Query 026481
Match_columns 238
No_of_seqs 16 out of 18
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 08:34:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026481.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026481hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14290 DUF4370: Domain of un 100.0 9E-123 2E-127 805.6 21.5 233 1-237 1-235 (239)
2 PLN02749 Uncharacterized prote 100.0 1E-108 2E-113 692.5 17.2 169 69-237 1-169 (173)
3 PRK15389 fumarate hydratase; P 76.7 8.2 0.00018 38.6 6.8 121 67-203 18-151 (536)
4 PRK00411 cdc6 cell division co 76.0 41 0.00088 29.6 10.3 151 73-225 197-372 (394)
5 PRK08230 tartrate dehydratase 73.6 7.7 0.00017 36.2 5.5 96 87-199 9-110 (299)
6 PRK08087 L-fuculose phosphate 67.5 20 0.00044 30.4 6.3 47 127-181 163-209 (215)
7 PF06798 PrkA: PrkA serine pro 64.6 7.7 0.00017 34.7 3.4 64 138-205 83-162 (254)
8 PRK02998 prsA peptidylprolyl i 64.4 59 0.0013 28.7 8.8 41 163-203 67-112 (283)
9 PRK07539 NADH dehydrogenase su 62.6 53 0.0012 26.8 7.7 104 107-233 6-123 (154)
10 PRK07490 hypothetical protein; 62.2 39 0.00083 29.5 7.2 50 127-184 175-224 (245)
11 COG1951 TtdA Tartrate dehydrat 60.8 24 0.00051 33.3 6.0 55 86-141 8-62 (297)
12 PF00268 Ribonuc_red_sm: Ribon 60.7 1.1E+02 0.0025 26.5 11.7 98 81-193 12-117 (281)
13 PRK06246 fumarate hydratase; P 60.5 21 0.00045 33.0 5.5 100 81-200 2-111 (280)
14 PLN03188 kinesin-12 family pro 52.4 60 0.0013 36.1 8.0 81 108-214 1137-1252(1320)
15 PF05681 Fumerase: Fumarate hy 52.2 28 0.0006 31.9 4.8 51 89-140 2-52 (271)
16 PRK07044 aldolase II superfami 51.5 62 0.0014 28.2 6.7 46 127-180 180-225 (252)
17 cd08048 TAF11 TATA Binding Pro 50.4 69 0.0015 24.6 6.1 37 137-175 45-82 (85)
18 PF00101 RuBisCO_small: Ribulo 49.0 14 0.00031 29.2 2.2 46 75-120 3-74 (99)
19 cd07119 ALDH_BADH-GbsA Bacillu 48.9 30 0.00065 32.2 4.6 51 75-125 24-82 (482)
20 COG2766 PrkA Putative Ser prot 48.8 38 0.00083 35.0 5.6 55 139-204 468-548 (649)
21 PRK10702 endonuclease III; Pro 48.2 13 0.00029 32.0 2.1 72 83-157 42-116 (211)
22 PF01388 ARID: ARID/BRIGHT DNA 48.0 33 0.00072 24.8 3.9 53 122-181 31-87 (92)
23 COG4423 Uncharacterized protei 47.6 47 0.001 26.2 4.9 47 82-128 4-51 (81)
24 cd03527 RuBisCO_small Ribulose 45.7 22 0.00049 28.3 2.9 26 75-100 4-29 (99)
25 TIGR00142 hycI hydrogenase mat 44.7 24 0.00053 28.0 3.0 35 155-189 109-146 (146)
26 PF01077 NIR_SIR: Nitrite and 44.6 16 0.00036 28.7 2.0 26 180-207 132-157 (157)
27 COG1107 Archaea-specific RecJ- 44.3 47 0.001 34.7 5.5 93 98-214 506-601 (715)
28 TIGR01237 D1pyr5carbox2 delta- 43.2 39 0.00085 32.1 4.5 49 76-124 59-113 (511)
29 PF11841 DUF3361: Domain of un 43.1 82 0.0018 27.1 6.0 58 88-145 37-98 (160)
30 PRK05255 hypothetical protein; 40.7 45 0.00097 28.8 4.1 47 131-185 22-76 (171)
31 PF02861 Clp_N: Clp amino term 40.2 28 0.0006 22.3 2.2 38 167-204 15-53 (53)
32 TIGR00722 ttdA_fumA_fumB hydro 39.9 54 0.0012 30.2 4.8 51 89-140 2-52 (273)
33 PF14355 Abi_C: Abortive infec 39.7 1.4E+02 0.0031 21.5 7.4 69 105-177 2-70 (80)
34 PF04751 DUF615: Protein of un 39.5 27 0.00057 29.5 2.6 45 133-185 13-65 (157)
35 TIGR00140 hupD hydrogenase exp 39.2 31 0.00068 26.6 2.7 35 155-189 96-134 (134)
36 PRK11241 gabD succinate-semial 38.7 42 0.00092 31.8 4.0 54 75-128 37-96 (482)
37 PF12631 GTPase_Cys_C: Catalyt 38.6 29 0.00063 25.1 2.3 32 144-181 41-72 (73)
38 PF02841 GBP_C: Guanylate-bind 38.0 1.6E+02 0.0034 26.2 7.2 57 153-211 57-113 (297)
39 COG5251 TAF40 Transcription in 37.1 22 0.00048 31.9 1.8 62 122-186 128-190 (199)
40 smart00501 BRIGHT BRIGHT, ARID 37.1 26 0.00056 25.9 1.9 51 130-188 33-87 (93)
41 cd01049 RNRR2 Ribonucleotide R 37.0 2.7E+02 0.0059 23.9 11.9 96 82-191 5-107 (288)
42 KOG0740 AAA+-type ATPase [Post 36.8 52 0.0011 32.2 4.3 117 60-190 298-425 (428)
43 COG0413 PanB Ketopantoate hydr 36.7 79 0.0017 29.6 5.3 70 125-194 157-262 (268)
44 PRK06833 L-fuculose phosphate 33.1 1.6E+02 0.0035 24.8 6.3 48 124-181 163-210 (214)
45 PF13758 Prefoldin_3: Prefoldi 33.1 45 0.00099 27.0 2.8 54 120-185 27-80 (99)
46 COG0248 GppA Exopolyphosphatas 33.0 86 0.0019 30.8 5.2 63 163-227 46-134 (492)
47 KOG4835 DNA-binding protein C1 32.5 86 0.0019 27.0 4.5 55 162-220 3-75 (144)
48 PLN02312 acyl-CoA oxidase 32.5 1.4E+02 0.003 30.2 6.7 39 158-196 625-663 (680)
49 PF10191 COG7: Golgi complex c 32.2 1.7E+02 0.0037 30.0 7.3 89 91-192 279-367 (766)
50 COG3215 PilZ Tfp pilus assembl 31.9 28 0.00061 29.1 1.5 20 187-206 86-107 (117)
51 PF10152 DUF2360: Predicted co 30.1 32 0.00069 28.3 1.6 31 177-221 115-145 (148)
52 TIGR01083 nth endonuclease III 30.1 2.7E+02 0.0059 23.1 7.1 73 82-157 38-113 (191)
53 TIGR02928 orc1/cdc6 family rep 29.6 3.8E+02 0.0082 23.3 9.4 60 73-132 189-251 (365)
54 PF01756 ACOX: Acyl-CoA oxidas 29.1 89 0.0019 25.6 4.0 76 113-196 66-144 (187)
55 PF13339 AATF-Che1: Apoptosis 29.0 2.8E+02 0.0061 21.6 7.3 56 132-187 56-123 (131)
56 PLN02289 ribulose-bisphosphate 28.5 48 0.001 29.4 2.4 31 70-101 64-94 (176)
57 PRK10880 adenine DNA glycosyla 28.4 57 0.0012 30.6 3.1 70 84-157 44-116 (350)
58 PF07849 DUF1641: Protein of u 27.8 50 0.0011 22.3 1.9 16 82-97 19-34 (42)
59 PRK06310 DNA polymerase III su 27.3 88 0.0019 27.3 3.9 106 99-218 130-239 (250)
60 COG0167 PyrD Dihydroorotate de 27.3 32 0.0007 32.0 1.3 89 74-181 133-238 (310)
61 PF04740 LXG: LXG domain of WX 26.2 3E+02 0.0064 22.4 6.5 41 163-203 59-108 (204)
62 TIGR02923 AhaC ATP synthase A1 26.0 1.4E+02 0.003 25.9 4.8 52 167-220 60-116 (343)
63 PF14363 AAA_assoc: Domain ass 25.7 1.1E+02 0.0024 23.2 3.8 42 166-207 2-53 (98)
64 PF02113 Peptidase_S13: D-Ala- 25.2 1.1E+02 0.0025 29.0 4.5 69 149-234 327-406 (444)
65 cd07149 ALDH_y4uC Uncharacteri 25.2 1.1E+02 0.0025 27.8 4.3 73 77-149 12-90 (453)
66 PF02436 PYC_OADA: Conserved c 24.8 1.5E+02 0.0033 25.8 4.8 100 85-190 56-163 (196)
67 TIGR01086 fucA L-fuculose phos 24.7 2.9E+02 0.0062 23.4 6.3 44 127-178 162-205 (214)
68 PF09531 Ndc1_Nup: Nucleoporin 24.6 1.6E+02 0.0034 28.5 5.3 32 165-196 564-599 (602)
69 KOG2120 SCF ubiquitin ligase, 24.3 93 0.002 30.7 3.7 56 97-165 95-150 (419)
70 PF13326 PSII_Pbs27: Photosyst 24.2 2E+02 0.0044 24.0 5.3 58 146-205 78-140 (145)
71 PF03789 ELK: ELK domain ; In 24.2 57 0.0012 20.2 1.5 15 138-152 7-21 (22)
72 PF06543 Lac_bphage_repr: Lact 24.1 59 0.0013 23.8 1.8 16 164-179 29-44 (49)
73 PRK13213 araD L-ribulose-5-pho 23.9 1.6E+02 0.0034 26.0 4.8 45 127-179 179-223 (231)
74 PF01261 AP_endonuc_2: Xylose 23.6 2.6E+02 0.0057 21.3 5.4 57 124-189 66-125 (213)
75 PF14526 Cass2: Integron-assoc 23.6 59 0.0013 24.5 1.9 33 164-196 99-136 (150)
76 TIGR03347 VI_chp_1 type VI sec 23.6 96 0.0021 27.9 3.5 21 155-176 67-87 (300)
77 PF06008 Laminin_I: Laminin Do 23.2 5E+02 0.011 22.5 8.7 66 125-191 79-147 (264)
78 PRK09614 nrdF ribonucleotide-d 22.9 5.5E+02 0.012 23.0 12.3 101 77-192 11-119 (324)
79 PF12887 SICA_alpha: SICA extr 22.7 1.3E+02 0.0029 25.5 4.0 81 141-221 1-96 (184)
80 PLN02466 aldehyde dehydrogenas 22.1 5E+02 0.011 25.3 8.2 49 75-123 84-140 (538)
81 COG2854 Ttg2D ABC-type transpo 22.1 1.2E+02 0.0026 27.1 3.8 39 168-206 31-69 (202)
82 TIGR02624 rhamnu_1P_ald rhamnu 22.0 2.6E+02 0.0057 25.1 5.9 42 127-176 218-259 (270)
83 PF05664 DUF810: Protein of un 21.7 1E+02 0.0022 31.7 3.6 46 150-195 567-613 (677)
84 cd00398 Aldolase_II Class II A 21.1 2.6E+02 0.0057 23.2 5.4 44 124-176 163-206 (209)
85 KOG0034 Ca2+/calmodulin-depend 21.1 89 0.0019 27.0 2.7 49 82-130 120-168 (187)
86 TIGR01408 Ube1 ubiquitin-activ 21.0 3E+02 0.0065 29.5 6.9 45 106-150 311-363 (1008)
87 PTZ00226 fumarate hydratase; P 20.8 2.2E+02 0.0048 29.2 5.7 65 76-140 64-128 (570)
88 TIGR01828 pyru_phos_dikin pyru 20.7 97 0.0021 32.4 3.3 26 165-190 109-141 (856)
89 PRK01433 hscA chaperone protei 20.7 8.4E+02 0.018 24.2 9.7 49 164-215 530-579 (595)
90 cd07118 ALDH_SNDH Gluconobacte 20.7 2E+02 0.0042 26.8 5.0 50 75-124 8-65 (454)
91 PTZ00433 tyrosine aminotransfe 20.5 89 0.0019 28.0 2.7 86 133-220 11-105 (412)
92 COG3562 KpsS Capsule polysacch 20.5 44 0.00096 32.8 0.8 33 196-235 293-334 (403)
93 PRK13967 nrdF1 ribonucleotide- 20.4 4E+02 0.0088 24.3 6.8 95 82-191 16-118 (322)
94 PF06470 SMC_hinge: SMC protei 20.4 23 0.00049 25.9 -0.9 32 153-185 2-33 (120)
95 PF05480 Staph_haemo: Staphylo 20.4 74 0.0016 22.6 1.7 29 87-115 7-35 (43)
96 TIGR03582 EF_0829 PRD domain p 20.3 1.7E+02 0.0037 23.7 4.0 38 158-195 55-96 (107)
97 PF03810 IBN_N: Importin-beta 20.2 1.1E+02 0.0024 20.7 2.5 25 91-115 39-71 (77)
98 PLN02926 histidinol dehydrogen 20.1 4.9E+02 0.011 25.8 7.7 88 98-190 6-100 (431)
99 COG2361 Uncharacterized conser 20.0 1.1E+02 0.0023 25.6 2.8 49 124-172 6-62 (117)
100 cd07957 Anticodon_Ia_Met Antic 20.0 3.5E+02 0.0075 19.5 5.5 31 163-193 34-64 (129)
101 PF11740 KfrA_N: Plasmid repli 20.0 2.7E+02 0.0058 20.9 4.8 44 140-183 28-76 (120)
No 1
>PF14290 DUF4370: Domain of unknown function (DUF4370)
Probab=100.00 E-value=8.6e-123 Score=805.59 Aligned_cols=233 Identities=62% Similarity=0.972 Sum_probs=222.6
Q ss_pred CchhhhHHHHHHHHHHhhhhhhHHHh--hhhhhhhhhccccccccCCCCCCCCCCCCCCCcCCcccccccccccccccCC
Q 026481 1 MEKIAVMSVRSIRRAACVRSSIIAAA--NNHHLRHLSSSRSLFSLSSPAASIPSKSIPFDCRSSLVMSIGCNRSFSEDVA 78 (238)
Q Consensus 1 mek~~m~~lrs~~r~a~~~s~~~~~~--~~~~~~h~s~~~sl~t~~~~~~~~ps~~~~~d~~~~~s~~~~~~R~fS~d~~ 78 (238)
||| ||+.||++||++|++|++.++. .+|+++|..+.+++++++++.+ +. ++++||++||+||||++|+||+|++
T Consensus 1 m~~-~~~~lr~~~R~~~~~s~~~~~~~~~~~~~~~~~~~~s~~~l~~~~~--~~-~~~s~~~~~~a~s~~~~R~fS~d~~ 76 (239)
T PF14290_consen 1 MEK-AMSALRSLLRSAALRSSRSSSASRSHHQIRHHLSSRSLFTLSSPSS--RN-RISSDCGGPFAMSWGSRRFFSEDVS 76 (239)
T ss_pred Cch-HHHHHHHHHHHHHHHHhhhhhhhcchhhhhhhhhhccccCCCCccc--cc-cccccccCCcccccchhhhcccccc
Confidence 887 5999999999999999987555 3377788558999999988873 33 8899999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCC
Q 026481 79 HMPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGL 158 (238)
Q Consensus 79 hlP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~Gl 158 (238)
|||+|+||||++|||||||+||+|||++||++|||||||||||+||||||+||||||||||||||+|++||||||||||+
T Consensus 77 hlP~i~Dp~i~~afKdLmAasW~elp~svv~~akkalSk~tdD~AGqeaL~nvfRAAeAvEeFgG~L~tLrm~idDl~Gl 156 (239)
T PF14290_consen 77 HLPAISDPEIEKAFKDLMAASWDELPDSVVNEAKKALSKNTDDKAGQEALKNVFRAAEAVEEFGGILVTLRMEIDDLCGL 156 (239)
T ss_pred cCCCCCCHHHHHHHHHHHhcchhhCCHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhhhhhcCCCCCcceeEEeeccccccccc
Q 026481 159 SGENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSKMIFLKMRCAGLGSEWGKVFYYGCQCHCGILA 237 (238)
Q Consensus 159 sGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LKmRcsGlgseWGKVtllGTSg~sGsy~ 237 (238)
||||||||||+++|||+|+|+||++|||||||||+|||||||+|||+|||||||||||||||||||||||||||||||.
T Consensus 157 sGEnv~PLP~~~~~Al~t~y~rY~~YL~sFgp~E~yLrKKVE~ELGtkmi~lKmRcsGlg~eWgkvtllGTSGlsGSYv 235 (239)
T PF14290_consen 157 SGENVKPLPDYIENALRTAYKRYMTYLDSFGPDEHYLRKKVEMELGTKMIHLKMRCSGLGSEWGKVTLLGTSGLSGSYV 235 (239)
T ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHhhhhHHHHhhhhcCCCcccceeeEeecCcCccchh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999995
No 2
>PLN02749 Uncharacterized protein At1g47420
Probab=100.00 E-value=1e-108 Score=692.48 Aligned_cols=169 Identities=66% Similarity=1.060 Sum_probs=167.7
Q ss_pred ccccccccCCCCCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026481 69 CNRSFSEDVAHMPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNI 148 (238)
Q Consensus 69 ~~R~fS~d~~hlP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sL 148 (238)
++|+||+|++|||+|+||+|++|||||||+||+|||++|+++||+|||||||||||||||+||||||||||||||+|++|
T Consensus 1 ~~R~fs~d~~~lP~i~Dp~i~~afkdLma~sW~elp~sv~~~~kkalsk~tddkagqeaL~nvfrAAeAveeFgG~L~sL 80 (173)
T PLN02749 1 LRRRFSEDVSHLPEISDPEILKAFKDLMAASWDELPDSVVNDAKKALSKNTDDKAGQEALKNVFRAAEAVEEFGGTLVSL 80 (173)
T ss_pred CccccccccccCCCCCCHHHHHHHHHHHhcchhhCChHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhhhhhcCCCCCcceeEEee
Q 026481 149 KMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSKMIFLKMRCAGLGSEWGKVFYYG 228 (238)
Q Consensus 149 rmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LKmRcsGlgseWGKVtllG 228 (238)
|||||||||+||||||||||+++|||+|+||||++|||||||||+|||||||+|||+|||||||||||||||||||||||
T Consensus 81 rmeidDl~GlsGEnv~PLPd~~~~Al~tay~rY~~YLdsFgp~E~yLrKKVE~ELG~kmi~lKmRcsGl~~eWgkvtllG 160 (173)
T PLN02749 81 RMEIDDLIGLSGENVKPLPDYIENALETAYQRYAAYLDSFGPEENYLKKKVEMELGTKMIHLKMRCSGLGSEWGKVTLLG 160 (173)
T ss_pred HHHHHHhcCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhHHHHHHHhhhcCCCcccceeeEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccc
Q 026481 229 CQCHCGILA 237 (238)
Q Consensus 229 TSg~sGsy~ 237 (238)
||||||||.
