew~ehh~~s~sede~d~~~r--k-s~p-~D~wdr~Fm~vDqemL~eI~laaNYL~i-kpLLd~gCKivaemirg 124 (158)
T COG5201 50 VLMKVQEWMEHHTSSLSEDENDLEIR--K-SKP-SDFWDRFFMEVDQEMLLEICLAANYLEI-KPLLDLGCKIVAEMIRG 124 (158)
T ss_pred HHHHHHHHHHhccccCCCccChHhhh--c-cCC-ccHHHHHHHHhhHHHHHHHHHhhccccc-hHHHHHHHHHHHHHHcc
Confidence 34567888887777665555553321 1 111 111123555665411 12222222211 13445667789999999
Q ss_pred CCHHHHhcccc
Q 033315 111 KQMQEVLSIKN 121 (122)
Q Consensus 111 KtleeA~~i~~ 121 (122)
|+.+|..+..+
T Consensus 125 kSpeeir~tfn 135 (158)
T COG5201 125 KSPEEIRETFN 135 (158)
T ss_pred CCHHHHHHHhC
Confidence 99999876543
No 38
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=27.76 E-value=45 Score=24.59 Aligned_cols=25 Identities=12% Similarity=0.137 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 97 AIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 97 s~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
|-==+..++++|.|+++++|..+.+
T Consensus 26 S~kk~r~va~~IRG~~v~~A~~~L~ 50 (153)
T PRK04223 26 SPKHSVEIAREIRGMKLDEAKAYLE 50 (153)
T ss_pred ChHHHHHHHHHHcCCcHHHHHHHHH
Confidence 3334677899999999999998764
No 39
>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=27.07 E-value=48 Score=24.41 Aligned_cols=31 Identities=3% Similarity=0.066 Sum_probs=23.2
Q ss_pred eccchHHHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 91 TFGCGSAIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 91 ~~GCais~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
+..--+|-==+-.++++|.|+++++|+.+.+
T Consensus 16 ~~~~riS~kk~r~va~~IrG~~v~~A~~~L~ 46 (150)
T TIGR01038 16 GRNLRVSFKNARETARAIRGMELDKARKYLE 46 (150)
T ss_pred eCCCcccHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 3344445555778999999999999998764
No 40
>CHL00034 rpl22 ribosomal protein L22
Probab=26.88 E-value=49 Score=23.19 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=17.2
Q ss_pred HHHHHHHHcCCCHHHHhccc
Q 033315 101 SSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 101 asi~~e~i~GKtleeA~~i~ 120 (122)
+-.++.+|.|+++++|..+.
T Consensus 24 ~r~va~~IRG~~v~~A~~~L 43 (117)
T CHL00034 24 ARRVIDQIRGRSYEEALMIL 43 (117)
T ss_pred HHHHHHHHcCCcHHHHHHHH
Confidence 46789999999999998764
No 41
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=26.54 E-value=1.5e+02 Score=18.39 Aligned_cols=28 Identities=21% Similarity=0.115 Sum_probs=22.9
Q ss_pred CcEEeeEEEeccchHHHHHHHHHHHHHc
Q 033315 82 GQIVDACFKTFGCGSAIASSSVATEWVK 109 (122)
Q Consensus 82 g~I~di~f~~~GCais~ASasi~~e~i~ 109 (122)
|++.=+-|.+..|..|.+....+.++..
T Consensus 1 gK~~ll~fwa~~c~~c~~~~~~l~~l~~ 28 (95)
T PF13905_consen 1 GKPVLLYFWASWCPPCKKELPKLKELYK 28 (95)
T ss_dssp TSEEEEEEE-TTSHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHHH
Confidence 5677889999999999999998888653
No 42
>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=26.40 E-value=28 Score=26.71 Aligned_cols=34 Identities=21% Similarity=0.213 Sum_probs=24.6
Q ss_pred cEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhcc
Q 033315 83 QIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (122)
Q Consensus 83 ~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i 119 (122)
++...+|.|.||.++- .+++.+++|+++++|.+.
