Query psy3972
Match_columns 77
No_of_seqs 106 out of 431
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 22:02:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3972hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1038 PycA Pyruvate carboxyl 99.7 1.5E-16 3.2E-21 136.0 6.5 55 6-61 1014-1068(1149)
2 KOG0369|consensus 99.5 1E-13 2.2E-18 118.0 6.4 56 7-62 1041-1096(1176)
3 TIGR01235 pyruv_carbox pyruvat 99.2 1.8E-11 3.9E-16 106.0 7.0 53 6-59 1009-1061(1143)
4 PRK12999 pyruvate carboxylase; 99.2 7.4E-11 1.6E-15 102.1 7.7 52 7-59 1012-1063(1146)
5 PRK14042 pyruvate carboxylase 99.1 2.5E-10 5.5E-15 93.8 5.8 47 8-57 464-510 (596)
6 PRK09282 pyruvate carboxylase 98.7 3.4E-08 7.4E-13 80.9 6.5 49 6-59 464-512 (592)
7 TIGR01108 oadA oxaloacetate de 97.3 0.00028 6.2E-09 58.1 3.9 38 21-60 459-496 (582)
8 PRK14040 oxaloacetate decarbox 95.7 0.014 3.1E-07 48.4 4.1 27 30-56 471-497 (593)
9 PF11321 DUF3123: Protein of u 82.8 2.7 5.8E-05 29.1 4.1 43 14-57 10-59 (113)
10 PF00394 Cu-oxidase: Multicopp 62.4 32 0.0007 23.1 5.4 41 9-55 59-99 (159)
11 PF11191 DUF2782: Protein of u 61.6 28 0.00061 22.5 4.9 22 34-55 47-68 (105)
12 KOG1263|consensus 57.0 35 0.00076 28.7 5.8 40 10-55 209-248 (563)
13 PF15417 DUF4624: Domain of un 56.7 23 0.00049 25.0 4.0 23 36-58 50-72 (132)
14 PF10618 Tail_tube: Phage tail 54.7 40 0.00087 22.6 4.8 39 4-42 71-112 (119)
15 PF07474 G2F: G2F domain; Int 54.0 37 0.00079 25.0 4.9 39 8-48 90-128 (192)
16 PLN02354 copper ion binding / 48.9 65 0.0014 26.7 6.1 40 10-55 207-246 (552)
17 PLN00044 multi-copper oxidase- 48.0 63 0.0014 27.3 5.9 39 11-55 218-256 (596)
18 PF14326 DUF4384: Domain of un 47.1 52 0.0011 20.0 4.2 34 6-43 5-38 (83)
19 PF11008 DUF2846: Protein of u 46.5 26 0.00056 22.7 2.8 14 10-24 61-74 (117)
20 PF12293 DUF3625: Protein of u 45.4 34 0.00073 25.8 3.7 44 7-55 32-75 (241)
21 KOG3721|consensus 45.4 19 0.00041 28.6 2.4 29 31-70 203-231 (302)
22 COG2080 CoxS Aerobic-type carb 45.3 23 0.00049 25.5 2.6 19 37-55 2-20 (156)
23 PF11012 DUF2850: Protein of u 43.7 50 0.0011 21.2 3.8 36 32-68 38-75 (79)
24 PF07523 Big_3: Bacterial Ig-l 43.0 56 0.0012 19.0 3.7 48 5-53 16-66 (67)
25 PF12894 Apc4_WD40: Anaphase-p 42.9 26 0.00057 20.0 2.2 20 24-47 25-44 (47)
26 PF02736 Myosin_N: Myosin N-te 42.7 44 0.00096 18.4 3.1 20 4-23 20-39 (42)
27 PLN02792 oxidoreductase 42.1 97 0.0021 25.7 6.1 39 11-55 194-232 (536)
28 PF11774 Lsr2: Lsr2 ; InterPr 41.3 29 0.00064 23.2 2.5 24 35-58 18-41 (110)
29 PF13757 VIT_2: Vault protein 41.2 62 0.0013 20.6 3.9 26 31-56 51-78 (78)
30 PF06697 DUF1191: Protein of u 40.8 77 0.0017 24.7 5.1 40 8-48 127-168 (278)
31 TIGR00192 urease_beta urease, 40.6 57 0.0012 22.1 3.8 28 11-45 68-95 (101)
32 PF07971 Glyco_hydro_92: Glyco 40.5 75 0.0016 26.3 5.2 37 8-48 442-478 (502)
33 PF00699 Urease_beta: Urease b 39.5 47 0.001 22.5 3.3 23 11-39 67-89 (100)
34 PRK13202 ureB urease subunit b 39.2 58 0.0012 22.2 3.7 23 11-39 69-91 (104)
35 PF08207 EFP_N: Elongation fac 38.7 62 0.0013 18.9 3.4 16 40-55 10-25 (58)
36 PF00609 DAGK_acc: Diacylglyce 38.7 41 0.00089 22.9 3.0 27 11-47 135-161 (161)
37 PRK13203 ureB urease subunit b 37.4 68 0.0015 21.8 3.8 28 11-45 68-95 (102)
38 PLN02991 oxidoreductase 36.6 1.4E+02 0.003 25.0 6.2 39 11-55 203-241 (543)
39 COG0231 Efp Translation elonga 36.4 93 0.002 21.2 4.5 36 40-77 14-51 (131)
40 COG0832 UreB Urea amidohydrola 35.9 58 0.0013 22.4 3.3 30 10-46 67-96 (106)
41 TIGR03389 laccase laccase, pla 35.6 1.4E+02 0.0029 24.5 5.9 39 10-54 187-225 (539)
42 cd00407 Urease_beta Urease bet 35.0 79 0.0017 21.4 3.8 18 11-28 68-85 (101)
43 PLN02168 copper ion binding / 34.1 1.5E+02 0.0033 24.7 6.1 40 10-55 201-240 (545)
44 PRK09908 xanthine dehydrogenas 33.8 51 0.0011 23.6 2.9 16 37-52 7-22 (159)
45 TIGR03198 pucE xanthine dehydr 33.8 42 0.00092 23.6 2.5 16 38-53 3-18 (151)
46 PLN02191 L-ascorbate oxidase 33.6 1.5E+02 0.0032 24.7 5.9 38 11-54 227-264 (574)
47 cd00255 nidG2 Nidogen, G2 doma 33.4 1.7E+02 0.0037 22.1 5.8 38 8-47 88-126 (224)
48 PRK13201 ureB urease subunit b 32.6 86 0.0019 22.4 3.8 29 11-46 68-96 (136)
49 smart00682 G2F G2 nidogen doma 32.6 1.6E+02 0.0035 22.3 5.6 38 8-47 90-127 (227)
50 TIGR03390 ascorbOXfungal L-asc 32.2 1.6E+02 0.0034 24.3 5.8 40 10-55 198-238 (538)
51 PF15657 Tox-HNH-EHHH: HNH/End 32.2 61 0.0013 20.5 2.8 28 37-66 13-47 (72)
52 PRK13198 ureB urease subunit b 32.1 78 0.0017 23.1 3.6 29 10-45 95-123 (158)
53 PF15406 PH_6: Pleckstrin homo 32.0 65 0.0014 22.3 3.1 32 21-53 66-97 (112)
54 cd01237 Unc112 Unc-112 pleckst 31.8 99 0.0021 20.8 3.9 27 15-46 63-89 (106)
55 KOG0005|consensus 31.3 32 0.00069 21.9 1.4 16 3-18 6-21 (70)
56 PF11113 Phage_head_chap: Head 31.2 1.3E+02 0.0028 18.4 4.8 33 8-43 3-35 (56)
57 TIGR03193 4hydroxCoAred 4-hydr 30.9 51 0.0011 23.3 2.5 15 39-53 2-16 (148)
58 PRK11433 aldehyde oxidoreducta 30.8 69 0.0015 24.1 3.3 19 35-53 48-66 (217)
59 TIGR03388 ascorbase L-ascorbat 30.3 1.7E+02 0.0037 23.9 5.7 40 10-55 203-242 (541)
60 PLN02835 oxidoreductase 30.2 1.7E+02 0.0037 24.2 5.7 38 11-54 203-240 (539)
61 PF05593 RHS_repeat: RHS Repea 29.9 93 0.002 16.4 3.4 23 32-55 12-34 (38)
62 TIGR00037 eIF_5A translation i 29.7 1.4E+02 0.0031 20.2 4.5 36 40-76 17-54 (130)
63 PRK05641 putative acetyl-CoA c 29.5 2E+02 0.0044 20.1 6.1 31 17-54 10-40 (153)
64 COG2306 Predicted RNA-binding 29.0 87 0.0019 23.3 3.5 39 15-53 40-78 (183)
65 PF03462 PCRF: PCRF domain; I 28.8 82 0.0018 20.6 3.1 26 20-46 81-106 (115)
66 PRK13204 ureB urease subunit b 28.0 1.1E+02 0.0024 22.4 3.8 28 11-45 91-118 (159)
67 PF13510 Fer2_4: 2Fe-2S iron-s 27.7 1E+02 0.0022 18.9 3.2 15 37-51 2-16 (82)
68 PLN02604 oxidoreductase 27.7 2.2E+02 0.0048 23.5 6.0 40 10-55 224-263 (566)
69 PF04283 CheF-arch: Chemotaxis 27.7 1.7E+02 0.0037 21.6 4.9 56 6-67 139-194 (221)
70 TIGR01633 phi3626_gp14_N putat 27.4 1.3E+02 0.0028 18.8 3.7 35 8-43 81-118 (124)
71 PRK03999 translation initiatio 27.4 1.6E+02 0.0034 20.0 4.4 11 42-52 18-28 (129)
72 PRK13205 ureB urease subunit b 26.7 1.1E+02 0.0024 22.4 3.6 18 11-28 68-85 (162)
73 PLN03107 eukaryotic translatio 26.4 1.6E+02 0.0036 20.8 4.5 38 40-77 31-69 (159)
74 PRK15123 lipopolysaccharide co 25.8 1.1E+02 0.0023 22.9 3.5 21 33-53 33-53 (268)
75 PRK02866 cyanate hydratase; Va 25.1 59 0.0013 23.1 2.0 20 27-47 122-141 (147)
76 PRK00529 elongation factor P; 24.6 1.8E+02 0.0039 20.7 4.4 37 40-76 12-48 (186)
77 smart00230 CysPc Calpain-like 24.3 1.3E+02 0.0029 22.8 3.9 24 32-55 98-121 (318)
78 TIGR00673 cynS cyanate hydrata 24.1 63 0.0014 23.1 2.0 20 27-47 125-144 (150)
79 PF02770 Acyl-CoA_dh_M: Acyl-C 23.8 37 0.0008 19.0 0.6 11 41-51 27-37 (52)
80 cd04880 ACT_AAAH-PDT-like ACT 22.9 1.6E+02 0.0036 16.9 3.6 15 32-46 37-51 (75)
81 PF04607 RelA_SpoT: Region fou 22.9 1.6E+02 0.0035 18.2 3.5 26 27-53 64-93 (115)
82 cd00044 CysPc Calpains, domain 22.0 1.6E+02 0.0034 22.0 3.9 24 32-55 106-129 (315)
83 PF00622 SPRY: SPRY domain; I 21.8 2E+02 0.0043 17.4 4.5 44 17-68 67-111 (124)
84 PF12142 PPO1_DWL: Polyphenol 21.7 47 0.001 20.0 0.8 21 35-55 9-29 (54)
85 PF01782 RimM: RimM N-terminal 21.5 1.1E+02 0.0025 18.2 2.5 24 35-58 29-53 (84)
86 cd06405 PB1_Mekk2_3 The PB1 do 21.4 99 0.0021 20.2 2.3 16 38-53 2-17 (79)
87 PF10370 DUF2437: Domain of un 21.2 1.7E+02 0.0037 16.5 4.0 22 36-57 1-22 (50)
88 PRK09918 putative fimbrial cha 21.0 2.1E+02 0.0045 20.9 4.2 31 11-44 77-107 (230)
89 PF14452 Multi_ubiq: Multiubiq 20.4 1.1E+02 0.0024 18.1 2.3 15 37-51 1-15 (72)
90 PF06832 BiPBP_C: Penicillin-B 20.4 2.1E+02 0.0046 17.2 4.4 25 18-48 30-54 (89)
91 PRK15299 fimbrial chaperone pr 20.1 1.9E+02 0.0041 21.0 3.9 31 11-44 78-109 (227)
92 PF00648 Peptidase_C2: Calpain 20.0 2.4E+02 0.0052 20.6 4.4 22 34-55 87-108 (298)
No 1
>COG1038 PycA Pyruvate carboxylase [Energy production and conversion]
Probab=99.65 E-value=1.5e-16 Score=135.99 Aligned_cols=55 Identities=38% Similarity=0.526 Sum_probs=52.0
Q ss_pred eeeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCceecc
Q psy3972 6 TTLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASKVR 61 (77)
Q Consensus 6 ~~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~~~ 61 (77)
.++|++|+|++||||+|+|++|| +||++|||+||||||||+|.|.|+|+++....
