Query psy9569
Match_columns 156
No_of_seqs 113 out of 157
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 22:57:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02284 COX5A: Cytochrome c o 100.0 4.3E-69 9.3E-74 407.9 11.1 108 37-145 1-108 (108)
2 cd00923 Cyt_c_Oxidase_Va Cytoc 100.0 5.7E-66 1.2E-70 388.2 11.1 103 40-143 1-103 (103)
3 KOG4077|consensus 100.0 1.7E-64 3.7E-69 398.5 13.0 146 1-147 1-149 (149)
4 PF08542 Rep_fac_C: Replicatio 83.7 6.3 0.00014 26.9 6.3 53 78-136 2-54 (89)
5 cd00620 Methyltransferase_Sun 81.6 7.8 0.00017 28.5 6.6 63 47-111 55-122 (126)
6 PF08822 DUF1804: Protein of u 76.9 4.3 9.4E-05 33.3 4.3 57 74-134 89-158 (165)
7 PF13812 PPR_3: Pentatricopept 74.4 6.1 0.00013 21.7 3.3 26 84-109 4-29 (34)
8 PF13041 PPR_2: PPR repeat fam 73.0 17 0.00036 22.3 5.4 45 79-124 1-46 (50)
9 PF12921 ATP13: Mitochondrial 70.3 38 0.00082 25.8 7.8 53 72-124 43-96 (126)
10 PF03732 Retrotrans_gag: Retro 69.5 15 0.00033 24.2 4.9 66 41-108 26-95 (96)
11 PF00617 RasGEF: RasGEF domain 68.3 5.9 0.00013 29.9 3.0 76 47-132 45-128 (188)
12 KOG2908|consensus 68.0 12 0.00027 34.5 5.4 37 78-114 72-108 (380)
13 PF13089 PP_kinase_N: Polyphos 66.2 2.4 5.1E-05 31.7 0.5 38 99-136 69-106 (109)
14 TIGR01837 PHA_granule_1 poly(h 66.1 4.1 9E-05 30.9 1.8 35 107-141 64-98 (118)
15 PF14559 TPR_19: Tetratricopep 65.8 19 0.00041 22.5 4.6 45 80-126 24-68 (68)
16 cd08183 Fe-ADH2 Iron-containin 65.7 11 0.00023 32.8 4.5 32 117-148 313-344 (374)
17 PRK09634 nusB transcription an 60.7 19 0.00042 30.2 5.0 53 58-112 147-199 (207)
18 PF01029 NusB: NusB family; I 59.2 12 0.00026 27.4 3.1 50 60-110 82-131 (134)
19 PF13174 TPR_6: Tetratricopept 59.0 19 0.00042 19.4 3.3 24 90-113 9-32 (33)
20 PF01535 PPR: PPR repeat; Int 58.9 18 0.00039 19.2 3.1 27 84-110 3-29 (31)
21 TIGR00756 PPR pentatricopeptid 56.6 22 0.00049 18.9 3.3 27 84-110 3-29 (35)
22 PF14853 Fis1_TPR_C: Fis1 C-te 55.0 43 0.00092 22.3 5.0 43 90-134 10-52 (53)
23 PF09597 IGR: IGR protein moti 53.7 9.2 0.0002 26.4 1.6 34 102-139 10-43 (57)
24 PF02637 GatB_Yqey: GatB domai 51.5 11 0.00025 28.6 2.0 35 102-137 1-35 (148)
25 PF00113 Enolase_C: Enolase, C 51.1 27 0.00059 30.6 4.5 69 42-110 133-224 (295)
26 cd00619 Terminator_NusB Transc 50.7 21 0.00046 26.1 3.3 51 60-111 73-126 (130)
27 TIGR01951 nusB transcription a 49.8 21 0.00046 26.0 3.1 48 62-110 78-125 (129)
28 PF12192 CBP: Fungal calcium b 48.8 29 0.00063 24.5 3.5 43 94-140 8-57 (59)
29 PF13428 TPR_14: Tetratricopep 48.6 51 0.0011 19.8 4.2 32 83-114 3-34 (44)
30 PF03704 BTAD: Bacterial trans 48.2 70 0.0015 23.1 5.6 32 82-113 63-94 (146)
31 PF13176 TPR_7: Tetratricopept 48.1 20 0.00044 21.0 2.3 18 89-106 7-24 (36)
32 KOG0991|consensus 47.7 45 0.00097 30.2 5.3 69 41-110 171-267 (333)
33 PLN03081 pentatricopeptide (PP 47.5 70 0.0015 29.6 6.8 62 62-123 407-469 (697)
34 PF04031 Las1: Las1-like ; In 45.8 1.5E+02 0.0032 23.4 8.6 88 43-137 6-115 (154)
35 PF00627 UBA: UBA/TS-N domain; 42.8 29 0.00063 20.8 2.5 23 80-104 15-37 (37)
36 cd08194 Fe-ADH6 Iron-containin 42.8 26 0.00056 30.5 3.1 30 118-147 311-340 (375)
37 cd08193 HVD 5-hydroxyvalerate 41.7 33 0.00071 29.8 3.5 32 117-148 313-345 (376)
38 TIGR02252 DREG-2 REG-2-like, H 41.4 1.4E+02 0.003 22.7 6.5 65 78-147 81-162 (203)
39 COG3325 ChiA Chitinase [Carboh 41.2 11 0.00025 35.3 0.7 22 116-137 193-214 (441)
40 PLN03081 pentatricopeptide (PP 40.5 98 0.0021 28.7 6.6 70 66-136 479-560 (697)
41 PF00607 Gag_p24: gag gene pro 40.4 41 0.00089 27.6 3.8 20 39-58 131-150 (206)
42 PF05597 Phasin: Poly(hydroxya 40.2 44 0.00096 26.2 3.8 39 102-141 72-111 (132)
43 cd08191 HHD 6-hydroxyhexanoate 40.2 33 0.00072 30.0 3.4 32 117-148 324-356 (386)
44 PLN03218 maturation of RBCL 1; 39.1 96 0.0021 31.7 6.7 43 67-109 493-535 (1060)
45 PRK10901 16S rRNA methyltransf 38.0 1.1E+02 0.0024 27.3 6.3 52 44-96 52-108 (427)
46 PLN03077 Protein ECB2; Provisi 37.6 1.1E+02 0.0023 29.1 6.5 72 64-135 572-653 (857)
47 cd08171 GlyDH-like2 Glycerol d 37.1 19 0.00042 30.9 1.4 28 121-148 285-313 (345)
48 KOG0036|consensus 36.4 1.6E+02 0.0035 28.1 7.3 90 41-139 6-117 (463)
49 KOG3103|consensus 35.1 17 0.00037 31.9 0.8 10 127-136 82-91 (249)
50 COG3189 Uncharacterized conser 34.8 36 0.00078 26.9 2.5 38 34-71 52-90 (117)
51 PLN00032 DNA-directed RNA poly 34.6 35 0.00076 24.8 2.2 27 110-136 9-41 (71)
52 smart00147 RasGEF Guanine nucl 34.5 49 0.0011 26.6 3.3 24 88-111 85-108 (242)
53 PRK04016 DNA-directed RNA poly 34.2 37 0.0008 24.1 2.2 27 110-136 9-41 (62)
54 PLN03218 maturation of RBCL 1; 33.8 1.4E+02 0.0031 30.5 7.0 64 61-124 734-797 (1060)
55 TIGR01428 HAD_type_II 2-haloal 33.5 2.1E+02 0.0046 21.6 7.4 83 61-147 56-150 (198)
56 PRK00202 nusB transcription an 33.3 47 0.001 24.7 2.8 48 63-111 81-128 (137)
57 PF14663 RasGEF_N_2: Rapamycin 33.2 60 0.0013 24.2 3.4 52 60-134 5-56 (115)
58 PF04336 DUF479: Protein of un 32.8 49 0.0011 24.2 2.8 84 40-123 13-104 (106)
59 PF02037 SAP: SAP domain; Int 32.8 34 0.00073 20.8 1.6 17 122-138 5-21 (35)
60 PF14726 RTTN_N: Rotatin, an a 32.8 98 0.0021 23.2 4.4 45 69-114 35-86 (98)
61 PF13925 Katanin_con80: con80 32.1 96 0.0021 24.4 4.5 30 84-113 30-61 (164)
62 PF15469 Sec5: Exocyst complex 32.0 79 0.0017 24.6 4.0 50 86-135 91-142 (182)
63 PLN03077 Protein ECB2; Provisi 29.6 3E+02 0.0064 26.3 8.0 71 65-136 641-723 (857)
64 PF01194 RNA_pol_N: RNA polyme 29.6 60 0.0013 22.8 2.6 27 110-136 9-41 (60)
65 PRK10015 oxidoreductase; Provi 29.4 2.1E+02 0.0045 25.4 6.6 56 53-108 369-427 (429)
66 PF12854 PPR_1: PPR repeat 29.0 1.3E+02 0.0027 17.6 3.8 32 76-107 2-33 (34)
67 cd00447 NusB_Sun RNA binding d 28.3 84 0.0018 22.7 3.4 51 59-110 73-124 (129)
68 cd08176 LPO Lactadehyde:propan 28.2 34 0.00074 29.7 1.5 30 119-148 317-347 (377)
69 PF05138 PaaA_PaaC: Phenylacet 28.1 37 0.0008 29.0 1.7 24 116-139 204-227 (263)
70 PRK00117 recX recombination re 27.9 1.8E+02 0.0039 22.1 5.2 50 53-107 19-71 (157)
71 PF07261 DnaB_2: Replication i 27.8 56 0.0012 21.5 2.2 14 80-93 31-44 (77)
72 PRK01611 argS arginyl-tRNA syn 27.5 1.6E+02 0.0035 27.0 5.7 60 81-141 435-507 (507)
73 COG1644 RPB10 DNA-directed RNA 27.2 50 0.0011 23.6 1.9 27 110-136 9-41 (63)
74 PF05746 DALR_1: DALR anticodo 27.1 27 0.00059 24.6 0.6 61 81-141 46-119 (119)
75 TIGR02158 PA_CoA_Oxy3 phenylac 27.0 60 0.0013 27.7 2.7 26 116-141 178-203 (237)
76 PRK15138 aldehyde reductase; P 26.9 1E+02 0.0022 27.3 4.2 32 117-148 321-353 (387)
77 PF13766 ECH_C: 2-enoyl-CoA Hy 26.7 61 0.0013 24.3 2.4 51 66-123 6-56 (118)
78 COG4710 Predicted DNA-binding 26.5 2.4E+02 0.0052 21.0 5.4 46 64-109 15-61 (80)
79 COG3888 Predicted transcriptio 26.4 52 0.0011 29.8 2.3 34 106-140 283-316 (321)
80 smart00513 SAP Putative DNA-bi 26.0 54 0.0012 19.6 1.7 16 123-138 6-21 (35)
81 cd08186 Fe-ADH8 Iron-containin 25.5 42 0.0009 29.4 1.6 29 120-148 317-346 (383)
82 TIGR03754 conj_TOL_TraD conjug 25.3 5.5E+02 0.012 25.3 9.1 83 47-136 320-410 (643)
83 cd08175 G1PDH Glycerol-1-phosp 25.1 34 0.00074 29.3 0.9 27 122-148 295-322 (348)
84 PF04282 DUF438: Family of unk 24.9 1.8E+02 0.0038 20.9 4.4 41 40-83 11-51 (71)
85 PF06293 Kdo: Lipopolysacchari 24.3 30 0.00064 27.3 0.4 17 129-145 67-83 (206)
86 cd08187 BDH Butanol dehydrogen 24.2 1.5E+02 0.0033 25.8 4.8 32 117-148 320-352 (382)
87 cd08182 HEPD Hydroxyethylphosp 24.2 45 0.00098 28.8 1.5 28 121-148 309-337 (367)
88 smart00351 PAX Paired Box doma 24.0 1.6E+02 0.0036 22.0 4.4 45 43-89 79-125 (125)
89 smart00386 HAT HAT (Half-A-TPR 23.8 1.2E+02 0.0026 15.7 3.0 29 95-124 1-29 (33)
90 KOG1154|consensus 23.5 82 0.0018 28.2 3.0 33 47-79 100-148 (285)
91 cd08188 Fe-ADH4 Iron-containin 23.5 48 0.001 28.9 1.6 29 120-148 318-347 (377)
92 cd00155 RasGEF Guanine nucleot 23.4 1E+02 0.0022 24.5 3.3 24 86-109 83-106 (237)
93 smart00633 Glyco_10 Glycosyl h 23.4 78 0.0017 25.9 2.7 62 45-110 60-148 (254)
94 PF00901 Orbi_VP5: Orbivirus o 23.3 1.7E+02 0.0036 28.3 5.1 54 61-114 248-308 (508)
95 PRK10586 putative oxidoreducta 23.2 71 0.0015 28.2 2.6 26 120-145 292-318 (362)
96 cd08192 Fe-ADH7 Iron-containin 23.2 49 0.0011 28.6 1.5 29 120-148 311-340 (370)
97 cd08185 Fe-ADH1 Iron-containin 23.1 51 0.0011 28.6 1.7 30 119-148 318-348 (380)
98 PRK01153 nicotinamide-nucleoti 22.7 1.1E+02 0.0024 24.4 3.4 29 54-83 121-150 (174)
99 PF14337 DUF4393: Domain of un 22.5 1.8E+02 0.0039 22.6 4.5 51 78-128 13-68 (186)
100 TIGR03405 Phn_Fe-ADH phosphona 22.4 54 0.0012 28.4 1.6 28 121-148 308-336 (355)
101 COG0576 GrpE Molecular chapero 22.4 96 0.0021 25.5 3.0 76 49-138 64-139 (193)
102 cd00194 UBA Ubiquitin Associat 22.3 1.3E+02 0.0027 17.6 2.8 32 69-104 5-36 (38)
103 TIGR02638 lactal_redase lactal 22.1 1.1E+02 0.0025 26.6 3.6 31 118-148 319-350 (379)
104 PF03705 CheR_N: CheR methyltr 22.0 1E+02 0.0023 19.3 2.6 39 102-141 7-47 (57)
105 cd08180 PDD 1,3-propanediol de 21.8 64 0.0014 27.5 2.0 29 119-147 268-297 (332)
106 PF12827 Peroxin-22: Peroxisom 21.7 57 0.0012 25.2 1.5 31 110-142 73-108 (117)
107 PF13419 HAD_2: Haloacid dehal 21.6 31 0.00068 24.3 0.0 50 97-147 79-135 (176)
108 COG5304 Uncharacterized protei 21.6 74 0.0016 24.3 2.0 68 41-126 17-84 (92)
109 PF00465 Fe-ADH: Iron-containi 21.5 76 0.0017 27.2 2.4 31 117-147 309-340 (366)
110 smart00165 UBA Ubiquitin assoc 21.3 1.3E+02 0.0029 17.4 2.8 32 69-104 5-36 (37)
111 KOG4281|consensus 21.3 1.2E+02 0.0025 26.7 3.4 42 100-144 4-45 (236)
112 TIGR00456 argS arginyl-tRNA sy 20.8 48 0.001 30.8 1.1 56 81-141 506-566 (566)
113 PHA02602 56 dCTP pyrophosphata 20.7 1.8E+02 0.004 24.4 4.3 52 62-134 35-89 (172)
114 PF05854 MC1: Non-histone chro 20.7 44 0.00096 25.5 0.7 9 85-93 26-34 (93)
115 PF10602 RPN7: 26S proteasome 20.1 1.2E+02 0.0026 24.0 3.1 68 41-126 13-80 (177)
No 1
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=100.00 E-value=4.3e-69 Score=407.88 Aligned_cols=108 Identities=62% Similarity=1.041 Sum_probs=89.4
Q ss_pred CCCCCCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCcc
Q psy9569 37 SHAVEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHD 116 (156)
Q Consensus 37 s~h~~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~ 116 (156)
|||++||||+|++||++|||+++||+||+||||||||||||||+|+||+|||||||||||||+||||||+||+|||++ +
T Consensus 1 sH~~~Et~eeF~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~-~ 79 (108)
T PF02284_consen 1 SHGSEETDEEFDARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNK-K 79 (108)
T ss_dssp -TS----HHHHHHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT--T
T ss_pred CCCcccCHHHHHHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh-H
Confidence 466899999999999999999999999999999999999999999999999999999999999999999999999998 6
Q ss_pred chhHHHHHhhhhhhHhhCCCCccccCCCC
Q psy9569 117 KIWPYIVQEITPTLKELGIETPAQLGYDK 145 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t~EeLgydk 145 (156)
+|||||+|||||||+||||+|||||||||
T Consensus 80 ~~Y~~~lqElkPtl~ELGI~t~EeLg~dk 108 (108)
T PF02284_consen 80 EIYPYILQELKPTLEELGIPTPEELGYDK 108 (108)
T ss_dssp THHHHHHHHHHHHHHHHT---TTTTTTT-
T ss_pred HHHHHHHHHHhhHHHHhCCCCHHHhCCCC
Confidence 69999999999999999999999999997
No 2
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=100.00 E-value=5.7e-66 Score=388.21 Aligned_cols=103 Identities=62% Similarity=1.055 Sum_probs=100.7
Q ss_pred CCCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchh
Q psy9569 40 VEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIW 119 (156)
Q Consensus 40 ~~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY 119 (156)
++||+|+|++||++|||+++||+||+||||||||||||||+|+||+|||||||||||||+||||||+||+|||++ ++||
T Consensus 1 ~~Et~EeF~aRye~~F~~~~iD~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~-~~~y 79 (103)
T cd00923 1 SEETDEEFDARYETYFNRPDIDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAH-KEIY 79 (103)
T ss_pred CcccHHHHHHHHHHHhCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCc-hhhH
Confidence 379999999999999999999999999999999999999999999999999999999999999999999999986 6899
Q ss_pred HHHHHhhhhhhHhhCCCCccccCC
Q psy9569 120 PYIVQEITPTLKELGIETPAQLGY 143 (156)
Q Consensus 120 ~~~lqElkPtl~ELGI~t~EeLgy 143 (156)
|||+|||||||+||||+|||||||
T Consensus 80 ~~~lqeikp~l~ELGI~t~EeLgy 103 (103)
T cd00923 80 PYILQEIKPTLKELGISTPEELGY 103 (103)
T ss_pred HHHHHHHhHHHHHHCCCCHHHhCc
Confidence 999999999999999999999998
No 3
>KOG4077|consensus
Probab=100.00 E-value=1.7e-64 Score=398.51 Aligned_cols=146 Identities=41% Similarity=0.701 Sum_probs=121.4
Q ss_pred ChHHHHHHHHhhhhHHHHh--hhcccCCc-cccccccccCCCCCCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCC
Q psy9569 1 MFRALASRLAASSSQVLRQ--TAVSKVKP-LTFAPIRSFSHAVEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDC 77 (156)
Q Consensus 1 Mlr~~~~~~~~~~r~~~~~--~~~~~~~~-~~~~~~r~~s~h~~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~Dl 77 (156)
||..++.+++-+.|.+... +++.+..+ ++...++.++.|..||+||||+||++|||+++||+||+||||||||+||+
T Consensus 1 ml~rAv~r~~i~~r~~~~a~~~~~~~~s~~~a~~~~~~~~~hg~et~EEfd~ry~~yf~r~~iD~wEvrkglN~l~~yDl 80 (149)
