Query 034824
Match_columns 82
No_of_seqs 14 out of 16
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 06:47:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07106 TBPIP: Tat binding pr 78.7 9.8 0.00021 26.0 5.8 60 5-66 102-164 (169)
2 PRK12277 50S ribosomal protein 76.9 0.57 1.2E-05 31.8 -0.7 40 42-82 32-77 (83)
3 PF10239 DUF2465: Protein of u 72.0 8.2 0.00018 30.3 4.5 43 9-51 148-192 (318)
4 PF01294 Ribosomal_L13e: Ribos 71.3 1.9 4.2E-05 32.4 0.9 40 43-82 69-117 (179)
5 PRK10079 phosphonate metabolis 63.8 22 0.00049 25.0 5.0 54 10-72 9-68 (241)
6 PF01687 Flavokinase: Riboflav 62.3 9.1 0.0002 26.2 2.7 20 14-33 106-125 (125)
7 PF11919 DUF3437: Domain of un 60.6 7.8 0.00017 25.5 2.1 43 3-66 11-59 (90)
8 PF08732 HIM1: HIM1; InterPro 60.3 6.2 0.00013 33.0 1.9 27 11-37 266-299 (410)
9 PF03224 V-ATPase_H_N: V-ATPas 57.4 15 0.00033 27.0 3.4 49 2-57 258-309 (312)
10 COG3388 Predicted transcriptio 56.3 12 0.00026 26.4 2.5 24 17-40 2-32 (101)
11 PF11672 DUF3268: Protein of u 51.8 16 0.00036 24.9 2.6 33 36-72 50-82 (102)
12 PF10642 Tom5: Mitochondrial i 50.6 35 0.00076 20.8 3.7 17 44-60 9-29 (49)
13 PF01923 Cob_adeno_trans: Coba 48.2 90 0.0019 21.6 6.1 49 14-62 81-130 (163)
14 PF10562 CaM_bdg_C0: Calmoduli 47.7 16 0.00035 20.8 1.7 12 55-66 16-27 (29)
15 cd07089 ALDH_CddD-AldA-like Rh 46.4 27 0.00059 27.2 3.4 42 36-78 9-50 (459)
16 PF10369 ALS_ss_C: Small subun 42.2 26 0.00056 21.7 2.2 18 22-41 46-63 (75)
17 COG5609 Uncharacterized conser 41.9 30 0.00065 25.0 2.8 34 14-53 12-45 (124)
18 smart00420 HTH_DEOR helix_turn 41.4 47 0.001 17.1 2.9 30 44-73 15-48 (53)
19 PRK14999 histidine utilization 41.0 81 0.0018 22.1 4.8 48 18-71 14-68 (241)
20 PF15127 DUF4565: Protein of u 40.9 28 0.00062 24.0 2.4 19 50-68 60-78 (91)
21 TIGR00586 mutt mutator mutT pr 39.2 16 0.00034 22.2 0.9 31 15-47 48-78 (128)
22 PF10224 DUF2205: Predicted co 38.7 54 0.0012 21.5 3.4 34 48-81 24-61 (80)
23 cd07036 TPP_PYR_E1-PDHc-beta_l 38.0 36 0.00077 23.8 2.6 37 5-43 126-167 (167)
24 cd07355 HN_L-delphilin-R2_like 37.6 30 0.00064 23.5 2.1 28 40-71 12-39 (80)
25 cd00256 VATPase_H VATPase_H, r 36.8 55 0.0012 26.9 3.9 54 2-62 247-308 (429)
26 PF02727 Cu_amine_oxidN2: Copp 36.7 25 0.00054 22.0 1.5 17 44-60 6-22 (86)
27 PF07870 DUF1657: Protein of u 36.4 44 0.00094 19.8 2.5 19 16-34 30-48 (50)
28 cd03199 GST_C_GRX2 GST_C famil 34.8 78 0.0017 22.2 3.9 33 15-50 59-92 (128)
29 PF14476 Chloroplast_duf: Peta 34.8 69 0.0015 26.3 4.1 20 15-34 92-111 (313)
30 PRK09764 DNA-binding transcrip 34.8 1.1E+02 0.0024 21.5 4.7 50 14-71 7-61 (240)
31 smart00062 PBPb Bacterial peri 33.8 94 0.002 18.5 3.7 38 35-79 181-218 (219)
32 PF09432 THP2: Tho complex sub 33.3 34 0.00074 25.0 2.0 15 54-68 88-102 (132)
33 COG2197 CitB Response regulato 32.6 65 0.0014 22.8 3.3 34 24-57 85-118 (211)
34 COG4352 RPL13 Ribosomal protei 32.6 22 0.00049 25.4 0.9 39 43-81 60-107 (113)
35 PF03328 HpcH_HpaI: HpcH/HpaI 32.2 59 0.0013 22.7 3.0 34 20-57 73-107 (221)
36 PF06837 Fijivirus_P9-2: Fijiv 32.0 31 0.00067 27.0 1.7 25 38-62 40-64 (214)
37 PF04402 SIMPL: Protein of unk 32.0 1.4E+02 0.003 19.8 4.6 45 23-68 93-142 (210)
38 PF05770 Ins134_P3_kin: Inosit 31.8 25 0.00054 27.6 1.1 16 35-50 51-66 (307)
39 COG3355 Predicted transcriptio 31.6 50 0.0011 23.3 2.5 44 22-72 27-75 (126)
40 KOG2550 IMP dehydrogenase/GMP 31.3 64 0.0014 28.0 3.5 25 22-48 75-99 (503)
41 TIGR01334 modD putative molybd 30.7 80 0.0017 24.4 3.7 46 25-74 198-243 (277)
42 smart00428 H3 Histone H3. 30.5 28 0.0006 23.8 1.1 19 8-26 29-47 (105)
43 PTZ00018 histone H3; Provision 30.5 28 0.00061 25.0 1.2 20 7-26 61-80 (136)
44 PF01023 S_100: S-100/ICaBP ty 30.2 37 0.0008 19.5 1.4 13 21-33 1-13 (44)
45 TIGR02977 phageshock_pspA phag 29.5 1.6E+02 0.0035 21.1 4.9 29 17-65 28-56 (219)
46 PF03480 SBP_bac_7: Bacterial 29.4 2.1E+02 0.0046 20.4 5.7 46 18-65 239-285 (286)
47 KOG0479 DNA replication licens 29.3 46 0.001 30.3 2.5 24 23-52 775-798 (818)
48 PLN00121 histone H3; Provision 28.6 35 0.00075 24.5 1.3 34 7-53 61-94 (136)
49 PF03147 FDX-ACB: Ferredoxin-f 28.5 75 0.0016 19.8 2.7 21 41-61 66-86 (94)
50 cd07098 ALDH_F15-22 Aldehyde d 28.2 78 0.0017 24.6 3.3 42 36-79 8-49 (465)
51 PF14769 CLAMP: Flagellar C1a 27.8 82 0.0018 20.1 2.9 41 40-80 8-49 (101)
52 PRK10386 curli assembly protei 27.3 92 0.002 22.3 3.3 33 46-78 96-128 (130)
53 PF13545 HTH_Crp_2: Crp-like h 27.2 1.3E+02 0.0028 17.1 3.8 42 33-74 18-63 (76)
54 TIGR03191 benz_CoA_bzdO benzoy 27.0 1.5E+02 0.0033 23.8 4.8 47 20-70 159-205 (430)
55 PF11473 B2: RNA binding prote 27.0 63 0.0014 21.7 2.3 15 49-63 45-59 (73)
56 PLN00160 histone H3; Provision 26.7 54 0.0012 22.3 1.9 19 7-25 20-38 (97)
57 cd07097 ALDH_KGSADH-YcbD Bacil 26.7 71 0.0015 25.0 2.8 46 30-77 17-66 (473)
58 TIGR02818 adh_III_F_hyde S-(hy 26.3 87 0.0019 23.1 3.1 35 23-57 320-357 (368)
59 PF14348 DUF4400: Domain of un 25.5 2.3E+02 0.005 19.8 5.0 28 11-38 5-32 (198)
60 PF03405 FA_desaturase_2: Fatt 25.1 34 0.00073 27.5 0.8 24 58-81 98-123 (330)
61 cd07144 ALDH_ALD2-YMR170C Sacc 24.8 95 0.0021 24.4 3.2 50 29-79 25-77 (484)
62 PF09682 Holin_LLH: Phage holi 24.8 93 0.002 20.3 2.8 25 37-67 84-108 (108)
63 cd07110 ALDH_F10_BADH Arabidop 24.7 1.1E+02 0.0024 23.7 3.5 40 36-77 9-48 (456)
64 cd07145 ALDH_LactADH_F420-Bios 24.6 1.1E+02 0.0024 23.7 3.5 40 36-77 11-50 (456)
65 PF03298 Stanniocalcin: Stanni 24.6 81 0.0017 24.3 2.7 23 16-38 181-203 (208)
66 PF10356 DUF2034: Protein of u 24.5 9.4 0.0002 28.2 -2.2 27 43-69 97-123 (185)
67 PF05193 Peptidase_M16_C: Pept 24.5 1.3E+02 0.0029 18.1 3.2 15 41-55 169-183 (184)
68 KOG1744 Histone H2B [Chromatin 24.1 42 0.00092 24.1 1.1 16 23-38 94-109 (127)
69 PF15266 DUF4594: Domain of un 24.1 19 0.00041 27.1 -0.7 32 47-78 75-107 (182)
70 PF10372 YojJ: Bacterial membr 24.1 81 0.0018 20.4 2.3 18 16-33 17-34 (70)
71 PRK09406 gabD1 succinic semial 23.9 90 0.0019 24.6 3.0 36 42-78 18-53 (457)
72 PF00534 Glycos_transf_1: Glyc 23.8 1.9E+02 0.0041 18.0 3.9 40 29-71 128-167 (172)
73 PF15617 C-C_Bond_Lyase: C-C_B 23.7 61 0.0013 26.4 2.0 40 16-58 251-298 (345)
74 cd07109 ALDH_AAS00426 Uncharac 23.6 97 0.0021 24.0 3.1 34 45-78 17-50 (454)
75 KOG1745 Histones H3 and H4 [Ch 23.4 54 0.0012 23.8 1.6 20 8-27 63-82 (137)
76 PF00171 Aldedh: Aldehyde dehy 23.4 94 0.002 24.1 2.9 35 43-78 25-59 (462)
77 cd07082 ALDH_F11_NP-GAPDH NADP 23.3 97 0.0021 24.1 3.0 36 43-78 34-69 (473)
78 PF00325 Crp: Bacterial regula 23.3 1.5E+02 0.0032 16.5 3.1 23 44-66 3-29 (32)
79 PF13094 CENP-Q: CENP-Q, a CEN 23.1 2.5E+02 0.0054 19.0 4.8 52 17-68 74-143 (160)
80 cd07225 Pat_PNPLA6_PNPLA7 Pata 23.1 70 0.0015 24.4 2.2 41 30-71 259-302 (306)
81 cd07088 ALDH_LactADH-AldA Esch 23.0 1E+02 0.0022 23.9 3.0 47 29-77 15-64 (468)
82 PF09548 Spore_III_AB: Stage I 22.6 27 0.00059 24.3 -0.1 61 11-79 48-113 (170)
83 PRK00507 deoxyribose-phosphate 22.5 1.7E+02 0.0037 21.5 4.0 45 14-58 101-147 (221)
84 PLN00179 acyl- [acyl-carrier p 22.2 34 0.00074 28.5 0.4 23 59-81 156-180 (390)
85 PF00675 Peptidase_M16: Insuli 22.1 1.2E+02 0.0026 19.1 2.8 21 43-63 99-119 (149)
86 PRK10673 acyl-CoA esterase; Pr 21.9 1.5E+02 0.0032 19.4 3.3 28 19-46 65-92 (255)
87 cd07117 ALDH_StaphAldA1 Unchar 21.9 1E+02 0.0022 24.5 2.9 47 30-78 19-68 (475)
88 COG1012 PutA NAD-dependent ald 21.6 1E+02 0.0022 25.0 2.9 34 43-77 32-65 (472)
89 TIGR01202 bchC 2-desacetyl-2-h 21.5 1E+02 0.0022 22.1 2.6 33 22-54 259-294 (308)
90 cd04268 ZnMc_MMP_like Zinc-dep 21.5 1.1E+02 0.0023 19.7 2.5 20 51-70 15-34 (165)
91 PLN00161 histone H3; Provision 21.4 63 0.0014 23.3 1.6 18 8-25 55-72 (135)
92 PF07332 DUF1469: Protein of u 21.2 1.1E+02 0.0024 19.4 2.5 19 10-28 100-118 (121)
93 PF01300 Sua5_yciO_yrdC: Telom 21.2 42 0.00091 23.0 0.6 23 21-43 62-84 (179)
94 TIGR03697 NtcA_cyano global ni 21.2 1.8E+02 0.004 18.7 3.6 40 34-73 133-177 (193)
95 PF09447 Cnl2_NKP2: Cnl2/NKP2 21.2 1.4E+02 0.0031 19.0 3.0 11 3-13 20-30 (67)
96 PTZ00192 60S ribosomal protein 21.2 28 0.00062 27.1 -0.3 41 42-82 78-127 (218)
97 PRK10309 galactitol-1-phosphat 21.0 1.3E+02 0.0029 21.4 3.2 34 23-56 297-333 (347)
98 cd08300 alcohol_DH_class_III c 20.7 1.4E+02 0.003 21.9 3.2 34 23-56 321-357 (368)
99 cd03431 DNA_Glycosylase_C DNA 20.6 1.1E+02 0.0024 17.9 2.3 16 33-48 59-74 (118)
100 PF12368 DUF3650: Protein of u 20.6 50 0.0011 18.5 0.7 15 38-52 10-24 (28)
101 PF04963 Sigma54_CBD: Sigma-54 20.5 74 0.0016 22.5 1.8 40 13-52 54-97 (194)
102 PF01399 PCI: PCI domain; Int 20.3 93 0.002 18.1 1.9 26 2-29 60-85 (105)
103 cd03725 SOCS_ASB6 SOCS (suppre 20.3 56 0.0012 19.1 0.9 29 52-80 10-40 (44)
104 cd08010 yceG_like proteins sim 20.2 41 0.00089 25.2 0.4 11 30-40 195-205 (245)
No 1
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=78.67 E-value=9.8 Score=26.02 Aligned_cols=60 Identities=20% Similarity=0.258 Sum_probs=45.0
Q ss_pred hhhhhhcCChHH---HHHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHHh
Q 034824 5 LSRLANALPFSR---LFRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLRN 66 (82)
Q Consensus 5 ~~~~~~~lPfs~---l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn 66 (82)
+..+.+.++-.+ .+.+|++++++.-.-|++-==|-.. .|++|+.++...-.++..-|+.-
T Consensus 102 L~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~--vs~ee~~~~~~~~~~~~k~w~kR 164 (169)
T PF07106_consen 102 LASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKP--VSPEEKEKLEKEYKKWRKEWKKR 164 (169)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 566777777444 4778899998888777763334433 88999999999999998888753
No 2
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=76.90 E-value=0.57 Score=31.80 Aligned_cols=40 Identities=23% Similarity=0.401 Sum_probs=32.2
Q ss_pred eccCHHHHHhHHHHHHH------HHHHHHHhhhhhcccchhhhhhhC
Q 034824 42 HKFSAEEVRQASATVER------AVQNWLRNAYQEQGSEILKDYIDK 82 (82)
Q Consensus 42 HkFs~~EI~~A~atv~r------AV~nWrrn~~lE~~~~ilkdyi~k 82 (82)
--||-+|+..|--+.+- |||.=|+|...| |-.-||.|..|
T Consensus 32 RGFsl~ELkaaGi~~~~ArtiGI~VD~RRrn~~~e-NVerLk~y~sk 77 (83)
T PRK12277 32 RGFSIGELEAAGLDIKNARKLGIRVDKRRKTVHEE-NVEALKKFLEQ 77 (83)
T ss_pred CCcCHHHHHHcCCCHHHhcccCeeecccccCCCHH-HHHHHHHHHHH
Confidence 35999999999655554 589999999877 88899999764
No 3
>PF10239 DUF2465: Protein of unknown function (DUF2465); InterPro: IPR018797 FAM98A, B and C are glycine-rich proteins found from worms to humans whose function is unknown.