T Consensus 1014 ~gEe~~v~ie~GktLii~l~aig-e~d~~G~r~v~felNGq~R~i~v~Drs~~~~~ 1068 (1149)
T COG1038 1014 PGEEIEVEIEKGKTLIIKLQAIG-EPDEKGMRTVYFELNGQPREIKVKDRSVGSSV 1068 (1149)
T ss_pred CCceEEEEecCCcEEEEEecccC-CCCcCCcEEEEEEeCCceeeeeeccccccccc
Confidence 57999999999999999999999 99999999999999999999999999877653
No 2
>KOG0369|consensus
Probab=99.46 E-value=1e-13 Score=118.01 Aligned_cols=56 Identities=55% Similarity=0.673 Sum_probs=50.5
Q ss_pred eeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCceeccc
Q psy3972 7 TLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASKVRN 62 (77)
Q Consensus 7 ~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~~~~ 62 (77)
.+|++|+||+||||+||++|+|...+..|+|+||||||||.|+|.|.|+++.++.+
T Consensus 1041 ~EE~~Veie~GKTL~ik~lAvg~~~~~~GqReVfFeLNGqlR~i~v~Dk~a~ke~v 1096 (1176)
T KOG0369|consen 1041 AEEFEVEIEQGKTLIIKLLAVGDLLKKTGQREVFFELNGQLRSIRVADKEAAKEIV 1096 (1176)
T ss_pred CceEEEEeccCcEEEEEeeecccccccCCceEEEEEecCceeeEEeechhhhhhhc
Confidence 58999999999999999999993345669999999999999999999999888765
No 3
>TIGR01235 pyruv_carbox pyruvate carboxylase. This enzyme plays a role in gluconeogensis but not glycolysis.
Probab=99.23 E-value=1.8e-11 Score=106.04 Aligned_cols=53 Identities=45% Similarity=0.582 Sum_probs=50.0
Q ss_pred eeeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCcee
Q psy3972 6 TTLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASK 59 (77)
Q Consensus 6 ~~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~ 59 (77)
.++|+.|++++||+++|||.++| ++|++|+|+|+|++|||+|+|.|+|.++..
T Consensus 1009 ~~~e~~v~~~~g~~~~i~~~~~~-~~~~~g~r~v~fElNGq~reV~V~D~s~~~ 1061 (1143)
T TIGR01235 1009 DGEEIEVDIEKGKTLIIKLQAVG-ATDSQGEREVFFELNGQPRRIKVPDRSHKA 1061 (1143)
T ss_pred CCcEEEEEecCCcEEEEEecccc-ccCCCCcEEEEEEECCeEEEEEecCccccc
Confidence 57899999999999999999999 999999999999999999999999997644
No 4
>PRK12999 pyruvate carboxylase; Reviewed
Probab=99.17 E-value=7.4e-11 Score=102.06 Aligned_cols=52 Identities=42% Similarity=0.569 Sum_probs=49.1
Q ss_pred eeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCcee
Q psy3972 7 TLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASK 59 (77)
Q Consensus 7 ~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~ 59 (77)
++|+.+++++||+++|+|.+++ +++++|+|+++|+||||+|+|.|+|.++.+
T Consensus 1012 ~e~~~~~~~~gk~~~i~~~~~~-~~~~~g~~~~~~~vnG~~~~V~v~d~~~~~ 1063 (1146)
T PRK12999 1012 GEEIEVEIEPGKTLIIKLEAIG-EPDEDGMRTVYFELNGQPREVQVRDRSVKS 1063 (1146)
T ss_pred CceEEeecCCCceeEEEeeccc-CcccCCcEEEEEEECCEEEEEEEecCcccc
Confidence 6899999999999999999999 999999999999999999999999987543
No 5
>PRK14042 pyruvate carboxylase subunit B; Provisional
Probab=99.06 E-value=2.5e-10 Score=93.82 Aligned_cols=47 Identities=15% Similarity=0.268 Sum_probs=43.4
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCc
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEA 57 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa 57 (77)
.|++|+ .+||+++|++.++| + +++|+|+||||+|||+|+|.|+|+++
T Consensus 464 ~e~~v~-~~Gk~~~Ikl~~~g-~-~~~G~r~v~fevng~~r~v~v~d~~~ 510 (596)
T PRK14042 464 SEFDII-LHGESYHVKVAGYG-M-IEHGQQSCFLWVDGVPEEVVVQHSEL 510 (596)
T ss_pred eEEEEE-ECCEEEEEEEeccc-c-ccCCceEEEEEEcCccceeecccccc
Confidence 489999 78999999999999 7 78899999999999999999999874
No 6
>PRK09282 pyruvate carboxylase subunit B; Validated
Probab=98.70 E-value=3.4e-08 Score=80.90 Aligned_cols=49 Identities=14% Similarity=0.232 Sum_probs=44.3
Q ss_pred eeeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCcee
Q psy3972 6 TTLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASK 59 (77)
Q Consensus 6 ~~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~ 59 (77)
.++|++|+++ ||+++|++.++| +++ +|+++|++|||+|+|.|+|+++..
T Consensus 464 ~~~~~~v~i~-Gk~~~i~~~~~g-~~~---~r~~~~~~ng~~~~v~v~d~~~~~ 512 (592)
T PRK09282 464 IPTEFKVEVD-GEKYEVKIEGVK-AEG---KRPFYLRVDGMPEEVVVEPLKEIV 512 (592)
T ss_pred CCeEEEEEEC-CEEEEEEEeecc-CCC---cceEEEEecCceeeeeccCccccc
Confidence 3578999999 999999999999 777 999999999999999999997543
No 7
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit. This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.
Probab=97.28 E-value=0.00028 Score=58.11 Aligned_cols=38 Identities=8% Similarity=0.008 Sum_probs=31.6
Q ss_pred EEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCceec
Q psy3972 21 GIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASKV 60 (77)
Q Consensus 21 iIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~~ 60 (77)
++++.++ +++++|.|+++|++|||+|.|.|.|.+....
T Consensus 459 ~~~~~~~--~~~~~g~~~~~~~vnG~~~~V~v~d~~~~~~ 496 (582)
T TIGR01108 459 HAQVVGK--YEETHASGSYTVEVEGKAFVVKVSPGGDVSQ 496 (582)
T ss_pred hhhcccc--ccccCCceEEEEEECCEEEEEEEcCCccccc
Confidence 5677776 5778899999999999999999999765433
No 8
>PRK14040 oxaloacetate decarboxylase; Provisional
Probab=95.69 E-value=0.014 Score=48.44 Aligned_cols=27 Identities=15% Similarity=0.202 Sum_probs=24.9
Q ss_pred CCCCCceEEEEEEECCeeeEEEEeecC
Q psy3972 30 DLTKNGEREVFFEMNGQLRSVFIRDKE 56 (77)
Q Consensus 30 e~de~G~R~V~FELNGq~R~V~V~D~s 56 (77)
+++++|.|+++|+|||++|.|.|.|.+
T Consensus 471 ~~~e~g~~~~~~~vnG~~~~V~v~~~~ 497 (593)
T PRK14040 471 KAEPAGSETYTVEVEGKAYVVKVSEGG 497 (593)
T ss_pred cCCCCCCeEEEEEECCEEEEEEECCCC
Confidence 567789999999999999999999986
No 9
>PF11321 DUF3123: Protein of unknown function (DUF3123); InterPro: IPR021470 This eukaryotic family of proteins has no known function.
Probab=82.82 E-value=2.7 Score=29.13 Aligned_cols=43 Identities=23% Similarity=0.258 Sum_probs=33.1
Q ss_pred eCCC-CEEEEEEeee--ccCCCCCceEEEEEEECCee----eEEEEeecCc
Q psy3972 14 IEKG-KTLGIKALAT--AADLTKNGEREVFFEMNGQL----RSVFIRDKEA 57 (77)
Q Consensus 14 ie~G-KtLiIkL~aI--g~e~de~G~R~V~FELNGq~----R~V~V~D~sa 57 (77)
|.-| ..|++.|-|+ | +.||||.-+|.|.-|=++ |.|+|--+.+
T Consensus 10 l~tg~~~LVLwL~AvVVS-~AdedG~l~VvY~~nfp~~DP~~tvrVA~~~v 59 (113)
T PF11321_consen 10 LGTGTRHLVLWLGAVVVS-AADEDGYLEVVYNGNFPRGDPFRTVRVARKDV 59 (113)
T ss_pred cccCceEEEEEeeeEEEe-cccCCCcEEEEecCCCCCCCCccceEechhhc
Confidence 4556 7788888887 8 889989999999988665 7777754433
No 10
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=62.44 E-value=32 Score=23.09 Aligned_cols=41 Identities=12% Similarity=0.319 Sum_probs=30.0
Q ss_pred EEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 9 LTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 9 ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
.-.+.+.+|+++.+++...+ ..+...|.+.|....|.-.|-
T Consensus 59 ~~~~~v~~g~~~rlRliNa~------~~~~~~~~i~gh~~~Via~DG 99 (159)
T PF00394_consen 59 PPVIKVKPGERYRLRLINAG------ASTSFNFSIDGHPMTVIAADG 99 (159)
T ss_dssp SGEEEEETTTEEEEEEEEES------SS-BEEEEETTBCEEEEEETT
T ss_pred cceEEEcCCcEEEEEEEecc------CCeeEEEEeeccceeEeeecc
Confidence 45688999999999998776 345777888888666655553
No 11
>PF11191 DUF2782: Protein of unknown function (DUF2782); InterPro: IPR021357 This is a bacterial family of proteins whose function is unknown.
Probab=61.56 E-value=28 Score=22.53 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=18.4
Q ss_pred CceEEEEEEECCeeeEEEEeec
Q psy3972 34 NGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 34 ~G~R~V~FELNGq~R~V~V~D~ 55 (77)
+|.+.=-|.+|||.++|+|+-+
T Consensus 47 ~~~~ieEyRv~G~l~~IkV~P~ 68 (105)
T PF11191_consen 47 GGSTIEEYRVNGQLYMIKVQPK 68 (105)
T ss_pred CCcEEEEEEECCeEeeEEEEeC
Confidence 3566677999999999999965
No 12
>KOG1263|consensus
Probab=57.03 E-value=35 Score=28.72 Aligned_cols=40 Identities=20% Similarity=0.306 Sum_probs=31.9
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
..+.+++|||...++...| -.-+++|.++|-...+.-.|.