T KOG4077|consen 1 MLTRAVTRLAIAGRTLVRARPSTRTPASGLGANTFIKYSMEHGPETAEEFDARYEKYFNRPEIDGWEVRKGLNNLFDYDL 80 (149)
T ss_pred ChHHHHHHHHHHhhhHhccccccccccCCccchhhhhhHhhcCcccHHHHHHHHHHHcCcccchHHHHHHHHHhhhcccc
Confidence 6766677666555555542 11111111 22223344455666799999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCCccccCCCCcc
Q psy9569 78 VPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQLGYDKPE 147 (156)
Q Consensus 78 VPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgydkpe 147 (156)
||+|+||+|||||||||||||+||||||+||+|||++ +++||||++||||||.||||+||||||++++|
T Consensus 81 VP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g~~-k~~Y~y~v~elkpvl~ELGI~t~EeLg~~~~~ 149 (149)
T KOG4077|consen 81 VPSPKVIEAALRACRRVNDFATAVRILEAIKDKCGAQ-KQVYPYYVKELKPVLNELGIPTPEELGFPSVE 149 (149)
T ss_pred CCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhcccH-HHHHHHHHHHHHHHHHHhCCCCHHHhCCCCCC
Confidence 9999999999999999999999999999999999998 66899999999999999999999999988875
No 4
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=83.69 E-value=6.3 Score=26.94 Aligned_cols=53 Identities=26% Similarity=0.281 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCC
Q psy9569 78 VPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIE 136 (156)
Q Consensus 78 VPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 136 (156)
+|.|++|+.-++.|.. ++|..+-..++.+... |=. ...++++|-..+-+..++
T Consensus 2 ~p~~~~i~~i~~~~~~-~~~~~~~~~~~~l~~~-G~s----~~~Il~~l~~~l~~~~~~ 54 (89)
T PF08542_consen 2 WPPPEVIEEILESCLN-GDFKEARKKLYELLVE-GYS----ASDILKQLHEVLVESDIP 54 (89)
T ss_dssp S--HHHHHHHHHHHHH-TCHHHHHHHHHHHHHT-T------HHHHHHHHHHHHHTSTSS
T ss_pred CCCHHHHHHHHHHHHh-CCHHHHHHHHHHHHHc-CCC----HHHHHHHHHHHHHHhhcc
Confidence 5899999999999988 6999999999999988 544 456677777666665444
No 5
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=81.57 E-value=7.8 Score=28.54 Aligned_cols=63 Identities=16% Similarity=0.111 Sum_probs=44.9
Q ss_pred HHHHHHHhhCCC--CCcHHH---HHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhc
Q psy9569 47 FVKRYVAFFNQP--DIDGWD---IRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKT 111 (156)
Q Consensus 47 F~aRy~~~F~~~--~iD~we---~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~ 111 (156)
.|.--.++-+++ .++.|+ +|=|+..++-.| +|...+|..|...|+..++ +.+-+|.-||=.+.
T Consensus 55 ld~~i~~~l~~~~~~~~~~~~~iLr~a~~el~~~~-~p~~avvneaVelak~~~~-~~~~~fVNaVLr~i 122 (126)
T cd00620 55 LDWIINPLLKKPDVGKDPDVRNLLRLGLYQLLYLD-VPPHAAVDETVEIAKIRKD-LGRAGLVNAVLRRF 122 (126)
T ss_pred HHHHHHHHhCCCccccCHHHHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhCC-CchhhHHHHHHHHH
Confidence 333333444443 245555 899999999889 9999999999999998865 35667777765543
No 6
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=76.90 E-value=4.3 Score=33.32 Aligned_cols=57 Identities=21% Similarity=0.368 Sum_probs=44.8
Q ss_pred cCCCCCCHHH---------HHHHHHHHHhh----hhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhC
Q psy9569 74 HDDCVPDPEI---------IIAALKAIRRV----NDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELG 134 (156)
Q Consensus 74 ~~DlVPeP~I---------i~AALrAcRRv----ND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 134 (156)
+.|+-|+-++ ...+..|+||+ +.+++|++++|.+-.-+ ++.||.-++.+-.+|++.|
T Consensus 89 ~~~~~~~~k~~~LasLaDsf~K~vaaskr~lPets~LavA~~vl~~l~~fv----~e~~P~h~~af~eiLepFg 158 (165)
T PF08822_consen 89 NEDMPPQEKVELLASLADSFSKMVAASKRVLPETSELAVAMEVLELLAAFV----QERYPQHLAAFLEILEPFG 158 (165)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHH----HhcCHHHHHHHHHHHHHHH
Confidence 4667666654 34567899998 99999999999766554 4569999998888888887
No 7
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=74.43 E-value=6.1 Score=21.71 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.4
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHhhh
Q psy9569 84 IIAALKAIRRVNDYALAIRFLETTEF 109 (156)
Q Consensus 84 i~AALrAcRRvND~alAVR~lE~iK~ 109 (156)
.++.++||.+-+|+..|.++|+..+.
T Consensus 4 y~~ll~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 4 YNALLRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999998876
No 8
>PF13041 PPR_2: PPR repeat family
Probab=73.02 E-value=17 Score=22.30 Aligned_cols=45 Identities=7% Similarity=0.205 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh-cCCCccchhHHHHH
Q psy9569 79 PDPEIIIAALKAIRRVNDYALAIRFLETTEFK-TGGSHDKIWPYIVQ 124 (156)
Q Consensus 79 PeP~Ii~AALrAcRRvND~alAVR~lE~iK~K-~~~~~~~iY~~~lq 124 (156)
|+-....+.++++-|-+++..|.++|+..+.+ +.+. ...|.-+++
T Consensus 1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~-~~Ty~~li~ 46 (50)
T PF13041_consen 1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPD-SYTYNILIN 46 (50)
T ss_pred CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCC-HHHHHHHHH
Confidence 55566778899999999999999999998866 3333 345665554
No 9
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=70.29 E-value=38 Score=25.78 Aligned_cols=53 Identities=13% Similarity=0.222 Sum_probs=40.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCc-cchhHHHHH
Q psy9569 72 LAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSH-DKIWPYIVQ 124 (156)
Q Consensus 72 l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~-~~iY~~~lq 124 (156)
.-+.-+-|.+.++.|-+-|==.-||+.+|+++++.+-.+-+-.. +..|..+++
T Consensus 43 ~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~ 96 (126)
T PF12921_consen 43 PPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE 96 (126)
T ss_pred CCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 34556889999999999998888999999999999988776321 345555443
No 10
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=69.47 E-value=15 Score=24.20 Aligned_cols=66 Identities=23% Similarity=0.190 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhh----hHHHHHHHHHHhh
Q psy9569 41 EESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVN----DYALAIRFLETTE 108 (156)
Q Consensus 41 ~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvN----D~alAVR~lE~iK 108 (156)
..|.++|...+.+.|..++ ....++.-|++|-. +==.--.-+..-.+.+++++ +=....+|++|++
T Consensus 26 ~~~W~~~~~~~~~~f~~~~-~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~~~~e~~~v~~f~~GL~ 95 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPD-RKEQARQELNSLRQ-GNESVREYVNRFRELARRAPPPMDEEMLVERFIRGLR 95 (96)
T ss_pred CCCHHHHHHHHHHHHhhhh-ccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCCCcCHHHHHHHHHHCCC
Confidence 4689999999999998864 56667777777766 33333333344444444444 3444555666654
No 11
>PF00617 RasGEF: RasGEF domain; InterPro: IPR001895 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. The balance between the GTP bound (active) and GDP bound (inactive) states is regulated by the opposite action of proteins activating the GTPase activity and that of proteins which promote the loss of bound GDP and the uptake of fresh GTP [, ]. The latter proteins are known as guanine-nucleotide dissociation stimulators (GDSs) (or also as guanine-nucleotide releasing (or exchange) factors (GRFs)). Proteins that act as GDS can be classified into at least two families, on the basis of sequence similarities, the CDC24 family (see IPR001331 from INTERPRO) and the CDC25 family. The size of the proteins of the CDC25 family range from 309 residues (LTE1) to 1596 residues (sos). The sequence similarity shared by all these proteins is limited to a region of about 250 amino acids generally located in their C-terminal section (currently the only exceptions are sos and ralGDS where this domain makes up the central part of the protein). This domain has been shown, in CDC25 an SCD25, to be essential for the activity of these proteins.; GO: 0005085 guanyl-nucleotide exchange factor activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IJE_S 3T6G_A 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=68.32 E-value=5.9 Score=29.90 Aligned_cols=76 Identities=20% Similarity=0.394 Sum_probs=44.5
Q ss_pred HHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCH--------HHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccch
Q psy9569 47 FVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDP--------EIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKI 118 (156)
Q Consensus 47 F~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP--------~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~i 118 (156)
--.++.++||. +-.|-..-- ... +++ +.|.-|.. |+.+|||..+.-|+-|+....-.+.+..
T Consensus 45 ~i~~~~~~~n~--ls~wv~~~I----l~~---~~~~~R~~~i~~~I~va~~-l~~l~Nf~s~~aI~~~L~s~~i~rL~~t 114 (188)
T PF00617_consen 45 NINKLIDRFNK--LSNWVISEI----LSQ---PDPEERAKIIEKFIQVAKK-LYELGNFNSLMAILSALNSSSIQRLKKT 114 (188)
T ss_dssp HHHHHHHHHHH--HHHHHHHHH----HTS---SSHHHHHHHHHHHHHHHHH-HHHTTBHHHHHHHHHHHTSHHHHT-HHH
T ss_pred hHHHHHHHhhh--HHHHHHHHh----hcc---ccHHHHHHHHHHHHhHHHH-HHHhcCchHHHHHHHHhccccccchhhh
Confidence 35667777775 455643222 221 233 34555555 9999999999999999987653333344
Q ss_pred hHHHHHhhhhhhHh
Q psy9569 119 WPYIVQEITPTLKE 132 (156)
Q Consensus 119 Y~~~lqElkPtl~E 132 (156)
|..+-++.+-++++
T Consensus 115 w~~l~~~~~~~~~~ 128 (188)
T PF00617_consen 115 WKSLSKKSKKTFEE 128 (188)
T ss_dssp HHTSHHHHHHHHHH
T ss_pred hhhhHHHHHHHHHH
Confidence 54444444433333
No 12
>KOG2908|consensus
Probab=68.03 E-value=12 Score=34.47 Aligned_cols=37 Identities=19% Similarity=0.162 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCC
Q psy9569 78 VPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGS 114 (156)
Q Consensus 78 VPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~ 114 (156)
|=.=+.|+-+|...++.||...|++|||.|++|..-.
T Consensus 72 INplslvei~l~~~~~~~D~~~al~~Le~i~~~~~~~ 108 (380)
T KOG2908|consen 72 INPLSLVEILLVVSEQISDKDEALEFLEKIIEKLKEY 108 (380)
T ss_pred cChHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhh
Confidence 4455789999999999999999999999999998654
No 13
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=66.24 E-value=2.4 Score=31.67 Aligned_cols=38 Identities=18% Similarity=0.237 Sum_probs=31.8
Q ss_pred HHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCC
Q psy9569 99 LAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIE 136 (156)
Q Consensus 99 lAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 136 (156)
++-..|+.|..++...++++|..+-++|.|-|++=||-
T Consensus 69 tP~eqL~~I~~~v~~l~~~q~~~~~~~Llp~L~~~GI~ 106 (109)
T PF13089_consen 69 TPQEQLDAIRKRVHELVEEQYEIYNEELLPELAEEGIH 106 (109)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHCTTEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 35567888888888877889999999999999999984
No 14
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=66.08 E-value=4.1 Score=30.90 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=26.0
Q ss_pred hhhhcCCCccchhHHHHHhhhhhhHhhCCCCcccc
Q psy9569 107 TEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 107 iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 141 (156)
++++.......+-+.+-+.++-+|..|||+|.+|+
T Consensus 64 ~~~~~~~~~~~le~~~~~~v~~~L~~lg~~tk~ev 98 (118)
T TIGR01837 64 TRDQVQRNWDKLEKAFDERVEQALNRLNIPSREEI 98 (118)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 33444333245677888899999999999999986
No 15
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=65.79 E-value=19 Score=22.50 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhh
Q psy9569 80 DPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEI 126 (156)
Q Consensus 80 eP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqEl 126 (156)
.+++.-.--+++-+.+++..|..+|+.+.....+. ..|..++.+|
T Consensus 24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~--~~~~~l~a~i 68 (68)
T PF14559_consen 24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDN--PEYQQLLAQI 68 (68)
T ss_dssp SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTH--HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCH--HHHHHHHhcC
Confidence 56666677788889999999999999999988874 4566665544
No 16
>cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria.
Probab=65.69 E-value=11 Score=32.78 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=27.2
Q ss_pred chhHHHHHhhhhhhHhhCCCCccccCCCCccc
Q psy9569 117 KIWPYIVQEITPTLKELGIETPAQLGYDKPEL 148 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t~EeLgydkpel 148 (156)
+.-...+++|+..+++||+|+..|+|.++.++
T Consensus 313 ~~a~~~~~~l~~l~~~lglP~L~e~gv~~~~~ 344 (374)
T cd08183 313 AAADDLVEWLEHWVDELGLPRLSDYGLTPDDL 344 (374)
T ss_pred HHHHHHHHHHHHHHHHcCCCChhhcCCCHHHH
Confidence 45567899999999999999889999987654
No 17
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=60.70 E-value=19 Score=30.19 Aligned_cols=53 Identities=21% Similarity=0.251 Sum_probs=43.1
Q ss_pred CCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcC
Q psy9569 58 PDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTG 112 (156)
Q Consensus 58 ~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~ 112 (156)
+.+|-.-+|-|+..++-.| +|.+.+|..|...|++..+- -+-+|.-||=.+..