T Consensus 161 TSGlsGSYv 169 (173)
T PLN02749 161 TSGLSGSYV 169 (173)
T ss_pred cCcccchhh
Confidence 999999995
No 3
>PRK15389 fumarate hydratase; Provisional
Probab=76.65 E-value=8.2 Score=38.62 Aligned_cols=121 Identities=13% Similarity=0.105 Sum_probs=77.1
Q ss_pred ccccccccccCCC-------CCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHH
Q 026481 67 IGCNRSFSEDVAH-------MPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVE 139 (238)
Q Consensus 67 ~~~~R~fS~d~~h-------lP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvE 139 (238)
.-.+|.|.++++- +=-|.-.+|.++.++|+-..=..||+.|+...++|+.+.-+...++.+|...+.-++..+
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~i~~~v~~l~~~a~~~lp~Dv~~aL~~a~~~~E~s~~ak~vl~~ileN~~iA~ 97 (536)
T PRK15389 18 TEYRLLTSDGVSVAEFEGREILKVEPEALTLLAEEAFHDISHLLRPAHLQQLAKILDDPEASDNDKFVALDLLKNANIAA 97 (536)
T ss_pred ceeEEeccCceEEEeeCCeeEEEECHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHh
Confidence 3444555554442 223455569999999999988999999999999998665667889999999888887766
Q ss_pred HHHHHHHHHhhhhhhccCC------CCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhh
Q 026481 140 EFIGIIMNIKMEFDDEIGL------SGENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETEL 203 (238)
Q Consensus 140 eFgGiL~sLrmeiDDl~Gl------sGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~EL 203 (238)
+-. +-+=+=.|+ -|++|. +...+++||+..-.| .| .|.|||+-+=.-|
T Consensus 98 ~~~-------~P~CQDTG~~~vfv~iG~~v~-~g~~l~~aI~eGV~~--ay------~~~pLR~svV~pl 151 (536)
T PRK15389 98 GGV-------LPMCQDTGTAIIMGKKGQRVW-TGGDDEEALSRGVYD--TY------TELNLRYSQNAPL 151 (536)
T ss_pred cCC-------CccccCCCcEEEEEEeCCCCC-CCchHHHHHHHHHHH--Hh------ccCCcchhhcCCC
Confidence 521 111111121 256776 444455555444333 22 2477998753334
No 4
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=76.01 E-value=41 Score=29.62 Aligned_cols=151 Identities=13% Similarity=0.102 Sum_probs=81.8
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHcccC--CCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH---HHHH
Q 026481 73 FSEDVAHMPVIRDPEIQRAFKDLMAADWG--ELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG---IIMN 147 (238)
Q Consensus 73 fS~d~~hlP~i~Dpei~~afKdLmA~sW~--elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG---iL~s 147 (238)
|....=++|.....++...+++-+...+. .+++.++..+-......+-| -+.|+.-.++|++..++-|- ....
T Consensus 197 ~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd--~r~a~~ll~~a~~~a~~~~~~~I~~~~ 274 (394)
T PRK00411 197 FRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGD--ARVAIDLLRRAGLIAEREGSRKVTEED 274 (394)
T ss_pred CCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCc--HHHHHHHHHHHHHHHHHcCCCCcCHHH
Confidence 33344589999999999999988765543 46666665543333221111 25566666777665544332 2334
Q ss_pred Hhhhhhhcc-CCCCCCCcCCchHHHHH----------------HHHHHHHHHHHHhhcCCCh---hHHHHHHHHhhhhhh
Q 026481 148 IKMEFDDEI-GLSGENVKPLSNELSSA----------------IRTVYQRYATYLDAFGPDE---SYLRKKVETELGSKM 207 (238)
Q Consensus 148 LrmeiDDl~-GlsGEnVkPLPd~~~~A----------------l~tay~rY~~YLdsFgpdE---~yLrKKVE~ELGtkm 207 (238)
++..++..- ...-+-+..||.+..-. +..+|++|..+.+.+|-+. ..+...+..=-...+
T Consensus 275 v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~gl 354 (394)
T PRK00411 275 VRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGI 354 (394)
T ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCC
Confidence 444444431 11112355666664433 3456788988888888643 555554433333445
Q ss_pred hhhhhhhcCCCCCcceeE
Q 026481 208 IFLKMRCAGLGSEWGKVF 225 (238)
Q Consensus 208 I~LKmRcsGlgseWGKVt 225 (238)
|..+++=.|....+=+|+
T Consensus 355 I~~~~~~~g~~g~~~~~~ 372 (394)
T PRK00411 355 INTRYSGKGGRGRTRLIS 372 (394)
T ss_pred eEEEEecCCCCCCeEEEE
Confidence 555554334433343343
No 5
>PRK08230 tartrate dehydratase subunit alpha; Validated
Probab=73.55 E-value=7.7 Score=36.23 Aligned_cols=96 Identities=15% Similarity=0.199 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCC------CC
Q 026481 87 EIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGL------SG 160 (238)
Q Consensus 87 ei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~Gl------sG 160 (238)
+|.++.++|+-..=..||+.|+...++|..+-+ +..++.+|++.+.-++..++-. +-+=+=.|+ -|
T Consensus 9 ~i~~~v~~l~~~a~~~lp~Dv~~al~~a~~~E~-s~~ak~~L~~ileN~~iA~~~~-------~PiCQDTG~~~~fv~iG 80 (299)
T PRK08230 9 KLTDIMAKFTAYISKRLPDDVTAKLKELKDAET-SPLAKIIYDTMFENQQLAIDLN-------RPSCQDTGVIQFFVKVG 80 (299)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHHhcCC-------CccccCCCcEEEEEEeC
Confidence 488999999999999999999999999999954 4557999999998888776532 222111222 26
Q ss_pred CCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHH
Q 026481 161 ENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKV 199 (238)
Q Consensus 161 EnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKV 199 (238)
++|. ++..+++||...-.| +-.|.||||-+
T Consensus 81 ~~v~-~~g~l~~aI~egVr~--------a~~~~~LR~s~ 110 (299)
T PRK08230 81 ARFP-LLGELESILKEAVEE--------ATVKAPLRHNA 110 (299)
T ss_pred CCcc-cCchHHHHHHHHHHH--------HhccCCCCccc
Confidence 7775 344466666554444 12578888874
No 6
>PRK08087 L-fuculose phosphate aldolase; Provisional
Probab=67.53 E-value=20 Score=30.35 Aligned_cols=47 Identities=19% Similarity=0.236 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRY 181 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY 181 (238)
-++.+|..+|.+|+.--+....+ ..|.++.|||++-.+.++..|.+|
T Consensus 163 ~~~~A~~~~e~lE~~a~~~~~a~--------~~g~~~~~l~~e~~~~~~~~~~~~ 209 (215)
T PRK08087 163 NLEKALWLAHEVEVLAQLYLKTL--------AITDPVPVLSDEEIAVVLEKFKTY 209 (215)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--------hcCCCCCCCCHHHHHHHHHHHHhc
Confidence 57888999999999877653332 246788999999988887766554
No 7
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=64.57 E-value=7.7 Score=34.69 Aligned_cols=64 Identities=20% Similarity=0.594 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHhhhhhhccCCCCCCCc-CCchHHHHHHHHHHHHHHHHHhhc---------------CCChhHHHHHHHH
Q 026481 138 VEEFIGIIMNIKMEFDDEIGLSGENVK-PLSNELSSAIRTVYQRYATYLDAF---------------GPDESYLRKKVET 201 (238)
Q Consensus 138 vEeFgGiL~sLrmeiDDl~GlsGEnVk-PLPd~~~~Al~tay~rY~~YLdsF---------------gpdE~yLrKKVE~ 201 (238)
.++|=.-|.++|.+.++.++ .+|. -+=-....+.++.+++|+.+.++| .|||.||| .+|.
T Consensus 83 ~~~y~~~l~~v~~~Y~~~v~---~EV~~A~~~~~ee~~~~l~~nYl~~v~a~~~~~~~~d~~TGe~~~pdE~~mr-sIEe 158 (254)
T PF06798_consen 83 RERYLEFLKSVRKEYDERVE---KEVQEAFYYSYEEQIQNLFENYLDHVEAWINDEKVKDPFTGEELEPDERFMR-SIEE 158 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHccHHHHHHHHHHHHHHHHHHhcCCeeeCCCCcccCCccHHHHH-HHHH
Confidence 56666678888888888775 1111 111223445678899999988875 38888887 5887
Q ss_pred hhhh
Q 026481 202 ELGS 205 (238)
Q Consensus 202 ELGt 205 (238)
.+|.
T Consensus 159 ~igi 162 (254)
T PF06798_consen 159 RIGI 162 (254)
T ss_pred hcCC
Confidence 7763
No 8
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=64.44 E-value=59 Score=28.72 Aligned_cols=41 Identities=20% Similarity=0.377 Sum_probs=31.9
Q ss_pred CcCCchHHHHHHHHHHHH----HHHHHhhcCC-ChhHHHHHHHHhh
Q 026481 163 VKPLSNELSSAIRTVYQR----YATYLDAFGP-DESYLRKKVETEL 203 (238)
Q Consensus 163 VkPLPd~~~~Al~tay~r----Y~~YLdsFgp-dE~yLrKKVE~EL 203 (238)
++.-.+++.+++.+.-++ |.++|.+-|- .+..+|+.++.+|
T Consensus 67 i~vsd~ev~~~i~~~~~~~~~~f~~~L~~~G~~~~~~~r~~i~~~l 112 (283)
T PRK02998 67 YKVSDEEAKKQVEEAKDKMGDNFKSTLEQVGLKNEDELKEKMKPEI 112 (283)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Confidence 455678888888887765 5778888898 5778899888876
No 9
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=62.64 E-value=53 Score=26.79 Aligned_cols=104 Identities=12% Similarity=0.145 Sum_probs=66.0
Q ss_pred HHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHh
Q 026481 107 VIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYLD 186 (238)
Q Consensus 107 vv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLd 186 (238)
...+++..+.+.. ..+++|-.+.+.+| ++||=|=...-.+|-+.+|+ |......|-|.|.-|. +.
T Consensus 6 ~~~~~~~i~~~~~---~~~~~ll~~L~~vQ--~~~g~ip~~~~~~iA~~l~v--------~~~~v~~v~tFY~~f~--~~ 70 (154)
T PRK07539 6 ELAAIEREIAKYP---RPRSAVIPALKIVQ--EQRGWVPDEAIEAVADYLGM--------PAIDVEEVATFYSMIF--RQ 70 (154)
T ss_pred HHHHHHHHHHHCC---CCHHHHHHHHHHHH--HHhCCCCHHHHHHHHHHhCc--------CHHHHHHHHHHHhhhC--cC
Confidence 3345555666643 34778888888888 66776766777777787774 5666777888888773 33
Q ss_pred hcCCChh--------H------HHHHHHHhhhhhhhhhhhhhcCCCCCcceeEEeeccccc
Q 026481 187 AFGPDES--------Y------LRKKVETELGSKMIFLKMRCAGLGSEWGKVFYYGCQCHC 233 (238)
Q Consensus 187 sFgpdE~--------y------LrKKVE~ELGtkmI~LKmRcsGlgseWGKVtllGTSg~s 233 (238)
--|.... + +-+.+|.+||-+ -|.-+++|+|+|..|.|++
T Consensus 71 p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~L~i~--------~g~tt~dg~~~l~~~~ClG 123 (154)
T PRK07539 71 PVGRHVIQVCTSTPCWLRGGEAILAALKKKLGIK--------PGETTADGRFTLLEVECLG 123 (154)
T ss_pred CCCCEEEEEcCCchHHHCCHHHHHHHHHHHhCCC--------CCCcCCCCeEEEEEccccC
Confidence 3443332 1 234455555411 1444689999999777764
No 10
>PRK07490 hypothetical protein; Provisional
Probab=62.16 E-value=39 Score=29.45 Aligned_cols=50 Identities=12% Similarity=0.241 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATY 184 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~Y 184 (238)
-+..+|..+|.+|+.--+....+ ..|+...|||++..+-+...|.+|-.+
T Consensus 175 ~~~eA~~~~e~lE~~a~~~l~a~--------~~G~~~~~l~~~~~~~~~~~~~~~~~~ 224 (245)
T PRK07490 175 TVAEAFDDLYYFERACQTYITAL--------STGQPLRVLSDAVAEKTARDWEDYPGF 224 (245)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--------hCCCCCCCCCHHHHHHHHHHHhhccch
Confidence 46788999999998877554332 247777899999877765555555433
No 11
>COG1951 TtdA Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]
Probab=60.79 E-value=24 Score=33.25 Aligned_cols=55 Identities=16% Similarity=0.282 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHH
Q 026481 86 PEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEF 141 (238)
Q Consensus 86 pei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeF 141 (238)
-++....+|+...-=+.||+.|++..++|+.+ .++.+++.+|+...+-+|-+++-
T Consensus 8 e~l~~~v~~a~~~as~~lp~Dv~~al~~a~~~-Ees~~ak~~l~~il~N~~ia~~~ 62 (297)
T COG1951 8 EDLTESVADAFQEASTYLPPDVVQALAKALER-EESEIAKYVLLQILENSRIAAKE 62 (297)
T ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHHhh-hcCHHHHHHHHHHHHHHHHHHhc
Confidence 45667777777777789999999999999999 88999999999999888887763
No 12
>PF00268 Ribonuc_red_sm: Ribonucleotide reductase, small chain; InterPro: IPR000358 Ribonucleotide reductase (1.17.4.1 from EC) [, ] catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O = ribonucleoside diphosphate + reduced thioredoxin It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain []. The small chain binds two iron atoms [] (three Glu, one Asp, and two His are involved in metal binding) and contains an active site tyrosine radical. The regions of the sequence that contain the metal-binding residues and the active site tyrosine are conserved in ribonucleotide reductase small chain from prokaryotes, eukaryotes and viruses. We have selected one of these regions as a signature pattern. It contains the active site residue as well as a glutamate and a histidine involved in the binding of iron.; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0009186 deoxyribonucleoside diphosphate metabolic process, 0055114 oxidation-reduction process; PDB: 1JK0_B 1SMS_B 2VUX_B 4DJN_B 3HF1_B 2RCC_B 2BQ1_I 1R2F_A 2R2F_A 2O1Z_A ....
Probab=60.66 E-value=1.1e+02 Score=26.48 Aligned_cols=98 Identities=16% Similarity=0.253 Sum_probs=58.1
Q ss_pred CCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH--HHHHHhhhhhhccCC
Q 026481 81 PVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG--IIMNIKMEFDDEIGL 158 (238)
Q Consensus 81 P~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG--iL~sLrmeiDDl~Gl 158 (238)
=+|++|......|.+.+.-|..=.=++-+|.+.--+ =+..-|++++.++..=-+.+..-+ ++..+...+.
T Consensus 12 ~pi~y~~~~~ly~k~~~~fW~peEi~~~~D~~~~~~---Ls~~e~~~~~~~l~~~~~~D~~v~~~l~~~i~~~~~----- 83 (281)
T PF00268_consen 12 NPIKYPWFWDLYKKAESNFWTPEEIDMSKDIKDWKK---LSEEEREAYKRILAFFAQLDSLVSENLLPNIMPEIT----- 83 (281)
T ss_dssp TS-SSHHHHHHHHHHHHT---GGGS-GGGHHHHHHH---S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-----
T ss_pred CCCCCHHHHHHHHHHHhCCCCchhcChhhhHHHHHh---CCHHHHHHHHHHHHHHHHHHhHHHhhHHHHHHHHcC-----
Confidence 459999999999999999998655556666554433 234568898888765443333222 1123333332
Q ss_pred CCCCCcCCchH-----HHHHHHHHHHH-HHHHHhhcCCChh
Q 026481 159 SGENVKPLSNE-----LSSAIRTVYQR-YATYLDAFGPDES 193 (238)
Q Consensus 159 sGEnVkPLPd~-----~~~Al~tay~r-Y~~YLdsFgpdE~ 193 (238)
.|+. .+.+.++.|++ |..+|+++++++.
