Query psy6209
Match_columns 115
No_of_seqs 104 out of 303
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 20:31:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6209.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6209hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02933 CDC48_2: Cell divisio 99.6 3E-15 6.4E-20 93.5 7.5 62 39-103 2-63 (64)
2 TIGR01243 CDC48 AAA family ATP 99.3 1.4E-11 3.1E-16 106.5 10.2 99 1-105 69-167 (733)
3 PF03152 UFD1: Ubiquitin fusio 98.7 2E-08 4.4E-13 74.3 5.8 92 1-97 80-171 (176)
4 KOG0730|consensus 98.6 1.1E-08 2.3E-13 88.0 1.7 102 2-108 77-178 (693)
5 KOG1816|consensus 98.2 1.5E-05 3.2E-10 63.1 9.3 97 1-102 92-189 (308)
6 PLN03086 PRLI-interacting fact 98.2 1.4E-05 3.1E-10 68.3 9.6 93 1-97 159-255 (567)
7 PF09262 PEX-1N: Peroxisome bi 97.2 0.00053 1.1E-08 44.8 4.0 73 24-98 1-79 (80)
8 KOG0735|consensus 96.7 0.012 2.7E-07 52.2 8.9 97 4-103 71-170 (952)
9 COG5140 UFD1 Ubiquitin fusion- 96.6 0.015 3.3E-07 45.7 8.1 98 1-102 100-200 (331)
10 COG1223 Predicted ATPase (AAA+ 95.8 0.051 1.1E-06 43.6 7.4 75 22-98 22-105 (368)
11 PF01272 GreA_GreB: Transcript 83.0 9.1 0.0002 24.0 7.2 70 6-82 5-76 (77)
12 KOG0741|consensus 78.0 19 0.00042 31.8 8.6 92 2-97 69-188 (744)
13 cd03450 NodN NodN (nodulation 76.8 4.7 0.0001 28.6 4.0 37 57-100 96-134 (149)
14 COG0361 InfA Translation initi 75.8 1.8 3.9E-05 28.0 1.5 18 1-18 40-58 (75)
15 COG0782 Uncharacterized conser 71.5 35 0.00075 24.5 7.5 73 2-83 75-150 (151)
16 cd04456 S1_IF1A_like S1_IF1A_l 68.3 3.5 7.6E-05 26.5 1.6 18 1-18 33-50 (78)
17 TIGR00008 infA translation ini 63.2 5.1 0.00011 25.3 1.5 18 1-18 38-56 (68)
18 PRK12442 translation initiatio 61.7 4.4 9.6E-05 26.9 1.1 17 1-17 40-57 (87)
19 cd05793 S1_IF1A S1_IF1A: Trans 60.2 5.8 0.00013 25.4 1.4 18 1-18 33-50 (77)
20 COG1047 SlpA FKBP-type peptidy 58.9 28 0.0006 25.9 5.0 57 25-83 59-115 (174)
21 PF07177 Neuralized: Neuralize 58.6 6.9 0.00015 24.5 1.5 30 54-83 34-69 (69)
22 PF03120 DNA_ligase_OB: NAD-de 57.6 5 0.00011 26.2 0.8 19 4-22 47-65 (82)
23 smart00652 eIF1a eukaryotic tr 56.6 7.5 0.00016 25.3 1.5 18 1-18 38-55 (83)
24 KOG0736|consensus 53.0 50 0.0011 30.4 6.4 58 42-100 304-382 (953)
25 smart00588 NEUZ domain in neur 52.3 16 0.00034 25.3 2.7 31 54-84 35-71 (123)
26 PF04014 Antitoxin-MazE: Antid 52.0 13 0.00029 21.0 1.9 29 2-34 16-44 (47)
27 PRK04012 translation initiatio 50.5 11 0.00023 25.5 1.5 18 1-18 54-71 (100)
28 PTZ00329 eukaryotic translatio 50.4 9.4 0.0002 27.9 1.3 17 1-17 65-81 (155)
29 COG0272 Lig NAD-dependent DNA 49.1 14 0.0003 32.8 2.4 27 4-30 365-392 (667)
30 TIGR00523 eIF-1A eukaryotic/ar 47.5 25 0.00054 23.6 3.0 21 1-22 52-72 (99)
31 cd05829 Sortase_E Sortase E (S 44.5 32 0.00068 24.1 3.3 24 58-81 72-96 (144)
32 PF00924 MS_channel: Mechanose 42.9 75 0.0016 22.7 5.2 36 44-83 46-81 (206)
33 PRK13691 (3R)-hydroxyacyl-ACP 42.7 77 0.0017 22.8 5.1 14 56-69 94-107 (166)
34 COG0186 RpsQ Ribosomal protein 41.2 48 0.001 22.0 3.5 27 4-30 53-79 (87)
35 smart00532 LIGANc Ligase N fam 40.9 26 0.00057 29.4 2.7 20 4-23 360-379 (441)
36 cd06166 Sortase_D_5 Sortase D 40.0 80 0.0017 21.4 4.7 23 59-81 65-87 (126)
37 TIGR02609 doc_partner putative 39.7 39 0.00084 21.2 2.8 28 2-34 19-46 (74)
38 COG1188 Ribosome-associated he 39.1 44 0.00096 22.7 3.1 27 56-82 46-72 (100)
39 PF01568 Molydop_binding: Moly 38.9 87 0.0019 20.0 4.6 26 57-82 42-67 (110)
40 cd03451 FkbR2 FkbR2 is a Strep 37.8 61 0.0013 21.8 3.8 12 57-68 90-101 (146)
41 PRK08097 ligB NAD-dependent DN 37.7 27 0.00058 30.4 2.4 26 4-29 357-383 (562)
42 COG0832 UreB Urea amidohydrola 37.6 26 0.00056 24.0 1.8 22 55-76 30-51 (106)
43 KOG1740|consensus 37.2 21 0.00045 24.5 1.3 26 7-32 50-75 (107)
44 TIGR00192 urease_beta urease, 37.2 18 0.0004 24.6 1.1 23 54-76 29-51 (101)
45 COG2847 Copper(I)-binding prot 36.7 1.2E+02 0.0025 22.1 5.2 60 9-82 78-144 (151)
46 PTZ00198 60S ribosomal protein 36.6 59 0.0013 22.9 3.5 39 30-70 27-65 (122)
47 COG0198 RplX Ribosomal protein 36.2 1.2E+02 0.0026 20.7 4.9 44 56-100 2-46 (104)
48 cd04473 S1_RecJ_like S1_RecJ_l 36.1 38 0.00082 20.9 2.3 26 6-32 52-77 (77)
49 PLN00208 translation initiatio 35.9 20 0.00044 25.9 1.2 17 1-17 65-81 (145)
50 PF01176 eIF-1a: Translation i 35.9 16 0.00035 22.3 0.6 18 1-18 36-53 (65)
51 TIGR00575 dnlj DNA ligase, NAD 35.9 30 0.00064 30.5 2.4 26 4-29 353-379 (652)
52 KOG3434|consensus 35.4 1E+02 0.0022 21.8 4.5 49 31-83 27-75 (125)
53 COG0668 MscS Small-conductance 35.1 1.2E+02 0.0027 22.9 5.5 53 44-96 133-190 (316)
54 cd05828 Sortase_D_4 Sortase D 34.7 57 0.0012 22.2 3.2 23 59-81 62-84 (127)
55 cd05830 Sortase_D_5 Sortase D 34.5 58 0.0012 22.5 3.3 23 59-81 66-88 (137)
56 PRK13202 ureB urease subunit b 34.2 23 0.00049 24.3 1.1 23 54-76 30-52 (104)
57 TIGR01076 sortase_fam LPXTG-si 34.2 58 0.0013 22.4 3.3 23 59-81 64-86 (136)
58 PRK11281 hypothetical protein; 34.2 70 0.0015 30.2 4.5 52 44-95 924-979 (1113)
59 TIGR03635 S17_bact 30S ribosom 33.2 70 0.0015 20.1 3.2 13 6-18 48-60 (71)
60 PRK13203 ureB urease subunit b 32.9 18 0.00039 24.7 0.5 23 54-76 29-51 (102)
61 PF13550 Phage-tail_3: Putativ 32.6 61 0.0013 22.1 3.2 26 57-82 138-163 (164)
62 PRK14350 ligA NAD-dependent DN 32.1 38 0.00083 30.1 2.4 20 4-23 362-381 (669)
63 cd00407 Urease_beta Urease bet 32.0 21 0.00046 24.3 0.7 23 54-76 29-51 (101)
64 PF11910 NdhO: Cyanobacterial 31.9 35 0.00076 21.5 1.6 42 59-100 1-44 (67)
65 PF13452 MaoC_dehydrat_N: N-te 31.7 37 0.0008 22.6 1.9 40 56-102 85-129 (132)
66 PRK07956 ligA NAD-dependent DN 31.7 42 0.00091 29.7 2.6 25 4-28 365-390 (665)
67 PF01776 Ribosomal_L22e: Ribos 31.3 70 0.0015 22.1 3.2 49 31-83 15-63 (112)
68 cd06165 Sortase_A_1 Sortase A 31.1 1.3E+02 0.0027 20.3 4.5 31 59-89 64-97 (127)
69 cd03452 MaoC_C MaoC_C The C-t 31.0 87 0.0019 21.5 3.7 31 57-94 87-120 (142)
70 PRK13692 (3R)-hydroxyacyl-ACP 30.9 1.9E+02 0.0041 20.5 5.6 12 57-68 95-106 (159)
71 smart00785 AARP2CN AARP2CN (NU 30.8 48 0.001 21.4 2.2 31 47-82 47-77 (83)
72 COG0233 Frr Ribosome recycling 30.7 55 0.0012 24.6 2.8 45 20-69 60-104 (187)
73 PRK05610 rpsQ 30S ribosomal pr 30.7 1E+02 0.0023 20.0 3.8 18 6-23 53-70 (84)
74 PRK05892 nucleoside diphosphat 30.6 71 0.0015 23.0 3.3 70 5-83 81-156 (158)
75 TIGR02227 sigpep_I_bact signal 29.9 2E+02 0.0044 20.3 5.9 46 57-103 50-97 (163)
76 PRK10334 mechanosensitive chan 29.5 1.2E+02 0.0026 23.8 4.7 51 45-95 116-170 (286)
77 PRK10737 FKBP-type peptidyl-pr 29.5 80 0.0017 23.7 3.5 26 58-83 89-114 (196)
78 PF08142 AARP2CN: AARP2CN (NUC 29.1 55 0.0012 21.1 2.3 31 47-82 49-79 (85)
79 PRK10929 putative mechanosensi 28.9 87 0.0019 29.6 4.3 52 44-95 921-976 (1109)
80 PRK13201 ureB urease subunit b 28.9 26 0.00055 25.1 0.7 22 54-75 29-50 (136)
81 PF11302 DUF3104: Protein of u 28.7 55 0.0012 21.1 2.2 34 60-93 29-66 (75)
82 COG4591 LolE ABC-type transpor 28.6 48 0.001 27.6 2.3 30 1-31 152-188 (408)
83 PTZ00194 60S ribosomal protein 28.5 2E+02 0.0044 20.7 5.3 46 56-101 44-91 (143)
84 KOG1728|consensus 28.2 86 0.0019 22.7 3.3 30 56-85 115-147 (156)
85 cd02775 MopB_CT Molybdopterin- 27.6 1.6E+02 0.0034 18.3 4.6 25 58-83 36-60 (101)
86 KOG4625|consensus 27.3 39 0.00084 29.6 1.6 33 54-86 133-171 (595)
87 TIGR02771 TraF_Ti conjugative 27.1 1.8E+02 0.004 21.0 5.0 23 81-104 90-112 (171)
88 PRK14351 ligA NAD-dependent DN 26.8 58 0.0013 29.0 2.7 26 4-29 387-413 (689)
89 PF08605 Rad9_Rad53_bind: Fung 26.8 35 0.00075 24.1 1.1 23 4-30 57-79 (131)
90 TIGR01462 greA transcription e 26.7 2.3E+02 0.005 19.9 7.0 68 6-82 80-151 (151)
91 CHL00142 rps17 ribosomal prote 26.5 1.4E+02 0.003 19.5 3.8 15 6-20 50-64 (84)
92 PRK10348 ribosome-associated h 26.2 1.1E+02 0.0023 21.8 3.5 28 56-83 46-73 (133)
93 cd03454 YdeM YdeM is a Bacillu 26.0 1.2E+02 0.0026 20.3 3.7 33 57-96 87-123 (140)
94 cd00004 Sortase Sortases are c 25.5 1E+02 0.0023 20.6 3.3 24 59-82 65-88 (128)
95 PF13742 tRNA_anti_2: OB-fold 25.3 1.3E+02 0.0028 19.7 3.6 28 56-83 66-99 (99)
96 PRK00226 greA transcription el 25.2 2.5E+02 0.0054 19.8 7.1 70 6-82 85-156 (157)
97 PRK13205 ureB urease subunit b 24.4 34 0.00074 25.1 0.7 23 54-76 29-51 (162)
98 PF08696 Dna2: DNA replication 24.4 1.2E+02 0.0025 22.7 3.6 14 56-69 22-35 (209)
99 PF12124 Nsp3_PL2pro: Coronavi 23.9 70 0.0015 19.6 1.9 21 58-78 31-51 (66)
100 PRK00083 frr ribosome recyclin 23.9 72 0.0016 23.6 2.4 45 20-69 58-102 (185)
101 PRK14720 transcript cleavage f 23.8 3.2E+02 0.0068 25.5 6.8 71 6-84 830-903 (906)
102 cd02792 MopB_CT_Formate-Dh-Na- 23.7 1.8E+02 0.004 18.8 4.2 33 58-90 48-82 (122)
103 TIGR01080 rplX_A_E ribosomal p 23.6 2.3E+02 0.005 19.5 4.7 31 56-86 39-70 (114)
104 PRK11033 zntA zinc/cadmium/mer 23.3 1.9E+02 0.0042 25.7 5.3 60 7-81 261-326 (741)
105 TIGR01439 lp_hng_hel_AbrB loop 23.2 1.1E+02 0.0024 16.2 2.6 27 2-32 16-42 (43)
106 PF00224 PK: Pyruvate kinase, 22.7 1.8E+02 0.0039 23.5 4.6 26 58-85 119-144 (348)
107 PRK11347 antitoxin ChpS; Provi 22.6 77 0.0017 20.5 2.0 27 2-33 21-47 (83)
108 COG3764 SrtA Sortase (surface 22.5 1.2E+02 0.0026 23.1 3.3 24 59-82 135-158 (210)
109 cd03446 MaoC_like MoaC_like 22.4 1.7E+02 0.0037 19.4 3.9 12 57-68 89-100 (140)
110 PRK11465 putative mechanosensi 22.4 2E+02 0.0044 26.0 5.2 54 43-96 558-615 (741)
111 COG0261 RplU Ribosomal protein 22.2 1E+02 0.0022 21.1 2.6 51 6-69 13-63 (103)
112 COG1974 LexA SOS-response tran 22.0 1.2E+02 0.0026 22.8 3.2 27 4-30 124-150 (201)
113 PRK13198 ureB urease subunit b 21.7 41 0.00088 24.7 0.6 23 54-76 57-79 (158)
114 PRK13204 ureB urease subunit b 21.6 41 0.00088 24.7 0.6 23 54-76 52-74 (159)
115 PRK10671 copA copper exporting 21.5 2.5E+02 0.0054 25.2 5.7 62 7-81 341-406 (834)
116 cd05827 Sortase_C_3 Sortase C 21.5 2.4E+02 0.0051 19.1 4.5 23 59-81 67-89 (131)
117 PRK14533 groES co-chaperonin G 21.1 1.9E+02 0.004 19.0 3.7 23 8-30 5-28 (91)
118 COG3127 Predicted ABC-type tra 21.1 51 0.0011 30.0 1.2 16 3-18 607-622 (829)
119 COG3971 2-keto-4-pentenoate hy 20.8 74 0.0016 25.2 2.0 29 46-74 211-239 (264)
120 COG2012 RPB5 DNA-directed RNA 20.6 1.5E+02 0.0034 19.3 3.1 14 4-17 52-65 (80)
121 COG1862 YajC Preprotein transl 20.4 2.8E+02 0.006 18.6 5.1 42 59-103 44-86 (97)
122 cd03448 HDE_HSD HDE_HSD The R 20.4 2.3E+02 0.0051 19.0 4.2 26 57-82 81-108 (122)
123 PF00699 Urease_beta: Urease b 20.1 18 0.0004 24.6 -1.3 23 54-76 28-50 (100)
124 PRK11507 ribosome-associated p 20.1 87 0.0019 19.8 1.8 15 2-16 48-62 (70)
No 1
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=99.61 E-value=3e-15 Score=93.50 Aligned_cols=62 Identities=31% Similarity=0.508 Sum_probs=56.4
Q ss_pred cccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCCceEEEcCcccc
Q psy6209 39 LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK 103 (115)
Q Consensus 39 i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~T~I~~~~~pv~ 103 (115)
+++++.+ |++++|. +||+++||.|.+...++.++|+|++|+|.++|+|+++|.|++.++|++
T Consensus 2 ~d~d~~~-~~~~~l~--~~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~~~p~~ 63 (64)
T PF02933_consen 2 FDGDFMA-YFKRQLE--GRPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIKEEPVE 63 (64)
T ss_dssp ECSHHHH-HHHHHHT--TEEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEESSTTBC
T ss_pred CCccHHH-HHHHHHc--CCCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEcccccc
Confidence 4566555 9999999 999999999999999999999999999999999999999999999875
No 2
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=99.30 E-value=1.4e-11 Score=106.53 Aligned_cols=99 Identities=23% Similarity=0.389 Sum_probs=86.3
Q ss_pred CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~ 80 (115)
+|+|+|+++||.|+|+++ ++++|++|+++|+... .+ +..+.+|++.+|. ++|+..||.+.+...+...+|.|++
T Consensus 69 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~~v~~ 142 (733)
T TIGR01243 69 LRANAGVTIGDTVTVERA-EVKEAKKVVLAPTQPI--RF-GRDFVDYVKEFLL--GKPISKGETVIVPVLEGALPFVVVS 142 (733)
T ss_pred HHhhcCCCCCCeEEEeec-CCCccceEeecccccc--cc-ccchHHHHHHHHc--CCCCCCCCEEEecccCcceeEEEEe
Confidence 589999999999999996 7999999999997532 23 3356789999999 8999999999998777789999999
Q ss_pred ecCCCcEEEcCCceEEEcCccccCc
Q psy6209 81 TDPAPYCIVAADTVIHCEGDPIKRE 105 (115)
Q Consensus 81 t~P~~~viVt~~T~I~~~~~pv~re 105 (115)
+.|.+++.++..|.+.+.+++..+.
