Query 039205
Match_columns 158
No_of_seqs 130 out of 680
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 07:20:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039205.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039205hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1546 Metacaspase involved i 100.0 5.8E-31 1.3E-35 220.9 10.7 138 1-155 111-337 (362)
2 PF00656 Peptidase_C14: Caspas 99.8 4.6E-20 1E-24 147.2 10.9 130 7-155 44-229 (248)
3 PF01650 Peptidase_C13: Peptid 98.9 4.8E-09 1E-13 86.9 8.3 110 8-156 79-233 (256)
4 cd00032 CASc Caspase, interleu 98.7 2.7E-07 5.9E-12 75.3 12.5 130 7-157 52-218 (243)
5 COG4249 Uncharacterized protei 98.7 1.5E-08 3.3E-13 88.2 3.4 101 6-138 111-257 (380)
6 smart00115 CASc Caspase, inter 98.6 9.6E-07 2.1E-11 72.2 13.4 127 7-157 50-214 (241)
7 PF14538 Raptor_N: Raptor N-te 98.0 3.9E-06 8.4E-11 64.8 3.3 46 7-53 70-151 (154)
8 KOG1517 Guanine nucleotide bin 95.7 0.015 3.2E-07 56.6 5.0 32 8-40 167-198 (1387)
9 KOG1348 Asparaginyl peptidases 94.7 0.023 5E-07 49.8 2.6 45 9-53 125-213 (477)
10 COG4249 Uncharacterized protei 93.3 0.056 1.2E-06 47.4 2.3 30 11-40 49-78 (380)
11 KOG1349 Gpi-anchor transamidas 92.6 0.6 1.3E-05 39.3 7.3 87 26-151 136-259 (309)
12 PF12770 CHAT: CHAT domain 92.3 0.12 2.7E-06 41.9 3.0 32 124-157 237-268 (287)
13 COG5206 GPI8 Glycosylphosphati 91.7 0.73 1.6E-05 39.1 6.9 55 85-152 203-260 (382)
14 KOG1321 Protoheme ferro-lyase 80.5 2 4.4E-05 37.3 3.5 35 6-40 197-237 (395)
15 PF01364 Peptidase_C25: Peptid 78.2 1.9 4.2E-05 37.0 2.8 24 9-40 226-249 (378)
16 COG0648 Nfo Endonuclease IV [D 77.0 3.1 6.7E-05 35.2 3.6 41 7-48 116-179 (280)
17 PF01878 EVE: EVE domain; Int 59.4 8.9 0.00019 28.4 2.5 17 21-37 36-52 (143)
18 KOG3425 Uncharacterized conser 59.0 11 0.00024 28.3 2.9 25 15-39 12-36 (128)
19 PF03568 Peptidase_C50: Peptid 53.2 20 0.00044 31.2 4.1 25 7-40 295-319 (383)
20 TIGR02219 phage_NlpC_fam putat 51.9 12 0.00027 27.6 2.3 14 23-36 75-88 (134)
21 PF13660 DUF4147: Domain of un 49.5 19 0.0004 29.8 3.1 36 8-43 94-131 (238)
22 COG1350 Predicted alternative 48.5 22 0.00047 31.4 3.4 12 29-40 405-416 (432)
23 PRK00809 hypothetical protein; 47.5 19 0.00041 27.3 2.7 20 20-39 30-50 (144)
24 COG1448 TyrB Aspartate/tyrosin 45.7 28 0.0006 31.0 3.7 31 16-55 160-190 (396)
25 COG2194 Predicted membrane-ass 45.5 29 0.00063 32.1 4.0 28 20-47 434-463 (555)
26 PF00254 FKBP_C: FKBP-type pep 45.4 16 0.00034 24.6 1.8 23 24-46 4-28 (94)
27 PF07317 YcgR: Flagellar regul 44.0 37 0.0008 24.2 3.6 40 10-53 6-60 (108)
28 TIGR01361 DAHP_synth_Bsub phos 43.9 48 0.001 27.4 4.8 42 9-51 143-207 (260)
29 PLN02895 phosphoacetylglucosam 42.8 11 0.00025 34.8 1.0 24 20-44 374-399 (562)
30 COG2947 Uncharacterized conser 41.4 24 0.00053 27.3 2.4 18 20-37 37-54 (156)
31 PRK00139 murE UDP-N-acetylmura 40.7 28 0.0006 30.8 3.1 28 13-40 409-436 (460)
32 PF12047 DNMT1-RFD: Cytosine s 39.6 33 0.00072 25.5 2.9 30 124-153 113-145 (146)
33 PTZ00302 N-acetylglucosamine-p 39.2 14 0.0003 34.4 0.9 25 20-45 406-432 (585)
34 COG0299 PurN Folate-dependent 39.1 14 0.00029 29.9 0.7 22 30-51 2-26 (200)
35 PF05066 HARE-HTH: HB1, ASXL, 37.9 39 0.00086 21.9 2.8 28 127-154 2-30 (72)
36 COG2379 GckA Putative glycerat 37.4 37 0.0008 30.3 3.2 26 20-45 104-129 (422)
37 TIGR00095 RNA methyltransferas 37.1 65 0.0014 25.1 4.3 37 4-40 26-62 (189)
38 PRK14022 UDP-N-acetylmuramoyla 37.1 32 0.0007 30.5 2.9 26 13-40 430-456 (481)
39 PF10557 Cullin_Nedd8: Cullin 36.4 29 0.00063 22.6 1.9 29 128-156 9-37 (68)
40 COG2830 Uncharacterized protei 35.5 37 0.00079 27.2 2.6 16 25-40 7-22 (214)
41 COG3376 HoxN High-affinity nic 34.6 46 0.00099 28.8 3.2 31 12-42 70-101 (342)
42 PF06672 DUF1175: Protein of u 34.5 24 0.00052 28.9 1.5 13 22-34 133-145 (216)
43 PF14338 Mrr_N: Mrr N-terminal 33.1 82 0.0018 21.5 3.9 28 128-155 5-33 (92)
44 PRK06260 threonine synthase; V 32.6 73 0.0016 27.7 4.4 33 8-40 334-368 (397)
45 KOG4530 Predicted flavoprotein 32.3 67 0.0014 25.5 3.6 28 13-40 104-131 (199)
46 PF00877 NLPC_P60: NlpC/P60 fa 32.1 27 0.00058 24.1 1.3 14 22-35 49-62 (105)
47 PRK14533 groES co-chaperonin G 32.0 28 0.0006 24.5 1.3 13 24-36 53-66 (91)
48 PRK15084 formate hydrogenlyase 31.5 26 0.00057 26.5 1.2 16 32-47 28-46 (133)
49 PRK07116 flavodoxin; Provision 31.5 32 0.00069 25.9 1.7 12 29-40 4-15 (160)
50 PF09791 Oxidored-like: Oxidor 31.3 19 0.00042 22.5 0.4 9 43-51 16-24 (48)
51 PF13404 HTH_AsnC-type: AsnC-t 31.0 73 0.0016 18.9 2.9 24 128-151 4-27 (42)
52 cd03768 SR_ResInv Serine Recom 31.0 55 0.0012 23.0 2.8 20 15-34 42-61 (126)
53 COG3536 Uncharacterized protei 31.0 39 0.00084 25.0 2.0 35 119-153 77-111 (120)
54 KOG0549 FKBP-type peptidyl-pro 31.0 34 0.00075 27.4 1.8 28 23-50 83-112 (188)
55 PRK05638 threonine synthase; V 30.3 85 0.0018 27.8 4.4 33 8-40 322-356 (442)
56 PRK10838 spr outer membrane li 30.2 32 0.0007 27.4 1.6 15 23-37 127-141 (190)
57 PF07450 HycH: Formate hydroge 30.1 28 0.00061 26.3 1.1 16 32-47 26-44 (131)
58 cd03767 SR_Res_par Serine reco 29.8 51 0.0011 24.5 2.6 20 15-34 47-66 (146)
59 PF07736 CM_1: Chorismate muta 29.6 68 0.0015 23.8 3.1 43 9-53 13-61 (118)
60 PRK09781 hypothetical protein; 29.1 7.3 0.00016 30.1 -2.2 31 85-130 52-82 (181)
61 PRK13413 mpi multiple promoter 28.6 46 0.00099 25.9 2.2 20 16-35 50-69 (200)
62 PF02671 PAH: Paired amphipath 28.5 1.2E+02 0.0026 17.9 3.7 26 131-156 6-33 (47)
63 PRK05569 flavodoxin; Provision 28.4 39 0.00085 24.4 1.7 12 29-40 3-14 (141)
64 TIGR03595 Obg_CgtA_exten Obg f 28.2 50 0.0011 21.8 2.0 12 23-34 52-63 (69)
65 TIGR02594 conserved hypothetic 27.8 34 0.00073 25.4 1.2 17 21-37 70-86 (129)
66 PRK07591 threonine synthase; V 27.6 1E+02 0.0022 27.2 4.4 32 9-40 358-391 (421)
67 PF07137 VDE: Violaxanthin de- 27.5 38 0.00081 27.4 1.5 14 26-39 128-141 (198)
68 PF11132 SplA: Transcriptional 27.0 50 0.0011 22.6 1.8 14 23-36 4-17 (75)
69 PRK11560 phosphoethanolamine t 26.8 53 0.0011 30.4 2.5 27 18-44 445-471 (558)
70 PF13768 VWA_3: von Willebrand 26.7 1.6E+02 0.0035 21.2 4.8 29 12-40 18-46 (155)
71 PRK10331 L-fuculokinase; Provi 26.7 67 0.0015 28.4 3.1 30 11-40 53-82 (470)
72 PF00884 Sulfatase: Sulfatase; 26.4 86 0.0019 24.7 3.5 31 16-46 222-256 (308)
73 PF04863 EGF_alliinase: Alliin 26.3 22 0.00048 23.0 -0.0 12 33-44 17-28 (56)
74 PLN02618 tryptophan synthase, 26.2 1.1E+02 0.0023 27.3 4.3 23 18-40 374-396 (410)
75 cd02185 AroH Chorismate mutase 26.0 71 0.0015 23.7 2.7 43 9-53 13-61 (117)
76 cd06406 PB1_P67 A PB1 domain i 26.0 36 0.00078 23.5 1.0 21 136-156 15-35 (80)
77 COG1961 PinR Site-specific rec 25.6 55 0.0012 25.8 2.2 21 15-35 50-71 (222)
78 PF14592 Chondroitinas_B: Chon 25.6 63 0.0014 29.0 2.7 25 16-40 5-39 (425)
79 TIGR00074 hypC_hupF hydrogenas 25.5 37 0.0008 23.1 1.0 15 21-35 32-46 (76)
80 TIGR01796 CM_mono_aroH monofun 25.1 76 0.0017 23.5 2.7 44 8-53 12-61 (117)
81 PRK05568 flavodoxin; Provision 24.8 49 0.0011 23.8 1.7 12 29-40 3-14 (142)
82 PRK10717 cysteine synthase A; 24.8 1.2E+02 0.0027 25.4 4.3 32 9-40 278-309 (330)
83 PF06720 Phi-29_GP16_7: Bacter 24.4 25 0.00054 26.1 0.0 11 30-40 13-23 (130)
84 PF02639 DUF188: Uncharacteriz 24.3 56 0.0012 24.4 1.9 14 19-32 43-56 (130)
85 COG1671 Uncharacterized protei 24.0 61 0.0013 25.1 2.1 15 19-33 58-72 (150)
86 COG1363 FrvX Cellulase M and r 24.0 1.2E+02 0.0025 26.6 4.0 44 9-53 183-244 (355)
87 TIGR02628 fuculo_kin_coli L-fu 24.0 70 0.0015 28.3 2.7 35 11-45 52-88 (465)
88 PF02938 GAD: GAD domain; Int 23.7 85 0.0018 21.6 2.6 11 24-34 74-84 (95)
89 KOG4107 MP1 adaptor interactin 23.5 91 0.002 22.9 2.7 25 16-40 5-39 (125)
90 PF12724 Flavodoxin_5: Flavodo 23.1 41 0.00088 24.7 0.9 10 31-40 1-10 (143)
91 cd03086 PGM3 PGM3 (phosphogluc 22.8 35 0.00077 31.1 0.6 27 18-45 340-368 (513)
92 PLN02569 threonine synthase 22.6 1.3E+02 0.0028 27.3 4.2 45 8-53 405-455 (484)
93 PRK02268 hypothetical protein; 22.6 65 0.0014 24.6 1.9 15 21-36 32-46 (141)
94 PF05095 DUF687: Protein of un 22.2 1E+02 0.0022 28.6 3.4 40 7-46 92-136 (541)
95 PF08541 ACP_syn_III_C: 3-Oxoa 22.2 1.3E+02 0.0028 19.9 3.3 28 13-40 52-81 (90)
96 PF06110 DUF953: Eukaryotic pr 22.2 1.2E+02 0.0025 22.4 3.2 22 16-37 6-28 (119)
97 PF02995 DUF229: Protein of un 22.1 1.1E+02 0.0023 27.8 3.6 27 14-40 318-344 (497)
98 PRK10649 hypothetical protein; 22.1 1.2E+02 0.0027 28.0 4.0 28 18-45 440-469 (577)
99 PF01455 HupF_HypC: HupF/HypC 22.0 39 0.00084 22.4 0.6 14 21-34 34-47 (68)
100 cd05007 SIS_Etherase N-acetylm 21.9 53 0.0011 27.0 1.5 33 12-46 33-69 (257)
101 COG1935 Uncharacterized conser 21.9 61 0.0013 24.1 1.6 16 22-37 36-51 (122)
102 PRK09598 lipid A phosphoethano 21.8 1.3E+02 0.0028 27.6 4.0 16 29-44 430-445 (522)
103 cd07364 PCA_45_Dioxygenase_B S 21.7 1.3E+02 0.0029 25.1 3.8 39 6-44 25-65 (277)
104 COG3673 Uncharacterized conser 21.5 1.3E+02 0.0028 26.7 3.7 30 11-40 104-133 (423)
105 PRK06721 threonine synthase; R 21.4 1.6E+02 0.0034 25.2 4.3 33 8-40 284-318 (352)
106 PRK06201 hypothetical protein; 21.1 1E+02 0.0022 24.8 3.0 22 17-40 69-90 (221)
107 PF03415 Peptidase_C11: Clostr 21.1 93 0.002 27.3 2.9 31 9-40 78-108 (397)
108 PRK09814 beta-1,6-galactofuran 20.9 1.3E+02 0.0027 25.2 3.6 28 12-39 49-76 (333)
109 PF09994 DUF2235: Uncharacteri 20.6 1.4E+02 0.003 24.7 3.8 31 10-40 73-103 (277)
110 PLN02433 uroporphyrinogen deca 20.4 70 0.0015 27.2 2.0 39 8-48 288-336 (345)
111 PF08496 Peptidase_S49_N: Pept 20.4 1.4E+02 0.003 23.0 3.4 25 12-36 115-139 (155)
112 TIGR01415 trpB_rel pyridoxal-p 20.3 1.6E+02 0.0034 26.2 4.2 29 11-40 375-406 (419)
113 PF08245 Mur_ligase_M: Mur lig 20.3 1.1E+02 0.0025 22.8 3.0 30 6-35 86-115 (188)
114 PF13412 HTH_24: Winged helix- 20.1 1.6E+02 0.0035 17.1 3.1 22 130-151 6-27 (48)
115 PRK08197 threonine synthase; V 20.1 1.6E+02 0.0035 25.5 4.2 33 8-40 347-381 (394)
No 1
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=5.8e-31 Score=220.92 Aligned_cols=138 Identities=39% Similarity=0.658 Sum_probs=112.2
Q ss_pred CCCCCCCcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC----------------------------------------
Q 039205 1 EDPDPLKWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS---------------------------------------- 40 (158)
Q Consensus 1 ~~~~~~~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~---------------------------------------- 40 (158)
+++++..+||++||++||.||++.++|||.+||||||||+
T Consensus 111 t~~s~~~~PT~~Nir~Al~wLV~~aq~gD~LvfHYSGHGtr~~~~~gDe~dG~DE~I~P~D~~t~G~iIdDe~~r~lV~p 190 (362)
T KOG1546|consen 111 TDESPVRIPTGKNIRRALRWLVESAQPGDSLVFHYSGHGTRQPDTNGDEVDGYDETIVPCDHNTQGPIIDDEIFRILVRP 190 (362)
T ss_pred CCCcccccCcHHHHHHHHHHHHhcCCCCCEEEEEecCCCCcCCCCCCCCCCCCcceeecccccccccccchHHHHHHHhc
Confidence 4667779999999999999999999999999999999999
Q ss_pred --------cccccCCCCCcCCcchhhccC---ccccccccccCCCC----C---------------Ccc-----------
Q 039205 41 --------CIIDACHSGTMLDLPFLCRMD---RRGRYIWEDHRPRS----G---------------TWK----------- 79 (158)
Q Consensus 41 --------~i~DcCHSG~~~r~p~~~~~~---~~g~~~~~~~~~~~----g---------------~~~----------- 79 (158)
+|+|+||||+++++|++++++ +.+++.|++.++.. | .+.