T Consensus 84 -------~~E~~~~l~~q~~~E~iH~~sYs~il~~l~~~~~ 117 (281)
T PF00268_consen 84 -------SPEIRAFLTFQAFMEAIHAESYSYILDSLGNDPK 117 (281)
T ss_dssp -------SHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSHH
T ss_pred -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChH
Confidence 2331 24556777776 8899999997663
No 13
>PRK06246 fumarate hydratase; Provisional
Probab=60.50 E-value=21 Score=32.96 Aligned_cols=100 Identities=28% Similarity=0.434 Sum_probs=68.6
Q ss_pred CCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCC--
Q 026481 81 PVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGL-- 158 (238)
Q Consensus 81 P~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~Gl-- 158 (238)
..|+-.+|.++..+++..-=..||+.|++..++|+.+ -++..++.+|+....-++..++-. +-+=+=.|+
T Consensus 2 ~~i~~~~i~~~v~~~~~~a~~~lp~Dv~~~l~~a~~~-E~s~~ak~~l~~ileN~~iA~~~~-------~P~CQDTG~~~ 73 (280)
T PRK06246 2 REIHVEDIIEAVAELCIEANYYLPDDVKEALKKAYEK-EESPIGKEILKAILENAEIAKEEQ-------VPLCQDTGMAV 73 (280)
T ss_pred ccccHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHh-ccChhHHHHHHHHHHHHHHHhcCC-------CccccCCCcEE
Confidence 3455556999999999988899999999999999986 555567889998888888777642 111111121
Q ss_pred ----CCCCCc----CCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHH
Q 026481 159 ----SGENVK----PLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVE 200 (238)
Q Consensus 159 ----sGEnVk----PLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE 200 (238)
-|++|. +|-+.+.++++.+| .|.|||+-|=
T Consensus 74 ~fv~iG~~v~~~~~~l~~ai~egv~~a~------------~~~pLR~s~V 111 (280)
T PRK06246 74 VFVEIGQDVHIEGGDLEDAINEGVRKGY------------EEGYLRKSVV 111 (280)
T ss_pred EEEEeCCCcccCCccHHHHHHHHHHHHh------------ccCCCchhcc
Confidence 366664 35555555666654 3668887654
No 14
>PLN03188 kinesin-12 family protein; Provisional
Probab=52.36 E-value=60 Score=36.06 Aligned_cols=81 Identities=25% Similarity=0.257 Sum_probs=54.7
Q ss_pred HHHHHhhhcccCCchhHHHHHHHHH------------------------------HHHHHHHHHHHHHHHHhhhhhhccC
Q 026481 108 IHDAKSALSRNNDDKAGQEVLKNVF------------------------------SAAEAVEEFIGIIMNIKMEFDDEIG 157 (238)
Q Consensus 108 v~~ak~alSk~tdDkAGqeaL~nvf------------------------------rAAeAvEeFgGiL~sLrmeiDDl~G 157 (238)
|.|||||..|++---||- ...|.+ --||||.-.|-.||.||.
T Consensus 1137 i~dvkkaaakag~kg~~~-~f~~alaae~s~l~~ereker~~~~~enk~l~~qlrdtaeav~aagellvrl~e------- 1208 (1320)
T PLN03188 1137 IDDVKKAAARAGVRGAES-KFINALAAEISALKVEREKERRYLRDENKSLQAQLRDTAEAVQAAGELLVRLKE------- 1208 (1320)
T ss_pred HHHHHHHHHHhccccchH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHH-------
Confidence 678999999977655552 222221 248999999999999985
Q ss_pred CCCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChh-----HHHHHHHHhhhhhhhhhhhhh
Q 026481 158 LSGENVKPLSNELSSAIRTVYQRYATYLDAFGPDES-----YLRKKVETELGSKMIFLKMRC 214 (238)
Q Consensus 158 lsGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~-----yLrKKVE~ELGtkmI~LKmRc 214 (238)
.+.|+-.+=+|++.-.. +-++. =||||-|+|+ +-||||.
T Consensus 1209 ------------aeea~~~a~~r~~~~eq--e~~~~~k~~~klkrkh~~e~----~t~~q~~ 1252 (1320)
T PLN03188 1209 ------------AEEALTVAQKRAMDAEQ--EAAEAYKQIDKLKRKHENEI----STLNQLV 1252 (1320)
T ss_pred ------------HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence 46777777788775432 11222 2788889985 4577765
No 15
>PF05681 Fumerase: Fumarate hydratase (Fumerase); InterPro: IPR004646 This entry represents various Fe-S type hydro-lyases, including the alpha subunit from both L-tartrate dehydratase (TtdA; 4.2.1.32 from EC) and class 1 fumarate hydratases (4.2.1.2 from EC), which includes both aerobic (FumA) and anaerobic (FumB) types []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this group is unknown. Fumarate hydratase (also known as fumarase) is a component of the citric acid cycle. In facultative anaerobes such as E. coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre [].; GO: 0016829 lyase activity
Probab=52.17 E-value=28 Score=31.87 Aligned_cols=51 Identities=24% Similarity=0.317 Sum_probs=41.0
Q ss_pred HHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHH
Q 026481 89 QRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEE 140 (238)
Q Consensus 89 ~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEe 140 (238)
.++..+|+-.-=..||+.|++..++|+.+.+.+. ++.+|+...+-++..++
T Consensus 2 ~~~v~~~~~~a~~~lp~Dv~~al~~a~~~E~~~~-ak~vl~~ileN~~iA~~ 52 (271)
T PF05681_consen 2 TEAVAELIIKASTYLPDDVLEALKKAYERETSPL-AKWVLEQILENAEIAAK 52 (271)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHccCCHH-HHHHHHHHHHHHHHHhh
Confidence 3456666666668999999999999999966555 99999998888887665
No 16
>PRK07044 aldolase II superfamily protein; Provisional
Probab=51.46 E-value=62 Score=28.22 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQR 180 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~r 180 (238)
-|..+|..+|.+|+.--+....+ ..|+++.++|++..+.++..+..
T Consensus 180 ~l~eA~~~~e~lE~~a~~~~~a~--------~lG~~~~~~~~~~~~~~~~~~~~ 225 (252)
T PRK07044 180 TVAEAFLLMYTLERACEIQVAAQ--------AGGGELVLPPPEVAERTARQSLF 225 (252)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--------hcCCCCCCCCHHHHHHHHHHHhh
Confidence 57789999999998876554333 25788899999998888777543
No 17
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=50.40 E-value=69 Score=24.65 Aligned_cols=37 Identities=30% Similarity=0.480 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhhhhhhccCCCCCCCcCC-chHHHHHHH
Q 026481 137 AVEEFIGIIMNIKMEFDDEIGLSGENVKPL-SNELSSAIR 175 (238)
Q Consensus 137 AvEeFgGiL~sLrmeiDDl~GlsGEnVkPL-Pd~~~~Al~ 175 (238)
....|=|-|++.=+++-|--|.. +.+|| |.|+..|.+
T Consensus 45 laKvFVGeivE~A~~V~~~~~~~--~~~Pl~P~HireA~r 82 (85)
T cd08048 45 IAKVFVGEIVEEARDVQEEWGEA--NTGPLQPRHLREAYR 82 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHhccc--cCCCCCcHHHHHHHH
Confidence 34578888888777777666554 57897 555544443
No 18
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=49.03 E-value=14 Score=29.24 Aligned_cols=46 Identities=26% Similarity=0.559 Sum_probs=30.9
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHc-----------------ccC--CCc-------hhHHHHHHhhhcccCC
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAA-----------------DWG--ELP-------ASVIHDAKSALSRNND 120 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~-----------------sW~--elp-------~svv~~ak~alSk~td 120 (238)
|+.+.||+++|.+|.+-+..|++- +|. .+| +.|+.+++.|++...+
T Consensus 3 et~S~lP~l~~~~i~~Qv~~ll~qG~~i~iE~ad~r~~r~~~W~mW~~p~~~~~~~~~Vl~el~~c~~~~p~ 74 (99)
T PF00101_consen 3 ETFSYLPPLTDEEIAKQVRYLLSQGWIIGIEHADPRRFRTSYWQMWKLPMFGCTDPAQVLAELEACLAEHPG 74 (99)
T ss_dssp STTTTSS---HHHHHHHHHHHHHTT-EEEEEEESCGGSTSSS-EEESSEBTTBSSHHHHHHHHHHHHHHSTT
T ss_pred cccccCCCCCHHHHHHHHHhhhhcCceeeEEecCCCCCCCCEeecCCCCCcCCCCHHHHHHHHHHHHHhCCC
Confidence 577899999999999999999985 455 554 4466666666665443
No 19
>cd07119 ALDH_BADH-GbsA Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like. Included in this CD is the NAD+-dependent, betaine aldehyde dehydrogenase (BADH, GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the synthesis of the osmoprotectant glycine betaine from choline or glycine betaine aldehyde.
Probab=48.94 E-value=30 Score=32.16 Aligned_cols=51 Identities=22% Similarity=0.389 Sum_probs=39.6
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHc----ccCCCc----hhHHHHHHhhhcccCCchhHH
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAA----DWGELP----ASVIHDAKSALSRNNDDKAGQ 125 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~----sW~elp----~svv~~ak~alSk~tdDkAGq 125 (238)
+-+..+|....-++..+++..-++ .|..+| -.++..+...|.++.|+.+--
T Consensus 24 ~~i~~~~~~~~~~v~~av~~A~~a~~~~~w~~~~~~~R~~~L~~~a~~l~~~~~~la~~ 82 (482)
T cd07119 24 EVIATVPEGTAEDAKRAIAAARRAFDSGEWPHLPAQERAALLFRIADKIREDAEELARL 82 (482)
T ss_pred CEEEEEeCCCHHHHHHHHHHHHHHcCCCchhhCCHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 346667888888999999988776 499999 556777888888888777643
No 20
>COG2766 PrkA Putative Ser protein kinase [Signal transduction mechanisms]
Probab=48.79 E-value=38 Score=34.99 Aligned_cols=55 Identities=31% Similarity=0.680 Sum_probs=40.2
Q ss_pred HHHHHHHH-HHhhhhhhccCCCCCCCcCCchHHHHHH--------HHHHHHHHHHHhhc---------------CCC--h
Q 026481 139 EEFIGIIM-NIKMEFDDEIGLSGENVKPLSNELSSAI--------RTVYQRYATYLDAF---------------GPD--E 192 (238)
Q Consensus 139 EeFgGiL~-sLrmeiDDl~GlsGEnVkPLPd~~~~Al--------~tay~rY~~YLdsF---------------gpd--E 192 (238)
++|-+-+. -+|.+++|.+| .+++.|+ +++|+||++|.++| .|| |
T Consensus 468 ~~yl~fv~~~~~~~Y~e~~~----------keVq~A~l~sy~E~~~~l~d~Yvdnv~Awi~d~~~~D~~TGee~~pd~le 537 (649)
T COG2766 468 ERYLDFVKGYLRPEYAEFIG----------KEVQKAYLESYSEYGQNLFDRYVDNVDAWINDQTVRDPATGEELNPDALE 537 (649)
T ss_pred HHHHHHHHHHHHHHHHHHHH----------HHHHHHHHhhhHHHHHHHHHHHHHHHHHHhccCcccCcccccccCccHHH
Confidence 45555444 88899999876 4667765 46899999999875 577 8
Q ss_pred hHHHHHHHHhhh
Q 026481 193 SYLRKKVETELG 204 (238)
Q Consensus 193 ~yLrKKVE~ELG 204 (238)
..||+ +|..+|
T Consensus 538 ~~L~~-iEe~~G 548 (649)
T COG2766 538 KELRS-IEEQAG 548 (649)
T ss_pred HHHHH-HHHhcC
Confidence 88874 676665
No 21
>PRK10702 endonuclease III; Provisional
Probab=48.22 E-value=13 Score=32.02 Aligned_cols=72 Identities=13% Similarity=0.118 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHHHHHc--ccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHH-HHHHHHHHHHhhhhhhccC
Q 026481 83 IRDPEIQRAFKDLMAA--DWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAV-EEFIGIIMNIKMEFDDEIG 157 (238)
Q Consensus 83 i~Dpei~~afKdLmA~--sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAv-EeFgGiL~sLrmeiDDl~G 157 (238)
-+|+.+.+++..|+.. +|..|-..=..+.+.+++..+=- ..--+++.++|+.+ |+|||.+-..+.+|-.|=|
T Consensus 42 t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y---~~kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpG 116 (211)
T PRK10702 42 ATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLY---NSKAENVIKTCRILLEQHNGEVPEDRAALEALPG 116 (211)
T ss_pred cCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCH---HHHHHHHHHHHHHHHHHcCCCCCchHHHHhcCCc
Confidence 3678888888888864 33333333355566666542210 12235667777776 7889977777776665555
No 22
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=48.02 E-value=33 Score=24.84 Aligned_cols=53 Identities=21% Similarity=0.377 Sum_probs=33.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHH-H-HHh--hhhhhccCCCCCCCcCCchHHHHHHHHHHHHH
Q 026481 122 KAGQEVLKNVFSAAEAVEEFIGII-M-NIK--MEFDDEIGLSGENVKPLSNELSSAIRTVYQRY 181 (238)
Q Consensus 122 kAGqeaL~nvfrAAeAvEeFgGiL-~-sLr--meiDDl~GlsGEnVkPLPd~~~~Al~tay~rY 181 (238)
..|+++ |.|+--.+|.++||-- + .-+ .+|-.-+|+...+. .....|++.|.||
T Consensus 31 i~g~~v--DL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~-----~~~~~L~~~Y~~~ 87 (92)
T PF01388_consen 31 IGGKPV--DLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSST-----SAAQQLRQHYEKY 87 (92)
T ss_dssp ETTSE---SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSC-----HHHHHHHHHHHHH
T ss_pred CCCEeC--cHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCC-----cHHHHHHHHHHHH
Confidence 455554 8899999999999942 2 222 35566666643222 2278899888876
No 23
>COG4423 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.65 E-value=47 Score=26.16 Aligned_cols=47 Identities=28% Similarity=0.328 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcc-cCCchhHHHHH
Q 026481 82 VIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSR-NNDDKAGQEVL 128 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk-~tdDkAGqeaL 128 (238)
.||||++-..-+.|-+.-=.-+-+.|+..++..|.+ ...-+.=.|+|
T Consensus 4 nIKDp~~d~lar~LA~rtg~S~t~AV~~Al~~~lar~r~r~~pL~~~l 51 (81)
T COG4423 4 NIKDPEVDRLARELAARTGESKTDAVRDALKERLARLRAREIPLRERL 51 (81)
T ss_pred ccCChHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhhhhHHHHH
Confidence 599999998888887766667788888888888888 33333333333
No 24
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=45.70 E-value=22 Score=28.32 Aligned_cols=26 Identities=19% Similarity=0.579 Sum_probs=23.4
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHccc
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAADW 100 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~sW 100 (238)
|..+-||+++|.+|.+.+..|++--|
T Consensus 4 ~t~sylp~lt~~~i~~QI~yll~qG~ 29 (99)
T cd03527 4 ETFSYLPPLTDEQIAKQIDYIISNGW 29 (99)
T ss_pred cccccCCCCCHHHHHHHHHHHHhCCC
Confidence 57889999999999999999998655
No 25
>TIGR00142 hycI hydrogenase maturation protease HycI. Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea.
Probab=44.67 E-value=24 Score=28.04 Aligned_cols=35 Identities=29% Similarity=0.470 Sum_probs=29.3
Q ss_pred ccCCCCCCC---cCCchHHHHHHHHHHHHHHHHHhhcC
Q 026481 155 EIGLSGENV---KPLSNELSSAIRTVYQRYATYLDAFG 189 (238)
Q Consensus 155 l~GlsGEnV---kPLPd~~~~Al~tay~rY~~YLdsFg 189 (238)
++|+.++++ .+|.+..++|+..+.++-.+++..||
T Consensus 109 ligi~~~~~~~g~~LS~~v~~a~~~~~~~i~~~i~~~~ 146 (146)
T TIGR00142 109 FLGIQPDIVGFYYPMSQPVKDAVETLYQRLIGWEGNGG 146 (146)
T ss_pred EEEEeeeeeecCCCCCHHHHHHHHHHHHHHHHHHhccC
Confidence 456666655 47999999999999999999999887
No 26
>PF01077 NIR_SIR: Nitrite and sulphite reductase 4Fe-4S domain; InterPro: IPR006067 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP) (IPR005117 from INTERPRO), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a siroheme through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. In the E. coli SiR-HP enzyme (1.8.1.2 from EC), the iron is bound to cysteine residues at positions 433, 439, 478 and 482, the latter also forming the siroheme ligand.; GO: 0016491 oxidoreductase activity, 0020037 heme binding, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1ZJ8_B 1ZJ9_A 2AKJ_A 3VKT_A 3VKR_A 3VKS_A 3B0M_A 3B0N_A 3VKP_A 3B0J_A ....
Probab=44.59 E-value=16 Score=28.67 Aligned_cols=26 Identities=31% Similarity=0.723 Sum_probs=20.2
Q ss_pred HHHHHHhhcCCChhHHHHHHHHhhhhhh
Q 026481 180 RYATYLDAFGPDESYLRKKVETELGSKM 207 (238)
Q Consensus 180 rY~~YLdsFgpdE~yLrKKVE~ELGtkm 207 (238)
|+..|++..|++ .+|+.||.+||-|+
T Consensus 132 r~~~~i~r~G~e--~~~~~v~~~~~~~~ 157 (157)
T PF01077_consen 132 RFKDFIERLGFE--KFREEVEERLGHKF 157 (157)
T ss_dssp SHHHHHHHHHHH--HHHHHHHHTSCGG-
T ss_pred CHHHHHHHHCHH--HHHHHHHHHhCcCC
Confidence 566788888875 58999999999764
No 27
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=44.29 E-value=47 Score=34.66 Aligned_cols=93 Identities=20% Similarity=0.256 Sum_probs=60.2
Q ss_pred cccCCCchhHH--HHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHH
Q 026481 98 ADWGELPASVI--HDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIR 175 (238)
Q Consensus 98 ~sW~elp~svv--~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~ 175 (238)
+-|.+.+.+=. ...+-+.++- -..|.|+.. +.|=.-|-|+=.-+.=|-=|+|+.|.+|+- +-|.+-+.
T Consensus 506 A~~gD~a~ape~~~Ylela~~~g----yd~e~L~~i-a~avd~EaFylrf~~gr~ii~dIL~~~gd~-----~rH~~Lv~ 575 (715)
T COG1107 506 AGVGDRAKAPEAEQYLELAAERG----YDREDLEKI-ALAVDYEAFYLRFMDGRGIIADILGTTGDA-----DRHRELVD 575 (715)
T ss_pred eeecccccChhHHHHHHHHHhcC----CCHHHHHHH-HHHHhHHHHHhhhcccchHHHHHhhcccch-----hHHHHHHH
Confidence 35888876622 2222222221 124556543 445566889888888888899999988874 23444444
Q ss_pred HHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhh-hhh
Q 026481 176 TVYQRYATYLDAFGPDESYLRKKVETELGSKMIFLK-MRC 214 (238)
Q Consensus 176 tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LK-mRc 214 (238)
..|. +-|++||++|-+.+-|+| +|.
