Query psy16496
Match_columns 245
No_of_seqs 221 out of 381
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:46:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16496hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01085 HH_signal: Hedgehog a 100.0 3.4E-52 7.3E-57 345.4 10.1 94 7-100 67-160 (160)
2 KOG3638|consensus 100.0 2.3E-46 5.1E-51 356.2 6.8 229 7-241 103-347 (414)
3 PF01079 Hint: Hint module; I 100.0 3.5E-40 7.6E-45 290.2 9.4 135 103-241 1-145 (217)
4 smart00306 HintN Hint (Hedgeho 99.8 2.6E-19 5.6E-24 135.9 11.3 99 114-221 1-99 (100)
5 cd00081 Hint Hedgehog/Intein d 99.8 4.5E-19 9.7E-24 141.8 11.0 117 115-241 1-123 (136)
6 PF07591 PT-HINT: Pretoxin HIN 99.6 3.8E-17 8.1E-22 133.5 1.9 90 121-225 1-90 (130)
7 PF14890 Intein_splicing: Inte 99.3 1.8E-11 4E-16 112.5 9.8 89 119-221 1-92 (323)
8 TIGR01445 intein_Nterm intein 99.2 2E-11 4.4E-16 90.3 6.7 72 116-191 1-81 (81)
9 PRK14714 DNA polymerase II lar 99.1 2.5E-10 5.3E-15 119.8 10.9 104 109-223 913-1042(1337)
10 PF14623 Vint: Hint-domain 99.1 5.1E-10 1.1E-14 94.8 7.7 84 114-219 1-86 (162)
11 PRK04132 replication factor C 99.0 5E-10 1.1E-14 115.4 8.7 102 110-222 49-163 (846)
12 PRK14898 DNA-directed RNA poly 99.0 2.1E-09 4.5E-14 111.2 11.8 113 95-222 61-197 (858)
13 PRK09519 recA DNA recombinatio 99.0 1.5E-09 3.4E-14 110.9 8.5 94 114-222 251-348 (790)
14 PF13403 Hint_2: Hint domain 99.0 2E-09 4.3E-14 89.7 7.6 102 115-223 2-117 (147)
15 PRK14715 DNA polymerase II lar 99.0 2.4E-09 5.3E-14 112.5 9.7 106 109-223 890-1017(1627)
16 PRK14845 translation initiatio 98.9 2.5E-09 5.4E-14 112.3 9.6 99 110-222 19-134 (1049)
17 PRK07773 replicative DNA helic 98.9 3.4E-09 7.3E-14 110.0 9.2 133 75-222 357-494 (886)
18 PRK14701 reverse gyrase; Provi 98.7 1.4E-08 2.9E-13 111.0 6.8 101 112-223 887-989 (1638)
19 PF05203 Hom_end_hint: Hom_end 98.7 3.5E-08 7.5E-13 87.3 6.1 70 115-193 1-73 (215)
20 PRK08332 ribonucleotide-diphos 98.6 1.9E-07 4.2E-12 101.8 9.7 108 108-223 295-430 (1740)
21 PF05951 Peptidase_M15_2: Bact 98.5 3.7E-07 8.1E-12 76.8 7.0 88 7-100 45-145 (152)
22 PF08291 Peptidase_M15_3: Pept 98.4 2E-07 4.4E-12 74.1 3.9 76 16-99 28-109 (110)
23 PRK14698 V-type ATP synthase s 98.4 1.5E-06 3.3E-11 91.5 9.4 105 110-222 236-361 (1017)
24 PRK08332 ribonucleotide-diphos 98.1 6E-06 1.3E-10 90.5 7.9 135 71-222 871-1044(1740)
25 smart00536 AXH domain in Ataxi 98.1 1E-05 2.2E-10 65.2 6.4 102 115-219 1-111 (116)
26 COG1372 Intein/homing endonucl 97.6 0.00019 4.1E-09 65.6 7.6 47 169-223 64-110 (420)
27 COG3108 Uncharacterized protei 97.3 0.00044 9.6E-09 59.8 5.7 82 14-101 84-176 (185)
28 PRK09532 DNA polymerase III su 97.1 0.00038 8.3E-09 72.8 4.1 77 113-193 773-852 (874)
29 PF01959 DHQS: 3-dehydroquinat 97.1 0.0028 6E-08 60.0 9.3 98 117-227 241-341 (354)
30 KOG4053|consensus 97.1 0.0017 3.7E-08 56.7 7.0 107 111-220 31-146 (224)
31 PRK02290 3-dehydroquinate synt 97.0 0.0033 7.1E-08 59.3 9.0 95 117-225 231-329 (344)
32 COG1465 Predicted alternative 96.7 0.011 2.4E-07 55.0 9.3 98 117-227 263-363 (376)
33 PF08517 AXH: Ataxin-1 and HBP 96.6 0.00067 1.5E-08 54.8 0.4 101 116-219 1-110 (115)
34 PF02557 VanY: D-alanyl-D-alan 93.4 0.18 3.9E-06 40.7 5.3 76 13-90 3-110 (132)
35 PRK10178 D-alanyl-D-alanine di 91.8 0.31 6.6E-06 42.5 4.9 56 13-70 41-112 (184)
36 PF15057 DUF4537: Domain of un 90.4 0.45 9.9E-06 38.6 4.4 60 132-193 53-114 (124)
37 PF15057 DUF4537: Domain of un 84.8 5.1 0.00011 32.5 7.3 67 138-223 1-67 (124)
38 PF01427 Peptidase_M15: D-ala- 76.9 6 0.00013 34.6 5.5 53 13-67 40-123 (198)
39 PF12059 DUF3540: Protein of u 73.2 17 0.00037 31.9 7.5 50 114-166 8-64 (202)
40 PF07591 PT-HINT: Pretoxin HIN 66.8 23 0.00049 28.7 6.4 30 117-146 59-88 (130)
41 PF01959 DHQS: 3-dehydroquinat 64.8 10 0.00022 36.3 4.5 38 122-159 313-350 (354)
42 PRK02290 3-dehydroquinate synt 64.7 9.5 0.00021 36.4 4.3 29 122-150 303-331 (344)
43 PF13539 Peptidase_M15_4: D-al 64.6 9 0.0002 27.4 3.3 39 52-90 5-55 (67)
44 PF13403 Hint_2: Hint domain 61.6 8.9 0.00019 31.8 3.2 21 205-225 14-34 (147)
45 cd06166 Sortase_D_5 Sortase D 61.3 64 0.0014 25.6 8.0 36 129-166 59-94 (126)
46 COG1862 YajC Preprotein transl 60.8 15 0.00033 28.8 4.2 42 130-183 39-80 (97)
47 TIGR00739 yajC preprotein tran 57.8 25 0.00054 26.6 4.8 41 131-183 34-74 (84)
48 PF07076 DUF1344: Protein of u 55.7 33 0.00073 24.8 4.8 36 117-152 14-56 (61)
49 TIGR02610 PHA_gran_rgn putativ 54.5 36 0.00078 26.2 5.2 55 16-81 15-74 (91)
50 PRK05585 yajC preprotein trans 54.1 37 0.00081 26.9 5.4 40 131-182 49-88 (106)
51 PRK05886 yajC preprotein trans 54.0 28 0.00062 27.9 4.7 42 131-184 35-76 (109)
52 cd05828 Sortase_D_4 Sortase D 53.7 87 0.0019 24.9 7.6 37 128-166 55-91 (127)
53 COG4787 FlgF Flagellar basal b 53.6 42 0.0009 30.4 6.1 118 15-144 31-155 (251)
54 TIGR00008 infA translation ini 53.2 17 0.00038 26.7 3.1 19 135-153 45-67 (68)
55 PF10772 DUF2597: Protein of u 51.7 73 0.0016 26.5 6.8 75 63-173 47-128 (134)
56 COG1902 NemA NADH:flavin oxido 50.6 11 0.00024 36.1 2.2 112 10-121 73-200 (363)
57 PRK10605 N-ethylmaleimide redu 50.2 20 0.00044 34.0 3.9 52 71-122 158-211 (362)
58 PRK14725 pyruvate kinase; Prov 48.6 46 0.001 34.2 6.3 25 132-157 266-290 (608)
59 PF11948 DUF3465: Protein of u 48.1 28 0.0006 28.9 3.9 34 130-167 81-117 (131)
60 PF08331 DUF1730: Domain of un 46.6 29 0.00062 25.6 3.5 25 15-39 49-73 (78)
61 PF00724 Oxidored_FMN: NADH:fl 46.0 13 0.00028 34.8 1.9 109 10-118 70-197 (341)
62 COG1465 Predicted alternative 45.5 18 0.00038 34.2 2.6 26 121-146 334-359 (376)
63 cd00081 Hint Hedgehog/Intein d 45.2 75 0.0016 24.6 5.9 28 117-144 69-99 (136)
64 PF02699 YajC: Preprotein tran 45.2 7.6 0.00016 29.2 0.2 41 131-183 33-73 (82)
65 KOG3209|consensus 42.9 42 0.00092 35.3 5.1 16 131-146 793-808 (984)
66 cd05829 Sortase_E Sortase E (S 42.5 93 0.002 25.5 6.3 25 129-154 67-92 (144)
67 COG3109 ProQ Activator of osmo 42.4 26 0.00056 30.7 3.0 51 131-190 158-208 (208)
68 PLN02411 12-oxophytodienoate r 41.6 20 0.00043 34.4 2.5 52 71-122 164-217 (391)
69 cd03701 IF2_IF5B_II IF2_IF5B_I 41.1 1.5E+02 0.0034 22.5 7.0 66 120-225 18-84 (95)
70 PRK11479 hypothetical protein; 40.3 29 0.00062 32.1 3.2 32 113-144 43-74 (274)
71 PRK12442 translation initiatio 39.7 41 0.0009 26.0 3.4 20 135-154 47-70 (87)
72 PF09650 PHA_gran_rgn: Putativ 39.5 71 0.0015 24.2 4.8 55 16-81 12-71 (87)
73 TIGR01076 sortase_fam LPXTG-si 39.5 1E+02 0.0022 24.8 6.1 37 128-166 57-93 (136)
74 PF01079 Hint: Hint module; I 39.3 73 0.0016 28.3 5.5 46 129-176 100-145 (217)
75 cd02931 ER_like_FMN Enoate red 37.4 26 0.00057 33.4 2.5 51 71-121 149-202 (382)
76 PF00970 FAD_binding_6: Oxidor 37.1 34 0.00074 25.3 2.7 24 129-153 76-99 (99)
77 TIGR03784 marine_sortase sorta 36.6 1.4E+02 0.0031 25.5 6.7 57 128-189 102-159 (174)
78 TIGR03689 pup_AAA proteasome A 36.4 1.4E+02 0.003 30.1 7.5 28 116-143 64-91 (512)
79 PRK00364 groES co-chaperonin G 36.3 43 0.00093 25.8 3.2 25 124-150 49-73 (95)
80 smart00306 HintN Hint (Hedgeho 35.0 39 0.00085 24.6 2.7 28 116-143 68-98 (100)
81 PRK09250 fructose-bisphosphate 34.4 29 0.00062 33.2 2.2 61 70-130 215-292 (348)
82 PF06904 Extensin-like_C: Exte 33.6 83 0.0018 27.2 4.8 48 18-66 60-111 (178)
83 PRK10862 SoxR reducing system 33.4 71 0.0015 26.8 4.2 22 116-142 44-66 (154)
84 cd05830 Sortase_D_5 Sortase D 33.4 1.5E+02 0.0032 23.9 6.1 29 129-159 60-88 (137)
85 PF14890 Intein_splicing: Inte 33.0 44 0.00096 30.6 3.2 29 115-144 64-92 (323)
86 cd06165 Sortase_A_1 Sortase A 32.9 1E+02 0.0022 24.3 5.0 57 129-189 58-114 (127)
87 cd04734 OYE_like_3_FMN Old yel 31.5 64 0.0014 30.2 4.1 108 9-117 66-188 (343)
88 COG5507 Uncharacterized conser 30.9 67 0.0014 25.7 3.4 30 16-47 16-45 (117)
89 PHA02584 34 long tail fiber, p 30.6 1.7E+02 0.0037 32.4 7.4 166 42-222 169-351 (1229)
90 PF07039 DUF1325: SGF29 tudor- 29.6 2.2E+02 0.0048 23.2 6.5 77 136-223 1-83 (130)
91 cd00004 Sortase Sortases are c 28.0 1.9E+02 0.0041 22.7 5.7 35 129-165 59-93 (128)
92 cd04747 OYE_like_5_FMN Old yel 27.7 16 0.00035 34.8 -0.7 110 12-123 70-197 (361)
93 PHA03356 tegument protein UL11 27.3 49 0.0011 25.5 2.0 21 172-192 17-37 (93)
94 PRK13523 NADPH dehydrogenase N 27.0 45 0.00097 31.4 2.2 50 71-120 141-192 (337)
95 PF13742 tRNA_anti_2: OB-fold 26.8 39 0.00085 26.0 1.5 40 93-144 37-78 (99)
96 cd00320 cpn10 Chaperonin 10 Kd 26.1 69 0.0015 24.5 2.7 24 125-150 49-72 (93)
97 cd02929 TMADH_HD_FMN Trimethyl 26.1 22 0.00047 33.8 -0.1 109 11-122 74-202 (370)
98 PRK11479 hypothetical protein; 25.8 59 0.0013 30.1 2.7 30 204-233 57-86 (274)
99 COG1370 Prefoldin, molecular c 25.7 58 0.0013 27.7 2.4 20 133-153 109-128 (155)
100 cd05827 Sortase_C_3 Sortase C 25.4 1.9E+02 0.0041 23.0 5.3 30 129-159 61-90 (131)
101 PF04203 Sortase: Sortase fami 24.8 97 0.0021 24.1 3.5 36 128-165 54-90 (128)
102 TIGR00002 S16 ribosomal protei 24.8 67 0.0015 24.2 2.4 15 228-242 31-45 (78)
103 PF15084 DUF4550: Domain of un 24.7 70 0.0015 25.3 2.5 28 114-142 24-51 (99)
104 PF06291 Lambda_Bor: Bor prote 24.6 42 0.00092 26.3 1.3 50 184-240 36-91 (97)
105 cd03703 aeIF5B_II aeIF5B_II: T 24.2 3.7E+02 0.0081 21.5 7.8 38 119-164 17-54 (110)
106 TIGR00074 hypC_hupF hydrogenas 24.0 58 0.0013 24.4 1.9 17 208-224 32-48 (76)
107 PF01455 HupF_HypC: HupF/HypC 23.4 53 0.0011 23.9 1.5 17 208-224 34-50 (68)
108 PF11094 UL11: Membrane-associ 22.8 57 0.0012 21.6 1.4 19 170-188 15-33 (39)
109 cd02930 DCR_FMN 2,4-dienoyl-Co 22.6 1.1E+02 0.0023 28.7 3.8 101 12-116 69-183 (353)
110 TIGR02228 sigpep_I_arch signal 22.2 4.4E+02 0.0095 22.1 7.1 14 133-146 59-72 (158)
111 cd04735 OYE_like_4_FMN Old yel 22.1 63 0.0014 30.4 2.2 111 12-122 70-196 (353)
112 PF00122 E1-E2_ATPase: E1-E2 A 22.0 60 0.0013 27.7 1.9 25 203-227 43-67 (230)
113 PRK09864 putative peptidase; P 21.9 1.9E+02 0.004 27.7 5.3 51 136-189 64-118 (356)
114 cd02803 OYE_like_FMN_family Ol 21.7 68 0.0015 29.3 2.3 47 71-118 140-189 (327)
115 PRK02268 hypothetical protein; 21.5 1.5E+02 0.0034 24.7 4.2 22 123-144 24-45 (141)
116 COG0361 InfA Translation initi 21.3 1.7E+02 0.0037 22.0 3.9 9 135-143 47-55 (75)
117 COG0503 Apt Adenine/guanine ph 20.3 1.5E+02 0.0033 25.2 4.0 89 62-150 26-130 (179)
118 COG2217 ZntA Cation transport 20.2 60 0.0013 33.9 1.7 28 117-144 210-239 (713)
No 1
>PF01085 HH_signal: Hedgehog amino-terminal signalling domain; InterPro: IPR000320 This domain identifies a group of sequences which belong to the MEROPS peptidase family C46 (clan CH). The type example is the hedgehog protein from Drosophila melanogaster (Fruit fly) which self-processes by a one-time cysteine dependent self cleavage. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. members of this family are composed of two domains. These proteins are autocatalytically cleaved by the C-terminal domain IPR001767 from INTERPRO. This family is the N-terminal domain that is responsible for both local and long-range signalling activities. The structure of this domain is known [] and reveals a tetrahedrally coordinated zinc ion that appears to be structurally analogous to the zinc coordination sites of zinc hydrolases, such as thermolysin and carboxypeptidase A. This putative catalytic site represents a distinct activity from the autoprocessing activity that resides in the carboxy-terminal domain.; GO: 0007267 cell-cell signaling, 0007275 multicellular organismal development; PDB: 2WFR_A 3N1Q_B 3N1G_B 2WFQ_A 2WG3_A 3MXW_A 3M1N_B 3HO5_H 3K7H_B 3N1O_B ....
Probab=100.00 E-value=3.4e-52 Score=345.42 Aligned_cols=94 Identities=77% Similarity=1.245 Sum_probs=84.3
Q ss_pred cccchhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCCCCCCcccceeeeeeEecCCCcchHHHHHhhhhhcCc
Q psy16496 7 NLTFLFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGF 86 (245)
Q Consensus 7 ~~~~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~~~~slh~egra~di~~s~~~~~k~g~La~la~~aGf 86 (245)
||||||+||||||+||+.||++||||||||||||||||||++||+++|||||||||||||||||++||||||+||++|||
T Consensus 67 ~tgadR~MTkRckdkL~~La~~V~nqwpgvkLrV~eaWded~~h~~~sLHyeGRAvdittsd~d~~k~g~LarLAv~AGF 146 (160)
T PF01085_consen 67 GTGADRLMTKRCKDKLNTLAISVMNQWPGVKLRVTEAWDEDGHHSPDSLHYEGRAVDITTSDRDRSKYGMLARLAVEAGF 146 (160)
T ss_dssp SSSGGGEE-HHHHHHHHHHHHHHHHHSTT--EEEEESS-SSSTSSTT-GGGGT-EEEEEETT--GGGHHHHHHHHHHTT-
T ss_pred cCCCcccchHHHHHHHHHHHHHHHHhCCCcEEEEEecccCcccCCchhccccceeEEEEeccccchhhHHHHHHHhhccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEcccceeeec
Q psy16496 87 DWVYYESRNHIHCS 100 (245)
Q Consensus 87 d~V~~~~r~~ih~~ 100 (245)
|||+|++++|||||
T Consensus 147 DwV~Yes~~hiHcS 160 (160)
T PF01085_consen 147 DWVYYESRNHIHCS 160 (160)
T ss_dssp SEEEEEETTEEEEE
T ss_pred CeEEecccceEecC
Confidence 99999999999997
No 2
>KOG3638|consensus
Probab=100.00 E-value=2.3e-46 Score=356.22 Aligned_cols=229 Identities=33% Similarity=0.495 Sum_probs=214.9
Q ss_pred cccchhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCCCCCCcccceeeeeeEecCCCcchHHHHHhhhhhcCc
Q psy16496 7 NLTFLFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGF 86 (245)
Q Consensus 7 ~~~~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~~~~slh~egra~di~~s~~~~~k~g~La~la~~aGf 86 (245)
+.|++ +|++||+.+++.+++.+||+|++ +.+++++||..++++.+++||++++.+++++++|.+++++++|.+++++|
T Consensus 103 ~~~l~-~~~d~g~~~v~~ge~~~g~ev~~-~~~~~~~fD~i~ni~~~~~~~g~~~y~~tv~r~~c~~~~~~~r~~~e~~~ 180 (414)
T KOG3638|consen 103 YEGLR-FSTDRGVATVSAGEIVVGGEVPG-RGNVQEAFDYISNVSKSVDEYGGVAYEVTVSRMNCLDYPQAARLAVEAGF 180 (414)
T ss_pred cccch-hhhhhhhccccCccEEEcceeec-cCCceeeeeeecceeeccCCCCceeccceeeecccCCccccccccccccc
Confidence 45666 99999999999999999999998 88999999999999999999999999999999999999999999999999
Q ss_pred ceEEEcccceeeeccccccccccccCcccccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 87 DWVYYESRNHIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 87 d~V~~~~r~~ih~~vks~~s~~aak~ggCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
+|..+...+++||+++++++ .+...++||+++++|.+..|+.|+|+||.+||+|||.|. .+++.|+||++||||+|++
T Consensus 181 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~cf~~~~~~~~~~~~~k~m~el~iGD~Vla~~~-~~~~~~spv~~~lhR~pe~ 258 (414)
T KOG3638|consen 181 DWETYRVVEHAHNSAKASSS-VAHQPPVCFPTDATVVLEQGGRKRMDELSIGDYVLAADQ-GGQTTYSPVALFLHREPEA 258 (414)
T ss_pred cccceeecccccceeeccCc-cccCCCCCCCCCCEeEEecCceeecCCCCCCCeeecccc-CCccccCchhhhhccCccc
Confidence 99999999999999999999 999999999999999999999999999999999999997 7999999999999999999
Q ss_pred eeceEEEEeCCCCeEEecCCCeeEeecCCCcccc------CCCcceEeCCCCCCCCEEEEcc--CCccc--------cce
Q psy16496 167 VHNFVQITTESGSLIKMTPSHLILRWHRPNAKSI------LNDIEYTYAERVRVNDSIIVHK--NGKAR--------NGI 230 (245)
Q Consensus 167 ~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~------~~~~~~v~A~~v~~GD~V~v~~--g~~~~--------~~~ 230 (245)
..+|+.|+|++|++|.||+.|+||+++ |...+ ....+.|||++|++||||++.. +.+++ +.+
T Consensus 259 ~~~F~~i~t~~g~~l~lT~~Hl~~~~~--c~~~~~~~~~~~~~~~~v~A~~l~~gdcv~~~~~~~~~~~~~~I~~i~~~~ 336 (414)
T KOG3638|consen 259 RAEFVVIETEQGETLQLTPQHLVFVAQ--CQQQPQQFQYGPAGLEAVFASRLRIGDCVLVAPGAGNKLRQQKIGAISRPV 336 (414)
T ss_pred cccceEEecCCCcccccchhheeecCC--CCCCccccccccCCcccccHhhCCcccEEEEecCCCCccceeecccccccc
Confidence 999999999999999999999999998 44321 2378999999999999999999 65543 899
Q ss_pred ecccCCCCCCC
Q psy16496 231 QRGAPIPPPRP 241 (245)
Q Consensus 231 ~~G~y~P~~~~ 241 (245)
+.|||||||..