T Consensus 143 ~~p~~~~~~~~~t~~~~~~~~~~~~ 167 (733)
T TIGR01243 143 TQPAGFVYVTEATEVEIREKPVREE 167 (733)
T ss_pred cCCCCcEEECCCceEEecCCccccc
Confidence 9999999999999999988887554
No 3
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=98.74 E-value=2e-08 Score=74.35 Aligned_cols=92 Identities=15% Similarity=0.208 Sum_probs=64.4
Q ss_pred CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~ 80 (115)
|-+|+++.-||.|.|+-+ ..+.|+.|+|.|-+..--.+. ....+|...|+ .+--+++||+|.|...+...+|.|++
T Consensus 80 mm~~L~l~~g~~V~v~~~-~LPkgt~vkLqP~~~~F~~i~--n~KavLE~~Lr-~ystLT~Gd~I~i~~~~~~y~l~V~e 155 (176)
T PF03152_consen 80 MMQNLGLQEGDIVRVEYV-SLPKGTFVKLQPQSSDFLDIS--NPKAVLERALR-NYSTLTKGDTISIEYNNKTYELDVVE 155 (176)
T ss_dssp HHHHHT--TTEEEEEEEE-E----SEEEEEESCHHHHCSS---HHHHHHHHHC-C-SEEETTSEEEEECTTEEEEEEEEE
T ss_pred HHhhcCCCCCCEEEEEEe-ECCCCCEEEEeECCCcccccc--chHHHHHhhcc-cCceeecCCEEEEEeCCEEEEEEEEE
Confidence 668999999999999985 999999999999743211232 24677888884 46679999999999999999999999
Q ss_pred ecCCCcEEEcCCceEEE
Q psy6209 81 TDPAPYCIVAADTVIHC 97 (115)
Q Consensus 81 t~P~~~viVt~~T~I~~ 97 (115)
++|++.+.|- +|.+++
T Consensus 156 ~kP~~aV~Ii-dTDl~v 171 (176)
T PF03152_consen 156 VKPENAVSII-DTDLEV 171 (176)
T ss_dssp ECSSSCEE-S-SS-SEE
T ss_pred EcCCCEEEEE-eCceEE
Confidence 9997754444 454444
No 4
>KOG0730|consensus
Probab=98.63 E-value=1.1e-08 Score=87.99 Aligned_cols=102 Identities=40% Similarity=0.694 Sum_probs=94.2
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEe
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
|.|+.++.|+.+.+.+...++.+.+++++|..++.+++.++.++.+.++|+..+++|+.+|+++ ..+..++|+++.+
T Consensus 77 r~~l~~~~~~~~~~~~~p~v~~~~~i~~l~~~~~~~~i~~~~~d~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~ 153 (693)
T KOG0730|consen 77 RSNLRLQLGRLLHSSDCPSVKRPARIAVLPVDDTSEGIAGELFDVLERPFLLEALRPLVKGDTF---AGLNPAEFKVLEL 153 (693)
T ss_pred ccchhhcccceecccCCCCccccceeeeeehhhccccchhhhhhhhhhhhhhhhhCccccccch---hhhhhhhhhcccc
Confidence 7899999999999998789999999999999999888998889999999999999999999998 4456789999999
Q ss_pred cCCCcEEEcCCceEEEcCccccCcccc
Q psy6209 82 DPAPYCIVAADTVIHCEGDPIKREGEE 108 (115)
Q Consensus 82 ~P~~~viVt~~T~I~~~~~pv~re~~~ 108 (115)
.|.. .++++|.+++.++++++++++
T Consensus 154 ~~~~--~v~~~t~~~~~~~~~~~~~~~ 178 (693)
T KOG0730|consen 154 DPSP--QVTPDTELSYLGEPAKREEEE 178 (693)
T ss_pred ccch--hcCccchhhhcCCCccccccc
Confidence 9988 899999999999999998776
No 5
>KOG1816|consensus
Probab=98.19 E-value=1.5e-05 Score=63.12 Aligned_cols=97 Identities=22% Similarity=0.275 Sum_probs=71.8
Q ss_pred CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~ 80 (115)
|=+|++..-||.|.|+-+ .++.|+-|.|.|- ++.-++-..-...|..-|+ ++--+++||.|.|..++...+|+|++
T Consensus 92 Mmq~L~le~gdlv~i~~v-~lpkgtyvKLqP~--s~dFLDItNpKAvLE~~LR-n~acLT~gDvi~i~Yn~k~y~i~V~e 167 (308)
T KOG1816|consen 92 MMQNLLLEEGDLVRIRSV-TLPKGTYVKLQPH--SVDFLDITNPKAVLENALR-NYACLTTGDVILINYNEKTYELKVVE 167 (308)
T ss_pred hhhhccCCCCCeEEEEEe-eccccceeeeccC--CCCccccCChHHHHHHHHh-hccccccCCEEEEecCCeEEEEEEEE
Confidence 678999999999999995 9999999999995 3322221111344444443 24469999999999999999999999
Q ss_pred ecCCC-cEEEcCCceEEEcCccc
Q psy6209 81 TDPAP-YCIVAADTVIHCEGDPI 102 (115)
Q Consensus 81 t~P~~-~viVt~~T~I~~~~~pv 102 (115)
++|+. ++||--+.++.. ..|+
T Consensus 168 ~kPa~aVsIiEtD~~VDF-~pP~ 189 (308)
T KOG1816|consen 168 TKPANAVSIIETDLNVDF-DPPL 189 (308)
T ss_pred ecCCceeEEEEcceeecc-cCCc
Confidence 99965 455665666665 3454
No 6
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.17 E-value=1.4e-05 Score=68.26 Aligned_cols=93 Identities=14% Similarity=0.157 Sum_probs=71.6
Q ss_pred CCcccCCCC---CCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEE
Q psy6209 1 MSFRLTTPC---RDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFK 77 (115)
Q Consensus 1 ~R~Nagv~i---GD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~Fk 77 (115)
|.+|+|..- |+.|+|+.+ .+|.|+.|.|.|-+..- ++-.....+|..+|.+ +--+++||+|.|..+....+|.
T Consensus 159 m~~~L~~~~~~~~~~v~v~~~-~Lpkgt~vklqP~~~~f--~di~npKavLE~~Lr~-~stLT~Gd~i~i~~~~~~y~~~ 234 (567)
T PLN03086 159 VWSNLFPSDPPDVPLVEVRYI-WLPKGTYAKLQPDGVGF--SDLPNHKAVLETALRQ-HATLSEDDVLVVNYGQLTYKLK 234 (567)
T ss_pred HHhhcCCCCCCCCCeEEEEEe-ecCCCCEEEEeeccCCc--CCcccHHHHHHHHhhc-CccccCCCEEEEecCCEEEEEE
Confidence 678998753 889999995 99999999999975321 1222346788888872 5579999999999888899999
Q ss_pred EEEecCC-CcEEEcCCceEEE
Q psy6209 78 IVDTDPA-PYCIVAADTVIHC 97 (115)
Q Consensus 78 Vv~t~P~-~~viVt~~T~I~~ 97 (115)
|++++|+ ++++|.-+=++.+
T Consensus 235 V~ev~P~~aVsiieTDi~VDf 255 (567)
T PLN03086 235 VLELKPASSVSVLETDIEVDI 255 (567)
T ss_pred EEEEcCCCeeEEEeCceEEEe
Confidence 9999997 5566654444444
No 7
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=97.22 E-value=0.00053 Score=44.80 Aligned_cols=73 Identities=22% Similarity=0.374 Sum_probs=44.8
Q ss_pred ccEEEEccCCCC-ccCcccchHHHHhhHhhhhCCCceecCCEEEEcc-CCceEEEEEEEecCCC----cEEEcCCceEEE
Q psy6209 24 GKRIHVLPIDDS-VQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG-GMRAVEFKIVDTDPAP----YCIVAADTVIHC 97 (115)
Q Consensus 24 A~~V~laP~~d~-i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~-~~~~v~FkVv~t~P~~----~viVt~~T~I~~ 97 (115)
|+.|.+.|.+.. =+ +-+ +-..|+...|++--|-|..|..|.+.. .+..+.|+|.++.|.. +++++++|+|.+
T Consensus 1 A~~V~veP~T~dDWE-IlE-l~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~~i~~~V~~i~p~~~~~~~~~L~~~TEv~V 78 (80)
T PF09262_consen 1 AKSVEVEPLTSDDWE-ILE-LHAEFLEDQLLSQIRVVFPGQVFPVWVSQNTVIKFKVVSIEPSSSAEGCARLSPDTEVIV 78 (80)
T ss_dssp -SEEEEEESSHHHHH-HHH-HS-SSHHHHHHHH--EE-TT-EEEEESSSS-EEEEEEEEEES--S---SEE--TT-EEEE
T ss_pred CcEEEEEcCCccHHH-HHH-HhHHHHHHHHHHhheeecCCCEEEEEEcCCeEEEEEEEEccCCCCceeEEEeCCCcEEEE
Confidence 678999996310 01 111 224667777776678999999999986 4678999999999954 799999999987
Q ss_pred c
Q psy6209 98 E 98 (115)
Q Consensus 98 ~ 98 (115)
.
T Consensus 79 a 79 (80)
T PF09262_consen 79 A 79 (80)
T ss_dssp -
T ss_pred C
Confidence 4
No 8
>KOG0735|consensus
Probab=96.68 E-value=0.012 Score=52.18 Aligned_cols=97 Identities=18% Similarity=0.194 Sum_probs=76.1
Q ss_pred ccCCCCCCeEEEEeCCCCCCccEEEEccCC-CCccCcccchHHHHhhHhhhhCCCceecCCEEEEccC-CceEEEEEEEe
Q psy6209 4 RLTTPCRDLLDRQRDIQIVYGKRIHVLPID-DSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG-MRAVEFKIVDT 81 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~A~~V~laP~~-d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~-~~~v~FkVv~t 81 (115)
-+|..-|+.|+++.++.+..|+.|++-|.. |.=+ |-+ +-..++...++.-.|-|+. .+|.|-.. +..+.|+|+++
T Consensus 71 ~l~L~e~~~V~l~~~~~v~~~~~V~VeP~TsdDWE-IiE-lnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl 147 (952)
T KOG0735|consen 71 TLGLAENQEVKLSIIDHVHEATQVEVEPVTSDDWE-IIE-LNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRL 147 (952)
T ss_pred hccCCCCCeEEEEEcCCccceeEEEEeeccCccHH-HHH-hhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeee
Confidence 368888999999999999999999999963 2222 222 2245666667666788888 77777544 57899999999
Q ss_pred cC-CCcEEEcCCceEEEcCcccc
Q psy6209 82 DP-APYCIVAADTVIHCEGDPIK 103 (115)
Q Consensus 82 ~P-~~~viVt~~T~I~~~~~pv~ 103 (115)
.| ..++.+..+|++-+..++-+
T Consensus 148 ~Ps~~~gRl~~~Tev~VaPK~~k 170 (952)
T KOG0735|consen 148 IPSMLYGRLLRGTEVLVAPKPNK 170 (952)
T ss_pred ecccceeeecCCceEEEecCccc
Confidence 99 68999999999999877664
No 9
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.60 E-value=0.015 Score=45.74 Aligned_cols=98 Identities=19% Similarity=0.235 Sum_probs=62.9
Q ss_pred CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCc--eEEEEE
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMR--AVEFKI 78 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~--~v~FkV 78 (115)
|=+-++...||.|.++- .+++-++-|.|.|- ++.-++-..-...|.+-|+ ++.-+++||.|.|..+++ .|.|.+
T Consensus 100 Mm~tLs~epgdlv~~~~-td~plG~fVKL~Pq--SVdFLdI~dpkavLEn~LR-NfstLt~~D~iei~ynd~v~~Ik~~~ 175 (331)
T COG5140 100 MMQTLSMEPGDLVVLRY-TDFPLGKFVKLIPQ--SVDFLDIEDPKAVLENCLR-NFSTLTEGDEIEIQYNDEVGSIKFTV 175 (331)
T ss_pred HHHhccCCCCcEEEEEe-ccccccceEEeccc--ccceEeccChHHHHHHHHh-hccccccCCEEEEEECCeeeEEEEEE
Confidence 44668889999999998 59999999999995 3422221111234444443 355799999999988764 567777
Q ss_pred EEecCCCcEEEcCCceEEE-cCccc
Q psy6209 79 VDTDPAPYCIVAADTVIHC-EGDPI 102 (115)
Q Consensus 79 v~t~P~~~viVt~~T~I~~-~~~pv 102 (115)
++.+|+..+|-.-+|.+.+ --.|+
T Consensus 176 v~pe~S~~~i~vveTDLvvDF~pPi 200 (331)
T COG5140 176 VHPEPSANAIYVVETDLVVDFLPPI 200 (331)
T ss_pred eccCCCcceEEEEecceeeeccCCc
Confidence 7777754433222344333 23455
No 10
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=95.80 E-value=0.051 Score=43.65 Aligned_cols=75 Identities=17% Similarity=0.298 Sum_probs=57.2
Q ss_pred CCccEEEEccCCCCccC-------c--ccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCC
Q psy6209 22 VYGKRIHVLPIDDSVQG-------L--TGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAAD 92 (115)
Q Consensus 22 ~~A~~V~laP~~d~i~~-------i--~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~ 92 (115)
++++-+.|.|...++.. + +.++|+-|.+...+ +.-+++||.+.=..+-...-|+|+++.|++..+++..
