Query 032325
Match_columns 143
No_of_seqs 104 out of 219
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 12:37:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032325hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3218 RNA polymerase, 25-kDa 100.0 1.7E-60 3.7E-65 372.0 14.8 140 3-142 4-144 (208)
2 PLN03111 DNA-directed RNA poly 100.0 1.4E-58 3E-63 365.5 15.4 142 1-142 1-142 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 5.4E-57 1.2E-61 356.0 15.4 138 5-142 2-141 (205)
4 PF03871 RNA_pol_Rpb5_N: RNA p 100.0 1.2E-38 2.5E-43 225.0 0.6 90 1-91 1-93 (93)
5 PF04471 Mrr_cat: Restriction 97.4 0.00051 1.1E-08 47.5 5.9 75 54-131 36-111 (115)
6 TIGR00640 acid_CoA_mut_C methy 80.9 8.5 0.00018 28.4 6.6 86 16-118 20-105 (132)
7 PRK03298 hypothetical protein; 79.7 3.7 8.1E-05 33.4 4.6 49 68-118 149-202 (224)
8 cd02072 Glm_B12_BD B12 binding 77.8 17 0.00037 27.0 7.4 74 17-107 18-91 (128)
9 PRK08485 DNA polymerase III su 73.5 8.9 0.00019 30.9 5.2 44 71-115 31-75 (206)
10 cd02067 B12-binding B12 bindin 72.2 28 0.0006 24.3 7.1 83 17-117 18-101 (119)
11 PF01939 DUF91: Protein of unk 71.7 5.6 0.00012 32.4 3.7 56 67-127 149-209 (228)
12 TIGR01501 MthylAspMutase methy 69.9 22 0.00048 26.5 6.4 74 16-106 19-92 (134)
13 COG1637 Predicted nuclease of 69.4 8.1 0.00017 32.1 4.2 59 68-127 175-238 (253)
14 KOG0975 Branched chain aminotr 68.8 2.5 5.5E-05 36.8 1.2 29 14-44 288-317 (379)
15 cd02071 MM_CoA_mut_B12_BD meth 66.0 37 0.0008 24.1 6.7 75 18-109 19-93 (122)
16 PRK02261 methylaspartate mutas 64.0 45 0.00096 24.6 7.0 73 17-106 22-94 (137)
17 PF13156 Mrr_cat_2: Restrictio 62.4 12 0.00027 27.8 3.7 81 38-118 16-99 (129)
18 PLN02559 chalcone--flavonone i 62.3 5.6 0.00012 32.5 2.0 79 35-116 128-206 (230)
19 PRK04280 arginine repressor; P 60.3 29 0.00064 26.2 5.5 87 17-118 23-113 (148)
20 PRK09545 znuA high-affinity zi 60.3 1E+02 0.0022 25.7 9.4 81 15-117 194-274 (311)
21 PRK05564 DNA polymerase III su 58.0 27 0.00059 28.7 5.4 42 74-115 69-114 (313)
22 COG1715 Mrr Restriction endonu 57.6 43 0.00094 28.6 6.5 54 66-119 214-268 (308)
23 PRK09539 tRNA-splicing endonuc 57.1 75 0.0016 23.6 7.1 56 21-94 43-98 (124)
24 PRK07993 DNA polymerase III su 54.7 40 0.00087 28.5 6.0 48 68-115 76-129 (334)
25 PRK08058 DNA polymerase III su 54.2 35 0.00075 28.6 5.5 48 68-115 80-131 (329)
26 PF13607 Succ_CoA_lig: Succiny 54.2 34 0.00075 25.4 4.9 80 16-114 15-99 (138)
27 cd02070 corrinoid_protein_B12- 53.9 75 0.0016 24.6 7.1 75 18-109 102-178 (201)
28 PRK06871 DNA polymerase III su 53.0 50 0.0011 28.0 6.3 48 68-115 76-128 (325)
29 PRK05917 DNA polymerase III su 50.7 44 0.00095 28.1 5.6 48 68-115 63-116 (290)
30 KOG1232 Proteins containing th 49.6 16 0.00034 32.6 2.8 40 2-42 365-404 (511)
31 PF11513 TA0956: Thermoplasma 48.1 60 0.0013 23.3 5.1 57 38-97 45-106 (110)
32 TIGR02370 pyl_corrinoid methyl 47.5 1.1E+02 0.0023 23.8 7.0 76 18-110 104-181 (197)
33 PRK04247 hypothetical protein; 46.1 42 0.00092 27.5 4.6 51 67-118 173-227 (238)
34 PF03345 DDOST_48kD: Oligosacc 45.2 90 0.0019 27.7 6.9 99 15-131 14-120 (423)
35 KOG3451 Uncharacterized conser 44.9 19 0.00042 24.1 2.1 42 94-138 3-50 (71)
36 KOG2130 Phosphatidylserine-spe 44.7 20 0.00043 31.2 2.6 50 77-131 117-168 (407)
37 cd02069 methionine_synthase_B1 44.4 88 0.0019 24.7 6.2 78 18-112 108-185 (213)
38 PF02310 B12-binding: B12 bind 42.4 1.1E+02 0.0024 20.9 7.5 97 16-130 18-114 (121)
39 PF13167 GTP-bdg_N: GTP-bindin 39.5 39 0.00085 23.8 3.1 88 34-135 6-93 (95)
40 TIGR03798 ocin_TIGR03798 bacte 38.8 36 0.00077 21.8 2.6 20 16-35 28-47 (64)
41 PF11985 DUF3486: Protein of u 38.7 20 0.00044 27.5 1.6 17 14-30 14-30 (180)
42 PRK03170 dihydrodipicolinate s 38.6 87 0.0019 25.5 5.5 49 68-117 9-62 (292)
43 PRK07276 DNA polymerase III su 37.0 88 0.0019 26.2 5.3 48 68-115 74-125 (290)
44 PRK00441 argR arginine repress 36.6 1.7E+02 0.0036 22.1 6.3 87 17-118 23-113 (149)
45 cd01019 ZnuA Zinc binding prot 36.3 2.4E+02 0.0051 23.0 9.4 72 22-116 177-248 (286)
46 PF07862 Nif11: Nitrogen fixat 35.8 21 0.00046 21.5 1.1 20 16-35 30-49 (49)
47 KOG0373 Serine/threonine speci 35.7 21 0.00046 29.6 1.4 86 23-117 83-176 (306)
48 PRK03094 hypothetical protein; 35.3 19 0.0004 24.8 0.9 15 17-31 12-26 (80)
49 PRK03341 arginine repressor; P 34.9 1.6E+02 0.0036 22.7 6.2 87 17-118 34-130 (168)
50 PF12687 DUF3801: Protein of u 34.5 1.2E+02 0.0025 24.1 5.4 67 15-92 21-92 (204)
51 cd01017 AdcA Metal binding pro 34.5 2.5E+02 0.0054 22.7 9.6 43 74-117 200-242 (282)
52 PRK05818 DNA polymerase III su 34.3 1.1E+02 0.0023 25.5 5.3 48 68-115 57-109 (261)
53 TIGR01529 argR_whole arginine 34.3 2E+02 0.0043 21.5 7.3 87 17-118 21-111 (146)
54 TIGR03249 KdgD 5-dehydro-4-deo 34.2 1.2E+02 0.0025 24.9 5.6 49 68-117 13-66 (296)
55 COG4889 Predicted helicase [Ge 34.2 68 0.0015 32.0 4.6 82 54-136 61-155 (1518)
56 PF04355 SmpA_OmlA: SmpA / Oml 33.2 1.1E+02 0.0024 19.4 4.3 53 26-78 1-67 (71)
57 PLN02925 4-hydroxy-3-methylbut 32.9 1.7E+02 0.0036 28.0 6.8 44 5-48 202-246 (733)
58 PF12641 Flavodoxin_3: Flavodo 32.2 1.3E+02 0.0028 22.8 5.1 52 66-117 68-123 (160)
59 TIGR02328 conserved hypothetic 32.1 47 0.001 24.6 2.5 24 8-31 47-70 (120)
60 cd00079 HELICc Helicase superf 31.1 1.6E+02 0.0035 19.6 6.1 46 64-116 27-72 (131)
61 PF03698 UPF0180: Uncharacteri 30.8 23 0.0005 24.3 0.7 15 17-31 12-26 (80)
62 PF01650 Peptidase_C13: Peptid 30.7 1.4E+02 0.003 24.4 5.4 49 61-109 102-162 (256)
63 PF01316 Arg_repressor: Argini 30.0 22 0.00048 23.7 0.5 26 16-41 23-48 (70)
64 PF10356 DUF2034: Protein of u 29.9 1E+02 0.0023 24.2 4.4 52 67-118 86-144 (185)
65 PRK07132 DNA polymerase III su 29.6 2E+02 0.0043 24.1 6.3 51 75-126 66-125 (299)
66 cd00315 Cyt_C5_DNA_methylase C 29.6 73 0.0016 25.9 3.6 71 12-92 121-193 (275)
67 TIGR00683 nanA N-acetylneurami 29.5 1.4E+02 0.003 24.5 5.3 49 68-117 8-62 (290)
68 TIGR02546 III_secr_ATP type II 29.2 1.7E+02 0.0036 25.8 6.0 35 81-118 221-255 (422)
69 cd02643 R3H_NF-X1 R3H domain o 28.8 1.1E+02 0.0024 20.2 3.8 48 81-129 16-63 (74)
70 PF05212 DUF707: Protein of un 28.7 49 0.0011 28.1 2.4 37 69-109 119-156 (294)
71 PRK06090 DNA polymerase III su 28.5 1.7E+02 0.0036 24.8 5.7 48 68-115 76-129 (319)
72 KOG1348 Asparaginyl peptidases 28.2 1.2E+02 0.0027 26.9 4.9 41 61-101 150-202 (477)
73 cd00951 KDGDH 5-dehydro-4-deox 28.0 1.6E+02 0.0035 24.1 5.4 47 69-116 9-60 (289)
74 cd01016 TroA Metal binding pro 28.0 1.7E+02 0.0038 23.7 5.6 43 73-116 189-231 (276)
75 PRK06581 DNA polymerase III su 27.7 1.6E+02 0.0035 24.6 5.3 40 76-115 67-110 (263)
76 PF13353 Fer4_12: 4Fe-4S singl 27.5 1.9E+02 0.0042 20.1 5.2 44 67-110 54-99 (139)
77 PRK09099 type III secretion sy 27.5 1.8E+02 0.0038 25.9 5.9 73 35-118 201-273 (441)
78 PRK09426 methylmalonyl-CoA mut 27.3 2.6E+02 0.0057 26.5 7.2 89 13-118 596-685 (714)
79 cd08616 PI-PLCXD1c Catalytic d 26.8 70 0.0015 26.5 3.1 39 76-114 197-235 (290)
80 TIGR00678 holB DNA polymerase 26.6 2.3E+02 0.0049 21.1 5.7 46 69-114 67-116 (188)
81 COG1137 YhbG ABC-type (unclass 26.5 90 0.002 25.7 3.5 52 51-104 145-197 (243)
82 PF06331 Tbf5: Transcription f 26.4 77 0.0017 21.0 2.6 40 94-136 3-46 (68)
83 smart00265 BH4 BH4 Bcl-2 homol 26.3 95 0.0021 17.1 2.6 25 1-30 1-25 (27)
84 PRK06964 DNA polymerase III su 26.2 2E+02 0.0043 24.6 5.8 39 77-115 111-153 (342)
85 cd01018 ZntC Metal binding pro 26.2 3.4E+02 0.0074 21.7 9.4 43 74-117 197-239 (266)
86 PRK07594 type III secretion sy 26.1 1.8E+02 0.0039 25.8 5.7 31 85-118 235-265 (433)
87 PRK05707 DNA polymerase III su 26.1 2E+02 0.0043 24.3 5.7 48 68-115 74-127 (328)
88 cd00950 DHDPS Dihydrodipicolin 26.0 1.9E+02 0.0041 23.3 5.4 49 68-117 8-61 (284)
89 KOG0147 Transcriptional coacti 25.6 1.3E+02 0.0029 27.6 4.7 92 13-120 177-268 (549)
90 TIGR02313 HpaI-NOT-DapA 2,4-di 25.6 1.1E+02 0.0023 25.3 3.9 48 68-116 8-60 (294)
91 cd01132 F1_ATPase_alpha F1 ATP 25.5 2.5E+02 0.0055 23.4 6.1 70 38-118 112-181 (274)
92 PF08011 DUF1703: Protein of u 25.3 1.5E+02 0.0033 20.4 4.2 44 17-73 9-53 (105)
93 cd03735 SOCS_SOCS1 SOCS (suppr 25.0 72 0.0016 19.3 2.1 33 12-46 8-40 (43)
94 PF14082 DUF4263: Domain of un 25.0 99 0.0021 23.0 3.4 56 77-132 86-164 (164)
95 PRK03620 5-dehydro-4-deoxygluc 24.7 2E+02 0.0044 23.7 5.5 47 69-116 16-67 (303)
96 COG1454 EutG Alcohol dehydroge 24.6 1.8E+02 0.0039 25.4 5.3 57 72-128 6-65 (377)
97 PF12646 DUF3783: Domain of un 24.6 1.9E+02 0.004 18.1 4.6 47 69-118 3-51 (58)
98 COG4123 Predicted O-methyltran 24.4 1.3E+02 0.0027 24.8 4.1 64 15-81 153-219 (248)
99 PF03374 ANT: Phage antirepres 24.1 1.7E+02 0.0038 20.0 4.3 28 15-42 38-66 (111)
100 PRK04147 N-acetylneuraminate l 23.9 2.2E+02 0.0048 23.2 5.5 48 68-116 11-64 (293)
101 PRK01889 GTPase RsgA; Reviewed 23.7 2.2E+02 0.0047 24.2 5.6 44 66-109 114-157 (356)
102 KOG1322 GDP-mannose pyrophosph 23.7 5E+02 0.011 22.8 7.8 95 19-126 107-221 (371)
103 PF00145 DNA_methylase: C-5 cy 23.6 37 0.0008 27.1 0.8 46 13-64 121-166 (335)
104 PF08479 POTRA_2: POTRA domain 23.5 75 0.0016 20.5 2.2 24 8-31 33-56 (76)
105 PF02222 ATP-grasp: ATP-grasp 23.4 99 0.0021 23.7 3.2 68 51-134 75-155 (172)
106 PF00919 UPF0004: Uncharacteri 23.3 2.6E+02 0.0056 19.3 5.7 39 81-119 53-91 (98)
107 COG1180 PflA Pyruvate-formate 23.3 4.1E+02 0.0088 21.6 7.3 52 67-119 85-136 (260)
108 TIGR00674 dapA dihydrodipicoli 23.0 2.3E+02 0.005 23.0 5.4 49 68-117 6-59 (285)
109 COG1787 Predicted endonuclease 22.7 1.2E+02 0.0026 24.6 3.6 58 76-137 157-214 (217)
110 PRK08769 DNA polymerase III su 22.7 2.2E+02 0.0048 24.1 5.4 39 77-115 92-134 (319)
111 PRK02118 V-type ATP synthase s 22.7 2.5E+02 0.0055 25.0 5.9 71 38-118 181-251 (436)
112 PLN02417 dihydrodipicolinate s 22.6 1.3E+02 0.0029 24.5 4.0 47 68-115 9-60 (280)
113 cd00408 DHDPS-like Dihydrodipi 22.5 1.3E+02 0.0028 24.1 3.8 48 68-116 5-57 (281)
114 cd03110 Fer4_NifH_child This p 22.2 3.2E+02 0.0069 19.9 6.0 41 66-107 116-156 (179)
115 PRK08699 DNA polymerase III su 22.2 3.5E+02 0.0077 22.7 6.5 40 77-116 92-135 (325)
116 PF03013 Pyr_excise: Pyrimidin 22.0 75 0.0016 23.6 2.2 27 8-34 58-84 (130)
117 PF05846 Chordopox_A15: Chordo 21.9 34 0.00074 24.1 0.3 12 129-140 48-59 (90)
118 PF13177 DNA_pol3_delta2: DNA 21.9 2.8E+02 0.0061 20.5 5.4 48 68-115 70-123 (162)
119 PF08190 PIH1: pre-RNA process 21.7 2.3E+02 0.005 23.1 5.2 49 81-143 8-58 (328)
120 COG1676 SEN2 tRNA splicing end 21.7 34 0.00074 26.8 0.3 14 18-31 94-107 (181)
121 COG3432 Predicted transcriptio 21.6 1.1E+02 0.0023 21.8 2.7 16 12-27 45-60 (95)
122 PF02113 Peptidase_S13: D-Ala- 21.4 2E+02 0.0043 25.4 5.0 33 66-98 82-114 (444)
123 cd02029 PRK_like Phosphoribulo 21.1 4.9E+02 0.011 21.9 7.0 101 5-114 150-268 (277)
124 PF02645 DegV: Uncharacterised 21.1 3.3E+02 0.0072 22.0 6.0 73 33-127 39-115 (280)
125 TIGR00454 conserved hypothetic 21.1 1.5E+02 0.0033 22.5 3.8 41 66-106 90-130 (183)
126 PTZ00096 40S ribosomal protein 21.0 63 0.0014 24.6 1.6 26 23-49 16-41 (143)
127 PF01297 TroA: Periplasmic sol 21.0 4.1E+02 0.0088 20.9 6.4 41 72-114 177-217 (256)
128 PF15472 DUF4638: Domain of un 20.9 55 0.0012 27.1 1.3 16 16-31 231-246 (268)
129 TIGR02764 spore_ybaN_pdaB poly 20.3 55 0.0012 24.7 1.1 21 76-96 163-183 (191)
130 smart00576 BTP Bromodomain tra 20.2 93 0.002 20.5 2.1 33 14-46 8-40 (77)
131 PF00701 DHDPS: Dihydrodipicol 20.1 1.6E+02 0.0035 23.8 3.9 49 68-117 9-62 (289)
132 PRK05922 type III secretion sy 20.0 3.4E+02 0.0073 24.2 6.1 36 80-118 232-267 (434)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=1.7e-60 Score=371.98 Aligned_cols=140 Identities=50% Similarity=0.773 Sum_probs=138.0
Q ss_pred CcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCC-CCCcceEEEeecCCCCCCcEEEEcCCCCccchh
Q 032325 3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN-MKREDLVINKALRNDSSDQIYVFFPDEQKVGVK 81 (143)
Q Consensus 3 ~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk 81 (143)
+++.|++||||+|||++||||||||.|+|+|++++|++|+++||+. |+|++|+|+|.|++||+++||||||++++||+|
T Consensus 4 ~~e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk 83 (208)
T KOG3218|consen 4 SKEEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVK 83 (208)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHH
Confidence 5689999999999999999999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325 82 TMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN 142 (143)
Q Consensus 82 ~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~ 142 (143)
+||.|+.+|+++|+++||+|+|++|||+|++++..++|+|+||+|+|+|||||||||+|||
T Consensus 84 ~~k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvP 144 (208)
T KOG3218|consen 84 TMKTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVP 144 (208)
T ss_pred HHHHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecC
Confidence 9999999999999999999999999999999999999999999999999999999999999
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=1.4e-58 Score=365.47 Aligned_cols=142 Identities=53% Similarity=0.818 Sum_probs=139.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccch
Q 032325 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGV 80 (143)
Q Consensus 1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv 80 (143)
|+++++|+.||||+|||++|||+||||.|+++|+++|+++|+++||++++|++|+|+|.+++||+++||||||++++||+
T Consensus 1 ~~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgv 80 (206)
T PLN03111 1 MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGV 80 (206)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCH
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN 142 (143)
Q Consensus 81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~ 142 (143)
|+||+|+++|+++|++|||||+|++|||+|+++++++++.|+||+|+|+|||||||+|+|||
T Consensus 81 k~ir~~~~~~~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVP 142 (206)
T PLN03111 81 KTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVP 142 (206)
T ss_pred HHHHHHHHHHhhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecC
Confidence 99999999999999999999999999999999999998889999999999999999999999
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=5.4e-57 Score=355.97 Aligned_cols=138 Identities=34% Similarity=0.552 Sum_probs=133.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCC-CCcceEEEeecCCCCCCcEEEEcCC-CCccchhH
Q 032325 5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-KREDLVINKALRNDSSDQIYVFFPD-EQKVGVKT 82 (143)
Q Consensus 5 ~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~-~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~ 82 (143)
++++.||||+|||++|||+||||.|+++|+++|+++|+++||+++ .|++|+|+|++++||+++||||||+ +++||+|+
T Consensus 2 ~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~ 81 (205)
T PTZ00061 2 DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKP 81 (205)
T ss_pred cHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHH
Confidence 378899999999999999999999999999999999999999985 5899999999999999999999999 57999999
Q ss_pred HHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325 83 MKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN 142 (143)
Q Consensus 83 ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~ 142 (143)
||+|+++|+++|++|||||+|++|||+|+++++++++.|+||+|+|+|||||||+|+|||
T Consensus 82 ir~~~~~~~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVP 141 (205)
T PTZ00061 82 IRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVP 141 (205)
T ss_pred HHHHHHHHhhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecC
Confidence 999999999999999999999999999999999999889999999999999999999999
No 4
>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....