T Consensus 576 ~L~~--------------q~~~~ve~qL~aa~~~vk~~~l 601 (715)
T COG1107 576 HLYE--------------QAKEAVEEQLRAALPHVKSERL 601 (715)
T ss_pred HHHH--------------HHHHHHHHHHHHhhhccceeec
Confidence 4443 347899999999999999 765
No 28
>TIGR01237 D1pyr5carbox2 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative. This enzyme is the second of two in the degradation of proline to glutamate. This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. Members of this branch may be associated with proline dehydrogenase (the other enzyme of the pathway from proline to glutamate) but have not been demonstrated experimentally. The branches are not as closely related to each other as some distinct aldehyde dehydrogenases are to some; separate models were built to let each model describe a set of equivalogs.
Probab=43.19 E-value=39 Score=32.06 Aligned_cols=49 Identities=14% Similarity=0.268 Sum_probs=37.5
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHc--ccCCCchh----HHHHHHhhhcccCCchhH
Q 026481 76 DVAHMPVIRDPEIQRAFKDLMAA--DWGELPAS----VIHDAKSALSRNNDDKAG 124 (238)
Q Consensus 76 d~~hlP~i~Dpei~~afKdLmA~--sW~elp~s----vv~~ak~alSk~tdDkAG 124 (238)
-+.++|..+..++..|++.--++ +|..+|.. ++..+...|.++.|+.+-
T Consensus 59 ~i~~~~~~~~~~v~~av~~A~~A~~~W~~~~~~~R~~~L~~~a~~l~~~~~~la~ 113 (511)
T TIGR01237 59 VVGKVGKASVEQAEHALQIAKKAFEAWKKTPVRERAGILRKAAAIMERRRHELNA 113 (511)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHCHHHHHH
Confidence 45568888888998888877664 79999976 567778888887777664
No 29
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=43.15 E-value=82 Score=27.11 Aligned_cols=58 Identities=22% Similarity=0.281 Sum_probs=46.7
Q ss_pred HHHHHHHHHH---cccCCCchhHHHHHHhhhcccC-CchhHHHHHHHHHHHHHHHHHHHHHH
Q 026481 88 IQRAFKDLMA---ADWGELPASVIHDAKSALSRNN-DDKAGQEVLKNVFSAAEAVEEFIGII 145 (238)
Q Consensus 88 i~~afKdLmA---~sW~elp~svv~~ak~alSk~t-dDkAGqeaL~nvfrAAeAvEeFgGiL 145 (238)
.+.||-.||. .+|+-++++.|+.+-.-++++. |...-|-+|...-.....-...++.+
T Consensus 37 ~L~af~eLMeHg~vsWd~l~~~FI~Kia~~Vn~~~~d~~i~q~sLaILEs~Vl~S~~ly~~V 98 (160)
T PF11841_consen 37 ALTAFVELMEHGIVSWDTLSDSFIKKIASYVNSSAMDASILQRSLAILESIVLNSPKLYQLV 98 (160)
T ss_pred HHHHHHHHHhcCcCchhhccHHHHHHHHHHHccccccchHHHHHHHHHHHHHhCCHHHHHHH
Confidence 5789999998 4999999999998888888777 78888888887777777666666643
No 30
>PRK05255 hypothetical protein; Provisional
Probab=40.66 E-value=45 Score=28.84 Aligned_cols=47 Identities=21% Similarity=0.327 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHH--------HHHHHHHHH
Q 026481 131 VFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRT--------VYQRYATYL 185 (238)
Q Consensus 131 vfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~t--------ay~rY~~YL 185 (238)
+=|.++|+.++|.-|+.|-..-=.- =|||+.+.+||.. +++|=+.|+
T Consensus 22 ~KRe~~alq~LG~~L~~Ls~~ql~~--------lpL~e~L~~Ai~ea~ri~~~eA~RRqlqyI 76 (171)
T PRK05255 22 IKRDAEALQDLGEELVELSKDQLAK--------LPLDEDLRDAILEAQRITSHEARRRQLQYI 76 (171)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHhc--------CCCCHHHHHHHHHHhhhccchHHHHHHHHH
Confidence 4488999999999999886532222 2999999999975 456666664
No 31
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=40.24 E-value=28 Score=22.26 Aligned_cols=38 Identities=26% Similarity=0.291 Sum_probs=27.4
Q ss_pred chHHHHHHHH-HHHHHHHHHhhcCCChhHHHHHHHHhhh
Q 026481 167 SNELSSAIRT-VYQRYATYLDAFGPDESYLRKKVETELG 204 (238)
Q Consensus 167 Pd~~~~Al~t-ay~rY~~YLdsFgpdE~yLrKKVE~ELG 204 (238)
|+|+--|+-. --.-....|..+|-+..-|++.+|..||
T Consensus 15 ~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg 53 (53)
T PF02861_consen 15 PEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG 53 (53)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 3455555322 2224667899999999999999999987
No 32
>TIGR00722 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=39.89 E-value=54 Score=30.18 Aligned_cols=51 Identities=22% Similarity=0.352 Sum_probs=40.6
Q ss_pred HHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHH
Q 026481 89 QRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEE 140 (238)
Q Consensus 89 ~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEe 140 (238)
.++..+|+-..=..||+.|.+..++|..+ -+...++.+|+....-++..++
T Consensus 2 ~~~v~~~~~~a~~~lp~Dv~~al~~a~~~-E~s~~ak~~l~~ileN~~iA~~ 52 (273)
T TIGR00722 2 TEAVKEAIKEAVTRLPEDVVDAIKEAYDR-EESEIAKINLEAILDNIEIAEK 52 (273)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHhh-cCCHHHHHHHHHHHHHHHHHhc
Confidence 45666777666788999999999999977 4555689999998888887765
No 33
>PF14355 Abi_C: Abortive infection C-terminus
Probab=39.69 E-value=1.4e+02 Score=21.53 Aligned_cols=69 Identities=14% Similarity=0.253 Sum_probs=43.4
Q ss_pred hhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHH
Q 026481 105 ASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTV 177 (238)
Q Consensus 105 ~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~ta 177 (238)
++++..++++|..+.++... +.++.+.+....+- --|.+||-...|-=|-......+-|.+-.=|+..+
T Consensus 2 ~~L~k~~~~~L~~~~~~~~~-~~ik~il~~l~~i~---~~i~~lRN~~g~~HG~~~~~~~~~~~~A~l~v~~a 70 (80)
T PF14355_consen 2 PKLVKKVKKALGLSPDSQSD-KDIKKILSSLNSIV---SGINELRNKYGDAHGRGSKPYELDPRHARLAVNAA 70 (80)
T ss_pred hHHHHHHHHHHccCCcccch-HHHHHHHHHHHHHH---HHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Confidence 35778899999888777776 66666666655544 23567888777666644444444444444444443
No 34
>PF04751 DUF615: Protein of unknown function (DUF615); InterPro: IPR006839 The proteins in this entry are functionally uncharacterised. The entry contains the Escherichia coli (strain K12) protein YjgA (P0A8X0 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2P0T_A.
Probab=39.49 E-value=27 Score=29.50 Aligned_cols=45 Identities=20% Similarity=0.326 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHH--------HHHHHHHHH
Q 026481 133 SAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRT--------VYQRYATYL 185 (238)
Q Consensus 133 rAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~t--------ay~rY~~YL 185 (238)
|.++|+..+|.-|+.|-..-=+-+ |||+++.+||.. +.+|=+.|+
T Consensus 13 Re~~~lq~Lg~~L~~L~~~ql~~l--------pL~e~l~~Ai~~a~ri~~~~arrRQ~qyI 65 (157)
T PF04751_consen 13 REMHALQDLGEELVELSPKQLAKL--------PLPEELRDAIMEARRITSHEARRRQLQYI 65 (157)
T ss_dssp ---HHHHHHHHHHTTS-HHHHTTS-----------HHHHHHHHHGGG--SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCHHHHhhC--------CCCHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence 788999999999998865433333 999999999965 456655554
No 35
>TIGR00140 hupD hydrogenase expression/formation protein. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease.
Probab=39.20 E-value=31 Score=26.57 Aligned_cols=35 Identities=29% Similarity=0.399 Sum_probs=29.5
Q ss_pred ccCCCCCCCc----CCchHHHHHHHHHHHHHHHHHhhcC
Q 026481 155 EIGLSGENVK----PLSNELSSAIRTVYQRYATYLDAFG 189 (238)
Q Consensus 155 l~GlsGEnVk----PLPd~~~~Al~tay~rY~~YLdsFg 189 (238)
++|+-++++. +|.+..++|+..+-++-.+.|+.||
T Consensus 96 ivgi~~~~~~~~g~~LS~~v~~av~~~~~~i~~~l~~~~ 134 (134)
T TIGR00140 96 LIGVQPEELEDYGGSLSPEVAEAIPPAIEIALAQLAEWG 134 (134)
T ss_pred EEEeeEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 5788888777 6899999999999888888888775
No 36
>PRK11241 gabD succinate-semialdehyde dehydrogenase I; Provisional
Probab=38.74 E-value=42 Score=31.81 Aligned_cols=54 Identities=20% Similarity=0.318 Sum_probs=39.7
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHc--ccCCCch----hHHHHHHhhhcccCCchhHHHHH
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAA--DWGELPA----SVIHDAKSALSRNNDDKAGQEVL 128 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~--sW~elp~----svv~~ak~alSk~tdDkAGqeaL 128 (238)
+-+..+|..+.-|+..|++..-++ .|..+|. .++..+...|.++.|+.+--..+
T Consensus 37 ~~v~~~~~~~~~~v~~av~~A~~a~~~W~~~~~~~R~~~L~~~a~~l~~~~~ela~~~~~ 96 (482)
T PRK11241 37 DKLGSVPKMGADETRAAIDAANRALPAWRALTAKERANILRRWFNLMMEHQDDLARLMTL 96 (482)
T ss_pred CEEEEEeCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 456778888888999999888765 6999983 46677777777777776554433
No 37
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=38.63 E-value=29 Score=25.06 Aligned_cols=32 Identities=9% Similarity=0.358 Sum_probs=22.7
Q ss_pred HHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHH
Q 026481 144 IIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRY 181 (238)
Q Consensus 144 iL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY 181 (238)
+-+.||.+++.|--++|+.+ .++-|..+|++|
T Consensus 41 ~a~~L~~A~~~L~~ItG~~~------~ediLd~IFs~F 72 (73)
T PF12631_consen 41 VAEDLREALESLGEITGEVV------TEDILDNIFSNF 72 (73)
T ss_dssp HHHHHHHHHHHHHHHCTSS--------HHHHHHHHCTS
T ss_pred HHHHHHHHHHHHHHHhCCCC------hHHHHHHHHHhh
Confidence 55689999999999999854 345556666654
No 38
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=37.98 E-value=1.6e+02 Score=26.18 Aligned_cols=57 Identities=14% Similarity=0.265 Sum_probs=35.9
Q ss_pred hhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhh
Q 026481 153 DDEIGLSGENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSKMIFLK 211 (238)
Q Consensus 153 DDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LK 211 (238)
+..+-+.-++..-|.+.|..+.+.|.+-|++ .+||-+..=..+++...|..++-+++
T Consensus 57 ~~~~~~P~~~~~eL~~~H~~~~~~A~~~F~~--~s~~d~~~~~~~~L~~~i~~~~~~~~ 113 (297)
T PF02841_consen 57 EQRVKLPTETLEELLELHEQCEKEALEVFMK--RSFGDEDQKYQKKLMEQIEKKFEEFC 113 (297)
T ss_dssp HHH--SS-SSHHHHHHHHHHHHHHHHHHHHH--H----GGGHHHHHHHHHHHHHHHHHH
T ss_pred HHHhCCCccCHHHHHHHHHHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444455666888999999999999997 78997544445677777777766654
No 39
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=37.14 E-value=22 Score=31.92 Aligned_cols=62 Identities=24% Similarity=0.260 Sum_probs=50.2
Q ss_pred hhHHHHHHHHHHHHHHHH-HHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHh
Q 026481 122 KAGQEVLKNVFSAAEAVE-EFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYLD 186 (238)
Q Consensus 122 kAGqeaL~nvfrAAeAvE-eFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLd 186 (238)
.+||.+-.|+-=+-+++- -|-|-+++|-|.+-|--|-+|- =+|+++-.|.|-.||||-.|+-
T Consensus 128 V~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgp---l~p~h~reayr~~~k~~~~~~~ 190 (199)
T COG5251 128 VANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGP---LIPFHKREAYRYKLKKYLKKLT 190 (199)
T ss_pred HhccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCC---CChHHHHHHHHHHHHhhhccch
Confidence 678877777766666654 3789999999999998887762 3689999999999999998875
No 40
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=37.11 E-value=26 Score=25.88 Aligned_cols=51 Identities=27% Similarity=0.420 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHH-HH---HhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHhhc
Q 026481 130 NVFSAAEAVEEFIGII-MN---IKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYLDAF 188 (238)
Q Consensus 130 nvfrAAeAvEeFgGiL-~s---LrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLdsF 188 (238)
|.|+-=.+|.++||-= ++ .=.+|-+.+|+..+ .......|+..|.|| |..|
T Consensus 33 dL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~-----~~~~~~~lk~~Y~k~---L~~y 87 (93)
T smart00501 33 DLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDT-----STSAASSLRKHYERY---LLPF 87 (93)
T ss_pred cHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcc-----cchHHHHHHHHHHHH---hHHH
Confidence 6777777899999932 22 33455566666422 234555666666665 5555
No 41
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-
Probab=37.05 E-value=2.7e+02 Score=23.91 Aligned_cols=96 Identities=18% Similarity=0.281 Sum_probs=61.3
Q ss_pred CCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH-HHHHHhhhhhhccCCCC
Q 026481 82 VIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG-IIMNIKMEFDDEIGLSG 160 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG-iL~sLrmeiDDl~GlsG 160 (238)
.|++|...+..|...+.-|..-.=++-+|++.--+. +..-|++++.++..=-+.+..=+ .+..+-+...
T Consensus 5 ~~~y~~~~~ly~~~~~~~W~p~ei~~~~D~~~~~~l---~~~er~~~~~~la~~~~~d~~v~~~~~~~~~~~~------- 74 (288)
T cd01049 5 PIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEKL---TEAERHFIKRVLAFLAALDSIVGENLVELFSRHV------- 74 (288)
T ss_pred ccccHHHHHHHHHHHHcCCChhhcchhhhHHHHhHC---CHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHc-------
Confidence 579999999999999999986666677776654332 45568999998876555444433 1111111110
Q ss_pred CCCcCCchH-----HHHHHHHHHHH-HHHHHhhcCCC
Q 026481 161 ENVKPLSNE-----LSSAIRTVYQR-YATYLDAFGPD 191 (238)
Q Consensus 161 EnVkPLPd~-----~~~Al~tay~r-Y~~YLdsFgpd 191 (238)
+.|+. .+-+.+++|.+ |..+|++++.+
T Consensus 75 ----~~~e~~~~~~~q~~~E~iH~e~Ys~il~~l~~~ 107 (288)
T cd01049 75 ----QIPEARAFYGFQAFMENIHSESYSYILDTLGKD 107 (288)
T ss_pred ----ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 12221 34556666655 77888999987
No 42
>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=36.77 E-value=52 Score=32.20 Aligned_cols=117 Identities=15% Similarity=0.256 Sum_probs=75.7
Q ss_pred CCcccccccccccccccCCCCCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHH
Q 026481 60 RSSLVMSIGCNRSFSEDVAHMPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVE 139 (238)
Q Consensus 60 ~~~~s~~~~~~R~fS~d~~hlP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvE 139 (238)
|-|+..--..+|.|. -.--+|-..+..=.-++++||..+ |..+...--.+|-+.||.-.|-++-..+=.||
T Consensus 298 N~P~e~Dea~~Rrf~-kr~yiplPd~etr~~~~~~ll~~~----~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~---- 368 (428)
T KOG0740|consen 298 NRPWELDEAARRRFV-KRLYIPLPDYETRSLLWKQLLKEQ----PNGLSDLDISLLAKVTEGYSGSDITALCKEAA---- 368 (428)
T ss_pred CCchHHHHHHHHHhh-ceeeecCCCHHHHHHHHHHHHHhC----CCCccHHHHHHHHHHhcCcccccHHHHHHHhh----
Confidence 445555555566666 333366666666666777777776 56666555566666677766666655544433
Q ss_pred HHHHHHHHHhhhhh--hccCCCCCCCcCC-chHHHHHHHHHH--------HHHHHHHhhcCC
Q 026481 140 EFIGIIMNIKMEFD--DEIGLSGENVKPL-SNELSSAIRTVY--------QRYATYLDAFGP 190 (238)
Q Consensus 140 eFgGiL~sLrmeiD--Dl~GlsGEnVkPL-Pd~~~~Al~tay--------~rY~~YLdsFgp 190 (238)
..-+|+-.+ |+.++..+++.|. +.+..+|+++++ .+|.++.+.||-
T Consensus 369 -----~~p~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~s~~~l~~~~~~~~~fg~ 425 (428)
T KOG0740|consen 369 -----MGPLRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSVSLEGLEKYEKWDKEFGS 425 (428)
T ss_pred -----cCchhhcccchhhhhcchhccCCCCcchHHHHHHhhccccCccccchhHHHhhhhcc
Confidence 223444444 7888888888875 678899999887 467777777774
No 43
>COG0413 PanB Ketopantoate hydroxymethyltransferase [Coenzyme metabolism]
Probab=36.70 E-value=79 Score=29.58 Aligned_cols=70 Identities=26% Similarity=0.418 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHH-------HHHHHhhhh------------------------hhccCCCCCCCcCCch---HH
Q 026481 125 QEVLKNVFSAAEAVEEFIG-------IIMNIKMEF------------------------DDEIGLSGENVKPLSN---EL 170 (238)
Q Consensus 125 qeaL~nvfrAAeAvEeFgG-------iL~sLrmei------------------------DDl~GlsGEnVkPLPd---~~ 170 (238)
++.-+.+|+-|.|+|+.|- +-..|=.+| +|++|++++-+.+.-. .+
T Consensus 157 ~~~a~~l~~dA~ale~AGaf~ivlE~Vp~~lA~~IT~~lsiPtIGIGAG~~cDGQvLV~~D~lGl~~~~~PkFvK~y~~l 236 (268)
T COG0413 157 EESAEKLLEDAKALEEAGAFALVLECVPAELAKEITEKLSIPTIGIGAGPGCDGQVLVMHDMLGLSGGHKPKFVKRYADL 236 (268)
T ss_pred HHHHHHHHHHHHHHHhcCceEEEEeccHHHHHHHHHhcCCCCEEeecCCCCCCceEEEeeeccccCCCCCCcHHHHHhcc
Confidence 4566778999999999985 334444443 7999998844433332 23
Q ss_pred HHHHHHHHHHHHHHHhh--cCCChhH
Q 026481 171 SSAIRTVYQRYATYLDA--FGPDESY 194 (238)
Q Consensus 171 ~~Al~tay~rY~~YLds--FgpdE~y 194 (238)
.+-+++|+++|+.=..+ |=.+||+
T Consensus 237 ~~~i~~A~~~Y~~eV~~g~FP~~~H~ 262 (268)
T COG0413 237 GEEIRAAVKQYAAEVKSGTFPEEEHS 262 (268)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCcccc
Confidence 44677889999887653 6555554
No 44
>PRK06833 L-fuculose phosphate aldolase; Provisional
Probab=33.15 E-value=1.6e+02 Score=24.84 Aligned_cols=48 Identities=29% Similarity=0.388 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHH
Q 026481 124 GQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRY 181 (238)
Q Consensus 124 GqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY 181 (238)
|+ -+.++|..+|++|+.--+....+ . .|+ ..|||++..+-++..|++|
T Consensus 163 G~-~~~eA~~~~e~lE~~a~~~~~a~-~-------~G~-~~~l~~~~~~~~~~~~~~~ 210 (214)
T PRK06833 163 AN-NLKNAFNIAEEIEFCAEIYYQTK-S-------IGE-PKLLPEDEMENMAEKFKTY 210 (214)
T ss_pred eC-CHHHHHHHHHHHHHHHHHHHHHH-h-------cCC-CCCCCHHHHHHHHHHHHHh
Confidence 44 57788999999998777554433 1 243 4889999888887777655
No 45
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=33.11 E-value=45 Score=26.95 Aligned_cols=54 Identities=22% Similarity=0.420 Sum_probs=38.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHH
Q 026481 120 DDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYL 185 (238)
Q Consensus 120 dDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YL 185 (238)
+|.+.++-|.. ..-+|||.|++ ..||++++|- |..+.-=|+++.++| +|=++|.