Probab=71.97 E-value=8.2 Score=30.28 Aligned_cols=43 Identities=23% Similarity=0.570 Sum_probs=37.2
Q ss_pred hhcCChHHHHHHHHHHHHHHHHhccCccce--eeeeccCHHHHHh
Q 034824 9 ANALPFSRLFRQLETEMETVVKVLQPGPLG--IIEHKFSAEEVRQ 51 (82)
Q Consensus 9 ~~~lPfs~l~RQlEqdvETVi~VLQPGPlG--IvEHkFs~~EI~~ 51 (82)
.+..+.++++.+++..++.+++-|.||.+| ++.+.+|++...+
T Consensus 148 ~~~i~~~~lf~~i~~ki~~~L~~lp~~~~~~PLl~~~L~~~Qw~~ 192 (318)
T PF10239_consen 148 PPNITASQLFSKIEAKIEELLSKLPPGHMGKPLLKKSLTDEQWEK 192 (318)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHhcCccccCCCCcCCCCCHHHHHH
Confidence 345568999999999999999999999888 7899999987644
No 4
>PF01294 Ribosomal_L13e: Ribosomal protein L13e; InterPro: IPR001380 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal protein L13e is widely found in vertebrates [], Drosophila melanogaster, plants, yeast, amongst others.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_U 4A1B_U 4A1D_U 4A19_U.
Probab=71.25 E-value=1.9 Score=32.37 Aligned_cols=40 Identities=30% Similarity=0.383 Sum_probs=25.2
Q ss_pred ccCHHHHHhHHHHHHHH------HHHHHHhhh---hhcccchhhhhhhC
Q 034824 43 KFSAEEVRQASATVERA------VQNWLRNAY---QEQGSEILKDYIDK 82 (82)
Q Consensus 43 kFs~~EI~~A~atv~rA------V~nWrrn~~---lE~~~~ilkdyi~k 82 (82)
-||-+|+..|--+.+-| ||-.|+|.. |+.|-.-||.|..|
T Consensus 69 GFsl~ELk~aGi~~~~A~tiGI~VD~RR~n~s~Esl~~Nv~RLkeY~sk 117 (179)
T PF01294_consen 69 GFSLEELKAAGISKKYARTIGISVDHRRKNKSEESLQANVQRLKEYKSK 117 (179)
T ss_dssp SB-HHHHHHHT--HHHHHHHTB-B-TT----SHHHHHHHHHHHHHHHHT
T ss_pred CcCHHHHHHcCCChHHccccCeeeccccCCccHHHHHHHHHHHHhhhhh
Confidence 59999999997766664 789999975 55677789999765
No 5
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=63.78 E-value=22 Score=24.96 Aligned_cols=54 Identities=13% Similarity=0.293 Sum_probs=34.8
Q ss_pred hcCC-hHHHHHHHHHHHHHHHHhccCccceeeeecc-CHHHHH----hHHHHHHHHHHHHHHhhhhhcc
Q 034824 10 NALP-FSRLFRQLETEMETVVKVLQPGPLGIIEHKF-SAEEVR----QASATVERAVQNWLRNAYQEQG 72 (82)
Q Consensus 10 ~~lP-fs~l~RQlEqdvETVi~VLQPGPlGIvEHkF-s~~EI~----~A~atv~rAV~nWrrn~~lE~~ 72 (82)
+..| +-++-++|.+.++. .++||= ++ |..|+- =.+.||++|++.=...-.+++.
T Consensus 9 ~~~p~Y~qi~~~L~~~I~~---~~~~G~------~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~ 68 (241)
T PRK10079 9 SYPTRYQEIAAKLEQELRQ---HYRCGD------YLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRR 68 (241)
T ss_pred CCCCHHHHHHHHHHHHHhc---ccCCCC------cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3345 56666777777652 689983 22 444444 3689999999987666555543
No 6
>PF01687 Flavokinase: Riboflavin kinase; InterPro: IPR015865 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents the riboflavin kinase domains from bacteria and eukaryotes.; GO: 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process; PDB: 1Q9S_A 1NB9_A 1P4M_A 1NB0_A 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A ....
Probab=62.29 E-value=9.1 Score=26.16 Aligned_cols=20 Identities=30% Similarity=0.438 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHHHHHhcc
Q 034824 14 FSRLFRQLETEMETVVKVLQ 33 (82)
Q Consensus 14 fs~l~RQlEqdvETVi~VLQ 33 (82)
+..|..|+++|+++.-+.||
T Consensus 106 ~e~L~~qI~~D~~~a~~~lq 125 (125)
T PF01687_consen 106 LEELKEQIKKDIEQARKYLQ 125 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHhcC
Confidence 67899999999999999987
No 7
>PF11919 DUF3437: Domain of unknown function (DUF3437); InterPro: IPR021843 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. ; PDB: 3L5Q_6 1VSY_5.
Probab=60.62 E-value=7.8 Score=25.45 Aligned_cols=43 Identities=26% Similarity=0.515 Sum_probs=26.0
Q ss_pred cchhhhhhcCC------hHHHHHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHHh
Q 034824 3 ASLSRLANALP------FSRLFRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLRN 66 (82)
Q Consensus 3 ~S~~~~~~~lP------fs~l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn 66 (82)
+.|++|..+.| ++.++..|= .-.+ .||||| .||++++.+|+|.
T Consensus 11 LGL~Alv~a~Py~vP~w~P~~l~~La----~~~~--~~~~I~---------------~tvk~tl~eFkrt 59 (90)
T PF11919_consen 11 LGLSALVLAFPYDVPPWMPEVLEELA----RHAN--DPQPIR---------------TTVKKTLSEFKRT 59 (90)
T ss_dssp HHHHHHHTT-S--SS-HHHHHHHHHH----TTSS--S-SSHH---------------HHTHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcccHHHHHHHHH----HHhC--CCchHH---------------HHHHHHHHHHHHh
Confidence 45778888888 344443332 2222 466664 7899999999874
No 8
>PF08732 HIM1: HIM1; InterPro: IPR014843 HIM1 (high induction of mutagenesis protein 1) plays a role in the control of spontaneous and induced mutagenesis []. It is thought to participate in the control of processing of mutational intermediates appearing during error-prone bypass of DNA damage.
Probab=60.27 E-value=6.2 Score=32.99 Aligned_cols=27 Identities=30% Similarity=0.780 Sum_probs=23.3
Q ss_pred cCChHHHHHHHHHHHHHHHH-------hccCccc
Q 034824 11 ALPFSRLFRQLETEMETVVK-------VLQPGPL 37 (82)
Q Consensus 11 ~lPfs~l~RQlEqdvETVi~-------VLQPGPl 37 (82)
.+|+.+.=-+||+|+-+-+. +|.||||
T Consensus 266 ~f~Yfk~K~~LE~dl~~~l~~~l~~lvILRPGpl 299 (410)
T PF08732_consen 266 MFPYFKTKGELENDLQNLLPPKLKHLVILRPGPL 299 (410)
T ss_pred hhhhhHHHHHHHHHHHhhcccccceEEEecCccc
Confidence 46899999999999998865 6999997
No 9
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=57.40 E-value=15 Score=27.04 Aligned_cols=49 Identities=20% Similarity=0.221 Sum_probs=34.3
Q ss_pred ccchhhhhhcCChHH--HHHH-HHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHH
Q 034824 2 PASLSRLANALPFSR--LFRQ-LETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVE 57 (82)
Q Consensus 2 ~~S~~~~~~~lPfs~--l~RQ-lEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~ 57 (82)
|++++-|++++.-+. .+.+ ++.++-.+++.|+ +.||+|+||.+.=..+.
T Consensus 258 Rv~la~l~Nl~~~~~~~~~~~mv~~~~l~~l~~L~-------~rk~~Dedl~edl~~L~ 309 (312)
T PF03224_consen 258 RVSLAILRNLLSKAPKSNIELMVLCGLLKTLQNLS-------ERKWSDEDLTEDLEFLK 309 (312)
T ss_dssp HHHHHHHHHTTSSSSTTHHHHHHHH-HHHHHHHHH-------SS--SSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHccHHHHHHHHh-------cCCCCCHHHHHHHHHHH
Confidence 788888998887444 4333 5777888888887 67899999998766554
No 10
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=56.30 E-value=12 Score=26.35 Aligned_cols=24 Identities=46% Similarity=0.837 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHH-------HhccCccceee
Q 034824 17 LFRQLETEMETVV-------KVLQPGPLGII 40 (82)
Q Consensus 17 l~RQlEqdvETVi-------~VLQPGPlGIv 40 (82)
++|.+=.|+||+- .|+.-+|+||+
T Consensus 2 ifr~i~~e~e~l~RHl~Vl~~v~eeqPiGI~ 32 (101)
T COG3388 2 IFREIINELETLKRHLSVLKVVLEEQPIGII 32 (101)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCCceeE
Confidence 4677777777753 46778999997
No 11
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=51.82 E-value=16 Score=24.89 Aligned_cols=33 Identities=24% Similarity=0.430 Sum_probs=26.5
Q ss_pred cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcc
Q 034824 36 PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQG 72 (82)
Q Consensus 36 PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~ 72 (82)
|||. +.++|.|+|+....+|.|.-.++..++++
T Consensus 50 PlGt----LAd~~lR~~R~~ah~~fd~lw~~~~~~R~ 82 (102)
T PF11672_consen 50 PLGT----LADAELRRARKAAHRAFDPLWQSGHMSRS 82 (102)
T ss_pred cCcc----cCCHHHHHHHHHHHHHHHHHHHhCcccHH
Confidence 6664 57899999999999999986666666654
No 12
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=50.60 E-value=35 Score=20.83 Aligned_cols=17 Identities=41% Similarity=0.421 Sum_probs=11.1
Q ss_pred cCHHHHHhHH----HHHHHHH
Q 034824 44 FSAEEVRQAS----ATVERAV 60 (82)
Q Consensus 44 Fs~~EI~~A~----atv~rAV 60 (82)
-|.|||+.++ .||++|+
T Consensus 9 pS~eE~k~~e~~A~~Tvk~a~ 29 (49)
T PF10642_consen 9 PSEEEIKAAEAQANFTVKNAA 29 (49)
T ss_pred CCHHHHHHHHHHHHHHHHHHH
Confidence 4889998655 4555554
No 13
>PF01923 Cob_adeno_trans: Cobalamin adenosyltransferase; InterPro: IPR002779 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation [], while EutT produces AdoCbl for ethanolamine utilisation []. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 2ZHY_A 2ZHZ_B 3KE5_C 3KE4_B 2AH6_C 1NOG_A 2IDX_C 3GAH_A 3CI1_A 3CI3_A ....
Probab=48.24 E-value=90 Score=21.58 Aligned_cols=49 Identities=20% Similarity=0.163 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHHhccCccceeeee-ccCHHHHHhHHHHHHHHHHH
Q 034824 14 FSRLFRQLETEMETVVKVLQPGPLGIIEH-KFSAEEVRQASATVERAVQN 62 (82)
Q Consensus 14 fs~l~RQlEqdvETVi~VLQPGPlGIvEH-kFs~~EI~~A~atv~rAV~n 62 (82)
...-+..||+.+...-+-+.|-.--|+-| .-..+.+.-|++.++||--.
T Consensus 81 ~~~~v~~Le~~i~~~~~~~~~~~~Filpgg~~~~a~Lh~aRtv~RraER~ 130 (163)
T PF01923_consen 81 TEEDVQELEEEIDEYSEELPPLKGFILPGGSPAAAALHVARTVCRRAERR 130 (163)
T ss_dssp -HHHHHHHHHHHHHHHHHS-SESSCEES-SSHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhcCCCCceeEeCCCCHHHHHHHHHHHHHHHHHHH
Confidence 45568889999988888877766667777 66788899999999998643
No 14
>PF10562 CaM_bdg_C0: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; InterPro: IPR018882 This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue [].
Probab=47.67 E-value=16 Score=20.77 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHh
Q 034824 55 TVERAVQNWLRN 66 (82)
Q Consensus 55 tv~rAV~nWrrn 66 (82)
..+.|++.||.|
T Consensus 16 lAr~a~dkWR~~ 27 (29)
T PF10562_consen 16 LARHAADKWRGN 27 (29)
T ss_pred HHHHHHHHHHhh
Confidence 456789999986
No 15
>cd07089 ALDH_CddD-AldA-like Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD.
Probab=46.41 E-value=27 Score=27.23 Aligned_cols=42 Identities=21% Similarity=0.205 Sum_probs=31.4
Q ss_pred cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 36 PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 36 PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
|+|-+ +.-|.+|+.+|=...++|...|+++...++...+|+.
