Query 026382
Match_columns 239
No_of_seqs 175 out of 452
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:18:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026382.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026382hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2768 Translation initiation 100.0 1.5E-54 3.2E-59 380.1 11.1 176 51-230 17-192 (231)
2 PRK03988 translation initiatio 100.0 1.9E-42 4.1E-47 287.0 12.9 113 115-233 4-116 (138)
3 TIGR00311 aIF-2beta translatio 100.0 9.7E-42 2.1E-46 281.2 12.6 111 117-233 1-111 (133)
4 PRK12336 translation initiatio 100.0 6.9E-40 1.5E-44 285.2 12.6 112 116-233 1-112 (201)
5 smart00653 eIF2B_5 domain pres 100.0 7.9E-38 1.7E-42 250.7 11.1 93 141-233 2-94 (110)
6 PF01873 eIF-5_eIF-2B: Domain 100.0 4.9E-38 1.1E-42 256.7 9.8 101 131-231 4-105 (125)
7 COG1601 GCD7 Translation initi 100.0 1.4E-32 3.1E-37 231.1 9.0 114 113-231 3-117 (151)
8 KOG2767 Translation initiation 99.9 3.5E-26 7.5E-31 213.0 4.9 95 139-233 12-110 (400)
9 PF01253 SUI1: Translation ini 94.3 0.13 2.9E-06 38.9 5.7 57 156-216 19-79 (83)
10 PRK00939 translation initiatio 90.9 0.39 8.4E-06 38.2 4.2 51 153-208 35-85 (99)
11 cd00474 SUI1_eIF1 The SUI1/eIF 90.2 0.51 1.1E-05 35.8 4.2 53 154-211 12-64 (77)
12 TIGR01158 SUI1_rel translation 88.2 0.95 2.1E-05 36.0 4.6 52 152-208 35-86 (101)
13 TIGR01159 DRP1 density-regulat 86.3 2 4.3E-05 37.5 5.9 56 156-215 103-162 (173)
14 COG0023 SUI1 Translation initi 82.5 3.6 7.7E-05 33.3 5.4 58 151-213 36-93 (104)
15 cd04762 HTH_MerR-trunc Helix-T 78.4 6.8 0.00015 24.8 4.8 46 162-212 2-47 (49)
16 TIGR01160 SUI1_MOF2 translatio 76.4 4 8.7E-05 33.2 4.0 60 151-215 34-98 (110)
17 PRK07451 translation initiatio 70.3 6.3 0.00014 32.4 3.8 51 154-209 51-101 (115)
18 PRK09019 translation initiatio 70.3 8.2 0.00018 31.4 4.4 52 154-210 44-95 (108)
19 PF04760 IF2_N: Translation in 66.7 5.9 0.00013 27.3 2.6 27 162-188 5-31 (54)
20 COG1163 DRG Predicted GTPase [ 65.6 4.6 0.0001 39.0 2.4 54 113-175 272-328 (365)
21 PRK06824 translation initiatio 64.8 13 0.00029 30.6 4.7 53 153-210 53-105 (118)
22 TIGR03826 YvyF flagellar opero 61.4 12 0.00026 31.6 3.8 48 161-232 47-94 (137)
23 PF00165 HTH_AraC: Bacterial r 53.6 20 0.00044 23.1 3.2 28 161-188 9-36 (42)
24 cd04761 HTH_MerR-SF Helix-Turn 53.2 34 0.00074 22.0 4.3 45 162-211 2-46 (49)
25 PF13936 HTH_38: Helix-turn-he 49.8 17 0.00038 24.2 2.5 22 161-182 21-42 (44)
26 PF08535 KorB: KorB domain; I 47.8 16 0.00036 27.7 2.4 39 163-205 6-44 (93)
27 PF06322 Phage_NinH: Phage Nin 42.8 36 0.00079 25.4 3.4 37 161-204 17-53 (64)
28 PF02591 DUF164: Putative zinc 42.5 15 0.00033 25.6 1.4 26 202-229 31-56 (56)
29 KOG2768 Translation initiation 42.4 9.3 0.0002 34.9 0.3 23 14-36 20-42 (231)
30 COG5631 Predicted transcriptio 40.9 25 0.00055 31.1 2.7 72 117-193 53-131 (199)
31 COG3741 HutG N-formylglutamate 40.1 4.5 9.8E-05 37.8 -2.1 66 157-222 64-132 (272)
32 smart00497 IENR1 Intron encode 38.4 86 0.0019 20.6 4.6 31 153-183 10-40 (53)
33 smart00422 HTH_MERR helix_turn 37.2 79 0.0017 21.8 4.4 46 162-211 2-47 (70)
34 PF12677 DUF3797: Domain of un 36.8 18 0.00038 25.8 0.9 13 216-228 10-22 (49)
35 PF08209 Sgf11: Sgf11 (transcr 35.2 15 0.00032 24.0 0.3 15 218-232 3-17 (33)
36 PRK01310 hypothetical protein; 34.7 91 0.002 25.0 4.9 40 175-216 55-102 (104)
37 PF05379 Peptidase_C23: Carlav 33.8 43 0.00094 26.0 2.8 25 163-187 7-31 (89)
38 smart00342 HTH_ARAC helix_turn 33.6 62 0.0013 22.2 3.4 28 161-188 51-79 (84)
39 TIGR01764 excise DNA binding d 33.0 1.3E+02 0.0027 18.9 4.9 47 160-212 1-47 (49)
40 PF09337 zf-H2C2: His(2)-Cys(2 33.0 25 0.00055 23.4 1.2 14 213-226 25-39 (39)
41 COG1579 Zn-ribbon protein, pos 32.7 43 0.00093 30.7 3.0 54 173-231 172-233 (239)
42 PRK10219 DNA-binding transcrip 32.7 59 0.0013 24.7 3.4 27 162-188 23-49 (107)
43 cd01106 HTH_TipAL-Mta Helix-Tu 31.8 98 0.0021 23.7 4.5 46 162-211 2-47 (103)
44 TIGR01371 met_syn_B12ind 5-met 29.8 82 0.0018 33.1 4.8 99 117-231 609-729 (750)
45 PF12728 HTH_17: Helix-turn-he 28.8 1.5E+02 0.0032 19.5 4.5 24 161-184 2-25 (51)
46 cd01279 HTH_HspR-like Helix-Tu 28.6 1.1E+02 0.0024 23.5 4.3 45 162-211 3-47 (98)
47 PRK11511 DNA-binding transcrip 28.1 74 0.0016 25.4 3.3 28 161-188 26-53 (127)
48 TIGR01464 hemE uroporphyrinoge 27.5 41 0.00089 31.0 2.0 53 173-230 265-323 (338)
49 PF02406 MmoB_DmpM: MmoB/DmpM 27.2 2E+02 0.0043 22.4 5.5 68 125-199 17-85 (87)
50 cd02983 P5_C P5 family, C-term 26.2 95 0.0021 25.2 3.7 43 176-218 70-117 (130)
51 cd01896 DRG The developmentall 26.1 90 0.002 27.4 3.8 94 120-227 92-188 (233)
52 smart00504 Ubox Modified RING 25.4 70 0.0015 21.8 2.4 21 211-231 27-47 (63)
53 PRK13501 transcriptional activ 25.4 78 0.0017 28.1 3.3 28 161-188 193-220 (290)
54 cd01104 HTH_MlrA-CarA Helix-Tu 23.9 2.4E+02 0.0052 19.3 5.0 45 162-211 2-47 (68)
55 PRK02048 4-hydroxy-3-methylbut 23.3 32 0.00069 35.6 0.5 53 177-230 465-529 (611)
56 smart00342 HTH_ARAC helix_turn 23.3 1.2E+02 0.0026 20.6 3.4 27 162-188 3-29 (84)
57 TIGR01463 mtaA_cmuA methyltran 23.3 44 0.00095 30.7 1.4 39 188-229 281-321 (340)
58 PLN02433 uroporphyrinogen deca 22.6 64 0.0014 30.1 2.3 54 173-231 264-322 (345)
59 cd04763 HTH_MlrA-like Helix-Tu 22.5 2.3E+02 0.005 19.8 4.7 46 162-212 2-48 (68)
60 PF13384 HTH_23: Homeodomain-l 22.1 84 0.0018 20.6 2.2 27 162-188 19-47 (50)
61 PF04423 Rad50_zn_hook: Rad50 21.9 58 0.0013 22.5 1.5 21 210-230 7-31 (54)
62 TIGR02609 doc_partner putative 21.8 3.3E+02 0.0072 20.0 5.9 46 174-219 15-65 (74)
63 KOG3239 Density-regulated prot 21.2 1.7E+02 0.0038 26.1 4.5 54 158-215 117-174 (193)
64 PF05042 Caleosin: Caleosin re 21.2 70 0.0015 28.2 2.1 25 187-217 83-107 (174)
65 cd00592 HTH_MerR-like Helix-Tu 21.0 1.8E+02 0.0039 21.8 4.2 45 162-211 2-46 (100)
66 smart00717 SANT SANT SWI3, AD 20.9 1.4E+02 0.0031 18.3 3.1 24 161-184 22-46 (49)
67 KOG1603 Copper chaperone [Inor 20.9 2.3E+02 0.005 20.5 4.6 40 175-214 20-61 (73)
68 PF11242 DUF2774: Protein of u 20.8 1.2E+02 0.0027 22.6 3.0 42 161-202 14-55 (63)
69 PF00249 Myb_DNA-binding: Myb- 20.8 1.2E+02 0.0026 20.0 2.8 22 162-183 23-46 (48)
70 COG4936 PocR Predicted sensor 20.5 78 0.0017 27.6 2.2 54 119-182 9-62 (169)
71 PRK13502 transcriptional activ 20.3 1.2E+02 0.0025 26.7 3.4 28 162-189 194-221 (282)
72 PF13921 Myb_DNA-bind_6: Myb-l 20.0 1.3E+02 0.0028 20.5 2.9 25 162-186 19-44 (60)
No 1
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-54 Score=380.09 Aligned_cols=176 Identities=58% Similarity=0.862 Sum_probs=147.9
Q ss_pred ccccCccccccccccccCCCccCcccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccHHHHHHHHHHHHH
Q 026382 51 SVSEGLESTFTGLKKKKKKPVESSLLNDEIGDAGDDLDGHVGEDDEADGSGGPRQRYPWEGSDRDYEYEELLGRVFNILR 130 (239)
Q Consensus 51 ~~~d~~~~~~~~~kKKkKK~~~~~~~~~e~~~~~e~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~y~YeeLL~R~~~~L~ 130 (239)
.++++++..+.++||||||++..+.++++...+++..+....++.++ + .+++.++|.|++++|.|++||.|+|++|+
T Consensus 17 ~~~~~l~~~~~~kKKKKkk~k~~s~~ee~~~~~~e~~~e~~~~~~e~-~--~~~~~~~~~g~e~dy~Y~ElL~rvf~ilr 93 (231)
T KOG2768|consen 17 EASERLDFLSLKKKKKKKKSKSLSALEEEDVNAGEFADEDKDPDKEV-R--QNQQGVSWVGSEPDYTYYELLSRVFNILR 93 (231)
T ss_pred chhhcccccccccccccCCCCchhhhHHHHHhccchhhhccChhhcc-c--cccccccccccCCCccHHHHHHHHHHHHH
Confidence 34566777777777777777766555555555554333222221121 1 23333999999999999999999999999
Q ss_pred hcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHH
Q 026382 131 ENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEG 210 (239)