Probab=100.00 E-value=1.2e-38 Score=224.98 Aligned_cols=90 Identities=62% Similarity=1.022 Sum_probs=75.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcEEEEcCCCCc
Q 032325 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQIYVFFPDEQK 77 (143)
Q Consensus 1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~ 77 (143)
|+ +++|++||||||||++|||+||||.|+++|+++|+++|+++||+ .++|++|+|+|.+++||+++|+||||++++
T Consensus 1 m~-~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~k 79 (93)
T PF03871_consen 1 MD-DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPK 79 (93)
T ss_dssp ---TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSC
T ss_pred Cc-cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCC
Confidence 55 56999999999999999999999999999999999999999999 688999999999999999999999999999
Q ss_pred cchhHHHHHHHHHh
Q 032325 78 VGVKTMKTYTNRMK 91 (143)
Q Consensus 78 vgvk~ik~~~~~~~ 91 (143)
||+|+||+|+++|+
T Consensus 80 vgvk~Ir~~~~~m~ 93 (93)
T PF03871_consen 80 VGVKTIRKYCERMK 93 (93)
T ss_dssp ESCCCCHHHCHHH-
T ss_pred cCHHHHHHHHHhcC
Confidence 99999999999985
No 5
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=97.40 E-value=0.00051 Score=47.51 Aligned_cols=75 Identities=19% Similarity=0.274 Sum_probs=42.5
Q ss_pred eEEEeecCCCCCCcEEEEcCC-CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceE
Q 032325 54 LVINKALRNDSSDQIYVFFPD-EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVF 131 (143)
Q Consensus 54 L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~EL 131 (143)
.-+.+.+.+.....++|.+-. ..+++.+.|+.++..+...+..++|+|+.+++||.|++.+.... .|+++.-++|
T Consensus 36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L 111 (115)
T PF04471_consen 36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDL 111 (115)
T ss_dssp EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH----------------
T ss_pred EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---cccccccccc
Confidence 334444433233467777633 35899999999999999999999999999999999999888754 4777766665
No 6
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=80.85 E-value=8.5 Score=28.37 Aligned_cols=86 Identities=10% Similarity=0.074 Sum_probs=56.4
Q ss_pred HHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC
Q 032325 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~ 95 (143)
+-+.-||++-||.|-+.-...|.++|.+..-+. +.+ +++. |.-..-.+..++..++.+++++.
T Consensus 20 ~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~-~ad---------------ii~i-Ssl~~~~~~~~~~~~~~L~~~g~ 82 (132)
T TIGR00640 20 KVIATAYADLGFDVDVGPLFQTPEEIARQAVEA-DVH---------------VVGV-SSLAGGHLTLVPALRKELDKLGR 82 (132)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCC---------------EEEE-cCchhhhHHHHHHHHHHHHhcCC
Confidence 445679999999999988889999998876432 111 1111 22112336678999999999887
Q ss_pred CeEEEEEcCCCCHHHHHHHHhcc
Q 032325 96 FRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 96 ~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
....+++.+.+.+.-...+.++.
T Consensus 83 ~~i~vivGG~~~~~~~~~l~~~G 105 (132)
T TIGR00640 83 PDILVVVGGVIPPQDFDELKEMG 105 (132)
T ss_pred CCCEEEEeCCCChHhHHHHHHCC
Confidence 65555566656655445555543
No 7
>PRK03298 hypothetical protein; Provisional
Probab=79.69 E-value=3.7 Score=33.43 Aligned_cols=49 Identities=22% Similarity=0.394 Sum_probs=36.7
Q ss_pred EEEEc--CCCCccchhHHHHHHHHHhhc---CCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 68 IYVFF--PDEQKVGVKTMKTYTNRMKSE---NVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 68 i~VfF--~~~~~vgvk~ik~~~~~~~~e---n~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
++|.. -.+.. ||.+++.|++.+..+ .-=|||||. +.+||.|+..+.+-.
T Consensus 149 V~vEvKRr~~id-aV~QL~RYve~l~rd~~~~~VRGIlvA-p~It~~Ar~Ll~drG 202 (224)
T PRK03298 149 VAVEIKRRGEID-GVEQLTRYLELLNRDPLLAPVRGVFAA-QEIKPQARTLAEDRG 202 (224)
T ss_pred EEEEEEecCCcc-HHHHHHHHHHHHhhCcCcCCceEEEEC-CcCCHHHHHHHHHcC
Confidence 55555 22223 899999999999765 346899997 589999999888643
No 8
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=77.75 E-value=17 Score=26.96 Aligned_cols=74 Identities=16% Similarity=0.240 Sum_probs=52.6
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCC
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVF 96 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~ 96 (143)
=+.-||++.||.|-+--...|.++|.+...+. +.+-+-+++- -.-.+..++...+.+.++++.
T Consensus 18 iv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~-~adiVglS~L----------------~t~~~~~~~~~~~~l~~~gl~ 80 (128)
T cd02072 18 ILDHAFTEAGFNVVNLGVLSPQEEFIDAAIET-DADAILVSSL----------------YGHGEIDCKGLREKCDEAGLK 80 (128)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEecc----------------ccCCHHHHHHHHHHHHHCCCC
Confidence 34559999999999988899999999987543 2222333321 123467788999999999996
Q ss_pred eEEEEEcCCCC
Q 032325 97 RAILVVQQNLT 107 (143)
Q Consensus 97 r~IlV~q~~lt 107 (143)
...+++.+.+.
T Consensus 81 ~v~vivGG~~~ 91 (128)
T cd02072 81 DILLYVGGNLV 91 (128)
T ss_pred CCeEEEECCCC
Confidence 66667777763
No 9
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=73.53 E-value=8.9 Score=30.88 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.5
Q ss_pred EcCCCCccchhHHHHHHHHHhh-cCCCeEEEEEcCCCCHHHHHHHH
Q 032325 71 FFPDEQKVGVKTMKTYTNRMKS-ENVFRAILVVQQNLTPFARTCIQ 115 (143)
Q Consensus 71 fF~~~~~vgvk~ik~~~~~~~~-en~~r~IlV~q~~ltp~Ar~~i~ 115 (143)
+|+.+ .+||.+||.+++.+.- .+-.+.|+.--..||+.|.-|+-
T Consensus 31 ~f~~~-~i~Vd~iReii~~~~~~~~~~k~iI~~a~~l~~~A~NaLL 75 (206)
T PRK08485 31 FFIKE-EFKIEDAKEVIAEAYIAESEEKIIVIAAPSYGIEAQNALL 75 (206)
T ss_pred EECCC-CCCHHHHHHHHHHHhhCCCCcEEEEEchHhhCHHHHHHHH
Confidence 34333 7999999999999742 33445565566678988876654
No 10
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=72.19 E-value=28 Score=24.26 Aligned_cols=83 Identities=22% Similarity=0.217 Sum_probs=51.4
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC-
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV- 95 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~- 95 (143)
=+..+|+..||.|..-..+.+.+++.+...+. +++- +.+.+..+ -....++.+++.+++.+-
T Consensus 18 ~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~~-~pdv--------------V~iS~~~~--~~~~~~~~~i~~l~~~~~~ 80 (119)
T cd02067 18 IVARALRDAGFEVIDLGVDVPPEEIVEAAKEE-DADA--------------IGLSGLLT--THMTLMKEVIEELKEAGLD 80 (119)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCE--------------EEEecccc--ccHHHHHHHHHHHHHcCCC
Confidence 35578999999998777788999998765322 1211 11222222 246888999999988866
Q ss_pred CeEEEEEcCCCCHHHHHHHHhc
Q 032325 96 FRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 96 ~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
.-.|+|.....+... +.+.++
T Consensus 81 ~~~i~vGG~~~~~~~-~~~~~~ 101 (119)
T cd02067 81 DIPVLVGGAIVTRDF-KFLKEI 101 (119)
T ss_pred CCeEEEECCCCChhH-HHHHHc
Confidence 444566555555433 334443
No 11
>PF01939 DUF91: Protein of unknown function DUF91; InterPro: IPR002793 The function of these prokaryotic proteins is unknown. Computational analysis suggests that they may form a restriction endonuclease-like fold, similar to that found in a variety of endonucleases and DNA repair enzymes [].; PDB: 2VLD_A.
Probab=71.71 E-value=5.6 Score=32.40 Aligned_cols=56 Identities=23% Similarity=0.389 Sum_probs=35.8
Q ss_pred cEEEEcCCC--CccchhHHHHHHHHHhhcC---CCeEEEEEcCCCCHHHHHHHHhccccceEeeec
Q 032325 67 QIYVFFPDE--QKVGVKTMKTYTNRMKSEN---VFRAILVVQQNLTPFARTCIQEISAKFHLEVFQ 127 (143)
Q Consensus 67 ~i~VfF~~~--~~vgvk~ik~~~~~~~~en---~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~ 127 (143)
-+.|+.--. ..=++.++..|++.+.++. --|||||.++ +|+.|+..+.+. .||+..
T Consensus 149 ~VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~~----glef~~ 209 (228)
T PF01939_consen 149 LVVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLEDR----GLEFVE 209 (228)
T ss_dssp EEEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHHH----T-EEEE
T ss_pred EEEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHHc----CCEEEE
Confidence 466666432 2346788888999886533 3489999865 999999988764 355554
No 12
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=69.88 E-value=22 Score=26.49 Aligned_cols=74 Identities=18% Similarity=0.262 Sum_probs=51.7
Q ss_pred HHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC
Q 032325 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~ 95 (143)
+-+.-||++.||.|-+-=...|.++|.+..-+. +.+-+-++... --....++...+.+.+++.
T Consensus 19 ~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~-~adiVglS~l~----------------~~~~~~~~~~~~~l~~~gl 81 (134)
T TIGR01501 19 KILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET-KADAILVSSLY----------------GHGEIDCKGLRQKCDEAGL 81 (134)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEeccc----------------ccCHHHHHHHHHHHHHCCC
Confidence 456779999999999988888999999986433 23333333211 1235568889999999998
Q ss_pred CeEEEEEcCCC
Q 032325 96 FRAILVVQQNL 106 (143)
Q Consensus 96 ~r~IlV~q~~l 106 (143)
....+|+.+.+
T Consensus 82 ~~~~vivGG~~ 92 (134)
T TIGR01501 82 EGILLYVGGNL 92 (134)
T ss_pred CCCEEEecCCc
Confidence 66556666653
No 13
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=69.38 E-value=8.1 Score=32.05 Aligned_cols=59 Identities=22% Similarity=0.326 Sum_probs=43.9
Q ss_pred EEEEcCCC--CccchhHHHHHHHHHhhcCCC--eEEEEEcCCCCHHHHHHHHhccccc-eEeeec
Q 032325 68 IYVFFPDE--QKVGVKTMKTYTNRMKSENVF--RAILVVQQNLTPFARTCIQEISAKF-HLEVFQ 127 (143)
Q Consensus 68 i~VfF~~~--~~vgvk~ik~~~~~~~~en~~--r~IlV~q~~ltp~Ar~~i~~~~~~~-~iE~F~ 127 (143)
+.|..--. .-.++.+++-|.+.+.+...- |||||.| .+|+.|++.+..-.=.| ++|-..
T Consensus 175 viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~VRGiLvAp-~it~~a~~ll~~~GLef~kle~~~ 238 (253)
T COG1637 175 VIIELKRRKAGLSAVSQLKRYVELLREDTGDKVRGILVAP-SITEQARRLLEDEGLEFVKLEPPK 238 (253)
T ss_pred EEEEEecccCCchHHHHHHHHHHHcccccCceEEEEEEcc-cccHHHHHHHHHcCceEEEcCCch
Confidence 45555332 357899999999999888877 9999975 79999999998733223 666555
No 14
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=68.77 E-value=2.5 Score=36.83 Aligned_cols=29 Identities=17% Similarity=0.508 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCC-cccchhhhccCHHHHHHH
Q 032325 14 IRRTVMQMLRDRG-YFVGDFEINMSKEQFIAK 44 (143)
Q Consensus 14 irrTv~eMl~DRG-Y~V~~~e~~~sl~~F~~~ 44 (143)
.|++++|+++|+| |.|.+ -+.|.++|++-
T Consensus 288 TR~sileLa~~~g~~~V~E--r~vtv~e~~~A 317 (379)
T KOG0975|consen 288 TRKSILELARDLGEFKVEE--RDVTVDELKTA 317 (379)
T ss_pred cHHHHHHHHHHhCceEEEE--EEEeHHHhhhh
Confidence 4899999999999 99987 55578888754
No 15
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=66.04 E-value=37 Score=24.13 Aligned_cols=75 Identities=12% Similarity=0.062 Sum_probs=49.0
Q ss_pred HHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCe
Q 032325 18 VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97 (143)
Q Consensus 18 v~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r 97 (143)
+.-|++..||.|..--.+.+.+++.+.-.+. +.+- +.+.+.. .-....++.+++.+++.+...
T Consensus 19 ~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~-~~d~--------------V~iS~~~--~~~~~~~~~~~~~L~~~~~~~ 81 (122)
T cd02071 19 IARALRDAGFEVIYTGLRQTPEEIVEAAIQE-DVDV--------------IGLSSLS--GGHMTLFPEVIELLRELGAGD 81 (122)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCE--------------EEEcccc--hhhHHHHHHHHHHHHhcCCCC
Confidence 3458999999998877778899998765322 1111 2222333 234667899999999987765
Q ss_pred EEEEEcCCCCHH
Q 032325 98 AILVVQQNLTPF 109 (143)
Q Consensus 98 ~IlV~q~~ltp~ 109 (143)
..+++.+...+.
T Consensus 82 i~i~~GG~~~~~ 93 (122)
T cd02071 82 ILVVGGGIIPPE 93 (122)
T ss_pred CEEEEECCCCHH
Confidence 555565555443
No 16
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=64.00 E-value=45 Score=24.62 Aligned_cols=73 Identities=19% Similarity=0.200 Sum_probs=49.6
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCC
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVF 96 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~ 96 (143)
-+.-||++.||.|..-=.+.+.++|.+.-.+. +.+-+- +.+... -....++.+++.+.+.+..
T Consensus 22 iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~-~~d~V~--------------lS~~~~--~~~~~~~~~~~~L~~~~~~ 84 (137)
T PRK02261 22 ILDRALTEAGFEVINLGVMTSQEEFIDAAIET-DADAIL--------------VSSLYG--HGEIDCRGLREKCIEAGLG 84 (137)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEE--------------EcCccc--cCHHHHHHHHHHHHhcCCC
Confidence 34568999999999866778999998864322 122222 222222 3577889999999988886
Q ss_pred eEEEEEcCCC
Q 032325 97 RAILVVQQNL 106 (143)
Q Consensus 97 r~IlV~q~~l 106 (143)
...+++.+.+
T Consensus 85 ~~~i~vGG~~ 94 (137)
T PRK02261 85 DILLYVGGNL 94 (137)
T ss_pred CCeEEEECCC
Confidence 6656677776
No 17
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=62.35 E-value=12 Score=27.82 Aligned_cols=81 Identities=10% Similarity=0.201 Sum_probs=54.2
Q ss_pred HHHHHHHhcCCCCCcceEEEeecCCCCC-CcEEE-EcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-CCCHHHHHHH
Q 032325 38 KEQFIAKFGENMKREDLVINKALRNDSS-DQIYV-FFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-NLTPFARTCI 114 (143)
Q Consensus 38 l~~F~~~y~~~~~r~~L~~~~~~~~dp~-~~i~V-fF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-~ltp~Ar~~i 114 (143)
..+|-.+++.+..-.-.-+++..+++.. --|-+ ||.++.+|..+.|-.|........+.+.|||.-. ++++.|.++|
T Consensus 16 w~dwp~~~~~~~~DtGIDLVA~~~~~g~~~AIQCKfY~~~~~I~k~didSF~s~sgk~~f~~rliisTt~~~s~nAe~~l 95 (129)
T PF13156_consen 16 WSDWPERYGWGGKDTGIDLVARTRDGGEYWAIQCKFYDPDHTIQKSDIDSFFSASGKSRFSRRLIISTTDKWSKNAEKAL 95 (129)
T ss_pred hhhhhHhhCCCCCCCCEeEEEEEcCCCcEEEEEEEeeCCCceEcHHHhhHHHHhcCCccccCcEEEEcCcHhhHHHHHHH
Confidence 4455555543322222555665444321 12433 4466679999999999999988889999888554 7999999999
Q ss_pred Hhcc
Q 032325 115 QEIS 118 (143)
Q Consensus 115 ~~~~ 118 (143)
..-.
T Consensus 96 ~~q~ 99 (129)
T PF13156_consen 96 ENQS 99 (129)
T ss_pred HcCC
Confidence 9765
No 18
>PLN02559 chalcone--flavonone isomerase
Probab=62.28 E-value=5.6 Score=32.54 Aligned_cols=79 Identities=18% Similarity=0.229 Sum_probs=44.4
Q ss_pred ccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHH
Q 032325 35 NMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114 (143)
Q Consensus 35 ~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i 114 (143)
.-.++.|.+-|-+..-+.--.|..... |..++.+-|+.|.++.-+..-.+-.+...+-+...+ |-..+.+|+||+++
T Consensus 128 ~~aLekF~~~Fk~~~fp~Gs~I~ft~s--p~g~L~isfs~dg~ipe~~~~~Ienk~l~eAv~e~~-IG~~~VSP~aK~sl 204 (230)
T PLN02559 128 AKAVEKFKEAFKEETFPPGSSILFTHS--PTGSLTVAFSKDSSVPEVGNAVIENKLLCEAVLESI-IGKHGVSPAAKLSL 204 (230)
T ss_pred HHHHHHHHHHhcCCCCCCCCEEEEEEC--CCCcEEEEEecCCCCCccceEEEechHHHHHHHHHH-ccCCCCCHHHHHHH
Confidence 447899999997653333333443333 556788888776543222211111222222222333 37788999999988
Q ss_pred Hh
Q 032325 115 QE 116 (143)
Q Consensus 115 ~~ 116 (143)
.+
T Consensus 205 A~ 206 (230)
T PLN02559 205 AA 206 (230)
T ss_pred HH
Confidence 75
No 19
>PRK04280 arginine repressor; Provisional
Probab=60.33 E-value=29 Score=26.17 Aligned_cols=87 Identities=10% Similarity=0.117 Sum_probs=44.5
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCc-EEEEcCCCCccchhHHHHHHHHH-hh-c
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQ-IYVFFPDEQKVGVKTMKTYTNRM-KS-E 93 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~-i~VfF~~~~~vgvk~ik~~~~~~-~~-e 93 (143)
-+.+.|+++|+.|+|.-+.-++.+ |.++ +..+++++ .|+.+.+...-....++..+... .+ +
T Consensus 23 eL~~~L~~~Gi~vTQATiSRDike-------------L~lv--Kv~~~~G~~~Y~lp~~~~~~~~~~l~~~~~~~v~sv~ 87 (148)
T PRK04280 23 ELVDRLREEGFNVTQATVSRDIKE-------------LHLV--KVPLPDGRYKYSLPADQRFNPLQKLKRALMDSFVKID 87 (148)
T ss_pred HHHHHHHHcCCCeehHHHHHHHHH-------------cCCE--EeecCCCcEEEeeccccccchHHHHHHHHHHHEEEEe
Confidence 467889999999999877544433 3333 23333333 56554432211122333333322 22 2
Q ss_pred CCCeEEEE-EcCCCCHHHHHHHHhcc
Q 032325 94 NVFRAILV-VQQNLTPFARTCIQEIS 118 (143)
Q Consensus 94 n~~r~IlV-~q~~ltp~Ar~~i~~~~ 118 (143)
.....|+| +..+-.+....+|+.+.