T Consensus 209 ~~l~v~pGktY~lRiiN~g------~~~~l~F~I~~H~ltvVe~Dg 248 (563)
T KOG1263|consen 209 PTLTVEPGKTYRLRIINAG------LNTSLNFSIANHQLTVVEVDG 248 (563)
T ss_pred eEEEEcCCCEEEEEEEccc------cccceEEEECCeEEEEEEecc
Confidence 5688999999999998887 233688999988877766665
No 13
>PF15417 DUF4624: Domain of unknown function (DUF4624)
Probab=56.67 E-value=23 Score=25.04 Aligned_cols=23 Identities=35% Similarity=0.706 Sum_probs=20.0
Q ss_pred eEEEEEEECCeeeEEEEeecCce
Q psy3972 36 EREVFFEMNGQLRSVFIRDKEAS 58 (77)
Q Consensus 36 ~R~V~FELNGq~R~V~V~D~sa~ 58 (77)
.-+|+|.++|+.--|.|+|+.+.
T Consensus 50 ~aEv~f~mDGe~~iVEiKd~~~d 72 (132)
T PF15417_consen 50 DAEVYFQMDGESGIVEIKDRKTD 72 (132)
T ss_pred eeEEEEEEcCccceEEeccCCcc
Confidence 45899999999999999999654
No 14
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=54.68 E-value=40 Score=22.61 Aligned_cols=39 Identities=23% Similarity=0.321 Sum_probs=28.4
Q ss_pred eeeeeEEEEEeCCCCEEEEEEeeeccCC--C-CCceEEEEEE
Q psy3972 4 ELTTLLTKVTIEKGKTLGIKALATAADL--T-KNGEREVFFE 42 (77)
Q Consensus 4 ~~~~~ei~Veie~GKtLiIkL~aIg~e~--d-e~G~R~V~FE 42 (77)
..+...+.++++.||+++..=.....++ + ++|.-+|.|+
T Consensus 71 ~~~~~tvt~e~~nG~~y~l~~aw~~~~~~~~~~~G~i~~~f~ 112 (119)
T PF10618_consen 71 DITDATVTFELDNGKVYVLSNAWTVEPPEVNTDDGTIEVKFE 112 (119)
T ss_pred CCcccEEEEEecCCcEEEecCeeEcCCccccCCCeEEEEEEe
Confidence 4567789999999999988766664133 4 5688777664
No 15
>PF07474 G2F: G2F domain; InterPro: IPR006605 Basement membranes are sheet-like extracellular matrices found at the basal surfaces of epithelia and condensed mesenchyma. By preventing cell mixing and providing a cell-adhesive substrate, they play crucial roles in tissue development and function. Basement menbranes are composed of an evolutionarily ancient set of large glycoproteins, which includes members of the laminin family, collagen IV, perlecan and nidogen/entactin. Nidogen/entactin is an important basement membrane component, which promotes cell attachment, neutrophil chemotaxis, trophoblast outgrowth, and angiogenesis. It consists of three globular regions, G1-G3. G1 and G2 are connected by a thread-like structure, whereas that between G2 and G3 is rod-like [, ]. The nidogen G2 region binds to collagen IV and perlecan. The nidogen G2 structure is composed of two domains, an N-terminal EGF-like domain and a much larger beta-barrel domain of ~230 residues. The nidogen G2 beta-barrel consists of an 11-stranded beta-barrel of complex topology, the interior of which is traversed by the hydrophobic, predominantly alpha helical segment connecting strands C and D. The N-terminal half of the barrel comprises two beta-meanders (strands A-C and D-F) linked by the buried alpha-helical segment. The polypeptide chain then crosses the bottom of the barrel and forms a five-stranded Greek key motif in the C- terminal half of the domain. Helix alpha3 caps the top of the barrel and forms the interface to the EGF-like domain. The nidogen G2 beta-barrel domain has unexpected structural similarity to green fluorescent protein, suggesting that they derive from a common ancestor. A large surface patch on the barrel surface is strikingly conserved in all metazoan nidogens. Site-directed mutagenesis demonstrates that the conserved residues in the conserved patch are involved in the binding of perlecan, and possibly also of collagen IV [].; PDB: 1GL4_A 1H4U_A.
Probab=54.02 E-value=37 Score=24.98 Aligned_cols=39 Identities=23% Similarity=0.257 Sum_probs=30.2
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeee
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLR 48 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R 48 (77)
-+.+|++++|..|.|+-.+-| .|++|.=.+--+++|+.=
T Consensus 90 ~~s~v~F~tGe~l~itq~~~G--lD~~~~L~~d~~i~G~vP 128 (192)
T PF07474_consen 90 RESEVEFATGERLTITQTARG--LDSDGYLLLDTVISGQVP 128 (192)
T ss_dssp EEEEEEESSS--EEEEEEEEE--E-TTS-EEEEEEEEEEE-
T ss_pred EEEEEEEeCCCEEEEEEEecc--cCCCCcEEEEEEEeccCC
Confidence 577888999999999999987 888899999999999873
No 16
>PLN02354 copper ion binding / oxidoreductase
Probab=48.87 E-value=65 Score=26.75 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=29.3
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
-.+.+++||+..+++...+ ..+..+|.+.|-...|.=.|-
T Consensus 207 ~~~~v~~Gk~yRlRiINa~------~~~~~~f~IdgH~~tVIa~DG 246 (552)
T PLN02354 207 PLFTMKPGKTYRYRICNVG------LKSSLNFRIQGHKMKLVEMEG 246 (552)
T ss_pred eEEEECCCCEEEEEEEecC------CCceEEEEECCceEEEEEeCC
Confidence 3578999999999998876 345677777776665555554
No 17
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=47.97 E-value=63 Score=27.32 Aligned_cols=39 Identities=13% Similarity=0.272 Sum_probs=29.7
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
.+++++||+..+++...+ ..+..+|.++|-...|.=.|-
T Consensus 218 ~i~V~~Gk~yRlRiINaa------~~~~~~fsIdgH~mtVIa~DG 256 (596)
T PLN00044 218 RINVDPGKTYRFRVHNVG------VATSLNFRIQGHNLLLVEAEG 256 (596)
T ss_pred eEEECCCCEEEEEEEEcc------CCceEEEEECCCEEEEEEeCC
Confidence 689999999999998776 346777777777665555554
No 18
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=47.07 E-value=52 Score=20.05 Aligned_cols=34 Identities=6% Similarity=0.084 Sum_probs=29.1
Q ss_pred eeeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEE
Q psy3972 6 TTLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEM 43 (77)
Q Consensus 6 ~~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FEL 43 (77)
.|+.+.+.+...+.-.+.|..+. .+|.-+++|--
T Consensus 5 ~Ge~v~~~~~~~~~~Yl~l~~~~----~~G~v~~L~Pn 38 (83)
T PF14326_consen 5 VGERVRFRVTSNRDGYLYLFYID----ADGKVTLLFPN 38 (83)
T ss_pred CCCEEEEEEEeCCCeEEEEEEEC----CCCCEEEEecC
Confidence 47889999999999999998886 78988888854
No 19
>PF11008 DUF2846: Protein of unknown function (DUF2846); InterPro: IPR022548 Some members in this group of proteins with unknown function are annotated as lipoproteins. However this cannot be confirmed.
Probab=46.55 E-value=26 Score=22.67 Aligned_cols=14 Identities=36% Similarity=0.342 Sum_probs=7.0
Q ss_pred EEEEeCCCCEEEEEE
Q psy3972 10 TKVTIEKGKTLGIKA 24 (77)
Q Consensus 10 i~Veie~GKtLiIkL 24 (77)
+.+++.+|+ +.|..
T Consensus 61 ~~~~v~pG~-h~i~~ 74 (117)
T PF11008_consen 61 FYVEVPPGK-HTISA 74 (117)
T ss_pred EEEEECCCc-EEEEE
Confidence 455555555 44444
No 20
>PF12293 DUF3625: Protein of unknown function (DUF3625); InterPro: IPR022073 This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 360 amino acids in length.
Probab=45.40 E-value=34 Score=25.83 Aligned_cols=44 Identities=11% Similarity=0.050 Sum_probs=33.0
Q ss_pred eeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 7 TLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 7 ~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
..-+.|++++|.+.-+--++.+ -..--+|+.-+|++|+|.-.+.
T Consensus 32 ~~sv~V~l~pGa~~p~ir~~~g-----~~s~l~F~D~tG~PWPI~~~~~ 75 (241)
T PF12293_consen 32 IRSVTVSLSPGASPPVIRTAPG-----YPSTLTFTDSTGAPWPIASVPI 75 (241)
T ss_pred EEEEEEccCCCCCCceEEeeCC-----CcEEEEEEcCCCCccceecccc
Confidence 3468899999987655444554 2255889999999999987766
No 21
>KOG3721|consensus
Probab=45.39 E-value=19 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.488 Sum_probs=22.4
Q ss_pred CCCCceEEEEEEECCeeeEEEEeecCceeccccceeeEEe
Q psy3972 31 LTKNGEREVFFEMNGQLRSVFIRDKEASKVRNPSHFLKIS 70 (77)
Q Consensus 31 ~de~G~R~V~FELNGq~R~V~V~D~sa~~~~~~~~~~~~~ 70 (77)
.+++|+-.|-|+|=|.+ ...+|.||.|+-
T Consensus 203 ~~~dgk~~VkYqVIG~n-----------~VAVPTHFfKVi 231 (302)
T KOG3721|consen 203 KEGDGKWYVKYQVIGNN-----------NVAVPTHFFKVI 231 (302)
T ss_pred ccCCCceEEEEEEeCCC-----------CcccccceeeEE
Confidence 36779999999998864 345799999973
No 22
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=45.33 E-value=23 Score=25.54 Aligned_cols=19 Identities=11% Similarity=0.218 Sum_probs=15.6
Q ss_pred EEEEEEECCeeeEEEEeec
Q psy3972 37 REVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 37 R~V~FELNGq~R~V~V~D~ 55 (77)
..+.|.|||+++.+.+...
T Consensus 2 ~~i~ltvNG~~~~~~~~p~ 20 (156)
T COG2080 2 MPITLTVNGEPVELDVDPR 20 (156)
T ss_pred CcEEEEECCeEEEEEeCCC
Confidence 3688999999999887654
No 23
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=43.66 E-value=50 Score=21.24 Aligned_cols=36 Identities=14% Similarity=0.224 Sum_probs=24.8
Q ss_pred CCCceEEEEEEECCeeeEEEEeecC--ceeccccceeeE
Q psy3972 32 TKNGEREVFFEMNGQLRSVFIRDKE--ASKVRNPSHFLK 68 (77)
Q Consensus 32 de~G~R~V~FELNGq~R~V~V~D~s--a~~~~~~~~~~~ 68 (77)
+=||. .|.|.+++..+.-.+.+.. --+-.+|+|+..
T Consensus 38 ~fDG~-~l~~~~G~~~~~y~~~~~~~s~mkr~~p~hy~~ 75 (79)
T PF11012_consen 38 EFDGK-TLEYRTGSGTYRYQISGENNSEMKRISPAHYQP 75 (79)
T ss_pred EECCC-EEEEEECCeEEEEEEcCCCchheEEcCCCCCCc
Confidence 34455 6777777777777777664 556778888754
No 24
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=43.01 E-value=56 Score=19.01 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=32.0
Q ss_pred eeeeEEEEEeCCCCEEEEEEeeeccC-C--CCCceEEEEEEECCeeeEEEEe
Q psy3972 5 LTTLLTKVTIEKGKTLGIKALATAAD-L--TKNGEREVFFEMNGQLRSVFIR 53 (77)
Q Consensus 5 ~~~~ei~Veie~GKtLiIkL~aIg~e-~--de~G~R~V~FELNGq~R~V~V~ 53 (77)
+++..+....+.|+++-..=..++ . . ..-|.-.|.+..+|....+.|.
