Query 034618
Match_columns 89
No_of_seqs 127 out of 1022
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 04:43:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034618.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034618hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11325 scaffold protein; Pro 99.9 1.2E-25 2.5E-30 152.8 7.8 71 1-72 56-126 (127)
2 TIGR01999 iscU FeS cluster ass 99.9 3E-25 6.5E-30 150.0 7.6 70 1-71 54-123 (124)
3 TIGR03419 NifU_clost FeS clust 99.9 3.1E-25 6.7E-30 149.5 7.4 71 1-72 50-121 (121)
4 COG0822 IscU NifU homolog invo 99.9 1.6E-22 3.5E-27 141.4 6.7 72 1-73 57-147 (150)
5 TIGR02000 NifU_proper Fe-S clu 99.9 6.7E-22 1.4E-26 150.2 7.3 72 1-73 55-127 (290)
6 PF01592 NifU_N: NifU-like N t 99.9 2E-21 4.4E-26 131.2 7.3 70 1-71 54-124 (126)
7 KOG3361 Iron binding protein i 99.9 2.4E-21 5.3E-26 134.6 7.8 73 2-75 83-155 (157)
8 cd06664 IscU_like Iron-sulfur 99.8 3E-20 6.6E-25 124.0 5.7 62 1-63 51-123 (123)
9 TIGR01994 SUF_scaf_2 SUF syste 99.8 2.6E-19 5.7E-24 122.9 5.7 64 1-65 54-137 (137)
10 PRK15019 CsdA-binding activato 92.3 0.72 1.6E-05 32.3 6.4 51 13-67 89-143 (147)
11 PRK09296 cysteine desufuration 92.0 0.84 1.8E-05 31.6 6.4 52 13-68 79-134 (138)
12 COG0351 ThiD Hydroxymethylpyri 91.6 0.24 5.2E-06 37.8 3.6 36 4-43 208-243 (263)
13 TIGR03391 FeS_syn_CsdE cystein 90.7 1.2 2.7E-05 30.7 6.1 48 13-64 84-135 (138)
14 cd00336 Ribosomal_L22 Ribosoma 84.8 3.7 7.9E-05 26.5 5.3 47 17-73 16-62 (105)
15 TIGR01044 rplV_bact ribosomal 84.6 3.6 7.9E-05 26.9 5.2 47 17-73 14-60 (103)
16 COG2166 sufE Cysteine desulfur 84.4 4 8.6E-05 28.7 5.6 50 13-66 84-137 (144)
17 PF08543 Phos_pyr_kin: Phospho 84.2 0.91 2E-05 33.1 2.4 35 2-40 195-229 (246)
18 PRK00565 rplV 50S ribosomal pr 84.1 3.7 8.1E-05 27.1 5.2 49 16-74 17-65 (112)
19 PTZ00493 phosphomethylpyrimidi 82.6 1.4 3E-05 34.4 2.9 36 3-42 247-282 (321)
20 PF02657 SufE: Fe-S metabolism 76.7 5.7 0.00012 26.7 4.2 38 13-51 70-111 (125)
21 PF00237 Ribosomal_L22: Riboso 76.3 12 0.00026 24.0 5.6 48 17-74 14-61 (105)
22 PRK04223 rpl22p 50S ribosomal 75.8 13 0.00029 26.2 6.0 55 16-70 30-104 (153)
23 TIGR01038 L22_arch ribosomal p 75.7 14 0.0003 26.0 6.1 54 16-69 26-101 (150)
24 cd01169 HMPP_kinase 4-amino-5- 75.1 3.6 7.8E-05 29.1 3.0 36 2-41 202-237 (242)
25 CHL00034 rpl22 ribosomal prote 74.3 13 0.00028 24.9 5.4 47 17-73 25-71 (117)
26 PTZ00178 60S ribosomal protein 73.9 14 0.0003 26.9 5.8 54 16-69 29-104 (181)
27 PRK12412 pyridoxal kinase; Rev 73.6 3.8 8.2E-05 30.1 2.9 35 5-43 210-244 (268)
28 cd01173 pyridoxal_pyridoxamine 71.4 5 0.00011 28.8 3.1 35 3-41 213-247 (254)
29 PRK08176 pdxK pyridoxal-pyrido 69.9 5.3 0.00012 29.7 3.0 36 2-41 227-262 (281)
30 PRK05756 pyridoxamine kinase; 69.5 5.6 0.00012 29.3 3.1 36 2-41 216-251 (286)
31 PRK08573 phosphomethylpyrimidi 69.0 12 0.00026 29.8 5.0 35 3-41 206-240 (448)
32 PRK12616 pyridoxal kinase; Rev 68.9 5.4 0.00012 29.4 2.9 36 4-43 212-247 (270)
33 PF01466 Skp1: Skp1 family, di 68.8 5.1 0.00011 24.6 2.3 23 14-36 34-56 (78)
34 PRK12279 50S ribosomal protein 67.6 18 0.00039 28.4 5.6 43 16-68 17-59 (311)
35 PLN02673 quinolinate synthetas 66.6 29 0.00063 30.2 7.0 52 10-67 155-211 (724)
36 PRK07105 pyridoxamine kinase; 64.3 8.2 0.00018 28.4 3.0 37 3-43 217-253 (284)
37 PRK06427 bifunctional hydroxy- 64.0 8.6 0.00019 27.8 3.1 35 2-40 209-243 (266)
38 TIGR00097 HMP-P_kinase phospho 62.7 9.2 0.0002 27.7 3.0 34 3-40 202-235 (254)
39 COG0091 RplV Ribosomal protein 57.9 37 0.0008 23.1 5.1 48 16-73 25-72 (120)
40 PTZ00347 phosphomethylpyrimidi 57.4 12 0.00026 30.2 3.1 37 3-43 440-476 (504)
41 PRK12413 phosphomethylpyrimidi 54.1 16 0.00036 26.1 3.1 35 3-41 204-238 (253)
42 PLN02898 HMP-P kinase/thiamin- 53.7 15 0.00033 29.6 3.1 37 3-43 215-251 (502)
43 PLN02978 pyridoxal kinase 50.8 19 0.0004 27.3 3.1 36 2-41 227-263 (308)
44 PRK09517 multifunctional thiam 50.8 16 0.00035 31.3 2.9 35 3-41 446-480 (755)
45 TIGR00718 sda_alpha L-serine d 48.6 1E+02 0.0023 24.0 6.9 54 14-67 176-235 (294)
46 PRK14713 multifunctional hydro 46.8 22 0.00048 29.0 3.1 34 3-40 234-267 (530)
47 KOG1724 SCF ubiquitin ligase, 45.4 21 0.00045 25.4 2.4 22 15-36 119-140 (162)
48 TIGR00687 pyridox_kin pyridoxa 44.9 25 0.00054 25.8 2.9 36 4-43 219-254 (286)
49 PF03313 SDH_alpha: Serine deh 43.7 89 0.0019 23.7 5.8 60 7-67 169-238 (282)
50 PF10312 Cactin_mid: Conserved 41.6 1.1E+02 0.0024 22.0 5.8 50 15-70 132-183 (191)
51 PTZ00344 pyridoxal kinase; Pro 38.2 38 0.00082 25.3 3.0 34 2-40 220-253 (296)
52 PRK14551 rnhB ribonuclease HII 37.9 42 0.0009 24.5 3.1 55 9-67 134-204 (212)
53 KOG2854 Possible pfkB family c 36.3 45 0.00098 26.6 3.2 32 3-36 291-322 (343)
54 PRK11470 hypothetical protein; 34.5 30 0.00066 25.4 1.9 21 45-65 111-131 (200)
55 cd01166 KdgK 2-keto-3-deoxyglu 32.2 45 0.00098 23.8 2.5 23 15-37 260-282 (294)
56 PRK10030 hypothetical protein; 31.1 30 0.00064 25.0 1.4 20 45-64 121-140 (197)
57 COG5201 SKP1 SCF ubiquitin lig 30.4 53 0.0012 23.2 2.5 22 15-36 114-135 (158)
58 PF13068 DUF3932: Protein of u 30.3 37 0.0008 21.3 1.5 22 52-73 27-48 (81)
59 PTZ00397 macrophage migration 27.2 48 0.001 21.3 1.7 28 24-51 67-97 (116)
60 cd01171 YXKO-related B.subtili 25.6 71 0.0015 22.9 2.6 30 3-36 197-226 (254)
61 PRK01964 4-oxalocrotonate taut 25.1 43 0.00094 19.2 1.1 28 23-50 9-39 (64)
62 PRK11316 bifunctional heptose 24.8 72 0.0016 25.1 2.6 29 5-37 261-289 (473)
63 TIGR02198 rfaE_dom_I rfaE bifu 24.7 76 0.0017 23.1 2.6 31 5-37 261-291 (315)
64 PF14131 DUF4298: Domain of un 24.2 51 0.0011 20.9 1.4 25 44-68 55-79 (90)
65 PRK00157 rplL 50S ribosomal pr 24.2 93 0.002 21.3 2.8 31 16-47 5-35 (123)
66 cd01945 ribokinase_group_B Rib 23.6 94 0.002 22.1 2.9 32 4-37 236-267 (284)
67 KOG2598 Phosphomethylpyrimidin 23.0 83 0.0018 26.4 2.7 33 4-40 246-278 (523)
68 PRK13508 tagatose-6-phosphate 22.8 96 0.0021 22.7 2.9 32 4-37 247-278 (309)
69 TIGR02947 SigH_actino RNA poly 22.8 1.7E+02 0.0036 19.9 3.9 36 37-72 151-187 (193)
70 PRK02220 4-oxalocrotonate taut 22.4 54 0.0012 18.4 1.2 29 22-50 8-39 (61)
71 PF13529 Peptidase_C39_2: Pept 22.1 76 0.0017 19.6 1.9 29 5-43 13-41 (144)
72 COG3580 Uncharacterized protei 21.5 1.5E+02 0.0033 23.7 3.8 65 3-78 279-344 (351)
73 COG0164 RnhB Ribonuclease HII 21.2 1.2E+02 0.0025 22.4 2.9 59 9-72 122-196 (199)
74 PRK10294 6-phosphofructokinase 20.8 1.1E+02 0.0025 22.3 2.9 32 4-37 250-281 (309)
75 PRK02919 oxaloacetate decarbox 20.7 84 0.0018 19.9 1.9 14 59-72 69-82 (82)
76 PF12854 PPR_1: PPR repeat 20.6 1.4E+02 0.003 15.1 2.8 31 7-37 2-32 (34)
77 PRK09813 fructoselysine 6-kina 20.6 1.2E+02 0.0025 21.6 2.9 33 3-37 216-248 (260)
78 TIGR00013 taut 4-oxalocrotonat 20.6 1.1E+02 0.0023 17.2 2.2 27 24-50 10-39 (63)
79 cd01170 THZ_kinase 4-methyl-5- 20.5 1E+02 0.0022 22.5 2.5 30 3-36 184-213 (242)
No 1
>PRK11325 scaffold protein; Provisional
Probab=99.93 E-value=1.2e-25 Score=152.82 Aligned_cols=71 Identities=54% Similarity=0.851 Sum_probs=68.2
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcC
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRT 72 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~ 72 (89)
++|+|+||++| +||+|+|+++++|||++|+..|+.+++.+.||+||+|+|||+|+|+||++||++|..++.