T Consensus 337 ~tGiyaPlT~~ 347 (414)
T KOG3638|consen 337 ATGIYAPLTSN 347 (414)
T ss_pred ccccccCcccC
Confidence 99999999976
No 3
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=100.00 E-value=3.5e-40 Score=290.23 Aligned_cols=135 Identities=38% Similarity=0.660 Sum_probs=99.0
Q ss_pred cccccccccCcccccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEE
Q psy16496 103 TETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIK 182 (245)
Q Consensus 103 s~~s~~aak~ggCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~ 182 (245)
||+| .|++++|||||+++|+++||++|+|+||++||+||++|. +|+++||||++|+||+|++.++|++|+|++|++|+
T Consensus 1 se~s-~a~~~ggCFpg~a~V~~~~G~~k~m~~L~iGD~Vla~d~-~G~~~yS~V~~flhr~~~~~~~F~~i~te~g~~l~ 78 (217)
T PF01079_consen 1 SESS-VAAKSGGCFPGDATVTLEDGGRKRMSDLKIGDRVLAVDS-DGKLVYSPVIMFLHRDPEQRAEFVVIETEDGRSLT 78 (217)
T ss_dssp -CCS-HCH-----B-TT-EEEBTTS-EEEGGG--TT-EEEEE-T-TS-EEEEEEEEEEEEEEEEEEEEEEEEETTS-EEE
T ss_pred Ccch-hhhhcCCCCCCCCEEEeCCCCEeEHHHCCCCCEEEEecC-CCcEEEEeEEEEeccCccccEEEEEEEcCCCCeEE
Confidence 5889 999999999999999999999999999999999999997 99999999999999999999999999999999999
Q ss_pred ecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc--CCcc--------ccceecccCCCCCCC
Q psy16496 183 MTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK--NGKA--------RNGIQRGAPIPPPRP 241 (245)
Q Consensus 183 lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~--g~~~--------~~~~~~G~y~P~~~~ 241 (245)
|||+||||+++++.. .....+++||++|++||+|++.. ++++ +.+.++|+|||||.+
T Consensus 79 LTp~HLI~v~~~~~~--~~~~~~~vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~ 145 (217)
T PF01079_consen 79 LTPNHLIFVADCNGS--ESSNFRAVFASDVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSH 145 (217)
T ss_dssp E-TT-EEEEEETTTT--EE---EEEEGGG--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESS
T ss_pred ecCCcEEEEecCCCC--cccccceeehhhCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCc
Confidence 999999999983221 11224799999999999999933 3332 388999999999986
No 4
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=99.81 E-value=2.6e-19 Score=135.86 Aligned_cols=99 Identities=32% Similarity=0.535 Sum_probs=83.6
Q ss_pred ccccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeec
Q psy16496 114 GCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWH 193 (245)
Q Consensus 114 gCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~ 193 (245)
|||+++|.|.+++|+.++|+||++||+|++.|..+++....+++.+.. ......++.|.+++|..|.+||+|+||+..
T Consensus 1 ~C~~~~t~V~~~~gg~~~i~~l~~g~~V~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 1 GCFPGDTLVLTEDGGIKKIEELEEGDKVLALDEGTLKYSPVKVFLVRE--PKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCcCCCCEEEcCCCCEEEHHHcCCCCEEEEecCCCcEEEEEEEEEEEc--CCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 799999999999988999999999999999997556655556554443 334567999999999999999999999997
Q ss_pred CCCccccCCCcceEeCCCCCCCCEEEEc
Q psy16496 194 RPNAKSILNDIEYTYAERVRVNDSIIVH 221 (245)
Q Consensus 194 ~~~~~~~~~~~~~v~A~~v~~GD~V~v~ 221 (245)
+ ....|++|++|++||.|++.
T Consensus 79 ~-------~~~~w~~a~~l~~gd~v~~~ 99 (100)
T smart00306 79 G-------GKLVWVFASELKPGDYVLVP 99 (100)
T ss_pred C-------CcEEEEEHHHCCCCCEEEec
Confidence 2 12569999999999999875
No 5
>cd00081 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Probab=99.80 E-value=4.5e-19 Score=141.79 Aligned_cols=117 Identities=33% Similarity=0.539 Sum_probs=99.9
Q ss_pred cccCCcEEEeeCCCceeccCCCC--CCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEee
Q psy16496 115 CFTGDSTVTLDNHKTINITDLNI--GDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRW 192 (245)
Q Consensus 115 CFpgdt~V~l~dG~~k~I~dL~~--GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~ 192 (245)
||+++|.|.++||+.+||+||.. ||+|++.|+ +|+..+++|..+++++ ....+++|.|++|..|.+||+|+||+.
T Consensus 1 C~~~~t~V~~~d~~~~~i~~l~~~~g~~V~~~d~-~~~~~~~~v~~~~~~~--~~~~~~~i~~~~g~~l~~T~~H~~~~~ 77 (136)
T cd00081 1 CFTGDTLVLLEDGGRKKIEELVEKKGDKVLALDE-TGKLVFSKVLKVLRRD--YEKKFYKIKTESGREITLTPDHLLFVL 77 (136)
T ss_pred CcCCCcEEEeccCcEEEhHHhhhccCCEEEEECC-CCCEEEEEeeEEEEEc--CCCcEEEEEECCCcEEEEcCCCEEEEE
Confidence 99999999999988999999999 999999999 9999999999999875 446799999999999999999999999
Q ss_pred cCCCccccCCCcceEeCCCCCCCCEEEEccCCccc----cceecccCCCCCCC
Q psy16496 193 HRPNAKSILNDIEYTYAERVRVNDSIIVHKNGKAR----NGIQRGAPIPPPRP 241 (245)
Q Consensus 193 ~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g~~~~----~~~~~G~y~P~~~~ 241 (245)
.. . ...|++|++|++||.|++....... ...+.+.|+|.+..
T Consensus 78 ~~-~------~~~~~~a~~l~~gd~l~~~~~~~v~~i~~~~~~~~vY~~~v~~ 123 (136)
T cd00081 78 ED-G------ELKWVFASDLKPGDYVLVPVLEKVKEIEEIEYTGGVYDLTVED 123 (136)
T ss_pred eC-C------eEEEEEHHHCCCCCEEEEccceEEEEEEEEccCCeEEccEEcC
Confidence 72 1 3689999999999999997543321 22224888887753
No 6
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=99.65 E-value=3.8e-17 Score=133.49 Aligned_cols=90 Identities=29% Similarity=0.405 Sum_probs=14.6
Q ss_pred EEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeecCCCcccc
Q psy16496 121 TVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSI 200 (245)
Q Consensus 121 ~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~ 200 (245)
+|.+++|. |||++|++||+|+|.|+.+|+..|.+|+....++. .+++.|++++ ..|.+||+||||+.+
T Consensus 1 lV~T~~G~-k~Ie~I~~GD~Vls~d~~tg~~~~~~V~~~f~~~~---~~l~~i~~~~-~~i~~T~~HPF~~~~------- 68 (130)
T PF07591_consen 1 LVHTADGL-KPIEDIKVGDRVLSYDEETGETEYKPVTATFVRET---DELVDITLED-ETITTTPNHPFWVEG------- 68 (130)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Cccccccc-ccccccccccccccccccccccccccccccccccc---cccccccccc-cccccccccccccch-------
Confidence 48899996 99999999999999999899999999998665543 4588898865 789999999999985
Q ss_pred CCCcceEeCCCCCCCCEEEEccCCc
Q psy16496 201 LNDIEYTYAERVRVNDSIIVHKNGK 225 (245)
Q Consensus 201 ~~~~~~v~A~~v~~GD~V~v~~g~~ 225 (245)
..|+.|++|++||.|+..+|..
T Consensus 69 ---~gWv~A~~L~~GD~L~~~~G~~ 90 (130)
T PF07591_consen 69 ---KGWVEAEDLKVGDRLLTADGSW 90 (130)
T ss_dssp ------EEGGG--TTSEEEEE-SSE
T ss_pred ---HhhhhHhhCCCCCEEEcCCCCE
Confidence 3699999999999999988864
No 7
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=99.27 E-value=1.8e-11 Score=112.49 Aligned_cols=89 Identities=26% Similarity=0.327 Sum_probs=71.9
Q ss_pred CcEEEeeCC-CceeccCC--CCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeecCC
Q psy16496 119 DSTVTLDNH-KTINITDL--NIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRP 195 (245)
Q Consensus 119 dt~V~l~dG-~~k~I~dL--~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~ 195 (245)
||+|.+++| ..++|+|| +.|..|+++|..+++++..+|..+.+. ..+..++|+|++|++|.+||+||+|+.+
T Consensus 1 dt~v~~~~~g~~~~i~ei~~~~~~~V~sl~~~~~k~~~~~v~~v~~~---g~k~v~ri~t~~GreI~~T~~H~~lt~~-- 75 (323)
T PF14890_consen 1 DTLVVLADTGRRVTIKEILEKKDVEVLSLDEDDLKLVKRKVSRVFHN---GEKPVYRIRTRSGREIKATPDHPFLTPD-- 75 (323)
T ss_dssp T-EEEBTTT--EEESGCCCC-SSEEEEEEETTTTEEEEEEEEEEEEE---EEEEEEEEEETTS-EEEEETT-EEEECC--
T ss_pred CcEEEeCCCCcEEehhHhhccCCCeEEEEeCCCCEEEEeeeeEEEEc---CCceEEEEEeCCCCEEEEcCCCcEEEcc--
Confidence 789999997 78899999 888999999976899999999888653 3567999999999999999999999997
Q ss_pred CccccCCCcceEeCCCCCCCCEEEEc
Q psy16496 196 NAKSILNDIEYTYAERVRVNDSIIVH 221 (245)
Q Consensus 196 ~~~~~~~~~~~v~A~~v~~GD~V~v~ 221 (245)
.|..+.+|++||.|.++
T Consensus 76 ---------~wk~~~~Lk~GD~I~v~ 92 (323)
T PF14890_consen 76 ---------GWKRLEELKPGDRIAVP 92 (323)
T ss_dssp ---------CCCECCC--TT-EEEEE
T ss_pred ---------CCEEhHHhhcccccccc
Confidence 36678999999999988
No 8
>TIGR01445 intein_Nterm intein N-terminal splicing region. This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein.
Probab=99.24 E-value=2e-11 Score=90.27 Aligned_cols=72 Identities=32% Similarity=0.479 Sum_probs=58.5
Q ss_pred ccCCcEEEeeCCCceeccCCCC---------CCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCC
Q psy16496 116 FTGDSTVTLDNHKTINITDLNI---------GDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPS 186 (245)
Q Consensus 116 Fpgdt~V~l~dG~~k~I~dL~~---------GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~ 186 (245)
|+|+|.|.+++|..++|+||.. |++|+++|. ++...++++..|.++.+. .++.|+|++|+.|.+||+
T Consensus 1 ~~~dt~V~~~~G~~~~i~el~~~~~~~~~~~~~~v~s~~~-~~~~~~~~~~~~~~~~~~---~~~~i~t~~g~~i~~T~~ 76 (81)
T TIGR01445 1 LTGDTKVLTEDGETVKIGELVEKEKDEKEPIKVKVLSLDG-GKIVKARPVVVWKRRAEG---KLIRIKTENGREIKATPD 76 (81)
T ss_pred CCCCCEEEeCCCCEEEHHHHHHHHhccCCccceEEEeecC-CcEEEeeceEEEEecCCC---cEEEEEeCCCCEEEECCC
Confidence 7899999999999899998866 789999987 444444444445555544 589999999999999999
Q ss_pred CeeEe
Q psy16496 187 HLILR 191 (245)
Q Consensus 187 Hlifv 191 (245)
|+||+
T Consensus 77 H~~~t 81 (81)
T TIGR01445 77 HPFLT 81 (81)
T ss_pred CcccC
Confidence 99985
No 9
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=99.13 E-value=2.5e-10 Score=119.78 Aligned_cols=104 Identities=23% Similarity=0.442 Sum_probs=85.5
Q ss_pred cccCcccccCCcEEEeeCCCc---eecc----------------------CCCCCCEEEEeeCCCCceeEEEEEEEE-ec
Q psy16496 109 NGKGAGCFTGDSTVTLDNHKT---INIT----------------------DLNIGDKVLTLNTITGEMEYSEVLLFL-HR 162 (245)
Q Consensus 109 aak~ggCFpgdt~V~l~dG~~---k~I~----------------------dL~~GDrVLa~d~~~G~~~yS~Vi~fl-~r 162 (245)
|+|.++||+|||.|.+.+|+. .+|+ +..-+=.|+++|. +|+++..+|...+ |+
T Consensus 913 AAKRRNCF~GDT~IlV~dgg~~~~vpIrelVEEl~el~~~~~d~~g~~~~~P~ddV~VlS~De-nGklv~~kVt~V~Khr 991 (1337)
T PRK14714 913 AAKRRNCFHGDTRILVQDDGGWHRDPIRIFVEERLDLEDPGYDDFGTVYQKPKRDVKVYSVDE-NGKVVLTDITSVSKHP 991 (1337)
T ss_pred hHhhcCCCCCCcEEEEEcCCceeeeeHHHHHHHHHhccccccccccccccccCCceEEeeecC-CCcEEEeeeeeEEecc
Confidence 578889999999999999983 2332 1122237999997 9999999998766 55
Q ss_pred CCCceeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 163 DPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 163 ~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
.+. .+++|+|++|++|++|++|++++.. + ....|+.|.+|++||.|.+...
T Consensus 992 apd---~LirIkt~~GRsL~VT~DHpvLv~~-g------ggl~wkkA~ELk~GD~I~ip~~ 1042 (1337)
T PRK14714 992 APD---HLIRFETERGRSLTVTPDHAMLVWD-G------GYLEKKRAFEVKEGDAVPVPEG 1042 (1337)
T ss_pred CCC---cEEEEEecCCceEEecCCceEEEec-C------CceEEEeHHHcCCCCEEeeccc
Confidence 554 4999999999999999999999997 3 2578999999999999999754
No 10
>PF14623 Vint: Hint-domain
Probab=99.05 E-value=5.1e-10 Score=94.78 Aligned_cols=84 Identities=25% Similarity=0.396 Sum_probs=64.7
Q ss_pred ccccCCcEEEeeCCCc-eeccCCCCCCEEEEeeCCCCceeEEEEEEEEecC-CCceeceEEEEeCCCCeEEecCCCeeEe
Q psy16496 114 GCFTGDSTVTLDNHKT-INITDLNIGDKVLTLNTITGEMEYSEVLLFLHRD-PNLVHNFVQITTESGSLIKMTPSHLILR 191 (245)
Q Consensus 114 gCFpgdt~V~l~dG~~-k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~-~~~~~~Fv~I~Te~g~~L~lTp~Hlifv 191 (245)
+||+|+|.|+|++|.. ++|++|+.||+|++.+. . ..|...+.-. .+....+.+| | .|.+||-|||.+
T Consensus 1 ~CFaG~s~V~l~~~~~~v~i~~lR~G~~V~tp~G---~---r~V~~Vlkt~v~~~~~~lc~v----g-~LlvTPwHPv~~ 69 (162)
T PF14623_consen 1 PCFAGSSLVTLASGRAPVRIDDLRAGDKVWTPRG---P---RKVAAVLKTPVESGSEDLCRV----G-GLLVTPWHPVRI 69 (162)
T ss_pred CcccCCcEEEEecCceeEEHHHccCCCEEECCCC---C---eEEEEEEEEeecCCceEEEEE----C-CEEEcCCCCeee
Confidence 6999999999999999 99999999999998763 3 4566666333 2323557777 3 699999999998
Q ss_pred ecCCCccccCCCcceEeCCCCCCCCEEE
Q psy16496 192 WHRPNAKSILNDIEYTYAERVRVNDSII 219 (245)
Q Consensus 192 ~~~~~~~~~~~~~~~v~A~~v~~GD~V~ 219 (245)
.. +|+|-.++.+++.++
T Consensus 70 ~g-----------~W~FP~~~~~~~~~~ 86 (162)
T PF14623_consen 70 GG-----------KWVFPADMASPQVVY 86 (162)
T ss_pred Cc-----------eeeCChhhccCcccc
Confidence 54 477877777776543
No 11
>PRK04132 replication factor C small subunit; Provisional
Probab=99.04 E-value=5e-10 Score=115.37 Aligned_cols=102 Identities=27% Similarity=0.449 Sum_probs=85.6
Q ss_pred ccCcccccCCcEEEeeCCCceeccCCC-------------CCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC
Q psy16496 110 GKGAGCFTGDSTVTLDNHKTINITDLN-------------IGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE 176 (245)
Q Consensus 110 ak~ggCFpgdt~V~l~dG~~k~I~dL~-------------~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te 176 (245)
.+.|.|+++||.|.+ +|..++|.||- .|-.|+++|. +|+++.+++..++... ....++|.|+
T Consensus 49 ~g~~~cl~~DtrV~~-~G~~v~I~ELv~~~~~g~~~~~~~~~i~V~slde-~gkl~~~~v~~v~k~g---~~~v~rI~t~ 123 (846)
T PRK04132 49 PGVGKCLTGDTKVIA-NGELFEIGELVEKISNGKFGPTPVNGLKVLGIDE-DGKLREFEVQYVYKDK---TNRLIKIKTR 123 (846)
T ss_pred CCCCcccccCCEEEe-cCceEEHHHHHHHHhcccccccCcCcceEEeecC-CCceeecchhhhhhcC---CceEEEEEeC
Confidence 567889999999987 78788998872 2458999998 8999999998777643 3679999999
Q ss_pred CCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 177 SGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 177 ~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
+|+.|.+||+||+|+... + +...|+.|.+|++||.|.++.
T Consensus 124 ~G~el~~T~~Hp~lv~~~-~-----g~~~W~~a~eL~~GD~vavpr 163 (846)
T PRK04132 124 LGRELKVTPYHPLLVNRK-N-----GEIKWVKAEELKPGDKLAIPR 163 (846)
T ss_pred CCcEEEecCCceEEEecc-C-----CceeeEEHhHcCCCCEEEecc
Confidence 999999999999999741 2 246899999999999998863
No 12
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.01 E-value=2.1e-09 Score=111.25 Aligned_cols=113 Identities=18% Similarity=0.271 Sum_probs=89.2
Q ss_pred ceeeeccccccccccccCcccccCCcEEEeeCCCce---ecc---------------------CCCCCCEEEEeeCCCCc
Q psy16496 95 NHIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTI---NIT---------------------DLNIGDKVLTLNTITGE 150 (245)
Q Consensus 95 ~~ih~~vks~~s~~aak~ggCFpgdt~V~l~dG~~k---~I~---------------------dL~~GDrVLa~d~~~G~ 150 (245)
|-+|..+..+ +.+.-|+++|+.|.+.+|..+ +|. ++..|..|+++|+ +++
T Consensus 61 G~~aaqsi~~-----~~~~~~~~~De~i~v~~~~~~~~~~Igelvd~~~~~~~~~~~~~~e~~~~~~~~~V~s~d~-~~k 134 (858)
T PRK14898 61 GIVAAQSIGE-----PGTQMSLPYDEKIIVKEGGETRVTEIGKLVDELIDKFGFEKIGGHEVCDLPIEIYALSLDQ-DEK 134 (858)
T ss_pred eeeeehhcCC-----CCccccCCCCceEEEecCCeeeEEEHHHHHHHHHhccCccccCCceEEecCCCcEEEEECC-CCc
Confidence 4455554444 333459999999999988754 333 2346789999999 899
Q ss_pred eeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 151 MEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 151 ~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
++..||..++.+.. ....+.|+|++|++|.+||+|++|+.. + ....++.|++|++||+|.+..
T Consensus 135 ~~~~~v~~v~r~~~--~~~l~~I~t~~Grei~vT~~H~~~v~~-~------g~~~~~~a~~l~~GD~i~~~~ 197 (858)
T PRK14898 135 VHWKRIISVIRHKA--NGKLIKIKTESGRTIRATPYHSFVTRK-D------NEVIPVEGSELKIGDWLPVVR 197 (858)
T ss_pred EEEEEeeeEEeccC--CCcEEEEEeCCCcEEEECCCCeEEEee-C------CeEEEeeHHhCCCCCEEeeee
Confidence 99999999885442 245999999999999999999999987 3 257899999999999998764
No 13
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=98.96 E-value=1.5e-09 Score=110.89 Aligned_cols=94 Identities=18% Similarity=0.327 Sum_probs=82.8
Q ss_pred ccccCCcEEEee-CCCceeccCCCCCCE---EEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCee
Q psy16496 114 GCFTGDSTVTLD-NHKTINITDLNIGDK---VLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLI 189 (245)
Q Consensus 114 gCFpgdt~V~l~-dG~~k~I~dL~~GDr---VLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hli 189 (245)
+|.|+++.|... +|..++|.||-.|.+ |+++|. ++++.-++|..|.+.-+. +.++|+|+.|+.|.+||+|||
T Consensus 251 ~cLpe~e~v~~i~tG~~v~i~elv~~~~~~~v~sl~~-d~~~~~~~v~~~f~tG~k---~v~rvrT~~G~~i~~T~~Hp~ 326 (790)
T PRK09519 251 KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAK-DGTLHARPVVSWFDQGTR---DVIGLRIAGGAIVWATPDHKV 326 (790)
T ss_pred CCCCCceEEEEecCCCEEEHHHhhcCccccceeeecc-ccceeeccceEEEEcCCc---eEEEEEeCCCcEEEEcCCCeE
Confidence 699999999644 799999999998864 999998 999999999999976544 478999999999999999999
Q ss_pred EeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 190 LRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 190 fv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
|+.. .|+.|++|++||+|.++.
T Consensus 327 lt~~-----------gw~~~~~L~~gD~ia~pr 348 (790)
T PRK09519 327 LTEY-----------GWRAAGELRKGDRVAQPR 348 (790)
T ss_pred EecC-----------CcEEHhHcCCCCEEecCc
Confidence 9875 689999999999997654
No 14
>PF13403 Hint_2: Hint domain
Probab=98.96 E-value=2e-09 Score=89.74 Aligned_cols=102 Identities=21% Similarity=0.200 Sum_probs=71.9
Q ss_pred cccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecC-C-----Cc--eeceEEEEe---CC---CCe
Q psy16496 115 CFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRD-P-----NL--VHNFVQITT---ES---GSL 180 (245)
Q Consensus 115 CFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~-~-----~~--~~~Fv~I~T---e~---g~~ 180 (245)
||+.+|.|.+.+|. ++|++|++||+|++.|. |- .+| .|+.+. - .. ...-+.|.- .+ .+.
T Consensus 2 cf~~GT~I~T~~G~-~~Ve~L~~GD~V~T~dg--g~---~~V-~wig~~~~~~~~~~~~~~~~pvri~a~alG~g~P~~d 74 (147)
T PF13403_consen 2 CFTAGTLIETPDGP-RPVEDLRPGDRVLTRDG--GF---QPV-RWIGRRTVSPADLPAPPRLAPVRIPAGALGNGRPSRD 74 (147)
T ss_pred ccCCCCEEecCCcC-eEeeccCCCCEEEecCC--CE---EEE-EEEEEEEecccccCcCCCcceEEEECCccCCCCCCcC
Confidence 99999999999996 89999999999999996 53 233 444322 1 11 223444443 23 357
Q ss_pred EEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 181 IKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 181 L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
|.|+|+|.+++........+......+.|.+|..|+.|.....
