Query psy10992
Match_columns 179
No_of_seqs 143 out of 1109
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 15:26:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10992hhsearch_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 1.6E-40 3.5E-45 255.6 15.5 124 49-172 2-125 (127)
2 TIGR01999 iscU FeS cluster ass 100.0 7E-40 1.5E-44 250.9 15.5 123 50-172 1-123 (124)
3 TIGR03419 NifU_clost FeS clust 100.0 1.7E-38 3.6E-43 242.4 15.3 120 50-173 1-121 (121)
4 COG0822 IscU NifU homolog invo 100.0 1.2E-36 2.5E-41 240.4 13.9 128 44-174 1-147 (150)
5 PF01592 NifU_N: NifU-like N t 100.0 5.1E-36 1.1E-40 229.7 15.2 123 49-173 1-125 (126)
6 TIGR01994 SUF_scaf_2 SUF syste 100.0 1E-35 2.2E-40 231.5 14.6 116 47-166 2-137 (137)
7 KOG3361|consensus 100.0 2E-35 4.2E-40 227.2 13.1 128 46-173 25-152 (157)
8 cd06664 IscU_like Iron-sulfur 100.0 2.8E-35 6.1E-40 223.6 13.7 112 49-164 1-123 (123)
9 TIGR02000 NifU_proper Fe-S clu 100.0 5.2E-34 1.1E-38 246.1 14.9 123 49-174 3-127 (290)
10 PF02657 SufE: Fe-S metabolism 93.6 1.9 4.2E-05 32.9 11.0 98 47-154 11-113 (125)
11 TIGR03391 FeS_syn_CsdE cystein 91.8 2.4 5.3E-05 33.1 9.5 96 47-152 26-126 (138)
12 PRK15019 CsdA-binding activato 91.2 6.3 0.00014 31.2 12.1 71 82-155 59-134 (147)
13 PRK09296 cysteine desufuration 90.6 6.9 0.00015 30.5 12.5 97 47-153 21-122 (138)
14 PLN02673 quinolinate synthetas 88.6 12 0.00027 36.6 13.1 81 82-165 127-212 (724)
15 COG2166 sufE Cysteine desulfur 87.7 6.4 0.00014 31.2 8.9 69 81-152 53-126 (144)
16 PTZ00178 60S ribosomal protein 75.6 12 0.00025 30.8 6.5 60 112-171 24-105 (181)
17 TIGR01038 L22_arch ribosomal p 74.4 15 0.00032 29.2 6.7 65 107-171 16-102 (150)
18 PRK04223 rpl22p 50S ribosomal 72.4 18 0.00038 28.9 6.7 57 115-171 28-104 (153)
19 cd00336 Ribosomal_L22 Ribosoma 67.4 15 0.00033 26.8 5.0 46 118-173 16-61 (105)
20 PRK00565 rplV 50S ribosomal pr 66.6 23 0.0005 26.4 5.9 45 117-171 17-61 (112)
21 TIGR01044 rplV_bact ribosomal 65.6 26 0.00055 25.8 5.9 45 117-171 13-57 (103)
22 PF10437 Lip_prot_lig_C: Bacte 65.2 10 0.00023 26.4 3.6 50 85-137 15-66 (86)
23 PF04205 FMN_bind: FMN-binding 64.3 8.9 0.00019 26.1 3.1 72 86-169 4-78 (81)
24 PF12637 TSCPD: TSCPD domain; 60.1 62 0.0014 23.3 8.1 46 83-133 6-61 (95)
25 CHL00034 rpl22 ribosomal prote 54.1 50 0.0011 25.0 5.9 45 117-171 24-68 (117)
26 PF02593 dTMP_synthase: Thymid 53.6 62 0.0014 27.2 6.9 72 89-165 134-216 (217)
27 PF00237 Ribosomal_L22: Riboso 52.3 70 0.0015 23.2 6.3 42 118-169 14-55 (105)
28 PF01466 Skp1: Skp1 family, di 50.5 26 0.00057 24.2 3.6 25 113-137 32-56 (78)
29 COG0351 ThiD Hydroxymethylpyri 48.8 38 0.00083 29.3 5.0 44 98-144 200-243 (263)
30 PTZ00493 phosphomethylpyrimidi 47.6 17 0.00036 32.3 2.7 44 98-144 240-283 (321)
31 PRK12279 50S ribosomal protein 45.9 53 0.0011 29.2 5.5 44 116-169 16-59 (311)
32 COG0091 RplV Ribosomal protein 44.9 68 0.0015 24.6 5.4 44 117-170 25-68 (120)
33 PF10650 zf-C3H1: Putative zin 42.7 14 0.00031 20.4 1.0 14 19-32 3-16 (23)
34 PF08543 Phos_pyr_kin: Phospho 36.2 21 0.00047 29.6 1.6 38 103-143 194-231 (246)
35 PF13103 TonB_2: TonB C termin 31.7 86 0.0019 21.2 3.8 22 86-107 26-47 (85)
36 PRK03822 lplA lipoate-protein 30.9 1.2E+02 0.0025 27.0 5.4 43 85-130 262-304 (338)
37 TIGR00545 lipoyltrans lipoyltr 30.2 85 0.0018 27.6 4.4 43 85-130 257-299 (324)
38 PF11604 CusF_Ec: Copper bindi 28.8 82 0.0018 21.3 3.3 24 81-104 42-67 (70)
39 PF03544 TonB_C: Gram-negative 28.2 80 0.0017 20.8 3.1 20 87-106 17-36 (79)
40 PF13509 S1_2: S1 domain; PDB: 27.0 93 0.002 20.4 3.2 21 81-101 37-57 (61)
41 TIGR00718 sda_alpha L-serine d 26.6 3.6E+02 0.0078 23.8 7.6 60 109-168 166-235 (294)
42 PF03313 SDH_alpha: Serine deh 26.3 2.1E+02 0.0045 24.7 6.0 60 109-168 169-238 (282)
43 PF00227 Proteasome: Proteasom 25.9 2.7E+02 0.0059 21.4 6.2 55 87-142 118-173 (190)
44 cd03752 proteasome_alpha_type_ 25.6 3.3E+02 0.0072 21.9 6.9 55 88-143 143-197 (213)
45 TIGR02870 spore_II_D stage II 24.9 1.7E+02 0.0036 26.2 5.3 44 90-135 285-328 (338)
46 cd04466 S1_YloQ_GTPase S1_YloQ 24.9 72 0.0016 20.6 2.4 23 81-103 37-59 (68)
47 TIGR03295 frhA coenzyme F420 h 23.9 2.1E+02 0.0045 26.0 5.8 45 88-138 17-61 (411)
48 PRK14061 unknown domain/lipoat 23.8 1.6E+02 0.0034 28.4 5.2 43 84-129 485-527 (562)
49 PRK14551 rnhB ribonuclease HII 23.6 88 0.0019 25.9 3.1 62 105-169 128-205 (212)
50 PF14410 GH-E: HNH/ENDO VII su 23.4 84 0.0018 21.6 2.5 20 51-71 43-62 (70)
51 PF03450 CO_deh_flav_C: CO deh 23.4 1.4E+02 0.003 21.2 3.8 44 88-131 18-61 (103)
52 TIGR02669 SpoIID_LytB SpoIID/L 23.2 1.5E+02 0.0034 25.3 4.6 43 91-135 216-258 (267)
53 PF05381 Peptidase_C21: Tymovi 22.9 26 0.00056 26.3 -0.2 29 2-30 32-71 (104)
54 COG3259 FrhA Coenzyme F420-red 22.8 1.7E+02 0.0037 27.3 5.0 21 89-109 18-38 (441)
55 TIGR00778 ahpD_dom alkylhydrop 22.4 1.8E+02 0.004 17.5 3.8 29 107-136 18-46 (50)
56 PF03891 DUF333: Domain of unk 22.3 38 0.00082 21.9 0.5 21 24-52 28-48 (50)
57 PRK12413 phosphomethylpyrimidi 21.9 92 0.002 25.5 2.9 40 102-144 201-240 (253)
58 KOG1724|consensus 21.8 94 0.002 24.9 2.8 25 112-136 115-139 (162)
59 PF11720 Inhibitor_I78: Peptid 21.5 1.1E+02 0.0023 20.2 2.6 17 86-104 42-58 (60)
60 PF13798 PCYCGC: Protein of un 21.1 2.5E+02 0.0055 22.6 5.1 47 94-141 99-146 (158)
61 COG3064 TolA Membrane protein 20.9 1.9E+02 0.0042 26.1 4.8 39 86-124 326-364 (387)
No 1
>PRK11325 scaffold protein; Provisional
Probab=100.00 E-value=1.6e-40 Score=255.57 Aligned_cols=124 Identities=81% Similarity=1.251 Sum_probs=116.8
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCC
Q psy10992 49 HYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKT 128 (179)
Q Consensus 49 lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKt 128 (179)
.|+++|++||+||+|+|.+++|+..++.++.+||.|||+|+|||+|+++|+|+|++|+++||++++||||+|+++++|||
T Consensus 2 ~Y~~~il~h~~~P~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~~~~I~d~~f~~~GC~is~Asas~~~e~~~Gkt 81 (127)
T PRK11325 2 AYSEKVIDHYENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVNDEGIIEDAKFKTYGCGSAIASSSLVTEWVKGKT 81 (127)
T ss_pred ccHHHHHHHHhCcCCCCCCCCCccccceEEecCCCCccEEEEEEEECCCCeEEEEEEEeeCCHHHHHHHHHHHHHHcCCC
Confidence 69999999999999999999998544566789999999999999997568999999999999999999999999999999
Q ss_pred HHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHhc
Q psy10992 129 VDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIKQ 172 (179)
Q Consensus 129 l~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k~ 172 (179)
++||..|+.+++.+.||+||+|+|||.|+|+||++|+++|+.++
T Consensus 82 l~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~~~~ 125 (127)
T PRK11325 82 LDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQ 125 (127)
T ss_pred HHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999998764
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=7e-40 Score=250.89 Aligned_cols=123 Identities=83% Similarity=1.254 Sum_probs=115.9
Q ss_pred hHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCH
Q psy10992 50 YHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTV 129 (179)
Q Consensus 50 Y~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl 129 (179)
|+++|++||.||+|+|.+++|+..+++++.+||.|||.|+|||+|+++++|++++|+++||++++||+|+|+++++|||+
T Consensus 1 Y~~~il~~~~~p~n~G~l~~~~~~~~~~~~~np~CGD~i~l~l~v~~~~~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl 80 (124)
T TIGR01999 1 YSEKVLDHYENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSL 80 (124)
T ss_pred CcHHHHHHHhCCCCCCCCCCCccccceEEeCCCCCccEEEEEEEECCCCeEEEEEEEecCcHHHHHHHHHHHHHHcCCCH