T Consensus 27 ~~~~~~e~l~~------i~r~f~g~lv~-~kEi~~ilG~-~~~i~Rt~~Qvv~~l----~RRiDYV 80 (99)
T PF13758_consen 27 DDDATREDLLR------IRRDFGGSLVT-EKEIKEILGE-GQGITRTREQVVDVL----SRRIDYV 80 (99)
T ss_pred cCCCCHHHHHH------HHHhcCccccc-HHHHHHHhCC-CCCCCcCHHHHHHHH----HHHHHHH
Confidence 46666766544 45689999988 4699999998 445556688888776 4556664
No 46
>COG0248 GppA Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]
Probab=33.02 E-value=86 Score=30.82 Aligned_cols=63 Identities=30% Similarity=0.441 Sum_probs=48.9
Q ss_pred CcCCchHHHHHHHHHHHHHHHHHhhcCCChh---------------HHHHHHHHhhhhhh-----------hhhhhhhcC
Q 026481 163 VKPLSNELSSAIRTVYQRYATYLDAFGPDES---------------YLRKKVETELGSKM-----------IFLKMRCAG 216 (238)
Q Consensus 163 VkPLPd~~~~Al~tay~rY~~YLdsFgpdE~---------------yLrKKVE~ELGtkm-----------I~LKmRcsG 216 (238)
-|.|+++-.+-...+.+||.+-++.|+++|. ..-++||.|+|-.. +++=+ .++
T Consensus 46 ~g~L~~eai~R~~~aL~~f~e~~~~~~~~~v~~vATsA~R~A~N~~eFl~rv~~~~G~~ievIsGeeEArl~~lGv-~~~ 124 (492)
T COG0248 46 TGNLSEEAIERALSALKRFAELLDGFGAEEVRVVATSALRDAPNGDEFLARVEKELGLPIEVISGEEEARLIYLGV-AST 124 (492)
T ss_pred cCCcCHHHHHHHHHHHHHHHHHHhhCCCCEEEEehhHHHHcCCCHHHHHHHHHHHhCCceEEeccHHHHHHHHHHH-Hhc
Confidence 3789988877778899999999999999993 35578999998653 33332 467
Q ss_pred CCCCcceeEEe
Q 026481 217 LGSEWGKVFYY 227 (238)
Q Consensus 217 lgseWGKVtll 227 (238)
++. ||++.|+
T Consensus 125 ~~~-~~~~lv~ 134 (492)
T COG0248 125 LPR-KGDGLVI 134 (492)
T ss_pred CCC-CCCEEEE
Confidence 777 8888776
No 47
>KOG4835 consensus DNA-binding protein C1D involved in regulation of double-strand break repair [Replication, recombination and repair]
Probab=32.55 E-value=86 Score=26.99 Aligned_cols=55 Identities=13% Similarity=0.223 Sum_probs=40.4
Q ss_pred CCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhh------------------hhhhhhcCCCCC
Q 026481 162 NVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSKMI------------------FLKMRCAGLGSE 220 (238)
Q Consensus 162 nVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI------------------~LKmRcsGlgse 220 (238)
--+|+|.++...|.. +-+||++-.|.+-=+-+++|.|.+..+- .+-.+|-|+|+.
T Consensus 3 ~~~~~p~~l~e~ln~----f~~~l~~l~~~le~~~s~~e~e~l~sl~~EqAKld~~~~ya~~sl~~~~l~~kG~da~ 75 (144)
T KOG4835|consen 3 SNDPEPESLIEYLNK----FLDNLEELKPPLEDMESISELEELRSLLLEQAKLDLTLAYAINSLFWSFLKLKGVDAS 75 (144)
T ss_pred CCCcChHHHHHHHHH----HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Confidence 346888888777765 7788888888777777777777776654 445678888864
No 48
>PLN02312 acyl-CoA oxidase
Probab=32.52 E-value=1.4e+02 Score=30.23 Aligned_cols=39 Identities=21% Similarity=0.355 Sum_probs=22.6
Q ss_pred CCCCCCcCCchHHHHHHHHHHHHHHHHHhhcCCChhHHH
Q 026481 158 LSGENVKPLSNELSSAIRTVYQRYATYLDAFGPDESYLR 196 (238)
Q Consensus 158 lsGEnVkPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLr 196 (238)
+|++.++.+...+..-+..+=.-=+...|+|+..+..|+
T Consensus 625 ls~~~~~~i~~~i~~L~~~lrp~Av~LvDaF~~~d~~L~ 663 (680)
T PLN02312 625 LSPDNVALVRKEVAKLCGELRPHALALVSSFGIPDAFLS 663 (680)
T ss_pred CCHHHHHHHHHHHHHHHHHHhHhHHHHhcccCCChHhcC
Confidence 355555555444444444444444567788888877764
No 49
>PF10191 COG7: Golgi complex component 7 (COG7); InterPro: IPR019335 The conserved oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis []. COG7 is required for normal Golgi morphology and trafficking. Mutation in COG7 causes a congenital disorder of glycosylation [].
Probab=32.22 E-value=1.7e+02 Score=29.99 Aligned_cols=89 Identities=19% Similarity=0.337 Sum_probs=59.9
Q ss_pred HHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHH
Q 026481 91 AFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNEL 170 (238)
Q Consensus 91 afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~ 170 (238)
.+-.|++..+..|.+++......++..+. +...|.......++.+.|+.-|..+-.+. .++ -. +..+
T Consensus 279 ~~~~ll~~~L~~L~PS~~~~l~~al~~~~----~~~~L~~L~~l~~~t~~Fa~~l~~~l~~~------~~~--~~-l~~~ 345 (766)
T PF10191_consen 279 VLPKLLAETLSALQPSFPSRLSSALKRAG----PETKLETLIELYQATEHFARNLEHLLSSL------PGE--SN-LSKV 345 (766)
T ss_pred HHHHHHHHHHHhcCccHHHHHHHHHhhcC----chhhHHHHHHHHHHHHHHHHHHHHHHhcc------ccc--cc-hHHH
Confidence 55566666778899998877777775432 22236666667778889988776664432 111 11 1245
Q ss_pred HHHHHHHHHHHHHHHhhcCCCh
Q 026481 171 SSAIRTVYQRYATYLDAFGPDE 192 (238)
Q Consensus 171 ~~Al~tay~rY~~YLdsFgpdE 192 (238)
.+.++++|.=|..|...||.-|
T Consensus 346 ~~l~~al~~PF~~~q~~Yg~lE 367 (766)
T PF10191_consen 346 EELLQALFEPFKPYQQRYGELE 367 (766)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 6778999999999999999755
No 50
>COG3215 PilZ Tfp pilus assembly protein PilZ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=31.87 E-value=28 Score=29.14 Aligned_cols=20 Identities=35% Similarity=0.564 Sum_probs=17.5
Q ss_pred hcCCChh--HHHHHHHHhhhhh
Q 026481 187 AFGPDES--YLRKKVETELGSK 206 (238)
Q Consensus 187 sFgpdE~--yLrKKVE~ELGtk 206 (238)
.|+.+|+ -+|.++|++||..
T Consensus 86 ~f~d~e~g~~vr~~IE~~Lg~~ 107 (117)
T COG3215 86 QFTDGENGLKVRNQIETLLGGT 107 (117)
T ss_pred eccCCCchhhHHHHHHHHHHhh
Confidence 5888998 8899999999975
No 51
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=30.12 E-value=32 Score=28.32 Aligned_cols=31 Identities=26% Similarity=0.444 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhhhhhcCCCCCc
Q 026481 177 VYQRYATYLDAFGPDESYLRKKVETELGSKMIFLKMRCAGLGSEW 221 (238)
Q Consensus 177 ay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LKmRcsGlgseW 221 (238)
.|.||-+.| .+|=-.. -|..||+--||++.|
T Consensus 115 ~y~kYfKMl-~~GvP~~-------------aVk~KM~~eGlDp~~ 145 (148)
T PF10152_consen 115 RYAKYFKML-KMGVPRE-------------AVKQKMQAEGLDPSL 145 (148)
T ss_pred cHHHHHHHH-HcCCCHH-------------HHHHHHHHcCCCHHH
Confidence 466666666 4553222 466788888988876
No 52
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=30.06 E-value=2.7e+02 Score=23.08 Aligned_cols=73 Identities=15% Similarity=0.162 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHc--ccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHH-HHHHHHHHHHhhhhhhccC
Q 026481 82 VIRDPEIQRAFKDLMAA--DWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAV-EEFIGIIMNIKMEFDDEIG 157 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA~--sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAv-EeFgGiL~sLrmeiDDl~G 157 (238)
..++..+.+++..|... +|..|-..-.++.+.+++..+=- .---+++...|+++ ++|+|.+...+.+|-.+=|
T Consensus 38 qt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~---~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~G 113 (191)
T TIGR01083 38 QATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLY---RNKAKNIIALCRILVERYGGEVPEDREELVKLPG 113 (191)
T ss_pred hCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhcCCh---HHHHHHHHHHHHHHHHHcCCCCchHHHHHHhCCC
Confidence 34677777787777753 12222111222333333332211 12235666777775 6788876666666555544
No 53
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=29.62 E-value=3.8e+02 Score=23.31 Aligned_cols=60 Identities=13% Similarity=0.181 Sum_probs=35.8
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHcccC--CCchhHHHHHHhhhc-ccCCchhHHHHHHHHH
Q 026481 73 FSEDVAHMPVIRDPEIQRAFKDLMAADWG--ELPASVIHDAKSALS-RNNDDKAGQEVLKNVF 132 (238)
Q Consensus 73 fS~d~~hlP~i~Dpei~~afKdLmA~sW~--elp~svv~~ak~alS-k~tdDkAGqeaL~nvf 132 (238)
|....=++|..+..++...++.-+...+. .+++.++..+..... .++|--....+|.+++
T Consensus 189 ~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~ 251 (365)
T TIGR02928 189 LCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAG 251 (365)
T ss_pred CCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 43345579999999999999988764443 467776655433222 2344333344444433
No 54
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=29.05 E-value=89 Score=25.56 Aligned_cols=76 Identities=24% Similarity=0.347 Sum_probs=34.7
Q ss_pred hhhcccCCchhHHHHHHHHHH--HHHHHHHHHHHHHHHhhhhhhccC-CCCCCCcCCchHHHHHHHHHHHHHHHHHhhcC
Q 026481 113 SALSRNNDDKAGQEVLKNVFS--AAEAVEEFIGIIMNIKMEFDDEIG-LSGENVKPLSNELSSAIRTVYQRYATYLDAFG 189 (238)
Q Consensus 113 ~alSk~tdDkAGqeaL~nvfr--AAeAvEeFgGiL~sLrmeiDDl~G-lsGEnVkPLPd~~~~Al~tay~rY~~YLdsFg 189 (238)
.++.+...|...+++|++++. |..-+++.-|-+.. -| +|++.++.|.+.+.+.+..+=.=-....|+||
T Consensus 66 ~~i~~~~~~~~~~~vL~~L~~Lyal~~i~~~~g~fl~--------~g~ls~~~~~~l~~~i~~l~~~lrp~av~LVDAF~ 137 (187)
T PF01756_consen 66 EAIQSSCADPEVRQVLRQLCQLYALSIIEENAGDFLE--------HGYLSPEQIKALRKAIEELCAELRPNAVALVDAFD 137 (187)
T ss_dssp HHTTSG-SSTTHHHHHHHHHHHHHHHHHHHTHHHHHH--------TTSS-HHHHHHHHHHHHHHHHHHGGGHHHHHHTT-
T ss_pred HHhcccCCChHHHHHHHHHHHHHhHHHHHHHHHHHHh--------CCcCCHHHHHHHHHHHHHHHHHHHhHHHHHHHhcC
Confidence 344434556666777776654 22223332221111 01 34555555554444444444333456778888
Q ss_pred CChhHHH
Q 026481 190 PDESYLR 196 (238)
Q Consensus 190 pdE~yLr 196 (238)
+.+..|+
T Consensus 138 ~~D~~L~ 144 (187)
T PF01756_consen 138 FPDFFLN 144 (187)
T ss_dssp --HHHHT
T ss_pred CCHHHHc
Confidence 8887775
No 55
>PF13339 AATF-Che1: Apoptosis antagonizing transcription factor
Probab=29.01 E-value=2.8e+02 Score=21.64 Aligned_cols=56 Identities=14% Similarity=0.234 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhccC-CCC-----------CCCcCCchHHHHHHHHHHHHHHHHHhh
Q 026481 132 FSAAEAVEEFIGIIMNIKMEFDDEIG-LSG-----------ENVKPLSNELSSAIRTVYQRYATYLDA 187 (238)
Q Consensus 132 frAAeAvEeFgGiL~sLrmeiDDl~G-lsG-----------EnVkPLPd~~~~Al~tay~rY~~YLds 187 (238)
-.+.+++...-..|.+||.++-|... ... +..+.-.+++...+...|++|..|-++
T Consensus 56 ~~~~~~~~~ll~~l~~Lq~~L~~~~~~~~~~~~~~~k~Kr~~~~~~~~~~~~~~~~~~~~~~~~~R~~ 123 (131)
T PF13339_consen 56 EEAEKALKKLLDSLLELQEELLEDNDSESEESDSKKKRKREKSSDRSLEEYWEEIQKLDKRLEPYRNS 123 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccccccccccccccccCCCCCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667777888999998872111 111 112235678889999999999999764
No 56
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=28.51 E-value=48 Score=29.43 Aligned_cols=31 Identities=23% Similarity=0.573 Sum_probs=28.0
Q ss_pred cccccccCCCCCCCCCHHHHHHHHHHHHcccC
Q 026481 70 NRSFSEDVAHMPVIRDPEIQRAFKDLMAADWG 101 (238)
Q Consensus 70 ~R~fS~d~~hlP~i~Dpei~~afKdLmA~sW~ 101 (238)
.|.| |+.+-||+++|.+|.+-..=|+.-.|.