T Consensus 16 ~~~~~v~at~~dG~~~~~~~~~vs-~~~d~~~~G~y~Vt~~y~~~t~t~~Vt 66 (67)
T PF07523_consen 16 PTGLFVTATYSDGTSLPLSDVTVS-GTVDTSKAGTYTVTYTYKGVTATFTVT 66 (67)
T ss_dssp HHCHEEEEEETTS-ES-GCCSEEE-S---TTS-CCEEEEEEECTEEEEEEEE
T ss_pred ccCCEEEEEEcCCCEeceeeeEEE-eeeecCCCceEEEEEEECCEEEEEEEE
Confidence 457788889999999443333344 3 3 3449999999999977776664
No 25
>PF12894 Apc4_WD40: Anaphase-promoting complex subunit 4 WD40 domain
Probab=42.87 E-value=26 Score=19.96 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=14.4
Q ss_pred EeeeccCCCCCceEEEEEEECCee
Q psy3972 24 ALATAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 24 L~aIg~e~de~G~R~V~FELNGq~ 47 (77)
|+|++ .++|. -..|.+|||.
T Consensus 25 LiA~~---t~~g~-v~v~Rl~~qr 44 (47)
T PF12894_consen 25 LIALG---TEDGE-VLVYRLNWQR 44 (47)
T ss_pred EEEEE---ECCCe-EEEEECCCcC
Confidence 56675 45677 6778889985
No 26
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=42.73 E-value=44 Score=18.38 Aligned_cols=20 Identities=30% Similarity=0.290 Sum_probs=14.3
Q ss_pred eeeeeEEEEEeCCCCEEEEE
Q psy3972 4 ELTTLLTKVTIEKGKTLGIK 23 (77)
Q Consensus 4 ~~~~~ei~Veie~GKtLiIk 23 (77)
+..+..+.|.+..|+++.++
T Consensus 20 ~~~g~~vtV~~~~G~~~tv~ 39 (42)
T PF02736_consen 20 EEEGDKVTVKTEDGKEVTVK 39 (42)
T ss_dssp EEESSEEEEEETTTEEEEEE
T ss_pred EEcCCEEEEEECCCCEEEeC
Confidence 45667778888778877665
No 27
>PLN02792 oxidoreductase
Probab=42.11 E-value=97 Score=25.69 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=28.6
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
.+++++||++.+++...+ ..+..+|.+.|-...|.-.|-
T Consensus 194 ~~~v~~Gk~yRlRliNa~------~~~~~~f~i~gH~~tVI~~DG 232 (536)
T PLN02792 194 SITVDKGKTYRFRISNVG------LQTSLNFEILGHQLKLIEVEG 232 (536)
T ss_pred eEEECCCCEEEEEEEEcC------CCceEEEEECCcEEEEEEeCC
Confidence 578899999999998776 345677777776665555554
No 28
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=41.28 E-value=29 Score=23.15 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=18.6
Q ss_pred ceEEEEEEECCeeeEEEEeecCce
Q psy3972 35 GEREVFFEMNGQLRSVFIRDKEAS 58 (77)
Q Consensus 35 G~R~V~FELNGq~R~V~V~D~sa~ 58 (77)
+..+|.|-|||....|-.-+.++.
T Consensus 18 a~etv~F~ldG~~YeIDLs~~na~ 41 (110)
T PF11774_consen 18 ADETVRFGLDGVDYEIDLSAENAA 41 (110)
T ss_dssp -SEEEEEEETTEEEEEEE-HHHHH
T ss_pred cceEEEEEECCeEEEEECCHHHHH
Confidence 447999999999999988776553
No 29
>PF13757 VIT_2: Vault protein inter-alpha-trypsin domain
Probab=41.17 E-value=62 Score=20.64 Aligned_cols=26 Identities=27% Similarity=0.477 Sum_probs=20.4
Q ss_pred CCCCceEEEEEE--ECCeeeEEEEeecC
Q psy3972 31 LTKNGEREVFFE--MNGQLRSVFIRDKE 56 (77)
Q Consensus 31 ~de~G~R~V~FE--LNGq~R~V~V~D~s 56 (77)
|-++|.+.+-|+ ++|+.+.+.|+|++
T Consensus 51 PL~e~~~V~gfea~i~gr~v~~~v~~rt 78 (78)
T PF13757_consen 51 PLDEGATVVGFEADIGGRIVTVQVQDRT 78 (78)
T ss_pred ecCCCcEEEEEEEEeCCcEEEEEeeecC
Confidence 346678888887 58999999999873
No 30
>PF06697 DUF1191: Protein of unknown function (DUF1191); InterPro: IPR010605 This family contains hypothetical plant proteins of unknown function.
Probab=40.83 E-value=77 Score=24.75 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=28.6
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCC--CceEEEEEEECCeee
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTK--NGEREVFFEMNGQLR 48 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de--~G~R~V~FELNGq~R 48 (77)
.|+.+... |+++.|+...+...++. .--+=|.|+.||...
T Consensus 127 ~el~l~a~-~~PI~V~F~~~~~~~~~~~~~~~Cv~F~~~G~~~ 168 (278)
T PF06697_consen 127 PELSLRAS-GKPILVDFSNVSPAPQPGMSVPKCVTFDLDGSVT 168 (278)
T ss_pred ceeeeecc-CCcEEEEecCCccCCCcccccceEEEEcCCCcEE
Confidence 47777777 99999999666512221 234889999999664
No 31
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=40.64 E-value=57 Score=22.12 Aligned_cols=28 Identities=29% Similarity=0.620 Sum_probs=21.3
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECC
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNG 45 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNG 45 (77)
.|.+|||.+--|.|..++ |.|.|+ =+||
T Consensus 68 avRFEPG~~k~V~LV~~g------G~r~v~-G~~g 95 (101)
T TIGR00192 68 AVRFEPGEEKSVELVAIG------GNRRIY-GFNG 95 (101)
T ss_pred eEeECCCCeEEEEEEEcc------CceEEE-ccCc
Confidence 578899999999999998 666653 3444
No 32
>PF07971 Glyco_hydro_92: Glycosyl hydrolase family 92; InterPro: IPR012939 This domain occurs within alpha-1,2-mannosidases, which remove alpha-1,2-linked mannose residues from Man(9)(GlcNAc)(2) by hydrolysis. They are critical for the maturation of N-linked oligosaccharides and ER-associated degradation [].; PDB: 2WW2_C 2WVY_B 2WVZ_B 2WW0_H 2WZS_D 2WVX_B 2WW1_D 2WW3_C.
Probab=40.52 E-value=75 Score=26.28 Aligned_cols=37 Identities=19% Similarity=0.175 Sum_probs=23.1
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeee
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLR 48 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R 48 (77)
..++|.+..||++.|+-...+ ++..=.=--.|||++.
T Consensus 442 ~~~~i~l~~g~~~~I~a~n~s----~~n~YIqsv~lNGk~~ 478 (502)
T PF07971_consen 442 DKVTIHLGNGKTFTIEAKNNS----AENIYIQSVTLNGKPL 478 (502)
T ss_dssp SEEEEE-CCC-EEEEE-TT-B----TTB-EEEEEEETTEEE
T ss_pred CeEEEEcCCCCEEEEEecCCC----CCCceEeEEEECCEEC
Confidence 368899999999999987776 3323233457899884
No 33
>PF00699 Urease_beta: Urease beta subunit CAUTION: The Prosite patterns do not match this subunit of the enzyme; InterPro: IPR002019 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plant seeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta, described in this entry, and gamma IPR002026 from INTERPRO). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism. This subunit is known (confusingly) as alpha in Helicobacter.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 1EJS_B 1EJW_B 1A5N_B 1A5K_B 1A5M_B 1EJR_B 1EJX_B 1A5L_B 1KRB_B 1FWA_B ....
Probab=39.50 E-value=47 Score=22.49 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=15.7
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEE
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREV 39 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V 39 (77)
.|.+|||.+--|.|..++ |.|.|
T Consensus 67 avRFEPG~~k~V~LV~~g------G~r~v 89 (100)
T PF00699_consen 67 AVRFEPGDTKEVELVPIG------GNRRV 89 (100)
T ss_dssp EEEE-TT-EEEEEEEE-S------TT-EE
T ss_pred eEEECCCCcEEEEEEEcc------CCeEE
Confidence 578899999999999997 56655
No 34
>PRK13202 ureB urease subunit beta; Reviewed
Probab=39.25 E-value=58 Score=22.23 Aligned_cols=23 Identities=30% Similarity=0.380 Sum_probs=19.1
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEE
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREV 39 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V 39 (77)
.|.+|||.+--|.|..++ |.|.|
T Consensus 69 avRFEPG~~k~V~LV~~g------G~r~v 91 (104)
T PRK13202 69 AVRFEPGIPQIVGLVPLG------GRREV 91 (104)
T ss_pred eEEECCCCeEEEEEEEcc------CCeEE
Confidence 578899999999999997 56555
No 35
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=38.74 E-value=62 Score=18.90 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=11.5
Q ss_pred EEEECCeeeEEEEeec
Q psy3972 40 FFEMNGQLRSVFIRDK 55 (77)
Q Consensus 40 ~FELNGq~R~V~V~D~ 55 (77)
++++||+++.|.=...
T Consensus 10 ~i~~~g~~~~V~~~~~ 25 (58)
T PF08207_consen 10 VIEIDGEPYVVLDFQH 25 (58)
T ss_dssp EEEETTEEEEEEEEEE
T ss_pred EEEECCEEEEEEEEEE
Confidence 6788999987765543
No 36
>PF00609 DAGK_acc: Diacylglycerol kinase accessory domain; InterPro: IPR000756 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The DAG kinase domain is assumed to be an accessory domain. Upon cell stimulation, DAG kinase converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It catalyses the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate. The enzyme is stimulated by calcium and phosphatidylserine and phosphorylated by protein kinase C. This domain is always associated with IPR001206 from INTERPRO.; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway
Probab=38.70 E-value=41 Score=22.91 Aligned_cols=27 Identities=19% Similarity=0.444 Sum_probs=18.7
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCee
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~ 47 (77)
...|.+|+++.|++.. . .++|.+||||
T Consensus 135 ~~rl~Q~~~i~i~~~~-~---------~~~~QvDGEp 161 (161)
T PF00609_consen 135 AKRLAQGRPIRIETKE-N---------KVPFQVDGEP 161 (161)
T ss_pred ceEeecCCEEEEEECC-C---------ceeEEeCCCC
Confidence 3567777777777632 1 7888888875
No 37
>PRK13203 ureB urease subunit beta; Reviewed
Probab=37.43 E-value=68 Score=21.79 Aligned_cols=28 Identities=32% Similarity=0.579 Sum_probs=21.2
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECC
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNG 45 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNG 45 (77)
.|.+|||.+--|.|+.++ |.|.|+ =+||
T Consensus 68 avRFEPG~~k~V~LV~~g------G~r~v~-G~ng 95 (102)
T PRK13203 68 AVRFEPGQTREVELVPLA------GARRVY-GFRG 95 (102)
T ss_pred eEeECCCCeEEEEEEEcc------CceEEE-ccCc
Confidence 578899999999999998 666553 3444
No 38
>PLN02991 oxidoreductase
Probab=36.56 E-value=1.4e+02 Score=24.96 Aligned_cols=39 Identities=15% Similarity=0.242 Sum_probs=25.8
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
.+++++||++-+++...+ ..+..+|.+.|-...|.-.|-
T Consensus 203 ~~~v~~G~~yRlRiINa~------~~~~~~~~idgH~~tVIa~DG 241 (543)
T PLN02991 203 TLNIEPGKTYRLRISNVG------LQNSLNFRIQNHTMKLVEVEG 241 (543)
T ss_pred eEEECCCCEEEEEEEecc------CCeeEEEEECCCEEEEEEeCC
Confidence 588999999999998776 234455555555544444443
No 39
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=36.36 E-value=93 Score=21.25 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=19.0
Q ss_pred EEEECCeeeEEEEeecCceeccccceeeE--EeeeeecCC
Q psy3972 40 FFEMNGQLRSVFIRDKEASKVRNPSHFLK--ISSVFNGAK 77 (77)
Q Consensus 40 ~FELNGq~R~V~V~D~sa~~~~~~~~~~~--~~~~~~~~~ 77 (77)
++.+||+++.|.=. +..+.-.-++|.+ ...+|+|++
T Consensus 14 ~i~~dg~~~~V~~~--~~~KpGKg~a~vrvk~k~l~tG~~ 51 (131)
T COG0231 14 YIVIDGEPYVVVEI--SHVKPGKGGAFVRVKLKNLFTGKK 51 (131)
T ss_pred EEEECCeEEEEEEE--EEccCCCCCcEEEEEEEEccCCCE
Confidence 45588888766544 3333322233654 445666653
No 40
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=35.88 E-value=58 Score=22.35 Aligned_cols=30 Identities=33% Similarity=0.578 Sum_probs=23.1
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCe
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQ 46 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq 46 (77)
..|.+|||..-.|.|+.++ |.|+| |=+||.