T Consensus 147 ~~idr~ILRlavyELl~l~-~P~~vaINEAVeLAK~~~~~-~~~~FVNaVLrri~ 199 (207)
T PRK09634 147 PRIDRDILRLAVVEILFLN-TPAAVAINEAVELAKRYSDE-QGRRFINGVLRRLQ 199 (207)
T ss_pred CHHHHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHHhCCC-cccchHHHHHHHHH
Confidence 4577888999999998887 89999999999999999874 44577777766553
No 18
>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....
Probab=59.20 E-value=12 Score=27.43 Aligned_cols=50 Identities=16% Similarity=0.172 Sum_probs=40.5
Q ss_pred CcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh
Q psy9569 60 IDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFK 110 (156)
Q Consensus 60 iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K 110 (156)
++.--+|-|+-.+.-.|=+|.+.+|..|...|++. .-..+.+|+-||=+|
T Consensus 82 ~~~~iLrla~~El~~~~~~p~~v~InEaVelak~~-~~~~~~~fVNaVL~~ 131 (134)
T PF01029_consen 82 VDRAILRLAIYELLFLDDIPPHVAINEAVELAKKY-GDEKSAGFVNAVLRR 131 (134)
T ss_dssp HHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHH-S-TTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHh-CCCCcchhHHHHHHH
Confidence 34556889999999999999999999999999998 445567777777554
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=58.97 E-value=19 Score=19.39 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=19.6
Q ss_pred HHHhhhhHHHHHHHHHHhhhhcCC
Q psy9569 90 AIRRVNDYALAIRFLETTEFKTGG 113 (156)
Q Consensus 90 AcRRvND~alAVR~lE~iK~K~~~ 113 (156)
+..+.+|+..|++.|+.+..+..+
T Consensus 9 ~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 9 CYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHccCHHHHHHHHHHHHHHCcC
Confidence 345689999999999999887654
No 20
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=58.89 E-value=18 Score=19.25 Aligned_cols=27 Identities=4% Similarity=0.171 Sum_probs=23.1
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHhhhh
Q psy9569 84 IIAALKAIRRVNDYALAIRFLETTEFK 110 (156)
Q Consensus 84 i~AALrAcRRvND~alAVR~lE~iK~K 110 (156)
...-+++|.+.+++..|.++++.++.+
T Consensus 3 y~~li~~~~~~~~~~~a~~~~~~M~~~ 29 (31)
T PF01535_consen 3 YNSLISGYCKMGQFEEALEVFDEMRER 29 (31)
T ss_pred HHHHHHHHHccchHHHHHHHHHHHhHC
Confidence 356789999999999999999988754
No 21
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=56.64 E-value=22 Score=18.91 Aligned_cols=27 Identities=4% Similarity=0.069 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHhhhh
Q psy9569 84 IIAALKAIRRVNDYALAIRFLETTEFK 110 (156)
Q Consensus 84 i~AALrAcRRvND~alAVR~lE~iK~K 110 (156)
..+-+++|-|.+++..|+++|..++.+
T Consensus 3 ~n~li~~~~~~~~~~~a~~~~~~M~~~ 29 (35)
T TIGR00756 3 YNTLIDGLCKAGRVEEALELFKEMLER 29 (35)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 356788999999999999999998764
No 22
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=54.96 E-value=43 Score=22.31 Aligned_cols=43 Identities=12% Similarity=0.145 Sum_probs=32.1
Q ss_pred HHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhC
Q psy9569 90 AIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELG 134 (156)
Q Consensus 90 AcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 134 (156)
++-|++||..|.+.++.+=..=.+ +.|...+.+.|+--+..=|
T Consensus 10 g~ykl~~Y~~A~~~~~~lL~~eP~--N~Qa~~L~~~i~~~i~kdg 52 (53)
T PF14853_consen 10 GHYKLGEYEKARRYCDALLEIEPD--NRQAQSLKELIEDKIQKDG 52 (53)
T ss_dssp HHHHTT-HHHHHHHHHHHHHHTTS---HHHHHHHHHHHHHHHHTT
T ss_pred HHHHhhhHHHHHHHHHHHHhhCCC--cHHHHHHHHHHHHHHhccC
Confidence 567999999999999998765544 4788888888877665443
No 23
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=53.75 E-value=9.2 Score=26.41 Aligned_cols=34 Identities=29% Similarity=0.351 Sum_probs=22.3
Q ss_pred HHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCCcc
Q psy9569 102 RFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPA 139 (156)
Q Consensus 102 R~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~E 139 (156)
|=.|.-.+|.++. |+.++.-=...|+|+|||...
T Consensus 10 R~~~~~~~kf~~~----w~~lf~~~s~~LK~~GIp~r~ 43 (57)
T PF09597_consen 10 RGCEEHAEKFESD----WEKLFTTSSKQLKELGIPVRQ 43 (57)
T ss_pred ccHHHHHHHHHHH----HHHHHhcCHHHHHHCCCCHHH
Confidence 3344444555442 677777777889999997653
No 24
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=51.49 E-value=11 Score=28.56 Aligned_cols=35 Identities=17% Similarity=0.270 Sum_probs=28.7
Q ss_pred HHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCC
Q psy9569 102 RFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIET 137 (156)
Q Consensus 102 R~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 137 (156)
.+||.+-.++.+. +....|++.||-+.+...|++.
T Consensus 1 d~Fe~~~~~~~~~-k~~anwi~~el~~~l~~~~~~~ 35 (148)
T PF02637_consen 1 DYFEEVVKKGKNP-KLAANWILNELLGLLNKKGLDI 35 (148)
T ss_dssp HHHHHHHCHSS-H-HHHHHHHHTHHHHHHHHHT--T
T ss_pred CHHHHHHHhcCCH-HHHHHHHHHHHHHHHHHCCCCh
Confidence 4789999999775 7899999999999999999854
No 25
>PF00113 Enolase_C: Enolase, C-terminal TIM barrel domain; InterPro: IPR020810 Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [, ]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer []. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [] to be evolutionary related to enolase. Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.; GO: 0000287 magnesium ion binding, 0004634 phosphopyruvate hydratase activity, 0006096 glycolysis, 0000015 phosphopyruvate hydratase complex; PDB: 2FYM_D 3H8A_C 1E9I_D 3TQP_B 2PU1_A 1OEP_A 2PA6_A 1PDY_A 1PDZ_A 3UJ2_E ....
Probab=51.11 E-value=27 Score=30.60 Aligned_cols=69 Identities=25% Similarity=0.510 Sum_probs=46.6
Q ss_pred CCHHHHHHHHHHh------------hCCCCCcHHH-HHHHhh---hhhcCCC-CCCHHHHHHHHH--HHH----hhhhHH
Q psy9569 42 ESDEEFVKRYVAF------------FNQPDIDGWD-IRRGLM---NLAHDDC-VPDPEIIIAALK--AIR----RVNDYA 98 (156)
Q Consensus 42 Et~eeF~aRy~~~------------F~~~~iD~we-~rrglN---~l~~~Dl-VPeP~Ii~AALr--AcR----RvND~a 98 (156)
-|-+|+..-|.++ |+..|.++|. +.+.+. .+.|.|| |..|+.|..|+. +|- ++|.+.
T Consensus 133 ~s~delid~y~~li~~YPIvsIEDpf~edD~e~w~~lt~~~g~~~~iVGDDl~vTn~~ri~~~i~~~~~na~llK~NQig 212 (295)
T PF00113_consen 133 KSSDELIDYYKDLIKKYPIVSIEDPFDEDDWEGWAKLTKRLGDKIQIVGDDLFVTNPKRIKKGIEKKACNALLLKPNQIG 212 (295)
T ss_dssp EEHHHHHHHHHHHHHHS-EEEEESSS-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHHS
T ss_pred cCHHHHHHHHHHHHHhcCeEEEEccccccchHHHHHHHHhhhcceeeecccccccchhhhhccchhhhccchhhhhhhhH
Confidence 4677777777665 6666777773 555555 4678886 577999999865 665 889998
Q ss_pred HHHHHHHHhhhh
Q psy9569 99 LAIRFLETTEFK 110 (156)
Q Consensus 99 lAVR~lE~iK~K 110 (156)
|--..+|++|.-
T Consensus 213 Tvte~lea~~~a 224 (295)
T PF00113_consen 213 TVTETLEAVKLA 224 (295)
T ss_dssp SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 888888888753
No 26
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=50.73 E-value=21 Score=26.12 Aligned_cols=51 Identities=20% Similarity=0.238 Sum_probs=40.6
Q ss_pred CcHHH---HHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhc
Q psy9569 60 IDGWD---IRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKT 111 (156)
Q Consensus 60 iD~we---~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~ 111 (156)
++.|+ +|-|+..++-.|=+|...+|..|...|++..+ +.+.+|.-||=.+.
T Consensus 73 l~~~~~~iLria~~el~~~~~~p~~~vinEaV~lak~~~~-~~~~~fVNaVLr~i 126 (130)
T cd00619 73 LAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGG-DDSHKFVNGVLDKI 126 (130)
T ss_pred hhHHHHHHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCC-CcchhHHHHHHHHH
Confidence 45554 89999999988878999999999999998765 46677777775554
No 27
>TIGR01951 nusB transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.
Probab=49.78 E-value=21 Score=26.02 Aligned_cols=48 Identities=19% Similarity=0.137 Sum_probs=37.4
Q ss_pred HHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh
Q psy9569 62 GWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFK 110 (156)
Q Consensus 62 ~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K 110 (156)
..-+|-|+..++-+|=+|...+|..|...|++.++ +-+.+|.-||=.+
T Consensus 78 ~~iLr~a~~el~~~~~~p~~avineaV~lak~~~~-~~~~~fVNaVLr~ 125 (129)
T TIGR01951 78 RAILRLAAYELLYRPDVPYKVVINEAVELAKKFGD-EDSHKFVNGVLDK 125 (129)
T ss_pred HHHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCC-CCchhhHHHHHHH
Confidence 33489999999888558999999999999998754 3566777776554
No 28
>PF12192 CBP: Fungal calcium binding protein; InterPro: IPR022013 This domain is found in eukaryotes, and is approximately 60 amino acids in length. There is a single completely conserved residue C that may be functionally important. This is a calcium binding domain from the fungal protein CBP (calcium binding protein). This protein is a virulence factor with unknown virulence mechanisms. CBP complexes as a highly intertwined homodimer. Each monomer is comprised of four alpha helices which adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids. ; PDB: 2JV7_A.
Probab=48.80 E-value=29 Score=24.55 Aligned_cols=43 Identities=23% Similarity=0.520 Sum_probs=31.8
Q ss_pred hhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhh-------hHhhCCCCccc
Q psy9569 94 VNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPT-------LKELGIETPAQ 140 (156)
Q Consensus 94 vND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPt-------l~ELGI~t~Ee 140 (156)
+|+|-.+|+.|+..|.-.|=. |..-+.-|-+. +.|||++.|-+
T Consensus 8 ~~~~n~~v~~F~kak~AA~Cd----Wl~CissLa~~sAaCaAA~~Elgl~~~~d 57 (59)
T PF12192_consen 8 LDMYNNAVTVFTKAKSAAGCD----WLACISSLAASSAACAAALAELGLNPPAD 57 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHT--------HHHHHHTT--HHHHHHHHSSSSTTTTH
T ss_pred HHHHHHHHHHHHHHHhccCCC----hHHHHHHHhhhHHHHHHHHHHhCCCcccc
Confidence 688999999999999888765 77888888774 78888877654
No 29
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=48.55 E-value=51 Score=19.83 Aligned_cols=32 Identities=22% Similarity=0.147 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCC
Q psy9569 83 IIIAALKAIRRVNDYALAIRFLETTEFKTGGS 114 (156)
Q Consensus 83 Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~ 114 (156)
+.-.-=++-++.+++..|++.|+.+-....+.
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 33444567789999999999999998888776
No 30
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=48.15 E-value=70 Score=23.12 Aligned_cols=32 Identities=19% Similarity=0.200 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCC
Q psy9569 82 EIIIAALKAIRRVNDYALAIRFLETTEFKTGG 113 (156)
Q Consensus 82 ~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~ 113 (156)
.++.....++.+.+|+..|++.++..=..-.-
T Consensus 63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~ 94 (146)
T PF03704_consen 63 DALERLAEALLEAGDYEEALRLLQRALALDPY 94 (146)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCC
Confidence 34555555566667777777766655544433
No 31
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=48.07 E-value=20 Score=21.00 Aligned_cols=18 Identities=33% Similarity=0.597 Sum_probs=15.3
Q ss_pred HHHHhhhhHHHHHHHHHH
Q psy9569 89 KAIRRVNDYALAIRFLET 106 (156)
Q Consensus 89 rAcRRvND~alAVR~lE~ 106 (156)
+++++.|||..|+.++|.
T Consensus 7 ~~~~~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 7 RIYRQQGDYEKAIEYYEQ 24 (36)
T ss_dssp HHHHHCT-HHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHH
Confidence 578999999999999987
No 32
>KOG0991|consensus
Probab=47.68 E-value=45 Score=30.20 Aligned_cols=69 Identities=26% Similarity=0.358 Sum_probs=47.5
Q ss_pred CCCHHHHHHHHHHhhCCC--CC--cHH---------HHHHHhhhhh----cCCCC-----------CCHHHHHHHHHHHH
Q psy9569 41 EESDEEFVKRYVAFFNQP--DI--DGW---------DIRRGLMNLA----HDDCV-----------PDPEIIIAALKAIR 92 (156)
Q Consensus 41 ~Et~eeF~aRy~~~F~~~--~i--D~w---------e~rrglN~l~----~~DlV-----------PeP~Ii~AALrAcR 92 (156)
.-||.+.-+|-..--... .+ ||- +.|+++|||- |+-+| |.|+.|+..|++|-
T Consensus 171 klsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g~g~Vn~enVfKv~d~PhP~~v~~ml~~~~ 250 (333)
T KOG0991|consen 171 KLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNGFGLVNQENVFKVCDEPHPLLVKKMLQACL 250 (333)
T ss_pred ccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHHHHHHHhccccccchhhhhhccCCCChHHHHHHHHHHH
Confidence 477888888865432111 11 333 5799999985 34443 99999999999996
Q ss_pred hhhhHHHHHHHHHHhhhh
Q psy9569 93 RVNDYALAIRFLETTEFK 110 (156)
Q Consensus 93 RvND~alAVR~lE~iK~K 110 (156)
. +++..|..+|..+-+.
