Query 031595
Match_columns 157
No_of_seqs 96 out of 98
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 02:42:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031595hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01106 NifU: NifU-like domai 99.8 8.7E-20 1.9E-24 125.6 7.4 60 86-152 1-63 (68)
2 COG0694 Thioredoxin-like prote 99.8 7E-19 1.5E-23 130.0 5.8 64 82-152 10-79 (93)
3 TIGR03341 YhgI_GntY IscR-regul 99.7 5.5E-18 1.2E-22 135.9 7.8 67 79-152 103-174 (190)
4 PRK11190 Fe/S biogenesis prote 99.7 9.7E-18 2.1E-22 135.0 6.7 64 82-152 107-176 (192)
5 TIGR02000 NifU_proper Fe-S clu 99.7 2.1E-16 4.5E-21 133.6 7.5 62 83-152 221-285 (290)
6 KOG2358 NifU-like domain-conta 98.9 4.5E-10 9.7E-15 94.1 2.1 70 77-153 120-194 (213)
7 KOG2358 NifU-like domain-conta 98.7 9.7E-09 2.1E-13 86.1 2.3 68 78-152 74-144 (213)
8 PF01883 DUF59: Domain of unkn 95.8 0.024 5.3E-07 37.8 4.8 65 83-152 1-68 (72)
9 TIGR02945 SUF_assoc FeS assemb 90.7 0.61 1.3E-05 32.9 4.7 63 84-151 4-70 (99)
10 TIGR03406 FeS_long_SufT probab 70.1 21 0.00044 29.0 6.6 60 91-151 76-146 (174)
11 KOG1664 Vacuolar H+-ATPase V1 69.3 9.3 0.0002 33.0 4.7 59 82-152 138-210 (220)
12 COG2151 PaaD Predicted metal-s 68.8 36 0.00078 26.1 7.3 66 81-146 5-78 (111)
13 PRK11670 antiporter inner memb 67.4 12 0.00027 32.7 5.2 68 80-152 11-81 (369)
14 PRK00135 scpB segregation and 63.2 17 0.00037 29.7 4.9 39 80-126 31-69 (188)
15 PF01545 Cation_efflux: Cation 62.5 47 0.001 26.5 7.2 32 121-152 240-272 (284)
16 TIGR02159 PA_CoA_Oxy4 phenylac 61.6 26 0.00057 27.6 5.5 44 104-147 10-55 (146)
17 PRK04217 hypothetical protein; 58.3 4.3 9.3E-05 30.9 0.6 66 36-101 19-90 (110)
18 PRK10718 RpoE-regulated lipopr 50.8 18 0.0004 30.5 3.2 59 67-131 41-102 (191)
19 PF02881 SRP54_N: SRP54-type p 50.7 25 0.00053 23.3 3.3 23 79-102 16-38 (75)
20 COG3414 SgaB Phosphotransferas 50.2 16 0.00035 27.0 2.5 25 123-147 2-29 (93)
21 PF09883 DUF2110: Uncharacteri 46.3 63 0.0014 28.1 5.8 54 85-152 10-67 (225)
22 PF11501 Nsp1: Non structural 43.1 23 0.00049 27.9 2.5 32 84-124 21-60 (115)
23 PRK08944 motB flagellar motor 42.7 90 0.0019 27.1 6.3 60 82-147 140-208 (302)
24 TIGR00281 segregation and cond 42.7 58 0.0013 26.7 4.9 39 83-129 32-70 (186)
25 PF04079 DUF387: Putative tran 42.3 56 0.0012 26.0 4.7 42 82-131 25-66 (159)
26 PF01491 Frataxin_Cyay: Fratax 41.8 83 0.0018 23.4 5.3 36 85-125 9-45 (109)
27 PF14454 Prok_Ub: Prokaryotic 41.4 36 0.00079 24.1 3.1 22 78-99 21-42 (65)
28 PF05642 Sporozoite_P67: Sporo 40.5 25 0.00055 34.7 2.9 22 72-93 579-600 (727)
29 PRK12784 hypothetical protein; 39.7 21 0.00046 26.9 1.8 19 103-121 46-65 (84)
30 TIGR00719 sda_beta L-serine de 38.8 22 0.00048 28.7 1.9 44 102-146 124-171 (208)
31 COG4803 Predicted membrane pro 38.3 22 0.00047 29.7 1.8 41 83-131 17-69 (170)
32 TIGR01327 PGDH D-3-phosphoglyc 37.2 26 0.00056 32.1 2.3 26 102-128 427-452 (525)
33 PRK03941 NTPase; Reviewed 36.8 52 0.0011 26.9 3.8 42 69-112 33-74 (174)
34 PF10646 Germane: Sporulation 36.6 71 0.0015 22.3 4.0 45 108-152 52-102 (117)
35 COG1782 Predicted metal-depend 36.0 91 0.002 30.7 5.8 57 86-148 3-62 (637)
36 PRK01215 competence damage-ind 35.8 1.4E+02 0.0031 25.2 6.4 65 81-156 189-261 (264)
37 cd02932 OYE_YqiM_FMN Old yello 35.7 2.8E+02 0.006 23.6 8.3 120 23-149 78-219 (336)
38 cd06155 eu_AANH_C_1 A group of 35.5 1.6E+02 0.0034 20.8 5.8 59 82-157 24-82 (101)
39 PF10865 DUF2703: Domain of un 34.6 68 0.0015 24.9 3.9 22 78-99 17-38 (120)
40 PF09105 SelB-wing_1: Elongati 34.2 88 0.0019 22.2 4.1 27 89-120 30-56 (61)
41 PF09840 DUF2067: Uncharacteri 33.8 92 0.002 25.7 4.8 40 82-131 7-46 (190)
42 TIGR01375 soxG sarcosine oxida 33.4 89 0.0019 23.6 4.4 37 84-129 51-87 (152)
43 cd06150 YjgF_YER057c_UK114_lik 33.1 1.6E+02 0.0036 20.7 5.4 59 82-157 27-85 (105)
44 PRK10005 dihydroxyacetone kina 33.0 41 0.00089 27.6 2.7 24 84-108 13-36 (210)
45 COG3270 Uncharacterized conser 32.9 25 0.00055 28.1 1.3 80 50-149 36-121 (127)
46 CHL00123 rps6 ribosomal protei 31.8 97 0.0021 22.5 4.2 29 80-115 17-45 (97)
47 cd04733 OYE_like_2_FMN Old yel 30.8 3.4E+02 0.0073 23.1 7.9 117 23-149 83-214 (338)
48 KOG3348 BolA (bacterial stress 30.5 47 0.001 25.1 2.4 64 79-151 1-66 (85)
49 TIGR00311 aIF-2beta translatio 29.7 2.4E+02 0.0053 22.1 6.3 62 78-148 37-98 (133)
50 PRK09038 flagellar motor prote 29.6 2.8E+02 0.0061 23.6 7.1 58 84-147 96-162 (281)
51 PF03982 DAGAT: Diacylglycerol 29.2 1.2E+02 0.0027 26.2 5.0 36 79-114 257-295 (297)
52 PF10437 Lip_prot_lig_C: Bacte 28.9 1.2E+02 0.0026 20.8 4.0 35 108-144 15-51 (86)
53 TIGR01297 CDF cation diffusion 28.8 1.9E+02 0.0042 22.9 5.7 18 135-152 242-259 (268)
54 PRK14438 acylphosphatase; Prov 28.5 71 0.0015 22.9 3.0 33 93-128 18-50 (91)
55 PRK03114 NTPase; Reviewed 28.4 87 0.0019 25.5 3.8 42 70-112 30-72 (169)
56 PF07634 RtxA: RtxA repeat; I 28.3 22 0.00048 19.2 0.3 11 103-113 9-19 (19)
57 PRK06778 hypothetical protein; 28.2 1.4E+02 0.0029 25.8 5.1 56 86-147 114-181 (289)
58 PRK05074 inosine/xanthosine tr 28.1 82 0.0018 25.8 3.6 43 69-112 37-81 (173)
59 PRK14447 acylphosphatase; Prov 27.8 89 0.0019 22.6 3.4 33 93-128 19-52 (95)
60 smart00411 BHL bacterial (prok 27.6 2E+02 0.0043 19.5 5.0 42 80-127 15-56 (90)
61 TIGR03422 mito_frataxin fratax 27.6 1.2E+02 0.0025 22.6 4.0 37 86-126 6-43 (97)
62 PRK14427 acylphosphatase; Prov 26.9 89 0.0019 22.6 3.3 47 93-147 21-67 (94)
63 PRK14445 acylphosphatase; Prov 26.5 99 0.0022 22.1 3.4 33 93-128 19-51 (91)
64 COG0776 HimA Bacterial nucleoi 26.5 1.2E+02 0.0027 22.6 4.0 26 83-116 23-48 (94)
65 PRK14424 acylphosphatase; Prov 26.1 84 0.0018 23.0 3.0 46 93-146 22-67 (94)
66 PRK14133 DNA polymerase IV; Pr 26.0 3.3E+02 0.0071 23.1 6.9 60 82-155 75-135 (347)
67 PF14280 DUF4365: Domain of un 25.7 75 0.0016 22.9 2.7 48 105-152 27-87 (138)
68 PRK00453 rpsF 30S ribosomal pr 25.6 1.4E+02 0.0031 21.5 4.2 29 80-115 13-41 (108)
69 TIGR00532 HMG_CoA_R_NAD hydrox 24.5 3.6E+02 0.0078 24.8 7.3 45 107-151 160-215 (393)
70 PF01250 Ribosomal_S6: Ribosom 24.4 1.7E+02 0.0036 20.3 4.1 59 80-145 12-79 (92)
71 TIGR00252 conserved hypothetic 24.4 2.6E+02 0.0055 21.3 5.5 49 108-156 36-98 (119)
72 PRK14449 acylphosphatase; Prov 24.3 1E+02 0.0023 21.9 3.2 33 93-128 18-50 (90)
73 cd07059 BMC_PduA 1,2-propanedi 24.3 1.4E+02 0.003 21.7 3.8 34 108-141 23-59 (85)
74 cd06154 YjgF_YER057c_UK114_lik 24.1 2.8E+02 0.0061 20.0 6.0 58 82-157 42-99 (119)
75 COG5005 Mu-like prophage prote 23.9 1.1E+02 0.0023 25.1 3.5 28 72-99 109-136 (140)
76 PRK14446 acylphosphatase; Prov 23.7 1E+02 0.0023 22.2 3.1 45 94-146 18-62 (88)
77 PRK14684 hypothetical protein; 23.7 2.8E+02 0.0061 21.2 5.6 49 108-156 36-97 (120)
78 PF14135 DUF4302: Domain of un 23.5 57 0.0012 26.7 1.9 31 105-137 110-142 (235)
79 PRK14429 acylphosphatase; Prov 23.5 1.1E+02 0.0023 21.8 3.1 47 93-147 17-63 (90)
80 PRK14422 acylphosphatase; Prov 23.4 93 0.002 22.5 2.8 47 93-147 21-67 (93)
81 PF11340 DUF3142: Protein of u 23.3 3.8E+02 0.0082 22.4 6.6 61 75-153 15-77 (181)
82 cd07057 BMC_CcmK Carbon dioxid 23.1 1.4E+02 0.0029 21.9 3.6 33 108-140 23-58 (88)
83 PF00708 Acylphosphatase: Acyl 23.1 1.2E+02 0.0026 21.1 3.2 50 93-150 19-68 (91)
84 PF00368 HMG-CoA_red: Hydroxym 22.9 2.8E+02 0.006 25.2 6.2 68 84-152 115-189 (373)
85 PRK14448 acylphosphatase; Prov 22.9 98 0.0021 22.2 2.8 46 93-146 17-62 (90)
86 PRK14441 acylphosphatase; Prov 22.8 1.3E+02 0.0028 21.7 3.5 46 93-146 20-65 (93)
87 COG0347 GlnK Nitrogen regulato 22.6 2.3E+02 0.005 22.1 5.0 39 81-124 65-103 (112)
88 PF11211 DUF2997: Protein of u 22.6 2.2E+02 0.0048 18.8 4.2 32 114-145 3-35 (48)
89 PRK09974 putative regulator Pr 22.4 1.4E+02 0.003 23.2 3.7 32 91-128 24-55 (111)
90 PF11774 Lsr2: Lsr2 ; InterPr 22.4 74 0.0016 24.1 2.2 27 73-99 27-53 (110)
91 PRK14688 hypothetical protein; 22.3 2.9E+02 0.0062 21.1 5.4 48 108-156 36-96 (121)
92 cd04470 S1_EF-P_repeat_1 S1_EF 22.2 1.3E+02 0.0028 20.2 3.1 37 77-125 24-60 (61)
93 PRK14686 hypothetical protein; 22.1 2.6E+02 0.0057 21.1 5.1 47 108-156 35-94 (119)
94 PF15585 Imm46: Immunity prote 22.0 4.2E+02 0.0091 21.2 6.4 41 83-131 20-62 (129)
95 PF00216 Bac_DNA_binding: Bact 21.8 1.6E+02 0.0036 19.7 3.6 30 80-113 15-44 (90)
96 PRK00285 ihfA integration host 21.6 2.5E+02 0.0054 19.8 4.7 42 79-127 16-58 (99)
97 PRK14676 hypothetical protein; 21.5 3.3E+02 0.0071 20.6 5.5 49 108-156 37-96 (117)
98 cd02933 OYE_like_FMN Old yello 21.5 5.4E+02 0.012 22.3 8.0 121 23-150 78-218 (338)
99 PRK08193 araD L-ribulose-5-pho 21.3 2.5E+02 0.0053 23.0 5.2 43 87-131 7-49 (231)
100 PRK13581 D-3-phosphoglycerate 21.2 68 0.0015 29.4 2.1 43 103-146 429-475 (526)
101 TIGR00258 inosine/xanthosine t 21.2 1.5E+02 0.0032 24.1 3.8 43 69-112 29-72 (163)
102 PF14908 DUF4496: Domain of un 20.9 3.4E+02 0.0074 20.2 5.5 41 81-128 94-134 (140)
103 PRK14682 hypothetical protein; 20.8 3.2E+02 0.007 20.7 5.4 48 108-156 35-96 (117)
104 PF05225 HTH_psq: helix-turn-h 20.5 89 0.0019 19.9 2.0 14 82-95 1-14 (45)
105 cd03764 proteasome_beta_archea 20.2 2.2E+02 0.0047 21.8 4.4 37 86-122 149-186 (188)
106 COG1820 NagA N-acetylglucosami 20.2 1.2E+02 0.0025 28.0 3.3 47 78-131 95-141 (380)
107 PRK14681 hypothetical protein; 20.2 3.8E+02 0.0082 21.7 5.9 41 107-147 72-126 (158)
108 PRK09019 translation initiatio 20.2 1.8E+02 0.0039 22.4 3.9 40 75-129 49-88 (108)
109 PF04539 Sigma70_r3: Sigma-70 20.2 14 0.0003 24.5 -1.9 36 78-115 29-64 (78)
110 PRK06105 aminotransferase; Pro 20.0 1E+02 0.0022 27.5 2.9 34 75-109 425-458 (460)
No 1
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 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 C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. 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: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=99.81 E-value=8.7e-20 Score=125.64 Aligned_cols=60 Identities=25% Similarity=0.343 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcCc
Q 031595 86 VRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 86 VE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI~ 152 (157)
|+++|++|||+|++ |||||||+++|++.|+|||+|+|.+ +.+|++.+||+.|++++||+.
T Consensus 1 V~~~l~~IrP~L~~-------dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~ 63 (68)
T PF01106_consen 1 VEEVLEEIRPYLQS-------DGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVK 63 (68)
T ss_dssp HHHHHHHCHHHHHH-------TTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-S
T ss_pred CHHHHHHhChHHHh-------cCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCc
Confidence 78999999999996 6999999999999999999999999 799999999999999999975
No 2
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=7e-19 Score=129.97 Aligned_cols=64 Identities=28% Similarity=0.330 Sum_probs=60.0
Q ss_pred chHHHHHHHH-HHHHHHHhhhccccccccceEEEEec--CCeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcCc
Q 031595 82 TEDNVRQVIA-DARGELAQLFDTSVGITGVAELAELD--GPFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 82 teENVE~vLd-eiRP~L~a~fD~sVGdGGdVELVeID--GpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI~ 152 (157)
..|+|+++|+ +|||+|++ |||||||++|| +++|+|||.|||.+ +.+|+|++||+.||++|||+.