T Consensus 88 ~~~~~vvikT~pG~A~~va~~iD~~~ 113 (148)
T PRK04280 88 GAGNLLVLKTLPGNANSIGALIDNLD 113 (148)
T ss_pred eeCCEEEEEcCCChHHHHHHHHHhCC
Confidence 23333333 33355666667777765
No 20
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=60.31 E-value=1e+02 Score=25.73 Aligned_cols=81 Identities=11% Similarity=0.147 Sum_probs=47.5
Q ss_pred HHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcC
Q 032325 15 RRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSEN 94 (143)
Q Consensus 15 rrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en 94 (143)
.+..+.-+.+|.+.+... .+.-|.+.||=. .... +-...+...+.+.|..+++.+++++
T Consensus 194 ~~~~l~~~~~~~~i~~H~----af~Yf~~~ygl~-------~~~~----------~~~~~~~eps~~~l~~l~~~ik~~~ 252 (311)
T PRK09545 194 IGNQLAPVKGKGYFVFHD----AYGYFEKHYGLT-------PLGH----------FTVNPEIQPGAQRLHEIRTQLVEQK 252 (311)
T ss_pred HHHHhhccCCCcEEEECc----hHHHHHHhCCCc-------eeee----------eccCCCCCCCHHHHHHHHHHHHHcC
Confidence 333444455566555332 566777777622 2110 1123344678999999999999999
Q ss_pred CCeEEEEEcCCCCHHHHHHHHhc
Q 032325 95 VFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 95 ~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
++ +|++=++.-++.++...++.
T Consensus 253 v~-~If~e~~~~~~~~~~la~e~ 274 (311)
T PRK09545 253 AT-CVFAEPQFRPAVIESVAKGT 274 (311)
T ss_pred CC-EEEecCCCChHHHHHHHHhc
Confidence 98 66665544444554444433
No 21
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=58.05 E-value=27 Score=28.71 Aligned_cols=42 Identities=14% Similarity=0.350 Sum_probs=32.3
Q ss_pred CCCccchhHHHHHHHHHh---hcCCCeEEEEEc-CCCCHHHHHHHH
Q 032325 74 DEQKVGVKTMKTYTNRMK---SENVFRAILVVQ-QNLTPFARTCIQ 115 (143)
Q Consensus 74 ~~~~vgvk~ik~~~~~~~---~en~~r~IlV~q-~~ltp~Ar~~i~ 115 (143)
+...+++.+||..++.+. -++=.|.+||.. ..||+.|..++-
T Consensus 69 ~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLL 114 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFL 114 (313)
T ss_pred cCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHH
Confidence 556799999999999764 356677888877 789987765554
No 22
>COG1715 Mrr Restriction endonuclease [Defense mechanisms]
Probab=57.57 E-value=43 Score=28.55 Aligned_cols=54 Identities=19% Similarity=0.341 Sum_probs=46.1
Q ss_pred CcEEEEc-CCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccc
Q 032325 66 DQIYVFF-PDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119 (143)
Q Consensus 66 ~~i~VfF-~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~ 119 (143)
|.|||-= ..+..||...|++|..-+.-...++|++|+-+.-|+.|+.-.+.+.+
T Consensus 214 d~iyiQAKR~~~tv~rpEIq~FagaL~g~kA~~GVFitTS~fs~~A~~~a~~i~~ 268 (308)
T COG1715 214 DRIYVQAKRWKNTVGRPEIQEFAGALEGHKAKRGVFITTSGFSAGARAYAERILG 268 (308)
T ss_pred eeEEEEeeecCCCcCCHHHHHHHHHhhhhccCCcEEEECCCCCHHHHHHHHhccC
Confidence 5677765 45668999999999999999999999999999999999777666554
No 23
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=57.09 E-value=75 Score=23.59 Aligned_cols=56 Identities=25% Similarity=0.205 Sum_probs=30.8
Q ss_pred HhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcC
Q 032325 21 MLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSEN 94 (143)
Q Consensus 21 Ml~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en 94 (143)
=||+|||.|.+. . +||. + +... ..+.+.-++....+...+....|-.+......-+
T Consensus 43 DLR~RGyvVk~G-~---------kfg~------~-~~~~-~~~~s~ylV~Vl~E~~~is~~eL~~~vr~a~svr 98 (124)
T PRK09539 43 DLKQRGRKTIDG-I---------DEIS------L-IIKD-KENKYTAMVLIVDENEKVSFKKILDKLHFSKSMN 98 (124)
T ss_pred hHHhCCCeeccC-C---------ceeE------E-EEec-CCCCceEEEEEecCCCccCHHHHHHHHHHHhhcc
Confidence 489999999772 1 1221 1 1111 2233333333346677899999977666555333
No 24
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=54.67 E-value=40 Score=28.54 Aligned_cols=48 Identities=17% Similarity=0.297 Sum_probs=35.3
Q ss_pred EEEEcCCC--CccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDE--QKVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~--~~vgvk~ik~~~~~~~---~en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
++..+|+. ..+||.+||.+.+.+. .+|-.+.+||- -..||+.|..++-
T Consensus 76 ~~~i~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLL 129 (334)
T PRK07993 76 YYTLTPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALL 129 (334)
T ss_pred EEEEecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHH
Confidence 66667775 3599999999999985 45666777775 3679987766554
No 25
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=54.17 E-value=35 Score=28.59 Aligned_cols=48 Identities=13% Similarity=0.247 Sum_probs=35.2
Q ss_pred EEEEcCCCCccchhHHHHHHHHHh---hcCCCeEEEEEc-CCCCHHHHHHHH
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMK---SENVFRAILVVQ-QNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~---~en~~r~IlV~q-~~ltp~Ar~~i~ 115 (143)
+....++...+++.+||..++.+. -++-.+.+||-. ..||..|..++-
T Consensus 80 ~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLL 131 (329)
T PRK08058 80 VHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLL 131 (329)
T ss_pred EEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHH
Confidence 444456667899999999999987 456677888866 668887655544
No 26
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=54.16 E-value=34 Score=25.36 Aligned_cols=80 Identities=10% Similarity=0.243 Sum_probs=42.8
Q ss_pred HHHHHHhcCCCcccc-----hhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHH
Q 032325 16 RTVMQMLRDRGYFVG-----DFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRM 90 (143)
Q Consensus 16 rTv~eMl~DRGY~V~-----~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~ 90 (143)
-++++++++||.-++ -.+..++..++.+.|.+. |.-++.+.|-+. ++.=+.|.+.+
T Consensus 15 ~~~~~~~~~~g~g~s~~vs~Gn~~dv~~~d~l~~~~~D---------------~~t~~I~ly~E~----~~d~~~f~~~~ 75 (138)
T PF13607_consen 15 TAILDWAQDRGIGFSYVVSVGNEADVDFADLLEYLAED---------------PDTRVIVLYLEG----IGDGRRFLEAA 75 (138)
T ss_dssp HHHHHHHHHTT-EESEEEE-TT-SSS-HHHHHHHHCT----------------SS--EEEEEES------S-HHHHHHHH
T ss_pred HHHHHHHHHcCCCeeEEEEeCccccCCHHHHHHHHhcC---------------CCCCEEEEEccC----CCCHHHHHHHH
Confidence 467889999988775 245577899999887654 444455555552 33348888888
Q ss_pred hhcCCCeEEEEEcCCCCHHHHHHH
Q 032325 91 KSENVFRAILVVQQNLTPFARTCI 114 (143)
Q Consensus 91 ~~en~~r~IlV~q~~ltp~Ar~~i 114 (143)
.+-...+=|++++.+-|+..+++.
T Consensus 76 ~~a~~~KPVv~lk~Grt~~g~~aa 99 (138)
T PF13607_consen 76 RRAARRKPVVVLKAGRTEAGARAA 99 (138)
T ss_dssp HHHCCCS-EEEEE-----------
T ss_pred HHHhcCCCEEEEeCCCchhhhhhh
Confidence 776666788888888877665543
No 27
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=53.94 E-value=75 Score=24.55 Aligned_cols=75 Identities=20% Similarity=0.228 Sum_probs=48.4
Q ss_pred HHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC--
Q 032325 18 VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV-- 95 (143)
Q Consensus 18 v~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~-- 95 (143)
+-.+++..||.|..--.+.+.++|.+.-... +++-+.++ +... -....++.+++.+++.+.
T Consensus 102 v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~-~~d~v~lS--------------~~~~--~~~~~~~~~i~~lr~~~~~~ 164 (201)
T cd02070 102 VATMLEANGFEVIDLGRDVPPEEFVEAVKEH-KPDILGLS--------------ALMT--TTMGGMKEVIEALKEAGLRD 164 (201)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEe--------------cccc--ccHHHHHHHHHHHHHCCCCc
Confidence 4457888999987655677888888765322 12222222 2222 236789999999998876
Q ss_pred CeEEEEEcCCCCHH
Q 032325 96 FRAILVVQQNLTPF 109 (143)
Q Consensus 96 ~r~IlV~q~~ltp~ 109 (143)
.--|+|-...+++.
T Consensus 165 ~~~i~vGG~~~~~~ 178 (201)
T cd02070 165 KVKVMVGGAPVNQE 178 (201)
T ss_pred CCeEEEECCcCCHH
Confidence 44567766667764
No 28
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=53.00 E-value=50 Score=28.02 Aligned_cols=48 Identities=13% Similarity=0.297 Sum_probs=34.1
Q ss_pred EEEEcCC-CCccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPD-EQKVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~-~~~vgvk~ik~~~~~~~---~en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
+++..|. ...+||.+||.+++.+. .+|-.+.++|- -..||+.|..|+-
T Consensus 76 ~~~i~p~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLL 128 (325)
T PRK06871 76 FHILEPIDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALL 128 (325)
T ss_pred EEEEccccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHH
Confidence 5555564 45699999999999875 45666777664 4569987766654
No 29
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=50.72 E-value=44 Score=28.05 Aligned_cols=48 Identities=15% Similarity=0.209 Sum_probs=35.0
Q ss_pred EEEEcCCCC--ccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDEQ--KVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~--~vgvk~ik~~~~~~~---~en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
+++.+|+.. .++|.+||.+.+.+. .++-.+.++|. ..+||+.|..++-
T Consensus 63 ~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLL 116 (290)
T PRK05917 63 IHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFL 116 (290)
T ss_pred EEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHH
Confidence 666678764 389999999999985 34666666664 5679988876654
No 30
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=49.58 E-value=16 Score=32.62 Aligned_cols=40 Identities=20% Similarity=0.488 Sum_probs=32.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHH
Q 032325 2 TLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFI 42 (143)
Q Consensus 2 ~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~ 42 (143)
+.|+.+..++|++|..+=+-|..-|| |-..++.+.++++-
T Consensus 365 a~d~~~~~~lW~~Re~ip~a~~~~g~-vyKyDvSLpL~d~Y 404 (511)
T KOG1232|consen 365 AQDEAEAQKLWKIRESIPEALQKAGG-VYKYDVSLPLEDLY 404 (511)
T ss_pred cCCHHHHHHHHHHHhccHHHHHhcCC-EEEeeccccHHHHH
Confidence 45678999999999999999999994 55667777777663
No 31
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=48.13 E-value=60 Score=23.27 Aligned_cols=57 Identities=11% Similarity=0.200 Sum_probs=35.9
Q ss_pred HHHHHHHhcCC----CCCcceEEEeecCCCCCCcEEEEcCCC-CccchhHHHHHHHHHhhcCCCe
Q 032325 38 KEQFIAKFGEN----MKREDLVINKALRNDSSDQIYVFFPDE-QKVGVKTMKTYTNRMKSENVFR 97 (143)
Q Consensus 38 l~~F~~~y~~~----~~r~~L~~~~~~~~dp~~~i~VfF~~~-~~vgvk~ik~~~~~~~~en~~r 97 (143)
+.+|.++|... |.-+..-|++-+++. .-+-|-|++- ..+ .+.||.+++..++.|++.
T Consensus 45 lmdFIsryARTDEImPEDKTvGFvviN~dK--K~mSvsFsdideNm-K~~i~ei~kkykd~Gykv 106 (110)
T PF11513_consen 45 LMDFISRYARTDEIMPEDKTVGFVVINKDK--KMMSVSFSDIDENM-KNSIEEIVKKYKDSGYKV 106 (110)
T ss_dssp HHHHHHHH---S---TTSEEEEEEEEETTT--TEEEEEE-S--CCH-HHHHHHHHHHHHCCS-EE
T ss_pred HHHHHHHhhcccccCCCCceeEEEEEecCC--eEEEEEecchhHHH-HHHHHHHHHHhhcCCcee
Confidence 88999999643 333445566554433 3478889863 444 788999999998888764
No 32
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=47.45 E-value=1.1e+02 Score=23.77 Aligned_cols=76 Identities=20% Similarity=0.167 Sum_probs=51.0
Q ss_pred HHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCC-
Q 032325 18 VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVF- 96 (143)
Q Consensus 18 v~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~- 96 (143)
+..|++..||.|..--.+.+.++|.+..-+. +++-+.+++. -. -.+..++.+++.+.+.+..
T Consensus 104 v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~-~pd~v~lS~~--------------~~--~~~~~~~~~i~~l~~~~~~~ 166 (197)
T TIGR02370 104 VVTMLRANGFDVIDLGRDVPIDTVVEKVKKE-KPLMLTGSAL--------------MT--TTMYGQKDINDKLKEEGYRD 166 (197)
T ss_pred HHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCCEEEEccc--------------cc--cCHHHHHHHHHHHHHcCCCC
Confidence 4568999999998877788899998875322 2333333332 21 2256689999999998775
Q ss_pred -eEEEEEcCCCCHHH
Q 032325 97 -RAILVVQQNLTPFA 110 (143)
Q Consensus 97 -r~IlV~q~~ltp~A 110 (143)
--|+|-...+++.-
T Consensus 167 ~v~i~vGG~~~~~~~ 181 (197)
T TIGR02370 167 SVKFMVGGAPVTQDW 181 (197)
T ss_pred CCEEEEEChhcCHHH
Confidence 34677776777653
No 33
>PRK04247 hypothetical protein; Provisional
Probab=46.08 E-value=42 Score=27.55 Aligned_cols=51 Identities=20% Similarity=0.291 Sum_probs=37.3
Q ss_pred cEEEEcCC--CCccchhHHHHHHHHHhhc--CCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 67 QIYVFFPD--EQKVGVKTMKTYTNRMKSE--NVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 67 ~i~VfF~~--~~~vgvk~ik~~~~~~~~e--n~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
-++|..-- ...=++.++..|.+.+.++ .-=|||+|. +.+||.|+..+.+-.
T Consensus 173 lViVEvKrr~~~~~~V~Ql~rY~~~~~~~~~~~VRGilvA-p~i~~~A~~ll~~~G 227 (238)
T PRK04247 173 LVVLELKRRRAGLSAVSQLKRYVEALRELHGDKVRGILVA-PSITDRARRLLEKEG 227 (238)
T ss_pred EEEEEEEEccCChhHHHHHHHHHHHHHhhcCCCcEEEEEC-CcCCHHHHHHHHHcC
Confidence 35666622 2456789999999999654 345899886 589999999888643
No 34
>PF03345 DDOST_48kD: Oligosaccharyltransferase 48 kDa subunit beta; InterPro: IPR005013 During N-linked glycosylation of proteins, oligosaccharide chains are assembled on the carrier molecule dolichyl pyrophosphate in the following order: 2 molecules of N-acetylglucosamine (GlcNAc), 9 molecules of mannose, and 3 molecules of glucose. These 14-residue oligosaccharide cores are then transferred to asparagine residues on nascent polypeptide chains in the endoplasmic reticulum (ER). As proteins progress through the Golgi apparatus, the oligosaccharide cores are modified by trimming and extension to generate a diverse array of glycosylated proteins [, ]. The oligosaccharyl transferase complex (OST complex) 2.4.1.119 from EC transfers 14-sugar branched oligosaccharides from dolichyl pyrophosphate to asparagine residues []. The complex contains nine protein subunits: Ost1p, Ost2p, Ost3p, Ost4p, Ost5p, Ost6p, Stt3p, Swp1p, and Wbp1p, all of which are integral membrane proteins of the ER. The OST complex interacts with the Sec61p pore complex [] involved in protein import into the ER. This entry represents subunits OST3 and OST6. OST3 is homologous to OST6 [], and several lines of evidence indicate that they are alternative members of the OST complex. Disruption of both OST3 and OST6 causes severe underglycosylation of soluble and membrane-bound glycoproteins and a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation []. This entry also includes the magnesium transporter protein 1, also known as OST3 homologue B, which might be involved in N-glycosylation through its association with the oligosaccharyl transferase (OST) complex. Wbp1p is the beta subunit of the OST complex, one of the original six subunits purified []. Wbp1 is essential [, ], but conditional mutants have decreased transferase activity [, ]. Wbp1p is homologous to mammalian OST48 [].; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0018279 protein N-linked glycosylation via asparagine, 0005789 endoplasmic reticulum membrane
Probab=45.24 E-value=90 Score=27.69 Aligned_cols=99 Identities=18% Similarity=0.272 Sum_probs=51.9
Q ss_pred HHHHHHHhcCCCcccchhhhc-cCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhc
Q 032325 15 RRTVMQMLRDRGYFVGDFEIN-MSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSE 93 (143)
Q Consensus 15 rrTv~eMl~DRGY~V~~~e~~-~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~e 93 (143)
+.+.++.|++|||.++=...+ -++.-| +||+. ..+.|-+...+.+. |. +++.+++|-.|++ .
T Consensus 14 yS~Ff~~L~~rg~~l~~~~~~d~~l~L~--~~ge~-~YD~LIif~~~~k~--------~g--~~ls~~~ll~Fvd----~ 76 (423)
T PF03345_consen 14 YSTFFNSLKERGYELTFKSADDESLSLF--KYGER-LYDHLIIFPPSVKE--------FG--GSLSPKTLLDFVD----N 76 (423)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcchh--hCChh-hcceEEEeCCcccc--------cC--CCCCHHHHHHHHh----C
Confidence 788899999999999632221 233333 23322 12333222211111 11 2466666665553 2
Q ss_pred CCCeEEEEEcCC-CCHHHHHHHHhcc----c--cceEeeeccceE
Q 032325 94 NVFRAILVVQQN-LTPFARTCIQEIS----A--KFHLEVFQVNVF 131 (143)
Q Consensus 94 n~~r~IlV~q~~-ltp~Ar~~i~~~~----~--~~~iE~F~E~EL 131 (143)
| ...+++.-+. ++...|..+.++. + ..-+..|..+..