T Consensus 9 ~i~~~-~~~~~~~v~~av~~A~~a~~~w~w~~~~~~R~~~L~~ 50 (459)
T cd07089 9 VIGTA-PDAGAADVDAAIAAARRAFDTGDWSTDAEERARCLRQ 50 (459)
T ss_pred EEEEE-eCCCHHHHHHHHHHHHHHHHhhhhcCCHHHHHHHHHH
Confidence 45554 5678899999999999999999745566666666554
No 16
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=42.25 E-value=26 Score=21.74 Aligned_cols=18 Identities=33% Similarity=0.864 Sum_probs=15.8
Q ss_pred HHHHHHHHHhccCccceeee
Q 034824 22 ETEMETVVKVLQPGPLGIIE 41 (82)
Q Consensus 22 EqdvETVi~VLQPGPlGIvE 41 (82)
+++++..++.|+| .||+|
T Consensus 46 ~~kid~fi~~l~~--~gi~E 63 (75)
T PF10369_consen 46 PEKIDAFIKLLKP--FGILE 63 (75)
T ss_dssp HHHHHHHHHHSTG--GGEEE
T ss_pred HHHHHHHHHHhhh--cCCEE
Confidence 5788999999998 89887
No 17
>COG5609 Uncharacterized conserved protein [Function unknown]
Probab=41.94 E-value=30 Score=25.04 Aligned_cols=34 Identities=24% Similarity=0.329 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHH
Q 034824 14 FSRLFRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQAS 53 (82)
Q Consensus 14 fs~l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~ 53 (82)
||+++||+|+| -|--||.-|.-|-|.++-|.--+
T Consensus 12 iS~~i~~~~ke------~lGrgp~sI~t~f~~nm~i~sL~ 45 (124)
T COG5609 12 ISKAITSLEKE------YLGRGPVSIKTDFLDNMAIISLE 45 (124)
T ss_pred HHHHHHHHHHH------HhCCCCceeEeehhhhhhhhhhh
Confidence 89999999998 48899999999988776654433
No 18
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.37 E-value=47 Score=17.11 Aligned_cols=30 Identities=17% Similarity=0.212 Sum_probs=22.9
Q ss_pred cCHHHHHhH----HHHHHHHHHHHHHhhhhhccc
Q 034824 44 FSAEEVRQA----SATVERAVQNWLRNAYQEQGS 73 (82)
Q Consensus 44 Fs~~EI~~A----~atv~rAV~nWrrn~~lE~~~ 73 (82)
+|..||.++ .+||.+.+++++...-+++..
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 577777776 789999999998876666543
No 19
>PRK14999 histidine utilization repressor; Provisional
Probab=40.96 E-value=81 Score=22.15 Aligned_cols=48 Identities=17% Similarity=0.358 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHH--HhccCccceeeeecc-CHHHHHh----HHHHHHHHHHHHHHhhhhhc
Q 034824 18 FRQLETEMETVV--KVLQPGPLGIIEHKF-SAEEVRQ----ASATVERAVQNWLRNAYQEQ 71 (82)
Q Consensus 18 ~RQlEqdvETVi--~VLQPGPlGIvEHkF-s~~EI~~----A~atv~rAV~nWrrn~~lE~ 71 (82)
-.|+..++..-| ..++|| .++ |..|+-+ .+.||++|++.=...-.+++
T Consensus 14 y~qi~~~i~~~I~~g~~~~G------~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 68 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPH------DRIPSEAELVAQYGFSRMTINRALRELTDEGWLVR 68 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCC------CcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 344444444444 478888 455 5666555 68999999998766655554
No 20
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=40.92 E-value=28 Score=23.99 Aligned_cols=19 Identities=26% Similarity=0.515 Sum_probs=15.1
Q ss_pred HhHHHHHHHHHHHHHHhhh
Q 034824 50 RQASATVERAVQNWLRNAY 68 (82)
Q Consensus 50 ~~A~atv~rAV~nWrrn~~ 68 (82)
|-++-.|.+||+.|-+|..
T Consensus 60 rLSqEIl~dAlqQWA~~n~ 78 (91)
T PF15127_consen 60 RLSQEILSDALQQWAENNI 78 (91)
T ss_pred HHHHHHHHHHHHHHHHhCc
Confidence 4566779999999998754
No 21
>TIGR00586 mutt mutator mutT protein. All proteins in this family for which functions are known are involved in repairing oxidative damage to dGTP (they are 8-oxo-dGTPases). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.20 E-value=16 Score=22.22 Aligned_cols=31 Identities=13% Similarity=0.101 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHhccCccceeeeeccCHH
Q 034824 15 SRLFRQLETEMETVVKVLQPGPLGIIEHKFSAE 47 (82)
Q Consensus 15 s~l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~ 47 (82)
..+.|.+..|.-.-+.+ ..++|.+.|.||..
T Consensus 48 ~~~~RE~~EE~g~~~~~--~~~~~~~~h~~~~~ 78 (128)
T TIGR00586 48 QAVVRELEEEIGIPQHF--SEFEKLEYEFYPRH 78 (128)
T ss_pred HHHHHHHHHHHCCccee--eeEEEEEEEECCCc
Confidence 45568777655332233 33589999999853
No 22
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=38.70 E-value=54 Score=21.54 Aligned_cols=34 Identities=24% Similarity=0.266 Sum_probs=22.1
Q ss_pred HHHhHHHHHHHHHH----HHHHhhhhhcccchhhhhhh
Q 034824 48 EVRQASATVERAVQ----NWLRNAYQEQGSEILKDYID 81 (82)
Q Consensus 48 EI~~A~atv~rAV~----nWrrn~~lE~~~~ilkdyi~ 81 (82)
||.+.+.++.--++ -=..|.-|+..|..|.+||.
T Consensus 24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~ 61 (80)
T PF10224_consen 24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444544442222 23467889999999999995
No 23
>cd07036 TPP_PYR_E1-PDHc-beta_like Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins. Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of the beta subunits of the E1 components of: human pyruvate dehydrogenase complex (E1- PDHc), the acetoin dehydrogenase complex (ADC), and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC), subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domain
Probab=38.00 E-value=36 Score=23.80 Aligned_cols=37 Identities=16% Similarity=0.274 Sum_probs=25.3
Q ss_pred hhhhhhcCC-----hHHHHHHHHHHHHHHHHhccCccceeeeec
Q 034824 5 LSRLANALP-----FSRLFRQLETEMETVVKVLQPGPLGIIEHK 43 (82)
Q Consensus 5 ~~~~~~~lP-----fs~l~RQlEqdvETVi~VLQPGPlGIvEHk 43 (82)
..++.+++| -|.=-.+.+.=+++.++ ++||.=|.|||
T Consensus 126 ~~a~lr~iPg~~V~~Psd~~e~~~~l~~~~~--~~~P~~~~e~k 167 (167)
T cd07036 126 LEAWFAHIPGLKVVAPSTPYDAKGLLKAAIR--DDDPVIFLEHK 167 (167)
T ss_pred HHHHHhcCCCCEEEeeCCHHHHHHHHHHHHh--CCCcEEEEecC
Confidence 346777777 23334555566777775 78999999997
No 24
>cd07355 HN_L-delphilin-R2_like Second harmonin_N_like domain (repeat 2) of L-delphilin, and related domains. This subgroup contains the second of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin), and related domains. Delphilin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain in L-delphilin follows the second PDZ protein-binding domain, PDZ2; it is also found in the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta). It is a putative protein-binding module based on its sequence similarity to the harmonin N-domain. The first harmonin_N_like domain of L-delphilin belongs to a different subgroup and is missing from S-delphilin.
Probab=37.59 E-value=30 Score=23.47 Aligned_cols=28 Identities=14% Similarity=0.431 Sum_probs=23.3
Q ss_pred eeeccCHHHHHhHHHHHHHHHHHHHHhhhhhc
Q 034824 40 IEHKFSAEEVRQASATVERAVQNWLRNAYQEQ 71 (82)
Q Consensus 40 vEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~ 71 (82)
+||-||..| +.++.+|..+.+++.+.+.
T Consensus 12 mehlLt~~E----R~~i~qaL~~y~~~Rnvd~ 39 (80)
T cd07355 12 MEHLLTPPE----RYGIKKALEDYFQHRNIDT 39 (80)
T ss_pred HHHhCCHHH----HHHHHHHHHHHHHhccHHH
Confidence 367789887 7899999999999988764
No 25
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=36.80 E-value=55 Score=26.94 Aligned_cols=54 Identities=11% Similarity=0.236 Sum_probs=36.3
Q ss_pred ccchhhhhhcCChHH-------H-HHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHH
Q 034824 2 PASLSRLANALPFSR-------L-FRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQN 62 (82)
Q Consensus 2 ~~S~~~~~~~lPfs~-------l-~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~n 62 (82)
|++++-|++++.-+. + ..-++-.+=.+++.|+ +-||+|+||.+.=..+...+++
T Consensus 247 Rv~l~~l~Nll~~~~~~~~~~~~~~~mv~~~l~~~l~~L~-------~rk~~DedL~edl~~L~e~L~~ 308 (429)
T cd00256 247 RIVLAIFRNLISKRVDREVKKTAALQMVQCKVLKTLQSLE-------QRKYDDEDLTDDLKFLTEELKN 308 (429)
T ss_pred HHHHHHHHHHhhcccccchhhhHHHHHHHcChHHHHHHHh-------cCCCCcHHHHHHHHHHHHHHHH
Confidence 678888888887431 1 2223335556666666 6789999999987777665543
No 26
>PF02727 Cu_amine_oxidN2: Copper amine oxidase, N2 domain; InterPro: IPR015800 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents one (N2) of the two N-terminal domains (N2/N3) that share a similar structure.; GO: 0005507 copper ion binding, 0008131 primary amine oxidase activity, 0048038 quinone binding, 0009308 amine metabolic process, 0055114 oxidation-reduction process; PDB: 1W2Z_A 1KSI_B 1US1_A 2C11_B 3ALA_E 2Y73_B 2C10_B 1PU4_B 2Y74_B 3SX1_A ....
Probab=36.70 E-value=25 Score=21.97 Aligned_cols=17 Identities=35% Similarity=0.493 Sum_probs=14.7
Q ss_pred cCHHHHHhHHHHHHHHH
Q 034824 44 FSAEEVRQASATVERAV 60 (82)
Q Consensus 44 Fs~~EI~~A~atv~rAV 60 (82)
+|++||..|.+.++.+.
T Consensus 6 Lt~~Ei~~a~~il~~~~ 22 (86)
T PF02727_consen 6 LTAEEIQAAAAILRDAH 22 (86)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHhcc
Confidence 57899999999998775
No 27
>PF07870 DUF1657: Protein of unknown function (DUF1657); InterPro: IPR012452 This domain appears to be restricted to the Bacillales.
Probab=36.39 E-value=44 Score=19.81 Aligned_cols=19 Identities=21% Similarity=0.656 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHhccC
Q 034824 16 RLFRQLETEMETVVKVLQP 34 (82)
Q Consensus 16 ~l~RQlEqdvETVi~VLQP 34 (82)
+.+.|.-+++|.||+-|+|
T Consensus 30 ~~y~~~a~~l~~ii~~L~~ 48 (50)
T PF07870_consen 30 QMYEQAAQQLEEIIQDLEP 48 (50)
T ss_pred HHHHHHHHHHHHHHHHhHc
Confidence 5688888999999999987
No 28
>cd03199 GST_C_GRX2 GST_C family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD (most GRXs range from 9-12kD). GRX2 adopts a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. It contains a redox active CXXC motif located in the N-terminal domain, but is not able to reduce ribonucleotide reductase like other GRXs. However, it catalyzes GSH-dependent protein disulfide reduction of other substrates efficiently. GRX2 is thought to function primarily in catalyzing the reversible glutathionylation of proteins in cellular redox regulation including stress responses.
Probab=34.82 E-value=78 Score=22.18 Aligned_cols=33 Identities=9% Similarity=0.295 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHhc-cCccceeeeeccCHHHHH
Q 034824 15 SRLFRQLETEMETVVKVL-QPGPLGIIEHKFSAEEVR 50 (82)
Q Consensus 15 s~l~RQlEqdvETVi~VL-QPGPlGIvEHkFs~~EI~ 50 (82)
++++.+||++++.+-..| .|+= +.+.+|-++|.
T Consensus 59 ~~~i~~l~~~L~~l~~ll~~~~~---~n~~ls~DDi~ 92 (128)
T cd03199 59 PQYIAALNALLEELDPLILSSEA---VNGQLSTDDII 92 (128)
T ss_pred HHHHHHHHHHHHHHHHHHcCccc---cCCcCCHHHHH
Confidence 488999999999999998 5553 56889988874
No 29
>PF14476 Chloroplast_duf: Petal formation-expressed
Probab=34.79 E-value=69 Score=26.30 Aligned_cols=20 Identities=40% Similarity=0.765 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHhccC
Q 034824 15 SRLFRQLETEMETVVKVLQP 34 (82)
Q Consensus 15 s~l~RQlEqdvETVi~VLQP 34 (82)
.+|++||+++++|.+.+=.|
T Consensus 92 tRLfkqL~~~I~t~la~~~~ 111 (313)
T PF14476_consen 92 TRLFKQLHSQIETTLALGNP 111 (313)
T ss_pred HHHHHHHHHHHHHHHhcCCc
Confidence 46799999999999876554
No 30
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=34.78 E-value=1.1e+02 Score=21.50 Aligned_cols=50 Identities=14% Similarity=0.385 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHHHHhccCccceeeeecc-CHHHHHh----HHHHHHHHHHHHHHhhhhhc
Q 034824 14 FSRLFRQLETEMETVVKVLQPGPLGIIEHKF-SAEEVRQ----ASATVERAVQNWLRNAYQEQ 71 (82)
Q Consensus 14 fs~l~RQlEqdvETVi~VLQPGPlGIvEHkF-s~~EI~~----A~atv~rAV~nWrrn~~lE~ 71 (82)
+.++.++|.++++. ..++|| .|+ |..|+.+ ++.||++|++.=...-.+++
T Consensus 7 y~qi~~~L~~~I~~--g~~~~G------~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r 61 (240)
T PRK09764 7 YRQIADRIREQIAR--GELKPG------DALPTESALQTEFGVSRVTVRQALRQLVEQQILES 61 (240)
T ss_pred HHHHHHHHHHHHHc--CCCCCC------CcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 34555555555433 478888 466 5555554 68999999998766665554
No 31
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=33.77 E-value=94 Score=18.49 Aligned_cols=38 Identities=8% Similarity=0.136 Sum_probs=24.4
Q ss_pred ccceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhhh
Q 034824 35 GPLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKDY 79 (82)
Q Consensus 35 GPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkdy 79 (82)
.|++|+=+|-++ +-...+.++++.++.+..++ +|++.|
T Consensus 181 ~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~~---~i~~~~ 218 (219)
T smart00062 181 EGYAFAVRKGDP----ELLDKINKALKELKADGTLK---KIYEKW 218 (219)
T ss_pred cceEEEEECCCH----HHHHHHHHHHHHHHhCchHH---HHHhcc
Confidence 788898888764 23344666777776665544 456655
No 32
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=33.32 E-value=34 Score=24.98 Aligned_cols=15 Identities=13% Similarity=0.357 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHhhh
Q 034824 54 ATVERAVQNWLRNAY 68 (82)
Q Consensus 54 atv~rAV~nWrrn~~ 68 (82)
.++.+.|..||++|.