T Consensus 10 ~~e~v~~~l~~~irP~l~~-------dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~ 79 (93)
T COG0694 10 LLERVEEVLDEKIRPQLAM-------DGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVK 79 (93)
T ss_pred HHHHHHHHHHhccCcceec-------cCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccc
Confidence 3679999999 99999986 79999999999 78999999999999 799999999999999999975
No 3
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=99.74 E-value=5.5e-18 Score=135.85 Aligned_cols=67 Identities=18% Similarity=0.203 Sum_probs=61.2
Q ss_pred cccchHHHHHHHH-HHHHHHHhhhccccccccceEEEEec-CCeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcCc
Q 031595 79 LDLTEDNVRQVIA-DARGELAQLFDTSVGITGVAELAELD-GPFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 79 LeLteENVE~vLd-eiRP~L~a~fD~sVGdGGdVELVeID-GpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI~ 152 (157)
-+-..+.|+++|+ +|||+|++ ||||||||+|+ +++|+|||+|+|.+ +.+|||.+||+.||+++|||.
T Consensus 103 ~~~~~~~i~~~l~~~irP~l~~-------dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~ 174 (190)
T TIGR03341 103 DAPLEERINYVLQSEINPQLAS-------HGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELK 174 (190)
T ss_pred chHHHHHHHHHHHhccCHHHHh-------cCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcc
Confidence 3335889999998 79999996 69999999998 67999999999999 799999999999999999985
No 4
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.72 E-value=9.7e-18 Score=135.00 Aligned_cols=64 Identities=17% Similarity=0.204 Sum_probs=59.6
Q ss_pred chHHHHHHHH-HHHHHHHhhhccccccccceEEEEec-CCeEEEEEeeccCc---chhhHHHHHHHHHHhhCC-cCc
Q 031595 82 TEDNVRQVIA-DARGELAQLFDTSVGITGVAELAELD-GPFVKIRLRGRFWH---KRSTVIARLANYLKQRIP-VSP 152 (157)
Q Consensus 82 teENVE~vLd-eiRP~L~a~fD~sVGdGGdVELVeID-GpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IP-EI~ 152 (157)
..+.|+++|+ +|||+|++ ||||||||+|| +++|+|||+|+|.+ +.+|||++||+.||+++| ||+
T Consensus 107 ~~~~i~~~l~~~irP~l~~-------dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~ 176 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAG-------HGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELK 176 (192)
T ss_pred HHHHHHHHHHhccChhHHh-------cCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhc
Confidence 5788999997 99999996 69999999998 57999999999999 799999999999999999 874
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=99.65 E-value=2.1e-16 Score=133.58 Aligned_cols=62 Identities=23% Similarity=0.285 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcCc
Q 031595 83 EDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 83 eENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI~ 152 (157)
.+.|+++|++|||+|++ ||||||||+|+|++|+|||+|+|.+ +.+||+. ||+.||+.+|||.
T Consensus 221 ~~~v~~~l~~irP~l~~-------dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~ 285 (290)
T TIGR02000 221 IQLIQKVLEEVRPVLQA-------DGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFV 285 (290)
T ss_pred HHHHHHHHHHhCchHhh-------cCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCce
Confidence 57899999999999996 6999999999999999999999999 7999999 9999999999985
No 6
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=4.5e-10 Score=94.05 Aligned_cols=70 Identities=14% Similarity=0.151 Sum_probs=61.5
Q ss_pred CCcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecC--CeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcC
Q 031595 77 PPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDG--PFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVS 151 (157)
Q Consensus 77 ~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDG--pvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI 151 (157)
+.-+.+.-+.|-+...|||.++. ||||+++++.|+ ++|++||||+|.+ +..|+|+|||+-|+.++||+
T Consensus 120 ~d~e~t~~ikelietRiRp~i~e-------dggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eV 192 (213)
T KOG2358|consen 120 SDPESTMTIKELIETRIRPKIQE-------DGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEV 192 (213)
T ss_pred CChhHHHHHHHHHHHhhhhhhhc-------cCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhccee
Confidence 33455666788888899999996 799999999996 6999999999999 68899999999999999998
Q ss_pred cC
Q 031595 152 PL 153 (157)
Q Consensus 152 ~~ 153 (157)
+-
T Consensus 193 K~ 194 (213)
T KOG2358|consen 193 KG 194 (213)
T ss_pred eE
Confidence 63
No 7
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.66 E-value=9.7e-09 Score=86.12 Aligned_cols=68 Identities=24% Similarity=0.290 Sum_probs=63.4
Q ss_pred CcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc---chhhHHHHHHHHHHhhCCcCc
Q 031595 78 PLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH---KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPEI~ 152 (157)
-+.+++||++.+|+..||+|++ |+|++-+-.|+|.++.++++|+|.. .+||+|++||.+|+..|||+-
T Consensus 74 v~k~~ee~~w~~L~p~i~~~~s-------d~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edg 144 (213)
T KOG2358|consen 74 VTKLTEENVWSVLDPEIPSLMS-------DGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDG 144 (213)
T ss_pred EeccchhhhHhhhchhhHHHHh-------ccccccchhhccchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccC
Confidence 3567999999999999999996 6999999999999999999999998 799999999999999999974
No 8
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=95.77 E-value=0.024 Score=37.76 Aligned_cols=65 Identities=17% Similarity=0.196 Sum_probs=46.2
Q ss_pred hHHHHHHHHHH-HHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc--chhhHHHHHHHHHHhhCCcCc
Q 031595 83 EDNVRQVIADA-RGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH--KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 83 eENVE~vLdei-RP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~--s~mTvk~gVe~~LKe~IPEI~ 152 (157)
++.|.++|..+ =|+++ .++-+-|-|+=++|+|+.|.|.|+=.+.+ ....++..|+..|+ .+|++.
T Consensus 1 k~~V~~aL~~v~dP~~~----~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~-~l~gv~ 68 (72)
T PF01883_consen 1 KQAVRDALKQVKDPELG----KDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPGVK 68 (72)
T ss_dssp HHHHHHHHTT-BETTTS----SBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT-S
T ss_pred CHHHHHHHhCCCCCCCC----CCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCCCc
Confidence 35566666655 35554 23555799999999999999999988766 46788999999999 888753
No 9
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=90.71 E-value=0.61 Score=32.86 Aligned_cols=63 Identities=14% Similarity=0.169 Sum_probs=42.2
Q ss_pred HHHHHHHHHHH-HHHHhhhccccccccceEEEEecC-CeEEEEEeeccCc--chhhHHHHHHHHHHhhCCcC
Q 031595 84 DNVRQVIADAR-GELAQLFDTSVGITGVAELAELDG-PFVKIRLRGRFWH--KRSTVIARLANYLKQRIPVS 151 (157)
Q Consensus 84 ENVE~vLdeiR-P~L~a~fD~sVGdGGdVELVeIDG-pvVkVrL~GaC~~--s~mTvk~gVe~~LKe~IPEI 151 (157)
++|.++|+.+. |+++ .++..-|.|.=++++| +.|.+.|.-.+.+ ....++..++..|.+ +|.+
T Consensus 4 ~~I~~~L~~v~dP~l~----~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~~l~~~i~~al~~-l~gv 70 (99)
T TIGR02945 4 DAVIEALKTVYDPEIP----VNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEVENAVRA-VPGV 70 (99)
T ss_pred HHHHHHHcCCCCCCCC----CCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHHHHHHHHHHHHh-CCCC
Confidence 45555555552 3332 3566678998899985 8888888775554 566788888888865 5554
No 10
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=70.12 E-value=21 Score=28.99 Aligned_cols=60 Identities=10% Similarity=0.109 Sum_probs=39.3
Q ss_pred HHHHHHHHhhhcc----ccccccceEEEEecC---C--eEEEEEeeccCcc--hhhHHHHHHHHHHhhCCcC
Q 031595 91 ADARGELAQLFDT----SVGITGVAELAELDG---P--FVKIRLRGRFWHK--RSTVIARLANYLKQRIPVS 151 (157)
Q Consensus 91 deiRP~L~a~fD~----sVGdGGdVELVeIDG---p--vVkVrL~GaC~~s--~mTvk~gVe~~LKe~IPEI 151 (157)
++|+-.|.+++|- ++-+-|-|.=++|++ + .|.|.|+=.+-++ .-.++..|++.|++ +|.+
T Consensus 76 e~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL~~-l~gV 146 (174)
T TIGR03406 76 DQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVLA-VPNV 146 (174)
T ss_pred HHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHHHh-CCCc
Confidence 3344445555552 233468888888886 5 7888888777774 44477778888864 5554
No 11
>KOG1664 consensus Vacuolar H+-ATPase V1 sector, subunit E [Energy production and conversion]
Probab=69.33 E-value=9.3 Score=32.99 Aligned_cols=59 Identities=24% Similarity=0.264 Sum_probs=40.8
Q ss_pred chHHHHHHHHHHHHHHHhhhccccc--------------cccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhh
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVG--------------ITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQR 147 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVG--------------dGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~ 147 (157)
...-||++++++-+.++.-+. +| ..|.|+|..-||.++ | .-||-+|++-.-++.
T Consensus 138 D~~lVe~~~~~a~~~y~~ka~--~~~e~~id~~~fL~~~~~GGVvl~s~dgkI~-------v---~NTLesRLeli~~q~ 205 (220)
T KOG1664|consen 138 DLKLVEAALPKAIEEYKEKAG--VGVEVQIDKKDFLPPDVAGGVVLYSRDGKIK-------V---SNTLESRLELIAEQK 205 (220)
T ss_pred hhHHHHHHHHHHHHHHHHHhc--CCceeeechhccCCccccCCeEEEcCCCceE-------e---cCcHHHHHHHHHHHh
Confidence 345599999999888875222 22 234555555555443 2 569999999999999
Q ss_pred CCcCc
Q 031595 148 IPVSP 152 (157)
Q Consensus 148 IPEI~ 152 (157)
.|||-
T Consensus 206 lPeIR 210 (220)
T KOG1664|consen 206 LPEIR 210 (220)
T ss_pred hHHHH
Confidence 99984
No 12
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=68.77 E-value=36 Score=26.11 Aligned_cols=66 Identities=17% Similarity=0.321 Sum_probs=47.0
Q ss_pred cchHHHHHHHHHHHHHHHhhhccccccc----cceEEEEecC--CeEEEEEeeccCcc--hhhHHHHHHHHHHh
Q 031595 81 LTEDNVRQVIADARGELAQLFDTSVGIT----GVAELAELDG--PFVKIRLRGRFWHK--RSTVIARLANYLKQ 146 (157)
Q Consensus 81 LteENVE~vLdeiRP~L~a~fD~sVGdG----GdVELVeIDG--pvVkVrL~GaC~~s--~mTvk~gVe~~LKe 146 (157)
.+++..+..++++.-.|.+.+|--+|+- |=|.=|+||| +.|+|+++...-++ ..-+..-|++.|++
T Consensus 5 ~~~~~~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~~ 78 (111)
T COG2151 5 IEEEAIKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALEE 78 (111)
T ss_pred cccchhhhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHHHHHHHHHHHHh
Confidence 3455677778888888888888655553 6677788874 48999999988774 44556667777654
No 13
>PRK11670 antiporter inner membrane protein; Provisional
Probab=67.39 E-value=12 Score=32.73 Aligned_cols=68 Identities=13% Similarity=0.047 Sum_probs=47.6
Q ss_pred ccchHHHHHHHHHH-HHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc--chhhHHHHHHHHHHhhCCcCc
Q 031595 80 DLTEDNVRQVIADA-RGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH--KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 80 eLteENVE~vLdei-RP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~--s~mTvk~gVe~~LKe~IPEI~ 152 (157)
..++|+|.++|..+ -|.++. ++-.-|-|.=++|+|+.|.+.|.-.... ..-.++..++..|++ +|++.
T Consensus 11 ~~~~~~v~~~l~~v~~p~~~~----~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 81 (369)
T PRK11670 11 EALRAMVAGTLANFQHPTLKH----NLTTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQCSAELLR-ITGAK 81 (369)
T ss_pred cchHHHHHHHHhcCCCCCCCC----ChhhhCCeeEEEEeCCEEEEEEEECCCCchHHHHHHHHHHHHHHh-cCCCc
Confidence 35667888888777 455552 2334577877889988888888765554 456688889998885 66653
No 14
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=63.24 E-value=17 Score=29.66 Aligned_cols=39 Identities=15% Similarity=0.233 Sum_probs=28.4
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEe
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLR 126 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~ 126 (157)
.+..+.|+++|++++-.+.. .+..+++++++|+ ..+.++
T Consensus 31 ~~~~~~v~~~l~~L~~~y~~-------~~~gi~i~~~~~~-y~l~tk 69 (188)
T PRK00135 31 ELEPTEVQQLLEELQEKYEG-------DDRGLKLIEFNDV-YKLVTK 69 (188)
T ss_pred CCCHHHHHHHHHHHHHHHhh-------CCCCEEEEEECCE-EEEEEc
Confidence 45567899999999888864 3667999999654 444443
No 15
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=62.48 E-value=47 Score=26.50 Aligned_cols=32 Identities=9% Similarity=0.243 Sum_probs=23.0
Q ss_pred EEEEEeeccCc-chhhHHHHHHHHHHhhCCcCc
Q 031595 121 VKIRLRGRFWH-KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 121 VkVrL~GaC~~-s~mTvk~gVe~~LKe~IPEI~ 152 (157)
++|+..+.+.- ....++..|++.|++++|+|.
T Consensus 240 i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~i~ 272 (284)
T PF01545_consen 240 IHVQVDPDMSVEEAHEIRERIEKRLREKFPGIY 272 (284)
T ss_dssp EEEEETTTSBHHHHHHHHHHHHHHHHHHSTTCE
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHHHHHhCCCcE
Confidence 34444455533 355688999999999999985
No 16
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=61.58 E-value=26 Score=27.59 Aligned_cols=44 Identities=14% Similarity=0.187 Sum_probs=35.8
Q ss_pred ccccccceEEEEecCCeEEEEEeeccCc--chhhHHHHHHHHHHhh
Q 031595 104 SVGITGVAELAELDGPFVKIRLRGRFWH--KRSTVIARLANYLKQR 147 (157)
Q Consensus 104 sVGdGGdVELVeIDGpvVkVrL~GaC~~--s~mTvk~gVe~~LKe~ 147 (157)
++.+-|.|.=|+++|+.|.|.|+=.+.+ ....++..|+..|++.
T Consensus 10 sIvdLG~Vr~V~v~gd~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~ 55 (146)
T TIGR02159 10 SVTDLGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRAL 55 (146)
T ss_pred CchhcCCeeEEEEECCEEEEEEEeCCCCCchHHHHHHHHHHHHHhc
Confidence 3445789988999988999999988888 4566888899999873
No 17
>PRK04217 hypothetical protein; Provisional
Probab=58.31 E-value=4.3 Score=30.90 Aligned_cols=66 Identities=15% Similarity=0.139 Sum_probs=41.6
Q ss_pred cCccccccccccccccCCCcceeeeecccc-ccccc-----cCCCCCCCcccchHHHHHHHHHHHHHHHhhh
Q 031595 36 AFNKQTTHCRQKKLSRRKPILLSTSIDRGY-LTRTA-----AGGVPPPPLDLTEDNVRQVIADARGELAQLF 101 (157)
Q Consensus 36 ~f~~~~~~~~~~~~~~~~~~~~~t~~~r~~-~~~~~-----~~~~~~~~LeLteENVE~vLdeiRP~L~a~f 101 (157)
||.||+.||+++-.|--+|.+.+-.-.+.. ..... ....+-..+.+++..|...|..++-.|.+..