T Consensus 191 lp~G~~lt~I~DSCHSGgliDlp~i~~~~~~ir~~~l~~e~~~d~l~~~tG~~~ge~~~i~~~l~d~f~~dts~~~~~~~ 270 (362)
T KOG1546|consen 191 LPKGCKLTAISDSCHSGGLIDLPEIERTKGVIRNRNLPWEDHRDLLKAQTGTDGGEVGKIRGCLDDIFGEDTSPLPNGTI 270 (362)
T ss_pred cCCCceEEEEeecccCCCcccchhheecccccccCccchHHhHHHHHhhcCCCCceeeeeecchhhhhcccCCCCCCcch
Confidence 999999999999999999986 56666666543110 0 000
Q ss_pred -------cCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHHHHHHHHHhcCCC-CCHHHHHHHH
Q 039205 80 -------GASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAITYSFIQASELGHG-TTYGRMLTSM 151 (158)
Q Consensus 80 -------~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT~all~~L~~~~~-~s~~~l~~~v 151 (158)
.....+.|++|+|+++|+|+++. ..|...||||+|+.++|.++++ .+..+|+-+.
T Consensus 271 ~~~~~~~~~~~d~~illSgcqadqtSad~~-----------------~~G~~~gAms~Aiq~i~~~n~g~~~~~~lvl~~ 333 (362)
T KOG1546|consen 271 GDLGRQLKDSHDNGILLSGCQADQTSADAS-----------------TYGHLYGAMSNAIQEILTENKGRITNKLLVLRA 333 (362)
T ss_pred hhhhhhcccCCCCceEEecccccccccccc-----------------cCCcchhHHHHHHHHHHhcCcccchhHHHHHHH
Confidence 13347899999999999999998 6788899999999999999776 5566666555
Q ss_pred HHHH
Q 039205 152 RSTI 155 (158)
Q Consensus 152 r~~v 155 (158)
|..+
T Consensus 334 ~~~~ 337 (362)
T KOG1546|consen 334 RGAL 337 (362)
T ss_pred hhhh
Confidence 5544
No 2
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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 sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=99.83 E-value=4.6e-20 Score=147.16 Aligned_cols=130 Identities=30% Similarity=0.345 Sum_probs=94.5
Q ss_pred CcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC--------------------------------------------cc
Q 039205 7 KWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS--------------------------------------------CI 42 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~--------------------------------------------~i 42 (158)
..||+++|.++|+++++.++++|.|+|||||||. +|
T Consensus 44 ~~~t~~~i~~~l~~l~~~~~~~D~~~~yfsGHG~~~~~~~~~~~~~~d~~~~~~d~~~~~~~~l~~~~~~~~~~~~k~~i 123 (248)
T PF00656_consen 44 DNATRANILKALRELLQRAQPGDSVVFYFSGHGIQVDGEGGDEDSGYDGYLLPLDANLILDDELRDLLCKSLPKKPKLFI 123 (248)
T ss_dssp ESSSHHHHHHHHHHHHTSGGTCSEEEEEEESEEETETTCCSTEEEETSSEEEEHHHHEEHHHHTSTTTTGGGTTS-EEEE
T ss_pred cchHHHHHHHHHhhhhccCCCCCeeEEEEeccccccCCccCcccccccceeeecchhhhHHHHHhhhhhhhccCCccEEe
Confidence 3599999999999999999999999999999995 89
Q ss_pred cccCCCCCcCCcchhhccCccccc--cccccCCCC--CCcccCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhh
Q 039205 43 IDACHSGTMLDLPFLCRMDRRGRY--IWEDHRPRS--GTWKGASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERA 118 (158)
Q Consensus 43 ~DcCHSG~~~r~p~~~~~~~~g~~--~~~~~~~~~--g~~~~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~ 118 (158)
+||||||.+.+............. ......... .......+.++++++||.++|+|+|..
T Consensus 124 lD~C~sg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~as~~~~~s~e~~---------------- 187 (248)
T PF00656_consen 124 LDCCRSGGFIDGLSSSSGESSKREERKLSSSIPPEDPNRSDVPSPSGFIVLSASRPGQTSYEDS---------------- 187 (248)
T ss_dssp EESESSSBTBCEEEEEESSSTSS-EECHCCCCCCSSCCSEEEETTTSEEEEESSSTTBCEEEEC----------------
T ss_pred eccccCCccCCccccccccccccccccccccccccccccccccCCCCcEEEEeccccceeeccc----------------
Confidence 999999999875432211000000 000000000 111234567899999999999999974
Q ss_pred ccCCCccchHHHHHHHHHhcC--------CCCCHHHHHHHHHHHH
Q 039205 119 LSNIPSIGAITYSFIQASELG--------HGTTYGRMLTSMRSTI 155 (158)
Q Consensus 119 ~~~g~~~GafT~all~~L~~~--------~~~s~~~l~~~vr~~v 155 (158)
+..+|+||++|+++|++. ...+..+++..+++.+
T Consensus 188 ---~~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~~~v~~~~ 229 (248)
T PF00656_consen 188 ---PGSGGLFTYALLEALKGNAADDPNQSWDELLEELLTEVNQKV 229 (248)
T ss_dssp ---TTTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHHHHHHHHH
T ss_pred ---CccCHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHhHC
Confidence 458999999999999752 1277788888888877
No 3
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 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 the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=98.92 E-value=4.8e-09 Score=86.86 Aligned_cols=110 Identities=15% Similarity=0.224 Sum_probs=80.5
Q ss_pred cchHHHHHHHHHHH-------HhhCCCCCEEEEEeccCCC----------------------------------cccccC
Q 039205 8 WPTKYNMRMALCWL-------MQGCQPGDSLVFHFSGHAS----------------------------------CIIDAC 46 (158)
Q Consensus 8 ~aTr~nI~~al~~L-------~~~a~~gD~v~f~fSGHG~----------------------------------~i~DcC 46 (158)
.-|.+|+++.|.-- +-...++|.||+||+|||+ +++|+|
T Consensus 79 ~v~~~~fl~vL~G~~~~~~~kvl~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC 158 (256)
T PF01650_consen 79 DVTPENFLNVLTGDKSVPSGKVLNSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEAC 158 (256)
T ss_pred ccCHHHHHHHhcCCCCCCccccccCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecc
Confidence 34566666666511 1156899999999999999 789999
Q ss_pred CCCCcCCcchhhccCccccccccccCCCCCCcccCCCCCeEEEEecCCCcccccccc-chhHHHHHHHHHHhhccCCCcc
Q 039205 47 HSGTMLDLPFLCRMDRRGRYIWEDHRPRSGTWKGASGGEAISFSSCDDNQTSADTSS-LTDIELFNLMLYERALSNIPSI 125 (158)
Q Consensus 47 HSG~~~r~p~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~i~lsAc~~~q~a~e~~~-~~~~~~~~~~~~~~~~~~g~~~ 125 (158)
+||++.+. . ....++++++|+..+|.|+-... .. .-+..-
T Consensus 159 ~SGs~~~~-L------------------------~~~~nv~~iTAa~~~e~Sy~~~~~~~--------------~~~~~l 199 (256)
T PF01650_consen 159 YSGSFFEG-L------------------------LKSPNVYVITAANADESSYGCYCSDD--------------SIGTYL 199 (256)
T ss_pred cccchhhc-c------------------------CCCCCEEEEecCCccccccccccccc--------------ccccEe
Confidence 99999662 0 11247899999999999987621 00 123333
Q ss_pred -chHHHHHHHHHhcCC--CCCHHHHHHHHHHHHh
Q 039205 126 -GAITYSFIQASELGH--GTTYGRMLTSMRSTIY 156 (158)
Q Consensus 126 -GafT~all~~L~~~~--~~s~~~l~~~vr~~v~ 156 (158)
-+|++.+++-+..++ ..|..++++.++..+.
T Consensus 200 ~d~fs~~~m~~~~~~~~~~~Tl~~~f~~v~~~~~ 233 (256)
T PF01650_consen 200 GDAFSYNWMEDSDSHPLSEETLDDQFEYVKRKTT 233 (256)
T ss_pred HHHHHHHhhhhhccCCccccCHHHHHHHHHHhcc
Confidence 489999999998865 4899999999998764
No 4
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=98.72 E-value=2.7e-07 Score=75.30 Aligned_cols=130 Identities=13% Similarity=-0.013 Sum_probs=86.2
Q ss_pred CcchHHHHHHHHHHHHh-hCCCCCEEEEEeccCCC-----------------------------------cccccCCCCC
Q 039205 7 KWPTKYNMRMALCWLMQ-GCQPGDSLVFHFSGHAS-----------------------------------CIIDACHSGT 50 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~-~a~~gD~v~f~fSGHG~-----------------------------------~i~DcCHSG~ 50 (158)
..+|++.|.++++.+.+ +.+..|.++++|+|||. +|+|+|-..-
T Consensus 52 ~nlt~~~~~~~l~~f~~~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl~~iqACRg~~ 131 (243)
T cd00032 52 NNLTAEEILEELKEFASPDHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKLFFIQACRGDE 131 (243)
T ss_pred CCCCHHHHHHHHHHHHhccCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcEEEEECCCCCc
Confidence 46899999999999985 78899999999999999 5555554332
Q ss_pred cCCcchhhccCccccccccccCCCCCCcccCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHHH
Q 039205 51 MLDLPFLCRMDRRGRYIWEDHRPRSGTWKGASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAITY 130 (158)
Q Consensus 51 ~~r~p~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT~ 130 (158)
..+............. ........+........+.++.-|+.++..|++.. ..++.|+.
T Consensus 132 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~p~~~d~lv~ysT~pG~~a~r~~--------------------~~gS~fi~ 190 (243)
T cd00032 132 LDLGVEVDSGADEPPD-VETEAEDDAVQTIPVEADFLVAYSTVPGYVSWRNT--------------------KKGSWFIQ 190 (243)
T ss_pred CCCceeccCccccccc-cccccccccccCCCCcccEEEEecCCCCeEeecCC--------------------CCCCEeHH
Confidence 2111000000000000 00000011112234456888888999999998644 25789999
Q ss_pred HHHHHHhc-CCCCCHHHHHHHHHHHHhc
Q 039205 131 SFIQASEL-GHGTTYGRMLTSMRSTIYH 157 (158)
Q Consensus 131 all~~L~~-~~~~s~~~l~~~vr~~v~~ 157 (158)
+|++.|++ ++..+-.+|+.+|+..|.+
T Consensus 191 ~l~~~l~~~~~~~~l~~il~~V~~~V~~ 218 (243)
T cd00032 191 SLCQVLRKYAHSLDLLDILTKVNRKVAE 218 (243)
T ss_pred HHHHHHHHhCCCCcHHHHHHHHHHHHhh
Confidence 99999988 4579999999999998864
No 5
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=98.66 E-value=1.5e-08 Score=88.17 Aligned_cols=101 Identities=23% Similarity=0.344 Sum_probs=76.0
Q ss_pred CCcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC---------------------------------------------
Q 039205 6 LKWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS--------------------------------------------- 40 (158)
Q Consensus 6 ~~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~--------------------------------------------- 40 (158)
...|++.+|...|..+...+.+.|..+|+|||||.
T Consensus 111 ~~~p~~~~V~~~~lD~~~~~~~~d~~~~~fsG~g~~~~~d~~~~lia~~t~p~~~a~~~~~~~s~~~~~~~~~~~~~~~q 190 (380)
T COG4249 111 IPLPARTKVRRVLLDAARDNPPADTILFFFSGHGATPGADGRAYLIAFDTRPGAVAYDGEGGISPYSVAQALHLSEPGNQ 190 (380)
T ss_pred ccCCchhHHHHHHHHHhhcCchhhhhhheeeccccccCCCCceeEEeecCChhhhcccCCCcccHHHHHHHHHhccCCce
Confidence 34788999999999999999999999999999999
Q ss_pred -cccccCCCCCcCCcchhhccCccccccccccCCCCCCcccCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhhc
Q 039205 41 -CIIDACHSGTMLDLPFLCRMDRRGRYIWEDHRPRSGTWKGASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERAL 119 (158)
Q Consensus 41 -~i~DcCHSG~~~r~p~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~ 119 (158)
..+|+||+|.+...-. .....|... ....+.....+.+|.++|.++|..
T Consensus 191 l~~~d~~~~~~~~~~~~------~~~~p~l~~-------s~~~~~~~~~~~~~ap~~~~~e~~----------------- 240 (380)
T COG4249 191 LVDLDACVRGDVFKATA------GQQRPWLAQ-------SLAREFGFGILDSCAPDQQSAEAP----------------- 240 (380)
T ss_pred eehhhhhcchhhhcccc------cccchHhhh-------hhhcceeeeeccCCCCCccccccc-----------------
Confidence 6677777777654210 000111111 012234678899999999999987
Q ss_pred cCCCccchHHHHHHHHHhc
Q 039205 120 SNIPSIGAITYSFIQASEL 138 (158)
Q Consensus 120 ~~g~~~GafT~all~~L~~ 138 (158)
-..+|+||++++.+|+.
T Consensus 241 --~~g~gv~t~al~~~l~~ 257 (380)
T COG4249 241 --ELGHGVFTDALLEGLRG 257 (380)
T ss_pred --cccCceeehhhhhcccc
Confidence 34699999999999987
No 6
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=98.64 E-value=9.6e-07 Score=72.16 Aligned_cols=127 Identities=13% Similarity=0.013 Sum_probs=85.0
Q ss_pred CcchHHHHHHHHHHHHhh--CCCCCEEEEEeccCCC-----------------------------------cccccCCCC
Q 039205 7 KWPTKYNMRMALCWLMQG--CQPGDSLVFHFSGHAS-----------------------------------CIIDACHSG 49 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~--a~~gD~v~f~fSGHG~-----------------------------------~i~DcCHSG 49 (158)
..+|++.|.++++++.+. .+..|.++++|+|||. +|+|+|--.
T Consensus 50 ~dlt~~em~~~l~~~~~~~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlffiqACRg~ 129 (241)
T smart00115 50 NNLTAEEMLEELKEFAERPEHSDSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLFFIQACRGD 129 (241)
T ss_pred cCCCHHHHHHHHHHHHhccccCCCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEEEEeCCCCC
Confidence 458999999999999874 4589999999999999 455555321
Q ss_pred CcCCcchhhccCccccccccccCCCCCCcccCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHH
Q 039205 50 TMLDLPFLCRMDRRGRYIWEDHRPRSGTWKGASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAIT 129 (158)
Q Consensus 50 ~~~r~p~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT 129 (158)
-..+. ...+ .............+..+.....+.++..|..++..|++.. ..+..|+
T Consensus 130 ~~~~g-~~~~---~~~~~~~~~~~~~~~~~~p~~~D~li~ysT~pG~va~r~~--------------------~~gS~fi 185 (241)
T smart00115 130 ELDGG-VPVE---DDVDDPPTEFEDDAIYKIPVEADFLAAYSTTPGYVSWRNP--------------------TRGSWFI 185 (241)
T ss_pred CCCCC-eecc---cccccccccccccccccCCCcCcEEEEEeCCCCeEeecCC--------------------CCCchHH
Confidence 11000 0000 0000000000011222334567889999999999998654 2578999
Q ss_pred HHHHHHHhc-CCCCCHHHHHHHHHHHHhc
Q 039205 130 YSFIQASEL-GHGTTYGRMLTSMRSTIYH 157 (158)
Q Consensus 130 ~all~~L~~-~~~~s~~~l~~~vr~~v~~ 157 (158)
.+|++.|++ ++..+-.+|+.+|+..|.+
T Consensus 186 ~~L~~~l~~~~~~~~l~~ilt~V~~~V~~ 214 (241)
T smart00115 186 QSLCQVLKEYARSLDLLDILTEVNRKVAV 214 (241)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhh
Confidence 999999998 5779999999999999864
No 7
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=98.04 E-value=3.9e-06 Score=64.83 Aligned_cols=46 Identities=22% Similarity=0.484 Sum_probs=40.8
Q ss_pred CcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC------------------------------------cccccCCCCC
Q 039205 7 KWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS------------------------------------CIIDACHSGT 50 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~------------------------------------~i~DcCHSG~ 50 (158)
..||-+.+.+.+..+-.+++. +.|+|||-|||. .||||..+|.