T Consensus 67 TAVRFEPG~~k~V~LV~~~------G~r~v-~Gf~~~ 96 (106)
T COG0832 67 TAVRFEPGDEKEVELVPLG------GKREV-YGFNGL 96 (106)
T ss_pred ceEeeCCCCccEEEEEEcc------CceEE-eccccc
Confidence 3578899999999999998 67666 455554
No 41
>TIGR03389 laccase laccase, plant. Members of this protein family include the copper-containing enzyme laccase (EC 1.10.3.2), often several from a single plant species, and additional, uncharacterized, closely related plant proteins termed laccase-like multicopper oxidases. This protein family shows considerable sequence similarity to the L-ascorbate oxidase (EC 1.10.3.3) family. Laccases are enzymes of rather broad specificity, and classification of all proteins scoring about the trusted cutoff of this model as laccases may be appropriate.
Probab=35.60 E-value=1.4e+02 Score=24.46 Aligned_cols=39 Identities=31% Similarity=0.432 Sum_probs=26.7
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEee
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRD 54 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D 54 (77)
..+.+++||++-++|+..| +.+...|.++|-...|.-.|
T Consensus 187 ~~i~v~~G~~~RlRlINa~------~~~~~~~~idgH~~~VIa~D 225 (539)
T TIGR03389 187 FKLTVEPGKTYLLRIINAA------LNDELFFAIANHTLTVVEVD 225 (539)
T ss_pred eEEEECCCCEEEEEEEecc------CCceEEEEECCCeEEEEEeC
Confidence 3688899999999998776 23456666666555444444
No 42
>cd00407 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=34.98 E-value=79 Score=21.42 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=15.6
Q ss_pred EEEeCCCCEEEEEEeeec
Q psy3972 11 KVTIEKGKTLGIKALATA 28 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg 28 (77)
.|.+|||.+--|.|..++
T Consensus 68 avRFEPG~~k~V~LV~~~ 85 (101)
T cd00407 68 AVRFEPGEEKEVELVPIG 85 (101)
T ss_pred eEEECCCCeEEEEEEEcc
Confidence 577889999999999887
No 43
>PLN02168 copper ion binding / pectinesterase
Probab=34.15 E-value=1.5e+02 Score=24.67 Aligned_cols=40 Identities=15% Similarity=0.127 Sum_probs=26.3
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
-.+++++||++-+++...+ ..+..+|.+.|-...|.-.|-
T Consensus 201 ~~~~v~~G~~yRlRiiNa~------~~~~~~~~IdgH~~tVIa~DG 240 (545)
T PLN02168 201 TFFAFEPGKTYRLRISNVG------LKTCLNFRIQDHDMLLVETEG 240 (545)
T ss_pred ceEEeCCCCEEEEEEEecc------CCceEEEEECCcEEEEEEECC
Confidence 3688999999999998876 133455555555544444443
No 44
>PRK09908 xanthine dehydrogenase subunit XdhC; Provisional
Probab=33.85 E-value=51 Score=23.62 Aligned_cols=16 Identities=13% Similarity=0.071 Sum_probs=13.3
Q ss_pred EEEEEEECCeeeEEEE
Q psy3972 37 REVFFEMNGQLRSVFI 52 (77)
Q Consensus 37 R~V~FELNGq~R~V~V 52 (77)
..+.|.|||+.+.+.+
T Consensus 7 ~~i~~~vNG~~~~~~~ 22 (159)
T PRK09908 7 ITIECTINGMPFQLHA 22 (159)
T ss_pred eeEEEEECCEEEEEec
Confidence 3688999999998754
No 45
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=33.77 E-value=42 Score=23.64 Aligned_cols=16 Identities=31% Similarity=0.333 Sum_probs=13.1
Q ss_pred EEEEEECCeeeEEEEe
Q psy3972 38 EVFFEMNGQLRSVFIR 53 (77)
Q Consensus 38 ~V~FELNGq~R~V~V~ 53 (77)
.+.|.|||+++.+.+.
T Consensus 3 ~i~f~vNG~~~~~~~~ 18 (151)
T TIGR03198 3 QFRFTVNGQAWEVAAV 18 (151)
T ss_pred cEEEEECCEEEEeecC
Confidence 4789999999988653
No 46
>PLN02191 L-ascorbate oxidase
Probab=33.62 E-value=1.5e+02 Score=24.72 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=26.1
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEee
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRD 54 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D 54 (77)
.+++++||++-+++...+ ..+...|.++|-...|.-.|
T Consensus 227 ~~~v~~G~~yRlRiINa~------~~~~~~~~idgH~~tVIa~D 264 (574)
T PLN02191 227 TLRVEPNKTYRIRLASTT------ALASLNLAVQGHKLVVVEAD 264 (574)
T ss_pred EEEEcCCCEEEEEEEecC------CceeEEEEECCCeEEEEEcC
Confidence 589999999999987665 34556666665554444444
No 47
>cd00255 nidG2 Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds collagen IV and perlecan. Also found in hemicentin, a protein which functions at various cell-cell and cell-matrix junctions and might assist in refining broad regions of cell contact into oriented, line-shaped junctions. Nidogen G2 consists of an N-terminal EGF-like domain (excluded from this alignment model) and an 11-stranded beta-barrel with a central helix, a topology that exhibits high structural similarity to the green flourescent proteins of Cnidaria.
Probab=33.42 E-value=1.7e+02 Score=22.10 Aligned_cols=38 Identities=24% Similarity=0.312 Sum_probs=33.1
Q ss_pred eEEEEEeCC-CCEEEEEEeeeccCCCCCceEEEEEEECCee
Q psy3972 8 LLTKVTIEK-GKTLGIKALATAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 8 ~ei~Veie~-GKtLiIkL~aIg~e~de~G~R~V~FELNGq~ 47 (77)
.+.+|++.+ |..|.|+-.+-| .|..|+=.+--+++|+.
T Consensus 88 ~~~~v~F~~~ge~l~I~Q~~~G--lD~~~~L~~~~~i~G~v 126 (224)
T cd00255 88 RQAEVTFYTGGEKLRITQVARG--LDSHGHLLLDTVISGRV 126 (224)
T ss_pred EEEEEEEcCCCEEEEEEEEEec--cCccCeEEEEEEEEeec
Confidence 456777788 999999999987 88899999999999987
No 48
>PRK13201 ureB urease subunit beta; Reviewed
Probab=32.63 E-value=86 Score=22.36 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=21.9
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCe
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQ 46 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq 46 (77)
.|.+|||.+--|.|+.++ |.|.|+ =+||.
T Consensus 68 AVRFEPG~~k~V~LV~ig------G~r~V~-Gfngl 96 (136)
T PRK13201 68 AVRFEPGDKKEVQLVEYA------GKRKIF-GFRGM 96 (136)
T ss_pred eEeECCCCeEEEEEEEcc------CceEEE-ccCcc
Confidence 578899999999999998 565553 34443
No 49
>smart00682 G2F G2 nidogen domain and fibulin.
Probab=32.59 E-value=1.6e+02 Score=22.29 Aligned_cols=38 Identities=32% Similarity=0.409 Sum_probs=33.3
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCee
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~ 47 (77)
-+.+|+++-|..|.|+-.+-| .|+.|+=.|--+++|+.
T Consensus 90 ~~s~v~F~~ge~l~i~Q~~~G--lD~~~~L~v~~~i~G~v 127 (227)
T smart00682 90 RETEVTFAGGEILRIKQTFSG--LDEHGYLKVKIEVSGRV 127 (227)
T ss_pred EEEEEEECCCCEEEEEEEEec--cCccccEEEEEEEEeec
Confidence 356777799999999999987 78899999999999987
No 50
>TIGR03390 ascorbOXfungal L-ascorbate oxidase, fungal type. This model describes a family of fungal ascorbate oxidases, within a larger family of multicopper oxidases that also includes plant ascorbate oxidases (TIGR03388), plant laccases and laccase-like proteins (TIGR03389), and related proteins. The member from Acremonium sp. HI-25 is characterized.
Probab=32.24 E-value=1.6e+02 Score=24.25 Aligned_cols=40 Identities=13% Similarity=0.238 Sum_probs=26.2
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCee-eEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQL-RSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~-R~V~V~D~ 55 (77)
-.+++++||++-++++..| ..+...|.+.|-. -.|.-.|-
T Consensus 198 ~~~~v~~G~~yRlRlINa~------~~~~~~~~idgH~~~~VIa~DG 238 (538)
T TIGR03390 198 PVIDVEPGKTYRLRFIGAT------ALSLISLGIEDHENLTIIEADG 238 (538)
T ss_pred eEEEECCCCEEEEEEEccC------CceEEEEEECCCCeEEEEEeCC
Confidence 3588899999999887665 3455566666555 44444443
No 51
>PF15657 Tox-HNH-EHHH: HNH/Endo VII superfamily nuclease toxins
Probab=32.15 E-value=61 Score=20.46 Aligned_cols=28 Identities=29% Similarity=0.489 Sum_probs=15.7
Q ss_pred EEEEE-EECCeeeEEEEeecCceecc------cccee
Q psy3972 37 REVFF-EMNGQLRSVFIRDKEASKVR------NPSHF 66 (77)
Q Consensus 37 R~V~F-ELNGq~R~V~V~D~sa~~~~------~~~~~ 66 (77)
|...| ..|| ..|.|+|.++...- .++||
T Consensus 13 R~yef~~~~g--~kivIqeHs~gh~~~~~~~~~gPHf 47 (72)
T PF15657_consen 13 REYEFTNPKG--EKIVIQEHSAGHRYGEGGGNQGPHF 47 (72)
T ss_pred eEEEEEcCCC--CEEEEEecCCCCccccCCCCCCCcc
Confidence 34455 3455 45556666666655 55565
No 52
>PRK13198 ureB urease subunit beta; Reviewed
Probab=32.14 E-value=78 Score=23.08 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=22.0
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECC
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNG 45 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNG 45 (77)
..|.+|||.+--|.|+.++ |.|.|+ =+||
T Consensus 95 TAVRFEPG~~k~V~LV~~g------G~r~V~-Gfng 123 (158)
T PRK13198 95 TAIRFEPGDETEVPLIPFG------GKQTLY-GFNN 123 (158)
T ss_pred CeEeeCCCCeeEEEEEEcc------CceEEE-ccCc
Confidence 3578999999999999998 666653 3444
No 53
>PF15406 PH_6: Pleckstrin homology domain
Probab=31.95 E-value=65 Score=22.25 Aligned_cols=32 Identities=16% Similarity=0.287 Sum_probs=27.2
Q ss_pred EEEEeeeccCCCCCceEEEEEEECCeeeEEEEe
Q psy3972 21 GIKALATAADLTKNGEREVFFEMNGQLRSVFIR 53 (77)
Q Consensus 21 iIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~ 53 (77)
||.|-.++ ++..+|.-.-.|..||.....+-.