T Consensus 251 ~-~~~~~A~~il~~lw~l 267 (333)
T KOG0991|consen 251 K-RNIDEALKILAELWKL 267 (333)
T ss_pred h-ccHHHHHHHHHHHHHc
Confidence 4 5677888888776544
No 33
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=47.45 E-value=70 Score=29.64 Aligned_cols=62 Identities=10% Similarity=0.085 Sum_probs=47.9
Q ss_pred HHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCc-cchhHHHH
Q psy9569 62 GWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSH-DKIWPYIV 123 (156)
Q Consensus 62 ~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~-~~iY~~~l 123 (156)
+-+.-+-++.+....+.|......+-|.||-+.+++..|.++|+.++.+.|... ...|..++
T Consensus 407 ~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li 469 (697)
T PLN03081 407 GTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMI 469 (697)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHH
Confidence 335555666777788999999999999999999999999999999986544321 34566554
No 34
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=45.78 E-value=1.5e+02 Score=23.44 Aligned_cols=88 Identities=20% Similarity=0.278 Sum_probs=63.1
Q ss_pred CHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcC----CCCCCHHHHHHHHHHHHhhh-----------------hHHHH-
Q psy9569 43 SDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHD----DCVPDPEIIIAALKAIRRVN-----------------DYALA- 100 (156)
Q Consensus 43 t~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~----DlVPeP~Ii~AALrAcRRvN-----------------D~alA- 100 (156)
+-+||.+=|..+|+.. .|.=+.++|++.+... .-+|-.--..+.|=.|.-.+ -|++|
T Consensus 6 ~~~Ew~~V~~~l~s~~-~~~~~~~~al~~v~~W~~R~~~lP~aVe~Ta~Ll~~~l~d~~~~~~~~~~~~~~lr~~ysmai 84 (154)
T PF04031_consen 6 SWSEWLQVYQWLYSSQ-DDPESRRRALERVSAWKSRGSKLPHAVESTASLLEAQLQDEEDPSSSGARSEQELRLSYSMAI 84 (154)
T ss_pred cHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHccCccccccccCCCHHHHHHHHHHhH
Confidence 5689999999999864 4777888898877532 57887776777776665333 26666
Q ss_pred HHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCC
Q psy9569 101 IRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIET 137 (156)
Q Consensus 101 VR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 137 (156)
|||.-|+=|.+.++ .| -.-+.-.-+++|||+
T Consensus 85 vRfVNgl~D~~Q~~---~~---a~si~~~A~~iglP~ 115 (154)
T PF04031_consen 85 VRFVNGLVDPSQQG---KY---ARSIASLAKEIGLPS 115 (154)
T ss_pred HHHHHHhhhHhhcc---ch---hhhHHHHHHHcCCCH
Confidence 69999998887543 22 256667778899973
No 35
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=42.77 E-value=29 Score=20.80 Aligned_cols=23 Identities=26% Similarity=0.284 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHH
Q psy9569 80 DPEIIIAALKAIRRVNDYALAIRFL 104 (156)
Q Consensus 80 eP~Ii~AALrAcRRvND~alAVR~l 104 (156)
+...+..||++|.- |...||.+|
T Consensus 15 ~~~~~~~AL~~~~~--nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNG--NVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTT--SHHHHHHHH
T ss_pred CHHHHHHHHHHcCC--CHHHHHHhC
Confidence 45678888888875 999998876
No 36
>cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions.
Probab=42.76 E-value=26 Score=30.48 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=25.8
Q ss_pred hhHHHHHhhhhhhHhhCCCCccccCCCCcc
Q psy9569 118 IWPYIVQEITPTLKELGIETPAQLGYDKPE 147 (156)
Q Consensus 118 iY~~~lqElkPtl~ELGI~t~EeLgydkpe 147 (156)
.=...+++|+-.+++||+|+..|+|.++.+
T Consensus 311 ~~~~~~~~i~~l~~~~glP~L~~~gv~~~~ 340 (375)
T cd08194 311 AAEKLIEALKELNRELEVPTLREYGIDKDA 340 (375)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHhcCCChHh
Confidence 345778999999999999999999998765
No 37
>cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene.
Probab=41.71 E-value=33 Score=29.77 Aligned_cols=32 Identities=16% Similarity=0.353 Sum_probs=25.6
Q ss_pred chhHHHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 117 KIWPYIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
+.-+..++.|+..+++||+|+ ..|+|.++.++
T Consensus 313 ~~~~~~~~~~~~l~~~lglp~~L~e~gi~~~~~ 345 (376)
T cd08193 313 EAAEALIDAMEALVADLGIPQRLREVGVTEDDL 345 (376)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 345678899999999999984 78999876554
No 38
>TIGR02252 DREG-2 REG-2-like, HAD superfamily (subfamily IA) hydrolase. Most likely, these sequences, like the vast majority of HAD sequences, represent phosphatase enzymes.
Probab=41.40 E-value=1.4e+02 Score=22.69 Aligned_cols=65 Identities=26% Similarity=0.414 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHh-hh------hHHHHHHHHHHhhhh---cCCCccchhHHHHHhhhhhhHhhCCC-------Cccc
Q psy9569 78 VPDPEIIIAALKAIRR-VN------DYALAIRFLETTEFK---TGGSHDKIWPYIVQEITPTLKELGIE-------TPAQ 140 (156)
Q Consensus 78 VPeP~Ii~AALrAcRR-vN------D~alAVR~lE~iK~K---~~~~~~~iY~~~lqElkPtl~ELGI~-------t~Ee 140 (156)
+|++.-+...+..+.+ +. =|+-+..+|+.+|.+ ++--.+ ... .++..++.+|+. +-++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~~L~~~g~~~~i~Sn-~~~----~~~~~l~~~~l~~~fd~i~~s~~ 155 (203)
T TIGR02252 81 VPDPESFEKIFEELYSYFATPEPWQVYPDAIKLLKDLRERGLILGVISN-FDS----RLRGLLEALGLLEYFDFVVTSYE 155 (203)
T ss_pred CCCchhHHHHHHHHHHHhcCCCcceeCcCHHHHHHHHHHCCCEEEEEeC-Cch----hHHHHHHHCCcHHhcceEEeecc
Confidence 4666666655555443 11 156678888888864 221111 111 234567777763 3456
Q ss_pred cCCCCcc
Q psy9569 141 LGYDKPE 147 (156)
Q Consensus 141 Lgydkpe 147 (156)
.|..||.
T Consensus 156 ~~~~KP~ 162 (203)
T TIGR02252 156 VGAEKPD 162 (203)
T ss_pred cCCCCCC
Confidence 7888876
No 39
>COG3325 ChiA Chitinase [Carbohydrate transport and metabolism]
Probab=41.23 E-value=11 Score=35.27 Aligned_cols=22 Identities=23% Similarity=0.462 Sum_probs=19.0
Q ss_pred cchhHHHHHhhhhhhHhhCCCC
Q psy9569 116 DKIWPYIVQEITPTLKELGIET 137 (156)
Q Consensus 116 ~~iY~~~lqElkPtl~ELGI~t 137 (156)
+.-|--+|||||--|++.|...
T Consensus 193 ~~ny~~Ll~eLR~~LD~a~~ed 214 (441)
T COG3325 193 KANYVLLLQELRKKLDKAGVED 214 (441)
T ss_pred HHHHHHHHHHHHHHHhhccccc
Confidence 4679999999999999999865
No 40
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=40.49 E-value=98 Score=28.70 Aligned_cols=70 Identities=17% Similarity=0.144 Sum_probs=48.9
Q ss_pred HHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHH------------HhhhhhhHhh
Q psy9569 66 RRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIV------------QEITPTLKEL 133 (156)
Q Consensus 66 rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~l------------qElkPtl~EL 133 (156)
..+++-+-.+-..|...+..+-|.||+..+++..|.+++|.+... ++.....|-.++ .++.-.|.+-
T Consensus 479 ~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~-~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~ 557 (697)
T PLN03081 479 DEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGM-GPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRK 557 (697)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCC-CCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 334444445667899999999999999999999999999987543 332133454443 3456667777
Q ss_pred CCC
Q psy9569 134 GIE 136 (156)
Q Consensus 134 GI~ 136 (156)
|+.
T Consensus 558 g~~ 560 (697)
T PLN03081 558 GLS 560 (697)
T ss_pred CCc
Confidence 875
No 41
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=40.41 E-value=41 Score=27.64 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHHHhhCCC
Q psy9569 39 AVEESDEEFVKRYVAFFNQP 58 (156)
Q Consensus 39 h~~Et~eeF~aRy~~~F~~~ 58 (156)
+..|+|.+|..|..+-..+.
T Consensus 131 Gp~Epf~dFv~rl~~a~~~~ 150 (206)
T PF00607_consen 131 GPKEPFADFVDRLQKAIRRE 150 (206)
T ss_dssp -TTSHHHHHHHHHHHHHHCS
T ss_pred ccccchHHHHHHHHHHHhhc
Confidence 46799999999999888775
No 42
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=40.22 E-value=44 Score=26.22 Aligned_cols=39 Identities=15% Similarity=0.317 Sum_probs=25.5
Q ss_pred HHHHHhhhhcCCCccchhHHHHH-hhhhhhHhhCCCCcccc
Q psy9569 102 RFLETTEFKTGGSHDKIWPYIVQ-EITPTLKELGIETPAQL 141 (156)
Q Consensus 102 R~lE~iK~K~~~~~~~iY~~~lq-ElkPtl~ELGI~t~EeL 141 (156)
...+.++.++...... -..+++ -+.-.|.-|||||.+|+
T Consensus 72 ~~~~~~~~~~~~~~dk-lE~~fd~rV~~aL~rLgvPs~~dv 111 (132)
T PF05597_consen 72 SRVDDVKERATGQWDK-LEQAFDERVARALNRLGVPSRKDV 111 (132)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCCCHHHH
Confidence 3556667776554222 223333 48899999999999876
No 43
>cd08191 HHD 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. 6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental pollutant. The degradation of these chemical compounds are through the cyclohexanol and cyclohexanone biological oxidation pathway. The intermediates of this pathway include cyclohexanol, cyclohexanone, e-caprolactone, 6-hydroxyhexanoate, 6-oxohexanoate and adipate. The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.
Probab=40.21 E-value=33 Score=29.98 Aligned_cols=32 Identities=25% Similarity=0.367 Sum_probs=25.2
Q ss_pred chhHHHHHhhhhhhHhhCCC-CccccCCCCccc
Q psy9569 117 KIWPYIVQEITPTLKELGIE-TPAQLGYDKPEL 148 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~-t~EeLgydkpel 148 (156)
+.-...+++|+..+++||+| +..|+|.++.++
T Consensus 324 ~~~~~~~~~l~~l~~~lglP~~L~e~gv~~~~~ 356 (386)
T cd08191 324 EQAAAAITRVEALLAAIGIPTTLAALGVTEADL 356 (386)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 34456789999999999999 478999876443
No 44
>PLN03218 maturation of RBCL 1; Provisional
Probab=39.12 E-value=96 Score=31.66 Aligned_cols=43 Identities=9% Similarity=0.018 Sum_probs=22.5
Q ss_pred HHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhh
Q psy9569 67 RGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEF 109 (156)
Q Consensus 67 rglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~ 109 (156)
+-++.+...++.|......+.+.+|.|.+++..|+++|+.++.
T Consensus 493 ~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~ 535 (1060)
T PLN03218 493 EVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRS 535 (1060)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3334444444555555555555555555555555555555543
No 45
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=37.97 E-value=1.1e+02 Score=27.28 Aligned_cols=52 Identities=12% Similarity=0.149 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhhCCC--CCcHHH---HHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhh
Q psy9569 44 DEEFVKRYVAFFNQP--DIDGWD---IRRGLMNLAHDDCVPDPEIIIAALKAIRRVND 96 (156)
Q Consensus 44 ~eeF~aRy~~~F~~~--~iD~we---~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND 96 (156)
....|.--.++..++ .++.++ +|-|.-.++-+| ||...+|..|.+.|++.++
T Consensus 52 ~~~lD~~i~~~~~~~~~~l~~~~r~iLrla~yell~~~-iP~~a~vneaVelak~~~~ 108 (427)
T PRK10901 52 LPRLEWLIAQLLAKPLKGKQRIVHALLLVGLYQLLYTR-IPAHAAVDETVEAAKALKR 108 (427)
T ss_pred HHHHHHHHHHHhCCCccccCHHHHHHHHHHHHHHhccC-CCcchHHHHHHHHHHhcCC
Confidence 344455445555432 455555 899999999899 9999999999999998765
No 46
>PLN03077 Protein ECB2; Provisional
Probab=37.57 E-value=1.1e+02 Score=29.14 Aligned_cols=72 Identities=17% Similarity=0.161 Sum_probs=52.3
Q ss_pred HHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCC-ccchhHHHH---------HhhhhhhHhh
Q psy9569 64 DIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGS-HDKIWPYIV---------QEITPTLKEL 133 (156)
Q Consensus 64 e~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~-~~~iY~~~l---------qElkPtl~EL 133 (156)
+..+-++......+.|+.....+.|.||-+-+++..|.++|+.++.+-|-. ..+.|..++ +|-.-+++++
T Consensus 572 ~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m 651 (857)
T PLN03077 572 MAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651 (857)
T ss_pred HHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHC
Confidence 344555666677899999999999999999999999999999998554422 135676665 4444555555
Q ss_pred CC
Q psy9569 134 GI 135 (156)
Q Consensus 134 GI 135 (156)
++
T Consensus 652 ~~ 653 (857)
T PLN03077 652 PI 653 (857)
T ss_pred CC
Confidence 43
No 47
>cd08171 GlyDH-like2 Glycerol dehydrogenase-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=37.07 E-value=19 Score=30.88 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=23.9
Q ss_pred HHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 121 YIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 121 ~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
..+++|+..+++||+|+ ..++|.++.++
T Consensus 285 ~~i~~i~~l~~~lglP~~L~~~gv~~~~l 313 (345)
T cd08171 285 EELERIYPFNKSIGLPVCLEDLGLTEDDL 313 (345)
T ss_pred HHHHHHHHHHHHcCCCCcHHHcCCCHHHH
Confidence 56899999999999994 89999987655
No 48
>KOG0036|consensus
Probab=36.40 E-value=1.6e+02 Score=28.08 Aligned_cols=90 Identities=32% Similarity=0.450 Sum_probs=63.2
Q ss_pred CCCHHHHHHHHHHhhCCCC------CcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHH-----hhhhHHHHH--------
Q psy9569 41 EESDEEFVKRYVAFFNQPD------IDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIR-----RVNDYALAI-------- 101 (156)
Q Consensus 41 ~Et~eeF~aRy~~~F~~~~------iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcR-----RvND~alAV-------- 101 (156)
-||++|=+.||..-|+.-| +|.=+|.+|+..|-.- -|.++...-=+++|- || ||..=.
T Consensus 6 ~~~~~er~~r~~~lf~~lD~~~~g~~d~~~l~k~~~~l~~~--~~~~~~~~~l~~~~d~~~dg~v-Dy~eF~~Y~~~~E~ 82 (463)
T KOG0036|consen 6 RETDEERDIRIRCLFKELDSKNDGQVDLDQLEKGLEKLDHP--KPNYEAAKMLFSAMDANRDGRV-DYSEFKRYLDNKEL 82 (463)
T ss_pred cCCcHHHHHHHHHHHHHhccCCCCceeHHHHHHHHHhcCCC--CCchHHHHHHHHhcccCcCCcc-cHHHHHHHHHHhHH
Confidence 5899999999998775433 4677899998776554 588888888888885 22 343333
Q ss_pred ---HHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCCcc
Q psy9569 102 ---RFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPA 139 (156)
Q Consensus 102 ---R~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~E 139 (156)
|+|-.|..+-..+ | -++||.+-|.+|||+..+
T Consensus 83 ~l~~~F~~iD~~hdG~---i---~~~Ei~~~l~~~gi~l~d 117 (463)
T KOG0036|consen 83 ELYRIFQSIDLEHDGK---I---DPNEIWRYLKDLGIQLSD 117 (463)
T ss_pred HHHHHHhhhccccCCc---c---CHHHHHHHHHHhCCccCH
Confidence 4555555544443 2 378999999999998554
No 49
>KOG3103|consensus
Probab=35.07 E-value=17 Score=31.91 Aligned_cols=10 Identities=60% Similarity=1.022 Sum_probs=9.3
Q ss_pred hhhhHhhCCC
Q psy9569 127 TPTLKELGIE 136 (156)
Q Consensus 127 kPtl~ELGI~ 136 (156)
+|+||||||+
T Consensus 82 pPLLEELgIn 91 (249)
T KOG3103|consen 82 PPLLEELGIN 91 (249)
T ss_pred CchHHHhCCC
Confidence 7999999997
No 50
>COG3189 Uncharacterized conserved protein [Function unknown]
Probab=34.77 E-value=36 Score=26.90 Aligned_cols=38 Identities=26% Similarity=0.206 Sum_probs=29.2
Q ss_pred cccCCCCCCCHHHHHHHHHHhhCCCC-CcHHHHHHHhhh
Q psy9569 34 RSFSHAVEESDEEFVKRYVAFFNQPD-IDGWDIRRGLMN 71 (156)
Q Consensus 34 r~~s~h~~Et~eeF~aRy~~~F~~~~-iD~we~rrglN~ 71 (156)
|.--+|..+-+.+|..||.+..+..+ .++++++..++.
T Consensus 52 Rkwf~Hdp~~w~~F~~rY~~EL~~~~~~~l~~L~~~~~~ 90 (117)
T COG3189 52 RKWFHHDPKKWDEFRERYRAELNAQDAQALEDLLDIASH 90 (117)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHhcccHHHHHHHHHHHcC
Confidence 55456778999999999999996543 358888887754
No 51
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=34.57 E-value=35 Score=24.82 Aligned_cols=27 Identities=19% Similarity=0.374 Sum_probs=20.4
Q ss_pred hcCCCccchhHHHHHhhh------hhhHhhCCC
Q psy9569 110 KTGGSHDKIWPYIVQEIT------PTLKELGIE 136 (156)
Q Consensus 110 K~~~~~~~iY~~~lqElk------Ptl~ELGI~ 136 (156)
-||..+..-|..|++-++ -+|++|||.