T Consensus 70 ~dpt~e~~~~~~~~~R~~a~~-~RvLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~dL~~~lg~Psi~V~DC~~AG~ 148 (154)
T PF14538_consen 70 LDPTVEDLKRLCQSLRRNAKD-ERVLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIYDLQSWLGSPSIYVFDCSNAGS 148 (154)
T ss_pred cCCCHHHHHHHHHHHHhhCCC-ceEEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHHHHHHhcCCCEEEEEECCcHHH
Confidence 468999999999998888776 999999999999 8999999998
Q ss_pred cCC
Q 039205 51 MLD 53 (158)
Q Consensus 51 ~~r 53 (158)
+++
T Consensus 149 il~ 151 (154)
T PF14538_consen 149 ILN 151 (154)
T ss_pred HHH
Confidence 754
No 8
>KOG1517 consensus Guanine nucleotide binding protein MIP1 [Cell cycle control, cell division, chromosome partitioning]
Probab=95.75 E-value=0.015 Score=56.63 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=23.3
Q ss_pred cchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 8 WPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
.||.+.+.+--..+- .-..+|.|+|||-|||.
T Consensus 167 DP~vddVrKlc~slR-r~ak~eRvLFHYNGHGV 198 (1387)
T KOG1517|consen 167 DPTVDDVRKLCTSLR-RNAKEERVLFHYNGHGV 198 (1387)
T ss_pred CCcHHHHHHHHHHHh-hhcCCceEEEEecCCCC
Confidence 467777665554443 34468999999999999
No 9
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=94.69 E-value=0.023 Score=49.80 Aligned_cols=45 Identities=24% Similarity=0.481 Sum_probs=33.8
Q ss_pred chHHHHHHHHHH---HHh-------hCCCCCEEEEEeccCCC----------------------------------cccc
Q 039205 9 PTKYNMRMALCW---LMQ-------GCQPGDSLVFHFSGHAS----------------------------------CIID 44 (158)
Q Consensus 9 aTr~nI~~al~~---L~~-------~a~~gD~v~f~fSGHG~----------------------------------~i~D 44 (158)
-|-+|.++-|.- -++ ..+|+|.||+||+-||+ +-+.
T Consensus 125 Vt~~Nf~aVllGd~savkGGsGKV~~SgpnDhiFiYytDHG~pGvl~mP~~~~l~akdlnevL~kmhk~k~Y~~mvfYlE 204 (477)
T KOG1348|consen 125 VTPQNFLAVLLGDASAVKGGSGKVLKSGPNDHIFIYYTDHGGPGVLGMPTSPDLYAKDLNEVLKKMHKSKTYKKMVFYLE 204 (477)
T ss_pred CCHHHHHHHHhcccccccCCCceeeccCCCceEEEEEecCCCCceEecCCCcchhHHHHHHHHHHHHhccchheEEEEee
Confidence 466676665541 111 35789999999999999 6678
Q ss_pred cCCCCCcCC
Q 039205 45 ACHSGTMLD 53 (158)
Q Consensus 45 cCHSG~~~r 53 (158)
+|-||+|..
T Consensus 205 ACESGSmfe 213 (477)
T KOG1348|consen 205 ACESGSMFE 213 (477)
T ss_pred eccCcchhh
Confidence 999999976
No 10
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=93.29 E-value=0.056 Score=47.43 Aligned_cols=30 Identities=23% Similarity=0.449 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 11 KYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 11 r~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
++....+|+...++++.=|.++|||||||-
T Consensus 49 ~~~~~~~L~~f~~da~ga~~al~~~aGhg~ 78 (380)
T COG4249 49 KSGLRRALRYFAEDAEGADVALIYYAGHGL 78 (380)
T ss_pred hHHHHhHHHHHHHHHHHHhHHHhhhccccc
Confidence 345667788889999999999999999998
No 11
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=92.59 E-value=0.6 Score=39.32 Aligned_cols=87 Identities=21% Similarity=0.316 Sum_probs=57.2
Q ss_pred CCCCEEEEEeccCCC----------------------------------cccccCCCCCcCCcchhhccCcccccccccc
Q 039205 26 QPGDSLVFHFSGHAS----------------------------------CIIDACHSGTMLDLPFLCRMDRRGRYIWEDH 71 (158)
Q Consensus 26 ~~gD~v~f~fSGHG~----------------------------------~i~DcCHSG~~~r~p~~~~~~~~g~~~~~~~ 71 (158)
..+..+++|--|||. +++|+|-+.++..-
T Consensus 136 De~SNIlIYmtGHGgd~FlKFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQaasly~~----------------- 198 (309)
T KOG1349|consen 136 DEGSNILIYLTGHGGDGFLKFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQAASLYER----------------- 198 (309)
T ss_pred cCCCcEEEEEccCCCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccchHHHHHh-----------------
Confidence 356789999999999 67777776665321
Q ss_pred CCCCCCcccCCCCCeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHHHHHHHHHhcCC---CCCHHHHH
Q 039205 72 RPRSGTWKGASGGEAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAITYSFIQASELGH---GTTYGRML 148 (158)
Q Consensus 72 ~~~~g~~~~~~~~~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT~all~~L~~~~---~~s~~~l~ 148 (158)
-.+ ++++.++++.-+|.|+.--...+ ++-.----|||+.++-|++.- .-|-.+|+
T Consensus 199 --------~~s-PNVLav~SS~~ge~SySh~~d~~-------------Igv~vIDrftyy~l~flek~~~~~~~~l~dl~ 256 (309)
T KOG1349|consen 199 --------FYS-PNVLAVASSLVGEPSYSHHSDSD-------------IGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLF 256 (309)
T ss_pred --------hcC-CCeEEEeecccCCcccccCCCcc-------------cceeeeccchHHHHHHHHhcccchhhhHHHHH
Confidence 112 27888888888888875443222 222234469999999999832 24566666
Q ss_pred HHH
Q 039205 149 TSM 151 (158)
Q Consensus 149 ~~v 151 (158)
+..
T Consensus 257 ~s~ 259 (309)
T KOG1349|consen 257 DSC 259 (309)
T ss_pred HhC
Confidence 543
No 12
>PF12770 CHAT: CHAT domain
Probab=92.33 E-value=0.12 Score=41.89 Aligned_cols=32 Identities=16% Similarity=0.205 Sum_probs=22.9
Q ss_pred ccchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 039205 124 SIGAITYSFIQASELGHGTTYGRMLTSMRSTIYH 157 (158)
Q Consensus 124 ~~GafT~all~~L~~~~~~s~~~l~~~vr~~v~~ 157 (158)
..-.|+..|.+.|.+ +.+..+-+...|..+++
T Consensus 237 ~a~~f~~~fY~~L~~--g~~~~~Al~~Ar~~l~~ 268 (287)
T PF12770_consen 237 AAARFMRRFYRALLQ--GQSVAEALRQARRALRR 268 (287)
T ss_pred HHHHHHHHHHHhhhc--CCCHHHHHHHHHHHHHh
Confidence 355788888888877 56777777777776654
No 13
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=91.73 E-value=0.73 Score=39.15 Aligned_cols=55 Identities=24% Similarity=0.282 Sum_probs=37.8
Q ss_pred CeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHHHHHHHHHhc---CCCCCHHHHHHHHH
Q 039205 85 EAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAITYSFIQASEL---GHGTTYGRMLTSMR 152 (158)
Q Consensus 85 ~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT~all~~L~~---~~~~s~~~l~~~vr 152 (158)
+++.+..++-+|.|+.--+... ++..----|||.+++-|++ +..+|-.+|+....
T Consensus 203 NvLavgsSeig~ssyShhsd~~-------------IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n 260 (382)
T COG5206 203 NVLAVGSSEIGQSSYSHHSDSL-------------IGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLN 260 (382)
T ss_pred ceEEEeccccCCccccccchhh-------------hhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcC
Confidence 7788888888888875442221 1112234699999999998 44599999987643
No 14
>KOG1321 consensus Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism]
Probab=80.46 E-value=2 Score=37.32 Aligned_cols=35 Identities=29% Similarity=0.516 Sum_probs=27.6
Q ss_pred CCcchHHHHHHHHHHHHhh-C----CC-CCEEEEEeccCCC
Q 039205 6 LKWPTKYNMRMALCWLMQG-C----QP-GDSLVFHFSGHAS 40 (158)
Q Consensus 6 ~~~aTr~nI~~al~~L~~~-a----~~-gD~v~f~fSGHG~ 40 (158)
.+|||++..+++|..+|+. + +| .|-|+++||-||-
T Consensus 197 drW~t~~glIkafA~~I~keL~~F~~~~r~~VVIlFSAHsl 237 (395)
T KOG1321|consen 197 DRWPTREGLIKAFAENIEKELQTFPEPVRDDVVILFSAHSL 237 (395)
T ss_pred ccccccchHHHHHHHHHHHHHHhcCCcccccEEEEEecCCC
Confidence 5799999999999877753 1 22 4778999999997
No 15
>PF01364 Peptidase_C25: Peptidase family C25 This family belongs to family C25 of the peptidase classification.; InterPro: IPR001769 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 C25 (gingipain, clan CD). The protein fold of the peptidase domain for members of this entry resembles that of caspase 1, the type example for clan CD. This is a protein family found only in the bacteria. Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=78.16 E-value=1.9 Score=37.03 Aligned_cols=24 Identities=33% Similarity=0.353 Sum_probs=14.3
Q ss_pred chHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 9 PTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 9 aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+++++|+++|+. |- .++.|.|||+
T Consensus 226 ~~~~~i~~~ln~-------G~-~~v~y~GHG~ 249 (378)
T PF01364_consen 226 GTRDNIINALNQ-------GA-GFVNYFGHGS 249 (378)
T ss_dssp --HHHHHHHHHH----------SEEEEES-B-
T ss_pred chHHHHHHHHhC-------CC-eEEEEecCCc
Confidence 688899999876 43 4557779998
No 16
>COG0648 Nfo Endonuclease IV [DNA replication, recombination, and repair]
Probab=76.99 E-value=3.1 Score=35.19 Aligned_cols=41 Identities=27% Similarity=0.260 Sum_probs=33.9
Q ss_pred CcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC-----------------------cccccCCC
Q 039205 7 KWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS-----------------------CIIDACHS 48 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~-----------------------~i~DcCHS 48 (158)
.....++|.++|+.+++. +....++...+|-|+ +.+|.||-
T Consensus 116 ~e~~l~~i~~~Ln~~~~~-~~v~i~~e~~agegs~~g~~F~~L~eii~~~~~~~~igvCiDtcH~ 179 (280)
T COG0648 116 KEEGLNRIAEALNELLEE-EGVIILLENTAGEGSGKGTQFGELAEIIDLIEEKERIGVCIDTCHA 179 (280)
T ss_pred HHHHHHHHHHHHHHHhhc-cCCeEEEEEeccccCccccchhhHHHHHHhhcccCceEEEEEchhh
Confidence 456778999999999986 556777889999998 88999994
No 17
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=59.39 E-value=8.9 Score=28.38 Aligned_cols=17 Identities=35% Similarity=0.751 Sum_probs=12.4
Q ss_pred HHhhCCCCCEEEEEecc
Q 039205 21 LMQGCQPGDSLVFHFSG 37 (158)
Q Consensus 21 L~~~a~~gD~v~f~fSG 37 (158)
.+++.++||.|+||=||
T Consensus 36 ~l~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 36 NLKRMKPGDKVIFYHSG 52 (143)
T ss_dssp HHHC--TT-EEEEEETS
T ss_pred hhhcCCCCCEEEEEEcC
Confidence 56689999999999998
No 18
>KOG3425 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.96 E-value=11 Score=28.31 Aligned_cols=25 Identities=12% Similarity=0.226 Sum_probs=21.4
Q ss_pred HHHHHHHHhhCCCCCEEEEEeccCC
Q 039205 15 RMALCWLMQGCQPGDSLVFHFSGHA 39 (158)
Q Consensus 15 ~~al~~L~~~a~~gD~v~f~fSGHG 39 (158)
.++|+.++++...|+.+|++|.|-=
T Consensus 12 ~e~~~~~~~~~~n~~~ifvlF~gsk 36 (128)
T KOG3425|consen 12 YESFEETLKNVENGKTIFVLFLGSK 36 (128)
T ss_pred HHHHHHHHHHHhCCceEEEEEeccc
Confidence 4788889999999999999999643
No 19
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 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 C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=53.22 E-value=20 Score=31.23 Aligned_cols=25 Identities=36% Similarity=0.611 Sum_probs=17.0
Q ss_pred CcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 7 KWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+.||.+.++.+|. .-| +|.|-|||+
T Consensus 295 ~~P~~~e~~~~l~-------~~d--lf~Y~GHG~ 319 (383)
T PF03568_consen 295 RAPTEEEFLQALT-------SSD--LFLYCGHGS 319 (383)
T ss_pred CCCCHHHHHHHHH-------hCC--eEEEecCCc
Confidence 4577777766664 234 566899999
No 20
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=51.94 E-value=12 Score=27.60 Aligned_cols=14 Identities=50% Similarity=0.973 Sum_probs=11.8
Q ss_pred hhCCCCCEEEEEec
Q 039205 23 QGCQPGDSLVFHFS 36 (158)
Q Consensus 23 ~~a~~gD~v~f~fS 36 (158)
++++|||+|||-+.
T Consensus 75 ~~~qpGDlvff~~~ 88 (134)
T TIGR02219 75 DAAQPGDVLVFRWR 88 (134)
T ss_pred hcCCCCCEEEEeeC
Confidence 57899999999863
No 21
>PF13660 DUF4147: Domain of unknown function (DUF4147); PDB: 1X3L_A 2B8N_A.
Probab=49.54 E-value=19 Score=29.76 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=23.9
Q ss_pred cchHHHHHHH--HHHHHhhCCCCCEEEEEeccCCCccc
Q 039205 8 WPTKYNMRMA--LCWLMQGCQPGDSLVFHFSGHASCII 43 (158)
Q Consensus 8 ~aTr~nI~~a--l~~L~~~a~~gD~v~f~fSGHG~~i~ 43 (158)
.|+...+..+ +-.++++++++|.|+|.-||=|+..+
T Consensus 94 ~Pd~~s~~aa~~il~~~~~~~~~dlvl~LiSGGgSALl 131 (238)
T PF13660_consen 94 LPDENSVRAARRILELARELTEDDLVLVLISGGGSALL 131 (238)
T ss_dssp S--HHHHHHHHHHHHHHCC--TTSEEEEEE-TTHHHHS
T ss_pred CCCHHHHHHHHHHHHHHhcCCCCCeEEEEecCChHHhh
Confidence 5666766643 44788899999999999999998443
No 22
>COG1350 Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) [General function prediction only]
Probab=48.53 E-value=22 Score=31.42 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=10.6
Q ss_pred CEEEEEeccCCC
Q 039205 29 DSLVFHFSGHAS 40 (158)
Q Consensus 29 D~v~f~fSGHG~ 40 (158)
-+++|-|||||-
T Consensus 405 kvI~fnlSGHGl 416 (432)
T COG1350 405 KVILFNLSGHGL 416 (432)
T ss_pred eEEEEeccCccc
Confidence 489999999995
No 23
>PRK00809 hypothetical protein; Provisional
Probab=47.53 E-value=19 Score=27.32 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=16.0
Q ss_pred HHHhhCCCCCEEEEEecc-CC
Q 039205 20 WLMQGCQPGDSLVFHFSG-HA 39 (158)
Q Consensus 20 ~L~~~a~~gD~v~f~fSG-HG 39 (158)
+.+.+.++||.|+||=|+ +|
T Consensus 30 n~lr~Mk~GD~v~fYhs~~~~ 50 (144)
T PRK00809 30 NTIEKVKPGDKLIIYVSQEYG 50 (144)
T ss_pred hHHhhCCCCCEEEEEECCccC
Confidence 445578999999999886 55
No 24
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=45.74 E-value=28 Score=30.96 Aligned_cols=31 Identities=19% Similarity=0.363 Sum_probs=24.6
Q ss_pred HHHHHHHhhCCCCCEEEEEeccCCCcccccCCCCCcCCcc
Q 039205 16 MALCWLMQGCQPGDSLVFHFSGHASCIIDACHSGTMLDLP 55 (158)
Q Consensus 16 ~al~~L~~~a~~gD~v~f~fSGHG~~i~DcCHSG~~~r~p 55 (158)
+.|-.-++++.+||+|++| -|||.-|..|+.