T Consensus 56 ~~f~~~GC~is-~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~~~~~ 126 (127)
T PRK11325 56 AKFKTYGCGSA-IASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQA 126 (127)
T ss_pred EEEEeeCCHHH-HHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHhhcC
Confidence 47999999999 999999999999999999999999999999999999999999999999999999988764
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=99.92 E-value=3e-25 Score=150.04 Aligned_cols=70 Identities=60% Similarity=0.835 Sum_probs=67.3
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhc
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKR 71 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~ 71 (89)
++|+|+||++| +||+|+|+|+++|||++|+..|+++++.+.||+||+|+|||.|+|+||++||++|+.++
T Consensus 54 ~~f~~~GC~~s-~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~~~~ 123 (124)
T TIGR01999 54 AKFKTFGCGSA-IASSSLATELIKGKSLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQ 123 (124)
T ss_pred EEEEecCcHHH-HHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHHhc
Confidence 47999999999 99999999999999999999999999999999999999999999999999999998765
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=99.92 E-value=3.1e-25 Score=149.54 Aligned_cols=71 Identities=41% Similarity=0.656 Sum_probs=67.8
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc-CCCCcchhhHHHHHHHHHHHHHHHHHhcC
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKRT 72 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L-glpp~Ri~CA~La~~AL~~Al~~y~~k~~ 72 (89)
++|+|+||++| +||+|+|+++++|||++|+..|+.+++.+.| ++||+|+|||+|+|+||++|+++|+.+++
T Consensus 50 ~~f~~~GC~is-~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~~~~ 121 (121)
T TIGR03419 50 VKFKTFGCGAA-IASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 (121)
T ss_pred EEEEEeccHHH-HHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHhccC
Confidence 47999999999 9999999999999999999999999999999 59999999999999999999999998864
No 4
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.87 E-value=1.6e-22 Score=141.41 Aligned_cols=72 Identities=43% Similarity=0.607 Sum_probs=64.6
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcch--hHHHHhhcC-----------------CCCcchhhHHHHHHHHH
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIK--NTEIAKHLS-----------------LPPVKLHCSMLAEDAIK 61 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~--~~~i~e~Lg-----------------lpp~Ri~CA~La~~AL~ 61 (89)
.+|+|.||++| +||+|||+|+++|||++||+.|+ ..++.+.+| +||.|+||++|+|+||+
T Consensus 57 ~~F~~~GC~is-~ASss~~te~v~Gkti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~ 135 (150)
T COG0822 57 AKFKGFGCAIS-IASSSMMTELVKGKTLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALK 135 (150)
T ss_pred EEeeecCcHHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhHhhhhhccccccccchhccHHHHH
Confidence 37999999999 99999999999999999999999 556665543 69999999999999999
Q ss_pred HHHHHHHHhcCC
Q 034618 62 AAVKDYEAKRTK 73 (89)
Q Consensus 62 ~Al~~y~~k~~~ 73 (89)
++|++|+.++..
T Consensus 136 ~ai~~~~~~~~~ 147 (150)
T COG0822 136 AAIKDYKGKAEE 147 (150)
T ss_pred HHHHHhhccccc
Confidence 999999988654
No 5
>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=99.86 E-value=6.7e-22 Score=150.18 Aligned_cols=72 Identities=32% Similarity=0.576 Sum_probs=67.9
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc-CCCCcchhhHHHHHHHHHHHHHHHHHhcCC
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L-glpp~Ri~CA~La~~AL~~Al~~y~~k~~~ 73 (89)
.+|+|+||++| +||+|+|+++++|||++|+..|+.+++.++| |+||+|+|||.|+|+||++||++|..+...
T Consensus 55 ~~F~~~GCais-~ASAs~~~eli~Gktv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~kp~~ 127 (290)
T TIGR02000 55 AGFQTFGCGSA-IASSSALTEMIKGLTLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLE 127 (290)
T ss_pred EEEEecCcHHH-HHHHHHHHHHHcCCCHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhcCccc
Confidence 37999999999 9999999999999999999999999999999 699999999999999999999999877554
No 6
>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=99.85 E-value=2e-21 Score=131.21 Aligned_cols=70 Identities=39% Similarity=0.575 Sum_probs=66.4
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc-CCCCcchhhHHHHHHHHHHHHHHHHHhc
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL-SLPPVKLHCSMLAEDAIKAAVKDYEAKR 71 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L-glpp~Ri~CA~La~~AL~~Al~~y~~k~ 71 (89)
++|+++||+++ +||+|+|+++++|||++||..|+.+++.+.| ++|+.|.||+.|++.||+++|++|+.|+
T Consensus 54 ~~f~~~GC~~~-~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~r~ 124 (126)
T PF01592_consen 54 AKFQGFGCAIS-IASASMMCELIKGKTLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPARH 124 (126)
T ss_dssp EEEEEESSHHH-HHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHHHC
T ss_pred EEEEeecChHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHhhh
Confidence 48999999998 9999999999999999999999999999999 5999999999999999999999999886
No 7
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=99.85 E-value=2.4e-21 Score=134.58 Aligned_cols=73 Identities=64% Similarity=0.926 Sum_probs=70.8
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCC
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTKPS 75 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~~~ 75 (89)
+|.+.||... +||+|++|||++|||+||+..|.+.+|...|.|||-+.||++|+.+|++.||+||+.||....