Confidence 89999999999999999999985445678899999999999999975589999999999999999999999999999999
Q ss_pred HHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHhc
Q psy10992 130 DEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIKQ 172 (179)
Q Consensus 130 ~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k~ 172 (179)
+|+..|+++++.+.||+||+|+|||.|+|+||++|+.+|+.++
T Consensus 81 ~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~~~~ 123 (124)
T TIGR01999 81 EEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQ 123 (124)
T ss_pred HHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999998764
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=1.7e-38 Score=242.45 Aligned_cols=120 Identities=58% Similarity=0.993 Sum_probs=113.3
Q ss_pred hHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCH
Q psy10992 50 YHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTV 129 (179)
Q Consensus 50 Y~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl 129 (179)
|+++|+|||+||+|+|++++|+. +++.+||.|||.|+|||+|+ +++|+|++|+++||++++||||+|+++++|||+
T Consensus 1 Y~~~il~~~~np~~~g~l~~~~~---~~~~~np~CGD~i~l~l~i~-~~~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l 76 (121)
T TIGR03419 1 YSEKVMDHFMNPRNVGEIENADG---VGEVGNPKCGDIMKIFLKVE-DDIIKDVKFKTFGCGAAIASSSMATEMIKGKTL 76 (121)
T ss_pred ChHHHHHHHhCCCCCCCCCCCCe---EEEeCCCCCccEEEEEEEEc-CCEEEEEEEEEeccHHHHHHHHHHHHHHcCCCH
Confidence 89999999999999999999984 46889999999999999997 689999999999999999999999999999999
Q ss_pred HHHHHhhhHhHHhhcC-CCCCcchhhHHHHHHHHHHHHHHHHhch
Q psy10992 130 DEALKLKNTDIAKELC-LPPVKLHCSMLAEDAIKAALSDYRIKQN 173 (179)
Q Consensus 130 ~Ea~~i~~~~i~~~L~-~~~~R~~CA~La~~AL~~Al~~y~~k~~ 173 (179)
+||..|..+++.+.|+ +||+|+|||+|+|+||++|+++|+.+.+
T Consensus 77 ~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~~~~ 121 (121)
T TIGR03419 77 EEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 (121)
T ss_pred HHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHhccC
Confidence 9999999988888885 8999999999999999999999998753
No 4
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=100.00 E-value=1.2e-36 Score=240.39 Aligned_cols=128 Identities=61% Similarity=0.949 Sum_probs=114.8
Q ss_pred cchHhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHH
Q psy10992 44 STPVLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEW 123 (179)
Q Consensus 44 ~~~~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~ 123 (179)
++.+.+|+++|++||.||+|.|.+++++. +.+..++|.|||.|+|||+++ +|+|+|++|+++||++++||+|+|+++
T Consensus 1 ~~~~~~y~~~Ildh~~np~~~g~l~~~~~--~~~~~~~~~CGD~i~l~lkv~-~~~I~d~~F~~~GC~is~ASss~~te~ 77 (150)
T COG0822 1 SNLDDLYSEKILDHYKNPRNVGVLDDADV--GVGHVGAPACGDVITLYLKVD-NGVIEDAKFKGFGCAISIASSSMMTEL 77 (150)
T ss_pred CcHHHHHHHHHHHHhcCCCcCCccCccch--hccccCCCCccceEEEEEEEc-CCEEEEEEeeecCcHHHHHHHHHHHHH
Confidence 35799999999999999999999999984 345667799999999999998 799999999999999999999999999
Q ss_pred hcCCCHHHHHHhhhH--hHHhhcC-----------------CCCCcchhhHHHHHHHHHHHHHHHHhchh
Q psy10992 124 VKGKTVDEALKLKNT--DIAKELC-----------------LPPVKLHCSMLAEDAIKAALSDYRIKQNS 174 (179)
Q Consensus 124 ~~GKtl~Ea~~i~~~--~i~~~L~-----------------~~~~R~~CA~La~~AL~~Al~~y~~k~~~ 174 (179)
++|||++||+.|++. ++.+.++ +||.|++|++|+|+||++++.+|+.++..
T Consensus 78 v~Gkti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~~ai~~~~~~~~~ 147 (150)
T COG0822 78 VKGKTLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALKAAIKDYKGKAEE 147 (150)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhHhhhhhccccccccchhccHHHHHHHHHHhhccccc
Confidence 999999999999954 4445443 79999999999999999999999887643
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=5.1e-36 Score=229.74 Aligned_cols=123 Identities=50% Similarity=0.944 Sum_probs=114.8
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCC-CcEEEeEEeeccchHHHHHHHHHHHHhcCC
Q psy10992 49 HYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDN-GKIIDAKFKTFGCGSAIASSSLATEWVKGK 127 (179)
Q Consensus 49 lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~-g~I~di~F~~~GCais~ASASil~e~~~GK 127 (179)
+|+++|++||.||+|+|.+++++. +++..+||+|||.|+|||+|+++ |+|+|++|+++||++++||+|+|+++++||
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 599999999999999999999984 25678999999999999999865 799999999999999999999999999999
Q ss_pred CHHHHHHhhhHhHHhhcC-CCCCcchhhHHHHHHHHHHHHHHHHhch
Q psy10992 128 TVDEALKLKNTDIAKELC-LPPVKLHCSMLAEDAIKAALSDYRIKQN 173 (179)
Q Consensus 128 tl~Ea~~i~~~~i~~~L~-~~~~R~~CA~La~~AL~~Al~~y~~k~~ 173 (179)
|++||..|+.+++.+.|+ +|+.|.+|+.|++.||++++.+|..|+.
T Consensus 79 ~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~r~~ 125 (126)
T PF01592_consen 79 TLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPARHK 125 (126)
T ss_dssp BHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHHHCH
T ss_pred CHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHhhhc
Confidence 999999999999999996 8999999999999999999999998863
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=1e-35 Score=231.54 Aligned_cols=116 Identities=37% Similarity=0.616 Sum_probs=103.4
Q ss_pred HhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcC
Q psy10992 47 VLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKG 126 (179)
Q Consensus 47 ~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~G 126 (179)
.++|+++|+|||+||+|+|.+++|+. +++.+||+|||+|+||++|+ +++|++++|+++||++++||||+|+++++|
T Consensus 2 ~~lY~~~Ileh~~~p~n~g~l~~~~~---~~~~~np~CGD~i~l~l~v~-~~~I~d~~f~~~GCais~Asas~~~e~i~G 77 (137)
T TIGR01994 2 DSLYRQVILDHYKNPRHRGKLEDATV---QERGHNPTCGDEITLTVKLE-GDRIEDIAFEGEGCSISQASASMMTELIKG 77 (137)
T ss_pred hHHHHHHHHHHHhCCCCCCCCCCCCe---eEEeCCCCCCcEEEEEEEEc-CCeEEEEEEEecccHHHHHHHHHHHHHHcC
Confidence 57999999999999999999999984 45789999999999999996 689999999999999999999999999999
Q ss_pred CCHHHHHHhhhHh---HH--------------hhc---CCCCCcchhhHHHHHHHHHHHH
Q psy10992 127 KTVDEALKLKNTD---IA--------------KEL---CLPPVKLHCSMLAEDAIKAALS 166 (179)
Q Consensus 127 Ktl~Ea~~i~~~~---i~--------------~~L---~~~~~R~~CA~La~~AL~~Al~ 166 (179)
||++|+..+.+.+ +. ..| ..+|+|++||+|||+||++||.
T Consensus 78 k~~~ea~~l~~~~~~ml~~~~~~~~~~~l~dl~~l~~v~~~p~R~~Ca~L~~~al~~al~ 137 (137)
T TIGR01994 78 KTVEEALSLVEAFSEMIQGQETDEDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137 (137)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCccccccchHHHhhccccCcchHHHHHHHHHHHHHHhC
Confidence 9999999999752 11 011 3489999999999999999873
No 7
>KOG3361|consensus
Probab=100.00 E-value=2e-35 Score=227.22 Aligned_cols=128 Identities=87% Similarity=1.273 Sum_probs=124.1
Q ss_pred hHhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhc
Q psy10992 46 PVLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVK 125 (179)
Q Consensus 46 ~~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~ 125 (179)
..-+|.+.++|||.||||.|.++..|..||+|.++-|.|||.++++++|+++|+|+|++|.++||+.++||+|+++||++
T Consensus 25 ~~rlYh~~VidHy~nPRNVGSldK~dpnVGtGlVGAPACGDVMkLqIkvd~~g~I~dakFKTFGCGSAIASSS~aTewvk 104 (157)
T KOG3361|consen 25 ASRLYHENVIDHYENPRNVGSLDKNDPNVGTGLVGAPACGDVMKLQIKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVK 104 (157)
T ss_pred hhhhcchhhhhcccCccccCccCCCCCCcccccccCccccceeeEEEEECCCCcEEEeeeeecccchHhhhhHHHHHHHc
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHhch
Q psy10992 126 GKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIKQN 173 (179)
Q Consensus 126 GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k~~ 173 (179)
|||++|+..|.+.+|..+|.+||.++||.+|+.+|++.|+.+|+.|+.