T Consensus 75 l~vsp~hrvl~~~~~~~~~~g~~~vlv~A~~Lv~~~~i~~~~~ 117 (147)
T PF13403_consen 75 LLVSPQHRVLLRGPRAELLFGRDEVLVPARDLVDGRGIRDTPP 117 (147)
T ss_pred eEECcccceeecchhhhhhcCCCceEEEHHHhcCCCCcEecCC
Confidence 9999999999996222222334567889999999999985443
No 15
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=98.95 E-value=2.4e-09 Score=112.52 Aligned_cols=106 Identities=15% Similarity=0.302 Sum_probs=83.7
Q ss_pred cccCcccccCCcEEEeeCCCce---eccCC-------------------CCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 109 NGKGAGCFTGDSTVTLDNHKTI---NITDL-------------------NIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 109 aak~ggCFpgdt~V~l~dG~~k---~I~dL-------------------~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
|||...||+++|.|...+++.. +|+++ ..+=+|.+.|+.+|+.+..++...+.+. .
T Consensus 890 AAKRRNCF~PDTkI~V~ddg~~~~iTIeELfel~~ee~~end~~Vrk~p~ddIkV~SfD~e~gKvvlt~i~~V~K~~--h 967 (1627)
T PRK14715 890 AAKRRNCFPGDTRILVNIDGNVERITLRELYELFDDEVYENMAYVRKKPKNDIKVYSFDPENKKVVLTDIEEVIKAQ--S 967 (1627)
T ss_pred hhhccCCCCCCceEEEecCCceeeccHHHHHHHhccccccccchhhccccccceeeeeccccCcceeeecceEEeec--c
Confidence 5888899999999999976642 12211 1223789999889999988887666432 2
Q ss_pred eeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 167 VHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 167 ~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
....++|.+.+|+++.+||+||+++.+ + +.+.|+.|.+|++||+|.++..
T Consensus 968 r~hLIrIKl~~GRSi~VTpdHPVLv~~-~------Gk~i~K~A~dlK~GD~vvIPK~ 1017 (1627)
T PRK14715 968 PNHLIRIELDLGRSFETTVDHPVMVYE-N------GKFIKKRAMDVKEGDLMLIPKL 1017 (1627)
T ss_pred CCcceEEEecCCeeeeecCCCceEEec-c------CccceeehhhcCcCceeecccc
Confidence 345999999999999999999999997 2 2578999999999999999864
No 16
>PRK14845 translation initiation factor IF-2; Provisional
Probab=98.95 E-value=2.5e-09 Score=112.33 Aligned_cols=99 Identities=17% Similarity=0.287 Sum_probs=80.8
Q ss_pred ccCcccccCCcEEEeeCCCceeccCCC-----------------CCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEE
Q psy16496 110 GKGAGCFTGDSTVTLDNHKTINITDLN-----------------IGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQ 172 (245)
Q Consensus 110 ak~ggCFpgdt~V~l~dG~~k~I~dL~-----------------~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~ 172 (245)
...|.||++||.|.+.+|..++|.||- .+.+|+++|. +|++...++..++-+. .....+.
T Consensus 19 pg~gKCl~~Dt~V~l~d~~~v~I~El~~~~~~~~~~~~~~ev~~~~i~V~sld~-~gk~~~~~~s~v~k~~--~~gkl~r 95 (1049)
T PRK14845 19 VDHGKCLLPEEKVILPEHGLITIKELFDLAKEVVEKDEEKEIRKLNIKVTGVGE-DGELSLLNAPYVWKVR--HKGKMIK 95 (1049)
T ss_pred CCCCcccCCCcEEEecCCCeeEHHHHHhhhcccccccCCceecccCceEEEecC-CCeEEEeecceEEecC--CCceeEE
Confidence 345579999999999998888777662 2567999998 8998888776665333 2235999
Q ss_pred EEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 173 ITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 173 I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
|+|++|++|++||+||+|+.. .|+.|++|++||+|.++.
T Consensus 96 Ikl~sGr~I~vT~~Hp~~t~~-----------gw~~~~eLk~gD~iavPr 134 (1049)
T PRK14845 96 VKLKNWHSVTVTPEHPFLTNR-----------GWVKADELKPGDYVAIPR 134 (1049)
T ss_pred EEecCCcEEEecCCceeEecC-----------CcEEHhhcccCCEEeeee
Confidence 999999999999999999986 489999999999997755
No 17
>PRK07773 replicative DNA helicase; Validated
Probab=98.92 E-value=3.4e-09 Score=110.01 Aligned_cols=133 Identities=20% Similarity=0.230 Sum_probs=98.2
Q ss_pred HHHHhhhhhcCcceEEEc--ccceeeeccccccccccccCcccccCCcEEEeeC-CCceeccCCC--CCCEEEEeeCCCC
Q psy16496 75 GLLARMAVEAGFDWVYYE--SRNHIHCSVKTETTHVNGKGAGCFTGDSTVTLDN-HKTINITDLN--IGDKVLTLNTITG 149 (245)
Q Consensus 75 g~La~la~~aGfd~V~~~--~r~~ih~~vks~~s~~aak~ggCFpgdt~V~l~d-G~~k~I~dL~--~GDrVLa~d~~~G 149 (245)
..|..||.+.++..+-.. +|+-=+-.-|...- .--+-.||.++||.|.+++ |...+|+||. .+-.|+++|..++
T Consensus 357 r~LK~lAkel~vpvi~lsQLnR~~e~r~~krP~l-sDlres~~~~~d~~V~~~d~G~~~~I~elv~~~~~~v~~~~~~~~ 435 (886)
T PRK07773 357 RHLKLLAKELEVPVVALSQLSRGVEQRTDKRPML-SDLRESGCLTGDTLILRADTGAEVPIGELVGERPFAVWALDERTL 435 (886)
T ss_pred HHHHHHHHHHCCcEEEecccCcchhccCCCCCCH-HHHhhcCcccCcceEEecCCCcEEEhHHhhccCCCceeeeccccc
Confidence 367888999998877422 22200000000000 1122359999999999999 8888999996 3335899998446
Q ss_pred ceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 150 EMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 150 ~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
+++.+++..|+.. ..+..++|+|++|+.|.+|++|++++.. .|+.++++++||.|.++.
T Consensus 436 ~~~~~~v~~~~~~---g~k~v~~v~t~~G~~i~~T~~H~~~t~~-----------gw~~~~~l~~gd~i~~pr 494 (886)
T PRK07773 436 RLVAAPVSNVFPT---GRKPVFRLRTRSGREIRATANHPFLTFE-----------GWKRLDELKVGDRLALPR 494 (886)
T ss_pred eeeeeehhhhhhc---CCceEEEEEeCCCcEEEEeCCCcEEecc-----------CCEEHHHCCCCCEEEecc
Confidence 8889999888753 3457999999999999999999999975 588999999999998864
No 18
>PRK14701 reverse gyrase; Provisional
Probab=98.74 E-value=1.4e-08 Score=110.96 Aligned_cols=101 Identities=26% Similarity=0.302 Sum_probs=84.1
Q ss_pred CcccccCCcEEEeeCCCceeccCCCCC--CEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCee
Q psy16496 112 GAGCFTGDSTVTLDNHKTINITDLNIG--DKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLI 189 (245)
Q Consensus 112 ~ggCFpgdt~V~l~dG~~k~I~dL~~G--DrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hli 189 (245)
.|-|..++|.|.|++|..++|+||..+ ..|++.|. ++...+.+..++-++. ....+.|.|++|+.|.+||+|+|
T Consensus 887 ~g~~~~p~t~V~l~dG~~~~I~el~e~~~~~vl~~~~--~~~~~~~~~~~~~~~~--~~~~~~i~~~~G~~i~~T~dH~~ 962 (1638)
T PRK14701 887 AGLCVTPDTYVSLHDGRIKEIDEIVEGSERNVLGLNG--LKPKEAKALKFWEIDY--NGPIKVITLKNNYEIKATPDHGL 962 (1638)
T ss_pred CceeeCCCceeecCchHHHHHHHHHhhccceeecccC--ceecccceeEEEEecc--CCcEEEEEECCCCEEEeCCCceE
Confidence 367999999999999998999999877 45887775 6666677766665552 34699999999999999999999
Q ss_pred EeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 190 LRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 190 fv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
|+.. + +...|+.|.+|++||+|.++..
T Consensus 963 lv~~-~------g~~~~~~a~~lk~gD~vav~~~ 989 (1638)
T PRK14701 963 LVMR-D------GKLGWVSAKNIREGDYVAFAFN 989 (1638)
T ss_pred Eeec-C------CceeeEEHHHCCcCCEEEeccc
Confidence 9996 2 2478999999999999998743
No 19
>PF05203 Hom_end_hint: Hom_end-associated Hint; InterPro: IPR007868 Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This domain corresponds to the protein-splicing domain.; GO: 0030908 protein splicing; PDB: 1LWT_A 1UM2_B 1JVA_B 1GPP_A 1VDE_A 1EF0_B 1DFA_A 1LWS_A.
Probab=98.67 E-value=3.5e-08 Score=87.28 Aligned_cols=70 Identities=21% Similarity=0.363 Sum_probs=48.8
Q ss_pred cccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC---CCCeEEecCCCeeEe
Q psy16496 115 CFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE---SGSLIKMTPSHLILR 191 (245)
Q Consensus 115 CFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te---~g~~L~lTp~Hlifv 191 (245)
||+.+|.|+|+||+.|+|++|++||+|++.| |.+ .+|+... .....+|.|... ++..+++|++|.|-+
T Consensus 1 c~~~gT~vlmaDG~~k~ie~i~~Gd~vmg~d---g~~--r~V~~~~----~g~~~my~i~~~~~~~~~~~~~~~~H~L~l 71 (215)
T PF05203_consen 1 CFAKGTRVLMADGSIKPIEDIKIGDQVMGPD---GRP--RRVTNVP----RGREEMYRITQKTKHKGEDFTCNANHILVL 71 (215)
T ss_dssp EEETT-EEEBTTS-EEEGGG--TT-EEEBTT---SSE--EEEEE------EEEEEEEEEEE-SSS--SEEEEETT-EEEE
T ss_pred CCCCCCEEEecCCCeeEEeecccCCEEECCC---CCc--EEEEEec----ccceeEEEEEEcccCCcceEEEcCCeEEEE
Confidence 9999999999999999999999999999977 442 2565542 234568898876 577899999999988
Q ss_pred ec
Q psy16496 192 WH 193 (245)
Q Consensus 192 ~~ 193 (245)
..
T Consensus 72 ~~ 73 (215)
T PF05203_consen 72 RT 73 (215)
T ss_dssp EE
T ss_pred ec
Confidence 74
No 20
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.57 E-value=1.9e-07 Score=101.78 Aligned_cols=108 Identities=17% Similarity=0.287 Sum_probs=77.7
Q ss_pred ccccCcccccCCcEEEeeCCC---ceeccCC-----------------------CCCCEEEEeeCCCCceeEEEEEEE-E
Q psy16496 108 VNGKGAGCFTGDSTVTLDNHK---TINITDL-----------------------NIGDKVLTLNTITGEMEYSEVLLF-L 160 (245)
Q Consensus 108 ~aak~ggCFpgdt~V~l~dG~---~k~I~dL-----------------------~~GDrVLa~d~~~G~~~yS~Vi~f-l 160 (245)
.....||||+|+|+|..++-. ...|+|+ .....|.+.|+ .+..+....+.+ +
T Consensus 295 i~k~~gG~~~~~tkil~~~d~~~~~~~~~e~y~~~~~~~~~~~~~~~~~~~~~~~~~i~V~s~d~-~~~~v~~~~~~~~~ 373 (1740)
T PRK08332 295 IQKAGGGCIDGNAKIIFENEGEEHLTTMAEMYERYKHLGEFYDEEYNRWGIDVSEVPIYVKSFDP-ETKRVVKGKVKVIW 373 (1740)
T ss_pred eeeecCccCCCCceEEEecCCcceeeeHHHHHHHHHhHHHHhhhccccccCccccCceEEEEecC-CCceEEeccceeEE
Confidence 445678999999999995533 3344441 23468999999 555556656566 3
Q ss_pred ecC-CCceeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 161 HRD-PNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 161 ~r~-~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
.++ |+.... +.|+|+.|++|.+||+||+||.. ++ ..+.+..|.+|++||.|.+...
T Consensus 374 k~~~p~~l~~-~~I~t~~G~~i~vTp~Hp~~V~~-~~-----g~~~~~~a~~l~~gD~i~~~~~ 430 (1740)
T PRK08332 374 KYELGEDVPK-YEIKTNKGTKILTSPWHPFFVLT-PD-----FKIVEKRADELKEGDILIGGMP 430 (1740)
T ss_pred eccCCCccee-EEEEecCCcEEEecCCcceEEec-CC-----CCcccchhhhcccCCEEeecCC
Confidence 333 443211 58999999999999999999995 22 2466779999999999998654
No 21
>PF05951 Peptidase_M15_2: Bacterial protein of unknown function (DUF882); InterPro: IPR010275 This family consists of proteins related to metallopeptidases belong to MEROPS peptidase family M15A. They are classed as non-peptidase homologues (M15A.UNA) and include A3D3U2 from SWISSPROT, where the metal ligands (marked by *) are conserved but the catalytic Asn has been replaced by Asp (+): 70 80 90 100 110 120 A3D3U2: QSKVLNDFNHLLRDHRQNVAAPMDKRLFDLLYSLKTTLNVDDEIHVISGYRSPKTNAMLA : .:. .:. : :.: ::.:: . :: . B1W1A6: PELNTCNSTWAGGKVAAGTARANALSSMWKLEALRHALG-DRSIRVTSGFRSASCNAAV- 20 30 40 50 60 70 * 130 * 140 150 160 170 * + A3D3U2: SNSGGVAKKSYHMRGMAMDIAIPSVKLKTLREAALSLKLGGV---GYYPNSGFVHVDCGP :: :..: :: : :.:.. .: :: . : . :. :: .. :::. :: B1W1A6: ---GG-ASNSRHMYGDAVDLGASPHSLCTLAKQARYHGFRGILGPGYVGHNDHVHVNQGP 80 90 100 110 120 B1W1A6 from SWISSPROT belongs to IPR013230 from INTERPRO, whcih contains peptidases belonging to the M15A family. The function of the proteins in this entry are not known.
Probab=98.48 E-value=3.7e-07 Score=76.82 Aligned_cols=88 Identities=23% Similarity=0.307 Sum_probs=69.4
Q ss_pred cccchhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCC----------CCCCcccceeeeeeEecCCCcchHHH
Q psy16496 7 NLTFLFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHH----------ASDSLHYEGRAVDITTSDRDSSKYGL 76 (245)
Q Consensus 7 ~~~~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~----------~~~slh~egra~di~~s~~~~~k~g~ 76 (245)
-||.---|.+++.|.|..|...+-. . -++.|++||+.+..| +.+|+|+.|+|+||.++.-+..++
T Consensus 45 r~~~~~~iDp~L~d~L~~~~~~~g~--~-~~i~iiSGYRsp~TN~~Lr~~~~gvA~~S~Hm~G~AiDi~ipgv~~~~l-- 119 (152)
T PF05951_consen 45 RTNEVHPIDPRLLDLLYELQQRLGS--R-NPIQIISGYRSPETNAMLRRRSGGVAKNSLHMQGKAIDIRIPGVPLRQL-- 119 (152)
T ss_pred CCCCceecCHHHHHHHHHHHHHhCC--C-CcEEEEeecCCHHHHHHHHhcCCCccccCccccceEEEEecCCCCHHHH--
Confidence 4666778999999999999887732 2 269999999998554 489999999999999987776666
Q ss_pred HHhhhhhcCcceE-EEcccc--eeeec
Q psy16496 77 LARMAVEAGFDWV-YYESRN--HIHCS 100 (245)
Q Consensus 77 La~la~~aGfd~V-~~~~r~--~ih~~ 100 (245)
.++|...+.--| +|..++ |||+=
T Consensus 120 -~~~A~~l~~GGVG~Yp~s~~~FVHvD 145 (152)
T PF05951_consen 120 -RRAALSLQRGGVGYYPRSGSKFVHVD 145 (152)
T ss_pred -HHHHHHcCCCeEEeeCCCCCCEEEeC
Confidence 666666667778 477777 99963
No 22
>PF08291 Peptidase_M15_3: Peptidase M15 ; InterPro: IPR013230 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents the C-terminal domain of zinc D-Ala-D-Ala carboxypeptidases from Streptomyces species and non-peptidase homologues that belong to MEROPS peptidase family M15 (subfamily M15A, clan MD) [].; PDB: 1LBU_A.
Probab=98.43 E-value=2e-07 Score=74.07 Aligned_cols=76 Identities=29% Similarity=0.437 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCC-----CCCCcccceeeeeeEecCCCcchHHHHHhhhhhcCcceEE
Q psy16496 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHH-----ASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVY 90 (245)
Q Consensus 16 ~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~-----~~~slh~egra~di~~s~~~~~k~g~La~la~~aGfd~V~ 90 (245)
+++.++|+. ++.+|.. ++.||+||+++.|| ++.|-|..|+|+||.+++.... .+++++...++..+.
T Consensus 28 ~~l~~~L~~----lR~~~g~-pi~ItSgyR~~~~N~~vGGa~~S~H~~G~A~Di~~~~~~~~---~~~~~~~~~~~~~~g 99 (110)
T PF08291_consen 28 PRLLNKLEK----LRDHFGK-PIIITSGYRCPDHNRAVGGAPNSQHMKGRAADIVVSGMSPE---EVAQIARSAGFFGIG 99 (110)
T ss_dssp HHHHHHHHH----HHHHTTS----EEE----HHHHHHHT--TT-GGGGT-EEEE--TTT-HH---HHHHHGGGTT-SEET
T ss_pred HHHHHHHHH----HHHHHCC-CeEEeeeecChhhchhhcCCCCCCCCCCEeEEEecCCCCHH---HHHHHHHHcCCCCee
Confidence 555555554 5555554 89999999999776 5899999999999999876444 447777778866653
Q ss_pred -Ecccceeee
Q psy16496 91 -YESRNHIHC 99 (245)
Q Consensus 91 -~~~r~~ih~ 99 (245)
+..+++||+
T Consensus 100 ~~~~~~~vHi 109 (110)
T PF08291_consen 100 IYRYSGFVHI 109 (110)
T ss_dssp STT-SSSEEE
T ss_pred eccCCCEEEe
Confidence 445689996
No 23
>PRK14698 V-type ATP synthase subunit A; Provisional
Probab=98.35 E-value=1.5e-06 Score=91.50 Aligned_cols=105 Identities=22% Similarity=0.278 Sum_probs=78.6
Q ss_pred ccCcccccCCcEEEeeCCCceeccCCCC---------------------CCEEEEeeCCCCceeEEEEEEEEecCCCcee
Q psy16496 110 GKGAGCFTGDSTVTLDNHKTINITDLNI---------------------GDKVLTLNTITGEMEYSEVLLFLHRDPNLVH 168 (245)
Q Consensus 110 ak~ggCFpgdt~V~l~dG~~k~I~dL~~---------------------GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~ 168 (245)
...|.|++++|.|.+.+|..++|.||-- ...|++++ +|+++..++..++... ..
T Consensus 236 ~G~GKCV~~dt~V~l~~g~~i~i~elve~~~g~~~~~~~g~e~~~~i~~~~~v~~~~--dgklv~~~~~~v~k~~---~~ 310 (1017)
T PRK14698 236 FGSGKCVDGDTLILTKEFGLIKIKDLYEILDGKGKKTVEGNEEWTELEEPITLYGYK--DGKIVEIKATHVYKGA---SA 310 (1017)
T ss_pred CCcCcccCCcceEeecCCceeEeccceEeccCCcceeeeccceeeecccccceeeec--cceEEEEeeeEEeecC---Cc
Confidence 4457899999999999988777777532 23366665 6999988887777633 23
Q ss_pred ceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 169 NFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 169 ~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
..+.|+|++|++|.+||+|++|+.. .... .....|++|++|++||+|.++.
T Consensus 311 ~v~rikt~~Gr~I~vT~~Hpflt~~-v~~~--G~~~~~~ka~eLk~GD~IavpR 361 (1017)
T PRK14698 311 GMIEIKTRTGRKIKVTPIHKLFTGR-VTKD--GLEIEEVMAKDIKKGDRIAVAK 361 (1017)
T ss_pred eeEEEEecCCcEEEEeecceeeeec-cccC--CcchhhhhhhhcCcCceEeecc
Confidence 4889999999999999999999631 0001 1135688999999999998875
No 24
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.12 E-value=6e-06 Score=90.46 Aligned_cols=135 Identities=20% Similarity=0.199 Sum_probs=88.7
Q ss_pred cchHHHHHhhhhhcCcceEEEccc-ceeeeccccc-cccccccCcccccCCcEEEeeCCCceeccCCC-----CCCEEEE
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYESR-NHIHCSVKTE-TTHVNGKGAGCFTGDSTVTLDNHKTINITDLN-----IGDKVLT 143 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~r-~~ih~~vks~-~s~~aak~ggCFpgdt~V~l~dG~~k~I~dL~-----~GDrVLa 143 (245)
+.-+..+++.+-+.|..++.+..+ |.-+- .... .- .-..+.-|++|||.|.+++|- .+++||- .|-++.+
T Consensus 871 reLw~~I~~~a~etGePgilF~D~iN~~n~-~~~~~~g-~I~aSNpCVtgdt~v~T~~G~-~~~~~l~~~~~~~g~~~~~ 947 (1740)
T PRK08332 871 KSLFEELAYMAWAKADPGVIFFDVINRRNV-LKEAKGG-PIRATNPCVVGDTRILTPEGY-IKAEELFSLAKERGKKEAV 947 (1740)
T ss_pred HHHHHHHHHHHHHhCCCcEEEhhhhhhhCC-CccccCC-eEEeecCCcCCCceeecccch-HHHHHHHHHHHhcCcceee
Confidence 345678889999999999875432 21111 1100 00 112234699999999999996 6899992 4655444
Q ss_pred e-e--CCCCcee-EEEEEE----------------------------EEecCCCceeceEEEEeCCCCeEEecCCCeeEe
Q psy16496 144 L-N--TITGEME-YSEVLL----------------------------FLHRDPNLVHNFVQITTESGSLIKMTPSHLILR 191 (245)
Q Consensus 144 ~-d--~~~G~~~-yS~Vi~----------------------------fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv 191 (245)
+ + +++|... |+..+. |++ ...+..++|.|.+|++|.+|++|+|++
T Consensus 948 ~~~g~~~~g~~~~~~~e~v~~g~~~~~~~~~~g~~~~~~~~~~~~~~~~~---tG~k~v~rl~T~~G~~i~~T~dH~~lt 1024 (1740)
T PRK08332 948 AVEGIAEEGEPYAYSVEILLPGEEEVKYETVHGKALAIADPVAVPAYVWK---VGKKKVARVRTKEGYEITATLDHKLMT 1024 (1740)
T ss_pred eeccccccCCcccccceeeccccccccccccCCcccccccccccccceee---cCcceEEEEEecCCcEEEecCCceeee
Confidence 3 1 0133321 111111 111 235668899999999999999999998
Q ss_pred ecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 192 WHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 192 ~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
.. .|+.|.+|++||.|.++.