T Consensus 160 ~~mla~L~~a~~~~vvLLH---------~CcHNPTG~D~t 190 (396)
T COG1448 160 DGMLADLKTAPEGSVVLLH---------GCCHNPTGIDPT 190 (396)
T ss_pred HHHHHHHHhCCCCCEEEEe---------cCCCCCCCCCCC
Confidence 4444556788999999997 499999999975
No 25
>COG2194 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]
Probab=45.53 E-value=29 Score=32.12 Aligned_cols=28 Identities=14% Similarity=0.204 Sum_probs=19.3
Q ss_pred HHHhhCCCC--CEEEEEeccCCCcccccCC
Q 039205 20 WLMQGCQPG--DSLVFHFSGHASCIIDACH 47 (158)
Q Consensus 20 ~L~~~a~~g--D~v~f~fSGHG~~i~DcCH 47 (158)
.++++.+.- |.++||+|-||-.+.|--+
T Consensus 434 ~vi~~Lk~~~~~~~liY~SDHGEslgEn~~ 463 (555)
T COG2194 434 KLIDQLKDKKDNTSLIYFSDHGESLGENGP 463 (555)
T ss_pred HHHHHHHhCCCCeEEEEEcCccHhhccCCc
Confidence 444444332 8999999999997666544
No 26
>PF00254 FKBP_C: FKBP-type peptidyl-prolyl cis-trans isomerase; InterPro: IPR001179 Synonym(s): Peptidylprolyl cis-trans isomerase FKBP-type peptidylprolyl isomerases (5.2.1.8 from EC) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms.; GO: 0006457 protein folding; PDB: 1IX5_A 3JXV_A 3JYM_A 1T11_A 1PBK_A 1FD9_A 2VCD_A 3B7X_A 1Q6H_B 1Q6I_B ....
Probab=45.41 E-value=16 Score=24.63 Aligned_cols=23 Identities=22% Similarity=0.560 Sum_probs=17.7
Q ss_pred hCCCCCEEEEEeccCC--CcccccC
Q 039205 24 GCQPGDSLVFHFSGHA--SCIIDAC 46 (158)
Q Consensus 24 ~a~~gD~v~f~fSGHG--~~i~DcC 46 (158)
.+++||.|.|||+|.= ..++|.-
T Consensus 4 ~~~~gd~V~i~y~~~~~~g~~~~~~ 28 (94)
T PF00254_consen 4 TPKEGDTVTIHYTGRLEDGKVFDSS 28 (94)
T ss_dssp SBSTTSEEEEEEEEEETTSEEEEET
T ss_pred cCCCCCEEEEEEEEEECCCcEEEEe
Confidence 4789999999999853 2556665
No 27
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=43.96 E-value=37 Score=24.18 Aligned_cols=40 Identities=10% Similarity=0.049 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHhhCCCCCEEEEEeccCCC---------------cccccCCCCCcCC
Q 039205 10 TKYNMRMALCWLMQGCQPGDSLVFHFSGHAS---------------CIIDACHSGTMLD 53 (158)
Q Consensus 10 Tr~nI~~al~~L~~~a~~gD~v~f~fSGHG~---------------~i~DcCHSG~~~r 53 (158)
++..|..-|+.|.++ .+.|.++ .++|. ++||+|......+
T Consensus 6 ~p~eI~~~Lr~L~~~---~~~l~v~-~~~g~~f~T~iL~VD~~~~~l~lD~~~~~~~n~ 60 (108)
T PF07317_consen 6 NPREILAVLRDLAKQ---RSPLTVR-HPRGQSFITSILAVDPDRGTLVLDEGSDEEENQ 60 (108)
T ss_dssp SHHHHHHHHHHHHHT---T--EEEE-TT-SSEEEE-EEEEETTTTEEEEE--BSGGGHH
T ss_pred CHHHHHHHHHHHHhC---CCeEEEE-eCCCCEEEEEEEEEeCCCCEEEEEcCCChHHHH
Confidence 456788888888755 8888888 77887 8899987665543
No 28
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.
Probab=43.94 E-value=48 Score=27.41 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=32.2
Q ss_pred chHHHHHHHHHHHHhhCCCCCEEEEE--eccC-CC--------------------cccccCCCCCc
Q 039205 9 PTKYNMRMALCWLMQGCQPGDSLVFH--FSGH-AS--------------------CIIDACHSGTM 51 (158)
Q Consensus 9 aTr~nI~~al~~L~~~a~~gD~v~f~--fSGH-G~--------------------~i~DcCHSG~~ 51 (158)
+|-+.|+.|.+.+.+. ...++++.| +|.+ +. +++|+.||++.
T Consensus 143 ~t~~e~~~Ave~i~~~-Gn~~i~l~~rG~s~y~~~~~~~~dl~~i~~lk~~~~~pV~~ds~Hs~G~ 207 (260)
T TIGR01361 143 NTIEEWLYAAEYILSS-GNGNVILCERGIRTFEKATRNTLDLSAVPVLKKETHLPIIVDPSHAAGR 207 (260)
T ss_pred CCHHHHHHHHHHHHHc-CCCcEEEEECCCCCCCCCCcCCcCHHHHHHHHHhhCCCEEEcCCCCCCc
Confidence 4889999999887643 345677777 6777 65 88999999774
No 29
>PLN02895 phosphoacetylglucosamine mutase
Probab=42.75 E-value=11 Score=34.79 Aligned_cols=24 Identities=21% Similarity=0.452 Sum_probs=14.8
Q ss_pred HHHhhCCCCCEEEEEe--ccCCCcccc
Q 039205 20 WLMQGCQPGDSLVFHF--SGHASCIID 44 (158)
Q Consensus 20 ~L~~~a~~gD~v~f~f--SGHG~~i~D 44 (158)
.|.+.++.-| +.||| ||||++||-
T Consensus 374 ~l~~~a~e~d-igvyfEaNGHGTviFs 399 (562)
T PLN02895 374 YLHEAAAEFD-IGVYFEANGHGTVLFS 399 (562)
T ss_pred HHHHHHHhcC-ceEEEccCCCeEEEEC
Confidence 3444455556 45555 999996654
No 30
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=41.41 E-value=24 Score=27.25 Aligned_cols=18 Identities=28% Similarity=0.270 Sum_probs=15.4
Q ss_pred HHHhhCCCCCEEEEEecc
Q 039205 20 WLMQGCQPGDSLVFHFSG 37 (158)
Q Consensus 20 ~L~~~a~~gD~v~f~fSG 37 (158)
+++.+.+.||.+|||-|-
T Consensus 37 NfmR~M~iGD~~fFYHSN 54 (156)
T COG2947 37 NFMRDMKIGDLGFFYHSN 54 (156)
T ss_pred HHHHhcccCceEEEEecC
Confidence 667778999999999884
No 31
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=40.74 E-value=28 Score=30.76 Aligned_cols=28 Identities=21% Similarity=0.439 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 13 NMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 13 nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+..+|++++.+.+++||+|++.=+||=.
T Consensus 409 d~~~Ai~~~~~~~~~gDvVLv~G~G~e~ 436 (460)
T PRK00139 409 DRAEAIRYAIAQAKPGDVVLIAGKGHED 436 (460)
T ss_pred CHHHHHHHHHHhcCCCCEEEEEEccCcc
Confidence 4567778888889999999998887755
No 32
>PF12047 DNMT1-RFD: Cytosine specific DNA methyltransferase replication foci domain; InterPro: IPR022702 This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties []. A structure exists for the human cytosine specific DNA methyltransferase replication foci domain. ; PDB: 3AV6_A 3AV5_A 3AV4_A 3EPZ_B.
Probab=39.57 E-value=33 Score=25.51 Aligned_cols=30 Identities=13% Similarity=0.150 Sum_probs=24.0
Q ss_pred ccchHHHHHHHHHhcCC---CCCHHHHHHHHHH
Q 039205 124 SIGAITYSFIQASELGH---GTTYGRMLTSMRS 153 (158)
Q Consensus 124 ~~GafT~all~~L~~~~---~~s~~~l~~~vr~ 153 (158)
..=.+|..+++.|++++ ..||.+++.+|..
T Consensus 113 ~~~~l~~~v~~~l~~~~~~~~~s~~d~l~~v~~ 145 (146)
T PF12047_consen 113 RKARLTVRVIHFLKKNPRASDLSYEDLLARVFR 145 (146)
T ss_dssp HHHHHHHHHHHHHHHHT---T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCcccccCCHHHHHHHHhc
Confidence 45578999999999987 8999999999864
No 33
>PTZ00302 N-acetylglucosamine-phosphate mutase; Provisional
Probab=39.24 E-value=14 Score=34.42 Aligned_cols=25 Identities=20% Similarity=0.353 Sum_probs=16.0
Q ss_pred HHHhhCCCCCEEEEEe--ccCCCccccc
Q 039205 20 WLMQGCQPGDSLVFHF--SGHASCIIDA 45 (158)
Q Consensus 20 ~L~~~a~~gD~v~f~f--SGHG~~i~Dc 45 (158)
.|...++.-| +.||| ||||++||--
T Consensus 406 ~l~~~a~e~d-i~iyfEaNGHGTvif~~ 432 (585)
T PTZ00302 406 NLHPKAHKYD-IGIYFEANGHGTVLFNE 432 (585)
T ss_pred HHHHHHHhcC-CeEEEccCCCEEEEECc
Confidence 4444555566 55665 9999976653
No 34
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=39.12 E-value=14 Score=29.94 Aligned_cols=22 Identities=36% Similarity=0.555 Sum_probs=18.9
Q ss_pred EEEEEeccCCC---cccccCCCCCc
Q 039205 30 SLVFHFSGHAS---CIIDACHSGTM 51 (158)
Q Consensus 30 ~v~f~fSGHG~---~i~DcCHSG~~ 51 (158)
.+.++.||.|+ +|+|.|++|..
T Consensus 2 ki~VlaSG~GSNlqaiida~~~~~~ 26 (200)
T COG0299 2 KIAVLASGNGSNLQAIIDAIKGGKL 26 (200)
T ss_pred eEEEEEeCCcccHHHHHHHHhcCCC
Confidence 36789999999 89999997755
No 35
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=37.92 E-value=39 Score=21.94 Aligned_cols=28 Identities=11% Similarity=0.185 Sum_probs=20.8
Q ss_pred hHHHHHHHHHhc-CCCCCHHHHHHHHHHH
Q 039205 127 AITYSFIQASEL-GHGTTYGRMLTSMRST 154 (158)
Q Consensus 127 afT~all~~L~~-~~~~s~~~l~~~vr~~ 154 (158)
.|..+-.++|++ +..+|+.+|.+.+.+.
T Consensus 2 t~~eaa~~vL~~~~~pm~~~eI~~~i~~~ 30 (72)
T PF05066_consen 2 TFKEAAYEVLEEAGRPMTFKEIWEEIQER 30 (72)
T ss_dssp -HHHHHHHHHHHH-S-EEHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCcCHHHHHHHHHHh
Confidence 356778889988 5569999999998764
No 36
>COG2379 GckA Putative glycerate kinase [Carbohydrate transport and metabolism]
Probab=37.41 E-value=37 Score=30.33 Aligned_cols=26 Identities=23% Similarity=0.394 Sum_probs=21.4
Q ss_pred HHHhhCCCCCEEEEEeccCCCccccc
Q 039205 20 WLMQGCQPGDSLVFHFSGHASCIIDA 45 (158)
Q Consensus 20 ~L~~~a~~gD~v~f~fSGHG~~i~Dc 45 (158)
.+++..+++|.|++..||=|+.+|-+
T Consensus 104 ~~v~~l~e~D~Vi~LISGGGSaL~e~ 129 (422)
T COG2379 104 ELVSGLTEDDLVIVLISGGGSALLEL 129 (422)
T ss_pred HHhcCCCCCcEEEEEEeCCchhhccC
Confidence 55778899999999999999955544
No 37
>TIGR00095 RNA methyltransferase, RsmD family. This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases.