Q Consensus 131 ~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~ 210 (239)
++|||++|++.+|.|+||||.|+| |||+|+||+|||+.|||+|+||++||++||||+|||||++||||+|||++++||+
T Consensus 94 eknpe~aGe~~k~v~~PPqvlReg-kkT~f~Nf~Dick~mhR~pdHv~~FLlAELgTsGSidg~~rLviKGrfq~kq~e~ 172 (231)
T KOG2768|consen 94 EKNPELAGEKRKFVMKPPQVLREG-KKTVFVNFADICKTMHRSPDHVMQFLLAELGTSGSIDGQQRLVIKGRFQQKQFEN 172 (231)
T ss_pred hcCchhcccccceeeCCHHHHhhc-cceeeeeHHHHHHHhccChHHHHHHHHHHhccccccCCCceEEEeccccHHHHHH
Confidence 999999999999999999999999 6999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccccCCCCcCcc
Q 026382 211 ILRRYVSKYFLKSSFVLNIY 230 (239)
Q Consensus 211 vL~kYI~eYVlC~~C~~~~~ 230 (239)
+||+||.+||+|..|.-|.+
T Consensus 173 VLRrYI~eyV~C~~CkSpdt 192 (231)
T KOG2768|consen 173 VLRRYIKEYVTCKTCKSPDT 192 (231)
T ss_pred HHHHHHHHheEeeecCChhH
Confidence 99999999999999998765
No 2
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=1.9e-42 Score=286.98 Aligned_cols=113 Identities=35% Similarity=0.646 Sum_probs=107.3
Q ss_pred CccHHHHHHHHHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCC
Q 026382 115 DYEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQ 194 (239)
Q Consensus 115 ~y~YeeLL~R~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~ 194 (239)
+|+|++||+|||+.| |+..++.+||+||+|+|.++|+ ||+|+||.+||++|||+|+||++||++||||+|+|+ +
T Consensus 4 ~~~Y~~lL~R~~~~l----p~~~~~~~R~~~p~~~v~~eG~-kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~-~ 77 (138)
T PRK03988 4 YYDYEELLDRAYEKL----PEKVFKESRFEVPKPDVRIEGN-RTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE-G 77 (138)
T ss_pred ccCHHHHHHHHHHHC----ccccCCCcceeCCCCeEEEEcC-cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeec-C
Confidence 689999999999999 8877888999999999999996 899999999999999999999999999999999996 5
Q ss_pred ceEEEEeecChHHHHHHHHHHHHhccccCCCCcCccCce
Q 026382 195 QRLVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYKSV 233 (239)
Q Consensus 195 ~rLII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~~~ 233 (239)
++|||+|+|++++|+++|++||++||+|++|..|.+.=+
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~ 116 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLI 116 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEE
Confidence 799999999999999999999999999999999987543
No 3
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=9.7e-42 Score=281.21 Aligned_cols=111 Identities=30% Similarity=0.574 Sum_probs=105.5
Q ss_pred cHHHHHHHHHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCce
Q 026382 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQR 196 (239)
Q Consensus 117 ~YeeLL~R~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~r 196 (239)
+|++||+|||+.| |+..++.+||+||+|+|.++|+ ||+|.||.+||++|||+|+||++||++||||+|++++ ++
T Consensus 1 ~Y~~lL~R~~~~l----~~~~~~~~R~~mP~~~v~~eG~-kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~~-~r 74 (133)
T TIGR00311 1 DYEKLLERAIDQL----PDEVFETKRFEVPKAYIVIEGN-RTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLEG-GR 74 (133)
T ss_pred CHHHHHHHHHHHC----ccccCCCccccCCCceEEEEcC-cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceecC-CE
Confidence 5999999999999 7877788999999999999996 8999999999999999999999999999999999985 69
Q ss_pred EEEEeecChHHHHHHHHHHHHhccccCCCCcCccCce
Q 026382 197 LVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYKSV 233 (239)
Q Consensus 197 LII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~~~ 233 (239)
|||+|+|++++|+++|++||++||+|++|..|.+.=+
T Consensus 75 lii~G~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~ 111 (133)
T TIGR00311 75 LILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRII 111 (133)
T ss_pred EEEEeecCHHHHHHHHHHHHhheEECCCCCCCCcEEE
Confidence 9999999999999999999999999999999998643
No 4
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=6.9e-40 Score=285.18 Aligned_cols=112 Identities=34% Similarity=0.663 Sum_probs=106.9
Q ss_pred ccHHHHHHHHHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCc
Q 026382 116 YEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQ 195 (239)
Q Consensus 116 y~YeeLL~R~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~ 195 (239)
|+|++||+|||+.| |+..++.+||+||+|+|.++|+ ||+|.||.+||++|||+|+||++||++||||+|+|++ +
T Consensus 1 ~~Y~~lL~r~~~~l----~~~~~~~~R~~~p~~~v~~eG~-kT~i~N~~~i~~~l~R~~~~~~ky~~~ELgt~~~~~~-~ 74 (201)
T PRK12336 1 MDYESLLDRAMEVL----PEPTKSGERFSIPEPKIFIEGK-TTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIEG-G 74 (201)
T ss_pred CCHHHHHHHHHHHC----CcccCCccceecCCceEEEEcC-cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCcceecC-C
Confidence 57999999999999 8888889999999999999995 9999999999999999999999999999999999986 5
Q ss_pred eEEEEeecChHHHHHHHHHHHHhccccCCCCcCccCce
Q 026382 196 RLVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYKSV 233 (239)
Q Consensus 196 rLII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~~~ 233 (239)
+|||+|+|++++|+++|++||++||+|++|..|.+.=+
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~ 112 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLV 112 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEE
Confidence 99999999999999999999999999999999988644
No 5
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=7.9e-38 Score=250.65 Aligned_cols=93 Identities=53% Similarity=0.880 Sum_probs=89.5
Q ss_pred cccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhcc
Q 026382 141 RRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVSKYF 220 (239)
Q Consensus 141 ~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~kYI~eYV 220 (239)
+||+||+|+|.++|++||+|.||.+||++|||+|+||++||++||||+|+||++++|||+|+|++++|+++|++||++||
T Consensus 2 ~R~~~p~~~v~~eG~~kTvi~Nf~~I~~~L~R~p~hv~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~l~~yI~~yV 81 (110)
T smart00653 2 YRFKMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIKEYV 81 (110)
T ss_pred CccccCCCeEEEEcCCeEEEEcHHHHHHHHCCCHHHHHHHHHHHhCCceeECCCCeEEEEEeeCHHHHHHHHHHHHHhcE
Confidence 69999999999999779999999999999999999999999999999999999889999999999999999999999999
Q ss_pred ccCCCCcCccCce
Q 026382 221 LKSSFVLNIYKSV 233 (239)
Q Consensus 221 lC~~C~~~~~~~~ 233 (239)
+|++|..|.+.=+
T Consensus 82 lC~~C~spdT~l~ 94 (110)
T smart00653 82 LCPECGSPDTELI 94 (110)
T ss_pred ECCCCCCCCcEEE
Confidence 9999999987644
No 6
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=100.00 E-value=4.9e-38 Score=256.71 Aligned_cols=101 Identities=44% Similarity=0.788 Sum_probs=92.0
Q ss_pred hcCCC-ccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 026382 131 ENNPE-LAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (239)
Q Consensus 131 ~~nPd-~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie 209 (239)
++||+ ..++..||+||+|+|.++|++||+|+||.|||++|||+|+||++||++||||+|+||++++|||+|+|++++|+
T Consensus 4 ~~np~~~~~~~~R~kmP~~~v~~eG~~KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~~~~lii~G~~~~~~i~ 83 (125)
T PF01873_consen 4 EKNPERSNSDKFRYKMPPPQVKIEGKKKTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDGKGRLIINGRFSSKQIQ 83 (125)
T ss_dssp CSSTTTSCSSSSS-CCCT--EEEETSTEEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEETTTEEEEESSSSCCHHH
T ss_pred HhCcCcccCCCcceecCCCeEEEEccceeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECCCCEEEEEEecCHHHHH
Confidence 45799 45666799999999999997799999999999999999999999999999999999997899999999999999
Q ss_pred HHHHHHHHhccccCCCCcCccC
Q 026382 210 GILRRYVSKYFLKSSFVLNIYK 231 (239)
Q Consensus 210 ~vL~kYI~eYVlC~~C~~~~~~ 231 (239)
++|++||++||+|++|..|.+.