T Consensus 9 TCGkvig~~we~y~~~~~~g~~~~~~LD~LG~~ 41 (71)
T PLN00032 9 TCGKVIGNKWDTYLDLLQADYSEGDALDALGLV 41 (71)
T ss_pred CCCCCcHHHHHHHHHHHhcCCCHHHHHHHhCch
Confidence 477766677888888774 589999984
No 52
>smart00147 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases.
Probab=34.54 E-value=49 Score=26.57 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=19.6
Q ss_pred HHHHHhhhhHHHHHHHHHHhhhhc
Q psy9569 88 LKAIRRVNDYALAIRFLETTEFKT 111 (156)
Q Consensus 88 LrAcRRvND~alAVR~lE~iK~K~ 111 (156)
-..|+.+|||..+.-|+-|+..-+
T Consensus 85 a~~l~~l~Nfns~~aI~~~L~~~~ 108 (242)
T smart00147 85 AKHCRELNNFNSLMAIVSALSSSP 108 (242)
T ss_pred HHHHHHhCCHHHHHHHHHHhCChH
Confidence 367889999999999998886533
No 53
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=34.15 E-value=37 Score=24.07 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=19.1
Q ss_pred hcCCCccchhHHHHHhhh------hhhHhhCCC
Q psy9569 110 KTGGSHDKIWPYIVQEIT------PTLKELGIE 136 (156)
Q Consensus 110 K~~~~~~~iY~~~lqElk------Ptl~ELGI~ 136 (156)
-||....+.|..|.+-++ -+|++||+.
T Consensus 9 TCGkvi~~~we~y~~~~~~g~~~~~vLd~Lg~~ 41 (62)
T PRK04016 9 TCGKVIAEKWEEFKERVEAGEDPGKVLDDLGVK 41 (62)
T ss_pred CCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCc
Confidence 366666666777766663 689999985
No 54
>PLN03218 maturation of RBCL 1; Provisional
Probab=33.78 E-value=1.4e+02 Score=30.50 Aligned_cols=64 Identities=13% Similarity=0.011 Sum_probs=44.9
Q ss_pred cHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHH
Q psy9569 61 DGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQ 124 (156)
Q Consensus 61 D~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lq 124 (156)
+..+..+-++.+....+.|......+-|.+|-+.+++..|..+++.++.+.-.....+|..++.
T Consensus 734 ~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIg 797 (1060)
T PLN03218 734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITG 797 (1060)
T ss_pred CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 3345555666666778888888888888888888888888888888765533332345666653
No 55
>TIGR01428 HAD_type_II 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.
Probab=33.53 E-value=2.1e+02 Score=21.63 Aligned_cols=83 Identities=16% Similarity=0.075 Sum_probs=44.1
Q ss_pred cHHHHH-HHhhhhhc-CCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh---cCCCccchhHHHHHhhhhhhHhhCC
Q psy9569 61 DGWDIR-RGLMNLAH-DDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFK---TGGSHDKIWPYIVQEITPTLKELGI 135 (156)
Q Consensus 61 D~we~r-rglN~l~~-~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K---~~~~~~~iY~~~lqElkPtl~ELGI 135 (156)
+.|++. ..++.++. +.+-+++..++....+..++.=++-+..+|+.+|.+ ++--.+... ..++..++.+||
T Consensus 56 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~g~~~~i~Sn~~~----~~~~~~l~~~gl 131 (198)
T TIGR01428 56 DFWDLTREALRYLLGRLGLEDDESAADRLAEAYLRLPPHPDVPAGLRALKERGYRLAILSNGSP----AMLKSLVKHAGL 131 (198)
T ss_pred CHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHCCCeEEEEeCCCH----HHHHHHHHHCCC
Confidence 445543 33443332 222245555555555555566677888889999876 221111111 223344566665
Q ss_pred C-------CccccCCCCcc
Q psy9569 136 E-------TPAQLGYDKPE 147 (156)
Q Consensus 136 ~-------t~EeLgydkpe 147 (156)
. +-++.|.-||.
T Consensus 132 ~~~fd~i~~s~~~~~~KP~ 150 (198)
T TIGR01428 132 DDPFDAVLSADAVRAYKPA 150 (198)
T ss_pred hhhhheeEehhhcCCCCCC
Confidence 3 45677888875
No 56
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=33.26 E-value=47 Score=24.73 Aligned_cols=48 Identities=23% Similarity=0.234 Sum_probs=35.9
Q ss_pred HHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhc
Q psy9569 63 WDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKT 111 (156)
Q Consensus 63 we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~ 111 (156)
.-||-|+..+.-.|=+|...||..|.+.|++..+ +-+.+|.-||=.++
T Consensus 81 ~iLr~a~~Ell~~~~~p~~~vinEaV~lak~~~~-~~~~~fVNaVLr~i 128 (137)
T PRK00202 81 AILRLALYELLFRDDVPYKVVINEAIELAKKFGD-EDSHKFVNGVLDKI 128 (137)
T ss_pred HHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCC-CCcchhHHHHHHHH
Confidence 3588899999888558999999999999997644 34556666555443
No 57
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=33.23 E-value=60 Score=24.20 Aligned_cols=52 Identities=29% Similarity=0.510 Sum_probs=32.1
Q ss_pred CcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhC
Q psy9569 60 IDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELG 134 (156)
Q Consensus 60 iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 134 (156)
...|-++-=++.|+. |+++|+.+|++. | -+-|..+ -|-.++=.++|.|+-||
T Consensus 5 f~~w~i~lLv~QL~D----~~~~V~~~A~~i-------------L---~e~c~~~---~~le~~v~~~p~l~~L~ 56 (115)
T PF14663_consen 5 FEDWGIELLVTQLYD----PSPEVVAAALEI-------------L---EEACEDK---EYLEYLVSLRPSLDHLG 56 (115)
T ss_pred HHHHHHHHHHHHhcC----CCHHHHHHHHHH-------------H---HHHHhch---hhHHHHHHcCcHHHHHH
Confidence 445777666666643 667998877654 2 2334333 35555566788888776
No 58
>PF04336 DUF479: Protein of unknown function, DUF479; InterPro: IPR007431 This entry contains the Escherichia coli gene yajB, now renamed acpH, which encodes an ACP hydrolase. AcpH converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP []. A mutant E. coli strain having a total deletion of the acpH grows normally, showing that phosphodiesterase activity is not essential for growth, although it is required for turnover of the ACP prosthetic group in vivo. AcpH is found only in Gram-negative organisms suggesting that it plays a role in some aspect of lipid metabolism that is unique to these organisms. The most obvious of which is biosynthesis of lipid A. Because AcpH is a hydrolase, it could possibly be an editing enzyme that intercepts acyl-ACPs that would give an inappropriate lipid A structure if used as acyl donors []. ; GO: 0008770 [acyl-carrier-protein] phosphodiesterase activity, 0006633 fatty acid biosynthetic process
Probab=32.83 E-value=49 Score=24.23 Aligned_cols=84 Identities=24% Similarity=0.221 Sum_probs=57.4
Q ss_pred CCCCHHHHHHHHHHhhCCC-CCcHHHHHHHhhhhhcCCCCC---CHHHHHHHHH----HHHhhhhHHHHHHHHHHhhhhc
Q psy9569 40 VEESDEEFVKRYVAFFNQP-DIDGWDIRRGLMNLAHDDCVP---DPEIIIAALK----AIRRVNDYALAIRFLETTEFKT 111 (156)
Q Consensus 40 ~~Et~eeF~aRy~~~F~~~-~iD~we~rrglN~l~~~DlVP---eP~Ii~AALr----AcRRvND~alAVR~lE~iK~K~ 111 (156)
+.++-++|.++.-.-.+.- .+=-=.+++-+..+..+|+.. +.+-|+.||. -.+|.|+++.|+..|+.-.+..
T Consensus 13 s~~~L~~f~~~~Y~~L~~~~~~lP~~~~~~~~~m~~~dWL~~Y~~~egi~~al~~m~~R~~~~~~l~~a~~~l~~~y~~l 92 (106)
T PF04336_consen 13 SDQPLEDFAQRFYQQLEANQPILPPRFQRMLPYMIEHDWLSSYRTLEGIERALQRMSRRLRRPNPLAGAIEELEEHYAEL 92 (106)
T ss_pred CcCCHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHhCHHHHcCCHHHHHHHHHHHHhccCchhhHHHHHHHHHHHHHHH
Confidence 4578888888876666542 111225677777888888775 4666776664 3457899999999999887777
Q ss_pred CCCccchhHHHH
Q psy9569 112 GGSHDKIWPYIV 123 (156)
Q Consensus 112 ~~~~~~iY~~~l 123 (156)
+..-.+.||.++
T Consensus 93 e~~F~~FfpdL~ 104 (106)
T PF04336_consen 93 EQDFLEFFPDLQ 104 (106)
T ss_pred HHHHHHHHHHHH
Confidence 665455666554
No 59
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=32.81 E-value=34 Score=20.75 Aligned_cols=17 Identities=41% Similarity=0.581 Sum_probs=13.9
Q ss_pred HHHhhhhhhHhhCCCCc
Q psy9569 122 IVQEITPTLKELGIETP 138 (156)
Q Consensus 122 ~lqElkPtl~ELGI~t~ 138 (156)
-+.|||-.+.++|+++-
T Consensus 5 ~v~eLk~~l~~~gL~~~ 21 (35)
T PF02037_consen 5 TVAELKEELKERGLSTS 21 (35)
T ss_dssp HHHHHHHHHHHTTS-ST
T ss_pred cHHHHHHHHHHCCCCCC
Confidence 47899999999999874
No 60
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=32.79 E-value=98 Score=23.15 Aligned_cols=45 Identities=27% Similarity=0.285 Sum_probs=28.5
Q ss_pred hhhhhcCCCCCCHHHHHHHH-------HHHHhhhhHHHHHHHHHHhhhhcCCC
Q psy9569 69 LMNLAHDDCVPDPEIIIAAL-------KAIRRVNDYALAIRFLETTEFKTGGS 114 (156)
Q Consensus 69 lN~l~~~DlVPeP~Ii~AAL-------rAcRRvND~alAVR~lE~iK~K~~~~ 114 (156)
|=.-|++.=+|.++-|=+-| .|+.-++++. |+|||..+|...++.
T Consensus 35 LleWFnf~~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG-~~~fL~klr~~~~~~ 86 (98)
T PF14726_consen 35 LLEWFNFPPVPMKEEVLALLLRLLKSPYAAQILRDIG-AVRFLSKLRPNVEPN 86 (98)
T ss_pred HHHHhCCCCCccHHHHHHHHHHHHhCcHHHHHHHHcc-HHHHHHHHHhcCCHH
Confidence 33345555566665443333 3667777775 788999999777775
No 61
>PF13925 Katanin_con80: con80 domain of Katanin
Probab=32.05 E-value=96 Score=24.38 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHhh--hhcCC
Q psy9569 84 IIAALKAIRRVNDYALAIRFLETTE--FKTGG 113 (156)
Q Consensus 84 i~AALrAcRRvND~alAVR~lE~iK--~K~~~ 113 (156)
+.+|+.+++|+||.+..+-+|-.+. .|-+.
T Consensus 30 ~k~ai~~~~~~~D~svlvD~L~vl~~~~~~~~ 61 (164)
T PF13925_consen 30 IKGAIEYAVRMNDPSVLVDVLSVLNQSLKPEK 61 (164)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHhcCcCc
Confidence 4678888889999998888888887 55443
No 62
>PF15469 Sec5: Exocyst complex component Sec5
Probab=32.02 E-value=79 Score=24.59 Aligned_cols=50 Identities=14% Similarity=0.165 Sum_probs=35.6
Q ss_pred HHHHHHHhhhhHHHHHHHHHHhhhhcCCC--ccchhHHHHHhhhhhhHhhCC
Q psy9569 86 AALKAIRRVNDYALAIRFLETTEFKTGGS--HDKIWPYIVQEITPTLKELGI 135 (156)
Q Consensus 86 AALrAcRRvND~alAVR~lE~iK~K~~~~--~~~iY~~~lqElkPtl~ELGI 135 (156)
.-|+.|=.-|||..||+-....|.-.+.. ...++..+.+|+..+++++=-
T Consensus 91 ~~L~~~i~~~dy~~~i~dY~kak~l~~~~~~~~~vf~~v~~eve~ii~~~r~ 142 (182)
T PF15469_consen 91 SNLRECIKKGDYDQAINDYKKAKSLFEKYKQQVPVFQKVWSEVEKIIEEFRE 142 (182)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 45566666788888888887777666554 356888888888877776543
No 63
>PLN03077 Protein ECB2; Provisional
Probab=29.65 E-value=3e+02 Score=26.28 Aligned_cols=71 Identities=17% Similarity=0.143 Sum_probs=47.8
Q ss_pred HHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHH------------HHhhhhhhHh
Q psy9569 65 IRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYI------------VQEITPTLKE 132 (156)
Q Consensus 65 ~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~------------lqElkPtl~E 132 (156)
+.++.+-+-.|.+-|++.+..+-|.|||.-++..+|-+..+.+-.- ++.....|--+ ..+++-.|++
T Consensus 641 ~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l-~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~ 719 (857)
T PLN03077 641 LTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFEL-DPNSVGYYILLCNLYADAGKWDEVARVRKTMRE 719 (857)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhh-CCCCcchHHHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3444444455678899999999999999989998888777666533 33312333322 2477788888
Q ss_pred hCCC
Q psy9569 133 LGIE 136 (156)
Q Consensus 133 LGI~ 136 (156)
-|+.
T Consensus 720 ~g~~ 723 (857)
T PLN03077 720 NGLT 723 (857)
T ss_pred cCCC
Confidence 8875
No 64
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=29.57 E-value=60 Score=22.81 Aligned_cols=27 Identities=19% Similarity=0.474 Sum_probs=18.8
Q ss_pred hcCCCccchhHHHHHhh------hhhhHhhCCC
Q psy9569 110 KTGGSHDKIWPYIVQEI------TPTLKELGIE 136 (156)
Q Consensus 110 K~~~~~~~iY~~~lqEl------kPtl~ELGI~ 136 (156)
-||..+..-|+.|++.+ +.+|++||+.
T Consensus 9 TCGkvi~~~~e~y~~~~~~~~~~~~~Ld~LG~~ 41 (60)
T PF01194_consen 9 TCGKVIGNKWEEYLERLENGEDPGDALDDLGLK 41 (60)
T ss_dssp TTTSBTCGHHHHHHHHHHTTS-HHHHHHHTT-S
T ss_pred CCCCChhHhHHHHHHHHHcCCCHHHHHHHhCCc
Confidence 36766667788888777 3578888874
No 65
>PRK10015 oxidoreductase; Provisional
Probab=29.44 E-value=2.1e+02 Score=25.38 Aligned_cols=56 Identities=9% Similarity=0.084 Sum_probs=41.1
Q ss_pred HhhCCCCCc---HHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhh
Q psy9569 53 AFFNQPDID---GWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTE 108 (156)
Q Consensus 53 ~~F~~~~iD---~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK 108 (156)
.+|.++.+- ..-+...|+++|..|-.|.+.+....+++.++..-+.++--.+.++|
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 427 (429)
T PRK10015 369 ALMENPRLFSQYPRMVADIMNDMFTIDGKPNQPVRKMIMGHAKKIGLINLLKDGIKGAT 427 (429)
T ss_pred hhhcCccHHHHHHHHHHHHHHHhcccCCccchHHHHHHHHHHHhccHHHHHHHHHHHHh
Confidence 445555331 24577889999999999999999999999987776666655555554
No 66
>PF12854 PPR_1: PPR repeat
Probab=29.04 E-value=1.3e+02 Score=17.63 Aligned_cols=32 Identities=13% Similarity=0.241 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHh
Q psy9569 76 DCVPDPEIIIAALKAIRRVNDYALAIRFLETT 107 (156)
Q Consensus 76 DlVPeP~Ii~AALrAcRRvND~alAVR~lE~i 107 (156)
.+.|.......-+.+.=|.+++..|.++|+..