T Consensus 1025 ~~-----------gW~~~~eLk~GD~i~lp~ 1044 (1740)
T PRK08332 1025 PE-----------GWKEVGDLKPGDKILLPR 1044 (1740)
T ss_pred cc-----------cCEEHhHcCCCCEEEecC
Confidence 75 699999999999998875
No 25
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=98.06 E-value=1e-05 Score=65.17 Aligned_cols=102 Identities=16% Similarity=0.165 Sum_probs=68.0
Q ss_pred cccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCc-eeEEEEEEEEecCCCceeceEEEEe----CCCC-eEEecCCCe
Q psy16496 115 CFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGE-MEYSEVLLFLHRDPNLVHNFVQITT----ESGS-LIKMTPSHL 188 (245)
Q Consensus 115 CFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~-~~yS~Vi~fl~r~~~~~~~Fv~I~T----e~g~-~L~lTp~Hl 188 (245)
||-.+|.|.|++|+.|.++||+..|-|.+.+..++. +.-+.|.+ ++.+ ....++.|.- ++++ .+.++++||
T Consensus 1 cF~kGT~I~l~~G~~krvEDl~teDfi~sa~~s~~~~l~~stv~~-i~~~--~~~~~v~itF~~g~~~~~v~~ev~~eHP 77 (116)
T smart00536 1 CFMKGTRLCLANGSNKKVEDLKTEDFIRSAECSNDEEIQMSTVKR-IGSS--GLPSVVTLTFDPGVEDALLTVECQVEHP 77 (116)
T ss_pred CccCCCEEEecCCCeeeeeccchhhhHhhhccCCcccccceeEEE-eCCC--CCcceEEEEEEecCccceEEEEEecCCC
Confidence 999999999999999999999999999998773343 33444443 3433 2234666543 2232 588999999
Q ss_pred eEeecCCCccc-cC--CCcceEeCCCCCCCCEEE
Q psy16496 189 ILRWHRPNAKS-IL--NDIEYTYAERVRVNDSII 219 (245)
Q Consensus 189 ifv~~~~~~~~-~~--~~~~~v~A~~v~~GD~V~ 219 (245)
+||....++.= +. ...--+.-.+|++||.=+
T Consensus 78 fFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl 111 (116)
T smart00536 78 FFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCL 111 (116)
T ss_pred eEEcCccccccChhhhhhhcCCcceecccCCEEe
Confidence 99997433210 00 011224578899999544
No 26
>COG1372 Intein/homing endonuclease [DNA replication, recombination, and repair]
Probab=97.61 E-value=0.00019 Score=65.57 Aligned_cols=47 Identities=30% Similarity=0.478 Sum_probs=41.2
Q ss_pred ceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEccC
Q psy16496 169 NFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKN 223 (245)
Q Consensus 169 ~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g 223 (245)
..+.|.|++|+.|.+||+|++|+. + ....|+.|+++++||.|.++..
T Consensus 64 ~~~~i~~~~G~ei~~T~~H~~l~~--~------~~~~~~~a~~lk~GD~i~~~~~ 110 (420)
T COG1372 64 KVIRIKTKSGREIKATPDHPFLTR--N------GELGWVKAGELKEGDRIAVPRR 110 (420)
T ss_pred eEEEEEecCCcEEEecCCCceEec--C------CeEEEEEhhhcccCCEeecccc
Confidence 589999999999999999999993 1 1468999999999999998774
No 27
>COG3108 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.32 E-value=0.00044 Score=59.77 Aligned_cols=82 Identities=23% Similarity=0.256 Sum_probs=59.0
Q ss_pred hcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCCC----------CCCcccceeeeeeEecCCCcchHHHHHhhhhh
Q psy16496 14 CFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHA----------SDSLHYEGRAVDITTSDRDSSKYGLLARMAVE 83 (245)
Q Consensus 14 m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~~----------~~slh~egra~di~~s~~~~~k~g~La~la~~ 83 (245)
|.+++-|.|..|.....-+ -++.||+||+.+.-|. ..|+|+.|.|.||-+. -..+-.|+..+..
T Consensus 84 mdp~l~dlv~~l~~~~g~~---~~i~V~SGYRSPatNr~lr~~s~gvAk~S~Hm~g~AmD~~i~---gV~l~~lr~~~~~ 157 (185)
T COG3108 84 MDPRLFDLVYQLKTLEGHR---RPVQVTSGYRSPATNRMLRSRSRGVAKKSLHMLGQAMDFQIP---GVSLWELRNAALS 157 (185)
T ss_pred cCcchHHHHHHHHHHhcCC---cceEEEeeccChhhhHHHHhhcccchhccccccceeeeeecC---CccHHHHHHHHHh
Confidence 5566777777776665444 4899999999996664 8999999999999995 3333344665554
Q ss_pred cCcceE-EEcccceeeecc
Q psy16496 84 AGFDWV-YYESRNHIHCSV 101 (245)
Q Consensus 84 aGfd~V-~~~~r~~ih~~v 101 (245)
.----| +|...++||+-|
T Consensus 158 ~~~GGVGyYp~s~sVH~Dv 176 (185)
T COG3108 158 MQGGGVGYYPHSNSVHMDV 176 (185)
T ss_pred CcCCceeeccCCCceEecc
Confidence 333567 577778888755
No 28
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=97.13 E-value=0.00038 Score=72.79 Aligned_cols=77 Identities=18% Similarity=0.246 Sum_probs=65.7
Q ss_pred cccccCCcEEEeeCCCceeccCCCCC---CEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCee
Q psy16496 113 AGCFTGDSTVTLDNHKTINITDLNIG---DKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLI 189 (245)
Q Consensus 113 ggCFpgdt~V~l~dG~~k~I~dL~~G---DrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hli 189 (245)
+=||+++|.|.+.+-+..||+++-++ ..|.|+|+ +|.+.-.+|..|.++- ..+-+.++|++|+.|..|++|++
T Consensus 773 ~Y~~~~~t~v~~~~yg~~~i~~~~~~~~~~~v~s~~~-~~~~~~~~~~~~~~~g---~~~v~~~~~~~g~~i~at~~h~~ 848 (874)
T PRK09532 773 EYCLSYDTEVLTVEYGLLPIGKIVEENIECTVYSVDP-NGFVYTQPIAQWHHRG---EQEVFEYCLEDGSIIRATKDHKF 848 (874)
T ss_pred CccccCCeeEEEeccceeeHHHhccccccceEEEEcC-CCcEEeecHHHHHHcC---CccceeEEcCCCCEEEeecCCcc
Confidence 34999999999888667999999655 57999999 9988888887777655 44588899999999999999999
Q ss_pred Eeec
Q psy16496 190 LRWH 193 (245)
Q Consensus 190 fv~~ 193 (245)
++.+
T Consensus 849 ~t~~ 852 (874)
T PRK09532 849 MTTD 852 (874)
T ss_pred ccCC
Confidence 9998
No 29
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=97.12 E-value=0.0028 Score=60.03 Aligned_cols=98 Identities=21% Similarity=0.225 Sum_probs=66.0
Q ss_pred cCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC-CCCeE--EecCCCeeEeec
Q psy16496 117 TGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE-SGSLI--KMTPSHLILRWH 193 (245)
Q Consensus 117 pgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te-~g~~L--~lTp~Hlifv~~ 193 (245)
|-.+-|.+++|.++-++||+.||+||++|. +|+..-..| .|-.-..+.++-|+.+ +|+.+ .|--+--|-...
T Consensus 241 aVHaYv~~pg~kT~YLSEL~sG~~VlvVd~-~G~tR~~~V----GRvKIE~RPLllIeA~~~g~~~svilQnaetIRlv~ 315 (354)
T PF01959_consen 241 AVHAYVLMPGGKTRYLSELRSGDEVLVVDA-DGRTRTAIV----GRVKIERRPLLLIEAEADGKRISVILQNAETIRLVG 315 (354)
T ss_pred cceeEEEcCCCceeehhhhcCCCEEEEEeC-CCCEEEEEe----eEEEEeecceEEEEEEeCCeEEEEEEecCcEEEEEC
Confidence 445668999999999999999999999999 998554444 3332335667778765 45432 222222222222
Q ss_pred CCCccccCCCcceEeCCCCCCCCEEEEccCCccc
Q psy16496 194 RPNAKSILNDIEYTYAERVRVNDSIIVHKNGKAR 227 (245)
Q Consensus 194 ~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g~~~~ 227 (245)
+....+-..+|++||.|++.-...-|
T Consensus 316 --------p~G~~vsVt~Lk~GD~vL~~~~~~~R 341 (354)
T PF01959_consen 316 --------PDGEPVSVTELKPGDEVLVYLEEAGR 341 (354)
T ss_pred --------CCCCEeeeeecCCCCEEEEEecCCCc
Confidence 23467889999999999987654433
No 30
>KOG4053|consensus
Probab=97.08 E-value=0.0017 Score=56.75 Aligned_cols=107 Identities=17% Similarity=0.156 Sum_probs=70.3
Q ss_pred cCcccccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCC-ceeEEEEEEEEecCCCceeceEEEEeCCC-----CeEEec
Q psy16496 111 KGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITG-EMEYSEVLLFLHRDPNLVHNFVQITTESG-----SLIKMT 184 (245)
Q Consensus 111 k~ggCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G-~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g-----~~L~lT 184 (245)
....||-.+|.+.+++|+.|.++||+.-|.|.+....++ ++.-|.|+. ++-. ...-+++|.-+-| -.|.+-
T Consensus 31 ~~ps~FmrGs~IqlAnGelkkVEDl~TeDFirsA~~S~~lkidsstVvr-I~~S--~~pg~vti~F~~g~h~akv~levq 107 (224)
T KOG4053|consen 31 YLPSHFMRGSIIQLANGELKKVEDLSTEDFIRSAEESDDLKIDSSTVVR-IKSS--GCPGSVTIIFEVGEHKAKVSLEVQ 107 (224)
T ss_pred cChhhhcccceeeecccceeehhhcchHHHHHHHHhcCCeEeecceEEE-eecc--CCCceEEEEEEeccccccceeecc
Confidence 456899999999999999999999999999998876344 333344433 3222 1223666654322 269999
Q ss_pred CCCeeEeecCCCcc-cc--CCCcceEeCCCCCCCCEEEE
Q psy16496 185 PSHLILRWHRPNAK-SI--LNDIEYTYAERVRVNDSIIV 220 (245)
Q Consensus 185 p~Hlifv~~~~~~~-~~--~~~~~~v~A~~v~~GD~V~v 220 (245)
+.||+||....+.. .+ ....--..-+.|++||.-+.
T Consensus 108 ~ehPfFVyGqGWsSC~P~rs~qly~L~C~~LqVgDVCis 146 (224)
T KOG4053|consen 108 VEHPFFVYGQGWSSCNPRRSGQLYGLPCEILQVGDVCIS 146 (224)
T ss_pred CCCceEEecccccccCccccccccCCcceeeeecCEEEE
Confidence 99999999632221 01 11122235788999996443
No 31
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=97.04 E-value=0.0033 Score=59.34 Aligned_cols=95 Identities=19% Similarity=0.196 Sum_probs=65.5
Q ss_pred cCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC-CCCeE--Ee-cCCCeeEee
Q psy16496 117 TGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE-SGSLI--KM-TPSHLILRW 192 (245)
Q Consensus 117 pgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te-~g~~L--~l-Tp~Hlifv~ 192 (245)
|-.+-|.+++|.++-++||+.||+||++|. +|+..-..| .|-.-..+.++-|+.+ +|+++ .| -+.|-=++.
T Consensus 231 aVhaYv~~pgg~T~YLsEL~sG~eVlvVd~-~G~tR~~~V----GRvKIE~RPL~lIeAe~~g~~~~viLQnaetIrlv~ 305 (344)
T PRK02290 231 AVHAYVRVPGDKTRYLSELRSGDEVLVVDA-DGNTREAIV----GRVKIEKRPLLLIEAEYGGKRIRTILQNAETIRLVT 305 (344)
T ss_pred cceeEEEcCCCcchhhHhhcCCCEEEEEeC-CCCEEEEEe----eEEEEeeccEEEEEEEeCCeEEEEEEecCcEEEEEC
Confidence 445668999999999999999999999999 998554443 3332334668888876 45432 22 222222222
Q ss_pred cCCCccccCCCcceEeCCCCCCCCEEEEccCCc
Q psy16496 193 HRPNAKSILNDIEYTYAERVRVNDSIIVHKNGK 225 (245)
Q Consensus 193 ~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g~~ 225 (245)
. ..+++-..+|++||.|++.-...
T Consensus 306 ~---------dG~~vsVt~Lk~GD~VL~~~~~~ 329 (344)
T PRK02290 306 P---------DGKPVSVVDLKPGDEVLGYLEEA 329 (344)
T ss_pred C---------CCCEeeeeecCCCCEEEEEecCC
Confidence 1 23578899999999999876543
No 32
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=96.69 E-value=0.011 Score=54.97 Aligned_cols=98 Identities=22% Similarity=0.244 Sum_probs=64.2
Q ss_pred cCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC-CCCeEE--ecCCCeeEeec
Q psy16496 117 TGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE-SGSLIK--MTPSHLILRWH 193 (245)
Q Consensus 117 pgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te-~g~~L~--lTp~Hlifv~~ 193 (245)
|=.+-|..++|.+|-+.+|+.||.|+-+|. +|+..-.-| .|-.-.++.++-|+-+ .|..|. |--+--|-...
T Consensus 263 ~VhaYi~vPg~kTkYLaEL~aGDeV~iVD~-dGr~R~aiV----GRvKIErRPl~lIeAey~g~~i~tiLQNAETIkLv~ 337 (376)
T COG1465 263 AVHAYIRVPGGKTKYLAELKAGDEVLIVDF-DGRTRSAIV----GRVKIERRPLMLIEAEYEGVEISTILQNAETIKLVN 337 (376)
T ss_pred ceeEEEEcCCCceEEhhhhcCCCeEEEEec-CCceeEEEE----EEEEeecCceEEEEEEecCcEEEEEeccceeEEEEc
Confidence 445678889999999999999999999998 898544322 3322223445666543 243322 22233333332
Q ss_pred CCCccccCCCcceEeCCCCCCCCEEEEccCCccc
Q psy16496 194 RPNAKSILNDIEYTYAERVRVNDSIIVHKNGKAR 227 (245)
Q Consensus 194 ~~~~~~~~~~~~~v~A~~v~~GD~V~v~~g~~~~ 227 (245)
+..+++...+|++||.|+++-+.+.|
T Consensus 338 --------~dG~pvSV~eLk~GD~vlv~~ee~aR 363 (376)
T COG1465 338 --------PDGEPVSVAELKPGDEVLVYLEEKAR 363 (376)
T ss_pred --------CCCcEeeeEecCCCCEEEEEehhccc
Confidence 23578899999999999998765433
No 33
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=96.56 E-value=0.00067 Score=54.78 Aligned_cols=101 Identities=14% Similarity=0.083 Sum_probs=56.2
Q ss_pred ccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEe--CCCC---eEEecCCCeeE
Q psy16496 116 FTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITT--ESGS---LIKMTPSHLIL 190 (245)
Q Consensus 116 Fpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~T--e~g~---~L~lTp~Hlif 190 (245)
|--+|.|.+++|+.|.++||+.-|-+.+....++.-.-+-.+.-++... ...++.|+- ...+ .|.++++||+|
T Consensus 1 F~kGs~I~l~~G~~krvEDl~teDf~~sa~~s~~l~l~~stV~~i~~~~--~~~~~~ltF~~g~~~~~v~~e~~~ehPFF 78 (115)
T PF08517_consen 1 FMKGSLIQLANGELKRVEDLRTEDFVQSAERSDDLKLDSSTVVRIEESS--GPGVVLLTFDVGEQQSQVTLECQVEHPFF 78 (115)
T ss_dssp BCTT-EEEETTSSEESGEEH-HHHHHHHHTCSSSECCCECEEEEEEEEE--TEEEEEEEEEESTGGEEEEEEEETT-EEE
T ss_pred CCCCCEEEecCCCeEeEeccchhHhhhhhhcCCCeeeeccEEEeeccCC--CCCEEEEEEEcCCCceEEEEEccCCCceE
Confidence 6779999999999999999999998888665233322222334443332 234555543 2222 58899999999
Q ss_pred eecCCCccccCCC----cceEeCCCCCCCCEEE
Q psy16496 191 RWHRPNAKSILND----IEYTYAERVRVNDSII 219 (245)
Q Consensus 191 v~~~~~~~~~~~~----~~~v~A~~v~~GD~V~ 219 (245)
|....++. ..+. .--+.-.+|++||.=+
T Consensus 79 V~gkGWsS-~~P~~T~~~ygL~C~~L~vGDvCl 110 (115)
T PF08517_consen 79 VKGKGWSS-CNPSLTVQLYGLPCRQLQVGDVCL 110 (115)
T ss_dssp ETTTEEEE-SSHHHHHHHHTS--EE--TT-EEE
T ss_pred EeCCcccc-cCcchhceecCCcccccccCCEEe
Confidence 99632221 0000 1113467888898544
No 34
>PF02557 VanY: D-alanyl-D-alanine carboxypeptidase; InterPro: IPR003709 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These proteins are metallopeptidases belonging to MEROPS peptidase family M15 (clan MD), subfamily M15B (vanY D-Ala-D-Ala carboxypeptidase) and M15C (Ply, L-alanyl-D-glutamate peptidase). Acquired VanA- and VanB-type glycopeptide resistance in enterococci is due to synthesis of modified peptidoglycan precursors terminating in D-lactate. As opposed to VanA-type strains which are resistant to both vancomycin and teicoplanin, VanB-type strains remain teicoplanin susceptible []. The vanY gene was necessary for synthesis of the vancomycin-inducible D,D-carboxypeptidase 3.4.16.4 from EC activity previously proposed to be responsible for glycopeptide resistance. However, this activity was not required for peptidoglycan synthesis in the presence of glycopeptides []. Bacteriophage lysins (Ply) or endolysins are phage-encoded cell wall lytic enzymes which are synthesised late during virus multiplication and mediate the release of progeny virions. Bacteriophages of the pathogen Listeria monocytogenes encode endolysin enzymes which specifically hydrolyse the cross-linking peptide bridges in Listeria peptidoglycan. Ply118 is a 30.8kDa L-alanoyl-D-glutamate peptidase and Ply511 (36.5 kDa) acts as N-acetylmuramoyl-L-alanine amidase (IPR002502 from INTERPRO). ; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4F78_A 2VO9_C.
Probab=93.39 E-value=0.18 Score=40.72 Aligned_cols=76 Identities=26% Similarity=0.338 Sum_probs=50.0
Q ss_pred hhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCC----------------------CCCCCCcccceeeeeeEecCCC
Q psy16496 13 FCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEG----------------------HHASDSLHYEGRAVDITTSDRD 70 (245)
Q Consensus 13 ~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~----------------------~~~~~slh~egra~di~~s~~~ 70 (245)
-|.++..+.|+.|......+ |+.|.|++||+... ..+-.|-|--|.|+||...+..
T Consensus 3 ~l~~~~~~~~~~l~~aa~~~--G~~l~i~SgyRs~~~Q~~ly~~~~~~~~~~~~~~~~a~pG~SeH~~GlAiDi~~~~~~ 80 (132)
T PF02557_consen 3 QLRPEAAKALNALVAAAKAE--GINLKITSGYRSYEEQQQLYDKYAQEYGKAGARVYVAPPGYSEHQTGLAIDIGIGDAP 80 (132)
T ss_dssp CCEHHHHHHHHHHHHHCCTT--TTSEEEEE----HHHHHHHHHHHHCCCSCCCHHHHS--TTSSGGGGT-EEEEEEC-TT
T ss_pred ccCHHHHHHHHHHHHHHHhc--CCCEEEEeecCCHHHHHHHHHHHHHhhhHhhhheecCCCCCCcccceeEEEeccCCCc
Confidence 37899999999998877665 89999999999730 1135799999999999997643
Q ss_pred c----------chHHHHHhhhhhcCcceEE
Q psy16496 71 S----------SKYGLLARMAVEAGFDWVY 90 (245)
Q Consensus 71 ~----------~k~g~La~la~~aGfd~V~ 90 (245)
. .-+--|.+.|.+-||-+-+
T Consensus 81 ~~~~~~~~~~~~~~~Wl~~na~~yGf~~rY 110 (132)
T PF02557_consen 81 GTNLEEDFANTPAYKWLEENAYRYGFILRY 110 (132)
T ss_dssp SESSCHHHHCCCCHCCHHHHGGGTTEEE--
T ss_pred cHhHhhccCCCHHHHHHHHHHHhCCEEEEC
Confidence 1 1222456667777777665
No 35
>PRK10178 D-alanyl-D-alanine dipeptidase; Provisional
Probab=91.76 E-value=0.31 Score=42.49 Aligned_cols=56 Identities=20% Similarity=0.295 Sum_probs=43.6
Q ss_pred hhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCC----------------CCCCCcccceeeeeeEecCCC
Q psy16496 13 FCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGH----------------HASDSLHYEGRAVDITTSDRD 70 (245)
Q Consensus 13 ~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~----------------~~~~slh~egra~di~~s~~~ 70 (245)
+.++...++|.+.+..+.. +|..|+|-+||++..- -...|-|-.|.|||+|+-|.+
T Consensus 41 ~l~~~aA~aL~~a~~~l~~--~G~~L~I~D~yRP~~aq~~~w~~~~~~~yVA~p~~~S~HsrG~AVDLTL~d~~ 112 (184)
T PRK10178 41 LLHKDAEAALRKAVSIAQL--AGLTLRIYDAYRPQQAQQVLWDACPDPQYVADLGRGSNHSRGTAIDLTLVDAH 112 (184)
T ss_pred EECHHHHHHHHHHHHHHHh--CCCeEEEEeccCCHHHHHHHHHhCCCcCeeeCCCCCCCCCCceEEEEEEECCC
Confidence 5677788888888888754 4899999999999410 124589999999999997743
No 36
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=90.45 E-value=0.45 Score=38.61 Aligned_cols=60 Identities=18% Similarity=0.148 Sum_probs=45.4
Q ss_pred ccCCCCCCEEEEeeCCCCceeEEEE--EEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeec
Q psy16496 132 ITDLNIGDKVLTLNTITGEMEYSEV--LLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWH 193 (245)
Q Consensus 132 I~dL~~GDrVLa~d~~~G~~~yS~V--i~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~ 193 (245)
-..|++||.|||.-+ .+...|-|= +.-..+. .....+++|..-||++..+-....+++.+
T Consensus 53 ~~~L~~GD~VLA~~~-~~~~~Y~Pg~V~~~~~~~-~~~~~~~~V~f~ng~~~~vp~~~~~~I~~ 114 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWE-PDDCRYGPGTVIAGPERR-ASEDKEYTVRFYNGKTAKVPRGEVIWISP 114 (124)
T ss_pred cCcCCCCCEEEEecC-cCCCEEeCEEEEECcccc-ccCCceEEEEEECCCCCccchhhEEECCH
Confidence 467899999999976 566668763 3333333 34456999999899999999999999876
No 37
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=84.77 E-value=5.1 Score=32.49 Aligned_cols=67 Identities=16% Similarity=0.144 Sum_probs=40.7
Q ss_pred CCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeEeecCCCccccCCCcceEeCCCCCCCCE
Q psy16496 138 GDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDS 217 (245)
Q Consensus 138 GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~ 217 (245)
|.+|||+.+++|-----.|..-+ +. .-+.|+-.++..-.+.....|+... .+ -..|++||+
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~----~~--~~~lV~f~~~~~~~v~~~~iI~~~~------------~~-~~~L~~GD~ 61 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV----SS--GQFLVEFDDGDTQEVPISDIIALSD------------AM-RHSLQVGDK 61 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc----CC--CEEEEEECCCCEEEeChHHeEEccC------------cc-cCcCCCCCE
Confidence 78999999888973222333333 11 1223343556555555566666554 12 667999999
Q ss_pred EEEccC
Q psy16496 218 IIVHKN 223 (245)
Q Consensus 218 V~v~~g 223 (245)
|+....