Probab=37.12 E-value=65 Score=25.09 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=30.5
Q ss_pred CCCCcchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 4 DPLKWPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 4 ~~~~~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+....||-+-++.+|-+++...-+|..|+=.|+|-|+
T Consensus 26 ~~~~rpt~~~vrea~f~~l~~~~~g~~vLDLfaGsG~ 62 (189)
T TIGR00095 26 GGSTRPTTRVVRELFFNILRPEIQGAHLLDVFAGSGL 62 (189)
T ss_pred CCCCCCchHHHHHHHHHHHHHhcCCCEEEEecCCCcH
Confidence 4467899999999988777655678888889999998
No 38
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=37.07 E-value=32 Score=30.52 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhhCC-CCCEEEEEeccCCC
Q 039205 13 NMRMALCWLMQGCQ-PGDSLVFHFSGHAS 40 (158)
Q Consensus 13 nI~~al~~L~~~a~-~gD~v~f~fSGHG~ 40 (158)
+..+|++.+.+.++ +||+|+| +|.|-
T Consensus 430 d~~~Ai~~a~~~a~~~gD~VLi--~G~G~ 456 (481)
T PRK14022 430 DRAEAIKHAMSITEGPGDAVII--AGKGA 456 (481)
T ss_pred CHHHHHHHHHHhcCCCCCEEEE--EecCC
Confidence 45566777777889 9998887 77774
No 39
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=36.43 E-value=29 Score=22.60 Aligned_cols=29 Identities=3% Similarity=0.110 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 039205 128 ITYSFIQASELGHGTTYGRMLTSMRSTIY 156 (158)
Q Consensus 128 fT~all~~L~~~~~~s~~~l~~~vr~~v~ 156 (158)
.--++++.|+....++|.+|+..|...++
T Consensus 9 I~AaIVrimK~~k~~~~~~L~~~v~~~l~ 37 (68)
T PF10557_consen 9 IDAAIVRIMKQEKKLSHDELINEVIEELK 37 (68)
T ss_dssp HHHHHHHHHHHSSEEEHHHHHHHHHHHTT
T ss_pred hhhheehhhhhcCceeHHHHHHHHHHHhc
Confidence 44578899999888999999999988875
No 40
>COG2830 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.50 E-value=37 Score=27.17 Aligned_cols=16 Identities=38% Similarity=0.933 Sum_probs=14.7
Q ss_pred CCCCCEEEEEeccCCC
Q 039205 25 CQPGDSLVFHFSGHAS 40 (158)
Q Consensus 25 a~~gD~v~f~fSGHG~ 40 (158)
++.||.+++||.|-|+
T Consensus 7 ~~qgd~LIvyFaGwgt 22 (214)
T COG2830 7 CKQGDHLIVYFAGWGT 22 (214)
T ss_pred ecCCCEEEEEEecCCC
Confidence 5679999999999999
No 41
>COG3376 HoxN High-affinity nickel permease [Inorganic ion transport and metabolism]
Probab=34.58 E-value=46 Score=28.81 Aligned_cols=31 Identities=26% Similarity=0.291 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHhhCCCCCEEEEEec-cCCCcc
Q 039205 12 YNMRMALCWLMQGCQPGDSLVFHFS-GHASCI 42 (158)
Q Consensus 12 ~nI~~al~~L~~~a~~gD~v~f~fS-GHG~~i 42 (158)
+.|-+.-++|.+|-|+-=.|=|||| ||-++|
T Consensus 70 AAIDN~tRKLmQqgK~p~~VG~fFSlGHStVV 101 (342)
T COG3376 70 AAIDNVTRKLMQQGKNPLGVGFFFSLGHSTVV 101 (342)
T ss_pred HHHHHHHHHHHhCCCCCceeeEEEecCchHHH
Confidence 4566677788999888888888998 999933
No 42
>PF06672 DUF1175: Protein of unknown function (DUF1175); InterPro: IPR009558 This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=34.48 E-value=24 Score=28.86 Aligned_cols=13 Identities=46% Similarity=1.009 Sum_probs=10.9
Q ss_pred HhhCCCCCEEEEE
Q 039205 22 MQGCQPGDSLVFH 34 (158)
Q Consensus 22 ~~~a~~gD~v~f~ 34 (158)
+++++|||++||+
T Consensus 133 l~~A~pGDL~Ff~ 145 (216)
T PF06672_consen 133 LEQARPGDLLFFH 145 (216)
T ss_pred hhhcCCCcEEEec
Confidence 5789999997776
No 43
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=33.13 E-value=82 Score=21.48 Aligned_cols=28 Identities=7% Similarity=0.144 Sum_probs=23.6
Q ss_pred HHHHHHHHHhc-CCCCCHHHHHHHHHHHH
Q 039205 128 ITYSFIQASEL-GHGTTYGRMLTSMRSTI 155 (158)
Q Consensus 128 fT~all~~L~~-~~~~s~~~l~~~vr~~v 155 (158)
|-..+|++|.+ +...+..++.+.|.+.+
T Consensus 5 ~~~piL~~L~~~g~~~~~~ei~~~v~~~~ 33 (92)
T PF14338_consen 5 LMPPILEALKDLGGSASRKEIYERVAERF 33 (92)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHHHh
Confidence 45678999998 77899999999998765
No 44
>PRK06260 threonine synthase; Validated
Probab=32.57 E-value=73 Score=27.69 Aligned_cols=33 Identities=18% Similarity=0.168 Sum_probs=25.8
Q ss_pred cchHHHHHHHHHHHHhh--CCCCCEEEEEeccCCC
Q 039205 8 WPTKYNMRMALCWLMQG--CQPGDSLVFHFSGHAS 40 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~--a~~gD~v~f~fSGHG~ 40 (158)
.|+-..-+.++.++.++ ..+++.|++..+|||-
T Consensus 334 epssaaalAa~~~l~~~g~i~~~~~VV~i~tG~gl 368 (397)
T PRK06260 334 EPASAASVAGLIKLVEEGVIDKDERVVCITTGHLL 368 (397)
T ss_pred CchHHHHHHHHHHHHHcCCCCCCCeEEEEeCCCcc
Confidence 45566667778777765 4689999999999996
No 45
>KOG4530 consensus Predicted flavoprotein [General function prediction only]
Probab=32.31 E-value=67 Score=25.52 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 13 NMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 13 nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
-..+||.||...-.---.+++.|-|||.
T Consensus 104 ~LKNAlD~lyheW~gKPalivSyGGhGG 131 (199)
T KOG4530|consen 104 PLKNALDWLYHEWAGKPALIVSYGGHGG 131 (199)
T ss_pred HHHHHHHHhhhhhcCCceEEEEecCCCC
Confidence 3456777777554334568889999998
No 46
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=32.07 E-value=27 Score=24.12 Aligned_cols=14 Identities=36% Similarity=0.600 Sum_probs=11.4
Q ss_pred HhhCCCCCEEEEEe
Q 039205 22 MQGCQPGDSLVFHF 35 (158)
Q Consensus 22 ~~~a~~gD~v~f~f 35 (158)
.++++|||++||..
T Consensus 49 ~~~~~pGDlif~~~ 62 (105)
T PF00877_consen 49 ISELQPGDLIFFKG 62 (105)
T ss_dssp GGG-TTTEEEEEEG
T ss_pred hhcCCcccEEEEeC
Confidence 46789999999998
No 47
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=32.01 E-value=28 Score=24.50 Aligned_cols=13 Identities=23% Similarity=0.718 Sum_probs=10.3
Q ss_pred hCCCCCEEEEE-ec
Q 039205 24 GCQPGDSLVFH-FS 36 (158)
Q Consensus 24 ~a~~gD~v~f~-fS 36 (158)
++++||.|+|. |+
T Consensus 53 ~Vk~GD~Vl~~~y~ 66 (91)
T PRK14533 53 DIKVGDKVIFSKYA 66 (91)
T ss_pred cccCCCEEEEccCC
Confidence 58999999875 55
No 48
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=31.54 E-value=26 Score=26.55 Aligned_cols=16 Identities=38% Similarity=0.627 Sum_probs=13.4
Q ss_pred EEEec---cCCCcccccCC
Q 039205 32 VFHFS---GHASCIIDACH 47 (158)
Q Consensus 32 ~f~fS---GHG~~i~DcCH 47 (158)
+.||| ||+.-|+||--
T Consensus 28 V~yYSLaIGHhvGvIDcle 46 (133)
T PRK15084 28 VMYYSLAIGHHVGVIDCLE 46 (133)
T ss_pred eeEEEeecccccceEecch
Confidence 67887 99999999854
No 49
>PRK07116 flavodoxin; Provisional
Probab=31.49 E-value=32 Score=25.85 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.7
Q ss_pred CEEEEEeccCCC
Q 039205 29 DSLVFHFSGHAS 40 (158)
Q Consensus 29 D~v~f~fSGHG~ 40 (158)
.++++|||++|.
T Consensus 4 k~lIvY~S~tGn 15 (160)
T PRK07116 4 KTLVAYFSATGT 15 (160)
T ss_pred cEEEEEECCCCc
Confidence 478999999999
No 50
>PF09791 Oxidored-like: Oxidoreductase-like protein, N-terminal; InterPro: IPR019180 This entry represents the N-terminal domain of various oxidoreductase-like proteins whose exact function is, as yet, unknown.
Probab=31.29 E-value=19 Score=22.45 Aligned_cols=9 Identities=33% Similarity=0.634 Sum_probs=7.0
Q ss_pred cccCCCCCc
Q 039205 43 IDACHSGTM 51 (158)
Q Consensus 43 ~DcCHSG~~ 51 (158)
-|||.||-.
T Consensus 16 ~~CCgSGC~ 24 (48)
T PF09791_consen 16 DECCGSGCA 24 (48)
T ss_pred ccccccCCc
Confidence 379999965
No 51
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=31.04 E-value=73 Score=18.89 Aligned_cols=24 Identities=4% Similarity=0.199 Sum_probs=17.3
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHH
Q 039205 128 ITYSFIQASELGHGTTYGRMLTSM 151 (158)
Q Consensus 128 fT~all~~L~~~~~~s~~~l~~~v 151 (158)
+-..+++.|..++..||.+|-+.+
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~l 27 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEEL 27 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHH
Confidence 346789999998889999887654
No 52
>cd03768 SR_ResInv Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some
Probab=31.01 E-value=55 Score=22.99 Aligned_cols=20 Identities=35% Similarity=0.476 Sum_probs=15.6
Q ss_pred HHHHHHHHhhCCCCCEEEEE
Q 039205 15 RMALCWLMQGCQPGDSLVFH 34 (158)
Q Consensus 15 ~~al~~L~~~a~~gD~v~f~ 34 (158)
...|+.|++.++++|+|+++
T Consensus 42 R~~~~~ll~~~~~~d~lvv~ 61 (126)
T cd03768 42 RPELQKLLEDLREGDTLVVT 61 (126)
T ss_pred CHHHHHHHHhCcCCCEEEEE
Confidence 35677788888899998776
No 53
>COG3536 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.98 E-value=39 Score=24.99 Aligned_cols=35 Identities=9% Similarity=0.221 Sum_probs=26.7
Q ss_pred ccCCCccchHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 039205 119 LSNIPSIGAITYSFIQASELGHGTTYGRMLTSMRS 153 (158)
Q Consensus 119 ~~~g~~~GafT~all~~L~~~~~~s~~~l~~~vr~ 153 (158)
|.+|...|+|||+-+.-|-.....-|.+-++.+.+
T Consensus 77 FdDgHDsGiy~W~YL~~lg~~~d~lw~~Yl~eLA~ 111 (120)
T COG3536 77 FDDGHDSGIYTWAYLHELGEEKDALWQAYLDELAA 111 (120)
T ss_pred ecCCcccCcccHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 46789999999999999977666667666665543
No 54
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=30.96 E-value=34 Score=27.36 Aligned_cols=28 Identities=25% Similarity=0.443 Sum_probs=23.1
Q ss_pred hhCCCCCEEEEEeccCCC--cccccCCCCC
Q 039205 23 QGCQPGDSLVFHFSGHAS--CIIDACHSGT 50 (158)
Q Consensus 23 ~~a~~gD~v~f~fSGHG~--~i~DcCHSG~ 50 (158)
++++.||.+-+||-|+=. .+||+-|+-.
T Consensus 83 ~kak~GD~l~~HY~g~leDGt~fdSS~~rg 112 (188)
T KOG0549|consen 83 EKAKKGDTLHVHYTGSLEDGTKFDSSYSRG 112 (188)
T ss_pred ccccCCCEEEEEEEEEecCCCEEeeeccCC
Confidence 568999999999998433 8899988766
No 55
>PRK05638 threonine synthase; Validated
Probab=30.34 E-value=85 Score=27.77 Aligned_cols=33 Identities=21% Similarity=0.143 Sum_probs=26.0
Q ss_pred cchHHHHHHHHHHHHhh--CCCCCEEEEEeccCCC
Q 039205 8 WPTKYNMRMALCWLMQG--CQPGDSLVFHFSGHAS 40 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~--a~~gD~v~f~fSGHG~ 40 (158)
.|+-+.-+.++.++.+. ..+|+.|++..+|||.
T Consensus 322 epssaaa~Aa~~~~~~~g~i~~~~~Vv~i~tG~g~ 356 (442)
T PRK05638 322 ELSSAVVMPALLKLGEEGYIEKGDKVVLVVTGSGL 356 (442)
T ss_pred cchHHHHHHHHHHHHHcCCCCCCCeEEEEeCCCCC
Confidence 45666667777777765 5789999999999997
No 56
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=30.22 E-value=32 Score=27.37 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=11.8
Q ss_pred hhCCCCCEEEEEecc
Q 039205 23 QGCQPGDSLVFHFSG 37 (158)
Q Consensus 23 ~~a~~gD~v~f~fSG 37 (158)
++++|||+|||...+
T Consensus 127 ~~lqpGDLVfF~~~~ 141 (190)
T PRK10838 127 SKLRTGDLVLFRAGS 141 (190)
T ss_pred CCCCCCcEEEECCCC
Confidence 567999999997543
No 57
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=30.08 E-value=28 Score=26.30 Aligned_cols=16 Identities=38% Similarity=0.627 Sum_probs=13.3
Q ss_pred EEEec---cCCCcccccCC
Q 039205 32 VFHFS---GHASCIIDACH 47 (158)
Q Consensus 32 ~f~fS---GHG~~i~DcCH 47 (158)
+.||| ||+.-|+||=-
T Consensus 26 V~yYSLaIGHhvGvIDcle 44 (131)
T PF07450_consen 26 VMYYSLAIGHHVGVIDCLE 44 (131)
T ss_pred eeEEEeeeccccceEeech
Confidence 67887 99999999854
No 58
>cd03767 SR_Res_par Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.
Probab=29.84 E-value=51 Score=24.48 Aligned_cols=20 Identities=35% Similarity=0.532 Sum_probs=15.3
Q ss_pred HHHHHHHHhhCCCCCEEEEE
Q 039205 15 RMALCWLMQGCQPGDSLVFH 34 (158)
Q Consensus 15 ~~al~~L~~~a~~gD~v~f~ 34 (158)
...|+.|++.+++||+|+++
T Consensus 47 Rp~~~~ll~~~~~gd~lvv~ 66 (146)
T cd03767 47 RPELFRLLDDAQSGDVLLVE 66 (146)
T ss_pred CHHHHHHHHHhhCCCEEEEE
Confidence 35677777788899987765
No 59
>PF07736 CM_1: Chorismate mutase type I; InterPro: IPR008243 Chorismate mutase (CM; 5.4.99.5 from EC) catalyses the reaction at the branch point of the biosynthetic pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. This entry represents a family of monofunctional (non-fused) chorismate mutases from Gram-positive bacteria (Firmicutes) and cyanobacteria. Trusted members of the family are found in operons with other enzymes of the chorismate pathways, both up- and downstream of CM (Listeria, Bacillus, Oceanobacillus) or are the sole CM in the genome where the other members of the chorismate pathways are found elsewhere in the genome (Nostoc, Thermosynechococcus). They are monofunctional, homotrimeric, nonallosteric enzymes and are not regulated by the end-product aromatic amino acids. The three types of CM are AroQ class, Prokaryotic type (e.g., IPR008239 from INTERPRO amongst others); AroQ class, Eukaryotic type (IPR008238 from INTERPRO); and AroH class. They fall into two structural folds (AroQ class and AroH class) which are completely unrelated []. The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved []. For additional information please see [, , , , , , ].; PDB: 2CHS_K 2CHT_L 1COM_J 1FNJ_A 1FNK_A 1DBF_C 1UI9_A 1ODE_A 1UFY_A 1XHO_C ....
Probab=29.60 E-value=68 Score=23.81 Aligned_cols=43 Identities=19% Similarity=0.181 Sum_probs=25.7
Q ss_pred chHHHHHHHHHHHHh------hCCCCCEEEEEeccCCCcccccCCCCCcCC
Q 039205 9 PTKYNMRMALCWLMQ------GCQPGDSLVFHFSGHASCIIDACHSGTMLD 53 (158)
Q Consensus 9 aTr~nI~~al~~L~~------~a~~gD~v~f~fSGHG~~i~DcCHSG~~~r 53 (158)
=|++.|+++-.+|++ +.+|.|++-++||-=.- +|+++=+...|
T Consensus 13 n~~e~I~~at~eLl~~i~~~N~l~~~dIvSi~FT~T~D--L~a~fPA~a~R 61 (118)
T PF07736_consen 13 NTPEEILEATRELLEEILERNELSPEDIVSIIFTVTPD--LDAAFPAAAAR 61 (118)
T ss_dssp SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEE-TT----SS-TCHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEEeCCC--cCccChHHHHH
Confidence 367888888777754 56899999999983322 45555444443
No 60
>PRK09781 hypothetical protein; Provisional
Probab=29.08 E-value=7.3 Score=30.11 Aligned_cols=31 Identities=26% Similarity=0.306 Sum_probs=22.2
Q ss_pred CeEEEEecCCCccccccccchhHHHHHHHHHHhhccCCCccchHHH
Q 039205 85 EAISFSSCDDNQTSADTSSLTDIELFNLMLYERALSNIPSIGAITY 130 (158)
Q Consensus 85 ~~i~lsAc~~~q~a~e~~~~~~~~~~~~~~~~~~~~~g~~~GafT~ 130 (158)
+.-+++||.|.|.++=.. -|.+|| ..|+|||
T Consensus 52 ga~vltacddrqvsy~~~--------Y~AIPE-------~~Gi~TW 82 (181)
T PRK09781 52 IIAVLTACDDRQVSYFPD--------YAAIPE-------QSGIWTW 82 (181)
T ss_pred hHHHhhhcccceeeeccc--------eeeccc-------cCCcEEe
Confidence 456789999999997443 134454 6788887
No 61
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=28.58 E-value=46 Score=25.90 Aligned_cols=20 Identities=25% Similarity=0.272 Sum_probs=15.7
Q ss_pred HHHHHHHhhCCCCCEEEEEe
Q 039205 16 MALCWLMQGCQPGDSLVFHF 35 (158)
Q Consensus 16 ~al~~L~~~a~~gD~v~f~f 35 (158)
..|+.|++.+++||+|+++=
T Consensus 50 ~~l~~ll~~~~~gd~lvv~~ 69 (200)
T PRK13413 50 RKLGKLLKKMRKGDILIVSE 69 (200)
T ss_pred ccHHHHHHHHhCCCEEEEEe
Confidence 36777788889999988864
No 62
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=28.48 E-value=1.2e+02 Score=17.91 Aligned_cols=26 Identities=4% Similarity=0.101 Sum_probs=20.9
Q ss_pred HHHHHHhc--CCCCCHHHHHHHHHHHHh
Q 039205 131 SFIQASEL--GHGTTYGRMLTSMRSTIY 156 (158)
Q Consensus 131 all~~L~~--~~~~s~~~l~~~vr~~v~ 156 (158)
.|++.|+. ...++..++.++|...++
T Consensus 6 ~FL~il~~y~~~~~~~~~v~~~v~~Ll~ 33 (47)
T PF02671_consen 6 EFLKILNDYKKGRISRSEVIEEVSELLR 33 (47)
T ss_dssp HHHHHHHHHHCTCSCHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence 57888876 566999999999988765
No 63
>PRK05569 flavodoxin; Provisional
Probab=28.42 E-value=39 Score=24.39 Aligned_cols=12 Identities=8% Similarity=0.088 Sum_probs=10.8
Q ss_pred CEEEEEeccCCC
Q 039205 29 DSLVFHFSGHAS 40 (158)
Q Consensus 29 D~v~f~fSGHG~ 40 (158)
.++++|||+||.