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 19 GFIPQVRHFYPAIPPVGPPKPPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred eccCCcceEeCCCCCccCCCCcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 799999999999988777766533222211 11100 0111223466788888888888888887644
No 18
>PRK10718 RpoE-regulated lipoprotein; Provisional
Probab=50.79 E-value=18 Score=30.51 Aligned_cols=59 Identities=14% Similarity=0.183 Sum_probs=36.7
Q ss_pred cccccCCCCCCCcccchHHHHHHHHHHHHHHHhhhccccc-cccceE-EEE-ecCCeEEEEEeeccCc
Q 031595 67 TRTAAGGVPPPPLDLTEDNVRQVIADARGELAQLFDTSVG-ITGVAE-LAE-LDGPFVKIRLRGRFWH 131 (157)
Q Consensus 67 ~~~~~~~~~~~~LeLteENVE~vLdeiRP~L~a~fD~sVG-dGGdVE-LVe-IDGpvVkVrL~GaC~~ 131 (157)
.++...+.++....+.++-+++.|+. +=.|.+ ..+ ..|+|- +.+ +++..|++-+.|. .+
T Consensus 41 vse~GVG~Ita~Tp~~~~aI~~~L~g-~y~lrs----Gm~t~~G~iv~~~qa~~~d~v~lvi~G~-~G 102 (191)
T PRK10718 41 VSEQGVGGITASTPLQEQAIADALDG-DYRLRS----GMKTANGNVVRFFQAMKGDQVAMVINGQ-QG 102 (191)
T ss_pred eccCccccccccCccCHHHHHhhcCC-CceEec----cccCCCCCEEEeeeeecCCceEEEEECC-CC
Confidence 34566777788888889999999887 112221 111 135442 222 5677889989887 44
No 19
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=50.73 E-value=25 Score=23.33 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=20.1
Q ss_pred cccchHHHHHHHHHHHHHHHhhhc
Q 031595 79 LDLTEDNVRQVIADARGELAQLFD 102 (157)
Q Consensus 79 LeLteENVE~vLdeiRP~L~a~fD 102 (157)
..+++++|+++|++++-.|.+ +|
T Consensus 16 ~~~~~~~i~~~l~ele~~Li~-aD 38 (75)
T PF02881_consen 16 IFLTEKDIEEFLEELEEALIE-AD 38 (75)
T ss_dssp SSCTHHHHHHHHHHHHHHHHH-TT
T ss_pred ccccHHhHHHHHHHHHHHHHH-cC
Confidence 556899999999999999987 77
No 20
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=50.21 E-value=16 Score=26.95 Aligned_cols=25 Identities=12% Similarity=0.211 Sum_probs=21.1
Q ss_pred EEEeeccCc---chhhHHHHHHHHHHhh
Q 031595 123 IRLRGRFWH---KRSTVIARLANYLKQR 147 (157)
Q Consensus 123 VrL~GaC~~---s~mTvk~gVe~~LKe~ 147 (157)
+++-=+||+ +++.+++.||++|+++
T Consensus 2 ~KIL~aCG~GvgSS~~ik~kve~~l~~~ 29 (93)
T COG3414 2 IKILAACGNGVGSSTMIKMKVEEVLKEL 29 (93)
T ss_pred cEEEEECCCCccHHHHHHHHHHHHHHHc
Confidence 355568998 8999999999999986
No 21
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.29 E-value=63 Score=28.10 Aligned_cols=54 Identities=17% Similarity=0.224 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHhhhccccccccceEE-EEec---CCeEEEEEeeccCcchhhHHHHHHHHHHhhCCcCc
Q 031595 85 NVRQVIADARGELAQLFDTSVGITGVAEL-AELD---GPFVKIRLRGRFWHKRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 85 NVE~vLdeiRP~L~a~fD~sVGdGGdVEL-VeID---GpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPEI~ 152 (157)
|.+.+|+.++.-+++ +=||+|. .+|+ +..|+|+|+|.=.. --.|.|+|+.-||.
T Consensus 10 d~~r~ld~L~~~v~n-------~lgdLdV~~~i~~~~~~wv~vtl~GeD~e-------va~Nll~eefGei~ 67 (225)
T PF09883_consen 10 DAERALDSLRSLVEN-------DLGDLDVEWDIGITKDDWVKVTLEGEDEE-------VAANLLREEFGEIV 67 (225)
T ss_pred cHHHHHHHHHHHHHH-------hhcCeeEEEEeccccCCceEEEEecCcHH-------HHHHHHHHHhCCCC
Confidence 458999999999986 2445442 1553 89999999998544 23577888777764
No 22
>PF11501 Nsp1: Non structural protein Nsp1; InterPro: IPR021590 Nsp1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing []. The specific function of the protein is unknown however the structure has been determined. The protein has a novel alpha/beta fold formed by a 6 stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel []. Nsp1 could be involved in the degradation of mRNA. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity, 0016788 hydrolase activity, acting on ester bonds, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2HSX_A 2GDT_A.
Probab=43.11 E-value=23 Score=27.94 Aligned_cols=32 Identities=31% Similarity=0.580 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccceEEEEec--------CCeEEEE
Q 031595 84 DNVRQVIADARGELAQLFDTSVGITGVAELAELD--------GPFVKIR 124 (157)
Q Consensus 84 ENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeID--------GpvVkVr 124 (157)
+.||.+|+++|..|. -|.+-+|++. .|.|.|+
T Consensus 21 d~vE~Al~eAR~hL~---------eGt~g~V~l~KG~l~qL~qP~vfv~ 60 (115)
T PF11501_consen 21 DSVEEALEEARVHLA---------EGTCGFVKLYKGVLPQLEQPYVFVK 60 (115)
T ss_dssp SSHHHHHHHHHHHHH---------HT-EEEE---TTSGGGS-S-EEEEE
T ss_pred hHHHHHHHHHHHHHh---------cCceEEEEecccccccccCCEEEEE
Confidence 469999999999997 5777777765 3666554
No 23
>PRK08944 motB flagellar motor protein MotB; Reviewed
Probab=42.73 E-value=90 Score=27.10 Aligned_cols=60 Identities=22% Similarity=0.316 Sum_probs=39.0
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEee--ccCc-------chhhHHHHHHHHHHhh
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRG--RFWH-------KRSTVIARLANYLKQR 147 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~G--aC~~-------s~mTvk~gVe~~LKe~ 147 (157)
..+++++..++++.+|.+. +..|.|+ |+.++.-|.|+|.+ -|.. ....+...|...|+..
T Consensus 140 ~~~~~~~~~~~l~~~l~~~-----~~~~~v~-v~~~~~~v~I~l~~~~~F~~gsa~L~~~~~~~L~~ia~~L~~~ 208 (302)
T PRK08944 140 AQEQIEDLVKKLAQQLEKE-----IEDGAIE-IESLGQQIIIRIREKGSFPSGSAFLQPKFKPVVRKIGELLKDV 208 (302)
T ss_pred HHHHHHHHHHHHHHHHHHH-----hhcCceE-EEEeCCEEEEEeCCCCeeCCCCcccCHHHHHHHHHHHHHHHhC
Confidence 4456777788888888752 3468888 45666678888864 4554 2334455577777765
No 24
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=42.70 E-value=58 Score=26.66 Aligned_cols=39 Identities=10% Similarity=0.142 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeecc
Q 031595 83 EDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRF 129 (157)
Q Consensus 83 eENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC 129 (157)
++.++.++++++-++.. ++..+++++++| ..+++++-.+
T Consensus 32 ~~~~~~~l~~l~~~~~~-------~~~gl~l~~~~~-~y~l~tk~e~ 70 (186)
T TIGR00281 32 AEKLNAIMELLEDYLSR-------DTAGIEIIKFGQ-SYSLVTKPAF 70 (186)
T ss_pred hHHHHHHHHHHHHHHhc-------CCCCEEEEEECC-EEEEEEhHHH
Confidence 45788999999888874 355699999954 4444444333
No 25
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=42.33 E-value=56 Score=25.96 Aligned_cols=42 Identities=19% Similarity=0.311 Sum_probs=30.8
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH 131 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~ 131 (157)
.++.|+++|++++-.+.. .+..++++++ |+...+..+-.+..
T Consensus 25 ~~~~v~~~l~~L~~~y~~-------~~~gl~l~~~-~~~y~l~tk~~~~~ 66 (159)
T PF04079_consen 25 SEDEVEEALEELQEEYNE-------EDRGLELVEV-GGGYRLQTKPEYAE 66 (159)
T ss_dssp -HHHHHHHHHHHHHHHHH-------CT-SEEEEEE-TTEEEEEE-GGGHH
T ss_pred CHHHHHHHHHHHHHHhcc-------CCCCEEEEEE-CCEEEEEEhHHHHH
Confidence 578899999999888864 4678999999 55667777666655
No 26
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
Probab=41.84 E-value=83 Score=23.36 Aligned_cols=36 Identities=17% Similarity=0.214 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHhhhcccccccc-ceEEEEecCCeEEEEE
Q 031595 85 NVRQVIADARGELAQLFDTSVGITG-VAELAELDGPFVKIRL 125 (157)
Q Consensus 85 NVE~vLdeiRP~L~a~fD~sVGdGG-dVELVeIDGpvVkVrL 125 (157)
-++++|+.|.-.|..+.| +.| +++ ++..|+++.|.+
T Consensus 9 lad~~l~~i~~~le~~~d----~~~~d~d-~e~~~gVLti~~ 45 (109)
T PF01491_consen 9 LADETLDSIEDALEELDD----EQDADID-VERSGGVLTIEF 45 (109)
T ss_dssp HHHHHHHHHHHHHHTCTT----SSSSTEE-EEEETTEEEEEE
T ss_pred HHHHHHHHHHHHHHHHhc----cCCCceE-EEccCCEEEEEE
Confidence 367888888888887555 333 555 445577887777
No 27
>PF14454 Prok_Ub: Prokaryotic Ubiquitin
Probab=41.39 E-value=36 Score=24.10 Aligned_cols=22 Identities=27% Similarity=0.320 Sum_probs=19.2
Q ss_pred CcccchHHHHHHHHHHHHHHHh
Q 031595 78 PLDLTEDNVRQVIADARGELAQ 99 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a 99 (157)
.-.++.|.|....+..-|+|..
T Consensus 21 ~p~~spe~V~~~ya~~YPeL~t 42 (65)
T PF14454_consen 21 NPSLSPEEVRDFYAAQYPELTT 42 (65)
T ss_pred CCCCCHHHHHHHHhhhChhhhe
Confidence 4478999999999999999974
No 28
>PF05642 Sporozoite_P67: Sporozoite P67 surface antigen; InterPro: IPR008845 This family consists of several Theileria P67 surface antigens. A stage specific surface antigen of Theileria parva, p67, is the basis for the development of an anti-sporozoite vaccine for the control of East Coast fever (ECF) in Bos taurus. The antigen has been shown to contain five distinct linear peptide sequences recognised by sporozoite-neutralising murine monoclonal antibodies [].
Probab=40.51 E-value=25 Score=34.72 Aligned_cols=22 Identities=36% Similarity=0.646 Sum_probs=19.5
Q ss_pred CCCCCCCcccchHHHHHHHHHH
Q 031595 72 GGVPPPPLDLTEDNVRQVIADA 93 (157)
Q Consensus 72 ~~~~~~~LeLteENVE~vLdei 93 (157)
.+...-.++|+||+|.++||||
T Consensus 579 ~ggslrg~dlteeev~kilde~ 600 (727)
T PF05642_consen 579 GGGSLRGLDLTEEEVKKILDEL 600 (727)
T ss_pred CCCcccCCccCHHHHHHHHHHH
Confidence 4566788999999999999998
No 29
>PRK12784 hypothetical protein; Provisional
Probab=39.71 E-value=21 Score=26.93 Aligned_cols=19 Identities=32% Similarity=0.552 Sum_probs=15.3
Q ss_pred cccccccceEEEEec-CCeE
Q 031595 103 TSVGITGVAELAELD-GPFV 121 (157)
Q Consensus 103 ~sVGdGGdVELVeID-GpvV 121 (157)
-.||+.|+|++|+++ |..|
T Consensus 46 v~vGiSG~I~~v~Ve~Gq~i 65 (84)
T PRK12784 46 VAVGISGNIRLVNVVVGQQI 65 (84)
T ss_pred EEEeeeeeEEEEEeecCcee
Confidence 358999999999998 6544
No 30
>TIGR00719 sda_beta L-serine dehydratase, iron-sulfur-dependent, beta subunit. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases.
Probab=38.78 E-value=22 Score=28.74 Aligned_cols=44 Identities=30% Similarity=0.385 Sum_probs=28.1
Q ss_pred ccccccccceEEEEecCCeEEEEEeecc---Cc-chhhHHHHHHHHHHh
Q 031595 102 DTSVGITGVAELAELDGPFVKIRLRGRF---WH-KRSTVIARLANYLKQ 146 (157)
Q Consensus 102 D~sVGdGGdVELVeIDGpvVkVrL~GaC---~~-s~mTvk~gVe~~LKe 146 (157)
.+|+| ||.+.+|+|||-.|.+..+|.- .+ .+--+-.+|...|-+
T Consensus 124 Gts~g-gg~~riv~idg~~vd~~~~g~~L~~~~~D~PG~Ig~vg~~Lg~ 171 (208)
T TIGR00719 124 GISIG-GGAIEITEINGFAIEFRGEHPAILLEHNDKFGTIAGVANLLAG 171 (208)
T ss_pred EEEeC-CCeEEEEEECCEEEEecCCccEEEEEeCCCCChHHHHHHHHHh
Confidence 35555 6889999999988888887741 22 244444555555433
No 31
>COG4803 Predicted membrane protein [Function unknown]
Probab=38.34 E-value=22 Score=29.74 Aligned_cols=41 Identities=27% Similarity=0.456 Sum_probs=27.1
Q ss_pred hHHHHHHHHHH-HHHHHhhhccccccccceEEEEec-CCeEEEE----------EeeccCc
Q 031595 83 EDNVRQVIADA-RGELAQLFDTSVGITGVAELAELD-GPFVKIR----------LRGRFWH 131 (157)
Q Consensus 83 eENVE~vLdei-RP~L~a~fD~sVGdGGdVELVeID-GpvVkVr----------L~GaC~~ 131 (157)
-|.|.+.|.++ +.||..| +|--.|-=| ++.||++ +.|+||+
T Consensus 17 Aeev~~~l~~LqkE~LI~L--------~DAvvvvk~~~gkvklkQ~~Nlt~aGa~sGafWG 69 (170)
T COG4803 17 AEEVRERLNELQKEYLITL--------EDAVVVVKDEDGKVKLKQLMNLTGAGAVSGAFWG 69 (170)
T ss_pred HHHHHHHHHHhhHHHheec--------cceEEEEeCCCCCeeHHHHhhhhhhccccccHHH
Confidence 46788888888 6677643 333333333 7777775 6788998
No 32
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=37.19 E-value=26 Score=32.05 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=20.3
Q ss_pred ccccccccceEEEEecCCeEEEEEeec
Q 031595 102 DTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 102 D~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
.+|+| ||.+++++|||-.|.+..+|.
T Consensus 427 G~s~g-Gg~~~I~~ing~~v~~~~~~~ 452 (525)
T TIGR01327 427 GTVFG-GFSPRIVEIDGFHVDLEPEGI 452 (525)
T ss_pred EEEec-CCcEEEEEECCEEEEEecCcc
Confidence 35555 789999999998888777663
No 33
>PRK03941 NTPase; Reviewed
Probab=36.84 E-value=52 Score=26.92 Aligned_cols=42 Identities=33% Similarity=0.493 Sum_probs=33.5
Q ss_pred cccCCCCCCCcccchHHHHHHHHHHHHHHHhhhccccccccceE
Q 031595 69 TAAGGVPPPPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAE 112 (157)
Q Consensus 69 ~~~~~~~~~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVE 112 (157)
+..|+++..|+- +|.++-++..++--|++=+|.+||+=|.|+
T Consensus 33 ~v~SgV~~QP~g--eET~~GA~nRA~~A~~~~ad~gVGiEgGv~ 74 (174)
T PRK03941 33 EVDSGVPDQPFG--EETVKGAINRAKNAYSPDFDFSVGIEAGLF 74 (174)
T ss_pred cCCCCCCCCCCC--HHHHHHHHHHHHHHHhcCCCEEEEEeeeEe
Confidence 456777777887 999999999999888854788888866665
No 34
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=36.61 E-value=71 Score=22.26 Aligned_cols=45 Identities=16% Similarity=0.312 Sum_probs=33.3
Q ss_pred ccceEEEEec-CCeEEEEEeeccC---c--chhhHHHHHHHHHHhhCCcCc
Q 031595 108 TGVAELAELD-GPFVKIRLRGRFW---H--KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 108 GGdVELVeID-GpvVkVrL~GaC~---~--s~mTvk~gVe~~LKe~IPEI~ 152 (157)
|=.+.=+.++ |+.++|.|...+. + ...-+...|.++|.+.+|+|.
T Consensus 52 ~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~ 102 (117)
T PF10646_consen 52 GTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVK 102 (117)
T ss_pred ccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCcc
Confidence 3334446677 6699999999884 3 366788889999998888763
No 35
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=36.03 E-value=91 Score=30.69 Aligned_cols=57 Identities=23% Similarity=0.466 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhhhccccccccceEEEEec--CCeEEEEEeeccCc-chhhHHHHHHHHHHhhC
Q 031595 86 VRQVIADARGELAQLFDTSVGITGVAELAELD--GPFVKIRLRGRFWH-KRSTVIARLANYLKQRI 148 (157)
Q Consensus 86 VE~vLdeiRP~L~a~fD~sVGdGGdVELVeID--GpvVkVrL~GaC~~-s~mTvk~gVe~~LKe~I 148 (157)
++++|+|+|....++.. ++++..+|+ ||.+.|=.+-+--- ..-.+-..++..||+||
T Consensus 3 ~~~~l~ei~~~i~~~~p------~~~~It~vefEGPelvvY~k~P~~~~~~~dlik~lAk~lrKRI 62 (637)
T COG1782 3 VREVLEEIRNKINEILP------SDVKITDVEFEGPELVVYTKNPELFAKDGDLIKDLAKDLRKRI 62 (637)
T ss_pred HHHHHHHHHHHHHHhCC------CcCceEEEEecCCeEEEEecCHHHhccchhHHHHHHHHHhhce
Confidence 67889999998887655 356666665 99988877654322 13356667888888887
No 36
>PRK01215 competence damage-inducible protein A; Provisional
Probab=35.84 E-value=1.4e+02 Score=25.25 Aligned_cols=65 Identities=14% Similarity=0.153 Sum_probs=39.9
Q ss_pred cchHHHHHHHHHHHHHHHhhhccccccccceEE------EEecCCeEEEEEeeccCc--chhhHHHHHHHHHHhhCCcCc
Q 031595 81 LTEDNVRQVIADARGELAQLFDTSVGITGVAEL------AELDGPFVKIRLRGRFWH--KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 81 LteENVE~vLdeiRP~L~a~fD~sVGdGGdVEL------VeIDGpvVkVrL~GaC~~--s~mTvk~gVe~~LKe~IPEI~ 152 (157)
+.|..+++.|+++-+. --++++ .....+.|.|||+++... ..-.+...++..|++++-+..