T Consensus 64 ~kkf-ETfSYLPpLtdeqI~kQVeYli~~GW~ 94 (176)
T PLN02289 64 KKKF-ETLSYLPDLTDEELAKEVDYLLRNKWV 94 (176)
T ss_pred ccce-eeeecCCCCCHHHHHHHHHHHHhCCCe
Confidence 4555 799999999999999999999999995
No 57
>PRK10880 adenine DNA glycosylase; Provisional
Probab=28.39 E-value=57 Score=30.61 Aligned_cols=70 Identities=16% Similarity=0.089 Sum_probs=44.0
Q ss_pred CCHHHHHHHHHHHHc--ccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHH-HHHHHHHHHHhhhhhhccC
Q 026481 84 RDPEIQRAFKDLMAA--DWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAV-EEFIGIIMNIKMEFDDEIG 157 (238)
Q Consensus 84 ~Dpei~~afKdLmA~--sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAv-EeFgGiL~sLrmeiDDl~G 157 (238)
+|..+..+|..||.. +|..|-++-.+++.++++.-+=- . --+|..++|+.+ +++||.+-..+.+|-.|=|
T Consensus 44 ~v~~v~~~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy---~-RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpG 116 (350)
T PRK10880 44 QVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYY---A-RARNLHKAAQQVATLHGGEFPETFEEVAALPG 116 (350)
T ss_pred cHHHHHHHHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChH---H-HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCC
Confidence 566777888888874 23333333345555555543321 1 256888999988 8899987766666555544
No 58
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=27.83 E-value=50 Score=22.28 Aligned_cols=16 Identities=44% Similarity=0.816 Sum_probs=12.9
Q ss_pred CCCCHHHHHHHHHHHH
Q 026481 82 VIRDPEIQRAFKDLMA 97 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA 97 (238)
.++||||++++-=+++
T Consensus 19 ~l~DpdvqrgL~~ll~ 34 (42)
T PF07849_consen 19 ALRDPDVQRGLGFLLA 34 (42)
T ss_pred HHcCHHHHHHHHHHHH
Confidence 4689999999877664
No 59
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=27.35 E-value=88 Score=27.28 Aligned_cols=106 Identities=12% Similarity=0.221 Sum_probs=50.6
Q ss_pred ccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcC----CchHHHHHH
Q 026481 99 DWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKP----LSNELSSAI 174 (238)
Q Consensus 99 sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkP----LPd~~~~Al 174 (238)
.|.+.|.--...+-+.+....++ -|.|+.||.-.|+-...+- ..++ .+++++-++.+++.| .=.+==..+
T Consensus 130 ~~~~~~~~~L~~l~~~~g~~~~~--aH~Al~Da~at~~vl~~l~---~~~~-~~~~l~~~~~~~~~~~~~~fGK~kG~~~ 203 (250)
T PRK06310 130 EYGDSPNNSLEALAVHFNVPYDG--NHRAMKDVEINIKVFKHLC---KRFR-TLEQLKQILSKPIKMKYMPLGKHKGRLF 203 (250)
T ss_pred hcccCCCCCHHHHHHHCCCCCCC--CcChHHHHHHHHHHHHHHH---Hhcc-cHHHHHHHhhcCcccccccCcccCCCCc
Confidence 36555543344444444443332 3888888887766544432 1111 335555555543311 000000011
Q ss_pred HHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhhhhhhhcCCC
Q 026481 175 RTVYQRYATYLDAFGPDESYLRKKVETELGSKMIFLKMRCAGLG 218 (238)
Q Consensus 175 ~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~LKmRcsGlg 218 (238)
..+=..|..++-.=|= ..||||++++ +||.||-|-+
T Consensus 204 ~~~~~~y~~w~~~~~~-~~~~~~~~~~-------~l~~~~~~~~ 239 (250)
T PRK06310 204 SEIPLEYLQWASKMDF-DQDLLFSIRS-------EIKHRKKGTG 239 (250)
T ss_pred ccCCHHHHHHHHhCCC-CcchHHHHHH-------HHHHhhccCc
Confidence 1111235555422121 2479999988 5789998854
No 60
>COG0167 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]
Probab=27.32 E-value=32 Score=32.00 Aligned_cols=89 Identities=26% Similarity=0.331 Sum_probs=50.5
Q ss_pred cccCCCCCCCC-CHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHH--HH--HHHH
Q 026481 74 SEDVAHMPVIR-DPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFI--GI--IMNI 148 (238)
Q Consensus 74 S~d~~hlP~i~-Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFg--Gi--L~sL 148 (238)
|-+..+++++. |||....+. +.+|+..++--==|-.- -..|+-..|+++++.| |+ ..|+
T Consensus 133 cPnt~g~~~l~~~~e~l~~l~---------------~~vk~~~~~Pv~vKl~P-~~~di~~iA~~~~~~g~Dgl~~~NT~ 196 (310)
T COG0167 133 CPNTPGGRALGQDPELLEKLL---------------EAVKAATKVPVFVKLAP-NITDIDEIAKAAEEAGADGLIAINTT 196 (310)
T ss_pred CCCCCChhhhccCHHHHHHHH---------------HHHHhcccCceEEEeCC-CHHHHHHHHHHHHHcCCcEEEEEeec
Confidence 44666788888 887655432 33333322110001110 2346667899999997 52 2323
Q ss_pred --hhhhhhcc----------CCCCCCCcCCchHHHHHHHHHHHHH
Q 026481 149 --KMEFDDEI----------GLSGENVKPLSNELSSAIRTVYQRY 181 (238)
Q Consensus 149 --rmeiDDl~----------GlsGEnVkPLPd~~~~Al~tay~rY 181 (238)
+|.||.-- ||||.-++|.+= +.|+.+|+|.
T Consensus 197 ~~~~~id~~~~~~~~~~~~GGLSG~~ikp~al---~~v~~l~~~~ 238 (310)
T COG0167 197 KSGMKIDLETKKPVLANETGGLSGPPLKPIAL---RVVAELYKRL 238 (310)
T ss_pred cccccccccccccccCcCCCCcCcccchHHHH---HHHHHHHHhc
Confidence 46576655 899999999864 3455555553
No 61
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=26.22 E-value=3e+02 Score=22.43 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=25.0
Q ss_pred CcCCchHHHHH---HHHHHHHHHHHHhhcCC------ChhHHHHHHHHhh
Q 026481 163 VKPLSNELSSA---IRTVYQRYATYLDAFGP------DESYLRKKVETEL 203 (238)
Q Consensus 163 VkPLPd~~~~A---l~tay~rY~~YLdsFgp------dE~yLrKKVE~EL 203 (238)
..||=..+.++ +...++.|..|...+++ +|-+|+..++..|
T Consensus 59 h~pll~~~~~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l 108 (204)
T PF04740_consen 59 HIPLLQGLILLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKL 108 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHH
Confidence 44555555444 34455677778888887 4788874444433
No 62
>TIGR02923 AhaC ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex.
Probab=26.04 E-value=1.4e+02 Score=25.94 Aligned_cols=52 Identities=15% Similarity=0.150 Sum_probs=36.3
Q ss_pred chHHHHHHHHHHHHHHHHHhhcCCChh--HHHH---HHHHhhhhhhhhhhhhhcCCCCC
Q 026481 167 SNELSSAIRTVYQRYATYLDAFGPDES--YLRK---KVETELGSKMIFLKMRCAGLGSE 220 (238)
Q Consensus 167 Pd~~~~Al~tay~rY~~YLdsFgpdE~--yLrK---KVE~ELGtkmI~LKmRcsGlgse 220 (238)
|..++.||+..+.++..+|-.|.|++. +++. +.|-+-=. .-||..++|.+++
T Consensus 60 ~~~iE~~L~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~di~Nik--~ilR~~~~g~~~~ 116 (343)
T TIGR02923 60 VDLIEHALDANLAKTYEKLFRISPGASRDLIRLYLKKWDVWNIK--TLIRAKYANASAE 116 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhHHHHH--HHHHHHHcCCCHH
Confidence 567899999999888888988888764 4443 45544444 4455558887654
No 63
>PF14363 AAA_assoc: Domain associated at C-terminal with AAA
Probab=25.73 E-value=1.1e+02 Score=23.18 Aligned_cols=42 Identities=26% Similarity=0.325 Sum_probs=32.0
Q ss_pred CchHHHHHHHHHHHHHHH-HHh---------hcCCChhHHHHHHHHhhhhhh
Q 026481 166 LSNELSSAIRTVYQRYAT-YLD---------AFGPDESYLRKKVETELGSKM 207 (238)
Q Consensus 166 LPd~~~~Al~tay~rY~~-YLd---------sFgpdE~yLrKKVE~ELGtkm 207 (238)
+|.++..++.+.++|... +.+ ..|-.++-|=..||.-|+++.
T Consensus 2 ~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g~~~N~ly~a~~~YL~s~~ 53 (98)
T PF14363_consen 2 LPHELRSYLRSLLRRLFSSRFSPYLTIVIPEFDGLSRNELYDAAQAYLSSKI 53 (98)
T ss_pred CCHHHHHHHHHHHHHHHhccCCCcEEEEEEeCCCccccHHHHHHHHHHhhcc
Confidence 799999999988877554 433 235666677789999999986
No 64
>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=25.21 E-value=1.1e+02 Score=29.00 Aligned_cols=69 Identities=29% Similarity=0.452 Sum_probs=46.9
Q ss_pred hhhhhhccCCCCCCCcCCchHHHHHHHHHHHH--HHHHHhhc---CCChhHHHHHHHHhhhhhhhhhhhhhc-----CCC
Q 026481 149 KMEFDDEIGLSGENVKPLSNELSSAIRTVYQR--YATYLDAF---GPDESYLRKKVETELGSKMIFLKMRCA-----GLG 218 (238)
Q Consensus 149 rmeiDDl~GlsGEnVkPLPd~~~~Al~tay~r--Y~~YLdsF---gpdE~yLrKKVE~ELGtkmI~LKmRcs-----Glg 218 (238)
-+.|+|=+|||-+|--+ |..+...|+.+|+. |..|++++ |-| || ||.|+. .-|
T Consensus 327 ~~~l~DGSGLSr~N~is-p~~l~~~L~~~~~~~~~~~~~~sLPiaG~d------------GT----L~~R~~~~~~~~~g 389 (444)
T PF02113_consen 327 GLVLVDGSGLSRYNRIS-PRQLVQLLRYMYKSPYFPDFLDSLPIAGVD------------GT----LKNRFKAPNTPAQG 389 (444)
T ss_dssp TCB-SSSSSSSTT-BBE-HHHHHHHHHHHHHTTTHHHHGGTS-BTTTS------------GG----GTTSSTHCTTTTTT
T ss_pred CcEEecCCCCCcccccC-HHHHHHHHHHHHhCccHHHHHhcCCcCCCC------------CC----hhhhccccCCCcCC
Confidence 34689999999888665 88999999999865 66788876 333 44 566766 233
Q ss_pred CCccee-EEeecccccc
Q 026481 219 SEWGKV-FYYGCQCHCG 234 (238)
Q Consensus 219 seWGKV-tllGTSg~sG 234 (238)
.-|+|= ||=|+++++|
T Consensus 390 ~v~aKTGtL~~v~sLaG 406 (444)
T PF02113_consen 390 RVRAKTGTLNGVSSLAG 406 (444)
T ss_dssp TEEEEEEEETTEEEEEE
T ss_pred cEEEeeecccCeEEeEE
Confidence 334554 4557788887
No 65
>cd07149 ALDH_y4uC Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (ORF name y4uC) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD.
Probab=25.18 E-value=1.1e+02 Score=27.82 Aligned_cols=73 Identities=18% Similarity=0.288 Sum_probs=40.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHc--ccCCCchh----HHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026481 77 VAHMPVIRDPEIQRAFKDLMAA--DWGELPAS----VIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIK 149 (238)
Q Consensus 77 ~~hlP~i~Dpei~~afKdLmA~--sW~elp~s----vv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLr 149 (238)
+.++|...-.++..+++..-++ .|..+|.. ++..+...|.++.|+.+-.....+=--.+||-.|+...+..|+
T Consensus 12 ~~~~~~~~~~~v~~av~~A~~A~~~w~~~~~~~R~~~L~~~a~~l~~~~~~la~~~~~e~Gk~~~~a~~ev~~~~~~l~ 90 (453)
T cd07149 12 IGRVPVASEEDVEKAIAAAKEGAKEMKSLPAYERAEILERAAQLLEERREEFARTIALEAGKPIKDARKEVDRAIETLR 90 (453)
T ss_pred EEEEeCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 3455666666676666665533 68888866 4566666777766665543333332233334445555555444
No 66
>PF02436 PYC_OADA: Conserved carboxylase domain; InterPro: IPR003379 This domain represents a conserved region in pyruvate carboxylase (PYC) (6.4.1.1 from EC), oxaloacetate decarboxylase alpha chain (OADA) (4.1.1.3 from EC), and transcarboxylase 5s subunit (2.1.3.1 from EC). The domain is found adjacent to the HMGL-like domain (IPR000891 from INTERPRO) and often close to the biotin_lipoyl domain (IPR000089 from INTERPRO) of biotin requiring enzymes.; PDB: 2NX9_B 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1S3H_A 1RQE_A 1U5J_A 1RQB_A 2QF7_B ....
Probab=24.75 E-value=1.5e+02 Score=25.76 Aligned_cols=100 Identities=16% Similarity=0.321 Sum_probs=60.5
Q ss_pred CHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH------HHHHHhhhhhhccCC
Q 026481 85 DPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG------IIMNIKMEFDDEIGL 158 (238)
Q Consensus 85 Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG------iL~sLrmeiDDl~Gl 158 (238)
|-++.++..+|....|..+|++|++-++.-+-+ +-..-..|..+.|...-++++.--| -+..+|.++.+..|-
T Consensus 56 ~qA~~nV~~~~~g~r~~~~p~~v~~~~~G~~G~-pp~~~~~~l~~~vl~~~~~i~~RP~~~l~p~d~~~~r~~l~~~~g~ 134 (196)
T PF02436_consen 56 DQAVFNVLNGLLGERYKDFPDSVVDYLLGKYGK-PPGGFPEELRKKVLKGEEPITGRPGDLLPPADLDKLRKELEEKAGR 134 (196)
T ss_dssp HHHHHHHHTT-HHTTTSS-BHHHHHHHTTTT----TTSS-HHHHHHHHTTS---SSSGGGCS----HHHHHHHHHHHCTS
T ss_pred HHHHHHHHhhhcCccccchhHHHHHHhCcccCC-CCCCCCHHHHHHHhcCCCCCCCCccccCChhhHHHHHHHHHHHcCC
Confidence 456666666666778999999999999988877 5555557777777766555544434 467888888888754
Q ss_pred CCCCCcCCchHHHH-HH-HHHHHHHHHHHhhcCC
Q 026481 159 SGENVKPLSNELSS-AI-RTVYQRYATYLDAFGP 190 (238)
Q Consensus 159 sGEnVkPLPd~~~~-Al-~tay~rY~~YLdsFgp 190 (238)
.. -.+++-. |+ =.+|..|.++-..||.
T Consensus 135 ~~-----~dedvlsyal~P~v~~~f~~~~~~~g~ 163 (196)
T PF02436_consen 135 EP-----TDEDVLSYALFPKVAEDFLKFRAKYGD 163 (196)
T ss_dssp TS-----CHHHHHHHHHCHHHHHHHHHHHHHHS-
T ss_pred CC-----CHHHHHHHhcCchhHHHHHHHHHhcCC
Confidence 32 2222211 11 2567888888888885
No 67
>TIGR01086 fucA L-fuculose phosphate aldolase. Members of this family are L-fuculose phosphate aldolase from various Proteobacteria, encoded in fucose utilization operons. Homologs in other bacteria given similar annotation may share extensive sequence similarity but are not experimenally characterized and are not found in apparent fucose utilization operons; we consider their annotation as L-fuculose phosphate aldolase to be tenuous. This model has been narrowed in scope from the previous version.
Probab=24.66 E-value=2.9e+02 Score=23.38 Aligned_cols=44 Identities=16% Similarity=0.124 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVY 178 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay 178 (238)
-++.+|..+|.+|+.--+....+ ..|-+..+||++-..++...|
T Consensus 162 ~l~eA~~~~e~lE~~a~~~~~a~--------~~g~~~~~l~~~~~~~~~~~~ 205 (214)
T TIGR01086 162 NLLKALWLAAEVEVLAAQYLKTL--------LAITDPPPLLSDEMIVVLLKF 205 (214)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--------HcCCCCccCCHHHHHHHHHHH
Confidence 46778888999999877543221 124356889888777664444
No 68
>PF09531 Ndc1_Nup: Nucleoporin protein Ndc1-Nup; InterPro: IPR019049 Ndc1 is a nucleoporin protein that is a component of the Nuclear Pore Complex, and, in fungi, also of the Spindle Pole Body. It consists of six transmembrane segments, three luminal loops, both concentrated at the N terminus and cytoplasmic domains largely at the C terminus, all of which are well conserved.
Probab=24.61 E-value=1.6e+02 Score=28.52 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=22.6
Q ss_pred CCchHHHHHHHHHHH----HHHHHHhhcCCChhHHH
Q 026481 165 PLSNELSSAIRTVYQ----RYATYLDAFGPDESYLR 196 (238)
Q Consensus 165 PLPd~~~~Al~tay~----rY~~YLdsFgpdE~yLr 196 (238)
+.-+.+.+|+++++. .|-.||+.++-+..-+|
T Consensus 564 ~~~~~l~~~l~~~l~~I~~~F~~~L~dl~L~~~~~k 599 (602)
T PF09531_consen 564 PEVSILRDALKSALYRIVTKFGPYLNDLRLSPDVIK 599 (602)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHH
Confidence 444666677766665 58889999887776555
No 69
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=24.27 E-value=93 Score=30.68 Aligned_cols=56 Identities=20% Similarity=0.479 Sum_probs=40.9
Q ss_pred HcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcC
Q 026481 97 AADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKP 165 (238)
Q Consensus 97 A~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkP 165 (238)
..+|+-|||.+....=++|.| |+..+++--|..|+|+=-.=+ +=-...++|.|..|
T Consensus 95 gv~~~slpDEill~IFs~L~k-----------k~LL~~~~VC~Rfyr~~~de~--lW~~lDl~~r~i~p 150 (419)
T KOG2120|consen 95 GVSWDSLPDEILLGIFSCLCK-----------KELLKVSGVCKRFYRLASDES--LWQTLDLTGRNIHP 150 (419)
T ss_pred CCCcccCCHHHHHHHHHhccH-----------HHHHHHHHHHHHHhhcccccc--ceeeeccCCCccCh
Confidence 457999999999999999988 678889999999999532111 11123356766665
No 70
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=24.20 E-value=2e+02 Score=24.02 Aligned_cols=58 Identities=16% Similarity=0.206 Sum_probs=38.3
Q ss_pred HHHhhhhhhccCCCCC--CCcCCchHHHHHHHHHHHHHHHHHhhcCCC---hhHHHHHHHHhhhh
Q 026481 146 MNIKMEFDDEIGLSGE--NVKPLSNELSSAIRTVYQRYATYLDAFGPD---ESYLRKKVETELGS 205 (238)
Q Consensus 146 ~sLrmeiDDl~GlsGE--nVkPLPd~~~~Al~tay~rY~~YLdsFgpd---E~yLrKKVE~ELGt 205 (238)
..+|.+|-|-++---- .|.=+| -...+.+|.+--..+..+|||- =.=+|++|+.||..