T Consensus 3 ki~iiY~S~tGn 14 (141)
T PRK05569 3 KVSIIYWSCGGN 14 (141)
T ss_pred eEEEEEECCCCH
Confidence 478999999999
No 64
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=28.20 E-value=50 Score=21.80 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=9.9
Q ss_pred hhCCCCCEEEEE
Q 039205 23 QGCQPGDSLVFH 34 (158)
Q Consensus 23 ~~a~~gD~v~f~ 34 (158)
..+++||+|.+.
T Consensus 52 ~G~~~GD~V~Ig 63 (69)
T TIGR03595 52 AGAKDGDTVRIG 63 (69)
T ss_pred cCCCCCCEEEEc
Confidence 368999999875
No 65
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=27.79 E-value=34 Score=25.38 Aligned_cols=17 Identities=18% Similarity=-0.031 Sum_probs=13.4
Q ss_pred HHhhCCCCCEEEEEecc
Q 039205 21 LMQGCQPGDSLVFHFSG 37 (158)
Q Consensus 21 L~~~a~~gD~v~f~fSG 37 (158)
-+++.+|||+|||...|
T Consensus 70 ~v~~p~~GDiv~f~~~~ 86 (129)
T TIGR02594 70 KLSKPAYGCIAVKRRGG 86 (129)
T ss_pred cCCCCCccEEEEEECCC
Confidence 35678999999998654
No 66
>PRK07591 threonine synthase; Validated
Probab=27.56 E-value=1e+02 Score=27.20 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=24.7
Q ss_pred chHHHHHHHHHHHHh--hCCCCCEEEEEeccCCC
Q 039205 9 PTKYNMRMALCWLMQ--GCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 9 aTr~nI~~al~~L~~--~a~~gD~v~f~fSGHG~ 40 (158)
|+-+.-+.++..+.+ ..++++.|++..+|||.
T Consensus 358 pssaaalAal~~l~~~g~i~~~~~VV~i~tG~G~ 391 (421)
T PRK07591 358 TAGGVTVAVLKKLVEAGKIDPDEETVVYITGNGL 391 (421)
T ss_pred chHHHHHHHHHHHHHhCCCCCCCeEEEEeCCCcc
Confidence 455555677777776 46789999999999997
No 67
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=27.46 E-value=38 Score=27.35 Aligned_cols=14 Identities=21% Similarity=0.541 Sum_probs=11.6
Q ss_pred CCCCEEEEEeccCC
Q 039205 26 QPGDSLVFHFSGHA 39 (158)
Q Consensus 26 ~~gD~v~f~fSGHG 39 (158)
+++|.+|+||.||-
T Consensus 128 ~~~~~vfVyYrG~n 141 (198)
T PF07137_consen 128 KPDDFVFVYYRGRN 141 (198)
T ss_dssp STT-EEEEEEEEEE
T ss_pred CCCCEEEEEEcccc
Confidence 58899999999986
No 68
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=27.01 E-value=50 Score=22.55 Aligned_cols=14 Identities=14% Similarity=0.332 Sum_probs=10.8
Q ss_pred hhCCCCCEEEEEec
Q 039205 23 QGCQPGDSLVFHFS 36 (158)
Q Consensus 23 ~~a~~gD~v~f~fS 36 (158)
++.++||.|++.|=
T Consensus 4 ~~~~~GD~VyViYr 17 (75)
T PF11132_consen 4 KPYHAGDIVYVIYR 17 (75)
T ss_pred cccCCCCEEEEEEc
Confidence 45688999988773
No 69
>PRK11560 phosphoethanolamine transferase; Provisional
Probab=26.76 E-value=53 Score=30.41 Aligned_cols=27 Identities=15% Similarity=0.300 Sum_probs=20.6
Q ss_pred HHHHHhhCCCCCEEEEEeccCCCcccc
Q 039205 18 LCWLMQGCQPGDSLVFHFSGHASCIID 44 (158)
Q Consensus 18 l~~L~~~a~~gD~v~f~fSGHG~~i~D 44 (158)
+.++++.++..+++++|+|-||..+-+
T Consensus 445 lg~ii~~Lk~~nTivIy~SDHGe~lge 471 (558)
T PRK11560 445 ISSVIDQLRDKKAIVFYAADHGESINE 471 (558)
T ss_pred HHHHHHHHHhcCeEEEEEcCCCCcCCC
Confidence 345566667789999999999996544
No 70
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=26.74 E-value=1.6e+02 Score=21.23 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 12 YNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 12 ~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+.+.++++.++++..|+|.+-+...|+..
T Consensus 18 ~~~k~al~~~l~~L~~~d~fnii~f~~~~ 46 (155)
T PF13768_consen 18 ELVKDALRAILRSLPPGDRFNIIAFGSSV 46 (155)
T ss_pred HHHHHHHHHHHHhCCCCCEEEEEEeCCEe
Confidence 78889999999999999999888888875
No 71
>PRK10331 L-fuculokinase; Provisional
Probab=26.74 E-value=67 Score=28.37 Aligned_cols=30 Identities=0% Similarity=-0.238 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 11 KYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 11 r~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
.+++.+.++.++++..+.++.-+-+||+|.
T Consensus 53 w~~~~~~~~~~~~~~~~~~I~~I~is~~~~ 82 (470)
T PRK10331 53 LQRFADCCRQINSELTECHIRGITVTTFGV 82 (470)
T ss_pred HHHHHHHHHHHHHhCCccceEEEEEecccc
Confidence 567778888888777677788899999877
No 72
>PF00884 Sulfatase: Sulfatase; InterPro: IPR000917 Sulphatases 3.1.6. from EC are enzymes that hydrolyze various sulphate esters. The sequence of different types of sulphatases are available and have shown to be structurally related [, , ]; these include: arylsulphatase A 3.1.6.8 from EC (ASA), a lysosomal enzyme which hydrolyses cerebroside sulphate; arylsulphatase B 3.1.6.12 from EC (ASB), which hydrolyses the sulphate ester group from N-acetylgalactosamine 4-sulphate residues of dermatan sulphate; arylsulphatase C (ASD) and E (ASE); steryl-sulphatase 3.1.6.2 from EC (STS), a membrane bound microsomal enzyme which hydrolyses 3-beta-hydroxy steroid sulphates; iduronate 2-sulphatase precursor 3.1.6.13 from EC (IDS), a lysosomal enzyme that hydrolyses the 2-sulphate groups from non-reducing-terminal iduronic acid residues in dermatan sulphate and heparan sulphate; N-acetylgalactosamine-6-sulphatase 3.1.6.4 from EC, which hydrolyses the 6-sulphate groups of the N-acetyl-d-galactosamine 6-sulphate units of chondroitin sulphate and the D-galactose 6-sulphate units of keratan sulphate; glucosamine-6-sulphatase 3.1.6.14 from EC (G6S), which hydrolyses the N-acetyl-D-glucosamine 6-sulphate units of heparan sulphate and keratan sulphate; N-sulphoglucosamine sulphohydrolase 3.10.1.1 from EC (sulphamidase), the lysosomal enzyme that catalyses the hydrolysis of N-sulpho-d-glucosamine into glucosamine and sulphate; sea urchin embryo arylsulphatase 3.1.6.1 from EC; green algae arylsulphatase 3.1.6.1 from EC, which plays an important role in the mineralisation of sulphates; and arylsulphatase 3.1.6.1 from EC from Escherichia coli (aslA), Klebsiella aerogenes (gene atsA) and Pseudomonas aeruginosa (gene atsA). ; GO: 0008484 sulfuric ester hydrolase activity, 0008152 metabolic process; PDB: 1P49_A 1FSU_A 2QZU_A 2W5Q_A 2W5T_A 2W5S_A 2W5R_A 3LXQ_A 1HDH_B 1E33_P ....
Probab=26.39 E-value=86 Score=24.74 Aligned_cols=31 Identities=10% Similarity=0.062 Sum_probs=22.3
Q ss_pred HHHHHHHhhC----CCCCEEEEEeccCCCcccccC
Q 039205 16 MALCWLMQGC----QPGDSLVFHFSGHASCIIDAC 46 (158)
Q Consensus 16 ~al~~L~~~a----~~gD~v~f~fSGHG~~i~DcC 46 (158)
++|..+++.+ ...+++++++|=||..+..++
T Consensus 222 ~~l~~~~~~l~~~~~~d~TiiiitsDHG~~~~e~~ 256 (308)
T PF00884_consen 222 DQLGRFIEYLKEQGLYDNTIIIITSDHGESFGENG 256 (308)
T ss_dssp HHHHHHHHHHHHTTCGGGEEEEEEESSSSSTGGHH
T ss_pred HHhhhhhhhhhhcCCcccceeEEecCcCccccccc
Confidence 3455555444 677999999999999876633
No 73
>PF04863 EGF_alliinase: Alliinase EGF-like domain; InterPro: IPR006947 Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system [].; GO: 0016846 carbon-sulfur lyase activity; PDB: 1LK9_B 2HOX_C 2HOR_A.
Probab=26.29 E-value=22 Score=22.99 Aligned_cols=12 Identities=33% Similarity=0.670 Sum_probs=7.0
Q ss_pred EEeccCCCcccc
Q 039205 33 FHFSGHASCIID 44 (158)
Q Consensus 33 f~fSGHG~~i~D 44 (158)
+.-||||.+.+|
T Consensus 17 i~CSGHGr~flD 28 (56)
T PF04863_consen 17 ISCSGHGRAFLD 28 (56)
T ss_dssp S--TTSEE--TT
T ss_pred CCcCCCCeeeec
Confidence 467999998888
No 74
>PLN02618 tryptophan synthase, beta chain
Probab=26.22 E-value=1.1e+02 Score=27.29 Aligned_cols=23 Identities=26% Similarity=0.287 Sum_probs=18.1
Q ss_pred HHHHHhhCCCCCEEEEEeccCCC
Q 039205 18 LCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 18 l~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
..++.++..+++.|++-+||+|.
T Consensus 374 a~~~a~~l~~~~~iVv~lsgrG~ 396 (410)
T PLN02618 374 LEKLCPTLPDGTKVVVNCSGRGD 396 (410)
T ss_pred HHHHhHhcCCCCEEEEEeCCCCc
Confidence 34555667889999999999994
No 75
>cd02185 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry.
Probab=26.02 E-value=71 Score=23.68 Aligned_cols=43 Identities=19% Similarity=0.142 Sum_probs=29.4
Q ss_pred chHHHHHHHHHHHHh------hCCCCCEEEEEeccCCCcccccCCCCCcCC
Q 039205 9 PTKYNMRMALCWLMQ------GCQPGDSLVFHFSGHASCIIDACHSGTMLD 53 (158)
Q Consensus 9 aTr~nI~~al~~L~~------~a~~gD~v~f~fSGHG~~i~DcCHSG~~~r 53 (158)
=|++.|++|-++|++ +.++.|++-+.||-= -=+|+|+=+...|
T Consensus 13 nt~e~I~~at~eLl~~i~~~N~l~~edivSv~FT~T--~DL~a~FPA~aaR 61 (117)
T cd02185 13 NTAEEILEATRELLEEIIERNNIKPEDIISVIFTVT--PDLDAAFPAKAAR 61 (117)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEEeC--CcccccChHHHHH
Confidence 478889988887764 568899999999822 2255555444433
No 76
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=26.00 E-value=36 Score=23.55 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=17.0
Q ss_pred HhcCCCCCHHHHHHHHHHHHh
Q 039205 136 SELGHGTTYGRMLTSMRSTIY 156 (158)
Q Consensus 136 L~~~~~~s~~~l~~~vr~~v~ 156 (158)
++-.++++|++|.+.|+++++
T Consensus 15 Irvp~~~~y~~L~~ki~~kLk 35 (80)
T cd06406 15 IQVARGLSYATLLQKISSKLE 35 (80)
T ss_pred EEcCCCCCHHHHHHHHHHHhC
Confidence 344567999999999999886
No 77
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=25.60 E-value=55 Score=25.79 Aligned_cols=21 Identities=33% Similarity=0.419 Sum_probs=18.5
Q ss_pred HHHHHHHHhhCCCC-CEEEEEe
Q 039205 15 RMALCWLMQGCQPG-DSLVFHF 35 (158)
Q Consensus 15 ~~al~~L~~~a~~g-D~v~f~f 35 (158)
.-+|+.|++.+++| |+|+++=
T Consensus 50 Rp~l~~ll~~i~~g~d~lvV~~ 71 (222)
T COG1961 50 RPGLQRLLEDIEEGKDTLVVYK 71 (222)
T ss_pred CHHHHHHHHHHHcCCcEEEEEE
Confidence 67899999999999 9999874
No 78
>PF14592 Chondroitinas_B: Chondroitinase B; PDB: 1OFM_A 1OFL_A 1DBO_A 1DBG_A.
Probab=25.57 E-value=63 Score=29.05 Aligned_cols=25 Identities=28% Similarity=0.591 Sum_probs=14.2
Q ss_pred HHHHHHHhhCCCCCEEEE----------EeccCCC
Q 039205 16 MALCWLMQGCQPGDSLVF----------HFSGHAS 40 (158)
Q Consensus 16 ~al~~L~~~a~~gD~v~f----------~fSGHG~ 40 (158)
++|+.-++.|+|||.+++ .|.|+|+
T Consensus 5 ~~lq~Ai~~a~pGD~I~L~~Gty~~~~i~~~~~GT 39 (425)
T PF14592_consen 5 AELQSAIDNAKPGDTIVLADGTYKDVEIVFKGSGT 39 (425)
T ss_dssp HHHHHHHHH--TT-EEEE-SEEEET-EEEE-S--B
T ss_pred HHHHHHHHhCCCCCEEEECCceeecceEEEEeccc
Confidence 566666778999999864 6788887
No 79
>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=25.48 E-value=37 Score=23.12 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=12.3
Q ss_pred HHhhCCCCCEEEEEe
Q 039205 21 LMQGCQPGDSLVFHF 35 (158)
Q Consensus 21 L~~~a~~gD~v~f~f 35 (158)
|+.++++||.|++|.
T Consensus 32 lv~~~~vGD~VLVH~ 46 (76)
T TIGR00074 32 LVGEVKVGDYVLVHV 46 (76)
T ss_pred eeCCCCCCCEEEEec
Confidence 456789999999885
No 80
>TIGR01796 CM_mono_aroH monofunctional chorismate mutase, gram positive type, clade 1. This model represents a family of monofunctional (non-fused) chorismate mutases from gram positive bacteria (Firmicutes) and cyanobacteria. Trusted members of the family are found in operons with other enzymes of the chorismate pathways, both up- and downstream of CM (Listeria, Bacillus, Oceanobacillus) or are the sole CM in the genome where the other members of the chorismate pathways are found elsewhere in the genome (Nostoc, Thermosynechococcus).