T Consensus 189 i~Es~l~~~l~~l~~~-----------~~~~~~~s~p~~~~~~~~~v~vrl~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 257 (264)
T PRK01215 189 VMESDLAPYVKELVKK-----------YDRVYVKSHPKGYEVSKPILEIQIAGSGEREEEAKVKVEKVLEELKELIKKLG 257 (264)
T ss_pred CCHHHHHHHHHHHHHh-----------CCCCEEecCccceecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5667777777666221 123443 223478899999987765 222344557788888776665
Q ss_pred CCCC
Q 031595 153 LPCR 156 (157)
Q Consensus 153 ~~~~ 156 (157)
..||
T Consensus 258 ~~~~ 261 (264)
T PRK01215 258 GIIR 261 (264)
T ss_pred Ceee
Confidence 5554
No 37
>cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.
Probab=35.72 E-value=2.8e+02 Score=23.59 Aligned_cols=120 Identities=14% Similarity=0.171 Sum_probs=58.1
Q ss_pred HHHHHHhhc-CccccCccccccccccccccCCCc----cee--eeecccccccc-ccCCCCCCCcccchHHHHHHHHHHH
Q 031595 23 FLRKILSTC-NHSKAFNKQTTHCRQKKLSRRKPI----LLS--TSIDRGYLTRT-AAGGVPPPPLDLTEDNVRQVIADAR 94 (157)
Q Consensus 23 ~l~~i~~~c-~~s~~f~~~~~~~~~~~~~~~~~~----~~~--t~~~r~~~~~~-~~~~~~~~~LeLteENVE~vLdeiR 94 (157)
-++|+.+.| .+....=.|++|.+....+..... .+. ..-.+...+.. ........+-++|+|+|+++.++..
T Consensus 78 ~~~~l~~~vh~~G~~~~~QL~H~G~~~~~~~~~~~~~~~~~~~~~~~~~~~ps~~~~~~~~~~p~~mt~~eI~~ii~~~~ 157 (336)
T cd02932 78 ALKRIVDFIHSQGAKIGIQLAHAGRKASTAPPWEGGGPLLPPGGGGWQVVAPSAIPFDEGWPTPRELTREEIAEVVDAFV 157 (336)
T ss_pred HHHHHHHHHHhcCCcEEEEccCCCcCCCCCCCccccccccccccCCCceeCCCCCcCCCCCCCCCcCCHHHHHHHHHHHH
Confidence 467888877 444455688999876654322100 000 00000000000 0011123457899999999999876
Q ss_pred HHHHhhhccccccccceEEEEecC-----------CeEEEEEeeccCc---chhhHHHHHHHHHHhhCC
Q 031595 95 GELAQLFDTSVGITGVAELAELDG-----------PFVKIRLRGRFWH---KRSTVIARLANYLKQRIP 149 (157)
Q Consensus 95 P~L~a~fD~sVGdGGdVELVeIDG-----------pvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IP 149 (157)
..-....+ ...+-|||.. |....|=-. .++ +++-+...|-+.+++.++
T Consensus 158 ~aA~~a~~------aGfDgVei~~~~gyLl~qFlsp~~N~R~D~-yGgsl~nr~rf~~eiv~aIR~~vG 219 (336)
T cd02932 158 AAARRAVE------AGFDVIEIHAAHGYLLHQFLSPLSNKRTDE-YGGSLENRMRFLLEVVDAVRAVWP 219 (336)
T ss_pred HHHHHHHH------cCCCEEEEccccccHHHHhcCCccCCCCcc-cCCCHHHHhHHHHHHHHHHHHHcC
Confidence 54432212 1122355542 223333221 122 455566667777777774
No 38
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=35.52 E-value=1.6e+02 Score=20.77 Aligned_cols=59 Identities=12% Similarity=0.104 Sum_probs=40.3
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhCCcCcCCCCC
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRIPVSPLPCRT 157 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPEI~~~~~~ 157 (157)
.++..+++|+.|+-.|.+ -|++. +.+|++++-= ..|.-...+.+..++++|+...|.|+
T Consensus 24 ~~~Q~~~v~~ni~~~L~~-------aG~~~------~dVv~~~iyl----~d~~~~~~~n~~~~~~f~~~~~Par~ 82 (101)
T cd06155 24 VEEQMESIFSKLREILQS-------NGLSL------SDILYVTLYL----RDMSDFAEVNSVYGTFFDKPNPPSRV 82 (101)
T ss_pred HHHHHHHHHHHHHHHHHH-------cCCCH------HHEEEEEEEE----CCHHHHHHHHHHHHHHcCCCCCCceE
Confidence 567899999999999987 22221 3455554321 23556677888888899887677764
No 39
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=34.61 E-value=68 Score=24.87 Aligned_cols=22 Identities=18% Similarity=0.202 Sum_probs=19.1
Q ss_pred CcccchHHHHHHHHHHHHHHHh
Q 031595 78 PLDLTEDNVRQVIADARGELAQ 99 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a 99 (157)
.-.-|.+++++|+.+++|.|..
T Consensus 17 RC~~Tg~~L~~av~~l~~~L~~ 38 (120)
T PF10865_consen 17 RCGDTGETLREAVKELAPVLAP 38 (120)
T ss_pred chhhHHHHHHHHHHHHHHHHHh
Confidence 3456899999999999999986
No 40
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=34.17 E-value=88 Score=22.16 Aligned_cols=27 Identities=15% Similarity=0.313 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhhhccccccccceEEEEecCCe
Q 031595 89 VIADARGELAQLFDTSVGITGVAELAELDGPF 120 (157)
Q Consensus 89 vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpv 120 (157)
-|+|-|..||+++- .|+|.|..+++..
T Consensus 30 sleetrkllqsmaa-----agqvtllrvendl 56 (61)
T PF09105_consen 30 SLEETRKLLQSMAA-----AGQVTLLRVENDL 56 (61)
T ss_dssp -HHHHHHHHHHHHH-----TTSEEEEEETTEE
T ss_pred cHHHHHHHHHHHHh-----cCceEEEEecccc
Confidence 36777888887655 8999999998654
No 41
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=33.76 E-value=92 Score=25.67 Aligned_cols=40 Identities=13% Similarity=0.197 Sum_probs=30.0
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH 131 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~ 131 (157)
+.+.+++.++.+.-... +-++ .+++++..|+|+++|-=-.
T Consensus 7 ~~~E~~~fle~l~~~~~---------~~~~-~v~~k~n~l~I~i~G~~~e 46 (190)
T PF09840_consen 7 DDEECEEFLERLSKMVK---------SIYI-YVEVKGNSLKIEIQGYEKE 46 (190)
T ss_pred ChHHHHHHHHHHHhhcc---------CcEE-EEEEeCCEEEEEEecChHH
Confidence 56778999999866654 3344 3788899999999996543
No 42
>TIGR01375 soxG sarcosine oxidase, gamma subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms.
Probab=33.39 E-value=89 Score=23.59 Aligned_cols=37 Identities=16% Similarity=0.263 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeecc
Q 031595 84 DNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRF 129 (157)
Q Consensus 84 ENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC 129 (157)
.+.++.++.++..+. +.++.++++.+..+.+.|||+=
T Consensus 51 ~~~~~~~~~l~~~~~---------~~~v~v~d~s~~~~~l~lqGP~ 87 (152)
T TIGR01375 51 PEGAVLMAALAAALG---------PEPHAVVDLSGGRTALRISGPM 87 (152)
T ss_pred cchHHHHHHHHHHhC---------CCccEEEEecCCEEEEEEEChh
Confidence 456777777777663 2258889998999999999973
No 43
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=33.08 E-value=1.6e+02 Score=20.72 Aligned_cols=59 Identities=17% Similarity=0.200 Sum_probs=38.2
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhCCcCcCCCCC
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRIPVSPLPCRT 157 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPEI~~~~~~ 157 (157)
.++..+++++.|+-.|.+ -|++. +.+||+++- -..|.-...+.+..++.+|+-..|.||
T Consensus 27 ~~~Q~~~~~~nl~~~L~~-------~G~~~------~dvvk~~vy----l~d~~~~~~~~~~~~~~f~~~~~Pa~t 85 (105)
T cd06150 27 ITGQTRQVLAKIDALLAE-------AGSDK------SRILSATIW----LADMADFAAMNAVWDAWVPPGHAPARA 85 (105)
T ss_pred HHHHHHHHHHHHHHHHHH-------cCCCH------HHEEEEEEE----EccHHHHHHHHHHHHHHcCCCCCCCeE
Confidence 578899999999999986 22222 245555532 123455566777778888875567664
No 44
>PRK10005 dihydroxyacetone kinase subunit DhaL; Provisional
Probab=33.02 E-value=41 Score=27.62 Aligned_cols=24 Identities=13% Similarity=0.302 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHhhhccccccc
Q 031595 84 DNVRQVIADARGELAQLFDTSVGIT 108 (157)
Q Consensus 84 ENVE~vLdeiRP~L~a~fD~sVGdG 108 (157)
+++.+.|.+.+|||.. .|+-+|||
T Consensus 13 ~~~~~~l~~~~~~Lt~-lD~~iGDG 36 (210)
T PRK10005 13 TRCGDIFTEESDYLTG-LDREIGDA 36 (210)
T ss_pred HHHHHHHHHhHHHHHH-HhccccCc
Confidence 3566677778999988 89889887
No 45
>COG3270 Uncharacterized conserved protein [Function unknown]
Probab=32.91 E-value=25 Score=28.14 Aligned_cols=80 Identities=21% Similarity=0.234 Sum_probs=53.1
Q ss_pred ccCCCcceeeeecccccccc-----ccCCCCCCCcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEec-CCeEEE
Q 031595 50 SRRKPILLSTSIDRGYLTRT-----AAGGVPPPPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELD-GPFVKI 123 (157)
Q Consensus 50 ~~~~~~~~~t~~~r~~~~~~-----~~~~~~~~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeID-GpvVkV 123 (157)
++|.-+.|+++++.+++..- .++.+.-...||++|. +|++.. |=||++-+=- .+-|-|
T Consensus 36 ~~r~GI~lg~~~kkg~r~s~e~~~al~p~~~~nsiELd~e~-------a~~w~r---------G~dV~~~~~~~~g~viv 99 (127)
T COG3270 36 KIHNGIKLGEIHKKGYRWSHEGGFALAPPAVRNSIELDEEE-------AREWMR---------GRDVEPQESGPAGWVIV 99 (127)
T ss_pred hhhcceEEEEEeccCeeEEeeEEEEeCChhhcceEEeCHHH-------HHhhhc---------CCccccCCCCCCceEEE
Confidence 34777888998888766533 4455555667787764 788886 7788743322 246888
Q ss_pred EEeeccCcchhhHHHHHHHHHHhhCC
Q 031595 124 RLRGRFWHKRSTVIARLANYLKQRIP 149 (157)
Q Consensus 124 rL~GaC~~s~mTvk~gVe~~LKe~IP 149 (157)
+.+|-.-+ +--+|.+.||..+|
T Consensus 100 ~~~~~~lG----~aK~vg~vlKN~~P 121 (127)
T COG3270 100 KFQGNGLG----LAKVVGNVLKNYFP 121 (127)
T ss_pred EECCcccc----eeeecCceecccCC
Confidence 88877666 33356777777777
No 46
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=31.80 E-value=97 Score=22.49 Aligned_cols=29 Identities=17% Similarity=0.170 Sum_probs=22.9
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEEEE
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAELAE 115 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVe 115 (157)
++++|+++++++.+...|.+ -||.|.-++
T Consensus 17 ~l~e~~~~~~~~~~~~~i~~-------~gg~i~~~~ 45 (97)
T CHL00123 17 DLNEEELLKWIENYKKLLRK-------RGAKNISVQ 45 (97)
T ss_pred CCCHHHHHHHHHHHHHHHHH-------CCCEEEEEE
Confidence 56899999999999999975 467664443
No 47
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=30.81 E-value=3.4e+02 Score=23.14 Aligned_cols=117 Identities=11% Similarity=0.152 Sum_probs=61.4
Q ss_pred HHHHHHhhc-CccccCccccccccccccccCCCcceeeeeccccccccccCCCCCCCcccchHHHHHHHHHHHHHHHhhh
Q 031595 23 FLRKILSTC-NHSKAFNKQTTHCRQKKLSRRKPILLSTSIDRGYLTRTAAGGVPPPPLDLTEDNVRQVIADARGELAQLF 101 (157)
Q Consensus 23 ~l~~i~~~c-~~s~~f~~~~~~~~~~~~~~~~~~~~~t~~~r~~~~~~~~~~~~~~~LeLteENVE~vLdeiRP~L~a~f 101 (157)
-++|+...| .+-+.+=-|++|.+....+.-....++.+-.. ...........+-++|+|.++++.++....-...-
T Consensus 83 ~~~~l~~~vh~~G~~~~~Ql~h~G~~~~~~~~~~~~~ps~~~---~~~~~~~~~~~p~~mt~~eI~~~i~~~~~aA~ra~ 159 (338)
T cd04733 83 AFREWAAAAKANGALIWAQLNHPGRQSPAGLNQNPVAPSVAL---DPGGLGKLFGKPRAMTEEEIEDVIDRFAHAARLAQ 159 (338)
T ss_pred HHHHHHHHHHhcCCEEEEEccCCCcCCCccCCCCCcCCCCCc---CcccccccCCCCCcCCHHHHHHHHHHHHHHHHHHH
Confidence 467888877 44445567899987764432211111110000 00000011124568999999999988754332211
Q ss_pred ccccccccceEEEEec-C----------CeEEEEEeeccCc---chhhHHHHHHHHHHhhCC
Q 031595 102 DTSVGITGVAELAELD-G----------PFVKIRLRGRFWH---KRSTVIARLANYLKQRIP 149 (157)
Q Consensus 102 D~sVGdGGdVELVeID-G----------pvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IP 149 (157)
. . ..+-|||. + |...-| +...++ +++-+-..|-+.+|+.++
T Consensus 160 ~-----a-GfDgVeih~a~gyLl~qFlsp~~N~R-~D~yGGslenR~rf~~EiI~aIR~avG 214 (338)
T cd04733 160 E-----A-GFDGVQIHAAHGYLLSQFLSPLTNKR-TDEYGGSLENRARLLLEIYDAIRAAVG 214 (338)
T ss_pred H-----c-CCCEEEEchhhhhHHHHhcCCcCCCC-CccCCCCHHHHHHHHHHHHHHHHHHcC
Confidence 1 1 13346665 2 333333 444444 567777778888888885
No 48
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=30.48 E-value=47 Score=25.07 Aligned_cols=64 Identities=19% Similarity=0.273 Sum_probs=37.4
Q ss_pred cccchHHHHHHHHH-HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHH-HHHHHHhhCCcC
Q 031595 79 LDLTEDNVRQVIAD-ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIAR-LANYLKQRIPVS 151 (157)
Q Consensus 79 LeLteENVE~vLde-iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~g-Ve~~LKe~IPEI 151 (157)
|..+++.+++-|.+ +.|+--..-|.|-|.|...+++ +|. -+|-|...--+-+ |...|+|.|+||
T Consensus 1 m~~~e~~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~-----IvS----~~FeGKs~L~rHRlVN~~L~Eeik~i 66 (85)
T KOG3348|consen 1 MTVTEERLEELLTEALEPEHVEVQDVSGGCGSMFDVV-----IVS----AAFEGKSLLARHRLVNSILAEEIKEI 66 (85)
T ss_pred CcchHHHHHHHHHhhcCceEEEEEEcCCCccceEEEE-----EEc----cccCChHHHHHHHHHHHHHHHHHHHH
Confidence 34566667666644 3666554557777777777755 222 2344422222222 788899988887
No 49
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=29.71 E-value=2.4e+02 Score=22.06 Aligned_cols=62 Identities=19% Similarity=0.381 Sum_probs=35.6
Q ss_pred CcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhC
Q 031595 78 PLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRI 148 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~I 148 (157)
|+-.+-.+|-++|..=-.++.+.|-...|..|+++ |+ .+.|+|++.. ..+...+.+|+++++
T Consensus 37 Tvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~-----~~--rlii~G~~~~--~~i~~~L~~yI~~yV 98 (133)
T TIGR00311 37 TIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLE-----GG--RLILQGKFTH--FLLNERIEDYVRKYV 98 (133)
T ss_pred EEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceec-----CC--EEEEEeecCH--HHHHHHHHHHHhheE
Confidence 33333333444433323444444445677788754 43 7899999876 346666777777654
No 50
>PRK09038 flagellar motor protein MotD; Reviewed
Probab=29.56 E-value=2.8e+02 Score=23.58 Aligned_cols=58 Identities=19% Similarity=0.351 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeec--cCc-------chhhHHHHHHHHHHhh
Q 031595 84 DNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR--FWH-------KRSTVIARLANYLKQR 147 (157)
Q Consensus 84 ENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga--C~~-------s~mTvk~gVe~~LKe~ 147 (157)
+.+++..++++.+|... +..|+|++- .++.-+.|+|.+. |.. ....+...|...|++.