T Consensus 83 kFKTFGCGSA-IASSS~aTewvkgkt~dea~kIkNteIAKeL~LPPVKLHCSMLAEDAIKaAikdyk~Kq~~~~ 155 (157)
T KOG3361|consen 83 KFKTFGCGSA-IASSSLATEWVKGKTLDEALKIKNTEIAKELSLPPVKLHCSMLAEDAIKAAIKDYKEKQNKPN 155 (157)
T ss_pred eeeecccchH-hhhhHHHHHHHccccHHHHHhcccHHHHHhccCCchhhhhHHHHHHHHHHHHHHHHHhccCCC
Confidence 7999999998 999999999999999999999999999999999999999999999999999999999998765
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=99.81 E-value=3e-20 Score=123.98 Aligned_cols=62 Identities=37% Similarity=0.496 Sum_probs=56.4
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhh----------c-CCCCcchhhHHHHHHHHHHH
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKH----------L-SLPPVKLHCSMLAEDAIKAA 63 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~----------L-glpp~Ri~CA~La~~AL~~A 63 (89)
++|.|+||++| +||+|+|+++++||+++|+..|+++++... + ++||+|+||++|+|+||+++
T Consensus 51 ~~f~~~GC~i~-~Asas~~~~~~~Gk~~~ea~~i~~~~~~~~~~~~~l~~~~~~~~~~~R~~Ca~L~~~Al~~a 123 (123)
T cd06664 51 AKFQGFGCAIS-IASASLLTELIKGKTLDEALKLLNKDIAMLDGKEELAALAGVGLPPARIHCALLAWKALKAA 123 (123)
T ss_pred EEEEecCcHHH-HHHHHHHHHHHcCCcHHHHHHHHHHHHHHhcCchhHHHhcccccCcccchHHHHHHHHHHhC
Confidence 47999999998 999999999999999999999999876554 2 57999999999999999874
No 9
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=99.78 E-value=2.6e-19 Score=122.85 Aligned_cols=64 Identities=28% Similarity=0.419 Sum_probs=54.4
Q ss_pred CceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHH---HH--------------hhc-CC--CCcchhhHHHHHHHH
Q 034618 1 MNYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTE---IA--------------KHL-SL--PPVKLHCSMLAEDAI 60 (89)
Q Consensus 1 ~~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~---i~--------------e~L-gl--pp~Ri~CA~La~~AL 60 (89)
++|+|+||+|| +||+|+|+++++|||++|+..+.+.. +. ..| ++ +|+|+||++|+|+||
T Consensus 54 ~~f~~~GCais-~Asas~~~e~i~Gk~~~ea~~l~~~~~~ml~~~~~~~~~~~l~dl~~l~~v~~~p~R~~Ca~L~~~al 132 (137)
T TIGR01994 54 IAFEGEGCSIS-QASASMMTELIKGKTVEEALSLVEAFSEMIQGQETDEDEEKLGDAEALAGVAKFPARIKCATLAWKAL 132 (137)
T ss_pred EEEEecccHHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCCCccccccchHHHhhccccCcchHHHHHHHHHHH
Confidence 47999999998 99999999999999999999998741 10 122 33 799999999999999
Q ss_pred HHHHH
Q 034618 61 KAAVK 65 (89)
Q Consensus 61 ~~Al~ 65 (89)
++||+
T Consensus 133 ~~al~ 137 (137)
T TIGR01994 133 ERALA 137 (137)
T ss_pred HHHhC
Confidence 99974
No 10
>PRK15019 CsdA-binding activator; Provisional
Probab=92.33 E-value=0.72 Score=32.30 Aligned_cols=51 Identities=16% Similarity=0.102 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHcchhHHHHhhcC----CCCcchhhHHHHHHHHHHHHHHH
Q 034618 13 GVSNVSATEWVKGKQIQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIKAAVKDY 67 (89)
Q Consensus 13 ~ASaS~~telikGktl~Ea~~i~~~~i~e~Lg----lpp~Ri~CA~La~~AL~~Al~~y 67 (89)
..=.+++.+.+.|+|.+|++.++.++..+.|| |.|.|.+ +..++-+.|+.|
T Consensus 89 kGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~N----Gl~ami~~I~~~ 143 (147)
T PRK15019 89 RGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQ----GLNALSEAIIAA 143 (147)
T ss_pred HHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCccHHH----HHHHHHHHHHHH
Confidence 46678999999999999999999988888886 6899987 556666666555
No 11
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=92.04 E-value=0.84 Score=31.56 Aligned_cols=52 Identities=12% Similarity=0.087 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHcchhHHHHhhcC----CCCcchhhHHHHHHHHHHHHHHHH
Q 034618 13 GVSNVSATEWVKGKQIQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIKAAVKDYE 68 (89)
Q Consensus 13 ~ASaS~~telikGktl~Ea~~i~~~~i~e~Lg----lpp~Ri~CA~La~~AL~~Al~~y~ 68 (89)
..=.+++...+.|+|.+|+.+++..+..+.|| |.|.|.+ ++.++-+-|+++-
T Consensus 79 kGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSpsR~n----Gl~aml~~ik~~a 134 (138)
T PRK09296 79 KGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTPSRSQ----GLEAMIRAIRAKA 134 (138)
T ss_pred HHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCccHHH----HHHHHHHHHHHHH
Confidence 46678999999999999999999776677775 6899987 5666666665553
No 12
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=91.64 E-value=0.24 Score=37.82 Aligned_cols=36 Identities=17% Similarity=0.175 Sum_probs=29.3
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
-|.||+.| +++.+++++|.++.||..---+.+...+
T Consensus 208 HGTGCTlS----aAIaa~LA~G~~l~~AV~~Ak~fv~~AI 243 (263)
T COG0351 208 HGTGCTLS----AAIAANLAKGLSLEEAVKKAKEFVTRAI 243 (263)
T ss_pred CCccHHHH----HHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 37799887 7888999999999999887777665554
No 13
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=90.70 E-value=1.2 Score=30.75 Aligned_cols=48 Identities=19% Similarity=0.165 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHcchhHHHHhhcC----CCCcchhhHHHHHHHHHHHH
Q 034618 13 GVSNVSATEWVKGKQIQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIKAAV 64 (89)
Q Consensus 13 ~ASaS~~telikGktl~Ea~~i~~~~i~e~Lg----lpp~Ri~CA~La~~AL~~Al 64 (89)
..=.+++.+.+.|+|.+|+..++.++....|| |.|.|.+ ++.++-+.|
T Consensus 84 kGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSpsR~N----Gl~am~~~I 135 (138)
T TIGR03391 84 RGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSASRSN----GLAALAAAI 135 (138)
T ss_pred HHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCccHHH----HHHHHHHHH
Confidence 46678999999999999999999988888885 6899987 444444443
No 14
>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=84.85 E-value=3.7 Score=26.48 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=38.0
Q ss_pred HHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCC
Q 034618 17 VSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 17 S~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~ 73 (89)
-.++.+++|++++||..+-..- ..+.+.+-.+.|+.|..+...+.+.
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~~~----------~kk~a~~i~k~l~sa~~nA~~~~~~ 62 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLEFV----------PKKAAKIILKLLKSAEANAENNGLD 62 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHHhC----------CHHHHHHHHHHHHHHHHhHHHcCCC
Confidence 3578899999999998766552 3678889999999999999876654
No 15
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=84.55 E-value=3.6 Score=26.85 Aligned_cols=47 Identities=15% Similarity=0.238 Sum_probs=37.4
Q ss_pred HHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCC
Q 034618 17 VSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 17 S~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~ 73 (89)
-.++.+|+|++++||..+-.- ...+.|..-.+.|+.|+.++....+.
T Consensus 14 ~~va~~IrG~~v~~A~~~L~f----------~pkk~a~~i~klL~sA~aNA~~~~~l 60 (103)
T TIGR01044 14 RLVADLIRGKSVSQALDILRF----------TPKKAAPLIKKVLASAIANAEHNYGL 60 (103)
T ss_pred HHHHHHHcCCcHHHHHHHHhh----------CCHhHHHHHHHHHHHHHHHHHHccCC
Confidence 457889999999999876652 36679999999999999998644443
No 16
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=84.36 E-value=4 Score=28.74 Aligned_cols=50 Identities=18% Similarity=0.203 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHcchhHHHHhhcC----CCCcchhhHHHHHHHHHHHHHH
Q 034618 13 GVSNVSATEWVKGKQIQEVLSIKNTEIAKHLS----LPPVKLHCSMLAEDAIKAAVKD 66 (89)
Q Consensus 13 ~ASaS~~telikGktl~Ea~~i~~~~i~e~Lg----lpp~Ri~CA~La~~AL~~Al~~ 66 (89)
-.=.+++.+.+.|+|.+|+..++..+..+.|| |+|.|.+ +.+++-+.|+.
T Consensus 84 rGL~aill~~~~G~t~~eI~~~~~~~~f~~LGL~~~LSpsR~n----Gl~am~~~i~~ 137 (144)
T COG2166 84 RGLLAILLAAYSGKTAAEILAFDPLDFFEELGLAQHLSPSRSN----GLEAMLKRIKR 137 (144)
T ss_pred HHHHHHHHHHHcCCCHHHHHcCCHHHHHHHhhHHHhcChHHhh----HHHHHHHHHHH
Confidence 45578999999999999999999988888886 6899977 44555444443
No 17
>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=84.18 E-value=0.91 Score=33.13 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=28.8
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
+|-|.||..| +.+++.+++|+++++|.....+.+.
T Consensus 195 ~~~GTGd~fs----s~laa~l~~g~~l~~Av~~A~~~v~ 229 (246)
T PF08543_consen 195 SFHGTGDLFS----SALAAFLAKGYSLEEAVEKAKNFVR 229 (246)
T ss_dssp GCTTHHHHHH----HHHHHHHHTTSSHHHHHHHHHHHHH
T ss_pred CCCCchhHHH----HHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 5778898887 7788889999999999888776544
No 18
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=84.12 E-value=3.7 Score=27.14 Aligned_cols=49 Identities=18% Similarity=0.309 Sum_probs=38.7
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCCC
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTKP 74 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~~ 74 (89)
.-.++.+|+|+++++|..+-.. ...+.|..-.+.|+.|+.+.....+.+
T Consensus 17 ~~~v~~~IrG~~v~~A~~~L~~----------~pkk~a~~i~k~L~sA~aNA~~~~g~d 65 (112)
T PRK00565 17 ARLVADLIRGKKVEEALAILKF----------SPKKAARLVKKVLKSAIANAENNHGLD 65 (112)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH----------CcHhHHHHHHHHHHHHHHHHHhccCCC
Confidence 3467889999999999887665 256778888999999999997655443
No 19
>PTZ00493 phosphomethylpyrimidine kinase; Provisional
Probab=82.58 E-value=1.4 Score=34.39 Aligned_cols=36 Identities=17% Similarity=-0.057 Sum_probs=29.2
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKH 42 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~ 42 (89)
|-|.||+.| +++++.+++|.++.+|..+..+.+...