T Consensus 22 ~~~k~lil~P~GyP~~~~~~e~pvv~dn~~~F~~YArdQW~--Ge~v~eg~ylFD~~~~pdyAfkvI~~~P~~~~i~~st 99 (368)
T COG1223 22 KSSKYLILRPMGYPLRESGMEYPVVDDNPEVFNIYARDQWL--GEVVREGDYLFDTRMFPDYAFKVIRVVPSGGGIITST 99 (368)
T ss_pred ccceEEEEccCCCccccccCCCceecCCHHHHHHHHHHhhc--ceeeecCceEeecccccccceeEEEEeCCCCceecce
Confidence 45677888886544421 1 12468889999988 9999999998776666778999999999999988866
Q ss_pred ceEEEc
Q psy6209 93 TVIHCE 98 (115)
Q Consensus 93 T~I~~~ 98 (115)
|.+.++
T Consensus 100 ~i~vl~ 105 (368)
T COG1223 100 TIFVLE 105 (368)
T ss_pred EEEEec
Confidence 665553
No 11
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=83.04 E-value=9.1 Score=23.97 Aligned_cols=70 Identities=9% Similarity=-0.015 Sum_probs=40.2
Q ss_pred CCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccch--HHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNL--FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~--~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.|++|.+|+++-. +-..-..++|....+. ....+. +..=|-.-|+ + -+.||.+.+...+...+|+|.+++
T Consensus 5 ~V~~Gs~V~l~~~-~~~~~~~~~lv~~~~~--~~~~~~IS~~SPLG~ALl--G--~~~Gd~v~~~~~~g~~~~~I~~I~ 76 (77)
T PF01272_consen 5 VVTIGSTVTLKDL-DDGEEETYTLVGPDEA--DPDNGKISIDSPLGKALL--G--KKVGDEVEVELPGGERKYEILEIE 76 (77)
T ss_dssp B-STTEEEEEEET-TTTEEEEEEEE-GGG---BSTSTEEETTSHHHHHHT--T---BTT-EEEEEETTBEEEEEEEEEE
T ss_pred EEEeCCEEEEEEC-CCCCEEEEEEEeEhHh--CCceeEEEecCHHHHHhc--C--CCCCCEEEEEeCCceEEEEEEEEE
Confidence 5889999999874 4455566666633221 111100 0122233333 3 378999999987778889998863
No 12
>KOG0741|consensus
Probab=77.98 E-value=19 Score=31.80 Aligned_cols=92 Identities=8% Similarity=0.021 Sum_probs=58.2
Q ss_pred CcccCCCCCCeEEEEeCCCCCCc----cEEEEcc-C-----CCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCC
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYG----KRIHVLP-I-----DDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGM 71 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A----~~V~laP-~-----~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~ 71 (115)
|+=|++++||.|.|++. ....+ ..++|-- | ..+ +.++++....-+++.|. +.+++.|+.+.....+
T Consensus 69 R~wa~~Sl~qev~V~~~-~~~~~~~~l~~m~le~dF~~k~~~~s-ep~Dad~ma~qF~~~y~--~q~fsvgQ~~~f~f~~ 144 (744)
T KOG0741|consen 69 RKWAGWSLGQEVEVKPF-TFDGSCDYLGSMTLEIDFLNKKNTTS-EPFDADEMAKQFKRQYN--SQAFSVGQQLVFEFNG 144 (744)
T ss_pred hhhhhcccCceeEEEec-ccCcccccceeEEEEehhhhcCCCCC-CCCCHHHHHHHHHHHhc--CcccCCccEEEEEecC
Confidence 66789999999999975 22222 2222220 0 011 13554433344455555 8999999999998765
Q ss_pred -ceEEEEEEEec---C--------------CCcEEEcCCceEEE
Q psy6209 72 -RAVEFKIVDTD---P--------------APYCIVAADTVIHC 97 (115)
Q Consensus 72 -~~v~FkVv~t~---P--------------~~~viVt~~T~I~~ 97 (115)
.-+-|+|.+++ | ...++++.+|+|..
T Consensus 145 ~~~l~l~v~~ie~~D~~~~~~~~a~~~~~~~~~G~l~~nT~i~F 188 (744)
T KOG0741|consen 145 NKLLGLKVKDIEAFDPGISEGESAVTKRQKIERGLLLGNTQIVF 188 (744)
T ss_pred ceEeeeEEEEEeeeccccccCCcccccccceeeeEeecCcEEEE
Confidence 56777777754 3 13589999999954
No 13
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=76.82 E-value=4.7 Score=28.62 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=28.7
Q ss_pred CceecCCEEEEccCCceEEEEEEEecCCCc--EEEcCCceEEEcCc
Q psy6209 57 RPVHKDDLFIVRGGMRAVEFKIVDTDPAPY--CIVAADTVIHCEGD 100 (115)
Q Consensus 57 rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~--viVt~~T~I~~~~~ 100 (115)
+||..||++.+. .+|.+.+++.. .+++-+++|++.|+
T Consensus 96 ~PV~~GDtl~~~-------~~V~~~~~~~~~~~~~~~~~~~~~~~~ 134 (149)
T cd03450 96 APVPVGSRVRGR-------FTLLSVEELKGGGVQVTLEVTVEIEGE 134 (149)
T ss_pred cceeCCcEEEEE-------EEEEEEEEcCCCeEEEEEEEEEEEeCC
Confidence 699999998875 45778777654 58888888888775
No 14
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=75.84 E-value=1.8 Score=27.97 Aligned_cols=18 Identities=17% Similarity=0.065 Sum_probs=16.1
Q ss_pred CCc-ccCCCCCCeEEEEeC
Q psy6209 1 MSF-RLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~-Nagv~iGD~V~V~k~ 18 (115)
||+ +.....||.|.|+.-
T Consensus 40 mr~~~i~I~~GD~V~Ve~~ 58 (75)
T COG0361 40 MRKNRIRILPGDVVLVELS 58 (75)
T ss_pred chheeEEeCCCCEEEEEec
Confidence 788 999999999999874
No 15
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=71.48 E-value=35 Score=24.45 Aligned_cols=73 Identities=10% Similarity=-0.041 Sum_probs=44.0
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEc-cCCCCc--cCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEE
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVL-PIDDSV--QGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKI 78 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~la-P~~d~i--~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkV 78 (115)
..+ .|..|-+|+++-. +-......+|. |.+-.. ..|+.. .=+-.-|. + -..||.+.+...+...++.|
T Consensus 75 ~~~-~V~~Gs~V~~~~~-~~ge~~~~~iVg~~ead~~~~~IS~~---SPig~aLl--G--k~vGd~v~v~~p~g~~~~~I 145 (151)
T COG0782 75 PPD-VVTFGSTVTLENL-DDGEEVTYTIVGPDEADPAKGKISVD---SPLGRALL--G--KKVGDTVEVNTPGGEKEVEI 145 (151)
T ss_pred CCC-EEecCCEEEEEEC-CCCCEEEEEEEcccccccccCceecc---CHHHHHHh--C--CCCCCEEEEecCCceEEEEE
Confidence 345 7899999999975 43555555554 321100 001110 11222233 3 26799999998888899999
Q ss_pred EEecC
Q psy6209 79 VDTDP 83 (115)
Q Consensus 79 v~t~P 83 (115)
.++.+
T Consensus 146 ~~I~~ 150 (151)
T COG0782 146 LSIEY 150 (151)
T ss_pred EEEec
Confidence 99865
No 16
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=68.34 E-value=3.5 Score=26.54 Aligned_cols=18 Identities=11% Similarity=-0.079 Sum_probs=16.5
Q ss_pred CCcccCCCCCCeEEEEeC
Q psy6209 1 MSFRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~ 18 (115)
||+|+-+..||.|.|.+.
T Consensus 33 ~Rk~iwI~~GD~VlV~~~ 50 (78)
T cd04456 33 LRKNIWIKRGDFLIVDPI 50 (78)
T ss_pred hccCEEEcCCCEEEEEec
Confidence 899999999999999874
No 17
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=63.18 E-value=5.1 Score=25.32 Aligned_cols=18 Identities=6% Similarity=-0.018 Sum_probs=15.0
Q ss_pred CC-cccCCCCCCeEEEEeC
Q psy6209 1 MS-FRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R-~Nagv~iGD~V~V~k~ 18 (115)
|| +...+..||+|+|..-
T Consensus 38 mr~~rI~I~~GD~V~Ve~s 56 (68)
T TIGR00008 38 IRMHYIRILPGDKVKVELS 56 (68)
T ss_pred chhccEEECCCCEEEEEEC
Confidence 77 4889999999999863
No 18
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=61.68 E-value=4.4 Score=26.89 Aligned_cols=17 Identities=18% Similarity=0.126 Sum_probs=14.2
Q ss_pred CCc-ccCCCCCCeEEEEe
Q psy6209 1 MSF-RLTTPCRDLLDRQR 17 (115)
Q Consensus 1 ~R~-Nagv~iGD~V~V~k 17 (115)
||+ .+.+..||+|+|+.
T Consensus 40 mR~~rIrIl~GD~V~VE~ 57 (87)
T PRK12442 40 MRKHRIRILAGDRVTLEL 57 (87)
T ss_pred eeeeeEEecCCCEEEEEE
Confidence 666 78899999998886
No 19
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=60.21 E-value=5.8 Score=25.42 Aligned_cols=18 Identities=17% Similarity=-0.084 Sum_probs=16.2
Q ss_pred CCcccCCCCCCeEEEEeC
Q psy6209 1 MSFRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~ 18 (115)
||+++.+..||.|.|...
T Consensus 33 ~rk~iwI~~GD~V~Ve~~ 50 (77)
T cd05793 33 MRKRVWINEGDIVLVAPW 50 (77)
T ss_pred hcccEEEcCCCEEEEEec
Confidence 789999999999999964
No 20
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=58.86 E-value=28 Score=25.89 Aligned_cols=57 Identities=11% Similarity=0.076 Sum_probs=36.2
Q ss_pred cEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecC
Q psy6209 25 KRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 25 ~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
..|.|.|-+ --...+.++.+.+=+..|...+ |+..|..|.+......++.+|+++..
T Consensus 59 ~~V~IpPE~-AfGe~~~~lvq~vp~~~F~~~~-~~~vGm~~~~~~~~~~~~~~V~~V~~ 115 (174)
T COG1047 59 FTVEIPPED-AFGEYDPDLVQRVPRDEFQGVG-ELEVGMEVEAEGGDGEIPGVVTEVSG 115 (174)
T ss_pred eEEEeCchH-hcCCCChHHeEEecHHHhCcCC-CCCCCcEEEEcCCCceeeEEEEEEcC
Confidence 345555532 1122334455455566676334 89999999998766778888888766
No 21
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=58.57 E-value=6.9 Score=24.48 Aligned_cols=30 Identities=23% Similarity=0.366 Sum_probs=15.7
Q ss_pred hCCCceecCCEEEEccC------CceEEEEEEEecC
Q psy6209 54 EAYRPVHKDDLFIVRGG------MRAVEFKIVDTDP 83 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~------~~~v~FkVv~t~P 83 (115)
++.||+..|+.|.|... ...+.|=|++.+|
T Consensus 34 FS~rPl~~~E~~~v~I~~~~~~wsG~L~~GvT~~~P 69 (69)
T PF07177_consen 34 FSSRPLRIGEKFEVRIDEVEPSWSGSLRIGVTSCDP 69 (69)
T ss_dssp EESS-B-TT-EEEEEEEEE-SSSSS--EEEEESS-C
T ss_pred EecCCccCCCEEEEEEEecCCCceeEEEEeeEccCC
Confidence 55999999999887531 2356666665555
No 22
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=57.60 E-value=5 Score=26.24 Aligned_cols=19 Identities=16% Similarity=0.125 Sum_probs=13.8
Q ss_pred ccCCCCCCeEEEEeCCCCC
Q psy6209 4 RLTTPCRDLLDRQRDIQIV 22 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~ 22 (115)
.+++++||.|.|+++.++-
T Consensus 47 ~~~i~~Gd~V~V~raGdVI 65 (82)
T PF03120_consen 47 ELDIRIGDTVLVTRAGDVI 65 (82)
T ss_dssp HTT-BBT-EEEEEEETTTE
T ss_pred HcCCCCCCEEEEEECCCcc
Confidence 4688999999999986653
No 23
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=56.56 E-value=7.5 Score=25.26 Aligned_cols=18 Identities=11% Similarity=-0.086 Sum_probs=16.3
Q ss_pred CCcccCCCCCCeEEEEeC
Q psy6209 1 MSFRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~ 18 (115)
||+++-+..||.|.|...
T Consensus 38 ~Rk~iwI~~GD~VlVe~~ 55 (83)
T smart00652 38 MRKKVWIRRGDIVLVDPW 55 (83)
T ss_pred hcccEEEcCCCEEEEEec
Confidence 789999999999999874
No 24
>KOG0736|consensus
Probab=53.04 E-value=50 Score=30.42 Aligned_cols=58 Identities=24% Similarity=0.318 Sum_probs=43.7
Q ss_pred chHHHHhhHhhhhCCCceecCCEEEEccCC------------------ceEEEEEEEecCC---CcEEEcCCceEEEcCc
Q psy6209 42 NLFEVYLKPYFLEAYRPVHKDDLFIVRGGM------------------RAVEFKIVDTDPA---PYCIVAADTVIHCEGD 100 (115)
Q Consensus 42 ~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~------------------~~v~FkVv~t~P~---~~viVt~~T~I~~~~~ 100 (115)
++....++.||+ ..|-++.||+|.|.... .-|-|+|++.+|+ .+++=+..|.+..-+.
T Consensus 304 ~~~~~~l~~~f~-t~ril~~gdvf~i~~~~~~~~~~~~~~l~l~~~~d~~v~~~v~~~ep~~~~~~~i~~~~T~lv~~~~ 382 (953)
T KOG0736|consen 304 GNIDVVLKKHFK-TPRILQSGDVFCIPINSQMANLNGYPELPLWRETDFLVYKKVIEAEPGNESAYIIDTNHTSLVLVGA 382 (953)
T ss_pred hHHHHHHHHHhC-cceeeecCCEEEEeehhhhcccccchhhHhhhhccceeEEEEeecCCCccceEEEcCCCceEEEccc
Confidence 345678899997 78999999999996432 2488999999993 3555666788877543
No 25
>smart00588 NEUZ domain in neuralized proteins.