T Consensus 96 ~~l~~l~~~l~~~l~~~-----~~~~~v~v~-~~~~gi~i~l~~~~lF~~gsa~l~~~~~~~L~~ia~~L~~~ 162 (281)
T PRK09038 96 DQLKTIADDLRKALGPL-----IESGQVTVR-RNELWIEIEINSSLLFGSGDAMLSDQAFAILEKVAEVLKPA 162 (281)
T ss_pred HHHHHHHHHHHHHHHhh-----hhcCceEEE-EeCCEEEEEeCCCCccCCCccccCHHHHHHHHHHHHHHHhC
Confidence 44566667777777642 236888854 5555678898764 322 3444556677788765
No 51
>PF03982 DAGAT: Diacylglycerol acyltransferase ; InterPro: IPR007130 The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT) [, ].; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=29.19 E-value=1.2e+02 Score=26.20 Aligned_cols=36 Identities=25% Similarity=0.325 Sum_probs=27.8
Q ss_pred cccchHHHHHHHHHHHHHHHhhhc---cccccccceEEE
Q 031595 79 LDLTEDNVRQVIADARGELAQLFD---TSVGITGVAELA 114 (157)
Q Consensus 79 LeLteENVE~vLdeiRP~L~a~fD---~sVGdGGdVELV 114 (157)
-+=|+|.|+++-+.-=..|++||| ..-|.-.|.+|+
T Consensus 257 ~~Pt~e~Vd~~H~~Y~~~L~~LFd~~K~~~g~~~d~~L~ 295 (297)
T PF03982_consen 257 ENPTQEDVDKLHARYIEALRELFDKHKAKYGYPPDTKLV 295 (297)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCeEE
Confidence 345789999999999999999998 345545677765
No 52
>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=28.94 E-value=1.2e+02 Score=20.81 Aligned_cols=35 Identities=26% Similarity=0.468 Sum_probs=22.8
Q ss_pred ccceEE-EEec-CCeEEEEEeeccCcchhhHHHHHHHHH
Q 031595 108 TGVAEL-AELD-GPFVKIRLRGRFWHKRSTVIARLANYL 144 (157)
Q Consensus 108 GGdVEL-VeID-GpvVkVrL~GaC~~s~mTvk~gVe~~L 144 (157)
+|.|++ ++|+ |-+-.+++.|-|-+... -..+++.|
T Consensus 15 ~G~v~v~~~V~~G~I~~i~i~gDf~~~~~--i~~le~~L 51 (86)
T PF10437_consen 15 WGTVEVHLNVKNGIIKDIKIYGDFFGPED--IEELEEAL 51 (86)
T ss_dssp TEEEEEEEEEETTEEEEEEEEECBS-CCC--HHHHHHHH
T ss_pred CceEEEEEEEECCEEEEEEEECCCCCchH--HHHHHHHH
Confidence 788885 4555 77778999999998422 23444444
No 53
>TIGR01297 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
Probab=28.77 E-value=1.9e+02 Score=22.93 Aligned_cols=18 Identities=11% Similarity=0.161 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHhhCCcCc
Q 031595 135 TVIARLANYLKQRIPVSP 152 (157)
Q Consensus 135 Tvk~gVe~~LKe~IPEI~ 152 (157)
.+...+|+.+++++|++.
T Consensus 242 ~i~~~i~~~i~~~~~~v~ 259 (268)
T TIGR01297 242 DIALEIEREILKRHPGIE 259 (268)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 445679999999999984
No 54
>PRK14438 acylphosphatase; Provisional
Probab=28.47 E-value=71 Score=22.88 Aligned_cols=33 Identities=18% Similarity=0.200 Sum_probs=26.1
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeec
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
.||+...+|. ..|..|-|. .++|+.|.+.++|.
T Consensus 18 FR~~~~~~A~-~~gl~G~V~--N~~dG~Vei~~qG~ 50 (91)
T PRK14438 18 FRHHTQQTAQ-RLNVSGWVK--NLPNGSVQGCFEGE 50 (91)
T ss_pred ccHHHHHHHH-HcCCEEEEE--ECCCCEEEEEEEEC
Confidence 3788877766 677888874 67799999999994
No 55
>PRK03114 NTPase; Reviewed
Probab=28.39 E-value=87 Score=25.55 Aligned_cols=42 Identities=24% Similarity=0.407 Sum_probs=33.0
Q ss_pred ccCCCCCCCcccchHHHHHHHHHHHHHHHhh-hccccccccceE
Q 031595 70 AAGGVPPPPLDLTEDNVRQVIADARGELAQL-FDTSVGITGVAE 112 (157)
Q Consensus 70 ~~~~~~~~~LeLteENVE~vLdeiRP~L~a~-fD~sVGdGGdVE 112 (157)
..|+++..|+-+ +|.++-++..++--|++. +|.+||+=|.|+
T Consensus 30 v~SgV~~QP~g~-eET~~GA~nRA~~A~~~~~aD~~VGiEgGv~ 72 (169)
T PRK03114 30 VPSGVAAQPFSD-EETMQGAINRAKRALEEGEADIGIGLEGGVM 72 (169)
T ss_pred CCCCcCCCCCCh-HHHHHHHHHHHHHHHhccCCCEEEEEeeeEe
Confidence 567777777763 889999999999888753 788899966665
No 56
>PF07634 RtxA: RtxA repeat; InterPro: IPR011509 This short repeat is found in the RtxA toxin family [].
Probab=28.34 E-value=22 Score=19.16 Aligned_cols=11 Identities=36% Similarity=0.428 Sum_probs=7.8
Q ss_pred cccccccceEE
Q 031595 103 TSVGITGVAEL 113 (157)
Q Consensus 103 ~sVGdGGdVEL 113 (157)
|.+|++|++.|
T Consensus 9 t~~G~~~~v~f 19 (19)
T PF07634_consen 9 THVGDGGNVSF 19 (19)
T ss_pred EEEecCCeEEC
Confidence 46788888764
No 57
>PRK06778 hypothetical protein; Validated
Probab=28.18 E-value=1.4e+02 Score=25.85 Aligned_cols=56 Identities=11% Similarity=0.125 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeec-----cCc-------chhhHHHHHHHHHHhh
Q 031595 86 VRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR-----FWH-------KRSTVIARLANYLKQR 147 (157)
Q Consensus 86 VE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga-----C~~-------s~mTvk~gVe~~LKe~ 147 (157)
+++..++++.++.. -+..|+|++ ++++.-+.|+|... |.. ....+...|...|++.
T Consensus 114 l~~l~~~l~~~l~~-----~~~~~~v~v-~~~~~Gl~i~l~~~~~~~lF~~gsa~L~~~~~~~L~~ia~~l~~~ 181 (289)
T PRK06778 114 LGELATSINTIARD-----AHMEANLEM-EIVPQGLRVLIKDDQNRNMFERGSAQIMPFFKTLLVELAPVFDSL 181 (289)
T ss_pred HHHHHHHHHHHHHH-----hhhcCCeEE-EEeCCeEEEEEecCCCCCCcCCCccccCHHHHHHHHHHHHHHHcC
Confidence 44555666666654 235788985 45555678889774 655 2334455566677665
No 58
>PRK05074 inosine/xanthosine triphosphatase; Reviewed
Probab=28.11 E-value=82 Score=25.78 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=32.8
Q ss_pred cccCCCCCCCcccchHHHHHHHHHHHHHHHhh--hccccccccceE
Q 031595 69 TAAGGVPPPPLDLTEDNVRQVIADARGELAQL--FDTSVGITGVAE 112 (157)
Q Consensus 69 ~~~~~~~~~~LeLteENVE~vLdeiRP~L~a~--fD~sVGdGGdVE 112 (157)
+..|+++..|+- .+|.++-++..++--+++. +|.+||+=|.|+
T Consensus 37 ~v~SgV~~QP~g-~eET~~GA~nRA~~a~~~~~~ad~gVGiEgGv~ 81 (173)
T PRK05074 37 AVPSGVPDQPMG-SEETRAGARNRVKNARQLRPEADFWVAIEAGID 81 (173)
T ss_pred ecCCCcCCCCCC-hHHHHHHHHHHHHHHHHhCCCCCEEEEEccccc
Confidence 345677777776 3788999999999998875 788899865553
No 59
>PRK14447 acylphosphatase; Provisional
Probab=27.79 E-value=89 Score=22.60 Aligned_cols=33 Identities=18% Similarity=0.268 Sum_probs=26.0
Q ss_pred HHHHHHhhhccccccccceEEEEecCC-eEEEEEeec
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGP-FVKIRLRGR 128 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGp-vVkVrL~Ga 128 (157)
.||+.+++|+ .-|+.|-|. ..+|+ .|.+.++|.
T Consensus 19 FR~~~~~~A~-~~gl~G~V~--N~~dG~~Vei~~qG~ 52 (95)
T PRK14447 19 FRQSMKEVAN-RNGVRGWVR--NRSDGRTVEAVLEGP 52 (95)
T ss_pred chHHHHHHHh-hcCeEEEEE--ECCCCCEEEEEEEeC
Confidence 4888888777 677888875 45677 699999996
No 60
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=27.64 E-value=2e+02 Score=19.45 Aligned_cols=42 Identities=12% Similarity=0.162 Sum_probs=25.9
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEee
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRG 127 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~G 127 (157)
.++...|+++|+.+--.+..-. ..|+.|+|-++ +..+++++.
T Consensus 15 ~~~~~~v~~vl~~l~~~i~~~L----~~g~~V~i~g~--G~F~~~~~~ 56 (90)
T smart00411 15 GLSKKDAKAAVDAFLEIITEAL----KKGEKVELRGF--GTFEVRERK 56 (90)
T ss_pred CCCHHHHHHHHHHHHHHHHHHH----hCCCeEEEeCc--EEEEEEeec
Confidence 4678888888877766555322 24776664333 566666665
No 61
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=27.56 E-value=1.2e+02 Score=22.56 Aligned_cols=37 Identities=11% Similarity=0.099 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHhhhccccccccceE-EEEecCCeEEEEEe
Q 031595 86 VRQVIADARGELAQLFDTSVGITGVAE-LAELDGPFVKIRLR 126 (157)
Q Consensus 86 VE~vLdeiRP~L~a~fD~sVGdGGdVE-LVeIDGpvVkVrL~ 126 (157)
++++|+.|--.|..+.| .++++. =++..|+++.|.+.
T Consensus 6 ad~~L~~ie~~le~~~d----~~~d~~~D~e~~~gVLti~~~ 43 (97)
T TIGR03422 6 ADEYLDHLLDKLEELGE----SRPDLDFDVEYSSGVLTLELP 43 (97)
T ss_pred HHHHHHHHHHHHHhhcc----cccccccccccCCCEEEEEEC
Confidence 45566666656654333 344553 13345778887774
No 62
>PRK14427 acylphosphatase; Provisional
Probab=26.95 E-value=89 Score=22.62 Aligned_cols=47 Identities=21% Similarity=0.269 Sum_probs=33.0
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQR 147 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~ 147 (157)
.||+..++|. .-|..|-|. .++++.|.+.++|.=. . .....++|++.
T Consensus 21 FR~fv~~~A~-~lgl~G~V~--N~~dGsVei~~qG~~~----~-i~~f~~~l~~~ 67 (94)
T PRK14427 21 FRYWTMRKAE-ELGLTGTVR--NLDDGSVALVAEGTGE----Q-VEKLLDWLNSD 67 (94)
T ss_pred ChHHHHHHHH-HcCCEEEEE--ECCCCeEEEEEEECHH----H-HHHHHHHHhhC
Confidence 3788887776 677889885 5678999999999422 1 34455666654
No 63
>PRK14445 acylphosphatase; Provisional
Probab=26.55 E-value=99 Score=22.07 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=26.0
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeec
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
.||+..++|. .-|..|-|. .++++.|.+.++|.
T Consensus 19 FR~~v~~~A~-~~gl~G~V~--N~~dG~Vei~~qG~ 51 (91)
T PRK14445 19 FRMFIDRAAS-ELNLSGWVR--NLPDGTVEIEAQGS 51 (91)
T ss_pred ChHHHHHHHh-hCCCEEEEE--ECCCCeEEEEEEEC
Confidence 3788887766 677888875 56788999999994
No 64
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=26.45 E-value=1.2e+02 Score=22.62 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccccceEEEEe
Q 031595 83 EDNVRQVIADARGELAQLFDTSVGITGVAELAEL 116 (157)
Q Consensus 83 eENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeI 116 (157)
++-|+.+||.|.-.|.+ |..|+|..+
T Consensus 23 ~~~v~~~~~~i~~aL~~--------G~~V~l~gF 48 (94)
T COG0776 23 EEAVDAFLEEITEALAK--------GERVELRGF 48 (94)
T ss_pred HHHHHHHHHHHHHHHHc--------CCeEEEeee
Confidence 34578888899999975 999999766
No 65
>PRK14424 acylphosphatase; Provisional
Probab=26.07 E-value=84 Score=22.98 Aligned_cols=46 Identities=20% Similarity=0.333 Sum_probs=32.2
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQ 146 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe 146 (157)
.||+...+|. .-|+.|-|. .++++.|.+.++|.=-. .....+.|++
T Consensus 22 FR~~v~~~A~-~~gl~G~V~--N~~dG~Vei~~qG~~~~-----v~~f~~~l~~ 67 (94)
T PRK14424 22 FRHATVREAH-ALGLRGWVA--NLEDGTVEAMIQGPAAQ-----IDRMLAWLRH 67 (94)
T ss_pred hHHHHHHHHH-HcCCeEEEE--ECCCCCEEEEEEECHHH-----HHHHHHHHHh
Confidence 4788887766 677889887 67788999999994322 3444455553
No 66
>PRK14133 DNA polymerase IV; Provisional
Probab=25.98 E-value=3.3e+02 Score=23.07 Aligned_cols=60 Identities=15% Similarity=0.234 Sum_probs=36.6
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhC-CcCcCCC
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRI-PVSPLPC 155 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~I-PEI~~~~ 155 (157)
..+.-+++++.+--+|.+. .-.||.+.||+ +.|.++|..++ - ..+.+.|+++| -+..++|
T Consensus 75 d~~~y~~~s~~i~~~l~~~-------s~~ve~~siDe--~~ldv~~~~~~-~----~~la~~i~~~i~~~~gl~~ 135 (347)
T PRK14133 75 RHERYKEVSKNIFKILYEV-------TPIVEPVSIDE--AYLDITNIKEE-P----IKIAKYIKKKVKKETGLTL 135 (347)
T ss_pred CHHHHHHHHHHHHHHHHHh-------CCceEEccCCe--EEEEccCCCCC-H----HHHHHHHHHHHHHHHCCcE
Confidence 4456677888888777763 34788888875 55666776533 2 23445555554 3444544
No 67
>PF14280 DUF4365: Domain of unknown function (DUF4365)
Probab=25.69 E-value=75 Score=22.89 Aligned_cols=48 Identities=21% Similarity=0.301 Sum_probs=32.5
Q ss_pred cccccceEEEE----ecCCeEEEEEeeccCc--------chhhH-HHHHHHHHHhhCCcCc
Q 031595 105 VGITGVAELAE----LDGPFVKIRLRGRFWH--------KRSTV-IARLANYLKQRIPVSP 152 (157)
Q Consensus 105 VGdGGdVELVe----IDGpvVkVrL~GaC~~--------s~mTv-k~gVe~~LKe~IPEI~ 152 (157)
.|+=|.||+++ ..|..+.|+|+|.-.- -...+ +.-++.+++..+|=|.