T Consensus 247 ~hGTGc~fA----SAIAa~LA~G~~l~~Av~~A~~fv~~a 282 (321)
T PTZ00493 247 IHGTGCTLS----TAIACYLAKKHNILQSCIESKKYIYNC 282 (321)
T ss_pred CCChHHHHH----HHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 578899887 778888899999999998887765443
No 20
>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=76.68 E-value=5.7 Score=26.74 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHcCCCHHHHHcchhHHHHhhcC----CCCcchh
Q 034618 13 GVSNVSATEWVKGKQIQEVLSIKNTEIAKHLS----LPPVKLH 51 (89)
Q Consensus 13 ~ASaS~~telikGktl~Ea~~i~~~~i~e~Lg----lpp~Ri~ 51 (89)
..-.+++.+.+.|+|.+|+..++.+ ..+.|| |+|.|.+
T Consensus 70 kGl~all~~~~~g~t~~eI~~~~~~-fl~~lgl~~~Ls~sR~n 111 (125)
T PF02657_consen 70 KGLLALLLEVLNGQTPEEILAFDPD-FLEQLGLSQHLSPSRSN 111 (125)
T ss_dssp HHHHHHHHHHTTT-BHHHHHHS-TH-HHHHHTSCCCSTHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHhCCHH-HHHHcCcccccCchHHH
Confidence 5678899999999999999999998 666664 6888877
No 21
>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=76.30 E-value=12 Score=24.04 Aligned_cols=48 Identities=10% Similarity=0.176 Sum_probs=37.9
Q ss_pred HHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCCC
Q 034618 17 VSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTKP 74 (89)
Q Consensus 17 S~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~~ 74 (89)
-.++.+++|+++++|...-..- ..+.|..-.+.|+.|+.+.....+.+
T Consensus 14 ~~v~~~Irg~~v~~A~~~L~~~----------~~k~a~~i~k~L~~a~~nA~~~~g~d 61 (105)
T PF00237_consen 14 REVARLIRGMSVDEAIAQLKFV----------PKKAAKFILKLLKSAIANAENNKGLD 61 (105)
T ss_dssp HHHHHHHTTSBHHHHHHHHHHH----------SSHHHHHHHHHHHHHHHHHHHHCTST
T ss_pred HHHHHHHcCCCHHHHHHHHHhC----------cHHHHHHHHhhHHHHHhhcccccccc
Confidence 3567899999999998776653 46788889999999999988555544
No 22
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=75.78 E-value=13 Score=26.16 Aligned_cols=55 Identities=16% Similarity=0.210 Sum_probs=40.3
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhh--c-------CC---------CC--cchhhHHHHHHHHHHHHHHHHHh
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKH--L-------SL---------PP--VKLHCSMLAEDAIKAAVKDYEAK 70 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~--L-------gl---------pp--~Ri~CA~La~~AL~~Al~~y~~k 70 (89)
+...+++|+|+++++|..+-..-+... + |+ +. --.+++.+-.+.|+.|+.+...+
T Consensus 30 ~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~KlL~sA~aNA~~~ 104 (153)
T PRK04223 30 SVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFLKLLENAEANAEYK 104 (153)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHHHHHHHHHHHHHhc
Confidence 346788999999999999887633221 1 11 11 24689999999999999998753
No 23
>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=75.66 E-value=14 Score=25.96 Aligned_cols=54 Identities=7% Similarity=0.103 Sum_probs=39.7
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhc---------CC-----------CC--cchhhHHHHHHHHHHHHHHHHH
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHL---------SL-----------PP--VKLHCSMLAEDAIKAAVKDYEA 69 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~L---------gl-----------pp--~Ri~CA~La~~AL~~Al~~y~~ 69 (89)
+-.++++|+|+++++|..+-..-+...- |+ .. --.+++.+-.+.|+.|+.+...
T Consensus 26 ~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~i~klL~sA~aNA~~ 101 (150)
T TIGR01038 26 ARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKFILKVLQNAEANAEY 101 (150)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHHHHHHHHHHHHHHHh
Confidence 3457889999999999998876332211 11 11 2468999999999999999865
No 24
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=75.13 E-value=3.6 Score=29.13 Aligned_cols=36 Identities=19% Similarity=0.177 Sum_probs=28.3
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
.+.|-||+.+ +.+++.+++|++++|+...-...+..
T Consensus 202 ~~~GaGD~f~----a~l~a~l~~g~~~~~A~~~A~~~~~~ 237 (242)
T cd01169 202 NTHGTGCTLS----SAIAANLAKGLSLEEAVREAKEYVTQ 237 (242)
T ss_pred CCCChHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 3457788776 78888899999999999887765543
No 25
>CHL00034 rpl22 ribosomal protein L22
Probab=74.30 E-value=13 Score=24.93 Aligned_cols=47 Identities=11% Similarity=0.111 Sum_probs=37.1
Q ss_pred HHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCC
Q 034618 17 VSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 17 S~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~ 73 (89)
-.++.+|.|+++++|..+-.. ...+.|.+-.+.|+.|+.+.....+.
T Consensus 25 r~va~~IRG~~v~~A~~~L~~----------~pkk~a~~i~klL~sA~aNA~~~~gl 71 (117)
T CHL00034 25 RRVIDQIRGRSYEEALMILEF----------MPYRACYPILKLVYSAAANASHNMGL 71 (117)
T ss_pred HHHHHHHcCCcHHHHHHHHHH----------CcHHHHHHHHHHHHHHHHHHHHccCC
Confidence 457889999999999877654 13788889999999999988654443
No 26
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=73.90 E-value=14 Score=26.92 Aligned_cols=54 Identities=15% Similarity=0.124 Sum_probs=39.7
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhcCC--------------------CC--cchhhHHHHHHHHHHHHHHHHH
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHLSL--------------------PP--VKLHCSMLAEDAIKAAVKDYEA 69 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~Lgl--------------------pp--~Ri~CA~La~~AL~~Al~~y~~ 69 (89)
+-.++++|+|+++++|..+-..-|...--+ ++ --.++|.+-.+.|+.|+.+...
T Consensus 29 ~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~GR~P~KaA~~i~KlL~SA~aNAe~ 104 (181)
T PTZ00178 29 TYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQGRWPEKSVKFVLSLLKNAEANAEA 104 (181)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccccccccCcCcHHHHHHHHHHHHHHHHHHHh
Confidence 356789999999999999887633211111 11 2468999999999999999873
No 27
>PRK12412 pyridoxal kinase; Reviewed
Probab=73.65 E-value=3.8 Score=30.15 Aligned_cols=35 Identities=23% Similarity=0.259 Sum_probs=27.7
Q ss_pred ecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 5 LRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 5 g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
|-||+.+ +.+++.+++|++++|+...-...+...+
T Consensus 210 GaGD~f~----aa~aa~l~~g~~l~eA~~~A~~~~~~~i 244 (268)
T PRK12412 210 GAGCTYS----AAITAELAKGKPVKEAVKTAKEFITAAI 244 (268)
T ss_pred chHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 6677776 7888899999999999988877554433
No 28
>cd01173 pyridoxal_pyridoxamine_kinase Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and require its precursors in the form of vitamin B6 (pyridoxal, pyridoxine, and pyridoxamine) from their diet. Pyridoxal kinase encoding genes are also found in many other species including yeast and bacteria.
Probab=71.36 E-value=5 Score=28.78 Aligned_cols=35 Identities=17% Similarity=0.122 Sum_probs=27.7
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
+-|-||+.+ +.++..+++|++++|+.+.-...+.+
T Consensus 213 ~~GaGD~f~----a~~~~~l~~g~~~~~a~~~A~~~~~~ 247 (254)
T cd01173 213 FNGTGDLFA----ALLLARLLKGKSLAEALEKALNFVHE 247 (254)
T ss_pred cCChHHHHH----HHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 456777776 78888999999999999888765543
No 29
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=69.88 E-value=5.3 Score=29.66 Aligned_cols=36 Identities=11% Similarity=0.059 Sum_probs=28.5
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
.+-|-||+.+ +.++..+++|++++|+.+...+.+..
T Consensus 227 ~~~GaGD~fa----a~~~a~l~~g~~l~~Av~~A~~~v~~ 262 (281)
T PRK08176 227 DLKGTGDLFC----AELVSGLLKGKALTDAAHRAGLRVLE 262 (281)
T ss_pred CCCChhHHHH----HHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 3567788776 77888899999999999888876543
No 30
>PRK05756 pyridoxamine kinase; Validated
Probab=69.54 E-value=5.6 Score=29.34 Aligned_cols=36 Identities=11% Similarity=0.118 Sum_probs=28.4
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
.+.|-||+.+ +.++..+++|++++|+.+.....+..
T Consensus 216 ~~~GaGD~f~----a~~~a~l~~g~~~~~al~~A~~~~~~ 251 (286)
T PRK05756 216 QPVGVGDLTS----ALFLARLLQGGSLEEALEHTTAAVYE 251 (286)
T ss_pred CCCChHHHHH----HHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 3567777776 78888999999999999888765543
No 31
>PRK08573 phosphomethylpyrimidine kinase; Provisional
Probab=68.97 E-value=12 Score=29.84 Aligned_cols=35 Identities=17% Similarity=0.067 Sum_probs=27.8
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
..|-||+.+ +.++..+++|+++.|+...-...+..