T Consensus 84 ~~L~~fI~~yVlC~~C~spdT~ 105 (125)
T PF01873_consen 84 DLLDKFIKEYVLCPECGSPDTE 105 (125)
T ss_dssp HHHHHHHCHHSSCTSTSSSSEE
T ss_pred HHHHHHHHHEEEcCCCCCCccE
Confidence 9999999999999999999874
No 7
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.4e-32 Score=231.09 Aligned_cols=114 Identities=34% Similarity=0.634 Sum_probs=107.2
Q ss_pred CCCccHHHHHHHHHHHHHhcCCCcccccc-ccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceee
Q 026382 113 DRDYEYEELLGRVFNILRENNPELAGDRR-RTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSL 191 (239)
Q Consensus 113 ~~~y~YeeLL~R~~~~L~~~nPd~~~~~~-Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsi 191 (239)
...+.|++||+|+|..+ |+..+... ||.||+|.|.++|+ +|+|.||.+||++|||+|+|+++||.+||||+|++
T Consensus 3 ~~~~~yeelLeR~~~~l----P~~~~~~~~R~~ip~~~i~~~g~-~Ti~~Nf~dia~~l~rDp~h~~k~l~kel~t~g~~ 77 (151)
T COG1601 3 EMEDDYEELLERAYSEL----PEKEVKNDERFRIPEPEINREGN-RTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSI 77 (151)
T ss_pred hhhhhHHHHHHHHHHhC----CccccccccceecCCcceecccc-hhHHHhHHHHHHHhcCCHHHHHHHHHHHhcccccc
Confidence 34678999999999777 99877655 99999999999997 99999999999999999999999999999999999
Q ss_pred cCCceEEEEeecChHHHHHHHHHHHHhccccCCCCcCccC
Q 026382 192 DGQQRLVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYK 231 (239)
Q Consensus 192 dg~~rLII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~ 231 (239)
++.++|||+|+|+++.|++.|++||..||.|+.|.-+++.
T Consensus 78 d~~~rlvl~g~f~~~~i~~~i~~yi~~yv~C~~c~s~dt~ 117 (151)
T COG1601 78 DGKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTE 117 (151)
T ss_pred CCcceEEEEecccHHHHHHHHHHHHHheeEeccCCCCchh
Confidence 9988999999999999999999999999999999998875
No 8
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=3.5e-26 Score=213.02 Aligned_cols=95 Identities=25% Similarity=0.341 Sum_probs=90.1
Q ss_pred cccccccCCCeEEEeC---ceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecC-CceEEEEeecChHHHHHHHHH
Q 026382 139 DRRRTVMRPPQVLREG---TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG-QQRLVVKGRFAPKNFEGILRR 214 (239)
Q Consensus 139 ~~~Rf~mP~p~V~reG---~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg-~~rLII~Grf~~k~Ie~vL~k 214 (239)
.-|||+||+++...|| ++||+|+|+.|||++|+|+|-|+++||++|||++++||. ++|+++||.|.+..||++|+.
T Consensus 12 ~FYRYKMPrl~aKvEGKGNGIKTvIvNm~eIakAL~RPp~Y~tKyFGcELGAQT~fd~kn~ryiVNG~Hd~~KLqdlLdg 91 (400)
T KOG2767|consen 12 PFYRYKMPRLQAKVEGKGNGIKTVIVNMVEIAKALGRPPLYPTKYFGCELGAQTKFDVKNGRYIVNGAHEASKLQDLLDG 91 (400)
T ss_pred hhhhhccchhhhhccccCCCeeeeeecHHHHHHHhCCCCCcccccceeeccccccccccCCeeeecccccHHHHHHHHHH
Confidence 3689999999999998 499999999999999999999999999999999999986 789999999999999999999
Q ss_pred HHHhccccCCCCcCccCce
Q 026382 215 YVSKYFLKSSFVLNIYKSV 233 (239)
Q Consensus 215 YI~eYVlC~~C~~~~~~~~ 233 (239)
||+.||+||+|+.|.+.-.
T Consensus 92 FIkKFVlC~~C~NPETel~ 110 (400)
T KOG2767|consen 92 FIKKFVLCPSCENPETELI 110 (400)
T ss_pred HHHHheeCcCCCCCceeEE
Confidence 9999999999999987543
No 9
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=94.32 E-value=0.13 Score=38.89 Aligned_cols=57 Identities=9% Similarity=0.082 Sum_probs=41.8
Q ss_pred eeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeec----CCceEEEEeecChHHHHHHHHHHH
Q 026382 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD----GQQRLVVKGRFAPKNFEGILRRYV 216 (239)
Q Consensus 156 kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsid----g~~rLII~Grf~~k~Ie~vL~kYI 216 (239)
.-|+|.||. .-.=+++-+++.|...+|++|++. .+..+.|+|.+...-.+-++.+|+
T Consensus 19 ~vT~V~gl~----~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~~ 79 (83)
T PF01253_consen 19 FVTIVSGLE----LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKGG 79 (83)
T ss_dssp EEEEEES------STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHCS
T ss_pred EEEEEECCc----ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhCC
Confidence 558899998 344578999999999999999992 245799999998887766666663
No 10
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=90.85 E-value=0.39 Score=38.24 Aligned_cols=51 Identities=14% Similarity=0.165 Sum_probs=40.2
Q ss_pred eCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHH
Q 026382 153 EGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNF 208 (239)
Q Consensus 153 eG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~I 208 (239)
-|+.-|+|.||..-. =++.-+++.|.+.+|+.|++.+ +.+.|+|-+.....
T Consensus 35 ~gK~VTiI~Gl~~~~----~~lk~l~k~lKk~~gcGgsvk~-~~I~iQGD~r~~v~ 85 (99)
T PRK00939 35 YGKEVTIIEGIDPKD----IDLKELAKKLKSKLACGGTVKD-GRIELQGDHRERVK 85 (99)
T ss_pred CCceEEEEeCCCCcc----hhHHHHHHHHHHHhCCCceEEC-CEEEEeCcHHHHHH
Confidence 355679999996422 2478899999999999999974 47999999876554
No 11
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=90.18 E-value=0.51 Score=35.84 Aligned_cols=53 Identities=13% Similarity=0.076 Sum_probs=41.8
Q ss_pred CceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 154 G~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
|+.-|+|.+|..-.. +++-+++.|.+.+|++|++.. +.+.|+|-+.....+-+
T Consensus 12 ~K~VT~I~Gl~~~~~----dlk~l~k~lKk~~~cggtv~~-~~I~lQGD~r~~v~~~L 64 (77)
T cd00474 12 GKTVTTVQGLDLEYA----DLKKLAKELKKKCACGGTVKD-EVIELQGDQRKKIKEFL 64 (77)
T ss_pred CccEEEEECCCCchH----hHHHHHHHHHHHcCCCcEEec-CEEEEeCcHHHHHHHHH
Confidence 445789999974332 689999999999999999975 59999998876655433
No 12
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=88.18 E-value=0.95 Score=36.01 Aligned_cols=52 Identities=13% Similarity=0.156 Sum_probs=40.9
Q ss_pred EeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHH
Q 026382 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNF 208 (239)
Q Consensus 152 reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~I 208 (239)
|-|+.-|+|.||..-. -+++-++++|.+.+|+.|++. ++.+.|+|-|.....
T Consensus 35 r~gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk-~~~IeiQGD~~~~v~ 86 (101)
T TIGR01158 35 RKGKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK-DGVIEIQGDHRDRVK 86 (101)
T ss_pred CCCCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe-CCEEEEeCcHHHHHH
Confidence 3456779999996322 257889999999999999997 458999999876544
No 13
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=86.32 E-value=2 Score=37.53 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=46.0
Q ss_pred eeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceee----cCCceEEEEeecChHHHHHHHHHH
Q 026382 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSL----DGQQRLVVKGRFAPKNFEGILRRY 215 (239)
Q Consensus 156 kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsi----dg~~rLII~Grf~~k~Ie~vL~kY 215 (239)
.-|+|.+|... .-++.-++++|..-+||+||+ .+++.++|+|-|....++=++.+|
T Consensus 103 ~VT~V~GLe~f----~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 103 FVTVIKGLETF----DIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred eEEEEeCCcCC----CcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 46899999753 457899999999999999877 246799999999988887777766
No 14
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=82.49 E-value=3.6 Score=33.34 Aligned_cols=58 Identities=14% Similarity=0.172 Sum_probs=45.8
Q ss_pred EEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 026382 151 LREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (239)
Q Consensus 151 ~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~ 213 (239)
.|-|+--|+|.+|.. -.-+++.+++.|-+-+|+.|++-.+ ...|+|-|..+..+=++.