T Consensus 190 ~~~~~~~~GTGd~fss---~laa~l~~g~~l~~Av~~ 223 (246)
T PF08543_consen 190 RIPTGSFHGTGDLFSS---ALAAFLAKGYSLEEAVEK 223 (246)
T ss_dssp EECTSGCTTHHHHHHH---HHHHHHHTTSSHHHHHHH
T ss_pred EEcCCCCCCchhHHHH---HHHHHHHcCCCHHHHHHH
Confidence 3444567788888764 456677889999999764
No 43
>PRK14887 KEOPS complex Pcc1-like subunit; Provisional
Probab=26.01 E-value=2e+02 Score=18.91 Aligned_cols=38 Identities=18% Similarity=0.144 Sum_probs=29.6
Q ss_pred CEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHc
Q 033315 69 DVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVK 109 (122)
Q Consensus 69 D~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~ 109 (122)
++.++.+.+++ ++|. +.|.+.==....|+.+.+.++++
T Consensus 35 ~rs~~~~~~~~--~~l~-i~i~A~D~~~LRAslNs~lr~i~ 72 (84)
T PRK14887 35 ERSKADLSLDG--NTIV-ITIEAEDLSALRASLNSWLRLIK 72 (84)
T ss_pred CceEEEEEEeC--CEEE-EEEEECcHHHHHHHHHHHHHHHH
Confidence 45566667766 5555 88899988999999999998874
No 44
>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=25.98 E-value=1.4e+02 Score=17.34 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=17.9
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEeeEEE
Q 033315 64 APACGDVMKLQIKVDEETGQIVDACFK 90 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di~f~ 90 (122)
=+.|+..-.|.+.+++ |+|..+.-.
T Consensus 8 C~~C~~gC~i~~~v~~--g~i~~v~g~ 32 (55)
T PF04879_consen 8 CPYCSSGCGIDVYVKD--GKIVKVEGD 32 (55)
T ss_dssp -SSCTT--EEEEEEET--TEEEEEEE-
T ss_pred CcCCcCCCcEEEEEec--CceEEEECC
Confidence 3679998888888888 999988765
No 45
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=25.77 E-value=1.4e+02 Score=18.51 Aligned_cols=22 Identities=14% Similarity=0.398 Sum_probs=14.8
Q ss_pred CEEEEEEEEeCCCCcEEeeEEEe
Q 033315 69 DVMKLQIKVDEETGQIVDACFKT 91 (122)
Q Consensus 69 D~i~l~l~vd~~~g~I~di~f~~ 91 (122)
-.+++.+.|+.+ |+|.+++...
T Consensus 26 ~~~~V~i~i~~d-G~v~~~~i~~ 47 (85)
T PF13103_consen 26 LSVTVRITIDPD-GRVISVRIVK 47 (85)
T ss_dssp --EEEEEEE-TT-SBEEEEEEEE
T ss_pred cEEEEEEEECCC-CCEEEEEEec
Confidence 367888888765 8998887764
No 46
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=25.64 E-value=1.8e+02 Score=18.19 Aligned_cols=38 Identities=16% Similarity=0.056 Sum_probs=28.1
Q ss_pred CCEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHH
Q 033315 68 GDVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWV 108 (122)
Q Consensus 68 GD~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i 108 (122)
++.++..+.+++ + ..-+.|.+.-=....|+.+-+.+++
T Consensus 30 ~~~~~~~~~~~~--~-~L~i~~~A~d~~~LRasvns~l~~l 67 (76)
T PF09341_consen 30 PSRVKRELSVDG--N-KLVITIEAEDLRSLRASVNSFLDLL 67 (76)
T ss_dssp S-SSEEEEEEES--S-EEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred CCcEEEEEEEeC--C-EEEEEEEECCHHHHHHHHHHHHHHH
Confidence 345667777776 4 4458888888888899988888876
No 47
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=25.26 E-value=1.3e+02 Score=18.11 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=21.8
Q ss_pred EEEEEEEEeCCCCcEEeeEEE-eccch-HHHHHHHHH
Q 033315 70 VMKLQIKVDEETGQIVDACFK-TFGCG-SAIASSSVA 104 (122)
Q Consensus 70 ~i~l~l~vd~~~g~I~di~f~-~~GCa-is~ASasi~ 104 (122)
++.+.+.|+.+ |.|.+++.. +.|-. +-.++-.++
T Consensus 17 ~v~v~~~I~~~-G~v~~~~v~~s~~~~~l~~~a~~~v 52 (79)
T PF03544_consen 17 TVVVEFTIDPD-GRVSDVRVIQSSGPPILDEAALRAV 52 (79)
T ss_dssp EEEEEEEEETT-TEEEEEEEEEESSSSCSHHHHHHHH
T ss_pred EEEEEEEEeCC-CCEEEEEEEEccCHHHHHHHHHHHH
Confidence 68888889865 999998754 33433 444444433
No 48
>PF15076 DUF4543: Domain of unknown function (DUF4543)
Probab=24.71 E-value=82 Score=20.44 Aligned_cols=17 Identities=24% Similarity=0.391 Sum_probs=13.8
Q ss_pred hHHHHHHHHHhCCCCCC
Q 033315 32 LYHENVIDHYNNPRNVG 48 (122)
Q Consensus 32 ~Y~~~Ile~~~~P~n~g 48 (122)
.-.+..+||+.||+.+.