T Consensus 88 ~~LtkEVn~Wr~ewd 102 (132)
T PF09432_consen 88 NQLTKEVNYWRKEWD 102 (132)
T ss_pred HHHHHHHHHHHHHHH
Confidence 357789999999995
No 33
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=32.62 E-value=65 Score=22.76 Aligned_cols=34 Identities=26% Similarity=0.357 Sum_probs=29.7
Q ss_pred HHHHHHHhccCccceeeeeccCHHHHHhHHHHHH
Q 034824 24 EMETVVKVLQPGPLGIIEHKFSAEEVRQASATVE 57 (82)
Q Consensus 24 dvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~ 57 (82)
|-+.|..+++-|+-|.+-...+.+++.+|=.+|.
T Consensus 85 ~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v~ 118 (211)
T COG2197 85 DPAYVIRALRAGADGYLLKDASPEELVEAIRAVA 118 (211)
T ss_pred CHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence 4567899999999999999999999998877664
No 34
>COG4352 RPL13 Ribosomal protein L13E [Translation, ribosomal structure and biogenesis]
Probab=32.60 E-value=22 Score=25.40 Aligned_cols=39 Identities=26% Similarity=0.337 Sum_probs=29.2
Q ss_pred ccCHHHHHhHHHHHHHH------HHHHHHhh---hhhcccchhhhhhh
Q 034824 43 KFSAEEVRQASATVERA------VQNWLRNA---YQEQGSEILKDYID 81 (82)
Q Consensus 43 kFs~~EI~~A~atv~rA------V~nWrrn~---~lE~~~~ilkdyi~ 81 (82)
-||..|...|--+++.| ||-=|+|. ++|.+-.-+|+|..
T Consensus 60 GFslgEl~aAGL~~~~AR~LGI~VD~RRr~~~~en~eal~k~ik~ll~ 107 (113)
T COG4352 60 GFSLGELKAAGLSARKARTLGIAVDHRRRNRNPENFEALVKRIKELLE 107 (113)
T ss_pred CccHHHHHHcCcCHHHHHhhCcceehhhccCCHHHHHHHHHHHHHHHh
Confidence 59999999998777775 88888875 45566666666654
No 35
>PF03328 HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family; InterPro: IPR005000 This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (4.1.2 from EC) and 4-hydroxy-2-oxovalerate aldolase (4.1.2 from EC). ; GO: 0016830 carbon-carbon lyase activity, 0006725 cellular aromatic compound metabolic process; PDB: 1DXF_B 1DXE_A 3QZ6_A 3QLL_C 3QQW_F 3OYZ_A 3PUG_A 3OYX_A 1IZC_A 2V5K_B ....
Probab=32.16 E-value=59 Score=22.70 Aligned_cols=34 Identities=41% Similarity=0.616 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhccCccceeeeecc-CHHHHHhHHHHHH
Q 034824 20 QLETEMETVVKVLQPGPLGIIEHKF-SAEEVRQASATVE 57 (82)
Q Consensus 20 QlEqdvETVi~VLQPGPlGIvEHkF-s~~EI~~A~atv~ 57 (82)
.+++|++ +|..||=||+==|. |.++++++...++
T Consensus 73 ~~~~Dl~----~l~~g~~gI~lP~ves~~~~~~~~~~~~ 107 (221)
T PF03328_consen 73 HIERDLE----ALDAGADGIVLPKVESAEDARQAVAALR 107 (221)
T ss_dssp HHHHHHH----HHHTTSSEEEETT--SHHHHHHHHHHHS
T ss_pred hhhhhhh----hcccCCCeeeccccCcHHHHHHHHHHHh
Confidence 4667777 88899999988777 5677776655543
No 36
>PF06837 Fijivirus_P9-2: Fijivirus P9-2 protein; InterPro: IPR009650 This family consists of several Fijivirus specific P9-2 proteins from Rice black streaked dwarf virus (RBSDV) and Fiji disease virus. The function of this family is unknown.
Probab=32.02 E-value=31 Score=26.97 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=21.4
Q ss_pred eeeeeccCHHHHHhHHHHHHHHHHH
Q 034824 38 GIIEHKFSAEEVRQASATVERAVQN 62 (82)
Q Consensus 38 GIvEHkFs~~EI~~A~atv~rAV~n 62 (82)
-|.||.|||.||-+-=.+++-+|+.
T Consensus 40 ~ife~~~sdse~Dd~vd~lE~~ve~ 64 (214)
T PF06837_consen 40 EIFERPLSDSELDDKVDKLETDVED 64 (214)
T ss_pred HHHcccCcchhHHHHHHHHhhhHHh
Confidence 4789999999999988888888753
No 37
>PF04402 SIMPL: Protein of unknown function (DUF541); InterPro: IPR007497 Members of this family have so far been found in bacteria and mouse UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entries. However possible family members have also been identified in translated rat (GenBank:AW144450) and human (GenBank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase). SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity []. Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerisation. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics []. In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane.
Probab=31.95 E-value=1.4e+02 Score=19.80 Aligned_cols=45 Identities=20% Similarity=0.311 Sum_probs=31.8
Q ss_pred HHHHHHHHhccC--cc---ceeeeeccCHHHHHhHHHHHHHHHHHHHHhhh
Q 034824 23 TEMETVVKVLQP--GP---LGIIEHKFSAEEVRQASATVERAVQNWLRNAY 68 (82)
Q Consensus 23 qdvETVi~VLQP--GP---lGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~ 68 (82)
.+++.++..|+- -+ ++-++-..|+.+..+ +.-...|+++++..|.
T Consensus 93 ~~l~~ll~~l~~~g~~~~~i~~i~~~~s~~~~~~-~e~~~~A~~~A~~kA~ 142 (210)
T PF04402_consen 93 KKLGKLLSALQSAGINNVSIGSIEFSLSDEDEAK-KEALKEAIKDAKEKAE 142 (210)
T ss_pred HHHHHHHHHHHhcCCccceecceEEEECCHHHHH-HHHHHHHHHHHHHHHH
Confidence 345556666655 23 577778888888877 6667899999988764
No 38
>PF05770 Ins134_P3_kin: Inositol 1, 3, 4-trisphosphate 5/6-kinase; InterPro: IPR008656 This entry represents inositol-tetrakisphosphate 1-kinase which is also called inositol 1,3,4-trisphosphate 5/6-kinase. Inositol-tetrakisphosphate 1-kinase can phosphorylate various inositol polyphosphate such as Ins(3,4,5,6)P4 or Ins(1,3,4)P3. This enzyme phosphorylates Ins(3,4,5,6)P4 at position 1 to form Ins(1,3,4,5,6)P5. This reaction is thought to have regulatory importance, since Ins(3,4,5,6)P4 is an inhibitor of plasma membrane Ca(2+)-activated Cl(-) channels, while Ins(1,3,4,5,6)P5 is not. It also phosphorylates Ins(1,3,4)P3 on O-5 and O-6 to form Ins(1,3,4,6)P4, an essential molecule in the hexakisphosphate (InsP6) pathway [, , , , ].; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0047325 inositol tetrakisphosphate 1-kinase activity, 0052725 inositol-1,3,4-trisphosphate 6-kinase activity, 0052726 inositol-1,3,4-trisphosphate 5-kinase activity, 0032957 inositol trisphosphate metabolic process, 0005622 intracellular; PDB: 1Z2P_X 1Z2O_X 1Z2N_X 2Q7D_A 2QB5_B 2ODT_X.
Probab=31.85 E-value=25 Score=27.65 Aligned_cols=16 Identities=38% Similarity=0.723 Sum_probs=9.5
Q ss_pred ccceeeeeccCHHHHH
Q 034824 35 GPLGIIEHKFSAEEVR 50 (82)
Q Consensus 35 GPlGIvEHkFs~~EI~ 50 (82)
||+-+|=||+|++++.
T Consensus 51 gpfDvIlHKltd~~~~ 66 (307)
T PF05770_consen 51 GPFDVILHKLTDEDWV 66 (307)
T ss_dssp --SCEEEE--CHCHHH
T ss_pred CCcEEEEEeCCCHHHH
Confidence 9999999999994433
No 39
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=31.64 E-value=50 Score=23.34 Aligned_cols=44 Identities=32% Similarity=0.521 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcc-CccceeeeeccCHHHHHh----HHHHHHHHHHHHHHhhhhhcc
Q 034824 22 ETEMETVVKVLQ-PGPLGIIEHKFSAEEVRQ----ASATVERAVQNWLRNAYQEQG 72 (82)
Q Consensus 22 EqdvETVi~VLQ-PGPlGIvEHkFs~~EI~~----A~atv~rAV~nWrrn~~lE~~ 72 (82)
|.|+|.....|+ -||+ |.+||.+ -++||.||++|--.---+++.
T Consensus 27 ~~Dv~v~~~LL~~~~~~-------tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 27 ELDVEVYKALLEENGPL-------TVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHHHHHHHHHHhhcCCc-------CHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 789999999995 6665 5566654 589999999997655444443
No 40
>KOG2550 consensus IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]
Probab=31.26 E-value=64 Score=27.99 Aligned_cols=25 Identities=36% Similarity=0.712 Sum_probs=19.9
Q ss_pred HHHHHHHHHhccCccceeeeeccCHHH
Q 034824 22 ETEMETVVKVLQPGPLGIIEHKFSAEE 48 (82)
Q Consensus 22 EqdvETVi~VLQPGPlGIvEHkFs~~E 48 (82)
|-||-.++..| |=||||-|.+|.|+
T Consensus 75 es~MAiaMAl~--ggIg~IHhNctpe~ 99 (503)
T KOG2550|consen 75 ESEMAIAMALL--GGIGFIHHNCTPED 99 (503)
T ss_pred hhHHHHHHHhc--CCceeeecCCCHHH
Confidence 66777777765 88999999999543
No 41
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=30.73 E-value=80 Score=24.39 Aligned_cols=46 Identities=15% Similarity=0.204 Sum_probs=34.5
Q ss_pred HHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccc
Q 034824 25 METVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSE 74 (82)
Q Consensus 25 vETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ 74 (82)
.|.+...++-|+=.|.=|+||.++++++-..++ +++.+..+|-.-+
T Consensus 198 leea~ea~~~GaDiI~lDn~~~e~l~~~v~~l~----~~~~~~~leasGG 243 (277)
T TIGR01334 198 IEQALTVLQASPDILQLDKFTPQQLHHLHERLK----FFDHIPTLAAAGG 243 (277)
T ss_pred HHHHHHHHHcCcCEEEECCCCHHHHHHHHHHHh----ccCCCEEEEEECC
Confidence 566778899999999999999999998865543 4555555654433
No 42
>smart00428 H3 Histone H3.
Probab=30.53 E-value=28 Score=23.84 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=15.6
Q ss_pred hhhcCChHHHHHHHHHHHH
Q 034824 8 LANALPFSRLFRQLETEME 26 (82)
Q Consensus 8 ~~~~lPfs~l~RQlEqdvE 26 (82)
+.+-+||++|+|.+-++..
T Consensus 29 LI~k~pF~RLVREI~~~~~ 47 (105)
T smart00428 29 LIRKAPFQRLVREIAQKFT 47 (105)
T ss_pred ccccccHHHHHHHHHHHcC
Confidence 4567899999999888864
No 43
>PTZ00018 histone H3; Provisional
Probab=30.53 E-value=28 Score=24.98 Aligned_cols=20 Identities=35% Similarity=0.720 Sum_probs=16.2
Q ss_pred hhhhcCChHHHHHHHHHHHH
Q 034824 7 RLANALPFSRLFRQLETEME 26 (82)
Q Consensus 7 ~~~~~lPfs~l~RQlEqdvE 26 (82)
-+.+-+||++|+|++-++..
T Consensus 61 lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 61 LLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred hccccccHHHHHHHHHHHcC
Confidence 35677899999999988863
No 44
>PF01023 S_100: S-100/ICaBP type calcium binding domain; InterPro: IPR013787 The calcium-binding domain found in S100 and CaBP-9k proteins is a subfamily of the EF-hand calcium-binding domain []. S100s are small dimeric acidic calcium and zinc-binding proteins abundant in the brain, with S100B playing an important role in modulating the proliferation and differentiation of neurons and glia cells []. S100 proteins have two different types of calcium-binding sites: a low affinity one with a special structure, and a 'normal' EF-hand type high-affinity site. Calbindin-D9k (CaBP-9k) also belong to this family of proteins, but it does not form dimers. CaBP-9k is a cytosolic protein expressed in a variety of tissues. Although its precise function is unknown, it appears to be under the control of the steroid hormones oestrogen and progesterone in the female reproductive system []. In the intestine, CaBP-9k may be involved in calcium absorption by mediating intracellular diffusion []. This entry represents a subdomain of the calcium-binding domain found in S100, CaBP-9k, and related proteins.; PDB: 2RGI_A 4DUQ_B 2KAY_B 2KAX_A 2CNP_A 1CNP_A 1A03_A 1JWD_B 2JTT_A 1XK4_B ....