T Consensus 66 iinLadas-e~~~~g~~kF~f~~~G~khtF~A~ 97 (112)
T PF15406_consen 66 IINLADAS-EPEKDGSNKFHFKIKGHKHTFEAA 97 (112)
T ss_pred eEehhhcc-ccccCCCceEEEEeCCceeeeecC
Confidence 78888888 999999999999999998776543
No 54
>cd01237 Unc112 Unc-112 pleckstrin homology (PH) domain. Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=31.77 E-value=99 Score=20.84 Aligned_cols=27 Identities=30% Similarity=0.439 Sum_probs=19.4
Q ss_pred CCCCEEEEEEeeeccCCCCCceEEEEEEECCe
Q psy3972 15 EKGKTLGIKALATAADLTKNGEREVFFEMNGQ 46 (77)
Q Consensus 15 e~GKtLiIkL~aIg~e~de~G~R~V~FELNGq 46 (77)
+++| ..|+|+- |-++|||++++..+.+
T Consensus 63 ~~~k-f~I~l~~----ps~~~~r~y~l~cdsE 89 (106)
T cd01237 63 AQQK-FHIKLLI----PTAEGMNEVWLRCDNE 89 (106)
T ss_pred cccc-eEEEEec----CCccCCeEEEEECCCH
Confidence 4555 8888833 3478999999987754
No 55
>KOG0005|consensus
Probab=31.28 E-value=32 Score=21.93 Aligned_cols=16 Identities=25% Similarity=0.223 Sum_probs=13.0
Q ss_pred ceeeeeEEEEEeCCCC
Q psy3972 3 TELTTLLTKVTIEKGK 18 (77)
Q Consensus 3 ~~~~~~ei~Veie~GK 18 (77)
.-||+.||+++|+|--
T Consensus 6 ktLt~KeIeidIep~D 21 (70)
T KOG0005|consen 6 KTLTGKEIEIDIEPTD 21 (70)
T ss_pred eeeccceEEEeeCcch
Confidence 4589999999998753
No 56
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=31.21 E-value=1.3e+02 Score=18.44 Aligned_cols=33 Identities=18% Similarity=0.200 Sum_probs=25.5
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEE
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEM 43 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FEL 43 (77)
.|+.+.+++|+.+++-+-.+. .+ +|.-.|-|.-
T Consensus 3 QEilI~l~dG~~hiVYi~~~~--~~-~G~l~vdfsT 35 (56)
T PF11113_consen 3 QEILITLEDGESHIVYITELH--YD-DGKLKVDFST 35 (56)
T ss_pred EEEEEEcCCCCEEEEEEEEEE--Ec-CCeEEEEEeC
Confidence 488899999999999887774 33 7777776654
No 57
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=30.85 E-value=51 Score=23.33 Aligned_cols=15 Identities=20% Similarity=0.346 Sum_probs=12.0
Q ss_pred EEEEECCeeeEEEEe
Q psy3972 39 VFFEMNGQLRSVFIR 53 (77)
Q Consensus 39 V~FELNGq~R~V~V~ 53 (77)
+.|.|||+++.+.+.
T Consensus 2 i~~~vNG~~~~~~~~ 16 (148)
T TIGR03193 2 LRLTVNGRWREDAVA 16 (148)
T ss_pred EEEEECCEEEEeecC
Confidence 469999999987653
No 58
>PRK11433 aldehyde oxidoreductase 2Fe-2S subunit; Provisional
Probab=30.77 E-value=69 Score=24.05 Aligned_cols=19 Identities=16% Similarity=0.242 Sum_probs=15.3
Q ss_pred ceEEEEEEECCeeeEEEEe
Q psy3972 35 GEREVFFEMNGQLRSVFIR 53 (77)
Q Consensus 35 G~R~V~FELNGq~R~V~V~ 53 (77)
.+..+.|.|||+.+.+.+.
T Consensus 48 ~~~~i~~~VNG~~~~~~v~ 66 (217)
T PRK11433 48 EISPVTLKVNGKTEQLEVD 66 (217)
T ss_pred cCceEEEEECCEEEEEecC
Confidence 3467999999999988764
No 59
>TIGR03388 ascorbase L-ascorbate oxidase, plant type. Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases.
Probab=30.31 E-value=1.7e+02 Score=23.93 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=29.7
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
..+++++||++-++|...+ +.+...|.++|..-.|.-.|-
T Consensus 203 ~~~~v~~g~~~RlRliNa~------~~~~~~~~id~h~~~VIa~DG 242 (541)
T TIGR03388 203 QILHVEPGKTYRLRIASTT------ALAALNFAIEGHKLTVVEADG 242 (541)
T ss_pred eEEEECCCCEEEEEEEccc------ccceEEEEECCCEEEEEEeCC
Confidence 3588999999999996665 456777777777766666654
No 60
>PLN02835 oxidoreductase
Probab=30.19 E-value=1.7e+02 Score=24.23 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=24.1
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEee
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRD 54 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D 54 (77)
.+++++||++-++|...+ . .+..+|.+.|-...|.=.|
T Consensus 203 ~~~v~~G~~yRlRliNa~-~-----~~~~~f~i~gH~~~VI~~D 240 (539)
T PLN02835 203 TFSGDQGKTYMFRISNVG-L-----STSLNFRIQGHTMKLVEVE 240 (539)
T ss_pred eEEECCCCEEEEEEEEcC-C-----CccEEEEECCCEEEEEEEC
Confidence 477899999999998776 1 2345555555444433333
No 61
>PF05593 RHS_repeat: RHS Repeat; InterPro: IPR006530 These sequences contain two tandem copies of a 21-residue extracellular repeat that is found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin [, , ].
Probab=29.88 E-value=93 Score=16.39 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=18.1
Q ss_pred CCCceEEEEEEECCeeeEEEEeec
Q psy3972 32 TKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 32 de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
|++|.++ .|+-|.+-|.+.+.|.
T Consensus 12 d~~G~~~-~y~YD~~g~l~~~t~~ 34 (38)
T PF05593_consen 12 DPDGRTT-RYTYDAAGRLTSVTDP 34 (38)
T ss_pred cCCCCEE-EEEECCCCCEEEEECC
Confidence 5677744 7999999888888875
No 62
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=29.74 E-value=1.4e+02 Score=20.25 Aligned_cols=36 Identities=8% Similarity=0.160 Sum_probs=18.4
Q ss_pred EEEECCeeeEEEEeecCceec--cccceeeEEeeeeecC
Q psy3972 40 FFEMNGQLRSVFIRDKEASKV--RNPSHFLKISSVFNGA 76 (77)
Q Consensus 40 ~FELNGq~R~V~V~D~sa~~~--~~~~~~~~~~~~~~~~ 76 (77)
++++||+|+.|.=...+.... .+. --+|.-.+|.|.
T Consensus 17 ~i~~~g~p~~V~e~~~~kpGkhG~A~-vr~k~knl~tG~ 54 (130)
T TIGR00037 17 YVVIDGRPCKIVDISTSKPGKHGHAK-ARVVAIGIFTGK 54 (130)
T ss_pred EEEECCEEEEEEEEEecCCCCCCcEE-EEEEEEECCCCC
Confidence 567788888764333322111 111 135566666664
No 63
>PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=29.49 E-value=2e+02 Score=20.11 Aligned_cols=31 Identities=10% Similarity=0.119 Sum_probs=24.1
Q ss_pred CCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEee
Q psy3972 17 GKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRD 54 (77)
Q Consensus 17 GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D 54 (77)
|..+-+.+..++ ++.....+||....|.|.+
T Consensus 10 g~~~~v~v~~~~-------~~~~~itvnG~~y~V~vee 40 (153)
T PRK05641 10 GVEYEVEVEELG-------PGKFRVSFEGKTYEVEAKG 40 (153)
T ss_pred CEEEEEEEEeec-------CccEEEEECCEEEEEEEEE
Confidence 666666666665 7778888999999998877
No 64
>COG2306 Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]
Probab=29.02 E-value=87 Score=23.33 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=31.4
Q ss_pred CCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEe
Q psy3972 15 EKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIR 53 (77)
Q Consensus 15 e~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~ 53 (77)
+.++++.+-|.+.+...-++|.|-++|-.||....|.+.
T Consensus 40 ~~~~pl~~~l~~q~~lv~~~Gyr~~~F~f~~K~~~i~~~ 78 (183)
T COG2306 40 SVFSPLFVYLEGQGWLVPSDGYRWVYFAFNGKDYDILKI 78 (183)
T ss_pred cCCCCcEEEEeeccEEEecCCceEEEEEecCccccceee
Confidence 567888888888654567899999999999988777654
No 65
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=28.76 E-value=82 Score=20.64 Aligned_cols=26 Identities=15% Similarity=0.308 Sum_probs=18.7
Q ss_pred EEEEEeeeccCCCCCceEEEEEEECCe
Q psy3972 20 LGIKALATAADLTKNGEREVFFEMNGQ 46 (77)
Q Consensus 20 LiIkL~aIg~e~de~G~R~V~FELNGq 46 (77)
+=++++... +.+..|.|.+.|+++|.
T Consensus 81 w~~~~l~~~-~~~~~G~k~a~~~I~G~ 106 (115)
T PF03462_consen 81 WKVEVLDYS-PGEEGGIKSATLEISGE 106 (115)
T ss_dssp -EEEEEEEE-E-SSSSEEEEEEEEEST
T ss_pred CEEEEEecC-CCCccceeEEEEEEEcC
Confidence 445666666 66667999999999985
No 66
>PRK13204 ureB urease subunit beta; Reviewed
Probab=27.95 E-value=1.1e+02 Score=22.36 Aligned_cols=28 Identities=29% Similarity=0.464 Sum_probs=21.7
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECC
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMNG 45 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNG 45 (77)
.|.+|||.+--|.|+.++ |.|.|+ =+||
T Consensus 91 AVRFEPG~~k~V~LV~~g------G~r~V~-Gfng 118 (159)
T PRK13204 91 AVRFEPGDEKEVTLVPFA------GKRFIF-GFNN 118 (159)
T ss_pred eEeECCCCeeEEEEEEcc------CceEEE-ccCc
Confidence 578999999999999998 666553 3454
No 67
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=27.74 E-value=1e+02 Score=18.93 Aligned_cols=15 Identities=20% Similarity=0.248 Sum_probs=12.6
Q ss_pred EEEEEEECCeeeEEE
Q psy3972 37 REVFFEMNGQLRSVF 51 (77)
Q Consensus 37 R~V~FELNGq~R~V~ 51 (77)
+.|-|.+||++..+.
