Query 028057
Match_columns 214
No_of_seqs 59 out of 61
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 05:34:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028057hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11909 NdhN: NADH-quinone ox 100.0 3.2E-79 6.8E-84 503.3 13.2 135 71-205 8-154 (154)
2 cd05797 Ribosomal_L10 Ribosoma 85.6 0.48 1E-05 37.5 1.6 26 157-182 105-130 (157)
3 PRK00099 rplJ 50S ribosomal pr 81.3 0.93 2E-05 36.7 1.7 26 157-182 106-131 (172)
4 PRK13361 molybdenum cofactor b 72.0 7.2 0.00016 34.4 4.8 60 60-122 67-130 (329)
5 TIGR02668 moaA_archaeal probab 68.7 11 0.00024 32.2 5.1 65 60-128 62-129 (302)
6 PF10902 DUF2693: Protein of u 67.9 2.3 5E-05 32.8 0.7 17 189-205 56-72 (83)
7 PF14085 DUF4265: Domain of un 67.1 15 0.00032 28.7 5.1 62 41-105 41-113 (117)
8 PRK00164 moaA molybdenum cofac 64.4 15 0.00033 31.9 5.1 63 60-123 71-135 (331)
9 TIGR02666 moaA molybdenum cofa 63.4 16 0.00035 31.9 5.1 60 60-122 65-128 (334)
10 TIGR03470 HpnH hopanoid biosyn 57.9 24 0.00053 31.3 5.3 61 57-118 75-136 (318)
11 cd02873 GH18_IDGF The IDGF's ( 51.1 9.2 0.0002 35.2 1.7 38 158-195 48-85 (413)
12 KOG2902 Dihydroorotase [Nucleo 49.9 2.8 6.1E-05 39.3 -1.8 52 140-191 121-174 (344)
13 TIGR00290 MJ0570_dom MJ0570-re 49.8 39 0.00085 29.5 5.2 62 56-117 85-148 (223)
14 TIGR02495 NrdG2 anaerobic ribo 48.6 46 0.001 26.3 5.1 113 60-183 68-183 (191)
15 TIGR03679 arCOG00187 arCOG0018 48.3 38 0.00083 28.7 4.8 62 56-117 86-149 (218)
16 PLN02951 Molybderin biosynthes 48.2 34 0.00074 31.3 4.8 60 60-122 112-175 (373)
17 PF02579 Nitro_FeMo-Co: Dinitr 47.4 13 0.00027 26.0 1.6 44 86-131 34-77 (94)
18 cd01994 Alpha_ANH_like_IV This 45.7 51 0.0011 27.5 5.2 59 59-117 91-151 (194)
19 PF09328 Phytochelatin_C: Doma 43.8 9 0.00019 35.2 0.4 58 119-176 20-84 (264)
20 cd06544 GH18_narbonin Narbonin 43.5 14 0.00031 32.3 1.6 25 172-196 58-82 (253)
21 PF15007 CEP44: Centrosomal sp 41.5 9 0.0002 31.6 0.1 35 93-127 5-40 (131)
22 PF01902 ATP_bind_4: ATP-bindi 39.2 62 0.0013 28.1 4.8 65 57-123 86-152 (218)
23 smart00775 LNS2 LNS2 domain. T 38.7 26 0.00055 28.2 2.3 31 96-126 34-67 (157)
24 PF11455 DUF3018: Protein of 36.5 19 0.00042 26.8 1.2 25 95-119 6-30 (65)
25 TIGR00289 conserved hypothetic 36.3 80 0.0017 27.6 5.1 61 56-117 85-147 (222)
26 cd02414 jag_KH jag_K homology 35.8 35 0.00076 24.4 2.4 33 162-196 41-76 (77)
27 cd02872 GH18_chitolectin_chito 34.8 29 0.00062 30.5 2.1 27 169-195 55-81 (362)
28 PF01548 DEDD_Tnp_IS110: Trans 34.7 26 0.00056 26.5 1.6 52 68-119 33-84 (144)
29 COG2083 Uncharacterized protei 34.2 45 0.00097 28.4 3.1 28 165-192 48-79 (140)
30 TIGR00027 mthyl_TIGR00027 meth 33.7 1.1E+02 0.0025 26.6 5.6 121 71-193 71-199 (260)
31 PF05822 UMPH-1: Pyrimidine 5' 32.4 24 0.00052 31.7 1.3 39 97-136 98-136 (246)
32 TIGR01689 EcbF-BcbF capsule bi 31.5 49 0.0011 26.5 2.8 24 97-120 32-55 (126)
33 PF08960 DUF1874: Domain of un 31.3 20 0.00044 28.7 0.6 52 111-173 40-96 (105)
34 COG0244 RplJ Ribosomal protein 30.5 39 0.00086 28.2 2.2 30 153-182 105-134 (175)
35 KOG1838 Alpha/beta hydrolase [ 30.1 49 0.0011 32.0 3.0 83 81-168 126-213 (409)
36 TIGR02109 PQQ_syn_pqqE coenzym 29.6 1.4E+02 0.0029 26.3 5.4 56 60-117 59-117 (358)
37 cd00379 Ribosomal_L10_P0 Ribos 28.2 38 0.00083 26.2 1.6 25 157-181 103-127 (155)
38 cd06344 PBP1_ABC_ligand_bindin 28.1 1.1E+02 0.0023 25.9 4.4 54 68-121 178-231 (332)
39 PF04784 DUF547: Protein of un 27.2 1.2E+02 0.0026 23.5 4.2 38 157-194 49-90 (117)
40 PRK05928 hemD uroporphyrinogen 26.5 1.6E+02 0.0035 23.4 5.0 101 75-182 93-199 (249)
41 cd04724 Tryptophan_synthase_al 26.2 88 0.0019 26.8 3.6 42 70-113 93-137 (242)
42 TIGR01482 SPP-subfamily Sucros 26.0 62 0.0013 25.7 2.5 35 97-131 23-57 (225)
43 PF12940 RAG1: Recombination-a 25.5 1.2E+02 0.0026 29.9 4.7 76 111-200 88-193 (442)
44 PRK11713 16S ribosomal RNA met 25.2 95 0.0021 26.4 3.6 34 81-114 178-211 (234)
45 PRK10985 putative hydrolase; P 24.9 65 0.0014 27.7 2.6 39 81-119 58-101 (324)
46 KOG0257 Kynurenine aminotransf 24.7 42 0.00091 32.7 1.5 21 163-183 185-205 (420)
47 PF11658 DUF3260: Protein of u 24.6 61 0.0013 32.4 2.6 26 69-94 384-411 (518)
48 PRK00726 murG undecaprenyldiph 24.6 1.1E+02 0.0023 26.0 3.8 28 86-113 7-37 (357)
49 PF04023 FeoA: FeoA domain; I 24.2 73 0.0016 21.7 2.3 41 146-190 2-42 (74)
50 PRK05301 pyrroloquinoline quin 24.2 1.8E+02 0.0039 25.9 5.3 57 59-116 67-125 (378)
51 smart00729 Elp3 Elongator prot 24.2 2.2E+02 0.0047 21.3 5.0 47 69-115 69-120 (216)
52 cd01427 HAD_like Haloacid deha 23.8 49 0.0011 22.6 1.4 33 96-129 31-63 (139)
53 cd06346 PBP1_ABC_ligand_bindin 23.3 1.3E+02 0.0027 25.3 3.9 53 68-120 179-231 (312)
54 PF09370 TIM-br_sig_trns: TIM- 22.8 80 0.0017 29.1 2.9 45 62-107 90-135 (268)
55 cd03413 CbiK_C Anaerobic cobal 22.2 2.4E+02 0.0051 21.5 4.9 50 67-117 41-103 (103)
56 PF04452 Methyltrans_RNA: RNA 21.9 1E+02 0.0022 25.9 3.1 33 82-114 176-208 (225)
57 TIGR01351 adk adenylate kinase 21.9 1.8E+02 0.0039 23.6 4.5 43 146-191 70-112 (210)
58 PRK06107 aspartate aminotransf 21.4 53 0.0012 29.0 1.4 29 162-190 178-206 (402)
59 PF14178 YppF: YppF-like prote 21.4 42 0.00091 24.9 0.7 24 60-83 32-55 (60)
60 PLN02486 aminoacyl-tRNA ligase 21.1 2E+02 0.0042 27.2 5.1 55 68-126 59-123 (383)
61 cd02019 NK Nucleoside/nucleoti 21.0 1.3E+02 0.0028 20.6 3.0 30 159-191 34-63 (69)
62 TIGR03368 cellulose_yhjU cellu 20.8 78 0.0017 31.7 2.5 25 69-93 381-407 (518)
63 PRK07324 transaminase; Validat 20.7 1.2E+02 0.0026 26.8 3.4 26 163-189 166-191 (373)
64 PF03944 Endotoxin_C: delta en 20.5 13 0.00029 29.3 -2.2 40 60-108 24-65 (143)
65 TIGR01359 UMP_CMP_kin_fam UMP- 20.2 1.3E+02 0.0028 23.2 3.2 33 159-191 78-112 (183)
66 PLN02511 hydrolase 20.2 1.3E+02 0.0029 27.0 3.7 41 80-120 99-144 (388)
No 1
>PF11909 NdhN: NADH-quinone oxidoreductase cyanobacterial subunit N; InterPro: IPR020874 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit N. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0016020 membrane
Probab=100.00 E-value=3.2e-79 Score=503.26 Aligned_cols=135 Identities=57% Similarity=1.007 Sum_probs=132.7
Q ss_pred hhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhhhhhcCCCCC-----Cce-------eEEe
Q 028057 71 GRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETTLTKVYPVCP-----QPI-------ARWY 138 (214)
Q Consensus 71 ~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeayLt~vHGVRP-----q~i-------~v~~ 138 (214)
.+|+|||||+||||||+|+||||||||+||||++||+|+++|||||||||+|||++||||| |+| +|||
T Consensus 8 ~~f~rdlEk~gaLavy~PlEGG~EgRy~RRLRa~GY~t~~~SArGLGD~~ayLt~~HGVRPpHLGk~~ig~~aavG~v~~ 87 (154)
T PF11909_consen 8 KKFIRDLEKSGALAVYAPLEGGYEGRYLRRLRAAGYRTLIISARGLGDPEAYLTKVHGVRPPHLGKQSIGRGAAVGEVYY 87 (154)
T ss_pred hHHHHHHHHcCceEEEcCCcCchhHHHHHHHHhcCceEEEecccCCCCHHHHHhccCCCCCCCCCccccccccccceeEE
Confidence 5899999999999999999999999999999999999999999999999999999999999 888 8999
Q ss_pred eCcchhhhhhcCCCCCcceEEEEEeceecCHHHHHHHHcCCCCCCCeEEEEEeCCeeeeeecchHHH
Q 028057 139 FPPEVDYRLAALPPSAKGLVVWIIEAKVLSKSELQFLALLPTLRPKVRVIAECGNWRKFMWKPLKEI 205 (214)
Q Consensus 139 vpP~v~yqL~~LPp~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~ePrvKVVvEmGG~R~frWqPL~~~ 205 (214)
+||+++|||++|||++||||||||||||||+|||+||++||++||||||||||||||+||||||+++
T Consensus 88 ~pP~~~y~Le~Lp~~~KglvLWiiEG~vLS~~El~~L~~Lp~~ePrvKvVvE~Gg~R~~rW~pL~~~ 154 (154)
T PF11909_consen 88 VPPIVNYQLENLPPKSKGLVLWIIEGQVLSRQELEYLCNLPQREPRVKVVVEMGGDRSFRWQPLKEI 154 (154)
T ss_pred eCchhhhhHhhcCCCCCcEEEEEEeccccCHHHHHHHHhccccCCCeEEEEEeCCceeEEeeecccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999875
No 2
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=85.62 E-value=0.48 Score=37.54 Aligned_cols=26 Identities=35% Similarity=0.452 Sum_probs=22.3
Q ss_pred eEEEEEeceecCHHHHHHHHcCCCCC
Q 028057 157 LVVWIIEAKVLSKSELQFLALLPTLR 182 (214)
Q Consensus 157 LVLWiiEG~VLS~~EL~~L~~Lp~~e 182 (214)
+.-=++||++||.+|++.|++||++|
T Consensus 105 ~~gg~~eg~~l~~~~v~~la~LPs~e 130 (157)
T cd05797 105 IKGGVVEGKVLDAEEVKALAKLPSRE 130 (157)
T ss_pred EEEEEECCEecCHHHHHHHhcCCCHH
Confidence 34457899999999999999999865
No 3
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=81.28 E-value=0.93 Score=36.71 Aligned_cols=26 Identities=38% Similarity=0.414 Sum_probs=22.2
Q ss_pred eEEEEEeceecCHHHHHHHHcCCCCC
Q 028057 157 LVVWIIEAKVLSKSELQFLALLPTLR 182 (214)
Q Consensus 157 LVLWiiEG~VLS~~EL~~L~~Lp~~e 182 (214)
+.-=++||++||.+|++.|++||.++
T Consensus 106 l~gg~~eg~~l~~~~i~~la~LPs~~ 131 (172)
T PRK00099 106 IKGGAIEGKVLDAEEVKALAKLPSRE 131 (172)
T ss_pred EEEEEECCEEcCHHHHHHHhcCCCHH
Confidence 33457899999999999999999864
No 4
>PRK13361 molybdenum cofactor biosynthesis protein A; Provisional
Probab=72.01 E-value=7.2 Score=34.36 Aligned_cols=60 Identities=22% Similarity=0.373 Sum_probs=45.3
Q ss_pred cccCc-ccCcchhhHHHHHHhcce---eEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhh
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKHKA---IAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETT 122 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~Ga---LAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeay 122 (214)
|.||+ |+..|+..+++.+.+.+- ++|- --|-.-.++.++|+.+|...+++|--++ |++.|
T Consensus 67 ~tGGEPllr~dl~~li~~i~~~~~l~~i~it--TNG~ll~~~~~~L~~aGl~~v~ISlDs~-~~e~~ 130 (329)
T PRK13361 67 LTGGEPLVRRGCDQLVARLGKLPGLEELSLT--TNGSRLARFAAELADAGLKRLNISLDTL-RPELF 130 (329)
T ss_pred EECcCCCccccHHHHHHHHHhCCCCceEEEE--eChhHHHHHHHHHHHcCCCeEEEEeccC-CHHHh
Confidence 34554 778899999999988764 4443 2354456789999999999999999887 66665
No 5
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A, archaeal. This model describes an archaeal family related, and predicted to be functionally equivalent, to molybdenum cofactor biosynthesis protein A (MoaA) of bacteria (see TIGR02666).