Probab=30.24 E-value=37 Score=19.53 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=10.5
Q ss_pred HHHHHHHHHHhcc
Q 034824 21 LETEMETVVKVLQ 33 (82)
Q Consensus 21 lEqdvETVi~VLQ 33 (82)
||+-|+++|+|-+
T Consensus 1 LE~ai~~iI~vFh 13 (44)
T PF01023_consen 1 LEKAIETIIDVFH 13 (44)
T ss_dssp HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHH
Confidence 6888999998863
No 45
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=29.54 E-value=1.6e+02 Score=21.13 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHH
Q 034824 17 LFRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLR 65 (82)
Q Consensus 17 l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrr 65 (82)
.++|+.+||+. ++.+|+..+.+++...++
T Consensus 28 ~l~q~irem~~--------------------~l~~ar~~lA~~~a~~k~ 56 (219)
T TIGR02977 28 MIRLIIQEMED--------------------TLVEVRTTSARTIADKKE 56 (219)
T ss_pred HHHHHHHHHHH--------------------HHHHHHHHHHHHHHHHHH
Confidence 57777777765 455666666666555544
No 46
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=29.44 E-value=2.1e+02 Score=20.38 Aligned_cols=46 Identities=20% Similarity=0.183 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHH-HHH
Q 034824 18 FRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQN-WLR 65 (82)
Q Consensus 18 ~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~n-Wrr 65 (82)
...++++.+..++.|+= -|+.=|.+|++|+.+-++.++..++. |.+
T Consensus 239 ~~~~~~~~~~~~~~~~~--~G~~v~~~s~~~~~~~~~~~~~~~~e~~~~ 285 (286)
T PF03480_consen 239 REYYEAEDEEALKELEE--NGVTVVELSDEELAAWREAAAPVWEEFFEE 285 (286)
T ss_dssp HHHHHHHHHHHHHHHHH--TT-EEEEGCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH--CcCEEeCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 33445555666666665 68888899999999999999888888 543
No 47
>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]
Probab=29.31 E-value=46 Score=30.31 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=17.8
Q ss_pred HHHHHHHHhccCccceeeeeccCHHHHHhH
Q 034824 23 TEMETVVKVLQPGPLGIIEHKFSAEEVRQA 52 (82)
Q Consensus 23 qdvETVi~VLQPGPlGIvEHkFs~~EI~~A 52 (82)
+++.+.||. ++.+||||++||..|
T Consensus 775 ~~i~esin~------~~~~~~fsa~E~~a~ 798 (818)
T KOG0479|consen 775 ADITESINN------QSGEEKFSADEIKAA 798 (818)
T ss_pred HHHHHHHhc------cCccCCcCHHHHHHH
Confidence 456777775 233999999999765
No 48
>PLN00121 histone H3; Provisional
Probab=28.55 E-value=35 Score=24.53 Aligned_cols=34 Identities=29% Similarity=0.566 Sum_probs=23.7
Q ss_pred hhhhcCChHHHHHHHHHHHHHHHHhccCccceeeeeccCHHHHHhHH
Q 034824 7 RLANALPFSRLFRQLETEMETVVKVLQPGPLGIIEHKFSAEEVRQAS 53 (82)
Q Consensus 7 ~~~~~lPfs~l~RQlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~ 53 (82)
-+.+-+||++|+|++-++..+ +..|+.+-|.--+
T Consensus 61 lLI~k~pF~RLVREI~~~~~~-------------~~Rf~~~Al~ALQ 94 (136)
T PLN00121 61 LLIRKLPFQRLVREIAQDFKT-------------DLRFQSSAVLALQ 94 (136)
T ss_pred cccccccHHHHHHHHHHHhCc-------------cceeeHHHHHHHH
Confidence 356678999999999888521 3578876554433
No 49
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=28.53 E-value=75 Score=19.78 Aligned_cols=21 Identities=19% Similarity=0.430 Sum_probs=15.4
Q ss_pred eeccCHHHHHhHHHHHHHHHH
Q 034824 41 EHKFSAEEVRQASATVERAVQ 61 (82)
Q Consensus 41 EHkFs~~EI~~A~atv~rAV~ 61 (82)
|+.+|++||.++...+..|+.
T Consensus 66 ~~TLt~~ev~~~~~~i~~~l~ 86 (94)
T PF03147_consen 66 DRTLTDEEVNEIHDKIIKALE 86 (94)
T ss_dssp SS---HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHH
Confidence 788999999999888888764
No 50
>cd07098 ALDH_F15-22 Aldehyde dehydrogenase family 15A1 and 22A1-like. Aldehyde dehydrogenase family members ALDH15A1 (Saccharomyces cerevisiae YHR039C) and ALDH22A1 (Arabidopsis thaliana, EC=1.2.1.3), and similar sequences, are in this CD. Significant improvement of stress tolerance in tobacco plants was observed by overexpressing the ALDH22A1 gene from maize (Zea mays) and was accompanied by a reduction of malondialdehyde derived from cellular lipid peroxidation.
Probab=28.22 E-value=78 Score=24.58 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=29.9
Q ss_pred cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhhh
Q 034824 36 PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKDY 79 (82)
Q Consensus 36 PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkdy 79 (82)
++|-+ +.-|.+++.+|=+..++|-..|++ ...++...+|+.+
T Consensus 8 ~i~~~-~~~~~~~v~~av~~A~~A~~~w~~-~~~~~R~~~L~~~ 49 (465)
T cd07098 8 HLGSV-PADTPEDVDEAIAAARAAQREWAK-TSFAERRKVLRSL 49 (465)
T ss_pred eeEEe-eCCCHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHH
Confidence 45544 566789999998889999999966 4555555665543
No 51
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=27.85 E-value=82 Score=20.11 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=33.4
Q ss_pred eeeccCHHHHHhHHHHHHHHHH-HHHHhhhhhcccchhhhhh
Q 034824 40 IEHKFSAEEVRQASATVERAVQ-NWLRNAYQEQGSEILKDYI 80 (82)
Q Consensus 40 vEHkFs~~EI~~A~atv~rAV~-nWrrn~~lE~~~~ilkdyi 80 (82)
.|..||.+++...=..+..-.+ ||....++|+.-..+|+.+
T Consensus 8 ~~~~fs~~q~s~~~~i~~~ll~~~i~~~~~~~~~~~~fk~~l 49 (101)
T PF14769_consen 8 KEQGFSWEQTSAFLSILKELLEKNIEKGMSLEDSFKYFKELL 49 (101)
T ss_pred hhCCCCHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence 4788999999888888888887 8888888888888887754
No 52
>PRK10386 curli assembly protein CsgE; Provisional
Probab=27.25 E-value=92 Score=22.26 Aligned_cols=33 Identities=15% Similarity=0.104 Sum_probs=27.4
Q ss_pred HHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 46 AEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 46 ~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
+++-.+|=.+|..++..|+.++.+.+..++-+|
T Consensus 96 k~~A~~Ai~~v~~~l~q~~~~~~~~~t~Dl~~d 128 (130)
T PRK10386 96 EKTVVFALDQTEEALNRRQIDQALLSTGDLARD 128 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCcC
Confidence 455667888999999999999999988887665
No 53
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=27.25 E-value=1.3e+02 Score=17.10 Aligned_cols=42 Identities=21% Similarity=0.160 Sum_probs=33.4
Q ss_pred cCccceeeeeccCHHHHHhH----HHHHHHHHHHHHHhhhhhcccc
Q 034824 33 QPGPLGIIEHKFSAEEVRQA----SATVERAVQNWLRNAYQEQGSE 74 (82)
Q Consensus 33 QPGPlGIvEHkFs~~EI~~A----~atv~rAV~nWrrn~~lE~~~~ 74 (82)
++|-=+.+...||-+||-+. +.||.|.+..|++.-.++...+
T Consensus 18 ~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 18 QDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp EETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred CCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 44556788899999999875 6789999999999887775443
No 54
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=26.99 E-value=1.5e+02 Score=23.76 Aligned_cols=47 Identities=11% Similarity=0.137 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhh
Q 034824 20 QLETEMETVVKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQE 70 (82)
Q Consensus 20 QlEqdvETVi~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE 70 (82)
-+-++++.++..|. .+...|||++.+++|=....|+...|++=..|-
T Consensus 159 Y~~~ql~~l~~~LE----e~tG~kit~e~L~eaI~n~nr~~~~~~e~~~l~ 205 (430)
T TIGR03191 159 YVANQLHDGIEFVE----KASGRKCDDELFIKAIKNEMRSTARWADICALN 205 (430)
T ss_pred HHHHHHHHHHHHHH----HHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444455555544 355679999999999999999999998866554
No 55
>PF11473 B2: RNA binding protein B2; InterPro: IPR024377 Protein B2 binds double-strand RNA (dsRNA) with high affinity and suppresses the host RNA silencing-based antiviral response. B2 is expressed by the insect Flock House virus (FHV) as a counter-defense mechanism against antiviral RNA silencing during infection. In vitro, B2 binds to dsRNA as a dimer and inhibits the cleavage of it by Dicer. B2 blocks cleavage of the FHV genome by Dicer and also the incorporation of FHV small interfering RNAs into the RNA-induced silencing complex [].; PDB: 2AZ2_A 2B9Z_A 2AZ0_A.
Probab=26.96 E-value=63 Score=21.67 Aligned_cols=15 Identities=40% Similarity=0.419 Sum_probs=13.1
Q ss_pred HHhHHHHHHHHHHHH
Q 034824 49 VRQASATVERAVQNW 63 (82)
Q Consensus 49 I~~A~atv~rAV~nW 63 (82)
..+|++|+.||++|-
T Consensus 45 L~K~e~T~~r~~~sL 59 (73)
T PF11473_consen 45 LNKAEATVFRATDSL 59 (73)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 567899999999986
No 56
>PLN00160 histone H3; Provisional
Probab=26.71 E-value=54 Score=22.31 Aligned_cols=19 Identities=47% Similarity=0.831 Sum_probs=15.6
Q ss_pred hhhhcCChHHHHHHHHHHH
Q 034824 7 RLANALPFSRLFRQLETEM 25 (82)
Q Consensus 7 ~~~~~lPfs~l~RQlEqdv 25 (82)
-+.+-+||++|+|.+-++.
T Consensus 20 lLI~k~pF~RLVREI~~~~ 38 (97)
T PLN00160 20 LLIRRLPFARLVREIQMEM 38 (97)
T ss_pred hhhccccHHHHHHHHHHHc
Confidence 3567789999999988775
No 57
>cd07097 ALDH_KGSADH-YcbD Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like. Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, tetrameric, 2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an enzyme involved in the catabolic pathway for D-arabinose in Sulfolobus solfataricus, also clusters in this group. This CD shows a distant phylogenetic relationship to the Azospirillum brasilense KGSADH-II (-III) group.
Probab=26.65 E-value=71 Score=24.99 Aligned_cols=46 Identities=28% Similarity=0.395 Sum_probs=31.3
Q ss_pred HhccCc----cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhh
Q 034824 30 KVLQPG----PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILK 77 (82)
Q Consensus 30 ~VLQPG----PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilk 77 (82)
.|..|. |+|-+ +.-|.+|+.+|=+..++|...|+.- ..++...+|+
T Consensus 17 ~v~~P~~~~~~i~~~-~~~~~~~v~~av~~A~~A~~~W~~~-~~~~R~~~L~ 66 (473)
T cd07097 17 ENRNPSDTSDVVGKY-ARASAEDADAAIAAAAAAFPAWRRT-SPEARADILD 66 (473)
T ss_pred eeECCCCCCeEEEEE-eCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHH
Confidence 456664 34443 3468899999999999999999764 3444445444
No 58
>TIGR02818 adh_III_F_hyde S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase. The members of this protein family show dual function. First, they remove formaldehyde, a toxic metabolite, by acting as S-(hydroxymethyl)glutathione dehydrogenase (1.1.1.284). S-(hydroxymethyl)glutathione can form spontaneously from formaldehyde and glutathione, and so this enzyme previously was designated glutathione-dependent formaldehyde dehydrogenase. These same proteins are also designated alcohol dehydrogenase (EC 1.1.1.1) of class III, for activities that do not require glutathione; they tend to show poor activity for ethanol among their various substrate alcohols.
Probab=26.34 E-value=87 Score=23.05 Aligned_cols=35 Identities=20% Similarity=0.413 Sum_probs=26.5
Q ss_pred HHHHHHHHhccCccc---eeeeeccCHHHHHhHHHHHH
Q 034824 23 TEMETVVKVLQPGPL---GIIEHKFSAEEVRQASATVE 57 (82)
Q Consensus 23 qdvETVi~VLQPGPl---GIvEHkFs~~EI~~A~atv~ 57 (82)
.+++.+++.++=|-+ -+|.|.|+-+|+.+|-+.++
T Consensus 320 ~~~~~~~~~~~~g~i~~~~~it~~~~l~~~~~A~~~~~ 357 (368)
T TIGR02818 320 TELPGIVEQYMKGEIALDDFVTHTMPLEDINEAFDLMH 357 (368)
T ss_pred HHHHHHHHHHHCCCCCchhheeEEecHHHHHHHHHHHh
Confidence 367778888877755 35899999999988866553
No 59
>PF14348 DUF4400: Domain of unknown function (DUF4400)
Probab=25.46 E-value=2.3e+02 Score=19.85 Aligned_cols=28 Identities=11% Similarity=0.020 Sum_probs=22.5
Q ss_pred cCChHHHHHHHHHHHHHHHHhccCccce
Q 034824 11 ALPFSRLFRQLETEMETVVKVLQPGPLG 38 (82)
Q Consensus 11 ~lPfs~l~RQlEqdvETVi~VLQPGPlG 38 (82)
.+|-.+..++.++|+++..+.|-+++-+
T Consensus 5 f~~~e~~~~~~~~e~~~~~~~lg~~~~~ 32 (198)
T PF14348_consen 5 FFWPEQGWRHSRAELQSELQWLGEDFTR 32 (198)
T ss_pred eeCchHHHHHHHHHHHHHHHHHccccch
Confidence 4566788999999999999998775433
No 60
>PF03405 FA_desaturase_2: Fatty acid desaturase; InterPro: IPR005067 Fatty acid desaturases are enzymes that catalyze the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related. Family 1 is composed of: - Stearoyl-CoA desaturase (SCD) (1.14.19.1 from EC) []. Family 2 is composed of: - Bacterial fatty acid desaturases. - Plant stearoyl-acyl-carrier-protein desaturase (1.14.19.1 from EC) [], this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils. - Cyanobacterial DesA [], an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids. This entry contains fatty acid desaturases belonging to Family 2. ; GO: 0045300 acyl-[acyl-carrier-protein] desaturase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 1OQ7_B 1AFR_A 2XZ0_B 1OQB_A 2J2F_E 1OQ4_B 1OQ9_A 2XZ1_A 1ZA0_A.