T Consensus 2 ~~v~i~idG~~v~~~ 16 (82)
T PF13510_consen 2 KMVTITIDGKPVEVP 16 (82)
T ss_dssp EEEEEEETTEEEEEE
T ss_pred CEEEEEECCEEEEEc
Confidence 578999999997765
No 68
>PLN02604 oxidoreductase
Probab=27.70 E-value=2.2e+02 Score=23.55 Aligned_cols=40 Identities=20% Similarity=0.273 Sum_probs=27.2
Q ss_pred EEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeec
Q psy3972 10 TKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 10 i~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
..+++++||+..++++..+ ..+...|.++|-...|.-.|-
T Consensus 224 ~~~~v~~g~~~RlRlINa~------~~~~~~~sidgH~~~VIa~DG 263 (566)
T PLN02604 224 YVLTVVPGKTYRLRISSLT------ALSALSFQIEGHNMTVVEADG 263 (566)
T ss_pred eEEEecCCCEEEEEEEecc------ccceEEEEECCCEEEEEEeCC
Confidence 3688999999999997766 345666666665554444443
No 69
>PF04283 CheF-arch: Chemotaxis signal transduction system protein F from archaea; InterPro: IPR007381 This is an archaeal protein of unknown function.
Probab=27.69 E-value=1.7e+02 Score=21.60 Aligned_cols=56 Identities=21% Similarity=0.159 Sum_probs=40.4
Q ss_pred eeeEEEEEeCCCCEEEEEEeeeccCCCCCceEEEEEEECCeeeEEEEeecCceeccccceee
Q psy3972 6 TTLLTKVTIEKGKTLGIKALATAADLTKNGEREVFFEMNGQLRSVFIRDKEASKVRNPSHFL 67 (77)
Q Consensus 6 ~~~ei~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~V~V~D~sa~~~~~~~~~~ 67 (77)
+..-+.+....|..+-|-|..|+ ... -..|+| ||+.|.|...+..-...++-+|.+
T Consensus 139 ~~~~i~~~~~~~~~~~I~l~~V~-~ve-~~~r~V----~g~~r~VL~I~H~~~g~sVtSyi~ 194 (221)
T PF04283_consen 139 TKKGIWFASSSGQFVSIDLDDVG-DVE-REERTV----NGKERPVLEIEHVEDGESVTSYIS 194 (221)
T ss_pred eccceEEEecCCceeEEEecccc-eee-eeeeec----CCccceEEEEEEecCCcEEEEEEe
Confidence 34446777777888888898887 553 347777 999999988877666666655544
No 70
>TIGR01633 phi3626_gp14_N putative phage tail component, N-terminal domain. This model represents the best-conserved region of about 125 amino acids, toward the N-terminus, of a family of proteins from temperate phage of a number of Gram-positive bacteria. These phage proteins range in length from 230 to 525 amino acids.
Probab=27.40 E-value=1.3e+02 Score=18.83 Aligned_cols=35 Identities=20% Similarity=0.111 Sum_probs=27.2
Q ss_pred eEEEEEeCCCCEEEEEEeeeccCCCC---CceEEEEEEE
Q psy3972 8 LLTKVTIEKGKTLGIKALATAADLTK---NGEREVFFEM 43 (77)
Q Consensus 8 ~ei~Veie~GKtLiIkL~aIg~e~de---~G~R~V~FEL 43 (77)
-++.+..+|++....++.+.. ++++ .|.-++-|.+
T Consensus 81 ~~L~f~dePd~yy~a~~~~~~-~~~~~~~~~~~titF~c 118 (124)
T TIGR01633 81 VPLIFSDEPDKTYYARVDEEI-DLDEDTTFGKGTLNFIC 118 (124)
T ss_pred cceEeccCCCcEEEEEEcCcc-CHHHhhcccEEEEEEEe
Confidence 467899999999999998877 6653 3666777766
No 71
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=27.36 E-value=1.6e+02 Score=19.99 Aligned_cols=11 Identities=9% Similarity=0.220 Sum_probs=6.0
Q ss_pred EECCeeeEEEE
Q psy3972 42 EMNGQLRSVFI 52 (77)
Q Consensus 42 ELNGq~R~V~V 52 (77)
++||+|+.|.=
T Consensus 18 ~~~g~p~~V~~ 28 (129)
T PRK03999 18 VIDGEPCKIVE 28 (129)
T ss_pred EECCEEEEEEE
Confidence 55666555443
No 72
>PRK13205 ureB urease subunit beta; Reviewed
Probab=26.71 E-value=1.1e+02 Score=22.40 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=16.3
Q ss_pred EEEeCCCCEEEEEEeeec
Q psy3972 11 KVTIEKGKTLGIKALATA 28 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg 28 (77)
.|.+|||.+--|.|+.++
T Consensus 68 AVRFEPGe~ktV~LV~ig 85 (162)
T PRK13205 68 AVRLEPGDARTVNLVAIG 85 (162)
T ss_pred eEeECCCCeEEEEEEEcc
Confidence 578899999999999997
No 73
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=26.43 E-value=1.6e+02 Score=20.80 Aligned_cols=38 Identities=13% Similarity=0.234 Sum_probs=20.9
Q ss_pred EEEECCeeeEEEEeecCceec-cccceeeEEeeeeecCC
Q psy3972 40 FFEMNGQLRSVFIRDKEASKV-RNPSHFLKISSVFNGAK 77 (77)
Q Consensus 40 ~FELNGq~R~V~V~D~sa~~~-~~~~~~~~~~~~~~~~~ 77 (77)
++.+||.|+.|.=...+.... -..---+|.-.+|+|.+
T Consensus 31 ~I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k 69 (159)
T PLN03107 31 YIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKK 69 (159)
T ss_pred EEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCE
Confidence 567799998875443322211 11111456677787753
No 74
>PRK15123 lipopolysaccharide core heptose(I) kinase RfaP; Provisional
Probab=25.81 E-value=1.1e+02 Score=22.88 Aligned_cols=21 Identities=24% Similarity=0.332 Sum_probs=16.7
Q ss_pred CCceEEEEEEECCeeeEEEEe
Q psy3972 33 KNGEREVFFEMNGQLRSVFIR 53 (77)
Q Consensus 33 e~G~R~V~FELNGq~R~V~V~ 53 (77)
.+|.|+|.|+++|+...|+..
T Consensus 33 ~~~rrvvr~~~~g~~~~vKr~ 53 (268)
T PRK15123 33 LEGRRTLRFELAGKSYFLKWH 53 (268)
T ss_pred CCCceEEEEEECCEEEEEEEe
Confidence 468899999999997666643
No 75
>PRK02866 cyanate hydratase; Validated
Probab=25.07 E-value=59 Score=23.11 Aligned_cols=20 Identities=20% Similarity=0.456 Sum_probs=15.6
Q ss_pred eccCCCCCceEEEEEEECCee
Q psy3972 27 TAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 27 Ig~e~de~G~R~V~FELNGq~ 47 (77)
|.+++|++|.| |...+||.-
T Consensus 122 v~k~~dp~Gdr-v~it~~GKf 141 (147)
T PRK02866 122 VDKVEDPKGDR-VVITLDGKF 141 (147)
T ss_pred eeeccCCCCCE-EEEEecccc
Confidence 44467888987 889999964
No 76
>PRK00529 elongation factor P; Validated
Probab=24.61 E-value=1.8e+02 Score=20.68 Aligned_cols=37 Identities=14% Similarity=0.186 Sum_probs=16.4
Q ss_pred EEEECCeeeEEEEeecCceeccccceeeEEeeeeecC
Q psy3972 40 FFEMNGQLRSVFIRDKEASKVRNPSHFLKISSVFNGA 76 (77)
Q Consensus 40 ~FELNGq~R~V~V~D~sa~~~~~~~~~~~~~~~~~~~ 76 (77)
++++||+++.|.=.+.+....-..---+|.-++++|.
T Consensus 12 ~I~~~g~~~~V~~~~~~kpGkg~A~vrvk~knL~tG~ 48 (186)
T PRK00529 12 VIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGS 48 (186)
T ss_pred EEEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCC
Confidence 3466887775543332211111111134555666654
No 77
>smart00230 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
Probab=24.34 E-value=1.3e+02 Score=22.77 Aligned_cols=24 Identities=25% Similarity=0.203 Sum_probs=21.1
Q ss_pred CCCceEEEEEEECCeeeEEEEeec
Q psy3972 32 TKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 32 de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
++.|.=.|.|-.||+.|.|.|-|.
T Consensus 98 ~~~G~y~vrl~~~G~w~~V~VDd~ 121 (318)
T smart00230 98 NYAGIFHFRFWRFGKWVDVVIDDR 121 (318)
T ss_pred ccCCEEEEEEEECCEEEEEEecCC
Confidence 366999999999999999998876
No 78
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=24.11 E-value=63 Score=23.07 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=15.6
Q ss_pred eccCCCCCceEEEEEEECCee
Q psy3972 27 TAADLTKNGEREVFFEMNGQL 47 (77)
Q Consensus 27 Ig~e~de~G~R~V~FELNGq~ 47 (77)
+.+++|++|.| |...+||.-
T Consensus 125 v~k~~dp~Gdr-v~it~~GKf 144 (150)
T TIGR00673 125 VEKVADPGGER-AVITLNGKY 144 (150)
T ss_pred eeeecCCCCCE-EEEEecccc
Confidence 44467889987 999999964
No 79
>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1.3.99.3 from EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [] prefers branched-chain substrates. The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; 1.3.3.6 from EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 3MDD_B 1UDY_C 3MDE_B 2UXW_A 3B96_A 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2D29_B ....
Probab=23.82 E-value=37 Score=19.04 Aligned_cols=11 Identities=36% Similarity=0.561 Sum_probs=9.5
Q ss_pred EEECCeeeEEE
Q psy3972 41 FEMNGQLRSVF 51 (77)
Q Consensus 41 FELNGq~R~V~ 51 (77)
|.|||+-+.|.
T Consensus 27 ~~L~G~K~~v~ 37 (52)
T PF02770_consen 27 YVLNGEKRFVS 37 (52)
T ss_dssp EEEEEEEEEEE
T ss_pred EEEeeEEEEEC
Confidence 89999998875
No 80
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=22.88 E-value=1.6e+02 Score=16.88 Aligned_cols=15 Identities=27% Similarity=0.392 Sum_probs=12.6
Q ss_pred CCCceEEEEEEECCe
Q psy3972 32 TKNGEREVFFEMNGQ 46 (77)
Q Consensus 32 de~G~R~V~FELNGq 46 (77)
++.|.+.+|.+++|.
T Consensus 37 ~~~~~~~f~id~~~~ 51 (75)
T cd04880 37 KGLWEYEFFVDFEGH 51 (75)
T ss_pred CCCceEEEEEEEECC
Confidence 456999999999984
No 81
>PF04607 RelA_SpoT: Region found in RelA / SpoT proteins; InterPro: IPR007685 The functions of Escherichia coli RelA and SpoT differ somewhat. RelA (2.7.6.5 from EC) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (3.1.7.2 from EC) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homologue to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. ; GO: 0015969 guanosine tetraphosphate metabolic process; PDB: 2BE3_B 1VJ7_B 3L9D_B.