T Consensus 36 rr~gK~VTiI~Gld~----~~~dlk~Lak~LKk~cacGGtvk~~-~IeiQGdhr~~v~~~L~~ 93 (104)
T COG0023 36 RRKGKTVTIIEGLDL----KDIDLKKLAKELKKKCACGGTVKDG-EIEIQGDHRDKVKELLIK 93 (104)
T ss_pred ecCCcEEEEEeCccc----chhhHHHHHHHHHHHcCCCceecCC-EEEEeChHHHHHHHHHHH
Confidence 355767899999986 2345789999999999999999744 999999998876654443
No 15
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=78.39 E-value=6.8 Score=24.79 Aligned_cols=46 Identities=11% Similarity=0.142 Sum_probs=33.7
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL 212 (239)
+..|+|+.|+.++..|.+|............ +++. +|+.+.|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~~-~~~~----~~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTP-GGHR----RFPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeCC-CCce----ecCHHHHHHHH
Confidence 5789999999999999999988665443322 2333 47888877765
No 16
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=76.45 E-value=4 Score=33.25 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=43.2
Q ss_pred EEeC-ceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecC----CceEEEEeecChHHHHHHHHHH
Q 026382 151 LREG-TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG----QQRLVVKGRFAPKNFEGILRRY 215 (239)
Q Consensus 151 ~reG-~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg----~~rLII~Grf~~k~Ie~vL~kY 215 (239)
.|-| +.-|+|.+|.+ .=+-.-+++.|.+.+|+.|++-. ++.+.|+|-+..+..+-+....
T Consensus 34 qR~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~g 98 (110)
T TIGR01160 34 QRNGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQG 98 (110)
T ss_pred EccCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHcC
Confidence 3445 34688888873 22347899999999999999953 3579999999876665555443
No 17
>PRK07451 translation initiation factor Sui1; Validated
Probab=70.35 E-value=6.3 Score=32.38 Aligned_cols=51 Identities=20% Similarity=0.354 Sum_probs=38.1
Q ss_pred CceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 026382 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (239)
Q Consensus 154 G~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie 209 (239)
|+.-|+|.+|..-.. +-.-+++.|-..+|+.|++.+ +.+.|+|-|..+..+
T Consensus 51 GK~VTvV~Gl~~~~~----dlk~LaK~LK~k~gcGGtvkd-~~IelQGD~r~~v~~ 101 (115)
T PRK07451 51 GKTVTVITGFQHKPE----TLAKLLKQLKTQCGSGGTVKD-NTIEIQGDHRQKILE 101 (115)
T ss_pred CCeEEEEeCCCCCHH----HHHHHHHHHHHHhcCCceEcC-CEEEEcCcHHHHHHH
Confidence 345799999863222 236789999999999999964 489999998765444
No 18
>PRK09019 translation initiation factor Sui1; Validated
Probab=70.30 E-value=8.2 Score=31.39 Aligned_cols=52 Identities=10% Similarity=0.002 Sum_probs=38.2
Q ss_pred CceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHH
Q 026382 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEG 210 (239)
Q Consensus 154 G~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~ 210 (239)
|..-|+|..|..-... -.-+++.|-+.+|+.|++-. +.+.|+|-|..+..+-
T Consensus 44 GK~VTiI~Gl~~~~~d----lk~l~K~lKkk~gcGGtvk~-~~IelQGD~r~~v~~~ 95 (108)
T PRK09019 44 GKGVCLITGLDLDDAE----LKKLAAELKKKCGCGGAVKD-GVIEIQGDKRDLLKSL 95 (108)
T ss_pred CCeEEEEeCCcCCHHH----HHHHHHHHHHHhcCCCeEEc-CEEEEcCcHHHHHHHH
Confidence 3346899988611111 36789999999999999974 5899999987654443
No 19
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=66.71 E-value=5.9 Score=27.26 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=22.9
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
...|+|+.|+.++..|++.|..++|..
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 357999999999999999999999998
No 20
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=65.61 E-value=4.6 Score=39.04 Aligned_cols=54 Identities=24% Similarity=0.441 Sum_probs=37.2
Q ss_pred CCCccHHHHHHHHHHHHHhcCCCccc---cccccccCCCeEEEeCceeeEEeehHHHHHHhCCChH
Q 026382 113 DRDYEYEELLGRVFNILRENNPELAG---DRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPD 175 (239)
Q Consensus 113 ~~~y~YeeLL~R~~~~L~~~nPd~~~---~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~pe 175 (239)
.+++.-++|++++|..|.- =..- ....-..++|.|.|.|+ | ..|+|..|||+--
T Consensus 272 ~~~~nld~L~e~i~~~L~l---iRVYtK~~g~~pd~~~PlIlr~Gs--T----V~Dvc~~IH~~l~ 328 (365)
T COG1163 272 KKGINLDELKERIWDVLGL---IRVYTKPPGEEPDFDEPLILRRGS--T----VGDVCRKIHRDLV 328 (365)
T ss_pred ccCCCHHHHHHHHHHhhCe---EEEEecCCCCCCCCCCCeEEeCCC--c----HHHHHHHHHHHHH
Confidence 4466789999999998820 0000 01223457899999996 5 4899999999743
No 21
>PRK06824 translation initiation factor Sui1; Validated
Probab=64.82 E-value=13 Score=30.58 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=39.1
Q ss_pred eCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHH
Q 026382 153 EGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEG 210 (239)
Q Consensus 153 eG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~ 210 (239)
-|..-|+|..|..-... -.-+++.|-+.+|+.|++-. +.+.|+|-|..+..+-
T Consensus 53 ~gK~VTvI~Gl~~~~~d----lk~l~K~LKkk~gcGGtvkd-~~IeiQGD~r~~v~~~ 105 (118)
T PRK06824 53 GGKTVTVITGVPLAEDA----LKELAKELKRRCGTGGTLKD-GVIEIQGDHVELLLAE 105 (118)
T ss_pred CCceEEEEeCCcCCHHH----HHHHHHHHHHHhcCCceEec-CEEEEcCcHHHHHHHH
Confidence 35567899988622111 36789999999999999964 5899999987665443
No 22
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=61.40 E-value=12 Score=31.55 Aligned_cols=48 Identities=13% Similarity=0.187 Sum_probs=38.0
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCcCccCc
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYKS 232 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~~ 232 (239)
.|+.+|++++.-++++|.+||- .|||.|.+ ++ +-+..|..|+.+|+.|
T Consensus 47 ati~eV~e~tgVs~~~I~~~Ir-----------eGRL~~~~-~~------------nl~~~CE~CG~~I~~G 94 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIR-----------EGRLQLKH-FP------------NLGYPCERCGTSIREG 94 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-----------cCCeeccC-CC------------CCcCcccccCCcCCCC
Confidence 5678999999999999999985 35777755 22 2368899999998877
No 23
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=53.56 E-value=20 Score=23.08 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=23.1
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
..+.+||..++=++.|+.+-|.+++|.+
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3578999999999999999999999974
No 24
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=53.15 E-value=34 Score=22.04 Aligned_cols=45 Identities=11% Similarity=0.099 Sum_probs=32.9
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
+..++|+.++-++..|-.|...-+.. ....++++ -+|+..+|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l~-~~~~~~~~----~~y~~~~v~~l 46 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLLS-PARTEGGY----RLYSDADLERL 46 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCC-CCcCCCCC----EEeCHHHHHHh
Confidence 46799999999999999998887766 33333333 24788877765
No 25
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=49.80 E-value=17 Score=24.21 Aligned_cols=22 Identities=18% Similarity=0.247 Sum_probs=16.4
Q ss_pred eehHHHHHHhCCChHHHHHHHH
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLL 182 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~ 182 (239)
..+.+||+.|+|++.-|.++|-
T Consensus 21 ~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHh
Confidence 3578999999999999998875
No 26
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=47.84 E-value=16 Score=27.70 Aligned_cols=39 Identities=21% Similarity=0.309 Sum_probs=22.1
Q ss_pred hHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecCh
Q 026382 163 FMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAP 205 (239)
Q Consensus 163 F~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~ 205 (239)
-.+||++|.|++.||.+||.- |..+-.|- .++-+|++..
T Consensus 6 q~eIA~~lGks~s~Vs~~l~L-l~lP~~i~---~~v~~g~~~~ 44 (93)
T PF08535_consen 6 QEEIAKRLGKSRSWVSNHLAL-LDLPEEIK---ELVRSGRISD 44 (93)
T ss_dssp HHHHHHHTT--HHHHHHHHGG-GS--HHHH---HHHHTTS---
T ss_pred HHHHHHHHCCCHHHHHHHHHH-HcCCHHHH---HHHHcCCCch
Confidence 479999999999999999863 33333332 3444455543
No 27
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=42.79 E-value=36 Score=25.44 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=29.8
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecC
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFA 204 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~ 204 (239)
-|..|+|..|+-.-.-|.+|.. -.++..-+|+||.+.