T Consensus 62 VLA~~~ 67 (124)
T PF15057_consen 62 VLAPWE 67 (124)
T ss_pred EEEecC
Confidence 998753
No 38
>PF01427 Peptidase_M15: D-ala-D-ala dipeptidase This is family M15 in the peptidase classification. ; InterPro: IPR000755 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M15 (clan MD), subfamily M15D (vanX D-Ala-D-Ala dipeptidase). The D-alanyl-D-alanine dipeptidase enzyme from Enterococcus faecalis is also known as the vancomycin resistance protein VanX, and hydrolyses D-ala-D-ala. It has a 250-fold differential in catalytic efficiency for hydrolysis of D-ala-D-ala versus D-ala-D-lactate. The latter therefore remains intact for subsequent incorporation into peptidoglycan precursors that terminate in the dipeptide D-ala-D-lactate rather than the dipeptide D-ala-D-ala, thereby preventing vancomycin from binding. The enzyme requires a metal cofactor, and is induced by vancomycin through regulation by VanS and VanR.; GO: 0008237 metallopeptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis, 0005618 cell wall; PDB: 1R44_B.
Probab=76.90 E-value=6 Score=34.61 Aligned_cols=53 Identities=26% Similarity=0.392 Sum_probs=35.5
Q ss_pred hhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC-------------CCC------------------CCCCcccceee
Q psy16496 13 FCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE-------------GHH------------------ASDSLHYEGRA 61 (245)
Q Consensus 13 ~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~-------------~~~------------------~~~slh~egra 61 (245)
+.++...++|...+.....+ |-+|.|-+||++. ..+ ...|-|-.|-|
T Consensus 40 ~l~~~~a~~L~~a~~~l~~~--g~~L~I~DayRP~~~Q~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~H~tG~A 117 (198)
T PF01427_consen 40 LLRKEAAERLAKAQAELPPQ--GYRLKIFDAYRPQSAQDAFKMWAAVPDPQYVAYPYYPRFWASPLFDPASPSPHSTGGA 117 (198)
T ss_dssp EEEHHHHHHHHHHHHHHHTT--TEEEEEEE----HHHHHHHHHHHTS----TTHHHH-TTS-CCHHCCS-SS-GGGGT-E
T ss_pred HcCHHHHHHHHHHHHHHHhC--CcEEEEEEEeCcHHHHHHHHHHHcCCchhhhhcccccccccccccccCCCCCccCCCC
Confidence 56788889998888777544 8899999999983 111 12499999999
Q ss_pred eeeEec
Q psy16496 62 VDITTS 67 (245)
Q Consensus 62 ~di~~s 67 (245)
||+|+-
T Consensus 118 VDlTL~ 123 (198)
T PF01427_consen 118 VDLTLV 123 (198)
T ss_dssp EEEEEE
T ss_pred CCccce
Confidence 999997
No 39
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=73.15 E-value=17 Score=31.94 Aligned_cols=50 Identities=24% Similarity=0.261 Sum_probs=35.5
Q ss_pred ccccCCcEEEeeCCCcee-------ccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 114 GCFTGDSTVTLDNHKTIN-------ITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 114 gCFpgdt~V~l~dG~~k~-------I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
+|++.+..|...+|. .+ +=+..+||+||-.+..++...| |+..|.|....
T Consensus 8 ~~~~~~~~v~~~~G~-~~arrAaSCLl~P~~GD~VLv~~~~d~~~~y--ILAVL~r~~~~ 64 (202)
T PF12059_consen 8 GREGDGLVVVDDDGE-WRARRAASCLLEPAVGDTVLVSGVADEERVY--ILAVLERADPG 64 (202)
T ss_pred EEeCCeEEEEcCCCE-EEEEeccccccCCCCCCEEEEeecCCCCcEE--EEEEEecCCCC
Confidence 577777778888886 33 5577999999987732455444 78899887443
No 40
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=66.76 E-value=23 Score=28.73 Aligned_cols=30 Identities=23% Similarity=0.428 Sum_probs=12.7
Q ss_pred cCCcEEEeeCCCceeccCCCCCCEEEEeeC
Q psy16496 117 TGDSTVTLDNHKTINITDLNIGDKVLTLNT 146 (245)
Q Consensus 117 pgdt~V~l~dG~~k~I~dL~~GDrVLa~d~ 146 (245)
+++=....+++++++.++|++||++++.|.
T Consensus 59 T~~HPF~~~~~gWv~A~~L~~GD~L~~~~G 88 (130)
T PF07591_consen 59 TPNHPFWVEGKGWVEAEDLKVGDRLLTADG 88 (130)
T ss_dssp -------------EEGGG--TTSEEEEE-S
T ss_pred ccccccccchHhhhhHhhCCCCCEEEcCCC
Confidence 455556667778899999999999998763
No 41
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=64.85 E-value=10 Score=36.31 Aligned_cols=38 Identities=21% Similarity=0.266 Sum_probs=27.0
Q ss_pred EEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEE
Q psy16496 122 VTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLF 159 (245)
Q Consensus 122 V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~f 159 (245)
+.-++|+.+++.+|++||+||..=+..|+-.--+|--|
T Consensus 313 lv~p~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~~I~E~ 350 (354)
T PF01959_consen 313 LVGPDGEPVSVTELKPGDEVLVYLEEAGRHFGMKIEEF 350 (354)
T ss_pred EECCCCCEeeeeecCCCCEEEEEecCCCcccceEeeeE
Confidence 34467888999999999999988664566444444333
No 42
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=64.65 E-value=9.5 Score=36.37 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=23.0
Q ss_pred EEeeCCCceeccCCCCCCEEEEeeCCCCc
Q psy16496 122 VTLDNHKTINITDLNIGDKVLTLNTITGE 150 (245)
Q Consensus 122 V~l~dG~~k~I~dL~~GDrVLa~d~~~G~ 150 (245)
+..+||..+++.+|++||+||..-+..|+
T Consensus 303 lv~~dG~~vsVt~Lk~GD~VL~~~~~~~R 331 (344)
T PRK02290 303 LVTPDGKPVSVVDLKPGDEVLGYLEEAAR 331 (344)
T ss_pred EECCCCCEeeeeecCCCCEEEEEecCCcc
Confidence 44567888899999999999988663444
No 43
>PF13539 Peptidase_M15_4: D-alanyl-D-alanine carboxypeptidase
Probab=64.59 E-value=9 Score=27.44 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=25.6
Q ss_pred CCCcccceeeeeeEecCCC------------cchHHHHHhhhhhcCcceEE
Q psy16496 52 SDSLHYEGRAVDITTSDRD------------SSKYGLLARMAVEAGFDWVY 90 (245)
Q Consensus 52 ~~slh~egra~di~~s~~~------------~~k~g~La~la~~aGfd~V~ 90 (245)
..|.|-.|.|+||....+. ...+-.+.+++.+.||.|=.
T Consensus 5 ~~S~H~~G~AiDin~~~np~~~~~~~~~~~~~~~~~~~~~~~~~~G~~WGG 55 (67)
T PF13539_consen 5 KLSNHSYGLAIDINPDENPYIQWNGDVDGYKIADYKEVVAIFEKLGFRWGG 55 (67)
T ss_pred cccccccEEEEEEccccCCeeeeCCccchhhhhhHHHHHHHHHhCCCEeCC
Confidence 4899999999999953222 12333556666677876653
No 44
>PF13403 Hint_2: Hint domain
Probab=61.63 E-value=8.9 Score=31.81 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=18.7
Q ss_pred ceEeCCCCCCCCEEEEccCCc
Q psy16496 205 EYTYAERVRVNDSIIVHKNGK 225 (245)
Q Consensus 205 ~~v~A~~v~~GD~V~v~~g~~ 225 (245)
.++..++|++||.|++.+++-
T Consensus 14 G~~~Ve~L~~GD~V~T~dgg~ 34 (147)
T PF13403_consen 14 GPRPVEDLRPGDRVLTRDGGF 34 (147)
T ss_pred cCeEeeccCCCCEEEecCCCE
Confidence 577899999999999999874
No 45
>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=61.27 E-value=64 Score=25.63 Aligned_cols=36 Identities=14% Similarity=0.331 Sum_probs=26.4
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
...+.+|++||.|.-.+. .+...|. |...-.-++..
T Consensus 59 F~~L~~l~~Gd~v~v~~~-~~~~~Y~-V~~~~~v~~~~ 94 (126)
T cd06166 59 FNRLDEVEKGDEIKVTTK-NGTYKYK-ITSIFVVEPTD 94 (126)
T ss_pred cCChHHCCCCCEEEEEEC-CEEEEEE-EEEEEEECCCc
Confidence 457999999999999887 6777776 55544445544
No 46
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=60.78 E-value=15 Score=28.78 Aligned_cols=42 Identities=29% Similarity=0.355 Sum_probs=25.5
Q ss_pred eeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEe
Q psy16496 130 INITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKM 183 (245)
Q Consensus 130 k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~l 183 (245)
+-+++|+.||+|++.... +-.|...- .+++.|++.++-.+++
T Consensus 39 ~ml~sL~kGD~VvT~gGi-----~G~V~~v~-------d~~v~I~l~~~~~i~~ 80 (97)
T COG1862 39 ELLNSLKKGDEVVTIGGI-----VGTVTKVG-------DDTVEIELGDGTKIKF 80 (97)
T ss_pred HHHHhccCCCEEEEcCCe-----EEEEEEEe-------cCcEEEEECCCeEEEE
Confidence 358999999999996531 22233221 2257777765555544
No 47
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=57.81 E-value=25 Score=26.63 Aligned_cols=41 Identities=29% Similarity=0.327 Sum_probs=26.0
Q ss_pred eccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEe
Q psy16496 131 NITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKM 183 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~l 183 (245)
-+++|++||+|.+... .|-.|... + .+++.|++..|-.+++
T Consensus 34 m~~~L~~Gd~VvT~gG-----i~G~V~~i-~------d~~v~vei~~g~~i~~ 74 (84)
T TIGR00739 34 LIESLKKGDKVLTIGG-----IIGTVTKI-A------ENTIVIELNDNTEITF 74 (84)
T ss_pred HHHhCCCCCEEEECCC-----eEEEEEEE-e------CCEEEEEECCCeEEEE
Confidence 4789999999998654 23344432 2 1367777766655544
No 48
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=55.67 E-value=33 Score=24.80 Aligned_cols=36 Identities=28% Similarity=0.410 Sum_probs=25.9
Q ss_pred cCCcEEEeeCCCce------eccCCCCCCEEE-EeeCCCCcee
Q psy16496 117 TGDSTVTLDNHKTI------NITDLNIGDKVL-TLNTITGEME 152 (245)
Q Consensus 117 pgdt~V~l~dG~~k------~I~dL~~GDrVL-a~d~~~G~~~ 152 (245)
+...+|+|.||..- .++.|++|.+|. +.|..+|+.+
T Consensus 14 ~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd~~~gk~v 56 (61)
T PF07076_consen 14 PETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYDEVDGKRV 56 (61)
T ss_pred CCceEEEecCCCEEECCCcccccccCCCCEEEEEEEccCCcEE
Confidence 34557889998754 488999999987 4465577643
No 49
>TIGR02610 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein. All members of this family are encoded by genes polyhydroxyalkanoic acid (PHA) biosynthesis and utilization genes, including proteins at found at the surface of PHA granules. Examples so far are found in the Pseudomonales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=54.46 E-value=36 Score=26.23 Aligned_cols=55 Identities=16% Similarity=0.383 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCCCCCCcccceeeee--eEecCCC---cchHHHHHhhh
Q psy16496 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVD--ITTSDRD---SSKYGLLARMA 81 (245)
Q Consensus 16 ~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~~~~slh~egra~d--i~~s~~~---~~k~g~La~la 81 (245)
...++++..|+.++.+++. +.+.|..| -|++.+.+|+ |.+.|.. .-++|+|....
T Consensus 15 ~eAr~~~e~~a~~l~~~~~-----~e~~W~GD------~l~F~~~gv~G~l~V~~d~v~v~v~Lg~Ll~~f 74 (91)
T TIGR02610 15 AAARAKAEDLARKLTDRYG-----LASHWEGD------TLRIARSGVDGAVHLGPQSIRVTAELGMLLSAM 74 (91)
T ss_pred HHHHHHHHHHHHHHHHHhC-----CEeEEeCC------EEEEEEeeeeEEEEEcCCeEEEEEEhHHHHHHH
Confidence 4688999999999998874 37889654 5777777777 4444322 24788776653
No 50
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=54.12 E-value=37 Score=26.87 Aligned_cols=40 Identities=28% Similarity=0.334 Sum_probs=26.2
Q ss_pred eccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEE
Q psy16496 131 NITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIK 182 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~ 182 (245)
-+++|++||+|.+... .|-.|+.. + .+.+.|++.+|-.++
T Consensus 49 ~~~~Lk~Gd~VvT~gG-----i~G~Vv~i-~------~~~v~lei~~g~~i~ 88 (106)
T PRK05585 49 MLSSLAKGDEVVTNGG-----IIGKVTKV-S------EDFVIIELNDDTEIK 88 (106)
T ss_pred HHHhcCCCCEEEECCC-----eEEEEEEE-e------CCEEEEEECCCeEEE
Confidence 4789999999998654 34445443 2 137778876664444
No 51
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=54.01 E-value=28 Score=27.86 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=27.4
Q ss_pred eccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEec
Q psy16496 131 NITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMT 184 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lT 184 (245)
-+++|++||+|.+... .|-.|+.. + .+++.|++.+|-.+++.
T Consensus 35 m~~~Lk~GD~VvT~gG-----i~G~V~~I-~------d~~v~leia~gv~i~~~ 76 (109)
T PRK05886 35 LHESLQPGDRVHTTSG-----LQATIVGI-T------DDTVDLEIAPGVVTTWM 76 (109)
T ss_pred HHHhcCCCCEEEECCC-----eEEEEEEE-e------CCEEEEEECCCeEEEEE
Confidence 4789999999999654 23334432 2 23888888766555543
No 52
>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=53.74 E-value=87 Score=24.89 Aligned_cols=37 Identities=19% Similarity=0.130 Sum_probs=27.1
Q ss_pred CceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 128 KTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 128 ~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
-...+.+|++||+|.-.+. .+...|. |......++..
T Consensus 55 ~F~~L~~l~~Gd~i~v~~~-~~~~~Y~-V~~~~~v~~~~ 91 (127)
T cd05828 55 HFRFLGELEPGDIITLQTL-GGTYTYR-VTSTRIVDADD 91 (127)
T ss_pred hhhChhcCCCCCEEEEEEC-CEEEEEE-EeeEEEECccc
Confidence 3558999999999999888 6777776 55554444443
No 53
>COG4787 FlgF Flagellar basal body rod protein [Cell motility and secretion]
Probab=53.62 E-value=42 Score=30.42 Aligned_cols=118 Identities=23% Similarity=0.277 Sum_probs=67.7
Q ss_pred cHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCC-CCCCcccceeeeeeEecCCCcchHHHHHhhhhhcCcceEE-Ec
Q psy16496 15 FQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHH-ASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVY-YE 92 (245)
Q Consensus 15 ~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~-~~~slh~egra~di~~s~~~~~k~g~La~la~~aGfd~V~-~~ 92 (245)
|...|.+|+.+ .+|.++-.+-+-|+-.--..++++ ++.+|-|-||-.||++. .. ..|+++. -|--+ |.
T Consensus 31 TtGFraql~a~-rav~v~g~~~ptrt~~~~s~pg~d~spG~l~~TgR~LDvaiq---~D-----GwlaVq~-~dG~EaYT 100 (251)
T COG4787 31 TTGFRAQLNAA-RAVQVHGDSLPTRTFVMASTPGTDMSPGSLDYTGRPLDVAIQ---GD-----GWLAVQD-ADGSEAYT 100 (251)
T ss_pred chhHHHHHHHh-hhccccCCCcchheeeecccCcccCCCccccccCCcceEEEc---cC-----ceEEEEc-CCCcchhe
Confidence 45566666543 334334344444555545556654 89999999999999993 21 1223321 12222 55
Q ss_pred ccceeeeccccccccc--cccCccc---ccCCcEEEeeCCCceeccCCCCCCEEEEe
Q psy16496 93 SRNHIHCSVKTETTHV--NGKGAGC---FTGDSTVTLDNHKTINITDLNIGDKVLTL 144 (245)
Q Consensus 93 ~r~~ih~~vks~~s~~--aak~ggC---Fpgdt~V~l~dG~~k~I~dL~~GDrVLa~ 144 (245)
+.++++...+.-.... -.-..|| .|.++.|+.+.-+ .|+.+.+||.=-++
T Consensus 101 RnG~~qI~a~g~lTiqg~pViG~ggpI~vPp~~~v~I~~DG--tIsa~~~g~~~~~v 155 (251)
T COG4787 101 RNGNIQIDATGQLTIQGHPVIGEGGPITVPPGAKVTIAADG--TISALNPGDPANTV 155 (251)
T ss_pred ecCceEECcccceecCCCeeecCCCccccCCCceEEEecCc--eEEeccCCCCCCce
Confidence 6677776655421100 0112255 7899999887665 47888888864433
No 54
>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=53.20 E-value=17 Score=26.69 Aligned_cols=19 Identities=32% Similarity=0.483 Sum_probs=11.5
Q ss_pred CCCCCEEEEe----eCCCCceeE
Q psy16496 135 LNIGDKVLTL----NTITGEMEY 153 (245)
Q Consensus 135 L~~GDrVLa~----d~~~G~~~y 153 (245)
+.+||+|+.- |.+.|+.+|
T Consensus 45 I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 45 ILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred ECCCCEEEEEECcccCCcEeEEe
Confidence 6799999732 333455544
No 55
>PF10772 DUF2597: Protein of unknown function (DUF2597); InterPro: IPR019708 This entry is represented by Bacteriophage HP1, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents proteins with unknown function and is restricted to Proteobacteria. One of the proteins is annotated to a predictive tail tube protein.
Probab=51.68 E-value=73 Score=26.51 Aligned_cols=75 Identities=27% Similarity=0.579 Sum_probs=46.0
Q ss_pred eeEecCCCcchHHHHHhhhhhcC-------cceEEEcccceeeeccccccccccccCcccccCCcEEEeeCCCceeccCC
Q psy16496 63 DITTSDRDSSKYGLLARMAVEAG-------FDWVYYESRNHIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINITDL 135 (245)
Q Consensus 63 di~~s~~~~~k~g~La~la~~aG-------fd~V~~~~r~~ih~~vks~~s~~aak~ggCFpgdt~V~l~dG~~k~I~dL 135 (245)
+|.+ |...|-.|...|..|| ||.+.|...+ +.. .-...-||= ..|++
T Consensus 47 EiEl---dt~nf~~l~~aA~~AGSwR~i~~~D~~fya~~g--------~ee-~kVEaFGck-------------l~lsd- 100 (134)
T PF10772_consen 47 EIEL---DTKNFNLLSEAAKSAGSWRGIPPFDILFYAKTG--------SEE-LKVEAFGCK-------------LKLSD- 100 (134)
T ss_pred EEEE---cHHHHHHHHHHHHhcCCccCCCcccEEEEeccC--------Cce-EEEEEeeeE-------------EEecc-
Confidence 4555 3445667788888888 8888887665 222 344455772 23443
Q ss_pred CCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEE
Q psy16496 136 NIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQI 173 (245)
Q Consensus 136 ~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I 173 (245)
+|.+|+ .|--.-..-+.|+-.+|+ |++|
T Consensus 101 -----lLdiD~-kGg~~~thKik~~VTsPd----FV~I 128 (134)
T PF10772_consen 101 -----LLDIDP-KGGSKSTHKIKFDVTSPD----FVRI 128 (134)
T ss_pred -----ceecCC-CCCcceeEEcceEecCCC----eEEE
Confidence 477888 443333444577776666 8877
No 56
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=50.59 E-value=11 Score=36.07 Aligned_cols=112 Identities=14% Similarity=0.082 Sum_probs=63.5
Q ss_pred chhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC--------CCCCCCCcc------cceeeeeeEecCCCcchHH
Q psy16496 10 FLFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE--------GHHASDSLH------YEGRAVDITTSDRDSSKYG 75 (245)
Q Consensus 10 ~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~--------~~~~~~slh------~egra~di~~s~~~~~k~g 75 (245)
.-.+.+...-+.|.+++..|+.+=.-+-+.+.-+.+.- .--+++.+= .+-|+.+..=-++-+..|.
T Consensus 73 ~~~l~~d~~i~~~~~vt~avH~~G~~i~iQL~H~Gr~~~~~~~~~~~~vapS~~~~~~~~~~~pr~mt~~eI~~ii~~f~ 152 (363)
T COG1902 73 QPGLWSDAQIPGLKRLTEAVHAHGAKIFIQLWHAGRKARASHPWLPSAVAPSAIPAPGGRRATPRELTEEEIEEVIEDFA 152 (363)
T ss_pred CCccCChhHhHHHHHHHHHHHhcCCeEEEEeccCcccccccccCCCcccCCCccccccCCCCCCccCCHHHHHHHHHHHH
Confidence 34567778889999999999886443334443333221 011121111 1222222111223356889
Q ss_pred HHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccCCcE
Q psy16496 76 LLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTGDST 121 (245)
Q Consensus 76 ~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpgdt~ 121 (245)
.-|+.|.+||||.|+.+. .+|+=.+--|..+ +-..++||+|-.-++
T Consensus 153 ~AA~rA~~AGFDgVEIH~AhGYLi~qFlsp~tN~RtD~YGGSlENR~R 200 (363)
T COG1902 153 RAARRAKEAGFDGVEIHGAHGYLLSQFLSPLTNKRTDEYGGSLENRAR 200 (363)
T ss_pred HHHHHHHHcCCCEEEEeeccchHHHHhcCCccCCCCCccCCcHHHHHH
Confidence 999999999999999775 3554443333322 245678898744333
No 57
>PRK10605 N-ethylmaleimide reductase; Provisional
Probab=50.17 E-value=20 Score=33.99 Aligned_cols=52 Identities=17% Similarity=0.215 Sum_probs=34.6
Q ss_pred cchHHHHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccCCcEE
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTGDSTV 122 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpgdt~V 122 (245)
...|+.=|+.|.+||||.|+.+- .+|+-.+--|..+ +-..++||++-.-++.