Probab=25.06 E-value=76 Score=23.53 Aligned_cols=44 Identities=14% Similarity=0.080 Sum_probs=30.4
Q ss_pred cchHHHHHHHHHHHHh------hCCCCCEEEEEeccCCCcccccCCCCCcCC
Q 039205 8 WPTKYNMRMALCWLMQ------GCQPGDSLVFHFSGHASCIIDACHSGTMLD 53 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~------~a~~gD~v~f~fSGHG~~i~DcCHSG~~~r 53 (158)
.=|++.|++|-++|++ +.++.|++-+.||- +-=+|+|+=+.+.|
T Consensus 12 ~nt~e~I~~at~eLl~~ii~~N~l~~edivSv~FT~--T~DL~a~FPA~aaR 61 (117)
T TIGR01796 12 RNEAEEIGEAVAELLTELMERNELTPEDLISVIFTV--TEDLHADFPAAAAR 61 (117)
T ss_pred CCCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEEe--cCcccccChHHHHH
Confidence 3478889988887764 56889999999982 22255666555444
No 81
>PRK05568 flavodoxin; Provisional
Probab=24.80 E-value=49 Score=23.83 Aligned_cols=12 Identities=17% Similarity=0.310 Sum_probs=10.8
Q ss_pred CEEEEEeccCCC
Q 039205 29 DSLVFHFSGHAS 40 (158)
Q Consensus 29 D~v~f~fSGHG~ 40 (158)
.++++|||++|.
T Consensus 3 ~~~IvY~S~~Gn 14 (142)
T PRK05568 3 KINIIYWSGTGN 14 (142)
T ss_pred eEEEEEECCCch
Confidence 378999999999
No 82
>PRK10717 cysteine synthase A; Provisional
Probab=24.80 E-value=1.2e+02 Score=25.40 Aligned_cols=32 Identities=16% Similarity=0.091 Sum_probs=23.3
Q ss_pred chHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 9 PTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 9 aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
|+-..-+.++.++.++..+++.|++-++|+|.
T Consensus 278 pssga~laa~~~l~~~~~~~~~Vv~v~~g~g~ 309 (330)
T PRK10717 278 GSSGINVAAALRLARELGPGHTIVTILCDSGE 309 (330)
T ss_pred ecHHHHHHHHHHHHHhcCCCCEEEEEECCCch
Confidence 34444455566666666788999999999997
No 83
>PF06720 Phi-29_GP16_7: Bacteriophage phi-29 early protein GP16.7; InterPro: IPR009595 The early-expressed gene 16.7 is conserved in bacteriophage phi-29 and related phages. It encodes a membrane protein, GP16.7, consisting of an N-terminal transmembrane domain and a C-terminal DNA-binding and dimerisation domain. GP16.7 plays an important role in organising membrane-associated bacteriophage DNA replication [, ]. The C-terminal domain has a similar secondary structure similar to homeodomains, but forms a fundamentally different tertiary structure consisting of a six-helical dimeric fold []. Multimerisation of this dimer leads to efficient DNA binding.; PDB: 2C5R_B 2BNK_A 1ZAE_B.
Probab=24.38 E-value=25 Score=26.08 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=0.0
Q ss_pred EEEEEeccCCC
Q 039205 30 SLVFHFSGHAS 40 (158)
Q Consensus 30 ~v~f~fSGHG~ 40 (158)
.++|+||||-.
T Consensus 13 ~~if~~sg~n~ 23 (130)
T PF06720_consen 13 CVIFLLSGRNN 23 (130)
T ss_dssp -----------
T ss_pred HHHHHhcCcCc
Confidence 36899999975
No 84
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=24.27 E-value=56 Score=24.37 Aligned_cols=14 Identities=21% Similarity=0.738 Sum_probs=12.0
Q ss_pred HHHHhhCCCCCEEE
Q 039205 19 CWLMQGCQPGDSLV 32 (158)
Q Consensus 19 ~~L~~~a~~gD~v~ 32 (158)
.|+++++++||+|+
T Consensus 43 ~~I~~~~~~gDiVI 56 (130)
T PF02639_consen 43 FYIVNHAKPGDIVI 56 (130)
T ss_pred HHHHHcCCCCCEEE
Confidence 38899999999986
No 85
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.04 E-value=61 Score=25.06 Aligned_cols=15 Identities=27% Similarity=0.567 Sum_probs=13.1
Q ss_pred HHHHhhCCCCCEEEE
Q 039205 19 CWLMQGCQPGDSLVF 33 (158)
Q Consensus 19 ~~L~~~a~~gD~v~f 33 (158)
.|+++.+++||+|+=
T Consensus 58 ~~Iv~~a~~gDlVVT 72 (150)
T COG1671 58 DWIVNLAEKGDLVVT 72 (150)
T ss_pred HHHHHhCCCCCEEEE
Confidence 489999999999974
No 86
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=23.98 E-value=1.2e+02 Score=26.63 Aligned_cols=44 Identities=18% Similarity=0.136 Sum_probs=32.9
Q ss_pred chHHHHHHHHHHHHhhCCCCCEEEEEec-----cCCC-------------cccccCCCCCcCC
Q 039205 9 PTKYNMRMALCWLMQGCQPGDSLVFHFS-----GHAS-------------CIIDACHSGTMLD 53 (158)
Q Consensus 9 aTr~nI~~al~~L~~~a~~gD~v~f~fS-----GHG~-------------~i~DcCHSG~~~r 53 (158)
+--+-++..++.| +..++.=.|+|.|| ||+. +.+|+|.+|-...
T Consensus 183 ~gva~lle~lk~l-~~~~~~~~vy~v~tvqEEVGlrGA~~~a~~i~pd~aiavd~~~~~d~~~ 244 (355)
T COG1363 183 AGVAALLELLKEL-KGIELPADVYFVASVQEEVGLRGAKTSAFRIKPDIAIAVDVTPAGDTPG 244 (355)
T ss_pred HhHHHHHHHHHHh-ccCCCCceEEEEEecchhhccchhhccccccCCCEEEEEecccccCCCC
Confidence 3445677778887 45566667899998 8887 8899999988744
No 87
>TIGR02628 fuculo_kin_coli L-fuculokinase. Members of this family are L-fuculokinase, from the clade that includes the L-fuculokinase of Escherichia coli. This enzyme catalyzes the second step in fucose catabolism. This family belongs to FGGY family of carbohydrate kinases (pfam02782, pfam00370). It is encoded by the kinase (K) gene of the fucose (fuc) operon.
Probab=23.98 E-value=70 Score=28.27 Aligned_cols=35 Identities=3% Similarity=-0.168 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEeccCCC--ccccc
Q 039205 11 KYNMRMALCWLMQGCQPGDSLVFHFSGHAS--CIIDA 45 (158)
Q Consensus 11 r~nI~~al~~L~~~a~~gD~v~f~fSGHG~--~i~Dc 45 (158)
.+++.+++++++.+..+.++.-|-+||+|. +.+|-
T Consensus 52 w~~~~~~~~~l~~~~~~~~I~aI~~s~~~~~~v~~D~ 88 (465)
T TIGR02628 52 WQKLADCCQQINSELTEKHIRGIAVTTFGVDGAPFDK 88 (465)
T ss_pred HHHHHHHHHHHHhhcChhceEEEEEeccccceEEECC
Confidence 577888888888666677899999999877 44444
No 88
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=23.67 E-value=85 Score=21.64 Aligned_cols=11 Identities=55% Similarity=1.096 Sum_probs=7.7
Q ss_pred hCCCCCEEEEE
Q 039205 24 GCQPGDSLVFH 34 (158)
Q Consensus 24 ~a~~gD~v~f~ 34 (158)
++++||+++|.
T Consensus 74 ~a~~GD~ll~~ 84 (95)
T PF02938_consen 74 GAKPGDLLLFV 84 (95)
T ss_dssp T--TTEEEEEE
T ss_pred CCCCCCEEEEE
Confidence 68999999885
No 89
>KOG4107 consensus MP1 adaptor interacting protein P14 [Signal transduction mechanisms]
Probab=23.46 E-value=91 Score=22.91 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=16.2
Q ss_pred HHHHHHHhhCCCCC----------EEEEEeccCCC
Q 039205 16 MALCWLMQGCQPGD----------SLVFHFSGHAS 40 (158)
Q Consensus 16 ~al~~L~~~a~~gD----------~v~f~fSGHG~ 40 (158)
+||-.++.|+.-|- =.++-|||.|.
T Consensus 5 KALtqVLsQaNTgGV~~tlLln~EG~LLAYsGygd 39 (125)
T KOG4107|consen 5 KALTQVLSQANTGGVDGTLLLNKEGLLLAYSGYGD 39 (125)
T ss_pred HHHHHHHhhcccCCccceEEEcCCCcEEEecccCc
Confidence 46667777776542 23677888887
No 90
>PF12724 Flavodoxin_5: Flavodoxin domain
Probab=23.12 E-value=41 Score=24.72 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=9.1
Q ss_pred EEEEeccCCC
Q 039205 31 LVFHFSGHAS 40 (158)
Q Consensus 31 v~f~fSGHG~ 40 (158)
+++|+|+||.
T Consensus 1 LIvY~S~~G~ 10 (143)
T PF12724_consen 1 LIVYFSKTGN 10 (143)
T ss_pred CEEEECCCch
Confidence 5899999999
No 91
>cd03086 PGM3 PGM3 (phosphoglucomutase 3), also known as PAGM (phosphoacetylglucosamine mutase) and AGM1 (N-acetylglucosamine-phosphate mutase), is an essential enzyme found in eukaryotes that reversibly catalyzes the conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate as part of the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway. UDP-GlcNAc is an essential metabolite that serves as the biosynthetic precursor of many glycoproteins and mucopolysaccharides. AGM1 is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. The alpha-D-phosphohexomutases have four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=22.79 E-value=35 Score=31.07 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=16.2
Q ss_pred HHHHHhhCCCCCEEEEEe--ccCCCccccc
Q 039205 18 LCWLMQGCQPGDSLVFHF--SGHASCIIDA 45 (158)
Q Consensus 18 l~~L~~~a~~gD~v~f~f--SGHG~~i~Dc 45 (158)
++|+.+.+..-| +.|+| ||||++||--
T Consensus 340 ~k~v~~~m~e~~-~~~ggE~sGHgtvif~~ 368 (513)
T cd03086 340 VKHLHHAAEEFD-IGVYFEANGHGTVLFSE 368 (513)
T ss_pred HHHHHHHHHHhC-cceEEeccCCEEEEECc
Confidence 455555555555 44554 9999955543
No 92
>PLN02569 threonine synthase
Probab=22.59 E-value=1.3e+02 Score=27.28 Aligned_cols=45 Identities=29% Similarity=0.224 Sum_probs=31.9
Q ss_pred cchHHHHHHHHHHHHhh--CCCCCEEEEEeccCCC----cccccCCCCCcCC
Q 039205 8 WPTKYNMRMALCWLMQG--CQPGDSLVFHFSGHAS----CIIDACHSGTMLD 53 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~--a~~gD~v~f~fSGHG~----~i~DcCHSG~~~r 53 (158)
.|+-+.-+.++.+|.++ .+++|.|++...|||. ..+| =|++...+
T Consensus 405 epssAaalAal~kl~~~g~i~~~~~VV~i~Tg~GlK~~~~~~~-~~~~~~~~ 455 (484)
T PLN02569 405 CPHTGVALAALKKLRASGVIGPTDRTVVVSTAHGLKFTQSKID-YHSKEIPD 455 (484)
T ss_pred CchHHHHHHHHHHHHHcCCCCCCCcEEEEeCCCcccChhHHHH-hccccccc
Confidence 35556666777877764 5789999999999998 3333 66665544
No 93
>PRK02268 hypothetical protein; Provisional
Probab=22.55 E-value=65 Score=24.56 Aligned_cols=15 Identities=27% Similarity=0.627 Sum_probs=11.3
Q ss_pred HHhhCCCCCEEEEEec
Q 039205 21 LMQGCQPGDSLVFHFS 36 (158)
Q Consensus 21 L~~~a~~gD~v~f~fS 36 (158)
-+++.+|||.|++| |
T Consensus 32 pl~RmkpGD~ivyY-s 46 (141)
T PRK02268 32 PLRRMKPGDWIIYY-S 46 (141)
T ss_pred hhhcCCCCCEEEEE-e
Confidence 35678999998765 5
No 94
>PF05095 DUF687: Protein of unknown function (DUF687); InterPro: IPR007787 This family contains uncharacterised Chlamydia proteins.
Probab=22.24 E-value=1e+02 Score=28.62 Aligned_cols=40 Identities=15% Similarity=0.249 Sum_probs=34.2
Q ss_pred CcchHHHHHHHHHHHHhhCC-CCCEEEEEeccCCC----cccccC
Q 039205 7 KWPTKYNMRMALCWLMQGCQ-PGDSLVFHFSGHAS----CIIDAC 46 (158)
Q Consensus 7 ~~aTr~nI~~al~~L~~~a~-~gD~v~f~fSGHG~----~i~DcC 46 (158)
.-|.-+.|++.|+.+..... +|-..+++|.|-|+ ..+||+
T Consensus 92 ~~p~~qAll~~w~~FFs~~~n~~~~fl~if~G~Gg~~Vq~aL~~~ 136 (541)
T PF05095_consen 92 MHPICQALLEVWNRFFSRHENPGSTFLQIFYGDGGAYVQEALDCT 136 (541)
T ss_pred CChHHHHHHHHHHHHhCcCCCCCCcEEEEEeCCcHHHHHHHHhCc
Confidence 45788999999999999887 99999999999999 567744
No 95
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=22.23 E-value=1.3e+02 Score=19.89 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=21.1
Q ss_pred HHHHHHHHHHh--hCCCCCEEEEEeccCCC
Q 039205 13 NMRMALCWLMQ--GCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 13 nI~~al~~L~~--~a~~gD~v~f~fSGHG~ 40 (158)
.+.-+|..+++ +.+|||.+++.=.|-|.
T Consensus 52 ~~~~~L~~~~~~g~~~~Gd~vl~~~~G~G~ 81 (90)
T PF08541_consen 52 SIPINLADALEEGRIKPGDRVLLVGFGAGF 81 (90)
T ss_dssp HHHHHHHHHHHTTSSCTTEEEEEEEEETTT
T ss_pred hHHHHHHHHHHcCCCCCCCEEEEEEEEhhh
Confidence 34556777777 78999999998777664
No 96
>PF06110 DUF953: Eukaryotic protein of unknown function (DUF953); InterPro: IPR010357 This family consists of several hypothetical eukaryotic proteins of unknown function that are thioredoxin-like.; PDB: 1V9W_A 1WOU_A.
Probab=22.20 E-value=1.2e+02 Score=22.37 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=13.3
Q ss_pred HHHHHHHhh-CCCCCEEEEEecc
Q 039205 16 MALCWLMQG-CQPGDSLVFHFSG 37 (158)
Q Consensus 16 ~al~~L~~~-a~~gD~v~f~fSG 37 (158)
+++..+++. .+++..+|++|.|
T Consensus 6 ~~~~~~~~~~~~~~~~~fl~F~g 28 (119)
T PF06110_consen 6 DEFEKLVEEYENSGKPLFLLFTG 28 (119)
T ss_dssp HHHHHHHHC--TTTSEEEEEEE-
T ss_pred HHHHHHHHHhhcCCCeEEEEEEc
Confidence 345555554 4567888888874
No 97
>PF02995 DUF229: Protein of unknown function (DUF229); InterPro: IPR004245 Members of this family are uncharacterised with a long conserved region that may contain several domains.
Probab=22.14 E-value=1.1e+02 Score=27.76 Aligned_cols=27 Identities=19% Similarity=0.117 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 14 MRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 14 I~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
+++.|+++.+.--=+++++|.+|-||.