T Consensus 2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence 35788888888999999999999999999864
No 67
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=28.25 E-value=84 Score=22.72 Aligned_cols=51 Identities=24% Similarity=0.206 Sum_probs=36.3
Q ss_pred CCcHHHHHHHhhhhhcCC-CCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh
Q psy9569 59 DIDGWDIRRGLMNLAHDD-CVPDPEIIIAALKAIRRVNDYALAIRFLETTEFK 110 (156)
Q Consensus 59 ~iD~we~rrglN~l~~~D-lVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K 110 (156)
.+|.|-++-++-.+.... =+|.+.+|..|...|++..+- .+-+|.-||=.+
T Consensus 73 ~~~~~il~l~~~el~~~~~~~p~~~vineaVelak~~~~~-~~~~fVNaVLr~ 124 (129)
T cd00447 73 KVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDD-DSAKFVNGVLRR 124 (129)
T ss_pred HHHHHHHHHHHHHHHhCcCCCCchhHHHHHHHHHHHHCCC-CcchhHHHHHHH
Confidence 467888777777776654 369999999999999987542 345566555444
No 68
>cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to
Probab=28.20 E-value=34 Score=29.75 Aligned_cols=30 Identities=13% Similarity=0.286 Sum_probs=24.4
Q ss_pred hHHHHHhhhhhhHhhCCC-CccccCCCCccc
Q psy9569 119 WPYIVQEITPTLKELGIE-TPAQLGYDKPEL 148 (156)
Q Consensus 119 Y~~~lqElkPtl~ELGI~-t~EeLgydkpel 148 (156)
=+..++.|+..+++||+| +..|+|+++.++
T Consensus 317 ~~~~~~~i~~l~~~lglP~~L~e~gv~~~~~ 347 (377)
T cd08176 317 AEAAIDAVRALSEDVGIPAGLRELGVKEEDF 347 (377)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 345788999999999998 578999987654
No 69
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid []. These proteins may form part of a dioxygenase complex.; PDB: 3PWQ_K 3PVT_B 1OTK_B 3PW1_B 3PW8_B 3PVR_B 3PVY_B 3Q1G_A 3PF7_B 3PM5_C ....
Probab=28.08 E-value=37 Score=28.99 Aligned_cols=24 Identities=29% Similarity=0.631 Sum_probs=18.8
Q ss_pred cchhHHHHHhhhhhhHhhCCCCcc
Q psy9569 116 DKIWPYIVQEITPTLKELGIETPA 139 (156)
Q Consensus 116 ~~iY~~~lqElkPtl~ELGI~t~E 139 (156)
.+..+..+++++|+++++|+..|+
T Consensus 204 ~~lr~~w~~~v~~~l~~~gL~~P~ 227 (263)
T PF05138_consen 204 EELRQRWLAEVVPVLEEAGLEVPE 227 (263)
T ss_dssp HHHHHHHHHHHHHHHHHTT---S-
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCC
Confidence 478999999999999999999999
No 70
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=27.91 E-value=1.8e+02 Score=22.05 Aligned_cols=50 Identities=20% Similarity=0.312 Sum_probs=37.6
Q ss_pred HhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHh---hhhHHHHHHHHHHh
Q psy9569 53 AFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRR---VNDYALAIRFLETT 107 (156)
Q Consensus 53 ~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRR---vND~alAVR~lE~i 107 (156)
.|-+..+.-.-||++-|..- |+ +|.+|+.+|.-+.. +||...|-.++..-
T Consensus 19 ~~L~~r~~s~~el~~kL~~k-g~----~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~ 71 (157)
T PRK00117 19 RLLARREHSRAELRRKLAAK-GF----SEEVIEAVLDRLKEEGLLDDERFAESFVRSR 71 (157)
T ss_pred HHHccchhHHHHHHHHHHhc-CC----CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 34444445567888887765 44 47999999999988 99998888888775
No 71
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=27.80 E-value=56 Score=21.50 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=10.2
Q ss_pred CHHHHHHHHHHHHh
Q psy9569 80 DPEIIIAALKAIRR 93 (156)
Q Consensus 80 eP~Ii~AALrAcRR 93 (156)
+|++|..|++-|-+
T Consensus 31 ~~~~v~~ai~~~~~ 44 (77)
T PF07261_consen 31 SPEVVNEAIEYALE 44 (77)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHH
Confidence 57788888877764
No 72
>PRK01611 argS arginyl-tRNA synthetase; Reviewed
Probab=27.55 E-value=1.6e+02 Score=26.96 Aligned_cols=60 Identities=20% Similarity=0.262 Sum_probs=37.3
Q ss_pred HHHHHHHHH------HHHhhhhHHHHH-HHHHHhhhhcCCC--cc----chhHHHHHhhhhhhHhhCCCCcccc
Q psy9569 81 PEIIIAALK------AIRRVNDYALAI-RFLETTEFKTGGS--HD----KIWPYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 81 P~Ii~AALr------AcRRvND~alAV-R~lE~iK~K~~~~--~~----~iY~~~lqElkPtl~ELGI~t~EeL 141 (156)
|.+|..|.+ +|+-+.+++.+. +|.+.++ ...+. .. ......-+-|+-.|+=|||++||.|
T Consensus 435 ~~~v~~a~~~~~p~~l~~yl~~la~~f~~fY~~~~-l~~~~~~~~~~Rl~L~~a~~~vl~~~l~lLgi~~~e~M 507 (507)
T PRK01611 435 PEVVESAAEELEPHRIANYLYELAGAFHSFYNRVL-LKDEEEELRNARLALVKATAQVLKNGLDLLGISAPERM 507 (507)
T ss_pred HHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHCC-CCCChHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccC
Confidence 566666653 566677776655 4555444 11221 00 1345667788888999999999976
No 73
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=27.16 E-value=50 Score=23.65 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=18.9
Q ss_pred hcCCCccchhHHHHHhh------hhhhHhhCCC
Q psy9569 110 KTGGSHDKIWPYIVQEI------TPTLKELGIE 136 (156)
Q Consensus 110 K~~~~~~~iY~~~lqEl------kPtl~ELGI~ 136 (156)
-||.....-|+.|.+-+ +.+|++|||.
T Consensus 9 sCGkvi~~~w~~y~~rv~~ge~p~~vLDdLGv~ 41 (63)
T COG1644 9 SCGKVIGHKWEEYKRRVEEGEDPGEVLDDLGVK 41 (63)
T ss_pred cCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCcH
Confidence 46766666777776544 5689999984
No 74
>PF05746 DALR_1: DALR anticodon binding domain; InterPro: IPR008909 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [].; GO: 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1F7V_A 1F7U_A 1BS2_A 1IQ0_A.
Probab=27.15 E-value=27 Score=24.62 Aligned_cols=61 Identities=20% Similarity=0.272 Sum_probs=32.4
Q ss_pred HHHHHHHHH------HHHhhhhHHHHH-HHHHHhhhhcCCCcc------chhHHHHHhhhhhhHhhCCCCcccc
Q psy9569 81 PEIIIAALK------AIRRVNDYALAI-RFLETTEFKTGGSHD------KIWPYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 81 P~Ii~AALr------AcRRvND~alAV-R~lE~iK~K~~~~~~------~iY~~~lqElkPtl~ELGI~t~EeL 141 (156)
|++++.|.+ .|+-+.+++.++ +|++.++-..++... .+...+.+-++-.|+=|||++||.|
T Consensus 46 ~~~l~~a~~~~~p~~l~~yL~~La~~f~~fy~~~~I~~~~~~~~~~~RL~Ll~~v~~vl~~~l~llgi~~~~~M 119 (119)
T PF05746_consen 46 PDVLEKAAKDLEPHKLCDYLYELAQAFNSFYDNVRILDEDEEIRKNNRLALLKAVRQVLKNGLDLLGIEPLEKM 119 (119)
T ss_dssp HHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHHS-STTSTTCHH-HHHHHHHHHHHHHHHHHHHHTT----S--
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccC
Confidence 455554443 455555555554 456666666565411 1456667778888899999999875
No 75
>TIGR02158 PA_CoA_Oxy3 phenylacetate-CoA oxygenase, PaaI subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=27.02 E-value=60 Score=27.70 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=23.2
Q ss_pred cchhHHHHHhhhhhhHhhCCCCcccc
Q psy9569 116 DKIWPYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 116 ~~iY~~~lqElkPtl~ELGI~t~EeL 141 (156)
.+..+..++.+.|+++++|+..|+.-
T Consensus 178 ~~Lr~~w~~~v~~~l~~agL~~P~~~ 203 (237)
T TIGR02158 178 ATLQAAWEKEVNAVLNEATLTLPQQT 203 (237)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCc
Confidence 47899999999999999999999753
No 76
>PRK15138 aldehyde reductase; Provisional
Probab=26.85 E-value=1e+02 Score=27.26 Aligned_cols=32 Identities=13% Similarity=0.262 Sum_probs=26.2
Q ss_pred chhHHHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 117 KIWPYIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
+.-...++.|+-.+++||||+ ..|+|.++.++
T Consensus 321 ~~~~~~i~~i~~l~~~lg~p~~L~~~gv~~~d~ 353 (387)
T PRK15138 321 ERIDAAIAATRNFFEQMGVPTRLSDYGLDGSSI 353 (387)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHcCCCHHHH
Confidence 456788999999999999996 78999876543
No 77
>PF13766 ECH_C: 2-enoyl-CoA Hydratase C-terminal region; PDB: 3JU1_A 3BPT_A.
Probab=26.66 E-value=61 Score=24.33 Aligned_cols=51 Identities=24% Similarity=0.120 Sum_probs=31.9
Q ss_pred HHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHH
Q psy9569 66 RRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIV 123 (156)
Q Consensus 66 rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~l 123 (156)
+..++.||+.| +.+=|.++|++ .+-.-|-..++.++.+|.-..+-.|..+-
T Consensus 6 ~~~I~~~F~~~---s~~eI~~~L~~----~~~~~a~~~~~~l~~~SP~Sl~vt~~~l~ 56 (118)
T PF13766_consen 6 LEAIDRCFSAD---SVEEIIEALEA----DGDEWAQKTLETLRSGSPLSLKVTFEQLR 56 (118)
T ss_dssp HHHHHHHTTSS---SHHHHHHHHHH----HS-HHHHHHHHHHCCS-HHHHHHHHHHHH
T ss_pred HHHHHHHhCCC---CHHHHHHHHHc----cCcHHHHHHHHHHHHCCHHHHHHHHHHHH
Confidence 45677888864 66667777877 44556777788887777654444444443
No 78
>COG4710 Predicted DNA-binding protein with an HTH domain [General function prediction only]
Probab=26.46 E-value=2.4e+02 Score=21.02 Aligned_cols=46 Identities=22% Similarity=0.319 Sum_probs=35.4
Q ss_pred HHHHHhhhhhcCCCCCCHHHHHHHHHHH-HhhhhHHHHHHHHHHhhh
Q psy9569 64 DIRRGLMNLAHDDCVPDPEIIIAALKAI-RRVNDYALAIRFLETTEF 109 (156)
Q Consensus 64 e~rrglN~l~~~DlVPeP~Ii~AALrAc-RRvND~alAVR~lE~iK~ 109 (156)
|+..-||+|...---|..-+|.-|+.+- --+-||-+|+-.||.||+
T Consensus 15 E~~eRL~~Ls~~tgrtkayyvrEaIE~~ieemED~ylA~~aler~k~ 61 (80)
T COG4710 15 ELKERLDNLSKNTGRTKAYYVREAIEAYIEEMEDFYLAVNALERLKD 61 (80)
T ss_pred HHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 5666777777777777776666666553 478999999999999986
No 79
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=26.40 E-value=52 Score=29.84 Aligned_cols=34 Identities=12% Similarity=0.092 Sum_probs=24.9
Q ss_pred HhhhhcCCCccchhHHHHHhhhhhhHhhCCCCccc
Q psy9569 106 TTEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQ 140 (156)
Q Consensus 106 ~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~Ee 140 (156)
.+|.-.++- .--|.+.+|++|--|+++|++-||+
T Consensus 283 ~v~~S~esY-~f~~k~d~~~~k~~le~igy~~~e~ 316 (321)
T COG3888 283 IVKESLESY-EFDYKLDLKEFKNYLEFIGYPIPEG 316 (321)
T ss_pred HHHHHHhcc-ccchhhcHHHHHHHHHhcCCCChhh
Confidence 345555554 2345568999999999999999886
No 80
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=25.98 E-value=54 Score=19.57 Aligned_cols=16 Identities=38% Similarity=0.584 Sum_probs=13.9
Q ss_pred HHhhhhhhHhhCCCCc
Q psy9569 123 VQEITPTLKELGIETP 138 (156)
Q Consensus 123 lqElkPtl~ELGI~t~ 138 (156)
.+|||-.++++|+++.
T Consensus 6 ~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 6 VSELKDELKKRGLSTS 21 (35)
T ss_pred HHHHHHHHHHcCCCCC
Confidence 6789999999999873
No 81
>cd08186 Fe-ADH8 Iron-containing alcohol dehydrogenase. Type III Iron-containing alcohol dehydrogenases (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. It was suggested that the type III ADHs in microorganisms are involved in acetaldehyde detoxication rather than in alcohol turnover.
Probab=25.46 E-value=42 Score=29.35 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=23.6
Q ss_pred HHHHHhhhhhhHhhCCC-CccccCCCCccc
Q psy9569 120 PYIVQEITPTLKELGIE-TPAQLGYDKPEL 148 (156)
Q Consensus 120 ~~~lqElkPtl~ELGI~-t~EeLgydkpel 148 (156)
...++.|+..+++||+| +..|+|.++.++
T Consensus 317 ~~~i~~l~~l~~~lglP~~L~~~gv~~~~~ 346 (383)
T cd08186 317 EKAAKAVEKWLFSIGITEKLSDYGFTEGDV 346 (383)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHcCCCHHHH
Confidence 46788999999999998 578999876543
No 82
>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family. Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.
Probab=25.27 E-value=5.5e+02 Score=25.26 Aligned_cols=83 Identities=23% Similarity=0.344 Sum_probs=47.9
Q ss_pred HHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCC-----HHH---HHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccch
Q psy9569 47 FVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPD-----PEI---IIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKI 118 (156)
Q Consensus 47 F~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPe-----P~I---i~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~i 118 (156)
|..--.++|...+-|.||.=+.+-+-....-+|- |+. +...++. .+++| .+++|+..-.... ++-
T Consensus 320 ~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~d-----~vl~gl~~~~~~d-r~~ 392 (643)
T TIGR03754 320 FMEYADKILPKHDPKAWELIEELIARLKDRNVPRNMQGRPPRVVAIEQYLKE-KRLYD-----PVLDGLRSAVRYD-KTY 392 (643)
T ss_pred HHHHHHHHHHhhCchHHHHHHHHHhhhhccccccccccchHHHHHHHHHHhh-hcccc-----hHHHHHHHHHhcC-HHH
Confidence 4444466776666789984232222112222442 222 2223332 23332 4567766666655 688
Q ss_pred hHHHHHhhhhhhHhhCCC
Q psy9569 119 WPYIVQEITPTLKELGIE 136 (156)
Q Consensus 119 Y~~~lqElkPtl~ELGI~ 136 (156)
|..|+.-|.|+|++|+-.
T Consensus 393 f~KivasL~p~L~~Lttg 410 (643)
T TIGR03754 393 FDKIVASLGPLLEKLTTG 410 (643)
T ss_pred HHHHHHHHHHHHHHHcCc
Confidence 999999999999999843
No 83
>cd08175 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific.