Probab=22.88 E-value=1.6e+02 Score=18.22 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=14.5
Q ss_pred eccCCCCCceEEEEEEE----CCeeeEEEEe
Q psy3972 27 TAADLTKNGEREVFFEM----NGQLRSVFIR 53 (77)
Q Consensus 27 Ig~e~de~G~R~V~FEL----NGq~R~V~V~ 53 (77)
+. .|+..|+|.+.+.+ +.....+.|+
T Consensus 64 i~-~~~~~GYrs~H~~v~~~~~~~~~~~EiQ 93 (115)
T PF04607_consen 64 IA-NPKSNGYRSLHYIVPENESFKGYPFEIQ 93 (115)
T ss_dssp TT-T--TTS--EEEEEEEETTECEEEEEEEE
T ss_pred cc-ccccCCcEeeEeeeeecccCCCceeeee
Confidence 45 78889999999999 4444444444
No 82
>cd00044 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
Probab=22.02 E-value=1.6e+02 Score=22.02 Aligned_cols=24 Identities=29% Similarity=0.321 Sum_probs=21.1
Q ss_pred CCCceEEEEEEECCeeeEEEEeec
Q psy3972 32 TKNGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 32 de~G~R~V~FELNGq~R~V~V~D~ 55 (77)
++.|.-.|.|-.||+.|.|.|-|.
T Consensus 106 ~~~G~y~v~l~~~G~w~~V~VDD~ 129 (315)
T cd00044 106 NYAGIYHFRFWKNGEWVEVVIDDR 129 (315)
T ss_pred CcCcEEEEEEEECCEEEEEEecCC
Confidence 467988999999999999999876
No 83
>PF00622 SPRY: SPRY domain; InterPro: IPR003877 The SPRY domain is of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin []. Ca2+-release from the sarcoplasmic or endoplasmic reticulum, the intracellular Ca2+ store, is mediated by the ryanodine receptor (RyR) and/or the inositol trisphosphate receptor (IP3R).; GO: 0005515 protein binding; PDB: 2V24_A 3EK9_A 2AFJ_A 2IWG_E 3EMW_A 2WL1_A 3TOJ_B 2VOK_A 2VOL_B 2FNJ_A ....
Probab=21.80 E-value=2e+02 Score=17.38 Aligned_cols=44 Identities=23% Similarity=0.224 Sum_probs=27.7
Q ss_pred CCEEEEEEeeeccCCCCCceEEEEEEECCeeeE-EEEeecCceeccccceeeE
Q psy3972 17 GKTLGIKALATAADLTKNGEREVFFEMNGQLRS-VFIRDKEASKVRNPSHFLK 68 (77)
Q Consensus 17 GKtLiIkL~aIg~e~de~G~R~V~FELNGq~R~-V~V~D~sa~~~~~~~~~~~ 68 (77)
|..+-+.|.... .+|.|-.||+... ...++-......-|+-.+.
T Consensus 67 ~dvIG~~lD~~~--------g~l~F~~ng~~~~~~~f~~~~~~~~l~P~v~~~ 111 (124)
T PF00622_consen 67 GDVIGCGLDLDN--------GELSFYKNGKFLGIYAFTDIDFSEPLYPAVSLG 111 (124)
T ss_dssp TSEEEEEEETTT--------TEEEEEETTEEEEEEEEESCTTSSSBEEEEEEE
T ss_pred CcEEEEEEeecc--------cEEEEEECCccceeEEEECCCCCCcEEEEEEec
Confidence 666666553221 2899999999977 5555454445666665554
No 84
>PF12142 PPO1_DWL: Polyphenol oxidase middle domain; InterPro: IPR022739 This domain is found in bacteria and eukaryotes and is approximately 50 amino acids in length. It is found in association with PF00264 from PFAM and PF12143 from PFAM. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process; PDB: 1BT3_A 1BUG_B 1BT1_B 1BT2_B 2P3X_A.
Probab=21.65 E-value=47 Score=20.05 Aligned_cols=21 Identities=38% Similarity=0.586 Sum_probs=14.8
Q ss_pred ceEEEEEEECCeeeEEEEeec
Q psy3972 35 GEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 35 G~R~V~FELNGq~R~V~V~D~ 55 (77)
...-+||.=|||.-.|.|+|-
T Consensus 9 ns~F~FYDen~~lVrv~vrD~ 29 (54)
T PF12142_consen 9 NSSFLFYDENGQLVRVKVRDV 29 (54)
T ss_dssp T-EEEEE-TTS-EEEEEGGGH
T ss_pred cCeeEEECCCCCEEEEEhhhc
Confidence 345689999999999999875
No 85
>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.
Probab=21.48 E-value=1.1e+02 Score=18.22 Aligned_cols=24 Identities=21% Similarity=0.448 Sum_probs=18.0
Q ss_pred ceEEEEEE-ECCeeeEEEEeecCce
Q psy3972 35 GEREVFFE-MNGQLRSVFIRDKEAS 58 (77)
Q Consensus 35 G~R~V~FE-LNGq~R~V~V~D~sa~ 58 (77)
....+++. -|++.+++.|..-...
T Consensus 29 ~~~~~~~~~~~~~~~~~~v~~~~~~ 53 (84)
T PF01782_consen 29 NLKQVYLEKRNGEWRPLKVESVRPH 53 (84)
T ss_dssp GSSCEEEE-ETTEEEEEEEEEEEEE
T ss_pred CCCeEEEEEcCCceEEEEEEEEEEe
Confidence 55577777 8999999999875433
No 86
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. 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, f
Probab=21.41 E-value=99 Score=20.22 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=12.5
Q ss_pred EEEEEECCeeeEEEEe
Q psy3972 38 EVFFEMNGQLRSVFIR 53 (77)
Q Consensus 38 ~V~FELNGq~R~V~V~ 53 (77)
.|-||.||+.|-+...
T Consensus 2 RiKfE~~gEKRIi~f~ 17 (79)
T cd06405 2 RIKFEHNGEKRIIQFP 17 (79)
T ss_pred eEEEEecCceEEEecC
Confidence 4779999998776654
No 87
>PF10370 DUF2437: Domain of unknown function (DUF2437); InterPro: IPR018833 This entry represents the N-terminal 50 amino acids of a group of bacterial proteins often annotated as fumarylacetoacetate hydrolase-containing enzymes. In most cases these proteins also contain IPR002529 from INTERPRO, which is found towards the C terminus. ; PDB: 3RR6_A 2DFU_D 3QDF_A.
Probab=21.23 E-value=1.7e+02 Score=16.49 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=18.1
Q ss_pred eEEEEEEECCeeeEEEEeecCc
Q psy3972 36 EREVFFEMNGQLRSVFIRDKEA 57 (77)
Q Consensus 36 ~R~V~FELNGq~R~V~V~D~sa 57 (77)
||-+.|.-+|+++.=.+.+..+
T Consensus 1 Mr~~Rf~~~g~~~~G~l~gd~v 22 (50)
T PF10370_consen 1 MRIVRFSHGGEIRYGVLEGDRV 22 (50)
T ss_dssp -EEEEEEETTEEEEEEEETTCE
T ss_pred CeEEEEeeCCCcEEEEEECCEE
Confidence 6889999999999988887764
No 88
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=20.98 E-value=2.1e+02 Score=20.86 Aligned_cols=31 Identities=13% Similarity=0.278 Sum_probs=20.0
Q ss_pred EEEeCCCCEEEEEEeeeccCCCCCceEEEEEEEC
Q psy3972 11 KVTIEKGKTLGIKALATAADLTKNGEREVFFEMN 44 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e~de~G~R~V~FELN 44 (77)
-+.|++|+.-.||+.-.+ +...| |+-.|.||
T Consensus 77 l~rl~pg~~q~vRii~~~-~lp~d--rEs~f~l~ 107 (230)
T PRK09918 77 VARVEPGQSQQVRFILKS-GSPLN--TEHLLRVS 107 (230)
T ss_pred eEEECCCCceEEEEEECC-CCCCC--eeEEEEEE
Confidence 467889999999987776 44333 34444444
No 89
>PF14452 Multi_ubiq: Multiubiquitin
Probab=20.43 E-value=1.1e+02 Score=18.14 Aligned_cols=15 Identities=20% Similarity=0.069 Sum_probs=11.1
Q ss_pred EEEEEEECCeeeEEE
Q psy3972 37 REVFFEMNGQLRSVF 51 (77)
Q Consensus 37 R~V~FELNGq~R~V~ 51 (77)
|..-|.|||++..+.
T Consensus 1 r~~~i~vn~~~~~~~ 15 (72)
T PF14452_consen 1 RTFRIIVNGRPYEWP 15 (72)
T ss_pred CeEEEEECCeEEEEC
Confidence 567889999876654
No 90
>PF06832 BiPBP_C: Penicillin-Binding Protein C-terminus Family; InterPro: IPR009647 This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (IPR001460 from INTERPRO). It is predicted to be a beta fold.
Probab=20.42 E-value=2.1e+02 Score=17.23 Aligned_cols=25 Identities=16% Similarity=0.287 Sum_probs=18.3
Q ss_pred CEEEEEEeeeccCCCCCceEEEEEEECCeee
Q psy3972 18 KTLGIKALATAADLTKNGEREVFFEMNGQLR 48 (77)
Q Consensus 18 KtLiIkL~aIg~e~de~G~R~V~FELNGq~R 48 (77)
+..-|.|.+.+ . +| .+++-|||++-
T Consensus 30 ~~~~l~l~a~~-~---~~--~~~W~vdg~~~ 54 (89)
T PF06832_consen 30 ERQPLVLKAAG-G---RG--PVYWFVDGEPL 54 (89)
T ss_pred ccceEEEEEeC-C---CC--cEEEEECCEEc
Confidence 46667777777 2 33 89999999984
No 91
>PRK15299 fimbrial chaperone protein StiB; Provisional
Probab=20.09 E-value=1.9e+02 Score=21.03 Aligned_cols=31 Identities=16% Similarity=0.377 Sum_probs=20.7
Q ss_pred EEEeCCCCEEEEEEeeeccC-CCCCceEEEEEEEC
Q psy3972 11 KVTIEKGKTLGIKALATAAD-LTKNGEREVFFEMN 44 (77)
Q Consensus 11 ~Veie~GKtLiIkL~aIg~e-~de~G~R~V~FELN 44 (77)
-+.|++|+.-.||+..++ + ...| |+-.|.||
T Consensus 78 l~rl~p~~~q~lRI~~~~-~~lP~D--rEslf~ln 109 (227)
T PRK15299 78 LFRLNGGQKNVLRIIRTG-GNLPED--RESLYWLD 109 (227)
T ss_pred eEEECCCCccEEEEEECC-CCCCCc--ceEEEEEE
Confidence 367899999999988886 4 3333 34445444
No 92
>PF00648 Peptidase_C2: Calpain family cysteine protease This is family C2 in the peptidase classification. ; InterPro: IPR001300 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 C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. Calpains are a family of cytosolic cysteine proteinases (see PDOC00126 from PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [, ]. The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs []. The crystal structure of calpain has been solved [, ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [][]. The profile covers the whole catalytic domain.; GO: 0004198 calcium-dependent cysteine-type endopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 2NQA_A 1KFU_L 1KFX_L 1QXP_B 2R9C_A 1TL9_A 2G8E_A 1KXR_B 2G8J_A 2NQG_A ....
Probab=20.05 E-value=2.4e+02 Score=20.60 Aligned_cols=22 Identities=36% Similarity=0.462 Sum_probs=19.2
Q ss_pred CceEEEEEEECCeeeEEEEeec
Q psy3972 34 NGEREVFFEMNGQLRSVFIRDK 55 (77)
Q Consensus 34 ~G~R~V~FELNGq~R~V~V~D~ 55 (77)
.|.-.|.|-.||+.+.|.|-|.
T Consensus 87 ~G~y~v~l~~~G~w~~V~VDd~ 108 (298)
T PF00648_consen 87 NGIYTVRLFKNGEWREVTVDDR 108 (298)
T ss_dssp SSEEEEEEEETTEEEEEEEES-
T ss_pred CceeeEeeccCCeeeeeccchh
Confidence 4999999999999999999876
Done!