T Consensus 206 t~GAGDaFs----Aa~aa~l~~G~~l~eAl~~A~~~~~~ 240 (448)
T PRK08573 206 THGTGCSFS----AAIAAGLAKGLDPEEAIKTAKKFITM 240 (448)
T ss_pred CCChHHHHH----HHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 457788776 67888899999999999988875443
No 32
>PRK12616 pyridoxal kinase; Reviewed
Probab=68.95 E-value=5.4 Score=29.39 Aligned_cols=36 Identities=19% Similarity=0.204 Sum_probs=28.5
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
.|-||+.+ +.+++.+++|++++|+.......+.+.|
T Consensus 212 ~GaGD~fs----aalaa~l~~g~~l~~Av~~A~~~~~~~i 247 (270)
T PRK12616 212 HGAGCTFS----AAVTAELAKGSEVKEAIYAAKEFITAAI 247 (270)
T ss_pred CcHHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 57788776 7888899999999999988876554433
No 33
>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=68.80 E-value=5.1 Score=24.57 Aligned_cols=23 Identities=17% Similarity=0.185 Sum_probs=17.7
Q ss_pred HHHHHHHHHHcCCCHHHHHcchh
Q 034618 14 VSNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 14 ASaS~~telikGktl~Ea~~i~~ 36 (89)
.++-.++.+++|||++|+..+-.
T Consensus 34 ~~~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 34 LCCKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHHHhcCCCHHHHHHHcC
Confidence 35667789999999999887765
No 34
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=67.58 E-value=18 Score=28.39 Aligned_cols=43 Identities=12% Similarity=0.232 Sum_probs=37.6
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHH
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYE 68 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~ 68 (89)
+-.++++|.|+++++|..+-... ..++|.+-.+.|+.|+.++.
T Consensus 17 ~R~Va~~IRGk~v~~Al~~L~~~----------PkKaA~~I~KlLkSA~ANAe 59 (311)
T PRK12279 17 ASLVIDLVRNKPVHEAIRILSNT----------PKKFAPIVLKLLNSAISNVQ 59 (311)
T ss_pred HHHHHHHHcCCcHHHHHHHHHhC----------CHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999877663 78899999999999999987
No 35
>PLN02673 quinolinate synthetase A
Probab=66.59 E-value=29 Score=30.25 Aligned_cols=52 Identities=13% Similarity=0.125 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc--CC---CCcchhhHHHHHHHHHHHHHHH
Q 034618 10 NLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL--SL---PPVKLHCSMLAEDAIKAAVKDY 67 (89)
Q Consensus 10 is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L--gl---pp~Ri~CA~La~~AL~~Al~~y 67 (89)
|. ..=.+++.+.+.|+|.+|++.++.+++ +.| |+ .|.|.+ +|.++-+.|+.+
T Consensus 155 IV-KGL~ALLl~~lsG~TpeEILavD~d~~-~~LGLGL~~~SPSRsN----GL~nML~~Iq~~ 211 (724)
T PLN02673 155 IT-KGFCSCLIWVLDGASPEEVLELKTEDL-AALNVGLPGGERSRVN----TWHNVLVSMQKR 211 (724)
T ss_pred HH-HHHHHHHHHHHcCCCHHHHHhCCHHHH-HHHhhhhcccCCchhH----HHHHHHHHHHHH
Confidence 44 677889999999999999999999877 554 43 789988 444554555444
No 36
>PRK07105 pyridoxamine kinase; Validated
Probab=64.26 E-value=8.2 Score=28.44 Aligned_cols=37 Identities=19% Similarity=0.131 Sum_probs=29.1
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
+-|-||+.+ +.++..+++|.+++++.......+...+
T Consensus 217 ~~GaGD~f~----aa~~~~l~~g~~l~~av~~A~~~~~~~i 253 (284)
T PRK07105 217 YPGTGDIFT----SVITGSLLQGDSLPIALDRAVQFIEKGI 253 (284)
T ss_pred cCChhHHHH----HHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 457788887 7788889999999999988877554444
No 37
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=63.98 E-value=8.6 Score=27.80 Aligned_cols=35 Identities=20% Similarity=0.183 Sum_probs=27.5
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
.+.|-||+.+ +.++..+++|.++.|+..+-...+.
T Consensus 209 ~~~GaGD~f~----a~l~~~l~~g~~l~~A~~~A~~~~~ 243 (266)
T PRK06427 209 NTHGTGCTLS----AAIAAELAKGASLLDAVQTAKDYVT 243 (266)
T ss_pred CCCChHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 3567788776 6788888999999999888776543
No 38
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase. This model represents phosphomethylpyrimidine kinase, the ThiD protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species.
Probab=62.69 E-value=9.2 Score=27.69 Aligned_cols=34 Identities=18% Similarity=0.113 Sum_probs=26.8
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
+.|-||+.+ +.+++.+++|.+++|+...-...+.
T Consensus 202 ~~GaGD~f~----aalaa~la~g~~l~eA~~~A~~~~~ 235 (254)
T TIGR00097 202 THGTGCTLS----AAIAANLAKGLSLKEAVKEAKEFVT 235 (254)
T ss_pred CCChHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 457788877 7788888999999999887776443
No 39
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=57.88 E-value=37 Score=23.08 Aligned_cols=48 Identities=17% Similarity=0.304 Sum_probs=35.8
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCC
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~ 73 (89)
+...+.++.|+++++|..+-... -.+-|-.-.+.|+.|+.+.+...+.
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~~~----------pkKaa~~v~KvL~sA~aNAe~n~gL 72 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILEFV----------PKKAAKLVKKVLESAIANAENNKGL 72 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHHhC----------hHHHHHHHHHHHHHHHhhHHhccCC
Confidence 45678999999999999885432 4566777788888888887764333
No 40
>PTZ00347 phosphomethylpyrimidine kinase; Provisional
Probab=57.41 E-value=12 Score=30.20 Aligned_cols=37 Identities=8% Similarity=0.038 Sum_probs=28.4
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
+-|-||+.+ +.+++.+++|+++.|+..+-...+...+
T Consensus 440 ~~GaGD~fs----aaiaa~la~G~~l~eAv~~A~~~v~~~i 476 (504)
T PTZ00347 440 THGTGCTLA----SAISSFLARGYTVPDAVERAIGYVHEAI 476 (504)
T ss_pred CCChHHHHH----HHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 457788887 6678888999999999988876554433
No 41
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=54.06 E-value=16 Score=26.12 Aligned_cols=35 Identities=23% Similarity=0.173 Sum_probs=25.6
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
..|-||+.+ +.++..+++|.+++|+...-...+..
T Consensus 204 ~~GaGDaf~----a~~~~~l~~g~~l~ea~~~A~~~~~~ 238 (253)
T PRK12413 204 NIGAGCTFA----SSIASQLVKGKSPLEAVKNSKDFVYQ 238 (253)
T ss_pred CCChHHHHH----HHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 345566654 77888899999999988877665443
No 42
>PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase
Probab=53.67 E-value=15 Score=29.62 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=29.3
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
+-|-||+.+ +.+++.+++|++++|+...-...+...+
T Consensus 215 t~GaGD~fs----aaiaa~l~~G~~l~eAv~~A~~~v~~ai 251 (502)
T PLN02898 215 THGTGCTLA----SCIAAELAKGSDMLSAVKVAKRYVETAL 251 (502)
T ss_pred CCchhhhHH----HHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 458888887 7788888999999999988887654443
No 43
>PLN02978 pyridoxal kinase
Probab=50.84 E-value=19 Score=27.30 Aligned_cols=36 Identities=6% Similarity=-0.079 Sum_probs=26.5
Q ss_pred ceeecchhhhHHHHHHHHHHHHcC-CCHHHHHcchhHHHHh
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKG-KQIQEVLSIKNTEIAK 41 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikG-ktl~Ea~~i~~~~i~e 41 (89)
.|-|-||..+ +.+++.+.+| .+++|+.......+..
T Consensus 227 ~~~GtGD~fs----A~laa~l~~g~~~l~~A~~~A~~~v~~ 263 (308)
T PLN02978 227 YFTGTGDLMA----ALLLGWSHKYPDNLDKAAELAVSSLQA 263 (308)
T ss_pred CCCCchHHHH----HHHHHHHhcCCcCHHHHHHHHHHHHHH
Confidence 3568888887 2477777888 7999998887765543
No 44
>PRK09517 multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase; Provisional
Probab=50.78 E-value=16 Score=31.29 Aligned_cols=35 Identities=14% Similarity=0.072 Sum_probs=27.6
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAK 41 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e 41 (89)
.-|-||+.+ +.+++.+++|++++|+.......+..
T Consensus 446 t~GaGDtfs----aaiaa~La~G~sl~eAv~~A~~~v~~ 480 (755)
T PRK09517 446 SHGTGCSLS----AALATLIAAGESVEKALEWATRWLNE 480 (755)
T ss_pred CcChHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 357788877 78888899999999998877765443
No 45
>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=48.57 E-value=1e+02 Score=23.96 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=37.5
Q ss_pred HHHHHHHHHHcCCCHHHHHcchhHHHHhhcCC--CCc----chhhHHHHHHHHHHHHHHH
Q 034618 14 VSNVSATEWVKGKQIQEVLSIKNTEIAKHLSL--PPV----KLHCSMLAEDAIKAAVKDY 67 (89)
Q Consensus 14 ASaS~~telikGktl~Ea~~i~~~~i~e~Lgl--pp~----Ri~CA~La~~AL~~Al~~y 67 (89)
+-++...-++.|-|.+++..-...-+...||+ -|. ++-|+.--.-+...|+.-.