T Consensus 27 ~GiD~~Ie~~~~~g~~tg~~i~VQlK~t~~~~~~~~~~~~~~~~~~~~l~y~~~~~~Pvil 87 (138)
T PF14280_consen 27 YGIDGEIEIVDDDGKPTGRRIAVQLKSTESYFYENDDGSFSFPLDKEHLNYWLNHPVPVIL 87 (138)
T ss_pred ccEeeEEEEEecCCcccCCEEEEEEcccCcccccCCCceEEEeeCHHHHHHHhcCCCCEEE
Confidence 67779999998 3478999999987653 12233 4556666666666543
No 68
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=25.56 E-value=1.4e+02 Score=21.51 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=23.2
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEEEE
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAELAE 115 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVe 115 (157)
+++++.++++++.+...|.. .||.|.-++
T Consensus 13 ~~~~~~~~~~~~~~~~~i~~-------~gg~i~~~~ 41 (108)
T PRK00453 13 DLSEEQVKALVERFKGVITE-------NGGTIHKVE 41 (108)
T ss_pred CCCHHHHHHHHHHHHHHHHH-------CCCEEEEEe
Confidence 46899999999999999985 477775554
No 69
>TIGR00532 HMG_CoA_R_NAD hydroxymethylglutaryl-CoA reductase, degradative. Most known examples of hydroxymethylglutaryl-CoA reductase are NADP-dependent (EC 1.1.1.34) from eukaryotes and archaea, involved in the biosynthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA. This model, in contrast, is built from the two examples in completed genomes of sequences closely related to the degradative, NAD-dependent hydroxymethylglutaryl-CoA reductase of Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source.
Probab=24.51 E-value=3.6e+02 Score=24.84 Aligned_cols=45 Identities=9% Similarity=0.220 Sum_probs=32.0
Q ss_pred cccceEEEE------ecCCeEEEEEeeccCc----c-hhhHHHHHHHHHHhhCCcC
Q 031595 107 ITGVAELAE------LDGPFVKIRLRGRFWH----K-RSTVIARLANYLKQRIPVS 151 (157)
Q Consensus 107 dGGdVELVe------IDGpvVkVrL~GaC~~----s-~mTvk~gVe~~LKe~IPEI 151 (157)
-||.+..++ ++|+.|+||+.=.|+- + .-|+...+..+|.+..|+-
T Consensus 160 rggg~~~i~~r~~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~Eav~~~i~~~~~~~ 215 (393)
T TIGR00532 160 LGGGCKDIEARVIDIIEGGILILHIIVDTCDAMGANALNSIAEKVAEFIELEFGGE 215 (393)
T ss_pred hcCCeEEEEEEeeecccCCEEEEEEEEecccccccHHHHHHHHHHHHHHHHhCCCc
Confidence 467666555 3488999999766554 2 3457778889999888763
No 70
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=24.44 E-value=1.7e+02 Score=20.27 Aligned_cols=59 Identities=22% Similarity=0.385 Sum_probs=35.8
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCC-----eEEEEEeeccCc----chhhHHHHHHHHHH
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGP-----FVKIRLRGRFWH----KRSTVIARLANYLK 145 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGp-----vVkVrL~GaC~~----s~mTvk~gVe~~LK 145 (157)
+++++.++++++.+.-.+.+ .||.|.-++-=|- .++=.-+|-++. +......-+++.|+
T Consensus 12 ~~~~~~~~~~~~~~~~~i~~-------~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~~~~f~~~~~~i~el~~~l~ 79 (92)
T PF01250_consen 12 DLSEEEIKKLIERVKKIIEK-------NGGVVRSVENWGKRRLAYPIKKQKEGHYFLFNFDASPSAIKELERKLR 79 (92)
T ss_dssp TSCHHHHHHHHHHHHHHHHH-------TTEEEEEEEEEEEEEESSEETTECEEEEEEEEEEESTTHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHH-------CCCEEEEEEEEeecccccCCCCCCEEEEEEEEEEeCHHHHHHHHHHhc
Confidence 45788999999999999975 5787765543221 111123444443 34455556666665
No 71
>TIGR00252 conserved hypothetical protein TIGR00252. the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment
Probab=24.42 E-value=2.6e+02 Score=21.29 Aligned_cols=49 Identities=22% Similarity=0.305 Sum_probs=31.7
Q ss_pred ccceEEEEecC-CeEEEEEeeccC----c--------chhhHHHHHHHHHHhhCCc-CcCCCC
Q 031595 108 TGVAELAELDG-PFVKIRLRGRFW----H--------KRSTVIARLANYLKQRIPV-SPLPCR 156 (157)
Q Consensus 108 GGdVELVeIDG-pvVkVrL~GaC~----~--------s~mTvk~gVe~~LKe~IPE-I~~~~~ 156 (157)
.|.|+||--|| -.|.|..+.+.. + .+--+....+.||.+.-|. -..|||
T Consensus 36 ~GEIDiIa~~~~~lvFVEVK~R~~~~~g~~~eaV~~~K~~ri~~aA~~yL~~~~~~~~~~~~R 98 (119)
T TIGR00252 36 WGEIDLIMHDTKTIAFVEVRTRSGGNYGGALLSVNARKQEKILQTANLWLASQNPSWSDWNCR 98 (119)
T ss_pred CCcEEEEEeeCCEEEEEEEEecCCCCCCChHHcCCHHHHHHHHHHHHHHHHhCCCCCCCCCEE
Confidence 69999999885 466777776543 3 2444555577899877443 234665
No 72
>PRK14449 acylphosphatase; Provisional
Probab=24.33 E-value=1e+02 Score=21.92 Aligned_cols=33 Identities=36% Similarity=0.328 Sum_probs=25.8
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeec
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
.||+..++|+ .-|..|-|. .++++.|.+.++|.
T Consensus 18 FR~fv~~~A~-~lgl~G~V~--N~~dG~Vei~~~G~ 50 (90)
T PRK14449 18 LRYSVYQKAV-SLGITGYAE--NLYDGSVEVVAEGD 50 (90)
T ss_pred hHHHHHHHHH-HcCCEEEEE--ECCCCeEEEEEEeC
Confidence 4888888776 567888864 56788999999994
No 73
>cd07059 BMC_PduA 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain. PduA is encoded within the 1,2-propanediol utilization (pdu) operon along with other homologous carboxysome shell proteins PduB, B', J, K, T, and U. PduA is thought to be required for the formation of the outer shell of bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduA might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, like PduU does, at present no experimental evidence directly supports this view.
Probab=24.33 E-value=1.4e+02 Score=21.72 Aligned_cols=34 Identities=21% Similarity=0.240 Sum_probs=25.1
Q ss_pred ccceEEEEec---CCeEEEEEeeccCcchhhHHHHHH
Q 031595 108 TGVAELAELD---GPFVKIRLRGRFWHKRSTVIARLA 141 (157)
Q Consensus 108 GGdVELVeID---GpvVkVrL~GaC~~s~mTvk~gVe 141 (157)
..||+|+.++ ++.+.+.++|.-+.-+.-+.++.+
T Consensus 23 aA~V~Li~~~~~~~G~~~v~v~GdVsaV~aAv~ag~~ 59 (85)
T cd07059 23 AANVTLVGKEQIGGGLVTVMVRGDVGAVKAATDAGAA 59 (85)
T ss_pred hCceEEEEEEecCCeEEEEEEEecHHHHHHHHHHHHH
Confidence 5799999885 789999999987764444444443
No 74
>cd06154 YjgF_YER057c_UK114_like_6 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=24.14 E-value=2.8e+02 Score=20.01 Aligned_cols=58 Identities=14% Similarity=0.055 Sum_probs=37.6
Q ss_pred chHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhCCcCcCCCCC
Q 031595 82 TEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRIPVSPLPCRT 157 (157)
Q Consensus 82 teENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPEI~~~~~~ 157 (157)
.++..+++|+.++-.|.+ -|++. +.+||++.-=.. +.-...+.+..++.+|+ ..|.||
T Consensus 42 ~~~Q~~~~~~ni~~~L~~-------aG~~~------~dVvk~~vyl~d----~~~~~~~~~~~~~~f~~-~~Part 99 (119)
T cd06154 42 AYEQTRQCLEIIEAALAE-------AGASL------EDVVRTRMYVTD----IADFEAVGRAHGEVFGD-IRPAAT 99 (119)
T ss_pred HHHHHHHHHHHHHHHHHH-------cCCCH------HHEEEEEEEECC----HHHHHHHHHHHHHHcCC-CCCceE
Confidence 578899999999999986 23332 456666543222 33344567777888887 457664
No 75
>COG5005 Mu-like prophage protein gpG [General function prediction only]
Probab=23.93 E-value=1.1e+02 Score=25.07 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=24.9
Q ss_pred CCCCCCCcccchHHHHHHHHHHHHHHHh
Q 031595 72 GGVPPPPLDLTEDNVRQVIADARGELAQ 99 (157)
Q Consensus 72 ~~~~~~~LeLteENVE~vLdeiRP~L~a 99 (157)
..++-|=|.|+.+..++.+|+|+-||+.
T Consensus 109 ~IpARpfl~l~~~deqei~d~i~~yf~~ 136 (140)
T COG5005 109 AIPARPFLGLTPDDEQEIMDDIQDYFSE 136 (140)
T ss_pred ccCCCcccccChhhHHHHHHHHHHHHHH
Confidence 4567788999999999999999999985
No 76
>PRK14446 acylphosphatase; Provisional
Probab=23.66 E-value=1e+02 Score=22.24 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=32.2
Q ss_pred HHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHh
Q 031595 94 RGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQ 146 (157)
Q Consensus 94 RP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe 146 (157)
|||-.++|+ .-|+.|-|. ..+|+.|.+.++|.= .-......+|++
T Consensus 18 R~fv~~~A~-~lgl~G~V~--N~~dGsVei~~qG~~-----~~l~~f~~~l~~ 62 (88)
T PRK14446 18 RASTRERAV-ALGLVGHAR--NQADGSVEVVAAGSA-----AALEALEAWLWQ 62 (88)
T ss_pred hHHHHHHHe-eCCeEEEEE--ECCCCCEEEEEEeCH-----HHHHHHHHHHhh
Confidence 888887776 677888775 667899999999942 134455666663
No 77
>PRK14684 hypothetical protein; Provisional
Probab=23.66 E-value=2.8e+02 Score=21.16 Aligned_cols=49 Identities=29% Similarity=0.468 Sum_probs=32.0
Q ss_pred ccceEEEEec-CCeEEEEEeeccC----c--------chhhHHHHHHHHHHhhCCcCcCCCC
Q 031595 108 TGVAELAELD-GPFVKIRLRGRFW----H--------KRSTVIARLANYLKQRIPVSPLPCR 156 (157)
Q Consensus 108 GGdVELVeID-GpvVkVrL~GaC~----~--------s~mTvk~gVe~~LKe~IPEI~~~~~ 156 (157)
.|.|+||-.| +-.|.|..+.+.. + .+..+....+.||.++=-.-..|||
T Consensus 36 ~GEIDiIa~~~~~lvFVEVK~R~~~~~g~~~eaV~~~K~~rl~r~A~~yL~~~~~~~~~~~R 97 (120)
T PRK14684 36 QGEIDLIMSDQSMLVFIEVRYRRFSDFIHPVATVTPLKQRRLIKTALHYLQKHRLLDKISCR 97 (120)
T ss_pred CCeEEEEEEeCCEEEEEEEeEcCCCCCCChHHcCCHHHHHHHHHHHHHHHHhCCCCCCCCEE
Confidence 6999999988 4566777776543 2 3555666678888665322244665
No 78
>PF14135 DUF4302: Domain of unknown function (DUF4302)
Probab=23.54 E-value=57 Score=26.74 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=24.0
Q ss_pred cccccceEEEEec--CCeEEEEEeeccCcchhhHH
Q 031595 105 VGITGVAELAELD--GPFVKIRLRGRFWHKRSTVI 137 (157)
Q Consensus 105 VGdGGdVELVeID--GpvVkVrL~GaC~~s~mTvk 137 (157)
.|.+||.||+=+. +. +|.|+|.-+++.|+|.
T Consensus 110 ~G~~gD~EF~i~~~~~d--~I~l~Gkk~~n~~~l~ 142 (235)
T PF14135_consen 110 KGLGGDFEFVIDSATND--SIKLKGKKNGNEMVLT 142 (235)
T ss_pred ccccccEEEEEEeccCC--EEEEEeeccCCEEEEE
Confidence 6778999998554 44 6778899999766665
No 79
>PRK14429 acylphosphatase; Provisional
Probab=23.54 E-value=1.1e+02 Score=21.84 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=32.2
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQR 147 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~ 147 (157)
.||+..++|. .-|..|-|. ..+++.|.+.++|.=.. .......|++.
T Consensus 17 FR~~v~~~A~-~~gl~G~V~--N~~dG~Vei~~qG~~~~-----i~~f~~~l~~g 63 (90)
T PRK14429 17 CRRATLTKAR-ALGVTGYVT--NCEDGSVEILAQGSDPA-----VDNLIAWCEVG 63 (90)
T ss_pred eHHHHHHHHH-HhCCEEEEE--ECCCCeEEEEEEeCHHH-----HHHHHHHHhhC
Confidence 3788877765 567888874 56789999999995322 34445556655
No 80
>PRK14422 acylphosphatase; Provisional
Probab=23.41 E-value=93 Score=22.48 Aligned_cols=47 Identities=21% Similarity=0.140 Sum_probs=32.5
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQR 147 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~ 147 (157)
.||+..++|. +-|..|-|. ..+++.|.+.++|.=.. .....+.|++.
T Consensus 21 FR~~v~~~A~-~~gl~G~V~--N~~dG~Vei~~~G~~~~-----i~~f~~~l~~g 67 (93)
T PRK14422 21 FRWWTRSRAL-ELGLTGYAA--NLADGRVQVVAEGPRAA-----CEKLLQLLRGD 67 (93)
T ss_pred cHHHHHHHHH-HcCCEEEEE--ECCCCCEEEEEEcCHHH-----HHHHHHHHHhC
Confidence 3888888776 677888875 56788899999994222 34455566655
No 81
>PF11340 DUF3142: Protein of unknown function (DUF3142); InterPro: IPR021488 This bacterial family of proteins has no known function.
Probab=23.30 E-value=3.8e+02 Score=22.41 Aligned_cols=61 Identities=21% Similarity=0.211 Sum_probs=40.5
Q ss_pred CCCCcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEec-CCeEEEEEeeccCcchhhHHHHHHHHHHhhCCc-Cc
Q 031595 75 PPPPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELD-GPFVKIRLRGRFWHKRSTVIARLANYLKQRIPV-SP 152 (157)
Q Consensus 75 ~~~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeID-GpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPE-I~ 152 (157)
..++|++.++.+..++..++-.=. -|-+|.=++|| | |.+++..-=...=+.||+++|. +.
T Consensus 15 r~~~Ld~~~~~~~~i~~~l~~W~~--------~G~~v~giQIDfD----------a~t~~L~~Y~~fL~~LR~~LP~~~~ 76 (181)
T PF11340_consen 15 RLPRLDWPEQVLARILQLLQRWQA--------AGNNVAGIQIDFD----------AATSRLPAYAQFLQQLRQRLPPDYR 76 (181)
T ss_pred ecccCCCCHHHHHHHHHHHHHHHH--------cCCCceEEEEecC----------ccccchHHHHHHHHHHHHhCCCCce
Confidence 345677767776666666544433 25578888898 5 5666666666677788999985 44
Q ss_pred C
Q 031595 153 L 153 (157)
Q Consensus 153 ~ 153 (157)
|
T Consensus 77 L 77 (181)
T PF11340_consen 77 L 77 (181)
T ss_pred E
Confidence 3
No 82
>cd07057 BMC_CcmK Carbon dioxide concentrating mechanism (CcmK); Bacterial Micro-Compartment (BCM) domain. CcmK1-4 and CcmL proteins found in Synechocystis sp. strain PCC 6803 make up the beta carboxysome shell. These CcmK proteins have been shown to form hexameric units, while the CcmL proteins have been shown to form pentameric units. Together these proteins further assemble into the flat facets of the polyhedral carboxysome shell. The structures suggest that the central pores and the gaps between hexamers limit the transport of metabolites into and out of the the carboxysome.
Probab=23.13 E-value=1.4e+02 Score=21.87 Aligned_cols=33 Identities=15% Similarity=0.192 Sum_probs=24.2
Q ss_pred ccceEEEEec---CCeEEEEEeeccCcchhhHHHHH
Q 031595 108 TGVAELAELD---GPFVKIRLRGRFWHKRSTVIARL 140 (157)
Q Consensus 108 GGdVELVeID---GpvVkVrL~GaC~~s~mTvk~gV 140 (157)
..||+|++++ ++.+.+.++|--+.-+.-+.++.