T Consensus 158 i~~f~~AA~rA~~AGfDGVEIh~ahGyLl~qFLSp~~N~RtDeYGGslENR~Rf 211 (362)
T PRK10605 158 VNDFRQAIANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARL 211 (362)
T ss_pred HHHHHHHHHHHHHcCCCEEEEcccccchHHHhcCCcCCCCCCcCCCcHHHHHHH
Confidence 46889999999999999999764 4555444444332 2456678876444433
No 58
>PRK14725 pyruvate kinase; Provisional
Probab=48.62 E-value=46 Score=34.16 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=17.9
Q ss_pred ccCCCCCCEEEEeeCCCCceeEEEEE
Q psy16496 132 ITDLNIGDKVLTLNTITGEMEYSEVL 157 (245)
Q Consensus 132 I~dL~~GDrVLa~d~~~G~~~yS~Vi 157 (245)
...|++||.+.-.|. -|+-.+=.|+
T Consensus 266 ~~~l~~Gd~i~~~Da-Rg~~R~l~V~ 290 (608)
T PRK14725 266 LARLEPGDELRFTDA-RGKKRKLTVT 290 (608)
T ss_pred hhhcCCCceeeeeec-cccceeeeEE
Confidence 577899999998887 6764444443
No 59
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=48.06 E-value=28 Score=28.90 Aligned_cols=34 Identities=35% Similarity=0.468 Sum_probs=26.1
Q ss_pred eeccCCCCCCEEEEeeCCCCceeEE---EEEEEEecCCCce
Q psy16496 130 INITDLNIGDKVLTLNTITGEMEYS---EVLLFLHRDPNLV 167 (245)
Q Consensus 130 k~I~dL~~GDrVLa~d~~~G~~~yS---~Vi~fl~r~~~~~ 167 (245)
.+|..|+.||.|-.. |+-.|+ .||-|-|++|...
T Consensus 81 prip~l~~GD~V~f~----GeYe~n~kggvIHWTH~dp~~~ 117 (131)
T PF11948_consen 81 PRIPWLQKGDQVEFY----GEYEWNPKGGVIHWTHHDPRGR 117 (131)
T ss_pred ccCcCcCCCCEEEEE----EEEEECCCCCEEEeeccCCCCC
Confidence 368899999999874 555555 4889999998753
No 60
>PF08331 DUF1730: Domain of unknown function (DUF1730); InterPro: IPR013542 This domain of unknown function occurs in iron-sulphur cluster-binding proteins together with the 4Fe-4S binding domain (IPR001450 from INTERPRO).
Probab=46.58 E-value=29 Score=25.58 Aligned_cols=25 Identities=32% Similarity=0.331 Sum_probs=21.4
Q ss_pred cHHHHHHHHHHHHHHhhhCCCceEE
Q psy16496 15 FQRLKEKLNTLAISVMNEWPGVRLR 39 (245)
Q Consensus 15 ~~~~~~~l~~l~~~v~~~w~~v~lr 39 (245)
++-+|+||+.|+..+.+++|+++-|
T Consensus 49 H~vlk~~L~~l~~~i~~~~~~~~~r 73 (78)
T PF08331_consen 49 HKVLKKKLEQLAEWIRELGPDFEYR 73 (78)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCeE
Confidence 5678999999999999999986544
No 61
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside []. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions []. The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GKA_B 3P67_A 3F03_K 2ABA_A 1VYR_A 1GVO_A 3KFT_B 3P8I_A 1GVQ_A 3P74_A ....
Probab=45.99 E-value=13 Score=34.77 Aligned_cols=109 Identities=17% Similarity=0.146 Sum_probs=58.7
Q ss_pred chhhhcHHHHHHHHHHHHHHhhhCCCceEEEE-eeeCCCCC----CC---------CCCcccceeee-eeEecC--CCcc
Q psy16496 10 FLFFCFQRLKEKLNTLAISVMNEWPGVRLRVI-EGWDEEGH----HA---------SDSLHYEGRAV-DITTSD--RDSS 72 (245)
Q Consensus 10 ~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~-~~w~~~~~----~~---------~~slh~egra~-di~~s~--~~~~ 72 (245)
.-.+-+..+.+.+.+|+..|+..=.-+-+.+. -|+..... .. +...++.|.-+ -+|..+ .-..
T Consensus 70 ~~~i~~d~~i~~~k~l~~~vh~~Ga~i~~QL~H~G~~~~~~~~~~~~~~psa~~~~~~~~~~~~~~~~~mt~~eI~~ii~ 149 (341)
T PF00724_consen 70 QPGIWDDEQIPGLKKLADAVHAHGAKIIAQLWHAGRQANPEYSGDPPVGPSAPSALPSPIKFMGYPPREMTEEEIEEIIE 149 (341)
T ss_dssp SEBSSSHHHHHHHHHHHHHHHHTTSEEEEEEE--GGGSSGCCSGGGCEESSCSSSSSTTTTETSCEEEE--HHHHHHHHH
T ss_pred cchhchhhHHHHHHHHHHHHHhcCccceeeccccccccCcccCCCCccCcccccccCcccccCCCCCeeCCHHHHHHHHH
Confidence 34566899999999999999886222222222 22222100 00 11111122222 233322 2346
Q ss_pred hHHHHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccC
Q psy16496 73 KYGLLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTG 118 (245)
Q Consensus 73 k~g~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpg 118 (245)
.|+.-|+.|.+||||.|+.+. .+|+-.+--|..+ +-..++||+|-.
T Consensus 150 ~f~~AA~~A~~AGfDGVEIH~ahGyLl~qFLSp~~N~RtDeYGGs~EN 197 (341)
T PF00724_consen 150 DFAQAARRAKEAGFDGVEIHAAHGYLLSQFLSPLTNRRTDEYGGSLEN 197 (341)
T ss_dssp HHHHHHHHHHHTT-SEEEEEESTTSHHHHHHSTTT---SSTTSSSHHH
T ss_pred HHHHHHHHHHHhccCeEeecccchhhhhheeeeccCCCchhhhhhhch
Confidence 899999999999999999765 4554444444322 245678887633
No 62
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=45.47 E-value=18 Score=34.25 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=21.6
Q ss_pred EEEeeCCCceeccCCCCCCEEEEeeC
Q psy16496 121 TVTLDNHKTINITDLNIGDKVLTLNT 146 (245)
Q Consensus 121 ~V~l~dG~~k~I~dL~~GDrVLa~d~ 146 (245)
++..+||....+.+|++||+||..=.
T Consensus 334 kLv~~dG~pvSV~eLk~GD~vlv~~e 359 (376)
T COG1465 334 KLVNPDGEPVSVAELKPGDEVLVYLE 359 (376)
T ss_pred EEEcCCCcEeeeEecCCCCEEEEEeh
Confidence 35567799899999999999998755
No 63
>cd00081 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Probab=45.19 E-value=75 Score=24.57 Aligned_cols=28 Identities=32% Similarity=0.292 Sum_probs=22.9
Q ss_pred cCCcEEEeeCC---CceeccCCCCCCEEEEe
Q psy16496 117 TGDSTVTLDNH---KTINITDLNIGDKVLTL 144 (245)
Q Consensus 117 pgdt~V~l~dG---~~k~I~dL~~GDrVLa~ 144 (245)
+++=.+.+.++ ..++.++|++||.|+..
T Consensus 69 T~~H~~~~~~~~~~~~~~a~~l~~gd~l~~~ 99 (136)
T cd00081 69 TPDHLLFVLEDGELKWVFASDLKPGDYVLVP 99 (136)
T ss_pred cCCCEEEEEeCCeEEEEEHHHCCCCCEEEEc
Confidence 56666777775 77899999999999875
No 64
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=45.18 E-value=7.6 Score=29.22 Aligned_cols=41 Identities=27% Similarity=0.396 Sum_probs=2.1
Q ss_pred eccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEe
Q psy16496 131 NITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKM 183 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~l 183 (245)
-+++|++||+|.+....-| .|+.. ..+.+.|++++|-.+++
T Consensus 33 m~~~Lk~Gd~VvT~gGi~G-----~V~~i-------~~~~v~lei~~g~~i~v 73 (82)
T PF02699_consen 33 MLASLKPGDEVVTIGGIYG-----TVVEI-------DDDTVVLEIAPGVEITV 73 (82)
T ss_dssp GGG--------------------------------------------------
T ss_pred HHHcCCCCCEEEECCcEEE-----EEEEE-------eCCEEEEEECCCeEEEE
Confidence 4789999999998765233 34433 23478888877655543
No 65
>KOG3209|consensus
Probab=42.94 E-value=42 Score=35.30 Aligned_cols=16 Identities=31% Similarity=0.682 Sum_probs=14.0
Q ss_pred eccCCCCCCEEEEeeC
Q psy16496 131 NITDLNIGDKVLTLNT 146 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~ 146 (245)
....|++||+|+|++.
T Consensus 793 RCgkLkVGDrilAVNG 808 (984)
T KOG3209|consen 793 RCGKLKVGDRILAVNG 808 (984)
T ss_pred hhccccccceEEEecC
Confidence 5778999999999974
No 66
>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=42.54 E-value=93 Score=25.45 Aligned_cols=25 Identities=28% Similarity=0.441 Sum_probs=20.0
Q ss_pred ceeccCCCCCCEEEEeeCCCC-ceeEE
Q psy16496 129 TINITDLNIGDKVLTLNTITG-EMEYS 154 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G-~~~yS 154 (245)
...+.+|++||+|.-.+. .| ...|.
T Consensus 67 F~~L~~l~~GD~I~v~~~-~g~~~~Y~ 92 (144)
T cd05829 67 FFRLGDLRKGDKVEVTRA-DGQTATFR 92 (144)
T ss_pred hcchhcCCCCCEEEEEEC-CCCEEEEE
Confidence 568999999999999886 56 46665
No 67
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=42.35 E-value=26 Score=30.69 Aligned_cols=51 Identities=22% Similarity=0.369 Sum_probs=34.6
Q ss_pred eccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCeeE
Q psy16496 131 NITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLIL 190 (245)
Q Consensus 131 ~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hlif 190 (245)
.|+.|.+|+.|-.--. .+.... .|+-. .++-+++..+||-.+.+++.||+|
T Consensus 158 ~~s~l~~g~~~kVk~G-~~a~~A-tvlEv-------~Kd~vRVqL~~Gl~m~V~AehL~~ 208 (208)
T COG3109 158 DISALTVGQALKVKAG-QNAMDA-TVLEI-------TKDGVRVQLNSGLSMIVRAEHLVF 208 (208)
T ss_pred HHHhhhccceeeeccc-cccccc-eEEEE-------eccceEEeecCCceEEEehhhhcC
Confidence 4889999998875433 222111 12222 244678889999999999999986
No 68
>PLN02411 12-oxophytodienoate reductase
Probab=41.59 E-value=20 Score=34.42 Aligned_cols=52 Identities=15% Similarity=0.161 Sum_probs=36.0
Q ss_pred cchHHHHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccCCcEE
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTGDSTV 122 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpgdt~V 122 (245)
...|+.=|+.|.+||||.|+.+- .+|+-.+--|..+ +-..++||.|-.-++.
T Consensus 164 i~~f~~AA~rA~~AGFDGVEIH~AhGYLl~QFLSp~tN~RtDeYGGSlENR~RF 217 (391)
T PLN02411 164 VEHYRQAALNAIRAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSIENRCRF 217 (391)
T ss_pred HHHHHHHHHHHHHcCCCEEEEccccchHHHHhCCCccCCCCCcCCCCHHHHhHH
Confidence 46889999999999999999774 4666655555533 1456678876444433
No 69
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=41.12 E-value=1.5e+02 Score=22.53 Aligned_cols=66 Identities=23% Similarity=0.367 Sum_probs=44.5
Q ss_pred cEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCC-CeEEecCCCeeEeecCCCcc
Q psy16496 120 STVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESG-SLIKMTPSHLILRWHRPNAK 198 (245)
Q Consensus 120 t~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g-~~L~lTp~Hlifv~~~~~~~ 198 (245)
++|.+.+|. |++||.+.+-.. .| +|-+.++- +| .-...+|..++.+..
T Consensus 18 atviV~~Gt------L~~Gd~iv~G~~-~G-----kVr~~~d~--------------~g~~v~~a~Ps~~v~i~g----- 66 (95)
T cd03701 18 ATVIVQNGT------LKKGDVIVAGGT-YG-----KIRTMVDE--------------NGKALLEAGPSTPVEILG----- 66 (95)
T ss_pred EEEEEEcCe------EecCCEEEECCc-cc-----eEEEEECC--------------CCCCccccCCCCCEEEee-----
Confidence 568888886 789999988544 34 45444432 23 247788999997775
Q ss_pred ccCCCcceEeCCCCCCCCEEEEccCCc
Q psy16496 199 SILNDIEYTYAERVRVNDSIIVHKNGK 225 (245)
Q Consensus 199 ~~~~~~~~v~A~~v~~GD~V~v~~g~~ 225 (245)
+=+....||.+++....+
T Consensus 67 ---------~~~~p~aGd~~~~~~~e~ 84 (95)
T cd03701 67 ---------LKDVPKAGDGVLVVASEK 84 (95)
T ss_pred ---------ecCCccCCCEEEEeCCCH
Confidence 234467788888776553
No 70
>PRK11479 hypothetical protein; Provisional
Probab=40.30 E-value=29 Score=32.14 Aligned_cols=32 Identities=31% Similarity=0.331 Sum_probs=27.3
Q ss_pred cccccCCcEEEeeCCCceeccCCCCCCEEEEe
Q psy16496 113 AGCFTGDSTVTLDNHKTINITDLNIGDKVLTL 144 (245)
Q Consensus 113 ggCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~ 144 (245)
+-=||.++...-..|..+++++|++||.|+.-
T Consensus 43 ~~~~pr~s~~q~~~g~~Vs~~~LqpGDLVFfs 74 (274)
T PRK11479 43 AVKFQHQSSFTEQGIKEITAPDLKPGDLLFSS 74 (274)
T ss_pred ceecCcccHHHHhCCcccChhhCCCCCEEEEe
Confidence 44578899888888888999999999999973
No 71
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=39.68 E-value=41 Score=25.99 Aligned_cols=20 Identities=20% Similarity=0.493 Sum_probs=10.7
Q ss_pred CCCCCEEEE----eeCCCCceeEE
Q psy16496 135 LNIGDKVLT----LNTITGEMEYS 154 (245)
Q Consensus 135 L~~GDrVLa----~d~~~G~~~yS 154 (245)
+.+||+|.. .|.+.|+++|.
T Consensus 47 Il~GD~V~VE~spYDltkGRIiyR 70 (87)
T PRK12442 47 ILAGDRVTLELSPYDLTKGRINFR 70 (87)
T ss_pred ecCCCEEEEEECcccCCceeEEEE
Confidence 457777753 23334555444
No 72
>PF09650 PHA_gran_rgn: Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=39.50 E-value=71 Score=24.24 Aligned_cols=55 Identities=24% Similarity=0.466 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCCCCCCcccceeeee--eEecCCC---cchHHHHHhhh
Q psy16496 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVD--ITTSDRD---SSKYGLLARMA 81 (245)
Q Consensus 16 ~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~~~~slh~egra~d--i~~s~~~---~~k~g~La~la 81 (245)
...++++..++.++.++++ +...|+.+ .|++.|..|+ |++.|.. .-++|+|....
T Consensus 12 ~eAr~~~~~~~~~l~~~~~-----~~~~W~gd------~l~f~~~gv~G~l~V~~d~v~l~v~Lg~Ll~~f 71 (87)
T PF09650_consen 12 EEARRRAEELAEKLAEEYG-----VECTWEGD------RLSFSGQGVDGTLDVADDHVRLEVKLGFLLSPF 71 (87)
T ss_pred HHHHHHHHHHHHHHHHHhC-----CEEEEEcC------EEEEEeCCceEEEEEcCCEEEEEEEcHHHHHHH
Confidence 3578888889998888764 46778844 5555566555 4443321 23788777653
No 73
>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=39.45 E-value=1e+02 Score=24.78 Aligned_cols=37 Identities=19% Similarity=0.160 Sum_probs=25.5
Q ss_pred CceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCc
Q psy16496 128 KTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNL 166 (245)
Q Consensus 128 ~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~ 166 (245)
-...+.+|++||.|.-.+. ++...|. |...-..++..
T Consensus 57 ~F~~L~~l~~GD~i~v~~~-~~~~~Y~-V~~~~~v~~~d 93 (136)
T TIGR01076 57 MFTNLDKLKKGDMLYLHVG-NEVLTYQ-VTSTKIVEPTD 93 (136)
T ss_pred ccCCHHHCCCCCEEEEEEC-CcEEEEE-EEEEEEECcCc
Confidence 3568999999999987776 6776776 44444444443
No 74
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=39.30 E-value=73 Score=28.29 Aligned_cols=46 Identities=20% Similarity=0.263 Sum_probs=28.3
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeC
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTE 176 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te 176 (245)
.+--+++++||.|+..+...+.+..++|+..--. .....|.+++.+
T Consensus 100 ~vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~--~~~G~yAPLT~~ 145 (217)
T PF01079_consen 100 AVFASDVRVGDCVLVSDEGGGKLRPSRVVRVSTV--EKRGVYAPLTSH 145 (217)
T ss_dssp EEEGGG--TT-EEEEE-TTT--EEEEEEEEEEEE--EEEEEEEEEESS
T ss_pred eeehhhCCCCCEEEEEEcCCCcEEEEEEEEEEEE--EEeeEEcCccCc
Confidence 4667899999999996664678888888765432 345667777653
No 75
>cd02931 ER_like_FMN Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent reduction of carbon-carbon double bonds of several molecules, including nonactivated 2-enoates, alpha,beta-unsaturated aldehydes, cyclic ketones, and methylketones. ERs are similar to 2,4-dienoyl-CoA reductase from E. coli and to the old yellow enzyme from Saccharomyces cerevisiae.
Probab=37.37 E-value=26 Score=33.39 Aligned_cols=51 Identities=24% Similarity=0.230 Sum_probs=32.8
Q ss_pred cchHHHHHhhhhhcCcceEEEcc-c-ceeeeccccc-cccccccCcccccCCcE
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYES-R-NHIHCSVKTE-TTHVNGKGAGCFTGDST 121 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~-r-~~ih~~vks~-~s~~aak~ggCFpgdt~ 121 (245)
...|+.-|+.|.+||||.|+.+. . +|+-.+--|. ..+...++||++-..++
T Consensus 149 i~~f~~AA~ra~~AGfDgVEih~ah~GyLl~qFLSp~~N~RtDeyGGslenR~r 202 (382)
T cd02931 149 VGKFGESAVIAKEAGFDGVEIHAVHEGYLLDQFTISLFNKRTDKYGGSLENRLR 202 (382)
T ss_pred HHHHHHHHHHHHHcCCCEEEEeccccChHHHHhcCCccCCCCCcCCCCHHHHhH
Confidence 46889999999999999999775 3 5443232222 22244567777644443
No 76
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=37.12 E-value=34 Score=25.27 Aligned_cols=24 Identities=25% Similarity=0.404 Sum_probs=20.2
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeE
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEY 153 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~y 153 (245)
+.-|.+|++||+|...-+ -|+..|
T Consensus 76 S~~L~~l~~Gd~v~i~gP-~G~f~y 99 (99)
T PF00970_consen 76 SRYLHQLKPGDEVEIRGP-YGNFTY 99 (99)
T ss_dssp HHHHHTSCTTSEEEEEEE-ESSEEE
T ss_pred HHHHHhCCCCCEEEEEEc-ccccCC
Confidence 347899999999999888 888766
No 77
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=36.58 E-value=1.4e+02 Score=25.46 Aligned_cols=57 Identities=14% Similarity=0.072 Sum_probs=35.8
Q ss_pred CceeccCCCCCCEEEEeeCCCCce-eEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCee
Q psy16496 128 KTINITDLNIGDKVLTLNTITGEM-EYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLI 189 (245)
Q Consensus 128 ~~k~I~dL~~GDrVLa~d~~~G~~-~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hli 189 (245)
....+.+|++||+|.-.+. +|+. .|. |...-.-+++.... +.-.+++.|+|.-=+|+
T Consensus 102 ~F~~L~~L~~GD~I~v~~~-~g~~~~Y~-V~~~~iV~~~d~~v---~~~~~~~~LtLiTC~Pf 159 (174)
T TIGR03784 102 HFAFLQELRPGDVIRLQTP-DGQWQSYQ-VTATRVVDESETGL---DLPADDSQLVLITCYPF 159 (174)
T ss_pred cCCChhhCCCCCEEEEEEC-CCeEEEEE-EeEEEEECCcccee---ccCCCCCEEEEEeCCCC
Confidence 4678999999999998887 7874 576 55544444443221 11123456776666664
No 78
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=36.38 E-value=1.4e+02 Score=30.06 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=20.7
Q ss_pred ccCCcEEEeeCCCceeccCCCCCCEEEE
Q psy16496 116 FTGDSTVTLDNHKTINITDLNIGDKVLT 143 (245)
Q Consensus 116 Fpgdt~V~l~dG~~k~I~dL~~GDrVLa 143 (245)
|.++-...+.=.......+|++|++|+-
T Consensus 64 ~~~g~~~~~~~~~~~~~~~l~~g~~v~l 91 (512)
T TIGR03689 64 FTAGRRMRVTVSPNVNAAELVPGQTVRL 91 (512)
T ss_pred EeCCceEEEEeCCCCCHHHCCCCCEEEE
Confidence 5566655555556678999999999984
No 79
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=36.29 E-value=43 Score=25.83 Aligned_cols=25 Identities=40% Similarity=0.651 Sum_probs=18.2
Q ss_pred eeCCCceeccCCCCCCEEEEeeCCCCc
Q psy16496 124 LDNHKTINITDLNIGDKVLTLNTITGE 150 (245)
Q Consensus 124 l~dG~~k~I~dL~~GDrVLa~d~~~G~ 150 (245)
..+|...|+ ++++||+|+--+. .|.
T Consensus 49 ~~~G~~~~~-~vk~GD~Vlf~~~-~g~ 73 (95)
T PRK00364 49 LDNGERVPL-DVKVGDKVLFGKY-AGT 73 (95)
T ss_pred CCCCCEeec-ccCCCCEEEEcCC-CCe
Confidence 345776777 7999999997554 554
No 80
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=35.05 E-value=39 Score=24.60 Aligned_cols=28 Identities=25% Similarity=0.317 Sum_probs=21.9
Q ss_pred ccCCcEEEeeCCC---ceeccCCCCCCEEEE
Q psy16496 116 FTGDSTVTLDNHK---TINITDLNIGDKVLT 143 (245)
Q Consensus 116 Fpgdt~V~l~dG~---~k~I~dL~~GDrVLa 143 (245)
-+++=.+.+.+|. .++.++|++||+|+.