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~-------D~~a~~HaIvNgvLM 53 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSR-------DKDAKRHAIVNGVLM 53 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhc-------ccccceEEEEcCEEE
Confidence 5899999999999999999974 445556778887764
No 28
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=42.51 E-value=15 Score=25.58 Aligned_cols=26 Identities=8% Similarity=0.176 Sum_probs=21.0
Q ss_pred ecChHHHHHHHHHHHHhccccCCCCcCc
Q 026382 202 RFAPKNFEGILRRYVSKYFLKSSFVLNI 229 (239)
Q Consensus 202 rf~~k~Ie~vL~kYI~eYVlC~~C~~~~ 229 (239)
..++..++.+... ++-|.||+|+..+
T Consensus 31 ~l~~~~~~~i~~~--~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 31 ELPPQELNEIRKG--DEIVFCPNCGRIL 56 (56)
T ss_pred EcCHHHHHHHHcC--CCeEECcCCCccC
Confidence 5678888888776 8899999998643
No 29
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=42.40 E-value=9.3 Score=34.87 Aligned_cols=23 Identities=35% Similarity=0.228 Sum_probs=15.9
Q ss_pred cccCCCCCCccccccccccCCCC
Q 026382 14 AELAPFDPTKKKKKKKVVIQDPS 36 (239)
Q Consensus 14 ~~l~~fd~~kKKKKKK~~~~d~~ 36 (239)
..|..|++.|||||||.......
T Consensus 20 ~~l~~~~~~kKKKKkk~k~~s~~ 42 (231)
T KOG2768|consen 20 ERLDFLSLKKKKKKKKSKSLSAL 42 (231)
T ss_pred hcccccccccccccCCCCchhhh
Confidence 45778888888887776655433
No 30
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=40.88 E-value=25 Score=31.13 Aligned_cols=72 Identities=21% Similarity=0.327 Sum_probs=45.8
Q ss_pred cHHHHHHHHHHHHHhcCCC-ccccccccccCCCeEEEe------CceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCce
Q 026382 117 EYEELLGRVFNILRENNPE-LAGDRRRTVMRPPQVLRE------GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSG 189 (239)
Q Consensus 117 ~YeeLL~R~~~~L~~~nPd-~~~~~~Rf~mP~p~V~re------G~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~g 189 (239)
..+.-|.|+|+....=.-. .+. ..-|.+.+|.+... ++- .-+.|||.+|||+.-|+..|-++-|-..|
T Consensus 53 EvEyaL~~ay~Af~rW~vrCmAa-ag~~~ls~~e~l~lH~irhrdR~----K~laDic~~ln~eDth~itYslrKL~k~g 127 (199)
T COG5631 53 EVEYALMRAYEAFGRWQVRCMAA-AGEFSLSGPENLLLHIIRHRDRP----KSLADICQMLNREDTHNITYSLRKLLKGG 127 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-hcCCCCcchHHHHHHHHhhcCch----hhHHHHHHHhccccchhHHHHHHHHHhcc
Confidence 5677888888766221100 000 11234444544322 322 23689999999999999999999998888
Q ss_pred eecC
Q 026382 190 SLDG 193 (239)
Q Consensus 190 sidg 193 (239)
-|.+
T Consensus 128 Lit~ 131 (199)
T COG5631 128 LITR 131 (199)
T ss_pred ceec
Confidence 8854
No 31
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=40.09 E-value=4.5 Score=37.76 Aligned_cols=66 Identities=20% Similarity=0.311 Sum_probs=54.6
Q ss_pred eeEEeehHHHHHHhCCChHHHHHH---HHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhcccc
Q 026382 157 KTVFVNFMDLCKTMHRQPDHVMTF---LLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVSKYFLK 222 (239)
Q Consensus 157 KTvi~NF~eI~k~L~R~peHv~kf---l~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~kYI~eYVlC 222 (239)
-++-.||.-.+=-+||+|.++.-| --..||+...+||.+.++--|+.+...+..-|+.|-+=|--|
T Consensus 64 ~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdge~l~~~g~~~~~~e~~~Rle~~~~PYHaa 132 (272)
T COG3741 64 TLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDGEPLYIYGGAPTPAEALARLETLWKPYHAA 132 (272)
T ss_pred hhhhccccceeEecCCCCCCCcCccccccCCccccccccCccccccCCCCCHHHHHHHHHHhhccHHHH
Confidence 455667777777899999999988 456789999999988999988999999999999987776543
No 32
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=38.35 E-value=86 Score=20.64 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=25.3
Q ss_pred eCceeeEEeehHHHHHHhCCChHHHHHHHHH
Q 026382 153 EGTKKTVFVNFMDLCKTMHRQPDHVMTFLLA 183 (239)
Q Consensus 153 eG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ 183 (239)
.|+.-..|..+.+.|+.|+.+..+|.+++-.
T Consensus 10 ~~~~i~~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 10 DGNLIGEFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred CCCEEEEecCHHHHHHHhCCCHHHHHHHHhC
Confidence 3442236899999999999999999999875
No 33
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=37.23 E-value=79 Score=21.84 Aligned_cols=46 Identities=7% Similarity=-0.010 Sum_probs=32.8
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
+..++|+.++.+|.+|..|...-+-.+..-+.+|+ .+|+..+|..+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g~----r~y~~~dl~~l 47 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGY----RLYSDEDLERL 47 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCC----EecCHHHHHHH
Confidence 46799999999999999998766655431222332 26888888755
No 34
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=36.81 E-value=18 Score=25.81 Aligned_cols=13 Identities=15% Similarity=0.023 Sum_probs=10.6
Q ss_pred HHhccccCCCCcC
Q 026382 216 VSKYFLKSSFVLN 228 (239)
Q Consensus 216 I~eYVlC~~C~~~ 228 (239)
...|+.||.|..+
T Consensus 10 ~~kY~~Cp~CGN~ 22 (49)
T PF12677_consen 10 SNKYCKCPKCGND 22 (49)
T ss_pred hhhhccCcccCCc
Confidence 4559999999875
No 35
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=35.23 E-value=15 Score=23.99 Aligned_cols=15 Identities=13% Similarity=-0.031 Sum_probs=10.5
Q ss_pred hccccCCCCcCccCc
Q 026382 218 KYFLKSSFVLNIYKS 232 (239)
Q Consensus 218 eYVlC~~C~~~~~~~ 232 (239)
.||.||+|..++-.+
T Consensus 3 ~~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 3 PYVECPNCGRPVAAS 17 (33)
T ss_dssp -EEE-TTTSSEEEGG
T ss_pred CeEECCCCcCCcchh
Confidence 589999999887544
No 36
>PRK01310 hypothetical protein; Validated
Probab=34.72 E-value=91 Score=25.03 Aligned_cols=40 Identities=23% Similarity=0.471 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhcCc--------eeecCCceEEEEeecChHHHHHHHHHHH
Q 026382 175 DHVMTFLLAELGTS--------GSLDGQQRLVVKGRFAPKNFEGILRRYV 216 (239)
Q Consensus 175 eHv~kfl~~ELGT~--------gsidg~~rLII~Grf~~k~Ie~vL~kYI 216 (239)
++|++||...||++ |.-.....+.|.| +++++...|..|+
T Consensus 55 ~ali~~LA~~l~v~ks~I~iv~G~tsR~K~v~I~~--~~~~l~~~l~~~~ 102 (104)
T PRK01310 55 RALIELLAKALGVPKSSVRLLSGATSRLKQLRIDG--DPEDLGEALRALT 102 (104)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC--CHHHHHHHHHHHh
Confidence 78999999999973 3333345677777 7888888888775
No 37
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=33.81 E-value=43 Score=26.01 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=21.9
Q ss_pred hHHHHHHhCCChHHHHHHHHHhhcC
Q 026382 163 FMDLCKTMHRQPDHVMTFLLAELGT 187 (239)
Q Consensus 163 F~eI~k~L~R~peHv~kfl~~ELGT 187 (239)
+..||++|+|.+..|++.|....+.
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~ 31 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGE 31 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCH
Confidence 4579999999999999999987774
No 38
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=33.57 E-value=62 Score=22.15 Aligned_cols=28 Identities=4% Similarity=0.052 Sum_probs=25.7
Q ss_pred eehHHHHHHhCC-ChHHHHHHHHHhhcCc
Q 026382 161 VNFMDLCKTMHR-QPDHVMTFLLAELGTS 188 (239)
Q Consensus 161 ~NF~eI~k~L~R-~peHv~kfl~~ELGT~ 188 (239)
.++.+||..++= ++.|+.+.|....|.+
T Consensus 51 ~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 51 LSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 578999999999 9999999999998875
No 39
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=33.05 E-value=1.3e+02 Score=18.88 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=31.0
Q ss_pred EeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 026382 160 FVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (239)
Q Consensus 160 i~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL 212 (239)
|.++.|+|+.|+-++..|.+++..-. .++...|+ + -+|....|+..|
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~~~~g~-i~~~~~g~-~----~~~~~~~l~~~~ 47 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRLIHEGE-LPAYRVGR-H----YRIPREDVDEYL 47 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHcCC-CCeEEeCC-e----EEEeHHHHHHHH
Confidence 35789999999999999999985432 23332332 2 245666665544
No 40
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=33.04 E-value=25 Score=23.45 Aligned_cols=14 Identities=7% Similarity=0.045 Sum_probs=7.8
Q ss_pred HHHHHhcc-ccCCCC
Q 026382 213 RRYVSKYF-LKSSFV 226 (239)
Q Consensus 213 ~kYI~eYV-lC~~C~ 226 (239)
++.|.+|| .|+.|+
T Consensus 25 ~~~V~~~ir~C~~Cq 39 (39)
T PF09337_consen 25 KKDVRRVIRSCPQCQ 39 (39)
T ss_pred HHHHHHHHhcCcccC
Confidence 33445555 577774
No 41
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=32.69 E-value=43 Score=30.75 Aligned_cols=54 Identities=6% Similarity=0.035 Sum_probs=31.0
Q ss_pred ChHHHHHHHHHhhcCc-----eeecC---CceEEEEeecChHHHHHHHHHHHHhccccCCCCcCccC
Q 026382 173 QPDHVMTFLLAELGTS-----GSLDG---QQRLVVKGRFAPKNFEGILRRYVSKYFLKSSFVLNIYK 231 (239)
Q Consensus 173 ~peHv~kfl~~ELGT~-----gsidg---~~rLII~Grf~~k~Ie~vL~kYI~eYVlC~~C~~~~~~ 231 (239)
-|.+++.|+..=..-. +-+.| +|+-+ ...+..+..|.. =+.-|.||+|+..+|.