Probab=25.08 E-value=34 Score=29.27 Aligned_cols=27 Identities=33% Similarity=0.543 Sum_probs=22.1
Q ss_pred HHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 122 IVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 122 ~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
.++.++..+++||||+ .+++|.++.++
T Consensus 295 ~~~~i~~l~~~lglP~~l~~~gv~~~~l 322 (348)
T cd08175 295 ASAKIEELLKKVGAPTHPEEIGIDKELF 322 (348)
T ss_pred cHHHHHHHHHHCCCCCCHHHcCCCHHHH
Confidence 4777899999999995 68999877554
No 84
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=24.89 E-value=1.8e+02 Score=20.87 Aligned_cols=41 Identities=22% Similarity=0.363 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHH
Q psy9569 40 VEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEI 83 (156)
Q Consensus 40 ~~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~I 83 (156)
.-++.|+-.++|.+.|.+ +|.-||-..-+.|.. +=+|.-+|
T Consensus 11 ~G~~~e~vk~~F~~~~~~--Vs~~EI~~~Eq~Li~-eG~~~eei 51 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSD--VSASEISAAEQELIQ-EGMPVEEI 51 (71)
T ss_pred CCCCHHHHHHHHHHHHCC--CCHHHHHHHHHHHHH-cCCCHHHH
Confidence 358999999999999997 589999999999998 55776555
No 85
>PF06293 Kdo: Lipopolysaccharide kinase (Kdo/WaaP) family; InterPro: IPR010440 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents lipopolysaccharide kinases which are related to protein kinases IPR000719 from INTERPRO. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of Salmonella enterica [].; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0009103 lipopolysaccharide biosynthetic process, 0016020 membrane
Probab=24.26 E-value=30 Score=27.28 Aligned_cols=17 Identities=41% Similarity=0.790 Sum_probs=14.2
Q ss_pred hhHhhCCCCccccCCCC
Q psy9569 129 TLKELGIETPAQLGYDK 145 (156)
Q Consensus 129 tl~ELGI~t~EeLgydk 145 (156)
.|.++||+||+=++|..
T Consensus 67 ~L~~~Gi~tP~pva~~~ 83 (206)
T PF06293_consen 67 RLREAGIPTPEPVAYGE 83 (206)
T ss_pred HHHHcCCCCCcEEEEEE
Confidence 46789999999998864
No 86
>cd08187 BDH Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold lower than that in the forward direction. The NADH-BDH had higher activity with longer chained aldehydes and was inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases.
Probab=24.21 E-value=1.5e+02 Score=25.83 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=26.3
Q ss_pred chhHHHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 117 KIWPYIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
+.-...+++|+..+++||+|+ ..|+|.++.++
T Consensus 320 ~~~~~~~~~i~~l~~~lglP~~L~~~gv~~~~l 352 (382)
T cd08187 320 ETALEGIEATEEFFKSLGLPTTLSELGIGEEDI 352 (382)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHcCCCHHHH
Confidence 456778999999999999994 78999987544
No 87
>cd08182 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. Members of this family are only found in bacteria.
Probab=24.19 E-value=45 Score=28.77 Aligned_cols=28 Identities=29% Similarity=0.356 Sum_probs=23.0
Q ss_pred HHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 121 YIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 121 ~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
..+++|+..+++||+|+ ..|+|.++.++
T Consensus 309 ~~~~~i~~l~~~~glp~~L~e~gv~~~~~ 337 (367)
T cd08182 309 EAAARIEALLKELGLPTRLAEYIVTREDI 337 (367)
T ss_pred HHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 46888999999999985 78999876543
No 88
>smart00351 PAX Paired Box domain.
Probab=24.03 E-value=1.6e+02 Score=21.99 Aligned_cols=45 Identities=27% Similarity=0.437 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHhhCCCCCcHHHHHHHhhhh--hcCCCCCCHHHHHHHHH
Q psy9569 43 SDEEFVKRYVAFFNQPDIDGWDIRRGLMNL--AHDDCVPDPEIIIAALK 89 (156)
Q Consensus 43 t~eeF~aRy~~~F~~~~iD~we~rrglN~l--~~~DlVPeP~Ii~AALr 89 (156)
..++|-..+.. ++|++-.||++..|-+- ..++-+|++.-|...|+
T Consensus 79 ~~~~~I~~~~~--~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 79 KVVKKIADYKQ--ENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHHH--HCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 34556555554 67889999999998763 77788999999887774
No 89
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=23.83 E-value=1.2e+02 Score=15.70 Aligned_cols=29 Identities=21% Similarity=0.182 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHhhhhcCCCccchhHHHHH
Q psy9569 95 NDYALAIRFLETTEFKTGGSHDKIWPYIVQ 124 (156)
Q Consensus 95 ND~alAVR~lE~iK~K~~~~~~~iY~~~lq 124 (156)
+|+..|..++|..-.+|... ..+|-.|++
T Consensus 1 ~~~~~~r~i~e~~l~~~~~~-~~~W~~y~~ 29 (33)
T smart00386 1 GDIERARKIYERALEKFPKS-VELWLKYAE 29 (33)
T ss_pred CcHHHHHHHHHHHHHHCCCC-hHHHHHHHH
Confidence 46777888888877777754 567777665
No 90
>KOG1154|consensus
Probab=23.53 E-value=82 Score=28.21 Aligned_cols=33 Identities=24% Similarity=0.418 Sum_probs=27.1
Q ss_pred HHHHHHHhhC------------CCCCcHHHHHHHhh----hhhcCCCCC
Q psy9569 47 FVKRYVAFFN------------QPDIDGWDIRRGLM----NLAHDDCVP 79 (156)
Q Consensus 47 F~aRy~~~F~------------~~~iD~we~rrglN----~l~~~DlVP 79 (156)
..++|+.-|. ++||+.|+-|++++ .|..|-.||
T Consensus 100 Lmalye~lF~Qy~~~iAQvLvT~~Di~d~~~r~Nl~~Ti~eLL~m~viP 148 (285)
T KOG1154|consen 100 LMALYETLFTQYGITIAQVLVTRNDILDEQQRKNLQNTISELLSMNVIP 148 (285)
T ss_pred HHHHHHHHHHHhccchheeeecCcchhhHHHHHHHHHHHHHHHhCCcee
Confidence 7889999886 68899999999876 477787777
No 91
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=23.48 E-value=48 Score=28.91 Aligned_cols=29 Identities=17% Similarity=0.392 Sum_probs=24.1
Q ss_pred HHHHHhhhhhhHhhCCC-CccccCCCCccc
Q psy9569 120 PYIVQEITPTLKELGIE-TPAQLGYDKPEL 148 (156)
Q Consensus 120 ~~~lqElkPtl~ELGI~-t~EeLgydkpel 148 (156)
...+++|+-.+++||+| +..|+|+++.++
T Consensus 318 ~~~~~~i~~l~~~lglp~~L~e~gv~~~~~ 347 (377)
T cd08188 318 LAVIEAVRRLRAALGVPETLGDLGVKREDI 347 (377)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 56789999999999998 578899887554
No 92
>cd00155 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
Probab=23.43 E-value=1e+02 Score=24.49 Aligned_cols=24 Identities=13% Similarity=0.224 Sum_probs=19.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHHhhh
Q psy9569 86 AALKAIRRVNDYALAIRFLETTEF 109 (156)
Q Consensus 86 AALrAcRRvND~alAVR~lE~iK~ 109 (156)
.....|+.+|||..+.-|+-|+..
T Consensus 83 ~ia~~l~~l~Nfns~~aI~~~L~~ 106 (237)
T cd00155 83 QVAKHCRELNNFNSLMAIVSALSS 106 (237)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCC
Confidence 344788899999999999988864
No 93
>smart00633 Glyco_10 Glycosyl hydrolase family 10.
Probab=23.41 E-value=78 Score=25.93 Aligned_cols=62 Identities=24% Similarity=0.399 Sum_probs=36.5
Q ss_pred HHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCC----------CCCCHHHHHHHHHHHHh--------hhhHHH------H
Q psy9569 45 EEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDD----------CVPDPEIIIAALKAIRR--------VNDYAL------A 100 (156)
Q Consensus 45 eeF~aRy~~~F~~~~iD~we~rrglN~l~~~D----------lVPeP~Ii~AALrAcRR--------vND~al------A 100 (156)
+.|...-.+.|... ++.|++= |.-+..+ =+.-|+.+..|.+++|+ +|||.+ .
T Consensus 60 ~~~i~~v~~ry~g~-i~~wdV~---NE~~~~~~~~~~~~~w~~~~G~~~i~~af~~ar~~~P~a~l~~Ndy~~~~~~~k~ 135 (254)
T smart00633 60 ENHIKTVVGRYKGK-IYAWDVV---NEALHDNGSGLRRSVWYQILGEDYIEKAFRYAREADPDAKLFYNDYNTEEPNAKR 135 (254)
T ss_pred HHHHHHHHHHhCCc-ceEEEEe---eecccCCCcccccchHHHhcChHHHHHHHHHHHHhCCCCEEEEeccCCcCccHHH
Confidence 44444445556554 6777652 3322221 01236899999999999 688762 2
Q ss_pred ---HHHHHHhhhh
Q psy9569 101 ---IRFLETTEFK 110 (156)
Q Consensus 101 ---VR~lE~iK~K 110 (156)
..+++.+++.
T Consensus 136 ~~~~~~v~~l~~~ 148 (254)
T smart00633 136 QAIYELVKKLKAK 148 (254)
T ss_pred HHHHHHHHHHHHC
Confidence 5566666554
No 94
>PF00901 Orbi_VP5: Orbivirus outer capsid protein VP5; InterPro: IPR000145 The orbivirus VP5 protein is one of the two proteins (with VP2) which make up the virus particle outer capsid. Cryoelectron microscopy indicates that VP5 is a trimer suggesting that there are 360 copies of VP5 per virion [].; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=23.25 E-value=1.7e+02 Score=28.29 Aligned_cols=54 Identities=19% Similarity=0.207 Sum_probs=44.3
Q ss_pred cHHHHHHHhhhhhcCCC----CC--CHHHHHHHHHHHHh-hhhHHHHHHHHHHhhhhcCCC
Q psy9569 61 DGWDIRRGLMNLAHDDC----VP--DPEIIIAALKAIRR-VNDYALAIRFLETTEFKTGGS 114 (156)
Q Consensus 61 D~we~rrglN~l~~~Dl----VP--eP~Ii~AALrAcRR-vND~alAVR~lE~iK~K~~~~ 114 (156)
-++-|.+-+|.|-|-|| +| .|.+|+..|.+=.. ++|-.|+.-+.+.++.--+++
T Consensus 248 g~yKLkkvI~aLtGidlsHl~~P~I~p~~iet~L~~~~~~i~D~~L~~~v~sK~~~v~E~~ 308 (508)
T PF00901_consen 248 GAYKLKKVINALTGIDLSHLRTPKIHPGTIETILTADTPEIPDKSLAQIVSSKLRHVEENE 308 (508)
T ss_pred HHHHHHHHHHHhhCCChhhccCCCcCHHHHHHHHhcCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 57889999999999998 56 59999999998776 999999988777666555444
No 95
>PRK10586 putative oxidoreductase; Provisional
Probab=23.22 E-value=71 Score=28.15 Aligned_cols=26 Identities=15% Similarity=0.243 Sum_probs=22.0
Q ss_pred HHHHHhhhhhhHhhCCCC-ccccCCCC
Q psy9569 120 PYIVQEITPTLKELGIET-PAQLGYDK 145 (156)
Q Consensus 120 ~~~lqElkPtl~ELGI~t-~EeLgydk 145 (156)
+..+++|+..++++|+|+ ..+||+++
T Consensus 292 ~~~~~~l~~~l~~lGLP~~L~dlGi~~ 318 (362)
T PRK10586 292 DDVLAQLIGAYQRFHLPTTLAELDVDI 318 (362)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHCCCCC
Confidence 346789999999999977 68999975
No 96
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=23.21 E-value=49 Score=28.60 Aligned_cols=29 Identities=31% Similarity=0.403 Sum_probs=23.7
Q ss_pred HHHHHhhhhhhHhhCCC-CccccCCCCccc
Q psy9569 120 PYIVQEITPTLKELGIE-TPAQLGYDKPEL 148 (156)
Q Consensus 120 ~~~lqElkPtl~ELGI~-t~EeLgydkpel 148 (156)
...++.|+-.+++||+| +..|+|.++.++
T Consensus 311 ~~~~~~i~~l~~~lglp~~L~e~gv~~~~~ 340 (370)
T cd08192 311 ADFADAILALNARLGIPHTLRELGVDEDDL 340 (370)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 45678899999999998 578999987654
No 97
>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.
Probab=23.07 E-value=51 Score=28.63 Aligned_cols=30 Identities=20% Similarity=0.440 Sum_probs=24.5
Q ss_pred hHHHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 119 WPYIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 119 Y~~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
-...++.|+..+++||+|+ ..|+|+++.++
T Consensus 318 ~~~~~~~i~~~~~~lglP~~L~e~gv~~~~~ 348 (380)
T cd08185 318 AEDFIEALRKLLKRIGLDDLLSDLGVTKEDI 348 (380)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 3456888999999999985 78999987665
No 98
>PRK01153 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=22.75 E-value=1.1e+02 Score=24.39 Aligned_cols=29 Identities=28% Similarity=0.614 Sum_probs=18.6
Q ss_pred hhCCCCCcHHHHHHHhhh-hhcCCCCCCHHH
Q psy9569 54 FFNQPDIDGWDIRRGLMN-LAHDDCVPDPEI 83 (156)
Q Consensus 54 ~F~~~~iD~we~rrglN~-l~~~DlVPeP~I 83 (156)
.|++.+|.++++|+.|-. ---.++|| |.|
T Consensus 121 ~~~~~~iSsT~IR~~i~~g~~w~~~VP-p~V 150 (174)
T PRK01153 121 MFNREEYSGTEIRRRMIEGDPWEELVP-KSV 150 (174)
T ss_pred ccccCCCCHHHHHHHHHcCCchhhhCC-HHH
Confidence 356777899999999831 01235688 444
No 99
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=22.52 E-value=1.8e+02 Score=22.60 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHhh-hhHHHHHHHHHHhhhhcCCCc----cchhHHHHHhhhh
Q psy9569 78 VPDPEIIIAALKAIRRV-NDYALAIRFLETTEFKTGGSH----DKIWPYIVQEITP 128 (156)
Q Consensus 78 VPeP~Ii~AALrAcRRv-ND~alAVR~lE~iK~K~~~~~----~~iY~~~lqElkP 128 (156)
.|.|+|+.-||.+++-. +|=.+.=.|-+-|-.-+.... .-.|-.||++|.|
T Consensus 13 ~~~~~i~~p~le~~~~~~~~e~Lremfa~LLass~d~~~~~~~hp~fv~Ii~qLsp 68 (186)
T PF14337_consen 13 EPPPKIAGPALEAASYEIDDEELREMFANLLASSMDKRKNDDVHPSFVEIIKQLSP 68 (186)
T ss_pred CCChhhhHHHHHhccCcCCcHHHHHHHHHHHHHHhCcCccccccHHHHHHHHhCCH
Confidence 46799999999999987 888888777777765555432 2367778888877
No 100
>TIGR03405 Phn_Fe-ADH phosphonate metabolism-associated iron-containing alcohol dehydrogenase. 2-hydroxyethylphosphonate (2-HEP), the presumed product of the reaction of Pald with an alcohol dehydrogenase, is a biologically novel but reasonable analog of 2-AEP and may be a constituent of as-yet undescribed natural products. In the case of Azoarcus, downstream of the dehydrogenase is a CDP-glycerol:glycerophosphate transferase homolog that may indicate the existence of a pathway for 2-HEP-derived phosphonolipid biosynthesis.
Probab=22.41 E-value=54 Score=28.44 Aligned_cols=28 Identities=25% Similarity=0.336 Sum_probs=23.2
Q ss_pred HHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 121 YIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 121 ~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
..++.|+-.+++||+|+ ..|+|+++.++
T Consensus 308 ~~~~~i~~l~~~lglP~~L~~~gv~~~~~ 336 (355)
T TIGR03405 308 SAPARLRAFLDTLGVKTRFADYGVSRDEA 336 (355)
T ss_pred HHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 57888999999999985 78999876554
No 101
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.36 E-value=96 Score=25.47 Aligned_cols=76 Identities=16% Similarity=0.218 Sum_probs=55.7
Q ss_pred HHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhh
Q psy9569 49 KRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITP 128 (156)
Q Consensus 49 aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkP 128 (156)
|-|++|..|-.-|.=++++-.+.=|..||+|.-.=++.||.+.--.+|.. -.+++|+ .-+.++|.-
T Consensus 64 Ae~eN~rkR~~re~e~~~k~a~e~~~~dlLpviDnlerAl~~~~~~~d~~--~~l~~Gv------------em~~~~l~~ 129 (193)
T COG0576 64 AEFENLRKRTEREREEAKKYAIEKFAKDLLPVIDNLERALEAAEDDKDPE--KALLEGV------------EMTLDQLLD 129 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchH--HHHHHHH------------HHHHHHHHH
Confidence 33556666666667778888888899999999888888888766666666 4455554 456677888
Q ss_pred hhHhhCCCCc
Q psy9569 129 TLKELGIETP 138 (156)
Q Consensus 129 tl~ELGI~t~ 138 (156)
+|+.+||.-.