T Consensus 176 amAAaai~~l~GGs~eqi~~Aa~~~l~~~lGlvCDpv~GlV~vpC~~Rna~~a~~A~~aa 235 (294)
T TIGR00718 176 AMAAAAIVEMAGGTPEQAAEAAAITIINMLGLVCDPIAGLVEVPCTFRNAMGAINAFIAA 235 (294)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHhccCCccCCccccccchhHHHHHHHHHHHHHHH
Confidence 33344445677889999988777777777886 477 8899876666666665544
No 46
>PRK14713 multifunctional hydroxymethylpyrimidine phosphokinase/4-amino-5-aminomethyl-2-methylpyrimidine hydrolase; Provisional
Probab=46.85 E-value=22 Score=28.99 Aligned_cols=34 Identities=15% Similarity=0.018 Sum_probs=26.8
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
+-|-||+.+ +.+++.+++|.++.++.......+.
T Consensus 234 t~GaGD~fs----aalaa~La~G~~l~eAv~~A~~~v~ 267 (530)
T PRK14713 234 THGTGCSLS----SALATRLGRGGDWAAALRWATAWLH 267 (530)
T ss_pred CCcHHHHHH----HHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 357788776 7788888999999999887776443
No 47
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=45.37 E-value=21 Score=25.37 Aligned_cols=22 Identities=27% Similarity=0.373 Sum_probs=17.6
Q ss_pred HHHHHHHHHcCCCHHHHHcchh
Q 034618 15 SNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 15 SaS~~telikGktl~Ea~~i~~ 36 (89)
++-.++.+++|||.+|.+.+.+
T Consensus 119 ~ck~va~mikgktpeEir~~f~ 140 (162)
T KOG1724|consen 119 TCKTVANMIKGKTPEEIREIFN 140 (162)
T ss_pred HHHHHHHHHccCCHHHHHHHcC
Confidence 4556789999999999887744
No 48
>TIGR00687 pyridox_kin pyridoxal kinase. ThiD and related proteins form an outgroup.
Probab=44.87 E-value=25 Score=25.83 Aligned_cols=36 Identities=14% Similarity=0.141 Sum_probs=27.0
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
.|-||+.+ +.++..+++|++++|+.......+...+
T Consensus 219 ~GaGD~f~----A~~l~~l~~g~~~~~al~~A~~~v~~~l 254 (286)
T TIGR00687 219 VGTGDLIA----ALLLATLLHGNSLKEALEKTVSAVYHVL 254 (286)
T ss_pred CChHHHHH----HHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 35566554 7788889999999999988887655444
No 49
>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=43.67 E-value=89 Score=23.71 Aligned_cols=60 Identities=15% Similarity=0.240 Sum_probs=40.7
Q ss_pred chhhhHHHHH----HHHHHHHcCCCHHHHHcchhHHHHhhcCC--CC----cchhhHHHHHHHHHHHHHHH
Q 034618 7 GFTNLYGVSN----VSATEWVKGKQIQEVLSIKNTEIAKHLSL--PP----VKLHCSMLAEDAIKAAVKDY 67 (89)
Q Consensus 7 GC~is~~ASa----S~~telikGktl~Ea~~i~~~~i~e~Lgl--pp----~Ri~CA~La~~AL~~Al~~y 67 (89)
||..- .+++ +...-++.|-+.+++..-...-+...+|+ -| .++-|+.--..+...|+.-.
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 GCQAE-AGAASAMAAAGIVYLLGGTPEQIEYAAANALGNLLGLICDGVAGLVKIPCALKNASGASAAISAA 238 (282)
T ss_pred hhhhh-hhhhHHHHHHHHHHHhCcCHHHHHHHHHHHhcccceeeCCCCcccccccHHHHHHHHHHHHHHHH
Confidence 66665 3332 22233567889999988877767777786 57 89999887666666666544
No 50
>PF10312 Cactin_mid: Conserved mid region of cactin; InterPro: IPR018816 This entry represents the conserved central domain of a family of proteins referred to as cactins. It contains two of three predicted coiled-coil motifs. Most proteins containing this domain also have IPR019134 from INTERPRO at the C-terminal end. Upstream of this domain in Drosophila proteins are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localisation signals, none of which are well-conserved. Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo [].
Probab=41.62 E-value=1.1e+02 Score=22.02 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=36.6
Q ss_pred HHHHHHHHHcCCCHHHHHcchhHHHHhhc--CCCCcchhhHHHHHHHHHHHHHHHHHh
Q 034618 15 SNVSATEWVKGKQIQEVLSIKNTEIAKHL--SLPPVKLHCSMLAEDAIKAAVKDYEAK 70 (89)
Q Consensus 15 SaS~~telikGktl~Ea~~i~~~~i~e~L--glpp~Ri~CA~La~~AL~~Al~~y~~k 70 (89)
..+=+..+++|||.+|...+-.+ |...| |=+.+--+ |.+|..-|.-|+.|
T Consensus 132 V~~dI~~il~gKs~~eL~~Le~q-I~~KL~s~~~~Dv~Y-----WE~lL~~L~v~kAk 183 (191)
T PF10312_consen 132 VAADIQKILSGKSYEELEELEQQ-IKAKLRSGEAIDVEY-----WESLLKQLKVFKAK 183 (191)
T ss_pred HHHHHHHHHccCCHHHHHHHHHH-HHHHhhcCCCccHHH-----HHHHHHHHHHHHHH
Confidence 34456678999999999998876 77777 44444444 88888888777655
No 51
>PTZ00344 pyridoxal kinase; Provisional
Probab=38.24 E-value=38 Score=25.25 Aligned_cols=34 Identities=6% Similarity=-0.134 Sum_probs=23.5
Q ss_pred ceeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 2 NYLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 2 ~F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
+|.|-||+.+ +.+++.+.+| ++.|+.......+.
T Consensus 220 ~~~GaGD~f~----A~~~a~l~~g-~~~~a~~~A~a~~~ 253 (296)
T PTZ00344 220 RYTGTGDLFA----ALLLAFSHQH-PMDLAVGKAMGVLQ 253 (296)
T ss_pred CCCCchHHHH----HHHHHHHhcC-CHHHHHHHHHHHHH
Confidence 3557777776 3466777888 99998877665443
No 52
>PRK14551 rnhB ribonuclease HII; Provisional
Probab=37.87 E-value=42 Score=24.49 Aligned_cols=55 Identities=5% Similarity=0.029 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHHHHHcCCCHHHHHcchh-------------HHHHhhc---CCCCcchhhHHHHHHHHHHHHHHH
Q 034618 9 TNLYGVSNVSATEWVKGKQIQEVLSIKN-------------TEIAKHL---SLPPVKLHCSMLAEDAIKAAVKDY 67 (89)
Q Consensus 9 ~is~~ASaS~~telikGktl~Ea~~i~~-------------~~i~e~L---glpp~Ri~CA~La~~AL~~Al~~y 67 (89)
..+ +|+||+++....-+-+++....-. +.+.+.+ |.+|. +...+|.+++..+.+.
T Consensus 134 ~~~-VAAASIlAKv~RD~~m~~l~~~y~~~GsGYpsd~~t~~~l~~~~~~~g~~p~---~~R~Sw~~~~~~~~~~ 204 (212)
T PRK14551 134 DPL-VGAASIVAKVARDAHVAALAAEYGDVGSGYPSDPTTREFLREYVREHGELPA---CARRSWSTCDDVLAAA 204 (212)
T ss_pred hHH-HHHHHHHHHHHHHHHHHHHHHHCCCCCCcCCCcHHHHHHHHHHHHHhCCCch---hhccCcHHHHHHHHHh
Confidence 356 899999999888887777765443 1222332 43331 4556699999988776
No 53
>KOG2854 consensus Possible pfkB family carbohydrate kinase [Carbohydrate transport and metabolism]
Probab=36.25 E-value=45 Score=26.61 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=26.7
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~ 36 (89)
++.+|+.-. ..+-.|+.+++|++++|..+.-.
T Consensus 291 vDtnGAGDa--FvgGFl~~l~qg~~l~~cir~g~ 322 (343)
T KOG2854|consen 291 VDTNGAGDA--FVGGFLSQLVQGKSLEECIRAGS 322 (343)
T ss_pred eeCCCchHH--HHHHHHHHHHcCCCHHHHHHHHH
Confidence 467888885 67789999999999999877654
No 54
>PRK11470 hypothetical protein; Provisional
Probab=34.53 E-value=30 Score=25.37 Aligned_cols=21 Identities=24% Similarity=0.290 Sum_probs=18.7
Q ss_pred CCCcchhhHHHHHHHHHHHHH
Q 034618 45 LPPVKLHCSMLAEDAIKAAVK 65 (89)
Q Consensus 45 lpp~Ri~CA~La~~AL~~Al~ 65 (89)
+.-+|+.|+.|.|++++.+..
T Consensus 111 ~~d~~~YCSElV~~~y~~a~~ 131 (200)
T PRK11470 111 YESSRQFCSKFVFDIYKEALC 131 (200)
T ss_pred CCCCceehHHHHHHHHHHhhC
Confidence 458899999999999999983
No 55
>cd01166 KdgK 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources.
Probab=32.24 E-value=45 Score=23.81 Aligned_cols=23 Identities=17% Similarity=0.243 Sum_probs=18.7
Q ss_pred HHHHHHHHHcCCCHHHHHcchhH
Q 034618 15 SNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 15 SaS~~telikGktl~Ea~~i~~~ 37 (89)
++.++..+++|++++++...-..