Probab=68.73 E-value=11 Score=32.15 Aligned_cols=65 Identities=25% Similarity=0.368 Sum_probs=48.2
Q ss_pred cccCc-ccCcchhhHHHHHHhcce--eEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhhhhhcCC
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKHKA--IAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETTLTKVYP 128 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~Ga--LAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeayLt~vHG 128 (214)
|.||+ ++..|+.++++.+.+.|- ++|.+ -|=.-.++..+|+.+|...+.+|--|+ |++.|- .++|
T Consensus 62 ~tGGEPll~~~l~~iv~~l~~~g~~~v~i~T--NG~ll~~~~~~l~~~g~~~v~iSld~~-~~~~~~-~i~~ 129 (302)
T TIGR02668 62 ITGGEPLLRKDLIEIIRRIKDYGIKDVSMTT--NGILLEKLAKKLKEAGLDRVNVSLDTL-DPEKYK-KITG 129 (302)
T ss_pred EECcccccccCHHHHHHHHHhCCCceEEEEc--CchHHHHHHHHHHHCCCCEEEEEecCC-CHHHhh-hccC
Confidence 45665 678899999999988873 44443 343445788899999999999999997 666654 4555
No 6
>PF10902 DUF2693: Protein of unknown function (DUF2693); InterPro: IPR024401 This family of proteins is found in bacteria and bacteriophages. Its function is unknown.
Probab=67.87 E-value=2.3 Score=32.78 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=14.6
Q ss_pred EEeCCeeeeeecchHHH
Q 028057 189 AECGNWRKFMWKPLKEI 205 (214)
Q Consensus 189 vEmGG~R~frWqPL~~~ 205 (214)
+|.++||+|+|..|-++
T Consensus 56 ve~~~WRSFk~dnLIsV 72 (83)
T PF10902_consen 56 VEKKGWRSFKIDNLISV 72 (83)
T ss_pred eccCceeeeeheeEEEE
Confidence 69999999999987554
No 7
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=67.07 E-value=15 Score=28.70 Aligned_cols=62 Identities=24% Similarity=0.223 Sum_probs=47.8
Q ss_pred cceeeEEeecCCccccccccccCcccCcchhhHHHHHHhcce---------eEEecCCCCCchh--hhhhHhhhcC
Q 028057 41 SKRVGVTNCSGNSGIEIGDFIGGDLLKPDLGRWLSDVEKHKA---------IAIYTPHEGGYEG--RYLNRLRYLG 105 (214)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~d~iggdl~~~d~~~FirDLEk~Ga---------LAvyaPlEGG~EG--Ry~RRLRaaG 105 (214)
.....+++.|||+.+=+--.-.+. -|+.+.+..|++.|| +||=+|..-+|+. .|+.+++.+|
T Consensus 41 ~~~~~~v~~sGnsTiRv~~~~~~~---~~~~~v~~~l~~lG~~~E~~~~~~lav~VP~~~~~~~i~~~L~~~~e~g 113 (117)
T PF14085_consen 41 LWFQKVVESSGNSTIRVIFDDPGP---DDIEAVREELEALGCTVEGFSERMLAVDVPPSVDFDAIKDYLDRGEEQG 113 (117)
T ss_pred EEEEEEEecCCCEEEEEEEcCCcc---hhHHHHHHHHHHcCCeEEccCCCEEEEEECCCCCHHHHHHHHHhhhhcC
Confidence 345667777888877665555554 688999999999987 7899999988885 6777777766
No 8
>PRK00164 moaA molybdenum cofactor biosynthesis protein A; Reviewed
Probab=64.41 E-value=15 Score=31.92 Aligned_cols=63 Identities=24% Similarity=0.310 Sum_probs=43.8
Q ss_pred cccCc-ccCcchhhHHHHHHhc-ceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhhh
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKH-KAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETTL 123 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~-GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeayL 123 (214)
|.||+ ++..|+.++++.+.+. |-.-|..---|=.-.++..+|+.+|...+.+|.-++ |++.|-
T Consensus 71 ~tGGEPll~~~l~~li~~i~~~~~~~~i~itTNG~ll~~~~~~L~~agl~~i~ISlds~-~~e~~~ 135 (331)
T PRK00164 71 LTGGEPLLRKDLEDIIAALAALPGIRDLALTTNGYLLARRAAALKDAGLDRVNVSLDSL-DPERFK 135 (331)
T ss_pred EECCCCcCccCHHHHHHHHHhcCCCceEEEEcCchhHHHHHHHHHHcCCCEEEEEeccC-CHHHhc
Confidence 44565 5678999999998776 323333333343345788999999999999999886 566553
No 9
>TIGR02666 moaA molybdenum cofactor biosynthesis protein A, bacterial. The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine.
Probab=63.39 E-value=16 Score=31.88 Aligned_cols=60 Identities=30% Similarity=0.410 Sum_probs=42.4
Q ss_pred cccCc-ccCcchhhHHHHHHhc-ce--eEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhh
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKH-KA--IAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETT 122 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~-Ga--LAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeay 122 (214)
|.||+ |+..|+.++++.+.+. |. +.|.. -|=.-.++..+|+.+|...+.+|--|+ |++.|
T Consensus 65 ltGGEPll~~~l~~li~~i~~~~gi~~v~itT--NG~ll~~~~~~L~~~gl~~v~ISld~~-~~~~~ 128 (334)
T TIGR02666 65 LTGGEPLLRKDLVELVARLAALPGIEDIALTT--NGLLLARHAKDLKEAGLKRVNVSLDSL-DPERF 128 (334)
T ss_pred EECccccccCCHHHHHHHHHhcCCCCeEEEEe--CchhHHHHHHHHHHcCCCeEEEecccC-CHHHh
Confidence 34443 6788999999998774 43 44433 343345688999999999999998887 44433
No 10
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=57.89 E-value=24 Score=31.26 Aligned_cols=61 Identities=18% Similarity=0.343 Sum_probs=46.5
Q ss_pred ccccccCc-ccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCC
Q 028057 57 IGDFIGGD-LLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGD 118 (214)
Q Consensus 57 ~~d~iggd-l~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGD 118 (214)
.=.|.||+ |+.+|+.++++-+.+.|. -++.---|-.-.+-..+|..+|+.++.+|--|+-+
T Consensus 75 ~V~i~GGEPLL~pdl~eiv~~~~~~g~-~v~l~TNG~ll~~~~~~l~~~~~~~i~VSLDG~~e 136 (318)
T TIGR03470 75 VVSIPGGEPLLHPEIDEIVRGLVARKK-FVYLCTNALLLEKKLDKFEPSPYLTFSVHLDGLRE 136 (318)
T ss_pred EEEEeCccccccccHHHHHHHHHHcCC-eEEEecCceehHHHHHHHHhCCCcEEEEEEecCch
Confidence 34567887 788999999999988774 45555556555566778999999999999988743
No 11
>cd02873 GH18_IDGF The IDGF's (imaginal disc growth factors) are a family of growth factors identified in insects that include at least five members, some of which are encoded by genes in a tight cluster. The IDGF's have an eight-stranded alpha/beta barrel fold and are related to the glycosyl hydrolase family 18 (GH18) chitinases, but they have an amino acid substitution known to abolish chitinase catalytic activity. IDGFs may have evolved from chitinases to gain new functions as growth factors, interacting with cell surface glycoproteins involved in growth-promoting processes.