T Consensus 172 l~~ell~~yeri~~~~kg~gvvpl~g~~C~GC~m---~l~~~~~~~V~~--~d~iv~CP~CgRILy~ 233 (239)
T COG1579 172 LDPELLSEYERIRKNKKGVGVVPLEGRVCGGCHM---KLPSQTLSKVRK--KDEIVFCPYCGRILYY 233 (239)
T ss_pred cCHHHHHHHHHHHhcCCCceEEeecCCcccCCee---eecHHHHHHHhc--CCCCccCCccchHHHh
Confidence 3677777776544332 22232 12222 334444444444 7789999999998873
No 42
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=32.67 E-value=59 Score=24.69 Aligned_cols=27 Identities=7% Similarity=-0.101 Sum_probs=25.0
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
++.+||+.++-++.|+.+.|...+|.+
T Consensus 23 ~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 23 NIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 689999999999999999999998874
No 43
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=31.77 E-value=98 Score=23.75 Aligned_cols=46 Identities=7% Similarity=0.010 Sum_probs=35.3
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
+..++|+.++-+|..|-.|....+..+...+++|+ ..|+..+|+.+
T Consensus 2 ti~eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~----R~y~~~di~~l 47 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGY----RLYTEEDLERL 47 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCc----eeeCHHHHHHH
Confidence 46899999999999999998777765655554432 35889888876
No 44
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase. This model describes the cobalamin-independent methionine synthase. A family of uncharacterized archaeal proteins is homologous to the C-terminal region of this family. That family is excluded from this model but, along with this family, belongs to pfam model pfam01717.
Probab=29.79 E-value=82 Score=33.12 Aligned_cols=99 Identities=10% Similarity=0.215 Sum_probs=58.3
Q ss_pred cHHHHHHHHHHHHHhcCCCccccccccccC-CCeEEEeCceeeEEeehHHHHHHhC------------CChHHHHHHHHH
Q 026382 117 EYEELLGRVFNILRENNPELAGDRRRTVMR-PPQVLREGTKKTVFVNFMDLCKTMH------------RQPDHVMTFLLA 183 (239)
Q Consensus 117 ~YeeLL~R~~~~L~~~nPd~~~~~~Rf~mP-~p~V~reG~kKTvi~NF~eI~k~L~------------R~peHv~kfl~~ 183 (239)
...+.|+.++..++.- .+ .+| ..+| +. .|.+-||.+|...|. |...+++..|..
T Consensus 609 ~~~~~l~~a~~~~~~~-----~~----~v~~~~~I---~~-H~C~g~~~~i~~~l~~l~vD~i~lE~~r~~~e~L~~~~~ 675 (750)
T TIGR01371 609 DWPEYLDWAVEAFRLA-----TS----GVKDETQI---HT-HMCYSEFNEIIESIADLDADVISIEASRSDMELLSAFKN 675 (750)
T ss_pred hHHHHHHHHHHHHHHH-----Hh----CCCCCCEE---EE-EEECCCcHHHHHHHHhCCCCEEEEEecCCChhHHHHhhh
Confidence 4577888888887421 01 123 2333 54 899999999998884 566667776633
Q ss_pred hhcCceeecCCceEEEEe----ecChHHHHHHHHHHHH-----hccccCCCCcCccC
Q 026382 184 ELGTSGSLDGQQRLVVKG----RFAPKNFEGILRRYVS-----KYFLKSSFVLNIYK 231 (239)
Q Consensus 184 ELGT~gsidg~~rLII~G----rf~~k~Ie~vL~kYI~-----eYVlC~~C~~~~~~ 231 (239)
-.+..-.+ +--||.| .=+...|...|++.++ .-.+.|.|.+-.+.
T Consensus 676 ~~~~~~~i---g~GVvD~~s~~ve~~eei~~~i~~a~~~i~~erl~vsPdCGL~tr~ 729 (750)
T TIGR01371 676 GFGYPNGI---GPGVYDIHSPRVPSVEEMADLIEKALQVLPAERLWVNPDCGLKTRN 729 (750)
T ss_pred hcccCCeE---EEEEEeCCCCCcCCHHHHHHHHHHHHHhcCcceEEEeCCCCCCcCC
Confidence 01211111 1223334 3345677777777755 45678999987753
No 45
>PF12728 HTH_17: Helix-turn-helix domain
Probab=28.76 E-value=1.5e+02 Score=19.51 Aligned_cols=24 Identities=4% Similarity=0.108 Sum_probs=20.9
Q ss_pred eehHHHHHHhCCChHHHHHHHHHh
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAE 184 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~E 184 (239)
.+..|+|+.|+-++..|.+++...
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 468899999999999999998654
No 46
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.60 E-value=1.1e+02 Score=23.52 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=32.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
++.++|+.++-++.+|-.|....|..+..-+++.| .|+..+|..+
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~Gli~p~r~~~g~R-----~Ys~~dv~~l 47 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGR-----RYSNNDLELL 47 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCe-----eECHHHHHHH
Confidence 78999999999999999998877766532233322 3677766654
No 47
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.05 E-value=74 Score=25.39 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=25.3
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
.++.++|+.++-+|.|+.+.|..++|.+
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 3468999999999999999999999975
No 48
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=27.51 E-value=41 Score=30.97 Aligned_cols=53 Identities=9% Similarity=0.128 Sum_probs=36.4
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHh------ccccCCCCcCcc
Q 026382 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVSK------YFLKSSFVLNIY 230 (239)
Q Consensus 173 ~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~kYI~e------YVlC~~C~~~~~ 230 (239)
+.....+.+.......|+++.. ++ .| +++.|++..++.|+. |++++.|.++..
T Consensus 265 dl~e~~~~~~~~~~i~Gni~p~--~l-~g--t~e~i~~~v~~~l~~~~~~~g~Il~~Gc~i~~~ 323 (338)
T TIGR01464 265 DLKEARKRVGPGVAIQGNLDPA--VL-YA--PEEALEEKVEKILEAFGGKSRYIFNLGHGILPD 323 (338)
T ss_pred CHHHHHHHhCCCeeEEeCCChH--Hh-cC--CHHHHHHHHHHHHHHhccCCCceecCCCcCCCC
Confidence 3334444444445667777642 33 56 788899988888885 799999998854
No 49
>PF02406 MmoB_DmpM: MmoB/DmpM family ; InterPro: IPR003454 This family consists of monooxygenase components such as MmoB methane monooxygenase (1.14.13.25 from EC) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen []. Also found in this family is DmpM or Phenol hydroxylase (1.14.13.7 from EC) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase []. Phenol hydroxylase catabolises phenol and some of its methylated derivatives in the first step of phenol biodegradation, and is required for growth on phenol. The multicomponent enzyme is made up of P0, P1, P2, P3, P4 and P5 polypeptides.; GO: 0004497 monooxygenase activity, 0006725 cellular aromatic compound metabolic process; PDB: 2INN_L 2INP_L 1CKV_A 3Q3M_H 3GE3_E 1G11_A 2BF2_B 3I5J_E 3Q3O_E 3I63_E ....
Probab=27.17 E-value=2e+02 Score=22.38 Aligned_cols=68 Identities=16% Similarity=0.286 Sum_probs=46.5
Q ss_pred HHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecC-CceEEE
Q 026382 125 VFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG-QQRLVV 199 (239)
Q Consensus 125 ~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg-~~rLII 199 (239)
+...+.+.||+..-. =.|.-|++++. ..+..++..|.+.|.|+=+ +..|...=-...|.++. ++++++
T Consensus 17 iveai~~dNP~v~V~-----d~~a~vrI~a~-g~l~i~~~tiee~LGr~~~-~~el~v~mss~~Gri~~~dD~~~~ 85 (87)
T PF02406_consen 17 IVEAIEEDNPGVTVE-----DRPAYVRIDAP-GRLVIRRETIEEALGRPFD-LQELEVNMSSFYGRIDEDDDEFVL 85 (87)
T ss_dssp HHHHHHHHSSTEEEE-----EESSEEEEEES-SEEEEEHHHHHHHCTSTCH-HHHHHHTECEEESEEEEESSEEEE
T ss_pred HHHHHHhhCCCeEEE-----ecCCEEEEecC-CeEEEEHHHHHHHhCCCCc-HHHHhhhhheeeeEEEEeCCEEEE
Confidence 346667779984211 13556777775 6788999999999999843 44666665666777754 556665
No 50
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=26.25 E-value=95 Score=25.16 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=26.4
Q ss_pred HHHHHHH-HhhcCceee--cC-CceEE-EEeecChHHHHHHHHHHHHh
Q 026382 176 HVMTFLL-AELGTSGSL--DG-QQRLV-VKGRFAPKNFEGILRRYVSK 218 (239)
Q Consensus 176 Hv~kfl~-~ELGT~gsi--dg-~~rLI-I~Grf~~k~Ie~vL~kYI~e 218 (239)
++++||. .+-+.+.-+ +. ++++. ..|.|+.+.|..-+..|+..