T Consensus 105 gkt~dea~kIkNteIAKeL~LPPVKLHCSMLAEDAIKaAikdyk~Kq~ 152 (157)
T KOG3361|consen 105 GKTLDEALKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKDYKEKQN 152 (157)
T ss_pred cccHHHHHhcccHHHHHhccCCchhhhhHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999999998865
No 8
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=100.00 E-value=2.8e-35 Score=223.65 Aligned_cols=112 Identities=58% Similarity=0.958 Sum_probs=103.9
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCC
Q psy10992 49 HYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKT 128 (179)
Q Consensus 49 lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKt 128 (179)
+|+++|++||.||+|.|.+++++. .++.+||.|||+|+||++|+ +++|++++|+++||++++||||+|+++++|||
T Consensus 1 ~y~~~il~~~~~p~~~g~l~~~~~---~~~~~n~~CGD~v~l~l~i~-~~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~ 76 (123)
T cd06664 1 LYSEIILDHYRNPRNVGRLEDADG---TGEVGNPLCGDEITLYLKVE-DGRITDAKFQGFGCAISIASASLLTELIKGKT 76 (123)
T ss_pred CcHHHHHHHhhCCCCCCCCCCCCe---EEEcCCCCCCceEEEEEEEc-CCEEEEEEEEecCcHHHHHHHHHHHHHHcCCc
Confidence 599999999999999999999874 46789999999999999997 58999999999999999999999999999999
Q ss_pred HHHHHHhhhHhHHhh-----------cCCCCCcchhhHHHHHHHHHH
Q psy10992 129 VDEALKLKNTDIAKE-----------LCLPPVKLHCSMLAEDAIKAA 164 (179)
Q Consensus 129 l~Ea~~i~~~~i~~~-----------L~~~~~R~~CA~La~~AL~~A 164 (179)
++|+..|..+++... .+.||+|++||+|||+||++|
T Consensus 77 ~~ea~~i~~~~~~~~~~~~~l~~~~~~~~~~~R~~Ca~L~~~Al~~a 123 (123)
T cd06664 77 LDEALKLLNKDIAMLDGKEELAALAGVGLPPARIHCALLAWKALKAA 123 (123)
T ss_pred HHHHHHHHHHHHHHhcCchhHHHhcccccCcccchHHHHHHHHHHhC
Confidence 999999999877653 368999999999999999874
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=5.2e-34 Score=246.08 Aligned_cols=123 Identities=50% Similarity=0.861 Sum_probs=115.2
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECC-CCcEEEeEEeeccchHHHHHHHHHHHHhcCC
Q psy10992 49 HYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDD-NGKIIDAKFKTFGCGSAIASSSLATEWVKGK 127 (179)
Q Consensus 49 lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~-~g~I~di~F~~~GCais~ASASil~e~~~GK 127 (179)
.|+++|++||+||+|+|.+++|+. +++.+||+|||.|+|||+|++ +++|+|++|+++||++++||||+|+++++||
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 499999999999999999999983 568899999999999999973 6899999999999999999999999999999
Q ss_pred CHHHHHHhhhHhHHhhc-CCCCCcchhhHHHHHHHHHHHHHHHHhchh
Q psy10992 128 TVDEALKLKNTDIAKEL-CLPPVKLHCSMLAEDAIKAALSDYRIKQNS 174 (179)
Q Consensus 128 tl~Ea~~i~~~~i~~~L-~~~~~R~~CA~La~~AL~~Al~~y~~k~~~ 174 (179)
|++||..++.+++.++| ++||+|+|||.|+|+||++|+.+|..+...
T Consensus 80 tv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~kp~~ 127 (290)
T TIGR02000 80 TLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLE 127 (290)
T ss_pred CHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhcCccc
Confidence 99999999999998888 599999999999999999999999887554
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=93.58 E-value=1.9 Score=32.94 Aligned_cols=98 Identities=20% Similarity=0.266 Sum_probs=63.0
Q ss_pred HhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeecc-chHHHHHHHHHHHHhc
Q psy10992 47 VLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFG-CGSAIASSSLATEWVK 125 (179)
Q Consensus 47 ~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~G-Cais~ASASil~e~~~ 125 (179)
|+.--+.|+++.+..+....-...+.. . -+.|-..|-|+...+++|++ .|.++. -.+...-.+++.+.+.
T Consensus 11 ~~~ry~~Li~lgk~lp~l~~~~~~~~~----~--V~GC~S~vWl~~~~~~~g~~---~f~adSda~ivkGl~all~~~~~ 81 (125)
T PF02657_consen 11 WEERYRYLIDLGKKLPPLPEELRTDEN----L--VHGCQSQVWLHVEEDEDGKV---HFRADSDARIVKGLLALLLEVLN 81 (125)
T ss_dssp HHHHHHHHHHHHHTS----CCCCSCCE----E--ETSSSS-EEEEEEEETTSEE---EEEEEESSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhcCCCCCHHHhcccc----c--CCCCccceeEeeeeccCCEE---EEEecCccHHHHHHHHHHHHHHc
Confidence 555556778999887654432222211 2 25899998885544456766 566653 4578888999999999
Q ss_pred CCCHHHHHHhhhHhHHhhcC----CCCCcchhh
Q psy10992 126 GKTVDEALKLKNTDIAKELC----LPPVKLHCS 154 (179)
Q Consensus 126 GKtl~Ea~~i~~~~i~~~L~----~~~~R~~CA 154 (179)
|+|.+|+..++.. +.+.+| +.|.|.+=.
T Consensus 82 g~t~~eI~~~~~~-fl~~lgl~~~Ls~sR~nGl 113 (125)
T PF02657_consen 82 GQTPEEILAFDPD-FLEQLGLSQHLSPSRSNGL 113 (125)
T ss_dssp T-BHHHHHHS-TH-HHHHHTSCCCSTHHHHHHH
T ss_pred CCCHHHHHhCCHH-HHHHcCcccccCchHHHHH
Confidence 9999999999999 555665 467777633
No 11
>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=91.79 E-value=2.4 Score=33.11 Aligned_cols=96 Identities=18% Similarity=0.130 Sum_probs=64.3
Q ss_pred HhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeecc-chHHHHHHHHHHHHhc
Q psy10992 47 VLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFG-CGSAIASSSLATEWVK 125 (179)
Q Consensus 47 ~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~G-Cais~ASASil~e~~~ 125 (179)
++.|+- |+++.+.-. .+++.... ....-+.|-..|=|...+.+||+ +.|.++. =.+...-++++.+.+.
T Consensus 26 e~ry~~-lI~lgk~Lp---~lpe~~r~---~~~~V~GCqS~VWl~~~~~~dg~---~~f~~dSDa~IvkGl~alL~~~~~ 95 (138)
T TIGR03391 26 EDRYRQ-LILLAKQLP---ALPEALKT---QATELTGCENRVWLGHQVLPDGT---LHFYGDSEGRIVRGLLAVLLTAVE 95 (138)
T ss_pred HHHHHH-HHHHHhhCC---CCChHHcC---hhhccCCcccceeeeeeecCCCE---EEEEecCccHHHHHHHHHHHHHHc
Confidence 455644 567766533 23332210 11123589888887766544564 4566663 4577888999999999
Q ss_pred CCCHHHHHHhhhHhHHhhcC----CCCCcch
Q psy10992 126 GKTVDEALKLKNTDIAKELC----LPPVKLH 152 (179)
Q Consensus 126 GKtl~Ea~~i~~~~i~~~L~----~~~~R~~ 152 (179)
|+|.+|+.+++..++...|| +.|.|.+
T Consensus 96 g~tp~eI~~~d~~~~~~~lGL~~~LSpsR~N 126 (138)
T TIGR03391 96 GKTPEQLLAQDPLALFDELGLRAQLSASRSN 126 (138)
T ss_pred CCCHHHHHHCCHHHHHHHcCchhccCccHHH
Confidence 99999999999977777776 5788876
No 12
>PRK15019 CsdA-binding activator; Provisional
Probab=91.24 E-value=6.3 Score=31.19 Aligned_cols=71 Identities=21% Similarity=0.165 Sum_probs=55.0
Q ss_pred CCCCcEEEEEEEECCCCcEEEeEEeecc-chHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhcC----CCCCcchhhH
Q psy10992 82 PACGDVMKLQIKVDDNGKIIDAKFKTFG-CGSAIASSSLATEWVKGKTVDEALKLKNTDIAKELC----LPPVKLHCSM 155 (179)
Q Consensus 82 p~CGD~I~l~l~i~~~g~I~di~F~~~G-Cais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L~----~~~~R~~CA~ 155 (179)
+.|-..|-|...++++|+ +.|.++. =.|...-++++.+.+.|+|++|+.+++..++...+| +.|.|..=..