Probab=51.14 E-value=9.2 Score=35.24 Aligned_cols=38 Identities=24% Similarity=0.273 Sum_probs=29.2
Q ss_pred EEEEEeceecCHHHHHHHHcCCCCCCCeEEEEEeCCee
Q 028057 158 VVWIIEAKVLSKSELQFLALLPTLRPKVRVIAECGNWR 195 (214)
Q Consensus 158 VLWiiEG~VLS~~EL~~L~~Lp~~ePrvKVVvEmGG~R 195 (214)
|.++-+...+-+.++..|..|-++.|.+||++-+|||-
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~lk~~~p~lKvllSiGGw~ 85 (413)
T cd02873 48 IKSLNEDLDLDKSHYRAITSLKRKYPHLKVLLSVGGDR 85 (413)
T ss_pred EEecCcccchhhhHHHHHHHHHhhCCCCeEEEeecCCC
Confidence 33333333444678899999999999999999999985
No 12
>KOG2902 consensus Dihydroorotase [Nucleotide transport and metabolism]
Probab=49.92 E-value=2.8 Score=39.26 Aligned_cols=52 Identities=21% Similarity=0.270 Sum_probs=39.1
Q ss_pred CcchhhhhhcCCCCCcceEEEEEeceecCHHH--HHHHHcCCCCCCCeEEEEEe
Q 028057 140 PPEVDYRLAALPPSAKGLVVWIIEAKVLSKSE--LQFLALLPTLRPKVRVIAEC 191 (214)
Q Consensus 140 pP~v~yqL~~LPp~~KgLVLWiiEG~VLS~~E--L~~L~~Lp~~ePrvKVVvEm 191 (214)
|-.-.-|=+|+|=+-.|=|-=.++|+|+..++ |..|-.|-++.|++|||.|-
T Consensus 121 Pvf~aMqe~nm~LnvHGEvpps~D~~Vf~aE~~Flptll~LhqrfP~LKivlEH 174 (344)
T KOG2902|consen 121 PVFEAMQEQNMPLNVHGEVPPSIDGHVFDAEKIFLPTLLQLHQRFPQLKIVLEH 174 (344)
T ss_pred HHHHHHHHcCceEEecCCCCCccCCceecchhhhHHHHHHHHHhCccceeHHHh
Confidence 33444566666666666666678899999877 56778899999999999983
No 13
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=49.79 E-value=39 Score=29.53 Aligned_cols=62 Identities=10% Similarity=0.113 Sum_probs=50.8
Q ss_pred cccccccCcccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEE--eccCCCC
Q 028057 56 EIGDFIGGDLLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLD--LSARGLG 117 (214)
Q Consensus 56 ~~~d~iggdl~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~--~SARGLG 117 (214)
|+--.+=||+.--+...+++.+=+.=-|-.+.||-|=-..-|++.+-+.|+++.. ++|.||+
T Consensus 85 gv~~vv~GdI~s~~qr~~~e~v~~~lgl~~~~PLW~~~~~~ll~e~i~~G~~aiIv~v~a~gL~ 148 (223)
T TIGR00290 85 DVEAVVFGAIYSEYQKTRIERVCRELGLKSFAPLWHRDPEKLMEEFVEEKFEARIIAVAAEGLD 148 (223)
T ss_pred CCCEEEECCcccHHHHHHHHHHHHhcCCEEeccccCCCHHHHHHHHHHcCCeEEEEEEecCCCC
Confidence 4555677888887888888877666668889999998888899999999999999 4567776
No 14
>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD.
Probab=48.63 E-value=46 Score=26.27 Aligned_cols=113 Identities=16% Similarity=0.147 Sum_probs=63.1
Q ss_pred cccCc-ccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCc-eEEEeccCCCCChhhhhhhcCCCCCCceeEE
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGY-YFLDLSARGLGDPETTLTKVYPVCPQPIARW 137 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY-~t~~~SARGLGDpeayLt~vHGVRPq~i~v~ 137 (214)
|.||| ++.+|+-.+++.+.+.| +-+..-. .|..-++..++..+|. .++.+|-.| +.+.|..-. |.... .+
T Consensus 68 ~sGGEPll~~~l~~li~~~~~~g-~~v~i~T-Ng~~~~~l~~l~~~g~~~~v~isl~~--~~~~~~~~~-g~~~~-~~-- 139 (191)
T TIGR02495 68 ITGGEPTLQAGLPDFLRKVRELG-FEVKLDT-NGSNPRVLEELLEEGLVDYVAMDVKA--PPEKYPELY-GLEKN-GS-- 139 (191)
T ss_pred EECCcccCcHhHHHHHHHHHHCC-CeEEEEe-CCCCHHHHHHHHhcCCCcEEEEeccC--ChHHHHHHH-CCCCc-hH--
Confidence 55777 45688999999999987 3444433 4455677888888885 678888887 455555432 33221 10
Q ss_pred eeCcchhhhhhcCCC-CCcceEEEEEeceecCHHHHHHHHcCCCCCC
Q 028057 138 YFPPEVDYRLAALPP-SAKGLVVWIIEAKVLSKSELQFLALLPTLRP 183 (214)
Q Consensus 138 ~vpP~v~yqL~~LPp-~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~eP 183 (214)
..+---++.|-. +-+-.|...+--...+.+|++.+...-+...
T Consensus 140 ---~~~~~~i~~l~~~gi~~~i~~~v~~~~~~~~ei~~~~~~l~~~~ 183 (191)
T TIGR02495 140 ---NNILKSLEILLRSGIPFELRTTVHRGFLDEEDLAEIATRIKENG 183 (191)
T ss_pred ---HHHHHHHHHHHHcCCCEEEEEEEeCCCCCHHHHHHHHHHhccCC
Confidence 001011111111 1122344444333455778888877665443
No 15
>TIGR03679 arCOG00187 arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes.
Probab=48.34 E-value=38 Score=28.66 Aligned_cols=62 Identities=19% Similarity=0.349 Sum_probs=51.8
Q ss_pred cccccccCcccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEE--eccCCCC
Q 028057 56 EIGDFIGGDLLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLD--LSARGLG 117 (214)
Q Consensus 56 ~~~d~iggdl~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~--~SARGLG 117 (214)
|+--.+=||+.--+-..++..+.+..-|-+++||-+=-..=+.+.+...|+++++ +++.||+
T Consensus 86 g~~~vv~G~i~sd~~~~~~e~v~~~~gl~~~~PLw~~~~~el~~~~~~~G~~~~i~~v~~~~l~ 149 (218)
T TIGR03679 86 GVEGIVTGAIASRYQKSRIERICEELGLKVFAPLWGRDQEEYLRELVERGFRFIIVSVSAYGLD 149 (218)
T ss_pred CCCEEEECCcccHhHHHHHHHHHHhCCCeEEeehhcCCHHHHHHHHHHCCCEEEEEEEecCCCC
Confidence 4445566777766678899999999999999999998888899999999999988 5566776
No 16
>PLN02951 Molybderin biosynthesis protein CNX2
Probab=48.21 E-value=34 Score=31.29 Aligned_cols=60 Identities=27% Similarity=0.330 Sum_probs=43.7
Q ss_pred cccCc-ccCcchhhHHHHHHhc-ce--eEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhh
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKH-KA--IAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETT 122 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~-Ga--LAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeay 122 (214)
|.||+ ++..|+.++++.+.+. |- ++|.+ -|=.-.+...+|+.+|-..+++|--|+ |++.|
T Consensus 112 ~tGGEPllr~dl~eli~~l~~~~gi~~i~itT--NG~lL~~~~~~L~~aGld~VnISLDsl-~~e~~ 175 (373)
T PLN02951 112 LTGGEPTLRKDIEDICLQLSSLKGLKTLAMTT--NGITLSRKLPRLKEAGLTSLNISLDTL-VPAKF 175 (373)
T ss_pred EECCCCcchhhHHHHHHHHHhcCCCceEEEee--CcchHHHHHHHHHhCCCCeEEEeeccC-CHHHH
Confidence 55665 5688999999888775 52 34432 332345678899999999999999997 77776
No 17
>PF02579 Nitro_FeMo-Co: Dinitrogenase iron-molybdenum cofactor; InterPro: IPR003731 This entry represents several Nif (B, X and Y) proteins, which are involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. The nitrogenase complex catalyses the reduction of atmospheric dinitrogen to ammonia, and is composed of an iron metalloprotein (dinitrogenase reductase; homodimer of NifH; IPR000392 from INTERPRO) and a Fe-Mo metalloprotein (dinitrogenase; heterotetramer of NifD and NifK; IPR000318 from INTERPRO). The pathway for the synthesis of the Fe-Mo cofactor involves several proteins, including NifB, NifE, NifH, NifN, NifQ, NifV and NifX. NifB appears to be an iron-sulphur source for FeMo-co biosynthesis, while NifX may be associated with the mature FeMo-co, in particular with the addition of homocitrate during the last step of biosynthesis []. The NifX protein shows sequence similarity with the C terminus of NifB [], as well as to the conserved protein MTH1175 from the archaeon Methanobacterium thermoautotrophicum, which displays a ribonuclease H-like motif of three layers, alpha/beta/alpha, with a single mixed beta-sheet [].; PDB: 2QTD_A 2KLA_A 1EO1_A 1P90_A 1RDU_A 2YX6_D 1O13_A 1T3V_A 2RE2_B 2WFB_A.
Probab=47.42 E-value=13 Score=26.03 Aligned_cols=44 Identities=18% Similarity=0.104 Sum_probs=26.8
Q ss_pred ecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhhhhhcCCCCC
Q 028057 86 YTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETTLTKVYPVCP 131 (214)
Q Consensus 86 yaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeayLt~vHGVRP 131 (214)
+.+.++|...+..+.|...|-.++ -++++|+.....++.+||++
T Consensus 34 ~~~~~~~~~~~~~~~l~~~~v~~l--i~~~iG~~~~~~L~~~gI~v 77 (94)
T PF02579_consen 34 ACNEGGGGGDKIAKFLAEEGVDVL--ICGGIGEGAFRALKEAGIKV 77 (94)
T ss_dssp ECCCSSCHSTHHHHHHHHTTESEE--EESCSCHHHHHHHHHTTSEE
T ss_pred ccccccccchhHHHHHHHcCCCEE--EEeCCCHHHHHHHHHCCCEE
Confidence 445556666666666666444433 34566777776666667665
No 18
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=45.72 E-value=51 Score=27.54 Aligned_cols=59 Identities=17% Similarity=0.204 Sum_probs=46.7
Q ss_pred ccccCcccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEE--eccCCCC
Q 028057 59 DFIGGDLLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLD--LSARGLG 117 (214)
Q Consensus 59 d~iggdl~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~--~SARGLG 117 (214)
-.+=||+.-=+...|+.++=+.=-|-.+.||-+=-..-|++.+-+.|+++++ ++|.||+
T Consensus 91 ~vv~G~i~sd~~~~~~e~~~~~~gl~~~~PLW~~~~~~ll~e~~~~g~~~~iv~v~~~~L~ 151 (194)
T cd01994 91 AVVFGAILSEYQRTRVERVCERLGLEPLAPLWGRDQEELLREMIEAGFKAIIIKVAAEGLD 151 (194)
T ss_pred EEEECccccHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHcCCeEEEEEeccCCCC
Confidence 3455777666667777777666668889999998888899999999999998 5677776
No 19
>PF09328 Phytochelatin_C: Domain of unknown function (DUF1984); InterPro: IPR015407 This entry represents the C-terminal region of plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process
Probab=43.84 E-value=9 Score=35.23 Aligned_cols=58 Identities=21% Similarity=0.207 Sum_probs=40.1
Q ss_pred hhhhhhhcCCCCCCceeEEeeCcchhhhhhcCCCCCcceEEEEEe-------ceecCHHHHHHHH
Q 028057 119 PETTLTKVYPVCPQPIARWYFPPEVDYRLAALPPSAKGLVVWIIE-------AKVLSKSELQFLA 176 (214)
Q Consensus 119 peayLt~vHGVRPq~i~v~~vpP~v~yqL~~LPp~~KgLVLWiiE-------G~VLS~~EL~~L~ 176 (214)
.+-||++-=.+==++-.+--++-++.--+.+||.|...+|-|+.| |+.||++|-+-|+
T Consensus 20 ~AKyL~eDvP~LLkse~v~~v~~vls~vf~SlPsn~~~FIKWVaEVRR~Edg~~~LS~EEk~RL~ 84 (264)
T PF09328_consen 20 MAKYLMEDVPRLLKSEDVKDVEEVLSVVFKSLPSNFGEFIKWVAEVRRQEDGGSSLSKEEKERLA 84 (264)
T ss_pred HHHHHHHHHHHHhhhcccCcHHHHHHHHHhcCchhHHHHhhhheeEEecccCCCCCCHHHHHHHH
Confidence 344555432221133344444555666789999999999999997 6889999998876
No 20
>cd06544 GH18_narbonin Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function. Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity. Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination. This family also includes the VfNOD32 nodulin from Vicia faba.