T Consensus 68 ~T~~H~~~~~~~~~~~w~~a~~l~~gd~v~~ 98 (100)
T smart00306 68 LTPDHLLLVRDGGKLVWVFASELKPGDYVLV 98 (100)
T ss_pred ECCCCEEEEecCCcEEEEEHHHCCCCCEEEe
Confidence 3566667777764 789999999999975
No 81
>PRK09250 fructose-bisphosphate aldolase; Provisional
Probab=34.42 E-value=29 Score=33.24 Aligned_cols=61 Identities=15% Similarity=0.217 Sum_probs=37.2
Q ss_pred CcchHHHHHhhhhhcCcceEE--Eccc--c--ee---------eeccccccc--cccccCcccccCCcEEEeeCCCce
Q psy16496 70 DSSKYGLLARMAVEAGFDWVY--YESR--N--HI---------HCSVKTETT--HVNGKGAGCFTGDSTVTLDNHKTI 130 (245)
Q Consensus 70 ~~~k~g~La~la~~aGfd~V~--~~~r--~--~i---------h~~vks~~s--~~aak~ggCFpgdt~V~l~dG~~k 130 (245)
+...++-.+++|.|.|-|.|. |..+ + -+ --....+++ ++.--.-+||.|...|..+.|..+
T Consensus 215 ~~d~Ia~AaRiaaELGADIVKv~yp~~~~~f~~v~~~~~~~~~~~~~~~~~~~~~~~~~V~ac~ag~vpVviAGG~k~ 292 (348)
T PRK09250 215 AADLTGQANHLAATIGADIIKQKLPTNNGGYKAINFGKTDDRVYSKLTSDHPIDLVRYQVANCYMGRRGLINSGGASK 292 (348)
T ss_pred cHHHHHHHHHHHHHHcCCEEEecCCCChhhHHHhhcccccccccccccccchHHHHHHHHHhhccCCceEEEeCCCCC
Confidence 456788889999999999985 3321 1 00 000011111 011113489999999999999865
No 82
>PF06904 Extensin-like_C: Extensin-like protein C-terminus; InterPro: IPR009683 This entry represents the C terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress []. Many proteins in this entry are hypothetical.
Probab=33.59 E-value=83 Score=27.25 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhhhCCCceEEEEeeeCCCCCC----CCCCcccceeeeeeEe
Q psy16496 18 LKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHH----ASDSLHYEGRAVDITT 66 (245)
Q Consensus 18 ~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~~~~----~~~slh~egra~di~~ 66 (245)
.++-+.-+|..+..+ +-++|+...+|.|.+-+ ..-|=|=.|.|+||.-
T Consensus 60 ~~~~v~paA~~~~gs-~v~~I~~~gsY~CR~~n~~~~~rlSEHA~gnAiDI~g 111 (178)
T PF06904_consen 60 VRHVVQPAARRHLGS-PVVRIEHAGSYACRNRNGRAGGRLSEHARGNAIDIAG 111 (178)
T ss_pred HHHhHHHHHHHHhCC-CceEEeeccceecCCcCCCCCCCcCccccccceeeee
Confidence 345555566666555 55899999999998644 5779999999999865
No 83
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=33.41 E-value=71 Score=26.76 Aligned_cols=22 Identities=18% Similarity=0.131 Sum_probs=14.0
Q ss_pred ccCCcE-EEeeCCCceeccCCCCCCEEE
Q psy16496 116 FTGDST-VTLDNHKTINITDLNIGDKVL 142 (245)
Q Consensus 116 Fpgdt~-V~l~dG~~k~I~dL~~GDrVL 142 (245)
|++.+. +.+++. .++++||+|.
T Consensus 44 ~~~~~~~~~v~~~-----~~~~vGD~V~ 66 (154)
T PRK10862 44 GPQTTHQLVVPSS-----QPLVPGQKVE 66 (154)
T ss_pred cCCCceEEEecCC-----CCCCCCCEEE
Confidence 555543 555443 4589999996
No 84
>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=33.37 E-value=1.5e+02 Score=23.88 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=22.7
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEE
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLF 159 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~f 159 (245)
...+++|++||.|.-.+. .|...|. |...
T Consensus 60 F~~L~~l~~Gd~i~v~~~-~~~~~Y~-V~~~ 88 (137)
T cd05830 60 FNDLDKLRPGDKIVVETA-DGWYTYV-VRSS 88 (137)
T ss_pred cccHhhCCCCCEEEEEEC-CeEEEEE-EeEE
Confidence 557999999999998887 7777775 4444
No 85
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=33.05 E-value=44 Score=30.61 Aligned_cols=29 Identities=17% Similarity=0.162 Sum_probs=21.2
Q ss_pred cccCCcEEEeeCCCceeccCCCCCCEEEEe
Q psy16496 115 CFTGDSTVTLDNHKTINITDLNIGDKVLTL 144 (245)
Q Consensus 115 CFpgdt~V~l~dG~~k~I~dL~~GDrVLa~ 144 (245)
.-+++=.+.+.+|. +++++|++||+|...
T Consensus 64 ~~T~~H~~lt~~~w-k~~~~Lk~GD~I~v~ 92 (323)
T PF14890_consen 64 KATPDHPFLTPDGW-KRLEELKPGDRIAVP 92 (323)
T ss_dssp EEETT-EEEECCCC-CECCC--TT-EEEEE
T ss_pred EEcCCCcEEEccCC-EEhHHhhcccccccc
Confidence 34888889999885 799999999999876
No 86
>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=32.90 E-value=1e+02 Score=24.32 Aligned_cols=57 Identities=19% Similarity=0.206 Sum_probs=33.9
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEecCCCee
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLI 189 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lTp~Hli 189 (245)
...+.+|++||.|.-.+. ++...|. |...---+|+....+. .+.+.+.|+|.-=++.
T Consensus 58 F~~L~~l~~Gd~I~l~~~-~~~~~Y~-V~~~~~v~~~~~~~~~--~~~~~~~ltLiTC~p~ 114 (127)
T cd06165 58 FSPLYKVKVGDKIYLTDK-DNVYEYK-VTSKKIVDPTRVDVID--DVPGKKLITLITCDDA 114 (127)
T ss_pred cCCHHHCcCCCEEEEEEC-CEEEEEE-EeeEEEECcccceeec--cCCCCCEEEEEecCCC
Confidence 457999999999998887 7788887 4443333444322111 1222456666555544
No 87
>cd04734 OYE_like_3_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.
Probab=31.52 E-value=64 Score=30.25 Aligned_cols=108 Identities=14% Similarity=0.053 Sum_probs=55.6
Q ss_pred cchhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC-----CCC--CCCC----cccceeeeeeEecC--CCcchHH
Q psy16496 9 TFLFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE-----GHH--ASDS----LHYEGRAVDITTSD--RDSSKYG 75 (245)
Q Consensus 9 ~~~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~-----~~~--~~~s----lh~egra~di~~s~--~~~~k~g 75 (245)
+.-+++++...+.|..|+..|+..=.-+-+.+.-+-+-. +.. ++.. .|+. ..-.+|..+ .-...|.
T Consensus 66 ~~~~l~~d~~i~~~~~l~~~vh~~g~~~~~Ql~H~G~~~~~~~~~~~~~~ps~~~~~~~~~-~~~~mt~~eI~~ii~~f~ 144 (343)
T cd04734 66 GNLNASDDEIIPGFRRLAEAVHAHGAVIMIQLTHLGRRGDGDGSWLPPLAPSAVPEPRHRA-VPKAMEEEDIEEIIAAFA 144 (343)
T ss_pred CccccCCHHHHHHHHHHHHHHHhcCCeEEEeccCCCcCcCcccCCCcccCCCCCCCCCCCC-CCCcCCHHHHHHHHHHHH
Confidence 345678899999999999999885222223332221110 000 1111 1111 011133321 2245778
Q ss_pred HHHhhhhhcCcceEEEccc-ceeeeccccccc-cccccCccccc
Q psy16496 76 LLARMAVEAGFDWVYYESR-NHIHCSVKTETT-HVNGKGAGCFT 117 (245)
Q Consensus 76 ~La~la~~aGfd~V~~~~r-~~ih~~vks~~s-~~aak~ggCFp 117 (245)
.-|+.|.++|||.|+.+.- +|+-.+--|... +-..++||++-
T Consensus 145 ~AA~ra~~aGfDgVeih~ahGyLl~qFlsp~~N~RtD~yGGsle 188 (343)
T cd04734 145 DAARRCQAGGLDGVELQAAHGHLIDQFLSPLTNRRTDEYGGSLE 188 (343)
T ss_pred HHHHHHHHcCCCEEEEccccchHHHHhhCCCcCCCCCcCCCCHH
Confidence 8899999999999986642 433222222211 12345666653
No 88
>COG5507 Uncharacterized conserved protein [Function unknown]
Probab=30.86 E-value=67 Score=25.68 Aligned_cols=30 Identities=30% Similarity=0.506 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC
Q psy16496 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE 47 (245)
Q Consensus 16 ~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~ 47 (245)
+.-+.||-++|-.|-.++. -||..|+|-.|
T Consensus 16 ~daYrk~a~~A~~v~kE~G--al~~VEc~~dD 45 (117)
T COG5507 16 KDAYRKLAAKAAPVWKEFG--ALRYVECWADD 45 (117)
T ss_pred HHHHHHHHHhhhHHHHHhC--chhhhhhcccC
Confidence 4556677777777755554 68999999887
No 89
>PHA02584 34 long tail fiber, proximal subunit; Provisional
Probab=30.61 E-value=1.7e+02 Score=32.38 Aligned_cols=166 Identities=13% Similarity=0.121 Sum_probs=91.1
Q ss_pred eeeCCCCCCCCCCcccceeeeeeE--ecCCCcchH-HHHHhhhhhcCcceEEEcccceeeeccccc-cc----------c
Q psy16496 42 EGWDEEGHHASDSLHYEGRAVDIT--TSDRDSSKY-GLLARMAVEAGFDWVYYESRNHIHCSVKTE-TT----------H 107 (245)
Q Consensus 42 ~~w~~~~~~~~~slh~egra~di~--~s~~~~~k~-g~La~la~~aGfd~V~~~~r~~ih~~vks~-~s----------~ 107 (245)
..|+.-...+..-|=|.|+.--+- ...++...+ +.-+.+..++|...+.-.+-+-|-..+..- +- .
T Consensus 169 ~~~~~T~p~s~~~fif~g~~W~~~~~~~~~~~~~v~~~~~~fq~q~g~~v~r~ts~g~I~~~LPk~aN~GD~I~t~DlD~ 248 (1229)
T PHA02584 169 ASVRITHPYSTNVFIFNGNLWQVYEAGYERRSVYVEPTGAGFQAQSGDTVFRRTSGGTITLTLPKYANHGDMITTVDLDG 248 (1229)
T ss_pred EEEEEccCCeEEEEEEcCcEEEEEeccCcccceEECCCccceeeccCcEEEEeccCceEEEEccCCCCCCCeEEEEeccc
Confidence 456555555666777788764433 333433222 222335556675555333334444333111 00 0
Q ss_pred ---ccccCcccccCCcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCCeEEec
Q psy16496 108 ---VNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMT 184 (245)
Q Consensus 108 ---~aak~ggCFpgdt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~~L~lT 184 (245)
..--.-.-||+..+..-+.|. ..|+..+-|+=++-.|. +. -.|---|-++...+-.|.. .+.++
T Consensus 249 l~~~~~~~~~vyp~~g~si~~~g~-~~~~~~~sg~G~fifd~--~~------~~W~v~dgD~~~rlr~i~~----d~~~~ 315 (1229)
T PHA02584 249 LNSVNHTTVEVYPGSGHSIGENGV-HSIESRTSGDGFFIFDS--TE------KLWRVWDGDQKVRLRVIRD----DTNLL 315 (1229)
T ss_pred cCcceEEEEEEeCCCCcCcccCce-eEEEEecccceEEEEcC--CC------ceEEEEcCCCceEEEEeec----ccccC
Confidence 011112356766666655554 67888888888877776 32 2333333334344555554 57889
Q ss_pred CCCeeEeecCCCccccCCCcceEeCCCCCCCCEEEEcc
Q psy16496 185 PSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222 (245)
Q Consensus 185 p~Hlifv~~~~~~~~~~~~~~~v~A~~v~~GD~V~v~~ 222 (245)
|+-.++|...+ .+........+-.+|..||.|.+.-
T Consensus 316 pne~v~v~~~~--~~~~~~vtlTLP~~va~GD~v~Is~ 351 (1229)
T PHA02584 316 PNEYVAVFGAN--NGTTQTVTLTLPTDVADGDRVKISM 351 (1229)
T ss_pred CCceEEEEcCC--CCCcceEEEeCCCccCCCcEEEEEh
Confidence 99988888622 2223346677899999999998743
No 90
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=29.56 E-value=2.2e+02 Score=23.16 Aligned_cols=77 Identities=10% Similarity=0.075 Sum_probs=42.9
Q ss_pred CCCCEEEEee---CCCCceeEEEEEEEEecCCCceeceEEEEeCC---CCeEEecCCCeeEeecCCCccccCCCcceEeC
Q psy16496 136 NIGDKVLTLN---TITGEMEYSEVLLFLHRDPNLVHNFVQITTES---GSLIKMTPSHLILRWHRPNAKSILNDIEYTYA 209 (245)
Q Consensus 136 ~~GDrVLa~d---~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~---g~~L~lTp~Hlifv~~~~~~~~~~~~~~~v~A 209 (245)
++||.|.+.- ...+..+-..|+.+.+.. ..|...-.+. .....++..|.|......+ ...--.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~----~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~-------~~~~~~ 69 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDG----NRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAP-------PDTDPL 69 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTT----TEEEEEETTTCTTTEEEEEEGGGEEEE-SB---------TTT-GG
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCC----CEEEEecCCCCCCCceEEeCHHHEEECCCccC-------CCCCch
Confidence 5899999853 226788888898877533 2244444432 2479999999999876111 112234
Q ss_pred CCCCCCCEEEEccC
Q psy16496 210 ERVRVNDSIIVHKN 223 (245)
Q Consensus 210 ~~v~~GD~V~v~~g 223 (245)
.+...|..||..-.
T Consensus 70 ~~f~~g~~VLAlYP 83 (130)
T PF07039_consen 70 AEFPKGTKVLALYP 83 (130)
T ss_dssp GS--TT-EEEEE-T
T ss_pred hhCCCCCEEEEECC
Confidence 55677877776543
No 91
>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=28.04 E-value=1.9e+02 Score=22.66 Aligned_cols=35 Identities=23% Similarity=0.347 Sum_probs=24.5
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCCC
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPN 165 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~ 165 (245)
...+.+|++||.|.-.+. .+...|. |.....-+++
T Consensus 59 F~~L~~l~~Gd~v~v~~~-~~~~~Y~-V~~~~~v~~~ 93 (128)
T cd00004 59 FSDLDNLKKGDKIYLTDG-GKTYVYK-VTSILTVTPT 93 (128)
T ss_pred cCCHHHCCCCCEEEEEEC-CEEEEEE-EEEEEEECCC
Confidence 457899999999998887 6677776 4444333444
No 92
>cd04747 OYE_like_5_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=27.74 E-value=16 Score=34.82 Aligned_cols=110 Identities=15% Similarity=0.052 Sum_probs=58.3
Q ss_pred hhhcHHHHHHHHHHHHHHhhhCCCceEEEEe-eeCCCCCC---------CCCCcccce----eeeeeEec--CCCcchHH
Q psy16496 12 FFCFQRLKEKLNTLAISVMNEWPGVRLRVIE-GWDEEGHH---------ASDSLHYEG----RAVDITTS--DRDSSKYG 75 (245)
Q Consensus 12 r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~-~w~~~~~~---------~~~slh~eg----ra~di~~s--~~~~~k~g 75 (245)
++-+..+.+.|++|+..|+..=.-+-+.+.- |.....+. ++..+-..+ |+ +|.. +.-...|+
T Consensus 70 ~~~~d~~i~~~~~l~d~vh~~Ga~i~~QL~H~Gr~~~~~~~~~~~~~~~~ps~~~~~~~~~p~~--mt~~eI~~ii~~f~ 147 (361)
T cd04747 70 RFHGEDALAGWKKVVDEVHAAGGKIAPQLWHVGAMRKLGTPPFPDVPPLSPSGLVGPGKPVGRE--MTEADIDDVIAAFA 147 (361)
T ss_pred ccCCHHHHHHHHHHHHHHHhcCCEEEEeccCCCCCcCcccCccCCCceeCCCCCCcCCCCCCcc--CCHHHHHHHHHHHH
Confidence 4557889999999999998762211222211 22111100 111110000 11 1111 11234778
Q ss_pred HHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccCCcEEE
Q psy16496 76 LLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTGDSTVT 123 (245)
Q Consensus 76 ~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpgdt~V~ 123 (245)
.-|+.|.+||||.|+.+- .+|+-.+--|..+ +-..++||+|-..++..
T Consensus 148 ~AA~~a~~aGfDgVeih~ahGyLl~qFLSp~~N~RtDeYGGslenR~Rf~ 197 (361)
T cd04747 148 RAAADARRLGFDGIELHGAHGYLIDQFFWAGTNRRADGYGGSLAARSRFA 197 (361)
T ss_pred HHHHHHHHcCCCEEEEecccchHHHHhcCCCCCCCCCCCCCCHHHHHHHH
Confidence 899999999999998664 3555444444333 24466788875555443
No 93
>PHA03356 tegument protein UL11; Provisional
Probab=27.34 E-value=49 Score=25.52 Aligned_cols=21 Identities=14% Similarity=0.170 Sum_probs=17.0
Q ss_pred EEEeCCCCeEEecCCCeeEee
Q psy16496 172 QITTESGSLIKMTPSHLILRW 192 (245)
Q Consensus 172 ~I~Te~g~~L~lTp~Hlifv~ 192 (245)
.|.|++|..|.||++|.=-|.
T Consensus 17 vL~Td~GEvvsLta~~fD~vd 37 (93)
T PHA03356 17 VLVTDRGETVSLTAHEFDAVD 37 (93)
T ss_pred eEEcCCCcEEEeeccccceEe
Confidence 578999999999999975444
No 94
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=27.01 E-value=45 Score=31.35 Aligned_cols=50 Identities=16% Similarity=0.097 Sum_probs=32.8
Q ss_pred cchHHHHHhhhhhcCcceEEEcc-cceeeeccccccc-cccccCcccccCCc
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYES-RNHIHCSVKTETT-HVNGKGAGCFTGDS 120 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~-r~~ih~~vks~~s-~~aak~ggCFpgdt 120 (245)
...|+.-|+.|.++|||.|+.+- .+|+-.+--|..+ +-..++||++-..+
T Consensus 141 i~~f~~aA~~a~~aGfDgVeih~ahGyLl~qFlSp~~N~RtD~yGGslenR~ 192 (337)
T PRK13523 141 VLAFKQAAVRAKEAGFDVIEIHGAHGYLINEFLSPLSNKRTDEYGGSPENRY 192 (337)
T ss_pred HHHHHHHHHHHHHcCCCEEEEccccchHHHHhcCCccCCcCCCCCCCHHHHH
Confidence 45788999999999999998663 3554444444422 24566777754433
No 95
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=26.81 E-value=39 Score=25.96 Aligned_cols=40 Identities=33% Similarity=0.385 Sum_probs=27.8
Q ss_pred ccceeeeccccccccccccCcccccCCcEEEeeCCCceec--cCCCCCCEEEEe
Q psy16496 93 SRNHIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINI--TDLNIGDKVLTL 144 (245)
Q Consensus 93 ~r~~ih~~vks~~s~~aak~ggCFpgdt~V~l~dG~~k~I--~dL~~GDrVLa~ 144 (245)
+++|+..++|-+. |.-.+.||.... ..+ .+|+.||+|++.
T Consensus 37 ~~gh~YftLkD~~---a~i~~~~~~~~~---------~~i~~~~l~~G~~V~v~ 78 (99)
T PF13742_consen 37 SSGHVYFTLKDEE---ASISCVIFRSRA---------RRIRGFDLKDGDKVLVR 78 (99)
T ss_pred CCceEEEEEEcCC---cEEEEEEEHHHH---------hhCCCCCCCCCCEEEEE
Confidence 4588888888753 466667775443 223 589999999984
No 96
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=26.14 E-value=69 Score=24.55 Aligned_cols=24 Identities=29% Similarity=0.566 Sum_probs=16.7
Q ss_pred eCCCceeccCCCCCCEEEEeeCCCCc
Q psy16496 125 DNHKTINITDLNIGDKVLTLNTITGE 150 (245)
Q Consensus 125 ~dG~~k~I~dL~~GDrVLa~d~~~G~ 150 (245)
.+|...++ ++++||+|+--.. .|.
T Consensus 49 ~~g~~~~~-~vk~GD~Vl~~~~-~g~ 72 (93)
T cd00320 49 ENGERVPL-SVKVGDKVLFPKY-AGT 72 (93)
T ss_pred CCCCCccc-cccCCCEEEECCC-Cce
Confidence 35655555 8999999996554 453
No 97
>cd02929 TMADH_HD_FMN Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain. TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a symetrical dimer with each subunit containing one 4Fe-4S cluster and one FMN cofactor. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN which is bent by ~25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This modification of the conformation of the flavin is thought to facilitate catalysis.The closely related histamine dehydrogenase catalyzes oxidative deamination of histamine.
Probab=26.14 E-value=22 Score=33.79 Aligned_cols=109 Identities=19% Similarity=0.153 Sum_probs=57.2
Q ss_pred hhhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC--------CC--CCCCCcccc------eeeeeeEecC--CCcc
Q psy16496 11 LFFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE--------GH--HASDSLHYE------GRAVDITTSD--RDSS 72 (245)
Q Consensus 11 ~r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~--------~~--~~~~slh~e------gra~di~~s~--~~~~ 72 (245)
-.+.+...-+.|+.|+..|+.. |.++ +..=|-.- +. -++.++-.. ...-.+|..+ .-.+
T Consensus 74 ~~l~~d~~i~~~~~l~~~vh~~--G~~i-~~QL~H~G~~~~~~~~~~~~~~ps~~~~~~~~~~~~~p~~mt~~eI~~ii~ 150 (370)
T cd02929 74 ARLWDDGDIRNLAAMTDAVHKH--GALA-GIELWHGGAHAPNRESRETPLGPSQLPSEFPTGGPVQAREMDKDDIKRVRR 150 (370)
T ss_pred cCcCCHHHHHHHHHHHHHHHHC--CCeE-EEecccCCCCCCccCCCCCccCCCCCCCCccccCCCCCccCCHHHHHHHHH
Confidence 3466888899999999999875 3232 11111110 00 011111100 0011122221 2245
Q ss_pred hHHHHHhhhhhcCcceEEEccc-ceeeeccccccc-cccccCcccccCCcEE
Q psy16496 73 KYGLLARMAVEAGFDWVYYESR-NHIHCSVKTETT-HVNGKGAGCFTGDSTV 122 (245)
Q Consensus 73 k~g~La~la~~aGfd~V~~~~r-~~ih~~vks~~s-~~aak~ggCFpgdt~V 122 (245)
.|+.-|+.|.++|||.|+.+.- +|+-.+--|..+ +...++||++-..++.