T Consensus 59 ~GCqS~VWL~~~~~~dg~---~~f~~dSDA~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~NGl~ 134 (147)
T PRK15019 59 AGCENRVWLGYTVAENGK---MHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLN 134 (147)
T ss_pred CCcccceeeeeeecCCCE---EEEEeeCccHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCccHHHHHH
Confidence 589888888777744563 4666653 357788899999999999999999999977777776 5788987433
No 13
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=90.58 E-value=6.9 Score=30.55 Aligned_cols=97 Identities=10% Similarity=0.109 Sum_probs=64.6
Q ss_pred HhhhHHHHHHHHhCCCCCCCCCCCCCcccceeecCCCCCcEEEEEEEECCCCcEEEeEEeecc-chHHHHHHHHHHHHhc
Q psy10992 47 VLHYHENVIDHYENPRNVGSLDKKDKNVGTGLVGAPACGDVMKLQIKVDDNGKIIDAKFKTFG-CGSAIASSSLATEWVK 125 (179)
Q Consensus 47 ~~lY~~~Ileh~~nP~n~G~l~~~d~~~~~g~~~np~CGD~I~l~l~i~~~g~I~di~F~~~G-Cais~ASASil~e~~~ 125 (179)
++.|+ .|+++.+.-+. +++... +....-+.|-..|-|...++++| .+.|.++. =.|...-++++...+.
T Consensus 21 e~Ry~-~LI~lgk~Lp~---lpe~~r---~~~~~V~GCqS~VWl~~~~~~~g---~~~f~~dSDa~ivkGl~alL~~~~~ 90 (138)
T PRK09296 21 EEKYL-YIIELGQRLPP---LTDEDR---SPQNLIQGCQSQVWIVMRQNAQG---IIELQGDSDAAIVKGLIAVVFILYQ 90 (138)
T ss_pred HHHHH-HHHHHHhhCCC---CCHHHc---CccccCCCcccceeeeEeecCCC---EEEEEEecccHHHHHHHHHHHHHHc
Confidence 44554 45777665433 333211 01112358988888877776556 34666664 3577788999999999
Q ss_pred CCCHHHHHHhhhHhHHhhcC----CCCCcchh
Q psy10992 126 GKTVDEALKLKNTDIAKELC----LPPVKLHC 153 (179)
Q Consensus 126 GKtl~Ea~~i~~~~i~~~L~----~~~~R~~C 153 (179)
|+|++|+.+++..++.+.|| +.|.|.+=
T Consensus 91 g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~nG 122 (138)
T PRK09296 91 QMTPQDIVNFDVRPWFEKLALTQHLTPSRSQG 122 (138)
T ss_pred CCCHHHHHhCChHHHHHHcCcccccCccHHHH
Confidence 99999999999765556676 57888873
No 14
>PLN02673 quinolinate synthetase A
Probab=88.57 E-value=12 Score=36.58 Aligned_cols=81 Identities=17% Similarity=0.170 Sum_probs=59.4
Q ss_pred CCCCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc--CC---CCCcchhhHH
Q psy10992 82 PACGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKEL--CL---PPVKLHCSML 156 (179)
Q Consensus 82 p~CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L--~~---~~~R~~CA~L 156 (179)
+.|-..|-|...++++|+ ..+.+..++ .|...-+.++.+.+.|+|.+|+++++.+++ ..| |+ .|+|..=..-
T Consensus 127 ~GCQSqVWL~~eldddGk-v~F~ADSDA-~IVKGL~ALLl~~lsG~TpeEILavD~d~~-~~LGLGL~~~SPSRsNGL~n 203 (724)
T PLN02673 127 MGCTAQVWLEAELDQDGK-MRFWADSDS-EITKGFCSCLIWVLDGASPEEVLELKTEDL-AALNVGLPGGERSRVNTWHN 203 (724)
T ss_pred CCcccceEEEEEEcCCCE-EEEEEeCcc-HHHHHHHHHHHHHHcCCCHHHHHhCCHHHH-HHHhhhhcccCCchhHHHHH
Confidence 589998988888765564 345555666 889999999999999999999999999877 444 32 7888874444
Q ss_pred HHHHHHHHH
Q psy10992 157 AEDAIKAAL 165 (179)
Q Consensus 157 a~~AL~~Al 165 (179)
..+++++..
T Consensus 204 ML~~Iq~~A 212 (724)
T PLN02673 204 VLVSMQKRT 212 (724)
T ss_pred HHHHHHHHH
Confidence 444443333
No 15
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=87.66 E-value=6.4 Score=31.16 Aligned_cols=69 Identities=23% Similarity=0.280 Sum_probs=53.6
Q ss_pred CCCCCcEEEEEEEECCCCcEEEeEEeeccc-hHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhcC----CCCCcch
Q psy10992 81 APACGDVMKLQIKVDDNGKIIDAKFKTFGC-GSAIASSSLATEWVKGKTVDEALKLKNTDIAKELC----LPPVKLH 152 (179)
Q Consensus 81 np~CGD~I~l~l~i~~~g~I~di~F~~~GC-ais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L~----~~~~R~~ 152 (179)
-+.|-..|-|....+++| .+.|.|+.= .|...-++++.+.+.|+|.+|+..++..++.+.|| +.|.|..
T Consensus 53 V~GC~S~vwL~~~~~~~~---~~~F~gdSdA~ivrGL~aill~~~~G~t~~eI~~~~~~~~f~~LGL~~~LSpsR~n 126 (144)
T COG2166 53 VPGCQSQVWLVTEQNDDG---TLHFFGDSDARIVRGLLAILLAAYSGKTAAEILAFDPLDFFEELGLAQHLSPSRSN 126 (144)
T ss_pred CCccccceeEEEeecCCc---eEEEeccchhHHHHHHHHHHHHHHcCCCHHHHHcCCHHHHHHHhhHHHhcChHHhh
Confidence 357888887777765433 457777754 46778889999999999999999999977777776 5788876
No 16
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=75.57 E-value=12 Score=30.80 Aligned_cols=60 Identities=15% Similarity=0.062 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc--------------------CCCCC--cchhhHHHHHHHHHHHHHHH
Q psy10992 112 SAIASSSLATEWVKGKTVDEALKLKNTDIAKEL--------------------CLPPV--KLHCSMLAEDAIKAALSDYR 169 (179)
Q Consensus 112 is~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L--------------------~~~~~--R~~CA~La~~AL~~Al~~y~ 169 (179)
+|-==+-.+++++.|+++++|..+....+...- +.++. -.+++.+-.+.|+.|+.+.+
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 444456788999999999999999998554211 11333 34899999999999999987
Q ss_pred Hh
Q psy10992 170 IK 171 (179)
Q Consensus 170 ~k 171 (179)
.+
T Consensus 104 ~~ 105 (181)
T PTZ00178 104 AK 105 (181)
T ss_pred hc
Confidence 43
No 17
>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=74.36 E-value=15 Score=29.17 Aligned_cols=65 Identities=11% Similarity=0.084 Sum_probs=46.9
Q ss_pred eccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc--------------------CCCC--CcchhhHHHHHHHHHH
Q psy10992 107 TFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKEL--------------------CLPP--VKLHCSMLAEDAIKAA 164 (179)
Q Consensus 107 ~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L--------------------~~~~--~R~~CA~La~~AL~~A 164 (179)
+..--+|-==+-.++.++.|+++++|..+....+...- +... -..+++.+-.+.|+.|
T Consensus 16 ~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~i~klL~sA 95 (150)
T TIGR01038 16 GRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKFILKVLQNA 95 (150)
T ss_pred eCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHHHHHHHHHH
Confidence 33334445556788999999999999999988654221 1111 2358999999999999
Q ss_pred HHHHHHh
Q psy10992 165 LSDYRIK 171 (179)
Q Consensus 165 l~~y~~k 171 (179)
+.+.+.+
T Consensus 96 ~aNA~~~ 102 (150)
T TIGR01038 96 EANAEYK 102 (150)
T ss_pred HHHHHhc
Confidence 9998754
No 18
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=72.40 E-value=18 Score=28.85 Aligned_cols=57 Identities=18% Similarity=0.145 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHhhhHhHHhh--c----------------CCCC--CcchhhHHHHHHHHHHHHHHHHh
Q psy10992 115 ASSSLATEWVKGKTVDEALKLKNTDIAKE--L----------------CLPP--VKLHCSMLAEDAIKAALSDYRIK 171 (179)
Q Consensus 115 ASASil~e~~~GKtl~Ea~~i~~~~i~~~--L----------------~~~~--~R~~CA~La~~AL~~Al~~y~~k 171 (179)
==+..++.++.|+++++|..+....+... + +.+. --.+++.+-.+.|+.|+.+.+.+
T Consensus 28 kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~KlL~sA~aNA~~~ 104 (153)
T PRK04223 28 KHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFLKLLENAEANAEYK 104 (153)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHHHHHHHHHHHHHhc
Confidence 34667899999999999999998755421 1 1122 23589999999999999998754
No 19
>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=67.40 E-value=15 Score=26.77 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=36.2
Q ss_pred HHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHhch
Q psy10992 118 SLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIKQN 173 (179)
Q Consensus 118 Sil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k~~ 173 (179)
-.+++++.|++++||..+..... .+.+..-.++|+.|..++..+..
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~~~~----------kk~a~~i~k~l~sa~~nA~~~~~ 61 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLEFVP----------KKAAKIILKLLKSAEANAENNGL 61 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHHhCC----------HHHHHHHHHHHHHHHHhHHHcCC
Confidence 46789999999999988775532 66778888999999988876543
No 20
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=66.57 E-value=23 Score=26.43 Aligned_cols=45 Identities=22% Similarity=0.392 Sum_probs=35.9
Q ss_pred HHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHh
Q psy10992 117 SSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIK 171 (179)
Q Consensus 117 ASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k 171 (179)
.-.++.++.|+++++|..+... ...+.+..-.+.|+.|+.+++..