T Consensus 49 raeEqflEhWlNPHC~P 65 (75)
T PF15076_consen 49 RAEEQFLEHWLNPHCKP 65 (75)
T ss_pred HHHHHHHHHhcCCCCCC
Confidence 34788999999998864
No 49
>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=24.11 E-value=2.3e+02 Score=20.14 Aligned_cols=49 Identities=20% Similarity=0.373 Sum_probs=37.4
Q ss_pred EEEEEEEEeCCCCcEEee-EEEeccchHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 70 VMKLQIKVDEETGQIVDA-CFKTFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 70 ~i~l~l~vd~~~g~I~di-~f~~~GCais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
.-.|| .++.. |.+.+. .|.+.|..-..+-.-+=..+-.+.|++||.++.
T Consensus 118 ~~~l~-~vd~~-G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~~ea~~~~ 167 (190)
T PF00227_consen 118 GPQLY-SVDPS-GSYIECKRFAAIGSGSQFAQPILEKLYKPDLSLEEAIELA 167 (190)
T ss_dssp EEEEE-EEETT-SEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSHHHHHHHH
T ss_pred cccee-eeccc-cccccccccccchhcchhhhHHHHhhccCCCCHHHHHHHH
Confidence 45565 55654 899999 599999877777666666666899999998764
No 50
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=23.24 E-value=60 Score=21.81 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=23.4
Q ss_pred eEEEeccchHHHHHHHHHHHHHcCCCH
Q 033315 87 ACFKTFGCGSAIASSSVATEWVKGKQM 113 (122)
Q Consensus 87 i~f~~~GCais~ASasi~~e~i~GKtl 113 (122)
+.+.+.||..-++=++.|...+...-.
T Consensus 2 v~i~T~GC~~N~~Dse~i~~~l~~~G~ 28 (98)
T PF00919_consen 2 VYIETLGCQMNQYDSERIASILQAAGY 28 (98)
T ss_pred EEEEECCCcccHHHHHHHHHHHHhcCC
Confidence 568899999999999999999877544
No 51
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=22.78 E-value=62 Score=24.65 Aligned_cols=29 Identities=7% Similarity=0.068 Sum_probs=22.2
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHhcccc
Q 033315 93 GCGSAIASSSVATEWVKGKQMQEVLSIKN 121 (122)
Q Consensus 93 GCais~ASasi~~e~i~GKtleeA~~i~~ 121 (122)
.--+|-==+-.++++|.|+++++|..+.+
T Consensus 21 ~~riSpkk~r~Va~~IRGk~v~~A~~~L~ 49 (181)
T PTZ00178 21 DLRVHFKNTYETARAIKGMKLARAQKYLE 49 (181)
T ss_pred CcccchHHHHHHHHHHcCCcHHHHHHHHH
Confidence 33344455678999999999999998764
No 52
>PF01294 Ribosomal_L13e: Ribosomal protein L13e; InterPro: IPR001380 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 [, ]. The ribosomal protein L13e is widely found in vertebrates [], Drosophila melanogaster, plants, yeast, amongst others.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_U 4A1B_U 4A1D_U 4A19_U.
Probab=22.32 E-value=71 Score=24.37 Aligned_cols=19 Identities=58% Similarity=0.837 Sum_probs=13.5
Q ss_pred hhhHHhHHHHhhhhCCCCCc
Q 033315 6 SKRLLRQATAAAVAAPRPVQ 25 (122)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~ 25 (122)
+.|..||+-|+++ +|||++
T Consensus 28 rRr~~R~~KA~~i-~prP~~ 46 (179)
T PF01294_consen 28 RRRQARQAKAAKI-APRPVS 46 (179)
T ss_dssp HHHHHHHHHHHHH-TTS-SS
T ss_pred HHHHHHHHHHHhc-CCCCcc
Confidence 4578888887765 688887
No 53
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=22.00 E-value=1.1e+02 Score=18.98 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=20.6
Q ss_pred eEEEeccchHHHHHHHHHHHHHcCC
Q 033315 87 ACFKTFGCGSAIASSSVATEWVKGK 111 (122)
Q Consensus 87 i~f~~~GCais~ASasi~~e~i~GK 111 (122)
+.|.+.+|+.|.....++-+.+.-.
T Consensus 3 i~~~a~~C~~C~~~~~~~~~~~~e~ 27 (76)
T TIGR00412 3 IQIYGTGCANCQMTEKNVKKAVEEL 27 (76)
T ss_pred EEEECCCCcCHHHHHHHHHHHHHHc
Confidence 6788999999999988887777543
No 54
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=21.19 E-value=75 Score=18.66 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=17.7
Q ss_pred EEEeccchHHHHHHHHHHHHH
Q 033315 88 CFKTFGCGSAIASSSVATEWV 108 (122)
Q Consensus 88 ~f~~~GCais~ASasi~~e~i 108 (122)
-|.+.+|+.|.....++.++.