Probab=25.08 E-value=34 Score=27.49 Aligned_cols=24 Identities=21% Similarity=0.428 Sum_probs=20.4
Q ss_pred HHHHHHHHhhhhhcccc--hhhhhhh
Q 034824 58 RAVQNWLRNAYQEQGSE--ILKDYID 81 (82)
Q Consensus 58 rAV~nWrrn~~lE~~~~--ilkdyi~ 81 (82)
+.-..|-+.||-|.|-| +|++|+.
T Consensus 98 ~~W~~wv~~WTAEEnRHg~~L~~YL~ 123 (330)
T PF03405_consen 98 SPWGRWVGRWTAEENRHGDALRDYLY 123 (330)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHcccccccccccHHHHHHHHH
Confidence 34678999999999988 9999974
No 61
>cd07144 ALDH_ALD2-YMR170C Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) and other similar sequences, are present in this CD.
Probab=24.79 E-value=95 Score=24.37 Aligned_cols=50 Identities=20% Similarity=0.423 Sum_probs=31.5
Q ss_pred HHhccCc---cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhhh
Q 034824 29 VKVLQPG---PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKDY 79 (82)
Q Consensus 29 i~VLQPG---PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkdy 79 (82)
+.|..|- ++|-+ +.-+.++|.+|=...++|...|.++...++...+|+.+
T Consensus 25 ~~~~~P~tg~~i~~~-~~~~~~~v~~ai~~A~~A~~~~w~~~~~~~R~~iL~~~ 77 (484)
T cd07144 25 IKTVNPSTGEVIASV-YAAGEEDVDKAVKAARKAFESWWSKVTGEERGELLDKL 77 (484)
T ss_pred EEeECCCCCCEEEEE-eCCCHHHHHHHHHHHHHHHHhhHhcCCHHHHHHHHHHH
Confidence 3455563 33322 34567889888888888888755455666666666543
No 62
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=24.78 E-value=93 Score=20.35 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=18.1
Q ss_pred ceeeeeccCHHHHHhHHHHHHHHHHHHHHhh
Q 034824 37 LGIIEHKFSAEEVRQASATVERAVQNWLRNA 67 (82)
Q Consensus 37 lGIvEHkFs~~EI~~A~atv~rAV~nWrrn~ 67 (82)
.|| +.|++||. .-++.||.....+|
T Consensus 84 ~gi---~~t~~~i~---~~IEaAV~~m~~~~ 108 (108)
T PF09682_consen 84 KGI---KVTDEQIE---GAIEAAVKEMNDEW 108 (108)
T ss_pred cCC---CCCHHHHH---HHHHHHHHHHhhcC
Confidence 466 88888865 45788888776654
No 63
>cd07110 ALDH_F10_BADH Arabidopsis betaine aldehyde dehydrogenase 1 and 2, ALDH family 10A8 and 10A9-like. Present in this CD are the Arabidopsis betaine aldehyde dehydrogenase (BADH) 1 (chloroplast) and 2 (mitochondria), also known as, aldehyde dehydrogenase family 10 member A8 and aldehyde dehydrogenase family 10 member A9, respectively, and are putative dehydration- and salt-inducible BADHs (EC 1.2.1.8) that catalyze the oxidation of betaine aldehyde to the compatible solute glycine betaine.
Probab=24.69 E-value=1.1e+02 Score=23.68 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=28.6
Q ss_pred cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhh
Q 034824 36 PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILK 77 (82)
Q Consensus 36 PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilk 77 (82)
|+|-+ +.-|.+|+.+|=...++|...|++ ...++...+|+
T Consensus 9 ~i~~~-~~~~~~~v~~av~~A~~A~~~w~~-~~~~~R~~~L~ 48 (456)
T cd07110 9 TIGEI-PAATAEDVDAAVRAARRAFPRWKK-TTGAERAKYLR 48 (456)
T ss_pred EEEEE-eCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHH
Confidence 45554 455889999998889999999975 45555555554
No 64
>cd07145 ALDH_LactADH_F420-Bios Methanocaldococcus jannaschii NAD+-dependent lactaldehyde dehydrogenase-like. NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22) involved the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii through the oxidation of lactaldehyde to lactate and generation of NAPH, and similar sequences are included in this CD.
Probab=24.62 E-value=1.1e+02 Score=23.66 Aligned_cols=40 Identities=25% Similarity=0.218 Sum_probs=29.2
Q ss_pred cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhh
Q 034824 36 PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILK 77 (82)
Q Consensus 36 PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilk 77 (82)
|+|-+ +.-+.+++.+|=+..++|-..|++ ...++...+|+
T Consensus 11 ~i~~~-~~~~~~~v~~av~~A~~A~~~w~~-~~~~~R~~~L~ 50 (456)
T cd07145 11 VIDTV-PSLSREEVREAIEVAEKAKDVMSN-LPAYKRYKILM 50 (456)
T ss_pred EEEEE-eCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHH
Confidence 45544 677889999999999999999975 45555555544
No 65
>PF03298 Stanniocalcin: Stanniocalcin family; InterPro: IPR004978 Stanniocalcin (STC) is a calcium- and phosphate-regulating hormone produced in bony fish by the corpuscles of Stannius, which are located close to the kidney. It is a major antihypercalcemic hormone in fish. Recent results suggest that the biological repertoires of STCs in mammals will be considerably larger than in fish and may not be limited to mineral metabolism.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=24.59 E-value=81 Score=24.28 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHhccCccce
Q 034824 16 RLFRQLETEMETVVKVLQPGPLG 38 (82)
Q Consensus 16 ~l~RQlEqdvETVi~VLQPGPlG 38 (82)
.+.-|++++|.+..+.||-+|-.
T Consensus 181 ~~~~~~g~~~~~l~~~lq~~~~~ 203 (208)
T PF03298_consen 181 SLMSQLGPNMASLFQLLQNCPCA 203 (208)
T ss_pred HHHHHHhhhHHHHHHHhccCCCc
Confidence 45668999999999999988864
No 66
>PF10356 DUF2034: Protein of unknown function (DUF2034); InterPro: IPR018828 This protein is expressed mainly in fungi but its function is unknown.
Probab=24.52 E-value=9.4 Score=28.19 Aligned_cols=27 Identities=33% Similarity=0.468 Sum_probs=24.2
Q ss_pred ccCHHHHHhHHHHHHHHHHHHHHhhhh
Q 034824 43 KFSAEEVRQASATVERAVQNWLRNAYQ 69 (82)
Q Consensus 43 kFs~~EI~~A~atv~rAV~nWrrn~~l 69 (82)
|.+..+|||-..|..+++.+||++.++
T Consensus 97 KvgP~~vRELeGt~~~~~~~~~~~~ti 123 (185)
T PF10356_consen 97 KVGPKLVRELEGTFSRAPPGWRRNSTI 123 (185)
T ss_pred CCChhhhhhhheeeecccCCCCCCCEE
Confidence 788999999999999999999977653
No 67
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues 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. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=24.46 E-value=1.3e+02 Score=18.11 Aligned_cols=15 Identities=33% Similarity=0.388 Sum_probs=10.7
Q ss_pred eeccCHHHHHhHHHH
Q 034824 41 EHKFSAEEVRQASAT 55 (82)
Q Consensus 41 EHkFs~~EI~~A~at 55 (82)
++.||++|+.+|+.+
T Consensus 169 ~~~~s~~el~~~k~~ 183 (184)
T PF05193_consen 169 EGGISEEELERAKNQ 183 (184)
T ss_dssp HHCS-HHHHHHHHHH
T ss_pred HcCCCHHHHHHHHhc
Confidence 344899999988865
No 68
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=24.11 E-value=42 Score=24.14 Aligned_cols=16 Identities=44% Similarity=0.806 Sum_probs=14.1
Q ss_pred HHHHHHHHhccCccce
Q 034824 23 TEMETVVKVLQPGPLG 38 (82)
Q Consensus 23 qdvETVi~VLQPGPlG 38 (82)
+|+.|++..|+||-|+
T Consensus 94 reiqta~rLllPgel~ 109 (127)
T KOG1744|consen 94 REIQTAVRLLLPGELA 109 (127)
T ss_pred HHHHHHHHHhCchHHh
Confidence 6899999999998765
No 69
>PF15266 DUF4594: Domain of unknown function (DUF4594)
Probab=24.11 E-value=19 Score=27.10 Aligned_cols=32 Identities=22% Similarity=0.385 Sum_probs=23.2
Q ss_pred HHHHhHH-HHHHHHHHHHHHhhhhhcccchhhh
Q 034824 47 EEVRQAS-ATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 47 ~EI~~A~-atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
++|-+|+ |-=+.|--+|||.|-+|+...+++|
T Consensus 75 eqID~eRlaRhR~a~G~WRReWD~dKa~~m~~d 107 (182)
T PF15266_consen 75 EQIDQERLARHRNAQGQWRREWDLDKAEPMFQD 107 (182)
T ss_pred HHHhHHHHHhhcccCCCcccccchhcccccccc
Confidence 4555554 2334567799999999999888876
No 70
>PF10372 YojJ: Bacterial membrane-spanning protein N-terminus; InterPro: IPR019457 This entry is found at the N terminus of a family of putative membrane-spanning bacterial proteins. These proteins often contain IPR003390 from INTERPRO towards the C terminus. ; PDB: 2FB5_A.
Probab=24.10 E-value=81 Score=20.39 Aligned_cols=18 Identities=22% Similarity=0.589 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHhcc
Q 034824 16 RLFRQLETEMETVVKVLQ 33 (82)
Q Consensus 16 ~l~RQlEqdvETVi~VLQ 33 (82)
+-++|+++|++.+++.|-
T Consensus 17 ~~L~~I~~~~~~i~~~ld 34 (70)
T PF10372_consen 17 QYLEQIEEEISQIIQTLD 34 (70)
T ss_dssp HHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 448899999999999885
No 71
>PRK09406 gabD1 succinic semialdehyde dehydrogenase; Reviewed
Probab=23.91 E-value=90 Score=24.60 Aligned_cols=36 Identities=14% Similarity=0.151 Sum_probs=26.0
Q ss_pred eccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 42 HKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 42 HkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
..-|.+|+.+|=+..++|...|++ -.+++...+|+.
T Consensus 18 ~~~~~~~v~~av~~A~~A~~~w~~-~~~~~R~~~L~~ 53 (457)
T PRK09406 18 TALTDDEVDAAIARAHARFRDYRT-TTFAQRARWANA 53 (457)
T ss_pred eCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHH
Confidence 346889999999999999999985 344444455543
No 72
>PF00534 Glycos_transf_1: Glycosyl transferases group 1; InterPro: IPR001296 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Proteins containign this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid. Mutations in this domain of the human N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein are the cause of paroxysmal nocturnal hemoglobinuria (PNH), an acquired hemolytic blood disorder characterised by venous thrombosis, erythrocyte hemolysis, infections and defective hematopoiesis.; GO: 0009058 biosynthetic process; PDB: 2L7C_A 2IV3_B 2IUY_B 2XA9_A 2XA1_B 2X6R_A 2XMP_B 2XA2_B 2X6Q_A 3QHP_B ....
Probab=23.81 E-value=1.9e+02 Score=17.96 Aligned_cols=40 Identities=13% Similarity=0.165 Sum_probs=27.5
Q ss_pred HHhccCccceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhc
Q 034824 29 VKVLQPGPLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQ 71 (82)
Q Consensus 29 i~VLQPGPlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~ 71 (82)
-.++.+|.-|++=+..+.+++.+ .+.++++++..-..+.+
T Consensus 128 ~e~~~~~~~g~~~~~~~~~~l~~---~i~~~l~~~~~~~~l~~ 167 (172)
T PF00534_consen 128 NEIINDGVNGFLFDPNDIEELAD---AIEKLLNDPELRQKLGK 167 (172)
T ss_dssp HHHSGTTTSEEEESTTSHHHHHH---HHHHHHHHHHHHHHHHH
T ss_pred ceeeccccceEEeCCCCHHHHHH---HHHHHHCCHHHHHHHHH
Confidence 35677788888877777777654 57788888755555443
No 73
>PF15617 C-C_Bond_Lyase: C-C_Bond_Lyase of the TIM-Barrel fold
Probab=23.74 E-value=61 Score=26.41 Aligned_cols=40 Identities=25% Similarity=0.416 Sum_probs=31.6
Q ss_pred HHHHHHHHHHH------HHHHhccCccceeee--eccCHHHHHhHHHHHHH
Q 034824 16 RLFRQLETEME------TVVKVLQPGPLGIIE--HKFSAEEVRQASATVER 58 (82)
Q Consensus 16 ~l~RQlEqdvE------TVi~VLQPGPlGIvE--HkFs~~EI~~A~atv~r 58 (82)
+|+|.++.|.. ||| +|-=+.+|+ +.-|.+|..+|.+.+..
T Consensus 251 gL~rEv~lD~anGlvGKTvI---HPsqI~~V~al~~Vs~eey~DA~~IL~~ 298 (345)
T PF15617_consen 251 GLIREVELDKANGLVGKTVI---HPSQIPVVQALYVVSHEEYEDALDILNS 298 (345)
T ss_pred HHHHHHHHHHhcCcccccee---chhhhhHHHHHhhcCHHHHHHHHHHhcc
Confidence 78888888886 555 588888887 56789999999887754
No 74
>cd07109 ALDH_AAS00426 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like. Uncharacterized aldehyde dehydrogenase of Saccharopolyspora spinosa (AAS00426) and other similar sequences, are present in this CD.
Probab=23.64 E-value=97 Score=23.97 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=26.3
Q ss_pred CHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 45 SAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 45 s~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
|.++|.+|=...++|-..|+++...++...+|+.