T Consensus 17 ~~~v~~~IrG~~v~~A~~~L~~----------~pkk~a~~i~k~L~sA~aNA~~~ 61 (112)
T PRK00565 17 ARLVADLIRGKKVEEALAILKF----------SPKKAARLVKKVLKSAIANAENN 61 (112)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH----------CcHhHHHHHHHHHHHHHHHHHhc
Confidence 4568899999999999987654 34556788889999999988763
No 21
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=65.63 E-value=26 Score=25.83 Aligned_cols=45 Identities=18% Similarity=0.380 Sum_probs=36.3
Q ss_pred HHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHh
Q psy10992 117 SSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIK 171 (179)
Q Consensus 117 ASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k 171 (179)
+-.++.++.|++++||..+.. + ...+.|..-.+.|+.|..+++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~--------f--~pkk~a~~i~klL~sA~aNA~~~ 57 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILR--------F--TPKKAAPLIKKVLASAIANAEHN 57 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHh--------h--CCHhHHHHHHHHHHHHHHHHHHc
Confidence 346789999999999988765 2 45568899999999999998643
No 22
>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=65.15 E-value=10 Score=26.44 Aligned_cols=50 Identities=18% Similarity=0.067 Sum_probs=33.5
Q ss_pred CcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCC--CHHHHHHhhh
Q psy10992 85 GDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGK--TVDEALKLKN 137 (179)
Q Consensus 85 GD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GK--tl~Ea~~i~~ 137 (179)
|-.|.+++.|+ +|+|+++++.|+-= ...-..-+.+.++|. +.+++.+...
T Consensus 15 ~G~v~v~~~V~-~G~I~~i~i~gDf~--~~~~i~~le~~L~G~~~~~~~i~~~l~ 66 (86)
T PF10437_consen 15 WGTVEVHLNVK-NGIIKDIKIYGDFF--GPEDIEELEEALIGCPYDREAIKEALN 66 (86)
T ss_dssp TEEEEEEEEEE-TTEEEEEEEEECBS---CCCHHHHHHHHTTCBSSHHHHHHHHH
T ss_pred CceEEEEEEEE-CCEEEEEEEECCCC--CchHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 45699999996 79999999987622 223356677778887 3444444433
No 23
>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=64.26 E-value=8.9 Score=26.13 Aligned_cols=72 Identities=18% Similarity=0.207 Sum_probs=40.7
Q ss_pred cEEEEEEEECCCCcEEEeEEeeccchHHHH---HHHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHH
Q psy10992 86 DVMKLQIKVDDNGKIIDAKFKTFGCGSAIA---SSSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIK 162 (179)
Q Consensus 86 D~I~l~l~i~~~g~I~di~F~~~GCais~A---SASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~ 162 (179)
..|++.+.|+++|+|.++.+....-..... ...-+.+.+.|+.+ ......-+-+-=|++.-+++.
T Consensus 4 g~i~v~v~i~~dg~I~~v~~~~~~et~~~~~~~~~~~~~~~~~g~~~------------~~~~~~vD~vSGAT~ss~a~~ 71 (81)
T PF04205_consen 4 GPITVTVTIDKDGKITDVKILEHNETPGYGKKAEIEEFFDQIVGKQI------------KKDSDDVDAVSGATISSKAIK 71 (81)
T ss_dssp EEEEEEEEEETTTEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCC------------TTTSCEETTCTTBHHHHHHHH
T ss_pred ceEEEEEEEeCCCEEEEEEEeeccCCcchhhhccHHHHHHHHHhccc------------cccCCCCCeeeCcchhHHHHH
Confidence 467888888766999999999864321111 12222233333322 001223344556788888888
Q ss_pred HHHHHHH
Q psy10992 163 AALSDYR 169 (179)
Q Consensus 163 ~Al~~y~ 169 (179)
+++.+..
T Consensus 72 ~av~~Al 78 (81)
T PF04205_consen 72 EAVQKAL 78 (81)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8877643
No 24
>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=60.07 E-value=62 Score=23.31 Aligned_cols=46 Identities=20% Similarity=0.526 Sum_probs=27.8
Q ss_pred CCCcEEEEEEEECCC-Cc----EEEeEEeeccchHHHHHHHHHHHHh-----cCCCHHHHH
Q psy10992 83 ACGDVMKLQIKVDDN-GK----IIDAKFKTFGCGSAIASSSLATEWV-----KGKTVDEAL 133 (179)
Q Consensus 83 ~CGD~I~l~l~i~~~-g~----I~di~F~~~GCais~ASASil~e~~-----~GKtl~Ea~ 133 (179)
.|| .+.|.+..++| |+ +.++++.+ || .+-.+.++.++ .|.+++++.
T Consensus 6 ~~g-~~yvtv~~d~d~g~p~Evf~~~~~~G-g~---~~~~~ai~rliS~~Lr~G~~~~~ii 61 (95)
T PF12637_consen 6 GCG-KLYVTVNFDEDNGRPFEVFINVGKAG-GC---SGNLEAIARLISLALRSGVPPEEII 61 (95)
T ss_pred ccc-ceEEEEEeeCCCCcceEEEEecCcCC-Cc---hHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 455 44444455544 64 44444333 56 67777788888 999988743
No 25
>CHL00034 rpl22 ribosomal protein L22
Probab=54.13 E-value=50 Score=24.97 Aligned_cols=45 Identities=11% Similarity=0.169 Sum_probs=36.1
Q ss_pred HHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHHh
Q psy10992 117 SSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRIK 171 (179)
Q Consensus 117 ASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~k 171 (179)
+-.++.++.|+++++|..+... ...+.+..-.+.|+.|+.+++..
T Consensus 24 ~r~va~~IRG~~v~~A~~~L~~----------~pkk~a~~i~klL~sA~aNA~~~ 68 (117)
T CHL00034 24 ARRVIDQIRGRSYEEALMILEF----------MPYRACYPILKLVYSAAANASHN 68 (117)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH----------CcHHHHHHHHHHHHHHHHHHHHc
Confidence 4578899999999999988763 22678888889999999888543
No 26
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=53.56 E-value=62 Score=27.20 Aligned_cols=72 Identities=26% Similarity=0.392 Sum_probs=48.5
Q ss_pred EEEEEECCCCcEEEeEEe-eccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhh-----cC-C----CCCcchhhHHH
Q psy10992 89 KLQIKVDDNGKIIDAKFK-TFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKE-----LC-L----PPVKLHCSMLA 157 (179)
Q Consensus 89 ~l~l~i~~~g~I~di~F~-~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~-----L~-~----~~~R~~CA~La 157 (179)
.|.+.++ +|+|++++-. +.=|+ |+..+++.++|++++++.......+... .+ . ..-.|....+-
T Consensus 134 ~~ei~v~-~~~I~~V~VlR~aPCG----sT~~vAk~l~G~~~~d~~~~~g~~~q~YPC~As~~~d~~~~d~~~h~Ag~i~ 208 (217)
T PF02593_consen 134 KVEIEVE-NGKIKDVKVLRSAPCG----STWFVAKRLIGKEVEDAPEKAGLAHQHYPCRASMGRDFELGDTILHKAGYIH 208 (217)
T ss_pred eEEEEec-CCcEEEEEEEecCCCc----cHHHHHHHhcCCccchhhhhhhhhheecccccccccccccccchhhhhHHHH
Confidence 3445555 6899998754 44454 6788999999999999988885433221 11 1 23355777777
Q ss_pred HHHHHHHH
Q psy10992 158 EDAIKAAL 165 (179)
Q Consensus 158 ~~AL~~Al 165 (179)
.+|+++||
T Consensus 209 ~~Ave~Al 216 (217)
T PF02593_consen 209 KEAVEKAL 216 (217)
T ss_pred HHHHHHhh
Confidence 88888876
No 27
>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=52.29 E-value=70 Score=23.21 Aligned_cols=42 Identities=17% Similarity=0.224 Sum_probs=34.2
Q ss_pred HHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHH
Q psy10992 118 SLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYR 169 (179)
Q Consensus 118 Sil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~ 169 (179)
-.++.++.|+++++|....... ..+.+..-.+.|+.|+.+.+
T Consensus 14 ~~v~~~Irg~~v~~A~~~L~~~----------~~k~a~~i~k~L~~a~~nA~ 55 (105)
T PF00237_consen 14 REVARLIRGMSVDEAIAQLKFV----------PKKAAKFILKLLKSAIANAE 55 (105)
T ss_dssp HHHHHHHTTSBHHHHHHHHHHH----------SSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHhC----------cHHHHHHHHhhHHHHHhhcc
Confidence 4678899999999998877653 35678888889999998887
No 28
>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=50.53 E-value=26 Score=24.18 Aligned_cols=25 Identities=20% Similarity=0.178 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHhhh
Q psy10992 113 AIASSSLATEWVKGKTVDEALKLKN 137 (179)
Q Consensus 113 s~ASASil~e~~~GKtl~Ea~~i~~ 137 (179)
...++..++.+++|||++|+..+-.