T Consensus 77 G-gNilv~~s~~~~~~~ir~~~~E~gi~~~~~~~~viDHf~~~~~ 120 (423)
T PF03345_consen 77 G-GNILVAGSSDAIPDSIREFANELGIEFDPKGSKVIDHFNYDSS 120 (423)
T ss_pred C-CcEEEEeCCCcCcHHHHHHHHHCCeEECCCCCEEEcCCCCccc
Confidence 3 3355556556 7777777777764 1 135666665443
No 35
>KOG3451 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.94 E-value=19 Score=24.14 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=29.5
Q ss_pred CCCeEEEEEcCCCCHHHHHHHHhcc------ccceEeeeccceEEeecccc
Q 032325 94 NVFRAILVVQQNLTPFARTCIQEIS------AKFHLEVFQVNVFSLMIYTC 138 (143)
Q Consensus 94 n~~r~IlV~q~~ltp~Ar~~i~~~~------~~~~iE~F~E~ELlVNIT~H 138 (143)
|+..|.+|... |+-++.|-.+. ++|.||...++-|+||...-
T Consensus 3 na~KGvlV~cD---p~~kqlilnmd~sm~~~skfii~eLDdthLfV~p~~v 50 (71)
T KOG3451|consen 3 NAKKGVLVTCD---PAFKQLILNMDDSMQLGSKFIIEELDDTHLFVNPSIV 50 (71)
T ss_pred ccccceEEecC---hhHHHHhhhccccCCCCCCeeEEEeccceeeecHHHH
Confidence 56677777543 44456665543 46899999999999997543
No 36
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=44.72 E-value=20 Score=31.18 Aligned_cols=50 Identities=18% Similarity=0.292 Sum_probs=33.2
Q ss_pred ccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHH--HHHHhccccceEeeeccceE
Q 032325 77 KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFAR--TCIQEISAKFHLEVFQVNVF 131 (143)
Q Consensus 77 ~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar--~~i~~~~~~~~iE~F~E~EL 131 (143)
+|.+| +|.|++.|+...=.+-+-|..++---.++ +.+.+ |.+=.|.++||
T Consensus 117 sv~MK-mkyY~~Ym~~~RddsPLYiFDssFgE~~~~rkLl~d----Y~VPk~F~dDl 168 (407)
T KOG2130|consen 117 SVKMK-MKYYIEYMKSTRDDSPLYIFDSSFGEHAPRRKLLED----YSVPKYFRDDL 168 (407)
T ss_pred ceeee-HHHHHHHHhccccCCCeEEecchhhcccchhhhhhh----cCcchhhhHHH
Confidence 56665 78999999987777788888777655554 54444 44544444443
No 37
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=44.39 E-value=88 Score=24.74 Aligned_cols=78 Identities=15% Similarity=0.160 Sum_probs=53.2
Q ss_pred HHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCe
Q 032325 18 VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97 (143)
Q Consensus 18 v~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r 97 (143)
+--||+..||.|..-=.+.+.++|.+...+. +++-+-+++ .. .-.+..++.+++.+.+.+..-
T Consensus 108 v~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~-~~~~V~lS~--------------~~--~~~~~~~~~~i~~L~~~~~~~ 170 (213)
T cd02069 108 VGVILSNNGYEVIDLGVMVPIEKILEAAKEH-KADIIGLSG--------------LL--VPSLDEMVEVAEEMNRRGIKI 170 (213)
T ss_pred HHHHHHhCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEcc--------------ch--hccHHHHHHHHHHHHhcCCCC
Confidence 4568999999998877788999998876432 222222222 22 234788999999999888865
Q ss_pred EEEEEcCCCCHHHHH
Q 032325 98 AILVVQQNLTPFART 112 (143)
Q Consensus 98 ~IlV~q~~ltp~Ar~ 112 (143)
-|+|-....|+....
T Consensus 171 ~i~vGG~~~~~~~~~ 185 (213)
T cd02069 171 PLLIGGAATSRKHTA 185 (213)
T ss_pred eEEEEChhcCHHHHh
Confidence 566766666755433
No 38
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=42.43 E-value=1.1e+02 Score=20.87 Aligned_cols=97 Identities=15% Similarity=0.134 Sum_probs=55.9
Q ss_pred HHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC
Q 032325 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~ 95 (143)
..+..+|++.||.|.--+.+.+.+++.+.-... +++-+-+++ .. .-.....+.+++.+++.+-
T Consensus 18 ~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~~~-~pd~V~iS~--------------~~--~~~~~~~~~l~~~~k~~~p 80 (121)
T PF02310_consen 18 LYLAAYLRKAGHEVDILDANVPPEELVEALRAE-RPDVVGISV--------------SM--TPNLPEAKRLARAIKERNP 80 (121)
T ss_dssp HHHHHHHHHTTBEEEEEESSB-HHHHHHHHHHT-TCSEEEEEE--------------SS--STHHHHHHHHHHHHHTTCT
T ss_pred HHHHHHHHHCCCeEEEECCCCCHHHHHHHHhcC-CCcEEEEEc--------------cC--cCcHHHHHHHHHHHHhcCC
Confidence 467889999999998766777777777643222 233233332 11 2346677888888766655
Q ss_pred CeEEEEEcCCCCHHHHHHHHhccccceEeeeccce
Q 032325 96 FRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNV 130 (143)
Q Consensus 96 ~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~E 130 (143)
.--|++-....|......++..+. +-.=++.|.|
T Consensus 81 ~~~iv~GG~~~t~~~~~~l~~~~~-~D~vv~GegE 114 (121)
T PF02310_consen 81 NIPIVVGGPHATADPEEILREYPG-IDYVVRGEGE 114 (121)
T ss_dssp TSEEEEEESSSGHHHHHHHHHHHT-SEEEEEETTS
T ss_pred CCEEEEECCchhcChHHHhccCcC-cceecCCChH
Confidence 544444444457776666654322 3344455544
No 39
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=39.51 E-value=39 Score=23.77 Aligned_cols=88 Identities=13% Similarity=0.129 Sum_probs=49.8
Q ss_pred hccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHH
Q 032325 34 INMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTC 113 (143)
Q Consensus 34 ~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~ 113 (143)
..-+++++++--... +-+-+.-...++..|+.+- -+|..-+..+.+.+...++. .+|+-..|||...+.
T Consensus 6 ~~~~l~El~~L~~t~-g~~vv~~~~q~~~~~~p~~--------~iG~GK~eei~~~~~~~~~d--~vvfd~~Lsp~Q~rN 74 (95)
T PF13167_consen 6 FEESLEELEELAETA-GYEVVGTVVQKRRKPDPKT--------YIGSGKVEEIKELIEELDAD--LVVFDNELSPSQQRN 74 (95)
T ss_pred HHHHHHHHHHHHHHC-CCeEEEEEEecCCCCCcce--------eechhHHHHHHHHHhhcCCC--EEEECCCCCHHHHHH
Confidence 344677777654322 2222322333333332111 25555566666777777774 445567899999998
Q ss_pred HHhccccceEeeeccceEEeec
Q 032325 114 IQEISAKFHLEVFQVNVFSLMI 135 (143)
Q Consensus 114 i~~~~~~~~iE~F~E~ELlVNI 135 (143)
|...- .++++.-..|+..|
T Consensus 75 Le~~~---~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 75 LEKAL---GVKVIDRTQLILEI 93 (95)
T ss_pred HHHHH---CCeeeccccHHHHH
Confidence 88755 46666666655443
No 40
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=38.84 E-value=36 Score=21.76 Aligned_cols=20 Identities=5% Similarity=0.255 Sum_probs=17.1
Q ss_pred HHHHHHhcCCCcccchhhhc
Q 032325 16 RTVMQMLRDRGYFVGDFEIN 35 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~ 35 (143)
.-+++..+..||.++.+|+.
T Consensus 28 e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 28 EDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHcCCCCCHHHHH
Confidence 45778899999999999984
No 41
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=38.71 E-value=20 Score=27.47 Aligned_cols=17 Identities=47% Similarity=0.546 Sum_probs=14.1
Q ss_pred HHHHHHHHhcCCCcccc
Q 032325 14 IRRTVMQMLRDRGYFVG 30 (143)
Q Consensus 14 irrTv~eMl~DRGY~V~ 30 (143)
+|..+.+||+|+||.-.
T Consensus 14 ir~~l~~~L~~~~~t~~ 30 (180)
T PF11985_consen 14 IREWLDQMLRDGGFTQY 30 (180)
T ss_pred HHHHHHHHHHhCCCChH
Confidence 78889999999997654
No 42
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=38.57 E-value=87 Score=25.46 Aligned_cols=49 Identities=12% Similarity=0.193 Sum_probs=38.1
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~~ 117 (143)
+..-|.++..|....++.+++.+.+.|++ ||+|..+ .||..-|+.+-+.
T Consensus 9 ~~TPf~~dg~iD~~~l~~~i~~l~~~Gv~-gi~~~Gs~GE~~~ls~~Er~~~~~~ 62 (292)
T PRK03170 9 LVTPFKEDGSVDFAALRKLVDYLIANGTD-GLVVVGTTGESPTLTHEEHEELIRA 62 (292)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECCcCCccccCCHHHHHHHHHH
Confidence 44557788899999999999999999998 7767655 4777777666543
No 43
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=36.97 E-value=88 Score=26.19 Aligned_cols=48 Identities=13% Similarity=0.229 Sum_probs=35.1
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~---en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
++++.|+...+++.+||.+.+.+.. ++-.+.+||- -..||+.|..++-
T Consensus 74 ~~~i~p~~~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~~AaNaLL 125 (290)
T PRK07276 74 VTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSLL 125 (290)
T ss_pred eeeecCCCCcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhcCHHHHHHHH
Confidence 6666777778999999999998853 5556666664 4568987766554
No 44
>PRK00441 argR arginine repressor; Provisional
Probab=36.62 E-value=1.7e+02 Score=22.05 Aligned_cols=87 Identities=14% Similarity=0.130 Sum_probs=43.1
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCC-cEEEEcCCCCccchhHHHHHHHHH-hh-c
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSD-QIYVFFPDEQKVGVKTMKTYTNRM-KS-E 93 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~-~i~VfF~~~~~vgvk~ik~~~~~~-~~-e 93 (143)
.+.+.|..+|+.|++.-+.-++.+ |.++ +..++++ ..|+.+.+...-....++..+... .+ +
T Consensus 23 eL~~~L~~~G~~vSqaTisRDl~~-------------L~lv--Kv~~~~G~~~Y~l~~~~~~~~~~~l~~~~~~~v~~v~ 87 (149)
T PRK00441 23 ELAEELKKMGFDVTQATVSRDIKE-------------LKLI--KVLSNDGKYKYATISKTESNLSDRLVNIFSNTVISVE 87 (149)
T ss_pred HHHHHHHhcCCCcCHHHHHHHHHH-------------cCcE--EeECCCCCEEEEeCcccccchHHHHHHHHHHHeeeEe
Confidence 456677777888777655333222 3333 3333333 467765543322233444444332 22 2
Q ss_pred CCCeEEEE-EcCCCCHHHHHHHHhcc
Q 032325 94 NVFRAILV-VQQNLTPFARTCIQEIS 118 (143)
Q Consensus 94 n~~r~IlV-~q~~ltp~Ar~~i~~~~ 118 (143)
.....|+| +..+-.+....+|+.+.
T Consensus 88 ~~~~lvvIkT~pG~A~~va~~iD~~~ 113 (149)
T PRK00441 88 NVDNMIVIKTISGSASAAAEAIDTLN 113 (149)
T ss_pred ecCCEEEEEeCCCcHHHHHHHHHhCC
Confidence 22333333 44566666667777765
No 45
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=36.27 E-value=2.4e+02 Score=23.01 Aligned_cols=72 Identities=15% Similarity=0.263 Sum_probs=43.2
Q ss_pred hcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEE
Q 032325 22 LRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILV 101 (143)
Q Consensus 22 l~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV 101 (143)
+.+|.+.+... ++.-|.++|| |.... ++-...+...+.+.|+.++..+++++++ +|++
T Consensus 177 ~~~~~~v~~H~----af~Yl~~~~g-------l~~~~----------~~~~~~~~eps~~~l~~l~~~ik~~~v~-~If~ 234 (286)
T cd01019 177 VKTKPFFVFHD----AYGYFEKRYG-------LTQAG----------VFTIDPEIDPGAKRLAKIRKEIKEKGAT-CVFA 234 (286)
T ss_pred cCCCeEEEecc----cHHHHHHHcC-------Cceee----------eecCCCCCCCCHHHHHHHHHHHHHcCCc-EEEe
Confidence 45555555432 5667777776 22221 1122345668899999999999999998 5544
Q ss_pred EcCCCCHHHHHHHHh
Q 032325 102 VQQNLTPFARTCIQE 116 (143)
Q Consensus 102 ~q~~ltp~Ar~~i~~ 116 (143)
- ...++..-+.|..
T Consensus 235 e-~~~~~~~~~~ia~ 248 (286)
T cd01019 235 E-PQFHPKIAETLAE 248 (286)
T ss_pred c-CCCChHHHHHHHH
Confidence 3 3444444444543
No 46
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=35.80 E-value=21 Score=21.46 Aligned_cols=20 Identities=25% Similarity=0.476 Sum_probs=15.9
Q ss_pred HHHHHHhcCCCcccchhhhc
Q 032325 16 RTVMQMLRDRGYFVGDFEIN 35 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~ 35 (143)
.-+....++.||.++.+|+.
T Consensus 30 ~e~~~lA~~~Gy~ft~~el~ 49 (49)
T PF07862_consen 30 EEVVALAREAGYDFTEEELE 49 (49)
T ss_pred HHHHHHHHHcCCCCCHHHhC
Confidence 34677889999999988863
No 47
>KOG0373 consensus Serine/threonine specific protein phosphatase involved in cell cycle control, PP2A-related [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=35.66 E-value=21 Score=29.63 Aligned_cols=86 Identities=22% Similarity=0.392 Sum_probs=54.3
Q ss_pred cCCCcccchhhhccCHHHHHHHhcCCCC-CcceEEEe-ecCCCCCCcEEEEcCC-CCccchhHHHHHHHHHh-----hcC
Q 032325 23 RDRGYFVGDFEINMSKEQFIAKFGENMK-REDLVINK-ALRNDSSDQIYVFFPD-EQKVGVKTMKTYTNRMK-----SEN 94 (143)
Q Consensus 23 ~DRGY~V~~~e~~~sl~~F~~~y~~~~~-r~~L~~~~-~~~~dp~~~i~VfF~~-~~~vgvk~ik~~~~~~~-----~en 94 (143)
-||||. |||.|.--+.-... +..+++.- .|.+..-.|+|-||-+ ..|-|-...-+||-+.= ..=
T Consensus 83 VDRGyy--------SLEtfT~l~~LkaryP~~ITLlRGNHEsRqitqVYGFydECq~KYGnan~wkycckVFD~LtlaAi 154 (306)
T KOG0373|consen 83 VDRGYY--------SLETFTLLLLLKARYPAKITLLRGNHESRQITQVYGFYDECQNKYGNANVWKYCCKVFDFLTLAAI 154 (306)
T ss_pred cccccc--------cHHHHHHHHHHhhcCCceeEEeeccchhhhhhhhhhhHHHHHhhcCCchHHHHHHHHHhhhhHHHH
Confidence 478886 66666544332211 34455543 2344444678888855 35888888888887752 344
Q ss_pred CCeEEEEEcCCCCHHHHHHHHhc
Q 032325 95 VFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 95 ~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
+..-|+-+.++++|..| .|+++
T Consensus 155 ID~~vLCVHGGLSPdir-tlDqi 176 (306)
T KOG0373|consen 155 IDEKVLCVHGGLSPDIR-TLDQI 176 (306)
T ss_pred hcCcEEEEcCCCCccce-eHHHH
Confidence 56668899999999874 45544
No 48
>PRK03094 hypothetical protein; Provisional
Probab=35.29 E-value=19 Score=24.85 Aligned_cols=15 Identities=40% Similarity=0.583 Sum_probs=12.8
Q ss_pred HHHHHhcCCCcccch
Q 032325 17 TVMQMLRDRGYFVGD 31 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~ 31 (143)
-|.|.|+.|||.|-+
T Consensus 12 ~i~~~L~~~GYeVv~ 26 (80)
T PRK03094 12 DVQQALKQKGYEVVQ 26 (80)
T ss_pred HHHHHHHHCCCEEEe
Confidence 367899999999975
No 49
>PRK03341 arginine repressor; Provisional
Probab=34.92 E-value=1.6e+02 Score=22.68 Aligned_cols=87 Identities=11% Similarity=0.221 Sum_probs=44.2
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCc--EEEEcCCCCc----c-chhHHHHHHHH
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQ--IYVFFPDEQK----V-GVKTMKTYTNR 89 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~--i~VfF~~~~~----v-gvk~ik~~~~~ 89 (143)
-+.+.|..+|+.|+|.-+.-.+.+.. +.+..+++++ .|+.+.+... . ....++..+..
T Consensus 34 eL~~~L~~~Gi~vTQaTiSRDl~eL~---------------~~Kv~~~~G~~~~Y~lp~~~~~~~~~~~~~~~l~~~~~~ 98 (168)
T PRK03341 34 ELAALLADEGIEVTQATLSRDLDELG---------------AVKLRGADGGLGVYVVPEEGGPRRGVAGGTERLRRLLGE 98 (168)
T ss_pred HHHHHHHHcCCcccHHHHHHHHHHhc---------------CEeeecCCCCEEEEEecccccccccccchHHHHHHHHHH
Confidence 45677888899998877755444432 1233444443 5666543221 1 22344443333
Q ss_pred H-hhcCCCeEEEEEcC--CCCHHHHHHHHhcc
Q 032325 90 M-KSENVFRAILVVQQ--NLTPFARTCIQEIS 118 (143)
Q Consensus 90 ~-~~en~~r~IlV~q~--~ltp~Ar~~i~~~~ 118 (143)
. .+-.....++|++. +..+....+|+.+.
T Consensus 99 ~v~sv~~~~~lvVIkT~pG~A~~va~~iD~~~ 130 (168)
T PRK03341 99 LLVSADASANLAVLRTPPGAAQYLASAIDRAA 130 (168)
T ss_pred HeEEEeeeCCEEEEEcCCChHHHHHHHHHhCC
Confidence 2 22222233444443 55566667777665
No 50
>PF12687 DUF3801: Protein of unknown function (DUF3801); InterPro: IPR024234 This functionally uncharacterised protein family is found in bacteria. Proteins found in this family are typically between 158 and 187 amino acids in length and include the PcfB protein.
Probab=34.54 E-value=1.2e+02 Score=24.11 Aligned_cols=67 Identities=13% Similarity=0.306 Sum_probs=36.1
Q ss_pred HHHHHHHhcCCCcccchhhh-ccCHHHHHH---HhcCCCCCcceEEEeec-CCCCCCcEEEEcCCCCccchhHHHHHHHH
Q 032325 15 RRTVMQMLRDRGYFVGDFEI-NMSKEQFIA---KFGENMKREDLVINKAL-RNDSSDQIYVFFPDEQKVGVKTMKTYTNR 89 (143)
Q Consensus 15 rrTv~eMl~DRGY~V~~~e~-~~sl~~F~~---~y~~~~~r~~L~~~~~~-~~dp~~~i~VfF~~~~~vgvk~ik~~~~~ 89 (143)
+.++-+|++.-+ .+..-++ +-.+.+|.. +|| +.|++.+ .+.+.+...|||..++ ...|....++
T Consensus 21 k~slk~L~k~g~-~l~~i~i~~~~lk~F~k~AkKyG-------V~yav~kdk~~~~~~~~V~FkA~D---a~~i~~af~~ 89 (204)
T PF12687_consen 21 KQSLKKLLKQGK-GLKNIEITDEDLKEFKKEAKKYG-------VDYAVKKDKSTGPGKYDVFFKAKD---ADVINRAFKE 89 (204)
T ss_pred ceeHHHHHhcCC-CceEEecCHhhHHHHHHHHHHcC-------CceEEeeccCCCCCcEEEEEEcCc---HHHHHHHHHH
Confidence 356778888633 3332222 113445544 465 5566655 2333347899997655 5555555555
Q ss_pred Hhh
Q 032325 90 MKS 92 (143)
Q Consensus 90 ~~~ 92 (143)
+..
T Consensus 90 ~~~ 92 (204)
T PF12687_consen 90 FSA 92 (204)
T ss_pred HHH
Confidence 543
No 51
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=34.53 E-value=2.5e+02 Score=22.69 Aligned_cols=43 Identities=19% Similarity=0.168 Sum_probs=30.7
Q ss_pred CCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 032325 74 DEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 74 ~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
.+...+.+.|+++++.++++|+. +|++=++--+..++...++.