T Consensus 17 ~~~dv~~av~~a~~A~~~~~~~~~~~~R~~~L~~ 50 (454)
T cd07109 17 GAADVDRAVQAARRAFESGWLRLSPAERGRLLLR 50 (454)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 6788888888888888888867777777776643
No 75
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=23.44 E-value=54 Score=23.82 Aligned_cols=20 Identities=40% Similarity=0.798 Sum_probs=17.0
Q ss_pred hhhcCChHHHHHHHHHHHHH
Q 034824 8 LANALPFSRLFRQLETEMET 27 (82)
Q Consensus 8 ~~~~lPfs~l~RQlEqdvET 27 (82)
+.+-+||.+|+|..+|+.-+
T Consensus 63 lI~K~PFqRlvrei~q~f~~ 82 (137)
T KOG1745|consen 63 LIRKLPFQRLVREIAQDFKT 82 (137)
T ss_pred HhhcCcHHHHhHHHHhcccc
Confidence 45679999999999998776
No 76
>PF00171 Aldedh: Aldehyde dehydrogenase family; InterPro: IPR015590 Aldehyde dehydrogenases (1.2.1.3 from EC and 1.2.1.5 from EC) are enzymes that oxidize a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor. In mammals at least four different forms of the enzyme are known []: class-1 (or Ald C) a tetrameric cytosolic enzyme, class-2 (or Ald M) a tetrameric mitochondrial enzyme, class- 3 (or Ald D) a dimeric cytosolic enzyme, and class IV a microsomal enzyme. Aldehyde dehydrogenases have also been sequenced from fungal and bacterial species. A number of enzymes are known to be evolutionary related to aldehyde dehydrogenases. A glutamic acid and a cysteine residue have been implicated in the catalytic activity of mammalian aldehyde dehydrogenase. These residues are conserved in all the enzymes of this entry. Some of the proteins in this entry are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 10 and Cla h 3.; GO: 0016491 oxidoreductase activity, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 3R31_A 3HAZ_A 1UXQ_A 1UXP_A 1UXR_A 1UXU_A 1UXN_A 1KY8_A 1UXT_A 1UXV_A ....
Probab=23.37 E-value=94 Score=24.09 Aligned_cols=35 Identities=23% Similarity=0.390 Sum_probs=25.3
Q ss_pred ccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 43 KFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 43 kFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
.-|.+++.+|=+.-++|-..|+. ...++...+|+.
T Consensus 25 ~~~~~~v~~av~~A~~A~~~w~~-~~~~~R~~iL~~ 59 (462)
T PF00171_consen 25 SATAEDVDRAVEAARAAFKEWSK-LPAAERARILER 59 (462)
T ss_dssp EBSHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHhhhh-hhhhhHHHHHHH
Confidence 45789999999999999999954 444444555543
No 77
>cd07082 ALDH_F11_NP-GAPDH NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11. NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9) catalyzes the irreversible oxidation of glyceraldehyde 3-phosphate to 3-phosphoglycerate generating NADPH for biosynthetic reactions. This CD also includes the Arabidopsis thaliana osmotic-stress-inducible ALDH family 11, ALDH11A3 and similar sequences. In autotrophic eukaryotes, NP-GAPDH generates NADPH for biosynthetic processes from photosynthetic glyceraldehyde-3-phosphate exported from the chloroplast and catalyzes one of the classic glycolytic bypass reactions unique to plants.
Probab=23.32 E-value=97 Score=24.11 Aligned_cols=36 Identities=25% Similarity=0.285 Sum_probs=26.5
Q ss_pred ccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 43 KFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 43 kFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
.-|.+++.+|=...++|-..|++....+....+|+.
T Consensus 34 ~~~~~~v~~av~~A~~A~~~w~~~~~~~~R~~~L~~ 69 (473)
T cd07082 34 ALSALEILEAAETAYDAGRGWWPTMPLEERIDCLHK 69 (473)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHH
Confidence 457889999999999999999887344444455543
No 78
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.27 E-value=1.5e+02 Score=16.46 Aligned_cols=23 Identities=17% Similarity=0.388 Sum_probs=15.4
Q ss_pred cCHHHHHh----HHHHHHHHHHHHHHh
Q 034824 44 FSAEEVRQ----ASATVERAVQNWLRN 66 (82)
Q Consensus 44 Fs~~EI~~----A~atv~rAV~nWrrn 66 (82)
+|-+||-+ +..||.|++..+++.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 45666655 467899999988875
No 79
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=23.07 E-value=2.5e+02 Score=19.00 Aligned_cols=52 Identities=25% Similarity=0.291 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHhccCccceeeeec--------------cC----HHHHHhHHHHHHHHHHHHHHhhh
Q 034824 17 LFRQLETEMETVVKVLQPGPLGIIEHK--------------FS----AEEVRQASATVERAVQNWLRNAY 68 (82)
Q Consensus 17 l~RQlEqdvETVi~VLQPGPlGIvEHk--------------Fs----~~EI~~A~atv~rAV~nWrrn~~ 68 (82)
+-++++++.+.+-.|||+++.+..+.. |+ ++||...-..+.+=+++=+.|..
T Consensus 74 ~~~e~~~~~~~~~~vL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~d~el~~l~~ql~~hl~s~~~n~~ 143 (160)
T PF13094_consen 74 LEREREEEEKKAHPVLQLDDSGVLELPELPQKSLLEASESRFAPTLCDEELLPLLKQLNKHLESMQNNLQ 143 (160)
T ss_pred HHHHHHHHHhccchhhccccccccccccccccccccccccccCcccchHHHHHHHHHHHHHHHHHHccHH
Confidence 467778888888999999877665542 21 77888887777777777666655
No 80
>cd07225 Pat_PNPLA6_PNPLA7 Patatin-like phospholipase domain containing protein 6 and protein 7. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are 60% identical to each other. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologous to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE
Probab=23.05 E-value=70 Score=24.36 Aligned_cols=41 Identities=20% Similarity=0.350 Sum_probs=27.1
Q ss_pred HhccCccceee-eeccCHH-H-HHhHHHHHHHHHHHHHHhhhhhc
Q 034824 30 KVLQPGPLGII-EHKFSAE-E-VRQASATVERAVQNWLRNAYQEQ 71 (82)
Q Consensus 30 ~VLQPGPlGIv-EHkFs~~-E-I~~A~atv~rAV~nWrrn~~lE~ 71 (82)
.++.| |++=+ +..|+.- | +....+..+++.+.|.++..+|.
T Consensus 259 ~~i~P-~v~~~~~~d~~kl~~~~~~Gy~~a~~~l~~~~~~~~~~~ 302 (306)
T cd07225 259 EYLRP-PIDKYKTLDFGKFDEICEVGYQHGKTVFDGWKRSGVLEK 302 (306)
T ss_pred EEEec-CccCCCCCChHHHHHHHHHHHHHHHHHHHHHHHcCcchh
Confidence 37899 66544 5444432 2 23345677888999999998875
No 81
>cd07088 ALDH_LactADH-AldA Escherichia coli lactaldehyde dehydrogenase AldA-like. Lactaldehyde dehydrogenase from Escherichia coli (AldA, LactADH, EC=1.2.1.22), an NAD(+)-dependent enzyme involved in the metabolism of L-fucose and L-rhamnose, and other similar sequences are present in this CD.
Probab=22.96 E-value=1e+02 Score=23.89 Aligned_cols=47 Identities=23% Similarity=0.372 Sum_probs=30.1
Q ss_pred HHhccCc---cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhh
Q 034824 29 VKVLQPG---PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILK 77 (82)
Q Consensus 29 i~VLQPG---PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilk 77 (82)
+.|..|. |+|-+ +.-|.+|+.+|=+..++|-..|+.- ..++...+|+
T Consensus 15 ~~~~~P~t~~~i~~~-~~~~~~~v~~av~~A~~A~~~w~~~-~~~~R~~~L~ 64 (468)
T cd07088 15 IDVLNPATGEVVATV-PAATAEDADRAVDAAEAAQKAWERL-PAIERAAYLR 64 (468)
T ss_pred EEeECCCCCCEEEEE-eCCCHHHHHHHHHHHHHHHHHHhhC-CHHHHHHHHH
Confidence 3455552 34422 4557789999999999999999863 3344444443
No 82
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=22.65 E-value=27 Score=24.25 Aligned_cols=61 Identities=20% Similarity=0.366 Sum_probs=36.7
Q ss_pred cCChHHHHHHHHHHHHHHHHhccCccceeeeeccCH----HHHHhHHHHHHHHHHHHHHhhhhhcccc-hhhhh
Q 034824 11 ALPFSRLFRQLETEMETVVKVLQPGPLGIIEHKFSA----EEVRQASATVERAVQNWLRNAYQEQGSE-ILKDY 79 (82)
Q Consensus 11 ~lPfs~l~RQlEqdvETVi~VLQPGPlGIvEHkFs~----~EI~~A~atv~rAV~nWrrn~~lE~~~~-ilkdy 79 (82)
..|+|++++.+=.. .+||++-+=+..++ .+-..+...-++|++.++.+..|.+..- +|+++
T Consensus 48 ~tpL~eal~~i~~~--------~~~~~~~~f~~~a~~L~~~~~~~~~~~w~~~~~~~~~~~~L~~~d~e~L~~l 113 (170)
T PF09548_consen 48 ATPLPEALERISRR--------SEGPIGEFFERVAERLEKNEGESFAEAWEEAVEKLLKESALKKEDKEILLEL 113 (170)
T ss_pred CCCHHHHHHHHHhc--------ccchHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhcCCCCHHHHHHHHHH
Confidence 45677766665433 36777766554432 2223455667788888888888864433 66665
No 83
>PRK00507 deoxyribose-phosphate aldolase; Provisional
Probab=22.46 E-value=1.7e+02 Score=21.52 Aligned_cols=45 Identities=22% Similarity=0.255 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHHHHHhccCcccee-ee-eccCHHHHHhHHHHHHH
Q 034824 14 FSRLFRQLETEMETVVKVLQPGPLGI-IE-HKFSAEEVRQASATVER 58 (82)
Q Consensus 14 fs~l~RQlEqdvETVi~VLQPGPlGI-vE-HkFs~~EI~~A~atv~r 58 (82)
.++-...+++|+..+.+...|-++=+ +| -.++++||.+|-..+..
T Consensus 101 ~~g~~~~v~~ei~~v~~~~~~~~lKvIlEt~~L~~e~i~~a~~~~~~ 147 (221)
T PRK00507 101 KSGDWDAVEADIRAVVEAAGGAVLKVIIETCLLTDEEKVKACEIAKE 147 (221)
T ss_pred cCCCHHHHHHHHHHHHHhcCCceEEEEeecCcCCHHHHHHHHHHHHH
Confidence 33447899999999999776656654 44 34899999776554443
No 84
>PLN00179 acyl- [acyl-carrier protein] desaturase
Probab=22.25 E-value=34 Score=28.54 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=19.4
Q ss_pred HHHHHHHhhhhhcccc--hhhhhhh
Q 034824 59 AVQNWLRNAYQEQGSE--ILKDYID 81 (82)
Q Consensus 59 AV~nWrrn~~lE~~~~--ilkdyi~ 81 (82)
+-..|-+.||-|.|-| +|.+|++
T Consensus 156 ~W~~Wvr~WTAEENRHgdlL~~YLy 180 (390)
T PLN00179 156 PWARWTRAWTAEENRHGDLLNKYLY 180 (390)
T ss_pred chhhhccccccccchHHHHHHHHHh
Confidence 3556999999999987 9999975
No 85
>PF00675 Peptidase_M16: Insulinase (Peptidase family M16) This is family M16 in the peptidase classification. ; InterPro: IPR011765 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The majority of the sequences in this entry are metallopeptidases and non-peptidase homologs belong to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C; they include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The proteins classified as non-peptidase homologues 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. ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3P7L_A 3P7O_A 3TUV_A 3GO9_A 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B ....
Probab=22.06 E-value=1.2e+02 Score=19.12 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=17.7
Q ss_pred ccCHHHHHhHHHHHHHHHHHH
Q 034824 43 KFSAEEVRQASATVERAVQNW 63 (82)
Q Consensus 43 kFs~~EI~~A~atv~rAV~nW 63 (82)
+|+++|+.+++..+...+..=
T Consensus 99 ~f~~~~~~~~r~~~~~ei~~~ 119 (149)
T PF00675_consen 99 SFDEEEFEREREQILQEIEEI 119 (149)
T ss_dssp GGCHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 899999999999888777653
No 86
>PRK10673 acyl-CoA esterase; Provisional
Probab=21.89 E-value=1.5e+02 Score=19.43 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHhccCccceeeeeccCH
Q 034824 19 RQLETEMETVVKVLQPGPLGIIEHKFSA 46 (82)
Q Consensus 19 RQlEqdvETVi~VLQPGPlGIvEHkFs~ 46 (82)
.++=+|+.++++-|.++++.+|-|-+-.
T Consensus 65 ~~~~~d~~~~l~~l~~~~~~lvGhS~Gg 92 (255)
T PRK10673 65 PAMAQDLLDTLDALQIEKATFIGHSMGG 92 (255)
T ss_pred HHHHHHHHHHHHHcCCCceEEEEECHHH
Confidence 4455688889999999999999886543
No 87
>cd07117 ALDH_StaphAldA1 Uncharacterized Staphylococcus aureus AldA1 (SACOL0154) aldehyde dehydrogenase-like. Uncharacterized aldehyde dehydrogenase from Staphylococcus aureus (AldA1, locus SACOL0154) and other similar sequences are present in this CD.
Probab=21.88 E-value=1e+02 Score=24.48 Aligned_cols=47 Identities=19% Similarity=0.374 Sum_probs=30.6
Q ss_pred HhccCc---cceeeeeccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhhh
Q 034824 30 KVLQPG---PLGIIEHKFSAEEVRQASATVERAVQNWLRNAYQEQGSEILKD 78 (82)
Q Consensus 30 ~VLQPG---PlGIvEHkFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilkd 78 (82)
.|..|. ++|-+ +.-|.+++.+|=+..++|..+|+.- ..++...+|+.
T Consensus 19 ~~~nP~t~~~i~~~-~~~~~~dv~~av~~A~~A~~~w~~~-~~~~R~~~L~~ 68 (475)
T cd07117 19 DSYNPANGETLSEI-TDATDADVDRAVKAAQEAFKTWRKT-TVAERANILNK 68 (475)
T ss_pred EeECCCCCCEEEEE-cCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHH
Confidence 444453 44432 3448899999999999999999763 44444455543
No 88
>COG1012 PutA NAD-dependent aldehyde dehydrogenases [Energy production and conversion]
Probab=21.57 E-value=1e+02 Score=24.99 Aligned_cols=34 Identities=32% Similarity=0.466 Sum_probs=24.8
Q ss_pred ccCHHHHHhHHHHHHHHHHHHHHhhhhhcccchhh
Q 034824 43 KFSAEEVRQASATVERAVQNWLRNAYQEQGSEILK 77 (82)
Q Consensus 43 kFs~~EI~~A~atv~rAV~nWrrn~~lE~~~~ilk 77 (82)
.-+.+++.+|-+..++|-..|++-.- ++...+|+
T Consensus 32 ~a~~~dv~~Av~aA~~a~~~W~~~~~-~eR~~iL~ 65 (472)
T COG1012 32 AATAEDVDAAVAAARAAFEAWSRLSA-EERAAILR 65 (472)
T ss_pred CCCHHHHHHHHHHHHHHHHHhhhCCH-HHHHHHHH
Confidence 35778999999988999999998444 44444444
No 89
>TIGR01202 bchC 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase.