T Consensus 260 ~a~~~~~l~~g~~~~~a~~~a~~ 282 (294)
T cd01166 260 AAGFLAGLLEGWDLEEALRFANA 282 (294)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 37788899999999999876653
No 56
>PRK10030 hypothetical protein; Provisional
Probab=31.10 E-value=30 Score=24.95 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=17.5
Q ss_pred CCCcchhhHHHHHHHHHHHH
Q 034618 45 LPPVKLHCSMLAEDAIKAAV 64 (89)
Q Consensus 45 lpp~Ri~CA~La~~AL~~Al 64 (89)
+..++++|+.|.|++++++.
T Consensus 121 ~~d~~~YCSELV~~ay~~a~ 140 (197)
T PRK10030 121 WSDDRIYCSELVWKVYQNAL 140 (197)
T ss_pred cCCCcEEeHHHHHHHHHHcc
Confidence 35789999999999999884
No 57
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=30.36 E-value=53 Score=23.25 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=17.5
Q ss_pred HHHHHHHHHcCCCHHHHHcchh
Q 034618 15 SNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 15 SaS~~telikGktl~Ea~~i~~ 36 (89)
++-+++++++||+.+|.....+
T Consensus 114 gCKivaemirgkSpeeir~tfn 135 (158)
T COG5201 114 GCKIVAEMIRGKSPEEIRETFN 135 (158)
T ss_pred HHHHHHHHHccCCHHHHHHHhC
Confidence 4456789999999999877654
No 58
>PF13068 DUF3932: Protein of unknown function (DUF3932)
Probab=30.34 E-value=37 Score=21.33 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHHHHHHHHhcCC
Q 034618 52 CSMLAEDAIKAAVKDYEAKRTK 73 (89)
Q Consensus 52 CA~La~~AL~~Al~~y~~k~~~ 73 (89)
-+.|-|.+||+.|++|...+..
T Consensus 27 paql~wttlkeliheytt~htn 48 (81)
T PF13068_consen 27 PAQLEWTTLKELIHEYTTSHTN 48 (81)
T ss_pred ccccchhHHHHHHHHHhccccc
Confidence 3456699999999999765443
No 59
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=27.18 E-value=48 Score=21.33 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=16.0
Q ss_pred cCCCHHHHHcchhH---HHHhhcCCCCcchh
Q 034618 24 KGKQIQEVLSIKNT---EIAKHLSLPPVKLH 51 (89)
Q Consensus 24 kGktl~Ea~~i~~~---~i~e~Lglpp~Ri~ 51 (89)
.|++.++=.++... .+.+.||+||+|+.
T Consensus 67 g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~ 97 (116)
T PTZ00397 67 GGISRSNNSSIAAAITKILASHLKVKSERVY 97 (116)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhCcCcccEE
Confidence 45565554444442 23455688888875
No 60
>cd01171 YXKO-related B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily.
Probab=25.62 E-value=71 Score=22.86 Aligned_cols=30 Identities=13% Similarity=-0.063 Sum_probs=21.3
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~ 36 (89)
.-|.||+.+ +.+.+-+.+|+++.|+..+-.
T Consensus 197 ~~GaGD~la----g~iaa~la~g~~~~eA~~~A~ 226 (254)
T cd01171 197 TGGSGDVLA----GIIAALLAQGLSPLEAAALAV 226 (254)
T ss_pred cCchHHHHH----HHHHHHHHcCCCHHHHHHHHH
Confidence 357777765 556666668999999877654
No 61
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=25.15 E-value=43 Score=19.18 Aligned_cols=28 Identities=14% Similarity=0.423 Sum_probs=18.4
Q ss_pred HcCCCHHHHHcchhH---HHHhhcCCCCcch
Q 034618 23 VKGKQIQEVLSIKNT---EIAKHLSLPPVKL 50 (89)
Q Consensus 23 ikGktl~Ea~~i~~~---~i~e~Lglpp~Ri 50 (89)
.+|+|.++-.+|... .+.+.||+|++.+
T Consensus 9 ~~grt~eqk~~l~~~it~~l~~~lg~p~~~v 39 (64)
T PRK01964 9 LEGRPEEKIKNLIREVTEAISATLDVPKERV 39 (64)
T ss_pred eCCCCHHHHHHHHHHHHHHHHHHhCcChhhE
Confidence 468888888887774 2344557766554
No 62
>PRK11316 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional
Probab=24.78 E-value=72 Score=25.12 Aligned_cols=29 Identities=24% Similarity=0.307 Sum_probs=23.2
Q ss_pred ecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 5 LRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 5 g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
|-|++.+ +.++..+++|++++++..+-..
T Consensus 261 GAGDaF~----aa~~~~l~~g~~~~~al~~A~a 289 (473)
T PRK11316 261 GAGDTVI----SVLAAALAAGNSLEEACALANA 289 (473)
T ss_pred CCcHHHH----HHHHHHHHcCCCHHHHHHHHHH
Confidence 4455554 7888999999999999988774
No 63
>TIGR02198 rfaE_dom_I rfaE bifunctional protein, domain I. RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. The longer, N-terminal domain I (this family) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (TIGR02199) adds ADP to yield ADP-D-glycero-D-manno-heptose.
Probab=24.72 E-value=76 Score=23.11 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=23.3
Q ss_pred ecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 5 LRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 5 g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
..||+-+ -++.++..+++|++++|+..+-..
T Consensus 261 t~GAGDa--f~ag~~~~l~~g~~~~~al~~A~~ 291 (315)
T TIGR02198 261 VTGAGDT--VIATLALALAAGASLEEACRLANA 291 (315)
T ss_pred CcCccHH--HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3455554 347788999999999999988764
No 64
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=24.24 E-value=51 Score=20.89 Aligned_cols=25 Identities=36% Similarity=0.430 Sum_probs=22.0
Q ss_pred CCCCcchhhHHHHHHHHHHHHHHHH
Q 034618 44 SLPPVKLHCSMLAEDAIKAAVKDYE 68 (89)
Q Consensus 44 glpp~Ri~CA~La~~AL~~Al~~y~ 68 (89)
|..|.-++|.+|+.+++=.++.++.
T Consensus 55 g~~~~~~~~gVLSEDaiyn~lgd~~ 79 (90)
T PF14131_consen 55 GDLPTDGKCGVLSEDAIYNALGDHY 79 (90)
T ss_pred CCCCCCcccCccCchHHHHHHHHHH
Confidence 5667899999999999999998875
No 65
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=24.19 E-value=93 Score=21.26 Aligned_cols=31 Identities=10% Similarity=0.190 Sum_probs=25.6
Q ss_pred HHHHHHHHcCCCHHHHHcchhHHHHhhcCCCC
Q 034618 16 NVSATEWVKGKQIQEVLSIKNTEIAKHLSLPP 47 (89)
Q Consensus 16 aS~~telikGktl~Ea~~i~~~~i~e~Lglpp 47 (89)
.+-+.+.+++.|+-|+..+... +.+.||+++
T Consensus 5 ~~~i~e~i~~LtllE~~eLv~~-lee~fgv~a 35 (123)
T PRK00157 5 KEQIIEALKEMTVLELSELVKA-LEEKFGVSA 35 (123)
T ss_pred HHHHHHHHHhCCHHHHHHHHHH-HHHHcCCCc
Confidence 3456789999999999999765 788898865
No 66
>cd01945 ribokinase_group_B Ribokinase-like subgroup B. Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time. .
Probab=23.60 E-value=94 Score=22.13 Aligned_cols=32 Identities=16% Similarity=0.220 Sum_probs=24.6
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
+..||.-+ -.+.++..+++|++++++..+-..
T Consensus 236 Dt~GAGDa--f~ag~l~~l~~g~~~~~al~~a~~ 267 (284)
T cd01945 236 DTTGAGDV--FHGAFAHALAEGMPLREALRFASA 267 (284)
T ss_pred cCCCcHHH--HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45677775 456777888999999999887764
No 67
>KOG2598 consensus Phosphomethylpyrimidine kinase [Coenzyme transport and metabolism; Transcription]
Probab=23.03 E-value=83 Score=26.39 Aligned_cols=33 Identities=12% Similarity=0.061 Sum_probs=23.3
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHH
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIA 40 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~ 40 (89)
-|.||+-+ +.+.+.++.|-++-++-.---+-+.
T Consensus 246 HGtgCtLa----SAIASnLA~g~sl~qAv~~ai~yvq 278 (523)
T KOG2598|consen 246 HGTGCTLA----SAIASNLARGYSLLQAVQGAIEYVQ 278 (523)
T ss_pred cCccchHH----HHHHHHHhhcCCHHHHHHHHHHHHH
Confidence 37788876 5677788999999887655444333
No 68
>PRK13508 tagatose-6-phosphate kinase; Provisional
Probab=22.80 E-value=96 Score=22.71 Aligned_cols=32 Identities=13% Similarity=0.012 Sum_probs=24.6
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
+..|++-+ -.+.++..+++|++++|+.++-..