Probab=52.31 E-value=16 Score=25.30 Aligned_cols=31 Identities=32% Similarity=0.506 Sum_probs=25.8
Q ss_pred hCCCceecCCEEEEccC------CceEEEEEEEecCC
Q psy6209 54 EAYRPVHKDDLFIVRGG------MRAVEFKIVDTDPA 84 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~------~~~v~FkVv~t~P~ 84 (115)
++.||+..|+.|.|... ...++|=|++.+|.
T Consensus 35 FS~rPl~~~E~~~v~i~~~~~~w~G~l~~G~Ts~dP~ 71 (123)
T smart00588 35 FSARPLRINELFEVKIEKVVRKWSGALRFGVTTCDPA 71 (123)
T ss_pred ecCCCCcCCCEEEEEEEEecCCccCceEEEEecCCcc
Confidence 55999999999999643 34799999999985
No 26
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=51.99 E-value=13 Score=21.00 Aligned_cols=29 Identities=14% Similarity=0.157 Sum_probs=21.6
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEccCCC
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDD 34 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d 34 (115)
|+-+|+..||.|.+... + . .++.|.|...
T Consensus 16 ~~~l~l~~Gd~v~i~~~-~--~-g~i~i~p~~~ 44 (47)
T PF04014_consen 16 REKLGLKPGDEVEIEVE-G--D-GKIVIRPVKR 44 (47)
T ss_dssp HHHTTSSTTTEEEEEEE-T--T-SEEEEEESTT
T ss_pred HHHcCCCCCCEEEEEEe-C--C-CEEEEEECCC
Confidence 55679999999999973 2 1 1788988753
No 27
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=50.50 E-value=11 Score=25.53 Aligned_cols=18 Identities=17% Similarity=-0.075 Sum_probs=16.3
Q ss_pred CCcccCCCCCCeEEEEeC
Q psy6209 1 MSFRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~ 18 (115)
||+++.+..||.|.|...
T Consensus 54 ~Rk~IwI~~GD~VlVe~~ 71 (100)
T PRK04012 54 MKKRMWIREGDVVIVAPW 71 (100)
T ss_pred hcccEEecCCCEEEEEec
Confidence 789999999999999974
No 28
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=50.37 E-value=9.4 Score=27.90 Aligned_cols=17 Identities=18% Similarity=0.051 Sum_probs=15.8
Q ss_pred CCcccCCCCCCeEEEEe
Q psy6209 1 MSFRLTTPCRDLLDRQR 17 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k 17 (115)
||+++.+..||.|.|..
T Consensus 65 mRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 65 MRKRVWINIGDIILVSL 81 (155)
T ss_pred ceeeEEecCCCEEEEec
Confidence 89999999999999975
No 29
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=49.09 E-value=14 Score=32.82 Aligned_cols=27 Identities=7% Similarity=-0.080 Sum_probs=20.4
Q ss_pred ccCCCCCCeEEEEeCCCC-CCccEEEEc
Q psy6209 4 RLTTPCRDLLDRQRDIQI-VYGKRIHVL 30 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v-~~A~~V~la 30 (115)
..+++|||+|.|+|+-++ |.--+|.+-
T Consensus 365 rkdIrIGDtV~V~kAGdVIP~V~~Vv~e 392 (667)
T COG0272 365 RKDIRIGDTVVVRKAGDVIPQVVGVVLE 392 (667)
T ss_pred hcCCCCCCEEEEEecCCCCcceeeeecc
Confidence 468999999999998776 444555554
No 30
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=47.45 E-value=25 Score=23.62 Aligned_cols=21 Identities=10% Similarity=-0.042 Sum_probs=17.2
Q ss_pred CCcccCCCCCCeEEEEeCCCCC
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQIV 22 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~v~ 22 (115)
||+.+-+..||.|.|.+- +..
T Consensus 52 ~Rk~iwI~~GD~VlVsp~-d~~ 72 (99)
T TIGR00523 52 LKKRIWIREGDVVIVKPW-EFQ 72 (99)
T ss_pred hcccEEecCCCEEEEEEc-cCC
Confidence 788899999999999874 444
No 31
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=44.54 E-value=32 Score=24.15 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=20.6
Q ss_pred ceecCCEEEEcc-CCceEEEEEEEe
Q psy6209 58 PVHKDDLFIVRG-GMRAVEFKIVDT 81 (115)
Q Consensus 58 PV~~Gd~i~v~~-~~~~v~FkVv~t 81 (115)
=+.+||.|.+.. .++...|+|.++
T Consensus 72 ~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 72 DLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred cCCCCCEEEEEECCCCEEEEEEeEE
Confidence 378999999988 678899999885
No 32
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=42.92 E-value=75 Score=22.73 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=20.7
Q ss_pred HHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecC
Q psy6209 44 FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 44 ~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
+.+++...+....+|+..||.|.+.+ ..=+|.++..
T Consensus 46 ~~n~~~gi~i~~~~pf~vGD~I~i~~----~~G~V~~I~l 81 (206)
T PF00924_consen 46 ISNFISGIIILFERPFKVGDRIEIGG----VEGRVEEIGL 81 (206)
T ss_dssp HHHHHHHHHHHCC-SS-TT-EEESSS-----EEEEEEE-S
T ss_pred HHHHHHHHHHhccCCccCCCEEEEEE----eehHHHhcCc
Confidence 44555555557789999999999975 3334555444
No 33
>PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional
Probab=42.69 E-value=77 Score=22.81 Aligned_cols=14 Identities=29% Similarity=0.320 Sum_probs=11.6
Q ss_pred CCceecCCEEEEcc
Q psy6209 56 YRPVHKDDLFIVRG 69 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~ 69 (115)
.+||..||++++..
T Consensus 94 ~rPV~~GDtL~~~~ 107 (166)
T PRK13691 94 HKPVLAGDKLWARM 107 (166)
T ss_pred eCCcCCCCEEEEEE
Confidence 47999999999863
No 34
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=41.18 E-value=48 Score=21.96 Aligned_cols=27 Identities=15% Similarity=0.108 Sum_probs=17.8
Q ss_pred ccCCCCCCeEEEEeCCCCCCccEEEEc
Q psy6209 4 RLTTPCRDLLDRQRDIQIVYGKRIHVL 30 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~A~~V~la 30 (115)
|..+++||.|+|.....+..-++-.|.
T Consensus 53 ~~~~k~GD~V~I~EtRPLSKtK~~~vv 79 (87)
T COG0186 53 CNEAKVGDIVRIAETRPLSKTKRFVVV 79 (87)
T ss_pred cccCCCCCEEEEEEccccCCcceEEEE
Confidence 567899999999876444444444443
No 35
>smart00532 LIGANc Ligase N family.
Probab=40.92 E-value=26 Score=29.43 Aligned_cols=20 Identities=5% Similarity=-0.024 Sum_probs=16.5
Q ss_pred ccCCCCCCeEEEEeCCCCCC
Q psy6209 4 RLTTPCRDLLDRQRDIQIVY 23 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~ 23 (115)
.+++++||+|.|+++.++-+
T Consensus 360 ~~~i~iGd~V~V~raGdVIP 379 (441)
T smart00532 360 EKDIRIGDTVVVRKAGDVIP 379 (441)
T ss_pred HcCCCCCCEEEEEECCCcCc
Confidence 36899999999999866644
No 36
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=39.95 E-value=80 Score=21.40 Aligned_cols=23 Identities=26% Similarity=0.271 Sum_probs=20.0
Q ss_pred eecCCEEEEccCCceEEEEEEEe
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
+.+||.|.+...+...+|+|.+.
T Consensus 65 l~~Gd~v~v~~~~~~~~Y~V~~~ 87 (126)
T cd06166 65 VEKGDEIKVTTKNGTYKYKITSI 87 (126)
T ss_pred CCCCCEEEEEECCEEEEEEEEEE
Confidence 57899999988888899999884
No 37
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=39.72 E-value=39 Score=21.15 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=21.7
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEccCCC
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDD 34 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d 34 (115)
+.-+|+..||.|.+..- + ..+.|.|...
T Consensus 19 ~~~lgl~~Gd~v~v~~~-~----~~iii~~~~~ 46 (74)
T TIGR02609 19 LESLGLKEGDTLYVDEE-E----GGLKLKRFDE 46 (74)
T ss_pred HHHcCcCCCCEEEEEEE-C----CEEEEEECCC
Confidence 45689999999998863 2 4688888865
No 38
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=39.05 E-value=44 Score=22.69 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=23.0
Q ss_pred CCceecCCEEEEccCCceEEEEEEEec
Q psy6209 56 YRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
..-|..||++.|..+...+.++|..+.
T Consensus 46 S~~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 46 SKEVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred ccccCCCCEEEEEeCCcEEEEEEEecc
Confidence 445899999999999899999999854
No 39
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=38.88 E-value=87 Score=20.03 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=19.5
Q ss_pred CceecCCEEEEccCCceEEEEEEEec
Q psy6209 57 RPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 57 rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
+=+..||.+.|......++++|.-++
T Consensus 42 ~Gi~~Gd~V~v~s~~G~v~~~v~~~~ 67 (110)
T PF01568_consen 42 LGIKDGDWVRVSSPRGSVEVRVKVTD 67 (110)
T ss_dssp CT--TTCEEEEEETTEEEEEEEEEET
T ss_pred hcCcCCCEEEEEeccceEeeeeEEec
Confidence 34889999999988788999886654
No 40
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=37.83 E-value=61 Score=21.82 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=9.7
Q ss_pred CceecCCEEEEc
Q psy6209 57 RPVHKDDLFIVR 68 (115)
Q Consensus 57 rPV~~Gd~i~v~ 68 (115)
+||..||++.+.
T Consensus 90 ~pv~~GDtl~~~ 101 (146)
T cd03451 90 APVFHGDTLYAE 101 (146)
T ss_pred CCCCCCCEEEEE
Confidence 689999988764
No 41
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=37.68 E-value=27 Score=30.42 Aligned_cols=26 Identities=8% Similarity=-0.202 Sum_probs=19.2
Q ss_pred ccCCCCCCeEEEEeCCCCCC-ccEEEE
Q psy6209 4 RLTTPCRDLLDRQRDIQIVY-GKRIHV 29 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~-A~~V~l 29 (115)
..++++||+|.|+|+.++-| -.+|..
T Consensus 357 ~~~I~iGD~V~V~raGdVIP~I~~vv~ 383 (562)
T PRK08097 357 QWDIAPGDQVLVSLAGQGIPRLDKVVW 383 (562)
T ss_pred HcCCCCCCEEEEEecCCCCcceeeeec
Confidence 36889999999999877644 345544
No 42
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=37.59 E-value=26 Score=24.00 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=16.6
Q ss_pred CCCceecCCEEEEccCCceEEE
Q psy6209 55 AYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 55 ~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
..||+..|.+|+....+.++.|
T Consensus 30 GDRPIQVGSHfHF~EvN~aL~F 51 (106)
T COG0832 30 GDRPIQVGSHFHFFEVNRALSF 51 (106)
T ss_pred CCCceEeecceeehhhCcceee
Confidence 3689999999998665555555
No 43
>KOG1740|consensus
Probab=37.21 E-value=21 Score=24.46 Aligned_cols=26 Identities=12% Similarity=0.063 Sum_probs=17.8
Q ss_pred CCCCCeEEEEeCCCCCCccEEEEccC
Q psy6209 7 TPCRDLLDRQRDIQIVYGKRIHVLPI 32 (115)
Q Consensus 7 v~iGD~V~V~k~~~v~~A~~V~laP~ 32 (115)
+++||.|++.+......-+.-.++++
T Consensus 50 cnvGD~VrlepsRPlSk~K~f~i~eI 75 (107)
T KOG1740|consen 50 CNVGDRVRLEPSRPLSKTKHFIIAEI 75 (107)
T ss_pred ccccceEEeccCCcccccceeehHHH
Confidence 68999999998644444455555553
No 44
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=37.21 E-value=18 Score=24.59 Aligned_cols=23 Identities=26% Similarity=0.367 Sum_probs=17.7
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||+.|.+++....+..++|
T Consensus 29 tGDRPIQVGSHyHF~E~N~aL~F 51 (101)
T TIGR00192 29 TGDRPIQVGSHFHFFEVNRALDF 51 (101)
T ss_pred CCCcceEEccccchhhcCcceee
Confidence 34799999999999766666655
No 45
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=36.74 E-value=1.2e+02 Score=22.09 Aligned_cols=60 Identities=15% Similarity=0.138 Sum_probs=34.0
Q ss_pred CCCeEEEEeCCC--CCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccC-----CceEEEEEEEe
Q psy6209 9 CRDLLDRQRDIQ--IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG-----MRAVEFKIVDT 81 (115)
Q Consensus 9 iGD~V~V~k~~~--v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~-----~~~v~FkVv~t 81 (115)
-||.-+.++++. ++....+.|.|=.+.+ .|.+..+|+.+||.|.+... ...++++|..-
T Consensus 78 ~~gvmkMr~v~~i~Ipa~~~v~lkpGgyHv--------------Mlm~lK~pl~eGd~v~vtL~f~~~~~~~v~~~v~~~ 143 (151)
T COG2847 78 DGGVMKMRKVPGIVIPAGGTVELKPGGYHV--------------MLMGLKKPLKEGDKVPVTLKFEKAGKVTVEAPVKKK 143 (151)
T ss_pred cCCeEEEEEcCcEEECCCceEEecCCCEEE--------------EEeccCCCccCCCEEEEEEEEecCCeEEEEEEEecc
Confidence 367777787642 2333445555533322 11234789999999999632 23456555543
Q ss_pred c
Q psy6209 82 D 82 (115)
Q Consensus 82 ~ 82 (115)
.
T Consensus 144 ~ 144 (151)
T COG2847 144 A 144 (151)
T ss_pred C
Confidence 3
No 46
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=36.55 E-value=59 Score=22.89 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=28.3
Q ss_pred ccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccC
Q psy6209 30 LPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70 (115)
Q Consensus 30 aP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~ 70 (115)
+|.+|.| ++...|+.||+..++-.++.=..|+.+.+...
T Consensus 27 ~PveD~I--~d~a~fekfL~erIKV~GK~gnLg~~V~v~~~ 65 (122)
T PTZ00198 27 IPAEDGI--IDLSGFEQFLQDRIKVDGKTGNLGNKVRVSRE 65 (122)
T ss_pred CcccCCc--ccHHHHHHHHHHhEEECCCcCccCCcEEEEEE
Confidence 4888865 44445789999999866777677787777543
No 47
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=36.16 E-value=1.2e+02 Score=20.68 Aligned_cols=44 Identities=23% Similarity=0.197 Sum_probs=28.8
Q ss_pred CCceecCCEEEEccC-CceEEEEEEEecCCCcEEEcCCceEEEcCc
Q psy6209 56 YRPVHKDDLFIVRGG-MRAVEFKIVDTDPAPYCIVAADTVIHCEGD 100 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~-~~~v~FkVv~t~P~~~viVt~~T~I~~~~~ 100 (115)
..+|.+||.+.|-.+ ..-=+=+|.++.|.. ++|-.=+.+.-.+.
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEGvnv~kkh~k 46 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEGVNVVKKHIK 46 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe-EEEECcEEEEecCC
Confidence 358999999999654 222344678888877 66655555554444
No 48
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=36.10 E-value=38 Score=20.90 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=19.4
Q ss_pred CCCCCCeEEEEeCCCCCCccEEEEccC
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIHVLPI 32 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~laP~ 32 (115)
..++||.++++-. .+.+..++.+.|.