Probab=21.51 E-value=1e+02 Score=22.14 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=26.2
Q ss_pred HHHHHHHHHhccCccce---eeeeccCHHHHHhHHH
Q 034824 22 ETEMETVVKVLQPGPLG---IIEHKFSAEEVRQASA 54 (82)
Q Consensus 22 EqdvETVi~VLQPGPlG---IvEHkFs~~EI~~A~a 54 (82)
-.+++.+++.++=|-+- +|.|.|+-+|+.+|=.
T Consensus 259 ~~~~~~~~~l~~~g~i~~~~~it~~~~l~~~~~A~~ 294 (308)
T TIGR01202 259 PGDLHAVRELIESGALSLDGLITHQRPASDAAEAYM 294 (308)
T ss_pred hhHHHHHHHHHHcCCCChhhccceeecHHHHHHHHH
Confidence 35788899998888775 4899999888887744
No 90
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=21.51 E-value=1.1e+02 Score=19.74 Aligned_cols=20 Identities=15% Similarity=0.275 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHHHHHhhhhh
Q 034824 51 QASATVERAVQNWLRNAYQE 70 (82)
Q Consensus 51 ~A~atv~rAV~nWrrn~~lE 70 (82)
+.++.+++|++.|.....+.
T Consensus 15 ~~r~~i~~A~~~W~~~~~i~ 34 (165)
T cd04268 15 KLRAAILDAIEAWNKAFAIG 34 (165)
T ss_pred HHHHHHHHHHHHHHHHhCcC
Confidence 45788999999999877543
No 91
>PLN00161 histone H3; Provisional
Probab=21.37 E-value=63 Score=23.34 Aligned_cols=18 Identities=50% Similarity=0.914 Sum_probs=14.7
Q ss_pred hhhcCChHHHHHHHHHHH
Q 034824 8 LANALPFSRLFRQLETEM 25 (82)
Q Consensus 8 ~~~~lPfs~l~RQlEqdv 25 (82)
+.+-+||++|+|.+=++.
T Consensus 55 LIpklPF~RLVREI~~~~ 72 (135)
T PLN00161 55 LIRKLPFARLVREISNEM 72 (135)
T ss_pred ccccccHHHHHHHHHHhc
Confidence 457789999999887765
No 92
>PF07332 DUF1469: Protein of unknown function (DUF1469); InterPro: IPR009937 This entry represents proteins found in hypothetical bacterial proteins where is is annotated as ycf49 or ycf49-like. The function is not known.
Probab=21.25 E-value=1.1e+02 Score=19.39 Aligned_cols=19 Identities=16% Similarity=0.464 Sum_probs=16.0
Q ss_pred hcCChHHHHHHHHHHHHHH
Q 034824 10 NALPFSRLFRQLETEMETV 28 (82)
Q Consensus 10 ~~lPfs~l~RQlEqdvETV 28 (82)
...||++..+|+.+|++..
T Consensus 100 ~~~~~~~t~~~l~~d~~~l 118 (121)
T PF07332_consen 100 APPPFEETIAELKEDIAAL 118 (121)
T ss_pred CCCCHHHHHHHHHHHHHHh
Confidence 3567999999999999864
No 93
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation []. The YrdC protein, which consists solely of this domain, forms an alpha/beta twisted open-sheet structure composed of seven alpha helices and seven beta strands []. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes []. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Sua5 is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for normal growth in yeast; however its exact function remains unknown []. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [].; PDB: 3L7V_A 1KK9_A 1K7J_A 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A 2EQA_A ....
Probab=21.24 E-value=42 Score=23.04 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhccCccceeeeec
Q 034824 21 LETEMETVVKVLQPGPLGIIEHK 43 (82)
Q Consensus 21 lEqdvETVi~VLQPGPlGIvEHk 43 (82)
+.......++-.-|||+.+|--+
T Consensus 62 ~~~~~~~l~~~~wPgp~t~I~~~ 84 (179)
T PF01300_consen 62 VSPKARRLLEKFWPGPLTLILPA 84 (179)
T ss_dssp --HHHHHHHHHCHSSSEEEEEEE
T ss_pred ccHHHHHHHHhccccCeeEeecc
Confidence 55677778888899999998653
No 94
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=21.23 E-value=1.8e+02 Score=18.69 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=31.0
Q ss_pred Cccce-eeeeccCHHHHHh----HHHHHHHHHHHHHHhhhhhccc
Q 034824 34 PGPLG-IIEHKFSAEEVRQ----ASATVERAVQNWLRNAYQEQGS 73 (82)
Q Consensus 34 PGPlG-IvEHkFs~~EI~~----A~atv~rAV~nWrrn~~lE~~~ 73 (82)
|++=| .+.-++|-+||-+ .+.||.|++..|++.-.++...
T Consensus 133 ~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 133 PGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 45555 3577899999977 4789999999999988776443
No 95
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=21.17 E-value=1.4e+02 Score=18.98 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=9.2
Q ss_pred cchhhhhhcCC
Q 034824 3 ASLSRLANALP 13 (82)
Q Consensus 3 ~S~~~~~~~lP 13 (82)
+|+-.|..++|
T Consensus 20 isl~qF~~LFP 30 (67)
T PF09447_consen 20 ISLEQFRKLFP 30 (67)
T ss_pred cCHHHHHHHcc
Confidence 67888888888
No 96
>PTZ00192 60S ribosomal protein L13; Provisional
Probab=21.17 E-value=28 Score=27.08 Aligned_cols=41 Identities=27% Similarity=0.335 Sum_probs=31.0
Q ss_pred eccCHHHHHhHHHHHHH------HHHHHHHhhhhh---cccchhhhhhhC
Q 034824 42 HKFSAEEVRQASATVER------AVQNWLRNAYQE---QGSEILKDYIDK 82 (82)
Q Consensus 42 HkFs~~EI~~A~atv~r------AV~nWrrn~~lE---~~~~ilkdyi~k 82 (82)
--||-+|+..|--..+- |||-=|+|...| .|-.-||.|..|
T Consensus 78 RGFtl~ELk~aGi~~~~ArtiGI~VD~RR~n~s~Esl~~Nv~rLk~Y~sk 127 (218)
T PTZ00192 78 RGFSLAELKAAGLNPRFARTIGIRVDRRRKNKSEEGMNVNVQRLKTYMSK 127 (218)
T ss_pred CCcCHHHHHHcCCCHHHhcccceeeccccccccHHHHHHHHHHHHHHHHh
Confidence 35999999998554444 589999998666 566679999764
No 97
>PRK10309 galactitol-1-phosphate dehydrogenase; Provisional
Probab=20.96 E-value=1.3e+02 Score=21.43 Aligned_cols=34 Identities=32% Similarity=0.348 Sum_probs=25.5
Q ss_pred HHHHHHHHhccCccc---eeeeeccCHHHHHhHHHHH
Q 034824 23 TEMETVVKVLQPGPL---GIIEHKFSAEEVRQASATV 56 (82)
Q Consensus 23 qdvETVi~VLQPGPl---GIvEHkFs~~EI~~A~atv 56 (82)
.+++.+++.++-|.+ -+|.|.|+-+|+.+|=..+
T Consensus 297 ~~~~~~~~~~~~g~i~~~~~i~~~~~l~~~~~A~~~~ 333 (347)
T PRK10309 297 QEWETASRLLTERKLSLEPLIAHRGSFESFAQAVRDL 333 (347)
T ss_pred hHHHHHHHHHHcCCCCchhheEEEeeHHHHHHHHHHH
Confidence 567778888887766 4689999988887765443
No 98
>cd08300 alcohol_DH_class_III class III alcohol dehydrogenases. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dim
Probab=20.73 E-value=1.4e+02 Score=21.86 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=25.1
Q ss_pred HHHHHHHHhccCccce---eeeeccCHHHHHhHHHHH
Q 034824 23 TEMETVVKVLQPGPLG---IIEHKFSAEEVRQASATV 56 (82)
Q Consensus 23 qdvETVi~VLQPGPlG---IvEHkFs~~EI~~A~atv 56 (82)
.+++.+++.+.-|-|- +|.|.|+-+|+.+|=+.+
T Consensus 321 ~~~~~~~~~~~~g~l~~~~~i~~~~~le~~~~A~~~~ 357 (368)
T cd08300 321 SQVPKLVEDYMKGKIKVDEFITHTMPLDEINEAFDLM 357 (368)
T ss_pred HHHHHHHHHHHcCCCChhhceeeeEcHHHHHHHHHHH
Confidence 4667777777766553 588999999988886554
No 99
>cd03431 DNA_Glycosylase_C DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to
Probab=20.65 E-value=1.1e+02 Score=17.91 Aligned_cols=16 Identities=31% Similarity=0.611 Sum_probs=12.0
Q ss_pred cCccceeeeeccCHHH
Q 034824 33 QPGPLGIIEHKFSAEE 48 (82)
Q Consensus 33 QPGPlGIvEHkFs~~E 48 (82)
...++|-+.|.||.-.
T Consensus 59 ~~~~~~~~~H~fth~~ 74 (118)
T cd03431 59 SLEPLGTVKHTFTHFR 74 (118)
T ss_pred ccccceeEEEecCCeE
Confidence 3456899999999653
No 100
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=20.57 E-value=50 Score=18.47 Aligned_cols=15 Identities=40% Similarity=0.463 Sum_probs=11.8
Q ss_pred eeeeeccCHHHHHhH
Q 034824 38 GIIEHKFSAEEVRQA 52 (82)
Q Consensus 38 GIvEHkFs~~EI~~A 52 (82)
=+.||.+|.+|+.+.
T Consensus 10 YV~eh~ls~ee~~~R 24 (28)
T PF12368_consen 10 YVKEHGLSEEEVAER 24 (28)
T ss_pred hHHhcCCCHHHHHHH
Confidence 367999999998653
No 101
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=20.55 E-value=74 Score=22.52 Aligned_cols=40 Identities=25% Similarity=0.370 Sum_probs=24.2
Q ss_pred ChHHHHHHH---HHHHHHHHHhccC-ccceeeeeccCHHHHHhH
Q 034824 13 PFSRLFRQL---ETEMETVVKVLQP-GPLGIIEHKFSAEEVRQA 52 (82)
Q Consensus 13 Pfs~l~RQl---EqdvETVi~VLQP-GPlGIvEHkFs~~EI~~A 52 (82)
|...+..++ +.+++.++++||= .|.||--..+..-=..++
T Consensus 54 ~~~eia~~l~~~~~~v~~~l~~lQ~leP~GigAr~l~EcLllQl 97 (194)
T PF04963_consen 54 SLEEIAEELGVSEEEVEKALELLQSLEPAGIGARDLQECLLLQL 97 (194)
T ss_dssp -HHHHHHHCTS-HHHHHHHHHHHHTTSS--TTTS-TTHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHcCCCCccCcCCHHHHHHHHH
Confidence 445555554 6789999998884 699998777665433333
No 102
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.35 E-value=93 Score=18.10 Aligned_cols=26 Identities=27% Similarity=0.454 Sum_probs=15.1
Q ss_pred ccchhhhhhcCChHHHHHHHHHHHHHHH
Q 034824 2 PASLSRLANALPFSRLFRQLETEMETVV 29 (82)
Q Consensus 2 ~~S~~~~~~~lPfs~l~RQlEqdvETVi 29 (82)
++|+..+...+.++. .++|.-+...|
T Consensus 60 ~i~~~~ia~~l~~~~--~~vE~~l~~~I 85 (105)
T PF01399_consen 60 SISISEIAKALQLSE--EEVESILIDLI 85 (105)
T ss_dssp EEEHHHHHHHHTCCH--HHHHHHHHHHH
T ss_pred ccchHHHHHHhccch--HHHHHHHHHHH
Confidence 456666777666665 44555444443
No 103
>cd03725 SOCS_ASB6 SOCS (suppressors of cytokine signaling) box of ASB6-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB6 interacts with the adaptor protein APS and recruits elongin B/C to the insulin receptor signaling complex. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=20.27 E-value=56 Score=19.08 Aligned_cols=29 Identities=14% Similarity=0.242 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHhhhhhcc--cchhhhhh
Q 034824 52 ASATVERAVQNWLRNAYQEQG--SEILKDYI 80 (82)
Q Consensus 52 A~atv~rAV~nWrrn~~lE~~--~~ilkdyi 80 (82)
.+-+|++.+..|+.......- ..-||||+
T Consensus 10 CR~~Ir~~lg~~~~~~~i~~LpLP~~Lk~yL 40 (44)
T cd03725 10 CRVFIRLCLRPWPVDVKVKALPLPDRLKWYL 40 (44)
T ss_pred HHHHHHHhcCccccccccccCCCCHHHHHHh
Confidence 456788888888765544433 36889986
No 104
>cd08010 yceG_like proteins similar to Escherichia coli yceG. The gene product of Escherichia coli yceG has been erroneously annotated as an aminodeoxychorismate lyase. Its overexpression has been reported to cause abnormal biofilm architecture, and it has been reported to be part of a putative five-gene operon. It might function as a periplasmic solute-binding protein. The family also includes Streptomyces caeruleus NovB, an uncharacterized member of the novobiocin biosynthetic gene cluster.
Probab=20.22 E-value=41 Score=25.15 Aligned_cols=11 Identities=45% Similarity=0.709 Sum_probs=8.5
Q ss_pred HhccCccceee
Q 034824 30 KVLQPGPLGII 40 (82)
Q Consensus 30 ~VLQPGPlGIv 40 (82)
+=|.||||+..
T Consensus 195 ~GLPPgPI~~P 205 (245)
T cd08010 195 KGLPPGPIANP 205 (245)
T ss_pred CCCCCCcCCCC
Confidence 45899999864
Done!