Probab=43.52 E-value=14 Score=32.28 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=21.1
Q ss_pred HHHHHcCCCCCCCeEEEEEeCCeee
Q 028057 172 LQFLALLPTLRPKVRVIAECGNWRK 196 (214)
Q Consensus 172 L~~L~~Lp~~ePrvKVVvEmGG~R~ 196 (214)
++.+..|-++.|.+||++-+|||..
T Consensus 58 ~~~~~~lK~~~p~lKvllSiGG~~~ 82 (253)
T cd06544 58 PEAVKSIKAQHPNVKVVISIGGRGV 82 (253)
T ss_pred HHHHHHHHHhCCCcEEEEEeCCCCC
Confidence 4567777889999999999999964
No 21
>PF15007 CEP44: Centrosomal spindle body, CEP44
Probab=41.55 E-value=9 Score=31.64 Aligned_cols=35 Identities=29% Similarity=0.252 Sum_probs=27.2
Q ss_pred chhhhhhHhhhcCce-EEEeccCCCCChhhhhhhcC
Q 028057 93 YEGRYLNRLRYLGYY-FLDLSARGLGDPETTLTKVY 127 (214)
Q Consensus 93 ~EGRy~RRLRaaGY~-t~~~SARGLGDpeayLt~vH 127 (214)
.-.|+++.||..+|- .++...=-.|||++||-=+|
T Consensus 5 ~l~~L~~~Lr~~~yp~~vd~~~l~~G~p~afLpil~ 40 (131)
T PF15007_consen 5 NLRRLEQELRSLKYPDEVDYQGLYKGDPSAFLPILH 40 (131)
T ss_pred HHHHHHHHHHHCCCCCccCHHHHhcCCHHHHHHHHH
Confidence 345889999999999 55555556799999996555
No 22
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=39.23 E-value=62 Score=28.05 Aligned_cols=65 Identities=20% Similarity=0.258 Sum_probs=40.9
Q ss_pred ccccccCcccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEec--cCCCCChhhhh
Q 028057 57 IGDFIGGDLLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLS--ARGLGDPETTL 123 (214)
Q Consensus 57 ~~d~iggdl~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~S--ARGLGDpeayL 123 (214)
+--.+=||+.--|.-.|++.+=+.=-|-.+.||-+=-..-|++.+-+.|+++.+++ +.|| ++.||
T Consensus 86 v~~vv~GdI~~~~~r~~~e~vc~~lGl~~~~PLW~~d~~~ll~e~i~~Gf~aiIv~V~~~~L--~~~~L 152 (218)
T PF01902_consen 86 VEAVVFGDIDSEYQRNWVERVCERLGLEAVFPLWGRDREELLREFIESGFEAIIVKVDADGL--DESFL 152 (218)
T ss_dssp -SEEE--TTS-HHHHHHHHHHHHHCT-EEE-TTTT--HHHHHHHHHHTT-EEEEEEEESTT----GGGT
T ss_pred CCEEEECcCCcHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHCCCeEEEEEEeccCC--ChHHC
Confidence 44456688877777788877655444778899999888899999999999999884 5555 34443
No 23
>smart00775 LNS2 LNS2 domain. This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins. SMP2 is involved in plasmid maintenance and respiration. Lipin proteins are involved in adipose tissue development and insulin resistance.
Probab=38.68 E-value=26 Score=28.18 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=26.1
Q ss_pred hhhhHhhhcCceEEEeccCCCCChh---hhhhhc
Q 028057 96 RYLNRLRYLGYYFLDLSARGLGDPE---TTLTKV 126 (214)
Q Consensus 96 Ry~RRLRaaGY~t~~~SARGLGDpe---ayLt~v 126 (214)
...++|+.+||..+..|+|...-.+ .||.++
T Consensus 34 ~a~~~l~~~G~~ivy~TGRp~~~~~~t~~~l~~~ 67 (157)
T smart00775 34 KLYRDIQNNGYKILYLTARPIGQADRTRSYLSQI 67 (157)
T ss_pred HHHHHHHHcCCeEEEEcCCcHHHHHHHHHHHHHh
Confidence 4678899999999999999998764 788763
No 24
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=36.52 E-value=19 Score=26.83 Aligned_cols=25 Identities=20% Similarity=0.211 Sum_probs=18.6
Q ss_pred hhhhhHhhhcCceEEEeccCCCCCh
Q 028057 95 GRYLNRLRYLGYYFLDLSARGLGDP 119 (214)
Q Consensus 95 GRy~RRLRaaGY~t~~~SARGLGDp 119 (214)
-||..|||++|++-+.|=..-.-+|
T Consensus 6 ~khR~~lRa~GLRPVqiWVPDtr~p 30 (65)
T PF11455_consen 6 RKHRERLRAAGLRPVQIWVPDTRRP 30 (65)
T ss_pred HHHHHHHHHcCCCcceeeCCCCCCh
Confidence 3799999999999887755543333
No 25
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=36.32 E-value=80 Score=27.55 Aligned_cols=61 Identities=11% Similarity=0.066 Sum_probs=49.3
Q ss_pred cccccccCcccCcchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEE--eccCCCC
Q 028057 56 EIGDFIGGDLLKPDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLD--LSARGLG 117 (214)
Q Consensus 56 ~~~d~iggdl~~~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~--~SARGLG 117 (214)
|+-..+=||+.--+...++.++=+.=-|-.+.||-+=-..-|. ++-+.|+++++ ++|.||+
T Consensus 85 gv~~vv~GdI~s~~qr~~~e~vc~~~gl~~~~PLW~~d~~~l~-e~i~~Gf~aiIv~v~~~gL~ 147 (222)
T TIGR00289 85 DVEALCIGAIESNYQKSRIDKVCRELGLKSIAPLWHADPEKLM-YEVAEKFEVIIVSVSAMGLD 147 (222)
T ss_pred CCCEEEECccccHHHHHHHHHHHHHcCCEEeccccCCCHHHHH-HHHHcCCeEEEEEEccCCCC
Confidence 5667788999888888888887777778889999987665565 78899999999 5677887
No 26
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=35.81 E-value=35 Score=24.42 Aligned_cols=33 Identities=30% Similarity=0.417 Sum_probs=24.3
Q ss_pred EeceecCHHHHHHHHcCC---CCCCCeEEEEEeCCeee
Q 028057 162 IEAKVLSKSELQFLALLP---TLRPKVRVIAECGNWRK 196 (214)
Q Consensus 162 iEG~VLS~~EL~~L~~Lp---~~ePrvKVVvEmGG~R~ 196 (214)
=.|+.|. -||||+++- ..+.+.+|+|+++|-|.
T Consensus 41 k~G~tL~--AlQ~L~~~~~~~~~~~~~~v~lDv~~YR~ 76 (77)
T cd02414 41 KRGKTLD--ALQYLANLVLNRNTGEYVRITLDVEGYRE 76 (77)
T ss_pred CCCccHH--HHHHHHHHHHhhccCCceEEEEECccccc
Confidence 3678884 366666654 34679999999999884
No 27
>cd02872 GH18_chitolectin_chitotriosidase This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases. The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases. The fold has a pronounced active-site cleft at the C-terminal end of the beta-barrel. The chitolectins lack a key active site glutamate (the proton donor required for hydrolytic activity) but retain highly conserved residues involved in oligosaccharide binding. Chitotriosidase is a chitinolytic enzyme expressed in maturing macrophages, which suggests that it plays a part in antimicrobial defense. Chitotriosidase hydrolyzes chitotriose, as well as colloidal chitin to yield chitobiose and is therefore considered an exochitinase. Chitotriosidase occurs in two major forms, the la
Probab=34.77 E-value=29 Score=30.49 Aligned_cols=27 Identities=15% Similarity=0.383 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCCCCCeEEEEEeCCee
Q 028057 169 KSELQFLALLPTLRPKVRVIAECGNWR 195 (214)
Q Consensus 169 ~~EL~~L~~Lp~~ePrvKVVvEmGG~R 195 (214)
.+.+..|..|-++.|.+||++-+||+-
T Consensus 55 ~~~~~~~~~lk~~~p~lkvlisiGG~~ 81 (362)
T cd02872 55 LGLYERFNALKEKNPNLKTLLAIGGWN 81 (362)
T ss_pred hhHHHHHHHHHhhCCCceEEEEEcCCC
Confidence 456777888899999999999999975
No 28
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition. This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=34.66 E-value=26 Score=26.46 Aligned_cols=52 Identities=13% Similarity=0.122 Sum_probs=40.6
Q ss_pred cchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCCh
Q 028057 68 PDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDP 119 (214)
Q Consensus 68 ~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDp 119 (214)
-++.+|...|++.+.+-|-.=..|||.-...+.|...||....+.++-+-..
T Consensus 33 ~~~~~l~~~l~~~~~~~v~~E~tg~y~~~l~~~L~~~g~~v~~vnp~~~~~~ 84 (144)
T PF01548_consen 33 AGLEKLLDWLASLGPVLVVMEATGGYWRPLADFLQDAGIEVVVVNPLQVKRF 84 (144)
T ss_pred cchhHHhhhhccccccccccccccccchhhhhheeccccccccccccccccc
Confidence 3568999999999844444444478888999999999999999888766544
No 29
>COG2083 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.24 E-value=45 Score=28.39 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=23.4
Q ss_pred eecCHHHHHHHHcCCCCC----CCeEEEEEeC
Q 028057 165 KVLSKSELQFLALLPTLR----PKVRVIAECG 192 (214)
Q Consensus 165 ~VLS~~EL~~L~~Lp~~e----PrvKVVvEmG 192 (214)
|-+-++||++|+++-..+ =|+-||+|++
T Consensus 48 hyfkr~ELE~La~~ldE~e~~rlrlPivlEi~ 79 (140)
T COG2083 48 HYFKRRELEFLAQILDEDEIPRLRLPIVLEIS 79 (140)
T ss_pred eeeeHHHHHHHHhhcchhhhhhccccEEEEec
Confidence 567899999999988777 4566899998
No 30
>TIGR00027 mthyl_TIGR00027 methyltransferase, putative, TIGR00027 family. This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants.