T Consensus 52 ~~~iGd~v~v~I~-~i~e~~~i~l~~~ 77 (77)
T cd04473 52 DYEVGDEVIVQVT-DIPENGNIDLIPV 77 (77)
T ss_pred cCCCCCEEEEEEE-EECCCCcEEEEEC
Confidence 3689999999974 5556678888763
No 49
>PLN00208 translation initiation factor (eIF); Provisional
Probab=35.94 E-value=20 Score=25.87 Aligned_cols=17 Identities=12% Similarity=0.044 Sum_probs=15.6
Q ss_pred CCcccCCCCCCeEEEEe
Q psy6209 1 MSFRLTTPCRDLLDRQR 17 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k 17 (115)
||+++.+..||.|.|..
T Consensus 65 mRKrIWI~~GD~VlVel 81 (145)
T PLN00208 65 MRKKVWIAAGDIILVGL 81 (145)
T ss_pred ceeeEEecCCCEEEEEc
Confidence 88999999999999985
No 50
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=35.91 E-value=16 Score=22.29 Aligned_cols=18 Identities=11% Similarity=0.030 Sum_probs=12.5
Q ss_pred CCcccCCCCCCeEEEEeC
Q psy6209 1 MSFRLTTPCRDLLDRQRD 18 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~ 18 (115)
||++.-+..||.|.|..-
T Consensus 36 ~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 36 FRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp HHTCC---TTEEEEEEES
T ss_pred eeeeEecCCCCEEEEEec
Confidence 578888999999999973
No 51
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=35.90 E-value=30 Score=30.53 Aligned_cols=26 Identities=12% Similarity=0.095 Sum_probs=19.0
Q ss_pred ccCCCCCCeEEEEeCCCCCC-ccEEEE
Q psy6209 4 RLTTPCRDLLDRQRDIQIVY-GKRIHV 29 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~-A~~V~l 29 (115)
.+++++||+|.|+++-++-| -.+|..
T Consensus 353 ~~~i~iGD~V~V~raGdVIP~i~~vv~ 379 (652)
T TIGR00575 353 ELDIRIGDTVVVRKAGDVIPKVVRVLL 379 (652)
T ss_pred HcCCCCCCEEEEEecCCcCceeeeecc
Confidence 46889999999999877755 234433
No 52
>KOG3434|consensus
Probab=35.39 E-value=1e+02 Score=21.81 Aligned_cols=49 Identities=14% Similarity=0.217 Sum_probs=31.7
Q ss_pred cCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecC
Q psy6209 31 PIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 31 P~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
|.+|.| ++...|+.||+...+-.+..=..|+.+.+...+..| -|++..+
T Consensus 27 p~eDgI--~d~A~fe~fLqerIKv~GK~gnLg~vv~ie~~kski--tV~s~~~ 75 (125)
T KOG3434|consen 27 PVEDGI--LDIADLEKFLQERIKVNGKVGNLGNVVTIERSKSKI--TVVSTVH 75 (125)
T ss_pred cccccc--ccHHHHHHHHHHHhhhcccccccCCeEEEecCCcEE--EEEecCC
Confidence 888876 553347899999998666666677766665443333 2555444
No 53
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=35.12 E-value=1.2e+02 Score=22.89 Aligned_cols=53 Identities=11% Similarity=0.155 Sum_probs=36.7
Q ss_pred HHHHhhHhhhhCCCceecCCEEEEc-cC-Cc--eEEEEEEEe-cCCCcEEEcCCceEE
Q psy6209 44 FEVYLKPYFLEAYRPVHKDDLFIVR-GG-MR--AVEFKIVDT-DPAPYCIVAADTVIH 96 (115)
Q Consensus 44 ~~~~lk~~l~~~~rPV~~Gd~i~v~-~~-~~--~v~FkVv~t-~P~~~viVt~~T~I~ 96 (115)
..+++...|....+|+..||.+.+. .. |. .+.++.+.+ .+.|..+.-++..+.
T Consensus 133 ~~n~~~Gi~il~~~~f~vGD~I~i~~~~~G~V~~i~~~~T~ir~~dg~~v~iPNs~i~ 190 (316)
T COG0668 133 LSNLIAGIFLLLERPFKVGDWIEIGSGVEGTVEDIGLRSTTIRTLDGRIVTIPNSKLF 190 (316)
T ss_pred HHHHHhhhHhheecCcCcCCEEEECCCceEEEEEEEEEEEEEEcCCCCEEEccchhhc
Confidence 3455555555668999999999997 34 33 345555555 678888888877654
No 54
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=34.72 E-value=57 Score=22.17 Aligned_cols=23 Identities=9% Similarity=0.236 Sum_probs=20.5
Q ss_pred eecCCEEEEccCCceEEEEEEEe
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
+.+||.|.+...++..+++|.++
T Consensus 62 l~~Gd~i~v~~~~~~~~Y~V~~~ 84 (127)
T cd05828 62 LEPGDIITLQTLGGTYTYRVTST 84 (127)
T ss_pred CCCCCEEEEEECCEEEEEEEeeE
Confidence 67899999998889999999985
No 55
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=34.48 E-value=58 Score=22.49 Aligned_cols=23 Identities=9% Similarity=0.140 Sum_probs=20.2
Q ss_pred eecCCEEEEccCCceEEEEEEEe
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
+.+||.|.+...+...+|+|.++
T Consensus 66 l~~Gd~i~v~~~~~~~~Y~V~~~ 88 (137)
T cd05830 66 LRPGDKIVVETADGWYTYVVRSS 88 (137)
T ss_pred CCCCCEEEEEECCeEEEEEEeEE
Confidence 78999999988777889999985
No 56
>PRK13202 ureB urease subunit beta; Reviewed
Probab=34.20 E-value=23 Score=24.27 Aligned_cols=23 Identities=26% Similarity=0.346 Sum_probs=17.6
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||+.|.+++.-..+..++|
T Consensus 30 tGDRPIQVGSHyHF~E~N~aL~F 52 (104)
T PRK13202 30 AGDRPVQVGSHVHLPQANRALSF 52 (104)
T ss_pred CCCCceEEccccchhhcCcceee
Confidence 34799999999998666666655
No 57
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=34.20 E-value=58 Score=22.42 Aligned_cols=23 Identities=17% Similarity=0.478 Sum_probs=19.7
Q ss_pred eecCCEEEEccCCceEEEEEEEe
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
+.+||.|.+...+...+++|+++
T Consensus 64 l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 64 LKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred CCCCCEEEEEECCcEEEEEEEEE
Confidence 67999999988778889999884
No 58
>PRK11281 hypothetical protein; Provisional
Probab=34.16 E-value=70 Score=30.22 Aligned_cols=52 Identities=12% Similarity=0.165 Sum_probs=34.0
Q ss_pred HHHHhhHhhhhCCCceecCCEEEEccC-C--ceEEEEEEEe-cCCCcEEEcCCceE
Q psy6209 44 FEVYLKPYFLEAYRPVHKDDLFIVRGG-M--RAVEFKIVDT-DPAPYCIVAADTVI 95 (115)
Q Consensus 44 ~~~~lk~~l~~~~rPV~~Gd~i~v~~~-~--~~v~FkVv~t-~P~~~viVt~~T~I 95 (115)
+.+|+.-.+....||++.||.|.+.+. | ..|.+..+.+ ++.+..++-+|..+
T Consensus 924 lsNfISGiiIl~eRPfrIGD~I~I~~~~G~V~~I~lRsT~Irt~D~~~ViIPNs~~ 979 (1113)
T PRK11281 924 FANFVSGLIILFERPVRIGDTVTIGTFSGTVSKIRIRATTITDFDRKEVIVPNKAF 979 (1113)
T ss_pred HHHHHHHHHHHHcCCcCCCCEEEECCEEEEEEEEEeEEEEEEcCCCCEEEEechhh
Confidence 445566666667899999999999754 2 2455666664 35666565555553
No 59
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=33.25 E-value=70 Score=20.13 Aligned_cols=13 Identities=8% Similarity=0.051 Sum_probs=11.4
Q ss_pred CCCCCCeEEEEeC
Q psy6209 6 TTPCRDLLDRQRD 18 (115)
Q Consensus 6 gv~iGD~V~V~k~ 18 (115)
.+.+||.|.|...
T Consensus 48 ~~k~GD~V~I~ec 60 (71)
T TIGR03635 48 ECKVGDVVRIIET 60 (71)
T ss_pred CCCCCCEEEEEEc
Confidence 5899999999975
No 60
>PRK13203 ureB urease subunit beta; Reviewed
Probab=32.86 E-value=18 Score=24.66 Aligned_cols=23 Identities=17% Similarity=0.222 Sum_probs=17.0
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||+.|.+++.-..+.+++|
T Consensus 29 tGDRPIQVGSH~HF~E~N~aL~F 51 (102)
T PRK13203 29 TGDRPIQVGSHYHFFEVNPALSF 51 (102)
T ss_pred CCCCceEEccccchhhcCcchhc
Confidence 34799999999998655555554
No 61
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=32.63 E-value=61 Score=22.14 Aligned_cols=26 Identities=15% Similarity=0.382 Sum_probs=19.9
Q ss_pred CceecCCEEEEccCCceEEEEEEEec
Q psy6209 57 RPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 57 rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.-+..||+|.+...+....|+|.+++
T Consensus 138 ~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 138 LALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred ccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 34788999999766777788887764
No 62
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=32.08 E-value=38 Score=30.06 Aligned_cols=20 Identities=10% Similarity=0.149 Sum_probs=16.7
Q ss_pred ccCCCCCCeEEEEeCCCCCC
Q psy6209 4 RLTTPCRDLLDRQRDIQIVY 23 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~ 23 (115)
.+++++||+|.|+++-++-|
T Consensus 362 ~~di~iGD~V~V~raGdVIP 381 (669)
T PRK14350 362 SIGLNVGDVVKISRRGDVIP 381 (669)
T ss_pred HcCCCCCCEEEEEecCCCCC
Confidence 46899999999999877654
No 63
>cd00407 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=31.97 E-value=21 Score=24.32 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=17.0
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||+.|.+++.-..+..++|
T Consensus 29 tGDRpIQVGSH~HF~E~N~aL~F 51 (101)
T cd00407 29 TGDRPIQVGSHYHFFEVNPALKF 51 (101)
T ss_pred CCCcceEEccccchhhcCccccc
Confidence 34799999999998655555554
No 64
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=31.89 E-value=35 Score=21.52 Aligned_cols=42 Identities=26% Similarity=0.381 Sum_probs=28.0
Q ss_pred eecCCEEEEc--cCCceEEEEEEEecCCCcEEEcCCceEEEcCc
Q psy6209 59 VHKDDLFIVR--GGMRAVEFKIVDTDPAPYCIVAADTVIHCEGD 100 (115)
Q Consensus 59 V~~Gd~i~v~--~~~~~v~FkVv~t~P~~~viVt~~T~I~~~~~ 100 (115)
+.+|+.+++. ...+++|-+.....|..|..=++...+.+.|+
T Consensus 1 lKKG~lVrv~re~~~nSlEa~ASD~~~P~Yife~~GEvl~ikgd 44 (67)
T PF11910_consen 1 LKKGSLVRVNREKYENSLEAKASDPRPPSYIFEGPGEVLDIKGD 44 (67)
T ss_pred CCcceEEEeehHhhcCchhhhhcCCCCCcceecCCCeEEEecCC
Confidence 3578888774 23456777777777777777777776666654
No 65
>PF13452 MaoC_dehydrat_N: N-terminal half of MaoC dehydratase; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1S9C_K 3OML_A 3KHP_A.
Probab=31.75 E-value=37 Score=22.63 Aligned_cols=40 Identities=18% Similarity=0.309 Sum_probs=22.7
Q ss_pred CCceecCCEEEEccCCceEEEEEEEecCC----CcEEEcCCceEE-EcCccc
Q psy6209 56 YRPVHKDDLFIVRGGMRAVEFKIVDTDPA----PYCIVAADTVIH-CEGDPI 102 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~----~~viVt~~T~I~-~~~~pv 102 (115)
.||+..||.+.+.. +|.++.++ ..++|+-.+++. -+|++|
T Consensus 85 h~Pl~~Gd~l~~~~-------~v~~v~~k~g~G~~~~v~~~~~~~~~~Ge~v 129 (132)
T PF13452_consen 85 HRPLRPGDTLTATS-------RVTDVYDKRGAGKGVFVTVETEYTDQDGELV 129 (132)
T ss_dssp SS--BSSEEEEEEE-------EEEEEEEES-TTSEEEEEEEEEEE-CTTEEE
T ss_pred eCCCCCCCEEEEEE-------EEEEEEEecCCCCEEEEEEEEEEECCCCCEE
Confidence 67999999998864 23333332 355666555554 566665
No 66
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.65 E-value=42 Score=29.70 Aligned_cols=25 Identities=12% Similarity=-0.000 Sum_probs=18.3
Q ss_pred ccCCCCCCeEEEEeCCCCCC-ccEEE
Q psy6209 4 RLTTPCRDLLDRQRDIQIVY-GKRIH 28 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~-A~~V~ 28 (115)
..++++||+|.|+++-++-| -.+|.
T Consensus 365 ~~~i~iGD~V~V~raGdVIP~i~~vv 390 (665)
T PRK07956 365 RKDIRIGDTVVVRRAGDVIPEVVGVV 390 (665)
T ss_pred HcCCCCCCEEEEEECCCccceeeeee
Confidence 36899999999999867644 33443
No 67
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 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 L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=31.29 E-value=70 Score=22.14 Aligned_cols=49 Identities=12% Similarity=0.263 Sum_probs=30.9
Q ss_pred cCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecC
Q psy6209 31 PIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 31 P~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
|.+|.| ++...|+.||+..++-.++.=..|+.+.+......|. |++.-|
T Consensus 15 pveD~I--~d~~~fe~fL~erIKV~gk~gnlg~~V~i~~~~~ki~--V~s~v~ 63 (112)
T PF01776_consen 15 PVEDGI--MDPADFEKFLQERIKVNGKTGNLGNKVTISRDKNKIT--VTSEVP 63 (112)
T ss_dssp SSSTS-----SHHHHHHHHHHHHHHSCSSSSTTTEEEEE-SSEEE--EEESSS
T ss_pred cccCce--ecHHHHHHHHHHheEeCCcccccCCeEEEEecCCEEE--EEeccc
Confidence 888865 5544578999998885566666688888865544443 444444
No 68
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=31.07 E-value=1.3e+02 Score=20.29 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=23.4
Q ss_pred eecCCEEEEccCCceEEEEEEEe---cCCCcEEE
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT---DPAPYCIV 89 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t---~P~~~viV 89 (115)
+.+||.|.+...+...+++|.+. +|.+.-++
T Consensus 64 l~~Gd~I~l~~~~~~~~Y~V~~~~~v~~~~~~~~ 97 (127)
T cd06165 64 VKVGDKIYLTDKDNVYEYKVTSKKIVDPTRVDVI 97 (127)
T ss_pred CcCCCEEEEEECCEEEEEEEeeEEEECcccceee
Confidence 45899999988888899999884 46554344
No 69
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=30.98 E-value=87 Score=21.46 Aligned_cols=31 Identities=29% Similarity=0.350 Sum_probs=18.0
Q ss_pred CceecCCEEEEccCCceEEEEEEEecCC---CcEEEcCCce
Q psy6209 57 RPVHKDDLFIVRGGMRAVEFKIVDTDPA---PYCIVAADTV 94 (115)
Q Consensus 57 rPV~~Gd~i~v~~~~~~v~FkVv~t~P~---~~viVt~~T~ 94 (115)
+||..||++.+. +.|++..++ +.++|+-.++
T Consensus 87 ~PV~~GDtl~~~-------~~V~~~~~~~~~~~~~v~~~~~ 120 (142)
T cd03452 87 EPVYPGDTIQVR-------LTCKRKIPRDGQDYGVVRWDAE 120 (142)
T ss_pred CCCCCCCEEEEE-------EEEEEEeecCCCCcEEEEEEEE
Confidence 588888888775 345665542 2345543333
No 70
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=30.92 E-value=1.9e+02 Score=20.52 Aligned_cols=12 Identities=17% Similarity=0.409 Sum_probs=10.5
Q ss_pred CceecCCEEEEc
Q psy6209 57 RPVHKDDLFIVR 68 (115)
Q Consensus 57 rPV~~Gd~i~v~ 68 (115)
+||..||++.+.