T Consensus 78 ~~ar~~in~~vs~YRr~~~v~g~~--Sf~~m~tAln~LaghY~s~g~raPlP~k~k~rll~el~~ 140 (145)
T PF13326_consen 78 AEARELINDYVSRYRRGPSVSGLP--SFTTMYTALNALAGHYSSYGNRAPLPEKLKERLLKELDQ 140 (145)
T ss_dssp HHHHHHHHHHHCCCCCCHHCCTSH--HHHHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCcCCcc--hHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Confidence 3567788888864322 233333 3445667777778888888975 34589999999864
No 71
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=24.19 E-value=57 Score=20.22 Aligned_cols=15 Identities=27% Similarity=0.693 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHhhhh
Q 026481 138 VEEFIGIIMNIKMEF 152 (238)
Q Consensus 138 vEeFgGiL~sLrmei 152 (238)
...++|-|.+||.||
T Consensus 7 lrkY~g~i~~Lr~Ef 21 (22)
T PF03789_consen 7 LRKYSGYISSLRQEF 21 (22)
T ss_pred HHHHhHhHHHHHHHh
Confidence 357899999999987
No 72
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=24.05 E-value=59 Score=23.80 Aligned_cols=16 Identities=25% Similarity=0.775 Sum_probs=14.7
Q ss_pred cCCchHHHHHHHHHHH
Q 026481 164 KPLSNELSSAIRTVYQ 179 (238)
Q Consensus 164 kPLPd~~~~Al~tay~ 179 (238)
+||+|+...|++.+|-
T Consensus 29 rPltdevK~a~k~i~~ 44 (49)
T PF06543_consen 29 RPLTDEVKEAMKLIFG 44 (49)
T ss_pred eeCCHHHHHHHHHHHh
Confidence 7999999999999885
No 73
>PRK13213 araD L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=23.87 E-value=1.6e+02 Score=26.03 Aligned_cols=45 Identities=13% Similarity=0.047 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQ 179 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~ 179 (238)
-|.++|..+|.+|+.--+.-..+. + .| .++|||++..+.+...|+
T Consensus 179 ~l~eA~~~~e~lE~~A~i~~~a~~-----l--~g-~~~~l~~~~~~~~~~~~~ 223 (231)
T PRK13213 179 NAANAVHNAVVLEEIAYMNLFTHQ-----L--TP-GVGDMQQTLLDKHYLRKH 223 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHh-----c--CC-CCCCCCHHHHHHHHHhhc
Confidence 578899999999999987544332 1 24 489999998888765543
No 74
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=23.64 E-value=2.6e+02 Score=21.32 Aligned_cols=57 Identities=14% Similarity=0.131 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCC---CCCcCCchHHHHHHHHHHHHHHHHHhhcC
Q 026481 124 GQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSG---ENVKPLSNELSSAIRTVYQRYATYLDAFG 189 (238)
Q Consensus 124 GqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsG---EnVkPLPd~~~~Al~tay~rY~~YLdsFg 189 (238)
-+++++..-++.++++++|.-. +.-.+| ..-....++..+.+...+++...|++.+|
T Consensus 66 r~~~~~~~~~~i~~a~~lg~~~---------i~~~~g~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~~g 125 (213)
T PF01261_consen 66 REEALEYLKKAIDLAKRLGAKY---------IVVHSGRYPSGPEDDTEENWERLAENLRELAEIAEEYG 125 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHTBSE---------EEEECTTESSSTTSSHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHHHHHHHhCCCc---------eeecCcccccccCCCHHHHHHHHHHHHHHHHhhhhhhc
Confidence 8889999999999999998633 222344 33344455677777778888888888777
No 75
>PF14526 Cass2: Integron-associated effector binding protein; PDB: 3GK6_A.
Probab=23.59 E-value=59 Score=24.50 Aligned_cols=33 Identities=27% Similarity=0.639 Sum_probs=19.3
Q ss_pred cCCchHHHHHHHHHHHHHH----HHHhhcCCC-hhHHH
Q 026481 164 KPLSNELSSAIRTVYQRYA----TYLDAFGPD-ESYLR 196 (238)
Q Consensus 164 kPLPd~~~~Al~tay~rY~----~YLdsFgpd-E~yLr 196 (238)
+|+|+.+.++-..+++... .|-.++||| |.|..
T Consensus 99 G~~~~~i~~~w~~i~~~~~~~~~~~~r~~~~dfE~Y~~ 136 (150)
T PF14526_consen 99 GPYPEAIIEAWQKIWEWFEEENNDYERAYGPDFEVYPE 136 (150)
T ss_dssp SSTTHHHHHHHHHHHHHH--------B--SEEEEE--S
T ss_pred CCChHHHHHHHHHHHHHHHhhCCCceeccCCCeEEEcC
Confidence 7788778787777766664 366679999 99854
No 76
>TIGR03347 VI_chp_1 type VI secretion protein, VC_A0111 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=23.58 E-value=96 Score=27.89 Aligned_cols=21 Identities=29% Similarity=0.423 Sum_probs=16.5
Q ss_pred ccCCCCCCCcCCchHHHHHHHH
Q 026481 155 EIGLSGENVKPLSNELSSAIRT 176 (238)
Q Consensus 155 l~GlsGEnVkPLPd~~~~Al~t 176 (238)
.+||+|-+ +|||.++.+-+..
T Consensus 67 flGL~G~~-gpLP~~ytE~~~~ 87 (300)
T TIGR03347 67 FLGLLGPN-GPLPLHYTELLLE 87 (300)
T ss_pred ecCccCCC-CCCcHHHHHHHHH
Confidence 78999976 9999988655443
No 77
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=23.16 E-value=5e+02 Score=22.53 Aligned_cols=66 Identities=21% Similarity=0.297 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHhhhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHHh--hcCCC
Q 026481 125 QEVLKNVFSAAEAVEEFIG-IIMNIKMEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYLD--AFGPD 191 (238)
Q Consensus 125 qeaL~nvfrAAeAvEeFgG-iL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YLd--sFgpd 191 (238)
.....+++.-|+..+.|-. +...+.--+.++.++.++...+-+..+.++++.| +|+...+. .|++.
T Consensus 79 ~~~t~~t~~~a~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea-~~mL~emr~r~f~~~ 147 (264)
T PF06008_consen 79 NNNTERTLQRAQDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQRALAEA-QRMLEEMRKRDFTPQ 147 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHH-HHHHHHHHhccchhH
Confidence 3556778888888888877 7777777778888888877777778888888887 67777772 37764
No 78
>PRK09614 nrdF ribonucleotide-diphosphate reductase subunit beta; Reviewed
Probab=22.89 E-value=5.5e+02 Score=22.96 Aligned_cols=101 Identities=16% Similarity=0.200 Sum_probs=65.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH--HHHHHhhhhhh
Q 026481 77 VAHMPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG--IIMNIKMEFDD 154 (238)
Q Consensus 77 ~~hlP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG--iL~sLrmeiDD 154 (238)
.-.+=.|++|...+..|...+.-|..-.=.+-+|++.- ++ =++.-|+++++++..=-+.+..-+ ++..+...+.+
T Consensus 11 ~~~~~~~~y~~~~~~y~~~~~~fW~peEi~~s~D~~dw-~~--Lt~~Er~~~~~~l~~~~~~D~~v~~~~~~~~~~~~~~ 87 (324)
T PRK09614 11 AINWNKIEDPWDYEAWKRLTANFWLPEEVPLSNDLKDW-KK--LSDEEKNLYTRVFGGLTLLDTLQNNNGMPNLMPDITT 87 (324)
T ss_pred cccCCCcccHHHHHHHHHHHhCCCCCccccccchHHHH-Hh--CCHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHCCc
Confidence 44556799999999999999999986666677777665 33 233557888888776444444433 12233333332
Q ss_pred ccCCCCCCCcCCch-----HHHHHHHHHHHH-HHHHHhhcCCCh
Q 026481 155 EIGLSGENVKPLSN-----ELSSAIRTVYQR-YATYLDAFGPDE 192 (238)
Q Consensus 155 l~GlsGEnVkPLPd-----~~~~Al~tay~r-Y~~YLdsFgpdE 192 (238)
|+ ..+.+.+.+|.+ |...|+++++++
T Consensus 88 ------------~E~~~~~~~q~~~E~iH~~sYs~il~tl~~~~ 119 (324)
T PRK09614 88 ------------PEEEAVLANIAFMEAVHAKSYSYIFSTLCSPE 119 (324)
T ss_pred ------------HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCh
Confidence 32 134556667755 888899998764
No 79
>PF12887 SICA_alpha: SICA extracellular alpha domain; InterPro: IPR024290 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-alpha domain.
Probab=22.74 E-value=1.3e+02 Score=25.47 Aligned_cols=81 Identities=16% Similarity=0.279 Sum_probs=49.4
Q ss_pred HHHHHHHHhhhhhhccCCCCCCC-cCCchHHHHHHHHHHHHHHHHHhhcCCChhHH-HHH---H----------HHhhhh
Q 026481 141 FIGIIMNIKMEFDDEIGLSGENV-KPLSNELSSAIRTVYQRYATYLDAFGPDESYL-RKK---V----------ETELGS 205 (238)
Q Consensus 141 FgGiL~sLrmeiDDl~GlsGEnV-kPLPd~~~~Al~tay~rY~~YLdsFgpdE~yL-rKK---V----------E~ELGt 205 (238)
|+|.+..=..+.-.--|.+|-++ +-+|+.+.+=|++.|+.-..||+..++.|.-= =.. + ..+|=.
T Consensus 1 ~~~L~~~Wl~~~~~~~~~~~~~~a~~i~~~Lk~~l~~~~~~L~~~l~~~~s~ei~~lC~~~~~~~~~~~~~~~~~K~lCk 80 (184)
T PF12887_consen 1 FTGLLQEWLQKLLKNGGTTGTGGAKEITEKLKKDLEEMFDELKSWLDRQESNEIANLCADGKLVWGGGGGKTDYMKNLCK 80 (184)
T ss_pred CcHHHHHHHHHHHhccCCCCCCchhHHHHHHHHHHHHHHHHHHHHHcccCchHHHHHhcCCCCCCCCCCCCcchHHHHhH
Confidence 34444444444433445666555 77899999999999999999999555544210 000 0 123445
Q ss_pred hhhhhhhhhcCCCCCc
Q 026481 206 KMIFLKMRCAGLGSEW 221 (238)
Q Consensus 206 kmI~LKmRcsGlgseW 221 (238)
-++.++.--+||...-
T Consensus 81 ~ivei~Yfm~Gl~~~~ 96 (184)
T PF12887_consen 81 AIVEIRYFMSGLKTKG 96 (184)
T ss_pred HHHHHHHHHhCCcccC
Confidence 5677777777776543
No 80
>PLN02466 aldehyde dehydrogenase family 2 member
Probab=22.10 E-value=5e+02 Score=25.33 Aligned_cols=49 Identities=24% Similarity=0.376 Sum_probs=31.4
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHc----ccCCCchh----HHHHHHhhhcccCCchh
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAA----DWGELPAS----VIHDAKSALSRNNDDKA 123 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~----sW~elp~s----vv~~ak~alSk~tdDkA 123 (238)
+-+.++|.....|+.+|++..-++ .|..+|.. ++..+...|.++.|+.+
T Consensus 84 ~~i~~v~~~~~~dv~~Av~aA~~a~~~~~w~~~~~~~R~~~L~~~a~~l~~~~~ela 140 (538)
T PLN02466 84 EVIAHVAEGDAEDVNRAVAAARKAFDEGPWPKMTAYERSRILLRFADLLEKHNDELA 140 (538)
T ss_pred CEEEEEeCCCHHHHHHHHHHHHHHcCcCccccCCHHHHHHHHHHHHHHHHHhHHHHH
Confidence 445677888888888888876665 48877754 34444455555555444
No 81
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.06 E-value=1.2e+02 Score=27.12 Aligned_cols=39 Identities=23% Similarity=0.232 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhh
Q 026481 168 NELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSK 206 (238)
Q Consensus 168 d~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtk 206 (238)
+.+++++..++++--.==..+--|+.|||-+||.||..-
T Consensus 31 ~~v~~~a~~~ls~lk~~~~~~k~dp~~l~~~v~~~l~p~ 69 (202)
T COG2854 31 SLVQEAADKVLSILKNNQAKIKQDPQYLRQIVDQELLPY 69 (202)
T ss_pred HHHHHHHHHHHHHHhccchhhccCHHHHHHHHHHHhhhh
Confidence 456778888888776666677889999999999999864
No 82
>TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase. Members of this family are the enzyme RhaD, rhamnulose-1-phosphate aldolase.
Probab=21.99 E-value=2.6e+02 Score=25.12 Aligned_cols=42 Identities=19% Similarity=0.243 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHH
Q 026481 127 VLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRT 176 (238)
Q Consensus 127 aL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~t 176 (238)
-++.+|..+|.+|+.--+....+. .|..+.+||++..+.+..
T Consensus 218 ~l~eA~~~~E~lE~~A~i~~~a~~--------lg~~~~~L~~e~l~~~~~ 259 (270)
T TIGR02624 218 SLDETFGLIETAEKSAEVYTKVYS--------QGGVKQTISDEQLIALAK 259 (270)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHh--------cCCCCCCCCHHHHHHHHH
Confidence 378899999999998887654432 255578899988777644
No 83
>PF05664 DUF810: Protein of unknown function (DUF810); InterPro: IPR008528 This family consists of several plant proteins of unknown function.
Probab=21.69 E-value=1e+02 Score=31.69 Aligned_cols=46 Identities=20% Similarity=0.256 Sum_probs=31.0
Q ss_pred hhhhhccCCCCCCCcCCchHHHHHHHHHHHHHHHHH-hhcCCChhHH
Q 026481 150 MEFDDEIGLSGENVKPLSNELSSAIRTVYQRYATYL-DAFGPDESYL 195 (238)
Q Consensus 150 meiDDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YL-dsFgpdE~yL 195 (238)
.-+|.+.+|...+---+-..+.+.|..+++||...+ +++|..+.|+
T Consensus 567 eTvd~ff~L~~~~~~~~l~~L~~gld~~lq~Y~~~v~~~~gsk~~li 613 (677)
T PF05664_consen 567 ETVDQFFQLPWPMHADFLQALSKGLDKALQRYCEKVEQSCGSKQSLI 613 (677)
T ss_pred HHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhcccccccC
Confidence 345666666432211122356678899999999999 9999888764
No 84
>cd00398 Aldolase_II Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
Probab=21.11 E-value=2.6e+02 Score=23.25 Aligned_cols=44 Identities=25% Similarity=0.268 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCCcCCchHHHHHHHH
Q 026481 124 GQEVLKNVFSAAEAVEEFIGIIMNIKMEFDDEIGLSGENVKPLSNELSSAIRT 176 (238)
Q Consensus 124 GqeaL~nvfrAAeAvEeFgGiL~sLrmeiDDl~GlsGEnVkPLPd~~~~Al~t 176 (238)
|+. +..+|..+|.+|+.--+....+. .|..+.+||++..+.+..
T Consensus 163 G~~-~~~A~~~~~~lE~~a~~~~~a~~--------~g~~~~~l~~~~~~~~~~ 206 (209)
T cd00398 163 GPT-LDEAFHLAVVLEVAAEIQLKALS--------MGGQLPPISLELLNKEYL 206 (209)
T ss_pred cCC-HHHHHHHHHHHHHHHHHHHHHHh--------cCCCCCCCCHHHHHHHHh
Confidence 553 67889999999998876544432 267788999988777654
No 85
>KOG0034 consensus Ca2+/calmodulin-dependent protein phosphatase (calcineurin subunit B), EF-Hand superfamily protein [Signal transduction mechanisms]
Probab=21.06 E-value=89 Score=26.97 Aligned_cols=49 Identities=8% Similarity=0.166 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHH
Q 026481 82 VIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKN 130 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~n 130 (238)
-|+-.|++..++.+...+|++..+.+...+.+.+.+..-|+-|+=-+..
T Consensus 120 ~I~reel~~iv~~~~~~~~~~~~e~~~~i~d~t~~e~D~d~DG~IsfeE 168 (187)
T KOG0034|consen 120 FISREELKQILRMMVGENDDMSDEQLEDIVDKTFEEADTDGDGKISFEE 168 (187)
T ss_pred cCcHHHHHHHHHHHHccCCcchHHHHHHHHHHHHHHhCCCCCCcCcHHH
Confidence 3888999999999999999998888889999999998888888754443
No 86
>TIGR01408 Ube1 ubiquitin-activating enzyme E1. This model represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (pfam00899), a repeat found in ubiquitin-activating proteins (pfam02134), and other regions.
Probab=21.02 E-value=3e+02 Score=29.54 Aligned_cols=45 Identities=9% Similarity=0.006 Sum_probs=23.2
Q ss_pred hHHHHHHhhhcccC--CchhHHHHHHHHHHHH-----HHHHHHHHH-HHHHhh
Q 026481 106 SVIHDAKSALSRNN--DDKAGQEVLKNVFSAA-----EAVEEFIGI-IMNIKM 150 (238)
Q Consensus 106 svv~~ak~alSk~t--dDkAGqeaL~nvfrAA-----eAvEeFgGi-L~sLrm 150 (238)
.++..++...++.. .+....+.++++.+-| --+--+||+ -+++-+
T Consensus 311 ~~~~~a~~i~~~~~~~~~~lde~li~~~~~~~~geisPv~Ai~GGi~aQEViK 363 (1008)
T TIGR01408 311 ELLKLATSISETLEEKVPDVDAKLVHWLSWTAQGFLSPMAAAVGGVVSQEVLK 363 (1008)
T ss_pred HHHHHHHHHHHhcCCCcccCCHHHHHHHHHhccccccHHHHHhchHHHHHHHH
Confidence 34444544433221 1335567788776543 445667884 344444
No 87
>PTZ00226 fumarate hydratase; Provisional
Probab=20.76 E-value=2.2e+02 Score=29.17 Aligned_cols=65 Identities=8% Similarity=-0.015 Sum_probs=51.4
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHH
Q 026481 76 DVAHMPVIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEE 140 (238)
Q Consensus 76 d~~hlP~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEe 140 (238)
+-..|-.|.-.+|..+.++++..-=..||+.+.+..++++........++.+|.+..+-|+..++
T Consensus 64 ~~~~m~~v~~e~l~~~~~~a~~~a~~~Lp~D~~~aL~~a~~d~E~s~~~k~vl~~iL~Na~iA~~ 128 (570)
T PTZ00226 64 GGKEILKVPPEALTKLTSYAFSDIQHFLRKSHLAQLRRILDDPEASDNDRFVAMTLLKNACIAAG 128 (570)
T ss_pred CCceeeeecHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHhCccCCHHHHHHHHHHHHHHHHHhc
Confidence 34556666534488899999988889999999999999998656666688888888888877665
No 88
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes.
Probab=20.72 E-value=97 Score=32.45 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=24.1
Q ss_pred CCchHHHHHHHH-------HHHHHHHHHhhcCC
Q 026481 165 PLSNELSSAIRT-------VYQRYATYLDAFGP 190 (238)
Q Consensus 165 PLPd~~~~Al~t-------ay~rY~~YLdsFgp 190 (238)
+|||.+.++|.+ +|+.|..++.+||.