T Consensus 318 ~~~~l~~~~~~g~l~nT~vi~~SDHG~ 344 (497)
T PF02995_consen 318 LLDFLEKLQEEGVLDNTFVIFMSDHGL 344 (497)
T ss_pred HHHHHHHhhhcCcccccEEEEEcCCCc
Confidence 334444444332246899999999999
No 98
>PRK10649 hypothetical protein; Provisional
Probab=22.11 E-value=1.2e+02 Score=27.96 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=20.0
Q ss_pred HHHHHhhCC--CCCEEEEEeccCCCccccc
Q 039205 18 LCWLMQGCQ--PGDSLVFHFSGHASCIIDA 45 (158)
Q Consensus 18 l~~L~~~a~--~gD~v~f~fSGHG~~i~Dc 45 (158)
+..+++.++ ..|++++|+|-||..+.|.
T Consensus 440 l~~ii~~Lk~~~~nt~iiy~SDHGe~~~~~ 469 (577)
T PRK10649 440 VASLIKDFKATDPNGFLVYFSDHGEEVYDT 469 (577)
T ss_pred HHHHHHHHhcCCCCeEEEEECCCCcccccC
Confidence 444444443 4689999999999987763
No 99
>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=21.96 E-value=39 Score=22.39 Aligned_cols=14 Identities=29% Similarity=0.579 Sum_probs=9.7
Q ss_pred HHhhCCCCCEEEEE
Q 039205 21 LMQGCQPGDSLVFH 34 (158)
Q Consensus 21 L~~~a~~gD~v~f~ 34 (158)
|+.++++||.|++|
T Consensus 34 lv~~v~~Gd~VLVH 47 (68)
T PF01455_consen 34 LVPDVKVGDYVLVH 47 (68)
T ss_dssp TCTSB-TT-EEEEE
T ss_pred EeCCCCCCCEEEEe
Confidence 45678999999987
No 100
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=21.91 E-value=53 Score=27.00 Aligned_cols=33 Identities=15% Similarity=0.240 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhhCCCCCEEEEEeccCCC----cccccC
Q 039205 12 YNMRMALCWLMQGCQPGDSLVFHFSGHAS----CIIDAC 46 (158)
Q Consensus 12 ~nI~~al~~L~~~a~~gD~v~f~fSGHG~----~i~DcC 46 (158)
.+|-++++.+++..+.|.. +||.|.|+ .++|++
T Consensus 33 ~~I~~av~~~~~~l~~ggr--l~~~GaGtSg~la~~da~ 69 (257)
T cd05007 33 PQIARAVDAAAERLRAGGR--LIYVGAGTSGRLGVLDAS 69 (257)
T ss_pred HHHHHHHHHHHHHHHcCCE--EEEEcCcHHHHHHHHHHH
Confidence 5677888888888888887 56777777 567764
No 101
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=21.85 E-value=61 Score=24.13 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=13.5
Q ss_pred HhhCCCCCEEEEEecc
Q 039205 22 MQGCQPGDSLVFHFSG 37 (158)
Q Consensus 22 ~~~a~~gD~v~f~fSG 37 (158)
+..++|||.||+.+.+
T Consensus 36 v~rl~~GDlVFlT~~~ 51 (122)
T COG1935 36 VLRLHEGDLVFLTSTS 51 (122)
T ss_pred hhcCCCCCEEEEehhH
Confidence 5678999999999863
No 102
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=21.84 E-value=1.3e+02 Score=27.60 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=13.7
Q ss_pred CEEEEEeccCCCcccc
Q 039205 29 DSLVFHFSGHASCIID 44 (158)
Q Consensus 29 D~v~f~fSGHG~~i~D 44 (158)
|++++|+|-||..+-|
T Consensus 430 ~t~iIy~SDHGe~lge 445 (522)
T PRK09598 430 PALMIYLSDHGESLGE 445 (522)
T ss_pred CeEEEEEccCcccccc
Confidence 9999999999986544
No 103
>cd07364 PCA_45_Dioxygenase_B Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate. Protocatechuate 4,5-dioxygenase (LigAB) catalyzes the oxidization and subsequent ring-opening of protocatechuate (or 3,4-dihydroxybenzoic acid, PCA), an intermediate in the breakdown of lignin and other compounds. Protocatechuate 4,5-dioxygenase is an aromatic ring opening dioxygenase belonging to the class III extradiol enzyme family, a group of enyzmes that cleaves aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon using a non-heme Fe(II). LigAB is composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. The B subunit (LigB) is the catalytic subunit of LigAB.
Probab=21.73 E-value=1.3e+02 Score=25.08 Aligned_cols=39 Identities=13% Similarity=-0.067 Sum_probs=29.0
Q ss_pred CCcchHHHHHHHHHHHHhhC--CCCCEEEEEeccCCCcccc
Q 039205 6 LKWPTKYNMRMALCWLMQGC--QPGDSLVFHFSGHASCIID 44 (158)
Q Consensus 6 ~~~aTr~nI~~al~~L~~~a--~~gD~v~f~fSGHG~~i~D 44 (158)
...+.++.++++++.+-+.+ ..=|+|++.+|=|...+++
T Consensus 25 ~~~~~~~~~~~a~~~~~~~~~~~~pD~vVvi~~dH~~~f~~ 65 (277)
T cd07364 25 TDEPYWKPLFKGYQPARDWIKKNKPDVAIIVYNDHASAFDL 65 (277)
T ss_pred CchHHHHHHHHHHHHHHHHHHHhCCCEEEEEcCchHHhhcc
Confidence 35678899999999886655 2348888888999884444
No 104
>COG3673 Uncharacterized conserved protein [Function unknown]
Probab=21.45 E-value=1.3e+02 Score=26.69 Aligned_cols=30 Identities=23% Similarity=0.311 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 11 KYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 11 r~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
..||..|..-|++.-+|||.+|.+=---|+
T Consensus 104 ~~nI~~AYrFL~~~yepGD~Iy~FGFSRGA 133 (423)
T COG3673 104 VQNIREAYRFLIFNYEPGDEIYAFGFSRGA 133 (423)
T ss_pred HHHHHHHHHHHHHhcCCCCeEEEeeccchh
Confidence 579999999999999999998766333455
No 105
>PRK06721 threonine synthase; Reviewed
Probab=21.36 E-value=1.6e+02 Score=25.22 Aligned_cols=33 Identities=15% Similarity=0.171 Sum_probs=24.1
Q ss_pred cchHHHHHHHHHHHHh--hCCCCCEEEEEeccCCC
Q 039205 8 WPTKYNMRMALCWLMQ--GCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~--~a~~gD~v~f~fSGHG~ 40 (158)
.|+...-+.++.++.+ +..+++.|++.++|+|.
T Consensus 284 epssgaalaa~~~~~~~~~~~~~~~Vv~v~~g~g~ 318 (352)
T PRK06721 284 EPGSNASLAGVMKHVQSGKIKKGETVVAVLTGNGL 318 (352)
T ss_pred CchHHHHHHHHHHHHHcCCCCCCCeEEEEeCCCCc
Confidence 3555566666666665 34678999999999997
No 106
>PRK06201 hypothetical protein; Validated
Probab=21.09 E-value=1e+02 Score=24.83 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=16.2
Q ss_pred HHHHHHhhCCCCCEEEEEeccCCC
Q 039205 17 ALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 17 al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
.+.+.++.++|||++++ .++|.
T Consensus 69 ~~~~ai~~~~pG~VlVi--d~~g~ 90 (221)
T PRK06201 69 MIHRALDLARPGDVIVV--DGGGD 90 (221)
T ss_pred HHHHHHhccCCCcEEEE--ECCCC
Confidence 34567888999999987 55554
No 107
>PF03415 Peptidase_C11: Clostripain family This family belongs to family C11 of the peptidase classification.; InterPro: IPR005077 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 the MEROPS peptidase family C11 (clostripain family, clan CD). ; PDB: 3UWS_A.
Probab=21.09 E-value=93 Score=27.30 Aligned_cols=31 Identities=13% Similarity=0.236 Sum_probs=19.5
Q ss_pred chHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 9 PTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 9 aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
...+.+.+-|+|..+.. |-|.-.+-+.+||.
T Consensus 78 ~dp~tL~~fi~~~~~~y-PA~~y~LIlw~HG~ 108 (397)
T PF03415_consen 78 GDPDTLSDFINWAKENY-PADRYGLILWDHGG 108 (397)
T ss_dssp TSHHHHHHHHHHHHHHS--ECEEEEEEES-B-
T ss_pred CCHHHHHHHHHHHHHhC-CcccEEEEEEECCC
Confidence 34455566666766554 77888889999998
No 108
>PRK09814 beta-1,6-galactofuranosyltransferase; Provisional
Probab=20.94 E-value=1.3e+02 Score=25.16 Aligned_cols=28 Identities=21% Similarity=0.395 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHhhCCCCCEEEEEeccCC
Q 039205 12 YNMRMALCWLMQGCQPGDSLVFHFSGHA 39 (158)
Q Consensus 12 ~nI~~al~~L~~~a~~gD~v~f~fSGHG 39 (158)
..+...++.++...++||+|+++|....
T Consensus 49 ~~~~~~~~~~~~~~~~~Dvv~~~~P~~~ 76 (333)
T PRK09814 49 SERSKRLDGILASLKPGDIVIFQFPTWN 76 (333)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEECCCCc
Confidence 3445556667788999999999987553
No 109
>PF09994 DUF2235: Uncharacterized alpha/beta hydrolase domain (DUF2235); InterPro: IPR018712 This domain has no known function.
Probab=20.57 E-value=1.4e+02 Score=24.66 Aligned_cols=31 Identities=19% Similarity=0.316 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHhhCCCCCEEEEEeccCCC
Q 039205 10 TKYNMRMALCWLMQGCQPGDSLVFHFSGHAS 40 (158)
Q Consensus 10 Tr~nI~~al~~L~~~a~~gD~v~f~fSGHG~ 40 (158)
-.++|.++.++|.+.-+|||.++++=-.-|+
T Consensus 73 ~~~~I~~ay~~l~~~~~~gd~I~lfGFSRGA 103 (277)
T PF09994_consen 73 IEARIRDAYRFLSKNYEPGDRIYLFGFSRGA 103 (277)
T ss_pred hHHHHHHHHHHHHhccCCcceEEEEecCccH
Confidence 3678999999999999999999877667788
No 110
>PLN02433 uroporphyrinogen decarboxylase
Probab=20.40 E-value=70 Score=27.20 Aligned_cols=39 Identities=13% Similarity=0.176 Sum_probs=30.2
Q ss_pred cchHHHHHHHHHHHHhhCCCCCEEEEEeccCCC----------cccccCCC
Q 039205 8 WPTKYNMRMALCWLMQGCQPGDSLVFHFSGHAS----------CIIDACHS 48 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~a~~gD~v~f~fSGHG~----------~i~DcCHS 48 (158)
.-|.+.|.+..+.+++.+.++- ++.=+|||. ++++++++
T Consensus 288 ~gt~e~i~~~v~~~i~~~~~~g--~Il~~Gc~i~~~tp~eNi~a~v~av~~ 336 (345)
T PLN02433 288 FGSKEAIEKEVRDVVKKAGPQG--HILNLGHGVLVGTPEENVAHFFDVARE 336 (345)
T ss_pred CCCHHHHHHHHHHHHHHcCCCC--eEEecCCCCCCCCCHHHHHHHHHHHHH
Confidence 4588999999999999864332 777799998 66777665
No 111
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=20.40 E-value=1.4e+02 Score=23.05 Aligned_cols=25 Identities=12% Similarity=0.324 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHhhCCCCCEEEEEec
Q 039205 12 YNMRMALCWLMQGCQPGDSLVFHFS 36 (158)
Q Consensus 12 ~nI~~al~~L~~~a~~gD~v~f~fS 36 (158)
++....+..++.-++|+|.|++=-=
T Consensus 115 ~~LReeisail~~a~~~DeV~~rLE 139 (155)
T PF08496_consen 115 ESLREEISAILSVATPEDEVLVRLE 139 (155)
T ss_pred HHHHHHHHHHHHhCCCCCeEEEEEe
Confidence 5666777788899999999997543
No 112
>TIGR01415 trpB_rel pyridoxal-phosphate dependent TrpB-like enzyme. This model represents a family of pyridoxal-phosphate dependent enzyme (pfam00291) closely related to the beta subunit of tryptophan synthase (TIGR00263). However, the only case in which a member of this family replaces a member of TIGR00263 is in Sulfolobus species which contain two sequences which hit this model, one of which is proximal to the alpha subunit. In every other case so far, either the species appears not to make tryptophan (there is no trp synthase alpha subunit), or a trp synthase beta subunit matching TIGR00263 is also found.
Probab=20.33 E-value=1.6e+02 Score=26.20 Aligned_cols=29 Identities=24% Similarity=0.513 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHhhCC-CCC--EEEEEeccCCC
Q 039205 11 KYNMRMALCWLMQGCQ-PGD--SLVFHFSGHAS 40 (158)
Q Consensus 11 r~nI~~al~~L~~~a~-~gD--~v~f~fSGHG~ 40 (158)
-.+|..++ ++.++.+ +|+ +|+|-.||||.
T Consensus 375 a~alaaai-~~a~~~~~~~~~~vvv~~lsG~G~ 406 (419)
T TIGR01415 375 AHAIAAAI-DEARKCRETGEEKVILFNLSGHGL 406 (419)
T ss_pred HHHHHHHH-HHHHhcCcCCCCeEEEEEcCCCCc
Confidence 34444444 3444443 243 78899999995
No 113
>PF08245 Mur_ligase_M: Mur ligase middle domain; InterPro: IPR013221 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [].; GO: 0005524 ATP binding, 0009058 biosynthetic process; PDB: 3LK7_A 2XJA_A 2WTZ_A 2GCA_A 1JBW_A 1JBV_A 2GC5_A 1FGS_A 2GCB_A 2GC6_A ....
Probab=20.28 E-value=1.1e+02 Score=22.84 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=25.7
Q ss_pred CCcchHHHHHHHHHHHHhhCCCCCEEEEEe
Q 039205 6 LKWPTKYNMRMALCWLMQGCQPGDSLVFHF 35 (158)
Q Consensus 6 ~~~aTr~nI~~al~~L~~~a~~gD~v~f~f 35 (158)
+..+|.++|.++...+++.+++++.+++-.
T Consensus 86 ~~~~s~~~~~~~k~~~~~~~~~~~~~v~n~ 115 (188)
T PF08245_consen 86 DRFGSIEEYAEAKAKIFRGLKPGGVAVLNA 115 (188)
T ss_dssp CCTSSHHHHHHHHHGGHTTTSTTSEEEEET
T ss_pred ccCCCHHHHHHHHHhhhhhcccceEEEecC
Confidence 455899999999999999999999887754
No 114
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=20.13 E-value=1.6e+02 Score=17.14 Aligned_cols=22 Identities=5% Similarity=-0.023 Sum_probs=15.8
Q ss_pred HHHHHHHhcCCCCCHHHHHHHH
Q 039205 130 YSFIQASELGHGTTYGRMLTSM 151 (158)
Q Consensus 130 ~all~~L~~~~~~s~~~l~~~v 151 (158)
+.++..|.++|.+|..+|-+.+
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~ 27 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKL 27 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHh
Confidence 4577888888888888876654
No 115
>PRK08197 threonine synthase; Validated
Probab=20.06 E-value=1.6e+02 Score=25.50 Aligned_cols=33 Identities=15% Similarity=0.107 Sum_probs=24.7
Q ss_pred cchHHHHHHHHHHHHhh--CCCCCEEEEEeccCCC
Q 039205 8 WPTKYNMRMALCWLMQG--CQPGDSLVFHFSGHAS 40 (158)
Q Consensus 8 ~aTr~nI~~al~~L~~~--a~~gD~v~f~fSGHG~ 40 (158)
.|+-..-+.++.++.++ .++|+.|++...|||.
T Consensus 347 epssaaala~~~~l~~~~~~~~~~~Vv~v~tG~g~ 381 (394)
T PRK08197 347 CPEGAATFAAARQLRESGWLKGDERVVLFNTGSGL 381 (394)
T ss_pred CchHHHHHHHHHHHHHcCCcCCCCcEEEEeCCCCc
Confidence 45566667777777764 5678999999999984
Done!