T Consensus 32 ~~~~~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 32 LDLCCKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHcC
Confidence 3456777899999999999988764
No 29
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=48.75 E-value=38 Score=29.32 Aligned_cols=44 Identities=20% Similarity=0.365 Sum_probs=33.7
Q ss_pred CcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc
Q psy10992 98 GKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKEL 144 (179)
Q Consensus 98 g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L 144 (179)
-||..=.-.|.||++|- ++.+++++|.++.||..--.+++...+
T Consensus 200 ~ri~t~~tHGTGCTlSa---AIaa~LA~G~~l~~AV~~Ak~fv~~AI 243 (263)
T COG0351 200 PRIPTKNTHGTGCTLSA---AIAANLAKGLSLEEAVKKAKEFVTRAI 243 (263)
T ss_pred cccCCCCCCCccHHHHH---HHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 35544445899999864 566777999999999998888876665
No 30
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=47.60 E-value=17 Score=32.25 Aligned_cols=44 Identities=11% Similarity=0.063 Sum_probs=32.7
Q ss_pred CcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc
Q psy10992 98 GKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKEL 144 (179)
Q Consensus 98 g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L 144 (179)
.+|..-.|.|.||.++-|-| +.++.|.++.+|.....+++...+
T Consensus 240 ~ri~~~~~hGTGc~fASAIA---a~LA~G~~l~~Av~~A~~fv~~aI 283 (321)
T PTZ00493 240 KRKPGKDIHGTGCTLSTAIA---CYLAKKHNILQSCIESKKYIYNCI 283 (321)
T ss_pred cccCCCCCCChHHHHHHHHH---HHHHcCCCHHHHHHHHHHHHHHHH
Confidence 35554567899999876555 455889999999999888765443
No 31
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=45.86 E-value=53 Score=29.20 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=38.0
Q ss_pred HHHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHH
Q psy10992 116 SSSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYR 169 (179)
Q Consensus 116 SASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~ 169 (179)
=+-.++.++.|+++++|..+.... ..++|.+-.+.|+.|+++++
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 356789999999999999887653 67899999999999999987
No 32
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=44.91 E-value=68 Score=24.57 Aligned_cols=44 Identities=20% Similarity=0.346 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCHHHHHHhhhHhHHhhcCCCCCcchhhHHHHHHHHHHHHHHHH
Q psy10992 117 SSLATEWVKGKTVDEALKLKNTDIAKELCLPPVKLHCSMLAEDAIKAALSDYRI 170 (179)
Q Consensus 117 ASil~e~~~GKtl~Ea~~i~~~~i~~~L~~~~~R~~CA~La~~AL~~Al~~y~~ 170 (179)
+..++.++.|+++++|..+.... ..+-+-...+.|+.|+.+.+.
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~~~----------pkKaa~~v~KvL~sA~aNAe~ 68 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILEFV----------PKKAAKLVKKVLESAIANAEN 68 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHHhC----------hHHHHHHHHHHHHHHHhhHHh
Confidence 56789999999999999985442 345556667777777777665
No 33
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=42.71 E-value=14 Score=20.35 Aligned_cols=14 Identities=29% Similarity=0.904 Sum_probs=11.8
Q ss_pred ccccCCCCcccCCc
Q psy10992 19 CSLHSSGGTCRTNN 32 (179)
Q Consensus 19 ~~~~~~~~~~~~~~ 32 (179)
|.....||+||-.+
T Consensus 3 C~yEl~Gg~Cnd~~ 16 (23)
T PF10650_consen 3 CPYELTGGVCNDPD 16 (23)
T ss_pred CccccCCCeeCCCC
Confidence 88888999998665
No 34
>PF08543 Phos_pyr_kin: Phosphomethylpyrimidine kinase; InterPro: IPR013749 This enzyme 2.7.4.7 from EC is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes []. ; PDB: 2DDW_B 2DDO_B 2DDM_A 3IBQ_A 3H74_A 3HYO_A 1UB0_A 1VI9_D 1TD2_B 2PHP_D ....
Probab=36.21 E-value=21 Score=29.64 Aligned_cols=38 Identities=24% Similarity=0.243 Sum_probs=28.9
Q ss_pred eEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhh
Q psy10992 103 AKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKE 143 (179)
Q Consensus 103 i~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~ 143 (179)
..|.|.||.++-+ +++.+++|+++++|......++...
T Consensus 194 ~~~~GTGd~fss~---laa~l~~g~~l~~Av~~A~~~v~~~ 231 (246)
T PF08543_consen 194 GSFHGTGDLFSSA---LAAFLAKGYSLEEAVEKAKNFVRRA 231 (246)
T ss_dssp SGCTTHHHHHHHH---HHHHHHTTSSHHHHHHHHHHHHHHH
T ss_pred CCCCCchhHHHHH---HHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 5677889988655 5556689999999999888766543
No 35
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=31.75 E-value=86 Score=21.18 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=15.2
Q ss_pred cEEEEEEEECCCCcEEEeEEee
Q psy10992 86 DVMKLQIKVDDNGKIIDAKFKT 107 (179)
Q Consensus 86 D~I~l~l~i~~~g~I~di~F~~ 107 (179)
-.+.|.+.|+.+|+|.++....
T Consensus 26 ~~~~V~i~i~~dG~v~~~~i~~ 47 (85)
T PF13103_consen 26 LSVTVRITIDPDGRVISVRIVK 47 (85)
T ss_dssp --EEEEEEE-TTSBEEEEEEEE
T ss_pred cEEEEEEEECCCCCEEEEEEec
Confidence 4578888888899998876653
No 36
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=30.91 E-value=1.2e+02 Score=27.02 Aligned_cols=43 Identities=19% Similarity=0.133 Sum_probs=31.3
Q ss_pred CcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHH
Q psy10992 85 GDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVD 130 (179)
Q Consensus 85 GD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~ 130 (179)
+-.|++.+.|+ +|+|+++++.++.-. ..--+-+.+.++|...+
T Consensus 262 ~G~v~i~~~v~-~g~I~~~~i~gD~~~--~~~~~~l~~~L~G~~~~ 304 (338)
T PRK03822 262 WGGVELHFDVE-KGHITRAQIFTDSLN--PAPLEALAGRLQGCLYR 304 (338)
T ss_pred CCcEEEEEEEE-CCEEEEEEEECCCCC--cccHHHHHHHhCCCCCC
Confidence 45689999996 799999999987433 33345677778887643
No 37
>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=30.16 E-value=85 Score=27.65 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=31.2
Q ss_pred CcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHH
Q psy10992 85 GDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVD 130 (179)
Q Consensus 85 GD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~ 130 (179)
+..|++++.|+ +|+|+++++.++--.. --.+-+.+.++|...+
T Consensus 257 ~G~v~i~l~v~-~g~I~~~~i~gDf~~~--~~~~~l~~~L~G~~~~ 299 (324)
T TIGR00545 257 AGGFELHVQVE-KGKIVDCKFFGDFLSV--ADITPVTNRLIGQKYD 299 (324)
T ss_pred CCcEEEEEEEe-CCEEEEEEEECCCCCc--ccHHHHHHHhCCCccC
Confidence 55799999996 6999999998774322 2256677778887643
No 38
>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=28.80 E-value=82 Score=21.34 Aligned_cols=24 Identities=21% Similarity=0.364 Sum_probs=16.9
Q ss_pred CCCCCcEEEEEEEECCCC--cEEEeE
Q psy10992 81 APACGDVMKLQIKVDDNG--KIIDAK 104 (179)
Q Consensus 81 np~CGD~I~l~l~i~~~g--~I~di~ 104 (179)
.-.-||.|.|.+...+++ +|++++
T Consensus 42 ~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 42 GLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp S-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred cCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 346699999999987666 677764
No 39
>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=28.22 E-value=80 Score=20.76 Aligned_cols=20 Identities=15% Similarity=0.499 Sum_probs=15.8
Q ss_pred EEEEEEEECCCCcEEEeEEe
Q psy10992 87 VMKLQIKVDDNGKIIDAKFK 106 (179)
Q Consensus 87 ~I~l~l~i~~~g~I~di~F~ 106 (179)
.+.+.+.|+.+|+|.+++-.
T Consensus 17 ~v~v~~~I~~~G~v~~~~v~ 36 (79)
T PF03544_consen 17 TVVVEFTIDPDGRVSDVRVI 36 (79)
T ss_dssp EEEEEEEEETTTEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEEEE
Confidence 57777888888999998644
No 40
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=26.98 E-value=93 Score=20.36 Aligned_cols=21 Identities=19% Similarity=0.526 Sum_probs=13.7
Q ss_pred CCCCCcEEEEEEEECCCCcEE
Q psy10992 81 APACGDVMKLQIKVDDNGKII 101 (179)
Q Consensus 81 np~CGD~I~l~l~i~~~g~I~ 101 (179)
...=||.|.+++..|.++++.
T Consensus 37 ~~~~Gd~v~VFvY~D~~~rl~ 57 (61)
T PF13509_consen 37 PLKVGDEVEVFVYLDKEGRLV 57 (61)
T ss_dssp ---TTSEEEEEEEE-TTS-EE
T ss_pred CCCCCCEEEEEEEECCCCCEE
Confidence 456799999999998767764
No 41
>TIGR00718 sda_alpha L-serine dehydratase, iron-sulfur-dependent, alpha subunit. This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This model describes the alpha chain of an iron-sulfur-dependent L-serine dehydratase, found in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of alpha chains from the homologous region of single chain forms such as found in Escherichia coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases.
Probab=26.57 E-value=3.6e+02 Score=23.78 Aligned_cols=60 Identities=27% Similarity=0.353 Sum_probs=42.0
Q ss_pred cc----hHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhcCC--CCC----cchhhHHHHHHHHHHHHHH
Q psy10992 109 GC----GSAIASSSLATEWVKGKTVDEALKLKNTDIAKELCL--PPV----KLHCSMLAEDAIKAALSDY 168 (179)
Q Consensus 109 GC----ais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L~~--~~~----R~~CA~La~~AL~~Al~~y 168 (179)
|| ..+-|-|+...-++.|-|.+|+..-....+...||+ .|. .+.|+.--.-+...|+...