T Consensus 151 ~f~~AA~ra~~aGfDgVEih~ahGyLl~QFlSp~~N~RtD~yGGslenR~Rf 202 (370)
T cd02929 151 WYVDAALRARDAGFDIVYVYAAHGYLPLQFLLPRYNKRTDEYGGSLENRARF 202 (370)
T ss_pred HHHHHHHHHHHcCCCEEEEcccccchHHHhhCccccCCccccCCChHhhhHH
Confidence 7889999999999999987643 444333333321 2445678877444443
No 98
>PRK11479 hypothetical protein; Provisional
Probab=25.82 E-value=59 Score=30.10 Aligned_cols=30 Identities=20% Similarity=0.159 Sum_probs=22.0
Q ss_pred cceEeCCCCCCCCEEEEccCCccccceecc
Q psy16496 204 IEYTYAERVRVNDSIIVHKNGKARNGIQRG 233 (245)
Q Consensus 204 ~~~v~A~~v~~GD~V~v~~g~~~~~~~~~G 233 (245)
...|-.+++++||.|+...++..++.|+.+
T Consensus 57 g~~Vs~~~LqpGDLVFfst~t~~S~~Ik~~ 86 (274)
T PRK11479 57 IKEITAPDLKPGDLLFSSSLGVTSFGIRVF 86 (274)
T ss_pred CcccChhhCCCCCEEEEecCCccccceecc
Confidence 346788999999999987766555555433
No 99
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=25.73 E-value=58 Score=27.71 Aligned_cols=20 Identities=30% Similarity=0.531 Sum_probs=16.4
Q ss_pred cCCCCCCEEEEeeCCCCceeE
Q psy16496 133 TDLNIGDKVLTLNTITGEMEY 153 (245)
Q Consensus 133 ~dL~~GDrVLa~d~~~G~~~y 153 (245)
.+|++||.||.+|+ ++++..
T Consensus 109 ~~iR~~dEvlVVne-~d~LlA 128 (155)
T COG1370 109 EEIRAGDEVLVVNE-DDELLA 128 (155)
T ss_pred cccCCCCeEEEECC-CCcEEE
Confidence 68999999999998 766543
No 100
>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=25.44 E-value=1.9e+02 Score=22.97 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=22.0
Q ss_pred ceeccCCCCCCEEEEeeCCCCceeEEEEEEE
Q psy16496 129 TINITDLNIGDKVLTLNTITGEMEYSEVLLF 159 (245)
Q Consensus 129 ~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~f 159 (245)
.-.|.+|+.||.|.-... .+...|.-+-.+
T Consensus 61 F~~L~~l~~gd~i~l~t~-~~~~~Y~V~~~~ 90 (131)
T cd05827 61 FTDLDKLKKGDKFYIHVL-GETLAYQVDQIE 90 (131)
T ss_pred cCCHHHCCCCCEEEEEEC-CeEEEEEEEEEE
Confidence 357999999999987666 677788744333
No 101
>PF04203 Sortase: Sortase family; InterPro: IPR005754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=24.81 E-value=97 Score=24.09 Aligned_cols=36 Identities=28% Similarity=0.420 Sum_probs=25.0
Q ss_pred CceeccCCCCCCEEEEeeCCCCce-eEEEEEEEEecCCC
Q psy16496 128 KTINITDLNIGDKVLTLNTITGEM-EYSEVLLFLHRDPN 165 (245)
Q Consensus 128 ~~k~I~dL~~GDrVLa~d~~~G~~-~yS~Vi~fl~r~~~ 165 (245)
-...+.++++||.|.-.++ .|+. .|. |.....-++.
T Consensus 54 ~F~~L~~~~~gd~i~~~~~-~g~~~~Y~-V~~~~~v~~~ 90 (128)
T PF04203_consen 54 MFSNLNKLKKGDEIYLTTP-DGKTYEYR-VTSVKIVDPD 90 (128)
T ss_dssp TTCGGGGGHTT-EEEEEET-SSEEEEEE-EEEEEEECTT
T ss_pred ccccccccCCCCEEEEEEe-cCEEEEEE-EEEEEEEcCC
Confidence 4457999999999999997 6877 776 5554433433
No 102
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=24.79 E-value=67 Score=24.17 Aligned_cols=15 Identities=13% Similarity=-0.064 Sum_probs=11.5
Q ss_pred cceecccCCCCCCCC
Q psy16496 228 NGIQRGAPIPPPRPK 242 (245)
Q Consensus 228 ~~~~~G~y~P~~~~~ 242 (245)
-..+-|+|.|++.++
T Consensus 31 ~iE~lG~YnP~~~~~ 45 (78)
T TIGR00002 31 YIEELGFYNPLTKES 45 (78)
T ss_pred ceeEeeeccCCCCCc
Confidence 356789999998754
No 103
>PF15084 DUF4550: Domain of unknown function (DUF4550)
Probab=24.71 E-value=70 Score=25.32 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=24.9
Q ss_pred ccccCCcEEEeeCCCceeccCCCCCCEEE
Q psy16496 114 GCFTGDSTVTLDNHKTINITDLNIGDKVL 142 (245)
Q Consensus 114 gCFpgdt~V~l~dG~~k~I~dL~~GDrVL 142 (245)
-||+..|.|.+++|. |-+.--+.||.|.
T Consensus 24 V~f~~~AKvF~e~~~-K~~~~w~~gd~~W 51 (99)
T PF15084_consen 24 VVFGNVAKVFLENES-KTVKPWHEGDQVW 51 (99)
T ss_pred EEecceeeEEEcCCc-eEeeeEecCCEEE
Confidence 699999999999998 7777777999886
No 104
>PF06291 Lambda_Bor: Bor protein; InterPro: IPR010438 This family consists of several Bacteriophage lambda Bor and Escherichia coli Iss proteins. Expression of bor significantly increases the survival of the E. coli host cell in animal serum. This property is a well known bacterial virulence determinant indeed, bor and its adjacent sequences are highly homologous to the iss serum resistance locus of the plasmid ColV2-K94, which confers virulence in animals. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis [].
Probab=24.64 E-value=42 Score=26.31 Aligned_cols=50 Identities=20% Similarity=0.122 Sum_probs=30.6
Q ss_pred cCCCeeEeecCCCccccCCCcceEeCCCCCCC-CEEE-EccC----CccccceecccCCCCCC
Q psy16496 184 TPSHLILRWHRPNAKSILNDIEYTYAERVRVN-DSII-VHKN----GKARNGIQRGAPIPPPR 240 (245)
Q Consensus 184 Tp~Hlifv~~~~~~~~~~~~~~~v~A~~v~~G-D~V~-v~~g----~~~~~~~~~G~y~P~~~ 240 (245)
+-.|.+|++. .....-+-|.++--| |.|. +... ..+-..+.-|||+|.+-
T Consensus 36 ~~~~~ffi~G-------l~q~~~vdaa~vCgg~~~v~kvetq~Tf~ngLl~~iT~GIYTP~~~ 91 (97)
T PF06291_consen 36 TVSHHFFISG-------LGQSKEVDAAQVCGGAEKVAKVETQQTFLNGLLSVITLGIYTPRTT 91 (97)
T ss_pred eeecceEEEe-------cCCcccccHHHhcCCCccEEEEEEeeehhhhhhhhEEEeeecCcEE
Confidence 3378888875 123345667777665 3343 3221 23457888999999864
No 105
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=24.18 E-value=3.7e+02 Score=21.46 Aligned_cols=38 Identities=24% Similarity=0.383 Sum_probs=25.1
Q ss_pred CcEEEeeCCCceeccCCCCCCEEEEeeCCCCceeEEEEEEEEecCC
Q psy16496 119 DSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDP 164 (245)
Q Consensus 119 dt~V~l~dG~~k~I~dL~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~ 164 (245)
-+.|.+.||. |+.||.|.+-.. .|.. -..|=+.++-.+
T Consensus 17 t~dvIl~~Gt------L~~GD~Iv~g~~-~Gpi-~tkVRaLl~~~~ 54 (110)
T cd03703 17 TIDVILYDGT------LREGDTIVVCGL-NGPI-VTKVRALLKPQP 54 (110)
T ss_pred EEEEEEECCe------EecCCEEEEccC-CCCc-eEEEeEecCCCC
Confidence 3568888886 799999998766 5643 334545554443
No 106
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=24.00 E-value=58 Score=24.36 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=14.1
Q ss_pred eCCCCCCCCEEEEccCC
Q psy16496 208 YAERVRVNDSIIVHKNG 224 (245)
Q Consensus 208 ~A~~v~~GD~V~v~~g~ 224 (245)
+-.++++||+|++..|-
T Consensus 32 lv~~~~vGD~VLVH~G~ 48 (76)
T TIGR00074 32 LVGEVKVGDYVLVHVGF 48 (76)
T ss_pred eeCCCCCCCEEEEecCh
Confidence 44789999999998874
No 107
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=23.40 E-value=53 Score=23.91 Aligned_cols=17 Identities=29% Similarity=0.434 Sum_probs=12.1
Q ss_pred eCCCCCCCCEEEEccCC
Q psy16496 208 YAERVRVNDSIIVHKNG 224 (245)
Q Consensus 208 ~A~~v~~GD~V~v~~g~ 224 (245)
+-.++++||+|++..|-
T Consensus 34 lv~~v~~Gd~VLVHaG~ 50 (68)
T PF01455_consen 34 LVPDVKVGDYVLVHAGF 50 (68)
T ss_dssp TCTSB-TT-EEEEETTE
T ss_pred EeCCCCCCCEEEEecCh
Confidence 45669999999998874
No 108
>PF11094 UL11: Membrane-associated tegument protein; InterPro: IPR024351 The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment []. UL11 is acylated, which is crucial for lipid raft association [].
Probab=22.76 E-value=57 Score=21.57 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=15.1
Q ss_pred eEEEEeCCCCeEEecCCCe
Q psy16496 170 FVQITTESGSLIKMTPSHL 188 (245)
Q Consensus 170 Fv~I~Te~g~~L~lTp~Hl 188 (245)
--+|.|++|..|.|++++.
T Consensus 15 ~N~LvT~~Ge~vsL~a~~F 33 (39)
T PF11094_consen 15 RNVLVTHSGETVSLDAEEF 33 (39)
T ss_pred cCEEEccCCeEEEeChhhc
Confidence 3467899999999998763
No 109
>cd02930 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provi
Probab=22.58 E-value=1.1e+02 Score=28.74 Aligned_cols=101 Identities=15% Similarity=0.168 Sum_probs=52.5
Q ss_pred hhhcHHHHHHHHHHHHHHhhhCCCceE--EEEeeeCCCCC-------CCCCCcccc-eeeeeeEecC--CCcchHHHHHh
Q psy16496 12 FFCFQRLKEKLNTLAISVMNEWPGVRL--RVIEGWDEEGH-------HASDSLHYE-GRAVDITTSD--RDSSKYGLLAR 79 (245)
Q Consensus 12 r~m~~~~~~~l~~l~~~v~~~w~~v~l--rv~~~w~~~~~-------~~~~slh~e-gra~di~~s~--~~~~k~g~La~ 79 (245)
.+.++.+.+.|+.|+..|+.. |.++ .+.-+-+...+ ..+.+.+++ =|+ +|..+ .-...|..-|+
T Consensus 69 ~~~~~~~i~~~~~l~~~vh~~--g~~~~~QL~h~G~~~~~~~~~~ps~~~~~~~~~~p~~--mt~~eI~~i~~~f~~aA~ 144 (353)
T cd02930 69 VLNSPRQAAGHRLITDAVHAE--GGKIALQILHAGRYAYHPLCVAPSAIRAPINPFTPRE--LSEEEIEQTIEDFARCAA 144 (353)
T ss_pred ccCCHHHHHHHHHHHHHHHHc--CCEEEeeccCCCCCCCCCCCcCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHH
Confidence 356788999999999999875 3332 22221111100 001112211 111 22221 23457888899
Q ss_pred hhhhcCcceEEEcc-cceeeecccccc-ccccccCcccc
Q psy16496 80 MAVEAGFDWVYYES-RNHIHCSVKTET-THVNGKGAGCF 116 (245)
Q Consensus 80 la~~aGfd~V~~~~-r~~ih~~vks~~-s~~aak~ggCF 116 (245)
.|.++|||.|+.+. .+|+-.+--|.. .+-..++||.+
T Consensus 145 ~a~~aGfDgVeih~ahGyLl~qFlsp~~N~RtD~yGGsl 183 (353)
T cd02930 145 LAREAGYDGVEIMGSEGYLINQFLAPRTNKRTDEWGGSF 183 (353)
T ss_pred HHHHcCCCEEEEecccchHHHHhcCCccCCCcCccCCCH
Confidence 99999999998643 233332322321 11345566654
No 110
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=22.19 E-value=4.4e+02 Score=22.07 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=8.4
Q ss_pred cCCCCCCEEEEeeC
Q psy16496 133 TDLNIGDKVLTLNT 146 (245)
Q Consensus 133 ~dL~~GDrVLa~d~ 146 (245)
++++.||-|....+
T Consensus 59 ~~~~~GDIVvf~~~ 72 (158)
T TIGR02228 59 NDIQVGDVITYKSP 72 (158)
T ss_pred CCCCCCCEEEEEEC
Confidence 45666666665554
No 111
>cd04735 OYE_like_4_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=22.08 E-value=63 Score=30.36 Aligned_cols=111 Identities=14% Similarity=0.124 Sum_probs=56.7
Q ss_pred hhhcHHHHHHHHHHHHHHhhhCCCceEEEEeeeCCC------CC--CCCCCc--ccc-ee-eeeeEecC--CCcchHHHH
Q psy16496 12 FFCFQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEE------GH--HASDSL--HYE-GR-AVDITTSD--RDSSKYGLL 77 (245)
Q Consensus 12 r~m~~~~~~~l~~l~~~v~~~w~~v~lrv~~~w~~~------~~--~~~~sl--h~e-gr-a~di~~s~--~~~~k~g~L 77 (245)
.++++.+-+.+..|+..|+..=.-+-+.+.-+-+.. +. -++... .+. +. .-.+|..+ .-...|..=
T Consensus 70 ~~~~d~~i~~~~~l~~~vh~~G~~i~~QL~h~G~~~~~~~~~~~~~~~ps~~~~~~~~~~~p~~mt~~eI~~ii~~f~~a 149 (353)
T cd04735 70 SADDDSDIPGLRKLAQAIKSKGAKAILQIFHAGRMANPALVPGGDVVSPSAIAAFRPGAHTPRELTHEEIEDIIDAFGEA 149 (353)
T ss_pred eecChhhhHHHHHHHHHHHhCCCeEEEEecCCCCCCCccccCCCceecCCCCcccCCCCCCCccCCHHHHHHHHHHHHHH
Confidence 567888999999999999875322222222111100 00 011111 011 10 11123322 234688889
Q ss_pred HhhhhhcCcceEEEcc-cceeeecccccccc-ccccCcccccCCcEE
Q psy16496 78 ARMAVEAGFDWVYYES-RNHIHCSVKTETTH-VNGKGAGCFTGDSTV 122 (245)
Q Consensus 78 a~la~~aGfd~V~~~~-r~~ih~~vks~~s~-~aak~ggCFpgdt~V 122 (245)
|+.|.++|||.|+.+- .+|+-.+--|..++ -..++||.+-..+++
T Consensus 150 A~~a~~aGfDgVeih~ahGyLl~qFlsp~~N~R~D~yGGslenR~r~ 196 (353)
T cd04735 150 TRRAIEAGFDGVEIHGANGYLIQQFFSPHSNRRTDEWGGSLENRMRF 196 (353)
T ss_pred HHHHHHcCCCEEEEccccchHHHHhcCCccCCCCcccCCcHHHHHHH
Confidence 9999999999998653 34433333333221 345677776444433
No 112
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=22.03 E-value=60 Score=27.72 Aligned_cols=25 Identities=12% Similarity=0.061 Sum_probs=19.2
Q ss_pred CcceEeCCCCCCCCEEEEccCCccc
Q psy16496 203 DIEYTYAERVRVNDSIIVHKNGKAR 227 (245)
Q Consensus 203 ~~~~v~A~~v~~GD~V~v~~g~~~~ 227 (245)
....+.+++|++||.|.+..|...+
T Consensus 43 ~~~~i~~~~L~~GDiI~l~~g~~vP 67 (230)
T PF00122_consen 43 RWQKIPSSELVPGDIIILKAGDIVP 67 (230)
T ss_dssp EEEEEEGGGT-TTSEEEEETTEBES
T ss_pred ccccchHhhccceeeeecccccccc
Confidence 3567899999999999998876543
No 113
>PRK09864 putative peptidase; Provisional
Probab=21.93 E-value=1.9e+02 Score=27.66 Aligned_cols=51 Identities=18% Similarity=0.339 Sum_probs=39.0
Q ss_pred CCCCEEEEeeCCCCceeEEEEEEEEecCCCceeceEEEEeCCCC----eEEecCCCee
Q psy16496 136 NIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQITTESGS----LIKMTPSHLI 189 (245)
Q Consensus 136 ~~GDrVLa~d~~~G~~~yS~Vi~fl~r~~~~~~~Fv~I~Te~g~----~L~lTp~Hli 189 (245)
.+|=.|..+++ +|.+.++++=-|..+.. ..+-+.|.|.+|. .+-.+|-|+.
T Consensus 64 evG~mV~~I~~-~G~l~~~~lGG~~~~~l--~~q~V~i~t~~g~~v~GVig~~~~H~~ 118 (356)
T PRK09864 64 EVGFMVTHIDE-SGFLRFTTIGGWWNQSM--LNHRVTIRTHKGVKIPGVIGSVAPHAL 118 (356)
T ss_pred ccCEEEEEECC-CCeEEEEeCCCcCcccc--CCCEEEEEeCCCCEEEEEEeCCccccC
Confidence 37899999999 99999998766665552 3458889998874 3667888886
No 114
>cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=21.70 E-value=68 Score=29.25 Aligned_cols=47 Identities=21% Similarity=0.236 Sum_probs=29.4
Q ss_pred cchHHHHHhhhhhcCcceEEEccc-ceeeeccccc--cccccccCcccccC
Q psy16496 71 SSKYGLLARMAVEAGFDWVYYESR-NHIHCSVKTE--TTHVNGKGAGCFTG 118 (245)
Q Consensus 71 ~~k~g~La~la~~aGfd~V~~~~r-~~ih~~vks~--~s~~aak~ggCFpg 118 (245)
...|..-|+.|.++|||.|+.+-- +|+-.+.-|. +. ...++||++-.
T Consensus 140 i~~~~~aA~~a~~aGfDgveih~~~gyL~~qFlsp~~n~-R~d~yGgs~en 189 (327)
T cd02803 140 IEDFAAAARRAKEAGFDGVEIHGAHGYLLSQFLSPYTNK-RTDEYGGSLEN 189 (327)
T ss_pred HHHHHHHHHHHHHcCCCEEEEcchhhhHHHHhcCccccC-CCcccCCCHHH
Confidence 457888999999999999986542 4332222222 22 34566777643
No 115
>PRK02268 hypothetical protein; Provisional
Probab=21.47 E-value=1.5e+02 Score=24.70 Aligned_cols=22 Identities=14% Similarity=0.238 Sum_probs=18.0
Q ss_pred EeeCCCceeccCCCCCCEEEEe
Q psy16496 123 TLDNHKTINITDLNIGDKVLTL 144 (245)
Q Consensus 123 ~l~dG~~k~I~dL~~GDrVLa~ 144 (245)
.+..|...||+-+++||+|+=.
T Consensus 24 qv~hgK~apl~RmkpGD~ivyY 45 (141)
T PRK02268 24 QVCHGKAAPLRRMKPGDWIIYY 45 (141)
T ss_pred EeCCCccchhhcCCCCCEEEEE
Confidence 4567888899999999999743
No 116
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=21.34 E-value=1.7e+02 Score=21.96 Aligned_cols=9 Identities=44% Similarity=0.527 Sum_probs=7.3
Q ss_pred CCCCCEEEE
Q psy16496 135 LNIGDKVLT 143 (245)
Q Consensus 135 L~~GDrVLa 143 (245)
+.+||.|+.
T Consensus 47 I~~GD~V~V 55 (75)
T COG0361 47 ILPGDVVLV 55 (75)
T ss_pred eCCCCEEEE
Confidence 679999975
No 117
>COG0503 Apt Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]
Probab=20.30 E-value=1.5e+02 Score=25.20 Aligned_cols=89 Identities=26% Similarity=0.267 Sum_probs=45.8
Q ss_pred eeeEecCCCcchH----HHHHhhhhhcCcceE-EEcccceeeecccccccc---ccccCcccccCCcEE---EeeCC-C-
Q psy16496 62 VDITTSDRDSSKY----GLLARMAVEAGFDWV-YYESRNHIHCSVKTETTH---VNGKGAGCFTGDSTV---TLDNH-K- 128 (245)
Q Consensus 62 ~di~~s~~~~~k~----g~La~la~~aGfd~V-~~~~r~~ih~~vks~~s~---~aak~ggCFpgdt~V---~l~dG-~- 128 (245)
.|++..+.+...+ +.+++...+.|+|.| ..+.++++....-+.... .-++..+=.|.++.+ .++.| .
T Consensus 26 ~d~~~~~~~~~~~~~~i~~~~~~~~~~~id~Iv~iea~Gi~~a~~vA~~Lgvp~v~vRK~~kl~~~~~~~~~~~~~~~~~ 105 (179)
T COG0503 26 VDITLLLGDPELLAKLIDELAERYKDDGIDKIVTIEARGIPLAAAVALELGVPFVPVRKKGKLPEESVVETYYLEYGSET 105 (179)
T ss_pred EecchhhcCcHHHHHHHHHHHHHhcccCCCEEEEEccccchhHHHHHHHhCCCEEEEEecCCCCCcceeEEEEEeccceE
Confidence 4556665555433 466777778889977 577788666333222110 111111111222211 12222 1
Q ss_pred -ceeccCCCCCCEEEEeeC--CCCc
Q psy16496 129 -TINITDLNIGDKVLTLNT--ITGE 150 (245)
Q Consensus 129 -~k~I~dL~~GDrVLa~d~--~~G~ 150 (245)
..+-..|++||+|+-+|+ .||.
T Consensus 106 l~~~~~~l~~G~rVlIVDDllaTGg 130 (179)
T COG0503 106 LELHKDALKPGDRVLIVDDLLATGG 130 (179)
T ss_pred EEEEhhhCCCCCEEEEEecchhcCh
Confidence 123456779999999996 2554
No 118
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=20.16 E-value=60 Score=33.95 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=22.3
Q ss_pred cCCcEEEeeCC--CceeccCCCCCCEEEEe
Q psy16496 117 TGDSTVTLDNH--KTINITDLNIGDKVLTL 144 (245)
Q Consensus 117 pgdt~V~l~dG--~~k~I~dL~~GDrVLa~ 144 (245)
|..+++...|| ..+|++||++||.|+-.
T Consensus 210 p~~A~~~~~~~~~~~v~v~~v~~GD~v~Vr 239 (713)
T COG2217 210 PKTATVVRGDGEEEEVPVEEVQVGDIVLVR 239 (713)
T ss_pred CCEEEEEecCCcEEEEEHHHCCCCCEEEEC
Confidence 55565777777 67799999999999864
Done!