T Consensus 200 ~~~eps~~~l~~l~~~ik~~~v~-~if~e~~~~~~~~~~la~~~ 242 (282)
T cd01017 200 PEVEPSPKQLAELVEFVKKSDVK-YIFFEENASSKIAETLAKET 242 (282)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCC-EEEEeCCCChHHHHHHHHHc
Confidence 45568899999999999999998 66665555455554433343
No 52
>PRK05818 DNA polymerase III subunit delta'; Validated
Probab=34.33 E-value=1.1e+02 Score=25.48 Aligned_cols=48 Identities=8% Similarity=0.215 Sum_probs=34.4
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcC----CCeEEEE-EcCCCCHHHHHHHH
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSEN----VFRAILV-VQQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en----~~r~IlV-~q~~ltp~Ar~~i~ 115 (143)
+++.||....+|+.+||.+.+.+.... -.+.++| -..+||+.|.-|+-
T Consensus 57 l~~i~p~~~~I~id~ir~l~~~l~~~s~e~~~~KV~II~~ae~m~~~AaNaLL 109 (261)
T PRK05818 57 FYLIFDQKNPIKKEDALSIINKLNRPSVESNGKKIYIIYGIEKLNKQSANSLL 109 (261)
T ss_pred EEEecCCcccCCHHHHHHHHHHHccCchhcCCCEEEEeccHhhhCHHHHHHHH
Confidence 666678877899999999999986433 3455555 35678987766553
No 53
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=34.27 E-value=2e+02 Score=21.47 Aligned_cols=87 Identities=11% Similarity=0.163 Sum_probs=43.5
Q ss_pred HHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCC-cEEEEcCCCCccchhHHHHHHHHH-hh-c
Q 032325 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSD-QIYVFFPDEQKVGVKTMKTYTNRM-KS-E 93 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~-~i~VfF~~~~~vgvk~ik~~~~~~-~~-e 93 (143)
-+.+.|+.+|+.|+++-+.- .+++ |.++..+. +++ ..|..+.+...-....++..+... .+ +
T Consensus 21 eL~~~L~~~G~~vsqaTIsR---dL~e----------lglvk~~~--~~g~~~Y~~~~~~~~~~~~~l~~~~~~~v~~v~ 85 (146)
T TIGR01529 21 ELVALLKAEGIEVTQATVSR---DLRE----------LGAVKVRD--EDGSYVYSLPADGVSDPTSKLKRLLKNLVLSID 85 (146)
T ss_pred HHHHHHHHhCCCcCHHHHHH---HHHH----------cCCEEEEC--CCCcEEEeeccccccchhHHHHHHHHHHeeEee
Confidence 46788899999999977743 3332 33332222 333 234443322111123344444332 21 3
Q ss_pred CCCeEEEE-EcCCCCHHHHHHHHhcc
Q 032325 94 NVFRAILV-VQQNLTPFARTCIQEIS 118 (143)
Q Consensus 94 n~~r~IlV-~q~~ltp~Ar~~i~~~~ 118 (143)
.....|+| +..+..+....+|+.+.
T Consensus 86 ~~~~~vvikT~pG~A~~va~~iD~~~ 111 (146)
T TIGR01529 86 RAGNLIVIRTKPGEASVIANLLDRLD 111 (146)
T ss_pred ccCCEEEEEeCCCcHHHHHHHHHhCC
Confidence 33334433 44556666667777765
No 54
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=34.16 E-value=1.2e+02 Score=24.95 Aligned_cols=49 Identities=14% Similarity=0.126 Sum_probs=37.5
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~~ 117 (143)
+..-|.++.+|..+.++..++.+.+.|++ ||+|..+ .||..-|+.+-+.
T Consensus 13 ~vTPf~~dg~iD~~~l~~li~~l~~~Gv~-gi~v~GstGE~~~Lt~eEr~~v~~~ 66 (296)
T TIGR03249 13 PVTPFDADGSFDEAAYRENIEWLLGYGLE-ALFAAGGTGEFFSLTPAEYEQVVEI 66 (296)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHhcCCC-EEEECCCCcCcccCCHHHHHHHHHH
Confidence 44557777899999999999999999998 7777543 5777766666543
No 55
>COG4889 Predicted helicase [General function prediction only]
Probab=34.15 E-value=68 Score=31.98 Aligned_cols=82 Identities=9% Similarity=0.146 Sum_probs=62.2
Q ss_pred eEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccc-------------
Q 032325 54 LVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK------------- 120 (143)
Q Consensus 54 L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~------------- 120 (143)
.-+++...++.-.-|..-|-. -+++...|-.|...+..-++++++||.-...++-|+++|++...-
T Consensus 61 idlva~~d~g~ytaiQcKFy~-nslak~di~sF~t~lgkt~f~~gliiSTtdw~sNA~~aieq~~~~~~~Iglsei~es~ 139 (1518)
T COG4889 61 IDLVAREDNGNYTAIQCKFYQ-NSLAKGDIDSFFTALGKTGFKNGLIISTTDWTSNAEKAIEQQRSPGMRIGLSEIAESP 139 (1518)
T ss_pred eeEEEEccCCCeEEEEeeeec-cccccccccHHHHHhccccccCceEEEecccchhHHHHHHhhhCccceecHHHHhcCC
Confidence 455665533332345555543 589999999999999999999999998888999999999876431
Q ss_pred ceEeeeccceEEeecc
Q 032325 121 FHLEVFQVNVFSLMIY 136 (143)
Q Consensus 121 ~~iE~F~E~ELlVNIT 136 (143)
.-.++|.-.||-+|++
T Consensus 140 IDW~~f~p~e~~~nl~ 155 (1518)
T COG4889 140 IDWDIFDPTELQDNLP 155 (1518)
T ss_pred CChhhcCccccccccc
Confidence 3457788889988886
No 56
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=33.20 E-value=1.1e+02 Score=19.42 Aligned_cols=53 Identities=21% Similarity=0.269 Sum_probs=31.6
Q ss_pred Ccccchhhh-----ccCHHHHHHHhcCCCC----CcceEEEeecCCCC-----CCcEEEEcCCCCcc
Q 032325 26 GYFVGDFEI-----NMSKEQFIAKFGENMK----REDLVINKALRNDS-----SDQIYVFFPDEQKV 78 (143)
Q Consensus 26 GY~V~~~e~-----~~sl~~F~~~y~~~~~----r~~L~~~~~~~~dp-----~~~i~VfF~~~~~v 78 (143)
||.++++.+ .||.++-.+..|.+.. ...-+........+ ..++.|.|.++..|
T Consensus 1 G~~~~~~~~~~i~~GmTk~qV~~lLG~P~~~~~~~~~~W~Y~~~~~~~~~~~~~~~l~V~Fd~~~~v 67 (71)
T PF04355_consen 1 GNVLTQEQLAQIKPGMTKDQVRALLGSPSLRDPFDPNRWYYVYSKRRGNGANEQRQLKVYFDDDGVV 67 (71)
T ss_dssp TSCTTSHHHTTT-TTSBHHHHHHHHTS-SEE-CTTSSEEEEEEEETTCSSSSCEEEEEEEECTTSBE
T ss_pred CCcCCHHHHHhhcCCCCHHHHHHhcCCCCccccccCCEEEEEEEEecCCCccEEEEEEEEEcCCCEE
Confidence 566665544 7899999999996522 12233333333222 34688888876644
No 57
>PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Probab=32.89 E-value=1.7e+02 Score=27.98 Aligned_cols=44 Identities=9% Similarity=0.184 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcccchhhhccCH-HHHHHHhcCC
Q 032325 5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSK-EQFIAKFGEN 48 (143)
Q Consensus 5 ~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl-~~F~~~y~~~ 48 (143)
.+|+.|+-.-..-+.+.|+++|=-+.=--=.=|| +.+.++||+.
T Consensus 202 ~~Ele~i~e~f~~~v~~ak~~~~~iRIGvN~GSLs~ri~~~yGdt 246 (733)
T PLN02925 202 QKELEHIEEVFTPLVEKCKKYGRAMRIGTNHGSLSDRIMSYYGDS 246 (733)
T ss_pred hhhHHHHHHHHHHHHHHHHHCCCCEEEecCCcCchHHHHHHhCCC
Confidence 4566677777778999999999666411111133 4777788754
No 58
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=32.19 E-value=1.3e+02 Score=22.84 Aligned_cols=52 Identities=10% Similarity=0.119 Sum_probs=33.7
Q ss_pred CcEEEEcCCCCccchhH----HHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 032325 66 DQIYVFFPDEQKVGVKT----MKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 66 ~~i~VfF~~~~~vgvk~----ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
.++++|=.-...-+... ++....-+.+.|.--|-+++|++++|..+..+..+
T Consensus 68 KkV~lF~T~G~~~~s~~~~~~~~~~~~~~~~~~~~lg~f~CqGk~~~~~~e~~~~~ 123 (160)
T PF12641_consen 68 KKVALFGTAGAGPDSEYAKKILKNVEALLPKGNEILGTFMCQGKMDPKVIEKYKKM 123 (160)
T ss_pred CeEEEEEecCCCCchHHHHHHHHHHHHhhccCCeecceEEeCCcCCHHHHHHHHhc
Confidence 45666654322223444 44444444455566678999999999999999888
No 59
>TIGR02328 conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown.
Probab=32.13 E-value=47 Score=24.56 Aligned_cols=24 Identities=33% Similarity=0.524 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHhcCCCcccch
Q 032325 8 IKRLFRIRRTVMQMLRDRGYFVGD 31 (143)
Q Consensus 8 ~~rL~rirrTv~eMl~DRGY~V~~ 31 (143)
...||.-..-|++-|..|||.++.
T Consensus 47 ~~~L~~yH~lv~~EM~~RGY~~~~ 70 (120)
T TIGR02328 47 PYKLFAYHLLVMEEMATRGYHVSK 70 (120)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCh
Confidence 367888888888888999999987
No 60
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=31.14 E-value=1.6e+02 Score=19.58 Aligned_cols=46 Identities=9% Similarity=0.235 Sum_probs=30.9
Q ss_pred CCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHh
Q 032325 64 SSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116 (143)
Q Consensus 64 p~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~ 116 (143)
+.++++||++. .+.+..+.+.+.+.+ -.+.++.+++++..++.+.+
T Consensus 27 ~~~~~lvf~~~-----~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~~~~~~~ 72 (131)
T cd00079 27 KGGKVLIFCPS-----KKMLDELAELLRKPG--IKVAALHGDGSQEEREEVLK 72 (131)
T ss_pred CCCcEEEEeCc-----HHHHHHHHHHHHhcC--CcEEEEECCCCHHHHHHHHH
Confidence 45668888876 455666666666533 35777888998877766553
No 61
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=30.81 E-value=23 Score=24.32 Aligned_cols=15 Identities=47% Similarity=0.731 Sum_probs=13.1
Q ss_pred HHHHHhcCCCcccch
Q 032325 17 TVMQMLRDRGYFVGD 31 (143)
Q Consensus 17 Tv~eMl~DRGY~V~~ 31 (143)
.|.|.|+.+||.|.+
T Consensus 12 ~v~~~L~~~GyeVv~ 26 (80)
T PF03698_consen 12 NVKEALREKGYEVVD 26 (80)
T ss_pred HHHHHHHHCCCEEEe
Confidence 467899999999987
No 62
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=30.66 E-value=1.4e+02 Score=24.40 Aligned_cols=49 Identities=12% Similarity=0.379 Sum_probs=35.5
Q ss_pred CCCCCCcEEEEcC-----------CCCccchhHHHHHHHHHhh-cCCCeEEEEEcCCCCHH
Q 032325 61 RNDSSDQIYVFFP-----------DEQKVGVKTMKTYTNRMKS-ENVFRAILVVQQNLTPF 109 (143)
Q Consensus 61 ~~dp~~~i~VfF~-----------~~~~vgvk~ik~~~~~~~~-en~~r~IlV~q~~ltp~ 109 (143)
.++++|.++|||. +.+.+..+.++..++.|.. ...+..++|+...=+.+
T Consensus 102 ~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs 162 (256)
T PF01650_consen 102 NSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYSGS 162 (256)
T ss_pred cCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccccc
Confidence 4577788888873 4556778899999999965 55577777776665544
No 63
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=30.04 E-value=22 Score=23.65 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=17.5
Q ss_pred HHHHHHhcCCCcccchhhhccCHHHH
Q 032325 16 RTVMQMLRDRGYFVGDFEINMSKEQF 41 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~~e~~~sl~~F 41 (143)
.-+.+.|.++||.|+|.-+.-.+.+.
T Consensus 23 ~eL~~~L~~~Gi~vTQaTiSRDLkeL 48 (70)
T PF01316_consen 23 EELVELLEEEGIEVTQATISRDLKEL 48 (70)
T ss_dssp HHHHHHHHHTT-T--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcchhHHHHHHHHc
Confidence 34678899999999998887666554
No 64
>PF10356 DUF2034: Protein of unknown function (DUF2034); InterPro: IPR018828 This protein is expressed mainly in fungi but its function is unknown.
Probab=29.87 E-value=1e+02 Score=24.23 Aligned_cols=52 Identities=19% Similarity=0.204 Sum_probs=39.0
Q ss_pred cEEEEcCC-CCccchhHHHHHHHHHhhcC------CCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 67 QIYVFFPD-EQKVGVKTMKTYTNRMKSEN------VFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 67 ~i~VfF~~-~~~vgvk~ik~~~~~~~~en------~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
+++|-=-. ..|+|-+.||++..-+.... -.=||||.+...|+.|+.++...+
T Consensus 86 ~VlvQCKa~~~KvgP~~vRELeGt~~~~~~~~~~~~tigiLvS~~~~Tk~~~~~l~~s~ 144 (185)
T PF10356_consen 86 RVLVQCKAFKKKVGPKLVRELEGTFSRAPPGWRRNSTIGILVSPRPFTKGALKALNSSR 144 (185)
T ss_pred eEEEECcCCCCCCChhhhhhhheeeecccCCCCCCCEEEEEECCCCCCHHHHHHHhhCc
Confidence 45665433 34899999999988875332 234789999999999999998765
No 65
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=29.64 E-value=2e+02 Score=24.06 Aligned_cols=51 Identities=8% Similarity=0.105 Sum_probs=34.8
Q ss_pred CCccchhHHHHHHHHHhhc----CCCeEEEEEc-CCCCHHHHHH----HHhccccceEeee
Q 032325 75 EQKVGVKTMKTYTNRMKSE----NVFRAILVVQ-QNLTPFARTC----IQEISAKFHLEVF 126 (143)
Q Consensus 75 ~~~vgvk~ik~~~~~~~~e----n~~r~IlV~q-~~ltp~Ar~~----i~~~~~~~~iE~F 126 (143)
...+++.+|+..++.+.-. |-.+.++|-. .+||..|..+ +.+.+ .+.+=+|
T Consensus 66 g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp-~~t~~il 125 (299)
T PRK07132 66 DKDLSKSEFLSAINKLYFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPP-KDTYFLL 125 (299)
T ss_pred CCcCCHHHHHHHHHHhccCCcccCCceEEEEecccccCHHHHHHHHHHhhCCC-CCeEEEE
Confidence 4679999999999998532 5677777766 7788866544 44433 3455444
No 66
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=29.59 E-value=73 Score=25.95 Aligned_cols=71 Identities=20% Similarity=0.181 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEc--CCCCccchhHHHHHHHH
Q 032325 12 FRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFF--PDEQKVGVKTMKTYTNR 89 (143)
Q Consensus 12 ~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF--~~~~~vgvk~ik~~~~~ 89 (143)
+..++.+++-|.+.||.+...-++- +.||-...|+++-+++.+.+.+. ..++ |.. .-...+++.++.+
T Consensus 121 ~~~~~~i~~~l~~~GY~~~~~~l~a------~~~GvPQ~R~R~~~ia~~~~~~~---~~~~~~p~~-~~~~~t~~d~l~~ 190 (275)
T cd00315 121 GNTLKVILNTLEELGYNVYWKLLNA------SDYGVPQNRERVFIIGIRKDLIL---NFFSPFPKP-SEKKKTLKDILRI 190 (275)
T ss_pred hHHHHHHHHHHHhCCcEEEEEEEEH------HHcCCCCCCcEEEEEEEeCCCCc---cccccCCCC-CCCCCcHHHHHhh
Confidence 4567788889999999998765543 24888888999999998765431 1111 221 1123466666655
Q ss_pred Hhh
Q 032325 90 MKS 92 (143)
Q Consensus 90 ~~~ 92 (143)
+.-
T Consensus 191 ~~~ 193 (275)
T cd00315 191 RDP 193 (275)
T ss_pred hcC
Confidence 543
No 67
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=29.46 E-value=1.4e+02 Score=24.52 Aligned_cols=49 Identities=16% Similarity=0.162 Sum_probs=38.2
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcC-CCeEEEEE-----cCCCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSEN-VFRAILVV-----QQNLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en-~~r~IlV~-----q~~ltp~Ar~~i~~~ 117 (143)
+..-|.++.+|....++..++++.+.| ++ ||+|. ...||..-|+.+-+.
T Consensus 8 ~~TPf~~dg~iD~~~~~~~i~~~i~~G~v~-gi~~~GstGE~~~Lt~eEr~~~~~~ 62 (290)
T TIGR00683 8 LLVSFNEDGTINEKGLRQIIRHNIDKMKVD-GLYVGGSTGENFMLSTEEKKEIFRI 62 (290)
T ss_pred eecCCCCCCCcCHHHHHHHHHHHHhCCCcC-EEEECCcccccccCCHHHHHHHHHH
Confidence 344577788999999999999999999 76 78786 456887777766543
No 68
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=29.22 E-value=1.7e+02 Score=25.76 Aligned_cols=35 Identities=26% Similarity=0.451 Sum_probs=23.6
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
-..-.+++...++| ++.++++ ..+|..| +|..+++
T Consensus 221 ~~a~~~AE~f~~~g-~~Vl~~~-Dsltr~a-~A~rei~ 255 (422)
T TIGR02546 221 YTATAIAEYFRDQG-KRVLLMM-DSLTRFA-RALREIG 255 (422)
T ss_pred HHHHHHHHHHHHCC-CcEEEEE-eCchHHH-HHHHHHH
Confidence 34455677777776 3444444 6899998 7888776
No 69
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=28.84 E-value=1.1e+02 Score=20.17 Aligned_cols=48 Identities=10% Similarity=0.126 Sum_probs=33.8
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccc
Q 032325 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVN 129 (143)
Q Consensus 81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ 129 (143)
++++.++....+. ...+=.+.-.+|++.-|+.+-+++..+.|+...+.
T Consensus 16 ~~l~~la~~~~~~-~~~~~~~~l~PM~~~eR~iIH~la~~~~l~S~S~G 63 (74)
T cd02643 16 KDLIELVESVNKG-KQTSRSHSFPPMNREKRRIVHELAEHFGIESVSYD 63 (74)
T ss_pred HHHHHHHHHHHhc-cccCCeeECCCCCHHHHHHHHHHHhhCCCEEEecC
Confidence 4566666666544 44555566789999999999988766677776654
No 70
>PF05212 DUF707: Protein of unknown function (DUF707); InterPro: IPR007877 This family consists of uncharacterised proteins from Arabidopsis thaliana.
Probab=28.69 E-value=49 Score=28.09 Aligned_cols=37 Identities=30% Similarity=0.421 Sum_probs=31.2
Q ss_pred EEEcCCCC-ccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHH
Q 032325 69 YVFFPDEQ-KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPF 109 (143)
Q Consensus 69 ~VfF~~~~-~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~ 109 (143)
|+|++||+ .|..-.+..|.+.++++|.. |.|.+|+|.