T Consensus 247 DttGAGDa--F~Agfi~~l~~g~~~~~al~~a~a 278 (309)
T PRK13508 247 NPVGSGDS--TVAGIASGLLHQEDDADLLKKANV 278 (309)
T ss_pred CCcChhHH--HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45577765 346678889999999999988764
No 69
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=22.76 E-value=1.7e+02 Score=19.91 Aligned_cols=36 Identities=17% Similarity=0.214 Sum_probs=24.1
Q ss_pred HHHHhhcCCCCcchhh-HHHHHHHHHHHHHHHHHhcC
Q 034618 37 TEIAKHLSLPPVKLHC-SMLAEDAIKAAVKDYEAKRT 72 (89)
Q Consensus 37 ~~i~e~Lglpp~Ri~C-A~La~~AL~~Al~~y~~k~~ 72 (89)
.+|.+.||+++.-++- ..-+.+.|++.|.++....+
T Consensus 151 ~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~ 187 (193)
T TIGR02947 151 KEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDVAGERG 187 (193)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3566777888777776 34567777888877665433
No 70
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=22.45 E-value=54 Score=18.37 Aligned_cols=29 Identities=10% Similarity=0.371 Sum_probs=19.1
Q ss_pred HHcCCCHHHHHcchhH---HHHhhcCCCCcch
Q 034618 22 WVKGKQIQEVLSIKNT---EIAKHLSLPPVKL 50 (89)
Q Consensus 22 likGktl~Ea~~i~~~---~i~e~Lglpp~Ri 50 (89)
+.+|+|.++-.+|... .+.+.+|+|++.+
T Consensus 8 ~~~Grs~eqk~~l~~~it~~l~~~~~~p~~~v 39 (61)
T PRK02220 8 LIEGRTEEQLKALVKDVTAAVSKNTGAPAEHI 39 (61)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHHHhCcChhhE
Confidence 4578888888887774 2344557766554
No 71
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=22.12 E-value=76 Score=19.62 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=14.1
Q ss_pred ecchhhhHHHHHHHHHHHHcCCCHHHHHcchhHHHHhhc
Q 034618 5 LRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNTEIAKHL 43 (89)
Q Consensus 5 g~GC~is~~ASaS~~telikGktl~Ea~~i~~~~i~e~L 43 (89)
..||.++ |++|+.... |++ ++..++.+.+
T Consensus 13 ~~~Cg~a---s~~mvl~~~-g~~------~~~~~l~~~~ 41 (144)
T PF13529_consen 13 SYGCGPA---SAAMVLNYY-GKN------ISQEDLADEA 41 (144)
T ss_dssp TT-HHHH---HHHHHHHHT-T----------HHHHHHHS
T ss_pred CCcCHHH---HHHHHHHHc-CCC------CCHHHHHHHh
Confidence 4578775 555555555 884 4445555555
No 72
>COG3580 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.48 E-value=1.5e+02 Score=23.71 Aligned_cols=65 Identities=25% Similarity=0.306 Sum_probs=41.2
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCC-HHHHHcchhHHHHhhcCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQ-IQEVLSIKNTEIAKHLSLPPVKLHCSMLAEDAIKAAVKDYEAKRTKPSAAS 78 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGkt-l~Ea~~i~~~~i~e~Lglpp~Ri~CA~La~~AL~~Al~~y~~k~~~~~~~~ 78 (89)
+...||++= ....|+.=|.+.|.+ +=-+++|++.. ++-.-|+. .++|+.+++.|..-+-..+..+
T Consensus 279 l~SFgCG~D-avttd~i~eIl~~~nk~ytvlkIDE~t-----n~gai~iR-----lesl~a~mkere~~~~k~~~~~ 344 (351)
T COG3580 279 LVSFGCGLD-AVTTDLIEEILEGHNKIYTVLKIDEGT-----NLGAIRIR-----LESLKAAMKERERNNVKNEERS 344 (351)
T ss_pred EeecccCcc-hhHHHHHHHHHHhCCCeeEEEEecCCC-----Ccchhhhh-----HHHHHHHHHHHHHhcccchhhc
Confidence 345789987 777777777777776 21333333321 11112333 7899999999988777776663
No 73
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=21.24 E-value=1.2e+02 Score=22.40 Aligned_cols=59 Identities=5% Similarity=-0.011 Sum_probs=41.9
Q ss_pred hhhHHHHHHHHHHHHcCCCHHHHHcchhH-------------HHHhhc--C-CCCcchhhHHHHHHHHHHHHHHHHHhcC
Q 034618 9 TNLYGVSNVSATEWVKGKQIQEVLSIKNT-------------EIAKHL--S-LPPVKLHCSMLAEDAIKAAVKDYEAKRT 72 (89)
Q Consensus 9 ~is~~ASaS~~telikGktl~Ea~~i~~~-------------~i~e~L--g-lpp~Ri~CA~La~~AL~~Al~~y~~k~~ 72 (89)
..+ +|+||+++.....+-+++....-++ -..+.+ | .++ |...+|..++..+.....++.
T Consensus 122 ~~~-IaAASIvAKV~RDr~m~~l~~~yp~Y~~~~~~GY~T~~h~~a~~~~~~~~~----~hR~Sf~~vk~~~~~~~~~~~ 196 (199)
T COG0164 122 SPS-IAAASILAKVTRDRLMEELAKEYPEYGFDKGSGYPTDPHTEALLKKGGTPG----IHRRSFAPVRRLLGLAKKRQL 196 (199)
T ss_pred hHH-HHHHHHHHHHHHHHHHHHHHhhCcCcCcccCCCCCChHHHHHHHHhCCCCc----eeecccHHHHHhhhhhhhhhh
Confidence 455 8999999999998888888877532 122333 3 332 666779999999988766543
No 74
>PRK10294 6-phosphofructokinase 2; Provisional
Probab=20.77 E-value=1.1e+02 Score=22.32 Aligned_cols=32 Identities=6% Similarity=0.091 Sum_probs=24.6
Q ss_pred eecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 4 LLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 4 ~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
+..||+-+ -.+.++..+++|++++++.++-..
T Consensus 250 DttGAGDa--f~ag~l~~l~~g~~~~~al~~a~a 281 (309)
T PRK10294 250 STVGAGDS--MVGAMTLKLAENASLEEMVRFGVA 281 (309)
T ss_pred CCcchHHH--HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45677765 345588999999999999988654
No 75
>PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=20.73 E-value=84 Score=19.88 Aligned_cols=14 Identities=21% Similarity=0.216 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHhcC
Q 034618 59 AIKAAVKDYEAKRT 72 (89)
Q Consensus 59 AL~~Al~~y~~k~~ 72 (89)
++..||++|+.+++
T Consensus 69 vIsAAI~~hR~~~~ 82 (82)
T PRK02919 69 VIAAAIHHHRRLNA 82 (82)
T ss_pred HHHHHHHHHHhcCC
Confidence 89999999998764
No 76
>PF12854 PPR_1: PPR repeat
Probab=20.59 E-value=1.4e+02 Score=15.06 Aligned_cols=31 Identities=13% Similarity=0.156 Sum_probs=21.7
Q ss_pred chhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 7 GFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 7 GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
||.+....=.+++.-+.+...++||..+-.+
T Consensus 2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHh
Confidence 5655523445666778899999999887653
No 77
>PRK09813 fructoselysine 6-kinase; Provisional
Probab=20.58 E-value=1.2e+02 Score=21.59 Aligned_cols=33 Identities=9% Similarity=0.121 Sum_probs=25.0
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchhH
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKNT 37 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~~ 37 (89)
.+..||.-+ -.+.++.-++.|++++|+..+-..
T Consensus 216 vDttGAGDa--F~ag~i~~~~~g~~~~~al~~a~~ 248 (260)
T PRK09813 216 VDTMGAGDS--FIAGFLCGWLAGMTLPQAMAQGTA 248 (260)
T ss_pred CCCCCchHH--HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 356788876 355677778999999999887654
No 78
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=20.56 E-value=1.1e+02 Score=17.18 Aligned_cols=27 Identities=11% Similarity=0.171 Sum_probs=18.0
Q ss_pred cCCCHHHHHcchhH---HHHhhcCCCCcch
Q 034618 24 KGKQIQEVLSIKNT---EIAKHLSLPPVKL 50 (89)
Q Consensus 24 kGktl~Ea~~i~~~---~i~e~Lglpp~Ri 50 (89)
+|+|.++-..|... .+.+.||+|++.+
T Consensus 10 ~grt~eqK~~l~~~it~~l~~~lg~~~~~v 39 (63)
T TIGR00013 10 EGRTDEQKRQLIEGVTEAMAETLGANLESI 39 (63)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCCCcccE
Confidence 68888888888775 2344557766544
No 79
>cd01170 THZ_kinase 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine and 1-deoxy-D-xylulose-5-phosphate.
Probab=20.51 E-value=1e+02 Score=22.51 Aligned_cols=30 Identities=17% Similarity=-0.114 Sum_probs=20.6
Q ss_pred eeecchhhhHHHHHHHHHHHHcCCCHHHHHcchh
Q 034618 3 YLLRGFTNLYGVSNVSATEWVKGKQIQEVLSIKN 36 (89)
Q Consensus 3 F~g~GC~is~~ASaS~~telikGktl~Ea~~i~~ 36 (89)
+-|.||+-+ +.+.+-+..|.++.+|....-
T Consensus 184 v~GtGdtLa----~aiAa~LA~g~~~~~A~~~A~ 213 (242)
T cd01170 184 ITGTGCLLG----AVIAAFLAVGDDPLEAAVSAV 213 (242)
T ss_pred CCchHHHHH----HHHHHHHhCCCCHHHHHHHHH
Confidence 358888887 455555667999888765443
Done!