T Consensus 23 aA~V~L~~~~~~~~Gk~~v~v~GdvsaV~aAv~ag~ 58 (88)
T cd07057 23 AARVTLVGYEKIGSGRCTVIVRGDVAEVKAAVEAGI 58 (88)
T ss_pred hCceEEEEEEecCCeEEEEEEEEcHHHHHHHHHHHH
Confidence 5799999887 78899999998766344444443
No 83
>PF00708 Acylphosphatase: Acylphosphatase; InterPro: IPR001792 Acylphosphatase (3.6.1.7 from EC) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly beta-sheet structure with 2 short alpha-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. While bacterial and archebacterial hypothetical proteins that are highly similar to that enzyme and that probably possess the same activity. These proteins include: Escherichia coli putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yccX). Bacillus subtilis putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yflL). Archaeoglobus fulgidus putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (O29440 from SWISSPROT). An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [, ].; PDB: 1APS_A 1GXT_A 1GXU_A 2HLT_A 2FHM_A 2HLU_A 3BR8_A 1ULR_A 3TRG_A 2BJD_A ....
Probab=23.07 E-value=1.2e+02 Score=21.07 Aligned_cols=50 Identities=22% Similarity=0.312 Sum_probs=31.6
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHhhCCc
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQRIPV 150 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe~IPE 150 (157)
.||+..++|. .-|..|-|. ..+++.|.+.++|.=.. ....-.+|++.-|.
T Consensus 19 FR~~v~~~A~-~~gl~G~V~--N~~dg~V~i~~~G~~~~-----l~~f~~~l~~g~p~ 68 (91)
T PF00708_consen 19 FRPFVKRIAR-KLGLTGWVR--NLPDGSVEIEAEGEEEQ-----LEEFIKWLKKGPPP 68 (91)
T ss_dssp HHHHHHHHHH-HTT-EEEEE--E-TTSEEEEEEEEEHHH-----HHHHHHHHHHSSTT
T ss_pred hhHHHHHHHH-HhCCceEEE--ECCCCEEEEEEEeCHHH-----HHHHHHHHHhCCCC
Confidence 4788877766 567788765 45688999999994222 33445556665553
No 84
>PF00368 HMG-CoA_red: Hydroxymethylglutaryl-coenzyme A reductase; InterPro: IPR002202 Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A reductase, HMG-CoA reductase. There are two distinct classes of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase enzymes: class I consists of eukaryotic and most archaeal enzymes (1.1.1.34 from EC), while class II consists of prokaryotic enzymes (1.1.1.88 from EC) [, ]. Class I HMG-CoA reductases catalyse the NADP-dependent synthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). In vertebrates, membrane-bound HMG-CoA reductase is the rate-limiting enzyme in the biosynthesis of cholesterol and other isoprenoids. In plants, mevalonate is the precursor of all isoprenoid compounds []. The reduction of HMG-CoA to mevalonate is regulated by feedback inhibition by sterols and non-sterol metabolites derived from mevalonate, including cholesterol. In archaea, HMG-CoA reductase is a cytoplasmic enzyme involved in the biosynthesis of the isoprenoids side chains of lipids []. Class I HMG-CoA reductases consist of an N-terminal membrane domain (lacking in archaeal enzymes), and a C-terminal catalytic region. The catalytic region can be subdivided into three domains: an N-domain (N-terminal), a large L-domain, and a small S-domain (inserted within the L-domain). The L-domain binds the substrate, while the S-domain binds NADP. Class II HMG-CoA reductases catalyse the reverse reaction of class I enzymes, namely the NAD-dependent synthesis of HMG-CoA from mevalonate and CoA []. Some bacteria, such as Pseudomonas mevalonii, can use mevalonate as the sole carbon source. Class II enzymes lack a membrane domain. Their catalytic region is structurally related to that of class I enzymes, but it consists of only two domains: a large L-domain and a small S-domain (inserted within the L-domain). As with class I enzymes, the L-domain binds substrate, but the S-domain binds NAD (instead of NADP in class I).; GO: 0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity, 0050662 coenzyme binding, 0015936 coenzyme A metabolic process, 0055114 oxidation-reduction process; PDB: 2Q6B_C 2Q6C_D 1HWI_C 1HWJ_C 3CD5_B 2R4F_C 1HWL_B 1HWK_C 1DQA_B 3CCT_D ....
Probab=22.94 E-value=2.8e+02 Score=25.15 Aligned_cols=68 Identities=16% Similarity=0.172 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccceEEE--EecCCeEEEEEeeccCc-----chhhHHHHHHHHHHhhCCcCc
Q 031595 84 DNVRQVIADARGELAQLFDTSVGITGVAELA--ELDGPFVKIRLRGRFWH-----KRSTVIARLANYLKQRIPVSP 152 (157)
Q Consensus 84 ENVE~vLdeiRP~L~a~fD~sVGdGGdVELV--eIDGpvVkVrL~GaC~~-----s~mTvk~gVe~~LKe~IPEI~ 152 (157)
..+.+.+.+-+..|.++|+ ++--||.+.=+ .++|+.|.|++.=.++- -..|....|..+|.+..|+..
T Consensus 115 ~~~~~~i~~~~~~l~~~a~-~~sr~ggl~~i~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~e~v~~~i~~~~~~~~ 189 (373)
T PF00368_consen 115 AAFKQWIEENFEELKEIAN-STSRGGGLRDIEVRIVGRFVHLRFHYDTGDAMGANMVNTATEAVCPWIEEQFGGMV 189 (373)
T ss_dssp HHHHHHHHHTHHHHHHHHH-HHCCTEEEEEEEEEECSTEEEEEEEEEETTC--HHHHHHHHHHHHHHHHHHHTSEE
T ss_pred HHHHHHHHHHHHHHHHhhh-hcCCceeeeEEEEEecCCEEEEEEEEEccccchhhHHHHHHHHHHHHHHHhcccce
Confidence 4456666666777777666 33345544333 44699999999766554 255677789999999877754
No 85
>PRK14448 acylphosphatase; Provisional
Probab=22.88 E-value=98 Score=22.17 Aligned_cols=46 Identities=22% Similarity=0.174 Sum_probs=31.7
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQ 146 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe 146 (157)
.||+..++|+ ..|..|-|. .++++.|.+.++|.=.. .......|++
T Consensus 17 FR~~v~~~A~-~lgl~G~V~--N~~dG~Vei~~~G~~~~-----v~~f~~~l~~ 62 (90)
T PRK14448 17 FRYFTWQEAT-KIGIKGYVK--NRPDGSVEVVAVGSDAQ-----IAAFRDWLQH 62 (90)
T ss_pred hHHHHHHHHH-HhCCEEEEE--ECCCCCEEEEEEeCHHH-----HHHHHHHHHh
Confidence 4888888776 677888874 56688899999995322 3444455553
No 86
>PRK14441 acylphosphatase; Provisional
Probab=22.78 E-value=1.3e+02 Score=21.65 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=31.7
Q ss_pred HHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCcchhhHHHHHHHHHHh
Q 031595 93 ARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWHKRSTVIARLANYLKQ 146 (157)
Q Consensus 93 iRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~s~mTvk~gVe~~LKe 146 (157)
.||+..++|. +-|..|-|. ..+|+.|.+-++|. .. -......+|++
T Consensus 20 FR~~v~~~A~-~lgL~G~V~--N~~dG~Vei~~qG~----~~-~i~~f~~~l~~ 65 (93)
T PRK14441 20 FRQSAADEAR-RLGVEGWVR--NLPDGRVEAEAEGE----RA-AVGALVRWCHA 65 (93)
T ss_pred chHHHHHHHh-hcCcEEEEE--ECCCCEEEEEEEEC----HH-HHHHHHHHHhh
Confidence 3788877766 678889875 66799999999994 22 23344455653
No 87
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=22.57 E-value=2.3e+02 Score=22.06 Aligned_cols=39 Identities=18% Similarity=0.346 Sum_probs=25.4
Q ss_pred cchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEE
Q 031595 81 LTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIR 124 (157)
Q Consensus 81 LteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVr 124 (157)
..+|.|++|++.|.+.++. - ..|| |-|=...| ...+++|
T Consensus 65 V~de~ve~vie~I~~~a~t-G--~~GD-GkIFV~~V-~~~irIR 103 (112)
T COG0347 65 VSDEDVDEVIEAIKKAART-G--KIGD-GKIFVSPV-EEVIRIR 103 (112)
T ss_pred EChHHHHHHHHHHHHHHhc-C--CCCC-eEEEEEEh-heEEEEe
Confidence 4789999999999999983 1 1222 34444444 4466666
No 88
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=22.55 E-value=2.2e+02 Score=18.80 Aligned_cols=32 Identities=16% Similarity=-0.040 Sum_probs=25.9
Q ss_pred EEec-CCeEEEEEeeccCcchhhHHHHHHHHHH
Q 031595 114 AELD-GPFVKIRLRGRFWHKRSTVIARLANYLK 145 (157)
Q Consensus 114 VeID-GpvVkVrL~GaC~~s~mTvk~gVe~~LK 145 (157)
+.|. |+.|.++.+|--+.+=..+...+|+.|-
T Consensus 3 ~~I~~dG~V~~~v~G~~G~~C~~~t~~lE~~LG 35 (48)
T PF11211_consen 3 FTIYPDGRVEEEVEGFKGSSCLEATAALEEALG 35 (48)
T ss_pred EEECCCcEEEEEEEeccChhHHHHHHHHHHHhC
Confidence 3466 8999999999999877777788887773
No 89
>PRK09974 putative regulator PrlF; Provisional
Probab=22.38 E-value=1.4e+02 Score=23.23 Aligned_cols=32 Identities=25% Similarity=0.136 Sum_probs=23.1
Q ss_pred HHHHHHHHhhhccccccccceEEEEecCCeEEEEEeec
Q 031595 91 ADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 91 deiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
.+||-.|+ ++.|+.|++.-.+|+.|.|+-..+
T Consensus 24 k~IR~~Lg------l~~GdkI~f~i~~dG~V~i~~~~~ 55 (111)
T PRK09974 24 APVRKALK------LKKRDSIHYEILPGGQVFICRLGD 55 (111)
T ss_pred HHHHHHcC------CCCCCEEEEEEeCCCEEEEEECCC
Confidence 36777786 567899998756677777776543
No 90
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=22.36 E-value=74 Score=24.05 Aligned_cols=27 Identities=15% Similarity=0.112 Sum_probs=21.8
Q ss_pred CCCCCCcccchHHHHHHHHHHHHHHHh
Q 031595 73 GVPPPPLDLTEDNVRQVIADARGELAQ 99 (157)
Q Consensus 73 ~~~~~~LeLteENVE~vLdeiRP~L~a 99 (157)
+...=.++|+++|-++..+.+.||+.+
T Consensus 27 dG~~YeIDLs~~na~~lr~~l~~yi~~ 53 (110)
T PF11774_consen 27 DGVDYEIDLSAENAAKLRDALAPYIAA 53 (110)
T ss_dssp TTEEEEEEE-HHHHHHHHHHHHHHHHH
T ss_pred CCeEEEEECCHHHHHHHHHHHHHHHHH
Confidence 344556889999999999999999984
No 91
>PRK14688 hypothetical protein; Provisional
Probab=22.32 E-value=2.9e+02 Score=21.14 Aligned_cols=48 Identities=23% Similarity=0.461 Sum_probs=30.7
Q ss_pred ccceEEEEec-CCeEEEEEeecc----Cc--------chhhHHHHHHHHHHhhCCcCcCCCC
Q 031595 108 TGVAELAELD-GPFVKIRLRGRF----WH--------KRSTVIARLANYLKQRIPVSPLPCR 156 (157)
Q Consensus 108 GGdVELVeID-GpvVkVrL~GaC----~~--------s~mTvk~gVe~~LKe~IPEI~~~~~ 156 (157)
.|.|+||--| +-.|.|..+-+. ++ .+.-+....+.||.+. |.-..|||
T Consensus 36 ~GEIDiIa~~~~~lVFVEVK~R~~~~~g~~~eaV~~~K~~ri~~aA~~yL~~~-~~~~~~~R 96 (121)
T PRK14688 36 EGEIDIVGQDGEYLVFIEVRTKRRLGYGLPAESVTPRKKAHLMASAESYIQKH-RLEHFPCR 96 (121)
T ss_pred CCcEeEEEeeCCEEEEEEEEecCCCCCCChHHcCCHHHHHHHHHHHHHHHHhC-CCCCCCEE
Confidence 6999999888 455566666543 33 3445555677899776 53245676
No 92
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=22.20 E-value=1.3e+02 Score=20.18 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=26.0
Q ss_pred CCcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEE
Q 031595 77 PPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRL 125 (157)
Q Consensus 77 ~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL 125 (157)
+..++..+. +.+..+||. +|-.+.++-.+|..+.|.|
T Consensus 24 eQ~~i~~~~----igd~~~~L~--------e~~~v~v~~~~~~~i~v~l 60 (61)
T cd04470 24 EQIELPKEA----LGDAAKFLK--------EGMEVIVLFYNGEPIGVEL 60 (61)
T ss_pred eEEEECHHH----hhhHHhhCc--------CCCEEEEEEECCEEEEEEC
Confidence 344555544 556789998 4888888777888888765
No 93
>PRK14686 hypothetical protein; Provisional
Probab=22.08 E-value=2.6e+02 Score=21.06 Aligned_cols=47 Identities=11% Similarity=0.231 Sum_probs=30.9
Q ss_pred ccceEEEEec-CCeEEEEEeeccC----c--------chhhHHHHHHHHHHhhCCcCcCCCC
Q 031595 108 TGVAELAELD-GPFVKIRLRGRFW----H--------KRSTVIARLANYLKQRIPVSPLPCR 156 (157)
Q Consensus 108 GGdVELVeID-GpvVkVrL~GaC~----~--------s~mTvk~gVe~~LKe~IPEI~~~~~ 156 (157)
.|.|+||-.| +-.|.|..+.+.. + ++.-+....+.||.+. + ...|||
T Consensus 35 ~GEIDlIa~~~~~lvFVEVKtR~~~~~g~~~eaV~~~K~~rl~~aA~~yl~~~-~-~~~~~R 94 (119)
T PRK14686 35 KAEIDIIAQKGNILVIVEVKTRSSSDFGNPQDFVKPKKIQLLVKAVNHYIEDK-D-LDVEIR 94 (119)
T ss_pred CCcEEEEECcCCEEEEEEEEecCCCCCCChhHcCCHHHHHHHHHHHHHHHHhC-C-CCCCEE
Confidence 6999999888 5566777776553 2 2344455567788766 3 356676
No 94
>PF15585 Imm46: Immunity protein 46
Probab=21.97 E-value=4.2e+02 Score=21.22 Aligned_cols=41 Identities=17% Similarity=0.301 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccccceEEEEec--CCeEEEEEeeccCc
Q 031595 83 EDNVRQVIADARGELAQLFDTSVGITGVAELAELD--GPFVKIRLRGRFWH 131 (157)
Q Consensus 83 eENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeID--GpvVkVrL~GaC~~ 131 (157)
+++.++++++|+-++.+ +| .+ .+++|. ++.-.|.+-|=-.|
T Consensus 20 ~~~~~~~~~~i~~~i~~-~~----~~---~~~~L~~~NG~~~l~~~g~~NH 62 (129)
T PF15585_consen 20 EAKLEKIIQEIQERISE-LD----WG---GLVDLRAMNGSYFLHFGGLSNH 62 (129)
T ss_pred hhhHHHHHHHHHHHHHh-cC----CC---CeEEEEecCCcEEEEEccccCC
Confidence 67899999999999987 33 13 455554 77888999887777
No 95
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=21.80 E-value=1.6e+02 Score=19.72 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=18.0
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccccccceEE
Q 031595 80 DLTEDNVRQVIADARGELAQLFDTSVGITGVAEL 113 (157)
Q Consensus 80 eLteENVE~vLdeiRP~L~a~fD~sVGdGGdVEL 113 (157)
.++...|+++|+++--.+.+... +|+.|+|
T Consensus 15 ~~s~~~v~~vl~~~~~~i~~~L~----~g~~V~l 44 (90)
T PF00216_consen 15 GLSKKDVEAVLDALFDVIKEALK----EGESVKL 44 (90)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHH----TT-EEEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHHh----cCCeEEe
Confidence 36788888888877555543222 4777654
No 96
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=21.57 E-value=2.5e+02 Score=19.83 Aligned_cols=42 Identities=12% Similarity=0.161 Sum_probs=25.3
Q ss_pred cccchHHHHHHHHHHHHHHHh-hhccccccccceEEEEecCCeEEEEEee
Q 031595 79 LDLTEDNVRQVIADARGELAQ-LFDTSVGITGVAELAELDGPFVKIRLRG 127 (157)
Q Consensus 79 LeLteENVE~vLdeiRP~L~a-~fD~sVGdGGdVELVeIDGpvVkVrL~G 127 (157)
..++...|+.+|+.+--.+.. |. .|+.|+|-++ +...++++.