T Consensus 119 YiflwDeDL~vd~f~~~ry~~Ivk~~gLe----ISQPALd~~ 156 (294)
T PF05212_consen 119 YIFLWDEDLGVDHFDINRYFEIVKKEGLE----ISQPALDPD 156 (294)
T ss_pred eEEecCCccCcCcCCHHHHHHHHHHhCCc----ccCcccCCC
Confidence 88888875 56667899999999999998 999999863
No 71
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=28.48 E-value=1.7e+02 Score=24.82 Aligned_cols=48 Identities=13% Similarity=0.285 Sum_probs=33.2
Q ss_pred EEEEcCCC--CccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDE--QKVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~--~~vgvk~ik~~~~~~~---~en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
+++..|++ ..++|.+||.+.+.+. .+|-.|.++|. -..||..|.-|+-
T Consensus 76 ~~~i~p~~~~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLL 129 (319)
T PRK06090 76 LHVIKPEKEGKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALL 129 (319)
T ss_pred EEEEecCcCCCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHH
Confidence 66666763 4699999999888874 35556777664 3558987765544
No 72
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=28.22 E-value=1.2e+02 Score=26.93 Aligned_cols=41 Identities=12% Similarity=0.425 Sum_probs=26.8
Q ss_pred CCCCCCcEEEEcCCC-----------CccchhHHHHHHHHHhhcC-CCeEEEE
Q 032325 61 RNDSSDQIYVFFPDE-----------QKVGVKTMKTYTNRMKSEN-VFRAILV 101 (143)
Q Consensus 61 ~~dp~~~i~VfF~~~-----------~~vgvk~ik~~~~~~~~en-~~r~IlV 101 (143)
.+.|+|.|||||.+- +.+-+|.+...+.+|-..+ .+.+.+-
T Consensus 150 ~SgpnDhiFiYytDHG~pGvl~mP~~~~l~akdlnevL~kmhk~k~Y~~mvfY 202 (477)
T KOG1348|consen 150 KSGPNDHIFIYYTDHGGPGVLGMPTSPDLYAKDLNEVLKKMHKSKTYKKMVFY 202 (477)
T ss_pred ccCCCceEEEEEecCCCCceEecCCCcchhHHHHHHHHHHHHhccchheEEEE
Confidence 468999999999553 4455667777777774444 4444443
No 73
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=28.01 E-value=1.6e+02 Score=24.06 Aligned_cols=47 Identities=13% Similarity=0.136 Sum_probs=36.1
Q ss_pred EEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHh
Q 032325 69 YVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQE 116 (143)
Q Consensus 69 ~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~ 116 (143)
..-|.++.+|..+.++..++++.+.|++ ||+|..+ .||..-|+.+-+
T Consensus 9 vTPf~~dg~iD~~~l~~l~~~l~~~Gv~-gi~v~GstGE~~~Ls~eEr~~l~~ 60 (289)
T cd00951 9 VTHFDADGSFDEDAYRAHVEWLLSYGAA-ALFAAGGTGEFFSLTPDEYAQVVR 60 (289)
T ss_pred ecCCCCCCCcCHHHHHHHHHHHHHcCCC-EEEECcCCcCcccCCHHHHHHHHH
Confidence 4457777899999999999999999998 7777653 467666665544
No 74
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=27.98 E-value=1.7e+02 Score=23.68 Aligned_cols=43 Identities=9% Similarity=0.159 Sum_probs=31.0
Q ss_pred CCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHh
Q 032325 73 PDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116 (143)
Q Consensus 73 ~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~ 116 (143)
..+...+.+.|.++++.+++++++ +|++=++.-++.++...++
T Consensus 189 ~~~~eps~~~l~~l~~~ik~~~v~-~if~e~~~~~~~~~~l~~~ 231 (276)
T cd01016 189 STDSEAGLRDINELVDLIVERKIK-AIFVESSVNQKSIEALQDA 231 (276)
T ss_pred CcccCCCHHHHHHHHHHHHHcCCC-EEEEeCCCCHHHHHHHHHH
Confidence 456678899999999999999998 6666555445555444343
No 75
>PRK06581 DNA polymerase III subunit delta'; Validated
Probab=27.74 E-value=1.6e+02 Score=24.61 Aligned_cols=40 Identities=3% Similarity=0.180 Sum_probs=30.1
Q ss_pred CccchhHHHHHHHHHh---hcCCCeEEEE-EcCCCCHHHHHHHH
Q 032325 76 QKVGVKTMKTYTNRMK---SENVFRAILV-VQQNLTPFARTCIQ 115 (143)
Q Consensus 76 ~~vgvk~ik~~~~~~~---~en~~r~IlV-~q~~ltp~Ar~~i~ 115 (143)
..+||.+||.+.+.+. .+|-.|.++| --..||+.|.-|+-
T Consensus 67 ~~I~IdqIReL~~~l~~~p~~g~~KViII~~ae~mt~~AANALL 110 (263)
T PRK06581 67 KNISIEQIRKLQDFLSKTSAISGYKVAIIYSAELMNLNAANSCL 110 (263)
T ss_pred CcccHHHHHHHHHHHhhCcccCCcEEEEEechHHhCHHHHHHHH
Confidence 4699999999999985 4566667766 45669988776654
No 76
>PF13353 Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A 3CB8_A 3T7V_A 2YX0_A 3CAN_A.
Probab=27.52 E-value=1.9e+02 Score=20.07 Aligned_cols=44 Identities=9% Similarity=-0.015 Sum_probs=31.8
Q ss_pred cEEEEcCCCCcc--chhHHHHHHHHHhhcCCCeEEEEEcCCCCHHH
Q 032325 67 QIYVFFPDEQKV--GVKTMKTYTNRMKSENVFRAILVVQQNLTPFA 110 (143)
Q Consensus 67 ~i~VfF~~~~~v--gvk~ik~~~~~~~~en~~r~IlV~q~~ltp~A 110 (143)
.-++++.+||-+ +.+.+..+++.+++++....++++-+......
T Consensus 54 ~~i~l~GGEPll~~~~~~l~~i~~~~k~~~~~~~~~~tng~~~~~~ 99 (139)
T PF13353_consen 54 KGIVLTGGEPLLHENYDELLEILKYIKEKFPKKIIILTNGYTLDEL 99 (139)
T ss_dssp CEEEEECSTGGGHHSHHHHHHHHHHHHHTT-SEEEEEETT--HHHH
T ss_pred eEEEEcCCCeeeeccHhHHHHHHHHHHHhCCCCeEEEECCCchhHH
Confidence 355566788888 89999999999999999667777755554444
No 77
>PRK09099 type III secretion system ATPase; Provisional
Probab=27.52 E-value=1.8e+02 Score=25.94 Aligned_cols=73 Identities=18% Similarity=0.170 Sum_probs=41.1
Q ss_pred ccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHH
Q 032325 35 NMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114 (143)
Q Consensus 35 ~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i 114 (143)
.-...+|.+..-.......-.++++..++| +...-...-+-=+++|...++|-+ .+++ -..+|-+| +|.
T Consensus 201 ~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p--------~~~r~~a~~~a~tiAEyfrd~G~~-VLl~-~DslTr~A-~A~ 269 (441)
T PRK09099 201 GREVREFIELILGEDGMARSVVVCATSDRS--------SIERAKAAYVATAIAEYFRDRGLR-VLLM-MDSLTRFA-RAQ 269 (441)
T ss_pred hHHHHHHHHHHhhcCCcceEEEEEECCCCC--------HHHHHHHHHHHHHHHHHHHHcCCC-EEEe-ccchhHHH-HHH
Confidence 334567877774444444455565555555 222212222333466777666643 4434 46899998 778
Q ss_pred Hhcc
Q 032325 115 QEIS 118 (143)
Q Consensus 115 ~~~~ 118 (143)
++++
T Consensus 270 REis 273 (441)
T PRK09099 270 REIG 273 (441)
T ss_pred HHHH
Confidence 8775
No 78
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=27.33 E-value=2.6e+02 Score=26.47 Aligned_cols=89 Identities=15% Similarity=0.039 Sum_probs=58.6
Q ss_pred HHHHH-HHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHh
Q 032325 13 RIRRT-VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMK 91 (143)
Q Consensus 13 rirrT-v~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~ 91 (143)
.+|.+ +--|+++-||.|.......|.++|.+...+. ++ -.|..|.-..-....++.+++.++
T Consensus 596 ~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa~~~--------------~a---~ivvlcs~d~~~~e~~~~l~~~Lk 658 (714)
T PRK09426 596 DRGAKVIATAFADLGFDVDIGPLFQTPEEAARQAVEN--------------DV---HVVGVSSLAAGHKTLVPALIEALK 658 (714)
T ss_pred hHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHHHHc--------------CC---CEEEEeccchhhHHHHHHHHHHHH
Confidence 44444 3468899999996555556888888876432 11 122224444556777899999999
Q ss_pred hcCCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 92 SENVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 92 ~en~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
+.|.....+++.+.+.|.....+.++.
T Consensus 659 ~~G~~~v~vl~GG~~~~~~~~~l~~aG 685 (714)
T PRK09426 659 KLGREDIMVVVGGVIPPQDYDFLYEAG 685 (714)
T ss_pred hcCCCCcEEEEeCCCChhhHHHHHhCC
Confidence 999776767777887776555555544
No 79
>cd08616 PI-PLCXD1c Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to
Probab=26.83 E-value=70 Score=26.54 Aligned_cols=39 Identities=21% Similarity=0.170 Sum_probs=31.2
Q ss_pred CccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHH
Q 032325 76 QKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114 (143)
Q Consensus 76 ~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i 114 (143)
.....+.+.++.+....++...+..|.|.-+||.++..+
T Consensus 197 nt~~~~~l~~~L~~~l~~~~~~~~~v~Q~ilTP~~~~i~ 235 (290)
T cd08616 197 NTTDPKKLIQFLETTLKERRPPGFHVSQGILTPDVKTIL 235 (290)
T ss_pred CCCCHHHHHHHHHHhhhcCCCCCEEEEEEEEcCcccchh
Confidence 345788899999988777777788999999998876654
No 80
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=26.56 E-value=2.3e+02 Score=21.10 Aligned_cols=46 Identities=13% Similarity=0.260 Sum_probs=28.7
Q ss_pred EEEcCCCCccchhHHHHHHHHHhh---cCCCeEEEEEc-CCCCHHHHHHH
Q 032325 69 YVFFPDEQKVGVKTMKTYTNRMKS---ENVFRAILVVQ-QNLTPFARTCI 114 (143)
Q Consensus 69 ~VfF~~~~~vgvk~ik~~~~~~~~---en~~r~IlV~q-~~ltp~Ar~~i 114 (143)
..+.++...+|+..||.+++.+.. .+-.+.|+|-. ..+++.|..++
T Consensus 67 ~~~~~~~~~~~~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~L 116 (188)
T TIGR00678 67 HRLEPEGQSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANAL 116 (188)
T ss_pred EEeccccCcCCHHHHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHH
Confidence 334455557899999988888764 45455555532 56777654433
No 81
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=26.49 E-value=90 Score=25.69 Aligned_cols=52 Identities=15% Similarity=0.301 Sum_probs=34.4
Q ss_pred CcceEEEeecCCCCCCcEEEE-cCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC
Q 032325 51 REDLVINKALRNDSSDQIYVF-FPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ 104 (143)
Q Consensus 51 r~~L~~~~~~~~dp~~~i~Vf-F~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~ 104 (143)
|.++.+......+|.=-++=. |++-+.+.|..|+.++..+.+.|+ ||+|+.-
T Consensus 145 RRR~EIARaLa~~P~fiLLDEPFAGVDPiaV~dIq~iI~~L~~rgi--GvLITDH 197 (243)
T COG1137 145 RRRVEIARALAANPKFILLDEPFAGVDPIAVIDIQRIIKHLKDRGI--GVLITDH 197 (243)
T ss_pred HHHHHHHHHHhcCCCEEEecCCccCCCchhHHHHHHHHHHHHhCCc--eEEEccc
Confidence 556666555555553111100 566678999999999999999887 5666643
No 82
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=26.42 E-value=77 Score=21.02 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=25.9
Q ss_pred CCCeEEEEEcCCCCHHHHHHHHhccc----cceEeeeccceEEeecc
Q 032325 94 NVFRAILVVQQNLTPFARTCIQEISA----KFHLEVFQVNVFSLMIY 136 (143)
Q Consensus 94 n~~r~IlV~q~~ltp~Ar~~i~~~~~----~~~iE~F~E~ELlVNIT 136 (143)
++.+|+||.. -|+.|+.+..+.. .|.||-..+.=|+|+-.
T Consensus 3 ~a~kGvLv~C---Dpa~Kq~il~ld~~~~~~FIIedLDdthlfV~~~ 46 (68)
T PF06331_consen 3 NAIKGVLVEC---DPAIKQFILHLDESMPHGFIIEDLDDTHLFVKPD 46 (68)
T ss_dssp EEEEEEEEES----HHHHHHHHHHHHHCCTSSEEEEECTTEEEE-CC
T ss_pred ceeeeEEEEc---CHHHHHHHHHHhcCCCCCeEEEEcCCCeEEEcHh
Confidence 3567888865 4566666655543 37888888888888744
No 83
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=26.29 E-value=95 Score=17.06 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=17.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCcccc
Q 032325 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVG 30 (143)
Q Consensus 1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~ 30 (143)
|+.+.+|+.--|--+| |..|||.-.
T Consensus 1 ~~~~nRelV~~yv~yK-----LsQrgy~w~ 25 (27)
T smart00265 1 SRLDNRELVVDYVTYK-----LSQNGYEWD 25 (27)
T ss_pred CCcchHHHHHHHHHHH-----HhhcCCCCC
Confidence 5566777766666655 778998654
No 84
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=26.19 E-value=2e+02 Score=24.60 Aligned_cols=39 Identities=8% Similarity=0.165 Sum_probs=28.1
Q ss_pred ccchhHHHHHHHHHh---hcCCCeEEEEEc-CCCCHHHHHHHH
Q 032325 77 KVGVKTMKTYTNRMK---SENVFRAILVVQ-QNLTPFARTCIQ 115 (143)
Q Consensus 77 ~vgvk~ik~~~~~~~---~en~~r~IlV~q-~~ltp~Ar~~i~ 115 (143)
.++|.+||.+++.+. .++-.|.+||.+ ..||+.|..++-
T Consensus 111 ~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLL 153 (342)
T PRK06964 111 EIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNVAAANALL 153 (342)
T ss_pred ccCHHHHHHHHHHhccCCccCCceEEEEechhhcCHHHHHHHH
Confidence 599999999999885 345566666643 458988766654
No 85
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=26.18 E-value=3.4e+02 Score=21.69 Aligned_cols=43 Identities=21% Similarity=0.194 Sum_probs=31.0
Q ss_pred CCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 032325 74 DEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 74 ~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
++...+.+.|+++.+.++++++. +|++-.+.-++.++....+.
T Consensus 197 ~~~eps~~~l~~l~~~ik~~~v~-~if~e~~~~~~~~~~la~~~ 239 (266)
T cd01018 197 EGKEPSPADLKRLIDLAKEKGVR-VVFVQPQFSTKSAEAIAREI 239 (266)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCC-EEEEcCCCCcHHHHHHHHHc
Confidence 44568899999999999999999 66665555555555443443
No 86
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=26.13 E-value=1.8e+02 Score=25.83 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=22.3
Q ss_pred HHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 85 TYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 85 ~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
+++|...++|-+ ++++-..+|-+| +|.++++
T Consensus 235 tiAEyfrd~G~~--VLl~~Dsltr~A-~A~REis 265 (433)
T PRK07594 235 TIAEFFRDNGKR--VVLLADSLTRYA-RAAREIA 265 (433)
T ss_pred HHHHHHHHCCCc--EEEEEeCHHHHH-HHHHHHH
Confidence 467777777766 334447999998 8888876
No 87
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=26.07 E-value=2e+02 Score=24.26 Aligned_cols=48 Identities=13% Similarity=0.237 Sum_probs=34.8
Q ss_pred EEEEcCCC--CccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDE--QKVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~--~~vgvk~ik~~~~~~~---~en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
++++.|++ ..+||.+||.+++.+. .++-.+.+||- -..||..|..++-
T Consensus 74 ~~~i~~~~~~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLL 127 (328)
T PRK05707 74 NFVLEPEEADKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALL 127 (328)
T ss_pred EEEEeccCCCCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHH
Confidence 66667765 3599999999999985 35667777663 3568987766654
No 88
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=25.99 E-value=1.9e+02 Score=23.29 Aligned_cols=49 Identities=12% Similarity=0.167 Sum_probs=36.6
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~~ 117 (143)
+..-|.++..|....++.+++++.+.|++ ||+|..+ .||..-|+.+-+.
T Consensus 8 ~~TPf~~dg~iD~~~~~~~i~~l~~~Gv~-gl~v~GstGE~~~lt~~Er~~l~~~ 61 (284)
T cd00950 8 LVTPFKDDGSVDFDALERLIEFQIENGTD-GLVVCGTTGESPTLSDEEHEAVIEA 61 (284)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECCCCcchhhCCHHHHHHHHHH
Confidence 34457777889999999999999999988 6666544 4677766666544
No 89
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=25.59 E-value=1.3e+02 Score=27.64 Aligned_cols=92 Identities=24% Similarity=0.272 Sum_probs=53.5
Q ss_pred HHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhh
Q 032325 13 RIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKS 92 (143)
Q Consensus 13 rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~ 92 (143)
|.+|||+=|+..+--. .-+|.+|-..+|.- |+-+-|.....-....-.||.|++..+|-.+. -+..
T Consensus 177 Rd~Rtvf~~qla~r~~------pRdL~efFs~~gkV--rdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai------aLsG 242 (549)
T KOG0147|consen 177 RDQRTVFCMQLARRNP------PRDLEEFFSIVGKV--RDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI------ALSG 242 (549)
T ss_pred HhHHHHHHHHHhhcCC------chhHHHHHHhhcCc--ceeEeeccccchhhcceeEEEEecccchhhHh------hhcC
Confidence 6789999888665422 44688998888743 33333333333333455899999988776554 2222
Q ss_pred cCCCeEEEEEcCCCCHHHHHHHHhcccc
Q 032325 93 ENVFRAILVVQQNLTPFARTCIQEISAK 120 (143)
Q Consensus 93 en~~r~IlV~q~~ltp~Ar~~i~~~~~~ 120 (143)
+-.-..=+++ .+|-.+|...+.+++.
T Consensus 243 qrllg~pv~v--q~sEaeknr~a~~s~a 268 (549)
T KOG0147|consen 243 QRLLGVPVIV--QLSEAEKNRAANASPA 268 (549)
T ss_pred CcccCceeEe--cccHHHHHHHHhcccc
Confidence 2222121222 4677777766666653
No 90
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=25.59 E-value=1.1e+02 Score=25.29 Aligned_cols=48 Identities=17% Similarity=0.099 Sum_probs=35.6
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHh
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQE 116 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~ 116 (143)
+..-|.++.+|..+.++.+++.+.+.|++ ||+|..+ .||..-|..+-+
T Consensus 8 ~~TPf~~dg~iD~~~l~~lv~~~~~~Gv~-gi~v~GstGE~~~Ls~~Er~~l~~ 60 (294)
T TIGR02313 8 LITPFKRNGDIDEEALRELIEFQIEGGSH-AISVGGTSGEPGSLTLEERKQAIE 60 (294)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECccCcccccCCHHHHHHHHH
Confidence 44557788899999999999999999998 7777543 356555544443
No 91
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=25.53 E-value=2.5e+02 Score=23.39 Aligned_cols=70 Identities=17% Similarity=0.149 Sum_probs=40.7
Q ss_pred HHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 032325 38 KEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 38 l~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
..+|.+.+-+....+.-.+++...++| +...-...-+-=+++|.+.++|-+ . +|+-..||..| +|.+++
T Consensus 112 v~e~~~~~~~~~~~~~tvvv~~t~d~~--------~~~r~~a~~~a~aiAE~fr~~G~~-V-lvl~DslTr~A-~A~rEi 180 (274)
T cd01132 112 VAQVVKTLEEHGAMEYTIVVAATASDP--------APLQYLAPYTGCAMGEYFMDNGKH-A-LIIYDDLSKQA-VAYRQM 180 (274)
T ss_pred HHHHHHHHHhcCccceeEEEEeCCCCc--------hhHHHHHHHHHHHHHHHHHHCCCC-E-EEEEcChHHHH-HHHHHH
Confidence 446777775544444455666655555 222222222334566777777654 3 34447999998 778887
Q ss_pred c
Q 032325 118 S 118 (143)
Q Consensus 118 ~ 118 (143)
+
T Consensus 181 s 181 (274)
T cd01132 181 S 181 (274)
T ss_pred H
Confidence 6
No 92
>PF08011 DUF1703: Protein of unknown function (DUF1703); InterPro: IPR012547 This family contains many hypothetical bacterial proteins.
Probab=25.31 E-value=1.5e+02 Score=20.40 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=29.6
Q ss_pred HHHHHhc-CCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcC
Q 032325 17 TVMQMLR-DRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFP 73 (143)
Q Consensus 17 Tv~eMl~-DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~ 73 (143)
.++-||. +.||.|..+.-. +.+|-+|.+. .+.+.+.....+.|-
T Consensus 9 ~~~~~l~~~~~y~v~sE~e~------------~~Gr~Dl~l~-~~~~~~~~~~IiElK 53 (105)
T PF08011_consen 9 FLLGYLSLSSGYEVKSERES------------GKGRIDLVLE-PPKPTPKYIYIIELK 53 (105)
T ss_pred HHHHHHHHcCCcEEEEEecC------------CCCeEEEEEE-EccCCCCeEEEEEEE
Confidence 4566777 889988763321 3458788888 455556667788885
No 93
>cd03735 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery.