Probab=33.67 E-value=1.1e+02 Score=26.59 Aligned_cols=121 Identities=14% Similarity=0.148 Sum_probs=65.8
Q ss_pred hhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhhhhhhcCCCCCCceeEEeeCcchh-hhhhc
Q 028057 71 GRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPETTLTKVYPVCPQPIARWYFPPEVD-YRLAA 149 (214)
Q Consensus 71 ~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpeayLt~vHGVRPq~i~v~~vpP~v~-yqL~~ 149 (214)
+.++++.=+.|. .-++=|.-|+.+|+.|---..+-+.+.+--...=+.-.-+.+.||..|.+ .+.+++==+. -..+.
T Consensus 71 D~~i~~~~~~g~-~qvV~LGaGlDTr~~Rl~~~~~~~~~EvD~P~v~~~K~~~l~~~~~~~~~-~~~~v~~Dl~~~w~~~ 148 (260)
T TIGR00027 71 DDFLLAAVAAGI-RQVVILGAGLDTRAYRLPWPDGTRVFEVDQPAVLAFKEKVLAELGAEPPA-HRRAVPVDLRQDWPAA 148 (260)
T ss_pred HHHHHHHHhcCC-cEEEEeCCccccHHHhcCCCCCCeEEECCChHHHHHHHHHHHHcCCCCCC-ceEEeccCchhhHHHH
Confidence 455655444564 56899999999999864223345555543222222223355566665521 1112221111 01122
Q ss_pred CCC---CCcceEEEEEecee--cCHHHHHHHH-cCCCCC-CCeEEEEEeCC
Q 028057 150 LPP---SAKGLVVWIIEAKV--LSKSELQFLA-LLPTLR-PKVRVIAECGN 193 (214)
Q Consensus 150 LPp---~~KgLVLWiiEG~V--LS~~EL~~L~-~Lp~~e-PrvKVVvEmGG 193 (214)
|.. +.+-=++|+.||-. |+.+++..|. .+.+.- |.-.|+.|.-+
T Consensus 149 L~~~gfd~~~ptl~i~EGvl~YL~~~~v~~ll~~i~~~~~~gs~l~~d~~~ 199 (260)
T TIGR00027 149 LAAAGFDPTAPTAWLWEGLLMYLTEEAVDALLAFIAELSAPGSRLAFDYVR 199 (260)
T ss_pred HHhCCCCCCCCeeeeecchhhcCCHHHHHHHHHHHHHhCCCCcEEEEEecc
Confidence 221 12234899999976 7888876543 343444 88999999754
No 31
>PF05822 UMPH-1: Pyrimidine 5'-nucleotidase (UMPH-1); InterPro: IPR006434 This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue []. The structure of mouse sequence has been reported []. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs [] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.; GO: 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0005737 cytoplasm; PDB: 2BDU_B 2G07_A 2G06_A 2G0A_A 2Q4T_A 2G09_A 2G08_A 2VKQ_A 2CN1_A 2JGA_A.
Probab=32.37 E-value=24 Score=31.71 Aligned_cols=39 Identities=23% Similarity=0.287 Sum_probs=29.2
Q ss_pred hhhHhhhcCceEEEeccCCCCChhhhhhhcCCCCCCceeE
Q 028057 97 YLNRLRYLGYYFLDLSARGLGDPETTLTKVYPVCPQPIAR 136 (214)
Q Consensus 97 y~RRLRaaGY~t~~~SARGLGDpeayLt~vHGVRPq~i~v 136 (214)
+.+.|...+--++..|| ||||.-...++.||+-|.++.|
T Consensus 98 ~f~~L~~~~IP~lIFSA-GlgdvI~~vL~q~~~~~~Nv~V 136 (246)
T PF05822_consen 98 FFDKLEEHNIPLLIFSA-GLGDVIEEVLRQAGVFHPNVKV 136 (246)
T ss_dssp HHHHHHCTT--EEEEEE-EEHHHHHHHHHHTT--BTTEEE
T ss_pred HHHHHHhcCCCEEEEeC-CcHHHHHHHHHHcCCCCCCeEE
Confidence 56778888888999997 9999988888888999988743
No 32
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=31.50 E-value=49 Score=26.48 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=20.1
Q ss_pred hhhHhhhcCceEEEeccCCCCChh
Q 028057 97 YLNRLRYLGYYFLDLSARGLGDPE 120 (214)
Q Consensus 97 y~RRLRaaGY~t~~~SARGLGDpe 120 (214)
.+++|+.+|+.....|||...+.+
T Consensus 32 ~L~~l~~~G~~IiiaTGR~~~~~~ 55 (126)
T TIGR01689 32 KLRHYKALGFEIVISSSRNMRTYE 55 (126)
T ss_pred HHHHHHHCCCEEEEECCCCchhhh
Confidence 367788999999999999987643
No 33
>PF08960 DUF1874: Domain of unknown function (DUF1874); InterPro: IPR015055 This entry is represented by Acidianus two-tailed virus, Orf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2J85_A 2X4I_C.
Probab=31.30 E-value=20 Score=28.71 Aligned_cols=52 Identities=31% Similarity=0.343 Sum_probs=23.5
Q ss_pred eccCCCCChhhhhhhcCCCCC-CceeEEeeCcchhhhhhcCCCCCcceEEEE----EeceecCHHHHH
Q 028057 111 LSARGLGDPETTLTKVYPVCP-QPIARWYFPPEVDYRLAALPPSAKGLVVWI----IEAKVLSKSELQ 173 (214)
Q Consensus 111 ~SARGLGDpeayLt~vHGVRP-q~i~v~~vpP~v~yqL~~LPp~~KgLVLWi----iEG~VLS~~EL~ 173 (214)
+||=|==|-+.+|...-|+.- .|--..++- +++|.+|.=+ =||+|||++|++
T Consensus 40 vSaIGH~sTa~lls~llg~~ip~NR~~i~~~-----------~Gd~alv~~L~~Rl~EG~Vl~~eEl~ 96 (105)
T PF08960_consen 40 VSAIGHDSTAQLLSELLGVNIPMNRIQIKLD-----------PGDKALVFQLKQRLPEGKVLSREELE 96 (105)
T ss_dssp EE----HHHHHHHHHHHT-----------B------------TT-EEEEEEESS---TT----HHHHH
T ss_pred EEeeCcHHHHHHHHHHhCCccccccEEEEec-----------CCCEEEEEEecccCCCCcCCCHHHHH
Confidence 567666678888888888875 222111122 3666666653 289999999998
No 34
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=30.50 E-value=39 Score=28.25 Aligned_cols=30 Identities=30% Similarity=0.280 Sum_probs=26.8
Q ss_pred CCcceEEEEEeceecCHHHHHHHHcCCCCC
Q 028057 153 SAKGLVVWIIEAKVLSKSELQFLALLPTLR 182 (214)
Q Consensus 153 ~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~e 182 (214)
+.-.+.-|++||++|+-++.+.+..||.++
T Consensus 105 ~~~~~~~~~~eg~~l~~~~v~~~aklp~~~ 134 (175)
T COG0244 105 DKAPIKGGVPEGKVLGAAEVIALAKLPSKE 134 (175)
T ss_pred ccceEEEEEecCcccCHHHHHHHhcCCcHH
Confidence 455678899999999999999999999876
No 35
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=30.13 E-value=49 Score=31.96 Aligned_cols=83 Identities=18% Similarity=0.233 Sum_probs=51.0
Q ss_pred ceeEEecCCCCCchhhhhh----HhhhcCceEEEeccCCCCChhhhhhhcCCCCCCce-eEEeeCcchhhhhhcCCCCCc
Q 028057 81 KAIAIYTPHEGGYEGRYLN----RLRYLGYYFLDLSARGLGDPETTLTKVYPVCPQPI-ARWYFPPEVDYRLAALPPSAK 155 (214)
Q Consensus 81 GaLAvyaPlEGG~EGRy~R----RLRaaGY~t~~~SARGLGDpeayLt~vHGVRPq~i-~v~~vpP~v~yqL~~LPp~~K 155 (214)
=.+-|-..+.||.+..|.| +++..||+.+.+-+||+|..+-.=... .+. -..-+-=.|+|.-...|..-.
T Consensus 126 P~vvilpGltg~S~~~YVr~lv~~a~~~G~r~VVfN~RG~~g~~LtTpr~-----f~ag~t~Dl~~~v~~i~~~~P~a~l 200 (409)
T KOG1838|consen 126 PIVVILPGLTGGSHESYVRHLVHEAQRKGYRVVVFNHRGLGGSKLTTPRL-----FTAGWTEDLREVVNHIKKRYPQAPL 200 (409)
T ss_pred cEEEEecCCCCCChhHHHHHHHHHHHhCCcEEEEECCCCCCCCccCCCce-----eecCCHHHHHHHHHHHHHhCCCCce
Confidence 3566667799999999998 568899999999999998654211000 000 001122345555555555555
Q ss_pred ceEEEEEeceecC
Q 028057 156 GLVVWIIEAKVLS 168 (214)
Q Consensus 156 gLVLWiiEG~VLS 168 (214)
--|=|-+-|-+|.
T Consensus 201 ~avG~S~Gg~iL~ 213 (409)
T KOG1838|consen 201 FAVGFSMGGNILT 213 (409)
T ss_pred EEEEecchHHHHH
Confidence 5566666666553
No 36
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E. This model describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.
Probab=29.59 E-value=1.4e+02 Score=26.31 Aligned_cols=56 Identities=25% Similarity=0.406 Sum_probs=41.0
Q ss_pred cccCc-ccCcchhhHHHHHHhcce-eEEecCCCCC-chhhhhhHhhhcCceEEEeccCCCC
Q 028057 60 FIGGD-LLKPDLGRWLSDVEKHKA-IAIYTPHEGG-YEGRYLNRLRYLGYYFLDLSARGLG 117 (214)
Q Consensus 60 ~iggd-l~~~d~~~FirDLEk~Ga-LAvyaPlEGG-~EGRy~RRLRaaGY~t~~~SARGLG 117 (214)
|.||+ ++..|+.++++.+.+.|- ..|. --|= ..-.+.++|+.+|...+.+|--|.-
T Consensus 59 ~~GGEPll~~~~~~ii~~~~~~g~~~~l~--TNG~ll~~e~~~~L~~~g~~~v~iSldg~~ 117 (358)
T TIGR02109 59 FSGGEPLARPDLVELVAHARRLGLYTNLI--TSGVGLTEARLDALADAGLDHVQLSFQGVD 117 (358)
T ss_pred EeCccccccccHHHHHHHHHHcCCeEEEE--eCCccCCHHHHHHHHhCCCCEEEEeCcCCC
Confidence 66787 567899999999988873 2332 2232 3456888999999999999988873
No 37
>cd00379 Ribosomal_L10_P0 Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been sho
Probab=28.24 E-value=38 Score=26.18 Aligned_cols=25 Identities=28% Similarity=0.295 Sum_probs=21.3
Q ss_pred eEEEEEeceecCHHHHHHHHcCCCC
Q 028057 157 LVVWIIEAKVLSKSELQFLALLPTL 181 (214)
Q Consensus 157 LVLWiiEG~VLS~~EL~~L~~Lp~~ 181 (214)
+.-=.+||+++|..++..++.||.+
T Consensus 103 ~k~g~~~~~v~~~~~~~~l~~lp~~ 127 (155)
T cd00379 103 AKGGVVAGKVLDPAGVTALAKLPSR 127 (155)
T ss_pred EEEEEEcCEecCHHHHHHHhcCCCH
Confidence 4445788999999999999999974
No 38
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=28.14 E-value=1.1e+02 Score=25.88 Aligned_cols=54 Identities=13% Similarity=-0.005 Sum_probs=43.2
Q ss_pred cchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChhh
Q 028057 68 PDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPET 121 (214)
Q Consensus 68 ~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpea 121 (214)
+|....+..+.+.++=+|+....|..-..+.+.++..|+....++.-++.++..