T Consensus 95 ~PV~~GDtL~~~ 106 (159)
T PRK13692 95 KPIVAGDKLYCD 106 (159)
T ss_pred CCccCCCEEEEE
Confidence 699999999875
No 71
>smart00785 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU PUBMED:15112237.
Probab=30.75 E-value=48 Score=21.39 Aligned_cols=31 Identities=16% Similarity=0.240 Sum_probs=24.2
Q ss_pred HhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209 47 YLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 47 ~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.+.-|+. +.++..++.|+|++.| .|++.+++
T Consensus 47 ~v~GyvR--G~~l~~n~lVHIpG~G---Dfqi~~I~ 77 (83)
T smart00785 47 VVYGYVR--GTGLNANQLVHIPGLG---DFQISKIE 77 (83)
T ss_pred EEEEEEc--CCCCCCCCEEEeCCcC---CeEeeEEe
Confidence 4677888 8999999999999875 46666654
No 72
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=30.71 E-value=55 Score=24.65 Aligned_cols=45 Identities=13% Similarity=0.229 Sum_probs=31.9
Q ss_pred CCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEcc
Q psy6209 20 QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG 69 (115)
Q Consensus 20 ~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~ 69 (115)
.+++|+.+.+.||+.+. +. ......+...|- --|...|+.|++..
T Consensus 60 svpe~r~l~I~p~Dks~--~~-~IekaI~~snLg--lnP~~dG~~IRv~~ 104 (187)
T COG0233 60 SVPEARTLVIKPFDKSM--VK-AIEKAILASNLG--LNPNNDGNVIRVPL 104 (187)
T ss_pred cCCCcceEEeecCccch--HH-HHHHHHHHcCCC--CCcCcCCCeEEecC
Confidence 67899999999997642 32 233445555544 66999999999853
No 73
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=30.65 E-value=1e+02 Score=19.98 Aligned_cols=18 Identities=6% Similarity=0.001 Sum_probs=13.4
Q ss_pred CCCCCCeEEEEeCCCCCC
Q psy6209 6 TTPCRDLLDRQRDIQIVY 23 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~ 23 (115)
.+++||.|.|.....+..
T Consensus 53 ~~k~GD~V~I~e~rPlSK 70 (84)
T PRK05610 53 EAKIGDVVRIMETRPLSK 70 (84)
T ss_pred CCCCCCEEEEEEcccCCC
Confidence 589999999997633333
No 74
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=30.56 E-value=71 Score=22.99 Aligned_cols=70 Identities=11% Similarity=0.058 Sum_probs=43.3
Q ss_pred cCCCCCCeEEEEeCCCCCCccEEEEccCCCC------ccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEE
Q psy6209 5 LTTPCRDLLDRQRDIQIVYGKRIHVLPIDDS------VQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKI 78 (115)
Q Consensus 5 agv~iGD~V~V~k~~~v~~A~~V~laP~~d~------i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkV 78 (115)
-.|.+|-+|+++- .+ .......|.|..+. ..-|+- ..=|-.-|. + -..||.+.+...+...+|.|
T Consensus 81 ~~V~~Gs~Vtl~~-~~-g~~~~~~IVg~~e~d~~~~~~~~IS~---~SPlG~ALl--G--k~vGD~v~v~~p~g~~~~eI 151 (158)
T PRK05892 81 ETLPGGTEVTLRF-PD-GEVETMHVISVVEETPVGREAETLTA---DSPLGQALA--G--HQAGDTVTYSTPQGPAQVEL 151 (158)
T ss_pred CEEEcCcEEEEEE-CC-CCEEEEEEeCchhcCcccccCCEEcc---CCHHHHHHh--C--CCCCCEEEEEcCCCcEEEEE
Confidence 3578999999985 33 35566778775332 101111 011222233 2 26899999987666789999
Q ss_pred EEecC
Q psy6209 79 VDTDP 83 (115)
Q Consensus 79 v~t~P 83 (115)
+++.|
T Consensus 152 ~~I~~ 156 (158)
T PRK05892 152 LAVKL 156 (158)
T ss_pred EEEEc
Confidence 99887
No 75
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=29.87 E-value=2e+02 Score=20.27 Aligned_cols=46 Identities=13% Similarity=0.141 Sum_probs=19.8
Q ss_pred CceecCCEEEEccC--CceEEEEEEEecCCCcEEEcCCceEEEcCcccc
Q psy6209 57 RPVHKDDLFIVRGG--MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK 103 (115)
Q Consensus 57 rPV~~Gd~i~v~~~--~~~v~FkVv~t~P~~~viVt~~T~I~~~~~pv~ 103 (115)
..+.+||++.+... ....-.|=+--.|++.+.+.+ -.++++|+++.
T Consensus 50 ~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~-~~l~vNg~~~~ 97 (163)
T TIGR02227 50 SDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRD-GKLYINGKKID 97 (163)
T ss_pred CCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEEC-CEEEECCEECc
Confidence 34555555555432 111222222233555554443 33555555543
No 76
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=29.54 E-value=1.2e+02 Score=23.82 Aligned_cols=51 Identities=16% Similarity=0.126 Sum_probs=32.4
Q ss_pred HHHhhHhhhhCCCceecCCEEEEccC-C--ceEEEEEEEec-CCCcEEEcCCceE
Q psy6209 45 EVYLKPYFLEAYRPVHKDDLFIVRGG-M--RAVEFKIVDTD-PAPYCIVAADTVI 95 (115)
Q Consensus 45 ~~~lk~~l~~~~rPV~~Gd~i~v~~~-~--~~v~FkVv~t~-P~~~viVt~~T~I 95 (115)
.+++.-.+....||++.||.|.+.+. | ..+.+..+.+. +.+..++-|+..+
T Consensus 116 ~N~~sGi~i~~~rpf~vGD~I~i~~~~G~V~~I~~r~T~i~t~d~~~v~IPNs~~ 170 (286)
T PRK10334 116 SNLAAGVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKI 170 (286)
T ss_pred HHHHHHHHHHhcCCCCCCCEEEECCEEEEEEEEEeEEEEEEcCCCCEEEEcchHh
Confidence 34444454466899999999999743 2 24555555544 4666666666654
No 77
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=29.54 E-value=80 Score=23.72 Aligned_cols=26 Identities=12% Similarity=0.171 Sum_probs=16.1
Q ss_pred ceecCCEEEEccCCceEEEEEEEecC
Q psy6209 58 PVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 58 PV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
.+..|+.|........+++.|++++.
T Consensus 89 ~l~~G~~~~~~~~~G~~~~~V~ev~~ 114 (196)
T PRK10737 89 ELQVGMRFLAETDQGPVPVEITAVED 114 (196)
T ss_pred CCCCCCEEEEeCCCCcEEEEEEEEcC
Confidence 35677777665443456777777655
No 78
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=29.11 E-value=55 Score=21.13 Aligned_cols=31 Identities=19% Similarity=0.311 Sum_probs=24.4
Q ss_pred HhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209 47 YLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 47 ~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.+.-|++ +.|+..+..|+|++.| .|++.+++
T Consensus 49 ~v~GyvR--G~~l~~n~lVHIpG~G---DFqi~~I~ 79 (85)
T PF08142_consen 49 KVYGYVR--GSPLSVNQLVHIPGVG---DFQISKIE 79 (85)
T ss_pred EEEEEEc--cccccCCCEEEeCCcC---CeEeeEee
Confidence 4667777 8899999999999876 56666654
No 79
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=28.93 E-value=87 Score=29.61 Aligned_cols=52 Identities=12% Similarity=0.201 Sum_probs=33.7
Q ss_pred HHHHhhHhhhhCCCceecCCEEEEccCCc---eEEEEEEEe-cCCCcEEEcCCceE
Q psy6209 44 FEVYLKPYFLEAYRPVHKDDLFIVRGGMR---AVEFKIVDT-DPAPYCIVAADTVI 95 (115)
Q Consensus 44 ~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~---~v~FkVv~t-~P~~~viVt~~T~I 95 (115)
+.+++.-.+....||++.||.|.+.+..+ .|.+..+.+ +..+..++-||..+
T Consensus 921 lsNfiSGIiIL~erPfrVGD~I~I~~~~GtV~~I~lRsT~Irt~Dg~~IiIPNs~~ 976 (1109)
T PRK10929 921 FANFISGLIILFEKPIRIGDTVTIRDLTGSVTKINTRATTISDWDRKEIIVPNKAF 976 (1109)
T ss_pred HHHHHHHHHHHHhCCCCCCCEEEECCEEEEEEEEeeeEEEEEeCCCCEEEEEChhh
Confidence 45566666667789999999999975432 344444443 35666666666654
No 80
>PRK13201 ureB urease subunit beta; Reviewed
Probab=28.86 E-value=26 Score=25.11 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=15.1
Q ss_pred hCCCceecCCEEEEccCCceEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVE 75 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~ 75 (115)
...|||+.|.+++....+..++
T Consensus 29 tGDRPIQVGSHyHF~EvN~aL~ 50 (136)
T PRK13201 29 TGDRPIQVGSHFHFYEANAALD 50 (136)
T ss_pred CCCcceEeccccchhhcCcccc
Confidence 3479999999998854444333
No 81
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=28.69 E-value=55 Score=21.10 Aligned_cols=34 Identities=26% Similarity=0.391 Sum_probs=24.3
Q ss_pred ecCCEEEEccCCc----eEEEEEEEecCCCcEEEcCCc
Q psy6209 60 HKDDLFIVRGGMR----AVEFKIVDTDPAPYCIVAADT 93 (115)
Q Consensus 60 ~~Gd~i~v~~~~~----~v~FkVv~t~P~~~viVt~~T 93 (115)
..|+++.+.++.+ .--|+|..++-+....|..+.
T Consensus 29 Wmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~ 66 (75)
T PF11302_consen 29 WMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADE 66 (75)
T ss_pred EEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchh
Confidence 4578888876532 223999999998888777654
No 82
>COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]
Probab=28.61 E-value=48 Score=27.61 Aligned_cols=30 Identities=17% Similarity=0.090 Sum_probs=22.6
Q ss_pred CCcccCCCCCCeEEEEeCCC-------CCCccEEEEcc
Q psy6209 1 MSFRLTTPCRDLLDRQRDIQ-------IVYGKRIHVLP 31 (115)
Q Consensus 1 ~R~Nagv~iGD~V~V~k~~~-------v~~A~~V~laP 31 (115)
|-+++||+.||+|++--. + .|..++.++.=
T Consensus 152 LA~~Lgv~~GD~v~li~p-~~~~~~g~~p~~~~f~V~G 188 (408)
T COG4591 152 LAEKLGVRVGDKVTLITP-ESNTPFGRGPRQKRFTVVG 188 (408)
T ss_pred HHHHcCCCCCCEEEEEee-cCCcccccCcceEEEEEEE
Confidence 357899999999999874 5 25567777764
No 83
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=28.55 E-value=2e+02 Score=20.68 Aligned_cols=46 Identities=26% Similarity=0.316 Sum_probs=29.1
Q ss_pred CCceecCCEEEEccC-CceEEEEEEEecCCCc-EEEcCCceEEEcCcc
Q psy6209 56 YRPVHKDDLFIVRGG-MRAVEFKIVDTDPAPY-CIVAADTVIHCEGDP 101 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~-~~~v~FkVv~t~P~~~-viVt~~T~I~~~~~p 101 (115)
..||.+||.+.|-.+ ...-+=+|+++.+... ++|..=+.+.-.++|
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~ 91 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP 91 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE
Confidence 449999999999654 2234467888888654 555544444444444
No 84
>KOG1728|consensus
Probab=28.24 E-value=86 Score=22.73 Aligned_cols=30 Identities=20% Similarity=0.402 Sum_probs=22.6
Q ss_pred CCceecCCEEEEcc---CCceEEEEEEEecCCC
Q psy6209 56 YRPVHKDDLFIVRG---GMRAVEFKIVDTDPAP 85 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~---~~~~v~FkVv~t~P~~ 85 (115)
+|-|..||++.+.. ++..+.|-|....+.+
T Consensus 115 Frdi~~gDiVtvGecrPLSKtvrfnVLkv~k~~ 147 (156)
T KOG1728|consen 115 FRDIQEGDIVTVGECRPLSKTVRFNVLKVIKAA 147 (156)
T ss_pred hhccccCCEEEEeecccccceEEEEEEEEeecC
Confidence 34588999999953 4677899998876643
No 85
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=27.63 E-value=1.6e+02 Score=18.26 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=19.1
Q ss_pred ceecCCEEEEccCCceEEEEEEEecC
Q psy6209 58 PVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 58 PV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
=+..||.+.+......+.++| .+++
T Consensus 36 gl~~Gd~v~v~~~~g~~~~~v-~~~~ 60 (101)
T cd02775 36 GIKDGDLVRVESRRGSVVLRA-KVTD 60 (101)
T ss_pred CCCCCCEEEEEcCCcEEEEEE-EECC
Confidence 467899999988777788877 4444
No 86
>KOG4625|consensus
Probab=27.31 E-value=39 Score=29.64 Aligned_cols=33 Identities=21% Similarity=0.371 Sum_probs=27.0
Q ss_pred hCCCceecCCEEEEccC------CceEEEEEEEecCCCc
Q psy6209 54 EAYRPVHKDDLFIVRGG------MRAVEFKIVDTDPAPY 86 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~------~~~v~FkVv~t~P~~~ 86 (115)
+++|||..|++|.|..- ...++|=|++++|+.+
T Consensus 133 FSnRPl~~~E~f~v~ieki~~~WSG~irlGvT~~dPe~i 171 (595)
T KOG4625|consen 133 FSNRPLRIGELFLVEIEKIERGWSGHLRLGVTSLDPEDI 171 (595)
T ss_pred eccCcCCCCcEEEEEEEEeccCccceeEeecccCCHhhc
Confidence 67999999999999642 3579999999999543
No 87
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=27.06 E-value=1.8e+02 Score=21.03 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=15.0
Q ss_pred ecCCCcEEEcCCceEEEcCccccC
Q psy6209 81 TDPAPYCIVAADTVIHCEGDPIKR 104 (115)
Q Consensus 81 t~P~~~viVt~~T~I~~~~~pv~r 104 (115)
--|.+.+.+.++ .++++|+++..
T Consensus 90 glpGD~V~i~~~-~v~INg~~~~~ 112 (171)
T TIGR02771 90 GLPGDRVTVRAD-VVAINGQLLPY 112 (171)
T ss_pred EeCCCEEEEECC-EEEECCEEccc
Confidence 347777767644 67788877643
No 88
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.79 E-value=58 Score=29.03 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=19.1
Q ss_pred ccCCCCCCeEEEEeCCCCC-CccEEEE
Q psy6209 4 RLTTPCRDLLDRQRDIQIV-YGKRIHV 29 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~-~A~~V~l 29 (115)
.+++++||+|.|+++-++- .-.+|..