Probab=25.02 E-value=72 Score=19.34 Aligned_cols=33 Identities=9% Similarity=0.189 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhc
Q 032325 12 FRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFG 46 (143)
Q Consensus 12 ~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~ 46 (143)
..||+||..-+ .|+.+....+.-++-+|.+.|.
T Consensus 8 hLCR~tI~~~~--~~~~i~~lpLP~~LKdyL~~y~ 40 (43)
T cd03735 8 ELCRKSIVATF--GRENLARIPLNPVLKDYLKSFP 40 (43)
T ss_pred HHHHHHHHHhc--CccccccCcCCHHHHHHHHhCC
Confidence 46899998876 3445544456667889988874
No 94
>PF14082 DUF4263: Domain of unknown function (DUF4263)
Probab=25.02 E-value=99 Score=22.98 Aligned_cols=56 Identities=11% Similarity=0.220 Sum_probs=39.7
Q ss_pred ccchhHHHHHHHHHhhc-------------------CCCeEEEEEc---CCCCHHHHHHHHhccccc-eEeeeccceEE
Q 032325 77 KVGVKTMKTYTNRMKSE-------------------NVFRAILVVQ---QNLTPFARTCIQEISAKF-HLEVFQVNVFS 132 (143)
Q Consensus 77 ~vgvk~ik~~~~~~~~e-------------------n~~r~IlV~q---~~ltp~Ar~~i~~~~~~~-~iE~F~E~ELl 132 (143)
.=++.+|..+...+.+. ---++|||.. ...+...++++......+ .||+-..+|||
T Consensus 86 ~~ai~Qi~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ilIiGr~~~~~~~~~r~~~e~~~~~~~~i~IiTyD~Ll 164 (164)
T PF14082_consen 86 SGAISQILDYKFWLEKNYNSIRFELHEGYKSSEPGIYNPKGILIIGRRSEYLNEEQRESFELFRRNLKNIEIITYDELL 164 (164)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHhhhccccccccCCccceeEEEEECCCCCCCCHHHHHHHHHHHcCCCCcEEEeccccC
Confidence 34567888777766421 1135777877 458888889898888765 78888888885
No 95
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=24.65 E-value=2e+02 Score=23.67 Aligned_cols=47 Identities=11% Similarity=0.095 Sum_probs=36.3
Q ss_pred EEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHh
Q 032325 69 YVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQE 116 (143)
Q Consensus 69 ~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~ 116 (143)
..-|.++..|..+.++..++.+.+.|++ ||+|..+ .||..-|+.+-+
T Consensus 16 vTPf~~dg~iD~~~l~~li~~l~~~Gv~-Gi~~~GstGE~~~Lt~eEr~~~~~ 67 (303)
T PRK03620 16 VTPFDADGSFDEAAYREHLEWLAPYGAA-ALFAAGGTGEFFSLTPDEYSQVVR 67 (303)
T ss_pred eCCCCCCCCcCHHHHHHHHHHHHHcCCC-EEEECcCCcCcccCCHHHHHHHHH
Confidence 3446777899999999999999999998 8878653 577776655544
No 96
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=24.65 E-value=1.8e+02 Score=25.40 Aligned_cols=57 Identities=23% Similarity=0.348 Sum_probs=40.6
Q ss_pred cCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCC--HHHHHHHHhccccc-eEeeecc
Q 032325 72 FPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLT--PFARTCIQEISAKF-HLEVFQV 128 (143)
Q Consensus 72 F~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~lt--p~Ar~~i~~~~~~~-~iE~F~E 128 (143)
.|..-..|-..++...+....-+++|+.||+-..+. +.+.+.++.+.... ..++|.+
T Consensus 6 ~p~~i~fG~g~l~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~ 65 (377)
T COG1454 6 LPTEILFGRGSLKELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDE 65 (377)
T ss_pred cCceEEecCChHHHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecC
Confidence 355556788899999999999999999999988764 44555555555432 4455644
No 97
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.62 E-value=1.9e+02 Score=18.12 Aligned_cols=47 Identities=6% Similarity=0.312 Sum_probs=34.0
Q ss_pred EEEcCCCCccchhHHHHHHHHHhhcCCCeEE--EEEcCCCCHHHHHHHHhcc
Q 032325 69 YVFFPDEQKVGVKTMKTYTNRMKSENVFRAI--LVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 69 ~VfF~~~~~vgvk~ik~~~~~~~~en~~r~I--lV~q~~ltp~Ar~~i~~~~ 118 (143)
+++|++ +.-+.+..++..+++.|+...+ ++++.++.=..+..+.++.
T Consensus 3 ~ll~~g---~~~~el~~~l~~~r~~~~~~~~kAvlT~tN~~Wt~~~L~~El~ 51 (58)
T PF12646_consen 3 FLLFSG---FSGEELDKFLDALRKAGIPIPLKAVLTPTNINWTLKDLLEELK 51 (58)
T ss_pred EEEECC---CCHHHHHHHHHHHHHcCCCcceEEEECCCcccCcHHHHHHHHH
Confidence 355664 5678999999999999996655 4567777666666666654
No 98
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=24.37 E-value=1.3e+02 Score=24.85 Aligned_cols=64 Identities=16% Similarity=0.203 Sum_probs=45.1
Q ss_pred HHHHHHHhcCCCccc--chhhhccCHHHHHHHhcC-CCCCcceEEEeecCCCCCCcEEEEcCCCCccchh
Q 032325 15 RRTVMQMLRDRGYFV--GDFEINMSKEQFIAKFGE-NMKREDLVINKALRNDSSDQIYVFFPDEQKVGVK 81 (143)
Q Consensus 15 rrTv~eMl~DRGY~V--~~~e~~~sl~~F~~~y~~-~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk 81 (143)
=++.-.+|+++||.. ...| .+.++.+..+. +-...+++++-.+.+.+...++|.+....+-|.+
T Consensus 153 i~~a~~~lk~~G~l~~V~r~e---rl~ei~~~l~~~~~~~k~i~~V~p~~~k~A~~vLv~~~k~~~~~l~ 219 (248)
T COG4123 153 IRAAAKLLKPGGRLAFVHRPE---RLAEIIELLKSYNLEPKRIQFVYPKIGKAANRVLVEAIKGGKSGLK 219 (248)
T ss_pred HHHHHHHccCCCEEEEEecHH---HHHHHHHHHHhcCCCceEEEEecCCCCCcceEEEEEEecCCCCCce
Confidence 466778999999765 3322 45566555544 4446779999988888889999999776664443
No 99
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=24.11 E-value=1.7e+02 Score=20.03 Aligned_cols=28 Identities=25% Similarity=0.545 Sum_probs=20.1
Q ss_pred HHHHHHHhcCCCcccc-hhhhccCHHHHH
Q 032325 15 RRTVMQMLRDRGYFVG-DFEINMSKEQFI 42 (143)
Q Consensus 15 rrTv~eMl~DRGY~V~-~~e~~~sl~~F~ 42 (143)
++++++.|+++||.-. ..--+..+..+.
T Consensus 38 ~~~l~~~Lr~~g~l~~~~~~~~~p~q~~~ 66 (111)
T PF03374_consen 38 RNKLFQWLREKGWLYRRGKGRNLPYQKYI 66 (111)
T ss_pred HHHHHHHHHhCCceEECCCCCcccChhhh
Confidence 6788999999999988 444455555543
No 100
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=23.89 E-value=2.2e+02 Score=23.21 Aligned_cols=48 Identities=8% Similarity=0.113 Sum_probs=36.5
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhh-cCCCeEEEEEc-----CCCCHHHHHHHHh
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKS-ENVFRAILVVQ-----QNLTPFARTCIQE 116 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~-en~~r~IlV~q-----~~ltp~Ar~~i~~ 116 (143)
+..-|.++..|..+.++.+++++.+ .|++ ||+|.. ..||..-|..+-+
T Consensus 11 ~~TPf~~dg~iD~~~~~~li~~l~~~~Gv~-gi~v~GstGE~~~Ls~eEr~~~~~ 64 (293)
T PRK04147 11 LLTPFDEDGQIDEQGLRRLVRFNIEKQGID-GLYVGGSTGEAFLLSTEEKKQVLE 64 (293)
T ss_pred eECcCCCCCCcCHHHHHHHHHHHHhcCCCC-EEEECCCccccccCCHHHHHHHHH
Confidence 3445777889999999999999999 9998 777754 3567666665544
No 101
>PRK01889 GTPase RsgA; Reviewed
Probab=23.74 E-value=2.2e+02 Score=24.23 Aligned_cols=44 Identities=9% Similarity=0.215 Sum_probs=37.9
Q ss_pred CcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHH
Q 032325 66 DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPF 109 (143)
Q Consensus 66 ~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~ 109 (143)
|+++|.++.++.+....|..|+..+...|+.-.|++.+..+-+.
T Consensus 114 D~vliV~s~~p~~~~~~ldr~L~~a~~~~i~piIVLNK~DL~~~ 157 (356)
T PRK01889 114 DTVFIVCSLNHDFNLRRIERYLALAWESGAEPVIVLTKADLCED 157 (356)
T ss_pred CEEEEEEecCCCCChhHHHHHHHHHHHcCCCEEEEEEChhcCCC
Confidence 67888888888899899999999999999999888888888543
No 102
>KOG1322 consensus GDP-mannose pyrophosphorylase/mannose-1-phosphate guanylyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=23.74 E-value=5e+02 Score=22.78 Aligned_cols=95 Identities=14% Similarity=0.274 Sum_probs=57.4
Q ss_pred HHHhcCCCcccchhhh--ccCHHHHHHHhcCCCCCcceEEEeecCCCCCC----------cEEEEcCCCCccchhHHHHH
Q 032325 19 MQMLRDRGYFVGDFEI--NMSKEQFIAKFGENMKREDLVINKALRNDSSD----------QIYVFFPDEQKVGVKTMKTY 86 (143)
Q Consensus 19 ~eMl~DRGY~V~~~e~--~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~----------~i~VfF~~~~~vgvk~ik~~ 86 (143)
+.--.|--|.|-..++ .|.|.+|.+-.-+. +.+-+++|.+.++|++ ....-|.+.|+
T Consensus 107 L~~~~~~~ffVLnsDvi~~~p~~~~vqfH~~~--gae~TI~~t~vdepSkyGvv~~d~~~grV~~F~EKPk--------- 175 (371)
T KOG1322|consen 107 LWVFEDAPFFVLNSDVICRMPYKEMVQFHRAH--GAEITIVVTKVDEPSKYGVVVIDEDTGRVIRFVEKPK--------- 175 (371)
T ss_pred hhhcCCCcEEEecCCeeecCCHHHHHHHHHhc--CCceEEEEEeccCccccceEEEecCCCceeEehhCch---------
Confidence 3333444577755554 78999999877544 5679999999998874 23444555553
Q ss_pred HHHHhhcCCCeEEEEEc--------CCCCHHHHHHHHhccccceEeee
Q 032325 87 TNRMKSENVFRAILVVQ--------QNLTPFARTCIQEISAKFHLEVF 126 (143)
Q Consensus 87 ~~~~~~en~~r~IlV~q--------~~ltp~Ar~~i~~~~~~~~iE~F 126 (143)
.+....+..||-|+. ..+|+..+..+..++....+..|
T Consensus 176 --d~vsnkinaGiYi~~~~vL~ri~~~ptSiekEifP~~a~~~~l~a~ 221 (371)
T KOG1322|consen 176 --DLVSNKINAGIYILNPEVLDRILLRPTSIEKEIFPAMAEEHQLYAF 221 (371)
T ss_pred --hhhhccccceEEEECHHHHhHhhhcccchhhhhhhhhhhcCceEEE
Confidence 344566667887753 23445555555544443344444
No 103
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=23.57 E-value=37 Score=27.08 Aligned_cols=46 Identities=20% Similarity=0.305 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCC
Q 032325 13 RIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDS 64 (143)
Q Consensus 13 rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp 64 (143)
.+++++++.|.+-||.|...-++.. .||-...|+++-+++...+-+
T Consensus 121 ~~~~~i~~~l~~lGY~v~~~vlna~------~yGvPQ~R~R~fivg~r~~~~ 166 (335)
T PF00145_consen 121 EVFKEILEELEELGYNVQWRVLNAA------DYGVPQNRERVFIVGIRKDLP 166 (335)
T ss_dssp HHHHHHHHHHHHTTEEEEEEEEEGG------GGTSSBE-EEEEEEEEEGGG-
T ss_pred cccccccccccccceeehhccccHh------hCCCCCceeeEEEEEECCCCC
Confidence 5678899999999999997777644 688888899999999877654
No 104
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=23.53 E-value=75 Score=20.50 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHhcCCCcccch
Q 032325 8 IKRLFRIRRTVMQMLRDRGYFVGD 31 (143)
Q Consensus 8 ~~rL~rirrTv~eMl~DRGY~V~~ 31 (143)
...|..+.+.+-+.++++||..+.
T Consensus 33 ~~~l~~~~~~l~~~y~~~GY~~s~ 56 (76)
T PF08479_consen 33 LADLQQLADALTNYYREKGYITSR 56 (76)
T ss_dssp HHHHHHHHHHHHHHHHHTT-TT-E
T ss_pred HHHHHHHHHHHHHHHHHcCceEEE
Confidence 456788999999999999999875
No 105
>PF02222 ATP-grasp: ATP-grasp domain; InterPro: IPR003135 The ATP-grasp domain has an unusual nucleotide-binding fold, also referred to as palmate, and is found in a superfamily of enzymes including D-alanine-D-alanine ligase, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, the ribosomal protein S6 modification enzyme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. This family does not contain all known ATP-grasp domain members. All the enzymes of this family possess ATP-dependent carboxylate-amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates.; PDB: 3K5H_C 3K5I_C 3AX6_A 3Q2O_B 3QFF_B 3R5H_A 3ORQ_B 3ORR_B 4E4T_B 2Z04_A ....
Probab=23.42 E-value=99 Score=23.72 Aligned_cols=68 Identities=13% Similarity=0.275 Sum_probs=39.2
Q ss_pred CcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccc----------
Q 032325 51 REDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK---------- 120 (143)
Q Consensus 51 r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~---------- 120 (143)
...+++.+....+ ++ .++||--+. ..++|+-+.- +++..+++...+.+.+++.+
T Consensus 75 ~~EiSvivaR~~~--G~-~~~yp~~en------------~~~~~il~~s-~~Pa~i~~~~~~~a~~ia~~i~~~l~~vGv 138 (172)
T PF02222_consen 75 DREISVIVARDQD--GE-IRFYPPVEN------------VHRDGILHES-IAPARISDEVEEEAKEIARKIAEALDYVGV 138 (172)
T ss_dssp SEEEEEEEEEETT--SE-EEEEEEEEE------------EEETTEEEEE-EESCSS-HHHHHHHHHHHHHHHHHHTSSEE
T ss_pred cEEEEEEEEEcCC--CC-EEEEcCceE------------EEECCEEEEE-ECCCCCCHHHHHHHHHHHHHHHHHcCcEEE
Confidence 4456666665333 34 455553221 1234444443 46777887766666665542
Q ss_pred ceEeeecc--ce-EEee
Q 032325 121 FHLEVFQV--NV-FSLM 134 (143)
Q Consensus 121 ~~iE~F~E--~E-LlVN 134 (143)
|.||.|.- .+ |+||
T Consensus 139 ~~VE~Fv~~~g~~v~vN 155 (172)
T PF02222_consen 139 LAVEFFVTKDGDEVLVN 155 (172)
T ss_dssp EEEEEEEETTSTEEEEE
T ss_pred EEEEEEEecCCCEEEEE
Confidence 69999986 65 9998
No 106
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=23.33 E-value=2.6e+02 Score=19.33 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccc
Q 032325 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119 (143)
Q Consensus 81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~ 119 (143)
..++..+.++.+.+=.++.+|+-+.+.......+.+..|
T Consensus 53 ~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p 91 (98)
T PF00919_consen 53 QKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFP 91 (98)
T ss_pred HHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCC
Confidence 334444445544443567778888998877777777665
No 107
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=23.32 E-value=4.1e+02 Score=21.58 Aligned_cols=52 Identities=15% Similarity=0.031 Sum_probs=42.1
Q ss_pred cEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccc
Q 032325 67 QIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119 (143)
Q Consensus 67 ~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~ 119 (143)
.-++|+-+||-+-..-+..+....+++|++.+ +++.+-+++.+..-+.+.-.
T Consensus 85 ~gvt~SGGEP~~q~e~~~~~~~~ake~Gl~~~-l~TnG~~~~~~~~~l~~~~D 136 (260)
T COG1180 85 GGVTFSGGEPTLQAEFALDLLRAAKERGLHVA-LDTNGFLPPEALEELLPLLD 136 (260)
T ss_pred CEEEEECCcchhhHHHHHHHHHHHHHCCCcEE-EEcCCCCCHHHHHHHHhhcC
Confidence 35666778899999999999999999999854 59999999998755555544
No 108
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=22.96 E-value=2.3e+02 Score=22.96 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=36.6
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~~ 117 (143)
+..-|.++..|....++.+++++.+.|++ ||++..+ .||..-|+.+-+.
T Consensus 6 ~~TPf~~~g~iD~~~~~~~i~~l~~~Gv~-Gi~~~GstGE~~~Ls~~Er~~~~~~ 59 (285)
T TIGR00674 6 LITPFKEDGSVDFAALEKLIDFQIENGTD-AIVVVGTTGESPTLSHEEHKKVIEF 59 (285)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECccCcccccCCHHHHHHHHHH
Confidence 34457778899999999999999999998 6666533 4677666666543
No 109
>COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]
Probab=22.75 E-value=1.2e+02 Score=24.63 Aligned_cols=58 Identities=16% Similarity=0.122 Sum_probs=46.8
Q ss_pred CccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccc
Q 032325 76 QKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYT 137 (143)
Q Consensus 76 ~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~ 137 (143)
..|+.+.|++++.---.-+...+++|+.+..|-.|++. +..+ .+|..+-+++.-||-.