T Consensus 16 ~~~s~~~v~~vl~~~~~~i~~~L~-----~g~~V~l~gf--G~F~~~~~~ 58 (99)
T PRK00285 16 VGLSKREAKELVELFFEEIRDALE-----NGEQVKLSGF--GNFQLRDKN 58 (99)
T ss_pred hCcCHHHHHHHHHHHHHHHHHHHH-----cCCeEEEcCC--EEEEEEEEC
Confidence 346777877777776555443 22 3888665444 466666664
No 97
>PRK14676 hypothetical protein; Provisional
Probab=21.52 E-value=3.3e+02 Score=20.64 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=27.8
Q ss_pred ccceEEEEecCC-eEEEEEe--eccCc--------chhhHHHHHHHHHHhhCCcCcCCCC
Q 031595 108 TGVAELAELDGP-FVKIRLR--GRFWH--------KRSTVIARLANYLKQRIPVSPLPCR 156 (157)
Q Consensus 108 GGdVELVeIDGp-vVkVrL~--GaC~~--------s~mTvk~gVe~~LKe~IPEI~~~~~ 156 (157)
.|.|+||-.||. .|.|..+ ..+++ ++--+....+.||.++=.+-..|||
T Consensus 37 ~GEIDiIa~~~~~lVFVEVKt~~~~g~~~eaV~~~K~~ri~~aA~~yL~~~~~~~~~~~R 96 (117)
T PRK14676 37 SGEIDLIAREGAEVIFIEVKKSKSHAAAAARLSRRQMDRIYGAASEFLAGEPRGQLTASR 96 (117)
T ss_pred CCeEEEEEeeCCEEEEEEEeeCCCCCChhHcCCHHHHHHHHHHHHHHHHhCCCCCCCCEE
Confidence 599999988854 4444444 34444 2333444467888665433344565
No 98
>cd02933 OYE_like_FMN Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes.
Probab=21.46 E-value=5.4e+02 Score=22.31 Aligned_cols=121 Identities=14% Similarity=0.095 Sum_probs=60.1
Q ss_pred HHHHHHhhc-CccccCccccccccccccccCC---Ccceeeeeccccc--cccccCCCCCCCcccchHHHHHHHHHHHHH
Q 031595 23 FLRKILSTC-NHSKAFNKQTTHCRQKKLSRRK---PILLSTSIDRGYL--TRTAAGGVPPPPLDLTEDNVRQVIADARGE 96 (157)
Q Consensus 23 ~l~~i~~~c-~~s~~f~~~~~~~~~~~~~~~~---~~~~~t~~~r~~~--~~~~~~~~~~~~LeLteENVE~vLdeiRP~ 96 (157)
-|+++.+.| .+.+-.=-|++|.+...-+... ...++-+-..... .....+.....+-++|+|.|++++++.+-.
T Consensus 78 ~lr~la~~vh~~ga~~~~QL~H~G~~~~~~~~~~~~~~~~ps~~~~~~~~~~~~~~~~~~~p~~mt~~eI~~ii~~f~~a 157 (338)
T cd02933 78 GWKKVTDAVHAKGGKIFLQLWHVGRVSHPSLLPGGAPPVAPSAIAAEGKVFTPAGKVPYPTPRALTTEEIPGIVADFRQA 157 (338)
T ss_pred HHHHHHHHHHhcCCeEEEEcccCccCCCcccccCCCCccCCCCCCCCcccccccccCCCCCCCCCCHHHHHHHHHHHHHH
Confidence 578888877 4444455689998865433211 1111110000000 000000112345789999999999887533
Q ss_pred HHhhhccccccccceEEEEecC-----------CeEEEEEeeccCc---chhhHHHHHHHHHHhhCCc
Q 031595 97 LAQLFDTSVGITGVAELAELDG-----------PFVKIRLRGRFWH---KRSTVIARLANYLKQRIPV 150 (157)
Q Consensus 97 L~a~fD~sVGdGGdVELVeIDG-----------pvVkVrL~GaC~~---s~mTvk~gVe~~LKe~IPE 150 (157)
-.-..+ ...+-|||.. |...-| +-..++ +++-+...|-..+|+.++.
T Consensus 158 A~~a~~------aGfDgVeih~ahGyLl~qFlSp~~N~R-~D~yGGslenR~rf~~eii~air~~vg~ 218 (338)
T cd02933 158 ARNAIE------AGFDGVEIHGANGYLIDQFLRDGSNKR-TDEYGGSIENRARFLLEVVDAVAEAIGA 218 (338)
T ss_pred HHHHHH------cCCCEEEEccccchhHHHhcCCccCCC-CCcCCCcHHHhhhHHHHHHHHHHHHhCC
Confidence 221111 1122355542 122222 222222 5777777788888888865
No 99
>PRK08193 araD L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=21.29 E-value=2.5e+02 Score=23.00 Aligned_cols=43 Identities=9% Similarity=0.022 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc
Q 031595 87 RQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH 131 (157)
Q Consensus 87 E~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~ 131 (157)
+++++-.|-... ..-..|.+|||....-+++.+.+.=+|.+++
T Consensus 7 ~~i~~~~~~l~~--~gl~~g~~GNiS~r~~~~~~~~ItpsG~~~~ 49 (231)
T PRK08193 7 QEVLEANLALPK--HGLVTFTWGNVSAIDRERGLFVIKPSGVDYD 49 (231)
T ss_pred HHHHHHHHHHHH--cCCCCCCCCeEEEEecCCCEEEEeCCCCChh
Confidence 344444444332 3456788999997544455666666666665
No 100
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=21.24 E-value=68 Score=29.40 Aligned_cols=43 Identities=28% Similarity=0.482 Sum_probs=25.5
Q ss_pred cccccccceEEEEecCCeEEEEEeec---cCc-chhhHHHHHHHHHHh
Q 031595 103 TSVGITGVAELAELDGPFVKIRLRGR---FWH-KRSTVIARLANYLKQ 146 (157)
Q Consensus 103 ~sVGdGGdVELVeIDGpvVkVrL~Ga---C~~-s~mTvk~gVe~~LKe 146 (157)
+|+| ||.+++++|||-.|.+..+|. +.+ .+--+.+.|...|-+
T Consensus 429 ~s~g-gg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~~v~~~L~~ 475 (526)
T PRK13581 429 TVFG-DGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVIGKVGTLLGE 475 (526)
T ss_pred EEec-CCceEEEEECCEEEEeeCCceEEEEEeCCcCChhHHHHHHHhh
Confidence 4444 678999999996666655442 111 244455556665543
No 101
>TIGR00258 inosine/xanthosine triphosphatase.
Probab=21.20 E-value=1.5e+02 Score=24.05 Aligned_cols=43 Identities=33% Similarity=0.485 Sum_probs=33.4
Q ss_pred cccCCCCCCCcccchHHHHHHHHHHHHHHHhh-hccccccccceE
Q 031595 69 TAAGGVPPPPLDLTEDNVRQVIADARGELAQL-FDTSVGITGVAE 112 (157)
Q Consensus 69 ~~~~~~~~~~LeLteENVE~vLdeiRP~L~a~-fD~sVGdGGdVE 112 (157)
+..|+++..|+- .+|.++-++..++--|.+. +|.+||+=|.|+
T Consensus 29 ~v~SgV~~QP~~-~eET~~GA~nRA~~a~~~~~ad~gVGiEgGv~ 72 (163)
T TIGR00258 29 EVESGVPEQPFG-LEETVRGARNRAKNAFRLLECDFSVGIEAGLD 72 (163)
T ss_pred cCCCCCCCCCCC-hHHHHHHHHHHHHHHHhccCCCEEEEEeeeEe
Confidence 345677777776 4889999999999988874 888899966665
No 102
>PF14908 DUF4496: Domain of unknown function (DUF4496)
Probab=20.90 E-value=3.4e+02 Score=20.15 Aligned_cols=41 Identities=15% Similarity=0.233 Sum_probs=28.9
Q ss_pred cchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeec
Q 031595 81 LTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGR 128 (157)
Q Consensus 81 LteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~Ga 128 (157)
++.+.||.+|+++--+|+.. +..|.+|++ ++ ++-++..++.
T Consensus 94 ~~kd~v~~~l~~~~~~l~~~----l~~~~~v~i-~f--gvG~L~~~~~ 134 (140)
T PF14908_consen 94 FSKDVVEACLREIFQALGDA----LRNGQNVEI-DF--GVGVLSIRNR 134 (140)
T ss_pred CCHHHHHHHHHHHHHHHHHH----HhCCCeEEE-EE--eEEEEEEECC
Confidence 68899999999998888753 335777763 35 4556655554
No 103
>PRK14682 hypothetical protein; Provisional
Probab=20.80 E-value=3.2e+02 Score=20.67 Aligned_cols=48 Identities=25% Similarity=0.453 Sum_probs=31.2
Q ss_pred ccceEEEEec-CCeEEEEEeeccC----c--------chhhHHHHHHHHHHhhCCc-CcCCCC
Q 031595 108 TGVAELAELD-GPFVKIRLRGRFW----H--------KRSTVIARLANYLKQRIPV-SPLPCR 156 (157)
Q Consensus 108 GGdVELVeID-GpvVkVrL~GaC~----~--------s~mTvk~gVe~~LKe~IPE-I~~~~~ 156 (157)
.|.|+||-.| +-.|.|..+.+.. + .+-.+....+.||.+. |. -..+||
T Consensus 35 ~GEIDiIa~~~~~lvFVEVKtR~~~~~g~~~eaV~~~K~~ri~~aA~~yL~~~-~~~~~~~~R 96 (117)
T PRK14682 35 YGEIDIIALDKDTLVFIEVKYRSKTKFAQAEEMLTYSKQQKLVNSASIYLQHN-PQYQDYQCR 96 (117)
T ss_pred CCcEEEEEeeCCEEEEEEEEecCCCCCCChHHcCCHHHHHHHHHHHHHHHHhC-CCCCCCCEE
Confidence 6999999998 5567777776543 2 3445556678888654 43 245665
No 104
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.49 E-value=89 Score=19.88 Aligned_cols=14 Identities=21% Similarity=0.544 Sum_probs=11.1
Q ss_pred chHHHHHHHHHHHH
Q 031595 82 TEDNVRQVIADARG 95 (157)
Q Consensus 82 teENVE~vLdeiRP 95 (157)
|||+++++|++++.
T Consensus 1 tee~l~~Ai~~v~~ 14 (45)
T PF05225_consen 1 TEEDLQKAIEAVKN 14 (45)
T ss_dssp -HHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHh
Confidence 68899999998873
No 105
>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the 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 both 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=20.24 E-value=2.2e+02 Score=21.78 Aligned_cols=37 Identities=5% Similarity=0.045 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHhhhccccccccceEEEEec-CCeEE
Q 031595 86 VRQVIADARGELAQLFDTSVGITGVAELAELD-GPFVK 122 (157)
Q Consensus 86 VE~vLdeiRP~L~a~fD~sVGdGGdVELVeID-GpvVk 122 (157)
.+++++.++--|....+.-+-.|+++|+.-|+ +++..
T Consensus 149 ~~ea~~l~~~~l~~~~~rd~~~~~~i~i~iv~~~g~~~ 186 (188)
T cd03764 149 VEEAKKLAIRAIKSAIERDSASGDGIDVVVITKDGYKE 186 (188)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCCcEEEEEECCCCeEe
Confidence 44455555555544444334567888888887 55443
No 106
>COG1820 NagA N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]
Probab=20.20 E-value=1.2e+02 Score=28.00 Aligned_cols=47 Identities=15% Similarity=0.238 Sum_probs=34.2
Q ss_pred CcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeeccCc
Q 031595 78 PLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRFWH 131 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC~~ 131 (157)
++.-+.|++.++|+.+|.|.++ -|-+|-=+-+|||+....=+|+=.-
T Consensus 95 ~iT~~~e~i~~al~~~~e~~~~-------~ga~ilGiHLEGP~ls~~kkGAh~~ 141 (380)
T COG1820 95 LITASLEKIKAALRAIREAIAK-------GGAQILGIHLEGPFLSPEKKGAHNP 141 (380)
T ss_pred cccCCHHHHHHHHHHHHHHHhc-------cCCceEEEEeecCccCHhhccCCCH
Confidence 3445889999999999999984 2334444667788888777776433
No 107
>PRK14681 hypothetical protein; Provisional
Probab=20.18 E-value=3.8e+02 Score=21.66 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=28.1
Q ss_pred cccceEEEEecC--CeEEEEEeeccCc------------chhhHHHHHHHHHHhh
Q 031595 107 ITGVAELAELDG--PFVKIRLRGRFWH------------KRSTVIARLANYLKQR 147 (157)
Q Consensus 107 dGGdVELVeIDG--pvVkVrL~GaC~~------------s~mTvk~gVe~~LKe~ 147 (157)
-.|.|+||-.|+ -.|.|..+.+... .+--+....+.||.+.
T Consensus 72 ~~GEIDIIa~d~~~~LVFVEVKtR~~~~~g~p~eaVt~~Kqrrl~raA~~yL~~~ 126 (158)
T PRK14681 72 RYGELDIVALNPEYTIVFVEVKTRRSMHYGYPQEAVTAAKQHNLRKAACDWLLER 126 (158)
T ss_pred CCCcEEEEEEcCCceEEEEEEEeccCCCCCChHHcCCHHHHHHHHHHHHHHHHhC
Confidence 369999999984 4777777765432 3444555577888764
No 108
>PRK09019 translation initiation factor Sui1; Validated
Probab=20.18 E-value=1.8e+02 Score=22.36 Aligned_cols=40 Identities=23% Similarity=0.413 Sum_probs=30.6
Q ss_pred CCCCcccchHHHHHHHHHHHHHHHhhhccccccccceEEEEecCCeEEEEEeecc
Q 031595 75 PPPPLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAELDGPFVKIRLRGRF 129 (157)
Q Consensus 75 ~~~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVeIDGpvVkVrL~GaC 129 (157)
....+++.++++++.+.+++..+. -||.|. |+ .|.|||--
T Consensus 49 iI~Gl~~~~~dlk~l~K~lKkk~g--------cGGtvk----~~---~IelQGD~ 88 (108)
T PRK09019 49 LITGLDLDDAELKKLAAELKKKCG--------CGGAVK----DG---VIEIQGDK 88 (108)
T ss_pred EEeCCcCCHHHHHHHHHHHHHHhc--------CCCeEE----cC---EEEEcCcH
Confidence 356778889999999999998886 489886 32 37788853
No 109
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=20.16 E-value=14 Score=24.49 Aligned_cols=36 Identities=22% Similarity=0.446 Sum_probs=26.4
Q ss_pred CcccchHHHHHHHHHHHHHHHhhhccccccccceEEEE
Q 031595 78 PLDLTEDNVRQVIADARGELAQLFDTSVGITGVAELAE 115 (157)
Q Consensus 78 ~LeLteENVE~vLdeiRP~L~a~fD~sVGdGGdVELVe 115 (157)
.|.++.+.|++++...+.+.- .|..+++.|+-+|.+
T Consensus 29 ~lgis~~~v~~~l~~~~~~~S--l~~~~~~~~~~~l~~ 64 (78)
T PF04539_consen 29 ELGISVEEVRELLQASRRPVS--LDLPVGDEDDSTLGD 64 (78)
T ss_dssp HHTS-HHHHHHHHHHHSCCEE--SSHCCSSSSSEEGGG
T ss_pred HHcccHHHHHHHHHhCCCCeE--EeeeecCCCCCchhh
Confidence 366889999999998877653 676677777777665
No 110
>PRK06105 aminotransferase; Provisional
Probab=20.03 E-value=1e+02 Score=27.52 Aligned_cols=34 Identities=24% Similarity=0.275 Sum_probs=26.1
Q ss_pred CCCCcccchHHHHHHHHHHHHHHHhhhcccccccc
Q 031595 75 PPPPLDLTEDNVRQVIADARGELAQLFDTSVGITG 109 (157)
Q Consensus 75 ~~~~LeLteENVE~vLdeiRP~L~a~fD~sVGdGG 109 (157)
..|+|..|+++++++++.+..-|.++++ .|-+||
T Consensus 425 l~Ppl~it~~eid~~~~~l~~~l~~~~~-~~~~~~ 458 (460)
T PRK06105 425 FCPPLIITAAQVDEMVDRFGRALDDVAA-WVAAGG 458 (460)
T ss_pred EECCCccCHHHHHHHHHHHHHHHHHHHH-HHhhcC
Confidence 4578889999999999998888877544 454565
Done!