T Consensus 70 ~~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 70 DLEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 3666665 222333332 33 23666 88999999888777777654
No 51
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=26.09 E-value=90 Score=27.40 Aligned_cols=94 Identities=12% Similarity=0.164 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEE
Q 026382 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVV 199 (239)
Q Consensus 120 eLL~R~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII 199 (239)
..++++.+.|.... -|+.-++|.|...++ .+-=.+|.--++..+=+.+.|.+ +++|.|... ..+.|
T Consensus 92 ~~~~~~~~~l~~~g-------i~l~~~~~~v~~~~~-~~ggi~~~~~~~~~~~~~~~v~~-~l~~~~i~~-----~~v~~ 157 (233)
T cd01896 92 GHREILERELEGVG-------IRLNKRPPNITIKKK-KKGGINITSTVPLTKLDEKTIKA-ILREYKIHN-----ADVLI 157 (233)
T ss_pred hHHHHHHHHHHHcC-------ceecCCCCeEEEEEE-ecCCEEEeccCCCCCCCHHHHHH-HHHHhCeee-----EEEEE
Confidence 36666666674322 145667888887764 33223333346666667788887 566888743 34688
Q ss_pred EeecChHHHHHHHH---HHHHhccccCCCCc
Q 026382 200 KGRFAPKNFEGILR---RYVSKYFLKSSFVL 227 (239)
Q Consensus 200 ~Grf~~k~Ie~vL~---kYI~eYVlC~~C~~ 227 (239)
.|..+-.+|.++|. .|+.-.+....|.+
T Consensus 158 ~~~~~~~~~~~~~~~~~~y~p~iiV~NK~Dl 188 (233)
T cd01896 158 REDITVDDLIDVIEGNRVYIPCLYVYNKIDL 188 (233)
T ss_pred ccCCCHHHHHHHHhCCceEeeEEEEEECccC
Confidence 88888888888886 56665555566665
No 52
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=25.39 E-value=70 Score=21.75 Aligned_cols=21 Identities=0% Similarity=-0.097 Sum_probs=14.9
Q ss_pred HHHHHHHhccccCCCCcCccC
Q 026382 211 ILRRYVSKYFLKSSFVLNIYK 231 (239)
Q Consensus 211 vL~kYI~eYVlC~~C~~~~~~ 231 (239)
.|.+|+.....||.|..++..
T Consensus 27 ~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 27 AIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred HHHHHHHHCCCCCCCcCCCCh
Confidence 344455557899999998854
No 53
>PRK13501 transcriptional activator RhaR; Provisional
Probab=25.37 E-value=78 Score=28.09 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=26.1
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
.++.++|.+++-+|.|+.+.|-+++|.+
T Consensus 193 ~sl~~lA~~~~lS~~~l~r~Fk~~~G~T 220 (290)
T PRK13501 193 FDMADFCHKNQLVERSLKQLFRQQTGMS 220 (290)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 4789999999999999999999999985
No 54
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=23.93 E-value=2.4e+02 Score=19.32 Aligned_cols=45 Identities=7% Similarity=0.137 Sum_probs=30.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceee-cCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSL-DGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsi-dg~~rLII~Grf~~k~Ie~v 211 (239)
...|+|+.+.-++..|.+|... .|..... +.+++ -.|++.+|+.+
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~-~g~~~~~r~~~~~----r~yt~~~v~~l 47 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR-YGLPAPQRTDGGH----RLYSEADVARL 47 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh-CCCCCCCcCCCCC----eecCHHHHHHH
Confidence 3679999999999999988754 3443322 22221 35888888765
No 55
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=23.33 E-value=32 Score=35.62 Aligned_cols=53 Identities=15% Similarity=0.220 Sum_probs=31.5
Q ss_pred HHHHHHHhhcCceeecC-CceEEEEee--cChHHHHHH---------HHHHHHhccccCCCCcCcc
Q 026382 177 VMTFLLAELGTSGSLDG-QQRLVVKGR--FAPKNFEGI---------LRRYVSKYFLKSSFVLNIY 230 (239)
Q Consensus 177 v~kfl~~ELGT~gsidg-~~rLII~Gr--f~~k~Ie~v---------L~kYI~eYVlC~~C~~~~~ 230 (239)
++=.-...+|+ =-+|| ++-+.|... .+...+.++ +|..=-+|+-||+|+.-++
T Consensus 465 ~~i~aa~~~G~-Ll~DGlgDgi~l~~~~~~~~~~~~~laf~ILQa~r~R~sKTEyISCPsCGRTLf 529 (611)
T PRK02048 465 LQLKAAADMGA-LIFDGLCDGIFLFNQGKLSHVVVDATAFGILQAGRLRTSKTEYISCPGCGRTLY 529 (611)
T ss_pred HHHHHHHhhhH-HHhCcccceEEEecCCCccHHHHHHHHHHHHHHhccccccceEEECCCCCcchh
Confidence 44444555554 23377 455666644 555544332 4455568999999998764
No 56
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=23.29 E-value=1.2e+02 Score=20.61 Aligned_cols=27 Identities=26% Similarity=0.491 Sum_probs=24.1
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~ 188 (239)
++.+||..++-++.++.+.|....|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s 29 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTT 29 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcC
Confidence 578999999999999999999888764
No 57
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.
Probab=23.28 E-value=44 Score=30.69 Aligned_cols=39 Identities=10% Similarity=0.239 Sum_probs=26.9
Q ss_pred ceeecCCceEEEEeecChHHHHHHHHHHHH--hccccCCCCcCc
Q 026382 188 SGSLDGQQRLVVKGRFAPKNFEGILRRYVS--KYFLKSSFVLNI 229 (239)
Q Consensus 188 ~gsidg~~rLII~Grf~~k~Ie~vL~kYI~--eYVlC~~C~~~~ 229 (239)
.|++|.. .+..+| +++.|.+..++-|+ .|++.+.|.++-
T Consensus 281 ~Gnidp~-~ll~~g--t~eeI~~~v~~~l~~~~~Il~~gcgi~~ 321 (340)
T TIGR01463 281 VGNLSPF-STLMNG--TPEKVKKLAKEVLYNGGDIVMPGCDIDW 321 (340)
T ss_pred EecCChH-HHhcCC--CHHHHHHHHHHHHHcCCeEECCCCCCCC
Confidence 4555432 233334 55778888888886 789999999974
No 58
>PLN02433 uroporphyrinogen decarboxylase
Probab=22.62 E-value=64 Score=30.06 Aligned_cols=54 Identities=19% Similarity=0.189 Sum_probs=35.1
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHh-----ccccCCCCcCccC
Q 026382 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVSK-----YFLKSSFVLNIYK 231 (239)
Q Consensus 173 ~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~vL~kYI~e-----YVlC~~C~~~~~~ 231 (239)
+.....+.+......+|+++. . ++.| +++.|++-.++.|+. |++++.|.++..-
T Consensus 264 dl~e~~~~~g~~~~l~GNi~p--~-ll~g--t~e~i~~~v~~~i~~~~~~g~Il~~Gc~i~~~t 322 (345)
T PLN02433 264 DMADARRRLGSDVAVQGNVDP--A-VLFG--SKEAIEKEVRDVVKKAGPQGHILNLGHGVLVGT 322 (345)
T ss_pred CHHHHHHHhCCCeEEEeCCCc--h-hhCC--CHHHHHHHHHHHHHHcCCCCeEEecCCCCCCCC
Confidence 334444445545556777763 2 3455 567788888888875 5899999988543
No 59
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.47 E-value=2.3e+02 Score=19.78 Aligned_cols=46 Identities=13% Similarity=0.176 Sum_probs=31.7
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCcee-ecCCceEEEEeecChHHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGS-LDGQQRLVVKGRFAPKNFEGIL 212 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gs-idg~~rLII~Grf~~k~Ie~vL 212 (239)
+..++|+.++-+|.+|-.| ..++|.... -+.+|+ ..|+..+|+.+.