T Consensus 109 glnd~~~~~l~~~~g~~~fa~d~yrRfi~~~g~ 141 (856)
T TIGR01828 109 GLNDETVEGLAKLTGNARFAYDSYRRFIQMFGD 141 (856)
T ss_pred CCCHHHHHHHHHhhCChHHHHHHHHHHHhhhcc
Confidence 699999999988 99999999999994
No 89
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=20.67 E-value=8.4e+02 Score=24.23 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=36.9
Q ss_pred cCCchHHHHHHHHHHHHHHHHHhhcCCChhHHHHHHHHhhhhhhhh-hhhhhc
Q 026481 164 KPLSNELSSAIRTVYQRYATYLDAFGPDESYLRKKVETELGSKMIF-LKMRCA 215 (238)
Q Consensus 164 kPLPd~~~~Al~tay~rY~~YLdsFgpdE~yLrKKVE~ELGtkmI~-LKmRcs 215 (238)
.+|+.+-.+.++.+-+++...|+ +.|..-++++. .||...+-+ |+.||.
T Consensus 530 ~~l~~~~~~~i~~~~~~~~~~l~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 579 (595)
T PRK01433 530 TLLSESEISIINSLLDNIKEAVH--ARDIILINNSI-KEFKSKIKKSMDTKLN 579 (595)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHh--cCCHHHHHHHH-HHHHHHHHHHHHHHhh
Confidence 35777888889999999999998 45666665554 467778877 888884
No 90
>cd07118 ALDH_SNDH Gluconobacter oxydans L-sorbosone dehydrogenase-like. Included in this CD is the L-sorbosone dehydrogenase (SNDH) from Gluconobacter oxydans UV10. In G. oxydans, D-sorbitol is converted to 2-keto-L-gulonate (a precursor of L-ascorbic acid) in sequential oxidation steps catalyzed by a FAD-dependent, L-sorbose dehydrogenase and an NAD(P)+-dependent, L-sorbosone dehydrogenase.
Probab=20.66 E-value=2e+02 Score=26.83 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=36.2
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHc----ccCCCchh----HHHHHHhhhcccCCchhH
Q 026481 75 EDVAHMPVIRDPEIQRAFKDLMAA----DWGELPAS----VIHDAKSALSRNNDDKAG 124 (238)
Q Consensus 75 ~d~~hlP~i~Dpei~~afKdLmA~----sW~elp~s----vv~~ak~alSk~tdDkAG 124 (238)
+-+.+.|..+..||..|++..-++ .|..+|-. ++..+...|.++.|+.+-
T Consensus 8 ~~i~~~~~~~~~~v~~av~~A~~a~~~~~w~~~~~~~R~~~l~~~a~~l~~~~~~la~ 65 (454)
T cd07118 8 VVVARYAEGTVEDVDAAVAAARKAFDKGPWPRMSGAERAAVLLKVADLIRARRERLAL 65 (454)
T ss_pred CEEEEEeCCCHHHHHHHHHHHHHHcCCCccccCCHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 345678888889999999888766 39888864 456666777776666553
No 91
>PTZ00433 tyrosine aminotransferase; Provisional
Probab=20.55 E-value=89 Score=28.03 Aligned_cols=86 Identities=14% Similarity=0.077 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHHHHhh--hhhhccCCCCCCCc-----CCchHHHHHHHHHHHH--HHHHHhhcCCChhHHHHHHHHhh
Q 026481 133 SAAEAVEEFIGIIMNIKM--EFDDEIGLSGENVK-----PLSNELSSAIRTVYQR--YATYLDAFGPDESYLRKKVETEL 203 (238)
Q Consensus 133 rAAeAvEeFgGiL~sLrm--eiDDl~GlsGEnVk-----PLPd~~~~Al~tay~r--Y~~YLdsFgpdE~yLrKKVE~EL 203 (238)
|++..-.++-.++.+++. .-.|++-++.-+.. +.|+.+.+|+..+.++ ...|-+..|- .-||+.+=.-+
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~g~p~~~~~~~p~~~~~~a~~~~~~~~~~~~Y~~~~G~--~~Lr~aia~~~ 88 (412)
T PTZ00433 11 HAGRVFNPLRTVTDNAKPSPSPKSIIKLSVGDPTLDGNLLTPAIQTKALVEAVDSQECNGYPPTVGS--PEAREAVATYW 88 (412)
T ss_pred HHHhhhccHHHHHHhhccCCCCCCeeecCCcCCCCcCCCCCCHHHHHHHHHHhhcCCCCCCCCCCCc--HHHHHHHHHHH
Confidence 444455556666666653 33344555433332 3588899999887765 2334444343 34899988888
Q ss_pred hhhhhhhhhhhcCCCCC
Q 026481 204 GSKMIFLKMRCAGLGSE 220 (238)
Q Consensus 204 GtkmI~LKmRcsGlgse 220 (238)
+..+.+-+.|-..++++
T Consensus 89 ~~~~~~~~~~~~~~~~~ 105 (412)
T PTZ00433 89 RNSFVHKESLKSTIKKD 105 (412)
T ss_pred HhhccccccccCCCChh
Confidence 87655433332233443
No 92
>COG3562 KpsS Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]
Probab=20.46 E-value=44 Score=32.81 Aligned_cols=33 Identities=15% Similarity=0.292 Sum_probs=24.1
Q ss_pred HHHHHHhhhhhhhhh---------hhhhcCCCCCcceeEEeeccccccc
Q 026481 196 RKKVETELGSKMIFL---------KMRCAGLGSEWGKVFYYGCQCHCGI 235 (238)
Q Consensus 196 rKKVE~ELGtkmI~L---------KmRcsGlgseWGKVtllGTSg~sGs 235 (238)
|++++-|+++..+++ .|=| |-|||=+|||||+-
T Consensus 293 ~~~~q~~v~~RvlYvhd~~lpvllr~a~-------GmVTvNsTsGlsal 334 (403)
T COG3562 293 RRFVQYEVKGRVLYVHDVPLPVLLRHAL-------GMVTVNSTSGLSAL 334 (403)
T ss_pred HHHHHhccCceEEEecCCCchHHHHhcc-------ceEEEccccchHHH
Confidence 456777777777665 3333 67999999999974
No 93
>PRK13967 nrdF1 ribonucleotide-diphosphate reductase subunit beta; Provisional
Probab=20.43 E-value=4e+02 Score=24.28 Aligned_cols=95 Identities=12% Similarity=0.129 Sum_probs=47.4
Q ss_pred CCCCHHHHHHHHHHHHcccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH-HHH-HHhhhhhhccCCC
Q 026481 82 VIRDPEIQRAFKDLMAADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG-IIM-NIKMEFDDEIGLS 159 (238)
Q Consensus 82 ~i~Dpei~~afKdLmA~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG-iL~-sLrmeiDDl~Gls 159 (238)
.++|+--++.++.+.+.-|..=.=.+-+|++.- .+-|| .-|++++.++..--+.+..=+ .+. .+...+
T Consensus 16 ~~~~~~~~~~~~~~~~~fW~peEI~ls~D~~dw-~~Lt~--~Er~~i~~~l~~lt~lDs~q~~~~~~~~~~~~------- 85 (322)
T PRK13967 16 RLLDAKDLQVWERLTGNFWLPEKIPLSNDLASW-QTLSS--TEQQTTIRVFTGLTLLDTAQATVGAVAMIDDA------- 85 (322)
T ss_pred CccchhhHHHHHHHHhCCCCccccCchhhHHHH-HhCCH--HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHhc-------
Confidence 456677777777777777753333344555433 12222 346677777654322221111 000 111111
Q ss_pred CCCCcCCchH-----HHHHHHHHHHH-HHHHHhhcCCC
Q 026481 160 GENVKPLSNE-----LSSAIRTVYQR-YATYLDAFGPD 191 (238)
Q Consensus 160 GEnVkPLPd~-----~~~Al~tay~r-Y~~YLdsFgpd 191 (238)
+-|+. .+-+.+++|.+ |.-.|++++++
T Consensus 86 -----~~~e~~~~l~~~~~~E~iHs~sYs~il~tl~~~ 118 (322)
T PRK13967 86 -----VTPHEEAVLTNMAFMESVHAKSYSSIFSTLCST 118 (322)
T ss_pred -----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 22332 23445666665 77888999863
No 94
>PF06470 SMC_hinge: SMC proteins Flexible Hinge Domain; InterPro: IPR010935 This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction [].; GO: 0005515 protein binding, 0005524 ATP binding, 0051276 chromosome organization, 0005694 chromosome; PDB: 2WD5_A 1GXL_C 1GXK_A 1GXJ_A 3NWC_B 3L51_A.
Probab=20.39 E-value=23 Score=25.93 Aligned_cols=32 Identities=6% Similarity=0.092 Sum_probs=26.8
Q ss_pred hhccCCCCCCCcCCchHHHHHHHHHHHHHHHHH
Q 026481 153 DDEIGLSGENVKPLSNELSSAIRTVYQRYATYL 185 (238)
Q Consensus 153 DDl~GlsGEnVkPLPd~~~~Al~tay~rY~~YL 185 (238)
++..|.-++.+.+ ++.++.||+++...|..++
T Consensus 2 ~gv~G~l~dli~v-~~~~~~Ave~~LG~~l~~i 33 (120)
T PF06470_consen 2 PGVLGRLADLIEV-DPKYEKAVEAALGGRLQAI 33 (120)
T ss_dssp TTEEEEGGGSEEE-SGGGHHHHHHHHGGGGGSE
T ss_pred CCeeeeHHhceec-CHHHHHHHHHHHHHhhceE
Confidence 4677888999999 9999999999988766654
No 95
>PF05480 Staph_haemo: Staphylococcus haemolytic protein; InterPro: IPR008846 This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus []. Gonococcal growth inhibitor from Staphylococcus acts on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death [].; GO: 0009405 pathogenesis
Probab=20.36 E-value=74 Score=22.59 Aligned_cols=29 Identities=17% Similarity=0.402 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHcccCCCchhHHHHHHhhh
Q 026481 87 EIQRAFKDLMAADWGELPASVIHDAKSAL 115 (238)
Q Consensus 87 ei~~afKdLmA~sW~elp~svv~~ak~al 115 (238)
.|.++.+.=...+|.+|--|.++.+.+.+
T Consensus 7 AI~n~V~Ag~~~Dwa~lgtsIv~iv~ngv 35 (43)
T PF05480_consen 7 AIKNTVQAGQNQDWAKLGTSIVDIVENGV 35 (43)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence 56777788888999999999999988754
No 96
>TIGR03582 EF_0829 PRD domain protein EF_0829/AHA_3910. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. This protein contains a PRD domain (see pfam00874). The function is unknown.
Probab=20.31 E-value=1.7e+02 Score=23.69 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=28.5
Q ss_pred CCCCCCcCCchHHHHHH----HHHHHHHHHHHhhcCCChhHH
Q 026481 158 LSGENVKPLSNELSSAI----RTVYQRYATYLDAFGPDESYL 195 (238)
Q Consensus 158 lsGEnVkPLPd~~~~Al----~tay~rY~~YLdsFgpdE~yL 195 (238)
.+||.+.|+.+++-+=| ....+.-.+++..+-|+|.||
T Consensus 55 ~~GE~lp~vD~~Lf~EIs~~sl~la~~v~~~f~~L~~~E~~l 96 (107)
T TIGR03582 55 TTGETLPEVDRSLFDEISKESIKLAEEVVAALGNLAEDEAYL 96 (107)
T ss_pred HcCCcCCccCHHHHHHHHHHHHHHHHHHHHHhcCCChhhHHH
Confidence 48999999998776554 345566666777788889887
No 97
>PF03810 IBN_N: Importin-beta N-terminal domain; InterPro: IPR001494 Karyopherins are a group of proteins involved in transporting molecules through the pores of the nuclear envelope. Karyopherins, which may act as importins or exportins, are part of the Importin-beta super-family, which all share a similar three-dimensional structure. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well. This entry represents the N-terminal domain of karyopherins that is important for the binding of the Ran protein []. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport; PDB: 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 1IBR_D 1QGR_A 3LWW_A 1F59_A 2Q5D_A ....
Probab=20.20 E-value=1.1e+02 Score=20.69 Aligned_cols=25 Identities=32% Similarity=0.639 Sum_probs=21.6
Q ss_pred HHHHHHHcccC--------CCchhHHHHHHhhh
Q 026481 91 AFKDLMAADWG--------ELPASVIHDAKSAL 115 (238)
Q Consensus 91 afKdLmA~sW~--------elp~svv~~ak~al 115 (238)
.||.....+|+ .+|+..-..+|..|
T Consensus 39 ~LKn~I~~~W~~~~~~~~~~~~~~~k~~Ik~~l 71 (77)
T PF03810_consen 39 LLKNLIKKNWSPSKQKGWSQLPEEEKEQIKSQL 71 (77)
T ss_dssp HHHHHHHHSGGHHHHHHHHGSSHHHHHHHHHHH
T ss_pred HHHHHHHHcCchhhccCCCCCCHHHHHHHHHHH
Confidence 58999999999 89999888888765
No 98
>PLN02926 histidinol dehydrogenase
Probab=20.12 E-value=4.9e+02 Score=25.80 Aligned_cols=88 Identities=19% Similarity=0.128 Sum_probs=49.7
Q ss_pred cccCCCchhHHHHHHhhhcccCCchhHHHHHHHHHHHHHHHHHHHH-HHHHHhhhhhhc----cCCCCC--CCcCCchHH
Q 026481 98 ADWGELPASVIHDAKSALSRNNDDKAGQEVLKNVFSAAEAVEEFIG-IIMNIKMEFDDE----IGLSGE--NVKPLSNEL 170 (238)
Q Consensus 98 ~sW~elp~svv~~ak~alSk~tdDkAGqeaL~nvfrAAeAvEeFgG-iL~sLrmeiDDl----~GlsGE--nVkPLPd~~ 170 (238)
.+|++++.+- .+..+.+...+ -.++.+.|-..-+.|.+-|- -|..+-..+|.. +-++.| -..-||.++
T Consensus 6 ~~~~~~~~~~---~~~~~~r~~~~--~~~~~~~V~~Il~~Vr~~GD~Al~~yt~~fD~~~~~~l~v~~~e~A~~~l~~~~ 80 (431)
T PLN02926 6 YRLSELSASE---VDSLKARPRID--FSSILETVNPIVENVRSRGDAAVKEYTSKFDKVALDSVVERVSDLPDPVLDADV 80 (431)
T ss_pred eecccCCHHH---HHHHhcCCCcc--hhhHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCCcccceeCHHHHHHhcCCHHH
Confidence 3677777654 33335554322 33355555555555555554 444444555522 011112 234479999
Q ss_pred HHHHHHHHHHHHHHHhhcCC
Q 026481 171 SSAIRTVYQRYATYLDAFGP 190 (238)
Q Consensus 171 ~~Al~tay~rY~~YLdsFgp 190 (238)
.+||+.+++|-.+|=..-=|
T Consensus 81 ~~ai~~A~~nI~~fh~~q~~ 100 (431)
T PLN02926 81 KEAFDVAYDNIYAFHLAQKS 100 (431)
T ss_pred HHHHHHHHHHHHHHHHHhCC
Confidence 99999999998888665444
No 99
>COG2361 Uncharacterized conserved protein [Function unknown]
Probab=20.04 E-value=1.1e+02 Score=25.58 Aligned_cols=49 Identities=20% Similarity=0.334 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHHhhh---hhh---ccCCCCCCCcCCchHHHH
Q 026481 124 GQEVLKNVFSAAEAVEEFIG--IIMNIKME---FDD---EIGLSGENVKPLSNELSS 172 (238)
Q Consensus 124 GqeaL~nvfrAAeAvEeFgG--iL~sLrme---iDD---l~GlsGEnVkPLPd~~~~ 172 (238)
-+.-|.+.+.|||.+++|=+ ...++.+. .|= -+=+-||.+|-||+++.+
T Consensus 6 ~~~yL~diL~a~~~i~~yT~~~d~~~F~~~~~~~dAvir~L~iIGEa~k~ip~~~re 62 (117)
T COG2361 6 DRVYLYDILQAAERIEEYTKDMDYEEFIADKLTQDAVIRNLEIIGEATKRIPKSFRE 62 (117)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCHHHHHHhHHHHHHHHHHHHHHHHHHhhcCHHHHH
Confidence 46678999999999999876 22222110 000 123569999999998874
No 100
>cd07957 Anticodon_Ia_Met Anticodon-binding domain of methionyl tRNA synthetases. This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA.
Probab=20.01 E-value=3.5e+02 Score=19.49 Aligned_cols=31 Identities=10% Similarity=0.142 Sum_probs=25.3
Q ss_pred CcCCchHHHHHHHHHHHHHHHHHhhcCCChh
Q 026481 163 VKPLSNELSSAIRTVYQRYATYLDAFGPDES 193 (238)
Q Consensus 163 VkPLPd~~~~Al~tay~rY~~YLdsFgpdE~ 193 (238)
..++...+.+.+...+++|.++++.|...+.
T Consensus 34 ~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a 64 (129)
T cd07957 34 LTEEDEELLEEAEELLEEVAEAMEELEFRKA 64 (129)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHhccHHHH
Confidence 5567788888889999999999998877653
No 101
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=20.01 E-value=2.7e+02 Score=20.89 Aligned_cols=44 Identities=16% Similarity=0.156 Sum_probs=27.1
Q ss_pred HHH-HHHHHHhhhhhhccCCCC----CCCcCCchHHHHHHHHHHHHHHH
Q 026481 140 EFI-GIIMNIKMEFDDEIGLSG----ENVKPLSNELSSAIRTVYQRYAT 183 (238)
Q Consensus 140 eFg-GiL~sLrmeiDDl~GlsG----EnVkPLPd~~~~Al~tay~rY~~ 183 (238)
..| |-..++...|++...--+ +..-+||+.+..++..+..+...
T Consensus 28 ~lG~GS~~ti~~~l~~w~~~~~~~~~~~~~~lP~~l~~~~~~~~~~~~~ 76 (120)
T PF11740_consen 28 RLGGGSMSTISKHLKEWREEREAQVSEAAPDLPEALQDALAELMARLWE 76 (120)
T ss_pred HHCCCCHHHHHHHHHHHHHhhhccccccccCCChhHHHHHHHHHHHHHH
Confidence 344 655666555555433222 45578999998777777766544
Done!