T Consensus 387 ~~di~iGD~V~V~raGdVIPkI~~vv~ 413 (689)
T PRK14351 387 ELGVNVGDRVRVKRAGDVIPYVEEVVE 413 (689)
T ss_pred HcCCCCCCEEEEEecCCccceeeeeec
Confidence 3678999999999986664 4345554
No 89
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=26.76 E-value=35 Score=24.12 Aligned_cols=23 Identities=17% Similarity=-0.090 Sum_probs=15.9
Q ss_pred ccCCCCCCeEEEEeCCCCCCccEEEEc
Q psy6209 4 RLTTPCRDLLDRQRDIQIVYGKRIHVL 30 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~A~~V~la 30 (115)
-|.++|||.|+|.- +.++-++..
T Consensus 57 ~LDlRIGD~Vkv~~----~k~~yiV~G 79 (131)
T PF08605_consen 57 YLDLRIGDTVKVDG----PKVTYIVVG 79 (131)
T ss_pred eeeeecCCEEEECC----CCccEEEEE
Confidence 36789999999985 444445543
No 90
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=26.75 E-value=2.3e+02 Score=19.89 Aligned_cols=68 Identities=7% Similarity=0.027 Sum_probs=38.4
Q ss_pred CCCCCCeEEEEeCCCCCCccEEEEc-cCCCCccCcccchHHHH---hhHhhhhCCCceecCCEEEEccCCceEEEEEEEe
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIHVL-PIDDSVQGLTGNLFEVY---LKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~la-P~~d~i~~i~~~~~~~~---lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
.|++|-+|+++-. +-.....++|. |-+- +...+.. .+ |-.-|. + -..||.+.+...+...+++|+++
T Consensus 80 ~V~~Gs~V~l~~~-~~g~~~~~~lVgp~e~---d~~~~~I-S~~SPlG~ALl--G--~~~Gd~v~v~~p~g~~~~~I~~I 150 (151)
T TIGR01462 80 VVGFGSTVTIKDL-DTGEEETYTIVGSWEA---DPKEGKI-SIDSPLGKALI--G--KKVGDVVEVQTPKGEKEYEILKI 150 (151)
T ss_pred EEeeCCEEEEEEC-CCCCEEEEEEECchhc---CccCCee-cCCCHHHHHHc--C--CCCCCEEEEEeCCCcEEEEEEEE
Confidence 5788999999863 33444555554 4321 1111110 11 122222 3 36799999987666688888876
Q ss_pred c
Q psy6209 82 D 82 (115)
Q Consensus 82 ~ 82 (115)
.
T Consensus 151 ~ 151 (151)
T TIGR01462 151 E 151 (151)
T ss_pred C
Confidence 3
No 91
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=26.49 E-value=1.4e+02 Score=19.45 Aligned_cols=15 Identities=7% Similarity=-0.121 Sum_probs=12.3
Q ss_pred CCCCCCeEEEEeCCC
Q psy6209 6 TTPCRDLLDRQRDIQ 20 (115)
Q Consensus 6 gv~iGD~V~V~k~~~ 20 (115)
.+.+||.|.|.....
T Consensus 50 ~~~~GD~V~I~e~RP 64 (84)
T CHL00142 50 ECNIGDQVLIEETRP 64 (84)
T ss_pred CCCCCCEEEEEEcCC
Confidence 589999999998633
No 92
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=26.21 E-value=1.1e+02 Score=21.76 Aligned_cols=28 Identities=11% Similarity=0.090 Sum_probs=24.3
Q ss_pred CCceecCCEEEEccCCceEEEEEEEecC
Q psy6209 56 YRPVHKDDLFIVRGGMRAVEFKIVDTDP 83 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~~~~v~FkVv~t~P 83 (115)
...|..||.+.|..++....++|..+..
T Consensus 46 s~~V~~gd~l~v~~~~~~~~v~Vl~l~~ 73 (133)
T PRK10348 46 SKIVELNATLTLRQGNDERTVIVKAITE 73 (133)
T ss_pred CCccCCCCEEEEEECCEEEEEEEeECcc
Confidence 7789999999999888889999988764
No 93
>cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=25.97 E-value=1.2e+02 Score=20.28 Aligned_cols=33 Identities=27% Similarity=0.422 Sum_probs=19.8
Q ss_pred CceecCCEEEEccCCceEEEEEEEecCC----CcEEEcCCceEE
Q psy6209 57 RPVHKDDLFIVRGGMRAVEFKIVDTDPA----PYCIVAADTVIH 96 (115)
Q Consensus 57 rPV~~Gd~i~v~~~~~~v~FkVv~t~P~----~~viVt~~T~I~ 96 (115)
+||..||.+.+. ..|.+..++ +.++|+-.+++.
T Consensus 87 ~pv~~Gd~l~~~-------~~v~~~~~~~~~~~~~~v~~~~~~~ 123 (140)
T cd03454 87 RPVRPGDTLSVE-------VEVLDKRPSRSRPDRGIVTLRSETL 123 (140)
T ss_pred CCCCCCCEEEEE-------EEEEEEeecCCCCCCeEEEEEEEEE
Confidence 588888888774 345555542 445555555544
No 94
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=25.48 E-value=1e+02 Score=20.62 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=20.0
Q ss_pred eecCCEEEEccCCceEEEEEEEec
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
+.+||.|.+...++..+++|.++.
T Consensus 65 l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 65 LKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred CCCCCEEEEEECCEEEEEEEEEEE
Confidence 566999999888888999998853
No 95
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=25.25 E-value=1.3e+02 Score=19.65 Aligned_cols=28 Identities=25% Similarity=0.377 Sum_probs=22.5
Q ss_pred CCceecCCEEEEcc------CCceEEEEEEEecC
Q psy6209 56 YRPVHKDDLFIVRG------GMRAVEFKIVDTDP 83 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~------~~~~v~FkVv~t~P 83 (115)
+.++..|+.+.+.+ ....+.|.|.+++|
T Consensus 66 ~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~i~P 99 (99)
T PF13742_consen 66 GFDLKDGDKVLVRGRVSFYEPRGSLSLIVEDIDP 99 (99)
T ss_pred CCCCCCCCEEEEEEEEEEECCCcEEEEEEEEeEC
Confidence 37899999999964 23569999999988
No 96
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=25.25 E-value=2.5e+02 Score=19.78 Aligned_cols=70 Identities=9% Similarity=0.030 Sum_probs=39.5
Q ss_pred CCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchH--HHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLF--EVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~--~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.|.+|-+|+++-. +-......+|....+ . +...+.. ..=|-.-|. + -..||.|.+...+....++|+++.
T Consensus 85 ~V~~Gs~V~l~~~-~~~~~~~~~lvg~~e-~-d~~~~~IS~~SPlG~aLl--G--k~~Gd~v~~~~p~g~~~~~I~~I~ 156 (157)
T PRK00226 85 KVKFGSTVTLKDL-DTDEEETYQIVGSDE-A-DPKQGKISIESPIARALI--G--KKVGDTVEVTTPGGEYEYEILSVE 156 (157)
T ss_pred EEecCCEEEEEEC-CCCCEEEEEEEChhh-c-CccCCeeccCChHHHHHh--C--CCCCCEEEEEcCCCcEEEEEEEEE
Confidence 5788999999863 433455566653321 1 1111000 011222233 2 378999999876667788888864
No 97
>PRK13205 ureB urease subunit beta; Reviewed
Probab=24.44 E-value=34 Score=25.10 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=15.5
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||..|.+++....+..+.|
T Consensus 29 tGDRPIQVGSHyHF~EvN~AL~F 51 (162)
T PRK13205 29 TGDRPVQIGSHFHFAEVNPSISF 51 (162)
T ss_pred CCCCceEeccccchhhcCccccc
Confidence 34789999999988544443333
No 98
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=24.42 E-value=1.2e+02 Score=22.72 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=11.7
Q ss_pred CCceecCCEEEEcc
Q psy6209 56 YRPVHKDDLFIVRG 69 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~ 69 (115)
.-|+..||+|++-+
T Consensus 22 ~t~v~~Gd~I~ii~ 35 (209)
T PF08696_consen 22 ETPVSPGDIIHIIG 35 (209)
T ss_pred cCCCcCCCEEEEEE
Confidence 55799999999965
No 99
>PF12124 Nsp3_PL2pro: Coronavirus polyprotein cleavage domain; InterPro: IPR022733 This domain is found in SARS coronaviruses, and is about 70 amino acids in length. It is found associated with various other coronavirus proteins due to the polyprotein nature of most viral translation. PL2pro is a domain of the non-structural protein nsp3. The domain performs three of the cleavages required to separate the translated polyprotein into its distinct proteins. ; 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: 2KAF_A 2KQW_A.
Probab=23.92 E-value=70 Score=19.55 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=14.6
Q ss_pred ceecCCEEEEccCCceEEEEE
Q psy6209 58 PVHKDDLFIVRGGMRAVEFKI 78 (115)
Q Consensus 58 PV~~Gd~i~v~~~~~~v~FkV 78 (115)
-+.+||-|..+..+..++|..
T Consensus 31 flkrgdkivyht~~~~iefh~ 51 (66)
T PF12124_consen 31 FLKRGDKIVYHTVENPIEFHM 51 (66)
T ss_dssp EEEETTEEEEE-SSSS--EEE
T ss_pred HHhcCCEEEEEecCCceEEEe
Confidence 367899999998888888853
No 100
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=23.89 E-value=72 Score=23.62 Aligned_cols=45 Identities=11% Similarity=0.144 Sum_probs=31.0
Q ss_pred CCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEcc
Q psy6209 20 QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG 69 (115)
Q Consensus 20 ~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~ 69 (115)
.++.|+.+.+.|++.+. + .........+.|. ..|...|+.+.++.
T Consensus 58 sv~~~~~l~I~p~D~~~--i-~~I~kAI~~s~lg--l~P~~dg~~Iri~i 102 (185)
T PRK00083 58 SVPEARTLLIQPWDKSM--L-KAIEKAIRASDLG--LNPSNDGTVIRLPI 102 (185)
T ss_pred ecCCCCEEEEEeCCHhH--H-HHHHHHHHHCCCC--CCcccCCCEEEecC
Confidence 45788899999996431 3 2244455566655 77999999998864
No 101
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=23.85 E-value=3.2e+02 Score=25.47 Aligned_cols=71 Identities=8% Similarity=0.080 Sum_probs=40.8
Q ss_pred CCCCCCeEEEEeCCCCCCccEEE-EccCCCCc-cC-cccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIH-VLPIDDSV-QG-LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~-laP~~d~i-~~-i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
.|++|-+|+++-. +-..-...+ +-|-+-.. .+ |+- ... |-.-|. |+ ..||.+.+...++..++.|++++
T Consensus 830 ~V~~GS~Vtl~d~-d~~ee~ty~IVGp~EaD~~~g~IS~--~SP-LGkALL--Gk--kvGD~V~v~~P~g~~~yeIl~I~ 901 (906)
T PRK14720 830 KVGFGTKVKLKNE-DTGEEESYSILGPWESDPEEGIISY--QSP-LGKSLL--GK--KEGDSLEFVINDTETRYTVLKIE 901 (906)
T ss_pred EEEeCCEEEEEEC-CCCCEEEEEEEChhhcCcCCCeECC--CCH-HHHHHc--CC--CCCCEEEEEECCceEEEEEEEEE
Confidence 5789999999863 322223344 44432111 01 111 011 122233 32 56999999887788899999998
Q ss_pred CC
Q psy6209 83 PA 84 (115)
Q Consensus 83 P~ 84 (115)
|-
T Consensus 902 ~~ 903 (906)
T PRK14720 902 RA 903 (906)
T ss_pred ee
Confidence 84
No 102
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.67 E-value=1.8e+02 Score=18.82 Aligned_cols=33 Identities=12% Similarity=0.081 Sum_probs=22.2
Q ss_pred ceecCCEEEEccCCceEEEEEEEe--cCCCcEEEc
Q psy6209 58 PVHKDDLFIVRGGMRAVEFKIVDT--DPAPYCIVA 90 (115)
Q Consensus 58 PV~~Gd~i~v~~~~~~v~FkVv~t--~P~~~viVt 90 (115)
=+..||.+.|.....++.++|.-+ -|.+.+.+-
T Consensus 48 gi~~Gd~V~v~s~~G~~~~~v~v~~~i~~g~v~~~ 82 (122)
T cd02792 48 GIKNGDMVWVSSPRGKIKVKALVTDRVKPHEVGIP 82 (122)
T ss_pred CCCCCCEEEEEcCCceEEEEEEECCCcCCCEEEEe
Confidence 478899999987766776666543 345555544
No 103
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=23.60 E-value=2.3e+02 Score=19.52 Aligned_cols=31 Identities=29% Similarity=0.364 Sum_probs=21.6
Q ss_pred CCceecCCEEEEccC-CceEEEEEEEecCCCc
Q psy6209 56 YRPVHKDDLFIVRGG-MRAVEFKIVDTDPAPY 86 (115)
Q Consensus 56 ~rPV~~Gd~i~v~~~-~~~v~FkVv~t~P~~~ 86 (115)
..++.+||.+.|-.+ ....+=+|+++.+...
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~ 70 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRY 70 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCCC
Confidence 458999999999655 2334556777777544
No 104
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=23.32 E-value=1.9e+02 Score=25.73 Aligned_cols=60 Identities=17% Similarity=0.205 Sum_probs=35.2
Q ss_pred CCCCCeEEEEeCCCCCCccEEEEccCCCCcc--CcccchHHHHhhHhhhhCCCceec--CCEEEEcc--CCceEEEEEEE
Q psy6209 7 TPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQ--GLTGNLFEVYLKPYFLEAYRPVHK--DDLFIVRG--GMRAVEFKIVD 80 (115)
Q Consensus 7 v~iGD~V~V~k~~~v~~A~~V~laP~~d~i~--~i~~~~~~~~lk~~l~~~~rPV~~--Gd~i~v~~--~~~~v~FkVv~ 80 (115)
+.+||.|.|++- +.-+|.-+.+.... .+. .++|+ ..||.+ ||.+.-.. ..+.+..+|++
T Consensus 261 l~~GDiv~v~~G-~~IP~Dg~vi~g~~-~vdes~lTGE-------------s~Pv~k~~Gd~V~aGt~~~~G~~~i~V~~ 325 (741)
T PRK11033 261 LRPGDVIEVAAG-GRLPADGKLLSPFA-SFDESALTGE-------------SIPVERATGEKVPAGATSVDRLVTLEVLS 325 (741)
T ss_pred CCCCCEEEECCC-CEEecceEEEECcE-EeecccccCC-------------CCCEecCCCCeeccCCEEcCceEEEEEEe
Confidence 678888888884 77777777776521 110 13332 456644 67655433 24567777776
Q ss_pred e
Q psy6209 81 T 81 (115)
Q Consensus 81 t 81 (115)
+
T Consensus 326 ~ 326 (741)
T PRK11033 326 E 326 (741)
T ss_pred c
Confidence 3
No 105
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=23.16 E-value=1.1e+02 Score=16.16 Aligned_cols=27 Identities=22% Similarity=0.150 Sum_probs=19.0
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEccC
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPI 32 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~ 32 (115)
|+.++...||.+.+... . ...+.|.|.
T Consensus 16 r~~l~~~~gd~~~i~~~-~---~~~l~l~p~ 42 (43)
T TIGR01439 16 REKLGLKEGDRLEVIRV-E---DGEIILRPA 42 (43)
T ss_pred HHHcCcCCCCEEEEEEe-C---CCEEEEEEC
Confidence 56788889999988863 1 235777663
No 106
>PF00224 PK: Pyruvate kinase, barrel domain; InterPro: IPR015793 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the two barrel domains, the beta/alpha-barrel, and the beta-barrel inserted within it.; GO: 0000287 magnesium ion binding, 0004743 pyruvate kinase activity, 0030955 potassium ion binding, 0006096 glycolysis; PDB: 3HQQ_W 3KTX_A 3E0V_A 3QV6_D 3QV7_D 1PKL_D 3HQP_A 3QV8_D 3HQO_C 3IS4_B ....