T Consensus 2 ~i~e~A~~~gVs~~tlr~y-e~~~gl~~~~r~~~g~----R~yt~~di~~l~ 48 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAW-EREFGLLKPQRSDGGH----RLFNDADIDRIL 48 (68)
T ss_pred CHHHHHHHHCcCHHHHHHH-HHhcCCCCCCcCCCCC----cccCHHHHHHHH
Confidence 5789999999999999877 444454432 222322 368999988763
No 60
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.08 E-value=84 Score=20.56 Aligned_cols=27 Identities=15% Similarity=0.262 Sum_probs=17.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHH--hhcCc
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLA--ELGTS 188 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~--ELGT~ 188 (239)
+..+||+.|+.++..|.+++.. +-|..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~ 47 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYREEGLE 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT--------
T ss_pred CHHHHHHHHCcCHHHHHHHHHHccccccc
Confidence 4679999999999999999865 45543
No 61
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.94 E-value=58 Score=22.46 Aligned_cols=21 Identities=10% Similarity=0.029 Sum_probs=13.0
Q ss_pred HHHHHHHHhcc----ccCCCCcCcc
Q 026382 210 GILRRYVSKYF----LKSSFVLNIY 230 (239)
Q Consensus 210 ~vL~kYI~eYV----lC~~C~~~~~ 230 (239)
..+.+||++.- .||=|+.+++
T Consensus 7 ~~~~k~i~~l~~~~~~CPlC~r~l~ 31 (54)
T PF04423_consen 7 EELKKYIEELKEAKGCCPLCGRPLD 31 (54)
T ss_dssp HHHHHHHHHHTT-SEE-TTT--EE-
T ss_pred HHHHHHHHHHhcCCCcCCCCCCCCC
Confidence 45677777776 9999999875
No 62
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=21.78 E-value=3.3e+02 Score=20.01 Aligned_cols=46 Identities=26% Similarity=0.265 Sum_probs=28.9
Q ss_pred hHHHHHHHHHhhcCceeecC-CceEEEEeecC----hHHHHHHHHHHHHhc
Q 026382 174 PDHVMTFLLAELGTSGSLDG-QQRLVVKGRFA----PKNFEGILRRYVSKY 219 (239)
Q Consensus 174 peHv~kfl~~ELGT~gsidg-~~rLII~Grf~----~k~Ie~vL~kYI~eY 219 (239)
|..++.-|.-.-|..-.+.- +++++|.=.-. ...|..++++.+++|
T Consensus 15 Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 15 PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 77777777777777777742 56788864333 244444566666665
No 63
>KOG3239 consensus Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only]
Probab=21.15 E-value=1.7e+02 Score=26.09 Aligned_cols=54 Identities=19% Similarity=0.332 Sum_probs=41.2
Q ss_pred eEEeehHHHHHHhCCChHHHHHHHHHhhcCceeecC----CceEEEEeecChHHHHHHHHHH
Q 026382 158 TVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG----QQRLVVKGRFAPKNFEGILRRY 215 (239)
Q Consensus 158 Tvi~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg----~~rLII~Grf~~k~Ie~vL~kY 215 (239)
|++.-+. ...-+-....+||..-++|..|+-+ ...++|+|-+...-+.=|..+|
T Consensus 117 T~V~GL~----~FdIdlk~aaK~fa~KFAtGaSVtk~a~kkdEIvIQGDv~dDi~d~I~ekw 174 (193)
T KOG3239|consen 117 TVVKGLE----TFDIDLKKAAKFFAQKFATGASVTKNAEKKDEIVIQGDVKDDIFDFIPEKW 174 (193)
T ss_pred EEEechh----hccccHHHHHHHHHHhhccCccccCCCCccceEEEeccchHHHHHHHHHhc
Confidence 4444443 4566678889999999999999976 6799999999887766555544
No 64
>PF05042 Caleosin: Caleosin related protein; InterPro: IPR007736 This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies []. The calcium binding domain is probably related to the calcium-binding EF-hands motif IPR002048 from INTERPRO.
Probab=21.15 E-value=70 Score=28.19 Aligned_cols=25 Identities=44% Similarity=0.930 Sum_probs=20.9
Q ss_pred CceeecCCceEEEEeecChHHHHHHHHHHHH
Q 026382 187 TSGSLDGQQRLVVKGRFAPKNFEGILRRYVS 217 (239)
Q Consensus 187 T~gsidg~~rLII~Grf~~k~Ie~vL~kYI~ 217 (239)
.+|.+|.+ |||.++.++++..+|-+
T Consensus 83 DSg~YD~e------GrFvp~kFe~iF~kya~ 107 (174)
T PF05042_consen 83 DSGAYDTE------GRFVPQKFEEIFSKYAK 107 (174)
T ss_pred CccccccC------CcCCHHHHHHHHHHhCC
Confidence 46777766 99999999999999954
No 65
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.05 E-value=1.8e+02 Score=21.80 Aligned_cols=45 Identities=7% Similarity=0.050 Sum_probs=32.9
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Grf~~k~Ie~v 211 (239)
+..++|+.++-+|..|..|...-+..+ ..+++|+. .|+..+|..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~~Gll~~-~~~~~g~r----~y~~~dv~~l 46 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYR----LYSEEDLERL 46 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCcCC-CcCCCCCc----ccCHHHHHHH
Confidence 578999999999999999987766553 33333332 5888888755
No 66
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=20.88 E-value=1.4e+02 Score=18.25 Aligned_cols=24 Identities=13% Similarity=0.126 Sum_probs=19.7
Q ss_pred eehHHHHHHhC-CChHHHHHHHHHh
Q 026382 161 VNFMDLCKTMH-RQPDHVMTFLLAE 184 (239)
Q Consensus 161 ~NF~eI~k~L~-R~peHv~kfl~~E 184 (239)
.|+..||..|. |.+..+..+...-
T Consensus 22 ~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 22 NNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57889999998 9999998887653
No 67
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=20.86 E-value=2.3e+02 Score=20.48 Aligned_cols=40 Identities=28% Similarity=0.354 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhc-CceeecC-CceEEEEeecChHHHHHHHHH
Q 026382 175 DHVMTFLLAELG-TSGSLDG-QQRLVVKGRFAPKNFEGILRR 214 (239)
Q Consensus 175 eHv~kfl~~ELG-T~gsidg-~~rLII~Grf~~k~Ie~vL~k 214 (239)
..|.+.|..--| -+..+|. ++++++.|.+.+..+...|++
T Consensus 20 ~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 20 RKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 367777877778 4556665 789999999999999998887
No 68
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=20.80 E-value=1.2e+02 Score=22.64 Aligned_cols=42 Identities=10% Similarity=0.244 Sum_probs=28.5
Q ss_pred eehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEee
Q 026382 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGR 202 (239)
Q Consensus 161 ~NF~eI~k~L~R~peHv~kfl~~ELGT~gsidg~~rLII~Gr 202 (239)
.||.|||+.++-.|..+.++...=-++-..+..-...+..-+
T Consensus 14 ~~FveIAr~~~i~a~e~a~~w~~Ve~Ak~kfk~rEkVVYRKr 55 (63)
T PF11242_consen 14 LSFVEIARKIGITAKEVAKAWAEVETAKEKFKTREKVVYRKR 55 (63)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccCceeeehh
Confidence 689999999999999999887654444433333334444444
No 69
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=20.78 E-value=1.2e+02 Score=20.03 Aligned_cols=22 Identities=18% Similarity=0.265 Sum_probs=19.1
Q ss_pred ehHHHHHHhC--CChHHHHHHHHH
Q 026382 162 NFMDLCKTMH--RQPDHVMTFLLA 183 (239)
Q Consensus 162 NF~eI~k~L~--R~peHv~kfl~~ 183 (239)
|+..||..|. |.+..+..++..
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHh
Confidence 8999999998 999998887653
No 70
>COG4936 PocR Predicted sensor domain [Signal transduction mechanisms / Transcription]
Probab=20.51 E-value=78 Score=27.57 Aligned_cols=54 Identities=19% Similarity=0.227 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHhcCCCccccccccccCCCeEEEeCceeeEEeehHHHHHHhCCChHHHHHHHH
Q 026382 119 EELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLL 182 (239)
Q Consensus 119 eeLL~R~~~~L~~~nPd~~~~~~Rf~mP~p~V~reG~kKTvi~NF~eI~k~L~R~peHv~kfl~ 182 (239)
..||+.+.+-..+ ...+-...|-+.|+--|-..||.-.|..|+-.|+|=.+--.
T Consensus 9 ~~ll~k~~d~Fs~----------at~lA~VvVdihG~evs~l~NftpfCqlirs~pk~~~rC~~ 62 (169)
T COG4936 9 IGLLQKFQDNFSE----------ATRLAAVVVDIHGKEVSKLSNFTPFCQLIRSTPKGEKRCAE 62 (169)
T ss_pred HHHHHHHHHHHHH----------hhceeEEEEecCCceecchhcccHHHHHHHhCcchhhHHHh
Confidence 5788888776621 12344567888898778899999999999999999766433
No 71
>PRK13502 transcriptional activator RhaR; Provisional
Probab=20.26 E-value=1.2e+02 Score=26.70 Aligned_cols=28 Identities=11% Similarity=0.132 Sum_probs=25.5
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCce
Q 026382 162 NFMDLCKTMHRQPDHVMTFLLAELGTSG 189 (239)
Q Consensus 162 NF~eI~k~L~R~peHv~kfl~~ELGT~g 189 (239)
...++|..++-+|.|+.+.|..++|.+-
T Consensus 194 ~~~~lA~~~~iS~~~L~r~fk~~~G~t~ 221 (282)
T PRK13502 194 ALDAFCQQEQCSERVLRQQFRAQTGMTI 221 (282)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 4689999999999999999999999853
No 72
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=20.01 E-value=1.3e+02 Score=20.52 Aligned_cols=25 Identities=12% Similarity=0.272 Sum_probs=20.5
Q ss_pred ehHHHHHHhC-CChHHHHHHHHHhhc
Q 026382 162 NFMDLCKTMH-RQPDHVMTFLLAELG 186 (239)
Q Consensus 162 NF~eI~k~L~-R~peHv~kfl~~ELG 186 (239)
|+..||+.|+ |.|..+..-+..-|.
T Consensus 19 ~W~~Ia~~l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 19 DWKKIAEHLGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp -HHHHHHHSTTS-HHHHHHHHHHTTS
T ss_pred CHHHHHHHHCcCCHHHHHHHHHHHCc
Confidence 7999999999 999999988888664
Done!