T Consensus 157 ~aV~~kaiqEivask~~Y~~eka~vvTn~~yt~~aqkl-a~~n---sv~l~~r~~~~~f~~~ 214 (217)
T COG1787 157 SAVSKKAIQEIVASKAYYGCEKAKVVTNGSYTYAAQKL-AQAN---SVELIDRDELSEFIRE 214 (217)
T ss_pred HhhhHHHHHHHHHhhhccCcceEEEecCCccchhHHHH-HHhh---cceEEecchHHhhhcc
Confidence 47999999999888888899999999999999888664 4444 5788888888777654
No 110
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=22.72 E-value=2.2e+02 Score=24.06 Aligned_cols=39 Identities=5% Similarity=0.202 Sum_probs=28.2
Q ss_pred ccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 77 KVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 77 ~vgvk~ik~~~~~~~~---en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
.++|.+||.+++.+.. +|-.|.+||. -..||..|..++-
T Consensus 92 ~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLL 134 (319)
T PRK08769 92 EIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALL 134 (319)
T ss_pred cccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHH
Confidence 3899999999998853 4555666663 3568987766654
No 111
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=22.68 E-value=2.5e+02 Score=25.05 Aligned_cols=71 Identities=20% Similarity=0.200 Sum_probs=37.1
Q ss_pred HHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 032325 38 KEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (143)
Q Consensus 38 l~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~ 117 (143)
..+|.+.+-+....++-.+++...++| |.+.-...-+-=+++|....++=++.+ ++-..||.+| +|.+++
T Consensus 181 ~~ef~~~~~~~~~l~rtvlv~~~adep--------~~~R~~~~~~AltiAEyfrd~g~~~VL-li~DdlTr~a-~A~REI 250 (436)
T PRK02118 181 YLFFKDTFENAGALDRTVMFIHTASDP--------PVECLLVPDMALAVAEKFALEGKKKVL-VLLTDMTNFA-DALKEI 250 (436)
T ss_pred HHHHHHHHhhCCCcceEEEEEECCCCC--------HHHHHHHHHHHHHHHHHHHhcCCCCEE-EeccCchHHH-HHHHHH
Confidence 345655554444444455555555555 222222233333466666666533333 3346788887 777776
Q ss_pred c
Q 032325 118 S 118 (143)
Q Consensus 118 ~ 118 (143)
+
T Consensus 251 s 251 (436)
T PRK02118 251 S 251 (436)
T ss_pred H
Confidence 5
No 112
>PLN02417 dihydrodipicolinate synthase
Probab=22.58 E-value=1.3e+02 Score=24.45 Aligned_cols=47 Identities=6% Similarity=0.030 Sum_probs=34.0
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHH
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~ 115 (143)
+..-|.++..|..+.++.+++++.+.|++ ||+|..+ .||..-|+.+-
T Consensus 9 ~~TPf~~~g~iD~~~~~~~i~~l~~~Gv~-Gi~~~GstGE~~~ls~~Er~~~~ 60 (280)
T PLN02417 9 IKTPYLPDGRFDLEAYDSLVNMQIENGAE-GLIVGGTTGEGQLMSWDEHIMLI 60 (280)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECccCcchhhCCHHHHHHHH
Confidence 34457777889999999999999999988 7777543 35555554443
No 113
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=22.55 E-value=1.3e+02 Score=24.10 Aligned_cols=48 Identities=17% Similarity=0.248 Sum_probs=34.7
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHh
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQE 116 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~ 116 (143)
+..-|.++..|....++.+++.+.+.|++ ||+|..+ .+|..-|+.+-+
T Consensus 5 ~~TPf~~dg~iD~~~~~~~i~~l~~~Gv~-gi~~~GstGE~~~ls~~Er~~l~~ 57 (281)
T cd00408 5 LVTPFTADGEVDLDALRRLVEFLIEAGVD-GLVVLGTTGEAPTLTDEERKEVIE 57 (281)
T ss_pred eeCCcCCCCCcCHHHHHHHHHHHHHcCCC-EEEECCCCcccccCCHHHHHHHHH
Confidence 34557778899999999999999999988 5666443 356655555543
No 114
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=22.22 E-value=3.2e+02 Score=19.94 Aligned_cols=41 Identities=7% Similarity=0.169 Sum_probs=26.8
Q ss_pred CcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCC
Q 032325 66 DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLT 107 (143)
Q Consensus 66 ~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~lt 107 (143)
|.+++....+ ..++..++...+.+++.+..-++++.+-...
T Consensus 116 D~vliv~~~~-~~~~~~~~~~~~~l~~~~~~~~vV~N~~~~~ 156 (179)
T cd03110 116 DAALLVTEPT-PSGLHDLERAVELVRHFGIPVGVVINKYDLN 156 (179)
T ss_pred CEEEEEecCC-cccHHHHHHHHHHHHHcCCCEEEEEeCCCCC
Confidence 4455554443 3577888888888887787766666555443
No 115
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=22.20 E-value=3.5e+02 Score=22.72 Aligned_cols=40 Identities=10% Similarity=0.248 Sum_probs=29.7
Q ss_pred ccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHHh
Q 032325 77 KVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQE 116 (143)
Q Consensus 77 ~vgvk~ik~~~~~~~~---en~~r~IlV~-q~~ltp~Ar~~i~~ 116 (143)
.+||.+||.+++.+.. ++-.+.|+|- -.+|++.|..++-.
T Consensus 92 ~I~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk 135 (325)
T PRK08699 92 QIKIDAVREIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLK 135 (325)
T ss_pred CcCHHHHHHHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHH
Confidence 4899999999999863 4656677663 34588888777664
No 116
>PF03013 Pyr_excise: Pyrimidine dimer DNA glycosylase; InterPro: IPR004260 Pyrimidine dimer DNA glycosylases are enzymes responsible for initiating the base excision repair pathway, excising pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond []. One such enzyme is T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway []. Bacteriophage T4 that are deficient in these enzymes are extremely sensitive to UV.; PDB: 2FCC_B 1ENJ_A 1ENI_A 1ENK_A 1VAS_A 2END_A.
Probab=21.96 E-value=75 Score=23.62 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHhcCCCcccchhhh
Q 032325 8 IKRLFRIRRTVMQMLRDRGYFVGDFEI 34 (143)
Q Consensus 8 ~~rL~rirrTv~eMl~DRGY~V~~~e~ 34 (143)
...|++=..=+++=|..|||.+.....
T Consensus 58 ~~~L~~rh~~l~~EM~~RGY~~~~~~~ 84 (130)
T PF03013_consen 58 LYYLYKRHQLLMAEMQRRGYKPNSPWF 84 (130)
T ss_dssp HHHHHHHHHHHHHHHHHTT---S--S-
T ss_pred HHHHHHHHHHHHHHHHHcCCCCChhhh
Confidence 456777778888888999999986544
No 117
>PF05846 Chordopox_A15: Chordopoxvirus A15 protein; InterPro: IPR008445 This family consists of several Chordopoxvirus A15 like sequences.
Probab=21.91 E-value=34 Score=24.12 Aligned_cols=12 Identities=8% Similarity=0.044 Sum_probs=9.6
Q ss_pred ceEEeeccccce
Q 032325 129 NVFSLMIYTCKL 140 (143)
Q Consensus 129 ~ELlVNIT~H~L 140 (143)
+=||||.|.|+|
T Consensus 48 silLVNPs~~~L 59 (90)
T PF05846_consen 48 SILLVNPSYIQL 59 (90)
T ss_pred eEEEECCCHHHH
Confidence 448899999887
No 118
>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A ....
Probab=21.88 E-value=2.8e+02 Score=20.51 Aligned_cols=48 Identities=15% Similarity=0.355 Sum_probs=32.5
Q ss_pred EEEEcCCCC--ccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHH
Q 032325 68 IYVFFPDEQ--KVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQ 115 (143)
Q Consensus 68 i~VfF~~~~--~vgvk~ik~~~~~~~~---en~~r~IlV~-q~~ltp~Ar~~i~ 115 (143)
++++=+++. .+++.+||.+.+.+.. ++-.+.|+|- -..||+.|..|+-
T Consensus 70 ~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLL 123 (162)
T PF13177_consen 70 FIIIKPDKKKKSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALL 123 (162)
T ss_dssp EEEEETTTSSSSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHH
T ss_pred eEEEecccccchhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHH
Confidence 444445554 6999999999999853 4456666663 4568988877765
No 119
>PF08190 PIH1: pre-RNA processing PIH1/Nop17
Probab=21.69 E-value=2.3e+02 Score=23.08 Aligned_cols=49 Identities=10% Similarity=0.073 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeec--cceEEeeccccceecC
Q 032325 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQ--VNVFSLMIYTCKLFNC 143 (143)
Q Consensus 81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~--E~ELlVNIT~H~LV~~ 143 (143)
+..++|++++..++=...++|.+.+ .|-|..+. ..-+-|||-+|..||+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~i~P~p--------------~f~ikt~~~~~~k~fiNic~~~~i~~ 58 (328)
T PF08190_consen 8 KEYEKEIQQLEKERKKDVIFIHPEP--------------GFVIKTKILKGKKVFINICSSDRIPP 58 (328)
T ss_pred HHHHHHHHHHHhccCCCeEEeCCCC--------------CeEEEEEecCCCEEEEEccCcccCCC
Confidence 6788899988665555566654322 13333332 2378999999999985
No 120
>COG1676 SEN2 tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=21.67 E-value=34 Score=26.79 Aligned_cols=14 Identities=57% Similarity=0.871 Sum_probs=12.1
Q ss_pred HHHHhcCCCcccch
Q 032325 18 VMQMLRDRGYFVGD 31 (143)
Q Consensus 18 v~eMl~DRGY~V~~ 31 (143)
|..+|+||||.|..
T Consensus 94 VY~dLr~rG~vvkt 107 (181)
T COG1676 94 VYRDLRDRGYVVKT 107 (181)
T ss_pred ehhhHHhCceEECc
Confidence 56799999999976
No 121
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=21.59 E-value=1.1e+02 Score=21.77 Aligned_cols=16 Identities=19% Similarity=0.580 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhcCCCc
Q 032325 12 FRIRRTVMQMLRDRGY 27 (143)
Q Consensus 12 ~rirrTv~eMl~DRGY 27 (143)
|+.-+.+++||-++|-
T Consensus 45 y~~~~~yi~~L~~~Gl 60 (95)
T COG3432 45 YKRAQKYIEMLVEKGL 60 (95)
T ss_pred HHHHHHHHHHHHhCCC
Confidence 7888999999999993
No 122
>PF02113 Peptidase_S13: D-Ala-D-Ala carboxypeptidase 3 (S13) family; InterPro: IPR000667 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The predicted active site residues for members of this family and family S12 occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components []; it is synthesised with a leader peptide to target it to the cell membrane []. After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor []. There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins []. Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. Proteases of family S11 have exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are C beta-lactamases [].; GO: 0004185 serine-type carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3F_B 3A3E_B 3A3D_A 3A3I_B 2Y59_C 1W8Q_A 3ZVT_B 3ZVW_B 2VGJ_B 1W79_D ....
Probab=21.36 E-value=2e+02 Score=25.38 Aligned_cols=33 Identities=9% Similarity=0.202 Sum_probs=29.7
Q ss_pred CcEEEEcCCCCccchhHHHHHHHHHhhcCCCeE
Q 032325 66 DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRA 98 (143)
Q Consensus 66 ~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~ 98 (143)
+.+++.+..||.++...+..+++++++.++.+.
T Consensus 82 G~L~l~G~GDP~l~~~~l~~la~~l~~~Gi~~I 114 (444)
T PF02113_consen 82 GDLYLKGGGDPSLTSEDLWALAAQLKAAGIKRI 114 (444)
T ss_dssp SEEEEEECSBTTBCHHHHHHHHHHHHHTT-SEE
T ss_pred CcEEEEecCCCccCHHHHHHHHHHHHHcCCCeE
Confidence 458999999999999999999999999999886
No 123
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=21.13 E-value=4.9e+02 Score=21.86 Aligned_cols=101 Identities=16% Similarity=0.214 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHH---hcC-CCCCcceEEEeecCCCCC------------C-c
Q 032325 5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAK---FGE-NMKREDLVINKALRNDSS------------D-Q 67 (143)
Q Consensus 5 ~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~---y~~-~~~r~~L~~~~~~~~dp~------------~-~ 67 (143)
+.++.-.||++|-+.| |||...+ +--++..+... |.. ...+.+..|..-+.-|.+ + -
T Consensus 150 ~~dlr~irRI~RD~~E----RGrs~Es--Vi~qilrrmpdy~~yI~PQ~~~tDI~fqr~p~vdts~pf~~~~~p~~~es~ 223 (277)
T cd02029 150 IINLEWIQKIHRDTAE----RGYSAEA--VMDTILRRMPDYINYICPQFSRTDINFQRVPTVDTSNPFIARDIPTADESF 223 (277)
T ss_pred cHHHHHHHHHHhhhHh----hCCCHHH--HHHHHHHhCchHHhhCCcccccCcEEEeccCcccCCCcccccCCCCCCcce
Confidence 4556667888886544 9998865 22222222222 322 233677777776643322 2 3
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeE-EEEEcCCCCHHHHHHH
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRA-ILVVQQNLTPFARTCI 114 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~-IlV~q~~ltp~Ar~~i 114 (143)
+.+-|.+...+.-..+- ..+..-=.+|+ -||++++=-..|-+.|
T Consensus 224 ~vi~~~~~~~~d~~~~~---~~~~~~~~s~~~~~v~~g~~~~~a~~~i 268 (277)
T cd02029 224 VVIHFRKPWGIDFPYLL---NMLHDSFMSRPNTIVVPGGKMGLAMELI 268 (277)
T ss_pred EEEEecCCCCCCHHHHH---HhhccchhcCCCcEEecCchHHHHHHHH
Confidence 56667664333333332 22232223333 3455555445554433
No 124
>PF02645 DegV: Uncharacterised protein, DegV family COG1307; InterPro: IPR003797 This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each other than to most homologs from other species. This suggests both recent paralogy and diversity of function.; PDB: 2DT8_A 3LUP_A 3NYI_B 3PL5_A 1PZX_B 1MGP_A 1VPV_B 3FYS_A 3EGL_C 3JR7_A ....
Probab=21.10 E-value=3.3e+02 Score=21.98 Aligned_cols=73 Identities=16% Similarity=0.289 Sum_probs=43.3
Q ss_pred hhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEE-EcCCCCH---
Q 032325 33 EINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILV-VQQNLTP--- 108 (143)
Q Consensus 33 e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV-~q~~ltp--- 108 (143)
..++|.++|-++....... |.........+.++.+++.+++....|.| +-+++|.
T Consensus 39 ~~~i~~~efy~~l~~~~~~---------------------p~TS~ps~~~~~~~f~~~~~~gyd~ii~i~iSs~LSgty~ 97 (280)
T PF02645_consen 39 GVDISPEEFYEKLRESGEI---------------------PKTSQPSPGEFEEAFEKLLEEGYDEIIVITISSGLSGTYN 97 (280)
T ss_dssp TTTSCHHHHHHHHHHTTSE---------------------EEEE---HHHHHHHHHHHHHTTTSEEEEEES-TTT-THHH
T ss_pred CCCCCHHHHHHHHHhcCCC---------------------ceecCCCHHHHHHHHHHHHHCCCCeEEEEeCCcchhhHHH
Confidence 3477888888876433211 11113447788888888888999988877 5566774
Q ss_pred HHHHHHHhccccceEeeec
Q 032325 109 FARTCIQEISAKFHLEVFQ 127 (143)
Q Consensus 109 ~Ar~~i~~~~~~~~iE~F~ 127 (143)
.|+.|.+.++ ..+|.+|.
T Consensus 98 ~a~~aa~~~~-~~~i~ViD 115 (280)
T PF02645_consen 98 SARLAAKMLP-DIKIHVID 115 (280)
T ss_dssp HHHHHHHHHT-TTEEEEEE
T ss_pred HHHHHHhhcC-cCEEEEEe
Confidence 4555666552 24666653
No 125
>TIGR00454 conserved hypothetical protein TIGR00454. At this time this gene appears to be present only in Archea
Probab=21.06 E-value=1.5e+02 Score=22.51 Aligned_cols=41 Identities=7% Similarity=0.069 Sum_probs=30.9
Q ss_pred CcEEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCC
Q 032325 66 DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNL 106 (143)
Q Consensus 66 ~~i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~l 106 (143)
+.++|.-+|-|-+.-++|+.+++.....+-.....+++...
T Consensus 90 ~~~lv~~~D~P~i~~~~i~~li~~~~~~~~~~~~~~~~~~~ 130 (183)
T TIGR00454 90 EPFLVVSSDLINLRSKIIDSIVDYYYCIKAPALAVMIPKEK 130 (183)
T ss_pred CCEEEEeCCcCcCCHHHHHHHHHHHHhcCCCceEEEecccc
Confidence 45888888889999999999999886665555555555443
No 126
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=21.00 E-value=63 Score=24.62 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=19.4
Q ss_pred cCCCcccchhhhccCHHHHHHHhcCCC
Q 032325 23 RDRGYFVGDFEINMSKEQFIAKFGENM 49 (143)
Q Consensus 23 ~DRGY~V~~~e~~~sl~~F~~~y~~~~ 49 (143)
.=|||.+.+ =++||+++|.+.+....
T Consensus 16 ~yRG~~l~~-L~~m~~~e~~~L~~aR~ 41 (143)
T PTZ00096 16 TYRGVELEK-LLALPEEELVELFRARQ 41 (143)
T ss_pred eeecCCHHH-HHcCCHHHHHHHcCccc
Confidence 348998865 35899999999885443
No 127
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=20.95 E-value=4.1e+02 Score=20.85 Aligned_cols=41 Identities=15% Similarity=0.174 Sum_probs=27.6
Q ss_pred cCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHH
Q 032325 72 FPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114 (143)
Q Consensus 72 F~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i 114 (143)
...+...+.+.+..+.+.++++++. +|+.-.+.-+..+ +.|
T Consensus 177 ~~~~~~ps~~~l~~l~~~ik~~~v~-~i~~e~~~~~~~~-~~l 217 (256)
T PF01297_consen 177 ISPGEEPSPKDLAELIKLIKENKVK-CIFTEPQFSSKLA-EAL 217 (256)
T ss_dssp SSSSSSS-HHHHHHHHHHHHHTT-S-EEEEETTS-THHH-HHH
T ss_pred cccccCCCHHHHHHHHHHhhhcCCc-EEEecCCCChHHH-HHH
Confidence 3456679999999999999999988 5555555445544 444
No 128
>PF15472 DUF4638: Domain of unknown function (DUF4638)
Probab=20.88 E-value=55 Score=27.09 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=14.6
Q ss_pred HHHHHHhcCCCcccch
Q 032325 16 RTVMQMLRDRGYFVGD 31 (143)
Q Consensus 16 rTv~eMl~DRGY~V~~ 31 (143)
+|++.+|+|-||.|.=
T Consensus 231 ~Tl~~lCkdaG~~vdi 246 (268)
T PF15472_consen 231 RTLLKLCKDAGMDVDI 246 (268)
T ss_pred HHHHHHHHHcCCCccc
Confidence 7999999999999974
No 129
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=20.27 E-value=55 Score=24.70 Aligned_cols=21 Identities=24% Similarity=0.276 Sum_probs=13.6
Q ss_pred CccchhHHHHHHHHHhhcCCC
Q 032325 76 QKVGVKTMKTYTNRMKSENVF 96 (143)
Q Consensus 76 ~~vgvk~ik~~~~~~~~en~~ 96 (143)
.+-.++.+..++..++++|++
T Consensus 163 ~~~t~~~l~~~i~~l~~~Gy~ 183 (191)
T TIGR02764 163 AKQTVKALPTIIKKLKEKGYE 183 (191)
T ss_pred cHhHHHHHHHHHHHHHHCCCE
Confidence 345566777777777776655
No 130
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=20.23 E-value=93 Score=20.50 Aligned_cols=33 Identities=15% Similarity=0.151 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCCcccchhhhccCHHHHHHHhc
Q 032325 14 IRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFG 46 (143)
Q Consensus 14 irrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~ 46 (143)
.|+.|.++|+.-||...+..---++.+..++|.
T Consensus 8 l~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl 40 (77)
T smart00576 8 LRIAVAQILESAGFDSFQESALETLTDILQSYI 40 (77)
T ss_pred HHHHHHHHHHHcCccccCHHHHHHHHHHHHHHH
Confidence 578899999999999987766556666666664
No 131
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=20.10 E-value=1.6e+02 Score=23.80 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=34.7
Q ss_pred EEEEcCCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-----CCCHHHHHHHHhc
Q 032325 68 IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-----NLTPFARTCIQEI 117 (143)
Q Consensus 68 i~VfF~~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~-----~ltp~Ar~~i~~~ 117 (143)
+..-|.++.+|..+.++.+++.+.+.|++ ||+|..+ .||..-|+.+-+.
T Consensus 9 ~~TPf~~dg~id~~~~~~~i~~l~~~Gv~-gl~~~GstGE~~~Lt~~Er~~l~~~ 62 (289)
T PF00701_consen 9 LITPFNADGSIDEDALKRLIDFLIEAGVD-GLVVLGSTGEFYSLTDEERKELLEI 62 (289)
T ss_dssp E---BETTSSB-HHHHHHHHHHHHHTTSS-EEEESSTTTTGGGS-HHHHHHHHHH
T ss_pred eeCCCCCCcCcCHHHHHHHHHHHHHcCCC-EEEECCCCcccccCCHHHHHHHHHH
Confidence 45558888899999999999999999988 8878643 4677666665443
No 132
>PRK05922 type III secretion system ATPase; Validated
Probab=20.01 E-value=3.4e+02 Score=24.18 Aligned_cols=36 Identities=14% Similarity=0.368 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325 80 VKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118 (143)
Q Consensus 80 vk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~ 118 (143)
..+-=+++|+..++|- +.+++ -..+|-+| +|.++++
T Consensus 232 ~~~a~tiAEyfrd~G~-~VLl~-~DslTR~A-~A~REis 267 (434)
T PRK05922 232 GRAAMTIAEYFRDQGH-RVLFI-MDSLSRWI-AALQEVA 267 (434)
T ss_pred HHHHHHHHHHHHHcCC-CEEEe-ccchhHHH-HHHHHHH
Confidence 3334457788877774 44444 47999998 8888876
Done!