T Consensus 178 ~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 231 (332)
T cd06344 178 FNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKGRLTLLGGDSLYTPDT 231 (332)
T ss_pred CCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCCCceEEecccccCHHH
Confidence 355557888999999999999888766778888999999888877777777643
No 39
>PF04784 DUF547: Protein of unknown function, DUF547; InterPro: IPR006869 This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans and Arabidopsis thaliana (Mouse-ear cress).
Probab=27.24 E-value=1.2e+02 Score=23.46 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=33.9
Q ss_pred eEEEEEeceecCHHHHHHHHcCC----CCCCCeEEEEEeCCe
Q 028057 157 LVVWIIEAKVLSKSELQFLALLP----TLRPKVRVIAECGNW 194 (214)
Q Consensus 157 LVLWiiEG~VLS~~EL~~L~~Lp----~~ePrvKVVvEmGG~ 194 (214)
-+.+.|.|+.+|-.++|.-..-+ ..+||+-..+=||..
T Consensus 49 ~~~y~Igg~~~SL~dIe~~ILR~~~~~~~DprihFaL~cgs~ 90 (117)
T PF04784_consen 49 KVRYNIGGQRFSLDDIEHGILRGNRPPWPDPRIHFALNCGSK 90 (117)
T ss_pred ceEEEECCEEecHHHHHHhhccCCCCCCCCCceeeeeecCCC
Confidence 37889999999999999988888 689999999998864
No 40
>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed
Probab=26.47 E-value=1.6e+02 Score=23.40 Aligned_cols=101 Identities=21% Similarity=0.124 Sum_probs=54.5
Q ss_pred HHHHhcceeEEecCCCCCchhhhh--hHhhhcCceEEEeccCC-CCChhhhhhhcCCCCCCceeEEeeCcch---hhhhh
Q 028057 75 SDVEKHKAIAIYTPHEGGYEGRYL--NRLRYLGYYFLDLSARG-LGDPETTLTKVYPVCPQPIARWYFPPEV---DYRLA 148 (214)
Q Consensus 75 rDLEk~GaLAvyaPlEGG~EGRy~--RRLRaaGY~t~~~SARG-LGDpeayLt~vHGVRPq~i~v~~vpP~v---~yqL~ 148 (214)
+-|++.|--.+++|.++..|+=-. -.....|-+.+.+...+ -+|....|. .+|..+..+.+|..-|.. .-.+.
T Consensus 93 ~~l~~~G~~~~~~~~~~~~~~l~~~l~~~~~~~~~ili~~~~~~~~~l~~~L~-~~G~~v~~~~~Y~~~~~~~~~~~~~~ 171 (249)
T PRK05928 93 LALKKLGGKVVFVPEDGESSELLLELPELLLKGKRVLYLRGNGGREVLGDTLE-ERGAEVDECEVYERVPPKLDGAELLA 171 (249)
T ss_pred HHHHHcCCCccccCCCCcChHHHHhChhhhcCCCEEEEECCCCCHHHHHHHHH-HCCCEEeEEEEEEeeCCCCChHHHHH
Confidence 456678877788887776664222 11213577777665543 334555554 468788777777654321 11111
Q ss_pred cCCCCCcceEEEEEeceecCHHHHHHHHcCCCCC
Q 028057 149 ALPPSAKGLVVWIIEAKVLSKSELQFLALLPTLR 182 (214)
Q Consensus 149 ~LPp~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~e 182 (214)
.+- .+-+-|++ .-|.+..+++..+....
T Consensus 172 ~~~---~~~~d~iv---ftS~~~v~~~~~~~~~~ 199 (249)
T PRK05928 172 RLQ---SGEVDAVI---FTSPSTVRAFFSLAPEL 199 (249)
T ss_pred HHH---hCCCCEEE---ECCHHHHHHHHHHhccc
Confidence 110 11223332 36888888887765543
No 41
>cd04724 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan.
Probab=26.19 E-value=88 Score=26.78 Aligned_cols=42 Identities=21% Similarity=0.298 Sum_probs=33.0
Q ss_pred hhhHHHHHHhcceeEEec---CCCCCchhhhhhHhhhcCceEEEecc
Q 028057 70 LGRWLSDVEKHKAIAIYT---PHEGGYEGRYLNRLRYLGYYFLDLSA 113 (214)
Q Consensus 70 ~~~FirDLEk~GaLAvya---PlEGG~EGRy~RRLRaaGY~t~~~SA 113 (214)
+++|++++.++|+=+|-. |.| .-.++.+++|..|-....+-+
T Consensus 93 ~~~fi~~~~~aG~~giiipDl~~e--e~~~~~~~~~~~g~~~i~~i~ 137 (242)
T cd04724 93 LERFLRDAKEAGVDGLIIPDLPPE--EAEEFREAAKEYGLDLIFLVA 137 (242)
T ss_pred HHHHHHHHHHCCCcEEEECCCCHH--HHHHHHHHHHHcCCcEEEEeC
Confidence 589999999999999998 665 334788888888876655444
No 42
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=26.04 E-value=62 Score=25.65 Aligned_cols=35 Identities=6% Similarity=0.029 Sum_probs=28.1
Q ss_pred hhhHhhhcCceEEEeccCCCCChhhhhhhcCCCCC
Q 028057 97 YLNRLRYLGYYFLDLSARGLGDPETTLTKVYPVCP 131 (214)
Q Consensus 97 y~RRLRaaGY~t~~~SARGLGDpeayLt~vHGVRP 131 (214)
-+++||.+|+.....|.|...+...++.+.....|
T Consensus 23 al~~l~~~Gi~~~~aTGR~~~~~~~~~~~l~~~~~ 57 (225)
T TIGR01482 23 AIRKAESVGIPVVLVTGNSVQFARALAKLIGTPDP 57 (225)
T ss_pred HHHHHHHCCCEEEEEcCCchHHHHHHHHHhCCCCe
Confidence 47889999999999999999998887765543334
No 43
>PF12940 RAG1: Recombination-activation protein 1 (RAG1); InterPro: IPR024627 This entry represents recombination activating protein 1 (RAG1), which is the catalytic component of the RAG complex. The RAG complex is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination []. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) []. Many of the proteins recognised by this entry are fragments.; GO: 0043565 sequence-specific DNA binding, 0033151 V(D)J recombination
Probab=25.54 E-value=1.2e+02 Score=29.93 Aligned_cols=76 Identities=21% Similarity=0.342 Sum_probs=45.9
Q ss_pred eccCCCCChhhhhhhcCCCCC----Cce------------------eEEeeCcchhhhhhcCCCCCcceEEEEEeceecC
Q 028057 111 LSARGLGDPETTLTKVYPVCP----QPI------------------ARWYFPPEVDYRLAALPPSAKGLVVWIIEAKVLS 168 (214)
Q Consensus 111 ~SARGLGDpeayLt~vHGVRP----q~i------------------~v~~vpP~v~yqL~~LPp~~KgLVLWiiEG~VLS 168 (214)
=|+-|+||++ .+||=-| |.+ -.-|-.|.-+..|. +|+|-|=+.+--
T Consensus 88 EscDGMGDVS----eKhgggp~vPEKAvRfSFtimsvsv~~d~~e~vtiF~e~KPNSel~-----ckPLclmfvDES--- 155 (442)
T PF12940_consen 88 ESCDGMGDVS----EKHGGGPAVPEKAVRFSFTIMSVSVLADEEEEVTIFTEPKPNSELS-----CKPLCLMFVDES--- 155 (442)
T ss_pred hhcccccchh----hhcCCCCCCCCCccceeEEeEEEEEEcCCCceeEEecCCCCcceee-----cccceeeeeccc---
Confidence 3788999998 7999888 433 12344555555554 788877666531
Q ss_pred HHHHHHHHcC-------CCCCCCeEEEEEeCC-eeeeeec
Q 028057 169 KSELQFLALL-------PTLRPKVRVIAECGN-WRKFMWK 200 (214)
Q Consensus 169 ~~EL~~L~~L-------p~~ePrvKVVvEmGG-~R~frWq 200 (214)
..| -|+.+ -..-..-+.|+++|| +|+||+.
T Consensus 156 dhe--tltaiL~pvvaER~amk~srLilsiggl~RsfrF~ 193 (442)
T PF12940_consen 156 DHE--TLTAILGPVVAERNAMKESRLILSIGGLPRSFRFH 193 (442)
T ss_pred cch--hhHHHhhHhhhhhHhHhhcEeeeeeCCCcceeEEE
Confidence 111 11111 111123568999998 6999874
No 44
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=25.18 E-value=95 Score=26.37 Aligned_cols=34 Identities=24% Similarity=0.414 Sum_probs=29.9
Q ss_pred ceeEEecCCCCCchhhhhhHhhhcCceEEEeccC
Q 028057 81 KAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSAR 114 (214)
Q Consensus 81 GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SAR 114 (214)
+.+.+.+=+||||.-+=..-|+.+|+..+++.-|
T Consensus 178 ~~i~viIGPEGGfs~~Ei~~l~~~g~~~vsLG~~ 211 (234)
T PRK11713 178 GKVLLLIGPEGGFSPEEIELLREAGFTPVSLGPR 211 (234)
T ss_pred CeEEEEECCCCCCCHHHHHHHHHCCCEEeccCCC
Confidence 4689999999999999999999999999887554
No 45
>PRK10985 putative hydrolase; Provisional
Probab=24.94 E-value=65 Score=27.70 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=27.4
Q ss_pred ceeEEecC-CCCCchhhhh----hHhhhcCceEEEeccCCCCCh
Q 028057 81 KAIAIYTP-HEGGYEGRYL----NRLRYLGYYFLDLSARGLGDP 119 (214)
Q Consensus 81 GaLAvyaP-lEGG~EGRy~----RRLRaaGY~t~~~SARGLGDp 119 (214)
..+-|+.+ +.|+....|. +.|..+||.++..--||.|+.
T Consensus 58 ~p~vll~HG~~g~~~~~~~~~~~~~l~~~G~~v~~~d~rG~g~~ 101 (324)
T PRK10985 58 KPRLVLFHGLEGSFNSPYAHGLLEAAQKRGWLGVVMHFRGCSGE 101 (324)
T ss_pred CCEEEEeCCCCCCCcCHHHHHHHHHHHHCCCEEEEEeCCCCCCC
Confidence 44555554 3444455555 468999999999999998753
No 46
>KOG0257 consensus Kynurenine aminotransferase, glutamine transaminase K [Amino acid transport and metabolism]
Probab=24.72 E-value=42 Score=32.71 Aligned_cols=21 Identities=33% Similarity=0.327 Sum_probs=19.7
Q ss_pred eceecCHHHHHHHHcCCCCCC
Q 028057 163 EAKVLSKSELQFLALLPTLRP 183 (214)
Q Consensus 163 EG~VLS~~EL~~L~~Lp~~eP 183 (214)
-|+|.|+.||+-|++||+..+
T Consensus 185 tGkvfsReeLe~ia~l~~k~~ 205 (420)
T KOG0257|consen 185 TGKVFSREELERIAELCKKHG 205 (420)
T ss_pred cCcccCHHHHHHHHHHHHHCC
Confidence 499999999999999999987
No 47
>PF11658 DUF3260: Protein of unknown function (DUF3260); InterPro: IPR017744 This protein was identified by the partial phylogenetic profiling algorithm [] as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation [].