T Consensus 166 GCqaEvg~A~amAAaai~~l~GGs~eqi~~Aa~~~l~~~lGlvCDpv~GlV~vpC~~Rna~~a~~A~~aa 235 (294)
T TIGR00718 166 GCQAECGSASAMAAAAIVEMAGGTPEQAAEAAAITIINMLGLVCDPIAGLVEVPCTFRNAMGAINAFIAA 235 (294)
T ss_pred CccccccHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhccCCccCCccccccchhHHHHHHHHHHHHHHH
Confidence 77 444444455555678889999988877777777886 466 8888877666666666544
No 42
>PF03313 SDH_alpha: Serine dehydratase alpha chain; InterPro: IPR005130 L-serine dehydratase is found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. This entry also describes a number of proteins with no known function.
Probab=26.27 E-value=2.1e+02 Score=24.74 Aligned_cols=60 Identities=20% Similarity=0.329 Sum_probs=41.8
Q ss_pred cchHHHHHH----HHHHHHhcCCCHHHHHHhhhHhHHhhcCC--CC----CcchhhHHHHHHHHHHHHHH
Q psy10992 109 GCGSAIASS----SLATEWVKGKTVDEALKLKNTDIAKELCL--PP----VKLHCSMLAEDAIKAALSDY 168 (179)
Q Consensus 109 GCais~ASA----Sil~e~~~GKtl~Ea~~i~~~~i~~~L~~--~~----~R~~CA~La~~AL~~Al~~y 168 (179)
||....+++ +...-++.|-|++|+..-....+...+|+ .| .+..|++--.-+...|+...
T Consensus 169 GC~~e~G~a~amAAagi~~l~gG~~~qi~~A~~~~l~n~~GliCDgv~g~vk~~Ca~k~a~~a~~A~~aa 238 (282)
T PF03313_consen 169 GCQAEAGAASAMAAAGIVYLLGGTPEQIEYAAANALGNLLGLICDGVAGLVKIPCALKNASGASAAISAA 238 (282)
T ss_pred hhhhhhhhhHHHHHHHHHHHhCcCHHHHHHHHHHHhcccceeeCCCCcccccccHHHHHHHHHHHHHHHH
Confidence 777664443 22223567889999988888877777786 56 78899887777666666544
No 43
>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=25.89 E-value=2.7e+02 Score=21.41 Aligned_cols=55 Identities=25% Similarity=0.420 Sum_probs=42.5
Q ss_pred EEEEEEEECCCCcEEEe-EEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHh
Q psy10992 87 VMKLQIKVDDNGKIIDA-KFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAK 142 (179)
Q Consensus 87 ~I~l~l~i~~~g~I~di-~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~ 142 (179)
.-.|| .+|..|.+.+. .|.+.|..-..+-.-+=..+-.+.|++||..+...-+..
T Consensus 118 ~~~l~-~vd~~G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~~ea~~~~~~~l~~ 173 (190)
T PF00227_consen 118 GPQLY-SVDPSGSYIECKRFAAIGSGSQFAQPILEKLYKPDLSLEEAIELALKALKE 173 (190)
T ss_dssp EEEEE-EEETTSEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHH
T ss_pred cccee-eeccccccccccccccchhcchhhhHHHHhhccCCCCHHHHHHHHHHHHHH
Confidence 45666 55778999999 699999877777666666666899999999998775543
No 44
>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=25.55 E-value=3.3e+02 Score=21.88 Aligned_cols=55 Identities=25% Similarity=0.321 Sum_probs=42.1
Q ss_pred EEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhh
Q psy10992 88 MKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKE 143 (179)
Q Consensus 88 I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~ 143 (179)
-.|| .+|..|.+....|.+.|..-..+-.-+=..+-.++|++|+.++...-+...
T Consensus 143 ~~ly-~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~y~~~ms~eea~~l~~~al~~~ 197 (213)
T cd03752 143 FQLY-QSDPSGNYSGWKATAIGNNNQAAQSLLKQDYKDDMTLEEALALAVKVLSKT 197 (213)
T ss_pred CEEE-EECCCCCeeeeeEEEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence 3465 456778888999999999888877777777777899999988876654433
No 45
>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=24.94 E-value=1.7e+02 Score=26.17 Aligned_cols=44 Identities=27% Similarity=0.306 Sum_probs=33.1
Q ss_pred EEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHh
Q psy10992 90 LQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKL 135 (179)
Q Consensus 90 l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i 135 (179)
|.++.++++.+..-+-.|+|-+.||--|..|++ +|++.+|++.-
T Consensus 285 F~i~~~~~~~~~~g~G~GHGVGMSQ~GA~~mA~--~G~~y~eIL~h 328 (338)
T TIGR02870 285 FTWKVQGDKIVITTIGYGHGVGMSQYGANAMAK--EGKTYDEILKH 328 (338)
T ss_pred eEEEEcCCEEEEEEeeecCCcCccHHHHHHHHH--cCCCHHHHHHH
Confidence 455555444455556668899999999999998 59999998753
No 46
>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=24.92 E-value=72 Score=20.62 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=13.7
Q ss_pred CCCCCcEEEEEEEECCCCcEEEe
Q psy10992 81 APACGDVMKLQIKVDDNGKIIDA 103 (179)
Q Consensus 81 np~CGD~I~l~l~i~~~g~I~di 103 (179)
.|.+||.|.+...-++.+.|.++
T Consensus 37 ~~~VGD~V~~~~~~~~~~~I~~v 59 (68)
T cd04466 37 PPAVGDRVEFEPEDDGEGVIEEI 59 (68)
T ss_pred CCCCCcEEEEEECCCCcEEEEEE
Confidence 47899999887532222345444
No 47
>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=23.89 E-value=2.1e+02 Score=25.97 Aligned_cols=45 Identities=22% Similarity=0.237 Sum_probs=31.1
Q ss_pred EEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhH
Q psy10992 88 MKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNT 138 (179)
Q Consensus 88 I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~ 138 (179)
++|.+.++++++|.+.+|...--- --+-.+++||+..++..+.+.
T Consensus 17 ~rl~l~vdge~vv~~~~~~~~~~~------RG~Ek~~egr~~~~~~~l~~R 61 (411)
T TIGR03295 17 AKLVLEVDDEGIVEKGDYLSITPV------RGFEKLLVGKTAEFAPIIVSR 61 (411)
T ss_pred eEEEEEEeCCCcEEEEEEeccCcC------cHHHHHHcCCCHHHHHHHHhH
Confidence 677777776688888867632111 225667889999999888863
No 48
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=23.77 E-value=1.6e+02 Score=28.35 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=30.8
Q ss_pred CCcEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCH
Q psy10992 84 CGDVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTV 129 (179)
Q Consensus 84 CGD~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl 129 (179)
-+..|++++.|+ +|+|+++++.++--.. .-.+-+.+.+.|...
T Consensus 485 ~~G~vei~l~V~-~G~I~~~ki~gDf~~~--~~i~~le~~L~G~~y 527 (562)
T PRK14061 485 SWGGVELHFDVE-KGHITRAQVFTDSLNP--APLEALAGRLQGCLY 527 (562)
T ss_pred ccccEEEEEEEe-CCEEEEEEEECCCCCc--ccHHHHHHHhCCCCc
Confidence 356789999996 6999999998874322 224557777788653
No 49
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=23.58 E-value=88 Score=25.92 Aligned_cols=62 Identities=8% Similarity=0.009 Sum_probs=40.1
Q ss_pred EeeccchHHHHHHHHHHHHhcCCCHHHHHHhhh-------------HhHHhh---cCCCCCcchhhHHHHHHHHHHHHHH
Q psy10992 105 FKTFGCGSAIASSSLATEWVKGKTVDEALKLKN-------------TDIAKE---LCLPPVKLHCSMLAEDAIKAALSDY 168 (179)
Q Consensus 105 F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~-------------~~i~~~---L~~~~~R~~CA~La~~AL~~Al~~y 168 (179)
..++.=..++|+||+++.-...+-+++....-. +.+.+. .|..| .++..+|+++++.+.++
T Consensus 128 ~KaD~~~~~VAAASIlAKv~RD~~m~~l~~~y~~~GsGYpsd~~t~~~l~~~~~~~g~~p---~~~R~Sw~~~~~~~~~~ 204 (212)
T PRK14551 128 HGADEEDPLVGAASIVAKVARDAHVAALAAEYGDVGSGYPSDPTTREFLREYVREHGELP---ACARRSWSTCDDVLAAA 204 (212)
T ss_pred ecccchhHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCcCCCcHHHHHHHHHHHHHhCCCc---hhhccCcHHHHHHHHHh
Confidence 345566789999999999888777777655432 112222 23333 25556799999888776
Q ss_pred H
Q psy10992 169 R 169 (179)
Q Consensus 169 ~ 169 (179)
+
T Consensus 205 ~ 205 (212)
T PRK14551 205 E 205 (212)
T ss_pred h
Confidence 3
No 50
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=23.41 E-value=84 Score=21.59 Aligned_cols=20 Identities=25% Similarity=0.622 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCCCCCCCCCC
Q psy10992 51 HENVIDHYENPRNVGSLDKKD 71 (179)
Q Consensus 51 ~~~Ileh~~nP~n~G~l~~~d 71 (179)
++.+++.|.+|.|+ +++.+.