Probab=22.74 E-value=1.8e+02 Score=23.46 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=20.8
Q ss_pred ceecCCEEEEccCCceEEEEEEEecCCC
Q psy6209 58 PVHKDDLFIVRGGMRAVEFKIVDTDPAP 85 (115)
Q Consensus 58 PV~~Gd~i~v~~~~~~v~FkVv~t~P~~ 85 (115)
-|..||.|.+.. ..+.|+|+++++..
T Consensus 119 ~v~~Gd~IlidD--G~i~l~V~~v~~~~ 144 (348)
T PF00224_consen 119 DVKPGDKILIDD--GKIELEVTEVDGDS 144 (348)
T ss_dssp HS-TTEEEEETT--TTEEEEEEEEESTE
T ss_pred hcCCCCEEEEcC--CCcEEEEEEEcCCc
Confidence 367899999974 35899999999987
No 107
>PRK11347 antitoxin ChpS; Provisional
Probab=22.61 E-value=77 Score=20.48 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=21.7
Q ss_pred CcccCCCCCCeEEEEeCCCCCCccEEEEccCC
Q psy6209 2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPID 33 (115)
Q Consensus 2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~ 33 (115)
.+.+|+..||.|.|... + .++.|.|..
T Consensus 21 l~~l~l~~G~~v~i~v~-~----~~iii~p~~ 47 (83)
T PRK11347 21 MKELNLQPGQSVEAQVS-N----NQLILTPIS 47 (83)
T ss_pred HHHcCCCCCCEEEEEEE-C----CEEEEEECC
Confidence 46789999999999973 3 569999974
No 108
>COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane]
Probab=22.47 E-value=1.2e+02 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=21.3
Q ss_pred eecCCEEEEccCCceEEEEEEEec
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDTD 82 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t~ 82 (115)
+.+||.|.+...+.....+|++++
T Consensus 135 lk~GD~iyv~~~~~~~~Y~v~~~~ 158 (210)
T COG3764 135 LKVGDKIYVTTKNETYVYKVTDIS 158 (210)
T ss_pred hcCCCEEEEEeCCcEEEEEEEEEE
Confidence 789999999998888999998864
No 109
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=22.40 E-value=1.7e+02 Score=19.42 Aligned_cols=12 Identities=25% Similarity=0.326 Sum_probs=9.7
Q ss_pred CceecCCEEEEc
Q psy6209 57 RPVHKDDLFIVR 68 (115)
Q Consensus 57 rPV~~Gd~i~v~ 68 (115)
+||..||++.+.
T Consensus 89 ~pv~~GD~l~~~ 100 (140)
T cd03446 89 NPVFIGDTIRAE 100 (140)
T ss_pred CCCCCCCEEEEE
Confidence 688888888775
No 110
>PRK11465 putative mechanosensitive channel protein; Provisional
Probab=22.37 E-value=2e+02 Score=26.05 Aligned_cols=54 Identities=11% Similarity=0.089 Sum_probs=34.9
Q ss_pred hHHHHhhHhhhhCCCceecCCEEEEccCCc---eEEEEEEEec-CCCcEEEcCCceEE
Q psy6209 43 LFEVYLKPYFLEAYRPVHKDDLFIVRGGMR---AVEFKIVDTD-PAPYCIVAADTVIH 96 (115)
Q Consensus 43 ~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~---~v~FkVv~t~-P~~~viVt~~T~I~ 96 (115)
...+++.-.|....+|+..||.|.+.+..+ .+.++-+.+. ..+..++-++.+|.
T Consensus 558 ~l~N~isGi~Il~e~pf~vGD~I~v~g~~GtVe~I~lRsT~iRt~dg~~i~IPNs~i~ 615 (741)
T PRK11465 558 LVKDIITGVFIQFENGMNTGDLVTIGPLTGTVERMSIRSVGVRQDTGAYHIIPWSSIT 615 (741)
T ss_pred HHHHHHHHHHHHHcCCcCCCCEEEECCeEEEEEEEeeeEEEEEcCCCCEEEEECCcce
Confidence 344556666666789999999999975432 3455555543 45666666666653
No 111
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=22.18 E-value=1e+02 Score=21.06 Aligned_cols=51 Identities=8% Similarity=0.067 Sum_probs=33.2
Q ss_pred CCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEcc
Q psy6209 6 TTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG 69 (115)
Q Consensus 6 gv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~ 69 (115)
.|.-||.++|+++ +......|.+-.. | -+.++- + + ..+.|...|-.+....
T Consensus 13 kV~~G~~i~vEkl-~~e~g~~v~f~~V---L-~v~~~~--~-v-----~iG~P~v~ga~V~aeV 63 (103)
T COG0261 13 KVEEGDVIKVEKL-DAEPGDKVEFDEV---L-MVGGGE--E-V-----KIGAPYVEGAKVTAEV 63 (103)
T ss_pred EEecCCEEEEEEc-CCCCCCEEEEEEE---E-EEcCCC--c-e-----EECCceecCcEEEEEE
Confidence 5788999999997 7777788887543 2 232210 0 0 1277888887777643
No 112
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=21.98 E-value=1.2e+02 Score=22.84 Aligned_cols=27 Identities=15% Similarity=0.001 Sum_probs=21.9
Q ss_pred ccCCCCCCeEEEEeCCCCCCccEEEEc
Q psy6209 4 RLTTPCRDLLDRQRDIQIVYGKRIHVL 30 (115)
Q Consensus 4 Nagv~iGD~V~V~k~~~v~~A~~V~la 30 (115)
++|..-||.|.|++..++.+++-|..+
T Consensus 124 ~~gi~dGDlvvV~~~~~a~~GdiVvA~ 150 (201)
T COG1974 124 DAGILDGDLVVVDPTEDAENGDIVVAL 150 (201)
T ss_pred cCcCCCCCEEEEcCCCCCCCCCEEEEE
Confidence 678889999999998777888855554
No 113
>PRK13198 ureB urease subunit beta; Reviewed
Probab=21.74 E-value=41 Score=24.66 Aligned_cols=23 Identities=30% Similarity=0.380 Sum_probs=16.6
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||..|.+++....+..++|
T Consensus 57 tGDRPIQVGSHyHF~EvN~aL~F 79 (158)
T PRK13198 57 TGDRPIQVGSHFHFFEVNRALEF 79 (158)
T ss_pred CCCCceEeccccchhhcCccccc
Confidence 44799999999998654544444
No 114
>PRK13204 ureB urease subunit beta; Reviewed
Probab=21.63 E-value=41 Score=24.68 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=16.4
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||..|.+++....+..++|
T Consensus 52 tGDRPIQVGSHyHF~EvN~aL~F 74 (159)
T PRK13204 52 TGDRPIQIGSHFHFFEVNRYLEF 74 (159)
T ss_pred CCCCceEeccccchhhcCccccc
Confidence 44799999999998654444444
No 115
>PRK10671 copA copper exporting ATPase; Provisional
Probab=21.54 E-value=2.5e+02 Score=25.22 Aligned_cols=62 Identities=15% Similarity=-0.069 Sum_probs=36.0
Q ss_pred CCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceec--CCEEEEccC--CceEEEEEEEe
Q psy6209 7 TPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHK--DDLFIVRGG--MRAVEFKIVDT 81 (115)
Q Consensus 7 v~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~--Gd~i~v~~~--~~~v~FkVv~t 81 (115)
+.+||.|.|++- +.-+|+-+.+.-. . .++.. .|-+-.+|+.+ ||.+.-... ...+..+|+.+
T Consensus 341 l~~GD~v~v~~G-~~iP~Dg~v~~g~---~-~vdeS--------~lTGEs~pv~k~~gd~V~aGt~~~~G~~~~~v~~~ 406 (834)
T PRK10671 341 VQPGMLLRLTTG-DRVPVDGEITQGE---A-WLDEA--------MLTGEPIPQQKGEGDSVHAGTVVQDGSVLFRASAV 406 (834)
T ss_pred cCCCCEEEEcCC-CEeeeeEEEEEce---E-EEeeh--------hhcCCCCCEecCCCCEEEecceecceeEEEEEEEE
Confidence 678899988884 7777777777531 1 12211 11122455544 787665432 35677777774
No 116
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=21.48 E-value=2.4e+02 Score=19.06 Aligned_cols=23 Identities=13% Similarity=0.248 Sum_probs=18.9
Q ss_pred eecCCEEEEccCCceEEEEEEEe
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDT 81 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t 81 (115)
+.+||.|.+...+...+++|.++
T Consensus 67 l~~gd~i~l~t~~~~~~Y~V~~~ 89 (131)
T cd05827 67 LKKGDKFYIHVLGETLAYQVDQI 89 (131)
T ss_pred CCCCCEEEEEECCeEEEEEEEEE
Confidence 56899999988777888888884
No 117
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=21.13 E-value=1.9e+02 Score=19.04 Aligned_cols=23 Identities=13% Similarity=-0.106 Sum_probs=14.2
Q ss_pred CCCCeEEEEeCC-CCCCccEEEEc
Q psy6209 8 PCRDLLDRQRDI-QIVYGKRIHVL 30 (115)
Q Consensus 8 ~iGD~V~V~k~~-~v~~A~~V~la 30 (115)
-+||+|-|++.. +-+.+.-+.|.
T Consensus 5 Pl~DRVLVk~~~~e~~T~gGI~Lp 28 (91)
T PRK14533 5 PLGERLLIKPIKEEKKTEGGIVLP 28 (91)
T ss_pred EcCCEEEEEEccccceecccEEec
Confidence 479999999852 22334445553
No 118
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.06 E-value=51 Score=30.02 Aligned_cols=16 Identities=19% Similarity=-0.103 Sum_probs=14.1
Q ss_pred cccCCCCCCeEEEEeC
Q psy6209 3 FRLTTPCRDLLDRQRD 18 (115)
Q Consensus 3 ~Nagv~iGD~V~V~k~ 18 (115)
+|+|+++||+||+--.
T Consensus 607 ~~LglKLGDtvTf~v~ 622 (829)
T COG3127 607 KRLGLKLGDTVTFMVL 622 (829)
T ss_pred HHhCCccCCEEEEEec
Confidence 6899999999999854
No 119
>COG3971 2-keto-4-pentenoate hydratase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.82 E-value=74 Score=25.21 Aligned_cols=29 Identities=14% Similarity=0.161 Sum_probs=24.1
Q ss_pred HHhhHhhhhCCCceecCCEEEEccCCceE
Q psy6209 46 VYLKPYFLEAYRPVHKDDLFIVRGGMRAV 74 (115)
Q Consensus 46 ~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v 74 (115)
-||.+.+...+.|+..||++.-.+.+..+
T Consensus 211 ~wLAn~~a~~G~~Lk~G~IVl~Gs~t~~v 239 (264)
T COG3971 211 AWLANKLAAYGVPLKAGDIVLTGSFTGPV 239 (264)
T ss_pred HHHHHHHHHcCCCcccCcEEecCccCccc
Confidence 67888888889999999999987765544
No 120
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=20.63 E-value=1.5e+02 Score=19.27 Aligned_cols=14 Identities=21% Similarity=0.188 Sum_probs=12.1
Q ss_pred ccCCCCCCeEEEEe
Q psy6209 4 RLTTPCRDLLDRQR 17 (115)
Q Consensus 4 Nagv~iGD~V~V~k 17 (115)
-+|+..||.|+|-+
T Consensus 52 ~lgak~GdvVkIvR 65 (80)
T COG2012 52 ALGAKPGDVVKIVR 65 (80)
T ss_pred HccCCCCcEEEEEe
Confidence 47899999999877
No 121
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=20.40 E-value=2.8e+02 Score=18.55 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=28.6
Q ss_pred eecCCEEEEccCCceEEEEEEEecCCCc-EEEcCCceEEEcCcccc
Q psy6209 59 VHKDDLFIVRGGMRAVEFKIVDTDPAPY-CIVAADTVIHCEGDPIK 103 (115)
Q Consensus 59 V~~Gd~i~v~~~~~~v~FkVv~t~P~~~-viVt~~T~I~~~~~pv~ 103 (115)
+.+||.+...++ +-=+|+++.-... +.++++|.+.+.-+.+.
T Consensus 44 L~kGD~VvT~gG---i~G~V~~v~d~~v~I~l~~~~~i~~~k~aI~ 86 (97)
T COG1862 44 LKKGDEVVTIGG---IVGTVTKVGDDTVEIELGDGTKIKFEKEAIA 86 (97)
T ss_pred ccCCCEEEEcCC---eEEEEEEEecCcEEEEECCCeEEEEEHHHHH
Confidence 899999998765 4445666666443 33667788888655553
No 122
>cd03448 HDE_HSD HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit.
Probab=20.37 E-value=2.3e+02 Score=19.02 Aligned_cols=26 Identities=15% Similarity=0.092 Sum_probs=16.6
Q ss_pred CceecCCEEEEccC--CceEEEEEEEec
Q psy6209 57 RPVHKDDLFIVRGG--MRAVEFKIVDTD 82 (115)
Q Consensus 57 rPV~~Gd~i~v~~~--~~~v~FkVv~t~ 82 (115)
+||..||++.+..- +..+.|.+...+
T Consensus 81 ~PV~~gDtl~~~~~~~~~~v~~~~~~~~ 108 (122)
T cd03448 81 SPVFPGETLRTEMWKEGNRVIFQTKVVE 108 (122)
T ss_pred CCccCCCEEEEEEEEeCCEEEEEEEEcc
Confidence 58999999888531 234555555544
No 123
>PF00699 Urease_beta: Urease beta subunit CAUTION: The Prosite patterns do not match this subunit of the enzyme; InterPro: IPR002019 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plant seeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta, described in this entry, and gamma IPR002026 from INTERPRO). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism. This subunit is known (confusingly) as alpha in Helicobacter.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 1EJS_B 1EJW_B 1A5N_B 1A5K_B 1A5M_B 1EJR_B 1EJX_B 1A5L_B 1KRB_B 1FWA_B ....
Probab=20.08 E-value=18 Score=24.57 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=13.4
Q ss_pred hCCCceecCCEEEEccCCceEEE
Q psy6209 54 EAYRPVHKDDLFIVRGGMRAVEF 76 (115)
Q Consensus 54 ~~~rPV~~Gd~i~v~~~~~~v~F 76 (115)
...|||+.|.+++.-..+..++|
T Consensus 28 ~GDRPIQVGSH~HF~E~N~aL~F 50 (100)
T PF00699_consen 28 TGDRPIQVGSHYHFFEVNPALEF 50 (100)
T ss_dssp -SSS-EEEETTS-GGGS-TTEES
T ss_pred CCCcceEEccccCHHHHhHHhhh
Confidence 34789999999888655554444
No 124
>PRK11507 ribosome-associated protein; Provisional
Probab=20.05 E-value=87 Score=19.83 Aligned_cols=15 Identities=7% Similarity=-0.099 Sum_probs=12.1
Q ss_pred CcccCCCCCCeEEEE
Q psy6209 2 SFRLTTPCRDLLDRQ 16 (115)
Q Consensus 2 R~Nagv~iGD~V~V~ 16 (115)
|+...++.||.|.+.
T Consensus 48 rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 48 RKRCKIVAGQTVSFA 62 (70)
T ss_pred ccCCCCCCCCEEEEC
Confidence 677888888888875
Done!