Probab=24.65 E-value=61 Score=32.43 Aligned_cols=26 Identities=27% Similarity=0.575 Sum_probs=22.1
Q ss_pred chhhHHHHHHhcc--eeEEecCCCCCch
Q 028057 69 DLGRWLSDVEKHK--AIAIYTPHEGGYE 94 (214)
Q Consensus 69 d~~~FirDLEk~G--aLAvyaPlEGG~E 94 (214)
|+++|+..|||+| ++=|.+|--|.+.
T Consensus 384 dl~~F~~~Le~SgR~v~vv~VPEHGAAl 411 (518)
T PF11658_consen 384 DLDRFFDELEKSGRKVMVVVVPEHGAAL 411 (518)
T ss_pred HHHHHHHHHHHcCCcEEEEEecCccccc
Confidence 8999999999998 6778888777653
No 48
>PRK00726 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional
Probab=24.57 E-value=1.1e+02 Score=26.04 Aligned_cols=28 Identities=21% Similarity=0.165 Sum_probs=16.1
Q ss_pred ecCCCCCchh---hhhhHhhhcCceEEEecc
Q 028057 86 YTPHEGGYEG---RYLNRLRYLGYYFLDLSA 113 (214)
Q Consensus 86 yaPlEGG~EG---Ry~RRLRaaGY~t~~~SA 113 (214)
.+--+||+|. -..+.|+.+||.+..++.
T Consensus 7 ~~~g~gG~~~~~~~la~~L~~~g~ev~vv~~ 37 (357)
T PRK00726 7 AGGGTGGHVFPALALAEELKKRGWEVLYLGT 37 (357)
T ss_pred EcCcchHhhhHHHHHHHHHHhCCCEEEEEEC
Confidence 3344566665 345556666666666654
No 49
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=24.22 E-value=73 Score=21.71 Aligned_cols=41 Identities=29% Similarity=0.396 Sum_probs=30.1
Q ss_pred hhhcCCCCCcceEEEEEeceecCHHHHHHHHcCCCCCCCeEEEEE
Q 028057 146 RLAALPPSAKGLVVWIIEAKVLSKSELQFLALLPTLRPKVRVIAE 190 (214)
Q Consensus 146 qL~~LPp~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~ePrvKVVvE 190 (214)
.|..+|++.++.|.++-+. +++-+.+|..+= ..|..+|-|.
T Consensus 2 ~L~~~~~g~~~~I~~i~~~---d~~~~~~L~~lG-l~~G~~i~v~ 42 (74)
T PF04023_consen 2 PLSELPPGERARIVRISDE---DPELLRRLADLG-LTPGSEITVI 42 (74)
T ss_dssp BGGGSSTTEEEEEEEESTS---SHHHHHHHHHCT--STTEEEEEE
T ss_pred ChhHCCCCCEEEEEEEECC---CHHHHHHHHHCC-CCCCCEEEEE
Confidence 4889999999999999863 677788888773 4455555444
No 50
>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional
Probab=24.18 E-value=1.8e+02 Score=25.92 Aligned_cols=57 Identities=23% Similarity=0.293 Sum_probs=39.6
Q ss_pred ccccCc-ccCcchhhHHHHHHhcceeEEecCCCCC-chhhhhhHhhhcCceEEEeccCCC
Q 028057 59 DFIGGD-LLKPDLGRWLSDVEKHKAIAIYTPHEGG-YEGRYLNRLRYLGYYFLDLSARGL 116 (214)
Q Consensus 59 d~iggd-l~~~d~~~FirDLEk~GaLAvyaPlEGG-~EGRy~RRLRaaGY~t~~~SARGL 116 (214)
.|.||+ ++.+|+-++++.+.+.|-. +..---|- ......++|+..|...+.+|--|.
T Consensus 67 ~~~GGEPll~~~~~~il~~~~~~g~~-~~i~TNG~ll~~~~~~~L~~~g~~~v~iSldg~ 125 (378)
T PRK05301 67 HFSGGEPLLRKDLEELVAHARELGLY-TNLITSGVGLTEARLAALKDAGLDHIQLSFQDS 125 (378)
T ss_pred EEECCccCCchhHHHHHHHHHHcCCc-EEEECCCccCCHHHHHHHHHcCCCEEEEEecCC
Confidence 356776 6688998888888777632 22222232 344678899999999999998875
No 51
>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Probab=24.15 E-value=2.2e+02 Score=21.27 Aligned_cols=47 Identities=17% Similarity=0.241 Sum_probs=26.7
Q ss_pred chhhHHHHHHhccee----EEecCCCCC-chhhhhhHhhhcCceEEEeccCC
Q 028057 69 DLGRWLSDVEKHKAI----AIYTPHEGG-YEGRYLNRLRYLGYYFLDLSARG 115 (214)
Q Consensus 69 d~~~FirDLEk~GaL----AvyaPlEGG-~EGRy~RRLRaaGY~t~~~SARG 115 (214)
++.++++.+.+.+.+ .+..=.-|+ ..-+..++|+..|...+.+|--.
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~tn~~~~~~~~~~~l~~~~~~~i~isl~~ 120 (216)
T smart00729 69 QLEELLEAIREILGLADDVEITIETRPGTLTEELLEALKEAGVNRVSLGVQS 120 (216)
T ss_pred HHHHHHHHHHHhCCCCCCeEEEEEeCcccCCHHHHHHHHHcCCCeEEEeccc
Confidence 356666666666532 122112233 34567777777777767666654
No 52
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=23.84 E-value=49 Score=22.57 Aligned_cols=33 Identities=12% Similarity=0.081 Sum_probs=23.1
Q ss_pred hhhhHhhhcCceEEEeccCCCCChhhhhhhcCCC
Q 028057 96 RYLNRLRYLGYYFLDLSARGLGDPETTLTKVYPV 129 (214)
Q Consensus 96 Ry~RRLRaaGY~t~~~SARGLGDpeayLt~vHGV 129 (214)
..+++|+.+||....+|++..-..+.++.. +|+
T Consensus 31 ~~l~~l~~~g~~i~ivS~~~~~~~~~~~~~-~~~ 63 (139)
T cd01427 31 EALKELKEKGIKLALATNKSRREVLELLEE-LGL 63 (139)
T ss_pred HHHHHHHHCCCeEEEEeCchHHHHHHHHHH-cCC
Confidence 567788888888888888875555555533 565
No 53
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=23.33 E-value=1.3e+02 Score=25.26 Aligned_cols=53 Identities=9% Similarity=-0.048 Sum_probs=41.0
Q ss_pred cchhhHHHHHHhcceeEEecCCCCCchhhhhhHhhhcCceEEEeccCCCCChh
Q 028057 68 PDLGRWLSDVEKHKAIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSARGLGDPE 120 (214)
Q Consensus 68 ~d~~~FirDLEk~GaLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SARGLGDpe 120 (214)
-|+...++.+.++++=+||...-+..-.++.+-++.+|+....+..-|+.|++
T Consensus 179 ~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~ 231 (312)
T cd06346 179 SSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFDKFLLTDGMKSDS 231 (312)
T ss_pred CCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCCceEeeccccChH
Confidence 46777888888888888888877777778888888888876666666777764
No 54
>PF09370 TIM-br_sig_trns: TIM-barrel signal transduction protein; InterPro: IPR009215 Members of this family are predicted to have a TIM barrel fold, based on PSI-BLAST analysis (iteration 4) and on SCOP prediction (using SMART). Interestingly, this novel domain also exists as an N-terminal domain of sigma54-dependent transcriptional activators (enhancer-binding proteins). Because sigma54 dependent activators typically have a three-domain structure: the variable N-terminal regulatory (activation) domain involved in signal recognition/receiving, the central AAA-type ATPase domain, and the DNA-binding domain (see PIRSF003187 from PIRSF, PIRSF005263 from PIRSF, PIRSF003184 from PIRSF, PIRSF005263 from PIRSF, IPR014443 from INTERPRO for details), the proteins of the current entry may be predicted to play a role in signal recognition/receiving and signal transduction.; PDB: 2P10_C.
Probab=22.76 E-value=80 Score=29.07 Aligned_cols=45 Identities=20% Similarity=0.378 Sum_probs=31.2
Q ss_pred cCcccCcchhhHHHHHHhcceeEEe-cCCCCCchhhhhhHhhhcCce
Q 028057 62 GGDLLKPDLGRWLSDVEKHKAIAIY-TPHEGGYEGRYLNRLRYLGYY 107 (214)
Q Consensus 62 ggdl~~~d~~~FirDLEk~GaLAvy-aPlEGG~EGRy~RRLRaaGY~ 107 (214)
+.|-.+ |+++|+++|.+.|.-||- -|--|..+|+|+.-|...|..
T Consensus 90 atDP~~-~~~~fl~~lk~~Gf~GV~NfPTvgliDG~fR~~LEe~Gmg 135 (268)
T PF09370_consen 90 ATDPFR-DMDRFLDELKELGFSGVQNFPTVGLIDGQFRQNLEETGMG 135 (268)
T ss_dssp TT-TT---HHHHHHHHHHHT-SEEEE-S-GGG--HHHHHHHHHTT--
T ss_pred CcCCCC-cHHHHHHHHHHhCCceEEECCcceeeccHHHHHHHhcCCC
Confidence 556664 999999999999999984 488899999999999888764
No 55
>cd03413 CbiK_C Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases, and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=22.19 E-value=2.4e+02 Score=21.53 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=37.1
Q ss_pred CcchhhHHHHHHhcceeEEec-CCC------------CCchhhhhhHhhhcCceEEEeccCCCC
Q 028057 67 KPDLGRWLSDVEKHKAIAIYT-PHE------------GGYEGRYLNRLRYLGYYFLDLSARGLG 117 (214)
Q Consensus 67 ~~d~~~FirDLEk~GaLAvya-PlE------------GG~EGRy~RRLRaaGY~t~~~SARGLG 117 (214)
.+++++-++.|.+.|+=-|+. |+- |--+.-++.||.++||..- ...+|||
T Consensus 41 ~P~i~~~l~~l~~~G~~~i~lvPl~L~~G~H~~~Dipge~~~SW~~~l~~~g~~v~-~~~~glg 103 (103)
T cd03413 41 YPGLDDVLAKLKKAGIKKVTLMPLMLVAGDHAHNDMAGDEPDSWKSILEAAGIKVE-TVLKGLG 103 (103)
T ss_pred CCCHHHHHHHHHHcCCCEEEEEehhheecccchhcCCCCCchhHHHHHHHCCCeeE-EEeccCC
Confidence 588899999998888766542 321 2235689999999999876 5678886
No 56
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=21.89 E-value=1e+02 Score=25.92 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=24.4
Q ss_pred eeEEecCCCCCchhhhhhHhhhcCceEEEeccC
Q 028057 82 AIAIYTPHEGGYEGRYLNRLRYLGYYFLDLSAR 114 (214)
Q Consensus 82 aLAvyaPlEGG~EGRy~RRLRaaGY~t~~~SAR 114 (214)
.+.|.+=+||||.-.=...|+.+|+..+++..|
T Consensus 176 ~i~i~IGPEGGfs~~E~~~~~~~g~~~vsLG~~ 208 (225)
T PF04452_consen 176 SIAIIIGPEGGFSEEEIEFLKEAGFQPVSLGPR 208 (225)
T ss_dssp EEEEEE--TT---HHHHHHHHHCTEEEEB-SSS
T ss_pred cEEEEECCCCCCCHHHHHHHHHCCCEEEEcCCC
Confidence 899999999999999999999999999987654
No 57
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=21.87 E-value=1.8e+02 Score=23.61 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=28.9
Q ss_pred hhhcCCCCCcceEEEEEeceecCHHHHHHHHcCCCCCCCeEEEEEe
Q 028057 146 RLAALPPSAKGLVVWIIEAKVLSKSELQFLALLPTLRPKVRVIAEC 191 (214)
Q Consensus 146 qL~~LPp~~KgLVLWiiEG~VLS~~EL~~L~~Lp~~ePrvKVVvEm 191 (214)
.+...+...+| |+|+|..-+..+.+.|..+-...|.+=|.+++
T Consensus 70 ~i~~~~~~~~~---~ilDGfPrt~~Qa~~l~~~~~~~~~~vi~L~~ 112 (210)
T TIGR01351 70 RLTQNQDNENG---FILDGFPRTLSQAEALDALLKEKIDAVIELDV 112 (210)
T ss_pred HHhcCcccCCc---EEEeCCCCCHHHHHHHHHHhccCCCEEEEEEC
Confidence 44444433454 89999999999988887765545665555554
No 58
>PRK06107 aspartate aminotransferase; Provisional
Probab=21.42 E-value=53 Score=29.03 Aligned_cols=29 Identities=31% Similarity=0.363 Sum_probs=26.1
Q ss_pred EeceecCHHHHHHHHcCCCCCCCeEEEEE
Q 028057 162 IEAKVLSKSELQFLALLPTLRPKVRVIAE 190 (214)
Q Consensus 162 iEG~VLS~~EL~~L~~Lp~~ePrvKVVvE 190 (214)
--|+++|.+|++.|+.++++.+++.||+.