T Consensus 43 ~ke~~d~~n~p~ny-rlE~~s 62 (70)
T PF14410_consen 43 RKEFLDWYNDPDNY-RLEDPS 62 (70)
T ss_pred HHHHHHHHhCccce-eecCCc
Confidence 67899999999998 577765
No 51
>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=23.35 E-value=1.4e+02 Score=21.17 Aligned_cols=44 Identities=25% Similarity=0.389 Sum_probs=28.0
Q ss_pred EEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHH
Q psy10992 88 MKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDE 131 (179)
Q Consensus 88 I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~E 131 (179)
+-+.+.++++|+|++++--.-|-+..---+.-+-+.+.|+.+.+
T Consensus 18 ~a~~~~~~~~~~i~~~ria~g~v~~~p~r~~~~E~~L~g~~~~~ 61 (103)
T PF03450_consen 18 VAVLVSVDDDGRIEDARIAVGGVAPTPVRAEEVEAALIGKPLSE 61 (103)
T ss_dssp EEEEEEEETTSEEEEEEEEEESSSSSTEE-HHHHHHTTTSBSSH
T ss_pred hhheEEEecCceEEEEEEEEeccccceeehHHHHHHHhhcchhh
Confidence 34455555555999998766665555445555666788987654
No 52
>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=23.18 E-value=1.5e+02 Score=25.32 Aligned_cols=43 Identities=23% Similarity=0.221 Sum_probs=31.5
Q ss_pred EEEECCCCcEEEeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHh
Q psy10992 91 QIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWVKGKTVDEALKL 135 (179)
Q Consensus 91 ~l~i~~~g~I~di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i 135 (179)
.+..++++.+..-+-.|+|...||--|..|++. |++.+|++..
T Consensus 216 ~i~~~~~~~~f~g~G~GHGvGmSQ~GA~~mA~~--G~~y~eIL~~ 258 (267)
T TIGR02669 216 SVKSRGNAILFTGKGYGHGVGMSQWGANGLAKL--GKDYREILKH 258 (267)
T ss_pred eeeecCCEEEEEEeecccCccCCHHHHHHHHHc--CCCHHHHHHh
Confidence 334433334445555688999999999999985 9999998764
No 53
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=22.89 E-value=26 Score=26.32 Aligned_cols=29 Identities=34% Similarity=0.661 Sum_probs=21.1
Q ss_pred cccccchhhhh-----------cccccCccccCCCCcccC
Q psy10992 2 SILLNKEMKTQ-----------LHFKFSCSLHSSGGTCRT 30 (179)
Q Consensus 2 ~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~ 30 (179)
|.|-|.|..++ .+|.|.|.+|+..|+...
T Consensus 32 SlL~n~ei~~~GLSTDhltaLa~~~~~~~~~hs~~~~~~~ 71 (104)
T PF05381_consen 32 SLLDNPEIRTLGLSTDHLTALAYRYHFQCTFHSDHGVLHY 71 (104)
T ss_pred hhcCchhhhhcCCcHHHHHHHHHHHheEEEEEcCCceEEe
Confidence 44556666543 367899999999998864
No 54
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]
Probab=22.77 E-value=1.7e+02 Score=27.30 Aligned_cols=21 Identities=43% Similarity=0.697 Sum_probs=15.8
Q ss_pred EEEEEECCCCcEEEeEEeecc
Q psy10992 89 KLQIKVDDNGKIIDAKFKTFG 109 (179)
Q Consensus 89 ~l~l~i~~~g~I~di~F~~~G 109 (179)
.+.+.|+++|.+++.+|.+.+
T Consensus 18 kv~i~vdd~G~V~~~~~~it~ 38 (441)
T COG3259 18 KVTIEVDDDGIVEDARFHITE 38 (441)
T ss_pred EEEEEEcCCCceeeeEEEecc
Confidence 455566777999999998654
No 55
>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=22.41 E-value=1.8e+02 Score=17.52 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=22.9
Q ss_pred eccchHHHHHHHHHHHHhcCCCHHHHHHhh
Q psy10992 107 TFGCGSAIASSSLATEWVKGKTVDEALKLK 136 (179)
Q Consensus 107 ~~GCais~ASASil~e~~~GKtl~Ea~~i~ 136 (179)
..||.++++.=+..+.. .|.|.+|+.++.
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 56999999998776654 699999887754
No 56
>PF03891 DUF333: Domain of unknown function (DUF333); InterPro: IPR005590 This family consists of bacterial proteins whose function has not been characterised.
Probab=22.27 E-value=38 Score=21.91 Aligned_cols=21 Identities=14% Similarity=0.134 Sum_probs=15.7
Q ss_pred CCCcccCCcccccccCCCCCcchHhhhHH
Q psy10992 24 SGGTCRTNNATTLLKSPKWASTPVLHYHE 52 (179)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~lY~~ 52 (179)
.-|.|.++||+.++ .|++|+.
T Consensus 28 ~~g~C~lpdG~~~~--------eW~l~r~ 48 (50)
T PF03891_consen 28 QVGYCVLPDGRRCE--------EWALYRG 48 (50)
T ss_pred eEeEEECCCCCEEe--------HHHHhhc
Confidence 45899999999854 4777763
No 57
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=21.92 E-value=92 Score=25.50 Aligned_cols=40 Identities=30% Similarity=0.365 Sum_probs=28.2
Q ss_pred EeEEeeccchHHHHHHHHHHHHhcCCCHHHHHHhhhHhHHhhc
Q psy10992 102 DAKFKTFGCGSAIASSSLATEWVKGKTVDEALKLKNTDIAKEL 144 (179)
Q Consensus 102 di~F~~~GCais~ASASil~e~~~GKtl~Ea~~i~~~~i~~~L 144 (179)
.+...|-||++ ++.+++.++.|.+++|+..+-...+.+.|
T Consensus 201 ~~~~~GaGDaf---~a~~~~~l~~g~~l~ea~~~A~~~~~~~l 240 (253)
T PRK12413 201 EKNNIGAGCTF---ASSIASQLVKGKSPLEAVKNSKDFVYQAI 240 (253)
T ss_pred CCCCCChHHHH---HHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 34455666666 55667777899999999988877655443
No 58
>KOG1724|consensus
Probab=21.83 E-value=94 Score=24.92 Aligned_cols=25 Identities=20% Similarity=0.182 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHhh
Q psy10992 112 SAIASSSLATEWVKGKTVDEALKLK 136 (179)
Q Consensus 112 is~ASASil~e~~~GKtl~Ea~~i~ 136 (179)
+.-.++-.++.+++|||.+|...+-
T Consensus 115 Ll~~~ck~va~mikgktpeEir~~f 139 (162)
T KOG1724|consen 115 LLDLTCKTVANMIKGKTPEEIREIF 139 (162)
T ss_pred HHHHHHHHHHHHHccCCHHHHHHHc
Confidence 4556677889999999999988774
No 59
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=21.45 E-value=1.1e+02 Score=20.19 Aligned_cols=17 Identities=35% Similarity=0.698 Sum_probs=11.9
Q ss_pred cEEEEEEEECCCCcEEEeE
Q psy10992 86 DVMKLQIKVDDNGKIIDAK 104 (179)
Q Consensus 86 D~I~l~l~i~~~g~I~di~ 104 (179)
|++.|. +|++|+|+++.
T Consensus 42 dRLnv~--~D~~g~I~~v~ 58 (60)
T PF11720_consen 42 DRLNVE--VDDDGVITRVR 58 (60)
T ss_pred CcEEEE--ECCCCcEEEEe
Confidence 556665 45678999885
No 60
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=21.14 E-value=2.5e+02 Score=22.56 Aligned_cols=47 Identities=15% Similarity=0.294 Sum_probs=31.9
Q ss_pred ECCCCcEEEeEEeeccchHHHHHHHHHHHH-hcCCCHHHHHHhhhHhHH
Q psy10992 94 VDDNGKIIDAKFKTFGCGSAIASSSLATEW-VKGKTVDEALKLKNTDIA 141 (179)
Q Consensus 94 i~~~g~I~di~F~~~GCais~ASASil~e~-~~GKtl~Ea~~i~~~~i~ 141 (179)
+.+||.|+ ---.+-.|.+|+--|.....+ =+|||+.|+++.+++.-.
T Consensus 99 ~~~dG~Vv-wd~Hg~~C~vCl~ia~~a~~~~~~Gks~~eIR~~ID~kYk 146 (158)
T PF13798_consen 99 IKEDGSVV-WDDHGTRCGVCLDIAVQAVQMYQEGKSPKEIRQYIDEKYK 146 (158)
T ss_pred ccCCCcee-ecccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 44567653 222366899998766655554 479999999998876433
No 61
>COG3064 TolA Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]
Probab=20.94 E-value=1.9e+02 Score=26.10 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=30.9
Q ss_pred cEEEEEEEECCCCcEEEeEEeeccchHHHHHHHHHHHHh
Q psy10992 86 DVMKLQIKVDDNGKIIDAKFKTFGCGSAIASSSLATEWV 124 (179)
Q Consensus 86 D~I~l~l~i~~~g~I~di~F~~~GCais~ASASil~e~~ 124 (179)
-+.+|.|++-+||.|.++.-.+---.+|+|+-|+++...
T Consensus 326 K~C~l~ikL~pdGtl~~~~~~~Gd~~lCqAalsAvAk~~ 364 (387)
T COG3064 326 KTCRLRIKLAPDGTLLDIKPEGGDPALCQAALSAVAKTA 364 (387)
T ss_pred ceeEEEEEEcCCcceeeccccCCChHHHHHHHHHHHHhc
Confidence 334666666678999999888888899999999888764
Done!