T Consensus 5 ~f~~~~C~~C~~~~~~l~~l~ 25 (67)
T cd02973 5 VFVSPTCPYCPDAVQAANRIA 25 (67)
T ss_pred EEECCCCCCcHHHHHHHHHHH
Confidence 467889999999999888764
No 55
>PRK07218 replication factor A; Provisional
Probab=21.15 E-value=2e+02 Score=24.64 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=28.5
Q ss_pred EEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhccc
Q 033315 70 VMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSIK 120 (122)
Q Consensus 70 ~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i~ 120 (122)
.+++...+|+.+|.|.-+-|. + +++.+.|+++++|.++.
T Consensus 323 dlrik~vLDDGtg~~~~~~~~-e-----------~~e~l~G~~~e~a~~~~ 361 (423)
T PRK07218 323 DLRIKAILDDGTGSVTVILDR-E-----------LTEIVYGGTLEDAEELA 361 (423)
T ss_pred eeEEEEEEECCCCeEEEEECh-h-----------hhHhHhCCCHHHHHHHH
Confidence 488888899877777644332 2 57788899999887764
No 56
>PTZ00192 60S ribosomal protein L13; Provisional
Probab=20.90 E-value=76 Score=24.92 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=14.2
Q ss_pred hhhHHhHHHHhhhhCCCCCc
Q 033315 6 SKRLLRQATAAAVAAPRPVQ 25 (122)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~ 25 (122)
+.|+.||+-|+++ +|||++
T Consensus 39 rRR~~R~~KA~~i-aPRP~~ 57 (218)
T PTZ00192 39 RRRRLRLLKAKKI-FPRPLK 57 (218)
T ss_pred HHHHHHHHHHHHh-CCCCCc
Confidence 5688888887765 688854
No 57
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=20.89 E-value=95 Score=18.51 Aligned_cols=23 Identities=30% Similarity=0.585 Sum_probs=13.8
Q ss_pred CCCCCCEEEEEEEEeCCCCcEEee
Q 033315 64 APACGDVMKLQIKVDEETGQIVDA 87 (122)
Q Consensus 64 np~CGD~i~l~l~vd~~~g~I~di 87 (122)
.|.+||.|.+... +++.+.|.++
T Consensus 37 ~~~VGD~V~~~~~-~~~~~~I~~v 59 (68)
T cd04466 37 PPAVGDRVEFEPE-DDGEGVIEEI 59 (68)
T ss_pred CCCCCcEEEEEEC-CCCcEEEEEE
Confidence 4789999988642 2221456543
No 58
>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=20.77 E-value=1.1e+02 Score=18.56 Aligned_cols=13 Identities=23% Similarity=0.304 Sum_probs=11.1
Q ss_pred CCCCCEEEEEEEE
Q 033315 65 PACGDVMKLQIKV 77 (122)
Q Consensus 65 p~CGD~i~l~l~v 77 (122)
+.+||.|.+.+..
T Consensus 41 ~~vGD~V~~~~~~ 53 (64)
T cd04451 41 ILPGDRVKVELSP 53 (64)
T ss_pred cCCCCEEEEEEee
Confidence 7899999988765
No 59
>PF02852 Pyr_redox_dim: Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; InterPro: IPR004099 This entry represents a dimerisation domain that is usually found at the C-terminal of both class I and class II oxidoreductases, as well as in NADH oxidases and peroxidases [, , ].; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0045454 cell redox homeostasis, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 3II4_B 2A8X_A 2BC0_B 2BC1_B 2W0H_A 2X50_B 2JK6_A 2YAU_A 2EQ9_E 2EQ6_B ....
Probab=20.57 E-value=2.6e+02 Score=18.30 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=36.8
Q ss_pred CEEEEEEEEeCCCCcEEeeEEEeccchHHHHHHHHHHHHHcCCCHHHHhcc
Q 033315 69 DVMKLQIKVDEETGQIVDACFKTFGCGSAIASSSVATEWVKGKQMQEVLSI 119 (122)
Q Consensus 69 D~i~l~l~vd~~~g~I~di~f~~~GCais~ASasi~~e~i~GKtleeA~~i 119 (122)
....+.|.++.++++|.-+..-+.+..-.+...+++.. .|.|++++...
T Consensus 47 ~~g~~Kli~d~~t~~IlGa~~vg~~a~e~I~~~~~ai~--~~~t~~~l~~~ 95 (110)
T PF02852_consen 47 TEGFVKLIFDKKTGRILGAQIVGPNASELINELALAIQ--NGLTVEDLADD 95 (110)
T ss_dssp TEEEEEEEEETTTTBEEEEEEEETTHHHHHHHHHHHHH--TTSBHHHHHTS
T ss_pred cceeeEEEEEeeccceeeeeeecCchHHHHHHHHHHHH--cCCCHHHHhCC
Confidence 46667777787679999999999887776666666555 58888876654
Done!