T Consensus 178 PtG~~~s~~~~~~l~~~a~~~~~~~iI~D 206 (402)
T PRK06107 178 PTGAVYSRAELRALADVLLRHPHVLVLTD 206 (402)
T ss_pred CCCcCcCHHHHHHHHHHHHHcCCeEEEEe
Confidence 36999999999999999999888888876
No 59
>PF14178 YppF: YppF-like protein
Probab=21.41 E-value=42 Score=24.93 Aligned_cols=24 Identities=17% Similarity=0.436 Sum_probs=18.4
Q ss_pred cccCcccCcchhhHHHHHHhccee
Q 028057 60 FIGGDLLKPDLGRWLSDVEKHKAI 83 (214)
Q Consensus 60 ~iggdl~~~d~~~FirDLEk~GaL 83 (214)
||=|++---|--..+|+||+.||.
T Consensus 32 Yi~gei~i~eYR~lvreLE~~GA~ 55 (60)
T PF14178_consen 32 YIQGEISINEYRNLVRELEANGAV 55 (60)
T ss_pred HHhCcccHHHHHHHHHHHHHhCCC
Confidence 356766666667788999999984
No 60
>PLN02486 aminoacyl-tRNA ligase
Probab=21.12 E-value=2e+02 Score=27.24 Aligned_cols=55 Identities=24% Similarity=0.123 Sum_probs=40.1
Q ss_pred cchhhHHHHHHhcceeEEecCCC--CC--ch-----hhhhhHhhhc-CceEEEeccCCCCChhhhhhhc
Q 028057 68 PDLGRWLSDVEKHKAIAIYTPHE--GG--YE-----GRYLNRLRYL-GYYFLDLSARGLGDPETTLTKV 126 (214)
Q Consensus 68 ~d~~~FirDLEk~GaLAvyaPlE--GG--~E-----GRy~RRLRaa-GY~t~~~SARGLGDpeayLt~v 126 (214)
=|+++++.++|+..-+.+|.--+ |. .= -...+.|..+ |...++. ++|+++|+.+.
T Consensus 59 rd~~~~l~~~e~~~~~~vYtG~~PSg~~lHlGHlv~~~~~~~lQ~~~~~~~~I~----iaD~e~~~~~~ 123 (383)
T PLN02486 59 RDLEEILDAYEKGEKFYLYTGRGPSSEALHLGHLIPFMFTKYLQDAFKVPLVIQ----LTDDEKFLWKN 123 (383)
T ss_pred cCHHHHHHHHhcCCCeEEEeCCCCCCccccHHHHHHHHHHHHHHHhCCCeEEEE----ecCHHHHhhcC
Confidence 38899999999999999998654 22 11 2335677766 6666666 77999999874
No 61
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=21.04 E-value=1.3e+02 Score=20.63 Aligned_cols=30 Identities=10% Similarity=0.040 Sum_probs=21.6
Q ss_pred EEEEeceecCHHHHHHHHcCCCCCCCeEEEEEe
Q 028057 159 VWIIEAKVLSKSELQFLALLPTLRPKVRVIAEC 191 (214)
Q Consensus 159 LWiiEG~VLS~~EL~~L~~Lp~~ePrvKVVvEm 191 (214)
.||+||..++..+++ ..=...+.++|.+..
T Consensus 34 ~~I~eg~~~~~~~~~---~~~~~~~d~~Iyld~ 63 (69)
T cd02019 34 IVILEGLYASYKSRD---ARIRDLADLKIYLDA 63 (69)
T ss_pred EEEecchhhhhhhHH---hhccccccEEEEEEe
Confidence 999999999998866 222345667777654
No 62
>TIGR03368 cellulose_yhjU cellulose synthase operon protein YhjU. This protein was identified by the partial phylogenetic profiling algorithm (PubMed:16930487) as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (PubMed:11929533).
Probab=20.80 E-value=78 Score=31.75 Aligned_cols=25 Identities=28% Similarity=0.658 Sum_probs=21.8
Q ss_pred chhhHHHHHHhcc--eeEEecCCCCCc
Q 028057 69 DLGRWLSDVEKHK--AIAIYTPHEGGY 93 (214)
Q Consensus 69 d~~~FirDLEk~G--aLAvyaPlEGG~ 93 (214)
|+++|+..|||+| ++=|++|--|++
T Consensus 381 dld~F~~~le~SgR~vvVv~VPEHGAA 407 (518)
T TIGR03368 381 DLDRFFDELEKSGRKVVVVLVPEHGAA 407 (518)
T ss_pred HHHHHHHHHHHcCCcEEEEEecCcchh
Confidence 8999999999998 677889977765
No 63
>PRK07324 transaminase; Validated
Probab=20.70 E-value=1.2e+02 Score=26.76 Aligned_cols=26 Identities=8% Similarity=0.171 Sum_probs=20.8
Q ss_pred eceecCHHHHHHHHcCCCCCCCeEEEE
Q 028057 163 EAKVLSKSELQFLALLPTLRPKVRVIA 189 (214)
Q Consensus 163 EG~VLS~~EL~~L~~Lp~~ePrvKVVv 189 (214)
-|.++|++|++.|+.++++ .++-||+
T Consensus 166 tG~~~~~~~l~~i~~~a~~-~~~~ii~ 191 (373)
T PRK07324 166 TGALMDRAYLEEIVEIARS-VDAYVLS 191 (373)
T ss_pred CCCCCCHHHHHHHHHHHHH-CCCEEEE
Confidence 4999999999999999865 4566555
No 64
>PF03944 Endotoxin_C: delta endotoxin; InterPro: IPR005638 This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain (IPR005639 from INTERPRO) involved in membrane insertion and pore formation; a beta-sheet central domain (IPR001178 from INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain that interacts with the N-terminal domain to form a channel [, ]. This entry represents the conserved C-terminal domain.; PDB: 1DLC_A 1JI6_A 1W99_A 1CIY_A 1I5P_A 2C9K_A 3EB7_A.
Probab=20.55 E-value=13 Score=29.34 Aligned_cols=40 Identities=28% Similarity=0.402 Sum_probs=26.1
Q ss_pred cccCcccCcchhhHHHHHHhccee--EEecCCCCCchhhhhhHhhhcCceE
Q 028057 60 FIGGDLLKPDLGRWLSDVEKHKAI--AIYTPHEGGYEGRYLNRLRYLGYYF 108 (214)
Q Consensus 60 ~iggdl~~~d~~~FirDLEk~GaL--AvyaPlEGG~EGRy~RRLRaaGY~t 108 (214)
|.|||+|++.- .+.+ .+-+....-.-.||+=|+|.|.=..
T Consensus 24 ~tGGdlv~l~~---------~~~~~~~~~v~~~~~~~~~YrIRiRYAs~~~ 65 (143)
T PF03944_consen 24 FTGGDLVKLSN---------SGSLSIKIRVTINNSSSQKYRIRIRYASNSN 65 (143)
T ss_dssp SSSS-EEEESS---------SCEECEEEEEEESSSSTEEEEEEEEEEESS-
T ss_pred ccCCcEEEEcC---------CCceEEEEEEEecCCCCceEEEEEEEEECCC
Confidence 89999998753 3433 3433333778889999999775433
No 65
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=20.24 E-value=1.3e+02 Score=23.25 Aligned_cols=33 Identities=15% Similarity=0.247 Sum_probs=24.3
Q ss_pred EEEEeceecCHHHHHHHHcCCC--CCCCeEEEEEe
Q 028057 159 VWIIEAKVLSKSELQFLALLPT--LRPKVRVIAEC 191 (214)
Q Consensus 159 LWiiEG~VLS~~EL~~L~~Lp~--~ePrvKVVvEm 191 (214)
-|+|+|..-|..+.+.+..+.. ..|.+-|++++
T Consensus 78 ~~vlDg~p~~~~q~~~~~~~~~~~~~~d~~i~l~~ 112 (183)
T TIGR01359 78 KFLIDGFPRNEENLEAWEKLMDNKVNFKFVLFFDC 112 (183)
T ss_pred cEEEeCCCCCHHHHHHHHHHHhcCCCCCEEEEEEC
Confidence 3899999999998888776543 35776555554
No 66
>PLN02511 hydrolase
Probab=20.15 E-value=1.3e+02 Score=27.04 Aligned_cols=41 Identities=27% Similarity=0.505 Sum_probs=30.4
Q ss_pred cceeEEecC-CCCCchhhhh----hHhhhcCceEEEeccCCCCChh
Q 028057 80 HKAIAIYTP-HEGGYEGRYL----NRLRYLGYYFLDLSARGLGDPE 120 (214)
Q Consensus 80 ~GaLAvyaP-lEGG~EGRy~----RRLRaaGY~t~~~SARGLGDpe 120 (214)
.+.+-|+.+ ++|+.+..|. ..+...||+++.+-.||.|+-+
T Consensus 99 ~~p~vvllHG~~g~s~~~y~~~~~~~~~~~g~~vv~~d~rG~G~s~ 144 (388)
T PLN02511 99 DAPVLILLPGLTGGSDDSYVRHMLLRARSKGWRVVVFNSRGCADSP 144 (388)
T ss_pred CCCEEEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEecCCCCCCC
Confidence 344566665 7788765554 4456899999999999999754
Done!