T Consensus 130 ~L~k~Gv~~i 139 (193)
T COG0576 130 ALEKLGVEEI 139 (193)
T ss_pred HHHHCCCEEe
Confidence 9999998433
No 102
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.29 E-value=1.3e+02 Score=17.58 Aligned_cols=32 Identities=28% Similarity=0.287 Sum_probs=21.7
Q ss_pred hhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHH
Q psy9569 69 LMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFL 104 (156)
Q Consensus 69 lN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~l 104 (156)
++.|..|= . +..-+..||++|. ||...|+.+|
T Consensus 5 v~~L~~mG-f-~~~~~~~AL~~~~--~d~~~A~~~L 36 (38)
T cd00194 5 LEQLLEMG-F-SREEARKALRATN--NNVERAVEWL 36 (38)
T ss_pred HHHHHHcC-C-CHHHHHHHHHHhC--CCHHHHHHHH
Confidence 34444443 2 2667778899998 5898888775
No 103
>TIGR02638 lactal_redase lactaldehyde reductase. This clade of genes encoding iron-containing alcohol dehydrogenase (pfam00465) proteins is generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in lactaldehyde which is reduced by this enzyme to 1,2 propanediol. This protein is alternatively known by the name 1,2 propanediol oxidoreductase. This enzyme is active under anaerobic conditions in E. coli while being inactivated by reactive oxygen species under aerobic conditions. Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase.
Probab=22.05 E-value=1.1e+02 Score=26.61 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=24.3
Q ss_pred hhHHHHHhhhhhhHhhCCCC-ccccCCCCccc
Q psy9569 118 IWPYIVQEITPTLKELGIET-PAQLGYDKPEL 148 (156)
Q Consensus 118 iY~~~lqElkPtl~ELGI~t-~EeLgydkpel 148 (156)
.-...++.|+-.+++||+|+ ..|+|.++.++
T Consensus 319 ~~~~~~~~i~~l~~~lglp~~L~e~gv~~~~~ 350 (379)
T TIGR02638 319 ARDAAVEAVKTLSKRVGIPEGLSELGVKEEDI 350 (379)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHcCCCHHHH
Confidence 34567888999999999984 78889876554
No 104
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=22.00 E-value=1e+02 Score=19.31 Aligned_cols=39 Identities=21% Similarity=0.333 Sum_probs=21.9
Q ss_pred HHHHHhhhhcCCCccchh--HHHHHhhhhhhHhhCCCCcccc
Q psy9569 102 RFLETTEFKTGGSHDKIW--PYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 102 R~lE~iK~K~~~~~~~iY--~~~lqElkPtl~ELGI~t~EeL 141 (156)
+|.+-|+.++|-... .| ..+..-|.+.|..+|+++.+++
T Consensus 7 ~~~~~i~~~~Gi~l~-~~K~~~l~rRl~~rm~~~~~~~~~~y 47 (57)
T PF03705_consen 7 RFRELIYRRTGIDLS-EYKRSLLERRLARRMRALGLPSFAEY 47 (57)
T ss_dssp HHHHHHHHHH------GGGHHHHHHHHHHHHHHHT---HHHH
T ss_pred HHHHHHHHHHCCCCc-hhhHHHHHHHHHHHHHHcCCCCHHHH
Confidence 466677888886532 23 3556678899999998877653
No 105
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=21.77 E-value=64 Score=27.50 Aligned_cols=29 Identities=31% Similarity=0.491 Sum_probs=23.5
Q ss_pred hHHHHHhhhhhhHhhCCCC-ccccCCCCcc
Q psy9569 119 WPYIVQEITPTLKELGIET-PAQLGYDKPE 147 (156)
Q Consensus 119 Y~~~lqElkPtl~ELGI~t-~EeLgydkpe 147 (156)
..|.+++|+-.+++||+|+ ..|+|+++.+
T Consensus 268 l~~~~~~i~~l~~~lglp~~L~~~gi~~~~ 297 (332)
T cd08180 268 IEFLIEAIKQLKKKLNIPETLKELGVDKEE 297 (332)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHcCCCHHH
Confidence 3346778999999999985 7899998764
No 106
>PF12827 Peroxin-22: Peroxisomal biogenesis protein family; InterPro: IPR024359 Peroxin-22 is an integral peroxisomal membrane protein. The N terminus of peroxin-22 is located in the matrix, while the C terminus is located in the cytosol. Peroxin-22 interacts with the ubiquitin-conjugating enzyme Pex4p, anchoring it at the peroxisomal membrane. Both proteins may act at the same step in peroxisome biogenesis [].; PDB: 2Y9O_B 2Y9M_B 2Y9P_B.
Probab=21.68 E-value=57 Score=25.22 Aligned_cols=31 Identities=23% Similarity=0.391 Sum_probs=21.0
Q ss_pred hcCCCccchhHHHHHhhhhh-----hHhhCCCCccccC
Q psy9569 110 KTGGSHDKIWPYIVQEITPT-----LKELGIETPAQLG 142 (156)
Q Consensus 110 K~~~~~~~iY~~~lqElkPt-----l~ELGI~t~EeLg 142 (156)
+|.+- +=|=..++-|||- .+|||+..|+|||
T Consensus 73 ~Cdt~--~G~~~~vK~Lk~d~llv~~ddl~~~ip~Di~ 108 (117)
T PF12827_consen 73 KCDTM--QGYWSCVKHLKPDQLLVCSDDLGISIPEDIN 108 (117)
T ss_dssp EESSH--HHHHHHHHHH--SEEEE-GGGT-SSS-GGGG
T ss_pred Eecch--hhHHHHHHhcCCCceEEehhhccccCHHHHH
Confidence 57775 4577788999994 6999999999976
No 107
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=21.61 E-value=31 Score=24.28 Aligned_cols=50 Identities=24% Similarity=0.319 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCC-------CccccCCCCcc
Q psy9569 97 YALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIE-------TPAQLGYDKPE 147 (156)
Q Consensus 97 ~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~-------t~EeLgydkpe 147 (156)
++-+..+|+.+|.+ |-+.--.=..-.+.++..++.+|+. +.++.|..||+
T Consensus 79 ~~~~~~~L~~l~~~-~~~~~i~Sn~~~~~~~~~l~~~~~~~~f~~i~~~~~~~~~Kp~ 135 (176)
T PF13419_consen 79 YPGVRELLERLKAK-GIPLVIVSNGSRERIERVLERLGLDDYFDEIISSDDVGSRKPD 135 (176)
T ss_dssp STTHHHHHHHHHHT-TSEEEEEESSEHHHHHHHHHHTTHGGGCSEEEEGGGSSSSTTS
T ss_pred hhhhhhhhhhcccc-cceeEEeecCCcccccccccccccccccccccccchhhhhhhH
Confidence 45677777777744 2110000011134556677777765 45677777774
No 108
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.58 E-value=74 Score=24.29 Aligned_cols=68 Identities=22% Similarity=0.192 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhH
Q psy9569 41 EESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWP 120 (156)
Q Consensus 41 ~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~ 120 (156)
-++|+||. +|-..+|+.++.-+.++-. --+=|+-=+||| .-++---||+||.|+..+ .=-|+
T Consensus 17 ~~~d~Eae-----~~l~Qdi~D~~~~~~fqk~-----------afe~lkkd~rin-iRlss~dLeaIK~kaSa~-GlpYQ 78 (92)
T COG5304 17 NALDEEAE-----NDLWQDIKDFEQEKHFQKA-----------AFEYLKKDTRIN-IRLSSSDLEAIKQKASAE-GLPYQ 78 (92)
T ss_pred hccchhhH-----HHHHHhhHHHHHHHHHHHH-----------HHHHhcccceee-EecCHHHHHHHHHHHhhc-CCcHH
Confidence 35566653 3334567777765543321 112233445665 234445689999999877 45699
Q ss_pred HHHHhh
Q psy9569 121 YIVQEI 126 (156)
Q Consensus 121 ~~lqEl 126 (156)
-|+.|+
T Consensus 79 tyIrei 84 (92)
T COG5304 79 TYIREI 84 (92)
T ss_pred HHHHHH
Confidence 999886
No 109
>PF00465 Fe-ADH: Iron-containing alcohol dehydrogenase ; InterPro: IPR001670 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Currently three, structurally and catalytically, different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Iron-containing ADH's have been found in yeast (gene ADH4) [], as well as in Zymomonas mobilis (gene adhB) []. These two iron-containing ADH's are closely related to the following enzymes: Escherichia coli propanediol oxidoreductase (1.1.1.77 from EC) (gene fucO) [], an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s). Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1 from EC) (genes adh1, bdhA and bdhB) [], an enzyme which has activity using butanol and ethanol as substrates. E. coli adhE [], an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10 from EC) and pyruvate-formate-lyase deactivase. Bacterial glycerol dehydrogenase (1.1.1.6 from EC) (gene gldA or dhaD) []. Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61 from EC). Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202 from EC) (gene dhaT). Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244 from EC) []. E. coli and Salmonella typhimurium ethanolamine utilization protein eutG. E. coli hypothetical protein yiaY. ; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1RRM_A 2BL4_A 2BI4_A 3BFJ_R 1KQ3_A 1JQ5_A 1JPU_A 1JQA_A 3JZD_A 3UHJ_A ....
Probab=21.48 E-value=76 Score=27.23 Aligned_cols=31 Identities=26% Similarity=0.449 Sum_probs=23.6
Q ss_pred chhHHHHHhhhhhhHhhCCCC-ccccCCCCcc
Q psy9569 117 KIWPYIVQEITPTLKELGIET-PAQLGYDKPE 147 (156)
Q Consensus 117 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkpe 147 (156)
+.-...+++|+-.+++||+|+ ..|+|++.-+
T Consensus 309 ~~a~~~~~~l~~l~~~lglp~~l~~~gi~~~~ 340 (366)
T PF00465_consen 309 EAADDAIDELRALLRSLGLPTRLSDLGIDEED 340 (366)
T ss_dssp HHHHHHHHHHHHHHHHTT--SSGGGGT-TGGG
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHcCCCHHH
Confidence 356788999999999999999 8999999743
No 110
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=21.35 E-value=1.3e+02 Score=17.45 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=20.2
Q ss_pred hhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHH
Q psy9569 69 LMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFL 104 (156)
Q Consensus 69 lN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~l 104 (156)
++.|..|= .| ..-+..||++|. ||...|+.+|
T Consensus 5 v~~L~~mG-f~-~~~a~~aL~~~~--~d~~~A~~~L 36 (37)
T smart00165 5 IDQLLEMG-FS-REEALKALRAAN--GNVERAAEYL 36 (37)
T ss_pred HHHHHHcC-CC-HHHHHHHHHHhC--CCHHHHHHHH
Confidence 34444443 33 346677888886 6788887765
No 111
>KOG4281|consensus
Probab=21.31 E-value=1.2e+02 Score=26.66 Aligned_cols=42 Identities=19% Similarity=0.281 Sum_probs=31.7
Q ss_pred HHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhCCCCccccCCC
Q psy9569 100 AIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQLGYD 144 (156)
Q Consensus 100 AVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgyd 144 (156)
.-|++..+|.-..+..-+..+.-||.||-+|+|| +||++|+.
T Consensus 4 vq~l~ntck~~fs~~~pg~~~~nlqkLr~vLd~l---kp~Dvgl~ 45 (236)
T KOG4281|consen 4 VQRLFNTCKEVFSTGGPGPFEENLQKLRSVLDEL---KPEDVGLE 45 (236)
T ss_pred hHHHHHHHHHHhcCCCCCccHHHHHHHHHHHhhC---CHhhcCcC
Confidence 4577788887766653357999999999999997 46777764
No 112
>TIGR00456 argS arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori.
Probab=20.78 E-value=48 Score=30.83 Aligned_cols=56 Identities=16% Similarity=0.160 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCC-c----cchhHHHHHhhhhhhHhhCCCCcccc
Q psy9569 81 PEIIIAALKAIRRVNDYALAIRFLETTEFKTGGS-H----DKIWPYIVQEITPTLKELGIETPAQL 141 (156)
Q Consensus 81 P~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~-~----~~iY~~~lqElkPtl~ELGI~t~EeL 141 (156)
..++...+.-|+.+|.|=..-|+|.. ++. . =......-+-|+-.|+=|||++||.|
T Consensus 506 ~~~~~~l~~La~~~N~yy~~~~Vl~~-----~~~~~~~~RL~L~~a~~~vl~~gL~lLGI~~~e~M 566 (566)
T TIGR00456 506 HVLTNYLYELASLFSSFYKACPVLDA-----ENENLAAARLALLKATRQTLKNGLQLLGIEPPERM 566 (566)
T ss_pred HHHHHHHHHHHHHHHHHHhcCccCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccC
Confidence 45566777777777777555455521 111 0 12456677888888999999999976
No 113
>PHA02602 56 dCTP pyrophosphatase; Provisional
Probab=20.71 E-value=1.8e+02 Score=24.37 Aligned_cols=52 Identities=21% Similarity=0.251 Sum_probs=35.3
Q ss_pred HHHHHHHhhhhhcCCC---CCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhHHHHHhhhhhhHhhC
Q psy9569 62 GWDIRRGLMNLAHDDC---VPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELG 134 (156)
Q Consensus 62 ~we~rrglN~l~~~Dl---VPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 134 (156)
-+++|++|+.-.+-+. +|.|. |..|+-.+|+-|+. +=.||.+|++.++.+||
T Consensus 35 m~dmQ~~lq~~l~~~~p~~~~~p~-------------~l~t~ge~l~W~~~--------~~~ai~dE~rEL~t~Lg 89 (172)
T PHA02602 35 MLDMQKSLQVRLANDKPEYNPHPD-------------ELKTCGEILDWLRN--------QDDYIADETRELYTSLG 89 (172)
T ss_pred HHHHHHHHHHHHcccccccCCCch-------------hHHHhhHHHHHHHH--------HHHHHHHHHHHHHHHhc
Confidence 5789999998877433 55554 44555555555543 34678888888888887
No 114
>PF05854 MC1: Non-histone chromosomal protein MC1; InterPro: IPR008674 This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation [].; GO: 0042262 DNA protection; PDB: 1T23_A 2KHL_A.
Probab=20.66 E-value=44 Score=25.51 Aligned_cols=9 Identities=78% Similarity=0.781 Sum_probs=8.4
Q ss_pred HHHHHHHHh
Q psy9569 85 IAALKAIRR 93 (156)
Q Consensus 85 ~AALrAcRR 93 (156)
+|||+|+||
T Consensus 26 qAAlKAA~R 34 (93)
T PF05854_consen 26 QAALKAARR 34 (93)
T ss_dssp HHHHHHHCC
T ss_pred HHHHHHhhc
Confidence 699999999
No 115
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=20.10 E-value=1.2e+02 Score=24.01 Aligned_cols=68 Identities=15% Similarity=0.072 Sum_probs=46.3
Q ss_pred CCCHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhcCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhcCCCccchhH
Q psy9569 41 EESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDKIWP 120 (156)
Q Consensus 41 ~Et~eeF~aRy~~~F~~~~iD~we~rrglN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~ 120 (156)
++.-++.++.-..|=++- --=++|+++.++..| -.+..|+..|++.++.++++|-+. +.+..
T Consensus 13 ~~~~~~Le~elk~~~~n~--~kesir~~~~~l~~~---------------~~~~Gd~~~A~k~y~~~~~~~~~~-~~~id 74 (177)
T PF10602_consen 13 AEELEKLEAELKDAKSNL--GKESIRMALEDLADH---------------YCKIGDLEEALKAYSRARDYCTSP-GHKID 74 (177)
T ss_pred HHHHHHHHHHHHHHHhcc--chHHHHHHHHHHHHH---------------HHHhhhHHHHHHHHHHHhhhcCCH-HHHHH
Confidence 455667777766665542 345889988887643 346789999999999999999765 44444
Q ss_pred HHHHhh
Q psy9569 121 YIVQEI 126 (156)
Q Consensus 121 ~~lqEl 126 (156)
-.+.-|
T Consensus 75 ~~l~~i 80 (177)
T PF10602_consen 75 MCLNVI 80 (177)
T ss_pred HHHHHH
Confidence 444433
Done!